bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microsphere Assisted Super-resolution Optical Imaging of Plasmonic Interaction between Gold Nanoparticles
Authors: Hou Beibei , Xie Mengran , He Ruoyu , Ji Minbiao , Trummer Sonja , Fink Rainer H. , Zhang Luning 
Published: October 2017

AbstractConventional far-field microscopy cannot directly resolve the sub-diffraction spatial distribution of localized surface plasmons in metal nanostructures. Using BaTiO3 microspheres as far-field superlenses by collecting the near-field signal, we can map the origin of enhanced two-photon photoluminescence signal from the gap region of gold nanosphere dimers and gold nanorod dimers beyond the diffraction limit, on a conventional far-field microscope. As the angle θ between dimer’s structural axis and laser polarisation changes, photoluminescence intensity varies with a cos4θ function, which agrees quantitatively with numerical simulations. An optical resolution of about λ/7 (λ: two-photon luminescence central wavelength) is demonstrated at dimer’s gap region.
Comparative Network Analysis of Patients with Non-Small Cell Lung Cancer and Smokers for Representing Potential Therapeutic Targets
Authors: Pazhouhandeh Mehrdad , Samiee Fatemeh , Boniadi Tahereh , Khedmat Abbas Fadaei , Vahedi Ensieh , Mirdamadi Mahsa , Sigari Naseh , Siadat Seyed Davar , Vaziri Farzam , Fateh Abolfazl , Ajorloo Faezeh , Tafsiri Elham , Ghanei Mostafa , Mahboudi Fereidoun , Rahimi Jamnani Fatemeh 
Published: October 2017

AbstractCigarette smoking is the leading cause of lung cancer worldwide. In this study, we evaluated the serum autoantibody (AAb) repertoires of non-small cell lung cancer (NSCLC) patients and smokers (SM), leading to the identification of overactivated pathways and hubs involved in the pathogenesis of NSCLC. Surface- and solution-phase biopanning were performed on immunoglobulin G purified from the sera of NSCLC and SM groups. In total, 20 NSCLC- and 12 SM-specific peptides were detected, which were used to generate NSCLC and SM protein datasets. NSCLC- and SM-related proteins were visualized using STRING and Gephi, and their modules were analyzed using Enrichr. By integrating the overrepresented pathways such as pathways in cancer, epithelial growth factor receptor, c-Met, interleukin-4 (IL-4) and IL-6 signaling pathways, along with a set of proteins (e.g. phospholipase D (PLD), IL-4 receptor, IL-17 receptor, laminins, collagens, and mucins) into the PLD pathway and inflammatory cytokines network as the most critical events in both groups, two super networks were made to elucidate new aspects of NSCLC pathogenesis and to determine the influence of cigarette smoking on tumour formation. Taken together, assessment of the AAb repertoires using a systems biology approach can delineate the hidden events involved in various disorders.
Graphene oxide electrodeposited electrode enhances start-up and selective enrichment of exoelectrogens in bioelectrochemical systems
Authors: Alonso R. M. , San-Martín M. I. , Sotres A. , Escapa A. 
Published: October 2017

AbstractThis study seeks to assess the impact that the anodic electrodeposition of graphene oxide (GO) has on the start-up process and on the development of microbial communities on the anode of BESs. The GO electrodeposited electrodes were characterised in abiotic conditions to verify the extent of the modification and were then transferred to a bioelectrochemical reactor. Results showed that the modified electrode allowed for a reduced start-up time compared to the control electrode. After three months, high throughput sequencing was performed, revealing that electrochemically reduced graphene oxide acts as a selective agent toward exoelectrogenic bacteria as Geobacter. Overall, this study shows that GO modified electrodes enhance biofilm build up in BES.
Improved emission of SiV diamond color centers embedded into concave plasmonic core-shell nanoresonators
Authors: Szenes András , Bánhelyi Balázs , Szabó Lóránt Zs. , Szabó Gábor , Csendes Tibor , Csete Mária 
Published: October 2017

