scholarly journals Signals interpreted as archaic introgression appear to be driven primarily by faster evolution in Africa

2020 ◽  
Vol 7 (7) ◽  
pp. 191900 ◽  
Author(s):  
William Amos
Keyword(s):  
Real Data ◽  
Heterozygous State ◽  
Opposite Pattern ◽  
Coalescent Simulations ◽  
Archaic Introgression ◽  
African Individual ◽  
D Values

Non-African humans appear to carry a few per cent archaic DNA due to ancient inter-breeding. This modest legacy and its likely recent timing imply that most introgressed fragments will be rare and hence will occur mainly in the heterozygous state. I tested this prediction by calculating D statistics, a measure of legacy size, for pairs of humans where one of the pair was conditioned always to be either homozygous or heterozygous. Using coalescent simulations, I confirmed that conditioning the non-African to be heterozygous increased D, while conditioning the non-African to be homozygous reduced D to zero. Repeating with real data reveals the exact opposite pattern. In African–non-African comparisons, D is near-zero if the African individual is held homozygous. Conditioning one of two Africans to be either homozygous or heterozygous invariably generates large values of D, even when both individuals are drawn from the same population. Invariably, the African with more heterozygous sites (conditioned heterozygous > unconditioned > conditioned homozygous) appears less related to the archaic. By contrast, the same analysis applied to pairs of non-Africans always yields near-zero D, showing that conditioning does not create large D without an underlying signal to expose. Large D values in humans are therefore driven almost entirely by heterozygous sites in Africans acting to increase divergence from related taxa such as Neanderthals. In comparison with heterozygous Africans, individuals that lack African heterozygous sites, whether non-African or conditioned homozygous African, always appear more similar to archaic outgroups, a signal previously interpreted as evidence for introgression. I hope these analyses will encourage others to consider increased divergence as well as increased similarity to archaics as mechanisms capable of driving asymmetrical base-sharing.

scholarly journals A test of the hypothesis that variable mutation rates create signals that have previously been interpreted as evidence of archaic introgression into humans

2020 ◽  
Author(s):  
William Amos
Keyword(s):  
Mutation Rate ◽  
Alternative Model ◽  
Mutation Rates ◽  
Human Populations ◽  
Common Cause ◽  
Coalescent Simulations ◽  
Recurrent Mutations ◽  
Archaic Introgression ◽  
Excess Base ◽  
Human Specific

AbstractIt is widely accepted that non-African humans carry 1-2% Neanderthal DNA due to historical inter-breeding. However, inferences about introgression rely on a critical assumption that mutation rate is constant and that back-mutations are too rare to be important. Both these assumptions have been challenged, and recent evidence points towards an alternative model where signals interpreted as introgression are driven mainly by higher mutation rates in Africa. In this model, non-Africans appear closer to archaics not because they harbour introgressed fragments but because Africans have diverged more. Here I test this idea by using the density of rare, human-specific variants (RHSVs) as a proxy for recent mutation rate. I find that sites that contribute most to the signal interpreted as introgression tend to occur in tightly defined regions spanning only a few hundred bases in which mutation rate differs greatly between the two human populations being compared. Mutation rate is invariably higher in the population into which introgression is not inferred. I confirmed that RHSV density reflects mutation rate by conducting a parallel analysis looking at the density of RHSVs around sites with three alleles, an independent class of site that also requires recurrent mutations to form. Near-identical peaks in RHSV density are found, suggesting a common cause. Similarly, coalescent simulations confirm that, with constant mutation rate, introgressed fragments do not occur preferentially in regions with a high density of rare, human-specific variants. Together, these observations are difficult to reconcile with a model where excess base-sharing is driven by archaic legacies but instead provide support for a higher mutation rate inside Africa driving increased divergence from the ancestral human state.

