bluuebunny/crossref_metadata_2025 huggingface dataset:
Ecology of fear: environment-dependent parasite avoidance among ovipositingDrosophila
Authors: Mierzejewski Monika K. , Horn Collin J. , Luong Lien T.
Published: June 2019

Habitat 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

A 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.
Probabilistic indigenization effects at the lexis–syntax interface
Authors: TAMAREDO IVÁN , RÖTHLISBERGER MELANIE , GRAFMILLER JASON , HELLER BENEDIKT
Published: June 2019

Szmrecsanyiet al.(2016) define probabilistic indigenization as the process whereby probabilistic constraints shape variation patterns in different ways, which eventually leads to more heterogeneity in the constraints governing syntactic variation across different varieties of English. The present study extends our knowledge of the heterogeneity of probabilistic grammars by sketching a corpus-based variationist method for calculating the similarity between varieties thereby drawing inspiration from the comparative sociolinguistics literature. Based on linguistic material from theInternational Corpus of English, we ascertain the degree of regional variability of five probabilistic constraints on the genitive, dative, particle placement and subject pronoun omission alternations across three varieties of English, namely British, Indian and Singapore English. Our results indicate that, of the four alternations under study, the genitive alternation is the most homogeneous one from a regional perspective, followed – in increasing order of heterogeneity – by subject pronoun omission, dative and particle placement alternations. On the basis of these findings, we evaluate claims in the literature according to which the extent of probabilistic indigenization is proportional to the lexical specificity of the syntactic phenomenon under study, a hypothesis that is borne out by our data.
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

We 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

Arctic 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.
Cascading Down the Mountain
Authors: Fan Xuanmei , Scaringi Gianvito , Xu Qiang , Huang Runqiu
Published: June 2019

Earthquakes in mountain ranges produce a cascade of geological disturbances and hazards, from enormous landslides to climate change.
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

Recent 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

The 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

One 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

In 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

The 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

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

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

In 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

Entanglement 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

Current 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.
Author Correction: Sequential transfection of RUNX2/SP7 and ATF4 coated onto dexamethasone-loaded nanospheres enhances osteogenesis
Authors: Kim Hye Jin , Park Ji Sun , Yi Se Won , Oh Hyun Jyung , Kim Jae-Hwan , Park Keun-Hong
Published: June 2019

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.
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

Low 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.
Pre-clinical evaluation of a quadrivalent HCV VLP vaccine in pigs following microneedle delivery
Authors: Christiansen D. , Earnest-Silveira L. , Grubor-Bauk B. , Wijesundara D. K. , Boo I. , Ramsland P. A. , Vincan E. , Drummer H. E. , Gowans E. J. , Torresi J.
Published: June 2019

The introduction of directly acting antiviral agents (DAAs) has produced significant improvements in the ability to cure chronic hepatitis C infection. However, with over 2% of the world’s population infected with HCV, complications arising from the development of cirrhosis of the liver, chronic hepatitis C infection remains the leading indication for liver transplantation. Several modelling studies have indicated that DAAs alone will not be sufficient to eliminate HCV, but if combined with an effective vaccine this regimen would provide a significant advance towards achieving this critical World Health Organisation goal. We have previously generated a genotype 1a, 1b, 2a, 3a HCV virus like particle (VLP) quadrivalent vaccine. The HCV VLPs contain the core and envelope proteins (E1 and E2) of HCV and the vaccine has been shown to produce broad humoral and T cell immune responses following vaccination of mice. In this report we further advanced this work by investigating vaccine responses in a large animal model. We demonstrate that intradermal microneedle vaccination of pigs with our quadrivalent HCV VLP based vaccine produces long-lived multi-genotype specific and neutralizing antibody (NAb) responses together with strong T cell and granzyme B responses and normal Th1 and Th2 cytokine responses. These responses were achieved without the addition of adjuvant. Our study demonstrates that our vaccine is able to produce broad immune responses in a large animal that, next to primates, is the closest animal model to humans. Our results are important as they show that the vaccine can produce robust immune responses in a large animal model before progressing the vaccine to human trials.
The Functional Mammalian CRES (Cystatin-Related Epididymal Spermatogenic) Amyloid is Antiparallel β-Sheet Rich and Forms a Metastable Oligomer During Assembly
Authors: Do Hoa Quynh , Hewetson Aveline , Myers Caitlyn , Khan Nazmul H. , Hastert Mary Catherine , M. Harsini Faraz , Latham Michael P. , Wylie Benjamin J. , Sutton R. Bryan , Cornwall Gail A.
Published: June 2019

