The number of human genomes being genotyped or sequenced increases exponentially and efficient haplotype estimation methods able to handle this amount of data are now required. Here we present a ...method, SHAPEIT4, which substantially improves upon other methods to process large genotype and high coverage sequencing datasets. It notably exhibits sub-linear running times with sample size, provides highly accurate haplotypes and allows integrating external phasing information such as large reference panels of haplotypes, collections of pre-phased variants and long sequencing reads. We provide SHAPEIT4 in an open source format and demonstrate its performance in terms of accuracy and running times on two gold standard datasets: the UK Biobank data and the Genome In A Bottle.
Introduction
Although the interdisciplinary management of the ageing individual is highly stressed, there is limited information on the outcomes of interprofessional education (IPE) activities of ...dental students in geriatrics. This systematic review aimed to identify studies with dentists participating in formal IPE courses in geriatrics and assess the outcomes reported.
Material and Methods
Electronic databases (PubMed, EMBASE, CINAHL and Scopus), reference lists from relevant studies and cited papers were investigated. The inclusion criteria were as follows: about formal interactive learning; learners from at least 2 disciplines; including dentists; related to geriatrics; any study design; reporting any outcome; only full papers; published in peer‐reviewed journals; English language.
Results
Of the 1259 records retrieved, 26 were assessed for eligibility based on defined inclusion criteria and 7 studies were included in the final analysis. Two studies reported specific outcomes for dentists with lower, or even negative, post‐training scores for interprofessional collaborative practice competences compared to other disciplines, but only one of them used a previously validated scale. There were no reports on the effect of IPE courses on dental trainees’ gerodontology skill improvements or on their attitudes towards the older persons.
Conclusion
The existing evidence is insufficient to determine any outcomes of formal interprofessional training of dentists in geriatrics. More studies with better experimental design should be developed. Among the strengths of IPE in geriatrics are the interdisciplinary nature of geriatric care, the sharing of common geriatric competences among participating disciplines and the opportunity to use nursing homes as a training site.
I congratulate the authors on a very interesting paper. My discussion focuses on the potential to combine the knockoff procedure with linear mixed model approaches that are now commonly used in ...genome-wide association studies and a concern about the validity of the nullity assumption in the situation of case-control studies. Since around 2011, a widely adopted strategy for analysing data from genome-wide association studies has been to use linear mixed models. In this approach, Y Y is an N×1 N×1 vector containing a quantitative phenotype, G G is an N×1 N×1 vector containing genotypes at a genetic marker, and the aim is to test for association between Y Y and G G.
Postbloom fruit drop (PFD) is an important citrus disease that causes up to 100% yield losses during years in which conditions are favourable for the occurrence of epidemics. The conidia of ...Colletotrichum acutatum and C. gloeosporioides, causal agents of PFD, are predominantly dispersed by rain splash. At the beginning of epidemics, the distribution of diseased plants is random and the disease progress rate is very high, which is unusual for pathogens spread by rain splash. As the pathogen produces abundant conidia on diseased petals, pollinating insects may contribute to disease dispersal. This study investigated honeybees (Apis mellifera) as dispersal agents of C. acutatum and C. gloeosporioides among citrus plants. Two experiments were carried out in a screenhouse in which citrus plants were protected (or not) in insect‐proof cages. The source of inoculum was placed on one side of the screenhouse, and a honeybee hive was placed on the opposite side. All uncaged plants showed symptoms of the disease, and none of the caged plants exhibited PFD symptoms. The monomolecular model showed a good fit to disease progress in both experiments. Conidium‐like structures of Colletotrichum spp. were identified attached to the bodies of the honeybees by scanning electron microscopy. These results have revealed that honeybees disperse Colletotrichum among citrus plants.
Cities and adjacent regions represent foci of intense human activity and provide unique opportunities for studying human-mediated dispersal and gene flow. We examined the effect of landscape features ...on gene flow in the invasive grass Brachypodium sylvaticum across an urban–rural interface at the edge of its expanding range. We used genome-wide single-nucleotide polymorphism surveys of individuals from 22 locations. Resistance surfaces were created for each landscape feature, using ResistanceGA to optimize resistance parameters. Our Structure analysis identified three distinct clusters, and diversity analyses support the existence of at least three local introductions. Multiple regression on distance matrices showed no evidence that development, roads, canopy cover or agriculture had a significant influence on genetic distance in B. sylvaticum. Geographical distance was a mediocre predictor of genetic distance and reflected geographical clustering. The model of rivers acting as a conduit explained a large portion of variation in genetic distance, but the lack of evidence of directional gene flow eliminated hydrochory as a dispersal mechanism. These results and observations of the distribution of populations in disturbed sites indicate that the influence of rivers on patterns of dispersal of B. sylvaticum probably reflects seed dispersal due to human recreational activity.
One of the main problems connected with the exploitation of CdTe and CdZnTe crystals for the preparation of X-ray imaging devices is the presence in the matrix of inclusions, mainly due to tellurium ...excess. It is important to set up characterization methods that permit one to map in three dimensions the presence and the diameter of inclusions. This is a key point for (both) a better understanding of the inclusion-formation mechanism and for the evaluation of crystal quality. For this purpose, we developed a system that can be implemented on standard transmission optical microscopes. The use of this tool in the characterization of Bridgman grown CdZnTe samples allowed us to uncover interesting features in the tellurium inclusion distribution.
