bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of Vegetation‐Generated Turbulence on the Critical, Near‐Bed, Wave‐Velocity for Sediment Resuspension
Authors: Tang Caihong , Lei Jiarui , Nepf Heidi M. 
Published: July 2019

AbstractLaboratory experiments examined the impact of model vegetation on wave‐driven resuspension. Model canopies were constructed from cylinders with three diameters (d = 0.32, 0.64, and 1.26 cm) and 12 densities (cylinders/m2) up to a solid volume fraction (ϕ) of 10%. The sediment bed consisted of spherical grains with d50 = 85 μm. For each experiment, the wave velocity was gradually adjusted by increasing the amplitude of 2‐s waves in a stepwise fashion. A Nortek Vectrino sampled the velocity at z = 1.3 cm above the bed. The critical wave orbital velocity for resuspension was inferred from records of suspended sediment concentration (measured with optical backscatter) as a function of wave velocity. The critical wave velocity decreased with increasing solid volume fraction. The reduction in critical wave velocity was linked to stem‐generated turbulence, which, for the same wave velocity, increased with increasing solid volume fraction. The measured turbulence was consistent with a wave‐modified version of a stem‐turbulence model. The measurements suggested that a critical value of turbulent kinetic energy was needed to initiate resuspension, and this was used to define the critical wave velocity as a function of solid volume fraction. The model predicted the measured critical wave velocity for stem diameters d = 0.64 to 2 cm. Combining the critical wave velocity with an existing model for wave damping defined the meadow size for which wave damping would be sufficient to suppress wave‐induced sediment suspension within the interior of the meadow.
Spatial Variation in the Responses of the Surface External and Induced Magnetic Field to the Solar Wind
Authors: Shore R. M. , Freeman M. P. , Coxon J. C. , Thomas E. G. , Gjerloev J. W. , Olsen N. 
Published: July 2019

AbstractWe analyze the spatial variation in the response of the surface geomagnetic field (or the equivalent ionospheric current) to variations in the solar wind. Specifically, we regress a reanalysis of surface external and induced magnetic field (SEIMF) variations onto measurements of the solar wind. The regression is performed in monthly sets, independently for 559 regularly spaced locations covering the entire northern polar region above 50° magnetic latitude. At each location, we find the lag applied to the solar wind data that maximizes the correlation with the SEIMF. The resulting spatial maps of these independent lags and regression coefficients provide a model of the localized SEIMF response to variations in the solar wind, which we call “Spatial Information from Distributed Exogenous Regression.” We find that the lag and regression coefficients vary systematically with ionospheric region, season, and solar wind driver. In the polar cap region the SEIMF is best described by the By component of the interplanetary magnetic field (50–75% of total variance explained) at a lag ∼20–25 min. Conversely, in the auroral zone the SEIMF is best described by the solar wind ϵ function (60–80% of total variance explained), with a lag that varies with season and magnetic local time (MLT), from ∼15–20 min for dayside and afternoon MLT (except in Oct–Dec) to typically 30–40 min for nightside and morning MLT and even longer (60–65 min) around midnight MLT.
Influence of Rainfall Over Eastern Arabian Sea on Its Salinity
Authors: Behara Ambica , Vinayachandran P. N. , Shankar D. 
Published: July 2019

AbstractThe west coast of India and the adjoining eastern Arabian Sea (EAS) is one of the high rainfall zones of Indian summer monsoon. The summer monsoon rainfall in this region is about 1,036 km3, which is comparable to the annual runoff of the Ganga‐Brahmaputra river system. We have investigated the impact of EAS rainfall and Bay of Bengal (BoB) low‐salinity water on the Arabian Sea salinity with a suite of experiments using an ocean general circulation model. The sea surface salinity (SSS) of EAS decreases progressively from June to September by 0.5 to 1 psu. A numerical experiment that isolates the effect of EAS rainfall suggests that this SSS decrease is largely due to local rainfall over the EAS. The spatial pattern of SSS decrease, however, is influenced by the prevailing West India Coastal Current. The role of low‐salinity water originating in the BoB on reducing the EAS salinity has also been examined. In the South Eastern Arabian Sea, during winter, the SSS decreases by about 1.5 psu. This freshening is caused by rainfall during the early winter in the southwestern BoB between 6°N and 15°N. Neither rainfall to the north of 15°N nor river runoff into the BoB contributes much to the South Eastern Arabian Sea freshening during winter.
Temporal and Topographic Source Effects on Tsunami Generation
Authors: Derakhti Morteza , Dalrymple Robert A. , Okal Emile A. , Synolakis Costas E. 
Published: July 2019

