bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bifunctional quorum-quenching and antibiotic-acylase MacQ forms a 170-kDa capsule-shaped molecule containing spacer polypeptides
Authors: Yasutake Yoshiaki , Kusada Hiroyuki , Ebuchi Teppei , Hanada Satoshi , Kamagata Yoichi , Tamura Tomohiro , Kimura Nobutada 
Published: August 2017

AbstractUnderstanding the molecular mechanisms of bacterial antibiotic resistance will help prepare against further emergence of multi-drug resistant strains. MacQ is an enzyme responsible for the multi-drug resistance of Acidovorax sp. strain MR-S7. MacQ has acylase activity against both N-acylhomoserine lactones (AHLs), a class of signalling compounds involved in quorum sensing, and β-lactam antibiotics. Thus, MacQ is crucial as a quencher of quorum sensing as well as in conferring antibiotic resistance in Acidovorax. Here, we report the X-ray structures of MacQ in ligand-free and reaction product complexes. MacQ forms a 170-kDa capsule-shaped molecule via face-to-face interaction with two heterodimers consisting of an α-chain and a β-chain, generated by the self-cleaving activity of a precursor polypeptide. The electron density of the spacer polypeptide in the hollow of the molecule revealed the close orientation of the peptide-bond atoms of Val20SP-Gly21SP to the active-site, implying a role of the residues in substrate binding. In mutational analyses, uncleaved MacQ retained degradation activity against both AHLs and penicillin G. These results provide novel insights into the mechanism of self-cleaving maturation and enzymatic function of N-terminal nucleophile hydrolases.
Three-dimensional plasmonic Ag/TiO2 nanocomposite architectures on flexible substrates for visible-light photocatalytic activity
Authors: Zhao Zhi-Jun , Hwang Soon Hyoung , Jeon Sohee , Hwang Boyeon , Jung Joo-Yun , Lee Jihye , Park Sang-Hu , Jeong Jun-Ho 
Published: August 2017

AbstractIn this study, a periodic three-dimensional (3D) Ag/TiO2nanocomposite architecture of nanowires was fabricated on a flexible substrate to enhance the plasmonic photocatalytic activity of the composite. Layer-by-layer nanofabrication based on nanoimprint lithography, vertical e-beam evaporation, nanotransfer, and nanowelding was applied in a new method to create different 3D Ag/TiO2nanocomposite architectures. The fabricated samples were characterized by scanning electron microscopy, transmission electron microscopy, focused ion-beam imaging, X-ray photoelectron spectrometry, and UV–visible spectroscopy. The experiment indicated that the 3D nanocomposite architectures could effectively enhance photocatalytic activity in the degradation of methylene blue solution under visible light irradiation. We believe that our method is efficient and stable, which could be applied to various fields, including photocatalysis, solar energy conversion, and biotechnology.
Ibuprofen and ketoprofen potentiate UVA-induced cell death by a photosensitization process
Authors: Bignon Emmanuelle , Marazzi Marco , Besancenot Vanessa , Gattuso Hugo , Drouot Guillaume , Morell Christophe , Eriksson Leif A. , Grandemange Stephanie , Dumont Elise , Monari Antonio 
Published: August 2017

AbstractNonsteroidal 2-arylproprionic acids are widely used, over-the-counter, anti-inflammatory drugs. Photosensitivity is a commonly overlooked adverse effect of these drugs. Based on the combined use of cell viability assays and molecular modeling, we prove and rationalize the photochemical pathways triggering photosensitization for two drugs, ibuprofen and ketoprofen. As its parent compound benzophenone, ketoprofen produces singlet oxygen, upon triplet manifold population. However, ibuprofen and ketoprofen photodissociate and hence may generate two highly reactive radicals. The formation of metastable aggregates between the two drugs and B-DNA is also directly probed by molecular dynamics. Our approach characterizes the coupled influence of the drug’s intrinsic photochemistry and the interaction pattern with DNA. The photosensitization activity of nonsteroidal 2-arylproprionic acids, being added to gels and creams for topical use, should be crucially analyzed and rationalized to enact the proper preventive measures.
Analysis of mononucleotides by tandem mass spectrometry: investigation of fragmentation pathways for phosphate- and ribose-modified nucleotide analogues
Authors: Strzelecka Dominika , Chmielinski Sebastian , Bednarek Sylwia , Jemielity Jacek , Kowalska Joanna 
Published: August 2017

