Architecture for the Next Generation System Management Tools

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gallard, Jerome; Lebre, I Adrien; Morin, Christine

2011-01-01

To get more results or greater accuracy, computational scientists execute their applications on distributed computing platforms such as Clusters, Grids and Clouds. These platforms are different in terms of hardware and software resources as well as locality: some span across multiple sites and multiple administrative domains whereas others are limited to a single site/domain. As a consequence, in order to scale their applica- tions up the scientists have to manage technical details for each target platform. From our point of view, this complexity should be hidden from the scientists who, in most cases, would prefer to focus on their researchmore » rather than spending time dealing with platform configuration concerns. In this article, we advocate for a system management framework that aims to automatically setup the whole run-time environment according to the applications needs. The main difference with regards to usual approaches is that they generally only focus on the software layer whereas we address both the hardware and the software expecta- tions through a unique system. For each application, scientists describe their requirements through the definition of a Virtual Platform (VP) and a Virtual System Environment (VSE). Relying on the VP/VSE definitions, the framework is in charge of: (i) the configuration of the physical infrastructure to satisfy the VP requirements, (ii) the setup of the VP, and (iii) the customization of the execution environment (VSE) upon the former VP. We propose a new formalism that the system can rely upon to successfully perform each of these three steps without burdening the user with the specifics of the configuration for the physical resources, and system management tools. This formalism leverages Goldberg s theory for recursive virtual machines by introducing new concepts based on system virtualization (identity, partitioning, aggregation) and emulation (simple, abstraction). This enables the definition of complex VP/VSE configurations without making assumptions about the hardware and the software re- sources. For each requirement, the system executes the corresponding operation with the appropriate management tool. As a proof of concept, we implemented a first prototype that currently interacts with several system management tools (e.g., OSCAR, the Grid 5000 toolkit, and XtreemOS) and that can be easily extended to integrate new resource brokers or cloud systems such as Nimbus, OpenNebula or Eucalyptus for instance.« less

Increasing Reasoning Awareness: Video Analysis of Students' Two-Party Virtual Patient Interactions.

PubMed

Edelbring, Samuel; Parodis, Ioannis; Lundberg, Ingrid E

2018-02-27

Collaborative reasoning occurs in clinical practice but is rarely developed during education. The computerized virtual patient (VP) cases allow for a stepwise exploration of cases and thus stimulate active learning. Peer settings during VP sessions are believed to have benefits in terms of reasoning but have received scant attention in the literature. The objective of this study was to thoroughly investigate interactions during medical students' clinical reasoning in two-party VP settings. An in-depth exploration of students' interactions in dyad settings of VP sessions was performed. For this purpose, two prerecorded VP sessions lasting 1 hour each were observed, transcribed in full, and analyzed. The transcriptions were analyzed using thematic analysis, and short clips from the videos were selected for subsequent analysis in relation to clinical reasoning and clinical aspects. Four categories of interactions were identified: (1) task-related dialogue, in which students negotiated a shared understanding of the task and strategies for information gathering; (2) case-related insights and perspectives were gained, and the students consolidated and applied preexisting biomedical knowledge into a clinical setting; (3) clinical reasoning interactions were made explicit. In these, hypotheses were followed up and clinical examples were used. The researchers observed interactions not only between students and the VP but also (4) interactions with other resources, such as textbooks. The interactions are discussed in relation to theories of clinical reasoning and peer learning. The dyad VP setting is conducive to activities that promote analytic clinical reasoning. In this setting, components such as peer interaction, access to different resources, and reduced time constraints provided a productive situation in which the students pursued different lines of reasoning. ©Samuel Edelbring, Ioannis Parodis, Ingrid E Lundberg. Originally published in JMIR Medical Education (http://mededu.jmir.org), 27.02.2018.

Increasing Reasoning Awareness: Video Analysis of Students’ Two-Party Virtual Patient Interactions

PubMed Central

Parodis, Ioannis; Lundberg, Ingrid E

2018-01-01

Background Collaborative reasoning occurs in clinical practice but is rarely developed during education. The computerized virtual patient (VP) cases allow for a stepwise exploration of cases and thus stimulate active learning. Peer settings during VP sessions are believed to have benefits in terms of reasoning but have received scant attention in the literature. Objective The objective of this study was to thoroughly investigate interactions during medical students’ clinical reasoning in two-party VP settings. Methods An in-depth exploration of students’ interactions in dyad settings of VP sessions was performed. For this purpose, two prerecorded VP sessions lasting 1 hour each were observed, transcribed in full, and analyzed. The transcriptions were analyzed using thematic analysis, and short clips from the videos were selected for subsequent analysis in relation to clinical reasoning and clinical aspects. Results Four categories of interactions were identified: (1) task-related dialogue, in which students negotiated a shared understanding of the task and strategies for information gathering; (2) case-related insights and perspectives were gained, and the students consolidated and applied preexisting biomedical knowledge into a clinical setting; (3) clinical reasoning interactions were made explicit. In these, hypotheses were followed up and clinical examples were used. The researchers observed interactions not only between students and the VP but also (4) interactions with other resources, such as textbooks. The interactions are discussed in relation to theories of clinical reasoning and peer learning. Conclusions The dyad VP setting is conducive to activities that promote analytic clinical reasoning. In this setting, components such as peer interaction, access to different resources, and reduced time constraints provided a productive situation in which the students pursued different lines of reasoning. PMID:29487043

A randomized trial of teaching clinical skills using virtual and live standardized patients.

PubMed

Triola, M; Feldman, H; Kalet, A L; Zabar, S; Kachur, E K; Gillespie, C; Anderson, M; Griesser, C; Lipkin, M

2006-05-01

We developed computer-based virtual patient (VP) cases to complement an interactive continuing medical education (CME) course that emphasizes skills practice using standardized patients (SP). Virtual patient simulations have the significant advantages of requiring fewer personnel and resources, being accessible at any time, and being highly standardized. Little is known about the educational effectiveness of these new resources. We conducted a randomized trial to assess the educational effectiveness of VPs and SPs in teaching clinical skills. To determine the effectiveness of VP cases when compared with live SP cases in improving clinical skills and knowledge. Randomized trial. Fifty-five health care providers (registered nurses 45%, physicians 15%, other provider types 40%) who attended a CME program. Participants were randomized to receive either 4 live cases (n=32) or 2 live and 2 virtual cases (n=23). Other aspects of the course were identical for both groups. Participants in both groups were equivalent with respect to pre-post workshop improvement in comfort level (P=.66) and preparedness to respond (P=.61), to screen (P=.79), and to care (P=.055) for patients using the skills taught. There was no difference in subjective ratings of effectiveness of the VPs and SPs by participants who experienced both (P=.79). Improvement in diagnostic abilities were equivalent in groups who experienced cases either live or virtually. Improvements in performance and diagnostic ability were equivalent between the groups and participants rated VP and SP cases equally. Including well-designed VPs has a potentially powerful and efficient place in clinical skills training for practicing health care workers.

Biochemical and Functional Characterization of the Ebola Virus VP24 Protein: Implications for a Role in Virus Assembly and Budding

PubMed Central

Han, Ziying; Boshra, Hani; Sunyer, J. Oriol; Zwiers, Susan H.; Paragas, Jason; Harty, Ronald N.

2003-01-01

The VP24 protein of Ebola virus is believed to be a secondary matrix protein and minor component of virions. In contrast, the VP40 protein of Ebola virus is the primary matrix protein and the most abundant virion component. The structure and function of VP40 have been well characterized; however, virtually nothing is known regarding the structure and function of VP24. Wild-type and mutant forms of VP24 were expressed in mammalian cells to gain a better understanding of the biochemical and functional nature of this viral protein. Results from these experiments demonstrated that (i) VP24 localizes to the plasma membrane and perinuclear region in both transfected and Ebola virus-infected cells, (ii) VP24 associates strongly with lipid membranes, (iii) VP24 does not contain N-linked sugars when expressed alone in mammalian cells, (iv) VP24 can oligomerize when expressed alone in mammalian cells, (v) progressive deletions at the N terminus of VP24 resulted in a decrease in oligomer formation and a concomitant increase in the formation of high-molecular-weight aggregates, and (vi) VP24 was present in trypsin-resistant virus like particles released into the media covering VP24-transfected cells. These data indicate that VP24 possesses structural features commonly associated with viral matrix proteins and that VP24 may have a role in virus assembly and budding. PMID:12525613

Virtual patient design: exploring what works and why. A grounded theory study

PubMed Central

Bateman, James; Allen, Maggie; Samani, Dipti; Kidd, Jane; Davies, David

2013-01-01

Objectives Virtual patients (VPs) are online representations of clinical cases used in medical education. Widely adopted, they are well placed to teach clinical reasoning skills. International technology standards mean VPs can be created, shared and repurposed between institutions. A systematic review has highlighted the lack of evidence to support which of the numerous VP designs may be effective, and why. We set out to research the influence of VP design on medical undergraduates. Methods This is a grounded theory study into the influence of VP design on undergraduate medical students. Following a review of the literature and publicly available VP cases, we identified important design properties. We integrated them into two substantial VPs produced for this research. Using purposeful iterative sampling, 46 medical undergraduates were recruited to participate in six focus groups. Participants completed both VPs, an evaluation and a 1-hour focus group discussion. These were digitally recorded, transcribed and analysed using grounded theory, supported by computer-assisted analysis. Following open, axial and selective coding, we produced a theoretical model describing how students learn from VPs. Results We identified a central core phenomenon designated ‘learning from the VP’. This had four categories: VP Construction; External Preconditions; Student–VP Interaction, and Consequences. From these, we constructed a three-layer model describing the interactions of students with VPs. The inner layer consists of the student's cognitive and behavioural preconditions prior to sitting a case. The middle layer considers the VP as an ‘encoded object’, an e-learning artefact and as a ‘constructed activity’, with associated pedagogic and organisational elements. The outer layer describes cognitive and behavioural change. Conclusions This is the first grounded theory study to explore VP design. This original research has produced a model which enhances understanding of how and why the delivery and design of VPs influence learning. The model may be of practical use to authors, institutions and researchers. PMID:23662877

A Scenario-Based Virtual Patient Program to Support Substance Misuse Education.

PubMed

Zlotos, Leon; Power, Ailsa; Hill, Duncan; Chapman, Paul

2016-04-25

Objective. To evaluate virtual patient (VP) programs for injecting equipment provision (IEP) and opiate substitution therapy (OST) services with respect to confidence and knowledge among preregistration pharmacist trainees. Methods. Preregistration trainee pharmacists pilot-tested the VP programs and were invited to complete pre/post and 6-month assessments of knowledge and perceived confidence. Results. One hundred six trainees participated and completed the pre/postassessments. Forty-six (43.4%) participants repeated the assessments at six months. Scores in perceived confidence increased in all domains at both time points postprogram. Knowledge scores were greater posteducation than preeducation. Knowledge scores were also greater six months after education than preeducation. Knowledge scores at six months were lower than posteducation for both programs. Conclusion. Virtual patients programs increased preregistration pharmacists' knowledge and confidence with regard to IEP and OST immediately after use and at six months postprogram. There was a loss of clinical knowledge over time but confidence change was sustained.

T helper cell-mediated interferon-gamma expression after human parvovirus B19 infection: persisting VP2-specific and transient VP1u-specific activity

PubMed Central

Franssila, R; Auramo, J; Modrow, S; Möbs, M; Oker-Blom, C; Käpylä, P; Söderlund-Venermo, M; Hedman, K

2005-01-01

Human parvovirus B19 is a small non-enveloped DNA virus with an icosahedral capsid consisting of proteins of only two species, the major protein VP2 and the minor protein VP1. VP2 is contained within VP1, which has an additional unique portion (VP1u) of 227 amino acids. We determined the ability of eukaryotically expressed parvovirus B19 virus-like particles consisting of VP1 and VP2 in the ratio recommended for vaccine use, or of VP2 alone, to stimulate, in an HLA class II restricted manner, peripheral blood mononuclear cells (PBMC) to proliferate and to secrete interferon gamma (IFN-γ) and interleukin (IL)-10 cytokines among recently and remotely B19 infected subjects. PBMC reactivity with VP1u was determined specifically with a prokaryotically expressed VP1u antigen. In general, B19-specific IFN-γ responses were stronger than IL-10 responses in both recent and remote infection; however, IL-10 responses were readily detectable among both groups, with the exception of patients with relapsed or persisting symptoms who showed strikingly low IL-10 responses. Whereas VP1u-specific IFN-γ responses were very strong among the recently infected subjects, the VP1u-specific IFN-γ and IL-10 responses were virtually absent among the remotely infected subjects. The disappearance of VP1u-specific IFN-γ expression is surprising, as B-cell immunity against VP1u is well maintained. PMID:16178856

Virtual patients design and its effect on clinical reasoning and student experience: a protocol for a randomised factorial multi-centre study.

PubMed

Bateman, James; Allen, Maggie E; Kidd, Jane; Parsons, Nick; Davies, David

2012-08-01

Virtual Patients (VPs) are web-based representations of realistic clinical cases. They are proposed as being an optimal method for teaching clinical reasoning skills. International standards exist which define precisely what constitutes a VP. There are multiple design possibilities for VPs, however there is little formal evidence to support individual design features. The purpose of this trial is to explore the effect of two different potentially important design features on clinical reasoning skills and the student experience. These are the branching case pathways (present or absent) and structured clinical reasoning feedback (present or absent). This is a multi-centre randomised 2 x 2 factorial design study evaluating two independent variables of VP design, branching (present or absent), and structured clinical reasoning feedback (present or absent).The study will be carried out in medical student volunteers in one year group from three university medical schools in the United Kingdom, Warwick, Keele and Birmingham. There are four core musculoskeletal topics. Each case can be designed in four different ways, equating to 16 VPs required for the research. Students will be randomised to four groups, completing the four VP topics in the same order, but with each group exposed to a different VP design sequentially. All students will be exposed to the four designs. Primary outcomes are performance for each case design in a standardized fifteen item clinical reasoning assessment, integrated into each VP, which is identical for each topic. Additionally a 15-item self-reported evaluation is completed for each VP, based on a widely used EViP tool. Student patterns of use of the VPs will be recorded.In one centre, formative clinical and examination performance will be recorded, along with a self reported pre and post-intervention reasoning score, the DTI. Our power calculations indicate a sample size of 112 is required for both primary outcomes. This trial will provide robust evidence to support the effectiveness of different designs of virtual patients, based on student performance and evaluation. The cases and all learning materials will be open access and available on a Creative Commons Attribution-Share-Alike license.

Integrated Computational Approach for Virtual Hit Identification against Ebola Viral Proteins VP35 and VP40.

PubMed

Mirza, Muhammad Usman; Ikram, Nazia

2016-10-26

The Ebola virus (EBOV) has been recognised for nearly 40 years, with the most recent EBOV outbreak being in West Africa, where it created a humanitarian crisis. Mortalities reported up to 30 March 2016 totalled 11,307. However, up until now, EBOV drugs have been far from achieving regulatory (FDA) approval. It is therefore essential to identify parent compounds that have the potential to be developed into effective drugs. Studies on Ebola viral proteins have shown that some can elicit an immunological response in mice, and these are now considered essential components of a vaccine designed to protect against Ebola haemorrhagic fever. The current study focuses on chemoinformatic approaches to identify virtual hits against Ebola viral proteins (VP35 and VP40), including protein binding site prediction, drug-likeness, pharmacokinetic and pharmacodynamic properties, metabolic site prediction, and molecular docking. Retrospective validation was performed using a database of non-active compounds, and early enrichment of EBOV actives at different false positive rates was calculated. Homology modelling and subsequent superimposition of binding site residues on other strains of EBOV were carried out to check residual conformations, and hence to confirm the efficacy of potential compounds. As a mechanism for artefactual inhibition of proteins through non-specific compounds, virtual hits were assessed for their aggregator potential compared with previously reported aggregators. These systematic studies have indicated that a few compounds may be effective inhibitors of EBOV replication and therefore might have the potential to be developed as anti-EBOV drugs after subsequent testing and validation in experiments in vivo.

Quantifying metal artefact reduction using virtual monochromatic dual-layer detector spectral CT imaging in unilateral and bilateral total hip prostheses.

PubMed

Wellenberg, R H H; Boomsma, M F; van Osch, J A C; Vlassenbroek, A; Milles, J; Edens, M A; Streekstra, G J; Slump, C H; Maas, M

2017-03-01

To quantify the impact of prosthesis material and design on the reduction of metal artefacts in total hip arthroplasties using virtual monochromatic dual-layer detector Spectral CT imaging. The water-filled total hip arthroplasty phantom was scanned on a novel 128-slice Philips IQon dual-layer detector Spectral CT scanner at 120-kVp and 140-kVp at a standard computed tomography dose index of 20.0mGy. Several unilateral and bilateral hip prostheses consisting of different metal alloys were inserted and combined which were surrounded by 18 hydroxyapatite calcium carbonate pellets representing bone. Images were reconstructed with iterative reconstruction and analysed at monochromatic energies ranging from 40 to 200keV. CT numbers in Hounsfield Units (HU), noise measured as the standard deviation in HU, signal-to-noise-ratios (SNRs) and contrast-to-noise-ratios (CNRs) were analysed within fixed regions-of-interests placed in and around the pellets. In 70 and 74keV virtual monochromatic images the CT numbers of the pellets were similar to 120-kVp and 140-kVp polychromatic results, therefore serving as reference. A separation into three categories of metal artefacts was made (no, mild/moderate and severe) where pellets were categorized based on HU deviations. At high keV values overall image contrast was reduced. For mild/moderate artefacts, the highest average CNRs were attained with virtual monochromatic 130keV images, acquired at 140-kVp. Severe metal artefacts were not reduced. In 130keV images, only mild/moderate metal artefacts were significantly reduced compared to 70 and 74keV images. Deviations in CT numbers, noise, SNRs and CNRs due to metal artefacts were decreased with respectively 64%, 57%, 62% and 63% (p<0.001) compared to unaffected pellets. Optimal keVs, based on CNRs, for different unilateral and bilateral metal hip prostheses consisting of different metal alloys varied from 74 to 150keV. The Titanium alloy resulted in less severe artefacts and were reduced more effectively compared to the Cobalt alloy. Virtual monochromatic dual-layer Spectral CT imaging results in a significant reduction of streak artefacts produced by beam-hardening in mild and moderate artefacts by improving CT number accuracy, SNRs and CNRs, while decreasing noise values in a total hip arthroplasty phantom. An optimal monochromatic energy of 130keV was found ranging from 74keV to 150keV for different unilateral and bilateral hip prostheses consisting of different metal alloys. Copyright © 2017 Elsevier Ireland Ltd. All rights reserved.

Automated flight path planning for virtual endoscopy.

PubMed

Paik, D S; Beaulieu, C F; Jeffrey, R B; Rubin, G D; Napel, S

1998-05-01

In this paper, a novel technique for rapid and automatic computation of flight paths for guiding virtual endoscopic exploration of three-dimensional medical images is described. While manually planning flight paths is a tedious and time consuming task, our algorithm is automated and fast. Our method for positioning the virtual camera is based on the medial axis transform but is much more computationally efficient. By iteratively correcting a path toward the medial axis, the necessity of evaluating simple point criteria during morphological thinning is eliminated. The virtual camera is also oriented in a stable viewing direction, avoiding sudden twists and turns. We tested our algorithm on volumetric data sets of eight colons, one aorta and one bronchial tree. The algorithm computed the flight paths in several minutes per volume on an inexpensive workstation with minimal computation time added for multiple paths through branching structures (10%-13% per extra path). The results of our algorithm are smooth, centralized paths that aid in the task of navigation in virtual endoscopic exploration of three-dimensional medical images.

Medical Students' Attitudes towards the Use of Virtual Patients

ERIC Educational Resources Information Center

Sobocan, M.; Klemenc-Ketis, Z.

2017-01-01

An increasing number of virtual patients (VPs) are being used in the classroom, which raises questions about how to implement VPs to improve students' satisfaction and enhance their learning. This study developed and validated a scale that measures acceptability and attitudes of medical students towards the use of the VP education tool in the…

Training staff to create simple interactive virtual patients: the impact on a medical and healthcare institution.

PubMed

Round, Jonathan; Conradi, Emily; Poulton, Terry

2009-08-01

Virtual patients (VPs) are excellent teaching tools for developing clinical decision-making skills and improving clinical competency, but are believed to be very expensive and time consuming to make. The aim of this study was to establish whether it was possible to design a workshop for VP creation, which would enable teaching staff to create interactive, immersive VPs quickly, and with limited technical support. The Centre for Medical and Healthcare Education at St George's University of London's (SGUL) medical school developed an ergonomic and generic 'model' for VP creation, simple enough for clinicians and educators to use, yet flexible enough to simulate real decisions through non-linear pathways. One-day workshops were set up to support the development of VPs by medical and healthcare educators. VP creation workshops have been successfully trialled, attracting a large number of clinicians and educators from a range of medicine and healthcare courses. Feedback from participants was very positive. Educators, organised into small groups, were unable to complete VPs within the workshop, but many groups completed a VP after the workshop. Interest was highest in mental health. The workshops catalysed a change in the awareness of the value of VPs, with staff directly integrating VPs into the curriculum.

Virtual surgical planning in endoscopic skull base surgery.

PubMed

Haerle, Stephan K; Daly, Michael J; Chan, Harley H L; Vescan, Allan; Kucharczyk, Walter; Irish, Jonathan C

2013-12-01

Skull base surgery (SBS) involves operative tasks in close proximity to critical structures in a complex three-dimensional (3D) anatomy. The aim was to investigate the value of virtual planning (VP) based on preoperative magnetic resonance imaging (MRI) for surgical planning in SBS and to compare the effects of virtual planning with 3D contours between the expert and the surgeon in training. Retrospective analysis. Twelve patients with manually segmented anatomical structures based on preoperative MRI were evaluated by eight surgeons in a randomized order using a validated National Aeronautics and Space Administration Task Load Index (NASA-TLX) questionnaire. Multivariate analysis revealed significant reduction of workload when using VP (P<.0001) compared to standard planning. Further, it showed that the experience level of the surgeon had a significant effect on the NASA-TLX differences (P<.05). Additional subanalysis did not reveal any significant findings regarding which type of surgeon benefits the most (P>.05). Preoperative anatomical segmentation with virtual surgical planning using contours in endoscopic SBS significantly reduces the workload for the expert and the surgeon in training. Copyright © 2013 The American Laryngological, Rhinological and Otological Society, Inc.

Web-Based Virtual Patients in Nursing Education: Development and Validation of Theory-Anchored Design and Activity Models

PubMed Central

2014-01-01

Background Research has shown that nursing students find it difficult to translate and apply their theoretical knowledge in a clinical context. Virtual patients (VPs) have been proposed as a learning activity that can support nursing students in their learning of scientific knowledge and help them integrate theory and practice. Although VPs are increasingly used in health care education, they still lack a systematic consistency that would allow their reuse outside of their original context. There is therefore a need to develop a model for the development and implementation of VPs in nursing education. Objective The aim of this study was to develop and evaluate a virtual patient model optimized to the learning and assessment needs in nursing education. Methods The process of modeling started by reviewing theoretical frameworks reported in the literature and used by practitioners when designing learning and assessment activities. The Outcome-Present State Test (OPT) model was chosen as the theoretical framework. The model was then, in an iterative manner, developed and optimized to the affordances of virtual patients. Content validation was performed with faculty both in terms of the relevance of the chosen theories but also its applicability in nursing education. The virtual patient nursing model was then instantiated in two VPs. The students’ perceived usefulness of the VPs was investigated using a questionnaire. The result was analyzed using descriptive statistics. Results A virtual patient Nursing Design Model (vpNDM) composed of three layers was developed. Layer 1 contains the patient story and ways of interacting with the data, Layer 2 includes aspects of the iterative process of clinical reasoning, and finally Layer 3 includes measurable outcomes. A virtual patient Nursing Activity Model (vpNAM) was also developed as a guide when creating VP-centric learning activities. The students perceived the global linear VPs as a relevant learning activity for the integration of theory and practice. Conclusions Virtual patients that are adapted to the nursing paradigm can support nursing students’ development of clinical reasoning skills. The proposed virtual patient nursing design and activity models will allow the systematic development of different types of virtual patients from a common model and thereby create opportunities for sharing pedagogical designs across technical solutions. PMID:24727709

The ebolavirus VP24 interferon antagonist

PubMed Central

Zhang, Adrianna P.P.; Abelson, Dafna M.; Bornholdt, Zachary A.; Liu, Tong; Woods, Jr, Virgil L.; Saphire, Erica Ollmann

2012-01-01

Suppression during the early phases of the immune system often correlates directly with a fatal outcome for the host. The ebolaviruses, some of the most lethal viruses known, appear to cripple initial stages of the host defense network via multiple distinct paths. Two of the eight viral proteins are critical for immunosuppression. One of these proteins is VP35, which binds double-stranded RNA and antagonizes several antiviral signaling pathways.1,2 The other protein is VP24, which binds transporter molecules to prevent STAT1 translocation.3 A more recent discovery is that VP24 also binds STAT1 directly,4 suggesting that VP24 may operate in at least two separate branches of the interferon pathway. New crystal structures of VP24 derived from pathogenic and nonpathogenic ebolaviruses reveal its novel, pyramidal fold, upon which can be mapped sites required for virulence and for STAT1 binding. These structures of VP24, and new information about its direct binding to STAT1, provide avenues by which we may explore its many roles in the viral life cycle, and reasons for differences in pathogenesis among the ebolaviruses. PMID:23076242

The ebolavirus VP24 interferon antagonist: know your enemy.

PubMed

Zhang, Adrianna P P; Abelson, Dafna M; Bornholdt, Zachary A; Liu, Tong; Woods, Virgil L; Saphire, Erica Ollmann

2012-08-15

Suppression during the early phases of the immune system often correlates directly with a fatal outcome for the host. The ebolaviruses, some of the most lethal viruses known, appear to cripple initial stages of the host defense network via multiple distinct paths. Two of the eight viral proteins are critical for immunosuppression. One of these proteins is VP35, which binds double-stranded RNA and antagonizes several antiviral signaling pathways. The other protein is VP24, which binds transporter molecules to prevent STAT1 translocation. A more recent discovery is that VP24 also binds STAT1 directly, suggesting that VP24 may operate in at least two separate branches of the interferon pathway. New crystal structures of VP24 derived from pathogenic and nonpathogenic ebolaviruses reveal its novel, pyramidal fold, upon which can be mapped sites required for virulence and for STAT1 binding. These structures of VP24, and new information about its direct binding to STAT1, provide avenues by which we may explore its many roles in the viral life cycle, and reasons for differences in pathogenesis among the ebolaviruses.

Renal Cyst Pseudoenhancement: Intraindividual Comparison Between Virtual Monochromatic Spectral Images and Conventional Polychromatic 120-kVp Images Obtained During the Same CT Examination and Comparisons Among Images Reconstructed Using Filtered Back Projection, Adaptive Statistical Iterative Reconstruction, and Model-Based Iterative Reconstruction

PubMed Central

Yamada, Yoshitake; Yamada, Minoru; Sugisawa, Koichi; Akita, Hirotaka; Shiomi, Eisuke; Abe, Takayuki; Okuda, Shigeo; Jinzaki, Masahiro

2015-01-01

Abstract The purpose of this study was to compare renal cyst pseudoenhancement between virtual monochromatic spectral (VMS) and conventional polychromatic 120-kVp images obtained during the same abdominal computed tomography (CT) examination and among images reconstructed using filtered back projection (FBP), adaptive statistical iterative reconstruction (ASIR), and model-based iterative reconstruction (MBIR). Our institutional review board approved this prospective study; each participant provided written informed consent. Thirty-one patients (19 men, 12 women; age range, 59–85 years; mean age, 73.2 ± 5.5 years) with renal cysts underwent unenhanced 120-kVp CT followed by sequential fast kVp-switching dual-energy (80/140 kVp) and 120-kVp abdominal enhanced CT in the nephrographic phase over a 10-cm scan length with a random acquisition order and 4.5-second intervals. Fifty-one renal cysts (maximal diameter, 18.0 ± 14.7 mm [range, 4–61 mm]) were identified. The CT attenuation values of the cysts as well as of the kidneys were measured on the unenhanced images, enhanced VMS images (at 70 keV) reconstructed using FBP and ASIR from dual-energy data, and enhanced 120-kVp images reconstructed using FBP, ASIR, and MBIR. The results were analyzed using the mixed-effects model and paired t test with Bonferroni correction. The attenuation increases (pseudoenhancement) of the renal cysts on the VMS images reconstructed using FBP/ASIR (least square mean, 5.0/6.0 Hounsfield units [HU]; 95% confidence interval, 2.6–7.4/3.6–8.4 HU) were significantly lower than those on the conventional 120-kVp images reconstructed using FBP/ASIR/MBIR (least square mean, 12.1/12.8/11.8 HU; 95% confidence interval, 9.8–14.5/10.4–15.1/9.4–14.2 HU) (all P < .001); on the other hand, the CT attenuation values of the kidneys on the VMS images were comparable to those on the 120-kVp images. Regardless of the reconstruction algorithm, 70-keV VMS images showed a lower degree of pseudoenhancement of renal cysts than 120-kVp images, while maintaining kidney contrast enhancement comparable to that on 120-kVp images. PMID:25881852

TU-A-12A-12: Improved Airway Measurement Accuracy for Low Dose Quantitative CT (qCT) Using Statistical (ASIR), at Reduced DFOV, and High Resolution Kernels in a Phantom and Swine Model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yadava, G; Imai, Y; Hsieh, J

2014-06-15

Purpose: Quantitative accuracy of Iodine Hounsfield Unit (HU) in conventional single-kVp scanning is susceptible to beam-hardening effect. Dual-energy CT has unique capabilities of quantification using monochromatic CT images, but this scanning mode requires the availability of the state-of-the-art CT scanner and, therefore, is limited in routine clinical practice. Purpose of this work was to develop a beam-hardening-correction (BHC) for single-kVp CT that can linearize Iodine projections at any nominal energy, apply this approach to study Iodine response with respect to keV, and compare with dual-energy based monochromatic images obtained from material-decomposition using 80kVp and 140kVp. Methods: Tissue characterization phantoms (Gammexmore » Inc.), containing solid-Iodine inserts of different concentrations, were scanned using GE multi-slice CT scanner at 80, 100, 120, and 140 kVp. A model-based BHC algorithm was developed where Iodine was estimated using re-projection of image volume and corrected through an iterative process. In the correction, the re-projected Iodine was linearized using a polynomial mapping between monochromatic path-lengths at various nominal energies (40 to 140 keV) and physically modeled polychromatic path-lengths. The beam-hardening-corrected 80kVp and 140kVp images (linearized approximately at effective energy of the beam) were used for dual-energy material-decomposition in Water-Iodine basis-pair followed by generation of monochromatic images. Characterization of Iodine HU and noise in the images obtained from singlekVp with BHC at various nominal keV, and corresponding dual-energy monochromatic images, was carried out. Results: Iodine HU vs. keV response from single-kVp with BHC and dual-energy monochromatic images were found to be very similar, indicating that single-kVp data may be used to create material specific monochromatic equivalent using modelbased projection linearization. Conclusion: This approach may enable quantification of Iodine contrast enhancement and potential reduction in injected contrast without using dual-energy scanning. However, in general, dual-energy scanning has unique value in material characterization and quantification, and its value cannot be discounted. GE Healthcare Employee.« less

A Scenario-Based Virtual Patient Program to Support Substance Misuse Education

PubMed Central

Power, Ailsa; Hill, Duncan; Chapman, Paul

2016-01-01

Objective. To evaluate virtual patient (VP) programs for injecting equipment provision (IEP) and opiate substitution therapy (OST) services with respect to confidence and knowledge among preregistration pharmacist trainees. Methods. Preregistration trainee pharmacists pilot-tested the VP programs and were invited to complete pre/post and 6-month assessments of knowledge and perceived confidence. Results. One hundred six trainees participated and completed the pre/postassessments. Forty-six (43.4%) participants repeated the assessments at six months. Scores in perceived confidence increased in all domains at both time points postprogram. Knowledge scores were greater posteducation than preeducation. Knowledge scores were also greater six months after education than preeducation. Knowledge scores at six months were lower than posteducation for both programs. Conclusion. Virtual patients programs increased preregistration pharmacists’ knowledge and confidence with regard to IEP and OST immediately after use and at six months postprogram. There was a loss of clinical knowledge over time but confidence change was sustained. PMID:27170819

Robotics virtual rail system and method

DOEpatents

Bruemmer, David J [Idaho Falls, ID; Few, Douglas A [Idaho Falls, ID; Walton, Miles C [Idaho Falls, ID

2011-07-05

A virtual track or rail system and method is described for execution by a robot. A user, through a user interface, generates a desired path comprised of at least one segment representative of the virtual track for the robot. Start and end points are assigned to the desired path and velocities are also associated with each of the at least one segment of the desired path. A waypoint file is generated including positions along the virtual track representing the desired path with the positions beginning from the start point to the end point including the velocities of each of the at least one segment. The waypoint file is sent to the robot for traversing along the virtual track.

SU-E-CAMPUS-J-06: The Impact of CT-Scan Energy On Range Uncertainty in Proton Therapy Planning

DOE Office of Scientific and Technical Information (OSTI.GOV)

Grantham, K; Li, H; Zhao, T

2014-06-15

Purpose: To investigate the impact of tube potential (kVp) on the CTnumber (HU) to proton stopping power ratio (PSPR) conversion table; the range uncertainty and the dosimetric change introduced by a mismatch in kVp between the CT and the HU to PSPR table used to calculate dose are analyzed. Methods: A CIRS CT-ED phantom was scanned with a Philips Brilliance 64-slice scanner under 90kVp and 120kVp tube potentials. Two HU to PSPR curves were then created. Using Eclipse (Varian) a treatment plan was created for a single beam in a water phantom (HU=0) passing through a wedge-shaped heterogeneity (HU=1488). Themore » dose was recalculated by changing only the HU to PSPR table used in the dose calculation. The change in range (the distal 90% isodose line) relative to a distal structure was recorded as a function of heterogeneity thickness in the beam. To show the dosimetric impact of a mismatch in kVp between the CT and the HU to PSPR table, we repeated this procedure using a clinical plan comparing DVH data. Results: The HU to PSPR tables diverge for low-density bone and higher density structures. In the phantom plan, the divergence of the tables results in a change in range of ~1mm per cm of bone in the beam path for the HU used. For the clinical plan, a mismatch in kVp showed a 28% increase in mean dose to the brainstem along with a 10% increase in maximum dose to the brainstem center. Conclusion: A mismatch in kVp between the CT and the HU to PSPR table can introduce significant uncertainty in the proton beam range. For dense bone, the measured range uncertainty is about 1mm per cm of bone in the beam. CT-scan energy verification should be employed, particularly when high-density media is in the proton beam path.« less

Introduction of virtual patients onto a final year anesthesia course: Hong Kong experience

PubMed Central

Leung, Joseph YC; Critchley, Lester AH; Yung, Alex LK; Kumta, Shekhar M

2011-01-01

e-Learning has revolutionized the way in which undergraduate medical education is delivered. One e-learning tool of note is the virtual patient (VP), a type of computer software that simulates real-life clinical scenarios, in which the learner emulates the role of health care provider to obtain the history, conduct examination, and make diagnoses and management decisions. VPs have been in use since 1993. Early designs were based on serial screen-cards of patient history, examination, investigations, diagnoses, treatment, and outcome, which the learner explored. With the development of web technology, VPs can now be accessed via the Internet and are more versatile, supporting different structural designs to suit a variety of learning objectives, and they can branch via different routes through a case. Using VPs has a number of advantages: 1) VPs improve access to learning material, 2) VPs help learners to acquire higher order cognitive skills like strategic thinking and decision making, 3) VPs provide a safe environment to practice, 4) VPs help to teach interdisciplinary care, and 5) VPs can be used instead of patients for examination. A number of well-known VP player systems are in use today: CASUS, CAMPUS, web-based Simulation of Patients, OpenLabyrinth, and vpSim. At the Chinese University of Hong Kong, we have also developed a web-based VP authoring and player system called Formative Assessment Case Studies (FACS), which is run by our Teaching and Learning Resources Centre. FACS has been integrated into Year-5 Anesthesia teaching since 2006. Three VP products have been developed: Anaesthesia FACS (six cases) that teaches preoperative assessment, Acute Pain Management FACS, and an eight-part longitudinal VP which tells the story of a patient’s stay, and anesthesia care, for routine gynecological surgery. Students spend about 3 hours on each during a 2-week clinical attachment. Our VPs have been well received and have overcome problems of providing adequate clinical exposure. PMID:23745078

Introduction of virtual patients onto a final year anesthesia course: Hong Kong experience.

PubMed

Leung, Joseph Yc; Critchley, Lester Ah; Yung, Alex Lk; Kumta, Shekhar M

2011-01-01

e-Learning has revolutionized the way in which undergraduate medical education is delivered. One e-learning tool of note is the virtual patient (VP), a type of computer software that simulates real-life clinical scenarios, in which the learner emulates the role of health care provider to obtain the history, conduct examination, and make diagnoses and management decisions. VPs have been in use since 1993. Early designs were based on serial screen-cards of patient history, examination, investigations, diagnoses, treatment, and outcome, which the learner explored. With the development of web technology, VPs can now be accessed via the Internet and are more versatile, supporting different structural designs to suit a variety of learning objectives, and they can branch via different routes through a case. Using VPs has a number of advantages: 1) VPs improve access to learning material, 2) VPs help learners to acquire higher order cognitive skills like strategic thinking and decision making, 3) VPs provide a safe environment to practice, 4) VPs help to teach interdisciplinary care, and 5) VPs can be used instead of patients for examination. A number of well-known VP player systems are in use today: CASUS, CAMPUS, web-based Simulation of Patients, OpenLabyrinth, and vpSim. At the Chinese University of Hong Kong, we have also developed a web-based VP authoring and player system called Formative Assessment Case Studies (FACS), which is run by our Teaching and Learning Resources Centre. FACS has been integrated into Year-5 Anesthesia teaching since 2006. Three VP products have been developed: Anaesthesia FACS (six cases) that teaches preoperative assessment, Acute Pain Management FACS, and an eight-part longitudinal VP which tells the story of a patient's stay, and anesthesia care, for routine gynecological surgery. Students spend about 3 hours on each during a 2-week clinical attachment. Our VPs have been well received and have overcome problems of providing adequate clinical exposure.

The use of a virtual patient case in an OSCE-based exam--a pilot study.

PubMed

Courteille, O; Bergin, R; Stockeld, D; Ponzer, S; Fors, U

2008-01-01

This study focuses on a skills test based clinical assessment where 118 fourth-year medical students at the four teaching hospitals of Karolinska Institutet participated in the same 12-module OSCE. The goal of one of the twelve examination modules was to assess the students' skills and ability to solve a virtual patient (VP) case (the ISP system), which included medical history taking, lab tests, physical examinations and suggestion of a preliminary diagnosis. The primary aim of this study was to evaluate the potential of a VP as a possible tool for assessment of clinical reasoning and problem solving ability among medical students. The feeling of realism of the VP and its possible affective impact on the student's confidence were also investigated. We observed and analysed students' reactions, engagement and performance (activity log files) during their interactive sessions with the simulation. An individual human assistant was provided along with the computer simulation and the videotaped interaction student/assistant was then analysed in detail and related to the students' outcomes. The results indicate possible advantages of using ISP-like systems for assessment. The VP was for instance able to reliably differentiate between students' performances but some weaknesses were also identified, like a confounding influence on students' outcomes by the assistants used. Significant differences, affecting the results, were found between the students in their degree of affective response towards the system as well as the perceived usefulness of assistance. Students need to be trained beforehand in mastering the assessment tool. Rating compliance needs to be targeted before VP-based systems like ISP can be used in exams and if such systems would be used in high-stake exams, the use of human assistants should be limited and scoring rubrics validated (and preferably automated).

Image reconstruction and system modeling techniques for virtual-pinhole PET insert systems

PubMed Central

Keesing, Daniel B; Mathews, Aswin; Komarov, Sergey; Wu, Heyu; Song, Tae Yong; O'Sullivan, Joseph A; Tai, Yuan-Chuan

2012-01-01

Virtual-pinhole PET (VP-PET) imaging is a new technology in which one or more high-resolution detector modules are integrated into a conventional PET scanner with lower-resolution detectors. It can locally enhance the spatial resolution and contrast recovery near the add-on detectors, and depending on the configuration, may also increase the sensitivity of the system. This novel scanner geometry makes the reconstruction problem more challenging compared to the reconstruction of data from a standalone PET scanner, as new techniques are needed to model and account for the non-standard acquisition. In this paper, we present a general framework for fully 3D modeling of an arbitrary VP-PET insert system. The model components are incorporated into a statistical reconstruction algorithm to estimate an image from the multi-resolution data. For validation, we apply the proposed model and reconstruction approach to one of our custom-built VP-PET systems – a half-ring insert device integrated into a clinical PET/CT scanner. Details regarding the most important implementation issues are provided. We show that the proposed data model is consistent with the measured data, and that our approach can lead to reconstructions with improved spatial resolution and lesion detectability. PMID:22490983

Bending the Curve: Sensitivity to Bending of Curved Paths and Application in Room-Scale VR.

PubMed

Langbehn, Eike; Lubos, Paul; Bruder, Gerd; Steinicke, Frank

2017-04-01

Redirected walking (RDW) promises to allow near-natural walking in an infinitely large virtual environment (VE) by subtle manipulations of the virtual camera. Previous experiments analyzed the human sensitivity to RDW manipulations by focusing on the worst-case scenario, in which users walk perfectly straight ahead in the VE, whereas they are redirected on a circular path in the real world. The results showed that a physical radius of at least 22 meters is required for undetectable RDW. However, users do not always walk exactly straight in a VE. So far, it has not been investigated how much a physical path can be bent in situations in which users walk a virtual curved path instead of a straight one. Such curved walking paths can be often observed, for example, when users walk on virtual trails, through bent corridors, or when circling around obstacles. In such situations the question is not, whether or not the physical path can be bent, but how much the bending of the physical path may vary from the bending of the virtual path. In this article, we analyze this question and present redirection by means of bending gains that describe the discrepancy between the bending of curved paths in the real and virtual environment. Furthermore, we report the psychophysical experiments in which we analyzed the human sensitivity to these gains. The results reveal encouragingly wider detection thresholds than for straightforward walking. Based on our findings, we discuss the potential of curved walking and present a first approach to leverage bent paths in a way that can provide undetectable RDW manipulations even in room-scale VR.

A Learner-Created Virtual Patient Curriculum for Surgical Residents: Successes and Failures.

PubMed

McKendy, Katherine M; Posel, Nancy; Fleiszer, David M; Vassiliou, Melina C

2016-01-01

To determine the feasibility and effectiveness of a learner-created virtual patient (VP) curriculum for postgraduate year 2 surgical residents. Using a social-constructivist model of learning, we designed a learner-created VP curriculum to help postgraduate year 2 residents prepare for their in-training surgical examination. Each resident was assigned to create a VP curriculum based on the learning objectives for this examination, and VP cases were then disseminated to all residents for completion. To measure the learning effects of the curriculum, participants completed 2 simulated in-training examinations, both at the beginning and at the end of the intervention. Study participants also participated in a focus group and completed an online questionnaire about the perceived learning value of the curriculum. The study was conducted at the McGill University Health Centre, a tertiary care hospital in Montreal, Canada. In total, 24 residents from 7 surgical specialties completed both the pretest and posttest, as well as took part in the creation of a VP curriculum. Of those 24 residents, only 19 residents completed the cases created by their peers, with 7 completing greater than 50% of the cases and 12 completing less than 50%. In all 17 residents responded to the online questionnaire and 11 residents participated in the focus group. The VP curriculum failed to improve scores from pretest (59.6%, standard deviation = 8.1) to posttest (55.4%, standard deviation = 6.6; p = 0.01) on the simulated in-training examination. Nonetheless, survey results demonstrated that most residents felt that creating a VP case (89%) and completing cases created by their peers (71%) had educational value. Overall, 71% preferred active participation in a curriculum to traditional didactic teaching. The focus group identified time-related constraints, concern about the quality of the peer-created cases, and questioning of the relationship between the curriculum and the Surgical Foundations examination as barriers to the success of the curriculum. Despite the fact that a learner-created VP curriculum did not improve scores on a mock in training examination, residents viewed this intervention as a valuable educational experience. Although there were barriers to the implementation of a learner-created curriculum, it is nonetheless important to try and integrate pedagogical concepts into the instructional design of curricula for surgical residents. Copyright © 2016 Association of Program Directors in Surgery. Published by Elsevier Inc. All rights reserved.

Dynamics of study strategies and teacher regulation in virtual patient learning activities: a cross sectional survey.

PubMed

Edelbring, Samuel; Wahlström, Rolf

2016-04-23

Students' self-regulated learning becomes essential with increased use of exploratory web-based activities such as virtual patients (VPs). The purpose was to investigate the interplay between students' self-regulated learning strategies and perceived benefit in VP learning activities. A cross-sectional study (n = 150) comparing students' study strategies and perceived benefit of a virtual patient learning activity in a clinical clerkship preparatory course. Teacher regulation varied among three settings and was classified from shared to strong. These settings were compared regarding their respective relations between regulation strategies and perceived benefit of the virtual patient activity. Self-regulation learning strategy was generally associated with perceived benefit of the VP activities (rho 0.27, p < 0.001), but was not true in all settings. The association was higher in the two strongly regulated settings. The external regulation strategy did generally associate weakly with perceived benefit (rho 0.17, p < 0.05) with large variations between settings. The flexible student-autonomous appeal of virtual patients should not lead to the dismissal of guidance and related course activities. External teacher and peer regulation seem to be productive for increasing learners' perceived benefit. Awareness of the interplay among teacher regulation (external) and various study strategies can increase the value of flexible web-based learning resources to students.

The role of intellectual property in creating, sharing and repurposing virtual patients.

PubMed

Campbell, Gabrielle; Miller, Angela; Balasubramaniam, Chara

2009-08-01

Medical schools are integrating more technology into the training of health care practitioners. Electronic Virtual Patients (VPs) provide interactive simulations to facilitate learning. The time, cost and effort required to create robust VPs on an individual school basis are significant; sharing of VPs by medical schools allows for access to a broad range of VPs across a variety of disciplines with lower investment. When this digital content is shared with other schools and distributed widely, digital copyright issues come into play. Unless all intellectual property rights (IPRs) and plans of the authors regarding the VP are confirmed upfront, the ability of the school to share the VP may be inhibited. Schools should also identify under what licensing/sharing model they plan to distribute the VPs - how do you plan to share the VPs and what will allow users to do with the VPs in the context of IPRs? This article highlights the role of IPRs in VPs and discusses a case-study of a European Virtual Patient collaboration to demonstrate how IPRs were managed.

Educational potential of a virtual patient system for caring for traumatized patients in primary care

PubMed Central

2013-01-01

Background Virtual Patients (VPs) have been used in undergraduate healthcare education for many years. This project is focused on using VPs for training professionals to care for highly vulnerable patient populations. The aim of the study was to evaluate if Refugee Trauma VPs was perceived as an effective and engaging learning tool by primary care professionals (PCPs) in a Primary Health Care Centre (PHC). Methods A VP system was designed to create realistic and engaging VP cases for Refugee Trauma for training refugee patient interview, use of established trauma and mental health instruments as well as to give feedback to the learners. The patient interview section was based on video clips with a Bosnian actor with a trauma story and mental health problems. The video clips were recorded in Bosnian language to further increase the realism, but also subtitled in English. The system was evaluated by 11 volunteering primary health clinicians at the Lynn Community Health Centre, Lynn, Massachusetts, USA. The participants were invited to provide insights/feedback about the system’s usefulness and educational value. A mixed methodological approach was used, generating both quantitative and qualitative data. Results Self-reported dimensions of clinical care, pre and post questionnaire questions on the PCPs clinical worldview, motivation to use the VP, and IT Proficiency. Construct items used in these questionnaires had previously demonstrated high face and construct validity. The participants ranked the mental status examination more positively after the simulation exercise compared to before the simulation. Follow up interviews supported the results. Conclusions Even though virtual clinical encounters are quite a new paradigm in PHC, the participants in the present study considered our VP case to be a relevant and promising educational tool. Next phase of our project will be a RCT study including comparison with specially prepared paper-cases and determinative input on improving clinical diagnosis and treatment of the traumatized refugee patient. PMID:23957962

Very preterm/very low birthweight infants' attachment: infant and maternal characteristics.

PubMed

Wolke, Dieter; Eryigit-Madzwamuse, Suna; Gutbrod, Tina

2014-01-01

To investigate whether there are differences in attachment security and disorganisation between very preterm or very low birthweight (VP/VLBW) (<32 weeks gestation or <1500 g birthweight) and full-term infants (37-42 weeks gestation) and whether the pathways to disorganised attachment differ between VP/VLBW and full-term infants. The sample with complete longitudinal data consisted of 71 VP/VLBW and 105 full-term children and their mothers matched for twin status, maternal age, income and maternal education. Infant attachment was assessed with the Strange Situation Assessment at 18 months of age. Maternal sensitivity in the VP/VLBW and full-term samples was rated by neonatal nurses and community midwives in the neonatal period, respectively, and mother-infant interaction was observed at 3 months. Infant difficultness was assessed by maternal report at 3 months and infant's developmental status was assessed with the Bayley Scales (BSID-II). Most VP/VLBW (61%) and full-term (72%) children were found to be securely attached. However, more VP/VLBW (32%) than full-term children (17%) had disorganised attachment. Longitudinal path analysis found that maternal sensitivity was predictive of attachment disorganisation in full-term children. In contrast, infant's distressing cry and infant's developmental delay, but not maternal sensitivity, were predictive of disorganised attachment in VP/VLBW children. A third of VP/VLBW children showed disorganised attachment. Underlying neurodevelopmental problems associated with VP/VLBW birth appear to be a common pathway to a range of social relationship problems in this group. Clinicians should be aware that disorganised attachment and relationship problems in VP/VLBW infants are frequent despite sensitive parenting.

Estimation of detection thresholds for redirected walking techniques.

PubMed

Steinicke, Frank; Bruder, Gerd; Jerald, Jason; Frenz, Harald; Lappe, Markus

2010-01-01

In immersive virtual environments (IVEs), users can control their virtual viewpoint by moving their tracked head and walking through the real world. Usually, movements in the real world are mapped one-to-one to virtual camera motions. With redirection techniques, the virtual camera is manipulated by applying gains to user motion so that the virtual world moves differently than the real world. Thus, users can walk through large-scale IVEs while physically remaining in a reasonably small workspace. In psychophysical experiments with a two-alternative forced-choice task, we have quantified how much humans can unknowingly be redirected on physical paths that are different from the visually perceived paths. We tested 12 subjects in three different experiments: (E1) discrimination between virtual and physical rotations, (E2) discrimination between virtual and physical straightforward movements, and (E3) discrimination of path curvature. In experiment E1, subjects performed rotations with different gains, and then had to choose whether the visually perceived rotation was smaller or greater than the physical rotation. In experiment E2, subjects chose whether the physical walk was shorter or longer than the visually perceived scaled travel distance. In experiment E3, subjects estimate the path curvature when walking a curved path in the real world while the visual display shows a straight path in the virtual world. Our results show that users can be turned physically about 49 percent more or 20 percent less than the perceived virtual rotation, distances can be downscaled by 14 percent and upscaled by 26 percent, and users can be redirected on a circular arc with a radius greater than 22 m while they believe that they are walking straight.

