scholarly journals Coevolution of structural variation and optimization in sound systems of human language

2018 ◽  
Author(s):  
Meng-Han Zhang ◽  
Tao Gong
Keyword(s):  
Large Scale ◽  
Structural Variation ◽  
Human Language ◽  
Linguistic Typology ◽  
Mixed Effect ◽  
World Languages ◽  
Mixed Effect Models ◽  
Gradual Evolution ◽  
Vowel Systems ◽  
Two Parameters

AbstractEvolution of sound systems of human language is an optimization process to improve communicative effectiveness: The intrinsic structures of sound systems are constantly organized with respect to constraints in speech production and perception. However, there lack sufficient quantitative descriptions of this process, large-scale investigations on universal tendencies in sound systems, and explicit evidence on whether demographic and/or geographic factors can influence linguistic typology of sound systems. Here, we proposed two composite parameters, namely structural variation and optimization, to capture linguistic typology of sound systems, vowel systems in particular. Synchronic comparisons based on a large-scale vowel corpus of world languages revealed a universal negative correlation between the two parameters. Phylogenetic comparative analyses identified a correlated evolution of the two, but with distinct evolutionary modes: a gradual evolution of the structural variation and a punctuated equilibrium of the optimization. Mixed-effect models also reported significant effects of speaker population size and longitude on shaping vowel systems of world languages. All these findings elaborate the intrinsic evolutionary mechanism of sound systems, clarify the extrinsic, non-linguistic effects on shaping human sound systems, and quantitatively describe and interpret the evolution and typology of sound systems.

scholarly journals Hybrid pointer networks for traveling salesman problems optimization

PLoS ONE ◽  
2021 ◽  
Vol 16 (12) ◽  
pp. e0260995
Author(s):  
Ahmed Stohy ◽  
Heba-Tullah Abdelhakam ◽  
Sayed Ali ◽  
Mohammed Elhenawy ◽  
Abdallah A. Hassan ◽  
...  
Keyword(s):  
Large Scale ◽  
Travelling Salesman Problem ◽  
Graph Embedding ◽  
Travelling Salesman ◽  
Traveling Salesman Problems ◽  
Original Graph ◽  
Mixed Effect ◽  
Mixed Effect Models ◽  
Benchmark Instances ◽  
The Cost

In this work, we proposed a hybrid pointer network (HPN), an end-to-end deep reinforcement learning architecture is provided to tackle the travelling salesman problem (TSP). HPN builds upon graph pointer networks, an extension of pointer networks with an additional graph embedding layer. HPN combines the graph embedding layer with the transformer’s encoder to produce multiple embeddings for the feature context. We conducted extensive experimental work to compare HPN and Graph pointer network (GPN). For the sack of fairness, we used the same setting as proposed in GPN paper. The experimental results show that our network significantly outperforms the original graph pointer network for small and large-scale problems. For example, it reduced the cost for travelling salesman problems with 50 cities/nodes (TSP50) from 5.959 to 5.706 without utilizing 2opt. Moreover, we solved benchmark instances of variable sizes using HPN and GPN. The cost of the solutions and the testing times are compared using Linear mixed effect models. We found that our model yields statistically significant better solutions in terms of the total trip cost. We make our data, models, and code publicly available https://github.com/AhmedStohy/Hybrid-Pointer-Networks.

scholarly journals Mixed effect models for genetic and areal dependencies in linguistic typology

2011 ◽  
Vol 15 (2) ◽  
Author(s):  
T. Florian Jaeger ◽  
Peter Graff ◽  
William Croft ◽  
Daniel Pontillo
Keyword(s):  
Linguistic Typology ◽  
Mixed Effect ◽  
Mixed Effect Models

CONTRIBUTION OF DNA COPY-NUMBER VARIATION (CNV) TO CANCER SUSCEPTIBILITY AND LARGE-SCALE GENOME ALTERATIONS IN OSTEOSARCOMA (OS)

2008 ◽  
Vol 31 (4) ◽  
pp. 19
Author(s):  
I Pasic ◽  
A Shlien ◽  
A Novokmet ◽  
C Zhang ◽  
U Tabori ◽  
...  
Keyword(s):  
Genomic Instability ◽  
Large Scale ◽  
Structural Variation ◽  
Age Of Onset ◽  
Cancer Susceptibility ◽  
Small Sample Size ◽  
Snp Array ◽  
Tumour Suppressor Gene ◽  
Small Sample ◽  
International Hapmap Project

