bluuebunny/crossref_metadata_2025 huggingface dataset:
Production and quality benefits of white clover inclusion into ryegrass swards at different nitrogen fertilizer rates
Authors: Enriquez-Hidalgo D. , Gilliland T. J. , Egan M. , Hennessy D.
Published: June 2018

A 4-year (2010–2013) plot study was undertaken to evaluate the effect of nitrogen (N) fertilizer rate (0, 60, 120, 196 and 240 kg N/ha/year) on seasonal responses and species persistency in frequently and tightly grazed (⩽4 cm) grass-only (GO) and grass white clover swards (GWc). Increasing N application rate increased herbage removed and pre-grazing sward height. Cows frequently grazed the GWc tighter than the GO. Increasing N rate reduced clover content, especially during the warmest months of the year, but less so up to 120 kg N/ha/year. The GWc had greater amounts of herbage removed than GO in the May–September period but the effect was less as N rate increased. Cumulative herbage removed from GWc was greater than GO swards receiving the same N rate and herbage quality was better in GWc than GO. Such effects were reduced as swards aged and with increasing N rate. It was concluded that under frequent and tight grazing management: (1) clover inclusion increased annual herbage removed; (2) herbage removed from GWc swards receiving no N was the same as the GO sward receiving 240 kg N/ha, and greater for the 240 GWc swards than the 240 GO swards; (3) clover inclusion benefits were mainly from summer onwards; (4) the management strategy applied in the current experiment may be capable of alleviating the detrimental effect of N fertilizer on clover, to a point between 60 and 120 kg N/ha.
Peroxisome proliferator-activated receptor β/δ does not regulate glucose uptake and lactose synthesis in bovine mammary epithelial cells cultivated in vitro
Authors: Lohakare Jayant , Osorio Johan S , Bionaz Massimo
Published: June 2018

The hypothesis of the study was that inhibition of PPARβ/δ increases glucose uptake and lactose synthesis in bovine mammary epithelial cells by reducing the expression of the glucose transporter mRNA destabiliser calreticulin. Three experiments were conducted to test the hypothesis using immortalised bovine mammary alveolar (MACT) and primary bovine mammary (PBMC) cells. In Experiment 1, the most effective dose to inhibit PPARβ/δ activity among two synthetic antagonists (GSK-3787 and PT-s58) was assessed using a gene reporter assay. In Experiment 2, the effect on glucose uptake and lactose synthesis was evaluated by measuring glucose and lactose in the media and expression of related key genes upon modulation of PPARβ/δ using GSK-3787, the synthetic PPARβ/δ agonist GW-501516, or a combination of the two in cells cultivated in plastic. In Experiment 3, the same treatments were applied to cells cultivated in Matrigel and glucose and lactose in media were measured. In Experiment 1 it was determined that a significant inhibition of PPARβ/δ in the presence or absence of fetal bovine serum was achieved with ≥ 1000 nm GSK-3787 but no significant inhibition was observed with PT-s58. In Experiment 2, inhibition of PPARβ/δ had no effect on glucose uptake and lactose synthesis but they were both increased by GW-501516 in PBMC. The mRNA abundance of PPARβ/δ target gene pyruvate dehydrogenase kinase 4 was increased but transcription of calreticulin was decreased (only in MACT cells) by GW-501516. Treatment with GSK-3787 did not affect the transcription of measured genes. No effects on glucose uptake or lactose synthesis were detected by modulation of PPARβ/δ activity on cells cultivated in Matrigel. The above data do not provide support for the original hypothesis and suggest that PPARβ/δ does not play a major role in glucose uptake and lactose synthesis in bovine mammary epithelial cells.
A process for assessing and prioritizing species conservation needs: going beyond the Red List
Authors: Johnson Kevin , Baker Anne , Buley Kevin , Carrillo Luis , Gibson Richard , Gillespie Graeme R. , Lacy Robert C. , Zippel Kevin
Published: June 2018

Conservation resources are limited, yet an increasing number of species are under threat. Assessing species for their conservation needs is, therefore, a vital first step in identifying and prioritizing species for both ex situ and in situ conservation actions. Using a transparent, logical and objective method, the Conservation Needs Assessment process developed by Amphibian Ark uses current knowledge of species in the wild to determine those with the most pressing conservation needs, and provides a foundation for the development of holistic conservation action plans that combine in situ and ex situ actions as appropriate. These assessments allow us to maximize the impact of limited conservation resources by identifying which measures could best serve those species requiring help. The Conservation Needs Assessment complements the IUCN Red List assessment, and together they provide a more holistic guide to conservation priorities and actions. Conservation Needs Assessments generate national prioritized lists of species recommended for conservation action. These can subsequently be used to assist in the development of species recovery plans and national action plans, or to inform national conservation priorities better. Additional tools that will evaluate the recommendations for ex situ rescues, to determine the best candidates for conservation breeding programmes, are currently under development.
TECHNOLOGICAL AND PROVENANCE ANALYSIS OF AN EARLY AND MIDDLE CYCLADIC POTTERY ASSEMBLAGE FROM THERASIA, GREECE
Authors: Kordatzaki Georgia , Sbonias Kostas , Farinetti Emeri , Tzachili Iris
Published: June 2018

