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Accelerating material design with the generative toolkit for scientific discovery

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npj Computational Materials 2023年第1期9卷 1649-1654页

作者： Matteo Manica Jannis Born Joris Cadow Dimitrios Christofidellis Ashish Dave Dean Clarke Yves Gaetan Nana Teukam Giorgio Giannone Samuel C.Hoffman Matthew Buchan Vijil Chenthamarakshan Timothy Donovan Hsiang Han Hsu Federico Zipoli Oliver Schilter Akihiro Kishimoto Lisa Hamada Inkit Padhi Karl Wehden Lauren McHugh Alexy Khrabrov Payel Das Seiji Takeda john r.smith IBM research Europe-Zurich RüschlikonSwitzerland IBM research-UK HursleyUK IBM research-Yorktown Heights New YorkUSA IBM research-Tokyo TokyoJapan IBM research-Almaden San JoseUSA

With the growing availability of data within various scientific domains,generative models hold enormous potential to accelerate scientific *** harness powerful representations learned from datasets to speed up the formulation of novel hypotheses with the potential to impact material discovery *** present the Generative Toolkit for Scientific Discovery(GT4SD).This extensible open-source library enables scientists,developers,and researchers to train and use state-of-the-art generative models to accelerate scientific discovery focused on organic material design.

关键词： enable scientific formulation

History and evaluation of national-scale geochemical data sets for the United States

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Geoscience Frontiers 2013年第2期4卷 167-183页

作者： David B.smith Steven M.smith john D.Horton U.S.Geological Survey.Denver Federal Center MS 973.DenverCO 80225USA

Six national-scale,or near national-scale,geochemical data sets for soils or stream sediments exist for the United *** earliest of these,here termed the ＇Shacklette＇ data set,was generated by a U.S. Geological Survey（USGS） project conducted from 1961 to *** project used soil collected from a depth of about 20 cm as the sampling medium at 1323 sites throughout the conterminous *** National Uranium resource Evaluation Hydrogeochemical and Stream Sediment reconnaissance（NUrEHSSr） Program of the *** of Energy was conducted from 1975 to 1984 and collected either stream sediments,lake sediments,or soils at more than 378,000 sites in both the conterminous *** *** sampled area represented about 65%of the *** Natural resources Conservation Service（NrCS）,from 1978 to 1982,collected samples from multiple soil horizons at sites within the major crop-growing regions of the conterminous *** data set contains analyses of more than 3000 *** National Geochemical Survey,a USGS project conducted from 1997 to 2009,used a subset of the NUrE-HSSr archival samples as its starting point and then collected primarily stream sediments, with occasional soils,in the parts of the *** covered by the NUrE-HSSr *** data set contains chemical analyses for more than 70,000 *** USGS,in collaboration with the Mexican Geological Survey and the Geological Survey of Canada,initiated soil sampling for the North American Soil Geochemical Landscapes Project in *** of three horizons or depths at more than 4800 sites in the *** completed in 2010,and chemical analyses are currently *** NrCS initiated a project in the 1990s to analyze the various soil horizons from selected pedons throughout the *** data set currently contains data from more than 1400 *** paper（1） discusses each data set in terms of its purpose,sample collection protocols,and analytical methods;and（2） evaluates each data set in terms

关键词： Geochemical mapping National-scale geochemical data Geochemical baselines United States

The Chemistry of Niobium Mineralisation at Bayan Obo,Inner Mongolia,China:Constraints on the Hydrothermal Precipitation and Alteration of Nb-Minerals

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地质学报 2012年第5期86卷 700-722页

作者： Martin smith john SPrATT School of Environment and Technology University of BrightonBrightonBN41 2HQU.K. Department of Mineralogy The Natural History MuseumLondonSW7 5BDU.K.

