bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ecology of fear: environment-dependent parasite avoidance among ovipositingDrosophila
Authors: Mierzejewski Monika K. , Horn Collin J. , Luong Lien T. 
Published: June 2019

AbstractHabitat avoidance is an anti-parasite behaviour exhibited by at-risk hosts that can minimize exposure to parasites. Because environments are often heterogeneous, host decision-making with regards to habitat use may be affected by the presence of parasites and habitat quality simultaneously. In this study we examine how the ovipositing behaviour of a cactiphilic fruit fly,Drosophila nigrospiracula, is affected by the presence of an ectoparasitic mite,Macrocheles subbadius, in conjunction with other environmental factors – specifically the presence or absence of conspecific eggs and host plant tissue. We hypothesized that the trade-off between site quality and parasite avoidance should favour ovipositing at mite-free sites even if it is of inferior quality. We found that although flies avoided mites in homogeneous environments (86% of eggs at mite-free sites), site quality overwhelmed mite avoidance. Both conspecific eggs (65% of eggs at infested sites with otherDrosophilaeggs) and host plant tissue (78% of eggs at infested sites with cactus) overpowered mite avoidance. Our results elucidate the context-dependent decision-making of hosts in response to the presence of parasites in variable environments, and suggest how the ecology of fear and associated trade-offs may influence the relative investment in anti-parasite behaviour in susceptible hosts.
Hybrid-Trajectory Based Terminal Sliding Mode Control of a Flexible Space Manipulator with an Elastic Base
Authors: Yu Xiaoyan 
Published: June 2019

SummaryA hybrid-trajectory based terminal sliding mode controller (TSMC) is addressed for a free-flying two-flexible-link space manipulator with an elastic base. In this system, there are unknown but bounded external disturbances and parameters. First, the Lagrange dynamic model of the manipulator was established by the momentum conservation. Second, a TSMC based on desired trajectory was proposed, by which the terminal trajectories were asymptotically tracked and periodic flexible vibrations were excited. Then based on virtual control force, hybrid trajectories were generated, in which the flexible variables, the joint angular displacement errors and the base’s attitude error were considered. Finally, a hybrid-trajectory TSMC was presented, by which the terminal trajectories were asymptotically tracked and the flexible vibrations were suppressed.
Genetic analysis of sugarcane brown rust resistance genes in wild sugarcane germplasm Erianthus rockii ‘Yundian 95-19’ and Erianthus rockii ‘Yundian 95-20’
Authors: Zhang Rong-Yue , Li Wen-Feng , Huang Ying-Kun , Lu Xin , Wang Xiao-Yan , Shan Hong-Li , Li Jie , Cang Xiao-Yan , Yin Jiong , Luo Zhi-Ming 
Published: June 2019

AbstractWe assessed inheritance of resistance to sugarcane brown rust (Puccinia melanocephala) in selfing F1 populations of wild sugarcane germplasm Erianthus rockii ‘Yundian 95-19’ and E. rockii ‘Yundian 95-20’. We tested parent and selfing F1 individuals for the brown rust resistance gene, Bru1, that has been shown to confer resistance to brown rust in sugarcane. The Bru1 gene was not detected in E. rockii ‘Yundian 95-19’, E. rockii ‘Yundian 95-20’ or their selfing F1 individuals, and we found there was segregation of resistance in the two selfing F1 populations (segregation ratio: 3:1). The results confirmed resistance in E. rockii ‘Yundian 95-19’ and E. rockii ‘Yundian 95-20’ to sugarcane brown rust is controlled by a novel, single dominant gene.
Long‐Term Measurements of Methane Ebullition From Thaw Ponds
Authors: Burke S. A. , Wik M. , Lang A. , Contosta A. R. , Palace M. , Crill P. M. , Varner R. K. 
Published: June 2019

