bluuebunny/crossref_metadata_2025_split huggingface dataset:
SAXS studies of RNA: structures, dynamics, and interactions with partners
Authors: Chen Yujie , Pollack Lois 
Published: April 2016

Small‐angle X‐ray scattering, SAXS, is a powerful and easily employed experimental technique that provides solution structures of macromolecules. The size and shape parameters derived from SAXS provide global structural information about these molecules in solution and essentially complement data acquired by other biophysical methods. As applied to protein systems, SAXS is a relatively mature technology: sophisticated tools exist to acquire and analyze data, and to create structural models that include dynamically flexible ensembles. Given the expanding appreciation of RNA’s biological roles, there is a need to develop comparable tools to characterize solution structures of RNA, including its interactions with important biological partners. We review the progress toward achieving this goal, focusing on experimental and computational innovations. The use of multiphase modeling, absolute calibration and contrast variation methods, among others, provides new and often unique ways of visualizing this important biological molecule and its essential partners: ions, other RNAs, or proteins. WIREs RNA 2016, 7:512–526. doi: 10.1002/wrna.1349This article is categorized under:

RNA Structure and Dynamics > RNA Structure, Dynamics, and Chemistry
RNA Interactions with Proteins and Other Molecules > RNA–Protein Complexes
Regulatory RNAs/RNAi/Riboswitches > Riboswitches
Convex polygons as carriers
Authors: Shephard G. C. 
Published: April 2016

We shall use the word ‘polyhedron’ to mean a connected, simply-connected 3-polytope of positive (non-zero) volume. The idea of thenetof a polyhedronPis well known. For example, the regular octahedron has eleven distinct nets, three of which are shown in Figure 1. A net consists of three parts:(a) A plane connected and simply-connected polygonQ(denoted by heavy lines in the diagrams), known as thecarrierof the net;(b) A set of lines knownas, fold-linesin the interior ofQ;(c) A labelling of the edges ofQ.If one cutsQout of paper or similar material, folds it along the fold-lines, and then pastes together edges with matching labels, one obtains a model of the polyhedronP.We say that a net isconvexif, and only if, its carrierQis convex.
Some properties of Kiepert lines of a triangle
Authors: Fox Michael 
Published: April 2016

This article describes an investigation into Kiepert lines, and leads to some surprising and little-known relationships between the Fermat, Napoleon and Vecten points of a triangle.If we draw similar isosceles triangles A'BC, B'CA and C'AB outwards on the sides of a given scalene triangle ABC as in Figure 1, Kiepert's theorem tells us that the lines A'A, B'B and C'C meet in a single point - a Kiepert point [1, Chapter 11]. Since its position depends on the common base angles θ of the isosceles triangles, I label it K(θ), taking θ as the parameter of this point.
Inverse kinematic solutions of 6-D.O.F. biopolymer segments
Authors: Kim Jin Seob , Chirikjian Gregory S. 
Published: April 2016

SUMMARYWe present two methods to find all the possible conformations of short six degree-of-freedom segments of biopolymers which satisfy end constraints in position and orientation. One of our methods is motivated by inverse kinematic solution techniques which have been developed for “general” 6R serial robotic manipulators. However, conventional robot kinematics methods are not directly applicable to the geometry of polymers, which can be treated as a degenerate case where all the “link lengths” are zero. Here, we propose a method which extends the elimination method of Kohli and Osvatic. This method can be applied directly to the geometry of biopolymers. We also propose a heuristic method based on a Lie-group-theoretic description. In this method, we utilize inverse iterations of the Jacobian matrix to obtain all conformations which satisfy end constraints. This can be easily implemented for both the general 6R manipulator and polymers. Although the extended elimination method is computationally faster than the Jacobian method, in cases where some of the joint angles are 180° (i.e., where the elimination method fails), we combine these two methods effectively to obtain the full set of inverse kinematic solutions. We demonstrate our approach with several numerical examples.
A premature low-birth-weight infant with congenital complete atrioventricular block and myocarditis successfully treated by staged pacemaker implantation
Authors: Fujioka Tao , Nii Masaki , Tanaka Yasuhiko 
Published: April 2016

