The VERA information environment

We present three components of a virtual research environment developed for the ongoing Roman excavation at Silchester. These components — Recycle Bridge, XDB cross-database search, and Arch3D — provide additional services around the existing core of the system, run on the Integrated Archaeological Database (IADB). They provide, respectively, embedding of legacy applications into portals, cross-database searching, and 3D visualisation of stratigraphic information.

What people study when they study Twitter: classifying Twitter related academic papers

PURPOSE: Since its introduction in 2006, messages posted to the microblogging system Twitter have provided a rich dataset for researchers, leading to the publication of over a thousand academic papers. This paper aims to identify this published work and to classify it in order to understand Twitter based research. DESIGN/METHODOLOGY/APPROACH: Firstly the papers on Twitter were identified. Secondly, following a review of the literature, a classification of the dimensions of microblogging research was established. Thirdly, papers were qualitatively classified using open coded content analysis, based on the paper’s title and abstract, in order to analyze method, subject, and approach. FINDINGS: The majority of published work relating to Twitter concentrates on aspects of the messages sent and details of the users. A variety of methodological approaches are used across a range of identified domains. RESEARCH LIMITATIONS/IMPLICATIONS: This work reviewed the abstracts of all papers available via database search on the term “Twitter” and this has two major implications: 1) the full papers are not considered and so works may be misclassified if their abstract is not clear, 2) publications not indexed by the databases, such as book chapters, are not included. ORIGINALITY/VALUE: To date there has not been an overarching study to look at the methods and purpose of those using Twitter as a research subject. Our major contribution is to scope out papers published on Twitter until the close of 2011. The classification derived here will provide a framework within which researchers studying Twitter related topics will be able to position and ground their work

Prevalence of dementia in Latin America: a collaborative study of population-based cohorts

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

The GHEP-EMPOP collaboration on mtDNA population data-A new resource for forensic casework

Mitochondrial DNA (mtDNA) population data for forensic purposes are still scarce for some populations, which may limit the evaluation of forensic evidence especially when the rarity of a haplotype needs to be determined in a database search. In order to improve the collection of mtDNA lineages from the Iberian and South American subcontinents, we here report the results of a collaborative study involving nine laboratories from the Spanish and Portuguese Speaking Working Group of the International Society for Forensic Genetics (GHEP-ISFG) and EMPOP. The individual laboratories contributed population data that were generated throughout the past 10 years, but in the majority of cases have not been made available to the scientific community. A total of 1019 haplotypes from Iberia (Basque Country, 2 general Spanish populations, 2 North and 1 Central Portugal populations), and Latin America (3 populations from São Paulo) were collected, reviewed and harmonized according to defined EMPOP criteria. The majority of data ambiguities that were found during the reviewing process (41 in total) were transcription errors confirming that the documentation process is still the most error-prone stage in reporting mtDNA population data, especially when performed manually. This GHEP-EMPOP collaboration has significantly improved the quality of the individual mtDNA datasets and adds mtDNA population data as valuable resource to the EMPOP database (www.empop.org). (C) 2010 Elsevier B.V. All rights reserved.

Effects of motor intervention in elderly patients with dementia: An analysis of randomized controlled trials

The objective of this study was to analyze randomized controlled trials published in the last decades involving motor intervention as a treatment for dementia, based on Physiotherapy Evidence Database (PEDro) criteria. A database search was performed using the following keywords: randomized controlled trial, dementia, physiotherapy, physical therapy, occupational therapy, physical education, motor approach, exercise, and physical activity. Ten trials were found: 4 related to physiotherapy, 3 to occupational therapy, 1 to physical education, and 2 to interdisciplinary motor intervention. The efficacy of motor intervention was confirmed in the following variables: psychosocial function, physical health and function, affective status, and caregiver's distress (P < .05). Results related to mobility were not significant (P > .05). Behavior, cognitive performance, activities of daily living, and risk of falls were not similar among the articles. From a total score of 10 points, with excellence characterized as the highest punctuation, the articles were classified between 3 and 7 by PEDro. Motor intervention was shown to be an alternative for minimizing physical and mental decline. PEDro has been confirmed as a very reliable tool to analyze studies and as an evaluation criteria, both qualitative and quantitative, allowing the establishment of motor intervention strategies for the treatment of patients with dementia. © 2007 Lippincott Williams & Wilkins, Inc.

