How well do regional or national Breeding Bird Survey data predict songbird population trends at an intact boreal site?

A study to monitor boreal songbird trends was initiated in 1998 in a relatively undisturbed and remote part of the boreal forest in the Northwest Territories, Canada. Eight years of point count data were collected over the 14 years of the study, 1998-2011. Trends were estimated for 50 bird species using generalized linear mixed-effects models, with random effects to account for temporal (repeat sampling within years) and spatial (stations within stands) autocorrelation and variability associated with multiple observers. We tested whether regional and national Breeding Bird Survey (BBS) trends could, on average, predict trends in our study area. Significant increases in our study area outnumbered decreases by 12 species to 6, an opposite pattern compared to Alberta (6 versus 15, respectively) and Canada (9 versus 20). Twenty-two species with relatively precise trend estimates (precision to detect > 30% decline in 10 years; observed SE ≤ 3.7%/year) showed nonsignificant trends, similar to Alberta (24) and Canada (20). Precision-weighted trends for a sample of 19 species with both reliable trends at our site and small portions of their range covered by BBS in Canada were, on average, more negative for Alberta (1.34% per year lower) and for Canada (1.15% per year lower) relative to Fort Liard, though 95% credible intervals still contained zero. We suggest that part of the differences could be attributable to local resource pulses (insect outbreak). However, we also suggest that the tendency for BBS route coverage to disproportionately sample more southerly, developed areas in the boreal forest could result in BBS trends that are not representative of range-wide trends for species whose range is centred farther north.

Concordância no diagnóstico radiológico da doença respiratória aguda baixa em crianças

Objetivo: Estudar a concordância no diagnóstico radiológico da doença respiratória aguda baixa (DRAB) em crianças. Métodos: Sessenta radiogramas do tórax de crianças menores de cinco anos foram avaliados, individualmente, por três médicos: um radiologista pediátrico (RP), um pneumologista pediatra (PP) e 1 pediatra experiente no atendimento de sala de emergências (PE). Todas as crianças tinham procurado atendimento por apresentar um quadro agudo de infecção respiratória com aparente participação pulmonar. Os avaliadores desconheciam os diagnósticos originais, mas receberam uma ficha padrão com dados clínicos e laboratoriais dos pacientes no momento da consulta inicial. Variáveis: Agrupadas em cinco categorias: a) qualidade técnica do filme; b) localização da alteração; c) padrões radiográficos; d) outras alterações radiográficas; e) diagnóstico. Análise Estatística: Para estudar a concordância entre as três duplas posíveis de observadores, utilizou-se a estatística de Kappa, aceitándo-se os valores ajustados para viés de prevalência (PABAK). Resultados: Os valores Kappa totais de cada dupla de observadores (RP x PP, RP x PE e PP x PE) foram 0.41, 0.43, e 0.39 respectivamente, o que representa em média, uma concordância interobservadores moderada (0.41). Outras variáveis: “qualidade técnica” teve uma concordância regular (0.30); com “localização”, foi moderada (0.48); com “padrões radiográficos” foi regular (0.29); com “outras alterações radiográficas” foi moderada (0,43); e com “diagnóstico”, regular (0.33). Quanto à concordância global intraobservadores, a mesma foi moderada (0.54), com valores menores dos descritos na literatura. Conclusões: A variabilidade interobservadores é inerente à interpretação dos achados radiológicos, e determinar o diagnóstico exato da DRAB nas crianças tem seus desafíos. Nossos resultados foram similares aos descritos na literatura.

Studio di marcatori immunoistochimici, analisi FISH e ruolo dei microRNA nelle neoplasie gliali di basso e di alto grado

Gliomas are the most common primary brain tumours. Despite advances in surgical techniques, postoperative supportive care, radiation and adjuvant systemic therapy, the life expectancy of patients with high grade glioma has remained essentially poor. Furthermore differential diagnosis among astrocytomas, oligodendrogliomas and oligoastrocytomas is very challenging and subject to inter-observer variability. The purpose of the research was: 1) to investigate a series of high grade and low grade gliomas at gene and protein (immunohistochemistry) levels to disclose possible genetic portraits of malignancy; 2) to verify the utility of Nogo-A, Olig-2 and synaptophysin in providing a correct histological diagnosis of oligodendroglioma and to investigate a possible complementary role in selecting the best areas suitable for detecting 1p/19q codeletion using FISH analysis; 3) to study the role of microRNA in high grade gliomas. In order to obtain these goals large series of brain tumors were studied with DNA microarrays, immunohistochemistry and RT-PCR The results demonstrated that: - Overexpression of IGFBP-2 and CDC20 is highly related to glioblastomas and their immunopositivity can be useful for the identification of glioblastoma in small biopsies. - Nogo-A is the most useful and specific marker in differentiating oigodendrogliomas from other gliomas. Furthermore, using a Nogo-A driven FISH analysis, it is possible to identify a larger number of 1p19q codeletions in gliomas. - microRNAs can be studied in paraffin embedded tissues better than in fresh tissues. A series of six microRNA, significatively deregulated in glioblastomas, may represent a genetic signature with prognostic and predictive value and could constitute candidates for novel anti-cancer therapeutics.

