bluuebunny/crossref_metadata_2025_split huggingface dataset:
Long-term observations of supraglacial streams on an Arctic glacier
Authors: St Germain Sarah L. , Moorman Brian J. 
Published: September 2019

AbstractSupraglacial streams are a significant part of the glacial hydrological system and important for understanding glacial hydrology and dynamics. Here we infer factors that influence the long-term development of perennial supraglacial streams, particularly in reference to canyon, incised and surface stream formation. Orthophotos and digital elevation models generated from high-resolution aerial imagery taken with unmanned aerial vehicles or piloted helicopters between 2010 and 2017 were used to compare seven streams on Fountain Glacier, Bylot Island, Canada over time. Results show canyon formation occurs from a combination of fluvial processes and the impact of solar radiation. The greater the discharge or slope, the faster the incision and higher the sinuosity. With greater sinuosity, the distance between the top of the valley banks increases, and cutoffs cause trapezoidal canyon-like valleys to form. Solar radiation causes the backward migration of the valley walls, further enhancing canyon area. Canyons are less likely to occur in areas of low discharge and slope. Less incised channels are also more likely to have water flow jumping the channel banks, changing the channel path. The presence of medial moraines and crevasses also increases rerouting of small streams. Lastly, windblown created snow-plugs may lead to stream diversion.
Effects of energy sources and inclusion levels of concentrate in sugarcane silage-based diets of finishing Nellore young bulls: Feeding behaviour, performance and blood parameters
Authors: Ferrari V. B. , Cônsolo N. R. B. , Sousa R. T. , Souza J. M. , Santana M. H. A. , Silva L. F. P. 
Published: September 2019

AbstractReplacing ground maize (GM) with steam-rolled maize typically increases feed efficiency in maize-silage-based diets. However, little is known about optimal carbohydrate supplementation in sugarcane silage-based diets. The objective was to quantify the effect of partially replacing GM with steam-rolled maize (SRM) or pelleted citrus pulp (PCP) at two concentrate levels (600 or 800 g/kg DM) in sugarcane-based diets on feeding behaviour, performance and blood parameters of finishing Nellore bulls. One hundred and eight young bulls were allocated to 36 pens in a randomized block design and fed for 84 d. Feeding 800 g/kg concentrate decreased time spending eating and ruminating, but improved G:F ratio, hot carcass weight and carcass dressing, compared to 600 g/kg concentrate. Bulls fed SRM and PCP diets with 600 g/kg concentrate had lower intake compared to GM. Both final weight and average daily gain decreased when bulls were fed PCP and SRM with 600 g/kg concentrate compared to GM diets, and when fed with PCP and 800 g/kg concentrate. Substituting PCP for GM decreased gain efficiency, carcass weight, rumination time and intake efficiency, indicating that the bulls consumed less feed per hour spent eating. Substituting SRM for GM increased backfat thickness and blood urea concentration. In conclusion, the replacement of GM with PCP reduces intake and enhances selection against large particles, decreasing rumination, performance and final carcass weight and dressing. Replacement of GM with SRM increases blood urea and fat deposition, with no impact on performance.
Nearly free curves and arrangements: a vector bundle point of view
Authors: MARCHESI SIMONE , VALLÈS JEAN 
Published: September 2019

AbstractOver the past forty years many papers have studied logarithmic sheaves associated to reduced divisors, in particular logarithmic bundles associated to plane curves. An interesting family of these curves are the so-called free ones for which the associated logarithmic sheaf is the direct sum of two line bundles. Terao conjectured thirty years ago that when a curve is a finite set of distinct lines (i.e. a line arrangement) its freeness depends solely on its combinatorics, but this has only been proved for sets of up to 12 lines. In looking for a counter-example to Terao’s conjecture, the nearly free curves introduced by Dimca and Sticlaru arise naturally. We prove here that the logarithmic bundle associated to a nearly free curve possesses a minimal non-zero section that vanishes on one single point, P say, called the jumping point, and that this characterises the bundle. We then give a precise description of the behaviour of P. Based on detailed examples we then show that the position of P relative to its corresponding nearly free arrangement of lines may or may not be a combinatorial invariant, depending on the chosen combinatorics.
Influence of Ocean Circulation and Benthic Exchange on Deep Northwest Atlantic Nd Isotope Records During the Past 30,000 Years
Authors: Pöppelmeier F. , Blaser P. , Gutjahr M. , Süfke F. , Thornalley D. J. R. , Grützner J. , Jakob K. A. , Link J. M. , Szidat S. , Lippold J. 
Published: September 2019