Implementation of dual-energy technique for virtual monochromatic and linearly mixed CBCTs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li Hao; Giles, William; Ren Lei

Purpose: To implement dual-energy imaging technique for virtual monochromatic (VM) and linearly mixed (LM) cone beam CTs (CBCTs) and to demonstrate their potential applications in metal artifact reduction and contrast enhancement in image-guided radiation therapy (IGRT). Methods: A bench-top CBCT system was used to acquire 80 kVp and 150 kVp projections, with an additional 0.8 mm tin filtration. To implement the VM technique, these projections were first decomposed into acrylic and aluminum basis material projections to synthesize VM projections, which were then used to reconstruct VM CBCTs. The effect of VM CBCT on the metal artifact reduction was evaluated withmore » an in-house titanium-BB phantom. The optimal VM energy to maximize contrast-to-noise ratio (CNR) for iodine contrast and minimize beam hardening in VM CBCT was determined using a water phantom containing two iodine concentrations. The LM technique was implemented by linearly combining the low-energy (80 kVp) and high-energy (150 kVp) CBCTs. The dose partitioning between low-energy and high-energy CBCTs was varied (20%, 40%, 60%, and 80% for low-energy) while keeping total dose approximately equal to single-energy CBCTs, measured using an ion chamber. Noise levels and CNRs for four tissue types were investigated for dual-energy LM CBCTs in comparison with single-energy CBCTs at 80, 100, 125, and 150 kVp. Results: The VM technique showed substantial reduction of metal artifacts at 100 keV with a 40% reduction in the background standard deviation compared to a 125 kVp single-energy scan of equal dose. The VM energy to maximize CNR for both iodine concentrations and minimize beam hardening in the metal-free object was 50 keV and 60 keV, respectively. The difference of average noise levels measured in the phantom background was 1.2% between dual-energy LM CBCTs and equivalent-dose single-energy CBCTs. CNR values in the LM CBCTs of any dose partitioning are better than those of 150 kVp single-energy CBCTs. The average CNR for four tissue types with 80% dose fraction at low-energy showed 9.0% and 4.1% improvement relative to 100 kVp and 125 kVp single-energy CBCTs, respectively. CNRs for low-contrast objects improved as dose partitioning was more heavily weighted toward low-energy (80 kVp) for LM CBCTs. Conclusions: Dual-energy CBCT imaging techniques were implemented to synthesize VM CBCT and LM CBCTs. VM CBCT was effective at achieving metal artifact reduction. Depending on the dose-partitioning scheme, LM CBCT demonstrated the potential to improve CNR for low contrast objects compared to single-energy CBCT acquired with equivalent dose.« less

Identification of novel Ebola virus (EBOV) VP24 inhibitor from Indonesian natural products through in silico drug design approach

NASA Astrophysics Data System (ADS)

Tambunan, U. S. F.; Nasution, M. A. F.

2017-07-01

Ebola remains as one of the deadliest diseases in the world, with almost 29,000 cases were reported and kill 11,000 of them, and yet neither treatment nor vaccine that can combat this disease effectively. This disease is caused by ebolavirus (EBOV), a primary member of Filoviridae family. The life cycle of this virus has been operated by several key proteins, one of them is VP24 protein, which has been known for its crucial role in the transcription and replication of EBOV. Therefore, targeting VP24 protein can be a solution for treating this pathogenic disease. In this study, virtual screening of Indonesian natural products as EBOV VP24 inhibitor was performed. About 2,020 ligands from many sources, including HerbalDB database, were obtained and screened by using DataWarrior software to measure its molecular and pharmacological properties, resulting 301 ligands in the process. Then, the molecular docking simulation was performed to check the ligand's binding interaction and affinity with EBOV VP24 protein; this simulation was done by using MOE 2014.09 software. This study resulted that cycloartocarpin was the best ligand to inhibit the EBOV VP24 protein. Therefore, this ligand should be checked its stability through molecular dynamics simulation and performed in vitro test to verify its bioactivity against the EBOV VP24 protein.

Qualitative and quantitative evaluation of rigid and deformable motion correction algorithms using dual-energy CT images in view of application to CT perfusion measurements in abdominal organs affected by breathing motion

PubMed Central

Skornitzke, S; Fritz, F; Klauss, M; Pahn, G; Hansen, J; Hirsch, J; Grenacher, L; Kauczor, H-U

2015-01-01

Objective: To compare six different scenarios for correcting for breathing motion in abdominal dual-energy CT (DECT) perfusion measurements. Methods: Rigid [RRComm(80 kVp)] and non-rigid [NRComm(80 kVp)] registration of commercially available CT perfusion software, custom non-rigid registration [NRCustom(80 kVp], demons algorithm) and a control group [CG(80 kVp)] without motion correction were evaluated using 80 kVp images. Additionally, NRCustom was applied to dual-energy (DE)-blended [NRCustom(DE)] and virtual non-contrast [NRCustom(VNC)] images, yielding six evaluated scenarios. After motion correction, perfusion maps were calculated using a combined maximum slope/Patlak model. For qualitative evaluation, three blinded radiologists independently rated motion correction quality and resulting perfusion maps on a four-point scale (4 = best, 1 = worst). For quantitative evaluation, relative changes in metric values, R2 and residuals of perfusion model fits were calculated. Results: For motion-corrected images, mean ratings differed significantly [NRCustom(80 kVp) and NRCustom(DE), 3.3; NRComm(80 kVp), 3.1; NRCustom(VNC), 2.9; RRComm(80 kVp), 2.7; CG(80 kVp), 2.7; all p < 0.05], except when comparing NRCustom(80 kVp) with NRCustom(DE) and RRComm(80 kVp) with CG(80 kVp). NRCustom(80 kVp) and NRCustom(DE) achieved the highest reduction in metric values [NRCustom(80 kVp), 48.5%; NRCustom(DE), 45.6%; NRComm(80 kVp), 29.2%; NRCustom(VNC), 22.8%; RRComm(80 kVp), 0.6%; CG(80 kVp), 0%]. Regarding perfusion maps, NRCustom(80 kVp) and NRCustom(DE) were rated highest [NRCustom(80 kVp), 3.1; NRCustom(DE), 3.0; NRComm(80 kVp), 2.8; NRCustom(VNC), 2.6; CG(80 kVp), 2.5; RRComm(80 kVp), 2.4] and had significantly higher R2 and lower residuals. Correlation between qualitative and quantitative evaluation was low to moderate. Conclusion: Non-rigid motion correction improves spatial alignment of the target region and fit of CT perfusion models. Using DE-blended and DE-VNC images for deformable registration offers no significant improvement. Advances in knowledge: Non-rigid algorithms improve the quality of abdominal CT perfusion measurements but do not benefit from DECT post processing. PMID:25465353

Effects of introducing a voluntary virtual patient module to a basic life support with an automated external defibrillator course: a randomised trial

PubMed Central

2012-01-01

Background The concept of virtual patients (VPs) encompasses a great variety of predominantly case-based e-learning modules with different complexity and fidelity levels. Methods for effective placement of VPs in the process of medical education are sought. The aim of this study was to determine whether the introduction of a voluntary virtual patients module into a basic life support with an automated external defibrillator (BLS-AED) course improved the knowledge and skills of students taking the course. Methods Half of the students were randomly assigned to an experimental group and given voluntary access to a virtual patient module consisting of six cases presenting BLS-AED knowledge and skills. Pre- and post-course knowledge tests and skills assessments were performed, as well as a survey of students' satisfaction with the VP usage. In addition, time spent using the virtual patient system, percentage of screen cards viewed and scores in the formative questions in the VP system throughout the course were traced and recorded. Results The study was conducted over a six week period and involved 226 first year medical students. The voluntary module was used by 61 (54%) of the 114 entitled study participants. The group that used VPs demonstrated better results in knowledge acquisition and in some key BLS-AED action skills than the group without access, or those students from the experimental group deliberately not using virtual patients. Most of the students rated the combination of VPs and corresponding teaching events positively. Conclusions The overall positive reaction of students and encouraging results in knowledge and skills acquisition suggest that the usage of virtual patients in a BLS-AED course on a voluntary basis is feasible and should be further investigated. PMID:22709278

Effects of introducing a voluntary virtual patient module to a basic life support with an automated external defibrillator course: a randomised trial.

PubMed

Kononowicz, Andrzej A; Krawczyk, Paweł; Cebula, Grzegorz; Dembkowska, Marta; Drab, Edyta; Frączek, Bartosz; Stachoń, Aleksandra J; Andres, Janusz

2012-06-18

The concept of virtual patients (VPs) encompasses a great variety of predominantly case-based e-learning modules with different complexity and fidelity levels. Methods for effective placement of VPs in the process of medical education are sought. The aim of this study was to determine whether the introduction of a voluntary virtual patients module into a basic life support with an automated external defibrillator (BLS-AED) course improved the knowledge and skills of students taking the course. Half of the students were randomly assigned to an experimental group and given voluntary access to a virtual patient module consisting of six cases presenting BLS-AED knowledge and skills. Pre- and post-course knowledge tests and skills assessments were performed, as well as a survey of students' satisfaction with the VP usage. In addition, time spent using the virtual patient system, percentage of screen cards viewed and scores in the formative questions in the VP system throughout the course were traced and recorded. The study was conducted over a six week period and involved 226 first year medical students. The voluntary module was used by 61 (54%) of the 114 entitled study participants. The group that used VPs demonstrated better results in knowledge acquisition and in some key BLS-AED action skills than the group without access, or those students from the experimental group deliberately not using virtual patients. Most of the students rated the combination of VPs and corresponding teaching events positively. The overall positive reaction of students and encouraging results in knowledge and skills acquisition suggest that the usage of virtual patients in a BLS-AED course on a voluntary basis is feasible and should be further investigated.

Comparison of path visualizations and cognitive measures relative to travel technique in a virtual environment.

PubMed

Zanbaka, Catherine A; Lok, Benjamin C; Babu, Sabarish V; Ulinski, Amy C; Hodges, Larry F

2005-01-01

We describe a between-subjects experiment that compared four different methods of travel and their effect on cognition and paths taken in an immersive virtual environment (IVE). Participants answered a set of questions based on Crook's condensation of Bloom's taxonomy that assessed their cognition of the IVE with respect to knowledge, understanding and application, and higher mental processes. Participants also drew a sketch map of the IVE and the objects within it. The users' sense of presence was measured using the Steed-Usoh-Slater Presence Questionnaire. The participants' position and head orientation were automatically logged during their exposure to the virtual environment. These logs were later used to create visualizations of the paths taken. Path analysis, such as exploring the overlaid path visualizations and dwell data information, revealed further differences among the travel techniques. Our results suggest that, for applications where problem solving and evaluation of information is important or where opportunity to train is minimal, then having a large tracked space so that the participant can walk around the virtual environment provides benefits over common virtual travel techniques.

TU-F-CAMPUS-I-02: Validation of a CT X-Ray Source Characterization Technique for Dose Computation Using An Anthropomorphic Thorax Phantom

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sommerville, M; Tambasco, M; Poirier, Y

2015-06-15

Purpose: To experimentally validate a rotational kV x-ray source characterization technique by computing CT dose in an anthropomorphic thorax phantom using an in-house dose computation algorithm (kVDoseCalc). Methods: The lateral variation in incident energy spectra of a GE Optima big bore CT scanner was found by measuring the HVL along the internal, full bow-tie filter axis. The HVL and kVp were used to generate the x-ray spectra using Spektr software, while beam fluence was derived by dividing the integral product of the spectra and in-air mass-energy absorption coefficients by in-air dose measurements along the bow-tie filter axis. Beams produced bymore » the GE Optima scanner were modeled at 80 and 140 kVp tube settings. kVDoseCalc calculates dose by solving the linear Boltzmann transport equation using a combination of deterministic and stochastic methods. Relative doses in an anthropomorphic thorax phantom (E2E SBRT Phantom) irradiated by the GE Optima scanner were measured using a (0.015 cc) PTW Freiburg ionization chamber, and compared to computations from kVDoseCalc. Results: The agreement in relative dose between dose computation and measurement for points of interest (POIs) within the primary path of the beam was within experimental uncertainty for both energies, however points outside the primary beam were not. The average absolute percent difference for POIs within the primary path of the beam was 1.37% and 5.16% for 80 and 140 kVp, respectively. The minimum and maximum absolute percent difference for both energies and all POIs within the primary path of the beam was 0.151% and 6.41%, respectively. Conclusion: The CT x-ray source characterization technique based on HVL measurements and kVp can be used to accurately compute CT dose in an anthropomorphic thorax phantom.« less

Architecture and design of optical path networks utilizing waveband virtual links

NASA Astrophysics Data System (ADS)

Ito, Yusaku; Mori, Yojiro; Hasegawa, Hiroshi; Sato, Ken-ichi

2016-02-01

We propose a novel optical network architecture that uses waveband virtual links, each of which can carry several optical paths, to directly bridge distant node pairs. Future photonic networks should not only transparently cover extended areas but also expand fiber capacity. However, the traversal of many ROADM nodes impairs the optical signal due to spectrum narrowing. To suppress the degradation, the bandwidth of guard bands needs to be increased, which degrades fiber frequency utilization. Waveband granular switching allows us to apply broader pass-band filtering at ROADMs and to insert sufficient guard bands between wavebands with minimum frequency utilization offset. The scheme resolves the severe spectrum narrowing effect. Moreover, the guard band between optical channels in a waveband can be minimized, which increases the number of paths that can be accommodated per fiber. In the network, wavelength path granular routing is done without utilizing waveband virtual links, and it still suffers from spectrum narrowing. A novel network design algorithm that can bound the spectrum narrowing effect by limiting the number of hops (traversed nodes that need wavelength path level routing) is proposed in this paper. This algorithm dynamically changes the waveband virtual link configuration according to the traffic distribution variation, where optical paths that need many node hops are effectively carried by virtual links. Numerical experiments demonstrate that the number of necessary fibers is reduced by 23% compared with conventional optical path networks.

Assessing progression of clinical reasoning through virtual patients: An exploratory study.

PubMed

Forsberg, Elenita; Ziegert, Kristina; Hult, Håkan; Fors, Uno

2016-01-01

To avoid test-driven learning, there have been discussions regarding the use of more formative assessments in health care education to promote students' deep learning. Feedback is important in formative assessment, but many students ignore it; therefore, interventions should be introduced which stimulate them to reflect on the new knowledge. The aim for this study was to explore if Virtual Patient (VP)-based formative assessments, in connection with self-evaluations, had an impact on postgraduate pediatric nursing students' development of clinical reasoning abilities. Students' self-evaluations served as the basis for measuring progress. Data was analysed using deductive content analysis. The findings showed a clear progression of the clinical reasoning ability of the students. After the first assessment, the students described feelings of uncertainty and that their knowledge gaps were exposed. At the mid-course assessment the awareness of improved clinical reasoning was obvious and the students were more certain of knowing how to solve the VP cases. In the final assessment, self-efficacy was expressed. VP-based assessments, in connection with self-evaluations, early in the education resulted in a gain of students' own identification of the concept of clinical reasoning, awareness of what to focus on during clinical practice and visualised expected clinical competence. Copyright © 2015 Elsevier Ltd. All rights reserved.

Virtual patients: the influence of case design and teamwork on students' perception and knowledge - a pilot study.

PubMed

Jäger, Frederik; Riemer, Martin; Abendroth, Martin; Sehner, Susanne; Harendza, Sigrid

2014-07-08

Virtual patient (VP) cases are an effective teaching method, although little is known about how to design and implement them for maximum effectiveness. The aim of this study was to explore the effect of case design and teamwork on students' learning outcome. One hundred forty-six undergraduate medical students participated in a mandatory medical computer science course consisting of five seminars. At the end of each seminar, they worked on one VP case, either in teams of two or individually. Each student filled out an introductory and a final survey and a feedback sheet after completing each case. Additionally, there was a surprise multiple choice (MC) test after the last seminar with three questions regarding each case. Students with more clinical experience and students who had worked in a team performed significantly better on MC questions. Students with less clinical experience more frequently used information which had been positioned less prominently on the case material. Certain aspects of case design were rated more positively by students who had an interest in e-learning. In general, students preferred to work on cases for less than 15 minutes. Clinically more advanced students and students working with a partner seem to benefit most from short VP cases with prominently presented information.

A Clinical Reasoning Tool for Virtual Patients: Design-Based Research Study.

PubMed

Hege, Inga; Kononowicz, Andrzej A; Adler, Martin

2017-11-02

Clinical reasoning is a fundamental process medical students have to learn during and after medical school. Virtual patients (VP) are a technology-enhanced learning method to teach clinical reasoning. However, VP systems do not exploit their full potential concerning the clinical reasoning process; for example, most systems focus on the outcome and less on the process of clinical reasoning. Keeping our concept grounded in a former qualitative study, we aimed to design and implement a tool to enhance VPs with activities and feedback, which specifically foster the acquisition of clinical reasoning skills. We designed the tool by translating elements of a conceptual clinical reasoning learning framework into software requirements. The resulting clinical reasoning tool enables learners to build their patient's illness script as a concept map when they are working on a VP scenario. The student's map is compared with the experts' reasoning at each stage of the VP, which is technically enabled by using Medical Subject Headings, which is a comprehensive controlled vocabulary published by the US National Library of Medicine. The tool is implemented using Web technologies, has an open architecture that enables its integration into various systems through an open application program interface, and is available under a Massachusetts Institute of Technology license. We conducted usability tests following a think-aloud protocol and a pilot field study with maps created by 64 medical students. The results show that learners interact with the tool but create less nodes and connections in the concept map than an expert. Further research and usability tests are required to analyze the reasons. The presented tool is a versatile, systematically developed software component that specifically supports the clinical reasoning skills acquisition. It can be plugged into VP systems or used as stand-alone software in other teaching scenarios. The modular design allows an extension with new feedback mechanisms and learning analytics algorithms. ©Inga Hege, Andrzej A Kononowicz, Martin Adler. Originally published in JMIR Medical Education (http://mededu.jmir.org), 02.11.2017.

Cognitive load of navigating without vision when guided by virtual sound versus spatial language.

PubMed

Klatzky, Roberta L; Marston, James R; Giudice, Nicholas A; Golledge, Reginald G; Loomis, Jack M

2006-12-01

A vibrotactile N-back task was used to generate cognitive load while participants were guided along virtual paths without vision. As participants stepped in place, they moved along a virtual path of linear segments. Information was provided en route about the direction of the next turning point, by spatial language ("left," "right," or "straight") or virtual sound (i.e., the perceived azimuth of the sound indicated the target direction). The authors hypothesized that virtual sound, being processed at direct perceptual levels, would have lower load than even simple language commands, which require cognitive mediation. As predicted, whereas the guidance modes did not differ significantly in the no-load condition, participants showed shorter distance traveled and less time to complete a path when performing the N-back task while navigating with virtual sound as guidance. Virtual sound also produced better N-back performance than spatial language. By indicating the superiority of virtual sound for guidance when cognitive load is present, as is characteristic of everyday navigation, these results have implications for guidance systems for the visually impaired and others.

[Virtual Patients and Medical Teaching].

PubMed

Gómez-Restrepo, Carlos; Narváez, Yamile Reveiz

2012-01-01

Biomedical advancements have evolved to the point where teaching software may be implemented to represent real-life scenarios. Virtual Patients or VPs are software programs that simulate clinical scenarios allowing students to generate a diagnosis and make treatment decisions. In this article, advantages and disadvantages regarding the use of this state-of-the-art technology are discussed. VP is a useful technique for psychiatry students. Copyright © 2012 Asociación Colombiana de Psiquiatría. Publicado por Elsevier España. All rights reserved.

A randomized trial of two e-learning strategies for teaching substance abuse management skills to physicians.

PubMed

Harris, John M; Sun, Huaping

2013-09-01

To compare the educational effectiveness of two virtual patient (VP)-based e-learning strategies, versus no training, in improving physicians' substance abuse management knowledge, attitudes, self-reported behaviors, and decision making. The 2011-2012 study was a posttest-only, three-arm, randomized controlled trial in 90 resident and 30 faculty physicians from five adult medicine primary care training programs. The intervention was one of two 2-hour VP-based e-learning programs, designed by national experts to teach structured screening, brief interventions, referral, and treatment skills. One used traditional problem solving with feedback (unworked example), and the other incorporated an expert demonstration first, followed by problem solving with feedback (worked example). The main outcome measure was performance on the Physicians' Competence in Substance Abuse Test (P-CSAT, maximum score = 315), a self-administered, previously validated measure of physicians' competence in managing substance abuse. The survey was completed at the outset of the study and two months later. Overall P-CSAT scores were virtually identical (202-211, P > .05) between both intervention groups and the no-training control group at both times. Average faculty P-CSAT scores (221.9, 224.6) were significantly higher (P < .01) than resident scores (203.7, 202.5) at both times. This study did not provide evidence that a brief, worked example, VP-based e-learning program or a traditional, unworked, VP-based e-learning program was superior to no training in improving physicians' substance abuse management skills. The study did provide additional evidence that the P-CSAT distinguishes between physicians who should possess different levels of substance abuse management skills.

Virtual patients: development in cancer nursing education.

PubMed

Moule, Pam; Pollard, Katherine; Armoogum, Julie; Messer, Simon

2015-07-01

The number of men diagnosed with prostate cancer is increasing and internationally there are high incidence rates. It is important that nurses and healthcare professionals are enabled to provide appropriate care to those men affected by prostate cancer and their families. Despite this need, there is recognition that many professionals feel ill prepared and lack knowledge in a number of areas. This paper presents the development of a Virtual Patient (VP) online resource to support practitioner learning. To develop five online VP simulation scenarios to meet the learning needs of nurses and health-care professionals caring for men with prostate cancer. Topic areas for the VPs were taken from previous work exploring the needs of health care professionals working with men with prostate cancer. An initial scoping exercise involving nursing practitioners, students and a prostate cancer charity confirmed the focus of the case study scenarios. Service users and specialist practitioners reviewed an outline of each case study to ensure fidelity of the simulations scenarios. Cases were entered into UChoose, a web based interactive VP player and authoring tool. The final case studies were reviewed by a sample of both registered and non-registered nurses and nursing students. The majority of respondents reported an increase in knowledge and suggested that they would recommend the resource to others. A number of positive aspects of the resource were highlighted. Respondents also commented about areas of weakness, a number of which have been addressed subsequently. The VP case studies provided an opportunity to develop knowledge and confidence in caring for men with prostate cancer. The mode of delivery and the content was acceptable for less experienced and knowledgeable staff. Copyright © 2015 Elsevier Ltd. All rights reserved.

Ab initio computational study of reaction mechanism of peptide bond formation on HF/6-31G(d,p) level

NASA Astrophysics Data System (ADS)

Siahaan, P.; Lalita, M. N. T.; Cahyono, B.; Laksitorini, M. D.; Hildayani, S. Z.

2017-02-01

Peptide plays an important role in modulation of various cell functions. Therefore, formation reaction of the peptide is important for chemical reactions. One way to probe the reaction of peptide synthesis is a computational method. The purpose of this research is to determine the reaction mechanism for peptide bond formation on Ac-PV-NH2 and Ac-VP-NH2 synthesis from amino acid proline and valine by ab initio computational approach. The calculations were carried out by theory and basis set HF/6-31G(d,p) for four mechanisms (path 1 to 4) that proposed in this research. The results show that the highest of the rate determining step between reactant and transition state (TS) for path 1, 2, 3, and 4 are 163.06 kJ.mol-1, 1868 kJ.mol-1, 5685 kJ.mol-1, and 1837 kJ.mol-1. The calculation shows that the most preferred reaction of Ac-PV-NH2 and Ac-VP-NH2 synthesis from amino acid proline and valine are on the path 1 (initiated with the termination of H+ in proline amino acid) that produce Ac-PV-NH2.

Virtual patients: the influence of case design and teamwork on students’ perception and knowledge – a pilot study

PubMed Central

2014-01-01

Background Virtual patient (VP) cases are an effective teaching method, although little is known about how to design and implement them for maximum effectiveness. The aim of this study was to explore the effect of case design and teamwork on students’ learning outcome. Methods One hundred forty-six undergraduate medical students participated in a mandatory medical computer science course consisting of five seminars. At the end of each seminar, they worked on one VP case, either in teams of two or individually. Each student filled out an introductory and a final survey and a feedback sheet after completing each case. Additionally, there was a surprise multiple choice (MC) test after the last seminar with three questions regarding each case. Results Students with more clinical experience and students who had worked in a team performed significantly better on MC questions. Students with less clinical experience more frequently used information which had been positioned less prominently on the case material. Certain aspects of case design were rated more positively by students who had an interest in e-learning. In general, students preferred to work on cases for less than 15 minutes. Conclusions Clinically more advanced students and students working with a partner seem to benefit most from short VP cases with prominently presented information. PMID:25000965

Evaluating progressive-rendering algorithms in appearance design tasks.

PubMed

Jiawei Ou; Karlik, Ondrej; Křivánek, Jaroslav; Pellacini, Fabio

2013-01-01

Progressive rendering is becoming a popular alternative to precomputational approaches to appearance design. However, progressive algorithms create images exhibiting visual artifacts at early stages. A user study investigated these artifacts' effects on user performance in appearance design tasks. Novice and expert subjects performed lighting and material editing tasks with four algorithms: random path tracing, quasirandom path tracing, progressive photon mapping, and virtual-point-light rendering. Both the novices and experts strongly preferred path tracing to progressive photon mapping and virtual-point-light rendering. None of the participants preferred random path tracing to quasirandom path tracing or vice versa; the same situation held between progressive photon mapping and virtual-point-light rendering. The user workflow didn’t differ significantly with the four algorithms. The Web Extras include a video showing how four progressive-rendering algorithms converged (at http://youtu.be/ck-Gevl1e9s), the source code used, and other supplementary materials.

Path following control of planar snake robots using virtual holonomic constraints: theory and experiments.

PubMed

Rezapour, Ehsan; Pettersen, Kristin Y; Liljebäck, Pål; Gravdahl, Jan T; Kelasidi, Eleni

This paper considers path following control of planar snake robots using virtual holonomic constraints. In order to present a model-based path following control design for the snake robot, we first derive the Euler-Lagrange equations of motion of the system. Subsequently, we define geometric relations among the generalized coordinates of the system, using the method of virtual holonomic constraints. These appropriately defined constraints shape the geometry of a constraint manifold for the system, which is a submanifold of the configuration space of the robot. Furthermore, we show that the constraint manifold can be made invariant by a suitable choice of feedback. In particular, we analytically design a smooth feedback control law to exponentially stabilize the constraint manifold. We show that enforcing the appropriately defined virtual holonomic constraints for the configuration variables implies that the robot converges to and follows a desired geometric path. Numerical simulations and experimental results are presented to validate the theoretical approach.

Simultaneous Determination of Average Thickness and P-wave Speed of the Crust by Virtual Deep Seismic Sounding (VDSS)

NASA Astrophysics Data System (ADS)

Kang, D.; Yu, C.; Ning, J.; TAO, K.; Chen, W. P.

2014-12-01

Using teleseismic S-waves, VDSS treats the SV-to-P conversion under the free surface (on the station-side) as a virtual source to generate strong, post-critical reflection off the Moho (SsPmp phase). With just a single, good-quality earthquake, arrival-time difference between SsPmp and the direct S-phase (TSsPmp-Ss) can effectively determine the crustal thickness (H) near the receiver. However, there is a strong trade-off between H and P-wave speed (Vp) in the crust. Here we extend VDSS to constrain both H and Vp by taking advantage of the variation in ray-parameters, or incident angles, as a function of epicentral distance. Note that in conventional receiver functions, information contained in data of different ray-parameters is usually lost, because stacking over move-out corrected data is required to get a clear signal. At a given station, we collect data from many events, each with a different ray-parameter of the direct S-phase (ps­). For each event, we 1) estimate the source wavelet of the direct S-wave through particle motion analysis; 2) deconvolve this wavelet from the vertical- and radial-component seismograms (Yu et al., GJI, 2013); and then 3) determine TSsPmp-Ss through waveform modeling. Finally, we analyze data pairs (ps2, T2SsPmp-Ss) to find the best-fitting values of H and Vp. Synthetic tests verify the robustness of the method even with 15% of white noise. Moreover, we applied the method to public domain data from Forrest (FORT), located in the Eucla basin of western Australia. Based on 30 earthquakes from a narrow back-azimuth range (105±15°) but with ps changing from 0.1221 to 0.1349 s/km, we estimate that near FORT, H and Vp are about 44±2 km and 6.67±0.35 km/s, respectively. This crustal thickness is consistent with previous reports - a surprisingly high value for a region where the elevation is less than 200 m. Together with the high Vp, our results imply that the crust has a dense, mafic component.

An innovative blended learning approach using virtual patients as preparation for skills laboratory training: perceptions of students and tutors

PubMed Central

2013-01-01

Background Currently only a few reports exist on how to prepare medical students for skills laboratory training. We investigated how students and tutors perceive a blended learning approach using virtual patients (VPs) as preparation for skills training. Methods Fifth-year medical students (N=617) were invited to voluntarily participate in a paediatric skills laboratory with four specially designed VPs as preparation. The cases focused on procedures in the laboratory using interactive questions, static and interactive images, and video clips. All students were asked to assess the VP design. After participating in the skills laboratory 310 of the 617 students were additionally asked to assess the blended learning approach through established questionnaires. Tutors’ perceptions (N=9) were assessed by semi-structured interviews. Results From the 617 students 1,459 VP design questionnaires were returned (59.1%). Of the 310 students 213 chose to participate in the skills laboratory; 179 blended learning questionnaires were returned (84.0%). Students provided high overall acceptance ratings of the VP design and blended learning approach. By using VPs as preparation, skills laboratory time was felt to be used more effectively. Tutors perceived students as being well prepared for the skills laboratory with efficient uses of time. Conclusion The overall acceptance of the blended learning approach was high among students and tutors. VPs proved to be a convenient cognitive preparation tool for skills training. PMID:23402663

Image-based path planning for automated virtual colonoscopy navigation

NASA Astrophysics Data System (ADS)

Hong, Wei

2008-03-01

Virtual colonoscopy (VC) is a noninvasive method for colonic polyp screening, by reconstructing three-dimensional models of the colon using computerized tomography (CT). In virtual colonoscopy fly-through navigation, it is crucial to generate an optimal camera path for efficient clinical examination. In conventional methods, the centerline of the colon lumen is usually used as the camera path. In order to extract colon centerline, some time consuming pre-processing algorithms must be performed before the fly-through navigation, such as colon segmentation, distance transformation, or topological thinning. In this paper, we present an efficient image-based path planning algorithm for automated virtual colonoscopy fly-through navigation without the requirement of any pre-processing. Our algorithm only needs the physician to provide a seed point as the starting camera position using 2D axial CT images. A wide angle fisheye camera model is used to generate a depth image from the current camera position. Two types of navigational landmarks, safe regions and target regions are extracted from the depth images. Camera position and its corresponding view direction are then determined using these landmarks. The experimental results show that the generated paths are accurate and increase the user comfort during the fly-through navigation. Moreover, because of the efficiency of our path planning algorithm and rendering algorithm, our VC fly-through navigation system can still guarantee 30 FPS.

Dual-layer DECT for multiphasic hepatic CT with 50 percent iodine load: a matched-pair comparison with a 120 kVp protocol.

PubMed

Nagayama, Yasunori; Nakaura, Takeshi; Oda, Seitaro; Utsunomiya, Daisuke; Funama, Yoshinori; Iyama, Yuji; Taguchi, Narumi; Namimoto, Tomohiro; Yuki, Hideaki; Kidoh, Masafumi; Hirata, Kenichiro; Nakagawa, Masataka; Yamashita, Yasuyuki

2018-04-01

To evaluate the image quality and lesion conspicuity of virtual-monochromatic-imaging (VMI) with dual-layer DECT (DL-DECT) for reduced-iodine-load multiphasic-hepatic CT. Forty-five adults with renal dysfunction who had undergone hepatic DL-DECT with 300-mgI/kg were included. VMI (40-70-keV, DL-DECT-VMI) was generated at each enhancement phase. As controls, 45 matched patients undergoing standard 120-kVp protocol (120-kVp, 600-mgI/kg, and iterative reconstruction) were included. We compared the size-specific dose estimate (SSDE), image noise, CT attenuation, and contrast-to-noise ratio (CNR) between protocols. Two radiologists scored the image quality and lesion conspicuity. SSDE was significantly lower in DL-DECT group (p < 0.01). Image noise of DL-DECT-VMI was almost constant at each keV (differences of ≤15%) and equivalent to or lower than of 120-kVp. As the energy decreased, CT attenuation and CNR gradually increased; the values of 55-60 keV images were almost equivalent to those of standard 120-kVp. The highest scores for overall quality and lesion conspicuity were assigned at 40-keV followed by 45 to 55-keV, all of which were similar to or better than of 120-kVp. For multiphasic-hepatic CT with 50% iodine-load, DL-DECT-VMI at 40- to 55-keV provides equivalent or better image quality and lesion conspicuity without increasing radiation dose compared with standard 120-kVp protocol. • 40-55-keV yields optimal image quality for half-iodine-load multiphasic-hepatic CT with DL-DECT. • DL-DECT protocol decreases radiation exposure compared with 120-kVp scans with iterative reconstruction. • 40-keV images maximise conspicuity of hepatocellular carcinoma especially at hepatic-arterial phase.

3-D Vp/Vs Ratio Distribution in the Geothermal Reservoir at Basel, Switzerland, from Microseismic Data

NASA Astrophysics Data System (ADS)

Kummerow, J.; Reshetnikov, A.; Häring, M.; Asanuma, H.

2012-12-01

Thousands of microseismic events occurred during and after the stimulation of the 4.5km deep Basel 1 well at the Deep Heat Mining Project in Basel, Switzerland, in December 2006. The located seismicity extends about 1km in vertical direction and also 1km in NNW-SSE direction, consistent with the orientation of the maximum horizontal stress. In this study, we analyze 2100 events with magnitudes Mw>0.0, which were recorded by six borehole seismometers between December 2, 2006, and June 7, 2007. We first identify event multiplets based on waveform similarity and apply an automatic, iterative arrival time optimization to calculate high-precision P and S time picks for the multiplet events. Local estimates of the Vp/Vs ratio in the stimulated Basel geothermal reservoir are then obtained from the slope of the demeaned differential S versus P arrival times. The average value of Vp/Vs=1.70 is close to the characteristic reservoir value of 1.72, which was determined independently from sonic log measurements. Also, in the vicinity of the borehole, the depth distribution of Vp/Vs correlates well with the low-pass filtered sonic log data: Vp/Vs values are less than 1.70 at the top of the seismicity cloud at <3.9km depth, close to average at 4.0-4.4km depth, and exceed the value of 1.75 at larger depth (4.4-4.6km), consistent with the sonic log data. Furthermore, we observe a correlation of anomalous Vp/Vs values with zones of enhanced seismic reflectivity which were resolved by microseismic reflection imaging. Away from the borehole, increased Vp/Vs ratios also seem to correlate with domains of high event density, possibly indicating fluid migration paths.

Interpersonal behaviors and socioemotional interaction of medical students in a virtual clinical encounter

PubMed Central

2014-01-01

Background The virtual clinical encounter (VCE) may function as an important support for medical students in or prior to clinical practice to train and ease communication and socioemotional interactions with patients. Few studies have however focused on the dynamics of interpersonal behaviors in clinical interviewing with a virtual patient (VP) and the affective responses evoked by such a learning experience. The study was designed to investigate the dynamics and congruence of interpersonal behaviors and socioemotional interaction exhibited during the learning experience in a VCE, and to evaluate which interaction design characteristics contribute most to the behavioral and affective engagement in medical students. Methods Thirty medical students (sixth semester) participated voluntarily in an exploratory observational study with a highly interactive VP case based on a trustworthy VP encounter with a natural and realistic dialogue interface. Students worked collaboratively in pairs. They were videotaped for further behavioral analysis and self-reported (in both a survey and an interview) their personal opinions, perceptions and attitudes about the VCE. A mixed methods approach was applied. Results All participants demonstrated an adequate, respectful and relevant clinical case management and to obtain psychosocial history. The collaborative workspace played its role and led to dynamic and engaged discussions fostering thus shared understanding. The results suggest that the VCE studied was perceived as a meaningful, intrinsically motivational and activating learning environment, and was found to socially and emotionally engage learners. We also found that VCEs have the potential to support the development of relevant and congruent interpersonal communication skills in trainees. Conclusions By taking advantage of socioemotional interaction, VCEs promote not only critical reflection skills or strategy-selection skills, but also to develop listening and nonverbal skills, induce self-awareness and target coping behaviours. We believe that, if applied in early medical education, this learning approach may facilitate clinical encounters at an early stage and contribute to responsible clinical decision making. PMID:24685070

Evaluation of a novel scoring and grading model for VP-based exams in postgraduate nurse education.

PubMed

Forsberg, Elenita; Ziegert, Kristina; Hult, Håkan; Fors, Uno

2015-12-01

For Virtual Patient-based exams, several scoring and grading methods have been proposed, but none have yet been validated. The aim of this study was to evaluate a new scoring and grading model for VP-based exams in postgraduate paediatric nurse education. The same student group of 19 students performed a VP-based exam in three consecutive courses. When using the scoring and grading assessment model, which contains a deduction system for unnecessary or unwanted actions, a progression was found in the three courses: 53% of the students passed the first exam, 63% the second and 84% passed the final exam. The most common reason for deduction of points was due to students asking too many interview questions or ordering too many laboratory tests. The results showed that the new scoring model made it possible to judge the students' clinical reasoning process as well as their progress. Copyright © 2015 Elsevier Ltd. All rights reserved.

Planar maneuvering control of underwater snake robots using virtual holonomic constraints.

PubMed

Kohl, Anna M; Kelasidi, Eleni; Mohammadi, Alireza; Maggiore, Manfredi; Pettersen, Kristin Y

2016-11-24

This paper investigates the problem of planar maneuvering control for bio-inspired underwater snake robots that are exposed to unknown ocean currents. The control objective is to make a neutrally buoyant snake robot which is subject to hydrodynamic forces and ocean currents converge to a desired planar path and traverse the path with a desired velocity. The proposed feedback control strategy enforces virtual constraints which encode biologically inspired gaits on the snake robot configuration. The virtual constraints, parametrized by states of dynamic compensators, are used to regulate the orientation and forward speed of the snake robot. A two-state ocean current observer based on relative velocity sensors is proposed. It enables the robot to follow the path in the presence of unknown constant ocean currents. The efficacy of the proposed control algorithm for several biologically inspired gaits is verified both in simulations for different path geometries and in experiments.

Grating Oriented Line-Wise Filtration (GOLF) for Dual-Energy X-ray CT

NASA Astrophysics Data System (ADS)

Xi, Yan; Cong, Wenxiang; Harrison, Daniel; Wang, Ge

2017-12-01

In medical X-ray Computed Tomography (CT), the use of two distinct X-ray source spectra (energies) allows dose-reduction and material discrimination relative to that achieved with only one source spectrum. Existing dual-energy CT methods include source kVp-switching, double-layer detection, dual-source gantry, and two-pass scanning. Each method suffers either from strong spectral correlation or patient-motion artifacts. To simultaneously address these problems, we propose to improve CT data acquisition with the Grating Oriented Line-wise Filtration (GOLF) method, a novel X-ray filter that is placed between the source and patient. GOLF uses a combination of absorption and filtering gratings that are moved relative to each other and in synchronization with the X-ray tube kVp-switching process and/or the detector view-sampling process. Simulation results show that GOLF can improve the spectral performance of kVp-switching to match that of dual-source CT while avoiding patient motion artifacts and dual imaging chains. Although significant flux is absorbed by this pre-patient filter, the proposed GOLF method is a novel path for cost-effectively extracting dual-energy or multi-energy data and reducing radiation dose with or without kVp switching.

Grating Oriented Line-Wise Filtration (GOLF) for Dual-Energy X-ray CT

PubMed Central

Xi, Yan; Cong, Wenxiang; Harrison, Daniel

2017-01-01

In medical X-ray Computed Tomography (CT), the use of two distinct X-ray source spectra (energies) allows dose-reduction and material discrimination relative to that achieved with only one source spectrum. Existing dual-energy CT methods include source kVp-switching, double-layer detection, dual-source gantry, and two-pass scanning. Each method suffers either from strong spectral correlation or patient-motion artifacts. To simultaneously address these problems, we propose to improve CT data acquisition with the Grating Oriented Line-wise Filtration (GOLF) method, a novel X-ray filter that is placed between the source and patient. GOLF uses a combination of absorption and filtering gratings that are moved relative to each other and in synchronization with the X-ray tube kVp-switching process and/or the detector view-sampling process. Simulation results show that GOLF can improve the spectral performance of kVp-switching to match that of dual-source CT while avoiding patient motion artifacts and dual imaging chains. Although significant flux is absorbed by this pre-patient filter, the proposed GOLF method is a novel path for cost-effectively extracting dual-energy or multi-energy data and reducing radiation dose with or without kVp switching. PMID:29333113

80-kVp CT Using Iterative Reconstruction in Image Space Algorithm for the Detection of Hypervascular Hepatocellular Carcinoma: Phantom and Initial Clinical Experience

PubMed Central

Hur, Saebeom; Kim, Soo Jin; Park, Ji Hoon; Han, Joon Koo; Choi, Byung Ihn

2012-01-01

Objective To investigate whether the low-tube-voltage (80-kVp), intermediate-tube-current (340-mAs) MDCT using the Iterative Reconstruction in Image Space (IRIS) algorithm improves lesion-to-liver contrast at reduced radiation dosage while maintaining acceptable image noise in the detection of hepatocellular carcinomas (HCC) in thin (mean body mass index, 24 ± 0.4 kg/m2) adults. Subjects and Methods A phantom simulating the liver with HCC was scanned at 50-400 mAs for 80, 100, 120 and 140-kVp. In addition, fifty patients with HCC who underwent multiphasic liver CT using dual-energy (80-kVp and 140-kVp) arterial scans were enrolled. Virtual 120-kVP scans (protocol A) and 80-kVp scans (protocol B) of the late arterial phase were reconstructed with filtered back-projection (FBP), while corresponding 80-kVp scans were reconstructed with IRIS (protocol C). Contrast-to-noise ratio (CNR) of HCCs and abdominal organs were assessed quantitatively, whereas lesion conspicuity, image noise, and overall image quality were assessed qualitatively. Results IRIS effectively reduced image noise, and yielded 29% higher CNR than the FBP at equivalent tube voltage and current in the phantom study. In the quantitative patient study, protocol C helped improve CNR by 51% and 172% than protocols A and B (p < 0.001), respectively, at equivalent radiation dosage. In the qualitative study, protocol C acquired the highest score for lesion conspicuity albeit with an inferior score to protocol A for overall image quality (p < 0.001). Mean effective dose was 2.63-mSv with protocol A and 1.12-mSv with protocols B and C. Conclusion CT using the low-tube-voltage, intermediate-tube-current and IRIS help improve lesion-to-liver CNR of HCC in thin adults during the arterial phase at a lower radiation dose when compared with the standard technique using 120-kVp and FBP. PMID:22438682

Path Complexity in Virtual Water Maze Navigation: Differential Associations with Age, Sex, and Regional Brain Volume.

PubMed

Daugherty, Ana M; Yuan, Peng; Dahle, Cheryl L; Bender, Andrew R; Yang, Yiqin; Raz, Naftali

2015-09-01

Studies of human navigation in virtual maze environments have consistently linked advanced age with greater distance traveled between the start and the goal and longer duration of the search. Observations of search path geometry suggest that routes taken by older adults may be unnecessarily complex and that excessive path complexity may be an indicator of cognitive difficulties experienced by older navigators. In a sample of healthy adults, we quantify search path complexity in a virtual Morris water maze with a novel method based on fractal dimensionality. In a two-level hierarchical linear model, we estimated improvement in navigation performance across trials by a decline in route length, shortening of search time, and reduction in fractal dimensionality of the path. While replicating commonly reported age and sex differences in time and distance indices, a reduction in fractal dimension of the path accounted for improvement across trials, independent of age or sex. The volumes of brain regions associated with the establishment of cognitive maps (parahippocampal gyrus and hippocampus) were related to path dimensionality, but not to the total distance and time. Thus, fractal dimensionality of a navigational path may present a useful complementary method of quantifying performance in navigation. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Experimental study of the P₁₁(1440) and D₁₃(1520) resonances from the CLAS data on ep→e 'π⁺π⁻p '

DOE PAGES

Mokeev, V. I.; Burkert, V. D.; Elouadrhiri, L.; ...

2012-09-13

The transition helicity amplitudes from the proton ground state to the P₁₁(1440) and D₁₃(1520) excited states (γ vpN* electrocouplings) were determined from the analysis of nine independent one-fold differential π⁺π⁻p electroproduction cross sections off a proton target, taken with CLAS at photon virtualities of 0.25vpN* electrocouplings offers clear evidence for the reliable extraction of these fundamental quantities from meson-electroproduction data. This analysis also led to the determination of the long-awaited hadronic branching ratios for the D₁₃(1520) decay into Δπ (24%–32%) and Nρ (8%–17%).

Changes in Search Path Complexity and Length During Learning of a Virtual Water Maze: Age Differences and Differential Associations with Hippocampal Subfield Volumes

PubMed Central

Daugherty, Ana M.; Bender, Andrew R.; Yuan, Peng; Raz, Naftali

2016-01-01

Impairment of hippocampus-dependent cognitive processes has been proposed to underlie age-related deficits in navigation. Animal studies suggest a differential role of hippocampal subfields in various aspects of navigation, but that hypothesis has not been tested in humans. In this study, we examined the association between volume of hippocampal subfields and age differences in virtual spatial navigation. In a sample of 65 healthy adults (age 19–75 years), advanced age was associated with a slower rate of improvement operationalized as shortening of the search path over 25 learning trials on a virtual Morris water maze task. The deficits were partially explained by greater complexity of older adults' search paths. Larger subiculum and entorhinal cortex volumes were associated with a faster decrease in search path complexity, which in turn explained faster shortening of search distance. Larger Cornu Ammonis (CA)1–2 volume was associated with faster distance shortening, but not in path complexity reduction. Age differences in regional volumes collectively accounted for 23% of the age-related variance in navigation learning. Independent of subfield volumes, advanced age was associated with poorer performance across all trials, even after reaching the asymptote. Thus, subiculum and CA1–2 volumes were associated with speed of acquisition, but not magnitude of gains in virtual maze navigation. PMID:25838036

The use of virtual patient scenarios as a vehicle for teaching professionalism.

PubMed

Marei, H F; Al-Eraky, M M; Almasoud, N N; Donkers, J; Van Merrienboer, J J G

2018-05-01

This study aimed to measure students' perceptions of virtual patient scenarios (VPs) for developing ethical reasoning skills and to explore features in VP design that are necessary to promote professionalism. Sixty-five dental students participated in learning sessions that involved collaborative practice with five VPs (four high fidelity and one low fidelity), followed by reflection sessions. Students' perceptions towards the use of VPs in developing ethical reasoning skills were assessed using a questionnaire that involved 10 closed and three open-ended questions. High-fidelity VPs were perceived as significantly better for developing ethical reasoning skills than low-fidelity VPs. Analyses of answers to open-ended questions revealed two new features that are specific for VPs intended for teaching professionalism, which are VP dramatic structure and how it should end. VPs intended for teaching professionalism need to have high fidelity, follow a specific dramatic structure and should include multiple plausible endings. The use of VPs as part of a collaborative activity that is followed by a reflection session is perceived as an effective tool for the development of ethical reasoning skills in dental education. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Changes in Search Path Complexity and Length During Learning of a Virtual Water Maze: Age Differences and Differential Associations with Hippocampal Subfield Volumes.

PubMed

Daugherty, Ana M; Bender, Andrew R; Yuan, Peng; Raz, Naftali

2016-06-01

Impairment of hippocampus-dependent cognitive processes has been proposed to underlie age-related deficits in navigation. Animal studies suggest a differential role of hippocampal subfields in various aspects of navigation, but that hypothesis has not been tested in humans. In this study, we examined the association between volume of hippocampal subfields and age differences in virtual spatial navigation. In a sample of 65 healthy adults (age 19-75 years), advanced age was associated with a slower rate of improvement operationalized as shortening of the search path over 25 learning trials on a virtual Morris water maze task. The deficits were partially explained by greater complexity of older adults' search paths. Larger subiculum and entorhinal cortex volumes were associated with a faster decrease in search path complexity, which in turn explained faster shortening of search distance. Larger Cornu Ammonis (CA)1-2 volume was associated with faster distance shortening, but not in path complexity reduction. Age differences in regional volumes collectively accounted for 23% of the age-related variance in navigation learning. Independent of subfield volumes, advanced age was associated with poorer performance across all trials, even after reaching the asymptote. Thus, subiculum and CA1-2 volumes were associated with speed of acquisition, but not magnitude of gains in virtual maze navigation. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Monolithic mm-wave phase shifter using optically activated superconducting switches

NASA Technical Reports Server (NTRS)

Romanofsky, Robert R. (Inventor); Bhasin, Kul B. (Inventor)

1992-01-01

A phase shifter is disclosed having a reference path and a delay path, light sources, and superconductive switches. Each of the superconductive switches is terminated in a virtual short circuit, which may be a radial stub. Switching between the reference path and delayed path is accomplished by illuminating the superconductive switches connected to the desired path, while not illuminating the superconductive switches connected to the other path.

Making the invisible visible: improving conspicuity of noncalcified gallstones using dual-energy CT.

PubMed

Uyeda, Jennifer W; Richardson, Ian J; Sodickson, Aaron D

2017-12-01

To determine whether virtual monochromatic imaging (VMI) increases detectability of noncalcified gallstones on dual-energy CT (DECT) compared with conventional CT imaging. This retrospective IRB-approved, HIPAA-compliant study included consecutive patients who underwent DECT of the abdomen in the Emergency Department during a 30-month period (July 1, 2013-December 31, 2015), with a comparison US or MR within 1-year. 51 patients (36F, 15M; mean age 52 years) fulfilled the inclusion criteria. All DECT were acquired on a dual-source 128 × 2 slice scanner using either 80/Sn140 or 100/Sn140 kVp pairs. Source images at high and low kVp were used for DE post-processing with VMI. Within 3 mm reconstructed images, regions of interest of 0.5 cm 2 were placed on noncalcified gallstones and bile to record hounsfield units (HU) at VMI energy levels ranging between 40 and 190 keV. Noncalcified gallstones uniformly demonstrated lowest HU at 40 keV and increase at higher keV; the HU of bile varied at higher keV. Few of the noncalcified stones are visible at 70 keV (simulating a conventional 120 kVp scan), with measured contrast (bile-stone HU difference) <10 HU in 78%, 10-20 HU in 20%, and >20 HU in 2%. Contrast was maximal at 40 keV, where 100% demonstrated >20 HU difference from surrounding bile, 75% >44 HU difference, and 50% >60 HU difference. A paired t test demonstrated a significant difference (p < 0.0001) between this stone-bile contrast at 40 vs. 70 keV and 70 vs. 190 keV. Low keV virtual monochromatic imaging increased conspicuity of noncalcified gallstones, improving their detectability.

