Penalized regression and clustering in high-dimensional data

The main goal of this Thesis is to describe numerous statistical techniques that deal with high-dimensional genomic data. The Thesis begins with a review of the literature on penalized regression models, with particular attention to least absolute shrinkage and selection operator (LASSO) or L1-penalty methods. L1 logistic/multinomial regression models are used for variable selection and discriminant analysis with a binary/categorical response variable. The Thesis discusses and compares several methods that are commonly utilized in genetics, and introduces new strategies to select markers according to their informative content and to discriminate clusters by offering reduced panels for popul…

Activation-Induced Rigidity in Neurologically and Cognitively Healthy Individuals Aged 18-90 Years: A Cross-Sectional Study.

2021

Background: Rigidity is a key clinical feature of Parkinson’s disease (PD), but in a very early phase of the disease it may be absent and can be enhanced through active movements of the arm contralateral to the one being tested. Objective: To evaluate in a large cohort of neurologically and cognitively healthy (NCH) subjects aged 18–90 years if activation-induced rigidity (AR) is present in all age classes, and if there are biological differences between subjects showing AR (AR+) and not showing AR (AR-). Methods: 2,228 NCH subjects categorized as young adult (18–44 years), adult (45–64 years), elderly (65–74 years), and old/oldest-old (75–90 years) were included in the analysis, and underw…

Nociceptive Primitive Reflexes in Neurologically and Cognitively Healthy Aging Subjects

2019

ABSTRACT:Background:To assess the prevalence of three nociceptive primitive reflexes (nPR), i.e., glabellar tap, snout reflex, and palmomental reflex, in neurologically and cognitively healthy (NCH) aging subjects.Objective:To investigate whether nPR are cross-sectionally associated with white matter hyperintensities (WMH), lacunes, atrophy of the caudate nuclei, and global brain atrophy.Methods:A total of 1246 NCH subjects aged 45–91 years were included in the study and underwent standard brain MRI. Atrophy of the caudate nuclei and global brain atrophy were assessed through the bicaudate ratio (BCr) and lateral ventricles to brain ratio (LVBr), respectively. WMH were assessed through visu…

Migration and students' performance: detecting geographical differences following a curves clustering approach

2020

Students’ migration mobility is the new form of migration: students migrate to improve their skills and become more valued for the job market. The data regard the migration of Italian Bachelors who enrolled at Master Degree level, moving typically from poor to rich areas. This paper investigates the migration and other possible determinants on the Master Degree students’ performance. The Clustering of Effects approach for Quantile Regression Coefficients Modelling has been used to cluster the effects of some variables on the students’ performance for three Italian macro-areas. Results show evidence of similarity between Southern and Centre students, with respect to the Northern ones.

A new approach for clustering of effects in quantile regression

2017

In this paper we aim at nding similarities among the coefficients from a multivariate regression. Using a quantile regression coefficients modeling, the effect of each covariate, given a response (also multivariate) is a curve in the multidimensional space of the percentiles. Collecting all the curves, describing the effects of each covariate on each response variable, we could be able to assess if only one or more covariates have same effects on different responses.

Genome-wide association study reveals the locus responsible for microtia in Valle del Belice sheep breed.

2018

Microtia is a congenital deformity of the outer ear with phenotypes varying from a small auricle to total absence (anotia). The genetic basis is still poorly understood, and very few studies have been performed in sheep. Valle del Belice sheep is a breed showing microtia. The aim of this study was to identify the potential genomic regions involved in microtia in sheep. A total of 40 individuals, 20 with microtia and 20 normal, were genotyped with the Illumina OvineSNP50 BeadChip. The comparison among the results from a genome-wide association study, Fisher's exact test and FST analysis revealed a single strong association signal: rs419889303 on chromosome 1, located within intron 3 of the C…

A penalized approach to covariate selection through quantile regression coefficient models

