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Honorio H, Boteon A, Kato M, Buzalaf M, Prakki A, Wang L, Rios D. Effect of cranberry and proanthocyanidin in dentin erosion prevention. Dent Mater 2016. [DOI: 10.1016/j.dental.2016.08.091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Marques N, Lourenço Neto N, Fernandes AP, Rodini C, Hungaro Duarte M, Rios D, Machado MA, Oliveira T. Pulp tissue response to Portland cement associated with different radio pacifying agents on pulpotomy of human primary molars. J Microsc 2015; 260:281-6. [PMID: 26258985 DOI: 10.1111/jmi.12294] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 06/25/2015] [Indexed: 12/01/2022]
Abstract
The objective of this research was to evaluate the response of Portland cement associated with different radio pacifying agents on pulp treatment of human primary teeth by clinical and radiographic exams and microscopic analysis. Thirty mandibular primary molars were randomly divided into the following groups: Group I - Portland cement; Group II - Portland cement with iodoform (Portland cement + CHI3 ); Group III - Portland cement with zirconium oxide (Portland cement + ZrO2 ); and treated by pulpotomy technique (removal of a portion of the pulp aiming to maintain the vitally of the remaining radicular pulp tissue using a therapeutic dressing). Clinical and radiographic evaluations were recorded at 6, 12 and 24 months follow-up. The teeth at the regular exfoliation period were extracted and processed for histological analysis. Data were tested using statistical analysis with a significance level of 5%. The microscopic findings were descriptively analysed. All treated teeth were clinically and radiographically successful at follow-up appointments. The microscopic analysis revealed positive response to pulp repair with hard tissue barrier formation and pulp calcification in the remaining roots of all available teeth. The findings of this study suggest that primary teeth pulp tissue exhibited satisfactory biological response to Portland cement associated with radio pacifying agents. However, further studies with long-term follow-up are needed to determine the safe clinical indication of this alternative material for pulp therapy of primary teeth.
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Powell JJ, Thomas-McKay E, Thoree V, Robertson J, Hewitt RE, Skepper JN, Brown A, Hernandez-Garrido JC, Midgley PA, Gomez-Morilla I, Grime GW, Kirkby KJ, Mabbott NA, Donaldson DS, Williams IR, Rios D, Girardin SE, Haas CT, Bruggraber SFA, Laman JD, Tanriver Y, Lombardi G, Lechler R, Thompson RPH, Pele LC. An endogenous nanomineral chaperones luminal antigen and peptidoglycan to intestinal immune cells. NATURE NANOTECHNOLOGY 2015; 10:361-9. [PMID: 25751305 PMCID: PMC4404757 DOI: 10.1038/nnano.2015.19] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 01/21/2015] [Indexed: 05/06/2023]
Abstract
In humans and other mammals it is known that calcium and phosphate ions are secreted from the distal small intestine into the lumen. However, why this secretion occurs is unclear. Here, we show that the process leads to the formation of amorphous magnesium-substituted calcium phosphate nanoparticles that trap soluble macromolecules, such as bacterial peptidoglycan and orally fed protein antigens, in the lumen and transport them to immune cells of the intestinal tissue. The macromolecule-containing nanoparticles utilize epithelial M cells to enter Peyer's patches, small areas of the intestine concentrated with particle-scavenging immune cells. In wild-type mice, intestinal immune cells containing these naturally formed nanoparticles expressed the immune tolerance-associated molecule 'programmed death-ligand 1', whereas in NOD1/2 double knockout mice, which cannot recognize peptidoglycan, programmed death-ligand 1 was undetected. Our results explain a role for constitutively formed calcium phosphate nanoparticles in the gut lumen and show how this helps to shape intestinal immune homeostasis.
