bluuebunny/crossref_metadata_2025_split huggingface dataset:
A walk in the maze: variation in Late Jurassic tridactyl dinosaur tracks from the Swiss Jura Mountains (NW Switzerland)
Authors: Castanera Diego , Belvedere Matteo , Marty Daniel , Paratte Géraldine , Lapaire-Cattin Marielle , Lovis Christel , Meyer Christian A. 
Published: April 2018

BackgroundMinute to medium-sized (footprint length (FL) less than 30 cm) tridactyl dinosaur tracks are the most abundant in the Late Jurassic tracksites of Highway A16 (Reuchenette Formation, Kimmeridgian) in the Jura Mountains (NW Switzerland). During excavations, two morphotypes, one gracile and one robust, were identified in the field. Furthermore, two large-sized theropod ichnospecies (Megalosauripus transjuranicusandJurabrontes curtedulensis) and an ornithopod-like morphotype (Morphotype II) have recently been described at these sites.MethodsThe quality of morphological preservation (preservation grade), the depth of the footprint, the shape variation, and the footprint proportions (FL/footprint width (FW) ratio and mesaxony) along the trackways have been analyzed using 3D models and false-color depth maps in order to determine the exact number of small to medium-sized morphotypes present in the tracksites.ResultsThe study of footprints (n= 93) recovered during the excavations has made it possible to identify and characterize the two morphotypes distinguished in the field. The gracile morphotype is mainly characterized by a high FL/FW ratio, high mesaxony, low divarication angles and clear, sharp claw marks, and phalangeal pads (2-3-4). By contrast, the robust morphotype is characterized by a lower FL/FW ratio, weaker mesaxony, slightly higher divarication angles and clear, sharp claw marks (when preserved), whereas the phalangeal pads are not clearly preserved although they might be present.DiscussionThe analysis does not allow the two morphotypes to be associated within the same morphological continuum. Thus, they cannot be extramorphological variations of similar tracks produced by a single trackmaker. Comparison of the two morphotypes with the larger morphotypes described in the formation (M. transjuranicus,J. curtedulensis, and Morphotype II) and the spatio-temporal relationships of the trackways suggest that the smaller morphotypes cannot reliably be considered as small individuals of any of the larger morphotypes. The morphometric data of some specimens of the robust morphotype (even lower values for the length/width ratio and mesaxony) suggest that more than one ichnotaxon might be represented within the robust morphotype. The features of the gracile morphotype (cf.Kalohipusisp.) are typical of “grallatorid” ichnotaxa with low mesaxony whereas those of the robust morphotype (cf.Therangospodusisp. andTherangospodus? isp.) are reminiscent ofTherangospodus pandemicus. This work sheds new light on combining an analysis of variations in footprint morphology through 3D models and false-color depth maps, with the study of possible ontogenetic variations and the identification of small-sized tridactyl ichnotaxa for the description of new dinosaur tracks.
PlasmidSeeker: identification of known plasmids from bacterial whole genome sequencing reads
Authors: Roosaare Märt , Puustusmaa Mikk , Möls Märt , Vaher Mihkel , Remm Maido 
Published: April 2018

BackgroundPlasmids play an important role in the dissemination of antibiotic resistance, making their detection an important task. Using whole genome sequencing (WGS), it is possible to capture both bacterial and plasmid sequence data, but short read lengths make plasmid detection a complex problem.ResultsWe developed a tool named PlasmidSeeker that enables the detection of plasmids from bacterial WGS data without read assembly. The PlasmidSeeker algorithm is based onk-mers and usesk-mer abundance to distinguish between plasmid and bacterial sequences. We tested the performance of PlasmidSeeker on a set of simulated and real bacterial WGS samples, resulting in 100% sensitivity and 99.98% specificity.ConclusionPlasmidSeeker enables quick detection of known plasmids and complements existing tools that assemble plasmids de novo. The PlasmidSeeker source code is stored on GitHub:https://github.com/bioinfo-ut/PlasmidSeeker.
Glycan‐metabolizing enzymes in microbe–host interactions: the Streptococcus pneumoniae paradigm
Authors: Hobbs Joanne K. , Pluvinage Benjamin , Boraston Alisdair B. 
Published: April 2018

