bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dust Detection via Voltage Power Spectroscopy on a CubeSat in Earth's Ionosphere
Authors: Maj Ronald , Cairns Iver H. 
Published: September 2018

AbstractDust detection is an important area of research, especially for determining the space environment in Earth orbit. Satellites such as the GPS constellation are vital for millions of people everyday and dust impacts on spacecraft can lead to catastrophic failure when particles are large enough (Caswell et al., 1995, https://doi.org/10.1016/0734-743X(95)99843-G). However, dust particles micron‐sized or smaller can be detected due to the plasma cloud that is released from their impact (Meyer‐Vernet, 1983, https://doi.org/10.1029/JA088iA10p08081). We investigate the practicality of using voltage power spectroscopy on a CubeSat with dipole antennas to measure the dust particles from such collisions and to characterize the Earth's ionosphere from 300‐ to 1,500‐km altitude. We find that the average power spectrum due to dust from space debris and interplanetary sources is at least 6 orders of magnitude smaller than the shot noise spectrum. Within 10 s of a 2009 Iridium‐COSMOS type satellite collision the average power spectrum due to dust impacts is at least 8 orders of magnitude smaller. Detection using the power spectrum is only possible for large enough single‐particle impact events, which are rare. For the average spectrum to be 3 times larger than the shot noise spectrum, the particle would need to be at least 5.4, 4.0, and 3.2 μm in diameter for a polar orbit at 300‐, 800‐, and 1,500‐km altitude, respectively, which corresponds to one hit every 2,150, 110, and 225 min, respectively. Direct time domain observation of the voltage signal of dust impact plasma clouds would be a more effective method for measuring dust particles in the ionosphere.
Smoothing of Fault Slip Surfaces by Scale‐Invariant Wear
Authors: Dascher‐Cousineau Kelian , Kirkpatrick James D. , Cooke Michele L. 
Published: September 2018

AbstractPrevious field observations suggest that fault slip surface roughness may decrease with slip. However, measurements have yet to confidently isolate the effect of slip from other possible controls, such as lithology or tectonic setting. We describe the evolution of slip surfaces in normal faults in SE Utah that cut well‐sorted, high‐porosity sandstones and accommodated regional extension at 1‐ to 4‐km depth. Tight controls on fault offset and uniform tectonic history allowed us to isolate the effect of slip during early stages of faulting (0‐ to 55‐m slip). Slip surfaces progress from rough joints and deformation bands toward smooth, continuous, and mirror‐like surfaces with increasing slip. We collected 123 scans of pristine slip surfaces, which measure surface geometry from micrometers to meters in length scale. Results indicate that slip surface roughness is systematically smoother than joint surfaces and deformation band edges. Over the best resolved length scales (0.1–10 mm), we observe roughness decreases with slip according to a power law with exponent −1 in the slip direction. Slip‐perpendicular profiles, though rougher, exhibit the same smoothing trend. The Hurst scaling exponent does not change with slip. These observations require wear to be multiscale. Boundary element method models suggest that mechanical wear of completely mated surfaces occurs by asperity failure and that the wear rate depends on the aspect ratio of asperities. These results indicate that at large slip, asperity failure at all length scales can cause slip surfaces to smooth while maintaining the fractal geometry characteristic of faults.
High Summertime Aerosol Loadings Over the Arabian Sea and Their Transport Pathways
Authors: Jin Qinjian , Wei Jiangfeng , Pu Bing , Yang Zong‐Liang , Parajuli Sagar Prasad 
Published: September 2018

