bluuebunny/crossref_metadata_2025_split huggingface dataset:
Isotopic fractionation in interstellar molecules
Authors: Furuya Kenji 
Published: September 2018

AbstractThe level of isotopic fractionation in molecules provides insights into their formation environments and how they formed. In this article, we review hydrogen and nitrogen isotopic fractionation in low-mass star-forming regions. Interstellar molecules are significantly enriched in deuterium. The importance of the nuclear spin states of light species on deuterium fractionation and the usefulness of singly and doubly deuterated molecules as chemical tracers are discussed. Observations have revealed that molecules in prestellar cores are enriched in or depleted in15N depending on molecules. Compared with deuterium fractionation chemistry, our understanding of15N fractionation chemistry is not well established. We briefly discuss potential15N fractionation routes, i.e., isotopic-exchange reactions and isotopic selective photodissociation of N2. In addition, the selective freeze-out of15N atoms onto dust grains around the transition between N atoms and N2is discussed as a potential mechanism that causes the depletion of15N in the gas phase.
The ALMA view of UV-irradiated cloud edges: unexpected structures and processes
Authors: Goicoechea Javier R. , Cuadrado S. , Pety J. , Aguado A. , Black J. H. , Bron E. , Cernicharo J. , Chapillon E. , Fuente A. , Gerin M. , Joblin C. , Roncero O. , Tercero B. 
Published: September 2018

AbstractFar-UV photons (FUV, E < 13.6 eV) from hot massive stars regulate, or at least influence, the heating, ionization, and chemistry of most of the neutral interstellar medium (H i and H2 clouds). Investigating the interaction between FUV radiation and interstellar matter (molecules, atoms and grains) thus plays an important role in astrochemistry.The Orion Bar, an interface region between the Orion A molecular cloud and the H ii region around the Trapezium cluster, is a textbook example of a strongly illuminated dense PDR (photodissociation region). The Bar is illuminated by a FUV field of a few 104 times the mean interstellar radiation field. Because of its proximity and nearly edge-on orientation, it provides a very good template to investigate the chemical content, structure, and dynamics of a strongly irradiated molecular cloud edge. We have used ALMA to mosaic a small field of the Bar where the critical transition from atomic to molecular gas takes place. These observations provide an unprecedented sharp view of this transition layer (≲ 1″ resolution or ≲ 414 AU). The resulting images (so far in the rotational emission of CO, HCO+, H13CO+, SO+, SO, and reactive ions SH+ and HOC+) show the small-scale structure in gas density and temperature, and the steep abundance gradients. The images reveal a pattern of high-density substructures, photo-ablative gas flows and instabilities at the edge of the molecular cloud. These first ALMA images thus show a more complex morphology than the classical clump/interclump static model of a PDR.In order to quantify the chemical content in strongly FUV-irradiated gas, we have also used the IRAM-30 m telescope to carry out a complete line-survey of the illuminated edge of the Bar in the millimeter domain. Our observations reveal the presence of complex organic molecules (and precursors) that were not expected in such a harsh environment. In particular, we have reported the first detection of the unstable cis conformer of formic acid (HCOOH) in the ISM. The energy barrier to internal rotation (the conversion from trans to cis) is approximately 4827 cm−1 (≈7000 K). Hence, this detection is surprising. The low inferred trans-to-cis abundance ratio of 2.8±1.0 supports a photoswitching mechanism: a given conformer absorbs a FUV stellar photon that radiatively excites the molecule to electronic states above the interconversion barrier. Subsequent fluorescent decay leaves the molecule in a different conformer form. This mechanism, which we have specifically studied with ab initio quantum calculations, was not considered so far in astrochemistry although it can affect the structure of a variety of molecules in PDRs.
On the Series of +CG Lightning Strokes in Dancing Sprite Events
Authors: Bór J. , Zelkó Z. , Hegedüs T. , Jäger Z. , Mlynarczyk J. , Popek M. , Betz H. D. 
Published: September 2018

