bluuebunny/crossref_metadata_2025_split huggingface dataset:
Simulated Greenland Surface Mass Balance in the GISS ModelE2 GCM: Role of the Ice Sheet Surface
Authors: Alexander P. M. , LeGrande A. N. , Fischer E. , Tedesco M. , Fettweis X. , Kelley M. , Nowicki S. M. J. , Schmidt G. A. 
Published: January 2019

AbstractThe rate of growth or retreat of the Greenland and Antarctic ice sheets remains a highly uncertain component of future sea level change. Here we examine the simulation of Greenland ice sheet surface mass balance (GrIS SMB) in a development branch of the ModelE2 version of the NASA Goddard Institute for Space Studies (GISS) general circulation model (GCM). GCMs are often limited in their ability to represent SMB compared with polar region regional climate models. We compare ModelE2‐simulated GrIS SMB for present‐day (1996–2005) simulations with fixed ocean conditions, at a spatial resolution of 2° latitude by 2.5° longitude (~200 km), with SMB simulated by the Modèle Atmosphérique Régionale (MAR) regional climate model (1996–2005 at a 25‐km resolution). ModelE2 SMB agrees well with MAR SMB on the whole, but there are distinct spatial patterns of differences and large differences in some SMB components. The impacts of changes to the ModelE2 surface are tested, including a subgrid‐scale representation of SMB with surface elevation classes. This has a minimal effect on ice sheet‐wide SMB but corrects local biases. Replacing fixed surface albedo with satellite‐derived values and an age‐dependent scheme has a larger impact, increasing simulated melt by 60%–100%. We also find that lower surface albedo can enhance the effects of elevation classes. Reducing ModelE2 surface roughness length to values closer to MAR reduces sublimation by ~50%. Further work is required to account for meltwater refreezing in ModelE2 and to understand how differences in atmospheric processes and model resolution influence simulated SMB.
Improved Spatiotemporal Representativeness and Bias Reduction of Satellite‐Based Evapotranspiration Retrievals via Use of In Situ Meteorology and Constrained Canopy Surface Resistance
Authors: Sullivan Ryan C. , Cook David R. , Ghate Virendra P. , Kotamarthi V. Rao , Feng Yan 
Published: January 2019

AbstractEvapotranspiration (ET) is a key component of the atmospheric and terrestrial water and energy budgets. Satellite‐based vegetation index approaches have used remotely sensed vegetation and reanalysis meteorological properties with surface energy balance models to estimate global ET (MOD16 ET). We reconstructed satellite retrievals using in situ meteorology (Argonne‐ET) and evaluated them using a dense network of surface turbulent heat flux measurements. Argonne‐ET resolves spatial heterogeneity of ET across the U.S. Southern Great Plains that is not well characterized by MOD16; MOD16 ET exhibits spatial autocorrelation (Moran's I significantly >0 in May–Aug.), whereas in situ and Argonne‐ET exhibit characteristics of a random spatial process (Moran's I not significantly different from 0). The skill in resolving ET temporal variability is not significantly different between MOD16 and Argonne‐ET (correlation coefficient = 0.75 and 0.72, respectively). However, the root‐mean‐square errors were significantly lower for Argonne‐ET (36 W/m2) than MOD16 (43 W/m2), and MOD16 exhibits substantial bias in annual ET relative to in situ measurements (−38%). This is attributed to overestimation in the dry canopy surface resistance (rs) parameterization. Using rs constrained to the range of typical measured values, Argonne‐ET substantially reduces the bias in the annual ET (+1%). The improved ET estimates are critical for regional water budget analyses. The methodology presented herein also demonstrates the ability to retrieve high temporally resolved (30 min; cf. 8‐day MOD16) ET that can be used for development of processed‐based diagnostics of model biases and to elucidate avenues to improve ET model parameterizations.
One‐ to 10‐Day Forecasts of Ionospheric Total Electron Content Using a Statistical Model
Authors: Lean J. L. 
Published: January 2019