AbstractNeodymium (Nd) isotopes extracted from authigenic sediment phases are increasingly used as a proxy for past variations in water mass provenance. To better constrain the controls of water mass provenance and nonconservative effects on the archived Nd isotope signal, we present a new depth transect of Nd isotope reconstructions from the Blake Bahama Outer Ridge along the North American continental margin covering the past 30 ka. We investigated five sediment cores that lie directly within the main flow path of the Deep Western Boundary Current, a major advection route of North Atlantic Deep Water. We found offsets between core tops and seawater Nd isotopic compositions that are observed elsewhere in the Northwest Atlantic. A possible explanation for this is the earlier suggested redistribution of sediment by nepheloid layers at intermediate as well as abyssal depths, transporting material downslope and along the continental margin. These processes potentially contributed to Nd isotope excursions recorded in Northwest Atlantic sediment cores during the Bølling‐Allerød and early Holocene. An Atlantic‐wide comparison of Nd isotope records shows that the early Holocene excursions had an additional contribution from conservative advection of unradiogenic dissolved Nd. Nevertheless, the trends of the Nd isotope records are in general agreement with previous reconstructions of water mass provenance from the entire Atlantic and also reveal millennial‐scale changes during the last deglaciation in temporal high resolution, which have rarely been reported before. Further, the new records confirm that during cold periods the Northwest Atlantic was bathed by an increased contribution of southern sourced water.
First‐principles Investigation of Frictional Characteristics of Brucite: An Application to Its Macroscopic Frictional Characteristics
Authors: Okuda Hanaya , Kawai Kenji , Sakuma Hiroshi 
Published: September 2019

AbstractBecause sheet‐structure minerals are often observed in natural faults and have lower friction coefficients than the other common rocks and rock‐forming minerals, it has been suggested that their frictional characteristics are related to fault strength. Despite their importance for understanding fault dynamics, what controls their frictional characteristics has not been clarified yet. Because the friction coefficients of these minerals depend on the mineral species, the atomic‐scale crystal structure can be a clue for understanding the mechanism. In this study, the variation of potential energy on the brucite (0001) shear plane (potential energy surface, PES) was calculated by using first‐principles calculations based on density functional theory. The shear stress along the sliding path is calculated by computing the displacement derivative of the PES. According to the adhesion theory of friction, we found that the atomic‐scale frictional parameters obtained by using the PES could explain the macroscopic friction coefficients when taking the experimental indentation strength into account. Then, we propose how to estimate the constitutive parameter a of the rate‐ and state‐dependent friction law from the PES of sheet‐structure minerals. The estimated value is consistent with the typical range for minerals investigated by previous experiments. The difference in the PES among sheet‐structure minerals can therefore be a key property to explain their frictional characteristics such as the tendency for frictional instability of natural faults.
New Cloud System Metrics to Assess Bulk Ice Cloud Schemes in a GCM
Authors: Stubenrauch Claudia J. , Bonazzola Marine , Protopapadaki Sofia E. , Musat Ionela 
Published: September 2019

AbstractBulk microphysical properties of ice clouds, such as fall speed and ice crystal size distribution, strongly impact the life time and the radiative effects of these clouds. Three coherent bulk ice schemes, with fall speed and effective ice crystal diameter depending on both ice water content and temperature, have been constructed from published parameterizations. We present a novel upper tropospheric cloud system concept to study the impact of these schemes on the LMDZ climate simulations. For this evaluation, cloud data from hyperspectral infrared sounders Atmospheric InfraRed Sounder and IR Atmospheric Sounding Interferometer are used, because they include cirrus with visible optical depths as low as 0.2. The analogous satellite observation simulator, developed for this purpose, is also presented. The cloud system concept, applied to the data and to the simulator outputs, allows a process‐oriented evaluation. In general, the new bulk ice schemes lead to a better agreement with the cloud data, in particular concerning the cloud system property distributions and the relation between cloud system properties and proxies mimicking the life stage and the convective depth. Sensitivity studies have demonstrated that both the introduction of the new schemes as well as the necessary adjustment of the relative width of the upper tropospheric subgrid water distribution lead to these improvements. Our studies also suggest to revise the formulation of the latter.
Metagenomic and chemical characterization of soil cobalamin production
Authors: Lu Xinda , Heal Katherine R , Ingalls Anitra E , Doxey Andrew C , Neufeld Josh D 
Published: September 2019

