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| 1 | The Open Quantum Materials Database (OQMD): assessing the accuracy of DFT formation energies显示文摘The Open Quantum Materials Database(OQMD)is a high-throughput database currently consisting of nearly 300,000 density functional theory(DFT)total energy calculations of compounds from the Inorganic Crystal Structure Database(ICSD)and decorations of commonly occurring crystal structures.To maximise the impact of these data,the entire database is being made available,without restrictions,at www.oqmd.org/download.In this paper,we outline the structure and contents of the database,and then use it to evaluate the accuracy of the calculations therein by comparing DFT predictions with experimental measurements for the stability of all elemental ground-state structures and 1,670 experimental formation energies of compounds.This represents the largest comparison between DFT and experimental formation energies to date.The apparent mean absolute error between experimental measurements and our calculations is 0.096 eV/atom.In order to estimate how much error to attribute to the DFT calculations,we also examine deviation between different experimental measurements themselves where multiple sources are available,and find a surprisingly large mean absolute error of 0.082 eV/atom.Hence,we suggest that a significant fraction of the error between DFT and experimental formation energies may be attributed to experimental uncertainties.Finally,we evaluate the stability of compounds in the OQMD(including compounds obtained from the ICSD as well as hypothetical structures),which allows us to predict the existence of~3,200 new compounds that have not been experimentally characterised and uncover trends in material discovery,based on historical data available within the ICSD. | Scott Kirklin James E Saal Bryce Meredig Alex Thompson Jeff W Doak Muratahan Aykol Stephan Rühl Chris Wolverton | 2015 | npj Computational Materials2015，，1： | 62 |
| 2 | Response of microbial communities to biochar-amended soils:a critical review显示文摘Application of biochar to soils changes soil physicochemical properties and stimulates the activities of soil microorganisms that influence soil quality and plant performance.Studying the response of soil microbial communities to biochar amendments is important for better understanding interactions of biochar with soil,as well as plants.However,the effect of biochar on soil microorganisms has received less attention than its influences on soil physicochemical properties.In this review,the following key questions are discussed:(i)how does biochar affect soil microbial activities,in particular soil carbon(C)mineralization,nutrient cycling,and enzyme activities?(ii)how do microorganisms respond to biochar amendment in contaminated soils?and(iii)what is the role of biochar as a growth promoter for soil microorganisms?Many studies have demonstrated that biochar-soil application enhances the soil microbial biomass with substantial changes in microbial community composition.Biochar amendment changes microbial habitats,directly or indirectly affects microbial metabolic activities,and modifies the soil microbial community in terms of their diversity and abundance.However,chemical properties of biochar,(especially pH and nutrient content),and physical properties such as pore size,pore volume,and specific surface area play significant roles in determining the efficacy of biochar on microbial performance as biochar provides suitable habitats for microorgan-isms.The mode of action of biochar leading to stimulation of microbial activities is complex and is influenced by the nature of biochar as well as soil conditions. | Kumuduni Niroshika Palansooriya James Tsz Fung Wong Yohey Hashimoto Longbin Huang Jörg Rinklebe Scott X.Chang Nanthi Bolan Hailong Wang Yong Sik Ok | 2019 | Biochar2019，1，1： | 34 |
