bluuebunny/crossref_metadata_2025_split huggingface dataset:
Recombinase-Mediated Cassette Exchange Provides a Versatile Platform for Gene Targeting: Knockout of miR-31b
Authors: Weng Ruifen , Chen Ya-Wen , Bushati Natascha , Cliffe Adam , Cohen Stephen M 
Published: June 2009

Abstract
A series of vectors has been designed to enhance the versatility of targeted homologous recombination. Recombinase-mediated cassette exchange permits sequential targeting at any locus and improves flexibility in making user-defined mutations. Application of RMCE to delete an intronic microRNA gene is described.
Systems-Level Engineering of Nonfermentative Metabolism in Yeast
Authors: Kennedy Caleb J , Boyle Patrick M , Waks Zeev , Silver Pamela A 
Published: June 2009

AbstractWe designed and experimentally validated an in silico gene deletion strategy for engineering endogenous one-carbon (C1) metabolism in yeast. We used constraint-based metabolic modeling and computer-aided gene knockout simulations to identify five genes (ALT2, FDH1, FDH2, FUM1, and ZWF1), which, when deleted in combination, predicted formic acid secretion in Saccharomyces cerevisiae under aerobic growth conditions. Once constructed, the quintuple mutant strain showed the predicted increase in formic acid secretion relative to a formate dehydrogenase mutant (fdh1 fdh2), while formic acid secretion in wild-type yeast was undetectable. Gene expression and physiological data generated post hoc identified a retrograde response to mitochondrial deficiency, which was confirmed by showing Rtg1-dependent NADH accumulation in the engineered yeast strain. Formal pathway analysis combined with gene expression data suggested specific modes of regulation that govern C1 metabolic flux in yeast. Specifically, we identified coordinated transcriptional regulation of C1 pathway enzymes and a positive flux control coefficient for the branch point enzyme 3-phosphoglycerate dehydrogenase (PGDH). Together, these results demonstrate that constraint-based models can identify seemingly unrelated mutations, which interact at a systems level across subcellular compartments to modulate flux through nonfermentative metabolic pathways.
GOVERNMENT OFFICES, WHITEHALL GARDENS. THE SPECIAL PROBLEM OF THE RE-SITING OF AN HISTORIC BUILDING. (INCLUDES PLATES).
Authors: SCOTT WHITE L , GARDNER G A 
Published: June 2009

Synopsis. The Paper describes in some detail the operation of underpinning and lowering a mediaeval building, constructed of masonry and vaulted brickwork, which was part of the Tudor Palace of Whitehall and used by Henry VIII as a wine cellar. The structure, which is 62 feet long, 32 feet wide, and 20 feet high, and which weighs approximately 1,000 tons, was moved 43 feet 6 inches laterally on to a staging; it was then lowered by screw-jacks through a height of 18 feet 9 inches and rolled back to a position beneath its original site. The building as it stood was in the way of the construction of important new government offices, but was of such historic interest that it was decided to preserve it intact. The task of lowering it into the basement of the new building was carried through within scheduled time without damaging the irreplaceable brick vaulting or extending any of the cracks in the old walls. This operation, although not new in kind, is probably unique in reapect of the age, nature, and size of the structure involved.
THIRD MAIN DRAIN, ICI, BILLINGHAM. (INCLUDES PHOTOGRAPHS AND PLATES).
Authors: SMITH L G , SHEPHERD B L 
Published: June 2009

Synopsis. This Paper describes the design and construction of a large brick-lined reinforced-concrete drainage culvert for conveying cooling water and effluents from the I.C.I. factory at Billingham, Co. Durham, to the River Tees. Important features are the special arrangements made to enable the new drain to be connected into existing cast-iron drains with the minimum interruption to the running of the factory, and to enable sections of main drain to be readily isolated for subsequent inspection and maintenance. The design conditions, the types of culvert, and the outfall are deecribed, together with the method of construction, and an example is given of the flow conditions, cross-connexions, and penstock control required to effect one of the major isolations. The main control chambers are fully described and the various stages of the programme for putting the new drain into commission are outlined. The special conditions associated with the drainage of cooling water from factories with a continuous process, and the advisability of providing in the early stages of design for the isolation of sections of drain for inspection and repair, will be apparent.
Semilunar Coronally Positioned Flap or Subepithelial Connective Tissue Graft for the Treatment of Gingival Recession: A 30‐Month Follow‐Up Study
Authors: Bittencourt Sandro , Ribeiro Érica Del Peloso , Sallum Enilson A. , Sallum Antônio W. , Nociti Francisco H. , Casati Márcio Zaffalon 
Published: June 2009

