bluuebunny/crossref_metadata_2025_split huggingface dataset:
Berry phase and band structure analysis of the Weyl semimetal NbP
Authors: Sergelius Philip , Gooth Johannes , Bäßler Svenja , Zierold Robert , Wiegand Christoph , Niemann Anna , Reith Heiko , Shekhar Chandra , Felser Claudia , Yan Binghai , Nielsch Kornelius 
Published: September 2016

AbstractWeyl semimetals are often considered the 3D-analogon of graphene or topological insulators. The evaluation of quantum oscillations in these systems remains challenging because there are often multiple conduction bands. We observe de Haas-van Alphen oscillations with several frequencies in a single crystal of the Weyl semimetal niobium phosphide. For each fundamental crystal axis, we can fit the raw data to a superposition of sinusoidal functions, which enables us to calculate the characteristic parameters of all individual bulk conduction bands using Fourier transform with an analysis of the temperature and magnetic field-dependent oscillation amplitude decay. Our experimental results indicate that the band structure consists of Dirac bands with low cyclotron mass, a non-trivial Berry phase and parabolic bands with a higher effective mass and trivial Berry phase.
Using rare earth elements to constrain particulate organic carbon flux in the East China Sea
Authors: Hung Chin-Chang , Chen Ya-Feng , Hsu Shih-Chieh , Wang Kui , Chen Jianfang , Burdige David J. 
Published: September 2016

AbstractFluxes of particulate organic carbon (POC) in the East China Sea (ECS) have been reported to decrease from the inner continental shelf towards the outer continental shelf. Recent research has shown that POC fluxes in the ECS may be overestimated due to active sediment resuspension. To better characterize the effect of sediment resuspension on particle fluxes in the ECS, rare earth elements (REEs) and organic carbon (OC) were used in separate two-member mixing models to evaluate trap-collected POC fluxes. The ratio of resuspended particles from sediments to total trap-collected particles in the ECS ranged from 82–94% using the OC mixing model, and 30–80% using the REEs mixing model, respectively. These results suggest that REEs may be better proxies for sediment resuspension than OC in high turbidity marginal seas because REEs do not appear to undergo degradation during particle sinking as compared to organic carbon. Our results suggest that REEs can be used as tracers to provide quantitative estimates of POC fluxes in marginal seas.
An Automated Microwell Platform for Large-Scale Single Cell RNA-Seq
Authors: Yuan Jinzhou , Sims Peter A. 
Published: September 2016

AbstractRecent developments have enabled rapid, inexpensive RNA sequencing of thousands of individual cells from a single specimen, raising the possibility of unbiased and comprehensive expression profiling from complex tissues. Microwell arrays are a particularly attractive microfluidic platform for single cell analysis due to their scalability, cell capture efficiency and compatibility with imaging. We report an automated microwell array platform for single cell RNA-Seq with significantly improved performance over previous implementations. We demonstrate cell capture efficiencies of >50%, compatibility with commercially available barcoded mRNA capture beads and parallel expression profiling from thousands of individual cells. We evaluate the level of cross-contamination in our platform by both tracking fluorescent cell lysate in sealed microwells and with a human-mouse mixed species RNA-Seq experiment. Finally, we apply our system to comprehensively assess heterogeneity in gene expression of patient-derived glioma neurospheres and uncover subpopulations similar to those observed in human glioma tissue.
Co-stimulation of HaCaT keratinization with mechanical stress and air-exposure using a novel 3D culture device
Authors: Jung Moon Hee , Jung Sang-Myung , Shin Hwa Sung 
Published: September 2016

AbstractArtificial skin or skin equivalents have been used for clinical purpose to skin graft and as substitutes for animal experiments. The culture of cell lines such as HaCaT has the potential to produce large amounts of artificial skin at a low cost. However, there is a limit to keratinization due to the restriction of differentiation in HaCaT. In this study, a culture device that mimics the in vivo keratinization mechanism, co-stimulated by air-exposure and mechanical stimulation, was developed to construct skin equivalents. The device can reconstruct the epidermal morphology, including the cornified layer, similar to its formation in vivo. Under the condition, epidermis was differentiated in the spinous and granular layers. Formation of the stratum corneum is consistent with the mRNA and protein expressions of differentiation markers. The device is the first of its kind to combine air-exposure with mechanical stress to co-stimulate keratinization, which can facilitate the economically viable production of HaCaT-based artificial skin substitutes.
Identifying and removing the cell-cycle effect from single-cell RNA-Sequencing data
Authors: Barron Martin , Li Jun 
Published: September 2016