AbstractCongenital complete atrioventricular block is a known lethal condition. Although antenatal diagnosis and the technical advances of pacemaker treatment have reduced its mortality, treatment of premature babies with significant myocardial damage remains a challenge. In this paper, we report the case of a premature low-birth-weight infant with congenital complete atrioventricular block and extremely low ventricular rate, fetal hydrops, and myocarditis who was successfully treated with staged permanent pacemaker implantation.
Determining Projections of Grain Boundaries from Diffraction Data in Transmission Electron Microscope
Authors: Kiss Ákos K. , Lábár János L. 
Published: April 2016

AbstractGrain boundaries (GB) are characterized by disorientation of the neighboring grains and the direction of the boundary plane between them. A new approach presented here determines the projection of GB that can be used to determine the latter one. The novelty is that an additional parameter of GB is quantified in addition to the ones provided by the orientation maps, namely the width of the projection of the GB is measured from the same set of diffraction patterns that were recorded for the orientation map, without the need to take any additional images. The diffraction patterns are collected in nanobeam diffraction mode in a transmission electron microscope, pixel-by-pixel, from an area containing two neighboring grains and the boundary between them. In our case, the diffraction patterns were recorded using the beam scanning function of a commercially available system (ASTAR). Our method is based on non-negative matrix factorization applied to the mentioned set of diffraction patterns. The method is encoded in a MATLAB environment, making the results easy to interpret and visualize. The measured GB-projection width is used to determine the orientation of the GB-plane, as given in the study by Kiss et al.
Evaluation of a video, telephone follow-ups, and an online forum as components of a psychoeducational intervention for caregivers of persons with advanced cancer
Authors: Leow Mabel Q.H. , Chan Sally W.C. 
Published: April 2016

AbstractObjective:Our aim was to evaluate caregivers' perceptions of a video, telephone follow-up, and online forum as components of a psychoeducational intervention.Method:Qualitative semistructured face-to-face interviews were conducted with 12 participants two weeks post-intervention. The study was conducted from September of 2012 to May of 2015. Family caregivers were recruited from four home hospice organizations (HCA Hospice Care, Metta Hospice, Singapore Cancer Centre, and Agape Methodist Hospice) and the National Cancer Centre outpatient clinic in Singapore. A purposive sample was employed, and participants were recruited until data saturation. Qualitative interviews were transcribed verbatim. Transcripts were coded and analyzed using content analysis. Two of the research team members were involved in the data analysis.Results:Two-thirds of participants were females (n= 8). Their ages ranged from 22 to 67 (mean = 50.50,SD= 11.53). About two-thirds were married (n= 7). Most participants were caring for a parent (n= 10), one for a spouse, and one for her mother-in-law. Caregivers favored the use of video for delivery of educational information. They liked the visual and audio aspects of the video. The ability to identify with the caregiver and scenarios in the video helped in the learning process. They appreciated telephone follow-ups from healthcare professionals for informational and emotional support. The online forum as a platform for sharing of information and provision of support was not received well by the caregivers in this study. The reasons for this included their being busy, not being computer savvy, rarely surfing the internet, and not feeling comfortable sharing with strangers on an online platform.Significance of Results:This study provided insight into caregivers' perceptions of various components of a psychoeducational intervention. It also gave us a better understanding of how future psychoeducational interventions and support for caregivers of persons with advanced cancer could be provided.
DIVISION A COMMISSION 19: ROTATION OF THE EARTH
Authors: Huang Chengli , Gross Richard , Seitz Florian , Schuh Harald , Bizouard Christian , Chao Ben , Kosek Wieslaw , Salstein David , Zharov Vladimir , Titov Oleg , Richter Bernd , Malkin Zinovy 
Published: April 2016

AbstractThe activities and some research progress of IAU Commission 19 (C19) - Rotation of the Earth - in the past triennial term (2012-2015) is reported in this paper, including the scientific session and business meeting of C19, as well as a business meeting of the IAU/IAG Joint Working Group of “Theory of Earth Rotation” (JWG_ThER) during the XXIX IAU General Assembly in Hawaii, USA. Three reports of JWG_ThER progress, IERS and IAG, eleven reports of national projects and individual institutions, a short summary of the history and heritage of C19, and an Overview of the status and outlook of new Commission A2 are also presented.
DIVISION F COMMISSION 15: PHYSICAL STUDY OF COMETS AND MINOR PLANETS
Authors: Bockelée-Morvan Dominique , Gil-Hutton Ricardo , Hestroffer Daniel , Belskaya Irina N. , Davidsson Björn J. R. , Dotto Elisabetta , Fitzsimmons Alan , Hestroffer Daniel , Kawakita Hideyo , Mothe-Diniz Thais , Licandro Javier , Wooden Diane H. , Yano Hajime 
Published: April 2016

