bluuebunny/crossref_metadata_2025_split huggingface dataset:
Generalizing Agarwal's Method for the Interpretation of Recovery Tests Under Non‐Ideal Conditions
Authors: Trabucchi Michela , Carrera Jesús , Fernàndez‐Garcia Daniel 
Published: August 2018

AbstractPumping tests are performed during aquifer characterization to gain conceptual understanding about the system through diagnostic plots and to estimate hydraulic properties. Recovery tests consist of measuring head response in observation and/or pumping wells after pumping termination. They are especially useful when the pumping rate cannot be accurately controlled. They have been traditionally interpreted using Theis' recovery method, which yields robust estimates of effective transmissivity but does not provide information about the conceptual model. Agarwal proposed a method that has become standard in the oil industry, to obtain both early and late time reservoir responses to pumping from recovery data. However, the validity of the method has only been tested to a limited extent. In this work, we analyze Agarwal's method in terms of both drawdowns and log derivatives for non‐ideal conditions: leaky aquifer, presence of boundaries, and one‐dimensional flow. Our results show that Agarwal's method provides excellent recovery plots (i.e., the drawdown curve that would be obtained during pumping) and parameter estimates for nearly all aquifer conditions, provided that a constant pumping rate is used and the log derivative at the end of pumping is constant, which is too limiting for groundwater hydrology practice, where observation wells are usually monitored. We generalize Agarwal's method by (1) deriving an improved equivalent time for time‐dependent pumping rate and (2) proposing to recover drawdown curves by extrapolating the pumping phase drawdowns. These yield excellent diagnostic plots, thus facilitating the conceptual model analysis for a broad range of conditions.
Second harmonic generation hotspot on a centrosymmetric smooth silver surface
Authors: Galanty Matan , Shavit Omer , Weissman Adam , Aharon Hannah , Gachet David , Segal Elad , Salomon Adi 
Published: August 2018

AbstractSecond harmonic generation (SHG) is forbidden for materials with inversion symmetry, such as bulk metals. Symmetry can be broken by morphological or dielectric discontinuities, yet SHG from a smooth continuous metallic surface is negligible. Using non-linear microscopy, we experimentally demonstrate enhanced SHG within an area of smooth silver film surrounded by nanocavities. Nanocavity-assisted SHG is locally enhanced by more than one order of magnitude compared to a neighboring silver surface area. Linear optical measurements and cathodoluminescence (CL) imaging substantiate these observations. We suggest that plasmonic modes launched from the edges of the nanocavities propagate onto the smooth silver film and annihilate, locally generating SHG. In addition, we show that these hotspots can be dynamically controlled in intensity and location by altering the polarization of the incoming field. Our results show that switchable nonlinear hotspots can be generated on smooth metallic films, with important applications in photocatalysis, single-molecule spectroscopy and non-linear surface imaging.
Microbial connectivity and sorting in a High Arctic watershed
Authors: Comte Jérôme , Culley Alexander I , Lovejoy Connie , Vincent Warwick F 
Published: August 2018

Abstract
Aquatic ecosystems in the High Arctic are facing unprecedented changes as a result of global warming effects on the cryosphere. Snow pack is a central feature of northern landscapes, but the snow microbiome and its microbial connectivity to adjacent and downstream habitats have been little explored. To evaluate these aspects, we sampled along a hydrologic continuum at Ward Hunt Lake (latitude 83°N) in the Canadian High Arctic, from snow banks, water tracks in the permafrost catchment, the upper and lower strata of the lake, and the lake outlet and its coastal marine mixing zone. The microbial communities were analyzed by high-throughput sequencing of 16 and 18S rRNA to determine the composition of potentially active Bacteria, Archaea and microbial Eukarya. Each habitat had distinct microbial assemblages, with highest species richness in the subsurface water tracks that connected the melting snow to the lake. However, up to 30% of phylotypes were shared along the hydrologic continuum, showing that many taxa originating from the snow can remain in the active fraction of downstream microbiomes. The results imply that changes in snowfall associated with climate warming will affect microbial community structure throughout all spatially connected habitats within snow-fed polar ecosystems.
Emergence of winner-takes-all connectivity paths in random nanowire networks
Authors: Manning Hugh G. , Niosi Fabio , da Rocha Claudia Gomes , Bellew Allen T. , O’Callaghan Colin , Biswas Subhajit , Flowers Patrick F. , Wiley Benjamin J. , Holmes Justin D. , Ferreira Mauro S. , Boland John J. 
Published: August 2018

