Search results for "DIMENSION"

Establishment and characterization of a highly immunogenic human renal carcinoma cell line.

2015

Renal cell carcinoma (RCC) is the most common kidney cancer, and accounts for ~3% of all adult malignancies. RCC has proven refractory to conventional treatment modalities but appears to be the only histological form that shows any consistent response to immunotherapeutic approaches. The development of a clinically effective vaccine remains a major strategic target for devising active specific immunotherapy in RCC. We aimed to identify a highly immunogenic antigenic format for immunotherapeutic approaches, so as to boost immune responses in RCC patients. We established and cloned an immunogenic cell line, RCC85#21 named Elthem, which was derived from a non-aggressive and non-metastatic clea…

LipidMS: An R Package for Lipid Annotation in Untargeted Liquid Chromatography-Data Independent Acquisition-Mass Spectrometry Lipidomics.

2018

High resolution LC-MS untargeted lipidomics using data independent acquisition (DIA) has the potential to increase lipidome coverage, as it enables the continuous and unbiased acquisition of all eluting ions. However, the loss of the link between the precursor and the product ions combined with the high dimensionality of DIA data sets hinder accurate feature annotation. Here, we present LipidMS, an R package aimed to confidently identify lipid species in untargeted LC-DIA-MS. To this end, LipidMS combines a coelution score, which links precursor and fragment ions with fragmentation and intensity rules. Depending on the MS evidence reached by the identification function survey, LipidMS provi…

Quantum clustering in non-spherical data distributions: Finding a suitable number of clusters

2017

Quantum Clustering (QC) provides an alternative approach to clustering algorithms, several of which are based on geometric relationships between data points. Instead, QC makes use of quantum mechanics concepts to find structures (clusters) in data sets by finding the minima of a quantum potential. The starting point of QC is a Parzen estimator with a fixed length scale, which significantly affects the final cluster allocation. This dependence on an adjustable parameter is common to other methods. We propose a framework to find suitable values of the length parameter σ by optimising twin measures of cluster separation and consistency for a given cluster number. This is an extension of the Se…

Analysis of Microstructure of the Cardiac Conduction System Based on Three-Dimensional Confocal Microscopy

2016

The specialised conducting tissues present in the ventricles are responsible for the fast distribution of the electrical impulse from the atrio-ventricular node to regions in the subendocardial myocardium. Characterisation of anatomical features of the specialised conducting tissues in the ventricles is highly challenging, in particular its most distal section, which is connected to the working myocardium via Purkinje-myocardial junctions. The goal of this work is to characterise the architecture of the distal section of the Purkinje network by differentiating Purkinje cells from surrounding tissue, performing a segmentation of Purkinje fibres at cellular scale, and mathematically describin…

Generation and Coherent Control of Pulsed Quantum Frequency Combs

2018

We present a method for the generation and coherent manipulation of pulsed quantum frequency combs. Until now, methods of preparing high-dimensional states on-chip in a practical way have remained elusive due to the increasing complexity of the quantum circuitry needed to prepare and process such states. Here, we outline how high-dimensional, frequency-bin entangled, two-photon states can be generated at a stable, high generation rate by using a nested-cavity, actively mode-locked excitation of a nonlinear micro-cavity. This technique is used to produce pulsed quantum frequency combs. Moreover, we present how the quantum states can be coherently manipulated using standard telecommunications…

A deeper look into natural sciences with physics-based and data-driven measures

2021

Summary With the development of machine learning in recent years, it is possible to glean much more information from an experimental data set to study matter. In this perspective, we discuss some state-of-the-art data-driven tools to analyze latent effects in data and explain their applicability in natural science, focusing on two recently introduced, physics-motivated computationally cheap tools—latent entropy and latent dimension. We exemplify their capabilities by applying them on several examples in the natural sciences and show that they reveal so far unobserved features such as, for example, a gradient in a magnetic measurement and a latent network of glymphatic channels from the mous…

Attraction in n ‐dimensional differential systems from network regulation theory

2018

Analysis of normal human retinal vascular network architecture using multifractal geometry

2017

AIM To apply the multifractal analysis method as a quantitative approach to a comprehensive description of the microvascular network architecture of the normal human retina. METHODS Fifty volunteers were enrolled in this study in the Ophthalmological Clinic of Cluj-Napoca, Romania, between January 2012 and January 2014. A set of 100 segmented and skeletonised human retinal images, corresponding to normal states of the retina were studied. An automatic unsupervised method for retinal vessel segmentation was applied before multifractal analysis. The multifractal analysis of digital retinal images was made with computer algorithms, applying the standard box-counting method. Statistical analyse…

Hsp40 Is Involved in Cilia Regeneration in Sea Urchin Embryos

2003

In a previous paper we demonstrated that, in Paracentrotus lividus embryos, deciliation represents a specific kind of stress that induces an increase in the levels of an acidic protein of about 40 kD (p40). Here we report that deciliation also induces an increase in Hsp40 chaperone levels and enhancement of its ectodermal localization. We suggest that Hsp40 might play a chaperoning role in cilia regeneration.

Single-cell trajectories reconstruction, exploration and mapping of omics data with STREAM

2019

Single-cell transcriptomic assays have enabled the de novo reconstruction of lineage differentiation trajectories, along with the characterization of cellular heterogeneity and state transitions. Several methods have been developed for reconstructing developmental trajectories from single-cell transcriptomic data, but efforts on analyzing single-cell epigenomic data and on trajectory visualization remain limited. Here we present STREAM, an interactive pipeline capable of disentangling and visualizing complex branching trajectories from both single-cell transcriptomic and epigenomic data. We have tested STREAM on several synthetic and real datasets generated with different single-cell techno…