Parafoveal preview benefit in unspaced and spaced Chinese reading.

PubMed

Cui, Lei; Drieghe, Denis; Bai, Xuejun; Yan, Guoli; Liversedge, Simon P

2014-01-01

In an eye movement experiment during reading, we compared parafoveal preview benefit during the reading of Chinese sentences either in the familiar, unspaced format or with spaces inserted between the words. Single-character words or the first of a two-character word were either presented normally or were replaced by a pseudocharacter in the preview. Results indicate that word spacing increased the parafoveal preview benefit but only for the one-character target words. We hypothesized that the incorrect preview of the first character of the two-character word prevented parafoveal processing of the ensuing character(s), effectively nullifying any benefits from the spacing. Our results suggest that word boundary demarcation allows for more precise focusing of attention.

Good, bad and ugly word stress--fMRI evidence for foot structure driven processing of prosodic violations.

PubMed

Domahs, Ulrike; Klein, Elise; Huber, Walter; Domahs, Frank

2013-06-01

Using a stress violation paradigm, we investigated whether metrical feet constrain the way prosodic patterns are processed and evaluated. Processing of correctly versus incorrectly stressed words was associated with activation in left posterior angular and retrosplenial cortex, indicating the recognition of an expected and familiar pattern, whereas the inverse contrast yielded enhanced bilateral activation in the superior temporal gyrus, reflecting higher costs in auditory (re-)analysis. More fine-grained analyses of severe versus mild stress violations revealed activations of the left superior temporal and left anterior angular gyrus whereas the opposite contrast led to frontal activations including Broca's area and its right-hemisphere homologue, suggesting that detection of mild violations lead to increased effort in working memory and deeper phonological processing. Our results provide first evidence that different incorrect stress patterns are processed in a qualitatively different way and that the underlying foot structure seems to determine potential stress positions in German words. Copyright © 2013 Elsevier Inc. All rights reserved.

Looking and touching: what extant approaches reveal about the structure of early word knowledge.

PubMed

Hendrickson, Kristi; Mitsven, Samantha; Poulin-Dubois, Diane; Zesiger, Pascal; Friend, Margaret

2015-09-01

The goal of the current study is to assess the temporal dynamics of vision and action to evaluate the underlying word representations that guide infants' responses. Sixteen-month-old infants participated in a two-alternative forced-choice word-picture matching task. We conducted a moment-by-moment analysis of looking and reaching behaviors as they occurred in tandem to assess the speed with which a prompted word was processed (visual reaction time) as a function of the type of haptic response: Target, Distractor, or No Touch. Visual reaction times (visual RTs) were significantly slower during No Touches compared to Distractor and Target Touches, which were statistically indistinguishable. The finding that visual RTs were significantly faster during Distractor Touches compared to No Touches suggests that incorrect and absent haptic responses appear to index distinct knowledge states: incorrect responses are associated with partial knowledge whereas absent responses appear to reflect a true failure to map lexical items to their target referents. Further, we found that those children who were faster at processing words were also those children who exhibited better haptic performance. This research provides a methodological clarification on knowledge measured by the visual and haptic modalities and new evidence for a continuum of word knowledge in the second year of life. © 2014 The Authors Developmental Science Published by John Wiley & Sons Ltd.

[Retrospective analysis of the use of the Spanish words severo and severidad in CIRUGIA ESPANOLA during 2007].

PubMed

Martínez-Ramos, David

2008-12-01

The Spanish words severo (severe) and severidad (severity) are usually used as a synonyms of grave (serious) and gravedad (seriousness), although the Spanish Royal Academy of Language (Real Academia Española [RAE]) specifically recommends not to use them in this sense. A retrospective analysis to evaluate the use of the words severo and severidad in Cirugía Española during 2007 was performed. All the articles published in Cirugía Española during 2007 were reviewed. The articles in which severo and/or severidad were present were selected. For each article, the month of publication, the type of article, the geographic origin and the exact sentence containing these words were analyzed. Correctness and incorrectness of their use was studied according to the RAE normative. A total of 33 articles were selected. Every month (except for January) had, at least, 2 articles. Thirty-one of the articles were from Spain whereas 2 were from Hispano-America. Eleven cases were original articles, 7 reviews, 6 case reports, 3 editorials, 3 special articles and 3 letters to the editor. The Spanish words severo and severidad are inadequately used too often in scientific texts. It must be avoided using them as a synonym of grave, importante or serio, incorrect translations of the English word severe.

Double jeopardy revisited: clinical decision making in unstable patients with, thoraco-abdominal stab wounds and, potential injuries in multiple body cavities.

PubMed

Clarke, Damian L; Gall, Tamara M H; Thomson, Sandie R

2011-05-01

In the setting of the hypovolaemic patient with a thoraco-abdominal stab wound and potential injuries in both the chest and abdomen, deciding which cavity to explore first may be difficult.Opening the incorrect body cavity can delay control of tamponade or haemorrhage and exacerbate hypothermia and fluid shifts. This situation has been described as one of double jeopardy. All stab victims from July 2007 to July 2009 requiring a thoracotomy and laparotomy at the same operation were identified from a database. Demographics, site and nature of injuries, admission observations and investigations as well as operative sequence were recorded. Correct sequencing was defined as first opening the cavity with most lethal injury. Incorrect sequencing was defined as opening a cavity and finding either no injury or an injury of less severity than a simultaneous injury in the unopened cavity. The primary outcome was survival or death. Sixteen stab victims underwent thoracotomy and laparotomy during the same operation. All were male with an age range of 18–40 (mean/median 27). Median systolic blood pressure on presentation was 90 mm Hg. (quartile range 80–90 mm Hg). Median base excess was 6.5 (quartile range 12 to 2.2). All the deaths were the result of cardiac injuries. Incorrect sequencing occurred in four patients (25%). In this group there were four negative abdominal explorations prior to thoracotomy with two deaths. There was one death in the correct sequencing group. Incorrect sequencing in stab victims who require both thoracotomy and laparotomy at the same sitting is associated with a high mortality. This is especially true when the abdomen is incorrectly entered first whilst the life threatening pathology is in the chest. Clinical signs may be confusing, leading to incorrect sequencing of exploration. The common causes for confusion include failure to appreciate that cardiac tamponade does not present with bleeding and difficulty in assessing peritonism in an unstable patient with multiple stab wounds. In the setting of the unstable patient with stab wounds and suspected dual cavity injuries the chest should be opened first followed by the abdomen. 2010 Elsevier Ltd. All rights reserved.

Instances of erroneous DNA barcoding of metazoan invertebrates: Are universal cox1 gene primers too "universal"?

PubMed

Mioduchowska, Monika; Czyż, Michał Jan; Gołdyn, Bartłomiej; Kur, Jarosław; Sell, Jerzy

2018-01-01

The cytochrome c oxidase subunit I (cox1) gene is the main mitochondrial molecular marker playing a pivotal role in phylogenetic research and is a crucial barcode sequence. Folmer's "universal" primers designed to amplify this gene in metazoan invertebrates allowed quick and easy barcode and phylogenetic analysis. On the other hand, the increase in the number of studies on barcoding leads to more frequent publishing of incorrect sequences, due to amplification of non-target taxa, and insufficient analysis of the obtained sequences. Consequently, some sequences deposited in genetic databases are incorrectly described as obtained from invertebrates, while being in fact bacterial sequences. In our study, in which we used Folmer's primers to amplify COI sequences of the crustacean fairy shrimp Branchipus schaefferi (Fischer 1834), we also obtained COI sequences of microbial contaminants from Aeromonas sp. However, when we searched the GenBank database for sequences closely matching these contaminations we found entries described as representatives of Gastrotricha and Mollusca. When these entries were compared with other sequences bearing the same names in the database, the genetic distance between the incorrect and correct sequences amplified from the same species was c.a. 65%. Although the responsibility for the correct molecular identification of species rests on researchers, the errors found in already published sequences data have not been re-evaluated so far. On the basis of the standard sampling technique we have estimated with 95% probability that the chances of finding incorrectly described metazoan sequences in the GenBank depend on the systematic group, and variety from less than 1% (Mollusca and Arthropoda) up to 6.9% (Gastrotricha). Consequently, the increasing popularity of DNA barcoding and metabarcoding analysis may lead to overestimation of species diversity. Finally, the study also discusses the sources of the problems with amplification of non-target sequences.

Confabulation behavior and false memories in Korsakoff's syndrome: role of source memory and executive functioning.

PubMed

Kessels, Roy P C; Kortrijk, Hans E; Wester, Arie J; Nys, Gudrun M S

2008-04-01

Confabulation behavior is common in patients with Korsakoff's syndrome. A distinction can be made between spontaneous and provoked confabulations, which may have different underlying cognitive mechanisms. Provoked confabulations may be related to intrusions on memory tests, whereas spontaneous confabulations may be due to executive dysfunction or a source memory deficit. In 19 chronic Korsakoff patients, spontaneous confabulations were quantified by third-party rating (Likert scale). Provoked confabulations were assessed using the Dalla Barba Confabulation Battery. Furthermore, assessment of executive function was performed using an extensive neuropsychological battery. False memories (i.e. intrusions) and source memory were measured using twoparallelversions of a word-list learning paradigm (a modification of the Rey Auditory Verbal Learning Test). There were deficits in source memory, in which patients incorrectly assigned previously learned words to an incorrect word list. Also, Korsakoff patients had extensive executive deficits, but no relationship between the severity of these deficits and the severity of confabulation or intrusions on a memory task was found. The present findings provide evidence for a dissociation between spontaneous confabulation, provoked confabulation and false memories.

Alpha phase determines successful lexical decision in noise.

PubMed

Strauß, Antje; Henry, Molly J; Scharinger, Mathias; Obleser, Jonas

2015-02-18

Psychophysical target detection has been shown to be modulated by slow oscillatory brain phase. However, thus far, only low-level sensory stimuli have been used as targets. The current human electroencephalography (EEG) study examined the influence of neural oscillatory phase on a lexical-decision task performed for stimuli embedded in noise. Neural phase angles were compared for correct versus incorrect lexical decisions using a phase bifurcation index (BI), which quantifies differences in mean phase angles and phase concentrations between correct and incorrect trials. Neural phase angles in the alpha frequency range (8-12 Hz) over right anterior sensors were approximately antiphase in a prestimulus time window, and thus successfully distinguished between correct and incorrect lexical decisions. Moreover, alpha-band oscillations were again approximately antiphase across participants for correct versus incorrect trials during a later peristimulus time window (∼500 ms) at left-central electrodes. Strikingly, lexical decision accuracy was not predicted by either event-related potentials (ERPs) or oscillatory power measures. We suggest that correct lexical decisions depend both on successful sensory processing, which is made possible by the alignment of stimulus onset with an optimal alpha phase, as well as integration and weighting of decisional information, which is coupled to alpha phase immediately following the critical manipulation that differentiated words from pseudowords. The current study constitutes a first step toward characterizing the role of dynamic oscillatory brain states for higher cognitive functions, such as spoken word recognition. Copyright © 2015 the authors 0270-6474/15/353256-07$15.00/0.

Processing of phonological variation in children with hearing loss: compensation for English place assimilation in connected speech.

PubMed

Skoruppa, Katrin; Rosen, Stuart

2014-06-01

In this study, the authors explored phonological processing in connected speech in children with hearing loss. Specifically, the authors investigated these children's sensitivity to English place assimilation, by which alveolar consonants like t and n can adapt to following sounds (e.g., the word ten can be realized as tem in the phrase ten pounds). Twenty-seven 4- to 8-year-old children with moderate to profound hearing impairments, using hearing aids (n = 10) or cochlear implants (n = 17), and 19 children with normal hearing participated. They were asked to choose between pictures of familiar (e.g., pen) and unfamiliar objects (e.g., astrolabe) after hearing t- and n-final words in sentences. Standard pronunciations (Can you find the pen dear?) and assimilated forms in correct (… pem please?) and incorrect contexts (… pem dear?) were presented. As expected, the children with normal hearing chose the familiar object more often for standard forms and correct assimilations than for incorrect assimilations. Thus, they are sensitive to word-final place changes and compensate for assimilation. However, the children with hearing impairment demonstrated reduced sensitivity to word-final place changes, and no compensation for assimilation. Restricted analyses revealed that children with hearing aids who showed good perceptual skills compensated for assimilation in plosives only.

Older and Wiser: Older Adults’ Episodic Word Memory Benefits from Sentence Study Contexts

PubMed Central

Matzen, Laura E.; Benjamin, Aaron S.

2013-01-01

A hallmark of adaptive cognition is the ability to modulate learning in response to the demands posed by different types of tests and different types of materials. Here we evaluate how older adults process words and sentences differently by examining patterns of memory errors. In two experiments, we explored younger and older adults’ sensitivity to lures on a recognition test following study of words in these two types of contexts. Among the studied words were compound words such as “blackmail” and “jailbird” that were related to conjunction lures (e.g. “blackbird”) and semantic lures (e.g. “criminal”). Participants engaged in a recognition test that included old items, conjunction lures, semantic lures, and unrelated new items. In both experiments, younger and older adults had the same general pattern of memory errors: more incorrect endorsements of semantic than conjunction lures following sentence study and more incorrect endorsements of conjunction than semantic lures following list study. The similar pattern reveals that older and younger adults responded to the constraints of the two different study contexts in similar ways. However, while younger and older adults showed similar levels of memory performance for the list study context, the sentence study context elicited superior memory performance in the older participants. It appears as though memory tasks that take advantage of greater expertise in older adults--in this case, greater experience with sentence processing--can reveal superior memory performance in the elderly. PMID:23834493

A proposal to rationalize within-species plant virus nomenclature: benefits and implications of inaction.

PubMed

Jones, Roger A C; Kehoe, Monica A

2016-07-01

Current approaches used to name within-species, plant virus phylogenetic groups are often misleading and illogical. They involve names based on biological properties, sequence differences and geographical, country or place-association designations, or any combination of these. This type of nomenclature is becoming increasingly unsustainable as numbers of sequences of the same virus from new host species and different parts of the world increase. Moreover, this increase is accelerating as world trade and agriculture expand, and climate change progresses. Serious consequences for virus research and disease management might arise from incorrect assumptions made when current within-species phylogenetic group names incorrectly identify properties of group members. This could result in development of molecular tools that incorrectly target dangerous virus strains, potentially leading to unjustified impediments to international trade or failure to prevent such strains being introduced to countries, regions or continents formerly free of them. Dangerous strains might be missed or misdiagnosed by diagnostic laboratories and monitoring programs, and new cultivars with incorrect strain-specific resistances released. Incorrect deductions are possible during phylogenetic analysis of plant virus sequences and errors from strain misidentification during molecular and biological virus research activities. A nomenclature system for within-species plant virus phylogenetic group names is needed which avoids such problems. We suggest replacing all other naming approaches with Latinized numerals, restricting biologically based names only to biological strains and removing geographically based names altogether. Our recommendations have implications for biosecurity authorities, diagnostic laboratories, disease-management programs, plant breeders and researchers.

Lax decision criteria lead to negativity bias: evidence from the emotional stroop task.

PubMed

Liu, Guofang; Xin, Ziqiang; Lin, Chongde

2014-06-01

Negativity bias means that negative information is usually given more emphasis than comparable positive information. Under signal detection theory, recent research found that people more frequently and incorrectly identify negative task-related words as having been presented originally than positive words, even when they were not presented. That is, people have lax decision criteria for negative words. However, the response biases for task-unrelated negative words and for emotionally important words are still unclear. This study investigated response bias for these two kinds of words. Study 1 examined the response bias for task-unrelated negative words using an emotional Stroop task. Proportions of correct recognition to negative and positive words were assessed by non-parametric signal detection analysis. Participants have lower (i.e., more lax) decision criteria for task-unrelated negative words than for positive words. Study 2 supported and expanded this result by investigating participants' response bias for highly emotional words. Participants have lower decision criteria for highly emotional words than for less emotional words. Finally, possible evolutionary sources of the response bias were discussed.

Dorsolateral pFC and the representation of the incorrect use of an object: the transcranial direct current stimulation effect on N400 for visual and linguistic stimuli.

PubMed

Balconi, Michela; Vitaloni, Silvia

2014-02-01

In this study, we explored the representation of an incongruent action (instrumentally incorrect use of an object) in comparison with sentences ending with an incongruent action word, taking into account the role of the activation of the left dorsolateral pFC (DLPFC). This activity was appositely modulated by transcranial direct current stimulation (tDCS). The effect of tDCS when participants processed congruent/incongruent object-related actions (Experiment 1) or sentences (Experiment 2) was verified by measuring changes in the ERP N400, error rates (ERs), and RTs. In Experiment 1, 30 participants performed the detection task within a dynamic context (video tapes representing a sequence of four action frames). In Experiment 2, 28 participants read sentences that represented object-related actions. The stimulation effect (a cathode applied to the DLPFC and an anode to the right supraorbital region) was analyzed by comparing the ER, RT, and ERP profiles before and after stimulation (or sham treatment). A significant reduction of the N400 was observed for incongruent stimuli in the case of cathodal (inhibitory) stimulation of the DLPFC in comparison with prestimulation conditions for Experiment 1, but not Experiment 2. Moreover, ERs were increased, and RTs were reduced in response to incongruent conditions after tDCS, but not after sham stimulation in Experiment 1. It is suggested that perturbation of the DLPFC may limit the ability to analyze a semantically anomalous action sequence as a reduced N400 ERP effect and increased random responses was observed. Finally, the contribution of the frontal area to the semantic processing of actions is discussed.

Word segmentation by alternating colors facilitates eye guidance in Chinese reading.

PubMed

Zhou, Wei; Wang, Aiping; Shu, Hua; Kliegl, Reinhold; Yan, Ming

2018-02-12

During sentence reading, low spatial frequency information afforded by spaces between words is the primary factor for eye guidance in spaced writing systems, whereas saccade generation for unspaced writing systems is less clear and under debate. In the present study, we investigated whether word-boundary information, provided by alternating colors (consistent or inconsistent with word-boundary information) influences saccade-target selection in Chinese. In Experiment 1, as compared to a baseline (i.e., uniform color) condition, word segmentation with alternating color shifted fixation location towards the center of words. In contrast, incorrect word segmentation shifted fixation location towards the beginning of words. In Experiment 2, we used a gaze-contingent paradigm to restrict the color manipulation only to the upcoming parafoveal words and replicated the results, including fixation location effects, as observed in Experiment 1. These results indicate that Chinese readers are capable of making use of parafoveal word-boundary knowledge for saccade generation, even if such information is unfamiliar to them. The present study provides novel support for the hypothesis that word segmentation is involved in the decision about where to fixate next during Chinese reading.

Phonological neighborhood and word frequency effects on the stuttered disfluencies of children who stutter: comments on Anderson (2007).

PubMed

Howell, Peter

2010-10-01

This letter comments on a study by Anderson (2007) that compared the effects of word frequency, neighborhood density, and phonological neighborhood frequency on part-word repetitions, prolongations, and single-syllable word repetitions produced by children who stutter. Anderson discussed her results with respect to 2 theories about stuttering: the covert repair hypothesis and execution planning (EXPLAN) theory. Her remarks about EXPLAN theory are examined. Anderson considered that EXPLAN does not predict the relationship between word and neighborhood frequency and stuttering for part-word repetitions and prolongations (she considered that EXPLAN predicts that stuttering occurs on simple words for children). The actual predictions that EXPLAN makes are upheld by her results. She also considered that EXPLAN cannot account for why stuttering is affected by the same variables that lead to speech errors, and it is shown that this is incorrect. The effects of word frequency, neighborhood density, and phonological neighborhood frequency on part-word repetitions, prolongations, and single-syllable word repetitions reported by Anderson (2007) are consistent with the predictions of the EXPLAN model.

Which button will I press? Preference for correctly ordered counting sequences in 18-month-olds.

PubMed

Ip, Martin Ho Kwan; Imuta, Kana; Slaughter, Virginia

2018-04-16

Correct counting respects the stable order principle whereby the count terms are recited in a fixed order every time. The 4 experiments reported here tested whether precounting infants recognize and prefer correct stable-ordered counting. The authors introduced a novel preference paradigm in which infants could freely press two buttons to activate videos of counting events. In the "correct" counting video, number words were always recited in the canonical order ("1, 2, 3, 4, 5, 6"). The "incorrect" counting video was identical except that the number words were recited in a random order (e.g., "5, 3, 1, 6, 4, 2"). In Experiment 1, 18-month-olds (n = 21), but not 15-month-olds (n = 24), significantly preferred to press the button that activated correct counting events. Experiment 2 revealed that English-learning 18-month-olds' (n = 21) preference for stable-ordered counting disappeared when the counting was done in Japanese. By contrast, Experiment 3 showed that multilingual 18-month-olds (n = 24) preferred correct stable-ordered counting in an unfamiliar foreign language. In Experiment 4, multilingual 18-month-olds (N = 21) showed no preference for stable-ordered alphabet sequences, ruling out some alternative explanations for the Experiment 3 results. Overall these findings are consistent with the idea that implicit recognition of the stable order principle of counting is acquired by 18 months of age, and that learning more than one language may accelerate infants' understanding of abstract counting principles. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

Effect of Context and Hearing Loss on Time-Gated Word Recognition in Children.

PubMed

Lewis, Dawna; Kopun, Judy; McCreery, Ryan; Brennan, Marc; Nishi, Kanae; Cordrey, Evan; Stelmachowicz, Pat; Moeller, Mary Pat

The purpose of this study was to examine word recognition in children who are hard of hearing (CHH) and children with normal hearing (CNH) in response to time-gated words presented in high- versus low-predictability sentences (HP, LP), where semantic cues were manipulated. Findings inform our understanding of how CHH combine cognitive-linguistic and acoustic-phonetic cues to support spoken word recognition. It was hypothesized that both groups of children would be able to make use of linguistic cues provided by HP sentences to support word recognition. CHH were expected to require greater acoustic information (more gates) than CNH to correctly identify words in the LP condition. In addition, it was hypothesized that error patterns would differ across groups. Sixteen CHH with mild to moderate hearing loss and 16 age-matched CNH participated (5 to 12 years). Test stimuli included 15 LP and 15 HP age-appropriate sentences. The final word of each sentence was divided into segments and recombined with the sentence frame to create series of sentences in which the final word was progressively longer by the gated increments. Stimuli were presented monaurally through headphones and children were asked to identify the target word at each successive gate. They also were asked to rate their confidence in their word choice using a five- or three-point scale. For CHH, the signals were processed through a hearing aid simulator. Standardized language measures were used to assess the contribution of linguistic skills. Analysis of language measures revealed that the CNH and CHH performed within the average range on language abilities. Both groups correctly recognized a significantly higher percentage of words in the HP condition than in the LP condition. Although CHH performed comparably with CNH in terms of successfully recognizing the majority of words, differences were observed in the amount of acoustic-phonetic information needed to achieve accurate word recognition. CHH needed more gates than CNH to identify words in the LP condition. CNH were significantly lower in rating their confidence in the LP condition than in the HP condition. CHH, however, were not significantly different in confidence between the conditions. Error patterns for incorrect word responses across gates and predictability varied depending on hearing status. The results of this study suggest that CHH with age-appropriate language abilities took advantage of context cues in the HP sentences to guide word recognition in a manner similar to CNH. However, in the LP condition, they required more acoustic information (more gates) than CNH for word recognition. Differences in the structure of incorrect word responses and their nomination patterns across gates for CHH compared with their peers with NH suggest variations in how these groups use limited acoustic information to select word candidates.

Computer Language Settings and Canadian Spellings

ERIC Educational Resources Information Center

Shuttleworth, Roger

2011-01-01

The language settings used on personal computers interact with the spell-checker in Microsoft Word, which directly affects the flagging of spellings that are deemed incorrect. This study examined the language settings of personal computers owned by a group of Canadian university students. Of 21 computers examined, only eight had their Windows…

Prefrontal neural correlates of memory for sequences.

PubMed

Averbeck, Bruno B; Lee, Daeyeol

2007-02-28

The sequence of actions appropriate to solve a problem often needs to be discovered by trial and error and recalled in the future when faced with the same problem. Here, we show that when monkeys had to discover and then remember a sequence of decisions across trials, ensembles of prefrontal cortex neurons reflected the sequence of decisions the animal would make throughout the interval between trials. This signal could reflect either an explicit memory process or a sequence-planning process that begins far in advance of the actual sequence execution. This finding extended to error trials such that, when the neural activity during the intertrial interval specified the wrong sequence, the animal also attempted to execute an incorrect sequence. More specifically, we used a decoding analysis to predict the sequence the monkey was planning to execute at the end of the fore-period, just before sequence execution. When this analysis was applied to error trials, we were able to predict where in the sequence the error would occur, up to three movements into the future. This suggests that prefrontal neural activity can retain information about sequences between trials, and that regardless of whether information is remembered correctly or incorrectly, the prefrontal activity veridically reflects the animal's action plan.

Quality Control Test for Sequence-Phenotype Assignments

PubMed Central

Ortiz, Maria Teresa Lara; Rosario, Pablo Benjamín Leon; Luna-Nevarez, Pablo; Gamez, Alba Savin; Martínez-del Campo, Ana; Del Rio, Gabriel

2015-01-01

Relating a gene mutation to a phenotype is a common task in different disciplines such as protein biochemistry. In this endeavour, it is common to find false relationships arising from mutations introduced by cells that may be depurated using a phenotypic assay; yet, such phenotypic assays may introduce additional false relationships arising from experimental errors. Here we introduce the use of high-throughput DNA sequencers and statistical analysis aimed to identify incorrect DNA sequence-phenotype assignments and observed that 10–20% of these false assignments are expected in large screenings aimed to identify critical residues for protein function. We further show that this level of incorrect DNA sequence-phenotype assignments may significantly alter our understanding about the structure-function relationship of proteins. We have made available an implementation of our method at http://bis.ifc.unam.mx/en/software/chispas. PMID:25700273

Rotary pin-in-maze discriminator

DOEpatents

Benavides, Gilbert L.

1997-01-01

A discriminator apparatus and method that discriminates between a unique signal and any other (incorrect) signal. The unique signal is a sequence of events; each event can assume one of two possible event states. Given the unique signal, a maze wheel is allowed to rotate fully in one direction. Given an incorrect signal, both the maze wheel and a pin wheel lock in position.

Misrepresenting "Choice Biographies"?: A Reply to Woodman

ERIC Educational Resources Information Center

Roberts, Steven

2010-01-01

This paper provides a reply to Woodman's (2009) recent argument that youth studies often incorrectly attribute the concept of "choice biographies" to the work of Ulrich Beck. Drawing heavily on Beck's own words, this paper contends that youth researchers might not be making this association unduly. Consideration is paid to some conceptual issues…

Stress errors in a case of developmental surface dyslexia in Filipino.

PubMed

Dulay, Katrina May; Hanley, J Richard

2015-01-01

This paper reports the case of a dyslexic boy (L.A.) whose impaired reading of Filipino is consistent with developmental surface dyslexia. Filipino has a transparent alphabetic orthography with stress typically falling on the penultimate syllable of multisyllabic words. However, exceptions to the typical stress pattern are not marked in the Filipino orthography. L.A. read words with typical stress patterns as accurately as controls, but made many more stress errors than controls when reading Filipino words with atypical stress. He regularized the pronunciation of many of these words by incorrectly placing the stress on the penultimate syllable. Since he also read nonwords as accurately and quickly as controls and performed well on tests of phonological awareness, L.A. appears to present a clear case of developmental surface dyslexia in a transparent orthography.

L2 Spelling Errors in Italian Children with Dyslexia.

PubMed

Palladino, Paola; Cismondo, Dhebora; Ferrari, Marcella; Ballagamba, Isabella; Cornoldi, Cesare

2016-05-01

The present study aimed to investigate L2 spelling skills in Italian children by administering an English word dictation task to 13 children with dyslexia (CD), 13 control children (comparable in age, gender, schooling and IQ) and a group of 10 children with an English learning difficulty, but no L1 learning disorder. Patterns of difficulties were examined for accuracy and type of errors, in spelling dictated short and long words (i.e. disyllables and three syllables). Notably, CD were poor in spelling English words. Furthermore, their errors were mainly related with phonological representation of words, as they made more 'phonologically' implausible errors than controls. In addition, CD errors were more frequent for short than long words. Conversely, the three groups did not differ in the number of plausible ('non-phonological') errors, that is, words that were incorrectly written, but whose reading could correspond to the dictated word via either Italian or English rules. Error analysis also showed syllable position differences in the spelling patterns of CD, children with and English learning difficulty and control children. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Effect of Context and Hearing Loss on Time-Gated Word Recognition in Children

PubMed Central

Lewis, Dawna E.; Kopun, Judy; McCreery, Ryan; Brennan, Marc; Nishi, Kanae; Cordrey, Evan; Stelmachowicz, Pat; Moeller, Mary Pat

2016-01-01

Objectives The purpose of this study was to examine word recognition in children who are hard of hearing (CHH) and children with normal hearing (CNH) in response to time-gated words presented in high- vs. low-predictability sentences (HP, LP), where semantic cues were manipulated. Findings inform our understanding of how CHH combine cognitive-linguistic and acoustic-phonetic cues to support spoken word recognition. It was hypothesized that both groups of children would be able to make use of linguistic cues provided by HP sentences to support word recognition. CHH were expected to require greater acoustic information (more gates) than CNH to correctly identify words in the LP condition. In addition, it was hypothesized that error patterns would differ across groups. Design Sixteen CHH with mild-to-moderate hearing loss and 16 age-matched CNH participated (5–12 yrs). Test stimuli included 15 LP and 15 HP age-appropriate sentences. The final word of each sentence was divided into segments and recombined with the sentence frame to create series of sentences in which the final word was progressively longer by the gated increments. Stimuli were presented monaurally through headphones and children were asked to identify the target word at each successive gate. They also were asked to rate their confidence in their word choice using a 5- or 3-point scale. For CHH, the signals were processed through a hearing aid simulator. Standardized language measures were used to assess the contribution of linguistic skills. Results Analysis of language measures revealed that the CNH and CHH performed within the average range on language abilities. Both groups correctly recognized a significantly higher percentage of words in the HP condition than in the LP condition. Although CHH performed comparably to CNH in terms of successfully recognizing the majority of words, differences were observed in the amount of acoustic-phonetic information needed to achieve accurate word recognition. CHH needed more gates than CNH to identify words in the LP condition. CNH were significantly lower in rating their confidence in the LP condition than in the HP condition. CHH, however, were not significantly different in confidence between the conditions. Error patterns for incorrect word responses across gates and predictability varied depending on hearing status. Conclusions The results of this study suggest that CHH with age-appropriate language abilities took advantage of context cues in the HP sentences to guide word recognition in a manner similar to CNH. However, in the LP condition, they required more acoustic information (more gates) than CNH for word recognition. Differences in the structure of incorrect word responses and their nomination patterns across gates for CHH compared to their peers with normal hearing suggest variations in how these groups use limited acoustic information to select word candidates. PMID:28045838

Rotary pin-in-maze discriminator

DOEpatents

Benavides, G.L.

1997-05-06

A discriminator apparatus and method that discriminates between a unique signal and any other (incorrect) signal are disclosed. The unique signal is a sequence of events; each event can assume one of two possible event states. Given the unique signal, a maze wheel is allowed to rotate fully in one direction. Given an incorrect signal, both the maze wheel and a pin wheel lock in position. 4 figs.

Investigating the technical adequacy of curriculum-based measurement in written expression for students who are deaf or hard of hearing.

PubMed

Cheng, Shu-Fen; Rose, Susan

2009-01-01

This study investigated the technical adequacy of curriculum-based measures of written expression (CBM-W) in terms of writing prompts and scoring methods for deaf and hard-of-hearing students. Twenty-two students at the secondary school-level completed 3-min essays within two weeks, which were scored for nine existing and alternative curriculum-based measurement (CBM) scoring methods. The technical features of the nine scoring methods were examined for interrater reliability, alternate-form reliability, and criterion-related validity. The existing CBM scoring method--number of correct minus incorrect word sequences--yielded the highest reliability and validity coefficients. The findings from this study support the use of the CBM-W as a reliable and valid tool for assessing general writing proficiency with secondary students who are deaf or hard of hearing. The CBM alternative scoring methods that may serve as additional indicators of written expression include correct subject-verb agreements, correct clauses, and correct morphemes.

BioWord: A sequence manipulation suite for Microsoft Word

PubMed Central

2012-01-01

Background The ability to manipulate, edit and process DNA and protein sequences has rapidly become a necessary skill for practicing biologists across a wide swath of disciplines. In spite of this, most everyday sequence manipulation tools are distributed across several programs and web servers, sometimes requiring installation and typically involving frequent switching between applications. To address this problem, here we have developed BioWord, a macro-enabled self-installing template for Microsoft Word documents that integrates an extensive suite of DNA and protein sequence manipulation tools. Results BioWord is distributed as a single macro-enabled template that self-installs with a single click. After installation, BioWord will open as a tab in the Office ribbon. Biologists can then easily manipulate DNA and protein sequences using a familiar interface and minimize the need to switch between applications. Beyond simple sequence manipulation, BioWord integrates functionality ranging from dyad search and consensus logos to motif discovery and pair-wise alignment. Written in Visual Basic for Applications (VBA) as an open source, object-oriented project, BioWord allows users with varying programming experience to expand and customize the program to better meet their own needs. Conclusions BioWord integrates a powerful set of tools for biological sequence manipulation within a handy, user-friendly tab in a widely used word processing software package. The use of a simple scripting language and an object-oriented scheme facilitates customization by users and provides a very accessible educational platform for introducing students to basic bioinformatics algorithms. PMID:22676326

BioWord: a sequence manipulation suite for Microsoft Word.

PubMed

Anzaldi, Laura J; Muñoz-Fernández, Daniel; Erill, Ivan

2012-06-07

The ability to manipulate, edit and process DNA and protein sequences has rapidly become a necessary skill for practicing biologists across a wide swath of disciplines. In spite of this, most everyday sequence manipulation tools are distributed across several programs and web servers, sometimes requiring installation and typically involving frequent switching between applications. To address this problem, here we have developed BioWord, a macro-enabled self-installing template for Microsoft Word documents that integrates an extensive suite of DNA and protein sequence manipulation tools. BioWord is distributed as a single macro-enabled template that self-installs with a single click. After installation, BioWord will open as a tab in the Office ribbon. Biologists can then easily manipulate DNA and protein sequences using a familiar interface and minimize the need to switch between applications. Beyond simple sequence manipulation, BioWord integrates functionality ranging from dyad search and consensus logos to motif discovery and pair-wise alignment. Written in Visual Basic for Applications (VBA) as an open source, object-oriented project, BioWord allows users with varying programming experience to expand and customize the program to better meet their own needs. BioWord integrates a powerful set of tools for biological sequence manipulation within a handy, user-friendly tab in a widely used word processing software package. The use of a simple scripting language and an object-oriented scheme facilitates customization by users and provides a very accessible educational platform for introducing students to basic bioinformatics algorithms.

Perception and Bias in the Processing of Compound versus Phrasal Stress: Evidence from Event-Related Brain Potentials

ERIC Educational Resources Information Center

McCauley, Stewart M; Hestvik, Arild; Vogel, Irene

2013-01-01

Previous research using picture/word matching tasks has demonstrated a tendency to incorrectly interpret phrasally stressed strings as compounds. Using event-related potentials, we sought to determine whether this pattern stems from poor perceptual sensitivity to the compound/phrasal stress distinction, or from a post-perceptual bias in behavioral…

Folk Etymology (In English and Elsewhere).

ERIC Educational Resources Information Center

Poruciuc, Adrian

Folk etymology is defined as a change in word or phrase form resulting from an incorrect popular idea of its origin or meaning. Irregular phonetic-semantic shifts are produced by inter-language borrowing or by intra-language passage from one period to another. These shifts are more common in periods when there are no, or few, normative factors…

On the Use of Lexical Stress in Reading Spanish

ERIC Educational Resources Information Center

Gutierrez-Palma, Nicolas; Palma-Reyes, Alfonso

2008-01-01

This paper investigates whether or not lexical stress is used for lexical access in Spanish. A lexical decision task and a masking priming procedure were used to compare correctly-versus-incorrectly stressed words (e.g., "tecla-TECLA vs. tecla-TECLA"). SOA (Stimulus Onset Asynchrony) was manipulated at 33, 66, 100, and 143 ms. The results showed…

Perception of Lexical Stress by Brain-Damaged Individuals: Effects on Lexical-Semantic Activation

ERIC Educational Resources Information Center

Shah, Amee P.; Baum, Shari R.

2006-01-01

A semantic priming, lexical-decision study was conducted to examine the ability of left- and right-brain damaged individuals to perceive lexical-stress cues and map them onto lexical-semantic representations. Correctly and incorrectly stressed primes were paired with related and unrelated target words to tap implicit processing of lexical prosody.…

Spelling in Written Stories by School-Age Children with Cochlear Implants

ERIC Educational Resources Information Center

Straley, Sara G.; Werfel, Krystal L.; Hendricks, Alison Eisel

2016-01-01

This study evaluated the spelling of 3rd to 6th grade children with cochlear implants in written stories. Spelling was analysed using traditional correct/incorrect scoring as well as the Spelling Sensitivity Score, which provides linguistic information about spelling attempts. Children with cochlear implants spelled 86 per cent of words in stories…

On avoided words, absent words, and their application to biological sequence analysis.

PubMed

Almirantis, Yannis; Charalampopoulos, Panagiotis; Gao, Jia; Iliopoulos, Costas S; Mohamed, Manal; Pissis, Solon P; Polychronopoulos, Dimitris

2017-01-01

The deviation of the observed frequency of a word w from its expected frequency in a given sequence x is used to determine whether or not the word is avoided . This concept is particularly useful in DNA linguistic analysis. The value of the deviation of w , denoted by [Formula: see text], effectively characterises the extent of a word by its edge contrast in the context in which it occurs. A word w of length [Formula: see text] is a [Formula: see text]-avoided word in x if [Formula: see text], for a given threshold [Formula: see text]. Notice that such a word may be completely absent from x . Hence, computing all such words naïvely can be a very time-consuming procedure, in particular for large k . In this article, we propose an [Formula: see text]-time and [Formula: see text]-space algorithm to compute all [Formula: see text]-avoided words of length k in a given sequence of length n over a fixed-sized alphabet. We also present a time-optimal [Formula: see text]-time algorithm to compute all [Formula: see text]-avoided words (of any length) in a sequence of length n over an integer alphabet of size [Formula: see text]. In addition, we provide a tight asymptotic upper bound for the number of [Formula: see text]-avoided words over an integer alphabet and the expected length of the longest one. We make available an implementation of our algorithm. Experimental results, using both real and synthetic data, show the efficiency and applicability of our implementation in biological sequence analysis. The systematic search for avoided words is particularly useful for biological sequence analysis. We present a linear-time and linear-space algorithm for the computation of avoided words of length k in a given sequence x . We suggest a modification to this algorithm so that it computes all avoided words of x , irrespective of their length, within the same time complexity. We also present combinatorial results with regards to avoided words and absent words.

Semantic Specificity in One-Year-Olds' Word Comprehension.

PubMed

Bergelson, Elika; Aslin, Richard

2017-01-01

The present study investigated infants' knowledge about familiar nouns. Infants (n = 46, 12-20-month-olds) saw two-image displays of familiar objects, or one familiar and one novel object. Infants heard either a matching word (e.g. "foot' when seeing foot and juice), a related word (e.g. "sock" when seeing foot and juice) or a nonce word (e.g. "fep" when seeing a novel object and dog). Across the whole sample, infants reliably fixated the referent on matching and nonce trials. On the critical related trials we found increasingly less looking to the incorrect (but related) image with age. These results suggest that one-year-olds look at familiar objects both when they hear them labeled and when they hear related labels, to similar degrees, but over the second year increasingly rely on semantic fit. We suggest that infants' initial semantic representations are imprecise, and continue to sharpen over the second postnatal year.

Sequence comparison alignment-free approach based on suffix tree and L-words frequency.

PubMed

Soares, Inês; Goios, Ana; Amorim, António

2012-01-01

The vast majority of methods available for sequence comparison rely on a first sequence alignment step, which requires a number of assumptions on evolutionary history and is sometimes very difficult or impossible to perform due to the abundance of gaps (insertions/deletions). In such cases, an alternative alignment-free method would prove valuable. Our method starts by a computation of a generalized suffix tree of all sequences, which is completed in linear time. Using this tree, the frequency of all possible words with a preset length L-L-words--in each sequence is rapidly calculated. Based on the L-words frequency profile of each sequence, a pairwise standard Euclidean distance is then computed producing a symmetric genetic distance matrix, which can be used to generate a neighbor joining dendrogram or a multidimensional scaling graph. We present an improvement to word counting alignment-free approaches for sequence comparison, by determining a single optimal word length and combining suffix tree structures to the word counting tasks. Our approach is, thus, a fast and simple application that proved to be efficient and powerful when applied to mitochondrial genomes. The algorithm was implemented in Python language and is freely available on the web.

The influence of phonological priming on variability in articulation

NASA Astrophysics Data System (ADS)

Babel, Molly E.; Munson, Benjamin

2004-05-01

Previous research [Sevald and Dell, Cognition 53, 91-127 (1994)] has found that reiterant sequences of CVC words are produced more quickly when the prime word and target word share VC sequences (i.e., sequences like sit sick) than when they are identical (sequences like sick sick). Even slower production rates are found when primes and targets share a CV sequence (sequences like kick sick). These data have been used to support a model of speech production in which lexical items and their constituent phonemes are activated sequentially. The current experiment investigated whether phonological priming also influences variability in the acoustic characteristics of words. Specifically, we examined whether greater variability in the acoustic characteristics of target words was noted in the CV-related prime context than in the identical-prime context, and whether less variability was noted in the VC-related context. Thirty adult subjects with typical speech, language, and hearing ability produced reiterant two-word sequences that varied in their phonological similarity. The duration, first, and second formant frequencies of the target-words' vowels were measured. Preliminary analyses indicate that phonological priming does not have a systematic effect on variability in these acoustic parameters.

Non-Adjacent Consonant Sequence Patterns in English Target Words during the First-Word Period

ERIC Educational Resources Information Center

Aoyama, Katsura; Davis, Barbara L.

2017-01-01

The goal of this study was to investigate non-adjacent consonant sequence patterns in target words during the first-word period in infants learning American English. In the spontaneous speech of eighteen participants, target words with a Consonant-Vowel-Consonant (C[subscript 1]VC[subscript 2]) shape were analyzed. Target words were grouped into…

Are There Separate Neural Systems for Spelling? New Insights into the Role of Rules and Memory in Spelling from Functional Magnetic Resonance Imaging.

PubMed

Norton, Elizabeth S; Kovelman, Ioulia; Petitto, Laura-Ann

2007-03-01

How do people spell the thousands of words at the tips of their tongues? Are words with regular sound-to-letter correspondences (e.g., "blink") spelled using the same neural systems as those with irregular correspondences (e.g., "yacht")? By offering novel neuroimaging evidence, we aim to advance contemporary debate about whether people use a single lexical memory process or whether dual mechanisms of lexical memory and sublexical phonological rules work in concert. We further aim to advance understanding of how people read by taking a fresh look at the related yet distinct capacity to spell. During functional magnetic resonance imaging scanning, 12 participants heard low-frequency regular words, irregular words, and nonwords (e.g., "shelm") and responded whether a visual presentation of the word was spelled correctly or incorrectly. While behavioral measures suggested some differences in accuracy and reaction time for the different word types, the neuroimaging results alone demonstrated robust differential processing and support a dual-route model of spelling, with implications for how spelling is taught and remediated in clinical and educational contexts.

Phonotactics, Neighborhood Activation, and Lexical Access for Spoken Words

PubMed Central

Vitevitch, Michael S.; Luce, Paul A.; Pisoni, David B.; Auer, Edward T.

2012-01-01

Probabilistic phonotactics refers to the relative frequencies of segments and sequences of segments in spoken words. Neighborhood density refers to the number of words that are phonologically similar to a given word. Despite a positive correlation between phonotactic probability and neighborhood density, nonsense words with high probability segments and sequences are responded to more quickly than nonsense words with low probability segments and sequences, whereas real words occurring in dense similarity neighborhoods are responded to more slowly than real words occurring in sparse similarity neighborhoods. This contradiction may be resolved by hypothesizing that effects of probabilistic phonotactics have a sublexical focus and that effects of similarity neighborhood density have a lexical focus. The implications of this hypothesis for models of spoken word recognition are discussed. PMID:10433774

Perception and the Temporal Properties of Speech.

DTIC Science & Technology

1993-01-11

conditions. In the embedded condition, phoneme sequences equivalent to these words formed the second syllable of a two-syllable word. In the unembedded ... unembedded in the sequence "warm lips". These priming sequences were based on the sequences used in Experiment 2. Each combinable priming sequence in...unrelated, to the embedded or unembedded prime word. The probes used in this experiment were identical to the ones used in Experiment 2. Subjects were tested

Attention and recognition memory bias for alcohol-related stimuli among alcohol-dependent patients attending residential treatment.

PubMed

Klein, Audrey A; Nelson, Lindsay M; Anker, Justin J

2013-03-01

Though studies have examined attentional bias for alcohol-related information among alcohol-dependent individuals, few have examined memory bias. This study examined attention and recognition memory biases for alcohol-related information among patients recently admitted to residential alcohol treatment (n=100; 40% female). Participants completed a computerized attentional task wherein they classified a centrally-presented digit as odd or even. On some trials, an alcohol word, neutral word, or anagram was presented along with the digit. On these dual trials participants first classified the digit and then classified the other stimulus as a word or nonword. Participants took longer to classify digits that appeared with alcohol words compared to neutral words; suggesting the alcohol words distracted them from processing the digit. In a subsequent recognition memory test, participants showed significantly higher hit rates (i.e., correctly classifying an old item as old) and false alarm rates (i.e., incorrectly classifying a new item as old) to the alcohol words compared to the neutral words, and they also showed a more liberal response bias to alcohol words. The findings suggest that alcohol-dependent individuals exhibit both attention and memory bias for alcohol-related information. Copyright © 2012 Elsevier Ltd. All rights reserved.

Listening beneath the Words: Parallel Processes in Music and Psychotherapy

ERIC Educational Resources Information Center

Shapiro, Yakov; Marks-Tarlow,Terry; Fridman, Joseph

2017-01-01

The authors investigate the parallels between musical performance and psychoanalytical therapy, using the former as a metaphor for the way therapist and patient jointly compose the therapeutic experience and better the treatment it offers. [Note: The volume and issue number (v9 n1) shown on this PDF is incorrect. The correct citation is v9 n2.

Transcranial magnetic stimulation of the left angular gyrus during encoding does not impair associative memory performance.

PubMed

Koen, Joshua D; Thakral, Preston P; Rugg, Michael D

2018-06-05

The left angular gyrus (AG) is thought to play a critical role in episodic retrieval and has been implicated in the recollection of specific details of prior episodes. Motivated by recent fMRI studies in which it was reported that elevated neural activity in left AG during study is predictive of subsequent associative memory, the present study investigated whether the region plays a causal role in associative memory encoding. Participants underwent online transcranial magnetic stimulation (TMS) while encoding word pairs prior to an associative memory test. We predicted that TMS to left AG during encoding would result in reduced subsequent memory accuracy, especially for estimates of recollection. The results did not support this prediction: estimates of both recollection and familiarity-driven recognition were essentially identical for words pairs encoded during TMS to left AG relative to a vertex control site. These results suggest that the left AG may not play a necessary role in associative memory encoding. TMS to left AG did however affect confidence for incorrect 'intact' judgments to rearranged pairs and incorrect 'rearranged' judgments to intact pairs. These findings suggest that the left AG supports encoding processes that contribute to aspects of subjective mnemonic experience.

Fast alignment-free sequence comparison using spaced-word frequencies.

PubMed

Leimeister, Chris-Andre; Boden, Marcus; Horwege, Sebastian; Lindner, Sebastian; Morgenstern, Burkhard

2014-07-15

Alignment-free methods for sequence comparison are increasingly used for genome analysis and phylogeny reconstruction; they circumvent various difficulties of traditional alignment-based approaches. In particular, alignment-free methods are much faster than pairwise or multiple alignments. They are, however, less accurate than methods based on sequence alignment. Most alignment-free approaches work by comparing the word composition of sequences. A well-known problem with these methods is that neighbouring word matches are far from independent. To reduce the statistical dependency between adjacent word matches, we propose to use 'spaced words', defined by patterns of 'match' and 'don't care' positions, for alignment-free sequence comparison. We describe a fast implementation of this approach using recursive hashing and bit operations, and we show that further improvements can be achieved by using multiple patterns instead of single patterns. To evaluate our approach, we use spaced-word frequencies as a basis for fast phylogeny reconstruction. Using real-world and simulated sequence data, we demonstrate that our multiple-pattern approach produces better phylogenies than approaches relying on contiguous words. Our program is freely available at http://spaced.gobics.de/. © The Author 2014. Published by Oxford University Press.

Statistical learning of an auditory sequence and reorganization of acquired knowledge: A time course of word segmentation and ordering.

PubMed

Daikoku, Tatsuya; Yatomi, Yutaka; Yumoto, Masato

2017-01-27

Previous neural studies have supported the hypothesis that statistical learning mechanisms are used broadly across different domains such as language and music. However, these studies have only investigated a single aspect of statistical learning at a time, such as recognizing word boundaries or learning word order patterns. In this study, we neutrally investigated how the two levels of statistical learning for recognizing word boundaries and word ordering could be reflected in neuromagnetic responses and how acquired statistical knowledge is reorganised when the syntactic rules are revised. Neuromagnetic responses to the Japanese-vowel sequence (a, e, i, o, and u), presented every .45s, were recorded from 14 right-handed Japanese participants. The vowel order was constrained by a Markov stochastic model such that five nonsense words (aue, eao, iea, oiu, and uoi) were chained with an either-or rule: the probability of the forthcoming word was statistically defined (80% for one word; 20% for the other word) by the most recent two words. All of the word transition probabilities (80% and 20%) were switched in the middle of the sequence. In the first and second quarters of the sequence, the neuromagnetic responses to the words that appeared with higher transitional probability were significantly reduced compared with those that appeared with a lower transitional probability. After switching the word transition probabilities, the response reduction was replicated in the last quarter of the sequence. The responses to the final vowels in the words were significantly reduced compared with those to the initial vowels in the last quarter of the sequence. The results suggest that both within-word and between-word statistical learning are reflected in neural responses. The present study supports the hypothesis that listeners learn larger structures such as phrases first, and they subsequently extract smaller structures, such as words, from the learned phrases. The present study provides the first neurophysiological evidence that the correction of statistical knowledge requires more time than the acquisition of new statistical knowledge. Copyright © 2016 Elsevier Ltd. All rights reserved.

Effects of Severe Bothersome Tinnitus on Cognitive Function Measured with Standardized Tests

PubMed Central

Pierce, Katherine J.; Kallogjeri, Dorina; Piccirillo, Jay F.; Garcia, Keith S.; Nicklaus, Joyce E.; Burton, Harold

2012-01-01

Neurocognitive tests compared abilities in people with bothersome tinnitus against an age, gender, and education matched normative population. Participants between 18 and 60 years had subjective, unilateral or bilateral, non-pulsatile tinnitus for >6 months, and a Tinnitus Handicap Inventory score of ≥38. Results from a first testing session showed deficits in learning, learning rates, immediate recall of heard words, and use of a serial order encoding strategy. Initial reliance on serial order encoding and later, increased intrusion of incorrect words towards normal levels might indicate a less demanding strategy to compensate for weakness in associative memory for semantic categories. PMID:22168528

Implicit and explicit mechanisms of word learning in a narrative context: an event-related potential study.

PubMed

Batterink, Laura; Neville, Helen

2011-11-01

The vast majority of word meanings are learned simply by extracting them from context rather than by rote memorization or explicit instruction. Although this skill is remarkable, little is known about the brain mechanisms involved. In the present study, ERPs were recorded as participants read stories in which pseudowords were presented multiple times, embedded in consistent, meaningful contexts (referred to as meaning condition, M+) or inconsistent, meaningless contexts (M-). Word learning was then assessed implicitly using a lexical decision task and explicitly through recall and recognition tasks. Overall, during story reading, M- words elicited a larger N400 than M+ words, suggesting that participants were better able to semantically integrate M+ words than M- words throughout the story. In addition, M+ words whose meanings were subsequently correctly recognized and recalled elicited a more positive ERP in a later time window compared with M+ words whose meanings were incorrectly remembered, consistent with the idea that the late positive component is an index of encoding processes. In the lexical decision task, no behavioral or electrophysiological evidence for implicit priming was found for M+ words. In contrast, during the explicit recognition task, M+ words showed a robust N400 effect. The N400 effect was dependent upon recognition performance, such that only correctly recognized M+ words elicited an N400. This pattern of results provides evidence that the explicit representations of word meanings can develop rapidly, whereas implicit representations may require more extensive exposure or more time to emerge.

Frequency Effects on ESL Compositional Multi-Word Sequence Processing

ERIC Educational Resources Information Center

Supasiraprapa, Sarut

2017-01-01

The current study investigated whether adult native English speakers and English-as-a-second-language (ESL) learners exhibit sensitivity to compositional English multi-word sequences, which have a meaning derivable from word parts (e.g., don't have to worry as opposed to sequences like He left the US for good, where for good cannot be taken apart…

The mechanism of suppression: a component of general comprehension skill.

PubMed

Gernsbacher, M A; Faust, M E

1991-03-01

We investigated whether the cognitive mechanism of suppression underlies differences in adult comprehension skill. Less skilled comprehenders reject less efficiently the inappropriate meanings of ambiguous words (e.g., the playing card vs. garden tool meaning of spade), the incorrect forms of homophones (e.g., patients vs. patience), the highly typical but absent members of scenes (e.g., a tractor in a farm scene), and words superimposed on pictures or pictures surrounding words. However, less skilled comprehenders are not less cognizant of what is contextually appropriate; in fact, they benefit from a biasing context just as much (and perhaps more) as more skilled comprehenders do. Thus, less skilled comprehenders do not have difficulty enhancing contextually appropriate information. Instead, we suggest that less skilled comprehenders suffer from a less efficient suppression mechanism, which we conclude is an important component of general comprehension skill.

Mapping the acquisition of the number word sequence in the first year of school

NASA Astrophysics Data System (ADS)

Gould, Peter

2017-03-01

Learning to count and to produce the correct sequence of number words in English is not a simple process. In NSW government schools taking part in Early Action for Success, over 800 students in each of the first 3 years of school were assessed every 5 weeks over the school year to determine the highest correct oral count they could produce. Rather than displaying a steady increase in the accurate sequence of the number words produced, the kindergarten data reported here identified clear, substantial hurdles in the acquisition of the counting sequence. The large-scale, longitudinal data also provided evidence of learning to count through the teens being facilitated by the semi-regular structure of the number words in English. Instead of occurring as hurdles to starting the next counting sequence, number words corresponding to some multiples of ten (10, 20 and 100) acted as if they were rest points. These rest points appear to be artefacts of how the counting sequence is acquired.

The low information content of Neurospora splicing signals: implications for RNA splicing and intron origin.

PubMed

Collins, Richard A; Stajich, Jason E; Field, Deborah J; Olive, Joan E; DeAbreu, Diane M

2015-05-01

When we expressed a small (0.9 kb) nonprotein-coding transcript derived from the mitochondrial VS plasmid in the nucleus of Neurospora we found that it was efficiently spliced at one or more of eight 5' splice sites and ten 3' splice sites, which are present apparently by chance in the sequence. Further experimental and bioinformatic analyses of other mitochondrial plasmids, random sequences, and natural nuclear genes in Neurospora and other fungi indicate that fungal spliceosomes recognize a wide range of 5' splice site and branchpoint sequences and predict introns to be present at high frequency in random sequence. In contrast, analysis of intronless fungal nuclear genes indicates that branchpoint, 5' splice site and 3' splice site consensus sequences are underrepresented compared with random sequences. This underrepresentation of splicing signals is sufficient to deplete the nuclear genome of splice sites at locations that do not comprise biologically relevant introns. Thus, the splicing machinery can recognize a wide range of splicing signal sequences, but splicing still occurs with great accuracy, not because the splicing machinery distinguishes correct from incorrect introns, but because incorrect introns are substantially depleted from the genome. © 2015 Collins et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Differences between conduction aphasia and Wernicke's aphasia.

PubMed

Anzaki, F; Izumi, S

2001-07-01

Conduction aphasia and Wernike's aphasia have been differentiated by the degree of auditory language comprehension. We quantitatively compared the speech sound errors of two conduction aphasia patients and three Wernicke's aphasia patients on various language modality tests. All of the patients were Japanese. The two conduction aphasia patients had "conduites d'approche" errors and phonological paraphasia. The patient with mild Wernicke's aphasia made various errors. In the patient with severe Wernicke's aphasia, neologism was observed. Phonological paraphasia in the two conduction aphasia patients seemed to occur when the examinee searched for the target word. They made more errors in vowels than in consonants of target words on the naming and repetition tests. They seemed to search the target word by the correct consonant phoneme and incorrect vocalic phoneme in the table of the Japanese alphabet. The Wernicke's aphasia patients who had severe impairment of auditory comprehension, made more errors in consonants than in vowels of target words. In conclusion, utterance of conduction aphasia and that of Wernicke's aphasia are qualitatively distinct.

Semantic Specificity in One-Year-Olds’ Word Comprehension

PubMed Central

Bergelson, Elika; Aslin, Richard

2017-01-01

The present study investigated infants’ knowledge about familiar nouns. Infants (n = 46, 12–20-month-olds) saw two-image displays of familiar objects, or one familiar and one novel object. Infants heard either a matching word (e.g. “foot’ when seeing foot and juice), a related word (e.g. “sock” when seeing foot and juice) or a nonce word (e.g. “fep” when seeing a novel object and dog). Across the whole sample, infants reliably fixated the referent on matching and nonce trials. On the critical related trials we found increasingly less looking to the incorrect (but related) image with age. These results suggest that one-year-olds look at familiar objects both when they hear them labeled and when they hear related labels, to similar degrees, but over the second year increasingly rely on semantic fit. We suggest that infants’ initial semantic representations are imprecise, and continue to sharpen over the second postnatal year. PMID:29200981

Is meaning implicated in illusory conjunctions?

PubMed

Virzi, R A; Egeth, H E

1984-08-01

According to feature-integration theory, when attention is diverted from a display, features from different objects in that display may be wrongly recombined, giving rise to "illusory conjunctions" (Treisman & Schmidt, 1982). Two experiments are reported that examine the nature of these illusory conjunctions. In displays that contain color names and adjectives printed in colored ink, subjects made two kinds of interesting and previously unreported errors. Consider, for example, a display that included the word BROWN in red ink and the word HEAVY in green ink. Subjects would sometimes incorrectly report that the word RED or the ink color brown had appeared in the display (e.g., RED in green ink or HEAVY in brown ink). It appears that subjects extract semantic representations from input and are sometimes confused about whether a particular representation has been extracted from a word or a color patch. Contrary to feature-integration theory, these findings suggest that illusory conjunctions may occur with high-level codes as well as with perceptual features.

Extracting DNA words based on the sequence features: non-uniform distribution and integrity.

PubMed

Li, Zhi; Cao, Hongyan; Cui, Yuehua; Zhang, Yanbo

2016-01-25

DNA sequence can be viewed as an unknown language with words as its functional units. Given that most sequence alignment algorithms such as the motif discovery algorithms depend on the quality of background information about sequences, it is necessary to develop an ab initio algorithm for extracting the "words" based only on the DNA sequences. We considered that non-uniform distribution and integrity were two important features of a word, based on which we developed an ab initio algorithm to extract "DNA words" that have potential functional meaning. A Kolmogorov-Smirnov test was used for consistency test of uniform distribution of DNA sequences, and the integrity was judged by the sequence and position alignment. Two random base sequences were adopted as negative control, and an English book was used as positive control to verify our algorithm. We applied our algorithm to the genomes of Saccharomyces cerevisiae and 10 strains of Escherichia coli to show the utility of the methods. The results provide strong evidences that the algorithm is a promising tool for ab initio building a DNA dictionary. Our method provides a fast way for large scale screening of important DNA elements and offers potential insights into the understanding of a genome.

Alcoholics' selective attention to alcohol stimuli: automated processing?

PubMed

Stormark, K M; Laberg, J C; Nordby, H; Hugdahl, K

2000-01-01

This study investigated alcoholics' selective attention to alcohol words in a version of the Stroop color-naming task. Alcoholic subjects (n = 23) and nonalcoholic control subjects (n = 23) identified the color of Stroop versions of alcohol, emotional, neutral and color words. Manual reaction times (RTs), skin conductance responses (SCRs) and heart rate (HR) were recorded. Alcoholics showed overall longer RTs than controls while both groups were slower in responding to the incongruent color words than to the other words. Alcoholics showed longer RTs to both alcohol (1522.7 milliseconds [ms]) and emotional words (1523.7 ms) than to neutral words (1450.8 ms) which suggests that the content of these words interfered with the ability to attend to the color of the words. There was also a negative correlation (r = -.41) between RT and response accuracy to alcohol words for the alcoholics, reflecting that the longer time the alcoholics used to respond to the color of the alcohol words, the more incorrect their responses were. The alcoholics also showed significantly greater SCRs to alcohol words (0.16 microSiemens) than to any of the other words (ranging from 0.04-0.08 microSiemens), probably reflecting the emotional significance of the alcohol words. Finally, the alcoholics evidenced smaller HR acceleration to alcohol (1.9 delta bpm) compared to neutral (2.8 delta bpm), which could be related to difficulties alcoholics experience in terminating their attention to the alcohol words. These findings indicate that it is difficult for alcoholics to regulate their attention to alcohol stimuli, suggesting that alcoholics' processing of alcohol information is automated.

Learning word order at birth: A NIRS study.

PubMed

Benavides-Varela, Silvia; Gervain, Judit

2017-06-01

In language, the relative order of words in sentences carries important grammatical functions. However, the developmental origins and the neural correlates of the ability to track word order are to date poorly understood. The current study therefore investigates the origins of infants' ability to learn about the sequential order of words, using near-infrared spectroscopy (NIRS) with newborn infants. We have conducted two experiments: one in which a word order change was implemented in 4-word sequences recorded with a list intonation (as if each word was a separate item in a list; list prosody condition, Experiment 1) and one in which the same 4-word sequences were recorded with a well-formed utterance-level prosodic contour (utterance prosody condition, Experiment 2). We found that newborns could detect the violation of the word order in the list prosody condition, but not in the utterance prosody condition. These results suggest that while newborns are already sensitive to word order in linguistic sequences, prosody appears to be a stronger cue than word order for the identification of linguistic units at birth. Copyright © 2017. Published by Elsevier Ltd.

Implicit and explicit mechanisms of word learning in a narrative context: an event-related potential study

PubMed Central

Batterink, Laura; Neville, Helen

2011-01-01

The vast majority of word meanings are learned simply by extracting them from context, rather than by rote memorization or explicit instruction. Although this skill is remarkable, little is known about the brain mechanisms involved. In the present study, ERPs were recorded as participants read stories in which pseudowords were presented multiple times, embedded in consistent, meaningful contexts (referred to as meaning condition, M+) or inconsistent, meaningless contexts (M−). Word learning was then assessed implicitly using a lexical decision task and explicitly through recall and recognition tasks. Overall, during story reading, M− words elicited a larger N400 than M+ words, suggesting that participants were better able to semantically integrate M+ words than M− words throughout the story. In addition, M+ words whose meanings were subsequently correctly recognized and recalled elicited a more positive ERP in a later time-window compared to M+ words whose meanings were incorrectly remembered, consistent with the idea that the late positive component (LPC) is an index of encoding processes. In the lexical decision task, no behavioral or electrophysiological evidence for implicit priming was found for M+ words. In contrast, during the explicit recognition task, M+ words showed a robust N400 effect. The N400 effect was dependent upon recognition performance, such that only correctly recognized M+ words elicited an N400. This pattern of results provides evidence that the explicit representations of word meanings can develop rapidly, while implicit representations may require more extensive exposure or more time to emerge. PMID:21452941

Predicting the host of influenza viruses based on the word vector.

PubMed

Xu, Beibei; Tan, Zhiying; Li, Kenli; Jiang, Taijiao; Peng, Yousong

2017-01-01

Newly emerging influenza viruses continue to threaten public health. A rapid determination of the host range of newly discovered influenza viruses would assist in early assessment of their risk. Here, we attempted to predict the host of influenza viruses using the Support Vector Machine (SVM) classifier based on the word vector, a new representation and feature extraction method for biological sequences. The results show that the length of the word within the word vector, the sequence type (DNA or protein) and the species from which the sequences were derived for generating the word vector all influence the performance of models in predicting the host of influenza viruses. In nearly all cases, the models built on the surface proteins hemagglutinin (HA) and neuraminidase (NA) (or their genes) produced better results than internal influenza proteins (or their genes). The best performance was achieved when the model was built on the HA gene based on word vectors (words of three-letters long) generated from DNA sequences of the influenza virus. This results in accuracies of 99.7% for avian, 96.9% for human and 90.6% for swine influenza viruses. Compared to the method of sequence homology best-hit searches using the Basic Local Alignment Search Tool (BLAST), the word vector-based models still need further improvements in predicting the host of influenza A viruses.

