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| 1 | Evolving concepts in bone infection: redefining “biofilm”,“acute vs. chronic osteomyelitis”, “the immune proteome” and “local antibiotic therapy”显示文摘Osteomyelitis is a devastating disease caused by microbial infection of bone. While the frequency of infection following elective orthopedic surgery is low, rates of reinfection are disturbingly high. Staphylococcus aureus is responsible for the majority of chronic osteomyelitis cases and is often considered to be incurable due to bacterial persistence deep within bone. Unfortunately, there is no consensus on clinical classifications of osteomyelitis and the ensuing treatment algorithm. Given the high patient morbidity,mortality, and economic burden caused by osteomyelitis, it is important to elucidate mechanisms of bone infection to inform novel strategies for prevention and curative treatment. Recent discoveries in this field have identified three distinct reservoirs of bacterial biofilm including: Staphylococcal abscess communities in the local soft tissue and bone marrow, glycocalyx formation on implant hardware and necrotic tissue, and colonization of the osteocyte-lacuno canalicular network(OLCN) of cortical bone. In contrast, S.aureus intracellular persistence in bone cells has not been substantiated in vivo, which challenges this mode of chronic osteomyelitis. There have also been major advances in our understanding of the immune proteome against S. aureus, from clinical studies of serum antibodies and media enriched for newly synthesized antibodies(MENSA), which may provide new opportunities for osteomyelitis diagnosis, prognosis, and vaccine development. Finally, novel therapies such as antimicrobial implant coatings and antibiotic impregnated 3D-printed scaffolds represent promising strategies for preventing and managing this devastating disease. Here, we review these recent advances and highlight translational opportunities towards a cure. | Elysia A. Masters Ryan P. Trombetta Karen L. de Mesy Bentley Brendan F Boyce Ann Lindley Gill Steven R. Gill Kohei Nishitani Masahiro Ishikawa Yugo Morita Hiromu Ito Sheila N. Bello-Irizarry Mark Ninomiya James D. Brodell Jr. Charles C. Lee Stephanie P. Hao Irvin Oh Chao Xie Hani A. Awad John L. Daiss John R. Owen Stephen L. Kates Edward M. Schwarz Gowrishankar Muthukrishnan | 2019 | Bone Research2019，7，3： | 19 |
| 2 | Modeling of elastic wave propagation on a curved free surface using an improved finite-difference algorithm显示文摘Based on existing direct and imaging methods of a staggered finite-difference scheme, an improved algorithm for staggered finite-difference is proposed to implement rugged topographic free boundary conditions. This method assumes that the free surface can be implemented with horizontal and vertical free surface segments and their corners; the free surface passes through the grid points of shear stress components, instead of the normal stress components. Imaging is carried out for stress components in both horizontal and vertical directions, thus increasing the accuracy. To update particle- velocities, imaging and updating are first performed in the horizontal direction, and then in the vertical direction. The numerical results for elastic flat horizontal free surface with the imaging method and those for flat free surfaces of various slope angles with the proposed method are compared, and are shown to be in good agreement. The advantage of the proposed method is that only the stresses are dealt with in implementing the free surface into the staggered algorithm, which improves computation efficiency. | WANG Xiuming1,3 & ZHANG Hailan2 1. CSIRO Petroleum, ARRC, PO BOX 1130, Technology Park, Bentley, WA 6102, Australia 2. Institute of Acoustics, Chinese Academy of Sciences, Beijing 100080, China 3. Present address: Institute of Acoustics, Chinese Academy of Sciences, Beijing 100080, China | 2004 | Science China(Physics,Mechanics & Astronomy)2004，47，5： | 11 |
