Computing Storyline Visualizations with Few Block Crossings

Storyline visualizations show the structure of a story, by depicting the interactions of the characters over time. Each character is represented by an x-monotone curve from left to right, and a meeting is represented by having the curves of the participating characters run close together for some time. There have been various approaches to drawing storyline visualizations in an automated way. In order to keep the visual complexity low, rather than minimizing pairwise crossings of curves, we count block crossings, that is, pairs of intersecting bundles of lines. Partly inspired by the ILP-based approach of Gronemann et al. [GD 2016] for minimizing the number of pairwise crossings, we model the problem as a satisfiability problem (since the straightforward ILP formulation becomes more complicated and harder to solve). Having restricted ourselves to a decision problem, we can apply powerful SAT solvers to find optimal drawings in reasonable time. We compare this SAT-based approach with two exact algorithms for block crossing minimization, using both the benchmark instances of Gronemann et al. and random instances. We show that the SAT approach is suitable for real-world instances and identify cases where the other algorithms are preferable.Comment: Appears in the Proceedings of the 25th International Symposium on Graph Drawing and Network Visualization (GD 2017

Illuminating Choices for Library Prep: A Comparison of Library Preparation Methods for Whole Genome Sequencing of Cryptococcus neoformans Using Illumina HiSeq.

The industry of next-generation sequencing is constantly evolving, with novel library preparation methods and new sequencing machines being released by the major sequencing technology companies annually. The Illumina TruSeq v2 library preparation method was the most widely used kit and the market leader; however, it has now been discontinued, and in 2013 was replaced by the TruSeq Nano and TruSeq PCR-free methods, leaving a gap in knowledge regarding which is the most appropriate library preparation method to use. Here, we used isolates from the pathogenic fungi Cryptococcus neoformans var. grubii and sequenced them using the existing TruSeq DNA v2 kit (Illumina), along with two new kits: the TruSeq Nano DNA kit (Illumina) and the NEBNext Ultra DNA kit (New England Biolabs) to provide a comparison. Compared to the original TruSeq DNA v2 kit, both newer kits gave equivalent or better sequencing data, with increased coverage. When comparing the two newer kits, we found little difference in cost and workflow, with the NEBNext Ultra both slightly cheaper and faster than the TruSeq Nano. However, the quality of data generated using the TruSeq Nano DNA kit was superior due to higher coverage at regions of low GC content, and more SNPs identified. Researchers should therefore evaluate their resources and the type of application (and hence data quality) being considered when ultimately deciding on which library prep method to use

Towards reference values of pericoronary adipose tissue attenuation:impact of coronary artery and tube voltage in coronary computed tomography angiography

Objectives: To determine normal pericoronary adipose tissue mean attenuation (PCATMA) values for left the anterior descending (LAD), left circumflex (LCX), and right coronary artery (RCA) in patients without plaques on coronary CT angiography (cCTA), taking into account tube voltage influence. Methods: This retrospective study included 192 patients (76 (39.6%) men; median age 49 years (range, 19–79)) who underwent cCTA with third-generation dual-source CT for the suspicion of CAD between 2015 and 2017. We selected patients without plaque on cCTA. PCATMA was measured semi-automatically on cCTA images in the proximal segment of the three main coronary arteries with 10 mm length. Paired t-testing was used to compare PCATMA between combinations of two coronary arteries within each patient, and one-way ANOVA testing was used to compare PCATMA in different kV groups. Results: The overall mean ± standard deviation (SD) PCATMA was − 90.3 ± 11.1 HU. PCATMA in men was higher than that in women: − 88.5 ± 10.5 HU versus − 91.5 ± 11.3 HU (p = 0.001). PCATMA of LAD, LCX, and RCA was − 92.4 ± 11.6 HU, − 88.4 ± 9.9 HU, and − 90.2 ± 11.4 HU, respectively. Pairwise comparison of the arteries showed significant difference in PCATMA: LAD and LCX (p < 0.001), LAD and RCA (p = 0.009), LCX and RCA (p = 0.033). PCATMA of the 70 kV, 80 kV, 90 kV, 100 kV, and 120 kV groups was − 95.6 ± 9.6 HU, − 90.2 ± 11.5 HU, − 87.3 ± 9.9 HU, − 82.7 ± 6.2 HU, and − 79.3 ± 6.8 HU, respectively (p < 0.001). Conclusions: In patients without plaque on cCTA, PCATMA varied by tube voltage, with minor differences in PCATMA between coronary arteries (LAD, LCX, RCA). PCATMA values need to be interpreted taking into account tube voltage setting. Key Points: • In patients without plaque on cCTA, PCATMAdiffers slightly by coronary artery (LAD, LCX, RCA). • Tube voltage of cCTA affects PCATMAmeasurement, with mean PCATMAincreasing linearly with increasing kV. • For longitudinal cCTA analysis of PCATMA, the use of equal kV setting is strongly recommended

