Introduction to the R package TDA

We present a short tutorial and introduction to using the R package TDA, which provides some tools for Topological Data Analysis. In particular, it includes implementations of functions that, given some data, provide topological information about the underlying space, such as the distance function, the distance to a measure, the kNN density estimator, the kernel density estimator, and the kernel distance. The salient topological features of the sublevel sets (or superlevel sets) of these functions can be quantified with persistent homology. We provide an R interface for the efficient algorithms of the C++ libraries GUDHI, Dionysus and PHAT, including a function for the persistent homology of the Rips filtration, and one for the persistent homology of sublevel sets (or superlevel sets) of arbitrary functions evaluated over a grid of points. The significance of the features in the resulting persistence diagrams can be analyzed with functions that implement recently developed statistical methods. The R package TDA also includes the implementation of an algorithm for density clustering, which allows us to identify the spatial organization of the probability mass associated to a density function and visualize it by means of a dendrogram, the cluster tree

“Feeling my Sister’s Pain”: Perceived Victim Suffering Moderates the Impact of Sexualized Music Videos on Fijian Women’s Responses to Men’s Intimate Partner Violence against Women

To better understand how sexualized music videos affect women’s responses to intimate partner violence (IPV), we examined the role of individual variability in perceived victim pain and perceived victim culpability in moderating and mediating (respectively) the priming effects of sexual music videos on women. Female Fijian college students (n = 243) were randomly assigned to one of three viewing conditions: stereotyped sexual music videos, non-stereotyped/non-sexual music videos, or neutral videos. All participants then read a portrayal of a male-toward-female IPV episode and their perceptions of the female victim and male perpetrator were assessed. Only women who minimized the victim’s pain were adversely affected by exposure to the stereotyped sexual videos. Specifically, for women who perceived low victim pain, those in the stereotyped video condition perceived the victim as more culpable and reported greater perpetrator-directed favorable responding than those in the other two conditions. For these women who perceived low victim pain, perceptions of victim culpability mediated the impact of video type on perpetrator-favorable responding. The findings help us better understand susceptibility to the negative impact of stereotypical sexual videos and highlight areas, such as emphasizing the suffering of victims and reducing myths about victim culpability, which may be worthy of particular emphasis in interventions

Subsampling Methods for Persistent Homology

Persistent homology is a multiscale method for analyzing the shape of sets and functions from point cloud data arising from an unknown distribution supported on those sets. When the size of the sample is large, direct computation of the persistent homology is prohibitive due to the combinatorial nature of the existing algorithms. We propose to compute the persistent homology of several subsamples of the data and then combine the resulting estimates. We study the risk of two estimators and we prove that the subsampling approach carries stable topological information while achieving a great reduction in computational complexity

On the Bootstrap for Persistence Diagrams and Landscapes

Persistent homology probes topological properties from point clouds and functions. By looking at multiple scales simultaneously, one can record the births and deaths of topological features as the scale varies. In this paper we use a statistical technique, the empirical bootstrap, to separate topological signal from topological noise. In particular, we derive confidence sets for persistence diagrams and confidence bands for persistence landscapes

Experimentally Manipulated Somatic Information and Somatization Tendencies and their Impact on Physical Symptom Reporting and Performance in a Physically Strenuous Task

This study attempts to determine whether the presentation of an experimentally manipulated somatic experience during a physically strenuous task can influence physical performance and symptom reporting. The study also compares the relative influence of experimentally manipulated somatic information (state somatization) with stable individual differences in the tendency to amplify physical symptoms (trait somatization) on performance and symptom reporting. 194 participants completed standardized measures of somatization tendencies, state anxiety, neuroticism and conscientiousness. Participants where then given a mock physical exam, with individuals randomly assigned to receive either favorable or unfavorable somatic information. All participants then had their body mass index assessed and completed a rigorous exercise task, with quantification of performance. Physiological measures of blood pressure and pulse were also assessed before and after the exercise task. The experimentally manipulated presentation of somatic information predicted both performance and physical symptoms, even after controlling for BMI, neuroticism, conscientiousness, and state anxiety. Moreover, expected performance uniquely and significantly predicted performance above and beyond condition, anxiety, BMI, neuroticism, and conscientiousness. Somatosensory amplification tendencies also predicted symptom endorsement, but not performance. Findings suggest that both state and trait expectations with respect to somatic experiences influence symptom reporting and to a lesser extent performance, even after controlling for variables known to strongly influence each of these outcomes. Results are consistent with the cognitive-perceptual and the cognitive-appraisal models of somatic interpretation