| 3 | 帕博利珠单抗治疗伴脑转移NSCLC患者的一项非随机、开放Ⅱ期试验的长期随访结果和生物标志物分析显示文摘背景与目的我们开展了一项帕博利珠单抗用于伴未治疗脑转移的非小细胞肺癌(non-small cell lung cancer,NSCLC)或黑色素瘤患者的疗效和安全性的II期试验,旨在评估程序性死亡受体1(programmed cell death 1,PD-1)抑制剂在中枢神经系统(central nervous system,CNS)中的疗效。中期结果已发表,现报道对NSCLC队列的更新分析结果。方法这是一项开放性、单中心、II期试验。纳入标准:年龄≥18岁,诊断为晚期NSCLC并伴有≥1个5 mm-20 mm脑转移病灶,既往从未治疗或之前放疗后进展,无神经系统症状,不需要激素治疗且美国东部肿瘤协作组(Eastern Cooperative Oncology Group,ECOG)<2分。患者每2周接受一次帕博利珠单抗(10 mg/kg)治疗。队列1为程序性死亡配体1(programmed cell death ligand 1,PD-L1)≥1%的患者,队列2为PD-L1<1%或未评估的患者。主要终点是脑转移患者缓解比例。所有经治患者均纳入疗效与安全性终点的分析。该研究已结束入组,并于Clinicaltrials.gov登记注册,注册号为NCT02085070。结果2014年3月31日-2018年5月21日,共42例患者接受治疗。中位随访时间为8.3个月(IQR:4.5个月-26.2个月)。队列1的37例患者中11例有脑转移缓解[29.7%(95%CI:15.9%-47.0%)]。队列2未观察到缓解。治疗相关的3级-4级不良事件(adverse events,AEs)包括2例肺炎、1例全身症状、1例结肠炎、1例肾上腺皮质功能不全、1例高血糖症和1例低钾血症。6例(14%)患者发生了治疗相关的严重不良事件,包括肺炎、急性肾损伤、低钾血症和肾上腺皮质功能不全。没有观察到治疗相关死亡病例。结论帕博利珠单抗治疗PD-L1≥1%的NSCLC伴脑转移患者有效,且对所有纳入的未经治疗的脑转移患者安全。需要进一步探索免疫治疗用于NSCLC合并CNS转移。 | Sarah B GOLDBERG Kurt A SCHALPER Scott N GETTINGER Amit MAHAJAN Roy S HERBST Anne C CHANG Rogerio LILENBAUM Frederick H WILSON Sacit Bulent OMAY James B YU Lucia JILAVEANU Thuy TRAN Kira PAVLIK Elin ROWEN Heather GERRSH Annette KOMLO Richa GUPTA Hailey WYATT Matthew RIBEIRO Yuval KLUGER Geyu ZHOU Wei WEI Veronica L CHANG Harriet M KLUGER 董晓荣(翻译/校对) | 2021 | 中国肺癌杂志2021，24，9： | 34 |
| 4 | 地下水铀污染的原位微生物还原与固定:在美国能源部田纳西橡树岭放射物污染现场的试验显示文摘总结了美国斯坦福大学和橡树岭国家实验室等在美国能源部田纳西州橡树岭综合试验基地进行的铀污染原位微生物修复阶段性试验结果.本试验利用微生物以乙醇为电子供体还原地下水和沉积物中的六价铀为不溶解的四价铀,使之原位固定化.随后通过加入溶解氧和硝酸盐来试验微生物还原后的地下水层中还原固定态铀的稳定性.通过预处理和长期间隔注入乙醇溶液,地下水中铀浓度从40~60mg·L-1降至0.03mg·L-1以下,达到了美国环保署饮用水的标准.还原的四价铀主要以U(Ⅳ)-Fe复合物的形态存在.结果表明,固定化后的四价铀只有在厌氧条件下才是稳定的,溶解氧和硝酸盐侵入地下水层后会使固定化的四价铀重新氧化为溶解态的六价铀.在试验过程中,采用多种分子生物学方法检测了微生物种群的变化和与铀氧化还原反应有关的功能微生物.本研究表明,在维持试验系统无氧和无硝酸盐的条件下,通过添加乙醇为电子供体可有效地促进地下水中土著功能微生物的活性,从而实现铀的原位还原固定与稳定. | 吴唯民 Jack Carley David Watson 顾宝华 Scott Brooks Shelly D.Kelly Kenneth Kemner Joy D.van Nostrand 吴力游 许玫英 周集中 罗剑 Erick Cardenas 黄家琪 Matthew W.Fields Terence L.Marsh James M.Tiedje Stefan J.Green Joel E.Kostka Peter K.Kitanidis Philip M.Jardme CraigS.Criddle | 2011 | 环境科学学报2011，31，3： | 28 |
| 5 | Updated Analysis of SWOG-Directed Intergroup Study 0116: A Phase III Trial of Adjuvant Radiochemotherapy Versus Observation After Curative Gastric Cancer Resection显示文摘 | Stephen R. Smalley Jacqueline K. Benedetti Daniel G. Haller Scott A. Hundahl Norman C. Estes Jaffer A. Ajani Leonard L. Gunderson Bryan Goldman James A. Martenson J. Milburn Jessup Grant N. Stemmermann Charles D. Blanke John S. Macdonald | 2012 | Journal of Clinical Oncology2012，，19： | 13 |