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Oliveira GC, Boteon AP, Ionta FQ, Moretto MJ, Honório HM, Wang L, Rios D. In Vitro Effects of Resin Infiltration on Enamel Erosion Inhibition. Oper Dent 2015; 40:492-502. [PMID: 25587972 DOI: 10.2341/14-162-l] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Resin-based materials that show promising effects for preventing the progression of erosion have been studied. This in vitro study evaluated the effects of applying resin-based materials, including resin infiltration, on previously eroded enamel subjected to erosive challenges. The influence of enamel surface etching prior to application of the material was also studied. Bovine enamel blocks were immersed in hydrochloric acid (HCl), 0.01 M (pH 2.3), for 30 seconds in order to form a softened erosion lesion. The blocks were then randomly divided into nine groups (n=12) and treated as follows: C = control without treatment; Hel = pit & fissure resin sealant (Helioseal Clear); Adh = two-step self-etching adhesive system (AdheSe); Tet = two-step conventional adhesive system (Tetric N-bond); and Inf = infiltrant (Icon). The Helno, Adhno, Tetno, and Infno groups received the same materials without (or with no) surface conditioning. The depth of the material's penetration into softened erosion lesions was qualitatively analyzed using reflection and fluorescence confocal microscopy. After application of the materials, the blocks were immersed in HCl for two minutes; this step was followed by immersion in artificial saliva for 120 minutes four times a day for five days (erosive cycling). Both the enamel alteration and material thickness were analyzed using profilometry, and the results were submitted to Kruskal-Wallis and Dunn tests (p>0.05). Images from the confocal microscopy showed minimal penetration of Adh/Adhno and deep penetration of Inf/Infno into the erosive lesions. The groups Hel, Adh, Inf, Tetno, and Infno resulted in the formation of a layer of material over the enamel, which was effective in inhibiting the progression of erosion. In conclusion, the infiltrant, with or without etching, was able to penetrate and protect the enamel against dental erosion. The other resin-based materials, except for the two-step conventional adhesive, were able to penetrate and inhibit the progression of erosive lesions only when they were applied after enamel etching.
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Mylvaganam G, Rios D, Williams I, Velu V, Amara R. Anti-viral CD8 T-cells with B-cell Follicle Homing Potential Contribute to Vaccine-mediated Enhanced Control of Pathogenic SIV Infection. AIDS Res Hum Retroviruses 2014. [DOI: 10.1089/aid.2014.5140a.abstract] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Rios D, Jansson KS, Martetschläger F, Boykin RE, Millett PJ, Wijdicks CA. Normal curvature of glenoid surface can be restored when performing an inlay osteochondral allograft: an anatomic computed tomographic comparison. Knee Surg Sports Traumatol Arthrosc 2014; 22:442-7. [PMID: 23344118 DOI: 10.1007/s00167-013-2391-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Accepted: 01/07/2013] [Indexed: 11/29/2022]
Abstract
PURPOSE The purpose of this study was to quantitatively measure the morphology of the glenoid and to assess feasibility of using the medial tibial plateau surface as a donor for osteoarticular allograft reconstruction of the glenoid. METHODS Using computed tomography (CT), 10 tibias and 10 scapular models from our database (5 males and 5 females in each group) were randomly selected. Commercial software (Mimics, Materialize, Inc., Plymouth, MI) was used to extract the bone contours from the CT images and to reconstruct the 3-dimensional (3D) geometry of the scapula and tibia. By utilizing the software Creo Elements/Pro 5.0 (Parametric Technology Corp., Needham, MA), mean length and width of both the glenoid and medial tibial plateau were calculated. Radius of curvature was then measured in each 3D CT model at three intermediate segment points that were established within the length line at 25, 50, and 75 percent from superior to inferior in the glenoid and from posterior to anterior in the medial tibial plateau. Statistical analysis was performed and determined to be significant for P < 0.05. RESULTS The mean (± SD) radius of curvature values at the established 25, 50, and 75 percent segments of the glenoid were 47.4 ± 17.5 mm, 51.2 ± 12.4 mm, and 45.9 ± 17.0 mm, respectively. For the medial tibial plateau, the radius of curvature at 25, 50, and 75 percent were 43.5 ± 9.7 mm, 37.4 ± 14.3 mm and 52.3 ± 21.5 mm, respectively. Values of the glenoid length were 34.0 ± 2.9 mm, and width values were 24.4 ± 2.3 mm. For the medial tibial plateau, the length was 42.6 ± 2.7 mm, and the width was 23.3 ± 4.3 mm. There was no statistical difference in the radius of curvature and dimensional surface area between the glenoid and medial tibial plateau surfaces. CONCLUSION The 3D CT-based anatomic study found that there is a statistically similar relationship in the radius of curvature of the glenoid and the medial tibial plateau surface. This concept may allow the medial tibial plateau to be used as a donor for osteoarticular allograft reconstruction of the glenoid, especially in young patients where previous studies have demonstrated that the success rate in shoulder replacements is not as good as in older patients.