2019

The coefficients of a quantile regression model are one-to-one functions of the order of the quantile. In standard quantile regression (QR), different quantiles are estimated one at a time. Another possibility is to model the coefficient functions parametrically, an approach that is referred to as quantile regression coefficients modeling (QRCM). Compared with standard QR, the QRCM approach facilitates estimation, inference and interpretation of the results, and generates more efficient estimators. We designed a penalized method that can address the selection of covariates in this particular modelling framework. Unlike standard penalized quantile regression estimators, in which model selec…

Genome-wide detection of signatures of selection in three Valdostana cattle populations

2020

International audience; The Valdostana is a local dual purpose cattle breed developed in Italy. Three populations are recognized within this breed, based on coat colour, production level, morphology and temperament: Valdostana Red Pied (VPR), Valdostana Black Pied (VPN) and Valdostana Chestnut (VCA). Here, we investigated putative genomic regions under selection among these three populations using the Bovine 50K SNP array by combining three different statistical methods based either on allele frequencies (F-ST) or extended haplotype homozygosity (iHS and Rsb). In total, 8, 5 and 8 chromosomes harbouring 13, 13 and 16 genomic regions potentially under selection were identified by at least tw…

The Joint Censored Gaussian Graphical Lasso Model

2022

The Gaussian graphical model is one of the most used tools for inferring genetic networks. Nowadays, the data are often collected from different sources or under different biological conditions, resulting in heterogeneous datasets that exhibit a dependency structure that varies across groups. The complex structure of these data is typically recovered using regularized inferential procedures that use two penalties, one that encourages sparsity within each graph and the other that encourages common structures among the different groups. To this date, these approaches have not been developed for handling the case of censored data. However, these data are often generated by gene expression tech…

cglasso: An R Package for Conditional Graphical Lasso Inference with Censored and Missing Values

2023

Sparse graphical models have revolutionized multivariate inference. With the advent of high-dimensional multivariate data in many applied fields, these methods are able to detect a much lower-dimensional structure, often represented via a sparse conditional independence graph. There have been numerous extensions of such methods in the past decade. Many practical applications have additional covariates or suffer from missing or censored data. Despite the development of these extensions of sparse inference methods for graphical models, there have been so far no implementations for, e.g., conditional graphical models. Here we present the general-purpose package cglasso for estimating sparse co…

The neglected status of the vermetid reefs in the Mediterranean Sea: A systematic map

2022

Studied since late 1800, vermetid reefs are marine bioconstructions of well-acknowledged importance in the Mediterranean Sea. Despite their persistence being jeopardized in the whole basin, recent studies have referred to this bioconstruction as a neglected habitat. In this study, we assessed the neglected status of the Mediterranean vermetid reefs in the scientific literature producing a systematic map through a multi-method bibliometric protocol. Scopus and Web of Science databases were jointly used for data collection. Vermetid reefs publication rate (i.e., number of publications per year) was investigated compared to the other Mediterranean bio-constructions using ANOVA analysis and Zer…

A distribution curves comparison approach to analyze the university moving students performance

2018

Da qualche anno anche l’Italia sta assistendo a un flusso migratorio di studenti, che da un povero Sud si dirige verso un più ricco Nord. Se un tempo la migrazione avveniva nel momento di cercare lavoro, adesso questa è anticipata da studenti che ritengono di avere meggiore successo se conseguono il titolo al Nord. L’obiettivo di questo studio è verificare la sensazione empirica secondo la quale in realtà gli studenti che restano per iscriversi alla Laurea Magistrale hanno un percorso simile rispetto a quelli che si iscrivono a un percorso magistrale del Nord. Considerate diverse misure di performance, e svolto i confronti attraverso una nuova procedura di raffronto tra curve di distribuzio…

Genome-wide scan for runs of homozygosity identifies potential candidate genes associated with local adaptation in Valle del Belice sheep

