bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatial Resolution in Scanning Electron Microscopy and Scanning Transmission Electron Microscopy Without a Specimen Vacuum Chamber
Authors: Nguyen Kayla X. , Holtz Megan E. , Richmond-Decker Justin , Muller David A. 
Published: July 2016

AbstractA long-standing goal of electron microscopy has been the high-resolution characterization of specimens in their native environment. However, electron optics require high vacuum to maintain an unscattered and focused probe, a challenge for specimens requiring atmospheric or liquid environments. Here, we use an electron-transparent window at the base of a scanning electron microscope’s objective lens to separate column vacuum from the specimen, enabling imaging under ambient conditions, without a specimen vacuum chamber. We demonstrate in-air imaging of specimens at nanoscale resolution using backscattered scanning electron microscopy (airSEM) and scanning transmission electron microscopy. We explore resolution and contrast using Monte Carlo simulations and analytical models. We find that nanometer-scale resolution can be obtained at gas path lengths up to 400μm, although contrast drops with increasing gas path length. As the electron-transparent window scatters considerably more than gas at our operating conditions, we observe that the densities and thicknesses of the electron-transparent window are the dominant limiting factors for image contrast at lower operating voltages. By enabling a variety of detector configurations, the airSEM is applicable to a wide range of environmental experiments including the imaging of hydrated biological specimens andin situchemical and electrochemical processes.
Where/when/how did life begin? A philosophical key for systematizing theories on the origin of life
Authors: Świeżyński Adam 
Published: July 2016

AbstractThe question of the origin of life interested people for centuries. All existing views on this subject can be classified into different areas of human knowledge about the world: natural sciences, philosophy, and theology (religion). It is interesting to look at them closer and to classify all the typical groups of the theories about the origins of life. We can then see links existing between them and relationships that indicate their own nature. Nowadays, driving forces of prebiological chemical evolution and the mode of explanation of the transition ‘non-life into life’ give a great variety of solutions. The differences between the theories, however, as well as the current controversies in the scientific community (what ‘in the beginning’ was?; where and when the prebiotic evolution may took place? etc.) will be shown as of secondary importance for the theories’ systematization in comparison with several much more profound philosophical assumptions underlying the origin-of-life-studies. My proposal to organize and classify different types of the theories of genesis of life allows for extracting conceptions of different kind: metaphysical and scientific, and also for comparing them with each other. Some of them answer the question of the emergence of life in general and others on the question of the origin of life on the Earth only. In the perspective of contemporary scientific research on the origin of life it seems interesting that two main ideas concerning the problem of the origin of life, spontaneous generation and panspermia, are still present as presuppositions of certain theories but have been modified. Thus a ‘philosophical key’ seems to be the most appropriate to systematize all kinds of theories on the origin of life. This paper is an attempt to justify the position adopted. Most important conclusion is that the philosophical basis or implications, which are irreducibly present and possible to be found within the scientific theories of the origin of life, indicates that this problem is not just the strictly scientific one; it is the philosophical problem, too; thus it cannot be fully solved merely through referring to the empirical aspect of biogenesis.
From climate models to planetary habitability: temperature constraints for complex life
Authors: Silva Laura , Vladilo Giovanni , Schulte Patricia M. , Murante Giuseppe , Provenzale Antonello 
Published: July 2016