AbstractIn dancing sprite events, sprite entities and groups appear in rapid succession together with a corresponding series of parent lightning strokes. Dancing sprite events, including a case with possible sprite rebrightening, were recorded on video simultaneously from two observation sites above a mesoscale convective system in Central Europe on the night of 6 August 2013. Joint analysis of triangulated locations of sprite elements, position, type, and peak current of lightning strokes from the LINET lightning detection network database and current moment waveforms deduced at the Hylaty station, Poland, showed that subsequent sprite‐parent lightning strokes occurred no further than 21 km from the closest preceding sprite entity in the cases analyzed in this study. Additionally, it was found that longer sprite delay times tend to correspond to larger sprite location offsets from the parent +CG stroke. These observations, the occurrence of +CG lightning stroke and sprite sequences, as well as sprite‐sprite delay times and displacements can be explained if +CG strokes are part of one extended lightning flash. A corresponding production mechanism based on previous findings on the formation of sprite‐producing and general +CG lightning discharges is suggested.
Measurement of Activation Volume for Creep of Dry Olivine at Upper‐Mantle Conditions
Authors: Dixon Nathaniel A. , Durham William B. 
Published: September 2018

AbstractOlivine is the most abundant and among the weakest phases in Earth's upper mantle, and thus, its rheological properties play a critical role in governing thermal structure and convective flow in the upper mantle. A persistent obstacle to constraining the in situ flow properties of olivine by laboratory experiment has been the difficulty in resolving the effect of pressure, which is weak within the 0‐ to ~2‐GPa pressure range of conventional laboratory deformation instruments but potentially strong over the 1‐ to ~14‐GPa range of the upper mantle. Using a deformation‐DIA, one of a new generation of bonafide deformation devices designed for operation to ≥10 GPa, we have deformed dry, polycrystalline San Carlos olivine in high‐temperature creep with the singular intent of providing the best achievable measurement of activation volume V* and a comprehensive statement of uncertainty. Under strictly dry conditions, at constant temperature (1,373 K) and strain rate (1 × 10−5 s−1), varying only pressure (1.8 to 8.8 GPa), we measure V* = 15 ± 5 cm3/mol. We have reproduced the well‐known mechanism change from [100]‐slip to [001]‐slip near 5 GPa and determined that, whatever the change in V* associated with the change in slip system, the effective value of 15 ± 5 cm3/mol is still accurate for modeling purposes in the 2‐ to 9‐GPa pressure range. This is a substantial pressure effect, which in the absence of a temperature gradient would represent a viscosity increase from the top to bottom of the upper mantle of 5 ± 2 orders of magnitude.
Plasmonic nanostructure design and characterization via Deep Learning
Authors: Malkiel Itzik , Mrejen Michael , Nagler Achiya , Arieli Uri , Wolf Lior , Suchowski Haim 
Published: September 2018

AbstractNanophotonics, the field that merges photonics and nanotechnology, has in recent years revolutionized the field of optics by enabling the manipulation of light–matter interactions with subwavelength structures. However, despite the many advances in this field, the design, fabrication and characterization has remained widely an iterative process in which the designer guesses a structure and solves the Maxwell’s equations for it. In contrast, the inverse problem, i.e., obtaining a geometry for a desired electromagnetic response, remains a challenging and time-consuming task within the boundaries of very specific assumptions. Here, we experimentally demonstrate that a novel Deep Neural Network trained with thousands of synthetic experiments is not only able to retrieve subwavelength dimensions from solely far-field measurements but is also capable of directly addressing the inverse problem. Our approach allows the rapid design and characterization of metasurface-based optical elements as well as optimal nanostructures for targeted chemicals and biomolecules, which are critical for sensing, imaging and integrated spectroscopy applications.
Entanglement and teleportation between polarization and wave-like encodings of an optical qubit
Authors: Sychev Demid V. , Ulanov Alexander E. , Tiunov Egor S. , Pushkina Anastasia A. , Kuzhamuratov A. , Novikov Valery , Lvovsky A. I. 
Published: September 2018

AbstractLight is an irreplaceable means of communication among various quantum information processing and storage devices. Due to their different physical nature, some of these devices couple more strongly to discrete, and some to continuous degrees of freedom of a quantum optical wave. It is therefore desirable to develop a technological capability to interconvert quantum information encoded in these degrees of freedom. Here we generate and characterize an entangled state between a dual-rail (polarization-encoded) single-photon qubit and a qubit encoded as a superposition of opposite-amplitude coherent states. We furthermore demonstrate the application of this state as a resource for the interfacing of quantum information between these encodings. In particular, we show teleportation of a polarization qubit onto a freely propagating continuous-variable qubit.
Dynamics of cellular states of fibro-adipogenic progenitors during myogenesis and muscular dystrophy
Authors: Malecova Barbora , Gatto Sole , Etxaniz Usue , Passafaro Magda , Cortez Amy , Nicoletti Chiara , Giordani Lorenzo , Torcinaro Alessio , De Bardi Marco , Bicciato Silvio , De Santa Francesca , Madaro Luca , Puri Pier Lorenzo 
Published: September 2018

