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| 1 | Design of 16S rRNA gene primers for 454 pyrosequencing of the human foregut microbiome显示文摘AIM:To design and validate broad-range 16S rRNA primers for use in high throughput sequencing to classify bacteria isolated from the human foregut microbiome.METHODS:A foregut microbiome dataset was constructed using 16S rRNA gene sequences obtained from oral,esophageal,and gastric microbiomes produced by Sanger sequencing in previous studies represented by 219 bacterial species.Candidate primers evaluated were from the European rRNA database.To assess the effect of sequence length on accuracy of classification,16S rRNA genes of various lengths were created by trimming the full length sequences.Sequences spanning various hypervariable regions were selected to simulate the amplicons that would be obtained using possible primer pairs.The sequences were compared with full length 16S rRNA genes for accuracy in taxonomic classification using online software at the Ribosomal Database Project (RDP).The universality of the primer set was evaluated using the RDP 16S rRNA database which is comprised of 433 306 16S rRNA genes,represented by 36 phyla.RESULTS:Truncation to 100 nucleotides(nt)downstream from the position corresponding to base 28 in the Escherichia coli 16S rRNA gene caused misclassification of 87(39.7%)of the 219 sequences,compared with misclassification of only 29(13.2%)sequences with truncation to 350 nt.Among 350-nt sequence reads within various regions of the 16S rRNA gene,the reverse read of an amplicon generated using the 343F/798R primers had the least(8.2%)effect on classification.In comparison,truncation to 900 nt mimicking single pass Sanger reads misclassified 5.0%of the 219 sequences.The 343F/798R amplicon accurately assigned 91.8%of the 219 sequences at the species level.Weighted by abundance of the species in the esophageal dataset,the 343F/798R amplicon yielded similar classification accuracy without a significant loss in species coverage(92%).Modification of the 343F/798R primers to 347F/803R increased their universality among foregut species.Assuming that a typicalpolymerase chain reaction can tolerate 2 mismatches between a primer and a template,the modified 347F and 803R primers should be able to anneal 98%and 99.6%of all 16S rRNA genes in the RDP database.CONCLUSION:347F/803R is the most suitable pair of primers for classification of foregut 16S rRNA genes but also possess universality suitable for analyses of other complex microbiomes. | Carlos W Nossa William E Oberdorf Jφrn A Aas Bruce J Paster Todd Z DeSantis Eoin L Brodie Daniel Malamud Michael A Poles Zhiheng Pei | 2010 | World Journal of Gastroenterology2010，16，33： | 16 |
| 2 | Neuroendocrine tumors of the gastrointestinal tract: Case reports and literature review显示文摘Neuroendocrine tumors(NET)previously called carcinoid tumors are neoplasms of enterochromaffin/neuroendocrine cell origin which display neurosecretory capacity that may result in the carcinoid syndrome.The annual incidence of patients with NET is 8.4 per 100000;yet many NET remain asymptomatic and clinically undetected.A majority of NET follows a benign course;however,some will display malignant characteristics.NET most commonly occur in the gastrointestinal tract(67%)and bronchopulmonary system(25%).Gastrointestinal NET occur within the stomach,small intestine,liver,and rectum.We report a retrospective study of 11 subjects:Eight with benign carcinoid tumors:duodenal bulb(n=2),terminal ileum(n=1),sigmoid colon(n=2),and rectum(n=3);three with malignant carcinoid:liver(n=1)and intra-abdominal site(n=2).The diagnosis,endoscopic images,outcome,treatment and review of the literature are presented. | William J Salyers Kenneth J Vega Juan Carlos Munoz Bruce W Trotman Silvio S Tanev | 2014 | World Journal of Gastrointestinal Oncology2014，6，8： | 8 |