Abstract
Cobalamin (vitamin B12) is an essential enzyme cofactor for most branches of life. Despite the potential importance of this cofactor for soil microbial communities, the producers and consumers of cobalamin in terrestrial environments are still unknown. Here we provide the first metagenome-based assessment of soil cobalamin-producing bacteria and archaea, quantifying and classifying genes encoding proteins for cobalamin biosynthesis, transport, remodeling, and dependency in 155 soil metagenomes with profile hidden Markov models. We also measured several forms of cobalamin (CN-, Me-, OH-, Ado-B12) and the cobalamin lower ligand (5,6-dimethylbenzimidazole; DMB) in 40 diverse soil samples. Metagenomic analysis revealed that less than 10% of soil bacteria and archaea encode the genetic potential for de novo synthesis of this important enzyme cofactor. Predominant soil cobalamin producers were associated with the Proteobacteria, Actinobacteria, Firmicutes, Nitrospirae, and Thaumarchaeota. In contrast, a much larger proportion of abundant soil genera lacked cobalamin synthesis genes and instead were associated with gene sequences encoding cobalamin transport and cobalamin-dependent enzymes. The enrichment of DMB and corresponding DMB synthesis genes, relative to corrin ring synthesis genes, suggests an important role for cobalamin remodelers in terrestrial habitats. Together, our results indicate that microbial cobalamin production and repair serve as keystone functions that are significantly correlated with microbial community size, diversity, and biogeochemistry of terrestrial ecosystems.
An ancestral NB-LRR with duplicated 3′UTRs confers stripe rust resistance in wheat and barley
Authors: Zhang Chaozhong , Huang Lin , Zhang Huifei , Hao Qunqun , Lyu Bo , Wang Meinan , Epstein Lynn , Liu Miao , Kou Chunlan , Qi Juan , Chen Fengjuan , Li Mengkai , Gao Ge , Ni Fei , Zhang Lianquan , Hao Ming , Wang Jirui , Chen Xianming , Luo Ming-Cheng , Zheng Youliang , Wu Jiajie , Liu Dengcai , Fu Daolin 
Published: September 2019

AbstractWheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a global threat to wheat production. Aegilops tauschii, one of the wheat progenitors, carries the YrAS2388 locus for resistance to Pst on chromosome 4DS. We reveal that YrAS2388 encodes a typical nucleotide oligomerization domain-like receptor (NLR). The Pst-resistant allele YrAS2388R has duplicated 3’ untranslated regions and is characterized by alternative splicing in the nucleotide-binding domain. Mutation of the YrAS2388R allele disrupts its resistance to Pst in synthetic hexaploid wheat; transgenic plants with YrAS2388R show resistance to eleven Pst races in common wheat and one race of P. striiformis f. sp. hordei in barley. The YrAS2388R allele occurs only in Ae. tauschii and the Ae. tauschii-derived synthetic wheat; it is absent in 100% (n = 461) of common wheat lines tested. The cloning of YrAS2388R will facilitate breeding for stripe rust resistance in wheat and other Triticeae species.
Magnetoelectric behavior via a spin state transition
Authors: Chikara Shalinee , Gu Jie , Zhang X.-G. , Cheng Hai-Ping , Smythe Nathan , Singleton John , Scott Brian , Krenkel Elizabeth , Eckert Jim , Zapf Vivien S. 
Published: September 2019

AbstractIn magnetoelectric materials, magnetic and dielectric/ferroelectric properties couple to each other. This coupling could enable lower power consumption and new functionalities in devices such as sensors, memories and transducers, since voltages instead of electric currents are sensing and controlling the magnetic state. We explore a different approach to magnetoelectric coupling in which we use the magnetic spin state instead of the more traditional ferro or antiferromagnetic order to couple to electric properties. In our molecular compound, magnetic field induces a spin crossover from the S = 1 to the S = 2 state of Mn3+, which in turn generates molecular distortions and electric dipoles. These dipoles couple to the magnetic easy axis, and form different polar, antipolar and paraelectric phases vs magnetic field and temperature. Spin crossover compounds are a large class of materials where the spin state can modify the structure, and here we demonstrate that this is a route to magnetoelectric coupling.
Similarities and differences in patterns of germline mutation between mice and humans
Authors: Lindsay Sarah J. , Rahbari Raheleh , Kaplanis Joanna , Keane Thomas , Hurles Matthew E. 
Published: September 2019

