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| 1 | The ReaxFF reactive force-field: development, applications and future directions显示文摘The reactive force-field(ReaxFF)interatomic potential is a powerful computational tool for exploring,developing and optimizing material properties.Methods based on the principles of quantum mechanics(QM),while offering valuable theoretical guidance at the electronic level,are often too computationally intense for simulations that consider the full dynamic evolution of a system.Alternatively,empirical interatomic potentials that are based on classical principles require significantly fewer computational resources,which enables simulations to better describe dynamic processes over longer timeframes and on larger scales.Such methods,however,typically require a predefined connectivity between atoms,precluding simulations that involve reactive events.The ReaxFF method was developed to help bridge this gap.Approaching the gap from the classical side,ReaxFF casts the empirical interatomic potential within a bond-order formalism,thus implicitly describing chemical bonding without expensive QM calculations.This article provides an overview of the development,application,and future directions of the ReaxFF method. | Thomas P Senftle Sungwook Hong Md Mahbubul Islam Sudhir B Kylasa Yuanxia Zheng Yun Kyung Shin Chad Junkermeier Roman Engel-Herbert Michael J Janik Hasan Metin Aktulga Toon Verstraelen Ananth Grama Adri CT van Duin | 2016 | npj Computational Materials2016，，1： | 22 |
| 2 | Intentional ingestions of foreign objects among prisoners: A review显示文摘The intentional ingestion of foreign objects(IIFO) is described more commonly in prison populations than in the general population, with an estimated annual incidence of 1 in 1900 inmates in our state correctional facilities. Incidents often involve ingestion of small metal objects(e.g., paperclips, razor blades) or other commonly available items like pens or eating utensils. Despite ingestion of relatively sharp objects, most episodes can be clinically managed with either observation or endoscopy. Surgery should be reserved for those with signs or symptoms of gastrointestinal perforation or obstruction. For those with a history of IIFO, efforts should focus on prevention of recurrenceas subsequent episodes are associated with higher morbidity, significant healthcare and security costs. The pattern of IIFO is often repetitive, with escalation both in frequency of ingestions and in number of items ingested. Little is known about successful prevention strategies, but efforts to monitor patients and provide psychiatric care are potential best-practice strategies. This article aims to provide state-of-the art review on the topic, followed by a set of basic recommendations. | David C Evans Thomas R Wojda Christian D Jones Andrew J Otey Stanislaw P Stawicki | 2015 | World Journal of Gastrointestinal Endoscopy2015，7，3： | 10 |
| 3 | Genetic association and epistatic interaction of the interleukin-10 signaling pathway in pediatric inflammatory bowel disease显示文摘AIM To study the genetic association and epistatic interaction of the interleukin(IL)-10 and IL-10/STAT3 pathways in pediatric inflammatory bowel disease(IBD). METHODS A total of 159 pediatric inflammatory IBD patients(Crohn's disease,n = 136; ulcerative colitis,n = 23) and 129 matched controls were studied for genetic association of selected single nucleotide polymorphisms(SNPs) of the IL-10 gene and the genes IL10 RA,IL10 RB,STAT3,and HO1,from the IL-10/STAT3 signaling pathway. As interactions between SNPs from different loci may significantly affect the associated risk for disease,additive(a) and dominant(d) modeling of SNP interactions was also performed to examine highorder epistasis between combinations of the individual SNPs. RESULTS The results showed that IL-10 rs304496 was associated with pediatric IBD(P = 0.022),but no association was found for two other IL-10 SNPs,rs1800872 and rs2034498,or for SNPs in genes IL10 RA,IL10 RB,STAT3,and HO1. However,analysis of epistatic interaction among these genes showed significant interactions:(1) between two IL-10 SNPs rs1800872 and rs3024496(additive-additive P = 0.00015,Bonferroni P value(Bp) = 0.003);(2) between IL-10 RB rs2834167 and HO1 rs2071746(dominant-additive,P = 0.0018,Bp = 0.039); and(3) among IL-10 rs1800872,IL10 RB rs2834167,and HO1 rs2071746(additivedominant-additive,P = 0.00015,Bp = 0.005),as well as weak interactions among IL-10 rs1800872,IL-10 rs3024496,and IL-10RA(additive-additive-additive,P = 0.003; Bp = 0.099),and among IL10 RA,IL10 RB,and HO1 genes(additive-dominant-additive,P = 0.008,Bp = 0.287).CONCLUSION These results indicate that both the IL-10 gene itself,and through epistatic interaction with genes within the IL-10/STAT3 signaling pathway,contribute to the risk of pediatric IBD. | Zhenwu Lin Zhong Wang John P Hegarty Tony R Lin Yunhua Wang Sue Deiling Rongling Wu Neal J Thomas Joanna Floros | 2017 | World Journal of Gastroenterology2017，23，27： | 5 |
