bluuebunny/crossref_metadata_2025_split huggingface dataset:
Decreased carbonyl reductase 1 expression promotes tumor growth via epithelial mesenchymal transition in uterine cervical squamous cell carcinomas
Authors: Nishimoto Yuki , Murakami Akihiro , Sato Shun , Kajimura Takuya , Nakashima Kengo , Yakabe Kazuyuki , Sueoka Kotaro , Sugino Norihiro 
Published: January 2018

AbstractPurposeCarbonyl reductase 1 (CBR1) is involved in cancer progression. Recently, the authors reported that the loss of CBR1 expression is associated with a poor prognosis in uterine cervical cancer. Here, we investigated whether the decreased CBR1 expression promotes cancer progression by inducing the epithelial mesenchymal transition (EMT).MethodsAntisense constructs of CBR1 complementary DNA (antisense clones) and the empty vectors (control clones) were transfected into human uterine cervical squamous cell carcinoma cell lines (SKG II and SiHa) and the proliferation and EMT marker expression of these clones were analyzed in vitro. In an in vivo study, 107 cells of the antisense and control clones were subcutaneously injected into nude mice and the tumorigenesis was observed for 8 weeks.ResultsWith the decreased CBR1 expression, the proliferation of the antisense clones increased, accompanied by a decrease in epithelial markers (E‐cadherin and cytokeratin) and an increase in mesenchymal markers (fibronectin, alpha‐smooth muscle actin, and N‐cadherin), which suggests EMT induction. In the in vivo study, the tumor volume in the antisense group was significantly larger than that in the control group.ConclusionDecreased CBR1 expression promotes tumor growth by inducing EMT in uterine cervical squamous cell carcinomas.
Distributed stochastic MPC for systems with parameter uncertainty and disturbances
Authors: Dai Li , Xia Yuanqing , Gao Yulong , Cannon Mark 
Published: January 2018

SummaryA distributed stochastic model predictive control algorithm is proposed for multiple linear subsystems with both parameter uncertainty and stochastic disturbances, which are coupled via probabilistic constraints. To handle the probabilistic constraints, the system dynamics is first decomposed into a nominal part and an uncertain part. The uncertain part is further divided into 2 parts: the first one is constrained to lie in probabilistic tubes that are calculated offline through the use of the probabilistic information on disturbances, whereas the second one is constrained to lie in polytopic tubes whose volumes are optimized online and whose facets' orientations are determined offline. By permitting a single subsystem to optimize at each time step, the probabilistic constraints are then reduced into a set of linear deterministic constraints, and the online optimization problem is transformed into a convex optimization problem that can be performed efficiently. Furthermore, compared to a centralized control scheme, the distributed stochastic model predictive control algorithm only requires message transmissions when a subsystem is optimized, thereby offering greater flexibility in communication. By designing a tailored invariant terminal set for each subsystem, the proposed algorithm can achieve recursive feasibility, which, in turn, ensures closed‐loop stability of the entire system. A numerical example is given to illustrate the efficacy of the algorithm.
Insights into the Effect of Structural Heterogeneity in Carbonized Electrospun Fibrous Mats for Flow Battery Electrodes by X‐Ray Tomography
Authors: Kok Matt D. R. , Jervis Rhodri , Brett Dan , Shearing Paul R. , Gostick Jeff T. 
Published: January 2018

AbstractElectrospun custom made flow battery electrodes are imaged in 3D using X‐ray computed tomography. A variety of computational methods and simulations are applied to the images to determine properties including the porosity, fiber size, and pore size distributions as well as the material permeability and flow distributions. The simulations are performed on materials before and after carbonization to determine the effect it has in the internal microstructure and material properties. It is found that the deposited fiber size is constantly changing throughout the electrospinning process. The results also show that the surfaces of the fibrous material are the most severely altered during carbonization and that the rest of the material remained intact. Pressure driven flow is modeled using the lattice Boltzmann method and excellent agreement with experimental results is found. The simulations coupled with the material analysis also demonstrate the highly heterogeneous nature of the flow. Most of the flow is concentrated to regions with high porosity while regions with low porosity shield other pores and starve them of flow. The importance of imaging these materials in 3D is highlighted throughout.
Sampling from Single Cells
Authors: Actis Paolo 
Published: January 2018