An amyloid matrix composed of several family 2 cystatins, including the reproductive cystatin CRES, is an integral structure in the mouse epididymal lumen and has proposed functions in sperm maturation and protection. Understanding how CRES amyloid assemblesin vitromay provide clues on how the epididymal amyloid matrix formsin vivo. We therefore purified full-length CRES under nondenaturing conditions and followed its aggregation from monomer to amyloid under conditions that may approximate those in the epididymal lumen. CRES transitioned into a metastable oligomer that was resistant to aggregation and only over extended time formed higher-ordered amyloids. High protein concentrations facilitated oligomer assembly and also were required to maintain the metastable state since following dilution the oligomer was no longer detected. Similar to other amyloid precursors, the formation of CRES amyloids correlated with a loss of α-helix and a gain of β-sheet content. However, CRES is unique in that its amyloids are rich in antiparallel β-sheets instead of the more common parallel β-sheets. Taken together, our studies suggest that early metastable oligomers may serve as building blocks for functional amyloid assembly and further reveal that antiparallel β-sheet-rich amyloids can be functional forms.
Differentiation between wild boar and domestic pig in food by targeting two gene loci by real-time PCR
Authors: Kaltenbrunner Maria , Mayer Walter , Kerkhoff Kirsten , Epp Rita , Rüggeberg Hermann , Hochegger Rupert , Cichna-Markl Margit
Published: June 2019

Studies indicate that many meat products are not authentic, most frequently because the meat species differ from those given on the food labels. At present, DNA based methods play the most important role in meat species authentication. Discrimination of wild boar and domestic pig meat in food is challenging because it is differentiation on the subspecies level. We developed and validated two singleplex real-time PCR assays targeting SNP rs81416363 on chromosome 9 and a duplex real-time PCR assay targeting SNP g.299084751 C > T in the NR6A1 gene located on chromosome 1. The singleplex real-time PCR assays led to some ambiguous results for Mangalica and Krškopolje pig breeds and wild boar individuals from Germany, the duplex real-time PCR assay particularly for the Turopolje pig breed. We demonstrate that the probability of misclassification can be substantially reduced if the results of both the singleplex real-time PCR assays and the duplex real-time PCR assay are taken into consideration. 86 (91.5%) of a total of 94 individuals, comprising 64 domestic pigs (14 different breeds and 6 cross-breeds) and 30 wild boars (from Austria, Germany, Romania, USA and Estonia), were classified correctly.
Winter storms accelerate the demise of sea ice in the Atlantic sector of the Arctic Ocean
Authors: Graham Robert M. , Itkin Polona , Meyer Amelie , Sundfjord Arild , Spreen Gunnar , Smedsrud Lars H. , Liston Glen E. , Cheng Bin , Cohen Lana , Divine Dmitry , Fer Ilker , Fransson Agneta , Gerland Sebastian , Haapala Jari , Hudson Stephen R. , Johansson A. Malin , King Jennifer , Merkouriadi Ioanna , Peterson Algot K. , Provost Christine , Randelhoff Achim , Rinke Annette , Rösel Anja , Sennéchael Nathalie , Walden Von P. , Duarte Pedro , Assmy Philipp , Steen Harald , Granskog Mats A.
Published: June 2019

A large retreat of sea-ice in the ‘stormy’ Atlantic Sector of the Arctic Ocean has become evident through a series of record minima for the winter maximum sea-ice extent since 2015. Results from the Norwegian young sea ICE (N-ICE2015) expedition, a five-month-long (Jan-Jun) drifting ice station in first and second year pack-ice north of Svalbard, showcase how sea-ice in this region is frequently affected by passing winter storms. Here we synthesise the interdisciplinary N-ICE2015 dataset, including independent observations of the atmosphere, snow, sea-ice, ocean, and ecosystem. We build upon recent results and illustrate the different mechanisms through which winter storms impact the coupled Arctic sea-ice system. These short-lived and episodic synoptic-scale events transport pulses of heat and moisture into the Arctic, which temporarily reduce radiative cooling and henceforth ice growth. Cumulative snowfall from each sequential storm deepens the snow pack and insulates the sea-ice, further inhibiting ice growth throughout the remaining winter season. Strong winds fracture the ice cover, enhance ocean-ice-atmosphere heat fluxes, and make the ice more susceptible to lateral melt. In conclusion, the legacy of Arctic winter storms for sea-ice and the ice-associated ecosystem in the Atlantic Sector lasts far beyond their short lifespan.
Generalization of the small-world effect on a model approaching the Erdős–Rényi random graph
Authors: Maier Benjamin F.
Published: June 2019