2017

Background Because very large numbers of single nucleotide polymorphisms (SNPs) are now available throughout the genome, they are particularly suitable for the detection of genomic regions where a reduction in heterozygosity has occurred and they offer new opportunities to improve the accuracy of inbreeding (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$F$$\end{document}F) estimates. Runs of homozygosity (ROH) are contiguous lengths of homozygous segments of the genome where the two haplotypes inherited from t…

A multivariate statistical test for differential expression analysis

2022

AbstractStatistical tests of differential expression usually suffer from two problems. Firstly, their statistical power is often limited when applied to small and skewed data sets. Secondly, gene expression data are usually discretized by applying arbitrary criteria to limit the number of false positives. In this work, a new statistical test obtained from a convolution of multivariate hypergeometric distributions, the Hy-test, is proposed to address these issues. Hy-test has been carried out on transcriptomic data from breast and kidney cancer tissues, and it has been compared with other differential expression analysis methods. Hy-test allows implicit discretization of the expression profi…

Apoe genotypes and brain imaging classes in normal cognition, mild cognitive impairment, and alzheimer’s disease: A longitudinal study

2020

Objective: To evaluate in 419 stroke-free cognitively normal subjects (CN) aged 45-82 years covering during a long prospective study (11.54 ± 1.47 years) the preclinical to dementia spectrum: 1) the distribution of small vessel disease (V) and brain atrophy (A) aggregated as following: V−/A−, V−/A+, V+/A−, V+/A+; 2) the relationship of these imaging classes with individual apolipoprotein E (APOE) genotypes; 3) the risk of progression to Alzheimer Disease (AD) of the individual APOE genotypes. Methods: Participants underwent one baseline (t0), and 4 clinical and neuropsychological assessments (t1,t2,t3, and t4). Brain MRI was performed in all subjects at t0, t2, t3 and t4.. White matter hyp…

A PCA-based clustering algorithm for the identification of stratiform and convective precipitation at the event scale: an application to the sub-hour…

2021

AbstractUnderstanding the structure of precipitation and its separation into stratiform and convective components is still today one of the important and interesting challenges for the scientific community. Despite this interest and the advances made in this field, the classification of rainfall into convective and stratiform components is still today not trivial. This study applies a novel criterion based on a clustering approach to analyze a high temporal resolution precipitation dataset collected for the period 2002–2018 over the Sicily (Italy). Starting from the rainfall events obtained from this dataset, the developed methodology makes it possible to classify the rainfall events into f…

Genome-wide association study between CNVs and milk production traits in Valle del Belice sheep.

2019

Copy number variation (CNV) is a major source of genomic structural variation. The aim of this study was to detect genomic CNV regions (CNVR) in Valle del Belice dairy sheep population and to identify those affecting milk production traits. The GO analysis identified possible candidate genes and pathways related to the selected traits. We identified CNVs in 416 individuals genotyped using the Illumina OvineSNP50 BeadChip array. The CNV association using a correlation-trend test model was examined with the Golden Helix SVS 8.7.0 tool. Significant CNVs were detected when their adjusted p-value was <0.01 after false discovery rate (FDR) correction. We identified 7,208 CNVs, which gave 365 C…

Isolated, Subtle Neurological Abnormalities in Mild Cognitive Impairment Types.

2019

Isolated, subtle neurological abnormalities (ISNA) are commonly seen in aging and have been related to cerebral small vessel disease (SVD) and subcortical atrophy in neurologically and cognitively healthy aging subjects.To investigate the frequency of ISNA in different mild cognitive impairment (MCI) types and to evaluate for each MCI type, the cross-sectional relation between ISNA and white matter hyperintensities (WMH), lacunes, caudate atrophy, and ventricular enlargement.One thousand two hundred fifty subjects with different MCI types were included in the analysis and underwent brain magnetic resonance imaging. WMHs were assessed through two visual rating scales. Lacunes were also rated…

Genome-Wide Analyses Identifies Known and New Markers Responsible of Chicken Plumage Color

