PERMUTOOLS: A MATLAB Package for Multivariate Permutation Testing

Statistical hypothesis testing and effect size measurement are routine parts of quantitative research. Advancements in computer processing power have greatly improved the capability of statistical inference through the availability of resampling methods. However, many of the statistical practices used today are based on traditional, parametric methods that rely on assumptions about the underlying population. These assumptions may not always be valid, leading to inaccurate results and misleading interpretations. Permutation testing, on the other hand, generates the sampling distribution empirically by permuting the observed data, providing distribution-free hypothesis testing. Furthermore, this approach lends itself to a powerful method for multiple comparison correction - known as max correction - which is less prone to type II errors than conventional correction methods. Parametric methods have also traditionally been utilized for estimating the confidence interval of various test statistics and effect size measures. However, these too can be estimated empirically using permutation or bootstrapping techniques. Whilst resampling methods are generally considered preferable, many popular programming languages and statistical software packages lack efficient implementations. Here, we introduce PERMUTOOLS, a MATLAB package for multivariate permutation testing and effect size measurement.Comment: 7 pages, 2 figures, for PERMUTOOLS toolbox, see https://github.com/mickcrosse/PERMUTOOL

Antineutrino Detectors Remain Impractical for Nuclear Explosion Monitoring

Fission explosions produce large numbers of antineutrinos. It is occasionally asked whether this distinctive, unshieldable emission could help reveal clandestine nuclear weapon explosions. The practical challenge encountered is that detectors large enough for this application are cost prohibitive, likely on the multi-billion-dollar scale. In this paper, we review several hypothetical use cases for antineutrino detectors as supplements to the seismic, infrasound, hydroacoustic, and airborne radionuclide sensors of the Comprehensive Nuclear-Test-Ban Treaty Organization's International Monitoring System. In each case, if an anti-neutrino detector could be constructed that would compete with existing capabilities, we conclude that the cost would considerably outstrip the value it might add to the existing monitoring network, compared to the significantly lower costs for the same or superior capability.Comment: 16 pages, 3 figure

Evidence for Pervasive Adaptive Protein Evolution in Wild Mice

The relative contributions of neutral and adaptive substitutions to molecular evolution has been one of the most controversial issues in evolutionary biology for more than 40 years. The analysis of within-species nucleotide polymorphism and between-species divergence data supports a widespread role for adaptive protein evolution in certain taxa. For example, estimates of the proportion of adaptive amino acid substitutions (alpha) are 50% or more in enteric bacteria and Drosophila. In contrast, recent estimates of alpha for hominids have been at most 13%. Here, we estimate alpha for protein sequences of murid rodents based on nucleotide polymorphism data from multiple genes in a population of the house mouse subspecies Mus musculus castaneus, which inhabits the ancestral range of the Mus species complex and nucleotide divergence between M. m. castaneus and M. famulus or the rat. We estimate that 57% of amino acid substitutions in murids have been driven by positive selection. Hominids, therefore, are exceptional in having low apparent levels of adaptive protein evolution. The high frequency of adaptive amino acid substitutions in wild mice is consistent with their large effective population size, leading to effective natural selection at the molecular level. Effective natural selection also manifests itself as a paucity of effectively neutral nonsynonymous mutations in M. m. castaneus compared to humans

Expression and trans-specific polymorphism of self-incompatibility RNases in Coffea (Rubiaceae)

Self-incompatibility (SI) is widespread in the angiosperms, but identifying the biochemical components of SI mechanisms has proven to be difficult in most lineages. Coffea (coffee; Rubiaceae) is a genus of old-world tropical understory trees in which the vast majority of diploid species utilize a mechanism of gametophytic self-incompatibility (GSI). The S-RNase GSI system was one of the first SI mechanisms to be biochemically characterized, and likely represents the ancestral Eudicot condition as evidenced by its functional characterization in both asterid (Solanaceae, Plantaginaceae) and rosid (Rosaceae) lineages. The S-RNase GSI mechanism employs the activity of class III RNase T2 proteins to terminate the growth of "self" pollen tubes. Here, we investigate the mechanism of Coffea GSI and specifically examine the potential for homology to S-RNase GSI by sequencing class III RNase T2 genes in populations of 14 African and Madagascan Coffea species and the closely related self-compatible species Psilanthus ebracteolatus. Phylogenetic analyses of these sequences aligned to a diverse sample of plant RNase T2 genes show that the Coffea genome contains at least three class III RNase T2 genes. Patterns of tissue-specific gene expression identify one of these RNase T2 genes as the putative Coffea S-RNase gene. We show that populations of SI Coffea are remarkably polymorphic for putative S-RNase alleles, and exhibit a persistent pattern of trans-specific polymorphism characteristic of all S-RNase genes previously isolated from GSI Eudicot lineages. We thus conclude that Coffea GSI is most likely homologous to the classic Eudicot S-RNase system, which was retained since the divergence of the Rubiaceae lineage from an ancient SI Eudicot ancestor, nearly 90 million years ago.United States National Science Foundation [0849186]; Society of Systematic Biologists; American Society of Plant Taxonomists; Duke University Graduate Schoolinfo:eu-repo/semantics/publishedVersio

