Methodological improvement of 3D fluoroscopic analysis for the robust quantification of 3D kinematics of human joints

3D video-fluoroscopy is an accurate but cumbersome technique to estimate natural or prosthetic human joint kinematics. This dissertation proposes innovative methodologies to improve the 3D fluoroscopic analysis reliability and usability. Being based on direct radiographic imaging of the joint, and avoiding soft tissue artefact that limits the accuracy of skin marker based techniques, the fluoroscopic analysis has a potential accuracy of the order of mm/deg or better. It can provide fundamental informations for clinical and methodological applications, but, notwithstanding the number of methodological protocols proposed in the literature, time consuming user interaction is exploited to obtain consistent results. The user-dependency prevented a reliable quantification of the actual accuracy and precision of the methods, and, consequently, slowed down the translation to the clinical practice. The objective of the present work was to speed up this process introducing methodological improvements in the analysis. In the thesis, the fluoroscopic analysis was characterized in depth, in order to evaluate its pros and cons, and to provide reliable solutions to overcome its limitations. To this aim, an analytical approach was followed. The major sources of error were isolated with in-silico preliminary studies as: (a) geometric distortion and calibration errors, (b) 2D images and 3D models resolutions, (c) incorrect contour extraction, (d) bone model symmetries, (e) optimization algorithm limitations, (f) user errors. The effect of each criticality was quantified, and verified with an in-vivo preliminary study on the elbow joint. The dominant source of error was identified in the limited extent of the convergence domain for the local optimization algorithms, which forced the user to manually specify the starting pose for the estimating process. To solve this problem, two different approaches were followed: to increase the optimal pose convergence basin, the local approach used sequential alignments of the 6 degrees of freedom in order of sensitivity, or a geometrical feature-based estimation of the initial conditions for the optimization; the global approach used an unsupervised memetic algorithm to optimally explore the search domain. The performances of the technique were evaluated with a series of in-silico studies and validated in-vitro with a phantom based comparison with a radiostereometric gold-standard. The accuracy of the method is joint-dependent, and for the intact knee joint, the new unsupervised algorithm guaranteed a maximum error lower than 0.5 mm for in-plane translations, 10 mm for out-of-plane translation, and of 3 deg for rotations in a mono-planar setup; and lower than 0.5 mm for translations and 1 deg for rotations in a bi-planar setups. The bi-planar setup is best suited when accurate results are needed, such as for methodological research studies. The mono-planar analysis may be enough for clinical application when the analysis time and cost may be an issue. A further reduction of the user interaction was obtained for prosthetic joints kinematics. A mixed region-growing and level-set segmentation method was proposed and halved the analysis time, delegating the computational burden to the machine. In-silico and in-vivo studies demonstrated that the reliability of the new semiautomatic method was comparable to a user defined manual gold-standard. The improved fluoroscopic analysis was finally applied to a first in-vivo methodological study on the foot kinematics. Preliminary evaluations showed that the presented methodology represents a feasible gold-standard for the validation of skin marker based foot kinematics protocols.

Recommendations for monitoring avian populations with point counts: a case study in southeastern Brazil

No hemisfério norte, o censo de aves é fundamental para gerar informações que auxiliam na compreensão de tendências populacionais. Tais censos, devido à marcada sazonalidade deste hemisfério, são realizados durante dois momentos distintos: na estação reprodutiva (aves residentes) e no inverno (quando as aves migratórias deixam determinadas regiões). Na região neotropical, porém, dependendo da localidade, as aves podem se reproduzir durante qualquer ou vários períodos do ano; podem ou não migrar, e aquelas que o fazem podem apresentar um padrão assincrônico. Em contraste com o hemisfério norte, tendências populacionais são desconhecidas, bem como o impacto das taxas rápidas de urbanização e desmatamento, que também são pouco monitoradas. Para melhor entender padrões temporais de riqueza e abundância de aves, e avaliar como um censo similar pode ser implementado na América tropical, foram utilizados pontos de escuta ao longo de 12 meses em uma localidade no Estado de São Paulo, sudeste do Brasil. Os censos ocorreram duas vezes por dia (manhãs/tardes) em uma floresta semidecidual ao longo de transecções com 10 pontos (20 pontos por dia) distantes 200 m entre si e com raio de detecção limitado em 100 m. Ambas as riquezas e abundâncias de aves foram maiores durante as manhãs, mas as curvas de acumulação sugerem que os censos vespertinos com maior esforço amostral podem fornecer resultados similares aos censos matutinos. Riqueza e abundância das aves não variam de acordo com estações (i.e., sem padrão aparente entre reprodução e migração), enquanto espécies exclusivas foram encontradas todos os meses e relativamente poucas espécies (20%) foram registradas em todos os meses do ano. Durante este ano, 84% de todas as aves florestais da área estudada foram registradas. Sugerimos que a metodologia de pontos de escuta pode ser utilizada à semelhança dos censos do hemisfério norte. Recomendamos ainda que o esforço amostral em transecções deva incluir ao menos 20 pontos, e que o início da contagem das aves deva ser sazonal, utilizando o período de migração das espécies austrais (e os seis meses seguintes) para coordenar pontos de escuta. Por último, sugerimos que os censos no Brasil e até mesmo na América Latina podem ajudar no entendimento de tendências populacionais, mas também demandam maior esforço do que o observado em latitudes temperadas, devido à maior riqueza de espécies e diferenças nas dinâmicas de reprodução e migração. Por meio do uso de censos de aves coordenados poderá ser desenvolvida uma técnica para os trópicos que irá gerar informações que permitam acompanhar tendências populacionais, com benefícios para a conservação das aves, similarmente aos censos realizados em países do hemisfério norte.

