Redox-neutral, metal-free tryptophan labeling of polypeptides in hexafluoroisopropanol (HFIP).

Despite the unmet needs for chemical tools to study biological roles of tryptophan in living systems, there has been a lack of chemical modification methods for tryptophan residues that can be used in cellular environments. Driven by a preliminary computational study of our previous research, this work experimentally examined our hypotheses to translate the metal-catalyzed tryptophan modification method in hexafluoroisopropanol (HFIP) into a metal-free process. While one of the hypotheses merely confirmed the superiority of the thiophene-ethanol reagent developed in the previous report, the second hypothesis resulted in the identification of a trifluoroborate salt and an acidic ionic liquid as alternatives for the catalysis. Labeling of lysates of a human cell line was achieved with the acidic ionic liquid catalyst, where negative impacts of the tryptophan labeling and HFIP medium on the cellular samples were apparently insignificant. Because the labeling process does not require any redox mediators and is a formal redox-neutral reaction, the metal-free approach would be of use for tryptophan biology research potentially related to their various redox roles.

An Upgraded, Highly Saturated Linkage Map of Japanese Plum (Prunus salicina Lindl.), and Identification of a New Major Locus Controlling the Flavan-3-ol Composition in Fruits.

Japanese plum fruits are rich in phenolic compounds, such as anthocyanins and flavan-3-ols, whose contents vary significantly among cultivars. Catechin (C) and epicatechin (EC) are flavan-3-ol monomers described in the fruits of this species and are associated with bitterness, astringency, antioxidant capacity, and susceptibility to enzymatic mesocarp browning. In this study, we aimed to identify quantitative trait loci (QTL) associated with the content of flavan-3-ol in Japanese plum fruits. We evaluated the content of C and EC in the mesocarp and exocarp of samples from 79 and 64 seedlings of an F1 progeny (<'98-99' × 'Angeleno'>) in the first and second seasons, respectively. We also constructed improved versions of linkage maps from '98-99' and 'Angeleno,' presently called single-nucleotide polymorphisms (SNPs) after mapping the already available GBS reads to Prunus salicina Lindl. cv. 'Sanyueli' v2.0 reference genome. These data allowed for describing a cluster of QTLs in the cultivar, 'Angeleno,' associated with the flavan-3-ol composition of mesocarp and exocarp, which explain up to 100% of the C/EC ratio. Additionally, we developed a C/EC metabolic marker, which was mapped between the markers with the highest log of odds (LOD) scores detected by the QTL analysis. The C/EC locus was located in the LG1, at an interval spanning 0.70 cM at 108.30-108.90 cM. Our results suggest the presence of a novel major gene controlling the preferential synthesis of C or EC in the Japanese plum fruits. This study is a significant advance in understanding the regulation of synthesizing compounds associated with fruit quality, postharvest, and human health promotion.

HisVA: A Visual Analytics System for Studying History.

Studying history involves many difficult tasks. Examples include searching for proper data in a large event space, understanding stories of historical events by time and space, and finding relationships among events that may not be apparent. Instructors who extensively use well-organized and well-argued materials (e.g., textbooks and online resources) can lead students to a narrow perspective in understanding history and prevent spontaneous investigation of historical events, with the students asking their own questions. In this article, we proposed HisVA, a visual analytics system that allows the efficient exploration of historical events from Wikipedia using three views: event, map, and resource. HisVA provides an effective event exploration space, where users can investigate relationships among historical events by reviewing and linking them in terms of space and time. To evaluate our system, we present two usage scenarios, a user study with a qualitative analysis of user exploration strategies, and in-class deployment results.

Multi-Scale 7DOF View Adjustment.

Multi-scale virtual environments contain geometric details ranging over several orders of magnitude and typically employ out-of-core rendering techniques. When displayed in virtual reality systems this entails using a 7 degree-of-freedom (DOF) view model where view scale is a separate 7th DOF in addition to 6DOF view pose. Dynamic adjustment of this and other view parameters become very important to usability. In this paper, we evaluate how two adjustment techniques interact with uni- and bi-manual 7DOF navigation in DesktopVR and a CAVE. The travel task has two stages, an initial targeted zoom and a detailed geometric inspection. The results show benefits of the auto-adjustments on completion time and stereo fusion issues, but only in certain circumstances. Peculiar view configuration examples show the difficulty of creating robust adjustment rules.

Urban Space Explorer: A Visual Analytics System for Urban Planning.

Understanding people's behavior is fundamental to many planning professions (including transportation, community development, economic development, and urban design) that rely on data about frequently traveled routes, places, and social and cultural practices. Based on the results of a practitioner survey, the authors designed Urban Space Explorer, a visual analytics system that utilizes mobile social media to enable interactive exploration of public-space-related activity along spatial, temporal, and semantic dimensions.

VAiRoma: A Visual Analytics System for Making Sense of Places, Times, and Events in Roman History.

Learning and gaining knowledge of Roman history is an area of interest for students and citizens at large. This is an example of a subject with great sweep (with many interrelated sub-topics over, in this case, a 3,000 year history) that is hard to grasp by any individual and, in its full detail, is not available as a coherent story. In this paper, we propose a visual analytics approach to construct a data driven view of Roman history based on a large collection of Wikipedia articles. Extracting and enabling the discovery of useful knowledge on events, places, times, and their connections from large amounts of textual data has always been a challenging task. To this aim, we introduce VAiRoma, a visual analytics system that couples state-of-the-art text analysis methods with an intuitive visual interface to help users make sense of events, places, times, and more importantly, the relationships between them. VAiRoma goes beyond textual content exploration, as it permits users to compare, make connections, and externalize the findings all within the visual interface. As a result, VAiRoma allows users to learn and create new knowledge regarding Roman history in an informed way. We evaluated VAiRoma with 16 participants through a user study, with the task being to learn about roman piazzas through finding relevant articles and new relationships. Our study results showed that the VAiRoma system enables the participants to find more relevant articles and connections compared to Web searches and literature search conducted in a roman library. Subjective feedback on VAiRoma was also very positive. In addition, we ran two case studies that demonstrate how VAiRoma can be used for deeper analysis, permitting the rapid discovery and analysis of a small number of key documents even when the original collection contains hundreds of thousands of documents.

Early adoption of robotic pulmonary lobectomy: feasibility and initial outcomes.

Despite the published benefits of minimally invasive video-assisted thoracoscopic surgery (VATS) for lobectomy, the majority of lobectomies in the United States continue to be performed through a thoracotomy. The low adoption rate of VATS has been attributed to its technical challenges and ergonomic inefficiencies. Robotic surgery has been proposed as an alternative minimally invasive technique that allows the replication of open lobectomy with wristed instruments and three-dimensional vision. Our aim was to analyze the transition from open to robotic lobectomy at our hospital where there had been no significant VATS lobectomy experience. We analyzed 88 open and 43 robotic lobectomies that met criteria for inclusion. Operative times were significantly longer with the robotic group but decreased with experience. The resection time of the latter half of the robotic cases decreased to within 20 minutes of the open cases. There were no conversions in the robotic cases to either VATS or open. Robotic lobectomy was associated with faster postoperative recovery with a 60 per cent decrease in length of stay. Complications were uncommon and there were no deaths in the robotic group. We conclude that the transition from open to robotic lobectomy can be achieved safely with excellent postoperative outcomes. This new technique is a viable alternative to VATS lobectomy.