AbstractIn an effort to derive temperature-based criteria of habitability for multicellular life, we investigated the thermal limits of terrestrial poikilotherms, i.e. organisms whose body temperature and the functioning of all vital processes is directly affected by the ambient temperature. Multicellular poikilotherms are the most common and evolutionarily ancient form of complex life on earth. The thermal limits for the active metabolism and reproduction of multicellular poikilotherms on earth are approximately bracketed by the temperature interval 0°C ≤ T ≤ 50°C. The same interval applies to the photosynthetic production of oxygen, an essential ingredient of complex life, and for the generation of atmospheric biosignatures observable in exoplanets. Analysis of the main mechanisms responsible for the thermal thresholds of terrestrial life suggests that the same mechanisms would apply to other forms of chemical life. We therefore propose a habitability index for complex life,h050, representing the mean orbital fraction of planetary surface that satisfies the temperature limits 0°C ≤ T ≤ 50°C. With the aid of a climate model tailored for the calculation of the surface temperature of Earth-like planets, we calculatedh050as a function of planet insolation,S, and atmospheric columnar mass,Natm, for a few earth-like atmospheric compositions with trace levels of CO2. By displayingh050as a function ofSandNatm, we built up an atmospheric mass habitable zone (AMHZ) for complex life. At variance with the classic habitable zone, the inner edge of the complex life habitable zone is not affected by the uncertainties inherent to the calculation of the runaway greenhouse limit. The complex life habitable zone is significantly narrower than the habitable zone of dry planets. Our calculations illustrate how changes in ambient conditions dependent onSandNatm, such as temperature excursions and surface dose of secondary particles of cosmic rays, may influence the type of life potentially present at different epochs of planetary evolution inside the AMHZ.
Mapping two-dimensional polar active fluids to two-dimensional soap and one-dimensional sandblasting
Authors: Chen Leiming , Lee Chiu Fan , Toner John 
Published: July 2016

AbstractActive fluids and growing interfaces are two well-studied but very different non-equilibrium systems. Each exhibits non-equilibrium behaviour distinct from that of their equilibrium counterparts. Here we demonstrate a surprising connection between these two: the ordered phase of incompressible polar active fluids in two spatial dimensions without momentum conservation, and growing one-dimensional interfaces (that is, the 1+1-dimensional Kardar–Parisi–Zhang equation), in fact belong to the same universality class. This universality class also includes two equilibrium systems: two-dimensional smectic liquid crystals, and a peculiar kind of constrained two-dimensional ferromagnet. We use these connections to show that two-dimensional incompressible flocks are robust against fluctuations, and exhibit universal long-ranged, anisotropic spatio-temporal correlations of those fluctuations. We also thereby determine the exact values of the anisotropy exponent ζ and the roughness exponents χx,y that characterize these correlations.
Tau mediates microtubule bundle architectures mimicking fascicles of microtubules found in the axon initial segment
Authors: Chung Peter J. , Song Chaeyeon , Deek Joanna , Miller Herbert P. , Li Youli , Choi Myung Chul , Wilson Leslie , Feinstein Stuart C. , Safinya Cyrus R. 
Published: July 2016

AbstractTau, an intrinsically disordered protein confined to neuronal axons, binds to and regulates microtubule dynamics. Although there have been observations of string-like microtubule fascicles in the axon initial segment (AIS) and hexagonal bundles in neurite-like processes in non-neuronal cells overexpressing Tau, cell-free reconstitutions have not replicated either geometry. Here we map out the energy landscape of Tau-mediated, GTP-dependent ‘active’ microtubule bundles at 37 °C, as revealed by synchrotron SAXS and TEM. Widely spaced bundles (wall-to-wall distance Dw–w≈25–41 nm) with hexagonal and string-like symmetry are observed, the latter mimicking bundles found in the AIS. A second energy minimum (Dw–w≈16–23 nm) is revealed under osmotic pressure. The wide spacing results from a balance between repulsive forces, due to Tau’s projection domain (PD), and a stabilizing sum of transient sub-kBT cationic/anionic charge–charge attractions mediated by weakly penetrating opposing PDs. This landscape would be significantly affected by charge-altering modifications of Tau associated with neurodegeneration.
Plexins function in epithelial repair in both Drosophila and zebrafish
Authors: Yoo Sa Kan , Pascoe Heath G. , Pereira Telmo , Kondo Shu , Jacinto Antonio , Zhang Xuewu , Hariharan Iswar K. 
Published: July 2016