| 4 | Sentinel-lymph-node resection compared with conventional axillary-lymph-node dissection in clinically node-negative patients with breast cancer: overall survival findings from the NSABP B-32 randomised phase 3 trial显示文摘 | David N Krag Stewart J Anderson Thomas B Julian Ann M Brown Seth P Harlow Joseph P Costantino Takamaru Ashikaga Donald L Weaver Eleftherios P Mamounas Lynne M Jalovec Thomas G Frazier R Dirk Noyes André Robidoux Hugh MC Scarth Norman Wolmark | 2010 | Lancet Oncology2010，，10： | 3 |
| 5 | A longitudinal study of SARS-CoV-2-infected patients reveals a high correlation between neutralizing antibodies and COVID-19 severity显示文摘Understanding the immune responses elicited by SARS-CoV-2 infection is critical in terms of protection against reinfection and,thus,for public health policy and vaccine development for COVID-19.In this study,using either live SARS-CoV-2 particles or retroviruses pseudotyped with the SARS-CoV-2 S viral surface protein(Spike),we studied the neutralizing antibody(nAb)response in serum samples from a cohort of 140 SARS-CoV-2 qPCR-confirmed infections,including patients with mild symptoms and also more severe forms,including those that required intensive care.We show that nAb titers correlated strongly with disease severity and with anti-spike IgG levels.Indeed,patients from intensive care units exhibited high nAb titers;conversely,patients with milder disease symptoms had heterogeneous nAb titers,and asymptomatic or exclusive outpatient-care patients had no or low nAbs.We found that nAb activity in SARS-CoV-2-infected patients displayed a relatively rapid decline after recovery compared to individuals infected with other coronaviruses.Moreover,we found an absence of cross-neutralization between endemic coronaviruses and SARS-CoV-2,indicating that previous infection by human coronaviruses may not generate protective nAbs against SARS-CoV-2.Finally,we found that the D614G mutation in the spike protein,which has recently been identified as the current major variant in Europe,does not allow neutralization escape.Altogether,our results contribute to our understanding of the immune correlates of SARS-CoV-2-induced disease,and rapid evaluation of the role of the humoral response in the pathogenesis of SARS-CoV-2 is warranted. | Vincent Legros Solène Denolly Manon Vogrig Bertrand Boson Eglantine Siret Josselin Rigaill Sylvie Pillet Florence Grattard Sylvie Gonzalo Paul Verhoeven Omran Allatif Philippe Berthelot Carole Pélissier Guillaume Thiery Elisabeth Botelho-Nevers Guillaume Millet Jérôme Morel Stéphane Paul Thierry Walzer François-Loïc Cosset Thomas Bourlet Bruno Pozzetto | 2021 | Cellular & Molecular Immunology2021，18，2： | 3 |
| 6 | Meeting report:a hard look at the state of enamel research显示文摘The Encouraging Novel Amelogenesis Models and Ex vivo cell Lines(ENAMEL) Development workshop was held on 23 June 2017 at the Bethesda headquarters of the National Institute of Dental and Craniofacial Research(NIDCR). Discussion topics included model organisms, stem cells/cell lines, and tissues/3 D cell culture/organoids. Scientists from a number of disciplines,representing institutions from across the United States, gathered to discuss advances in our understanding of enamel, as well as future directions for the field. | ophir d klein olivier duverger wendy shaw rodrigo s lacruz derk joester janet moradian-oldak megan k pugach j timothy wright sarah e millar ashok b kulkarni john d bartlett thomas gh diekwisch pamela den besten james p simmer | 2017 | International Journal of Oral Science2017，9，4： | 3 |
