bluuebunny/crossref_metadata_2025_split huggingface dataset:
Experimental Measurement of the Solid Particle Concentration in Geophysical Turbulent Gas‐Particle Mixtures
Authors: Weit A. , Roche O. , Dubois T. , Manga M. 
Published: May 2018

AbstractDilute gas‐particle mixtures in which the particles are carried by the turbulent fluid are found in various geophysical contexts, from cold snow avalanches to hot pyroclastic density currents. Though previous studies suggest that such mixtures have maximum particle concentrations of a few volume percent, the dependence of this maximum concentration on the Reynolds number is unclear. We addressed this issue through laboratory experiments in a vertical pipe, where dilute gas‐particle mixtures were created by injecting a turbulent air flow from below. Nearly monodisperse mixtures of glass beads of different grain sizes (77 to 1,550 μm) were used with varying bulk concentrations from 0.025 to 8 vol. %. To create quasi‐static mixtures, the mean air velocity matched the terminal settling velocity for the grain sizes investigated. The maximum Reynolds numbers of the mixtures were ~104–106. The air pressure indicated full support of the particle weight at concentrations down to 0.025 vol. %. Above a critical particle concentration, at which all the particles were suspended, subsequent additional particles were not maintained in the mixture and led to the formation of clusters that settled downward in the pipe to form a dense fluidized bed. Maximum mean particle concentrations of the dilute mixtures increased from ~1 to ~2.8 vol. % and reached a plateau at increasing mixture Reynolds number. These results give insights into the maximum particle concentrations of geophysical turbulent gas‐particle mixtures and may serve to constrain observations as well as the input and output data of models.
Polarization insensitive frequency conversion for an atom-photon entanglement distribution via a telecom network
Authors: Ikuta Rikizo , Kobayashi Toshiki , Kawakami Tetsuo , Miki Shigehito , Yabuno Masahiro , Yamashita Taro , Terai Hirotaka , Koashi Masato , Mukai Tetsuya , Yamamoto Takashi , Imoto Nobuyuki 
Published: May 2018

AbstractLong-lifetime quantum storages accessible to the telecom photonic infrastructure are essential to long-distance quantum communication. Atomic quantum storages have achieved subsecond storage time corresponding to 1000 km transmission time for a telecom photon through a quantum repeater algorithm. However, the telecom photon cannot be directly interfaced to typical atomic storages. Solid-state quantum frequency conversions fill this wavelength gap. Here we report on the experimental demonstration of a polarization-insensitive solid-state quantum frequency conversion to a telecom photon from a short-wavelength photon entangled with an atomic ensemble. Atom–photon entanglement has been generated with a Rb atomic ensemble and the photon has been translated to telecom range while retaining the entanglement by our nonlinear-crystal-based frequency converter in a Sagnac interferometer.
Interpretable dimensionality reduction of single cell transcriptome data with deep generative models
Authors: Ding Jiarui , Condon Anne , Shah Sohrab P. 
Published: May 2018

AbstractSingle-cell RNA-sequencing has great potential to discover cell types, identify cell states, trace development lineages, and reconstruct the spatial organization of cells. However, dimension reduction to interpret structure in single-cell sequencing data remains a challenge. Existing algorithms are either not able to uncover the clustering structures in the data or lose global information such as groups of clusters that are close to each other. We present a robust statistical model, scvis, to capture and visualize the low-dimensional structures in single-cell gene expression data. Simulation results demonstrate that low-dimensional representations learned by scvis preserve both the local and global neighbor structures in the data. In addition, scvis is robust to the number of data points and learns a probabilistic parametric mapping function to add new data points to an existing embedding. We then use scvis to analyze four single-cell RNA-sequencing datasets, exemplifying interpretable two-dimensional representations of the high-dimensional single-cell RNA-sequencing data.
Large quantum-spin-Hall gap in single-layer 1T′ WSe2
Authors: Chen P. , Pai Woei Wu , Chan Y.-H. , Sun W.-L. , Xu C.-Z. , Lin D.-S. , Chou M. Y. , Fedorov A.-V. , Chiang T.-C. 
Published: May 2018