AbstractSingle-cell RNA-Sequencing (scRNA-Seq) is a revolutionary technique for discovering and describing cell types in heterogeneous tissues, yet its measurement of expression often suffers from large systematic bias. A major source of this bias is the cell cycle, which introduces large within-cell-type heterogeneity that can obscure the differences in expression between cell types. The current method for removing the cell-cycle effect is unable to effectively identify this effect and has a high risk of removing other biological components of interest, compromising downstream analysis. We present ccRemover, a new method that reliably identifies the cell-cycle effect and removes it. ccRemover preserves other biological signals of interest in the data and thus can serve as an important pre-processing step for many scRNA-Seq data analyses. The effectiveness of ccRemover is demonstrated using simulation data and three real scRNA-Seq datasets, where it boosts the performance of existing clustering algorithms in distinguishing between cell types.
Measuring Method for Lightning Channel Temperature
Authors: Li X. , Zhang J. , Chen L. , Xue Q. , Zhu R. 
Published: September 2016

AbstractIn this paper, we demonstrate the temperature of lightning channel utilizing the theory of lightning spectra and the model of local thermodynamic equilibrium (LTE). The impulse current generator platform (ICGS) was used to simulate the lightning discharge channel, and the spectral energy of infrared spectroscopy (930 nm) and the visible spectroscopy (648.2 nm) of the simulated lightning has been calculated. Results indicate that the peaks of luminous intensity of both infrared and visible spectra increase with the lightning current intensity in range of 5–50 kA. Based on the results, the temperature of the lightning channel is derived to be 6140.8–10424 K. Moreover, the temperature of the channel is approximately exponential to the lightning current intensity, which shows good agreement with that of the natural lightning cases.
HB-GAM (pleiotrophin) reverses inhibition of neural regeneration by the CNS extracellular matrix
Authors: Paveliev Mikhail , Fenrich Keith K. , Kislin Mikhail , Kuja-Panula Juha , Kulesskiy Evgeny , Varjosalo Markku , Kajander Tommi , Mugantseva Ekaterina , Ahonen-Bishopp Anni , Khiroug Leonard , Kulesskaya Natalia , Rougon Geneviève , Rauvala Heikki 
Published: September 2016

AbstractChondroitin sulfate (CS) glycosaminoglycans inhibit regeneration in the adult central nervous system (CNS). We report here that HB-GAM (heparin-binding growth-associated molecule; also known as pleiotrophin), a CS-binding protein expressed at high levels in the developing CNS, reverses the role of the CS chains in neurite growth of CNS neurons in vitro from inhibition to activation. The CS-bound HB-GAM promotes neurite growth through binding to the cell surface proteoglycan glypican-2; furthermore, HB-GAM abrogates the CS ligand binding to the inhibitory receptor PTPσ (protein tyrosine phosphatase sigma). Our in vivo studies using two-photon imaging of CNS injuries support the in vitro studies and show that HB-GAM increases dendrite regeneration in the adult cerebral cortex and axonal regeneration in the adult spinal cord. Our findings may enable the development of novel therapies for CNS injuries.
Biocompatibility and biodistribution of functionalized carbon nano-onions (f-CNOs) in a vertebrate model
Authors: d’ Amora Marta , Rodio Marina , Bartelmess Juergen , Sancataldo Giuseppe , Brescia Rosaria , Cella Zanacchi Francesca , Diaspro Alberto , Giordani Silvia 
Published: September 2016

AbstractFunctionalized carbon nano-onions (f-CNOs) are of great interest as platforms for imaging, diagnostic and therapeutic applications due to their high cellular uptake and low cytotoxicity. To date, the toxicological effects of f-CNOs on vertebrates have not been reported. In this study, the possible biological impact of f-CNOs on zebrafish during development is investigated, evaluating different toxicity end-points such as the survival rate, hatching rate, and heart beat rate. Furthermore, a bio-distribution study of boron dipyrromethene (BODIPY) functionalized CNOs in zebrafish larvae is performed by utilizing inverted selective plane illumination microscopy (iSPIM), due to its intrinsic capability of allowing for fast 3D imaging. Our in vivo findings indicate that f-CNOs exhibit no toxicity, good biocompatibility (in the concentration range of 5–100 μg mL−1) and a homogenous biodistribution in zebrafish larvae.
Experimental factors affecting the robustness of DNA methylation analysis
Authors: Pharo Heidi D. , Honne Hilde , Vedeld Hege M. , Dahl Christina , Andresen Kim , Liestøl Knut , Jeanmougin Marine , Guldberg Per , Lind Guro E. 
Published: September 2016