AbstractFibro-adipogenic progenitors (FAPs) are currently defined by their anatomical position, expression of non-specific membrane-associated proteins, and ability to adopt multiple lineages in vitro. Gene expression analysis at single-cell level reveals that FAPs undergo dynamic transitions through a spectrum of cell states that can be identified by differential expression levels of Tie2 and Vcam1. Different patterns of Vcam1-negative Tie2high or Tie2low and Tie2low/Vcam1-expressing FAPs are detected during neonatal myogenesis, response to acute injury and Duchenne Muscular Dystrophy (DMD). RNA sequencing analysis identified cell state-specific transcriptional profiles that predict functional interactions with satellite and inflammatory cells. In particular, Vcam1-expressing FAPs, which exhibit a pro-fibrotic expression profile, are transiently activated by acute injury in concomitance with the inflammatory response. Aberrant persistence of Vcam1-expressing FAPs is detected in DMD muscles or upon macrophage depletion, and is associated with muscle fibrosis, thereby revealing how disruption of inflammation-regulated FAPs dynamics leads to a pathogenic outcome.
Reconstruction of the cropland cover changes in eastern China between the 10th century and 13th century using historical documents
Authors: Li Meijiao , He Fanneng , Li Shicheng , Yang Fan 
Published: September 2018

AbstractTo evaluate and improve datasets of anthropogenic land cover change used in local and global climate models, great efforts were made to reconstruct historical land use, including the LandCover 6k project which dedicated to reconstructing human land use over the past 10,000 years. In this study, we utilized historical records, including taxed-cropland and cropland measurement areas, and data on the number of households in eastern China between the 10th century and 13th century in concert with coefficient calibration, model allocation, and per capita cropland estimation to reconstruct areas of provincial cropland for 22 provinces over five time periods. Our reconstructions indicate that total cropland areas of eastern China for AD 1000, 1066, 1078, 1162, and 1215 are 34.74 × 106 ha, 49.42 × 106 ha, 51.62 × 106 ha, 35.21 × 106 ha, and 51.21 × 106 ha, respectively. And the cropland area fluctuated because of dynasty shift and went through three phases. Cropland expansion and contraction mainly occurred in the middle and lower reaches of the Yangtze and Yellow Rivers as well as the Huaihe River Basin, while in some regions far away from battlefields, including northeastern and southern China, cropland area expanded continuously throughout the study period.
Single cell genomes of Prochlorococcus, Synechococcus, and sympatric microbes from diverse marine environments
Authors: Berube Paul M. , Biller Steven J. , Hackl Thomas , Hogle Shane L. , Satinsky Brandon M. , Becker Jamie W. , Braakman Rogier , Collins Sara B. , Kelly Libusha , Berta-Thompson Jessie , Coe Allison , Bergauer Kristin , Bouman Heather A. , Browning Thomas J. , De Corte Daniele , Hassler Christel , Hulata Yotam , Jacquot Jeremy E. , Maas Elizabeth W. , Reinthaler Thomas , Sintes Eva , Yokokawa Taichi , Lindell Debbie , Stepanauskas Ramunas , Chisholm Sallie W. 
Published: September 2018

AbstractProchlorococcus and Synechococcus are the dominant primary producers in marine ecosystems and perform a significant fraction of ocean carbon fixation. These cyanobacteria interact with a diverse microbial community that coexists with them. Comparative genomics of cultivated isolates has helped address questions regarding patterns of evolution and diversity among microbes, but the fraction that can be cultivated is miniscule compared to the diversity in the wild. To further probe the diversity of these groups and extend the utility of reference sequence databases, we report a data set of single cell genomes for 489 Prochlorococcus, 50 Synechococcus, 9 extracellular virus particles, and 190 additional microorganisms from a diverse range of bacterial, archaeal, and viral groups. Many of these uncultivated single cell genomes are derived from samples obtained on GEOTRACES cruises and at well-studied oceanographic stations, each with extensive suites of physical, chemical, and biological measurements. The genomic data reported here greatly increases the number of available Prochlorococcus genomes and will facilitate studies on evolutionary biology, microbial ecology, and biological oceanography.
Chemotactic responses of growing neurites to precisely controlled gradients of nerve growth factor
Authors: Bicknell Brendan A. , Pujic Zac , Feldner Julia , Vetter Irina , Goodhill Geoffrey J. 
Published: September 2018