Characterization of Midface Fractures Incurred in Recent Wars

DTIC Science & Technology

2012-11-01

reconstruction . Key Words: Maxillofacial, facial fractures, early rigid fixation, blast injury (J Craniofac Surg 2012;23: 1587 1591) The percentage of...evaluated by a facial trauma expert that some of these findings are made. Conversely, it is not uncommon to find fractures that are incorrectly...þ Robert G. Hale, DDS,þ and Rodney K. Chan, MDþ Background: Facial injuries sustained by US military personnel during the wars in Iraq and

DEEPEN: A negation detection system for clinical text incorporating dependency relation into NegEx

PubMed Central

Mehrabi, Saeed; Krishnan, Anand; Sohn, Sunghwan; Roch, Alexandra M; Schmidt, Heidi; Kesterson, Joe; Beesley, Chris; Dexter, Paul; Schmidt, C. Max; Liu, Hongfang; Palakal, Mathew

2018-01-01

In Electronic Health Records (EHRs), much of valuable information regarding patients’ conditions is embedded in free text format. Natural language processing (NLP) techniques have been developed to extract clinical information from free text. One challenge faced in clinical NLP is that the meaning of clinical entities is heavily affected by modifiers such as negation. A negation detection algorithm, NegEx, applies a simplistic approach that has been shown to be powerful in clinical NLP. However, due to the failure to consider the contextual relationship between words within a sentence, NegEx fails to correctly capture the negation status of concepts in complex sentences. Incorrect negation assignment could cause inaccurate diagnosis of patients’ condition or contaminated study cohorts. We developed a negation algorithm called DEEPEN to decrease NegEx’s false positives by taking into account the dependency relationship between negation words and concepts within a sentence using Stanford dependency parser. The system was developed and tested using EHR data from Indiana University (IU) and it was further evaluated on Mayo Clinic dataset to assess its generalizability. The evaluation results demonstrate DEEPEN, which incorporates dependency parsing into NegEx, can reduce the number of incorrect negation assignment for patients with positive findings, and therefore improve the identification of patients with the target clinical findings in EHRs. PMID:25791500

Reconsidering the role of temporal order in spoken word recognition.

PubMed

Toscano, Joseph C; Anderson, Nathaniel D; McMurray, Bob

2013-10-01

Models of spoken word recognition assume that words are represented as sequences of phonemes. We evaluated this assumption by examining phonemic anadromes, words that share the same phonemes but differ in their order (e.g., sub and bus). Using the visual-world paradigm, we found that listeners show more fixations to anadromes (e.g., sub when bus is the target) than to unrelated words (well) and to words that share the same vowel but not the same set of phonemes (sun). This contrasts with the predictions of existing models and suggests that words are not defined as strict sequences of phonemes.

The span of correlations in dolphin whistle sequences

NASA Astrophysics Data System (ADS)

Ferrer-i-Cancho, Ramon; McCowan, Brenda

2012-06-01

Long-range correlations are found in symbolic sequences from human language, music and DNA. Determining the span of correlations in dolphin whistle sequences is crucial for shedding light on their communicative complexity. Dolphin whistles share various statistical properties with human words, i.e. Zipf's law for word frequencies (namely that the probability of the ith most frequent word of a text is about i-α) and a parallel of the tendency of more frequent words to have more meanings. The finding of Zipf's law for word frequencies in dolphin whistles has been the topic of an intense debate on its implications. One of the major arguments against the relevance of Zipf's law in dolphin whistles is that it is not possible to distinguish the outcome of a die-rolling experiment from that of a linguistic or communicative source producing Zipf's law for word frequencies. Here we show that statistically significant whistle-whistle correlations extend back to the second previous whistle in the sequence, using a global randomization test, and to the fourth previous whistle, using a local randomization test. None of these correlations are expected by a die-rolling experiment and other simple explanations of Zipf's law for word frequencies, such as Simon's model, that produce sequences of unpredictable elements.

Syntactic Prediction in Language Comprehension: Evidence From Either…or

PubMed Central

Staub, Adrian; Clifton, Charles

2006-01-01

Readers’ eye movements were monitored as they read sentences in which two noun phrases or two independent clauses were connected by the word or (NP-coordination and S-coordination, respectively). The word either could be present or absent earlier in the sentence. When either was present, the material immediately following or was read more quickly, across both sentence types. In addition, there was evidence that readers misanalyzed the S-coordination structure as an NP-coordination structure only when either was absent. The authors interpret the results as indicating that the word either enabled readers to predict the arrival of a coordination structure; this predictive activation facilitated processing of this structure when it ultimately arrived, and in the case of S-coordination sentences, enabled readers to avoid the incorrect NP-coordination analysis. The authors argue that these results support parsing theories according to which the parser can build predictable syntactic structure before encountering the corresponding lexical input. PMID:16569157

Repeated readings and science: Fluency with expository passages

NASA Astrophysics Data System (ADS)

Kostewicz, Douglas E.

The current study investigated the effects of repeated readings to a fluency criterion (RRFC) for seven students with disabilities using science text. The study employed a single subject design, specifically, two multiple probe multiple baselines across subjects, to evaluate the effects of the RRFC intervention. Results indicated that students met criterion (200 or more correct words per minute with 2 or fewer errors) on four consecutive passages. A majority of students displayed accelerations to correct words per minute and decelerations to incorrect words per minute on successive initial, intervention readings suggesting reading transfer. Students' reading scores during posttest and maintenance out performed pre-test and baseline readings provided additional measures of reading transfer. For a relationship to comprehension, students scored higher on oral retell measures after meeting criterion as compared to initial readings. Overall, the research findings suggested that the RRFC intervention improves science reading fluency for students with disabilities, and may also indirectly benefit comprehension.

Conflict and bias in heuristic judgment.

PubMed

Bhatia, Sudeep

2017-02-01

Conflict has been hypothesized to play a key role in recruiting deliberative processing in reasoning and judgment tasks. This claim suggests that changing the task so as to add incorrect heuristic responses that conflict with existing heuristic responses can make individuals less likely to respond heuristically and can increase response accuracy. We tested this prediction in experiments involving judgments of argument strength and word frequency, and found that participants are more likely to avoid heuristic bias and respond correctly in settings with 2 incorrect heuristic response options compared with similar settings with only 1 heuristic response option. Our results provide strong evidence for conflict as a mechanism influencing the interaction between heuristic and deliberative thought, and illustrate how accuracy can be increased through simple changes to the response sets offered to participants. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Incorrectly predicted genes in rice?

PubMed

Cruveiller, Stéphane; Jabbari, Kamel; Clay, Oliver; Bernardi, Giorgio

2004-05-26

Between one third and one half of the proposed rice genes appear to have no homologs in other species, including Arabidopsis. Compositional considerations, and a comparison of curated rice sequences with ex novo predictions, suggest that many or most of the putative genes without homologs may be false positive predictions, i.e., sequences that are never translated into functional proteins in vivo.

Attentional capture by taboo words: A functional view of auditory distraction.

PubMed

Röer, Jan P; Körner, Ulrike; Buchner, Axel; Bell, Raoul

2017-06-01

It is well established that task-irrelevant, to-be-ignored speech adversely affects serial short-term memory (STM) for visually presented items compared with a quiet control condition. However, there is an ongoing debate about whether the semantic content of the speech has the capacity to capture attention and to disrupt memory performance. In the present article, we tested whether taboo words are more difficult to ignore than neutral words. Taboo words or neutral words were presented as (a) steady state sequences in which the same distractor word was repeated, (b) changing state sequences in which different distractor words were presented, and (c) auditory deviant sequences in which a single distractor word deviated from a sequence of repeated words. Experiments 1 and 2 showed that taboo words disrupted performance more than neutral words. This taboo effect did not habituate and it did not differ between individuals with high and low working memory capacity. In Experiments 3 and 4, in which only a single deviant taboo word was presented, no taboo effect was obtained. These results do not support the idea that the processing of the auditory distractors' semantic content is the result of occasional attention switches to the auditory modality. Instead, the overall pattern of results is more in line with a functional view of auditory distraction, according to which the to-be-ignored modality is routinely monitored for potentially important stimuli (e.g., self-relevant or threatening information), the detection of which draws processing resources away from the primary task. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Research and Implementation of Tibetan Word Segmentation Based on Syllable Methods

NASA Astrophysics Data System (ADS)

Jiang, Jing; Li, Yachao; Jiang, Tao; Yu, Hongzhi

2018-03-01

Tibetan word segmentation (TWS) is an important problem in Tibetan information processing, while abbreviated word recognition is one of the key and most difficult problems in TWS. Most of the existing methods of Tibetan abbreviated word recognition are rule-based approaches, which need vocabulary support. In this paper, we propose a method based on sequence tagging model for abbreviated word recognition, and then implement in TWS systems with sequence labeling models. The experimental results show that our abbreviated word recognition method is fast and effective and can be combined easily with the segmentation model. This significantly increases the effect of the Tibetan word segmentation.

Green love is ugly: emotions elicited by synesthetic grapheme-color perceptions.

PubMed

Callejas, Alicia; Acosta, Alberto; Lupiáñez, Juan

2007-01-05

Synesthetes who experience grapheme-color synesthesia often report feeling uneasy when dealing with incongruently colored graphemes although no empirical data is available to confirm this phenomenon. We studied this affective reaction related to synesthetic perceptions by means of an evaluation task. We found that the perception of an incorrectly colored word affects the judgments of emotional valence. Furthermore, this effect competed with the word's emotional valence in a categorization task thus supporting the automatic nature of this synesthetically elicited affective reaction. When manipulating word valence and word color-photism congruence, we found that responses were slower (and less accurate) for inconsistent conditions than for consistent conditions. Inconsistent conditions were defined as those where semantics and color-photism congruence did not produce a similar assessment and therefore gave rise to a negative affective reaction (i.e., positive-valence words presented in a color different from the synesthete's photism or negative-valence words presented in the photism's color). We therefore observed a modulation of the congruency effect (i.e., faster reaction times to congruently colored words than incongruently colored words). Although this congruence effect has been taken as an index of the true experience of synesthesia, we observed that it can be reversed when the experimental manipulations turn an incongruently colored word into a consistent stimulus. To our knowledge, this is the first report of an affective reaction elicited by the congruency between the synesthetically induced color of a word and the color in which the word is actually presented. The underlying neural mechanisms that might be involved in this phenomenon are discussed.

How long-term memory and accentuation interact during spoken language comprehension.

PubMed

Li, Xiaoqing; Yang, Yufang

2013-04-01

Spoken language comprehension requires immediate integration of different information types, such as semantics, syntax, and prosody. Meanwhile, both the information derived from speech signals and the information retrieved from long-term memory exert their influence on language comprehension immediately. Using EEG (electroencephalogram), the present study investigated how the information retrieved from long-term memory interacts with accentuation during spoken language comprehension. Mini Chinese discourses were used as stimuli, with an interrogative or assertive context sentence preceding the target sentence. The target sentence included one critical word conveying new information. The critical word was either highly expected or lowly expected given the information retrieved from long-term memory. Moreover, the critical word was either consistently accented or inconsistently de-accented. The results revealed that for lowly expected new information, inconsistently de-accented words elicited a larger N400 and larger theta power increases (4-6 Hz) than consistently accented words. In contrast, for the highly expected new information, consistently accented words elicited a larger N400 and larger alpha power decreases (8-14 Hz) than inconsistently de-accented words. The results suggest that, during spoken language comprehension, the effect of accentuation interacted with the information retrieved from long-term memory immediately. Moreover, our results also have important consequences for our understanding of the processing nature of the N400. The N400 amplitude is not only enhanced for incorrect information (new and de-accented word) but also enhanced for correct information (new and accented words). Copyright © 2013 Elsevier Ltd. All rights reserved.

Importance Sampling of Word Patterns in DNA and Protein Sequences

PubMed Central

Chan, Hock Peng; Chen, Louis H.Y.

2010-01-01

Abstract Monte Carlo methods can provide accurate p-value estimates of word counting test statistics and are easy to implement. They are especially attractive when an asymptotic theory is absent or when either the search sequence or the word pattern is too short for the application of asymptotic formulae. Naive direct Monte Carlo is undesirable for the estimation of small probabilities because the associated rare events of interest are seldom generated. We propose instead efficient importance sampling algorithms that use controlled insertion of the desired word patterns on randomly generated sequences. The implementation is illustrated on word patterns of biological interest: palindromes and inverted repeats, patterns arising from position-specific weight matrices (PSWMs), and co-occurrences of pairs of motifs. PMID:21128856

Complete Mitochondrial Genomes of the Cherskii's Sculpin Cottus czerskii and Siberian Taimen Hucho taimen Reveal GenBank Entry Errors: Incorrect Species Identification and Recombinant Mitochondrial Genome.

PubMed

Balakirev, Evgeniy S; Saveliev, Pavel A; Ayala, Francisco J

2017-01-01

The complete mitochondrial (mt) genome is sequenced in 2 individuals of the Cherskii's sculpin Cottus czerskii . A surprisingly high level of sequence divergence (10.3%) has been detected between the 2 genomes of C czerskii studied here and the GenBank mt genome of C czerskii (KJ956027). At the same time, a surprisingly low level of divergence (1.4%) has been detected between the GenBank C czerskii (KJ956027) and the Amur sculpin Cottus szanaga (KX762049, KX762050). We argue that the observed discrepancies are due to incorrect taxonomic identification so that the GenBank accession number KJ956027 represents actually the mt genome of C szanaga erroneously identified as C czerskii . Our results are of consequence concerning the GenBank database quality, highlighting the potential negative consequences of entry errors, which once they are introduced tend to be propagated among databases and subsequent publications. We illustrate the premise with the data on recombinant mt genome of the Siberian taimen Hucho taimen (NCBI Reference Sequence Database NC_016426.1; GenBank accession number HQ897271.1), bearing 2 introgressed fragments (≈0.9 kb [kilobase]) from 2 lenok subspecies, Brachymystax lenok and Brachymystax lenok tsinlingensis , submitted to GenBank on June 12, 2011. Since the time of submission, the H taimen recombinant mt genome leading to incorrect phylogenetic inferences was propagated in multiple subsequent publications despite the fact that nonrecombinant H taimen genomes were also available (submitted to GenBank on August 2, 2014; KJ711549, KJ711550). Other examples of recombinant sequences persisting in GenBank are also considered. A GenBank Entry Error Depositary is urgently needed to monitor and avoid a progressive accumulation of wrong biological information.

Characterizing the D2 statistic: word matches in biological sequences.

PubMed

Forêt, Sylvain; Wilson, Susan R; Burden, Conrad J

2009-01-01

Word matches are often used in sequence comparison methods, either as a measure of sequence similarity or in the first search steps of algorithms such as BLAST or BLAT. The D2 statistic is the number of matches of words of k letters between two sequences. Recent advances have been made in the characterization of this statistic and in the approximation of its distribution. Here, these results are extended to the case of approximate word matches. We compute the exact value of the variance of the D2 statistic for the case of a uniform letter distribution, and introduce a method to provide accurate approximations of the variance in the remaining cases. This enables the distribution of D2 to be approximated for typical situations arising in biological research. We apply these results to the identification of cis-regulatory modules, and show that this method detects such sequences with a high accuracy. The ability to approximate the distribution of D2 for both exact and approximate word matches will enable the use of this statistic in a more precise manner for sequence comparison, database searches, and identification of transcription factor binding sites.

What is autologous blood transfusion?

PubMed

Sansom, A

1993-07-01

The word autologous is Greek in origin. The definition is exact 'autos' means self and 'logus' means relation. Thus, the meaning is 'related to self'. Autologous blood transfusion, which also is referred to frequently but incorrectly and imprecisely as auto transfusion, designates the reinfusion of blood or blood components to the same individual from whom they were taken. Homologous blood is blood or blood components, from another human donor, taken and stored for later transfusion as required.

Military Implications of United Nations Peacekeeping Operations

DTIC Science & Technology

1993-06-01

between the UN’s growing list of negotiated agreements and its ability to underwrite them with 30 WILLIAM H. LEWIS effective forces was revealed during the... rapidly changing situation. Words like "peace- making" and "peace-enforcement," used freely without any underlying doctrinal agreement as to what they...enforcement. The term "Second Generation" operations refers to a growing range of contingencies. sometimes incorrectly described as "peacekeeping" in

Dissociating parafoveal preview benefit and parafovea-on-fovea effects during reading: A combined eye tracking and EEG study.

PubMed

Niefind, Florian; Dimigen, Olaf

2016-12-01

During reading, the parafoveal processing of an upcoming word n+1 can influence word recognition in two ways: It can affect fixation behavior during the preceding fixation on word n (parafovea-on-fovea effect, POF), and it can facilitate subsequent foveal processing once word n+1 is fixated (preview benefit). While preview benefits are established, evidence for POF effects is mixed. Recently, it has been suggested that POF effects exist, but have a delayed impact on saccade planning and thus coincide with preview benefits measured on word n+1. We combined eye movement and EEG recordings to investigate and separate neural correlates of POF and preview benefit effects. Participants read lists of nouns either in a boundary paradigm or the RSVP-with-flankers paradigm, while we recorded fixation- or event-related potentials (FRPs/ERPs), respectively. The validity and lexical frequency of the word shown as preview for the upcoming word n+1 were orthogonally manipulated. Analyses focused on the first fixation on word n+1. Preview validity (correct vs. incorrect preview) strongly modulated fixation times and electrophysiological N1 amplitudes, replicating previous findings. Importantly, gaze durations and FRPs measured on word n+1 were also affected by the frequency of the word shown as preview, with low-frequency previews eliciting a sustained, N400-like centroparietal negativity. Results support the idea that POF effects exist but affect word recognition with a delay. Lastly, once word n+1 was fixated, its frequency also modulated N1 amplitudes in ERPs and FRPs. Taken together, we separated immediate and delayed effects of parafoveal processing on brain correlates of word recognition. © 2016 Society for Psychophysiological Research.

Magnetoencephalographic--features related to mild cognitive impairment.

PubMed

Püregger, E; Walla, P; Deecke, L; Dal-Bianco, P

2003-12-01

We recorded changes of brain activity from 10 MCI patients and 10 controls related to shallow (nonsemantic) and deep (semantic) word encoding using a whole-head MEG. During the following recognition tasks, all participants had to recognize the previously encoded words, which were presented again together with new words. In both groups recognition performance significantly varied as a function of depth of processing. No significant differences were found between the groups. Reaction times related to correctly classified new words (correct rejections) and incorrectly classified repetitions (misses) of MCI patients showed a strong tendency toward prolongation compared to controls, although no statistically significant differences occurred. Strikingly, in patients the neurophysiological data associated with nonsemantic and semantic word encoding differed significantly between 250 and 450 ms after stimulus onset mainly over left frontal and left temporal sensors. They showed higher electrophysiological activation during shallow encoding as compared to deep encoding. No such significant differences were found in controls. The present results might reflect a dysfunction with respect to shallow encoding of visually presented verbal information. It is interpreted that additional neural activation is needed to compensate for neurodegeneration. This finding is suggested to be an additional tool for MCI diagnosis.

Decision-related factors in pupil old/new effects: Attention, response execution, and false memory.

PubMed

Brocher, Andreas; Graf, Tim

2017-07-28

In this study, we investigate the effects of decision-related factors on recognition memory in pupil old/new paradigms. In Experiment 1, we used an old/new paradigm with words and pseudowords and participants made lexical decisions during recognition rather than old/new decisions. Importantly, participants were instructed to focus on the nonword-likeness of presented items, not their word-likeness. We obtained no old/new effects. In Experiment 2, participants discriminated old from new words and old from new pseudowords during recognition, and they did so as quickly as possible. We found old/new effects for both words and pseudowords. In Experiment 3, we used materials and an old/new design known to elicit a large number of incorrect responses. For false alarms ("old" response for new word), we found larger pupils than for correctly classified new items, starting at the point at which response execution was allowed (2750ms post stimulus onset). In contrast, pupil size for misses ("new" response for old word) was statistically indistinguishable from pupil size in correct rejections. Taken together, our data suggest that pupil old/new effects result more from the intentional use of memory than from its automatic use. Copyright © 2017 Elsevier Ltd. All rights reserved.

Coval: Improving Alignment Quality and Variant Calling Accuracy for Next-Generation Sequencing Data

PubMed Central

Kosugi, Shunichi; Natsume, Satoshi; Yoshida, Kentaro; MacLean, Daniel; Cano, Liliana; Kamoun, Sophien; Terauchi, Ryohei

2013-01-01

Accurate identification of DNA polymorphisms using next-generation sequencing technology is challenging because of a high rate of sequencing error and incorrect mapping of reads to reference genomes. Currently available short read aligners and DNA variant callers suffer from these problems. We developed the Coval software to improve the quality of short read alignments. Coval is designed to minimize the incidence of spurious alignment of short reads, by filtering mismatched reads that remained in alignments after local realignment and error correction of mismatched reads. The error correction is executed based on the base quality and allele frequency at the non-reference positions for an individual or pooled sample. We demonstrated the utility of Coval by applying it to simulated genomes and experimentally obtained short-read data of rice, nematode, and mouse. Moreover, we found an unexpectedly large number of incorrectly mapped reads in ‘targeted’ alignments, where the whole genome sequencing reads had been aligned to a local genomic segment, and showed that Coval effectively eliminated such spurious alignments. We conclude that Coval significantly improves the quality of short-read sequence alignments, thereby increasing the calling accuracy of currently available tools for SNP and indel identification. Coval is available at http://sourceforge.net/projects/coval105/. PMID:24116042

Effects of classwide peer tutoring on the acquisition, maintenance, and generalization of science vocabulary words for seventh grade students with learning disabilities and/or low achievement

NASA Astrophysics Data System (ADS)

Nobel, Michele Mcmahon

2005-07-01

This study investigated the effects of classwide peer tutoring (CWPT) on the acquisition, maintenance, and generalization of science vocabulary words and definitions. Participants were 14 seventh grade students at-risk for failure in a general education science course; 3 students had learning disabilities and 2 had a communication disorder. CWPT was conducted daily for 20 minutes during the last period of the school day. Procedures for CWPT were consistent with the Ohio State University CWPT model. Students were engaged in dyadic, reciprocal tutoring. Tutors presented word cards to tutees to identify the word and definition. Tutors praised correct responses and used a correction procedure for incorrect responses. After practicing their vocabulary words, students completed a daily testing procedure and recorded and plotted data. Many of the study's findings are consistent with previous studies using CWPT to teach word identification. Results of this study indicate a functional relationship between CWPT and acquisition of science vocabulary. All students were able to acquire words and definitions. Results for maintenance and generalization varied. When acquisition criterion was changed, maintenance and generalization scores increased for some students, while other students remained consistently high. All students reported that they enjoyed CWPT, and all but student stated it helped them learn science vocabulary.

Long frame sync words for binary PSK telemetry

NASA Technical Reports Server (NTRS)

Levitt, B. K.

1975-01-01

Correlation criteria have previously been established for identifying whether a given binary sequence would be a good frame sync word for phase-shift keyed telemetry. In the past, the search for a good K-bit sync word has involved the application of these criteria to the entire set of 2 exponent K binary K-tuples. It is shown that restricting this search to a much smaller subset consisting of K-bit prefixes of pseudonoise sequences results in sync words of comparable quality, with greatly reduced computer search times for larger values of K. As an example, this procedure is used to find good sync words of length 16-63; from a storage viewpoint, each of these sequences can be generated by a 5- or 6-bit linear feedback shift register.

Optimal choice of word length when comparing two Markov sequences using a χ 2-statistic.

PubMed

Bai, Xin; Tang, Kujin; Ren, Jie; Waterman, Michael; Sun, Fengzhu

2017-10-03

Alignment-free sequence comparison using counts of word patterns (grams, k-tuples) has become an active research topic due to the large amount of sequence data from the new sequencing technologies. Genome sequences are frequently modelled by Markov chains and the likelihood ratio test or the corresponding approximate χ 2 -statistic has been suggested to compare two sequences. However, it is not known how to best choose the word length k in such studies. We develop an optimal strategy to choose k by maximizing the statistical power of detecting differences between two sequences. Let the orders of the Markov chains for the two sequences be r 1 and r 2 , respectively. We show through both simulations and theoretical studies that the optimal k= max(r 1 ,r 2 )+1 for both long sequences and next generation sequencing (NGS) read data. The orders of the Markov chains may be unknown and several methods have been developed to estimate the orders of Markov chains based on both long sequences and NGS reads. We study the power loss of the statistics when the estimated orders are used. It is shown that the power loss is minimal for some of the estimators of the orders of Markov chains. Our studies provide guidelines on choosing the optimal word length for the comparison of Markov sequences.

Markov model plus k-word distributions: a synergy that produces novel statistical measures for sequence comparison.

PubMed

Dai, Qi; Yang, Yanchun; Wang, Tianming

2008-10-15

Many proposed statistical measures can efficiently compare biological sequences to further infer their structures, functions and evolutionary information. They are related in spirit because all the ideas for sequence comparison try to use the information on the k-word distributions, Markov model or both. Motivated by adding k-word distributions to Markov model directly, we investigated two novel statistical measures for sequence comparison, called wre.k.r and S2.k.r. The proposed measures were tested by similarity search, evaluation on functionally related regulatory sequences and phylogenetic analysis. This offers the systematic and quantitative experimental assessment of our measures. Moreover, we compared our achievements with these based on alignment or alignment-free. We grouped our experiments into two sets. The first one, performed via ROC (receiver operating curve) analysis, aims at assessing the intrinsic ability of our statistical measures to search for similar sequences from a database and discriminate functionally related regulatory sequences from unrelated sequences. The second one aims at assessing how well our statistical measure is used for phylogenetic analysis. The experimental assessment demonstrates that our similarity measures intending to incorporate k-word distributions into Markov model are more efficient.

Improving ESL Writing Using an Online Formulaic Sequence Word-Combination Checker

ERIC Educational Resources Information Center

Grami, G. M. A.; Alkazemi, B. Y.

2016-01-01

Writing correct English sentences can be challenging. Furthermore, writing correct formulaic sequences can be especially difficult because accepted combinations do not follow clear rules governing which words appear together in a sequence. One solution is to provide examples of correct usage accompanied by statistical feedback from web-based…

Learning about Spelling Sequences: The Role of Onsets and Rimes in Analogies in Reading.

ERIC Educational Resources Information Center

Goswami, Usha

1991-01-01

In one experiment, children learned more about consonant blends at the onset than at the end of words. In a second experiment, children learned more about rhyming vowel-consonant blend sequences at the end of words than those at the beginning of words, where the vowel extended the onset. (BC)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lapidus, Alla L.

From the date its role in heredity was discovered, DNA has been generating interest among scientists from different fields of knowledge: physicists have studied the three dimensional structure of the DNA molecule, biologists tried to decode the secrets of life hidden within these long molecules, and technologists invent and improve methods of DNA analysis. The analysis of the nucleotide sequence of DNA occupies a special place among the methods developed. Thanks to the variety of sequencing technologies available, the process of decoding the sequence of genomic DNA (or whole genome sequencing) has become robust and inexpensive. Meanwhile the assembly ofmore » whole genome sequences remains a challenging task. In addition to the need to assemble millions of DNA fragments of different length (from 35 bp (Solexa) to 800 bp (Sanger)), great interest in analysis of microbial communities (metagenomes) of different complexities raises new problems and pushes some new requirements for sequence assembly tools to the forefront. The genome assembly process can be divided into two steps: draft assembly and assembly improvement (finishing). Despite the fact that automatically performed assembly (or draft assembly) is capable of covering up to 98% of the genome, in most cases, it still contains incorrectly assembled reads. The error rate of the consensus sequence produced at this stage is about 1/2000 bp. A finished genome represents the genome assembly of much higher accuracy (with no gaps or incorrectly assembled areas) and quality ({approx}1 error/10,000 bp), validated through a number of computer and laboratory experiments.« less

Increase in posterior alpha activity during rehearsal predicts successful long-term memory formation of word sequences.

PubMed

Meeuwissen, Esther B; Takashima, Atsuko; Fernández, Guillén; Jensen, Ole

2011-12-01

It is becoming increasingly clear that demanding cognitive tasks rely on an extended network engaging task-relevant areas and, importantly, disengaging task-irrelevant areas. Given that alpha activity (8-12 Hz) has been shown to reflect the disengagement of task-irrelevant regions in attention and working memory tasks, we here ask if alpha activity plays a related role for long-term memory formation. Subjects were instructed to encode and maintain the order of word sequences while the ongoing brain activity was recorded using magnetoencephalography (MEG). In each trial, three words were presented followed by a 3.4 s rehearsal interval. Considering the good temporal resolution of MEG this allowed us to investigate the word presentation and rehearsal interval separately. The sequences were grouped in trials where word order either could be tested immediately (working memory trials; WM) or later (LTM trials) according to instructions. Subjects were tested on their ability to retrieve the order of the three words. The data revealed that alpha power in parieto-occipital regions was lower during word presentation compared to rehearsal. Our key finding was that parieto-occipital alpha power during the rehearsal period was markedly stronger for successfully than unsuccessfully encoded LTM sequences. This subsequent memory effect demonstrates that high posterior alpha activity creates an optimal brain state for successful LTM formation possibly by actively reducing parieto-occipital activity that might interfere with sequence encoding. Copyright © 2010 Wiley Periodicals, Inc.

Automaticity of higher cognitive functions: neurophysiological evidence for unconscious syntactic processing of masked words.

PubMed

Jiménez-Ortega, Laura; García-Milla, Marcos; Fondevila, Sabela; Casado, Pilar; Hernández-Gutiérrez, David; Martín-Loeches, Manuel

2014-12-01

Models of language comprehension assume that syntactic processing is automatic, at least at early stages. However, the degree of automaticity of syntactic processing is still controversial. Evidence of automaticity is either indirect or has been observed for pairs of words, which might provide a poor syntactic context in comparison to sentences. The present study investigates the automaticity of syntactic processing using event-related brain potentials (ERPs) during sentence processing. To this end, masked adjectives that could either be syntactically correct or incorrect relative to a sentence being processed appeared just prior to the presentation of supraliminal adjectives. The latter could also be correct or incorrect. According to our data, subliminal gender agreement violations embedded in a sentence trigger an early anterior negativity-like modulation, whereas supraliminal gender agreement violations elicited a later anterior negativity. First-pass syntactic parsing thus appears to be unconsciously and automatically elicited. Interestingly, a P600-like modulation of short duration and early latency could also be observed for masked violations. In addition, masked violations also modulated the P600 component elicited by unmasked targets, probably reflecting that the mechanisms of revising a structural mismatch appear affected by subliminal information. According to our findings, both conscious and unconscious processes apparently contribute to syntactic processing. These results are discussed in line with most recent theories of automaticity and syntactic processing. Copyright © 2014 Elsevier B.V. All rights reserved.

The Effects of Within-Sequence Acoustic Similarity on the Short-Term Retention of Consonants and Words

ERIC Educational Resources Information Center

Marcer, D.; And Others

1977-01-01

Compares the rates of forgetting of five-item sequences of acoustically similar and dissimilar consonants and words in the absence of proactive and retroactive interference in order to test whether within sequence similarity rather than stimulus length would have a greater influence on retention. (Author/RK)

Effects of Temporal Sequencing and Auditory Discrimination on Children's Memory Patterns for Tones, Numbers, and Nonsense Words

ERIC Educational Resources Information Center

Gromko, Joyce Eastlund; Hansen, Dee; Tortora, Anne Halloran; Higgins, Daniel; Boccia, Eric

2009-01-01

The purpose of this study was to determine whether children's recall of tones, numbers, and words was supported by a common temporal sequencing mechanism; whether children's patterns of memory for tones, numbers, and nonsense words were the same despite differences in symbol systems; and whether children's recall of tones, numbers, and nonsense…

Improving word reading speed: individual differences interact with a training focus on successes or failures.

PubMed

Steenbeek-Planting, Esther G; van Bon, Wim H J; Schreuder, Robert

2012-10-01

The effect of two training procedures on the development of reading speed in poor readers is examined. One training concentrates on the words the children read correctly (successes), the other on the words they read incorrectly (failures). Children were either informed or not informed about the training focus. A randomized controlled trial was conducted with 79 poor readers. They repeatedly read regularly spelled Dutch consonant-vowel-consonant words, some children their successes, others their failures. The training used a computerized flashcards format. The exposure duration of the words was varied to maintain an accuracy rate at a constant level. Reading speed improved and transferred to untrained, orthographically more complex words. These transfer effects were characterized by an Aptitude-Treatment Interaction. Poor readers with a low initial reading level improved most in the training focused on successes. For poor readers with a high initial reading level, however, it appeared to be more profitable to practice with their failures. Informing students about the focus of the training positively affected training: The exposure duration needed for children informed about the focus of the training decreased more than for children who were not informed. This study suggests that neither of the two interventions is superior to the other in general. Rather, the improvement of general reading speed in a transparent orthography is closely related to both the children's initial reading level and the type of words they practice with: common and familiar words when training their successes and uncommon and less familiar words with training their failures.

Phonological and Semantic Cues to Learning from Word-Types

PubMed Central

Richtsmeier, Peter

2017-01-01

Word-types represent the primary form of data for many models of phonological learning, and they often predict performance in psycholinguistic tasks. Word-types are often tacitly defined as phonologically unique words. Yet, an explicit test of this definition is lacking, and natural language patterning suggests that word meaning could also act as a cue to word-type status. This possibility was tested in a statistical phonotactic learning experiment in which phonological and semantic properties of word-types varied. During familiarization, the learning targets—word-medial consonant sequences—were instantiated either by four related word-types or by just one word-type (the experimental frequency factor). The expectation was that more word-types would lead participants to generalize the target sequences. Regarding semantic cues, related word-types were either associated with different referents or all with a single referent. Regarding phonological cues, related word-types differed from each other by one, two, or more phonemes. At test, participants rated novel wordforms for their similarity to the familiarization words. When participants heard four related word-types, they gave higher ratings to test words with the same consonant sequences, irrespective of the phonological and semantic manipulations. The results support the existing phonological definition of word-types. PMID:29187914

Dual coding theory, word abstractness, and emotion: a critical review of Kousta et al. (2011).

PubMed

Paivio, Allan

2013-02-01

Kousta, Vigliocco, Del Campo, Vinson, and Andrews (2011) questioned the adequacy of dual coding theory and the context availability model as explanations of representational and processing differences between concrete and abstract words. They proposed an alternative approach that focuses on the role of emotional content in the processing of abstract concepts. Their dual coding critique is, however, based on impoverished and, in some respects, incorrect interpretations of the theory and its implications. This response corrects those gaps and misinterpretations and summarizes research findings that show predicted variations in the effects of dual coding variables in different tasks and contexts. Especially emphasized is an empirically supported dual coding theory of emotion that goes beyond the Kousta et al. emphasis on emotion in abstract semantics. 2013 APA, all rights reserved

Extrinsic Cognitive Load Impairs Spoken Word Recognition in High- and Low-Predictability Sentences.

PubMed

Hunter, Cynthia R; Pisoni, David B

Listening effort (LE) induced by speech degradation reduces performance on concurrent cognitive tasks. However, a converse effect of extrinsic cognitive load on recognition of spoken words in sentences has not been shown. The aims of the present study were to (a) examine the impact of extrinsic cognitive load on spoken word recognition in a sentence recognition task and (b) determine whether cognitive load and/or LE needed to understand spectrally degraded speech would differentially affect word recognition in high- and low-predictability sentences. Downstream effects of speech degradation and sentence predictability on the cognitive load task were also examined. One hundred twenty young adults identified sentence-final spoken words in high- and low-predictability Speech Perception in Noise sentences. Cognitive load consisted of a preload of short (low-load) or long (high-load) sequences of digits, presented visually before each spoken sentence and reported either before or after identification of the sentence-final word. LE was varied by spectrally degrading sentences with four-, six-, or eight-channel noise vocoding. Level of spectral degradation and order of report (digits first or words first) were between-participants variables. Effects of cognitive load, sentence predictability, and speech degradation on accuracy of sentence-final word identification as well as recall of preload digit sequences were examined. In addition to anticipated main effects of sentence predictability and spectral degradation on word recognition, we found an effect of cognitive load, such that words were identified more accurately under low load than high load. However, load differentially affected word identification in high- and low-predictability sentences depending on the level of sentence degradation. Under severe spectral degradation (four-channel vocoding), the effect of cognitive load on word identification was present for high-predictability sentences but not for low-predictability sentences. Under mild spectral degradation (eight-channel vocoding), the effect of load was present for low-predictability sentences but not for high-predictability sentences. There were also reliable downstream effects of speech degradation and sentence predictability on recall of the preload digit sequences. Long digit sequences were more easily recalled following spoken sentences that were less spectrally degraded. When digits were reported after identification of sentence-final words, short digit sequences were recalled more accurately when the spoken sentences were predictable. Extrinsic cognitive load can impair recognition of spectrally degraded spoken words in a sentence recognition task. Cognitive load affected word identification in both high- and low-predictability sentences, suggesting that load may impact both context use and lower-level perceptual processes. Consistent with prior work, LE also had downstream effects on memory for visual digit sequences. Results support the proposal that extrinsic cognitive load and LE induced by signal degradation both draw on a central, limited pool of cognitive resources that is used to recognize spoken words in sentences under adverse listening conditions.

The role of word order in the interpretation of canonical and non-canonical graphic symbol utterances: A developmental study.

PubMed

Trudeau, Natacha; Morford, Jill P; Sutton, Ann

2010-06-01

Graphic symbols are often used to represent words in Augmentative and Alternative Communication systems. Previous findings suggest that different processes operate when using graphic symbols and when using speech. This study assessed the ability of native speakers of French with no communication disorders from four age groups to interpret graphic-symbol sequences of varying length and canonicity. Results reveal that, as they get older, participants show an increase in their capacity to interpret graphic-symbol sequences. Constituent order played an important role in the interpretation of the sequences. However, the specific word-order strategies used varied depending on the age group and the type of sequence presented.

Optimal word sizes for dissimilarity measures and estimation of the degree of dissimilarity between DNA sequences.

PubMed

Wu, Tiee-Jian; Huang, Ying-Hsueh; Li, Lung-An

2005-11-15

Several measures of DNA sequence dissimilarity have been developed. The purpose of this paper is 3-fold. Firstly, we compare the performance of several word-based or alignment-based methods. Secondly, we give a general guideline for choosing the window size and determining the optimal word sizes for several word-based measures at different window sizes. Thirdly, we use a large-scale simulation method to simulate data from the distribution of SK-LD (symmetric Kullback-Leibler discrepancy). These simulated data can be used to estimate the degree of dissimilarity beta between any pair of DNA sequences. Our study shows (1) for whole sequence similiarity/dissimilarity identification the window size taken should be as large as possible, but probably not >3000, as restricted by CPU time in practice, (2) for each measure the optimal word size increases with window size, (3) when the optimal word size is used, SK-LD performance is superior in both simulation and real data analysis, (4) the estimate beta of beta based on SK-LD can be used to filter out quickly a large number of dissimilar sequences and speed alignment-based database search for similar sequences and (5) beta is also applicable in local similarity comparison situations. For example, it can help in selecting oligo probes with high specificity and, therefore, has potential in probe design for microarrays. The algorithm SK-LD, estimate beta and simulation software are implemented in MATLAB code, and are available at http://www.stat.ncku.edu.tw/tjwu

Exceptional motifs in different Markov chain models for a statistical analysis of DNA sequences.

PubMed

Schbath, S; Prum, B; de Turckheim, E

1995-01-01

Identifying exceptional motifs is often used for extracting information from long DNA sequences. The two difficulties of the method are the choice of the model that defines the expected frequencies of words and the approximation of the variance of the difference T(W) between the number of occurrences of a word W and its estimation. We consider here different Markov chain models, either with stationary or periodic transition probabilities. We estimate the variance of the difference T(W) by the conditional variance of the number of occurrences of W given the oligonucleotides counts that define the model. Two applications show how to use asymptotically standard normal statistics associated with the counts to describe a given sequence in terms of its outlying words. Sequences of Escherichia coli and of Bacillus subtilis are compared with respect to their exceptional tri- and tetranucleotides. For both bacteria, exceptional 3-words are mainly found in the coding frame. E. coli palindrome counts are analyzed in different models, showing that many overabundant words are one-letter mutations of avoided palindromes.

Rejecting familiar distracters during recognition in young adults with traumatic brain injury and in healthy older adults.

PubMed

Ozen, Lana J; Skinner, Erin I; Fernandes, Myra A

2010-05-01

The most common cognitive complaint reported by healthy older adults and young adults with traumatic brain injury (TBI) is memory difficulties. We investigated the effects of normal aging and the long-term effects of TBI in young adults on the susceptibility to incorrectly endorse distracter information on a memory test. Prior to a study phase, participants viewed a "pre-exposure" list containing distracter words, presented once or three times, and half of the target study words. Subsequently, during the study phase, all target words were presented such that, across lists, study words were viewed either once or three times. On the recognition test, TBI and older adult participants were more likely to falsely endorse "pre-exposed" distracter words viewed three times as being from the target study list, compared to non-head-injured young controls. Normal aging and head injury in young may similarly compromise one's ability to reject highly familiar, but distracting, information during recognition. Older adult and TBI participants were also slower to complete the Trail Making task and had poorer output on a Digit Span task, suggesting these two populations share a deficit in executive function and working memory. Similar changes in frontal lobe function may underlie these shared cognitive deficits.

Preparation and applicability of a test of speech perception with pictures.

PubMed

Souza, Laís Flavia de; Braga, Gabriela Rosito Alvarez Bernardez; Mota, Ana Lúcia Rios; Zamberlan-Amorim, Nelma Ellen; Reis, Ana Cláudia Mirândola Barbosa

2016-01-01

To prepare and apply support material for responses to the Speech Recognition Percentage Index (SRPI) test in children. This is a descriptive, exploratory study conducted in two phases: in the first phase, 31 speech-language pathologists (referees) prepared material composed of regular, frequently used monosyllabic and disyllabic words belonging to the vocabulary of children and figures that could represent these words; the second phase consisted in the application of this material to 30 normal-hearing children aged 2 to 4 years and 11 months. The material consisted of 25 words and six boards with six figures each. The word selection criterion adopted by the referees included the initial phoneme and real, colorful figures familiar to the children. The mean scores of the children in the SRPI test were 93% (SD ± 8%) with the support of figures and 64% (SD ± 25%) without figure support. Comparison between the results obtained with and without the support of figures showed significant difference for 15 of the 25 test words, with higher scores with the use of supporting figures. Comparison between correct and incorrect responses using the support of figures showed significant difference only for the word "dog" ("cão") (p=0.0079). There was agreement among the referees with respect to the words and figures. The SRPI test can be rapidly and easily applied, allowing evaluation and systematic monitoring of speech perception ability regardless of child verbalization capacity.

Code-Switching to Know a TL Equivalent of an L1 Word: Request-Provision-Acknowledgement (RPA) Sequence

ERIC Educational Resources Information Center

Lucero, Edgar

2011-01-01

This article focuses on the learner's use of Code-switching to learn the TL (Target Language) equivalent of an L1 word. The interactional pattern that this situation creates defines the Request-Provision-Acknowledgement (RPA) sequence. The article explains each of the turns of the sequence under the combination of the Ethnomethodological…

Normal and compound poisson approximations for pattern occurrences in NGS reads.

PubMed

Zhai, Zhiyuan; Reinert, Gesine; Song, Kai; Waterman, Michael S; Luan, Yihui; Sun, Fengzhu

2012-06-01

Next generation sequencing (NGS) technologies are now widely used in many biological studies. In NGS, sequence reads are randomly sampled from the genome sequence of interest. Most computational approaches for NGS data first map the reads to the genome and then analyze the data based on the mapped reads. Since many organisms have unknown genome sequences and many reads cannot be uniquely mapped to the genomes even if the genome sequences are known, alternative analytical methods are needed for the study of NGS data. Here we suggest using word patterns to analyze NGS data. Word pattern counting (the study of the probabilistic distribution of the number of occurrences of word patterns in one or multiple long sequences) has played an important role in molecular sequence analysis. However, no studies are available on the distribution of the number of occurrences of word patterns in NGS reads. In this article, we build probabilistic models for the background sequence and the sampling process of the sequence reads from the genome. Based on the models, we provide normal and compound Poisson approximations for the number of occurrences of word patterns from the sequence reads, with bounds on the approximation error. The main challenge is to consider the randomness in generating the long background sequence, as well as in the sampling of the reads using NGS. We show the accuracy of these approximations under a variety of conditions for different patterns with various characteristics. Under realistic assumptions, the compound Poisson approximation seems to outperform the normal approximation in most situations. These approximate distributions can be used to evaluate the statistical significance of the occurrence of patterns from NGS data. The theory and the computational algorithm for calculating the approximate distributions are then used to analyze ChIP-Seq data using transcription factor GABP. Software is available online (www-rcf.usc.edu/∼fsun/Programs/NGS_motif_power/NGS_motif_power.html). In addition, Supplementary Material can be found online (www.liebertonline.com/cmb).

Groundwater, A century of word evolution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Diefendorf, A.F.

1995-08-01

Words, especially those that apply directly to more than one discipline, often become the object of intense debate among professionals in those disciplines. This is particularly true with those people who have to deal with technical jargon on a day-to-day basis and who are concerned that scientific facts get communicated in as clear and concise a manner as possible. Communications regarding environmental restoration projects for the US Department of Energy are no exception. Lockheed Martin Energy Systems, Inc., its subcontractors and other prime contractors often disagree about the spelling and use of compound words. This frequently results in inconsistent spellingmore » between project reports and incorrect spelling of referenced document titles. The following discussion is an attempt to provide an objective, in-depth examination of the evolution of one particular word and recommendations for its proper and consistent use. This discussion is the result of an extensive literature search conducted within the library system at Oak Ridge National Laboratory as well as the personal geologic libraries of the author and colleagues. The author has attempted to cite only those works produced by recognized names in the related disciplines or those works that constitute common references or glossaries.« less

Complete Mitochondrial Genomes of the Cherskii’s Sculpin Cottus czerskii and Siberian Taimen Hucho taimen Reveal GenBank Entry Errors: Incorrect Species Identification and Recombinant Mitochondrial Genome

PubMed Central

Balakirev, Evgeniy S; Saveliev, Pavel A; Ayala, Francisco J

2017-01-01

The complete mitochondrial (mt) genome is sequenced in 2 individuals of the Cherskii’s sculpin Cottus czerskii. A surprisingly high level of sequence divergence (10.3%) has been detected between the 2 genomes of C czerskii studied here and the GenBank mt genome of C czerskii (KJ956027). At the same time, a surprisingly low level of divergence (1.4%) has been detected between the GenBank C czerskii (KJ956027) and the Amur sculpin Cottus szanaga (KX762049, KX762050). We argue that the observed discrepancies are due to incorrect taxonomic identification so that the GenBank accession number KJ956027 represents actually the mt genome of C szanaga erroneously identified as C czerskii. Our results are of consequence concerning the GenBank database quality, highlighting the potential negative consequences of entry errors, which once they are introduced tend to be propagated among databases and subsequent publications. We illustrate the premise with the data on recombinant mt genome of the Siberian taimen Hucho taimen (NCBI Reference Sequence Database NC_016426.1; GenBank accession number HQ897271.1), bearing 2 introgressed fragments (≈0.9 kb [kilobase]) from 2 lenok subspecies, Brachymystax lenok and Brachymystax lenok tsinlingensis, submitted to GenBank on June 12, 2011. Since the time of submission, the H taimen recombinant mt genome leading to incorrect phylogenetic inferences was propagated in multiple subsequent publications despite the fact that nonrecombinant H taimen genomes were also available (submitted to GenBank on August 2, 2014; KJ711549, KJ711550). Other examples of recombinant sequences persisting in GenBank are also considered. A GenBank Entry Error Depositary is urgently needed to monitor and avoid a progressive accumulation of wrong biological information. PMID:28890653

Counting of oligomers in sequences generated by markov chains for DNA motif discovery.

PubMed

Shan, Gao; Zheng, Wei-Mou

2009-02-01

By means of the technique of the imbedded Markov chain, an efficient algorithm is proposed to exactly calculate first, second moments of word counts and the probability for a word to occur at least once in random texts generated by a Markov chain. A generating function is introduced directly from the imbedded Markov chain to derive asymptotic approximations for the problem. Two Z-scores, one based on the number of sequences with hits and the other on the total number of word hits in a set of sequences, are examined for discovery of motifs on a set of promoter sequences extracted from A. thaliana genome. Source code is available at http://www.itp.ac.cn/zheng/oligo.c.

Estimation of pairwise sequence similarity of mammalian enhancers with word neighbourhood counts.

PubMed

Göke, Jonathan; Schulz, Marcel H; Lasserre, Julia; Vingron, Martin

2012-03-01

The identity of cells and tissues is to a large degree governed by transcriptional regulation. A major part is accomplished by the combinatorial binding of transcription factors at regulatory sequences, such as enhancers. Even though binding of transcription factors is sequence-specific, estimating the sequence similarity of two functionally similar enhancers is very difficult. However, a similarity measure for regulatory sequences is crucial to detect and understand functional similarities between two enhancers and will facilitate large-scale analyses like clustering, prediction and classification of genome-wide datasets. We present the standardized alignment-free sequence similarity measure N2, a flexible framework that is defined for word neighbourhoods. We explore the usefulness of adding reverse complement words as well as words including mismatches into the neighbourhood. On simulated enhancer sequences as well as functional enhancers in mouse development, N2 is shown to outperform previous alignment-free measures. N2 is flexible, faster than competing methods and less susceptible to single sequence noise and the occurrence of repetitive sequences. Experiments on the mouse enhancers reveal that enhancers active in different tissues can be separated by pairwise comparison using N2. N2 represents an improvement over previous alignment-free similarity measures without compromising speed, which makes it a good candidate for large-scale sequence comparison of regulatory sequences. The software is part of the open-source C++ library SeqAn (www.seqan.de) and a compiled version can be downloaded at http://www.seqan.de/projects/alf.html. Supplementary data are available at Bioinformatics online.

Minimal Absent Words in Four Human Genome Assemblies

PubMed Central

Garcia, Sara P.; Pinho, Armando J.

2011-01-01

Minimal absent words have been computed in genomes of organisms from all domains of life. Here, we aim to contribute to the catalogue of human genomic variation by investigating the variation in number and content of minimal absent words within a species, using four human genome assemblies. We compare the reference human genome GRCh37 assembly, the HuRef assembly of the genome of Craig Venter, the NA12878 assembly from cell line GM12878, and the YH assembly of the genome of a Han Chinese individual. We find the variation in number and content of minimal absent words between assemblies more significant for large and very large minimal absent words, where the biases of sequencing and assembly methodologies become more pronounced. Moreover, we find generally greater similarity between the human genome assemblies sequenced with capillary-based technologies (GRCh37 and HuRef) than between the human genome assemblies sequenced with massively parallel technologies (NA12878 and YH). Finally, as expected, we find the overall variation in number and content of minimal absent words within a species to be generally smaller than the variation between species. PMID:22220210

Twisted trees and inconsistency of tree estimation when gaps are treated as missing data - The impact of model mis-specification in distance corrections.

PubMed

McTavish, Emily Jane; Steel, Mike; Holder, Mark T

2015-12-01

Statistically consistent estimation of phylogenetic trees or gene trees is possible if pairwise sequence dissimilarities can be converted to a set of distances that are proportional to the true evolutionary distances. Susko et al. (2004) reported some strikingly broad results about the forms of inconsistency in tree estimation that can arise if corrected distances are not proportional to the true distances. They showed that if the corrected distance is a concave function of the true distance, then inconsistency due to long branch attraction will occur. If these functions are convex, then two "long branch repulsion" trees will be preferred over the true tree - though these two incorrect trees are expected to be tied as the preferred true. Here we extend their results, and demonstrate the existence of a tree shape (which we refer to as a "twisted Farris-zone" tree) for which a single incorrect tree topology will be guaranteed to be preferred if the corrected distance function is convex. We also report that the standard practice of treating gaps in sequence alignments as missing data is sufficient to produce non-linear corrected distance functions if the substitution process is not independent of the insertion/deletion process. Taken together, these results imply inconsistent tree inference under mild conditions. For example, if some positions in a sequence are constrained to be free of substitutions and insertion/deletion events while the remaining sites evolve with independent substitutions and insertion/deletion events, then the distances obtained by treating gaps as missing data can support an incorrect tree topology even given an unlimited amount of data. Copyright © 2015 Elsevier Inc. All rights reserved.

Accommodation of end-state comfort reveals subphonemic planning in speech

PubMed Central

Gick, Bryan

2015-01-01

Applying Rosenbaum’s “end-state comfort” hypothesis (Rosenbaum et al., 1992, 1996) to tongue motion provides evidence of long-distance subphonemic planning in speech. Speakers’ tongue postures may anticipate upcoming speech up to three segments, two syllables, and a morpheme or word boundary later. We used m-mode ultrasound imaging to measure the direction of tongue tip/blade movements for known variants of flap/tap allophones of North American English /t/ and /d/. Results show that speakers produce different flap variants early in words or word sequences so as to facilitate the kinematic needs of flap/tap or other /r/ variants that appear later in the word or word sequence. Similar results were also observed across word boundaries, indicating that this is not a lexical effect. PMID:25790787

Working memory for pitch, timbre, and words

PubMed Central

Tillmann, Barbara

2012-01-01

Aiming to further our understanding of fundamental mechanisms of auditory working memory (WM), the present study compared performance for three auditory materials (words, tones, timbres). In a forward recognition task (Experiment 1) participants indicated whether the order of the items in the second sequence was the same as in the first sequence. In a backward recognition task (Experiment 2) participants indicated whether the items of the second sequence were played in the correct backward order. In Experiment 3 participants performed an articulatory suppression task during the retention delay of the backward task. To investigate potential length effects the number of items per sequence was manipulated. Overall findings underline the benefit of a cross-material experimental approach and suggest that human auditory WM is not a unitary system. Whereas WM processes for timbres differed from those for tones and words, similarities and differences were observed for words and tones: Both types of stimuli appear to rely on rehearsal mechanisms, but might differ in the involved sensorimotor codes. PMID:23116413

Keeping it together: Semantic coherence stabilizes phonological sequences in short-term memory.

PubMed

Savill, Nicola; Ellis, Rachel; Brooke, Emma; Koa, Tiffany; Ferguson, Suzie; Rojas-Rodriguez, Elena; Arnold, Dominic; Smallwood, Jonathan; Jefferies, Elizabeth

2018-04-01

Our ability to hold a sequence of speech sounds in mind, in the correct configuration, supports many aspects of communication, but the contribution of conceptual information to this basic phonological capacity remains controversial. Previous research has shown modest and inconsistent benefits of meaning on phonological stability in short-term memory, but these studies were based on sets of unrelated words. Using a novel design, we examined the immediate recall of sentence-like sequences with coherent meaning, alongside both standard word lists and mixed lists containing words and nonwords. We found, and replicated, substantial effects of coherent meaning on phoneme-level accuracy: The phonemes of both words and nonwords within conceptually coherent sequences were more likely to be produced together and in the correct order. Since nonwords do not exist as items in long-term memory, the semantic enhancement of phoneme-level recall for both item types cannot be explained by a lexically based item reconstruction process employed at the point of retrieval ("redintegration"). Instead, our data show, for naturalistic input, that when meaning emerges from the combination of words, the phonological traces that support language are reinforced by a semantic-binding process that has been largely overlooked by past short-term memory research.

LESS SKILLED READERS HAVE LESS EFFICIENT SUPPRESSION MECHANISMS.

PubMed

Gernsbacher, Morton Ann

1993-09-01

One approach to understanding the component processes and mechanisms underlying adult reading skill is to compare the performance of more skilled and less skilled readers on laboratory experiments. The results of some recent experiments employing this approach demonstrate that less skilled adult readers suppress less efficiently the inappropriate meanings of ambiguous words (e.g., the playing card vs. garden tool meanings of spade ), the incorrect forms of homophones (e.g., patients vs. patience ), the typical-but-absent members of scenes (e.g., a tractor in a farm scene), and words superimposed on pictures. Less skilled readers are not less efficient in activating contextually appropriate information; in fact, they activate contextually appropriate information more strongly than more skilled readers do. Therefore, one conclusion that can be drawn from these experiments is that less skilled adult readers suffer from less efficient suppression mechanisms.

Author Response to LTE CLC 22970 of John Madias: Brain-heart pathway to injury in takotsubo syndrome.

PubMed

Marafioti, Vincenzo; Turri, Giulia; Carbone, Vincenzo; Monaco, Salvatore

2018-05-26

We would like to thank John Madias for his interest in our review about the mystery of the pathogenesis of Takotsubo cardiomyopathy (TC) . 1 We agree with his semantic restraint of the eponym Wellens electrocardiographic (ECG) pattern, which needs a contextual disambiguation. Indeed, as stressed by Dr. Madias in a previous letter to the editor, this term is often used incorrectly in the literature 2,3 . In this respect, through the words of Cato: "Nos vera vocabula rerum amisimus "4 (we have lost the real names of things), we would like to emphasize how the scientific world suffers from a sort of daily linguistic Babel, where words seem to have lost their capacity to communicate. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

I 5683 you: dialing phone numbers on cell phones activates key-concordant concepts.

PubMed

Topolinski, Sascha

2011-03-01

When people perform actions, effects associated with the actions are activated mentally, even if those effects are not apparent. This study tested whether sequences of simulations of virtual action effects can be integrated into a meaning of their own. Cell phones were used to test this hypothesis because pressing a key on a phone is habitually associated with both digits (dialing numbers) and letters (typing text messages). In Experiment 1, dialing digit sequences induced the meaning of words that share the same key sequence (e.g., 5683, LOVE). This occurred even though the letters were not labeled on the keypad, and participants were not aware of the digit-letter correspondences. In Experiment 2, subjects preferred dialing numbers implying positive words (e.g., 37326, DREAM) over dialing numbers implying negative words (e.g., 75463, SLIME). In Experiment 3, subjects preferred companies with phone numbers implying a company-related word (e.g., LOVE for a dating agency, CORPSE for a mortician) compared with companies with phone numbers implying a company-unrelated word.

Congenital amusia: a short-term memory deficit for non-verbal, but not verbal sounds.

PubMed

Tillmann, Barbara; Schulze, Katrin; Foxton, Jessica M

2009-12-01

Congenital amusia refers to a lifelong disorder of music processing and is linked to pitch-processing deficits. The present study investigated congenital amusics' short-term memory for tones, musical timbres and words. Sequences of five events (tones, timbres or words) were presented in pairs and participants had to indicate whether the sequences were the same or different. The performance of congenital amusics confirmed a memory deficit for tone sequences, but showed normal performance for word sequences. For timbre sequences, amusics' memory performance was impaired in comparison to matched controls. Overall timbre performance was found to be correlated with melodic contour processing (as assessed by the Montreal Battery of Evaluation of Amusia). The present findings show that amusics' deficits extend to non-verbal sound material other than pitch, in this case timbre, while not affecting memory for verbal material. This is in line with previous suggestions about the domain-specificity of congenital amusia.

Verification of Ribosomal Proteins of Aspergillus fumigatus for Use as Biomarkers in MALDI-TOF MS Identification.

PubMed

Nakamura, Sayaka; Sato, Hiroaki; Tanaka, Reiko; Yaguchi, Takashi

2016-01-01

We have previously proposed a rapid identification method for bacterial strains based on the profiles of their ribosomal subunit proteins (RSPs), observed using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). This method can perform phylogenetic characterization based on the mass of housekeeping RSP biomarkers, ideally calculated from amino acid sequence information registered in public protein databases. With the aim of extending its field of application to medical mycology, this study investigates the actual state of information of RSPs of eukaryotic fungi registered in public protein databases through the characterization of ribosomal protein fractions extracted from genome-sequenced Aspergillus fumigatus strains Af293 and A1163 as a model. In this process, we have found that the public protein databases harbor problems. The RSP names are in confusion, so we have provisionally unified them using the yeast naming system. The most serious problem is that many incorrect sequences are registered in the public protein databases. Surprisingly, more than half of the sequences are incorrect, due chiefly to mis-annotation of exon/intron structures. These errors could be corrected by a combination of in silico inspection by sequence homology analysis and MALDI-TOF MS measurements. We were also able to confirm conserved post-translational modifications in eleven RSPs. After these verifications, the masses of 31 expressed RSPs under 20,000 Da could be accurately confirmed. These RSPs have a potential to be useful biomarkers for identifying clinical isolates of A. fumigatus .

The effect of object processing in content-dependent source memory

PubMed Central

2013-01-01

Background Previous studies have suggested that the study condition of an item influences how the item is encoded. However, it is still unclear whether subsequent source memory effects are dependent upon stimulus content when the item and context are unitized. The present fMRI study investigated the effect of encoding activity sensitive to stimulus content in source memory via unitization. In the scanner, participants were instructed to integrate a study item, an object in either a word or a picture form, with perceptual context into a single image. Results Subsequent source memory effects independent of stimulus content were identified in the left lateral frontal and parietal regions, bilateral fusiform areas, and the left perirhinal cortex extending to the anterior hippocampus. Content-dependent subsequent source memory effects were found only with words in the left medial frontal lobe, the ventral visual stream, and bilateral parahippocampal regions. Further, neural activity for source memory with words extensively overlapped with the region where pictures were preferentially processed than words, including the left mid-occipital cortex and the right parahippocampal cortex. Conclusions These results indicate that words that were accurately remembered with correct contextual information were processed more like pictures mediated by integrated imagery operation, compared to words that were recognized with incorrect context. In contrast, such processing did not discriminate subsequent source memory with pictures. Taken together, these findings suggest that unitization supports source memory for both words and pictures and that the requirement of the study task interacts with the nature of stimulus content in unitized source encoding. PMID:23848969

The relationship between children's sensitivity to dominant and non-dominant patterns of lexical stress and reading accuracy.

PubMed

Arciuli, Joanne

2017-05-01

This study reports on a new task for assessing children's sensitivity to lexical stress for words with different stress patterns and demonstrates that this task is useful in examining predictors of reading accuracy during the elementary years. In English, polysyllabic words beginning with a strong syllable exhibit the most common or dominant pattern of lexical stress (e.g., "coconut"), whereas polysyllabic words beginning with a weak syllable exhibit a less common non-dominant pattern (e.g., "banana"). The new Aliens Talking Underwater task assesses children's ability to match low-pass filtered recordings of words to pictures of objects. Via filtering, phonetic detail is removed but prosodic contour information relating to lexical stress is retained. In a series of two-alternative forced choice trials, participants see a picture and are asked to choose which of two filtered recordings matches the name of that picture; one recording exhibits the correct lexical stress of the target word, and the other recording reverses the pattern of stress over the initial two syllables of the target word rendering it incorrect. Target words exhibit either dominant stress or non-dominant stress. Analysis of data collected from 192 typically developing children aged 5 to 12years revealed that sensitivity to non dominant lexical stress was a significant predictor of reading accuracy even when age and phonological awareness were taken into account. A total of 76.3% of variance in children's reading accuracy was explained by these variables. Crown Copyright © 2016. Published by Elsevier Inc. All rights reserved.

How Well Do Patients Understand Written Instructions?

PubMed Central

Wong, Peter K.K.; Christie, Laura; Johnston, Jenny; Bowling, Alison; Freeman, Diane; Joshua, Fred; Bird, Paul; Chia, Karen; Bagga, Hanish

2014-01-01

Abstract The aim of this study was to assess health literacy (word recognition and comprehension) in patients at a rural rheumatology practice and to compare this to health literacy levels in patients from an urban rheumatology practice. Inclusion criteria for this cross-sectional study were as follows: ≥18-year-old patients at a rural rheumatology practice (Mid-North Coast Arthritis Clinic, Coffs Harbour, Australia) and an urban Sydney rheumatology practice (Combined Rheumatology Practice, Kogarah, Australia). Exclusion criteria were as follows: ill-health precluding participation; poor vision/hearing, non-English primary language. Word recognition was assessed using the Rapid Estimate of Adult Literacy in Medicine (REALM). Comprehension was assessed using the Test of Functional Health Literacy in Adults (TOFHLA). Practical comprehension and numeracy were assessed by asking patients to follow prescribing instructions for 5 common rheumatology medications. At the rural practice (Mid-North Coast Arthritis Clinic), 124/160 patients agreed to participate (F:M 83:41, mean age 60.3 ± 12.2) whereas the corresponding number at the urban practice (Combined Rheumatology Practice) was 99/119 (F:M 69:30, mean age 60.7 ± 17.5). Urban patients were more likely to be born overseas, speak another language at home, and be employed. There was no difference in REALM or TOFHLA scores between the 2 sites, and so data were pooled. REALM scores indicated 15% (33/223) of patients had a reading level ≤Grade 8 whereas 8% (18/223) had marginal or inadequate functional health literacy as assessed by the TOFHLA. Dosing instructions for ibuprofen and methotrexate were incorrectly understood by 32% (72/223) and 21% (46/223) of patients, respectively. Up to 15% of rural and urban patients had low health literacy and <1/3 of patients incorrectly followed dosing instructions for common rheumatology drugs. There was no significant difference in word recognition, functional health literacy, and numeracy between rural and urban rheumatology patients. PMID:25437024

rasbhari: Optimizing Spaced Seeds for Database Searching, Read Mapping and Alignment-Free Sequence Comparison.