AbstractNanowire networks are promising memristive architectures for neuromorphic applications due to their connectivity and neurosynaptic-like behaviours. Here, we demonstrate a self-similar scaling of the conductance of networks and the junctions that comprise them. We show this behavior is an emergent property of any junction-dominated network. A particular class of junctions naturally leads to the emergence of conductance plateaus and a “winner-takes-all” conducting path that spans the entire network, and which we show corresponds to the lowest-energy connectivity path. The memory stored in the conductance state is distributed across the network but encoded in specific connectivity pathways, similar to that found in biological systems. These results are expected to have important implications for development of neuromorphic devices based on reservoir computing.
Iridophores as a source of robustness in zebrafish stripes and variability in Danio patterns
Authors: Volkening Alexandria , Sandstede Björn 
Published: August 2018

AbstractZebrafish (Danio rerio) feature black and yellow stripes, while related Danios display different patterns. All these patterns form due to the interactions of pigment cells, which self-organize on the fish skin. Until recently, research focused on two cell types (melanophores and xanthophores), but newer work has uncovered the leading role of a third type, iridophores: by carefully orchestrated transitions in form, iridophores instruct the other cells, but little is known about what drives their form changes. Here we address this question from a mathematical perspective: we develop a model (based on known interactions between the original two cell types) that allows us to assess potential iridophore behavior. We identify a set of mechanisms governing iridophore form that is consistent across a range of empirical data. Our model also suggests that the complex cues iridophores receive may act as a key source of redundancy, enabling both robust patterning and variability within Danio.
Neonatal brain injury causes cerebellar learning deficits and Purkinje cell dysfunction
Authors: Sathyanesan Aaron , Kundu Srikanya , Abbah Joseph , Gallo Vittorio 
Published: August 2018

AbstractPremature infants are more likely to develop locomotor disorders than term infants. In a chronic sub-lethal hypoxia (Hx) mouse model of neonatal brain injury, we recently demonstrated the presence of cellular and physiological changes in the cerebellar white matter. We also observed Hx-induced delay in Purkinje cell (PC) arborization. However, the behavioral consequences of these cellular alterations remain unexplored. Using the Erasmus Ladder to study cerebellar behavior, we report the presence of locomotor malperformance and long-term cerebellar learning deficits in Hx mice. Optogenetics experiments in Hx mice reveal a profound reduction in spontaneous and photoevoked PC firing frequency. Finally, treatment with a gamma-aminobutyric acid (GABA) reuptake inhibitor partially rescues locomotor performance and improves PC firing. Our results demonstrate a long-term miscoordination phenotype characterized by locomotor malperformance and cerebellar learning deficits in a mouse model of neonatal brain injury. Our findings also implicate the developing GABA network as a potential therapeutic target for prematurity-related locomotor deficits.
Universal holonomic quantum gates over geometric spin qubits with polarised microwaves
Authors: Nagata Kodai , Kuramitani Kouyou , Sekiguchi Yuhei , Kosaka Hideo 
Published: August 2018

AbstractA microwave shares a nonintuitive phase called the geometric phase with an interacting electron spin after an elastic scattering. The geometric phase, generally discarded as a global phase, allows universal holonomic gating of an ideal logical qubit, which we call a geometric spin qubit, defined in the degenerate subspace of the triplet spin qutrit. We here experimentally demonstrate nonadiabatic and non-abelian holonomic quantum gates over the geometric spin qubit on an electron or nitrogen nucleus. We manipulate purely the geometric phase with a polarised microwave in a nitrogen-vacancy centre in diamond under a zero-magnetic field at room temperature. We also demonstrate a two-qubit holonomic gate to show universality by manipulating the electron−nucleus entanglement. The universal holonomic gates enable fast and fault-tolerant manipulation for realising quantum repeaters interfacing between universal quantum computers and secure communication networks.
Uphill production of dihydrogen by enzymatic oxidation of glucose without an external energy source
Authors: Suraniti Emmanuel , Merzeau Pascal , Roche Jérôme , Gounel Sébastien , Mark Andrew G. , Fischer Peer , Mano Nicolas , Kuhn Alexander 
Published: August 2018