AbstractConfiguration of three different concave silver core-shell nanoresonators was numerically optimized to enhance the excitation and emission of embedded silicon vacancy (SiV) diamond color centers simultaneously. Conditional optimization was performed to ensure ~20–30–40 and 50% apparent quantum efficiency (cQE) of SiV color centers. The enhancement spectra, as well as the near-field and charge distribution were inspected to uncover the underlying nanophotonical phenomena. The conditionally optimized coupled systems were qualified by the product of the radiative rate enhancements at the excitation and emission, which is nominated as Px factor. The optimized spherical core-shell nanoresonator containing a centralized emitter is capable of enhancing the emission considerably via bonding dipolar resonance. The Px factor is 529-fold with 49.7% cQE at the emission. Decentralization of the emitter leads to appearance of higher order nonradiative multipolar modes. Transversal and longitudinal dipolar resonance of the optimized ellipsoidal core-shell resonator was tuned to the excitation and emission, which results in 6.2∙105Px factor with 50.6% cQE at the emission. Rod-shaped concave core-shell nanoresonators exploit similar transversal and longitudinal dipolar resonance, moreover they enhance the fluorescence more significantly due to their antenna-like geometry. Px factor indicating 8.34∙105 enhancement is achievable while the cQE is 50.3% at the emission.
Endogenous physical regulation of population density in the freshwater protozoan Paramecium caudatum
Authors: Fels Daniel 
Published: October 2017

AbstractStudies confirm physical long-range cell-cell communication, most evidently based on electromagnetic fields. Effects concern induction or inhibition of cell growth. Their natural function is unclear. With the protozoan Paramecium caudatum I tested whether the signals regulate cell density and are electromagnetic. Up to 300 cells/mL, cell growth in clones of this study is decreasingly pronounced. Using cuvettes as chemical barriers enabling physical communication I placed 5 indicator cells/mL, the inducer populations, into smaller cuvettes that stand in bigger and contained 50, 100, 200 or 300 cells/mL. Under conditions of total darkness such pairs were mutually exposed for 48 hours. The hypothesis was that indicator cells, too, grow less the more neighbor cells there are. The bigger inducer populations were in the beginning the less they grew. The indicator populations grew accordingly; the more cells they were surrounded by the less they grew. The suppressing neighbors-effect disappeared when inner cuvettes were shielded by graphite known to shield electromagnetic radiation from GHz to PHz, i.e. to absorb energy from microwaves to light. These are the first results demonstrating non-contact physical quorum sensing for cell population density regulation. I assume rules intrinsic to electromagnetic fields interacting with matter and life.
Gene expression atlas of fruit ripening and transcriptome assembly from RNA-seq data in octoploid strawberry (Fragaria × ananassa)
Authors: Sánchez-Sevilla José F. , Vallarino José G. , Osorio Sonia , Bombarely Aureliano , Posé David , Merchante Catharina , Botella Miguel A. , Amaya Iraida , Valpuesta Victoriano 
Published: October 2017

AbstractRNA-seq has been used to perform global expression analysis of the achene and the receptacle at four stages of fruit ripening, and of the roots and leaves of strawberry (Fragaria × ananassa). About 967 million reads and 191 Gb of sequence were produced, using Illumina sequencing. Mapping the reads in the related genome of the wild diploid Fragaria vesca revealed differences between the achene and receptacle development program, and reinforced the role played by ethylene in the ripening receptacle. For the strawberry transcriptome assembly, a de novo strategy was followed, generating separate assemblies for each of the ten tissues and stages sampled. The Trinity program was used for these assemblies, resulting in over 1.4 M isoforms. Filtering by a threshold of 0.3 FPKM, and doing Blastx (E-value < 1 e-30) against the UniProt database of plants reduced the number to 472,476 isoforms. Their assembly with the MIRA program (90% homology) resulted in 26,087 contigs. From these, 91.34 percent showed high homology to Fragaria vesca genes and 87.30 percent Fragaria iinumae (BlastN E-value < 1 e-100). Mapping back the reads on the MIRA contigs identified polymorphisms at nucleotide level, using FREEBAYES, as well as estimate their relative abundance in each sample.
Enhanced Cell Adhesion on a Nano-Embossed, Sticky Surface Prepared by the Printing of a DOPA-Bolaamphiphile Assembly Ink
Authors: Lee Chaemyeong , Kim Seung-Hyun , Jang Jae-Hyung , Lee Sang-Yup 
Published: October 2017