As well as world class Fe and rEE resources the Bayan Obo mineral deposits also hosts significant niobium resources(estimated as 2.2 Mt Nb with an average grade of 0.13 wt% Nb).Niobium in this study is primarily hosted in aeschynite-(Ce) and(Nd),but with subsidiary amounts of pyrochlore,fergusonite-(Ce),fersmite and *** we report on the paragenetic and textural setting of aeschynite,pyrochlore and fergusonite in the main ore bodies and in a carbonatite *** in a carbonatite sample is hosted in a phase tentatively(due to significant Ca,Mn and Ti contents) identified as fergusonite-(Ce).Aeschynite occurs overgrowing foliation in banded ores,in fractures and vugs in aegirine-rich rocks and in calcite *** composition in all settings is similar,but some examples in banded ores develop significant zonation in Y,Th and the rEE,inferred to relate to buffering of halogen acid species to low levels by dissolution and fluoritisation of calcite,and the preferential precipitation of LrEE from solution due to lower mineral solubility products compared to the *** lower in total concentration the ratios of rEE in pyrochlore are similar to those of aeschynite and suggest the same metal *** crystallisation of pyrochlore probably relates to growth in paragenetic settings where carbonates had already been eliminated and hence the buffering of F-species activities in the hydrothermal fluid was *** aeschynite and pyrochlore show evidence of *** alteration of aeschynite resulted in leaching of A-site cations(Ca,rEE,Th) and Nb,addition of Fe,and ultimately replacement by Ba-Ti phases(baotite and bafertisite).Secondary,metamictisation enhanced,possibly supergene alteration of pyrochlore resulted in hydration,leaching of A-site cations leading to the development of lattice vacancies and increases in *** presence of hydrothermal Nb resources at Bayan Obo suggests there may be potential for further Nb discoveries in the area,

关键词：地质学地层成矿 LrEE

The role of organic electron donors in the initiation of BHAS base-induced coupling reactions between haloarenes and arenes

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Science China Chemistry 2019年第11期62卷 1425-1438页

作者： Andrew J.smith Darren L.Poole john A.Murphy Department of Pure and Applied Chemistry University of StrathclydeStrathclydeGlasgow G11XLUnited Kingdom Flexible Discovery Unit GlaxoSmithKline Medicines Research CentreStevenageSG12NYUnited Kingdom

Coupling reactions between haloarenes and arenes(including heteroarenes)that are conducted without added transition metals but in the presence of KOtBu or NaOtBu,have been a topic of great interest since their discovery in *** organic structures act as additives that assist these *** additives are converted into organic electron donors by the butoxide base and this leads to initiation of the coupling reactions,which proceed by radical chain *** review provides an overview of the initiation stages of these reactions.

关键词： organic electron donor potassium tert-butoxide electron transfer base-promoted homolytic aromatic substitution(BHAS) coupling benzyne

Polymorphisms in salivary-gland transcripts of russian wheat aphid biotypes 1 and 2

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Insect Science 2012年第4期19卷 429-440页

作者： Feng Cui Michael smith john reese Owain Edwards Gerald reeck Department of Biochemistry Kansas State UniversityManhattanKansasUSA State Key Laboratory of Integrated Managementof Pest Insects&rodents Institute of ZoologyChinese Academy of SciencesBeijingChina Department of Entomology Kansas StateUniversityManhattanKansasUSA CSIrO Entomology Canberra CooperaEve research Centre for Plant Biosecufity CanberraAustralia

The russian wheat aphid （rWA）, Diuraphis noxia （Mordvilko）（Homoptera： Aphididae）, is a major pest of small grains. As with plant-feeding aphids in general, the interaction between rWA and host plants is governed, on the insect side, by proteins and enzymes in saliva. In this work, we examined sequence variations in transcripts encoding proteins and enzymes of rWA salivary glands. We conducted reverse transcription - polymerase chain reaction in rWA biotypes 1 and 2 using primers derived from pea aphid orthologs, and cloned regions of 17 putative salivary gland transcripts. For four of the transcripts, we observed no difference in sequences between the two biotypes. For the other 13 transcripts, for example, the transcripts encoding sucrase, trehalase and protein C002, large amount of variations, both within each biotype and between the two biotypes, were observed. Usually the two biotypes shared only one variant, which was typically the most common variant in both biotypes. Most of the transcripts had more non-synonymous than synonymous codon changes among their variants. Our results offer possible molecular markers for distinguishing the two biotypes and insights into their evolution.

