Grade of membership models, also known as "admixture models", "topic models" or "Latent Dirichlet Allocation", are a generalization of cluster models that allow each sample to have membership in ...multiple clusters. These models are widely used in population genetics to model admixed individuals who have ancestry from multiple "populations", and in natural language processing to model documents having words from multiple "topics". Here we illustrate the potential for these models to cluster samples of RNA-seq gene expression data, measured on either bulk samples or single cells. We also provide methods to help interpret the clusters, by identifying genes that are distinctively expressed in each cluster. By applying these methods to several example RNA-seq applications we demonstrate their utility in identifying and summarizing structure and heterogeneity. Applied to data from the GTEx project on 53 human tissues, the approach highlights similarities among biologically-related tissues and identifies distinctively-expressed genes that recapitulate known biology. Applied to single-cell expression data from mouse preimplantation embryos, the approach highlights both discrete and continuous variation through early embryonic development stages, and highlights genes involved in a variety of relevant processes-from germ cell development, through compaction and morula formation, to the formation of inner cell mass and trophoblast at the blastocyst stage. The methods are implemented in the Bioconductor package CountClust.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Physiological and molecular processes initiated during implantation for pregnancy success are complex but highly organized. This review primarily highlights adverse ripple effects arising from ...defects during the peri-implantation period that perpetuate throughout pregnancy. These defects are reflected in aberrations in embryo spacing, decidualization, placentation and intrauterine embryonic growth, manifesting in preeclampsia, miscarriages and/or preterm birth. Understanding molecular signaling networks that coordinate strategies for successful implantation and decidualization may lead to approaches to improve the outcome of natural pregnancy and pregnancy conceived from in vitro fertilization.
Celotno besedilo
Dostopno za:
DOBA, IJS, IZUM, KILJ, NUK, PILJ, PNG, SAZU, UILJ, UKNU, UL, UM, UPUK
Preterm labor Romero, Roberto; Dey, Sudhansu K.; Fisher, Susan J.
Science (American Association for the Advancement of Science),
08/2014, Letnik:
345, Številka:
6198
Journal Article
Recenzirano
Odprti dostop
Preterm birth is associated with 5 to 18% of pregnancies and is a leading cause of infant morbidity and mortality. Spontaneous preterm labor, a syndrome caused by multiple pathologic processes, leads ...to 70% of preterm births. The prevention and the treatment of preterm labor have been long-standing challenges. We summarize the current understanding of the mechanisms of disease implicated in this condition and review advances relevant to intra-amniotic infection, decidual senescence, and breakdown of maternal-fetal tolerance. The success of progestogen treatment to prevent preterm birth in a subset of patients at risk is a cause for optimism. Solving the mystery of preterm labor, which compromises the health of future generations, is a formidable scientific challenge worthy of investment.
Regulated expression of the H19 long noncoding RNA gene has been well characterized as a paradigm for genomic imprinting, but the H19 RNA's biological function remains largely unclear. H19 is ...abundantly expressed maternally in embryonic tissues but is strongly repressed after birth, and significant transcription persists only in skeletal muscle. Thus, we examined the role of the H19 RNA in skeletal muscle differentiation and regeneration. Knockdown of H19 RNA in myoblast cells and H19 knockout mouse satellite cells decreases differentiation. H19 exon1 encodes two conserved microRNAs, miR-675-3p and miR-675-5p, both of which are induced during skeletal muscle differentiation. The inhibition of myogenesis by H19 depletion during myoblast differentiation is rescued by exogenous expression of miR-675-3p and miR-675-5p. H19-deficient mice display abnormal skeletal muscle regeneration after injury, which is rectified by reintroduction of miR-675-3p and miR-675-5p. miR-675-3p and miR-675-5p function by directly targeting and down-regulating the anti-differentiation Smad transcription factors critical for the bone morphogenetic protein (BMP) pathway and the DNA replication initiation factor Cdc6. Therefore, the H19 long noncoding RNA has a critical trans-regulatory function in skeletal muscle differentiation and regeneration that is mediated by the microRNAs encoded within H19.
Supplier evaluation and selection problem has been studied extensively. Various decision making approaches have been proposed to tackle the problem. In contemporary supply chain management, the ...performance of potential suppliers is evaluated against multiple criteria rather than considering a single factor-cost. This paper reviews the literature of the multi-criteria decision making approaches for supplier evaluation and selection. Related articles appearing in the international journals from 2000 to 2008 are gathered and analyzed so that the following three questions can be answered: (i) Which approaches were prevalently applied? (ii) Which evaluating criteria were paid more attention to? (iii) Is there any inadequacy of the approaches? Based on the inadequacy, if any, some improvements and possible future work are recommended. This research not only provides evidence that the multi-criteria decision making approaches are better than the traditional cost-based approach, but also aids the researchers and decision makers in applying the approaches effectively.
