Evaluating named entity recognition tools for extracting social networks from novels.

The analysis of literary works has experienced a surge in computer-assisted processing. To obtain insights into the community structures and social interactions portrayed in novels, the creation of social networks from novels has gained popularity. Many methods rely on identifying named entities and relations for the construction of these networks, but many of these tools are not specifically created for the literary domain. Furthermore, many of the studies on information extraction from literature typically focus on 19th and early 20th century source material. Because of this, it is unclear if these techniques are as suitable to modern-day literature as they are to those older novels. We present a study in which we evaluate natural language processing tools for the automatic extraction of social networks from novels as well as their network structure. We find that there are no significant differences between old and modern novels but that both are subject to a large amount of variance. Furthermore, we identify several issues that complicate named entity recognition in our set of novels and we present methods to remedy these. We see this work as a step in creating more culturally-aware AI systems.

A lifelong study of a pack Rhodesian ridgeback dogs reveals subclinical and clinical tick-borne Anaplasma phagocytophilum infections with possible reinfection or persistence.

BACKGROUND: Various tick-borne infections often occur without specific clinical signs and are therefore notoriously hard to diagnose separately in veterinary practice. Longitudinal studies over multiple tick seasons performing clinical, serological and molecular investigations in parallel, may elucidate the relationship between infection and disease. In this regard, six related Rhodesian Ridgeback dogs living as a pack became subject of lifetime studies due to ongoing tick infestations and recurring clinical problems. Blood samples for diagnostic tests were obtained throughout the years 2000 to 2009. METHODS: Data collected from clinical observations, hemograms, serology and detection of Anaplasma phagocytophilum, either by microscopy or by DNA amplification and typing, were placed in a time line. This dataset essentially presents as a prospective study enabling the association of the Anaplasma infections with occurring disease. RESULTS: All six dogs were infected, and two of them developed particular clinical symptoms that could be associated with Anaplasma infections over time. More specifically, episodes of general malaise with fever and purpura with thrombocytopenia and bacterial inclusions in granulocytes, were found concurrently with Anaplasma DNA and specific antibodies in peripheral blood samples. DNA from A. phagocytophilum variant 4 (of 16S rRNA) was found in multiple and sequential samples. DNA-sequences from variant 1 and the human granulocytic ehrlichiosis (HGE) agent were also detected. CONCLUSIONS: In this study two lifelong cases of canine anaplasmosis (CGA) are presented. The data show that dogs can be naturally infected concurrently with A. phagocytophilum variant 1, variant 4 and the HGE agent. The ongoing presence of specific antibodies and Anaplasma DNA in one dog indicates one year of persisting infection. Treatment with doxycycline during recurring clinical episodes in the other dog resulted in transient clinical improvement and subsequent disappearance of specific antibodies and DNA suggesting that re-infection occurred.

Effect of Simultaneous Exposure of Pigs to Streptococcus suis Serotypes 2 and 9 on Their Colonization and Transmission, and on Mortality.

The distribution of Streptococcus suis serotypes isolated from clinically infected pigs differs between geographical areas, and varies over time. In several European countries, predomination of serotype 2 has changed to serotype 9. We hypothesize a relation, with one serotype affecting the other in colonization and invasion. The aim of this study was to evaluate whether simultaneous exposure of pigs to serotypes 2 and 9 affects colonization and transmission of each type, and mortality. Thirty-six caesarean-derived/colostrum-deprived piglets were randomly assigned to three groups, and there housed pair-wise. At six weeks old, one pig per pair was inoculated with either one (serotype 2 or 9; mono-group) or two serotypes simultaneously (dual-group); the other pig was contact-exposed. Tonsillar and nasal samples were collected within three weeks post inoculation. Bacterial loads in samples were quantified using multiplex real-time polymerase chain reaction (PCR). Transmission rates of the serotypes among pigs were estimated using a mathematical Susceptible-Infectious (SI) model. Bacterial loads and transmission rates did not differ significantly between serotypes. Compared to the mono-group, in the dual-group the average serotype 2 load in tonsillar samples from contact pigs was reduced on days 1 to 4 and on day 6. Simultaneous exposure to the serotypes reduced the mortality hazard 6.3 times (95% C.I.: 2.0-19.8) compared to exposure to serotype 2 only, and increased it 6.6 times (95% C.I.: 1.4-30.9) compared to exposure to serotype 9 only. This study indicates that serotype 2 load and mortality were affected in pigs exposed to these two serotypes.

Simultaneous Quantification and Differentiation of Streptococcus suis Serotypes 2 and 9 by Quantitative Real-Time PCR, Evaluated in Tonsillar and Nasal Samples of Pigs.

