bluuebunny/crossref_metadata_2025_split huggingface dataset:
Atlas Toolkit: Fast registration of 3D morphological datasets in the absence of landmarks
Authors: Grocott Timothy , Thomas Paul , Münsterberg Andrea E. 
Published: February 2016

AbstractImage registration is a gateway technology for Developmental Systems Biology, enabling computational analysis of related datasets within a shared coordinate system. Many registration tools rely on landmarks to ensure that datasets are correctly aligned; yet suitable landmarks are not present in many datasets. Atlas Toolkit is a Fiji/ImageJ plugin collection offering elastic group-wise registration of 3D morphological datasets, guided by segmentation of the interesting morphology. We demonstrate the method by combinatorial mapping of cell signalling events in the developing eyes of chick embryos and use the integrated datasets to predictively enumerate Gene Regulatory Network states.
hCLE/C14orf166, a cellular protein required for viral replication, is incorporated into influenza virus particles
Authors: Rodriguez-Frandsen Ariel , de Lucas Susana , Pérez-González Alicia , Pérez-Cidoncha Maite , Roldan-Gomendio Alejandro , Pazo Alejandra , Marcos-Villar Laura , Landeras-Bueno Sara , Ortín Juan , Nieto Amelia 
Published: February 2016

AbstractThe influenza A virus polymerase associates with a number of cellular transcription-related factors, including the RNA polymerase II (RNAP II). We previously described that the cellular protein hCLE/C14orf166 interacts with and stimulates influenza virus polymerase as well as RNAP II activities. Here we show that, despite the considerable cellular shut-off observed in infected cells, which includes RNAP II degradation, hCLE protein levels increase throughout infection in a virus replication-dependent manner. Human and avian influenza viruses of various subtypes increase hCLE levels, but other RNA or DNA viruses do not. hCLE colocalises and interacts with viral ribonucleoproteins (vRNP) in the nucleus, as well as in the cytoplasm late in infection. Furthermore, biochemical analysis of purified virus particles and immunoelectron microscopy of infected cells show hCLE in virions, in close association with viral vRNP. These findings indicate that hCLE, a cellular protein important for viral replication, is one of the very few examples of transcription factors that are incorporated into particles of an RNA-containing virus.
Optical Dark Rogue Wave
Authors: Frisquet Benoit , Kibler Bertrand , Morin Philippe , Baronio Fabio , Conforti Matteo , Millot Guy , Wabnitz Stefan 
Published: February 2016

AbstractPhotonics enables to develop simple lab experiments that mimic water rogue wave generation phenomena, as well as relativistic gravitational effects such as event horizons, gravitational lensing and Hawking radiation. The basis for analog gravity experiments is light propagation through an effective moving medium obtained via the nonlinear response of the material. So far, analogue gravity kinematics was reproduced in scalar optical wave propagation test models. Multimode and spatiotemporal nonlinear interactions exhibit a rich spectrum of excitations, which may substantially expand the range of rogue wave phenomena and lead to novel space-time analogies, for example with multi-particle interactions. By injecting two colliding and modulated pumps with orthogonal states of polarization in a randomly birefringent telecommunication optical fiber, we provide the first experimental demonstration of an optical dark rogue wave. We also introduce the concept of multi-component analog gravity, whereby localized spatiotemporal horizons are associated with the dark rogue wave solution of the two-component nonlinear Schrödinger system.
Use of whole-genome sequencing to trace, control and characterize the regional expansion of extended-spectrum β-lactamase producing ST15 Klebsiella pneumoniae
Authors: Zhou Kai , Lokate Mariette , Deurenberg Ruud H. , Tepper Marga , Arends Jan P. , Raangs Erwin G. C. , Lo-Ten-Foe Jerome , Grundmann Hajo , Rossen John W. A. , Friedrich Alexander W. 
Published: February 2016