AbstractSynthetic nucleotide and nucleic acid analogues are useful research tools and modern therapeutics. Hence, methods for the rapid and unambiguous identification of mononucleotides derived from organic syntheses or biological materials are of broad interest. Here, we analysed over 150 mononucleotides (mostly nucleoside 5′-mono-, 5′-di-, and 5′-triphosphates) and their structurally related nucleobase-, phosphate-, and ribose-modified analogues by electrospray tandem mass spectrometry (ESI/MS/MS), identifying characteristic fragmentation ions that may be helpful in structure determination. While positive-ion mode yielded fragments derived mainly from nucleobases, negative-ion mode provided insight into the structures of phosphoryl and phosphoribosyl moieties, enabling the determination of structural features such as the number of phosphate groups and the presence of ribose or phosphate substitutions. Based on these data, we proposed fragmentation pathways that were confirmed by experiments with [18O]-isotopologues. We demonstrated the utility of ESI(−)/MS/MS in the analysis of structurally related compounds by analysing isomeric and isobaric nucleotides and applying ESI(−)/MS/MS to rapid identification of nucleotide synthesis products. We formulated general rules regarding nucleotide structure–fragmentation pattern relationships and indicating characteristic fragmentation ions for the interpretation of ESI(−)/MS/MS spectra of nucleotides and their analogues. The ESI(−)/MS/MS spectra of all nucleotides are available in an on-line database, msTide, at www.msTide-db.com.
Chemotherapy with cisplatin: insights into intracellular pH and metabolic landscape of cancer cells in vitro and in vivo
Authors: Shirmanova Marina V. , Druzhkova Irina N. , Lukina Maria M. , Dudenkova Varvara V. , Ignatova Nadezhda I. , Snopova Ludmila B. , Shcheslavskiy Vladislav I. , Belousov Vsevolod V. , Zagaynova Elena V. 
Published: August 2017

AbstractAlthough cisplatin plays a central role in cancer chemotherapy, the mechanisms of cell response to this drug have been unexplored. The present study demonstrates the relationships between the intracellular pH (pHi), cell bioenergetics and the response of cervical cancer to cisplatin. pHi was measured using genetically encoded sensor SypHer2 and metabolic state was accessed by fluorescence intensities and lifetimes of endogenous cofactors NAD(P)H and FAD. Our data support the notion that cisplatin induces acidification of the cytoplasm early after the treatment. We revealedin vitrothat a capacity of cells to recover and maintain alkaline pHi after the initial acidification is the crucial factor in mediating the cellular decision to survive and proliferate at a vastly reduced rate or to undergo cell death. Additionally, we showed for the first time that pHi acidification occurs after prolonged therapyin vitroandin vivo, and this, likely, favors metabolic reorganization of cells. A metabolic shift from glycolysis towards oxidative metabolism accompanied the cisplatin-induced inhibition of cancer cell growthin vitroandin vivo. Overall, these findings contribute to an understanding of the mechanisms underlying the responsiveness of an individual cell and tumor to therapy and are valuable for developing new therapeutic strategies.
TRAF4 promotes lung cancer aggressiveness by modulating tumor microenvironment in normal fibroblasts
Authors: Kim EunGi , Kim Wanyeon , Lee Sungmin , Chun Jahyun , Kang JiHoon , Park Gaeul , Han IkJoon , Yang Hee Jung , Youn HyeSook , Youn BuHyun 
Published: August 2017

AbstractNormal fibroblasts surrounding tumor cells play a crucial role in cancer progression through formation of the tumor microenvironment. Because factors secreted from normal fibroblasts can modulate the tumor microenvironment, it is necessary to identify key factors associated with regulation of secreted factors and to investigate the molecular mechanisms contributing to the tumor microenvironment formation process. In this study, we found that radiation induced the expression and K63-linkage poly-ubiquitination of TRAF4 in normal lung fibroblasts. The K63-linkage poly-ubiquitinated TRAF4 formed complexes with NOX2 or NOX4 by mediating phosphorylated p47-phox in normal lung fibroblasts. Moreover, we showed that TRAF4 stabilized NOX complexes by decreasing lysosomal degradation of NOX2 and NOX4 after irradiation. NOX complexes increased endosomal ROS levels that were permeable into cytoplasm, leading to NF-κB-mediated ICAM1 up-regulation. Soluble ICAM1 was subsequently secreted into conditioned media of radiation-activated normal lung fibroblasts. The conditioned media from irradiated normal fibroblasts enhanced proliferation and epithelial-mesenchymal transition of non-small cell lung cancer cells both in vitro and in vivo. These results demonstrate that TRAF4 in irradiated fibroblasts is positively associated with aggressiveness of adjacent cancer cells by altering the tumor microenvironment. Thus, we suggest that regulation of TRAF4 might be a promising strategy for cancer therapy.
Characterization and structural determination of a new anti-MET function-blocking antibody with binding epitope distinct from the ligand binding domain
Authors: DiCara Danielle M. , Chirgadze Dimitri Y. , Pope Anthony R. , Karatt-Vellatt Aneesh , Winter Anja , Slavny Peter , van den Heuvel Joop , Parthiban Kothai , Holland Jane , Packman Len C. , Mavria Georgia , Hoffmann Jens , Birchmeier Walter , Gherardi Ermanno , McCafferty John 
Published: August 2017