AbstractSatellite observations show high aerosol loadings over the Arabian Sea in boreal summer, which have great impacts on the Indian monsoon due to absorbing dust aerosols. However, the compositions, origins, transport pathways, and decadal trends of these aerosols have not been well studied. In this study, using multiple satellite retrievals, a back trajectory model, and reanalysis data, we found that (1) aerosol optical depth (AOD) over the Arabian Sea and Arabian Peninsula have a summer peak and dust aerosols dominate the AOD; aerosol reanalysis data tend to considerably underestimate dust AOD compared to satellite data, indicating challenges of extracting dust from total AOD; (2) aerosols over the Arabian Sea are largely transported from South and East Arabian Peninsula by cyclonic winds in the lower troposphere (850 hPa) and from Iran–Afghanistan–Pakistan by anticyclonic winds in the middle troposphere (500 hPa); (3) both case studies and composite analyses show that extremely high aerosol loadings over the Arabian Sea is associated with an abnormally low pressure over the Arabian Sea and the Middle East; and (4) significant positive trends in AOD over the Arabian Peninsula and the Arabian Sea exist during 2000–2011 but disappear during 2000–2016, indicating a strong interdecadal variability of dust activities. This study revealed pathways linking dust emissions in the Middle East to high summertime AOD over the Arabian Sea and identified the atmospheric conditions favorable for dust emissions and transport.
Population Density and Risk of Inflammatory Bowel Disease: A Prospective Population-Based Study in 13 Countries or Regions in Asia-Pacific
Authors: Ng Siew C. , Kaplan Gilaad G. , Tang Whitney , Banerjee Rupa , Adigopula Bhargavi , Underwood Fox E. , Tanyingoh Divine , Wei Shu-Chen , Lin Wei-Chen , Lin Hung-Hsin , Li Jin , Bell Sally , Niewiadomski Olga , Kamm Michael A. , Zeng Zhirong , Chen Minhu , Hu Pinjin , Ong David , Ooi Choon Jin , Ling Khoon-Lin , Miao Yinglei , Miao Jiarong , Janaka de Silva H. , Niriella Madunil , Aniwan Satimai , Limsrivilai Julajak , Pisespongsa Pises , Wu Kaichun , Yang Hong , Ng Ka Kei , Yu Hon Ho , Wang Yufang , Ouyang Qin , Abdullah Murdani , Simadibrata Marcellus , Gunawan Jeffri , Hilmi Ida , Lee Goh Khean , Cao Qian , Sheng Hong , Ong-Go Arlinking , Chong Vui Heng , Ching Jessica Y. L. , Wu Justin C. Y. , Chan Francis K. L. , Sung Joseph J. Y. 
Published: September 2018

INTRODUCTION:
Living in an urban environment may increase the risk of developing inflammatory bowel disease (IBD). It is unclear if this observation is seen globally. We conducted a population-based study to assess the relationship between urbanization and incidence of IBD in the Asia-Pacific region.

METHODS:
Newly diagnosed IBD cases between 2011 and 2013 from 13 countries or regions in Asia-Pacific were included. Incidence was calculated with 95% confidence interval (CI) and pooled using random-effects model. Meta-regression analysis was used to assess incidence rates and their association with population density, latitude, and longitude.

RESULTS:
We identified 1175 ulcerative colitis (UC), 656 Crohn’s disease (CD), and 37 IBD undetermined (IBD-U). Mean annual IBD incidence per 100 000 was 1.50 (95% CI: 1.43–1.57). India (9.31; 95% CI: 8.38–10.31) and China (3.64; 95% CI, 2.97–4.42) had the highest IBD incidence in Asia. Incidence of overall IBD (incidence rate ratio [IRR]: 2.19; 95% CI: 1.01–4.76]) and CD (IRR: 3.28; 95% CI: 1.83–9.12) was higher across 19 areas of Asia with a higher population density. In China, incidence of IBD (IRR: 2.37; 95% CI: 1.10–5.16) and UC (IRR: 2.63; 95% CI: 1.2–5.8) was positively associated with gross domestic product. A south-to-north disease gradient (IRR: 0.94; 95% CI: 0.91–0.98) was observed for IBD incidence and a west-to-east gradient (IRR: 1.14; 95% CI: 1.05–1.24) was observed for CD incidence in China. This study received IRB approval.