| 6 | Consequences of bullying victimization in childhood and adolescence:A systematic review and meta-analysis显示文摘AIM To identify health and psychosocial problems associated with bullying victimization and conduct a meta-analysis summarizing the causal evidence.METHODS A systematic review was conducted using Pub Med, EMBASE, ERIC and Psyc INFO electronic databases up to 28 February 2015. The study included published longitudinal and cross-sectional articles that examined health and psychosocial consequences of bullying victimization. All meta-analyses were based on qualityeffects models. Evidence for causality was assessed using Bradford Hill criteria and the grading system developed by the World Cancer Research Fund.RESULTS Out of 317 articles assessed for eligibility, 165 satisfied the predetermined inclusion criteria for meta-analysis.Statistically significant associations were observed between bullying victimization and a wide range of adverse health and psychosocial problems. The evidence was strongest for causal associations between bullying victimization and mental health problems such as depression, anxiety, poor general health and suicidal ideation and behaviours. Probable causal associations existed between bullying victimization and tobacco and illicit drug use. CONCLUSION Strong evidence exists for a causal relationship between bullying victimization, mental health problems and substance use. Evidence also exists for associations between bullying victimization and other adverse health and psychosocial problems, however, there is insufficient evidence to conclude causality. The strong evidence that bullying victimization is causative of mental illness highlights the need for schools to implement effective interventions to address bullying behaviours. | Sophie E Moore Rosana E Norman Shuichi Suetani Hannah J Thomas Peter D Sly James G Scott | 2017 | World Journal of Psychiatry2017，7，1： | 12 |
| 7 | Diagnosis and Management of the Metabolic Syndrome: An American Heart Association/National Heart, Lung, and Blood Institute Scientific Statement显示文摘 | Scott M. Grundy James I. Cleeman Stephen R. Daniels Karen A. Donato Robert H. Eckel Barry A. Franklin David J. Gordon Ronald M. Krauss Peter J. Savage Sidney C. Smith John A. Spertus Fernando Costa | 2005 | Circulation2005，，17： | 7 |
| 8 | Tight junction disruption: Helicobacter pylori and dysregulation of the gastric mucosal barrier显示文摘Long-term chronic infection with Helicobacter pylori(H. pylori) is a risk factor for gastric cancer development. In the multi-step process that leads to gastric cancer,tight junction dysfunction is thought to occur and serve as a risk factor by permitting the permeation of luminal contents across an otherwise tight mucosa. Mechanisms that regulate tight junction function and structure in the normal stomach,or dysfunction in the infected stomach,however,are largely unknown. Although conventional tight junction components are expressed in gastric epithelial cells,claudins regulate paracellular permeability and are likely the target of inflammation or H. pylori itself. There are 27 different claudin molecules,each with unique properties that render the mucosa an intact barrier that is permselective in a way that is consistent with cell physiology. Understanding the architecture of tight junctions in the normal stomach and then changes that occur during infection is important but challenging,because most of the reports that catalog claudin expression in gastric cancer pathogenesis are contradictory. Furthermore,the role of H. pylori virulence factors,such as cytotoxin-associated gene A and vacoulating cytotoxin,in regulating tight junction dysfunction during infection is inconsistent in different gastric cell lines and in vivo,likely because non-gastric epithelial cell cultures were initially used to unravel the details of their effects on the stomach. Hampering further study,as well,is the relative lack of cultured cell models that have tight junction claudins that are consistent with native tissues. This summary will review the current state of knowledge about gastric tight junctions,normally and in H. pylori infection,and make predictions about the consequences of claudin reorganization during H. pylori infection. | Tyler J Caron Kathleen E Scott James G Fox Susan J Hagen | 2015 | World Journal of Gastroenterology2015，21，40： | 7 |