AbstractCommission 15 of the International Astronomical Union (IAU), entitled Physical Study of Comets and Minor Planets, was founded in 1935 and dissolved in 2015, following the reorganization of IAU. In 80 years of Commission 15, tremendous progress has been made on the knowledge of these objets, thanks to the combined efforts of ground- and space-based observations, space mission rendezvous and flybys, laboratory simulation and analyses of returned samples, and theoretical and numerical modeling. Together with dynamical studies of the Solar System, this discipline has provided a much deeper understanding of how the Solar System formed and evolved. We present a legacy report of Commission 15, which highlights key milestones in the exploration and knowledge of the small bodies of the Solar System.
The rate of quasiparticle recombination probes the onset of coherence in cuprate superconductors
Authors: Hinton J. P. , Thewalt E. , Alpichshev Z. , Mahmood F. , Koralek J. D. , Chan M. K. , Veit M. J. , Dorow C. J. , Barišić N. , Kemper A. F. , Bonn D. A. , Hardy W. N. , Liang Ruixing , Gedik N. , Greven M. , Lanzara A. , Orenstein J. 
Published: April 2016

AbstractIn the underdoped copper-oxides, high-temperature superconductivity condenses from a nonconventional metallic ”pseudogap” phase that exhibits a variety of non-Fermi liquid properties. Recently, it has become clear that a charge density wave (CDW) phase exists within the pseudogap regime. This CDW coexists and competes with superconductivity (SC) below the transition temperature Tc, suggesting that these two orders are intimately related. Here we show that the condensation of the superfluid from this unconventional precursor is reflected in deviations from the predictions of BSC theory regarding the recombination rate of quasiparticles. We report a detailed investigation of the quasiparticle (QP) recombination lifetime, τqp, as a function of temperature and magnetic field in underdoped HgBa2CuO4+δ (Hg-1201) and YBa2Cu3O6+x (YBCO) single crystals by ultrafast time-resolved reflectivity. We find that τqp(T ) exhibits a local maximum in a small temperature window near Tc that is prominent in underdoped samples with coexisting charge order and vanishes with application of a small magnetic field. We explain this unusual, non-BCS behavior by positing that Tc marks a transition from phase-fluctuating SC/CDW composite order above to a SC/CDW condensate below. Our results suggest that the superfluid in underdoped cuprates is a condensate of coherently-mixed particle-particle and particle-hole pairs.
Testing the island effect on phenotypic diversification: insights from the Hemidactylus geckos of the Socotra Archipelago
Authors: Garcia-Porta Joan , Šmíd Jiří , Sol Daniel , Fasola Mauro , Carranza Salvador 
Published: April 2016

AbstractIsland colonization is often assumed to trigger extreme levels of phenotypic diversification. Yet, empirical evidence suggests that it does not always so. In this study we test this hypothesis using a completely sampled mainland-island system, the arid clade ofHemidactylus, a group of geckos mainly distributed across Africa, Arabia and the Socotra Archipelago. To such purpose, we generated a new molecular phylogeny of the group on which we mapped body size and head proportions. We then explored whether island and continental taxa shared the same morphospace and differed in their disparities and tempos of evolution. Insular species produced the most extreme sizes of the radiation, involving accelerated rates of evolution and higher disparities compared with most (but not all) of the continental groups. In contrast, head proportions exhibited constant evolutionary rates across the radiation and similar disparities in islands compared with the continent. These results, although generally consistent with the notion that islands promote high morphological disparity, reveal at the same time a complex scenario in which different traits may experience different evolutionary patterns in the same mainland-island system and continental groups do not always present low levels of morphological diversification compared to insular groups.
Evaluation of in vitro and in vivo biocompatibility of a myo-inositol hexakisphosphate gelated polyaniline hydrogel in a rat model
Authors: Sun Kwang-Hsiao , Liu Zhao , Liu Changjian , Yu Tong , Shang Tao , Huang Chen , Zhou Min , Liu Cheng , Ran Feng , Li Yun , Shi Yi , Pan Lijia 
Published: April 2016