| 3 | Macrophage migration inhibitory factor gene polymorphisms in inflammatory bowel disease: An association study in New Zealand Caucasians and meta-analysis显示文摘AIM:To investigate the association of macrophage migration inhibitory factor(MIF)promoter polymorphisms with inflammatory bowel disease(IBD)risk.METHODS:One thousand and six New Zealand Caucasian cases and 540 Caucasian controls were genotyped for the MIF SNP-173G>C(rs755622)and the repeat polymorphism CATT5-8(rs5844572)using a predesigned TaqMan SNP assay and capillary electrophoresis,respectively.Data were analysed for single site and haplotype association with IBD risk and phenotype.Meta-analysis was employed,to assess cumulative evidence of association of MIF-173G>C with IBD.All published genotype data for MIF-173G>C in IBD were identified using PubMed and subsequently searching the references of all PubMed-identified studies.Imputed genotypes for MIF-173G>C were generated from the Wellcome Trust Case Control Consortium(and National Institute of Diabetes and Digestive and Kidney Diseases).Separate meta-analyses were performed on Caucasian Crohn’s disease(CD)(3863 patients,6031controls),Caucasian ulcerative colitis(UC)(1260 patients,1987 controls),and East Asian UC(416 patients and 789 controls)datasets using the Mantel-Haenszel method.The New Zealand dataset had 93%power,and the meta-analyses had 100%power to detect an effect size of OR=1.40 atα=0.05,respectively.RESULTS:In our New Zealand dataset,single-site analysis found no evidence of association of MIF polymorphisms with overall risk of CD,UC,and IBD or disease phenotype(all P values>0.05).Haplotype analysis found the CATT5/-173C haplotype occurred at a higher frequency in New Zealand controls compared to IBD patients(0.6 vs 0.01;P=0.03,OR=0.22;95%CI:0.05-0.99),but this association did not survive bonferroni correction.Meta-analysis of our New Zealand MIF-173G>C data with data from seven additional Caucasian datasets using a random effects model found no association of MIF polymorphisms with CD,UC,or overall IBD.Similarly,meta-analysis of all published MIF-173G>C data from East Asian datasets(416UC patients,789 controls)found no association of this promoter polymorphism with UC. | James D Falvey Robert W Bentley Tony R Merriman Mark B Hampton Murray L Barclay Richard B Gearry Rebecca L Roberts | 2013 | World Journal of Gastroenterology2013，19，39： | 9 |
| 4 | Heterologous Expression of the Mevalonic Acid Pathway in Cyanobacteria Enhances Endogenous Carbon Partitioning to Isoprene显示文摘在 cyanobacterium Synechocystis PCC 6803 的异戌二烯 synthase 基因的 Heterologous 表示在这些微生物之上授与光合的异戌二烯(C5H8 ) 的性质烃生产。从 CO2 和 H2O 的异戌二烯的连续生产在光被完成,经由内长的 methylerythritol 磷酸盐(MEP ) 发生小径,与 Synechocystis 的生长一起。这个工作处理了光合的碳在 Synechocystis 在异戌二烯和生物资源之间划分的问题。证据被介绍显示出 heterologous genomic 集成和 mevalonic 酸(MVA ) 的细胞的表示在为碳流动扩大资助一条外国人小径到 isopentenyl-diphosphate (IPP ) 和 dimethylallyl-diphosphate (DMAPP ) 的 Synechocystis 的小径基因异戌二烯的先锋。在有 MVA 小径酶的联合的异戌二烯 synthase 的 Heterologous 表示由近似 2.5 褶层导致了光合的异戌二烯收益改进,与在仅仅与异戌二烯 synthase 基因转变的 cyanobacteria 测量了那相比。这些结果建议 MVA 小径介绍一在在到 IPP 和 DMAPP 的 Synechocystis 的内长的细胞的底层的流动的 bypass,克服本国的 MEP 小径的流动限制。工作在 Synechocystis 采用了新奇 chromosomal 集成和合成基因操纵子的表示,包括直到在一个单身的倡导者的控制下面的四基因,并且同时表示三操纵子。这是有七 recombinant 酶的一条全部 biosynthetic 小径 heterologously 在光合的微生物被表示了的第一次。它为有感染力的产品的可更新的产生在光合的途径的追求组成贡献到光合的微生物和一个范例的遗传工程工具箱。 | Fiona K. Bentley Andreas Zurbriggen Anastasios Melis | 2014 | Molecular Plant2014，7，1： | 4 |