AbstractA new, rapid, nonassimilative technique is demonstrated for forecasting the ionosphere's vertical total electron content (TEC) on time scales longer than 1 day. The approach uses a statistical model constructed by regressing solar extreme ultraviolet irradiance and seasonal, diurnal, and geomagnetic predictors at multiple lags against the 2‐hourly International Global Navigation Satellite Systems Service observations, with a formulation that accounts for solar modulation of the seasonal oscillations and solar and seasonal modulation of the diurnal oscillations. Solar irradiance inputs to the statistical model are forecast at successive 2‐hr intervals from 1999 to 2015 using an autoregressive model of irradiance variations during the prior 100 days. As the forecast time increment increases from 1 to 10 days, the average over the globe of the mean absolute error of TEC observations and the forecasts increases from 2.5 to 3.2 TECU (total electron content unit, 1 TECU = 1016 el/m2); the root‐mean‐square error increases from 3.7 to 4.8 TECU. Averaged over the equatorial ionization anomaly region (30°S–30°N) the mean absolute error of the forecasts increases from 3.2 to 4.3 TECU and the root‐mean‐square error increases from 4.6 to 6.4 TECU. The skill of the TEC forecasts at time increments of 3, 5, and 8 days ahead exceeds persistence by 9%, 13%, and 15% and climatology by 9%, 12%, and 10%, respectively. Forecast skill is higher in April than in July. Long‐range, multiyear forecasts from 2018 to 2030 are demonstrated based on current expectations that solar activity in cycle 25 will be comparable to that in cycle 24.
Using phenome-wide association to investigate the function of a schizophrenia risk locus at SLC39A8
Authors: McCoy Thomas H. , Pellegrini Amelia M. , Perlis Roy H. 
Published: January 2019

AbstractWhile nearly all common genomic variants associated with schizophrenia have no known function, one corresponds to a missense variant associated with change in efficiency of a metal ion transporter, ZIP8, coded by SLC39A8. This variant has been linked to a range of phenotypes and is believed to be under recent selection pressure, but its impact on health is poorly understood. We sought to understand phenotypic implications of this variant in a large genomic biobank using an unbiased phenome-wide approach. Specifically, we generated 50 topics based on diagnostic codes using latent Dirichlet allocation, and examined them for association with the risk variant. Then, any significant topics were further characterized by examining association with individual diagnostic codes contributing to the topic. Among 50 topics, 1 was associated at an experiment-wide significance threshold (beta = 0.003, uncorrected p = 0.00049), comprising predominantly brain-related codes, including intracranial hemorrhage, cerebrovascular disease, and delirium/dementia. These results suggest that a functional variant previously associated with schizophrenia risk also increases liability to cerebrovascular disease. They further illustrate the utility of a topic-based approach to phenome-wide association.
Towards maximized volumetric capacity via pore-coordinated design for large-volume-change lithium-ion battery anodes
Authors: Ma Jiyoung , Sung Jaekyung , Hong Jaehyung , Chae Sujong , Kim Namhyung , Choi Seong-Hyeon , Nam Gyutae , Son Yoonkook , Kim Sung Youb , Ko Minseong , Cho Jaephil 
Published: January 2019

AbstractTo achieve the urgent requirement for high volumetric energy density in lithium-ion batteries, alloy-based anodes have been spotlighted as next-generation alternatives. Nonetheless, for the veritable accomplishment with regards to high-energy demand, alloy-based anodes must be evaluated considering several crucial factors that determine volumetric capacity. In particular, the electrode swelling upon cycling must be contemplated if these anodes are to replace conventional graphite anodes in terms of volumetric capacity. Herein, we propose macropore-coordinated graphite-silicon composite by incorporating simulation and mathematical calculation of numerical values from experimental data. This unique structure exhibits minimized electrode swelling comparable to conventional graphite under industrial electrode fabrication conditions. Consequently, this hybrid anode, even with high specific capacity (527 mAh g−1) and initial coulombic efficiency (93%) in half-cell, achieves higher volumetric capacity (493.9 mAh cm−3) and energy density (1825.7 Wh L−1) than conventional graphite (361.4 mAh cm−3 and 1376.3 Wh L−1) after 100 cycles in the full-cell configuration.
Genome-wide association analyses of chronotype in 697,828 individuals provides insights into circadian rhythms
Authors: Jones Samuel E. , Lane Jacqueline M. , Wood Andrew R. , van Hees Vincent T. , Tyrrell Jessica , Beaumont Robin N. , Jeffries Aaron R. , Dashti Hassan S. , Hillsdon Melvyn , Ruth Katherine S. , Tuke Marcus A. , Yaghootkar Hanieh , Sharp Seth A. , Jie Yingjie , Thompson William D. , Harrison Jamie W. , Dawes Amy , Byrne Enda M. , Tiemeier Henning , Allebrandt Karla V. , Bowden Jack , Ray David W. , Freathy Rachel M. , Murray Anna , Mazzotti Diego R. , Gehrman Philip R. , Lawlor Debbie A. , Frayling Timothy M. , Rutter Martin K. , Hinds David A. , Saxena Richa , Weedon Michael N. 
Published: January 2019