Statistical methods for analysis and processing of medical ultrasound: applications to segmentation and restoration

In this thesis two major topics inherent with medical ultrasound images are addressed: deconvolution and segmentation. In the first case a deconvolution algorithm is described allowing statistically consistent maximum a posteriori estimates of the tissue reflectivity to be restored. These estimates are proven to provide a reliable source of information for achieving an accurate characterization of biological tissues through the ultrasound echo. The second topic involves the definition of a semi automatic algorithm for myocardium segmentation in 2D echocardiographic images. The results show that the proposed method can reduce inter- and intra observer variability in myocardial contours delineation and is feasible and accurate even on clinical data.

Software zur automatischen Tumordiagnose in der funktionalen MRT der weiblichen Brust

In den westlichen Industrieländern ist das Mammakarzinom der häufigste bösartige Tumor der Frau. Sein weltweiter Anteil an allen Krebserkrankungen der Frau beläuft sich auf etwa 21 %. Inzwischen ist jede neunte Frau bedroht, während ihres Lebens an Brustkrebs zu erkranken. Die alterstandardisierte Mortalitätrate liegt derzeit bei knapp 27 %.rnrnDas Mammakarzinom hat eine relative geringe Wachstumsrate. Die Existenz eines diagnostischen Verfahrens, mit dem alle Mammakarzinome unter 10 mm Durchmesser erkannt und entfernt werden, würden den Tod durch Brustkrebs praktisch beseitigen. Denn die 20-Jahres-Überlebungsrate bei Erkrankung durch initiale Karzinome der Größe 5 bis 10 mm liegt mit über 95 % sehr hoch.rnrnMit der Kontrastmittel gestützten Bildgebung durch die MRT steht eine relativ junge Untersuchungsmethode zur Verfügung, die sensitiv genug zur Erkennung von Karzinomen ab einer Größe von 3 mm Durchmesser ist. Die diagnostische Methodik ist jedoch komplex, fehleranfällig, erfordert eine lange Einarbeitungszeit und somit viel Erfahrung des Radiologen.rnrnEine Computer unterstützte Diagnosesoftware kann die Qualität einer solch komplexen Diagnose erhöhen oder zumindest den Prozess beschleunigen. Das Ziel dieser Arbeit ist die Entwicklung einer vollautomatischen Diagnose Software, die als Zweitmeinungssystem eingesetzt werden kann. Meines Wissens existiert eine solche komplette Software bis heute nicht.rnrnDie Software führt eine Kette von verschiedenen Bildverarbeitungsschritten aus, die dem Vorgehen des Radiologen nachgeahmt wurden. Als Ergebnis wird eine selbstständige Diagnose für jede gefundene Läsion erstellt: Zuerst eleminiert eine 3d Bildregistrierung Bewegungsartefakte als Vorverarbeitungsschritt, um die Bildqualität der nachfolgenden Verarbeitungsschritte zu verbessern. Jedes kontrastanreichernde Objekt wird durch eine regelbasierte Segmentierung mit adaptiven Schwellwerten detektiert. Durch die Berechnung kinetischer und morphologischer Merkmale werden die Eigenschaften der Kontrastmittelaufnahme, Form-, Rand- und Textureeigenschaften für jedes Objekt beschrieben. Abschließend werden basierend auf den erhobenen Featurevektor durch zwei trainierte neuronale Netze jedes Objekt in zusätzliche Funde oder in gut- oder bösartige Läsionen klassifiziert.rnrnDie Leistungsfähigkeit der Software wurde auf Bilddaten von 101 weiblichen Patientinnen getested, die 141 histologisch gesicherte Läsionen enthielten. Die Vorhersage der Gesundheit dieser Läsionen ergab eine Sensitivität von 88 % bei einer Spezifität von 72 %. Diese Werte sind den in der Literatur bekannten Vorhersagen von Expertenradiologen ähnlich. Die Vorhersagen enthielten durchschnittlich 2,5 zusätzliche bösartige Funde pro Patientin, die sich als falsch klassifizierte Artefakte herausstellten.rn

