The Retreat from Locative Overgeneralisation Errors: A Novel Verb Grammaticality Judgment Study

Whilst some locative verbs alternate between the ground- and figure-locative constructions (e.g. Lisa sprayed the flowers with water/Lisa sprayed water onto the flowers), others are restricted to one construction or the other (e.g. *Lisa filled water into the cup/*Lisa poured the cup with water). The present study investigated two proposals for how learners (aged 5–6, 9–10 and adults) acquire this restriction, using a novel-verb-learning grammaticality-judgment paradigm. In support of the semantic verb class hypothesis, participants in all age groups used the semantic properties of novel verbs to determine the locative constructions (ground/figure/both) in which they could and could not appear. In support of the frequency hypothesis, participants'' tolerance of overgeneralisation errors decreased with each increasing level of verb frequency (novel/low/high). These results underline the need to develop an integrated account of the roles of semantics and frequency in the retreat from argument structure overgeneralisation.     

Influence of Precision of Emission Characteristic Parameters on Model Prediction Error of VOCs/Formaldehyde from Dry Building Material

Mass transfer models are useful in predicting the emissions of volatile organic compounds (VOCs) and formaldehyde from building materials in indoor environments. They are also useful for human exposure evaluation and in sustainable building design. The measurement errors in the emission characteristic parameters in these mass transfer models, i.e., the initial emittable concentration (C ₀), the diffusion coefficient (D), and the partition coefficient (K), can result in errors in predicting indoor VOC and formaldehyde concentrations. These errors have not yet been quantitatively well analyzed in the literature. This paper addresses this by using modelling to assess these errors for some typical building conditions. The error in C ₀, as measured in environmental chambers and applied to a reference living room in Beijing, has the largest influence on the model prediction error in indoor VOC and formaldehyde concentration, while the error in K has the least effect. A correlation between the errors in D, K, and C ₀ and the error in the indoor VOC and formaldehyde concentration prediction is then derived for engineering applications. In addition, the influence of temperature on the model prediction of emissions is investigated. It shows the impact of temperature fluctuations on the prediction errors in indoor VOC and formaldehyde concentrations to be less than 7% at 23±0.5°C and less than 30% at 23±2°C.     

Comparing Different Models of the Development of Verb Inflection in Early Child Spanish

How children acquire knowledge of verb inflection is a long-standing question in language acquisition research. In the present study, we test the predictions of some current constructivist and generativist accounts of the development of verb inflection by focusing on data from two Spanish-speaking children between the ages of 2;0 and 2;6. The constructivist claim that children’s early knowledge of verb inflection is only partially productive is tested by comparing the average number of different inflections per verb in matched samples of child and adult speech. The generativist claim that children’s early use of verb inflection is essentially error-free is tested by investigating the rate at which the children made subject-verb agreement errors in different parts of the present tense paradigm. Our results show: 1) that, although even adults’ use of verb inflection in Spanish tends to look somewhat lexically restricted, both children’s use of verb inflection was significantly less flexible than that of their caregivers, and 2) that, although the rate at which the two children produced subject-verb agreement errors in their speech was very low, this overall error rate hid a consistent pattern of error in which error rates were substantially higher in low frequency than in high frequency contexts, and substantially higher for low frequency than for high frequency verbs. These results undermine the claim that children’s use of verb inflection is fully productive from the earliest observable stages, and are consistent with the constructivist claim that knowledge of verb inflection develops only gradually.     