AbstractRecent advances in understanding the interaction between electricity and cells/biomolecules have generated great interest in developing biocompatible electrically conductive materials. In this study, we investigated the biocompatibility of a myo-inositol hexakisphosphate gelated polyaniline hydrogel using in vitro and in vivo experiments in a rat model. The polyaniline hydrogel was used to coat a polycaprolactone scaffold and was cultured with rat endothelial progenitor cells differentiated from rat adipose-derived stem cells. Compared with the control sample on a pristine polycaprolactone scaffold, the treated polyaniline hydrogel had the same non-poisonous/cytotoxicity grade, enhanced cell adhesion, and a higher cell proliferation/growth rate. In implant studies, the polyaniline hydrogel sample induced milder inflammatory responses than did the control at the same time points. Combining the advantages of a biocompatible hydrogel and an organic conductor, the inositol phosphate-gelated polyaniline hydrogel could be used in bioelectronics applications such as biosensors, neural probes, cell stimulators, medical electrodes, tissue engineering, and electro-controlled drug delivery.
A novel and highly sensitive nanocatalytic surface plasmon resonance-scattering analytical platform for detection of trace Pb ions
Authors: Ye Lingling , Wen Guiqing , Ouyang Huixiang , Liu Qingye , Liang Aihui , Jiang Zhiliang 
Published: April 2016

AbstractGold nanoparticles (AuNP) have catalysis on the reaction of HAuCl4-H2O2. The produced AuNP have strong resonance Rayleigh scattering (RRS) effect and surface-enhanced resonance Raman scattering (SERS) effect when Victoria blue B (VBB) and rhodamine S (RhS) were used as probes. The increased RRS/SERS intensity respond linearly with the concentration of gold nanoparticles (AuNPB) which synthesized by NaBH4 over 0.038–76 ng/mL, 19–285 ng/mL, 3.8–456 ng/mL respectively. Four kinds of tested nanoparticles have catalysis on the HAuCl4-H2O2 particles reaction. Thus, a novel nanocatalysis surface plasmon resonance-scattering (SPR-S) analytical platform was developed for AuNP. The DNAzyme strand hybridized with the substrate strand to form double-stranded DNA (dsDNA) which couldn’t protect AuNPc to aggregate to AuNPc aggregations, having strong RRS effect. Upon addition of Pb2+, dsDNA could be cracked by Pb2+ to produce single-stranded DNA (ssDNA) that adsorbed on the AuNPc surface to form AuNPc-ssDNA conjugates. The conjugates have strong catalysis on HAuCl4-H2O2 reaction. With increased Pb2+ concentration, the concentration of AuNPc-ssDNA increased and lead to the catalytic activity stronger. The increased RRS intensity responds linearly with Pb2+ concentration over 16.7–666.7 nmol/L. The SERS intensity responded linearly with the concentration of Pb2+ over 50–500 nmol/L.
Characterisation of synovial fluid and infrapatellar fat pad derived mesenchymal stromal cells: The influence of tissue source and inflammatory stimulus
Authors: Garcia John , Wright Karina , Roberts Sally , Kuiper Jan Herman , Mangham Chas , Richardson James , Mennan Claire 
Published: April 2016

AbstractThe infrapatellar fat pad (FP) and synovial fluid (SF) in the knee serve as reservoirs of mesenchymal stromal cells (MSCs) with potential therapeutic benefit. We determined the influence of the donor on the phenotype of donor matched FP and SF derived MSCs and examined their immunogenic and immunomodulatory properties before and after stimulation with the pro-inflammatory cytokine interferon-gamma (IFN-γ). Both cell populations were positive for MSC markers CD73, CD90 and CD105 and displayed multipotency. FP-MSCs had a significantly faster proliferation rate than SF-MSCs. CD14 positivity was seen in both FP-MSCs and SF-MSCs and was positively correlated to donor age but only for SF-MSCs. Neither cell population was positive for the co-stimulatory markers CD40, CD80 and CD86, but both demonstrated increased levels of human leukocyte antigen-DR (HLA-DR) following IFN-γ stimulation. HLA-DR production was positively correlated with donor age for FP-MSCs but not SF-MSCs. The immunomodulatory molecule, HLA-G, was constitutively produced by both cell populations, unlike indoleamine 2, 3-dioxygenase which was only produced following IFN-γ stimulation. FP and SF are accessible cell sources which could be utilised in the treatment of cartilage injuries, either by transplantation following ex-vivo expansion or endogenous targeting and mobilisation of cells close to the site of injury.
Islands of spatially discordant APD alternans underlie arrhythmogenesis by promoting electrotonic dyssynchrony in models of fibrotic rat ventricular myocardium
Authors: Majumder Rupamanjari , Engels Marc C. , de Vries Antoine A. F. , Panfilov Alexander V. , Pijnappels Daniël A. 
Published: April 2016

