High-performing plastic clones best explain the spread of yellow monkeyflower from lowland to higher elevation areas in New Zealand.

The relative contribution of adaptation and phenotypic plasticity can vary between core and edge populations, with implications for invasive success. We investigated the spread of the invasive yellow monkeyflower, Erythranthe gutatta in New Zealand, where it is spreading from lowland agricultural land into high-elevation conservation areas. We investigated the extent of phenotypic variation among clones from across the South Island, looked for adaptation and compared degrees of plasticity among lowland core versus montane range-edge populations. We grew 34 clones and measured their vegetative and floral traits in two common gardens, one in the core range at 9 m a.s.l. and one near the range-edge at 560 m a.s.l. Observed trait variation was explained by a combination of genotypic diversity (as identified through common gardens) and high phenotypic plasticity. We found a subtle signature of local adaptation to lowland habitats but all clones were plastic and able to survive and reproduce in both gardens. In the range-edge garden, above-ground biomass was on average almost double and stolon length almost half that of the same clone in the core garden. Clones from low-elevation sites showed higher plasticity on average than those from higher elevation sites. The highest performing clones in the core garden were also top performers in the range-edge garden. These results suggest some highly fit general-purpose genotypes, possibly pre-adapted to New Zealand montane conditions, best explains the spread of E. gutatta from lowland to higher elevation areas.

Eliciting real cravings with virtual food: Using immersive technologies to explore the effects of food stimuli in virtual reality.

In this paper, we explore the current technical possibilities of eating in virtual reality (VR) and show how this could be used to influence eating behaviors. Cue-based exposure therapy is a well-known method used to treat eating disorders. There are several benefits to using VR in combination with cue-based therapy. However, before VR-based cue-exposure can be used for therapeutic purposes, the ability of the VR environment to elicit craving responses in participants must be assessed. This was the objective of the first part of the study, where we assessed whether our VR environment elicited food craving responses in participants. Results showed that our VR environment elicited food craving responses: Salivation Magnitude, Food Craving State and Urge to Eat was significantly different from the neutral baseline. In addition, results showed that food cravings measured through the salivation magnitude in response to the virtual condition were not significantly different from the real condition, thus showing that VR had a comparable effect on producing food cravings. The second part of the study was conducted to determine whether the addition of olfactory and interaction cues in VR increased the development of food cravings. The results of this part showed that adding synthetic olfactory cues, paired with visual cues, to our system, provided a significant further increase in food cravings. Our results demonstrate that the use of food cues in VR can increase the development of food cravings and that it is possible to provide a simple yet convincing eating experience in VR. Inevitably, food interaction in VR is still underexplored territory and further research is needed to improve utility and application in disciplines related to food and eating.

An Evaluation of the P300 Brain-Computer Interface, EyeLink Board, and Eye-Tracking Camera as Augmentative and Alternative Communication Devices.

PURPOSE: Augmentative and alternative communication (AAC) systems are important to support communication for individuals with complex communication needs. A recent addition to AAC system options is the brain-computer interface (BCI). This study aimed to compare the clinical application of the P300 speller BCI with two more common AAC systems, the EyeLink board, and an eye-tracking camera. METHOD: Ten participants without communication impairment (18-35 years of age) used each of the three AAC systems to spell three-letter words in one session. Accuracy and speed of letter selection were measured, and questionnaires were administered to evaluate usability, cognitive workload, and user preferences. RESULTS: The results showed that the BCI was significantly less accurate, slower, and with lower usability and higher cognitive workload compared to the eye-tracking camera and EyeLink board. Participants rated the eye-tracking camera as the most favorable AAC system on all measures. CONCLUSIONS: The results demonstrated that while the P300 speller BCI was usable by most participants, it did not function as well as the eye-tracking camera and EyeLink board. The clinical use of the BCI is, therefore, currently difficult to justify for most individuals, particularly when considering the substantial cost and setup resourcing needed. SUPPLEMENTAL MATERIAL: https://doi.org/10.23641/asha.21291384.

Distance assessment of detours by jumping spiders.

To take an indirect route (detour) in order to reach a specific target requires complex cognitive processes. Yet more demanding, from the cognitive point of view, is when the goal is only visible at the beginning of the detour. In spiders from the family Salticidae, vision is a key sensory modality mediating navigation and prey search. Their acute vision allows them to perform complicated detours, possibly as a consequence of the multitude of potential routes in their typically complex 3-dimensional habitats. We used a 4-route choice test, in which routes differed in being either short or long and in the presence or absence of a lure of a prey item, to investigate route assessment in 2 salticid species, Trite planiceps and Marpissa marina. Although both species showed evidence of motivation to follow lured-routes, judging by the number of times they re-oriented toward them while detouring, we found that Trite chose short routes in preference to long routes, but did not prefer the lured-routes. In contrast, Marpissa exhibited random route choice, although it oriented toward lured-routes more often than control routes (lure absent). Our results suggest that decision-making processes about which route to take occurs before embarking on a route, but this is cognitively challenging. Spiders exhibited cognitive limitations in which the lack of visibility of the goal affected success. However, the severity of cognitive limitations depended on species. We suggest that variability in spatial ability across the Salticidae may be related to the habitat complexity inhabited by each species.