AbstractDiverging methylation frequencies are often reported for the same locus in the same disease, underscoring the need for limiting technical variability in DNA methylation analyses. We have investigated seven likely sources of variability at different steps of bisulfite PCR-based DNA methylation analyses using a fully automated quantitative methylation-specific PCR setup of six gene promoters across 20 colon cancer cell lines. Based on >15,000 individual PCRs, all tested parameters affected the normalized percent of methylated reference (PMR) differences, with a fourfold varying magnitude. Additionally, large variations were observed across the six genes analyzed. The highest variation was seen using single-copy genes as reference for normalization, followed by different amounts of template in the PCR, different amounts of DNA in the bisulfite reaction and storage of bisulfite converted samples. Finally, when a highly standardized pipeline was repeated, the difference in PMR value for the same assay in the same cell line was on average limited to five (on a 0–100 scale). In conclusion, a standardized pipeline is essential for consistent methylation results, where parameters are kept constant for all samples. Nevertheless, a certain level of variation in methylation values must be expected, underscoring the need for careful interpretation of data.
High Resolution non-Markovianity in NMR
Authors: Bernardes Nadja K. , Peterson John P. S. , Sarthour Roberto S. , Souza Alexandre M. , Monken C. H. , Roditi Itzhak , Oliveira Ivan S. , Santos Marcelo F. 
Published: September 2016

AbstractMemoryless time evolutions are ubiquitous in nature but often correspond to a resolution-induced approximation, i.e. there are correlations in time whose effects are undetectable. Recent advances in the dynamical control of small quantum systems provide the ideal scenario to probe some of these effects. Here we experimentally demonstrate the precise induction of memory effects on the evolution of a quantum coin (qubit) by correlations engineered in its environment. In particular, we design a collisional model in Nuclear Magnetic Resonance (NMR) and precisely control the strength of the effects by changing the degree of correlation in the environment and its time of interaction with the qubit. We also show how these effects can be hidden by the limited resolution of the measurements performed on the qubit. The experiment reinforces NMR as a test bed for the study of open quantum systems and the simulation of their classical counterparts.
Increased levels of 3-hydroxykynurenine parallel disease severity in human acute pancreatitis
Authors: Skouras Christos , Zheng Xiaozhong , Binnie Margaret , Homer Natalie Z. M. , Murray Toby B. J. , Robertson Darren , Briody Lesley , Paterson Finny , Spence Heather , Derr Lisa , Hayes Alastair J. , Tsoumanis Andreas , Lyster Dawn , Parks Rowan W. , Garden O. James , Iredale John P. , Uings Iain J. , Liddle John , Wright Wayne L. , Dukes George , Webster Scott P. , Mole Damian J. 
Published: September 2016

AbstractInhibition of kynurenine 3-monooxygenase (KMO) protects against multiple organ dysfunction (MODS) in experimental acute pancreatitis (AP). We aimed to precisely define the kynurenine pathway activation in relation to AP and AP-MODS in humans, by carrying out a prospective observational study of all persons presenting with a potential diagnosis of AP for 90 days. We sampled peripheral venous blood at 0, 3, 6, 12, 24, 48, 72 and 168 hours post-recruitment. We measured tryptophan metabolite concentrations and analysed these in the context of clinical data and disease severity indices, cytokine profiles and C-reactive protein (CRP) concentrations. 79 individuals were recruited (median age: 59.6 years; 47 males, 59.5%). 57 met the revised Atlanta definition of AP: 25 had mild, 23 moderate, and 9 severe AP. Plasma 3-hydroxykynurenine concentrations correlated with contemporaneous APACHE II scores (R2 = 0.273; Spearman rho = 0.581; P < 0.001) and CRP (R2 = 0.132; Spearman rho = 0.455, P < 0.001). Temporal profiling showed early tryptophan depletion and contemporaneous 3-hydroxykynurenine elevation. Furthermore, plasma concentrations of 3-hydroxykynurenine paralleled systemic inflammation and AP severity. These findings support the rationale for investigating early intervention with a KMO inhibitor, with the aim of reducing the incidence and severity of AP-associated organ dysfunction.
Solving Set Cover with Pairs Problem using Quantum Annealing
Authors: Cao Yudong , Jiang Shuxian , Perouli Debbie , Kais Sabre 
Published: September 2016