Introduction: OS, a common Li-Fraumeni syndrome (LFS)-associated neoplasm, is a common bone malignancy of children and adolescents. Sporadic OS is also characterized by young age of onset and high genomic instability, suggesting a genetic contribution to disease. This study examined the contribution of novel DNA structural variation elements, CNVs, to OS susceptibility. Given our finding of excessive constitutional DNA CNV in LFS patients, which often coincide with cancer-related genes, we hypothesized that constitutional CNV may also provide clues about the aetiology of LFS-related sporadic neoplasms like OS. Methods: CNV in blood DNA of 26 patients with sporadic OS was compared to that of 263 normal control samples from the International HapMap project, as well as 62 local controls. Analysis was performed on DNA hybridized to Affymetrix genome-wide human SNP array 6.0 by Partek Genomic Suite. Results: There was no detectable difference in average number of CNVs, CNV length, and total structural variation (product of average CNV number and length) between individuals with OS and controls. While this data is preliminary (small sample size), it argues against the presence of constitutional genomic instability in individuals with sporadic OS. Conclusion: We found that the majority of tumours from patients with sporadic OS show CN loss at chr3q13.31, raising the possibility that chr3q13.31 may represent a “driver” region in OS aetiology. In at least one OS tumour, which displays CN loss at chr3q13.31, we demonstrate decreased expression of a known tumour suppressor gene located at chr3q13.31. We are investigating the role ofchr3q13.31 in development of OS.

scholarly journals Relationship between large-scale ionospheric field-aligned currents and electron/ion precipitations: DMSP observations

2020 ◽  
Vol 72 (1) ◽  
Author(s):  
Chao Xiong ◽  
Claudia Stolle ◽  
Patrick Alken ◽  
Jan Rauberg
Keyword(s):  
Time Distribution ◽  
Large Scale ◽  
Particle Flux ◽  
Particle Energy ◽  
Lower Latitude ◽  
Particle Precipitation ◽  
Data Set ◽  
The Mean ◽  
Two Parameters ◽  
Meteorological Satellite

Abstract In this study, we have derived field-aligned currents (FACs) from magnetometers onboard the Defense Meteorological Satellite Project (DMSP) satellites. The magnetic latitude versus local time distribution of FACs from DMSP shows comparable dependences with previous findings on the intensity and orientation of interplanetary magnetic field (IMF) By and Bz components, which confirms the reliability of DMSP FAC data set. With simultaneous measurements of precipitating particles from DMSP, we further investigate the relation between large-scale FACs and precipitating particles. Our result shows that precipitation electron and ion fluxes both increase in magnitude and extend to lower latitude for enhanced southward IMF Bz, which is similar to the behavior of FACs. Under weak northward and southward Bz conditions, the locations of the R2 current maxima, at both dusk and dawn sides and in both hemispheres, are found to be close to the maxima of the particle energy fluxes; while for the same IMF conditions, R1 currents are displaced further to the respective particle flux peaks. Largest displacement (about 3.5°) is found between the downward R1 current and ion flux peak at the dawn side. Our results suggest that there exists systematic differences in locations of electron/ion precipitation and large-scale upward/downward FACs. As outlined by the statistical mean of these two parameters, the FAC peaks enclose the particle energy flux peaks in an auroral band at both dusk and dawn sides. Our comparisons also found that particle precipitation at dawn and dusk and in both hemispheres maximizes near the mean R2 current peaks. The particle precipitation flux maxima closer to the R1 current peaks are lower in magnitude. This is opposite to the known feature that R1 currents are on average stronger than R2 currents.

scholarly journals MegaLMM: Mega-scale linear mixed models for genomic predictions with thousands of traits

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Daniel E. Runcie ◽  
Jiayi Qu ◽  
Hao Cheng ◽  
Lorin Crawford
Keyword(s):  
Genomic Prediction ◽  
Large Scale ◽  
Mixed Model ◽  
Human Genetics ◽  
Linear Mixed Effect Model ◽  
Mixed Effect ◽  
Statistical Framework ◽  
Effect Model ◽  
Plant Data ◽  
Genetic Value

AbstractLarge-scale phenotype data can enhance the power of genomic prediction in plant and animal breeding, as well as human genetics. However, the statistical foundation of multi-trait genomic prediction is based on the multivariate linear mixed effect model, a tool notorious for its fragility when applied to more than a handful of traits. We present , a statistical framework and associated software package for mixed model analyses of a virtually unlimited number of traits. Using three examples with real plant data, we show that can leverage thousands of traits at once to significantly improve genetic value prediction accuracy.

