bluuebunny/crossref_metadata_2025_split huggingface dataset:
The secreted Ly6/uPAR-related protein-1 suppresses neutrophil binding, chemotaxis, and transmigration through human umbilical vein endothelial cells
Authors: Swamynathan Sudha , Tiwari Anil , Loughner Chelsea L. , Gnalian John , Alexander Nicholas , Jhanji Vishal , Swamynathan Shivalingappa K. 
Published: April 2019

AbstractThe secreted Ly-6/uPAR Related Protein-1 (SLURP1) is an immunomodulatory protein that promotes corneal immune- and angiogenic-privilege. Here, we have examined the influence of SLURP1 on neutrophil-vascular endothelial cell interactions using human umbilical vein endothelial cells (HUVEC) and differentiated neutrophil-like HL-60 (dHL-60) cells, or primary human neutrophils. SLURP1 blocked the tumor necrosis factor-alpha (TNF-α)-activated dHL-60 cells (i) binding to TNF-α-activated HUVEC with a concurrent reduction in endothelial cell adhesion molecule E-selectin, (ii) transmigration through TNF-α-activated confluent HUVEC monolayer by stabilizing VE-cadherin and β-catenin on endothelial cell cytoplasmic membranes, (iii) chemotaxis towards chemoattractant formyl Met-Leu-Phe (fMLP) coupled with their decreased polarization, and (iv) TNF-α-stimulated matrix metalloproteinase-9 (MMP9) expression and activity. SLURP1 also suppressed the primary human neutrophil chemotaxis, and interaction with HUVEC. Furthermore, SLURP1 suppressed fMLP-induced phosphorylation of protein kinase-B (AKT) in dHL-60 cells. Collectively, these results provide evidence that SLURP1 suppresses neutrophil (i) docking on HUVEC cells by decreasing endothelial cell adhesion molecule E-Selectin production, (ii) transmigration through HUVEC monolayer by stabilizing endothelial cell membrane localization of VE-cadherin and β-catenin complex and promoting their barrier function, and (iii) chemotaxis by modulating their polarization and TNF-α-stimulated MMP9 production.
Microchannel Structural Design For a Room-Temperature Liquid Metal Based Super-stretchable Sensor
Authors: Gao Qinwu , Li Hui , Zhang Jinjie , Xie Zhenwen , Zhang Jinyong , Wang Lei 
Published: April 2019

AbstractRoom-temperature liquid metal has been widely used in flexible and stretchable sensors, focusing on embedding liquid metal in microchannels, liquid metal microdroplets formation, captive sensors, and liquid metal nanoparticles, etc. In this paper, a facile Eutectic Galium-Indium (EGaln) liquid-based microfluidic high-sensitivity, skin-mountable, and ultra-soft stretchable sensor is developed. It comprises Ecoflex microfluidic assembly filled with EGaln, which serves as the working fluid of the stretchable sensor. The lithography method is applied to achieve microfluidic channel. The microfluidic channel is optimized by using topology method and finite element analysis, making this device with high conformability and high stretchability. This method achieved an outstanding effect on elastomer-encapsulated strain gauge, which displays an approximately linear behavior with a gauge factor (GF). The GF could reach as high as 4.95 when the strain ultimately reached 550%. Applications of detection of the joints, fingers, and wrists has been conducted and showed excellent results. This work can further facilitate the exploration and potential realization of a functional liquid-state device technology with superior mechanical flexibility and conformability.
Adaptively Weighted and Robust Mathematical Programming for the Discovery of Driver Gene Sets in Cancers
Authors: Xu Xiaolu , Qin Pan , Gu Hong , Wang Jia , Wang Yang 
Published: April 2019

AbstractHigh coverage and mutual exclusivity (HCME), which are considered two combinatorial properties of mutations in a collection of driver genes in cancers, have been used to develop mathematical programming models for distinguishing cancer driver gene sets. In this paper, we summarize a weak HCME pattern to justify the description of practical mutation datasets. We then present AWRMP, a method for identifying driver gene sets through the adaptive assignment of appropriate weights to gene candidates to tune the balance between coverage and mutual exclusivity. It embeds the genetic algorithm into the subsampling strategy to provide the optimization results robust against the uncertainty and noise in the data. Using biological datasets, we show that AWRMP can identify driver gene sets that satisfy the weak HCME pattern and outperform the state-of-arts methods in terms of robustness.
MiRNA-506 inhibits rheumatoid arthritis fibroblast-like synoviocytes proliferation and induces apoptosis by targetting TLR4
Authors: Li Dan , Zhou Qingchen , Hu Gaojian , Wang Gang 
Published: April 2019