Children Use Statistics and Semantics in the Retreat from Overgeneralization

How do children learn to restrict their productivity and avoid ungrammatical utterances? The present study addresses this question by examining why some verbs are used with un- prefixation (e.g., unwrap) and others are not (e.g., *unsqueeze). Experiment 1 used a priming methodology to examine children''s (3–4; 5–6) grammatical restrictions on verbal un- prefixation. To elicit production of un-prefixed verbs, test trials were preceded by a prime sentence, which described reversal actions with grammatical un- prefixed verbs (e.g., Marge folded her arms and then she unfolded them). Children then completed target sentences by describing cartoon reversal actions corresponding to (potentially) un- prefixed verbs. The younger age-group''s production probability of verbs in un- form was negatively related to the frequency of the target verb in bare form (e.g., squeez/e/ed/es/ing), while the production probability of verbs in un- form for both age groups was negatively predicted by the frequency of synonyms to a verb''s un- form (e.g., release/*unsqueeze). In Experiment 2, the same children rated the grammaticality of all verbs in un- form. The older age-group''s grammaticality judgments were (a) positively predicted by the extent to which each verb was semantically consistent with a semantic “cryptotype” of meanings - where “cryptotype” refers to a covert category of overlapping, probabilistic meanings that are difficult to access - hypothesised to be shared by verbs which take un-, and (b) negatively predicted by the frequency of synonyms to a verb''s un- form. Taken together, these experiments demonstrate that children as young as 4;0 employ pre-emption and entrenchment to restrict generalizations, and that use of a semantic cryptotype to guide judgments of overgeneralizations is also evident by age 6;0. Thus, even early developmental accounts of children''s restriction of productivity must encompass a mechanism in which a verb''s semantic and statistical properties interact.     

Sensorimotor Recalibration Depends on Attribution of Sensory Prediction Errors to Internal Causes

Sensorimotor learning critically depends on error signals. Learning usually tries to minimise these error signals to guarantee optimal performance. Errors can, however, have both internal causes, resulting from one’s sensorimotor system, and external causes, resulting from external disturbances. Does learning take into account the perceived cause of error information? Here, we investigated the recalibration of internal predictions about the sensory consequences of one’s actions. Since these predictions underlie the distinction of self- and externally produced sensory events, we assumed them to be recalibrated only by prediction errors attributed to internal causes. When subjects were confronted with experimentally induced visual prediction errors about their pointing movements in virtual reality, they recalibrated the predicted visual consequences of their movements. Recalibration was not proportional to the externally generated prediction error, but correlated with the error component which subjects attributed to internal causes. We also revealed adaptation in subjects’ motor performance which reflected their recalibrated sensory predictions. Thus, causal attribution of error information is essential for sensorimotor learning.     

A comprehensive analysis of translational missense errors in the yeast Saccharomyces cerevisiae

The process of protein synthesis must be sufficiently rapid and sufficiently accurate to support continued cellular growth. Failure in speed or accuracy can have dire consequences, including disease in humans. Most estimates of the accuracy come from studies of bacterial systems, principally Escherichia coli, and have involved incomplete analysis of possible errors. We recently used a highly quantitative system to measure the frequency of all types of misreading errors by a single tRNA in E. coli. That study found a wide variation in error frequencies among codons; a major factor causing that variation is competition between the correct (cognate) and incorrect (near-cognate) aminoacyl-tRNAs for the mutant codon. Here we extend that analysis to measure the frequency of missense errors by two tRNAs in a eukaryote, the yeast Saccharomyces cerevisiae. The data show that in yeast errors vary by codon from a low of 4 × 10⁻⁵ to a high of 6.9 × 10⁻⁴ per codon and that error frequency is in general about threefold lower than in E. coli, which may suggest that yeast has additional mechanisms that reduce missense errors. Error rate again is strongly influenced by tRNA competition. Surprisingly, missense errors involving wobble position mispairing were much less frequent in S. cerevisiae than in E. coli. Furthermore, the error-inducing aminoglycoside antibiotic, paromomycin, which stimulates errors on all error-prone codons in E. coli, has a more codon-specific effect in yeast.     