Streptococcus pneumoniae is a frequent colonizer of the upper airways; however, it is also an accomplished pathogen capable of causing life‐threatening diseases. To colonize and cause invasive disease, this bacterium relies on a complex array of factors to mediate the host–bacterium interaction. The respiratory tract is rich in functionally important glycoconjugates that display a vast range of glycans, and, thus, a key component of the pneumococcus–host interaction involves an arsenal of bacterial carbohydrate‐active enzymes to depolymerize these glycans and carbohydrate transporters to import the products. Through the destruction of host glycans, the glycan‐specific metabolic machinery deployed by S. pneumoniae plays a variety of roles in the host–pathogen interaction. Here, we review the processing and metabolism of the major host‐derived glycans, including N‐ and O‐linked glycans, Lewis and blood group antigens, proteoglycans, and glycogen, as well as some dietary glycans. We discuss the role of these metabolic pathways in the S. pneumoniae–host interaction, speculate on the potential of key enzymes within these pathways as therapeutic targets, and relate S. pneumoniae as a model system to glycan processing in other microbial pathogens.
Velocity Structure of the Subducted Yakutat Terrane, Alaska: Insights From Guided Waves
Authors: Coulson S. , Garth T. , Rietbrock A. 
Published: April 2018

AbstractDispersed P wave arrivals from intermediate‐depth earthquakes in the Alaskan subduction zone provide insight into the low‐velocity structure of the subducting oceanic crust. P wave arrivals from 41 earthquakes in the eastern section of the arc show significant guided wave dispersion, with high‐frequency (>1 Hz) energy delayed by up to 2–3 s. We simulate this dispersion using a 2‐D finite difference waveform propagation model, systematically varying both P wave velocity and low‐velocity layer thickness parameters to find the lowest misfit between the observed and synthetic waveforms. We infer a 6 to 10 km thick low‐velocity layer with a P wave velocity contrast of 7–15% with the overriding mantle, velocities which cannot be entirely accounted for by metamorphosed mid‐ocean ridge basalt compositions. We postulate that this structure is the remnant of the subducted Yakutat terrane, significantly thinned at depth by metamorphism or delamination of material during subduction.
Laboratory Strategies for Hydrate Formation in Fine‐Grained Sediments
Authors: Lei L. , Santamarina J. C. 
Published: April 2018

AbstractFine‐grained sediments limit hydrate nucleation, shift the phase boundary, and hinder gas supply. Laboratory experiments in this study explore different strategies to overcome these challenges, including the use of a more soluble guest molecule rather than methane, grain‐scale gas‐storage within porous diatoms, ice‐to‐hydrate transformation to grow lenses at predefined locations, forced gas injection into water saturated sediments, and long‐term guest molecule transport. Tomographic images and thermal and pressure data provide rich information on hydrate formation and morphology. Results show that hydrate formation is inherently displacive in fine‐grained sediments; lenses are thicker and closer to each other in compressible, high specific surface area sediments subjected to low effective stress. Temperature and pressure trajectories follow a shifted phase boundary that is consistent with capillary effects. Exo‐pore growth results in freshly formed hydrate with a striped and porous structure; this open structure becomes an effective pathway for gas transport to the growing hydrate front. Ice‐to‐hydrate transformation goes through a liquid stage at premelt temperatures; then, capillarity and cryogenic suction compete, and some water becomes imbibed into the sediment faster than hydrate reformation. The geometry of hydrate lenses and the internal hydrate structure continue evolving long after the exothermal response to hydrate formation has completely decayed. Multiple time‐dependent processes occur during hydrate formation, including gas, water and heat transport, sediment compressibility, reaction rate, and the stochastic nucleation process. Hydrate formation strategies conceived for this study highlight the inherent difficulties in emulating hydrate formation in fine‐grained sediments within the relatively short time scale available for laboratory experiments.
Evaluating the Impact of Emissions Regulations on the Emissions Reduction During the 2015 China Victory Day Parade With an Ensemble Square Root Filter
Authors: Chu Kekuan , Peng Zhen , Liu Zhiquan , Lei Lili , Kou Xingxia , Zhang Yi , Bo Xin , Tian Jun 
Published: April 2018