During the archaeological survey research project ‘Island Cultures in a Diachronic Perspective: the case of Therasia’, large amounts of pottery were recorded throughout the island of Therasia, ranging in date from the Bronze Age to modern times. Focusing on the prehistoric period, pottery of the Early Cycladic and late Middle Cycladic periods was recovered at Panaghia Koimisis, which is situated on the southern part of the island. This paper presents the petrographic data and results of the analysis carried out on pottery samples which are representative of variable surface treatments and different macro-fabrics of these two prehistoric periods. Tackling issues of provenance and technology, the current scientific analysis attests the coexistence of Theran and off-Theran pottery fabrics already at Panaghia Koimisis in the Early Cycladic period. The majority of the pottery fabrics at Panaghia Koimisis were identified as Theran and the analysis demonstrates intensive contacts between the southern parts of Thera and Therasia throughout the Early and late Middle Cycladic phases. Moreover, adding support to previous studies, this research indicates a wide Cycladic pottery network, in which the site participated as a consumer. During the late Middle Cycladic period major changes in the Theran production are documented, including the disappearance of the earlier pottery recipe, which had been prevalent at Panaghia Koimisis.
L2 DEVELOPMENT OF PERCEPTUAL CATEGORIZATION OF DIALECTAL SOUNDS
Authors: Schmidt Lauren B.
Published: June 2018

The present study examined second language (L2) development in the perceptual identification of a dialectal sound of the target language, through an investigation of the role of individual learner experiences in L2 phonological development. A total of 213 English-speaking learners of Spanish across five levels of study and with varying dialect contact experiences completed an identification task, which tested perceptual categorization of Spanish dialectal aspirated-s (e.g.,siesta[ˈsi̯eh-ta]). In accordance with postulates of L2 speech perception models (PAM-L2, SLM, L2LP), findings revealed influence of the first language phonology on categorization at early levels shifting toward nativelike, dialect-specific categorizations of aspirated-s for more experienced learners. Dialect contact factors of prior study abroad location, native speaker social contacts, and metalinguistic training were found to be predictors of the dialectal perceptual targets toward which the L2 learners developed—for those learners past intermediate-level language courses—highlighting how individual experiences shape L2 perceptual abilities.
In Search of Greene's Argument
Authors: PAULO NORBERT
Published: June 2018

The moral psychologist Joshua Greene has proposed a number of arguments for the normative significance of empirical research and for the unreliability of deontological intuitions. For these arguments, much hinges on the combination of various components of Greene's research – namely the dual-process theory of moral judgement, ‘personalness’ as a factor in moral decision-making, and his functional understanding of deontology and consequentialism. Incorporating these components, I reconstruct three distinct arguments and show that the Personalness Argument for the claim that empirical research can advance normative ethics and the Combined Argument against deontology are both sound and interesting in themselves. They do not, however, cast doubt on traditional deontology or reserve a specific role for neuroscience. The Indirect Route argument overcomes some of the other arguments’ limitations. It is, however, invalid. I conclude by pointing out the broader philosophical relevance of Greene's arguments as shedding light on second-order morality.
Institutional complementarities between labour laws and innovation
Authors: BELLOC FILIPPO
Published: June 2018

We analyse how institutional complementarities between employee representation laws and dismissal restrictions influence aggregate innovation outcomes. We argue that greater employee voice, due to improved employee representation legislations, may spur innovative effort by employees only when shareholders cannot renegotiate ex-ante agreements with workers over revenue sharing, by threatening dismissal. We perform a panel regression analysis, exploiting country-sector panel data over the 1977–2005 period, and find that stronger employee representation laws in the presence of stricter firing restrictions are in fact associated with higher patenting activity. Consistently with our theoretical argument, the magnitude of this empirical relationship is seen to be relatively larger in those sectors where the human capital contribution to production is higher. Implications for the analysis of economic institutions and for legal policy making are proposed.
CPW slot antenna with Y-shaped central monopole and matching arms
Authors: Inserra Daniele , Fang Xiaochuan , Huang Yongjun , Wen Guangjun
Published: June 2018

A coplanar waveguide slot antenna is herein presented. A rectangular slot is excited by a Y-shaped monopole etched on a single FR4 substrate. This structure exhibits two resonances due to the presence of the slot and the central monopole which can be used to design a dual-band or a wideband antenna. A parametric analysis is presented to describe the impedance matching mechanism for the two impedance bandwidths (BWs), as well as for the wideband antenna. The latter is fabricated and provides a measured impedance BW from 2.28 to 3.6 GHz, and gain larger than 2 dBi, yielding an outstanding BW/size trade-off. Finally, a 60 mm × 60 mm back metallic reflector is used to achieve a directive antenna with 6 dBi of measured gain, and an impedance BW from 2.16 to 3.59 GHz.
Influence of Plant Growth Stage and Temperature on Glyphosate Efficacy in Common Lambsquarters (Chenopodium album)
Authors: DeGreeff Randy D. , Varanasi Aruna V. , Dille J. Anita , Peterson Dallas E. , Jugulam Mithila
Published: June 2018

