bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation ofKpandDstPredictions Using ACE and DSCOVR Solar Wind Data
Authors: Wintoft P. , Wik M. 
Published: December 2018

AbstractModels that predict theKpandDstindices are evaluated using solar wind data at L1. The models consist of ensembles of neural networks that have been developed using ACE Level 2 data from the period 1998–2015. The use of ensembles is motivated by the difficulty of generating functions that generalize well in regions of the input‐output space that are poorly sampled, which typically occurs during stronger events. Since the launch of the DSCOVR spacecraft, providing measurements from about August 2016, new and independent data have become available to test the models. ACE Level 2 data for almost the same period are also available, representing another independent set collected after 2015. We evaluate the models using plots and various statistical measures. We also study the performance of the predictions for lead times up to 3 hr. The results show that the models perform better when using ACE or cleaned DSCOVR data compared to the real‐time DSCOVR data and that lead times of L1‐Earth travel time plus a maximum of 1 hr are possible. As the models use only solar wind for their inputs, and the temporal dynamics ofKpandDstare very different, we see significant differences in the error distributions that we believe are related to long‐term changes inDstthat are not captured by theDstprediction model.
Comparing TanDEM‐X Data With Frequently Used DEMs for Flood Inundation Modeling
Authors: Archer L. , Neal J. C. , Bates P. D. , House J. I. 
Published: December 2018

AbstractFlood risk, particularly in Small Island Developing States, is increasing. Although spaceborne Digital Elevation Models (DEMs) have provided a capacity to model flooding at the global scale, their relatively coarse resolution (~90 m) has led to a limited ability to provide fine‐scale flood assessments in smaller catchments such as those in Small Island Developing States. Following the release of the TanDEM‐X DEM at ~12‐m resolution, the aim of this research is to determine whether TanDEM‐X can improve flood estimates in comparison to Shuttle Radar Topography Mission (SRTM) and Multi‐Error‐Removed Improved‐Terrain (MERIT) DEMs. Suitable methods to process TanDEM‐X to a Digital Terrain Model (DTM) are identified through testing of seven DTMs produced through combinations of different vegetation removal approaches. Methods include Progressive Morphological Filtering and Image Classification of two TanDEM‐X auxiliary data sets—a Height Error Map and Amplitude map. The LISFLOOD‐FP hydrodynamic model output flood extent and water surface elevation for the TanDEM‐X DTMs, SRTM, and MERIT are compared against the LiDAR model for a catchment in Fiji. The main findings show that the unprocessed TanDEM‐X has improved predictive capacity over SRTM, but not MERIT. The TanDEM‐X processing method combining Image Classification of the Amplitude map and Progressive Morphological Filtering produces the DTM with the highest flood model skill in comparison to all tested DEMs. This DTM reports a 12–14 percentage point higher flood model skill score than MERIT and a lower water surface elevation root‐mean‐square error of 0.11–0.21 m, indicating the suitability of TanDEM‐X for flood modeling.
Dynamin-related protein 1 has membrane constricting and severing abilities sufficient for mitochondrial and peroxisomal fission
Authors: Kamerkar Sukrut C. , Kraus Felix , Sharpe Alice J. , Pucadyil Thomas J. , Ryan Michael T. 
Published: December 2018

AbstractDynamin-related protein 1 (Drp1) is essential for mitochondrial and peroxisomal fission. Recent studies propose that Drp1 does not sever but rather constricts mitochondrial membranes allowing dynamin 2 (Dnm2) to execute final scission. Here, we report that unlike Drp1, Dnm2 is dispensable for peroxisomal and mitochondrial fission, as these events occurred in Dnm2 knockout cells. Fission events were also observed in mouse embryonic fibroblasts lacking Dnm1, 2 and 3. Using reconstitution experiments on preformed membrane tubes, we show that Drp1 alone both constricts and severs membrane tubes. Scission required the membrane binding, self-assembling and GTPase activities of Drp1 and occurred on tubes up to 250 nm in radius. In contrast, Dnm2 exhibited severely restricted fission capacity with occasional severing of tubes below 50 nm in radius. We conclude that Drp1 has both membrane constricting and severing abilities and is the dominant dynamin performing mitochondrial and peroxisomal fission.
Transmembrane but not soluble helices fold inside the ribosome tunnel
Authors: Bañó-Polo Manuel , Baeza-Delgado Carlos , Tamborero Silvia , Hazel Anthony , Grau Brayan , Nilsson IngMarie , Whitley Paul , Gumbart James C. , von Heijne Gunnar , Mingarro Ismael 
Published: December 2018