AbstractChemotaxis plays a key role in many biological systems. In particular in the context of the developing nervous system, growing neurites can respond in vitro to shallow gradients of chemotropic molecules such as nerve growth factor (NGF). However, in such studies the gradient parameters are often not well controlled. Here we present a dataset of ~3500 images of early postnatal rat dorsal root ganglion (DRG) explants growing in 40 different precisely controlled combinations of absolute concentration and gradient steepness of NGF. Each image has been segmented into neurite and explant-body regions. We provide computer code for exploration and quantification of the data, including a Fourier analysis of the outer contour of neurite growth, which allows quantities such as outgrowth and guidance as a function of concentration and gradient steepness to be easily extracted. This is the most comprehensive quantitative dataset of chemotactic responses yet available for any biological system, which we hope will be useful for exploring the biological mechanisms governing chemotaxis.
Galbanic Acid-Coated Fe3O4 Magnetic Nanoparticles with Enhanced Cytotoxicity to Prostate Cancer Cells
Authors: Mohtashami Leila , Ghows Narjes , Tayarani-Najaran Zahra , Iranshahi Mehrdad 
Published: September 2018

AbstractGalbanic acid is a natural sesquiterpene coumarin compound with different biological activities, particularly cytotoxicity against LNCaP (an androgen-dependent prostate cancer cell line). Galbanic acid induces apoptosis in LNCaP via down-regulation of androgen receptor. However, the poor water-solubility of galbanic acid limits further in vitro and in vivo studies. In this study we present the synthesis of galbanic acid-coated Fe3O4 magnetic nanoparticles and their cytotoxicity evaluation on three prostate cancer cell lines, including PC3 (an androgen-independent cell line), LNCaP, and DU145 (an androgen-independent cell line). The synthesized nanoparticles were characterized by X-ray diffraction spectroscopy, Fourier transform infrared spectroscopy, transmission electron microscopy, scattering electron microscopy, energy-dispersive X-ray spectroscopy, dynamic light scattering, and vibrating sample magnetometry. Our cytotoxicity evaluation demonstrated that galbanic acid was cytotoxic only against LNCaP cells, while the galbanic acid-coated Fe3O4 nanoparticles showed cytotoxicity on all tested cells, including androgen-dependent and -independent cell lines. This indicates that other mechanisms are involved in the cytotoxicity of galbanic acid in addition to androgen receptor down-regulation. In conclusion, the loading of galbanic acid on the surface of Fe3O4 magnetic nanoparticles turned out to be a successful approach to enhance the solubility and cytotoxicity of this compound.
Colorectal Lymphoma: A Review
Authors: Gay Nathan , Chen Andy , Okada Craig 
Published: September 2018

AbstractNon-Hodgkin lymphoma (NHL) that primarily involves the colon is rare and should be distinguished from the more common systemic nodal lymphoma. It has unique clinical expectations and management consideration. Different histologic subtypes of NHL involve the colon, which varies in the clinical behavior and likelihood of obtaining durable remissions with treatment. This article will review the current understanding of the different histologic subtypes of primary colorectal lymphoma and propose management algorithms.
Small Bowel and Colorectal Carcinoids
Authors: Byrne Raphael , Pommier Rodney 
Published: September 2018

AbstractNeuroendocrine tumors, or carcinoid tumors, of both the midgut and hindgut are quite rare, but their incidence is increasing. Surgery is the treatment of choice in patients who can tolerate an operation and have operable disease. Options for the treatment of metastatic disease include cytoreductive surgery, somatostatin analogues, interferon α, local liver therapies (hepatic arterial embolization, ablation), chemotherapy, Peptide-Receptor Radionucleotide Radiotherapy, angiogenesis inhibitors, and mammalian target of rapamycin inhibitors.
The Role of Factor VII in Haemostasis: Infusion Studies of Factor VIIa in a Canine Model of Factor VIII Deficiency
Authors: Mertens Koen , Briët Ernest , Giles Alan R 
Published: September 2018