Plant growth stage and temperature influence the activity of glyphosate on common lambsquarters. A biotype of common lambsquarters in Dickinson County, KS (DK) was not controlled upon treatment with glyphosate in the field. In a greenhouse dose–response study, the DK biotype expressed 1.5-fold less sensitivity to glyphosate compared to a known susceptible biotype from Riley County, KS (RL). Common lambsquarters plants were treated at different growth stages (5 to 7, 10 to 12, 15 to 17, or 19 to 21 cm tall) with glyphosate at a field rate (840 g ae ha–1), and, regardless of the biotype, plants were more susceptible to glyphosate when they were 5 to 7 cm tall. Common lambsquarters plants were treated with glyphosate (840 g ae ha–1) after growing at different temperatures (25/15, 32.5/22.5, or 40/30 C day/night), and regardless of the biotype, plants were more susceptible to glyphosate when grown at 25/15 C. The results suggest that the DK biotype exhibits reduced sensitivity to glyphosate compared to the RL biotype, and glyphosate applied at field rate would be more effective on smaller common lambsquarters plants and at cooler temperatures. Common lambsquarters seedlings tend to emerge when temperatures are cooler, early in the spring relative to other summer annual weeds. Therefore, plants should be identified and treated earlier in the growing season for best efficacy with glyphosate.
Spatiotemporal Features of Intraseasonal Oceanic Variability in the Philippine Sea From Mooring Observations and Numerical Simulations
Authors: Hu Shijian , Sprintall Janet , Guan Cong , Sun Bowen , Wang Fan , Yang Guang , Jia Fan , Wang Jianing , Hu Dunxin , Chai Fei
Published: June 2018

The Philippine Sea is located within the pathway of the propagating Madden‐Julian Oscillation system and is also the destination for the North Pacific mesoscale oceanic eddies and waves. As such, the Philippine Sea is characterized by striking intraseasonal variability (ISV; 20–90 days) that plays a key role in bridging weather and climate. Spatial patterns and temporal features of intraseasonal oceanic variability along the Philippine coast are investigated using mooring observations and outputs from an eddy‐resolving general circulation model. The amplitude of ISV determined from sea level anomaly is found to decrease from the northern and coastal Philippine Sea to the south and interior Pacific Ocean. In contrast, eddy kinetic energy features a northward decreasing gradient with a maximum at about 6°N. The meridional distribution of sea level anomaly and eddy kinetic energy spectra indicates that the ISV period increases with latitude and is symmetrical about the equator. Mesoscale eddies in the upper layer are tracked to explore the statistical distribution. Westward propagating mesoscale eddies and intraseasonal Rossby waves related to dynamic instabilities are an important source of the oceanic ISV in the Philippine Sea. Clear coastal propagation of ISVs related to coastal Kelvin waves is detected the south of about 14°N. Composite analysis shows that the Madden‐Julian Oscillation is another important forcing shaping the spatial features of Philippine ISV intensity and contributes close to half of the observed total ISV.
Evaluation and Intercomparison of Five North American Dry Deposition Algorithms at a Mixed Forest Site
Authors: Wu Zhiyong , Schwede Donna B. , Vet Robert , Walker John T. , Shaw Mike , Staebler Ralf , Zhang Leiming
Published: June 2018

To quantify differences between dry deposition algorithms commonly used in North America, five models were selected to calculate dry deposition velocity (Vd) for O3 and SO2 over a temperate mixed forest in southern Ontario, Canada, where a 5‐year flux database had previously been developed. The models performed better in summer than in winter with correlation coefficients for hourly Vd between models and measurements being approximately 0.6 and 0.3, respectively. Differences in mean Vd values between models were on the order of a factor of 2 in both summer and winter. All models produced lower Vd values than the measurements of O3 in summer and SO2 in summer and winter, although the measured Vd may be biased. There was not a consistent tendency in the models to overpredict or underpredict for O3 in winter. Several models produced magnitudes of the diel variation of Vd (O3) comparable to the measurements, while all models produced slightly smaller diel variations than the measurements of Vd (SO2) in summer. A few models produced larger diel variations than the measurements of Vd for O3 and SO2 in winter. Model differences were mainly due to different surface resistance parameterizations for stomatal and nonstomatal uptake pathways, while differences in aerodynamic and quasi‐laminar resistances played only a minor role. It is recommended to use ensemble modeling results for ecosystem impact assessment studies, which provides mean values of all the used models and thus can avoid too much overestimations or underestimations.
The Case of the Missing Lunar Heat Flow Data Is Finally Solved
Authors: Stanley Sarah
Published: June 2018

Decades-old data analyzed for the first time suggest that astronauts’ disturbance of the Moon surface increased solar heat intake, warming the ground below.
Evidence Connecting Mercury's Magnesium Exosphere to Its Magnesium‐Rich Surface Terrane
Authors: Merkel Aimee W. , Vervack Ronald J. , Killen Rosemary M. , Cassidy Timothy A. , McClintock William E. , Nittler Larry R. , Burger Matthew H.
Published: June 2018

Mercury is surrounded by a tenuous, collisionless exosphere where the surface of the planet is directly exposed to the space environment. As a consequence, impacts and space weathering processes are expected to eject atoms and molecules from the surface into the exosphere, implying a direct link between the exospheric composition and the planet's regolith material. However, observational evidence demonstrating this link has been elusive. Here we report that exospheric magnesium, a species recently discovered and systematically measured by the Mercury Surface, Space ENvironment, GEochemistry, and Ranging mission, is enhanced when observed over a portion of the planet's surface regolith rich in magnesium. These observations confirm a direct link between Mercury's magnesium exosphere and the underlying crustal surface composition, providing strong evidence supporting theoretical arguments that impact vaporization can directly supply material to the exosphere from the regolith of a rocky, airless body.
Response of Mesospheric HO2and O3to Large Solar Proton Events
Authors: Zou Zicheng , Xue Xianghui , Shen Chenglong , Yi Wen , Wu Jianfei , Chen Tingdi , Dou Xiankang
Published: June 2018