AbstractThe growth and motility factor Hepatocyte Growth Factor/Scatter Factor (HGF/SF) and its receptor, the product of the MET proto-oncogene, promote invasion and metastasis of tumor cells and have been considered potential targets for cancer therapy. We generated a new Met-blocking antibody which binds outside the ligand-binding site, and determined the crystal structure of the Fab in complex with its target, which identifies the binding site as the Met Ig1 domain. The antibody, 107_A07, inhibited HGF/SF-induced cell migration and proliferation in vitro and inhibited growth of tumor xenografts in vivo. In biochemical assays, 107_A07 competes with both HGF/SF and its truncated splice variant NK1 for MET binding, despite the location of the antibody epitope on a domain (Ig1) not reported to bind NK1 or HGF/SF. Overlay of the Fab-MET crystal structure with the InternalinB-MET crystal structure shows that the 107_A07 Fab comes into close proximity with the HGF/SF-binding SEMA domain when MET is in the “compact”, InternalinB-bound conformation, but not when MET is in the “open” conformation. These findings provide further support for the importance of the “compact” conformation of the MET extracellular domain, and the relevance of this conformation to HGF/SF binding and signaling.
Low TIM3 expression indicates poor prognosis of metastatic prostate cancer and acts as an independent predictor of castration resistant status
Authors: Wu Junlong , Lin Guowen , Zhu Yao , Zhang Hailiang , Shi Guohai , Shen Yijun , Zhu Yiping , Dai Bo , Ye Dingwei 
Published: August 2017

AbstractT cell immunoglobulin 3 (TIM3) is a cell surface star molecule expressed on T cells, and also marks dysfunctional CD8+ T cells in various kinds of cancers. However, there are few studies focusing on the expression of TIM3 in tumor cells. In our study, we recruited 139 patients with metastatic prostate cancer (mPCa) who received transurethral resection of the prostate (TURP) consecutively to examine whether TIM3 expression level is associated with overall survival (OS) in mPCa patients. Immunohistochemistry was performed to determine TIM3 expression in prostate cancer tissues and then patients were divided into two groups. In multivariate Cox analysis, we revealed that mPCa patients with negative TIM3 expression, younger age, no radiotherapy, higher Gleason score, higher cT stage and patients of mCRPC had a shorter OS. Therefore, a predictive nomogram was generated with identified independent prognostic factors to assess patients’ OS at 3 years. Multivariate logistic regression revealed that higher cT stage, higher Gleason score and low TIM3 expression were independent predictors of metastatic castration resistant prostate cancer (mCRPC). In conclusion, low expression level of TIM3 in prostate cancer tissues is an independent prognostic factor of poor prognosis for mPCa patients, and also an independent predictor of mCRPC.
A Faraday laser lasing on Rb 1529 nm transition
Authors: Chang Pengyuan , Peng Huanfa , Zhang Shengnan , Chen Zhangyuan , Luo Bin , Chen Jingbiao , Guo Hong 
Published: August 2017

AbstractWe present the design and performance characterization of a Faraday laser directly lasing on the Rb 1529 nm transition (Rb, 5P3/2 − 4D5/2) with high stability, narrow spectral linewidth and low cost. This system does not need an additional frequency-stabilized pump laser as a prerequisite to preparing Rb atom from 5S to 5P excited state. Just by using a performance-improved electrodeless discharge lamp-based excited-state Faraday anomalous dispersion optical filter (LESFADOF), we realized a heterogeneously Faraday laser with the frequency corresponding to atomic transition, working stably over a range of laser diode (LD) current from 85 mA to 171 mA and the LD temperature from 11 °C to 32 °C, as well as the 24-hour long-term frequency fluctuation range of no more than 600 MHz. Both the laser linewidth and relative intensity noisy (RIN) are measured. The Faraday laser lasing on Rb 1529 nm transition (telecom C-band) can be applied to further research on metrology, microwave photonics and optical communication systems. Besides, since the transitions correspongding to the populated excited-states of alkali atoms within lamp are extraordinarily rich, this scheme can increase the flexibility for choosing proper wavelengths for Faraday laser and greatly expand the coverage of wavelength corresponding to atomic transmission for laser frequency stabilization.
NMR and Rheological Study of Anion Size Influence on the Properties of Two Imidazolium-based Ionic Liquids
Authors: Green Stephen M. , Ries Michael E. , Moffat Jamie , Budtova Tatiana 
Published: August 2017

