Ventilation/perfusion SPECT or SPECT/CT for lung function imaging in patients with pulmonary emphysema?

PURPOSE To evaluate the utility of attenuation correction (AC) of V/P SPECT images for patients with pulmonary emphysema. MATERIALS AND METHODS Twenty-one patients (mean age 67.6 years) with pulmonary emphysema who underwent V/P SPECT/CT were included. AC/non-AC V/P SPECT images were compared visually and semiquantitatively. Visual comparison of AC/non-AC images was based on a 5-point likert scale. Semiquantitative comparison assessed absolute counts per lung (aCpLu) and lung lobe (aCpLo) for AC/non-AC images using software-based analysis; percentage counts (PC = (aCpLo/aCpLu) × 100) were calculated. Correlation between AC/non-AC V/P SPECT images was analyzed using Spearman's rho correlation coefficient; differences were tested for significance with the Wilcoxon rank sum test. RESULTS Visual analysis revealed high conformity for AC and non-AC V/P SPECT images. Semiquantitative analysis of PC in AC/non-AC images had an excellent correlation and showed no significant differences in perfusion (ρ = 0.986) or ventilation (ρ = 0.979, p = 0.809) SPECT/CT images. CONCLUSION AC of V/P SPECT images for lung lobe-based function imaging in patients with pulmonary emphysema do not improve visual or semiquantitative image analysis.

Pollen and charcoal in lake sediments compared with historically documented forest fires in southern Switzerland since AD 1920

Charcoal in unlaminated sediments dated by 210Pb was analysed by the pollen-slide and thin-section methods. The results were compared with the number and area of forest fires on different spatial scales in the area around Lago di Origlio as listed in the wildfire database of southern Switzerland since AD 1920. The influx of the number of charcoal particles > 75 µm2 in pollen slides correlates well with the number of annual forest fires recorded within a distance of 20-50 km from the coring site. Hence a size-class distinction or an area measurement by image analysis may not be absolutely necessary for the reconstruction of regional fire history. A regression equation was computed and tested against an independent data set. Its use makes it possible to estimate the charcoal area influx (or concentration) from the particle number influx (or concentration). Local fires within a radius of 2 km around the coring site correlate well with the area influx of charcoal particles estimated by the thin-section method measuring the area of charcoal particles larger than 20 000 µm2 or longer than 50 µm. Pollen percentages and influx values suggest that intensive agriculture and Castanea sativa cultivation were reduced 30-40 years ago, followed by an increase of forest area and a development to more natural woodlands. The traditional Castanea sativa cultivation was characterized by a complete use of the biomass produced, so abandonment of chestnut led to an increasing accumulation of dead biomass, thereby raising the fire risk. On the other hand, the pollen record of the regional vegetation does not show any clear response to the increase of fire frequency during the last three decades in this area.

Dish Detection and Segmentation for Dietary Assessment on Smartphones

Diet-related chronic diseases severely affect personal and global health. However, managing or treating these diseases currently requires long training and high personal involvement to succeed. Computer vision systems could assist with the assessment of diet by detecting and recognizing different foods and their portions in images. We propose novel methods for detecting a dish in an image and segmenting its contents with and without user interaction. All methods were evaluated on a database of over 1600 manually annotated images. The dish detection scored an average of 99% accuracy with a .2s/image run time, while the automatic and semi-automatic dish segmentation methods reached average accuracies of 88% and 91% respectively, with an average run time of .5s/image, outperforming competing solutions.

High intratumoral levels of FoxP3+ lymphocytes are associated with better prognosis in primary resected esophageal adenocarcinomas.

