bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transplantation of human-induced pluripotent stem cells carried by self-assembling peptide nanofiber hydrogel improves bone regeneration in rat calvarial bone defects
Authors: Hayashi Kamichika , Ochiai-Shino Hiromi , Shiga Takeaki , Onodera Shoko , Saito Akiko , Shibahara Takahiko , Azuma Toshifumi 
Published: January 2016

Abstract
Objectives/Aims:
The requisite conditions for successful bone tissue engineering are efficient stem cell differentiation into osteogenic cells and a suitable scaffold. In this study, we investigated in vivo bone regeneration from transplanted induced pluripotent stem cells (iPSCs).

Materials and Methods:
Two critical-sized calvarial bone defects were created in 36 rats. The surgical sites were randomly assigned to one of three treatments to test the healing effectiveness of the scaffold alone, scaffold with iPSCs or a salt solution as a control. The effectiveness of the treatments was evaluated after 2 or 4 weeks using radiographic and histological analyses of bone regeneration in the six groups.

Results:
Micro-computed tomography (CT) analysis of the bone defects found minimal bone regeneration with the salt solution and nanofiber scaffold and increased bone regeneration in defects repaired with iPSCs delivered in the nanofiber scaffold.

Conclusion:
Transplanted iPSCs encapsulated in a nanofiber scaffold can regenerate bone in critical-sized defects.
Ecological succession reveals potential signatures of marine–terrestrial transition in salt marsh fungal communities
Authors: Dini-Andreote Francisco , Pylro Victor Satler , Baldrian Petr , van Elsas Jan Dirk , Salles Joana Falcão 
Published: January 2016

Abstract
Marine-to-terrestrial transition represents one of the most fundamental shifts in microbial life. Understanding the distribution and drivers of soil microbial communities across coastal ecosystems is critical given the roles of microbes in soil biogeochemistry and their multifaceted influence on landscape succession. Here, we studied the fungal community dynamics in a well-established salt marsh chronosequence that spans over a century of ecosystem development. We focussed on providing high-resolution assessments of community composition, diversity and ecophysiological shifts that yielded patterns of ecological succession through soil formation. Notably, despite containing 10- to 100-fold lower fungal internal transcribed spacer abundances, early-successional sites revealed fungal richnesses comparable to those of more mature soils. These newly formed sites also exhibited significant temporal variations in β-diversity that may be attributed to the highly dynamic nature of the system imposed by the tidal regime. The fungal community compositions and ecophysiological assignments changed substantially along the successional gradient, revealing a clear signature of ecological replacement and gradually transforming the environment from a marine into a terrestrial system. Moreover, distance-based linear modelling revealed soil physical structure and organic matter to be the best predictors of the shifts in fungal β-diversity along the chronosequence. Taken together, our study lays the basis for a better understanding of the spatiotemporally determined fungal community dynamics in salt marshes and highlights their ecophysiological traits and adaptation in an evolving ecosystem.
A Phytophthora infestans RXLR effector targets plant PP1c isoforms that promote late blight disease
Authors: Boevink Petra C. , Wang Xiaodan , McLellan Hazel , He Qin , Naqvi Shaista , Armstrong Miles R. , Zhang Wei , Hein Ingo , Gilroy Eleanor M. , Tian Zhendong , Birch Paul R. J. 
Published: January 2016

AbstractPlant pathogens deliver effectors to alter host processes. Knowledge of how effectors target and manipulate host proteins is critical to understand crop disease. Here, we show that in planta expression of the RXLR effector Pi04314 enhances leaf colonization by Phytophthora infestans via activity in the host nucleus and attenuates induction of jasmonic and salicylic acid-responsive genes. Pi04314 interacts with three host protein phosphatase 1 catalytic (PP1c) isoforms, causing their re-localization from the nucleolus to the nucleoplasm. Re-localization of PP1c-1 also occurs during infection and is dependent on an R/KVxF motif in the effector. Silencing the PP1c isoforms or overexpression of a phosphatase-dead PP1c-1 mutant attenuates infection, demonstrating that host PP1c activity is required for disease. Moreover, expression of PP1c–1mut abolishes enhanced leaf colonization mediated by in planta Pi04314 expression. We argue that PP1c isoforms are susceptibility factors forming holoenzymes with Pi04314 to promote late blight disease.
Arrhythmogenesis in Timothy Syndrome is associated with defects in Ca2+-dependent inactivation
Authors: Dick Ivy E. , Joshi-Mukherjee Rosy , Yang Wanjun , Yue David T. 
Published: January 2016