The famous Watts–Strogatz (WS) small-world network model does not approach the Erdős–Rényi (ER) random graph model in the limit of total randomization which can lead to confusion and complicates certain analyses. In this paper we discuss a simple alternative which was first introduced by Song and Wang, where instead of rewiring, edges are drawn between pairs of nodes with a distance-based connection probability. We show that this model is simpler to analyze, approaches the true ER random graph model in the completely randomized limit, and demonstrate that the WS model and the alternative model may yield different quantitative results using the example of a random walk temporal observable. An efficient sampling algorithm for the alternative model is proposed. Analytic results regarding the degree distribution, degree variance, number of two-stars per node, number of triangles per node, clustering coefficient, and random walk mixing time are presented. Subsequently, the small-world effect is illustrated by showing that the clustering coefficient decreases much slower than an upper bound on the message delivery time with increasing long-range connection probability which generalizes the small-world effect from informed searches to random search strategies. Due to its accessibility for analytic evaluations, we propose that this modified model should be used as an alternative reference model for studying the influence of small-world topologies on dynamic systems as well as a simple model to introduce numerous topics when teaching network science.
Physical activity associates with subarachnoid hemorrhage risk– a population-based long-term cohort study
Authors: Lindbohm Joni V. , Rautalin Ilari , Jousilahti Pekka , Salomaa Veikko , Kaprio Jaakko , Korja Miikka
Published: June 2019

Benefit of physical activity in prevention of aneurysmal subarachnoid hemorrhage (SAH) is unclear. We aimed to clarify this by studying how different types of physical activity associate with SAH risk. By following 65 521 population-based FINRISK participants prospectively from medical and autopsy registries since 1972 until 2014, we detected 543 incident SAHs. At baseline, we measured leisure-time physical activity (LTPA), occupational physical activity (OPA), and commuting physical activity (CPA) levels. The Cox model adjusted for all well-known SAH risk factors and for socioeconomic status, provided hazard ratios (HRs) for physical activity variables. Every 30-minute increase in weekly LTPA decreased SAH risk linearly in men and women HR = 0.95 (95% CI = 0.90–1.00). CPA reduced SAH risk as well, but the association diminished as participants retired. In contrast, individuals with moderate (1.41, 1.04–1.92) and high OPA (1.34, 0.99–1.81) had elevated SAH risk. Protective association of LTPA persisted in all age and hypertension groups, and was even greater in current smokers 0.88 (0.81–0.96) than non-smokers (p = 0.04 for difference). Commuting and leisure time physical activity seem to reduce SAH risk in men and women and is most beneficial for smokers. Future intervention studies should investigate whether physical activity can reduce the rupture risk of intracranial aneurysms.
How typhoons trigger turbidity currents in submarine canyons
Authors: Sequeiros Octavio E. , Bolla Pittaluga Michele , Frascati Alessandro , Pirmez Carlos , Masson Douglas G. , Weaver Philip , Crosby Alexander R. , Lazzaro Gianluca , Botter Gianluca , Rimmer Jeffrey G.
Published: June 2019

Intense turbidity currents occur in the Malaylay Submarine Canyon off the northern coast of Mindoro Island in the Philippines. They start in very shallow waters at the shelf break and reach deeper waters where a gas pipeline is located. The pipeline was displaced by a turbidity current in 2006 and its rock berm damaged by another 10 years later. Here we propose that they are triggered near the mouth of the Malaylay and Baco rivers by direct sediment resuspension in the shallow shelf and transport to the canyon heads by typhoon-induced waves and currents. We show these rivers are unlikely to generate hyperpycnal flows and trigger turbidity currents by themselves. Characteristic signatures of turbidity currents, in the form of bed shear stress obtained by numerical simulations, match observed erosion/deposition and rock berm damage patterns recorded by repeat bathymetric surveys before and after typhoon Nock-ten in December 2016. Our analysis predicts a larger turbidity current triggered by typhoon Durian in 2006; and reveals the reason for the lack of any significant turbidity current associated with typhoon Melor in December 2015. Key factors to assess turbidity current initiation are typhoon proximity, strength, and synchronicity of typhoon induced waves and currents. Using data from a 66-year hindcast we estimate a ~8-year return period of typhoons with capacity to trigger large turbidity currents.
Alpha-band oscillations reflect external spatial coding for tactile stimuli in sighted, but not in congenitally blind humans
Authors: Schubert Jonathan T. W. , Buchholz Verena N. , Föcker Julia , Engel Andreas K. , Röder Brigitte , Heed Tobias
Published: June 2019