AbstractTwo-dimensional (2D) topological insulators (TIs) are promising platforms for low-dissipation spintronic devices based on the quantum-spin-Hall (QSH) effect, but experimental realization of such systems with a large band gap suitable for room-temperature applications has proven difficult. Here, we report the successful growth on bilayer graphene of a quasi-freestanding WSe2 single layer with the 1T′ structure that does not exist in the bulk form of WSe2. Using angle-resolved photoemission spectroscopy (ARPES) and scanning tunneling microscopy/spectroscopy (STM/STS), we observe a gap of 129 meV in the 1T′ layer and an in-gap edge state located near the layer boundary. The system′s 2D TI characters are confirmed by first-principles calculations. The observed gap diminishes with doping by Rb adsorption, ultimately leading to an insulator–semimetal transition. The discovery of this large-gap 2D TI with a tunable band gap opens up opportunities for developing advanced nanoscale systems and quantum devices.
Continuous addition of progenitors forms the cardiac ventricle in zebrafish
Authors: Felker Anastasia , Prummel Karin D. , Merks Anne M. , Mickoleit Michaela , Brombacher Eline C. , Huisken Jan , Panáková Daniela , Mosimann Christian 
Published: May 2018

AbstractThe vertebrate heart develops from several progenitor lineages. After early-differentiating first heart field (FHF) progenitors form the linear heart tube, late-differentiating second heart field (SHF) progenitors extend the atrium and ventricle, and form inflow and outflow tracts (IFT/OFT). However, the position and migration of late-differentiating progenitors during heart formation remains unclear. Here, we track zebrafish heart development using transgenics based on the cardiopharyngeal gene tbx1. Live imaging uncovers a tbx1 reporter-expressing cell sheath that continuously disseminates from the lateral plate mesoderm towards the forming heart tube. High-speed imaging and optogenetic lineage tracing corroborates that the zebrafish ventricle forms through continuous addition from the undifferentiated progenitor sheath followed by late-phase accrual of the bulbus arteriosus (BA). FGF inhibition during sheath migration reduces ventricle size and abolishes BA formation, refining the window of FGF action during OFT formation. Our findings consolidate previous end-point analyses and establish zebrafish ventricle formation as a continuous process.
Tomographic and multimodal scattering-type scanning near-field optical microscopy with peak force tapping mode
Authors: Wang Haomin , Wang Le , Jakob Devon S. , Xu Xiaoji G. 
Published: May 2018

AbstractScattering-type scanning near-field optical microscopy (s-SNOM) enables nanoscale spectroscopic imaging and has been instrumental for many nano-photonic discoveries and in situ studies. However, conventional s-SNOM techniques with atomic force microscopy tapping mode operation and lock-in detections do not provide direct tomographic information with explicit tip−sample distance. Here, we present a non-traditional s-SNOM technique, named peak force scattering-type scanning near-field optical microscopy (PF-SNOM), by combination of peak force tapping mode and time-gated light detection. PF-SNOM enables direct sectioning of vertical near-field signals from a sample surface for both three-dimensional near-field imaging and spectroscopic analysis. Tip-induced relaxation of surface phonon polaritons are revealed and modeled by considering tip damping. PF-SNOM also delivers a spatial resolution of 5 nm and can simultaneously measure mechanical and electrical properties together with optical near-field signals. PF-SNOM is expected to facilitate three-dimensional nanoscale near-field characterizations and correlative in situ investigations on light-induced mechanical and electrical effects.
A unified formulation of dichroic signals using the Borrmann effect and twisted photon beams
Authors: Collins Stephen P. , Lovesey Stephen W. 
Published: May 2018

AbstractDichroic X-ray signals derived from the Borrmann effect and a twisted photon beam with topological charge l = 1 are formulated with an effective wavevector. The unification applies for non-magnetic and magnetic materials. Electronic degrees of freedom associated with an ion are encapsulated in multipoles previously used to interpret conventional dichroism and Bragg diffraction enhanced by an atomic resonance. A dichroic signal exploiting the Borrmann effect with a linearly polarized beam presents charge-like multipoles that include a hexadecapole. A difference between dichroic signals obtained with a twisted beam carrying spin polarization (circular polarization) and opposite winding numbers presents charge-like atomic multipoles, whereas a twisted beam carrying linear polarization alone presents magnetic (time-odd) multipoles. Charge-like multipoles include a quadrupole, and magnetic multipoles include a dipole and an octupole. We discuss the practicalities and relative merits of spectroscopy exploiting the two remarkably closely-related processes. Signals using beams with topological charges l ≥ 2 present additional atomic multipoles.
Molecular Size Modulates Pharmacokinetics, Biodistribution, and Renal Deposition of the Drug Delivery Biopolymer Elastin-like Polypeptide
Authors: Kuna Marija , Mahdi Fakhri , Chade Alejandro R. , Bidwell Gene L. 
Published: May 2018