AbstractIn most multicellular organisms, homeostasis is contingent upon maintaining epithelial integrity. When unanticipated insults breach epithelial barriers, dormant programmes of tissue repair are immediately activated. However, many of the mechanisms that repair damaged epithelia remain poorly characterized. Here we describe a role for Plexin A (PlexA), a protein with particularly well-characterized roles in axonal pathfinding, in the healing of damaged epithelia in Drosophila. Semaphorins, which are PlexA ligands, also regulate tissue repair. We show that Drosophila PlexA has GAP activity for the Rap1 GTPase, which is known to regulate the stability of adherens junctions. Our observations suggest that the inhibition of Rap1 activity by PlexA in damaged Drosophila epithelia allows epithelial remodelling, thus facilitating wound repair. We also demonstrate a role for Plexin A1, a zebrafish orthologue of Drosophila PlexA, in epithelial repair in zebrafish tail fins. Thus, plexins function in epithelial wound healing in diverse taxa.
Dynamics of extinction debt across five taxonomic groups
Authors: Halley John M. , Monokrousos Nikolaos , Mazaris Antonios D. , Newmark William D. , Vokou Despoina 
Published: July 2016

AbstractSpecies extinction following habitat loss is well documented. However, these extinctions do not happen immediately. The biodiversity surplus (extinction debt) declines with some delay through the process of relaxation. Estimating the time constants of relaxation, mainly the expected time to first extinction and the commonly used time for half the extinction debt to be paid off (half-life), is crucial for conservation purposes. Currently, there is no agreement on the rate of relaxation and the factors that it depends on. Here we find that half-life increases with area for all groups examined in a large meta-analysis of extinction data. A common pattern emerges if we use average number of individuals per species before habitat loss as an area index: for mammals, birds, reptiles and plants, the relationship has an exponent close to a half. We also find that the time to first determined extinction is short and increases slowly with area.
Single microwave-photon detector using an artificial Λ-type three-level system
Authors: Inomata Kunihiro , Lin Zhirong , Koshino Kazuki , Oliver William D. , Tsai Jaw-Shen , Yamamoto Tsuyoshi , Nakamura Yasunobu 
Published: July 2016

AbstractSingle-photon detection is a requisite technique in quantum-optics experiments in both the optical and the microwave domains. However, the energy of microwave quanta are four to five orders of magnitude less than their optical counterpart, making the efficient detection of single microwave photons extremely challenging. Here we demonstrate the detection of a single microwave photon propagating through a waveguide. The detector is implemented with an impedance-matched artificial Λ system comprising the dressed states of a driven superconducting qubit coupled to a microwave resonator. Each signal photon deterministically induces a Raman transition in the Λ system and excites the qubit. The subsequent dispersive readout of the qubit produces a discrete ‘click’. We attain a high single-photon-detection efficiency of 0.66±0.06 with a low dark-count probability of 0.014±0.001 and a reset time of ∼400 ns. This detector can be exploited for various applications in quantum sensing, quantum communication and quantum information processing.
Comparative transcriptomic analysis reveals the oncogenic fusion protein PAX3-FOXO1 globally alters mRNA and miRNA to enhance myoblast invasion
Authors: Loupe J M , Miller P J , Bonner B P , Maggi E C , Vijayaraghavan J , Crabtree J S , Taylor C M , Zabaleta J , Hollenbach A D 
Published: July 2016

AbstractRhabdomyosarcoma, one of the most common childhood sarcomas, is comprised of two main subtypes, embryonal and alveolar (ARMS). ARMS, the more aggressive subtype, is primarily characterized by the t(2;13)(p35;p14) chromosomal translocation, which fuses two transcription factors, PAX3 and FOXO1 to generate the oncogenic fusion protein PAX3-FOXO1. Patients with PAX3-FOXO1-postitive tumors have a poor prognosis, in part due to the enhanced local invasive capacity of these cells, which leads to the increased metastatic potential for this tumor. Despite this knowledge, little is known about the role that the oncogenic fusion protein has in this increased invasive potential. In this report we use large-scale comparative transcriptomic analyses in physiologically relevant primary myoblasts to demonstrate that the presence of PAX3-FOXO1 is sufficient to alter the expression of 70 mRNA and 27 miRNA in a manner predicted to promote cellular invasion. In contrast the expression of PAX3 alters 60 mRNA and 23 miRNA in a manner predicted to inhibit invasion. We demonstrate that these alterations in mRNA and miRNA translate into changes in the invasive potential of primary myoblasts with PAX3-FOXO1 increasing invasion nearly 2-fold while PAX3 decreases invasion nearly 4-fold. Taken together, these results allow us to build off of previous reports and develop a more expansive molecular model by which the presence of PAX3-FOXO1 alters global gene regulatory networks to enhance the local invasiveness of cells. Further, the global nature of our observed changes highlights the fact that instead of focusing on a single-gene target, we must develop multi-faceted treatment regimens targeting multiple genes of a single oncogenic phenotype or multiple genes that target different oncogenic phenotypes for tumor progression.
Exploring lateral genetic transfer among microbial genomes using TF-IDF
Authors: Cong Yingnan , Chan Yao-ban , Ragan Mark A. 
Published: July 2016

