bluuebunny/crossref_metadata_2025_split huggingface dataset:
Three-Phase 3D Reconstruction of a LiCoO2 Cathode via FIB-SEM Tomography
Authors: Liu Zhao , Chen-Wiegart Yu-chen K. , Wang Jun , Barnett Scott A. , Faber Katherine T. 
Published: January 2016

AbstractThree-phase three-dimensional (3D) microstructural reconstructions of lithium-ion battery electrodes are critical input for 3D simulations of electrode lithiation/delithiation, which provide a detailed understanding of battery operation. In this report, 3D images of a LiCoO2 electrode are achieved using focused ion beam-scanning electron microscopy (FIB-SEM), with clear contrast among the three phases: LiCoO2 particles, carbonaceous phases (carbon and binder) and the electrolyte space. The good contrast was achieved by utilizing an improved FIB-SEM sample preparation method that combined infiltration of the electrolyte space with a low-viscosity silicone resin and triple ion-beam polishing. Morphological parameters quantified include phase volume fraction, surface area, feature size distribution, connectivity, and tortuosity. Electrolyte tortuosity was determined using two different geometric calculations that were in good agreement. The electrolyte tortuosity distribution versus position within the electrode was found to be highly inhomogeneous; this will lead to inhomogeneous electrode lithiation/delithiation at high C-rates that could potentially cause battery degradation.
Externalities as a basis for regulation: a philosophical view
Authors: CLAASSEN RUTGER 
Published: January 2016

AbstractExternalities are an important concept in economic theories of market failure, aiming to justify state regulation of the economy. This paper explores the concept of externalities from a philosophical perspective. It criticizes the utilitarian nature of economic analyses of externalities, showing how they cannot take into account values like freedom and justice. It then develops the analogy between the concept of externalities and the ‘harm principle’ in political philosophy. It argues that the harm principle points to the need for a theory of basic interests to judge when a harm is imposed. Similarly, externality analyses should use such a theory of basic interests as the basis for judgments about legitimate state intervention. This proposal is defended against objections, and illustrated with a case study of the US Supreme Court's ruling on the Affordable Care Act, which shows how the judicial reasoning implicitly interprets externalities in terms of basic interests.
PCB pollution continues to impact populations of orcas and other dolphins in European waters
Authors: Jepson Paul D. , Deaville Rob , Barber Jonathan L. , Aguilar Àlex , Borrell Asunción , Murphy Sinéad , Barry Jon , Brownlow Andrew , Barnett James , Berrow Simon , Cunningham Andrew A. , Davison Nicholas J. , ten Doeschate Mariel , Esteban Ruth , Ferreira Marisa , Foote Andrew D. , Genov Tilen , Giménez Joan , Loveridge Jan , Llavona Ángela , Martin Vidal , Maxwell David L. , Papachlimitzou Alexandra , Penrose Rod , Perkins Matthew W. , Smith Brian , de Stephanis Renaud , Tregenza Nick , Verborgh Philippe , Fernandez Antonio , Law Robin J. 
Published: January 2016

AbstractOrganochlorine (OC) pesticides and the more persistent polychlorinated biphenyls (PCBs) have well-established dose-dependent toxicities to birds, fish and mammals in experimental studies, but the actual impact of OC pollutants on European marine top predators remains unknown. Here we show that several cetacean species have very high mean blubber PCB concentrations likely to cause population declines and suppress population recovery. In a large pan-European meta-analysis of stranded (n = 929) or biopsied (n = 152) cetaceans, three out of four species:- striped dolphins (SDs), bottlenose dolphins (BNDs) and killer whales (KWs) had mean PCB levels that markedly exceeded all known marine mammal PCB toxicity thresholds. Some locations (e.g. western Mediterranean Sea, south-west Iberian Peninsula) are global PCB “hotspots” for marine mammals. Blubber PCB concentrations initially declined following a mid-1980s EU ban, but have since stabilised in UK harbour porpoises and SDs in the western Mediterranean Sea. Some small or declining populations of BNDs and KWs in the NE Atlantic were associated with low recruitment, consistent with PCB-induced reproductive toxicity. Despite regulations and mitigation measures to reduce PCB pollution, their biomagnification in marine food webs continues to cause severe impacts among cetacean top predators in European seas.
Generation of attosecond electron packets via conical surface plasmon electron acceleration
Authors: Greig S. R. , Elezzabi A. Y. 
Published: January 2016

