Breast Mass Segmentation Using a Semi-automatic Procedure Based on Fuzzy C-means Clustering

Mammography is the primary modality that helped in the early detection and diagnosis of women breast diseases. Further, the process of extracting the masses in mammogram represents a challenging task facing the radiologists, due to problems such as fuzzy or speculated borders, low contrast and the presence of intensity inhomogeneities. Aims to help the radiologists in the diagnosis of breast cancer, many approaches have been conducted to automatically segment the masses in mammograms. Towards this aim, in this paper, we present a new approach for extraction of tumors from region-of-interest (ROI) using the algorithm of Fuzzy C-Means (FCM) setting two clusters for semi-automated segmentation. The proposed method meant to select as input data the set of pixels that enable to get the meaningful information required to segment the masses with high accuracy. This could be accomplished through eliminating unnecessary pixels, which influence on this process through separating it outside of the input data using an optimal threshold given by monitoring the change of clusters rate during the process of threshold decrementing. The proposed methodology has successfully segmented the masses, with an average sensitivity of 82.02% and specificity of 98.23%

Energy-based Self-attentive Learning of Abstractive Communities for Spoken Language Understanding

Abstractive community detection is an important spoken language understanding task, whose goal is to group utterances in a conversation according to whether they can be jointly summarized by a common abstractive sentence. This paper provides a novel approach to this task. We first introduce a neural contextual utterance encoder featuring three types of self-attention mechanisms. We then train it using the siamese and triplet energy-based meta-architectures. Experiments on the AMI corpus show that our system outperforms multiple energy-based and non-energy based baselines from the state-of-the-art. Code and data are publicly available.Comment: Update baseline

An Integrated Fuzzy Clustering Cooperative Game Data Envelopment Analysis Model with application in Hospital Efficiency

Hospitals are the main sub-section of health care systems and evaluation of hospitals is one of the most important issue for health policy makers. Data Envelopment Analysis (DEA) is a nonparametric method that has recently been used for measuring efficiency and productivity of Decision Making Units (DMUs) and commonly applied for comparison of hospitals. However, one of the important assumption in DEA is that DMUs must be homogenous. The crucial issue in hospital efficiency is that hospitals are providing different services and so may not be comparable. In this paper, we propose an integrated fuzzy clustering cooperative game DEA approach. In fact, due to the lack of homogeneity among DMUs, we first propose to use a fuzzy C-means technique to cluster the DMUs. Then we apply DEA combined with the game theory where each DMU is considered as a player, using Core and Shapley value approaches within each cluster. The procedure has successfully been applied for performances measurement of 288 hospitals in 31 provinces of Iran. Finally, since the classical DEA model is not capable to distinguish between efficient DMUs, efficient hospitals within each cluster, are ranked using combined DEA model and cooperative game approach. The results show that the Core and Shapley values are suitable for fully ranking of efficient hospitals in the healthcare systems

A Self-Adaptive Online Brain Machine Interface of a Humanoid Robot through a General Type-2 Fuzzy Inference System

This paper presents a self-adaptive general type-2 fuzzy inference system (GT2 FIS) for online motor imagery (MI) decoding to build a brain-machine interface (BMI) and navigate a bi-pedal humanoid robot in a real experiment, using EEG brain recordings only. GT2 FISs are applied to BMI for the first time in this study. We also account for several constraints commonly associated with BMI in real practice: 1) maximum number of electroencephalography (EEG) channels is limited and fixed, 2) no possibility of performing repeated user training sessions, and 3) desirable use of unsupervised and low complexity features extraction methods. The novel learning method presented in this paper consists of a self-adaptive GT2 FIS that can both incrementally update its parameters and evolve (a.k.a. self-adapt) its structure via creation, fusion and scaling of the fuzzy system rules in an online BMI experiment with a real robot. The structure identification is based on an online GT2 Gath-Geva algorithm where every MI decoding class can be represented by multiple fuzzy rules (models). The effectiveness of the proposed method is demonstrated in a detailed BMI experiment where 15 untrained users were able to accurately interface with a humanoid robot, in a single thirty-minute experiment, using signals from six EEG electrodes only

White adipose remodeling during browning in mice involves YBX1 to drive thermogenic commitment

Objective: Increasing adaptive thermogenesis by stimulating browning in white adipose tissue is a promising method of improving metabolic health. However, the molecular mechanisms underlying this transition remain elusive. Our study examined the molecular determinants driving the differentiation of precursor cells into thermogenic adipocytes. Methods: In this study, we conducted temporal high-resolution proteomic analysis of subcutaneous white adipose tissue (scWAT) after cold exposure in mice. This was followed by loss- and gain-of-function experiments using siRNA-mediated knockdown and CRISPRa-mediated induction of gene expression, respectively, to evaluate the function of the transcriptional regulator Y box-binding protein 1 (YBX1) during adipogenesis of brown pre-adipocytes and mesenchymal stem cells. Transcriptomic analysis of mesenchymal stem cells following induction of endogenous Ybx1 expression was conducted to elucidate transcriptomic events controlled by YBX1 during adipogenesis. Results: Our proteomics analysis uncovered 509 proteins differentially regulated by cold in a time-dependent manner. Overall, 44 transcriptional regulators were acutely upregulated following cold exposure, among which included the cold-shock domain containing protein YBX1, peaking after 24 h. Cold-induced upregulation of YBX1 also occurred in brown adipose tissue, but not in visceral white adipose tissue, suggesting a role of YBX1 in thermogenesis. This role was confirmed by Ybx1 knockdown in brown and brite preadipocytes, which significantly impaired their thermogenic potential. Conversely, inducing Ybx1 expression in mesenchymal stem cells during adipogenesis promoted browning concurrent with an increased expression of thermogenic markers and enhanced mitochondrial respiration. At a molecular level, our transcriptomic analysis showed that YBX1 regulates a subset of genes, including the histone H3K9 demethylase Jmjd1c, to promote thermogenic adipocyte differentiation. Conclusion: Our study mapped the dynamic proteomic changes of murine scWAT during browning and identified YBX1 as a novel factor coordinating the genomic mechanisms by which preadipocytes commit to brite/beige lineage