| 3 | Melanization in living organisms: a perspective of species evolution显示文摘Eumelanin is a heteropolymer that is generally composed of hydroxylated indole residues and plays diverse protective functions in various species.Melanin is derived from the amino acid tyrosine and production of melanin is a highly complex oxidative process with a number of steps that can either proceed enzymatically or non-enzymatically.Although melanin plays important protective roles in many species,during melanization,particularly in steps that can proceed non-enzymatically,many toxic intermediates are produced,including semiquinones,dopaquinone,indole-quinones and moreover,the production of many reactive oxygen species.To mitigate the production of reactive species,a number of proteins that regulate the biochemical process of melanization have evolved in various living species,which is closely related to adaptation and physiological requirements.In this communication,we discuss differences between non-enzymatic and enzymatic processes of melanization and the enzymatic regulation of melanization in difference species with an emphasis on differences between mammals and insects.Comparison between melanization and insect sclerotization is also emphasized which raises some interesting questions about the current models of these pathways. | Christopher J Vavricka Bruce M.Christensen Jianyong Li | 2010 | Protein & Cell2010，1，9： | 5 |
| 4 | 新西兰黄土和中国黄土的对比研究显示文摘根据野外观测和实验室分析,本文详细地论述了新西兰黄土在分布、粒度组成、矿物成分、化学成分、石英砂表面微结构及古土壤等方面的特征,并通过与中国黄土的对比,指出新西兰黄土形成于比较潮湿的气候条件之下,其物源主要来自当地的河流泛滥平原、冰水平原和低海面时的大陆架平原,是风力就地吹扬堆积的产物。 | 夏正楷 Bruce J G Crozier M J | 1993 | 地理学报1993，48，4： | 4 |
| 5 | Staining for p53 and Ki-67 increases the sensitivity of EUS-FNA to detect pancreatic malignancy显示文摘AIM:To investigate whether tumor marker staining can improve the sensitivity of endoscopic ultrasound-guided fine needle aspiration(EUS-FNA)to diagnose pancreatic malignancy. METHODS:Patients who underwent EUS-FNA were retrospectively identified.Each EUS-FNA specimen was evaluated by routine cytology and stained for tumor markers p53,Ki-67,carcinoembryonic antigen(CEA) and CA19-9.Sensitivity,specificity,positive and negative predictive values(PPV and NPV),and positive and negative likelihood ratios(PLR and NLR)were calculated in order to evaluate the performance of each test to detect malignancy. RESULTS:Sixty-one specimens had complete sets of stains,yielding 49 and 12 specimens from pancreatic adenocarcinomas and benign pancreatic lesions due to pancreatitis,respectively.Cytology alone had sensitivity and specificity of 41%and 100%to detect malignancy, respectively.In 46%of the specimens,routine cytology alone was deemed indeterminate.The addition of either p53 or Ki-67 increased the sensitivity to 51%and 53%,respectively,with perfect specificity,PPV and PLR (100%,100%and infinite).Both stains in combination increased the sensitivity to 57%.While additional staining with CEA and CA19-9 further increased the sensitivity to 86%,the specificity,PPV and PLR were significantly reduced(at minimum 42%,84%and 1,respectively).Markers in all combinations performed poorly as a negative test(NPV 26%to 47%,and NLR 0.27 and 0.70).CONCLUSION:Immunohistochemical staining for p53 and Ki-67 can improve the sensitivity of EUS-FNA to diagnose pancreatic adenocarcinoma. | Alexander W Jahng Sonya Reicher David Chung Donna Varela Rahul Chhablani Anil Dev Binh Pham Jose Nieto Rose J Venegas Samuel W French Bruce E Stabile Viktor E Eysselein | 2010 | World Journal of Gastrointestinal Endoscopy2010，2，11： | 3 |
| 6 | Mortality Risk for Dialysis Patients With Different Levels of Serum Calcium, Phosphorus, and PTH: The Dialysis Outcomes and Practice Patterns Study (DOPPS)显示文摘 | Francesca Tentori Margaret J. Blayney Justin M. Albert Brenda W. Gillespie Peter G. Kerr Jürgen Bommer Eric W. Young Tadao Akizawa Takashi Akiba Ronald L. Pisoni Bruce M. Robinson Friedrich K. Port | 2008 | American Journal of Kidney Diseases2008，，3： | 3 |
| 7 | Diagnostic accuracy of tests for Helicobacter pylori in an Alaska Native population显示文摘AIM:To evaluate the accuracy of two non-invasivetests in a population of Alaska Native persons. Highrates of Helico bacter pylori(H. pylori) infection,H. pylori treatment failure,and gastric cancer in this population necessitate documentation of infection status atmultiple time points over a patient's life.METHODS:In 280 patients undergoing endoscopy,H. pylori was diagnosed by culture,histology,rapidurease test,13C urea breath test(UBT) ,and immuno-globulin G antibodies to H. pylori in serum. The performances of 13C-UBT and antibody test were compared to a gold standard defined by a positive H. pylori testby culture or,in case of a negative culture result,bypositive histology