Abstract
Fibroblast-like synoviocytes (FLSs) play a crucial role in rheumatoid arthritis (RA) pathogenesis. While miRNA (miR)-506 has been implicated in the progression of multiple diseases, its role in RA remains to be explored. The present study evaluated the function of miR-506 in the regulation of RA-FLSs. FLSs were prepared from RA and healthy synovial tissues. The expression of miR-506 was measured by quantitative real time PCR (qRT-PCR). The effects of miR-506 on RA-FLSs proliferation and apoptosis were detected by cell counting Kit-8 and flow cytometry assays, respectively. The determination of TNF-α, IL-6, and IL-1β concentrations in RA-FLSs supernatant were done by ELISA. The levels of miR-506 were detected to be significantly lower in the synovial tissues and FLSs of RA than in the synovial tissues and FLSs of healthy controls. The miR-506 up-regulation in RA-FLSs significantly inhibited the proliferation and promoted cell cycle arrest at the G0/G1 phase. The overexpression of miR-506 induced apoptosis, along with an increase in activities of caspase-3 and -8. A target gene Toll-like receptor 4 (TLR4) under the direct regulation of miR-506 was identified through the luciferase assay, qRT-PCR and western blot analysis. Forced overexpression of TLR4 in the rescue experiments showed that TLR4 effectively reversed the effect on proliferation and apoptosis in miR-506-overexpressing RA-FLSs. Thus, miR-506 may be a potential target for RA prevention and therapy of RA.
L-securinine inhibits cell growth and metastasis of human androgen-independent prostate cancer DU145 cells via regulating mitochondrial and AGTR1/MEK/ERK/STAT3/PAX2 apoptotic pathways
Authors: Zhang Dongxu , Liu Houxian , Yang Binbin , Hu Jiasheng , Cheng Yue 
Published: April 2019

Abstract
The present study aims to evaluate the anticancer effect of L-securinine on androgen-independent prostate cancer (AIPC) DU145 cells. L-securinine (2.5, 5, and 10 μM) treatment for 24, 48 and 72 h displayed strong growth inhibitory effect on DU145 cells in a concentration and time-dependent fashion but has less toxicity toward normal androgen-dependent LNCaP cells. Hoechst 332582 staining of DU145 cells and Annexin V-FITC/ PI dual-labeling followed by flow cytometry assay identified that this growth inhibition by L-securinine would be due to the induction of apoptosis. Moreover Transwell assay revealed that L-securinine significantly inhibited the cell migration/invasion ability of DU145 cells. Furthermore, results of western blotting showed that the involvement of mitochondrial apoptotic pathway in the L-securinine-induced apoptosis of DU145 cell, as evidenced by an increase in the protein expression of Bax, cleaved caspase-9, cleaved caspase-3, cytosolic cytochrome c, and cleaved PARP, together with a unchanged cleaved caspase-8 and decreased Bcl-2 protein expression. Also, L-securinine-induced antimetastatic activity in DU145 cells was associated with decreased protein expression of MMP-2 and MMP-9 and concurrent reduction of VEGF. In addition, further studies revealed that L-securinine may inhibit the protein expression of AGTR1, p-MEK1/2, p-ERK1/2, p-STAT3, PAX2, and p-PAX2, while the expression of ERK1/2, MEK1/2, and STAT3 protein retains intact. These findings suggest that L-securinine may be a promising chemopreventive agent against AIPC.
Wirkung von Aqua-Cycling als Bewegungstherapie bei der
Diagnose Lipödem
Authors: Burger R. , Jung M. , Becker J. , Krominus J. , Lampe M. , Kleinschmidt J. , Kleinschmidt B. 
Published: April 2019