AbstractIn order to guarantee good air quality for the 15th International Association of Athletics Federations World Championships (22–30 August) and the China Victory Day parade (3 September) in Beijing, a series of comprehensive emissions regulations were implemented in Beijing and the surrounding provinces from 20 August to 3 September 2015. During this period, the intensity of the emissions regulation was enhanced step by step in the run‐up to the event. This period therefore allowed us to quantitatively estimate the reduction in emissions as a result of the emissions regulations under different intensity and strategy scenarios. The ensemble square root filter was employed to optimize the initial conditions and the emissions simultaneously. Numerical results showed that the variations of the anthropogenic emissions before, during, and after the emissions regulations were reasonably simulated. The updated emissions were about 80% and 50% of the prior anthropogenic emissions during the regular‐ and stringent‐regulations periods, respectively. As a result, the PM2.5 concentrations consistently reduced during the regulations period, and the largest reduction occurred under the stringent‐regulations period. Sensitivity simulations forced by the averaged emissions before the regulations and during the regular‐ and stringent‐regulation periods further highlighted the valuable impacts of emissions regulations, under different strategy and intensity scenarios, on the improvement of air quality. More intense emissions regulation will lead to a greater reduction in PM2.5 concentrations.
Controls on Yardang Development and Morphology: 2. Numerical Modeling
Authors: Pelletier Jon D. 
Published: April 2018

AbstractHere I present a set of mathematical modeling results, constrained by the results of the companion paper, aimed at improving our understanding of yardang development and controls on yardang morphology. The classic model for yardang development posits that yardangs evolve to an aspect ratio of ≈4 in order to minimize aerodynamic drag. Computational fluid dynamics model results presented here, however, demonstrate that yardangs with an aspect ratio of 4 do not minimize drag. As an alternative, I propose that yardang aspect ratios are primarily controlled by the lateral downwind expansion of wind and wind‐blown sediments focused into the troughs among yardangs, which can be quantified using previous studies of wall‐bounded turbulent jets. This approach predicts yardangs with aspect ratios in the range of 5 to 10, that is, similar to those of natural yardangs. In addition to aerodynamics, yardang aspect ratios are influenced by the strikes and dips of strata, as demonstrated in the companion paper. To better understand the aerodynamic and bedrock structural controls on yardang morphology, I developed a landscape evolution model that combines the physics of boundary layer flow and abrasion by eolian sediment transport with a model for the erosion of the tops and lee sides of yardangs by water‐driven erosional processes. Yardang formation in the model is enhanced in substrates with greater heterogeneity (i.e., alternating strong and weak strata). Yardang morphology is controlled by the strikes and dips of strata as well as the topographic diffusivity associated with water‐driven erosional processes.
Tunable, Electrically Small, Inductively Coupled Antenna for Transportable Ionospheric Heating
Authors: Esser Benedikt , Mauch Daniel , Dickens James , Mankowski John , Neuber Andreas 
Published: April 2018

AbstractAn electrically small antenna is evaluated for use as the principle radiating element in a mobile ionospheric heating array. Consisting of a small loop antenna inductively coupled to a capacitively loaded loop, the electrically small antenna provides high efficiency with the capability of being tuned within the range of ionospheric heating. At a factor 60 smaller in area than a High‐Frequency Active Auroral Research Program element, this antenna provides a compact, efficient radiating element for mobile ionospheric heating. A prototype antenna at 10 MHz was built to study large‐scale feasibility and possible use with photoconductive semiconductor switch‐based drivers. Based on the experimental study, the design has been extrapolated to a small 6 × 4 array of antennas. At a total power input of 16.1 MW this array is predicted to provide 3.6‐GW effective radiated power typically required for ionospheric heating. Array cross talk is addressed, including effects upon individual antenna port parameters. Tuning within the range of ionospheric heating, 3–10 MHz, is made possible without the use of lossy dielectrics through a large capacitive area suited to tune the antenna. Considerations for high power operation across the band are provided including a method of driving the antenna with a simple switcher requiring no radio frequency cabling. Source matching may be improved via adjustment of the coupling between small loop antenna and capacitively loaded loop improving |S11| from −1 to −21 dB at 3 MHz.
Modeling the Mechanisms Behind Yardang Evolution
Authors: Barchyn Thomas E. 
Published: April 2018