AbstractInspired by adhesive mussel proteins, nanospherical self-assemblies were prepared from bolaamphiphiles containing 3,4-dihydroxyphenylalanine (DOPA) moieties, and a suspension of the bolaamphiphile assemblies was used for the preparation of a patterned surface that enhanced cell adhesion and viability. The abundant surface-exposed catechol groups on the robust bolaamphiphile self-assemblies were responsible for their outstanding adhesivity to various surfaces and showed purely elastic mechanical behaviour in response to tensile stress. Compared to other polydopamine coatings, the spherical DOPA-bolaamphiphile assemblies were coated uniformly and densely on the surface, yielding a nano-embossed surface. Cell culture tests on the surface modified by DOPA-bolaamphiphiles also showed enhanced cellular adhesivity and increased viability compared to surfaces decorated with other catecholic compounds. Furthermore, the guided growth of a cell line was demonstrated on the patterned surface, which was prepared by inkjet printing using a suspension of the self-assembled particles as an ink. The self-assembly of DOPA-bolaamphiphiles shows that they are a promising adhesive, biocompatible material with the potential to modify various substances.
DDX3 regulates endoplasmic reticulum stress-induced ATF4 expression
Authors: Adjibade Pauline , Grenier St-Sauveur Valérie , Bergeman Jonathan , Huot Marc-Etienne , Khandjian Edouard W. , Mazroui Rachid 
Published: October 2017

AbstractAccumulation of unfolded and potentially toxic proteins in the endoplasmic reticulum (ER) activates a cell stress adaptive response, which involves a reprogramming of general gene expression. ATF4 is a master stress-induced transcription factor that orchestrates gene expression in cells treated with various ER stress inducers including those used to treat cancers. ER stress-induced ATF4 expression occurs mainly at the translational level involving the activity of the phosphorylated (P) translation initiation factor (eIF) eIF2α. While it is well established that under ER stress PeIF2α drives ATF4 expression through a specialised mode of translation re-initiation, factors (e.g. RNA-binding proteins and specific eIFs) involved in PeIF2α-mediated ATF4 translation remain unknown. Here we identified the RNA-binding protein named DDX3 as a promotor of ATF4 expression in cancer cells treated with sorafenib, an ER stress inducer used as a chemotherapeutic. Depletion experiments showed that DDX3 is required for PeIF2α-mediated ATF4 expression. Luciferase and polyribosomes assays showed that DDX3 drives ER stress-induced ATF4 mRNA expression at the translational level. Protein-interaction assays showed that DDX3 binds the eIF4F complex, which we found to be required for ER stress-induced ATF4 expression. This study thus showed that PeIF2α-mediated ATF4 mRNA translation requires DDX3 as a part of the eIF4F complex.
Identification of a Different Agonist-Binding Site and Activation Mechanism of the Human P2Y1 Receptor
Authors: Li Yang , Yin Can , Liu Pi , Li Dongmei , Lin Jianping 
Published: October 2017

AbstractThe human P2Y1 receptor (P2Y1R) is a purinergic G-protein-coupled receptor (GPCR) that functions as a receptor for adenosine 5′-diphosphate (ADP). An antagonist of P2Y1R might potentially have antithrombotic effects, whereas agonists might serve as antidiabetic agents. On the basis of the antagonist-bound MRS2500-P2Y1R crystal structure, we constructed computational models of apo-P2Y1R and the agonist-receptor complex 2MeSADP-P2Y1R. We then performed conventional molecular dynamics (cMD) and accelerated molecular dynamics (aMD) simulations to study the conformational dynamics after binding with agonist/antagonist as well as the P2Y1R activation mechanism. We identified a new agonist-binding site of P2Y1R that is consistent with previous mutagenesis data. This new site is deeper than those of the agonist ADP in the recently simulated ADP-P2Y1R structure and the antagonist MRS2500 in the MRS2500-P2Y1R crystal structure. During P2Y1R activation, the cytoplasmic end of helix VI shifts outward 9.1 Å, the Ser1463.47-Tyr2375.58 hydrogen bond breaks, a Tyr2375.58-Val2626.37 hydrogen bond forms, and the conformation of the χ1 rotamer of Phe2696.44 changes from parallel to perpendicular to helix VI. The apo-P2Y1R system and the MRS2500-P2Y1R system remain inactive. The newly identified agonist binding site and activation mechanism revealed in this study may aid in the design of P2Y1R antagonists/agonists as antithrombotic/antidiabetic agents, respectively.
Computer-aided evaluation of the correlation between MRI morphology and immunohistochemical biomarkers or molecular subtypes in breast cancer
Authors: Jiang Sen , Hong You-Jia , Zhang Fan , Li Yang-Kang 
Published: October 2017