Assessing and developing the written reflective practice skills of speech-language pathology students.

PURPOSE: Written reflective practice aims to support critical thinking and problem solving skills in speech-language pathology (SLP) clinical education programmes. Yet, there has been limited investigation of students' development of written reflective practice skills over time and during a real-time clinical experience. The purpose of this study was to investigate students' development of breadth and depth of written reflective practice across a six-week clinical experience. METHOD: Participants were 59 undergraduate and 14 postgraduate SLP students. Participants wrote critical reflections describing an interaction with a client/s at the conclusion of weeks two, four and six of their clinical experience. Formative feedback was provided after each submission. Breadth and depth of reflection were coded using a modification of Plack et al.'s coding schema. RESULT: There was a statistically significant association between time and likelihood of development of breadth of reflection for the elements process and content. Depth of reflection improved significantly across time. The majority of participants were classified as "reflectors" or critical reflector at the conclusion of the study. CONCLUSION: SLP students can make significant improvements in both breadth and depth of written reflective practice over a six-week period. Implications for clinical teaching are discussed.

Identification of the minimum effective dose for normally distributed data using a Bayesian variable selection approach.

The identification of the minimum effective dose is of high importance in the drug development process. In early stage screening experiments, establishing the minimum effective dose can be translated into a model selection based on information criteria. The presented alternative, Bayesian variable selection approach, allows for selection of the minimum effective dose, while taking into account model uncertainty. The performance of Bayesian variable selection is compared with the generalized order restricted information criterion on two dose-response experiments and through the simulations study. Which method has performed better depends on the complexity of the underlying model and the effect size relative to noise.

Methionine restriction inhibits chemically-induced malignant transformation in the BALB/c 3T3 cell transformation assay.

High consumption of red meat entails a higher risk of developing colorectal cancer. Methionine, which is more frequently a component of animal proteins, and folic acid are members of the one carbon cycle and as such important players in DNA methylation and cancer development. Therefore, dietary modifications involving altered methionine and folic acid content might inhibit colon cancer development. In the present study, the BALB/c 3T3 cell transformation assay was used to investigate whether methionine and folic acid are able to influence the malignant transformation of mouse fibroblasts after treatment with the known tumour initiator 3-methylcholanthrene. Three different methionine concentrations (representing a -40%, a "normal" and a +40% cell culture medium concentration, respectively) and two different folic acid concentrations (6 and 20 µM) were thereby investigated. Methionine restriction led to a decrease of type III foci, while enhancement of both methionine and folic acid did not significantly increase the cell transformation rate. Interestingly, the focus-lowering effect of methionine was only significant in conjunction with an elevated folic acid concentration. In summary, we conclude that the malignant transformation of mouse fibroblasts is influenced by methionine levels and that methionine restriction could be a possible approach to reduce cancer development.

Modeling the oxygen uptake kinetics during exercise testing of patients with chronic obstructive pulmonary diseases using nonlinear mixed models.

BACKGROUND: The six-minute walk test (6MWT) is commonly used to quantify exercise capacity in patients with several cardio-pulmonary diseases. Oxygen uptake ([Formula: see text]O2) kinetics during 6MWT typically follow 3 distinct phases (rest, exercise, recovery) that can be modeled by nonlinear regression. Simultaneous modeling of multiple kinetics requires nonlinear mixed models methodology. To the best of our knowledge, no such curve-fitting approach has been used to analyze multiple [Formula: see text]O2 kinetics in both research and clinical practice so far. METHODS: In the present study, we describe functionality of the R package medrc that extends the framework of the commonly used packages drc and nlme and allows fitting nonlinear mixed effects models for automated nonlinear regression modeling. The methodology was applied to a data set including 6MWT [Formula: see text]O2 kinetics from 61 patients with chronic obstructive pulmonary disease (disease severity stage II to IV). The mixed effects approach was compared to a traditional curve-by-curve approach. RESULTS: A six-parameter nonlinear regression model was jointly fitted to the set of [Formula: see text]O2 kinetics. Significant differences between disease stages were found regarding steady state [Formula: see text]O2 during exercise, [Formula: see text]O2 level after recovery and [Formula: see text]O2 inflection point in the recovery phase. Estimates obtained by the mixed effects approach showed standard errors that were consistently lower as compared to the curve-by-curve approach. CONCLUSIONS: Hereby we demonstrate the novelty and usefulness of this methodology in the context of physiological exercise testing.

