Panoptes: web-based exploration of large scale genome variation data.

MOTIVATION: The size and complexity of modern large-scale genome variation studies demand novel approaches for exploring and sharing the data. In order to unlock the potential of these data for a broad audience of scientists with various areas of expertise, a unified exploration framework is required that is accessible, coherent and user-friendly. RESULTS: Panoptes is an open-source software framework for collaborative visual exploration of large-scale genome variation data and associated metadata in a web browser. It relies on technology choices that allow it to operate in near real-time on very large datasets. It can be used to browse rich, hybrid content in a coherent way, and offers interactive visual analytics approaches to assist the exploration. We illustrate its application using genome variation data of Anopheles gambiae, Plasmodium falciparum and Plasmodium vivax. AVAILABILITY AND IMPLEMENTATION: Freely available at https://github.com/cggh/panoptes, under the GNU Affero General Public License. CONTACT: paul.vauterin@gmail.com.

Genomic analysis of local variation and recent evolution in Plasmodium vivax.

The widespread distribution and relapsing nature of Plasmodium vivax infection present major challenges for the elimination of malaria. To characterize the genetic diversity of this parasite in individual infections and across the population, we performed deep genome sequencing of >200 clinical samples collected across the Asia-Pacific region and analyzed data on >300,000 SNPs and nine regions of the genome with large copy number variations. Individual infections showed complex patterns of genetic structure, with variation not only in the number of dominant clones but also in their level of relatedness and inbreeding. At the population level, we observed strong signals of recent evolutionary selection both in known drug resistance genes and at new loci, and these varied markedly between geographical locations. These findings demonstrate a dynamic landscape of local evolutionary adaptation in the parasite population and provide a foundation for genomic surveillance to guide effective strategies for control and elimination of P. vivax.

Thoracic epidural versus intercostal nerve catheter plus patient-controlled analgesia: a randomized study.

BACKGROUND: Pain control is an important issue after thoracotomy. Ideal methods should have a high success rate, with easy implementation and minimal complications. Debate exists over the optimal pain control method. This randomized trial was designed to compare epidural (EPI) and intercostal nerve catheter with patient-controlled analgesia (ICN-PCA) for pain control after thoracotomy. METHODS: The study included 124 randomized patients; 91 had sufficient data for analysis (44 EPI, 47 ICN-PCA). The primary endpoint was pain measurement using a composite of a visual analogue scale, numerical rating, and categorical rating. A second endpoint was the success rate of each method. Pulmonary function tests, antibiotics, intensive care unit (ICU), and hospital days, and use of nonprotocol pain medications were also compared. RESULTS: There were 12 pain observations per patient (90% completed on days 1 to 5). The pain composite revealed an average postoperative pain score of 2.4 on a scale from 0 (no pain) to 10 (worst pain). There was no difference between the groups. Failures of the planned method of analgesia included 9 in the EPI group and 4 in the ICN group (p = 0.23). Another 20 patients were excluded (no difference between groups) due to unsuspected mediastinal metastases precluding thoracotomy (n = 13), and other miscellaneous factors precluding follow-up (n = 7). The EPI group had an increased number of urinary catheter days (2.5 days vs 1.7, p = 0.002) and increased narcotic supplements (p = 0.03) compared with ICN. Mean ICU days (0.9) and hospital days (6.2) were similar for both groups, and there were no differences in arrhythmias, pneumonias, transfusions, and antibiotic use. Significant differences were seen (p = 0.001) between preoperative and postoperative pulmonary function tests in both groups. However, there were no differences in pulmonary function when the groups were compared with each other. CONCLUSIONS: Satisfactory pain control was achieved after thoracotomy using either EPI or ICN-PCA. The ICN-PCA achieved equivalent pain control compared with EPI, and was placed by the surgeon with no delays in surgery, and demonstrated a decreased requirement for Foley catheter duration.