PubMed

Hahn, Lars; Leimeister, Chris-André; Ounit, Rachid; Lonardi, Stefano; Morgenstern, Burkhard

2016-10-01

Many algorithms for sequence analysis rely on word matching or word statistics. Often, these approaches can be improved if binary patterns representing match and don't-care positions are used as a filter, such that only those positions of words are considered that correspond to the match positions of the patterns. The performance of these approaches, however, depends on the underlying patterns. Herein, we show that the overlap complexity of a pattern set that was introduced by Ilie and Ilie is closely related to the variance of the number of matches between two evolutionarily related sequences with respect to this pattern set. We propose a modified hill-climbing algorithm to optimize pattern sets for database searching, read mapping and alignment-free sequence comparison of nucleic-acid sequences; our implementation of this algorithm is called rasbhari. Depending on the application at hand, rasbhari can either minimize the overlap complexity of pattern sets, maximize their sensitivity in database searching or minimize the variance of the number of pattern-based matches in alignment-free sequence comparison. We show that, for database searching, rasbhari generates pattern sets with slightly higher sensitivity than existing approaches. In our Spaced Words approach to alignment-free sequence comparison, pattern sets calculated with rasbhari led to more accurate estimates of phylogenetic distances than the randomly generated pattern sets that we previously used. Finally, we used rasbhari to generate patterns for short read classification with CLARK-S. Here too, the sensitivity of the results could be improved, compared to the default patterns of the program. We integrated rasbhari into Spaced Words; the source code of rasbhari is freely available at http://rasbhari.gobics.de/.

Roles of frontal and temporal regions in reinterpreting semantically ambiguous sentences

PubMed Central

Vitello, Sylvia; Warren, Jane E.; Devlin, Joseph T.; Rodd, Jennifer M.

2014-01-01

Semantic ambiguity resolution is an essential and frequent part of speech comprehension because many words map onto multiple meanings (e.g., “bark,” “bank”). Neuroimaging research highlights the importance of the left inferior frontal gyrus (LIFG) and the left posterior temporal cortex in this process but the roles they serve in ambiguity resolution are uncertain. One possibility is that both regions are engaged in the processes of semantic reinterpretation that follows incorrect interpretation of an ambiguous word. Here we used fMRI to investigate this hypothesis. 20 native British English monolinguals were scanned whilst listening to sentences that contained an ambiguous word. To induce semantic reinterpretation, the disambiguating information was presented after the ambiguous word and delayed until the end of the sentence (e.g., “the teacher explained that the BARK was going to be very damp”). These sentences were compared to well-matched unambiguous sentences. Supporting the reinterpretation hypothesis, these ambiguous sentences produced more activation in both the LIFG and the left posterior inferior temporal cortex. Importantly, all but one subject showed ambiguity-related peaks within both regions, demonstrating that the group-level results were driven by high inter-subject consistency. Further support came from the finding that activation in both regions was modulated by meaning dominance. Specifically, sentences containing biased ambiguous words, which have one more dominant meaning, produced greater activation than those with balanced ambiguous words, which have two equally frequent meanings. Because the context always supported the less frequent meaning, the biased words require reinterpretation more often than balanced words. This is the first evidence of dominance effects in the spoken modality and provides strong support that frontal and temporal regions support the updating of semantic representations during speech comprehension. PMID:25120445

Lexical ambiguity in sentence comprehension

PubMed Central

Mason, Robert A.; Just, Marcel Adam

2009-01-01

An event-related fMRI paradigm was used to investigate brain activity during the reading of sentences containing either a lexically ambiguous word or an unambiguous control word. Higher levels of activation occurred during the reading of sentences containing a lexical ambiguity. Furthermore, the activated cortical network differed, depending on: (1) whether the sentence contained a balanced (i.e., both meanings equally likely) or a biased (i.e., one meaning more likely than other meanings) ambiguous word; and, (2) the working memory capacity of the individual as assessed by reading span. The findings suggest that encountering a lexical ambiguity is dealt with by activating multiple meanings utilizing processes involving both hemispheres. When an early interpretation of a biased ambiguous word is later disambiguated to the subordinate meaning, the superior frontal cortex activates in response to the coherence break and the right inferior frontal gyrus and the insula activate, possibly to suppress the incorrect interpretation. Negative correlations between reading span scores and activation in the right hemisphere for both types of ambiguous words suggest that readers with lower spans are more likely to involve show right hemisphere involvement in the processing of the ambiguity. A positive correlation between reading span scores and insula activation appearing only for biased sentences disambiguated to the subordinate meaning indicates that individuals with higher spans were more likely to initially maintain both meanings and as a result had to suppress the unintended dominant meaning. PMID:17433891

Treatment of Not-Administered Items on Individually Administered Intelligence Tests

ERIC Educational Resources Information Center

He, Wei; Wolfe, Edward W.

2012-01-01

In administration of individually administered intelligence tests, items are commonly presented in a sequence of increasing difficulty, and test administration is terminated after a predetermined number of incorrect answers. This practice produces stochastically censored data, a form of nonignorable missing data. By manipulating four factors…

Evaluating approaches to find exon chains based on long reads.

PubMed

Kuosmanen, Anna; Norri, Tuukka; Mäkinen, Veli

2018-05-01

Transcript prediction can be modeled as a graph problem where exons are modeled as nodes and reads spanning two or more exons are modeled as exon chains. Pacific Biosciences third-generation sequencing technology produces significantly longer reads than earlier second-generation sequencing technologies, which gives valuable information about longer exon chains in a graph. However, with the high error rates of third-generation sequencing, aligning long reads correctly around the splice sites is a challenging task. Incorrect alignments lead to spurious nodes and arcs in the graph, which in turn lead to incorrect transcript predictions. We survey several approaches to find the exon chains corresponding to long reads in a splicing graph, and experimentally study the performance of these methods using simulated data to allow for sensitivity/precision analysis. Our experiments show that short reads from second-generation sequencing can be used to significantly improve exon chain correctness either by error-correcting the long reads before splicing graph creation, or by using them to create a splicing graph on which the long-read alignments are then projected. We also study the memory and time consumption of various modules, and show that accurate exon chains lead to significantly increased transcript prediction accuracy. The simulated data and in-house scripts used for this article are available at http://www.cs.helsinki.fi/group/gsa/exon-chains/exon-chains-bib.tar.bz2.

Mojibake - The rehearsal of word fragments in verbal recall.

PubMed

Lange-Küttner, Christiane; Sykorova, Eva

2015-01-01

Theories of verbal rehearsal usually assume that whole words are being rehearsed. However, words consist of letter sequences, or syllables, or word onset-vowel-coda, amongst many other conceptualizations of word structure. A more general term is the 'grain size' of word units (Ziegler and Goswami, 2005). In the current study, a new method measured the quantitative percentage of correctly remembered word structure. The amount of letters in the correct letter sequence as per cent of word length was calculated, disregarding missing or added letters. A forced rehearsal was tested by repeating each memory list four times. We tested low frequency (LF) English words versus geographical (UK) town names to control for content. We also tested unfamiliar international (INT) non-words and names of international (INT) European towns to control for familiarity. An immediate versus distributed repetition was tested with a between-subject design. Participants responded with word fragments in their written recall especially when they had to remember unfamiliar words. While memory of whole words was sensitive to content, presentation distribution and individual sex and language differences, recall of word fragments was not. There was no trade-off between memory of word fragments with whole word recall during the repetition, instead also word fragments significantly increased. Moreover, while whole word responses correlated with each other during repetition, and word fragment responses correlated with each other during repetition, these two types of word recall responses were not correlated with each other. Thus there may be a lower layer consisting of free, sparse word fragments and an upper layer that consists of language-specific, orthographically and semantically constrained words.

Facilitatory Effects of Multi-Word Units in Lexical Processing and Word Learning: A Computational Investigation.

PubMed

Grimm, Robert; Cassani, Giovanni; Gillis, Steven; Daelemans, Walter

2017-01-01

Previous studies have suggested that children and adults form cognitive representations of co-occurring word sequences. We propose (1) that the formation of such multi-word unit (MWU) representations precedes and facilitates the formation of single-word representations in children and thus benefits word learning, and (2) that MWU representations facilitate adult word recognition and thus benefit lexical processing. Using a modified version of an existing computational model (McCauley and Christiansen, 2014), we extract MWUs from a corpus of child-directed speech (CDS) and a corpus of conversations among adults. We then correlate the number of MWUs within which each word appears with (1) age of first production and (2) adult reaction times on a word recognition task. In doing so, we take care to control for the effect of word frequency, as frequent words will naturally tend to occur in many MWUs. We also compare results to a baseline model which randomly groups words into sequences-and find that MWUs have a unique facilitatory effect on both response variables, suggesting that they benefit word learning in children and word recognition in adults. The effect is strongest on age of first production, implying that MWUs are comparatively more important for word learning than for adult lexical processing. We discuss possible underlying mechanisms and formulate testable predictions.

Fast and accurate phylogeny reconstruction using filtered spaced-word matches

PubMed Central

Sohrabi-Jahromi, Salma; Morgenstern, Burkhard

2017-01-01

Abstract Motivation: Word-based or ‘alignment-free’ algorithms are increasingly used for phylogeny reconstruction and genome comparison, since they are much faster than traditional approaches that are based on full sequence alignments. Existing alignment-free programs, however, are less accurate than alignment-based methods. Results: We propose Filtered Spaced Word Matches (FSWM), a fast alignment-free approach to estimate phylogenetic distances between large genomic sequences. For a pre-defined binary pattern of match and don’t-care positions, FSWM rapidly identifies spaced word-matches between input sequences, i.e. gap-free local alignments with matching nucleotides at the match positions and with mismatches allowed at the don’t-care positions. We then estimate the number of nucleotide substitutions per site by considering the nucleotides aligned at the don’t-care positions of the identified spaced-word matches. To reduce the noise from spurious random matches, we use a filtering procedure where we discard all spaced-word matches for which the overall similarity between the aligned segments is below a threshold. We show that our approach can accurately estimate substitution frequencies even for distantly related sequences that cannot be analyzed with existing alignment-free methods; phylogenetic trees constructed with FSWM distances are of high quality. A program run on a pair of eukaryotic genomes of a few hundred Mb each takes a few minutes. Availability and Implementation: The program source code for FSWM including a documentation, as well as the software that we used to generate artificial genome sequences are freely available at http://fswm.gobics.de/ Contact: chris.leimeister@stud.uni-goettingen.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:28073754

Fast and accurate phylogeny reconstruction using filtered spaced-word matches.

PubMed

Leimeister, Chris-André; Sohrabi-Jahromi, Salma; Morgenstern, Burkhard

2017-04-01

Word-based or 'alignment-free' algorithms are increasingly used for phylogeny reconstruction and genome comparison, since they are much faster than traditional approaches that are based on full sequence alignments. Existing alignment-free programs, however, are less accurate than alignment-based methods. We propose Filtered Spaced Word Matches (FSWM) , a fast alignment-free approach to estimate phylogenetic distances between large genomic sequences. For a pre-defined binary pattern of match and don't-care positions, FSWM rapidly identifies spaced word-matches between input sequences, i.e. gap-free local alignments with matching nucleotides at the match positions and with mismatches allowed at the don't-care positions. We then estimate the number of nucleotide substitutions per site by considering the nucleotides aligned at the don't-care positions of the identified spaced-word matches. To reduce the noise from spurious random matches, we use a filtering procedure where we discard all spaced-word matches for which the overall similarity between the aligned segments is below a threshold. We show that our approach can accurately estimate substitution frequencies even for distantly related sequences that cannot be analyzed with existing alignment-free methods; phylogenetic trees constructed with FSWM distances are of high quality. A program run on a pair of eukaryotic genomes of a few hundred Mb each takes a few minutes. The program source code for FSWM including a documentation, as well as the software that we used to generate artificial genome sequences are freely available at http://fswm.gobics.de/. chris.leimeister@stud.uni-goettingen.de. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press.

When Words Collide: Facilitation and Interference in the Report of Repeated Words From Rapidly Presented Lists

ERIC Educational Resources Information Center

Masson, Michael E. J.

2004-01-01

Inhibited encoding is the basis of some accounts of repetition blindness--impaired report of the second occurrence of a repeated word in a rapidly presented word sequence. The author presents evidence for the claim that repetition effects arise from constructive processes of perception and memory that occur to some extent after the word sequence…

Word structures of Granada Spanish-speaking preschoolers with typical versus protracted phonological development.

PubMed

Bernhardt, B May; Hanson, R; Perez, D; Ávila, C; Lleó, C; Stemberger, J P; Carballo, G; Mendoza, E; Fresneda, D; Chávez-Peón, M

2015-01-01

Research on children's word structure development is limited. Yet, phonological intervention aims to accelerate the acquisition of both speech-sounds and word structure, such as word length, stress or shapes in CV sequences. Until normative studies and meta-analyses provide in-depth information on this topic, smaller investigations can provide initial benchmarks for clinical purposes. To provide preliminary reference data for word structure development in a variety of Spanish with highly restricted coda use: Granada Spanish (similar to many Hispano-American varieties). To be clinically applicable, such data would need to show differences by age, developmental typicality and word structure complexity. Thus, older typically developing (TD) children were expected to show higher accuracy than younger children and those with protracted phonological development (PPD). Complex or phonologically marked forms (e.g. multisyllabic words, clusters) were expected to be late developing. Participants were 59 children aged 3-5 years in Granada, Spain: 30 TD children, and 29 with PPD and no additional language impairments. Single words were digitally recorded by a native Spanish speaker using a 103-word list and transcribed by native Spanish speakers, with confirmation by a second transcriber team and acoustic analysis. The program Phon 1.5 provided quantitative data. In accordance with expectations, the TD and older age groups had better-established word structures than the younger children and those with PPD. Complexity was also relevant: more structural mismatches occurred in multisyllabic words, initial unstressed syllables and clusters. Heterosyllabic consonant sequences were more accurate than syllable-initial sequences. The most common structural mismatch pattern overall was consonant deletion, with syllable deletion most common in 3-year-olds and children with PPD. The current study provides preliminary reference data for word structure development in a Spanish variety with restricted coda use, both by age and types of word structures. Between ages 3 and 5 years, global measures (whole word match, word shape match) distinguished children with typical versus protracted phonological development. By age 4, children with typical development showed near-mastery of word structures, whereas 4- and 5-year-olds with PPD continued to show syllable deletion and cluster reduction, especially in multisyllabic words. The results underline the relevance of multisyllabic words and words with clusters in Spanish phonological assessment and the utility of word structure data for identification of protracted phonological development. © 2014 Royal College of Speech and Language Therapists.

The parietal memory network activates similarly for true and associative false recognition elicited via the DRM procedure.

PubMed

McDermott, Kathleen B; Gilmore, Adrian W; Nelson, Steven M; Watson, Jason M; Ojemann, Jeffrey G

2017-02-01

Neuroimaging investigations of human memory encoding and retrieval have revealed that multiple regions of parietal cortex contribute to memory. Recently, a sparse network of regions within parietal cortex has been identified using resting state functional connectivity (MRI techniques). The regions within this network exhibit consistent task-related responses during memory formation and retrieval, leading to its being called the parietal memory network (PMN). Among its signature patterns are: deactivation during initial experience with an item (e.g., encoding); activation during subsequent repetitions (e.g., at retrieval); greater activation for successfully retrieved familiar words than novel words (e.g., hits relative to correctly-rejected lures). The question of interest here is whether novel words that are subjectively experienced as having been recently studied would elicit PMN activation similar to that of hits. That is, we compared old items correctly recognized to two types of novel items on a recognition test: those correctly identified as new and those incorrectly labeled as old due to their strong associative relation to the studied words (in the DRM false memory protocol). Subjective oldness plays a strong role in driving activation, as hits and false alarms activated similarly (and greater than correctly-rejected lures). Copyright © 2016 Elsevier Ltd. All rights reserved.

Mojibake – The rehearsal of word fragments in verbal recall

PubMed Central

Lange-Küttner, Christiane; Sykorova, Eva

2015-01-01

Theories of verbal rehearsal usually assume that whole words are being rehearsed. However, words consist of letter sequences, or syllables, or word onset-vowel-coda, amongst many other conceptualizations of word structure. A more general term is the ‘grain size’ of word units (Ziegler and Goswami, 2005). In the current study, a new method measured the quantitative percentage of correctly remembered word structure. The amount of letters in the correct letter sequence as per cent of word length was calculated, disregarding missing or added letters. A forced rehearsal was tested by repeating each memory list four times. We tested low frequency (LF) English words versus geographical (UK) town names to control for content. We also tested unfamiliar international (INT) non-words and names of international (INT) European towns to control for familiarity. An immediate versus distributed repetition was tested with a between-subject design. Participants responded with word fragments in their written recall especially when they had to remember unfamiliar words. While memory of whole words was sensitive to content, presentation distribution and individual sex and language differences, recall of word fragments was not. There was no trade-off between memory of word fragments with whole word recall during the repetition, instead also word fragments significantly increased. Moreover, while whole word responses correlated with each other during repetition, and word fragment responses correlated with each other during repetition, these two types of word recall responses were not correlated with each other. Thus there may be a lower layer consisting of free, sparse word fragments and an upper layer that consists of language-specific, orthographically and semantically constrained words. PMID:25941500

Word Structures of Granada Spanish-Speaking Preschoolers with Typical versus Protracted Phonological Development

ERIC Educational Resources Information Center

May Bernhardt, B.; Hanson, R.; Perez, D.; Ávila, C.; Lleó, C.; Stemberger, J. P.; Carballo, G.; Mendoza, E.; Fresneda, D.; Chávez-Peón, M.

2015-01-01

Background: Research on children's word structure development is limited. Yet, phonological intervention aims to accelerate the acquisition of both speech-sounds and word structure, such as word length, stress or shapes in CV sequences. Until normative studies and meta-analyses provide in-depth information on this topic, smaller investigations can…

A Preliminary Investigation of Racial Bias in Early Writing Curriculum-Based Measures

ERIC Educational Resources Information Center

Kondisko, Joseph E.

2017-01-01

Using de-identified data, this study investigated the relationship between racial categories with curriculum-based early writing measures (CBM-W), which included word dictation, picture word sentence writing, and story prompt tasks for over 300 participants in Grades 1, 2, and 3. Words written, words spelled correctly, correct letter sequences,…

The production and phonetic representation of fake geminates in English

PubMed Central

Oh, Grace E.; Redford, Melissa A.

2011-01-01

The current study focused on the production of non-contrastive geminates across different boundary types in English to investigate the hypothesis that word-internal heteromorphemic geminates may differ from those that arise across a word boundary. In this study, word-internal geminates arising from affixation, and described as either assimilated or concatenated, were matched to heteromorphemic geminates arising from sequences of identical consonants that spanned a word boundary and to word-internal singletons. Word-internal geminates were found to be longer than matched singletons in absolute and relative terms. By contrast, heteromorphemic geminates that occurred at word boundaries were only longer than matched singletons in absolute terms. In addition, heteromorphemic geminates in two word phrases were typically “pulled apart” in careful speech; that is, speakers marked the boundaries between free morphemes with pitch changes and pauses. Morpheme boundaries in words with bound affixes were very rarely highlighted in this way. These results are taken to indicate that most word-internal heteromorphemic geminates are represented as a single long consonant in the speech plan rather than as a consonant sequence. Only those geminates that arise in two word phrases exhibit phonetic characteristics that are fully consistent with the representation of two identical consonants crossing a morpheme boundary. PMID:22611293

A knowledge engineering approach to recognizing and extracting sequences of nucleic acids from scientific literature.

PubMed

García-Remesal, Miguel; Maojo, Victor; Crespo, José

2010-01-01

In this paper we present a knowledge engineering approach to automatically recognize and extract genetic sequences from scientific articles. To carry out this task, we use a preliminary recognizer based on a finite state machine to extract all candidate DNA/RNA sequences. The latter are then fed into a knowledge-based system that automatically discards false positives and refines noisy and incorrectly merged sequences. We created the knowledge base by manually analyzing different manuscripts containing genetic sequences. Our approach was evaluated using a test set of 211 full-text articles in PDF format containing 3134 genetic sequences. For such set, we achieved 87.76% precision and 97.70% recall respectively. This method can facilitate different research tasks. These include text mining, information extraction, and information retrieval research dealing with large collections of documents containing genetic sequences.

Caffeine enhances real-world language processing: evidence from a proofreading task.

PubMed

Brunyé, Tad T; Mahoney, Caroline R; Rapp, David N; Ditman, Tali; Taylor, Holly A

2012-03-01

Caffeine has become the most prevalently consumed psychostimulant in the world, but its influences on daily real-world functioning are relatively unknown. The present work investigated the effects of caffeine (0 mg, 100 mg, 200 mg, 400 mg) on a commonplace language task that required readers to identify and correct 4 error types in extended discourse: simple local errors (misspelling 1- to 2-syllable words), complex local errors (misspelling 3- to 5-syllable words), simple global errors (incorrect homophones), and complex global errors (incorrect subject-verb agreement and verb tense). In 2 placebo-controlled, double-blind studies using repeated-measures designs, we found higher detection and repair rates for complex global errors, asymptoting at 200 mg in low consumers (Experiment 1) and peaking at 400 mg in high consumers (Experiment 2). In both cases, covariate analyses demonstrated that arousal state mediated the relationship between caffeine consumption and the detection and repair of complex global errors. Detection and repair rates for the other 3 error types were not affected by caffeine consumption. Taken together, we demonstrate that caffeine has differential effects on error detection and repair as a function of dose and error type, and this relationship is closely tied to caffeine's effects on subjective arousal state. These results support the notion that central nervous system stimulants may enhance global processing of language-based materials and suggest that such effects may originate in caffeine-related right hemisphere brain processes. Implications for understanding the relationships between caffeine consumption and real-world cognitive functioning are discussed. PsycINFO Database Record (c) 2012 APA, all rights reserved.

Inference of Markovian properties of molecular sequences from NGS data and applications to comparative genomics.

PubMed

Ren, Jie; Song, Kai; Deng, Minghua; Reinert, Gesine; Cannon, Charles H; Sun, Fengzhu

2016-04-01

Next-generation sequencing (NGS) technologies generate large amounts of short read data for many different organisms. The fact that NGS reads are generally short makes it challenging to assemble the reads and reconstruct the original genome sequence. For clustering genomes using such NGS data, word-count based alignment-free sequence comparison is a promising approach, but for this approach, the underlying expected word counts are essential.A plausible model for this underlying distribution of word counts is given through modeling the DNA sequence as a Markov chain (MC). For single long sequences, efficient statistics are available to estimate the order of MCs and the transition probability matrix for the sequences. As NGS data do not provide a single long sequence, inference methods on Markovian properties of sequences based on single long sequences cannot be directly used for NGS short read data. Here we derive a normal approximation for such word counts. We also show that the traditional Chi-square statistic has an approximate gamma distribution ,: using the Lander-Waterman model for physical mapping. We propose several methods to estimate the order of the MC based on NGS reads and evaluate those using simulations. We illustrate the applications of our results by clustering genomic sequences of several vertebrate and tree species based on NGS reads using alignment-free sequence dissimilarity measures. We find that the estimated order of the MC has a considerable effect on the clustering results ,: and that the clustering results that use a N: MC of the estimated order give a plausible clustering of the species. Our implementation of the statistics developed here is available as R package 'NGS.MC' at http://www-rcf.usc.edu/∼fsun/Programs/NGS-MC/NGS-MC.html fsun@usc.edu Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Some Principles Involved in the Acquisition of Number Words.

ERIC Educational Resources Information Center

Pollmann, Thijs

2003-01-01

Offers linguistic insights into number acquisition. Argues that the particular rhythmical structure of speech forms for numerical sequence provides children with the raw material to develop a concept "decade word. Children have to learn by rote a second sequence--decade numbers (10, 20, 20, etc). This is an important step in the detection of the…

Lindamood Phonemic Sequencing (LiPS) [R]. What Works Clearinghouse Intervention Report

ERIC Educational Resources Information Center

What Works Clearinghouse, 2008

2008-01-01

The Lindamood Phonemic Sequencing (LiPS)[R] program (formerly called the Auditory Discrimination in Depth[R] [ADD] program) is designed to teach students skills to decode words and to identify individual sounds and blends in words. The program is individualized to meet student needs and is often used with students who have learning disabilities or…

Verification of Ribosomal Proteins of Aspergillus fumigatus for Use as Biomarkers in MALDI-TOF MS Identification

PubMed Central

Nakamura, Sayaka; Sato, Hiroaki; Tanaka, Reiko; Yaguchi, Takashi

2016-01-01

We have previously proposed a rapid identification method for bacterial strains based on the profiles of their ribosomal subunit proteins (RSPs), observed using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). This method can perform phylogenetic characterization based on the mass of housekeeping RSP biomarkers, ideally calculated from amino acid sequence information registered in public protein databases. With the aim of extending its field of application to medical mycology, this study investigates the actual state of information of RSPs of eukaryotic fungi registered in public protein databases through the characterization of ribosomal protein fractions extracted from genome-sequenced Aspergillus fumigatus strains Af293 and A1163 as a model. In this process, we have found that the public protein databases harbor problems. The RSP names are in confusion, so we have provisionally unified them using the yeast naming system. The most serious problem is that many incorrect sequences are registered in the public protein databases. Surprisingly, more than half of the sequences are incorrect, due chiefly to mis-annotation of exon/intron structures. These errors could be corrected by a combination of in silico inspection by sequence homology analysis and MALDI-TOF MS measurements. We were also able to confirm conserved post-translational modifications in eleven RSPs. After these verifications, the masses of 31 expressed RSPs under 20,000 Da could be accurately confirmed. These RSPs have a potential to be useful biomarkers for identifying clinical isolates of A. fumigatus. PMID:27843740

Metabolic network prediction through pairwise rational kernels.

PubMed

Roche-Lima, Abiel; Domaratzki, Michael; Fristensky, Brian

2014-09-26

Metabolic networks are represented by the set of metabolic pathways. Metabolic pathways are a series of biochemical reactions, in which the product (output) from one reaction serves as the substrate (input) to another reaction. Many pathways remain incompletely characterized. One of the major challenges of computational biology is to obtain better models of metabolic pathways. Existing models are dependent on the annotation of the genes. This propagates error accumulation when the pathways are predicted by incorrectly annotated genes. Pairwise classification methods are supervised learning methods used to classify new pair of entities. Some of these classification methods, e.g., Pairwise Support Vector Machines (SVMs), use pairwise kernels. Pairwise kernels describe similarity measures between two pairs of entities. Using pairwise kernels to handle sequence data requires long processing times and large storage. Rational kernels are kernels based on weighted finite-state transducers that represent similarity measures between sequences or automata. They have been effectively used in problems that handle large amount of sequence information such as protein essentiality, natural language processing and machine translations. We create a new family of pairwise kernels using weighted finite-state transducers (called Pairwise Rational Kernel (PRK)) to predict metabolic pathways from a variety of biological data. PRKs take advantage of the simpler representations and faster algorithms of transducers. Because raw sequence data can be used, the predictor model avoids the errors introduced by incorrect gene annotations. We then developed several experiments with PRKs and Pairwise SVM to validate our methods using the metabolic network of Saccharomyces cerevisiae. As a result, when PRKs are used, our method executes faster in comparison with other pairwise kernels. Also, when we use PRKs combined with other simple kernels that include evolutionary information, the accuracy values have been improved, while maintaining lower construction and execution times. The power of using kernels is that almost any sort of data can be represented using kernels. Therefore, completely disparate types of data can be combined to add power to kernel-based machine learning methods. When we compared our proposal using PRKs with other similar kernel, the execution times were decreased, with no compromise of accuracy. We also proved that by combining PRKs with other kernels that include evolutionary information, the accuracy can also also be improved. As our proposal can use any type of sequence data, genes do not need to be properly annotated, avoiding accumulation errors because of incorrect previous annotations.

Evaluating the Pedagogic Value of Multi-word Expressions Based on EFL Teachers' and Advanced Learners' Value Judgments

ERIC Educational Resources Information Center

Omidian, Taha; Shahriari, Hesamoddin; Ghonsooly, Behzad

2017-01-01

Multi-word expressions play an important role in second language acquisition, comprehension, and production. Therefore, there is great need for a list of frequent, useful multi-word expressions in language teaching classrooms. Despite multiple attempts at defining multi-word sequences, researchers and teaching experts are divided over the nature…

Stress Sensitivity and Reading Performance in Spanish: A Study with Children

ERIC Educational Resources Information Center

Gutierrez-Palma, Nicolas; Reyes, Alfonso Palma

2007-01-01

This paper investigates the relationship between ability to detect changes in prosody and reading performance in Spanish. Participants were children aged 7-8 years. Their tasks consisted of reading words, reading non-words, stressing non-words and reproducing sequences of two, three or four non-words by pressing the corresponding keys on the…

Building a dictionary for genomes: Identification of presumptive regulatory sites by statistical analysis

PubMed Central

Bussemaker, Harmen J.; Li, Hao; Siggia, Eric D.

2000-01-01

The availability of complete genome sequences and mRNA expression data for all genes creates new opportunities and challenges for identifying DNA sequence motifs that control gene expression. An algorithm, “MobyDick,” is presented that decomposes a set of DNA sequences into the most probable dictionary of motifs or words. This method is applicable to any set of DNA sequences: for example, all upstream regions in a genome or all genes expressed under certain conditions. Identification of words is based on a probabilistic segmentation model in which the significance of longer words is deduced from the frequency of shorter ones of various lengths, eliminating the need for a separate set of reference data to define probabilities. We have built a dictionary with 1,200 words for the 6,000 upstream regulatory regions in the yeast genome; the 500 most significant words (some with as few as 10 copies in all of the upstream regions) match 114 of 443 experimentally determined sites (a significance level of 18 standard deviations). When analyzing all of the genes up-regulated during sporulation as a group, we find many motifs in addition to the few previously identified by analyzing the subclusters individually to the expression subclusters. Applying MobyDick to the genes derepressed when the general repressor Tup1 is deleted, we find known as well as putative binding sites for its regulatory partners. PMID:10944202

Yeast identification: reassessment of assimilation tests as sole universal identifiers.

PubMed

Spencer, J; Rawling, S; Stratford, M; Steels, H; Novodvorska, M; Archer, D B; Chandra, S

2011-11-01

To assess whether assimilation tests in isolation remain a valid method of identification of yeasts, when applied to a wide range of environmental and spoilage isolates. Seventy-one yeast strains were isolated from a soft drinks factory. These were identified using assimilation tests and by D1/D2 rDNA sequencing. When compared to sequencing, assimilation test identifications (MicroLog™) were 18·3% correct, a further 14·1% correct within the genus and 67·6% were incorrectly identified. The majority of the latter could be attributed to the rise in newly reported yeast species. Assimilation tests alone are unreliable as a universal means of yeast identification, because of numerous new species, variability of strains and increasing coincidence of assimilation profiles. Assimilation tests still have a useful role in the identification of common species, such as the majority of clinical isolates. It is probable, based on these results, that many yeast identifications reported in older literature are incorrect. This emphasizes the crucial need for accurate identification in present and future publications. © 2011 The Authors. Letters in Applied Microbiology © 2011 The Society for Applied Microbiology.

On the Time Course of Accessing Meaning in a Second Language: An Electrophysiological and Behavioral Investigation of Translation Recognition

PubMed Central

Guo, Taomei; Misra, Maya; Tam, Joyce W.; Kroll, Judith F.

2012-01-01

In 2 experiments, relatively proficient Chinese–English bilinguals decided whether Chinese words were the correct translations of English words. Critical trials were those on which incorrect translations were related in lexical form or meaning to the correct translation. In Experiment 1, behavioral interference was revealed for both distractor types, but event-related potentials (ERPs) revealed a different time course for the 2 conditions. Semantic distractors elicited effects primarily on the N400 and late positive component (LPC), with a smaller N400 and a smaller LPC over the posterior scalp but a larger LPC over the anterior scalp relative to unrelated controls. In contrast, translation form distractors elicited a larger P200 and a larger LPC than did unrelated controls. To determine whether the translation form effects were enabled by the relatively long, 750-ms stimulus onset asynchrony (SOA) between words, a 2nd ERP experiment was conducted using a shorter, 300-ms, SOA. The behavioral results revealed interference for both types of distractors, but the ERPs again revealed different loci for the 2 effects. Taken together, the data suggest that proficient bilinguals activate 1st-language translations of words in the 2nd language after they have accessed the meaning of those words. The implications of this pattern for claims about the nature of cross-language activation when bilinguals read in 1 or both languages are discussed. PMID:22686844

Effects of Working Memory Capacity on Metacognitive Monitoring: A Study of Group Differences Using a Listening Span Test.

PubMed

Komori, Mie

2016-01-01

Monitoring is an executive function of working memory that serves to update novel information, focusing attention on task-relevant targets, and eliminating task-irrelevant noise. The present research used a verbal working memory task to examine how working memory capacity limits affect monitoring. Participants performed a Japanese listening span test that included maintenance of target words and listening comprehension. On each trial, participants responded to the target word and then immediately estimated confidence in recall performance for that word (metacognitive judgment). The results confirmed significant differences in monitoring accuracy between high and low capacity groups in a multi-task situation. That is, confidence judgments were superior in high vs. low capacity participants in terms of absolute accuracy and discrimination. The present research further investigated how memory load and interference affect underestimation of successful recall. The results indicated that the level of memory load that reduced word recall performance and led to an underconfidence bias varied according to participants' memory capacity. In addition, irrelevant information associated with incorrect true/ false decisions (secondary task) and word recall within the current trial impaired monitoring accuracy in both participant groups. These findings suggest that interference from unsuccessful decisions only influences low, but not high, capacity participants. Therefore, monitoring accuracy, which requires high working memory capacity, improves metacognitive abilities by inhibiting task-irrelevant noise and focusing attention on detecting task-relevant targets or useful retrieval cues, which could improve actual cognitive performance.

"I know your name, but not your number"--Patients with verbal short-term memory deficits are impaired in learning sequences of digits.

PubMed

Bormann, Tobias; Seyboth, Margret; Umarova, Roza; Weiller, Cornelius

2015-06-01

Studies on verbal learning in patients with impaired verbal short-term memory (vSTM) have revealed dissociations among types of verbal information. Patients with impaired vSTM are able to learn lists of known words but fail to acquire new word forms. This suggests that vSTM is involved in new word learning. The present study assessed both new word learning and the learning of digit sequences in two patients with impaired vSTM. In two experiments, participants were required to learn people's names, ages and professions, or their four digit 'phone numbers'. The STM patients were impaired on learning unknown family names and phone numbers, but managed to acquire other verbal information. In contrast, a patient with a severe verbal episodic memory impairment was impaired across information types. These results indicate verbal STM involvement in the learning of digit sequences. Copyright © 2015 Elsevier Ltd. All rights reserved.

The Impact of Transcription Writing Interventions for First-Grade Students

PubMed Central

Wanzek, Jeanne; Gatlin, Brandy; Al Otaiba, Stephanie; Kim, Young-Suk Grace

2016-01-01

We examined the effects of transcription instruction for students in first grade. Students in the lowest 70% of the participating schools were selected for the study. These 81 students were randomly assigned to: (a) spelling instruction, (b) handwriting instruction, (c) combination spelling and handwriting instruction, or (d) no intervention. Intervention was provided in small groups of 4 students, 25 min a day, 4 days a week for 8 weeks. Students in the spelling condition outperformed the control group on spelling measures with moderate effect sizes noted on curriculum-based writing measures (e.g., correct word sequence; g range = 0.34 to 0.68). Students in the handwriting condition outperformed the control group on correct word sequences with small to moderate effects on other handwriting and writing measures (g range = 0.31 to 0.71). Students in the combined condition outperformed the control group on correct word sequences with a small effect on total words written (g range = 0.39 to 0.84). PMID:28989267

Using stochastic language models (SLM) to map lexical, syntactic, and phonological information processing in the brain.

PubMed

Lopopolo, Alessandro; Frank, Stefan L; van den Bosch, Antal; Willems, Roel M

2017-01-01

Language comprehension involves the simultaneous processing of information at the phonological, syntactic, and lexical level. We track these three distinct streams of information in the brain by using stochastic measures derived from computational language models to detect neural correlates of phoneme, part-of-speech, and word processing in an fMRI experiment. Probabilistic language models have proven to be useful tools for studying how language is processed as a sequence of symbols unfolding in time. Conditional probabilities between sequences of words are at the basis of probabilistic measures such as surprisal and perplexity which have been successfully used as predictors of several behavioural and neural correlates of sentence processing. Here we computed perplexity from sequences of words and their parts of speech, and their phonemic transcriptions. Brain activity time-locked to each word is regressed on the three model-derived measures. We observe that the brain keeps track of the statistical structure of lexical, syntactic and phonological information in distinct areas.

"I know you can hear me": neural correlates of feigned hearing loss.

PubMed

McPherson, Bradley; McMahon, Katie; Wilson, Wayne; Copland, David

2012-08-01

In the assessment of human hearing, it is often important to determine whether hearing loss is organic or nonorganic in nature. Nonorganic, or functional, hearing loss is often associated with deceptive intention on the part of the listener. Over the past decade, functional neuroimaging has been used to study the neural correlates of deception, and studies have consistently highlighted the contribution of the prefrontal cortex in such behaviors. Can patterns of brain activity be similarly used to detect when an individual is feigning a hearing loss? To answer this question, 15 adult participants were requested to respond to pure tones and simple words correctly, incorrectly, randomly, or with the intent to feign a hearing loss. As predicted, more activity was observed in the prefrontal cortices (as measured by functional magnetic resonance imaging), and delayed behavioral reaction times were noted, when the participants feigned a hearing loss or responded randomly versus when they responded correctly or incorrectly. The results suggest that cortical imaging techniques could play a role in identifying individuals who are feigning hearing loss. Copyright © 2011 Wiley Periodicals, Inc.

Level statistics of words: Finding keywords in literary texts and symbolic sequences

NASA Astrophysics Data System (ADS)

Carpena, P.; Bernaola-Galván, P.; Hackenberg, M.; Coronado, A. V.; Oliver, J. L.

2009-03-01

Using a generalization of the level statistics analysis of quantum disordered systems, we present an approach able to extract automatically keywords in literary texts. Our approach takes into account not only the frequencies of the words present in the text but also their spatial distribution along the text, and is based on the fact that relevant words are significantly clustered (i.e., they self-attract each other), while irrelevant words are distributed randomly in the text. Since a reference corpus is not needed, our approach is especially suitable for single documents for which no a priori information is available. In addition, we show that our method works also in generic symbolic sequences (continuous texts without spaces), thus suggesting its general applicability.

System for information discovery

DOEpatents

Pennock, Kelly A [Richland, WA; Miller, Nancy E [Kennewick, WA

2002-11-19

A sequence of word filters are used to eliminate terms in the database which do not discriminate document content, resulting in a filtered word set and a topic word set whose members are highly predictive of content. These two word sets are then formed into a two dimensional matrix with matrix entries calculated as the conditional probability that a document will contain a word in a row given that it contains the word in a column. The matrix representation allows the resultant vectors to be utilized to interpret document contents.

When a hit sounds like a kiss: An electrophysiological exploration of semantic processing in visual narrative.

PubMed

Manfredi, Mirella; Cohn, Neil; Kutas, Marta

2017-06-01

Researchers have long questioned whether information presented through different sensory modalities involves distinct or shared semantic systems. We investigated uni-sensory cross-modal processing by recording event-related brain potentials to words replacing the climactic event in a visual narrative sequence (comics). We compared Onomatopoeic words, which phonetically imitate action sounds (Pow!), with Descriptive words, which describe an action (Punch!), that were (in)congruent within their sequence contexts. Across two experiments, larger N400s appeared to Anomalous Onomatopoeic or Descriptive critical panels than to their congruent counterparts, reflecting a difficulty in semantic access/retrieval. Also, Descriptive words evinced a greater late frontal positivity compared to Onomatopoetic words, suggesting that, though plausible, they may be less predictable/expected in visual narratives. Our results indicate that uni-sensory cross-model integration of word/letter-symbol strings within visual narratives elicit ERP patterns typically observed for written sentence processing, thereby suggesting the engagement of similar domain-independent integration/interpretation mechanisms. Copyright © 2017 Elsevier Inc. All rights reserved.

When a hit sounds like a kiss: an electrophysiological exploration of semantic processing in visual narrative

PubMed Central

Manfredi, Mirella; Cohn, Neil; Kutas, Marta

2017-01-01

Researchers have long questioned whether information presented through different sensory modalities involves distinct or shared semantic systems. We investigated uni-sensory cross-modal processing by recording event-related brain potentials to words replacing the climactic event in a visual narrative sequence (comics). We compared Onomatopoeic words, which phonetically imitate action sounds (Pow!), with Descriptive words, which describe an action (Punch!), that were (in)congruent within their sequence contexts. Across two experiments, larger N400s appeared to Anomalous Onomatopoeic or Descriptive critical panels than to their congruent counterparts, reflecting a difficulty in semantic access/retrieval. Also, Descriptive words evinced a greater late frontal positivity compared to Onomatopoetic words, suggesting that, though plausible, they may be less predictable/expected in visual narratives. Our results indicate that uni-sensory cross-model integration of word/letter-symbol strings within visual narratives elicit ERP patterns typically observed for written sentence processing, thereby suggesting the engagement of similar domain-independent integration/interpretation mechanisms. PMID:28242517

Domain-specific and domain-general constraints on word and sequence learning.

PubMed

Archibald, Lisa M D; Joanisse, Marc F

2013-02-01

The relative influences of language-related and memory-related constraints on the learning of novel words and sequences were examined by comparing individual differences in performance of children with and without specific deficits in either language or working memory. Children recalled lists of words in a Hebbian learning protocol in which occasional lists repeated, yielding improved recall over the course of the task on the repeated lists. The task involved presentation of pictures of common nouns followed immediately by equivalent presentations of the spoken names. The same participants also completed a paired-associate learning task involving word-picture and nonword-picture pairs. Hebbian learning was observed for all groups. Domain-general working memory constrained immediate recall, whereas language abilities impacted recall in the auditory modality only. In addition, working memory constrained paired-associate learning generally, whereas language abilities disproportionately impacted novel word learning. Overall, all of the learning tasks were highly correlated with domain-general working memory. The learning of nonwords was additionally related to general intelligence, phonological short-term memory, language abilities, and implicit learning. The results suggest that distinct associations between language- and memory-related mechanisms support learning of familiar and unfamiliar phonological forms and sequences.

Distinguishing Functional DNA Words; A Method for Measuring Clustering Levels

NASA Astrophysics Data System (ADS)

Moghaddasi, Hanieh; Khalifeh, Khosrow; Darooneh, Amir Hossein

2017-01-01

Functional DNA sub-sequences and genome elements are spatially clustered through the genome just as keywords in literary texts. Therefore, some of the methods for ranking words in texts can also be used to compare different DNA sub-sequences. In analogy with the literary texts, here we claim that the distribution of distances between the successive sub-sequences (words) is q-exponential which is the distribution function in non-extensive statistical mechanics. Thus the q-parameter can be used as a measure of words clustering levels. Here, we analyzed the distribution of distances between consecutive occurrences of 16 possible dinucleotides in human chromosomes to obtain their corresponding q-parameters. We found that CG as a biologically important two-letter word concerning its methylation, has the highest clustering level. This finding shows the predicting ability of the method in biology. We also proposed that chromosome 18 with the largest value of q-parameter for promoters of genes is more sensitive to dietary and lifestyle. We extended our study to compare the genome of some selected organisms and concluded that the clustering level of CGs increases in higher evolutionary organisms compared to lower ones.

Library Design-Facilitated High-Throughput Sequencing of Synthetic Peptide Libraries.

PubMed

Vinogradov, Alexander A; Gates, Zachary P; Zhang, Chi; Quartararo, Anthony J; Halloran, Kathryn H; Pentelute, Bradley L

2017-11-13

A methodology to achieve high-throughput de novo sequencing of synthetic peptide mixtures is reported. The approach leverages shotgun nanoliquid chromatography coupled with tandem mass spectrometry-based de novo sequencing of library mixtures (up to 2000 peptides) as well as automated data analysis protocols to filter away incorrect assignments, noise, and synthetic side-products. For increasing the confidence in the sequencing results, mass spectrometry-friendly library designs were developed that enabled unambiguous decoding of up to 600 peptide sequences per hour while maintaining greater than 85% sequence identification rates in most cases. The reliability of the reported decoding strategy was additionally confirmed by matching fragmentation spectra for select authentic peptides identified from library sequencing samples. The methods reported here are directly applicable to screening techniques that yield mixtures of active compounds, including particle sorting of one-bead one-compound libraries and affinity enrichment of synthetic library mixtures performed in solution.

Phenotypic and genotypic discrepancy of Streptococcus pneumoniae strains isolated from Asian countries.

PubMed

Ko, Kwan Soo; Oh, Won Sup; Peck, Kyong Ran; Lee, Jang Ho; Lee, Nam Yong; Song, Jae-Hoon

2005-07-01

Non-typeable isolates of Streptococcus pneumoniae collected from Asian countries were characterized by optochin susceptibility test, bile solubility test, multilocus sequence typing of housekeeping genes, amplification of virulence-related genes, 16S rDNA-RsaI digestion, and 16S rDNA sequencing. Six of 54 non-typeable pneumococcal isolates showed divergence of gene sequences of recP and xpt from typical pneumococcal strains. Of these six atypical pneumococcal strains, two showed different results in optochin susceptibility or bile solubility test from typical pneumococcal strains. All six isolates showed high sequence dissimilarities of multilocus sequence typing, 16S rDNA sequences, and lytA sequences from typical S. pneumoniae strains. Data from this study suggest that classic tests such as optochin susceptibility and bile solubility tests may lead to incorrect identification of S. pneumoniae. These atypical strains may belong to different bacterial species from S. pneumoniae.

Effects of Sequences of Cognitions on Group Performance Over Time

PubMed Central

Molenaar, Inge; Chiu, Ming Ming

2017-01-01

Extending past research showing that sequences of low cognitions (low-level processing of information) and high cognitions (high-level processing of information through questions and elaborations) influence the likelihoods of subsequent high and low cognitions, this study examines whether sequences of cognitions are related to group performance over time; 54 primary school students (18 triads) discussed and wrote an essay about living in another country (32,375 turns of talk). Content analysis and statistical discourse analysis showed that within each lesson, groups with more low cognitions or more sequences of low cognition followed by high cognition added more essay words. Groups with more high cognitions, sequences of low cognition followed by low cognition, or sequences of high cognition followed by an action followed by low cognition, showed different words and sequences, suggestive of new ideas. The links between cognition sequences and group performance over time can inform facilitation and assessment of student discussions. PMID:28490854

Effects of Sequences of Cognitions on Group Performance Over Time.

PubMed

Molenaar, Inge; Chiu, Ming Ming

2017-04-01

Extending past research showing that sequences of low cognitions (low-level processing of information) and high cognitions (high-level processing of information through questions and elaborations) influence the likelihoods of subsequent high and low cognitions, this study examines whether sequences of cognitions are related to group performance over time; 54 primary school students (18 triads) discussed and wrote an essay about living in another country (32,375 turns of talk). Content analysis and statistical discourse analysis showed that within each lesson, groups with more low cognitions or more sequences of low cognition followed by high cognition added more essay words. Groups with more high cognitions, sequences of low cognition followed by low cognition, or sequences of high cognition followed by an action followed by low cognition, showed different words and sequences, suggestive of new ideas. The links between cognition sequences and group performance over time can inform facilitation and assessment of student discussions.

Aging and interference in story recall.

PubMed

Mund, Iris; Bell, Raoul; Buchner, Axel

2012-01-01

BACKGROUND/STUDY CONTEXT: According to inhibitory deficit theory, older adults should be more impaired by visual distractors than younger adults when reading texts. Studies using a multiple-choice recognition test to examine age differences in the impairment of text comprehension due to distractor words yielded inconsistent results. In the present study, younger participants and older participants were required to read short texts comprising unrelated, related, or no distractor words. Visual acuity was equated between groups. Text recall was assessed using a gist-based propositional scoring procedure. There were pronounced age differences in reading with distraction. Older adults were slowed down more than younger adults by the presence of distractor words when reading. Furthermore, older adults' story recall was clearly impaired by the presence of distractor material, whereas younger adults' recall performance was not. In addition, older adults were more likely to make intrusion errors. Consistent with inhibitory deficit theory, the findings suggest that older adults were less able than younger adults to establish a correct mental representation of the target text when distractors were present. Furthermore, older adults were more likely than younger adults to build up incorrect memory representations that comprise distractor concepts. Thus, there are pronounced age differences in the impairment of text comprehension by distracting information.

Uses and Functions of Formulaic Sequences in Second-Language Speech: An Exploration of the Foundations of Fluency

ERIC Educational Resources Information Center

Wood, David

2006-01-01

Formulaic sequences are fixed combinations of words that have a range of functions and uses in speech production and communication, and seem to be cognitively stored and retrieved by speakers as if they were single words. They can facilitate fluency in speech by making pauses shorter and less frequent, and allowing longer runs of speech between…

The impact of visual sequencing of graphic symbols on the sentence construction output of children who have acquired language.

PubMed

Alant, Erna; du Plooy, Amelia; Dada, Shakila

2007-01-01

Although the sequence of graphic or pictorial symbols displayed on a communication board can have an impact on the language output of children, very little research has been conducted to describe this. Research in this area is particularly relevant for prioritising the importance of specific visual and graphic features in providing more effective and user-friendly access to communication boards. This study is concerned with understanding the impact ofspecific sequences of graphic symbol input on the graphic and spoken output of children who have acquired language. Forty participants were divided into two comparable groups. Each group was exposed to graphic symbol input with a certain word order sequence. The structure of input was either in typical English word order sequence Subject- Verb-Object (SVO) or in the word order sequence of Subject-Object-Verb (SOV). Both input groups had to answer six questions by using graphic output as well as speech. The findings indicated that there are significant differences in the PCS graphic output patterns of children who are exposed to graphic input in the SOV and SVO sequences. Furthermore, the output produced in the graphic mode differed considerably to the output produced in the spoken mode. Clinical implications of these findings are discussed

Wild Birds Use an Ordering Rule to Decode Novel Call Sequences.

PubMed

Suzuki, Toshitaka N; Wheatcroft, David; Griesser, Michael

2017-08-07

The generative power of human language depends on grammatical rules, such as word ordering, that allow us to produce and comprehend even novel combinations of words [1-3]. Several species of birds and mammals produce sequences of calls [4-6], and, like words in human sentences, their order may influence receiver responses [7]. However, it is unknown whether animals use call ordering to extract meaning from truly novel sequences. Here, we use a novel experimental approach to test this in a wild bird species, the Japanese tit (Parus minor). Japanese tits are attracted to mobbing a predator when they hear conspecific alert and recruitment calls ordered as alert-recruitment sequences [7]. They also approach in response to recruitment calls of heterospecific individuals in mixed-species flocks [8, 9]. Using experimental playbacks, we assess their responses to artificial sequences in which their own alert calls are combined into different orderings with heterospecific recruitment calls. We find that Japanese tits respond similarly to mixed-species alert-recruitment call sequences and to their own alert-recruitment sequences. Importantly, however, tits rarely respond to mixed-species sequences in which the call order is reversed. Thus, Japanese tits extract a compound meaning from novel call sequences using an ordering rule. These results demonstrate a new parallel between animal communication systems and human language, opening new avenues for exploring the evolution of ordering rules and compositionality in animal vocal sequences. Copyright © 2017 Elsevier Ltd. All rights reserved.

Pigeons acquire multiple categories in parallel via associative learning: A parallel to human word learning?

PubMed Central

Wasserman, Edward A.; Brooks, Daniel I.; McMurray, Bob

2014-01-01

Might there be parallels between category learning in animals and word learning in children? To examine this possibility, we devised a new associative learning technique for teaching pigeons to sort 128 photographs of objects into 16 human language categories. We found that pigeons learned all 16 categories in parallel, they perceived the perceptual coherence of the different object categories, and they generalized their categorization behavior to novel photographs from the training categories. More detailed analyses of the factors that predict trial-by-trial learning implicated a number of factors that may shape learning. First, we found considerable trial-by-trial dependency of pigeons’ categorization responses, consistent with several recent studies that invoke this dependency to claim that humans acquire words via symbolic or inferential mechanisms; this finding suggests that such dependencies may also arise in associative systems. Second, our trial-by-trial analyses divulged seemingly irrelevant aspects of the categorization task, like the spatial location of the report responses, which influenced learning. Third, those trial-by-trial analyses also supported the possibility that learning may be determined both by strengthening correct stimulus-response associations and by weakening incorrect stimulus-response associations. The parallel between all these findings and important aspects of human word learning suggests that associative learning mechanisms may play a much stronger part in complex human behavior than is commonly believed. PMID:25497520

The Influence of Phonotactic Probability on Word Recognition in Toddlers

ERIC Educational Resources Information Center

MacRoy-Higgins, Michelle; Shafer, Valerie L.; Schwartz, Richard G.; Marton, Klara

2014-01-01

This study examined the influence of phonotactic probability on word recognition in English-speaking toddlers. Typically developing toddlers completed a preferential looking paradigm using familiar words, which consisted of either high or low phonotactic probability sound sequences. The participants' looking behavior was recorded in response to…

Word Reading Fluency as a Serial Naming Task

ERIC Educational Resources Information Center

Protopapas, Athanassios; Katopodi, Katerina; Altani, Angeliki; Georgiou, George K.

2018-01-01

Word list reading fluency is theoretically expected to depend on single word reading speed. Yet the correlation between the two diminishes with increasing fluency, while fluency remains strongly correlated to serial digit naming. We hypothesized that multi-element sequence processing is an important component of fluency. We used confirmatory…

Jungle Quest: Adventures in Creating a HyperStudio Word Study Program.

ERIC Educational Resources Information Center

Ludwig, Jessica; Green, Lauren

This paper describes the development, design, and implementation of an educational multimedia program. The program, "Jungle Quest," combined HyperStudio and word study in a game for classroom use. Methods for word study provide a carefully sequenced teaching of phonics, vocabulary, and spelling following children's natural stages of…

The neural correlates of statistical learning in a word segmentation task: An fMRI study

PubMed Central

Karuza, Elisabeth A.; Newport, Elissa L.; Aslin, Richard N.; Starling, Sarah J.; Tivarus, Madalina E.; Bavelier, Daphne

2013-01-01

Functional magnetic resonance imaging (fMRI) was used to assess neural activation as participants learned to segment continuous streams of speech containing syllable sequences varying in their transitional probabilities. Speech streams were presented in four runs, each followed by a behavioral test to measure the extent of learning over time. Behavioral performance indicated that participants could discriminate statistically coherent sequences (words) from less coherent sequences (partwords). Individual rates of learning, defined as the difference in ratings for words and partwords, were used as predictors of neural activation to ask which brain areas showed activity associated with these measures. Results showed significant activity in the pars opercularis and pars triangularis regions of the left inferior frontal gyrus (LIFG). The relationship between these findings and prior work on the neural basis of statistical learning is discussed, and parallels to the frontal/subcortical network involved in other forms of implicit sequence learning are considered. PMID:23312790

Two- and Three-Year-Olds Track a Single Meaning during Word Learning: Evidence for Propose-but-Verify

ERIC Educational Resources Information Center

Woodard, Kristina; Gleitman, Lila R.; Trueswell, John C.

2016-01-01

A child word-learning experiment is reported that examines 2- and 3-year-olds' ability to learn the meanings of novel words across multiple, referentially ambiguous, word occurrences. Children were told they were going on an animal safari in which they would learn the names of unfamiliar animals. Critical trial sequences began with hearing a novel…

Comparison between BIDE, PrefixSpan, and TRuleGrowth for Mining of Indonesian Text

NASA Astrophysics Data System (ADS)

Sa'adillah Maylawati, Dian; Irfan, Mohamad; Budiawan Zulfikar, Wildan

2017-01-01

Mining proscess for Indonesian language still be an interesting research. Multiple of words representation was claimed can keep the meaning of text better than bag of words. In this paper, we compare several sequential pattern algortihm, among others BIDE (BIDirectional Extention), PrefixSpan, and TRuleGrowth. All of those algorithm produce frequent word sequence to keep the meaning of text. However, the experiment result, with 14.006 of Indonesian tweet from Twitter, shows that BIDE can produce more efficient frequent word sequence than PrefixSpan and TRuleGrowth without missing the meaning of text. Then, the average of time process of PrefixSpan is faster than BIDE and TRuleGrowth. In the other hand, PrefixSpan and TRuleGrowth is more efficient in using memory than BIDE.

APPLIED MECHANICS REVIEWS, WADEX WORD AND AUTHOR INDEX, VOLUME XVI, 1963,

DTIC Science & Technology

Author inDEX ) an IBM 1401 prepared mechanical index, extension of KWIC. WADEX usable for browsing and searching. This second WADEX is based on 8,000 titles of APPLIED MECHANICS REVIEWS (AMR), Vol. 16, 1963, an international critical review magazine. In WADEX, titles printed fully with author names, and as many lines used as necessary (60 characters per line). WADEX entry: word in title (except forbidden word) or author’s name. Alphabetically sequenced entries printed out of context. Words are single words or hypenated word pairs or ’Tagged Words’ (TW).

A modularized pulse programmer for NMR spectroscopy

NASA Astrophysics Data System (ADS)

Mao, Wenping; Bao, Qingjia; Yang, Liang; Chen, Yiqun; Liu, Chaoyang; Qiu, Jianqing; Ye, Chaohui

2011-02-01

A modularized pulse programmer for a NMR spectrometer is described. It consists of a networked PCI-104 single-board computer and a field programmable gate array (FPGA). The PCI-104 is dedicated to translate the pulse sequence elements from the host computer into 48-bit binary words and download these words to the FPGA, while the FPGA functions as a sequencer to execute these binary words. High-resolution NMR spectra obtained on a home-built spectrometer with four pulse programmers working concurrently demonstrate the effectiveness of the pulse programmer. Advantages of the module include (1) once designed it can be duplicated and used to construct a scalable NMR/MRI system with multiple transmitter and receiver channels, (2) it is a totally programmable system in which all specific applications are determined by software, and (3) it provides enough reserve for possible new pulse sequences.

Hippocampal activations in mesial temporal lobe epilepsy due to hippocampal sclerosis- an observational study on intramural encoding-delayed recall paradigms using task-based memory fMRI.

PubMed

Rajesh, P G; Thomas, Bejoy; Pammi, V S Chandrasekhar; Kesavadas, C; Alexander, Aley; Radhakrishnan, Ashalatha; Thomas, S V; Menon, R N

2018-05-26

To validate concurrent utility of within-scanner encoding and delayed recognition-memory paradigms to ascertain hippocampal activations during task-based memory fMRI. Memory paradigms were designed for faces, word-pairs and abstract designs. A deep-encoding task was designed comprising of a total of 9 cycles run within a 1.5T MRI scanner. A recall session was performed after 1 h within the scanner using an event-related design. Group analysis was done with 'correct-incorrect' responses applied as parametric modulators in Statistical Parametric Mapping version 8 using boot-strap method to enable estimation of laterality indices (LI) using custom anatomical masks involving the medio-basal temporal structures. Twenty seven subjects with drug-resistant mesial temporal lobe epilepsy due to hippocampal sclerosis (MTLE-HS) [17 patients of left-MTLE and 10 patients of right-MTLE] and 21 right handed age-matched healthy controls (HC) were recruited. For the encoding paradigm blood oxygen level dependent (BOLD) responses in HC demonstrated right laterality for faces, left laterality for word pairs, and bilaterality for design encoding over the regions of interest. Both right and left MTLE-HS groups revealed left lateralisation for word-pair encoding, bilateral activation for face encoding, with design encoding in right MTLE-HS demonstrating a left shift. As opposed to lateralization shown in controls, group analysis of cued-recall BOLD signals acquired within scanner in left MTLE-HS demonstrated right lateralization for word-pairs with bilaterality for faces and designs. The right MTLE-HS group demonstrated bilateral activations for faces, word-pairs and designs. Recall-based fMRI paradigms indicate hippocampal plasticity in MTLE-HS, maximal for word-pair associate recall tasks. Copyright © 2018 Elsevier B.V. All rights reserved.

Errors Detection by 5- to 8-Year-Olds Listening to a Wrong French Sequence of Number Words: Music before Lyrics?

ERIC Educational Resources Information Center

Gauderat-Bagault, Laurence; Lehalle, Henri

Children, ages 5 to 8 years (n=71), were required to listen and detect errors out of a partly wrong sequence of tape-recorded French number words from 1 to 100. Children (from several schools near Montpellier, France) were from preschool, grade 1, and grade 2. Results show that wrong syntactic rules were better detected than omissions, whereas…

Neural correlates of visualizations of concrete and abstract words in preschool children: a developmental embodied approach

PubMed Central

D’Angiulli, Amedeo; Griffiths, Gordon; Marmolejo-Ramos, Fernando

2015-01-01

The neural correlates of visualization underlying word comprehension were examined in preschool children. On each trial, a concrete or abstract word was delivered binaurally (part 1: post-auditory visualization), followed by a four-picture array (a target plus three distractors; part 2: matching visualization). Children were to select the picture matching the word they heard in part 1. Event-related potentials (ERPs) locked to each stimulus presentation and task interval were averaged over sets of trials of increasing word abstractness. ERP time-course during both parts of the task showed that early activity (i.e., <300 ms) was predominant in response to concrete words, while activity in response to abstract words became evident only at intermediate (i.e., 300–699 ms) and late (i.e., 700–1000 ms) ERP intervals. Specifically, ERP topography showed that while early activity during post-auditory visualization was linked to left temporo-parietal areas for concrete words, early activity during matching visualization occurred mostly in occipito-parietal areas for concrete words, but more anteriorly in centro-parietal areas for abstract words. In intermediate ERPs, post-auditory visualization coincided with parieto-occipital and parieto-frontal activity in response to both concrete and abstract words, while in matching visualization a parieto-central activity was common to both types of words. In the late ERPs for both types of words, the post-auditory visualization involved right-hemispheric activity following a “post-anterior” pathway sequence: occipital, parietal, and temporal areas; conversely, matching visualization involved left-hemispheric activity following an “ant-posterior” pathway sequence: frontal, temporal, parietal, and occipital areas. These results suggest that, similarly, for concrete and abstract words, meaning in young children depends on variably complex visualization processes integrating visuo-auditory experiences and supramodal embodying representations. PMID:26175697

Do you remember where sounds, pictures and words came from? The role of the stimulus format in object location memory.

PubMed

Delogu, Franco; Lilla, Christopher C

2017-11-01

Contrasting results in visual and auditory spatial memory stimulate the debate over the role of sensory modality and attention in identity-to-location binding. We investigated the role of sensory modality in the incidental/deliberate encoding of the location of a sequence of items. In 4 separated blocks, 88 participants memorised sequences of environmental sounds, spoken words, pictures and written words, respectively. After memorisation, participants were asked to recognise old from new items in a new sequence of stimuli. They were also asked to indicate from which side of the screen (visual stimuli) or headphone channel (sounds) the old stimuli were presented in encoding. In the first block, participants were not aware of the spatial requirement while, in blocks 2, 3 and 4 they knew that their memory for item location was going to be tested. Results show significantly lower accuracy of object location memory for the auditory stimuli (environmental sounds and spoken words) than for images (pictures and written words). Awareness of spatial requirement did not influence localisation accuracy. We conclude that: (a) object location memory is more effective for visual objects; (b) object location is implicitly associated with item identity during encoding and (c) visual supremacy in spatial memory does not depend on the automaticity of object location binding.

Can the meaning of multiple words be integrated unconsciously?

PubMed

van Gaal, Simon; Naccache, Lionel; Meuwese, Julia D I; van Loon, Anouk M; Leighton, Alexandra H; Cohen, Laurent; Dehaene, Stanislas

2014-05-05

What are the limits of unconscious language processing? Can language circuits process simple grammatical constructions unconsciously and integrate the meaning of several unseen words? Using behavioural priming and electroencephalography (EEG), we studied a specific rule-based linguistic operation traditionally thought to require conscious cognitive control: the negation of valence. In a masked priming paradigm, two masked words were successively (Experiment 1) or simultaneously presented (Experiment 2), a modifier ('not'/'very') and an adjective (e.g. 'good'/'bad'), followed by a visible target noun (e.g. 'peace'/'murder'). Subjects indicated whether the target noun had a positive or negative valence. The combination of these three words could either be contextually consistent (e.g. 'very bad - murder') or inconsistent (e.g. 'not bad - murder'). EEG recordings revealed that grammatical negations could unfold partly unconsciously, as reflected in similar occipito-parietal N400 effects for conscious and unconscious three-word sequences forming inconsistent combinations. However, only conscious word sequences elicited P600 effects, later in time. Overall, these results suggest that multiple unconscious words can be rapidly integrated and that an unconscious negation can automatically 'flip the sign' of an unconscious adjective. These findings not only extend the limits of subliminal combinatorial language processes, but also highlight how consciousness modulates the grammatical integration of multiple words.