| 9 | Small molecules enable OCT4-mediated direct reprogramming into expandable human neural stem cells显示文摘 | Saiyong Zhu Raiesh Ambasudhan Woong Sun Hyun Jung Kim Maria Talantova Xiaojing Wang Mingliang Zhang Yu Zhang Timothy Laurent James Parker Han-Seop Kim Jeffrey D Zaremba Sofiyan Saleem Sara Sanz-Blasco Eliezer Masliah Scott R McKercher Yee Sook Cho Stuart A Lipton Janghwan Kim Sheng Ding | 2014 | Cell Research2014，24，1： | 6 |
| 10 | Double Fertilization in Arabidopsis thaliana Involves a Polyspermy Block on the Egg but Not the Central Cell显示文摘在动物复制,几千个精子可以竞争使肥沃一颗单个卵,而是 polyspermy 块阻止将不那样导致胚胎的死亡的多重授精。在 flowering 植物,成功的种子开发要求仅仅二个精子被送到胚胎囊,在各个必须使肥沃的地方女配偶子(鸡蛋或中央房间) 到生产胚胎和内乳。因此, polyspermy 必须被避免,不是仅仅加倍授精在后代阻止畸形,但是保证。它没被理解精子怎么各使肥沃仅仅一女配偶子,也不 polyspermy 障碍的存在是直接在 vivo 测试了。这里,我们用 polyspermic 四分芽胞(tes ) 在被子植物为 polyspermy 块寻求了证据 Arabidopsis 变异,它与多重男配偶子允许鸡蛋和中央房间的 in-vivo 挑战。我们证明 tes 异种花粉试管能从超过一对把超过一精子对传给胚胎囊,和那个精子能参予授精。我们与能仅仅源于多重授精的 ploidies 检测了内乳然而并非胚胎。我们的结果因此在卵,然而并非 flowering 植物的中央房间上表明 in-vivo polyspermy 块。 | Rod J. Scott Susan J. Armstrong James Doughty Melissa Spielman | 2008 | Molecular Plant2008，1，4： | 6 |
| 11 | Implications of Recent Clinical Trials for the National Cholesterol Education Program Adult Treatment Panel III Guidelines显示文摘 | Scott M. Grundy James I. Cleeman C. Noel Bairey Merz H. Bryan Brewer Luther T. Clark Donald B. Hunninghake Richard C. Pasternak Sidney C. Smith Neil J. Stone | 2004 | Circulation: Journal of the American Heart Association2004，，2： | 6 |
| 12 | 代谢综合征的诊断和治疗——美国心脏协会/国立心肺血液研究所指南概要显示文摘 | Scott M. Grundy James I. Cleeman Stephen R. Daniels Karen A. Donato Robert H. Eckel Barry A.Franklin David J. Gordon Ronald M. Krauss Peter J. Savage Sidney C. Smith John A. Spertus Fernando Costa | 2006 | 世界核心医学期刊文摘(心脏病学分册)2006，2，4： | 5 |
| 13 | 棉铃虫的自然庇护所、抗性发展以及中国的零庇护所政策显示文摘本文旨在讨论天然庇护所作物在减缓棉铃虫抗性发展中的作用以及中国是否需要为转基因抗虫棉制定专门的庇护所政策.首先,描述了在制定庇护所政策时所需要考虑的各种因素;其次,为了科学合理地分析这些因素的影响,构建了一个生物经济学模型并利用实证数据进行了量化分析.在模型分析过程中,考虑了多种方案以增强分析结果的稳定性和可靠性.结果表明,中国多样性的种植结构使玉米等作物成为棉铃虫的天然庇护所.换言之,在此情况下仍然要求农民种植一定比例的非转基因抗虫棉作为棉铃虫的专门庇护所是不经济的. | 乔方彬 黄季煜 ROZELLE Scott WILEN James | 2010 | 中国科学:生命科学2010，40，11： | 5 |
| 14 | Natural refuge crops, buildup of resistance, and zero-refuge strategy for Bt cotton in China显示文摘In the context of genetically modified crops expressing the Bacillus thuringiensis (Bt) toxin, a ‘refuge’ refers to a crop of the same or a related species that is planted nearby to enable growth and reproduction of the target pest without the selection pres- sure imposed by the Bt toxin. The goal of this study is to discuss the role of natural refuge crops in slowing down the buildup of resistance of cotton bollworm (CBW), and to evaluate China’s no-refuge policy for Bt cotton. We describe in detail the dif- ferent factors that China should consider in relation to the refuge policy. Drawing on a review of scientific data, economic analyses of other cases, and a simulation exercise using a bio-economic model, we show that in the case of Bt cotton in China, the no-refuge policy is defensible. | ROZELLE Scott WILEN James | 2010 | Science China(Life Sciences)2010，53，10： | 4 |
