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High-quality antibody (Ab) production depends on the availability of immunologically relevant antigens. We present a potentially universal platform for generating soluble antigens from bacterial hosts, tailored to immunized animals for Ab production. A novel RNA-dependent chaperone, in which the target antigen is genetically fused with an RNA-interacting domain (RID) docking tag derived from the immunized host, promotes the solubility and robust folding of the target antigen. We selected the N-terminal tRNA-binding domain of lysyl-tRNA synthetase (LysRS) as the RID for fusion with viral proteins and demonstrated the expression of the RID fusion proteins in their soluble and native conformations; immunization predominantly elicited Ab responses to the target antigen, whereas the self RID tag remained nonimmunogenic. Differential immunogenicity of the fusion proteins greatly enriched and simplified the screening of hybridoma clones of monoclonal antibodies (mAbs), enabling specific and sensitive serodiagnosis of MERS-CoV infection. Moreover, mAbs against the consensus influenza hemagglutinin stalk domain enabled a novel assay for trivalent seasonal influenza vaccines. The Fc-mediated effector function was demonstrated, which could be harnessed for the design of next-generation universal influenza vaccines. The nonimmunogenic built-in antigen folding module tailored to a repertoire of immunized animal hosts will drive immunochemical diagnostics, therapeutics, and designer vaccines.

Graphs are the natural data structure to represent relational and structural information in many domains. To cover the broad range of graph-data applications including graph classification as well as graph generation, it is desirable to have a general and flexible model consisting of an encoder and a decoder that can handle graph data. Although the representative encoder-decoder model, Transformer, shows superior performance in various tasks especially of natural language processing, it is not immediately available for graphs due to their non-sequential characteristics. To tackle this incompatibility, we propose GRaph-Aware Transformer (GRAT), the first Transformer-based model which can encode and decode whole graphs in end-to-end fashion. GRAT is featured with a self-attention mechanism adaptive to the edge information and an auto-regressive decoding mechanism based on the two-path approach consisting of sub-graph encoding path and node-and-edge generation path for each decoding step. We empirically evaluated GRAT on multiple setups including encoder-based tasks such as molecule property predictions on QM9 datasets and encoder-decoder-based tasks such as molecule graph generation in the organic molecule synthesis domain. GRAT has shown very promising results including state-of-the-art performance on 4 regression tasks in QM9 benchmark.

Over the past decade, the proliferation of mobile devices has generated a variety of data at an unprecedented rate. The trend will be further accelerated by the advent of the Internet-of- Things era. Such data include signals, texts, photos, and videos tagged with date, time, and geo coordinates. The data are structured, semi-structured, or unstructured. Data-processing systems that aim to ingest, store, index, and analyze Big Data must deal with such data efficiently. In response, we have developed Apache AsterixDB, a parallel, semi-structured information management platform, that provides the ability to ingest, store, index, query, and analyze mass quantities of data.The key contributions of this thesis fall in two major parts. First, in order to store and index newly generated data and make them queryable in a timely manner, a record-level transaction model was designed and implemented in AsterixDB based on the read-committed isolation level. Second, due to the importance of efficient query processing for such dynamic geo- tagged data, we implemented five variants of representative, disk-resident spatial indexing methods on top of the Log-Structured Merge-tree-based (LSM) storage layer in AsterixDB and evaluated their pros and cons in light of the dynamic characteristics of geo-tagged Big Data.

A novel protein-folding function of RNA has been recognized, which can outperform previously known molecular chaperone proteins. The RNA as a molecular chaperone (chaperna) activity is intrinsic to some ribozymes and is operational during viral infections. Our purpose was to test whether influenza hemagglutinin (HA) can be assembled in a soluble, trimeric, and immunologically activating conformation by means of an RNA molecular chaperone (chaperna) activity. An RNA-interacting domain (RID) from the host being immunized was selected as a docking tag for RNA binding, which served as a transducer for the chaperna function for de novo folding and trimeric assembly of RID-HA1. Mutations that affect tRNA binding greatly increased the soluble aggregation defective in trimer assembly, suggesting that RNA interaction critically controls the kinetic network in the folding/assembly pathway. Immunization of mice resulted in strong hemagglutination inhibition and high titers of a neutralizing antibody, providing sterile protection against a lethal challenge and confirming the immunologically relevant HA conformation. The results may be translated into a rapid response to a new influenza pandemic. The harnessing of the novel chaperna described herein with immunologically tailored antigen-folding functions should serve as a robust prophylactic and diagnostic tool for viral infections.