Bang for Your Buck: A Single-Case Experimental Design Study of Practice Amount and Distribution in Treatment for Childhood Apraxia of Speech

2019 ◽  
Vol 62 (9) ◽  
pp. 3160-3182 ◽  
Author(s):  
Edwin Maas ◽  
Christina Gildersleeve-Neumann ◽  
Kathy Jakielski ◽  
Nicolette Kovacs ◽  
Ruth Stoeckel ◽  
...  
Keyword(s):  
Single Case ◽  
Evidence Base ◽  
Distributed Practice ◽  
Single Subject ◽  
Single Subject Design ◽  
Apraxia Of Speech ◽  
Childhood Apraxia Of Speech ◽  
Opposite Pattern ◽  
Massed Practice ◽  
Treatment Conditions

Purpose The aim of this study was to examine 2 aspects of treatment intensity in treatment for childhood apraxia of speech (CAS): practice amount and practice distribution. Method Using an alternating-treatments single-subject design with multiple baselines, we compared high versus low amount of practice, and massed versus distributed practice, in 6 children with CAS. Conditions were manipulated in the context of integral stimulation treatment. Changes in perceptual accuracy, scored by blinded analysts, were quantified with effect sizes. Results Four children showed an advantage for high amount of practice, 1 showed an opposite effect, and 1 showed no condition difference. For distribution, 4 children showed a clear advantage for massed over distributed practice post treatment; 1 showed an opposite pattern, and 1 showed no clear difference. Follow-up revealed a similar pattern. All children demonstrated treatment effects (larger gains for treated than untreated items). Conclusions High practice amount and massed practice were associated with more robust speech motor learning in most children with CAS, compared to low amount and distributed practice, respectively. Variation in effects across children warrants further research to determine factors that predict optimal treatment conditions. Finally, this study adds to the evidence base supporting the efficacy of integral stimulation treatment for CAS. Supplemental Material https://doi.org/10.23641/asha.9630599

Detecting Random Responses in a Personality Scale Using IRT-Based Person-Fit Indices

2019 ◽  
Vol 35 (1) ◽  
pp. 126-136 ◽  
Author(s):  
Tour Liu ◽  
Tian Lan ◽  
Tao Xin
Keyword(s):  
Experimental System ◽  
Real Data ◽  
Fit Indices ◽  
Random Response ◽  
Person Fit ◽  
Index Method ◽  
Single Person ◽  
Person Fit Index ◽  
Random Responses ◽  
Response Behaviors

Abstract. Random response is a very common aberrant response behavior in personality tests and may negatively affect the reliability, validity, or other analytical aspects of psychological assessment. Typically, researchers use a single person-fit index to identify random responses. This study recommends a three-step person-fit analysis procedure. Unlike the typical single person-fit methods, the three-step procedure identifies both global misfit and local misfit individuals using different person-fit indices. This procedure was able to identify more local misfit individuals than single-index method, and a graphical method was used to visualize those particular items in which random response behaviors appear. This method may be useful to researchers in that it will provide them with more information about response behaviors, allowing better evaluation of scale administration and development of more plausible explanations. Real data were used in this study instead of simulation data. In order to create real random responses, an experimental test administration was designed. Four different random response samples were produced using this experimental system.

Is the Future the Right Time?

2010 ◽  
Vol 57 (4) ◽  
pp. 308-314 ◽  
Author(s):  
Marc Ouellet ◽  
Julio Santiago ◽  
Ziv Israeli ◽  
Shai Gabay
Keyword(s):  
Auditory Task ◽  
English Speakers ◽  
Visual Modality ◽  
Opposite Pattern ◽  
Time Line ◽  
Temporal Reference ◽  
Left Hand ◽  
Reading Direction ◽  
Mental Time Line ◽  
The Right

Spanish and English speakers tend to conceptualize time as running from left to right along a mental line. Previous research suggests that this representational strategy arises from the participants’ exposure to a left-to-right writing system. However, direct evidence supporting this assertion suffers from several limitations and relies only on the visual modality. This study subjected to a direct test the reading hypothesis using an auditory task. Participants from two groups (Spanish and Hebrew) differing in the directionality of their orthographic system had to discriminate temporal reference (past or future) of verbs and adverbs (referring to either past or future) auditorily presented to either the left or right ear by pressing a left or a right key. Spanish participants were faster responding to past words with the left hand and to future words with the right hand, whereas Hebrew participants showed the opposite pattern. Our results demonstrate that the left-right mapping of time is not restricted to the visual modality and that the direction of reading accounts for the preferred directionality of the mental time line. These results are discussed in the context of a possible mechanism underlying the effects of reading direction on highly abstract conceptual representations.