| 5 | Hydrocarbon accumulation in network and its application in the continental rift basin显示文摘The concept of hydrocarbon accumulation in network was presented on basis of the overall analysis of the formation and evolution characteristics of the continental faulted basin and of the systemic re-search on the major controlling factors on the hydrocarbon accumulation. The hydrocarbon accumu-lation in network can be defined as hydrocarbon accumulation in a three-dimensional network system which is constituted by the hydrocarbon migration passages under multiple dynamics,following the hydrocarbon generation from source rocks. The research shows that the hydrocarbon accumulation in network is composed of four elements,i.e.,hydrocarbon source (source rock kitchen),hydrocarbon accumulation terminal (trap),network pathway connecting source and terminal (transporting system),and network potential driving hydrocarbon migration in the network pathway (migration dynamics). Compared with other networks,hydrocarbon accumulation in network has three basic characteristics: the irreversible geological process of material and information flow in the network; the loss of material and information in the flow process in the network; the multiple dynamics in the flow process. Interac-tion of all the elements in the geological process can be called hydrocarbon accumulation in network. There are three basic models for hydrocarbon accumulation in network,that is,hydrocarbon accumu-lation in the network source area,hydrocarbon accumulation in the network pathway,and hydrocarbon accumulation in the network terminal. The key in the application of the hydrocarbon accumulation models in network in practice is to confirm the major accumulation stage and the function range of the four elements controlling the hydrocarbon firstly,to predict the profitable accumulation region by su-perposition of the favorable areas confirmed by four elements consequently,and to evaluate the oil-bearing property of the trap as well as confirm drilling targets. This paper takes the Dongying De-pression in the Bohai Bay Basin as an application example. | PANG XiongQi1,2,CHEN DongXia1,ZHANG ShanWen3,HAO Fang1,LIU Zheng1,LIU KeYu3,SONG GuoQi4,WANG YongShi4,LUO XiaoRong5 & WU XiaoChun61 State Key Laboratory of Petroleum Resource and Prospecting,Chinese University of Petroleum,Beijing 102249,China 2 Basin and Reservoir Center,Chinese University of Petroleum,Beijing 102249,China 3 SINOPEC Shengli Oilfield,Dongying 257051,China 4 CSIRO Petroleum,P. O. Box 1130,Bentley,WA 6102,Australia 5 Institute of Geology and Geophysics,Chinese Academy of Science,Beijing 100029,China 6 China National Petroleum Corporation,Beijing 100724,China | 2008 | Science China Earth Sciences2008，51，S2： | 3 |
| 6 | 国际卒中遗传学联盟的推荐意见(第1部分):标准化表型数据收集显示文摘与几乎所有复杂疾病一样,卒中的患病风险和临床转归也是多基因作用的[1]。探索相关基因突变有望为新型个体化治疗方法奠定基础,从而显著减少卒中对全球健康造成的毁灭性影响。为了达到足够的统计学效能以确认多个风险性等位基因,需要很大的样本量。尽管卒中是全世界范围内第二大致死病因和成年人致残的主要原因[2],但没有任何一家研究机构能独立收集到足够的样本。在认识到这一挑战之后,来自世界各地的卒中研究者们于2007年成立了国际卒中遗传学联盟( International Stroke Genetics Consortium, ISGC; http://www. strokegenetics.org),其使命是通过研究在全球多个研究机构入组的患者来识别影响卒中患病风险、临床预后和治疗效果的遗传学因素。尽管先前已取得了一些成功[3-5],仍有大量工作有待进行,这不仅是为了发现风险性等位基因从而达到卒中个体化医疗的最终目标,更是为了开发综合性卒中风险评估手段以及得到足以改变临床实践的结果[6]。根据糖尿病和冠状动脉疾病等其他复杂疾病的研究进展,为了识别与卒中相关的所有基因突变,需要100000~200000个样本。为了达到这个样本量,需要进行更为广泛的协作。 | Jennifer J. Majersik John W.Cole Jonathan Golledge Natalia S. Rost Yu-Feng Yvonne Chan M. Edip Gurol Ame G. Lindgren Daniel Woo Israel Fernandez-Cadenas Donna T. Chen Vincent Thijs Bradford B. Worrall Ayeesha Kamal Paul Bentley Joanna M. Wardlaw Ynte M. Ruigrok Thomas W.K Battey Reinhold Schmidt Joan Montaner Anne-Katrin Giese Jaume Roquer Jordi Jimenez-Conde Chaeyoung Lee Hakan Ay Juan Jose Martin 李海峰 岳耀先 徐军 | 2015 | 国际脑血管病杂志2015，23，9： | 3 |
