bluuebunny/crossref_metadata_2025_split huggingface dataset:
3DI: A novel ion composition and three-dimensional velocity analyzer for the topside ionosphere
Authors: Ogasawara Keiichi , George Don E. , Goldstein Jerry , Hwang Kyoung-Joo , Nishimura Yukitoshi , Ruggles David A. , Stange Jason L. 
Published: May 2020

AbstractA new ion composition and three-dimensional velocity analyzer, 3-Dimensional ion velocity and mass Imager (3DI), measures 3D velocity distribution functions (VDFs) for each major ion species in Earth’s topside ionosphere. The 3DI instrument is composed of a miniaturized electrostatic analyzer (ESA) and a deflector, backed by a static, magnet-based, mass spectrometer. We have developed a micro-pixel read-out anode technique that significantly saves power in the particle detection system, and integrated it into an imaging microchannel plate (MCP). We tested the ESA and deflector, magnet-based mass spectrometer, and anode in the laboratory to demonstrate the 3DI prototype’s performance. We have applied numerical calculations to evaluate and discuss 3DI’s performance and dynamic range. Due to complexities associated with imaging 3D distribution functions during fast spacecraft motion, we also discuss the operation strategy for 3DI to capture and resolve the VDF within the field of view. Once applied to flight investigations, the 3DI observations will be extremely useful in identifying ionosphere composition, mass-dependent ion transport such as upflows, and mass-dependent ion heating. Furthermore, the precise measurement of non-thermal plasma VDFs provides information to improve ionospheric environment modeling and ground-based radar observations.
Controlled Structure and Growth Mechanism behind Hydrothermal Growth of TiO2 Nanorods
Authors: Prathan Aschariya , Sanglao Jongrak , Wang Tao , Bhoomanee Chawalit , Ruankham Pipat , Gardchareon Atcharawon , Wongratanaphisan Duangmanee 
Published: May 2020

AbstractFabrication of uniform vertically-aligned titanium dioxide nanorods (TiO2 NRs) was achieved by hydrothermal growth on a fluorine-doped tin oxide (FTO) glass substrate. The substrate was coated by a TiO2 seed layer composed of titanium (IV) butoxide (TBO) as a precursor in an HCl solution. To reduce the amount of toxic substances used in this work, a minimal amount of HCl was used. On a larger scale, this method would require less precursor and therefore be a cost-savings. The aim of the present work is to achieve high crystalline orientations of TiO2 NRs for low quantities of both TBO precursor and HCl solutions. Results showed that the 0.7% TBO TiO2 NRs after 1.5 h of hydrothermal treatment exhibited the optimal crystalline orientation along [001] while the (002) plane is the dominant facet. The results demonstrate high transmittance of visible light and well-formed crystalline structures that offer a fast electron pathway along the length of the TiO2 NRs with less grain boundaries. Lastly, TiO2 NRs and their growth mechanism are discussed. This work offers a promising hydrothermal method for growing well-aligned TiO2 single-crystal NRs that can be employed in solar cell applications.
Genetic population structure of invasive raccoons (Procyon lotor) in Hokkaido, Japan: Unique phenomenon caused by pet escape or abandonment
Authors: Okuyama Minami W. , Shimozuru Michito , Nakai Mariko , Yamaguchi Emi , Fujii Kei , Shimada Ken-ichiro , Ikeda Tohru , Tsubota Toshio 
Published: May 2020

AbstractPhylogeographic studies can resolve relationships between genetic population structure of organisms and geographical distributions. Raccoons have become feral in Japan, and in Hokkaido island, they have been rapidly increasing in number and spreading since the 1970s. We analyzed mitochondrial (mtDNA) and microsatellite DNA to understand the current phylogenetic distribution and invasive founder events. Overall, Hokkaido raccoons maintained high genetic diversity (i.e., the level of heterozygosity was comparable to the original habitat, North America). Based on mtDNA distribution and microsatellite diversity, Hokkaido raccoons were divided into six management units. However, mtDNA haplotype distributions and genetic structures based on microsatellites did not always correspond to each other (e.g., two geographically and genetically separated populations showed similar mtDNA distributions). In addition, a high degree of genetic admixture was observed in every unit, and the degree of genetic differentiation was low even between regions separated by long distances. Compared with other countries in Europe where genetic distribution of introduced raccoons is more clearly structured, the current results represent a unique and complex phenomenon of pet escape/abandonment in Hokkaido: i.e., genetically related colonies were introduced into multiple regions as founder events, resulting in the current state in which raccoons are not clearly genetically differentiated even 40 years after introduction.
Long-term sediment decline causes ongoing shrinkage of the Mekong megadelta, Vietnam
Authors: Tamura Toru , Nguyen Van Lap , Ta Thi Kim Oanh , Bateman Mark D. , Gugliotta Marcello , Anthony Edward J. , Nakashima Rei , Saito Yoshiki 
Published: May 2020