A lot of solar proton events (SPEs) have happened during the ongoing solar cycle 24 including extremely large events. Seven large SPEs from 2012 to 2017 were chosen to find the response of polar atmosphere to them. Three SPEs happened in 2012, and the other four SPEs happened in 2013, 2014, 2015, and 2017, respectively. The National Oceanic and Atmospheric Administration Geostationary Operational Environmental Satellites 13 proton observations were used to illustrate the proton flux toward the Earth during each SPE. These energetic protons are deposited in the middle and upper atmosphere and ionize the neutral atmosphere constituents and create radicals HOx(H, OH, and HO2). Enhancements in the upper atmospheric hydroperoxyl radical (HO2) of both polar regions of over 1 ppbv are found in the Aura Microwave Limb Sounder measurements immediately after some SPEs happened. The Microwave Limb Sounder observations of ozone (O3) show decreases of >10% in both polar middle and upper atmosphere for a few days with a peak value of >20–60% over 1–3 days. The compositions of HO2and ozone for all the selected SPEs indicate that the polar ozone depletions during the SPEs in a way are the result of the HO2enhancements.
South Atlantic Subtropical Gyre Late Twentieth Century Changes
Authors: Marcello Fernanda , Wainer Ilana , Rodrigues Regina R.
Published: June 2018

This study builds upon existing research suggesting recent changes in the circulation of global subtropical gyres with respect to the South Atlantic Ocean using simulation results from the ocean component of the Community Earth System Model version 1—the Parallel Ocean Program version 2. The results point to an intensification of the total anticyclonic circulation of the subtropical gyre and a southward displacement of the system, as revealed by the wind stress curl, sea surface height, and barotropic stream function fields. Increased values of these variables were found within the dynamical limits of the South Atlantic Subtropical Gyre (SASG), while their basin‐scale structure seemed to be concurrently drifting poleward. The southern branch of the South Equatorial Current (sSEC) marks the northern boundary of the SASG. When reaching the South American coast, it bifurcates into the North Brazil Undercurrent to the north and the Brazil Current to the south. The sSEC bifurcation latitude (SBL) dictates the partition between the waters flowing poleward to recirculate within the SASG and those flowing toward the equatorial region and the Northern Hemisphere. A southward migration of the SBL at a rate of −0.11°± 0.03°/year was observed, associated with a substantial increase in the equatorward advection of waters within the sSEC‐SBL‐North Brazil Undercurrent system.
Drivers of Interannual Variability of Summer Mixed Layer Depth in the Southern Ocean Between 2002 and 2011
Authors: Panassa E. , Völker C. , Wolf‐Gladrow D. , Hauck J.
Published: June 2018

Climate change projections indicate that there will be warming and an intensification of westerly winds in the Southern Ocean (SO) in the future. These two forcings potentially have opposing effects on the depth of the surface mixed layer. Here we investigate how interannual to decadal variability of atmospheric surface air temperature (SAT) and zonal wind speed (uwind) impact mixed layer depth (MLD) in the SO (south of 30°S) during summer, the season of main biological activity. We use gridded MLD data from observations and atmospheric reanalysis data of uwind and SAT in the SO to assess summer MLD variability and its potential drivers. With a model‐based sensitivity experiment, we quantify the relative contributions of uwind versus SAT forcing on the summer MLD in the decade 2002–2011. Wind‐induced changes dominate over temperature‐induced changes of the MLD between 2002 and 2011. We find a positive trend of summer MLD in the Antarctic Zone of the Atlantic and Indian Ocean sectors. Our model‐based sensitivity study suggests that the summer MLD shows a zonally asymmetric response to recent atmospheric forcing. In the Pacific and Australian sectors, cooling and intensification of uwind jointly result in a deepening of the mixed layer. In the Atlantic and Indian sectors, the MLD responds differently north and south of the Antarctic Polar Front (APF). A deepening south of the APF is caused by the increase in uwind, whereas the decrease in uwind and warming act in concert to result in a shoaling of the MLD north of the APF.
Temporal Variability in Surface Water pCO2 in Adventfjorden (West Spitsbergen) With Emphasis on Physical and Biogeochemical Drivers
Authors: Ericson Y. , Falck E. , Chierici M. , Fransson A. , Kristiansen S. , Platt S. M. , Hermansen O. , Myhre C. L.
Published: June 2018