Background: The objective of this prospective, controlled clinical trial was to evaluate the long‐term outcomes of subepithelial connective tissue graft (SCTG) or semilunar coronally positioned flap (SCPF) for the treatment of Miller Class I gingival recession defects.Methods: Seventeen patients with bilateral Miller Class I gingival recessions (≤4.0 mm) in maxillary canines or premolars were selected. The recessions were randomly assigned to receive SCPF or SCTG. Recession height (RH), recession width (RW), width of keratinized tissue (WKT), thickness of keratinized tissue (TKT), probing depth (PD), and clinical attachment level (CAL) were measured at baseline and at 6 and 30 months post‐surgery. Patient satisfaction with esthetics and root sensitivity was also evaluated.Results: The root‐coverage outcomes obtained at 6 months were maintained throughout the study. At the 30‐month examination, the average percentage of root coverage was 89.25% for SCPF and 96.83% for SCTG (P >0.05); complete root coverage was observed in 58.82% and 88.24% of patients, respectively. SCTG maintained a statistically significant increase in TKT (P <0.05) at 30 months. At this time, there were no significant differences between the two groups with regard to RH, RW, WKT, PD, and CAL. The evaluation of the esthetic outcome by the patient showed a preference for the SCTG treatment. Furthermore, in this group, no patient complained of residual or additional root hypersensitivity. In the SCPF group, three patients had this complaint at 30 months.Conclusions: SCPF and SCTG can be successfully used to treat Class I gingival recession, presenting outcomes with long‐term stability. However, patient‐oriented outcomes, such as esthetics and root sensitivity, favor SCTG therapy.
Guided Tissue Regeneration–Based Root Coverage With a Platelet Concentrate Graft: A 3‐Year Follow‐Up Case Series
Authors: Griffin Terrence J. , Cheung Wai S. 
Published: June 2009

Background: A platelet concentrate graft (PCG) was applied underneath the barrier membrane in guided tissue regeneration (GTR)–based root coverage procedures. The purpose of this case study was to assess the effectiveness of the technique and the long‐term outcomes.Methods: Thirty‐seven Miller Class I or II recession defects in six patients were treated using the PCG and a collagen membrane covered by an advanced mucogingival flap. Clinical parameters, such as vertical gingival recession depth (VRD), clinical attachment level (CAL), probing depth (PD), and width of keratinized tissue (WKT), were recorded presurgery (at baseline [BL]) and at 6 and 36 months of follow‐up. The Wilcoxon signed‐rank test and the Mann‐Whitney test were used to assess statistical significance (α = 0.05).Results: Between BL and 6 months, there was a statistically significant reduction in VRD (from 2.81 ± 0.88 mm to 0.30 ± 0.48 mm) and PD (from 2.59 ± 0.50 mm to 1.14 ± 0.35 mm), as well as an improvement in CAL (from 5.41 ± 0.86 mm to 1.43 ± 0.66 mm). These results remained stable over the following 30 months. There was no statistically significant change in WKT during the initial 6 months; however, the increase in WKT was statistically significant at the 36‐month follow‐up. When comparing the healing between the maxillary and mandibular teeth at 6 months, the VRD reduction was statistically significantly greater in the maxillary teeth, but the difference was not statistically significant 30 months later. The average root coverage at 6 and 36 months was 89.86% ± 15.85% and 85.86% ± 18.16%, respectively, with complete root coverage in 24 (64.86%) and 21 (56.76%) of the 37 teeth.Conclusions: The GTR–based technique using PCG was effective in reducing gingival recession. The outcomes remained stable for 3 years.
Real‐Time Polymerase Chain Reaction to Determine the Prevalence and Copy Number of Epstein‐Barr Virus and Cytomegalovirus DNA in Subgingival Plaque at Individual Healthy and Periodontal Disease Sites
Authors: Dawson Dolphus R. , Wang Chunmei , Danaher Robert J. , Lin Yushun , Kryscio Richard J. , Jacob Robert J. , Miller Craig S. 
Published: June 2009