AbstractSince the 1990s the Mekong River delta has suffered a large decline in sediment supply causing coastal erosion, following catchment disturbance through hydropower dam construction and sand extraction. However, our new geological reconstruction of 2500-years of delta shoreline changes show that serious coastal erosion actually started much earlier. Data shows the sandy coast bounding river mouths accreted consistently at a rate of +2 to +4 km2/year. In contrast, we identified a variable accretion rate of the muddy deltaic protrusion at Camau; it was < +1 km2/year before 1400 years ago but increased drastically around 600 years ago, forming the entire Camau Peninsula. This high level of mud supply had sharply declined by the early 20th century after a vast canal network was built on the delta. Since then the Peninsula has been eroding, promoted by the conjunction of mud sequestration in the delta plain driven by expansion of rice cultivation, and hysteresis of long-term muddy sedimentation that left the protrusion exposed to wave erosion. Natural mitigation would require substantial increases in sediment supply well above the pre-1990s levels.
The geometry as an eyed fish feels it in spontaneous and rewarded spatial reorientation tasks
Authors: Sovrano Valeria Anna , Baratti Greta , Potrich Davide , Bertolucci Cristiano 
Published: May 2020

AbstractDisoriented human beings and animals, the latter both sighted and blind, are able to use spatial geometric information (metric and sense properties) to guide their reorientation behaviour in a rectangular environment. Here we aimed to investigate reorientation spatial skills in three fish species (Danio rerio, Xenotoca eiseni, Carassius auratus) in an attempt to discover the possible involvement of extra-visual senses during geometric navigation. We observed the fish’s behaviour under different experimental procedures (spontaneous social cued task and rewarded exit task), providing them different temporal opportunities to experience the environmental shape (no experience, short and prolonged experience). Results showed that by using spontaneous social cued memory tasks, fishes were not able to take advantage of extra-visual senses to encode the spatial geometry, neither allowing them short time-periods of environmental exploration. Contrariwise, by using a reference memory procedure, during the rewarded exit tasks, thus providing a prolonged extra-visual experience, fishes solved the geometric task, showing also differences in terms of learning times among species.
Statistical characterization of urban CO2 emission signals observed by commercial airliner measurements
Authors: Umezawa Taku , Matsueda Hidekazu , Oda Tomohiro , Higuchi Kaz , Sawa Yousuke , Machida Toshinobu , Niwa Yosuke , Maksyutov Shamil 
Published: May 2020

AbstractCities are responsible for the largest anthropogenic CO2 emissions and are key to effective emission reduction strategies. Urban CO2 emissions estimated from vertical atmospheric measurements can contribute to an independent quantification of the reporting of national emissions and will thus have political implications. We analyzed vertical atmospheric CO2 mole fraction data obtained onboard commercial aircraft in proximity to 36 airports worldwide, as part of the Comprehensive Observation Network for Trace gases by Airliners (CONTRAIL) program. At many airports, we observed significant flight-to-flight variations of CO2 enhancements downwind of neighboring cities, providing advective fingerprints of city CO2 emissions. Observed CO2 variability increased with decreasing altitude, the magnitude of which varied from city to city. We found that the magnitude of CO2 variability near the ground (~1 km altitude) at an airport was correlated with the intensity of CO2 emissions from a nearby city. Our study has demonstrated the usefulness of commercial aircraft data for city-scale anthropogenic CO2 emission studies.
Shared and Independent Genetic Basis of Resistance to Bt Toxin Cry2Ab in Two Strains of Pink Bollworm
Authors: Fabrick Jeffrey A. , LeRoy Dannialle M. , Unnithan Gopalan C. , Yelich Alex J. , Carrière Yves , Li Xianchun , Tabashnik Bruce E. 
Published: May 2020