Invasive Streptococcus suis (S. suis) infections in pigs are often associated with serotypes 2 and 9. Mucosal sites of healthy pigs can be colonized with these serotypes, often multiple serotypes per pig. To unravel the contribution of these serotypes in pathogenesis and epidemiology, simultaneous quantification of serotypes is needed. A quantitative real-time PCR (qPCR) targeting cps2J (serotypes 2 and 1/2) and cps9H (serotype 9) was evaluated with nasal and tonsillar samples from S. suis exposed pigs. qPCR specifically detected serotypes in all pig samples. The serotypes loads in pig samples estimated by qPCR showed, except for serotype 9 in tonsillar samples (correlation coefficient = 0.25), moderate to strong correlation with loads detected by culture (correlation coefficient > 0.65), and also in pigs exposed to both serotypes (correlation coefficient > 0.75). This qPCR is suitable for simultaneous differentiation and quantification of important S. suis serotypes.

How psychophysical methods influence optimizations of color difference formulas.

For developing color difference formulas, there are several choices to be made on the psychophysical method used for gathering visual (observer) data. We tested three different psychophysical methods: gray scales, constant stimuli, and two-alternative forced choice (2AFC). Our results show that when using gray scales or constant stimuli, assessments of color differences are biased toward lightness differences. This bias is particularly strong in LCD monitor experiments, and also present when using physical paint samples. No such bias is found when using 2AFC. In that case, however, observer responses are affected by other factors that are not accounted for by current color difference formulas. For accurate prediction of relative color differences, our results show, in agreement with other works, that modern color difference formulas do not perform well. We also investigated if the use of digital images as presented on LCD displays is a good alternative to using physical samples. Our results indicate that there are systematic differences between these two media.

How color difference formulas depend on reference pairs in the underlying constant stimuli experiment.

For calculating color differences, the CIEDE2000 and CIE94 equations are widely used and recommended. These equations were derived more than a decade ago, based for a large part on the RIT-Dupont set of visual data. This data was collected from a series of psychophysical tests that use the method of constant stimuli. In this method, observers need to compare the color difference within a sample pair to that between a reference pair. In the current investigation, we show that the color difference equation significantly changes if reference pairs are chosen in the underlying visual experiments that differ from what was used when creating the RIT-Dupont dataset. The investigation is done using metallic paint samples representing two color centers, red and yellow-green. We show that the reproducibility differs for three different reference pairs, and that for modeling the visual data for the yellow-green color center, extra model terms are required as compared to the CIEDE2000 equation. Our results suggest that observers differ in their ability to mentally convert a color difference recognized in a sample pair into an equivalent color difference along the color difference direction represented by the reference pair. We also find that in these tests the tolerance to lightness differences is widened by a factor of 1.3 to 1.6, and that for the red color center the tolerance ellipsoid is rotated by 30° as compared to the CIEDE2000 equation. The latter observations are possibly due to the metallic texture in the samples used for the current experiment.

3D assessment of stent cell size and side branch access in intravascular optical coherence tomographic pullback runs.

We present a semi-automatic approach to assess the maximum circular unsupported surface area (MCUSA) of selected stent cells and the side branch access through stent cells in intravascular optical coherence tomography (IVOCT) pullback runs. Such 3D information may influence coronary interventions, stent design, blood flow analysis or prognostic evaluation. First, the stent struts are detected automatically and stent cells are reconstructed with users' assistance. Using cylinder fitting, a 2D approximation of the stent cell is generated for MCUSA detection and measurement. Next, a stent surface is reconstructed and stent-covered side branches are detected. Both the stent cell contours and side branch lumen contours are projected onto the stent surface to indicate their areas, and the overlapping regions are measured as the side branch access through these stent cells. The method was evaluated on phantom data sets and the accuracy of the MCUSA and side branch access was found to be 95% and 91%, respectively. The usability of this approach for clinical research was proved on 12 in vivo IVOCT pullback runs.

Effects of chromatic image statistics on illumination induced color differences.

We measure the color fidelity of visual scenes that are rendered under different (simulated) illuminants and shown on a calibrated LCD display. Observers make triad illuminant comparisons involving the renderings from two chromatic test illuminants and one achromatic reference illuminant shown simultaneously. Four chromatic test illuminants are used: two along the daylight locus (yellow and blue), and two perpendicular to it (red and green). The observers select the rendering having the best color fidelity, thereby indirectly judging which of the two test illuminants induces the smallest color differences compared to the reference. Both multicolor test scenes and natural scenes are studied. The multicolor scenes are synthesized and represent ellipsoidal distributions in CIELAB chromaticity space having the same mean chromaticity but different chromatic orientations. We show that, for those distributions, color fidelity is best when the vector of the illuminant change (pointing from neutral to chromatic) is parallel to the major axis of the scene's chromatic distribution. For our selection of natural scenes, which generally have much broader chromatic distributions, we measure a higher color fidelity for the yellow and blue illuminants than for red and green. Scrambled versions of the natural images are also studied to exclude possible semantic effects. We quantitatively predict the average observer response (i.e., the illuminant probability) with four types of models, differing in the extent to which they incorporate information processing by the visual system. Results show different levels of performance for the models, and different levels for the multicolor scenes and the natural scenes. Overall, models based on the scene averaged color difference have the best performance. We discuss how color constancy algorithms may be improved by exploiting knowledge of the chromatic distribution of the visual scene.