and a positive rapid urease test.RESULTS:The sensitivity and specificity of the 13C-UBT were 93% and 88%,respectively,relative to thegold standard. The antibody test had an equivalents ensitivity of 93% with a reduced specificity of 68%.The false positive results for the antibody test were as-sociated with previous treatment for an H. pylori infection [relative risk(RR) = 2.8]. High levels of antibodiesto H. pylori were associated with chronic gastritis and male gender,while high scores in the 13C-UBT testwere associated with older age and with the H. pyloribacteria load on histological examination(RR = 4.4) .CONCLUSION:The 13C-UBT out performed the anti-body test for H. pylori and could be used when a non-invasive test is clinically necessary to document treatment out come or when monitoring for reinfection. | Dana L Bruden Michael G Bruce Karen M Miernyk Julie Morris Debby Hurlburt Thomas W Hennessy Helen Peters Frank Sacco Alan J Parkinson Brian J McMahon | 2011 | World Journal of Gastroenterology2011，17，42： | 3 |
| 8 | Bovine immunoglobulin protein isolates for the nutritional management of enteropathy显示文摘The gastrointestinal tract is responsible for a multitude of digestive and immune functions which depend upon the balanced interaction of the intestinal microbiota, diet, gut barrier function, and mucosal immune response. Disruptions in one or more of these factors can lead to intestinal disorders or enteropathies which are characterized by intestinal inflammation, increased gut permeability, and reduced capacity to absorb nutrients. Enteropathy is frequently associated with human immunodeficiency virus(HIV) infection, inflammatory bowel disease, autoimmune enteropathy, radiation enteritis, and irritable bowel syndrome(IBS), where pathologic changes in the intestinal tract lead to abdominal discomfort, bloating, abnormal bowel function(e.g., diarrhea, urgency, constipation and malabsorption). Unfortunately, effective therapies for the management ofenteropathy and restoring intestinal health are still not available. An accumulating body of preclinical studies has demonstrated that oral administration of plasmaor serum-derived protein concentrates containing high levels of immunoglobulins can improve weight, normalize gut barrier function, and reduce the severity of enteropathy in animal models. Recent studies in humans, using serum-derived bovine immunoglobulin/protein isolate, demonstrate that such protein preparations are safe and improve symptoms, nutritional status, and various biomarkers associated with enteropathy. Benefits have been shown in patients with HIV infection or diarrhea-predominant IBS. This review summarizes preclinical and clinical studies with plasma/serum protein concentrates and describes the effects on host nutrition, intestinal function, and markers of intestinal inflammation. It supports the concept that immunoglobulin-containing protein preparations may offer a new strategy for restoring functional homeostasis in the intestinal tract of patients with enteropathy. | Bryon W Petschow Anthony T Blikslager Eric M Weaver Joy M Campbell Javier Polo Audrey L Shaw Bruce P Burnett Gerald L Klein J Marc Rhoads | 2014 | World Journal of Gastroenterology2014，20，33： | 2 |
| 9 | Hematopoietic AMPK [Beta]1 reduces mouse adipose tissue macrophage inflammation and insulin resistance in obesity显示文摘 | Galic Sandra Fullerton Morgan D Schertzer Jonathan D Sikkema Sarah Marcinko Katarina Walkley Carl R Izon David Honeyman Jane Chen Zhi-Ping van Denderen Bryce J Kemp Bruce E Steinberg Gregory R | 2011 | Journal of Clinical Investigation2011，，12： | 2 |
| 10 | Effects of fibrates on cardiovascular outcomes: a systematic review and meta-analysis显示文摘 | Min Jun Celine Foote Jicheng Lv Bruce Neal Anushka Patel Stephen J Nicholls Diederick E Grobbee Alan Cass John Chalmers Vlado Perkovic | 2010 | The Lancet . 2010 (9729)2010，，9729： | 2 |
