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hierarchical generative model

Cesar Alvarado, Nicole A Fider, Helen J Wearing, Natalia L Komarova
In order to maintain homeostasis, mature cells removed from the top compartment of hierarchical tissues have to be replenished by means of differentiation and self-renewal events happening in the more primitive compartments. As each cell division is associated with a risk of mutation, cell division patterns have to be optimized, in order to minimize or delay the risk of malignancy generation. Here we study this optimization problem, focusing on the role of division tree length, that is, the number of layers of cells activated in response to the loss of terminally differentiated cells, which is related to the balance between differentiation and self-renewal events in the compartments...
February 15, 2018: PLoS Computational Biology
Qing Song, Meng Li, Xiaolei Li
Accurate and fast path computation is essential for applications such as onboard navigation systems and traffic network routing. While a number of heuristic algorithms have been developed in the past few years for faster path queries, the accuracy of them are always far below satisfying. In this paper, we first develop an agglomerative graph partitioning method for generating high balanced traverse distance partitions, and we constitute a three-level graph model based on the graph partition scheme for structuring the urban road network...
2018: PloS One
Carmen Murciano, Salvador Cazorla-Vázquez, Javier Gutiérrez, Juan Antonio Hijano, Josefa Ruiz-Sánchez, Laura Mesa-Almagro, Flores Martín-Reyes, Tahía Diana Fernández, Manuel Marí-Beffa
The amputation of a teleost fin rapidly triggers an intricate maze of hierarchically regulated signalling processes which ultimately reconstruct the diverse tissues of the appendage. Whereas the generation of the fin pattern along the proximodistal axis brings with it several well-known developmental regulators, the mechanisms by which the fin widens along its dorsoventral axis remain poorly understood. Utilizing the zebrafish as an experimental model of fin regeneration and studying more than 1000 actinopterygian species, we hypothesized a connection between specific inter-ray regulatory mechanisms and the morphological variability of inter-ray membranes found in nature...
February 14, 2018: Journal of Anatomy
Margriet M Palm, Marjet Elemans, Joost B Beltman
Tumors consist of a hierarchical population of cells that differ in their phenotype and genotype. This hierarchical organization of cells means that a few clones (i.e., cells and several generations of offspring) are abundant while most are rare, which is called clonal dominance. Such dominance also occurred in published in vitro iterated growth and passage experiments with tumor cells in which genetic barcodes were used for lineage tracing. A potential source for such heterogeneity is that dominant clones derive from cancer stem cells with an unlimited self-renewal capacity...
February 12, 2018: PLoS Computational Biology
James Burridge
We provide a unified mathematical explanation of two classical forms of spatial linguistic spread. The wave model describes the radiation of linguistic change outwards from a central focus. Changes can also jump between population centres in a process known as hierarchical diffusion. It has recently been proposed that the spatial evolution of dialects can be understood using surface tension at linguistic boundaries. Here we show that the inclusion of long-range interactions in the surface tension model generates both wave-like spread, and hierarchical diffusion, and that it is surface tension that is the dominant effect in deciding the stable distribution of dialect patterns...
January 2018: Royal Society Open Science
Marc Tittgemeyer, Lionel Rigoux, Thomas R Knösche
One of the major challenges in systems neuroscience is to identify brain networks and unravel their significance for brain function -this has led to the concept of the 'connectome'. Connectomes are currently extensively studied in large-scale international efforts at multiple scales, and follow different definitions with respect to their connections as well as their elements. Perhaps the most promising avenue for defining the elements of connectomes originates from the notion that individual brain areas maintain distinct (long-range) connection profiles...
January 30, 2018: NeuroImage
S Chauhan, A Kumar
Hierarchical QSAR technology (HiT QSAR) was used for consensus QSAR modelling of 65 SIRT1 activators. Simplex representation of molecular structure (SiRMS) has been used for descriptor generation. The predictive QSAR models were developed using the partial least squares (PLS) method. The QSAR models were built up according to OECD principles. One hundred rounds of Y-scrambling were performed for each selected model to exclude chance correlations. A successful consensus model (r2 = 0.830, [Formula: see text] = 0...