Effect of spatial separation of pigs on spread of Streptococcus suis serotype 9.

The spread of an infectious agent in a population can be reduced by interfering in the infectiousness or susceptibility of individuals, and/or in their contact structure. The aim of this study was to quantify the effect of prevention of direct contact between infectious and susceptible pigs on the transmission of Streptococcus suis (S. suis). In three replicate experiments, S. suis-free pigs were housed in boxes either in pairs (25 pairs) or alone (15 pigs). The distance between the boxes was ±1 m. At 7 weeks of age, one pig of each pair was inoculated intranasally with S. suis serotype 9; the other pigs were exposed to S. suis by either direct (pairs) or indirect contact (individually housed pigs). Tonsillar brush and saliva swab samples from all pigs were collected regularly for 4 weeks post inoculation to monitor colonization with S. suis. All inoculated pigs became infected, and their pen mates became colonized within 2 days. Thirteen indirectly exposed pigs became positive within 7-25 days after exposure. The rate of direct transmission ßdir was estimated to be 3.58 per pig per day (95% CI: 2.29-5.60). The rate of indirect transmission increased in time, depending on the cumulative number of days pigs tested positive for the presence of S. suis. The estimate ß'ind was 0.001 (95% CI: 0.0006-0.0017) new infections per pig per day for each day that an infected pig was tested positive for S. suis. We conclude that prevention of direct contact reduces the rate at which susceptible pigs become colonized. Simulation studies using these parameters showed, however, that such intervention measure would not limit S. suis serotype 9 spread in a commercial pig farm to a relevant extent, implying that spatial separation of groups op pigs within a compartment would not be effective on a farm.

Automatic stent strut detection in intravascular optical coherence tomographic pullback runs.

We developed and evaluated an automatic stent strut detection method in intravascular optical coherence tomography (IVOCT) pullback runs. Providing very high resolution images, IVOCT has been rapidly accepted as a coronary imaging modality for the optimization of the stenting procedure and its follow-up evaluation based on stent strut analysis. However, given the large number of struts visible in a pullback run, quantitative three-dimensional analysis is only feasible when the strut detection is performed automatically. The presented method first detects the candidate pixels using both a global intensity histogram and the intensity profile of each A-line. Gaussian smoothing is applied followed by specified Prewitt compass filters to detect the trailing shadow of each strut. Next, the candidate pixels are clustered using the shadow information. In the final step, several filters are applied to remove the false positives such as the guide wire. Our new method requires neither a priori knowledge of the strut status nor the lumen/vessel contours. In total, 10 IVOCT pullback runs from a 1-year follow-up study were used for validation purposes. 18,311 struts were divided into three strut status categories (malapposition, apposition or covered) and classified based on the image quality (high, medium or low). The inter-observer agreement is 95%. The sensitivity was defined as the ratio of the number of true positives and the total number of struts in the expert defined result. The proposed approach demonstrated an average sensitivity of 94%. For malapposed, apposed and covered stent struts, the sensitivity of the method is respectively 91, 93 and 94%, which shows the robustness towards different situations. The presented method can detect struts automatically regardless of the strut status or the image quality, and thus can be used for quantitative measurement, 3D reconstruction and visualization of the stents in IVOCT pullback runs.

Evaluation of cost functions for gray value matching of two-dimensional images in radiotherapy.

In external beam radiotherapy, portal imaging is applied for verification of the patient setup. Current automatic methods for portal image registration, which are often based on segmentation of anatomical structures, are especially successful for images of the pelvic region. For portal images of more complicated anatomical structures, e.g., lung, these techniques are less successful. It is desirable to have a method for image registration that is applicable for a wide range of treatment sites. In this study, a registration method for two-dimensional (2D) registration of portal and reference images based on intensity values was tested on portal images of various anatomical sites. Tests were performed with and without preprocessing (unsharp mask filtering followed by histogram equalization) for 96 image pairs and six cost functions. The images were obtained from treatments of the rectum, salivary gland, brain, prostate, and lung. To get insight into the behavior of the various cost functions, cost function values were computed for each portal image for 20,000 transformations of the corresponding reference image, translating the reference image in a range of +/- 1 cm and rotating +/- 10 degrees with respect to the clinical match. The automatic match was defined as the transformation associated with the global minimum (found by an exhaustive search). Without preprocessing, the registration reliability was low (less than 27%). With preprocessing, about 90% of the matches were successful, with a difference with our gold standard (manual registration) of about 1 mm and 1 degree SD. All tested cost functions performed similarly. However, the number of local minima using mutual information was larger than for the other tested cost functions. A cost function based on the mean product of the corresponding pixel values had the least number of local minima. In conclusion, gray value based registration of portal images is applicable for a wide range of treatment sites. However, pre-processing of the images is essential.