AbstractWe present a systematic study of the influence on tsunami waves generated by the uplift of a rectangular plug, of the rise time of the deformation, and of its topographic details (e.g., the presence of a sill). We are motivated by the fact that most simulation codes use an instantaneous deformation of a flat ocean floor as an initial condition of the problem, although Hammack (1973, http://resolver.caltech.edu/CaltechAUTHORS:HAMjfm73) performed pioneering laboratory studies as well as analytical computations featuring variable rise times. Here, we consider three 2‐D source shapes, including a flat seafloor, a simple elevated piston, and additional trapezoidal sill on top of it, all with variable rise times, and simulate the resulting waves using the fully nonlinear smooth particle hydrodynamic model graphics processing unit smooth particle hydrodynamic. We validate our results against Hammack's (1973) laboratory measurements and analytical results. We find that a relatively large sill, with height and width of more than half of the local depth and width of the source, has a profound effect on the spatiotemporal structure of the generated free surface wavefield. Specifically, we show that the maximum water surface elevation over the source region is not always the same as the bottom displacement, as assumed in most tsunami propagation models. Next, we obtain simple scaling relationships to predict the maximum height of the generated tsunami over and outside the source, based on the geometry of the sill and the nondimensional bed rise time. Last, we show that inertial effects may lead to an initial free surface displacement over the generation region greater than the maximum vertical displacement of the displaced seabed.
The Gravitational Signature of Martian Volcanoes
Authors: Broquet A. , Wieczorek M. A. 
Published: July 2019

AbstractBy modeling the elastic flexure of the Martian lithosphere under imposed loads, we provide a systematic study of the old and low‐relief volcanoes (>3.2 Ga, 0.5 to 7.4 km) and the younger and larger prominent constructs within the Tharsis and Elysium provinces (<3 Ga, 5.8 to 21.9 km). We fit the theoretical gravitational signal to observations in order to place constraints on 18 volcanic structures. Inverted parameters include the bulk density of the load, the elastic thickness required to support the volcanic edifice at the time it was emplaced (Te), the heat flow, the volume of extruded lava, and the ratio of volcanic products that form within (Vi) and above the preexisting surface (Ve). The bulk density of the volcanic structures is found to have a mean value of 3,206±190 kg/m3, which is representative of iron‐rich basalts as sampled by the Martian basaltic meteorites. Te beneath the small volcanoes is found to be small, less than 15 km, which implies that the lithosphere was weak and hot when these volcanoes formed. Conversely, most large volcanoes display higher values of Te, which is consistent with the bulk of their emplacement occurring later in geologic history, when the elastic lithosphere was colder and thicker. Our estimates for the volumes of volcanic edifices are about 10 times larger than those that neglect the flexure of the lithosphere. Constraints on the magnitude of subsurface loads imply that the ratio Vi/Ve is generally 3:5, which is smaller than for the Hawaiian volcanoes on Earth.
24(S)-Hydroxycholesterol induces ER dysfunction-mediated unconventional cell death
Authors: Urano Yasuomi , Ho Vo Diep-Khanh , Hirofumi Araki , Noguchi Noriko 
Published: July 2019

AbstractEndoplasmic reticulum (ER) stress induced by disruption of protein folding activates the unfolded protein response (UPR), which while generally pro-survival in effect can also induce cell death under severe ER stress. 24(S)-hydroxycholesterol (24S-OHC), which is enzymatically produced in the ER of neurons, plays an important role in maintaining brain cholesterol homeostasis but also shows neurotoxicity when subjected to esterification by acyl-CoA:cholesterol acyltransferase 1 (ACAT1) in the ER. In this study, we demonstrated that the accumulation of 24S-OHC esters in human neuroblastoma SH-SY5Y cells evoked the UPR with substantially no pro-survival adaptive response but with significant activation of pro-death UPR signaling via regulated IRE1-dependent decay (RIDD). We further found that accumulation of 24S-OHC esters caused disruption of ER membrane integrity and release of ER luminal proteins into cytosol. We also found that de novo synthesis of global proteins was robustly suppressed in 24S-OHC-treated cells. Collectively, these results show that ER dysfunction and the accompanying RIDD-mediated pro-death UPR signaling and global protein synthesis inhibition are responsible for 24S-OHC ester-induced unconventional cell death.
Development of a high-throughput strategy for discovery of potent analogues of antibiotic lysocin E
Authors: Itoh Hiroaki , Tokumoto Kotaro , Kaji Takuya , Paudel Atmika , Panthee Suresh , Hamamoto Hiroshi , Sekimizu Kazuhisa , Inoue Masayuki 
Published: July 2019