AbstractThe study describes the transmission of a CTX-M-15-producing ST15 Klebsiella pneumoniae between patients treated in a single center and the subsequent inter-institutional spread by patient referral occurring between May 2012 and September 2013. A suspected epidemiological link between clinical K. pneumoniae isolates was supported by patient contact tracing and genomic phylogenetic analysis from May to November 2012. By May 2013, a patient treated in three institutions in two cities was involved in an expanding cluster caused by this high-risk clone (HiRiC) (local expansion, CTX-M-15 producing, and containing hypervirulence factors). A clone-specific multiplex PCR was developed for patient screening by which another patient was identified in September 2013. Genomic phylogenetic analysis including published ST15 genomes revealed a close homology with isolates previously found in the USA. Environmental contamination and lack of consistent patient screening were identified as being responsible for the clone dissemination. The investigation addresses the advantages of whole-genome sequencing in the early detection of HiRiC with a high propensity of nosocomial transmission and prolonged circulation in the regional patient population. Our study suggests the necessity for inter-institutional/regional collaboration for infection/outbreak management of K. pneumoniae HiRiCs.
Randomized, Multicenter, Double–Blind Study of the Safety and Efficacy of 1%D-3-Hydroxybutyrate eye drops for Dry Eye Disease
Authors: Kawakita Tetsuya , Uchino Miki , Fukagawa Kazumi , Yoshino Kenichi , Shimazaki Seika , Toda Ikuko , Tanaka Mari , Arai Hiroyuki , Sakatani Keiko , Hata Seiichiro , Okano Takashi , Tsubota Kazuo 
Published: February 2016

AbstractIn a previous study, we demonstrated that topical D-beta-hydroxybutyrate ameliorates corneal epithelial erosion and superficial punctate keratopathy in a rat model of dry eye disease. In the current investigation, we performed a prospective, randomized, multicentre, double-blind, placebo-controlled study to assess the safety and efficacy of 1% D-3-hydroxybutyrate eye drops in patients with dry eye disease. A total of 65 patients were randomly assigned to either the placebo group or the 1% D-3-hydroxybutyrate group and the treatments were administered 6 times a day for 4 weeks. We then evaluated corneal fluorescein staining, corneal and conjunctival rose Bengal staining, tear film break-up time (BUT), Schirmer score and subjective symptoms. At both 2 and 4 weeks, the corneal rose Bengal score was significantly better in the 1% D-3-hydroxybutyrate group than in the placebo group. Among patients with an initial Schirmer score of ≤5 mm, the corneal fluorescein staining score was significantly better in the 1% D-3-hydroxybutyrate group than in the placebo group at two weeks. Mild ocular symptoms occurred in both groups and these spontaneously resolved. The present study suggested that 1% D-3-hydroxybutyrate eye drops are safe and effective in treating ocular surface disorders in patients with tear-deficient dry eye disease.
Hippocampal subfield volumetry in patients with subcortical vascular mild cognitive impairment
Authors: Li Xinwei , Li Deyu , Li Qiongling , Li Yuxia , Li Kuncheng , Li Shuyu , Han Ying 
Published: February 2016

AbstractMemory impairment is a typical characteristic of patients with subcortical vascular mild cognitive impairment (svMCI) or with amnestic mild cognitive impairment (aMCI). The hippocampus, which plays an important role in the consolidation of information from short-term memory to long-term memory, is a heterogeneous structure that consists of several anatomically and functionally distinct subfields. However, whether distinct hippocampal subfields are differentially and selectively affected by svMCI pathology and whether these abnormal changes in hippocampal subfields are different between svMCI and aMCI patients are largely unknown. A total of 26 svMCI patients, 26 aMCI patients and 26 healthy controls matched according to age, gender and years of education were enrolled in this study. We utilized an automated hippocampal subfield segmentation method provided by FreeSurfer to estimate the volume of several hippocampal subfields, including the cornu ammonis (CA) areas, the dentate gyrus (DG), the subiculum and the presubiculum. Compared with controls, the left subiculum and presubiculum and the right CA4/DG displayed significant atrophy in patients with svMCI. Interestingly, we also found significant differences in the volume of the right CA1 between the svMCI and aMCI groups. Taken together, our results reveal region-specific vulnerability of hippocampal subfields to svMCI pathology and identify distinct hippocampal subfield atrophy patterns between svMCI and aMCI patients.
Focal Adhesion Kinase Signaling Mediated the Enhancement of Osteogenesis of Human Mesenchymal Stem Cells Induced by Extracorporeal Shockwave
Authors: Hu Jun , Liao Haojie , Ma Zebin , Chen Hongjiang , Huang Zhonglian , Zhang Yuantao , Yu Menglei , Chen Youbin , Xu Jiankun 
Published: February 2016