AbstractBeing a morning person is a behavioural indicator of a person’s underlying circadian rhythm. Using genome-wide data from 697,828 UK Biobank and 23andMe participants we increase the number of genetic loci associated with being a morning person from 24 to 351. Using data from 85,760 individuals with activity-monitor derived measures of sleep timing we find that the chronotype loci associate with sleep timing: the mean sleep timing of the 5% of individuals carrying the most morningness alleles is 25 min earlier than the 5% carrying the fewest. The loci are enriched for genes involved in circadian regulation, cAMP, glutamate and insulin signalling pathways, and those expressed in the retina, hindbrain, hypothalamus, and pituitary. Using Mendelian Randomisation, we show that being a morning person is causally associated with better mental health but does not affect BMI or risk of Type 2 diabetes. This study offers insights into circadian biology and its links to disease in humans.
Indirect tail states formation by thermal-induced polar fluctuations in halide perovskites
Authors: Wu Bo , Yuan Haifeng , Xu Qiang , Steele Julian A. , Giovanni David , Puech Pascal , Fu Jianhui , Ng Yan Fong , Jamaludin Nur Fadilah , Solanki Ankur , Mhaisalkar Subodh , Mathews Nripan , Roeffaers Maarten B. J. , Grätzel Michael , Hofkens Johan , Sum Tze Chien 
Published: January 2019

AbstractHalide perovskites possess enormous potential for various optoelectronic applications. Presently, a clear understanding of the interplay between the lattice and electronic effects is still elusive. Specifically, the weakly absorbing tail states and dual emission from perovskites are not satisfactorily described by existing theories based on the Urbach tail and reabsorption effect. Herein, through temperature-dependent and time-resolved spectroscopy on metal halide perovskite single crystals with organic or inorganic A-site cations, we confirm the existence of indirect tail states below the direct transition edge to arise from a dynamical Rashba splitting effect, caused by the PbBr6 octahedral thermal polar distortions at elevated temperatures. This dynamic effect is distinct from the static Rashba splitting effect, caused by non-spherical A-site cations or surface induced lattice distortions. Our findings shed fresh perspectives on the electronic-lattice relations paramount for the design and optimization of emergent perovskites, revealing broad implications for light harvesting/photo-detection and light emission/lasing applications.
Frustrated supercritical collapse in tunable charge arrays on graphene
Authors: Lu Jiong , Tsai Hsin-Zon , Tatan Alpin N. , Wickenburg Sebastian , Omrani Arash A. , Wong Dillon , Riss Alexander , Piatti Erik , Watanabe Kenji , Taniguchi Takashi , Zettl Alex , Pereira Vitor M. , Crommie Michael F. 
Published: January 2019

AbstractThe photon-like behavior of electrons in graphene causes unusual confinement properties that depend strongly on the geometry and strength of the surrounding potential. We report bottom-up synthesis of atomically-precise one-dimensional (1D) arrays of point charges on graphene that allow exploration of a new type of supercritical confinement of graphene carriers. The arrays were synthesized by arranging F4TCNQ molecules into a 1D lattice on back-gated graphene, allowing precise tuning of both the molecular charge and the array periodicity. While dilute arrays of ionized F4TCNQ molecules are seen to behave like isolated subcritical charges, dense arrays show emergent supercriticality. In contrast to compact supercritical clusters, these extended arrays display both supercritical and subcritical characteristics and belong to a new physical regime termed “frustrated supercritical collapse”. Here carriers in the far-field are attracted by a supercritical charge distribution, but their fall to the center is frustrated by subcritical potentials in the near-field, similar to trapping of light by a dense cluster of stars in general relativity.
Porous supraparticle assembly through self-lubricating evaporating colloidal ouzo drops
Authors: Tan Huanshu , Wooh Sanghyuk , Butt Hans-Jürgen , Zhang Xuehua , Lohse Detlef 
Published: January 2019