AbstractEvolution of pest resistance threatens the benefits of crops genetically engineered to produce insecticidal proteins from Bacillus thuringiensis (Bt). Field populations of the pink bollworm (Pectinophora gossypiella), a global pest of cotton, have evolved practical resistance to transgenic cotton producing Bt toxin Cry2Ab in India, but not in the United States. Previous results show that recessive mutations disrupting an autosomal ATP-binding cassette gene (PgABCA2) are associated with pink bollworm resistance to Cry2Ab in field-selected populations from India and in one lab-selected strain from the United States (Bt4-R2). Here we discovered that an independently derived, lab-selected Cry2Ab-resistant pink bollworm strain from the United States (BX-R) also harbors mutations that disrupt PgABCA2. Premature stop codons introduced by mis-splicing of PgABCA2 pre-mRNA were prevalent in field-selected larvae from India and in both lab-selected strains. The most common mutation in field-selected larvae from India was also detected in both lab-selected strains. Results from interstrain crosses indicate BX-R has at least one additional mechanism of resistance to Cry2Ab that does not involve PgABCA2 and is not completely recessive or autosomal. We conclude that recessive mutations disrupting PgABCA2 are the primary, but not the only, mechanism of resistance to Cry2Ab in pink bollworm.
Quantum driven proton diffusion in brucite-like minerals under high pressure
Authors: Schaack Sofiane , Depondt Philippe , Huppert Simon , Finocchi Fabio 
Published: May 2020

AbstractTransport of hydrogen in hydrous minerals under high pressure is a key step for the water cycle within the Earth interior. Brucite Mg(OH)2 is one of the simplest minerals containing hydroxyl groups and is believed to decompose under the geological condition of the deep Earth’s mantle. In the present study, we investigate the proton diffusion in brucite under high pressure, which results from a complex interplay between two processes: the O–H reorientations motion around the c axis and O–H covalent bond dissociations. First-principle path-integral molecular dynamics simulations reveal that the increasing pressure tends to lock the former motion, while, in contrast, it activates the latter which is mainly triggered by nuclear quantum effects. These two competing effects therefore give rise to a pressure sweet spot for proton diffusion within the mineral. In brucite Mg(OH)2, proton diffusion reaches a maximum for pressures close to 70GPa, while the structurally similar portlandite Ca(OH)2 never shows proton diffusion within the pressure range and time scale that we explored. We analyze the different behavior of brucite and portlandite, which might constitute two prototypes for other minerals with same structure.
Circulating and tumor-infiltrating arginase 1-expressing cells in gastric adenocarcinoma patients were mainly immature and monocytic Myeloid-derived suppressor cells
Authors: Ren WeiHong , Zhang XuRan , Li WenBo , Feng Qian , Feng HuiJie , Tong Yan , Rong Hao , Wang Wei , Zhang Dai , Zhang ZhenQiang , Tu ShiChun 
Published: May 2020

AbstractMyeloid-derived suppressor cells (MDSCs) are a group of heterogeneous cells derived from immature myeloid cells (IMCs). MDSCs are known to play important roles in tumor immune evasion. While we know that there are a large number of circulating and tumor-infiltrating MDSCs existing in gastric cancer (GC) patients, the phenotypic characteristics and arginase 1 (ARG1) expression levels of these MDSCs remain very unclear. In our study, flow cytometric analysis of circulating MDSCs from 20 gastric adenocarcinoma (GAC) patients found that ≥80% ARG1-expressing MDSCs were mainly early-stage MDSCs (HLA-DR−CD33+CD14−CD15−MDSCs). In addition, our investigation showed that tumor-infiltrating MDSCs from 6 GAC patients consisted of >35% ARG1-expressing naïve MDSCs (HLA-DR−CD33−CD11b−CD14−CD15−MDSCs), >15% early-stage MDSCs and >40% monocytic MDSCs (HLA-DR−CD14+MDSCs). This preliminary study describes the phenotypic characteristics and ARG1 expression levels of MDSCs from GAC patients and shows that circulating and tumor-infiltrating ARG1-expressing cells were mainly immature and monocytic MDSCs, which provides information to better understand the mechanisms that allow gastric cancer cells to evade the immune system.
Generation of Pseudo-CT using High-Degree Polynomial Regression on Dual-Contrast Pelvic MRI Data
Authors: Leu Samuel C. , Huang Zhibin , Lin Ziwei 
Published: May 2020