SummaryThe role of factor VIIa in haemostasis has been studied using a canine model of factor VIII deficiency. Highly purified human factor VIIa was administered to dogs at a dosage of 0.5 μg/kg. At selected times pre- and post-infusion, haemostasis was evaluated by the cuticle bleeding time. Plasma was collected for the assay of various parameters, including fibrinopeptide A (FPA) as a marker for thrombin generation in vivo. Factor VIIa infusion resulted in a 6-fold increase of factor VII clotting activity with z t1/2 of 2 h. FPA levels which were 1.4 ng/ml before infusion, did not increase significantly in haemophilic dogs. In normal dogs, however, FPA levels rose to a mean value of 190 ng/ml 30 min post-infusion. It appeared that thrombin generation by factor VIIa infusion had occurred mainly via the intrinsic, factor VIIIdependent pathway. In factor VIII-deficient dogs, factor VIIa infusion did not correct cuticle bleeding, but an inconsistent haemostatic effect was observed 15–30 min post-infusion. Similar results were obtained in haemophilic dogs with circulating antibodies against factor VIII. The haemostatic effectivity could not be improved by increasing the factor VIIa dosage up to 40-fold. Although these data suggest that the extrinsic, factor VIIdependent factor X activation provides only a minor pathway of thrombin generation in vivo, it is possible that the suboptimal haemostatic effect noted may be promoted in bleeding situations where tissue factor availability is less limited. As such, factor VIIa may prove useful in the treatment of haemophilia A patients with acquired inhibitors to factor VIII.
A Point Mutation in an Invariant Splice Acceptor Site Results in a Decreased mRNA Level in a Patient with Severe Coagulation Factor XIII Subunit A Deficiency
Authors: Vreken Peter , Niessen René W L M , Peters Marjolein , Schaap Marianne C L , Zuithoff-Rijntjes Johanna G M , Sturk Augueste 
Published: September 2018

SummaryAmplification and sequencing of exons I-XV of the gene encoding subunit A of coagulation factor XIII (FXIII) in a patient with severe subunit A deficiency revealed a single G → A base substitution at the last position of intron E, mutating the invariant AG dinucleotide splice acceptor site to AA. Northern blot analysis of FXIII subunit A mRNA levels in peripheral mononuclear leukocytes showed that this mutation leads to an undetectable FXIII subunit A mRNA level, suggesting that the mutant transcript is either highly unstable or only spliced at low efficiency. Despite this low mRNA level we were able to amplify cDNA fragments containing the exonV-exonVI junction. Sequence analysis showed that the AA dinucleotide is not recognized by the splicing machinery. Instead, an AG dinucleotide located seven bases downstream of the mutated splice acceptor site is used as alternative acceptor. The resulting, alternatively spliced, FXIII subunit A transcript contains a deletion of the first seven bases of exon VI, while translation continues out of frame and leads to a premature stop codon 27 bases thereafter.
Infants distinguish between leaders and bullies
Authors: Margoni Francesco , Baillargeon Renée , Surian Luca 
Published: September 2018

SignificancePrior research indicates that infants can represent power asymmetries and expect them to both endure over time and extend across situations. Building on these efforts, we examined whether 21-month-old infants could distinguish between two different bases of social power. Infants first saw three protagonists interact with a powerful character who was either a leader (with respect-based power) or a bully (with fear-based power). Next, the character gave an order to the protagonists. Infants expected the protagonists to continue to obey the leader’s order after she left the scene, but they expected the protagonists to obey the bully’s order only when she remained present. Thus, by 21 months of age, infants can already distinguish between respect-based and fear-based power relations.
FcαRI binding at the IgA1 CH2–CH3 interface induces long-range conformational changes that are transmitted to the hinge region
Authors: Posgai Monica T. , Tonddast-Navaei Sam , Jayasinghe Manori , Ibrahim George M. , Stan George , Herr Andrew B. 
Published: September 2018

SignificanceAntibodies binding to their cognate cellular receptors can trigger important downstream immune responses. We mapped out critical amino acids on the IgA1 antibody that govern binding to its specific receptor, FcαRI. We found that two of the most important amino acids were located on a different IgA1 domain than the rest of the binding site, separated by a flexible linker. To better understand the interplay between receptor binding and dynamic motions in IgA1, we conducted dynamics simulations on the system. The results indicate that receptor binding perturbs IgA1 conformational dynamics over long distances and can link the receptor binding site to the hinge region of IgA1. We validate this finding experimentally, which has implications for the kidney disease IgA nephropathy.