Comparing empirical ROC curves using a Java application: CERCUS

Receiver Operating Characteristic (ROC) analysis is a methodology that has gained much popularity in our days, especially in Medicine, since through the ROC curves, it provides a useful tool to evaluate and specify problems in the performance of a diagnostic indicator. The area under empirical ROC curve (AUC) it’s an indicator that can be used to compare two or more ROC curves. This work arose from the necessity of the existence of software that allows the calculation of the necessary measures to compare systems based on ROC curves. Several software, commercial and non-commercial, are available to perform the calculation of the measures associated to the ROC analysis. However, they present some flaws, especially when there is a need to compare independent samples with different dimensions, or also to compare two ROC curves that intersect. In this paper is presented a new application called CERCUS (Comparison of Empirical ROC Curves). This was developed using a programming language (Java) and stands out for the possibility of comparing two or more ROC curves that cross each other. The main objective of CERCUS is the calculation of several ROC estimates using different methods and make the ROC curves comparison, even if there is an intersection, either for independent or paired samples. It also allows the graph representation of the ROC curve in a unitary plan as well the graph of the area between curves in comparison. This paper presents the program’s versatility in data entry, test menus and visualization of graphs and results.This work has been supported by FCT – Fundação para a Ciência e Tecnologia within the Project Scope: UID/CEC/00319/201

Optical clearing methods: An overview of the techniques used for the imaging of 3D spheroids

Spheroids have emerged as in vitro models that reproduce in a great extent the architectural microenvironment found in human tissues. However, the imaging of 3D cell cultures is highly challenging due to its high thickness, which results in a light-scattering phenomenon that limits light penetration. Therefore, several optical clearing methods, widely used in the imaging of animal tissues, have been recently explored to render spheroids with enhanced transparency. These methods are aimed to homogenize the microtissue refractive index (RI) and can be grouped into four different categories, namely (a) simple immersion in an aqueous solution with high RI; (b) delipidation and dehydration followed by RI matching; (c) delipidation and hyperhydration followed by RI matching; and (d) hydrogel embedding followed by delipidation and RI matching. In this review, the main optical clearing methods, their mechanism of action, advantages, and disadvantages are described. Furthermore, the practical examples of the optical clearing methods application for the imaging of 3D spheroids are highlighted.info:eu-repo/semantics/publishedVersio

Glutathione status and antioxidant enzymes in a crocodilian species from the swamps of the Brazilian Pantanal

AbstractIn a previous study oxidative damage markers – lipid peroxidation and protein oxidation – were determined in organs of wild Caiman yacare captured in winter-2001 and summer-2002 at various developmental stages. An increase in oxidative damage occurred in the hatchling-juvenile transition (but not in the juvenile-adult transition) and winter–summer transition (in juveniles), suggesting that oxidative stress is associated with development and season. Herein the effect of development and season on glutathione (GSH) metabolism and the effect of development on the activity of antioxidant enzymes (catalase, glutathione peroxidase, glutathione reductase and glutathione S-transferase) and glucose 6-phosphate dehydrogenase were analyzed. The ratio GSSG:GSH-eq increased in lung, liver, kidney and brain by 1.8- to 4-fold in the embryo/hatchling to juvenile transition. No changes occurred in juvenile–adult transition. GSSG:GSH-eq across seasons was significantly elevated in summer. Total-glutathione content was mostly stable in various organs; in liver it increased in the embryo–juvenile transition. Enzyme activities were only determined in summer-animals (embryos, hatchlings and juveniles). For most antioxidant enzymes, activities increased from embryo/hatchling to juvenile in liver and Kidney. In lung, there was an inverse trend for enzyme activities and total glutathione content. Thus, increased metabolic rates during early caiman growth – in embryo–juvenile transition – appears to be related to redox imbalance as suggested by increased GSSG:GSH-eq and activation of antioxidant defenses. Differences in oxidative stress across seasons were related with summer–winter nocturnal temperatures. These results, as a whole, were interpreted in the context of ecological biochemistry

PRÉ-HABILITAÇÃO E PROGNÓSTICO PÓS-OPERATÓRIO EM DOENTES ONCOLÓGICOS DE ALTO RISCO: UMA REVISÃO SISTEMÁTICA E META-ANÁLISE