Seasonal and interannual variability in surface water partial pressure of CO2 (pCO2) and air‐sea CO2 fluxes from a West Spitsbergen fjord (IsA Station, Adventfjorden) are presented, and the associated driving forces are evaluated. Marine CO2 system data together with temperature, salinity, and nutrients, were collected at the IsA Station between March 2015 and June 2017. The surface waters were undersaturated in pCO2 with respect to atmospheric pCO2 all year round. The effects of biological activity (primary production/respiration) followed by thermal forcing on pCO2 were the most important drivers on a seasonal scale. The ocean was a sink for atmospheric CO2 with annual air‐sea CO2 fluxes of −36 ± 2 and −31 ± 2 g C·m−2·year−1 for 2015–2016 and 2016–2017, respectively, as estimated from the month of April. Waters of an Arctic origin dominated in 2015 and were replaced in 2016 by waters of a transformed Atlantic source. The CO2 uptake rates over the period of Arctic origin waters were significantly higher (2 mmol C·m−2·day−1) than the rates of the Atlantic origin waters of the following year.
Exaggerated Effect of Urbanization in the Diurnal Temperature Range Via “Observation minus Reanalysis” and the Physical Causes
Authors: Wang Jun , Yan Zhongwei , Feng Jinming
Published: June 2018

The observation minus reanalysis (OMR) method is widely used to investigate the impact of urbanization and land use changes on regional climate. Based on homogenized temperature observations and the National Centers for Environmental Prediction/Department of Energy Atmospheric Model Intercomparison Project II reanalysis surface temperatures, we estimate the trend in diurnal temperature range (DTR) using the OMR method to be −0.324 ± 0.063 °C per decade for the period of 1980–2009 in eastern China. However, we find that reanalysis data produce a positive trend in downward surface solar radiation, while the observations do not, because the reanalysis data significantly overestimate the negative trend in total cloud coverage in the region. Moreover, the reanalysis considerably overestimates the negative trend in the local precipitation. These systematic biases cause an overestimation of the warming rate in daily maximum temperature in the reanalysis and therefore lead to the exaggerated effect of urbanization on the DTR via the OMR analysis. After adjusting the systematic bias in the trend of daily maximum temperature in the reanalysis data, the regional mean OMR trend in the DTR is estimated to be −0.065 °C per decade, which becomes much smaller than previous OMR calculations, and is more consistent with the previous estimates based on the comparison of urban and rural stations. These results not only indicate the methodological problem of the OMR method in many studies of urbanization effects but also hint at important aspects for improving the current reanalysis system.
Making Sense of Massive Carbon Isotope Excursions With an Inverse Carbon Cycle Model
Authors: Miyazaki Yoshinori , Planavsky Noah J. , Bolton Edward W. , Reinhard Christopher T.
Published: June 2018

The beginning and end of the Proterozoic Eon are marked by extreme variations in carbonate carbon isotope values that have been interpreted to record massive perturbations to the global carbon cycle. The lower Proterozoic contains an extended interval of strata characterized by positive carbonate δ13C values. Conversely, uppermost Proterozoic carbonate strata contain thick intervals with extremely negative δ13C values and multiple large swings in carbonate δ13C. Previous attempts to model these pronounced carbon isotope excursions as shifts in the global marine dissolved inorganic carbon (DIC) reservoir have proved to be problematic, as the direction and magnitude of these positive and negative carbon isotope excursions require unrealistic amounts of either organic carbon burial or organic carbon oxidation, respectively. Here we present a modified global carbon cycle model—coupled with oxygen and sulfur cycle mass balances—that includes a parameterization of the recycling of sedimentary isotope anomalies and allows the extent of organic carbon oxidation to vary as a function of atmospheric oxygen levels. Our model is designed to match carbon isotope records while maintaining redox and mass balance with a given set of initial conditions and carbon cycle parameterizations. Using this approach, we demonstrate that there is a range of plausible biogeochemical perturbations that could induce substantial δ13C excursions in the global marine DIC reservoir. However, we also find that there are multiple, nonunique Earth system states for any observed marine δ13C value.
Tree Mortality From Insect Infestation Enhances Carbon Stabilization in Southern Appalachian Forest Soils
Authors: Fraterrigo Jennifer M. , Ream Kelsey , Knoepp Jennifer D.
Published: June 2018

Forest insect and pathogen outbreaks may exacerbate anthropogenic climate change if they accelerate soil carbon loss to the atmosphere. We quantified soil respiration and carbon content for nearly a decade after girdling or natural infestation of hemlock (Tsuga canadensis L. Carr., a codominant species in southern Appalachian forests) by hemlock woolly adelgid (Adelges tsugae) to improve understanding of soil carbon response to disturbance from forest insect and pathogens. From 2005 to 2013, net soil respiration was similar among hemlock mortality (~50% basal area reduction) and reference hardwood plots, but both girdled and hemlock woolly adelgid‐infested plots showed greater activities of β‐glucosidase (a cellulose‐hydrolyzing extracellular enzyme), decreased O‐horizon, and decreased fine root biomass. During this period, mineral soil carbon accumulated at a higher rate in hemlock mortality plots than in reference plots in both surface (0–10 cm) and subsurface (10–30 cm) soils, driven by increases in the mineral‐associated fraction of the soil organic matter. In contrast, particulate organic matter (POM) carbon accrued slowly in surface soils and declined in the subsurface of girdled plots. δ13C values of the POM fraction demonstrate increased microbial processing of surface soil organic matter over time, suggesting enhanced decomposition of organic matter in this pool. These findings indicate that hemlock mortality in this system has led to enhanced soil carbon stabilization through the transformation and translocation of carbon from detrital and POM pools to the mineral‐associated organic matter pool. Accelerated responses in the girdled versus naturally infested treatments highlight limitations associated with using girdling to simulate natural mortality.
Benthic Biotic Response to Climate Changes Over the Last 700,000 Years in a Deep Marginal Sea: Impacts of Deoxygenation and the Mid‐Brunhes Event
Authors: Huang Huai‐Hsuan M. , Yasuhara Moriaki , Iwatani Hokuto , Alvarez Zarikian Carlos A. , Bassetti Maria‐Angela , Sagawa Takuya
Published: June 2018