Hepatitis C virus (HCV) alters mitochondrial dynamics associated with persistent viral infection and suppression of innate immunity. Mitochondrial dysfunction is also a pathologic feature of direct-acting antiviral (DAA) treatment. Despite the high efficacy of DAAs, their use in treating patients with chronic hepatitis C in interferon-sparing regimens occasionally produces undesirable side effects such as fatigue, migraine, and other conditions, which may be linked to mitochondrial dysfunction. Here, we show that clinically prescribed DAAs, including sofosbuvir, affect mitochondrial dynamics. To counter these adverse effects, we examined HCV-induced and DAA-induced aberrant mitochondrial dynamics modulated by ginsenoside, which is known to support healthy mitochondrial physiology and the innate immune system. We screened several ginsenoside compounds showing antiviral activity using a robust HCV cell culture system. We investigated the role of ginsenosides in antiviral efficacy, alteration of mitochondrial transmembrane potential, abnormal mitochondrial fission, its upstream signaling, and mitophagic process caused by HCV infection or DAA treatment. Only one of the compounds, ginsenoside Rg3 (G-Rg3), exhibited notable and promising anti-HCV potential. Treatment of HCV-infected cells with G-Rg3 increased HCV core protein-mediated reduction in the expression level of cytosolic p21, required for increasing cyclin-dependent kinase 1 activity, which catalyzes Ser616 phosphorylation of dynamin-related protein 1. The HCV-induced mitophagy, which follows mitochondrial fission, was also rescued by G-Rg3 treatment.ConclusionG-Rg3 inhibits HCV propagation. Its antiviral mechanism involves restoring the HCV-induced dynamin-related protein 1-mediated aberrant mitochondrial fission process, thereby resulting in suppression of persistent HCV infection. (Hepatology 2017;66:758-771).

Ji Hyeon Joo, Yeon Joo Kim, Young Seok Kim, Young Pil Cho, Ho Yeon Lee, Chang Young Jeong, Jungwon Kwak, Byung Chul Cho Department of Radiation Oncology, Asan Medical Center, University of Ulsan, College of Medicine, Seoul, Republic of Korea Background: The authors conducted this prospective study to analyze the amount of interfractional prostate bed motion (PBM) and quantify its components with the use of an endorectal balloon (ERB).Methods: A total of 1,348 cone beam computed tomography images from 46 patients who underwent postprostatectomy radiotherapy were analyzed. For the pilot image, electronic portal imaging, guided by skin marks was performed to ensure proper positioning and inflation of the ERB. Then, for bone matching, manual or automatic registration of the planning and each cone beam computed tomography was performed, based on the bony anatomy of the pelvis. Shifts (bony misalignment [BM]) in three directions were recorded at each treatment session. For prostate bed matching, manual matching was conducted based on the anterior rectal wall and the shift (PBM) was recorded. Total setup error was defined as the shift from the skin mark to the prostate bed matching, based on anterior rectal wall stretched by the ERB. PBM was defined as the difference between the total setup error and BM.Results: Systematic errors for the total setup error were 1.0, 1.3, and 1.0 mm in the right–left, anterior–posterior, and superior–inferior directions, with random errors of 1.9, 2.4, and 1.9 mm, respectively. Systematic errors were 1.6, 1.6, and 0.3 mm for BM and 0.8, 1.1, and 0.9 mm for PBM, with random errors of 2.4, 2.5, and 1.1 mm for BM and 1.8, 2.2, and 1.9 mm for PBM.Conclusion: The BM was the main component of the total setup error, suggesting that interfractional PBM was well controlled by the ERB device. Planning target volume margins of <5 mm were needed to include 95% of the interfractional variations when