Motormouth: mere exposure depends on stimulus-specific motor simulations.

PubMed

Topolinski, Sascha; Strack, Fritz

2009-03-01

The authors apply an embodied account to mere exposure, arguing that through the repeated exposure of a particular stimulus, motor responses specifically associated to that stimulus are repeatedly simulated, thus trained, and become increasingly fluent. This increased fluency drives preferences for repeated stimuli. This hypothesis was tested by blocking stimulus-specific motor simulations during repeated exposure. In Experiment 1, chewing gum while evaluating stimuli destroyed mere exposure effects (MEEs) for words but not for visual characters. However, concurrently kneading a ball left both MEEs unaffected. In Experiment 2, concurrently whispering an unrelated word destroyed MEEs for words but not for characters, even when implemented either exclusively during the initial presentation or during the test phase and when the first presentation involved an evaluation or a mere study of the stimuli. In Experiment 3, a double dissociation between 2 classes of stimuli was demonstrated, namely, words (oral) and tunes (vocal). A concurrent oral task (tongue movements) destroyed MEEs for words but not for tone sequences. A concurrent vocal task (humming "mm-hm") destroyed MEEs for tone sequences but not for words. (c) 2009 APA, all rights reserved

Relationships between Eye Movements during Sentence Reading Comprehension, Word Spelling and Reading, and DTI and fmri Connectivity In Students with and without Dysgraphia or Dyslexia

PubMed Central

Yagle, Kevin; Richards, Todd; Askren, Katie; Mestre, Zoe; Beers, Scott; Abbott, Robert; Nagy, William; Boord, Peter; Berninger, Virginia

2017-01-01

While eye movements were recorded and brains scanned, 29 children with and without specific learning disabilities (SLDs) decided if sentences they read (half with only correctly spelled words and half with homonym foils) were meaningful. Significant main effects were found for diagnostic groups (non-SLD control, dysgraphia control, and dyslexia) in total fixation (dwell) time, total number of fixations, and total regressions in during saccades; the dyslexia group had longer and more fixations and made more regressions in during saccades than either control group. The dyslexia group also differed from both control groups in (a) fractional anisotropy in left optic radiation and (b) silent word reading fluency on a task in which surrounding letters can be distracting, consistent with Rayner's selective attention dyslexia model. Different profiles for non-SLD control, dysgraphia, and dyslexia groups were identified in correlations between total fixation time, total number of fixations, regressions in during saccades, magnitude of gray matter connectivity during the fMRI sentence reading comprehension from left occipital temporal cortex seed with right BA44 and from left inferior frontal gyrus with right inferior frontoccipital fasciculus, and normed word-specific spelling and silent word reading fluency measures. The dysgraphia group was more likely than the non-SLD control or dyslexia groups to show negative correlations between eye movement outcomes and sentences containing incorrect homonym foils. Findings are discussed in reference to a systems approach in future sentence reading comprehension research that integrates eye movement, brain, and literacy measures. PMID:28936361

Relationships between Eye Movements during Sentence Reading Comprehension, Word Spelling and Reading, and DTI and fmri Connectivity In Students with and without Dysgraphia or Dyslexia.

PubMed

Yagle, Kevin; Richards, Todd; Askren, Katie; Mestre, Zoe; Beers, Scott; Abbott, Robert; Nagy, William; Boord, Peter; Berninger, Virginia

2017-01-01

While eye movements were recorded and brains scanned, 29 children with and without specific learning disabilities (SLDs) decided if sentences they read (half with only correctly spelled words and half with homonym foils) were meaningful. Significant main effects were found for diagnostic groups (non-SLD control, dysgraphia control, and dyslexia) in total fixation (dwell) time, total number of fixations, and total regressions in during saccades; the dyslexia group had longer and more fixations and made more regressions in during saccades than either control group. The dyslexia group also differed from both control groups in (a) fractional anisotropy in left optic radiation and (b) silent word reading fluency on a task in which surrounding letters can be distracting, consistent with Rayner's selective attention dyslexia model. Different profiles for non-SLD control, dysgraphia, and dyslexia groups were identified in correlations between total fixation time, total number of fixations, regressions in during saccades, magnitude of gray matter connectivity during the fMRI sentence reading comprehension from left occipital temporal cortex seed with right BA44 and from left inferior frontal gyrus with right inferior frontoccipital fasciculus, and normed word-specific spelling and silent word reading fluency measures. The dysgraphia group was more likely than the non-SLD control or dyslexia groups to show negative correlations between eye movement outcomes and sentences containing incorrect homonym foils. Findings are discussed in reference to a systems approach in future sentence reading comprehension research that integrates eye movement, brain, and literacy measures.

Cognitive inhibition in students with and without dyslexia and dyscalculia.

PubMed

Wang, Li-Chih; Tasi, Hung-Ju; Yang, Hsien-Ming

2012-01-01

The present study presents a comparison of the cognitive inhibition abilities of dyslexic, dyscalculic, and control students. The participants were 45 dyslexic students, 45 dyscalculic students, and 45 age-, gender-, and IQ-matched control students. The major evaluation tools included six cognitive inhibition tasks which were restructured during principal component analysis into three categories: graph inhibition, number inhibition, and word inhibition. Comparisons of the 3 groups of students revealed that in graph inhibition, dyscalculic students performed worst of the 3 groups, with dyslexic students also performing worse than control students in this category. For number inhibition, the control students' performances were equal to those of dyslexic students, with both groups performing better than dyscalculic students. For word inhibition, control students' performances were equal to those of dyscalculic students; both groups had shorter response times and lower incorrect rates than dyslexic students. These results suggest the complexity of the different cognitive inhibition abilities displayed by dyslexic, dyscalculic, and control students. However, some regular patterns occurred. Copyright © 2012 Elsevier Ltd. All rights reserved.

Can Chunk Size Differences Explain Developmental Changes in Lexical Learning?

PubMed Central

Smalle, Eleonore H. M.; Bogaerts, Louisa; Simonis, Morgane; Duyck, Wouter; Page, Michael P. A.; Edwards, Martin G.; Szmalec, Arnaud

2016-01-01

In three experiments, we investigated Hebb repetition learning (HRL) differences between children and adults, as a function of the type of item (lexical vs. sub-lexical) and the level of item-overlap between sequences. In a first experiment, it was shown that when non-repeating and repeating (Hebb) sequences of words were all permutations of the same words, HRL was slower than when the sequences shared no words. This item-overlap effect was observed in both children and adults. In a second experiment, we used syllable sequences and we observed reduced HRL due to item-overlap only in children. The findings are explained within a chunking account of the HRL effect on the basis of which we hypothesize that children, compared with adults, chunk syllable sequences in smaller units. By hypothesis, small chunks are more prone to interference from anagram representations included in the filler sequences, potentially explaining the item-overlap effect in children. This hypothesis was tested in a third experiment with adults where we experimentally manipulated the chunk size by embedding pauses in the syllable sequences. Interestingly, we showed that imposing a small chunk size caused adults to show the same behavioral effects as those observed in children. Departing from the analogy between verbal HRL and lexical development, the results are discussed in light of the less-is-more hypothesis of age-related differences in language acquisition. PMID:26779065

Songs as an aid for language acquisition.

PubMed

Schön, Daniele; Boyer, Maud; Moreno, Sylvain; Besson, Mireille; Peretz, Isabelle; Kolinsky, Régine

2008-02-01

In previous research, Saffran and colleagues [Saffran, J. R., Aslin, R. N., & Newport, E. L. (1996). Statistical learning by 8-month-old infants. Science, 274, 1926-1928; Saffran, J. R., Newport, E. L., & Aslin, R. N. (1996). Word segmentation: The role of distributional cues. Journal of Memory and Language, 35, 606-621.] have shown that adults and infants can use the statistical properties of syllable sequences to extract words from continuous speech. They also showed that a similar learning mechanism operates with musical stimuli [Saffran, J. R., Johnson, R. E. K., Aslin, N., & Newport, E. L. (1999). Abstract Statistical learning of tone sequences by human infants and adults. Cognition, 70, 27-52.]. In this work we combined linguistic and musical information and we compared language learning based on speech sequences to language learning based on sung sequences. We hypothesized that, compared to speech sequences, a consistent mapping of linguistic and musical information would enhance learning. Results confirmed the hypothesis showing a strong learning facilitation of song compared to speech. Most importantly, the present results show that learning a new language, especially in the first learning phase wherein one needs to segment new words, may largely benefit of the motivational and structuring properties of music in song.

Phonotactic Probability of Brand Names: I'd buy that!

PubMed Central

Vitevitch, Michael S.; Donoso, Alexander J.

2011-01-01

Psycholinguistic research shows that word-characteristics influence the speed and accuracy of various language-related processes. Analogous characteristics of brand names influence the retrieval of product information and the perception of risks associated with that product. In the present experiment we examined how phonotactic probability—the frequency with which phonological segments and sequences of segments appear in a word—might influence consumer behavior. Participants rated brand names that varied in phonotactic probability on the likelihood that they would buy the product. Participants indicated that they were more likely to purchase a product if the brand name was comprised of common segments and sequences of segments rather than less common segments and sequences of segments. This result suggests that word-characteristics may influence higher-level cognitive processes, in addition to language-related processes. Furthermore, the benefits of using objective measures of word characteristics in the design of brand names are discussed. PMID:21870135

Cognitive performance of young and elderly subjects on the free word recall memory test: effect of presentation order on recall order.

PubMed

Santos-Galduróz, R F; Oliveira, F G; Galduróz, J C F; Bueno, O F A

2009-10-01

The influence of aging on memory has been extensively studied, but the importance of short-term memory and recall sequence has not. The objective of the current study was to examine the recall order of words presented on lists and to determine if age affects recall sequence. Physically and psychologically healthy male subjects were divided into two groups according to age, i.e., 23 young subjects (20 to 30 years) and 50 elderly subjects (60 to 70 years) submitted to the Wechsler Adult Intelligence Scale-Revised and the free word recall test. The order of word presentation significantly affected the 3rd and 4th words recalled (P < 0.01; F = 14.6). In addition, there was interaction between the presentation order and the type of list presented (P < 0.05; F = 9.7). Also, both groups recalled the last words presented from each list (words 13-15) significantly more times 3rd and 4th than words presented in all remaining positions (P < 0.01). The order of word presentation also significantly affected the 5th and 6th words recalled (P = 0.05; F = 7.5) and there was a significant interaction between the order of presentation and the type of list presented (P < 0.01; F = 20.8). The more developed the cognitive functions, resulting mainly from formal education, the greater the cognitive reserve, helping to minimize the effects of aging on the long-term memory (episodic declarative).

The disease of the moon: the linguistic and pathological evolution of the English term "lunatic".

PubMed

Riva, M A; Tremolizzo, L; Spicci, M; Ferrarese, C; De Vito, G; Cesana, G C; Sironi, V A

2011-01-01

The public opinion and the scientific community incorrectly believe that the English term "lunatic" was originally related only to insanity, but it also referred to epileptic people. The aim of this article is to clarify the original meaning of the English word "lunatic" by analyzing the evolution of the relationship between psychiatric and neurological diseases and by pointing out the influence of the moon in the history of medicine, in popular traditions, and in English literature. The article also contains a detailed and accurate review of the modern scientific literature on the relationship between moon and epilepsy/psychiatric disorders.

Marks of Change in Sequences

NASA Astrophysics Data System (ADS)

Jürgensen, H.

2011-12-01

Given a sequence of events, how does one recognize that a change has occurred? We explore potential definitions of the concept of change in a sequence and propose that words in relativized solid codes might serve as indicators of change.

The Influence of Formulaic Language on L2 Listener Decoding in Extended Discourse

ERIC Educational Resources Information Center

Yeldham, Michael

2018-01-01

This study investigated the effect of formulaic language on L2 learners' ability to decode words in listening texts. One possibility was that formulas would facilitate listening by reducing the need to process every word of the sequences. However, a contrasting possibility was that the commonly reduced nature of formulaic words would hinder…

The Effect of Sonority on Word Segmentation: Evidence for the Use of a Phonological Universal

ERIC Educational Resources Information Center

Ettlinger, Marc; Finn, Amy S.; Hudson Kam, Carla L.

2012-01-01

It has been well documented how language-specific cues may be used for word segmentation. Here, we investigate what role a language-independent phonological universal, the sonority sequencing principle (SSP), may also play. Participants were presented with an unsegmented speech stream with non-English word onsets that juxtaposed adherence to the…

SUGGESTIONS FOR DEVELOPING INDEPENDENT WORD ATTACK IN READING, FOR USE IN BASIC INSTITUTE MEETINGS, GRADES THREE AND FOUR.

ERIC Educational Resources Information Center

REECE, THOMAS E.; AND OTHERS

A GUIDE FOR PLANNING SPECIFIC INSTRUCTION FOR DEVELOPING INDEPENDENT WORD ATTACK PRESENTS THE SKILLS NECESSARY FOR MASTERING SIGHT VOCABULARY, WORD RECOGNITION, AND THE USE OF THE DICTIONARY. SPECIFIC DEFINITIONS OF TERMS AND EXAMPLES OF TEACHING TECHNIQUES WITH THE SEQUENCE OF INSTRUCTION FOR THE DEVELOPMENT OF PHONETIC AND STRUCTURAL ANALYSIS…

Models of Vocabulary Acquisition: Direct Tests and Text-Derived Simulations of Vocabulary Growth

ERIC Educational Resources Information Center

Biemiller, Andrew; Rosenstein, Mark; Sparks, Randall; Landauer, Thomas K.; Foltz, Peter W.

2014-01-01

Determining word meanings that ought to be taught or introduced is important for educators. A sequence for vocabulary growth can be inferred from many sources, including testing children's knowledge of word meanings at various ages, predicting from print frequency, or adult-recalled Age of Acquisition. A new approach, Word Maturity, is based on…

The effect of native-language experience on the sensory-obligatory components, the P1–N1–P2 and the T-complex

PubMed Central

Wagner, Monica; Shafer, Valerie L.; Martin, Brett; Steinschneider, Mitchell

2013-01-01

The influence of native-language experience on sensory-obligatory auditory-evoked potentials (AEPs) was investigated in native-English and native-Polish listeners. AEPs were recorded to the first word in nonsense word pairs, while participants performed a syllable identification task to the second word in the pairs. Nonsense words contained phoneme sequence onsets (i.e., /pt/, /pət/, /st/ and /sət/) that occur in the Polish and English languages, with the exception that /pt/ at syllable onset is an illegal phonotactic form in English. P1–N1–P2 waveforms from fronto-central electrode sites were comparable in English and Polish listeners, even though, these same English participants were unable to distinguish the nonsense words having /pt/ and /pət/ onsets. The P1–N1–P2 complex indexed the temporal characteristics of the word stimuli in the same manner for both language groups. Taken together, these findings suggest that the fronto-central P1–N1–P2 complex reflects acoustic feature processing of speech and is not significantly influenced by exposure to the phoneme sequences of the native-language. In contrast, the T-complex from bilateral posterior temporal sites was found to index phonological as well as acoustic feature processing to the nonsense word stimuli. An enhanced negativity for the /pt/ cluster relative to its contrast sequence (i.e., /pət/) occurred only for the Polish listeners, suggesting that neural networks within non-primary auditory cortex may be involved in early cortical phonological processing. PMID:23643857

An experimental phylogeny to benchmark ancestral sequence reconstruction

PubMed Central

Randall, Ryan N.; Radford, Caelan E.; Roof, Kelsey A.; Natarajan, Divya K.; Gaucher, Eric A.

2016-01-01

Ancestral sequence reconstruction (ASR) is a still-burgeoning method that has revealed many key mechanisms of molecular evolution. One criticism of the approach is an inability to validate its algorithms within a biological context as opposed to a computer simulation. Here we build an experimental phylogeny using the gene of a single red fluorescent protein to address this criticism. The evolved phylogeny consists of 19 operational taxonomic units (leaves) and 17 ancestral bifurcations (nodes) that display a wide variety of fluorescent phenotypes. The 19 leaves then serve as ‘modern' sequences that we subject to ASR analyses using various algorithms and to benchmark against the known ancestral genotypes and ancestral phenotypes. We confirm computer simulations that show all algorithms infer ancient sequences with high accuracy, yet we also reveal wide variation in the phenotypes encoded by incorrectly inferred sequences. Specifically, Bayesian methods incorporating rate variation significantly outperform the maximum parsimony criterion in phenotypic accuracy. Subsampling of extant sequences had minor effect on the inference of ancestral sequences. PMID:27628687

Sleep-Driven Computations in Speech Processing

PubMed Central

Frost, Rebecca L. A.; Monaghan, Padraic

2017-01-01

Acquiring language requires segmenting speech into individual words, and abstracting over those words to discover grammatical structure. However, these tasks can be conflicting—on the one hand requiring memorisation of precise sequences that occur in speech, and on the other requiring a flexible reconstruction of these sequences to determine the grammar. Here, we examine whether speech segmentation and generalisation of grammar can occur simultaneously—with the conflicting requirements for these tasks being over-come by sleep-related consolidation. After exposure to an artificial language comprising words containing non-adjacent dependencies, participants underwent periods of consolidation involving either sleep or wake. Participants who slept before testing demonstrated a sustained boost to word learning and a short-term improvement to grammatical generalisation of the non-adjacencies, with improvements after sleep outweighing gains seen after an equal period of wake. Thus, we propose that sleep may facilitate processing for these conflicting tasks in language acquisition, but with enhanced benefits for speech segmentation. PMID:28056104

Sleep-Driven Computations in Speech Processing.

PubMed

Frost, Rebecca L A; Monaghan, Padraic

2017-01-01

Acquiring language requires segmenting speech into individual words, and abstracting over those words to discover grammatical structure. However, these tasks can be conflicting-on the one hand requiring memorisation of precise sequences that occur in speech, and on the other requiring a flexible reconstruction of these sequences to determine the grammar. Here, we examine whether speech segmentation and generalisation of grammar can occur simultaneously-with the conflicting requirements for these tasks being over-come by sleep-related consolidation. After exposure to an artificial language comprising words containing non-adjacent dependencies, participants underwent periods of consolidation involving either sleep or wake. Participants who slept before testing demonstrated a sustained boost to word learning and a short-term improvement to grammatical generalisation of the non-adjacencies, with improvements after sleep outweighing gains seen after an equal period of wake. Thus, we propose that sleep may facilitate processing for these conflicting tasks in language acquisition, but with enhanced benefits for speech segmentation.

Psychoactive drugs and false memory: comparison of dextroamphetamine and delta-9-tetrahydrocannabinol on false recognition

PubMed Central

Ballard, Michael E.; Gallo, David A.; de Wit, Harriet

2014-01-01

Rationale Several psychoactive drugs are known to influence episodic memory. However, these drugs’ effects on false memory, or the tendency to incorrectly remember nonstudied information, remain poorly understood. Objectives Here, we examined the effects of two commonly used psychoactive drugs, one with memory-enhancing properties (dextroamphetamine; AMP), and another with memory-impairing properties (Δ9-tetrahydrocannabinol; THC), on false memory using the Deese/Roediger–McDermott (DRM) illusion. Methods Two parallel studies were conducted in which healthy volunteers received either AMP (0, 10, and 20 mg) or THC (0, 7.5, and 15 mg) in within-subjects, randomized, double-blind designs. Participants studied DRM word lists under the influence of the drugs, and their recognition memory for the studied words was tested 2 days later, under sober conditions. Results As expected, AMP increased memory of studied words relative to placebo, and THC reduced memory of studied words. Although neither drug significantly affected false memory relative to placebo, AMP increased false memory relative to THC. Across participants, both drugs’ effects on true memory were positively correlated with their effects on false memory. Conclusions Our results indicate that AMP and THC have opposing effects on true memory, and these effects appear to correspond to similar, albeit more subtle, effects on false memory. These findings are consistent with previous research using the DRM illusion and provide further evidence that psychoactive drugs can affect the encoding processes that ultimately result in the creation of false memories. PMID:21647577

Psychoactive drugs and false memory: comparison of dextroamphetamine and δ-9-tetrahydrocannabinol on false recognition.

PubMed

Ballard, Michael E; Gallo, David A; de Wit, Harriet

2012-01-01

Several psychoactive drugs are known to influence episodic memory. However, these drugs' effects on false memory, or the tendency to incorrectly remember nonstudied information, remain poorly understood. Here, we examined the effects of two commonly used psychoactive drugs, one with memory-enhancing properties (dextroamphetamine; AMP), and another with memory-impairing properties (Δ(9)-tetrahydrocannabinol; THC), on false memory using the Deese/Roediger-McDermott (DRM) illusion. Two parallel studies were conducted in which healthy volunteers received either AMP (0, 10, and 20 mg) or THC (0, 7.5, and 15 mg) in within-subjects, randomized, double-blind designs. Participants studied DRM word lists under the influence of the drugs, and their recognition memory for the studied words was tested 2 days later, under sober conditions. As expected, AMP increased memory of studied words relative to placebo, and THC reduced memory of studied words. Although neither drug significantly affected false memory relative to placebo, AMP increased false memory relative to THC. Across participants, both drugs' effects on true memory were positively correlated with their effects on false memory. Our results indicate that AMP and THC have opposing effects on true memory, and these effects appear to correspond to similar, albeit more subtle, effects on false memory. These findings are consistent with previous research using the DRM illusion and provide further evidence that psychoactive drugs can affect the encoding processes that ultimately result in the creation of false memories.

Spoken Word Recognition Errors in Speech Audiometry: A Measure of Hearing Performance?

PubMed Central

Coene, Martine; van der Lee, Anneke; Govaerts, Paul J.

2015-01-01

This report provides a detailed analysis of incorrect responses from an open-set spoken word-repetition task which is part of a Dutch speech audiometric test battery. Single-consonant confusions were analyzed from 230 normal hearing participants in terms of the probability of choice of a particular response on the basis of acoustic-phonetic, lexical, and frequency variables. The results indicate that consonant confusions are better predicted by lexical knowledge than by acoustic properties of the stimulus word. A detailed analysis of the transmission of phonetic features indicates that “voicing” is best preserved whereas “manner of articulation” yields most perception errors. As consonant confusion matrices are often used to determine the degree and type of a patient's hearing impairment, to predict a patient's gain in hearing performance with hearing devices and to optimize the device settings in view of maximum output, the observed findings are highly relevant for the audiological practice. Based on our findings, speech audiometric outcomes provide a combined auditory-linguistic profile of the patient. The use of confusion matrices might therefore not be the method best suited to measure hearing performance. Ideally, they should be complemented by other listening task types that are known to have less linguistic bias, such as phonemic discrimination. PMID:26557717

Does test-enhanced learning transfer for triple associates?

PubMed

Pan, Steven C; Wong, Carol M; Potter, Zachary E; Mejia, Jonathan; Rickard, Timothy C

2016-01-01

Test-enhanced learning and transfer for triple-associate word stimuli was assessed in three experiments. In each experiment, training and final-test trials involved the presentation of two words per triple associate (triplet), with the third word having to be retrieved. In agreement with the prior literature on different stimuli, training through testing with feedback yielded markedly better final-test performance than did restudy. However, in contrast to the positive transfer reported for paired associate stimuli, minimal or no positive transfer was observed, relative to a restudy control, from a trained cue combination (e.g., A, B, ?) to other cue combinations from the same triplet that required a different response (e.g., B, C, ?). That result also held when two unique cue combinations per triplet were tested during training, and for triplets with low and high average associative strengths. Supplementary analyses provided insight into the overall transfer effect: An incorrect response during training appears to yield positive transfer relative to restudy, whereas a correct response appears to yield no, or even negative, transfer. Cross-experiment analyses indicated that test-enhanced learning is not diminished when two or three cue combinations are presented during training. Thus, even though learning through testing is highly specific, testing on all possible stimulus-response combinations remains the most efficient strategy for the learning of triple associates.

Deficient relational binding processes in adolescents with psychosis: evidence from impaired memory for source and temporal context.

PubMed

Doré, Marie-Claire; Caza, Nicole; Gingras, Nathalie; Rouleau, Nancie

2007-11-01

Findings from the literature consistently revealed episodic memory deficits in adolescents with psychosis. However, the nature of the dysfunction remains unclear. Based on a cognitive neuropsychological approach, a theoretically driven paradigm was used to generate valid interpretations about the underlying memory processes impaired in these patients. A total of 16 inpatient adolescents with psychosis and 19 individually matched controls were assessed using an experimental task designed to measure memory for source and temporal context of studied words. Retrospective confidence judgements for source and temporal context responses were also assessed. On word recognition, patients had more difficulty than controls discriminating target words from neutral distractors. In addition, patients identified both source and temporal context features of recognised items less often than controls. Confidence judgements analyses revealed that the difference between the proportions of correct and incorrect responses made with high confidence was lower in patients than in controls. In addition, the proportion of high-confident responses that were errors was higher in patients compared to controls. These findings suggest impaired relational binding processes in adolescents with psychosis, resulting in a difficulty to create unified memory representations. Our findings on retrospective confidence data point to impaired monitoring of retrieved information that may also impair memory performance in these individuals.

Universal Entropy of Word Ordering Across Linguistic Families

PubMed Central

Montemurro, Marcelo A.; Zanette, Damián H.

2011-01-01

Background The language faculty is probably the most distinctive feature of our species, and endows us with a unique ability to exchange highly structured information. In written language, information is encoded by the concatenation of basic symbols under grammatical and semantic constraints. As is also the case in other natural information carriers, the resulting symbolic sequences show a delicate balance between order and disorder. That balance is determined by the interplay between the diversity of symbols and by their specific ordering in the sequences. Here we used entropy to quantify the contribution of different organizational levels to the overall statistical structure of language. Methodology/Principal Findings We computed a relative entropy measure to quantify the degree of ordering in word sequences from languages belonging to several linguistic families. While a direct estimation of the overall entropy of language yielded values that varied for the different families considered, the relative entropy quantifying word ordering presented an almost constant value for all those families. Conclusions/Significance Our results indicate that despite the differences in the structure and vocabulary of the languages analyzed, the impact of word ordering in the structure of language is a statistical linguistic universal. PMID:21603637

How Does Context Play "a Part" in Splitting Words "Apart"? Production and Perception of Word Boundaries in Casual Speech

ERIC Educational Resources Information Center

Kim, Dahee; Stephens, Joseph D. W.; Pitt, Mark A.

2012-01-01

Four experiments examined listeners' segmentation of ambiguous schwa-initial sequences (e.g., "a long" vs. "along") in casual speech, where acoustic cues can be unclear, possibly increasing reliance on contextual information to resolve the ambiguity. In Experiment 1, acoustic analyses of talkers' productions showed that the one-word and two-word…

Effects of Self-Graphing on Written Expression of Fourth Grade Students with High-Incidence Disabilities

ERIC Educational Resources Information Center

Stotz, Kate E.; Itoi, Madoka; Konrad, Moira; Alber-Morgan, Sheila R.

2008-01-01

The purpose of this study was to determine the effects of self-graphing on the writing of 3 fourth grade students with high-incidence disabilities. Measures of written expression included total number of words written and number of correct word sequences. During intervention, students self-graphed their total number of words written in response to…

Linking sounds to meanings: infant statistical learning in a natural language.

PubMed

Hay, Jessica F; Pelucchi, Bruna; Graf Estes, Katharine; Saffran, Jenny R

2011-09-01

The processes of infant word segmentation and infant word learning have largely been studied separately. However, the ease with which potential word forms are segmented from fluent speech seems likely to influence subsequent mappings between words and their referents. To explore this process, we tested the link between the statistical coherence of sequences presented in fluent speech and infants' subsequent use of those sequences as labels for novel objects. Notably, the materials were drawn from a natural language unfamiliar to the infants (Italian). The results of three experiments suggest that there is a close relationship between the statistics of the speech stream and subsequent mapping of labels to referents. Mapping was facilitated when the labels contained high transitional probabilities in the forward and/or backward direction (Experiment 1). When no transitional probability information was available (Experiment 2), or when the internal transitional probabilities of the labels were low in both directions (Experiment 3), infants failed to link the labels to their referents. Word learning appears to be strongly influenced by infants' prior experience with the distribution of sounds that make up words in natural languages. Copyright © 2011 Elsevier Inc. All rights reserved.

A mapping of an ensemble of mitochondrial sequences for various organisms into 3D space based on the word composition.

PubMed

Aita, Takuyo; Nishigaki, Koichi

2012-11-01

To visualize a bird's-eye view of an ensemble of mitochondrial genome sequences for various species, we recently developed a novel method of mapping a biological sequence ensemble into Three-Dimensional (3D) vector space. First, we represented a biological sequence of a species s by a word-composition vector x(s), where its length [absolute value]x(s)[absolute value] represents the sequence length, and its unit vector x(s)/[absolute value]x(s)[absolute value] represents the relative composition of the K-tuple words through the sequence and the size of the dimension, N=4(K), is the number of all possible words with the length of K. Second, we mapped the vector x(s) to the 3D position vector y(s), based on the two following simple principles: (1) [absolute value]y(s)[absolute value]=[absolute value]x(s)[absolute value] and (2) the angle between y(s) and y(t) maximally correlates with the angle between x(s) and x(t). The mitochondrial genome sequences for 311 species, including 177 Animalia, 85 Fungi and 49 Green plants, were mapped into 3D space by using K=7. The mapping was successful because the angles between vectors before and after the mapping highly correlated with each other (correlation coefficients were 0.92-0.97). Interestingly, the Animalia kingdom is distributed along a single arc belt (just like the Milky Way on a Celestial Globe), and the Fungi and Green plant kingdoms are distributed in a similar arc belt. These two arc belts intersect at their respective middle regions and form a cross structure just like a jet aircraft fuselage and its wings. This new mapping method will allow researchers to intuitively interpret the visual information presented in the maps in a highly effective manner. Copyright © 2012 Elsevier Inc. All rights reserved.

A frequency-based linguistic approach to protein decoding and design: Simple concepts, diverse applications, and the SCS Package

PubMed Central

Motomura, Kenta; Nakamura, Morikazu; Otaki, Joji M.

2013-01-01

Protein structure and function information is coded in amino acid sequences. However, the relationship between primary sequences and three-dimensional structures and functions remains enigmatic. Our approach to this fundamental biochemistry problem is based on the frequencies of short constituent sequences (SCSs) or words. A protein amino acid sequence is considered analogous to an English sentence, where SCSs are equivalent to words. Availability scores, which are defined as real SCS frequencies in the non-redundant amino acid database relative to their probabilistically expected frequencies, demonstrate the biological usage bias of SCSs. As a result, this frequency-based linguistic approach is expected to have diverse applications, such as secondary structure specifications by structure-specific SCSs and immunological adjuvants with rare or non-existent SCSs. Linguistic similarities (e.g., wide ranges of scale-free distributions) and dissimilarities (e.g., behaviors of low-rank samples) between proteins and the natural English language have been revealed in the rank-frequency relationships of SCSs or words. We have developed a web server, the SCS Package, which contains five applications for analyzing protein sequences based on the linguistic concept. These tools have the potential to assist researchers in deciphering structurally and functionally important protein sites, species-specific sequences, and functional relationships between SCSs. The SCS Package also provides researchers with a tool to construct amino acid sequences de novo based on the idiomatic usage of SCSs. PMID:24688703

A frequency-based linguistic approach to protein decoding and design: Simple concepts, diverse applications, and the SCS Package.

PubMed

Motomura, Kenta; Nakamura, Morikazu; Otaki, Joji M

2013-01-01

Protein structure and function information is coded in amino acid sequences. However, the relationship between primary sequences and three-dimensional structures and functions remains enigmatic. Our approach to this fundamental biochemistry problem is based on the frequencies of short constituent sequences (SCSs) or words. A protein amino acid sequence is considered analogous to an English sentence, where SCSs are equivalent to words. Availability scores, which are defined as real SCS frequencies in the non-redundant amino acid database relative to their probabilistically expected frequencies, demonstrate the biological usage bias of SCSs. As a result, this frequency-based linguistic approach is expected to have diverse applications, such as secondary structure specifications by structure-specific SCSs and immunological adjuvants with rare or non-existent SCSs. Linguistic similarities (e.g., wide ranges of scale-free distributions) and dissimilarities (e.g., behaviors of low-rank samples) between proteins and the natural English language have been revealed in the rank-frequency relationships of SCSs or words. We have developed a web server, the SCS Package, which contains five applications for analyzing protein sequences based on the linguistic concept. These tools have the potential to assist researchers in deciphering structurally and functionally important protein sites, species-specific sequences, and functional relationships between SCSs. The SCS Package also provides researchers with a tool to construct amino acid sequences de novo based on the idiomatic usage of SCSs.

Development of a Serial Order in Speech Constrained by Articulatory Coordination

PubMed Central

Oohashi, Hiroki; Watanabe, Hama; Taga, Gentaro

2013-01-01

Universal linguistic constraints seem to govern the organization of sound sequences in words. However, our understanding of the origin and development of these constraints is incomplete. One possibility is that the development of neuromuscular control of articulators acts as a constraint for the emergence of sequences in words. Repetitions of the same consonant observed in early infancy and an increase in variation of consonantal sequences over months of age have been interpreted as a consequence of the development of neuromuscular control. Yet, it is not clear how sequential coordination of articulators such as lips, tongue apex and tongue dorsum constrains sequences of labial, coronal and dorsal consonants in words over the course of development. We examined longitudinal development of consonant-vowel-consonant(-vowel) sequences produced by Japanese children between 7 and 60 months of age. The sequences were classified according to places of articulation for corresponding consonants. The analyses of individual and group data show that infants prefer repetitive and fronting articulations, as shown in previous studies. Furthermore, we reveal that serial order of different places of articulations within the same organ appears earlier and then gradually develops, whereas serial order of different articulatory organs appears later and then rapidly develops. In the same way, we also analyzed the sequences produced by English children and obtained similar developmental trends. These results suggest that the development of intra- and inter-articulator coordination constrains the acquisition of serial orders in speech with the complexity that characterizes adult language. PMID:24223827

Word and frame synchronization with verification for PPM optical communications

NASA Technical Reports Server (NTRS)

Marshall, William K.

1986-01-01

A method for obtaining word and frame synchronization in pulse position modulated optical communication systems is described. The method uses a short sync sequence inserted at the beginning of each data frame and a verification procedure to distinguish between inserted and randomly occurring sequences at the receiver. This results in an easy to implement sync system which provides reliable synchronization even at high symbol error rates. Results are given for the application of this approach to a highly energy efficient 256-ary PPM test system.

Newly-acquired words are more phonologically robust in verbal short-term memory when they have associated semantic representations.

PubMed

Savill, Nicola; Ellis, Andrew W; Jefferies, Elizabeth

2017-04-01

Verbal short-term memory (STM) is a crucial cognitive function central to language learning, comprehension and reasoning, yet the processes that underlie this capacity are not fully understood. In particular, although STM primarily draws on a phonological code, interactions between long-term phonological and semantic representations might help to stabilise the phonological trace for words ("semantic binding hypothesis"). This idea was first proposed to explain the frequent phoneme recombination errors made by patients with semantic dementia when recalling words that are no longer fully understood. However, converging evidence in support of semantic binding is scant: it is unusual for studies of healthy participants to examine serial recall at the phoneme level and also it is difficult to separate the contribution of phonological-lexical knowledge from effects of word meaning. We used a new method to disentangle these influences in healthy individuals by training new 'words' with or without associated semantic information. We examined phonological coherence in immediate serial recall (ISR), both immediately and the day after training. Trained items were more likely to be recalled than novel nonwords, confirming the importance of phonological-lexical knowledge, and items with semantic associations were also produced more accurately than those with no meaning, at both time points. For semantically-trained items, there were fewer phoneme ordering and identity errors, and consequently more complete target items were produced in both correct and incorrect list positions. These data show that lexical-semantic knowledge improves the robustness of verbal STM at the sub-item level, even when the effect of phonological familiarity is taken into account. Copyright © 2016 Elsevier Ltd. All rights reserved.

The Influence of Phonotactic Probability on Nonword Repetition and Fast Mapping in 3-Year-Olds With a History of Expressive Language Delay.

PubMed

MacRoy-Higgins, Michelle; Dalton, Kevin Patrick

2015-12-01

The purpose of this study was to examine the influence of phonotactic probability on sublexical (phonological) and lexical representations in 3-year-olds who had a history of being late talkers in comparison with their peers with typical language development. Ten 3-year-olds who were late talkers and 10 age-matched typically developing controls completed nonword repetition and fast mapping tasks; stimuli for both experimental procedures differed in phonotactic probability. Both participant groups repeated nonwords containing high phonotactic probability sequences more accurately than nonwords containing low phonotactic probability sequences. Participants with typical language showed an early advantage for fast mapping high phonotactic probability words; children who were late talkers required more exposures to the novel words to show the same advantage for fast mapping high phonotactic probability words. Children who were late talkers showed similar sensitivities to phonotactic probability in nonword repetition and word learning when compared with their peers with no history of language delay. However, word learning in children who were late talkers appeared to be slower when compared with their peers.

A New Perspective on Visual Word Processing Efficiency

PubMed Central

Houpt, Joseph W.; Townsend, James T.; Donkin, Christopher

2013-01-01

As a fundamental part of our daily lives, visual word processing has received much attention in the psychological literature. Despite the well established advantage of perceiving letters in a word or in a pseudoword over letters alone or in random sequences using accuracy, a comparable effect using response times has been elusive. Some researchers continue to question whether the advantage due to word context is perceptual. We use the capacity coefficient, a well established, response time based measure of efficiency to provide evidence of word processing as a particularly efficient perceptual process to complement those results from the accuracy domain. PMID:24334151

Processing Rhythmic Pattern during Chinese Sentence Reading: An Eye Movement Study

PubMed Central

Luo, Yingyi; Duan, Yunyan; Zhou, Xiaolin

2015-01-01

Prosodic constraints play a fundamental role during both spoken sentence comprehension and silent reading. In Chinese, the rhythmic pattern of the verb-object (V-O) combination has been found to rapidly affect the semantic access/integration process during sentence reading (Luo and Zhou, 2010). Rhythmic pattern refers to the combination of words with different syllabic lengths, with certain combinations disallowed (e.g., [2 + 1]; numbers standing for the number of syllables of the verb and the noun respectively) and certain combinations preferred (e.g., [1 + 1] or [2 + 2]). This constraint extends to the situation in which the combination is used to modify other words. A V-O phrase could modify a noun by simply preceding it, forming a V-O-N compound; when the verb is disyllabic, however, the word order has to be O-V-N and the object is preferred to be disyllabic. In this study, we investigated how the reader processes the rhythmic pattern and word order information by recording the reader's eye-movements. We created four types of sentences by crossing rhythmic pattern and word order in compounding. The compound, embedding a disyllabic verb, could be in the correct O-V-N or the incorrect V-O-N order; the object could be disyllabic or monosyllabic. We found that the reader spent more time and made more regressions on and after the compounds when either type of anomaly was detected during the first pass reading. However, during re-reading (after all the words in the sentence have been viewed), less regressive eye movements were found for the anomalous rhythmic pattern, relative to the correct pattern; moreover, only the abnormal rhythmic pattern, not the violated word order, influenced the regressive eye movements. These results suggest that while the processing of rhythmic pattern and word order information occurs rapidly during the initial reading of the sentence, the process of recovering from the rhythmic pattern anomaly may ease the reanalysis processing at the later stage of sentence integration. Thus, rhythmic pattern in Chinese can dynamically affect both local phrase analysis and global sentence integration during silent reading. PMID:26696942

Processing Rhythmic Pattern during Chinese Sentence Reading: An Eye Movement Study.

PubMed

Luo, Yingyi; Duan, Yunyan; Zhou, Xiaolin

2015-01-01

Prosodic constraints play a fundamental role during both spoken sentence comprehension and silent reading. In Chinese, the rhythmic pattern of the verb-object (V-O) combination has been found to rapidly affect the semantic access/integration process during sentence reading (Luo and Zhou, 2010). Rhythmic pattern refers to the combination of words with different syllabic lengths, with certain combinations disallowed (e.g., [2 + 1]; numbers standing for the number of syllables of the verb and the noun respectively) and certain combinations preferred (e.g., [1 + 1] or [2 + 2]). This constraint extends to the situation in which the combination is used to modify other words. A V-O phrase could modify a noun by simply preceding it, forming a V-O-N compound; when the verb is disyllabic, however, the word order has to be O-V-N and the object is preferred to be disyllabic. In this study, we investigated how the reader processes the rhythmic pattern and word order information by recording the reader's eye-movements. We created four types of sentences by crossing rhythmic pattern and word order in compounding. The compound, embedding a disyllabic verb, could be in the correct O-V-N or the incorrect V-O-N order; the object could be disyllabic or monosyllabic. We found that the reader spent more time and made more regressions on and after the compounds when either type of anomaly was detected during the first pass reading. However, during re-reading (after all the words in the sentence have been viewed), less regressive eye movements were found for the anomalous rhythmic pattern, relative to the correct pattern; moreover, only the abnormal rhythmic pattern, not the violated word order, influenced the regressive eye movements. These results suggest that while the processing of rhythmic pattern and word order information occurs rapidly during the initial reading of the sentence, the process of recovering from the rhythmic pattern anomaly may ease the reanalysis processing at the later stage of sentence integration. Thus, rhythmic pattern in Chinese can dynamically affect both local phrase analysis and global sentence integration during silent reading.

Learning builds on learning: Infants' use of native language sound patterns to learn words

PubMed Central

Graf Estes, Katharine

2014-01-01

The present research investigated how infants apply prior knowledge of environmental regularities to support new learning. The experiments tested whether infants could exploit experience with native language (English) phonotactic patterns to facilitate associating sounds with meanings during word learning. Fourteen-month-olds heard fluent speech that contained cues for detecting target words; they were embedded in sequences that occur across word boundaries. A separate group heard the target words embedded without word boundary cues. Infants then participated in an object label-learning task. With the opportunity to use native language patterns to segment the target words, infants subsequently learned the labels. Without this experience, infants failed. Novice word learners can take advantage of early learning about sounds scaffold lexical development. PMID:24980741

Effects of Systematic and Strategic Analogy-Based Phonics on Grade 2 Students' Word Reading and Reading Comprehension

ERIC Educational Resources Information Center

White, Thomas G.

2005-01-01

Fifteen regular grade 2 teachers used a set of 150 written lessons that were designed to develop, over the course of a school year, low and normally achieving students' ability to decode by analogy (i.e., to read unknown words using known words). The lessons provided (1) a planned sequence for teaching phonic elements including common spelling…

Word learning emerges from the interaction of online referent selection and slow associative learning

PubMed Central

McMurray, Bob; Horst, Jessica S.; Samuelson, Larissa K.

2013-01-01

Classic approaches to word learning emphasize the problem of referential ambiguity: in any naming situation the referent of a novel word must be selected from many possible objects, properties, actions, etc. To solve this problem, researchers have posited numerous constraints, and inference strategies, but assume that determining the referent of a novel word is isomorphic to learning. We present an alternative model in which referent selection is an online process that is independent of long-term learning. This two timescale approach creates significant power in the developing system. We illustrate this with a dynamic associative model in which referent selection is simulated as dynamic competition between competing referents, and learning is simulated using associative (Hebbian) learning. This model can account for a range of findings including the delay in expressive vocabulary relative to receptive vocabulary, learning under high degrees of referential ambiguity using cross-situational statistics, accelerating (vocabulary explosion) and decelerating (power-law) learning rates, fast-mapping by mutual exclusivity (and differences in bilinguals), improvements in familiar word recognition with development, and correlations between individual differences in speed of processing and learning. Five theoretical points are illustrated. 1) Word learning does not require specialized processes – general association learning buttressed by dynamic competition can account for much of the literature. 2) The processes of recognizing familiar words are not different than those that support novel words (e.g., fast-mapping). 3) Online competition may allow the network (or child) to leverage information available in the task to augment performance or behavior despite what might be relatively slow learning or poor representations. 4) Even associative learning is more complex than previously thought – a major contributor to performance is the pruning of incorrect associations between words and referents. 5) Finally, the model illustrates that learning and referent selection/word recognition, though logically distinct, can be deeply and subtly related as phenomena like speed of processing and mutual exclusivity may derive in part from the way learning shapes the system. As a whole, this suggests more sophisticated ways of describing the interaction between situation- and developmental-time processes and points to the need for considering such interactions as a primary determinant of development and processing in children. PMID:23088341

Metacognitive unawareness of the errorful generation benefit and its effects on self-regulated learning.

PubMed

Yang, Chunliang; Potts, Rosalind; Shanks, David R

2017-07-01

Generating errors followed by corrective feedback enhances retention more effectively than does reading-the benefit of errorful generation-but people tend to be unaware of this benefit. The current research explored this metacognitive unawareness, its effect on self-regulated learning, and how to alleviate or reverse it. People's beliefs about the relative learning efficacy of generating errors followed by corrective feedback compared to reading, and the effects of generation fluency, are also explored. In Experiments 1 and 2, lower judgments of learning (JOLs) were consistently given to incorrectly generated word pairs than to studied (read) pairs and led participants to distribute more study resources to incorrectly generated pairs, even though superior recall of these pairs was exhibited in the final test. In Experiment 3, a survey revealed that people believe that generating errors followed by corrective feedback is inferior to reading. Experiment 4 was designed to alter participants' metacognition by informing them of the errorful generation benefit prior to study. Although metacognitive misalignment was partly countered, participants still tended to be unaware of this benefit when making item-by-item JOLs. In Experiment 5, in a delayed JOL condition, higher JOLs were given to incorrectly generated pairs and read pairs were more likely to be selected for restudy. The current research reveals that people tend to underestimate the learning efficiency of generating errors followed by corrective feedback relative to reading when making immediate item-by-item JOLs. Informing people of the errorful generation benefit prior to study and asking them to make delayed JOLs are effective ways to alleviate this metacognitive miscalibration. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Microcomputers and Preschoolers.

ERIC Educational Resources Information Center

Evans, Dina

Preschool children can benefit by working with microcomputers. Thinking skills are enhanced by software games that focus on logic, memory, problem solving, and pattern recognition. Counting, sequencing, and matching games develop mathematics skills, and word games focusing on basic letter symbol and word recognition develop language skills.…

Novel technique used to treat melanoma and epithelial tumors in new clinical trial | Center for Cancer Research

Cancer.gov

Exomic sequencing allows researchers to read the “letters” in the part of your DNA that makes proteins to see where the letters are correct and where the letters are incorrect. This information allows white blood cells engineered from the patient to recognize these tumor-specific mutations and be made into vaccines, called dendritic cell (DC) vaccines, to test effects on

A universal cue for grammatical categories in the input to children: Frequent frames.

PubMed

Moran, Steven; Blasi, Damián E; Schikowski, Robert; Küntay, Aylin C; Pfeiler, Barbara; Allen, Shanley; Stoll, Sabine

2018-06-01

How does a child map words to grammatical categories when words are not overtly marked either lexically or prosodically? Recent language acquisition theories have proposed that distributional information encoded in sequences of words or morphemes might play a central role in forming grammatical classes. To test this proposal, we analyze child-directed speech from seven typologically diverse languages to simulate maximum variation in the structures of the world's languages. We ask whether the input to children contains cues for assigning syntactic categories in frequent frames, which are frequently occurring nonadjacent sequences of words or morphemes. In accord with aggregated results from previous studies on individual languages, we find that frequent word frames do not provide a robust distributional pattern for accurately predicting grammatical categories. However, our results show that frames are extremely accurate cues cross-linguistically at the morpheme level. We theorize that the nonadjacent dependency pattern captured by frequent frames is a universal anchor point for learners on the morphological level to detect and categorize grammatical categories. Whether frames also play a role on higher linguistic levels such as words is determined by grammatical features of the individual language. Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.

Lateralized effects of orthographical irregularity and auditory memory load on the kinematics of transcription typewriting.

PubMed

Bloemsaat, Gijs; Van Galen, Gerard P; Meulenbroek, Ruud G J

2003-05-01

This study investigated the combined effects of orthographical irregularity and auditory memory load on the kinematics of finger movements in a transcription-typewriting task. Eight right-handed touch-typists were asked to type 80 strings of ten seven-letter words. In half the trials an irregularly spelt target word elicited a specific key press sequence of either the left or right index finger. In the other trials regularly spelt target words elicited the same key press sequence. An auditory memory load was added in half the trials by asking participants to remember the pitch of a tone during task performance. Orthographical irregularity was expected to slow down performance. Auditory memory load, viewed as a low level stressor, was expected to affect performance only when orthographically irregular words needed to be typed. The hypotheses were confirmed. Additional analysis showed differential effects on the left and right hand, possibly related to verbal-manual interference and hand dominance. The results are discussed in relation to relevant findings of recent neuroimaging studies.

What is preexisting strength? Predicting free association probabilities, similarity ratings, and cued recall probabilities.

PubMed

Nelson, Douglas L; Dyrdal, Gunvor M; Goodmon, Leilani B

2005-08-01

Measuring lexical knowledge poses a challenge to the study of the influence of preexisting knowledge on the retrieval of new memories. Many tasks focus on word pairs, but words are embedded in associative networks, so how should preexisting pair strength be measured? It has been measured by free association, similarity ratings, and co-occurrence statistics. Researchers interpret free association response probabilities as unbiased estimates of forward cue-to-target strength. In Study 1, analyses of large free association and extralist cued recall databases indicate that this interpretation is incorrect. Competitor and backward strengths bias free association probabilities, and as with other recall tasks, preexisting strength is described by a ratio rule. In Study 2, associative similarity ratings are predicted by forward and backward, but not by competitor, strength. Preexisting strength is not a unitary construct, because its measurement varies with method. Furthermore, free association probabilities predict extralist cued recall better than do ratings and co-occurrence statistics. The measure that most closely matches the criterion task may provide the best estimate of the identity of preexisting strength.

Feature Migration in Time: Reflection of Selective Attention on Speech Errors

PubMed Central

Nozari, Nazbanou; Dell, Gary S.

2012-01-01

This paper describes an initial study of the effect of focused attention on phonological speech errors. In three experiments, participants recited four-word tongue-twisters, and focused attention on one (or none) of the words. The attended word was singled out differently in each experiment; participants were under instructions to either avoid errors on the attended word, to stress it, or to say it silently. The experiments showed that all methods of attending to a word decreased errors on that word, while increasing errors on the surrounding words. However, this error increase did not result from a relative increase in phonemic migrations originating from the attended word. This pattern is inconsistent with conceptualizing attention either as higher activation of the attended word or greater inhibition of the unattended words throughout the production of the sequence. Instead, it is consistent with a model which presumes that attention exerts its effect at the time of production of the attended word, without lingering effects on the past or the future. PMID:22268910

Frequency, Contingency and Online Processing of Multiword Sequences: An Eye-Tracking Study

ERIC Educational Resources Information Center

Yi, Wei; Lu, Shiyi; Ma, Guojie

2017-01-01

Frequency and contingency are two primary statistical factors that drive the acquisition and processing of language. This study explores the role of phrasal frequency and contingency (the co-occurrence probability/statistical association of the constituent words in multiword sequences) during online processing of multiword sequences. Meanwhile, it…

Long-Branch Attraction Bias and Inconsistency in Bayesian Phylogenetics

PubMed Central

Kolaczkowski, Bryan; Thornton, Joseph W.

2009-01-01

Bayesian inference (BI) of phylogenetic relationships uses the same probabilistic models of evolution as its precursor maximum likelihood (ML), so BI has generally been assumed to share ML's desirable statistical properties, such as largely unbiased inference of topology given an accurate model and increasingly reliable inferences as the amount of data increases. Here we show that BI, unlike ML, is biased in favor of topologies that group long branches together, even when the true model and prior distributions of evolutionary parameters over a group of phylogenies are known. Using experimental simulation studies and numerical and mathematical analyses, we show that this bias becomes more severe as more data are analyzed, causing BI to infer an incorrect tree as the maximum a posteriori phylogeny with asymptotically high support as sequence length approaches infinity. BI's long branch attraction bias is relatively weak when the true model is simple but becomes pronounced when sequence sites evolve heterogeneously, even when this complexity is incorporated in the model. This bias—which is apparent under both controlled simulation conditions and in analyses of empirical sequence data—also makes BI less efficient and less robust to the use of an incorrect evolutionary model than ML. Surprisingly, BI's bias is caused by one of the method's stated advantages—that it incorporates uncertainty about branch lengths by integrating over a distribution of possible values instead of estimating them from the data, as ML does. Our findings suggest that trees inferred using BI should be interpreted with caution and that ML may be a more reliable framework for modern phylogenetic analysis. PMID:20011052

Long-branch attraction bias and inconsistency in Bayesian phylogenetics.

PubMed

Kolaczkowski, Bryan; Thornton, Joseph W

2009-12-09

Bayesian inference (BI) of phylogenetic relationships uses the same probabilistic models of evolution as its precursor maximum likelihood (ML), so BI has generally been assumed to share ML's desirable statistical properties, such as largely unbiased inference of topology given an accurate model and increasingly reliable inferences as the amount of data increases. Here we show that BI, unlike ML, is biased in favor of topologies that group long branches together, even when the true model and prior distributions of evolutionary parameters over a group of phylogenies are known. Using experimental simulation studies and numerical and mathematical analyses, we show that this bias becomes more severe as more data are analyzed, causing BI to infer an incorrect tree as the maximum a posteriori phylogeny with asymptotically high support as sequence length approaches infinity. BI's long branch attraction bias is relatively weak when the true model is simple but becomes pronounced when sequence sites evolve heterogeneously, even when this complexity is incorporated in the model. This bias--which is apparent under both controlled simulation conditions and in analyses of empirical sequence data--also makes BI less efficient and less robust to the use of an incorrect evolutionary model than ML. Surprisingly, BI's bias is caused by one of the method's stated advantages--that it incorporates uncertainty about branch lengths by integrating over a distribution of possible values instead of estimating them from the data, as ML does. Our findings suggest that trees inferred using BI should be interpreted with caution and that ML may be a more reliable framework for modern phylogenetic analysis.

Robust Vocabulary Instruction in a Readers' Workshop

ERIC Educational Resources Information Center

Feezell, Greg

2012-01-01

This article presents strategies for integrating explicit vocabulary instruction within a reading workshop. The author begins by describing a process for involving students in word selection. The author then provides a weeklong instructional sequence using student-selected words. Finally, the author briefly examines the role of vocabulary…

Apical Coarticulation at Juncture Boundaries

ERIC Educational Resources Information Center

Lewis, J.; And Others

1975-01-01

Sentences were read by six informants to determine the presence or absence of /n/ in /nth/ sequences. The sentences contained seven different levels of juncture with /nth/ occurring in word final position, intervocalically, and across word boundaries, among other places. Dental coarticulation was not hindered by most junctures. (SC)

A Functional Syntax of German.

ERIC Educational Resources Information Center

Fichtner, Edward G.

Students in intermediate language courses, especially conversational courses, can benefit from a simple set of instructions for combining words and phrases into sentences. A description of the basic concepts determining word order in German--the fundamental sequence of clause elements, the "infrastructure," and the movement rules by which the…

Event-related brain potentials index cue-based retrieval interference during sentence comprehension.

PubMed

Martin, Andrea E; Nieuwland, Mante S; Carreiras, Manuel

2012-01-16

Successful language use requires access to products of past processing within an evolving discourse. A central issue for any neurocognitive theory of language then concerns the role of memory variables during language processing. Under a cue-based retrieval account of language comprehension, linguistic dependency resolution (e.g., retrieving antecedents) is subject to interference from other information in the sentence, especially information that occurs between the words that form the dependency (e.g., between the antecedent and the retrieval site). Retrieval interference may then shape processing complexity as a function of the match of the information at retrieval with the antecedent versus other recent or similar items in memory. To address these issues, we studied the online processing of ellipsis in Castilian Spanish, a language with morphological gender agreement. We recorded event-related brain potentials while participants read sentences containing noun-phrase ellipsis indicated by the determiner otro/a ('another'). These determiners had a grammatically correct or incorrect gender with respect to their antecedent nouns that occurred earlier in the sentence. Moreover, between each antecedent and determiner, another noun phrase occurred that was structurally unavailable as an antecedent and that matched or mismatched the gender of the antecedent (i.e., a local agreement attractor). In contrast to extant P600 results on agreement violation processing, and inconsistent with predictions from neurocognitive models of sentence processing, grammatically incorrect determiners evoked a sustained, broadly distributed negativity compared to correct ones between 400 and 1000ms after word onset, possibly related to sustained negativities as observed for referential processing difficulties. Crucially, this effect was modulated by the attractor: an increased negativity was observed for grammatically correct determiners that did not match the gender of the attractor, suggesting that structurally unavailable noun phrases were at least temporarily considered for grammatically correct ellipsis. These results constitute the first ERP evidence for cue-based retrieval interference during comprehension of grammatical sentences. Copyright © 2011 Elsevier Inc. All rights reserved.

The effects of bilingual language proficiency on recall accuracy and semantic clustering in free recall output: evidence for shared semantic associations across languages.

PubMed

Francis, Wendy S; Taylor, Randolph S; Gutiérrez, Marisela; Liaño, Mary K; Manzanera, Diana G; Penalver, Renee M

2018-05-19

Two experiments investigated how well bilinguals utilise long-standing semantic associations to encode and retrieve semantic clusters in verbal episodic memory. In Experiment 1, Spanish-English bilinguals (N = 128) studied and recalled word and picture sets. Word recall was equivalent in L1 and L2, picture recall was better in L1 than in L2, and the picture superiority effect was stronger in L1 than in L2. Semantic clustering in word and picture recall was equivalent in L1 and L2. In Experiment 2, Spanish-English bilinguals (N = 128) and English-speaking monolinguals (N = 128) studied and recalled word sequences that contained semantically related pairs. Data were analyzed using a multinomial processing tree approach, the pair-clustering model. Cluster formation was more likely for semantically organised than for randomly ordered word sequences. Probabilities of cluster formation, cluster retrieval, and retrieval of unclustered items did not differ across languages or language groups. Language proficiency has little if any impact on the utilisation of long-standing semantic associations, which are language-general.

Qualitative features of semantic fluency performance in mesial and lateral frontal patients.

PubMed

Reverberi, Carlo; Laiacona, Marcella; Capitani, Erminio

2006-01-01

Semantic verbal fluency is widely used in clinical and experimental studies. This task is highly sensitive to the presence of brain pathology and is frequently impaired after frontal lesions. Besides the total number of words generated, a qualitative analysis of their sequence can add valuable information about the impaired cognitive components. Thirty-four frontal patients and a group of matched controls were examined. Besides the number of words and subcategories retrieved by each group, we analysed two distinct aspects of the word sequence: the search strategy through a semantically organised store and the ability to switch from one subcategory to another. We checked whether the pattern of impairment changed according to the lesion site within the frontal lobe. Overall, patients produced fewer words than controls. However, only lateral frontal patients presented a reduced semantic relatedness between contiguously produced words and a specifically increased proportion of switches to different subcategories. The performance of lateral frontal patients was in line with the hypothesis of a search strategy impairment and cannot be attributed to a switching deficit. The performance of mesial frontal patients could be ascribed to a general deficit of activation.

'Necessary and sufficient' in biology is not necessarily necessary - confusions and erroneous conclusions resulting from misapplied logic in the field of biology, especially neuroscience.

PubMed

Yoshihara, Motojiro; Yoshihara, Motoyuki

In this article, we describe an incorrect use of logic which involves the careless application of the 'necessary and sufficient' condition originally used in formal logic. This logical fallacy is causing frequent confusion in current biology, especially in neuroscience. In order to clarify this problem, we first dissect the structure of this incorrect logic (which we refer to as 'misapplied-N&S') to show how necessity and sufficiency in misapplied-N&S are not matching each other. Potential pitfalls of utilizing misapplied-N&S are exemplified by cases such as the discrediting of command neurons and other potentially key neurons, the distorting of truth in optogenetic studies, and the wrongful justification of studies with little meaning. In particular, the use of the word 'sufficient' in optogenetics tends to generate misunderstandings by opening up multiple interpretations. To avoid the confusion caused by the misleading logic, we now recommend using 'indispensable and inducing' instead of using 'necessary and sufficient.' However, we ultimately recommend fully articulating the limits of what our experiments suggest, not relying on such simple phrases. Only after this problem is fully understood and more rigorous language is demanded, can we finally interpret experimental results in an accurate way.

String Mining in Bioinformatics

NASA Astrophysics Data System (ADS)

Abouelhoda, Mohamed; Ghanem, Moustafa

Sequence analysis is a major area in bioinformatics encompassing the methods and techniques for studying the biological sequences, DNA, RNA, and proteins, on the linear structure level. The focus of this area is generally on the identification of intra- and inter-molecular similarities. Identifying intra-molecular similarities boils down to detecting repeated segments within a given sequence, while identifying inter-molecular similarities amounts to spotting common segments among two or multiple sequences. From a data mining point of view, sequence analysis is nothing but string- or pattern mining specific to biological strings. For a long time, this point of view, however, has not been explicitly embraced neither in the data mining nor in the sequence analysis text books, which may be attributed to the co-evolution of the two apparently independent fields. In other words, although the word "data-mining" is almost missing in the sequence analysis literature, its basic concepts have been implicitly applied. Interestingly, recent research in biological sequence analysis introduced efficient solutions to many problems in data mining, such as querying and analyzing time series [49,53], extracting information from web pages [20], fighting spam mails [50], detecting plagiarism [22], and spotting duplications in software systems [14].

String Mining in Bioinformatics

NASA Astrophysics Data System (ADS)

Abouelhoda, Mohamed; Ghanem, Moustafa

Sequence analysis is a major area in bioinformatics encompassing the methods and techniques for studying the biological sequences, DNA, RNA, and proteins, on the linear structure level. The focus of this area is generally on the identification of intra- and inter-molecular similarities. Identifying intra-molecular similarities boils down to detecting repeated segments within a given sequence, while identifying inter-molecular similarities amounts to spotting common segments among two or multiple sequences. From a data mining point of view, sequence analysis is nothing but string- or pattern mining specific to biological strings. For a long time, this point of view, however, has not been explicitly embraced neither in the data mining nor in the sequence analysis text books, which may be attributed to the co-evolution of the two apparently independent fields. In other words, although the word “data-mining” is almost missing in the sequence analysis literature, its basic concepts have been implicitly applied. Interestingly, recent research in biological sequence analysis introduced efficient solutions to many problems in data mining, such as querying and analyzing time series [49,53], extracting information from web pages [20], fighting spam mails [50], detecting plagiarism [22], and spotting duplications in software systems [14].

Mechanism-based strategies for protein thermostabilization.

PubMed

Mozhaev, V V

1993-03-01

Strategies for stabilizing enzymes can be derived from a two-step model of irreversible inactivation that involves preliminary reversible unfolding, followed by an irreversible step. Reversible unfolding is best prevented by covalent immobilization, whereas methods such as covalent modification of amino acid residues or 'medium engineering' (by the addition of low-molecular-weight compounds) are effective against irreversible 'incorrect' refolding. Genetic modification of the protein sequence is the most effective approach for preventing chemical deterioration.

Computer decision support as a source of interpretation error: the case of electrocardiograms.

PubMed

Tsai, Theodore L; Fridsma, Douglas B; Gatti, Guido

2003-01-01

The aim of this study was to determine the effect that the computer interpretation (CI) of electrocardiograms (EKGs) has on the accuracy of resident (noncardiologist) physicians reading EKGs. A randomized, controlled trial was conducted in a laboratory setting from February through June 2001, using a two-period crossover design with matched pairs of subjects randomly assigned to sequencing groups. Subjects' interpretive accuracy of discrete, cardiologist-determined EKG findings were measured as judged by a board-certified internist. Without the CI, subjects interpreted 48.9% (95% confidence interval, 45.0% to 52.8%) of the findings correctly. With the CI, subjects interpreted 55.4% (51.9% to 58.9%) correctly (p < 0.0001). When the CIs that agreed with the gold standard (Correct CIs) were not included, 53.1% (47.7% to 58.5%) of the findings were interpreted correctly. When the correct CI was included, accuracy increased to 68.1% (63.2% to 72.7%; p < 0.0001). When computer advice that did not agree with the gold standard (Incorrect CI) was not provided to the subjects, 56.7% (48.5% to 64.5%) of findings were interpreted correctly. Accuracy dropped to 48.3% (40.4% to 56.4%) when the incorrect computer advice was provided (p = 0.131). Subjects erroneously agreed with the incorrect CI more often when it was presented with the EKG 67.7% (57.2% to 76.7%) than when it was not 34.6% (23.8% to 47.3%; p < 0.0001). Computer decision support systems can generally improve the interpretive accuracy of internal medicine residents in reading EKGs. However, subjects were influenced significantly by incorrect advice, which tempers the overall usefulness of computer-generated advice in this and perhaps other areas.