AbstractStudies using tumor circularity (TC), a quantitative MRI morphologic index, to evaluate breast cancer are scarce. The purpose of this study is to evaluate the correlation between TC and immunohistochemical biomarkers or molecular subtypes in breast cancer. 146 patients with 150 breast cancers were selected. All tumors were confirmed by histopathology and examined by 3.0T MRI. TC was calculated by computer-aided software. The associations between TC and patient age, tumor size, histological grade, molecular subtypes, and immunohistochemical biomarkers including estrogen receptor (ER), progesterone receptor (PR), human epidermal growth factor receptor 2 (HER2), and Ki67 were analyzed. TC correlated inversely with tumor size (r = −0.224, P < 0.001), ER (r = −0.490, P < 0.001) and PR (r = −0.484, P < 0.001). However, TC correlated positively with Ki67 (r = 0.332, P < 0.001) and histological grade (r = 0.309, P < 0.001). In multiple linear regression analysis, tumor size, ER, PR and Ki67 were independent influential factors of TC. Compared with HER2-overexpressed (61.6%), luminal A (54.7%) and luminal B (52.3%) subtypes, triple-negative breast cancer (TNBC) showed the highest score of TC (70.8%, P < 0.001). Our study suggests that TC can be used as an imaging biomarker to predict the aggressiveness of newly diagnosed breast cancers. TNBC seems to present as an orbicular appearance when comparing with other subtypes.
Localised genetic heterogeneity provides a novel mode of evolution in dsDNA phages
Authors: Magill Damian J. , Kucher Phillip A. , Krylov Victor N. , Pleteneva Elena A. , Quinn John P. , Kulakov Leonid A. 
Published: October 2017

AbstractThe Red Queen hypothesis posits that antagonistic co-evolution between interacting species results in recurrent natural selection via constant cycles of adaptation and counter-adaptation. Interactions such as these are at their most profound in host-parasite systems, with bacteria and their viruses providing the most intense of battlefields. Studies of bacteriophage evolution thus provide unparalleled insight into the remarkable elasticity of living entities. Here, we report a novel phenomenon underpinning the evolutionary trajectory of a group of dsDNA bacteriophages known as the phiKMVviruses. Employing deep next generation sequencing (NGS) analysis of nucleotide polymorphisms we discovered that this group of viruses generates enhanced intraspecies heterogeneity in their genomes. Our results show the localisation of variants to genes implicated in adsorption processes, as well as variation of the frequency and distribution of SNPs within and between members of the phiKMVviruses. We link error-prone DNA polymerase activity to the generation of variants. Critically, we show trans-activity of this phenomenon (the ability of a phiKMVvirus to dramatically increase genetic variability of a co-infecting phage), highlighting the potential of phages exhibiting such capabilities to influence the evolutionary path of other viruses on a global scale.
11β-hydroxysteroid dehydrogenase type 1 has no effect on survival during experimental malaria but affects parasitemia in a parasite strain-specific manner
Authors: Vandermosten L. , De Geest C. , Knoops S. , Thijs G. , Chapman K. E. , De Bosscher K. , Opdenakker G. , Van den Steen P. E. 
Published: October 2017

AbstractMalaria is a global disease associated with considerable mortality and morbidity. An appropriately balanced immune response is crucial in determining the outcome of malarial infection. The glucocorticoid (GC) metabolising enzyme, 11β-hydroxysteroid dehydrogenase-1 (11β-HSD1) converts intrinsically inert GCs into active GCs. 11β-HSD1 shapes endogenous GC action and is immunomodulatory. We investigated the role of 11β-HSD1 in two mouse models of malaria. 11β-HSD1 deficiency did not affect survival after malaria infection, but it increased disease severity and parasitemia in mice infected with Plasmodium chabaudi AS. In contrast, 11β-HSD1 deficiency rather decreased parasitemia in mice infected with the reticulocyte-restricted parasite Plasmodium berghei NK65 1556Cl1. Malaria-induced antibody production and pathology were unaltered by 11β-HSD1 deficiency though plasma levels of IL-4, IL-6 and TNF-α were slightly affected by 11β-HSD1 deficiency, dependent on the infecting parasite. These data suggest that 11β-HSD1 is not crucial for survival of experimental malaria, but alters its progression in a parasite strain-specific manner.
Alpha-1 antitrypsin augmentation therapy decreases miR-199a-5p, miR-598 and miR-320a expression in monocytes via inhibition of NFκB
Authors: Hassan Tidi , de Santi Chiara , Mooney Catherine , McElvaney Noel G. , Greene Catherine M. 
Published: October 2017