AbstractMany microbes can acquire genetic material from their environment and incorporate it into their genome, a process known as lateral genetic transfer (LGT). Computational approaches have been developed to detect genomic regions of lateral origin, but typically lack sensitivity, ability to distinguish donor from recipient and scalability to very large datasets. To address these issues we have introduced an alignment-free method based on ideas from document analysis, term frequency-inverse document frequency (TF-IDF). Here we examine the performance of TF-IDF on three empirical datasets: 27 genomes of Escherichia coli and Shigella, 110 genomes of enteric bacteria and 143 genomes across 12 bacterial and three archaeal phyla. We investigate the effect of k-mer size, gap size and delineation of groups on the inference of genomic regions of lateral origin, finding an interplay among these parameters and sequence divergence. Because TF-IDF identifies donor groups and delineates regions of lateral origin within recipient genomes, aggregating these regions by gene enables us to explore, for the first time, the mosaic nature of lateral genes including the multiplicity of biological sources, ancestry of transfer and over-writing by subsequent transfers. We carry out Gene Ontology enrichment tests to investigate which biological processes are potentially affected by LGT.
Controllable Phase Transformation and Mid-infrared Emission from Er3+-Doped Hexagonal-/Cubic-NaYF4 Nanocrystals
Authors: Yang Dandan , Chen Dongdan , He Huilin , Pan Qiwen , Xiao Quanlan , Qiu Jianrong , Dong Guoping 
Published: July 2016

AbstractThe morphology of hexagonal phase NaYF4:Er3+ nanorods synthesized by hydrothermal method changed greatly after a continuing calcination, along with a phase transformation to cubic phase. Photoluminescence (PL) spectra indicated that mid-infrared (MIR) emission was obtained in both hexagonal and cubic phase NaYF4:Er3+ nanocrystals for the first time. And the MIR emission of NaYF4:Er3+ nanocrystals enhanced remarkably at higher calcination temperature. To prevent uncontrollable morphology from phase transformation, the cubic phase NaYF4:Er3+ nanospheres with an average size of ~100 nm were prepared via a co-precipitation method directly. In contrast, the results showed better morphology and size of cubic phase NaYF4:Er3+ nanocrystals have realized when calcined at different temperatures. And PL spectra demonstrated a more intense MIR emission in the cubic phase NaYF4:Er3+ nanocrystals with an increasing temperature. Besides, the MIR emission peak of Er3+ ions had an obvious splitting in cubic phase NaYF4. Therefore, cubic phase NaYF4:Er3+ nanospheres with more excellent MIR luminescent properties seems to provide a new material for nanocrystal-glass composites, which is expected to open a broad new field for the realization of MIR lasers gain medium.
Association of MIF, but not type I interferon-induced chemokines, with increased disease activity in Asian patients with systemic lupus erythematosus
Authors: Connelly K. L. , Kandane-Rathnayake R. , Hoi A. , Nikpour Mandana , Morand E. F. 
Published: July 2016

