Anatomically compliant modes of variations: New tools for brain connectivity.

Anatomical complexity and data dimensionality present major issues when analysing brain connectivity data. The functional and anatomical aspects of the connections taking place in the brain are in fact equally relevant and strongly intertwined. However, due to theoretical challenges and computational issues, their relationship is often overlooked in neuroscience and clinical research.

Analyzing data in complicated 3D domains: Smoothing, semiparametric regression, and functional principal component analysis.

In this work, we introduce a family of methods for the analysis of data observed at locations scattered in three-dimensional (3D) domains, with possibly complicated shapes. The proposed family of methods includes smoothing, regression, and functional principal component analysis for functional signals defined over (possibly nonconvex) 3D domains, appropriately complying with the nontrivial shape of the domain. This constitutes an important advance with respect to the literature, because the available methods to analyze data observed in 3D domains rely on Euclidean distances, which are inappropriate when the shape of the domain influences the phenomenon under study.

A PDE-regularized smoothing method for space-time data over manifolds with application to medical data.

We propose an innovative statistical-numerical method to model spatio-temporal data, observed over a generic two-dimensional Riemanian manifold. The proposed approach consists of a regression model completed with a regularizing term based on the heat equation. The model is discretized through a finite element scheme set on the manifold, and solved by resorting to a fixed point-based iterative algorithm.

A Functional Data Analysis Approach to Left Ventricular Remodeling Assessment.

Left ventricular remodeling is a mechanism common to various cardiovascular diseases affecting myocardial morphology. It can be often overlooked in clinical practice since the parameters routinely employed in the diagnostic process (e.g.

A look at the spatio-temporal mortality patterns in Italy during the COVID-19 pandemic through the lens of mortality densities.

With the tools and perspective of Object Oriented Spatial Statistics, we analyze official daily data on mortality from all causes in the provinces and municipalities of Italy for the year 2020, the first of the COVID-19 pandemic. By comparison with mortality data from 2011 to 2019, we assess the local impact of the pandemic as perturbation factor of the natural spatio-temporal death process. For each Italian province and year, mortality data are represented by the densities of time of death during the calendar year.

FunChIP: an R/Bioconductor package for functional classification of ChIP-seq shapes.

Summary: Chromatin Immunoprecipitation followed by sequencing (ChIP-seq) generates local accumulations of sequencing reads on the genome ("peaks"), which correspond to specific protein-DNA interactions or chromatin modifications. Peaks are detected by considering their total area above a background signal, usually neglecting their shapes, which instead may convey additional biological information. We present FunChIP, an R/Bioconductor package for clustering peaks according to a functional representation of their shapes: after approximating their profiles with cubic B-splines, FunChIP minimizes their functional distance and classifies the peaks applying a k-mean alignment and clustering algorithm.

Peak shape clustering reveals biological insights.

Background: ChIP-seq experiments are widely used to detect and study DNA-protein interactions, such as transcription factor binding and chromatin modifications. However, downstream analysis of ChIP-seq data is currently restricted to the evaluation of signal intensity and the detection of enriched regions (peaks) in the genome. Other features of peak shape are almost always neglected, despite the remarkable differences shown by ChIP-seq for different proteins, as well as by distinct regions in a single experiment.

A Combination of Cisplatin and 5-Fluorouracil With a Taxane in Patients Who Underwent Lymph Node Dissection for Nodal Metastases From Squamous Cell Carcinoma of the Penis: Treatment Outcome and Survival Analyses in Neoadjuvant and Adjuvant Settings.

Background: The role of chemotherapy in nodal metastases from penile squamous cell carcinoma is not defined. We evaluated the efficacy of a combination of T-PF (a taxane, cisplatin, and 5-fluorouracil) in neoadjuvant and adjuvant settings.

Patients And Methods: Since June of 2004, T-PF was administered to stage N2 to 3 patients.

Object Oriented Data Analysis: A few methodological challenges.

This is a discussion of the paper "Overview of object oriented data analysis" by J. Steve Marron and Andrés M. Alonso.

An introduction with medical applications to functional data analysis.

Functional data are data that can be represented by suitable functions, such as curves (potentially multi-dimensional) or surfaces. This paper gives an introduction to some basic but important techniques for the analysis of such data, and we apply the techniques to two datasets from biomedicine. One dataset is about white matter structures in the brain in multiple sclerosis patients; the other dataset is about three-dimensional vascular geometries collected for the study of cerebral aneurysms.

Identification and predictive value of interleukin-6+ interleukin-10+ and interleukin-6- interleukin-10+ cytokine patterns in ST-elevation acute myocardial infarction.

Rationale: At the onset of ST-elevation acute myocardial infarction (STEMI), patients can present with very high circulating interleukin-6 (IL-6(+)) levels or very low-IL-6(-) levels.

Objective: We compared these 2 groups of patients to understand whether it is possible to define specific STEMI phenotypes associated with outcome based on the cytokine response.

Methods And Results: We compared 109 patients with STEMI in the top IL-6 level (median, 15.

Invariant NKT cell reconstitution in pediatric leukemia patients given HLA-haploidentical stem cell transplantation defines distinct CD4+ and CD4- subset dynamics and correlates with remission state.

Immune reconstitution plays a crucial role on the outcome of patients given T cell-depleted HLA-haploidentical hematopoietic stem cell transplantation (hHSCT) for hematological malignancies. CD1d-restricted invariant NKT (iNKT) cells are innate-like, lipid-reactive T lymphocytes controlling infections, cancer, and autoimmunity. Adult mature iNKT cells are divided in two functionally distinct CD4(+) and CD4(-) subsets that express the NK receptor CD161 and derive from thymic CD4(+)CD161(-) precursors.

pT1 penile squamous cell carcinoma: a clinicopathologic study of 56 cases treated by CO2 laser therapy.

Objective: To evaluate the pathologic characteristics that are associated with outcomes in pT1 penile squamous cell carcinoma (SCC) treated with laser excision.

Study Design: Peniscopic magnification and 5% acetic acid application were performed prior to CO2 laser excision. Specimens were reviewed to reassess stage, grade, invasion depth, carcinoma in situ, margins, tumor extension, lymphovascular invasion and human papillomavirus infection.