AbstractNew work by Pelletier et al. (2018, https://doi.org/10.1002/2017JF004461) and Pelletier (2018, https://doi.org/10.1002/2017JF004462) quantitatively explains how arid landscapes can be sculpted into regular “teardrop”‐shaped hills known as yardangs. A diversity of theories have been proposed to explain these perplexing hills. Pelletier (2018) helpfully clarifies that the most likely suite of mechanisms involves an interplay between wind‐ and water‐driven erosion. Using detailed field measurements from Ocotillo Wells, California, a model is developed that explains how yardangs achieve their characteristic form and spacing. Although couched around the iconic yardang, the work contributes a general and robust template for understanding landscapes where both wind and water erosion are present.
Formation of Aldehydes and Ketones by Reduction of Phenols, Carboxylic Acids and Deriatives, and Nitriles
Authors: Larock Richard C. , Dubrovskiy Anton V. , Markina Nataliya A. 
Published: April 2018

AbstractPhenols and DerivativesAcylsilanesCarboxylic AcidsAcid HalidesAnhydridesEstersThioestersSelenoestersLactonesAmides and ImidesNitriles and Acyl Nitriles4,5‐Dihydrooxazoles and 2‐Imidazolines
Formation of Aldehydes and Ketones by Cyclization and Annulation Reactions
Authors: Larock Richard C. , Dubrovskiy Anton V. , Markina Nataliya A. 
Published: April 2018

AbstractCyclizationSpirocyclization and SpiroannulationOne‐Carbon AnnulationTwo‐Carbon AnnulationThree‐Carbon AnnulationFour‐Carbon AnnulationFive‐Carbon AnnulationFive‐ and Six‐Carbon AnnulationSix‐Carbon Annulation
Elevated LGI1‐IgG CSF index predicts worse neurological outcome
Authors: Gadoth Avi , Zekeridou Anastasia , Klein Christopher J. , Thoreson Colton J. , Majed Masoud , Dubey Divyanshu , Flanagan Eoin P. , McKeon Andrew , Jenkins Sarah M. , Lennon Vanda A. , Pittock Sean J. 
Published: April 2018

AbstractTo determine whether CSF leucine‐rich glioma‐inactivated 1(LGI1)‐IgG titer, index or IgG subclass has prognostic significance, we tested serum and CSF specimens collected concomitantly from 39 seropositive patients. LGI1‐IgG index was elevated (>1) in 21 patients (54%), suggesting intrathecal synthesis. Patients with worse outcome at last follow‐up (modified Rankin Scale >2) had significantly higher index (median 6.57 vs. 0.5, P = 0.048) compared to those with better outcome. Higher CSF LGI1‐IgG4 subclass‐specific titer and index correlated with worse outcome (P < 0.005 for both). These data suggest that evidence of intrathecal LGI1‐IgG synthesis may correlate with neuronal injury and warrant consideration of aggressive immunotherapy.
UV resistance and water barrier properties of PP/PLA/MAH/TiO2 functional hybrid biocomposite films for packaging application
Authors: Jiang Qian , Pei Xin , Wu Liwei , Li Ting‐Ting , Lin Jia‐Horng 
Published: April 2018

AbstractSynthetic polymers have been commonly used in the packaging engineering field due to the excellent properties. However, they also generate non‐biodegradable waste which causes environmental pollutions. Therefore, a new material is expected to accelerate the degradation of packaging materials, making them naturally degraded and keeping the excellent properties meanwhile. One solution to address this problem is using hybrid biocomposites that are made of traditional polymer matrices, biodegradable polymers, and nanofiller using a melt‐blending process. Polylactic acid is added for dispersion phase and polypropylene is used as a matrix, during which maleic anhydride is used as a compatibilizer and nano‐TiO2 is added as fillers. The melt‐blending process is used to make the materials into biodegradable composite films with functions in terms of UV resistance and water barrier properties. The composite films are tested for different properties in order to obtain the optimal amount of nano‐TiO2. The test results show that comparing to the control group that contains 0 wt% nano‐TiO2, adding 1 wt% nano‐TiO2 improves the tensile strength and elastic modulus of the functional hybrid biocomposite films by 22% and 31%, respectively. The thermal resistance of hybrid biocomposite films is superior under 400°C. In addition, the functional hybrid biocomposite films have a UV transmittance that is less than 1%. After exposure to the medium waves (UVB) for 144 hr, the functional hybrid biocomposite films have tensile strength retention of 84.61%. The water contact angle of hybrid biocomposite films with 1 wt% nano‐TiO2 is 112.7°, showing good water barrier property.
Phylotranscriptomic analysis and genome evolution of the Cypripedioideae (Orchidaceae)
Authors: Unruh Sarah A. , McKain Michael R. , Lee Yung‐I , Yukawa Tomohisa , McCormick Melissa K. , Shefferson Richard P. , Smithson Ann , Leebens‐Mack James H. , Pires J. Chris 
Published: April 2018