AbstractArctic regions are experiencing rapid warming, leading to permafrost thaw and formation of numerous water bodies. Although small ponds in particular are considered hot spots for methane (CH4) release, long‐term studies of CH4 efflux from these surfaces are rare. We have collected an extensive data set of CH4 ebullition (bubbling) measurements from eight small thaw ponds (<0.001 km2) with different physical and hydrological characteristics over four summer seasons, the longest set of observations from thaw ponds to date. The measured fluxes were highly variable with an average of 20.0 mg CH4 · m−2 · day−1 (median: 4.1 mg CH4 · m−2 · day−1, n = 2,063) which is higher than that of most nearby lakes. The ponds were categorized into four types based on clear and significant differences in bubble flux. We found that the amount of CH4 released as bubbles from ponds was very weakly correlated with environmental variables, like air temperature and atmospheric pressure, and was potentially more related to differences in physical characteristics of the ponds. Using our measured average daily bubble flux plus the available literature, we estimate circumpolar thaw ponds <0.001 km2 in size to emit between 0.2 and 1.0 Tg of CH4 through ebullition. Our findings exemplify the importance of high‐frequency measurements over long study periods in order to adequately capture the variability of these water bodies. Through the expansion of current spatial and temporal monitoring efforts, we can increase our ability to estimate CH4 emissions from permafrost pond ecosystems now and in the future.
The Effect of QBO Phase on the Atmospheric Response to Projected Arctic Sea Ice Loss in Early Winter
Authors: Labe Zachary , Peings Yannick , Magnusdottir Gudrun 
Published: June 2019

AbstractRecent modeling studies have shown an important role for stratosphere‐troposphere coupling in the large‐scale atmospheric response to Arctic sea ice loss. Evidence is growing that the Quasi‐biennial Oscillation (QBO) can contribute to or even mitigate teleconnections from surface forcing. Here, the influence of QBO phase on the atmospheric response to projected Arctic sea ice loss is examined using an atmospheric general circulation model with a well‐resolved stratosphere and a QBO prescribed from observations. The role of the QBO is determined by compositing seasons with easterly phase (QBO‐E) separately from seasons with westerly phase (QBO‐W). In response to the sea ice forcing in early winter, the polar vortex during QBO‐E weakens with strong stratosphere‐troposphere wave‐1 coupling and a negative Northern Annular Mode‐type response. At the surface, this results in more severe Siberian cold spells. For QBO‐W, the polar vortex strengthens in response to the sea ice forcing.
Timescales of the Climate Record in the South Polar Ice Cap of Mars
Authors: Becerra Patricio , Sori Michael M. , Thomas Nicolas , Pommerol Antoine , Simioni Emanuele , Sutton Sarah S. , Tulyakov Stepan , Cremonese Gabriele 
Published: June 2019

AbstractThe South Polar Layered Deposits (SPLD) are the largest water ice reservoirs on Mars. Their accumulation is believed to result from climate oscillations that drive the movement of ice and dust on the surface. The High‐Resolution Imaging Science Experiment and the Colour and Stereo Surface Imaging System have imaged exposures of its internal structure in troughs and marginal scarps. Here we use the stereo imaging products of these instruments to extract stratigraphic profiles representative of various locations throughout the SPLD. Through wavelet and series‐matching analyses of these profiles, we reveal periodicities in the stratigraphy that correlate to the orbital oscillations that drive climate change on Mars and that have been observed to force the accumulation of the north polar cap. We infer that the water ice and dust of the SPLD were deposited at variable rates of 0.13–0.39 mm/year, taking a minimum of 10–30 Myr to accumulate.
New Homogeneous Composite Of Energetic Electron Fluxes From POES: 2. Intercalibration of SEM‐1 and SEM‐2
Authors: Asikainen T. 
Published: June 2019

AbstractOne of the most popular long‐term data sets of energetic particles used in, for example, long‐term radiation belt studies and in atmospheric/climate studies is perhaps the NOAA/POES (Polar Orbiting Environmental Satellites) data set, which extends nearly continuously from 1979 to present. The present study aims to construct a new homogeneous long‐term composite record of daily latitude distributions of energetic electrons based on the MEPED (Medium Energy Proton and Electron Detector) data. Part 1 of this study corrected the data for temporally varying background noise related to cosmic rays and for the drift in the orientation of satellite orbital planes. The present paper addresses the final and most severe problem for the data homogeneity, caused by the difference of telescope pointing directions in older SEM‐1 and newer SEM‐2 versions of the MEPED instrument. Because the telescope pitch angles and the electron pitch angle distribution change with latitude, the difference in SEM‐1 and SEM‐2 fluxes depends on latitude and varies from time to time. The systematic flux differences between SEM‐1 and SEM‐2 can range between a factor of 1.5 to more than an order of magnitude. Novel statistical methodology based on principal components and canonical correlation mapping is presented here to robustly transform the daily SEM‐1 electron latitude distributions into SEM‐2 level. The data from different POES satellites are then combined into a spatially and temporally homogeneous composite series, which is well suited, for example, for long‐term studies of radiation belts and precipitation related atmospheric ionization and its chemical and dynamical effects in the atmosphere/climate system.
On the Balance Between Plasma and Magnetic Pressure Across Equatorial Plasma Depletions
Authors: Rodríguez‐Zuluaga J. , Stolle C. , Yamazaki Y. , Lühr H. , Park J. , Scherliess L. , Chau J. L. 
Published: June 2019