AbstractWe present a method for the generation of high kinetic energy attosecond electron packets via magnetostatic and aperture filtering of conical surface plasmon (SP) accelerated electrons. The conical SP waves are excited by coupling an ultrafast radially polarized laser beam to a conical silica lens coated with an Ag film. Electromagnetic and particle tracking models are employed to characterize the ultrafast electron packets.
Application of FDM three-dimensional printing technology in the digital manufacture of custom edentulous mandible trays
Authors: Chen Hu , Yang Xu , Chen Litong , Wang Yong , Sun Yuchun 
Published: January 2016

AbstractThe objective was to establish and evaluate a method for manufacture of custom trays for edentulous jaws using computer aided design and fused deposition modeling (FDM) technologies. A digital method for design the custom trays for edentulous jaws was established. The tissue surface data of ten standard mandibular edentulous plaster models, which was used to design the digital custom tray in a reverse engineering software, were obtained using a 3D scanner. The designed tray was printed by a 3D FDM printing device. Another ten hand-made custom trays were produced as control. The 3-dimentional surface data of models and custom trays was scanned to evaluate the accuracy of reserved impression space, while the difference between digitally made trays and hand-made trays were analyzed. The digitally made custom trays achieved a good matching with the mandibular model, showing higher accuracy than the hand-made ones. There was no significant difference of the reserved space between different models and its matched digitally made trays. With 3D scanning, CAD and FDM technology, an efficient method of custom tray production was established, which achieved a high reproducibility and accuracy.
Radiation-induced alternative transcription and splicing events and their applicability to practical biodosimetry
Authors: Macaeva Ellina , Saeys Yvan , Tabury Kevin , Janssen Ann , Michaux Arlette , Benotmane Mohammed A. , De Vos Winnok H. , Baatout Sarah , Quintens Roel 
Published: January 2016

AbstractAccurate assessment of the individual exposure dose based on easily accessible samples (e.g. blood) immediately following a radiological accident is crucial. We aimed at developing a robust transcription-based signature for biodosimetry from human peripheral blood mononuclear cells irradiated with different doses of X-rays (0.1 and 1.0 Gy) at a dose rate of 0.26 Gy/min. Genome-wide radiation-induced changes in mRNA expression were evaluated at both gene and exon level. Using exon-specific qRT-PCR, we confirmed that several biomarker genes are alternatively spliced or transcribed after irradiation and that different exons of these genes exhibit significantly different levels of induction. Moreover, a significant number of radiation-responsive genes were found to be genomic neighbors. Using three different classification models we found that gene and exon signatures performed equally well on dose prediction, as long as more than 10 features are included. Together, our results highlight the necessity of evaluating gene expression at the level of single exons for radiation biodosimetry in particular and transcriptional biomarker research in general. This approach is especially advisable for practical gene expression-based biodosimetry, for which primer- or probe-based techniques would be the method of choice.
Antinociceptive effects of vitexin in a mouse model of postoperative pain
Authors: Zhu Qing , Mao Li-Na , Liu Cheng-Peng , Sun Yue-Hua , Jiang Bo , Zhang Wei , Li Jun-Xu 
Published: January 2016

AbstractVitexin, a C-glycosylated flavone present in several medicinal herbs, has showed various pharmacological activities including antinociception. The present study investigated the antinociceptive effects of vitexin in a mouse model of postoperative pain. This model was prepared by making a surgical incision on the right hindpaw and von Frey filament test was used to assess mechanical hyperalgesia. Isobolographical analysis method was used to examine the interaction between vitexin and acetaminophen. A reliable mechanical hyperalgesia was observed at 2 h post-surgery and lasted for 4 days. Acute vitexin administration (3–10 mg/kg, i.p.) dose-dependently relieved this hyperalgesia, which was also observed from 1 to 3 days post-surgery during repeated daily treatment. However, repeated vitexin administration prior to surgery had no preventive value. The 10 mg/kg vitexin-induced antinociception was blocked by the opioid receptor antagonist naltrexone or the GABAAreceptor antagonist bicuculline. The doses of vitexin used did not significantly suppress the locomotor activity. In addition, the combination of vitexin and acetaminophen produced an infra-additive effect in postoperative pain. Together, though vitexin-acetaminophen combination may not be useful for treating postoperative pain, vitexin exerts behaviorally-specific antinociception against postoperative pain mediated through opioid receptors and GABAAreceptors, suggesting that vitexin may be useful for the control of postoperative pain.
Nanofibril scaffold assisted MEMS artificial hydrogel neuromasts for enhanced sensitivity flow sensing
Authors: Kottapalli Ajay Giri Prakash , Bora Meghali , Asadnia Mohsen , Miao Jianmin , Venkatraman Subbu S. , Triantafyllou Michael 
Published: January 2016