We investigated the function of oscillatory alpha-band activity in the neural coding of spatial information during tactile processing. Sighted humans concurrently encode tactile location in skin-based and, after integration with posture, external spatial reference frames, whereas congenitally blind humans preferably use skin-based coding. Accordingly, lateralization of alpha-band activity in parietal regions during attentional orienting in expectance of tactile stimulation reflected external spatial coding in sighted, but skin-based coding in blind humans. Here, we asked whether alpha-band activity plays a similar role in spatial coding for tactile processing, that is, after the stimulus has been received. Sighted and congenitally blind participants were cued to attend to one hand in order to detect rare tactile deviant stimuli at this hand while ignoring tactile deviants at the other hand and tactile standard stimuli at both hands. The reference frames encoded by oscillatory activity during tactile processing were probed by adopting either an uncrossed or crossed hand posture. In sighted participants, attended relative to unattended standard stimuli suppressed the power in the alpha-band over ipsilateral centro-parietal and occipital cortex. Hand crossing attenuated this attentional modulation predominantly over ipsilateral posterior-parietal cortex. In contrast, although contralateral alpha-activity was enhanced for attended versus unattended stimuli in blind participants, no crossing effects were evident in the oscillatory activity of this group. These findings suggest that oscillatory alpha-band activity plays a pivotal role in the neural coding of external spatial information for touch.
Evidence of nitrite acting as a stable and robust inducer of non-cultivability in Mycobacterium tuberculosis with physiological relevance
Authors: Gample Suwarna P. , Agrawal Sonia , Sarkar Dhiman
Published: June 2019

Tuberculosis (TB) is the ninth leading cause of death worldwide, ranking above human immunodeficiency virus. Latency is the major obstacle in the eradication of this disease. How the physiology of the pathogen changes in transition to the latent stage needs to be understood. The latent bacteria extracted from animal hosts exist in a nonculturable (NC) phase, whereas bacteria extracted from most in vitro models are culture-positive. In the present study, we observed that nitrite, up to a concentration of 5 mM, shows the growth of Mycobacterium tuberculosis (MTB) in liquid media, but this effect starts reversing at higher concentrations. At a concentration of 10 mM, nitrite induces rapid nonculturability of MTB at the aerobic stage. This noncultivable dormancy was confirmed by analyzing the characteristics of NC bacteria. Further differential gene expression analyses clearly supported the formation of a dormancy phenotype. This study will be helpful for the use of this bacillus as a dormancy model in future studies on TB latency.
Silver content dependent thermal conductivity and thermoelectric properties of electrodeposited antimony telluride thin films
Authors: Ferrer-Argemi Laia , Yu Ziqi , Kim Jiwon , Myung Nosang V. , Lim Jae-Hong , Lee Jaeho
Published: June 2019

While electrodeposited antimony telluride thin films with silver contents demonstrated promising thermoelectric properties, their thermal conductivity and the silver content dependence remain unknown. Here, we report the thermal conductivities of Ag3.9Sb33.6Te62.5 and AgSbTe2 thin films with controlled annealing and temperature conditions and demonstrate the impact of silver content on thermal transport. After annealing at 160 °C, the room-temperature thermal conductivity of Ag3.9Sb33.6Te62.5 and AgSbTe2 thin films increases from 0.24 to 1.59 Wm−1 K−1 and from 0.17 to 0.56 Wm−1 K−1, respectively. Using phonon transport models and X-ray diffraction measurements, we attribute the thermal conductivity increases to the crystal growth and explain the thermal conductivity variations with the degree of crystallization. Unlike electrical properties reported in previous studies, the presence of silver contents has little impact on the thermal conductivity of Ag3.9Sb33.6Te62.5 and leads to a strong reduction in the thermal conductivity of AgSbTe2 thin films. By performing transient thermal conductivity measurements at 94 °C, we find the crystallization activation energy of Ag3.9Sb33.6Te62.5 and AgSbTe2 films as 1.14 eV and 1.16 eV, respectively. Their differences reveal the role of silver in inhibiting the nucleation and growth of Sb2Te3 crystals and impeding thermal transport. These findings provide guidance for optimizing doping and annealing conditions of antimony tellurides for near-room-temperature thermoelectric applications.
Unusual Flavones from Primula macrocalyx as Inhibitors of OAT1 and OAT3 and as Antifungal Agents against Candida rugosa
Authors: Li Xue , Wang Xue , Li Caiyu , Khutsishvili Manana , Fayvush George , Atha Daniel , Zhang Youcai , Borris Robert P.
Published: June 2019