Computer Decision Support as a Source of Interpretation Error: The Case of Electrocardiograms

PubMed Central

Tsai, Theodore L.; Fridsma, Douglas B.; Gatti, Guido

2003-01-01

Objective: The aim of this study was to determine the effect that the computer interpretation (CI) of electrocardiograms (EKGs) has on the accuracy of resident (noncardiologist) physicians reading EKGs. Design: A randomized, controlled trial was conducted in a laboratory setting from February through June 2001, using a two-period crossover design with matched pairs of subjects randomly assigned to sequencing groups. Measurements: Subjects' interpretive accuracy of discrete, cardiologist-determined EKG findings were measured as judged by a board-certified internist. Results: Without the CI, subjects interpreted 48.9% (95% confidence interval, 45.0% to 52.8%) of the findings correctly. With the CI, subjects interpreted 55.4% (51.9% to 58.9%) correctly (p < 0.0001). When the CIs that agreed with the gold standard (Correct CIs) were not included, 53.1% (47.7% to 58.5%) of the findings were interpreted correctly. When the correct CI was included, accuracy increased to 68.1% (63.2% to 72.7%; p < 0.0001). When computer advice that did not agree with the gold standard (Incorrect CI) was not provided to the subjects, 56.7% (48.5% to 64.5%) of findings were interpreted correctly. Accuracy dropped to 48.3% (40.4% to 56.4%) when the incorrect computer advice was provided (p = 0.131). Subjects erroneously agreed with the incorrect CI more often when it was presented with the EKG 67.7% (57.2% to 76.7%) than when it was not 34.6% (23.8% to 47.3%; p < 0.0001). Conclusions: Computer decision support systems can generally improve the interpretive accuracy of internal medicine residents in reading EKGs. However, subjects were influenced significantly by incorrect advice, which tempers the overall usefulness of computer-generated advice in this and perhaps other areas. PMID:12807810

A model linking immediate serial recall, the Hebb repetition effect and the learning of phonological word forms

PubMed Central

Page, M. P. A.; Norris, D.

2009-01-01

We briefly review the considerable evidence for a common ordering mechanism underlying both immediate serial recall (ISR) tasks (e.g. digit span, non-word repetition) and the learning of phonological word forms. In addition, we discuss how recent work on the Hebb repetition effect is consistent with the idea that learning in this task is itself a laboratory analogue of the sequence-learning component of phonological word-form learning. In this light, we present a unifying modelling framework that seeks to account for ISR and Hebb repetition effects, while being extensible to word-form learning. Because word-form learning is performed in the service of later word recognition, our modelling framework also subsumes a mechanism for word recognition from continuous speech. Simulations of a computational implementation of the modelling framework are presented and are shown to be in accordance with data from the Hebb repetition paradigm. PMID:19933143

Is attention confined to one word at a time? The spatial distribution of parafoveal preview benefits during reading.

PubMed

Wang, Chin-An; Inhoff, Albrecht W; Radach, Ralph

2009-10-01

Eye movements were recorded while participants read declarative sentences. Each sentence contained a critical three-word sequence with a three-letter target word (n), a spatially adjacent post-target word (n+1), and a subsequent nonadjacent post-target word (n+2). The parafoveal previews of words n and n+2 were manipulated so that they were either fully visible or masked until they were fixated. The results revealed longer word n and word n+1 viewing durations when word n had been masked in the parafovea, and this occurred irrespective of whether the target was skipped or fixated. Furthermore, masking of word n diminished the usefulness of the preview of word n+2. These results indicate that the effect of a parafoveally available target preview was not strictly localized. Instead, it influenced target viewing and the viewing of the two subsequent words in the text. These results are difficult to reconcile with the assumption that attention is confined to one word at a time until that word is recognized and that attention is then shifted from the recognized word to the next.

Bilingual Performance on Nonword Repetition in Spanish and English

ERIC Educational Resources Information Center

Summers, Connie; Bohman, Thomas M.; Gillam, Ronald B.; Pena, Elizabeth D.; Bedore, Lisa M.

2010-01-01

Background: Nonword repetition (NWR) involves the ability to perceive, store, recall and reproduce phonological sequences. These same abilities play a role in word and morpheme learning. Cross-linguistic studies of performance on NWR tasks, word learning, and morpheme learning yield patterns of increased performance on all three tasks as a…

Phonological learning in semantic dementia.

PubMed

Jefferies, Elizabeth; Bott, Samantha; Ehsan, Sheeba; Lambon Ralph, Matthew A

2011-04-01

Patients with semantic dementia (SD) have anterior temporal lobe (ATL) atrophy that gives rise to a highly selective deterioration of semantic knowledge. Despite pronounced anomia and poor comprehension of words and pictures, SD patients have well-formed, fluent speech and normal digit span. Given the intimate connection between phonological STM and word learning revealed by both neuropsychological and developmental studies, SD patients might be expected to show good acquisition of new phonological forms, even though their ability to map these onto meanings is impaired. In contradiction of these predictions, a limited amount of previous research has found poor learning of new phonological forms in SD. In a series of experiments, we examined whether SD patient, GE, could learn novel phonological sequences and, if so, under which circumstances. GE showed normal benefits of phonological knowledge in STM (i.e., normal phonotactic frequency and phonological similarity effects) but reduced support from semantic memory (i.e., poor immediate serial recall for semantically degraded words, characterised by frequent item errors). Next, we demonstrated normal learning of serial order information for repeated lists of single-digit number words using the Hebb paradigm: these items were well-understood allowing them to be repeated without frequent item errors. In contrast, patient GE showed little learning of nonsense syllable sequences using the same Hebb paradigm. Detailed analysis revealed that both GE and the controls showed a tendency to learn their own errors as opposed to the target items. Finally, we showed normal learning of phonological sequences for GE when he was prevented from repeating his errors. These findings confirm that the ATL atrophy in SD disrupts phonological processing for semantically degraded words but leaves the phonological architecture intact. Consequently, when item errors are minimised, phonological STM can support the acquisition of new phoneme sequences in patients with SD. Copyright © 2011 Elsevier Ltd. All rights reserved.

Three speech sounds, one motor action: evidence for speech-motor disparity from English flap production.

PubMed

Derrick, Donald; Stavness, Ian; Gick, Bryan

2015-03-01

The assumption that units of speech production bear a one-to-one relationship to speech motor actions pervades otherwise widely varying theories of speech motor behavior. This speech production and simulation study demonstrates that commonly occurring flap sequences may violate this assumption. In the word "Saturday," a sequence of three sounds may be produced using a single, cyclic motor action. Under this view, the initial upward tongue tip motion, starting with the first vowel and moving to contact the hard palate on the way to a retroflex position, is under active muscular control, while the downward movement of the tongue tip, including the second contact with the hard palate, results from gravity and elasticity during tongue muscle relaxation. This sequence is reproduced using a three-dimensional computer simulation of human vocal tract biomechanics and differs greatly from other observed sequences for the same word, which employ multiple targeted speech motor actions. This outcome suggests that a goal of a speaker is to produce an entire sequence in a biomechanically efficient way at the expense of maintaining parity within the individual parts of the sequence.

High resolution identity testing of inactivated poliovirus vaccines

PubMed Central

Mee, Edward T.; Minor, Philip D.; Martin, Javier

2015-01-01

Background Definitive identification of poliovirus strains in vaccines is essential for quality control, particularly where multiple wild-type and Sabin strains are produced in the same facility. Sequence-based identification provides the ultimate in identity testing and would offer several advantages over serological methods. Methods We employed random RT-PCR and high throughput sequencing to recover full-length genome sequences from monovalent and trivalent poliovirus vaccine products at various stages of the manufacturing process. Results All expected strains were detected in previously characterised products and the method permitted identification of strains comprising as little as 0.1% of sequence reads. Highly similar Mahoney and Sabin 1 strains were readily discriminated on the basis of specific variant positions. Analysis of a product known to contain incorrect strains demonstrated that the method correctly identified the contaminants. Conclusion Random RT-PCR and shotgun sequencing provided high resolution identification of vaccine components. In addition to the recovery of full-length genome sequences, the method could also be easily adapted to the characterisation of minor variant frequencies and distinction of closely related products on the basis of distinguishing consensus and low frequency polymorphisms. PMID:26049003

Perceptual recovery from consonant-cluster simplification in Korean using language-specific phonological knowledge.

PubMed

Cho, Taehong; McQueen, James M

2011-08-01

Two experiments examined whether perceptual recovery from Korean consonant-cluster simplification is based on language-specific phonological knowledge. In tri-consonantal C1C2C3 sequences such as /lkt/ and /lpt/ in Seoul Korean, either C1 or C2 can be completely deleted. Seoul Koreans monitored for C2 targets (/p/ or / k/, deleted or preserved) in the second word of a two-word phrase with an underlying /l/-C2-/t/ sequence. In Experiment 1 the target-bearing words had contextual lexical-semantic support. Listeners recovered deleted targets as fast and as accurately as preserved targets with both Word and Intonational Phrase (IP) boundaries between the two words. In Experiment 2, contexts were low-pass filtered. Listeners were still able to recover deleted targets as well as preserved targets in IP-boundary contexts, but better with physically-present targets than with deleted targets in Word-boundary contexts. This suggests that the benefit of having target acoustic-phonetic information emerges only when higher-order (contextual and phrase-boundary) information is not available. The strikingly efficient recovery of deleted phonemes with neither acoustic-phonetic cues nor contextual support demonstrates that language-specific phonological knowledge, rather than language-universal perceptual processes which rely on fine-grained phonetic details, is employed when the listener perceives the results of a continuous-speech process in which reduction is phonetically complete.

Memory for tonal pitches: a music-length effect hypothesis.

PubMed

Akiva-Kabiri, Lilach; Vecchi, Tomaso; Granot, Roni; Basso, Demis; Schön, Daniele

2009-07-01

One of the most studied effects of verbal working memory (WM) is the influence of the length of the words that compose the list to be remembered. This work aims to investigate the nature of musical WM by replicating the word length effect in the musical domain. Length and rate of presentation were manipulated in a recognition task of tone sequences. Results showed significant effects for both factors (length and presentation rate) as well as their interaction, suggesting the existence of different strategies (e.g., chunking and rehearsal) for the immediate memory of musical information, depending upon the length of the sequences.

Errorless discrimination and picture fading as techniques for teaching sight words to TMR students.

PubMed

Walsh, B F; Lamberts, F

1979-03-01

The effectiveness of two approaches for teaching beginning sight words to 30 TMR students was compared. In Dorry and Zeaman's picture-fading technique, words are taught through association with pictures that are faded out over a series of trials, while in the Edmark program errorless-discrimination technique, words are taught through shaped sequences of visual and auditory--visual matching-to-sample, with the target word first appearing alone and eventually appearing with orthographically similar words. Students were instructed on two lists of 10 words each, one list in the picture-fading and one in the discrimination method, in a double counter-balanced, repeated-measures design. Covariance analysis on three measures (word identification, word recognition, and picture--word matching) showed highly significant differences between the two methods. Students' performance was better after instruction with the errorless-discrimination method than after instruction with the picture-fading method. The findings on picture fading were interpreted as indicating a possible failure of the shifting of control from picture to printed word that earlier researchers have hypothesized as occurring.

Comment on 'Semitransparency effects in the moving mirror model for Hawking radiation'

DOE Office of Scientific and Technical Information (OSTI.GOV)

Elizalde, Emilio; Haro, Jaume

2010-06-15

Particle production by a semitransparent mirror accelerating on trajectories which simulate the Hawking effect was recently discussed in 3. This author points out that some results in 1 are incorrect. We show here that, contrary to statements therein, the main results and conclusions of the last paper remain valid, only Eq. (41) there and some particular implication are not. The misunderstanding actually comes from comparing two very different parameter regions, and from the fact that, in our work, the word statistics was used in an unusual way related to the sign of the {beta}-Bogoliubov coefficient, and not with its ordinarymore » meaning, connected with the number of particles emitted per mode.« less

Identification of Critical Residues for the Tight Binding of Both Correct and Incorrect Nucleotides to Human DNA Polymerase λ

PubMed Central

Brown, Jessica A.; Pack, Lindsey R.; Sherrer, Shanen M.; Kshetry, Ajay K.; Newmister, Sean A.; Fowler, Jason D.; Taylor, John-Stephen; Suo, Zucai

2010-01-01

DNA polymerase λ (Pol λ) is a novel X-family DNA polymerase that shares 34% sequence identity with DNA polymerase β (Pol β). Pre-steady state kinetic studies have shown that the Pol λ•DNA complex binds both correct and incorrect nucleotides 130-fold tighter on average than the Pol β•DNA complex, although, the base substitution fidelity of both polymerases is 10−4 to 10−5. To better understand Pol λ’s tight nucleotide binding affinity, we created single- and double-substitution mutants of Pol λ to disrupt interactions between active site residues and an incoming nucleotide or a template base. Single-turnover kinetic assays showed that Pol λ binds to an incoming nucleotide via cooperative interactions with active site residues (R386, R420, K422, Y505, F506, A510, and R514). Disrupting protein interactions with an incoming correct or incorrect nucleotide impacted binding with each of the common structural moieties in the following order: triphosphate ≫ base > ribose. In addition, the loss of Watson-Crick hydrogen bonding between the nucleotide and template base led to a moderate increase in the Kd. The fidelity of Pol λ was maintained predominantly by a single residue, R517, which has minor groove interactions with the DNA template. PMID:20851705

Suitability of partial 16S ribosomal RNA gene sequence analysis for the identification of dangerous bacterial pathogens.

PubMed

Ruppitsch, W; Stöger, A; Indra, A; Grif, K; Schabereiter-Gurtner, C; Hirschl, A; Allerberger, F

2007-03-01

In a bioterrorism event a rapid tool is needed to identify relevant dangerous bacteria. The aim of the study was to assess the usefulness of partial 16S rRNA gene sequence analysis and the suitability of diverse databases for identifying dangerous bacterial pathogens. For rapid identification purposes a 500-bp fragment of the 16S rRNA gene of 28 isolates comprising Bacillus anthracis, Brucella melitensis, Burkholderia mallei, Burkholderia pseudomallei, Francisella tularensis, Yersinia pestis, and eight genus-related and unrelated control strains was amplified and sequenced. The obtained sequence data were submitted to three public and two commercial sequence databases for species identification. The most frequent reason for incorrect identification was the lack of the respective 16S rRNA gene sequences in the database. Sequence analysis of a 500-bp 16S rDNA fragment allows the rapid identification of dangerous bacterial species. However, for discrimination of closely related species sequencing of the entire 16S rRNA gene, additional sequencing of the 23S rRNA gene or sequencing of the 16S-23S rRNA intergenic spacer is essential. This work provides comprehensive information on the suitability of partial 16S rDNA analysis and diverse databases for rapid and accurate identification of dangerous bacterial pathogens.

Reading Speed Does Not Benefit from Increased Line Spacing in AMD Patients

PubMed Central

CHUNG, SUSANA T. L.; JARVIS, SAMUEL H.; WOO, STANLEY Y.; HANSON, KARA; JOSE, RANDALL T.

2009-01-01

Purpose Crowding, the adverse spatial interaction due to the proximity of adjacent targets, has been suggested as an explanation for slow reading in peripheral vision. Previously, we showed that increased line spacing, which presumably reduces crowding between adjacent lines of text, improved reading speed in the normal periphery (Chung, Optom Vis Sci 2004;81:525–35). The purpose of this study was to examine whether or not individuals with age-related macular degeneration (AMD) would benefit from increased line spacing for reading. Methods Experiment 1: Eight subjects with AMD read aloud 100-word passages rendered at five line spacings: the standard single spacing, 1.5×, 2×, 3×, and 4× the standard spacing. Print sizes were 1× and 2× of the critical print size. Reading time and number of reading errors for each passage were measured to compute the reading speed. Experiment 2: Four subjects with AMD read aloud sequences of six 4-letter words, presented on a computer monitor using the rapid serial visual presentation (RSVP) paradigm. Target words were presented singly, or flanked above and below by two other words that changed in synchrony with the target word, at various vertical word separations. Print size was 2× the critical print size. Reading speed was calculated based on the RSVP exposure duration that yielded 80% of the words read correctly. Results Averaged across subjects, reading speeds for passages were virtually constant for the range of line spacings tested. For sequences of unrelated words, reading speeds were also virtually constant for the range of vertical word separations tested, except at the smallest (standard) separation at which reading speed was lower. Conclusions Contrary to the previous finding that reading speed improved in normal peripheral vision, increased line spacing in passages, or increased vertical separation between words in RSVP, did not lead to improved reading speed in people with AMD. PMID:18772718

MRO DKF Post-Processing Tool

NASA Technical Reports Server (NTRS)

Ayap, Shanti; Fisher, Forest; Gladden, Roy; Khanampompan, Teerapat

2008-01-01

This software tool saves time and reduces risk by automating two labor-intensive and error-prone post-processing steps required for every DKF [DSN (Deep Space Network) Keyword File] that MRO (Mars Reconnaissance Orbiter) produces, and is being extended to post-process the corresponding TSOE (Text Sequence Of Events) as well. The need for this post-processing step stems from limitations in the seq-gen modeling resulting in incorrect DKF generation that is then cleaned up in post-processing.

Novel technique used to treat melanoma and epithelial tumors in new clinical trial | Center for Cancer Research

Cancer.gov

Exomic sequencing allows researchers to read the “letters” in the part of your DNA that makes proteins to see where the letters are correct and where the letters are incorrect. This information allows white blood cells engineered from the patient to recognize these tumor-specific mutations and be made into vaccines, called dendritic cell (DC) vaccines, to test effects on melanoma and epithelial tumors. Read more…

Best practices for evaluating single nucleotide variant calling methods for microbial genomics

PubMed Central

Olson, Nathan D.; Lund, Steven P.; Colman, Rebecca E.; Foster, Jeffrey T.; Sahl, Jason W.; Schupp, James M.; Keim, Paul; Morrow, Jayne B.; Salit, Marc L.; Zook, Justin M.

2015-01-01

Innovations in sequencing technologies have allowed biologists to make incredible advances in understanding biological systems. As experience grows, researchers increasingly recognize that analyzing the wealth of data provided by these new sequencing platforms requires careful attention to detail for robust results. Thus far, much of the scientific Communit’s focus for use in bacterial genomics has been on evaluating genome assembly algorithms and rigorously validating assembly program performance. Missing, however, is a focus on critical evaluation of variant callers for these genomes. Variant calling is essential for comparative genomics as it yields insights into nucleotide-level organismal differences. Variant calling is a multistep process with a host of potential error sources that may lead to incorrect variant calls. Identifying and resolving these incorrect calls is critical for bacterial genomics to advance. The goal of this review is to provide guidance on validating algorithms and pipelines used in variant calling for bacterial genomics. First, we will provide an overview of the variant calling procedures and the potential sources of error associated with the methods. We will then identify appropriate datasets for use in evaluating algorithms and describe statistical methods for evaluating algorithm performance. As variant calling moves from basic research to the applied setting, standardized methods for performance evaluation and reporting are required; it is our hope that this review provides the groundwork for the development of these standards. PMID:26217378

A Randomized Field Trial of the Fast ForWord Language Computer-Based Training Program

ERIC Educational Resources Information Center

Borman, Geoffrey D.; Benson, James G.; Overman, Laura

2009-01-01

This article describes an independent assessment of the Fast ForWord Language computer-based training program developed by Scientific Learning Corporation. Previous laboratory research involving children with language-based learning impairments showed strong effects on their abilities to recognize brief and fast sequences of nonspeech and speech…

The Color-Word Interference Test and Its Relation to Performance Impairment under Auditory Distraction.

ERIC Educational Resources Information Center

Thackray, Richard I.; And Others

The ability to resist distraction is an important requirement for air traffic controllers. The study examined the relationship between performance on the Stroop color-word interference test (a suggested measure of distraction susceptibility) and impairment under auditory distraction on a task requiring the subject to generate random sequences of…

The Independent Effects of Phonotactic Probability and Neighbourhood Density on Lexical Acquisition by Preschool Children

ERIC Educational Resources Information Center

Storkel, Holly L.; Lee, Su-Yeon

2011-01-01

The goal of this research was to disentangle effects of phonotactic probability, the likelihood of occurrence of a sound sequence, and neighbourhood density, the number of phonologically similar words, in lexical acquisition. Two-word learning experiments were conducted with 4-year-old children. Experiment 1 manipulated phonotactic probability…

Statistical Segmentation of Tone Sequences Activates the Left Inferior Frontal Cortex: A Near-Infrared Spectroscopy Study

ERIC Educational Resources Information Center

Abla, Dilshat; Okanoya, Kazuo

2008-01-01

Word segmentation, that is, discovering the boundaries between words that are embedded in a continuous speech stream, is an important faculty for language learners; humans solve this task partly by calculating transitional probabilities between sounds. Behavioral and ERP studies suggest that detection of sequential probabilities (statistical…

A Visual Literacy Approach to Developmental and Remedial Reading.

ERIC Educational Resources Information Center

Barley, Steven D.

Photography, films, and other visual materials offer a different approach to teaching reading. For example, photographs may be arranged in sequences analogous to the ways words form sentences and sentences for stories. If, as is possible, children respond first to pictures and later to words, training they receive in visual literacy may help them…

Attention Is Required for Knowledge-Based Sequential Grouping: Insights from the Integration of Syllables into Words.

PubMed

Ding, Nai; Pan, Xunyi; Luo, Cheng; Su, Naifei; Zhang, Wen; Zhang, Jianfeng

2018-01-31

How the brain groups sequential sensory events into chunks is a fundamental question in cognitive neuroscience. This study investigates whether top-down attention or specific tasks are required for the brain to apply lexical knowledge to group syllables into words. Neural responses tracking the syllabic and word rhythms of a rhythmic speech sequence were concurrently monitored using electroencephalography (EEG). The participants performed different tasks, attending to either the rhythmic speech sequence or a distractor, which was another speech stream or a nonlinguistic auditory/visual stimulus. Attention to speech, but not a lexical-meaning-related task, was required for reliable neural tracking of words, even when the distractor was a nonlinguistic stimulus presented cross-modally. Neural tracking of syllables, however, was reliably observed in all tested conditions. These results strongly suggest that neural encoding of individual auditory events (i.e., syllables) is automatic, while knowledge-based construction of temporal chunks (i.e., words) crucially relies on top-down attention. SIGNIFICANCE STATEMENT Why we cannot understand speech when not paying attention is an old question in psychology and cognitive neuroscience. Speech processing is a complex process that involves multiple stages, e.g., hearing and analyzing the speech sound, recognizing words, and combining words into phrases and sentences. The current study investigates which speech-processing stage is blocked when we do not listen carefully. We show that the brain can reliably encode syllables, basic units of speech sounds, even when we do not pay attention. Nevertheless, when distracted, the brain cannot group syllables into multisyllabic words, which are basic units for speech meaning. Therefore, the process of converting speech sound into meaning crucially relies on attention. Copyright © 2018 the authors 0270-6474/18/381178-11$15.00/0.

Dysgraphia in Patients with Primary Lateral Sclerosis: A Speech-Based Rehearsal Deficit?

PubMed Central

Zago, S.; Poletti, B.; Corbo, M.; Adobbati, L.; Silani, V.

2008-01-01

The present study aims to demonstrate that errors when writing are more common than expected in patients affected by primary lateral sclerosis (PLS) with severe dysarthria or complete mutism, independent of spasticity. Sixteen patients meeting Pringle’s et al. [34] criteria for PLS underwent standard neuropsychological tasks and evaluation of writing. We assessed writing abilities in spelling through dictation in which a set of words, non-words and short phrases were presented orally and by composing words using a set of preformed letters. Finally, a written copying task was performed with the same words. Relative to controls, PLS patients made a greater number of spelling errors in all writing conditions, but not in copy task. The error types included: omissions, transpositions, insertions and letter substitutions. These were equally distributed on the writing task and the composition of words with a set of preformed letters. This pattern of performance is consistent with a spelling impairment. The results are consistent with the concept that written production is critically dependent on the subvocal articulatory mechanism of rehearsal, perhaps at the level of retaining the sequence of graphemes in a graphemic buffer. In PLS patients a disturbance in rehearsal opportunity may affect the correct sequencing/assembly of an orthographic representation in the written process. PMID:19096141

Word segmentation in phonemically identical and prosodically different sequences using cochlear implants: A case study.

PubMed

Basirat, Anahita

2017-01-01

Cochlear implant (CI) users frequently achieve good speech understanding based on phoneme and word recognition. However, there is a significant variability between CI users in processing prosody. The aim of this study was to examine the abilities of an excellent CI user to segment continuous speech using intonational cues. A post-lingually deafened adult CI user and 22 normal hearing (NH) subjects segmented phonemically identical and prosodically different sequences in French such as 'l'affiche' (the poster) versus 'la fiche' (the sheet), both [lafiʃ]. All participants also completed a minimal pair discrimination task. Stimuli were presented in auditory-only and audiovisual presentation modalities. The performance of the CI user in the minimal pair discrimination task was 97% in the auditory-only and 100% in the audiovisual condition. In the segmentation task, contrary to the NH participants, the performance of the CI user did not differ from the chance level. Visual speech did not improve word segmentation. This result suggests that word segmentation based on intonational cues is challenging when using CIs even when phoneme/word recognition is very well rehabilitated. This finding points to the importance of the assessment of CI users' skills in prosody processing and the need for specific interventions focusing on this aspect of speech communication.

Rehearsal in immediate serial recall.

PubMed

Tan, Lydia; Ward, Geoff

2008-06-01

We report for the first time overt rehearsal data in immediate serial recall (ISR) undertaken at three presentation rates (1, 2.5, and 5 sec/word). Two groups of participants saw lists of six words for ISR and were required either to engage in overt rehearsal or to remain silent after reading aloud the word list during its presentation. Typical ISR serial position effects were obtained for both groups, and recall increased with slower rates. When participants rehearsed, they tended to do so in a cumulative forward order up to Serial Position 4, after which the amount of rehearsal decreased substantially. There were similarities between rehearsal and recall data: Both broke down toward the end of longer sequences, and there were strong positive correlations between the maximum sequence of participants' rehearsals and their ISR performance. We interpret these data as suggesting that similar mechanisms underpin both rehearsal and recall in ISR.

Ideational apraxia in Parkinson disease.

PubMed

Qureshi, Mohammad; Williamson, John B; Heilman, Kenneth M

2011-09-01

: The objective of the study was to determine whether ideational apraxia (IA), a loss of ability to plan the sequence of actions needed to achieve a goal, is associated with Parkinson disease (PD). : The frontal lobes play an important role in planning and sequencing, and many patients with PD have frontal lobe dysfunction. : Ten right-handed patients with PD and 10 right-handed neurologically and psychiatrically healthy people participated. To assess for IA, participants were given sets of pictures that showed the steps in completing a task, but the steps were shown out of order. The participants were required to point to the pictures in the correct sequence to complete each task. The participants also performed a control task of sequencing randomly arranged printed single words to create a sentence that described an accompanying picture. : The patients with PD performed more poorly than the controls on the action-sequencing tasks (P<0.05). Errors were predominantly in sequencing rather than repetition or omission, indicating that the poor performance was not caused by perseveration. There were no group differences in the task of sequencing words to make a sentence. : These results indicate that patients with PD do have IA, an action-sequence planning deficit. Further research is needed to better understand mechanisms, ecological implications, and potential treatments.

PhyloTreePruner: A Phylogenetic Tree-Based Approach for Selection of Orthologous Sequences for Phylogenomics.

PubMed

Kocot, Kevin M; Citarella, Mathew R; Moroz, Leonid L; Halanych, Kenneth M

2013-01-01

Molecular phylogenetics relies on accurate identification of orthologous sequences among the taxa of interest. Most orthology inference programs available for use in phylogenomics rely on small sets of pre-defined orthologs from model organisms or phenetic approaches such as all-versus-all sequence comparisons followed by Markov graph-based clustering. Such approaches have high sensitivity but may erroneously include paralogous sequences. We developed PhyloTreePruner, a software utility that uses a phylogenetic approach to refine orthology inferences made using phenetic methods. PhyloTreePruner checks single-gene trees for evidence of paralogy and generates a new alignment for each group containing only sequences inferred to be orthologs. Importantly, PhyloTreePruner takes into account support values on the tree and avoids unnecessarily deleting sequences in cases where a weakly supported tree topology incorrectly indicates paralogy. A test of PhyloTreePruner on a dataset generated from 11 completely sequenced arthropod genomes identified 2,027 orthologous groups sampled for all taxa. Phylogenetic analysis of the concatenated supermatrix yielded a generally well-supported topology that was consistent with the current understanding of arthropod phylogeny. PhyloTreePruner is freely available from http://sourceforge.net/projects/phylotreepruner/.

Processing Stages Underlying Word Recognition in the Anteroventral Temporal Lobe

PubMed Central

Halgren, Eric; Wang, Chunmao; Schomer, Donald L.; Knake, Susanne; Marinkovic, Ksenija; Wu, Julian; Ulbert, Istvan

2006-01-01

The anteroventral temporal lobe integrates visual, lexical, semantic and mnestic aspects of word-processing, through its reciprocal connections with the ventral visual stream, language areas, and the hippocampal formation. We used linear microelectrode arrays to probe population synaptic currents and neuronal firing in different cortical layers of the anteroventral temporal lobe, during semantic judgments with implicit priming, and overt word recognition. Since different extrinsic and associative inputs preferentially target different cortical layers, this method can help reveal the sequence and nature of local processing stages at a higher resolution than was previously possible. The initial response in inferotemporal and perirhinal cortices is a brief current sink beginning at ~120ms, and peaking at ~170ms. Localization of this initial sink to middle layers suggests that it represents feedforward input from lower visual areas, and simultaneously increased firing implies that it represents excitatory synaptic currents. Until ~800ms, the main focus of transmembrane current sinks alternates between middle and superficial layers, with the superficial focus becoming increasingly dominant after ~550ms. Since superficial layers are the target of local and feedback associative inputs, this suggests an alternation in predominant synaptic input between feedforward and feedback modes. Word repetition does not affect the initial perirhinal and inferotemporal middle layer sink, but does decrease later activity. Entorhinal activity begins later (~200ms), with greater apparent excitatory postsynaptic currents and multiunit activity in neocortically-projecting than hippocampal-projecting layers. In contrast to perirhinal and entorhinal responses, entorhinal responses are larger to repeated words during memory retrieval. These results identify a sequence of physiological activation, beginning with a sharp activation from lower level visual areas carrying specific information to middle layers. This is followed by feedback and associative interactions involving upper cortical layers, which are abbreviated to repeated words. Following bottom-up and associative stages, top-down recollective processes may be driven by entorhinal cortex. Word processing involves a systematic sequence of fast feedforward information transfer from visual areas to anteroventral temporal cortex, followed by prolonged interactions of this feedforward information with local associations, and feedback mnestic information from the medial temporal lobe. PMID:16488158

Sequence-structure mapping errors in the PDB: OB-fold domains

PubMed Central

Venclovas, Česlovas; Ginalski, Krzysztof; Kang, Chulhee

2004-01-01

The Protein Data Bank (PDB) is the single most important repository of structural data for proteins and other biologically relevant molecules. Therefore, it is critically important to keep the PDB data, as much as possible, error-free. In this study, we have analyzed PDB crystal structures possessing oligonucleotide/oligosaccharide binding (OB)-fold, one of the highly populated folds, for the presence of sequence-structure mapping errors. Using energy-based structure quality assessment coupled with sequence analyses, we have found that there are at least five OB-structures in the PDB that have regions where sequences have been incorrectly mapped onto the structure. We have demonstrated that the combination of these computation techniques is effective not only in detecting sequence-structure mapping errors, but also in providing guidance to correct them. Namely, we have used results of computational analysis to direct a revision of X-ray data for one of the PDB entries containing a fairly inconspicuous sequence-structure mapping error. The revised structure has been deposited with the PDB. We suggest use of computational energy assessment and sequence analysis techniques to facilitate structure determination when homologs having known structure are available to use as a reference. Such computational analysis may be useful in either guiding the sequence-structure assignment process or verifying the sequence mapping within poorly defined regions. PMID:15133161

Nanopore Kinetic Proofreading of DNA Sequences

NASA Astrophysics Data System (ADS)

Ling, Xinsheng Sean

The concept of DNA sequencing using the time dependence of the nanopore ionic current was proposed in 1996 by Kasianowicz, Brandin, Branton, and Deamer (KBBD). The KBBD concept has generated tremendous amount interests in recent decade. In this talk, I will review the current understanding of the DNA ``translocation'' dynamics and how it can be described by Schrodinger's 1915 paper on first-passage-time distribution function. Schrodinger's distribution function can be used to give a rigorous criterion for achieving nanopore DNA sequencing which turns out to be identical to that of gel electrophoresis used by Sanger in the first-generation Sanger method. A nanopore DNA sequencing technology also requires discrimination of bases with high accuracies. I will describe a solid-state nanopore sandwich structure that can function as a proofreading device capable of discriminating between correct and incorrect hybridization probes with an accuracy rivaling that of high-fidelity DNA polymerases. The latest results from Nanjing will be presented. This work is supported by China 1000-Talent Program at Southeast University, Nanjing, China.

Using machine learning for sequence-level automated MRI protocol selection in neuroradiology.

PubMed

Brown, Andrew D; Marotta, Thomas R

2018-05-01

Incorrect imaging protocol selection can lead to important clinical findings being missed, contributing to both wasted health care resources and patient harm. We present a machine learning method for analyzing the unstructured text of clinical indications and patient demographics from magnetic resonance imaging (MRI) orders to automatically protocol MRI procedures at the sequence level. We compared 3 machine learning models - support vector machine, gradient boosting machine, and random forest - to a baseline model that predicted the most common protocol for all observations in our test set. The gradient boosting machine model significantly outperformed the baseline and demonstrated the best performance of the 3 models in terms of accuracy (95%), precision (86%), recall (80%), and Hamming loss (0.0487). This demonstrates the feasibility of automating sequence selection by applying machine learning to MRI orders. Automated sequence selection has important safety, quality, and financial implications and may facilitate improvements in the quality and safety of medical imaging service delivery.

The effect of response modality on immediate serial recall in dementia of the Alzheimer type.

PubMed

Macé, Anne-Laure; Ergis, Anne-Marie; Caza, Nicole

2012-09-01

Contrary to traditional models of verbal short-term memory (STM), psycholinguistic accounts assume that temporary retention of verbal materials is an intrinsic property of word processing. Therefore, memory performance will depend on the nature of the STM tasks, which vary according to the linguistic representations they engage. The aim of this study was to explore the effect of response modality on verbal STM performance in individuals with dementia of the Alzheimer Type (DAT), and its relationship with the patients' word-processing deficits. Twenty individuals with mild DAT and 20 controls were tested on an immediate serial recall (ISR) task using the same items across two response modalities (oral and picture pointing) and completed a detailed language assessment. When scoring of ISR performance was based on item memory regardless of item order, a response modality effect was found for all participants, indicating that they recalled more items with picture pointing than with oral response. However, this effect was less marked in patients than in controls, resulting in an interaction. Interestingly, when recall of both item and order was considered, results indicated similar performance between response modalities in controls, whereas performance was worse for pointing than for oral response in patients. Picture-naming performance was also reduced in patients relative to controls. However, in the word-to-picture matching task, a similar pattern of responses was found between groups for incorrectly named pictures of the same items. The finding of a response modality effect in item memory for all participants is compatible with the assumption that semantic influences are greater in picture pointing than in oral response, as predicted by psycholinguistic models. Furthermore, patients' performance was modulated by their word-processing deficits, showing a reduced advantage relative to controls. Overall, the response modality effect observed in this study for item memory suggests that verbal STM performance is intrinsically linked with word processing capacities in both healthy controls and individuals with mild DAT, supporting psycholinguistic models of STM.

Neural Correlates of Encoding Within- and Across-Domain Inter-Item Associations

PubMed Central

Park, Heekyeong; Rugg, Michael D.

2012-01-01

The neural correlates of the encoding of associations between pairs of words, pairs of pictures, and word-picture pairs were compared. The aims were to determine first, whether the neural correlates of associative encoding vary according to study material and second, whether encoding of across- versus within-material item pairs is associated with dissociable patterns of hippocampal and perirhinal activity, as predicted by the ‘domain dichotomy’ hypothesis of medial temporal lobe (MTL) function. While undergoing fMRI scanning, subjects (n = 24) were presented with the three classes of study pairs, judging which of the denoted objects fit into the other. Outside of the scanner, subjects then undertook an associative recognition task, discriminating between intact study pairs, rearranged pairs comprising items that had been presented on different study trials, and unstudied item pairs. The neural correlates of successful associative encoding – subsequent associative memory effects – were operationalized as the difference in activity between study pairs correctly judged intact versus pairs incorrectly judged rearranged on the subsequent memory test. Pair type-independent subsequent memory effects were evident in the left inferior frontal gyrus (IFG) and the hippocampus. Picture-picture pairs elicited material-selective effects in regions of fusiform cortex that were also activated to a greater extent on picture trials than word trials, while word-word pairs elicited material-selective subsequent memory effects in left lateral temporal cortex. Contrary to the domain-dichotomy hypothesis, neither hippocampal nor perirhinal subsequent memory effects differed depending on whether they were elicited by within- versus across-material study pairs. It is proposed that the left IFG plays a domain-general role in associative encoding, that associative encoding can also be facilitated by enhanced processing in material-selective cortical regions, and that the hippocampus and perirhinal cortex contribute equally to the formation of inter-item associations regardless of whether the items belong to the same or to different processing domains. PMID:21254802

Filtering large-scale event collections using a combination of supervised and unsupervised learning for event trigger classification.

PubMed

Mehryary, Farrokh; Kaewphan, Suwisa; Hakala, Kai; Ginter, Filip

2016-01-01

Biomedical event extraction is one of the key tasks in biomedical text mining, supporting various applications such as database curation and hypothesis generation. Several systems, some of which have been applied at a large scale, have been introduced to solve this task. Past studies have shown that the identification of the phrases describing biological processes, also known as trigger detection, is a crucial part of event extraction, and notable overall performance gains can be obtained by solely focusing on this sub-task. In this paper we propose a novel approach for filtering falsely identified triggers from large-scale event databases, thus improving the quality of knowledge extraction. Our method relies on state-of-the-art word embeddings, event statistics gathered from the whole biomedical literature, and both supervised and unsupervised machine learning techniques. We focus on EVEX, an event database covering the whole PubMed and PubMed Central Open Access literature containing more than 40 million extracted events. The top most frequent EVEX trigger words are hierarchically clustered, and the resulting cluster tree is pruned to identify words that can never act as triggers regardless of their context. For rarely occurring trigger words we introduce a supervised approach trained on the combination of trigger word classification produced by the unsupervised clustering method and manual annotation. The method is evaluated on the official test set of BioNLP Shared Task on Event Extraction. The evaluation shows that the method can be used to improve the performance of the state-of-the-art event extraction systems. This successful effort also translates into removing 1,338,075 of potentially incorrect events from EVEX, thus greatly improving the quality of the data. The method is not solely bound to the EVEX resource and can be thus used to improve the quality of any event extraction system or database. The data and source code for this work are available at: http://bionlp-www.utu.fi/trigger-clustering/.

5W1H Information Extraction with CNN-Bidirectional LSTM

NASA Astrophysics Data System (ADS)

Nurdin, A.; Maulidevi, N. U.

2018-03-01

In this work, information about who, did what, when, where, why, and how on Indonesian news articles were extracted by combining Convolutional Neural Network and Bidirectional Long Short-Term Memory. Convolutional Neural Network can learn semantically meaningful representations of sentences. Bidirectional LSTM can analyze the relations among words in the sequence. We also use word embedding word2vec for word representation. By combining these algorithms, we obtained F-measure 0.808. Our experiments show that CNN-BLSTM outperforms other shallow methods, namely IBk, C4.5, and Naïve Bayes with the F-measure 0.655, 0.645, and 0.595, respectively.

Identification and correction of abnormal, incomplete and mispredicted proteins in public databases.

PubMed

Nagy, Alinda; Hegyi, Hédi; Farkas, Krisztina; Tordai, Hedvig; Kozma, Evelin; Bányai, László; Patthy, László

2008-08-27

Despite significant improvements in computational annotation of genomes, sequences of abnormal, incomplete or incorrectly predicted genes and proteins remain abundant in public databases. Since the majority of incomplete, abnormal or mispredicted entries are not annotated as such, these errors seriously affect the reliability of these databases. Here we describe the MisPred approach that may provide an efficient means for the quality control of databases. The current version of the MisPred approach uses five distinct routines for identifying abnormal, incomplete or mispredicted entries based on the principle that a sequence is likely to be incorrect if some of its features conflict with our current knowledge about protein-coding genes and proteins: (i) conflict between the predicted subcellular localization of proteins and the absence of the corresponding sequence signals; (ii) presence of extracellular and cytoplasmic domains and the absence of transmembrane segments; (iii) co-occurrence of extracellular and nuclear domains; (iv) violation of domain integrity; (v) chimeras encoded by two or more genes located on different chromosomes. Analyses of predicted EnsEMBL protein sequences of nine deuterostome (Homo sapiens, Mus musculus, Rattus norvegicus, Monodelphis domestica, Gallus gallus, Xenopus tropicalis, Fugu rubripes, Danio rerio and Ciona intestinalis) and two protostome species (Caenorhabditis elegans and Drosophila melanogaster) have revealed that the absence of expected signal peptides and violation of domain integrity account for the majority of mispredictions. Analyses of sequences predicted by NCBI's GNOMON annotation pipeline show that the rates of mispredictions are comparable to those of EnsEMBL. Interestingly, even the manually curated UniProtKB/Swiss-Prot dataset is contaminated with mispredicted or abnormal proteins, although to a much lesser extent than UniProtKB/TrEMBL or the EnsEMBL or GNOMON-predicted entries. MisPred works efficiently in identifying errors in predictions generated by the most reliable gene prediction tools such as the EnsEMBL and NCBI's GNOMON pipelines and also guides the correction of errors. We suggest that application of the MisPred approach will significantly improve the quality of gene predictions and the associated databases.

Remembering Plurals: Unit of Coding and Form of Coding during Serial Recall.

ERIC Educational Resources Information Center

Van Der Molen, Hugo; Morton, John

1979-01-01

Adult females recalled lists of six words, including some plural nouns, presented visually in sequence. A frequent error was to detach the plural from its root. This supports a morpheme-based as opposed to a unitary word code. Evidence for a primarily phonological coding of the plural morpheme was obtained. (Author/RD)

Using Explicit C-R-A Instruction to Teach Fraction Word Problem Solving to Low-Performing Asian English Learners

ERIC Educational Resources Information Center

Kim, Sun A.; Wang, Peishi; Michaels, Craig A.

2015-01-01

This article investigates the effects of fraction word problem-solving instruction involving explicit teaching of the concrete-representational-abstract sequence with culturally relevant teaching examples for 3 low-performing Asian immigrant English learners who spoke a language other than English at home. We used a multiple probe design across…

Structuring Word Problems for Diagnostic Teaching: Helping Teachers Meet the Needs of Children with Mild Disabilities.

ERIC Educational Resources Information Center

Parmar, Rene S.; Cawley, John F.

1994-01-01

Matrix organization can be used to construct math word problems for children with mild disabilities. Matrix organization specifies the characteristics of problems, such as problem theme or setting, operations, level of computation complexity, reading vocabulary level, and need for classification. A sample scope and sequence and 16 sample word…

Teaching Formulaic Sequences: The Same as or Different from Teaching Single Words?

ERIC Educational Resources Information Center

Alali, Fatima A.; Schmitt, Norbert

2012-01-01

Formulaic language is an important component of discourse and needs to be addressed in teaching pedagogy. Unfortunately, there has been little research into the most effective ways of teaching formulaic language. In this study, Kuwaiti students were taught words and idioms using the same teaching methodologies, and their learning was measured. The…

A Formal Criterion for Identifying Lexical Phrases: Implication from a Classroom Experiment

ERIC Educational Resources Information Center

Yu, Xia

2009-01-01

This study investigates whether two different means of learning the word sequence "despite the fact (that)" lead to differential outcomes of the acquisition of the grammatical structure imbedded in the word string which is, due to L1 transfer, especially problematic for Chinese learners of English. The participants of the study were randomly…

Congenital Amusia: A Short-Term Memory Deficit for Non-Verbal, but Not Verbal Sounds

ERIC Educational Resources Information Center

Tillmann, Barbara; Schulze, Katrin; Foxton, Jessica M.

2009-01-01

Congenital amusia refers to a lifelong disorder of music processing and is linked to pitch-processing deficits. The present study investigated congenital amusics' short-term memory for tones, musical timbres and words. Sequences of five events (tones, timbres or words) were presented in pairs and participants had to indicate whether the sequences…

Determinants of Multiple Semantic Priming: A Meta-Analysis and Spike Frequency Adaptive Model of a Cortical Network

ERIC Educational Resources Information Center

Lavigne, Frederic; Dumercy, Laurent; Darmon, Nelly

2011-01-01

Recall and language comprehension while processing sequences of words involves multiple semantic priming between several related and/or unrelated words. Accounting for multiple and interacting priming effects in terms of underlying neuronal structure and dynamics is a challenge for current models of semantic priming. Further elaboration of current…

Statistical Clustering and the Contents of the Infant Vocabulary

ERIC Educational Resources Information Center

Swingley, Daniel

2005-01-01

Infants parse speech into word-sized units according to biases that develop in the first year. One bias, present before the age of 7 months, is to cluster syllables that tend to co-occur. The present computational research demonstrates that this statistical clustering bias could lead to the extraction of speech sequences that are actual words,…

Similarity as an organising principle in short-term memory.

PubMed

LeCompte, D C; Watkins, M J

1993-03-01

The role of stimulus similarity as an organising principle in short-term memory was explored in a series of seven experiments. Each experiment involved the presentation of a short sequence of items that were drawn from two distinct physical classes and arranged such that item class changed after every second item. Following presentation, one item was re-presented as a probe for the 'target' item that had directly followed it in the sequence. Memory for the sequence was considered organised by class if probability of recall was higher when the probe and target were from the same class than when they were from different classes. Such organisation was found when one class was auditory and the other was visual (spoken vs. written words, and sounds vs. pictures). It was also found when both classes were auditory (words spoken in a male voice vs. words spoken in a female voice) and when both classes were visual (digits shown in one location vs. digits shown in another). It is concluded that short-term memory can be organised on the basis of sensory modality and on the basis of certain features within both the auditory and visual modalities.

Learning of grammar-like visual sequences by adults with and without language-learning disabilities.

PubMed

Aguilar, Jessica M; Plante, Elena

2014-08-01

Two studies examined learning of grammar-like visual sequences to determine whether a general deficit in statistical learning characterizes this population. Furthermore, we tested the hypothesis that difficulty in sustaining attention during the learning task might account for differences in statistical learning. In Study 1, adults with normal language (NL) or language-learning disability (LLD) were familiarized with the visual artificial grammar and then tested using items that conformed or deviated from the grammar. In Study 2, a 2nd sample of adults with NL and LLD were presented auditory word pairs with weak semantic associations (e.g., groom + clean) along with the visual learning task. Participants were instructed to attend to visual sequences and to ignore the auditory stimuli. Incidental encoding of these words would indicate reduced attention to the primary task. In Studies 1 and 2, both groups demonstrated learning and generalization of the artificial grammar. In Study 2, neither the NL nor the LLD group appeared to encode the words presented during the learning phase. The results argue against a general deficit in statistical learning for individuals with LLD and demonstrate that both NL and LLD learners can ignore extraneous auditory stimuli during visual learning.

Improvement of training set structure in fusion data cleaning using Time-Domain Global Similarity method

NASA Astrophysics Data System (ADS)

Liu, J.; Lan, T.; Qin, H.

2017-10-01

Traditional data cleaning identifies dirty data by classifying original data sequences, which is a class-imbalanced problem since the proportion of incorrect data is much less than the proportion of correct ones for most diagnostic systems in Magnetic Confinement Fusion (MCF) devices. When using machine learning algorithms to classify diagnostic data based on class-imbalanced training set, most classifiers are biased towards the major class and show very poor classification rates on the minor class. By transforming the direct classification problem about original data sequences into a classification problem about the physical similarity between data sequences, the class-balanced effect of Time-Domain Global Similarity (TDGS) method on training set structure is investigated in this paper. Meanwhile, the impact of improved training set structure on data cleaning performance of TDGS method is demonstrated with an application example in EAST POlarimetry-INTerferometry (POINT) system.

A note on chaotic unimodal maps and applications.

PubMed

Zhou, C T; He, X T; Yu, M Y; Chew, L Y; Wang, X G

2006-09-01

Based on the word-lift technique of symbolic dynamics of one-dimensional unimodal maps, we investigate the relation between chaotic kneading sequences and linear maximum-length shift-register sequences. Theoretical and numerical evidence that the set of the maximum-length shift-register sequences is a subset of the set of the universal sequence of one-dimensional chaotic unimodal maps is given. By stabilizing unstable periodic orbits on superstable periodic orbits, we also develop techniques to control the generation of long binary sequences.

Phonotactic Probability Effects in Children Who Stutter

PubMed Central

Anderson, Julie D.; Byrd, Courtney T.

2008-01-01

Purpose The purpose of this study was to examine the influence of phonotactic probability, the frequency of different sound segments and segment sequences, on the overall fluency with which words are produced by preschool children who stutter (CWS), as well as to determine whether it has an effect on the type of stuttered disfluency produced. Method A 500+ word language sample was obtained from 19 CWS. Each stuttered word was randomly paired with a fluently produced word that closely matched it in grammatical class, word length, familiarity, word and neighborhood frequency, and neighborhood density. Phonotactic probability values were obtained for the stuttered and fluent words from an online database. Results Phonotactic probability did not have a significant influence on the overall susceptibility of words to stuttering, but it did impact the type of stuttered disfluency produced. In specific, single-syllable word repetitions were significantly lower in phonotactic probability than fluently produced words, as well as part-word repetitions and sound prolongations. Conclusions In general, the differential impact of phonotactic probability on the type of stuttering-like disfluency produced by young CWS provides some support for the notion that different disfluency types may originate in the disruption of different levels of processing. PMID:18658056

Line and word bisection in right-brain-damaged patients with left spatial neglect.

PubMed

Veronelli, Laura; Vallar, Giuseppe; Marinelli, Chiara V; Primativo, Silvia; Arduino, Lisa S

2014-01-01

Right-brain-damaged patients with left unilateral spatial neglect typically set the mid-point of horizontal lines to the right of the objective center. By contrast, healthy participants exhibit a reversed bias (pseudoneglect). The same effect has been described also when bisecting orthographic strings. In particular, for this latter kind of stimulus, some recent studies have shown that visuo-perceptual characteristics, like stimulus length, may contribute to both the magnitude and the direction bias of the bisection performance (Arduino et al. in Neuropsychologia 48:2140-2146, 2010). Furthermore, word stress was shown to modulate reading performances in both healthy participants, and patients with left spatial neglect and neglect dyslexia (Cubelli and Beschin in Brain Lang 95:319-326, 2005; Rusconi et al. in Neuropsychology 18:135-140, 2004). In Experiment I, 22 right-brain-damaged patients (11 with left visuo-spatial neglect) and 11 matched neurologically unimpaired control participants were asked to set the subjective mid-point of word letter strings, and of lines of comparable length. Most patients exhibited an overall disproportionate rightward bias, sensitive to stimulus length, and similar for words and lines. Importantly, in individual patients, biases differed according to stimulus type (words vs. lines), indicating that at least partly different mechanisms may be involved. In Experiment II, the putative effects on the bisection bias of ortho-phonological information (i.e., word stress endings), arising from the non-neglected right hand side of the stimulus were investigated. The orthographic cue induced a rightward shift of the perceived mid-point in both patients and controls, with short words stressed on the antepenultimate final sequence inducing a smaller rightward deviation with respect to short words stressed on the penultimate final sequence. In conclusion, partly different mechanisms, including both visuo-spatial and lexical factors, may support line and word bisection performance of right-brain-damaged patients with left spatial neglect, and healthy participants.

Pre-Attentive Auditory Processing of Lexicality

ERIC Educational Resources Information Center

Jacobsen, Thomas; Horvath, Janos; Schroger, Erich; Lattner, Sonja; Widmann, Andreas; Winkler, Istvan

2004-01-01

The effects of lexicality on auditory change detection based on auditory sensory memory representations were investigated by presenting oddball sequences of repeatedly presented stimuli, while participants ignored the auditory stimuli. In a cross-linguistic study of Hungarian and German participants, stimulus sequences were composed of words that…

Surface errors without semantic impairment in acquired dyslexia: a voxel-based lesion–symptom mapping study

PubMed Central

Pillay, Sara B.; Humphries, Colin J.; Gross, William L.; Graves, William W.; Book, Diane S.

2016-01-01

Patients with surface dyslexia have disproportionate difficulty pronouncing irregularly spelled words (e.g. pint), suggesting impaired use of lexical-semantic information to mediate phonological retrieval. Patients with this deficit also make characteristic ‘regularization’ errors, in which an irregularly spelled word is mispronounced by incorrect application of regular spelling-sound correspondences (e.g. reading plaid as ‘played’), indicating over-reliance on sublexical grapheme–phoneme correspondences. We examined the neuroanatomical correlates of this specific error type in 45 patients with left hemisphere chronic stroke. Voxel-based lesion–symptom mapping showed a strong positive relationship between the rate of regularization errors and damage to the posterior half of the left middle temporal gyrus. Semantic deficits on tests of single-word comprehension were generally mild, and these deficits were not correlated with the rate of regularization errors. Furthermore, the deep occipital-temporal white matter locus associated with these mild semantic deficits was distinct from the lesion site associated with regularization errors. Thus, in contrast to patients with surface dyslexia and semantic impairment from anterior temporal lobe degeneration, surface errors in our patients were not related to a semantic deficit. We propose that these patients have an inability to link intact semantic representations with phonological representations. The data provide novel evidence for a post-semantic mechanism mediating the production of surface errors, and suggest that the posterior middle temporal gyrus may compute an intermediate representation linking semantics with phonology. PMID:26966139

Emergence of good conduct, scaling and zipf laws in human behavioral sequences in an online world.

PubMed

Thurner, Stefan; Szell, Michael; Sinatra, Roberta

2012-01-01

We study behavioral action sequences of players in a massive multiplayer online game. In their virtual life players use eight basic actions which allow them to interact with each other. These actions are communication, trade, establishing or breaking friendships and enmities, attack, and punishment. We measure the probabilities for these actions conditional on previous taken and received actions and find a dramatic increase of negative behavior immediately after receiving negative actions. Similarly, positive behavior is intensified by receiving positive actions. We observe a tendency towards antipersistence in communication sequences. Classifying actions as positive (good) and negative (bad) allows us to define binary 'world lines' of lives of individuals. Positive and negative actions are persistent and occur in clusters, indicated by large scaling exponents α ~ 0.87 of the mean square displacement of the world lines. For all eight action types we find strong signs for high levels of repetitiveness, especially for negative actions. We partition behavioral sequences into segments of length n (behavioral 'words' and 'motifs') and study their statistical properties. We find two approximate power laws in the word ranking distribution, one with an exponent of κ ~ -1 for the ranks up to 100, and another with a lower exponent for higher ranks. The Shannon n-tuple redundancy yields large values and increases in terms of word length, further underscoring the non-trivial statistical properties of behavioral sequences. On the collective, societal level the timeseries of particular actions per day can be understood by a simple mean-reverting log-normal model.

Effects of Noise on Speech Recognition and Listening Effort in Children With Normal Hearing and Children With Mild Bilateral or Unilateral Hearing Loss.

PubMed

Lewis, Dawna; Schmid, Kendra; O'Leary, Samantha; Spalding, Jody; Heinrichs-Graham, Elizabeth; High, Robin

2016-10-01

This study examined the effects of stimulus type and hearing status on speech recognition and listening effort in children with normal hearing (NH) and children with mild bilateral hearing loss (MBHL) or unilateral hearing loss (UHL). Children (5-12 years of age) with NH (Experiment 1) and children (8-12 years of age) with MBHL, UHL, or NH (Experiment 2) performed consonant identification and word and sentence recognition in background noise. Percentage correct performance and verbal response time (VRT) were assessed (onset time, total duration). In general, speech recognition improved as signal-to-noise ratio (SNR) increased both for children with NH and children with MBHL or UHL. The groups did not differ on measures of VRT. Onset times were longer for incorrect than for correct responses. For correct responses only, there was a general increase in VRT with decreasing SNR. Findings indicate poorer sentence recognition in children with NH and MBHL or UHL as SNR decreases. VRT results suggest that greater effort was expended when processing stimuli that were incorrectly identified. Increasing VRT with decreasing SNR for correct responses also supports greater effort in poorer acoustic conditions. The absence of significant hearing status differences suggests that VRT was not differentially affected by MBHL, UHL, or NH for children in this study.

Facilitatory Effects of Multi-Word Units in Lexical Processing and Word Learning: A Computational Investigation

PubMed Central

Grimm, Robert; Cassani, Giovanni; Gillis, Steven; Daelemans, Walter

2017-01-01

Previous studies have suggested that children and adults form cognitive representations of co-occurring word sequences. We propose (1) that the formation of such multi-word unit (MWU) representations precedes and facilitates the formation of single-word representations in children and thus benefits word learning, and (2) that MWU representations facilitate adult word recognition and thus benefit lexical processing. Using a modified version of an existing computational model (McCauley and Christiansen, 2014), we extract MWUs from a corpus of child-directed speech (CDS) and a corpus of conversations among adults. We then correlate the number of MWUs within which each word appears with (1) age of first production and (2) adult reaction times on a word recognition task. In doing so, we take care to control for the effect of word frequency, as frequent words will naturally tend to occur in many MWUs. We also compare results to a baseline model which randomly groups words into sequences—and find that MWUs have a unique facilitatory effect on both response variables, suggesting that they benefit word learning in children and word recognition in adults. The effect is strongest on age of first production, implying that MWUs are comparatively more important for word learning than for adult lexical processing. We discuss possible underlying mechanisms and formulate testable predictions. PMID:28450842

Retrieving handwriting by combining word spotting and manifold ranking

NASA Astrophysics Data System (ADS)

Peña Saldarriaga, Sebastián; Morin, Emmanuel; Viard-Gaudin, Christian

2012-01-01

Online handwritten data, produced with Tablet PCs or digital pens, consists in a sequence of points (x, y). As the amount of data available in this form increases, algorithms for retrieval of online data are needed. Word spotting is a common approach used for the retrieval of handwriting. However, from an information retrieval (IR) perspective, word spotting is a primitive keyword based matching and retrieval strategy. We propose a framework for handwriting retrieval where an arbitrary word spotting method is used, and then a manifold ranking algorithm is applied on the initial retrieval scores. Experimental results on a database of more than 2,000 handwritten newswires show that our method can improve the performances of a state-of-the-art word spotting system by more than 10%.

Spatiotemporal Dynamics of Bilingual Word Processing

PubMed Central

Leonard, Matthew K.; Brown, Timothy T.; Travis, Katherine E.; Gharapetian, Lusineh; Hagler, Donald J.; Dale, Anders M.; Elman, Jeffrey L.; Halgren, Eric

2009-01-01

Studies with monolingual adults have identified successive stages occurring in different brain regions for processing single written words. We combined magnetoencephalography and magnetic resonance imaging to compare these stages between the first (L1) and second (L2) languages in bilingual adults. L1 words in a size judgment task evoked a typical left-lateralized sequence of activity first in ventral occipitotemporal cortex (VOT: previously associated with visual word-form encoding), and then ventral frontotemporal regions (associated with lexico-semantic processing). Compared to L1, words in L2 activated right VOT more strongly from ~135 ms; this activation was attenuated when words became highly familiar with repetition. At ~400ms, L2 responses were generally later than L1, more bilateral, and included the same lateral occipitotemporal areas as were activated by pictures. We propose that acquiring a language involves the recruitment of right hemisphere and posterior visual areas that are not necessary once fluency is achieved. PMID:20004256

Cross-Curricular Sequence: An Approach for Teaching Business Communication.

ERIC Educational Resources Information Center

Clarke, Lillian W.; Franklin, Carl M.

1985-01-01

The Cross-Curricular Sequencing (CCS) approach to teaching business communications is explored. Its uses in word processing, principles of management, and business policy courses are discussed. Techniques for integrating materials from these courses into business communication classes are described. The implications of CCS for business…

High resolution identity testing of inactivated poliovirus vaccines.

PubMed

Mee, Edward T; Minor, Philip D; Martin, Javier

2015-07-09

Definitive identification of poliovirus strains in vaccines is essential for quality control, particularly where multiple wild-type and Sabin strains are produced in the same facility. Sequence-based identification provides the ultimate in identity testing and would offer several advantages over serological methods. We employed random RT-PCR and high throughput sequencing to recover full-length genome sequences from monovalent and trivalent poliovirus vaccine products at various stages of the manufacturing process. All expected strains were detected in previously characterised products and the method permitted identification of strains comprising as little as 0.1% of sequence reads. Highly similar Mahoney and Sabin 1 strains were readily discriminated on the basis of specific variant positions. Analysis of a product known to contain incorrect strains demonstrated that the method correctly identified the contaminants. Random RT-PCR and shotgun sequencing provided high resolution identification of vaccine components. In addition to the recovery of full-length genome sequences, the method could also be easily adapted to the characterisation of minor variant frequencies and distinction of closely related products on the basis of distinguishing consensus and low frequency polymorphisms. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

Historic origin of the "Arcade of Struthers".

PubMed

De Jesus, Ramon; Dellon, A Lee

2003-05-01

John Struthers wrote in 1848 and 1854 about sites of compression of the median nerve from axilla to elbow. He is best known for describing the rare median nerve entrapment by a ligament from a supracondylar process extending to the medial humeral epicondyle. In 1973, observation of ulnar nerve entrapment associated with a midshaft humeral fracture and subsequent anatomic dissections led to the creation of the term "Arcade of Struthers." Review of Struthers' original writings fails to identify either the use of word "arcade" or description of ulnar nerve compression. Review of published anatomic dissections identifies variations in the origin of the medial head of the triceps, not described by Struthers, that may cause failure of an anterior transposition of the ulnar nerve. Continued use of the term "Arcade of Struthers" is historically incorrect.

Assessing Feedback in a Mobile Videogame.

PubMed

Brand, Leah; Beltran, Alicia; Hughes, Sheryl; O'Connor, Teresia; Baranowski, Janice; Nicklas, Theresa; Chen, Tzu-An; Dadabhoy, Hafza R; Diep, Cassandra S; Buday, Richard; Baranowski, Tom

2016-06-01

Player feedback is an important part of serious games, although there is no consensus regarding its delivery or optimal content. "Mommio" is a serious game designed to help mothers motivate their preschoolers to eat vegetables. The purpose of this study was to assess optimal format and content of player feedback for use in "Mommio." The current study posed 36 potential "Mommio" gameplay feedback statements to 20 mothers using a Web survey and interview. Mothers were asked about the meaning and helpfulness of each feedback statement. Several themes emerged upon thematic analysis, including identifying an effective alternative in the case of corrective feedback, avoiding vague wording, using succinct and correct grammar, avoiding provocation of guilt, and clearly identifying why players' game choice was correct or incorrect. Guidelines are proposed for future feedback statements.

Disentangling fast and slow attentional influences of negative and taboo spoken words in the emotional Stroop paradigm.

PubMed

Bertels, Julie; Kolinsky, Régine

2016-09-01

Although the influence of the emotional content of stimuli on attention has been considered as occurring within trial, recent studies revealed that the presentation of such stimuli would also involve a slow component. The aim of the present study was to investigate fast and slow effects of negative (Exp. 1) and taboo (Exp. 2) spoken words. For this purpose, we used an auditory variant of the emotional Stroop paradigm in which each emotional word was followed by a sequence of neutral words. Replicating results from our previous study, we observed slow but no fast effects of negative and taboo words, which we interpreted as reflecting difficulties to disengage attention from their emotional dimension. Interestingly, while the presentation of a negative word only delayed the processing of the immediately subsequent neutral word, slow effects of taboo words were long-lasting. Nevertheless, such attentional effects were only observed when the emotional words were presented in the first block of trials, suggesting that once participants develop strategies to perform the task, attention-grabbing effects of emotional words disappear. Hence, far from being automatic, the occurrence of these effects would depend on participants' attentional set.

Reading through a Noisy Channel: Why There's Nothing Special about the Perception of Orthography

ERIC Educational Resources Information Center

Norris, Dennis; Kinoshita, Sachiko

2012-01-01

The goal of research on how letter identity and order are perceived during reading is often characterized as one of "cracking the orthographic code." Here, we suggest that there is no orthographic code to crack: Words are perceived and represented as sequences of letters, just as in a dictionary. Indeed, words are perceived and represented in…

Teaching Problem Solving to Students Receiving Tiered Interventions Using the Concrete-Representational-Abstract Sequence and Schema-Based Instruction

ERIC Educational Resources Information Center

Flores, Margaret M.; Hinton, Vanessa M.; Burton, Megan E.