AbstractWe present the development and testing of superficial neuromast-inspired flow sensors that also attain high sensitivity and resolution through a biomimetic hyaulronic acid-based hydrogel cupula dressing. The inspiration comes from the spatially distributed neuromasts of the blind cavefish that live in completely dark undersea caves; the sensors enable the fish to form three-dimensional flow and object maps, enabling them to maneuver efficiently in cluttered environments. A canopy shaped electrospun nanofibril scaffold, inspired by the cupular fibrils, assists the drop-casting process allowing the formation of a prolate spheroid-shaped artificial cupula. Rheological and nanoindentation characterizations showed that the Young’s modulus of the artificial cupula closely matches the biological cupula (10–100 Pa). A comparative experimental study conducted to evaluate the sensitivities of the naked hair cell sensor and the cupula-dressed sensor in sensing steady-state flows demonstrated a sensitivity enhancement by 3.5–5 times due to the presence of hydrogel cupula. The novel strategies of sensor development presented in this report are applicable to the design and fabrication of other biomimetic sensors as well. The developed sensors can be used in the navigation and maneuvering of underwater robots, but can also find applications in biomedical and microfluidic devices.
Comparative transcriptome and metabolome provides new insights into the regulatory mechanisms of accelerated senescence in litchi fruit after cold storage
Authors: Yun Ze , Qu Hongxia , Wang Hui , Zhu Feng , Zhang Zhengke , Duan Xuewu , Yang Bao , Cheng Yunjiang , Jiang Yueming 
Published: January 2016

AbstractLitchi is a non-climacteric subtropical fruit of high commercial value. The shelf life of litchi fruit under ambient conditions (AC) is approximately 4–6 days. Post-harvest cold storage prolongs the life of litchi fruit for up to 30 days with few changes in pericarp browning and total soluble solids. However, the shelf life of litchi fruits at ambient temperatures after pre-cold storage (PCS) is only 1–2 days. To better understand the mechanisms involved in the rapid fruit senescence induced by pre-cold storage, a transcriptome of litchi pericarp was constructed to assemble the reference genes, followed by comparative transcriptomic and metabolomic analyses. Results suggested that the senescence of harvested litchi fruit was likely to be an oxidative process initiated by ABA, including oxidation of lipids, polyphenols and anthocyanins. After cold storage, PCS fruit exhibited energy deficiency and respiratory burst was elicited through aerobic and anaerobic respiration, which was regulated specifically by an up-regulated calcium signal, G-protein-coupled receptor signalling pathway and small GTPase-mediated signal transduction. The respiratory burst was largely associated with increased production of reactive oxygen species, up-regulated peroxidase activity and initiation of the lipoxygenase pathway, which were closely related to the accelerated senescence of PCS fruit.
Fabrication of in-situ grown graphene reinforced Cu matrix composites
Authors: Chen Yakun , Zhang Xiang , Liu Enzuo , He Chunnian , Shi Chunsheng , Li Jiajun , Nash Philip , Zhao Naiqin 
Published: January 2016

