Search results for "CLUSTER"

Preparing for Winter: The Transcriptomic Response Associated with Different Day Lengths in Drosophila montana

2016

The work has been supported by a Natural Environment Research Council studentship to D.J.P. and an Academy of Finland grant to M.K. (project 268214). At northern latitudes, the most robust cue for assessing the onset of winter is the shortening of day lengths. Many species use day length as a cue to increase their cold tolerance and/or enter into diapause, but little is known about changes in gene expression that occur under different day lengths. We investigate the gene expression changes associated with differences in light/dark cycles in Drosophila montana, a northerly distributed species with a strong adult photoperiodic reproductive diapause. To examine gene expression changes induced …

Nano-delivery system targeting to cancer stem cell cluster of differentiation biomarkers

2017

Cancer stem cells (CSCs) are one of the most important origins of cancer progression and metastasis. CSCs have unique self-renewal properties and diverse cell membrane receptors that induced the resistance to the conventional chemotherapeutic agents. Therefore, the therapeutic removal of CSCs could result in the cancer cure with lack of recurrence and metastasis. In this regard, targeting CSCs in accordance to their specific biomarkers is a talented attitude in cancer therapy. Various CSCs surface biomarkers have been described, which some of them exhibited similarities on different cancer cell types, while the others are cancer specific and have just been reported on one or a few types of …

2016

Focal demyelinated lesions, diffuse white matter (WM) damage and grey matter (GM) atrophy influence directly the disease progression in patients with multiple sclerosis. The aim of this study was to identify specific characteristics of GM and WM structural networks in subjects with clinically isolated syndrome (CIS) in comparison to patients with early relapsing-remitting multiple sclerosis (RRMS). Twenty patients with CIS, thirty three with RRMS and forty healthy subjects were investigated using 3 T-MRI. Diffusion tensor imaging was applied, together with probabilistic tractography and fractional anisotropy (FA) maps for WM and cortical thickness correlation analysis for GM, to determine t…

Active and Secretory IgA-Coated Bacterial Fractions Elucidate Dysbiosis in Clostridium difficile Infection

2016

C. difficile is a major enteric pathogen with worldwide distribution. Its expansion is associated with broad-spectrum antibiotics which disturb the normal gut microbiome. In this study, the DNA sequencing of highly active bacteria and bacteria opsonized by intestinal secretory immunoglobulin A (SIgA) separated from the whole bacterial community by FACS elucidated how the gut dysbiosis promotes C. difficile infection (CDI). Bacterial groups with inhibitory effects on C. difficile growth, such as Lactobacillales, were mostly inactive in the CDI patients. C. difficile was typical for the bacterial fraction opsonized by SIgA in patients with CDI, while Fusobacterium was characteristic for the S…

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…

The IgG1 B-cell receptor provides survival and proliferative signals analogue to the Igα but not the Igβ co-receptor.

2016

The function of the IgM B-cell receptor (BCR) is dependent on intact signaling of the co-receptors Igα and Igβ, both of which contain a cytoplasmic tail bearing an immunoreceptor tyrosine-based activation motif. We have previously demonstrated that the cytoplasmic tail of the IgG1 BCR can partially compensate for the loss of the signaling moiety of Igα. Here, we show that unlike Igα, Igβ signaling is indispensable for the development and function of IgG1-expressing B cells. Deletion of the cytoplasmic signaling tail of Igβ compromised the survival and proliferation not only of IgM(+) B cells but also of IgG1-expressing B cells. In the absence of the signaling tail of Igβ, the transcription …

Collective behavior of quorum-sensing run-and-tumble particles in confinement

2016

We study a generic model for quorum-sensing bacteria in circular confinement. Every bacterium produces signaling molecules, the local concentration of which triggers a response when a certain threshold is reached. If this response lowers the motility then an aggregation of bacteria occurs, which differs fundamentally from standard motility-induced phase separation due to the long-ranged nature of the concentration of signal molecules. We analyze this phenomenon analytically and by numerical simulations employing two different protocols leading to stationary cluster and ring morphologies, respectively.

Application of Graph Clustering and Visualisation Methods to Analysis of Biomolecular Data

2018

In this paper we present an approach based on integrated use of graph clustering and visualisation methods for semi-supervised discovery of biologically significant features in biomolecular data sets. We describe several clustering algorithms that have been custom designed for analysis of biomolecular data and feature an iterated two step approach involving initial computation of thresholds and other parameters used in clustering algorithms, which is followed by identification of connected graph components, and, if needed, by adjustment of clustering parameters for processing of individual subgraphs.

Network-Wide Adaptive Burst Detection Depicts Neuronal Activity with Improved Accuracy

2017

Neuronal networks are often characterized by their spiking and bursting statistics. Previously, we introducedan adaptive burst analysis methodwhich enhances the analysis power for neuronal networks with highly varying firing dynamics. The adaptation is based on single channels analyzing each element of a network separately. Such kind of analysis was adequate for the assessment of local behavior, where the analysis focuses on the neuronal activity in the vicinity of a single electrode. However, the assessment of the whole network may be hampered, if parts of the network are analyzed using different rules. Here, we test how using multiple channels and measurement time points affect adaptive b…

Revealing community structures by ensemble clustering using group diffusion

2018

We propose an ensemble clustering approach using group diffusion to reveal community structures in data. We represent data points as a directed graph and assume each data point belong to single cluster membership instead of multiple memberships. The method is based on the concept of ensemble group diffusion with a parameter to represent diffusion depth in clustering. The ability to modulate the diffusion-depth parameter by varying it within a certain interval allows for more accurate construction of clusters. Depending on the value of the diffusion-depth parameter, the presented approach can determine very well both local clusters and global structure of data. At the same time, the ability …