AbstractExtracorporeal shockwave (ESW) has been shown of great potential in promoting the osteogenesis of bone marrow mesenchymal stem cells (BMSCs), but it is unknown whether this osteogenic promotion effect can also be achieved in other MSCs (i.e., tendon-derived stem cells (TDSCs) and adipose-derived stem cells (ADSCs)). In the current study, we aimed not only to compare the osteogenic effects of BMSCs induced by ESW to those of TDSCs and ADSCs; but also to investigate the underlying mechanisms. We show here that ESW (0.16 mj/mm2) significantly promoted the osteogenic differentiation in all the tested types of MSCs, accompanied with the downregulation of miR-138, but the activation of FAK, ERK1/2 and RUNX2. The enhancement of osteogenesis in these MSCs was consistently abolished when the cells were pretreated with one of the following conditions: overexpression of miR-138, FAK knockdown using specific siRNA and U0126, implying that all of these elements are indispensable for mediating the effect of ESW. Moreover, our study provides converging genetic and molecular evidence that the miR-138-FAK-ERK1/2-RUNX2 machinery can be generally activated in ESW-preconditioned MSCs, suggesting that ESW may be a promising therapeutic strategy for the enhancement of osteogenesis of MSCs, regardless of their origins.
W-box and G-box elements play important roles in early senescence of rice flag leaf
Authors: Liu Li , Xu Wei , Hu Xuesong , Liu Haoju , Lin Yongjun 
Published: February 2016

AbstractPlant cis-elements play important roles in global regulation of gene expression. Based on microarray data from rice flag leaves during early senescence, we identified W-box and G-box cis-elements as positive regulators of senescence in the important rice variety Minghui 63. Both cis-elements were bound by leaf senescence-specific proteins in vitro and influenced senescence in vivo. Furthermore, combination of the two elements drove enhanced expression during leaf senescence and copy numbers of the cis-elements significantly affected the levels of expression. The W-box is the cognate cis-element for WRKY proteins, while the G-box is the cognate cis-element for bZIP, bHLH and NAC proteins. Consistent with this, WRKY, bZIP, bHLH and NAC family members were overrepresented among transcription factor genes up-regulated according during senescence. Crosstalk between ABA, CTK, BR, auxin, GA and JA during senescence was uncovered by comparing expression patterns of senescence up-regulated transcription factors. Together, our results indicate that hormone-mediated signaling could converge on leaf senescence at the transcriptional level through W-box and G-box elements. Considering that there are very few documented early senescence-related cis-elements, our results significantly contribute to understanding the regulation of flag leaf senescence and provide prioritized targets for stay-green trait improvement.
Allopatric divergence of Stuckenia filiformis (Potamogetonaceae) on the Qinghai-Tibet Plateau and its comparative phylogeography with S. pectinata in China
Authors: Du Zhi-Yuan , Wang Qing-Feng 
Published: February 2016

AbstractIn the aquatic genus Stuckenia, the wide geographic range of S. pectinata and S. filiformis make them suited for examination of topographic and climatic effects on plant evolution. Using nuclear ITS sequence and ten chloroplast sequences, we conducted comparative phylogeographical analyses to investigate their distribution regions and hybrid zones in China and compare their phylogeographical patterns and demographical histories. These two species were allopatric in China. S. filiformis occurred only on the Qinghai-Tibet Plateau (QTP), whereas S. pectinata occupied a wide range of habitats. These two species formed hybrid zones on the northeastern edge of QTP. Most of the genetic variance of S. filiformis was between the southern and eastern groups on the QTP, showing a significant phylogeographic structure. The geographical isolations caused by the Nyenchen Tanglha Mountains and the Tanggula Mountains promoted intraspecific diversification of alpine plants on the QTP. This study revealed the lack of phylogeographic structure in S. pectinata, due to the continued gene flow among its distribution regions. The ecological niche modeling showed that the distribution ranges of these two herbaceous species did not contract too much during the glacial period.
Probing electron-phonon excitations in molecular junctions by quantum interference
Authors: Bessis C. , Della Rocca M. L. , Barraud C. , Martin P. , Lacroix J. C. , Markussen T. , Lafarge P. 
Published: February 2016