A bioactivity guided program exploring the interaction of phytochemicals in the entire plant Primula macrocalyx with the organic anion transporters (OAT1 and OAT3) and microorganisms led to the elucidation of ten known flavones (1–4, 6–10, 12) and two previously undescribed flavones (5, 11). The structures of the compounds were determined by extensive analysis of spectroscopic data, as well as by comparison with data from previous reports. Two known flavones (9, 12) are reported for the first time from the family Primulaceae. All compounds were evaluated for inhibition of OAT1 and OAT3. Six flavones (2, 3, 6–8, 12) showed potent inhibitory activity on OAT1, while seven flavones (2, 3, 6–9, 12) showed marked inhibitory activity on OAT3, with IC50 ≤ 10.0 µM. Antimicrobial activities of crude fractions against sixteen microorganisms were tested to give a target yeast strain Candida rugosa for further evaluation of MICs on the isolates. Three flavones (7, 8, 12) showed marked antifungal activity with MIC < 2.0 µM. To our knowledge, this study is the first to evaluate these flavones as inhibitors of the OAT1 and OAT3, and as antifungal agents.
Antibody-driven capture of synaptic vesicle proteins on the plasma membrane enables the analysis of their interactions with other synaptic proteins
Authors: Richter Katharina N. , Patzelt Christina , Phan Nhu T. N. , Rizzoli Silvio O.
Published: June 2019

Many organelles from the secretory pathway fuse to the plasma membrane, to exocytose different cargoes. Their proteins are then retrieved from the plasma membrane by endocytosis, and the organelles are re-formed. It is generally unclear whether the organelle proteins colocalize when they are on the plasma membrane, or whether they disperse. To address this, we generated here a new approach, which we tested on synaptic vesicles, organelles that are known to exo- and endocytose frequently. We tagged the synaptotagmin molecules of newly exocytosed vesicles using clusters of primary and secondary antibodies targeted against the luminal domains of these molecules. The antibody clusters are too large for endocytosis, and thus sequestered the synaptotagmin molecules on the plasma membrane. Immunostainings for other synaptic molecules then revealed whether they colocalized with the sequestered synaptotagmin molecules. We suggest that such assays may be in the future extended to other cell types and other organelles.
Insights into the water status in hydrous minerals using terahertz time-domain spectroscopy
Authors: Ma Yuanyuan , Huang Haochong , Hao Sibo , Qiu Kunfeng , Gao Hua , Gao Lu , Tang Weichong , Zhang Zili , Zheng Zhiyuan
Published: June 2019

The determinations of water status incorporated in hydrous minerals are of considerable significances in geoscience fields. Coincidentally, the aqueous sensitivity of terahertz radiation has motivated numerous explorations in several cross-domain applications. Terahertz time-domain spectroscopy is employed as a major probing technique coupling of traditional detecting methods to uncover the mask of water status in copper sulfate pentahydrate as well as mineral quartz in this article. Based on the quantitative identification of water status in copper sulfate pentahydrate, the water incorporated in mineral quartz is verified qualitatively. Notable differences of optical constants originating from the water content are obtained for copper sulfate pentahydrate and mineral quartz. These present works indicate that terahertz technology can be considered as a promising method to satisfy the ever-increasing requirements in hydrous mineral analyses.
Quantifying Uncertainty Due to Stochastic Weather Generators in Climate Change Impact Studies
Authors: Vesely Fosco M. , Paleari Livia , Movedi Ermes , Bellocchi Gianni , Confalonieri Roberto
Published: June 2019

Climate change studies involve complex processes translating coarse climate change projections in locally meaningful terms. We analysed the behaviour of weather generators while downscaling precipitation and air temperature data. With multiple climate indices and alternative weather generators, we directly quantified the uncertainty associated with using weather generators when site specific downscaling is performed. We extracted the influence of weather generators on climate variability at local scale and the uncertainty that could affect impact assessment. For that, we first designed the downscaling experiments with three weather generators (CLIMAK, LARS-WG, WeaGETS) to interpret future projections. Then we assessed the impacts of estimated changes of precipitation and air temperature for a sample of 15 sites worldwide using a rice yield model and an extended set of climate metrics. We demonstrated that the choice of a weather generator in the downscaling process may have a higher impact on crop yield estimates than the climate scenario adopted. Should they be confirmed, these results would indicate that widely accepted outcomes of climate change studies using this downscaling technique need reconsideration.