An investigation of the shortcomings of the CONSORT 2010 statement for the reporting of group sequential randomised controlled trials: a methodological systematic review

Background It can be argued that adaptive designs are underused in clinical research. We have explored concerns related to inadequate reporting of such trials, which may influence their uptake. Through a careful examination of the literature, we evaluated the standards of reporting of group sequential (GS) randomised controlled trials, one form of a confirmatory adaptive design. Methods We undertook a systematic review, by searching Ovid MEDLINE from the 1st January 2001 to 23rd September 2014, supplemented with trials from an audit study. We included parallel group, confirmatory, GS trials that were prospectively designed using a Frequentist approach. Eligible trials were examined for compliance in their reporting against the CONSORT 2010 checklist. In addition, as part of our evaluation, we developed a supplementary checklist to explicitly capture group sequential specific reporting aspects, and investigated how these are currently being reported. Results Of the 284 screened trials, 68(24%) were eligible. Most trials were published in “high impact” peer-reviewed journals. Examination of trials established that 46(68%) were stopped early, predominantly either for futility or efficacy. Suboptimal reporting compliance was found in general items relating to: access to full trials protocols; methods to generate randomisation list(s); details of randomisation concealment, and its implementation. Benchmarking against the supplementary checklist, GS aspects were largely inadequately reported. Only 3(7%) trials which stopped early reported use of statistical bias correction. Moreover, 52(76%) trials failed to disclose methods used to minimise the risk of operational bias, due to the knowledge or leakage of interim results. Occurrence of changes to trial methods and outcomes could not be determined in most trials, due to inaccessible protocols and amendments. Discussion and Conclusions There are issues with the reporting of GS trials, particularly those specific to the conduct of interim analyses. Suboptimal reporting of bias correction methods could potentially imply most GS trials stopping early are giving biased results of treatment effects. As a result, research consumers may question credibility of findings to change practice when trials are stopped early. These issues could be alleviated through a CONSORT extension. Assurance of scientific rigour through transparent adequate reporting is paramount to the credibility of findings from adaptive trials. Our systematic literature search was restricted to one database due to resource constraints.

Application of the comet assay in erythrocytes of Oreochromis niloticus (Pisces): a methodological comparison

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Measurement of melatonin in body fluids: Standards, protocols and procedures

Background and Purpose: The circadian rhythm of melatonin in saliva or plasma, or of the melatonin metabolite 6-sulfatoxymelatonin (a6MTs) in urine, is a defining feature of suprachiasmatic nucleus (SCN) function, the body's endogenous oscillatory pacemaker. The primary objective of this review is to ascertain the clinical benefits and limitations of current methodologies employed for detection and quantification of melatonin in biological fluids and tissues. Data Identification: A search of the English-language literature (Medline) and a systematic review of published articles were carried out. Study Selection: Articles that specified both the methodology for quantifying melatonin and indicated the clinical purpose were chosen for inclusion in the review. Data Extraction: The authors critically evaluated the methodological issues associated with various tools and techniques (e.g. standards, protocols, and procedures). Results of Data Synthesis: Melatonin measurements are useful for evaluating problems related to the onset or offset of sleep and for assessing phase delays or advances of rhythms in entrained individuals. They have also become an important tool for psychiatric diagnosis, their use being recommended for phase typing in patients suffering from sleep and mood disorders. Additionally, there has been a continuous interest in the use of melatonin as a marker for neoplasms of the pineal region. Melatonin decreases such as found with aging are or post pinealectomy can cause alterations in the sleep/wake cycle. The development of sensitive and selective methods for the precise detection of melatonin in tissues and fluids has increasingly been shown to have direct relevance for clinical decision making. Conclusions: Due to melatonin's low concentration, as well as the coexistence of numerous other compounds in the blood, the routine determination of melatonin has been an analytical challenge. The available evidence indicates however that these challenges can be overcome and consequently that evaluation of melatonin's presence and activity can be an accessible and useful tool for clinical diagnosis. © Springer-Verlag 2010.