AbstractIntegral membrane proteins are assembled into the ER membrane via a continuous ribosome-translocon channel. The hydrophobicity and thickness of the core of the membrane bilayer leads to the expectation that transmembrane (TM) segments minimize the cost of harbouring polar polypeptide backbones by adopting a regular pattern of hydrogen bonds to form α-helices before integration. Co-translational folding of nascent chains into an α-helical conformation in the ribosomal tunnel has been demonstrated previously, but the features governing this folding are not well understood. In particular, little is known about what features influence the propensity to acquire α-helical structure in the ribosome. Using in vitro translation of truncated nascent chains trapped within the ribosome tunnel and molecular dynamics simulations, we show that folding in the ribosome is attained for TM helices but not for soluble helices, presumably facilitating SRP (signal recognition particle) recognition and/or a favourable conformation for membrane integration upon translocon entry.
Macromolecular-clustered facial amphiphilic antimicrobials
Authors: Rahman Md Anisur , Bam Marpe , Luat Edgar , Jui Moumita Sharmin , Ganewatta Mitra S. , Shokfai Tinom , Nagarkatti Mitzi , Decho Alan W. , Tang Chuanbing 
Published: December 2018

AbstractBacterial infections and antibiotic resistance, particularly by Gram-negative pathogens, have become a global healthcare crisis. We report the design of a class of cationic antimicrobial polymers that cluster local facial amphiphilicity from repeating units to enhance interactions with bacterial membranes without requiring a globally conformational arrangement associated with highly unfavorable entropic loss. This concept of macromolecular architectures is demonstrated with a series of multicyclic natural product-based cationic polymers. We have shown that cholic acid derivatives with three charged head groups are more potent and selective than lithocholic and deoxycholic counterparts, particularly against Gram-negative bacteria. This is ascribed to the formation of true facial amphiphilicity with hydrophilic ion groups oriented on one face and hydrophobic multicyclic hydrocarbon structures on the opposite face. Such local facial amphiphilicity is clustered via a flexible macromolecular backbone in a concerted way when in contact with bacterial membranes.
Sub-picosecond photon-efficient 3D imaging using single-photon sensors
Authors: Heide Felix , Diamond Steven , Lindell David B. , Wetzstein Gordon 
Published: December 2018

AbstractActive 3D imaging systems have broad applications across disciplines, including biological imaging, remote sensing and robotics. Applications in these domains require fast acquisition times, high timing accuracy, and high detection sensitivity. Single-photon avalanche diodes (SPADs) have emerged as one of the most promising detector technologies to achieve all of these requirements. However, these detectors are plagued by measurement distortions known as pileup, which fundamentally limit their precision. In this work, we develop a probabilistic image formation model that accurately models pileup. We devise inverse methods to efficiently and robustly estimate scene depth and reflectance from recorded photon counts using the proposed model along with statistical priors. With this algorithm, we not only demonstrate improvements to timing accuracy by more than an order of magnitude compared to the state-of-the-art, but our approach is also the first to facilitate sub-picosecond-accurate, photon-efficient 3D imaging in practical scenarios where widely-varying photon counts are observed.
Atmospheric CO2 captured by biogenic polyamines is transferred as a possible substrate to Rubisco for the carboxylation reaction
Authors: Yasumoto Ko , Sakata Tsuyoshi , Yasumoto Jun , Yasumoto-Hirose Mina , Sato Shun-ichi , Mori-Yasumoto Kanami , Jimbo Mitsuru , Kusumi Takenori , Watabe Shugo 
Published: December 2018