AbstractTimothy Syndrome (TS) is a multisystem disorder, prominently featuring cardiac action potential prolongation with paroxysms of life-threatening arrhythmias. The underlying defect is a single de novo missense mutation in CaV1.2 channels, either G406R or G402S. Notably, these mutations are often viewed as equivalent, as they produce comparable defects in voltage-dependent inactivation and cause similar manifestations in patients. Yet, their effects on calcium-dependent inactivation (CDI) have remained uncertain. Here, we find a significant defect in CDI in TS channels, and uncover a remarkable divergence in the underlying mechanism for G406R versus G402S variants. Moreover, expression of these TS channels in cultured adult guinea pig myocytes, combined with a quantitative ventricular myocyte model, reveals a threshold behaviour in the induction of arrhythmias due to TS channel expression, suggesting an important therapeutic principle: a small shift in the complement of mutant versus wild-type channels may confer significant clinical improvement.
Pure-quartic solitons
Authors: Blanco-Redondo Andrea , de Sterke C. Martijn , Sipe J.E. , Krauss Thomas F. , Eggleton Benjamin J. , Husko Chad 
Published: January 2016

AbstractTemporal optical solitons have been the subject of intense research due to their intriguing physics and applications in ultrafast optics and supercontinuum generation. Conventional bright optical solitons result from the interaction of anomalous group-velocity dispersion and self-phase modulation. Here we experimentally demonstrate a class of bright soliton arising purely from the interaction of negative fourth-order dispersion and self-phase modulation, which can occur even for normal group-velocity dispersion. We provide experimental and numerical evidence of shape-preserving propagation and flat temporal phase for the fundamental pure-quartic soliton and periodically modulated propagation for the higher-order pure-quartic solitons. We derive the approximate shape of the fundamental pure-quartic soliton and discover that is surprisingly Gaussian, exhibiting excellent agreement with our experimental observations. Our discovery, enabled by precise dispersion engineering, could find applications in communications, frequency combs and ultrafast lasers.
DNA methylation outliers in normal breast tissue identify field defects that are enriched in cancer
Authors: Teschendorff Andrew E , Gao Yang , Jones Allison , Ruebner Matthias , Beckmann Matthias W. , Wachter David L. , Fasching Peter A. , Widschwendter Martin 
Published: January 2016

AbstractIdentifying molecular alterations in normal tissue adjacent to cancer is important for understanding cancer aetiology and designing preventive measures. Here we analyse the DNA methylome of 569 breast tissue samples, including 50 from cancer-free women and 84 from matched normal cancer pairs. We use statistical algorithms for dissecting intra- and inter-sample cellular heterogeneity and demonstrate that normal tissue adjacent to breast cancer is characterized by tens to thousands of epigenetic alterations. We show that their genomic distribution is non-random, being strongly enriched for binding sites of transcription factors specifying chromatin architecture. We validate the field defects in an independent cohort and demonstrate that over 30% of the alterations exhibit increased enrichment within matched cancer samples. Breast cancers highly enriched for epigenetic field defects, exhibit adverse clinical outcome. Our data support a model where clonal epigenetic reprogramming towards reduced differentiation in normal tissue is an important step in breast carcinogenesis.
E2F function in muscle growth is necessary and sufficient for viability in Drosophila
Authors: Zappia Maria Paula , Frolov Maxim V. 
Published: January 2016

AbstractThe E2F transcription factor is a key cell cycle regulator. However, the inactivation of the entire E2F family in Drosophila is permissive throughout most of animal development until pupation when lethality occurs. Here we show that E2F function in the adult skeletal muscle is essential for animal viability since providing E2F function in muscles rescues the lethality of the whole-body E2F-deficient animals. Muscle-specific loss of E2F results in a significant reduction in muscle mass and thinner myofibrils. We demonstrate that E2F is dispensable for proliferation of muscle progenitor cells, but is required during late myogenesis to directly control the expression of a set of muscle-specific genes. Interestingly, E2f1 provides a major contribution to the regulation of myogenic function, while E2f2 appears to be less important. These findings identify a key function of E2F in skeletal muscle required for animal viability, and illustrate how the cell cycle regulator is repurposed in post-mitotic cells.
Theory of antiskyrmions in magnets
Authors: Koshibae Wataru , Nagaosa Naoto 
Published: January 2016