CONCLUSIONS:
Regions in Asia with a high population density had a higher CD and UC incidence. Coastal areas within China had higher IBD incidence. With increasing urbanization and a shift from rural areas to cities, disease incidence may continue to climb in Asia.
Mapping molecular landmarks of human skeletal ontogeny and pluripotent stem cell-derived articular chondrocytes
Authors: Ferguson Gabriel B. , Van Handel Ben , Bay Maxwell , Fiziev Petko , Org Tonis , Lee Siyoung , Shkhyan Ruzanna , Banks Nicholas W. , Scheinberg Mila , Wu Ling , Saitta Biagio , Elphingstone Joseph , Larson A. Noelle , Riester Scott M. , Pyle April D. , Bernthal Nicholas M. , Mikkola Hanna KA , Ernst Jason , van Wijnen Andre J. , Bonaguidi Michael , Evseenko Denis 
Published: September 2018

AbstractTissue-specific gene expression defines cellular identity and function, but knowledge of early human development is limited, hampering application of cell-based therapies. Here we profiled 5 distinct cell types at a single fetal stage, as well as chondrocytes at 4 stages in vivo and 2 stages during in vitro differentiation. Network analysis delineated five tissue-specific gene modules; these modules and chromatin state analysis defined broad similarities in gene expression during cartilage specification and maturation in vitro and in vivo, including early expression and progressive silencing of muscle- and bone-specific genes. Finally, ontogenetic analysis of freshly isolated and pluripotent stem cell-derived articular chondrocytes identified that integrin alpha 4 defines 2 subsets of functionally and molecularly distinct chondrocytes characterized by their gene expression, osteochondral potential in vitro and proliferative signature in vivo. These analyses provide new insight into human musculoskeletal development and provide an essential comparative resource for disease modeling and regenerative medicine.
High-throughput chromatin accessibility profiling at single-cell resolution
Authors: Mezger Anja , Klemm Sandy , Mann Ishminder , Brower Kara , Mir Alain , Bostick Magnolia , Farmer Andrew , Fordyce Polly , Linnarsson Sten , Greenleaf William 
Published: September 2018

AbstractHere we develop a high-throughput single-cell ATAC-seq (assay for transposition of accessible chromatin) method to measure physical access to DNA in whole cells. Our approach integrates fluorescence imaging and addressable reagent deposition across a massively parallel (5184) nano-well array, yielding a nearly 20-fold improvement in throughput (up to ~1800 cells/chip, 4–5 h on-chip processing time) and library preparation cost (~81¢ per cell) compared to prior microfluidic implementations. We apply this method to measure regulatory variation in peripheral blood mononuclear cells (PBMCs) and show robust, de novo clustering of single cells by hematopoietic cell type.
Liquid-state quantitative SERS analyzer on self-ordered metal liquid-like plasmonic arrays
Authors: Tian Li , Su Mengke , Yu Fanfan , Xu Yue , Li Xiaoyun , Li Lei , Liu Honglin , Tan Weihong 
Published: September 2018

AbstractLiquid interfacial plasmonic platform is emerging for new sensors, catalysis, and tunable optical devices, but also promises an alternative for practical applications of surface-enhanced Raman spectroscopy (SERS). Here we show that vigorous mixing of chloroform with citrate-capped gold nanorod sols triggers the rapid self-assembly of three-dimensional plasmonic arrays at the chloroform/water (O/W) interface and produces a self-healing metal liquid-like brilliant golden droplet. The O phase itself generates stable SERS fingerprints and is a good homogeneous internal standard for quantitative analysis. This platform presents reversible O/W encasing in a common cuvette determined just by surface wettability of the container. Both O-in-W and W-in-O platforms exhibit excellent SERS sensitivity and reproducibility for different analytes by the use of a portable Raman device. It paves the way toward a practical and quantitative liquid-state SERS analyzer, likened to a simple UV–Vis spectrometer, that is far superior to typical solid substrate-based or nanoparticle sol-based analysis.
Tropical peatland carbon storage linked to global latitudinal trends in peat recalcitrance
Authors: Hodgkins Suzanne B. , Richardson Curtis J. , Dommain René , Wang Hongjun , Glaser Paul H. , Verbeke Brittany , Winkler B. Rose , Cobb Alexander R. , Rich Virginia I. , Missilmani Malak , Flanagan Neal , Ho Mengchi , Hoyt Alison M. , Harvey Charles F. , Vining S. Rose , Hough Moira A. , Moore Tim R. , Richard Pierre J. H. , De La Cruz Florentino B. , Toufaily Joumana , Hamdan Rasha , Cooper William T. , Chanton Jeffrey P. 
Published: September 2018