February 1, 2018: SAR and QSAR in Environmental Research
Rima Chaudhuri, James R Krycer, Daniel J Fazakerley, Kelsey H Fisher-Wellman, Zhiduan Su, Kyle L Hoehn, Jean Yee Hwa Yang, Zdenka Kuncic, Fatemeh Vafaee, David E James
Insulin resistance is a major risk factor for metabolic diseases such as Type 2 diabetes. Although the underlying mechanisms of insulin resistance remain elusive, oxidative stress is a unifying driver by which numerous extrinsic signals and cellular stresses trigger insulin resistance. Consequently, we sought to understand the cellular response to oxidative stress and its role in insulin resistance. Using cultured 3T3-L1 adipocytes, we established a model of physiologically-derived oxidative stress by inhibiting the cycling of glutathione and thioredoxin, which induced insulin resistance as measured by impaired insulin-stimulated 2-deoxyglucose uptake...
January 29, 2018: Scientific Reports
Cao Xiao, Ying Li, Inci M Baytas, Jiayu Zhou, Fei Wang
Delayed drug safety insights can impact patients, pharmaceutical companies, and the whole society. Post-market drug safety surveillance plays a critical role in providing drug safety insights, where real world evidence such as spontaneous reporting systems (SRS) and a series of disproportional analysis serve as a cornerstone of proactive and predictive drug safety surveillance. However, they still face several challenges including concomitant drugs confounders, rare adverse drug reaction (ADR) detection, data bias, and the under-reporting issue...
January 29, 2018: Scientific Reports
Raymund E Horch, Annika Weigand, Harald Wajant, Jürgen Groll, Aldo R Boccaccini, Andreas Arkudas
BACKGROUND: The advent of Tissue Engineering (TE) in the early 1990ies was fostered by the increasing need for functional tissue and organ replacement. Classical TE was based on the combination of carrier matrices, cells and growth factors to reconstitute lost or damaged tissue and organs. Despite considerable results in vitro and in experimental settings the lack of early vascularization has hampered its translation into daily clinical practice so far. A new field of research, called "biofabrication" utilizing latest 3D printing technologies aims at hierarchically and spatially incorporating different cells, biomaterials and molecules into a matrix to alleviate a directed maturation of artificial tissue...
January 29, 2018: Handchirurgie, Mikrochirurgie, Plastische Chirurgie
Lieke Heil, Johan Kwisthout, Stan van Pelt, Iris van Rooij, Harold Bekkering
Evidence is accumulating that our brains process incoming information using top-down predictions. If lower level representations are correctly predicted by higher level representations, this enhances processing. However, if they are incorrectly predicted, additional processing is required at higher levels to "explain away" prediction errors. Here, we explored the potential nature of the models generating such predictions. More specifically, we investigated whether a predictive processing model with a hierarchical structure and causal relations between its levels is able to account for the processing of agent-caused events...
January 1, 2018: Quarterly Journal of Experimental Psychology: QJEP
Dewei Yang, Lingxing Xu, Xueli Gao, Qinghai Guo, Ning Huang
Waste-related greenhouse gas (GHG) emissions have been recognized as one of the prominent contributors to global warming. Current urban waste regulations, however, face increasing challenges from stakeholders' trade-offs and hierarchic management. A combined method, i.e., life cycle inventories and scenario analysis, was employed to investigate waste-related GHG emissions during 1995-2015 and to project future scenarios of waste-driven carbon emissions by 2050 in a pilot low carbon city, Xiamen, China. The process-based carbon analysis of waste generation (prevention and separation), transportation (collection and transfer) and disposal (treatment and recycling) shows that the main contributors of carbon emissions are associated with waste disposal processes, solid waste, the municipal sector and Xiamen Mainland...
January 19, 2018: Science of the Total Environment
Zhifeng Jiang, Weiming Wan, Huaming Li, Shouqi Yuan, Huijun Zhao, Po Keung Wong
The challenge in the artificial photosynthesis of fossil resources from CO2 by utilizing solar energy is to achieve stable photocatalysts with effective CO2 adsorption capacity and high charge-separation efficiency. A hierarchical direct Z-scheme system consisting of urchin-like hematite and carbon nitride provides an enhanced photocatalytic activity of reduction of CO2 to CO, yielding a CO evolution rate of 27.2 µmol g-1 h-1 without cocatalyst and sacrifice reagent, which is >2.2 times higher than that produced by g-C3 N4 alone (10...
January 19, 2018: Advanced Materials
Eric R Gamazon, Matthew R Trendowski, Yujia Wen, Claudia Wing, Shannon M Delaney, Won Huh, Shan Wong, Nancy J Cox, M Eileen Dolan
Pemetrexed is indicated for non-small cell lung carcinoma and mesothelioma, but often has limited efficacy due to drug resistance. To probe the molecular mechanisms underlying chemotherapeutic response, we performed mRNA and microRNA (miRNA) expression profiling of pemetrexed treated and untreated lymphoblastoid cell lines (LCLs) and applied a hierarchical Bayesian method. We identified genetic variation associated with gene expression in human lung tissue for the most significant differentially expressed genes (Benjamini-Hochberg [BH] adjusted p < 0...