scholarly journals A hierarchical bivariate meta-analysis of diagnostic test accuracy to provide direct comparisons of immunoassays vs. indirect immunofluorescence for initial screening of connective tissue diseases

2020 ◽  
Vol 0 (0) ◽  
Author(s):  
Michelle Elaine Orme ◽  
Carmen Andalucia ◽  
Sigrid Sjölander ◽  
Xavier Bossuyt
Keyword(s):  
Connective Tissue ◽  
Indirect Immunofluorescence ◽  
Meta Analysis ◽  
Connective Tissue Diseases ◽  
Test Accuracy ◽  
Initial Screening ◽  
Case Control Studies ◽  
Cross Sectional ◽  
Mixed Effect ◽  
Mixed Effect Models

AbstractObjectivesTo compare indirect immunofluorescence (IIF) for antinuclear antibodies (ANA) against immunoassays (IAs) as an initial screening test for connective tissue diseases (CTDs).MethodsA systematic literature review identified cross-sectional or case-control studies reporting test accuracy data for IIF and enzyme-linked immunosorbent assays (ELISA), fluorescence enzyme immunoassay (FEIA), chemiluminescent immunoassay (CLIA) or multiplex immunoassay (MIA). The meta-analysis used hierarchical, bivariate, mixed-effect models with random-effects by test.ResultsDirect comparisons of IIF with ELISA showed that both tests had good sensitivity (five studies, 2321 patients: ELISA: 90.3% [95% confidence interval (CI): 80.5%, 95.5%] vs. IIF at a cut-off of 1:80: 86.8% [95% CI: 81.8%, 90.6%]; p = 0.4) but low specificity, with considerable variance across assays (ELISA: 56.9% [95% CI: 40.9%, 71.5%] vs. IIF 1:80: 68.0% [95% CI: 39.5%, 87.4%]; p = 0.5). FEIA sensitivity was lower than IIF sensitivity (1:80: p = 0.005; 1:160: p = 0.051); however, FEIA specificity was higher (seven studies, n = 12,311, FEIA 93.6% [95% CI: 89.9%, 96.0%] vs. IIF 1:80 72.4% [95% CI: 62.2%, 80.7%]; p < 0.001; seven studies, n = 3251, FEIA 93.5% [95% CI: 91.1%, 95.3%] vs. IIF 1:160 81.1% [95% CI: 73.4%, 86.9%]; p < 0.0001). CLIA sensitivity was similar to IIF (1:80) with higher specificity (four studies, n = 1981: sensitivity 85.9% [95% CI: 64.7%, 95.3%]; p = 0.86; specificity 86.1% [95% CI: 78.3%, 91.4%]). More data are needed to make firm inferences for CLIA vs. IIF given the wide prediction region. There were too few studies for the meta-analysis of MIA vs. IIF (MIA sensitivity range 73.7%–86%; specificity 53%–91%).ConclusionsFEIA and CLIA have good specificity compared to IIF. A positive FEIA or CLIA test is useful to support the diagnosis of a CTD. A negative IIF test is useful to exclude a CTD.

scholarly journals Neurophysiological and behavioural effects of conventional and high definition tDCS

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Fabio Masina ◽  
Giorgio Arcara ◽  
Eleonora Galletti ◽  
Isabella Cinque ◽  
Luciano Gamberini ◽  
...  
Keyword(s):  
Response Times ◽  
Power Reduction ◽  
Alpha Power ◽  
High Definition ◽  
Mixed Effect ◽  
State Dependency ◽  
Mixed Effect Models ◽  
Beta Power ◽  
Neurophysiological Data ◽  
Spectrum Density