AbstractIn magnetized plasmas such as the ionosphere, electric currents develop in regions of strong density gradients to balance the resulting plasma pressure gradients. These currents, usually known as diamagnetic currents decrease the magnetic pressure where the plasma pressure increases, and vice versa. In the low‐latitude ionosphere, equatorial plasma depletions (EPDs) are well known for their steep plasma density gradients and adverse effect on radio wave propagation. In this paper, we use continuous measurements of the magnetic field and electron density from the European Space Agency's Swarm constellation mission to assess the balance between plasma and magnetic pressure across large‐scale EPDs. The analysis is based on the magnetic fluctuations related to diamagnetic currents flowing at the edges of EPDs. This study shows that most of the EPDs detected by Swarm present a decrease of the plasma pressure relative to the ambient plasma. However, EPDs with high plasma pressure are also identified mainly in the vicinity of the South Atlantic magnetic anomaly. From the electron density measurements, we deduce that such an increase in plasma pressure within EPDs might be possible by temperatures inside the EPD as high as twice the temperature of the ambient plasma. Due to the distinct location of the high‐pressure EPDs, we suggest that a possible heating mechanism might be due to precipitation of particle from the radiation belts. This finding corresponds to the first observational evidence of plasma pressure enhancements in regions of depleted plasma density in the ionosphere.
Long‐Term Hydroclimatic Patterns in the Truckee‐Carson Basin of the Eastern Sierra Nevada, USA
Authors: Biondi F. , Meko D. M. 
Published: June 2019

AbstractThe Truckee/Carson Basin, like other semiarid basins in the western United States, faces challenges to water management and planning under a changing climate. We analyzed tree‐ring data, along with instrumental climatic and hydrologic records, to provide a perspective on extreme drought in the 21st century. Drought indices highlighted a recent increase in the average duration of hydroclimatic episodes: in the new millennium average duration was 74% longer for the 24‐month Standardized Precipitation Index (SPI‐24) and 62% longer for the Palmer Drought Severity Index (PDSI) than in the previous century. Average snow water equivalent (SWE) declined 7% per decade from 1965 to 2018. The 2012‐2015 drought, in particular, stood out for its intensity and expression in snowpack, streamflow, and drought indices. Likely because of recent warming, this 4‐year drought event had a very low likelihood based on observed Carson River flows from the first half of the 20th century. A 501‐year tree‐ring reconstruction (1500‐2000 CE) of average water‐year streamflow for the Carson River indicated that positive (wet) spells had slightly longer duration (mean of 2.7 years and range from 1 to 10 years) than negative (dry) intervals (mean of 2.4 years and range from 1 to 9 years). The early 1900s pluvial, that is, 1905‐1911 in this record, was the third strongest episode in the entire reconstruction. The driest years were 1580 and 1934, both well‐known widespread and severe droughts in the western United States. Noise‐added reconstructions suggest that 2012‐2015, while not unique in the 401 years prior to the start of the Carson River gaged flows in 1901, was a less than one‐in‐a‐century event.
Visualization and prediction of CRISPR incidence in microbial trait-space to identify drivers of antiviral immune strategy
Authors: Weissman J L , Laljani Rohan M R , Fagan William F , Johnson Philip L F 
Published: June 2019