Background: Detection of cytomegalovirus (CMV) and Epstein‐Barr virus (EBV) in plaque from patients with periodontal disease provides support for the theory that these viruses play a role in the pathogenesis of periodontitis. This study sought to further define this relationship by determining the prevalence of these viruses at individual disease and healthy sites of patients with periodontal disease and to determine whether the presence and amount of viral DNA correlate with disease severity.Methods: Subgingival plaque from three healthy and three disease sites of 65 patients who had chronic periodontitis were evaluated for the presence and amount of EBV, CMV, and Fusobacterium nucleatum DNA using real‐time polymerase chain reaction. Patient serum was evaluated for antibodies against EBV and CMV using enzyme‐linked immunosorbent assays.Results: EBV DNA was detected in 18.5% of subgingival plaque samples (72/390) and in at least one of the six plaque samples in 44.6% (29/65) of the patients. CMV DNA was detected in one plaque sample (0.3%). EBV was significantly more prevalent in disease sites (28.2%; 55/195) than in healthy sites (8.7%; 17/195; P = 0.002). However, neither EBV prevalence nor its amount correlated with increased probing depth >5 mm or attachment loss >2 mm, whereas the amount of F. nucleatum DNA did. Sites positive for EBV had a median copy number of eight. Antibodies against EBV and CMV were detected in 85.7% and 78.6% of persons evaluated, respectively.Conclusion: EBV was infrequent and CMV was rarely present in individual subgingival sites affected by chronic periodontitis.
Within‐Subject Variability in Repeated Measures of Salivary Analytes in Healthy Adults
Authors: Thomas Mark V. , Branscum Adam , Miller Craig S. , Ebersole Jeffrey , Al‐Sabbagh Mohanad , Schuster Julie L. 
Published: June 2009

Background: Saliva contains a large number of biomolecules, some of which have putative diagnostic usefulness. A potential problem with the use of biomolecules in diagnosis is day‐to‐day fluctuation due to within‐subject variability. This study evaluated the intraindividual variability of six salivary analytes in healthy adults and determined their normal range.Methods: Unstimulated whole saliva (5 ml) was collected every 2 to 3 days on six occasions from 30 subjects in good oral and systemic health. Four of the samples were collected in the clinic, and two were collected by the subject at home. The concentration ranges of interleukin (IL)‐1β, IL‐6, matrix metalloproteinase‐8, prostaglandin E2, tumor necrosis factor‐alpha, interferon‐alpha, and albumin were examined. Descriptive statistics were computed, and a one‐way random‐effects model was used to quantify within‐ and between‐subject components of variability. Intraclass correlation coefficients (ICCs) were calculated for each subject/analyte combination.Results: Within‐subject coefficients of variation for these analytes ranged from 67.6% to 172.1% for the in‐clinic samples and from 111.9% to 201.0% for the at‐home samples. The ICC for the various analytes ranged from 41% to 61% for the in‐clinic samples. The at‐home samples exhibited significantly more variability than did those obtained in the clinic under supervision.Conclusions: There was marked within‐subject variation in the salivary concentrations of these analytes. With increased interest in salivary diagnostics, the within‐subject variability, normal range, and threshold levels for abnormal levels of individual salivary analytes need to be determined if these diagnostics tests are to have clinical usefulness.
B‐1a Cells in Experimental Gingivitis in Humans
Authors: Donati Mauro , Liljenberg Birgitta , Zitzmann Nicola U. , Berglundh Tord 
Published: June 2009

Background: Although previous studies revealed the presence of autoreactive B cells (B‐1a cells) in periodontitis lesions, no evidence was provided for an active role of such cells in the host response to microbial challenge. The aim of the present investigation was to study the reaction of B‐1a cells to de novo plaque formation in subjects who were treated for severe chronic periodontitis.Methods: Fifteen white subjects with generalized, severe chronic periodontitis volunteered. Surgical periodontal therapy was performed in all quadrants of each subject after a period of infection control. After 6 months of healing (baseline), two gingival biopsies were harvested from each patient (probing depth <4 mm and no bleeding on probing; healed sites). The experimental gingivitis model was applied, and plaque accumulation was allowed for 3 weeks. Two additional biopsies were collected and prepared for immunohistochemical analysis on day 21.Results: The biopsies retrieved after 3 weeks of plaque accumulation contained larger proportions of CD19+ and CD5+ cells (B‐1a cells) than biopsies representing baseline (healed sites) (7.38% ± 2.80% versus 5.96% ± 2.48%). The tissue fraction of cells carrying the markers for CD3 (T cells), CD19 (B cells), and Bcl2 (apoptosis‐associated marker) were significantly larger in tissue samples collected after 3 weeks of plaque accumulation than in specimens from baseline (healed sites).Conclusion: Autoreactive B cells (B‐1a cells) are involved in the host response to microbial challenge in subjects with chronic periodontitis.
Bone Strain and Interfacial Sliding Analyses of Platform Switching and Implant Diameter on an Immediately Loaded Implant: Experimental and Three‐Dimensional Finite Element Analyses
Authors: Hsu Jui‐Ting , Fuh Lih‐Jyh , Lin Dan‐Jae , Shen Yen‐Wen , Huang Heng‐Li 
Published: June 2009