Focal pericoronary adipose tissue attenuation is related to plaque presence, plaque type, and stenosis severity in coronary CTA

Objectives To investigate the association of pericoronary adipose tissue mean attenuation (PCAT(MA)) with coronary artery disease (CAD) characteristics on coronary computed tomography angiography (CCTA). Methods We retrospectively investigated 165 symptomatic patients who underwent third-generation dual-source CCTA at 70kVp: 93 with and 72 without CAD (204 arteries with plaque, 291 without plaque). CCTA was evaluated for presence and characteristics of CAD per artery. PCAT(MA) was measured proximally and across the most severe stenosis. Patient-level, proximal PCAT(MA) was defined as the mean of the proximal PCAT(MA) of the three main coronary arteries. Analyses were performed on patient and vessel level. Results Mean proximal PCAT(MA) was -96.2 +/- 7.1 HU and -95.6 +/- 7.8HU for patients with and without CAD (p = 0.644). In arteries with plaque, proximal and lesion-specific PCAT(MA) was similar (-96.1 +/- 9.6 HU, -95.9 +/- 11.2 HU, p = 0.608). Lesion-specific PCAT(MA) of arteries with plaque (-94.7 HU) differed from proximal PCAT(MA) of arteries without plaque (-97.2 HU, p = 0.015). Minimal stenosis showed higher lesion-specific PCAT(MA) (-94.0 HU) than severe stenosis (-98.5 HU, p = 0.030). Lesion-specific PCAT(MA) of non-calcified, mixed, and calcified plaque was -96.5 HU, -94.6 HU, and -89.9 HU (p = 0.004). Vessel-based total plaque, lipid-rich necrotic core, and calcified plaque burden showed a very weak to moderate correlation with proximal PCAT(MA). Conclusions Lesion-specific PCAT(MA) was higher in arteries with plaque than proximal PCAT(MA) in arteries without plaque. Lesion-specific PCAT(MA) was higher in non-calcified and mixed plaques compared to calcified plaques, and in minimal stenosis compared to severe; proximal PCAT(MA) did not show these relationships. This suggests that lesion-specific PCAT(MA) is related to plaque development and vulnerability

Comparison of computed tomography image features extracted by radiomics, self-supervised learning and end-to-end deep learning for outcome prediction of oropharyngeal cancer

Background and purpose: To compare the prediction performance of image features of computed tomography (CT) images extracted by radiomics, self-supervised learning and end-to-end deep learning for local control (LC), regional control (RC), locoregional control (LRC), distant metastasis-free survival (DMFS), tumor-specific survival (TSS), overall survival (OS) and disease-free survival (DFS) of oropharyngeal squamous cell carcinoma (OPSCC) patients after (chemo)radiotherapy.Methods and materials: The OPC-Radiomics dataset was used for model development and independent internal testing and the UMCG-OPC set for external testing. Image features were extracted from the Gross Tumor Volume contours of the primary tumor (GTVt) regions in CT scans when using radiomics or a self-supervised learning-based method (autoencoder). Clinical and combined (radiomics, autoencoder or end-to-end) models were built using multivariable Cox proportional-hazard analysis with clinical features only and both clinical and image features for LC, RC, LRC, DMFS, TSS, OS and DFS prediction, respectively.Results: In the internal test set, combined autoencoder models performed better than clinical models and combined radiomics models for LC, RC, LRC, DMFS, TSS and DFS prediction (largest improvements in C-index: 0.91 vs. 0.76 in RC and 0.74 vs. 0.60 in DMFS). In the external test set, combined radiomics models performed better than clinical and combined autoencoder models for all endpoints (largest improvements in LC, 0.82 vs. 0.71). Furthermore, combined models performed better in risk stratification than clinical models and showed good calibration for most endpoints.Conclusions: Image features extracted using self-supervised learning showed best internal prediction performance while radiomics features have better external generalizability.</p

A diet rich in fish oil and Leucine Ameliorates Hypercalcemia in tumour-induced cachectic mice

Background: Dietary supplementation with leucine and fish oil rich in omega-3 fatty acids docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA) has previously been shown to reduce cachexia-related outcomes in C26 tumour-bearing mice. To further explore associated processes and mechanisms we investigated changes in plasma Ca2+ levels, the involvement of parathyroid hormone related protein (PTHrP), and its possible interactions with cyclooxygenase 2 (COX-2). Methods: CD2F1 mice were subcutaneously inoculated with C26 adenocarcinoma cells or sham treated and divided in: (1) controls, (2) tumour-bearing controls, and (3) tumour-bearing receiving experimental diets. After 20 days, body and organ masses and total plasma Ca2+ levels were determined. Furthermore, effects of DHA, EPA and leucine on production of PTHrP were studied in cultured C26 cells. Results: The combination of leucine and fish oil reduced tumour-associated hypercalcemia. Plasma Ca2+ levels negatively correlated with carcass mass and multiple organ masses. DHA was able to reduce PTHrP production by C26 cells in vitro. Results indicate that this effect occurred independently of COX-2 inhibition. Conclusion: Our results suggest that cancer-related hypercalcemia may be ameliorated by a nutritional intervention rich in leucine and fish oil. The effect of fish oil possibly relates to a DHA-induced reduction of PTHrP excretion by the tumour