ZusammenfassungIn der folgenden Übersicht werden die allgemeinen Vorteile von
Bewegungsinterventionen im Wasser innerhalb der physikalischen
Therapiemöglichkeiten sowie bei den Diagnosen Lip- und Lymphödem angesprochen.
Aufgrund von positiven Erfahrungen bei Lymphödempatientinnen werden hier
Einzelfallkasuistiken bzgl. des Einsatzes von Aqua-Cycling bei Lipödem
vorgestellt, die weitere Untersuchungen anstoßen sollten.
Effects of Enantiomerically Pure β-Carboline Alkaloids from Picrasma quassioides on Human Hepatoma Cells
Authors: Zhao Wen-Yu , Chen Jing-Jie , Zou Chun-Xin , Zhou Wei-Yu , Yao Guo-Dong , Wang Xiao-Bo , Lin Bin , Huang Xiao-Xiao , Song Shao-Jiang 
Published: April 2019

AbstractFour pairs of β-carboline enantiomers (1a/1b–4a/4b), 2 β-carboline derivatives (5 – 6) with a single enantiomeric configuration, together with 2 known achiral congeners (7 – 8) were isolated from the stems of Picrasma quassioides. Their structures were elucidated on the basis of extensive spectroscopic analyses and quantum mechanical calculations. Compound 5 possesses a 4,5-seco β-carboline framework and represents the first example of this type of β-carboline alkaloids from nature. A possible biosynthetic pathway is proposed to generate the racemate 4 and the enantiomerically pure compounds 5 and 6. All isolates were screened for their cytotoxicity against hepatocellular carcinoma Hep3B and HepG2 cells, which revealed that enantiomeric compounds 4a and 4b had distinctive effects in HepG2 cells. Further investigation showed that 4b could induce apoptosis in HepG2 cells.
Dispersion forces in nanoscience
Authors: Rusanov Anatoly I. , Brodskaya Elena N. 
Published: April 2019

The 21st century was marked by a new outbreak of interest in dispersion forces in nanoscale systems. However, now the consideration is conducted at a different level. Whereas earlier the main object of study was infinite plane-parallel films, now it is a question of calculations for systems of a more complex configuration with non-parallel and finite surfaces of various shapes. On the other hand, it is not the average interaction force that is estimated, but the detailed mechanical state of the interacting bodies, for which statistical mechanics and the Irving – Kirkwood stress tensor are involved. This review summarizes the theoretical studies of plane-parallel, but finite-area films, wedge-shaped films, systems with spherical, cylindrical, and conical surfaces. Particular consideration is given to interactions involving nanoparticles. Spheroidal particles, rod-like and disc-shaped particles are analyzed. The shape factor of the interaction of particles with a flat surface is estimated. The calculation of the contribution of dispersion forces to surface, line and point tension is explained. Among the latest news is the calculation (brought to numbers) of the contribution of dispersion forces to the graphene point energy.
The bibliography includes 109 references.
Metal complex catalysis in the chemistry of lower diamondoids
Authors: Khusnutdinov Ravil I. , Shchadneva Nina A. 
Published: April 2019

The review presents the first survey of published data on the use of compounds, complexes and nanoparticles of transition metals (Fe, Co, Ni, Mn, V, Mo, Cu, Pd, Pt, Rh, Ru, Os, Au, Re and Th) in the catalytic transformations of lower diamondoids — adamantane, diamantane and their derivatives. Catalytic halogenation, oxidation, alkylation and cross-coupling reactions are considered, and the formation pathways of C–N, C–S and C–Se bonds in the series of adamantanoids are discussed. Reaction conditions, appropriate catalytic systems and the structures of products are presented.
The bibliography includes 242 references.
Quasinormal modes of Dirac spinors in the background of rotating black holes in four and five dimensions
Authors: Blázquez-Salcedo Jose Luis , Knoll Christian 
Published: April 2019