AbstractElectron-phonon coupling is a fundamental inelastic interaction in condensed matter and in molecules. Here we probe phonon excitations using quantum interference in electron transport occurring in short chains of anthraquinone based molecular junctions. By studying the dependence of molecular junction’s conductance as a function of bias voltage and temperature, we show that inelastic scattering of electrons by phonons can be detected as features in conductance resulting from quenching of quantum interference. Our results are in agreement with density functional theory calculations and are well described by a generic two-site model in the framework of non-equilibrium Green’s functions formalism. The importance of the observed inelastic contribution to the current opens up new ways for exploring coherent electron transport through molecular devices.
Assessment of the latest NGS enrichment capture methods in clinical context
Authors: García-García Gema , Baux David , Faugère Valérie , Moclyn Mélody , Koenig Michel , Claustres Mireille , Roux Anne-Françoise 
Published: February 2016

AbstractEnrichment capture methods for NGS are widely used, however, they evolve rapidly and it is necessary to periodically measure their strengths and weaknesses before transfer to diagnostic services. We assessed two recently released custom DNA solution-capture enrichment methods for NGS, namely Illumina NRCCE and Agilent SureSelectQXT, against a reference method NimbleGen SeqCap EZ Choice on a similar gene panel, sharing 678 kb and 110 genes. Two Illumina MiSeq runs of 12 samples each have been performed, for each of the three methods, using the same 24 patients (affected with sensorineural disorders). Technical outcomes have been computed and compared, including depth and evenness of coverage, enrichment in targeted regions, performance in GC-rich regions and ability to generate consistent variant datasets. While we show that the three methods resulted in suitable datasets for standard DNA variant discovery, we describe significant differences between the results for the above parameters. NimbleGen offered the best depth of coverage and evenness, while NRCCE showed the highest on target levels but high duplicate rates. SureSelectQXT showed an overall quality close to that of NimbleGen. The new methods exhibit reduced preparation time but behave differently. These findings will guide laboratories in their choice of library enrichment approach.
High-mobility capacitively-induced two-dimensional electrons in a lateral superlattice potential
Authors: Lu T. M. , Laroche D. , Huang S.-H. , Chuang Y. , Li J.-Y. , Liu C. W. 
Published: February 2016

AbstractIn the presence of a lateral periodic potential modulation, two-dimensional electrons may exhibit interesting phenomena, such as a graphene-like energy-momentum dispersion, Bloch oscillations, or the Hofstadter butterfly band structure. To create a sufficiently strong potential modulation using conventional semiconductor heterostructures, aggressive device processing is often required, unfortunately resulting in strong disorder that masks the sought-after effects. Here, we report a novel fabrication process flow for imposing a strong lateral potential modulation onto a capacitively induced two-dimensional electron system, while preserving the host material quality. Using this process flow, the electron density in a patterned Si/SiGe heterostructure can be tuned over a wide range, from 4.4 × 1010 cm−2 to 1.8 × 1011 cm−2, with a peak mobility of 6.4 × 105 cm2/V·s. The wide density tunability and high electron mobility allow us to observe sequential emergence of commensurability oscillations as the density, the mobility, and in turn the mean free path, increase. Magnetic-field-periodic quantum oscillations associated with various closed orbits also emerge sequentially with increasing density. We show that, from the density dependence of the quantum oscillations, one can directly extract the steepness of the imposed superlattice potential. This result is then compared to a conventional lateral superlattice model potential.
Role of C–N Configurations in the Photoluminescence of Graphene Quantum Dots Synthesized by a Hydrothermal Route
Authors: Permatasari Fitri Aulia , Aimon Akfiny Hasdi , Iskandar Ferry , Ogi Takashi , Okuyama Kikuo 
Published: February 2016

AbstractGraphene quantum dots (GQDs) containing N atoms were successfully synthesized using a facile, inexpensive and environmentally friendly hydrothermal reaction of urea and citric acid and the effect of the GQDs’ C–N configurations on their photoluminescence (PL) properties were investigated. High-resolution transmission electron microscopy (HR-TEM) images confirmed that the dots were spherical, with an average diameter of 2.17 nm. X-ray photoelectron spectroscopy (XPS) analysis indicated that the C–N configurations of the GQDs substantially affected their PL intensity. Increased PL intensity was obtained in areas with greater percentages of pyridinic-N and lower percentages of pyrrolic-N. This enhanced PL was attributed to delocalized π electrons from pyridinic-N contributing to the C system of the GQDs. On the basis of energy electron loss spectroscopy (EELS) and UV-Vis spectroscopy analyses, we propose a PL mechanism for hydrothermally synthesized GQDs.
Biomineral shell formation under ocean acidification: a shift from order to chaos
Authors: Fitzer Susan C. , Chung Peter , Maccherozzi Francesco , Dhesi Sarnjeet S. , Kamenos Nicholas A. , Phoenix Vernon R. , Cusack Maggie 
Published: February 2016