Class II malocclusion treatment using high-pull headgear with a splint: a systematic review

Objective: To systematically review the scientific evidence pertaining to the effectiveness of high-pull headgear in growing Class II subjects. Methods: A literature survey was performed by electronic database search. The survey covered the period from January 1966 to December 2008 and used Medical Subject Headings (MeSH). Articles were initially selected based on their titles and abstracts; the full articles were then retrieved. The inclusion criteria included growing subjects between 8 to 15 years of age, Class II malocclusion treatment with high-pull headgear, and a control group with Class II malocclusion. References from selected articles were hand-searched for additional publications. Selected studies were evaluated methodologically. Results: Four articles were selected; none were randomized controlled trials. All of the articles clearly formulated their objectives and used appropriate measures. The studies showed that high-pull headgear treatment improves skeletal and dental relationship, distal displacement of the maxilla, vertical eruption control and upper molars distalization. One of the studies showed a slight clockwise rotation of the palatal plane; the others showed no significant treatment effect. The mandible was not affected by the treatment. Conclusion: While there is still a lack of strong evidence demonstrating the effects of high-pull headgear with a splint, other studies indicate that the AP relations improve due to distalization of the maxilla and upper molars, with little or no treatment effects in the mandible. Greater attention to the design should be given to improve the quality of such trials. © 2013 Dental Press Journal of Orthodontics.

Implants in the zygomatic bone for maxillary prosthetic rehabilitation: a systematic review

The purpose of this systematic review was to evaluate clinical studies on the follow-up survival of implants inserted in the zygomatic bone for maxillary rehabilitation. A comprehensive search of studies published from 2000 to July 2012 and listed in the PubMed/MEDLINE, Embase, and Cochrane Library databases was performed in accordance with the PRISMA statement. Relevant studies were selected according to predetermined inclusion and exclusion criteria. The initial database search yielded 751 titles. After filtering, 313 abstracts were selected, culminating in 42 full text articles. Application of eligibility criteria led to the elimination of 17 articles. Hence 25 full-text articles were considered clinically relevant and were included. Calculations of the interval survival rates and cumulative survival rates of implants could be carried out on the data extracted from the final list of included studies for the different time intervals. These studies reported the insertion of a total of 1541 zygomatic implants and 33 implant failures. Failure generally occurred during the first year interval and was related to clinical complications, such as recurrent acute and chronic sinusitis. After a 36-month follow-up, the survival rate was 97.86%. Additional studies with longer follow-up periods, including the number of zygomatic implants inserted and details of the variations in the surgical techniques used and the impact of the maxillary morphology are still required.

Photodynamic antimicrobial chemotherapy for prevention and treatment of dental caries: a critical review

Introduction: Photodynamic antimicrobial chemotherapy studies regarding dental caries have been present more frequently in the literature. However, photodynamic antimicrobial chemotherapy depends on the adjustment of variables such as the type of light source and, photosensitisers target microorganism; this makes it difficult to draw meaningful comparisons. The purpose of this paper was to provide a critical review related to this coadjuvant approach in the prevention and treatment of dental caries. Materials and Methods: A database search was made via Medline/PubMed (keywords: photodynamic therapy and dental caries) and 33 articles were found. Results: Twelve articles were included after using the filter tool, being excluded reviews and manuscripts reporting works not related to the studied area. Conclusion: The manuscripts showed that photodynamic therapy presents optimal results against dental caries, even though better understanding of photodynamic antimicrobial chemotherapy and its components are necessary before the clinical application of this alternative modality in the dental practice.