Fish exposure to nano-TiO2 under different experimental conditions: Methodological aspects for nanoecotoxicology investigations

The ecotoxicology of nano-TiO2 has been extensively studied in recent years; however, few toxicological investigations have considered the photocatalytic properties of the substance, which can increase its toxicity to aquatic biota. The aim of this work was to evaluate the effects on fish exposed to different nano-TiO2 concentrations and illumination conditions. The interaction of these variables was investigated by observing the survival of the organisms, together with biomarkers of biochemical and genetic alterations. Fish (Piaractus mesopotamicus) were exposed for 96h to 0, 1, 10, and 100mg/L of nano-TiO2, under visible light, and visible light with ultraviolet (UV) light (22.47J/cm2/h). The following biomarkers of oxidative stress were monitored in the liver: concentrations of lipid hydroperoxide and carbonylated protein, and specific activities of superoxide dismutase, catalase, and glutathione S-transferase. Other biomarkers of physiological function were also studied: the specific activities of acid phosphatase and Na,K-ATPase were analyzed in the liver and brain, respectively, and the concentration of metallothionein was measured in the gills. In addition, micronucleus and comet assays were performed with blood as genotoxic biomarkers. Nano-TiO2 caused no mortality under any of the conditions tested, but induced sublethal effects that were influenced by illumination condition. Under both illumination conditions tested, exposure to 100mg/L showed an inhibition of acid phosphatase activity. Under visible light, there was an increase in metallothionein level in fish exposed to 1mg/L of nano-TiO2. Under UV light, protein carbonylation was reduced in groups exposed to 1 and 10mg/L, while nucleus alterations in erythrocytes were higher in fish exposed to 10mg/L. As well as improving the understanding of nano-TiO2 toxicity, the findings demonstrated the importance of considering the experimental conditions in nanoecotoxicological tests. This work provides information for the development of protocols to study substances whose toxicity is affected by illumination conditions. © 2013 Elsevier B.V..

Application of the comet assay in erythrocytes of Oreochromis niloticus (Pisces): a methodological comparison

The present study applied the comet assay to erythrocytes of Oreochromis niloticus with the aim of improving protocols to detect DNA damage in these cells, by using two distinct pHs (pH = 12.1 and pH > 13) and evaluating whether there is a correspondence between silver and ethidium bromide staining. Comets were visually examined and, the frequency of cells with and without damage was obtained, as well as the distribution of classes and scores. By using the Kruskal-Wallis test, our results revealed that pH 12.1 is more effective, although both pHs can be used. Our findings also suggest that silver staining can substitute ethidium bromide, an expensive and highly toxic stain that requires specific equipment for examination.

A naturalistic comparison of two right unilateral electroconvulsive therapy dosing protocols: 2-3X seizure threshold versus fixed high-dose

The aim of this study was to compare the outcomes associated with two differing right unilateral (RUL) electroconvulsive therapy (ECT) dosing protocols: 2-3X seizure threshold (2-3X ST) and fixed high dose (FHD) at 353 mC. A retrospective chart review was performed to compare patient outcomes during the implementation of two different dosing protocols: 2-3X ST from October 2000 to May 2001 and FHD from June 2001 to February 2002. A total of 56 patients received ECT under the 2-3X ST protocol, and 46 received ECT under the FHD protocol. In total, 13.6% of patients receiving ECT according to the 2-3X ST protocol received more than 12 ECT, whereas none of the FHD group received more than 12 ECT. The mean number of ECT per treatment course reduced significantly from 7.6 to 5.7 following the switch from the 2-3X ST protocol to the FHD protocol. There were no significant differences between the two groups in the incidence of adverse cognitive effects. ECT practitioners adhered to the 2-3X ST protocol for only 51.8% of ECT courses, with protocol adherence improving to 87% following introduction of the FHD protocol. Although this naturalistic retrospective chart survey had significant methodological limitations, it found that practitioners are more likely to correctly adhere to a fixed dose protocol, therefore, increasing its 'real world' effectiveness in comparison to titrated suprathreshold dosing techniques. The FHD protocol was associated with shorter courses of ECT than the 2-3X ST protocol, with no significant difference between the two protocols in clinically discernable adverse cognitive effects.