AbstractWhole genome sequencing (WGS) studies have estimated the human germline mutation rate per basepair per generation (~1.2 × 10−8) to be higher than in mice (3.5–5.4 × 10−9). In humans, most germline mutations are paternal in origin and numbers of mutations per offspring increase with paternal and maternal age. Here we estimate germline mutation rates and spectra in six multi-sibling mouse pedigrees and compare to three multi-sibling human pedigrees. In both species we observe a paternal mutation bias, a parental age effect, and a highly mutagenic first cell division contributing to the embryo. We also observe differences between species in mutation spectra, in mutation rates per cell division, and in the parental bias of mutations in early embryogenesis. These differences between species likely result from both species-specific differences in cellular genealogies of the germline, as well as biological differences within the same stage of embryogenesis or gametogenesis.
A second open reading frame in human enterovirus determines viral replication in intestinal epithelial cells
Authors: Guo Haoran , Li Yan , Liu Guanchen , Jiang Yunhe , Shen Siyu , Bi Ran , Huang Honglan , Cheng Tong , Wang Chunxi , Wei Wei 
Published: September 2019

AbstractHuman enteroviruses (HEVs) of the family Picornaviridae, which comprises non-enveloped RNA viruses, are ubiquitous worldwide. The majority of EV proteins are derived from viral polyproteins encoded by a single open reading frame (ORF). Here, we characterize a second ORF in HEVs that is crucial for viral intestinal infection. Disruption of ORF2p expression decreases the replication capacity of EV-A71 in human intestinal epithelial cells (IECs). Ectopic expression of ORF2p proteins derived from diverse enteric enteroviruses sensitizes intestinal cells to the replication of ORF2p-defective EV-A71 and respiratory enterovirus EV-D68. We show that the highly conserved WIGHPV domain of ORF2p is important for ORF2p-dependent viral intestinal infection. ORF2p expression is required for EV-A71 particle release from IECs and can support productive EV-D68 infection in IECs by facilitating virus release. Our results indicate that ORF2p is a determining factor for enteric enterovirus replication in IECs.
Pathogen-targeting glycovesicles as a therapy for salmonellosis
Authors: Mu Haibo , Bai Hu , Sun Feifei , Liu Yinyin , Lu Chunbo , Qiu Yuanhao , Chen Peng , Yang Yu , Kong Lili , Duan Jinyou 
Published: September 2019

AbstractAntibiotic therapy is usually not recommended for salmonellosis, as it is associated with prolonged fecal carriage without reducing symptom duration or severity. Here we show that antibiotics encapsulated in hydrogen sulfide (H2S)-responsive glycovesicles may be potentially useful for the treatment of salmonellosis. The antibiotics are released in the presence of Salmonella, which is known to produce H2S. This approach prevents the quick absorption of antibiotics into the bloodstream, allows localized targeting of the pathogen in the gut, and alleviates disease symptoms in a mouse infection model. In addition, it reduces antibiotic-induced changes in the gut microbiota, and increases the abundance of potentially beneficial lactobacilli due to the release of prebiotic xylooligosaccharide analogs.
In vitro role of Rad54 in Rad51-ssDNA filament-dependent homology search and synaptic complexes formation
Authors: Tavares Eliana Moreira , Wright William Douglass , Heyer Wolf-Dietrich , Le Cam Eric , Dupaigne Pauline 
Published: September 2019

