bluuebunny/crossref_metadata_2025_split huggingface dataset:
Antagonistic effects of IL-17 and D-resolvins on endothelial Del-1 expression through a GSK-3β-C/EBPβ pathway
Authors: Maekawa Tomoki , Hosur Kavita , Abe Toshiharu , Kantarci Alpdogan , Ziogas Athanasios , Wang Baomei , Van Dyke Thomas E. , Chavakis Triantafyllos , Hajishengallis George 
Published: September 2015

AbstractDel-1 is an endothelial cell-secreted anti-inflammatory protein. In humans and mice, Del-1 expression is inversely related to that of IL-17, which inhibits Del-1 through hitherto unidentified mechanism(s). Here we show that IL-17 downregulates human endothelial cell expression of Del-1 by targeting a critical transcription factor, C/EBPβ. Specifically, IL-17 causes GSK-3β-dependent phosphorylation of C/EBPβ, which is associated with diminished C/EBPβ binding to the Del-1 promoter and suppressed Del-1 expression. This inhibitory action of IL-17 can be reversed at the GSK-3β level by PI3K/Akt signalling induced by D-resolvins. The biological relevance of this regulatory network is confirmed in a mouse model of inflammatory periodontitis. Intriguingly, resolvin-D1 (RvD1) confers protection against IL-17-driven periodontal bone loss in a Del-1-dependent manner, indicating an RvD1-Del-1 axis against IL-17-induced pathological inflammation. The dissection of signalling pathways regulating Del-1 expression provides potential targets to treat inflammatory diseases associated with diminished Del-1 expression, such as periodontitis and multiple sclerosis.
Nonlinear spin-wave excitations at low magnetic bias fields
Authors: Bauer Hans G. , Majchrak Peter , Kachel Torsten , Back Christian H. , Woltersdorf Georg 
Published: September 2015

AbstractNonlinear magnetization dynamics is essential for the operation of numerous spintronic devices ranging from magnetic memory to spin torque microwave generators. Examples are microwave-assisted switching of magnetic structures and the generation of spin currents at low bias fields by high-amplitude ferromagnetic resonance. Here we use X-ray magnetic circular dichroism to determine the number density of excited magnons in magnetically soft Ni80Fe20 thin films. Our data show that the common model of nonlinear ferromagnetic resonance is not adequate for the description of the nonlinear behaviour in the low magnetic field limit. Here we derive a model of parametric spin-wave excitation, which correctly predicts nonlinear threshold amplitudes and decay rates at high and at low magnetic bias fields. In fact, a series of critical spin-wave modes with fast oscillations of the amplitude and phase is found, generalizing the theory of parametric spin-wave excitation to large modulation amplitudes.
Ligand-dependent genomic function of glucocorticoid receptor in triple-negative breast cancer
Authors: Chen Zhong , Lan Xun , Wu Dayong , Sunkel Benjamin , Ye Zhenqing , Huang Jiaoti , Liu Zhihua , Clinton Steven K. , Jin Victor X. , Wang Qianben 
Published: September 2015

AbstractGlucocorticoids (GCs) have been widely used as coadjuvants in the treatment of solid tumours, but GC treatment may be associated with poor pharmacotherapeutic response or prognosis. The genomic action of GC in these tumours is largely unknown. Here we find that dexamethasone (Dex, a synthetic GC)-regulated genes in triple-negative breast cancer (TNBC) cells are associated with drug resistance. Importantly, these GC-regulated genes are aberrantly expressed in TNBC patients and are associated with unfavourable clinical outcomes. Interestingly, in TNBC cells, Compound A (CpdA, a selective GR modulator) only regulates a small number of genes not involved in carcinogenesis and therapy resistance. Mechanistic studies using a ChIP-exo approach reveal that Dex- but not CpdA-liganded glucocorticoid receptor (GR) binds to a single glucocorticoid response element (GRE), which drives the expression of pro-tumorigenic genes. Our data suggest that development of safe coadjuvant therapy should consider the distinct genomic function between Dex- and CpdA-liganded GR.
Estimation of a biofilm-specific reaction rate: kinetics of bacterial urea hydrolysis in a biofilm
Authors: Connolly James M , Jackson Benjamin , Rothman Adam P , Klapper Isaac , Gerlach Robin 
Published: September 2015

