CAVASS: A Computer-Assisted Visualization and Analysis Software System

The Medical Image Processing Group at the University of Pennsylvania has been developing (and distributing with source code) medical image analysis and visualization software systems for a long period of time. Our most recent system, 3DVIEWNIX, was first released in 1993. Since that time, a number of significant advancements have taken place with regard to computer platforms and operating systems, networking capability, the rise of parallel processing standards, and the development of open-source toolkits. The development of CAVASS by our group is the next generation of 3DVIEWNIX. CAVASS will be freely available and open source, and it is integrated with toolkits such as Insight Toolkit and Visualization Toolkit. CAVASS runs on Windows, Unix, Linux, and Mac but shares a single code base. Rather than requiring expensive multiprocessor systems, it seamlessly provides for parallel processing via inexpensive clusters of work stations for more time-consuming algorithms. Most importantly, CAVASS is directed at the visualization, processing, and analysis of 3-dimensional and higher-dimensional medical imagery, so support for digital imaging and communication in medicine data and the efficient implementation of algorithms is given paramount importance

CIDI-Lung-Seg: A Single-Click Annotation Tool for Automatic Delineation of Lungs from CT Scans

Accurate and fast extraction of lung volumes from computed tomography (CT) scans remains in a great demand in the clinical environment because the available methods fail to provide a generic solution due to wide anatomical variations of lungs and existence of pathologies. Manual annotation, current gold standard, is time consuming and often subject to human bias. On the other hand, current state-of-the-art fully automated lung segmentation methods fail to make their way into the clinical practice due to their inability to efficiently incorporate human input for handling misclassifications and praxis. This paper presents a lung annotation tool for CT images that is interactive, efficient, and robust. The proposed annotation tool produces an "as accurate as possible" initial annotation based on the fuzzy-connectedness image segmentation, followed by efficient manual fixation of the initial extraction if deemed necessary by the practitioner. To provide maximum flexibility to the users, our annotation tool is supported in three major operating systems (Windows, Linux, and the Mac OS X). The quantitative results comparing our free software with commercially available lung segmentation tools show higher degree of consistency and precision of our software with a considerable potential to enhance the performance of routine clinical tasks.Comment: 4 pages, 6 figures; to appear in the proceedings of 36th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC 2014

Identification of quantitative trait loci controlling root and shoot traits associated with drought tolerance in a lentil (Lens culinaris Medik.) recombinant inbred line population

Drought is one of the major abiotic stresses limiting lentil productivity in rainfed production systems. Specific rooting patterns can be associated with drought avoidance mechanisms that can be used in lentil breeding programs. In all, 252 co-dominant and dominant markers were used for Quantitative Trait Loci (QTL) analysis on 132 lentil recombinant inbred lines based on greenhouse experiments for root and shoot traits during two seasons under progressive drought-stressed conditions. Eighteen QTLs controlling a total of 14 root and shoot traits were identified. A QTL-hotspot genomic region related to a number of root and shoot characteristics associated with drought tolerance such as dry root biomass, root surface area, lateral root number, dry shoot biomass and shoot length was identified. Interestingly, a QTL (QRSratioIX-2.30) related to root-shoot ratio, an important trait for drought avoidance, explaining the highest phenotypic variance of 27.6 and 28.9% for the two consecutive seasons, respectively, was detected. This QTL was closed to the co-dominant SNP marker TP6337 and also flanked by the two SNP TP518 and TP1280. An important QTL (QLRNIII-98.64) related to lateral root number was found close to TP3371 and flanked by TP5093 and TP6072 SNP markers. Also, a QTL (QSRLIV-61.63) associated with specific root length was identified close to TP1873 and flanked by F7XEM6b SRAP marker and TP1035 SNP marker. These two QTLs were detected in both seasons. Our results could be used for marker-assisted selection in lentil breeding programs targeting root and shoot characteristics conferring drought avoidance as an efficient alternative to slow and labor-intensive conventional breeding methods

Drug package inserts: how accessible is the information?

Background: Information given in drug package inserts is often not easily accessible by patients and practitioners. Presentation of important information in an easily accessible manner fulfills the very purpose of inserts. In the present study, accessibility of important information in drug package inserts is evaluated.Methods: We evaluated 110 package inserts. Accessibility to important information was noted under following headings: use of box, use of special/bigger font or color, use of table of contents and information in front sheet. Each of these parameters was given a point. Cumulative accessibility score of more than three considered as accessible. Provision of toll free numbers and internet addresses of the companies noted.Results: Information in inserts regarding posology, method of administration, precautions under special conditions, contraindications, pharmacokinetics, interactions, pregnancy and lactation, driving, and machine use precautions were adequate and orderly in most. Only seven drug inserts mentioned important information with special font/different color. 18 drug inserts had used boxes. About 13 inserts used bigger font size for revealing important information. We observed a mean accessible score was 0.37 a insert. Only two inserts carried toll free numbers.Conclusion: Important information in drug package inserts is not easily accessible. Display of toll free numbers and internet addresses for queries and reporting adverse drug reactions is highly recommended