AbstractSkyrmions and antiskyrmions are swirling topological magnetic textures realized as emergent particles in magnets. A skyrmion is stabilized by the Dzyaloshinskii–Moriya interaction in chiral magnets and/or a dipolar interaction in thin film magnets, which prefer the twist of the magnetic moments. Here we show by a numerical simulation of the Landau–Lifshitz–Gilbert equation that pairs of skyrmions and antiskyrmions are created from the helix state as the magnetic field is increased. Antiskyrmions are unstable and disappear immediately in chiral magnets, whereas they are metastable and survive in dipolar magnets. The collision between a skyrmion and an antiskyrmion in a dipolar magnet is also studied. It is found that the collision depends on their relative direction, and the pair annihilation occurs in some cases and only the antiskyrmion is destroyed in the other cases. These results indicate that the antiskyrmion offers a unique opportunity to study particles and antiparticles in condensed-matter systems.
Genome-wide association study and targeted metabolomics identifies sex-specific association of CPS1 with coronary artery disease
Authors: Hartiala Jaana A. , Wilson Tang W. H. , Wang Zeneng , Crow Amanda L. , Stewart Alexandre F. R. , Roberts Robert , McPherson Ruth , Erdmann Jeanette , Willenborg Christina , Hazen Stanley L. , Allayee Hooman 
Published: January 2016

AbstractMetabolites derived from dietary choline and L-carnitine, such as trimethylamine N-oxide and betaine, have recently been identified as novel risk factors for atherosclerosis in mice and humans. We sought to identify genetic factors associated with plasma betaine levels and determine their effect on risk of coronary artery disease (CAD). A two-stage genome-wide association study (GWAS) identified two significantly associated loci on chromosomes 2q34 and 5q14.1. The lead variant on 2q24 (rs715) localizes to carbamoyl-phosphate synthase 1 (CPS1), which encodes a mitochondrial enzyme that catalyses the first committed reaction and rate-limiting step in the urea cycle. Rs715 is also significantly associated with decreased levels of urea cycle metabolites and increased plasma glycine levels. Notably, rs715 yield a strikingly significant and protective association with decreased risk of CAD in only women. These results suggest that glycine metabolism and/or the urea cycle represent potentially novel sex-specific mechanisms for the development of atherosclerosis.
Probable involvement of p11 with interferon alpha induced depression
Authors: Guo Jiqiang , Zhang Wen , Zhang Lili , Ding Huaxia , Zhang Jingjing , Song Chen , Zhang Yanfei , Xia Namei , Li Mingfang , Liang Yinming , Hu Xianzhang , Luan Haojiang , Wang Hui 
Published: January 2016

AbstractDepression is one of the major side effects of interferon alpha (IFN-α) treatment, but the molecular mechanism underlying IFN-α-induced depression remains unclear. Several studies have shown that the serotonin receptors 5-HTR1b and 5-HTR4 play key roles in the anti-depression effects associated with p11 (S100A10). We investigated the effects of IFN-α on the regulation of p11, 5-HTR1b and 5-HTR4 in mice and human neuroblastoma cells (SH-sy5y). We found that intraperitoneal injection with IFN-α in Balb/c mice resulted in an increased immobility in FST and TST and potently lowered the protein levels of p11, 5-HTR1b and 5-HTR4 in the hippocampus or cingulate gyrus. IFN-α significantly down-regulated the protein levels of p11, 5-HTR1b and 5-HTR4 in SH-sy5y cells, in a time- and dose-dependent manner. Our study revealed that over-expression of p11 could prevent the IFN-α-induced down-regulation of 5-HTR1b and 5-HTR4. The results indicated that IFN-α treatment resulted in p11 down-regulation, which subsequently decreased 5-HTR1b and 5-HTR4 in vitro or in vivo. Our findings suggested that p11 might be a potential regulator on 5-HTR1b and 5-HTR4 as well as a predictor of or a therapeutic target for IFN-α-induced depression.
Normothermic Mouse Functional MRI of Acute Focal Thermostimulation for Probing Nociception
Authors: Reimann Henning Matthias , Hentschel Jan , Marek Jaroslav , Huelnhagen Till , Todiras Mihail , Kox Stefanie , Waiczies Sonia , Hodge Russ , Bader Michael , Pohlmann Andreas , Niendorf Thoralf 
Published: January 2016