| 15 | An improved understanding of soil Cd risk to humans and low cost methods to phytoextract Cd from contaminated soils to prevent soil Cd risks显示文摘 | Rufus L. Chaney Philip G. Reeves James A. Ryan Robert W. Simmons Ross M. Welch J. Scott Angle | 2004 | BioMetals2004，，5： | 4 |
| 16 | Quality in the technical performance of colonoscopy and the continuous quality improvement process for colonoscopy: recommendations of the U.S. Multi-Society Task Force on Colorectal Cancer显示文摘 | Douglas K Rex John H Bond Sidney Winawer Theodore R Levin Randall W Burt David A Johnson Lynne M Kirk Scott Litlin David A Lieberman Jerome D Waye James Church John B Marshall Robert H Riddell | 2002 | The American Journal of Gastroenterology2002，，6： | 3 |
| 17 | The Cost-Effectiveness of Neoadjuvant Chemoradiation is Superior to a Surgery-First Approach in the Treatment of Pancreatic Head Adenocarcinoma显示文摘 | Daniel E. Abbott Ching-Wei David Tzeng Ryan P. Merkow Scott B. Cantor George J. Chang Matthew Harold Katz David J. Bentrem Karl Y. Bilimoria Christopher H. Crane Gauri R. Varadhachary James L. Abbruzzese Robert A. Wolff Jeffrey E. Lee Douglas B. Evans Jas | 2013 | Annals of Surgical Oncology2013，，3： | 3 |
| 18 | Brain metastasis in advanced colorectal cancer: results from the South Australian metastatic colorectal cancer (SAmCRC) registry显示文摘Objective:Brain metastasis is considered rare in metastatic colorectal cancer(mCRC);thus,surveillance imaging does not routinely include the brain.The reported incidence of brain metastases ranges from 0.6% to 3.2%.Methods:The South Australian mCRC Registry(SAmCRC)was analyzed to assess the number of patients presenting with brain metastasis during their lifetime.Due to small numbers,a descriptive analysis is presented.Results:Only 59 patients of 4,100 on the registry at the time of analysis had developed brain metastasis(1.4%).The clinical characteristics of those with brain metastasis were as follows:the median age was 65.3 years and 51% were female.Where the V-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog(KRAS)mutation status of the tumor was known,the majority harbored a KRAS mutation(55%);31(53%)underwent craniotomy and 55(93%)underwent whole-brain radiotherapy.The median survival time from diagnosis of brain metastasis was 4.2 months(95% confidence interval 2.9–5.5).Patients who underwent craniotomy and radiotherapy had superior survival compared to those who underwent whole-brain radiotherapy(8.5 months vs.2.2 months,respectively).Data from the SAmCRC(a population-based registry)confirm that brain metastases are rare and the median time to development is approximately 2 years.Conclusions:Brain metastasis is a rare outcome in advanced CRC.Patients within the registry tended to be female,young in age,and harbored with higher rates of KRAS mutations.Whether routine surveillance brain scanning should be considered remains controversial given the relative rarity of developing brain metastases in mCRC and ultimately,most patients with central nervous system involvement die from their extracranial disease. | Gonzalo Tapia Rico Timothy J. Price Christos Karapetis Cynthia Piantadosi Rob Padbury Amitesh Roy Guy Maddern James Moore Scott Carruthers David Roder Amanda R. Townsend | 2017 | Cancer Biology & Medicine2017，14，4： | 3 |