Temporal Correlations and Persistence in the Kinetic Ising Model: the Role of Temperature

We study the statistical properties of the sum $S_t=\int_{0}^{t}dt' \sigma_{t'}$, that is the difference of time spent positive or negative by the spin $\sigma_{t}$, located at a given site of a $D$-dimensional Ising model evolving under Glauber dynamics from a random initial configuration. We investigate the distribution of $S_{t}$ and the first-passage statistics (persistence) of this quantity. We discuss successively the three regimes of high temperature ($T>T_{c}$), criticality ($T=T_c$), and low temperature ($T<T_{c}$). We discuss in particular the question of the temperature dependence of the persistence exponent $\theta$, as well as that of the spectrum of exponents $\theta(x)$, in the low temperature phase. The probability that the temporal mean $S_t/t$ was always larger than the equilibrium magnetization is found to decay as $t^{-\theta-\frac12}$. This yields a numerical determination of the persistence exponent $\theta$ in the whole low temperature phase, in two dimensions, and above the roughening transition, in the low-temperature phase of the three-dimensional Ising model.Comment: 21 pages, 11 PostScript figures included (1 color figure

Optimising Subsidiary Crop Applications in Rotations (OSCAR): A Perspective for the North Africa Region

Background: For sustainable improvement of wheat-based farming systems in the North Africa, there is a need to improve plant health, soil health and fertility. One approach to achieve this is by integrating subsidiary crops (SC) as living or dead mulches or cover crops with the main crops in rotations, which will increase plant species and microbial diversity and reducing water demand in dry climates. Methods: A collaborative research project funded by EU FP 7 (Project No. 289277) was initiated in April 2012, in partnership with European Union (public research organizations and private sector small and medium enterprises of Germany, Norway, Sweden, Denmark, the Netherland, UK, Poland, Switzerland and Italy), Brazil and Morocco (INRA-Morocco and ICARDA), in order to enhance understanding and use of SC systems, develop suitable farm technologies, increase the range of SC species, and enhance understanding of impact of SC on soil ecology, biology and microbial diversity and crop pests and diseases. Results: Based on two field experiments in Morocco (Sidi AI-Aidi and Sidi Allal-Tazi), the project will assess the economic and ecological impact including legume root health and soil health, fertility and microbial diversity and compare the results with other sites in Europe. Screening of new species and genotypes will result in identification of range of potentially useful plant species for SC for the North Africa and Europe. The identified SC species will be tested for their potential as forage and for extraction of useful biochemicals. Conclusion: The results of the project as a whole will be of use for and improve sustainability in low-input, organic, and conventional farming systems in the North Africa, Latin America and Europe

Towards identification of novel legume species of potential interest as cover crops and living mulches for the North Africa region.

Subsidiary crops (SC) grown either as cover crops (CC) preceding or following the main crops, or as living mulches (LM) together with the main crops can deliver multiple ecological services within farming systems. These include increasing the duration of soil cover in the rotation, increasing plant and microbial diversity, improving plant health, soil health and fertility, minimizing the use of tillage and agrochemicals, enhancing biological N fixation and soil C content, and reducing water demand in dry climates. However, species available for growing as SC for dry areas are limited. To identify species of potential interest to CC and LM, we screened 197 accessions from the ICARDA genebank, belonging to 142 species/sub-species at Rabat, Morocco in one square meter plots. The preliminary assessments based on visual observations enabled us to identify: (1) 21 accessions belonging to Medicago and Trifolium species with prostrate growth habit, early maturity and senescence, determinate growth cycle and good potential for seed production, as potentially suitable for LM; and (2) 28 accessions belonging to Vicia, Lathyrus, Medicago and Trifolium species with high biomass and competitive ability, and also good potential for seed production, as potentially suitable for CC or green manure crops. Further evaluations in replicated trials are in progress. The selected accessions have been planted in the field during autumn 2013 at Sidi El Aidi

Segmentation and Evaluation of Adipose Tissue from Whole Body MRI Scans

Accurate quantification of total body and the distribution of regional adipose tissue using manual segmentation is a challenging problem due to the high variation between manual delineations. Manual segmentation also requires highly trained experts with knowledge of anatomy. We present a hybrid segmentation method that provides robust delineation results for adipose tissue from whole body MRI scans. A formal evaluation of accuracy of the segmentation method is performed. This semi-automatic segmentation algorithm reduces significantly the time required for quantification of adipose tissue, and the accuracy measurements show that the results are close to the ground truth obtained from manual segmentations