2020

Simple Summary In order to assess sources of variation related to Polverara breed plumage color (black vs. white), we carried out genome-wide analyses to identify the genomic regions involved in this trait. The present work has revealed new candidate genes involved in the phenotypic variability in local chicken populations. These results also contribute insights into the genetic basis for plumage color in poultry, and confirm the great complexity of the mechanisms that control this trait. Abstract Through the development of the high-throughput genotyping arrays, molecular markers and genes related to phenotypic traits have been identified in livestock species. In poultry, plumage color is a…

IMPLEMENTAZIONE DI UN ALGORITMO DI CLUSTERING PER L’IDENTIFICAZIONE DELLE PRECIPITAZIONI STRATIFORMI E CONVETTIVE ALLA SCALA D’EVENTO: UN’APPLICAZION…

SPARSE INFERENCE IN COVARIATE ADJUSTED CENSORED GAUSSIAN GRAPHICAL MODELS

2021

The covariate adjusted glasso is one of the most used estimators for inferring genetic networks. Despite its diffusion, there are several fields in applied research where the limits of detection of modern measurement technologies make the use of this estimator theoretically unfounded, even when the assumption of a multivariate Gaussian distribution is satisfied. In this paper we propose an extension to censored data.

A model-based approach for assessing bronchodilator responsiveness in children: The conventional cutoff revisited

2020

An increase in FEV1 >=12% has been proposed in international guidelines as a clue to airway reversibility for diagnosing asthma in both adults and children. However, the validity of this cut-off has been questioned in the pediatric population. The aim of this study was to provide evidence that different cut-off values in BDR may be associated with better performance in discriminating among outpatient children with naïve asthma (A) and without asthma (NA). We compared three approaches: i) the conventional cutoff (12%); ii) the cut-off estimated by Youden's criteria; and iii) the cut-off based on a model-driven approach. we found that the conventional cut-off of 12% showed poor sensitivity in…

A combined genome-wide approach identifies a new potential candidate marker associated with the coat color sidedness in cattle

2019

Abstract Coat color is one of the most important phenotypic features in livestock breeds. Cinisara is a local cattle breed generally of uniform black color which occasionally presents a particular phenotype, with animals typically display a white band along their spine, from the head to the tail, and on the ventral line (color sidedness). Therefore, this breed provides an ideal model to study the genetic components underlying phenotypic variation in coat color. A total of 63 animals, ten with sidedness phenotype and 53 with uniform black color were genotyped with Illumina Bovine 50 K. The comparison among genome-wide association study and FST analysis revealed a single nucleotide polymorphi…

Association Between Atrophy of the Caudate Nuclei, Global Brain Atrophy, Cerebral Small Vessel Disease and Mild Parkinsonian Signs in Neurologically …

2017

Background: Mild Parkinsonian signs (MPS) are commonly seen in aging, and have been related to cerebral Small Vessel Diseases (SVD) with no univocal results. Objective: The aim of this study was to investigate the cross-sectional relation between MPS and White Matter Hyperintensities (WMH), lacunes, caudate atrophy, and global cerebral atrophy in a large cohort of Neurologically and Cognitively Healthy (NCH) aging individuals. Method: 1,219 NCH individuals were included in the analysis, and underwent standard brain MRI. The items of the motor section of the Unified Parkinson’s Disease Rating Scale were used to evaluate tremor, rigidity, bradykinesia, and gait/balance/axial dysfunction. Cau…

An extension of the censored gaussian lasso estimator

2019

The conditional glasso is one of the most used estimators for inferring genetic networks. Despite its diffusion, there are several fields in applied research where the limits of detection of modern measurement technologies make the use of this estimator theoretically unfounded, even when the assumption of a multivariate Gaussian distribution is satisfied. In this paper we propose an extension to censored data.

Genome-wide analyses reveal the regions involved in the phenotypic diversity in Sicilian pigs.