关键词： biotype molecular marker polymorphism russian wheat aphid salivarygland transcript

A stability evaluation method for deep-seated toppling in the upper Lancang river,Southwestern China

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Journal of rock Mechanics and Geotechnical Engineering 2024年第7期16卷 2388-2410页

作者： Yibing Ning Huiming Tang Jianbing Peng Yanjun Shen john V.smith Bocheng Zhang College of Geological Engineering and Geomatics Chang’an UniversityXi’an710054China Academy of Yellow river Sciences of Shaanxi Province Chang’an UniversityXi’an710054China Badong National Observation and research Station of Geohazards China University of GeosciencesWuhan430074China School of Engineering RMIT UniversityMelbourne3001Australia

Deep-seated toppling in the upper reaches of the Lancang river,southwest China involves deformations exceeding 100 m in *** slope deformation is initiated by river downcutting and evolves distinctive characteristics with a depth of river *** this study,we propose a system for evaluating the stability of deep-seated toppled slopes in different evolutionary *** system contains identification criteria for each evolutionary stage and provides the corresponding stability evaluation *** on the mechanical and kinematic analysis of slope blocks,the specific stage of slope movement can be identified in the field through outcrop mapping,in situ tests,surface displacement monitoring,and adit and borehole *** stability evaluation methods are established based on the limiting equilibrium theory and the strain compatibility between the undisturbed zone and the toppled ***,several sample slopes in different evolution stages have been investigated to verify the applicability and accuracy of the proposed stability evaluation *** results indicate that intense tectonic activity and rapid river incision lead to a maximum principal stress ratio exceeding 10 near the slope surface,thus triggering widespread toppling deformations along the river *** considering the losses of joint cohesion during the further rotation process,the safety factor of the slope drops by 7%e28%.The self-stabilization of toppling deformation can be recognized by the layer symmetry configuration after the free rotation of the deflected *** toppled rock blocks mainly suffer sliding failures beyond the layer symmetry *** factor of safety of the K73 rockslide decreased from 1.17 to 0.87 by considering the development of the potential sliding surface and the toesaturated zone.

关键词： Stability evaluation Deep-seated toppling Evolutionary process reservoir impoundment rock slope

recent laser upgrades at Sandia's Z-backlighter facility in order to accommodate new requirements for magnetized liner inertial fusion on the Z-machine

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High Power Laser Science and Engineering 2016年第4期4卷 1-12页

作者： Jens Schwarz Patrick rambo Darrell Armstrong Marius Schollmeier Ian smith Jonathan Shores Matthias Geissel Mark Kimmel john Porter Sandia National Laboratories

The Z-backlighter laser facility primarily consists of two high energy, high-power laser systems. Z-Beamlet laser(ZBL)(rambo et al., Appl. Opt. 44, 2421(2005)) is a multi-kJ-class, nanosecond laser operating at 1054 nm which is frequency doubled to 527 nm in order to provide x-ray backlighting of high energy density events on the Z-machine. Z-Petawatt(ZPW)(Schwarz et al., J. Phys.: Conf. Ser. 112, 032020(2008)) is a petawatt-class system operating at 1054 nm delivering up to 500 J in 500 fs for backlighting and various short-pulse laser experiments(see also Figure 10 for a facility overview). With the development of the magnetized liner inertial fusion(MagLIF) concept on the Z-machine, the primary backlighting missions of ZBL and ZPW have been adjusted accordingly. As a result, we have focused our recent efforts on increasing the output energy of ZBL from 2 to 4 kJ at 527 nm by modifying the fiber front end to now include extra bandwidth(for stimulated Brillouin scattering suppression). The MagLIF concept requires a well-defined/behaved beam for interaction with the pressurized fuel. Hence we have made great efforts to implement an adaptive optics system on ZBL and have explored the use of phase plates. We are also exploring concepts to use ZPW as a backlighter for ZBL driven MagLIF experiments. Alternatively, ZPW could be used as an additional fusion fuel pre-heater or as a temporally flexible high energy pre-pulse. All of these concepts require the ability to operate the ZPW in a nanosecond long-pulse mode, in which the beam can co-propagate with ZBL. Some of the proposed modifications are complete and most of them are well on their way.