AbstractThe cell is the fundamental unit of biology. Major methodological advances in engineering and molecular biology have enabled the 'omics analysis of individual cells and supported biologists in understanding the deepest difference between health and disease. These advancements were based on the assumption that a single cell needs to be lysed or fixed before any in‐depth analysis can be performed. Here, a picture is painted of the innovative methods used for extracting the contents of living cells without affecting their viability. These novel methods are now empowering the biological community to repeatedly interrogate a single cell over time, thus giving a dynamic representation of the cell's 'omics rather than a snapshot at a particular time point.
Prediction of quality using ANN based on Teaching‐Learning Optimization in component‐based software systems
Authors: Tomar Pradeep , Mishra Rajesh , Sheoran Kavita 
Published: January 2018

SummaryThe primary objective of our research work is to enhance the prediction of the quality of a component‐based software system and to develop an artificial neural network (ANN) model for the system reliability optimization problem. In this paper, we introduced the ANN‐supported Teaching‐Learning Optimization by transforming constraints to objective functions. Artificial neural network techniques are found to be powerful in the modeling software package quality metrics compared with the ancient statistical techniques. Therefore, by using the neural network, the quality characteristics of software components of the proposed work are predicted. A nonlinear differentiable transfer function of ANN used in the proposed approach is hyperbolic tangent sigmoid. A new efficient optimization methodology referred to as the Teaching‐Learning–based Optimization is proposed in this paper to optimize reliability and different cost functions. The weight values of the network are then adjusted consistent with a proposed optimization rule, therefore minimizing the network error. The proposed work is implemented in MATLAB by using the Neural Network Toolbox. The proposed work provides improved performance in terms of sensitivity, precision, specificity, negative predictive value, fall‐out or false positive rate, false discovery rate, accuracy, Matthews correlation coefficient, and rate of convergence.
Uncovering cell type‐specific complexities of gene expression and RNA metabolism by TU‐tagging and EC‐tagging
Authors: Cleary Michael D. 
Published: January 2018

Cell type‐specific transcription is a key determinant of cell fate and function. An ongoing challenge in biology is to develop robust and stringent biochemical methods to explore gene expression with cell type specificity. This challenge has become even greater as researchers attempt to apply high‐throughput RNA analysis methods under in vivo conditions. TU‐tagging and EC‐tagging are in vivo biosynthetic RNA tagging techniques that allow spatial and temporal specificity in RNA purification. Spatial specificity is achieved through targeted expression of pyrimidine salvage enzymes (uracil phosphoribosyltransferase and cytosine deaminase) and temporal specificity is achieved by controlling exposure to bioorthogonal substrates of these enzymes (4‐thiouracil and 5‐ethynylcytosine). Tagged RNAs can be purified from total RNA extracted from an animal or tissue and used in transcriptome profiling analyses. In addition to identifying cell type‐specific mRNA profiles, these techniques are applicable to noncoding RNAs and can be used to measure RNA transcription and decay. Potential applications of TU‐tagging and EC‐tagging also include fluorescent RNA imaging and selective definition of RNA–protein interactions. TU‐tagging and EC‐tagging hold great promise for supporting research at the intersection of RNA biology and developmental biology.This article is categorized under:

Technologies > Analysis of the Transcriptome
Chromatin modifications in metabolic disease: Potential mediators of long‐term disease risk
Authors: Costello Kevin R. , Schones Dustin E. 
Published: January 2018