AbstractHere we consider using quantum annealing to solve Set Cover with Pairs (SCP), an NP-hard combinatorial optimization problem that plays an important role in networking, computational biology and biochemistry. We show an explicit construction of Ising Hamiltonians whose ground states encode the solution of SCP instances. We numerically simulate the time-dependent Schrödinger equation in order to test the performance of quantum annealing for random instances and compare with that of simulated annealing. We also discuss explicit embedding strategies for realizing our Hamiltonian construction on the D-wave type restricted Ising Hamiltonian based on Chimera graphs. Our embedding on the Chimera graph preserves the structure of the original SCP instance and in particular, the embedding for general complete bipartite graphs and logical disjunctions may be of broader use than that the specific problem we deal with.
Controllably releasing long-lived quantum memory for photonic polarization qubit into multiple spatially-separate photonic channels
Authors: Chen Lirong , Xu Zhongxiao , Zeng Weiqing , Wen Yafei , Li Shujing , Wang Hai 
Published: September 2016

AbstractWe report an experiment in which long-lived quantum memories for photonic polarization qubits (PPQs) are controllably released into any one of multiple spatially-separate channels. The PPQs are implemented with an arbitrarily-polarized coherent signal light pulses at the single-photon level and are stored in cold atoms by means of electromagnetic-induced-transparency scheme. Reading laser pulses propagating along the direction at a small angle relative to quantum axis are applied to release the stored PPQs into an output channel. By changing the propagating directions of the read laser beam, we controllably release the retrieved PPQs into 7 different photonic output channels, respectively. At a storage time of δt = 5 μs, the least quantum-process fidelity in 7 different output channels is ~89%. At one of the output channels, the measured maximum quantum-process fidelity for the PPQs is 94.2% at storage time of δt = 0.85 ms. At storage time of 6 ms, the quantum-process fidelity is still beyond the bound of 78% to violate the Bell’s inequality. The demonstrated controllable release of the stored PPQs may extend the capabilities of the quantum information storage technique.
Desmoteplase for Acute Ischemic Stroke within 3 to 9 Hours after Symptom Onset: Evidence from Randomized Controlled Trials
Authors: Shi Ligen , Liang Feng , Li Yunping , Shao Anwen , Zhou Keren , Yu Jun , Zhang Jianmin 
Published: September 2016

AbstractRecent studies have shown inconsistent results regarding the value of desmoteplase for treating acute ischemic stroke (AIS) when administered within an extended time window. We performed a meta-analysis to explore the value of desmoteplase in AIS treatment. The MEDLINE, EMBASE, and Cochrane Library databases were searched for randomized controlled trials (RCTs) that had evaluated desmoteplase versus placebo for AIS. The primary outcomes were intracranial hemorrhage (ICH) within 72 hours and favorable outcome at Day 90. We pooled 819 patients from 5 RCTs. Desmoteplase treatment showed a neutral effect on favorable outcome (P = 0.42) but a favorable safety profile in terms of ICH (P = 0.64) compared with the placebo group. In the subgroup analysis, 90 μg/kg desmoteplase, a late time to treatment (6–9 hours), and serious stroke symptoms at baseline (NIHSS > 12) subgroups showed high risks of ICH (P ≤ 0.02). A high dose of desmoteplase (125 μg/kg) showed a tendency to improve recanalization (P = 0.05), but was also associated with an increased risk of death (P = 0.04). In conclusion, desmoteplase administered over an extended time window had no significant effect on functional recovery but exhibited a favorable safety profile in patients with AIS.
Reduced graphene oxide enwrapped phosphors for long-term thermally stable phosphor converted white light emitting diodes
Authors: Anoop Gopinathan , Rani Janardhanan R. , Lim Juhwan , Jang Myoung Soo , Suh Dong Wook , Kang Shinill , Jun Seong Chan , Yoo Jae Soo 
Published: September 2016