Background: Strain gauge analysis and finite element (FE) simulations were used to estimate the bone strain and micromovement at the bone–implant interface (BII) for platform switching and different diameters of a single, immediately loaded mandibular implant.Methods: Four models were created, including 5‐mm‐diameter implants assembled with abutments that were 5 or 4 mm in diameter on bonded (delay‐loading treatment) and contact (immediate‐loading treatment) BIIs; a model with an implant diameter of 3.75 mm was also analyzed. Vertical and lateral loads of 130 N were applied to all models.Results: During lateral loading, the strains were highly concentrated on one side of the mandible in the experimental and validation FE models. Bone strains were reduced by <10% when platform switching was used compared to no platform switching. However, increasing implant diameter decreased the surrounding bone strain significantly. The sliding and gap distances at the BII did not differ significantly among all models considered.Conclusions: Bone strain was reduced more by increasing the diameter of the implant than by using platform switching in the immediately loaded implant. However, neither a wide implant nor platform switching reduced micromotion at the BII for enhancing implant stability.
The Influence of Atopy in the Prognosis of the Replantation of Avulsed Teeth
Authors: Roskamp Liliane , Westphalen Vânia P.D. , Lima José H.C. , Carneiro Everdan , Fariniuk Luiz F. , Silva Neto Ulisses X. , Westphalen Fernando H. 
Published: June 2009

Background: Replantation is the most indicated procedure for traumatic dental avulsion, but it invariably results in a greater or lower degree of root resorption. The outcomes of these cases can be affected by some well‐known factors. Because studies have shown the importance of the innate and acquired immune response in the mechanisms involved in the resorption of bone tissues, an endeavor was made to verify if such an influence applies to dental resorption.Methods: Fifty‐seven avulsed, endodontically treated teeth were assessed in the Endodontics Clinic, Pontifical Catholic University of Paraná. Follow‐up of the replanted teeth included periodical clinical examinations and radiographs, in accordance with the control rules of the International Association of Dental Traumatology. The evaluation of atopy was based on the patient's personal and family history in conjunction with the skin‐prick test for five allergen extracts.Results: Of the 46 teeth with a favorable outcome, 33 (71.74%) were in atopic patients, and 13 (28.26%) were in non‐atopic patients. Of the 11 teeth with an unfavorable outcome, four (36.36%) were in atopic patients, and seven (63.64%) were in non‐atopic patients; a greater prevalence of unfavorable prognoses occurred in non‐atopic patients.Conclusion: The outcome after 1 year for avulsed and replanted teeth is more favorable in atopic patients.
Coronally Advanced Flap With and Without Vertical Releasing Incisions for the Treatment of Multiple Gingival Recessions: A Comparative Controlled Randomized Clinical Trial
Authors: Zucchelli G. , Mele M. , Mazzotti C. , Marzadori M. , Montebugnoli L. , De Sanctis M. 
Published: June 2009

Background: Vertical releasing incisions might damage the blood supply to the flap and result in unesthetic visible white scars. The aim of the present study was to compare root coverage and esthetic outcomes of the coronally advanced flap (CAF) with and without vertical releasing incisions in the treatment of multiple gingival recessions.Methods: Thirty‐two systemically and periodontally healthy subjects with esthetic complaints due to the exposure of Miller Class I and II multiple (at least two) gingival recession defects (≥1 mm) affecting adjacent teeth of the same quadrant of the upper jaw were enrolled in the study. Sixteen patients (with 45 gingival recessions) were randomly assigned to the control group, and the other 16 patients (with 47 recession defects) were assigned to the test group. All recessions were treated with a CAF; vertical releasing incisions were performed in the control group, whereas an envelope‐type flap was used in the test group. The patient's postoperative morbidity was assessed 1 week after the surgery, whereas the esthetic evaluation, made by the patient and independent periodontist, and the clinical evaluation were made 1 year later.Results: Surgical time was significantly shorter in the envelope‐type CAF group. No statistically significant difference was demonstrated between the two groups in terms of recession reduction and clinical attachment level gain. A statistically greater probability of complete root coverage (adjusted odds ratio, 3.76; 95% confidence interval: 0.92 to 15.33; P <0.05) and a greater increase in buccal keratinized tissue height were observed with the envelope type of CAF. Patient satisfaction with esthetics was very high in both treatment groups, with no statistically significant differences between them. A better postoperative course and better results in the esthetic evaluation made by an independent periodontist were demonstrated in patients treated with the envelope type of CAF.Conclusions: Both CAF techniques were effective in reducing recession depth. The envelope type of CAF was associated with an increased probability of achieving complete root coverage and with a better postoperative course. Keloid formation along the vertical releasing incisions was responsible for the worst esthetic evaluation made by an independent expert periodontist.
Fusobacterium nucleatum Enters Normal Human Oral Fibroblasts In Vitro
Authors: Dabija‐Wolter Gabriela , Cimpan Mihaela‐Roxana , Costea Daniela E. , Johannessen Anne Christine , Sørnes Steinar , Neppelberg Evelyn , Al‐Haroni Mohammed , Skaug Nils , Bakken Vidar 
Published: June 2009