Clinical application and reliability of a post abdominal surgery pain assessment scale (PASPAS) in horses

The aim of this study was to refine a multi-dimensional scale based on physiological and behavioural parameters, known as the post abdominal surgery pain assessment scale (PASPAS), to quantify pain after laparotomy in horses. After a short introduction, eight observers used the scale to assess eight horses at multiple time points after laparotomy. In addition, a single observer was used to test the correlation of each parameter with the total pain index in 34 patients, and the effect of general anaesthesia on PASPAS was investigated in a control group of eight horses. Inter-observer variability was low (coefficient of variation 0.3), which indicated good reliability of PASPAS. The correlation of individual parameters with the total pain index differed between parameters. PASPAS, which was not influenced by general anaesthesia, was a useful tool to evaluate pain in horses after abdominal surgery and may also be useful to investigate analgesic protocols or for teaching purposes.

How reliable is Ki-67 immunohistochemistry in grade 2 breast carcinomas? A QA study of the Swiss Working Group of Breast- and Gynecopathologists

Adjuvant chemotherapy decisions in breast cancer are increasingly based on the pathologist's assessment of tumor proliferation. The Swiss Working Group of Gyneco- and Breast Pathologists has surveyed inter- and intraobserver consistency of Ki-67-based proliferative fraction in breast carcinomas. Methods Five pathologists evaluated MIB-1-labeling index (LI) in ten breast carcinomas (G1, G2, G3) by counting and eyeballing. In the same way, 15 pathologists all over Switzerland then assessed MIB-1-LI on three G2 carcinomas, in self-selected or pre-defined areas of the tumors, comparing centrally immunostained slides with slides immunostained in the different laboratoires. To study intra-observer variability, the same tumors were re-examined 4 months later. Results The Kappa values for the first series of ten carcinomas of various degrees of differentiation showed good to very good agreement for MIB-1-LI (Kappa 0.56–0.72). However, we found very high inter-observer variabilities (Kappa 0.04–0.14) in the read-outs of the G2 carcinomas. It was not possible to explain the inconsistencies exclusively by any of the following factors: (i) pathologists' divergent definitions of what counts as a positive nucleus (ii) the mode of assessment (counting vs. eyeballing), (iii) immunostaining technique, and (iv) the selection of the tumor area in which to count. Despite intensive confrontation of all participating pathologists with the problem, inter-observer agreement did not improve when the same slides were re-examined 4 months later (Kappa 0.01–0.04) and intra-observer agreement was likewise poor (Kappa 0.00–0.35). Conclusion Assessment of mid-range Ki-67-LI suffers from high inter- and intra-observer variability. Oncologists should be aware of this caveat when using Ki-67-LI as a basis for treatment decisions in moderately differentiated breast carcinomas.

Graph-Based Multi-Surface Segmentation of OCT Data Using Trained Hard and Soft Constraints

Optical coherence tomography (OCT) is a well-established image modality in ophthalmology and used daily in the clinic. Automatic evaluation of such datasets requires an accurate segmentation of the retinal cell layers. However, due to the naturally low signal to noise ratio and the resulting bad image quality, this task remains challenging. We propose an automatic graph-based multi-surface segmentation algorithm that internally uses soft constraints to add prior information from a learned model. This improves the accuracy of the segmentation and increase the robustness to noise. Furthermore, we show that the graph size can be greatly reduced by applying a smart segmentation scheme. This allows the segmentation to be computed in seconds instead of minutes, without deteriorating the segmentation accuracy, making it ideal for a clinical setup. An extensive evaluation on 20 OCT datasets of healthy eyes was performed and showed a mean unsigned segmentation error of 3.05 ±0.54 μm over all datasets when compared to the average observer, which is lower than the inter-observer variability. Similar performance was measured for the task of drusen segmentation, demonstrating the usefulness of using soft constraints as a tool to deal with pathologies.

Whole-body MRI of multiple myeloma: comparison of different MRI sequences in assessment of different growth patterns