AbstractThe long-term instability of the presently available best commercial phosphor-converted light-emitting diodes (pcLEDs) is the most serious obstacle for the realization of low-cost and energy-saving lighting applications. Emission from pcLEDs starts to degrade after approximately 200 h of operation because of thermal degradation of the phosphors. We propose a new strategy to overcome this thermal degradation problem of phosphors by wrapping the phosphor particles with reduced graphene oxide (rGO). Through the rGO wrapping, we have succeeded in controlling the thermal degradation of phosphors and improving the stability of fabricated pcLEDs. We have fabricated pcLEDs with long-term stability that maintain nearly 98% of their initial luminescence emission intensity even after 800 h of continuous operation at 85 °C and 85% relative humidity. The pcLEDs fabricated using SrBaSi2O2N2:Eu2+ phosphor particles wrapped with reduced graphene oxide are thermally stable because of enhanced heat dissipation that prevents the ionization of Eu2+ to Eu3+. We believe that this technique can be applied to other rare-earth doped phosphors for the realization of highly efficient and stable white LEDs.
In-vivo, non-invasive detection of hyperglycemic states in animal models using mm-wave spectroscopy
Authors: Martín-Mateos Pedro , Dornuf Fabian , Duarte Blanca , Hils Bernhard , Moreno-Oyervides Aldo , Bonilla-Manrique Oscar Elias , Larcher Fernando , Krozer Viktor , Acedo Pablo 
Published: September 2016

AbstractChronic or sustained hyperglycemia associated to diabetes mellitus leads to many medical complications, thus, it is necessary to track the evolution of patients for providing the adequate management of the disease that is required for the restoration of the carbohydrate metabolism to a normal state. In this paper, a novel monitoring approach based on mm-wave spectroscopy is comprehensively described and experimentally validated using living animal models as target. The measurement method has proved the possibility of non-invasive, in-vivo, detection of hyperglycemia-associated conditions in different mouse models, making possible to clearly differentiate between several hyperglycemic states.
Flow-induced HDAC1 phosphorylation and nuclear export in angiogenic sprouting
Authors: Bazou Despina , Ng Mei Rosa , Song Jonathan W. , Chin Shan Min , Maimon Nir , Munn Lance L. 
Published: September 2016

AbstractAngiogenesis requires the coordinated growth and migration of endothelial cells (ECs), with each EC residing in the vessel wall integrating local signals to determine whether to remain quiescent or undergo morphogenesis. These signals include vascular endothelial growth factor (VEGF) and flow-induced mechanical stimuli such as interstitial flow, which are both elevated in the tumor microenvironment. However, it is not clear how VEGF signaling and mechanobiological activation due to interstitial flow cooperate during angiogenesis. Here, we show that endothelial morphogenesis is histone deacetylase-1- (HDAC1) dependent and that interstitial flow increases the phosphorylation of HDAC1, its activity and its export from the nucleus. Furthermore, we show that HDAC1 inhibition decreases endothelial morphogenesis and matrix metalloproteinase-14 (MMP14) expression. Our results suggest that HDAC1 modulates angiogenesis in response to flow, providing a new target for modulating vascularization in the clinic.
Displacement correlations between a single mesenchymal-like cell and its nucleus effectively link subcellular activities and motility in cell migration analysis
Authors: Lan Tian , Cheng Kai , Ren Tina , Arce Stephen Hugo , Tseng Yiider 
Published: September 2016

AbstractCell migration is an essential process in organism development and physiological maintenance. Although current methods permit accurate comparisons of the effects of molecular manipulations and drug applications on cell motility, effects of alterations in subcellular activities on motility cannot be fully elucidated from those methods. Here, we develop a strategy termed cell-nuclear (CN) correlation to parameterize represented dynamic subcellular activities and to quantify their contributions in mesenchymal-like migration. Based on the biophysical meaning of the CN correlation, we propose a cell migration potential index (CMPI) to measure cell motility. When the effectiveness of CMPI was evaluated with respect to one of the most popular cell migration analysis methods, Persistent Random Walk, we found that the cell motility estimates among six cell lines used in this study were highly consistent between these two approaches. Further evaluations indicated that CMPI can be determined using a shorter time period and smaller cell sample size, and it possesses excellent reliability and applicability, even in the presence of a wide range of noise, as might be generated from individual imaging acquisition systems. The novel approach outlined here introduces a robust strategy through an analysis of subcellular locomotion activities for single cell migration assessment.