| 7 | Formation mechanisms of heavy oils in the Liaohe Western Depression,Bohai Gulf Basin显示文摘The Liaohe Oilfield in the Liaohe Western Depression of the Bohai Gulf Basin is the third-largest oil producing province and the largest heavy oil producing oilfield in China. A total of 65 oil samples,35 rock samples and 36 reservoir sandstone samples were collected and analyzed utilizing conventional geochemical and biogeochemical approaches to unravel the mechanisms of the formation of the heavy oils. Investigation of the oils with the lowest maturity compared with the oils in the Gaosheng and Niuxintuo oilfields indicates no apparent relation between the maturity and physical properties of the heavy oils. It is suggested that the heavy oil with primary origin is not likely the main mechanism re-sponsible for the majority of the heavy oils in the Liaohe Western Slope. The absence and/or depletion of n-alkanes etc.,with relatively low molecular weight and the occurrence of 25-norhopane series in the heavy oils as well as the relatively high acidity of the oils all suggest that the majority of the heavy oils once experienced secondary alteration. The fingerprints of the total scanning fluorescence (TSF) of the inner adsorbed hydrocarbons on the reservoir grains and the included hydrocarbons in fluid inclusions are similar to that of the normal oils in the area but are different from the outer adsorbed and reser-voired free oils at present,further indicating that most of the heavy oils are secondary in origin. Analyses of bacteria (microbes) in 7 oil samples indicate that anaerobic and hyperthermophilic Ar-chaeoglobus sp. are the dominant microbes relevant to oil biodegradation,which coincides with the shallow commercial gas reservoirs containing anaerobic bacteria derived gas in the Gaosheng and Leijia teotonic belts. The biodegradation most likely occurs at the water/oil interface,where the forma-tion water is essential for microbe removal and nutrient transportation. We think that biodegradation,water washing and oxidization are interrelated and are the main mechanisms for the formation of the heavy oils. Biodegradation was the predominant process with water washing being a prerequisite,and oxidization acting as a metabolic manifestation. This study provides unique approaches for further investigation of the formation mechanisms of heavy oils in general,and may provide some important insight for the exploration of shallow biogas in the area. | LI SuMei1,2,PANG XiongQi1,2,LIU KeYu3,GAO XianZhi1,2,LI XiaoGuang4,CHEN ZhenYan4 & LIU BaoHong41 State Key Laboratory of Petroleum Resource and Prospecting,China University of Petroleam,Beijing 102249,China 2 Basin and Reservoir Research Center,China University of Petroleum,Beijing 102249,China 3 CSIRO Petroleum,P.O. Box 1130,Bentley WA 6102,Australia 4 Liaohe Oilfield Co. Ltd,PetroChina,Panjin 124010,China | 2008 | Science China Earth Sciences2008，51，S2： | 2 |
| 8 | Quieting cross talk- the quorum sensing regulator LsrR as a possible target for fighting bacterial infections显示文摘 | Christopher M Byrd | 2009 | Cell Research2009，19，11： | 2 |