AbstractChemical systems do not allow the coupling of energy from several simple reactions to drive a subsequent reaction, which takes place in the same medium and leads to a product with a higher energy than the one released during the first reaction. Gibbs energy considerations thus are not favorable to drive e.g., water splitting by the direct oxidation of glucose as a model reaction. Here, we show that it is nevertheless possible to carry out such an energetically uphill reaction, if the electrons released in the oxidation reaction are temporarily stored in an electromagnetic system, which is then used to raise the electrons’ potential energy so that they can power the electrolysis of water in a second step. We thereby demonstrate the general concept that lower energy delivering chemical reactions can be used to enable the formation of higher energy consuming reaction products in a closed system.
Combining spectroscopic and isotopic techniques gives a dynamic view of phosphorus cycling in soil
Authors: Helfenstein Julian , Tamburini Federica , von Sperber Christian , Massey Michael S. , Pistocchi Chiara , Chadwick Oliver A. , Vitousek Peter M. , Kretzschmar Ruben , Frossard Emmanuel 
Published: August 2018

AbstractCurrent understanding of phosphorus (P) cycling in soils can be enhanced by integrating previously discrete findings concerning P speciation, exchange kinetics, and the underlying biological and geochemical processes. Here, we combine sequential extraction with P K-edge X-ray absorption spectroscopy and isotopic methods (33P and 18O in phosphate) to characterize P cycling on a climatic gradient in Hawaii. We link P pools to P species and estimate the turnover times for commonly considered P pools. Dissolved P turned over in seconds, resin-extractable P in minutes, NaOH-extractable inorganic P in weeks to months, and HCl-extractable P in years to millennia. Furthermore, we show that in arid-zone soils, some primary mineral P remains even after 150 ky of soil development, whereas in humid-zone soils of the same age, all P in all pools has been biologically cycled. The integrative information we provide makes possible a more dynamic, process-oriented conceptual model of P cycling in soils.
Ductile deformation mechanism in semiconductor α-Ag2S
Authors: Li Guodong , An Qi , Morozov Sergey I. , Duan Bo , Goddard William A. , Zhang Qingjie , Zhai Pengcheng , Snyder G. Jeffrey 
Published: August 2018

AbstractInorganic semiconductor α-Ag2S exhibits a metal-like ductile behavior at room temperature, but the origin of this high ductility has not been fully explored yet. Based on density function theory simulations on the intrinsic mechanical properties of α-Ag2S, its underlying ductile mechanism is attributed to the following three factors: (i) the low ideal shear strength and multiple slip pathways under pressure, (ii) easy movement of Ag–S octagon framework without breaking Ag−S bonds, and (iii) a metallic Ag−Ag bond forms which suppresses the Ag–S frameworks from slipping and holds them together. The easy slip pathways (or easy rearrangement of atoms without breaking bonds) in α-Ag2S provide insight into the understanding of the plastic deformation mechanism of ductile semiconductor materials, which is beneficial for devising and developing flexible semiconductor materials and electronic devices.
Evidence for Ussurian tube-nosed bats (Murina ussuriensis) hibernating in snow
Authors: Hirakawa Hirofumi , Nagasaka Yu 
Published: August 2018

AbstractSurviving winter is a challenge for endothermic animals living at high latitudes. In bats, some species migrate to milder climates in winter, but others presumably stay and hibernate in thermally buffered roosts. However, we know little about where, or in what roosts bats hibernate. Ussurian tube-nosed bats (Murina ussuriensis) have occasionally been observed under or near the surface of snow. We collected the details of those accounts and used our own observations to conclude that these bats hibernate in snow. To our knowledge, this is the first evidence of hibernation in snow for bats, and second for mammals, following polar bears (Ursus maritimus) denning in snow.
PMLPR: A novel method for predicting subcellular localization based on recommender systems
Authors: Mirzaei Mehrabad Elnaz , Hassanzadeh Reza , Eslahchi Changiz 
Published: August 2018