Introduction. Prehabilitation aims to optimize patients before surgical treatment in order to improve postsurgical recovery. While its efficacy to improve major postoperative clinical outcomes have been recognized for the broader low-risk surgical population, it remains unclear if the high-risk surgical population also benefits. This meta-analysis assessed the impact of prehabilitation on postoperative outcomes in high-risk surgical cancer patients Methodology: We searched for experimental (randomized and non- randomized) and observational studies investigating the impact of prehabilitation in the frequency and/or severity (e.g minor and major complications) of post-surgical complications (primary outcome), type of complications, functional capacity, hospital readmissions, length of hospital stay and 30 day post-surgical mortality (secondary outcomes). High-risk patients for adverse surgical events were defined as frail and / or age ≥70 years and / or with an ASA score of >III. Results: 136 articles were found, of which only 6 were eligible for qualitative and quantitative evaluation (3 randomized and 3 observational studies). The analysis resulted in a total of 674 participants, with an average age of 78 years, mostly male. Prehabilitation resulted in a lower risk of major complications (risk difference –0.09, 95% CI: –0.15, – 0.03, p = 0.005; i2 = 27%, p = 0.24) and surgical complications (RR 0.62, 95% CI 0.43 to 0.89, p=0.01; I2 = 33%, p = 0.22) in comparison to patients receiving standard care. Also, prehabilitation reduced the length of hospital stay (mean difference of – 2.7, 95% CI: –5.37 to –0.17, p = 0.04) and improved functional recovery as assessed by the distance covered in the 6 MWT (mean difference 29.06 meters, 95% CI 26.55 to 31.57, I2 = 42%, p < 0.001). No differences were observed for the rate of overall complications, medical complications 30-day postoperative mortality or hospital readmission. Conclusion: Our work suggests that prehabilitation is effective in reducing postoperative burden in high-risk cancer patients. Future randomized controlled trials for the high-risk surgical patients, using well-established and clinically relevant outcome measures, and with appropriate sample size calculation are needed.Introdução: A pré-habilitação visa otimizar os doentes antes do tratamento cirúrgico, com o objetivo de melhorar a sua recuperação pós-cirúrgica. Embora a eficácia desta intervenção para melhorar os principais desfechos clínicos pós-operatórios tenha sido reconhecida para a população cirúrgica de baixo risco, ainda não está claro até que ponto estes benefícios serão extensíveis também para doentes considerados de alto risco. Esta meta-análise avaliou o impacto da pré-habilitação em desfechos pós-operatórios de doentes oncológicos cirúrgicos de alto risco. Metodologia: Procuramos estudos experimentais (randomizados e não randomizados) e observacionais que avaliaram o impacto da pré-habilitação na frequência e / ou gravidade (major e minor) das complicações pós-cirúrgicas (desfecho primário), tipo de complicações, capacidade funcional, readmissões hospitalares, tempo de hospitalização e mortalidade pós-cirúrgica até 30 dias (desfechos secundários). Doentes de alto risco para eventos cirúrgicos adversos foram definidos como frágeis e / ou com idade ≥70 anos e / ou com score ASA> III. Resultados: foram encontrados 136 artigos, dos quais apenas 6 foram elegíveis para avaliação qualitativa e quantitativa (3 estudos randomizados e 3 estudos observacionais). A análise global incluiu um total de 674 participantes, com idade média de 78 anos, a maioria do sexo masculino. A pré-habilitação reduziu o risco de complicações major (diferença do risco –0,09, IC 95%: –0,15, – 0,03, p = 0,005; i2 = 27%, p = 0,24) e de complicações cirúrgicas (RR 0,62, IC 95% 0,43 a 0,89, p = 0,01; I2 = 33%, p = 0,22) em comparação com doentes que receberam o tratamento habitual. Além disso, a pré-habilitação reduziu o tempo de hospitalização (diferença média de – 2,7, IC 95%: –5,37 a –0,17, p = 0,04) e melhorou a recuperação funcional avaliada pela distância percorrida no teste de marcha de 6 minutos (diferença média de 29,06 metros, IC de 95% 26,55 a 31,57, I2 = 42%, p <0,001). Não foram observadas diferenças para as complicações gerais, complicações médicas, mortalidade pós-operatória até 30 dias ou na readmissão hospitalar. Conclusão: O nosso trabalho sugere que a pré-habilitação é eficaz na melhoria do prognóstico pós-operatório de doentes oncológicos considerados de “alto risco” para complicações cirúrgicas. Ficou evidente a necessidade de desenvolver ensaios clínicos randomizados especialmente focados em doentes cirúrgicos de alto risco, usando medidas de desfecho bem estabelecidas e clinicamente relevantes, e com cálculo de tamanho amostral adequado

Non-invasive assessment of peri-implant mucosal thickness: A cross-sectional study.