An opposite pattern of cognitive performance in autistic individuals with and without alexithymia.

2019 ◽  
Vol 128 (7) ◽  
pp. 735-737
Author(s):  
Eya-Mist Rødgaard ◽  
Kristian Jensen ◽  
Laurent Mottron
Keyword(s):  
Cognitive Performance ◽  
Opposite Pattern

Exergy and sensibility analysis of each individual effect in a kraft multiple effect evaporator

TAPPI Journal ◽  
2019 ◽  
Vol 18 (10) ◽  
pp. 607-618
Author(s):  
JÉSSICA MOREIRA ◽  
BRUNO LACERDA DE OLIVEIRA CAMPOS ◽  
ESLY FERREIRA DA COSTA JUNIOR ◽  
ANDRÉA OLIVEIRA SOUZA DA COSTA
Keyword(s):  
Optimization Problem ◽  
Real Data ◽  
Kraft Pulping ◽  
Steam Temperature ◽  
Input Flow ◽  
Transfer Coefficients ◽  
Heat Transfer Coefficients ◽  
Multiple Effect ◽  
Sensibility Analysis ◽  
Exergetic Analysis

The multiple effect evaporator (MEE) is an energy intensive step in the kraft pulping process. The exergetic analysis can be useful for locating irreversibilities in the process and pointing out which equipment is less efficient, and it could also be the object of optimization studies. In the present work, each evaporator of a real kraft system has been individually described using mass balance and thermodynamics principles (the first and the second laws). Real data from a kraft MEE were collected from a Brazilian plant and were used for the estimation of heat transfer coefficients in a nonlinear optimization problem, as well as for the validation of the model. An exergetic analysis was made for each effect individually, which resulted in effects 1A and 1B being the least efficient, and therefore having the greatest potential for improvement. A sensibility analysis was also performed, showing that steam temperature and liquor input flow rate are sensible parameters.

Influence of corneal biomechanical properties on IOP indices in patients with keratoconus

The Eye ◽  
2019 ◽  
Vol 21 (128) ◽  
pp. 15-19
Author(s):  
Irina Bubnova ◽  
Veronica Averich ◽  
Elena Belousova
Keyword(s):  
Disease Progression ◽  
Corneal Thickness ◽  
Central Zone ◽  
Biomechanical Properties ◽  
Resistance Factor ◽  
Corneal Resistance Factor ◽  
Mean Values ◽  
Coefficient Of Elasticity ◽  
D Values ◽  
Corneal Biomechanical Properties

Purpose: Evaluation of corneal biomechanical prop¬erties and their influence on IOP indices in patients with keratoconus. Material and methods. The study included 194 eyes with keratoconus (113 patients aged from 23 to 36 years old). Corneal refraction in central zone varied from 48.25 to 56.75 D, values of corneal thickness ranged from 279 to 558 μm. Patients were divided into 4 groups according to Amsler classification: I stage – 40 eyes; II stage – 78 eyes; III stage – 54 eyes and IV stage – 22 eyes. Standard ophthal¬mological examination was carried out including pneumo¬tonometry. IOP indices and values of biomechanical prop¬erties were evaluated by dynamic bidirectional pneumatic applanation and pneumatic impression. Results. Study of corneal biomechanical properties in patients with keratoconus showed a decrease of such biomechanical indices as corneal hysteresis (CH) on aver¬age to 8.42±1.12 mm Hg, corneal resistance factor (CRF) – to 7.45±0.96 mm Hg, coefficient of elasticity (CE) – 5.35± 0.87 mm Hg. Values of these indices strongly depended on the stage of keratoconus. In the whole sample, the aver¬age corneal compensated IOP (IOPcc) amounted to 15.08± 2.43 mm Hg, Goldman IOP (IOPg) was 11.61±2.37 mm Hg and pneumatic tonometry IOP (IOPp) was 10.13±2.94 mm Hg. IOPcc indices didn’t have any statistically significant differ¬ence in dependence on the stage of keratoconus (р>0.473), while in process of disease progression IOPg and IOPp indi¬ces showed statistically significant decrease of mean values. Conclusion. Progression of keratoconus led to a de¬crease in corneal biomechanical properties which deter¬mine reduction of such indices as IOPg and IOPp in contrast to IOPcc.