Background: Fusobacterium nucleatum, a commensal opportunistic oral bacterium, is capable of invading gingival epithelial cells, but the entrance into human primary oral fibroblast cells has not been documented. This study evaluated the ability of three strains of F. nucleatum (F. nucleatum ssp. nucleatum, F. nucleatum ssp. polymorphum, and F. nucleatum ssp. vincentii) to enter gingival fibroblasts (GFs) and periodontal ligament fibroblasts (PLFs).Methods: GFs and PLFs were cocultured for various periods of time with different strains of F. nucleatum. Scanning and transmission electron microscopy, together with confocal laser scanning microscopy, were used to visualize the entrance and presence of bacteria in host cells. Flow cytometry was performed to compare the load of internalized bacteria in GFs and PLFs exposed for 3 and 5 hours to live F. nucleatum labeled with fluorescein isothiocyanate.Results: All three strains of F. nucleatum were found entering and located in the cytoplasm of GFs and PLFs after 1 hour of exposure. Flow cytometry tests revealed a significant increase in the fluorescent signal, compared to baseline, derived from bacteria internalized in fibroblasts exposed for 3 hours (P <0.001); a further increase was found at 5 hours. The greatest bacterial mass in exposed fibroblasts of both types was of F. nucleatum ssp. polymorphum; the smallest was of F. nucleatum ssp. vincentii. Although not statistically significant, PLFs had a higher bacterial load than corresponding GFs.Conclusion: F. nucleatum was capable of entering GFs and PLFs in a manner that is dependent on the cell type and the bacterial strain.
The American Journal of Cardiology and Journal of Periodontology Editors' Consensus: Periodontitis and Atherosclerotic Cardiovascular Disease
Authors: Friedewald Vincent E. , Kornman Kenneth S. , Beck James D. , Genco Robert , Goldfine Allison , Libby Peter , Offenbacher Steven , Ridker Paul M. , Van Dyke Thomas E. , Roberts William C. 
Published: June 2009

Acknowledgment: This Editors' Consensus is supported by an educational grant from Colgate‐Palmolive, Inc., New York, New York, and is based on a meeting of the authors held in Boston, Massachusetts, on January 9, 2009.Disclosure: Dr. Friedewald has received honoraria for speaking from Novartis, East Hanover, New Jersey. Dr. Kornman is a full‐time employee and shareholder of Interleukin Genetics, Waltham, Massachusetts, which owns patents on genetic biomarkers for chronic inflammatory diseases. Dr. Genco is a consultant to Merck, Whitehouse Station, New Jersey. Dr. Ridker has received research support from AstraZeneca, Wilmington, Delaware; Novartis; Pfizer, New York, New York; Roche, Nutley, New Jersey; Sanofi‐Aventis, Bridgewater, New Jersey; and Abbott Laboratories, Abbott Park, Illinois. Dr. Ridker has received non‐financial research support from Amgen, Thousand Oaks, California. Dr. Ridker is a co‐inventor on patents held by Brigham and Women's Hospital that relate to the use of inflammatory biomarkers in cardiovascular disease. Dr. Ridker is a research consultant for Schering‐Plough, Kenilworth, New Jersey; Sanofi‐Aventis; AstraZeneca; Isis, Carlsbad, California; Novartis; and Vascular Biogenics, Tel Aviv, Israel. Dr. Van Dyke is a co‐inventor on patents held by Boston University, Boston, Massachusetts, that relate to inflammation control, including consulting fees. Dr. Roberts has received honoraria for speaking from Merck, Schering‐Plough, AstraZeneca, and Novartis. All other individuals in a position to control content disclosed no relevant financial relationships.