Metabolic diseases such as obesity and diabetes are complex diseases resulting from multiple genetic and environmental factors, such as diet and activity levels. These factors are well known contributors to the development of metabolic diseases. One manner by which environmental factors can influence metabolic disease progression is through modifications to chromatin. These modifications can lead to altered gene regulatory programs, which alters disease risk. Furthermore, there is evidence that parents exposed to environmental factors can influence the metabolic health of offspring, especially if exposures are during intrauterine growth periods. In this review, we outline the evidence that chromatin modifications are associated with metabolic diseases, including diabetes and obesity. We also consider evidence that these chromatin modifications can lead to long‐term disease risk and contribute to disease risk for future generations.This article is categorized under:

Biological Mechanisms > Metabolism
Developmental Biology > Developmental Processes in Health and Disease
Physiology > Organismal Responses to Environment
Cysto‐cholecystostomy: A More Physiological Procedure for Hepatic Cysts with Biliary Communications and Cystic Dilatations of Main Intrahepatic Ducts
Authors: Diao Mei , Li Long , Cheng Wei 
Published: January 2018

AbstractObjectiveHepatic cysts with biliary communications (HC) and cystic dilatations of main intrahepatic ducts (CIHD) can cause biliary obstruction, cholestasis, stone formation, cholangitis, liver damage and carcinoma. Conventionally, Roux‐Y cysto‐jejunostomy is employed to manage these conditions. However, it is technically demanding and may be complicated with major biliary disruption and bacteria migration from intestine to intrahepatic duct. We have carried out laparoscopic cysto‐cholecystostomies for HC with biliary communication and CIHD and evaluated outcomes.MethodsTwenty patients with HC (n = 10) or CIHD (n = 10) who successfully underwent laparoscopic cysto‐cholecystostomies in our center, between September 2010 and March 2017, were reviewed.ResultsThe mean age of the patients at surgery was 2.06 and 2.23 years for HC and CIHD groups, respectively. Eighteen patients were symptomatic, with abdominal pain, fever, vomiting and jaundice. Laboratory results showed abnormal liver functions in 8 patients. Pathological results verified hepatic cellular damages in 8 patients. The mean operative time was 0.97 and 0.92 h for HC and CIHD patients, respectively. The median follow‐up duration was 27 months (1–54 months) and 35 months (1–79 months) for HC and CIHD groups, respectively. No patient developed bile leak, anastomotic stenosis, stone formation or cholangitis. Liver function normalized postoperatively.ConclusionsLaparoscopic cysto‐cholecystostomy is a simpler and more physiological surgical alternative for managing HC with biliary communication and CIHD.
Inverse formulas of parameterized orthogonal wavelets
Authors: Herrera-Alcántara Oscar , González-Mendoza Miguel 
Published: January 2018

AbstractWe review the parameterization of orthogonal wavelet based filters of length 4, 6, 8, and 10, and present their inverse formulas, which means to determine the parameter values from filter coefficients. Experimental results support the validity of these inverse formulas when parameters are restricted to $$[0, 2\pi )$$

[
0
,
2
π
)

for practical applications, such as image processing where parameters are optimized to maximize the number of negligible wavelet coefficients.
Reproductive Decision Support: Preferences and Needs of Couples at Risk for Hereditary Cancer and Clinical Geneticists
Authors: Reumkens Kelly , van Oudheusden A. J. G. , Gietel‐Habets J. J. G. , Tummers M. H. E. , de Die‐Smulders C. E. M. , van Osch L. A. D. M. 
Published: January 2018