AbstractFibrosis and altered gap junctional coupling are key features of ventricular remodelling and are associated with abnormal electrical impulse generation and propagation. Such abnormalities predispose to reentrant electrical activity in the heart. In the absence of tissue heterogeneity, high-frequency impulse generation can also induce dynamic electrical instabilities leading to reentrant arrhythmias. However, because of the complexity and stochastic nature of such arrhythmias, the combined effects of tissue heterogeneity and dynamical instabilities in these arrhythmias have not been explored in detail. Here, arrhythmogenesis was studied using in vitro and in silico monolayer models of neonatal rat ventricular tissue with 30% randomly distributed cardiac myofibroblasts and systematically lowered intercellular coupling achieved in vitro through graded knockdown of connexin43 expression. Arrhythmia incidence and complexity increased with decreasing intercellular coupling efficiency. This coincided with the onset of a specialized type of spatially discordant action potential duration alternans characterized by island-like areas of opposite alternans phase, which positively correlated with the degree of connexinx43 knockdown and arrhythmia complexity. At higher myofibroblast densities, more of these islands were formed and reentrant arrhythmias were more easily induced. This is the first study exploring the combinatorial effects of myocardial fibrosis and dynamic electrical instabilities on reentrant arrhythmia initiation and complexity.
The gut microbiome and degradation enzyme activity of wild freshwater fishes influenced by their trophic levels
Authors: Liu Han , Guo Xianwu , Gooneratne Ravi , Lai Ruifang , Zeng Cong , Zhan Fanbin , Wang Weimin 
Published: April 2016

AbstractVertebrate gut microbiome often underpins the metabolic capability and provides many beneficial effects on their hosts. However, little was known about how host trophic level influences fish gut microbiota and metabolic activity. In this study, more than 985,000 quality-filtered sequences from 24 16S rRNA libraries were obtained and the results revealed distinct compositions and diversities of gut microbiota in four trophic categories. PCoA test showed that gut bacterial communities of carnivorous and herbivorous fishes formed distinctly different clusters in PCoA space. Although fish in different trophic levels shared a large size of OTUs comprising a core microbiota community, at the genus level a strong distinction existed. Cellulose-degrading bacteria Clostridium, Citrobacter and Leptotrichia were dominant in the herbivorous, while Cetobacterium and protease-producing bacteria Halomonas were dominant in the carnivorous. PICRUSt predictions of metagenome function revealed that fishes in different trophic levels affected the metabolic capacity of their gut microbiota. Moreover, cellulase and amylase activities in herbivorous fishes were significantly higher than in the carnivorous, while trypsin activity in the carnivorous was much higher than in the herbivorous. These results indicated that host trophic level influenced the structure and composition of gut microbiota, metabolic capacity and gut content enzyme activity.
GPER signalling in both cancer-associated fibroblasts and breast cancer cells mediates a feedforward IL1β/IL1R1 response
Authors: De Marco Paola , Lappano Rosamaria , Francesco Ernestina Marianna De , Cirillo Francesca , Pupo Marco , Avino Silvia , Vivacqua Adele , Abonante Sergio , Picard Didier , Maggiolini Marcello 
Published: April 2016

AbstractCancer-associated fibroblasts (CAFs) contribute to the malignant aggressiveness through secreted factors like IL1β, which may drive pro-tumorigenic inflammatory phenotypes mainly acting via the cognate receptor named IL1R1. Here, we demonstrate that signalling mediated by the G protein estrogen receptor (GPER) triggers IL1β and IL1R1 expression in CAFs and breast cancer cells, respectively. Thereby, ligand-activation of GPER generates a feedforward loop coupling IL1β induction by CAFs to IL1R1 expression by cancer cells, promoting the up-regulation of IL1β/IL1R1 target genes such as PTGES, COX2, RAGE and ABCG2. This regulatory interaction between the two cell types induces migration and invasive features in breast cancer cells including fibroblastoid cytoarchitecture and F-actin reorganization. A better understanding of the mechanisms involved in the regulation of pro-inflammatory cytokines by GPER-integrated estrogen signals may be useful to target these stroma-cancer interactions.