AbstractGraphene/Cu composites were fabricated through a graphene in-situ grown approach, which involved ball-milling of Cu powders with PMMA as solid carbon source, in-situ growth of graphene on flaky Cu powders and vacuum hot-press sintering. SEM and TEM characterization results indicated that graphene in-situ grown on Cu powders guaranteed a homogeneous dispersion and a good combination between graphene and Cu matrix, as well as the intact structure of graphene, which was beneficial to its strengthening effect. The yield strength of 244 MPa and tensile strength of 274 MPa were achieved in the composite with 0.95 wt.% graphene, which were separately 177% and 27.4% enhancement over pure Cu. Strengthening effect of in-situ grown graphene in the matrix was contributed to load transfer and dislocation strengthening.
Enhanced OCT4 transcriptional activity substitutes for exogenous SOX2 in cellular reprogramming
Authors: Marthaler Adele G. , Adachi Kenjiro , Tiemann Ulf , Wu Guangming , Sabour Davood , Velychko Sergiy , Kleiter Ingo , Schöler Hans R. , Tapia Natalia 
Published: January 2016

AbstractAdenoviral early region 1A (E1A) is a viral gene that can promote cellular proliferation and de-differentiation in mammalian cells, features required for the reprogramming of somatic cells to a pluripotent state. E1A has been shown to interact with OCT4 and as a consequence, to increase OCT4 transcriptional activity. Indeed, E1A and OCT4 are sufficient to revert neuroepithelial hybrids to pluripotency, as demonstrated in previous cell fusion experiments. However, the role that E1A might play in the generation of induced pluripotent stem cells (iPSCs) has not been investigated yet. In this report, we show that E1A can generate iPSCs in combination with OCT4 and KLF4, thus replacing exogenous SOX2. The generated iPSCs are bona fide pluripotent cells as shown by in vitro and in vivo tests. Overall, our study suggests that E1A might replace SOX2 through enhancing OCT4 transcriptional activity at the early stages of reprogramming.
Evolutionary Footprints of Short Tandem Repeats in Avian Promoters
Authors: Abe Hideaki , Gemmell Neil J. 
Published: January 2016

AbstractShort tandem repeats (STRs) or microsatellites are well-known sequence elements that may change the spacing between transcription factor binding sites (TFBSs) in promoter regions by expansion or contraction of repetitive units. Some of these mutations have the potential to contribute to phenotypic diversity by altering patterns of gene expression. To explore how repetitive sequence motifs within promoters have evolved in avian lineages under mutation-selection balance, more than 400 evolutionary conserved STRs (ecSTRs) were identified in this study by comparing the 2 kb upstream promoter sequences of chicken against those of other birds (turkey, duck, zebra finch and flycatcher). The rate of conservation was significantly higher in AG dinucleotide repeats than in AC or AT repeats, with the expansion of AG motifs being noticeably constrained in passerines. Analysis of the relative distance between ecSTRs and TFBSs revealed a significantly higher rate of conserved TFBSs in the vicinity of ecSTRs in both chicken-duck and chicken-passerine comparisons. Our comparative study provides a novel insight into which intrinsic factors have influenced the degree of constraint on repeat expansion/contraction during avian promoter evolution.
Bonding and Anti-bonding Modes of Plasmon Coupling Effects in TiO2-Ag Core-shell Dimers
Authors: Li Quanshui , Zhang Zhili 
Published: January 2016

AbstractBonding and anti-bonding modes of plasmon coupling effects are numerically investigated in TiO2-Ag core-shell nano dimers. First, splitting phenomena of the coupled anti-bonding modes are observed under the longitudinal polarization when the distance between the monomers decreases to a certain level. Second, one of the split resonance modes is identified to be formed by the dipole anti-bonding mode of the monomers from charge density distribution patterns. Those split modes have similar redshift behaviors as the coupled dipole bonding modes in the same situations. Furthermore, the intensities of those anti-bonding modes weaken with decreasing distance between the monomers, because of the interaction of the induced dipole moment in the monomers and the charge distribution variation on the facing surfaces of the gap by the coulomb attraction. Other split bands are the higher-order mode (octupole-like or triakontadipole-like), which do not have obvious peak-shift behavior and the intensities have very little attenuation with decreasing distance. Finally, the coupling of the bonding and anti-bonding modes under the longitudinal polarization is symmetric (bonding).
Thermal modelling of transfer‐bonded thin‐film gallium arsenide laser diode
Authors: Quan Zhi H. , Justice John , Mooney Marcus B. , Gubbins Mark A. , Parbrook Peter J. , Corbett Brian 
Published: January 2016