| 7 | Macrophage secretory products induce an inflammatory phenotype in hepatocytes显示文摘AIM:To investigate the influence of macrophages on hepatocyte phenotype and function.METHODS:Macrophages were differentiated from THP-1 monocytes via phorbol myristate acetate stimulation and the effects of monocyte or macrophageconditioned medium on HepG2 mRNA and protein expression determined.The in vivo relevance of these findings was confirmed using liver biopsies from 147 patients with hepatitis C virus(HCV)infection.RESULTS:Conditioned media from macrophages,but not monocytes,induced a transient morphological change in hepatocytes associated with upregulation of vimentin(7.8±2.5-fold,P=0.045)and transforming growth factor(TGF)-β1(2.6±0.2-fold,P<0.001)and downregulation of epithelial cadherin(1.7±0.02-fold,P=0.017)mRNA expression.Microarray analysis revealed significant upregulation of lipocalin-2(17-fold,P <0.001)and pathways associated with inflammation,and substantial downregulation of pathways related to hepatocyte function.In patients with chronic HCV,realtime polymerase chain reaction and immunohistochemistry confirmed an increase in lipocalin-2 mRNA(F0 1.0 ±0.3,F1 2.2±0.2,F2 3.0±9.3,F3/4 4.0±0.8,P= 0.003)and protein expression(F1 1.0±0.5,F2 1.3± 0.4,F3/4 3.6±0.4,P=0.014)with increasing liver injury.High performance liquid chromatography-tandem mass spectrometry analysis identified elevated levels of matrix metalloproteinase(MMP)-9 in macrophageconditioned medium,and a chemical inhibitor of MMP-9 attenuated the change in morphology and mRNA expression of TGF-β1(2.9±0.2 vs 1.04±0.1,P<0.001) in macrophage-conditioned media treated HepG2 cells.In patients with chronic HCV infection,hepatic mRNA expression of CD163(F0 1.0±0.2,F1/2 2.8±0.3,F3/4 5.3±1.0,P=0.001)and MMP-9(F0 1.0±0.4,F1/2 2.8±0.3,F3/4 4.1±0.8,P=0.011)was significantly associated with increasing stage of fibrosis.CONCLUSION:Secreted macrophage products alter the phenotype and function of hepatocytes,with increased expression of inflammatory mediators,suggesting that hepatocytes actively participate in liver injury. | Michelle Melino Victoria L Gadd Gene V Walker Richard Skoien Helen D Barrie Dinesh Jothimani Leigh Horsfall Alun Jones Matthew J Sweet Gethin P Thomas Andrew D Clouston Julie R Jonsson Elizabeth E Powell | 2012 | World Journal of Gastroenterology2012，18，15： | 3 |
| 8 | Senescent human hepatocytes express a unique secretory phenotype and promote macrophage migration显示文摘AIM:To develop a model of stress-induced senescence to study the hepatocyte senescence associated secretory phenotype(SASP).METHODS:Hydrogen peroxide treatment was used to induce senescence in the human Hep G2 hepatocyte cell line.Senescence was confirmed by cytochemical staining for a panel of markers including Ki67,p21,heterochromatin protein 1β,and senescence-associated-β-galactosidase activity.Senescent hepatocytes were characterised by gene expression arrays and quantitative polymerase chain reaction(q PCR),and conditioned media was used in proteomic analyses,a human chemokine protein array,and cell migration assays to characterise the composition and function of the hepatocyte SASP.RESULTS:Senescent hepatocytes induced classical markers of senescence(p21,heterochromatin protein1β,and senescence-associated-β-galactosidase activity);and downregulated the proliferation marker,Ki67.Hepatocyte senescence induced a 4.6-fold increase in total secreted protein(P=0.06)without major alterations in the protein profile.Senescence-induced genes were identified by microarray(Benjamini Hochbergcorrected P<0.05);and,consistent with the increase in secreted protein,gene ontology analysis revealed a significant enrichment of secreted proteins among inducible genes.The hepatocyte SASP included characteristic factors such as interleukin(IL)-8 and IL-6,as well as novel components such as SAA4,IL-32and Fibrinogen,which were validated by q PCR and/or chemokine protein array.Senescent hepatocyteconditioned medium elicited migration of inflammatory(granulocyte-macrophage colony stimulating factor,GM-CSF-derived),but not non-inflammatory(CSF-1-derived)human macrophages(P=0.022),which could contribute to a pro-inflammatory microenvironment in vivo,or facilitate the clearance of senescent cells.CONCLUSION:Our novel model of hepatocyte senescence provides insights into mechanisms by which senescent hepatocytes may promote chronic liver disease pathogenesis. | Katharine M Irvine Richard Skoien Nilesh J Bokil Michelle Melino Gethin P Thomas Dorothy Loo Brian Gabrielli Michelle M Hill Matthew J Sweet Andrew D Clouston Elizabeth E Powell | 2014 | World Journal of Gastroenterology2014，20，47： | 2 |
| 9 | Direct control of the grid point distribution in meshs generated by elliptic equations显示文摘 | P D Thomas J F Middlecoff | 1980 | AIAA Journal1980，18，6： | 2 |