Retinal vessel analysis:flicker reproducibility, methodological standardisations and practical limitations

The Retinal Vessel Analyser (RVA) is a commercially available ophthalmoscopic instrument capable of acquiring vessel diameter fluctuations in real time and in high temporal resolution. Visual stimulation by means of flickering light is a unique exploration tool of neurovascular coupling in the human retina. Vessel reactivity as mediated by local vascular endothelial vasodilators and vasoconstrictors can be assessed non-invasively, in vivo. In brief, the work in this thesis • deals with interobserver and intraobserver reproducibility of the flicker responses in healthy volunteers • explains the superiority of individually analysed reactivity parameters over vendorgenerated output • links in static retinal measures with dynamic ones • highlights practical limitations in the use of the RVA that may undermine its clinical usefulness • provides recommendations for standardising measurements in terms of vessel location and vessel segment length and • presents three case reports of essential hypertensives in a -year follow-up. Strict standardisation of measurement procedures is a necessity when utilising the RVA system. Agreement between research groups on implemented protocols needs to be met, before it could be considered a clinically useful tool in detecting or predicting microvascular dysfunction.

Characterization of microplastics ingested by marine benthos - a methodological and field-experimental study

Microplastics have become ubiquitous pollutants in the marine environment. Ingestion of microplastics by a wide range of marine organisms has been recorded both in laboratory and field studies. Despite growing concern for microplastics, few studies have evaluated their concentrations and distribution in wild populations. Further, there is a need to identify cost-effective standardized methodologies for microplastics extraction and analysis in organisms. In this thesis I present: (i) the results of a multi-scale field sampling to quantify and characterize microplastics occurrence and distribution in 4 benthic marine invertebrates from saltmarshes along the North Adriatic Italian coastal lagoons; (ii) a comparison of the effects and cost-effectiveness of two extraction protocols for microplastics isolation on microfibers and on wild collected organisms; (iii) the development of a novel field- based technique to quantify and characterize the microplastic uptake rates of wild and farmed populations of mussels (Mytilus galloprovincialis) through the analysis of their biodeposits. I found very low and patchy amounts of microplastics in the gastrointestinal tracts of sampled organisms. The omnivorous crab Carcinus aestuarii was the species with the highest amounts of microplastics, but there was a notable variation among individuals. There were no substantial differences between enzymatic and alkaline extraction methods. However, the alkaline extraction was quicker and cheaper. Biodeposit traps proved to be an effective method to estimate mussel ingestion rates. However their performance differed significantly among sites, suggesting that the method, as currently designed, is sensible to local environmental conditions. There were no differences in the ingestion rates of microplastics between farmed and wild mussels. The estimates of microplastic ingestion and the validated procedures for their extraction provide a strong basis for future work on microplastic pollution.

A Microleakage Study Of Gutta-percha/ah Plus And Resilon/real Self-etch Systems After Different Irrigation Protocols.

The development and maintenance of the sealing of the root canal system is the key to the success of root canal treatment. The resin-based adhesive material has the potential to reduce the microleakage of the root canal because of its adhesive properties and penetration into dentinal walls. Moreover, the irrigation protocols may have an influence on the adhesiveness of resin-based sealers to root dentin. The objective of the present study was to evaluate the effect of different irrigant protocols on coronal bacterial microleakage of gutta-percha/AH Plus and Resilon/Real Seal Self-etch systems. One hundred ninety pre-molars were used. The teeth were divided into 18 experimental groups according to the irrigation protocols and filling materials used. The protocols used were: distilled water; sodium hypochlorite (NaOCl)+eDTA; NaOCl+H3PO4; NaOCl+eDTA+chlorhexidine (CHX); NaOCl+H3PO4+CHX; CHX+eDTA; CHX+ H3PO4; CHX+eDTA+CHX and CHX+H3PO4+CHX. Gutta-percha/AH Plus or Resilon/Real Seal Se were used as root-filling materials. The coronal microleakage was evaluated for 90 days against Enterococcus faecalis. Data were statistically analyzed using Kaplan-Meier survival test, Kruskal-Wallis and Mann-Whitney tests. No significant difference was verified in the groups using chlorhexidine or sodium hypochlorite during the chemo-mechanical preparation followed by eDTA or phosphoric acid for smear layer removal. The same results were found for filling materials. However, the statistical analyses revealed that a final flush with 2% chlorhexidine reduced significantly the coronal microleakage. A final flush with 2% chlorhexidine after smear layer removal reduces coronal microleakage of teeth filled with gutta-percha/AH Plus or Resilon/Real Seal SE.