Background: Tumor infiltrating T-lymphocytes (TILs) have been shown to play an important prognostic role in many carcinomas. The identification of prognostic relevant morphological or molecular factors is a major area of interest in the diagnostic process and for the treatment of highly aggressive esophageal adenocarcinoma. Studies about the impact of TILs in this tumor have not shown completely congruent results yet. We present a comprehensive study about the clinical and pathological impact of TIL in esophageal adenocarcinomas. Methods: A next generation tissue microarray (TMA) of 117 primary resected esophageal adenocarcinomas was analyzed for CD3+, CD8+ and FoxP3+ TIL using immunohistochemistry. The TMA contained three cores of the tumor center and the tumor periphery per each case. Slides were scanned with a high-resolution scanner (ScanScope CS; Aperio) and an image analysis software (Aperio Image Scope) was used to determine the TIL counts. The results were correlated with clinicopathological parameters. Results: CD3+, CD8+ and FoxP3+ TIL counts showed a significant correlation among each other (p<0.001 each, range: 0.27-0.77). TIL counts were categorized as high and low levels, according to the median. Tumors with high FoxP3+ intratumoral lymphocyte counts were more frequently of lower pT category (p<0.001) and without lymph node metastasis (p=0.04). High levels of FoxP3+ lymphocytes in the tumor center and the periphery were also associated with better prognosis (p<0.001 and p=0.041, respectively) in univariate analysis. A similar prognostic impact was seen for high levels of CD3+ and CD8+ TIL in the tumor center, but not in the periphery (p=0.047 and p=0.011, respectively). In multivariate analysis high central FoxP3+TIL levels were an independent prognostic factor (HR=0.4; p=0.023) which was similar to a combination score of CD3+/CD8+/FoxP3+ TIL (HR=0.54; p=0.027) or CD8+/Foxp3+ TIL (HR=0.052; p=0.020) and superior to pT- and pN category (p>0.05 each). Conclusion: This study demonstrates a significant beneficial prognostic impact of high TIL counts in the tumor center of esophageal adenocarcinomas, in particular with regards to the subpopulation of FoxP3+ and CD8+ T-regulatory cells. The determination of intratumoral lymphocytic counts and application of TIL scores can improve prognostic accuracy of pathologic reports of these tumors and may be helpful for better risk stratification of esophageal adenocarcinoma patients.

Lung Pattern Classification for Interstitial Lung Diseases Using a Deep Convolutional Neural Network

Automated tissue characterization is one of the most crucial components of a computer aided diagnosis (CAD) system for interstitial lung diseases (ILDs). Although much research has been conducted in this field, the problem remains challenging. Deep learning techniques have recently achieved impressive results in a variety of computer vision problems, raising expectations that they might be applied in other domains, such as medical image analysis. In this paper, we propose and evaluate a convolutional neural network (CNN), designed for the classification of ILD patterns. The proposed network consists of 5 convolutional layers with 2×2 kernels and LeakyReLU activations, followed by average pooling with size equal to the size of the final feature maps and three dense layers. The last dense layer has 7 outputs, equivalent to the classes considered: healthy, ground glass opacity (GGO), micronodules, consolidation, reticulation, honeycombing and a combination of GGO/reticulation. To train and evaluate the CNN, we used a dataset of 14696 image patches, derived by 120 CT scans from different scanners and hospitals. To the best of our knowledge, this is the first deep CNN designed for the specific problem. A comparative analysis proved the effectiveness of the proposed CNN against previous methods in a challenging dataset. The classification performance (~85.5%) demonstrated the potential of CNNs in analyzing lung patterns. Future work includes, extending the CNN to three-dimensional data provided by CT volume scans and integrating the proposed method into a CAD system that aims to provide differential diagnosis for ILDs as a supportive tool for radiologists.

Carbohydrate Estimation by a Mobile Phone-Based System Versus Self-Estimations of Individuals With Type 1 Diabetes Mellitus: A Comparative Study

Background: Diabetes mellitus is spreading throughout the world and diabetic individuals have been shown to often assess their food intake inaccurately; therefore, it is a matter of urgency to develop automated diet assessment tools. The recent availability of mobile phones with enhanced capabilities, together with the advances in computer vision, have permitted the development of image analysis apps for the automated assessment of meals. GoCARB is a mobile phone-based system designed to support individuals with type 1 diabetes during daily carbohydrate estimation. In a typical scenario, the user places a reference card next to the dish and acquires two images using a mobile phone. A series of computer vision modules detect the plate and automatically segment and recognize the different food items, while their 3D shape is reconstructed. Finally, the carbohydrate content is calculated by combining the volume of each food item with the nutritional information provided by the USDA Nutrient Database for Standard Reference. Objective: The main objective of this study is to assess the accuracy of the GoCARB prototype when used by individuals with type 1 diabetes and to compare it to their own performance in carbohydrate counting. In addition, the user experience and usability of the system is evaluated by questionnaires. Methods: The study was conducted at the Bern University Hospital, “Inselspital” (Bern, Switzerland) and involved 19 adult volunteers with type 1 diabetes, each participating once. Each study day, a total of six meals of broad diversity were taken from the hospital’s restaurant and presented to the participants. The food items were weighed on a standard balance and the true amount of carbohydrate was calculated from the USDA nutrient database. Participants were asked to count the carbohydrate content of each meal independently and then by using GoCARB. At the end of each session, a questionnaire was completed to assess the user’s experience with GoCARB. Results: The mean absolute error was 27.89 (SD 38.20) grams of carbohydrate for the estimation of participants, whereas the corresponding value for the GoCARB system was 12.28 (SD 9.56) grams of carbohydrate, which was a significantly better performance ( P=.001). In 75.4% (86/114) of the meals, the GoCARB automatic segmentation was successful and 85.1% (291/342) of individual food items were successfully recognized. Most participants found GoCARB easy to use. Conclusions: This study indicates that the system is able to estimate, on average, the carbohydrate content of meals with higher accuracy than individuals with type 1 diabetes can. The participants thought the app was useful and easy to use. GoCARB seems to be a well-accepted supportive mHealth tool for the assessment of served-on-a-plate meals.