| 11 | 术中应用荧光素钠有利于胶质母细胞瘤浸润边缘的手术切除(英文)显示文摘Objective Extent of resection is an important prognostic factor in patients undergoing surgery for glioblastoma( GBM).Recent evidence suggests that intravenously administered fluorescein sodium associates with tumor tissue,facilitating safe maximal resection of GBM. In this study,the authors evaluate the safety and utility of intraoperative fluorescein guidance for the prediction of histopathological alteration both in the contrast-enhancing( CE) regions,where this relationship has been established,and into the nonCE( NCE),diffusely infiltrated margins. Methods Thirty-two patients received fluorescein sodium( 3 mg/kg) intravenously prior to resection. Fluorescence was intraoperatively visualized using a Zeiss Pentero surgical microscope equipped with a YELLOW 560 filter.Stereotactically localized biopsy specimens were acquired from CE and NCE regions based on preoperative MRI in conjunction with neuronavigation. The fluorescence intensity of these specimens was subjectively classified in real time with subsequent quantitative image analysis,histopathological evaluation of localized biopsy specimens,and radiological volumetric assessment of the extent of resection.Results Bright fluorescence was observed in all GBMs and localized to the CE regions and portions of the NCE margins of the tumors,thus serving as a visual guide during resection. Gross-total resection( GTR) was achieved in 84% of the patients with an average resected volume of 95%,and this rate was higher among patients for whom GTR was the surgical goal( GTR achieved in 93. 1% of patients,average resected volume of 99. 7%). Intraoperative fluorescein staining correlated with histopathological alteration in both CE and NCE regions,with positive predictive values by subjective fluorescence evaluation greater than 96% in NCE regions. Conclusions Intraoperative administration of fluorescein provides an easily visualized marker for glioma pathology in both CE and NCE regions of GBM. These findingssupport the use of fluorescein as a microsurgical adjunct for guiding GBM resection to facilitate safe maximal removal. | Neira JA Ung TH Sims J Malone HR Chow DS Samanamud JL Zanazzi GJ Guo X Bowden SG Zhao B Sheth SA McKhann GM 2nd Sisti MB Canoll P D'Amico RS Bruce JN | 2016 | 中华神经外科疾病研究杂志2016，15，5： | 2 |
| 12 | Tooth loss and alveolar remodeling in Sinosaurus triassicus (Dinosauria: Theropoda) from the Lower Jurassic strata of the Lufeng Basin, China显示文摘Pathological or traumatic loss of teeth often results in the resorption and remodeling of the affected alveoli in mammals. However, instances of alveolar remodeling in reptiles are rare. A remodeled alveolus in the maxilla of the Chinese theropod Sinosaurus (Lower Jurassic Lower Lufeng Formation) is the first confirmed example of such dental pathology in a dinosaur. Given the known relationship between feeding behavior and tooth damage in theropods (teeth with spalled enamel, tooth crowns embedded in bone) and the absence of dentary, maxillary, and premaxillary osteomyelitis, traumatic loss of a tooth is most likely the cause of alveolar remodeling. Based on the extent of remodeling, the injury and subsequent tooth loss were non-fatal in this individual. | XING LiDa BELL Phil R ROTHSCHILD Bruce M RAN Hao ZHANG JianPing DONG ZhiMing ZHANG Wei CURRIE Philip J | 2013 | Chinese Science Bulletin2013，58，16： | 2 |
| 13 | Elicitation of lignin biosynthesis and iso peroxidase activity by pectic fragnents insuspension cultures caster bean显示文摘 | Bruce R J West C A | 1989 | PlantPhysiol1989，91，： | 1 |
| 14 | Organizational Form and Environment: An Analysis of Between-form and Within-form Responses to Environmental Change显示文摘 | James J Hoffman Bruce T Lamont | 2000 | Strategic Management Journal2000，21，8： | 1 |
| 15 | Multiple scattering from random rough surfaces using the kirchhoff approximation显示文摘 | Bruce N C Dainty J C | 1991 | Journal of Modern Optics1991，38，3： | 1 |
| 16 | Sulfur and nitrogen fertility affects flavour of field-grown onions显示文摘 | McCallum J Noel P Bruce S | 2005 | Plant Soil2005，289，： | 1 |
| 17 | The potential of world cropland soils to sequester C and mitigate the greenhouse effect显示文摘 | Lal R Bruce J P | 1999 | Environmental Science & Policy1999，2，： | 1 |
| 18 | The tibial plateau fracture:the Toronto experience 1968 -1975 显示文摘 | Schatzker J McBroom R Bruce D | 1979 | Clin Orthop1979，，138： | 1 |
| 19 | Phosphine residues from phostoxin- treated grain 显示文摘 | Bruce R B Robbins A J Tuft T O | 1962 | Journal of Agricultural and Food Chemistry1962，10，1： | 1 |
| 20 | The Profession:Public Intrests andCommom Good显示文摘 | Bruce J Callahan D Wolf S M | 1987 | Hasting Center Report1987，，： | 1 |
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