Virtual Enhancement to Physical Spaces: A QR Code Based Orientation Game

University orientations are typically passive events for students, with activities that include sitting and listening to speakers and perhaps talking to others seated nearby. In this project, the authors sought to provide a more active and collaborative component to a university orientation via a team-based game that incorporated content included in a typical orientation and modeled appropriate instructional technology use. This mobile orientation game used QR codes and videos to augment the physical environment of an academic building. This paper describes the design and development process for this game, and presents the results of an evaluation conducted at the end. The game, which lasted an hour, both helped players learn more about the people and key locations within the new program they were joining and, most importantly, helped participants meet and interact with their new peers prior to the beginning of classes

Whole Genome Analysis of the Red-Crowned Crane Provides Insight into Avian Longevity

The red-crowned crane (Grus japonensis) is an endangered, large-bodied crane native to East Asia. It is a traditional symbol of longevity and its long lifespan has been confirmed both in captivity and in the wild. Lifespan in birds is known to be positively correlated with body size and negatively correlated with metabolic rate, though the genetic mechanisms for the red-crowned crane's long lifespan have not previously been investigated. Using whole genome sequencing and comparative evolutionary analyses against the grey-crowned crane and other avian genomes, including the long-lived common ostrich, we identified red-crowned crane candidate genes with known associations with longevity. Among these are positively selected genes in metabolism and immunity pathways (NDUFA5, NDUFA8, NUDT12, SOD3, CTH, RPA1, PHAX, HNMT, HS2ST1, PPCDC, PSTK CD8B, GP9, IL-9R, and PTPRC). Our analyses provide genetic evidence for low metabolic rate and longevity, accompanied by possible convergent adaptation signatures among distantly related large and long-lived birds. Finally, we identified low genetic diversity in the red-crowned crane, consistent with its listing as an endangered species, and this genome should provide a useful genetic resource for future conservation studies of this rare and iconic species

Steering Algorithm for a Flexible Microrobot to Enhance Guidewire Control in a Coronary Angioplasty Application

Magnetically driven microrobots have been widely studied for various biomedical applications in the past decade. An important application of these biomedical microrobots is heart disease treatment. In intravascular treatments, a particular challenge is the submillimeter-sized guidewire steering; this requires a new microrobotic approach. In this study, a flexible microrobot was fabricated by the replica molding method, which consists of three parts: (1) a flexible polydimethylsiloxane (PDMS) body, (2) two permanent magnets, and (3) a micro-spring connector. A mathematical model was developed to describe the relationship between the magnetic field and the deformation. A system identification approach and an algorithm were proposed for steering. The microrobot was fabricated, and the models for steering were experimentally validated under a magnetic field intensity of 15 mT. Limitations to control were identified, and the microrobot was steered in an arbitrary path using the proposed model. Furthermore, the flexible microrobot was steered using the guidewire within a three-dimensional (3D) transparent phantom of the right coronary artery filled with water, to show the potential application in a realistic environment. The flexible microrobot presented here showed promising results for enhancing guidewire steering in percutaneous coronary intervention (PCI)

Genomic profile analysis of diffuse-type gastric cancers

Background: Stomach cancer is the third deadliest among all cancers worldwide. Although incidence of the intestinal-type gastric cancer has decreased, the incidence of diffuse-type is still increasing and its progression is notoriously aggressive. There is insufficient information on genome variations of diffuse-type gastric cancer because its cells are usually mixed with normal cells, and this low cellularity has made it difficult to analyze the genome. Results: We analyze whole genomes and corresponding exomes of diffuse-type gastric cancer, using matched tumor and normal samples from 14 diffuse-type and five intestinal-type gastric cancer patients. Somatic variations found in the diffuse-type gastric cancer are compared to those of the intestinal-type and to previously reported variants. We determine the average exonic somatic mutation rate of the two types. We find associated candidate driver genes, and identify seven novel somatic mutations in CDH1, which is a well-known gastric cancer-associated gene. Three-dimensional structure analysis of the mutated E-cadherin protein suggests that these new somatic mutations could cause significant functional perturbations of critical calcium-binding sites in the EC1-2 junction. Chromosomal instability analysis shows that the MDM2 gene is amplified. After thorough structural analysis, a novel fusion gene TSC2-RNF216 is identified, which may simultaneously disrupt tumor-suppressive pathways and activate tumorigenesis. Conclusions: We report the genomic profile of diffuse-type gastric cancers including new somatic variations, a novel fusion gene, and amplification and deletion of certain chromosomal regions that contain oncogenes and tumor suppressors.open121