AbstractIncreasing interests in using magnetic resonance imaging only in radiation therapy require methods for predicting the computed tomography numbers from MRI data. Here we propose a simple voxel method to generate the pseudo-CT (pCT) image using dual-contrast pelvic MRI data. The method is first trained with the CT data and dual-contrast MRI data (two sets of MRI with different sequences) of multiple patients, where the anatomical structures in the images after deformable image registration are segmented into several regions, and after MRI intensity normalizations a regression analysis is used to determine a two-variable polynomial function for each region to relate a voxel’s two MRI intensity values to its CT number. We first evaluate the accuracy via the Hounsfield unit (HU) difference between the pseudo-CT and reference-CT (rCT) images and obtain the average mean absolute error as 40.3 ± 2.9 HU from leave-one-out-cross-validation (LOOCV) across all six patients, which is better than most previous results and comparable to another study using the more complicated atlas-based method. We also perform a dosimetric evaluation of the treatment plans based on pCT and rCT images and find the average passing rate within 2% dose difference to be 95.4% in point-to-point dose comparisons. Therefore, our method shows encouraging results in predicting the CT numbers. This polynomial method needs less computer storage than the interpolation method and can be readily extended to the case of more than two MRI sequences.
Methodology for the identification of small molecule inhibitors of the Fanconi Anaemia ubiquitin E3 ligase complex
Authors: Sharp Michael F. , Murphy Vince J. , Twest Sylvie Van , Tan Winnie , Lui Jennii , Simpson Kaylene J. , Deans Andrew J. , Crismani Wayne 
Published: May 2020

AbstractDNA inter-strand crosslinks (ICLs) threaten genomic stability by creating a physical barrier to DNA replication and transcription. ICLs can be caused by endogenous reactive metabolites or from chemotherapeutics. ICL repair in humans depends heavily on the Fanconi Anaemia (FA) pathway. A key signalling step of the FA pathway is the mono-ubiquitination of Fanconi Anaemia Complementation Group D2 (FANCD2), which is achieved by the multi-subunit E3 ligase complex. FANCD2 mono-ubiquitination leads to the recruitment of DNA repair proteins to the site of the ICL. The loss of FANCD2 mono-ubiquitination is a common clinical feature of FA patient cells. Therefore, molecules that restore FANCD2 mono-ubiquitination could lead to a potential drug for the management of FA. On the other hand, in some cancers, FANCD2 mono-ubiquitination has been shown to be essential for cell survival. Therefore, inhibition of FANCD2 mono-ubiquitination represents a possible therapeutic strategy for cancer specific killing. We transferred an 11-protein FANCD2 mono-ubiquitination assay to a high-throughput format. We screened 9,067 compounds for both activation and inhibition of the E3 ligase complex. The use of orthogonal assays revealed that candidate compounds acted via non-specific mechanisms. However, our high-throughput biochemical assays demonstrate the feasibility of using sophisticated and robust biochemistry to screen for small molecules that modulate a key step in the FA pathway. The future identification of FA pathway modulators is anticipated to guide future medicinal chemistry projects with drug leads for human disease.
Development of Small Molecule MEIS Inhibitors that modulate HSC activity
Authors: Turan Raife Dilek , Albayrak Esra , Uslu Merve , Siyah Pinar , Alyazici Lamia Yazgi , Kalkan Batuhan Mert , Aslan Galip Servet , Yucel Dogacan , Aksoz Merve , Tuysuz Emre Can , Meric Neslihan , Durdagi Serdar , Gulbas Zafer , Kocabas Fatih 
Published: May 2020