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Gong Y, Vallet V, del Carmen Michelini M, Rios D, Gibson JK. Activation of Gas-Phase Uranyl: From an Oxo to a Nitrido Complex. J Phys Chem A 2013; 118:325-30. [DOI: 10.1021/jp4113798] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Kobayashi TY, Gurgel CV, Cota AL, Rios D, Machado MAA, Oliveira TM. The usefulness of cone beam computed tomography for treatment of complex odontoma. Eur Arch Paediatr Dent 2013; 14:185-9. [PMID: 23633234 DOI: 10.1007/s40368-013-0036-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Accepted: 02/21/2013] [Indexed: 01/12/2023]
Abstract
BACKGROUND Odontomas are odontogenic tumours, resulting from epithelial growth and differentiated mesenchymal cells, clinically asymptomatic, and often associated with changes to the eruption of the permanent dentition. In recent years, cone beam computed tomography (CBCT) has been used in the diagnosis and treatment planning of this condition. CASE REPORT A 9-year-old male patient, with an unerupted permanent maxillary right central incisor (tooth 11) presented to our clinic. The panoramic radiograph showed impaction of tooth 11 with incomplete root development and the suspicion of an odontome and supernumerary tooth. CBCT was performed and enabled the visualisation of a radiopaque image compatible with an odontome, confirming the presence of an impacted supernumerary tooth on the palatal surface of tooth 11. TREATMENT Surgical excision of the odontome and the supernumerary tooth was performed. FOLLOW-UP Clinical and radiographic evaluations 2 months after the removal of the lesion showed lack of space for the eruption of tooth 11. The patient was referred for orthodontic treatment and a Hyrax appliance was fitted. The patient has been followed for 12 months. CONCLUSION CBCT is an important auxiliary tool, aiding in both correct diagnosis and accurate treatment planning. It is currently a technology accessible to most paediatric dentists and should be beneficial considering the diagnostic information provided as well as the cost-benefit ratio for the patient.
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Millett PJ, Horan MP, Pennock AT, Rios D. Comprehensive Arthroscopic Management (CAM) procedure: clinical results of a joint-preserving arthroscopic treatment for young, active patients with advanced shoulder osteoarthritis. Arthroscopy 2013; 29:440-8. [PMID: 23544687 DOI: 10.1016/j.arthro.2012.10.028] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Revised: 10/22/2012] [Accepted: 10/23/2012] [Indexed: 02/02/2023]
Abstract
PURPOSE The purpose of this study was to examine the surgical outcomes of 29 active patients (30 shoulders) with end-stage, symptomatic glenohumeral arthritis undergoing the comprehensive arthroscopic management (CAM) procedure. METHODS In this institutional review board-approved study, patients with advanced glenohumeral osteoarthritis (OA) underwent the CAM procedure, a joint-preserving arthroscopic treatment. All subjects were candidates for shoulder arthroplasty. The CAM procedure involves the combination of glenohumeral chondroplasty; removal of loose bodies if present; humeral osteoplasty and osteophyte resection (goat's beard deformity); anterior, posterior, and inferior capsular release; subacromial decompression; axillary nerve neurolysis; and biceps tenodesis. Outcome measures included pain, American Shoulder and Elbow Surgeons score, Single Assessment Numeric Evaluation score, QuickDASH (short version of Disabilities of the Arm, Shoulder and Hand questionnaire) score, and satisfaction. For survivorship analysis, failure was defined as progression to shoulder arthroplasty. RESULTS The mean age was 52 years (range, 33 to 68 years), and there were 23 men and 6 women. Of the 30 shoulders, 6 progressed to an arthroplasty at a mean of 1.9 years (range, 0.9 to 3.4 years). Patients with less than 2.0 mm of joint space on radiographs were more likely to undergo arthroplasty (P = .037). For shoulders that did not progress to arthroplasty (n = 24), the mean follow-up was 2.6 years (range, 2.1 to 4.7 years). The American Shoulder and Elbow Surgeons scores significantly improved from 58 points (SE, 2.4) to 83 points (SE, 3.3) (P < .001), and pain levels decreased with activities of daily living, work, recreation, and sleep (P < .05). The median patient satisfaction rating was 9 (range, 3 to 10). Survivorship analysis showed a 92% survival rate at 1 year and 85% at 2 years. Patients with larger osteophytes had greater improvement in postoperative range of motion but were less satisfied (r = 0.479, P = .038). CONCLUSIONS The CAM procedure reduced pain, improved function, and provided reasonable short-term durability for our cohort of young, active patients with advanced shoulder OA and may serve as a joint-preserving alternative to arthroplasty. Patients with less than 2 mm of joint space had a significantly higher failure rate. The CAM procedure is a viable surgical option in young, active patients with advanced OA, showing survivorship of 85% at 2 years. LEVEL OF EVIDENCE Level IV, therapeutic case series.