Variation block-based genomics method for crop plants

BACKGROUND: In contrast with wild species, cultivated crop genomes consist of reshuffled recombination blocks, which occurred by crossing and selection processes. Accordingly, recombination block-based genomics analysis can be an effective approach for the screening of target loci for agricultural traits. RESULTS: We propose the variation block method, which is a three-step process for recombination block detection and comparison. The first step is to detect variations by comparing the short-read DNA sequences of the cultivar to the reference genome of the target crop. Next, sequence blocks with variation patterns are examined and defined. The boundaries between the variation-containing sequence blocks are regarded as recombination sites. All the assumed recombination sites in the cultivar set are used to split the genomes, and the resulting sequence regions are termed variation blocks. Finally, the genomes are compared using the variation blocks. The variation block method identified recurring recombination blocks accurately and successfully represented block-level diversities in the publicly available genomes of 31 soybean and 23 rice accessions. The practicality of this approach was demonstrated by the identification of a putative locus determining soybean hilum color. CONCLUSIONS: We suggest that the variation block method is an efficient genomics method for the recombination block-level comparison of crop genomes. We expect that this method will facilitate the development of crop genomics by bringing genomics technologies to the field of crop breeding

A Magnetically Controlled Soft Microrobot Steering a Guidewire in a Three-Dimensional Phantom Vascular Network

Magnetically actuated soft robots may improve the treatment of disseminated intravascular coagulation. Significant progress has been made in the development of soft robotic systems that steer catheters. A more challenging task, however, is the development of systems that steer sub-millimeter-diameter guidewires during intravascular treatments; a novel microrobotic approach is required for steering. In this article, we develop a novel, magnetically actuated, soft microrobotic system, increasing the steerability of a conventional guidewire. The soft microrobot is attached to the tip of the guidewire, and it is magnetically steered by changing the direction and intensity of an external magnetic field. The microrobot is fabricated via replica molding and features a soft body made of polydimethylsiloxane, two permanent magnets, and a microspring. We developed a mathematical model mapping deformation of the soft microrobot using a feed-forward approach toward steering. Then, we used the model to steer a guidewire. The angulation of the microrobot can be controlled from 21.1° to 132.7° by using a magnetic field of an intensity of 15 mT. Steerability was confirmed by two-dimensional in vitro tracking. Finally, a guidewire with the soft microrobot was tested by using a three-dimensional (3D) phantom of the coronary artery to verify steerability in 3D space

COMUS: Clinician-Oriented locus-specific MUtation detection and deposition System

Background: A disease-causing mutation refers to a heritable genetic change that is associated with a specific phenotype (disease). The detection of a mutation from a patient's sample is critical for the diagnosis, treatment, and prognosis of the disease. There are numerous databases and applications with which to archive mutation data. However, none of them have been implemented with any automated bioinformatics tools for mutation detection and analysis starting from raw data materials from patients. We present a Locus Specific mutation DB (LSDB) construction system that supports both mutation detection and deposition in one package. Results: COMUS (Clinician-Oriented locus specific MUtation detection and deposition System) is a mutation detection and deposition system for developing specific LSDBs. COMUS contains 1) a DNA sequence mutation analysis method for clinicians' mutation data identification and deposition and 2) a curation system for variation detection from clinicians' input data. To embody the COMUS system and to validate its clinical utility, we have chosen the disease hemophilia as a test database. A set of data files from bench experiments and clinical information from hemophilia patients were tested on the LSDB, KoHemGene http://www.kohemgene.org, which has proven to be a clinician-friendly interface for mutation detection and deposition. Conclusion: COMUS is a bioinformatics system for detecting and depositing new mutations from patient DNA with a clinician-friendly interface. LSDBs made using COMUS will promote the clinical utility of LSDBs. COMUS is available at http://www.comus.info. © 2009 Jho et al; licensee BioMed Central Ltdclose