AbstractBiogenic polyamines are involved in a wide range of plant cellular processes, including cell division, morphogenesis and stress responses. However, the exact roles of biogenic polyamines are not well understood. We recently reported that biogenic polyamines that have multiple amino groups can react with CO2 and accelerate calcium carbonate formation in seawater. The ability of biogenic polyamines to capture atmospheric CO2 prompted us to examine their roles in photosynthesis. Here, we demonstrated that atmospheric CO2 captured by biogenic polyamines is a candidate substrate for the carboxylation reaction of ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco), which is an enzyme involved in the first major step of carbon fixation during photosynthesis, and that biogenic polyamines can accelerate the carboxylation reaction of this enzyme because of their specific affinity for CO2. Moreover, the results of our nuclear magnetic resonance (NMR) analysis showed that putrescine, which is the most common biogenic polyamine, reacts with atmospheric CO2 and promotes the formation of carbamate derivatives and bicarbonate in aqueous environments. A sufficient amount of CO2 is well known to be produced by carbonic anhydrase from bicarbonate in vivo. The present study indicates that CO2 would be also produced by the equilibrium reaction from carbonate produced by biogenic polyamines and would be used as a substrate of Rubisco, too. Our results may suggest a new photosynthetic research strategy that involves CO2-concentrating mechanisms and also possibly constitutes a potential tool for reducing atmospheric CO2 levels and, consequently, global warming.
Physical and thermodynamic characterization of the rice gibberellin receptor/gibberellin/DELLA protein complex
Authors: Xiang Hongyu , Okamura Hideyasu , Kezuka Yuichiro , Katoh Etsuko 
Published: December 2018

AbstractGibberellins (GAs) are phytohormones that regulate various developmental processes in plants. The initial GA signalling events involve the binding of a GA to the soluble GA receptor protein GID1, followed by the binding of the complex to the negative transcriptional regulator of GA signaling, the DELLA protein. Although X-ray structures for certain Arabidopsis GID1/GA/DELLA protein complexes have previously been determined, examination of these complexes did not fully clarify how a DELLA protein recognizes and binds to a GID1/GA complex. Herein, we present a study aimed at physically defining, via a combination of gel chromatography, isothermal titration calorimetry (ITC), small-angle X-ray scattering experiments (SAXS), NMR spectroscopy and mutagenesis, how the rice DELLA protein (SLR1) binds to the rice GID1/GA complex. We have identified the shortest SLR1 sequence (M28-A112) that binds the rice GID/GA complex tightly. The binding constant for the ternary complex that includes SLR1(M28-A112) is 2.9 × 107 M−1; the binding is enthalpically driven and does not depend on the chemical nature of the bound GA. Furthermore, the results of SAXS, ITC, and gel filtration experiments indicate that when free in solution, SLR1(M28-A112) is a natively unfolded protein. The NMR experiments expand this observation to show that the unfolded mutant also contains a small amount of marginally stable secondary structure. Conversely, the protein has a highly ordered structure when bound one-to-one to GID1/GA.
Fano resonance between coherent acoustic phonon oscillations and electronic states near the bandgap of photoexcited GaAs
Authors: Vinod M. , Raghavan G. , Sivasubramanian V. 
Published: December 2018

AbstractImpulsive photo-excitation of solids results in a travelling strain pulse which manifests itself as coherent acoustic phonon oscillations. These oscillations have been extensively studied using time-resolved pump-probe spectroscopy. In the present work, we report the generation of extremely long-lived, coherent longitudinal acoustic phonon oscillations in intrinsic GaAs (100), with clear and unambiguous evidence of Fano interference between these oscillations and the continuum of electronic states close to the bandgap. Fano resonance is a widespread phenomenon observed in atomic systems and condensed media that arises from quantum interference between a continuum of quantum states and a discrete quantum state. Among other techniques, Fano resonance has been investigated with respect to optical phonons studied with Raman Spectroscopy. In the present work, we investigate Fano resonance in coherent phonon oscillations generated without the aid of any capping layer, dopants or substrate/interface effects. Since Fano resonance is sensitive to changes in electronic structure, doping and defects, these observations are important to the field of picosecond ultrasonics which is used for non-destructive depth profiling of solids and for carrier diffusion studies.
Chemosynthesis and characterization of site-specific N-terminally PEGylated Alpha-momorcharin as apotential agent
Authors: Sun Wenkui , Sun Jinghui , Zhang Haowen , Meng Yanfa , Li Linli , Li Gangrui , Zhang Xu , Meng Yao 
Published: December 2018