Effective distance adaptation traffic dispatching in software defined IP over optical network

NASA Astrophysics Data System (ADS)

Duan, Zhiwei; Li, Hui; Liu, Yuze; Ji, Yuefeng; Li, Hongfa; Lin, Yi

2017-10-01

The rapid growth of IP traffic has contributed to the wide deployment of optical devices (ROADM/OXC, etc.). Meanwhile, with the emergence and application of high-performance network services such as ultra-high video transmission, people are increasingly becoming more and more particular about the quality of service (QoS) of network. However, the pass-band shape of WSSs which is utilized in the ROADM/OXC is not ideal, causing narrowing of spectrum. Spectral narrowing can lead to signal impairment. Therefore, guard-bands need to be inserted between adjacent paths. In order to minimize the bandwidth waste due to guard bands, we propose an effective distance-adaptation traffic dispatching algorithm in IP over optical network based on SDON architecture. We use virtualization technology to set up virtual resources direct links by extracting part of the resources on paths which meet certain specific constraints. We also assign different bandwidth to each IP request based on path length. There is no need for guard-bands between the adjacent paths on the virtual link, which can effectively reduce the number of guard-bands and save the spectrum.

How a joint interpretation of seismic scattering, velocity, and attenuation models explains the nature of the Campi Flegrei (Italy).

NASA Astrophysics Data System (ADS)

Calo, M.; Tramelli, A.

2017-12-01

Seismic P and S velocity models (and their ratio Vp/Vs) help illuminating the geometrical structure of the bodies and give insight on the presence of water, molten or gas saturated regions. Seismic attenuation represents the anelastic behavior of the medium. Due to its dependence on temperature, fluid contents and cracks presence, this parameter is also largely used to characterize the structures of volcanoes and geothermal areas. Scattering attenuation is related, in the upper crust, to the amount, size and organization of the fractures giving complementary information on the state of the medium.Therefore a joint interpretation of these models provides an exhaustive view of the elastic parameters in volcanic regions. Campi Flegrei is an active Caldera marked by strong vertical deformations of the ground called bradyseisms and several models have been proposed to describe the nature and the geometry of the bodies responsible of the bradyseisms. Here we show Vp, Vp/Vs, Qp and scattering models carried out by applying an enhanced seismic tomography method that combines de double difference approach (Zhang and Thurber, 2003) and the Weigthed Average Method (Calò et al., 2009, Calò et al., 2011, 2013). The data used are the earthquakes recorded during the largest bradyseism crisis of the 80's. Our method allowed to image structures with linear dimension of 0.5-1.2km, resulting in an improvement of the resolving power at least two times of the other published models (e.g. Priolo et al., 2012). The joint interpretation of seismic models allowed to discern small anomalous bodies at shallow depth (0.5-2.0 km) marked by relatively low Vp, high Vp/Vs ratio and low Qp values associated with the presence of shallow geothermal water saturated reservoir from regions with low Vp, low Vp/Vs and low Qp related to the gas saturated part of the reservoir. At deeper depth (2-3.5 km) bodies with high Vp and Vp/Vs and low Qp are associated with magmatic intrusions. The Scattering model highlights the highly fractured part of the caldera suggesting the main paths of the fluid/heath transportation. This work was supported by UNAM-PAPIIT:IA100416.

Development, implementation and pilot evaluation of a Web-based Virtual Patient Case Simulation environment – Web-SP

PubMed Central

Zary, Nabil; Johnson, Gunilla; Boberg, Jonas; Fors, Uno GH

2006-01-01

Background The Web-based Simulation of Patients (Web-SP) project was initiated in order to facilitate the use of realistic and interactive virtual patients (VP) in medicine and healthcare education. Web-SP focuses on moving beyond the technology savvy teachers, when integrating simulation-based education into health sciences curricula, by making the creation and use of virtual patients easier. The project strives to provide a common generic platform for design/creation, management, evaluation and sharing of web-based virtual patients. The aim of this study was to evaluate if it was possible to develop a web-based virtual patient case simulation environment where the entire case authoring process might be handled by teachers and which would be flexible enough to be used in different healthcare disciplines. Results The Web-SP system was constructed to support easy authoring, management and presentation of virtual patient cases. The case authoring environment was found to facilitate for teachers to create full-fledged patient cases without the assistance of computer specialists. Web-SP was successfully implemented at several universities by taking into account key factors such as cost, access, security, scalability and flexibility. Pilot evaluations in medical, dentistry and pharmacy courses shows that students regarded Web-SP as easy to use, engaging and to be of educational value. Cases adapted for all three disciplines were judged to be of significant educational value by the course leaders. Conclusion The Web-SP system seems to fulfil the aim of providing a common generic platform for creation, management and evaluation of web-based virtual patient cases. The responses regarding the authoring environment indicated that the system might be user-friendly enough to appeal to a majority of the academic staff. In terms of implementation strengths, Web-SP seems to fulfil most needs from course directors and teachers from various educational institutions and disciplines. The system is currently in use or under implementation in several healthcare disciplines at more than ten universities worldwide. Future aims include structuring the exchange of cases between teachers and academic institutions by building a VP library function. We intend to follow up the positive results presented in this paper with other studies looking at the learning outcomes, critical thinking and patient management. Studying the potential of Web-SP as an assessment tool will also be performed. More information about Web-SP: PMID:16504041

Development, implementation and pilot evaluation of a Web-based Virtual Patient Case Simulation environment--Web-SP.

PubMed

Zary, Nabil; Johnson, Gunilla; Boberg, Jonas; Fors, Uno G H

2006-02-21

The Web-based Simulation of Patients (Web-SP) project was initiated in order to facilitate the use of realistic and interactive virtual patients (VP) in medicine and healthcare education. Web-SP focuses on moving beyond the technology savvy teachers, when integrating simulation-based education into health sciences curricula, by making the creation and use of virtual patients easier. The project strives to provide a common generic platform for design/creation, management, evaluation and sharing of web-based virtual patients. The aim of this study was to evaluate if it was possible to develop a web-based virtual patient case simulation environment where the entire case authoring process might be handled by teachers and which would be flexible enough to be used in different healthcare disciplines. The Web-SP system was constructed to support easy authoring, management and presentation of virtual patient cases. The case authoring environment was found to facilitate for teachers to create full-fledged patient cases without the assistance of computer specialists. Web-SP was successfully implemented at several universities by taking into account key factors such as cost, access, security, scalability and flexibility. Pilot evaluations in medical, dentistry and pharmacy courses shows that students regarded Web-SP as easy to use, engaging and to be of educational value. Cases adapted for all three disciplines were judged to be of significant educational value by the course leaders. The Web-SP system seems to fulfil the aim of providing a common generic platform for creation, management and evaluation of web-based virtual patient cases. The responses regarding the authoring environment indicated that the system might be user-friendly enough to appeal to a majority of the academic staff. In terms of implementation strengths, Web-SP seems to fulfil most needs from course directors and teachers from various educational institutions and disciplines. The system is currently in use or under implementation in several healthcare disciplines at more than ten universities worldwide. Future aims include structuring the exchange of cases between teachers and academic institutions by building a VP library function. We intend to follow up the positive results presented in this paper with other studies looking at the learning outcomes, critical thinking and patient management. Studying the potential of Web-SP as an assessment tool will also be performed. More information about Web-SP: http://websp.lime.ki.se.

The evaluation of a virtual education system based on the DeLone and McLean model:  A path analysis.

PubMed

Mahmoodi, Zohreh; Esmaelzadeh-Saeieh, Sara; Lotfi, Razieh; Baradaran Eftekhari, Monir; Akbari Kamrani, Mahnaz; Mehdizadeh Tourzani, Zahra; Salehi, Katayoun

2017-01-01

Background : The Internet has dramatically influenced the introduction of virtual education. Virtual education is a term that involves online education and e-learning. This study was conducted to evaluate a virtual education system based on the DeLone and McLean model. Methods : This descriptive analytical study was conducted using the census method on all the students of the Nursing and Midwifery Department of Alborz University of Medical Sciences who had taken at least one online course in 2016-2017. Data were collected using a researcher-made questionnaire based on the DeLone and McLean model in six domains and then analyzed in SPSS-16 and LISREL-8.8 using the path analysis. Results : The goodness of fit indices (GFI) of the model represent the desirability and good fit of the model, and the rational nature of the adjusted relationships between the variables based on a conceptual model (GFI = 0.98; RMSEA = 0.014).The results showed that system quality has the greatest impact on the net benefits of the system through both direct and indirect paths (β=0.52), service quality through the indirect path (β=0.03) and user satisfaction through the direct path (β=0.73). Conclusions : According to the results, system quality has the greatest overall impact on the net benefits of the system, both directly and indirectly by affecting user satisfaction and the intention to use. System quality should therefore be further emphasized, to use these systems more efficiently.

Visual influence on path integration in darkness indicates a multimodal representation of large-scale space

PubMed Central

Tcheang, Lili; Bülthoff, Heinrich H.; Burgess, Neil

2011-01-01

Our ability to return to the start of a route recently performed in darkness is thought to reflect path integration of motion-related information. Here we provide evidence that motion-related interoceptive representations (proprioceptive, vestibular, and motor efference copy) combine with visual representations to form a single multimodal representation guiding navigation. We used immersive virtual reality to decouple visual input from motion-related interoception by manipulating the rotation or translation gain of the visual projection. First, participants walked an outbound path with both visual and interoceptive input, and returned to the start in darkness, demonstrating the influences of both visual and interoceptive information in a virtual reality environment. Next, participants adapted to visual rotation gains in the virtual environment, and then performed the path integration task entirely in darkness. Our findings were accurately predicted by a quantitative model in which visual and interoceptive inputs combine into a single multimodal representation guiding navigation, and are incompatible with a model of separate visual and interoceptive influences on action (in which path integration in darkness must rely solely on interoceptive representations). Overall, our findings suggest that a combined multimodal representation guides large-scale navigation, consistent with a role for visual imagery or a cognitive map. PMID:21199934

Virtual Learning Environment for Interactive Engagement with Advanced Quantum Mechanics

ERIC Educational Resources Information Center

Pedersen, Mads Kock; Skyum, Birk; Heck, Robert; Müller, Romain; Bason, Mark; Lieberoth, Andreas; Sherson, Jacob F.

2016-01-01

A virtual learning environment can engage university students in the learning process in ways that the traditional lectures and lab formats cannot. We present our virtual learning environment "StudentResearcher," which incorporates simulations, multiple-choice quizzes, video lectures, and gamification into a learning path for quantum…

How to tell a patient's story? Influence of the case narrative design on the clinical reasoning process in virtual patients.

PubMed

Hege, Inga; Dietl, Anita; Kiesewetter, Jan; Schelling, Jörg; Kiesewetter, Isabel

2018-02-28

Virtual patients (VPs) are narrative-based educational activities to train clinical reasoning in a safe environment. Our aim was to explore the influence of the design of the narrative and level of difficulty on the clinical reasoning process, diagnostic accuracy and time-on-task. In a randomized controlled trial, we analyzed the clinical reasoning process of 46 medical students with six VPs in three different variations: (1) patients showing a friendly behavior, (2) patients showing a disruptive behavior and (3) a version without a patient story. For easy VPs, we did not see a significant difference in diagnostic accuracy. For difficult VPs, the diagnostic accuracy was significantly higher for participants who worked on the friendly VPs compared to the other two groups. Independent from VP difficulty, participants identified significantly more problems and tests for disruptive than for friendly VPs; time on task was comparable for these two groups. The extrinsic motivation of participants working on the VPs without a patient story was significantly lower than for the students working on the friendly VPs. Our results indicate that the measured VP difficulty has a higher influence on the clinical reasoning process and diagnostic accuracy than the variations in the narratives.

The effectiveness of integration of virtual patients in a collaborative learning activity.

PubMed

Marei, Hesham F; Donkers, Jeroen; Van Merrienboer, Jeroen J G

2018-05-07

Virtual patients (VPs) have been recently integrated within different learning activities. To compare between the effect of using VPs in a collaborative learning activity and using VPs in an independent learning activity on students' knowledge acquisition, retention and transfer. For two different topics, respectively 82 and 76 dental students participated in teaching, learning and assessment sessions with VPs. Students from a female campus and from a male campus have been randomly assigned to condition (collaborative and independent), yielding four experimental groups. Each group received a lecture followed by a learning session using two VPs per topic. Students were administrated immediate and delayed written tests as well as transfer tests using two VPs to assess their knowledge in diagnosis and treatment. For the treatment items of the immediate and delayed written tests, females outperformed males in the collaborative VP group but not in the independent VP group. On the female campus, the use of VPs in a collaborative learning activity is more effective than its use as an independent learning activity in enhancing students' knowledge acquisition and retention. However, the collaborative use of VPs by itself is not enough to produce consistent results across different groups of students and attention should be given to all the factors that would affect students' interaction.

Marine derived compounds as binders of the White spot syndrome virus VP28 envelope protein: In silico insights from molecular dynamics and binding free energy calculations.

PubMed

Sivakumar, K C; Sajeevan, T P; Bright Singh, I S

2016-10-01

White spot syndrome virus (WSSV) remains as one of the most dreadful pathogen of the shrimp aquaculture industry owing to its high virulence. The cumulative mortality reaches up to 100% within in 2-10days in a shrimp farm. Currently, no chemotherapeutics are available to control WSSV. The viral envelope protein, VP28, located on the surface of the virus particle acts as a vital virulence factor in the initial phases of inherent WSSV infection in shrimp. Hence, inhibition of envelope protein VP28 could be a novel way to deal with infection by inhibiting its interaction in the endocytic pathway. In this direction, a timely attempt was made to recognize a potential drug candidate of marine origin against WSSV using VP28 as a target by employing in silico docking and molecular dynamic simulations. A virtual library of 388 marine bioactive compounds was extracted from reports published in Marine Drugs. The top ranking compounds from docking studies were chosen from the flexible docking based on the binding affinities (ΔGb). In addition, the MD simulation and binding free energy analysis were implemented to validate and capture intermolecular interactions. The results suggested that the two compounds obtained a negative binding free energy with -40.453kJ/mol and -31.031kJ/mol for compounds with IDs 30797199 and 144162 respectively. The RMSD curve indicated that 30797199 moves into the hydrophobic core, while the position of 144162 atoms changes abruptly during simulation and is mostly stabilized by water bridges. The shift in RMSD values of VP28 corresponding to ligand RMSD gives an insight into the ligand induced conformational changes in the protein. This study is first of its kind to elucidate the explicit binding of chemical inhibitor to WSSV major structural protein VP28. Copyright © 2016 Elsevier Ltd. All rights reserved.

Biplane reconstruction and visualization of virtual endoscopic and fluoroscopic views for interventional device navigation

NASA Astrophysics Data System (ADS)

Wagner, Martin G.; Strother, Charles M.; Schafer, Sebastian; Mistretta, Charles A.

2016-03-01

Biplane fluoroscopic imaging is an important tool for minimally invasive procedures for the treatment of cerebrovascular diseases. However, finding a good working angle for the C-arms of the angiography system as well as navigating based on the 2D projection images can be a difficult task. The purpose of this work is to propose a novel 4D reconstruction algorithm for interventional devices from biplane fluoroscopy images and to propose new techniques for a better visualization of the results. The proposed reconstruction methods binarizes the fluoroscopic images using a dedicated noise reduction algorithm for curvilinear structures and a global thresholding approach. A topology preserving thinning algorithm is then applied and a path search algorithm minimizing the curvature of the device is used to extract the 2D device centerlines. Finally, the 3D device path is reconstructed using epipolar geometry. The point correspondences are determined by a monotonic mapping function that minimizes the reconstruction error. The three dimensional reconstruction of the device path allows the rendering of virtual fluoroscopy images from arbitrary angles as well as 3D visualizations like virtual endoscopic views or glass pipe renderings, where the vessel wall is rendered with a semi-transparent material. This work also proposes a combination of different visualization techniques in order to increase the usability and spatial orientation for the user. A combination of synchronized endoscopic and glass pipe views is proposed, where the virtual endoscopic camera position is determined based on the device tip location as well as the previous camera position using a Kalman filter in order to create a smooth path. Additionally, vessel centerlines are displayed and the path to the target is highlighted. Finally, the virtual endoscopic camera position is also visualized in the glass pipe view to further improve the spatial orientation. The proposed techniques could considerably improve the workflow of minimally invasive procedures for the treatment of cerebrovascular diseases.

Dynamic-Stark-effect-induced coherent mixture of virtual paths in laser-dressed helium: energetic electron impact excitation

NASA Astrophysics Data System (ADS)

Agueny, Hicham; Makhoute, Abdelkader; Dubois, Alain

2017-06-01

We theoretically investigate quantum virtual path interference caused by the dynamic Stark effect in bound-bound electronic transitions. The effect is studied in an intermediate resonant region and in connection with the energetic electron impact excitation of a helium atom embedded in a weak low-frequency laser field. The process under investigation is dealt with via a Born-Floquet approach. Numerical calculations show a resonant feature in laser-assisted cross sections. The latter is found to be sensitive to the intensity of the laser field dressing. We show that this feature is a signature of quantum beats which result from the coherent mixture of different quantum virtual pathways, and that excitation may follow in order to end up with a common final channel. This mixture arises from the dynamic Stark effect, which produces a set of avoided crossings in laser-dressed states. The effect allows one to coherently control quantum virtual path interference by varying the intensity of the laser field dressing. Our findings suggest that the combination of an energetic electron and a weak laser field is a useful tool for the coherent control of nonadiabatic transitions in an intermediate resonant region.

Artificial pheromone for path selection by a foraging swarm of robots.

PubMed

Campo, Alexandre; Gutiérrez, Alvaro; Nouyan, Shervin; Pinciroli, Carlo; Longchamp, Valentin; Garnier, Simon; Dorigo, Marco

2010-11-01

Foraging robots involved in a search and retrieval task may create paths to navigate faster in their environment. In this context, a swarm of robots that has found several resources and created different paths may benefit strongly from path selection. Path selection enhances the foraging behavior by allowing the swarm to focus on the most profitable resource with the possibility for unused robots to stop participating in the path maintenance and to switch to another task. In order to achieve path selection, we implement virtual ants that lay artificial pheromone inside a network of robots. Virtual ants are local messages transmitted by robots; they travel along chains of robots and deposit artificial pheromone on the robots that are literally forming the chain and indicating the path. The concentration of artificial pheromone on the robots allows them to decide whether they are part of a selected path. We parameterize the mechanism with a mathematical model and provide an experimental validation using a swarm of 20 real robots. We show that our mechanism favors the selection of the closest resource is able to select a new path if a selected resource becomes unavailable and selects a newly detected and better resource when possible. As robots use very simple messages and behaviors, the system would be particularly well suited for swarms of microrobots with minimal abilities.

Objective structured clinical interview training using a virtual human patient.

PubMed

Parsons, Thomas D; Kenny, Patrick; Ntuen, Celestine A; Pataki, Caroly S; Pato, Michele T; Rizzo, Albert A; St-George, Cheryl; Sugar, Jeffery

2008-01-01

Effective interview skills are a core competency for psychiatry residents and developing psychotherapists. Although schools commonly make use of standardized patients to teach interview skills, the diversity of the scenarios standardized patients can characterize is limited by availability of human actors. Further, there is the economic concern related to the time and money needed to train standardized patients. Perhaps most damaging is the "standardization" of standardized patients -- will they in fact consistently proffer psychometrically reliable and valid interactions with the training clinicians. Virtual Human Agent (VHA) technology has evolved to a point where researchers may begin developing mental health applications that make use of virtual reality patients. The work presented here is a preliminary attempt at what we believe to be a large application area. Herein we describe an ongoing study of our virtual patients (VP). We present an approach that allows novice mental health clinicians to conduct an interview with a virtual character that emulates an adolescent male with conduct disorder. This study illustrates the ways in which a variety of core research components developed at the University of Southern California facilitates the rapid development of mental health applications.

Virtual screening of the inhibitors targeting at the viral protein 40 of Ebola virus.

PubMed

Karthick, V; Nagasundaram, N; Doss, C George Priya; Chakraborty, Chiranjib; Siva, R; Lu, Aiping; Zhang, Ge; Zhu, Hailong

2016-02-17

The Ebola virus is highly pathogenic and destructive to humans and other primates. The Ebola virus encodes viral protein 40 (VP40), which is highly expressed and regulates the assembly and release of viral particles in the host cell. Because VP40 plays a prominent role in the life cycle of the Ebola virus, it is considered as a key target for antiviral treatment. However, there is currently no FDA-approved drug for treating Ebola virus infection, resulting in an urgent need to develop effective antiviral inhibitors that display good safety profiles in a short duration. This study aimed to screen the effective lead candidate against Ebola infection. First, the lead molecules were filtered based on the docking score. Second, Lipinski rule of five and the other drug likeliness properties are predicted to assess the safety profile of the lead candidates. Finally, molecular dynamics simulations was performed to validate the lead compound. Our results revealed that emodin-8-beta-D-glucoside from the Traditional Chinese Medicine Database (TCMD) represents an active lead candidate that targets the Ebola virus by inhibiting the activity of VP40, and displays good pharmacokinetic properties. This report will considerably assist in the development of the competitive and robust antiviral agents against Ebola infection.

Coordinated path following of multiple underacutated marine surface vehicles along one curve.

PubMed

Liu, Lu; Wang, Dan; Peng, Zhouhua

2016-09-01

This paper investigates the coordinated path following problem for a fleet of underactuated marine surface vehicles (MSVs) along one curve. The dedicated control design is divided into two tasks. One is to steer individual underactuated MSV to track the given spatial path, and the other is to force the vehicles dispersed on a parameterized path subject to the constraints of a communication network. Specifically, a robust individual path following controller is developed based on a line-of-sight (LOS) guidance law and a reduced-order extended state observer (ESO). The vehicle sideslip angle due to environmental disturbances can be exactly identified. Then, the vehicle coordination is achieved by a path variable containment approach, under which the path variables are evenly dispersed between two virtual leaders. Another reduced-order ESO is developed to identify the composite disturbance related to the speed of virtual leaders and neighboring vehicles. The proposed coordination design is distributed since the reference speed does not need to be known by all vehicles as a priori. The input-to-state stability of the closed-loop network system is established via cascade theory. Simulation results demonstrate the effectiveness of the proposed design method. Copyright © 2016 ISA. Published by Elsevier Ltd. All rights reserved.

Three-dimensional Image Fusion Guidance for Transjugular Intrahepatic Portosystemic Shunt Placement.

PubMed

Tacher, Vania; Petit, Arthur; Derbel, Haytham; Novelli, Luigi; Vitellius, Manuel; Ridouani, Fourat; Luciani, Alain; Rahmouni, Alain; Duvoux, Christophe; Salloum, Chady; Chiaradia, Mélanie; Kobeiter, Hicham

2017-11-01

To assess the safety, feasibility and effectiveness of image fusion guidance with pre-procedural portal phase computed tomography with intraprocedural fluoroscopy for transjugular intrahepatic portosystemic shunt (TIPS) placement. All consecutive cirrhotic patients presenting at our interventional unit for TIPS creation from January 2015 to January 2016 were prospectively enrolled. Procedures were performed under general anesthesia in an interventional suite equipped with flat panel detector, cone-beam computed tomography (CBCT) and image fusion technique. All TIPSs were placed under image fusion guidance. After hepatic vein catheterization, an unenhanced CBCT acquisition was performed and co-registered with the pre-procedural portal phase CT images. A virtual path between hepatic vein and portal branch was made using the virtual needle path trajectory software. Subsequently, the 3D virtual path was overlaid on 2D fluoroscopy for guidance during portal branch cannulation. Safety, feasibility, effectiveness and per-procedural data were evaluated. Sixteen patients (12 males; median age 56 years) were included. Procedures were technically feasible in 15 of the 16 patients (94%). One procedure was aborted due to hepatic vein catheterization failure related to severe liver distortion. No periprocedural complications occurred within 48 h of the procedure. The median dose-area product was 91 Gy cm 2 , fluoroscopy time 15 min, procedure time 40 min and contrast media consumption 65 mL. Clinical benefit of the TIPS placement was observed in nine patients (56%). This study suggests that 3D image fusion guidance for TIPS is feasible, safe and effective. By identifying virtual needle path, CBCT enables real-time multiplanar guidance and may facilitate TIPS placement.

A systematic investigation of navigation impairment in chronic stroke patients: Evidence for three distinct types.

PubMed

Claessen, Michiel H G; Visser-Meily, Johanna M A; Meilinger, Tobias; Postma, Albert; de Rooij, Nicolien K; van der Ham, Ineke J M

2017-08-01

In a recent systematic review, Claessen and van der Ham (2017) have analyzed the types of navigation impairment in the single-case study literature. Three dissociable types related to landmarks, locations, and paths were identified. This recent model as well as previous models of navigation impairment have never been verified in a systematic manner. The aim of the current study was thus to investigate the prevalence of landmark-based, location-based, and path-based navigation impairment in a large sample of stroke patients. Navigation ability of 77 stroke patients in the chronic phase and 60 healthy participants was comprehensively evaluated using the Virtual Tübingen test, which contains twelve subtasks addressing various aspects of knowledge about landmarks, locations, and paths based on a newly learned virtual route. Participants also filled out the Wayfinding Questionnaire to allow for making a distinction between stroke patients with and without significant subjective navigation-related complaints. Analysis of responses on the Wayfinding Questionnaire indicated that 33 of the 77 participating stroke patients had significant navigation-related complaints. An examination of their performance on the Virtual Tübingen test established objective evidence for navigation impairment in 27 patients. Both landmark-based and path-based navigation impairment occurred in isolation, while location-based navigation impairment was only found along with the other two types. The current study provides the first empirical support for the distinction between landmark-based, location-based, and path-based navigation impairment. Future research relying on other assessment instruments of navigation ability might be helpful to further validate this distinction. Copyright © 2017 Elsevier Ltd. All rights reserved.

On-demand virtual optical network access using 100 Gb/s Ethernet.

PubMed

Ishida, Osamu; Takamichi, Toru; Arai, Sachine; Kawate, Ryusuke; Toyoda, Hidehiro; Morita, Itsuro; Araki, Soichiro; Ichikawa, Toshiyuki; Hoshida, Takeshi; Murai, Hitoshi

2011-12-12

Our Terabit LAN initiatives attempt to enhance the scalability and utilization of lambda resources. This paper describes bandwidth-on-demand virtualized 100GE access to WDM networks on a field fiber test-bed using multi-domain optical-path provisioning. © 2011 Optical Society of America

Navigating Mythic Space in the Digital Age

ERIC Educational Resources Information Center

Foley, Drew Thomas

2012-01-01

In prior ages, alternate worlds are associated with symbolic expressions of storied space, here termed "mythic space." The digital age brings new forms of virtual space that are co-existent with physical space. These virtual spaces may be understood as a contemporary representation of mythic space. This dissertation explores the paths by…

Virtually Unpacking Your Backpack: Educational Philosophy and Pedagogical Praxis

ERIC Educational Resources Information Center

Franklin, Yvette

2014-01-01

In this autoethnographic, conceptual philosophical reflection, the author inquires: "Can my students and I, in a technologically mediated virtual space, harness the work of philosophy of education scholars to engage in a shared experience of (re)considering paths to sensitivity to diversity for equity and equality?" The author engages…

Examining Factors That Affect Students' Knowledge Sharing within Virtual Teams

ERIC Educational Resources Information Center

He, Jinxia; Gunter, Glenda

2015-01-01

The purpose of this study was to examine factors that might impact student knowledge sharing within virtual teams through online discussion boards. These factors include: trust, mutual influence, conflict, leadership, and cohesion. A path model was developed to determine whether relationships exist among knowledge sharing from asynchronous group…

Distance comparisons in virtual reality: effects of path, context, and age

PubMed Central

van der Ham, Ineke J. M.; Baalbergen, Heleen; van der Heijden, Peter G. M.; Postma, Albert; Braspenning, Merel; van der Kuil, Milan N. A.

2015-01-01

In this large scale, individual differences study (N = 521), the effects of cardinal axes of an environment and the path taken between locations on distance comparisons were assessed. The main goal was to identify if and to what extent previous findings in simple 2D tasks can be generalized to a more dynamic, three-dimensional virtual reality environment. Moreover, effects of age and gender were assessed. After memorizing the locations of six objects in a circular environment, participants were asked to judge the distance between objects they encountered. Results indicate that categorization (based on the cardinal axes) was present, as distances within one quadrant were judged as being closer together, even when no visual indication of the cardinal axes was given. Moreover, strong effects of the path taken between object locations were found; objects that were near on the path taken were perceived as being closer together than objects that were further apart on this path, regardless of the metric distance between the objects. Males outperformed females in distance comparison, but did not differ in the extent of the categorization and path effects. Age also affected performance; the categorization and path effects were highly similar across the age range tested, but the general ability to estimate distances does show a clear pattern increase during development and decrease with aging. PMID:26321968

Secondary metabolites extracted from marine sponge associated Comamonas testosteroni and Citrobacter freundii as potential antimicrobials against MDR pathogens and hypothetical leads for VP40 matrix protein of Ebola virus: an in vitro and in silico investigation.

PubMed

Skariyachan, Sinosh; Acharya, Archana B; Subramaniyan, Saumya; Babu, Sumangala; Kulkarni, Shruthi; Narayanappa, Rajeswari

2016-09-01

The current study explores therapeutic potential of metabolites extracted from marine sponge (Cliona sp.)-associated bacteria against MDR pathogens and predicts the binding prospective of probable lead molecules against VP40 target of Ebola virus. The metabolite-producing bacteria were characterized by agar overlay assay and as per the protocols in Bergey's manual of determinative bacteriology. The antibacterial activities of extracted metabolites were tested against clinical pathogens by well-diffusion assay. The selected metabolite producers were characterized by 16S rDNA sequencing. Chemical screening and Fourier Transform Infrared (FTIR) analysis for selected compounds were performed. The probable lead molecules present in the metabolites were hypothesized based on proximate analysis, FTIR data, and literature survey. The drug-like properties and binding potential of lead molecules against VP40 target of Ebola virus were hypothesized by computational virtual screening and molecular docking. The current study demonstrated that clear zones around bacterial colonies in agar overlay assay. Antibiotic sensitivity profiling demonstrated that the clinical isolates were multi-drug resistant, however; most of them showed sensitivity to secondary metabolites (MIC-15 μl/well). The proximate and FTIR analysis suggested that probable metabolites belonged to alkaloids with O-H, C-H, C=O, and N-H groups. 16S rDNA characterization of selected metabolite producers demonstrated that 96% and 99% sequence identity to Comamonas testosteroni and Citrobacter freundii, respectively. The docking studies suggested that molecules such as Gymnastatin, Sorbicillactone, Marizomib, and Daryamide can designed as probable lead candidates against VP40 target of Ebola virus.

Real-time path planning in dynamic virtual environments using multiagent navigation graphs.

PubMed

Sud, Avneesh; Andersen, Erik; Curtis, Sean; Lin, Ming C; Manocha, Dinesh

2008-01-01

We present a novel approach for efficient path planning and navigation of multiple virtual agents in complex dynamic scenes. We introduce a new data structure, Multi-agent Navigation Graph (MaNG), which is constructed using first- and second-order Voronoi diagrams. The MaNG is used to perform route planning and proximity computations for each agent in real time. Moreover, we use the path information and proximity relationships for local dynamics computation of each agent by extending a social force model [Helbing05]. We compute the MaNG using graphics hardware and present culling techniques to accelerate the computation. We also address undersampling issues and present techniques to improve the accuracy of our algorithm. Our algorithm is used for real-time multi-agent planning in pursuit-evasion, terrain exploration and crowd simulation scenarios consisting of hundreds of moving agents, each with a distinct goal.

Examining Factors that Affect Knowledge Sharing and Students' Attitude toward Their Learning Experience within Virtual Teams

ERIC Educational Resources Information Center

He, Jinxia

2009-01-01

This study examined factors that might impact student knowledge sharing within virtual teams through online discussion boards. These factors included: trust, mutual influence, conflict, leadership, and cohesion. A path model was developed to determine whether relationships exist among knowledge sharing from asynchronous group discussion and the…

Virtual hybrid test control of sinuous crack

NASA Astrophysics Data System (ADS)

Jailin, Clément; Carpiuc, Andreea; Kazymyrenko, Kyrylo; Poncelet, Martin; Leclerc, Hugo; Hild, François; Roux, Stéphane

2017-05-01

The present study aims at proposing a new generation of experimental protocol for analysing crack propagation in quasi brittle materials. The boundary conditions are controlled in real-time to conform to a predefined crack path. Servo-control is achieved through a full-field measurement technique to determine the pre-set fracture path and a simple predictor model based on linear elastic fracture mechanics to prescribe the boundary conditions on the fly so that the actual crack path follows at best the predefined trajectory. The final goal is to identify, for instance, non-local damage models involving internal lengths. The validation of this novel procedure is performed via a virtual test-case based on an enriched damage model with an internal length scale, a prior chosen sinusoidal crack path and a concrete sample. Notwithstanding the fact that the predictor model selected for monitoring the test is a highly simplified picture of the targeted constitutive law, the proposed protocol exhibits a much improved sensitivity to the sought parameters such as internal lengths as assessed from the comparison with other available experimental tests.

Dual-energy CT revisited with multidetector CT: review of principles and clinical applications.

PubMed

Karçaaltıncaba, Muşturay; Aktaş, Aykut

2011-09-01

Although dual-energy CT (DECT) was first conceived in the 1970s, it was not widely used for CT indications. Recently, the simultaneous acquisition of volumetric dual-energy data has been introduced using multidetector CT (MDCT) with two X-ray tubes and rapid kVp switching (gemstone spectral imaging). Two major advantages of DECT are material decomposition by acquiring two image series with different kVp and the elimination of misregistration artifacts. Hounsfield unit measurements by DECT are not absolute and can change depending on the kVp used for an acquisition. Typically, a combination of 80/140 kVp is used for DECT, but for some applications, 100/140 kVp is preferred. In this study, we summarized the clinical applications of DECT and included images that were acquired using the dual-source CT and rapid kVp switching. In general, unenhanced images can be avoided by using DECT for body and neurological applications; iodine can be removed from the image, and a virtual, non-contrast (water) image can be obtained. Neuroradiological applications allow for the removal of bone and calcium from the carotid and brain CT angiography. Thorax applications include perfusion imaging in patients with pulmonary thromboemboli and other chest diseases, xenon ventilation-perfusion imaging and solitary nodule characterization. Cardiac applications include dual-energy cardiac perfusion, viability and cardiac iron detection. The removal of calcific plaques from arteries, bone removal and aortic stent graft evaluation may be achieved in the vascular system. Abdominal applications include the detection and characterization of liver and pancreas masses, the diagnosis of steatosis and iron overload, DECT colonoscopy and CT cholangiography. Urinary system applications are urinary calculi characterization (uric acid vs. non-uric acid), renal cyst characterization and mass characterization. Musculoskeletal applications permit the differentiation of gout from pseudogout and a reduction of metal artifacts. Recent introduction of iterative reconstruction techniques can increase the use of DECT techniques; the use of dual energy in patients with a high BMI is limited due to noise and the radiation dose. DECT may be a good alternative to PET-CT. Iodine map images can quantify iodine uptake, and this approach may be more effective than obtaining non-contrast and post-contrast images for the diagnosis of a solid mass. Thus, computer-aided detection may be used more effectively in CT applications. DECT is a promising technique with potential clinical applications.

Imaging Basin Structure with Teleseismic Virtual Source Reflection Profiles

NASA Astrophysics Data System (ADS)

Yang, Z.; Sheehan, A. F.; Yeck, W. L.; Miller, K. C.; Worthington, L. L.; Erslev, E.; Harder, S. H.; Anderson, M. L.; Siddoway, C. S.

2011-12-01

We demonstrate a case of using teleseisms recorded on single channel high frequency geophones to image upper crustal structure across the Bighorn Arch in north-central Wyoming. The dataset was obtained through the EarthScope FlexArray Bighorn Arch Seismic Experiment (BASE). In addition to traditional active and passive source seismic data acquisition, BASE included a 12 day continuous (passive source) deployment of 850 geophones with 'Texan' dataloggers. The geophones were deployed in three E-W lines in north-central Wyoming extending from the Powder River Basin across the Bighorn Mountains and across the Bighorn Basin, and two N-S lines on east and west flanks of the Bighorn Mountains. The station interval is roughly 1.5-2 km, good for imaging coherent shallow structures. The approach used in this study uses the surface reflection as virtual seismic source and reverberated teleseismic P-wave phase (PpPdp) (teleseismic P-wave reflected at receiver side free surface and then reflected off crustal seismic interface) to construct seismic profiles. These profiles are equivalent to conventional active source seismic reflection profiles except that high-frequency (up to 2.4 Hz) transmitted wave fields from distant earthquakes are used as sources. On the constructed seismic profiles, the coherent PpPdp phases beneath Powder River and Bighorn Basins are distinct after the source wavelet is removed from the seismograms by deconvolution. Under the Bighorn Arch, no clear coherent signals are observed. We combine phases PpPdp and Ps to constrain the averaged Vp/Vs: 2.05-2.15 for the Powder River Basin and 1.9-2.0 for the Bighorn Basin. These high Vp/Vs ratios suggest that the layers within which P-wave reverberates are sedimentary. Assuming Vp as 4 km/s under the Powder River Basin, the estimated thickness of sedimentary layer above reflection below the profile is 3-4.5 km, consistent with the depth of the top of the Tensleep Fm. Therefore we interpret the coherent PpPdp phases about 1-3 s after direct P-wave arrival as the reflections off the interface between the Paleozoic carbonates/sandstones and Mesozoic shales.

Learning through a virtual patient vs. recorded lecture: a comparison of knowledge retention in a trauma case.

PubMed

Courteille, Olivier; Fahlstedt, Madelen; Ho, Johnson; Hedman, Leif; Fors, Uno; von Holst, Hans; Felländer-Tsai, Li; Möller, Hans

2018-03-28

To compare medical students' and residents' knowledge retention of assessment, diagnosis and treatment procedures, as well as a learning experience, of patients with spinal trauma after training with either a Virtual Patient case or a video-recorded traditional lecture. A total of 170 volunteers (85 medical students and 85 residents in orthopedic surgery) were randomly allocated (stratified for student/resident and gender) to either a video-recorded standard lecture or a Virtual Patient-based training session where they interactively assessed a clinical case portraying a motorcycle accident. The knowledge retention was assessed by a test immediately following the educational intervention and repeated after a minimum of 2 months. Participants' learning experiences were evaluated with exit questionnaires. A repeated-measures analysis of variance was applied on knowledge scores. A total of 81% (n = 138) of the participants completed both tests. There was a small but significant decline in first and second test results for both groups (F (1, 135) = 18.154, p = 0.00). However, no significant differences in short-term and long-term knowledge retention were observed between the two teaching methods. The Virtual Patient group reported higher learning experience levels in engagement, stimulation, general perception, and expectations. Participants' levels engagement were reported in favor of the VP format. Similar knowledge retention was achieved through either a Virtual Patient or a recorded lecture.

Quantitative Comparison of Virtual Monochromatic Images of Dual Energy Computed Tomography Systems: Beam Hardening Artifact Correction and Variance in Computed Tomography Numbers: A Phantom Study.

PubMed

Wu, Rongli; Watanabe, Yoshiyuki; Satoh, Kazuhiko; Liao, Yen-Peng; Takahashi, Hiroto; Tanaka, Hisashi; Tomiyama, Noriyuki

2018-05-21

The aim of this study was to quantitatively compare the reduction in beam hardening artifact (BHA) and variance in computed tomography (CT) numbers of virtual monochromatic energy (VME) images obtained with 3 dual-energy computed tomography (DECT) systems at a given radiation dose. Five different iodine concentrations were scanned using dual-energy and single-energy (120 kVp) modes. The BHA and CT number variance were evaluated. For higher iodine concentrations, 40 and 80 mgI/mL, BHA on VME imaging was significantly decreased when the energy was higher than 50 keV (P = 0.003) and 60 keV (P < 0.001) for GE, higher than 80 keV (P < 0.001) and 70 keV (P = 0.002) for Siemens, and higher than 40 keV (P < 0.001) and 60 keV (P < 0.001) for Toshiba, compared with single-energy CT imaging. Virtual monochromatic energy imaging can decrease BHA and improve CT number accuracy in different dual-energy computed tomography systems, depending on energy levels and iodine concentrations.

The Knowledge Development Model: Responding to the Changing Landscape of Learning in Virtual Environments

ERIC Educational Resources Information Center

Adams, Nan B.

2017-01-01

Society's relationship to knowledge and what is considered to be factual is changing. Effective teaching models focused on leveraging strategic control of the knowledge from teachers to learners in virtual learning environments are critical to insuring a positive path is charted. The Knowledge Development Model serves as the guide for determining…

Virtual Heritage Tours: Developing Interactive Narrative-Based Environments for Historical Sites

NASA Astrophysics Data System (ADS)

Tuck, Deborah; Kuksa, Iryna

In the last decade there has been a noticeable growth in the use of virtual reality (VR) technologies for reconstructing cultural heritage sites. However, many of these virtual reconstructions evidence little of sites' social histories. Narrating the Past is a research project that aims to re-address this issue by investigating methods for embedding social histories within cultural heritage sites and by creating narrative based virtual environments (VEs) within them. The project aims to enhance the visitor's knowledge and understanding by developing a navigable 3D story space, in which participants are immersed. This has the potential to create a malleable virtual environment allowing the visitor to configure their own narrative paths.

Formal integration of controlled-source and passive seismic data: Utilization of the CD-ROM experiment

NASA Astrophysics Data System (ADS)

Rumpfhuber, E.; Keller, G. R.; Velasco, A. A.

2005-12-01

Many large-scale experiments conduct both controlled-source and passive deployments to investigate the lithospheric structure of a targeted region. Many of these studies utilize each data set independently, resulting in different images of the Earth depending on the data set investigated. In general, formal integration of these data sets, such as joint inversions, with other data has not been performed. The CD-ROM experiment, which included both 2-D controlled-source and passive recording along a profile extending from southern Wyoming to northern New Mexico serves as an excellent data set to develop a formal integration strategy between both controlled source and passive experiments. These data are ideal to develop this strategy because: 1) the analysis of refraction/wide-angle reflection data yields Vp structure, and sometimes Vs structure, of the crust and uppermost mantle; 2) analysis of the PmP phase (Moho reflection) yields estimates of the average Vp of the crust for the crust; and 3) receiver functions contain full-crustal reverberations and yield the Vp/Vs ratio, but do not constrain the absolute P and S velocity. Thus, a simple form of integration involves using the Vp/Vs ratio from receiver functions and the average Vp from refraction measurements, to solve for the average Vs of the crust. When refraction/ wide-angle reflection data and several receiver functions nearby are available, an integrated 2-D model can be derived. In receiver functions, the PS conversion gives the S-wave travel-time (ts) through the crust along the raypath traveled from the Moho to the surface. Since the receiver function crustal reverberation gives the Vp/Vs ratio, it is also possible to use the arrival time of the converted phase, PS, to solve for the travel time of the direct teleseismic P-wave through the crust along the ray path. Raytracing can yield the point where the teleseismic wave intersects the Moho. In this approach, the conversion point is essentially a pseudo-shotpoint, thus the converted arrival at the surface can be jointly modeled with refraction data using a 3-D inversion code. Employing the combined CD-ROM data sets, we will be investigating the joint inversion results of controlled source data and receiver functions.

Tier identification (TID) for tiered memory characteristics

DOEpatents

Chang, Jichuan; Lim, Kevin T; Ranganathan, Parthasarathy

2014-03-25

A tier identification (TID) is to indicate a characteristic of a memory region associated with a virtual address in a tiered memory system. A thread may be serviced according to a first path based on the TID indicating a first characteristic. The thread may be serviced according to a second path based on the TID indicating a second characteristic.

Control devices and steering strategies in pathway surgery.

PubMed

Fan, Chunman; Jelínek, Filip; Dodou, Dimitra; Breedveld, Paul

2015-02-01

For pathway surgery, that is, minimally invasive procedures carried out transluminally or through instrument-created pathways, handheld maneuverable instruments are being developed. As the accompanying control interfaces of such instruments have not been optimized for intuitive manipulation, we investigated the effect of control mode (1DoF or 2DoF), and control device (joystick or handgrip) on human performance in a navigation task. The experiments were conducted using the Endo-PaC (Endoscopic-Path Controller), a simulator that emulates the shaft and handle of a maneuverable instrument, combined with custom-developed software animating pathway surgical scenarios. Participants were asked to guide a virtual instrument without collisions toward a target located at the end of a virtual curved tunnel. The performance was assessed in terms of task completion time, path length traveled by the virtual instrument, motion smoothness, collision metrics, subjective workload, and personal preference. The results indicate that 2DoF control leads to faster task completion and fewer collisions with the tunnel wall combined with a strong subjective preference compared with 1DoF control. Handgrip control appeared to be more intuitive to master than joystick control. However, the participants experienced greater physical demand and had longer path lengths with handgrip than joystick control. Copyright © 2015 Elsevier Inc. All rights reserved.

Virtual patients to explore and develop clinical case summary statement skills amongst Japanese resident physicians: a mixed methods study.

PubMed

Heist, Brian S; Kishida, Naoki; Deshpande, Gautam; Hamaguchi, Sugihiro; Kobayashi, Hiroyuki

2016-02-01

In Western clinical training, formulation of a summary statement (SS) is a core exercise for articulation, evaluation, and improvement of clinical reasoning (CR). In Japanese clinical training, structured guidance in developing CR, including opportunity for SS practice, is uncommon, and the present status of case summarization skills is unclear. We used Virtual Patients (VPs) to explore Japanese junior residents' SS styles and the effectiveness of VPs on improving SS quality. All first-year junior resident physicians at 4 residency programs (n = 54) were assigned randomized sequences of 5 VP modules, rolled out at 6 day intervals. During each module, participants free-texted a case summary and then reviewed a model summary. Thematic analysis was used to identify SS styles and each SS was categorized accordingly. Frequency of SS styles, and SS CR quality determined by 1) an internally developed Key Feature rubric and 2) demonstration of semantic qualification, were compared across modules. Four SS styles were identified: numbered features matched to differential diagnoses, differential diagnoses with supportive comments, feature listing, and narrative summarization. From module #1 to #5, significant increases in the narrative summarization SS style (p = 0.016), SS CR quality score (p = 0.021) and percentage of semantically driven SS (p = 0.003) were observed. Our study of Japanese junior residents identified distinct clinical case summary statement styles, and observed adoption of the narrative summarization style and improvement in the CR quality of summary statements during a series of VP cases.

Virtual patient simulation in psychiatric care - A pilot study of digital support for collaborate learning.

PubMed

Sunnqvist, Charlotta; Karlsson, Karin; Lindell, Lisbeth; Fors, Uno

2016-03-01

Psychiatric and mental health nursing is built on a trusted nurse and patient relationship. Therefore communication and clinical reasoning are two important issues. Our experiences as teachers in psychiatric educational programmes are that the students feel anxiety and fear before they start their clinical practices in psychiatry. Therefore there is a need for bridging over the fear. Technology enhanced learning might support such activities so we used Virtual patients (VPs), an interactive computer simulations of real-life clinical scenarios. The aim of this study was to investigate 4th term nursing students' opinions on the use of Virtual Patients for assessment in a Mental Health and Ill-health course module. We asked 24 volunteering students to practise with five different VP cases during almost 10 weeks before the exam. The participants were gathered together for participating in a written and an oral evaluation. The students were positive to the use of VPs in psychiatry and were very positive to use VPs in their continued nursing education. It seems that Virtual Patients can be an activity producing pedagogic model promoting students' independent knowledge development, critical thinking, reflection and problem solving ability for nurse students in psychiatric care. Copyright © 2016 Elsevier Ltd. All rights reserved.

Creating objects and object categories for studying perception and perceptual learning.

PubMed

Hauffen, Karin; Bart, Eugene; Brady, Mark; Kersten, Daniel; Hegdé, Jay

2012-11-02

In order to quantitatively study object perception, be it perception by biological systems or by machines, one needs to create objects and object categories with precisely definable, preferably naturalistic, properties. Furthermore, for studies on perceptual learning, it is useful to create novel objects and object categories (or object classes) with such properties. Many innovative and useful methods currently exist for creating novel objects and object categories (also see refs. 7,8). However, generally speaking, the existing methods have three broad types of shortcomings. First, shape variations are generally imposed by the experimenter, and may therefore be different from the variability in natural categories, and optimized for a particular recognition algorithm. It would be desirable to have the variations arise independently of the externally imposed constraints. Second, the existing methods have difficulty capturing the shape complexity of natural objects. If the goal is to study natural object perception, it is desirable for objects and object categories to be naturalistic, so as to avoid possible confounds and special cases. Third, it is generally hard to quantitatively measure the available information in the stimuli created by conventional methods. It would be desirable to create objects and object categories where the available information can be precisely measured and, where necessary, systematically manipulated (or 'tuned'). This allows one to formulate the underlying object recognition tasks in quantitative terms. Here we describe a set of algorithms, or methods, that meet all three of the above criteria. Virtual morphogenesis (VM) creates novel, naturalistic virtual 3-D objects called 'digital embryos' by simulating the biological process of embryogenesis. Virtual phylogenesis (VP) creates novel, naturalistic object categories by simulating the evolutionary process of natural selection. Objects and object categories created by these simulations can be further manipulated by various morphing methods to generate systematic variations of shape characteristics. The VP and morphing methods can also be applied, in principle, to novel virtual objects other than digital embryos, or to virtual versions of real-world objects. Virtual objects created in this fashion can be rendered as visual images using a conventional graphical toolkit, with desired manipulations of surface texture, illumination, size, viewpoint and background. The virtual objects can also be 'printed' as haptic objects using a conventional 3-D prototyper. We also describe some implementations of these computational algorithms to help illustrate the potential utility of the algorithms. It is important to distinguish the algorithms from their implementations. The implementations are demonstrations offered solely as a 'proof of principle' of the underlying algorithms. It is important to note that, in general, an implementation of a computational algorithm often has limitations that the algorithm itself does not have. Together, these methods represent a set of powerful and flexible tools for studying object recognition and perceptual learning by biological and computational systems alike. With appropriate extensions, these methods may also prove useful in the study of morphogenesis and phylogenesis.

Electrochemical cell structure including an ionomeric barrier

DOEpatents

Lambert, Timothy N.; Hibbs, Michael

2017-06-20

An apparatus includes an electrochemical half-cell comprising: an electrolyte, an anode; and an ionomeric barrier positioned between the electrolyte and the anode. The anode may comprise a multi-electron vanadium phosphorous alloy, such as VP.sub.x, wherein x is 1-5. The electrochemical half-cell is configured to oxidize the vanadium and phosphorous alloy to release electrons. A method of mitigating corrosion in an electrochemical cell includes disposing an ionomeric barrier in a path of electrolyte or ion flow to an anode and mitigating anion accumulation on the surface of the anode.