关键词： adaptive optics high energy lasers MagLIF OPCPA petawatt lasers SBS suppression

Inhibition of hepatitis C virus replication by single-stranded rNA structural mimics

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World Journal of Gastroenterology 2010年第17期16卷 2100-2108页

作者： robert Smolic Martina Smolic john H Andorfer Catherine H Wu robert M smith George Y Wu Department of Medicine Division of Gastroenterology-HepatologyUniversity of Connecticut Health Center263 Farmington Ave.FarmingtonCT 06030-1845United States

AIM: To examine the effect of hepatitis C virus (HCV) structural mimics of regulatory regions of the genome on HCV ***: HCV rNA structural mimics were constructed and tested in a HCV genotype 1b aBB7 replicon,and a Japanese fulminant hepatitis-1 (JFH-1) HCV genotype 2a infection *** sequences were computer-predicted to adopt stem-loop structures identical to the corresponding elements in full-length viral ***7.5 cells bearing the BB7 replicon or infected with JFH-1 virus were transfected with expression vectors generating HCV mimics and *** HCV rNA and protein levels were quantified by real-time polymerase chain reaction and Western blotting,*** evaluate possible antisense effects,complementary rNAs spanning a mimic were ***: In the BB7 genotype 1b replicon system,mimics of the polymerase (NS-5B),X and BA regions inhibited replication by more than 90%,50%,and 60%,*** the JFH-1 genotype 2 infection system,mimics that were only 74% and 46% identical in sequence relative to the corresponding region in JFH-1 inhibited HCV replication by 91.5% and 91.2%,respectively,as effectively as a mimic with complete identity to HCV genotype *** inhibitory effects were confirmed by NS3 protein *** rNA molecules spanning the 74% identical mimic had no significant ***: HCV rNA structural mimics can inhibit HCV rNA replication in replicon and infectious HCV systems and do so independent of close sequence identity with the target.

关键词： Hepatitis C virus Japanese fulminant hepatitis virus Complementarity rNA sequence Hybridization

Time-series prediction of shellfish farm closure: A comparison of alternatives

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Information Processing in Agriculture 2014年第1期1卷 42-50页

作者： Ashfaqur rahman Md Sumon Shahriar Claire D’Este Greg smith john McCulloch Greg Timms Autonomous Systems Program CSIRO Computational InformaticsHobartTAS 7000Australia

Shellfish farms are closed for harvest when microbial pollutants are *** pollutants are typically present in rainfall runoff from various land uses in *** currently use a number of observable parameters(river flow,rainfall,salinity)as proxies to determine when to close *** have proposed using the short term historical rainfall data as a time-series prediction problem where we aim to predict the closure of shellfish farms based only on ***-series event prediction consists of two steps:(i)feature extraction,and(ii)prediction.A number of data mining challenges exist for these scenarios:(i)which feature extraction method best captures the rainfall pattern over successive days that leads to opening or closure of the farms?,(ii)The farm closure events occur infrequently and this leads to a class imbalance problem;the question is what is the best way to deal with this problem?In this paper we have analysed and compared different combinations of balancing methods(under-sampling and over-sampling),feature extraction methods(cluster profile,curve fitting,Fourier Transform,Piecewise Aggregate Approximation,and Wavelet Transform)and learning algorithms(neural network,support vector machine,k-nearest neighbour,decision tree,and Bayesian Network)to predict closure events accurately considering the above data mining *** have identified the best combination of techniques to accurately predict shellfish farm closure from rainfall,given the above data mining challenges.

关键词： Aquaculture Shellfish farm closure Data mining Time series data