A permutation approach for ranking of multivariate populations

Design of experiments and machine learning with application to industrial experiments

In the context of product innovation, there is an emerging trend to use Machine Learning (ML) models with the support of Design Of Experiments (DOE). The paper aims firstly to review the most suitable designs and ML models to use jointly in an Active Learning (AL) approach; it then reviews ALPERC, a novel AL approach, and proves the validity of this method through a case study on amorphous metallic alloys, where this algorithm is used in combination with a Random Forest model.

A robust Spearman correlation coefficient permutation test

In this work, we show that Spearman's correlation coefficient test about H 0 : ρ s = 0 found in most statistical software is theoretically incorrect and performs poorly when bivariate normality assumptions are not met or the sample size is small. There is common misconception that the tests about ρ s = 0 are robust to deviations from bivariate normality. However, we found under certain scenarios violation of the bivariate normality assumption has severe effects on type I error control for the common tests. To address this issue, we developed a robust permutation test for testing the hypothesis H 0 : ρ s = 0 based on an appropriately studentized statistic. We will show that the test is asymptotically valid in general settings. This was demonstrated by a comprehensive set of simulation studies, where the proposed test exhibits robust type I error control, even when the sample size is small. We also demonstrated the application of this test in two real world examples.

The primary visual cortex of Cetartiodactyls: organization, cytoarchitectonics and comparison with perissodactyls and primates

Cetartiodactyls include terrestrial and marine species, all generally endowed with a comparatively lateral position of their eyes and a relatively limited binocular field of vision. To this day, our understanding of the visual system in mammals beyond the few studied animal models remains limited. In the present study, we examined the primary visual cortex of Cetartiodactyls that live on land (sheep, Père David deer, giraffe); in the sea (bottlenose dolphin, Risso’s dolphin, long-finned pilot whale, Cuvier’s beaked whale, sperm whale and fin whale); or in an amphibious environment (hippopotamus). We also sampled and studied the visual cortex of the horse (a closely related perissodactyl) and two primates (chimpanzee and pig-tailed macaque) for comparison. Our histochemical and immunohistochemical results indicate that the visual cortex of Cetartiodactyls is characterized by a peculiar organization, structure, and complexity of the cortical column. We noted a general lesser lamination compared to simians, with diminished density, and an apparent simplification of the intra- and extra-columnar connections. The presence and distribution of calcium-binding proteins indicated a notable absence of parvalbumin in water species and a strong reduction of layer 4, usually enlarged in the striated cortex, seemingly replaced by a more diffuse distribution in neighboring layers. Consequently, thalamo-cortical inputs are apparently directed to the higher layers of the column. Computer analyses and statistical evaluation of the data confirmed the results and indicated a substantial correlation between eye placement and cortical structure, with a markedly segregated pattern in cetaceans compared to other mammals. Furthermore, cetacean species showed several types of cortical lamination which may reflect differences in function, possibly related to depth of foraging and consequent progressive disappearance of light, and increased importance of echolocation.

Multi-aspect testing and ranking inference to quantify dimorphism in the cytoarchitecture of cerebellum of male, female and intersex individuals: a model applied to bovine brains

The dimorphism among male, female and freemartin intersex bovines, focusing on the vermal lobules VIII and IX, was analyzed using a novel data analytics approach to quantify morphometric differences in the cytoarchitecture of digitalized sections of the cerebellum. This methodology consists of multivariate and multi-aspect testing for cytoarchitecture-ranking, based on neuronal cell complexity among populations defined by factors, such as sex, age or pathology. In this context, we computed a set of shape descriptors of the neural cell morphology, categorized them into three domains named size, regularity and density, respectively. The output and results of our methodology are multivariate in nature, allowing an in-depth analysis of the cytoarchitectonic organization and morphology of cells. Interestingly, the Purkinje neurons and the underlying granule cells revealed the same morphological pattern: female possessed larger, denser and more irregular neurons than males. In the Freemartin, Purkinje neurons showed an intermediate setting between males and females, while the granule cells were the largest, most regular and dense. This methodology could be a powerful instrument to carry out morphometric analysis providing robust bases for objective tissue screening, especially in the field of neurodegenerative pathologies.