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Rios D, Schoendorff G, Van Stipdonk MJ, Gordon MS, Windus TL, Gibson JK, de Jong WA. Roles of Acetone and Diacetone Alcohol in Coordination and Dissociation Reactions of Uranyl Complexes. Inorg Chem 2012; 51:12768-75. [DOI: 10.1021/ic3015964] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Rios D, del Carmen Michelini M, Lucena AF, Marçalo J, Gibson JK. On the Origins of Faster Oxo Exchange for Uranyl(V) versus Plutonyl(V). J Am Chem Soc 2012; 134:15488-96. [DOI: 10.1021/ja305800q] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Rios D, Michelini MC, Lucena AF, Marçalo J, Bray TH, Gibson JK. Gas-Phase Uranyl, Neptunyl, and Plutonyl: Hydration and Oxidation Studied by Experiment and Theory. Inorg Chem 2012; 51:6603-14. [DOI: 10.1021/ic3001625] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Rios D, Knoop K, Kumar N, Tawde S, Chablani L, D'Souza M, Williams I. Conditional deletion of RANK in intestinal epithelial cells of mice results in loss of Peyer’s patch M cells and impaired acquisition of orally delivered antigen (49.2). THE JOURNAL OF IMMUNOLOGY 2012. [DOI: 10.4049/jimmunol.188.supp.49.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abstract
Microfold (M) cells are antigen-sampling intestinal epithelial cells found in the follicle-associated epithelium (FAE) of Peyer’s patches (PPs). M cells initiate mucosal immune responses by transcytosis of particulate antigens for delivery to antigen-presenting cells that traffic through the intraepithelial pocket of M cells. We previously showed that RANKL from stromal cells in the subepithelial dome of PPs is necessary and sufficient for inducing M cell differentiation. To determine how selective loss of intestinal M cells affects host immune responses to antigens encountered in the gut lumen, we generated mice with a floxed allele of RANK deleted only in intestinal epithelial cells (IEC) by a villin-cre transgene (RANKΔIEC mice). The FAE of PP in RANKΔIEC mice lacked any cells expressing the M-cell marker GP2, proving that RANKL promotes M cell differentiation from intestinal stem cells via a direct action on RANK-expressing IEC. An OT-II T cell adoptive transfer model was used to analyze ovalbumin (OVA)-specific T cell responses 2 to 3 days after gavage with various forms of OVA. RANKΔIEC mice had compromised T cell responses to both soluble OVA and particulate OVA (OVA encapsulated in acid-stable microparticles prepared by spray drying). The RANKΔIEC mouse provides a first-of-its-kind mouse model for the specific assessment of the contribution of intestinal M cells to uptake of protein antigens and pathogenic microorganisms encountered in the intestinal lumen.