AbstractLysocin E, a 37-membered natural depsipeptide, induces rapid bacteriolysis in methicillin-resistant Staphylococcus aureus via a unique menaquinone-dependent mechanism, presenting a promising therapeutic lead. Despite the great medical importance, exploring the potential utility of its derivatives as new platform structures for antibiotic development has remained a significant challenge. Here, we report a high-throughput strategy that enabled the preparation of thousands of analogues of lysocin E and large-scale structure-activity relationship analyses. We integrate 26-step total synthesis of 2401 cyclic peptides, tandem mass spectrometry-sequencing, and two microscale activity assays to identify 23 candidate compounds. Re-synthesis of these candidates shows that 11 of them (A1–A11) exhibit antimicrobial activity superior or comparable to that of lysocin E, and that lysocin E and A1–A11 share l-Leu-6 and l-Ile-11. Therefore, the present strategy allows us to efficiently decipher biologically crucial residues and identify potentially useful agents for the treatment of infectious diseases.
Accurate estimation of cell-type composition from gene expression data
Authors: Tsoucas Daphne , Dong Rui , Chen Haide , Zhu Qian , Guo Guoji , Yuan Guo-Cheng 
Published: July 2019

AbstractThe rapid development of single-cell transcriptomic technologies has helped uncover the cellular heterogeneity within cell populations. However, bulk RNA-seq continues to be the main workhorse for quantifying gene expression levels due to technical simplicity and low cost. To most effectively extract information from bulk data given the new knowledge gained from single-cell methods, we have developed a novel algorithm to estimate the cell-type composition of bulk data from a single-cell RNA-seq-derived cell-type signature. Comparison with existing methods using various real RNA-seq data sets indicates that our new approach is more accurate and comprehensive than previous methods, especially for the estimation of rare cell types. More importantly, our method can detect cell-type composition changes in response to external perturbations, thereby providing a valuable, cost-effective method for dissecting the cell-type-specific effects of drug treatments or condition changes. As such, our method is applicable to a wide range of biological and clinical investigations.
Interaction between the nasal microbiota and S. pneumoniae in the context of live-attenuated influenza vaccine
Authors: de Steenhuijsen Piters Wouter A. A. , Jochems Simon P. , Mitsi Elena , Rylance Jamie , Pojar Sherin , Nikolaou Elissavet , German Esther L. , Holloway Mark , Carniel Beatriz F. , Chu Mei Ling J. N. , Arp Kayleigh , Sanders Elisabeth A. M. , Ferreira Daniela M. , Bogaert Debby 
Published: July 2019

AbstractStreptococcus pneumoniae is the main bacterial pathogen involved in pneumonia. Pneumococcal acquisition and colonization density is probably affected by viral co-infections, the local microbiome composition and mucosal immunity. Here, we report the interactions between live-attenuated influenza vaccine (LAIV), successive pneumococcal challenge, and the healthy adult nasal microbiota and mucosal immunity using an experimental human challenge model. Nasal microbiota profiles at baseline are associated with consecutive pneumococcal carriage outcome (non-carrier, low-dense and high-dense pneumococcal carriage), independent of LAIV co-administration. Corynebacterium/Dolosigranulum-dominated profiles are associated with low-density colonization. Lowest rates of natural viral co-infection at baseline and post-LAIV influenza replication are detected in the low-density carriers. Also, we detected the fewest microbiota perturbations and mucosal cytokine responses in the low-density carriers compared to non-carriers or high-density carriers. These results indicate that the complete respiratory ecosystem affects pneumococcal behaviour following challenge, with low-density carriage representing the most stable ecological state.
The transcription factor OsSUF4 interacts with SDG725 in promoting H3K36me3 establishment
Authors: Liu Bing , Liu Yuhao , Wang Baihui , Luo Qiang , Shi Jinlei , Gan Jianhua , Shen Wen-Hui , Yu Yu , Dong Aiwu 
Published: July 2019