AbstractThe importance of protein subcellular localization problem is due to the importance of protein’s functions in different cell parts. Moreover, prediction of subcellular locations helps to identify the potential molecular targets for drugs and has an important role in genome annotation. Most of the existing prediction methods assign only one location for each protein. But, since some proteins move between different subcellular locations, they can have multiple locations. In recent years, some multiple location predictors have been introduced. However, their performances are not accurate enough and there is much room for improvement. In this paper, we introduced a method, PMLPR, to predict locations for a protein. PMLPR predicts a list of locations for each protein based on recommender systems and it can properly overcome the multiple location prediction problem. For evaluating the performance of PMLPR, we considered six datasets RAT, FLY, HUMAN, Du et al., DBMLoc and Höglund. The performance of this algorithm is compared with six state-of-the-art algorithms, YLoc, WOLF-PSORT, prediction channel, MDLoc, Du et al. and MultiLoc2-HighRes. The results indicate that our proposed method is significantly superior on RAT and Fly proteins, and decent on HUMAN proteins. Moreover, on the datasets introduced by Du et al., DBMLoc and Höglund, PMLPR has comparable results. For the case study, we applied the algorithms on 8 proteins which are important in cancer research. The results of comparison with other methods indicate the efficiency of PMLPR.
Mitochondrial ribosomal proteins involved in tellurite resistance in yeast Saccharomyces cerevisiae
Authors: Pontieri Paola , Hartings Hans , Di Salvo Marco , Massardo Domenica R. , De Stefano Mario , Pizzolante Graziano , Romano Roberta , Troisi Jacopo , Del Giudice Angelica , Alifano Pietro , Del Giudice Luigi 
Published: August 2018

AbstractA considerable body of evidence links together mitochondrial dysfunctions, toxic action of metalloid oxyanions, and system and neurodegenerative disorders. In this study we have used the model yeast Saccharomyces cerevisiae to investigate the genetic determinants associated with tellurite resistance/sensitivity. Nitrosoguanidine-induced K2TeO3-resistant mutants were isolated, and one of these mutants, named Sc57-Te5R, was characterized. Both random spore analysis and tetrad analysis and growth of heterozygous (TeS/Te5R) diploid from Sc57-Te5R mutant revealed that nuclear and recessive mutation(s) was responsible for the resistance. To get insight into the mechanisms responsible for K2TeO3-resistance, RNA microarray analyses were performed with K2TeO3-treated and untreated Sc57-Te5R cells. A total of 372 differentially expressed loci were identified corresponding to 6.37% of the S. cerevisiae transcriptome. Of these, 288 transcripts were up-regulated upon K2TeO3 treatment. About half of up-regulated transcripts were associated with the following molecular functions: oxidoreductase activity, structural constituent of cell wall, transporter activity. Comparative whole-genome sequencing allowed us to identify nucleotide variants distinguishing Sc57-Te5R from parental strain Sc57. We detected 15 CDS-inactivating mutations, and found that 3 of them affected genes coding mitochondrial ribosomal proteins (MRPL44 and NAM9) and mitochondrial ribosomal biogenesis (GEP3) pointing out to alteration of mitochondrial ribosome as main determinant of tellurite resistance.
Endogenous HIF2A reporter systems for high-throughput functional screening
Authors: Zaini M. Nazhif , Patel Saroor A. , Syafruddin Saiful E. , Rodrigues Paulo , Vanharanta Sakari 
Published: August 2018

AbstractTissue-specific transcriptional programs control most biological phenotypes, including disease states such as cancer. However, the molecular details underlying transcriptional specificity is largely unknown, hindering the development of therapeutic approaches. Here, we describe novel experimental reporter systems that allow interrogation of the endogenous expression of HIF2A, a critical driver of renal oncogenesis. Using a focused CRISPR-Cas9 library targeting chromatin regulators, we provide evidence that these reporter systems are compatible with high-throughput screening. Our data also suggests redundancy in the control of cancer type-specific transcriptional traits. Reporter systems such as those described here could facilitate large-scale mechanistic dissection of transcriptional programmes underlying cancer phenotypes, thus paving the way for novel therapeutic approaches.
Differential interactions of bacterial lipopolysaccharides with lipid membranes: implications for TRPA1-mediated chemosensation
Authors: Startek Justyna B. , Talavera Karel , Voets Thomas , Alpizar Yeranddy A. 
Published: August 2018