Methods for preparing and counting biochemical varves

Four different preparation and counting methods for biochemical varves were compared in order to assess counting errors and to standardize these techniques. The properties of two embedding methods, namely the shock-freeze, freeze-dry and the water-acetone-epoxy-exchange method, are discussed. Varve counts were carried out on fresh sediment and on sediment thin-sections, on the latter by manual and by automated counting using image-analysis software. Counting on fresh sediment and using image-analysis generally underestimated the number of varves, especially in sections with inconspicuous varves. A comparison between multiple varve counts carried out by a single analyst and different analysts showed no significant differences in the mean varve counts.

Inactivation and self -association of CaM kinase: Effects of ATP, substrate binding domains, and isozymic forms

Calcium/calmodulin-dependent protein kinase II (CaM kinase) is a multifunctional Ser/Thr protein kinase, that is highly enriched in brain and is involved in regulating many aspects of neuronal function. We observed that forebrain CaM kinase from crude homogenates, cytosolic fractions and purified preparations inactivates and translocates into the particulate fraction following autophosphorylation. Using purified forebrain CaM kinase as well as recombinant $\alpha$ isozyme, we determined that the formation of particulate enzyme was due to enzyme self-association. The conditions of autophosphorylation determine whether enzyme self-association and/or inactivation will occur. Self-association of CaM kinase is sensitive to pH, ATP concentration, and enzyme autophosphorylation. This process is prevented by saturating concentrations of ATP. However, in limiting ATP, pH is the dominant factor, and enzyme self-association occurs at pH values $\rm{<}7.0.$ Site-specific mutants were produced by substituting Ala for Thr286, Thr253, or Thr305,306 to determine whether these sites of autophosphorylation affect enzyme inactivation and self-association. The only mutation that influenced these processes was Ala286, which removed the protective effect afforded by autophosphorylation in saturating ATP. Enzyme inactivation occurs in the presence and absence of self-association and appears predominantly sensitive to nucleotide concentration, because saturating concentrations of $\rm Mg\sp{2+}/ADP$ or $\rm Mg\sp{2+}/ATP$ prevent this process. These data implicate the ATP binding pocket in both inactivation and self-association. We also observed that select peptide substrates and peptide inhibitors modeled after the autoregulatory domain of CaM kinase prevented these processes. The $\alpha$ and $\beta$ isozymes of CaM kinase were characterized independently, and were observed to exhibit differences in both enzyme inactivation and self-association. The $\beta$ isozyme was less sensitive to inactivation, and was never observed to self-associate. Biophysical characterization, and transmission electron microscopy coupled with image analysis indicated both isozymes were multimeric, however, the $\alpha$ and $\beta$ isozymes appeared structurally different. We hypothesize that the $\alpha$ subunit of CaM kinase plays both a structural and enzymatic role, and the $\beta$ subunit plays an enzymatic role. The ramifications for the functional differences observed for inactivation and self-association are discussed based on potential structural differences and autoregulation of the $\alpha$ and $\beta$ isozymes in both calcium-induced physiological and pathological processes. ^

Faecal pellet production of copepoda collected in water depth up to 30 meters in the eastern Mediterranean Sea in Oktober 2008 during SES_GR2