PURPOSE: To determine sensitivity, specificity and inter-observer variability of different whole-body MRI (WB-MRI) sequences in patients with multiple myeloma (MM). METHODS AND MATERIALS: WB-MRI using a 1.5T MRI scanner was performed in 23 consecutive patients (13 males, 10 females; mean age 63+/-12 years) with histologically proven MM. All patients were clinically classified according to infiltration (low-grade, n=7; intermediate-grade, n=7; high-grade, n=9) and to the staging system of Durie and Salmon PLUS (stage I, n=12; stage II, n=4; stage III, n=7). The control group consisted of 36 individuals without malignancy (25 males, 11 females; mean age 57+/-13 years). Two observers independently evaluated the following WB-MRI sequences: T1w-TSE (T1), T2w-TIRM (T2), and the combination of both sequences, including a contrast-enhanced T1w-TSE with fat-saturation (T1+/-CE/T2). They had to determine growth patterns (focal and/or diffuse) and the MRI sequence that provided the highest confidence level in depicting the MM lesions. Results were calculated on a per-patient basis. RESULTS: Visual detection of MM was as follows: T1, 65% (sensitivity)/85% (specificity); T2, 76%/81%; T1+/-CE/T2, 67%/88%. Inter-observer variability was as follows: T1, 0.3; T2, 0.55; T1+/-CE/T2, 0.55. Sensitivity improved depending on infiltration grade (T1: 1=60%; 2=36%; 3=83%; T2: 1=70%; 2=71%; 3=89%; T1+/-CE/T2: 1=50%; 2=50%; 3=89%) and clinical stage (T1: 1=58%; 2=63%; 3=79%; T2: 1=58%; 2=88%; 3=100%; T1+/-CE/T2: 1=50%; 2=63%; 3=100%). T2w-TIRM sequences achieved the best reliability in depicting the MM lesions (65% in the mean of both readers). CONCLUSIONS: T2w-TIRM sequences achieved the highest level of sensitivity and best reliability, and thus might be valuable for initial assessment of MM. For an exact staging and grading the examination protocol should encompass unenhanced and enhanced T1w-MRI sequences, in addition to T2w-TIRM.

Accuracy and reproducibility of aortic annulus sizing using a dedicated three-dimensional computed tomography reconstruction tool in patients evaluated for transcatheter aortic valve replacement

Aims: To evaluate the accuracy and reproducibility of aortic annulus sizing using a multislice computed tomography (MSCT) based aortic root reconstruction tool compared with conventional imaging among patients evaluated for transcatheter aortic valve replacement (TAVR). Methods and results: Patients referred for TAVR underwent standard preprocedural assessment of aortic annulus parameters using MSCT, angiography and transoesophageal echocardiography (TEE). Three-dimensional (3-D) reconstruction of MSCT images of the aortic root was performed using 3mensio (3mensio Medical Imaging BV, Bilthoven, The Netherlands), allowing for semi-automated delineation of the annular plane and assessment of annulus perimeter, area, maximum, minimum and virtual diameters derived from area and perimeter (aVD and pVD). A total of 177 patients were enrolled. We observed a good inter-observer variability of 3-D reconstruction assessments with concordance coefficients for agreement of 0.91 (95% CI: 0.87-0.93) and 0.91 (0.88-0.94) for annulus perimeter and area assessments, respectively. 3-D derived pVD and aVD correlated very closely with a concordance coefficient of 0.97 (0.96-0.98) with a mean difference of 0.5±0.3 mm (pVD-aVD). 3-D derived pVD showed the best, but moderate concordance with diameters obtained from coronal MSCT (0.67, 0.56-0.75; 0.3±1.8 mm), and the lowest concordance with diameters obtained from TEE (0.42, 0.31-0.52; 1.9±1.9 mm). Conclusions: MSCT-based 3-D reconstruction of the aortic annulus using the 3mensio software enables accurate and reproducible assessment of aortic annulus dimensions.

Automatic estimation of noise parameters in Fourier-domain optical coherence tomography cross sectional images using statistical information

We present an application and sample independent method for the automatic discrimination of noise and signal in optical coherence tomography Bscans. The proposed algorithm models the observed noise probabilistically and allows for a dynamic determination of image noise parameters and the choice of appropriate image rendering parameters. This overcomes the observer variability and the need for a priori information about the content of sample images, both of which are challenging to estimate systematically with current systems. As such, our approach has the advantage of automatically determining crucial parameters for evaluating rendered image quality in a systematic and task independent way. We tested our algorithm on data from four different biological and nonbiological samples (index finger, lemon slices, sticky tape, and detector cards) acquired with three different experimental spectral domain optical coherence tomography (OCT) measurement systems including a swept source OCT. The results are compared to parameters determined manually by four experienced OCT users. Overall, our algorithm works reliably regardless of which system and sample are used and estimates noise parameters in all cases within the confidence interval of those found by observers.