AbstractPeatlands represent large terrestrial carbon banks. Given that most peat accumulates in boreal regions, where low temperatures and water saturation preserve organic matter, the existence of peat in (sub)tropical regions remains enigmatic. Here we examined peat and plant chemistry across a latitudinal transect from the Arctic to the tropics. Near-surface low-latitude peat has lower carbohydrate and greater aromatic content than near-surface high-latitude peat, creating a reduced oxidation state and resulting recalcitrance. This recalcitrance allows peat to persist in the (sub)tropics despite warm temperatures. Because we observed similar declines in carbohydrate content with depth in high-latitude peat, our data explain recent field-scale deep peat warming experiments in which catotelm (deeper) peat remained stable despite temperature increases up to 9 °C. We suggest that high-latitude deep peat reservoirs may be stabilized in the face of climate change by their ultimately lower carbohydrate and higher aromatic composition, similar to tropical peats.
Necroptosis mediates myofibre death in dystrophin-deficient mice
Authors: Morgan Jennifer E. , Prola Alexandre , Mariot Virginie , Pini Veronica , Meng Jinhong , Hourde Christophe , Dumonceaux Julie , Conti Francesco , Relaix Frederic , Authier Francois-Jerôme , Tiret Laurent , Muntoni Francesco , Bencze Maximilien 
Published: September 2018

AbstractDuchenne muscular dystrophy (DMD) is a severe degenerative disorder caused by mutations in the dystrophin gene. Dystrophin-deficient muscles are characterised by progressive myofibre necrosis in which inflammation plays a deleterious role. However, the molecular mechanisms underlying inflammation-induced necrosis in muscle cells are unknown. Here we show that necroptosis is a mechanism underlying myofibre death in dystrophin-deficient muscle. RIPK1, RIPK3 and MLKL are upregulated in dystrophic mouse myofibres. In human DMD samples, there is strong immunoreactivity to RIPK3 and phospho-MLKL in myofibres. In vitro, TNFα can elicit necroptosis in C2C12 myoblasts, and RIPK3 overexpression sensitises myoblasts to undergo TNF-induced death. Furthermore, genetic ablation of Ripk3 in mdx mice reduces myofibre degeneration, inflammatory infiltrate, and muscle fibrosis, and eventually improves muscle function. These findings provide the first evidence of necroptotic cell death in a disease affecting skeletal muscle and identify RIPK3 as a key player in the degenerative process in dystrophin-deficient muscles.
Focused clamping of a single neuronal SNARE complex by complexin under high mechanical tension
Authors: Shon Min Ju , Kim Haesoo , Yoon Tae-Young 
Published: September 2018

AbstractNeuronal soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) catalyze synaptic vesicle fusion with presynaptic membranes through the formation of SNARE complexes. Complexin (Cpx) is the only presynaptic protein that tightly binds to SNAREs and regulates membrane fusion, but how it modulates the energy landscape of SNARE complex assembly, especially under mechanical tension on the complex, remains unclear. Here, using magnetic tweezers, we report how Cpx interacts with single SNARE complexes. The effects of Cpx manifest only under high mechanical tensions above 13 pN. Cpx stabilizes the central four-helix bundle of SNARE motifs and, at the same time, prevents the complete zippering of SNAREs by inhibiting linker-domain assembly. These results suggest that Cpx generates a focused clamp for the neuronal SNARE complex in a linker-open conformation. Our results provide a hint as to how Cpx cooperates with neuronal SNAREs to prime synaptic vesicles in preparation for synchronous neurotransmitter release.
Analysis By Deep Sequencing of Discontinued Neurotropic Yellow Fever Vaccine Strains
Authors: Beck Andrew S. , Wood Thomas G. , Widen Steven G. , Thompson Jill K , Barrett Alan D. T. 
Published: September 2018