2019

Nero Siciliano (Sicilian Black, SB) is a local pig breed generally of uniform black color. In addition to this officially recognized breed, there are animals showing morphological characteristics resembling the SB but with gray hair (Sicilian Grey, SG). The SG, compared with the SB, also shows a more compact structure with greater transverse diameters, higher average daily gains and lower thickness of the back fat. In this study, using the Illumina PorcineSNP60 BeadChip, we run genome-wide analyses to identify regions that may explain the phenotypic differences between SB (n = 21) and SG (n = 27) individuals. Combining the results of the two case–control approaches (GWAS and FST), we identi…

The conditional censored graphical lasso estimator

2020

© 2020, Springer Science+Business Media, LLC, part of Springer Nature. In many applied fields, such as genomics, different types of data are collected on the same system, and it is not uncommon that some of these datasets are subject to censoring as a result of the measurement technologies used, such as data generated by polymerase chain reactions and flow cytometer. When the overall objective is that of network inference, at possibly different levels of a system, information coming from different sources and/or different steps of the analysis can be integrated into one model with the use of conditional graphical models. In this paper, we develop a doubly penalized inferential procedure for…

Manuale tecnico applicativo Progetto: “Innova Uva Mazzarone I.U.M.

2014

Combined approaches to identify genomic regions involved in phenotypic differentiation between low divergent breeds: Application in Sardinian sheep p…

2019

Selective breeding has led to modifications in the genome of many livestock breeds. In this study, we identified the genomic regions that may explain some of the phenotypic differences between two closely related breeds from Sardinia. A total of 44 animals, 20 Sardinian Ancestral Black (SAB) and 24 Sardinian White (SW), were genotyped using the Illumina Ovine 50K array. A total of 68, 38 and 15 significant markers were identified using the case–control genome-wide association study (GWAS), the Bayesian population differentiation analysis (FST) and the Rsb metric, respectively. Comparisons among the approaches revealed a total of 22 overlapping markers between GWAS and FST and one marker bet…

Covariate adjusted censored gaussian lasso estimator

2021

The covariate adjusted glasso is one of the most used estimators for in- ferring genetic networks. Despite its diffusion, there are several fields in applied research where the limits of detection of modern measurement technologies make the use of this estimator theoretically unfounded, even when the assumption of a multivariate Gaussian distribution is satisfied. In this paper we propose an extension to censored data.

An association analysis to identify genetic variants linked to asthma and rhinoconjunctivitis in a cohort of Sicilian children

2018

Abstract Asthma and rhino-conjunctivitis are common chronic diseases in childhood. In this cross-sectional study, we performed a gene association analysis with current asthma and rhino-conjunctivitis in a cohort of Sicilian children aged 10–15 years. Overall, our findings reveal the importance of different genetic variants at 4p14, 16p12.1, 17q12, 6p12.2 and 17q21.1, identifying possible candidate genes responsible for susceptibility to asthma and rhino-conjunctivitis.

The Induced Smoothed lasso: A practical framework for hypothesis testing in high dimensional regression.

2020

This paper focuses on hypothesis testing in lasso regression, when one is interested in judging statistical significance for the regression coefficients in the regression equation involving a lot of covariates. To get reliable p-values, we propose a new lasso-type estimator relying on the idea of induced smoothing which allows to obtain appropriate covariance matrix and Wald statistic relatively easily. Some simulation experiments reveal that our approach exhibits good performance when contrasted with the recent inferential tools in the lasso framework. Two real data analyses are presented to illustrate the proposed framework in practice.

Penalized classification for optimal statistical selection of markers from high-throughput genotyping: application in sheep breeds

2018

The identification of individuals’ breed of origin has several practical applications in livestock and is useful in different biological contexts such as conservation genetics, breeding and authentication of animal products. In this paper, penalized multinomial regression was applied to identify the minimum number of single nucleotide polymorphisms (SNPs) from high-throughput genotyping data for individual assignment to dairy sheep breeds reared in Sicily. The combined use of penalized multinomial regression and stability selection reduced the number of SNPs required to 48. A final validation step on an independent population was carried out obtaining 100% correctly classified individuals. …