2016-01-01

Mathematical word problems are the most common form of mathematics problem solving implemented in K-12 schools. Identifying key words is a frequent strategy taught in classrooms in which students struggle with problem solving and show low success rates in mathematics. Researchers show that using the concrete-representational-abstract (CRA)…

Paced Reading in Semantic Dementia: Word Knowledge Contributes to Phoneme Binding in Rapid Speech Production

ERIC Educational Resources Information Center

Jefferies, Elizabeth; Grogan, John; Mapelli, Cristina; Isella, Valeria

2012-01-01

Patients with semantic dementia (SD) show deficits in phoneme binding in immediate serial recall: when attempting to reproduce a sequence of words that they no longer fully understand, they show frequent migrations of phonemes between items (e.g., cap, frog recalled as "frap, cog"). This suggests that verbal short-term memory emerges directly from…

Syntactic Universals and the Acquisition of Spanish Word Order by Quechua-Speaking Children.

ERIC Educational Resources Information Center

Lujan, Marta; Liliana Minaya

Because of the syntactic differences between Spanish and Quechua, Quechua-speaking children must make major word order adjustments to learn the Peruvian Spanish taught in school. This study investigates whether the order or time sequence in which these changes are adopted reflects any general constraint, or is in any way predicted by a theory of…

Noun or Verb? Adult Readers' Sensitivity to Spelling Cues to Grammatical Category in Word Endings

ERIC Educational Resources Information Center

Kemp, Nenagh; Nilsson, Jodi; Arciuli, Joanne

2009-01-01

The spelling of many disyllabic English word endings holds cues to their grammatical category, beyond obvious inflectional endings such as "-ing" for verbs. For example, some letter sequences are clearly associated with nouns (e.g., "-oon") and others with verbs (e.g., "-erge"). This study extended recent research by Arciuli and Cupples (2006),…

Textual emotion recognition for enhancing enterprise computing

NASA Astrophysics Data System (ADS)

Quan, Changqin; Ren, Fuji

2016-05-01

The growing interest in affective computing (AC) brings a lot of valuable research topics that can meet different application demands in enterprise systems. The present study explores a sub area of AC techniques - textual emotion recognition for enhancing enterprise computing. Multi-label emotion recognition in text is able to provide a more comprehensive understanding of emotions than single label emotion recognition. A representation of 'emotion state in text' is proposed to encompass the multidimensional emotions in text. It ensures the description in a formal way of the configurations of basic emotions as well as of the relations between them. Our method allows recognition of the emotions for the words bear indirect emotions, emotion ambiguity and multiple emotions. We further investigate the effect of word order for emotional expression by comparing the performances of bag-of-words model and sequence model for multi-label sentence emotion recognition. The experiments show that the classification results under sequence model are better than under bag-of-words model. And homogeneous Markov model showed promising results of multi-label sentence emotion recognition. This emotion recognition system is able to provide a convenient way to acquire valuable emotion information and to improve enterprise competitive ability in many aspects.

Individual differences in language and working memory affect children's speech recognition in noise.

PubMed

McCreery, Ryan W; Spratford, Meredith; Kirby, Benjamin; Brennan, Marc

2017-05-01

We examined how cognitive and linguistic skills affect speech recognition in noise for children with normal hearing. Children with better working memory and language abilities were expected to have better speech recognition in noise than peers with poorer skills in these domains. As part of a prospective, cross-sectional study, children with normal hearing completed speech recognition in noise for three types of stimuli: (1) monosyllabic words, (2) syntactically correct but semantically anomalous sentences and (3) semantically and syntactically anomalous word sequences. Measures of vocabulary, syntax and working memory were used to predict individual differences in speech recognition in noise. Ninety-six children with normal hearing, who were between 5 and 12 years of age. Higher working memory was associated with better speech recognition in noise for all three stimulus types. Higher vocabulary abilities were associated with better recognition in noise for sentences and word sequences, but not for words. Working memory and language both influence children's speech recognition in noise, but the relationships vary across types of stimuli. These findings suggest that clinical assessment of speech recognition is likely to reflect underlying cognitive and linguistic abilities, in addition to a child's auditory skills, consistent with the Ease of Language Understanding model.

Segmenting words from natural speech: subsegmental variation in segmental cues.

PubMed

Rytting, C Anton; Brew, Chris; Fosler-Lussier, Eric

2010-06-01

Most computational models of word segmentation are trained and tested on transcripts of speech, rather than the speech itself, and assume that speech is converted into a sequence of symbols prior to word segmentation. We present a way of representing speech corpora that avoids this assumption, and preserves acoustic variation present in speech. We use this new representation to re-evaluate a key computational model of word segmentation. One finding is that high levels of phonetic variability degrade the model's performance. While robustness to phonetic variability may be intrinsically valuable, this finding needs to be complemented by parallel studies of the actual abilities of children to segment phonetically variable speech.

Electrophysiological Correlates of Emotional Source Memory in High-Trait-Anxiety Individuals

PubMed Central

Cui, Lixia; Shi, Guangyuan; He, Fan; Zhang, Qin; Oei, Tian P. S.; Guo, Chunyan

2016-01-01

The interaction between recognition memory and emotion has become a research hotspot in recent years. Dual process theory posits that familiarity and recollection are two separate processes contributing to recognition memory, but further experimental evidence is needed. The present study explored the emotional context effects on successful and unsuccessful source retrieval amongst 15 high-trait-anxiety college students by using event-related potentials (ERPs) measurement. During study, a happy, fearful, or neutral face picture first was displayed, then a Chinese word was superimposed centrally on the picture and subjects were asked to remember the word and the corresponding type of picture. During the test participants were instructed to press one of four buttons to indicate whether the displayed word was an old or new word. And then, for the old word, indicate whether it had been shown with a fearful, happy, or neutral face during the study. ERPs were generally more positive for remembered words than for new words and the ERP difference was termed as an old/new effect. It was found that, for successful source retrieval (it meant both the item and the source were remembered accurately) between 500 and 700 ms (corresponding to a late positive component, LPC), there were significant old/new effects in all contexts. However, for unsuccessful source retrieval (it meant the correct recognition of old items matched with incorrect source attribution), there were no significant old/new effects in happy and neutral contexts, though significant old/new effects were observed in the fearful context. Between 700 and 1200 ms (corresponding to a late slow wave, LSW), there were significant old/new effects for successful source retrieval in happy and neutral contexts. However, in the fearful context, the old/new effects were reversed, ERPs were more negative for successful source retrieval compared to correct rejections. Moreover, there were significant emotion effects for successful source retrieval at this time window. Further analysis showed ERPs of old items were more negative in fearful context than in neutral context. The results showed that early unsuccessful fearful source retrieval processes (related to familiarity) were enhanced, but late successful fearful source retrieval processes during source retrieval monitoring (related to recollection) were weakened. This provided preliminary evidence for the dual processing theory. PMID:27462288

Accurate protein structure modeling using sparse NMR data and homologous structure information.

PubMed

Thompson, James M; Sgourakis, Nikolaos G; Liu, Gaohua; Rossi, Paolo; Tang, Yuefeng; Mills, Jeffrey L; Szyperski, Thomas; Montelione, Gaetano T; Baker, David

2012-06-19

While information from homologous structures plays a central role in X-ray structure determination by molecular replacement, such information is rarely used in NMR structure determination because it can be incorrect, both locally and globally, when evolutionary relationships are inferred incorrectly or there has been considerable evolutionary structural divergence. Here we describe a method that allows robust modeling of protein structures of up to 225 residues by combining (1)H(N), (13)C, and (15)N backbone and (13)Cβ chemical shift data, distance restraints derived from homologous structures, and a physically realistic all-atom energy function. Accurate models are distinguished from inaccurate models generated using incorrect sequence alignments by requiring that (i) the all-atom energies of models generated using the restraints are lower than models generated in unrestrained calculations and (ii) the low-energy structures converge to within 2.0 Å backbone rmsd over 75% of the protein. Benchmark calculations on known structures and blind targets show that the method can accurately model protein structures, even with very remote homology information, to a backbone rmsd of 1.2-1.9 Å relative to the conventional determined NMR ensembles and of 0.9-1.6 Å relative to X-ray structures for well-defined regions of the protein structures. This approach facilitates the accurate modeling of protein structures using backbone chemical shift data without need for side-chain resonance assignments and extensive analysis of NOESY cross-peak assignments.

Working Memory Capacity and Stroop Interference: Global versus Local Indices of Executive Control

ERIC Educational Resources Information Center

Meier, Matt E.; Kane, Michael J.

2013-01-01

Two experiments examined the relations among working memory capacity (WMC), congruency-sequence effects, proportion-congruency effects, and the color-word Stroop effect to test whether congruency-sequence effects might inform theoretical claims regarding WMC's prediction of Stroop interference. In Experiment 1, subjects completed either a…

Derivational Suffixes as Cues to Stress Position in Reading Greek

ERIC Educational Resources Information Center

Grimani, Aikaterini; Protopapas, Athanassios

2017-01-01

Background: In languages with lexical stress, reading aloud must include stress assignment. Stress information sources across languages include word-final letter sequences. Here, we examine whether such sequences account for stress assignment in Greek and whether this is attributable to absolute rules involving accenting morphemes or to…

Stimulus-Dependent Flexibility in Non-Human Auditory Pitch Processing

ERIC Educational Resources Information Center

Bregman, Micah R.; Patel, Aniruddh D.; Gentner, Timothy Q.

2012-01-01

Songbirds and humans share many parallels in vocal learning and auditory sequence processing. However, the two groups differ notably in their abilities to recognize acoustic sequences shifted in absolute pitch (pitch height). Whereas humans maintain accurate recognition of words or melodies over large pitch height changes, songbirds are…

Trellises and Trellis-Based Decoding Algorithms for Linear Block Codes. Part 3; The Map and Related Decoding Algirithms

NASA Technical Reports Server (NTRS)

Lin, Shu; Fossorier, Marc

1998-01-01

In a coded communication system with equiprobable signaling, MLD minimizes the word error probability and delivers the most likely codeword associated with the corresponding received sequence. This decoding has two drawbacks. First, minimization of the word error probability is not equivalent to minimization of the bit error probability. Therefore, MLD becomes suboptimum with respect to the bit error probability. Second, MLD delivers a hard-decision estimate of the received sequence, so that information is lost between the input and output of the ML decoder. This information is important in coded schemes where the decoded sequence is further processed, such as concatenated coding schemes, multi-stage and iterative decoding schemes. In this chapter, we first present a decoding algorithm which both minimizes bit error probability, and provides the corresponding soft information at the output of the decoder. This algorithm is referred to as the MAP (maximum aposteriori probability) decoding algorithm.

A novel algorithm for validating peptide identification from a shotgun proteomics search engine.

PubMed

Jian, Ling; Niu, Xinnan; Xia, Zhonghang; Samir, Parimal; Sumanasekera, Chiranthani; Mu, Zheng; Jennings, Jennifer L; Hoek, Kristen L; Allos, Tara; Howard, Leigh M; Edwards, Kathryn M; Weil, P Anthony; Link, Andrew J

2013-03-01

Liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) has revolutionized the proteomics analysis of complexes, cells, and tissues. In a typical proteomic analysis, the tandem mass spectra from a LC-MS/MS experiment are assigned to a peptide by a search engine that compares the experimental MS/MS peptide data to theoretical peptide sequences in a protein database. The peptide spectra matches are then used to infer a list of identified proteins in the original sample. However, the search engines often fail to distinguish between correct and incorrect peptides assignments. In this study, we designed and implemented a novel algorithm called De-Noise to reduce the number of incorrect peptide matches and maximize the number of correct peptides at a fixed false discovery rate using a minimal number of scoring outputs from the SEQUEST search engine. The novel algorithm uses a three-step process: data cleaning, data refining through a SVM-based decision function, and a final data refining step based on proteolytic peptide patterns. Using proteomics data generated on different types of mass spectrometers, we optimized the De-Noise algorithm on the basis of the resolution and mass accuracy of the mass spectrometer employed in the LC-MS/MS experiment. Our results demonstrate De-Noise improves peptide identification compared to other methods used to process the peptide sequence matches assigned by SEQUEST. Because De-Noise uses a limited number of scoring attributes, it can be easily implemented with other search engines.

The dependence of frequency distributions on multiple meanings of words, codes and signs

NASA Astrophysics Data System (ADS)

Yan, Xiaoyong; Minnhagen, Petter

2018-01-01

The dependence of the frequency distributions due to multiple meanings of words in a text is investigated by deleting letters. By coding the words with fewer letters the number of meanings per coded word increases. This increase is measured and used as an input in a predictive theory. For a text written in English, the word-frequency distribution is broad and fat-tailed, whereas if the words are only represented by their first letter the distribution becomes exponential. Both distribution are well predicted by the theory, as is the whole sequence obtained by consecutively representing the words by the first L = 6 , 5 , 4 , 3 , 2 , 1 letters. Comparisons of texts written by Chinese characters and the same texts written by letter-codes are made and the similarity of the corresponding frequency-distributions are interpreted as a consequence of the multiple meanings of Chinese characters. This further implies that the difference of the shape for word-frequencies for an English text written by letters and a Chinese text written by Chinese characters is due to the coding and not to the language per se.

Mining protein loops using a structural alphabet and statistical exceptionality

PubMed Central

2010-01-01

Background Protein loops encompass 50% of protein residues in available three-dimensional structures. These regions are often involved in protein functions, e.g. binding site, catalytic pocket... However, the description of protein loops with conventional tools is an uneasy task. Regular secondary structures, helices and strands, have been widely studied whereas loops, because they are highly variable in terms of sequence and structure, are difficult to analyze. Due to data sparsity, long loops have rarely been systematically studied. Results We developed a simple and accurate method that allows the description and analysis of the structures of short and long loops using structural motifs without restriction on loop length. This method is based on the structural alphabet HMM-SA. HMM-SA allows the simplification of a three-dimensional protein structure into a one-dimensional string of states, where each state is a four-residue prototype fragment, called structural letter. The difficult task of the structural grouping of huge data sets is thus easily accomplished by handling structural letter strings as in conventional protein sequence analysis. We systematically extracted all seven-residue fragments in a bank of 93000 protein loops and grouped them according to the structural-letter sequence, named structural word. This approach permits a systematic analysis of loops of all sizes since we consider the structural motifs of seven residues rather than complete loops. We focused the analysis on highly recurrent words of loops (observed more than 30 times). Our study reveals that 73% of loop-lengths are covered by only 3310 highly recurrent structural words out of 28274 observed words). These structural words have low structural variability (mean RMSd of 0.85 Å). As expected, half of these motifs display a flanking-region preference but interestingly, two thirds are shared by short (less than 12 residues) and long loops. Moreover, half of recurrent motifs exhibit a significant level of amino-acid conservation with at least four significant positions and 87% of long loops contain at least one such word. We complement our analysis with the detection of statistically over-represented patterns of structural letters as in conventional DNA sequence analysis. About 30% (930) of structural words are over-represented, and cover about 40% of loop lengths. Interestingly, these words exhibit lower structural variability and higher sequential specificity, suggesting structural or functional constraints. Conclusions We developed a method to systematically decompose and study protein loops using recurrent structural motifs. This method is based on the structural alphabet HMM-SA and not on structural alignment and geometrical parameters. We extracted meaningful structural motifs that are found in both short and long loops. To our knowledge, it is the first time that pattern mining helps to increase the signal-to-noise ratio in protein loops. This finding helps to better describe protein loops and might permit to decrease the complexity of long-loop analysis. Detailed results are available at http://www.mti.univ-paris-diderot.fr/publication/supplementary/2009/ACCLoop/. PMID:20132552

Mining protein loops using a structural alphabet and statistical exceptionality.

PubMed

Regad, Leslie; Martin, Juliette; Nuel, Gregory; Camproux, Anne-Claude

2010-02-04

Protein loops encompass 50% of protein residues in available three-dimensional structures. These regions are often involved in protein functions, e.g. binding site, catalytic pocket... However, the description of protein loops with conventional tools is an uneasy task. Regular secondary structures, helices and strands, have been widely studied whereas loops, because they are highly variable in terms of sequence and structure, are difficult to analyze. Due to data sparsity, long loops have rarely been systematically studied. We developed a simple and accurate method that allows the description and analysis of the structures of short and long loops using structural motifs without restriction on loop length. This method is based on the structural alphabet HMM-SA. HMM-SA allows the simplification of a three-dimensional protein structure into a one-dimensional string of states, where each state is a four-residue prototype fragment, called structural letter. The difficult task of the structural grouping of huge data sets is thus easily accomplished by handling structural letter strings as in conventional protein sequence analysis. We systematically extracted all seven-residue fragments in a bank of 93000 protein loops and grouped them according to the structural-letter sequence, named structural word. This approach permits a systematic analysis of loops of all sizes since we consider the structural motifs of seven residues rather than complete loops. We focused the analysis on highly recurrent words of loops (observed more than 30 times). Our study reveals that 73% of loop-lengths are covered by only 3310 highly recurrent structural words out of 28274 observed words). These structural words have low structural variability (mean RMSd of 0.85 A). As expected, half of these motifs display a flanking-region preference but interestingly, two thirds are shared by short (less than 12 residues) and long loops. Moreover, half of recurrent motifs exhibit a significant level of amino-acid conservation with at least four significant positions and 87% of long loops contain at least one such word. We complement our analysis with the detection of statistically over-represented patterns of structural letters as in conventional DNA sequence analysis. About 30% (930) of structural words are over-represented, and cover about 40% of loop lengths. Interestingly, these words exhibit lower structural variability and higher sequential specificity, suggesting structural or functional constraints. We developed a method to systematically decompose and study protein loops using recurrent structural motifs. This method is based on the structural alphabet HMM-SA and not on structural alignment and geometrical parameters. We extracted meaningful structural motifs that are found in both short and long loops. To our knowledge, it is the first time that pattern mining helps to increase the signal-to-noise ratio in protein loops. This finding helps to better describe protein loops and might permit to decrease the complexity of long-loop analysis. Detailed results are available at http://www.mti.univ-paris-diderot.fr/publication/supplementary/2009/ACCLoop/.

Analysis of quality raw data of second generation sequencers with Quality Assessment Software.

PubMed

Ramos, Rommel Tj; Carneiro, Adriana R; Baumbach, Jan; Azevedo, Vasco; Schneider, Maria Pc; Silva, Artur

2011-04-18

Second generation technologies have advantages over Sanger; however, they have resulted in new challenges for the genome construction process, especially because of the small size of the reads, despite the high degree of coverage. Independent of the program chosen for the construction process, DNA sequences are superimposed, based on identity, to extend the reads, generating contigs; mismatches indicate a lack of homology and are not included. This process improves our confidence in the sequences that are generated. We developed Quality Assessment Software, with which one can review graphs showing the distribution of quality values from the sequencing reads. This software allow us to adopt more stringent quality standards for sequence data, based on quality-graph analysis and estimated coverage after applying the quality filter, providing acceptable sequence coverage for genome construction from short reads. Quality filtering is a fundamental step in the process of constructing genomes, as it reduces the frequency of incorrect alignments that are caused by measuring errors, which can occur during the construction process due to the size of the reads, provoking misassemblies. Application of quality filters to sequence data, using the software Quality Assessment, along with graphing analyses, provided greater precision in the definition of cutoff parameters, which increased the accuracy of genome construction.

Integrating alignment-based and alignment-free sequence similarity measures for biological sequence classification.

PubMed

Borozan, Ivan; Watt, Stuart; Ferretti, Vincent

2015-05-01

Alignment-based sequence similarity searches, while accurate for some type of sequences, can produce incorrect results when used on more divergent but functionally related sequences that have undergone the sequence rearrangements observed in many bacterial and viral genomes. Here, we propose a classification model that exploits the complementary nature of alignment-based and alignment-free similarity measures with the aim to improve the accuracy with which DNA and protein sequences are characterized. Our model classifies sequences using a combined sequence similarity score calculated by adaptively weighting the contribution of different sequence similarity measures. Weights are determined independently for each sequence in the test set and reflect the discriminatory ability of individual similarity measures in the training set. Because the similarity between some sequences is determined more accurately with one type of measure rather than another, our classifier allows different sets of weights to be associated with different sequences. Using five different similarity measures, we show that our model significantly improves the classification accuracy over the current composition- and alignment-based models, when predicting the taxonomic lineage for both short viral sequence fragments and complete viral sequences. We also show that our model can be used effectively for the classification of reads from a real metagenome dataset as well as protein sequences. All the datasets and the code used in this study are freely available at https://collaborators.oicr.on.ca/vferretti/borozan_csss/csss.html. ivan.borozan@gmail.com Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.

Integrating alignment-based and alignment-free sequence similarity measures for biological sequence classification

PubMed Central

Borozan, Ivan; Watt, Stuart; Ferretti, Vincent

2015-01-01

Motivation: Alignment-based sequence similarity searches, while accurate for some type of sequences, can produce incorrect results when used on more divergent but functionally related sequences that have undergone the sequence rearrangements observed in many bacterial and viral genomes. Here, we propose a classification model that exploits the complementary nature of alignment-based and alignment-free similarity measures with the aim to improve the accuracy with which DNA and protein sequences are characterized. Results: Our model classifies sequences using a combined sequence similarity score calculated by adaptively weighting the contribution of different sequence similarity measures. Weights are determined independently for each sequence in the test set and reflect the discriminatory ability of individual similarity measures in the training set. Because the similarity between some sequences is determined more accurately with one type of measure rather than another, our classifier allows different sets of weights to be associated with different sequences. Using five different similarity measures, we show that our model significantly improves the classification accuracy over the current composition- and alignment-based models, when predicting the taxonomic lineage for both short viral sequence fragments and complete viral sequences. We also show that our model can be used effectively for the classification of reads from a real metagenome dataset as well as protein sequences. Availability and implementation: All the datasets and the code used in this study are freely available at https://collaborators.oicr.on.ca/vferretti/borozan_csss/csss.html. Contact: ivan.borozan@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25573913

Phylogenetic tree construction using trinucleotide usage profile (TUP).

PubMed

Chen, Si; Deng, Lih-Yuan; Bowman, Dale; Shiau, Jyh-Jen Horng; Wong, Tit-Yee; Madahian, Behrouz; Lu, Henry Horng-Shing

2016-10-06

It has been a challenging task to build a genome-wide phylogenetic tree for a large group of species containing a large number of genes with long nucleotides sequences. The most popular method, called feature frequency profile (FFP-k), finds the frequency distribution for all words of certain length k over the whole genome sequence using (overlapping) windows of the same length. For a satisfactory result, the recommended word length (k) ranges from 6 to 15 and it may not be a multiple of 3 (codon length). The total number of possible words needed for FFP-k can range from 4 6 =4096 to 4 15 . We propose a simple improvement over the popular FFP method using only a typical word length of 3. A new method, called Trinucleotide Usage Profile (TUP), is proposed based only on the (relative) frequency distribution using non-overlapping windows of length 3. The total number of possible words needed for TUP is 4 3 =64, which is much less than the total count for the recommended optimal "resolution" for FFP. To build a phylogenetic tree, we propose first representing each of the species by a TUP vector and then using an appropriate distance measure between pairs of the TUP vectors for the tree construction. In particular, we propose summarizing a DNA sequence by a matrix of three rows corresponding to three reading frames, recording the frequency distribution of the non-overlapping words of length 3 in each of the reading frame. We also provide a numerical measure for comparing trees constructed with various methods. Compared to the FFP method, our empirical study showed that the proposed TUP method is more capable of building phylogenetic trees with a stronger biological support. We further provide some justifications on this from the information theory viewpoint. Unlike the FFP method, the TUP method takes the advantage that the starting of the first reading frame is (usually) known. Without this information, the FFP method could only rely on the frequency distribution of overlapping words, which is the average (or mixture) of the frequency distributions of three possible reading frames. Consequently, we show (from the entropy viewpoint) that the FFP procedure could dilute important gene information and therefore provides less accurate classification.

Background Adjusted Alignment-Free Dissimilarity Measures Improve the Detection of Horizontal Gene Transfer.

PubMed

Tang, Kujin; Lu, Yang Young; Sun, Fengzhu

2018-01-01

Horizontal gene transfer (HGT) plays an important role in the evolution of microbial organisms including bacteria. Alignment-free methods based on single genome compositional information have been used to detect HGT. Currently, Manhattan and Euclidean distances based on tetranucleotide frequencies are the most commonly used alignment-free dissimilarity measures to detect HGT. By testing on simulated bacterial sequences and real data sets with known horizontal transferred genomic regions, we found that more advanced alignment-free dissimilarity measures such as CVTree and [Formula: see text] that take into account the background Markov sequences can solve HGT detection problems with significantly improved performance. We also studied the influence of different factors such as evolutionary distance between host and donor sequences, size of sliding window, and host genome composition on the performances of alignment-free methods to detect HGT. Our study showed that alignment-free methods can predict HGT accurately when host and donor genomes are in different order levels. Among all methods, CVTree with word length of 3, [Formula: see text] with word length 3, Markov order 1 and [Formula: see text] with word length 4, Markov order 1 outperform others in terms of their highest F 1 -score and their robustness under the influence of different factors.

Reactivity to stress and the cognitive components of math disability in grade 1 children.

PubMed

MacKinnon McQuarrie, Maureen A; Siegel, Linda S; Perry, Nancy E; Weinberg, Joanne

2014-01-01

This study investigated the relationship among working memory, processing speed, math performance, and reactivity to stress in 83 Grade 1 children. Specifically, 39 children with math disability (MD) were compared to 44 children who are typically achieving (TA) in mathematics. It is the first study to use a physiological index of stress (salivary cortisol levels) to measure children's reactivity while completing tasks that assess the core components of MD: working memory for numbers, working memory for words, digits backward, letter number sequence, digit span forward, processing speed for numbers and words, block rotation, and math tasks. Grade 1 children with MD obtained significantly lower scores on the letter number sequence and quantitative concepts tasks. Higher levels of reactivity significantly predicted poorer performance on the working memory for numbers, working memory for words, and quantitative concepts tasks for Grade 1 children, regardless of math ability. Grade 1 children with MD and higher reactivity had significantly lower scores on the letter number sequence task than the children with MD and low reactivity. The findings suggest that high reactivity impairs performance in working memory and math tasks in Grade 1 children, and young children with high reactivity may benefit from interventions aimed at lowering anxiety in stressful situations, which may improve learning. © Hammill Institute on Disabilities 2012.

Reactivity to Stress and the Cognitive Components of Math Disability in Grade 1 Children

PubMed Central

MacKinnon McQuarrie, Maureen A.; Siegel, Linda S.; Perry, Nancy E.; Weinberg, Joanne

2016-01-01

This study investigated the relationship among working memory, processing speed, math performance, and reactivity to stress in 83 Grade 1 children. Specifically, 39 children with math disability (MD) were compared to 44 children who are typically achieving (TA) in mathematics. It is the first study to use a physiological index of stress (salivary cortisol levels) to measure children’s reactivity while completing tasks that assess the core components of MD: working memory for numbers, working memory for words, digits backward, letter number sequence, digit span forward, processing speed for numbers and words, block rotation, and math tasks. Grade 1 children with MD obtained significantly lower scores on the letter number sequence and quantitative concepts tasks. Higher levels of reactivity significantly predicted poorer performance on the working memory for numbers, working memory for words, and quantitative concepts tasks for Grade 1 children, regardless of math ability. Grade 1 children with MD and higher reactivity had significantly lower scores on the letter number sequence task than the children with MD and low reactivity. The findings suggest that high reactivity impairs performance in working memory and math tasks in Grade 1 children, and young children with high reactivity may benefit from interventions aimed at lowering anxiety in stressful situations, which may improve learning. PMID:23124381

Schizophrenia patients demonstrate a dissociation on declarative and non-declarative memory tests.

PubMed

Perry, W; Light, G A; Davis, H; Braff, D L

2000-12-15

Declarative memory refers to the recall and recognition of factual information. In contrast, non-declarative memory entails a facilitation of memory based on prior exposure and is typically assessed with priming and perceptual-motor sequencing tasks. In this study, schizophrenia patients were compared to normal comparison subjects on two computerized memory tasks: the Word-stem Priming Test (n=30) and the Pattern Sequence Learning Test (n=20). Word-stem Priming includes recall, recognition (declarative) and priming (non-declarative) components of memory. The schizophrenia patients demonstrated an impaired performance on recall of words with relative improvement during the recognition portion of the test. Furthermore, they performed normally on the priming portion of the test. Thus, on tests of declarative memory, the patients had retrieval deficits with intact performance on the non-declarative memory component. The Pattern Sequence Learning Test utilizes a serial reaction time paradigm to assess non-declarative memory. The schizophrenia patients' serial reaction time was significantly slower than that of comparison subjects. However, the patients' rate of acquisition was not different from the normal comparison group. The data suggest that patients with schizophrenia process more slowly than normal, but have an intact non-declarative memory. The schizophrenia patients' dissociation on declarative vs. non-declarative memory tests is discussed in terms of possible underlying structural impairment.

First learned words are not forgotten: Age-of-acquisition effects in the tip-of-the-tongue experience.

PubMed

Navarrete, Eduardo; Pastore, Massimiliano; Valentini, Rosa; Peressotti, Francesca

2015-10-01

A large body of evidence indicates that the age at which a word is acquired predicts the time required to retrieve that word during speech production. Here we explored whether age of acquisition also predicts the experience of being unable to produce a known word at a particular moment. Italian speakers named a sequence of pictures in Experiment 1 or retrieved a word as a response to a definition in Experiment 2. In both experiments, the participants were instructed to indicate when they were in a tip-of-the-tongue (TOT) state. Generalized mixed-effects models performed on the TOT and correct responses revealed that word frequency and age of acquisition predicted the TOT states. Specifically, low-frequency words elicited more TOTs than did high-frequency words, replicating previous findings. In addition, late-acquired words elicited more TOTs than did early-acquired words. Further analyses revealed that the age of acquisition was a better predictor of TOTs than was word frequency. The effects of age of acquisition were similar with subjective and objective measures of age of acquisition, and persisted when several psycholinguistic variables were taken into consideration as predictors in the generalized mixed-effects models. We explained these results in terms of weaker semantic-to-phonological connections in the speech production system for late-acquired words.

Morphable Word Clouds for Time-Varying Text Data Visualization.

PubMed

Chi, Ming-Te; Lin, Shih-Syun; Chen, Shiang-Yi; Lin, Chao-Hung; Lee, Tong-Yee

2015-12-01

A word cloud is a visual representation of a collection of text documents that uses various font sizes, colors, and spaces to arrange and depict significant words. The majority of previous studies on time-varying word clouds focuses on layout optimization and temporal trend visualization. However, they do not fully consider the spatial shapes and temporal motions of word clouds, which are important factors for attracting people's attention and are also important cues for human visual systems in capturing information from time-varying text data. This paper presents a novel method that uses rigid body dynamics to arrange multi-temporal word-tags in a specific shape sequence under various constraints. Each word-tag is regarded as a rigid body in dynamics. With the aid of geometric, aesthetic, and temporal coherence constraints, the proposed method can generate a temporally morphable word cloud that not only arranges word-tags in their corresponding shapes but also smoothly transforms the shapes of word clouds over time, thus yielding a pleasing time-varying visualization. Using the proposed frame-by-frame and morphable word clouds, people can observe the overall story of a time-varying text data from the shape transition, and people can also observe the details from the word clouds in frames. Experimental results on various data demonstrate the feasibility and flexibility of the proposed method in morphable word cloud generation. In addition, an application that uses the proposed word clouds in a simulated exhibition demonstrates the usefulness of the proposed method.

Pitch enhancement facilitates word learning across visual contexts

PubMed Central

Filippi, Piera; Gingras, Bruno; Fitch, W. Tecumseh

2014-01-01

This study investigates word-learning using a new experimental paradigm that integrates three processes: (a) extracting a word out of a continuous sound sequence, (b) inferring its referential meanings in context, (c) mapping the segmented word onto its broader intended referent, such as other objects of the same semantic category, and to novel utterances. Previous work has examined the role of statistical learning and/or of prosody in each of these processes separately. Here, we combine these strands of investigation into a single experimental approach, in which participants viewed a photograph belonging to one of three semantic categories while hearing a complex, five-word utterance containing a target word. Six between-subjects conditions were tested with 20 adult participants each. In condition 1, the only cue to word-meaning mapping was the co-occurrence of word and referents. This statistical cue was present in all conditions. In condition 2, the target word was sounded at a higher pitch. In condition 3, random words were sounded at a higher pitch, creating an inconsistent cue. In condition 4, the duration of the target word was lengthened. In conditions 5 and 6, an extraneous acoustic cue and a visual cue were associated with the target word, respectively. Performance in this word-learning task was significantly higher than that observed with simple co-occurrence only when pitch prominence consistently marked the target word. We discuss implications for the pragmatic value of pitch marking as well as the relevance of our findings to language acquisition and language evolution. PMID:25566144

Effects of Word Width and Word Length on Optimal Character Size for Reading of Horizontally Scrolling Japanese Words

PubMed Central

Teramoto, Wataru; Nakazaki, Takuyuki; Sekiyama, Kaoru; Mori, Shuji

2016-01-01

The present study investigated, whether word width and length affect the optimal character size for reading of horizontally scrolling Japanese words, using reading speed as a measure. In Experiment 1, three Japanese words, each consisting of four Hiragana characters, sequentially scrolled on a display screen from right to left. Participants, all Japanese native speakers, were instructed to read the words aloud as accurately as possible, irrespective of their order within the sequence. To quantitatively measure their reading performance, we used rapid serial visual presentation paradigm, where the scrolling rate was increased until the participants began to make mistakes. Thus, the highest scrolling rate at which the participants’ performance exceeded 88.9% correct rate was calculated for each character size (0.3°, 0.6°, 1.0°, and 3.0°) and scroll window size (5 or 10 character spaces). Results showed that the reading performance was highest in the range of 0.6° to 1.0°, irrespective of the scroll window size. Experiment 2 investigated whether the optimal character size observed in Experiment 1 was applicable for any word width and word length (i.e., the number of characters in a word). Results showed that reading speeds were slower for longer than shorter words and the word width of 3.6° was optimal among the word lengths tested (three, four, and six character words). Considering that character size varied depending on word width and word length in the present study, this means that the optimal character size can be changed by word width and word length in scrolling Japanese words. PMID:26909052

Effects of Word Width and Word Length on Optimal Character Size for Reading of Horizontally Scrolling Japanese Words.

PubMed

Teramoto, Wataru; Nakazaki, Takuyuki; Sekiyama, Kaoru; Mori, Shuji

2016-01-01

The present study investigated, whether word width and length affect the optimal character size for reading of horizontally scrolling Japanese words, using reading speed as a measure. In Experiment 1, three Japanese words, each consisting of four Hiragana characters, sequentially scrolled on a display screen from right to left. Participants, all Japanese native speakers, were instructed to read the words aloud as accurately as possible, irrespective of their order within the sequence. To quantitatively measure their reading performance, we used rapid serial visual presentation paradigm, where the scrolling rate was increased until the participants began to make mistakes. Thus, the highest scrolling rate at which the participants' performance exceeded 88.9% correct rate was calculated for each character size (0.3°, 0.6°, 1.0°, and 3.0°) and scroll window size (5 or 10 character spaces). Results showed that the reading performance was highest in the range of 0.6° to 1.0°, irrespective of the scroll window size. Experiment 2 investigated whether the optimal character size observed in Experiment 1 was applicable for any word width and word length (i.e., the number of characters in a word). Results showed that reading speeds were slower for longer than shorter words and the word width of 3.6° was optimal among the word lengths tested (three, four, and six character words). Considering that character size varied depending on word width and word length in the present study, this means that the optimal character size can be changed by word width and word length in scrolling Japanese words.

Concurrent Validity and Classification Accuracy of Curriculum-Based Measurement for Written Expression

ERIC Educational Resources Information Center

Furey, William M.; Marcotte, Amanda M.; Hintze, John M.; Shackett, Caroline M.

2016-01-01

The study presents a critical analysis of written expression curriculum-based measurement (WE-CBM) metrics derived from 3- and 10-min test lengths. Criterion validity and classification accuracy were examined for Total Words Written (TWW), Correct Writing Sequences (CWS), Percent Correct Writing Sequences (%CWS), and Correct Minus Incorrect…

Speech Sequence Skill Learning in Adults Who Stutter

ERIC Educational Resources Information Center

Bauerly, Kim R.; De Nil, Luc F.

2011-01-01

The present study compared the ability of 12 people who stutter (PWS) and 12 people who do not stutter (PNS) to consolidate a novel sequential speech task. Participants practiced 100 repetitions of a single, monosyllabic, nonsense word sequence during an initial practice session and returned 24-h later to perform an additional 50 repetitions.…

Structured Semantic Knowledge Can Emerge Automatically from Predicting Word Sequences in Child-Directed Speech

PubMed Central

Huebner, Philip A.; Willits, Jon A.

2018-01-01

Previous research has suggested that distributional learning mechanisms may contribute to the acquisition of semantic knowledge. However, distributional learning mechanisms, statistical learning, and contemporary “deep learning” approaches have been criticized for being incapable of learning the kind of abstract and structured knowledge that many think is required for acquisition of semantic knowledge. In this paper, we show that recurrent neural networks, trained on noisy naturalistic speech to children, do in fact learn what appears to be abstract and structured knowledge. We trained two types of recurrent neural networks (Simple Recurrent Network, and Long Short-Term Memory) to predict word sequences in a 5-million-word corpus of speech directed to children ages 0–3 years old, and assessed what semantic knowledge they acquired. We found that learned internal representations are encoding various abstract grammatical and semantic features that are useful for predicting word sequences. Assessing the organization of semantic knowledge in terms of the similarity structure, we found evidence of emergent categorical and hierarchical structure in both models. We found that the Long Short-term Memory (LSTM) and SRN are both learning very similar kinds of representations, but the LSTM achieved higher levels of performance on a quantitative evaluation. We also trained a non-recurrent neural network, Skip-gram, on the same input to compare our results to the state-of-the-art in machine learning. We found that Skip-gram achieves relatively similar performance to the LSTM, but is representing words more in terms of thematic compared to taxonomic relations, and we provide reasons why this might be the case. Our findings show that a learning system that derives abstract, distributed representations for the purpose of predicting sequential dependencies in naturalistic language may provide insight into emergence of many properties of the developing semantic system. PMID:29520243

Associations among measures of sequential processing in motor and linguistics tasks in adults with and without a family history of childhood apraxia of speech: a replication study.

PubMed

Button, Le; Peter, Beate; Stoel-Gammon, Carol; Raskind, Wendy H

2013-03-01

The purpose of this study was to address the hypothesis that childhood apraxia of speech (CAS) is influenced by an underlying deficit in sequential processing that is also expressed in other modalities. In a sample of 21 adults from five multigenerational families, 11 with histories of various familial speech sound disorders, 3 biologically related adults from a family with familial CAS showed motor sequencing deficits in an alternating motor speech task. Compared with the other adults, these three participants showed deficits in tasks requiring high loads of sequential processing, including nonword imitation, nonword reading and spelling. Qualitative error analyses in real word and nonword imitations revealed group differences in phoneme sequencing errors. Motor sequencing ability was correlated with phoneme sequencing errors during real word and nonword imitation, reading and spelling. Correlations were characterized by extremely high scores in one family and extremely low scores in another. Results are consistent with a central deficit in sequential processing in CAS of familial origin.

Associations among measures of sequential processing in motor and linguistics tasks in adults with and without a family history of childhood apraxia of speech: A replication study

PubMed Central

BUTTON, LE; PETER, BEATE; STOEL-GAMMON, CAROL; RASKIND, WENDY H.

2013-01-01

The purpose of this study was to address the hypothesis that childhood apraxia of speech (CAS) is influenced by an underlying deficit in sequential processing that is also expressed in other modalities. In a sample of 21 adults from five multigenerational families, 11 with histories of various familial speech sound disorders, 3 biologically related adults from a family with familial CAS showed motor sequencing deficits in an alternating motor speech task. Compared with the other adults, these three participants showed deficits in tasks requiring high loads of sequential processing, including nonword imitation, nonword reading and spelling. Qualitative error analyses in real word and nonword imitations revealed group differences in phoneme sequencing errors. Motor sequencing ability was correlated with phoneme sequencing errors during real word and nonword imitation, reading and spelling. Correlations were characterized by extremely high scores in one family and extremely low scores in another. Results are consistent with a central deficit in sequential processing in CAS of familial origin. PMID:23339292

Association mining of dependency between time series

NASA Astrophysics Data System (ADS)

Hafez, Alaaeldin

2001-03-01

Time series analysis is considered as a crucial component of strategic control over a broad variety of disciplines in business, science and engineering. Time series data is a sequence of observations collected over intervals of time. Each time series describes a phenomenon as a function of time. Analysis on time series data includes discovering trends (or patterns) in a time series sequence. In the last few years, data mining has emerged and been recognized as a new technology for data analysis. Data Mining is the process of discovering potentially valuable patterns, associations, trends, sequences and dependencies in data. Data mining techniques can discover information that many traditional business analysis and statistical techniques fail to deliver. In this paper, we adapt and innovate data mining techniques to analyze time series data. By using data mining techniques, maximal frequent patterns are discovered and used in predicting future sequences or trends, where trends describe the behavior of a sequence. In order to include different types of time series (e.g. irregular and non- systematic), we consider past frequent patterns of the same time sequences (local patterns) and of other dependent time sequences (global patterns). We use the word 'dependent' instead of the word 'similar' for emphasis on real life time series where two time series sequences could be completely different (in values, shapes, etc.), but they still react to the same conditions in a dependent way. In this paper, we propose the Dependence Mining Technique that could be used in predicting time series sequences. The proposed technique consists of three phases: (a) for all time series sequences, generate their trend sequences, (b) discover maximal frequent trend patterns, generate pattern vectors (to keep information of frequent trend patterns), use trend pattern vectors to predict future time series sequences.

Speculation detection for Chinese clinical notes: Impacts of word segmentation and embedding models.

PubMed

Zhang, Shaodian; Kang, Tian; Zhang, Xingting; Wen, Dong; Elhadad, Noémie; Lei, Jianbo

2016-04-01

Speculations represent uncertainty toward certain facts. In clinical texts, identifying speculations is a critical step of natural language processing (NLP). While it is a nontrivial task in many languages, detecting speculations in Chinese clinical notes can be particularly challenging because word segmentation may be necessary as an upstream operation. The objective of this paper is to construct a state-of-the-art speculation detection system for Chinese clinical notes and to investigate whether embedding features and word segmentations are worth exploiting toward this overall task. We propose a sequence labeling based system for speculation detection, which relies on features from bag of characters, bag of words, character embedding, and word embedding. We experiment on a novel dataset of 36,828 clinical notes with 5103 gold-standard speculation annotations on 2000 notes, and compare the systems in which word embeddings are calculated based on word segmentations given by general and by domain specific segmenters respectively. Our systems are able to reach performance as high as 92.2% measured by F score. We demonstrate that word segmentation is critical to produce high quality word embedding to facilitate downstream information extraction applications, and suggest that a domain dependent word segmenter can be vital to such a clinical NLP task in Chinese language. Copyright © 2016 Elsevier Inc. All rights reserved.

BAIT: Organizing genomes and mapping rearrangements in single cells.

PubMed

Hills, Mark; O'Neill, Kieran; Falconer, Ester; Brinkman, Ryan; Lansdorp, Peter M

2013-01-01

Strand-seq is a single-cell sequencing technique to finely map sister chromatid exchanges (SCEs) and other rearrangements. To analyze these data, we introduce BAIT, software which assigns templates and identifies and localizes SCEs. We demonstrate BAIT can refine completed reference assemblies, identifying approximately 21 Mb of incorrectly oriented fragments and placing over half (2.6 Mb) of the orphan fragments in mm10/GRCm38. BAIT also stratifies scaffold-stage assemblies, potentially accelerating the assembling and finishing of reference genomes. BAIT is available at http://sourceforge.net/projects/bait/.

An Alternative to Mapping a Word onto a Concept in Language Acquisition: Pragmatic Frames

PubMed Central

Rohlfing, Katharina J.; Wrede, Britta; Vollmer, Anna-Lisa; Oudeyer, Pierre-Yves

2016-01-01

The classic mapping metaphor posits that children learn a word by mapping it onto a concept of an object or event. However, we believe that a mapping metaphor cannot account for word learning, because even though children focus attention on objects, they do not necessarily remember the connection between the word and the referent unless it is framed pragmatically, that is, within a task. Our theoretical paper proposes an alternative mechanism for word learning. Our main premise is that word learning occurs as children accomplish a goal in cooperation with a partner. We follow Bruner’s (1983) idea and further specify pragmatic frames as the learning units that drive language acquisition and cognitive development. These units consist of a sequence of actions and verbal behaviors that are co-constructed with a partner to achieve a joint goal. We elaborate on this alternative, offer some initial parametrizations of the concept, and embed it in current language learning approaches. PMID:27148105

Perception of resyllabification in French.

PubMed

Gaskell, M Gareth; Spinelli, Elsa; Meunier, Fanny

2002-07-01

In three experiments, we examined the effects of phonological resyllabification processes on the perception of French speech. Enchainment involves the resyllabification of a word-final consonant across a syllable boundary (e.g., in chaque avion, the /k/ crosses the syllable boundary to become syllable initial). Liaison involves a further process of realization of a latent consonant, alongside resyllabification (e.g., the /t/ in petit avion). If the syllable is a dominant unit of perception in French (Mehler, Dommergues, Frauenfelder, & Segui, 1981), these processes should cause problems for recognition of the following word. A cross-modal priming experiment showed no cost attached to either type of resyllabification in terms of reduced activation of the following word. Furthermore, word- and sequence-monitoring experiments again showed no cost and suggested that the recognition of vowel-initial words may be facilitated when they are preceded by a word that had undergone resyllabification through enchainment or liaison. We examine the sources of information that could underpin facilitation and propose a refinement of the syllable's role in the perception of French speech.

Acquisition of Malay word recognition skills: lessons from low-progress early readers.

PubMed

Lee, Lay Wah; Wheldall, Kevin

2011-02-01

Malay is a consistent alphabetic orthography with complex syllable structures. The focus of this research was to investigate word recognition performance in order to inform reading interventions for low-progress early readers. Forty-six Grade 1 students were sampled and 11 were identified as low-progress readers. The results indicated that both syllable awareness and phoneme blending were significant predictors of word recognition, suggesting that both syllable and phonemic grain-sizes are important in Malay word recognition. Item analysis revealed a hierarchical pattern of difficulty based on the syllable and the phonic structure of the words. Error analysis identified the sources of errors to be errors due to inefficient syllable segmentation, oversimplification of syllables, insufficient grapheme-phoneme knowledge and inefficient phonemic code assembly. Evidence also suggests that direct instruction in syllable segmentation, phonemic awareness and grapheme-phoneme correspondence is necessary for low-progress readers to acquire word recognition skills. Finally, a logical sequence to teach grapheme-phoneme decoding in Malay is suggested. Copyright © 2010 John Wiley & Sons, Ltd.

Orthographic recognition in late adolescents: an assessment through event-related brain potentials.

PubMed

González-Garrido, Andrés Antonio; Gómez-Velázquez, Fabiola Reveca; Rodríguez-Santillán, Elizabeth

2014-04-01

Reading speed and efficiency are achieved through the automatic recognition of written words. Difficulties in learning and recognizing the orthography of words can arise despite reiterative exposure to texts. This study aimed to investigate, in native Spanish-speaking late adolescents, how different levels of orthographic knowledge might result in behavioral and event-related brain potential differences during the recognition of orthographic errors. Forty-five healthy high school students were selected and divided into 3 equal groups (High, Medium, Low) according to their performance on a 5-test battery of orthographic knowledge. All participants performed an orthographic recognition task consisting of the sequential presentation of a picture (object, fruit, or animal) followed by a correctly, or incorrectly, written word (orthographic mismatch) that named the picture just shown. Electroencephalogram (EEG) recording took place simultaneously. Behavioral results showed that the Low group had a significantly lower number of correct responses and increased reaction times while processing orthographical errors. Tests showed significant positive correlations between higher performance on the experimental task and faster and more accurate reading. The P150 and P450 components showed higher voltages in the High group when processing orthographic errors, whereas N170 seemed less lateralized to the left hemisphere in the lower orthographic performers. Also, trials with orthographic errors elicited a frontal P450 component that was only evident in the High group. The present results show that higher levels of orthographic knowledge correlate with high reading performance, likely because of faster and more accurate perceptual processing, better visual orthographic representations, and top-down supervision, as the event-related brain potential findings seem to suggest.

Short-term memory for serial order supports vocabulary development: new evidence from a novel word learning paradigm.

PubMed

Majerus, Steve; Boukebza, Claire

2013-12-01

Although recent studies suggest a strong association between short-term memory (STM) for serial order and lexical development, the precise mechanisms linking the two domains remain to be determined. This study explored the nature of these mechanisms via a microanalysis of performance on serial order STM and novel word learning tasks. In the experiment, 6- and 7-year-old children were administered tasks maximizing STM for either item or serial order information as well as paired-associate learning tasks involving the learning of novel words, visual symbols, or familiar word pair associations. Learning abilities for novel words were specifically predicted by serial order STM abilities. A measure estimating the precision of serial order coding predicted the rate of correct repetitions and the rate of phoneme migration errors during the novel word learning process. In line with recent theoretical accounts, these results suggest that serial order STM supports vocabulary development via ordered and detailed reactivation of the novel phonological sequences that characterize new words. Copyright © 2013 Elsevier Inc. All rights reserved.

Spotting handwritten words and REGEX using a two stage BLSTM-HMM architecture

NASA Astrophysics Data System (ADS)

Bideault, Gautier; Mioulet, Luc; Chatelain, Clément; Paquet, Thierry

2015-01-01

In this article, we propose a hybrid model for spotting words and regular expressions (REGEX) in handwritten documents. The model is made of the state-of-the-art BLSTM (Bidirectional Long Short Time Memory) neural network for recognizing and segmenting characters, coupled with a HMM to build line models able to spot the desired sequences. Experiments on the Rimes database show very promising results.

AGILE: Autonomous Global Integrated Language Exploitation

DTIC Science & Technology

2008-04-01

training is extending the pronunciation dictionary to cover any additional words. For many languages this is relatively straightforward via grapheme-to...into one or more word sequences and look up the constituent parts in the Master dictionary or apply Buckwalter to them. The Buckwalter prefix table was...errors involve the article ’Al’. As a result of this analysis, the pronunciation dictionary was extended to add alternate pronunciations for the

Climbing the Tower of Babel: Perfecting Machine Translation

DTIC Science & Technology

2011-02-16

Center) used MT tools to translate extraordinary numbers of Russian technical documents. 10 For the Air Force, the manpower and time savings were...recognition.htm. Granted, this number is tempered by the rules of a specific language that would disallow specific word orderings, or mandate particular word...sequences, (e.g., in English, prepositions can only be followed by articles, etc) but the overall numbers convey the complexity of the machine

Synthesis of Polysyllabic Sequences of Thai Tones Using a Generative Model of Fundamental Frequency Contours

NASA Astrophysics Data System (ADS)

Seresangtakul, Pusadee; Takara, Tomio

In this paper, the distinctive tones of Thai in running speech are studied. We present rules to synthesize F0 contours of Thai tones in running speech by using the generative model of F0 contours. Along with our method, the pitch contours of Thai polysyllabic words, both disyllabic and trisyllabic words, were analyzed. The coarticulation effect of Thai tones in running speech were found. Based on the analysis of the polysyllabic words using this model, rules are derived and applied to synthesize Thai polysyllabic tone sequences. We performed listening tests to evaluate intelligibility of the rules for Thai tones generation. The average intelligibility scores became 98.8%, and 96.6% for disyllabic and trisyllabic words, respectively. From these result, the rule of the tones' generation was shown to be effective. Furthermore, we constructed the connecting rules to synthesize suprasegmental F0 contours using the trisyllable training rules' parameters. The parameters of the first, the third, and the second syllables were selected and assigned to the initial, the ending, and the remaining syllables in a sentence, respectively. Even such a simple rule, the synthesized phrases/senetences were completely identified in listening tests. The MOSs (Mean Opinion Score) was 3.50 while the original and analysis/synthesis samples were 4.82 and 3.59, respectively.

Napping to renew learning capacity: enhanced encoding after stimulation of sleep slow oscillations.

PubMed

Antonenko, Daria; Diekelmann, Susanne; Olsen, Cathrin; Born, Jan; Mölle, Matthias

2013-04-01

As well as consolidating memory, sleep has been proposed to serve a second important function for memory, i.e. to free capacities for the learning of new information during succeeding wakefulness. The slow wave activity (SWA) that is a hallmark of slow wave sleep could be involved in both functions. Here, we aimed to demonstrate a causative role for SWA in enhancing the capacity for encoding of information during subsequent wakefulness, using transcranial slow oscillation stimulation (tSOS) oscillating at 0.75 Hz to induce SWA in healthy humans during an afternoon nap. Encoding following the nap was tested for hippocampus-dependent declarative materials (pictures, word pairs, and word lists) and procedural skills (finger sequence tapping). As compared with a sham stimulation control condition, tSOS during the nap enhanced SWA and significantly improved subsequent encoding on all three declarative tasks (picture recognition, cued recall of word pairs, and free recall of word lists), whereas procedural finger sequence tapping skill was not affected. Our results indicate that sleep SWA enhances the capacity for encoding of declarative materials, possibly by down-scaling hippocampal synaptic networks that were potentiated towards saturation during the preceding period of wakefulness. © 2013 Federation of European Neuroscience Societies and Blackwell Publishing Ltd.

Generalizability of carry-over effects in the emotional Stroop task.

PubMed

Waters, Andrew J; Sayette, Michael A; Franken, Ingmar H A; Schwartz, Joseph E

2005-06-01

The emotional Stroop task has been the most widely used task to examine attentional bias to emotionally salient stimuli. In one format of this task, words are presented to participants in a mixed randomized or quasi-randomized sequence. Using a mixed smoking Stroop task, we have previously demonstrated that smokers are slower to respond to words which follow smoking-related words than words which follow neutral words. Here we show that this carry-over effect is present in heroin addicts-but not control subjects-in a heroin Stroop task, and in normal subjects in a stress Stroop task. Thus, the effect generalizes to other populations. In addition, an examination of the studies that have collected data from both mixed and blocked formats provides converging evidence for the presence of carry-over effects. We discuss the implications of the carry-over effect for research using the emotional Stroop task.

Assessing Feedback in a Mobile Videogame

PubMed Central

Brand, Leah; Beltran, Alicia; Hughes, Sheryl; O'Connor, Teresia; Baranowski, Janice; Nicklas, Theresa; Chen, Tzu-An; Dadabhoy, Hafza R.; Diep, Cassandra S.; Buday, Richard

2016-01-01

Abstract Background: Player feedback is an important part of serious games, although there is no consensus regarding its delivery or optimal content. “Mommio” is a serious game designed to help mothers motivate their preschoolers to eat vegetables. The purpose of this study was to assess optimal format and content of player feedback for use in “Mommio.” Materials and Methods: The current study posed 36 potential “Mommio” gameplay feedback statements to 20 mothers using a Web survey and interview. Mothers were asked about the meaning and helpfulness of each feedback statement. Results: Several themes emerged upon thematic analysis, including identifying an effective alternative in the case of corrective feedback, avoiding vague wording, using succinct and correct grammar, avoiding provocation of guilt, and clearly identifying why players' game choice was correct or incorrect. Conclusions: Guidelines are proposed for future feedback statements. PMID:27058403

Differentiation in Coregonus zenithicus in Lake Superior

USGS Publications Warehouse

Todd, Thomas N.; Smith, Gerald R.

1980-01-01

Morphological variation in Coregonus zenithicus has long plagued biologists working on Lake Superior ciscoes. Some of this variation is due to allometric growth; earlier workers incorrectly recognized large C. zenithicus as a distinct species, C. nigripinnis cyanopterus. Coregonus reighardi dymondi is a variant of C. zenithicus in northern bays of Lake Superior and Lake Nipigon. The morphological differences between members of spring and fall spawning populations of C. zenithicus in Lake Superior are no greater than those between geographically separate populations. We conclude that spawning time and geographic isolation act similarly in effecting differentiation of coregonine populations, and that populations with different spawning times do not necessarily represent different species.Key words: Coregonus zenithicus, cisco, Great Lakes, multivariate morphometrics, endangered species, taxonomy

Being Active and Impulsive: The Role of Goals for Action and Inaction in Self-Control.

PubMed

Hepler, Justin; Albarracin, Dolores; McCulloch, Kathleen C; Noguchi, Kenji

2012-12-01

Although self-control often requires behavioral inaction (i.e., not eating a piece of cake), the process of inhibiting impulsive behavior is commonly characterized as cognitively active (i.e., actively exerting self-control). Two experiments examined whether motivation for action or inaction facilitates self-control behavior in the presence of tempting stimuli. Experiment 1 used a delay discounting task to assess the ability to delay gratification with respect to money. Experiment 2 used a Go/No-Go task to assess the ability to inhibit a dominant but incorrect motor response to the words "condom" and "sex". The results demonstrate that goals for inaction promote self-control, whereas goals for action promote impulsive behavior. These findings are discussed in light of recent evidence suggesting that goals for action and inaction modulate physiological resources that promote behavioral execution.

BlackOPs: increasing confidence in variant detection through mappability filtering.

PubMed

Cabanski, Christopher R; Wilkerson, Matthew D; Soloway, Matthew; Parker, Joel S; Liu, Jinze; Prins, Jan F; Marron, J S; Perou, Charles M; Hayes, D Neil

2013-10-01

Identifying variants using high-throughput sequencing data is currently a challenge because true biological variants can be indistinguishable from technical artifacts. One source of technical artifact results from incorrectly aligning experimentally observed sequences to their true genomic origin ('mismapping') and inferring differences in mismapped sequences to be true variants. We developed BlackOPs, an open-source tool that simulates experimental RNA-seq and DNA whole exome sequences derived from the reference genome, aligns these sequences by custom parameters, detects variants and outputs a blacklist of positions and alleles caused by mismapping. Blacklists contain thousands of artifact variants that are indistinguishable from true variants and, for a given sample, are expected to be almost completely false positives. We show that these blacklist positions are specific to the alignment algorithm and read length used, and BlackOPs allows users to generate a blacklist specific to their experimental setup. We queried the dbSNP and COSMIC variant databases and found numerous variants indistinguishable from mapping errors. We demonstrate how filtering against blacklist positions reduces the number of potential false variants using an RNA-seq glioblastoma cell line data set. In summary, accounting for mapping-caused variants tuned to experimental setups reduces false positives and, therefore, improves genome characterization by high-throughput sequencing.

Conceptual issues in Bayesian divergence time estimation

PubMed Central

2016-01-01

Bayesian inference of species divergence times is an unusual statistical problem, because the divergence time parameters are not identifiable unless both fossil calibrations and sequence data are available. Commonly used marginal priors on divergence times derived from fossil calibrations may conflict with node order on the phylogenetic tree causing a change in the prior on divergence times for a particular topology. Care should be taken to avoid confusing this effect with changes due to informative sequence data. This effect is illustrated with examples. A topology-consistent prior that preserves the marginal priors is defined and examples are constructed. Conflicts between fossil calibrations and relative branch lengths (based on sequence data) can cause estimates of divergence times that are grossly incorrect, yet have a narrow posterior distribution. An example of this effect is given; it is recommended that overly narrow posterior distributions of divergence times should be carefully scrutinized. This article is part of the themed issue ‘Dating species divergences using rocks and clocks’. PMID:27325831

Conceptual issues in Bayesian divergence time estimation.

PubMed

Rannala, Bruce

2016-07-19

Bayesian inference of species divergence times is an unusual statistical problem, because the divergence time parameters are not identifiable unless both fossil calibrations and sequence data are available. Commonly used marginal priors on divergence times derived from fossil calibrations may conflict with node order on the phylogenetic tree causing a change in the prior on divergence times for a particular topology. Care should be taken to avoid confusing this effect with changes due to informative sequence data. This effect is illustrated with examples. A topology-consistent prior that preserves the marginal priors is defined and examples are constructed. Conflicts between fossil calibrations and relative branch lengths (based on sequence data) can cause estimates of divergence times that are grossly incorrect, yet have a narrow posterior distribution. An example of this effect is given; it is recommended that overly narrow posterior distributions of divergence times should be carefully scrutinized.This article is part of the themed issue 'Dating species divergences using rocks and clocks'. © 2016 The Author(s).

Archaeal phylogeny: reexamination of the phylogenetic position of Archaeoglobus fulgidus in light of certain composition-induced artifacts

NASA Technical Reports Server (NTRS)

Woese, C. R.; Achenbach, L.; Rouviere, P.; Mandelco, L.

1991-01-01

A major and too little recognized source of artifact in phylogenetic analysis of molecular sequence data is compositional difference among sequences. The problem becomes particularly acute when alignments contain ribosomal RNAs from both mesophilic and thermophilic species. Among prokaryotes the latter are considerably higher in G + C content than the former, which often results in artificial clustering of thermophilic lineages and their being placed artificially deep in phylogenetic trees. In this communication we review archaeal phylogeny in the light of this consideration, focusing in particular on the phylogenetic position of the sulfate reducing species Archaeoglobus fulgidus, using both 16S rRNA and 23S rRNA sequences. The analysis shows clearly that the previously reported deep branching of the A. fulgidus lineage (very near the base of the euryarchaeal side of the archaeal tree) is incorrect, and that the lineage actually groups with a previously recognized unit that comprises the Methanomicrobiales and extreme halophiles.

Adult Age Differences in Production and Monitoring in Dual-List Free Recall

PubMed Central

Wahlheim, Christopher N.; Ball, B. Hunter; Richmond, Lauren L.

2017-01-01

The present experiment examined adult age differences in the production and monitoring of responses in dual-list free recall. Younger and older adults studied two lists of unrelated words and were instructed to recall from List 1, List 2, or List 1 and List 2. An externalized free recall (EFR) procedure required participants to: 1) report all responses that came to mind while recalling from specific lists, 2) classify responses as correct or incorrect, and 3) provide confidence judgments for their accuracy classifications. Relative to younger adults, older adults showed a monitoring deficit by misclassifying proportionally more responses and discriminating more poorly between correct and incorrect responses in their confidence judgments. This deficit was especially pronounced under conditions of retroactive interference that occurred when participants recalled from List 1 only. A comparison of retrieval dynamics for all responses produced and for those that participants were reasonably confident were correct provided information about age differences in preretrieval context reinstatement and postretrieval monitoring of retrieved context. One noteworthy finding was that total production when recalling from List 1 showed that List 2 responses remained more accessible across the first several retrieval attempts for older than younger adults, which indicated a substantial age difference in the ability to reinstate List 1 context. Overall, the present findings provide a nuanced characterization of age differences in the operation of production and monitoring mechanisms under conditions of proactive and retroactive interference that can inform models of free recall. PMID:28206784

Adult age differences in production and monitoring in dual-list free recall.

PubMed

Wahlheim, Christopher N; Ball, B Hunter; Richmond, Lauren L

2017-06-01

The present experiment examined adult age differences in the production and monitoring of responses in dual-list free recall. Younger and older adults studied 2 lists of unrelated words and were instructed to recall from List 1, List 2, or List 1 and List 2. An externalized free recall procedure required participants to: (a) report all responses that came to mind while recalling from specific lists, (b) classify responses as correct or incorrect, and (c) provide confidence judgments for their accuracy classifications. Relative to younger adults, older adults showed a monitoring deficit by misclassifying proportionally more responses and discriminating more poorly between correct and incorrect responses in their confidence judgments. This deficit was especially pronounced under conditions of retroactive interference that occurred when participants recalled from List 1 only. A comparison of retrieval dynamics for all responses produced and for those that participants were reasonably confident were correct provided information about age differences in preretrieval context reinstatement and postretrieval monitoring of retrieved context. One noteworthy finding was that total production when recalling from List 1 showed that List 2 responses remained more accessible across the first several retrieval attempts for older than younger adults, which indicated a substantial age difference in the ability to reinstate List 1 context. Overall, the present findings provide a nuanced characterization of age differences in the operation of production and monitoring mechanisms under conditions of proactive and retroactive interference that can inform models of free recall. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Reduced Performance During a Sentence Repetition Task by Continuous Theta-Burst Magnetic Stimulation of the Pre-supplementary Motor Area.

PubMed

Dietrich, Susanne; Hertrich, Ingo; Müller-Dahlhaus, Florian; Ackermann, Hermann; Belardinelli, Paolo; Desideri, Debora; Seibold, Verena C; Ziemann, Ulf

2018-01-01

The pre-supplementary motor area (pre-SMA) is engaged in speech comprehension under difficult circumstances such as poor acoustic signal quality or time-critical conditions. Previous studies found that left pre-SMA is activated when subjects listen to accelerated speech. Here, the functional role of pre-SMA was tested for accelerated speech comprehension by inducing a transient "virtual lesion" using continuous theta-burst stimulation (cTBS). Participants were tested (1) prior to (pre-baseline), (2) 10 min after (test condition for the cTBS effect), and (3) 60 min after stimulation (post-baseline) using a sentence repetition task (formant-synthesized at rates of 8, 10, 12, 14, and 16 syllables/s). Speech comprehension was quantified by the percentage of correctly reproduced speech material. For high speech rates, subjects showed decreased performance after cTBS of pre-SMA. Regarding the error pattern, the number of incorrect words without any semantic or phonological similarity to the target context increased, while related words decreased. Thus, the transient impairment of pre-SMA seems to affect its inhibitory function that normally eliminates erroneous speech material prior to speaking or, in case of perception, prior to encoding into a semantically/pragmatically meaningful message.