Abstract
Background/Objectives:
Biofilms and specifically urea-hydrolysing biofilms are of interest to the medical community (for example, urinary tract infections), scientists and engineers (for example, microbially induced carbonate precipitation). To appropriately model these systems, biofilm-specific reaction rates are required. A simple method for determining biofilm-specific reaction rates is described and applied to a urea-hydrolysing biofilm.

Methods:
Biofilms were grown in small silicon tubes and influent and effluent urea concentrations were determined. Immediately after sampling, the tubes were thin sectioned to estimate the biofilm thickness profile along the length of the tube. Urea concentration and biofilm thickness data were used to construct an inverse model for the estimation of the urea hydrolysis rate.

Results/Conclusions:
It was found that urea hydrolysis in Escherichia coli MJK2 biofilms is well approximated by first-order kinetics between urea concentrations of 0.003 and 0.221 mol/l (0.186 and 13.3 g/l). The first-order rate coefficient (k1) was estimated to be 23.2±6.2 h−1. It was also determined that advection dominated the experimental system rather than diffusion, and that urea hydrolysis within the biofilms was not limited by diffusive transport. Beyond the specific urea-hydrolysing biofilm discussed in this work, the method has the potential for wide application in cases where biofilm-specific rates must be determined.
Effects of Nanotexture on Electrical Profiling of Single Tumor Cell and Detection of Cancer from Blood in Microfluidic Channels
Authors: Islam Muhymin , Motasim Bellah Mohammad , Sajid Adeel , Raziul Hasan Mohammad , Kim Young-tae , Iqbal Samir M. 
Published: September 2015

AbstractMicrofluidic channels have been implemented to detect cancer cells from blood using electrical measurement of each single cell from the sample. Every cell provided characteristic current profile based on its mechano-physical properties. Cancer cells not only showed higher translocation time and peak amplitude compared to blood cells, their pulse shape was also distinctively different. Prevalent microfluidic channels are plain but we created nanotexture on the channel walls using micro reactive ion etching (micro-RIE). The translocation behaviors of the metastatic renal cancer cells through plain and nanotextured PDMS microchannels showed clear differences. Nanotexture enhanced the cell-surface interactions and more than 50% tumor cells exhibited slower translocation through nanotextured channels compared to plain devices. On the other hand, most of the blood cells had very similar characteristics in both channels. Only 7.63% blood cells had slower translocation in nanotextured microchannels. The tumor cell detection efficiency from whole blood increased by 14% in nanotextured microchannels compared to plain channels. This interesting effect of nanotexture on translocation behavior of tumor cells is important for the early detection of cancer.
Robust bioengineered 3D functional human intestinal epithelium
Authors: Chen Ying , Lin Yinan , Davis Kimberly M. , Wang Qianrui , Rnjak-Kovacina Jelena , Li Chunmei , Isberg Ralph R. , Kumamoto Carol A. , Mecsas Joan , Kaplan David L. 
Published: September 2015