The Sea of Japan is a marginal sea, connecting to adjacent seas by four shallow straits (water depths <130 m). Marginal seas are ideal for studying biotic responses to large‐scale environmental changes as they often are sensitive to glacial‐interglacial and stadial‐interstadial climatic cycles. However, only a limited number of studies cover time periods beyond the last two glacial‐interglacial cycles. Here we present a 700,000‐year record of benthic biotic response to paleoceanographic changes in the southern Sea of Japan, covering the past seven glacial‐interglacial cycles, based on ostracode assemblages at the Integrated Ocean Drilling Program (IODP) Site U1427. The results indicate that long‐term oxygen variability in the bottom water has been the major control impacting the marginal‐sea biota. Five local extirpation events were recognized as barren zones during glacial maxima immediately before terminations I, II, IV, V, and VII, which are probably caused by bottom‐water deoxygenation. Results of multivariate analyses indicated clear faunal cyclicity influenced by glacial‐interglacial oxygen variability with a succession from opportunistic species dominance through tolerant infauna dominance to barren zone during the deoxygenation processes and the opposite succession during the recovery processes. The Sea of Japan ostracode faunal composition showed distinct difference between the post‐MBE and pre‐MBE (Mid‐Brunhes Event) periods, indicating the MBE as a major disturbance event in marginal‐sea ecosystems. The MBE shortened the duration of the extirpation events, fostered dominance of warmer‐water species, and amplified the glacial‐interglacial faunal cyclicity. Our long‐term biotic response study clearly indicates that deep marginal sea ecosystems are dynamic and vulnerable to climate changes.
Orbitally Forced Hydrological Balance During the Messinian Salinity Crisis: Insights From Strontium Isotopes (87Sr/86Sr) in the Vena del Gesso Basin (Northern Apennines, Italy)
Authors: Reghizzi Matteo , Lugli Stefano , Manzi Vinicio , Rossi Francesco Paolo , Roveri Marco
Published: June 2018

The87Sr/86Sr ratio is a proxy of the hydrologic structure of marginal basins characterized by the mixing between marine and continental waters. This reliable paleoceanographic and paleoclimatic tool is considered a key to the reconstruction of high‐amplitude hydrologic changes that governed the evolution of the Mediterranean region during the Messinian salinity crisis (MSC), when reduced connections with the global ocean resulted in the deposition of the most studied Earth's salt giant. Paleohydrological dynamics leading to the deposition of the Primary Lower Gypsum during the first stage of the MSC were revealed by the study of the87Sr/86Sr composition of 114 samples from the Vena del Gesso basin (Northern Apennines, Italy). The analysis of seven high‐resolution87Sr/86Sr profiles from individual gypsum beds suggests a climatic influence of precessional‐scale orbital parameters during evaporite deposition. The variations of Sr isotope ratios over time indicate that gypsum precipitation started from a seawater body dominated by continental contributions, followed by a relative increase of marine input. The overall results show a gradual upward detachment from the global ocean87Sr/86Sr curve, with crucial steps corresponding to the most extreme eccentricity minima, suggesting an orbital influence on the hydrological balance of the basin. Given the sedimentological and geochemical analogies shared by the Mediterranean marginal basins that hosted the Primary Lower Gypsum deposition, the87Sr/86Sr evolution of the Vena del Gesso basin may be considered as indicative of Mediterranean‐scale hydrologic dynamics, driven by gradual reduction of exchanges with the Atlantic and variable freshwater input.
Complete characterization of ultrashort optical pulses with a phase-shifting wedged reversal shearing interferometer
Authors: Lam Billy , Guo Chunlei
Published: June 2018

The ability of an interferometer to characterize the spatial information of a light beam is often limited by the temporal profile of the beam, with femtosecond pulse characterization being particularly challenging. In this study, we developed a simple, stable, controllable shearing and vectorial phase-shifting wedged reversal shearing interferometer that is able to characterize all types of coherent and partially coherent light beams. The proposed interferometer consists of only a single beam splitter cube with one wedged entrance face and is insensitive to environmental vibration due to its common path configuration. A near zero-path length difference of the proposed interferometer ensures its operation for ultrashort pulses, providing, for the first time, a simple and stable interferometric tool to fully characterize sub-100  fs laser pulses. All common beam characterization can be carried out with the interferometer, such as the amplitude, phase, polarization, wavelength, and pulse duration. Furthermore, this technique is sensitive to the wavefront tilt and can be used for precise beam alignment. Therefore, this interferometer can be an essential tool for beam characterization, optical imaging, and the testing required for a wide range of applications, including astronomy, biomedicine, ophthalmology, optical testing and imaging systems, and adaptive optics.
Subnanometer localization accuracy in widefield optical microscopy
Authors: Copeland Craig R. , Geist Jon , McGray Craig D. , Aksyuk Vladimir A. , Liddle J. Alexander , Ilic B. Robert , Stavis Samuel M.
Published: June 2018