Premise of the StudyThe slipper orchids (Cypripedioideae) are a morphologically distinct subfamily of Orchidaceae. They also have some of the largest genomes in the orchids, which may be due to polyploidy or some other mechanism of genome evolution. We generated 10 transcriptomes and incorporated existing RNA‐seq data to infer a multilocus nuclear phylogeny of the Cypripedioideae and to determine whether a whole‐genome duplication event (WGD) correlated with the large genome size of this subfamily. Knowing more about timing of ancient polyploidy events can help us understand the evolution of one of the most species‐rich plant families.MethodsTranscriptome data were used to identify low‐copy orthologous genes to infer a phylogeny of Orchidaceae and to identify paralogs to place any WGD events on the species tree.Key ResultsOur transcriptome phylogeny confirmed relationships published in previous studies that used fewer markers but incorporated more taxa. We did not find a WGD event at the base of the slipper orchids; however, we did identify one on the Orchidaceae stem lineage. We also confirmed the presence of a previously identified WGD event deeper in the monocot phylogeny.ConclusionsAlthough WGD has played a role in the evolution of Orchidaceae, polyploidy does not appear to be responsible for the large genome size of slipper orchids. The conserved set of 775 largely single‐copy nuclear genes identified in this study should prove useful in future studies of orchid evolution.
Ancient DNA reveals temporal population structure within the South‐Central Andes area
Authors: Russo M. Gabriela , Mendisco Fanny , Avena Sergio A. , Crespo Cristian M. , Arencibia Valeria , Dejean Cristina B. , Seldes Verónica 
Published: April 2018

AbstractObjectivesThe main aim of this work was to contribute to the knowledge of pre‐Hispanic genetic variation and population structure among the South‐central Andes Area by studying individuals from Quebrada de Humahuaca, North‐western (NW) Argentina.Materials and methodsWe analyzed 15 autosomal STRs in 19 individuals from several archaeological sites in Quebrada de Humahuaca, belonging to the Regional Developments Period (900–1430 AD). Compiling autosomal, mitochondrial, and Y‐chromosome data, we evaluated population structure and differentiation among eight South‐central Andean groups from the current territories of NW Argentina and Peru.ResultsAutosomal data revealed a structuring of the analyzed populations into two clusters which seemed to represent different temporalities in the Andean pre‐Hispanic history: pre‐Inca and Inca. All pre‐Inca samples fell into the same cluster despite being from the two different territories of NW Argentina and Peru. Also, they were systematically differentiated from the Peruvian Inca group. These results were mostly confirmed by mitochondrial and Y‐chromosome analyses. We mainly found a clearly different haplotype composition between clusters.DiscussionPopulation structure in South America has been mostly studied on current native groups, mainly showing a west‐to‐east differentiation between the Andean and lowland regions. Here we demonstrated that genetic population differentiation preceded the European contact and might have been more complex than thought, being found within the South‐central Andes Area. Moreover, divergence among temporally different populations might be reflecting socio‐political changes occurred in the evermore complex pre‐Hispanic Andean societies.
Atomic Layer Deposition of the Metal Pyrites FeS2, CoS2, and NiS2
Authors: Guo Zheng , Wang Xinwei 
Published: April 2018

AbstractAtomic layer deposition (ALD) of the pyrite‐type metal disulfides FeS2, CoS2, and NiS2 is reported for the first time. The deposition processes use iron, cobalt, and nickel amidinate compounds as the corresponding metal precursors and the H2S plasma as the sulfur source. All the processes are demonstrated to follow ideal self‐limiting ALD growth behavior to produce fairly pure, smooth, well‐crystallized, stoichiometric pyrite FeS2, CoS2, and NiS2 films. By these processes, the FeS2, CoS2, and NiS2 films can also be uniformly and conformally deposited into deep narrow trenches with aspect ratios as high as 10:1, which thereby highlights the broad and promising applicability of these ALD processes for conformal film coatings on complex high‐aspect‐ratio 3D architectures in general.