AbstractCombining mouse genomics and functional magnetic resonance imaging (fMRI) provides a promising tool to unravel the molecular mechanisms of chronic pain. Probing murine nociception via the blood oxygenation level-dependent (BOLD) effect is still challenging due to methodological constraints. Here we report on the reproducible application of acute noxious heat stimuli to examine the feasibility and limitations of functional brain mapping for central pain processing in mice. Recent technical and procedural advances were applied for enhanced BOLD signal detection and a tight control of physiological parameters. The latter includes the development of a novel mouse cradle designed to maintain whole-body normothermia in anesthetized mice during fMRI in a way that reflects the thermal status of awake, resting mice. Applying mild noxious heat stimuli to wildtype mice resulted in highly significant BOLD patterns in anatomical brain structures forming the pain matrix, which comprise temporal signal intensity changes of up to 6% magnitude. We also observed sub-threshold correlation patterns in large areas of the brain, as well as alterations in mean arterial blood pressure (MABP) in response to the applied stimulus.
Towards a phylogenetic classification of Leptothecata (Cnidaria, Hydrozoa)
Authors: Maronna Maximiliano M. , Miranda Thaís P. , Peña Cantero Álvaro L. , Barbeitos Marcos S. , Marques Antonio C. 
Published: January 2016

AbstractLeptothecata are hydrozoans whose hydranths are covered by perisarc and gonophores and whose medusae bear gonads on their radial canals. They develop complex polypoid colonies and exhibit considerable morphological variation among species with respect to growth, defensive structures and mode of development. For instance, several lineages within this order have lost the medusa stage. Depending on the author, traditional taxonomy in hydrozoans may be either polyp- or medusa-oriented. Therefore, the absence of the latter stage in some lineages may lead to very different classification schemes. Molecular data have proved useful in elucidating this taxonomic challenge. We analyzed a super matrix of new and published rRNA gene sequences (16S, 18S and 28S), employing newly proposed methods to measure branch support and improve phylogenetic signal. Our analysis recovered new clades not recognized by traditional taxonomy and corroborated some recently proposed taxa. We offer a thorough taxonomic revision of the Leptothecata, erecting new orders, suborders, infraorders and families. We also discuss the origination and diversification dynamics of the group from a macroevolutionary perspective.
Ru/Al Multilayers Integrate Maximum Energy Density and Ductility for Reactive Materials
Authors: Woll K. , Bergamaschi A. , Avchachov K. , Djurabekova F. , Gier S. , Pauly C. , Leibenguth P. , Wagner C. , Nordlund K. , Mücklich F. 
Published: January 2016

AbstractEstablished and already commercialized energetic materials, such as those based on Ni/Al for joining, lack the adequate combination of high energy density and ductile reaction products. To join components, this combination is required for mechanically reliable bonds. In addition to the improvement of existing technologies, expansion into new fields of application can also be anticipated which triggers the search for improved materials. Here, we present a comprehensive characterization of the key parameters that enables us to classify the Ru/Al system as new reactive material among other energetic systems. We finally found that Ru/Al exhibits the unusual integration of high energy density and ductility. For example, we measured reaction front velocities up to 10.9 (±0.33) ms−1 and peak reaction temperatures of about 2000 °C indicating the elevated energy density. To our knowledge, such high temperatures have never been reported in experiments for metallic multilayers. In situ experiments show the synthesis of a single-phase B2-RuAl microstructure ensuring improved ductility. Molecular dynamics simulations corroborate the transformation behavior to RuAl. This study fundamentally characterizes a Ru/Al system and demonstrates its enhanced properties fulfilling the identification requirements of a novel nanoscaled energetic material.
Structural basis for the recognition of two consecutive mutually interacting DPF motifs by the SGIP1 μ homology domain
Authors: Shimada Atsushi , Yamaguchi Atsuko , Kohda Daisuke 
Published: January 2016