AbstractBiomineral production in marine organisms employs transient phases of amorphous calcium carbonate (ACC) in the construction of crystalline shells. Increasing seawater pCO2 leads to ocean acidification (OA) with a reduction in oceanic carbonate concentration which could have a negative impact on shell formation and therefore survival. We demonstrate significant changes in the hydrated and dehydrated forms of ACC in the aragonite and calcite layers of Mytilus edulis shells cultured under acidification conditions (1000 μatm pCO2) compared to present day conditions (380 μatm pCO2). In OA conditions, Mytilus edulis has more ACC at crystalisation sites. Here, we use the high-spatial resolution of synchrotron X-ray Photo Emission Electron Microscopy (XPEEM) combined with X-ray Absorption Spectroscopy (XAS) to investigate the influence of OA on the ACC formation in the shells of adult Mytilus edulis. Electron Backscatter Diffraction (EBSD) confirms that OA reduces crystallographic control of shell formation. The results demonstrate that OA induces more ACC formation and less crystallographic control in mussels suggesting that ACC is used as a repair mechanism to combat shell damage under OA. However, the resultant reduced crystallographic control in mussels raises concerns for shell protective function under predation and changing environments.
Simulation shows that HLA-matched stem cell donors can remain unidentified in donor searches
Authors: Sauter Jürgen , Solloch Ute V. , Giani Anette S. , Hofmann Jan A. , Schmidt Alexander H. 
Published: February 2016

AbstractThe heterogeneous nature of HLA information in real-life stem cell donor registries may hamper unrelated donor searches. It is even possible that fully HLA-matched donors with incomplete HLA information are not identified. In our simulation study, we estimated the probability of these unnecessarily failed donor searches. For that purpose, we carried out donor searches in several virtual donor registries. The registries differed by size, composition with respect to HLA typing levels, and genetic diversity. When up to three virtual HLA typing requests were allowed within donor searches, the share of unnecessarily failed donor searches ranged from 1.19% to 4.13%, thus indicating that non-identification of completely HLA-matched stem cell donors is a problem of practical relevance. The following donor registry characteristics were positively correlated with the share of unnecessarily failed donor searches: large registry size, high genetic diversity, and, most strongly correlated, large fraction of registered donors with incomplete HLA typing. Increasing the number of virtual HLA typing requests within donor searches up to ten had a smaller effect. It follows that the problem of donor non-identification can be substantially reduced by complete high-resolution HLA typing of potential donors.
Downregulation of vimentin in macrophages infected with live Mycobacterium tuberculosis is mediated by Reactive Oxygen Species
Authors: Mahesh P. P. , Retnakumar R. J. , Mundayoor Sathish 
Published: February 2016

AbstractMycobacterium tuberculosis persists primarily in macrophages after infection and manipulates the host defence pathways in its favour. 2D gel electrophoresis results showed that vimentin, an intermediate filament protein, is downregulated in macrophages infected with live Mycobacterium tuberculosis H37Rv when compared to macrophages infected with heat- killed H37Rv. The downregulation was confirmed by Western blot and quantitative RT-PCR. Besides, the expression of vimentin in avirulent strain, Mycobacterium tuberculosis H37Ra- infected macrophages was similar to the expression in heat-killed H37Rv- infected macrophages. Increased expression of vimentin in H2O2- treated live H37Rv-infected macrophages and decreased expression of vimentin both in NAC and DPI- treated heat-killed H37Rv-infected macrophages showed that vimentin expression is positively regulated by ROS. Ectopic expression of ESAT-6 in macrophages decreased both the level of ROS and the expression of vimentin which implies that Mycobacterium tuberculosis-mediated downregulation of vimentin is at least in part due to the downregulation of ROS by the pathogen. Interestingly, the incubation of macrophages with anti-vimentin antibody increased the ROS production and decreased the survival of H37Rv. In addition, we also showed that the pattern of phosphorylation of vimentin in macrophages by PKA/PKC is different from monocytes, emphasizing a role for vimentin phosphorylation in macrophage differentiation.