AbstractThe assembly of colloidal particles from evaporating suspension drops is seen as a versatile route for the fabrication of supraparticles for various applications. However, drop contact line pining leads to uncontrolled shapes of the emerging supraparticles, hindering this technique. Here we report how the pinning problem can be overcome by self-lubrication. The colloidal particles are dispersed in ternary drops (water, ethanol, and anise-oil). As the ethanol evaporates, oil microdroplets form (‘ouzo effect’). The oil microdroplets coalesce and form an oil ring at the contact line, levitating the evaporating colloidal drop (‘self-lubrication’). Then the water evaporates, leaving behind a porous supraparticle, which easily detaches from the surface. The dispersed oil microdroplets act as templates, leading to multi-scale, fractal-like structures inside the supraparticle. Employing this method, we could produce a large number of supraparticles with tunable shapes and high porosity on hydrophobic surfaces.
Integrative analysis with expanded DNA methylation data reveals common key regulators and pathways in cancers
Authors: Fan Shicai , Tang Jianxiong , Li Nan , Zhao Ying , Ai Rizi , Zhang Kai , Wang Mengchi , Du Wei , Wang Wei 
Published: February 2019

AbstractThe integration of genomic and DNA methylation data has been demonstrated as a powerful strategy in understanding cancer mechanisms and identifying therapeutic targets. The TCGA consortium has mapped DNA methylation in thousands of cancer samples using Illumina Infinium Human Methylation 450 K BeadChip (Illumina 450 K array) that only covers about 1.5% of CpGs in the human genome. Therefore, increasing the coverage of the DNA methylome would significantly leverage the usage of the TCGA data. Here, we present a new model called EAGLING that can expand the Illumina 450 K array data 18 times to cover about 30% of the CpGs in the human genome. We applied it to analyze 13 cancers in TCGA. By integrating the expanded methylation, gene expression, and somatic mutation data, we identified the genes showing differential patterns in each of the 13 cancers. Many of the triple-evidenced genes identified in majority of the cancers are biomarkers or potential biomarkers. Pan-cancer analysis also revealed the pathways in which the triple-evidenced genes are enriched, which include well known ones as well as new ones, such as axonal guidance signaling pathway and pathways related to inflammatory processing or inflammation response. Triple-evidenced genes, particularly TNXB, RRM2, CELSR3, SLC16A3, FANCI, MMP9, MMP11, SIK1, and TRIM59 showed superior predictive power in both tumor diagnosis and prognosis. These results have demonstrated that the integrative analysis using the expanded methylation data is powerful in identifying critical genes/pathways that may serve as new therapeutic targets.
Basic clinical features do not predict dopamine transporter binding in idiopathic REM behavior disorder
Authors: Chahine L. M. , Iranzo A. , Fernández-Arcos A. , Simuni T. , Seedorff N. , Caspell-Garcia C. , Amara A. W. , Comella C. , Högl B. , Hamilton J. , Marek K. , Mayer G. , Mollenhauer B. , Postuma R. , Tolosa E. , Trenkwalder C. , Videnovic A. , Oertel W. ,   the PPMI Sleep Working Group, Kumar B. , James L. , Nomikos G. , Cedarbaum J. , Yang M. , Brys M. , Irzhevesky V. , Schmidt K. , Jennings N. , Reith A. , Tattersall D. , Sanchez M. , Daegele N. , Min C. , Malkani R. , Peterschmitt J. , Sardi P. , Bozzi S. , Fischer T. , Evans R. , Kiyasova V. , Simen A. , Siderowf A. 
Published: January 2019

AbstractREM sleep behavior disorder (RBD) is strongly associated with development of Parkinson’s Disease and other α-synuclein-related disorders. Dopamine transporter (DAT) binding deficit predicts conversion to α-synuclein-related disorders in individuals with RBD. In turn, identifying which individuals with RBD have the highest likelihood of having abnormal DAT binding would be useful. The objective of this analysis was to examine if there are basic clinical predictors of DAT deficit in RBD. Participants referred for inclusion in the RBD cohort of the Parkinson Progression Markers Initiative were included. Assessments at the screening visit including DAT SPECT imaging, physical examination, cognitive function screen, and questionnaire-based non-motor assessment. The group with DAT binding deficit (n = 49) was compared to those without (n = 26). There were no significant differences in demographic or clinical features between the two groups. When recruiting RBD cohorts enriched for high risk of neurodegenerative disorders, our data support the need for objective biomarker assessments.
Structure, function, and inhibition of drug reactivating human gut microbial β-glucuronidases
Authors: Biernat Kristen A. , Pellock Samuel J. , Bhatt Aadra P. , Bivins Marissa M. , Walton William G. , Tran Bich Ngoc T. , Wei Lianjie , Snider Michael C. , Cesmat Andrew P. , Tripathy Ashutosh , Erie Dorothy A. , Redinbo Matthew R. 
Published: January 2019