AbstractIntestinal functions are central to human physiology, health and disease. Options to study these functions with direct relevance to the human condition remain severely limited when using conventional cell cultures, microfluidic systems, organoids, animal surrogates or human studies. To replicate in vitro the tissue architecture and microenvironments of native intestine, we developed a 3D porous protein scaffolding system, containing a geometrically-engineered hollow lumen, with adaptability to both large and small intestines. These intestinal tissues demonstrated representative human responses by permitting continuous accumulation of mucous secretions on the epithelial surface, establishing low oxygen tension in the lumen and interacting with gut-colonizing bacteria. The newly developed 3D intestine model enabled months-long sustained access to these intestinal functions in vitro, readily integrable with a multitude of different organ mimics and will therefore ensure a reliable ex vivo tissue system for studies in a broad context of human intestinal diseases and treatments.
Super-Resolution Imaging Conditions for enhanced Yellow Fluorescent Protein (eYFP) Demonstrated on DNA Origami Nanorulers
Authors: Jusuk Ija , Vietz Carolin , Raab Mario , Dammeyer Thorben , Tinnefeld Philip 
Published: September 2015

AbstractPhotostability is one of the crucial properties of a fluorophore which strongly influences the quality of single molecule-based super-resolution imaging. Enhanced yellow fluorescent protein (eYFP) is one of the most widely used versions of fluorescent proteins in modern cell biology exhibiting fast intrinsic blinking and reversible photoactivation by UV light. Here, we developed an assay for studying photostabilization of single eYFP molecules with respect to fast blinking and demonstrated a 6-fold enhanced photostability of single eYFP molecules with a beneficial influence on the blinking kinetics under oxygen removal and addition of aliphatic thiols (dSTORM-buffer). Conjugation to single stranded DNA and immobilization via DNA hybridization on a DNA origami 12 helix bundle in aqueous solution allowed photophyiscal studies of eYFP at the single-molecule level and at close to physiological conditions. The benefit of improved photophysical properties for localization-based super-resolution microscopy is demonstrated and quantitatively characterized by imaging 12 helix bundle DNA origami nanorulers with binding sites at designed distances of 160 and 100 nm and by imaging microtubules in fixed mammalian Vero cells.
Standardization of the antibody-dependent respiratory burst assay with human neutrophils and Plasmodium falciparum malaria
Authors: Llewellyn David , Miura Kazutoyo , Fay Michael P. , Williams Andrew R. , Murungi Linda M. , Shi Jianguo , Hodgson Susanne H. , Douglas Alexander D. , Osier Faith H. , Fairhurst Rick M. , Diakite Mahamadou , Pleass Richard J. , Long Carole A. , Draper Simon J. 
Published: September 2015

AbstractThe assessment of naturally-acquired and vaccine-induced immunity to blood-stagePlasmodium falciparummalaria is of long-standing interest. However, the field has suffered from a paucity ofin vitroassays that reproducibly measure the anti-parasitic activity induced by antibodies in conjunction with immune cells. Here we optimize the antibody-dependent respiratory burst (ADRB) assay, which assesses the ability of antibodies to activate the release of reactive oxygen species from human neutrophils in response toP. falciparumblood-stage parasites. We focus particularly on assay parameters affecting serum preparation and concentration and importantly assess reproducibility. Our standardized protocol involves testing each serum sample in singlicate with three independent neutrophil donors and indexing responses against a standard positive control of pooled hyper-immune Kenyan sera. The protocol can be used to quickly screen large cohorts of samples from individuals enrolled in immuno-epidemiological studies or clinical vaccine trials and requires only 6 μL of serum per sample. Using a cohort of 86 samples, we show that malaria-exposed individuals induce higher ADRB activity than malaria-naïve individuals. The development of the ADRB assay complements the use of cell-independent assays in blood-stage malaria, such as the assay of growth inhibitory activity and provides an important standardized cell-based assay in the field.
Shape-controlled synthesis and influence of W doping and oxygen nonstoichiometry on the phase transition of VO2
Authors: Chen Ru , Miao Lei , Liu Chengyan , Zhou Jianhua , Cheng Haoliang , Asaka Toru , Iwamoto Yuji , Tanemura Sakae 
Published: September 2015