Runs of homozygosity reveal genome-wide autozygosity in Italian sheep breeds

2018

The availability of dense single nucleotide polymorphism (SNP) assays allows for the determination of autozygous segments based on runs of consecutive homozygous genotypes (ROH). The aim of the present study was to investigate the occurrence and distribution of ROH in 21 Italian sheep breeds using medium-density SNP genotypes in order to characterize autozygosity and identify genomic regions that frequently appeared in ROH within individuals, namely ROH islands. After filtering, the final number of animals and SNPs retained for analyses were 502 and 46 277 respectively. A total of 12 302 ROH were identified. The mean number of ROH per breed ranged from 10.58 (Comisana) to 44.54 (Valle del B…

Parametric estimation of non-crossing quantile functions

2021

Quantile regression (QR) has gained popularity during the last decades, and is now considered a standard method by applied statisticians and practitioners in various fields. In this work, we applied QR to investigate climate change by analysing historical temperatures in the Arctic Circle. This approach proved very flexible and allowed to investigate the tails of the distribution, that correspond to extreme events. The presence of quantile crossing, however, prevented using the fitted model for prediction and extrapolation. In search of a possible solution, we first considered a different version of QR, in which the QR coefficients were described by parametric functions. This alleviated th…

MOESM2 of Genome-wide scan for runs of homozygosity identifies potential candidate genes associated with local adaptation in Valle del Belice sheep

2017

Additional file 2: Figure S2. Total number of runs of homozygosity (ROH) longer than 1Â Mb and total length of genome (Mb) covered by ROH segments per individual. Observed (black) vs simulated (red) data.

Clusters of effects curves in quantile regression models

2018

In this paper, we propose a new method for finding similarity of effects based on quantile regression models. Clustering of effects curves (CEC) techniques are applied to quantile regression coefficients, which are one-to-one functions of the order of the quantile. We adopt the quantile regression coefficients modeling (QRCM) framework to describe the functional form of the coefficient functions by means of parametric models. The proposed method can be utilized to cluster the effect of covariates with a univariate response variable, or to cluster a multivariate outcome. We report simulation results, comparing our approach with the existing techniques. The idea of combining CEC with QRCM per…

Non-crossing parametric quantile functions: an application to extreme temperatures

2019

Quantile regression can be used to obtain a non-parametric estimate of a conditional quantile function. The presence of quantile crossing, however, leads to an invalid distribution of the response and makes it difficult to use the fitted model for prediction. In this work, we show that crossing can be alleviated by modelling the quantile function parametrically. We then describe an algorithm for constrained optimisation that can be used to estimate parametric quantile functions with the noncrossing property. We investigate climate change by modelling the long-term trends of extreme temperatures in the Arctic Circle.

Refining the genetic structure and relationships of European cattle breeds through meta-analysis of worldwide genomic SNP data, focusing on Italian c…

2020

AbstractThe availability of genotyping assays has allowed the detailed evaluation of cattle genetic diversity worldwide. However, these comprehensive studies did not include some local European populations, including autochthonous Italian cattle. In this study, we assembled a large-scale, genome-wide dataset of single nucleotide polymorphisms scored in 3,283 individuals from 205 cattle populations worldwide to assess genome-wide autozygosity and understand better the genetic relationships among these populations. We prioritized European cattle, with a special focus on Italian breeds. Moderate differences in estimates of molecular inbreeding calculated from runs of homozygosity (FROH) were o…

Genome-wide analysis identifies potentially causative genes explaining the phenotypic variability in Pinzirita sheep

2019

Genome-wide analysis identifies potentially causative genes explaining the phenotypic variability in Pinzirita sheep

Depth-based methods for clustering of functional data.