Selection for minimization of translational frameshifting errors as a factor in the evolution of codon usage

In a wide range of genomes, it was observed that the usage of synonymous codons is biased toward specific codons and codon patterns. Factors that are implicated in the selection for codon usage include facilitation of fast and accurate translation. There are two types of translational errors: missense errors and processivity errors. There is considerable evidence in support of the hypothesis that codon usage is optimized to minimize missense errors. In contrast, little is known about the relationship between codon usage and frameshifting errors, an important form of processivity errors, which appear to occur at frequencies comparable to the frequencies of missense errors. Based on the recently proposed pause-and-slip model of frameshifting, we developed Frameshifting Robustness Score (FRS). We used this measure to test if the pattern of codon usage indicates optimization against frameshifting errors. We found that the FRS values of protein-coding sequences from four analyzed genomes (the bacteria Bacillus subtilis and Escherichia coli, and the yeasts Saccharomyces cerevisiae and Schizosaccharomyce pombe) were typically higher than expected by chance. Other properties of FRS patterns observed in B. subtilis, S. cerevisiae and S. pombe, such as the tendency of FRS to increase from the 5′- to 3′-end of protein-coding sequences, were also consistent with the hypothesis of optimization against frameshifting errors in translation. For E. coli, the results of different tests were less consistent, suggestive of a much weaker optimization, if any. Collectively, the results fit the concept of selection against mistranslation-induced protein misfolding being one of the factors shaping the evolution of both coding and non-coding sequences.     

If You’re House Is Still Available,Send Me an Email: Personality Influences Reactions to Written Errors in Email Messages

The increasing prevalence of social media means that we often encounter written language characterized by both stylistic variation and outright errors. How does the personality of the reader modulate reactions to non-standard text? Experimental participants read ‘email responses’ to an ad for a housemate that either contained no errors or had been altered to include either typos (e.g., teh) or homophonous grammar errors (grammos, e.g., to/too, it’s/its). Participants completed a 10-item evaluation scale for each message, which measured their impressions of the writer. In addition participants completed a Big Five personality assessment and answered demographic and language attitude questions. Both typos and grammos had a negative impact on the evaluation scale. This negative impact was not modulated by age, education, electronic communication frequency, or pleasure reading time. In contrast, personality traits did modulate assessments, and did so in distinct ways for grammos and typos.     

Measurement of the electrode dispersion in very low frequency DNA solutions

Based on the four electrodes technique, an apparatus is described which measures the Very Low Frequency (VLF) conductivity of ionic solutions, all electrode effects being completely eliminated. It is thus possible to measure the conductivity frequency dependence between 0.8 and 500 cps, with a relative error of 10^?4. Applying this method to DNA solutions, one always finds a conductivity dispersion in the VLF range, which disappears when the biopolymer is heat-denatured. The relaxation time is different from one solution to another, but is always greater than 10 msee. approximately, sometimes even greater than 0.1 sec., the upper limit which one can estimate with our apparatus. The different, explanations of the DNA very low frequency polarization, assuming that its relaxation is connected with the rotational diffusion of the biopolymer long axis, is discussed.     

Draft versus finished sequence data for DNA and protein diagnostic signature development

Sequencing pathogen genomes is costly, demanding careful allocation of limited sequencing resources. We built a computational Sequencing Analysis Pipeline (SAP) to guide decisions regarding the amount of genomic sequencing necessary to develop high-quality diagnostic DNA and protein signatures. SAP uses simulations to estimate the number of target genomes and close phylogenetic relatives (near neighbors or NNs) to sequence. We use SAP to assess whether draft data are sufficient or finished sequencing is required using Marburg and variola virus sequences. Simulations indicate that intermediate to high-quality draft with error rates of 10⁻³–10⁻⁵ (~8× coverage) of target organisms is suitable for DNA signature prediction. Low-quality draft with error rates of ~1% (3× to 6× coverage) of target isolates is inadequate for DNA signature prediction, although low-quality draft of NNs is sufficient, as long as the target genomes are of high quality. For protein signature prediction, sequencing errors in target genomes substantially reduce the detection of amino acid sequence conservation, even if the draft is of high quality. In summary, high-quality draft of target and low-quality draft of NNs appears to be a cost-effective investment for DNA signature prediction, but may lead to underestimation of predicted protein signatures.     