AbstractFCHo1, FCHo2 and SGIP1 are key regulators of clathrin-mediated endocytosis. Their μ homology domains (μHDs) interact with the C-terminal region of an endocytic scaffold protein, Eps15, containing fifteen Asp-Pro-Phe (DPF) motifs. Here, we show that the high-affinity μHD-binding site in Eps15 is a region encompassing six consecutive DPF motifs, while the minimal μHD-binding unit is two consecutive DPF motifs. We present the crystal structures of the SGIP1 μHD in complex with peptides containing two DPF motifs. The peptides bind to a novel ligand-binding site of the μHD, which is distinct from those of other distantly related μHD-containing proteins. The two DPF motifs, which adopt three-dimensional structures stabilized by sequence-specific intramotif and intermotif interactions, are extensively recognized by the μHD and are both required for binding. Thus, consecutive and singly scattered DPF motifs play distinct roles in μHD binding.
Site-selective local fluorination of graphene induced by focused ion beam irradiation
Authors: Li Hu , Daukiya Lakshya , Haldar Soumyajyoti , Lindblad Andreas , Sanyal Biplab , Eriksson Olle , Aubel Dominique , Hajjar-Garreau Samar , Simon Laurent , Leifer Klaus 
Published: January 2016

AbstractThe functionalization of graphene remains an important challenge for numerous applications expected by this fascinating material. To keep advantageous properties of graphene after modification or functionalization of its structure, local approaches are a promising road. A novel technique is reported here that allows precise site-selective fluorination of graphene. The basic idea of this approach consists in the local radicalization of graphene by focused ion beam (FIB) irradiation and simultaneous introduction of XeF2 gas. A systematic series of experiments were carried out to outline the relation between inserted defect creation and the fluorination process. Based on a subsequent X-ray photoelectron spectroscopy (XPS) analysis, a 6-fold increase of the fluorine concentration on graphene under simultaneous irradiation was observed when compared to fluorination under normal conditions. The fluorine atoms are predominately localized at the defects as indicated from scanning tunneling microscopy (STM). The experimental findings are confirmed by density functional theory which predicts a strong increase of the binding energy of fluorine atoms when bound to the defect sites. The developed technique allows for local fluorination of graphene without using resists and has potential to be a general enabler of site-selective functionalization of graphene using a wide range of gases.
Quantum Hash function and its application to privacy amplification in quantum key distribution, pseudo-random number generation and image encryption
Authors: Yang Yu-Guang , Xu Peng , Yang Rui , Zhou Yi-Hua , Shi Wei-Min 
Published: January 2016

AbstractQuantum information and quantum computation have achieved a huge success during the last years. In this paper, we investigate the capability of quantum Hash function, which can be constructed by subtly modifying quantum walks, a famous quantum computation model. It is found that quantum Hash function can act as a hash function for the privacy amplification process of quantum key distribution systems with higher security. As a byproduct, quantum Hash function can also be used for pseudo-random number generation due to its inherent chaotic dynamics. Further we discuss the application of quantum Hash function to image encryption and propose a novel image encryption algorithm. Numerical simulations and performance comparisons show that quantum Hash function is eligible for privacy amplification in quantum key distribution, pseudo-random number generation and image encryption in terms of various hash tests and randomness tests. It extends the scope of application of quantum computation and quantum information.
White-nose syndrome without borders: Pseudogymnoascus destructans infection tolerated in Europe and Palearctic Asia but not in North America
Authors: Zukal Jan , Bandouchova Hana , Brichta Jiri , Cmokova Adela , Jaron Kamil S. , Kolarik Miroslav , Kovacova Veronika , Kubátová Alena , Nováková Alena , Orlov Oleg , Pikula Jiri , Presetnik Primož , Šuba Jurģis , Zahradníková Alexandra , Martínková Natália 
Published: January 2016

AbstractA striking feature of white-nose syndrome, a fungal infection of hibernating bats, is the difference in infection outcome between North America and Europe. Here we show high WNS prevalence both in Europe and on the West Siberian Plain in Asia. Palearctic bat communities tolerate similar fungal loads of Pseudogymnoascus destructans infection as their Nearctic counterparts and histopathology indicates equal focal skin tissue invasiveness pathognomonic for WNS lesions. Fungal load positively correlates with disease intensity and it reaches highest values at intermediate latitudes. Prevalence and fungal load dynamics in Palearctic bats remained persistent and high between 2012 and 2014. Dominant haplotypes of five genes are widespread in North America, Europe and Asia, expanding the source region of white-nose syndrome to non-European hibernacula. Our data provides evidence for both endemicity and tolerance to this persistent virulent fungus in the Palearctic, suggesting that host-pathogen interaction equilibrium has been established.