Dose-Response Analysis Using R.

Dose-response analysis can be carried out using multi-purpose commercial statistical software, but except for a few special cases the analysis easily becomes cumbersome as relevant, non-standard output requires manual programming. The extension package drc for the statistical environment R provides a flexible and versatile infrastructure for dose-response analyses in general. The present version of the package, reflecting extensions and modifications over the last decade, provides a user-friendly interface to specify the model assumptions about the dose-response relationship and comes with a number of extractors for summarizing fitted models and carrying out inference on derived parameters. The aim of the present paper is to provide an overview of state-of-the-art dose-response analysis, both in terms of general concepts that have evolved and matured over the years and by means of concrete examples.

Re-evaluation of groundwater monitoring data for glyphosate and bentazone by taking detection limits into account.

Current regulatory assessment of pesticide contamination of Danish groundwater is exclusively based on samples with pesticide concentrations above detection limit. Here we demonstrate that a realistic quantification of pesticide contamination requires the inclusion of "non-detect" samples i.e. samples with concentrations below the detection limit, as left-censored observations. The median calculated pesticide concentrations are shown to be reduced 10(4) to 10(5) fold for two representative herbicides (glyphosate and bentazone) relative to the median concentrations based upon observations above detection limits alone.

Estimating marginal properties of quantitative real-time PCR data using nonlinear mixed models.

A unified modeling framework based on a set of nonlinear mixed models is proposed for flexible modeling of gene expression in real-time PCR experiments. Focus is on estimating the marginal or population-based derived parameters: cycle thresholds and ΔΔc(t), but retaining the conditional mixed model structure to adequately reflect the experimental design. Additionally, the calculation of model-average estimates allows incorporation of the model selection uncertainty. The methodology is applied for estimating the differential expression of a phosphate transporter gene OsPT6 in rice in comparison to a reference gene at several states after phosphate resupply. In a small simulation study the performance of the proposed method is evaluated and compared to a standard method.

Human embryonic stem cell-derived test systems for developmental neurotoxicity: a transcriptomics approach.

Developmental neurotoxicity (DNT) and many forms of reproductive toxicity (RT) often manifest themselves in functional deficits that are not necessarily based on cell death, but rather on minor changes relating to cell differentiation or communication. The fields of DNT/RT would greatly benefit from in vitro tests that allow the identification of toxicant-induced changes of the cellular proteostasis, or of its underlying transcriptome network. Therefore, the 'human embryonic stem cell (hESC)-derived novel alternative test systems (ESNATS)' European commission research project established RT tests based on defined differentiation protocols of hESC and their progeny. Valproic acid (VPA) and methylmercury (MeHg) were used as positive control compounds to address the following fundamental questions: (1) Does transcriptome analysis allow discrimination of the two compounds? (2) How does analysis of enriched transcription factor binding sites (TFBS) and of individual probe sets (PS) distinguish between test systems? (3) Can batch effects be controlled? (4) How many DNA microarrays are needed? (5) Is the highest non-cytotoxic concentration optimal and relevant for the study of transcriptome changes? VPA triggered vast transcriptional changes, whereas MeHg altered fewer transcripts. To attenuate batch effects, analysis has been focused on the 500 PS with highest variability. The test systems differed significantly in their responses (<20 % overlap). Moreover, within one test system, little overlap between the PS changed by the two compounds has been observed. However, using TFBS enrichment, a relatively large 'common response' to VPA and MeHg could be distinguished from 'compound-specific' responses. In conclusion, the ESNATS assay battery allows classification of human DNT/RT toxicants on the basis of their transcriptome profiles.

Model-specific tests on variance heterogeneity for detection of potentially interacting genetic loci.

BACKGROUND: Trait variances among genotype groups at a locus are expected to differ in the presence of an interaction between this locus and another locus or environment. A simple maximum test on variance heterogeneity can thus be used to identify potentially interacting single nucleotide polymorphisms (SNPs). RESULTS: We propose a multiple contrast test for variance heterogeneity that compares the mean of Levene residuals for each genotype group with their average as an alternative to a global Levene test. We applied this test to a Bogalusa Heart Study dataset to screen for potentially interacting SNPs across the whole genome that influence a number of quantitative traits. A user-friendly implementation of this method is available in the R statistical software package multcomp. CONCLUSIONS: We show that the proposed multiple contrast test of model-specific variance heterogeneity can be used to test for potential interactions between SNPs and unknown alleles, loci or covariates and provide valuable additional information compared with traditional tests. Although the test is statistically valid for severely unbalanced designs, care is needed in interpreting the results at loci with low allele frequencies.