Stochastic Convergence of Persistence Landscapes and Silhouettes

Persistent homology is a widely used tool in Topological Data Analysis that encodes multiscale topological information as a multi-set of points in the plane called a persistence diagram. It is difficult to apply statistical theory directly to a random sample of diagrams. Instead, we can summarize the persistent homology with the persistence landscape, introduced by Bubenik, which converts a diagram into a well-behaved real-valued function. We investigate the statistical properties of landscapes, such as weak convergence of the average landscapes and convergence of the bootstrap. In addition, we introduce an alternate functional summary of persistent homology, which we call the silhouette, and derive an analogous statistical theory

Suppression of Sleep Spindle Rhythmogenesis in Mice with Deletion of CaV3.2 and CaV3.3 T-type Ca(2+) Channels.

STUDY OBJECTIVES: Low-threshold voltage-gated T-type Ca(2+) channels (T-channels or CaV3 channels) sustain oscillatory discharges of thalamocortical (TC) and nucleus Reticularis thalami (nRt) cells. The CaV3.3 subtype dominates nRt rhythmic bursting and mediates a substantial fraction of spindle power in the NREM sleep EEG. CaV3.2 channels are also found in nRt, but whether these contribute to nRt-dependent spindle generation is unexplored. We investigated thalamic rhythmogenesis in mice lacking this subtype in isolation (CaV3.2KO mice) or in concomitance with CaV3.3 deletion (CaV3.double-knockout (DKO) mice). METHODS: We examined discharge characteristics of thalamic cells and intrathalamic evoked synaptic transmission in brain slices from wild-type, CaV3.2KO and CaV3.DKO mice through patch-clamp recordings. The sleep profile of freely behaving CaV3.2KO and CaV3.DKO mice was assessed by polysomnographic recordings. RESULTS: CaV3.2 channel deficiency left nRt discharge properties largely unaltered, but additional deletion of CaV3.3 channels fully abolished low-threshold whole-cell Ca(2+) currents and bursting, and suppressed burst-mediated inhibitory responses in TC cells. CaV3.DKO mice had more fragmented sleep, with shorter NREM sleep episodes and more frequent microarousals. The NREM sleep EEG power spectrum displayed a relative suppression of the σ frequency band (10-15 Hz), which was accompanied by an increase in the δ band (1-4 Hz). CONCLUSIONS: Consistent with previous findings, CaV3.3 channels dominate nRt rhythmogenesis, but the lack of CaV3.2 channels further aggravates neuronal, synaptic, and EEG deficits. Therefore, CaV3.2 channels can boost intrathalamic synaptic transmission, and might play a modulatory role adjusting the relative presence of NREM sleep EEG rhythms

Search for Neutron Flux Generation in a Plasma Discharge Electrolytic Cell

Following some recent unexpected hints of neutron production in setups like high-voltage atmospheric discharges and plasma discharges in electrolytic cells, we present a measurement of the neutron flux in a configuration similar to the latter. We use two different types of neutron detectors, poly-allyl-diglicol-carbonate (PADC, aka CR-39) tracers and Indium disks. At 95% C.L. we provide an upper limit of 1.5 neutrons cm^-2 s^-1 for the thermal neutron flux at ~5 cm from the center of the cell. Allowing for a higher energy neutron component the largest allowed flux is 64 neutrons cm^-2 s^-1. This upper limit is two orders of magnitude smaller than what previously claimed in an electrolytic cell plasma discharge experiment. Furthermore the behavior of the CR-39 is discussed to point our possible sources of spurious signals.Comment: 4 pages, 3 figure