Abstract
Bacteria and archaea are locked in a near-constant battle with their viral pathogens. Despite previous mechanistic characterization of numerous prokaryotic defense strategies, the underlying ecological drivers of different strategies remain largely unknown and predicting which species will take which strategies remains a challenge. Here, we focus on the CRISPR immune strategy and develop a phylogenetically-corrected machine learning approach to build a predictive model of CRISPR incidence using data on over 100 traits across over 2600 species. We discover a strong but hitherto-unknown negative interaction between CRISPR and aerobicity, which we hypothesize may result from interference between CRISPR-associated proteins and non-homologous end-joining DNA repair due to oxidative stress. Our predictive model also quantitatively confirms previous observations of an association between CRISPR and temperature. Finally, we contrast the environmental associations of different CRISPR system types (I, II, III) and restriction modification systems, all of which act as intracellular immune systems.
Microbiome analysis as a platform R&D tool for parasitic nematode disease management
Authors: Hogan Glenn , Walker Sidney , Turnbull Frank , Curiao Tania , Morrison Alison A , Flores Yensi , Andrews Leigh , Claesson Marcus J , Tangney Mark , Bartley Dave J 
Published: June 2019

Abstract
The relationship between bacterial communities and their host is being extensively investigated for the potential to improve the host’s health. Little is known about the interplay between the microbiota of parasites and the health of the infected host. Using nematode co-infection of lambs as a proof-of-concept model, the aim of this study was to characterise the microbiomes of nematodes and that of their host, enabling identification of candidate nematode-specific microbiota member(s) that could be exploited as drug development tools or for targeted therapy. Deep sequencing techniques were used to elucidate the microbiomes of different life stages of two parasitic nematodes of ruminants, Haemonchus contortus and Teladorsagia circumcincta, as well as that of the co-infected ovine hosts, pre- and post infection. Bioinformatic analyses demonstrated significant differences between the composition of the nematode and ovine microbiomes. The two nematode species also differed significantly. The data indicated a shift in the constitution of the larval nematode microbiome after exposure to the ovine microbiome, and in the ovine intestinal microbial community over time as a result of helminth co-infection. Several bacterial species were identified in nematodes that were absent from their surrounding abomasal environment, the most significant of which included Escherichia coli/Shigella. The ability to purposefully infect nematode species with engineered E. coli was demonstrated in vitro, validating the concept of using this bacterium as a nematode-specific drug development tool and/or drug delivery vehicle. To our knowledge, this is the first description of the concept of exploiting a parasite’s microbiome for drug development and treatment purposes.
Lzts1 controls both neuronal delamination and outer radial glial-like cell generation during mammalian cerebral development
Authors: Kawaue T. , Shitamukai A. , Nagasaka A. , Tsunekawa Y. , Shinoda T. , Saito K. , Terada R. , Bilgic M. , Miyata T. , Matsuzaki F. , Kawaguchi A. 
Published: June 2019

AbstractIn the developing central nervous system, cell departure from the apical surface is the initial and fundamental step to form the 3D, organized architecture. Both delamination of differentiating cells and repositioning of progenitors to generate outer radial glial cells (oRGs) contribute to mammalian neocortical expansion; however, a comprehensive understanding of their mechanisms is lacking. Here, we demonstrate that Lzts1, a molecule associated with microtubule components, promotes both cell departure events. In neuronally committed cells, Lzts1 functions in apical delamination by altering apical junctional organization. In apical RGs (aRGs), Lzts1 expression is variable, depending on Hes1 expression levels. According to its differential levels, Lzts1 induces diverse RG behaviors: planar division, oblique divisions of aRGs that generate oRGs, and their mitotic somal translocation. Loss-of-function of lzts1 impairs all these cell departure processes. Thus, Lzts1 functions as a master modulator of cellular dynamics, contributing to increasing complexity of the cerebral architecture during evolution.
Quantifying entanglement in a 68-billion-dimensional quantum state space
Authors: Schneeloch James , Tison Christopher C. , Fanto Michael L. , Alsing Paul M. , Howland Gregory A. 
Published: June 2019