BACKGROUND This study aimed to evaluate the reliability and reproducibility of different non-invasive methods for the assessment of peri-implant mucosal thickness. METHODS Subjects with two adjacent dental implants in the central maxillary region were included in this study. Three different methods to assess facial mucosal thickness (FMT) were compared: digital file superimposition using Digital Imaging and Communication in Medicine (DICOM) and stereolithography (STL) files of the arch of interest (DICOM-STL), DICOM files alone, and non-ionizing ultrasound (US). Inter-rater reliability agreements between different assessment methods were analyzed using inter-class correlation coefficients (ICCs). RESULTS A total of 50 subjects with 100 bone-level implants constituted the study population. Assessment of FMT using STL and DICOM files demonstrated excellent inter-rater reliability agreement. Mean ICC values of 0.97 and 0.95 were observed in the DICOM-STL and DICOM groups, respectively. Comparison between the DICOM-STL and US revealed good agreement, with an ICC of 0.82 (95% CI: 0.74 to 0.88) and a mean difference of -0.13 ± 0.50 mm (-1.13 to 0.86). Comparison between DICOM files alone versus US showed good agreement, with an ICC of 0.81 (95% CI: 0.73 to 0.89) and a mean difference of -0.23 ± 0.46 mm (-1.12 to 0.67). Comparison between DICOM-STL and DICOM files revealed excellent agreement, with an ICC of 0.94 (95% CI: 0.91 to 0.96) and a mean difference of 0.1 ± 0.29 mm (LOA -0.47 to 0.46). CONCLUSIONS Quantification of peri-implant mucosal thickness via analysis of DICOM-STL files, DICOM files, or US assessment are comparably reliable and reproducible methods

The liver transcriptome of suckermouth armoured catfish (Pterygoplichthys anisitsi, Loricariidae) : identification of expansions in defensome gene families

© The Author(s), 2016. This is the author's version of the work. It is posted here under a nonexclusive, irrevocable, paid-up, worldwide license granted to WHOI. It is made available for personal use, not for redistribution. The definitive version was published in Marine Pollution Bulletin 115 (2017): 352-361, doi:10.1016/j.marpolbul.2016.12.012.Pterygoplichthys is a genus of related suckermouth armoured catfish native to South America that has invaded tropical and subtropical regions worldwide. Physiological features, including an augmented resistance to organic xenobiotics, may have aided their settlement in foreign habitats. The liver transcriptome of Pterygoplichthys anisitsi was sequenced and used to characterize the diversity of mRNAs potentially involved in the responses to natural and anthropogenic chemicals. In total, 66,642 transcripts were assembled. Among the identified defensome genes, cytochromes P450 (CYP) were the most abundant, followed by nuclear receptors (NR), sulfotransferases (SULT) and ATP binding cassette transporters (ABC). A novel expansion in the CYP2Y subfamily was identified, as well as an independent expansion of the CYP2AAs. Two expansions were also observed among SULT1. Thirty-nine transcripts were classified into twelve subfamilies of NR, while 21 encoded ABC transporters. The diversity of defensome transcripts sequenced herein could contribute to this species resistance to organic xenobiotics.This study was supported by a PEER grant from USAID (PGA-2000003446 and PGA-2000004790) associated with NSF grant DEB-1120263. T.E.P, D.A.M, and M.G.P.M receives independent fellowships from the Brazilian funding agency CAPES

Actualización SIOSE en Andalucía 2009

Tras la finalización a finales de 2009 del proyecto SIOSE 2005 en Andalucía, se denota un alto grado de desactualización de la cartografía, en especial para las funciones de apoyo a la gestión a las que en principio estaba destinada. Es por ello que el lanzamiento de un nuevo proyecto de actualización de SIOSE a nivel estatal por parte de la Dirección General del Instituto Geográfico Nacional es percibido como una oportunidad para actualizar asimismo la base de referencia SIOSE Andalucía 1:10.000. Valiéndonos de la experiencia adquirida, se propone acometer una actualización metodológica que participe de la hoja de ruta trazada en la primera versión en muchos aspectos (colaboración entre Administraciones, uso de procedimientos técnicos desarrollados ex profeso, fotointerpretación descentralizada…), mejorándola en otros. Además, para poder dotar a las bases de esta dimensión gerenciales imprescindible que los plazos de ejecución no provoquen una brecha temporal que haga que las bases nazcan desactualizadas. Por tanto, además de la optimización de los recursos económicos, tan escasos en estos momentos, hay que procurar la maximización de la productividad, sin olvidar un elevado nivel de calidad de los productos finales, que garantice la compleción y la veracidad de los datos ofrecidos.On accomplishing the Andalusian project SIOSE 2005 in late 2009, the cartography is perceived highly outdated, especially regarding its suitability for management support, for which it was initially conceived. This is why the release of an update project for SIOSE at national level, supported by Directorate General of the National Geographic Institute, is seen as an opportunity for also updating de Andalusia’s SIOSE reference database on a 1:10.000 scale. Leaning on the experience acquired to this point, we propose to tackle a methodological update that could be integrated within the first release’s roadmap in many aspects (cooperation between administrations, use of specifically developed technical procedures, decentralized photo interpretation…), but also improving it in many others. Moreover, to be able to provide the databases with this managerial scope, it is essential that the implementation schedule avoid time gaps causing them to be outdated on their very release. Therefore, as well as optimizing economic resources, so limited for the time being, we have to focus on maximizing productivity, without neglecting a high-end product quality guaranteeing comprehensiveness and veracity of the offered data