AbstractElastin-like polypeptides (ELP) are engineered proteins that consist of repetitions of a five amino acid motif, and their composition is easily modified to adjust their physical properties and attach therapeutics. Because of the repetitive nature of the ELP sequence, polymer size is particularly amenable to manipulation. ELP fusion proteins are being actively developed as therapeutics for many disease applications, and how the ELP size and shape affects its pharmacokinetics and biodistribution is a critical question for the general field of ELP drug delivery. To address this, we generated a library of ELPs ranging in size from 25 kDa to 110 kDa. Terminal plasma half-life was directly proportional to polymer size, and organ biodistribution was also size dependent. The kidneys accumulated the highest levels of ELP of all sizes, followed by the liver. Within the kidney, most ELP was found in the proximal tubule, but intra-renal localization shifted from exclusively cortical to a mixture of cortical and medullary as ELP size increased.
Metabolic Reprogramming in Leaf Lettuce Grown Under Different Light Quality and Intensity Conditions Using Narrow-Band LEDs
Authors: Kitazaki Kazuyoshi , Fukushima Atsushi , Nakabayashi Ryo , Okazaki Yozo , Kobayashi Makoto , Mori Tetsuya , Nishizawa Tomoko , Reyes-Chin-Wo Sebastian , Michelmore Richard W. , Saito Kazuki , Shoji Kazuhiro , Kusano Miyako 
Published: May 2018

AbstractLight-emitting diodes (LEDs) are an artificial light source used in closed-type plant factories and provide a promising solution for a year-round supply of green leafy vegetables, such as lettuce (Lactuca sativaL.). Obtaining high-quality seedlings using controlled irradiation from LEDs is critical, as the seedling health affects the growth and yield of leaf lettuce after transplantation. Because key molecular pathways underlying plant responses to a specific light quality and intensity remain poorly characterised, we used a multi-omics–based approach to evaluate the metabolic and transcriptional reprogramming of leaf lettuce seedlings grown under narrow-band LED lighting. Four types of monochromatic LEDs (one blue, two green and one red) and white fluorescent light (control) were used at low and high intensities (100 and 300 μmol·m−2·s−1, respectively). Multi-platform mass spectrometry-based metabolomics and RNA-Seq were used to determine changes in the metabolome and transcriptome of lettuce plants in response to different light qualities and intensities. Metabolic pathway analysis revealed distinct regulatory mechanisms involved in flavonoid and phenylpropanoid biosynthetic pathways under blue and green wavelengths. Taken together, these data suggest that the energy transmitted by green light is effective in creating a balance between biomass production and the production of secondary metabolites involved in plant defence.
Dark septate endophytes isolated from a xerophyte plant promote the growth of Ammopiptanthus mongolicus under drought condition
Authors: Li Xia , He Xueli , Hou Lifeng , Ren Ying , Wang Shaojie , Su Fang 
Published: May 2018

AbstractDark septate endophytes (DSE) may facilitate plant growth and stress tolerance in stressful ecosystems. However, little is known about the response of plants to non-host DSE fungi isolated from other plants, especially under drought condition. This study aimed to seek and apply non-host DSE to evaluate their growth promoting effects in a desert species, Ammopiptanthus mongolicus, under drought condition. Nine DSE strains isolated from a super-xerophytic shrub, Gymnocarpos przewalskii, were identified and used as the non-host DSE. And DSE colonization rate (30–35%) and species composition in the roots of G. przewalskii were first reported. The inoculation results showed that all DSE strains were effective colonizers and formed a strain-dependent symbiosis with A. mongolicus. Specifically, one Darksidea strain, Knufia sp., and Leptosphaeria sp. increased the total biomass of A. mongolicus compared to non-inoculated plants. Two Paraconiothyrium strains, Phialophora sp., and Embellisia chlamydospora exhibited significantly positive effects on plant branch number, potassium and calcium content. Two Paraconiothyrium and Darksidea strains particularly decreased plant biomass or element content. As A. mongolicus plays important roles in fixing moving sand and delay desertification, the ability of certain DSE strains to promote desert plant growth indicates their potential use for vegetation recovery in arid environments.
Highly Bactericidal Macroporous Antimicrobial Polymeric Gel for Point-of-Use Water Disinfection
Authors: Kumar Amit , Boyer Cyrille , Nebhani Leena , Wong Edgar H. H. 
Published: May 2018