There are many ways to detect activation patterns in a time series of observations at a single voxel in a functional magnetic resonance imaging study. The critical problem is to estimate the ...statistical significance, which depends on the estimation of both the magnitude of the response to the stimulus and the serial dependence of the time series and especially on the assumptions made in that estimation. We show that for experimental designs with periodic stimuli, only a few aspects of the serial dependence are important and these can be estimated reliably via nonparametric estimation of the spectral density of the time series, whereas existing techniques are biased by their assumptions. The linear model with (stationary) serially dependent errors can be analyzed entirely in frequency domain, and doing so provides many insights. In particular, we introduce a technique to detect periodic activations and show that it has a distribution theory that enables us to assign significance levels down to 1 in 100,000, levels which are needed when a whole brain image is under consideration. Nonparametric spectral density estimation is shown to be self-calibrating and accurate when compared to several other time-domain approaches. The technique is especially resistant to high frequency artefacts that we have found in some datasets and we demonstrate that time-domain approaches may be sufficiently susceptible to these effects to give misleading results. The method is easily generalized to handle event-related designs. We found it necessary to consider the trends in the time series carefully and use nonlinear filters to remove the trends and robust techniques to remove “spikes.” Using this in connection with our techniques allows us to detect activations in clumps of a few (even one) voxel in periodic designs, yet produce essentially no false positive detections at any voxels in null datasets.
Introduction:
Although the population is aging and retaining more teeth, there is a lack of studies that address the longevity of dental restorations placed among older adults.
Objectives:
This study ...aimed to describe the survival trajectory of dental restorations placed in an outpatient population of geriatric and adult special needs patients over a 15-y span, with particular interest in the longevity of subsequent restorations in teeth that received multiple restorations over time.
Methods:
Dental restorations of different types and sizes in patients aged ≥65 y treated between 2000 and 2014 at the University of Iowa College of Dentistry were followed until they incurred an event (i.e., restoration replacement, extraction of the tooth, or endodontic treatment of the tooth). Survival analysis and extended Cox regression models were used to generate hazard ratios for selected predictor variables.
Results and Conclusion:
A total of 9,184 restorations were followed among 1,551 unique patients. During the follow-up period, 28.7% of these restorations incurred an event, and overall the restorations had a median life span of 6.2 y. In multivariable regression models, after controlling for sex and age, a greater number of restoration surfaces were associated with higher risks of failure, and the initial restoration recorded in the database for each participant tended to have a lower risk of failure than that of restorations that included any of those same surfaces that were placed later. This information could be helpful to older adult patients considering various restorative treatment options during the dental treatment–planning and informed consent process.
Knowledge Transfer Statement:
Informed decision making with regard to potential treatment options is an important component of health and well-being. The present study could contribute to the improved health of older adult dental patients by providing baseline information that clinicians can use as they discuss different restorative treatment options with these patients and their caregivers during the informed consent process.
Introduction
Identification and assessment of Evidence‐based dentistry (EBD) outcomes have been elusive. Our objective was to describe EBD skill acquisition during the second (D2) year of ...pre‐doctoral dental education and student competency at the end of the year.
Methods
The first and fourth (final) curricular‐required EBD Exercises (ie, application of the first 4 steps of the 5‐Step evidence‐based practice process applied to a real or hypothetical situation) completed by D2 students (n = 151) during 2014‐2015 and 2015‐2016 were evaluated to measure skill acquisition through use of a novel rubric with measures of performance from novice to expert. Exercises were evaluated on the performance for each step, identification of manuscript details and reflective commentary on manuscript components. Changes in performance were evaluated using the chi‐square test for trend and the Wilcoxon signed‐rank test.
Results
Seventy‐eight per cent of students scored competent or higher on the Ask step at the beginning of the D2 year; scores improved with 58% scoring proficient or expert on the fourth Exercise (P < .001). Most students were advanced beginners or higher in the Acquire, Appraise and Apply steps at the beginning of the D2 year, with minimal growth observed during the year. Identification of manuscript details improved between the first and fourth Exercises (P = .015); however, depth of commentary skills did not change.
Discussion
Unlike previous investigations evaluating EBD knowledge or behaviour in a testing situation, we evaluated skill acquisition using applied Exercises.
Conclusion
Consistent with their clinical and scientific maturity, D2 students minimally performed as advanced beginners at the end of their D2 year.
Abstract
Background and Aims
Phenotypic plasticity and genetic differentiation both play important roles in the establishment and spread of species after extra-range dispersal; however, the adaptive ...potential of plasticity and genetic divergence in successful invasions remains unclear.
Methods
We measured six anatomical traits associated with drought tolerance in contrasting water environments for individuals from the invasive and native range of the bunchgrass Brachypodium sylvaticum. To represent sources contributing to admixed genotypes in the invasive range accurately, we used unique alleles to determine probabilities of genetic contribution, and utilized these as weights in our analyses. The adaptive values of plasticity and genetic differentiation were assessed using regression.
Key Results
No plasticity was found in response to water availability for any of the measured traits. Bulliform cell area and three traits related to xylem morphology displayed genetic differentiation between invasive and native ranges, indicating a shift in the invasive range towards drought-tolerant phenotypes. Genetic divergence was not consistently in the direction indicated by selection, suggesting that responses are limited by trade-offs with other traits or physical constraints.
Conclusions
Our results indicate that invasive adaptation is the consequence of post-introduction selection leading to genetic differentiation. Selection, rather than plasticity, is driving B. sylvaticum success in its invaded range.
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