AbstractAlpha-1 antitrypsin (AAT) augmentation therapy involves infusion of plasma-purified AAT to AAT deficient individuals. Whether treatment affects microRNA expression has not been investigated. This study’s objectives were to evaluate the effect of AAT augmentation therapy on altered miRNA expression in monocytes and investigate the mechanism. Monocytes were isolated from non-AAT deficient (MM) and AAT deficient (ZZ) individuals, and ZZs receiving AAT. mRNA (qRT-PCR, microarray), miRNA (miRNA profiling, qRT-PCR), and protein (western blotting) analyses were performed. Twenty one miRNAs were differentially expressed 3-fold between ZZs and MMs. miRNA validation studies demonstrated that in ZZ monocytes receiving AAT levels of miR-199a-5p, miR-598 and miR-320a, which are predicted to be regulated by NFκB, were restored to levels similar to MMs. Validated targets co-regulated by these miRNAs were reciprocally increased in ZZs receiving AAT in vivo and in vitro. Expression of these miRNAs could be increased in ZZ monocytes treated ex vivo with an NFκB agonist and decreased by NFκB inhibition. p50 and p65 mRNA and protein were significantly lower in ZZs receiving AAT than untreated ZZs. AAT augmentation therapy inhibits NFκB and decreases miR-199a-5p, miR-598 and miR-320a in ZZ monocytes. These NFκB-inhibitory properties may contribute to the anti-inflammatory effects of AAT augmentation therapy.
RNA sequencing analysis of activated macrophages treated with the anti-HIV ABX464 in intestinal inflammation
Authors: Manchon Laurent , Chebli Karim , Papon Laura , Paul Conception , Garcel Aude , Campos Noëlie , Scherrer Didier , Ehrlich Hartmut , Hahne Michael , Tazi Jamal 
Published: October 2017

AbstractRNA-Seq enables the generation of extensive transcriptome information providing the capability to characterize transcripts (including alternative isoforms and polymorphism), to quantify expression and to identify differential regulation in a single experiment. To reveal the capacity of new anti-HIV ABX464 candidate in modulating the expression of genes, datasets were generated and validated using RNA-seq approach. This comprehensive dataset will be useful to deepen the comprehensive understanding of the progression of human immunodeficiency virus (HIV) associated with mucosal damage in the gastrointestinal (GI) tract and subsequent inflammation, providing an opportunity to generate new therapies, diagnoses, and preventive strategies.
Fossil group origins
Authors: Aguerri J. A. L. , Longobardi A. , Zarattini S. , Kundert A. , D’Onghia E. , Domínguez-Palmero L. 
Published: October 2017

Context. It is thought that fossil systems are relics of structure formation in the primitive Universe. They are galaxy aggregations that have assembled their mass at high redshift with few or no subsequent accretion. Observationally these systems are selected by large magnitude gaps between their 1st and 2nd ranked galaxies (Δm12). Nevertheless, there is still debate over whether or not this observational criterium selects dynamically evolved ancient systems.
Aims. We have studied the properties of the nearby fossil group RX J075243.6+455653 in order to understand the mass assembly of this system.
Methods. Deep spectroscopic observations allow us to construct the galaxy luminosity function (LF) of RX J075243.6+455653 down to Mr*+6. The analysis of the faint-end of the LF in groups and clusters provides valuable information about the mass assembly of the system. In addition, we have analyzed the nearby large-scale structure around this group.
Results. We identified 26 group members within r200 ~ 0.96 Mpc. These galaxies are located at Vc = 15551 ± 65 km s-1 and have a velocity dispersion of σc = 333 ± 46 km s-1. The X-ray luminosity of the group is LX = 2.2 × 1043 h70-2 erg s-1, resulting in a mass of M = 4.2 × 1013 h70-1 within 0.5r200. The group has Δm12 = 2.1 within 0.5r200, confirming the fossil nature of this system. RX J075243.6+455653 has a central brightest group galaxy (BGG) with Mr = −22.67, one of the faintest BGGs observed in fossil systems. The LF of the group shows a flat faint-end slope (α = −1.08 ± 0.33). This low density of dwarf galaxies is confirmed by the low value of the dwarf-to-giant ratio (DGR = 0.99 ± 0.49) for this system. Both the lack of dwarf galaxies and the low luminosity of the BGG suggests that RX J075243.6+455653 still has to accrete mass from its nearby environment. This mass accretion will be achieved because it is the dominant structure of a rich environment formed by several groups of galaxies (15) within ~ 7 Mpc from the group center and with ± 1000 km s-1.
Conclusions. RX J075243.6+455653 is a group of galaxies that has not yet completed the process of its mass assembly. This new mass accretion will change the fossil state of the group. This group is an example of a galaxy aggregation selected by a large magnitude gap but still in the process of the accretion of its mass.