Instrument Motion Metrics for Laparoscopic Skills Assessment in Virtual Reality and Augmented Reality.

PubMed

Fransson, Boel A; Chen, Chi-Ya; Noyes, Julie A; Ragle, Claude A

2016-11-01

To determine the construct and concurrent validity of instrument motion metrics for laparoscopic skills assessment in virtual reality and augmented reality simulators. Evaluation study. Veterinarian students (novice, n = 14) and veterinarians (experienced, n = 11) with no or variable laparoscopic experience. Participants' minimally invasive surgery (MIS) experience was determined by hospital records of MIS procedures performed in the Teaching Hospital. Basic laparoscopic skills were assessed by 5 tasks using a physical box trainer. Each participant completed 2 tasks for assessments in each type of simulator (virtual reality: bowel handling and cutting; augmented reality: object positioning and a pericardial window model). Motion metrics such as instrument path length, angle or drift, and economy of motion of each simulator were recorded. None of the motion metrics in a virtual reality simulator showed correlation with experience, or to the basic laparoscopic skills score. All metrics in augmented reality were significantly correlated with experience (time, instrument path, and economy of movement), except for the hand dominance metric. The basic laparoscopic skills score was correlated to all performance metrics in augmented reality. The augmented reality motion metrics differed between American College of Veterinary Surgeons diplomates and residents, whereas basic laparoscopic skills score and virtual reality metrics did not. Our results provide construct validity and concurrent validity for motion analysis metrics for an augmented reality system, whereas a virtual reality system was validated only for the time score. © Copyright 2016 by The American College of Veterinary Surgeons.

The virtual lover: variable and easily guided 3D fish animations as an innovative tool in mate-choice experiments with sailfin mollies-I. Design and implementation

PubMed Central

Smielik, Ievgen; Hütwohl, Jan-Marco; Gierszewski, Stefanie; Witte, Klaudia; Kuhnert, Klaus-Dieter

2017-01-01

Abstract Animal behavior researchers often face problems regarding standardization and reproducibility of their experiments. This has led to the partial substitution of live animals with artificial virtual stimuli. In addition to standardization and reproducibility, virtual stimuli open new options for researchers since they are easily changeable in morphology and appearance, and their behavior can be defined. In this article, a novel toolchain to conduct behavior experiments with fish is presented by a case study in sailfin mollies Poecilia latipinna. As the toolchain holds many different and novel features, it offers new possibilities for studies in behavioral animal research and promotes the standardization of experiments. The presented method includes options to design, animate, and present virtual stimuli to live fish. The designing tool offers an easy and user-friendly way to define size, coloration, and morphology of stimuli and moreover it is able to configure virtual stimuli randomly without any user influence. Furthermore, the toolchain brings a novel method to animate stimuli in a semiautomatic way with the help of a game controller. These created swimming paths can be applied to different stimuli in real time. A presentation tool combines models and swimming paths regarding formerly defined playlists, and presents the stimuli onto 2 screens. Experiments with live sailfin mollies validated the usage of the created virtual 3D fish models in mate-choice experiments. PMID:29491963

The virtual lover: variable and easily guided 3D fish animations as an innovative tool in mate-choice experiments with sailfin mollies-I. Design and implementation.

PubMed

Müller, Klaus; Smielik, Ievgen; Hütwohl, Jan-Marco; Gierszewski, Stefanie; Witte, Klaudia; Kuhnert, Klaus-Dieter

2017-02-01

Animal behavior researchers often face problems regarding standardization and reproducibility of their experiments. This has led to the partial substitution of live animals with artificial virtual stimuli. In addition to standardization and reproducibility, virtual stimuli open new options for researchers since they are easily changeable in morphology and appearance, and their behavior can be defined. In this article, a novel toolchain to conduct behavior experiments with fish is presented by a case study in sailfin mollies Poecilia latipinna . As the toolchain holds many different and novel features, it offers new possibilities for studies in behavioral animal research and promotes the standardization of experiments. The presented method includes options to design, animate, and present virtual stimuli to live fish. The designing tool offers an easy and user-friendly way to define size, coloration, and morphology of stimuli and moreover it is able to configure virtual stimuli randomly without any user influence. Furthermore, the toolchain brings a novel method to animate stimuli in a semiautomatic way with the help of a game controller. These created swimming paths can be applied to different stimuli in real time. A presentation tool combines models and swimming paths regarding formerly defined playlists, and presents the stimuli onto 2 screens. Experiments with live sailfin mollies validated the usage of the created virtual 3D fish models in mate-choice experiments.

Detecting Pore Fluid Pressure Changes by Using the Vp/Vs Ratio

NASA Astrophysics Data System (ADS)

Vanorio, T.; Mavko, G.

2006-12-01

A central problem in studies aimed at predicting the dynamic behavior of faults is monitoring and quantifying fluid changes in areas prone to overpressure. Experimental and modeling studies show the Vp/Vs ratio to be a good determinant of the saturation state of a rock formation as well as of its inner pore pressure condition. Dectecting pore pressure changes depends, among other causes, on the reliability of laboratory data to calibrate the in-situ measured velocities. Ideally, laboratory experiments performed under controlled conditions would identify the fundamental mechanisms responsible for changes in the measured acoustic properties. However, technical limitations in the laboratory together with the assumptions driving the experimental and modeling approaches rise spouriuos mechanisms which hinder our present understanding of the actual role of high pore pressure on the elastic and poroelastic parameters. Critical issues unclude: a) the frequencies used in the laboratory are responsible for high-frequency fluid effects which induce velocity dispersion. As a result, both the effective stress parameter and velocities (and their pressure-dependence) estimated from high- frequency ultrasonic data are different from those applicable to crustal low frequency wave propagation; b) laboratory measurements made at dry, drained conditions are assumed to mimic those in gas pressured rocks. However, in dry, drained conditions, no pore pressure is exerted in the pore space, and the pore gas is infinitely compressible; c) when using room-dry, drained measurements as the baseline to model pressured rock formations, the unloading path (i.e. decreasing confining pressure) is supposed to mimic the inflationary path due to pore pressure increase. Doing so, it is assumed that the amount of crack opening due to pore pressure is equal to that of crack closure caused by the overburden stress and thus, the effective stress coefficient is implicitely assumed equal to 1. To minimize the assumptions and limitations described above, we designed a laboratory experiment which used gas as pore fluid medium. Experimental results show that in gas-pressured saturated rocks the Vp/Vs ratio, while remaining lower than values reported for liquid saturation conditions, increases with decreasing differential pressure, similarly to the trend observed in liquid saturated rocks.

LapSim virtual reality laparoscopic simulator reflects clinical experience in German surgeons.

PubMed

Langelotz, C; Kilian, M; Paul, C; Schwenk, W

2005-11-01

The aim of this study was to analyze the ability of a training module on a virtual laparoscopic simulator to assess surgical experience in laparoscopy. One hundred and fifteen participants at the 120th annual convent of the German surgical society took part in this study. All participants were stratified into two groups, one with laparoscopic experience of less than 50 operations (group 1, n=61) and one with laparoscopic experience of more than 50 laparoscopic operations (group 2, n=54). All subjects completed a laparoscopic training module consisting of five different exercises for navigation, coordination, grasping, cutting and clipping. The time to perform each task was measured, as were the path lengths of the instruments and their respective angles representing the economy of the movements. Results between groups were compared using chi(2) or Mann-Whitney U-test. Group 1 needed more time for completion of the exercises (median 424 s, range 99-1,376 s) than group 2 (median 315 s, range 168-625 s) (P<0.01). Instrument movements were less economic in group 1 with larger angular pathways, e.g. in the cutting exercise (median 352 degrees , range 104-1,628 degrees vs median 204 degrees , range 107-444 degrees , P<0.01), and longer path lengths (each instrument P<0.05). As time for completion of exercises, instrument path lengths and angular paths are indicators of clinical experience, it can be concluded that laparoscopic skills acquired in the operating room transfer into virtual reality. A laparoscopic simulator can serve as an instrument for the assessment of experience in laparoscopic surgery.

A molecular epidemiology study based on VP2 gene sequences reveals that a new genotype of infectious bursal disease virus is dominantly prevalent in Italy.

PubMed

Lupini, Caterina; Giovanardi, Davide; Pesente, Patrizia; Bonci, Michela; Felice, Viviana; Rossi, Giulia; Morandini, Emilio; Cecchinato, Mattia; Catelli, Elena

2016-08-01

A distinctive infectious bursal disease (IBD) virus genotype (ITA) was detected in IBD-live vaccinated broilers in Italy without clinical signs of IBD. It was isolated in specific-pathogen-free eggs and molecularly characterized in the hypervariable region of the virus protein (VP) 2. Phylogenetic analysis showed that ITA strains clustered separately from other homologous reference sequences of IBDVs, either classical or very virulent, retrieved from GenBank or previously reported in Italy, and from vaccine strains. The new genotype shows peculiar molecular characteristics in key positions of the VP2 hypervariable region, which affect charged or potentially glycosylated amino acids virtually associated with important changes in virus properties. Characterization of 41 IBDV strains detected in Italy between 2013 and 2014 showed that ITA is emergent in densely populated poultry areas of Italy, being 68% of the IBDV detections made during routine diagnostic activity over a two-year period, in spite of the immunity induced by large-scale vaccination. Four very virulent strains (DV86) and one classical strain (HPR2), together with eight vaccine strains, were also detected. The currently available epidemiological and clinical data do not allow the degree of pathogenicity of the ITA genotype to be defined. Only in vivo experimental pathogenicity studies conducted in secure isolation conditions, through the evaluation of clinical signs and macro/microscopic lesions, will clarify conclusively the virulence of the new Italian genotype.

Introduction of Virtualization Technology to Multi-Process Model Checking

NASA Technical Reports Server (NTRS)

Leungwattanakit, Watcharin; Artho, Cyrille; Hagiya, Masami; Tanabe, Yoshinori; Yamamoto, Mitsuharu

2009-01-01

Model checkers find failures in software by exploring every possible execution schedule. Java PathFinder (JPF), a Java model checker, has been extended recently to cover networked applications by caching data transferred in a communication channel. A target process is executed by JPF, whereas its peer process runs on a regular virtual machine outside. However, non-deterministic target programs may produce different output data in each schedule, causing the cache to restart the peer process to handle the different set of data. Virtualization tools could help us restore previous states of peers, eliminating peer restart. This paper proposes the application of virtualization technology to networked model checking, concentrating on JPF.

A Virtual Water Maze Revisited: Two-Year Changes in Navigation Performance and their Neural Correlates in Healthy Adults

PubMed Central

Daugherty, Ana M.; Raz, Naftali

2016-01-01

Age-related declines in spatial navigation are associated with deficits in procedural and episodic memory and deterioration of their neural substrates. For the lack of longitudinal evidence, the pace and magnitude of these declines and their neural mediators remain unclear. Here we examined virtual navigation in healthy adults (N=213, age 18–77 years) tested twice, two years apart, with complementary indices of navigation performance (path length and complexity) measured over six learning trials at each occasion. Slopes of skill acquisition curves and longitudinal change therein were estimated in structural equation modeling, together with change in regional brain volumes and iron content (R2* relaxometry). Although performance on the first trial did not differ between occasions separated by two years, the slope of path length improvement over trials was shallower and end-of-session performance worse at follow-up. Advanced age, higher pulse pressure, smaller cerebellar and caudate volumes, and greater caudate iron content were associated with longer search paths, i.e. poorer navigation performance. In contrast, path complexity diminished faster over trials at follow-up, albeit less so in older adults. Improvement in path complexity after two years was predicted by lower baseline hippocampal iron content and larger parahippocampal volume. Thus, navigation path length behaves as an index of perceptual-motor skill that is vulnerable to age-related decline, whereas path complexity may reflect cognitive mapping in episodic memory that improves with repeated testing, although not enough to overcome age-related deficits. PMID:27659539

A virtual water maze revisited: Two-year changes in navigation performance and their neural correlates in healthy adults.

PubMed

Daugherty, Ana M; Raz, Naftali

2017-02-01

Age-related declines in spatial navigation are associated with deficits in procedural and episodic memory and deterioration of their neural substrates. For the lack of longitudinal evidence, the pace and magnitude of these declines and their neural mediators remain unclear. Here we examined virtual navigation in healthy adults (N=213, age 18-77 years) tested twice, two years apart, with complementary indices of navigation performance (path length and complexity) measured over six learning trials at each occasion. Slopes of skill acquisition curves and longitudinal change therein were estimated in structural equation modeling, together with change in regional brain volumes and iron content (R2* relaxometry). Although performance on the first trial did not differ between occasions separated by two years, the slope of path length improvement over trials was shallower and end-of-session performance worse at follow-up. Advanced age, higher pulse pressure, smaller cerebellar and caudate volumes, and greater caudate iron content were associated with longer search paths, i.e. poorer navigation performance. In contrast, path complexity diminished faster over trials at follow-up, albeit less so in older adults. Improvement in path complexity after two years was predicted by lower baseline hippocampal iron content and larger parahippocampal volume. Thus, navigation path length behaves as an index of perceptual-motor skill that is vulnerable to age-related decline, whereas path complexity may reflect cognitive mapping in episodic memory that improves with repeated testing, although not enough to overcome age-related deficits. Copyright © 2016 Elsevier Inc. All rights reserved.

Sensors and Algorithms for an Unmanned Surf-Zone Robot

DTIC Science & Technology

2015-12-01

71 3. Data Fusion and Filtering................................................ 74 C. VIRTUAL POTENTIAL FIELD (VPF) PATH PLANNING ...iron effects are clearly seen: Soft iron de - calibration (sphere distortion) was caused by proximity of circuit boards. Offset of the center of the...information to perform global tasks such as path- planning , sensors and actuators commands, external communications, etc. Python3 is used as the primary

Novices in surgery are the target group of a virtual reality training laboratory.

PubMed

Hassan, Iyad; Maschuw, Katja; Rothmund, Matthias; Koller, Michael; Gerdes, Berthold

2006-01-01

This study aims to establish which physicians represent the suitable target group of a virtual training laboratory. Novices (48 physicians with fewer than 10 laparoscopic operations) and intermediate trainees (19 physicians who performed 30-50 laparoscopic operations) participated in this study. Each participant performed the basic module 'clip application' at the beginning and after a 1-hour short training course on the LapSim. The course consisted of the tasks coordination, lift and grasp, clip application, cutting with diathermy and fine dissection at increasing difficulty levels. The time taken to complete the tasks, number of errors, and economy of motion parameters (path length and angular path) were analyzed. Following training with the simulator, novices completed the task significantly faster (p = 0.001), demonstrated a greater economy of motion [path length (p = 0.04) and angular path (p = 0.01)]. In contrast, the intermediate trainees showed a reduction of their errors, but without reaching statistical significance. They showed no improvement in economy of motion and completed the task significantly slower (p = 0.03). Novices, in comparison to intermediate trainees, tend to benefit most during their first exposure to a laparoscopy simulator.

A multi-criteria approach to camera motion design for volume data animation.

PubMed

Hsu, Wei-Hsien; Zhang, Yubo; Ma, Kwan-Liu

2013-12-01

We present an integrated camera motion design and path generation system for building volume data animations. Creating animations is an essential task in presenting complex scientific visualizations. Existing visualization systems use an established animation function based on keyframes selected by the user. This approach is limited in providing the optimal in-between views of the data. Alternatively, computer graphics and virtual reality camera motion planning is frequently focused on collision free movement in a virtual walkthrough. For semi-transparent, fuzzy, or blobby volume data the collision free objective becomes insufficient. Here, we provide a set of essential criteria focused on computing camera paths to establish effective animations of volume data. Our dynamic multi-criteria solver coupled with a force-directed routing algorithm enables rapid generation of camera paths. Once users review the resulting animation and evaluate the camera motion, they are able to determine how each criterion impacts path generation. In this paper, we demonstrate how incorporating this animation approach with an interactive volume visualization system reduces the effort in creating context-aware and coherent animations. This frees the user to focus on visualization tasks with the objective of gaining additional insight from the volume data.

Technical Note: Quantitative accuracy evaluation for spectral images from a detector-based spectral CT scanner using an iodine phantom.

PubMed

Duan, Xinhui; Arbique, Gary; Guild, Jeffrey; Xi, Yin; Anderson, Jon

2018-05-01

The purpose of this study was to evaluate the quantitative accuracy of spectral images from a detector-based spectral CT scanner using a phantom with iodine-loaded inserts. A 40-cm long-body phantom with seven iodine inserts (2-20 mg/ml of iodine) was used in the study. The inserts could be placed at 5.5 or 10.5 cm from the phantom axis. The phantom was scanned five times for each insert configuration using 120 kVp tube voltage. A set of iodine, virtual noncontrast, effective atomic number, and virtual monoenergetic spectral CT images were generated and measurements were made for all the iodine rods. Measured values were compared with reference values calculated from the chemical composition information provided by the phantom manufacturer. Radiation dose from the spectral CT was compared to a conventional CT using a CTDI (32 cm) phantom. Good agreement between measurements and reference values was achieved for all types of spectral images. The differences ranged from -0.46 to 0.1 mg/ml for iodine concentration, -9.95 to 6.41 HU for virtual noncontrast images, 0.12 to 0.35 for effective Z images, and -17.7 to 55.7 HU for virtual monoenergetic images. For a similar CTDIvol, image noise from the conventional CT was 10% lower than the spectral CT. The detector-based spectral CT can achieve accurate spectral measurements on iodine concentration, virtual non-contrast images, effective atomic numbers, and virtual monoenergetic images. © 2018 American Association of Physicists in Medicine.

Dynamic Test Generation for Large Binary Programs

DTIC Science & Technology

2009-11-12

the fuzzing@whitestar.linuxbox.orgmailing list, including Jared DeMott, Disco Jonny, and Ari Takanen, for discussions on fuzzing tradeoffs. Martin...as is the case for large applications where exercising all execution paths is virtually hopeless anyway. This point will be further discussed in...consumes trace files generated by iDNA and virtually re-executes the recorded runs. TruScan offers several features that substantially simplify symbolic

Virtual endoscopy using spherical QuickTime-VR panorama views.

PubMed

Tiede, Ulf; von Sternberg-Gospos, Norman; Steiner, Paul; Höhne, Karl Heinz

2002-01-01

Virtual endoscopy needs some precomputation of the data (segmentation, path finding) before the diagnostic process can take place. We propose a method that precomputes multinode spherical panorama movies using Quick-Time VR. This technique allows almost the same navigation and visualization capabilities as a real endoscopic procedure, a significant reduction of interaction input is achieved and the movie represents a document of the procedure.

Expression and purification of recombinant polyomavirus VP2 protein and its interactions with polyomavirus proteins

NASA Technical Reports Server (NTRS)

Cai, X.; Chang, D.; Rottinghaus, S.; Consigli, R. A.; Spooner, B. S. (Principal Investigator)

1994-01-01

Recombinant polyomavirus VP2 protein was expressed in Escherichia coli (RK1448), using the recombinant expression system pFPYV2. Recombinant VP2 was purified to near homogeneity by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, electroelution, and Extracti-Gel chromatography. Polyclonal serum to this protein which reacted specifically with recombinant VP2 as well as polyomavirus virion VP2 and VP3 on Western blots (immunoblots) was produced. Purified VP2 was used to establish an in vitro protein-protein interaction assay with polyomavirus structural proteins and purified recombinant VP1. Recombinant VP2 interacted with recombinant VP1, virion VP1, and the four virion histones. Recombinant VP1 coimmunoprecipitated with recombinant VP2 or truncated VP2 (delta C12VP2), which lacked the carboxy-terminal 12 amino acids. These experiments confirmed the interaction between VP1 and VP2 and revealed that the carboxyterminal 12 amino acids of VP2 and VP3 were not necessary for formation of this interaction. In vivo VP1-VP2 interaction study accomplished by cotransfection of COS-7 cells with VP2 and truncated VP1 (delta N11VP1) lacking the nuclear localization signal demonstrated that VP2 was capable of translocating delta N11VP1 into the nucleus. These studies suggest that complexes of VP1 and VP2 may be formed in the cytoplasm and cotransported to the nucleus for virion assembly to occur.

Virtually assisted optical colonoscopy

NASA Astrophysics Data System (ADS)

Marino, Joseph; Qiu, Feng; Kaufman, Arie

2008-03-01

We present a set of tools used to enhance the optical colonoscopy procedure in a novel manner with the aim of improving both the accuracy and efficiency of this procedure. In order to better present the colon information to the gastroenterologist performing a conventional (optical) colonoscopy, we undistort the radial distortion of the fisheye view of the colonoscope. The radial distortion is modeled with a function that converts the fisheye view to the perspective view, where the shape and size of polyps can be more readily observed. The conversion, accelerated on the graphics processing unit and running in real-time, calculates the corresponding position in the fisheye view of each pixel on the perspective image. We also merge our previous work in computer-aided polyp detection for virtual colonoscopy into the optical colonoscopy environment. The physical colonoscope path in the optical colonoscopy is approximated with the hugging corner shortest path, which is correlated with the centerline in the virtual colonoscopy. With the estimated distance that the colonoscope has been inserted, we are able to provide the gastroenterologist with visual cues along the observation path as to the location of possible polyps found by the detection process. In order to present the information to the gastroenterologist in a non-intrusive manner, we have developed a friendly user interface to enhance the optical colonoscopy without being cumbersome, distracting, or resulting in a more lackadaisical inspection by the gastroenterologist.

Construct validity and expert benchmarking of the haptic virtual reality dental simulator.

PubMed

Suebnukarn, Siriwan; Chaisombat, Monthalee; Kongpunwijit, Thanapohn; Rhienmora, Phattanapon

2014-10-01

The aim of this study was to demonstrate construct validation of the haptic virtual reality (VR) dental simulator and to define expert benchmarking criteria for skills assessment. Thirty-four self-selected participants (fourteen novices, fourteen intermediates, and six experts in endodontics) at one dental school performed ten repetitions of three mode tasks of endodontic cavity preparation: easy (mandibular premolar with one canal), medium (maxillary premolar with two canals), and hard (mandibular molar with three canals). The virtual instrument's path length was registered by the simulator. The outcomes were assessed by an expert. The error scores in easy and medium modes accurately distinguished the experts from novices and intermediates at the onset of training, when there was a significant difference between groups (ANOVA, p<0.05). The trend was consistent until trial 5. From trial 6 on, the three groups achieved similar scores. No significant difference was found between groups at the end of training. Error score analysis was not able to distinguish any group at the hard level of training. Instrument path length showed a difference in performance according to groups at the onset of training (ANOVA, p<0.05). This study established construct validity for the haptic VR dental simulator by demonstrating its discriminant capabilities between that of experts and non-experts. The experts' error scores and path length were used to define benchmarking criteria for optimal performance.

The effect of extended sensory range via the EyeCane sensory substitution device on the characteristics of visionless virtual navigation.

PubMed

Maidenbaum, Shachar; Levy-Tzedek, Shelly; Chebat, Daniel Robert; Namer-Furstenberg, Rinat; Amedi, Amir

2014-01-01

Mobility training programs for helping the blind navigate through unknown places with a White-Cane significantly improve their mobility. However, what is the effect of new assistive technologies, offering more information to the blind user, on the underlying premises of these programs such as navigation patterns? We developed the virtual-EyeCane, a minimalistic sensory substitution device translating single-point-distance into auditory cues identical to the EyeCane's in the real world. We compared performance in virtual environments when using the virtual-EyeCane, a virtual-White-Cane, no device and visual navigation. We show that the characteristics of virtual-EyeCane navigation differ from navigation with a virtual-White-Cane or no device, and that virtual-EyeCane users complete more levels successfully, taking shorter paths and with less collisions than these groups, and we demonstrate the relative similarity of virtual-EyeCane and visual navigation patterns. This suggests that additional distance information indeed changes navigation patterns from virtual-White-Cane use, and brings them closer to visual navigation.

Applications of virtual reality technology in pathology.

PubMed

Grimes, G J; McClellan, S A; Goldman, J; Vaughn, G L; Conner, D A; Kujawski, E; McDonald, J; Winokur, T; Fleming, W

1997-01-01

TelePath(SM) a telerobotic system utilizing virtual microscope concepts based on high quality still digital imaging and aimed at real-time support for surgery by remote diagnosis of frozen sections. Many hospitals and clinics have an application for the remote practice of pathology, particularly in the area of reading frozen sections in support of surgery, commonly called anatomic pathology. The goal is to project the expertise of the pathologist into the remote setting by giving the pathologist access to the microscope slides with an image quality and human interface comparable to what the pathologist would experience at a real rather than a virtual microscope. A working prototype of a virtual microscope has been defined and constructed which has the needed performance in both the image quality and human interface areas for a pathologist to work remotely. This is accomplished through the use of telerobotics and an image quality which provides the virtual microscope the same diagnostic capabilities as a real microscope. The examination of frozen sections is performed a two-dimensional world. The remote pathologist is in a virtual world with the same capabilities as a "real" microscope, but response times may be slower depending on the specific computing and telecommunication environments. The TelePath system has capabilities far beyond a normal biological microscope, such as the ability to create a low power image of the entire sample using multiple images digitally matched together; the ability to digitally retrace a viewing trajectory; and the ability to archive images using CD ROM and other mass storage devices.

Characterization and protective efficacy in an animal model of a novel truncated rotavirus VP8 subunit parenteral vaccine candidate.

PubMed

Xue, Miaoge; Yu, Linqi; Che, Yaojian; Lin, Haijun; Zeng, Yuanjun; Fang, Mujin; Li, Tingdong; Ge, Shengxiang; Xia, Ningshao

2015-05-21

The cell-attachment protein VP8* of rotavirus is a potential candidate parenteral vaccine. However, the yield of full-length VP8 protein (VP8*, residues 1-231) expressed in Escherichia coli was low, and a truncated VP8 protein (ΔVP8*, residues 65-231) cannot elicit efficient protective immunity in a mouse model. In this study, tow novel truncated VP8 proteins, VP8-1 (residues 26-231) and VP8-2 (residues 51-231), were expressed in E. coli and evaluated for immunogenicity and protective efficacy, compared with VP8* and ΔVP8*. As well as ΔVP8*, the protein VP8-1 and VP8-2 were successfully expressed in high yield and purified in homogeneous dimeric forms, while the protein VP8* was expressed with lower yield and prone to aggregation and degradation in solution. Although the immunogenicity of the protein VP8*, VP8-1, VP8-2 and ΔVP8* was comparable, immunization of VP8* and VP8-1 elicited significantly higher neutralizing antibody titers than that of VP8-2 and ΔVP8* in mice. Furthermore, when assessed using a mouse maternal antibody model, the efficacy of VP8-1 to protect against rotavirus-induced diarrhea in pups was comparable to that of VP8*, both were dramatically higher than that of VP8-2 and ΔVP8*. Taken together, the novel truncated protein VP8-1, with increased yield, improved homogeneity and high protective efficacy, is a viable candidate for further development of a parenterally administrated prophylactic vaccine against rotavirus infection. Copyright © 2015 Elsevier Ltd. All rights reserved.

Virtual Estimator for Piecewise Linear Systems Based on Observability Analysis

PubMed Central

Morales-Morales, Cornelio; Adam-Medina, Manuel; Cervantes, Ilse; Vela-Valdés and, Luis G.; García Beltrán, Carlos Daniel

2013-01-01

This article proposes a virtual sensor for piecewise linear systems based on observability analysis that is in function of a commutation law related with the system's outpu. This virtual sensor is also known as a state estimator. Besides, it presents a detector of active mode when the commutation sequences of each linear subsystem are arbitrary and unknown. For the previous, this article proposes a set of virtual estimators that discern the commutation paths of the system and allow estimating their output. In this work a methodology in order to test the observability for piecewise linear systems with discrete time is proposed. An academic example is presented to show the obtained results. PMID:23447007

Logical optical line terminal technologies towards flexible and highly reliable metro- and access-integrated networks

NASA Astrophysics Data System (ADS)

Okamoto, Satoru; Sato, Takehiro; Yamanaka, Naoaki

2017-01-01

In this paper, flexible and highly reliable metro and access integrated networks with network virtualization and software defined networking technologies will be presented. Logical optical line terminal (L-OLT) technologies and active optical distribution networks (ODNs) are the key to introduce flexibility and high reliability into the metro and access integrated networks. In the Elastic Lambda Aggregation Network (EλAN) project which was started in 2012, a concept of the programmable optical line terminal (P-OLT) has been proposed. A role of the P-OLT is providing multiple network services that have different protocols and quality of service requirements by single OLT box. Accommodated services will be Internet access, mobile front-haul/back-haul, data-center access, and leased line. L-OLTs are configured within the P-OLT box to support the functions required for each network service. Multiple P-OLTs and programmable optical network units (P-ONUs) are connected by the active ODN. Optical access paths which have flexible capacity are set on the ODN to provide network services from L-OLT to logical ONUs (L-ONUs). The L-OLT to L-ONU path on the active ODN provides a logical connection. Therefore, introducing virtualization technologies becomes possible. One example is moving an L-OLT from one P-OLT to another P-OLT like a virtual machine. This movement is called L-OLT migration. The L-OLT migration provides flexible and reliable network functions such as energy saving by aggregating L-OLTs to a limited number of P-OLTs, and network wide optical access path restoration. Other L-OLT virtualization technologies and experimental results will be also discussed in the paper.

Comparison of Path Length and Ranges of Movement of the Center of Pressure and Reaction Time and Between Paired-Play and Solo-Play of a Virtual Reality Game.

PubMed

Portnoy, Sigal; Hersch, Ayelet; Sofer, Tal; Tresser, Sarit

2017-06-01

To test whether paired-play will induce longer path length and ranges of movement of the center of pressure (COP), which reflects on balance performance and stability, compared to solo-play and to test the difference in the path length and ranges of movement of the COP while playing the virtual reality (VR) game with the dominant hand compared to playing it with the nondominant hand. In this cross-sectional study 20 children (age 6.1 ± 0.7 years old) played an arm movement controlled VR game alone and with a peer while each of them stood on a pressure measuring pad to track the path length and ranges of movement of the COP. The total COP path was significantly higher during the paired-play (median 295.8 cm) compared to the COP path during the solo-play (median 189.2 cm). No significant differences were found in the reaction time and the mediolateral and anterior-posterior COP ranges between solo-play and paired-play. No significant differences were found between the parameters extracted during paired-play with the dominant or nondominant hand. Our findings imply that the paired-play is advantageous compared to solo-play since it induces a greater movement for the child, during which, higher COP velocities are reached that may contribute to improving the balance control of the child. Apart from the positive social benefits of paired-play, this positive effect on the COP path length is a noteworthy added value in the clinical setting when treating children with balance disorder.

Colour as an Environmental Cue when Learning a Route in a Virtual Environment: Typical and Atypical Development

ERIC Educational Resources Information Center

Farran, Emily K.; Courbois, Yannick; Van Herwegen, Jo; Cruickshank, Alice G.; Blades, Mark

2012-01-01

Typically developing (TD) 6-year-olds and 9-year-olds, and older children and adults with Williams syndrome (WS) navigated through brick-wall mazes in a virtual environment. Participants were shown a route through three mazes, each with 6 turns. In each maze the floor of each path section was a different colour such that colour acted as an…

The Nature of Nurture: Using a Virtual-Parent Design to Test Parenting Effects on Children's Educational Attainment in Genotyped Families.

PubMed

Bates, Timothy C; Maher, Brion S; Medland, Sarah E; McAloney, Kerrie; Wright, Margaret J; Hansell, Narelle K; Kendler, Kenneth S; Martin, Nicholas G; Gillespie, Nathan A

2018-04-01

Research on environmental and genetic pathways to complex traits such as educational attainment (EA) is confounded by uncertainty over whether correlations reflect effects of transmitted parental genes, causal family environments, or some, possibly interactive, mixture of both. Thus, an aggregate of thousands of alleles associated with EA (a polygenic risk score; PRS) may tap parental behaviors and home environments promoting EA in the offspring. New methods for unpicking and determining these causal pathways are required. Here, we utilize the fact that parents pass, at random, 50% of their genome to a given offspring to create independent scores for the transmitted alleles (conventional EA PRS) and a parental score based on alleles not transmitted to the offspring (EA VP_PRS). The formal effect of non-transmitted alleles on offspring attainment was tested in 2,333 genotyped twins for whom high-quality measures of EA, assessed at age 17 years, were available, and whose parents were also genotyped. Four key findings were observed. First, the EA PRS and EA VP_PRS were empirically independent, validating the virtual-parent design. Second, in this family-based design, children's own EA PRS significantly predicted their EA (β = 0.15), ruling out stratification confounds as a cause of the association of attainment with the EA PRS. Third, parental EA PRS predicted the SES environment parents provided to offspring (β = 0.20), and parental SES and offspring EA were significantly associated (β = 0.33). This would suggest that the EA PRS is at least as strongly linked to social competence as it is to EA, leading to higher attained SES in parents and, therefore, a higher experienced SES for children. In a full structural equation model taking account of family genetic relatedness across multiple siblings the non-transmitted allele effects were estimated at similar values; but, in this more complex model, confidence intervals included zero. A test using the forthcoming EA3 PRS may clarify this outcome. The virtual-parent method may be applied to clarify causality in other phenotypes where observational evidence suggests parenting may moderate expression of other outcomes, for instance in psychiatry.

Cleavage sites within the poliovirus capsid protein precursors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Larsen, G.R.; Anderson, C.W.; Dorner, A.J.

1982-01-01

Partial amino-terminal sequence analysis was performed on radiolabeled poliovirus capsid proteins VP1, VP2, and VP3. A computer-assisted comparison of the amino acid sequences obtained with that predicted by the nucleotide sequence of the poliovirus genome allows assignment of the amino terminus of each capsid protein to a unique position within the virus polyprotein. Sequence analysis of trypsin-digested VP4, which has a blocked amino terminus, demonstrates that VP4 is encoded at or very near to the amino terminus of the polyprotein. The gene order of the capsid proteins is VP4-VP2-VP3-VP1. Cleavage of VP0 to VP4 and VP2 is shown to occurmore » between asparagine and serine, whereas the cleavages that separate VP2/VP3 and VP3/VP1 occur between glutamine and glycine residues. This finding supports the hypothesis that the cleavage of VP0, which occurs during virion morphogenesis, is distinct from the cleavages that separate functional regions of the polyprotein.« less

Improving Shipboard Applications of Non-Intrusive Load Monitoring

DTIC Science & Technology

2008-06-01

EVENTS_LIST (EventNum) .EVENTCODE) case 0 %Unclassifiable case 1 %VP On STATE.VP.ON = STATE.VP.ON + 1; STATE.VP.START = true; PICTURES.RUNNING.VP.SHOW...true; case 2 %VP Off STATE.VP.STOP = true; PICTURES. RUNNING.VP. SHOW false; case 3 %DP On 149 STATE.DP.ON = STATE.DP.ON + 1; STATE.DP.START = true...PICTURES.RUNNING.DP.SHOW true; case 4 %DP Off STATE.DP.STOP = true; PICTURES.RUNNING.DP.SHOW = false; case 5 %VP On (Clogged) STATE.VP.ON = STATE.VP.ON

New approaches to virtual environment surgery

NASA Technical Reports Server (NTRS)

Ross, M. D.; Twombly, A.; Lee, A. W.; Cheng, R.; Senger, S.

1999-01-01

This research focused on two main problems: 1) low cost, high fidelity stereoscopic imaging of complex tissues and organs; and 2) virtual cutting of tissue. A further objective was to develop these images and virtual tissue cutting methods for use in a telemedicine project that would connect remote sites using the Next Generation Internet. For goal one we used a CT scan of a human heart, a desktop PC with an OpenGL graphics accelerator card, and LCD stereoscopic glasses. Use of multiresolution meshes ranging from approximately 1,000,000 to 20,000 polygons speeded interactive rendering rates enormously while retaining general topography of the dataset. For goal two, we used a CT scan of an infant skull with premature closure of the right coronal suture, a Silicon Graphics Onyx workstation, a Fakespace Immersive WorkBench and CrystalEyes LCD glasses. The high fidelity mesh of the skull was reduced from one million to 50,000 polygons. The cut path was automatically calculated as the shortest distance along the mesh between a small number of hand selected vertices. The region outlined by the cut path was then separated from the skull and translated/rotated to assume a new position. The results indicate that widespread high fidelity imaging in virtual environment is possible using ordinary PC capabilities if appropriate mesh reduction methods are employed. The software cutting tool is applicable to heart and other organs for surgery planning, for training surgeons in a virtual environment, and for telemedicine purposes.

Creating Objects and Object Categories for Studying Perception and Perceptual Learning

PubMed Central

Hauffen, Karin; Bart, Eugene; Brady, Mark; Kersten, Daniel; Hegdé, Jay

2012-01-01

In order to quantitatively study object perception, be it perception by biological systems or by machines, one needs to create objects and object categories with precisely definable, preferably naturalistic, properties1. Furthermore, for studies on perceptual learning, it is useful to create novel objects and object categories (or object classes) with such properties2. Many innovative and useful methods currently exist for creating novel objects and object categories3-6 (also see refs. 7,8). However, generally speaking, the existing methods have three broad types of shortcomings. First, shape variations are generally imposed by the experimenter5,9,10, and may therefore be different from the variability in natural categories, and optimized for a particular recognition algorithm. It would be desirable to have the variations arise independently of the externally imposed constraints. Second, the existing methods have difficulty capturing the shape complexity of natural objects11-13. If the goal is to study natural object perception, it is desirable for objects and object categories to be naturalistic, so as to avoid possible confounds and special cases. Third, it is generally hard to quantitatively measure the available information in the stimuli created by conventional methods. It would be desirable to create objects and object categories where the available information can be precisely measured and, where necessary, systematically manipulated (or 'tuned'). This allows one to formulate the underlying object recognition tasks in quantitative terms. Here we describe a set of algorithms, or methods, that meet all three of the above criteria. Virtual morphogenesis (VM) creates novel, naturalistic virtual 3-D objects called 'digital embryos' by simulating the biological process of embryogenesis14. Virtual phylogenesis (VP) creates novel, naturalistic object categories by simulating the evolutionary process of natural selection9,12,13. Objects and object categories created by these simulations can be further manipulated by various morphing methods to generate systematic variations of shape characteristics15,16. The VP and morphing methods can also be applied, in principle, to novel virtual objects other than digital embryos, or to virtual versions of real-world objects9,13. Virtual objects created in this fashion can be rendered as visual images using a conventional graphical toolkit, with desired manipulations of surface texture, illumination, size, viewpoint and background. The virtual objects can also be 'printed' as haptic objects using a conventional 3-D prototyper. We also describe some implementations of these computational algorithms to help illustrate the potential utility of the algorithms. It is important to distinguish the algorithms from their implementations. The implementations are demonstrations offered solely as a 'proof of principle' of the underlying algorithms. It is important to note that, in general, an implementation of a computational algorithm often has limitations that the algorithm itself does not have. Together, these methods represent a set of powerful and flexible tools for studying object recognition and perceptual learning by biological and computational systems alike. With appropriate extensions, these methods may also prove useful in the study of morphogenesis and phylogenesis. PMID:23149420

Expression and characterization of highly antigenic domains of chicken anemia virus viral VP2 and VP3 subunit proteins in a recombinant E. coli for sero-diagnostic applications

PubMed Central

2013-01-01

Background Chicken anemia virus (CAV) is an important viral pathogen that causes anemia and severe immunodeficiency syndrome in chickens worldwide. Generally, CAV infection occurs via vertical transmission in young chicks that are less than two weeks old, which are very susceptible to the disease. Therefore, epidemiological investigations of CAV infection and/or the evaluation of the immunization status of chickens is necessary for disease control. Up to the present, systematically assessing viral protein antigenicity and/or determining the immunorelevant domain(s) of viral proteins during serological testing for CAV infection has never been performed. The expression, production and antigenic characterization of CAV viral proteins such as VP1, VP2 and VP3, and their use in the development of diagnostic kit would be useful for CAV infection prevention. Results Three CAV viral proteins VP1, VP2 and VP3 was separately cloned and expressed in recombinant E. coli. The purified recombinant CAV VP1, VP2 and VP3 proteins were then used as antigens in order to evaluate their reactivity against chicken sera using indirect ELISA. The results indicated that VP2 and VP3 show good immunoreactivity with CAV-positive chicken sera, whereas VP1 was found to show less immunoreactivity than VP2 and VP3. To carry out the further antigenic characterization of the immunorelevant domains of the VP2 and VP3 proteins, five recombinant VP2 subunit proteins (VP2-435N, VP2-396N, VP2-345N, VP2-171C and VP2-318C) and three recombinant VP3 subunit proteins (VP3-123N, VP3-246M, VP3-366C), spanning the defined regions of VP2 and VP3 were separately produced by an E. coli expression system. These peptides were then used as antigens in indirect ELISAs against chicken sera. The results of these ELISAs using truncated recombinant VP2 and VP3 subunit proteins as coating antigen showed that VP2-345N, VP2-396N and VP3-246M gave good immunoreactivity with CAV-positive chicken sera compared to the other subunit proteins. Moreover, the VP2-396N and VP2-345 based ELISAs had better sensitivity (97.5%) and excellent specificity (100%) during serodiagnosis testing using a mean plus three standard deviations cut-off. The VP3-246M based ELISA showed a sensitivity of 85% and a specificity of 100% at the same cut-off value. Conclusions This is the first report to systematically assess the antigenic characteristics of CAV viral proteins for sero-diagnosis purposes. Purified recombinant VP2-396N and VP2-345N subunit proteins, which span defined regions of VP2, were demonstrated to have good antigenicity and higher sensitivities than VP3-246M and were able to recognize CAV-positive chicken serum using an ELISA assay. The defined antigenicity potential of these chimeric subunit proteins produced by expression in E. coli seem to have potential and could be useful in the future for the development of the CAV diagnostic tests based on a subunit protein ELISA system. PMID:23937712

VP24-Karyopherin Alpha Binding Affinities Differ between Ebolavirus Species, Influencing Interferon Inhibition and VP24 Stability

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schwarz, Toni M.; Edwards, Megan R.; Diederichs, Audrey

ABSTRACT Zaire ebolavirus(EBOV),Bundibugyo ebolavirus(BDBV), andReston ebolavirus(RESTV) belong to the same genus but exhibit different virulence properties. VP24 protein, a structural protein present in all family members, blocks interferon (IFN) signaling and likely contributes to virulence. Inhibition of IFN signaling by EBOV VP24 (eVP24) involves its interaction with the NPI-1 subfamily of karyopherin alpha (KPNA) nuclear transporters. Here, we evaluated eVP24, BDBV VP24 (bVP24), and RESTV VP24 (rVP24) interactions with three NPI-1 subfamily KPNAs (KPNA1, KPNA5, and KPNA6). Using purified proteins, we demonstrated that each VP24 binds to each of the three NPI-1 KPNAs. bVP24, however, exhibited approximately 10-fold-lower KPNA bindingmore » affinity than either eVP24 or rVP24. Cell-based assays also indicate that bVP24 exhibits decreased KPNA interaction, decreased suppression of IFN induced gene expression, and a decreased half-life in transfected cells compared to eVP24 or rVP24. Amino acid sequence alignments between bVP24 and eVP24 also identified residues within and surrounding the previously defined eVP24-KPNA5 binding interface that decrease eVP24-KPNA affinity or bVP24-KPNA affinity. VP24 mutations that lead to reduced KPNA binding affinity also decrease IFN inhibition and shorten VP24 half-lives. These data identify novel functional differences in VP24-KPNA interaction and reveal a novel impact of the VP24-KPNA interaction on VP24 stability. IMPORTANCEThe interaction of Ebola virus (EBOV) VP24 protein with host karyopherin alpha (KPNA) proteins blocks type I interferon (IFN) signaling, which is a central component of the host innate immune response to viral infection. Here, we quantitatively compared the interactions of VP24 proteins from EBOV and two members of theEbolavirusgenus, Bundibugyo virus (BDBV) and Reston virus (RESTV). The data reveal lower binding affinity of the BDBV VP24 (bVP24) for KPNAs and demonstrate that the interaction with KPNA modulates inhibition of IFN signaling and VP24 stability. The effect of KPNA interaction on VP24 stability is a novel functional consequence of this virus-host interaction, and the differences identified between viral species may contribute to differences in pathogenesis.« less

VP24-Karyopherin Alpha Binding Affinities Differ between Ebolavirus Species, Influencing Interferon Inhibition and VP24 Stability.

PubMed

Schwarz, Toni M; Edwards, Megan R; Diederichs, Audrey; Alinger, Joshua B; Leung, Daisy W; Amarasinghe, Gaya K; Basler, Christopher F

2017-02-15

Zaire ebolavirus (EBOV), Bundibugyo ebolavirus (BDBV), and Reston ebolavirus (RESTV) belong to the same genus but exhibit different virulence properties. VP24 protein, a structural protein present in all family members, blocks interferon (IFN) signaling and likely contributes to virulence. Inhibition of IFN signaling by EBOV VP24 (eVP24) involves its interaction with the NPI-1 subfamily of karyopherin alpha (KPNA) nuclear transporters. Here, we evaluated eVP24, BDBV VP24 (bVP24), and RESTV VP24 (rVP24) interactions with three NPI-1 subfamily KPNAs (KPNA1, KPNA5, and KPNA6). Using purified proteins, we demonstrated that each VP24 binds to each of the three NPI-1 KPNAs. bVP24, however, exhibited approximately 10-fold-lower KPNA binding affinity than either eVP24 or rVP24. Cell-based assays also indicate that bVP24 exhibits decreased KPNA interaction, decreased suppression of IFN induced gene expression, and a decreased half-life in transfected cells compared to eVP24 or rVP24. Amino acid sequence alignments between bVP24 and eVP24 also identified residues within and surrounding the previously defined eVP24-KPNA5 binding interface that decrease eVP24-KPNA affinity or bVP24-KPNA affinity. VP24 mutations that lead to reduced KPNA binding affinity also decrease IFN inhibition and shorten VP24 half-lives. These data identify novel functional differences in VP24-KPNA interaction and reveal a novel impact of the VP24-KPNA interaction on VP24 stability. The interaction of Ebola virus (EBOV) VP24 protein with host karyopherin alpha (KPNA) proteins blocks type I interferon (IFN) signaling, which is a central component of the host innate immune response to viral infection. Here, we quantitatively compared the interactions of VP24 proteins from EBOV and two members of the Ebolavirus genus, Bundibugyo virus (BDBV) and Reston virus (RESTV). The data reveal lower binding affinity of the BDBV VP24 (bVP24) for KPNAs and demonstrate that the interaction with KPNA modulates inhibition of IFN signaling and VP24 stability. The effect of KPNA interaction on VP24 stability is a novel functional consequence of this virus-host interaction, and the differences identified between viral species may contribute to differences in pathogenesis. Copyright © 2017 American Society for Microbiology.

Virtual local target method for avoiding local minimum in potential field based robot navigation.

PubMed

Zou, Xi-Yong; Zhu, Jing

2003-01-01

A novel robot navigation algorithm with global path generation capability is presented. Local minimum is a most intractable but is an encountered frequently problem in potential field based robot navigation. Through appointing appropriately some virtual local targets on the journey, it can be solved effectively. The key concept employed in this algorithm are the rules that govern when and how to appoint these virtual local targets. When the robot finds itself in danger of local minimum, a virtual local target is appointed to replace the global goal temporarily according to the rules. After the virtual target is reached, the robot continues on its journey by heading towards the global goal. The algorithm prevents the robot from running into local minima anymore. Simulation results showed that it is very effective in complex obstacle environments.

Enhancement of VP6 immunogenicity and protective efficacy against rotavirus by VP2 in a genetic immunization.

PubMed

Lopez-Guerrero, D V; Arias, N; Gutierrez-Xicotencatl, L; Chihu-Amparan, L; González, A; Pedroza-Saavedra, A; Rosas-Salgado, G; Villegas-Garcia, J C; Badillo-Godinez, O; Fernandez, G; Lopez, S; Esquivel-Guadarrama, F

2018-05-24

VP2/VP6 virus like particles (VLPs) are very effective in inducing protection against the rotavirus infection in animal models. Individually, VP6 can also induce protection. However, there is no information about the immunogenicity of VP2. The aim of this work was to evaluate the efficacy of DNA vaccines codifying for VP2 or VP6, alone or combined, to induce protection against the rotavirus infection. Murine rotavirus VP2 and VP6 genes were cloned into the pcDNA3 vector. Adult BALB/c mice were inoculated three times by intramuscular (i.m.) injections with 100 or 200µg of pcDNA3-VP2 or pcDNA3-VP6 alone or co-administered with 100µg of pcDNA3-VP2/100µg of pcDNA3-VP6. Two weeks after the last inoculation, mice were challenged with the wild type murine rotavirus strain epizootic diarrhea of infant mice (EDIM wt ). We found that both plasmids, pcDNA3-VP2 and pcDNA3-VP6, were able to induce rotavirus-specific serum antibodies, but not intestinal rotavirus-specific IgA; only 200µg of pcDNA3-VP6 induced 35% protection against the infection. A similar level of protection was found when mice were co-administered with 100µg of pcDNA3-VP2/100µg of pcDNA3-VP6 (1:1 ratio). However, the best protection (up to 58%) occurred when mice were inoculated with 10µg of pcDNA3-VP2/100µg of pcDNA3-VP6 (1:10 ratio). These results indicate that the DNA plasmid expressing VP6 is a better vaccine candidate that the one expressing VP2. However, when co-expressed, VP2 potentiates the immunogenicity and protective efficacy of VP6. Copyright © 2017. Published by Elsevier Ltd.