AbstractAlpha-momorcharin (α-MC), a type I ribosome-inactivating protein (RIP) isolated from Momordica charantia seeds, has been extensively studied for its antitumor, antiviral and antifungal activities. However, as an exogenous protein, problems associated with short half-life and strong immunogenicity have limited its clinical application. Poly (ethylene glycol) (PEG), as a polyether compound, is a well established and efficient modifier to develop it as a potential agent. Nevertheless, conventional PEGylation is not site-controlled and the conjugates are often not homogenous due to the generation of multi-PEGylated derivatives. To obtain a homogenous mono-PEGylated α-MC, the PEGylation was carried out by coupling a 20 kDa mPEG-butyraldehyde (mPEG-ALD) with α-MC. The product was separated and purified by MacroCap SP chromatography. Results from SDS-PAGE and MALDI-TOF MS revealed that the PEGylated α-MC consisted of one molecule mPEG and α-MC. Edman degradation confirmed that the N-terminal residue of α-MC was successfully coupled with mPEG-ALD. The mono-PEGylated α-MC possessed an extremely similar secondary structure to native α-MC through spectral analyses. In addition, it also showed low immunogenicity by double immunodiffusion and preserved moderate antitumor activity to three kinds of tumor cell lines in vitro. Finally, trypsin resistance was also considerably improved.
Using a three-compartment model improves the estimation of iohexol clearance to assess glomerular filtration rate
Authors: Taubert Max , Ebert Natalie , Martus Peter , van der Giet Markus , Fuhr Uwe , Schaeffner Elke 
Published: December 2018

AbstractPlasma clearance of iohexol is a key tool to precisely determine glomerular filtration rate (GFR) in clinical research and clinical practice. Despite evidence that iohexol pharmacokinetics are described best by three-compartment models, two-compartment approaches (Schwartz approach) are customary, which might result in avoidable bias and imprecision. We aimed to provide a population pharmacokinetic (popPK) model of iohexol by re-evaluating data from the Berlin Initiative Study (BIS) to compare respective clearance estimates to the Schwartz approach and to assess the impact of revised clearance estimates on the BIS equations. A popPK model was developed based on iohexol plasma samples (8–10 per subject, iohexol dose 3235 mg) from 570 elderly patients. A three-compartment model appropriately described the pharmacokinetics of iohexol (clearance 57.4 mL/min, CV 33%). Compared to the three-compartment model, clearance values were overestimated by the Schwartz approach (bias 6.5 mL/min), resulting in limited effects on regression coefficients of the BIS equations (e.g., proportionality factor of BIS2 changed from 767 to 720). Predictions based on the BIS2 equation were biased (5.4 mL/min/1.73 m²) and the sensitivity to detect a GFR < 60 mL/min/1.73 m² was low compared to the revised equation (72% versus 89%). Three-compartment models should be employed to assess iohexol pharmacokinetics.
Pheromone-Induced Odor Associative Fear Learning in Rats
Authors: Carew Samantha J. , Mukherjee Bandhan , MacIntyre Iain T. K. , Ghosh Abhinaba , Li Sa , Kirouac Gilbert J. , Harley Carolyn W. , Yuan Qi 
Published: December 2018

AbstractAlarm pheromones alert conspecifics to the presence of danger. Can pheromone communication aid in learning specific cues? Such facilitation has an evident evolutionary advantage. We use two associative learning paradigms to test this hypothesis. The first is stressed cage mate-induced conditioning. One pair-housed adult rat received 4 pairings of terpinene + shock over 30 min. Ten minutes after return to the home cage, its companion rat was removed and exposed to terpinene. Single-housed controls were exposed to either terpinene or shock only. Companion rats showed terpinene-specific freezing, which was prevented by β-adrenoceptor blockade. Using Arc to index neuronal activation in response to terpinene re-exposure, stressed cage-mate induced associative learning was measured. Companion rats showed increased neuronal activity in the accessory olfactory bulb, while terpinene + shock-conditioned rats showed increased activity in the main olfactory bulb. Both groups had enhanced activity in the anterior basolateral amygdala and central amygdala. To test involvement of pheromone mediation, in the 2nd paradigm, we paired terpinene with soiled bedding from odor + shock rats or a rat alarm pheromone. Both conditioning increased rats’ freezing to terpinene. Blocking NMDA receptors in the basolateral amygdala prevented odor-specific learning suggesting shock and pheromone-paired pathways converge in the amygdala. An alarm pheromone thus enables cue-specific learning as well as signalling danger.
Patterns of wild carnivore attacks on humans in urban areas
Authors: Bombieri Giulia , Delgado María del Mar , Russo Luca Francesco , Garrote Pedro José , López-Bao José Vicente , Fedriani José M. , Penteriani Vincenzo 
Published: December 2018