| 19 | Effect of fiber supplementation on the microbiota in critically ill patients显示文摘AIM:To determine tolerance to fiber supplementation of semi-elemental tube feeds in critically ill patients and measure its effect on colonic microbiota and fermentation.METHODS:Thirteen intensive care unit patients receiving jejunal feeding with a semi-elemental diet for predominantly necrotizing pancreatitis were studied.The study was divided into 2 parts:first,short-term (3-9 d)clinical tolerance and colonic fermentation as assessed by fecal short chain fatty acid(SCFA)concentrations and breath hydrogen and methane was measured in response to progressive fiber supplementation increasing from 4 g tid up to normal requirement levels of 8 g tid;second,4 patients with diarrhea were studied for 2-5 wk with maximal supplementation to additionally assess its influence on fecal microbiota quantitated by quantitative polymerase chain reaction (qPCR)of microbial 16S rRNA genes and Human Intestinal Tract Chip(HITChip)microarray analysis.Nearly all patients were receiving antibiotics(10/13)and acid suppressants(11/13)at some stage during the studies.RESULTS:In group 1,tolerance to progressive fiber supplementation was good with breath hydrogen and methane evidence(P=0.008 and P<0.0001,respectively)of increased fermentation with no exacerbation of abdominal symptoms and resolution of diarrhea in 2 of 4 patients.In group 2 before supplementation,fecal microbiota mass and their metabolites,SCFA,were dramatically lower in patients compared to healthy volunteers.From qPCR and HITChip analyses we calculated that there was a 97%reduction in the predominant potential butyrate producers and starch degraders.Following 2-5 wk of fiber supplementation there was a significant increase in fecal SCFA(acetate 28.4±4.1μmol/g to 42.5±3.1μmol/g dry weight,P=0.01;propionate 1.6±0.5 vs 6.22±1.1,P=0.006 and butyrate 2.5±0.6 vs 5.9±1.1,P=0.04)and microbial counts of specific butyrate producers,with resolution of diarrhea in 3 of 4 patients.CONCLUSION:Conventional management of critically ill patients,which includes the use of elemental diets and broad-spectrum antibiotics,was associated with gross suppression of the colonic microbiota and their production of essential colonic fuels,i.e.,SCFA.Our investigations show that fiber supplementation of the feeds has the potential to improve microbiota mass and function,thereby reducing the risks of diarrhea due to dysbiosis. | Stephen JD O'Keefe Junhai Ou James P DeLany Scott Curry Erwin Zoetendal H Rex Gaskins Scott Gunn | 2011 | World Journal of Gastrointestinal Pathophysiology2011，2，6： | 3 |
| 20 | Laparoscopic resection of gastrointestinal stromal tumors:Does laparoscopic surgery provide an adequate oncologic resection?显示文摘Gastrointestinal stromal tumors (GISTs) are rare tumors of the GI tract.Surgical resection remains the mainstay of non-metastatic disease.However,the ability to provide an adequate oncologic resection using laparoscopic surgery is still an area of debate.This is a thorough review of the current literature,looking particularly at the use of laparoscopic surgery for larger GISTs and the long-term oncologic outcomes compared to the results of open surgery.Laparoscopic resections provide an adequate oncologic result for GISTs of all sizes,including those greater than 5 cm in size. | Joseph J Kim James Y Lim Scott Q Nguyen | 2017 | World Journal of Gastrointestinal Endoscopy2017，9，9： | 3 |
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