AbstractDeep sequencing of live-attenuated viral vaccines has focused on vaccines in current use. Here we report characterization of a discontinued live yellow fever (YF) vaccine associated with severe adverse events. The French neurotropic vaccine (FNV) strain of YF virus was derived empirically in 1930 by 260 passages of wild-type French viscerotropic virus (FVV) in mouse brain. The vaccine was administered extensively in French-speaking Africa until discontinuation in 1982, due to high rates of post-vaccination encephalitis in children. Using rare archive strains of FNV, viral RNAs were sequenced and analyzed by massively parallel, in silico methods. Diversity and specific population structures were compared in reference to the wild-type parental strain FVV, and between the vaccine strains themselves. Lower abundance of polymorphism content was observed for FNV strains relative to FVV. Although the vaccines were of lower diversity than FVV, heterogeneity between the vaccines was observed. Reversion to wild-type identity was variably observed in the FNV strains. Specific population structures were recovered from vaccines with neurotropic properties; loss of neurotropism in mice was associated with abundance of wild-type RNA populations. The analysis provides novel sequence evidence that FNV is genetically unstable, and that adaptation of FNV contributed to the neurotropic adverse phenotype.
Deep soils modify environmental consequences of increased nitrogen fertilizer use in intensifying Amazon agriculture
Authors: Jankowski KathiJo , Neill Christopher , Davidson Eric A. , Macedo Marcia N. , Costa Ciniro , Galford Gillian L. , Maracahipes Santos Leonardo , Lefebvre Paul , Nunes Darlisson , Cerri Carlos E. P. , McHorney Richard , O’Connell Christine , Coe Michael T. 
Published: September 2018

AbstractAgricultural intensification offers potential to grow more food while reducing the conversion of native ecosystems to croplands. However, intensification also risks environmental degradation through emissions of the greenhouse gas nitrous oxide (N2O) and nitrate leaching to ground and surface waters. Intensively-managed croplands and nitrogen (N) fertilizer use are expanding rapidly in tropical regions. We quantified fertilizer responses of maize yield, N2O emissions, and N leaching in an Amazon soybean-maize double-cropping system on deep, highly-weathered soils in Mato Grosso, Brazil. Application of N fertilizer above 80 kg N ha−1 yr−1 increased maize yield and N2O emissions only slightly. Unlike experiences in temperate regions, leached nitrate accumulated in deep soils with increased fertilizer and conversion to cropping at N fertilization rates >80 kg N ha−1, which exceeded maize demand. This raises new questions about the capacity of tropical agricultural soils to store nitrogen, which may determine when and how much nitrogen impacts surface waters.
Comparison of the Rat and Human Dorsal Root Ganglion Proteome
Authors: Schwaid Adam G. , Krasowka-Zoladek Alicja , Chi An , Cornella-Taracido Ivan 
Published: September 2018