Placement of dental implants in the maxillary tuberosity: a systematic review

The aim of this systematic review was to identify clinical studies on implants placed in the tuberosity region to determine the survival rate of these implants when compared to implants placed in other regions of the maxilla. A search for data published up until March 2014 was undertaken using the PubMed, Cochrane Library, Embase, and ScienceDirect databases. Eligible studies were selected according to inclusion and exclusion criteria. The first database search revealed 310 titles. After inclusion and exclusion criteria were applied, five studies remained for the detailed analysis. A total of 113 patients were followed for a period of 6-144 months; 289 implants were placed in the patients evaluated. There were eight failures/losses of dental implants in the tuberosity region; the overall survival rate was 94.63% for these implants. In controlled studies, the cumulative survival rates for implants placed in the maxillary tuberosity and other maxillary regions were 96.1% and 95%, respectively. In conclusion, implants placed into the maxillary tuberosity are a predictable alternative for the treatment of patients with insufficient bone volume in the maxillary region. However, randomized trials are needed to assess the effectiveness of this treatment.

Peptidomics of Three Bothrops Snake Venoms: Insights Into the Molecular Diversification of Proteomes and Peptidomes

Snake venom proteomes/peptidomes are highly complex and maintenance of their integrity within the gland lumen is crucial for the expression of toxin activities. There has been considerable progress in the field of venom proteomics, however, peptidomics does not progress as fast, because of the lack of comprehensive venom sequence databases for analysis of MS data. Therefore, in many cases venom peptides have to be sequenced manually by MS/MS analysis or Edman degradation. This is critical for rare snake species, as is the case of Bothrops cotiara (BC) and B. fonsecai (BF), which are regarded as near threatened with extinction. In this study we conducted a comprehensive analysis of the venom peptidomes of BC, BF, and B. jararaca (BJ) using a combination of solid-phase extraction and reversed-phase HPLC to fractionate the peptides, followed by nano-liquid chromatography-tandem MS (LC-MS/MS) or direct infusion electrospray ionization-(ESI)-MS/MS or MALDI-MS/MS analyses. We detected marked differences in the venom peptidomes and identified peptides ranging from 7 to 39 residues in length by de novo sequencing. Forty-four unique sequences were manually identified, out of which 30 are new peptides, including 17 bradykinin-potentiating peptides, three poly-histidine-poly-glycine peptides and interestingly, 10 L-amino acid oxidase fragments. Some of the new bradykinin-potentiating peptides display significant bradykinin potentiating activity. Automated database search revealed fragments from several toxins in the peptidomes, mainly from L-amino acid oxidase, and allowed the determination of the peptide bond specificity of proteinases and amino acid occurrences for the P4-P4' sites. We also demonstrate that the venom lyophilization/resolubilization process greatly increases the complexity of the peptidome because of the imbalance caused to the venom proteome and the consequent activity of proteinases on venom components. The use of proteinase inhibitors clearly showed different outcomes in the peptidome characterization and suggested that degradomic-peptidomic analysis of snake venoms is highly sensitive to the conditions of sampling procedures. Molecular & Cellular Proteomics 11: 10.1074/mcp.M112.019331, 1245-1262, 2012.

Lipid fingerprinting in women with early-onset preeclampsia: A first look

Objectives: The aim of this preliminary study was to characterize the plasma lipid profiling of women with preeclampsia. Design and methods: Plasma samples of 8 pregnant women with early-onset preeclampsia and 8 normal pregnant women were evaluated. Lipids were extracted from plasma using the Bligh-Dyer protocol. The extracts were subjected to MALDI-MS. Data matrix was exported for partial least squares discriminant analysis (PLS-DA) and a parameter VIP was employed to reflect the variable importance in the discriminant analysis. The major discriminant variables were selected and underwent to Mann-Whitney U test. Results: A total of 1290 ions were initially identified and twelve m/z signals were highlighted as the most important lipids for the discrimination of patients with preeclampsia. The identification of these differential lipids was carried out through Lipid Database Search. Conclusions: The main classes identified were glycerophosphocholines [GP01], glycerophosphoserines [GP03], glycerophosphoglycerols [GP04], glycosyldiradylglycerols [GL05] and glycerophosphates [GP10]. (C) 2012 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