AbstractBacterial β-glucuronidase (GUS) enzymes cause drug toxicity by reversing Phase II glucuronidation in the gastrointestinal tract. While many human gut microbial GUS enzymes have been examined with model glucuronide substrates like p-nitrophenol-β-D-glucuronide (pNPG), the GUS orthologs that are most efficient at processing drug-glucuronides remain unclear. Here we present the crystal structures of GUS enzymes from human gut commensals Lactobacillus rhamnosus, Ruminococcus gnavus, and Faecalibacterium prausnitzii that possess an active site loop (Loop 1; L1) analogous to that found in E. coli GUS, which processes drug substrates. We also resolve the structure of the No Loop GUS from Bacteroides dorei. We then compare the pNPG and diclofenac glucuronide processing abilities of a panel of twelve structurally diverse GUS proteins, and find that the new L1 GUS enzymes presented here process small glucuronide substrates inefficiently compared to previously characterized L1 GUS enzymes like E. coli GUS. We further demonstrate that our GUS inhibitors, which are effective against some L1 enzymes, are not potent towards all. Our findings pinpoint active site structural features necessary for the processing of drug-glucuronide substrates and the inhibition of such processing.
Biochemical and Proteomic Characterization of Recombinant Human α/β Hydrolase Domain 6
Authors: Shields Christina Miyabe , Zvonok Nikolai , Zvonok Alexander , Makriyannis Alexandros 
Published: January 2019

AbstractHuman alpha/beta hydrolase domain 6 (hABHD6) is an enzyme that hydrolyzes 2-arachidonoylglycerol (2-AG), a potent agonist at both cannabinoid CB1 and CB2 receptors. In vivo modulation of ABHD6 expression has been shown to have potential therapeutic applications, making the enzyme a promising drug target. However, the lack of structural information on hABHD6 limits the discovery and design of selective inhibitors. We have performed E. coli expression, purification and activity profiling screening of different hABHD6 constructs and identified a truncated variant without N-terminal transmembrane (TM) domain, hΔ29-3-ABHD6, as the most promising protein for further characterization. The elimination of the TM domain did not affect 2-AG or fluorogenic arachidonoyl, 7-hydroxy-6-methoxy-4-methylcoumarin ester (AHMMCE) substrates hydrolysis, suggesting that the TM is not essential for enzyme catalytic activity. The hΔ29-3-ABHD6 variant was purified in a single step using Immobilized Metal Affinity Chromatography (IMAC), in-solution trypsin digested, and proteomically characterized by Matrix Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS). The N-terminal peptide without methionine was identified indicating on a post-translational modification of the recombinant protein. The mechanism of inhibition of hABHD6 with AM6701 and WWL70 covalent probes was elucidated based on MS analysis of trypsin digested hABHD6 following the Ligand Assisted Protein Structure (LAPS) approach. We identified the carbamylated peptides containing catalytic serine (Ser148) suggesting a selective carbamylation of the enzyme by AM6701 or WWL70 and confirming an essential role of this residue in catalysis. The ability to produce substantial quantities of functional, pure hABHD6 will aid in the downstream structural characterization, and development of potent, selective inhibitors.
Large-scale experiments into the tsunamigenic potential of different iceberg calving mechanisms
Authors: Heller Valentin , Chen Fan , Brühl Markus , Gabl Roman , Chen Xuexue , Wolters Guido , Fuchs Helge 
Published: January 2019

AbstractMass balance analysis of ice sheets is a key component to understand the effects of global warming. A significant component of ice sheet and shelf mass balance is iceberg calving, which can generate large tsunamis endangering human beings and coastal infrastructure. Such iceberg-tsunamis have reached amplitudes of 50 m and destroyed harbours. Calving icebergs interact with the surrounding water through different mechanisms and we investigate five; A: capsizing, B: gravity-dominated fall, C: buoyancy-dominated fall, D: gravity-dominated overturning and E: buoyancy-dominated overturning. Gravity-dominated icebergs essentially fall into the water body whereas buoyancy-dominated icebergs rise to the water surface. We find with unique large-scale laboratory experiments that iceberg-tsunami heights from gravity-dominated mechanisms (B and D) are roughly an order of magnitude larger than from A, C and E. A theoretical model for released iceberg energy supports this finding and the measured wave periods upscaled to Greenlandic outlet glaciers agree with field observations. Whilst existing empirical equations for landslide-tsunamis establish estimates of an upper envelope of the maximum iceberg-tsunami heights, they fail to capture the physics of most iceberg-tsunami mechanisms.