AbstractFor couples at high risk of transmitting a cancer predisposition to offspring, reproductive decision‐making can be challenging. As the choice between available reproductive options is preference‐sensitive, the use of a decision aid can support these couples in their decisional process. The present study aims to investigate preferences and needs of involved stakeholders regarding the development and implementation of a patient decision aid. Semi‐structured interviews assessing the needs and preferences regarding the content and functionalities of a decision support program were conducted among seven couples at risk for hereditary cancer and among eight clinical geneticists involved in oncogenetic counseling. Many similarities were found between the expressed preferences and needs of both stakeholder groups concerning the content, barriers and facilitating factors regarding the use of the decision aid, and its implementation. Emphasis was placed on the use of simple non‐medical language, an extensive explanation of the procedures and techniques used in prenatal diagnosis (PND) and preimplantation genetic diagnosis (PGD), and the role of health care providers to refer couples to the decision aid. Both stakeholder groups were in favor of incorporating narrative stories in the decision aid. Integrating the present findings with knowledge on reproductive decisional motives and considerations is essential in guiding the development of a decision aid that corresponds to the preferences and needs of end‐users. Trial registration: NTR5467
Effect of Temperature on the Fracture Toughness of Hot Isostatically Pressed 304L Stainless Steel
Authors: Cooper A. J. , Brayshaw W. J. , Sherry A. H. 
Published: January 2018

Abstract
Herein, we have performed J-Resistance multi-specimen fracture toughness testing of hot isostatically pressed (HIP’d) and forged 304L austenitic stainless steel, tested at elevated (300 °C) and cryogenic (− 140 °C) temperatures. The work highlights that although both materials fail in a pure ductile fashion, stainless steel manufactured by HIP displays a marked reduction in fracture toughness, defined using J
0.2BL, when compared to equivalently graded forged 304L, which is relatively constant across the tested temperature range.
Nonlinear phase-resolved reconstruction of irregular water waves
Authors: Qi Yusheng , Wu Guangyu , Liu Yuming , Kim Moo-Hyun , Yue Dick K. P. 
Published: January 2018

We develop and validate a high-order reconstruction (HOR) method for the phase-resolved reconstruction of a nonlinear wave field given a set of wave measurements. HOR optimizes the amplitude and phase of $L$ free wave components of the wave field, accounting for nonlinear wave interactions up to order $M$ in the evolution, to obtain a wave field that minimizes the reconstruction error between the reconstructed wave field and the given measurements. For a given reconstruction tolerance, $L$ and $M$ are provided in the HOR scheme itself. To demonstrate the validity and efficacy of HOR, we perform extensive tests of general two- and three-dimensional wave fields specified by theoretical Stokes waves, nonlinear simulations and physical wave fields in tank experiments which we conduct. The necessary $L$, for general broad-banded wave fields, is shown to be substantially less than the free and locked modes needed for the nonlinear evolution. We find that, even for relatively small wave steepness, the inclusion of high-order effects in HOR is important for prediction of wave kinematics not in the measurements. For all the cases we consider, HOR converges to the underlying wave field within a nonlinear spatial-temporal predictable zone ${\mathcal{P}}_{NL}$ which depends on the measurements and wave nonlinearity. For infinitesimal waves, ${\mathcal{P}}_{NL}$ matches the linear predictable zone ${\mathcal{P}}_{L}$, verifying the analytic solution presented in Qi et al. (Wave Motion, vol. 77, 2018, pp. 195–213). With increasing wave nonlinearity, we find that ${\mathcal{P}}_{NL}$ contains and is generally greater than ${\mathcal{P}}_{L}$. Thus ${\mathcal{P}}_{L}$ provides a (conservative) estimate of ${\mathcal{P}}_{NL}$ when the underlying wave field is not known.
Propagation of a strong shock over a random bed of spherical particles
Authors: Mehta Y. , Neal C. , Salari K. , Jackson T. L. , Balachandar S. , Thakur S. 
Published: January 2018