Water-soluble organic compounds in air particulate matter analyzed by HPLC-DAD-MS and HPLC-MS/MS: abundance, sources and transformation of carboxylic acids, nitrophenols and nitrated proteins

Wasserlösliche organische Verbindungen (WSOCs) sind Hauptbestandteile atmosphärischer Aerosole, die bis zu ~ 50% und mehr der organischen Aerosolfraktion ausmachen. Sie können die optischen Eigenschaften sowie die Hygroskopizität von Aerosolpartikeln und damit deren Auswirkungen auf das Klima beeinflussen. Darüber hinaus können sie zur Toxizität und Allergenität atmosphärischer Aerosole beitragen.In dieser Studie wurde Hochleistungsflüssigchromatographie gekoppelt mit optischen Diodenarraydetektion und Massenspektrometrie (HPLC-DAD-MS und HPLC-MS/MS) angewandt, um WSOCs zu analysieren, die für verschiedene Aerosolquellen und -prozesse charakteristisch sind. Niedermolekulare Carbonsäuren und Nitrophenole wurden als Indikatoren für die Verbrennung fossiler Brennstoffe und die Entstehung sowie Alterung sekundärer organischer Aerosole (SOA) aus biogenen Vorläufern untersucht. Protein-Makromoleküle wurden mit Blick auf den Einfluss von Luftverschmutzung und Nitrierungsreaktionen auf die Allergenität primärer biologischer Aerosolpartikel – wie Pollen und Pilzsporen – untersucht.rnFilterproben von Grob- und Feinstaubwurden über ein Jahr hinweg gesammelt und auf folgende WSOCs untersucht: die Pinen-Oxidationsprodukte Pinsäure, Pinonsäure und 3-Methyl-1,2,3-Butantricarbonsäure (3-MBTCA) sowie eine Vielzahl anderer Dicarbonsäuren und Nitrophenole. Saisonale Schwankungen und andere charakteristische Merkmale werden mit Blick auf Aerosolquellen und -senken im Vergleich zu Daten anderen Studien und Regionen diskutiert. Die Verhätlnisse von Adipinsäure und Phthalsäure zu Azelainsäure deuten darauf hin, dass die untersuchten Aerosolproben hauptsächlich durch biogene Quellen beeinflusst werden. Eine ausgeprägte Arrhenius-artige Korrelation wurde zwischen der 3-MBTCA-¬Konzentration und der inversen Temperatur beobachtet (R2 = 0.79, Ea = 126±10 kJ mol-1, Temperaturbereich 275–300 K). Modellrechnungen zeigen, dass die Temperaturabhängigkeit auf eine Steigerung der photochemischen Produktionsraten von 3-MBTCA durch erhöhte OH-Radikal-Konzentrationen bei erhöhten Temperaturen zurückgeführt werden kann. Im Vergleich zur chemischen Reaktionskinetik scheint der Einfluss von Gas-Partikel-Partitionierungseffekten nur eine untergeordnete Rolle zu spielen. Die Ergebnisse zeigen, dass die OH-initiierte Oxidation von Pinosäure der geschwindigkeitsbestimmende Schritt der Bildung von 3-MBTCA ist. 3-MBTCA erscheint somit als Indikator für die chemische Alterung von biogener sekundärer organischer Aerosole (SOA) durch OH-Radikale geeignet. Eine Arrhenius-artige Temperaturabhängigkeit wurde auch für Pinäure beobachtet und kann durch die Temperaturabhängigkeit der biogenen Pinen-Emissionen als geschwindigkeitsbestimmender Schritt der Pinsäure-Bildung erklärt werden (R2 = 0.60, Ea = 84±9 kJ mol-1).rn rnFür die Untersuchung von Proteinnitrierungreaktionen wurde nitrierte Protein¬standards durch Flüssigphasenreaktion von Rinderserumalbumin (BSA) und Ovalbumin (OVA) mit Tetranitromethan (TNM) synthetisiert.Proteinnitrierung erfolgt vorrangig an den Resten der aromatischen Aminosäure Tyrosin auf, und mittels UV-Vis-Photometrie wurde der Proteinnnitrierungsgrad (ND) bestimmt. Dieser ist definiert als Verhältnis der mittleren Anzahl von Nitrotyrosinresten zur Tyrosinrest-Gesamtzahl in den Proteinmolekülen. BSA und OVA zeigten verschiedene Relationen zwischen ND und TNM/Tyrosin-Verhältnis im Reaktionsgemisch, was vermutlich auf Unterschiede in den Löslichkeiten und den molekularen Strukturen der beiden Proteine zurück zu führen ist.rnDie Nitrierung von BSA und OVA durch Exposition mit einem Gasgemisch aus Stickstoffdioxid (NO2) und Ozon (O3) wurde mit einer neu entwickelten HPLC-DAD-¬Analysemethode untersucht. Diese einfache und robuste Methode erlaubt die Bestimmung des ND ohne Hydrolyse oder Verdau der untersuchten Proteine und ernöglicht somit eine effiziente Untersuchung der Kinetik von Protein¬nitrierungs-Reaktionen. Für eine detaillierte Produktstudien wurden die nitrierten Proteine enzymatisch verdaut, und die erhaltenen Oligopeptide wurden mittels HPLC-MS/MS und Datenbankabgleich mit hoher Sequenzübereinstimmung analysiert. Die Nitrierungsgrade individueller Nitrotyrosin-Reste (NDY) korrelierten gut mit dem Gesamt-Proteinnitrierungsgrad (ND), und unterschiedliche Verhältnisse von NDY zu ND geben Aufschluss über die Regioselektivität der Reaktion. Die Nitrierungmuster von BSA und OVA nach Beahndlung mit TNM deuten darauf hin, dass die Nachbarschaft eines negativ geladenen Aminosäurerestes die Tyrosinnitrierung fördert. Die Behandlung von BSA durch NO2 und O3 führte zu anderend Nitrierungemustern als die Behandlung mit TNM, was darauf hindeutet, dass die Regioselektivität der Nitrierung vom Nitrierungsmittel abhängt. Es zeigt sich jedoch, dass Tyrosinreste in Loop-Strukturen bevorzugt und unabhängig vom Reagens nitriert werden.Die Methoden und Ergebnisse dieser Studie bilden eine Grundlage für weitere, detaillierte Untersuchungen der Reaktionskinetik sowie der Produkte und Mechanismen von Proteinnitrierungreaktionen. Sie sollen helfen, die Zusammenhänge zwischen verkehrsbedingten Luftschadstoffen wie Stickoxiden und Ozon und der Allergenität von Luftstaub aufzuklären.rn