AbstractHomologous recombination (HR) uses a homologous template to accurately repair DNA double-strand breaks and stalled replication forks to maintain genome stability. During homology search, Rad51 nucleoprotein filaments probe and interact with dsDNA, forming the synaptic complex that is stabilized on a homologous sequence. Strand intertwining leads to the formation of a displacement-loop (D-loop). In yeast, Rad54 is essential for HR in vivo and required for D-loop formation in vitro, but its exact role remains to be fully elucidated. Using electron microscopy to visualize the DNA-protein complexes, here we find that Rad54 is crucial for Rad51-mediated synaptic complex formation and homology search. The Rad54−K341R ATPase-deficient mutant protein promotes formation of synaptic complexes but not D-loops and leads to the accumulation of stable heterologous associations, suggesting that the Rad54 ATPase is involved in preventing non-productive intermediates. We propose that Rad51/Rad54 form a functional unit operating in homology search, synaptic complex and D-loop formation.
Success rates of re-excision after positive margins for invasive lobular carcinoma of the breast
Authors: Piper Merisa L. , Wong Jasmine , Fahrner-Scott Kelly , Ewing Cheryl , Alvarado Michael , Esserman Laura J. , Mukhtar Rita A. 
Published: September 2019

AbstractRates of positive margins after surgical resection of invasive lobular carcinoma (ILC) are high (ranging from 18 to 60%), yet the efficacy of re-excision lumpReceptor subtypeectomy for clearing positive margins is unknown. Concerns about the diffuse nature of ILC may drive increased rates of completion mastectomy to treat positive margins, thus lowering breast conservation rates. We therefore determined the success rate of re-excision lumpectomy in women with ILC and positive margins after surgical resection. We identified 314 cases of stage I-III ILC treated with breast conserving surgery (BCS) at the University of California, San Francisco. Surgical procedures, pathology reports, and outcomes were analyzed using univariate and multivariate statistics and Cox-proportional hazards models. We evaluated outcomes before and after the year 2014, when new margin management consensus guidelines were published. Positive initial margins occurred in 118 (37.6%) cases. Of these, 62 (52.5%) underwent re-excision lumpectomy, which cleared the margin in 74.2%. On multivariate analysis, node negativity was significantly associated with successful re-excision (odds ratio [OR] 3.99, 95% CI 1.15–13.81, p = 0.029). After 2014, we saw fewer initial positive margins (42.7% versus 25.5%, p = 0.009), second surgeries (54.6% versus 20.2%, p < 0.001), and completion mastectomies (27.7% versus 4.5%, p < 0.001). In this large cohort of women with ILC, re-excision lumpectomy was highly successful at clearing positive margins. Additionally, positive margins and completion mastectomy rates significantly decreased over time. These findings highlight improvements in management of ILC, and suggest that completion mastectomy may not be required for those with positive margins after initial BCS.
Universality of fold-encoded localized vibrations in enzymes
Authors: Chalopin Yann , Piazza Francesco , Mayboroda Svitlana , Weisbuch Claude , Filoche Marcel 
Published: September 2019

AbstractEnzymes speed up biochemical reactions at the core of life by as much as 15 orders of magnitude. Yet, despite considerable advances, the fine dynamical determinants at the microscopic level of their catalytic proficiency are still elusive. In this work, we use a powerful mathematical approach to show that rate-promoting vibrations in the picosecond range, specifically encoded in the 3D protein structure, are localized vibrations optimally coupled to the chemical reaction coordinates at the active site. Remarkably, our theory also exposes an hithertho unknown deep connection between the unique localization fingerprint and a distinct partition of the 3D fold into independent, foldspanning subdomains that govern long-range communication. The universality of these features is demonstrated on a pool of more than 900 enzyme structures, comprising a total of more than 10,000 experimentally annotated catalytic sites. Our theory provides a unified microscopic rationale for the subtle structure-dynamics-function link in proteins.
A New Route for Indirect Mineralization of Carbon Dioxide–Sodium Oxalate as a Detergent Builder
Authors: Li Chen , Wang Lijie , Yuan Min , Xu Hong , Dong Jinxiang 
Published: September 2019

AbstractHere, we bridge the gap between carbon mineralization and laundry detergent builder with sodium oxalate. Daily laundry can help mineralize carbon dioxide. First, we screen an environment-friendly process to produce sodium oxalate, using CO2 as a raw material. Then, we evaluate the properties of sodium oxalate as a detergent builder and prove the formation of calcium oxalate under laundry conditions. Our data suggest that sodium oxalate has excellent calcium-removing properties. Detergents based on sodium oxalate have good detergency. Furthermore, solid calcium oxalates (calcium oxalate monohydrate or calcium oxalate dihydrate, which has good stability in water and thermal stability), is obtained from washing waters. These results demonstrate the possibility of using sodium oxalate as detergent builder. The whole process can transform the greenhouse gas CO2 into commodity chemicals and can mineralize carbon.