Reduced Performance During a Sentence Repetition Task by Continuous Theta-Burst Magnetic Stimulation of the Pre-supplementary Motor Area

PubMed Central

Dietrich, Susanne; Hertrich, Ingo; Müller-Dahlhaus, Florian; Ackermann, Hermann; Belardinelli, Paolo; Desideri, Debora; Seibold, Verena C.; Ziemann, Ulf

2018-01-01

The pre-supplementary motor area (pre-SMA) is engaged in speech comprehension under difficult circumstances such as poor acoustic signal quality or time-critical conditions. Previous studies found that left pre-SMA is activated when subjects listen to accelerated speech. Here, the functional role of pre-SMA was tested for accelerated speech comprehension by inducing a transient “virtual lesion” using continuous theta-burst stimulation (cTBS). Participants were tested (1) prior to (pre-baseline), (2) 10 min after (test condition for the cTBS effect), and (3) 60 min after stimulation (post-baseline) using a sentence repetition task (formant-synthesized at rates of 8, 10, 12, 14, and 16 syllables/s). Speech comprehension was quantified by the percentage of correctly reproduced speech material. For high speech rates, subjects showed decreased performance after cTBS of pre-SMA. Regarding the error pattern, the number of incorrect words without any semantic or phonological similarity to the target context increased, while related words decreased. Thus, the transient impairment of pre-SMA seems to affect its inhibitory function that normally eliminates erroneous speech material prior to speaking or, in case of perception, prior to encoding into a semantically/pragmatically meaningful message. PMID:29896086

Dynamic Encoding of Speech Sequence Probability in Human Temporal Cortex

PubMed Central

Leonard, Matthew K.; Bouchard, Kristofer E.; Tang, Claire

2015-01-01

Sensory processing involves identification of stimulus features, but also integration with the surrounding sensory and cognitive context. Previous work in animals and humans has shown fine-scale sensitivity to context in the form of learned knowledge about the statistics of the sensory environment, including relative probabilities of discrete units in a stream of sequential auditory input. These statistics are a defining characteristic of one of the most important sequential signals humans encounter: speech. For speech, extensive exposure to a language tunes listeners to the statistics of sound sequences. To address how speech sequence statistics are neurally encoded, we used high-resolution direct cortical recordings from human lateral superior temporal cortex as subjects listened to words and nonwords with varying transition probabilities between sound segments. In addition to their sensitivity to acoustic features (including contextual features, such as coarticulation), we found that neural responses dynamically encoded the language-level probability of both preceding and upcoming speech sounds. Transition probability first negatively modulated neural responses, followed by positive modulation of neural responses, consistent with coordinated predictive and retrospective recognition processes, respectively. Furthermore, transition probability encoding was different for real English words compared with nonwords, providing evidence for online interactions with high-order linguistic knowledge. These results demonstrate that sensory processing of deeply learned stimuli involves integrating physical stimulus features with their contextual sequential structure. Despite not being consciously aware of phoneme sequence statistics, listeners use this information to process spoken input and to link low-level acoustic representations with linguistic information about word identity and meaning. PMID:25948269

Higher quality of molecular testing, an unfulfilled priority: Results from external quality assessment for KRAS mutation testing in colorectal cancer.

PubMed

Tembuyser, Lien; Ligtenberg, Marjolijn J L; Normanno, Nicola; Delen, Sofie; van Krieken, J Han; Dequeker, Elisabeth M C

2014-05-01

Precision medicine is now a key element in clinical oncology. RAS mutational status is a crucial predictor of responsiveness to anti-epidermal growth factor receptor agents in metastatic colorectal cancer. In an effort to guarantee high-quality testing services in molecular pathology, the European Society of Pathology has been organizing an annual KRAS external quality assessment program since 2009. In 2012, 10 formalin-fixed, paraffin-embedded samples, of which 8 from invasive metastatic colorectal cancer tissue and 2 artificial samples of cell line material, were sent to more than 100 laboratories from 26 countries with a request for routine KRAS testing. Both genotyping and clinical reports were assessed independently. Twenty-seven percent of the participants genotyped at least 1 of 10 samples incorrectly. In total, less than 5% of the distributed specimens were genotyped incorrectly. Genotyping errors consisted of false negatives, false positives, and incorrectly genotyped mutations. Twenty percent of the laboratories reported a technical error for one or more samples. A review of the written reports showed that several essential elements were missing, most notably a clinical interpretation of the test result, the method sensitivity, and the use of a reference sequence. External quality assessment serves as a valuable educational tool in assessing and improving molecular testing quality and is an important asset for monitoring quality assurance upon incorporation of new biomarkers in diagnostic services. Copyright © 2014 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

Seeing a Phrase "Time and Again" Matters: The Role of Phrasal Frequency in the Processing of Multiword Sequences

ERIC Educational Resources Information Center

Siyanova-Chanturia, Anna; Conklin, Kathy; van Heuven, Walter J. B.

2011-01-01

Are speakers sensitive to the frequency with which phrases occur in language? The authors report an eye-tracking study that investigates this by examining the processing of multiword sequences that differ in phrasal frequency by native and proficient nonnative English speakers. Participants read sentences containing 3-word binomial phrases…

The Development of Long-Term Lexical Representations through Hebb Repetition Learning

ERIC Educational Resources Information Center

Szmalec, Arnaud; Page, Mike P. A.; Duyck, Wouter

2012-01-01

This study clarifies the involvement of short- and long-term memory in novel word-form learning, using the Hebb repetition paradigm. In Experiment 1, participants recalled sequences of visually presented syllables (e.g., "la"-"va"-"bu"-"sa"-"fa"-"ra"-"re"-"si"-"di"), with one particular (Hebb) sequence repeated on every third trial. Crucially,…

Two Distinct Origins of Long-Term Learning Effects in Verbal Short-Term Memory

ERIC Educational Resources Information Center

Majerus, Steve; Perez, Trecy Martinez; Oberauer, Klaus

2012-01-01

Verbal short-term memory (STM) is highly sensitive to learning effects: digit sequences or nonword sequences which have been rendered more familiar via repeated exposure are recalled more accurately. In this study we show that sublist-level, incidental learning of item co-occurrence regularities affects immediate serial recall of words and…

On the Edge of Language Acquisition: Inherent Constraints on Encoding Multisyllabic Sequences in the Neonate Brain

ERIC Educational Resources Information Center

Ferry, Alissa L.; Fló, Ana; Brusini, Perrine; Cattarossi, Luigi; Macagno, Francesco; Nespor, Marina; Mehler, Jacques

2016-01-01

To understand language, humans must encode information from rapid, sequential streams of syllables--tracking their order and organizing them into words, phrases, and sentences. We used Near-Infrared Spectroscopy (NIRS) to determine whether human neonates are born with the capacity to track the positions of syllables in multisyllabic sequences.…

Errors detected in pediatric oral liquid medication doses prepared in an automated workflow management system.

PubMed

Bledsoe, Sarah; Van Buskirk, Alex; Falconer, R James; Hollon, Andrew; Hoebing, Wendy; Jokic, Sladan

2018-02-01

The effectiveness of barcode-assisted medication preparation (BCMP) technology on detecting oral liquid dose preparation errors. From June 1, 2013, through May 31, 2014, a total of 178,344 oral doses were processed at Children's Mercy, a 301-bed pediatric hospital, through an automated workflow management system. Doses containing errors detected by the system's barcode scanning system or classified as rejected by the pharmacist were further reviewed. Errors intercepted by the barcode-scanning system were classified as (1) expired product, (2) incorrect drug, (3) incorrect concentration, and (4) technological error. Pharmacist-rejected doses were categorized into 6 categories based on the root cause of the preparation error: (1) expired product, (2) incorrect concentration, (3) incorrect drug, (4) incorrect volume, (5) preparation error, and (6) other. Of the 178,344 doses examined, 3,812 (2.1%) errors were detected by either the barcode-assisted scanning system (1.8%, n = 3,291) or a pharmacist (0.3%, n = 521). The 3,291 errors prevented by the barcode-assisted system were classified most commonly as technological error and incorrect drug, followed by incorrect concentration and expired product. Errors detected by pharmacists were also analyzed. These 521 errors were most often classified as incorrect volume, preparation error, expired product, other, incorrect drug, and incorrect concentration. BCMP technology detected errors in 1.8% of pediatric oral liquid medication doses prepared in an automated workflow management system, with errors being most commonly attributed to technological problems or incorrect drugs. Pharmacists rejected an additional 0.3% of studied doses. Copyright © 2018 by the American Society of Health-System Pharmacists, Inc. All rights reserved.

A Web-based interface to calculate phonotactic probability for words and nonwords in English

PubMed Central

VITEVITCH, MICHAEL S.; LUCE, PAUL A.

2008-01-01

Phonotactic probability refers to the frequency with which phonological segments and sequences of phonological segments occur in words in a given language. We describe one method of estimating phonotactic probabilities based on words in American English. These estimates of phonotactic probability have been used in a number of previous studies and are now being made available to other researchers via a Web-based interface. Instructions for using the interface, as well as details regarding how the measures were derived, are provided in the present article. The Phonotactic Probability Calculator can be accessed at http://www.people.ku.edu/~mvitevit/PhonoProbHome.html. PMID:15641436

One Time Passwords in Everything (OPIE): Experiences with Building and Using Stringer Authentication

DTIC Science & Technology

1995-01-01

opiepasswd(1). The name change brings it more in line with its UNIX counterpart passwd (1), which should make both programs easier to remember for users. This...char * passwd ) int opiehash(char *x, unsigned algorithm) The one-time password schemes implemented in OPIE, as rst described in [Hal94], compute a...seed, passwd ); while (sequence-- != 0) opiehash(result, algorithm); opiebtoe(result,words); Send words. : : : 6 Deployment Every machine that has

Noise-robust speech recognition through auditory feature detection and spike sequence decoding.

PubMed

Schafer, Phillip B; Jin, Dezhe Z

2014-03-01

Speech recognition in noisy conditions is a major challenge for computer systems, but the human brain performs it routinely and accurately. Automatic speech recognition (ASR) systems that are inspired by neuroscience can potentially bridge the performance gap between humans and machines. We present a system for noise-robust isolated word recognition that works by decoding sequences of spikes from a population of simulated auditory feature-detecting neurons. Each neuron is trained to respond selectively to a brief spectrotemporal pattern, or feature, drawn from the simulated auditory nerve response to speech. The neural population conveys the time-dependent structure of a sound by its sequence of spikes. We compare two methods for decoding the spike sequences--one using a hidden Markov model-based recognizer, the other using a novel template-based recognition scheme. In the latter case, words are recognized by comparing their spike sequences to template sequences obtained from clean training data, using a similarity measure based on the length of the longest common sub-sequence. Using isolated spoken digits from the AURORA-2 database, we show that our combined system outperforms a state-of-the-art robust speech recognizer at low signal-to-noise ratios. Both the spike-based encoding scheme and the template-based decoding offer gains in noise robustness over traditional speech recognition methods. Our system highlights potential advantages of spike-based acoustic coding and provides a biologically motivated framework for robust ASR development.

Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical Information

PubMed Central

McDonald, Daniel; Gonzalez, Antonio; Navas-Molina, Jose A.; Jiang, Lingjing; Xu, Zhenjiang Zech; Winker, Kevin; Kado, Deborah M.; Orwoll, Eric; Manary, Mark; Mirarab, Siavash

2018-01-01

ABSTRACT Recent algorithmic advances in amplicon-based microbiome studies enable the inference of exact amplicon sequence fragments. These new methods enable the investigation of sub-operational taxonomic units (sOTU) by removing erroneous sequences. However, short (e.g., 150-nucleotide [nt]) DNA sequence fragments do not contain sufficient phylogenetic signal to reproduce a reasonable tree, introducing a barrier in the utilization of critical phylogenetically aware metrics such as Faith’s PD or UniFrac. Although fragment insertion methods do exist, those methods have not been tested for sOTUs from high-throughput amplicon studies in insertions against a broad reference phylogeny. We benchmarked the SATé-enabled phylogenetic placement (SEPP) technique explicitly against 16S V4 sequence fragments and showed that it outperforms the conceptually problematic but often-used practice of reconstructing de novo phylogenies. In addition, we provide a BSD-licensed QIIME2 plugin (https://github.com/biocore/q2-fragment-insertion) for SEPP and integration into the microbial study management platform QIITA. IMPORTANCE The move from OTU-based to sOTU-based analysis, while providing additional resolution, also introduces computational challenges. We demonstrate that one popular method of dealing with sOTUs (building a de novo tree from the short sequences) can provide incorrect results in human gut metagenomic studies and show that phylogenetic placement of the new sequences with SEPP resolves this problem while also yielding other benefits over existing methods. PMID:29719869

A strategy for complex dimer formation when biomimicry fails: total synthesis of ten coccinellid alkaloids.

PubMed

Sherwood, Trevor C; Trotta, Adam H; Snyder, Scott A

2014-07-09

Although dimeric natural products can often be synthesized in the laboratory by directly merging advanced monomers, these approaches sometimes fail, leading instead to non-natural architectures via incorrect unions. Such a situation arose during our studies of the coccinellid alkaloids, when attempts to directly dimerize Nature's presumed monomeric precursors in a putative biomimetic sequence afforded only a non-natural analogue through improper regiocontrol. Herein, we outline a unique strategy for dimer formation that obviates these difficulties, one which rapidly constructs the coccinellid dimers psylloborine A and isopsylloborine A through a terminating sequence of two reaction cascades that generate five bonds, five rings, and four stereocenters. In addition, a common synthetic intermediate is identified which allows for the rapid, asymmetric formal or complete total syntheses of eight monomeric members of the class.

Hybrid generative-discriminative human action recognition by combining spatiotemporal words with supervised topic models

NASA Astrophysics Data System (ADS)

Sun, Hao; Wang, Cheng; Wang, Boliang

2011-02-01

We present a hybrid generative-discriminative learning method for human action recognition from video sequences. Our model combines a bag-of-words component with supervised latent topic models. A video sequence is represented as a collection of spatiotemporal words by extracting space-time interest points and describing these points using both shape and motion cues. The supervised latent Dirichlet allocation (sLDA) topic model, which employs discriminative learning using labeled data under a generative framework, is introduced to discover the latent topic structure that is most relevant to action categorization. The proposed algorithm retains most of the desirable properties of generative learning while increasing the classification performance though a discriminative setting. It has also been extended to exploit both labeled data and unlabeled data to learn human actions under a unified framework. We test our algorithm on three challenging data sets: the KTH human motion data set, the Weizmann human action data set, and a ballet data set. Our results are either comparable to or significantly better than previously published results on these data sets and reflect the promise of hybrid generative-discriminative learning approaches.

Character Decomposition and Transposition Processes in Chinese Compound Words Modulates Attentional Blink.

PubMed

Cao, Hongwen; Gao, Min; Yan, Hongmei

2016-01-01

The attentional blink (AB) is the phenomenon in which the identification of the second of two targets (T2) is attenuated if it is presented less than 500 ms after the first target (T1). Although the AB is eliminated in canonical word conditions, it remains unclear whether the character order in compound words affects the magnitude of the AB. Morpheme decomposition and transposition of Chinese two-character compound words can provide an effective means to examine AB priming and to assess combinations of the component representations inherent to visual word identification. In the present study, we examined the processing of consecutive targets in a rapid serial visual presentation (RSVP) paradigm using Chinese two-character compound words in which the two characters were transposed to form meaningful words or meaningless combinations (reversible, transposed, or canonical words). We found that when two Chinese characters that form a compound word, regardless of their order, are presented in an RSVP sequence, the likelihood of an AB for the second character is greatly reduced or eliminated compared to when the two characters constitute separate words rather than a compound word. Moreover, the order of the report for the two characters is more likely to be reversed when the normal order of the two characters in a compound word is reversed, especially when the interval between the presentation of the two characters is extremely short. These findings are more consistent with the cognitive strategy hypothesis than the resource-limited hypothesis during character decomposition and transposition of Chinese two-character compound words. These results suggest that compound characters are perceived as a unit, rather than two separate words. The data further suggest that readers could easily understand the text with character transpositions in compound words during Chinese reading.

SA-Search: a web tool for protein structure mining based on a Structural Alphabet

PubMed Central

Guyon, Frédéric; Camproux, Anne-Claude; Hochez, Joëlle; Tufféry, Pierre

2004-01-01

SA-Search is a web tool that can be used to mine for protein structures and extract structural similarities. It is based on a hidden Markov model derived Structural Alphabet (SA) that allows the compression of three-dimensional (3D) protein conformations into a one-dimensional (1D) representation using a limited number of prototype conformations. Using such a representation, classical methods developed for amino acid sequences can be employed. Currently, SA-Search permits the performance of fast 3D similarity searches such as the extraction of exact words using a suffix tree approach, and the search for fuzzy words viewed as a simple 1D sequence alignment problem. SA-Search is available at http://bioserv.rpbs.jussieu.fr/cgi-bin/SA-Search. PMID:15215446

SA-Search: a web tool for protein structure mining based on a Structural Alphabet.

PubMed

Guyon, Frédéric; Camproux, Anne-Claude; Hochez, Joëlle; Tufféry, Pierre

2004-07-01

SA-Search is a web tool that can be used to mine for protein structures and extract structural similarities. It is based on a hidden Markov model derived Structural Alphabet (SA) that allows the compression of three-dimensional (3D) protein conformations into a one-dimensional (1D) representation using a limited number of prototype conformations. Using such a representation, classical methods developed for amino acid sequences can be employed. Currently, SA-Search permits the performance of fast 3D similarity searches such as the extraction of exact words using a suffix tree approach, and the search for fuzzy words viewed as a simple 1D sequence alignment problem. SA-Search is available at http://bioserv.rpbs.jussieu.fr/cgi-bin/SA-Search.

Incidental orthographic learning during a color detection task.

PubMed

Protopapas, Athanassios; Mitsi, Anna; Koustoumbardis, Miltiadis; Tsitsopoulou, Sofia M; Leventi, Marianna; Seitz, Aaron R

2017-09-01

Orthographic learning refers to the acquisition of knowledge about specific spelling patterns forming words and about general biases and constraints on letter sequences. It is thought to occur by strengthening simultaneously activated visual and phonological representations during reading. Here we demonstrate that a visual perceptual learning procedure that leaves no time for articulation can result in orthographic learning evidenced in improved reading and spelling performance. We employed task-irrelevant perceptual learning (TIPL), in which the stimuli to be learned are paired with an easy task target. Assorted line drawings and difficult-to-spell words were presented in red color among sequences of other black-colored words and images presented in rapid succession, constituting a fast-TIPL procedure with color detection being the explicit task. In five experiments, Greek children in Grades 4-5 showed increased recognition of words and images that had appeared in red, both during and after the training procedure, regardless of within-training testing, and also when targets appeared in blue instead of red. Significant transfer to reading and spelling emerged only after increased training intensity. In a sixth experiment, children in Grades 2-3 showed generalization to words not presented during training that carried the same derivational affixes as in the training set. We suggest that reinforcement signals related to detection of the target stimuli contribute to the strengthening of orthography-phonology connections beyond earlier levels of visually-based orthographic representation learning. These results highlight the potential of perceptual learning procedures for the reinforcement of higher-level orthographic representations. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Alignment-free genetic sequence comparisons: a review of recent approaches by word analysis

PubMed Central

Steele, Joe; Bastola, Dhundy

2014-01-01

Modern sequencing and genome assembly technologies have provided a wealth of data, which will soon require an analysis by comparison for discovery. Sequence alignment, a fundamental task in bioinformatics research, may be used but with some caveats. Seminal techniques and methods from dynamic programming are proving ineffective for this work owing to their inherent computational expense when processing large amounts of sequence data. These methods are prone to giving misleading information because of genetic recombination, genetic shuffling and other inherent biological events. New approaches from information theory, frequency analysis and data compression are available and provide powerful alternatives to dynamic programming. These new methods are often preferred, as their algorithms are simpler and are not affected by synteny-related problems. In this review, we provide a detailed discussion of computational tools, which stem from alignment-free methods based on statistical analysis from word frequencies. We provide several clear examples to demonstrate applications and the interpretations over several different areas of alignment-free analysis such as base–base correlations, feature frequency profiles, compositional vectors, an improved string composition and the D2 statistic metric. Additionally, we provide detailed discussion and an example of analysis by Lempel–Ziv techniques from data compression. PMID:23904502

Application of Logic to Integer Sequences: A Survey

NASA Astrophysics Data System (ADS)

Makowsky, Johann A.

Chomsky and Schützenberger showed in 1963 that the sequence d L (n), which counts the number of words of a given length n in a regular language L, satisfies a linear recurrence relation with constant coefficients for n, or equivalently, the generating function g_L(x)=sumn d_L(n) x^n is a rational function. In this talk we survey results concerning sequences a(n) of natural numbers which satisfy linear recurrence relations over ℤ or ℤ m , and

Storage and retrieval properties of dual codes for pictures and words in recognition memory.

PubMed

Snodgrass, J G; McClure, P

1975-09-01

Storage and retrieval properties of pictures and words were studied within a recognition memory paradigm. Storage was manipulated by instructing subjects either to image or to verbalize to both picture and word stimuli during the study sequence. Retrieval was manipulated by representing a proportion of the old picture and word items in their opposite form during the recognition test (i.e., some old pictures were tested with their corresponding words and vice versa). Recognition performance for pictures was identical under the two instructional conditions, whereas recognition performance for words was markedly superior under the imagery instruction condition. It was suggested that subjects may engage in dual coding of simple pictures naturally, regardless of instructions, whereas dual coding of words may occur only under imagery instructions. The form of the test item had no effect on recognition performance for either type of stimulus and under either instructional condition. However, change of form of the test item markedly reduced item-by-item correlations between the two instructional conditions. It is tentatively proposed that retrieval is required in recognition, but that the effect of a form change is simply to make the retrieval process less consistent, not less efficient.

Next-generation sequencing can reveal in vitro-generated PCR crossover products: some artifactual sequences correspond to HLA alleles in the IMGT/HLA database.

PubMed

Holcomb, C L; Rastrou, M; Williams, T C; Goodridge, D; Lazaro, A M; Tilanus, M; Erlich, H A

2014-01-01

The high-resolution human leukocyte antigen (HLA) genotyping assay that we developed using 454 sequencing and Conexio software uses generic polymerase chain reaction (PCR) primers for DRB exon 2. Occasionally, we observed low abundance DRB amplicon sequences that resulted from in vitro PCR 'crossing over' between DRB1 and DRB3/4/5. These hybrid sequences, revealed by the clonal sequencing property of the 454 system, were generally observed at a read depth of 5%-10% of the true alleles. They usually contained at least one mismatch with the IMGT/HLA database, and consequently, were easily recognizable and did not cause a problem for HLA genotyping. Sometimes, however, these artifactual sequences matched a rare allele and the automatic genotype assignment was incorrect. These observations raised two issues: (1) could PCR conditions be modified to reduce such artifacts? and (2) could some of the rare alleles listed in the IMGT/HLA database be artifacts rather than true alleles? Because PCR crossing over occurs during late cycles of PCR, we compared DRB genotypes resulting from 28 and (our standard) 35 cycles of PCR. For all 21 cell line DNAs amplified for 35 cycles, crossover products were detected. In 33% of the cases, these hybrid sequences corresponded to named alleles. With amplification for only 28 cycles, these artifactual sequences were not detectable. To investigate whether some rare alleles in the IMGT/HLA database might be due to PCR artifacts, we analyzed four samples obtained from the investigators who submitted the sequences. In three cases, the sequences were generated from true alleles. In one case, our 454 sequencing revealed an error in the previously submitted sequence. © 2013 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

The Effects of Phonotactic Probability and Neighborhood Density on Adults' Word Learning in Noisy Conditions

PubMed Central

Storkel, Holly L.; Lee, Jaehoon; Cox, Casey

2016-01-01

Purpose Noisy conditions make auditory processing difficult. This study explores whether noisy conditions influence the effects of phonotactic probability (the likelihood of occurrence of a sound sequence) and neighborhood density (phonological similarity among words) on adults' word learning. Method Fifty-eight adults learned nonwords varying in phonotactic probability and neighborhood density in either an unfavorable (0-dB signal-to-noise ratio [SNR]) or a favorable (+8-dB SNR) listening condition. Word learning was assessed using a picture naming task by scoring the proportion of phonemes named correctly. Results The unfavorable 0-dB SNR condition showed a significant interaction between phonotactic probability and neighborhood density in the absence of main effects. In particular, adults learned more words when phonotactic probability and neighborhood density were both low or both high. The +8-dB SNR condition did not show this interaction. These results are inconsistent with those from a prior adult word learning study conducted under quiet listening conditions that showed main effects of word characteristics. Conclusions As the listening condition worsens, adult word learning benefits from a convergence of phonotactic probability and neighborhood density. Clinical implications are discussed for potential populations who experience difficulty with auditory perception or processing, making them more vulnerable to noise. PMID:27788276

The Effects of Phonotactic Probability and Neighborhood Density on Adults' Word Learning in Noisy Conditions.

PubMed

Han, Min Kyung; Storkel, Holly L; Lee, Jaehoon; Cox, Casey

2016-11-01

Noisy conditions make auditory processing difficult. This study explores whether noisy conditions influence the effects of phonotactic probability (the likelihood of occurrence of a sound sequence) and neighborhood density (phonological similarity among words) on adults' word learning. Fifty-eight adults learned nonwords varying in phonotactic probability and neighborhood density in either an unfavorable (0-dB signal-to-noise ratio [SNR]) or a favorable (+8-dB SNR) listening condition. Word learning was assessed using a picture naming task by scoring the proportion of phonemes named correctly. The unfavorable 0-dB SNR condition showed a significant interaction between phonotactic probability and neighborhood density in the absence of main effects. In particular, adults learned more words when phonotactic probability and neighborhood density were both low or both high. The +8-dB SNR condition did not show this interaction. These results are inconsistent with those from a prior adult word learning study conducted under quiet listening conditions that showed main effects of word characteristics. As the listening condition worsens, adult word learning benefits from a convergence of phonotactic probability and neighborhood density. Clinical implications are discussed for potential populations who experience difficulty with auditory perception or processing, making them more vulnerable to noise.

HMM-based lexicon-driven and lexicon-free word recognition for online handwritten Indic scripts.

PubMed

Bharath, A; Madhvanath, Sriganesh

2012-04-01

Research for recognizing online handwritten words in Indic scripts is at its early stages when compared to Latin and Oriental scripts. In this paper, we address this problem specifically for two major Indic scripts--Devanagari and Tamil. In contrast to previous approaches, the techniques we propose are largely data driven and script independent. We propose two different techniques for word recognition based on Hidden Markov Models (HMM): lexicon driven and lexicon free. The lexicon-driven technique models each word in the lexicon as a sequence of symbol HMMs according to a standard symbol writing order derived from the phonetic representation. The lexicon-free technique uses a novel Bag-of-Symbols representation of the handwritten word that is independent of symbol order and allows rapid pruning of the lexicon. On handwritten Devanagari word samples featuring both standard and nonstandard symbol writing orders, a combination of lexicon-driven and lexicon-free recognizers significantly outperforms either of them used in isolation. In contrast, most Tamil word samples feature the standard symbol order, and the lexicon-driven recognizer outperforms the lexicon free one as well as their combination. The best recognition accuracies obtained for 20,000 word lexicons are 87.13 percent for Devanagari when the two recognizers are combined, and 91.8 percent for Tamil using the lexicon-driven technique.

Strategic deployment of orthographic knowledge in phoneme detection.

PubMed

Cutler, Anne; Treiman, Rebecca; van Ooijen, Brit

2010-01-01

The phoneme detection task is widely used in spoken-word recognition research. Alphabetically literate participants, however, are more used to explicit representations of letters than of phonemes. The present study explored whether phoneme detection is sensitive to how target phonemes are, or may be, orthographically realized. Listeners detected the target sounds [b, m, t, f, s, k] in word-initial position in sequences of isolated English words. Response times were faster to the targets [b, m, t], which have consistent word-initial spelling, than to the targets [f, s, k], which are inconsistently spelled, but only when spelling was rendered salient by the presence in the experiment of many irregularly spelled filler words. Within the inconsistent targets [f, s, k], there was no significant difference between responses to targets in words with more usual (foam, seed, cattle) versus less usual (phone, cede, kettle) spellings. Phoneme detection is thus not necessarily sensitive to orthographic effects; knowledge of spelling stored in the lexical representations of words does not automatically become available as word candidates are activated. However, salient orthographic manipulations in experimental input can induce such sensitivity. We attribute this to listeners' experience of the value of spelling in everyday situations that encourage phonemic decisions (such as learning new names).

Word-Synchronous Optical Sampling of Periodically Repeated OTDM Data Words for True Waveform Visualization

NASA Astrophysics Data System (ADS)

Benkler, Erik; Telle, Harald R.

2007-06-01

An improved phase-locked loop (PLL) for versatile synchronization of a sampling pulse train to an optical data stream is presented. It enables optical sampling of the true waveform of repetitive high bit-rate optical time division multiplexed (OTDM) data words such as pseudorandom bit sequences. Visualization of the true waveform can reveal details, which cause systematic bit errors. Such errors cannot be inferred from eye diagrams and require word-synchronous sampling. The programmable direct-digital-synthesis circuit used in our novel PLL approach allows flexible adaption of virtually any problem-specific synchronization scenario, including those required for waveform sampling, for jitter measurements by slope detection, and for classical eye-diagrams. Phase comparison of the PLL is performed at 10-GHz OTDM base clock rate, leading to a residual synchronization jitter of less than 70 fs.

Reading a standing wave: figure-ground-alternation masking of primes in evaluative priming.

PubMed

Bermeitinger, Christina; Kuhlmann, Michael; Wentura, Dirk

2012-09-01

We propose a new masking technique for masking word stimuli. Drawing on the phenomena of metacontrast and paracontrast, we alternately presented two prime displays of the same word with the background color in one display matching the font color in the other display and vice versa. The sequence of twenty alterations (spanning approx. 267 ms) was sandwich-masked by structure masks. Using this masking technique, we conducted evaluative priming experiments with positive and negative target and prime words. Significant priming effects were found - for primes and targets drawn from the same as well as from different word sets. Priming effects were independent of prime discrimination performance in direct tests and they were still significant after the sample was restricted to those participants who showed random responding in the direct test. Copyright © 2012 Elsevier Inc. All rights reserved.

Description of 3D digital curves using the theory free groups

NASA Astrophysics Data System (ADS)

Imiya, Atsushi; Oosawa, Muneaki

1999-09-01

In this paper, we propose a new descriptor for two- and three- dimensional digital curves using the theory of free groups. A spatial digital curve is expressed as a word which is an element of the free group which consists from three elements. These three symbols correspond to the directions of the orthogonal coordinates, respectively. Since a digital curve is treated as a word which is a sequence of alphabetical symbols, this expression permits us to describe any geometric operation as rewriting rules for words. Furthermore, the symbolic derivative of words yields geometric invariants of digital curves for digital Euclidean motion. These invariants enable us to design algorithms for the matching and searching procedures of partial structures of digital curves. Moreover, these symbolic descriptors define the global and local distances for digital curves as an editing distance.

Music listening for maintaining attention of older adults with cognitive impairments.

PubMed

Gregory, Dianne

2002-01-01

Twelve older adults with cognitive impairments who were participants in weekly community-based group music therapy sessions, 6 older adults in an Alzheimer's caregivers' group, and 6 college student volunteers listened to a 3.5 minute prepared audiotape of instrumental excerpts of patriotic selections. The tape consisted of 7 excerpts ranging from 18 s to 34 s in duration. Each music excerpt was followed by a 7-9 s period of silence, a "wait" excerpt. Listeners were instructed to move a Continuous Response Digital Interface (CRDI) to the name of the music excerpt depicted on the CRDI overlay when they heard a music excerpt. Likewise, they were instructed to move the dial to the word "WAIT" when there was no music. They were also instructed to maintain the dial position for the duration of each music or silence excerpt. Statistical analysis indicated no significant differences between the caregivers' and the college students' group means for total dial changes, correct and incorrect recognitions, correct and incorrect responses to silence excerpts, and reaction times. The mean scores of these 2 groups were combined and compared with the mean scores of the group of elderly adults with cognitive impairments. The mean total dial changes were significantly lower for the listeners with cognitive impairments, resulting in significant differences in all of the other response categories except incorrect recognitions. In addition, their mean absence of response to silence excerpts was significantly higher than their mean absence of responding to music excerpts. Their mean reaction time was significantly slower than the comparison group's reaction time. To evaluate training effects, 10 of the original 12 music therapy participants repeated the listening task with assistance from the therapist (treatment) immediately following the first listening (baseline). A week later the order was reversed for the 2 listening trials. Statistical and graphic analysis of responses between first and second baseline responses indicate significant improvement in responses to silence and music excerpts over the 2 sessions. Applications of the findings to music listening interventions for maintaining attention, eliciting social interaction between clients or caregivers and their patients, and evaluating this population's affective responses to music are discussed.

The impact of food supplementation on infant weight gain in rural Bangladesh; an assessment of the Bangladesh Integrated Nutritional Program (BINP).

PubMed

Begum, Housne Ara; Mascie-Taylor, Cgn; Nahar, Shamsun

2007-01-01

To examine the efficiency of the Bangladesh Integrated Nutritional Program (BINP) in identifying which infants should be supplemented, whether full supplementation was given for the stipulated period of time, and whether the correct exit criteria from the supplementation programme were used. To test whether targeted food supplementation of infants between 6-12 months of age resulted in enhanced weight gain. Mallickbari Union, Bhaluka, a rural area located about 100 km north of Dhaka, Bangladesh. Five hundred and twenty-six infants followed for 6 to 12 months. Of the 526 infants studied, 368 should have received supplementation based on BINP criteria but only 111 infants (30%) did so, while a further 13% were incorrectly given supplementation. So in total over half (52.8%) of the sample was incorrectly identified for supplementation. In addition, less than a quarter of the infants received the full 90 days of supplementation and close to half of the infants exited the programme without the requisite weight gain. Infants were assigned to one of four groups: correctly supplemented, correctly non-supplemented, incorrectly supplemented or incorrectly non-supplemented. This classification provided natural controls; the correctly supplemented infants versus the incorrectly non-supplemented infants, and the correctly non-supplemented infants versus the incorrectly supplemented infants. There were no significant differences in weight gain between the correctly supplemented group and the incorrectly non-supplemented group or between the correctly non-supplemented and the incorrectly supplemented groups, nor was there any evidence of growth faltering in the incorrectly non-supplemented group. This study found serious programmatic deficiencies - inability to identify growth faltering in infants, failure to supplement for the full time period and incorrect exit procedures. There was no evidence that food supplementation had any impact on improving infant weight gain.

Learners' choices and beliefs about self-testing.

PubMed

Kornell, Nate; Son, Lisa K

2009-07-01

Students have to make scores of practical decisions when they study. We investigated the effectiveness of, and beliefs underlying, one such practical decision: the decision to test oneself while studying. Using a flashcards-like procedure, participants studied lists of word pairs. On the second of two study trials, participants either saw the entire pair again (pair mode) or saw the cue and attempted to generate the target (test mode). Participants were asked either to rate the effectiveness of each study mode (Experiment 1) or to choose between the two modes (Experiment 2). The results demonstrated a mismatch between metacognitive beliefs and study choices: Participants (incorrectly) judged that the pair mode resulted in the most learning, but chose the test mode most frequently. A post-experimental questionnaire suggested that self-testing was motivated by a desire to diagnose learning rather than a desire to improve learning.

A glossary of terms to assist the recognition and diagnosis of skin conditions associated with lower-limb chronic oedema.

PubMed

Elwell, Rebecca; Craven, Nicholas

2015-04-01

There are a number of recognised skin conditions associated with chronic oedema, but the lack of agreed definitions and terminology often leads to poor recognition and a delay in treatment. Many patients are given a diagnostic 'label' (e.g. varicose eczema) that often turns out to be incorrect, leading to an interruption in the patient pathway. Every skin condition can be described in a variety of ways and each professional group adheres to certain phrases and words that, within each discipline, are recognised, but when making onward referral or working between professions, it helps to have clear and concise definitions. This article aims is to standardise the terminology used to describe skin conditions of the lower limbs among health professionals, removing some of the discrepancy, and to develop a glossary to aid recognition, definition and hence diagnosis to ensure prompt and appropriate management is implemented.

Grammar, Punctuation, and Capitalization: a Handbook for Technical Writers and Editors

NASA Technical Reports Server (NTRS)

Mccaskill, Mary K.

1990-01-01

Writing problems are addressed which are often encountered in technical documents and preferences are indicated (Langley's) when authorities do not agree. It is directed toward professional writers, editors, and proofreaders. Those whose profession lies in other areas (for example, research or management), but who have occasion to write or review others' writing will also find this information useful. A functional attitude toward grammar and punctuation is presented. Chapter 1 on grammar presents grammatical problems related to each part of speech. Chapter 2 on sentence structure concerns syntax, that is, effective arrangement of words, with emphasis on methods of revision to improve writing effectiveness. Chapter 3 addresses punctuation marks, presenting their function, situations when they are required or incorrect, and situations when they are appropriate but optional. Chapter 4 presents capitalization, which is mostly a matter of editorial style and preference rather than a matter of generally accepted rules. An index and glossary are included.

Infants can use distributional cues to form syntactic categories.

PubMed

Gerken, LouAnn; Wilson, Rachel; Lewis, William

2005-05-01

Nearly all theories of language development emphasize the importance of distributional cues for segregating words and phrases into syntactic categories like noun, feminine or verb phrase. However, questions concerning whether such cues can be used to the exclusion of referential cues have been debated. Using the headturn preference procedure, American children aged 1;5 were briefly familiarized with a partial Russian gender paradigm, with a subset of the paradigm members withheld. During test, infants listened on alternate trials to previously withheld grammatical items and ungrammatical items with incorrect gender markings on previously heard stems. Across three experiments, infants discriminated new grammatical from ungrammatical items, but like adults in previous studies, were only able to do so when a subset of familiarization items was double marked for gender category. The results suggest that learners can use distributional cues to category structure, to the exclusion of referential cues, from relatively early in the language learning process.

Reply to Gopalswamy et al.

NASA Technical Reports Server (NTRS)

Cane, H. V.; Richardson, I. G.

2003-01-01

The comment of Gopalswamy et al. (thereafter GMY) relates to a letter discussing coronal mass ejections (CMEs), interplanetary ejecta and geomagnetic storms. GMY contend that Cane et al. incorrectly identified ejecta (interplanetary CMEs) and hypothesize that this is because Cane et al. fail to understand how to separate ejecta from "shock sheaths" when interpreting solar wind and energetic particle data sets. They (GMY) are wrong be cause the relevant section of the paper was concerned with the propagation time to 1 AU of any potentially geoeffective structures caused by CMEs, i.e. upstream compression regions with or without shocks, or ejecta. In other words, the travel times used by Cane et al. were purposefully and deliberately distinct from ejecta travel times (except for those slow ejecta, approx. 30% of their events, which generated no upstream features), and no error in identification was involved. The confusion of GMY stems from the description did not characterize the observations sufficiently clearly.

WordSeeker: concurrent bioinformatics software for discovering genome-wide patterns and word-based genomic signatures

PubMed Central

2010-01-01

Background An important focus of genomic science is the discovery and characterization of all functional elements within genomes. In silico methods are used in genome studies to discover putative regulatory genomic elements (called words or motifs). Although a number of methods have been developed for motif discovery, most of them lack the scalability needed to analyze large genomic data sets. Methods This manuscript presents WordSeeker, an enumerative motif discovery toolkit that utilizes multi-core and distributed computational platforms to enable scalable analysis of genomic data. A controller task coordinates activities of worker nodes, each of which (1) enumerates a subset of the DNA word space and (2) scores words with a distributed Markov chain model. Results A comprehensive suite of performance tests was conducted to demonstrate the performance, speedup and efficiency of WordSeeker. The scalability of the toolkit enabled the analysis of the entire genome of Arabidopsis thaliana; the results of the analysis were integrated into The Arabidopsis Gene Regulatory Information Server (AGRIS). A public version of WordSeeker was deployed on the Glenn cluster at the Ohio Supercomputer Center. Conclusion WordSeeker effectively utilizes concurrent computing platforms to enable the identification of putative functional elements in genomic data sets. This capability facilitates the analysis of the large quantity of sequenced genomic data. PMID:21210985

Communication training in mute autistic adolescents using the written work.

PubMed

LaVigna, G W

1977-06-01

The expressive and receptive use of three written words was taught to three mute autistic adolescents using a procedure based on Terrace's errorless discrimination model and Premack's language training with chimps. Expressive language was measured by the subject's selection of the appropriate word card from among the available alternatives when the corresponding object was presented. Receptive language was measured by the subject's selection of the appropriate object from among the available alternatives when the corresponding word card was presented. The sequence of the presentations and the order of placement of the available alternatives were randomized. The three subjects required 979, 1,791, and 1,644 trails, respectively, to master both the expressive and receptive use of the three words. The correct response rates for the three subjects over the entire training program were 92, 92, and 90%, respectively. It was concluded that, as concrete visual symbols, written words may provide a viable communication system for the mute autistic. The implications for treatment are discussed and suggestions for future research are made.

Contributions of Domain-General Cognitive Resources and Different Forms of Arithmetic Development to Pre-Algebraic Knowledge

PubMed Central

Fuchs, Lynn S.; Compton, Donald L.; Fuchs, Douglas; Powell, Sarah R.; Schumacher, Robin F.; Hamlett, Carol L.; Vernier, Emily; Namkung, Jessica M.; Vukovic, Rose K.

2012-01-01

The purpose of this study was to investigate the contributions of domain-general cognitive resources and different forms of arithmetic development to individual differences in pre-algebraic knowledge. Children (n=279; mean age=7.59 yrs) were assessed on 7 domain-general cognitive resources as well as arithmetic calculations and word problems at start of 2nd grade and on calculations, word problems, and pre-algebraic knowledge at end of 3rd grade. Multilevel path analysis, controlling for instructional effects associated with the sequence of classrooms in which students were nested across grades 2–3, indicated arithmetic calculations and word problems are foundational to pre-algebraic knowledge. Also, results revealed direct contributions of nonverbal reasoning and oral language to pre-algebraic knowledge, beyond indirect effects that are mediated via arithmetic calculations and word problems. By contrast, attentive behavior, phonological processing, and processing speed contributed to pre-algebraic knowledge only indirectly via arithmetic calculations and word problems. PMID:22409764

Identification of the sequence variations of 15 autosomal STR loci in a Chinese population.

PubMed

Chen, Wenjing; Cheng, Jianding; Ou, Xueling; Chen, Yong; Tong, Dayue; Sun, Hongyu

2014-01-01

DNA sequence variation including base(s) changes and insertion or deletion in the primer binding region may cause a null allele and, if this changes the length of the amplified fragment out of the allelic ladder, off-ladder (OL) alleles may be detected. In order to provide accurate and reliable DNA evidence for forensic DNA analysis, it is essential to clarify sequence variations in prevalently used STR loci. Suspected null alleles and OL alleles of PlowerPlex16® System from 21,934 unrelated Chinese individuals were verified by alternative systems and sequenced. A total of 17 cases with null alleles were identified, including 12 kinds of point mutations in 16 cases and a 19-base deletion in one case. The total frequency of null alleles was 7.751 × 10(-4). Eight hundred and forty-four OL alleles classified as being of 97 different kinds were observed at 15 STR loci of the PowerPlex®16 system except vWA. All the frequencies of OL alleles were under 0.01. Null alleles should be confirmed by alternative primers and OL alleles should be named appropriately. Particular attention should be paid to sequence variation, since incorrect designation could lead to false conclusions.

Horizontal Transfer of Segments of the 16S rRNA Genes between Species of the Streptococcus anginosus Group

PubMed Central

Schouls, Leo M.; Schot, Corrie S.; Jacobs, Jan A.

2003-01-01

The nature in variation of the 16S rRNA gene of members of the Streptococcus anginosus group was investigated by hybridization and DNA sequencing. A collection of 708 strains was analyzed by reverse line blot hybridization. This revealed the presence of distinct reaction patterns representing 11 different hybridization groups. The 16S rRNA genes of two strains of each hybridization group were sequenced to near-completion, and the sequence data confirmed the reverse line blot hybridization results. Closer inspection of the sequences revealed mosaic-like structures, strongly suggesting horizontal transfer of segments of the 16S rRNA gene between different species belonging to the Streptococcus anginosus group. Southern blot hybridization further showed that within a single strain all copies of the 16S rRNA gene had the same composition, indicating that the apparent mosaic structures were not PCR-induced artifacts. These findings indicate that the highly conserved rRNA genes are also subject to recombination and that these events may be fixed in the population. Such recombination may lead to the construction of incorrect phylogenetic trees based on the 16S rRNA genes. PMID:14645285

Enzyme-Free Replication with Two or Four Bases.

PubMed

Richert, Clemens; Hänle, Elena

2018-05-20

All known forms of life encode their genetic information in a sequence of bases of a genetic polymer and produce copies of their genes via semiconservative replication. How this process started before polymerase enzymes had been evolved is unclear. Enzyme-free copying of short stretches of DNA or RNA sequence has been demonstrated, using activated nucleotides, but not replication. We have developed a methodology for replication. It involves extension with reversible termination, enzyme-free ligation, and strand capture and allowed us to monitor nucleotide incorporation for an entire helical turn of DNA, both during a first and a second round of copying. When tracking replication mass spectrometrically, we found that with all four bases (A/C/G/T) an 'error catastrophe' occurs, with the correct sequence being 'overwhelmed' by incorrect ones. When only C and G were used, approx. half of all daughter strands had the mass of the correct sequence after 20 nonenzymatic copying steps. We conclude that enzyme-free replication is more likely to be successful with the two strongly pairing bases, rather than all four bases of the genetic alphabet. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Mathematics, thermodynamics, and modeling to address ten common misconceptions about protein structure, folding, and stability.

PubMed

Robic, Srebrenka

2010-01-01

To fully understand the roles proteins play in cellular processes, students need to grasp complex ideas about protein structure, folding, and stability. Our current understanding of these topics is based on mathematical models and experimental data. However, protein structure, folding, and stability are often introduced as descriptive, qualitative phenomena in undergraduate classes. In the process of learning about these topics, students often form incorrect ideas. For example, by learning about protein folding in the context of protein synthesis, students may come to an incorrect conclusion that once synthesized on the ribosome, a protein spends its entire cellular life time in its fully folded native confirmation. This is clearly not true; proteins are dynamic structures that undergo both local fluctuations and global unfolding events. To prevent and address such misconceptions, basic concepts of protein science can be introduced in the context of simple mathematical models and hands-on explorations of publicly available data sets. Ten common misconceptions about proteins are presented, along with suggestions for using equations, models, sequence, structure, and thermodynamic data to help students gain a deeper understanding of basic concepts relating to protein structure, folding, and stability.

The type specimens of Hekstra's owl

USGS Publications Warehouse

Browning, M.R.

1989-01-01

Twenty-four new subspecies of New World owls of the genus Otus were named in a paper by Hekstra (1982b) issued 17 December 1982. These same new names also appeared in Hekstra's (1982a) unpublished thesis. The holotypes of the new taxa are in 10 different collections, most of which are in the United States. Incorrect information was published with regard to museum designation, museum number, and collecting locality of many of the holotypes. I here list the holotypes with their correct specimen label data. The species names are here presented in the sequence proposed by Marshall & King (1988). The subspecies are generally arranged from north to south. The type localities given are standardized, and the spellings are corrected where required. Abbreviations for museum designations are given under acknowledgments. The numbers following the names refer to the pages where the descriptions were given (Hekstra 1982b). Several of the scientific names proposed were spelled incorrectly and these have been emended in accord with Article 31c and Appendix D of the International Code (International Commission on Zoological Nomenclature 1985). Taxonomic comments are appended for a small number of Hekstra's proposed taxa. The remaining forms he named require further study.

Words and possible words in early language acquisition.

PubMed

Marchetto, Erika; Bonatti, Luca L

2013-11-01

In order to acquire language, infants must extract its building blocks-words-and master the rules governing their legal combinations from speech. These two problems are not independent, however: words also have internal structure. Thus, infants must extract two kinds of information from the same speech input. They must find the actual words of their language. Furthermore, they must identify its possible words, that is, the sequences of sounds that, being morphologically well formed, could be words. Here, we show that infants' sensitivity to possible words appears to be more primitive and fundamental than their ability to find actual words. We expose 12- and 18-month-old infants to an artificial language containing a conflict between statistically coherent and structurally coherent items. We show that 18-month-olds can extract possible words when the familiarization stream contains marks of segmentation, but cannot do so when the stream is continuous. Yet, they can find actual words from a continuous stream by computing statistical relationships among syllables. By contrast, 12-month-olds can find possible words when familiarized with a segmented stream, but seem unable to extract statistically coherent items from a continuous stream that contains minimal conflicts between statistical and structural information. These results suggest that sensitivity to word structure is in place earlier than the ability to analyze distributional information. The ability to compute nontrivial statistical relationships becomes fully effective relatively late in development, when infants have already acquired a considerable amount of linguistic knowledge. Thus, mechanisms for structure extraction that do not rely on extensive sampling of the input are likely to have a much larger role in language acquisition than general-purpose statistical abilities. Copyright © 2013. Published by Elsevier Inc.

Quantification of sequence exchange events between PMS2 and PMS2CL provides a basis for improved mutation scanning of Lynch syndrome patients.

PubMed

van der Klift, Heleen M; Tops, Carli M J; Bik, Elsa C; Boogaard, Merel W; Borgstein, Anne-Marijke; Hansson, Kerstin B M; Ausems, Margreet G E M; Gomez Garcia, Encarna; Green, Andrew; Hes, Frederik J; Izatt, Louise; van Hest, Liselotte P; Alonso, Angel M; Vriends, Annette H J T; Wagner, Anja; van Zelst-Stams, Wendy A G; Vasen, Hans F A; Morreau, Hans; Devilee, Peter; Wijnen, Juul T

2010-05-01

Heterozygous mutations in PMS2 are involved in Lynch syndrome, whereas biallelic mutations are found in Constitutional mismatch repair-deficiency syndrome patients. Mutation detection is complicated by the occurrence of sequence exchange events between the duplicated regions of PMS2 and PMS2CL. We investigated the frequency of such events with a nonspecific polymerase chain reaction (PCR) strategy, co-amplifying both PMS2 and PMS2CL sequences. This allowed us to score ratios between gene and pseudogene-specific nucleotides at 29 PSV sites from exon 11 to the end of the gene. We found sequence transfer at all investigated PSVs from intron 12 to the 3' end of the gene in 4 to 52% of DNA samples. Overall, sequence exchange between PMS2 and PMS2CL was observed in 69% (83/120) of individuals. We demonstrate that mutation scanning with PMS2-specific PCR primers and MLPA probes, designed on PSVs, in the 3' duplicated region is unreliable, and present an RNA-based mutation detection strategy to improve reliability. Using this strategy, we found 19 different putative pathogenic PMS2 mutations. Four of these (21%) are lying in the region with frequent sequence transfer and are missed or called incorrectly as homozygous with several PSV-based mutation detection methods. (c) 2010 Wiley-Liss, Inc.

The minimal unit of phonological encoding: prosodic or lexical word.

PubMed

Wheeldon, Linda R; Lahiri, Aditi

2002-09-01

Wheeldon and Lahiri (Journal of Memory and Language 37 (1997) 356) used a prepared speech production task (Sternberg, S., Monsell, S., Knoll, R. L., & Wright, C. E. (1978). The latency and duration of rapid movement sequences: comparisons of speech and typewriting. In G. E. Stelmach (Ed.), Information processing in motor control and learning (pp. 117-152). New York: Academic Press; Sternberg, S., Wright, C. E., Knoll, R. L., & Monsell, S. (1980). Motor programs in rapid speech: additional evidence. In R. A. Cole (Ed.), The perception and production of fluent speech (pp. 507-534). Hillsdale, NJ: Erlbaum) to demonstrate that the latency to articulate a sentence is a function of the number of phonological words it comprises. Latencies for the sentence [Ik zoek het] [water] 'I seek the water' were shorter than latencies for sentences like [Ik zoek] [vers] [water] 'I seek fresh water'. We extend this research by examining the prepared production of utterances containing phonological words that are less than a lexical word in length. Dutch compounds (e.g. ooglid 'eyelid') form a single morphosyntactic word and a phonological word, which in turn includes two phonological words. We compare their prepared production latencies to those syntactic phrases consisting of an adjective and a noun (e.g. oud lid 'old member') which comprise two morphosyntactic and two phonological words, and to morphologically simple words (e.g. orgel 'organ') which comprise one morphosyntactic and one phonological word. Our findings demonstrate that the effect is limited to phrasal level phonological words, suggesting that production models need to make a distinction between lexical and phrasal phonology.

The Inhibitory Mechanism in Learning Ambiguous Words in a Second Language

PubMed Central

Lu, Yao; Wu, Junjie; Dunlap, Susan; Chen, Baoguo

2017-01-01

Ambiguous words are hard to learn, yet little is known about what causes this difficulty. The current study aimed to investigate the relationship between the representations of new and prior meanings of ambiguous words in second language (L2) learning, and to explore the function of inhibitory control on L2 ambiguous word learning at the initial stage of learning. During a 4-day learning phase, Chinese–English bilinguals learned 30 novel English words for 30 min per day using bilingual flashcards. Half of the words to be learned were unambiguous (had one meaning) and half were ambiguous (had two semantically unrelated meanings learned in sequence). Inhibitory control was introduced as a subject variable measured by a Stroop task. The semantic representations established for the studied items were probed using a cross-language semantic relatedness judgment task, in which the learned English words served as the prime, and the targets were either semantically related or unrelated to the prime. Results showed that response latencies for the second meaning of ambiguous words were slower than for the first meaning and for unambiguous words, and that performance on only the second meaning of ambiguous words was predicted by inhibitory control ability. These results suggest that, at the initial stage of L2 ambiguous word learning, the representation of the second meaning is weak, probably interfered with by the representation of the prior learned meaning. Moreover, inhibitory control may modulate learning of the new meanings, such that individuals with better inhibitory control may more effectively suppress interference from the first meaning, and thus learn the new meaning more quickly. PMID:28496423

The Inhibitory Mechanism in Learning Ambiguous Words in a Second Language.

PubMed

Lu, Yao; Wu, Junjie; Dunlap, Susan; Chen, Baoguo

2017-01-01

Ambiguous words are hard to learn, yet little is known about what causes this difficulty. The current study aimed to investigate the relationship between the representations of new and prior meanings of ambiguous words in second language (L2) learning, and to explore the function of inhibitory control on L2 ambiguous word learning at the initial stage of learning. During a 4-day learning phase, Chinese-English bilinguals learned 30 novel English words for 30 min per day using bilingual flashcards. Half of the words to be learned were unambiguous (had one meaning) and half were ambiguous (had two semantically unrelated meanings learned in sequence). Inhibitory control was introduced as a subject variable measured by a Stroop task. The semantic representations established for the studied items were probed using a cross-language semantic relatedness judgment task, in which the learned English words served as the prime, and the targets were either semantically related or unrelated to the prime. Results showed that response latencies for the second meaning of ambiguous words were slower than for the first meaning and for unambiguous words, and that performance on only the second meaning of ambiguous words was predicted by inhibitory control ability. These results suggest that, at the initial stage of L2 ambiguous word learning, the representation of the second meaning is weak, probably interfered with by the representation of the prior learned meaning. Moreover, inhibitory control may modulate learning of the new meanings, such that individuals with better inhibitory control may more effectively suppress interference from the first meaning, and thus learn the new meaning more quickly.

The Deinococcus-Thermus phylum and the effect of rRNA composition on phylogenetic tree construction

NASA Technical Reports Server (NTRS)

Weisburg, W. G.; Giovannoni, S. J.; Woese, C. R.

1989-01-01

Through comparative analysis of 16S ribosomal RNA sequences, it can be shown that two seemingly dissimilar types of eubacteria Deinococcus and the ubiquitous hot spring organism Thermus are distantly but specifically related to one another. This confirms an earlier report based upon 16S rRNA oligonucleotide cataloging studies (Hensel et al., 1986). Their two lineages form a distinctive grouping within the eubacteria that deserved the taxonomic status of a phylum. The (partial) sequence of T. aquaticus rRNA appears relatively close to those of other thermophilic eubacteria. e.g. Thermotoga maritima and Thermomicrobium roseum. However, this closeness does not reflect a true evolutionary closeness; rather it is due to a "thermophilic convergence", the result of unusually high G+C composition in the rRNAs of thermophilic bacteria. Unless such compositional biases are taken into account, the branching order and root of phylogenetic trees can be incorrectly inferred.

Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors.

PubMed

Haghverdi, Laleh; Lun, Aaron T L; Morgan, Michael D; Marioni, John C

2018-06-01

Large-scale single-cell RNA sequencing (scRNA-seq) data sets that are produced in different laboratories and at different times contain batch effects that may compromise the integration and interpretation of the data. Existing scRNA-seq analysis methods incorrectly assume that the composition of cell populations is either known or identical across batches. We present a strategy for batch correction based on the detection of mutual nearest neighbors (MNNs) in the high-dimensional expression space. Our approach does not rely on predefined or equal population compositions across batches; instead, it requires only that a subset of the population be shared between batches. We demonstrate the superiority of our approach compared with existing methods by using both simulated and real scRNA-seq data sets. Using multiple droplet-based scRNA-seq data sets, we demonstrate that our MNN batch-effect-correction method can be scaled to large numbers of cells.

Spectral analysis of variable-length coded digital signals

NASA Astrophysics Data System (ADS)

Cariolaro, G. L.; Pierobon, G. L.; Pupolin, S. G.

1982-05-01

A spectral analysis is conducted for a variable-length word sequence by an encoder driven by a stationary memoryless source. A finite-state sequential machine is considered as a model of the line encoder, and the spectral analysis of the encoded message is performed under the assumption that the sourceword sequence is composed of independent identically distributed words. Closed form expressions for both the continuous and discrete parts of the spectral density are derived in terms of the encoder law and sourceword statistics. The jump part exhibits jumps at multiple integers of per lambda(sub 0)T, where lambda(sub 0) is the greatest common divisor of the possible codeword lengths, and T is the symbol period. The derivation of the continuous part can be conveniently factorized, and the theory is applied to the spectral analysis of BnZS and HDBn codes.

Distinct frontal regions for processing sentence syntax and story grammar.

PubMed

Sirigu, A; Cohen, L; Zalla, T; Pradat-Diehl, P; Van Eeckhout, P; Grafman, J; Agid, Y

1998-12-01

Time is a fundamental dimension of cognition. It is expressed in the sequential ordering of individual elements in a wide variety of activities such as language, motor control or in the broader domain of long range goal-directed actions. Several studies have shown the importance of the frontal lobes in sequencing information. The question addressed in this study is whether this brain region hosts a single supramodal sequence processor, or whether separate mechanisms are required for different kinds of temporally organised knowledge structures such as syntax and action knowledge. Here we show that so-called agrammatic patients, with lesions in Broca's area, ordered word groups correctly to form a logical sequence of actions but they were severely impaired when similar word groups had to be ordered as a syntactically well-formed sentence. The opposite performance was observed in patients with dorsolateral prefrontal lesions, that is, while their syntactic processing was intact at the sentence level, they demonstrated a pronounced deficit in producing temporally coherent sequences of actions. Anatomical reconstruction of lesions from brain scans revealed that the sentence and action grammar deficits involved distinct, non-overlapping sites within the frontal lobes. Finally, in a third group of patients whose lesions encompassed both Broca's area and the prefrontal cortex, the two types of deficits were found. We conclude that sequence processing is specific to knowledge domains and involves different networks within the frontal lobes.

Sure, or unsure? Measuring students' confidence and the potential impact on patient safety in multiple-choice questions.

PubMed

Rangel, Rafael Henrique; Möller, Leona; Sitter, Helmut; Stibane, Tina; Strzelczyk, Adam

2017-11-01

Multiple-choice questions (MCQs) provide useful information about correct and incorrect answers, but they do not offer information about students' confidence. Ninety and another 81 medical students participated each in a curricular neurology multiple-choice exam and indicated their confidence for every single MCQ. Each MCQ had a defined level of potential clinical impact on patient safety (uncritical, risky, harmful). Our first objective was to detect informed (IF), guessed (GU), misinformed (MI), and uninformed (UI) answers. Further, we evaluated whether there were significant differences for confidence at correct and incorrect answers. Then, we explored if clinical impact had a significant influence on students' confidence. There were 1818 IF, 635 GU, 71 MI, and 176 UI answers in exam I and 1453 IF, 613 GU, 92 MI, and 191 UI answers in exam II. Students' confidence was significantly higher for correct than for incorrect answers at both exams (p < 0.001). For exam I, students' confidence was significantly higher for incorrect harmful than for incorrect risky classified MCQs (p = 0.01). At exam II, students' confidence was significantly higher for incorrect harmful than for incorrect benign (p < 0.01) and significantly higher for correct benign than for correct harmful categorized MCQs (p = 0.01). We were pleased to see that there were more informed than guessed, more uninformed than misinformed answers and higher students' confidence for correct than for incorrect answers. Our expectation that students state higher confidence in correct and harmful and lower confidence in incorrect and harmful MCQs could not be confirmed.

Area Determination of Diabetic Foot Ulcer Images Using a Cascaded Two-Stage SVM-Based Classification.

PubMed

Wang, Lei; Pedersen, Peder C; Agu, Emmanuel; Strong, Diane M; Tulu, Bengisu

2017-09-01

The standard chronic wound assessment method based on visual examination is potentially inaccurate and also represents a significant clinical workload. Hence, computer-based systems providing quantitative wound assessment may be valuable for accurately monitoring wound healing status, with the wound area the best suited for automated analysis. Here, we present a novel approach, using support vector machines (SVM) to determine the wound boundaries on foot ulcer images captured with an image capture box, which provides controlled lighting and range. After superpixel segmentation, a cascaded two-stage classifier operates as follows: in the first stage, a set of k binary SVM classifiers are trained and applied to different subsets of the entire training images dataset, and incorrectly classified instances are collected. In the second stage, another binary SVM classifier is trained on the incorrectly classified set. We extracted various color and texture descriptors from superpixels that are used as input for each stage in the classifier training. Specifically, color and bag-of-word representations of local dense scale invariant feature transformation features are descriptors for ruling out irrelevant regions, and color and wavelet-based features are descriptors for distinguishing healthy tissue from wound regions. Finally, the detected wound boundary is refined by applying the conditional random field method. We have implemented the wound classification on a Nexus 5 smartphone platform, except for training which was done offline. Results are compared with other classifiers and show that our approach provides high global performance rates (average sensitivity = 73.3%, specificity = 94.6%) and is sufficiently efficient for a smartphone-based image analysis.

Intonation and dialog context as constraints for speech recognition.

PubMed

Taylor, P; King, S; Isard, S; Wright, H

1998-01-01

This paper describes a way of using intonation and dialog context to improve the performance of an automatic speech recognition (ASR) system. Our experiments were run on the DCIEM Maptask corpus, a corpus of spontaneous task-oriented dialog speech. This corpus has been tagged according to a dialog analysis scheme that assigns each utterance to one of 12 "move types," such as "acknowledge," "query-yes/no" or "instruct." Most ASR systems use a bigram language model to constrain the possible sequences of words that might be recognized. Here we use a separate bigram language model for each move type. We show that when the "correct" move-specific language model is used for each utterance in the test set, the word error rate of the recognizer drops. Of course when the recognizer is run on previously unseen data, it cannot know in advance what move type the speaker has just produced. To determine the move type we use an intonation model combined with a dialog model that puts constraints on possible sequences of move types, as well as the speech recognizer likelihoods for the different move-specific models. In the full recognition system, the combination of automatic move type recognition with the move specific language models reduces the overall word error rate by a small but significant amount when compared with a baseline system that does not take intonation or dialog acts into account. Interestingly, the word error improvement is restricted to "initiating" move types, where word recognition is important. In "response" move types, where the important information is conveyed by the move type itself--for example, positive versus negative response--there is no word error improvement, but recognition of the response types themselves is good. The paper discusses the intonation model, the language models, and the dialog model in detail and describes the architecture in which they are combined.

Deep learning for pharmacovigilance: recurrent neural network architectures for labeling adverse drug reactions in Twitter posts.