Propagation of a strong incident shock through a bed of particles results in complex wave dynamics such as a reflected shock, a transmitted shock, and highly unsteady flow inside the particle bed. In this paper we present three-dimensional numerical simulations of shock propagation in air over a random bed of particles. We assume the flow is inviscid and governed by the Euler equations of gas dynamics. Simulations are carried out by varying the volume fraction of the particle bed at a fixed shock Mach number. We compute the unsteady inviscid streamwise and transverse drag coefficients as a function of time for each particle in the random bed for different volume fractions. We show that (i) there are significant variations in the peak drag for the particles in the bed, (ii) the mean peak drag as a function of streamwise distance through the bed decreases with a slope that increases as the volume fraction increases, and (iii) the deviation from the mean peak drag does not correlate with local volume fraction. We also present the local Mach number and pressure contours for the different volume fractions to explain the various observed complex physical mechanisms occurring during the shock–particle interactions. Since the shock interaction with the random bed of particles leads to transmitted and reflected waves, we compute the average flow properties to characterize the strength of the transmitted and reflected shock waves and quantify the energy dissipation inside the particle bed. Finally, to better understand the complex wave dynamics in a random bed, we consider a simpler approximation of a planar shock propagating in a duct with a sudden area change. We obtain Riemann solutions to this problem, which are used to compare with fully resolved numerical simulations.
COVERS OF GENERALIZED QUADRANGLES
Authors: THAS JOSEPH A. , THAS KOEN 
Published: January 2018

AbstractWe solve a problem posed by Cardinali and Sastry (Elliptic ovoids and their rosettes in a classical generalized quadrangle of even order.Proc. Indian Acad. Sci. Math. Sci.126(2016), 591–612) about factorization of 2-covers of finite classical generalized quadrangles (GQs). To that end, we develop a general theory of cover factorization for GQs, and in particular, we study the isomorphism problem for such covers and associated geometries. As a byproduct, we obtain new results about semi-partial geometries coming from θ-covers, and consider related problems.
A new species-level taxonomy forTrapelia(Trapeliaceae, Ostropomycetidae) with special reference to Great Britain and the Falkland Islands
Authors: ORANGE Alan 
Published: January 2018

AbstractTrapeliais a small genus of worldwide distribution.Trapelia coarctatahas long been regarded as a morphologically variable species and phylogenetic studies have suggested that it is non-monophyletic, or at least that species are frequently misidentified. The phylogenetic relationships of freshly-collected material ofTrapeliawere studied using ITS, mitochondrial SSU rDNA and to a small extent also beta-tubulin sequence data, together with chemical and morphological characters. Sequence data combined with morphology and chemistry confirm that the diversity of the genus at species-level has been underestimated.Trapelia coarctatais defined in a more restricted way and many specimens previously referable to this taxon are assigned to the reinstated speciesT. elacista, which differs in subtle morphological characters including a crack separating the thallus and apothecium in well-developed thalli.Trapelia involutais reinstated as a separate, though closely related, species toT. glebulosabased on sequence data, morphology and chemistry, and is lectotypified.Trapelia collarisis a distinctive species described as new from Great Britain which has an extensive, cracked thallus with abruptly thickening marginal areoles arising on an inconspicuous prothallus, relatively small apothecia (rarely exceeding 300 µm diameter) and contains 5-O-methylhiascic acid as the major secondary substance.Trapelia obtegensis shown to include frequent non-sorediate morphs which have doubtless been misidentified as other species. The number of species ofTrapeliaconsidered to occur in Europe is thus raised from five to eight. The genus is newly reported for the Falkland Islands where seven species occur:T. coarctata,T. placodioides,T. sitienssp. nov. (with a thin, extensive thallus, sessile apothecia, 5-O-methylhiascic acid as the major secondary substance and the presence of conidiomata),T. tristissp. nov. (with relatively small apothecia up to 460 µm diameter, presence of gyrophoric acid as the major substance and an absence of conidiomata) and three unidentified species represented by very sparse material. All the species studied, with the possible exception of the three unidentified species, can usually be distinguished by morphological features, particularly the method of development of the thallus and the shape and distribution of the areoles, but morphological variation in response to microhabitat variation is likely to make a proportion of specimens difficult to assign to species in the absence of sequence data.