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Rios D, Gibson JK. Activation of Gas-Phase Uranyl Diacetone Alcohol Coordination Complexes by Spectator Ligand Addition. Eur J Inorg Chem 2012. [DOI: 10.1002/ejic.201200024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Rios D, Rutkowski PX, Shuh DK, Bray TH, Gibson JK, Van Stipdonk MJ. Electron transfer dissociation of dipositive uranyl and plutonyl coordination complexes. JOURNAL OF MASS SPECTROMETRY : JMS 2011; 46:1247-1254. [PMID: 22223415 DOI: 10.1002/jms.2011] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Reported here is a comparison of electron transfer dissociation (ETD) and collision-induced dissociation (CID) of solvent-coordinated dipositive uranyl and plutonyl ions generated by electrospray ionization. Fundamental differences between the ETD and CID processes are apparent, as are differences between the intrinsic chemistries of uranyl and plutonyl. Reduction of both charge and oxidation state, which is inherent in ETD activation of [An(VI) O(2) (CH(3) COCH(3) )(4) ](2+) , [An(VI) O(2) (CH(3) CN)(4) ](2) , [U(VI) O(2) (CH(3) COCH(3) )(5) ](2+) and [U(VI) O(2) (CH(3) CN)(5) ](2+) (An = U or Pu), is accompanied by ligand loss. Resulting low-coordinate uranyl(V) complexes add O(2) , whereas plutonyl(V) complexes do not. In contrast, CID of the same complexes generates predominantly doubly-charged products through loss of coordinating ligands. Singly-charged CID products of [U(VI) O(2) (CH(3) COCH(3) )(4,5) ](2+) , [U(VI) O(2) (CH(3) CN)(4,5) ](2+) and [Pu(VI) O(2) (CH(3) CN)(4) ](2+) retain the hexavalent metal oxidation state with the addition of hydroxide or acetone enolate anion ligands. However, CID of [Pu(VI) O(2) (CH(3) COCH(3) )(4) ](2+) generates monopositive plutonyl(V) complexes, reflecting relatively more facile reduction of Pu(VI) to Pu(V).
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Rutkowski PX, Rios D, Gibson JK, Van Stipdonk MJ. Gas-phase coordination complexes of U(VI)O2(2+), Np(VI)O2(2+), and Pu(VI)O2(2+) with dimethylformamide. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:2042-2048. [PMID: 21952769 DOI: 10.1007/s13361-011-0226-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2011] [Revised: 07/30/2011] [Accepted: 07/30/2011] [Indexed: 05/31/2023]
Abstract
Electrospray ionization of actinyl perchlorate solutions in H(2)O with 5% by volume of dimethylformamide (DMF) produced the isolatable gas-phase complexes, [An(VI)O(2)(DMF)(3)(H(2)O)](2+) and [An(VI)O(2)(DMF)(4)](2+), where An = U, Np, and Pu. Collision-induced dissociation confirmed the composition of the dipositive coordination complexes, and produced doubly- and singly-charged fragment ions. The fragmentation products reveal differences in underlying chemistries of uranyl, neptunyl, and plutonyl, including the lower stability of Np(VI) and Pu(VI) compared with U(VI).
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Schoendorff G, de Jong WA, Van Stipdonk MJ, Gibson JK, Rios D, Gordon MS, Windus TL. Correction to On the Formation of “Hypercoordinated” Uranyl Complexes. Inorg Chem 2011. [DOI: 10.1021/ic202173r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Schoendorff G, de Jong WA, Van Stipdonk MJ, Gibson JK, Rios D, Gordon MS, Windus TL. On the Formation of “Hypercoordinated” Uranyl Complexes. Inorg Chem 2011; 50:8490-3. [DOI: 10.1021/ic201080z] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Rios D, Rutkowski PX, Van Stipdonk MJ, Gibson JK. Gas-Phase Coordination Complexes of Dipositive Plutonyl, PuO22+: Chemical Diversity Across the Actinyl Series. Inorg Chem 2011; 50:4781-90. [DOI: 10.1021/ic2005375] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Rios D, Gillett-Kunnath MM, Taylor JD, Oliver AG, Sevov SC. Addition of a Thallium Vertex to Empty and Centered Nine-Atom Deltahedral Zintl Ions of Germanium and Tin. Inorg Chem 2011; 50:2373-7. [DOI: 10.1021/ic102152e] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Wang L, Francisconi L, Casas-Apayco L, Calábria M, Honório H, Rios D, Buzalaf M, Carrilho M. Chlorhexidine preserves the bond strength to eroded dentin. Dent Mater 2011. [DOI: 10.1016/j.dental.2011.08.460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Flicek P, Amode MR, Barrell D, Beal K, Brent S, Chen Y, Clapham P, Coates G, Fairley S, Fitzgerald S, Gordon L, Hendrix M, Hourlier T, Johnson N, Kähäri A, Keefe D, Keenan S, Kinsella R, Kokocinski F, Kulesha E, Larsson P, Longden I, McLaren W, Overduin B, Pritchard B, Riat HS, Rios D, Ritchie GRS, Ruffier M, Schuster M, Sobral D, Spudich G, Tang YA, Trevanion S, Vandrovcova J, Vilella AJ, White S, Wilder SP, Zadissa A, Zamora J, Aken BL, Birney E, Cunningham F, Dunham I, Durbin R, Fernández-Suarez XM, Herrero J, Hubbard TJP, Parker A, Proctor G, Vogel J, Searle SMJ. Ensembl 2011. Nucleic Acids Res 2011; 39:D800-6. [PMID: 21045057 PMCID: PMC3013672 DOI: 10.1093/nar/gkq1064] [Citation(s) in RCA: 564] [Impact Index Per Article: 43.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2010] [Accepted: 10/13/2010] [Indexed: 11/13/2022] Open