AbstractThe different genome-wide distributions of tri-methylation at H3K36 (H3K36me3) in various species suggest diverse mechanisms for H3K36me3 establishment during evolution. Here, we show that the transcription factor OsSUF4 recognizes a specific 7-bp DNA element, broadly distributes throughout the rice genome, and recruits the H3K36 methyltransferase SDG725 to target a set of genes including the key florigen genes RFT1 and Hd3a to promote flowering in rice. Biochemical and structural analyses indicate that several positive residues within the zinc finger domain are vital for OsSUF4 function in planta. Our results reveal a regulatory mechanism contributing to H3K36me3 distribution in plants.
Emergent symmetries in block copolymer epitaxy
Authors: Ding Yi , Gadelrab Karim R. , Mizrahi Rodriguez Katherine , Huang Hejin , Ross Caroline A. , Alexander-Katz Alfredo 
Published: July 2019

AbstractThe directed self-assembly (DSA) of block copolymers (BCPs) has shown promise in fabricating customized two-dimensional (2D) geometries at the nano- and meso-scale. Here, we discover spontaneous symmetry breaking and superlattice formation in DSA of BCP. We observe the emergence of low symmetry phases in high symmetry templates for BCPs that would otherwise not exhibit these phases in the bulk or thin films. The emergence phenomena are found to be a general behavior of BCP in various template layouts with square local geometry, such as 44 and 32434 Archimedean tilings and octagonal quasicrystals. To elucidate the origin of this phenomenon and confirm the stability of the emergent phases, we implement self-consistent field theory (SCFT) simulations and a strong-stretching theory (SST)-based analytical model. Our work demonstrates an emergent behavior of soft matter and draws an intriguing connection between 2-dimensional soft matter self-assembly at the mesoscale and inorganic epitaxy at the atomic scale.
AWD regulates timed activation of BMP signaling in intestinal stem cells to maintain tissue homeostasis
Authors: Tracy Cai Xiaoyu , Li Hongjie , Safyan Abu , Gawlik Jennifer , Pyrowolakis George , Jasper Heinrich 
Published: July 2019

AbstractPrecise control of stem cell (SC) proliferation ensures tissue homeostasis. In the Drosophila intestine, injury-induced regeneration involves initial activation of intestinal SC (ISC) proliferation and subsequent return to quiescence. These two phases of the regenerative response are controlled by differential availability of the BMP type I receptor Thickveins (Tkv), yet how its expression is dynamically regulated remains unclear. Here we show that during homeostasis, the E3 ubiquitin ligase Highwire and the ubiquitin-proteasome system maintain low Tkv protein expression. After ISC activation, Tkv is stabilized by proteasome inhibition and undergoes endocytosis due to the induction of the nucleoside diphosphate kinase Abnormal Wing Disc (AWD). Tkv internalization is required for the activation of the Smad protein Mad, and for the return to quiescence after a regenerative episode. Our data provide insight into the mechanisms ensuring tissue homeostasis by dynamic control of somatic stem cell activity.
Genomic signatures and correlates of widespread population declines in salmon
Authors: Lehnert S. J. , Kess T. , Bentzen P. , Kent M. P. , Lien S. , Gilbey J. , Clément M. , Jeffery N. W. , Waples R. S. , Bradbury I. R. 
Published: July 2019

AbstractGlobal losses of biodiversity are occurring at an unprecedented rate, but causes are often unidentified. Genomic data provide an opportunity to isolate drivers of change and even predict future vulnerabilities. Atlantic salmon (Salmo salar) populations have declined range-wide, but factors responsible are poorly understood. Here, we reconstruct changes in effective population size (Ne) in recent decades for 172 range-wide populations using a linkage-based method. Across the North Atlantic, Ne has significantly declined in >60% of populations and declines are consistently temperature-associated. We identify significant polygenic associations with decline, involving genomic regions related to metabolic, developmental, and physiological processes. These regions exhibit changes in presumably adaptive diversity in declining populations consistent with contemporary shifts in body size and phenology. Genomic signatures of widespread population decline and associated risk scores allow direct and potentially predictive links between population fitness and genotype, highlighting the power of genomic resources to assess population vulnerability.
Enhancing laser beam performance by interfering intense laser beamlets
Authors: Morace A. , Iwata N. , Sentoku Y. , Mima K. , Arikawa Y. , Yogo A. , Andreev A. , Tosaki S. , Vaisseau X. , Abe Y. , Kojima S. , Sakata S. , Hata M. , Lee S. , Matsuo K. , Kamitsukasa N. , Norimatsu T. , Kawanaka J. , Tokita S. , Miyanaga N. , Shiraga H. , Sakawa Y. , Nakai M. , Nishimura H. , Azechi H. , Fujioka S. , Kodama R. 
Published: July 2019