AbstractNMR self-diffusion and relaxation, coupled with viscosity, were used to study the properties and structure of two imidazolium-based ionic liquids, 1-ethyl-3-methylimidazolium acetate [C2MIM][OAc] and 1-ethyl-3-methylimidazolium octanoate [C2MIM][OOct]. The experimental results point to the formation of different types of aggregates in each ionic liquid. These aggregates are small and stable under flow and temperature in [C2MIM][OAc], whereas the aggregates are large and sensitive to flow and temperature in [C2MIM][OOct]. In the latter case the size of aggregates decreases both under flow and temperature increase.
Composite Photocatalysts Containing BiVO4 for Degradation of Cationic Dyes
Authors: Pingmuang Kanlaya , Chen Jun , Kangwansupamonkon Wiyong , Wallace Gordon G. , Phanichphant Sukon , Nattestad Andrew 
Published: August 2017

AbstractThe creation of composite structures is a commonly employed approach towards enhanced photocatalytic performance, with one of the key rationales for doing this being to separate photoexcited charges, affording them longer lifetimes in which to react with adsorbed species. Here we examine three composite photocatalysts using either WO3, TiO2 or CeO2 with BiVO4 for the degradation of model dyes Methylene Blue and Rhodamine B. Each of these materials (WO3, TiO2 or CeO2) has a different band edge energy offset with respect to BiVO4, allowing for a systematic comparison of these different arrangements. It is seen that while these offsets can afford beneficial charge transfer (CT) processes, they can also result in the deactivation of certain reactions. We also observed the importance of localized dye concentrations, resulting from a strong affinity between it and the surface, in attaining high overall photocatalytic performance, a factor not often acknowledged. It is hoped in the future that these observations will assist in the judicious selection of semiconductors for use as composite photocatalysts.
Excellent low-voltage operating flexible ferroelectric organic transistor nonvolatile memory with a sandwiching ultrathin ferroelectric film
Authors: Xu Ting , Xiang Lanyi , Xu Meili , Xie Wenfa , Wang Wei 
Published: August 2017

AbstractThe high operating voltage is a primary issue preventing the commercial application of the ferroelectric organic field-effect transistor (Fe-OFET) nonvolatile memory (NVM). In this work, we propose a novel route to resolve this issue by employing two ultrathin AlOX interfacial layers sandwiching an ultrathin ferroelectric polymer film with a low coercive field, in the fabricated flexible Fe-OFET NVM. The operation voltage of Fe-OFET NVMs decreases with the downscaling thickness of the ferroelectric film. By inserting two ultrathin AlOX interfacial layers at both sides of the ultrathin ferroelectric film, not only the gate leakage is prominently depressed but also the mobility is greatly improved. Excellent memory performances, with large mobility of 1.7 ~ 3.3 cm2 V−1 s−1, high reliable memory switching endurance over 2700 cycles, high stable data storage retention capability over 8 × 104 s with memory on-off ratio larger than 102, are achieved at the low operating voltage of 4 V, which is the lowest value reported to data for all Fe-OFET NVMs. Simultaneously, outstanding mechanical fatigue property with the memory performances maintaining well over 7500 bending cycles at a bending radius of 5.5 mm is also achieved in our flexible FE-OFET NVM.
The profile of selected single nucleotide polymorphisms in patients with hypertension and heart failure with preserved and mid-range ejection fraction
Authors: Bielecka-Dabrowa Agata , Sakowicz Agata , Pietrucha Tadeusz , Misztal Małgorzata , Chruściel Piotr , Rysz Jacek , Banach Maciej 
Published: August 2017