Experimental study of the P11(1440) and D13(1520) resonances from the CLAS data on ep→e'π+π-p'

NASA Astrophysics Data System (ADS)

Mokeev, V. I.; Burkert, V. D.; Elouadrhiri, L.; Fedotov, G. V.; Golovatch, E. N.; Gothe, R. W.; Ishkhanov, B. S.; Isupov, E. L.; Adhikari, K. P.; Aghasyan, M.; Anghinolfi, M.; Avakian, H.; Baghdasaryan, H.; Ball, J.; Baltzell, N. A.; Battaglieri, M.; Batourine, V.; Bedlinskiy, I.; Biselli, A. S.; Bookwalter, C.; Boiarinov, S.; Briscoe, W. J.; Brooks, W. K.; Carman, D. S.; Celentano, A.; Charles, G.; Cole, P. L.; Contalbrigo, M.; Crede, V.; D'Angelo, A.; Daniel, A.; Dashyan, N.; De Vita, R.; De Sanctis, E.; Deur, A.; Djalali, C.; Doughty, D.; Dupre, R.; El Alaoui, A.; Eugenio, P.; Fegan, S.; Fradi, A.; Giovanetti, K. L.; Girod, F. X.; Gohn, W.; Graham, L.; Griffioen, K. A.; Guegan, B.; Guidal, M.; Guo, L.; Hafidi, K.; Hakobyan, H.; Hanretty, C.; Hicks, K.; Ho, D.; Holtrop, M.; Ilieva, Y.; Ireland, D. G.; Jo, H. S.; Joo, K.; Keller, D.; Khandaker, M.; Khetarpal, P.; Kim, A.; Kim, W.; Klein, A.; Klein, F. J.; Koirala, S.; Kubarovsky, A.; Kubarovsky, V.; Kuleshov, S. V.; Kvaltine, N. D.; Livingston, K.; Lu, H. Y.; MacGregor, I. J. D.; Mao, Y.; Markov, N.; Martinez, D.; Mayer, M.; McKinnon, B.; Meyer, C. A.; Mineeva, T.; Mirazita, M.; Moutarde, H.; Munevar, E.; Nadel-Turonski, P.; Nepali, C. S.; Ostrovidov, A. I.; Pappalardo, L. L.; Paremuzyan, R.; Park, K.; Park, S.; Pasyuk, E.; Pereira, S. Anefalos; Pisano, S.; Pogorelko, O.; Pozdniakov, S.; Price, J. W.; Procureur, S.; Protopopescu, D.; Raue, B. A.; Ricco, G.; Rimal, D.; Ripani, M.; Rosner, G.; Rossi, P.; Sabatié, F.; Saini, M. S.; Salgado, C.; Schott, D.; Schumacher, R. A.; Seder, E.; Seraydaryan, H.; Sharabian, Y. G.; Smith, G. D.; Smith, L. C.; Sober, D. I.; Sokhan, D.; Stepanyan, S.; Stepanyan, S. S.; Stoler, P.; Strakovsky, I. I.; Strauch, S.; Tang, W.; Taylor, C. E.; Tian, Ye; Tkachenko, S.; Trivedi, A.; Ungaro, M.; Vineyard, M. F.; Voskanyan, H.; Voutier, E.; Walford, N. K.; Wood, M. H.; Zachariou, N.; Zhao, Z. W.; Zonta, I.

2012-09-01

The transition helicity amplitudes from the proton ground state to the P11(1440) and D13(1520) excited states (γvpN* electrocouplings) were determined from the analysis of nine independent one-fold differential π+π-p electroproduction cross sections off a proton target, taken with CLAS at photon virtualities of 0.25

LACUS Forum XXV, [1998].

ERIC Educational Resources Information Center

Hwang, Shin Ja J., Ed.; Lommel, Arle R., Ed.

Papers from the conference include: "English and Human Morphology: 'Naturalness' in Counting and Measuring" (Sullivan); "Phonetic and Phonemic Change Revisited" (Lockwood); "Virtual Reality" (Langacker); "Path Directions in ASL Agreement Verbs are Predictable on Semantic Grounds" (Taub); "Temporal…

Redundancy, Self-Motion, and Motor Control

PubMed Central

Martin, V.; Scholz, J. P.; Schöner, G.

2011-01-01

Outside the laboratory, human movement typically involves redundant effector systems. How the nervous system selects among the task-equivalent solutions may provide insights into how movement is controlled. We propose a process model of movement generation that accounts for the kinematics of goal-directed pointing movements performed with a redundant arm. The key element is a neuronal dynamics that generates a virtual joint trajectory. This dynamics receives input from a neuronal timer that paces end-effector motion along its path. Within this dynamics, virtual joint velocity vectors that move the end effector are dynamically decoupled from velocity vectors that do not. Moreover, the sensed real joint configuration is coupled back into this neuronal dynamics, updating the virtual trajectory so that it yields to task-equivalent deviations from the dynamic movement plan. Experimental data from participants who perform in the same task setting as the model are compared in detail to the model predictions. We discover that joint velocities contain a substantial amount of self-motion that does not move the end effector. This is caused by the low impedance of muscle joint systems and by coupling among muscle joint systems due to multiarticulatory muscles. Back-coupling amplifies the induced control errors. We establish a link between the amount of self-motion and how curved the end-effector path is. We show that models in which an inverse dynamics cancels interaction torques predict too little self-motion and too straight end-effector paths. PMID:19718817

Localized double-array stacking analysis of PcP: D″ and ULVZ structure beneath the Cocos plate, Mexico, central Pacific, and north Pacific

USGS Publications Warehouse

Hutko, Alexander R.; Lay, Thorne; Revenaugh, Justin

2009-01-01

A large, high quality P-wave data set comprising short-period and broadband signals sampling four separate regions in the lowermost mantle beneath the Cocos plate, Mexico, the central Pacific, and the north Pacific is analyzed using regional one-dimensional double-array stacking and modelling with reflectivity synthetics. A data-screening criterion retains only events with stable PcP energy in the final data stacks used for modelling and interpretation. This significantly improves the signal stacks relative to including unscreened observations, allows confident alignment on the PcP arrival and allows tight bounds to be placed on P-wave velocity structure above the core–mantle boundary (CMB). The PcP reflections under the Cocos plate are well modelled without any ultra-low velocity zone from 5 to 20°N. At latitudes from 15 to 20°N, we find evidence for two P-wave velocity discontinuities in the D″ region. The first is ∼182 km above the CMB with a δln Vp of +1.5%, near the same depth as a weaker discontinuity (<+0.5%) observed from 5 to 15°N in prior work. The other reflector is ∼454 km above the CMB, with a δln Vp of +0.4%; this appears to be a shallower continuation of the joint P- and S-wave discontinuity previously detected south of 15° N, which is presumed to be the perovskite to post-perovskite phase transition. The data stacks for paths bottoming below Mexico have PcP images that are well matched with the simple IASP91 structure, contradicting previous inferences of ULVZ presence in this region. These particular data are not very sensitive to any D″ discontinuities, and simply bound them to be <∼2%, if present. Data sampling the lowermost mantle beneath the central Pacific confirm the presence of a ∼15-km thick ultra-low velocity zone (ULVZ) just above the CMB, with δln Vp and δln Vs of around −3 to −4% and −4 to −8%, respectively. The ULVZ models predict previous S-wave data stacks well. The data for this region indicate laterally varying Vp discontinuities in D″, with one subregion having a δln Vp of 0.5% 140 km above the CMB. Beneath the north Pacific, the PcP arrivals are compatible with only weak ULVZ (δln Vp ∼ 0 to −3%), and there is a weak D″ reflector with δln Vp = 0.5%, near 314 km above the CMB. These results indicate localized occurrence of detectable ULVZ structures rather than ubiquitous ULVZ structure and emphasize the distinctiveness between the large low shear velocity province under the central Pacific and circum-Pacific regions.

Elastic and electrical properties and permeability of serpentinites from Atlantis Massif, Mid-Atlantic Ridge

NASA Astrophysics Data System (ADS)

Falcon-Suarez, Ismael; Bayrakci, Gaye; Minshull, Tim A.; North, Laurence J.; Best, Angus I.; Rouméjon, Stéphane

2017-11-01

Serpentinized peridotites co-exist with mafic rocks in a variety of marine environments including subduction zones, continental rifts and mid-ocean ridges. Remote geophysical methods are crucial to distinguish between them and improve the understanding of the tectonic, magmatic and metamorphic history of the oceanic crust. But, serpentinite peridotites exhibit a wide range of physical properties that complicate such a distinction. We analysed the ultrasonic P- and S-wave velocities (Vp, Vs) and their respective attenuation (Qp-1, Qs-1), electrical resistivity and permeability of four serpentinized peridotite samples from the southern wall of the Atlantis Massif, Mid-Atlantic Ridge, collected during International Ocean Discovery Program Expedition 357. The measurements were taken over a range of loading-unloading stress paths (5-45 MPa), using ∼1.7 cm length, 5 cm diameter samples horizontally extracted from the original cores drilled on the seafloor. The measured parameters showed variable degrees of stress dependence, but followed similar trends. Vp, Vs, resistivity and permeability show good inter-correlations, while relationships that included Qp-1 and Qs-1 are less clear. Resistivity showed high contrast between highly serpentinized ultramafic matrix (>50 Ω m) and mechanically/geochemically altered (magmatic/hydrothermal-driven alteration) domains (<20 Ω m). This information together with the elastic constants (Vp/Vs ratio and bulk moduli) of the samples allowed us to infer useful information about the degree of serpentinization and the alteration state of the rock, contrasted by petrographic analysis. This study shows the potential of combining seismic techniques and controlled source electromagnetic surveys for understanding tectonomagmatic processes and fluid pathways in hydrothermal systems.

The study of the intercellular trafficking of the fusion proteins of herpes simplex virus protein VP22.

PubMed

Xue, Xiaodong; Huang, Jianhua; Wang, Huishan

2014-01-01

Genetic modifications can improve the therapeutic efficacy of mesenchymal stem cell (MSC) transplantation in myocardial infarction. However, so far, the efficiency of MSC modification is very low. Seeking for a more efficient way of MSC modification, we investigated the possibility of employing the intercellular trafficking capacity of the herpes simplex virus type-1 tegument protein VP22 on the enhancement of MSC modification. Plasmids pVP22-myc, pVP22-EGFP, pEGFP-VP22, pVP22-hBcl-xL and phBcl-xL-VP22 were constructed for the expressions of the myc-tagged VP22 and the fusion proteins VP22-EGFP, EGFP-VP22, VP22-hBcl-xL and hBcl-xL-VP22. MSCs were isolated from rat bone marrow and the surface markers were identified by Flowcytometry. COS-1 cells were transfected with the above plasmids and co-cultured with untransfected MSCs, the intercellular transportations of the constructed proteins were studied by immunofluorescence. The solubility of VP22-hBcl-xL and hBcl-xL-VP22 was analyzed by Western blot. VP22-myc could be expressed in and spread between COS-1 cells, which indicates the validity of our VP22 expression construct. Flowcytometry analysis revealed that the isolated MSCs were CD29, CD44, and CD90 positive and were negative for the hematopoietic markers, CD34 and CD45. The co-culturing and immunofluorescence assay showed that VP22-myc, VP22-EGFP and EGFP-VP22 could traffic between COS-1 cells and MSCs, while the evidence of intercellular transportation of VP22-hBcl-xL and hBcl-xL-VP22 was not detected. Western blot analysis showed that VP22-hBcl-xL and hBcl-xL-VP22 were both insoluble in the cell lysate suggesting interactions of the fusion proteins with other cellular components. The intercellular trafficking of VP22-myc, VP22-EGFP and EGFP-VP22 between COS-1 cells and MSCs presents an intriguing prospect in the therapeutic application of VP22 as a delivery vehicle which enhances genetic modifications of MSCs. However, VP22-hBcl-xL and hBcl-xL-VP22 failed to spread between cells, which are due to the insolubility of the fusion protein incurred by interactions with other cellular components.

The Study of the Intercellular Trafficking of the Fusion Proteins of Herpes Simplex Virus Protein VP22

PubMed Central

Xue, Xiaodong; Huang, Jianhua; Wang, Huishan

2014-01-01

Background Genetic modifications can improve the therapeutic efficacy of mesenchymal stem cell (MSC) transplantation in myocardial infarction. However, so far, the efficiency of MSC modification is very low. Seeking for a more efficient way of MSC modification, we investigated the possibility of employing the intercellular trafficking capacity of the herpes simplex virus type-1 tegument protein VP22 on the enhancement of MSC modification. Methods Plasmids pVP22-myc, pVP22-EGFP, pEGFP-VP22, pVP22-hBcl-xL and phBcl-xL-VP22 were constructed for the expressions of the myc-tagged VP22 and the fusion proteins VP22-EGFP, EGFP-VP22, VP22-hBcl-xL and hBcl-xL-VP22. MSCs were isolated from rat bone marrow and the surface markers were identified by Flowcytometry. COS-1 cells were transfected with the above plasmids and co-cultured with untransfected MSCs, the intercellular transportations of the constructed proteins were studied by immunofluorescence. The solubility of VP22-hBcl-xL and hBcl-xL-VP22 was analyzed by Western blot. Results VP22-myc could be expressed in and spread between COS-1 cells, which indicates the validity of our VP22 expression construct. Flowcytometry analysis revealed that the isolated MSCs were CD29, CD44, and CD90 positive and were negative for the hematopoietic markers, CD34 and CD45. The co-culturing and immunofluorescence assay showed that VP22-myc, VP22-EGFP and EGFP-VP22 could traffic between COS-1 cells and MSCs, while the evidence of intercellular transportation of VP22-hBcl-xL and hBcl-xL-VP22 was not detected. Western blot analysis showed that VP22-hBcl-xL and hBcl-xL-VP22 were both insoluble in the cell lysate suggesting interactions of the fusion proteins with other cellular components. Conclusions The intercellular trafficking of VP22-myc, VP22-EGFP and EGFP-VP22 between COS-1 cells and MSCs presents an intriguing prospect in the therapeutic application of VP22 as a delivery vehicle which enhances genetic modifications of MSCs. However, VP22-hBcl-xL and hBcl-xL-VP22 failed to spread between cells, which are due to the insolubility of the fusion protein incurred by interactions with other cellular components. PMID:24955582

MO-FG-CAMPUS-JeP1-04: Evaluating DECT Vs SECT Range Differences in Proton Therapy Using Clinical Data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hudobivnik, N; Dedes, G; Parodi, K

Purpose: Range uncertainty from X-ray CT number conversion to stopping power ratio (SPR) is one of the key factors limiting the potential of proton therapy. The large margins required for deep seated tumors degrade the organ sparing achievable with the technology. Of interest is the application of dual energy CT (DECT) to SPR estimation. In this planning study proton range differences between SECT and DECT have been quantified for brain cases. Methods: A last generation dual source DECT scanner was used to acquire SECT (150 kVp with Sn filtration) and DECT (additionally 90 kVp) scans of phantoms and 5 headmore » trauma patients, acting as surrogate cancer patients. Phantom materials were characterized in terms of SPR in a particle beam to obtain reference values. IMPT treatment plans were generated on the basis of SECT and DECT SPR images for hypothetical brain tumors using a short and a long beam path. Range differences between SECT and DECT from plan recalculations were evaluated in beam-eye-view (BEV) by comparing the 80% isodose. Results: For the 18 phantom materials the SECT RMS SPR errors were 2.6% compared to 1.1% for DECT. Group median relative range differences between SECT and DECT plans were −1.0% for the short beam path over the 5 patients investigated in this study. For the long beam path the median difference was −1.4%. These relative range differences corresponded to −0.5 mm and −1.4 mm shifts respectively. Conclusion: This is the first study performing proton therapy treatment planning on DECT patient images. Important range differences of more than 1 mm were observed between SECT and DECT treatment plans, and DECT SPR accuracy was found superior on the basis of phantom measurements. While the patients investigated in this study did not have brain tumors, the findings we observed should apply to cancer patients. Deutsche Forschungsgemeinschaft (MAP); Bundesministerium fur Bildung und Forschung (01IB13001)« less

Psychomotor performance measured in a virtual environment correlates with technical skills in the operating room.

PubMed

Kundhal, Pavi S; Grantcharov, Teodor P

2009-03-01

This study was conducted to validate the role of virtual reality computer simulation as an objective method for assessing laparoscopic technical skills. The authors aimed to investigate whether performance in the operating room, assessed using a modified Objective Structured Assessment of Technical Skill (OSATS), correlated with the performance parameters registered by a virtual reality laparoscopic trainer (LapSim). The study enrolled 10 surgical residents (3 females) with a median of 5.5 years (range, 2-6 years) since graduation who had similar limited experience in laparoscopic surgery (median, 5; range, 1-16 laparoscopic cholecystectomies). All the participants performed three repetitions of seven basic skills tasks on the LapSim laparoscopic trainer and one laparoscopic cholecystectomy in the operating room. The operating room procedure was video recorded and blindly assessed by two independent observers using a modified OSATS rating scale. Assessment in the operating room was based on three parameters: time used, error score, and economy of motion score. During the tasks on the LapSim, time, error (tissue damage and millimeters of tissue damage [tasks 2-6], error score [incomplete target areas, badly placed clips, and dropped clips [task 7]), and economy of movement parameters (path length and angular path) were registered. The correlation between time, economy, and error parameters during the simulated tasks and the operating room procedure was statistically assessed using Spearman's test. Significant correlations were demonstrated between the time used to complete the operating room procedure and time used for task 7 (r (s) = 0.74; p = 0.015). The error score demonstrated during the laparoscopic cholecystectomy correlated well with the tissue damage in three of the seven tasks (p < 0.05), the millimeters of tissue damage during two of the tasks, and the error score in task 7 (r (s) = 0.67; p = 0.034). Furthermore, statistically significant correlations were observed between the economy of motion score from the operative procedure and LapSim's economy parameters (path length and angular path in six of the tasks) (p < 0.05). The current study demonstrated significant correlations between operative performance in the operating room (assessed using a well-validated rating scale) and psychomotor performance in virtual environment assessed by a computer simulator. This provides strong evidence for the validity of the simulator system as an objective tool for assessing laparoscopic skills. Virtual reality simulation can be used in practice to assess technical skills relevant for minimally invasive surgery.

Halon Replacement Program for Aviation, Aircraft Engine Nacelle Application Phase II - Operational Comparison of Selected Extinguishants

DTIC Science & Technology

1997-05-01

Control Butterfly Hi-Pressure High Flow Control Butterfly Ejector Primary Clycol Control Valve Scrubber Fan Pressure Control Butterfly 8" Venturi ...the scrubber . 20 ■ SCRUBBER FAN BLOWER INLET VALVE VP-2 VP-3 VP-4 VP-5 VP-6 VP-7 VP-8 VP-9 VP-10 SV-1 SV-2 DESCRIPTION Atmospheric...Blower Bypass Butterfly 24" Venturi Control Butterfly 24" Test Section Exit Butterfly Ejector 10’ Secondary Inlet-Butterfly Hi-pressure Low Flow

Advances in edge-diffraction modeling for virtual-acoustic simulations

NASA Astrophysics Data System (ADS)

Calamia, Paul Thomas

In recent years there has been growing interest in modeling sound propagation in complex, three-dimensional (3D) virtual environments. With diverse applications for the military, the gaming industry, psychoacoustics researchers, architectural acousticians, and others, advances in computing power and 3D audio-rendering techniques have driven research and development aimed at closing the gap between the auralization and visualization of virtual spaces. To this end, this thesis focuses on improving the physical and perceptual realism of sound-field simulations in virtual environments through advances in edge-diffraction modeling. To model sound propagation in virtual environments, acoustical simulation tools commonly rely on geometrical-acoustics (GA) techniques that assume asymptotically high frequencies, large flat surfaces, and infinitely thin ray-like propagation paths. Such techniques can be augmented with diffraction modeling to compensate for the effect of surface size on the strength and directivity of a reflection, to allow for propagation around obstacles and into shadow zones, and to maintain soundfield continuity across reflection and shadow boundaries. Using a time-domain, line-integral formulation of the Biot-Tolstoy-Medwin (BTM) diffraction expression, this thesis explores various aspects of diffraction calculations for virtual-acoustic simulations. Specifically, we first analyze the periodic singularity of the BTM integrand and describe the relationship between the singularities and higher-order reflections within wedges with open angle less than 180°. Coupled with analytical approximations for the BTM expression, this analysis allows for accurate numerical computations and a continuous sound field in the vicinity of an arbitrary wedge geometry insonified by a point source. Second, we describe an edge-subdivision strategy that allows for fast diffraction calculations with low error relative to a numerically more accurate solution. Third, to address the considerable increase in propagation paths due to diffraction, we describe a simple procedure for identifying and culling insignificant diffraction components during a virtual-acoustic simulation. Finally, we present a novel method to find GA components using diffraction parameters that ensures continuity at reflection and shadow boundaries.

Radiation dose reduction using 100-kVp and a sinogram-affirmed iterative reconstruction algorithm in adolescent head CT: Impact on grey-white matter contrast and image noise.

PubMed

Nagayama, Yasunori; Nakaura, Takeshi; Tsuji, Akinori; Urata, Joji; Furusawa, Mitsuhiro; Yuki, Hideaki; Hirarta, Kenichiro; Kidoh, Masafumi; Oda, Seitaro; Utsunomiya, Daisuke; Yamashita, Yasuyuki

2017-07-01

To retrospectively evaluate the image quality and radiation dose of 100-kVp scans with sinogram-affirmed iterative reconstruction (IR) for unenhanced head CT in adolescents. Sixty-nine patients aged 12-17 years underwent head CT under 120- (n = 34) or 100-kVp (n = 35) protocols. The 120-kVp images were reconstructed with filtered back-projection (FBP), 100-kVp images with FBP (100-kVp-F) and sinogram-affirmed IR (100-kVp-S). We compared the effective dose (ED), grey-white matter (GM-WM) contrast, image noise, and contrast-to-noise ratio (CNR) between protocols in supratentorial (ST) and posterior fossa (PS). We also assessed GM-WM contrast, image noise, sharpness, artifacts, and overall image quality on a four-point scale. ED was 46% lower with 100- than 120-kVp (p < 0.001). GM-WM contrast was higher, and image noise was lower, on 100-kVp-S than 120-kVp at ST (p < 0.001). CNR of 100-kVp-S was higher than of 120-kVp (p < 0.001). GM-WM contrast of 100-kVp-S was subjectively rated as better than of 120-kVp (p < 0.001). There were no significant differences in the other criteria between 100-kVp-S and 120-kVp (p = 0.072-0.966). The 100-kVp with sinogram-affirmed IR facilitated dramatic radiation reduction and better GM-WM contrast without increasing image noise in adolescent head CT. • 100-kVp head CT provides 46% radiation dose reduction compared with 120-kVp. • 100-kVp scanning improves subjective and objective GM-WM contrast. • Sinogram-affirmed IR decreases head CT image noise, especially in supratentorial region. • 100-kVp protocol with sinogram-affirmed IR is suited for adolescent head CT.

Virtual Learning Environment for Interactive Engagement with Advanced Quantum Mechanics

NASA Astrophysics Data System (ADS)

Pedersen, Mads Kock; Skyum, Birk; Heck, Robert; Müller, Romain; Bason, Mark; Lieberoth, Andreas; Sherson, Jacob F.

2016-06-01

A virtual learning environment can engage university students in the learning process in ways that the traditional lectures and lab formats cannot. We present our virtual learning environment StudentResearcher, which incorporates simulations, multiple-choice quizzes, video lectures, and gamification into a learning path for quantum mechanics at the advanced university level. StudentResearcher is built upon the experiences gathered from workshops with the citizen science game Quantum Moves at the high-school and university level, where the games were used extensively to illustrate the basic concepts of quantum mechanics. The first test of this new virtual learning environment was a 2014 course in advanced quantum mechanics at Aarhus University with 47 enrolled students. We found increased learning for the students who were more active on the platform independent of their previous performances.

Industry careers for the biomedical engineer.

PubMed

Munzner, Robert F

2004-01-01

This year's conference theme is "linkages for innovation in biomedicine." Biomedical engineers, especially those transitioning their career from academic study into medical device industry, will play a critical role in converting the fruits of scientific research into the reality of modern medical devices. This special session is organized to help biomedical engineers to achieve their career goals more effectively. Participants will have opportunities to hear from and interact with leading industrial experts on many issues. These may include but not limited to 1) career paths for biomedical engineers (industrial, academic, or federal; technical vs. managerial track; small start-up or large established companies); 2) unique design challenges and regulatory requirements in medical device development; 3) aspects of a successful biomedical engineering job candidate (such as resume, interview, follow-up). Suggestions for other topics are welcome and should be directed to xkong@ieee.org The distinguished panelists include: Xuan Kong, Ph.D., VP of Research, NEUROMetrix Inc, Waltham, MA Robert F. Munzner, Ph.D., Medical Device Consultant, Doctor Device, Herndon, VA Glen McLaughlin, Ph.D., VP of Engineering and CTO, Zonare Medical System Inc., Mountain View, CA Grace Bartoo, Ph.D., RAC, General Manager, Decus Biomedical LLC San Carlos, CA.

Weak measurements measure probability amplitudes (and very little else)

NASA Astrophysics Data System (ADS)

Sokolovski, D.

2016-04-01

Conventional quantum mechanics describes a pre- and post-selected system in terms of virtual (Feynman) paths via which the final state can be reached. In the absence of probabilities, a weak measurement (WM) determines the probability amplitudes for the paths involved. The weak values (WV) can be identified with these amplitudes, or their linear combinations. This allows us to explain the ;unusual; properties of the WV, and avoid the ;paradoxes; often associated with the WM.

Are visual cues helpful for virtual spatial navigation and spatial memory in patients with mild cognitive impairment or Alzheimer's disease?

PubMed

Cogné, Mélanie; Auriacombe, Sophie; Vasa, Louise; Tison, François; Klinger, Evelyne; Sauzéon, Hélène; Joseph, Pierre-Alain; N Kaoua, Bernard

2018-05-01

To evaluate whether visual cues are helpful for virtual spatial navigation and memory in Alzheimer's disease (AD) and patients with mild cognitive impairment (MCI). 20 patients with AD, 18 patients with MCI and 20 age-matched healthy controls (HC) were included. Participants had to actively reproduce a path that included 5 intersections with one landmark at each intersection that they had seen previously during a learning phase. Three cueing conditions for navigation were offered: salient landmarks, directional arrows and a map. A path without additional visual stimuli served as control condition. Navigation time and number of trajectory mistakes were recorded. With the presence of directional arrows, no significant difference was found between groups concerning the number of trajectory mistakes and navigation time. The number of trajectory mistakes did not differ significantly between patients with AD and patients with MCI on the path with arrows, the path with salient landmarks and the path with a map. There were significant correlations between the number of trajectory mistakes under the arrow condition and executive tests, and between the number of trajectory mistakes under the salient landmark condition and memory tests. Visual cueing such as directional arrows and salient landmarks appears helpful for spatial navigation and memory tasks in patients with AD and patients with MCI. This study opens new research avenues for neuro-rehabilitation, such as the use of augmented reality in real-life settings to support the navigational capabilities of patients with MCI and patients with AD. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

Spatial awareness in immersive virtual environments revealed in open-loop walking

NASA Astrophysics Data System (ADS)

Turano, Kathleen A.; Chaudhury, Sidhartha

2005-03-01

People are able to walk without vision to previously viewed targets in the real world. This ability to update one"s position in space has been attributed to a path integration system that uses internally generated self-motion signals together with the perceived object-to-self distance of the target. In a previous study using an immersive virtual environment (VE), we found that many subjects were unable to walk without vision to a previously viewed target located 4 m away. Their walking paths were influenced by the room structure that varied trial to trial. In this study we investigated whether the phenomenon is specific to a VE by testing subjects in a real world and a VE. The real world was viewed with field restricting goggles and via cameras using the same head-mounted display as in the VE. The results showed that only in the VE were walking paths influenced by the room structure. Women were more affected than men, and the effect decreased over trials and after subjects performed the task in the real world. The results also showed that a brief (<0.5 s) exposure to the visual scene during self-motion was sufficient to reduce the influence of the room structure on walking paths. The results are consistent with the idea that without visual experience within the VE, the path integration system is unable to effectively update one"s spatial position. As a result, people rely on other cues to define their position in space. Women, unlike men, choose to use visual cues about environmental structure to reorient.

Radiation dose reduction in digital breast tomosynthesis (DBT) by means of deep-learning-based supervised image processing

NASA Astrophysics Data System (ADS)

Liu, Junchi; Zarshenas, Amin; Qadir, Ammar; Wei, Zheng; Yang, Limin; Fajardo, Laurie; Suzuki, Kenji

2018-03-01

To reduce cumulative radiation exposure and lifetime risks for radiation-induced cancer from breast cancer screening, we developed a deep-learning-based supervised image-processing technique called neural network convolution (NNC) for radiation dose reduction in DBT. NNC employed patched-based neural network regression in a convolutional manner to convert lower-dose (LD) to higher-dose (HD) tomosynthesis images. We trained our NNC with quarter-dose (25% of the standard dose: 12 mAs at 32 kVp) raw projection images and corresponding "teaching" higher-dose (HD) images (200% of the standard dose: 99 mAs at 32 kVp) of a breast cadaver phantom acquired with a DBT system (Selenia Dimensions, Hologic, CA). Once trained, NNC no longer requires HD images. It converts new LD images to images that look like HD images; thus the term "virtual" HD (VHD) images. We reconstructed tomosynthesis slices on a research DBT system. To determine a dose reduction rate, we acquired 4 studies of another test phantom at 4 different radiation doses (1.35, 2.7, 4.04, and 5.39 mGy entrance dose). Structural SIMilarity (SSIM) index was used to evaluate the image quality. For testing, we collected half-dose (50% of the standard dose: 32+/-14 mAs at 33+/-5 kVp) and full-dose (standard dose: 68+/-23 mAs at 33+/-5 kvp) images of 10 clinical cases with the DBT system at University of Iowa Hospitals and Clinics. NNC converted half-dose DBT images of 10 clinical cases to VHD DBT images that were equivalent to full dose DBT images. Our cadaver phantom experiment demonstrated 79% dose reduction.

Low-dose dual-energy electronic cleansing for fecal-tagging CT Colonography

NASA Astrophysics Data System (ADS)

Cai, Wenli; Zhang, Da; Lee, June-Goo; Yoshida, Hiroyuki

2013-03-01

Dual-energy electronic cleansing (DE-EC) provides a promising means for cleansing the tagged fecal materials in fecaltagging CT colonography (CTC). However, the increased radiation dose due to the double exposures in dual-energy CTC (DE-CTC) scanning is a major limitation for the use of DE-EC in clinical practice. The purpose of this study was to develop and evaluate a low-dose DE-EC scheme in fecal-tagging DE-CTC. In this study, a custom-made anthropomorphic colon phantom, which was filled with simulated tagged materials by non-ionic iodinated contrast agent (Omnipaque iohexol, GE Healthcare), was scanned by a dual-source CT scanner (SOMATON Definition Flash, Siemens Healthcare) at two photon energies: 80 kVp and 140 kVp with nine different tube current settings ranging from 12 to 74 mAs for 140 kVp, and then reconstructed by soft-tissue reconstruction kernel (B30f). The DE-CTC images were subjected to a low-dose DE-EC scheme. First, our image-space DE-CTC denoising filter was applied for reduction of image noise. Then, the noise-reduced images were processed by a virtual lumen tagging method for reduction of partial volume effect and tagging inhomogeneity. The results were compared with the registered CTC images of native phantom without fillings. Preliminary results showed that our low-dose DE-EC scheme achieved the cleansing ratios, defined by the proportion of the cleansed voxels in the tagging mask, between 93.18% (12 mAs) and 96.62% (74 mAs). Also, the soft-tissue preservation ratios, defined by the proportion of the persevered voxels in the soft-tissue mask, were maintained in the range between 94.67% and 96.41%.

Formation of Covalently Modified Folding Intermediates of Simian Virus 40 Vp1 in Large T Antigen-Expressing Cells

PubMed Central

Watanabe, Marika; Phamduong, Ellen; Huang, Chu-Han; Itoh, Noriko; Bernal, Janie; Nakanishi, Akira; Rundell, Kathleen; Gjoerup, Ole

2013-01-01

The folding and pentamer assembly of the simian virus 40 (SV40) major capsid protein Vp1, which take place in the infected cytoplasm, have been shown to progress through disulfide-bonded Vp1 folding intermediates. In this report, we further demonstrate the existence of another category of Vp1 folding or assembly intermediates: the nonreducible, covalently modified mdVp1s. These species were present in COS-7 cells that expressed a recombinant SV40 Vp1, Vp1ΔC, through plasmid transfection. The mdVp1s persisted under cell and lysate treatment and SDS-PAGE conditions that are expected to have suppressed the formation of artifactual disulfide cross-links. As shown through a pulse-chase analysis, the mdVp1s were derived from the newly synthesized Vp1ΔC in the same time frame as Vp1's folding and oligomerization. The apparent covalent modifications occurred in the cytoplasm within the core region of Vp1 and depended on the coexpression of the SV40 large T antigen (LT) in the cells. Analogous covalently modified species were found with the expression of recombinant polyomavirus Vp1s and human papillomavirus L1s in COS-7 cells. Furthermore, the mdVp1s formed multiprotein complexes with LT, Hsp70, and Hsp40, and a fraction of the largest mdVp1, md4, was disulfide linked to the unmodified Vp1ΔC. Both mdVp1 formation and most of the multiprotein complex formation were blocked by a Vp1 folding mutation, C87A-C254A. Our observations are consistent with a role for LT in facilitating the folding process of SV40 Vp1 by stimulating certain covalent modifications of Vp1 or by recruiting certain cellular proteins. PMID:23427157

Vaccination with multimeric recombinant VP28 induces high protection against white spot syndrome virus in shrimp.

PubMed

Taengchaiyaphum, Suparat; Nakayama, Hideki; Srisala, Jiraporn; Khiev, Ratny; Aldama-Cano, Diva January; Thitamadee, Siripong; Sritunyalucksana, Kallaya

2017-11-01

To improve the efficacy of WSSV protection, multimeric (tetrameric) recombinant VP28 (4XrVP28) was produced and tested in comparison with those of monomeric VP28 (1XrVP28). In vitro binding of either 1XrVP28 or 4XrVP28 to shrimp hemocyte surface was evident as early as 10 min after protein inoculation. Similar results were obtained in vivo when shrimp were injected with recombinant proteins that the proteins bound to the hemocyte surface could be detected since 5 min after injection. Comparison of the WSSV protection efficiencies of 1XrVP28 or 4XrVP28 were performed by injection the purified 1XrVP28 or 4XrVP28 (22.5 μg/shrimp) and WSSV inoculum (1000 copies/shrimp) into shrimp. At 10 dpi, while shrimp injected with WSSV inoculum reached 100% mortality, shrimp injected with 1XrVP28 + WSSV or 4XrVP28 + WSSV showed relative percent survival (RPS) of 67% and 81%, respectively. PCR quantification revealed high number of WSSV in the moribund shrimp of WSSV- and 1XrVP28+WSSV-injected group. In contrast, lower number of WSSV copies were found in the survivors both from 1XrVP28+WSSV- or 4XrVP28+WSSV- injected groups. Histopathological analysis demonstrated the WSSV infected lesions found in the moribund from WSSV-infected group and 1XrVP28+WSSV-injected group, but less or none in the survivors. ELISA demonstrated that 4XrVP28 exhibited higher affinity binding to rPmRab7, a WSSV binding protein essential for WSSV entry to the cell than 1XrVP28. Taken together, the protection against WSSV in shrimp could be improved by application of multimeric rVP28. Copyright © 2017 Elsevier Ltd. All rights reserved.

[Escherichia coli heat-labile enterotoxin B subunit enhances the immune response against canine parvovirus VP2 in mice immunized by VP2 DNA vaccine].

PubMed

Han, Dongmei; Zhong, Fei; Li, Xiujin; Wang, Wei; Wang, Xingxing; Pan, Sumin

2011-01-01

To investigate the effect of Escherichia coli heat-labile enterotoxin (LT) B subunit (LTB) gene on canine parvovirus (CPV) VP2 gene vaccine. The LTB gene was amplified by PCR from genomic DNA of E. coli 44815 strain. The VP2-70 fragment (210 bp) encoding major epitope of VP2 (70 amino acids) was amplified by PCR from a plasmid encoding VP2 gene. VP2-70 and LTB genes were inserted into the eukaryotic vector to construct VP2-70 gene,LTB gene and VP2-70-LTB fused gene vectors. The mice were immunized with VP2-70 vector, VP2-70-LTB fused vector, or VP2-70 vector plus LTB vector, respectively. The antibody titers at the different time were measured by using ELISA method. The spleen lymphocyte proliferation activity was analyzed by 3-(4, 5-Dimethylthiazol-2-yl)-2, 5-diphenyltetrazolium bromide (MTT) assay. The sequence of VP2-70 and LTB genes was identified. The recombinant VP2-70 and LTB proteins could be expressed in HEK293T cells in a secretory manner. The mice immunized with VP2-70 vector, VP2-70-LTB vector or VP2-70 vector plus LTB vector could generate the specific antibody against VP2 protein. The antibody titer immunized with VP2-70-LTB vector reached 1:5120 at 35 d post immunization, significantly higher than that of other two groups (P < 0.01). For antibody isotype analysis, the IgG1 isotype antibody titers in all test groups were significantly higher than of IgG2a (P < 0.01). The high-level spleen lymphocyte stimulation index was observed in the three test groups under the stimulation with Con A, higher than that in control groups (P < 0.01). LTB gene could enhance the humoral immune response of CPV VP2 gene vaccine in mice.

Full protection against African horsesickness (AHS) in horses induced by baculovirus-derived AHS virus serotype 4 VP2, VP5 and VP7.

PubMed

Martínez-Torrecuadrada, J L; Díaz-Laviada, M; Roy, P; Sánchez, C; Vela, C; Sánchez-Vizcaíno, J M; Casal, J I

1996-06-01

African horsesickness virus serotype 4 (AHSV-4) outer capsid protein VP2, or VP2 and VP5 plus inner capsid protein VP7, derived from single or dual recombinant baculovirus expression vectors were used in different combinations to immunize horses. When the proteins were purified by affinity chromatography, the combination of all three proteins induced low levels of neutralizing antibodies and conferred protection against virulent virus challenge. However, purified VP2 or VP2 and VP5 in the absence of VP7 failed to induce neutralizing antibodies and protection. Immunization with non-purified proteins enhanced the titres of neutralizing antibodies. Again, the combination of the three proteins was able to confer total protection to immunized horses, which showed absence of viraemia. The antigenicity of recombinant VP2 was analysed with a collection of 30 MAbs. Both purified and unpurified recombinant VP2 proteins showed different antigenic patterns in comparison to that of VP2 on virions. An immunization experiment with four more horses confirmed these results. The vaccine described here would not only prevent the disease, but would drastically reduce the propagation of the virus by vectors.

Identification and modification of dominant noise sources in diesel engines

NASA Astrophysics Data System (ADS)

Hayward, Michael D.

Determination of dominant noise sources in diesel engines is an integral step in the creation of quiet engines, but is a process which can involve an extensive series of expensive, time-consuming fired and motored tests. The goal of this research is to determine dominant noise source characteristics of a diesel engine in the near and far-fields with data from fewer tests than is currently required. Pre-conditioning and use of numerically robust methods to solve a set of cross-spectral density equations results in accurate calculation of the transfer paths between the near- and far-field measurement points. Application of singular value decomposition to an input cross-spectral matrix determines the spectral characteristics of a set of independent virtual sources, that, when scaled and added, result in the input cross spectral matrix. Each virtual source power spectral density is a singular value resulting from the decomposition performed over a range of frequencies. The complex relationship between virtual and physical sources is estimated through determination of virtual source contributions to each input measurement power spectral density. The method is made more user-friendly through use of a percentage contribution color plotting technique, where different normalizations can be used to help determine the presence of sources and the strengths of their contributions. Convolution of input measurements with the estimated path impulse responses results in a set of far-field components, to which the same singular value contribution plotting technique can be applied, thus allowing dominant noise source characteristics in the far-field to also be examined. Application of the methods presented results in determination of the spectral characteristics of dominant noise sources both in the near- and far-fields from one fired test, which significantly reduces the need for extensive fired and motored testing. Finally, it is shown that the far-field noise time history of a physically altered engine can be simulated through modification of singular values and recalculation of transfer paths between input and output measurements of previously recorded data.

Pangea, the geoid, and the paths of virtual geomagnetic poles during polarity reversals

NASA Astrophysics Data System (ADS)

Vizán, H.; Mena, M.; Vilas, J. F.

1992-11-01

The elongated distribution of virtual geomagnetic poles (VGPs) of South American Jurassic units has been interpreted as reflecting: 1) the behavior of the Earth's magnetic field (EMF), and 2) apparent polar shift of the South American plate before the breakup of Gondwana. New paleomagnetic data do not support the latter. We analyze these Jurassic VGPs together with those of other Pangean continents, considering a model based on the following assumptions: 1) Pangea was assembled over the present African-Atlantic geoid high; 2) the hotspot framework has not been significantly deformed over the last 200 Ma; 3) the present geoid matches the present topography of the core mantle boundary (CMB); 4) the overall topography of the CMB remains unchanged for long periods of time. We plotted Jurassic VGPs of Pangean continents, previously returned to a fixed-hotspot framework, on a map of the present topography of the CMB. The VGPs seem to follow the trend of regions of increased CMB seismic velocities. When a polarity reversal was registered by a Jurassic unit, the path of the VGPs was channeled on zones that have been observed in translational paths for the last 10 Ma.

Plasma membrane association facilitates conformational changes in the Marburg virus protein VP40 dimer.

PubMed

Bhattarai, Nisha; Gc, Jeevan B; Gerstman, Bernard S; Stahelin, Robert V; Chapagain, Prem P

2017-04-26

Filovirus infections cause hemorrhagic fever in humans and non-human primates that often results in high fatality rates. The Marburg virus is a lipid-enveloped virus from the Filoviridae family and is closely related to the Ebola virus. The viral matrix layer underneath the lipid envelope is formed by the matrix protein VP40 (VP40), which is also involved in other functions during the viral life-cycle. As in the Ebola virus VP40 (eVP40), the recently determined X-ray crystal structure of the Marburg virus VP40 (mVP40) features loops containing cationic residues that form a lipid binding basic patch. However, the mVP40 basic patch is significantly flatter with a more extended surface than in eVP40, suggesting the possibility of differences in the plasma membrane interactions and phospholipid specificity between the VP40 dimers. In this paper, we report on molecular dynamics simulations that investigate the roles of various residues and lipid types in PM association as well as the conformational changes of the mVP40 dimer facilitated by membrane association. We compared the structural changes of the mVP40 dimer with the mVP40 dimer in both lipid free and membrane associated conditions. Despite the significant structural differences in the crystal structure, the Marburg VP40 dimer is found to adopt a configuration very similar to the Ebola VP40 dimer after associating with the membrane. This conformational rearrangement upon lipid binding allows Marburg VP40 to localize and stabilize at the membrane surface in a manner similar to the Ebola VP40 dimer. Consideration of the structural information in its lipid-interacting condition may be important in targeting mVP40 for novel drugs to inhibit viral budding from the plasma membrane.

Herpes simplex virus 2 VP22 phosphorylation induced by cellular and viral kinases does not influence intracellular localization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Geiss, Brian J.; Cano, Gina L.; Tavis, John E.

2004-12-05

Phosphorylation of the herpes simplex virus (HSV) VP22 protein is regulated by cellular kinases and the UL13 viral kinase, but the sites at which these enzymes induce phosphorylation of HSV-2 VP22 are not known. Using serine-to-alanine mutants to map phosphorylation sites on HSV-2 VP22 in cells, we made three major observations. First, phosphorylation by a cellular kinase mapped to serines 70, 71, and/or 72 within CKII consensus sites analogous to previously identified phosphorylation sites in HSV-1 VP22. Second, we mapped UL13-mediated phosphorylation of HSV-2 VP22 to serines 28 and 34, describing for the first time UL13-dependent phosphorylation sites on VP22.more » Third, previously identified VP22-associated cellular kinase sites in HSV-1 VP22 (serines 292 and 294) were not phosphorylated in HSV-2 VP22 (serines 291 and 293). VP22 expressed alone accumulated in the cytoplasm and to a lesser extent in the nucleus. Phosphorylation by endogenous cellular kinase(s) did not alter the localization of VP22. Co-expression of HSV-2 VP22 with active UL13, but not with enzymatically inactive UL13, resulted in nuclear accumulation of VP22 and altered nuclear morphology. Surprisingly, redistribution of VP22 to the nucleus occurred independently of UL13-induced phosphorylation of VP22. The altered nuclear morphology of UL13-expressing cells was not due to apoptosis. These results demonstrate that phosphorylation of HSV-2 VP22 at multiple serine residues is induced by UL13 and cellular kinase(s), and that the nuclear/cytoplasmic distribution of VP22 is independent of its phosphorylation status but is controlled indirectly by UL13 kinase activity.« less

Expression and characterization of a novel truncated rotavirus VP4 for the development of a recombinant rotavirus vaccine.

PubMed

Li, Yijian; Xue, Miaoge; Yu, Linqi; Luo, Guoxing; Yang, Han; Jia, Lianzhi; Zeng, Yuanjun; Li, Tingdong; Ge, Shengxiang; Xia, Ningshao

2018-04-12

The outer capsid protein VP4 is an important target for the development of a recombinant rotavirus vaccine because it mediates the attachment and penetration of rotavirus. Due to the poor solubility of full-length VP4, VP8 was explored as candidate rotavirus vaccines in the past years. In previous studies, it has been found that the N-terminal truncated VP8 protein, VP8-1 (aa26-231), could be expressed in soluble form with improved immunogenicity compared to the core of VP8 (aa65-223). However, this protein stimulated only a weak immune response when aluminum hydroxide was used as an adjuvant. In addition, it should be noted that the protective efficacy of VP4 was higher than that of VP8 and VP5. In this study, it was found that when the N-terminal 25 amino acids were deleted, the truncated VP4 ∗ (aa26-476) containing VP8 and the stalk domain of VP5 could be expressed in soluble form in E. coli and purified to homogeneous trimers. Furthermore, the truncated VP4 could induce high titers of neutralizing antibodies when aluminum adjuvant was used and conferred high protective efficacy in reducing the severity of diarrhea and rotavirus shedding in stools in animal models. The immunogenicity of the truncated VP4 was significantly higher than that of VP8 ∗ and VP5 ∗ alone. Taken together, the truncated VP4 ∗ (aa26-476), with enhanced immunogenicity and immunoprotectivity, could be considered as a viable candidate for further development and has the potential to become a parenterally administered rotavirus vaccine. Copyright © 2018 Elsevier Ltd. All rights reserved.

Helmet Mounted Eye Tracking for Virtual Panoramic Displays. Volume 1: Review of Current Eye Movement Measurement Technology

DTIC Science & Technology

1989-08-01

paths for integration with the off-aperture and dual-mirror VPD designs. PREFACE The goal of this work was to explore integration of an eye line-of- gaze ...Relationship in one plane between point-of- gaze on a flat scene and relative eye, detector, and scene positions...and eye line-of- gaze measurement. As a first step towards the design of an appropriate eye trac.<ing system for interface with the virtual cockpit

Simulation of dental collisions and occlusal dynamics in the virtual environment.

PubMed

Stavness, I K; Hannam, A G; Tobias, D L; Zhang, X

2016-04-01

Semi-adjustable articulators have often been used to simulate occlusal dynamics, but advances in intra-oral scanning and computer software now enable dynamics to be modelled mathematically. Computer simulation of occlusal dynamics requires accurate virtual casts, records to register them and methods to handle mesh collisions during movement. Here, physical casts in a semi-adjustable articulator were scanned with a conventional clinical intra-oral scanner. A coordinate measuring machine was used to index their positions in intercuspation, protrusion, right and left laterotrusion, and to model features of the articulator. Penetrations between the indexed meshes were identified and resolved using restitution forces, and the final registrations were verified by distance measurements between dental landmarks at multiple sites. These sites were confirmed as closely approximating via measurements made from homologous transilluminated vinylpolysiloxane interocclusal impressions in the mounted casts. Movements between the indexed positions were simulated with two models in a custom biomechanical software platform. In model DENTAL, 6 degree-of-freedom movements were made to minimise deviation from a straight line path and also shaped by dynamic mesh collisions detected and resolved mathematically. In model ARTIC, the paths were further constrained by surfaces matching the control settings of the articulator. Despite these differences, the lower mid-incisor point paths were very similar in both models. The study suggests that mathematical simulation utilising interocclusal 'bite' registrations can closely replicate the primary movements of casts mounted in a semi-adjustable articulator. Additional indexing positions and appropriate software could, in some situations, replace the need for mechanical semi-adjustable articulation and/or its virtual representation. © 2015 John Wiley & Sons Ltd.

VP1 amino acid residue 145 of enterovirus 71 is a key residue for its receptor attachment and resistance to neutralizing antibody during cynomolgus monkey infection.

PubMed

Fujii, Ken; Sudaka, Yui; Takashino, Ayako; Kobayashi, Kyousuke; Kataoka, Chikako; Suzuki, Tadaki; Iwata-Yoshikawa, Naoko; Kotani, Osamu; Ami, Yasushi; Shimizu, Hiroyuki; Nagata, Noriyo; Mizuta, Katsumi; Matsuzaki, Yoko; Koike, Satoshi

2018-05-30

Enterovirus 71 (EV71) is a causative agent of hand, foot, and mouth disease and sometimes causes severe or fatal neurological complications. The amino acid at VP1-145 determines virological characteristics of EV71. Viruses with glutamic acid (E) at VP1-145 (VP1-145E) are virulent in neonatal mice and transgenic mice expressing human scavenger receptor B2, whereas those with glutamine (Q) or glycine (G) are not. However, the contribution of this variation to pathogenesis in humans is not fully understood. We compared the virulence of VP1-145E and VP1-145G viruses of Isehara and C7/Osaka backgrounds in cynomolgus monkeys. VP1-145E, but not VP1-145G, viruses induced neurological symptoms. VP1-145E viruses were frequently detected in the tissues of infected monkeys. VP1-145G viruses were detected less frequently and disappeared quickly. Instead, mutants that had a G to E mutation at VP1-145 emerged, suggesting that VP1-145E viruses have a replication advantage in the monkeys. This is consistent with our hypothesis proposed in the accompanying paper that the VP1-145G virus is attenuated due to its adsorption by heparan sulfate. Monkeys infected with both viruses produced neutralizing antibodies before the onset of the disease. Interestingly, VP1-145E viruses were more resistant to neutralizing antibodies than VP1-145G viruses in vitro A small amount of neutralizing antibody raised in the early phase of infection may not be sufficient to block the dissemination of VP1-145E viruses. The different resistance of the VP1-145 variants to neutralizing antibodies may be one of the reasons for the difference in virulence. IMPORTANCE The contribution of VP1-145 variants in humans is not fully understood. In some reports, VP1-145G/Q viruses were more frequently isolated from severely affected than from mildly affected patients, suggesting that VP1-145G/Q viruses are more virulent. In the accompanying paper, we showed that VP1-145E viruses are more virulent than VP1-145G viruses in human SCARB2 transgenic mice. Heparan sulfate acts as a decoy to specifically trap the VP1-145G viruses and leads to abortive infection. Here, we demonstrated that VP1-145G was attenuated in cynomolgus monkeys, suggesting that this hypothesis is also true in a non-human primate model. VP1-145E viruses, but not VP1-145G viruses, were highly resistant to neutralizing antibodies. We propose the difference in resistance against neutralizing antibodies as another mechanism of EV71 virulence. In summary, VP1-145 contributes to virulence determination by controlling attachment receptor usage and antibody sensitivity. Copyright © 2018 American Society for Microbiology.

Training to acquire psychomotor skills for endoscopic endonasal surgery using a personal webcam trainer.