AbstractAccess to clean and safe water supply remains inadequate in many developing countries. One of the key challenges is to remove pathogenic bacteria from the water supply via effective water disinfection technologies to prevent the spread of diseases and to ensure the safety of consumers. Herein, a highly effective point-of-use (on-demand) water disinfection technology, in the form of a polymeric scaffold called macroporous antimicrobial polymeric gel (MAPG), is demonstrated. MAPG is easy to fabricate, completely organic and possess inherent antimicrobial property which makes it non-reliant on inorganic compounds such as silver where the long-term toxicity remains unknown. MAPG is highly bactericidal and can disinfect bacteria-contaminated water (ca. 108 CFU mL−1) at a capacity of about >50 times the mass of the organic material used, inactivating >99% of both Gram-negative and Gram-positive bacteria including Escherichia coli, Vibrio cholerae and Staphylococcus aureus within 20 minutes of treatment. When fabricated in a syringe, MAPG eliminates E. coli from contaminated water source by >8.0 log10 reduction in bacteria counts (i.e., no viable bacteria were detected after treatment), and the syringe can be reused multiple times without losing potency. The MAPG technology is not only restricted to water disinfection but may also be applicable in other bacteria inactivation applications.
Well-protected quantum state transfer in a dissipative spin chain
Authors: Behzadi Naghi , Ektesabi Abbas , Ahansaz Bahram 
Published: May 2018

AbstractIn this work, a mechanism is investigated for improving the quantum state transfer efficiency in a spin chain, which is in contact with a dissipative structured reservoir. The efficiency of the method is based on the addition of similar non-interacting auxiliary chains into the reservoir. In this way, we obtain the exact solution for the master equation of the spin chain in the presence of dissipation. It is found out that entering more auxiliary chains into the reservoir causes, in general, the better improvement of the fidelity of state transfer along the mentioned chain. Furthermore, it is reveal that the protocol has better efficiency for a chain with longer length. Therefore, by this method, quantum state transfer along a linear chain with an arbitrary number of qubits, can be well-protected against the dissipative noises.
Whole-genome analysis of Mustela erminea finds that pulsed hybridization impacts evolution at high latitudes
Authors: Colella Jocelyn P. , Lan Tianying , Schuster Stephan C. , Talbot Sandra L. , Cook Joseph A. , Lindqvist Charlotte 
Published: May 2018

AbstractAt high latitudes, climatic shifts hypothetically initiate recurrent episodes of divergence by isolating populations in glacial refugia—ice-free regions that enable terrestrial species persistence. Upon glacial recession, populations subsequently expand and often come into contact with other independently diverging populations, resulting in gene flow. To understand how recurrent periods of isolation and contact may have impacted evolution at high latitudes, we investigated introgression dynamics in the stoat (Mustela erminea), a Holarctic mammalian carnivore, using whole-genome sequences. We identify two spatio-temporally distinct episodes of introgression coincident with large-scale climatic shifts: contemporary introgression in a mainland contact zone and ancient contact ~200 km south of the contemporary zone, in the archipelagos along North America’s North Pacific Coast. Repeated episodes of gene flow highlight the central role of cyclic climates in structuring high-latitude diversity, through refugial divergence and introgressive hybridization. When introgression is followed by allopatric isolation (e.g., insularization) it may ultimately expedite divergence.
The electronic Rothamsted Archive (e-RA), an online resource for data from the Rothamsted long-term experiments
Authors: Perryman Sarah A. M. , Castells-Brooke Nathalie I. D. , Glendining Margaret J. , Goulding Keith W. T. , Hawkesford Malcolm J. , Macdonald Andy J. , Ostler Richard J. , Poulton Paul R. , Rawlings Christopher J. , Scott Tony , Verrier Paul J. 
Published: May 2018