2017

The problem of detecting clusters is a common issue in the analysis of functional data and some interesting intuitions from approaches relied on depth measures can be considered for construction of basic tools for clustering of curves. Motivated by recent contributions on the problem clustering and alignment of functional data, we also consider the problem of aligning a set of curves when classification procedures are implemented. The variability among curves can be interpreted in terms of two components, phase and amplitude; phase variability, or misalignment, can be eliminated by aligning the curves, according to a similarity index and a warping function. Some approaches address the misal…

MOESM3 of Genome-wide scan for runs of homozygosity identifies potential candidate genes associated with local adaptation in Valle del Belice sheep

2017

Additional file 3: Figures S3, S4, S5, S6. Plot of SNP occurrences (%) in ROH against the genomic regions of QTL for OAR chromosomes with the highest inbreeding coefficient (OAR 2, 4, 11, 23).

Identification of breed informative single nucleotide polymorphisms for assigning individual in Sicilian dairy sheep

2015

Assignment tests using genetic information to establish population membership of individuals, provide the most direct methods to determine the population of origin of unknown individuals. The identification of the breed or population of origin of individuals potentially offers unbiased tools in livestock and is useful in a variety of biological contexts. The aim of this study was to identify the minimum number of informative SNPs from highthroughput genotyping data in Sicilian dairy sheep breeds, and to investigate their usefulness for breed assignment purposes. Individuals of Valle del Belice (48), Comisana (48) and Pinzirita (53) sheep breeds were genotyped using Illumina OvineSNP50K Geno…

MOESM1 of Genome-wide scan for runs of homozygosity identifies potential candidate genes associated with local adaptation in Valle del Belice sheep

2017

Additional file 1: Figure S1. Mean sum of runs of homozygosity (ROH) per animal estimated within four different generation categories. ROH were mapped according to their genetic positions (i.e. linkage map positions). ROH length (l cM) within each category was determined using 100/2 g, replacing g with the number of generations of interest.

Mild Parkinsonian Signs in a Hospital-based Cohort of Mild Cognitive Impairment Types: A Cross-sectional Study

2018

Background:Mild Parkinsonian Signs (MPS) have been associated with Mild Cognitive Impairment (MCI) types with conflicting results.Objective:To investigate the association of individual MPS with different MCI types using logistic ridge regression analysis, and to evaluate for each MCI type, the association of MPS with caudate atrophy, global cerebral atrophy, and the topographical location of White Matter Hyperintensities (WMH), and lacunes.Methods:A cross-sectional study was performed among 1,168 subjects with different types of MCI aged 45-97 (70,52 ± 9,41) years, who underwent brain MRI. WMH were assessed through two visual rating scales. The number and location of lacunes were also rated…

Robust estimation and regression with parametric quantile functions

2022

A new, broad family of quantile-based estimators is described, and theoretical and empirical evidence is provided for their robustness to outliers in the response. The proposed method can be used to estimate all types of parameters, including location, scale, rate and shape parameters, extremes, regression coefficients and hazard ratios, and can be extended to censored and truncated data. The described estimator can be utilized to construct robust versions of common parametric and semiparametric methods, such as linear (Normal) regression, generalized linear models, and proportional hazards models. A variety of significant results and applications is presented to show the flexibility of the…

MOESM4 of Genome-wide scan for runs of homozygosity identifies potential candidate genes associated with local adaptation in Valle del Belice sheep

2017

Additional file 4: Figure S7. Plot of SNP occurrences in ROH against recombination rate. Recombination rate is the solid red line and the occurrence of a SNP in a ROH is represented by blue dots. (A) OAR2, (B) OAR4, (C) OAR11, and (D) OAR23. Recombination rate (cM/Mb) was estimated every 500Â kb.

MOESM5 of Genome-wide scan for runs of homozygosity identifies potential candidate genes associated with local adaptation in Valle del Belice sheep

2017

Additional file 5: Table S1. List of 239 SNPs considered as candidate markers under directional selection in the Valle del Belice sheep breed.

MOESM6 of Genome-wide scan for runs of homozygosity identifies potential candidate genes associated with local adaptation in Valle del Belice sheep

2017

Additional file 6: Table S2. List of 107 potential candidate genes under directional selection in the Valle del Belice sheep breed.