January 15, 2018: Scientific Reports
Edward Koifman, Michael J Lipinski, Kyle Buchanan, Won Yu Kang, Ricardo O Escarcega, Ron Waksman, Nelson L Bernardo
OBJECTIVES: We sought to compare treatment strategies in a Bayesian network meta-analysis of randomized controlled trials. BACKGROUND: Peripheral artery disease (PAD) is a prevalent morbidity that is treated with various strategies. METHODS: We performed a MEDLINE search for randomized studies comparing at least 2 treatment strategies, including bypass surgery, percutaneous transluminal angioplasty (PTA) balloons, stents, covered stents, drug-eluting stents (DES), and drug-coated balloons (DCB), in patients with native femoro-popliteal disease...
January 14, 2018: Catheterization and Cardiovascular Interventions
Chang-Yu Hsieh, Jianshu Cao
We use the "generalized hierarchical equation of motion" proposed in Paper I [C.-Y. Hsieh and J. Cao, J. Chem. Phys. 148, 014103 (2018)] to study decoherence in a system coupled to a spin bath. The present methodology allows a systematic incorporation of higher-order anharmonic effects of the bath in dynamical calculations. We investigate the leading order corrections to the linear response approximations for spin bath models. Two kinds of spin-based environments are considered: (1) a bath of spins discretized from a continuous spectral density and (2) a bath of localized nuclear or electron spins...
January 7, 2018: Journal of Chemical Physics
Tatiana M Medvedeva, Marina V Sysoeva, Gilles van Luijtelaar, Ilya V Sysoev
PURPOSE: The organization of neural networks and the mechanisms, which generate the highly stereotypical for absence epilepsy spike-wave discharges (SWDs) is heavily debated. Here we describe such a model which can both reproduce the characteristics of SWDs and dynamics of coupling between brain regions, relying mainly on properties of hierarchically organized networks of a large number of neuronal oscillators. MODEL: We used a two level mesoscale model. The first level consists of three structures: the nervus trigeminus serving as an input, the thalamus and the somatosensory cortex; the second level of a group of nearby situated neurons belonging to one of three modeled structures...
December 13, 2017: Neural Networks: the Official Journal of the International Neural Network Society
Goma Kumari Khatri, Thach Duc Tran, Sushil Baral, Jane Fisher
BACKGROUND: Antenatal mental health problems are of concern globally not only because of the burden and limits to participation experienced by women but also because of risks for foetal neurocognitive development and adverse birth outcomes. The aim was to describe the indicative prevalence of and risk and protective factors for clinically-significant symptoms of antenatal common mental disorders (CMDs) among women who experienced the 2015 Nepal earthquakes during pregnancy. METHODS: A population-based cross-sectional study in Bhaktapur, one of 14 districts highly affected by the 2015 Nepal earthquakes...
December 9, 2017: Journal of Affective Disorders
Ming Wang, Stephen A Matthews, Khaled Iskandarani, Yimei Li, Zheng Li, Vernon M Chinchilli, Lijun Zhang
Prostate cancer is the most common cancer diagnosed among males, and the incidence in Pennsylvania, USA is considerably higher than nationally. Knowledge of regional differences and time trends in prostate cancer incidence may contribute to a better understanding of aetiologic factors and racial disparities in outcomes, and to improvements in preventive intervention and screening efforts. We used Pennsylvania Cancer Registry data on reported prostate cancer diagnoses between 2000 and 2011 to study the regional distribution and temporal trends of prostate cancer incidence in both Pennsylvania White males and Philadelphia metropolitan area Black males...
November 28, 2017: Geospatial Health
Xianfeng Lin, Jiaxin Chen, Pengcheng Qiu, Qi Zhang, Shengyu Wang, Mingzhen Su, Yunbin Chen, Keke Jin, An Qin, Shunwu Fan, Pengfei Chen, Xing Zhao
OBJECTIVE: To investigate the effect of decellularized osteochondral extracellular matrix (ECM) scaffold for osteochondral defect regeneration. DESIGN: We compared the histological features and microstructure of degenerated cartilage to normal articular cartilage. We also generated and evaluated osteochondral ECM scaffolds through decellularization technology. Then scaffolds were implanted to osteochondral defect in rabbit model. After 12 weeks surgery, regeneration tissues were analyzed by histology, immunohistochemistry evaluation...
December 9, 2017: Osteoarthritis and Cartilage
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