Event-related alpha suppression in response to facial motion

This article has been made available through the Brunel Open Access Publishing Fund.While biological motion refers to both face and body movements, little is known about the visual perception of facial motion. We therefore examined alpha wave suppression as a reduction in power is thought to reflect visual activity, in addition to attentional reorienting and memory processes. Nineteen neurologically healthy adults were tested on their ability to discriminate between successive facial motion captures. These animations exhibited both rigid and non-rigid facial motion, as well as speech expressions. The structural and surface appearance of these facial animations did not differ, thus participants decisions were based solely on differences in facial movements. Upright, orientation-inverted and luminance-inverted facial stimuli were compared. At occipital and parieto-occipital regions, upright facial motion evoked a transient increase in alpha which was then followed by a significant reduction. This finding is discussed in terms of neural efficiency, gating mechanisms and neural synchronization. Moreover, there was no difference in the amount of alpha suppression evoked by each facial stimulus at occipital regions, suggesting early visual processing remains unaffected by manipulation paradigms. However, upright facial motion evoked greater suppression at parieto-occipital sites, and did so in the shortest latency. Increased activity within this region may reflect higher attentional reorienting to natural facial motion but also involvement of areas associated with the visual control of body effectors. © 2014 Girges et al

Os mártires e a cristianização do território na América portuguesa, séculos XVI e XVII

O artigo investiga um grupo de atores sociais bastante relevante para viabilizar a cristianização na América portuguesa: os mártires cristãos, indivíduos muito especiais, dispostos a regar a terra com seu próprio sangue, de forma a tornar definitiva e irreversível a ocupação cristã do território. Os mártires - e principalmente a narrativa em torno deles - parecem ter sido bastante acionados para integrar a América portuguesa e seus habitantes nativos à temporalidade e territorialidade cristã. Os mártires dos séculos XVI e XVII, principalmente missionários, reeditavam os martírios do início da cristandade, que espalharam o cristianismo rumo a diversas partes do mundo na antiguidade. Dessa forma, viabilizaram a cristianização das novas fronteiras, consagrando o solo com seu sangue divino e viabilizando posteriores processos de urbanização. Além da função estratégica dos mártires para os cristãos, o texto mostra que eles também tiveram significado peculiar na interlocução com as culturas ameríndias, que tinha como um de seus principais personagens o grande guerreiro, disposto a perder seu sangue em prol de seu grupo.This paper looks into a group of social agents who played a significant role in the Christianization of Portuguese America, namely, the Christian martyrs - very special individuals who were ready to wet the land with their own blood in order to make possible a definitive and irreversible occupation of the territory by Christian settlers. The martyrs, and above all the stories told about them, seem to have been called upon to integrate Portuguese America and its native inhabitants into the temporalities and territory of Christendom. Mostly made up of missionaries, this group of 16th and 17th-century martyrs reedited the martyrdom of early Christians, who spread their creed across numerous parts of the Ancient World. They enabled the Christianization of new frontiers by consecrating the soil with their divine blood and paving the way for subsequent processes of urban development. In addition to their strategic significance for Christianity, the text also shows that their martyrdom played a specific role in the Christian settlers' interaction with Amerindian culture, whose main cults included the figure of the great warrior, ever ready to shed his own blood for his group

Benefits of Stimulus Congruency for Multisensory Facilitation of Visual Learning

Background. Studies of perceptual learning have largely focused on unisensory stimuli. However, multisensory interactions are ubiquitous in perception, even at early processing stages, and thus can potentially play a role in learning. Here, we examine the effect of auditory-visual congruency on visual learning. Methodology/Principle Findings. Subjects were trained over five days on a visual motion coherence detection task with either congruent audiovisual, or incongruent audiovisual stimuli. Comparing performance on visual-only trials, we find that training with congruent audiovisual stimuli produces significantly better learning than training with incongruent audiovisual stimuli or with only visual stimuli. Conclusions/ Significance. This advantage from stimulus congruency during training suggests that the benefits of multisensory training may result from audiovisual interactions at a perceptual rather than cognitive level

Polygenic Risk for Alzheimer's Disease is not Associated with Cognitive Ability or Cognitive Aging in Non-Demented Older People

Peer reviewedPublisher PD

Audiovisual Non-Verbal Dynamic Faces Elicit Converging fMRI and ERP Responses

In an everyday social interaction we automatically integrate another’s facial movements and vocalizations, be they linguistic or otherwise. This requires audiovisual integration of a continual barrage of sensory input—a phenomenon previously well-studied with human audiovisual speech, but not with non-verbal vocalizations. Using both fMRI and ERPs, we assessed neural activity to viewing and listening to an animated female face producing non-verbal, human vocalizations (i.e. coughing, sneezing) under audio-only (AUD), visual-only (VIS) and audiovisual (AV) stimulus conditions, alternating with Rest (R). Underadditive effects occurred in regions dominant for sensory processing, which showed AV activation greater than the dominant modality alone. Right posterior temporal and parietal regions showed an AV maximum in which AV activation was greater than either modality alone, but not greater than the sum of the unisensory conditions. Other frontal and parietal regions showed Common-activation in which AV activation was the same as one or both unisensory conditions. ERP data showed an early superadditive effect (AV > AUD + VIS, no rest), mid-range underadditive effects for auditory N140 and face-sensitive N170, and late AV maximum and common-activation effects. Based on convergence between fMRI and ERP data, we propose a mechanism where a multisensory stimulus may be signaled or facilitated as early as 60 ms and facilitated in sensory-specific regions by increasing processing speed (at N170) and efficiency (decreasing amplitude in auditory and face-sensitive cortical activation and ERPs). Finally, higher-order processes are also altered, but in a more complex fashion