Personalized Tests in Paralympic Athletes: Aerobic and Anaerobic Performance Profile of Elite Wheelchair Rugby Players

In Paralympic sports, the goal of functional classifications is to minimize the impact of impairment on the outcome of the competition. The present cross-sectional study aimed to investigate aerobic and anaerobic personalized tests in Paralympic athletes and to correlate them with the classification of the international wheelchair rugby federation (IWRF). Sixteen elite players of the Italian wheelchair rugby team volunteered for the study. Aerobic (incremental test to exhaustion) and anaerobic (Wingate 30s all-out test, 5 and 10-meter sprint test, shuttle test, isometric test) sport-performance measurements were correlated singularly or grouped (Z scores) with the classification point. Moreover, a multivariate permutation-based ranking analysis investigated possible differences in the overall level of performance among the adjacent classified groups of players, considering the scores of each test. A statistically significant correlation between the performance parameters and the IWRF functional classification considering both aerobic and anaerobic personalized tests was detected (0.58 ≤ r ≤ 0.88; 0.0260 ≤ p ≤ 0.0001). The multivariate permutation-based ranking analysis showed differences only for the low-pointers versus mid-pointers (p = 0.0195) and high-pointers (p = 0.0075). Although single performance parameters correlated with athletes’ classification point, results of the multivariate permutation-based ranking analysis seem to suggest considering only the most significant anaerobic and sport-specific performance parameters among athletes. These should be combined with the physical assessment and the qualitative observation, which are already part of the classification process to improve its effectiveness.

An Assay System to Evaluate Riboflavin/UV-A Corneal Phototherapy Efficacy in a Porcine Corneal Organ Culture Model

Simple summary

The scope of this study is to quantitatively evaluate, with an automated digital image analysis method, the efficacy of riboflavin/UV-A corneal phototherapy on the cornea in a porcine corneal organ culture model of ulcerative melting keratitis. Riboflavin/UV-A corneal phototherapy provided a favorable outcome in the corneal wound healing process after chemical injury: the treatment restores the damaged corneas to the texture of healthy corneas. This automated image analysis method may be compared to clinical diagnostic methods, such as optical coherence tomography (OCT) imaging, for in vivo damaged ocular structural investigations. Positive results from this research could provide an opportunity for studying the effects of this method in other economically and emotionally valued species, such as dogs, cats, and horses. The relatively overall low treatment cost and the ease of performing the procedure make riboflavin/UV-A corneal phototherapy accessible to the veterinary market.

Abstract

The purpose of this study was to investigate the response of porcine corneal organ cultures to riboflavin/UV-A phototherapy in the injury healing of induced lesions. A porcine corneal organ culture model was established. Corneal alterations in the stroma were evaluated using an assay system, based on an automated image analysis method able to (i) localize the holes and gaps within the stroma and (ii) measure the brightness values in these patches. The analysis has been performed by dividing the corneal section in 24 regions of interest (ROIs) and integrating the data analysis with a “multi-aspect approach.” Three group of corneas were analyzed: healthy, injured, and injured-and-treated. Our study revealed a significant effect of the riboflavin/UV-A phototherapy in the injury healing of porcine corneas after induced lesions. The injured corneas had significant differences of brightness values in comparison to treated (p < 0.00) and healthy (p < 0.001) corneas, whereas the treated and healthy corneas showed no significant difference (p = 0.995). Riboflavin/UV-A phototherapy shows a significant effect in restoring the brightness values of damaged corneas to the values of healthy corneas, suggesting treatment restores the injury healing of corneas after lesions. Our assay system may be compared to clinical diagnostic methods, such as optical coherence tomography (OCT) imaging, for in vivo damaged ocular structure investigations.