Recommendations from GEC ESTRO Breast Cancer Working Group (I): Target definition and target delineation for accelerated or boost Partial Breast Irradiation using multicatheter interstitial brachytherapy after breast conserving closed cavity surgery

OBJECTIVE The aim was to develop a delineation guideline for target definition for APBI or boost by consensus of the Breast Working Group of GEC-ESTRO. PROPOSED RECOMMENDATIONS Appropriate delineation of CTV (PTV) with low inter- and intra-observer variability in clinical practice is complex and needs various steps as: (1) Detailed knowledge of primary surgical procedure, of all details of pathology, as well as of preoperative imaging. (2) Definition of tumour localization before breast conserving surgery inside the breast and translation of this information in the postoperative CT imaging data set. (3) Calculation of the size of total safety margins. The size should be at least 2 cm. (4) Definition of the target. (5) Delineation of the target according to defined rules. CONCLUSION Providing guidelines based on the consensus of a group of experts should make it possible to achieve a reproducible and consistent definition of CTV (PTV) for Accelerated Partial Breast Irradiation (APBI) or boost irradiation after breast conserving closed cavity surgery, and helps to define it after selected cases of oncoplastic surgery.

Epidemiologic and methodological issues in serial measurements of blood pressure: The blood pressure study in Mexican children

The Blood Pressure Study in Mexican Children (BPSMC) is a short term longitudinal study of serial blood pressure collected in three observation periods by standardized examinations of 233 female children, 10 to 12 years of age, enrolled in public and private primary schools in Tlalpan, Mexico. Study objectives were: (1) to describe from baseline information the distribution and relationship of blood pressure to age and selected anthropometric factors, as well as to compare the BPSMC results with other blood pressure studies, (2) to examine the sources and amount of variation present in serial blood pressure of 123 children, and (3) to evaluate observer performance by means of intra- and inter-observer variability.^ Stepwise regression results from baseline revealed that of all anthropometric factors and age, weight was the best predictor for blood pressure.^ The results of serial blood pressure measurements show that, besides the known sources of blood pressure variability (subject, day, reading), the physiologic event of menarche has an important bearing upon the variability and characterization of blood pressure in young girls. The assessment of the effects of blood pressure variability and reliability upon the design and analysis of epidemiologic studies, became apparent among post-menarcheal girls; where blood pressure measurements taken from them have low reliability. Research is needed to propose alternatives for assessing blood pressure during puberty.^ Finally, observer performance of blood pressure and anthropometry were evaluated. Anthropometric measurements had reliabilities in excess of R = 0.96. Acceptable reliabilities (R = 0.88 to 0.95) were obtained for systolic and diastolic (phase 4 and 5) blood pressures. The BPSMC showed a 50 percent decrease in measurement error from the first to the third observation periods. ^

Measuring color differences in automotive samples with lightness flop: a test of the AUDI2000 color-difference formula

From a set of gonioapparent automotive samples from different manufacturers we selected 28 low-chroma color pairs with relatively small color differences predominantly in lightness. These color pairs were visually assessed with a gray scale at six different viewing angles by a panel of 10 observers. Using the Standardized Residual Sum of Squares (STRESS) index, the results of our visual experiment were tested against predictions made by 12 modern color-difference formulas. From a weighted STRESS index accounting for the uncertainty in visual assessments, the best prediction of our whole experiment was achieved using AUDI2000, CAM02-SCD, CAM02-UCS and OSA-GP-Euclidean color-difference formulas, which were no statistically significant different among them. A two-step optimization of the original AUDI2000 color-difference formula resulted in a modified AUDI2000 formula which performed both, significantly better than the original formula and below the experimental inter-observer variability. Nevertheless the proposal of a new revised AUDI2000 color-difference formula requires additional experimental data.

Measuring color differences in gonioapparent materials used in the automotive industry

This paper illustrates how to design a visual experiment to measure color differences in gonioapparent materials and how to assess the merits of different advanced color-difference formulas trying to predict the results of such experiment. Successful color-difference formulas are necessary for industrial quality control and artificial color-vision applications. A color- difference formula must be accurate under a wide variety of experimental conditions including the use of challenging materials like, for example, gonioapparent samples. Improving the experimental design in a previous paper [Melgosaet al., Optics Express 22, 3458-3467 (2014)], we have tested 11 advanced color-difference formulas from visual assessments performed by a panel of 11 observers with normal colorvision using a set of 56 nearly achromatic colorpairs of automotive gonioapparent samples. Best predictions of our experimental results were found for the AUDI2000 color-difference formula, followed by color-difference formulas based on the color appearance model CIECAM02. Parameters in the original weighting function for lightness in the AUDI2000 formula were optimized obtaining small improvements. However, a power function from results provided by the AUDI2000 formula considerably improved results, producing values close to the inter-observer variability in our visual experiment. Additional research is required to obtain a modified AUDI2000 color-difference formula significantly better than the current one.