| 10 | Effect of hepatic artery embolization on liver hypertrophy response in a rabbit liver VX2tumor model显示文摘BACKGROUND:Portal vein embolization not only induces hypertrophy of the non-embolized liver,but also enhances tumor growth.The latter could be prevented by embolizing the hepatic arteries supplying the tumor-bearing liver segments.This study aimed to determine the effects of transcatheter arterial embolization(TAE)on tumor volume and liver regeneration in a rabbit VX2 tumor model.METHODS:Twenty-three rabbits underwent subcapsular tumor implantation with a VX2 tumor.Two weeks after implantation,18 rabbits were used for TAE experiments,5were for sham controls.Tumor response and liver regeneration response of the embolized cranial and non-embolized caudal liver lobes were assessed by CT volumetry,liver to body weight index,and the amount of proliferating hepatocytes.RESULTS:All super-selective arterial tumor embolization procedures were performed successfully.Despite embolization,the tumor volume increased after an initial steady state.The tumor volume after embolization was smaller than that of the sham group,but this difference was not significant.Massive necrosis of the tumor,however,was seen after embolization,without damage of the surrounding liver parenchyma.There was a significant atrophy response of the tumor bearing cranial lobe after super-selective arterial embolization of the tumor with a concomitant hypertrophy response of the non-embolized,caudal lobe.This regeneration response was confirmed histologically by a significantly higher number of proliferating hepatocytes on the Ki-67 stained slides.CONCLUSIONS:Super-selective,bland arterial coil embolization causes massive necrosis of the tumor,despite increase of volume on CT scan.Atrophy of the tumor bearing liver lobe is seen after arterial embolization of the tumor with a concomitant hypertrophy response of the non-embolized lobe,despite absence of histological damage of the tumor-surrounding liver parenchyma. | Krijn P van Lienden Lisette T Hoekstra Jessica D van Trigt Joris J Roelofs Otto M van Delden Thomas M van Gulik | 2013 | Hepatobiliary & Pancreatic Diseases International2013，12，6： | 2 |
| 11 | Axitinib versus sorafenib as first-line therapy in patients with metastatic renal-cell carcinoma: a randomised open-label phase 3 trial显示文摘 | Thomas E Hutson Vladimir Lesovoy Salman Al-Shukri Viktor P Stus Oleg N Lipatov Angel H Bair Brad Rosbrook Connie Chen Sinil Kim Nicholas J Vogelzang | 2013 | Lancet Oncology2013，，13： | 2 |
| 12 | Morbidity and mortality in compensated cirrhosis type C: A retrospective follow-up study of 384 patients显示文摘 | G Fattovich G Giustina F Degos F Tremolada G Diodati P Almasio F Nevens A Solinas D Mura JT Brouwer H Thomas C Njapoum C Casarin P Bonetti P Fuschi J Basho A Tocco A Bhalla R Galassini F Noventa SW Schalm G Realdi | 1997 | Gastroenterology1997，，2： | 2 |
| 13 | Technical outcomes of sentinel-lymph-node resection and conventional axillary-lymph-node dissection in patients with clinically node-negative breast cancer: results from the NSABP B-32 randomised phase III trial显示文摘 | David N Krag Stewart J Anderson Thomas B Julian Ann M Brown Seth P Harlow Takamaru Ashikaga Donald L Weaver Barbara J Miller Lynne M Jalovec Thomas G Frazier R Dirk Noyes André Robidoux Hugh MC Scarth Denise M Mammolito David R McCready Eleftherios P Mamo | 2007 | Lancet Oncology2007，，10： | 2 |
| 14 | Effective primary isolation of wild-type canine distemper virus in MDCK,MV1 Lu and Vero cells without nucleotide sequence changes within the entire haemagglutinin protein gene and in subgenomic sections of the fusion and phospho protein genes显示文摘 | John A L Thomas P M Michael J K | 2004 | Virology2004，118，： | 1 |
| 15 | Three dimensional transonic aeroelasticity using proper orthogonal decompo- sition-based reduced order models显示文摘 | Thomas J P Dowell E H Hall K C | 2003 | Journal of Aircraft2003，40，3： | 1 |
| 16 | Improved acid neutralisation capacity assessment of iron carbonates by titration and theoretical calculation显示文摘 | Weber P A Thomas J E Skinner W M | 2004 | Applied Geochemistry2004，19，： | 1 |
| 17 | Involvement of preexisting lipid hydroperoxides in Cu(2+)-stimulated oxidation of low-density lipoprotein显示文摘 | THOMAS J P KALYANARAMAN B GIROTTI A W | 1994 | Arch Biochem Biophys1994，315，2： | 1 |
| 18 | Quantitation of asbestos in synthetic mixtures using instrumental neutron activation analysis 显示文摘 | Pravin P P Richard J J James S W Thomas M S | 1992 | Analytical Chemistry1992，64，3： | 1 |
| 19 | Treatment for secondary postpartum haemorrhage显示文摘 | Alexander J Thomas P Sanghera J | 2002 | Cochrane Syst Rev2002，2，1： | 1 |
| 20 | Gold and trace element zonation in pyrite using a laser imaging technique: Implications for the timing of gold in orogenic and Carlin- style sediment- hosted deposits 显示文摘 | R R Large L Danyushevsky C Hollit V Maslennikov S Meffer S Gilbert S Bull R Scott P Emsbo H Thomas B Singh J Foster | 2009 | Economic Geology2009，104，5： | 1 |
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