AbstractEthnicity is a key factor impacting on disease severity in SLE, but molecular mechanisms of these associations are unknown. Type I IFN and MIF have each been associated with SLE pathogenesis. We investigated whether increased SLE severity in Asian patients is associated with either MIF or Type I IFN. SLE patients (n = 151) had prospective recording of disease variables. Serum MIF, and a validated composite score of three Type I IFN-inducible chemokines (IFNCK:CCL2, CXCL10, CCL19) were measured. Associations of MIF and IFNCK score with disease activity were assessed, with persistent active disease (PAD) used as a marker of high disease activity over a median 2.6 years follow up. In univariable analysis, MIF, IFNCK score and Asian ethnicity were significantly associated with PAD. Asian ethnicity was associated with higher MIF but not IFNCK score. In multivariable logistic regression analysis, MIF (OR3.62 (95% CI 1.14,11.5), p = 0.03) and Asian ethnicity (OR3.00 (95% CI 1.39,6.46), p < 0.01) but not IFNCK were significantly associated with PAD. These results potentially support an effect of MIF, but not Type I IFN, in heightened SLE disease severity in Asian SLE. The associations of MIF and Asian ethnicity with PAD are at least partly independent.
The inhibition of calpains ameliorates vascular restenosis through MMP2/TGF-β1 pathway
Authors: Tang Lianghu , Pei Haifeng , Yang Yi , Wang Xiong , Wang Ting , Gao Erhe , Li De , Yang Yongjian , Yang Dachun 
Published: July 2016

AbstractRestenosis limits the efficacy of vascular percutaneous intervention, in which vascular smooth muscle cell (VSMC) proliferation and activation of inflammation are two primary causal factors. Calpains influence VSMC proliferation and collagen synthesis. However, the roles of calpastatin and calpains in vascular restenosis remain unclear. Here, restenosis was induced by ligating the left carotid artery and VSMCs were pretreated with platelet-derived growth factor (PDGF)-BB. Adenovirus vector carrying MMP2 sequence and specific small interfering RNA against calpain-1/2 were introduced. Finally, restenosis enhanced the expression of calpain-1/2, but reduced calpastatin content. In calpastatin transgenic mice, lumen narrowing was attenuated gradually and peaked on days 14–21. Cell proliferation and migration as well as collagen synthesis were inhibited in transgenic mice and expression of calpain-1/2 and MMP2/transforming growth factor-β1 (TGF-β1). Consistently, in VSMCs pretreated with PDGF-BB, calpastatin induction and calpains inhibition suppressed the proliferation and migration of VSMCs and collagen synthesis and reduced expression of calpain-1/2 and MMP2/TGF-β1. Moreover, simvastatin improved restenosis indicators by suppressing the HIF-1α/calpains/MMP2/TGF-β1 pathway. However, MMP2 supplementation eliminated the vascular protection of calpastatin induction and simvastatin. Collectively, calpains inhibition plays crucial roles in vascular restenosis by preventing neointimal hyperplasia at the early stage via suppression of the MMP2/TGF-β1 pathway.
N-dimensional measurement-device-independent quantum key distribution with N + 1 un-characterized sources: zero quantum-bit-error-rate case
Authors: Hwang Won-Young , Su Hong-Yi , Bae Joonwoo 
Published: July 2016

AbstractWe study N-dimensional measurement-device-independent quantum-key-distribution protocol where one checking state is used. Only assuming that the checking state is a superposition of other N sources, we show that the protocol is secure in zero quantum-bit-error-rate case, suggesting possibility of the protocol. The method may be applied in other quantum information processing.
Effects of grazing on photosynthetic features and soil respiration of rangelands in the Tianshan Mountains of Northwest China
Authors: Liu Hua , Zang Runguo , Chen Han Y. H. 
Published: July 2016

AbstractRangelands play a critical role in the global carbon cycle. However, the eco-physiological mechanisms associated with the effects of grazing on leaf photosynthesis and soil respiration remain poorly understood. To examine the impacts of grazing on leaf photosynthesis and soil respiration, we measured the photosynthetic parameters of the dominant species (Trifolium repens) and the soil respiration in grazed and ungrazed rangelands in the Tianshan Mountains of China. We found that grazing reduced the daily maximum net photosynthetic rate and increased soil respiration rates by 35% and 15%, respectively. The photosynthetic quantum yield, dark respiratory rate, and water use efficiency ofT. repensleaves were reduced in grazed plots by 33.3%, 69.2%, and 21.5%, respectively. Our results demonstrated that grazing reduced carbon assimilation while increasing soil respiration within the rangelands in the Tianshan Mountains.