AbstractMonoclinic VO2(M) in nanostructure is a prototype material for interpreting correlation effects in solids with fully reversible phase transition and for the advanced applications to smart devices. Here, we report a facile one-step hydrothermal method for the controlled growth of single crystalline VO2(M/R) nanorods. Through tuning the hydrothermal temperature, duration of the hydrothermal time and W-doped level, single crystalline VO2(M/R) nanorods with controlled aspect ratio can be synthesized in large quantities and the crucial parameter for the shape-controlled synthesis is the W-doped content. The dopant greatly promotes the preferential growth of (110) to form pure phase VO2(R) nanorods with high aspect ratio for the W-doped level = 2.0 at% sample. The shape-controlled process of VO2(M/R) nanorods upon W-doping are systematically studied. Moreover, the phase transition temperature (Tc) of VO2 depending on oxygen nonstoichiometry is investigated in detail.
M1 Muscarinic Receptor Deficiency Attenuates Azoxymethane-Induced Chronic Liver Injury in Mice
Authors: Rachakonda Vikrant , Jadeja Ravirajsinh N. , Urrunaga Nathalie H. , Shah Nirish , Ahmad Daniel , Cheng Kunrong , Twaddell William S. , Raufman Jean-Pierre , Khurana Sandeep 
Published: September 2015

AbstractCholinergic nervous system regulates liver injury. However, the role of M1 muscarinic receptors (M1R) in modulating chronic liver injury is uncertain. To address this gap in knowledge we treated M1R-deficient and WT mice with azoxymethane (AOM) for six weeks and assessed liver injury responses 14 weeks after the last dose of AOM. Compared to AOM-treated WT mice, M1R-deficient mice had attenuated liver nodularity, fibrosis and ductular proliferation, α-SMA staining and expression of α1 collagen, Tgfβ-R, Pdgf-R, Mmp-2, Timp-1 and Timp-2. In hepatocytes, these findings were associated with reductions of cleaved caspase-3 staining and Tnf-α expression. In response to AOM treatment, M1R-deficient mice mounted a vigorous anti-oxidant response by upregulating Gclc and Nqo1 expression and attenuating peroxynitrite generation. M1R-deficient mouse livers had increased expression of Trail-R2, a promotor of stellate cell apoptosis; dual staining for TUNNEL and α-SMA revealed increased stellate cells apoptosis in livers from M1R-deficient mice compared to those from WT. Finally, pharmacological inhibition of M1R reduced H2O2-induced hepatocyte apoptosis in vitro. These results indicate that following liver injury, anti-oxidant response in M1R-deficient mice attenuates hepatocyte apoptosis and reduces stellate cell activation, thereby diminishing fibrosis. Therefore, targeting M1R expression and activation in chronic liver injury may provide therapeutic benefit.
Protective role of ALDH2 against acetaldehyde-derived DNA damage in oesophageal squamous epithelium
Authors: Amanuma Yusuke , Ohashi Shinya , Itatani Yoshiro , Tsurumaki Mihoko , Matsuda Shun , Kikuchi Osamu , Nakai Yukie , Miyamoto Shin’ichi , Oyama Tsunehiro , Kawamoto Toshihiro , Whelan Kelly A. , Nakagawa Hiroshi , Chiba Tsutomu , Matsuda Tomonari , Muto Manabu 
Published: September 2015