The common assumption that precision is the limit of accuracy in localization microscopy and the typical absence of comprehensive calibration of optical microscopes lead to a widespread issue—overconfidence in measurement results with nanoscale statistical uncertainties that can be invalid due to microscale systematic errors. In this article, we report a comprehensive solution to this underappreciated problem. We develop arrays of subresolution apertures into the first reference materials that enable localization errors approaching the atomic scale across a submillimeter field. We present novel methods for calibrating our microscope system using aperture arrays and develop aberration corrections that reach the precision limit of our reference materials. We correct and register localization data from multiple colors and test different sources of light emission with equal accuracy, indicating the general applicability of our reference materials and calibration methods. In a first application of our new measurement capability, we introduce the concept of critical-dimension localization microscopy, facilitating tests of nanofabrication processes and quality control of aperture arrays. In a second application, we apply these stable reference materials to answer open questions about the apparent instability of fluorescent nanoparticles that commonly serve as fiducial markers. Our study establishes a foundation for subnanometer localization accuracy in widefield optical microscopy.
TGF-β signaling alters H4K20me3 status via miR-29 and contributes to cellular senescence and cardiac aging
Authors: Lyu Guoliang , Guan Yiting , Zhang Chao , Zong Le , Sun Lei , Huang Xiaoke , Huang Li , Zhang Lijun , Tian Xiao-Li , Zhou Zhongjun , Tao Wei
Published: June 2018

Cellular senescence is a well-orchestrated programmed process involved in age-related pathologies, tumor suppression and embryonic development. TGF-β/Smad is one of the predominant pathways that regulate damage-induced and developmentally programmed senescence. Here we show that canonical TGF-β signaling promotes senescence via miR-29-induced loss of H4K20me3. Mechanistically, oxidative stress triggers TGF-β signaling. Activated TGF-β signaling gives rise to acute accumulation of miR-29a and miR-29c, both of which directly suppress their novel target, Suv4-20h, thus reducing H4K20me3 abundance in a Smad-dependent manner, which compromises DNA damage repair and genome maintenance. Loss of H4K20me3 mediated by the senescent TGF-β/miR-29 pathway contributes to cardiac aging in vivo. Disruption of TGF-β signaling restores H4K20me3 and improves cardiac function in aged mice. Our study highlights the sequential mechanisms underlying the regulation of senescence, from senescence-inducing triggers to activation of responsive signaling followed by specific epigenetic alterations, shedding light on potential therapeutic interventions in cardiac aging.
Dedicated surveillance mechanism controls G-quadruplex forming non-coding RNAs in human mitochondria
Authors: Pietras Zbigniew , Wojcik Magdalena A. , Borowski Lukasz S. , Szewczyk Maciej , Kulinski Tomasz M. , Cysewski Dominik , Stepien Piotr P. , Dziembowski Andrzej , Szczesny Roman J.
Published: June 2018

The GC skew in vertebrate mitochondrial genomes results in synthesis of RNAs that are prone to form G-quadruplexes (G4s). Such RNAs, although mostly non-coding, are transcribed at high rates and are degraded by an unknown mechanism. Here we describe a dedicated mechanism of degradation of G4-containing RNAs, which is based on cooperation between mitochondrial degradosome and quasi-RNA recognition motif (qRRM) protein GRSF1. This cooperation prevents accumulation of G4-containing transcripts in human mitochondria. In vitro reconstitution experiments show that GRSF1 promotes G4 melting that facilitates degradosome-mediated decay. Among degradosome and GRSF1 regulated transcripts we identified one that undergoes post-transcriptional modification. We show that GRSF1 proteins form a distinct qRRM group found only in vertebrates. The appearance of GRSF1 coincided with changes in the mitochondrial genome, which allows the emergence of G4-containing RNAs. We propose that GRSF1 appearance is an evolutionary adaptation enabling control of G4 RNA.
Nuclear microtubule filaments mediate non-linear directional motion of chromatin and promote DNA repair
Authors: Oshidari Roxanne , Strecker Jonathan , Chung Daniel K. C. , Abraham Karan J. , Chan Janet N. Y. , Damaren Christopher J. , Mekhail Karim
Published: June 2018

Damaged DNA shows increased mobility, which can promote interactions with repair-conducive nuclear pore complexes (NPCs). This apparently random mobility is paradoxically abrogated upon disruption of microtubules or kinesins, factors that typically cooperate to mediate the directional movement of macromolecules. Here, we resolve this paradox by uncovering DNA damage-inducible intranuclear microtubule filaments (DIMs) that mobilize damaged DNA and promote repair. Upon DNA damage, relief of centromeric constraint induces DIMs that cooperate with the Rad9 DNA damage response mediator and Kar3 kinesin motor to capture DNA lesions, which then linearly move along dynamic DIMs. Decreasing and hyper-inducing DIMs respectively abrogates and hyper-activates repair. Accounting for DIM dynamics across cell populations by measuring directional changes of damaged DNA reveals that it exhibits increased non-linear directional behavior in nuclear space. Abrogation of DIM-dependent processes or repair-promoting factors decreases directional behavior. Thus, inducible and dynamic nuclear microtubule filaments directionally mobilize damaged DNA and promote repair.
Migrating the SNP array-based homologous recombination deficiency measures to next generation sequencing data of breast cancer
Authors: Sztupinszki Zsofia , Diossy Miklos , Krzystanek Marcin , Reiniger Lilla , Csabai István , Favero Francesco , Birkbak Nicolai J. , Eklund Aron C. , Syed Ali , Szallasi Zoltan
Published: June 2018