Integration of genetic and physical maps of the Primula vulgaris S locus and localization by chromosome in situ hybridization

•Heteromorphic flower development in Primula is controlled by the S locus. The S locus genes, which control anther position, pistil length and pollen size in pin and thrum flowers, have not yet been characterized. We have integrated S-linked genes, marker sequences and mutant phenotypes to create a map of the P. vulgaris S locus region that will facilitate the identification of key S locus genes. We have generated, sequenced and annotated BAC sequences spanning the S locus, and identified its chromosomal location. •We have employed a combination of classical genetics and three-point crosses with molecular genetic analysis of recombinants to generate the map. We have characterized this region by Illumina sequencing and bioinformatic analysis, together with chromosome in situ hybridization. •We present an integrated genetic and physical map across the P. vulgaris S locus flanked by phenotypic and DNA sequence markers. BAC contigs encompass a 1.5-Mb genomic region with 1 Mb of sequence containing 82 S-linked genes anchored to overlapping BACs. The S locus is located close to the centromere of the largest metacentric chromosome pair. •These data will facilitate the identification of the genes that orchestrate heterostyly in Primula and enable evolutionary analyses of the S locus

Appearance of the weight-bearing lateral radiograph in retrocalcaneal bursitis

Background and purpose A retrocalcaneal bursitis is caused by repetitive impingement of the bursa between the Achilles tendon and the posterosuperior calcaneus. The bursa is situated in the posteroinferior corner of Kager's triangle (retrocalcaneal recess), which is a radiolucency with sharp borders on the lateral radiograph of the ankle. If there is inflammation, the fluid-filled bursa is less radiolucent, making it difficult to delineate the retrocalcaneal recess. We assessed whether the radiographic appearance of the retrocalcaneal recess on plain digital (filmless) radiographs could be used in the diagnosis of a retrocalcaneal bursitis. Methods Whether or not there was obliteration of the retrocalcaneal recess (yes/no) on 74 digital weight-bearing lateral radiographs of the ankle was independently assessed by 2 observers. The radiographs were from 24 patients (25 heels) with retrocalcaneal bursitis (confirmed on endoscopic calcaneoplasty); the control group consisted of 50 patients (59 heels). Results The sensitivity of the test was 83% for observer 1 and 79% for observer 2. Specificity was 100% and 98%, respectively. The kappa value of the interobserver reliability test was 0.86. For observer 1, intraobserver reliability was 0.96 and for observer 2 it was 0.92. Interpretation On digital weight-bearing lateral radiographs of a retrocalcaneal bursitis, the retrocalcaneal recess has a typical appearanc

Risk Factors for Pre-Treatment Mortality among HIV-Infected Children in Rural Zambia: A Cohort Study

Many HIV-infected children in sub-Saharan Africa enter care at a late stage of disease. As preparation of the child and family for antiretroviral therapy (ART) can take several clinic visits, some children die prior to ART initiation. This study was undertaken to determine mortality rates and clinical predictors of mortality during the period prior to ART initiation.A prospective cohort study of HIV-infected treatment-naïve children was conducted between September 2007 and September 2010 at the HIV clinic at Macha Hospital in rural Southern Province, Zambia. HIV-infected children younger than 16 years of age who were treatment-naïve at study enrollment were eligible for analysis. Mortality rates prior to ART initiation were calculated and risk factors for mortality were evaluated.351 children were included in the study, of whom 210 (59.8%) were eligible for ART at study enrollment. Among children ineligible for ART at enrollment, 6 children died (mortality rate: 0.33; 95% CI:0.15, 0.74). Among children eligible at enrollment, 21 children died before initiation of ART and their mortality rate (2.73 per 100 person-years; 95% CI:1.78, 4.18) was significantly higher than among children ineligible for ART (incidence rate ratio: 8.20; 95% CI:3.20, 24.83). In both groups, mortality was highest in the first three months of follow-up. Factors associated with mortality included younger age, anemia and lower weight-for-age z-score at study enrollment.These results underscore the need to increase efforts to identify HIV-infected children at an earlier age and stage of disease progression so they can enroll in HIV care and treatment programs prior to becoming eligible for ART and these deaths can be prevented