AbstractAcetaldehyde is an ethanol-derived definite carcinogen that causes oesophageal squamous cell carcinoma (ESCC). Aldehyde dehydrogenase 2 (ALDH2) is a key enzyme that eliminates acetaldehyde and impairment of ALDH2 increases the risk of ESCC. ALDH2 is produced in various tissues including the liver, heart and kidney, but the generation and functional roles of ALDH2 in the oesophagus remain elusive. Here, we report that ethanol drinking increased ALDH2 production in the oesophagus of wild-type mice. Notably, levels of acetaldehyde-derived DNA damage represented by N2-ethylidene-2′-deoxyguanosine were higher in the oesophagus of Aldh2-knockout mice than in wild-type mice upon ethanol consumption. In vitro experiments revealed that acetaldehyde induced ALDH2 production in both mouse and human oesophageal keratinocytes. Furthermore, the N2-ethylidene-2′-deoxyguanosine levels increased in both Aldh2-knockout mouse keratinocytes and ALDH2-knockdown human keratinocytes treated with acetaldehyde. Conversely, forced production of ALDH2 sharply diminished the N2-ethylidene-2′-deoxyguanosine levels. Our findings provide new insight into the preventive role of oesophageal ALDH2 against acetaldehyde-derived DNA damage.
Micelle PCR reduces chimera formation in 16S rRNA profiling of complex microbial DNA mixtures
Authors: Boers Stefan A. , Hays John P. , Jansen Ruud 
Published: September 2015

Abstract16S rRNA gene profiling has revolutionized the field of microbial ecology. Many researchers in various fields have embraced this technology to investigate bacterial compositions of samples derived from many different ecosystems. However, it is important to acknowledge the current limitations and drawbacks of 16S rRNA gene profiling. Although sample handling, DNA extraction methods and the choice of universal 16S rRNA gene PCR primers are well known factors that could seriously affect the final results of microbiota profiling studies, inevitable amplification artifacts, such as chimera formation and PCR competition, are seldom appreciated. Here we report on a novel micelle based amplification strategy, which overcomes these limitations via the clonal amplification of targeted DNA molecules. Our results show that micelle PCR drastically reduces chimera formation by a factor of 38 (1.5% vs. 56.9%) compared with traditional PCR, resulting in improved microbial diversity estimates. In addition, compartmentalization during micelle PCR prevents PCR competition due to unequal amplification rates of different 16S template molecules, generating robust and accurate 16S microbiota profiles required for comparative studies (e.g. longitudinal surveys).
Background-free in-vivo Imaging of Vitamin C using Time-gateable Responsive Probe
Authors: Song Bo , Ye Zhiqing , Yang Yajie , Ma Hua , Zheng Xianlin , Jin Dayong , Yuan Jingli 
Published: September 2015

AbstractSensitive optical imaging of active biomolecules in the living organism requires both a molecular probe specifically responsive to the target and a high-contrast approach to remove the background interference from autofluorescence and light scatterings. Here, a responsive probe for ascorbic acid (vitamin C) has been developed by conjugating two nitroxide radicals with a long-lived luminescent europium complex. The nitroxide radical withholds the probe on its “off” state (barely luminescent), until the presence of vitamin C will switch on the probe by forming its hydroxylamine derivative. The probe showed a linear response to vitamin C concentration with a detection limit of 9.1 nM, two orders of magnitude lower than that achieved using electrochemical methods. Time-gated luminescence microscopy (TGLM) method has further enabled real-time, specific and background-free monitoring of cellular uptake or endogenous production of vitamin C and mapping of vitamin C in living Daphnia magna. This work suggests a rational design of lanthanide complexes for background-free small animal imaging of biologically functional molecules.
Novel lithium-nitrogen compounds at ambient and high pressures
Authors: Shen Yanqing , Oganov Artem R. , Qian Guangri , Zhang Jin , Dong Huafeng , Zhu Qiang , Zhou Zhongxiang 
Published: September 2015

AbstractUsing ab initio evolutionary simulations, we predict the existence of five novel stable Li-N compounds at pressures from 0 to 100 GPa (Li13N, Li5N, Li3N2, LiN2and LiN5). Structures of these compounds contain isolated N atoms, N2dimers, polyacetylene-like N chains and N5rings, respectively. The structure of Li13N consists of Li atoms and Li12N icosahedra (with N atom in the center of the Li12icosahedron) – such icosahedra are not described by Wade-Jemmis electron counting rules and are unique. Electronic structure of Li-N compounds is found to dramatically depend on composition and pressure, making this system ideal for studying metal-insulator transitions. For example, the sequence of lowest-enthalpy structures of LiN3shows peculiar electronic structure changes with increasing pressure: metal-insulator-metal-insulator. This work also resolves the previous controversies of theory and experiment on Li2N2.
Three-dimensional morphogenesis of MDCK cells induced by cellular contractile forces on a viscous substrate
Authors: Imai Misako , Furusawa Kazuya , Mizutani Takeomi , Kawabata Kazushige , Haga Hisashi 
Published: September 2015