Abstract
We study the quasinormal modes of massive Dirac spinors in the background of rotating black holes. In particular, we consider the Kerr geometry as well as the five dimensional Myers–Perry spacetime with equal angular momenta. We decouple the equations using the standard methods from the literature. In the five dimensional Myers–Perry black hole the angular equation is solved analytically. Using the continued fraction method, we calculate the spectrum of quasinormal modes for the ground modes and first excited modes. For the case of the Kerr black hole we also study some features of the modes with high overtone number. We analyze, in a systematic way, its dependence on the different parameters of the black hole and fermionic field. We compare our values with previous results available in the literature for Kerr and for the static limit. The numerical results show several differences between the four and five dimensional cases. For instance, in five dimensions the symmetry between the positive and negative (real) frequency of the modes breaks down, which results in a richer spectrum.
Residual flatness and scale calibration for a point autofocus surface topography measuring instrument
Authors: Maculotti Giacomo , Feng Xiaobing , Su Rong , Galetto Maurizio , Leach Richard 
Published: April 2019

Abstract
Point autofocus instruments are often used for measuring the surface topography of objects with complex geometry. Determining the metrological characteristics of the instrument is key to ensuring a traceable areal surface topography measurement. In this work, several metrological characteristics, as outlined in ISO/FDIS 25178-600, are determined for a commercial point autofocus instrument, including flatness deviation, the amplification and linearity of the lateral and vertical axes, and the perpendicularity between the axes. Calibrated material measures including an optical flat, step heights and areal cross gratings are used to determine the metrological characteristics. The impact of the point autofocus operating principle and the evaluation method on the metrological characteristics is discussed.
van der Waals-corrected density functional study of electric field noise heating in ion traps caused by electrode surface adsorbates
Authors: Ray Keith G , Rubenstein Brenda M , Gu Wenze , Lordi Vincenzo 
Published: April 2019

Abstract
In order to realize the full potential of ion trap quantum computers, an improved understanding is required of the motional heating that trapped ions experience. Experimental studies of the temperature-, frequency-, and ion–electrode distance-dependence of the electric field noise responsible for motional heating, as well as the noise before and after ion bombardment cleaning of trap electrodes, suggest that fluctuations of adsorbate dipoles are a likely source of so-called ‘anomalous heating,’ or motional heating of the trapped ions at a rate much higher than the Johnson noise limit. Previous computational studies have investigated how the fluctuation of model adsorbate dipoles affects anomalous heating. However, the way in which specific adsorbates affect the electric field noise has not yet been examined, and an electric dipole model employed in previous studies is only accurate for a small subset of possible adsorbates. Here, we analyze the behavior of both in-plane and out-of-plane vibrational modes of twenty-one adsorbate–electrode combinations within the independent fluctuating dipole model, utilizing accurate first principles computational methods to determine the surface-induced dipole moments. We find the chemical specificity of the adsorbate can change the electric field noise by seven orders of magnitude and specifically that soft in-plane modes of weakly-adsorbed hydrocarbons produce the greatest noise and ion heating. We discuss the dynamics captured by the fluctuating dipole model, namely the adsorbate-dependent turn-on temperature and electric field noise magnitude, and also discuss the model’s failure to reproduce the measured 1/ω noise frequency scaling with a single adsorbate species. We suggest future research directions for improved, quantitatively predictive models based on extensions of the present framework to multiple interacting adsorbates.
Novel Contributors and Mechanisms of Cellular Senescence in Hypertension-Associated Premature Vascular Aging
Authors: McCarthy Cameron G , Wenceslau Camilla F , Webb R Clinton , Joe Bina 
Published: April 2019

Abstract
Hypertension has been described as a condition of premature vascular aging, relative to actual chronological age. In fact, many factors that contribute to the deterioration of vascular function as we age are accelerated in hypertension. Nonetheless, the precise mechanisms that underlie the aged phenotype of arteries from hypertensive patients and animals remain elusive. Cellular senescence is an age-related physiologic process in which cells undergo irreversible growth arrest. Although controlled senescence negatively regulates cell proliferation and promotes tissue regeneration, uncontrolled senescence can contribute to disease pathogenesis by presenting the senescence-associated secretory phenotype, in which molecules such as proinflammatory cytokines, matrix metalloproteases, and reactive oxygen species are released into tissue microenvironments. This review will address and critically evaluate the current literature on the role of cellular senescence in hypertension, with particular emphasis on cells types that mediate and modulate vascular function and structure.
Role of Pendrin in the Pathophysiology of Aldosterone-Induced Hypertension
Authors: Shibata Shigeru 
Published: April 2019