The first genomic scar-based homologous recombination deficiency (HRD) measures were produced using SNP arrays. As array-based technology has been largely replaced by next generation sequencing approaches, it has become important to develop algorithms that derive the same type of genomic scar scores from next generation sequencing (whole exome “WXS”, whole genome “WGS”) data. In order to perform this analysis, we introduce here the scarHRD R package and show that using this method the SNP array-based and next generation sequencing-based derivation of HRD scores show good correlation (Pearson correlation between 0.73 and 0.87 depending on the actual HRD measure) and that the NGS-based HRD scores distinguish similarly well between BRCA mutant and BRCA wild-type cases in a cohort of triple-negative breast cancer patients of the TCGA data set.
Competing Coulomb and electron–phonon interactions in NbS2
Authors: van Loon Erik G. C. P. , Rösner Malte , Schönhoff Gunnar , Katsnelson Mikhail I. , Wehling Tim O.
Published: June 2018

The interplay of Coulomb and electron–phonon interactions with thermal and quantum fluctuations facilitates rich phase diagrams in two-dimensional electron systems. Layered transition metal dichalcogenides hosting charge, excitonic, spin and superconducting order form an epitomic material class in this respect. Theoretical studies of materials like NbS2 have focused on the electron–phonon coupling, whereas the Coulomb interaction, particularly strong in the monolayer limit, remained essentially untouched. Here, we analyze the interplay of short- and long-range Coulomb as well as electron–phonon interactions in NbS2 monolayers. The combination of these interactions causes electronic correlations that are fundamentally different to what would be expected from the interaction terms separately. The fully interacting electronic spectral function resembles the non-interacting band structure but with appreciable broadening. An unexpected coexistence of strong charge and spin fluctuations puts NbS2 close to spin and charge order, suggesting monolayer NbS2 as a platform for atomic scale engineering of electronic quantum phases.
Production, quality control, stability, and potency of cGMP-produced Plasmodium falciparum RH5.1 protein vaccine expressed in Drosophila S2 cells
Authors: Jin Jing , Tarrant Richard D. , Bolam Emma J. , Angell-Manning Philip , Soegaard Max , Pattinson David J. , Dulal Pawan , Silk Sarah E. , Marshall Jennifer M. , Dabbs Rebecca A. , Nugent Fay L. , Barrett Jordan R. , Hjerrild Kathryn A. , Poulsen Lars , Jørgensen Thomas , Brenner Tanja , Baleanu Ioana N. , Parracho Helena M. , Tahiri-Alaoui Abdessamad , Whale Gary , Moyle Sarah , Payne Ruth O. , Minassian Angela M. , Higgins Matthew K. , Detmers Frank J. , Lawrie Alison M. , Douglas Alexander D. , Smith Robert , de Jongh Willem A. , Berrie Eleanor , Ashfield Rebecca , Draper Simon J.
Published: June 2018

Plasmodium falciparum reticulocyte-binding protein homolog 5 (PfRH5) is a leading asexual blood-stage vaccine candidate for malaria. In preparation for clinical trials, a full-length PfRH5 protein vaccine called “RH5.1” was produced as a soluble product under cGMP using the ExpreS2 platform (based on a Drosophila melanogaster S2 stable cell line system). Following development of a high-producing monoclonal S2 cell line, a master cell bank was produced prior to the cGMP campaign. Culture supernatants were processed using C-tag affinity chromatography followed by size exclusion chromatography and virus-reduction filtration. The overall process yielded >400 mg highly pure RH5.1 protein. QC testing showed the MCB and the RH5.1 product met all specified acceptance criteria including those for sterility, purity, and identity. The RH5.1 vaccine product was stored at −80 °C and is stable for over 18 months. Characterization of the protein following formulation in the adjuvant system AS01B showed that RH5.1 is stable in the timeframe needed for clinical vaccine administration, and that there was no discernible impact on the liposomal formulation of AS01B following addition of RH5.1. Subsequent immunization of mice confirmed the RH5.1/AS01B vaccine was immunogenic and could induce functional growth inhibitory antibodies against blood-stage P. falciparum in vitro. The RH5.1/AS01B was judged suitable for use in humans and has since progressed to phase I/IIa clinical trial. Our data support the future use of the Drosophila S2 cell and C-tag platform technologies to enable cGMP-compliant biomanufacture of other novel and “difficult-to-express” recombinant protein-based vaccines.
Potential formula of an m × n globe network and its application
Authors: Tan Zhen , Tan Zhi-Zhong
Published: June 2018

Searching for the explicit solutions of the potential function in an arbitrary resistor network is important but difficult in physics. We investigate the problem of potential formula in an arbitrary m × n globe network of resistors, which has not been resolved before (the previous study only calculated the resistance). In this paper, an exact potential formula of an arbitrary m × n globe network is discovered by means of the Recursion-Transform method with current parameters (RT-I). The key process of RT method is to set up matrix equation and to transform two-dimensional matrix equation into one-dimensional matrix equation. In order to facilitate practical application, we deduced a series of interesting results of potential by means of the general formula, and the effective resistance between two nodes in the m × n globe network is derived naturally by making use of potential formula.