Validation of fatty acid predictions in milk using mid-infrared spectrometry across cattle breeds

The aim of this study was to investigate the accuracy to predict detailed fatty acid (FA) composition of bovine milk by mid-infrared spectrometry, for a cattle population that partly differed in terms of country, breed and methodology used to measure actual FA composition compared with the calibration data set. Calibration equations for predicting FA composition using mid-infrared spectrometry were developed in the European project RobustMilk and based on 1236 milk samples from multiple cattle breeds from Ireland, Scotland and the Walloon Region of Belgium. The validation data set contained 190 milk samples from cows in the Netherlands across four breeds: Dutch Friesian, Meuse-Rhine-Yssel, Groningen White Headed (GWH) and Jersey (JER). The FA measurements were performed using gas–liquid partition chromatography (GC) as the gold standard. Some FAs and groups of FAs were not considered because of differences in definition, as the capillary column of the GC was not the same as used to develop the calibration equations. Differences in performance of the calibration equations between breeds were mainly found by evaluating the standard error of validation and the average prediction error. In general, for the GWH breed the smallest differences were found between predicted and reference GC values and least variation in prediction errors, whereas for JER the largest differences were found between predicted and reference GC values and most variation in prediction errors. For the individual FAs 4:0, 6:0, 8:0, 10:0, 12:0, 14:0 and 16:0 and the groups’ saturated FAs, short-chain FAs and medium-chain FAs, predictions assessed for all breeds together were highly accurate (validation R² > 0.80) with limited bias. For the individual FAs cis-14:1, cis-16:1 and 18:0, the calibration equations were moderately accurate (R² in the range of 0.60 to 0.80) and for the individual FA 17:0 predictions were less accurate (R² < 0.60) with considerable bias. FA concentrations in the validation data set of our study were generally higher than those in the calibration data. This difference in the range of FA concentrations, mainly due to breed differences in our study, can cause lower accuracy. In conclusion, the RobustMilk calibration equations can be used to predict most FAs in milk from the four breeds in the Netherlands with only a minor loss of accuracy.     

Analyzing nested experimental designs—A user-friendly resampling method to determine experimental significance

While hierarchical experimental designs are near-ubiquitous in neuroscience and biomedical research, researchers often do not take the structure of their datasets into account while performing statistical hypothesis tests. Resampling-based methods are a flexible strategy for performing these analyses but are difficult due to the lack of open-source software to automate test construction and execution. To address this, we present Hierarch, a Python package to perform hypothesis tests and compute confidence intervals on hierarchical experimental designs. Using a combination of permutation resampling and bootstrap aggregation, Hierarch can be used to perform hypothesis tests that maintain nominal Type I error rates and generate confidence intervals that maintain the nominal coverage probability without making distributional assumptions about the dataset of interest. Hierarch makes use of the Numba JIT compiler to reduce p-value computation times to under one second for typical datasets in biomedical research. Hierarch also enables researchers to construct user-defined resampling plans that take advantage of Hierarch’s Numba-accelerated functions.     

Intake of dietary fats and colorectal cancer risk: Prospective findings from the UK Dietary Cohort Consortium

Introduction: Epidemiologic evidence for an association between colorectal cancer (CRC) risk and total dietary fat, saturated fat (SF), monounsaturated fat (MUFA) and polyunsaturated fat (PUFA) is inconsistent. Previous studies have used food frequency questionnaires (FFQ) to assess diet, but data from food diaries may be less prone to severe measurement error than data from FFQ. Methods: We conducted a case–control study nested within seven prospective UK cohort studies, comprising 579 cases of incident CRC and 1996 matched controls. Standardized dietary data from 4- to 7-day food diaries and from FFQ were used to estimate odds ratios for CRC risk associated with intake of fat and subtypes of fat using conditional logistic regression. We also calculated multivariate measurement error corrected odds ratios for CRC using repeated food diary measurements. Results: We observed no associations between intakes of total dietary fat or types of fat and CRC risk, irrespective of whether dietary data were obtained using food diaries or FFQ. Conclusion: Our results do not support the hypothesis that intakes of total dietary fat, SF, MUFA or PUFA are linked to risk of CRC.     