Mechanical and technical risks in implant therapy

PURPOSE: To systematically appraise the impact of mechanical/technical risk factors on implant-supported reconstructions. MATERIAL AND METHODS: A MEDLINE (PubMed) database search from 1966 to April 2008 was conducted. The search strategy was a combination of MeSH terms and the key words: design, dental implant(s), risk, prosthodontics, fixed prosthodontics, fixed partial denture(s), fixed dental prosthesis (FDP), fixed reconstruction(s), oral rehabilitation, bridge(s), removable partial denture(s), overdenture(s). Randomized controlled trials, controlled trials, and prospective and retrospective cohort studies with a mean follow-up of at least 4 years were included. The material evaluated in each study had to include cases with/without exposure to the risk factor. RESULTS: From 3,568 articles, 111 were selected for full text analysis. Of the 111 articles, 33 were included for data extraction after grouping the outcomes into 10 risk factors: type of retentive elements supporting overdentures, presence of cantilever extension(s), cemented versus screw-retained FDPs, angled/angulated abutments, bruxism, crown/implant ratio, length of the suprastructure, prosthetic materials, number of implants supporting an FDP, and history of mechanical/technical complications. CONCLUSIONS: The absence of a metal framework in overdentures, the presence of cantilever extension(s) > 15 mm and of bruxism, the length of the reconstruction, and a history of repeated complications were associated with increased mechanical/technical complications. The type of retention, the presence of angled abutments, the crown-implant ratio, and the number of implants supporting an FDP were not associated with increased mechanical/technical complications. None of the mechanical/technical risk factors had an impact on implant survival and success rates.