| 9 | NOD2 and ATG16L1 polymorphisms affect monocyte responses in Crohn's disease显示文摘AIM:To assess whether polymorphisms in NOD2 and ATG16L1 affect cytokine responses and mycobacterium avium subspecies paratuberculosis (MAP) survival in monocytes from Crohn's disease (CD) patients.METHODS:Monocytes were isolated from peripheral blood of CD patients of known genotype for common single nucleotide polymorphisms of NOD2 and ATG16L1.Monocytes were challenged with MAP and bacterial persistence assessed at subsequent time-points.Cytokine responses were assayed using a Milliplex multi-analyte profiling assay for 13 cytokines.RESULTS:Monocytes heterozygous for a NOD2 polymorphism (R702W,P268S,or 1007fs) were more permissive for growth of MAP (P=0.045) than those without.There was no effect of NOD2 genotype on subsequent cytokine expression.The T300A polymorphism ofATG16L1 did not affect growth of MAP in our model (P=0.175),but did increase expression of cytokines interleukin (IL)-10 (P=0.047) and IL-6 (P=0.019).CONCLUSION:CD-associated polymorphisms affected the elimination of MAP fromex vivo monocytes (NOD2),or expression of certain cytokines (ATG16L1),implying independent but contributory roles in the pathogenesis of CD. | Dylan M Glubb Richard B Gearry Murray L Barclay Rebecca L Roberts John Pearson Jacqui I Keenan Judy McKenzie Robert W Bentley | 2011 | World Journal of Gastroenterology2011，17，23： | 2 |
| 10 | Computational simulation of wave propagation problems in infinite domains显示文摘This paper deals with the computational simulation of both scalar wave and vector wave propagation problems in infinite domains. Due to its advantages in simulating complicated geometry and complex material properties, the finite element method is used to simulate the near field of a wave propagation problem involving an infinite domain. To avoid wave reflection and refraction at the common boundary between the near field and the far field of an infinite domain, we have to use some special treatments to this boundary. For a wave radiation problem, a wave absorbing boundary can be applied to the common boundary between the near field and the far field of an infinite domain, while for a wave scattering problem, the dynamic infinite element can be used to propagate the incident wave from the near field to the far field of the infinite domain. For the sake of illustrating how these two different approaches are used to simulate the effect of the far field, a mathematical expression for a wave absorbing boundary of high-order accuracy is derived from a two-dimensional scalar wave radiation problem in an infinite domain, while the detailed mathematical formulation of the dynamic infinite element is derived from a two-dimensional vector wave scattering problem in an infinite domain. Finally, the coupled method of finite elements and dynamic infinite elements is used to investigate the effects of topographical conditions on the free field motion along the surface of a canyon. | ZHAO ChongBin1,2* 1 Computational Geosciences Research Centre, Central South University, Changsha 410083, China 2 CSIRO Division of Exploration and Mining, P. O. Box 1130, Bentley, WA 6102, Australia | 2010 | Science China(Physics,Mechanics & Astronomy)2010，53，8： | 2 |