AbstractThe electronic Rothamsted Archive, e-RA (www.era.rothamsted.ac.uk) provides a permanent managed database to both securely store and disseminate data from Rothamsted Research’s long-term field experiments (since 1843) and meteorological stations (since 1853). Both historical and contemporary data are made available via this online database which provides the scientific community with access to a unique continuous record of agricultural experiments and weather measured since the mid-19th century. Qualitative information, such as treatment and management practices, plans and soil information, accompanies the data and are made available on the e-RA website. e-RA was released externally to the wider scientific community in 2013 and this paper describes its development, content, curation and the access process for data users. Case studies illustrate the diverse applications of the data, including its original intended purposes and recent unforeseen applications. Usage monitoring demonstrates the data are of increasing interest. Future developments, including adopting FAIR data principles, are proposed as the resource is increasingly recognised as a unique archive of data relevant to sustainable agriculture, agroecology and the environment.
Field-recorded data on the diet of six species of European Hydromantes cave salamanders
Authors: Lunghi Enrico , Cianferoni Fabio , Ceccolini Filippo , Mulargia Manuela , Cogoni Roberto , Barzaghi Benedetta , Cornago Lorenzo , Avitabile Domenico , Veith Michael , Manenti Raoul , Ficetola Gentile Francesco , Corti Claudia 
Published: May 2018

AbstractThe availability of data on the feeding habits of species of conservation value may be of great importance to develop analyses for both scientific and management purposes. Stomach flushing is a harmless technique that allowed us to collect extensive data on the feeding habits of six Hydromantes species. Here, we present two datasets originating from a three-year study performed in multiple seasons (spring and autumn) on 19 different populations of cave salamanders. The first dataset contains data of the stomach content of 1,250 salamanders, where 6,010 items were recognized; the second one reports the size of the intact prey items found in the stomachs. These datasets integrate considerably data already available on the diet of the European plethodontid salamanders, being also of potential use for large scale meta-analyses on amphibian diet.
A pair of datasets for microRNA expression profiling to examine the use of careful study design for assigning arrays to samples
Authors: Qin Li-Xuan , Huang Huei-Chung , Villafania Liliana , Cavatore Magali , Olvera Narciso , Levine Douglas A. 
Published: May 2018

AbstractWe set out to demonstrate the logistic feasibility of careful experimental design for microarray studies and its level of scientific benefits for improving the accuracy and reproducibility of data inference. Towards this end, we conducted a study of microRNA expression using endometrioid endometrial tumours (n=96) and serous ovarian tumours (n=96) that were primary, untreated, and collected from 2000 to 2012 at Memorial Sloan Kettering Cancer Center. The same set of tumour tissue samples were profiled twice using the Agilent microRNA microarrays: once under an ideal experimental condition with balanced array-to-sample allocation and uniform handling; a second time by mimicking typical practice, with arrays assigned in the order of sample collection and processed by two technicians in multiple batches. This paper provides a detailed description of the generation and validation of this unique dataset pair so that the research community can re-use it to investigate other statistical questions regarding microarray study design and data analysis, and to address biological questions on the relevance of microRNA expression in gynaecologic cancer.
HYSOGs250m, global gridded hydrologic soil groups for curve-number-based runoff modeling
Authors: Ross C. Wade , Prihodko Lara , Anchang Julius , Kumar Sanath , Ji Wenjie , Hanan Niall P. 
Published: May 2018

AbstractHydrologic soil groups (HSGs) are a fundamental component of the USDA curve-number (CN) method for estimation of rainfall runoff; yet these data are not readily available in a format or spatial-resolution suitable for regional- and global-scale modeling applications. We developed a globally consistent, gridded dataset defining HSGs from soil texture, bedrock depth, and groundwater. The resulting data product—HYSOGs250m—represents runoff potential at 250 m spatial resolution. Our analysis indicates that the global distribution of soil is dominated by moderately high runoff potential, followed by moderately low, high, and low runoff potential. Low runoff potential, sandy soils are found primarily in parts of the Sahara and Arabian Deserts. High runoff potential soils occur predominantly within tropical and sub-tropical regions. No clear pattern could be discerned for moderately low runoff potential soils, as they occur in arid and humid environments and at both high and low elevations. Potential applications of this data include CN-based runoff modeling, flood risk assessment, and as a covariate for biogeographical analysis of vegetation distributions.