AbstractIncreasing the laser energy absorption into energetic particle beams represents a longstanding quest in intense laser-plasma physics. During the interaction with matter, part of the laser energy is converted into relativistic electron beams, which are the origin of secondary sources of energetic ions, γ-rays and neutrons. Here we experimentally demonstrate that using multiple coherent laser beamlets spatially and temporally overlapped, thus producing an interference pattern in the laser focus, significantly improves the laser energy conversion efficiency into hot electrons, compared to one beam with the same energy and nominal intensity as the four beamlets combined. Two-dimensional particle-in-cell simulations support the experimental results, suggesting that beamlet interference pattern induces a periodical shaping of the critical density, ultimately playing a key-role in enhancing the laser-to-electron energy conversion efficiency. This method is rather insensitive to laser pulse contrast and duration, making this approach robust and suitable to many existing facilities.
Dissecting a heterotic gene through GradedPool-Seq mapping informs a rice-improvement strategy
Authors: Wang Changsheng , Tang Shican , Zhan Qilin , Hou Qingqing , Zhao Yan , Zhao Qiang , Feng Qi , Zhou Congcong , Lyu Danfeng , Cui Lingling , Li Yan , Miao Jiashun , Zhu Chuanrang , Lu Yiqi , Wang Yongchun , Wang Ziqun , Zhu Jingjie , Shangguan Yingying , Gong Junyi , Yang Shihua , Wang Wuqi , Zhang Jianfu , Xie Huaan , Huang Xuehui , Han Bin 
Published: July 2019

AbstractHybrid rice breeding for exploiting hybrid vigor, heterosis, has greatly increased grain yield. However, the heterosis-related genes associated with rice grain production remain largely unknown, partly because comprehensive mapping of heterosis-related traits is still labor-intensive and time-consuming. Here, we present a quantitative trait locus (QTL) mapping method, GradedPool-Seq, for rapidly mapping QTLs by whole-genome sequencing of graded-pool samples from F2 progeny via bulked-segregant analysis. We implement this method and map-based cloning to dissect the heterotic QTL GW3p6 from the female line. We then generate the near isogenic line NIL-FH676::GW3p6 by introgressing the GW3p6 allele from the female line Guangzhan63-4S into the male inbred line Fuhui676. The NIL-FH676::GW3p6 exhibits grain yield highly increased compared to Fuhui676. This study demonstrates that it may be possible to achieve a high level of grain production in inbred rice lines without the need to construct hybrids.
Global analysis reveals climatic controls on the oxygen isotope composition of cave drip water
Authors: Baker Andy , Hartmann Andreas , Duan Wuhui , Hankin Stuart , Comas-Bru Laia , Cuthbert Mark O. , Treble Pauline C. , Banner Jay , Genty Dominique , Baldini Lisa M. , Bartolomé Miguel , Moreno Ana , Pérez-Mejías Carlos , Werner Martin 
Published: July 2019

AbstractThe oxygen isotope composition of speleothems is a widely used proxy for past climate change. Robust use of this proxy depends on understanding the relationship between precipitation and cave drip water δ18O. Here, we present the first global analysis, based on data from 163 drip sites, from 39 caves on five continents, showing that drip water δ18O is most similar to the amount-weighted precipitation δ18O where mean annual temperature (MAT) is < 10 °C. By contrast, for seasonal climates with MAT > 10 °C and < 16 °C, drip water δ18O records the recharge-weighted δ18O. This implies that the δ18O of speleothems (formed in near isotopic equilibrium) are most likely to directly reflect meteoric precipitation in cool climates only. In warmer and drier environments, speleothems will have a seasonal bias toward the precipitation δ18O of recharge periods and, in some cases, the extent of evaporative fractionation of stored karst water.