Yeon Joo Kim, Jin-hong Park, In-Ha Yun, Young Seok KimDepartment of Radiation Oncology, Asan Medical Center, College of Medicine, University of Ulsan, Seoul, Republic of KoreaPurpose: To compare the acute intestinal toxicity of whole pelvic (WP) and small field (SF) intensity-modulated radiotherapy (IMRT) for prostate cancer using dosimetric and metabolic parameters as well as clinical findings.Methods: Patients who received IMRT in either a definitive or postoperative setting were prospectively enrolled. Target volume and organs at risk including intestinal cavity (IC) were delineated in every patient by a single physician. The IC volume that received a 10–50 Gy dose at 5-Gy intervals (V10–V50) and the percentage of irradiated volume as a fraction of total IC volume were calculated. Plasma citrulline levels, as an objective biological marker, were checked at three time points: baseline and after exposure to 30 Gy and 60 Gy.Results: Of the 41 patients, only six experienced grade 1 acute intestinal toxicity. Although all dose–volume parameters were significantly worse following WP than SF IMRT, there was no statistically significant relationship between these dosimetric parameters and clinical symptoms. Plasma citrulline levels did not show a serial decrease by radiotherapy volume difference (WP versus SF) and were not relevant to the irradiated doses.Conclusion: Given that WP had comparable acute intestinal toxicities to those associated with SF, WP IMRT appears to be a feasible approach for the treatment of prostate cancer despite dosimetric disadvantages.Keywords: prostate cancer, intensity-modulated radiotherapy, intestinal toxicity, citrulline

AsterixDB is a new, full-function BDMS (Big Data Management System) with a feature set that distinguishes it from other platforms in today's open source Big Data ecosystem. Its features make it well-suited to applications like web data warehousing, social data storage and analysis, and other use cases related to Big Data. AsterixDB has a flexible NoSQL style data model; a query language that supports a wide range of queries; a scalable runtime; partitioned, LSM-based data storage and indexing (including B+-tree, R-tree, and text indexes); support for external as well as natively stored data; a rich set of built-in types; support for fuzzy, spatial, and temporal types and queries; a built-in notion of data feeds for ingestion of data; and transaction support akin to that of a NoSQL store. Development of AsterixDB began in 2009 and led to a mid-2013 initial open source release. This paper is the first complete description of the resulting open source AsterixDB system. Covered herein are the system's data model, its query language, and its software architecture. Also included are a summary of the current status of the project and a first glimpse into how AsterixDB performs when compared to alternative technologies, including a parallel relational DBMS, a popular NoSQL store, and a popular Hadoop-based SQL data analytics platform, for things that both technologies can do. Also included is a brief description of some initial trials that the system has undergone and the lessons learned (and plans laid) based on those early "customer" engagements.

Noninvasive serial monitoring of the fate of transplanted cells would be invaluable to evaluate the potential therapeutic use of human hepatocyte transplantation. Therefore, we assessed the feasibility of bioluminescent imaging using double or triple fusion lentiviral vectors in a NOD-SCID mouse model transplanted with immortalized human fetal hepatocytes. Lentiviral vectors driven by the CMV promoter were constructed carrying reporter genes: firefly luciferase and green fluorescence protein with or without herpes simplex virus type 1 thymidine kinase. Human fetal hepatocytes immortalized by telomerase reconstitution (FH-hTERT) were successfully transduced with either of these fusion vectors. Two million stably transduced cells selected by fluorescence-activated cell sorting were injected into the spleens of NOD-SCID mice pretreated with methylcholanthrene and monocrotaline. The transplanted mice were serially imaged with a bioluminescence charged-coupled device camera after D-luciferin injection. Bioluminescence signal intensity was highest on day 3 (6.10 +/- 2.02 x 10(5) p/s/cm2/sr, mean +/- SEM), but decreased to 2.26 +/- 1.54 x 10(5) and 7.47 +/- 3.09 x 10(4) p/s/cm2/sr on day 7 and 10, respectively (p = 0.001). ELISA for human albumin in mice sera showed that levels were similar to those of control mice on day 2 (3.25 +/- 0.92 vs. 2.84 +/- 0.59 ng/ml, mean +/- SEM), peaked at 18.04 +/- 3.11 ng/ml on day 7, and decreased to 8.93 +/- 1.40 and 3.54 +/- 0.87 ng/ml on day 14 and 21, respectively (p = 0.02). Real-time quantitative RT-PCR showed gene expression levels of human albumin, alpha1-antitrypsin, and transferrin in mouse liver were 60.7 +/- 6.5%, 26.0 +/- 1.4%, and 156.8 +/- 62.4% of those of primary human adult hepatocytes, respectively, and immunohistochemistry revealed cells with human albumin and alpha1-antitrypsin expression in the mouse liver. In conclusion, our study demonstrated that bioluminescent imaging appears to be a sensitive, noninvasive modali