Abstract
The recent advances in genetics and molecular biology have resulted in the characterization of key components that critically regulate renal NaCl transport and blood pressure. Pendrin is a Cl−/HCO3− exchanger that is highly expressed in thyroid, inner ear, and kidney. In the kidney, it is selectively present at the apical membrane in non-α intercalated cells of the connecting tubules and cortical collecting duct. Besides its role in acid/base homeostasis, accumulating studies using various genetically modified animals have provided compelling evidence that pendrin regulates extracellular fluid volume and electrolyte balance at the downstream of aldosterone signaling. We have shown that angiotensin II and aldosterone cooperatively control pendrin abundance partly through mammalian target of rapamycin signaling and mineralocorticoid receptor dephosphorylation, which is necessary for the kidney to prevent extracellular fluid loss and electrolyte disturbances under physiologic perturbations. In line with the experimental observations, several clinical data indicated that the impaired pendrin function can cause fluid and electrolyte abnormalities in humans. The purpose of this review is to provide an update on the recent progress regarding the role of pendrin in fluid and electrolyte homeostasis, as well as in the pathophysiology of hypertension associated with mineralocorticoid receptor signaling.
An overview of diffusion models for intracellular dynamics analysis
Authors: Briane Vincent , Vimond Myriam , Kervrann Charles 
Published: April 2019

AbstractWe present an overview of diffusion models commonly used for quantifying the dynamics of intracellular particles (e.g. biomolecules) inside eukaryotic living cells. It is established that inference on the modes of mobility of molecules is central in cell biology since it reflects interactions between structures and determines functions of biomolecules in the cell. In that context, Brownian motion is a key component in short distance transportation (e.g. connectivity for signal transduction). Another dynamical process that has been heavily studied in the past decade is the motor-mediated transport (e.g. dynein, kinesin and myosin) of molecules. Primarily supported by actin filament and microtubule network, it ensures spatial organization and temporal synchronization in the intracellular mechanisms and structures. Nevertheless, the complexity of internal structures and molecular processes in the living cell influence the molecular dynamics and prevent the systematic application of pure Brownian or directed motion modeling. On the one hand, cytoskeleton density will hinder the free displacement of the particle, a phenomenon called subdiffusion. On the other hand, the cytoskeleton elasticity combined with thermal bending can contribute a phenomenon called superdiffusion. This paper discusses the basics of diffusion modes observed in eukariotic cells, by introducing the essential properties of these processes. Applications of diffusion models include protein trafficking and transport and membrane diffusion.
PEPred-Suite: improved and robust prediction of therapeutic peptides using adaptive feature representation learning
Authors: Wei Leyi , Zhou Chen , Su Ran , Zou Quan 
Published: April 2019

Abstract

Motivation
Prediction of therapeutic peptides is critical for the discovery of novel and efficient peptide-based therapeutics. Computational methods, especially machine learning based methods, have been developed for addressing this need. However, most of existing methods are peptide-specific; currently, there is no generic predictor for multiple peptide types. Moreover, it is still challenging to extract informative feature representations from the perspective of primary sequences.

Results
In this study, we have developed PEPred-Suite, a bioinformatics tool for the generic prediction of therapeutic peptides. In PEPred-Suite, we introduce an adaptive feature representation strategy that can learn the most representative features for different peptide types. To be specific, we train diverse sequence-based feature descriptors, integrate the learnt class information into our features, and utilize a two-step feature optimization strategy based on the area under receiver operating characteristic curve to extract the most discriminative features. Using the learnt representative features, we trained eight random forest models for eight different types of functional peptides, respectively. Benchmarking results showed that as compared with existing predictors, PEPred-Suite achieves better and robust performance for different peptides. As far as we know, PEPred-Suite is currently the first tool that is capable of predicting so many peptide types simultaneously. In addition, our work demonstrates that the learnt features can reliably predict different peptides.

Availability and implementation
The user-friendly webserver implementing the proposed PEPred-Suite is freely accessible at http://server.malab.cn/PEPred-Suite.

Supplementary information
Supplementary data are available at Bioinformatics online.