AbstractHigh-definition transcranial direct current stimulation (HD-tDCS) seems to overcome a drawback of traditional bipolar tDCS: the wide-spread diffusion of the electric field. Nevertheless, most of the differences that characterise the two techniques are based on mathematical simulations and not on real, behavioural and neurophysiological, data. The study aims to compare a widespread tDCS montage (i.e., a Conventional bipolar montage with extracephalic return electrode) and HD-tDCS, investigating differences both at a behavioural level, in terms of dexterity performance, and a neurophysiological level, as modifications of alpha and beta power as measured with EEG. Thirty participants took part in three sessions, one for each montage: Conventional tDCS, HD-tDCS, and sham. In all the conditions, the anode was placed over C4, while the cathode/s placed according to the montage. At baseline, during, and after each stimulation condition, dexterity was assessed with a Finger Tapping Task. In addition, resting-state EEG was recorded at baseline and after the stimulation. Power spectrum density was calculated, selecting two frequency bands: alpha (8–12 Hz) and beta (18–22 Hz). Linear mixed effect models (LMMs) were used to analyse the modulation induced by tDCS. To evaluate differences among the montages and consider state-dependency phenomenon, the post-stimulation measurements were covariate-adjusted for baseline levels. We observed that HD-tDCS induced an alpha power reduction in participants with lower alpha at baseline. Conversely, Conventional tDCS induced a beta power reduction in participants with higher beta at baseline. Furthermore, data showed a trend towards a behavioural effect of HD-tDCS in participants with lower beta at baseline showing faster response times. Conventional and HD-tDCS distinctively modulated cortical activity. The study highlights the importance of considering state-dependency to determine the effects of tDCS on individuals.

scholarly journals Recombining Your Way Out of Trouble: The Genetic Architecture of Hybrid Fitness under Environmental Stress

2019 ◽  
Vol 37 (1) ◽  
pp. 167-182 ◽  
Author(s):  
Zebin Zhang ◽  
Devin P Bendixsen ◽  
Thijs Janzen ◽  
Arne W Nolte ◽  
Duncan Greig ◽  
...  
Keyword(s):  
Environmental Stress ◽  
Evolutionary Potential ◽  
Genetic Trait ◽  
Hybrid Fitness ◽  
Mixed Effect ◽  
Mixed Effect Models ◽  
Hybrid Genome ◽  
Chromosome Associations ◽  
Low Coverage ◽  
Negative Epistasis

Abstract Hybridization between species can either promote or impede adaptation. But we know very little about the genetic basis of hybrid fitness, especially in nondomesticated organisms, and when populations are facing environmental stress. We made genetically variable F2 hybrid populations from two divergent Saccharomyces yeast species. We exposed populations to ten toxins and sequenced the most resilient hybrids on low coverage using ddRADseq to investigate four aspects of their genomes: 1) hybridity, 2) interspecific heterozygosity, 3) epistasis (positive or negative associations between nonhomologous chromosomes), and 4) ploidy. We used linear mixed-effect models and simulations to measure to which extent hybrid genome composition was contingent on the environment. Genomes grown in different environments varied in every aspect of hybridness measured, revealing strong genotype–environment interactions. We also found selection against heterozygosity or directional selection for one of the parental alleles, with larger fitness of genomes carrying more homozygous allelic combinations in an otherwise hybrid genomic background. In addition, individual chromosomes and chromosomal interactions showed significant species biases and pervasive aneuploidies. Against our expectations, we observed multiple beneficial, opposite-species chromosome associations, confirmed by epistasis- and selection-free computer simulations, which is surprising given the large divergence of parental genomes (∼15%). Together, these results suggest that successful, stress-resilient hybrid genomes can be assembled from the best features of both parents without paying high costs of negative epistasis. This illustrates the importance of measuring genetic trait architecture in an environmental context when determining the evolutionary potential of genetically diverse hybrid populations.

scholarly journals Human language reveals a universal positivity bias

2015 ◽  
Vol 112 (8) ◽  
pp. 2389-2394 ◽  
Author(s):  
Peter Sheridan Dodds ◽  
Eric M. Clark ◽  
Suma Desu ◽  
Morgan R. Frank ◽  
Andrew J. Reagan ◽  
...  
Keyword(s):  
Real Time ◽  
Large Scale ◽  
Emotional Content ◽  
Human Language ◽  
Present Evidence ◽  
Word Use ◽  
Positivity Bias ◽  
Human Evaluation ◽  
Offline Measurement

Using human evaluation of 100,000 words spread across 24 corpora in 10 languages diverse in origin and culture, we present evidence of a deep imprint of human sociality in language, observing that (i) the words of natural human language possess a universal positivity bias, (ii) the estimated emotional content of words is consistent between languages under translation, and (iii) this positivity bias is strongly independent of frequency of word use. Alongside these general regularities, we describe interlanguage variations in the emotional spectrum of languages that allow us to rank corpora. We also show how our word evaluations can be used to construct physical-like instruments for both real-time and offline measurement of the emotional content of large-scale texts.

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