Changes in the Oligodendrocyte Progenitor Cell Proteome with Ageing.

Following central nervous system (CNS) demyelination, adult oligodendrocyte progenitor cells (OPCs) can differentiate into new myelin-forming oligodendrocytes in a regenerative process called remyelination. Although remyelination is very efficient in young adults, its efficiency declines progressively with ageing. Here we performed proteomic analysis of OPCs freshly isolated from the brains of neonate, young and aged female rats. Approximately 50% of the proteins are expressed at different levels in OPCs from neonates compared with their adult counterparts. The amount of myelin-associated proteins, and proteins associated with oxidative phosphorylation, inflammatory responses and actin cytoskeletal organization increased with age, whereas cholesterol-biosynthesis, transcription factors and cell cycle proteins decreased. Our experiments provide the first ageing OPC proteome, revealing the distinct features of OPCs at different ages. These studies provide new insights into why remyelination efficiency declines with ageing and potential roles for aged OPCs in other neurodegenerative diseases

Genomic and transcriptomic analyses reveal polygenic architecture for ecologically important traits in aspen (Populus tremuloides Michx.)

Intraspecific genetic variation in foundation species such as aspen (Populus tremuloides Michx.) shapes their impact on forest structure and function. Identifying genes underlying ecologically important traits is key to understanding that impact. Previous studies, using single-locus genome-wide association (GWA) analyses to identify candidate genes, have identified fewer genes than anticipated for highly heritable quantitative traits. Mounting evidence suggests that polygenic control of quantitative traits is largely responsible for this "missing heritability" phenomenon. Our research characterized the genetic architecture of 30 ecologically important traits using a common garden of aspen through genomic and transcriptomic analyses. A multilocus association model revealed that most traits displayed a highly polygenic architecture, with most variation explained by loci with small effects (likely below the detection levels of single-locus GWA methods). Consistent with a polygenic architecture, our single-locus GWA analyses found only 38 significant SNPs in 22 genes across 15 traits. Next, we used differential expression analysis on a subset of aspen genets with divergent concentrations of salicinoid phenolic glycosides (key defense traits). This complementary method to traditional GWA discovered 1243 differentially expressed genes for a polygenic trait. Soft clustering analysis revealed three gene clusters (241 candidate genes) involved in secondary metabolite biosynthesis and regulation. Our work reveals that ecologically important traits governing higher-order community- and ecosystem-level attributes of a foundation forest tree species have complex underlying genetic structures and will require methods beyond traditional GWA analyses to unravel

Application of fuzzy c-means clustering for analysis of chemical ionization mass spectra: insights into the gas-phase chemistry of NO3-initiated oxidation of isoprene

Oxidation of volatile organic compounds (VOCs) can lead to the formation of secondary organic aerosol, a significant component of atmospheric fine particles, which can affect air quality, human health, and climate change. However, current understanding of the formation mechanism of SOA is still incomplete, which is not only due to the complexity of the chemistry, but also relates to analytical challenges in SOA precursor detection and quantification. Recent instrumental advances, especially the developments of high-resolution time-of-flight chemical ionization mass spectrometry (CIMS), greatly enhanced the capability to detect low- and extremely low-volatility organic molecules (L/ELVOCs). Although detection and characterization of low volatility vapors largely improved our understanding of SOA formation, analyzing and interpreting complex mass spectrometric data remains a challenging task. This necessitates the use of dimension-reduction techniques to simplify mass spectrometric data with the purpose of extracting chemical and kinetic information of the investigated system. Here we present an approach by using fuzzy c-means clustering (FCM) to analyze CIMS data from chamber experiments aiming to investigate the gas-phase chemistry of nitrate radical initiated oxidation of isoprene. The performance of FCM was evaluated and validated. By applying FCM various oxidation products were classified into different groups according to their chemical and kinetic properties, and the common patterns of their time series were identified, which gave insights into the chemistry of the system investigated. The chemical properties are characterized by elemental ratios and average carbon oxidation state, and the kinetic behaviors are parameterized with generation number and effective rate coefficient (describing the average reactivity of a species) by using the gamma kinetic parameterization model. In addition, the fuzziness of FCM algorithm provides a possibility to separate isomers or different chemical processes species are involved in, which could be useful for mechanism development. Overall FCM is a well applicable technique to simplify complex mass spectrometric data, and the chemical and kinetic properties derived from clustering can be utilized to understand the reaction system of interest.</p