Two‐dimensional temperature distributions of thin‐film edge‐emitting gallium arsenide (GaAs) 3 μm wide ridge lasers transfer‐bonded to substrates with different thermal conductivities, k, were simulated in COMSOL. The thermal resistance, Rth, is compared with a simplified steady‐state analytic expression. The effects of laser cavity length, thickness of dielectric passivation layer, contact metal layer thickness and submount material are investigated in order to reduce the thermal resistance of the laser when referenced to lasers with the native GaAs substrate. The simulations show the importance in reducing the GaAs substrate thickness especially for short cavity lengths. The Rth of a 200 μm long laser with the substrate fully removed is 37.5 K/W, compared with 230 K/W for the laser with a 100 μm thick GaAs substrate. Increased p‐contact metal thickness and reduced dielectric layer thickness further reduce Rth. If alumina (k = 1.35 W/mK) is used as a submount, its thickness above a perfect heat sink should be minimised to decrease the junction temperature. A 10 μm thick silicon submount (k = 150 W/mK) above a perfect heat sink provides an acceptably low Rth.
Pain and distress caused by endotracheal suctioning in neonates is better quantified by behavioural than physiological items: a comparison based on item response theory modelling
Authors: Välitalo Pyry A.J. , van Dijk Monique , Krekels Elke H.J. , Gibbins Sharyn , Simons Sinno H.P. , Tibboel Dick , Knibbe Catherijne A.J. 
Published: January 2016

Abstract
Pain cannot be directly measured in neonates. Therefore, scores based on indirect behavioural signals such as crying, or physiological signs such as blood pressure, are used to quantify neonatal pain both in clinical practice and in clinical studies. The aim of this study was to determine which of the physiological and behavioural items of 2 validated pain assessment scales (COMFORT and premature infant pain profile) are best able to detect pain during endotracheal and nasal suctioning in ventilated newborns. We analysed a total of 516 PIPP and COMFORT scores from 118 newborns. A graded response model was built to describe the data and item information was calculated for each of the behavioural and physiological items. We found that the graded response model was able to well describe the data, as judged by agreement between the observed data and model simulations. Furthermore, a good agreement was found between the pain estimated by the graded response model and the investigator-assessed visual analogue scale scores (Spearman rho correlation coefficient = 0.80). The information scores for the behavioural items ranged from 1.4 to 27.2 and from 0.0282 to 0.131 for physiological items. In these data with mild to moderate pain levels, behavioural items were vastly more informative of pain and distress than were physiological items. The items that were the most informative of pain are COMFORT items “calmness/agitation,” “alertness,” and “facial tension.”
Comparative Analysis of Single-Cell RNA Sequencing Methods
Authors: Ziegenhain Christoph , Vieth Beate , Parekh Swati , Reinius Björn , Smets Martha , Leonhardt Heinrich , Hellmann Ines , Enard Wolfgang 
Published: January 2016

AbstractBackgroundSingle-cell RNA sequencing (scRNA-seq) offers exciting possibilities to address biological and medical questions, but a systematic comparison of recently developed protocols is still lacking.ResultsWe generated data from 447 mouse embryonic stem cells using Drop-seq, SCRB-seq, Smart-seq (on Fluidigm C1) and Smart-seq2 and analyzed existing data from 35 mouse embryonic stem cells prepared with CEL-seq. We find that Smart-seq2 is the most sensitive method as it detects the most genes per cell and across cells. However, it shows more amplification noise than CEL-seq, Drop-seq and SCRB-seq as it cannot use unique molecular identifiers (UMIs). We use simulations to model how the observed combinations of sensitivity and amplification noise affects detection of differentially expressed genes and find that SCRB-seq reaches 80% power with the fewest number of cells. When considering cost-efficiency at different sequencing depths at 80% power, we find that Drop-seq is preferable when quantifying transcriptomes of a large numbers of cells with low sequencing depth, SCRB-seq is preferable when quantifying transcriptomes of fewer cells and Smart-seq2 is preferable when annotating and/or quantifying transcriptomes of fewer cells as long one can use in-house produced transposase.ConclusionsOur analyses allows an informed choice among five prominent scRNA-seq protocols and provides a solid framework for benchmarking future improvements in scRNA-seq methodologies.