Curing lights for orthodontic bonding: a systematic review and meta-analysis

INTRODUCTION Light cure of resin-based adhesives is the mainstay of orthodontic bonding. In recent years, alternatives to conventional halogen lights offering reduced curing time and the potential for lower attachment failure rates have emerged. The relative merits of curing lights in current use, including halogen-based lamps, light-emitting diodes (LEDs), and plasma arc lights, have not been analyzed systematically. In this study, we reviewed randomized controlled trials and controlled clinical trials to assess the risks of attachment failure and bonding time in orthodontic patients in whom brackets were cured with halogen lights, LEDs, or plasma arc systems. METHODS Multiple electronic database searches were undertaken, including MEDLINE, EMBASE, and the Cochrane Oral Health Group's Trials Register, CENTRAL. Language restrictions were not applied. Unpublished literature was searched on ClinicalTrials.gov, the National Research Register, Pro-Quest Dissertation Abstracts, and Thesis database. Search terms included randomized controlled trial, controlled clinical trial, random allocation, double blind method, single blind method, orthodontics, LED, halogen, bond, and bracket. Authors of primary studies were contacted as required, and reference lists of the included studies were screened. RESULTS Randomized controlled trials and clinical controlled trials directly comparing conventional halogen lights, LEDs, or plasma arc systems involving patients with full arch, fixed, or bonded orthodontic appliances (not banded) with follow-up periods of a minimum of 6 months were included. Using predefined forms, 2 authors undertook independent extraction of articles; disagreements were resolved by discussion. The assessment of the risk of bias of the randomized controlled trials was based on the Cochrane Risk of Bias tool. Ten studies met the inclusion criteria; 2 were excluded because of high risk of bias. In the comparison of bond failure risk with halogen lights and plasma arc lights, 1851 brackets were included in both groups. Little statistical heterogeneity was observed in this analysis (I(2) = 4.8%; P = 0.379). There was no statistical difference in bond failure risk between the groups (OR, 0.92; 95% CI, 0.68-1.23; prediction intervals, 0.54, 1.56). Similarly, no statistical difference in bond failure risk was observed in the meta-analysis comparing halogen lights and LEDs (OR, 0.96; 95% CI, 0.64-1.44; prediction intervals, 0.07, 13.32). The pooled estimates from both comparisons were OR, 0.93; 95% CI, 0.74-1.17; and prediction intervals, 0.69, 1.17. CONCLUSIONS There is no evidence to support the use of 1 light cure type over another based on risk of attachment failure.

Facts and myths regarding the maxillary midline frenum and its treatment: a systematic review of the literature

OBJECTIVE To systematically review the current literature on the maxillary midline frenum and associated conditions and complications, as well as the recommended treatment options. METHOD AND MATERIALS A detailed MEDLINE database search was carried out to provide evidence about the epidemiology, associated pathologies, and treatment options regarding the maxillary frenum. Of the 206 initially identified articles, 48 met the inclusion criteria. RESULTS The maxillary frenum is highly associated with a number of syndromes and developmental abnormalities. A hypertrophic frenum may be involved in the etiology of the midline diastema. There is also a tendency by orthodontists to suggest posttreatment removal of the frenum (frenectomy). Studies on the cause of gingival recession due to the maxillary frenum are inconclusive. An injured frenum in combination with other traumas and doubtful history might point to child abuse. The involvement of hyperplastic frena in the pathogenesis of peri-implant diseases remains uncertain. There seems to be a clinical interest regarding lasers for surgery for treatment of maxillary frena. The superiority of laser treatment in relation to conventional surgical methods has not yet been demonstrated in the literature. CONCLUSION A maxillary frenum is a clinical symptom in numerous syndromic conditions and plays a role in the development of the median midline diastema. Nevertheless, the contribution to gingival recession and peri-implant diseases in the region of the maxillary incisors is rather controversial. Laser techniques are reported as the method of choice for the surgical removal of frena; however, this needs to be substantiated by appropriate prospective controlled studies.