| 11 | A review of physical supply and EROI of fossil fuels in China显示文摘This paper reviews China's future fossil fuel supply from the perspectives of physical output and net energy output. Comprehensive analyses of physical output of fossil fuels suggest that China's total oil production will likely reach its peak, at about 230 Mt/year(or 9.6 EJ/year),in 2018; its total gas production will peak at around350 Bcm/year(or 13.6 EJ/year) in 2040, while coal production will peak at about 4400 Mt/year(or 91.9 EJ/year)around 2020 or so. In terms of the forecast production of these fuels, there are significant differences among current studies. These differences can be mainly explained by different ultimately recoverable resources assumptions, the nature of the models used, and differences in the historical production data. Due to the future constraints on fossil fuels production, a large gap is projected to grow between domestic supply and demand, which will need to be met by increasing imports. Net energy analyses show that both coal and oil and gas production show a steady declining trend of EROI(energy return on investment) due to the depletion of shallow-buried coal resources and conventional oil and gas resources, which is generally consistent with the approaching peaks of physical production of fossil fuels. The peaks of fossil fuels production, coupled with the decline in EROI ratios, are likely to challenge the sustainable development of Chinese society unless new abundant energy resources with high EROI values can be found. | Jian-Liang Wang Jiang-Xuan Feng Yongmei Bentley Lian-Yong Feng Hui Qu | 2017 | Petroleum Science2017，14，4： | 2 |
| 12 | Cardiopulmonary Resuscitation Quality: Improving Cardiac Resuscitation Outcomes Both Inside and Outside the Hospital: A Consensus Statement From the American Heart Association显示文摘 | Peter A. Meaney Bentley J. Bobrow Mary E. Mancini Jim Christenson Allan R. de Caen Farhan Bhanji Benjamin S. Abella Monica E. Kleinman Dana P. Edelson Robert A. Berg Tom P. Aufderheide Venu Menon Marion Leary | 2013 | Circulation2013，，4： | 2 |
| 13 | The shikimate pathway-a metabolic tree with many brances显示文摘 | Bentley R | 1990 | Crit Rev Biochem Mol Bio1990，25，： | 2 |
| 14 | Malignancy in Endometriosis: Frequency and Comparison of Ovarian and Extraovarian Types显示文摘 | Robert C. Stern Rajesh Dash Rex C. Bentley Matthew J. Snyder Arthur F. Haney Stanley J. Robboy | 2001 | International Journal of Gynecological Pathology2001，，2： | 2 |
| 15 | HPV genotypes and cervical intraepithelial neoplasia in a multiethnic cohort in the southeastern USA显示文摘 | Adriana C. Vidal Jennifer S. Smith Fidel Valea Rex Bentley Maggie Gradison Kimberly S. H. Yarnall Anne Ford Francine Overcash Kathy Grant Susan K. Murphy Cathrine Hoyo | 2014 | Cancer Causes & Control2014，，8： | 2 |
| 16 | Chemistry for peptide and protein PEGylation 显示文摘 | ROBERT MJ BENTLEY MD HARRIS JM | 2002 | Adv Drug Deliver Rev2002，54，4： | 1 |
| 17 | APFIM and AEM Investigation of CF8 and CF8M Primary Coolant Pipe Steels 显示文摘 | Miller M K Bentley J | 1990 | Materials Science and Technology1990，6，3： | 1 |
| 18 | Complete genomes of two clinical Staphylococcus aureus strains:evidence for the rapid evolution of virulence and drug resistance显示文摘 | Holden MT Feil EJ Lindsay JA Peacock SJ Day NP Enright MC Foster TJ Moore CE Hurst L Atkin R Barron A Bason N Bentley SD Chillingworth C Chillingworth T Churcher C Clark L Corton C Cronin A Doggett J Dowd L Feltwell T Hance Z Harris B Hauser H Holroyd S Jagels K James KD Lennard N Line A Mayes R Moule S Mungall K Ormond D Quail MA Rabbinowitsch E Rutherford K Sanders M Sharp S Simmonds M Stevens K Whitehead S Barrell BG Spratt BG Parkhill J | 2004 | Proc Natl Acad Sci USA2004，101，26： | 1 |
| 19 | An algorithm for finding best matches in logari - thmic expected time 显示文摘 | Friedman J H Bentley J L Finkel R A | 1977 | ACM Transactions on Mathematical Software1977，，3： | 1 |
| 20 | Accurate whole human genome sequencing using reversible terminator chemistry显示文摘 | Bentley DR Balasubramanian S Swerdlow HP | 2008 | Nature2008，456，7218： | 1 |
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