PubMed

Hirayama, Ryuichi; Fujimoto, Yasunori; Umegaki, Masao; Kagawa, Naoki; Kinoshita, Manabu; Hashimoto, Naoya; Yoshimine, Toshiki

2013-05-01

Existing training methods for neuroendoscopic surgery have mainly emphasized the acquisition of anatomical knowledge and procedures for operating an endoscope and instruments. For laparoscopic surgery, various training systems have been developed to teach handling of an endoscope as well as the manipulation of instruments for speedy and precise endoscopic performance using both hands. In endoscopic endonasal surgery (EES), especially using a binostril approach to the skull base and intradural lesions, the learning of more meticulous manipulation of instruments is mandatory, and it may be necessary to develop another type of training method for acquiring psychomotor skills for EES. Authors of the present study developed an inexpensive, portable personal trainer using a webcam and objectively evaluated its utility. Twenty-five neurosurgeons volunteered for this study and were divided into 2 groups, a novice group (19 neurosurgeons) and an experienced group (6 neurosurgeons). Before and after the exercises of set tasks with a webcam box trainer, the basic endoscopic skills of each participant were objectively assessed using the virtual reality simulator (LapSim) while executing 2 virtual tasks: grasping and instrument navigation. Scores for the following 11 performance variables were recorded: instrument time, instrument misses, instrument path length, and instrument angular path (all of which were measured in both hands), as well as tissue damage, max damage, and finally overall score. Instrument time was indicated as movement speed; instrument path length and instrument angular path as movement efficiency; and instrument misses, tissue damage, and max damage as movement precision. In the novice group, movement speed and efficiency were significantly improved after the training. In the experienced group, significant improvement was not shown in the majority of virtual tasks. Before the training, significantly greater movement speed and efficiency were demonstrated in the experienced group, but no difference in movement precision was shown between the 2 groups. After the training, no significant differences were shown between the 2 groups in the majority of the virtual tasks. Analysis revealed that the webcam trainer improved the basic skills of the novices, increasing movement speed and efficiency without sacrificing movement precision. Novices using this unique webcam trainer showed improvement in psychomotor skills for EES. The authors believe that training in terms of basic endoscopic skills is meaningful and that the webcam training system can play a role in daily off-the-job training for EES.

Red Hat Enterprise Virtualization - KVM-based infrastructure services at BNL

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cortijo, D.

2011-06-14

Over the past 18 months, BNL has moved a large percentage of its Linux-based servers and services into a Red Hat Enterprise Virtualization (RHEV) environment. This presentation will address our approach to virtualization, critical decision points, and a discussion of our implementation. Specific topics will include an overview of hardware and software requirements, networking, and storage; discussion of the decision of Red Hat solution over competing products (VMWare, Xen, etc); details on some of the features of RHEV - both current and on their roadmap; Review of performance and reliability gains since deployment completion; path forward for RHEV at BNLmore » and caveats and potential problems.« less

Lloviu virus VP24 and VP35 proteins function as innate immune antagonists in human and bat cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Feagins, Alicia R.; Basler, Christopher F., E-mail: chris.basler@mssm.edu

Lloviu virus (LLOV) is a new member of the filovirus family that also includes Ebola virus (EBOV) and Marburg virus (MARV). LLOV has not been cultured; however, its genomic RNA sequence indicates the coding capacity to produce homologs of the EBOV and MARV VP24, VP35, and VP40 proteins. EBOV and MARV VP35 proteins inhibit interferon (IFN)-alpha/beta production and EBOV VP35 blocks activation of the antiviral kinase PKR. The EBOV VP24 and MARV VP40 proteins inhibit IFN signaling, albeit by different mechanisms. Here we demonstrate that LLOV VP35 suppresses Sendai virus induced IFN regulatory factor 3 (IRF3) phosphorylation, IFN-α/β production, andmore » PKR phosphorylation. Additionally, LLOV VP24 blocks tyrosine phosphorylated STAT1 binding to karyopherin alpha 5 (KPNA5), STAT1 nuclear accumulation, and IFN-induced gene expression. LLOV VP40 lacks detectable IFN antagonist function. These activities parallel EBOV IFN inhibitory functions. EBOV and LLOV VP35 and VP24 proteins also inhibit IFN responses in bat cells. These data suggest that LLOV infection will block innate immune responses in a manner similar to EBOV. - Highlights: • Lloviu virus (LLOV) is a new member of the filovirus family. • LLOV VP35 blocks IRF3 phosphorylation, IFN-α/β production and PKR phosphorylation. • LLOV VP24 inhibits IFN responses by targeting phospho-STAT1 KPNA interaction. • Infection by LLOV may block innate immune responses in a manner similar to EBOV.« less

Pre-harvest sprouting resistance and haplotype variation of ThVp-1 gene in the collection of wheat-wheatgrass hybrids

PubMed Central

Kocheshkova, A. A.; Kroupin, P. Yu.; Bazhenov, M. S.; Karlov, G. I.; Pochtovyy, A. A.; Upelniek, V. P.; Belov, V. I.

2017-01-01

The germplasm collection of 87 wheat-wheatgrass hybrids developed in Tsitisin Main Botanical Garden (Russia, Moscow) was evaluated for resistance to pre-harvest sprouting (PHS) by spike sprouting (SS) and germination index (GI) assays as well as for spike and grain features. The PHS resistance variation and haplotype polymorphism of the wheatgrass ThVp-1 and wheat TaVp-1B genes orthologues of Vp-1 was revealed in the studied collection. Four haplotypes of ThVp-1 were revealed: ThVp-1a (41% of the entries), ThVp-1b (13%), ThVp-1c (29%), and ThVp-1d (15%). The association between the allelic state of ThVp-1 and PHS resistance in the wheat-wheatgrass hybrids was shown: haplotype ThVp-1d of the wheatgrass Vp-1 gene is significantly associated with reduced PHS in the wheat-wheatgrass hybrids (mean SS 0.33, mean GI 0.64). The resistant entries may be perspective as a source of PHS resistance in the development of commercial cultivars of perennial wheat. PMID:29131854

Cyclophilin A Interacts with Viral VP4 and Inhibits the Replication of Infectious Bursal Disease Virus.

PubMed

Wang, Nian; Zhang, Lizhou; Chen, Yuming; Lu, Zhen; Gao, Li; Wang, Yongqiang; Gao, Yulong; Gao, Honglei; Cui, Hongyu; Li, Kai; Liu, Changjun; Zhang, Yanping; Qi, Xiaole; Wang, Xiaomei

2015-01-01

Nonstructural protein VP4, a serine protease of infectious bursal disease virus (IBDV) that catalyzes the hydrolysis of polyprotein pVP2-VP4-VP3 to form the viral proteins VP2, VP4, and VP3, is essential to the replication of IBDV. However, the interacting partners of VP4 in host cells and the effects of the interaction on the IBDV lifecycle remain incompletely elucidated. In this study, using the yeast two-hybrid system, the putative VP4-interacting partner cyclophilin A (CypA) was obtained from a chicken embryo fibroblast (CEF) expression library. CypA was further confirmed to interact with VP4 of IBDV using co-immunoprecipitation (CO-IP), GST pull-down, and confocal microscopy assays. Moreover, we found that the overexpression of CypA suppressed IBDV replication, whereas the knock-down of CypA by small interfering RNAs promoted the replication of IBDV. Taken together, our findings indicate that the host cell protein CypA interacts with viral VP4 and inhibits the replication of IBDV.

P and S velocity structure of the crust and the upper mantle beneath central Java from local tomography inversion

NASA Astrophysics Data System (ADS)

Koulakov, I.; Bohm, M.; Asch, G.; Lühr, B.-G.; Manzanares, A.; Brotopuspito, K. S.; Fauzi, Pak; Purbawinata, M. A.; Puspito, N. T.; Ratdomopurbo, A.; Kopp, H.; Rabbel, W.; Shevkunova, E.

2007-08-01

Here we present the results of local source tomographic inversion beneath central Java. The data set was collected by a temporary seismic network. More than 100 stations were operated for almost half a year. About 13,000 P and S arrival times from 292 events were used to obtain three-dimensional (3-D) Vp, Vs, and Vp/Vs models of the crust and the mantle wedge beneath central Java. Source location and determination of the 3-D velocity models were performed simultaneously based on a new iterative tomographic algorithm, LOTOS-06. Final event locations clearly image the shape of the subduction zone beneath central Java. The dipping angle of the slab increases gradually from almost horizontal to about 70°. A double seismic zone is observed in the slab between 80 and 150 km depth. The most striking feature of the resulting P and S models is a pronounced low-velocity anomaly in the crust, just north of the volcanic arc (Merapi-Lawu anomaly (MLA)). An algorithm for estimation of the amplitude value, which is presented in the paper, shows that the difference between the fore arc and MLA velocities at a depth of 10 km reaches 30% and 36% in P and S models, respectively. The value of the Vp/Vs ratio inside the MLA is more than 1.9. This shows a probable high content of fluids and partial melts within the crust. In the upper mantle we observe an inclined low-velocity anomaly which links the cluster of seismicity at 100 km depth with MLA. This anomaly might reflect ascending paths of fluids released from the slab. The reliability of all these patterns was tested thoroughly.

Computed tomographic venography for varicose veins of the lower extremities: prospective comparison of 80-kVp and conventional 120-kVp protocols.

PubMed

Cho, Eun-Suk; Kim, Joo Hee; Kim, Sungjun; Yu, Jeong-Sik; Chung, Jae-Joon; Yoon, Choon-Sik; Lee, Hyeon-Kyeong; Lee, Kyung Hee

2012-01-01

To prospectively investigate the feasibility of an 80-kilovolt (peak) (kVp) protocol in computed tomographic venography for varicose veins of the lower extremities by comparison with conventional 120-kVp protocol. Attenuation values and signal-to-noise ratio of iodine contrast medium (CM) were determined in a water phantom for 2 tube voltages (80 kVp and 120 kVp). Among 100 patients, 50 patients were scanned with 120 kVp and 150 effective milliampere second (mAs(eff)), and the other 50 patients were scanned with 80 kVp and 390 mAs(eff) after the administration of 1.7-mL/kg CM (370 mg of iodine per milliliter). The 2 groups were compared for venous attenuation, contrast-to-noise ratio, and subjective degree of venous enhancement, image noise, and overall diagnostic image quality. In the phantom, the attenuation value and signal-to-noise ratio value for iodine CM at 80 kVp were 63.8% and 33.0% higher, respectively, than those obtained at 120 kVp. The mean attenuation of the measured veins of the lower extremities was 148.3 Hounsfield units (HU) for the 80-kVp protocol and 94.8 HU for the 120-kVp protocol. Contrast-to-noise ratio was also significantly higher with the 80-kVp protocol. The overall diagnostic image quality of the 3-dimensional volume-rendered images was good with both protocols. The subjective score for venous enhancement was higher at the 80-kVp protocol. The mean volume computed tomography dose index of the 80-kVp (5.6 mGy) protocol was 23.3% lower than that of the 120-kVp (7.3 mGy) protocol. The use of the 80-kVp protocol improved overall venous attenuation, especially in perforating vein, and provided similarly high diagnostic image quality with a lower radiation dose when compared to the conventional 120-kVp protocol.

Assembly of the Herpes Simplex Virus Capsid: Preformed Triplexes Bind to the Nascent Capsid

PubMed Central

Spencer, Juliet V.; Newcomb, William W.; Thomsen, Darrell R.; Homa, Fred L.; Brown, Jay C.

1998-01-01

The herpes simplex virus type 1 (HSV-1) capsid is a T=16 icosahedral shell that forms in the nuclei of infected cells. Capsid assembly also occurs in vitro in reaction mixtures created from insect cell extracts containing recombinant baculovirus-expressed HSV-1 capsid proteins. During capsid formation, the major capsid protein, VP5, and the scaffolding protein, pre-VP22a, condense to form structures that are extended into procapsids by addition of the triplex proteins, VP19C and VP23. We investigated whether triplex proteins bind to the major capsid-scaffold protein complexes as separate polypeptides or as preformed triplexes. Assembly products from reactions lacking one triplex protein were immunoprecipitated and examined for the presence of the other. The results showed that neither triplex protein bound unless both were present, suggesting that interaction between VP19C and VP23 is required before either protein can participate in the assembly process. Sucrose density gradient analysis was employed to determine the sedimentation coefficients of VP19C, VP23, and VP19C-VP23 complexes. The results showed that the two proteins formed a complex with a sedimentation coefficient of 7.2S, a value that is consistent with formation of a VP19C-VP232 heterotrimer. Furthermore, VP23 was observed to have a sedimentation coefficient of 4.9S, suggesting that this protein exists as a dimer in solution. Deletion analysis of VP19C revealed two domains that may be required for attachment of the triplex to major capsid-scaffold protein complexes; none of the deletions disrupted interaction of VP19C with VP23. We propose that preformed triplexes (VP19C-VP232 heterotrimers) interact with major capsid-scaffold protein complexes during assembly of the HSV-1 capsid. PMID:9557680

Hepatitis A Virus Capsid Protein VP1 Has a Heterogeneous C Terminus

PubMed Central

Graff, Judith; Richards, Oliver C.; Swiderek, Kristine M.; Davis, Michael T.; Rusnak, Felicia; Harmon, Shirley A.; Jia, Xi-Yu; Summers, Donald F.; Ehrenfeld, Ellie

1999-01-01

Hepatitis A virus (HAV) encodes a single polyprotein which is posttranslationally processed into the functional structural and nonstructural proteins. Only one protease, viral protease 3C, has been implicated in the nine protein scissions. Processing of the capsid protein precursor region generates a unique intermediate, PX (VP1-2A), which accumulates in infected cells and is assumed to serve as precursor to VP1 found in virions, although the details of this reaction have not been determined. Coexpression in transfected cells of a variety of P1 precursor proteins with viral protease 3C demonstrated efficient production of PX, as well as VP0 and VP3; however, no mature VP1 protein was detected. To identify the C-terminal amino acid residue of HAV VP1, we performed peptide sequence analysis by protease-catalyzed [18O]H2O incorporation followed by liquid chromatography ion-trap microspray tandem mass spectrometry of HAV VP1 isolated from purified virions. Two different cell culture-adapted isolates of HAV, strains HM175pE and HM175p35, were used for these analyses. VP1 preparations from both virus isolates contained heterogeneous C termini. The predominant C-terminal amino acid in both virus preparations was VP1-Ser274, which is located N terminal to a methionine residue in VP1-2A. In addition, the analysis of HM175pE recovered smaller amounts of amino acids VP1-Glu273 and VP1-Thr272. In the case of HM175p35, which contains valine at amino acid position VP1-273, VP1-Thr272 was found in addition to VP1-Ser274. The data suggest that HAV 3C is not the protease responsible for generation of the VP1 C terminus. We propose the involvement of host cell protease(s) in the production of HAV VP1. PMID:10364353

A Framework for Simulation of Aircraft Flyover Noise Through a Non-Standard Atmosphere

NASA Technical Reports Server (NTRS)

Arntzen, Michael; Rizzi, Stephen A.; Visser, Hendrikus G.; Simons, Dick G.

2012-01-01

This paper describes a new framework for the simulation of aircraft flyover noise through a non-standard atmosphere. Central to the framework is a ray-tracing algorithm which defines multiple curved propagation paths, if the atmosphere allows, between the moving source and listener. Because each path has a different emission angle, synthesis of the sound at the source must be performed independently for each path. The time delay, spreading loss and absorption (ground and atmosphere) are integrated along each path, and applied to each synthesized aircraft noise source to simulate a flyover. A final step assigns each resulting signal to its corresponding receiver angle for the simulation of a flyover in a virtual reality environment. Spectrograms of the results from a straight path and a curved path modeling assumption are shown. When the aircraft is at close range, the straight path results are valid. Differences appear especially when the source is relatively far away at shallow elevation angles. These differences, however, are not significant in common sound metrics. While the framework used in this work performs off-line processing, it is conducive to real-time implementation.

Search for temporal changes in shear-wave splitting associated with the 2012 Te Maari Eruptions at Mount Tongariro, New Zealand

NASA Astrophysics Data System (ADS)

Godfrey, Holly J.; Shelley, Adrian; Savage, Martha K.

2014-10-01

We investigate changes in shear wave splitting and VP/VS ratios of local earthquakes from the GeoNet catalogue during a 16 month period beginning a year before the first Te Maari eruption at Mount Tongariro on August 6, 2012, focusing on four permanent seismographs located in proximity to the volcano. We identify four time periods bounded by sharp transitions that comprise the study period, during which moving averages of the shear-wave splitting parameters, Φ (fast direction) and δt (delay time), are fairly constant. At all stations, VP/VS is steady throughout most of the study period at 1.75. Small variations occur during the earthquake swarm at the volcano, which started a month before the first eruption, and for some low magnitude events occurring after a change in earthquake location method. Analysis of data sets in which epicentre location, hypocentre depth and event magnitude are restricted illustrates that observed temporal changes in shear-wave splitting parameters are likely due to the spatial variation of paths. This in turn is governed by the spatial distribution of seismicity and measurement quality. We think the short term variation in VP/VS ratios is due to event origin time uncertainty of low magnitude earthquakes or incorrect S-phase arrival timing for events in the Tongariro swarm. These results suggest that any volcanic processes able to cause changes in shear-wave splitting or VP/VS associated with the two eruptions during our study period were too localised to Te Maari to be observed at the seismographs studied using our methods. Dominant Φ observed during the study period are oriented approximately tangential to the Tongariro/Ngauruhoe massif at all four stations. We suggest that this may result from gravitational loading of Tongariro and Ngauruhoe mountains inducing fracturing or dilatation of tangentially oriented microcracks. There may also be some effect from layered material causing horizontal propagating rays yielding faster speed SH waves than SV at station NGZ. Measurements from shallow earthquakes in immediate proximity to the seismographs indicate the potential presence of a shallow, highly anisotropic body in the volcano.

Anisotropic imaging performance in breast tomosynthesis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Badano, Aldo; Kyprianou, Iacovos S.; Jennings, Robert J.

We describe the anisotropy in imaging performance caused by oblique x-ray incidence in indirect detectors for breast tomosynthesis based on columnar scintillator screens. We use MANTIS, a freely available combined x-ray, electron, and optical Monte Carlo transport package which models the indirect detection processes in columnar screens, interaction by interaction. The code has been previously validated against published optical distributions. In this article, initial validation results are provided concerning the blur for particular designs of phosphor screens for which some details with respect to the columnar geometry are available from scanning electron microscopy. The polyenergetic x-ray spectrum utilized comes frommore » a database of experimental data for three different anode/filter/kVp combinations: Mo/Mo at 28 kVp, Rh/Rh at 28 kVp, and W/Al at 42 kVp. The x-ray spectra were then filtered with breast tissue (3, 4, and 6 cm thickness), compression paddle, and support base, according to the oblique paths determined by the incidence angle. The composition of the breast tissue was 50%/50% adipose/glandular tissue mass ratio. Results are reported on the pulse-height statistics of the light output and on spatial blur, expressed as the response of the detector to a pencil beam with a certain incidence angle. Results suggest that the response is nonsymmetrical and that the resolution properties of a tomosynthesis system vary significantly with the angle of x-ray incidence. In contrast, it is found that the noise due to the variability in the number of light photons detected per primary x-ray interaction changes only a few percent. The anisotropy in the response is not less in screens with absorptive backings while the noise introduced by variations in the depth-dependent light output and optical transport is larger. The results suggest that anisotropic imaging performance across the detector area can be incorporated into reconstruction algorithms for improving the image quality of breast tomosynthesis. This study also demonstrates that the assessment of image quality of breast tomosynthesis systems requires a more complete description of the detector response beyond local, center measurements of resolution and noise that assume some degree of symmetry in the detector performance.« less

Localization of the herpes simplex virus type 1 major capsid protein VP5 to the cell nucleus requires the abundant scaffolding protein VP22a.

PubMed

Nicholson, P; Addison, C; Cross, A M; Kennard, J; Preston, V G; Rixon, F J

1994-05-01

The intracellular distributions of three herpes simplex virus type 1 (HSV-1) capsid proteins, VP23, VP5 and VP22a, were examined using vaccinia virus and plasmid expression systems. During infection of cells with HSV-1 wild-type virus, all three proteins were predominantly located in the nucleus, which is the site of capsid assembly. However, when expressed in the absence of any other HSV-1 proteins, although VP22a was found exclusively in the nucleus as expected, VP5 and VP23 were distributed throughout the cell. Thus nuclear localization is not an intrinsic property of these proteins but must be mediated by one or more HSV-1-induced proteins. Co-expression experiments demonstrated that VP5 was efficiently transported to the nucleus in the presence of VP22a, but the distribution of VP23 was unaffected by the presence of either or both of the other two proteins.

Characterization of putative toxin/antitoxin systems in Vibrio parahaemolyticus.

PubMed

Hino, M; Zhang, J; Takagi, H; Miyoshi, T; Uchiumi, T; Nakashima, T; Kakuta, Y; Kimura, M

2014-07-01

To obtain more information about the toxin/antitoxin (TA) systems in the Vibrio genus and also to examine their involvement in the induction of a viable but nonculturable (VBNC) state, we searched homologues of the Escherichia coli TA systems in the Vibrio parahaemolyticus genome. We found that a gene cluster, vp1842/vp1843, in the V. parahaemolyticus genome database has homology to that encoding the E. coli TA proteins, DinJ/YafQ. Expression of the putative toxin gene vp1843 in E. coli cells strongly inhibited the cell growth, while coexpression with the putative antitoxin gene vp1842 neutralized this effect. Mutational analysis identified Lys37 and Pro45 in the gene product VP1843 of vp1843 as crucial residues for the growth retardation of E. coli cells. VP1843, unlike the E. coli toxin YafQ, has no protein synthesis inhibitory activity, and that instead the expression of vp1843 in E. coli caused morphological change of the cells. The gene cluster vp1842/vp1843 encodes the V. parahaemolyticus TA system; VP1843 inhibits cell growth, whereas VP1842 serves as an antitoxin by forming a stable complex with VP1843. The putative toxin, VP1843, may be involved in the induction of the VBNC state in V. parahaemolyticus by inhibiting cell division. © 2014 The Society for Applied Microbiology.

Incidental Findings in Abdominal Dual-Energy Computed Tomography: Correlation Between True Noncontrast and Virtual Noncontrast Images Considering Renal and Liver Cysts and Adrenal Masses.

PubMed

Slebocki, Karin; Kraus, Bastian; Chang, De-Hua; Hellmich, Martin; Maintz, David; Bangard, Christopher

To assess correlation between attenuation measurements of incidental findings in abdominal second generation dual-energy computed tomography (CT) on true noncontrast (TNC) and virtual noncontrast (VNC) images. Sixty-three patients underwent arterial dual-energy CT (Somatom Definition Flash, Siemens; pitch factor, 0.75-1.0; gantry rotation time, 0.28 seconds) after endovascular aneurysm repair, consisting of a TNC single energy CT scan (collimation, 128 × 0.6 mm; 120 kVp) and a dual-energy arterial phase scan (collimation, 32 × 0.6 mm, 140 and 100 kVp; blended, 120 kVp data set). Attenuation measurements in Hounsfield units (HU) of liver parenchyma and incidental findings like renal and hepatic cysts and adrenal masses on TNC and VNC images were done by drawing regions of interest. Statistical analysis was performed by paired t test and Pearson correlation. Incidental findings were detected in 56 (89%) patients. There was excellent correlation for both renal (n = 40) and hepatic cysts (n = 12) as well as adrenal masses (n = 6) with a Pearson correlation of 0.896, 0.800, and 0.945, respectively, and mean attenuation values on TNC and VNC images of 10.6 HU ± 12.8 versus 5.1 HU ± 17.5 (attenuation value range from -8.8 to 59.1 HU vs -11.8 to 73.4 HU), 6.4 HU ± 5.8 versus 6.3 HU ± 4.6 (attenuation value range from 2.0 to 16.2 HU vs -3.0 to 15.9 HU), and 12.8 HU ± 11.2 versus 12.4 HU ± 10.2 (attenuation value range from -2.3 to 27.5 HU vs -2.2 to 23.6 HU), respectively. As proof of principle, liver parenchyma measurements also showed excellent correlation between TNC and VNC (n = 40) images with a Pearson correlation of 0.839 and mean attenuation values on TNC and VNC images of 47.2 HU ± 10.5 versus 43.8 HU ± 8.7 (attenuation value range from 21.9 to 60.2 HU vs 4.5 to 65.3 HU). In conclusion, attenuation measurements of incidental findings like renal cysts or adrenal masses on TNC and VNC images derived from second generation dual-energy CT scans show excellent correlation providing considerable dose savings, favorable for future application in clinical routine.

A Comparative Analysis of 2D and 3D Tasks for Virtual Reality Therapies Based on Robotic-Assisted Neurorehabilitation for Post-stroke Patients

PubMed Central

Lledó, Luis D.; Díez, Jorge A.; Bertomeu-Motos, Arturo; Ezquerro, Santiago; Badesa, Francisco J.; Sabater-Navarro, José M.; García-Aracil, Nicolás

2016-01-01

Post-stroke neurorehabilitation based on virtual therapies are performed completing repetitive exercises shown in visual electronic devices, whose content represents imaginary or daily life tasks. Currently, there are two ways of visualization of these task. 3D virtual environments are used to get a three dimensional space that represents the real world with a high level of detail, whose realism is determinated by the resolucion and fidelity of the objects of the task. Furthermore, 2D virtual environments are used to represent the tasks with a low degree of realism using techniques of bidimensional graphics. However, the type of visualization can influence the quality of perception of the task, affecting the patient's sensorimotor performance. The purpose of this paper was to evaluate if there were differences in patterns of kinematic movements when post-stroke patients performed a reach task viewing a virtual therapeutic game with two different type of visualization of virtual environment: 2D and 3D. Nine post-stroke patients have participated in the study receiving a virtual therapy assisted by PUPArm rehabilitation robot. Horizontal movements of the upper limb were performed to complete the aim of the tasks, which consist in reaching peripheral or perspective targets depending on the virtual environment shown. Various parameter types such as the maximum speed, reaction time, path length, or initial movement are analyzed from the data acquired objectively by the robotic device to evaluate the influence of the task visualization. At the end of the study, a usability survey was provided to each patient to analysis his/her satisfaction level. For all patients, the movement trajectories were enhanced when they completed the therapy. This fact suggests that patient's motor recovery was increased. Despite of the similarity in majority of the kinematic parameters, differences in reaction time and path length were higher using the 3D task. Regarding the success rates were very similar. In conclusion, the using of 2D environments in virtual therapy may be a more appropriate and comfortable way to perform tasks for upper limb rehabilitation of post-stroke patients, in terms of accuracy in order to effectuate optimal kinematic trajectories. PMID:27616992

Two potential recombinant rabies vaccines expressing canine parvovirus virion protein 2 induce immunogenicity to canine parvovirus and rabies virus.

PubMed

Luo, Jun; Shi, Hehe; Tan, Yeping; Niu, Xuefeng; Long, Teng; Zhao, Jing; Tian, Qin; Wang, Yifei; Chen, Hao; Guo, Xiaofeng

2016-08-17

Both rabies virus (RABV) and canine parvovirus (CPV) cause lethal diseases in dogs. In this study, both high egg passage Flury (HEP-Flury) strains of RABV and recombinant RABV carrying double RABV glycoprotein (G) gene were used to express the CPV virion protein 2 (VP2) gene, and were designated rHEP-VP2 and, rHEP-dG-VP2 respectively. The two recombinant RABVs maintained optimal virus titration according to their viral growth kinetics assay compared with the parental strain HEP-Flury. Western blotting indicated that G protein and VP2 were expressed in vitro. The expression of VP2 in Crandell feline kidney cells post-infection by rHEP-VP2 and rHEP-dG-VP2 was confirmed by indirect immunofluorescence assay with antibody against VP2. Immunogenicity of recombinant rabies viruses was tested in Kunming mice. Both rHEP-VP2 and rHEP-dG-VP2 induced high levels of rabies antibody compared with HEP-Flury. Mice immunized with rHEP-VP2 and rHEP-dG-VP2 both had a high level of antibodies against VP2, which can protect against CPV infection. A challenge experiment indicated that more than 80% mice immunized with recombinant RABVs survived after infection of challenge virus standard 24 (CVS-24). Together, this study showed that recombinant RABVs expressing VP2 induced protective immune responses to RABV and CPV. Therefore, rHEP-VP2 and rHEP-dG-VP2 might be potential combined vaccines for RABV and CPV. Copyright © 2016 Elsevier Ltd. All rights reserved.

Enterovirus 71 viral capsid protein linear epitopes: Identification and characterization

PubMed Central

2012-01-01

Background To characterize the human humoral immune response against enterovirus 71 (EV71) infection and map human epitopes on the viral capsid proteins. Methods A series of 256 peptides spanning the capsid proteins (VP1, VP2, VP3) of BJ08 strain (genomic C4) were synthesized. An indirect enzyme-linked immunosorbent assay (ELISA) was carried out to detect anti-EV71 IgM and IgG in sera of infected children in acute or recovery phase. The partially overlapped peptides contained 12 amino acids and were coated in the plate as antigen (0.1 μg/μl). Sera from rabbits immunized with inactivated BJ08 virus were also used to screen the peptide panel. Results A total of 10 human anti-EV71 IgM epitopes (vp1-14 in VP1; vp2-6, 21, 40 and 50 in VP2 and vp3-10, 12, 15, 24 and 75 in VP3) were identified in acute phase sera. In contrast, only one anti-EV71 IgG epitope in VP1 (vp1-15) was identified in sera of recovery stage. Four rabbit anti-EV71 IgG epitopes (vp1-14, 31, 54 and 71) were identified and mapped to VP1. Conclusion These data suggested that human IgM epitopes were mainly mapped to VP2 and VP3 with multi-epitope responses occurred at acute infection, while the only IgG epitope located on protein VP1 was activated in recovery phase sera. The dynamic changes of humoral immune response at different stages of infection may have public health significance in evaluation of EV71 vaccine immunogenicity and the clinical application of diagnostic reagents. PMID:22264266

The organization of orientation selectivity throughout macaque visual cortex.

PubMed

Vanduffel, Wim; Tootell, Roger B H; Schoups, Aniek A; Orban, Guy A

2002-06-01

A double-label deoxyglucose technique was used to study orientation columns throughout visual cortex in awake behaving macaques. Four macaques were trained to fixate while contrastreversing, stationary gratings or one-dimensional noise of a single orientation or an orthogonal orientation were presented, during uptake of [14C]deoxyglucose ([14C]DG) or [3H]DG, respectively. The two orthogonal stimulus orientations produced DG-labeled columns that were maximally separated in the two isotope maps (inter-digitated) in four areas: V1, V2, V3 and VP. The topographic change from interdigitated to overlapping columns occurred abruptly rather than gradually, at corresponding cortical area borders (e.g. VP and V4v, respectively). In addition, the data suggest that orientation column topography systematically changes with retinotopic eccentricity. In V1, the orientation columns systematically avoided the cytochrome oxidase blobs in the parafoveal representation, but converged closer to the blobs in the foveal representation. A control experiment indicated that this was unlikely to reflect eccentricity-dependent differences in cortical spatial frequency sensitivity. A similar eccentricity-dependent change in the topography of orientation columns occurred in V2. In parafoveal but not foveal visual field representations of V2, the orientation columns were centered on the thick cytochrome oxidase stripes, extended into the adjacent interstripe region, but were virtually absent in the thin stripes.

Updates on the Studies of $${\\varvec{N}}^\\mathbf{*}$$ N * Structure with CLAS and the Prospects with CLAS12

DOE PAGES

Mokeev, V. I.

2016-06-16

Here, the recent results onmore » $$\\gamma_vpN^*$$ electrocouplings from analyses of the data on exclusive meson electroproduction off protons measured with the CLAS detector at Jefferson Lab are presented. The impact of these results on the exploration of the excited nucleon state structure and non-perturbative strong interaction dynamics behind its formation is outlined. The future extension of these studies in the experiments with the CLAS12 detector in the upgraded Hall-B at JLab will provide for the first time $$\\gamma_vpN^*$$ electrocouplings of all prominent resonances at the still unexplored distance scales that correspond to extremely low (0.05~GeV$^2 < Q^2 <$ 0.5~GeV$^2$) and the highest photon virtualities (5.0~GeV$^2 < Q^2 <$ 12.0~GeV$^2$) ever achieved in the exclusive electroproduction measurements. The expected results will address the most important open problems of the Standard Model: on the nature of more than 98\\% of hadron mass, quark-gluon confinement and emergence of the excited nucleon state structure from the QCD Lagrangian, as well as allowing a search for the new states of hadron matter predicted from the first principles of QCD, the so-called hybrid baryons.« less

Updates on the Studies of {\\varvec{N}}^* Structure with CLAS and the Prospects with CLAS12

NASA Astrophysics Data System (ADS)

Mokeev, V. I.

2016-10-01

The recent results on γ _vpN^* electrocouplings from analyses of the data on exclusive meson electroproduction off protons measured with the CLAS detector at Jefferson Lab are presented. The impact of these results on the exploration of the excited nucleon state structure and non-perturbative strong interaction dynamics behind its formation is outlined. The future extension of these studies in the experiments with the CLAS12 detector in the upgraded Hall-B at JLab will provide for the first time γ _vpN^* electrocouplings of all prominent resonances at the still unexplored distance scales that correspond to extremely low (0.05 GeV^2 < Q^2< 0.5 GeV^2) and the highest photon virtualities (5.0 GeV^2 < Q^2< 12.0 GeV^2) ever achieved in the exclusive electroproduction measurements. The expected results will address the most important open problems of the Standard Model: on the nature of more than 98 % of hadron mass, quark-gluon confinement and emergence of the excited nucleon state structure from the QCD Lagrangian, as well as allowing a search for the new states of hadron matter predicted from the first principles of QCD, the so-called hybrid baryons.

Overexpression of VpEIFP1, a novel F-box/Kelch-repeat protein from wild Chinese Vitis pseudoreticulata, confers higher tolerance to powdery mildew by inducing thioredoxin z proteolysis.

PubMed

Wang, Jie; Yao, Wenkong; Wang, Lei; Ma, Fuli; Tong, Weihuo; Wang, Chen; Bao, Rui; Jiang, Changyue; Yang, Yazhou; Zhang, Jianxia; Xu, Yan; Wang, Xiping; Zhang, Chaohong; Wang, Yuejin

2017-10-01

An F-box protein (VpEIFP1) induced by Erysiphe necator was isolated from Vitis pseudoreticulata, a wild Chinese grapevine species naturally resistant to powdery mildew (PM). It contains an F-box domain and two Kelch-repeat motifs. Expression profiles indicate the VpEIFP1 is strongly induced at both transcriptional and translational levels by PM infection. A subcellular localisation assay showed that VpEIFP1 is predominantly located in the nucleus and cytoplasm. Overexpression of VpEIFP1 accelerated the accumulation of hydrogen peroxide (H 2 O 2 ) and up-regulated the expressions of ICS2, NPR1 and PR1 involved in defence responses, resulting in suppression of PM germination and growth. As an F-box protein, VpEIFP1 interacts with thioredoxin z (VpTrxz) in the yeast-two-hybrid (Y2H) assay and in the bimolecular fluorescence complementation (BiFC) assay. Decreased amounts of VpTrxz protein in transgenic grapevine leaves overexpressing VpEIFP1 were restored by proteasome inhibitor MG132, implying that VpEIFP1 mediated VpTrxz for degradation through the SCF VpEIFP1 (Skp1-Cullin-F-box) E3 ubiquitin ligase complex. The RNA interference line of VpTrxz showed increased H 2 O 2 accumulation following PM inoculation. We propose VpEIFP1 positively modulates the grapevine defence response to PM by inducing the degradation of VpTrxz via the ubiquitin/26S proteasome system. Copyright © 2017 Elsevier B.V. All rights reserved.

The immunogenicity of recombinant vaccines based on modified Vaccinia Ankara (MVA) viruses expressing African horse sickness virus VP2 antigens depends on the levels of expressed VP2 protein delivered to the host.

PubMed

Calvo-Pinilla, Eva; Gubbins, Simon; Mertens, Peter; Ortego, Javier; Castillo-Olivares, Javier

2018-06-01

African horse sickness (AHS) is a lethal equine disease transmitted by Culicoides biting midges and caused by African horse sickness virus (AHSV). AHS is endemic to sub-Saharan Africa, but devastating outbreaks have been recorded periodically outside this region. The perceived risk of an AHS outbreak occurring in Europe has increased following the frequent epidemics caused in ruminants by bluetongue virus, closely related to AHSV. Attenuated vaccines for AHS are considered unsuitable for use in non-endemic countries due bio-safety concerns. Further, attenuated and inactivated vaccines are not compatible with DIVA (differentiate infected from vaccinated animals) strategies. All these factors stimulated the development of novel AHS vaccines that are safer, more efficacious and DIVA compatible. We showed previously that recombinant modified Vaccinia Ankara virus (MVA) vaccines encoding the outer capsid protein of AHSV (AHSV-VP2) induced virus neutralising antibodies (VNAb) and protection against AHSV in a mouse model and also in the horse. Passive immunisation studies demonstrated that immunity induced by MVA-VP2 was associated with pre-challenge VNAb titres in the vaccinates. Analyses of the inoculum of these MVA-VP2 experimental vaccines showed that they contained pre-formed AHSV-VP2. We continued studying the influence of pre-formed AHSV-VP2, present in the inoculum of MVA-VP2 vaccines, in the immunogenicity of MVA-VP2 vaccines. Thus, we compared correlates of immunity in challenged mice that were previously vaccinated with: a) MVA-VP2 (live); b) MVA-VP2 (live and sucrose gradient purified); c) MVA-VP2 (UV light inactivated); d) MVA-VP2 (UV light inactivated and diluted); e) MVA-VP2 (heat inactivated); f) MVA-VP2 (UV inactivated) + MVA-VP2 (purified); g) MVA-VP2 (heat inactivated) + MVA-VP2 (purified); and h) wild type-MVA (no insert). The results of these experiments showed that protection was maximal using MVA-VP2 (live) vaccine and that the protection conferred by all other vaccines correlated strongly with the levels of pre-formed AHSV-VP2 in the vaccine inoculum. Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.

Proteomic analysis reveals differential accumulation of small heat shock proteins and late embryogenesis abundant proteins between ABA-deficient mutant vp5 seeds and wild-type Vp5 seeds in maize

PubMed Central

Wu, Xiaolin; Gong, Fangping; Yang, Le; Hu, Xiuli; Tai, Fuju; Wang, Wei

2014-01-01

ABA is a major plant hormone that plays important roles during many phases of plant life cycle, including seed development, maturity and dormancy, and especially the acquisition of desiccation tolerance. Understanding of the molecular basis of ABA-mediated plant response to stress is of interest not only in basic research on plant adaptation but also in applied research on plant productivity. Maize mutant viviparous-5 (vp5), deficient in ABA biosynthesis in seeds, is a useful material for studying ABA-mediated response in maize. Due to carotenoid deficiency, vp5 endosperm is white, compared to yellow Vp5 endosperm. However, the background difference at proteome level between vp5 and Vp5 seeds is unclear. This study aimed to characterize proteome alterations of maize vp5 seeds and to identify ABA-dependent proteins during seed maturation. We compared the embryo and endosperm proteomes of vp5 and Vp5 seeds by gel-based proteomics. Up to 46 protein spots, most in embryos, were found to be differentially accumulated between vp5 and Vp5. The identified proteins included small heat shock proteins (sHSPs), late embryogenesis abundant (LEA) proteins, stress proteins, storage proteins and enzymes among others. However, EMB564, the most abundant LEA protein in maize embryo, accumulated in comparable levels between vp5 and Vp5 embryos, which contrasted to previously characterized, greatly lowered expression of emb564 mRNA in vp5 embryos. Moreover, LEA proteins and sHSPs displayed differential accumulations in vp5 embryos: six out of eight identified LEA proteins decreased while nine sHSPs increased in abundance. Finally, we discussed the possible causes of global proteome alterations, especially the observed differential accumulation of identified LEA proteins and sHSPs in vp5 embryos. The data derived from this study provides new insight into ABA-dependent proteins and ABA-mediated response during maize seed maturation. PMID:25653661

Clinical reasoning in nursing, a think-aloud study using virtual patients - a base for an innovative assessment.

PubMed

Forsberg, Elenita; Ziegert, Kristina; Hult, Håkan; Fors, Uno

2014-04-01

In health-care education, it is important to assess the competencies that are essential for the professional role. To develop clinical reasoning skills is crucial for nursing practice and therefore an important learning outcome in nursing education programmes. Virtual patients (VPs) are interactive computer simulations of real-life clinical scenarios and have been suggested for use not only for learning, but also for assessment of clinical reasoning. The aim of this study was to investigate how experienced paediatric nurses reason regarding complex VP cases and how they make clinical decisions. The study was also aimed to give information about possible issues that should be assessed in clinical reasoning exams for post-graduate students in diploma specialist paediatric nursing education. The information from this study is believed to be of high value when developing scoring and grading models for a VP-based examination for the specialist diploma in paediatric nursing education. Using the think-aloud method, data were collected from 30 RNs working in Swedish paediatric departments, and child or school health-care centres. Content analysis was used to analyse the data. The results indicate that experienced nurses try to consolidate their hypotheses by seeing a pattern and judging the value of signs, symptoms, physical examinations, laboratory tests and radiology. They show high specific competence but earlier experience of similar cases was also of importance for the decision making. The nurses thought it was an innovative assessment focusing on clinical reasoning and clinical decision making. They thought it was an enjoyable way to be assessed and that all three main issues could be assessed using VPs. In conclusion, VPs seem to be a possible model for assessing the clinical reasoning process and clinical decision making, but how to score and grade such exams needs further research. © 2013.

From planes to brains: parallels between military development of virtual reality environments and virtual neurological surgery.

PubMed

Schmitt, Paul J; Agarwal, Nitin; Prestigiacomo, Charles J

2012-01-01

Military explorations of the practical role of simulators have served as a driving force for much of the virtual reality technology that we have today. The evolution of 3-dimensional and virtual environments from the early flight simulators used during World War II to the sophisticated training simulators in the modern military followed a path that virtual surgical and neurosurgical devices have already begun to parallel. By understanding the evolution of military simulators as well as comparing and contrasting that evolution with current and future surgical simulators, it may be possible to expedite the development of appropriate devices and establish their validity as effective training tools. As such, this article presents a historical perspective examining the progression of neurosurgical simulators, the establishment of effective and appropriate curricula for using them, and the contributions that the military has made during the ongoing maturation of this exciting treatment and training modality. Copyright © 2012. Published by Elsevier Inc.

System and method for multi-stage bypass, low operating temperature suppressor for automatic weapons

DOEpatents

Moss, William C.; Anderson, Andrew T.

2015-06-09

The present disclosure relates to a suppressor for use with a weapon. The suppressor may be formed to have a body portion having a bore extending concentric with a bore axis of the weapon barrel. An opening in the bore extends at least substantially circumferentially around the bore. A flow path communicates with the opening and defines a channel for redirecting gasses flowing in the bore out from the bore, through the opening, into a rearward direction in the flow path. The flow path raises a pressure at the opening to generate a Mach disk within the bore at a location approximately coincident with the opening. The Mach disk forms as a virtual baffle to divert at least a portion of the gasses into the opening and into the flow path.

Dynamic Phosphorylation of VP30 Is Essential for Ebola Virus Life Cycle.

PubMed

Biedenkopf, Nadine; Lier, Clemens; Becker, Stephan

2016-05-15

Ebola virus is the causative agent of a severe fever with high fatality rates in humans and nonhuman primates. The regulation of Ebola virus transcription and replication currently is not well understood. An important factor regulating viral transcription is VP30, an Ebola virus-specific transcription factor associated with the viral nucleocapsid. Previous studies revealed that the phosphorylation status of VP30 impacts viral transcription. Together with NP, L, and the polymerase cofactor VP35, nonphosphorylated VP30 supports viral transcription. Upon VP30 phosphorylation, viral transcription ceases. Phosphorylation weakens the interaction between VP30 and the polymerase cofactor VP35 and/or the viral RNA. VP30 thereby is excluded from the viral transcription complex, simultaneously leading to increased viral replication which is supported by NP, L, and VP35 alone. Here, we use an infectious virus-like particle assay and recombinant viruses to show that the dynamic phosphorylation of VP30 is critical for the cotransport of VP30 with nucleocapsids to the sites of viral RNA synthesis, where VP30 is required to initiate primary viral transcription. We further demonstrate that a single serine residue at amino acid position 29 was sufficient to render VP30 active in primary transcription and to generate a recombinant virus with characteristics comparable to those of wild-type virus. In contrast, the rescue of a recombinant virus with a single serine at position 30 in VP30 was unsuccessful. Our results indicate critical roles for phosphorylated and dephosphorylated VP30 during the viral life cycle. The current Ebola virus outbreak in West Africa has caused more than 28,000 cases and 11,000 fatalities. Very little is known regarding the molecular mechanisms of how the Ebola virus transcribes and replicates its genome. Previous investigations showed that the transcriptional support activity of VP30 is activated upon VP30 dephosphorylation. The current study reveals that the situation is more complex and that primary transcription as well as the rescue of recombinant Ebola virus also requires the transient phosphorylation of VP30. VP30 encodes six N-proximal serine residues that serve as phosphorylation acceptor sites. The present study shows that the dynamic phosphorylation of serine at position 29 alone is sufficient to activate primary viral transcription. Our results indicate a series of phosphorylation/dephosphorylation events that trigger binding to and release from the nucleocapsid and transcription complex to be essential for the full activity of VP30. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Sexual dimorphism of human vallate papillae: an in vivo study of normative morphology.

PubMed

Zdilla, M J; Gibson, L N; Hunt, A J

2015-01-01

The perimeters of vallate papillae (VP) house approximately half of the taste buds on the human tongue. However, little information exists regarding perimeter measurements of VP. Likewise, great diversity exists among reports of the number of VP and diameter of VP, in general. The research presents an analysis of the perimeters, counts, and diameters of VP in vivo. Endoscopic examination was performed on 79 individuals (40 females, 39 males) between 18 and 26 years of age. A total of 583 VP were counted, 565 of which were able to be measured. Data revealed a statistically significant difference between male and female VP count (t(75.6) = 4.5; p = 0.00003). Females had, on average, 2.22 more VP than males. Males were found to have larger mean VP diameter per person and mean VP perimeter per person than females (t(58.9) = -2.4; p = 0.021 and t(59.3) = -2.4; p = 0.019, respectively). The report demonstrates that VP are sexually dimorphic at the gross anatomical level.

Independent segregation of two antigenic specificities (VP3 and VP7) involved in neutralization of rotavirus infectivity.

PubMed Central

Hoshino, Y; Sereno, M M; Midthun, K; Flores, J; Kapikian, A Z; Chanock, R M

1985-01-01

Antiserum prepared against the M37 strain of rotavirus, recovered from an asymptomatic newborn infant in Venezuela, neutralized two prototype human rotaviruses that define two separate serotypes: serotype 1 (Wa) and serotype 4 (ST3). Thus, the M37 strain is a naturally occurring intertypic rotavirus. Analysis of reassortant viruses produced during coinfection in vitro indicated that the observed dual serotype specificity of M37 resulted from sharing a related outer capsid protein, VP3, with the ST3 virus and another related outer capsid protein, VP7, with the Wa virus. Analysis of single (VP3)-gene-substitution reassortants indicated that VP3 was as potent an immunogen as VP7. In addition, direct evidence was obtained that the serotype specificity of neutralizing antibody elicited by VP3 can differ from the serotype specificity of neutralizing antibody elicited by VP7, indicating the need for a dual system of rotavirus classification in which the neutralization specificity of both VP3 and VP7 outer capsid proteins are identified. Images PMID:3001716

Remote sensing measurements of sea surface temperature as an indicator of Vibrio parahaemolyticus in oyster meat and human illnesses.

PubMed

Konrad, Stephanie; Paduraru, Peggy; Romero-Barrios, Pablo; Henderson, Sarah B; Galanis, Eleni

2017-08-31

Vibrio parahaemolyticus (Vp) is a naturally occurring bacterium found in marine environments worldwide. It can cause gastrointestinal illness in humans, primarily through raw oyster consumption. Water temperatures, and potentially other environmental factors, play an important role in the growth and proliferation of Vp in the environment. Quantifying the relationships between environmental variables and indicators or incidence of Vp illness is valuable for public health surveillance to inform and enable suitable preventative measures. This study aimed to assess the relationship between environmental parameters and Vp in British Columbia (BC), Canada. The study used Vp counts in oyster meat from 2002-2015 and laboratory confirmed Vp illnesses from 2011-2015 for the province of BC. The data were matched to environmental parameters from publicly available sources, including remote sensing measurements of nighttime sea surface temperature (SST) obtained from satellite readings at a spatial resolution of 1 km. Using three separate models, this paper assessed the relationship between (1) daily SST and Vp counts in oyster meat, (2) weekly mean Vp counts in oysters and weekly Vp illnesses, and (3) weekly mean SST and weekly Vp illnesses. The effects of salinity and chlorophyll a were also evaluated. Linear regression was used to quantify the relationship between SST and Vp, and piecewise regression was used to identify SST thresholds of concern. A total of 2327 oyster samples and 293 laboratory confirmed illnesses were included. In model 1, both SST and salinity were significant predictors of log(Vp) counts in oyster meat. In model 2, the mean log(Vp) count in oyster meat was a significant predictor of Vp illnesses. In model 3, weekly mean SST was a significant predictor of weekly Vp illnesses. The piecewise regression models identified a SST threshold of approximately 14 o C for both model 1 and 3, indicating increased risk of Vp in oyster meat and Vp illnesses at higher temperatures. Monitoring of SST, particularly through readily accessible remote sensing data, could serve as a warning signal for Vp and help inform the introduction and cessation of preventative or control measures.

Expression of goose parvovirus whole VP3 protein and its epitopes in Escherichia coli cells.

PubMed

Tarasiuk, K; Woźniakowski, G; Holec-Gąsior, L

2015-01-01

The aim of this study was the expression of goose parvovirus capsid protein (VP3) and its epitopes in Escherichia coli cells. Expression of the whole VP3 protein provided an insufficient amount of protein. In contrast, the expression of two VP3 epitopes (VP3ep4, VP3ep6) in E. coli, resulted in very high expression levels. This may suggest that smaller parts of the GPV antigenic determinants are more efficiently expressed than the complete VP3 gene.

An optimization method of VON mapping for energy efficiency and routing in elastic optical networks

NASA Astrophysics Data System (ADS)

Liu, Huanlin; Xiong, Cuilian; Chen, Yong; Li, Changping; Chen, Derun

2018-03-01

To improve resources utilization efficiency, network virtualization in elastic optical networks has been developed by sharing the same physical network for difference users and applications. In the process of virtual nodes mapping, longer paths between physical nodes will consume more spectrum resources and energy. To address the problem, we propose a virtual optical network mapping algorithm called genetic multi-objective optimize virtual optical network mapping algorithm (GM-OVONM-AL), which jointly optimizes the energy consumption and spectrum resources consumption in the process of virtual optical network mapping. Firstly, a vector function is proposed to balance the energy consumption and spectrum resources by optimizing population classification and crowding distance sorting. Then, an adaptive crossover operator based on hierarchical comparison is proposed to improve search ability and convergence speed. In addition, the principle of the survival of the fittest is introduced to select better individual according to the relationship of domination rank. Compared with the spectrum consecutiveness-opaque virtual optical network mapping-algorithm and baseline-opaque virtual optical network mapping algorithm, simulation results show the proposed GM-OVONM-AL can achieve the lowest bandwidth blocking probability and save the energy consumption.