Two new approaches to improve the analysis of BALB/c 3T3 cell transformation assay data.

Validation activities of the BALB/c 3T3 cell transformation assay (CTA) - a test method used for the assessment of the carcinogenic potential of compounds - have revealed the need for statistical analysis tailored to specific features of BALB/c 3T3 CTA data. Whereas a standard statistical approach for the Syrian hamster embryo (SHE) CTA was considered sufficient, an international expert group was gathered by the European Centre for the Validation of Alternative Methods (ECVAM) to review commonly applied statistical approaches for BALB/c 3T3 CTA. As it was concluded that none of the commonly applied approaches is entirely appropriate, two novel statistical approaches were found to be recommended for the evaluation of BALB/c 3T3 CTA data accounting for possible non-monotone concentration-response relationship and variance heterogeneity: a negative binomial generalised linear model with William's-type downturn-protected trend tests and a normalisation of the data by a specific transformation allowing for application of a general linear model that estimates effects assuming a normal distribution with William's-type protected tests. Both approaches are described in this article and their performance and the quality of the results they generate is demonstrated using exemplary data. Our work confirmed that both approaches are suitable for the statistical analysis of BALB/c 3T3 CTA data and that each of them is superior to commonly used methods. Furthermore, a procedure dichotomising data into negatives and positives is proposed which allows re-testing in cases where inconclusive data are encountered. The scripts of the statistical evaluation programs written in R - a freely available statistical software - are appended including exemplary outputs (Appendix A).

Statistical aspects of design and validation of microtitre-plate-based linear and non-linear parallel in vitro bioassays.

Assay validation was performed using four consecutive experiments with the related statistical evaluation. A cell-based assay on microtitre plates measured repeatedly within 1 day and on consecutive days was chosen as the model. The following problems were addressed: (i) choosing an appropriate design on a plate to avoid heterogeneities, (ii) quantification of all sources of variability and (iii) selecting between linear and non-linear parallel line assays. A mixed model was used with the random factors: rows, columns and plates and fixed effect factors with either linear or non-linear parallel line models.

Detection of a related difference in efficacy of azadirachtin treatments for the control of whiteflies on Gerbera jamesonii by testing for interactions in generalised linear models.

BACKGROUND: Within a project cluster, systemical effects of two neem treatments (Neem Azal U and Neem Pellet) on the number of Trialeurodes vaporariorum (Westw.) in Gerbera jamesonii Flori Line Maxi were investigated. In order to minimise adverse ecological effects of a product, a new plant protection product can be declared as superior to a reference if it shows the same or a higher effect at a lower dosage. RESULTS: Based on a negative binomial model, the efficacy of the two treatments is compared by applying a user-defined interaction contrast in a multiple-contrast test framework. The corresponding calculation of simultaneous confidence intervals for the ratio of model parameters provides conclusions about statistical significance and biological relevance. The validity of the approach is shown by a small simulation study. As a result of the experiment, besides a significant difference between two negative control treatments, no significant difference between the efficiency of the two neem treatments (Neem Azal U and Neem Pellet) could be detected. CONCLUSIONS: Simultaneous confidence intervals for linear combinations of parameters of generalised linear models provide a useful way to compare the efficiency of two plant protection products. The results for the azadirachtin experiment indicate that large differences between any application effects of either Neem Azal U or Neem Pellet cannot be expected.

Rank transformation in Haseman-Elston regression using scores for location-scale alternatives.

The Haseman-Elston method is a simple regression approach for detecting genetic linkage to quantitative traits in sib-pair studies. Although this method and especially the new extended Haseman-Elston approach are quite robust, there might be some loss of power for non-normally distributed traits. We propose using rank transformation techniques, which either combine the information on a trend in locations and in scales or detect a trend only for a subset of the trait variables for genetically different sibs under linkage. As this rank transformation is based on linear regression, no exact grouping of identity by descent proportions has to be assumed. Simulation results indicate a gain in power compared to recently suggested nonparametric methods.

Statistical evaluation of the in vivo micronucleus assay.

The statistical evaluation of the in vivo micronucleus assay is focused on multiple contrast tests for comparisons versus the negative control for count data taking the between-animals variability into account. For a possible claim the compound is not genotoxic in the micronucleus assay a proof of safety approach is proposed. For these statistical approaches user-friendly software is free available.