Targeted single molecule mutation detection with massively parallel sequencing

Next-generation sequencing (NGS) technologies have transformed genomic research and have the potential to revolutionize clinical medicine. However, the background error rates of sequencing instruments and limitations in targeted read coverage have precluded the detection of rare DNA sequence variants by NGS. Here we describe a method, termed CypherSeq, which combines double-stranded barcoding error correction and rolling circle amplification (RCA)-based target enrichment to vastly improve NGS-based rare variant detection. The CypherSeq methodology involves the ligation of sample DNA into circular vectors, which contain double-stranded barcodes for computational error correction and adapters for library preparation and sequencing. CypherSeq is capable of detecting rare mutations genome-wide as well as those within specific target genes via RCA-based enrichment. We demonstrate that CypherSeq is capable of correcting errors incurred during library preparation and sequencing to reproducibly detect mutations down to a frequency of 2.4 × 10⁻⁷ per base pair, and report the frequency and spectra of spontaneous and ethyl methanesulfonate-induced mutations across the Saccharomyces cerevisiae genome.     

A low-cost integrator for preparative ultracentrifuges

An integrator is described for the measurement of the time integral ∫₀^t rpm²dt in preparative ultracentrifuge where linearity exists either (a) between tachometer generator ac voltage amplitude and rpm (e.g., Sorvall RC2-B) or dc voltage and rpm, or (b) between the square-wave frequency from the tachometer generator and rpm (e.g., Beckman L2-65B). The construction and the precision levels of an integrator for Sorvall RC2-B preparative ultracentrifuge in the range 0–10,000 rpm and for Beckman L2-65B preparative ultracentrifuge in the range 0–40,000 rpm are described.     

Negative Phototaxis from Blue Light and the Role of Third Rhodopsinlike Pigment in Halobacterium Cutirubrum

Wild-type cells of Halobacterium cutirubrum show phototaxis. In negative phototaxis the cells are repelled by blue-near ultraviolet light, and in positive phototaxis the cells are attracted to green-red light. The extent of the responses are measured by monitoring the changes in the reversal frequency of the swimming direction of cells using a computer-linked automated method as described previously (Takahashi, T., and Y. Kobatake, 1982, Cell. Struct. Funct., 7:183-192). When the intensity of the background light (illumination for the observation) was dramatically reduced, the sensitivity of the cells to the repellent light decreased markedly. This result has been previously explained by Bogomolni and Spudich (1982, Proc. Natl. Acad. Sci. USA, 79:6250-6254), who proposed that the photoreceptor for negative phototaxis is the long-lifetime intermediate in the photocycle of slow-rhodospin. The behavioral response in the negative phototaxis is dependent upon the intensity of the actinic light and the background light. This agrees quantitatively with our model based on the aforementioned hypothesis.     

The reliability of surface electromyography to assess quadriceps fatigue during multi joint tasks in healthy and painful knees

This study’s aim was to determine the between days reliability of surface EMG recordings from the superficial quadriceps during a multi joint sub-maximal fatiguing protocol. Three subject groups (healthy n = 29; patellofemoral pain syndrome n = 74; knee osteoarthritis n = 55) performed the task at 60 maximum voluntary isometric contraction on three separate days. Spectral and amplitude EMG parameters were recorded from vastus medialis oblique, vastus lateralis and rectus femoris and were analysed for between days reliability using intraclass correlation coefficient (ICC_(2,1)), the standard errors of measure and smallest detectable differences. For frequency results, initial and final frequency values had ‘good’ or ‘excellent’ reliability in all groups for all muscles. ICCs for median frequency slopes for vastus medialis oblique, vastus lateralis, and rectus femoris respectively, in the osteoarthritis group were 0.04, 0.55, and 0.72; in the patellofemoral pain group were 0.41, 0.17, and 0.33; in the healthy group were 0.68, 0.64, and 0.31. The standard errors of measurement and smallest detectable differences for all groups and for all muscles were unacceptably high. For amplitude results, ICC root mean squared initial and final values were ‘good’ to ‘excellent’ for all groups and all muscles, albeit with high measurement error. The ICCs for root mean squared slopes in all tests were ‘poor’ with extremely high measurement error. The poor between days reliability and high measurement error suggests that surface EMG should not be adopted to assess fatigue during multi joint sub-maximal isometric quadriceps testing.