Estudo sobre o nivel de participação, num programa de atividade fisica e saude e suas relações com as doenças cronicas não transmissiveis e a qualidade de vida : um estudo de caso

Universidade Estadual de Campinas. Faculdade de Educação Física

Effectiveness of different final irrigation protocols in removing debris in flattened root canals

This study evaluated in vitro the capacity of debris removal from the apical third of flattened root canals, using different final irrigation protocols. Thirty human mandibular central incisors with a mesiodistal flattened root were prepared using rotary instrumentation by Endo-Flare 25.12 and Hero 642 30.06, 35.02, 40.02 files, irrigated with 2 mL of 1% NaOCl after each file. The specimens were randomly distributed into 5 groups according to the final irrigation of root canals: Group I: 10 mL of distilled water (control), Group II: 10 mL of 1% NaOCl for 8 min, Group III: 2 mL of 1% NaOCl for 2 min (repeated 4 times), Group IV: 10 mL of 2.5% NaOCl for 8 min, and Group V: 10 mL of 2.5% NaOCl for 2 min (repeated 4 times). The apical thirds of the specimens were subjected to histological processing and 6-μm cross-sections were obtained and stained with hematoxylin-eosin. The specimens were examined under optical microscopy at ×40 magnification and the images were subjected to morphometric analysis using the Scion image-analysis software. The total area of root canal and the area with debris were measured in square millimeters. Analysis of variance showed no statistically significant difference (p>0.05) among the groups GI (2.39 ± 3.59), GII (2.91 ± 2.21), GIII (0.73 ± 1.36), GIV (0.95 ± 0.84) and GV (0.51 ± 0.22). In conclusion, the final irrigation protocols evaluated in this study using the Luer syringe presented similar performance in the removal of debris from the apical third of flattened root canals.

Temperature of denture base resin under different protocols of microwave irradiation

This in vitro study evaluated the temperature of dentures after different microwave irradiation protocols. Two complete dentures (one maxillary and one mandibular denture) were irradiated separately 4 times for each of the following 5 protocols: dentures immersed in water (G1- 6 min, G2- 3 min); dentures kept dry (G3- 6 min); dentures placed in the steam sterilizer (G4- 6 min, G5- 3 min). The final temperature of the dentures was gauged in a thin and in a thick area of each denture with an infrared thermometer. All groups presented an increase in the resin base temperature. The thin areas of the dentures underwent greater heating than the thick areas. There was no significant difference (p>0.05) between the final mean temperatures of dentures immersed in water for 6 (G1) and 3 min (G2). However, the final mean temperatures recorded in G1 and G2 exceeded 71°C and were significantly higher (<0.001) than the final mean temperatures recorded in the other groups. It may be concluded that denture base resins subjected to microwave irradiation immersed in water may be exposed to deleterious temperatures.

Protocols for obtainment and isolation of two mesenchymal stem cell sources in sheep

PURPOSE: To evaluate different protocols to isolate stem cells from ovine umbilical cord blood and adipose tissue. METHODS: There were used 5 samples of umbilical blood and 5 samples of perirenal adipose tissue from 10 female sheep. All the samples were obtained through surgery, to harvest aseptic samples. There were used 3 protocols for obtainment and culture of umbilical cord blood stem cells and 4 protocols for ovine adipose tissue stem cells. RESULTS: It was possible to observe only one successful protocol for the obtainment of umbilical cord blood stem cells. When analyzing the techniques used to obtain adipose tissue stem cells, only one of the methods was effective as well. Through colony forming unit assay, there were obtained 58 colonies of cells after seven days in culture. Flow citometry tests revealed the cells were positive to CD44 and exhibited negative reaction to CD38, CD45, CD41/61. These cells showed a growth curve with very well defined phases LOG, LAG and PLATEAU. This phases are typically seem in mesenchymal stem cells growth curves. CONCLUSIONS: The isolation and culture of mesenchymal stem cells from ovine umbilical cord blood are complex and request more detailed assays. Stem cells from fat tissue sheep showed mesenchymal characteristics, according to their cell growth curve, ability to origin colonies of fibroblastoid cells and positive reactivity with the antibody CD44 by flow citometry.