Ecological validity of virtual environments to assess human navigation ability

PubMed Central

van der Ham, Ineke J. M.; Faber, Annemarie M. E.; Venselaar, Matthijs; van Kreveld, Marc J.; Löffler, Maarten

2015-01-01

Route memory is frequently assessed in virtual environments. These environments can be presented in a fully controlled manner and are easy to use. Yet they lack the physical involvement that participants have when navigating real environments. For some aspects of route memory this may result in reduced performance in virtual environments. We assessed route memory performance in four different environments: real, virtual, virtual with directional information (compass), and hybrid. In the hybrid environment, participants walked the route outside on an open field, while all route information (i.e., path, landmarks) was shown simultaneously on a handheld tablet computer. Results indicate that performance in the real life environment was better than in the virtual conditions for tasks relying on survey knowledge, like pointing to start and end point, and map drawing. Performance in the hybrid condition however, hardly differed from real life performance. Performance in the virtual environment did not benefit from directional information. Given these findings, the hybrid condition may offer the best of both worlds: the performance level is comparable to that of real life for route memory, yet it offers full control of visual input during route learning. PMID:26074831

A sensor network based virtual beam-like structure method for fault diagnosis and monitoring of complex structures with Improved Bacterial Optimization

NASA Astrophysics Data System (ADS)

Wang, H.; Jing, X. J.

2017-02-01

This paper proposes a novel method for the fault diagnosis of complex structures based on an optimized virtual beam-like structure approach. A complex structure can be regarded as a combination of numerous virtual beam-like structures considering the vibration transmission path from vibration sources to each sensor. The structural 'virtual beam' consists of a sensor chain automatically obtained by an Improved Bacterial Optimization Algorithm (IBOA). The biologically inspired optimization method (i.e. IBOA) is proposed for solving the discrete optimization problem associated with the selection of the optimal virtual beam for fault diagnosis. This novel virtual beam-like-structure approach needs less or little prior knowledge. Neither does it require stationary response data, nor is it confined to a specific structure design. It is easy to implement within a sensor network attached to the monitored structure. The proposed fault diagnosis method has been tested on the detection of loosening screws located at varying positions in a real satellite-like model. Compared with empirical methods, the proposed virtual beam-like structure method has proved to be very effective and more reliable for fault localization.

Folding units in calcium vector protein of amphioxus: Structural and functional properties of its amino- and carboxy-terminal halves.

PubMed

Baladi, S; Tsvetkov, P O; Petrova, T V; Takagi, T; Sakamoto, H; Lobachov, V M; Makarov, A A; Cox, J A

2001-04-01

Muscle of amphioxus contains large amounts of a four EF-hand Ca2+-binding protein, CaVP, and its target, CaVPT. To study the domain structure of CaVP and assess the structurally important determinants for its interaction with CaVPT, we expressed CaVP and its amino (N-CaVP) and carboxy-terminal halves (C-CaVP). The interactive properties of recombinant and wild-type CaVP are very similar, despite three post-translational modifications in the wild-type protein. N-CaVP does not bind Ca2+, shows a well-formed hydrophobic core, and melts at 44 degrees C. C-CaVP binds two Ca2+ with intrinsic dissociation constants of 0.22 and 140 microM (i.e., very similar to the entire CaVP). The metal-free domain in CaVP and C-CaVP shows no distinct melting transition, whereas its 1Ca2+ and 2Ca2+) forms melt in the 111 degrees -123 degrees C range, suggesting that C-CaVP and the carboxy- domain of CaVP are natively unfolded in the metal-free state and progressively gain structure upon binding of 1Ca2+ and 2Ca2+. Thermal denaturation studies provide evidence for interdomain interaction: the apo, 1Ca2+ and 2Ca2+ states of the carboxy-domain destabilize to different degrees the amino-domain. Only C-CaVP forms a Ca2+-dependent 1:1 complex with CaVPT. Our results suggest that the carboxy-terminal domain of CaVP interacts with CaVPT and that the amino-terminal lobe modulates this interaction.

Folding units in calcium vector protein of amphioxus: Structural and functional properties of its amino- and carboxy-terminal halves

PubMed Central

Baladi, Sibyl; Tsvetkov, Philipp O.; Petrova, Tatiana V.; Takagi, Takashi; Sakamoto, Hiroshi; Lobachov, Vladimir M.; Makarov, Alexander A.; Cox, Jos A.

2001-01-01

Muscle of amphioxus contains large amounts of a four EF-hand Ca2+-binding protein, CaVP, and its target, CaVPT. To study the domain structure of CaVP and assess the structurally important determinants for its interaction with CaVPT, we expressed CaVP and its amino (N-CaVP) and carboxy-terminal halves (C-CaVP). The interactive properties of recombinant and wild-type CaVP are very similar, despite three post-translational modifications in the wild-type protein. N-CaVP does not bind Ca2+, shows a well-formed hydrophobic core, and melts at 44°C. C-CaVP binds two Ca2+ with intrinsic dissociation constants of 0.22 and 140 μM (i.e., very similar to the entire CaVP). The metal-free domain in CaVP and C-CaVP shows no distinct melting transition, whereas its 1Ca2+ and 2Ca2+ forms melt in the 111°–123°C range, suggesting that C-CaVP and the carboxy- domain of CaVP are natively unfolded in the metal-free state and progressively gain structure upon binding of 1Ca2+ and 2Ca2+. Thermal denaturation studies provide evidence for interdomain interaction: the apo, 1Ca2+ and 2Ca2+ states of the carboxy-domain destabilize to different degrees the amino-domain. Only C-CaVP forms a Ca2+-dependent 1:1 complex with CaVPT. Our results suggest that the carboxy-terminal domain of CaVP interacts with CaVPT and that the amino-terminal lobe modulates this interaction. PMID:11274468

Crystal Structures of Yellowtail Ascites Virus VP4 Protease

PubMed Central

Chung, Ivy Yeuk Wah; Paetzel, Mark

2013-01-01

Yellowtail ascites virus (YAV) is an aquabirnavirus that causes ascites in yellowtail, a fish often used in sushi. Segment A of the YAV genome codes for a polyprotein (pVP2-VP4-VP3), where processing by its own VP4 protease yields the capsid protein precursor pVP2, the ribonucleoprotein-forming VP3, and free VP4. VP4 protease utilizes the rarely observed serine-lysine catalytic dyad mechanism. Here we have confirmed the existence of an internal cleavage site, preceding the VP4/VP3 cleavage site. The resulting C-terminally truncated enzyme (ending at Ala716) is active, as shown by a trans full-length VP4 cleavage assay and a fluorometric peptide cleavage assay. We present a crystal structure of a native active site YAV VP4 with the internal cleavage site trapped as trans product complexes and trans acyl-enzyme complexes. The acyl-enzyme complexes confirm directly the role of Ser633 as the nucleophile. A crystal structure of the lysine general base mutant (K674A) reveals the acyl-enzyme and empty binding site states of VP4, which allows for the observation of structural changes upon substrate or product binding. These snapshots of three different stages in the VP4 protease reaction mechanism will aid in the design of anti-birnavirus compounds, provide insight into previous site-directed mutagenesis results, and contribute to understanding of the serine-lysine dyad protease mechanism. In addition, we have discovered that this protease contains a channel that leads from the enzyme surface (adjacent to the substrate binding groove) to the active site and the deacylating water. PMID:23511637

Crystal structures of yellowtail ascites virus VP4 protease: trapping an internal cleavage site trans acyl-enzyme complex in a native Ser/Lys dyad active site.

PubMed

Chung, Ivy Yeuk Wah; Paetzel, Mark

2013-05-03

Yellowtail ascites virus (YAV) is an aquabirnavirus that causes ascites in yellowtail, a fish often used in sushi. Segment A of the YAV genome codes for a polyprotein (pVP2-VP4-VP3), where processing by its own VP4 protease yields the capsid protein precursor pVP2, the ribonucleoprotein-forming VP3, and free VP4. VP4 protease utilizes the rarely observed serine-lysine catalytic dyad mechanism. Here we have confirmed the existence of an internal cleavage site, preceding the VP4/VP3 cleavage site. The resulting C-terminally truncated enzyme (ending at Ala(716)) is active, as shown by a trans full-length VP4 cleavage assay and a fluorometric peptide cleavage assay. We present a crystal structure of a native active site YAV VP4 with the internal cleavage site trapped as trans product complexes and trans acyl-enzyme complexes. The acyl-enzyme complexes confirm directly the role of Ser(633) as the nucleophile. A crystal structure of the lysine general base mutant (K674A) reveals the acyl-enzyme and empty binding site states of VP4, which allows for the observation of structural changes upon substrate or product binding. These snapshots of three different stages in the VP4 protease reaction mechanism will aid in the design of anti-birnavirus compounds, provide insight into previous site-directed mutagenesis results, and contribute to understanding of the serine-lysine dyad protease mechanism. In addition, we have discovered that this protease contains a channel that leads from the enzyme surface (adjacent to the substrate binding groove) to the active site and the deacylating water.

Tandem truncated rotavirus VP8* subunit protein with T cell epitope as non-replicating parenteral vaccine is highly immunogenic.

PubMed

Wen, Xiaobo; Cao, Dianjun; Jones, Ronald W; Hoshino, Yasutaka; Yuan, Lijuan

2015-01-01

The two currently available live oral rotavirus vaccines, Rotarix(®) and RotaTeq(®), are highly efficacious in the developed countries. However, the efficacy of such vaccines in resource deprived countries in Africa and Southeast Asia is low. We reported previously that a bacterially-expressed rotavirus P2-P[8] ΔVP8* subunit vaccine candidate administered intramuscularly elicited high-titers of neutralizing antibodies in guinea pigs and mice and significantly shortened the duration of diarrhea in neonatal gnotobiotic pigs upon oral challenge with virulent human rotavirus Wa strain. To further improve its vaccine potential and provide wider coverage against rotavirus strains of global and regional epidemiologic importance, we constructed 2 tandem recombinant VP8* proteins, P2-P[8] ΔVP8*-P[8] ΔVP8* and P2-P[8] ΔVP8*-P[6] ΔVP8* based on Escherichia coli expression system. The two resulting recombinant tandem proteins were highly soluble and P2-P[8] ΔVP8*-P[8] ΔVP8* was generated with high yield. Moreover, guinea pigs immunized intramuscularly by 3 doses of the P2-P[8] ΔVP8*-P[8] ΔVP8* or P2-P[8] ΔVP8*-P[6] ΔVP8* vaccine with aluminum phosphate adjuvant developed high titers of homotypic and heterotypic neutralizing antibodies against human rotaviruses bearing G1-G4, G8, G9 and G12 with P[8], P[4] or P[6] combination. The results suggest that these 2 subunit vaccines in monovalent or bivalent formulation can provide antigenic coverage to almost all the rotavirus G (VP7) types and major P (VP4) types of global as well as regional epidemiologic importance.

Molecular basis for ebolavirus VP35 suppression of human dendritic cell maturation.

PubMed

Yen, Benjamin; Mulder, Lubbertus C F; Martinez, Osvaldo; Basler, Christopher F

2014-11-01

Zaire ebolavirus (EBOV) VP35 is a double-stranded RNA (dsRNA)-binding protein that inhibits RIG-I signaling and alpha/beta interferon (IFN-α/β) responses by both dsRNA-binding-dependent and -independent mechanisms. VP35 also suppresses dendritic cell (DC) maturation. Here, we define the pathways and mechanisms through which VP35 impairs DC maturation. Wild-type VP35 (VP35-WT) and two well-characterized VP35 mutants (F239A and R322A) that independently ablate dsRNA binding and RIG-I inhibition were delivered to primary human monocyte-derived DCs (MDDCs) using a lentivirus-based expression system. VP35-WT suppressed not only IFN-α/β but also proinflammatory responses following stimulation of MDDCs with activators of RIG-I-like receptor (RLR) signaling, including RIG-I activators such as Sendai virus (SeV) or 5'-triphosphate RNA, or MDA5 activators such as encephalomyocarditis virus (EMCV) or poly(I · C). The F239A and R322A mutants exhibited greatly reduced suppression of IFN-α/β and proinflammatory cytokine production following treatment of DCs with RLR agonists. VP35-WT also blocked the upregulation of DC maturation markers and the stimulation of allogeneic T cell responses upon SeV infection, whereas the mutants did not. In contrast to the RLR activators, VP35-WT and the VP35 mutants impaired IFN-β production induced by Toll-like receptor 3 (TLR3) or TLR4 agonists but failed to inhibit proinflammatory cytokine production induced by TLR2, TLR3, or TLR4 agonists. Furthermore, VP35 did not prevent lipopolysaccharide (LPS)-induced upregulation of surface markers of MDDC maturation and did not prevent LPS-triggered allogeneic T cell stimulation. Therefore, VP35 is a general antagonist of DC responses to RLR activation. However, TLR agonists can circumvent many of the inhibitory effects of VP35. Therefore, it may be possible to counteract EBOV immune evasion by using treatments that bypass the VP35-imposed block to DC maturation. The VP35 protein, which is an inhibitor of RIG-I signaling and alpha/beta interferon (IFN-α/β) responses, has been implicated as an EBOV-encoded factor that contributes to suppression of dendritic cell (DC) function. We used wild-type VP35 and previously characterized VP35 mutants to clarify VP35-DC interactions. Our data demonstrate that VP35 is a general inhibitor of RIG-I-like receptor (RLR) signaling that blocks not only RIG-I- but also MDA5-mediated induction of IFN-α/β responses. Furthermore, in DCs, VP35 also impairs the RLR-mediated induction of proinflammatory cytokine production, upregulation of costimulatory markers, and activation of T cells. These inhibitory activities require VP35 dsRNA-binding activity, an activity previously correlated to VP35 RIG-I inhibitory function. In contrast, while VP35 can inhibit IFN-α/β production induced by TLR3 or TLR4 agonists, this occurs in a dsRNA-independent fashion, and VP35 does not inhibit TLR-mediated expression of proinflammatory cytokines. These data suggest strategies to overcome VP35 inhibition of DC function. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Structures of Rotavirus Reassortants Demonstrate Correlation of Altered Conformation of the VP4 Spike and Expression of Unexpected VP4-Associated Phenotypes

PubMed Central

Pesavento, Joseph B.; Billingsley, Angela M.; Roberts, Ed J.; Ramig, Robert F.; Prasad, B. V. Venkataram

2003-01-01

Numerous prior studies have indicated that viable rotavirus reassortants containing structural proteins of heterologous parental origin may express unexpected phenotypes, such as changes in infectivity and immunogenicity. To provide a structural basis for alterations in phenotypic expression, a three-dimensional structural analysis of these reassortants was conducted. The structures of the reassortants show that while VP4 generally maintains the parental structure when moved to a heterologous protein background, in certain reassortants, there are subtle alterations in the conformation of VP4. The alterations in VP4 conformation correlated with expression of unexpected VP4-associated phenotypes. Interactions between heterologous VP4 and VP7 in reassortants expressing unexpected phenotypes appeared to induce the conformational alterations seen in VP4. PMID:12584352

Effects of community-based virtual reality treadmill training on balance ability in patients with chronic stroke.

PubMed

Kim, Nara; Park, YuHyung; Lee, Byoung-Hee

2015-03-01

[Purpose] We aimed to examine the effectiveness of a community-based virtual reality treadmill training (CVRTT) program on static balance abilities in patients with stroke. [Subjects and Methods] Patients (n = 20) who suffered a stroke at least 6 months prior to the study were recruited. All subjects underwent conventional physical therapy for 60 min/day, 5 days/week, for 4 weeks. Additionally, the CVRTT group underwent community-based virtual reality scene exposure combined with treadmill training for 30 min/day, 3 days/week, for 4 weeks, whereas the control group underwent conventional physical therapy, including muscle strengthening, balance training, and indoor and outdoor gait training, for 30 min/day, 3 days/week, for 4 weeks. Outcome measurements included the anteroposterior, mediolateral, and total postural sway path lengths and speed, which were recorded using the Balancia Software on a Wii Fit(™) balance board. [Results] The postural sway speed and anteroposterior and total postural sway path lengths were significantly decreased in the CVRTT group. Overall, the CVRTT group showed significantly greater improvement than the control group. [Conclusions] The present study results can be used to support the use of CVRTT for effectively improving balance in stroke patients. Moreover, we determined that a CVRTT program for stroke patients is both feasible and suitable.

Ubiquitin Ligase WWP1 Interacts with Ebola Virus VP40 To Regulate Egress.

PubMed

Han, Ziying; Sagum, Cari A; Takizawa, Fumio; Ruthel, Gordon; Berry, Corbett T; Kong, Jing; Sunyer, J Oriol; Freedman, Bruce D; Bedford, Mark T; Sidhu, Sachdev S; Sudol, Marius; Harty, Ronald N

2017-10-15

Ebola virus (EBOV) is a member of the Filoviridae family and the cause of hemorrhagic fever outbreaks. The EBOV VP40 (eVP40) matrix protein is the main driving force for virion assembly and budding. Indeed, expression of eVP40 alone in mammalian cells results in the formation and budding of virus-like particles (VLPs) which mimic the budding process and morphology of authentic, infectious EBOV. To complete the budding process, eVP40 utilizes its PPXY L-domain motif to recruit a specific subset of host proteins containing one or more modular WW domains that then function to facilitate efficient production and release of eVP40 VLPs. In this report, we identified additional host WW-domain interactors by screening for potential interactions between mammalian proteins possessing one or more WW domains and WT or PPXY mutant peptides of eVP40. We identified the HECT family E3 ubiquitin ligase WWP1 and all four of its WW domains as strong interactors with the PPXY motif of eVP40. The eVP40-WWP1 interaction was confirmed by both peptide pulldown and coimmunoprecipitation assays, which also demonstrated that modular WW domain 1 of WWP1 was most critical for binding to eVP40. Importantly, the eVP40-WWP1 interaction was found to be biologically relevant for VLP budding since (i) small interfering RNA (siRNA) knockdown of endogenous WWP1 resulted in inhibition of eVP40 VLP egress, (ii) coexpression of WWP1 and eVP40 resulted in ubiquitination of eVP40 and a subsequent increase in eVP40 VLP egress, and (iii) an enzymatically inactive mutant of WWP1 (C890A) did not ubiquitinate eVP40 or enhance eVP40 VLP egress. Last, our data show that ubiquitination of eVP40 by WWP1 enhances egress of VLPs and concomitantly decreases cellular levels of higher-molecular-weight oligomers of eVP40. In sum, these findings contribute to our fundamental understanding of the functional interplay between host E3 ligases, ubiquitination, and regulation of EBOV VP40-mediated egress. IMPORTANCE Ebola virus (EBOV) is a high-priority, emerging human pathogen that can cause severe outbreaks of hemorrhagic fever with high mortality rates. As there are currently no approved vaccines or treatments for EBOV, a better understanding of the biology and functions of EBOV-host interactions that promote or inhibit viral budding is warranted. Here, we describe a physical and functional interaction between EBOV VP40 (eVP40) and WWP1, a host E3 ubiquitin ligase that ubiquitinates VP40 and regulates VLP egress. This viral PPXY-host WW domain-mediated interaction represents a potential new target for host-oriented inhibitors of EBOV egress. Copyright © 2017 American Society for Microbiology.

Architectural Methodology Report

NASA Technical Reports Server (NTRS)

Dhas, Chris

2000-01-01

The establishment of conventions between two communicating entities in the end systems is essential for communications. Examples of the kind of decisions that need to be made in establishing a protocol convention include the nature of the data representation, the for-mat and the speed of the date representation over the communications path, and the sequence of control messages (if any) which are sent. One of the main functions of a protocol is to establish a standard path between the communicating entities. This is necessary to create a virtual communications medium with certain desirable characteristics. In essence, it is the function of the protocol to transform the characteristics of the physical communications environment into a more useful virtual communications model. The final function of a protocol is to establish standard data elements for communications over the path; that is, the protocol serves to create a virtual data element for exchange. Other systems may be constructed in which the transferred element is a program or a job. Finally, there are special purpose applications in which the element to be transferred may be a complex structure such as all or part of a graphic display. NASA's Glenn Research Center (GRC) defines and develops advanced technology for high priority national needs in communications technologies for application to aeronautics and space. GRC tasked Computer Networks and Software Inc. (CNS) to describe the methodologies used in developing a protocol architecture for an in-space Internet node. The node would support NASA:s four mission areas: Earth Science; Space Science; Human Exploration and Development of Space (HEDS); Aerospace Technology. This report presents the methodology for developing the protocol architecture. The methodology addresses the architecture for a computer communications environment. It does not address an analog voice architecture.

Expression and responses to dehydration and salinity stresses of V-PPase gene members in wheat.

PubMed

Wang, Yuezhi; Xu, Haibin; Zhang, Guangxiang; Zhu, Huilan; Zhang, Lixia; Zhang, Zhengzhi; Zhang, Caiqin; Ma, Zhengqiang

2009-12-01

Vacuolar H(+)-translocating pyrophosphatase (V-PPase) is a key enzyme related to plant growth as well as abiotic stress tolerance. In this work, wheat V-PPase genes TaVP1, TaVP2 and TaVP3 were identified. TaVP1 and TaVP2 are more similar to each other than to TaVP3. Their deduced polypeptide sequences preserve the topological structure and essential residues of V-PPases. Phylogenetic studies suggested that monocot plants, at least monocot grasses, have three VP paralogs. TaVP3 transcripts were only detected in developing seeds, and no TaVP2 transcripts were found in germinating seeds. TaVP2 was mainly expressed in shoot tissues and down-regulated in leaves under dehydration. Its expression was up-regulated in roots under high salinity. TaVP1 was relatively more ubiquitously and evenly expressed than TaVP2. Its expression level in roots was highest among the tissues examined, and was inducible by salinity stress. These results indicated that the V-PPase gene paralogs in wheat are differentially regulated spatially and in response to dehydration and salinity stresses. 2009 Institute of Genetics and Developmental Biology and the Genetics Society of China. Published by Elsevier Ltd. All rights reserved.

Spontaneous Evolution of Nanostructure in Composite Films Consisting of Mixtures of Two Different Block Copolymer Micelles

NASA Astrophysics Data System (ADS)

Kim, Sehee; Char, Kookheon; Sohn, Byeong-Hyeok

2010-03-01

Diblock copolymers consisting of two immiscible polymer blocks covalently bonded together form various self-assembled nanostructures such as spheres, cylinders, and lamellae in bulk phase. In a selective solvent, however, they assemble into micelles with soluble corona brushes and immiscible cores. Both polystyrene-poly(4-vinylpyridine) (PS-b-P4VP) and polystyrene-poly(2-vinylpyridine) (PS-b-P2VP) diblock copolymers form micelles with PS coronas and P4VP or P2VP cores in a PS selective solvent (toluene). By varying the mixture ratio between PS-b-P4VP and PS-b-P2VP, composite films based on the micellar mixtures of PS-b-P4VP and PS-b-P2VP were obtained by spin-coating, followed by the solvent annealing with tetrahydrofuran (THF) vapor. Since THF is a solvent for both PS and P2VP blocks and, at the same time, a non-solvent for the P4VP block, PS-P2VP micelles transformed to lamellar multilayers while PS-P4VP micelles remained intact during the THF annealing. The spontaneous evolution of nanostructure in composite films consisting of lamellae layers with BCP micelles were investigated in detail by cross-sectional TEM and AFM.

Cryo-Electron Microscopy Reconstruction Shows Poliovirus 135S Particles Poised for Membrane Interaction and RNA Release

PubMed Central

Butan, Carmen; Filman, David J.

2014-01-01

During infection, binding of mature poliovirus to cell surface receptors induces an irreversible expansion of the capsid, to form an infectious cell-entry intermediate particle that sediments at 135S. In these expanded virions, the major capsid proteins (VP1 to VP3) adopt an altered icosahedral arrangement to open holes in the capsid at 2-fold and quasi-3-fold axes, and internal polypeptides VP4 and the N terminus of VP1, which can bind membranes, become externalized. Cryo-electron microscopy images for 117,330 particles were collected using Leginon and reconstructed using FREALIGN. Improved rigid-body positioning of major capsid proteins established reliably which polypeptide segments become disordered or rearranged. The virus-to-135S transition includes expansion of 4%, rearrangements of the GH loops of VP3 and VP1, and disordering of C-terminal extensions of VP1 and VP2. The N terminus of VP1 rearranges to become externalized near its quasi-3-fold exit, binds to rearranged GH loops of VP3 and VP1, and attaches to the top surface of VP2. These details improve our understanding of subsequent stages of infection, including endocytosis and RNA transfer into the cytoplasm. PMID:24257617

Maturation of the Hepatitis A Virus Capsid Protein VP1 Is Not Dependent on Processing by the 3Cpro Proteinase

PubMed Central

Martin, Annette; Bénichou, Danièle; Chao, Shih-Fong; Cohen, Lisette M.; Lemon, Stanley M.

1999-01-01

Most details of the processing of the hepatitis A virus (HAV) polyprotein are known. Unique among members of the family Picornaviridae, the primary cleavage of the HAV polyprotein is mediated by 3Cpro, the only proteinase known to be encoded by the virus, at the 2A/2B junction. All other cleavages of the polyprotein have been considered to be due to 3Cpro, although the precise location and mechanism responsible for the VP1/2A cleavage have been controversial. Here we present data that argue strongly against the involvement of the HAV 3Cpro proteinase in the maturation of VP1 from its VP1-2A precursor. Using a heterologous expression system based on recombinant vaccinia viruses directing the expression of full-length or truncated capsid protein precursors, we show that the C terminus of the mature VP1 capsid protein is located near residue 764 of the polyprotein. However, a proteolytically active HAV 3Cpro that was capable of directing both VP0/VP3 and VP3/VP1 cleavages in vaccinia virus-infected cells failed to process the VP1-2A precursor. Using site-directed mutagenesis of an infectious molecular clone of HAV, we modified potential VP1/2A cleavage sites that fit known 3Cpro recognition criteria and found that a substitution that ablates the presumed 3Cpro dipeptide recognition sequence at Glu764-Ser765 abolished neither infectivity nor normal VP1 maturation. Altered electrophoretic mobility of VP1 from a viable mutant virus with an Arg764 substitution indicated that this residue is present in VP1 and that the VP1/2A cleavage occurs downstream of this residue. These data indicate that maturation of the HAV VP1 capsid protein is not dependent on 3Cpro processing and may thus be uniquely dependent on a cellular proteinase. PMID:10400711

Optimal learning in a virtual patient simulation of cranial nerve palsies: the interaction between social learning context and student aptitude.

PubMed

Johnson, Teresa R; Lyons, Rebecca; Chuah, Joon Hao; Kopper, Regis; Lok, Benjamin C; Cendan, Juan C

2013-01-01

Simulation in medical education provides students with opportunities to practice interviews, examinations, and diagnosis formulation related to complex conditions without risks to patients. To examine differences between individual and team participation on learning outcomes and student perspectives through use of virtual patients (VPs) for teaching cranial nerve (CN) evaluation. Fifty-seven medical students were randomly assigned to complete simulation exercises either as individuals or as members of three-person teams. Students interviewed, examined, and diagnosed VPs with possible CN damage in the neurological exam rehearsal virtual environment (NERVE). Knowledge of CN abnormalities was assessed pre- and post-simulation. Student perspectives of system usability were evaluated post-simulation. An aptitude-treatment interaction (ATI) effect was detected; at pre-test scores ≤ 50%, students in teams scored higher (83%) at post-test than did students as individuals (62%, p = 0.02). Post-simulation, students in teams reported greater confidence in their ability to diagnose CN abnormalities than did students as individuals (p = 0.02; mean rating = 4.0/5.0 and 3.4/5.0, respectively). The ATI effect allows us to begin defining best practices for the integration of VP simulators into the medical curriculum. We are persuaded to implement future NERVE exercises with small teams of medical students.

Optimal learning in a virtual patient simulation of cranial nerve palsies: The interaction between social learning context and student aptitude

PubMed Central

JOHNSON, TERESA R.; LYONS, REBECCA; CHUAH, JOON HAO; KOPPER, REGIS; LOK, BENJAMIN C.; CENDAN, JUAN C.

2013-01-01

Background Simulation in medical education provides students with opportunities to practice interviews, examinations, and diagnosis formulation related to complex conditions without risks to patients. Aim To examine differences between individual and team participation on learning outcomes and student perspectives through use of virtual patients (VPs) for teaching cranial nerve (CN) evaluation. Methods Fifty-seven medical students were randomly assigned to complete simulation exercises either as individuals or as members of three-person teams. Students interviewed, examined, and diagnosed VPs with possible CN damage in the Neurological Exam Rehearsal Virtual Environment (NERVE). Knowledge of CN abnormalities was assessed pre- and post-simulation. Student perspectives of system usability were evaluated post-simulation. Results An aptitude-treatment interaction (ATI) effect was detected; at pre-test scores ≤50%, students in teams scored higher (83%) at post-test than did students as individuals (62%, p = 0.02). Post-simulation, students in teams reported greater confidence in their ability to diagnose CN abnormalities than did students as individuals (p = 0.02; mean rating = 4.0/5.0 and 3.4/5.0, respectively). Conclusion The ATI effect allows us to begin defining best practices for the integration of VP simulators into the medical curriculum. We are persuaded to implement future NERVE exercises with small teams of medical students. PMID:22938679

Joint Video Stitching and Stabilization from Moving Cameras.

PubMed

Guo, Heng; Liu, Shuaicheng; He, Tong; Zhu, Shuyuan; Zeng, Bing; Gabbouj, Moncef

2016-09-08

In this paper, we extend image stitching to video stitching for videos that are captured for the same scene simultaneously by multiple moving cameras. In practice, videos captured under this circumstance often appear shaky. Directly applying image stitching methods for shaking videos often suffers from strong spatial and temporal artifacts. To solve this problem, we propose a unified framework in which video stitching and stabilization are performed jointly. Specifically, our system takes several overlapping videos as inputs. We estimate both inter motions (between different videos) and intra motions (between neighboring frames within a video). Then, we solve an optimal virtual 2D camera path from all original paths. An enlarged field of view along the virtual path is finally obtained by a space-temporal optimization that takes both inter and intra motions into consideration. Two important components of this optimization are that (1) a grid-based tracking method is designed for an improved robustness, which produces features that are distributed evenly within and across multiple views, and (2) a mesh-based motion model is adopted for the handling of the scene parallax. Some experimental results are provided to demonstrate the effectiveness of our approach on various consumer-level videos and a Plugin, named "Video Stitcher" is developed at Adobe After Effects CC2015 to show the processed videos.

Ebola Virus VP35-VP40 Interaction Is Sufficient for Packaging 3E-5E Minigenome RNA into Virus-Like Particles

PubMed Central

Johnson, Reed F.; McCarthy, Sarah E.; Godlewski, Peter J.; Harty, Ronald N.

2006-01-01

The packaging of viral genomic RNA into nucleocapsids and subsequently into virions is not completely understood. Phosphoprotein (P) and nucleoprotein (NP) interactions link NP-RNA complexes with P-L (polymerase) complexes to form viral nucleocapsids. The nucleocapsid then interacts with the viral matrix protein, leading to specific packaging of the nucleocapsid into the virion. A mammalian two-hybrid assay and confocal microscopy were used to demonstrate that Ebola virus VP35 and VP40 interact and colocalize in transfected cells. VP35 was packaged into budding virus-like particles (VLPs) as observed by protease protection assays. Moreover, VP40 and VP35 were sufficient for packaging an Ebola virus minignome RNA into VLPs. Results from immunoprecipitation-reverse transcriptase PCR experiments suggest that VP35 confers specificity of the nucleocapsid for viral genomic RNA by direct VP35-RNA interactions. PMID:16698994

A conserved carboxy-terminal domain in the major tegument structural protein VP22 facilitates virion packaging of a chimeric protein during productive herpes simplex virus 1 infection

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schlegel, Elisabeth F.M.; Blaho, John A., E-mail: john.blaho@mssm.ed

2009-05-10

Recombinant virus HSV-1(RF177) was previously generated to examine tegument protein VP22 function by inserting the GFP gene into the gene encoding VP22. During a detailed analysis of this virus, we discovered that RF177 produces a novel fusion protein between the last 15 amino acids of VP22 and GFP, termed GCT-VP22. Thus, the VP22 carboxy-terminal specific antibody 22-3 and two anti-GFP antibodies reacted with an approximately 28 kDa protein from RF177-infected Vero cells. GCT-VP22 was detected at 1 and 3 hpi. Examination of purified virions indicated that GCT-VP22 was incorporated into RF177 virus particles. These observations imply that at least amore » portion of the information required for virion targeting is located in this domain of VP22. Indirect immunofluorescence analyses showed that GCT-VP22 also localized to areas of marginalized chromatin during RF177 infection. These results indicate that the last fifteen amino acids of VP22 participate in virion targeting during HSV-1 infection.« less

Interplay Among Constitutes of Ebola Virus: Nucleoprotein, Polymerase L, Viral Proteins

NASA Astrophysics Data System (ADS)

Zhang, Minchuan; He, Peiming; Su, Jing; Singh, Dadabhai T.; Su, Hailei; Su, Haibin

Ebola virus is a highly lethal filovirus, claimed thousands of people in its recent outbreak. Seven viral proteins constitute ebola viral structure, and four of them (nucleoprotein (NP), polymerase L, VP35 and VP30) participate majorly in viral replication and transcription. We have elucidated a conformation change of NP cleft by VP35 NP-binding protein domains through superimposing two experimental NP structure images and discussed the function of this conformation change in the replication and transcription with polymerase complex (L, VP35 and VP30). The important roles of VP30 in viral RNA synthesis have also been discussed. A “tapping” model has been proposed in this paper for a better understanding of the interplay among the four viral proteins (NP, polymerase L, VP35 and VP30). Moreover, we have pinpointed some key residue changes on NP (both NP N- and C-terminal) and L between Reston and Zaire by computational studies. Together, this paper provides a description of interactions among ebola viral proteins (NP, L, VP35, VP30 and VP40) in viral replication and transcription, and sheds light on the complex system of viral reproduction.

Comprehensive evaluation of broad-beam transmission of patient supports from three fluoroscopy-guided interventional systems.

PubMed

DeLorenzo, Matthew C; Yang, Kai; Li, Xinhua; Liu, Bob

2018-04-01

The purpose of the study was to measure, evaluate, and model the broad-beam x-ray transmission of the patient supports from representative modern fluoroscopy-guided interventional systems, for patient skin dose calculation. Broad-beam transmission was evaluated by varying incident angle, kVp, added copper (Cu) filter, and x-ray field size for three fluoroscopy systems: General Electric (GE) Innova 4100 with Omega V table and pad, Siemens Axiom Artis with Siemens tabletop "narrow" (CARD) table and pad, and Siemens Zeego with Trumpf TruSystem 7500 table and pad. Field size was measured on the table using a lead ruler for all setups in this study. Exposure rates were measured in service mode using a calibrated Radcal 10 × 6-60 ion chamber above the patient support at the assumed skin location. Broad-beam transmission factors were calculated by the ratio of air kerma rates measured with and without a patient support in the beam path. First, angle dependency was investigated on the GE system, with the chamber at isocenter, for angles of 0°, 15°, 30°, and 40°, for a variety of kVp, added Cu filters, and for two field sizes (small and large). Second, the broad-beam transmission factor at normal incidence was evaluated for all three fluoroscopes by varying kVp, added Cu filter, and field size (small, medium, and large). An analytical equation was created to fit the data as to maximize R 2 and minimize maximum percentage difference across all measurements for each system. For all patient supports, broad-beam transmission factor increased with field size, kVp, and added Cu filtration and decreased with incident angle. Oblique incidence measurements show that the transmission decreased by about 1%, 3%, and 6% for incident angles of 15°, 30°, and 40°, respectively. The broad-beam transmission factors at 0° for the table and table plus pad ranged from 0.73 to 0.96 and from 0.59 to 0.89, respectively. The GE and Siemens transmission factors were comparable, while the Trumpf transmission factors were the lowest. The data were successfully fitted to a function of angle, field size, kVp, and added Cu filtration using nine parameters, with an average R 2 value of 0.977 and maximum percentage difference of 4.08%. This study evaluated the broad-beam transmission for three representative fluoroscopy systems and their dependency on angle, kVp, added Cu filter, and field size. The comprehensive data provided for patient support transmission will facilitate accurate calculation of peak skin dose (PSD) and may potentially be integrated into real-time and retrospective dose monitoring with access to Radiation Dose Structured Reports (RDSR) and radiation event data. © 2018 American Association of Physicists in Medicine.

JAVA PathFinder

NASA Technical Reports Server (NTRS)

Mehhtz, Peter

2005-01-01

JPF is an explicit state software model checker for Java bytecode. Today, JPF is a swiss army knife for all sort of runtime based verification purposes. This basically means JPF is a Java virtual machine that executes your program not just once (like a normal VM), but theoretically in all possible ways, checking for property violations like deadlocks or unhandled exceptions along all potential execution paths. If it finds an error, JPF reports the whole execution that leads to it. Unlike a normal debugger, JPF keeps track of every step how it got to the defect.

A sparse representation of the pathologist's interaction with whole slide images to improve the assigned relevance of regions of interest

NASA Astrophysics Data System (ADS)

Santiago, Daniel; Corredor, Germán.; Romero, Eduardo

2017-11-01

During a diagnosis task, a Pathologist looks over a Whole Slide Image (WSI), aiming to find out relevant pathological patterns. Nonetheless, a virtual microscope captures these structures, but also other cellular patterns with different or none diagnostic meaning. Annotation of these images depends on manual delineation, which in practice becomes a hard task. This article contributes a new method for detecting relevant regions in WSI using the routine navigations in a virtual microscope. This method constructs a sparse representation or dictionary of each navigation path and determines the hidden relevance by maximizing the incoherence between several paths. The resulting dictionaries are then projected onto each other and relevant information is set to the dictionary atoms whose similarity is higher than a custom threshold. Evaluation was performed with 6 pathological images segmented from a skin biopsy already diagnosed with basal cell carcinoma (BCC). Results show that our proposal outperforms the baseline by more than 20%.

Vibrons in finite size molecular lattices: a route for high-fidelity quantum state transfer at room temperature.

PubMed

Pouthier, Vincent

2012-11-07

A communication protocol is proposed in which vibron-mediated quantum state transfer takes place in a molecular lattice. We consider two distant molecular groups grafted on each side of the lattice. These groups form two quantum computers where vibrational qubits are implemented and received. The lattice defines the communication channel along which a vibron delocalizes and interacts with a phonon bath. Using quasi-degenerate perturbation theory, vibron-phonon entanglement is taken into account through the effective Hamiltonian concept. A vibron is thus dressed by a virtual phonon cloud whereas a phonon is clothed by virtual vibronic transitions. It is shown that three quasi-degenerate dressed states define the relevant paths followed by a vibron to tunnel between the computers. When the coupling between the computers and the lattice is judiciously chosen, constructive interference takes place between these paths. Phonon-induced decoherence is minimized and a high-fidelity quantum state transfer occurs over a broad temperature range.

A Dynamic Bayesian Observer Model Reveals Origins of Bias in Visual Path Integration.

PubMed

Lakshminarasimhan, Kaushik J; Petsalis, Marina; Park, Hyeshin; DeAngelis, Gregory C; Pitkow, Xaq; Angelaki, Dora E

2018-06-20

Path integration is a strategy by which animals track their position by integrating their self-motion velocity. To identify the computational origins of bias in visual path integration, we asked human subjects to navigate in a virtual environment using optic flow and found that they generally traveled beyond the goal location. Such a behavior could stem from leaky integration of unbiased self-motion velocity estimates or from a prior expectation favoring slower speeds that causes velocity underestimation. Testing both alternatives using a probabilistic framework that maximizes expected reward, we found that subjects' biases were better explained by a slow-speed prior than imperfect integration. When subjects integrate paths over long periods, this framework intriguingly predicts a distance-dependent bias reversal due to buildup of uncertainty, which we also confirmed experimentally. These results suggest that visual path integration in noisy environments is limited largely by biases in processing optic flow rather than by leaky integration. Copyright © 2018 Elsevier Inc. All rights reserved.

[The relevance of junctional rhythm during neurocardiogenic reaction provoked by tilt testing].

PubMed

Zyśko, Dorota; Gajek, Jacek; Agrawal, Anil Kumar; Rudnicki, Jerzy

2012-01-01

During neurocardiogenic reaction provoked by tilt testing (TT), different arrhythmias such as sinus bradycardia, sinus arrest, atrioventricular block or junctional rhythm or beats (JR) may occur. The characteristics of the JR during neurocardiogenic reaction have not yet been systematically assessed. It is not known whether the presence of JR during neurocardiogenic reaction is related to clinical characteristics of syncopal patients or the outcome of TT. To assess whether clinical outcome of TT and clinical data are related to the presence of JR during TT. The study group consisted of 532 patients aged 43.3 ± 18.2 years with positive TT, divided into four groups on the basis of the presence of JR and/or a ventricular pause (VP) during neurocardiogenic reaction: group VP(-)/JR(+) - JR present and VP absent, group VP(+)/JR(+) - both JR and VP present, group VP(+)/JR(-) - JR absent and VP present, and group VP(-)/JR(-) - both JR and VP absent. The control group consisted of 53 patients with no history of syncope or presyncope, including 46 patients with negative TT and seven patients with false positive TT. Total loss of consciousness during TT occurred in group VP(-)/JR(+) less frequently than in groups VP(+)/JR(+) and VP(+)/JR(-), and more frequently than in group VP(-)/JR(-) (80% vs 96% vs 94% vs 62%; p 〈 0.05 for both comparisons). Group VP(-)/JR(+) was significantly younger than group VP(-)/JR(-) (37.3 ± 16.3 years vs 45.8 ± 18.9 years; p 〈 0.05) and had a lower number of syncopal events than group VP(+)/JR(+) and VP(+)/JR(-) (median [IQ]: 2.5 (1-6) vs 4 (2-12) and 4 (2-10), respectively; p 〈 0.05) and lower rate of traumatic injuries than group VP(+)/JR(+) and VP(+)/JR(-) (22% vs 45% and 39%, respectively; p 〈 0.05). Logistic regression analysis revealed that the presence of JR was associated with younger age, male gender, history of blood-instrumentation-injection phobia and higher number of syncopal spells in medical history. The ROC curve analysis revealed that a junctional rate of no more than 49 bpm was related to the total loss of consciousness during TT (p 〈 0.05). 1. JR frequently occurs during positive TT and in no subjects with negative TT. 2. Among patients with JR, two groups may be chosen on the basis of a VP occurrence, and these groups differ in respect to clinical characteristics and TT outcome. 3. Relatively rapid JR without VP is related to consciousness preservation during neurocardiogenic reaction at TT and fewer syncopal spells as well as syncope associated with injury in the past. 4. In patients with JR and VP, the JR is slower, of shorter duration, and more frequently single or pairs of junctional beats occur, which indicates high parasympathetic activity, whereas relatively rapid and stable JR may be the symptom of simultaneously increased sympathetic and parasympathetic activity.

Trypsin activation pathway of rotavirus infectivity.

PubMed Central

Arias, C F; Romero, P; Alvarez, V; López, S

1996-01-01

The infectivity of rotaviruses is increased by and most probably is dependent on trypsin treatment of the virus. This proteolytic treatment specifically cleaves VP4, the protein that forms the spikes on the surface of the virions, to polypeptides VP5 and VP8. This cleavage has been reported to occur in rotavirus SA114fM at two conserved, closely spaced arginine residues located at VP4 amino acids 241 and 247. In this work, we have characterized the VP4 cleavage products of rotavirus SA114S generated by in vitro treatment of the virus with increasing concentrations of trypsin and with proteases AspN and alpha-chymotrypsin. The VP8 and VP5 polypeptides were analyzed by gel electrophoresis and by Western blotting (immunoblotting) with antibodies raised to synthetic peptides that mimic the terminal regions of VP4 generated by the trypsin cleavage. It was shown that in addition to arginine residues 241 and 247, VP4 is cleaved at arginine residue 231. These three sites were found to have different susceptibilities to trypsin, Arg-241 > Arg-231 > Arg-247, with the enhancement of infectivity correlating with cleavage at Arg-247 rather than at Arg-231 or Arg-241. Proteases AspN and alpha-chymotrypsin cleaved VP4 at Asp-242 and Tyr-246, respectively, with no significant enhancement of infectivity, although this enhancement could be achieved by further treatment of the virus with trypsin. The VP4 end products of trypsin treatment were a homogeneous VP8 polypeptide comprising VP4 amino acids 1 to 231 and a heterogeneous VP5, which is formed by two polypeptide species (present at a ratio of approximately 1:5) as a result of cleavage at either Arg-241 or Arg-247. A pathway for the trypsin activation of rotavirus infectivity is proposed. PMID:8709201

Image quality and radiation dose of brain computed tomography in children: effects of decreasing tube voltage from 120 kVp to 80 kVp.

PubMed

Park, Ji Eun; Choi, Young Hun; Cheon, Jung-Eun; Kim, Woo Sun; Kim, In-One; Cho, Hyun Suk; Ryu, Young Jin; Kim, Yu Jin

2017-05-01

Computed tomography (CT) has generated public concern associated with radiation exposure, especially for children. Lowering the tube voltage is one strategy to reduce radiation dose. To assess the image quality and radiation dose of non-enhanced brain CT scans acquired at 80 kilo-voltage peak (kVp) compared to those at 120 kVp in children. Thirty children who had undergone both 80- and 120-kVp non-enhanced brain CT were enrolled. For quantitative analysis, the mean attenuation of white and gray matter, attenuation difference, noise, signal-to-noise ratio, contrast-to-noise ratio and posterior fossa artifact index were measured. For qualitative analysis, noise, gray-white matter differentiation, artifact and overall image quality were scored. Radiation doses were evaluated by CT dose index, dose-length product and effective dose. The mean attenuations of gray and white matter and contrast-to-noise ratio were significantly increased at 80 kVp, while parameters related to image noise, i.e. noise, signal-to-noise ratio and posterior fossa artifact index were higher at 80 kVp than at 120 kVp. In qualitative analysis, 80-kVp images showed improved gray-white differentiation but more artifacts compared to 120-kVp images. Subjective image noise and overall image quality scores were similar between the two scans. Radiation dose parameters were significantly lower at 80 kVp than at 120 kVp. In pediatric non-enhanced brain CT scans, a decrease in tube voltage from 120 kVp to 80 kVp resulted in improved gray-white matter contrast, comparable image quality and decreased radiation dose.

Recombination and Population Mosaic of a Multifunctional Viral Gene, Adeno-Associated Virus cap

PubMed Central

Takeuchi, Yasuhiro; Myers, Richard; Danos, Olivier

2008-01-01

Homologous recombination is a dominant force in evolution and results in genetic mosaics. To detect evidence of recombination events and assess the biological significance of genetic mosaics, genome sequences for various viral populations of reasonably large size are now available in the GenBank. We studied a multi-functional viral gene, the adeno-associated virus (AAV) cap gene, which codes for three capsid proteins, VP1, VP2 and VP3. VP1-3 share a common C-terminal domain corresponding to VP3, which forms the viral core structure, while the VP1 unique N-terminal part contains an enzymatic domain with phospholipase A2 activity. Our recombinant detection program (RecI) revealed five novel recombination events, four of which have their cross-over points in the N-terminal, VP1 and VP2 unique region. Comparison of phylogenetic trees for different cap gene regions confirmed discordant phylogenies for the recombinant sequences. Furthermore, differences in the phylogenetic tree structures for the VP1 unique (VP1u) region and the rest of cap highlighted the mosaic nature of cap gene in the AAV population: two dominant forms of VP1u sequences were identified and these forms are linked to diverse sequences in the rest of cap gene. This observation together with the finding of frequent recombination in the VP1 and 2 unique regions suggests that this region is a recombination hot spot. Recombination events in this region preserve protein blocks of distinctive functions and contribute to convergence in VP1u and divergence of the rest of cap. Additionally the possible biological significance of two dominant VP1u forms is inferred. PMID:18286191

Value of 100 kVp scan with sinogram-affirmed iterative reconstruction algorithm on a single-source CT system during whole-body CT for radiation and contrast medium dose reduction: an intra-individual feasibility study.

PubMed

Nagayama, Y; Nakaura, T; Oda, S; Tsuji, A; Urata, J; Furusawa, M; Tanoue, S; Utsunomiya, D; Yamashita, Y

2018-02-01

To perform an intra-individual investigation of the usefulness of a contrast medium (CM) and radiation dose-reduction protocol using single-source computed tomography (CT) combined with 100 kVp and sinogram-affirmed iterative reconstruction (SAFIRE) for whole-body CT (WBCT; chest-abdomen-pelvis CT) in oncology patients. Forty-three oncology patients who had undergone WBCT under both 120 and 100 kVp protocols at different time points (mean interscan intervals: 98 days) were included retrospectively. The CM doses for the 120 and 100 kVp protocols were 600 and 480 mg iodine/kg, respectively; 120 kVp images were reconstructed with filtered back-projection (FBP), whereas 100 kVp images were reconstructed with FBP (100 kVp-F) and the SAFIRE (100 kVp-S). The size-specific dose estimate (SSDE), iodine load and image quality of each protocol were compared. The SSDE and iodine load of 100 kVp protocol were 34% and 21%, respectively, lower than of 120 kVp protocol (SSDE: 10.6±1.1 versus 16.1±1.8 mGy; iodine load: 24.8±4versus 31.5±5.5 g iodine, p<0.01). Contrast enhancement, objective image noise, contrast-to-noise-ratio, and visual score of 100 kVp-S were similar to or better than of 120 kVp protocol. Compared with the 120 kVp protocol, the combined use of 100 kVp and SAFIRE in WBCT for oncology assessment with an SSCT facilitated substantial reduction in the CM and radiation dose while maintaining image quality. Copyright © 2017 The Royal College of Radiologists. Published by Elsevier Ltd. All rights reserved.

Investigating Ebola virus pathogenicity using molecular dynamics.

PubMed

Pappalardo, Morena; Collu, Francesca; Macpherson, James; Michaelis, Martin; Fraternali, Franca; Wass, Mark N

2017-08-11

Ebolaviruses have been known to cause deadly disease in humans for 40 years and have recently been demonstrated in West Africa to be able to cause large outbreaks. Four Ebolavirus species cause severe disease associated with high mortality in humans. Reston viruses are the only Ebolaviruses that do not cause disease in humans. Conserved amino acid changes in the Reston virus protein VP24 compared to VP24 of other Ebolaviruses have been suggested to alter VP24 binding to host cell karyopherins resulting in impaired inhibition of interferon signalling, which may explain the difference in human pathogenicity. Here we used protein structural analysis and molecular dynamics to further elucidate the interaction between VP24 and KPNA5. As a control experiment, we compared the interaction of wild-type and R137A-mutant (known to affect KPNA5 binding) Ebola virus VP24 with KPNA5. Results confirmed that the R137A mutation weakens direct VP24-KPNA5 binding and enables water molecules to penetrate at the interface. Similarly, Reston virus VP24 displayed a weaker interaction with KPNA5 than Ebola virus VP24, which is likely to reduce the ability of Reston virus VP24 to prevent host cell interferon signalling. Our results provide novel molecular detail on the interaction of Reston virus VP24 and Ebola virus VP24 with human KPNA5. The results indicate a weaker interaction of Reston virus VP24 with KPNA5 than Ebola virus VP24, which is probably associated with a decreased ability to interfere with the host cell interferon response. Hence, our study provides further evidence that VP24 is a key player in determining Ebolavirus pathogenicity.