Abstract
The Ensembl project (http://www.ensembl.org) seeks to enable genomic science by providing high quality, integrated annotation on chordate and selected eukaryotic genomes within a consistent and accessible infrastructure. All supported species include comprehensive, evidence-based gene annotations and a selected set of genomes includes additional data focused on variation, comparative, evolutionary, functional and regulatory annotation. The most advanced resources are provided for key species including human, mouse, rat and zebrafish reflecting the popularity and importance of these species in biomedical research. As of Ensembl release 59 (August 2010), 56 species are supported of which 5 have been added in the past year. Since our previous report, we have substantially improved the presentation and integration of both data of disease relevance and the regulatory state of different cell types.
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McLaren W, Pritchard B, Rios D, Chen Y, Flicek P, Cunningham F. Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor. Bioinformatics 2010; 26:2069-70. [PMID: 20562413 PMCID: PMC2916720 DOI: 10.1093/bioinformatics/btq330] [Citation(s) in RCA: 1270] [Impact Index Per Article: 90.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2010] [Revised: 05/27/2010] [Accepted: 06/15/2010] [Indexed: 01/17/2023] Open
Abstract
SUMMARY A tool to predict the effect that newly discovered genomic variants have on known transcripts is indispensible in prioritizing and categorizing such variants. In Ensembl, a web-based tool (the SNP Effect Predictor) and API interface can now functionally annotate variants in all Ensembl and Ensembl Genomes supported species. AVAILABILITY The Ensembl SNP Effect Predictor can be accessed via the Ensembl website at http://www.ensembl.org/. The Ensembl API (http://www.ensembl.org/info/docs/api/api_installation.html for installation instructions) is open source software.
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Rios D, Sevov SC. The Elusive closo-Ge102− Zintl Ion: Finally “Captured” as a Ligand in the Complex [Ge10Mn(CO)4]3−. Inorg Chem 2010; 49:6396-8. [DOI: 10.1021/ic100877u] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Rios D, McLaren WM, Chen Y, Birney E, Stabenau A, Flicek P, Cunningham F. A database and API for variation, dense genotyping and resequencing data. BMC Bioinformatics 2010; 11:238. [PMID: 20459810 PMCID: PMC2882931 DOI: 10.1186/1471-2105-11-238] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2009] [Accepted: 05/11/2010] [Indexed: 11/15/2022] Open
Abstract
Background Advances in sequencing and genotyping technologies are leading to the widespread availability of multi-species variation data, dense genotype data and large-scale resequencing projects. The 1000 Genomes Project and similar efforts in other species are challenging the methods previously used for storage and manipulation of such data necessitating the redesign of existing genome-wide bioinformatics resources. Results Ensembl has created a database and software library to support data storage, analysis and access to the existing and emerging variation data from large mammalian and vertebrate genomes. These tools scale to thousands of individual genome sequences and are integrated into the Ensembl infrastructure for genome annotation and visualisation. The database and software system is easily expanded to integrate both public and non-public data sources in the context of an Ensembl software installation and is already being used outside of the Ensembl project in a number of database and application environments. Conclusions Ensembl's powerful, flexible and open source infrastructure for the management of variation, genotyping and resequencing data is freely available at http://www.ensembl.org.
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