AbstractMeis1, which belongs to TALE-type class of homeobox gene family, appeared as one of the key regulators of hematopoietic stem cell (HSC) self-renewal and a potential therapeutical target. However, small molecule inhibitors of MEIS1 remained unknown. This led us to develop inhibitors of MEIS1 that could modulate HSC activity. To this end, we have established a library of relevant homeobox family inhibitors and developed a high-throughputin silicoscreening strategy against homeodomain of MEIS proteins using the AutoDock Vina and PaDEL-ADV platform. We have screened over a million druggable small moleculesin silicoand selected putative MEIS inhibitors (MEISi) with no predicted cytotoxicity or cardiotoxicity. This was followed byin vitrovalidation of putative MEIS inhibitors using MEIS dependent luciferase reporter assays and analysis in theex vivoHSC assays. We have shown that small molecules named MEISi-1 and MEISi-2 significantly inhibit MEIS-luciferase reportersin vitroand induce murine (LSKCD34l°wcells) and human (CD34+, CD133+, and ALDHhicells) HSC self-renewalex vivo. In addition, inhibition of MEIS proteins results in downregulation ofMeis1and MEIS1 target gene expression including Hif-1α, Hif-2α and HSC quiescence modulators. MEIS inhibitors are effectivein vivoas evident by induced HSC content in the murine bone marrow and downregulation of expression of MEIS target genes. These studies warrant identification of first-in-class MEIS inhibitors as potential pharmaceuticals to be utilized in modulation of HSC activity and bone marrow transplantation studies.
An automated data processing and analysis pipeline for transmembrane proteins in detergent solutions
Authors: Molodenskiy Dmitry S. , Mertens Haydyn D. T. , Svergun Dmitri I. 
Published: May 2020

AbstractThe application of small angle X-ray scattering (SAXS) to the structural characterization of transmembrane proteins (MPs) in detergent solutions has become a routine procedure at synchrotron BioSAXS beamlines around the world. SAXS provides overall parameters and low resolution shapes of solubilized MPs, but is also meaningfully employed in hybrid modeling procedures that combine scattering data with information provided by high-resolution techniques (eg. macromolecular crystallography, nuclear magnetic resonance and cryo-electron microscopy). Structural modeling of MPs from SAXS data is non-trivial, and the necessary computational procedures require further formalization and facilitation. We propose an automated pipeline integrated with the laboratory-information management system ISPyB, aimed at preliminary SAXS analysis and the first-step reconstruction of MPs in detergent solutions, in order to streamline high-throughput studies, especially at synchrotron beamlines. The pipeline queries an ISPyB database for available a priori information via dedicated services, estimates model-free SAXS parameters and generates preliminary models utilizing either ab initio, high-resolution-based, or mixed/hybrid methods. The results of the automated analysis can be inspected online using the standard ISPyB interface and the estimated modeling parameters may be utilized for further in-depth modeling beyond the pipeline. Examples of the pipeline results for the modelling of the tetrameric alpha-helical membrane channel Aquaporin0 and mechanosensitive channel T2, solubilized by n-Dodecyl β-D-maltoside are presented. We demonstrate how increasing the amount of a priori information improves model resolution and enables deeper insights into the molecular structure of protein-detergent complexes.
Effects of local hypothermia–rewarming on physiology, metabolism and inflammation of acutely injured human spinal cord
Authors: Gallagher Mathew J. , Hogg Florence R. A. , Kearney Siobhan , Kopp Marcel A. , Blex Christian , Serdani Leonarda , Sherwood Oliver , Schwab Jan M. , Zoumprouli Argyro , Papadopoulos Marios C. , Saadoun Samira 
Published: May 2020

AbstractIn five patients with acute, severe thoracic traumatic spinal cord injuries (TSCIs), American spinal injuries association Impairment Scale (AIS) grades A–C, we induced cord hypothermia (33 °C) then rewarming (37 °C). A pressure probe and a microdialysis catheter were placed intradurally at the injury site to monitor intraspinal pressure (ISP), spinal cord perfusion pressure (SCPP), tissue metabolism and inflammation. Cord hypothermia–rewarming, applied to awake patients, did not cause discomfort or neurological deterioration. Cooling did not affect cord physiology (ISP, SCPP), but markedly altered cord metabolism (increased glucose, lactate, lactate/pyruvate ratio (LPR), glutamate; decreased glycerol) and markedly reduced cord inflammation (reduced IL1β, IL8, MCP, MIP1α, MIP1β). Compared with pre-cooling baseline, rewarming was associated with significantly worse cord physiology (increased ICP, decreased SCPP), cord metabolism (increased lactate, LPR; decreased glucose, glycerol) and cord inflammation (increased IL1β, IL8, IL4, IL10, MCP, MIP1α). The study was terminated because three patients developed delayed wound infections. At 18-months, two patients improved and three stayed the same. We conclude that, after TSCI, hypothermia is potentially beneficial by reducing cord inflammation, though after rewarming these benefits are lost due to increases in cord swelling, ischemia and inflammation. We thus urge caution when using hypothermia–rewarming therapeutically in TSCI.