AbstractAttacks by wild carnivores on humans represent an increasing problem in urban areas across North America and their frequency is expected to rise following urban expansion towards carnivore habitats. Here, we analyzed records of carnivore attacks on humans in urban areas of the U.S. and Canada between 1980 and 2016 to analyze the general patterns of the attacks, as well as describe the landscape structure and, for those attacks occurring at night, the light conditions at the site of the attacks. We found that several behavioral and landscape-related factors were recurrent elements in the attacks recorded. The species for which the attack locations were available (coyote and black bear) attacked in areas with different conditions of landscape structure and artificial light. Specifically, black bears attacked more frequently in areas with abundant and aggregated vegetation cover and scarce buildings and roads, while coyotes attacked in a broader range of landscape conditions. At night, black bears attacked in generally darker areas than coyotes. By providing a comprehensive perspective of the phenomenon, this study will improve our understanding of how effective strategies aimed at reducing the frequency of risky encounters in urban areas should be developed.
Task-Based Model Observer Assessment of A Partial Model-Based Iterative Reconstruction Algorithm in Thoracic Oncologic Multidetector CT
Authors: Rotzinger David C. , Racine Damien , Beigelman-Aubry Catherine , Alfudhili Khalid M. , Keller Nathalie , Monnin Pascal , Verdun Francis R. , Becce Fabio 
Published: December 2018

AbstractTo investigate the impact of a partial model-based iterative reconstruction (ASiR-V) on image quality in thoracic oncologic multidetector computed tomography (MDCT), using human and mathematical model observers. Twenty cancer patients examined with regular-dose thoracic-abdominal-pelvic MDCT were retrospectively included. Thoracic images reconstructed using a sharp kernel and filtered back-projection (reference) or ASiR-V (0–100%, 20% increments; follow-up) were analysed by three thoracic radiologists. Advanced quantitative physical metrics, including detectability indexes of simulated 4-mm-diameter solid non-calcified nodules and ground-glass opacities, were computed at regular and reduced doses using a custom-designed phantom. All three radiologists preferred higher ASiR-V levels (best = 80%). Increasing ASiR-V substantially decreased noise magnitude, with slight changes in noise texture. For high-contrast objects, changing the ASiR-V level had no major effect on spatial resolution; whereas for lower-contrast objects, increasing ASiR-V substantially decreased spatial resolution, more markedly at reduced dose. For both high- and lower-contrast pulmonary lesions, detectability remained excellent, regardless of ASiR-V and dose levels, and increased significantly with increasing ASiR-V levels (all p < 0.001). While high ASiR-V levels (80%) are recommended to detect solid non-calcified nodules and ground-glass opacities in regular-dose thoracic oncologic MDCT, care must be taken because, for lower-contrast pulmonary lesions, high ASiR-V levels slightly change noise texture and substantially decrease spatial resolution, more markedly at reduced dose.
Insight into Elongation Stages of Peptidoglycan Processing in Bacterial Cytoplasmic Membranes
Authors: Kim Seonghoon , Pires Marcos M. , Im Wonpil 
Published: December 2018

AbstractPeptidoglycan (PG) biosynthesis and assembly are needed for bacterial cell wall formation. Lipid II is the precursor in the PG biosynthetic pathway and carries a nascent PG unit that is processed by glycosyltransferases. Despite its immense therapeutic value as a target of several classes of antibiotics, the conformational ensemble of lipid II in bacterial membranes and its interactions with membrane-anchored enzymes remain elusive. In this work, lipid II and its elongated forms (lipid VI and lipid XII) were modeled and simulated in bilayers of POPE (palmitoyl-oleoyl-phosphatidyl-ethanolamine) and POPG (palmitoyl-oleoyl-phosphatidyl-glycerol) that mimic the prototypical composition of Gram-negative cytoplasmic membranes. In addition, penicillin-binding protein 1b (PBP1b) from Escherichia coli was modeled and simulated in the presence of a nascent PG to investigate their interactions. Trajectory analysis reveals that as the glycan chain grows, the non-reducing end of the nascent PG displays much greater fluctuation along the membrane normal and minimally interacts with the membrane surface. In addition, dihedral angles within the pyrophosphate moiety are determined by the length of the PG moiety and its surrounding environment. When a nascent PG is bound to PBP1b, the stem peptide remains in close contact with PBP1b by structural rearrangement of the glycan chain. Most importantly, the number of nascent PG units required to reach the transpeptidase domain are determined to be 7 or 8. Our findings complement experimental results to further understand how the structure of nascent PG can dictate the assembly of the PG scaffold.