PubMed

Cocos, Anne; Fiks, Alexander G; Masino, Aaron J

2017-07-01

Social media is an important pharmacovigilance data source for adverse drug reaction (ADR) identification. Human review of social media data is infeasible due to data quantity, thus natural language processing techniques are necessary. Social media includes informal vocabulary and irregular grammar, which challenge natural language processing methods. Our objective is to develop a scalable, deep-learning approach that exceeds state-of-the-art ADR detection performance in social media. We developed a recurrent neural network (RNN) model that labels words in an input sequence with ADR membership tags. The only input features are word-embedding vectors, which can be formed through task-independent pretraining or during ADR detection training. Our best-performing RNN model used pretrained word embeddings created from a large, non-domain-specific Twitter dataset. It achieved an approximate match F-measure of 0.755 for ADR identification on the dataset, compared to 0.631 for a baseline lexicon system and 0.65 for the state-of-the-art conditional random field model. Feature analysis indicated that semantic information in pretrained word embeddings boosted sensitivity and, combined with contextual awareness captured in the RNN, precision. Our model required no task-specific feature engineering, suggesting generalizability to additional sequence-labeling tasks. Learning curve analysis showed that our model reached optimal performance with fewer training examples than the other models. ADR detection performance in social media is significantly improved by using a contextually aware model and word embeddings formed from large, unlabeled datasets. The approach reduces manual data-labeling requirements and is scalable to large social media datasets. © The Author 2017. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com

The Effect of Intensified Language Exposure on Accommodating Talker Variability.

PubMed

Antoniou, Mark; Wong, Patrick C M; Wang, Suiping

2015-06-01

This study systematically examined the role of intensified exposure to a second language on accommodating talker variability. English native listeners (n = 37) were compared with Mandarin listeners who had either lived in the United States for an extended period of time (n = 33) or had lived only in China (n = 44). Listeners responded to target words in an English word-monitoring task in which sequences of words were randomized. Half of the sequences were spoken by a single talker and the other half by multiple talkers. Mandarin listeners living in China were slower and less accurate than both English listeners and Mandarin listeners living in the United States. Mandarin listeners living in the United States were less accurate than English natives only in the more cognitively demanding mixed-talker condition. Mixed-talker speech affects processing in native and nonnative listeners alike, although the decrement is larger in nonnatives and further exaggerated in less proficient listeners. Language immersion improves listeners' ability to resolve talker variability, and this suggests that immersion may automatize nonnative processing, freeing cognitive resources that may play a crucial role in speech perception. These results lend support to the active control model of speech perception.

PanGEA: identification of allele specific gene expression using the 454 technology.

PubMed

Kofler, Robert; Teixeira Torres, Tatiana; Lelley, Tamas; Schlötterer, Christian

2009-05-14

Next generation sequencing technologies hold great potential for many biological questions. While mainly used for genomic sequencing, they are also very promising for gene expression profiling. Sequencing of cDNA does not only provide an estimate of the absolute expression level, it can also be used for the identification of allele specific gene expression. We developed PanGEA, a tool which enables a fast and user-friendly analysis of allele specific gene expression using the 454 technology. PanGEA allows mapping of 454-ESTs to genes or whole genomes, displaying gene expression profiles, identification of SNPs and the quantification of allele specific gene expression. The intuitive GUI of PanGEA facilitates a flexible and interactive analysis of the data. PanGEA additionally implements a modification of the Smith-Waterman algorithm which deals with incorrect estimates of homopolymer length as occuring in the 454 technology To our knowledge, PanGEA is the first tool which facilitates the identification of allele specific gene expression. PanGEA is distributed under the Mozilla Public License and available at: http://www.kofler.or.at/bioinformatics/PanGEA

PanGEA: Identification of allele specific gene expression using the 454 technology

PubMed Central

Kofler, Robert; Teixeira Torres, Tatiana; Lelley, Tamas; Schlötterer, Christian

2009-01-01

Background Next generation sequencing technologies hold great potential for many biological questions. While mainly used for genomic sequencing, they are also very promising for gene expression profiling. Sequencing of cDNA does not only provide an estimate of the absolute expression level, it can also be used for the identification of allele specific gene expression. Results We developed PanGEA, a tool which enables a fast and user-friendly analysis of allele specific gene expression using the 454 technology. PanGEA allows mapping of 454-ESTs to genes or whole genomes, displaying gene expression profiles, identification of SNPs and the quantification of allele specific gene expression. The intuitive GUI of PanGEA facilitates a flexible and interactive analysis of the data. PanGEA additionally implements a modification of the Smith-Waterman algorithm which deals with incorrect estimates of homopolymer length as occuring in the 454 technology Conclusion To our knowledge, PanGEA is the first tool which facilitates the identification of allele specific gene expression. PanGEA is distributed under the Mozilla Public License and available at: PMID:19442283

Vocabulary development in children with hearing loss: the role of child, family, and educational variables.

PubMed

Coppens, Karien M; Tellings, Agnes; van der Veld, William; Schreuder, Robert; Verhoeven, Ludo

2012-01-01

In the present study we examined the effect of hearing status on reading vocabulary development. More specifically, we examined the change of lexical competence in children with hearing loss over grade 4-7 and the predictors of this change. Therefore, we used a multi-factor longitudinal design with multiple outcomes, measuring the reading vocabulary knowledge in children with hearing loss from grades 4 and 5, and of children without hearing loss from grade 4, for 3 years with two word tasks: a lexical decision task and a use decision task. With these tasks we measured word form recognition and (in)correct usage recognition, respectively. A GLM repeated measures procedure indicated that scores and growth rates on the two tasks were affected by hearing status. Moreover, with structural equation modeling we observed that the development of lexical competence in children with hearing loss is stable over time, and a child's lexical competence can be explained best by his or her lexical competence assessed on a previous measurement occasion. If you look back, differences in lexical competence among children with hearing loss stay unfortunately the same. Educational placement, use of sign language at home, intelligence, use of hearing devices, and onset of deafness can account for the differences among children with hearing loss. Copyright © 2011 Elsevier Ltd. All rights reserved.

Distinct but Overlapping Patterns of Response to Words and Faces in the Fusiform Gyrus.

PubMed

Harris, Richard J; Rice, Grace E; Young, Andrew W; Andrews, Timothy J

2016-07-01

Converging evidence suggests that the fusiform gyrus is involved in the processing of both faces and words. We used fMRI to investigate the extent to which the representation of words and faces in this region of the brain is based on a common neural representation. In Experiment 1, a univariate analysis revealed regions in the fusiform gyrus that were only selective for faces and other regions that were only selective for words. However, we also found regions that showed both word-selective and face-selective responses, particularly in the left hemisphere. We then used a multivariate analysis to measure the pattern of response to faces and words. Despite the overlap in regional responses, we found distinct patterns of response to both faces and words in the left and right fusiform gyrus. In Experiment 2, fMR adaptation was used to determine whether information about familiar faces and names is integrated in the fusiform gyrus. Distinct regions of the fusiform gyrus showed adaptation to either familiar faces or familiar names. However, there was no adaptation to sequences of faces and names with the same identity. Taken together, these results provide evidence for distinct, but overlapping, neural representations for words and faces in the fusiform gyrus. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

The effect of incremental changes in phonotactic probability and neighborhood density on word learning by preschool children

PubMed Central

Storkel, Holly L.; Bontempo, Daniel E.; Aschenbrenner, Andrew J.; Maekawa, Junko; Lee, Su-Yeon

2013-01-01

Purpose Phonotactic probability or neighborhood density have predominately been defined using gross distinctions (i.e., low vs. high). The current studies examined the influence of finer changes in probability (Experiment 1) and density (Experiment 2) on word learning. Method The full range of probability or density was examined by sampling five nonwords from each of four quartiles. Three- and 5-year-old children received training on nonword-nonobject pairs. Learning was measured in a picture-naming task immediately following training and 1-week after training. Results were analyzed using multi-level modeling. Results A linear spline model best captured nonlinearities in phonotactic probability. Specifically word learning improved as probability increased in the lowest quartile, worsened as probability increased in the midlow quartile, and then remained stable and poor in the two highest quartiles. An ordinary linear model sufficiently described neighborhood density. Here, word learning improved as density increased across all quartiles. Conclusion Given these different patterns, phonotactic probability and neighborhood density appear to influence different word learning processes. Specifically, phonotactic probability may affect recognition that a sound sequence is an acceptable word in the language and is a novel word for the child, whereas neighborhood density may influence creation of a new representation in long-term memory. PMID:23882005

The role of short-term memory impairment in nonword repetition, real word repetition, and nonword decoding: A case study.

PubMed

Peter, Beate

2018-01-01

In a companion study, adults with dyslexia and adults with a probable history of childhood apraxia of speech showed evidence of difficulty with processing sequential information during nonword repetition, multisyllabic real word repetition and nonword decoding. Results suggested that some errors arose in visual encoding during nonword reading, all levels of processing but especially short-term memory storage/retrieval during nonword repetition, and motor planning and programming during complex real word repetition. To further investigate the role of short-term memory, a participant with short-term memory impairment (MI) was recruited. MI was confirmed with poor performance during a sentence repetition and three nonword repetition tasks, all of which have a high short-term memory load, whereas typical performance was observed during tests of reading, spelling, and static verbal knowledge, all with low short-term memory loads. Experimental results show error-free performance during multisyllabic real word repetition but high counts of sequence errors, especially migrations and assimilations, during nonword repetition, supporting short-term memory as a locus of sequential processing deficit during nonword repetition. Results are also consistent with the hypothesis that during complex real word repetition, short-term memory is bypassed as the word is recognized and retrieved from long-term memory prior to producing the word.

Alignment-free genetic sequence comparisons: a review of recent approaches by word analysis.

PubMed

Bonham-Carter, Oliver; Steele, Joe; Bastola, Dhundy

2014-11-01

Modern sequencing and genome assembly technologies have provided a wealth of data, which will soon require an analysis by comparison for discovery. Sequence alignment, a fundamental task in bioinformatics research, may be used but with some caveats. Seminal techniques and methods from dynamic programming are proving ineffective for this work owing to their inherent computational expense when processing large amounts of sequence data. These methods are prone to giving misleading information because of genetic recombination, genetic shuffling and other inherent biological events. New approaches from information theory, frequency analysis and data compression are available and provide powerful alternatives to dynamic programming. These new methods are often preferred, as their algorithms are simpler and are not affected by synteny-related problems. In this review, we provide a detailed discussion of computational tools, which stem from alignment-free methods based on statistical analysis from word frequencies. We provide several clear examples to demonstrate applications and the interpretations over several different areas of alignment-free analysis such as base-base correlations, feature frequency profiles, compositional vectors, an improved string composition and the D2 statistic metric. Additionally, we provide detailed discussion and an example of analysis by Lempel-Ziv techniques from data compression. © The Author 2013. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

Contingency learning without awareness: evidence for implicit control.

PubMed

Schmidt, James R; Crump, Matthew J C; Cheesman, Jim; Besner, Derek

2007-06-01

The results of four experiments provide evidence for controlled processing in the absence of awareness. Participants identified the colour of a neutral distracter word. Each of four words (e.g., MOVE) was presented in one of the four colours 75% of the time (Experiments 1 and 4) or 50% of the time (Experiments 2 and 3). Colour identification was faster when the words appeared in the colour they were most often presented in relative to when they appeared in another colour, even for participants who were subjectively unaware of any contingencies between the words and the colours. An analysis of sequence effects showed that participants who were unaware of the relation between distracter words and colours nonetheless controlled the impact of the word on performance depending on the nature of the previous trial. A block analysis of contingency-unaware participants revealed that contingencies were learned rapidly in the first block of trials. Experiment 3 showed that the contingency effect does not depend on the level of awareness, thus ruling out explicit strategy accounts. Finally, Experiment 4 showed that the contingency effect results from behavioural control and not from semantic association or stimulus familiarity. These results thus provide evidence for implicit control.

Evidence for Human Fronto-Central Gamma Activity during Long-Term Memory Encoding of Word Sequences

PubMed Central

Meeuwissen, Esther Berendina; Takashima, Atsuko; Fernández, Guillén; Jensen, Ole

2011-01-01

Although human gamma activity (30–80 Hz) associated with visual processing is often reported, it is not clear to what extend gamma activity can be reliably detected non-invasively from frontal areas during complex cognitive tasks such as long term memory (LTM) formation. We conducted a memory experiment composed of 35 blocks each having three parts: LTM encoding, working memory (WM) maintenance and LTM retrieval. In the LTM encoding and WM maintenance parts, participants had to respectively encode or maintain the order of three sequentially presented words. During LTM retrieval subjects had to reproduce these sequences. Using magnetoencephalography (MEG) we identified significant differences in the gamma and beta activity. Robust gamma activity (55–65 Hz) in left BA6 (supplementary motor area (SMA)/pre-SMA) was stronger during LTM rehearsal than during WM maintenance. The gamma activity was sustained throughout the 3.4 s rehearsal period during which a fixation cross was presented. Importantly, the difference in gamma band activity correlated with memory performance over subjects. Further we observed a weak gamma power difference in left BA6 during the first half of the LTM rehearsal interval larger for successfully than unsuccessfully reproduced word triplets. In the beta band, we found a power decrease in left anterior regions during LTM rehearsal compared to WM maintenance. Also this suppression of beta power correlated with memory performance over subjects. Our findings show that an extended network of brain areas, characterized by oscillatory activity in different frequency bands, supports the encoding of word sequences in LTM. Gamma band activity in BA6 possibly reflects memory processes associated with language and timing, and suppression of beta activity at left frontal sensors is likely to reflect the release of inhibition directly associated with the engagement of language functions. PMID:21738641

Early dynamics of the semantic priming shift

PubMed Central

Lavigne, Frédéric; Chanquoy, Lucile; Dumercy, Laurent; Vitu, Françoise

2013-01-01

Semantic processing of sequences of words requires the cognitive system to keep several word meanings simultaneously activated in working memory with limited capacity. The real- time updating of the sequence of word meanings relies on dynamic changes in the associates to the words that are activated. Protocols involving two sequential primes report a semantic priming shift from larger priming of associates to the first prime to larger priming of associates to the second prime, in a range of long SOAs (stimulus-onset asynchronies) between the second prime and the target. However, the possibility for an early semantic priming shift is still to be tested, and its dynamics as a function of association strength remain unknown. Three multiple priming experiments are proposed that cross-manipulate association strength between each of two successive primes and a target, for different values of short SOAs and prime durations. Results show an early priming shift ranging from priming of associates to the first prime only to priming of strong associates to the first prime and all of the associates to the second prime. We investigated the neural basis of the early priming shift by using a network model of spike frequency adaptive cortical neurons (e.g., Deco & Rolls, 2005), able to code different association strengths between the primes and the target. The cortical network model provides a description of the early dynamics of the priming shift in terms of pro-active and retro-active interferences within populations of excitatory neurons regulated by fast and unselective inhibitory feedback. PMID:23717346

Sub-Audible Speech Recognition Based upon Electromyographic Signals

NASA Technical Reports Server (NTRS)

Jorgensen, Charles C. (Inventor); Agabon, Shane T. (Inventor); Lee, Diana D. (Inventor)

2012-01-01

Method and system for processing and identifying a sub-audible signal formed by a source of sub-audible sounds. Sequences of samples of sub-audible sound patterns ("SASPs") for known words/phrases in a selected database are received for overlapping time intervals, and Signal Processing Transforms ("SPTs") are formed for each sample, as part of a matrix of entry values. The matrix is decomposed into contiguous, non-overlapping two-dimensional cells of entries, and neural net analysis is applied to estimate reference sets of weight coefficients that provide sums with optimal matches to reference sets of values. The reference sets of weight coefficients are used to determine a correspondence between a new (unknown) word/phrase and a word/phrase in the database.

42 CFR 489.40 - Definition of incorrect collection.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 42 Public Health 5 2011-10-01 2011-10-01 false Definition of incorrect collection. 489.40 Section 489.40 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) STANDARDS AND CERTIFICATION PROVIDER AGREEMENTS AND SUPPLIER APPROVAL Handling of Incorrect...

42 CFR 489.40 - Definition of incorrect collection.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 42 Public Health 5 2010-10-01 2010-10-01 false Definition of incorrect collection. 489.40 Section 489.40 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) STANDARDS AND CERTIFICATION PROVIDER AGREEMENTS AND SUPPLIER APPROVAL Handling of Incorrect...

Deficits in sequential processing manifest in motor and linguistic tasks in a multigenerational family with childhood apraxia of speech

PubMed Central

PETER, BEATE; BUTTON, LE; STOEL-GAMMON, CAROL; CHAPMAN, KATHY; RASKIND, WENDY H.

2013-01-01

The purpose of this study was to evaluate a global deficit in sequential processing as candidate endophenotypein a family with familial childhood apraxia of speech (CAS). Of 10 adults and 13 children in a three-generational family with speech sound disorder (SSD) consistent with CAS, 3 adults and 6 children had past or present SSD diagnoses. Two preschoolers with unremediated CAS showed a high number of sequencing errors during single-word production. Performance on tasks with high sequential processing loads differentiated between the affected and unaffected family members, whereas there were no group differences in tasks with low processing loads. Adults with a history of SSD produced more sequencing errors during nonword and multisyllabic real word imitation, compared to those without such a history. Results are consistent with a global deficit in sequential processing that influences speech development as well as cognitive and linguistic processing. PMID:23339324

Pattern statistics on Markov chains and sensitivity to parameter estimation

PubMed Central

Nuel, Grégory

2006-01-01

Background: In order to compute pattern statistics in computational biology a Markov model is commonly used to take into account the sequence composition. Usually its parameter must be estimated. The aim of this paper is to determine how sensitive these statistics are to parameter estimation, and what are the consequences of this variability on pattern studies (finding the most over-represented words in a genome, the most significant common words to a set of sequences,...). Results: In the particular case where pattern statistics (overlap counting only) computed through binomial approximations we use the delta-method to give an explicit expression of σ, the standard deviation of a pattern statistic. This result is validated using simulations and a simple pattern study is also considered. Conclusion: We establish that the use of high order Markov model could easily lead to major mistakes due to the high sensitivity of pattern statistics to parameter estimation. PMID:17044916

Pattern statistics on Markov chains and sensitivity to parameter estimation.

PubMed

Nuel, Grégory

2006-10-17

In order to compute pattern statistics in computational biology a Markov model is commonly used to take into account the sequence composition. Usually its parameter must be estimated. The aim of this paper is to determine how sensitive these statistics are to parameter estimation, and what are the consequences of this variability on pattern studies (finding the most over-represented words in a genome, the most significant common words to a set of sequences,...). In the particular case where pattern statistics (overlap counting only) computed through binomial approximations we use the delta-method to give an explicit expression of sigma, the standard deviation of a pattern statistic. This result is validated using simulations and a simple pattern study is also considered. We establish that the use of high order Markov model could easily lead to major mistakes due to the high sensitivity of pattern statistics to parameter estimation.

Is scanning in probed order recall articulatory?

PubMed

Farrell, Simon; Lelièvre, Anna

2009-09-01

We consider how theories of serial recall might apply to other short-term memory tasks involving recall of order. In particular, we consider the possibility that when participants are cued to recall an item at an arbitrary position in a sequence, they covertly serially recall the list up to the cued position. One question is whether such "scanning" is articulatory in nature. Two experiments are presented in which the syllabic length of words preceding and following target positions were manipulated, to test the prediction of an articulatory-based mechanism that time to recall an item at a particular position will depend on the number of preceding long words. Although latency was dependent on target position, no word length effects on latency were observed. Additionally, the effects of word length on accuracy replicate recent demonstrations in serial recall that recall accuracy is dependent on the word length of all list items, not just that of target items, in line with distinctiveness assumptions. It is concluded that if scanning does occur, it is not carried out by covert or overt articulation.

Information processing of visually presented picture and word stimuli by young hearing-impaired and normal-hearing children.

PubMed

Kelly, R R; Tomlison-Keasey, C

1976-12-01

Eleven hearing-impaired children and 11 normal-hearing children (mean = four years 11 months) were visually presented familiar items in either picture or word form. Subjects were asked to recognize the stimuli they had seen from cue cards consisting of pictures or words. They were then asked to recall the sequence of stimuli by arranging the cue cards selected. The hearing-impaired group and normal-hearing subjects performed differently with the picture/picture (P/P) and word/word (W/W) modes in the recognition phase. The hearing impaired performed equally well with both modes (P/P and W/W), while the normal hearing did significantly better on the P/P mode. Furthermore, the normal-hearing group showed no difference in processing like modes (P/P and W/W) when compared to unlike modes (W/P and P/W). In contrast, the hearing-impaired subjects did better on like modes. The results were interpreted, in part, as supporting the position that young normal-hearing children dual code their visual information better than hearing-impaired children.

The augmentation algorithm and molecular phylogenetic trees

NASA Technical Reports Server (NTRS)

Holmquist, R.

1978-01-01

Moore's (1977) augmentation procedure is discussed, and it is concluded that the procedure is valid for obtaining estimates of the total number of fixed nucleotide substitutions both theoretically and in practice, for both simulated and real data, and in agreement, for experimentally dense data sets, with stochastic estimates of the divergence, provided the restrictions on codon mutability resulting from natural selection are explicitly allowed for. Tateno and Nei's (1978) critique that the augmentation procedure has a systematic bias toward overestimation of the total number of nucleotide replacements is disputed, and a data analysis suggests that ancestral sequences inferred by the method of parsimony contain a large number of incorrectly assigned nucleotides.

Console test report for shuttle task 501 shuttle carrier aircraft transceiver console (SED 36115353-301)

NASA Technical Reports Server (NTRS)

Lane, J. H.

1976-01-01

Performance tests completed on the Space Shuttle Carrier Aircraft (SCA) transceiver console, verifying its design objectives, were described. These tests included: (1) check of power supply voltages for correct output voltage and energization at the proper point in the turn on sequence, (2) check of cooling system (LRU blower, overload sensors and circuitry, and thermocouple probe), (3) check of control circuits logic, including the provisions for remote control and display, (4) check of the LRU connector for presence of correct voltages and absence of incorrect voltages under both energized and deenergized conditions, and (5) check of the AGC and power output monitor circuits.

Realising the Promise of Cancer Predisposition Genes

PubMed Central

Rahman, Nazneen

2016-01-01

Genes in which germline mutations confer high or moderate increased risks of cancer are called cancer predisposition genes (CPG). Over 100 CPGs have been identified providing important scientific insights in many areas, particularly mechanisms of cancer causation. Moreover, clinical utilisation of CPGs has had substantial impact in diagnosis, optimised management and prevention of cancer. The recent transformative advances in DNA sequencing bring the promise of many more CPG discoveries and greater, broader clinical applications. However, there is also considerable potential for incorrect inferences and inappropriate clinical applications. Realising the promise of cancer predisposition genes for science and medicine will thus require careful navigation. PMID:24429628

Reading speed benefits from increased vertical word spacing in normal peripheral vision.

PubMed

Chung, Susana T L

2004-07-01

Crowding, the adverse spatial interaction due to proximity of adjacent targets, has been suggested as an explanation for slow reading in peripheral vision. The purposes of this study were to (1) demonstrate that crowding exists at the word level and (2) examine whether or not reading speed in central and peripheral vision can be enhanced with increased vertical word spacing. Five normal observers read aloud sequences of six unrelated four-letter words presented on a computer monitor, one word at a time, using rapid serial visual presentation (RSVP). Reading speeds were calculated based on the RSVP exposure durations yielding 80% correct. Testing was conducted at the fovea and at 5 degrees and 10 degrees in the inferior visual field. Critical print size (CPS) for each observer and at each eccentricity was first determined by measuring reading speeds for four print sizes using unflanked words. We then presented words at 0.8x or 1.4x CPS, with each target word flanked by two other words, one above and one below the target word. Reading speeds were determined for vertical word spacings (baseline-to-baseline separation between two vertically separated words) ranging from 0.8x to 2x the standard single-spacing, as well as the unflanked condition. At the fovea, reading speed increased with vertical word spacing up to about 1.2x to 1.5x the standard spacing and remained constant and similar to the unflanked reading speed at larger vertical word spacings. In the periphery, reading speed also increased with vertical word spacing, but it remained below the unflanked reading speed for all spacings tested. At 2x the standard spacing, peripheral reading speed was still about 25% lower than the unflanked reading speed for both eccentricities and print sizes. Results from a control experiment showed that the greater reliance of peripheral reading speed on vertical word spacing was also found in the right visual field. Increased vertical word spacing, which presumably decreases the adverse effect of crowding between adjacent lines of text, benefits reading speed. This benefit is greater in peripheral than central vision.

78 FR 33204 - Airworthiness Directives; Bell Helicopter Textron, Inc. (Bell) Helicopters

Federal Register 2010, 2011, 2012, 2013, 2014

2013-06-04

... manufactured seal material is installed on the bearing. This AD is prompted by a report that certain bearings were manufactured with an incorrect seal material that does not meet Bell specifications. The actions... June 2012 were manufactured with incorrect seal material. The incorrect seal material does not meet...

26 CFR 31.3406-0 - Outline of the backup withholding regulations.

Code of Federal Regulations, 2013 CFR

2013-04-01

... incorrect name/TIN combination. (2) Definition of account. (3) Definition of business day. (4) Certain exceptions. (c) Notice regarding an incorrect name/TIN combination. (1) In general. (2) Additional... of receipt. (d) Notice from payors of backup withholding due to an incorrect name/TIN combination. (1...

78 FR 47527 - Airworthiness Directives; Dassault Aviation Airplanes

Federal Register 2010, 2011, 2012, 2013, 2014

2013-08-06

... and correct an incorrect angle signal causing an un-commanded nose wheel deflection, which could... incorrect angle signal resulting in un-commanded nose wheel deflection which could not be countered by the... adoption of this rule because an incorrect angle signal causing an un-commanded nose wheel deflection could...

Recall is not necessary for verbal sequence learning.

PubMed

Kalm, Kristjan; Norris, Dennis

2016-01-01

The question of whether overt recall of to-be-remembered material accelerates learning is important in a wide range of real-world learning settings. In the case of verbal sequence learning, previous research has proposed that recall either is necessary for verbal sequence learning (Cohen & Johansson Journal of Verbal Learning and Verbal Behavior, 6, 139-143, 1967; Cunningham, Healy, & Williams Journal of Experimental Psychology: Learning, Memory, and Cognition, 10, 575-597, 1984), or at least contributes significantly to it (Glass, Krejci, & Goldman Journal of Memory and Language, 28, 189-199, 1989; Oberauer & Meyer Memory, 17, 774-781, 2009). In contrast, here we show that the amount of previous spoken recall does not predict learning and is not necessary for it. We suggest that previous research may have underestimated participants' learning by using suboptimal performance measures, or by using manual or written recall. However, we show that the amount of spoken recall predicted how much interference from other to-be-remembered sequences would be observed. In fact, spoken recall mediated most of the error learning observed in the task. Our data support the view that the learning of overlapping auditory-verbal sequences is driven by learning the phonological representations and not the articulatory motor responses. However, spoken recall seems to reinforce already learned representations, whether they are correct or incorrect, thus contributing to a participant identifying a specific stimulus as either "learned" or "new" during the presentation phase.

Visual management of large scale data mining projects.

PubMed

Shah, I; Hunter, L

2000-01-01

This paper describes a unified framework for visualizing the preparations for, and results of, hundreds of machine learning experiments. These experiments were designed to improve the accuracy of enzyme functional predictions from sequence, and in many cases were successful. Our system provides graphical user interfaces for defining and exploring training datasets and various representational alternatives, for inspecting the hypotheses induced by various types of learning algorithms, for visualizing the global results, and for inspecting in detail results for specific training sets (functions) and examples (proteins). The visualization tools serve as a navigational aid through a large amount of sequence data and induced knowledge. They provided significant help in understanding both the significance and the underlying biological explanations of our successes and failures. Using these visualizations it was possible to efficiently identify weaknesses of the modular sequence representations and induction algorithms which suggest better learning strategies. The context in which our data mining visualization toolkit was developed was the problem of accurately predicting enzyme function from protein sequence data. Previous work demonstrated that approximately 6% of enzyme protein sequences are likely to be assigned incorrect functions on the basis of sequence similarity alone. In order to test the hypothesis that more detailed sequence analysis using machine learning techniques and modular domain representations could address many of these failures, we designed a series of more than 250 experiments using information-theoretic decision tree induction and naive Bayesian learning on local sequence domain representations of problematic enzyme function classes. In more than half of these cases, our methods were able to perfectly discriminate among various possible functions of similar sequences. We developed and tested our visualization techniques on this application.

Representation Learning of Logic Words by an RNN: From Word Sequences to Robot Actions

PubMed Central

Yamada, Tatsuro; Murata, Shingo; Arie, Hiroaki; Ogata, Tetsuya

2017-01-01

An important characteristic of human language is compositionality. We can efficiently express a wide variety of real-world situations, events, and behaviors by compositionally constructing the meaning of a complex expression from a finite number of elements. Previous studies have analyzed how machine-learning models, particularly neural networks, can learn from experience to represent compositional relationships between language and robot actions with the aim of understanding the symbol grounding structure and achieving intelligent communicative agents. Such studies have mainly dealt with the words (nouns, adjectives, and verbs) that directly refer to real-world matters. In addition to these words, the current study deals with logic words, such as “not,” “and,” and “or” simultaneously. These words are not directly referring to the real world, but are logical operators that contribute to the construction of meaning in sentences. In human–robot communication, these words may be used often. The current study builds a recurrent neural network model with long short-term memory units and trains it to learn to translate sentences including logic words into robot actions. We investigate what kind of compositional representations, which mediate sentences and robot actions, emerge as the network's internal states via the learning process. Analysis after learning shows that referential words are merged with visual information and the robot's own current state, and the logical words are represented by the model in accordance with their functions as logical operators. Words such as “true,” “false,” and “not” work as non-linear transformations to encode orthogonal phrases into the same area in a memory cell state space. The word “and,” which required a robot to lift up both its hands, worked as if it was a universal quantifier. The word “or,” which required action generation that looked apparently random, was represented as an unstable space of the network's dynamical system. PMID:29311891

Representation Learning of Logic Words by an RNN: From Word Sequences to Robot Actions.

PubMed

Yamada, Tatsuro; Murata, Shingo; Arie, Hiroaki; Ogata, Tetsuya

2017-01-01

An important characteristic of human language is compositionality. We can efficiently express a wide variety of real-world situations, events, and behaviors by compositionally constructing the meaning of a complex expression from a finite number of elements. Previous studies have analyzed how machine-learning models, particularly neural networks, can learn from experience to represent compositional relationships between language and robot actions with the aim of understanding the symbol grounding structure and achieving intelligent communicative agents. Such studies have mainly dealt with the words (nouns, adjectives, and verbs) that directly refer to real-world matters. In addition to these words, the current study deals with logic words, such as "not," "and," and "or" simultaneously. These words are not directly referring to the real world, but are logical operators that contribute to the construction of meaning in sentences. In human-robot communication, these words may be used often. The current study builds a recurrent neural network model with long short-term memory units and trains it to learn to translate sentences including logic words into robot actions. We investigate what kind of compositional representations, which mediate sentences and robot actions, emerge as the network's internal states via the learning process. Analysis after learning shows that referential words are merged with visual information and the robot's own current state, and the logical words are represented by the model in accordance with their functions as logical operators. Words such as "true," "false," and "not" work as non-linear transformations to encode orthogonal phrases into the same area in a memory cell state space. The word "and," which required a robot to lift up both its hands, worked as if it was a universal quantifier. The word "or," which required action generation that looked apparently random, was represented as an unstable space of the network's dynamical system.

Evaluation of electrical test conditions in MIL-M-38510 slash sheets

NASA Astrophysics Data System (ADS)

Sandgren, K.

1980-08-01

Adequacy of MIL-M-38510 slash sheet requirements for electrical test conditions in an automated test environment were evaluated. Military temperature range commercial devices of 13 types from 6 manufacturers were purchased. Software for testing these devices and for varying the test conditions was written for the Tektronix S-3260 test system. The devices were tested to evaluate the effects of pin-condition settling time, measurement sequence of the same and different D-C parameters, temperature sequence, differently defined temperature ambients, variable measurement conditions, sequence of time measurements, pin-application sequence, and undesignated pin condition ambiguity. An alternative to current tri-state enable and disable time measurements is proposed; S-3260 'open' and 'ground' conditions are characterized; and suggestions for changes in MIL-M-38510 slash sheet specifications and MIL-STD-883 test methods are proposed, both to correct errors and ambiguities and to facilitate the gathering of repeatable data on automated test equipment. Data obtained showed no sensitivity to measurement or temperature sequence nor to temperature ambient, provided that test times were not excessive. V sub ICP tests and some low current measurements required allowance for a pin condition settling time because of the test system speed. Some pin condition application sequences yielded incorrect measurements. Undefined terminal conditions of output pins were found to affect I sub OS and propagation delay time measurements. Truth table test results varied with test frequency and V sub IL for low-power Schottky devices.

Fastidious Gram-Negatives: Identification by the Vitek 2 Neisseria-Haemophilus Card and by Partial 16S rRNA Gene Sequencing Analysis.

PubMed

Sönksen, Ute Wolff; Christensen, Jens Jørgen; Nielsen, Lisbeth; Hesselbjerg, Annemarie; Hansen, Dennis Schrøder; Bruun, Brita

2010-12-31

Taxonomy and identification of fastidious Gram negatives are evolving and challenging. We compared identifications achieved with the Vitek 2 Neisseria-Haemophilus (NH) card and partial 16S rRNA gene sequence (526 bp stretch) analysis with identifications obtained with extensive phenotypic characterization using 100 fastidious Gram negative bacteria. Seventy-five strains represented 21 of the 26 taxa included in the Vitek 2 NH database and 25 strains represented related species not included in the database. Of the 100 strains, 31 were the type strains of the species. Vitek 2 NH identification results: 48 of 75 database strains were correctly identified, 11 strains gave `low discrimination´, seven strains were unidentified, and nine strains were misidentified. Identification of 25 non-database strains resulted in 14 strains incorrectly identified as belonging to species in the database. Partial 16S rRNA gene sequence analysis results: For 76 strains phenotypic and sequencing identifications were identical, for 23 strains the sequencing identifications were either probable or possible, and for one strain only the genus was confirmed. Thus, the Vitek 2 NH system identifies most of the commonly occurring species included in the database. Some strains of rarely occurring species and strains of non-database species closely related to database species cause problems. Partial 16S rRNA gene sequence analysis performs well, but does not always suffice, additional phenotypical characterization being useful for final identification.

Fastidious Gram-Negatives: Identification by the Vitek 2 Neisseria-Haemophilus Card and by Partial 16S rRNA Gene Sequencing Analysis

PubMed Central

Sönksen, Ute Wolff; Christensen, Jens Jørgen; Nielsen, Lisbeth; Hesselbjerg, Annemarie; Hansen, Dennis Schrøder; Bruun, Brita

2010-01-01

Taxonomy and identification of fastidious Gram negatives are evolving and challenging. We compared identifications achieved with the Vitek 2 Neisseria-Haemophilus (NH) card and partial 16S rRNA gene sequence (526 bp stretch) analysis with identifications obtained with extensive phenotypic characterization using 100 fastidious Gram negative bacteria. Seventy-five strains represented 21 of the 26 taxa included in the Vitek 2 NH database and 25 strains represented related species not included in the database. Of the 100 strains, 31 were the type strains of the species. Vitek 2 NH identification results: 48 of 75 database strains were correctly identified, 11 strains gave `low discrimination´, seven strains were unidentified, and nine strains were misidentified. Identification of 25 non-database strains resulted in 14 strains incorrectly identified as belonging to species in the database. Partial 16S rRNA gene sequence analysis results: For 76 strains phenotypic and sequencing identifications were identical, for 23 strains the sequencing identifications were either probable or possible, and for one strain only the genus was confirmed. Thus, the Vitek 2 NH system identifies most of the commonly occurring species included in the database. Some strains of rarely occurring species and strains of non-database species closely related to database species cause problems. Partial 16S rRNA gene sequence analysis performs well, but does not always suffice, additional phenotypical characterization being useful for final identification. PMID:21347215

Inflation and deflation timing of the AutoCAT 2 WAVE intra-aortic balloon pump using the autoPilot mode in a clinical setting.

PubMed

Bakker, E W M; Visser, K; van der Wal, A; Kuiper, M A; Koopmans, M; Breedveld, R

2012-09-01

The primary goal of this observational clinical study was to register the occurrence of incorrect inflation and deflation timing of an intra-aortic balloon pump in autoPilot mode. The secondary goal was to identify possible causes of incorrect timing. During IABP assistance of 60 patients, every four hours a strip was printed with the IABP frequency set to 1:2. Strips were examined for timing discrepancies beyond 40 ms from the dicrotic notch (inflation) and the end of the diastolic phase (deflation). In this way, 320 printed strips were examined. A total of 52 strips (16%) showed incorrect timing. On 24 of these strips, the incorrect timing was called incidental, as it showed on only one or a few beats. The other 28 cases of erroneous timing were called consistent, as more than 50% of the beats on the strip showed incorrect timing. We observed arrhythmia in 69% of all cases of incorrect timing. When timing was correct, arrhythmia was found on 13 (5%) of 268 strips. A poor quality electrocardiograph (ECG) signal showed on 37% of all strips with incorrect timing and 11% of all strips with proper timing. We conclude that inflation and deflation timing of the IABP is not always correct when using the autoPilot mode. The quality of the ECG input signal and the occurrence of arrhythmia appear to be related to erroneous timing. Switching from autoPilot mode to operator mode may not always prevent incorrect timing.

What can Written-Words Tell us About Lexical Retrieval in Speech Production?

PubMed Central

Navarrete, Eduardo; Mahon, Bradford Z.; Lorenzoni, Anna; Peressotti, Francesca

2016-01-01

In recent decades, researchers have exploited semantic context effects in picture naming tasks in order to investigate the mechanisms involved in the retrieval of words from the mental lexicon. In the blocked naming paradigm, participants name target pictures that are either blocked or not blocked by semantic category. In the continuous naming task, participants name a sequence of target pictures that are drawn from multiple semantic categories. Semantic context effects in both tasks are a highly reliable phenomenon. The empirical evidence is, however, sparse and inconsistent when the target stimuli are printed-words instead of pictures. In the first part of the present study we review the empirical evidence regarding semantic context effects with written-word stimuli in the blocked and continuous naming tasks. In the second part, we empirically test whether semantic context effects are transferred from picture naming trials to word reading trials, and from word reading trials to picture naming trials. The results indicate a transfer of semantic context effects from picture naming to subsequently read within-category words. There is no transfer of semantic effects from target words that were read to subsequently named within-category pictures. These results replicate previous findings (Navarrete et al., 2010) and are contrary to predictions from a recent theoretical analysis by Belke (2013). The empirical evidence reported in the literature together with the present results, are discussed in relation to current accounts of semantic context effects in speech production. PMID:26779090

Resolving prokaryotic taxonomy without rRNA: longer oligonucleotide word lengths improve genome and metagenome taxonomic classification.

PubMed

Alsop, Eric B; Raymond, Jason

2013-01-01

Oligonucleotide signatures, especially tetranucleotide signatures, have been used as method for homology binning by exploiting an organism's inherent biases towards the use of specific oligonucleotide words. Tetranucleotide signatures have been especially useful in environmental metagenomics samples as many of these samples contain organisms from poorly classified phyla which cannot be easily identified using traditional homology methods, including NCBI BLAST. This study examines oligonucleotide signatures across 1,424 completed genomes from across the tree of life, substantially expanding upon previous work. A comprehensive analysis of mononucleotide through nonanucleotide word lengths suggests that longer word lengths substantially improve the classification of DNA fragments across a range of sizes of relevance to high throughput sequencing. We find that, at present, heptanucleotide signatures represent an optimal balance between prediction accuracy and computational time for resolving taxonomy using both genomic and metagenomic fragments. We directly compare the ability of tetranucleotide and heptanucleotide world lengths (tetranucleotide signatures are the current standard for oligonucleotide word usage analyses) for taxonomic binning of metagenome reads. We present evidence that heptanucleotide word lengths consistently provide more taxonomic resolving power, particularly in distinguishing between closely related organisms that are often present in metagenomic samples. This implies that longer oligonucleotide word lengths should replace tetranucleotide signatures for most analyses. Finally, we show that the application of longer word lengths to metagenomic datasets leads to more accurate taxonomic binning of DNA scaffolds and have the potential to substantially improve taxonomic assignment and assembly of metagenomic data.

Real-time inference of word relevance from electroencephalogram and eye gaze

NASA Astrophysics Data System (ADS)

Wenzel, M. A.; Bogojeski, M.; Blankertz, B.

2017-10-01

Objective. Brain-computer interfaces can potentially map the subjective relevance of the visual surroundings, based on neural activity and eye movements, in order to infer the interest of a person in real-time. Approach. Readers looked for words belonging to one out of five semantic categories, while a stream of words passed at different locations on the screen. It was estimated in real-time which words and thus which semantic category interested each reader based on the electroencephalogram (EEG) and the eye gaze. Main results. Words that were subjectively relevant could be decoded online from the signals. The estimation resulted in an average rank of 1.62 for the category of interest among the five categories after a hundred words had been read. Significance. It was demonstrated that the interest of a reader can be inferred online from EEG and eye tracking signals, which can potentially be used in novel types of adaptive software, which enrich the interaction by adding implicit information about the interest of the user to the explicit interaction. The study is characterised by the following novelties. Interpretation with respect to the word meaning was necessary in contrast to the usual practice in brain-computer interfacing where stimulus recognition is sufficient. The typical counting task was avoided because it would not be sensible for implicit relevance detection. Several words were displayed at the same time, in contrast to the typical sequences of single stimuli. Neural activity was related with eye tracking to the words, which were scanned without restrictions on the eye movements.

Support for Struggling Students in Algebra: Contributions of Incorrect Worked Examples

ERIC Educational Resources Information Center

Barbieri, Christina; Booth, Julie L.

2016-01-01

Middle school algebra students (N = 125) randomly assigned within classroom to a Problem-solving control group, a Correct worked examples control group, or an Incorrect worked examples group, completed an experimental classroom study to assess the differential effects of incorrect examples versus the two control groups on students' algebra…

78 FR 56150 - Airworthiness Directives; Piper Aircraft, Inc. Airplanes

Federal Register 2010, 2011, 2012, 2013, 2014

2013-09-12

..., PA-46-350P, PA-46R-350T, and PA-46-500TP airplanes. There is an incorrect reference to a paragraph designation, four instances of an incorrect reference to the paragraph in the service bulletin that references... instances of an incorrect reference to the paragraph in the service bulletin that references an...

Innovative /ye/ and /we/ sequences in recent loans in Japanese

NASA Astrophysics Data System (ADS)

Vance, Timothy; Matsugu, Yuka

2005-04-01

The GV sequences /ye/ and /we/ do not occur in Japanese except perhaps in recent loans. Katakana spellings of the relevant loans in authoritative dictionaries are inconsistent, and it is not clear whether native speakers treat them as containing the GV sequences /ye/ and /we/ or as containing the VV sequences /ie/ and /ue/. Native speakers of Japanese with minimal exposure to spoken English were recorded producing some relevant loans in response to picture prompts. The same speakers were also recorded producing some native words containing uncontroversial /ie/ and /ue/ sequences. All the productions are being analyzed acoustically to determine whether they show the expected contrast between GV and VV sequences. A VV sequence is disyllabic (and bimoraic) and should therefore have greater duration and more gradual formant movements than a monosyllabic (and monomoraic) GV sequence. Utterance-initially, a VV sequence should have a LH pitch pattern and should be preceded by a nondistinctive glottal stop, whereas a GV sequence should have a H pitch pattern and should have smooth onset.

Subcortical roles in lexical task processing: Inferences from thalamic and subthalamic event-related potentials.

PubMed

Tiedt, Hannes O; Ehlen, Felicitas; Krugel, Lea K; Horn, Andreas; Kühn, Andrea A; Klostermann, Fabian

2017-01-01

Subcortical functions for language capacities are poorly defined, but may be investigated in the context of deep brain stimulation. Here, we studied event-related potentials recorded from electrodes in the subthalamic nucleus (STN) and the thalamic ventral intermediate nucleus (VIM) together with surface-EEG. Participants completed a lexical decision task (LDT), which required the differentiation of acoustically presented words from pseudo-words by button press. Target stimuli were preceded by prime-words. In recordings from VIM, a slow potential shift apparent at the lower electrode contacts persisted during target stimulus presentation (equally for words and pseudo-words). In contrast, recordings from STN electrodes showed a short local activation on prime-words but not target-stimuli. In both depth-recording regions, further components related to contralateral motor responses to target words were evident. On scalp level, mid-central activations on (pseudo)lexical stimuli were obtained, in line with the expression of N400 potentials. The prolonged activity recorded from VIM, exclusively accompanying the relevant LDT phase, is in line with the idea of thalamic "selective engagement" for supporting the realization of the behavioral focus demanded by the task. In contrast, the phasic prime related activity rather indicates "procedural" STN functions, for example, for trial sequencing or readiness inhibition of prepared target reactions. Hum Brain Mapp 38:370-383, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Constitutional Mutations in RTEL1 Cause Severe Dyskeratosis Congenita

PubMed Central

Walne, Amanda J.; Vulliamy, Tom; Kirwan, Michael; Plagnol, Vincent; Dokal, Inderjeet

2013-01-01

Dyskeratosis congenita (DC) and its phenotypically severe variant, Hoyeraal-Hreidarsson syndrome (HHS), are multisystem bone-marrow-failure syndromes in which the principal pathology is defective telomere maintenance. The genetic basis of many cases of DC and HHS remains unknown. Using whole-exome sequencing, we identified biallelic mutations in RTEL1, encoding a helicase essential for telomere maintenance and regulation of homologous recombination, in an individual with familial HHS. Additional screening of RTEL1 identified biallelic mutations in 6/23 index cases with HHS but none in 102 DC or DC-like cases. All 11 mutations in ten HHS individuals from seven families segregated in an autosomal-recessive manner, and telomere lengths were significantly shorter in cases than in controls (p = 0.0003). This group had significantly higher levels of telomeric circles, produced as a consequence of incorrect processing of telomere ends, than did controls (p = 0.0148). These biallelic RTEL1 mutations are responsible for a major subgroup (∼29%) of HHS. Our studies show that cells harboring these mutations have significant defects in telomere maintenance, but not in homologous recombination, and that incorrect resolution of T-loops is a mechanism for telomere shortening and disease causation in humans. They also demonstrate the severe multisystem consequences of its dysfunction. PMID:23453664

A Quantitative Tool to Distinguish Isobaric Leucine and Isoleucine Residues for Mass Spectrometry-Based De Novo Monoclonal Antibody Sequencing

NASA Astrophysics Data System (ADS)

Poston, Chloe N.; Higgs, Richard E.; You, Jinsam; Gelfanova, Valentina; Hale, John E.; Knierman, Michael D.; Siegel, Robert; Gutierrez, Jesus A.

2014-07-01

De novo sequencing by mass spectrometry (MS) allows for the determination of the complete amino acid (AA) sequence of a given protein based on the mass difference of detected ions from MS/MS fragmentation spectra. The technique relies on obtaining specific masses that can be attributed to characteristic theoretical masses of AAs. A major limitation of de novo sequencing by MS is the inability to distinguish between the isobaric residues leucine (Leu) and isoleucine (Ile). Incorrect identification of Ile as Leu or vice versa often results in loss of activity in recombinant antibodies. This functional ambiguity is commonly resolved with costly and time-consuming AA mutation and peptide sequencing experiments. Here, we describe a set of orthogonal biochemical protocols, which experimentally determine the identity of Ile or Leu residues in monoclonal antibodies (mAb) based on the selectivity that leucine aminopeptidase shows for n-terminal Leu residues and the cleavage preference for Leu by chymotrypsin. The resulting observations are combined with germline frequencies and incorporated into a logistic regression model, called Predictor for Xle Sites (PXleS) to provide a statistical likelihood for the identity of Leu at an ambiguous site. We demonstrate that PXleS can generate a probability for an Xle site in mAbs with 96% accuracy. The implementation of PXleS precludes the expression of several possible sequences and, therefore, reduces the overall time and resources required to go from spectra generation to a biologically active sequence for a mAb when an Ile or Leu residue is in question.

Context and meter enhance long-range planning in music performance

PubMed Central

Mathias, Brian; Pfordresher, Peter Q.; Palmer, Caroline

2015-01-01

Neural responses demonstrate evidence of resonance, or oscillation, during the production of periodic auditory events. Music contains periodic auditory events that give rise to a sense of beat, which in turn generates a sense of meter on the basis of multiple periodicities. Metrical hierarchies may aid memory for music by facilitating similarity-based associations among sequence events at different periodic distances that unfold in longer contexts. A fundamental question is how metrical associations arising from a musical context influence memory during music performance. Longer contexts may facilitate metrical associations at higher hierarchical levels more than shorter contexts, a prediction of the range model, a formal model of planning processes in music performance (Palmer and Pfordresher, 2003; Pfordresher et al., 2007). Serial ordering errors, in which intended sequence events are produced in incorrect sequence positions, were measured as skilled pianists performed musical pieces that contained excerpts embedded in long or short musical contexts. Pitch errors arose from metrically similar positions and further sequential distances more often when the excerpt was embedded in long contexts compared to short contexts. Musicians’ keystroke intensities and error rates also revealed influences of metrical hierarchies, which differed for performances in long and short contexts. The range model accounted for contextual effects and provided better fits to empirical findings when metrical associations between sequence events were included. Longer sequence contexts may facilitate planning during sequence production by increasing conceptual similarity between hierarchically associated events. These findings are consistent with the notion that neural oscillations at multiple periodicities may strengthen metrical associations across sequence events during planning. PMID:25628550

A quantitative tool to distinguish isobaric leucine and isoleucine residues for mass spectrometry-based de novo monoclonal antibody sequencing.

PubMed

Poston, Chloe N; Higgs, Richard E; You, Jinsam; Gelfanova, Valentina; Hale, John E; Knierman, Michael D; Siegel, Robert; Gutierrez, Jesus A

2014-07-01

De novo sequencing by mass spectrometry (MS) allows for the determination of the complete amino acid (AA) sequence of a given protein based on the mass difference of detected ions from MS/MS fragmentation spectra. The technique relies on obtaining specific masses that can be attributed to characteristic theoretical masses of AAs. A major limitation of de novo sequencing by MS is the inability to distinguish between the isobaric residues leucine (Leu) and isoleucine (Ile). Incorrect identification of Ile as Leu or vice versa often results in loss of activity in recombinant antibodies. This functional ambiguity is commonly resolved with costly and time-consuming AA mutation and peptide sequencing experiments. Here, we describe a set of orthogonal biochemical protocols, which experimentally determine the identity of Ile or Leu residues in monoclonal antibodies (mAb) based on the selectivity that leucine aminopeptidase shows for n-terminal Leu residues and the cleavage preference for Leu by chymotrypsin. The resulting observations are combined with germline frequencies and incorporated into a logistic regression model, called Predictor for Xle Sites (PXleS) to provide a statistical likelihood for the identity of Leu at an ambiguous site. We demonstrate that PXleS can generate a probability for an Xle site in mAbs with 96% accuracy. The implementation of PXleS precludes the expression of several possible sequences and, therefore, reduces the overall time and resources required to go from spectra generation to a biologically active sequence for a mAb when an Ile or Leu residue is in question.

Transfers of stimulus function during roulette wagering.

PubMed

Dixon, Mark R; Enoch, Mary Rachel; Belisle, Jordan

2017-10-01

Twenty-five recreational gamblers were initially asked to place bets on either red or black positions on a roulette board in a simulated casino setting. Each participant was then exposed to a stimulus pairing observing procedure which attempted to develop equivalence classes between one color (black or red) and traditionally positive words (e.g., love, happy, sex) and another color (black or red) and traditionally negative words (e.g., death, cancer, taxes), in the absence of consequence manipulations. Twenty-one of the twenty-five participants demonstrated greater response allocation to the color position on the roulette board that participated in a relational network with the positive words. Variations in sequencing of experimental conditions had no impact on poststimulus-pairing wagers, but did impact tests for equivalence accuracy. © 2017 Society for the Experimental Analysis of Behavior.

Multiunit Sequences in First Language Acquisition.

PubMed

Theakston, Anna; Lieven, Elena

2017-07-01

Theoretical and empirical reasons suggest that children build their language not only out of individual words but also out of multiunit strings. These are the basis for the development of schemas containing slots. The slots are putative categories that build in abstraction while the schemas eventually connect to other schemas in terms of both meaning and form. Evidence comes from the nature of the input, the ways in which children construct novel utterances, the systematic errors that children make, and the computational modeling of children's grammars. However, much of this research is on English, which is unusual in its rigid word order and impoverished inflectional morphology. We summarize these results and explore their implications for languages with more flexible word order and/or much richer inflectional morphology. Copyright © 2017 Cognitive Science Society, Inc.

Toward a model for lexical access based on acoustic landmarks and distinctive features

NASA Astrophysics Data System (ADS)

Stevens, Kenneth N.

2002-04-01

This article describes a model in which the acoustic speech signal is processed to yield a discrete representation of the speech stream in terms of a sequence of segments, each of which is described by a set (or bundle) of binary distinctive features. These distinctive features specify the phonemic contrasts that are used in the language, such that a change in the value of a feature can potentially generate a new word. This model is a part of a more general model that derives a word sequence from this feature representation, the words being represented in a lexicon by sequences of feature bundles. The processing of the signal proceeds in three steps: (1) Detection of peaks, valleys, and discontinuities in particular frequency ranges of the signal leads to identification of acoustic landmarks. The type of landmark provides evidence for a subset of distinctive features called articulator-free features (e.g., [vowel], [consonant], [continuant]). (2) Acoustic parameters are derived from the signal near the landmarks to provide evidence for the actions of particular articulators, and acoustic cues are extracted by sampling selected attributes of these parameters in these regions. The selection of cues that are extracted depends on the type of landmark and on the environment in which it occurs. (3) The cues obtained in step (2) are combined, taking context into account, to provide estimates of ``articulator-bound'' features associated with each landmark (e.g., [lips], [high], [nasal]). These articulator-bound features, combined with the articulator-free features in (1), constitute the sequence of feature bundles that forms the output of the model. Examples of cues that are used, and justification for this selection, are given, as well as examples of the process of inferring the underlying features for a segment when there is variability in the signal due to enhancement gestures (recruited by a speaker to make a contrast more salient) or due to overlap of gestures from neighboring segments.

Bayesian Recurrent Neural Network for Language Modeling.

PubMed

Chien, Jen-Tzung; Ku, Yuan-Chu

2016-02-01

A language model (LM) is calculated as the probability of a word sequence that provides the solution to word prediction for a variety of information systems. A recurrent neural network (RNN) is powerful to learn the large-span dynamics of a word sequence in the continuous space. However, the training of the RNN-LM is an ill-posed problem because of too many parameters from a large dictionary size and a high-dimensional hidden layer. This paper presents a Bayesian approach to regularize the RNN-LM and apply it for continuous speech recognition. We aim to penalize the too complicated RNN-LM by compensating for the uncertainty of the estimated model parameters, which is represented by a Gaussian prior. The objective function in a Bayesian classification network is formed as the regularized cross-entropy error function. The regularized model is constructed not only by calculating the regularized parameters according to the maximum a posteriori criterion but also by estimating the Gaussian hyperparameter by maximizing the marginal likelihood. A rapid approximation to a Hessian matrix is developed to implement the Bayesian RNN-LM (BRNN-LM) by selecting a small set of salient outer-products. The proposed BRNN-LM achieves a sparser model than the RNN-LM. Experiments on different corpora show the robustness of system performance by applying the rapid BRNN-LM under different conditions.

Fractionating nonword repetition: The contributions of short-term memory and oromotor praxis are different

PubMed Central

Alcock, Katherine J.; Carey, Daniel; Bergström, Lina; Karmiloff-Smith, Annette; Dick, Frederic

2017-01-01

The ability to reproduce novel words is a sensitive marker of language impairment across a variety of developmental disorders. Nonword repetition tasks are thought to reflect phonological short-term memory skills. Yet, when children hear and then utter a word for the first time, they must transform a novel speech signal into a series of coordinated, precisely timed oral movements. Little is known about how children’s oromotor speed, planning and co-ordination abilities might influence their ability to repeat novel nonwords, beyond the influence of higher-level cognitive and linguistic skills. In the present study, we tested 35 typically developing children between the ages of 5−8 years on measures of nonword repetition, digit span, memory for non-verbal sequences, reading fluency, oromotor praxis, and oral diadochokinesis. We found that oromotor praxis uniquely predicted nonword repetition ability in school-age children, and that the variance it accounted for was additional to that of digit span, memory for non-verbal sequences, articulatory rate (measured by oral diadochokinesis) as well as reading fluency. We conclude that the ability to compute and execute novel sensorimotor transformations affects the production of novel words. These results have important implications for understanding motor/language relations in neurodevelopmental disorders. PMID:28704379

Neural correlate of the construction of sentence meaning

PubMed Central

Fedorenko, Evelina; Brunner, Peter; Pritchett, Brianna; Kanwisher, Nancy

2016-01-01

The neural processes that underlie your ability to read and understand this sentence are unknown. Sentence comprehension occurs very rapidly, and can only be understood at a mechanistic level by discovering the precise sequence of underlying computational and neural events. However, we have no continuous and online neural measure of sentence processing with high spatial and temporal resolution. Here we report just such a measure: intracranial recordings from the surface of the human brain show that neural activity, indexed by γ-power, increases monotonically over the course of a sentence as people read it. This steady increase in activity is absent when people read and remember nonword-lists, despite the higher cognitive demand entailed, ruling out accounts in terms of generic attention, working memory, and cognitive load. Response increases are lower for sentence structure without meaning (“Jabberwocky” sentences) and word meaning without sentence structure (word-lists), showing that this effect is not explained by responses to syntax or word meaning alone. Instead, the full effect is found only for sentences, implicating compositional processes of sentence understanding, a striking and unique feature of human language not shared with animal communication systems. This work opens up new avenues for investigating the sequence of neural events that underlie the construction of linguistic meaning. PMID:27671642

Visualization and Analysis of Geology Word Vectors for Efficient Information Extraction

NASA Astrophysics Data System (ADS)

Floyd, J. S.

2016-12-01

When a scientist begins studying a new geographic region of the Earth, they frequently begin by gathering relevant scientific literature in order to understand what is known, for example, about the region's geologic setting, structure, stratigraphy, and tectonic and environmental history. Experienced scientists typically know what keywords to seek and understand that if a document contains one important keyword, then other words in the document may be important as well. Word relationships in a document give rise to what is known in linguistics as the context-dependent nature of meaning. For example, the meaning of the word `strike' in geology, as in the strike of a fault, is quite different from its popular meaning in baseball. In addition, word order, such as in the phrase `Cretaceous-Tertiary boundary,' often corresponds to the order of sequences in time or space. The context of words and the relevance of words to each other can be derived quantitatively by machine learning vector representations of words. Here we show the results of training a neural network to create word vectors from scientific research papers from selected rift basins and mid-ocean ridges: the Woodlark Basin of Papua New Guinea, the Hess Deep rift, and the Gulf of Mexico basin. The word vectors are statistically defined by surrounding words within a given window, limited by the length of each sentence. The word vectors are analyzed by their cosine distance to related words (e.g., `axial' and `magma'), classified by high dimensional clustering, and visualized by reducing the vector dimensions and plotting the vectors on a two- or three-dimensional graph. Similarity analysis of `Triassic' and `Cretaceous' returns `Jurassic' as the nearest word vector, suggesting that the model is capable of learning the geologic time scale. Similarity analysis of `basalt' and `minerals' automatically returns mineral names such as `chlorite', `plagioclase,' and `olivine.' Word vector analysis and visualization allow one to extract information from hundreds of papers or more and find relationships in less time than it would take to read all of the papers. As machine learning tools become more commonly available, more and more scientists will be able to use and refine these tools for their individual needs.

Impact of Cyrillic on Native English Speakers' Phono-lexical Acquisition of Russian.

PubMed

Showalter, Catherine E

2018-03-01

We investigated the influence of grapheme familiarity and native language grapheme-phoneme correspondences during second language lexical learning. Native English speakers learned Russian-like words via auditory presentations containing only familiar first language phones, pictured meanings, and exposure to either Cyrillic orthographic forms (Orthography condition) or the sequence (No Orthography condition). Orthography participants saw three types of written forms: familiar-congruent (e.g., -[kom]), familiar-incongruent (e.g., -[rɑt]), and unfamiliar (e.g., <ФИЛ>-[fil]). At test, participants determined whether pictures and words matched according to what they saw during word learning. All participants performed near ceiling in all stimulus conditions, except for Orthography participants on words containing incongruent grapheme-phoneme correspondences. These results suggest that first language grapheme-phoneme correspondences can cause interference during second language phono-lexical acquisition. In addition, these results suggest that orthographic input effects are robust enough to interfere even when the input does not contain novel phones.

Programmable Pulse Generator

NASA Technical Reports Server (NTRS)

Rhim, W. K.; Dart, J. A.

1982-01-01

New pulse generator programmed to produce pulses from several ports at different pulse lengths and intervals and virtually any combination and sequence. Unit contains a 256-word-by-16-bit memory loaded with instructions either manually or by computer. Once loaded, unit operates independently of computer.

An improved model for whole genome phylogenetic analysis by Fourier transform.

PubMed

Yin, Changchuan; Yau, Stephen S-T

2015-10-07

DNA sequence similarity comparison is one of the major steps in computational phylogenetic studies. The sequence comparison of closely related DNA sequences and genomes is usually performed by multiple sequence alignments (MSA). While the MSA method is accurate for some types of sequences, it may produce incorrect results when DNA sequences undergone rearrangements as in many bacterial and viral genomes. It is also limited by its computational complexity for comparing large volumes of data. Previously, we proposed an alignment-free method that exploits the full information contents of DNA sequences by Discrete Fourier Transform (DFT), but still with some limitations. Here, we present a significantly improved method for the similarity comparison of DNA sequences by DFT. In this method, we map DNA sequences into 2-dimensional (2D) numerical sequences and then apply DFT to transform the 2D numerical sequences into frequency domain. In the 2D mapping, the nucleotide composition of a DNA sequence is a determinant factor and the 2D mapping reduces the nucleotide composition bias in distance measure, and thus improving the similarity measure of DNA sequences. To compare the DFT power spectra of DNA sequences with different lengths, we propose an improved even scaling algorithm to extend shorter DFT power spectra to the longest length of the underlying sequences. After the DFT power spectra are evenly scaled, the spectra are in the same dimensionality of the Fourier frequency space, then the Euclidean distances of full Fourier power spectra of the DNA sequences are used as the dissimilarity metrics. The improved DFT method, with increased computational performance by 2D numerical representation, can be applicable to any DNA sequences of different length ranges. We assess the accuracy of the improved DFT similarity measure in hierarchical clustering of different DNA sequences including simulated and real datasets. The method yields accurate and reliable phylogenetic trees and demonstrates that the improved DFT dissimilarity measure is an efficient and effective similarity measure of DNA sequences. Due to its high efficiency and accuracy, the proposed DFT similarity measure is successfully applied on phylogenetic analysis for individual genes and large whole bacterial genomes. Copyright © 2015 Elsevier Ltd. All rights reserved.

[Analysis of causes of incorrect use of dose aerosols].

PubMed

Petro, W; Gebert, P; Lauber, B

1994-03-01

Preparations administered by inhalation make relatively high demands on the skill and knowledge of the patient in handling this form of application, for the effectivity of the therapy is inseparably linked to its faultless application. The present article aims at analysing possible mistakes in handling and at finding the most effective way of avoiding them. Several groups of patients with different previous knowledge were analysed in respect of handling skill and the influence of training on an improvement of the same; the patients' self-assessment was analysed by questioning them. Most mistakes are committed by patients whose only information consists of the contents of the package circular. Written instructions alone cannot convey sufficient information especially on how to synchronize the release operations. Major mistakes are insufficient expiration before application in 85.6% of the patients and lack of synchronisation in 55.9%, while the lowest rate of errors in respect of handling was seen in patients who had undergone training and instruction. Training in application associated with demonstration and subsequent exercise reduces the error ratio to a tolerable level. Pulverizers free from propelling gas and preparations applied by means of a spacer are clearly superior to others in respect of a comparatively low error rate. 99.3% of all patients believe they are correctly following the instructions, but on going into the question more deeply it becomes apparent that 37.1% of them make incorrect statements. Hence, practical training in application should get top priority in the treatment of obstructive diseases of the airways. The individual steps of inhalation technique must be explained in detail and demonstrated by means of a placebo dosage aerosol.(ABSTRACT TRUNCATED AT 250 WORDS)

The Impact of Incorrect Examples on Learning Fractions: A Field Experiment with 6th Grade Students

ERIC Educational Resources Information Center

Heemsoth, Tim; Heinze, Aiso

2014-01-01

Educational research indicates that error reflection, especially reflection on incorrect examples, has a positive effect on knowledge acquisition. The benefit of error reflections might be explained by the extended knowledge of incorrect strategies and concepts (negative knowledge) which fosters the learning of new content. In a field experiment…