Abstract
MicroRNAs are involved in the crucial processes of development and diseases and have emerged as a new class of biomarkers. The field of DNA nanotechnology has shown great promise in the ...creation of novel microRNA biosensors that have utility in lab-based biosensing and potential for disease diagnostics. In this Survey and Summary, we explore and review DNA nanotechnology approaches for microRNA detection, surveying the literature for microRNA detection in three main areas of DNA nanostructures: DNA tetrahedra, DNA origami, and DNA devices and motifs. We take a critical look at the reviewed approaches, advantages and disadvantages of these methods in general, and a critical comparison of specific approaches. We conclude with a brief outlook on the future of DNA nanotechnology in biosensing for microRNA and beyond.
Integrated supplier selection and order allocation is an important decision for both designing and operating supply chains. This decision is often influenced by the concerned stakeholders, suppliers, ...plant operators and customers in different tiers. As firms continue to seek competitive advantage through supply chain design and operations they aim to create optimized supply chains. This calls for on one hand consideration of multiple conflicting criteria and on the other hand consideration of uncertainties of demand and supply. Although there are studies on supplier selection using advanced mathematical models to cover a stochastic approach, multiple criteria decision making techniques and multiple stakeholder requirements separately, according to authors׳ knowledge there is no work that integrates these three aspects in a common framework. This paper proposes an integrated method for dealing with such problems using a combined Analytic Hierarchy Process–Quality Function Deployment (AHP–QFD) and chance constrained optimization algorithm approach that selects appropriate suppliers and allocates orders optimally between them. The effectiveness of the proposed decision support system has been demonstrated through application and validation in the bioenergy industry.
•A new model for integrating stakeholder requirements to the supplier selection and order allocation decision process.•Integrates the AHP–QFD method with chance constrained programming.•Applied to the bioenergy industry.
Various suspensions containing Al2O3 nanoparticles (<50 nm) in a car engine coolant have been prepared using oleic acid as the surfactant and are tested to be stable for more than 80 days. Thermal ...conductivity and viscosity of the nanofluids have been investigated both as a function of concentration of Al2O3 nanoparticles as well as temperature between 10 and 80 degree C. The prepared nanofluid, containing only 0.035 volume fraction of Al2O3 nanoparticles, displays a fairly higher thermal conductivity than the base fluid and a maximum enhancement (knf/kbf) of ~10.41% is observed at room temperature. The thermal conductivity enhancement of the Al2O3 nanofluid based on engine coolant is proportional to the volume fraction of Al2O3. The volume fraction and temperature dependence of the thermal conductivity of the studied nanofluids present excellent correspondence with the model proposed by Prasher et al (2005 Phys. Rev. Lett. 94 025901), which takes into account the role of translational Brownian motion, interparticle potential and convection in fluid arising from Brownian movement of nanoparticles for thermal energy transfer in nanofluids. Viscosity data demonstrate transition from Newtonian characteristics for the base fluid to non-Newtonian behaviour with increasing content of Al2O3 in the base fluid (coolant). The data also show that the viscosity increases with an increase in concentration and decreases with an increase in temperature. An empirical correlation of the type log( Delta *mnf) = A exp(-BT) explains the observed temperature dependence of the measured viscosity of Al2O3 nanofluid based on car engine coolant. We further confirm that Al2O3 nanoparticle concentration dependence of the viscosity of nanofluids is very well predicted on the basis of a recently reported theoretical model (Masoumi et al 2009 J. Phys. D: Appl. Phys. 42 055501), which considers Brownian motion of nanoparticles in the nanofluid.
During implantation, uterine luminal epithelial (LE) cells first interact with the blastocyst trophectoderm. Within 30 hours after the initiation of attachment, LE cells surrounding the blastocyst in ...the implantation chamber (crypt) disappear, allowing trophoblast cells to make direct physical contact with the underneath stroma for successful implantation. The mechanism for the extraction of LE cells was thought to be mediated by apoptosis. Here we show that LE cells in direct contact with the blastocyst are endocytosed by trophoblast cells by adopting the nonapoptotic cell-in-cell invasion process (entosis) in the absence of Caspase3 activation. Our in vivo observations were reinforced by the results of co-culture experiments with primary uterine epithelial cells with trophoblast stem cells or blastocysts showing internalization of epithelial cells by trophoblasts. We have identified entosis as a mechanism to remove LE cells by trophoblast cells in implantation, conferring a role for entosis in an important physiological process.
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Blastocyst trophoblasts engulf uterine epithelial cells by entosis (cell-eat-cell)Entosis allows prompt entry of trophoblasts to the underlying stromaThis non-apoptotic process of entosis occurrs without Caspase 3 activationEntosis is thus a central concept in embryo implantation
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