Testing and ranking on round-robin design for data sport analytics with application to basketball

By modelling results of sport matches as a set of paired fixed effect linear models, the goal of the present article is showing that traditional scoring outputs can be used to do inference on parameters related to the net relative strength or weakness of teams within a league. As hypothesis testing method, we propose either a normal-based and a non-parametric permutation-based approach. As an extension to round-robin of the ranking methodology recently proposed by Arboretti Giancristofaro et al. (2014) and Corain et al. (2016) , results of pairwise testing are then exploited to provide a ranking of teams within a league. Through an extensive Monte Carlo simulation study, we investigated the properties of the proposed testing and ranking methodology where we proved its validity under different random distributions. In its simplest univariate version, the proposed methodology allows us to infer on the teams average net scoring within a league, while in its more intriguing multivariate layout it is suitable for looking for any team-related global dominance using a wide set of performance indicators. Finally, by using traditional basketball box scores, we present an application to the Italian Basket League.

The bovine anterior hypothalamus: Characterization of the vasopressin-oxytocin containing nucleus and changes in relation to sexual differentiation

In an effort to systematically describe the neurochemical anatomy of the bovine anterior hypothalamus, we used a series of immunocytochemical markers such as acetylcholine esterase (AChE), arginine-vasopressin (AVP), calbindin (Calb), galanin (Gal), neuropeptide-Y (NPY), oxytocin (OXT), somatostatin (SST), and vasoactive intestinal peptide (VIP). We also investigated the potential sex difference present in the suprachiasmatic nucleus (SCN) and the vasopressin-oxytocin containing nucleus (VON) of six male and six female Bos taurus. Our study revealed that the cytochemical structure of the cattle anterior hypothalamus follows the blueprint of other mammals. The VON, which was never described before in cattle, showed a sex difference with a 33.7% smaller volume and 23.2% fewer magnocellular neurons (approximately 20-30 μm) in the male. The SCN also did show a sex difference in VIP neurons and volume with a 36.1% larger female nucleus with 28.1% more cells. Additionally, we included five heifers with freemartin syndrome as a new animal model relevant to sexual differentiation in the brain. This is, to the best of our knowledge, the first freemartin study in relation to the brain. Surprisingly, the SCN of freemartin heifers was 32.5% larger than its control male and female counterparts with 29% more VIP cells. Conversely, the freemartin VON had an intermediary size between male and female. To analyze our data, a classical statistical analysis and a novel multivariate and multi-aspect approach were applied. These findings shed new light on sexual dimorphism in the bovine brain and present this species with freemartins as a valuable animal model in neuroscience.

Sexually Diergic Trophic Effects of Estradiol Exposure on Developing Bovine Cerebellar Granule Cells

In the mammalian brain, the differentiation of neural cells and the developmental organization of the underlying circuitry are influenced by steroid hormones. The estrogen 17-β estradiol (E2) is one of the most potent regulators of neural growth during prenatal life, synthetized locally from steroid precursors including prenatal testicular testosterone. Estradiol promotes brain differentiation counting sexually dimorphic neural circuits by binding to the estrogen receptors, ER-α and ER-β. The cerebellum has been described as a site of estrogen action and a potentially sexually dimorphic area. The goal of this study was to analyze the capacity of E2 to affect the growth of male and female fetal bovine cerebellar granule. We performed primary cultures of fetal cerebellar granules, and verified the mRNA expression of the ER-α and ER-β in both sexes. Moreover, the distribution of ERs in the male and female cerebellar granules of the second fetal stage was characterized by immunohistochemistry. We measured morphological parameters in presence (or absence) of estradiol administration, focusing on the variations of the dendritic branching pattern of granule neurons. By using the nonparametric combination and permutation testing approach, we proposed a sophisticated multivariate statistical analysis to demonstrate that E2 induces multifarious and dimorphic changes in the granule cells. E2 exerts trophic effects in both female and male granules and this effect is stronger in female. Male granules treated with E2 became similar to female control granule. Bos taurus species has a long gestation and a large brain that offers an interesting alternative in comparative neuroscience.