AbstractThe study aimed to assess the clinical significance of selected single nucleotide polymorphisms (SNPs) in patients with diastolic heart failure (HF): inflammation [-174 G/C Interleukin -6 (IL-6) rs1800795, tumor necrosis factor (TNF)-608 G/A rs1800629], fibrosis [Arg25Pro transforming growth factor β (TGF β) rs1800471], endothelial function [-786 T/C nitric oxide synthase (NOS) rs2070744], glucose and lipid metabolism [Pro12Ala peroxisome proliferator activated receptor (PPAR)γ rs1801282], and vitamin D metabolism [cytochrome P450 27B1 (CYP27B1) C-1260A].110 patients with HF with preserved and mid-range ejection fraction (HFpEF and HFmrEF) were recruited. GG homozygotes in 174 G/C of IL6 polymorphism are characterized by higher values of estimated glomerular filtration rate based on the study Modification of Diet in Renal Disease (eGFR MDRD) and C allele in the NOS polymorphism and AA profile in C-1260A of CYP27B1 polymorphism correlated with a lower eGFR (MDRD). In multivariate analysis the CG genotype for 174 G/C of IL-6 and allele A in C-1260A of CYP27B1 are the only SNPs independently associated with worse course of HFpEF and HFmrEF. These data confirm the importance of the selected SNPs in aggravation and complications of hypertension.
Thickness-controlled electronic structure and thermoelectric performance of ultrathin SnS2 nanosheets
Authors: Li Jun , Shen Jinni , Ma Zuju , Wu Kechen 
Published: August 2017

AbstractThe thermoelectric conversion efficiency of a material relies on a dimensionless parameter (ZT = S2σT/κ). It is a great challenge in enhancing the ZT value basically due to that the related transport factors of most of the bulk materials are inter-conditioned to each other, making it very difficult to simultaneously optimize these parameters. In this report, the negative correlation between power factor and thermal conductivity of nano-scaled SnS2 multilayers is predicted by high-level first-principle computations combined with Boltzmann transport theory. By diminishing the thickness of SnS2 nanosheet to about 3 L, the S and σ along a direction simultaneously increase whereas κ decreases, achieving a high ZT value of 1.87 at 800 K. The microscopic mechanisms for this unusual negative correlation in nano-scaled two dimensional (2D) material are elucidated and attributed to the quantum confinement effect. The results may open a way to explore the high ZT thermoelectric nano-devices for the practical thermoelectric applications.
Experimental Study of Hysteresis behavior of Foam Generation in Porous Media
Authors: Kahrobaei S. , Vincent-Bonnieu S. , Farajzadeh R. 
Published: August 2017

AbstractFoam can be used for gas mobility control in different subsurface applications. The success of foam-injection process depends on foam-generation and propagation rate inside the porous medium. In some cases, foam properties depend on the history of the flow or concentration of the surfactant, i.e., the hysteresis effect. Foam may show hysteresis behavior by exhibiting multiple states at the same injection conditions, where coarse-textured foam is converted into strong foam with fine texture at a critical injection velocity or pressure gradient. This study aims to investigate the effects of injection velocity and surfactant concentration on foam generation and hysteresis behavior as a function of foam quality. We find that the transition from coarse-foam to strong-foam (i.e., the minimum pressure gradient for foam generation) is almost independent of flowrate, surfactant concentration, and foam quality. Moreover, the hysteresis behavior in foam generation occurs only at high-quality regimes and when the pressure gradient is below a certain value regardless of the total flow rate and surfactant concentration. We also observe that the rheological behavior of foam is strongly dependent on liquid velocity.
Functional and proteomic analysis of Ceratonova shasta (Cnidaria: Myxozoa) polar capsules reveals adaptations to parasitism
Authors: Piriatinskiy Gadi , Atkinson Stephen D. , Park Sinwook , Morgenstern David , Brekhman Vera , Yossifon Gilad , Bartholomew Jerri L. , Lotan Tamar 
Published: August 2017

AbstractMyxozoa is a diverse, speciose group of microscopic parasites, recently placed within the phylum Cnidaria. Myxozoans are highly reduced in size and complexity relative to free-living cnidarians, yet they have retained specialized organelles known as polar capsules, akin to the nematocyst stinging capsules of free-living species. Whereas in free-living cnidarians the stinging capsules are used for prey capture or defense, in myxozoans they have the essential function of initiating the host infection process. To explore the evolutionary adaptation of polar capsules to parasitism, we used as a model organism Ceratonova shasta, which causes lethal disease in salmonids. Here, we report the first isolation of C. shasta myxospore polar capsules using a tailored dielectrophoresis-based microfluidic chip. Using electron microscopy and functional analysis we demonstrated that C. shasta tubules have no openings and are likely used to anchor the spore to the host. Proteomic analysis of C. shasta polar capsules suggested that they have retained typical structural and housekeeping proteins found in nematocysts of jellyfish, sea anemones and Hydra, but have lost the most important functional group in nematocysts, namely toxins. Our findings support the hypothesis that polar capsules and nematocysts are homologous organelles, which have adapted to their distinct functions.