THE DEVELOPMENT OF THE MATHEMATICAL MODEL OF PREDICTING THE INDICATORS OF ACCREDITATION OF TECHNICAL UNIVERSITIES IN THE RUSSIAN FEDERATION

2017 ◽  
pp. 27-38
Author(s):  
Olga Mikhaylovna Tikhonova ◽  
Alexander Fedorovich Rezchikov ◽  
Vladimir Andreevich Ivashchenko ◽  
Vadim Alekseevich Kushnikov
Keyword(s):  
Mathematical Model ◽  
System Dynamics ◽  
Regression Model ◽  
Oriented Graph ◽  
Real Data ◽  
Educational Process ◽  
Proposed Model ◽  
Linear Differential ◽  
The University ◽  
The Mathematical Model

The paper presents the system of predicting the indicators of accreditation of technical universities based on J. Forrester mechanism of system dynamics. According to analysis of cause-and-effect relationships between selected variables of the system (indicators of accreditation of the university) there was built the oriented graph. The complex of mathematical models developed to control the quality of training engineers in Russian higher educational institutions is based on this graph. The article presents an algorithm for constructing a model using one of the simulated variables as an example. The model is a system of non-linear differential equations, the modelling characteristics of the educational process being determined according to the solution of this system. The proposed algorithm for calculating these indicators is based on the system dynamics model and the regression model. The mathematical model is constructed on the basis of the model of system dynamics, which is further tested for compliance with real data using the regression model. The regression model is built on the available statistical data accumulated during the period of the university's work. The proposed approach is aimed at solving complex problems of managing the educational process in universities. The structure of the proposed model repeats the structure of cause-effect relationships in the system, and also provides the person responsible for managing quality control with the ability to quickly and adequately assess the performance of the system.

Investigation of Timing Anomalies in the Russian Stock Market in the Post-Crisis Period

2019 ◽  
Vol 12 (3) ◽  
pp. 37-47
Author(s):  
I. Ya. Lukasevich
Keyword(s):  
Stock Market ◽  
Information Technologies ◽  
Real Data ◽  
Weak Form ◽  
Fair Value ◽  
Presidential Decree ◽  
Day Of The Week ◽  
Russian Stock Market ◽  
Economic Growth Rates ◽  
Global And Local

The implementation of the May presidential decree aimed at Russia’s joining the top five global economies and achieving economic growth rates above the world’s average while maintaining macroeconomic stability requires a highly developed and efficient stock market ensuring the accumulation of capital and its deployment in the most promising and productive sectors of the economy.The subject of the research is timing anomalies in the Russian stock market in 2012–2018. The relevance of the research is due to the information inefficiency of the Russian stock market and its imperfections leading to significant price deviations from the «fair» value of assets and depriving investors of the opportunity to form various strategies for deriving additional revenues not related to fundamental economic factors and objective processes occurring in the global and local economies and the economy of an individual business entity. Based on the trend analysis of the Broad Market USD Index (RUBMI), the paper demonstrates a methodology for simulating the analysis of price anomalies on large arrays of real data using statistical data processing methods and modern information technologies. The paper concludes that though the Russian stock market lacks even the weak form of efficiency, such well-known timing anomalies as the “day-of-the-week” effect and the “month” effect have not been observed in the recent years. Therefore, investors could not use these anomalies to derive regular revenues above the market average.

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