AbstractBacterial lipopolysaccharides (LPS) activate the TRPA1 cation channels in sensory neurons, leading to acute pain and inflammation in mice and to aversive behaviors in fruit flies. However, the precise mechanisms underlying this effect remain elusive. Here we assessed the hypothesis that TRPA1 is activated by mechanical perturbations induced upon LPS insertion in the plasma membrane. We asked whether the effects of different LPS on TRPA1 relate to their ability to induce mechanical alterations in artificial and cellular membranes. We found that LPS from E. coli, but not from S. minnesota, activates TRPA1. We then assessed the effects of these LPS on lipid membranes using dyes whose fluorescence properties change upon alteration of the local lipid environment. E. coli LPS was more effective than S. minnesota LPS in shifting Laurdan’s emission spectrum towards lower wavelengths, increasing the fluorescence anisotropy of diphenylhexatriene and reducing the fluorescence intensity of merocyanine 540. These data indicate that E. coli LPS induces stronger changes in the local lipid environment than S. minnesota LPS, paralleling its distinct ability to activate TRPA1. Our findings indicate that LPS activate TRPA1 by producing mechanical perturbations in the plasma membrane and suggest that TRPA1-mediated chemosensation may result from primary mechanosensory mechanisms.
Plasma metabolomic analysis in mature female common bottlenose dolphins: profiling the characteristics of metabolites after overnight fasting by comparison with data in beagle dogs
Authors: Suzuki Miwa , Yoshioka Motoi , Ohno Yoshito , Akune Yuichiro 
Published: August 2018

AbstractThe present study was aimed at determining the characteristics of plasma metabolites in bottlenose dolphins to provide a greater understanding of their metabolism and to obtain information for the health management of cetaceans. Capillary electrophoresis-time-of-flight mass spectrometry (CE-TOFMS) and liquid chromatograph-time-of-flight mass spectrometry (LC-TOFMS) were conducted on plasma samples after overnight fasting from three common bottlenose dolphins as well as three beagle dogs (representative terrestrial carnivores) for comparison. In total, 257 and 227 plasma metabolites were identified in the dolphins and the dogs, respectively. Although a small number of animals were used for each species, the heatmap patterns, a principal component analysis and a cluster analysis confirmed that the composition of metabolites could be segregated from each other. Of 257 compounds detected in dolphin plasma, 24 compounds including branched amino acids, creatinine, urea, and methylhistidine were more abundant than in dogs; 26 compounds including long-chained acyl-carnitines and fatty acids, astaxanthin, and pantothenic acid were detected only in dolphins. In contrast, 25 compounds containing lactic acid and glycerol 3-phosphate were lower in dolphins compared to dogs. These data imply active protein metabolism, differences in usage of lipids, a unique urea cycle, and a low activity of the glycolytic pathway in dolphins.
A Novel Frequency Selectivity Approach Based on Travelling Wave Propagation in Mechanoluminescence Basilar Membrane for Artificial Cochlea
Authors: Kim Yooil , Kim Ji-Sik , Kim Gi-Woo 
Published: August 2018

AbstractThis study presents the initial assessment for a new approach to frequency selectivity aimed at mimicking the function of the basilar membrane within the human cochlea. The term cochlea tonotopy refers to the passive frequency selectivity and a transformation from the acoustic wave into a frequency signal assisted by the hair cells in the organ of Corti. While high-frequency sound waves vibrate near the base of the cochlea (near the oval windows), low-frequency waves vibrate near the apex (at the maximum distance from the base), which suggests the existence of continuous frequency selectivity. Over the past few decades, frequency selectivity using artificial membranes has been utilized in acoustic transducers by mimicking cochlea tonotopy using cantilever-beam arrays with defined physical parameters such as length and thickness. Unlike the conventional cantilever-beam array type, the travelling wave propagation based-mechanoluminescence (ML) membrane made of ZnS:Cu- polydimethylsiloxane (ZnS:Cu-PDMS) composite that we describe here provides new frequency selectivity more similar to that demonstrated by the human membrane. Here, we explored the potential of the ML membrane to deliver new frequency selectivity by using a non-contact image sensor to measure visualized frequencies. We report that the ML basilar membrane can provide effective visualization of the distribution of strain rate associated with the position of maximal amplitude of the travelling wave.