Mesozooplankton is collected by vertical tows within the Black sea water body mass layer in the NE Aegean, using a WP-2 200 µm net equipped with a large non-filtering cod-end (10 l). Macrozooplankton organisms are removed using a 2000 µm net. A few unsorted animals (approximately 100) are placed inside several glass beaker of 250 ml filled with GF/F or 0.2 µm Nucleopore filtered seawater and with a 100 µm net placed 1 cm above the beaker bottom. Beakers are then placed in an incubator at natural light and maintaining the in situ temperature. After 1 hour pellets are separated from animals and placed in separated flasks and preserved with formalin. Pellets are counted and measured using an inverted microscope. Animals are scanned and counted using an image analysis system. Carbon- Specific faecal pellet production is calculated from a) faecal pellet production, b) individual carbon: Animals are scanned and their body area is measured using an image analysis system. Body volume is then calculated as an ellipsoid using the major and minor axis of an ellipse of same area as the body. Individual carbon is calculated from a carbon- total body volume of organisms (relationship obtained for the Mediterranean Sea by Alcaraz et al. (2003) divided by the total number of individuals scanned and c) faecal pellet carbon: Faecal pellet length and width is measured using an inverted microscope. Faecal pellet volume is calculated from length and width assuming cylindrical shape. Conversion of faecal pellet volume to carbon is done using values obtained in the Mediterranean from: a) faecal pellet density 1,29 g cm**3 (or pg µm**3) from Komar et al. (1981); b) faecal pellet DW/WW=0,23 from Elder and Fowler (1977) and c) faecal pellet C%DW=25,5 Marty et al. (1994).

El color en las aceitunas negras naturales de mesa : nueva técnica de mensura digitalizada para optimizar el método de oscurecimiento natural

Se aplicó un nuevo método para la evaluación objetiva del color en aceitunas de mesa, basado en el análisis de la intensidad de reflexión de cada uno de los colores primarios que componen la luz blanca (rojo, verde y azul), según las longitudes de onda del Sistema RGB. Se trabajó con programas informáticos para el análisis de imágenes digitales color tipo BMP de 24 bits. Este trabajo proporciona mayor información sobre el pardeamiento de las aceitunas naturales en salmuera, lo que sería muy útil para incrementar la efectividad del proceso. El método propuesto es rápido y no destructivo, prometiendo ser muy práctico ya que permite que una misma muestra pueda ser evaluada en el tiempo. Se investigaron los cambios de color en aceitunas elaboradas naturalmente, con diferentes grados de madurez (pintas, rojas y negras) y a diferentes valores de pH (3,6 - 4,0 - 4,5), expuestas al aire durante períodos crecientes de tiempo. Se cuantificó el grado de oscurecimiento a través de Índices de Intensidad de Reflexión. La evolución del índice de reflexión en función del tiempo generó una curva polinomial de 4° grado que reveló el comportamiento sigmoidal del fenómeno de pardeamiento enzimático, con la máxima correlación a las 8 horas de aireación. Esta función permitiría predecir el fenómeno de pardeamiento en las aceitunas negras y representa una medición objetiva del grado relativo de pardeamiento. La evolución del color rojo (λ = 700,0 nm) exhibió la mayor correlación con el proceso de pardeamiento. Las aceitunas rojas naturales a pH 4,5 presentaron óptimo pardeamiento. El espectro de reflexión para el color azul (λ = 435,8 nm) se sugiere como medida de la actividad de la enzima PPO (polifenoloxidasa).

Mensura digitalizada de la evolución del color en aceitunas según el grado de madurez del fruto

Se desarrolló un nuevo método para la valoración objetiva del color en las aceitunas, mediante el análisis de la intensidad de la reflexión de los colores primarios (rojo, verde y azul) que componen la luz blanca. Se trabajó con programas informáticos para el análisis de imágenes digitales color tipo BMP de 24 bits. Este método es rápido, objetivo, no destructivo y puede ser muy útil cuando se requiere una técnica eficiente para determinar el grado de madurez de las aceitunas o de otros alimentos.

Mass estimates and morphometric meassurements of Discoaster species and Sphenolithus from Ceara Rise ODP Site 927

Mass estimates for Late Miocene and Pliocene (8.6-3.25 Ma) Discoaster species and Sphenolithus are determined using samples of the equatorial Atlantic (Ceara Rise: ODP Site 927). Based on morphometric measurements, 3D computer models were created for 11 Discoaster species and their volumes calculated. From these, shape factors (ks) were derived to allow calculation of mass for different-sized discoasters and Sphenolithus abies. The mass estimates were then used to calculate the contribution of nannofossils to the total nannofossil carbonate. The discoaster contribution ranges from 10% to 40%, with a decreasing trend through the investigated interval. However, our estimates of total nannofossil carbonate from size-corrected abundance data are consistently 30-50% lower than estimates from grain-size measurement; this suggests that data based on mass estimates need to be interpreted with caution.