AbstractDorsal root ganglion (DRG) are a key tissue in the nervous system that have a role in neurological disease, particularly pain. Despite the importance of this tissue, the proteome of DRG is poorly understood, and it is unknown whether the proteome varies between organisms or different DRG along the spine. Therefore, we profiled the proteome of human and rat DRG. We identified 5,245 proteins in human DRG and 4959 proteins in rat DRG. Across species the proteome is largely conserved with some notable differences. While the most abundant proteins in both rat and human DRG played a role in extracellular functions and myelin sheeth, proteins detected only in humans mapped to roles in immune function whereas those detected only in rat mapped to roles in localization and transport. The DRG proteome between human T11 and L2 vertebrae was nearly identical indicating DRG from different vertebrae are representative of one another. Finally, we asked if this data could be used to enhance translatability by identifying mechanisms that modulate cellular phenotypes representative of pain in different species. Based on our data we tested and discovered that MAP4K4 inhibitor treatment increased neurite outgrowth in rat DRG as in human SH-SY5Y cells.
Novel insight into the reaction of nitro, nitroso and hydroxylamino benzothiazinones and of benzoxacinones with Mycobacterium tuberculosis DprE1
Authors: Richter Adrian , Rudolph Ines , Möllmann Ute , Voigt Kerstin , Chung Chun-wa , Singh Onkar M. P. , Rees Michael , Mendoza-Losana Alfonso , Bates Robert , Ballell Lluís , Batt Sarah , Veerapen Natacha , Fütterer Klaus , Besra Gurdyal , Imming Peter , Argyrou Argyrides 
Published: September 2018

AbstractNitro-substituted 1,3-benzothiazinones (nitro-BTZs) are mechanism-based covalent inhibitors of Mycobacterium tuberculosis decaprenylphosphoryl-β-D-ribose-2′-oxidase (DprE1) with strong antimycobacterial properties. We prepared a number of oxidized and reduced forms of nitro-BTZs to probe the mechanism of inactivation of the enzyme and to identify opportunities for further chemistry. The kinetics of inactivation of DprE1 was examined using an enzymatic assay that monitored reaction progress up to 100 min, permitting compound ranking according to kinact/Ki values. The side-chain at the 2-position and heteroatom identity at the 1-position of the BTZs were found to be important for inhibitory activity. We obtained crystal structures with several compounds covalently bound. The data suggest that steps upstream from the covalent end-points are likely the key determinants of potency and reactivity. The results of protein mass spectrometry using a 7-chloro-nitro-BTZ suggest that nucleophilic reactions at the 7-position do not operate and support a previously proposed mechanism in which BTZ activation by a reduced flavin intermediate is required. Unexpectedly, a hydroxylamino-BTZ showed time-dependent inhibition and mass spectrometry corroborated that this hydroxylamino-BTZ is a mechanism-based suicide inhibitor of DprE1. With this BTZ derivative, we propose a new covalent mechanism of inhibition of DprE1 that takes advantage of the oxidation cycle of the enzyme.
Mechanism(s) of action of heavy metals to investigate the regulation of plastidic glucose-6-phosphate dehydrogenase
Authors: De Lillo Alessia , Cardi Manuela , Landi Simone , Esposito Sergio 
Published: September 2018

AbstractThe regulation of recombinant plastidic glucose-6P dehydrogenase from Populus trichocarpa (PtP2-G6PDH - EC 1.1.1.49) was investigated by exposing wild type and mutagenized isoforms to heavy metals. Nickel and Cadmium caused a marked decrease in PtP2-G6PDH WT activity, suggesting their poisoning effect on plant enzymes; Lead (Pb++) was substantially ineffective. Copper (Cu++) and Zinc (Zn++) exposition resulted in strongest decrease in enzyme activity, thus suggesting a physiological competition with Magnesium, a well-known activator of G6PDH activity. Kinetic analyses confirmed a competitive inhibition by Copper, and a mixed inhibition by (Cd++). Mutagenized enzymes were differently affected by HMs: the reduction of disulfide (C175–C183) exposed the NADP+ binding sites to metals; C145 participates to NADP+ cofactor binding; C194 and C242 are proposed to play a role in the regulation of NADP+/NADPH binding. Copper (and possibly Zinc) is able to occupy competitively Magnesium (Mg++) sites and/or bind to NADP+, resulting in a reduced access of NADP+ sites on the enzyme. Hence, heavy metals could be used to describe specific roles of cysteine residues present in the primary protein sequence; these results are discussed to define the biochemical mechanism(s) of inhibition of plant plastidic G6PDH.