AbstractSubstrate physical properties are essential for many physiological events such as embryonic development and 3D tissue formation. Physical properties of the extracellular matrix such as viscoelasticity and geometrical constraints are understood as factors that affect cell behaviour. In this study, we focused on the relationship between epithelial cell 3D morphogenesis and the substrate viscosity. We observed that Madin-Darby Canine Kidney (MDCK) cells formed 3D structures on a viscous substrate (Matrigel). The structures appear as a tulip hat. We then changed the substrate viscosity by genipin (GP) treatment. GP is a cross-linker of amino groups. Cells cultured on GP-treated-matrigel changed their 3D morphology in a substrate viscosity-dependent manner. Furthermore, to elucidate the spatial distribution of the cellular contractile force, localization of mono-phosphorylated and di-phosphorylated myosin regulatory light chain (P-MRLCs) was visualized by immunofluorescence. P-MRLCs localized along the periphery of epithelial sheets. Treatment with Y-27632, a Rho-kinase inhibitor, blocked the P-MRLCs localization at the edge of epithelial sheets and halted 3D morphogenesis. Our results indicate that the substrate viscosity, the substrate deformation and the cellular contractile forces induced by P-MRLCs play crucial roles in 3D morphogenesis.
Dynamical crossover line in supercritical water
Authors: Fomin Yu. D. , Ryzhov V. N. , Tsiok E. N. , Brazhkin V. V. 
Published: September 2015

AbstractDynamical crossover in water is studied by means of computer simulation. The crossover temperature is calculated from the behavior of velocity autocorrelation functions. The results are compared with experimental data. It is shown that the qualitative behavior of the dynamical crossover line is similar to the melting curve behavior. Importantly, the crossover line belongs to experimentally achievable (P, T) region which stimulates the experimental investigation in this field.
Parity and endometrial cancer risk: a meta-analysis of epidemiological studies
Authors: Wu Qi-Jun , Li Yuan-Yuan , Tu Chao , Zhu Jingjing , Qian Ke-Qing , Feng Tong-Bao , Li Changwei , Wu Lang , Ma Xiao-Xin 
Published: September 2015

AbstractThe association between parity and endometrial cancer risk is inconsistent from observational studies. We aimed to quantitatively assess the relationship by summarizing all relevant epidemiological studies. PubMed (MEDLINE), Embase and Scopus were searched up to February 2015 for eligible case–control studies and prospective studies. Random-effects model was used to pool risk estimations. Ten prospective studies, 35 case-control studies and 1 pooled analysis of 10 cohort and 14 case-control studies including 69681 patients were identified. Pooled analysis revealed that there was a significant inverse association between parity and risk of endometrial cancer (relative risk (RR) for parous versus nulliparous: 0.69, 95% confidence interval (CI) 0.65–0.74; I2 = 76.9%). By evaluating the number of parity, we identified that parity number of 1, 2 or 3 versus nulliparous demonstrated significant negative association (RR = 0.73, 95% CI 0.64–0.84, I2 = 88.3%; RR = 0.62, 95% CI 0.53–0.74, I2 = 92.1%; and RR = 0.68, 95% CI 0.65–0.70, I2 = 20.0% respectively). The dose-response analysis suggested a nonlinear relationship between the number of parity and endometrial cancer risk. The RR decreased when the number of parity increased. This meta-analysis suggests that parity may be associated with a decreased risk of endometrial cancer. Further studies are warranted to replicate our findings.