AbstractEntanglement is the powerful and enigmatic resource central to quantum information processing, which promises capabilities in computing, simulation, secure communication, and metrology beyond what is possible for classical devices. Exactly quantifying the entanglement of an unknown system requires completely determining its quantum state, a task which demands an intractable number of measurements even for modestly-sized systems. Here we demonstrate a method for rigorously quantifying high-dimensional entanglement from extremely limited data. We improve an entropic, quantitative entanglement witness to operate directly on compressed experimental data acquired via an adaptive, multilevel sampling procedure. Only 6,456 measurements are needed to certify an entanglement-of-formation of 7.11 ± .04 ebits shared by two spatially-entangled photons. With a Hilbert space exceeding 68 billion dimensions, we need 20-million-times fewer measurements than the uncompressed approach and 1018-times fewer measurements than tomography. Our technique offers a universal method for quantifying entanglement in any large quantum system shared by two parties.
Infection with multiple hepatitis C virus genotypes detected using commercial tests should be confirmed using next generation sequencing
Authors: Fernández-Caso Belén , Fernández-Caballero Jose Ángel , Chueca Natalia , Rojo Eukene , de Salazar Adolfo , García Buey Luisa , Cardeñoso Laura , García Federico 
Published: June 2019

AbstractCurrent HCV genotyping methods may have some limitations in detecting mixed infections. We aimed to determine the accuracy of genotyping and the detection of mixed-genotype infections using the Abbott-RealTime HCV Genotype II assay (Abbott-RT-PCR) in comparison with a Roche-Next Generation Sequencing assay (Roche-NGS). Plasma samples collected from 139 HCV-infected patients tested with Abbott-RT-PCR, 114 with single genotype (GT) and 25 with mixed GTs were genotyped using Roche-NGS. Roche-NGS confirmed all single GTs obtained with Abbott-RT-PCR. One case of Abbott GT 4 was found as GT 1a using Roche-NGS. Genotype 5 was confirmed using Roche-NGS in 75% cases (3 out of 4 cases). Twenty-five patients were identified as having mixed HCVinfections using Abbott-RT-PCR. The concordance between Abbott-RT-PCR and Roche-NGS was 76% (19 out of 25 cases). Three mixed-GT infections identified with the Abbott assay (two (1b + 4); one (1a + 3)) were reported as pure 1b using Roche-NGS. Very divergent results were found for the other three samples. When compared to Roche-NGS, Abbott-RT-PCR has performed excellently for the determination of patients infected with single GTs. For patients that are categorized as having a mixed infection using Abbott-RT-PCR, we recommend an NGS assay as a confirmation test.
Novel insights into pore-scale dynamics of wettability alteration during low salinity waterflooding
Authors: Aziz Rimsha , Joekar-Niasar Vahid , Martínez-Ferrer Pedro J. , Godinez-Brizuela Omar E. , Theodoropoulos Constantinos , Mahani Hassan 
Published: June 2019

AbstractLow salinity waterflooding has proven to accelerate oil production at core and field scales. Wettability alteration from a more oil-wetting to a more water-wetting condition has been established as one of the most notable effects of low salinity waterflooding. To induce the wettability alteration, low salinity water should be transported to come in contact with the oil-water interfaces. Transport under two-phase flow conditions can be highly influenced by fluids topology that creates connected pathways as well as dead-end regions. It is known that under two-phase flow conditions, the pore space filled by a fluid can be split into flowing (connected pathways) and stagnant (deadend) regions due to fluids topology. Transport in flowing regions is advection controlled and transport in stagnant regions is predominantly diffusion controlled. To understand the full picture of wettability alteration of a rock by injection of low salinity water, it is important to know i) how the injected low salinity water displaces and mixes with the high salinity water, ii) how continuous wettability alteration impacts the redistribution of two immiscible fluids and (ii) role of hydrodynamic transport and mixing between the low salinity water and the formation brine (high salinity water) in wettability alteration. To address these two issues, computational fluid dynamic simulations of coupled dynamic two-phase flow, hydrodynamic transport and wettability alteration in a 2D domain were carried out using the volume of fluid method. The numerical simulations show that when low salinity water was injected, the formation brine (high salinity water) was swept out from the flowing regions by advection. However, the formation brine residing in stagnant regions was diffused very slowly to the low salinity water. The presence of formation brine in stagnant regions created heterogeneous wettability conditions at the pore scale, which led to remarkable two-phase flow dynamics and internal redistribution of oil, which is referred to as the "pull-push" behaviour and has not been addressed before in the literature. Our simulation results imply that the presence of stagnant regions in the tertiary oil recovery impedes the potential of wettability alteration for additional oil recovery. Hence, it would be favorable to inject low salinity water from the beginning of waterflooding to avoid stagnant saturation. We also observed that oil ganglia size was reduced under tertiary mode of low salinity waterflooding compared to the high salinity waterflooding.