New results from the studies of the Ν (1440) 1/2 +, Ν (1520) 3/2 –, and Δ (1620) 1/2 – resonances in exclusive ep → e'p'π +π – electroproduction with the CLAS detector

DOE PAGES

Mokeev, Viktor I.; Burkert, Volker D.; Carman, Daniel S.; ...

2016-02-25

In this study, the transition helicity amplitudes from the proton ground state to the N(1440)1/2 +, N(1520)3/2 –, and Δ(1620)1/2 – resonances (γvpN* electrocouplings) were determined from the analysis of nine independent onefold differential π +π –p electroproduction cross sections off a proton target, taken with CLAS at photon virtualities 0.5GeV 2 < Q 2 < 1.5 GeV 2. The phenomenological reaction model employed for separation of the resonant and nonresonant contributions to this exclusive channel was further developed.

Characterization of the DNA binding properties of polyomavirus capsid protein

NASA Technical Reports Server (NTRS)

Chang, D.; Cai, X.; Consigli, R. A.; Spooner, B. S. (Principal Investigator)

1993-01-01

The DNA binding properties of the polyomavirus structural proteins VP1, VP2, and VP3 were studied by Southwestern analysis. The major viral structural protein VP1 and host-contributed histone proteins of polyomavirus virions were shown to exhibit DNA binding activity, but the minor capsid proteins VP2 and VP3 failed to bind DNA. The N-terminal first five amino acids (Ala-1 to Lys-5) were identified as the VP1 DNA binding domain by genetic and biochemical approaches. Wild-type VP1 expressed in Escherichia coli (RK1448) exhibited DNA binding activity, but the N-terminal truncated VP1 mutants (lacking Ala-1 to Lys-5 and Ala-1 to Cys-11) failed to bind DNA. The synthetic peptide (Ala-1 to Cys-11) was also shown to have an affinity for DNA binding. Site-directed mutagenesis of the VP1 gene showed that the point mutations at Pro-2, Lys-3, and Arg-4 on the VP1 molecule did not affect DNA binding properties but that the point mutation at Lys-5 drastically reduced DNA binding affinity. The N-terminal (Ala-1 to Lys-5) region of VP1 was found to be essential and specific for DNA binding, while the DNA appears to be non-sequence specific. The DNA binding domain and the nuclear localization signal are located in the same N-terminal region.

Two-dimensional seismic image of the San Andreas Fault in the Northern Gabilan Range, central California: Evidence for fluids in the fault zone

USGS Publications Warehouse

Thurber, C.; Roecker, S.; Ellsworth, W.; Chen, Y.; Lutter, W.; Sessions, R.

1997-01-01

A joint inversion for two-dimensional P-wave velocity (Vp), P-to-S velocity ratio (Vp/Vs), and earthquake locations along the San Andreas fault (SAF) in central California reveals a complex relationship among seismicity, fault zone structure, and the surface fault trace. A zone of low Vp and high Vp/Vs lies beneath the SAF surface trace (SAFST), extending to a depth of about 6 km. Most of the seismic activity along the SAF occurs at depths of 3 to 7 km in a southwest-dipping zone that roughly intersects the SAFST, and lies near the southwest edge of the low Vp and high Vp/Vs zones. Tests indicate that models in which this seismic zone is significantly closer to vertical can be confidently rejected. A second high Vp/Vs zone extends to the northeast, apparently dipping beneath the Diablo Range. Another zone of seismicity underlies the northeast portion of this Vp/Vs high. The high Vp/Vs zones cut across areas of very different Vp values, indicating that the high Vp/Vs values are due to the presence of fluids, not just lithology. The close association between the zones of high Vp/Vs and seismicity suggests a direct involvement of fluids in the faulting process. Copyright 1997 by the American Geophysical Union.

Expression, purification, crystallization and preliminary X-ray diffraction analysis of the VP8* sialic acid-binding domain of porcine rotavirus strain OSU

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Yang-De, E-mail: zhangyd1960@yahoo.com.cn; Li, Hao; Liu, Hui

2007-02-01

Porcine rotavirus strain OSU VP8* domain has been expressed, purified and crystallized. X-ray diffraction data from different crystal forms of the VP8* domain have been collected to 2.65 and 2.2 Å resolution, respectively. The rotavirus outer capsid spike protein VP4 is utilized in the process of rotavirus attachment to and membrane penetration of host cells. VP4 is cleaved by trypsin into two domains: VP8* and VP5*. The VP8* domain is implicated in initial interaction with sialic acid-containing cell-surface carbohydrates and triggers subsequent virus invasion. The VP8* domain from porcine OSU rotavirus was cloned and expressed in Escherichia coli. Different crystalmore » forms (orthorhombic P2{sub 1}2{sub 1}2{sub 1} and tetragonal P4{sub 1}2{sub 1}2) were harvested from two distinct crystallization conditions. Diffraction data have been collected to 2.65 and 2.2 Å resolution and the VP8*{sub 65–224} structure was determined by molecular replacement.« less

Antigenicity analysis of human parvovirus B19-VP1u protein in the induction of anti-phospholipid syndrome.

PubMed

Lin, Chun-Yu; Chiu, Chun-Ching; Cheng, Ju; Lin, Chia-Yun; Shi, Ya-Fang; Tsai, Chun-Chou; Tzang, Bor-Show; Hsu, Tsai-Ching

2018-01-01

Mounting evidence suggests a connection between human parvovirus B19 (B19) and autoimmune diseases, and especially an association between the B19-VP1 unique region (VP1u) and anti-phospholipid syndrome (APS). However, little is known about the antigenicity of B19-VP1u in the induction of APS-like syndrome. To elucidate the antigenicity of B19-VP1u in the induction of APS, N-terminal truncated B19-VP1u (tVP1u) proteins were prepared to immunize Balb/c mice to generate antibodies against B19-tVP1u proteins. The secreted phospholipase A2 (sPLA2) activities and binding specificity of mice anti-B19-tVP1u antibodies with cardiolipin (CL) and beta-2-glycoprotein I (β2GPI) were evaluated by performing immunoblot, ELISA and absorption experiments. A mice model of passively induced APS was adopted. Although sPLA2 activities were identified in all B19-tVP1u proteins, only amino acid residues 61-227 B19-tVP1u exhibited a higher sPLA2 activity. Autoantibodies against CL and β2GPI exhibited binding activities with all B19-tVP1u proteins. IgG that was purified from mice that had been immunized with amino acid residues 21-227 to 121-227 B19-tVP1u proteins exhibited significantly higher binding activity with CL. IgG that was purified from mice that had been immunized with amino acid residues 21-227, 31-227, 82-227 and 91-227 B19-tVP1u proteins exhibited significantly higher binding activity with β2GPI. Accordingly, significantly higher binding inhibition of CL was detected in the presence of amino acid residues 61-227 and 101-227 B19-tVP1u. Significantly higher binding inhibition of β2GPI was detected in the presence of amino acid residues 21-227, 31-227, 82-227 and 91-227 B19-tVP1u. The mice that received amino acid residues 31-227 or 61-227 anti-tB19-VP1u IgG revealed significant thrombocytopenia and those that received amino acid residues 21-227, 31-227, 61-227, 71-227, 82-227, 91-227, 101-227 or 114-227 anti-tB19-VP1u IgG exhibited significantly prolonged aPTT. These findings provide further information concerning the role of B19-VP1u antigenicity in APS-like autoimmunity.

Purification of recombinant budgerigar fledgling disease virus VP1 capsid protein and its ability for in vitro capsid assembly

NASA Technical Reports Server (NTRS)

Rodgers, R. E.; Chang, D.; Cai, X.; Consigli, R. A.; Spooner, B. S. (Principal Investigator)

1994-01-01

A recombinant system for the major capsid VP1 protein of budgerigar fledgling disease virus has been established. The VP1 gene was inserted into a truncated form of the pFlag-1 vector and expressed in Escherichia coli. The budgerigar fledgling disease virus VP1 protein was purified to near homogeneity by immunoaffinity chromatography. Fractions containing highly purified VP1 were pooled and found to constitute 3.3% of the original E. coli-expressed VP1 protein. Electron microscopy revealed that the VP1 protein was isolated as pentameric capsomeres. Electron microscopy also revealed that capsid-like particles were formed in vitro from purified VP1 capsomeres with the addition of Ca2+ ions and the removal of chelating and reducing agents.

Genetic Diversity of Hepatitis A Virus in China: VP3-VP1-2A Genes and Evidence of Quasispecies Distribution in the Isolates

PubMed Central

Cao, Jingyuan; Zhou, Wenting; Yi, Yao; Jia, Zhiyuan; Bi, Shengli

2013-01-01

Hepatitis A virus (HAV) is the most common cause of infectious hepatitis throughout the world, spread largely by the fecal-oral route. To characterize the genetic diversity of the virus circulating in China where HAV in endemic, we selected the outbreak cases with identical sequences in VP1-2A junction region and compiled a panel of 42 isolates. The VP3-VP1-2A regions of the HAV capsid-coding genes were further sequenced and analyzed. The quasispecies distribution was evaluated by cloning the VP3 and VP1-2A genes in three clinical samples. Phylogenetic analysis demonstrated that the same genotyping results could be obtained whether using the complete VP3, VP1, or partial VP1-2A genes for analysis in this study, although some differences did exist. Most isolates clustered in sub-genotype IA, and fewer in sub-genotype IB. No amino acid mutations were found at the published neutralizing epitope sites, however, several unique amino acid substitutions in the VP3 or VP1 region were identified, with two amino acid variants closely located to the immunodominant site. Quasispecies analysis showed the mutation frequencies were in the range of 7.22x10-4 -2.33x10-3 substitutions per nucleotide for VP3, VP1, or VP1-2A. When compared with the consensus sequences, mutated nucleotide sites represented the minority of all the analyzed sequences sites. HAV replicated as a complex distribution of closely genetically related variants referred to as quasispecies, and were under negative selection. The results indicate that diverse HAV strains and quasispecies inside the viral populations are presented in China, with unique amino acid substitutions detected close to the immunodominant site, and that the possibility of antigenic escaping mutants cannot be ruled out and needs to be further analyzed. PMID:24069343

Determinants of the VP1/2A junction cleavage by the 3C protease in foot-and-mouth disease virus-infected cells.

PubMed

Kristensen, Thea; Normann, Preben; Gullberg, Maria; Fahnøe, Ulrik; Polacek, Charlotta; Rasmussen, Thomas Bruun; Belsham, Graham J

2017-03-01

The foot-and-mouth disease virus (FMDV) capsid precursor, P1-2A, is cleaved by FMDV 3C protease to yield VP0, VP3, VP1 and 2A. Cleavage of the VP1/2A junction is the slowest. Serotype O FMDVs with uncleaved VP1-2A (having a K210E substitution in VP1; at position P2 in cleavage site) have been described previously and acquired a second site substitution (VP1 E83K) during virus rescue. Furthermore, introduction of the VP1 E83K substitution alone generated a second site change at the VP1/2A junction (2A L2P, position P2' in cleavage site). These virus adaptations have now been analysed using next-generation sequencing to determine sub-consensus level changes in the virus; this revealed other variants within the E83K mutant virus population that changed residue VP1 K210. The construction of serotype A viruses with a blocked VP1/2A cleavage site (containing K210E) has now been achieved. A collection of alternative amino acid substitutions was made at this site, and the properties of the mutant viruses were determined. Only the presence of a positively charged residue at position P2 in the cleavage site permitted efficient cleavage of the VP1/2A junction, consistent with analyses of diverse FMDV genome sequences. Interestingly, in contrast to the serotype O virus results, no second site mutations occurred within the VP1 coding region of serotype A viruses with the blocked VP1/2A cleavage site. However, some of these viruses acquired changes in the 2C protein that is involved in enterovirus morphogenesis. These results have implications for the testing of potential antiviral agents targeting the FMDV 3C protease.

Comparative characteristics of the VP7 and VP4 antigenic epitopes of the rotaviruses circulating in Russia (Nizhny Novgorod) and the Rotarix and RotaTeq vaccines.

PubMed

Morozova, O V; Sashina, T A; Fomina, S G; Novikova, N A

2015-07-01

Two live, attenuated rotavirus A (RVA) vaccines, Rotarix and RotaTeq, have been successfully introduced into national immunization programs worldwide. The parent strains of both vaccines were obtained more than 30 years ago. Nonetheless, only very limited data are available on the molecular similarity of the vaccine strains and their genetic relationships to the wild-type strains circulating within the territory of Russian Federation. In this study, we have determined the nucleotide sequences of the genes encoding the viral proteins VP7 and VP4 (the globular domain VP8*) of vaccine strains and natural isolates of rotaviruses in Nizhny Novgorod, Russia. The VP7 and VP4 proteins contain antigenic sites that are the main targets of neutralizing antibodies. Phylogenetic analysis based on VP4 and VP7 showed that the majority of the natural RVA isolates from Nizhny Novgorod and the vaccine strains belong to different clusters. Four amino acids within the VP7 antigenic sites were common in both the wild-type and vaccine strains. The largest number of amino acid differences was found between the vaccine strain Rotarix and the Nizhny Novgorod G2 strains (19 residues out of 29). From 3 to 5 amino acid differences per strain were identified in the antigenic sites of VP4 (domain VP8*) between wild-type strains and the vaccine RotaTeq, and 6-8 substitutions were found when they were compared with the vaccine strain Rotarix. For the first time, immunodominant T-cell epitopes of VP7 were analyzed, and differences in the sequences between the vaccine and the wild-type strains were found. The accumulation of amino acid substitutions in the VP7 and VP4 antigenic sites may potentially reduce the immune protection of vaccinated children from wild-type strains of rotavirus.

Clinical clues for differential diagnosis between verruca plana and verruca plana-like seborrheic keratosis.

PubMed

Kim, Won-Jeong; Lee, Won-Ku; Song, Margaret; Kim, Hoon-Soo; Ko, Hyun-Chang; Kim, Byung-Soo; Kim, Moon-Bum

2015-04-01

Sometimes the clinical differentiation between verruca plana (VP) and VP-like seborrheic keratosis (SK) could be challenged. However, there have been no studies on this issue to date. The aim of this study was to elucidate clinical and dermoscopic differences between these two diseases, and also to suggest a diagnostic algorithm of VP and VP-like SK without skin biopsy. The patients who had lesions clinically considered as VP or VP-like SK were the target of our study. We took clinical and dermoscopic photos with informed consent and conducted a questionnaire. All patients had their diagnoses confirmed by biopsy. Thirty-three patients were enrolled in our study. Seventeen patients were finally diagnosed with VP (51.5%) and 16 patients with VP-like SK (48.5%). In clinical findings, VP-like SK showed significantly more scattered distribution than VP (P = 0.039), which exhibited more clustered or grouped distribution (P = 0.039). In dermoscopic findings, brain-like appearance was more commonly observed in VP-like SK (P = 0.003) whereas VP showed more red dots or globular vessels (P = 0.017) and even-colored light brown to yellow patch (P < 0.001). Sex, onset age, the size of each lesion, location, color and shape showed no significant differences between them (P > 0.05). Based on our results, we suggest a diagnostic algorithm using Koebner's phenomenon, dermoscopic findings, distribution of each lesion and biopsy for multiple VP-like lesions in adults, and we think it will be a very useful diagnostic tool in daily clinical dermatological practice. © 2015 Japanese Dermatological Association.

Expression and immunogenic analysis of recombinant polypeptides derived from capsid protein VP1 for developing subunit vaccine material against hepatitis A virus.

PubMed

Jang, Kyoung Ok; Park, Jong-Hwa; Lee, Hyun Ho; Chung, Dae Kyun; Kim, Wonyong; Chung, In Sik

2014-08-01

Three recombinant polypeptides, VP1-His, VP1-3N-His, and 3D2-His, were produced by Escherichia coli expression system. Recombinant VP1-His, VP1-3N-His, and 3D2-His were expressed as bands with molecular weights of 32, 38, and 30 kDa, respectively. These were purified by affinity chromatography using Ni-NTA Fast-flow resin and/or ion-exchange chromatography using DEAE-Sepharose Fast-flow resin. Intraperitoneal immunizations of recombinant polypeptides successfully elicited the productions of VP1-His, VP1-3N-His, and 3D2-His specific IgG antibodies (IgG subclass distribution of IgG1>IgG2a>IgG2b>IgG3) in sera and induced the secretions of cytokines IFN-γ and IL-6 in spleen cells. Sera from recombinant VP1-His-, VP1-3N-His-, and 3D2-His-immunized mice neutralized the propagation of HAV. The highest neutralizing activity was shown in sera from recombinant VP1-3N-His-immunized mice. These results suggest that recombinant VP1-3N-His can be a useful source for developing hepatitis A virus (HAV) subunit vaccine candidates. Copyright © 2014 Elsevier Inc. All rights reserved.

Immunogenicity and protective efficacy of rotavirus VP8* fused to cholera toxin B subunit in a mouse model.

PubMed

Xue, Miaoge; Yu, Linqi; Jia, Lianzhi; Li, Yijian; Zeng, Yuanjun; Li, Tingdong; Ge, Shengxiang; Xia, Ningshao

2016-11-01

In attempts to develop recombinant subunit vaccines against rotavirus disease, it was previously shown that the N-terminal truncated VP8* protein, VP8-1 (aa26-231), is a good vaccine candidate when used for immunization in combination with Freund's adjuvant. However, this protein stimulated only weak immune response when aluminum hydroxide was used as an adjuvant. In this study, the nontoxic B subunit of cholera toxin (CTB) was employed as intra-molecular adjuvant to improve the immunogenicity of VP8-1. Both, the N-terminal and C-terminal fusion proteins, were purified to homogeneity, at which stage they formed pentamers, and showed significantly higher immunogenicity and protective efficacy than a VP8-1/aluminum hydroxide mixture in a mouse model. Compared to VP8-1-CTB, CTB-VP8-1 showed higher binding activity to both, GM1 and the conformation sensitive neutralizing monoclonal antibodies specific to VP8. More importantly, CTB-VP8-1 elicited higher titers of neutralizing antibodies and conferred higher protective efficacy than VP8-1-CTB. Therefore, the protein CTB-VP8-1, with enhanced immunogenicity and immunoprotectivity, could be considered as a viable candidate for further development of an alternative, replication-incompetent, parenterally administered vaccine against rotavirus disease.

Immunogenicity of virus-like particles containing modified goose parvovirus VP2 protein.

PubMed

Chen, Zongyan; Li, Chuanfeng; Zhu, Yingqi; Wang, Binbin; Meng, Chunchun; Liu, Guangqing

2012-10-01

The major capsid protein VP2 of goose parvovirus (GPV) expressed using a baculovirus expression system (BES) assembles into virus-like particles (VLPs). To optimize VP2 gene expression in Sf9 cells, we converted wild-type VP2 (VP2) codons into codons that are more common in insect genes. This change greatly increased VP2 protein production in Sf9 cells. The protein generated from the codon-optimized VP2 (optVP2) was detected by immunoblotting and an indirect immunofluorescence assay (IFA). Transmission electron microscopy analysis revealed the formation of VLPs. These findings indicate that optVP2 yielded stable and high-quality VLPs. Immunogenicity assays revealed that the VLPs are highly immunogenic, elicit a high level of neutralizing antibodies and provide protection against lethal challenge. The antibody levels appeared to be directly related to the number of GP-Ag-positive hepatocytes. The variation trends for GP-Ag-positive hepatocytes were similar in the vaccine groups. In comparison with the control group, the optVP2 VLPs groups exhibited obviously better responses. These data indicate that the VLPs retained immunoreactivity and had strong immunogenicity in susceptible geese. Thus, GPV optVP2 appears to be a good candidate for the vaccination of goslings. Copyright © 2012 Elsevier B.V. All rights reserved.

Surface modification of silicon wafer by grafting zwitterionic polymers to improve its antifouling property

NASA Astrophysics Data System (ADS)

Sun, Yunlong; Chen, Changlin; Xu, Heng; Lei, Kun; Xu, Guanzhe; Zhao, Li; Lang, Meidong

2017-10-01

Silicon (111) wafer was modified by triethoxyvinylsilane containing double bond as an intermedium, and then P4VP (polymer 4-vinyl pyridine) brush was "grafted" onto the surface of silicon wafer containing reactive double bonds by adopting the "grafting from" way and Si-P4VP substrate (silicon wafer grafted by P4VP) was obtained. Finally, P4VP brush of Si-P4VP substrate was modified by 1,3-propanesulfonate fully to obtain P4VP-psl brush (zwitterionic polypyridinium salt) and the functional Si-P4VP-psl substrate (silicon wafer grafted by zwitterionic polypyridinium salt based on polymer 4-vinyl pyridine) was obtained successfully. The antifouling property of the silicon wafer, the Si-P4VP substrate and the Si-P4VP-psl substrate was investigated by using bovine serum albumin, mononuclear macrophages (RAW 264.7) and Escherichia coli (E. coli) ATTC25922 as model bacterium. The results showed that compared with the blank sample-silicon wafer, the Si-P4VP-psl substrate had excellent anti-adhesion ability against bovine serum albumin, cells and bacterium, due to zwitterionic P4VP-psl brush (polymer 4-vinyl pyridine salt) having special functionality like antifouling ability on biomaterial field.

Subunit Vaccine Preparation of Bovine Rotavirus and Its Efficacy in Mice.

PubMed

Suocheng, Wei; Tuanjie, Che; Changjun, Song; Fengling, Tian; Zhongren, Ma

2015-09-01

Rotaviruses (RV) are important viral diarrheal agents in calves. Vaccination is an optimum measure to prevent bovine rotaviruses (BRV) infection. However, little research on BRV VP7 vaccine has been done and currently there is no BRV vaccine. To prepare a subunit vaccine of BRV and investigate its efficacy. Total RNA was extracted from MA104 cells infected with bovine rotavirus (BRV) strain GSB01. BRV VP7 gene was amplified using real time fluorescence quantitative PCR (qPCR). The pEASY-T3-VP7 plasmid was digested using HindⅢ and BamHI restriction endonucleases, then recombined into the prokaryotic expression vector pET32a. The pET32a-VP7 and pET32a-VP7-LTB (heat-labile enterotoxin B subunit) were transformed into BL21 (DE3) competent cells of Escherichia coli, respectively, and induced with IPTG, then analyzed using SDS-PAGE. Sixty mice were randomly divided into three groups (n=20). Group A mice was used as His-tag control and mice in group B and C were inoculated with pET32a-VP7 and pET32a-VP7-LTB, respectively. VP7 IgG antibody titers and protection efficiency of pET32a-VP7-LTB were further determined in neonatal mice challenged with GSB01 BRV strain. SDS-PAGE analysis showed that the pET32a-VP7 was highly expressed in the BL21 (DE3) cells. PET32a-VP7 and pET32a-VP7-LTB protein could promote VP7 IgG antibody titer（8.33×103 vs. 17.26×103）in mice. Immunization protection ratios of pET32a-VP7 and pET32a-VP7-LTB proteins in the neonatal mice were 86.4% and 91.7%, respectively. The fusion protein of pET32a-VP7-LTB had excellent immunogenicity and protected mice from BRV infection. Our findings can be used for further developing of a high-efficiency subunit vaccine of BRV.

Virtual animation of victim-specific 3D models obtained from CT scans for forensic reconstructions: Living and dead subjects.

PubMed

Villa, C; Olsen, K B; Hansen, S H

2017-09-01

Post-mortem CT scanning (PMCT) has been introduced at several forensic medical institutions many years ago and has proved to be a useful tool. 3D models of bones, skin, internal organs and bullet paths can rapidly be generated using post-processing software. These 3D models reflect the individual physiognomics and can be used to create whole-body 3D virtual animations. In such way, virtual reconstructions of the probable ante-mortem postures of victims can be constructed and contribute to understand the sequence of events. This procedure is demonstrated in two victims of gunshot injuries. Case #1 was a man showing three perforating gunshot wounds, who died due to the injuries of the incident. Whole-body PMCT was performed and 3D reconstructions of bones, relevant internal organs and bullet paths were generated. Using 3ds Max software and a human anatomy 3D model, a virtual animated body was built and probable ante-mortem postures visualized. Case #2 was a man presenting three perforating gunshot wounds, who survived the incident: one in the left arm and two in the thorax. Only CT scans of the thorax, abdomen and the injured arm were provided by the hospital. Therefore, a whole-body 3D model reflecting the anatomical proportions of the patient was made combining the actual bones of the victim with those obtained from the human anatomy 3D model. The resulted 3D model was used for the animation process. Several probable postures were also visualized in this case. It has be shown that in Case #1 the lesions and the bullet path were not consistent with an upright standing position; instead, the victim was slightly bent forward, i.e. he was sitting or running when he was shot. In Case #2, one of the bullets could have passed through the arm and continued into the thorax. In conclusion, specialized 3D modelling and animation techniques allow for the reconstruction of ante-mortem postures based on both PMCT and clinical CT. Copyright © 2017 Elsevier B.V. All rights reserved.

Modeling the disruption of vascular development in a Virtual Embryo using ToxCast HTS Bioactivity Profiles

EPA Science Inventory

Blood vessel formation is an important aspect of embryo development and teratogenesis. Recent studies address the signaling networks responsible for vasculogenesis and how they might be targeted by certain chemicals. For example, disruption of vasculogenesis and angiogenesis path...

Dynamic phosphorylation of Ebola virus VP30 in NP-induced inclusion bodies.

PubMed

Lier, Clemens; Becker, Stephan; Biedenkopf, Nadine

2017-12-01

Zaire Ebolavirus (EBOV) causes a severe feverish disease with high case fatality rates. Transcription of EBOV is dependent on the activity of the nucleocapsid protein VP30 which represents an essential viral transcription factor. Activity of VP30 is regulated via phosphorylation at six N-terminal serine residues. Recent data demonstrated that dynamic phosphorylation and dephosphorylation of serine residue 29 is essential for transcriptional support activity of VP30. To analyze the spatio/temporal dynamics of VP30 phosphorylation, we generated a peptide antibody recognizing specifically VP30 phosphorylated at serine 29. Using this antibody we could demonstrate that (i) the majority of VP30 molecules in EBOV-infected cells is dephosphorylated at the crucial position serine 29, (ii) both, VP30 phosphorylation and dephosphorylation take place in viral inclusion bodies that are induced by the nucleoprotein NP and (iii) NP influences the phosphorylation state of VP30. Copyright © 2017 Elsevier Inc. All rights reserved.

First study conducted in Northern India that identifies group C rotavirus as the etiological agent of severe diarrhea in children in Delhi.

PubMed

Tiku, Vasundhara Razdan; Jiang, Baoming; Kumar, Praveen; Aneja, Satender; Bagga, Arvind; Bhan, Maharaj Kishen; Ray, Pratima

2017-05-30

Group C Rotavirus (RVC) is an enteric pathogen responsible for acute gastroenteritis in children and adults globally. At present there are no surveillance studies on group C Rotaviruses in India and therefore their prevalence in India remains unknown. The present study aimed to evaluate group C rotavirus infection among <5 years old children hospitalized with acute gastroenteritis in New Delhi. A total of 350 fecal specimens were collected during September 2013 to November 2014 from <5 years old diarrheal patients admitted at KSCH hospital, Delhi. The samples found negative for group A rotavirus (N = 180) by Enzyme immunoassay were screened for group C rotavirus by RT-PCR with VP6, VP7 and VP4 gene specific primers. The PCR products were further sequenced (VP6, VP7, VP4) and analyzed to ascertain their origin and G and P genotypes. Six out of 180 (group A rotavirus negative) samples were found positive for group C rotavirus by VP6 gene specific RT-PCR, of which 3 were also found positive for VP7 and VP4 genes. Phylogenetic analysis of VP7 and VP4 genes of these showed them to be G4 and P[2] genotypes. Overall, the nucleotide sequence data (VP6, VP7 and VP4) revealed a close relationship with the human group C rotavirus with no evidence of animal ancestry. Interestingly, the nucleotide sequence analysis of various genes also indicated differences in their origin. While the identity matrix of VP4 gene (n = 3) showed high amino acid sequence identity (97.60 to 98.20%) with Korean strain, the VP6 gene (n = 6) showed maximum identity with Nigerian strain (96.40 to 97.60%) and VP7 gene (n = 3) with Bangladeshi and USA strains. This is true for all analyzed samples. Our study demonstrated the group C rotavirus as the cause of severe diarrhea in young children in Delhi and provides insights on the origin of group C rotavirus genes among the local strains indicating their source of transmission. Our study also highlights the need for a simple and reliable diagnostic test that can be utilized to determine the disease burden due to group C rotavirus in India.

CdS/C60 binary nanocomposite films prepared via phase transition of PS-b-P2VP block copolymer.

PubMed

Lee, Jung-Pil; Koh, Haeng-Deog; Shin, Won-Jeong; Kang, Nam-Goo; Park, Soojin; Lee, Jae-Suk

2014-03-01

We demonstrate the well-defined control of phase transition of a polystyrene-b-poly(2-vinylpyridine) (PS-b-P2VP) block copolymer from spherical micelles to lamellar structures, in which CdS and C60 nanoparticles (NPs) are selectively positioned at the P2VP domains. The CdS NPs are in situ synthesized using PS-b-P2VP block copolymer templates that are self-assembled in PS-selective solvents. The CdS-PS-b-P2VP micellar structures are transformed to lamellar phase by adjusting a solvent selectivity for both blocks. In addition, a binary system of CdS/C60 embedded in PS-b-P2VP lamellar structures (CdS/C60-PS-b-P2VP) is fabricated by embedding C60 molecules into P2VP domain though charge-transfer complexation between pyridine units of PS-b-P2VP and C60 molecules. The CdS/C60-PS-b-P2VP nanostructured films are characterized by transmission electron microscopy (TEM) and UV-Vis spectrometer. Copyright © 2013 Elsevier Inc. All rights reserved.

Molecular Tectonic Model of Virus Structural Transitions: the Putative Cell Entry States of Poliovirus

PubMed Central

Belnap, David M.; Filman, David J.; Trus, Benes L.; Cheng, Naiqian; Booy, Frank P.; Conway, James F.; Curry, Stephen; Hiremath, Chaitanya N.; Tsang, Simon K.; Steven, Alasdair C.; Hogle, James M.

2000-01-01

Upon interacting with its receptor, poliovirus undergoes conformational changes that are implicated in cell entry, including the externalization of the viral protein VP4 and the N terminus of VP1. We have determined the structures of native virions and of two putative cell entry intermediates, the 135S and 80S particles, at ∼22-Å resolution by cryo-electron microscopy. The 135S and 80S particles are both ∼4% larger than the virion. Pseudoatomic models were constructed by adjusting the beta-barrel domains of the three capsid proteins VP1, VP2, and VP3 from their known positions in the virion to fit the 135S and 80S reconstructions. Domain movements of up to 9 Å were detected, analogous to the shifting of tectonic plates. These movements create gaps between adjacent subunits. The gaps at the sites where VP1, VP2, and VP3 subunits meet are plausible candidates for the emergence of VP4 and the N terminus of VP1. The implications of these observations are discussed for models in which the externalized components form a transmembrane pore through which viral RNA enters the infected cell. PMID:10627545

Molecular tectonic model of virus structural transitions: the putative cell entry states of poliovirus.

PubMed

Belnap, D M; Filman, D J; Trus, B L; Cheng, N; Booy, F P; Conway, J F; Curry, S; Hiremath, C N; Tsang, S K; Steven, A C; Hogle, J M

2000-02-01

Upon interacting with its receptor, poliovirus undergoes conformational changes that are implicated in cell entry, including the externalization of the viral protein VP4 and the N terminus of VP1. We have determined the structures of native virions and of two putative cell entry intermediates, the 135S and 80S particles, at approximately 22-A resolution by cryo-electron microscopy. The 135S and 80S particles are both approximately 4% larger than the virion. Pseudoatomic models were constructed by adjusting the beta-barrel domains of the three capsid proteins VP1, VP2, and VP3 from their known positions in the virion to fit the 135S and 80S reconstructions. Domain movements of up to 9 A were detected, analogous to the shifting of tectonic plates. These movements create gaps between adjacent subunits. The gaps at the sites where VP1, VP2, and VP3 subunits meet are plausible candidates for the emergence of VP4 and the N terminus of VP1. The implications of these observations are discussed for models in which the externalized components form a transmembrane pore through which viral RNA enters the infected cell.

A novel oral delivery system consisting in "drug-in cyclodextrin-in nanostructured lipid carriers" for poorly water-soluble drug: vinpocetine.

PubMed

Lin, Congcong; Chen, Fen; Ye, Tiantian; Zhang, Lina; Zhang, Wenji; Liu, Dandan; Xiong, Wei; Yang, Xinggang; Pan, Weisan

2014-04-25

The purpose of this study was to develop a new delivery system based on drug cyclodextrin (CD) complexation and loading into nanostructured lipid carriers (NLC) to improve the oral bioavailability of vinpocetine (VP). Three different CDs and three different methods to obtain solid vinpocetine-cyclodextrin-tartaric acid complexes (VP-CD-TA) were contrasted. The co-evaporation vinpocetine-β-cyclodextrin-tartaric acid loaded NLC (VP-β-CD-TA COE-loaded NLC) was obtained by emulsification ultrasonic dispersion method. VP-β-CD-TA COE-loaded NLC was suitably characterized for particle size, polydispersity index, zeta potential, entrapment efficiency and the morphology. The crystallization of drug in VP-CD-TA and NLC was investigated by differential scanning calorimetry (DSC). The in vitro release study was carried out at pH 1.2, pH 6.8 and pH 7.4 medium. New Zealand rabbits were applied to investigate the pharmacokinetic behavior in vivo. The VP-β-CD-TA COE-loaded NLC presented a superior physicochemical property and selected to further study. In the in vitro release study, VP-β-CD-TA COE-loaded NLC exhibited a higher dissolution rate in the pH 6.8 and pH 7.4 medium than VP suspension and VP-NLC. The relative bioavailability of VP-β-CD-TA COE-loaded NLC was 592% compared with VP suspension and 92% higher than VP-NLC. In conclusion, the new formulation significantly improved bioavailability of VP for oral delivery, demonstrated a perspective way for oral delivery of poorly water-soluble drugs. Copyright © 2014 Elsevier B.V. All rights reserved.

Antigenic profile of African horse sickness virus serotype 4 VP5 and identification of a neutralizing epitope shared with bluetongue virus and epizootic hemorrhagic disease virus.

PubMed

Martínez-Torrecuadrada, J L; Langeveld, J P; Venteo, A; Sanz, A; Dalsgaard, K; Hamilton, W D; Meloen, R H; Casal, J I

1999-05-10

African horse sickness virus (AHSV) causes a fatal disease in horses. The virus capsid is composed of a double protein layer, the outermost of which is formed by two proteins: VP2 and VP5. VP2 is known to determine the serotype of the virus and to contain the neutralizing epitopes. The biological function of VP5, the other component of the capsid, is unknown. In this report, AHSV VP5, expressed in insect cells alone or together with VP2, was able to induce AHSV-specific neutralizing antibodies. Moreover, two VP5-specific monoclonal antibodies (MAbs) that were able to neutralize the virus in a plaque reduction assay were generated. To dissect the antigenic structure of AHSV VP5, the protein was cloned in Escherichia coli using the pET3 system. The immunoreactivity of both MAbs, and horse and rabbit polyclonal antisera, with 17 overlapping fragments from VP5 was analyzed. The most immunodominant region was found in the N-terminal 330 residues of VP5, defining two antigenic regions, I (residues 151-200) and II (residues 83-120). The epitopes were further defined by PEPSCAN analysis with 12mer peptides, which determined eight antigenic sites in the N-terminal half of the molecule. Neutralizing epitopes were defined at positions 85-92 (PDPLSPGE) for MAb 10AE12 and at 179-185 (EEDLRTR) for MAb 10AC6. Epitope 10AE12 is highly conserved between the different orbiviruses. MAb 10AE12 was able to recognize bluetongue virus VP5 and epizootic hemorrhagic disease virus VP5 by several techniques. These data will be especially useful for vaccine development and diagnostic purposes. Copyright 1999 Academic Press.

Marburg Virus VP24 Protein Relieves Suppression of the NF-κB Pathway Through Interaction With Kelch-like ECH-Associated Protein 1.

PubMed

Edwards, Megan R; Basler, Christopher F

2015-10-01

Marburg virus (MARV) is an emerging zoonotic pathogen that causes hemorrhagic fever. MARV VP24 (mVP24) protein interacts with the host cell protein Kelch-like-ECH-associated protein 1 (Keap1). Keap1 interacts with and promotes the degradation of IκB kinase β (IKKβ), a component of the IκB kinase (IKK) complex that regulates nuclear factor-κB (NF-κB) activity. We studied whether mVP24 could relieve Keap1 repression of the NF-κB pathway. Coimmunoprecipitation assays were used to examine the interaction between Keap1 and IKKβ in the presence of wild-type mVP24 and mutants of mVP24 defective for binding to Keap1. Western blotting was used to determine levels of IKKβ expression in the presence of Keap1 and mVP24. NF-κB promoter-luciferase assays were used to determine the effect of mVP24 on Keap1-induced repression of activity. Expression of wild-type mVP24 disrupted the interaction of IKKβ and Keap1, whereas weakly interacting and noninteracting mVP24 mutants did not disrupt the interaction between Keap1 and IKKβ. The interaction of mVP24 with Keap1 enhanced IKKβ levels in the presence of Keap1. The interaction of mVP24 with Keap1 also relieved Keap1 repression of NF-κB reporter activity. mVP24 can relieve Keap1 repression of the NF-κB pathway through its interaction with Keap1. © The Author 2015. Published by Oxford University Press on behalf of the Infectious Diseases Society of America. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

The Acheta domesticus Densovirus, Isolated from the European House Cricket, Has Evolved an Expression Strategy Unique among Parvoviruses▿†

PubMed Central

Liu, Kaiyu; Li, Yi; Jousset, Françoise-Xavière; Zadori, Zoltan; Szelei, Jozsef; Yu, Qian; Pham, Hanh Thi; Lépine, François; Bergoin, Max; Tijssen, Peter

2011-01-01

The Acheta domesticus densovirus (AdDNV), isolated from crickets, has been endemic in Europe for at least 35 years. Severe epizootics have also been observed in American commercial rearings since 2009 and 2010. The AdDNV genome was cloned and sequenced for this study. The transcription map showed that splicing occurred in both the nonstructural (NS) and capsid protein (VP) multicistronic RNAs. The splicing pattern of NS mRNA predicted 3 nonstructural proteins (NS1 [576 codons], NS2 [286 codons], and NS3 [213 codons]). The VP gene cassette contained two VP open reading frames (ORFs), of 597 (ORF-A) and 268 (ORF-B) codons. The VP2 sequence was shown by N-terminal Edman degradation and mass spectrometry to correspond with ORF-A. Mass spectrometry, sequencing, and Western blotting of baculovirus-expressed VPs versus native structural proteins demonstrated that the VP1 structural protein was generated by joining ORF-A and -B via splicing (splice II), eliminating the N terminus of VP2. This splice resulted in a nested set of VP1 (816 codons), VP3 (467 codons), and VP4 (429 codons) structural proteins. In contrast, the two splices within ORF-B (Ia and Ib) removed the donor site of intron II and resulted in VP2, VP3, and VP4 expression. ORF-B may also code for several nonstructural proteins, of 268, 233, and 158 codons. The small ORF-B contains the coding sequence for a phospholipase A2 motif found in VP1, which was shown previously to be critical for cellular uptake of the virus. These splicing features are unique among parvoviruses and define a new genus of ambisense densoviruses. PMID:21775445

The Ebola virus VP35 protein binds viral immunostimulatory and host RNAs identified through deep sequencing.

PubMed

Dilley, Kari A; Voorhies, Alexander A; Luthra, Priya; Puri, Vinita; Stockwell, Timothy B; Lorenzi, Hernan; Basler, Christopher F; Shabman, Reed S

2017-01-01

Ebola virus and Marburg virus are members of the Filovirdae family and causative agents of hemorrhagic fever with high fatality rates in humans. Filovirus virulence is partially attributed to the VP35 protein, a well-characterized inhibitor of the RIG-I-like receptor pathway that triggers the antiviral interferon (IFN) response. Prior work demonstrates the ability of VP35 to block potent RIG-I activators, such as Sendai virus (SeV), and this IFN-antagonist activity is directly correlated with its ability to bind RNA. Several structural studies demonstrate that VP35 binds short synthetic dsRNAs; yet, there are no data that identify viral immunostimulatory RNAs (isRNA) or host RNAs bound to VP35 in cells. Utilizing a SeV infection model, we demonstrate that both viral isRNA and host RNAs are bound to Ebola and Marburg VP35s in cells. By deep sequencing the purified VP35-bound RNA, we identified the SeV copy-back defective interfering (DI) RNA, previously identified as a robust RIG-I activator, as the isRNA bound by multiple filovirus VP35 proteins, including the VP35 protein from the West African outbreak strain (Makona EBOV). Moreover, RNAs isolated from a VP35 RNA-binding mutant were not immunostimulatory and did not include the SeV DI RNA. Strikingly, an analysis of host RNAs bound by wild-type, but not mutant, VP35 revealed that select host RNAs are preferentially bound by VP35 in cell culture. Taken together, these data support a model in which VP35 sequesters isRNA in virus-infected cells to avert RIG-I like receptor (RLR) activation.

Identification of a T-helper cell epitope on the rotavirus VP6 protein.

PubMed Central

Baños, D M; Lopez, S; Arias, C F; Esquivel, F R

1997-01-01

In this work, we have studied the T-helper (Th)-cell response against rotavirus, in a mouse model. Adult BALB/c mice were inoculated parenterally with porcine rotavirus YM, and the Th-cell response from spleen cells against the virus and two overlapping fragments of the major capsid protein VP6 (VP6(1-192) and VP6(171-397)) were evaluated in vitro. The Th cells recognized the YM virus and the two protein fragments, suggesting that there are at least two Th-cell epitopes on the VP6 molecule. To study the specificity of Th cells against VP6 at the clonal level, we established two Th-cell hybridomas cross-reactive for the VP6 protein of rotavirus strains YM and SA11. Both hybridomas recognized the VP6(171-397) polypeptide, and a synthetic peptide comprising the amino acids 289 to 302 (RLSFQLVRPPNMTP) of YM VP6 in the context of the major histocompatibility complex class II IEd molecule. The Th-cell hybridomas recognized rotavirus VP6 in a highly cross-reactive fashion, since they could be stimulated by eight different strains of rotavirus, including the murine rotavirus EDIM, that represent five G serotypes and at least two subgroups. The amino acid sequence of the VP6 epitope is highly conserved in most group A rotavirus strains sequenced so far. On the other hand, it was found that Th cells specific for the VP6 epitope may constitute an important proportion of the total polyclonal Th-cell response against rotavirus YM in spleen cells. These results demonstrate that VP6 can be a target for highly cross-reactive Th cells. PMID:8985366

Genetic diversity of G1P[8] rotavirus VP7 and VP8* antigens in Finland over a 20-year period: No evidence for selection pressure by universal mass vaccination with RotaTeq® vaccine.

PubMed

Hemming, Maria; Vesikari, Timo

2013-10-01

Two live-attenuated oral vaccines (Rotarix™ and Rotateq®) against rotavirus gastroenteritis were licensed in 2006 and have been introduced into National Immunization Programs (NIPs) of several countries. Large scale use of rotavirus vaccines might cause antigenic pressure on circulating rotavirus types or lead to selection of new rotaviruses thus decreasing vaccine efficacy. We examined the nucleotide and amino acid sequences of the surface proteins VP7 and VP4 (cleaved to VP8(*) and VP5(*)) of a total of 108 G1P[8] rotavirus strains collected over a 20-year period from 1992, including the years 2006-2009 when rotavirus vaccine (mainly Rotarix™) was available, and the years 2009-2012 after implementation of RotaTeq® vaccine into the NIP of Finland. In G1 VP7 no changes at amino acid level were observed. In VP8(*) periodical fluctuation of the sublineage over the study period was found with multiple changes both at nucleotide and amino acid levels. Most amino acid changes were in the dominant antigenic epitopes of VP8(*). A change in VP8(*) sublineage occurred between 2008 and 2009, with a temporal correlation to the use of Rotarix™ up to 30% coverage in the period. In contrast, no antigenic changes in the VP8(*) protein appeared to be correlated to the exclusive use of RotaTeq® vaccine after 2009. Nevertheless, long-term surveillance of antigenic changes in VP4 and also VP7 proteins in wild-type rotavirus strains is warranted in countries with large scale use of the currently licensed live oral rotavirus vaccines. Copyright © 2013 Elsevier B.V. All rights reserved.

Alphavirus Replicon DNA Vectors Expressing Ebola GP and VP40 Antigens Induce Humoral and Cellular Immune Responses in Mice

PubMed Central

Ren, Shoufeng; Wei, Qimei; Cai, Liya; Yang, Xuejing; Xing, Cuicui; Tan, Feng; Leavenworth, Jianmei W.; Liang, Shaohui; Liu, Wenquan

2018-01-01

Ebola virus (EBOV) causes severe hemorrhagic fevers in humans, and no approved therapeutics or vaccine is currently available. Glycoprotein (GP) is the major protective antigen of EBOV, and can generate virus-like particles (VLPs) by co-expression with matrix protein (VP40). In this study, we constructed a recombinant Alphavirus Semliki Forest virus (SFV) replicon vector DREP to express EBOV GP and matrix viral protein (VP40). EBOV VLPs were successfully generated and achieved budding from 293 cells after co-transfection with DREP-based GP and VP40 vectors (DREP-GP+DREP-VP40). Vaccination of BALB/c mice with DREP-GP, DREP-VP40, or DREP-GP+DREP-VP40 vectors, followed by immediate electroporation resulted in a mixed IgG subclass production, which recognized EBOV GP and/or VP40 proteins. This vaccination regimen also led to the generation of both Th1 and Th2 cellular immune responses in mice. Notably, vaccination with DREP-GP and DREP-VP40, which produces both GP and VP40 antigens, induced a significantly higher level of anti-GP IgG2a antibody and increased IFN-γ secreting CD8+ T-cell responses relative to vaccination with DREP-GP or DREP-VP40 vector alone. Our study indicates that co-expression of GP and VP40 antigens based on the SFV replicon vector generates EBOV VLPs in vitro, and vaccination with recombinant DREP vectors containing GP and VP40 antigens induces Ebola antigen-specific humoral and cellular immune responses in mice. This novel approach provides a simple and efficient vaccine platform for Ebola disease prevention. PMID:29375526

A cationic, C-terminal patch and structural rearrangements in Ebola virus matrix VP40 protein control its interactions with phosphatidylserine.

PubMed

Del Vecchio, Kathryn; Frick, Cary T; Gc, Jeevan B; Oda, Shun-Ichiro; Gerstman, Bernard S; Saphire, Erica Ollmann; Chapagain, Prem P; Stahelin, Robert V

2018-03-02

Ebola virus (EBOV) is a filamentous lipid-enveloped virus that causes hemorrhagic fever with a high fatality rate. Viral protein 40 (VP40) is the major EBOV matrix protein and regulates viral budding from the plasma membrane. VP40 is a transformer/morpheein that can structurally rearrange its native homodimer into either a hexameric filament that facilitates viral budding or an RNA-binding octameric ring that regulates viral transcription. VP40 associates with plasma-membrane lipids such as phosphatidylserine (PS), and this association is critical to budding from the host cell. However, it is poorly understood how different VP40 structures interact with PS, what essential residues are involved in this association, and whether VP40 has true selectivity for PS among different glycerophospholipid headgroups. In this study, we used lipid-binding assays, MD simulations, and cellular imaging to investigate the molecular basis of VP40-PS interactions and to determine whether different VP40 structures ( i.e. monomer, dimer, and octamer) can interact with PS-containing membranes. Results from quantitative analysis indicated that VP40 associates with PS vesicles via a cationic patch in the C-terminal domain (Lys 224, 225 and Lys 274, 275 ). Substitutions of these residues with alanine reduced PS-vesicle binding by >40-fold and abrogated VP40 localization to the plasma membrane. Dimeric VP40 had 2-fold greater affinity for PS-containing membranes than the monomer, whereas binding of the VP40 octameric ring was reduced by nearly 10-fold. Taken together, these results suggest the different VP40 structures known to form in the viral life cycle harbor different affinities for PS-containing membranes. © 2018 by The American Society for Biochemistry and Molecular Biology, Inc.

Optimizing CT technique to reduce radiation dose: effect of changes in kVp, iterative reconstruction, and noise index on dose and noise in a human cadaver.

PubMed

Chang, Kevin J; Collins, Scott; Li, Baojun; Mayo-Smith, William W

2017-06-01

For assessment of the effect of varying the peak kilovoltage (kVp), the adaptive statistical iterative reconstruction technique (ASiR), and automatic dose modulation on radiation dose and image noise in a human cadaver, a cadaver torso underwent CT scanning at 80, 100, 120 and 140 kVp, each at ASiR settings of 0, 30 and 50 %, and noise indices (NIs) of 5.5, 11 and 22. The volume CT dose index (CTDI vol ), image noise, and attenuation values of liver and fat were analyzed for 20 data sets. Size-specific dose estimates (SSDEs) and liver-to-fat contrast-to-noise ratios (CNRs) were calculated. Values for different combinations of kVp, ASiR, and NI were compared. The CTDI vol varied by a power of 2 with kVp values between 80 and 140 without ASiR. Increasing ASiR levels allowed a larger decrease in CTDI vol and SSDE at higher kVp than at lower kVp while image noise was held constant. In addition, CTDI vol and SSDE decreased with increasing NI at each kVp, but the decrease was greater at higher kVp than at lower kVp. Image noise increased with decreasing kVp despite a fixed NI; however, this noise could be offset with the use of ASiR. The CT number of the liver remained unchanged whereas that of fat decreased as the kVp decreased. Image noise and dose vary in a complicated manner when the kVp, ASiR, and NI are varied in a human cadaver. Optimization of CT protocols will require balancing of the effects of each of these parameters to maximize image quality while minimizing dose.

The Ebola virus VP35 protein binds viral immunostimulatory and host RNAs identified through deep sequencing

PubMed Central

Voorhies, Alexander A.; Luthra, Priya; Puri, Vinita; Stockwell, Timothy B.; Lorenzi, Hernan; Basler, Christopher F.; Shabman, Reed S.

2017-01-01

Ebola virus and Marburg virus are members of the Filovirdae family and causative agents of hemorrhagic fever with high fatality rates in humans. Filovirus virulence is partially attributed to the VP35 protein, a well-characterized inhibitor of the RIG-I-like receptor pathway that triggers the antiviral interferon (IFN) response. Prior work demonstrates the ability of VP35 to block potent RIG-I activators, such as Sendai virus (SeV), and this IFN-antagonist activity is directly correlated with its ability to bind RNA. Several structural studies demonstrate that VP35 binds short synthetic dsRNAs; yet, there are no data that identify viral immunostimulatory RNAs (isRNA) or host RNAs bound to VP35 in cells. Utilizing a SeV infection model, we demonstrate that both viral isRNA and host RNAs are bound to Ebola and Marburg VP35s in cells. By deep sequencing the purified VP35-bound RNA, we identified the SeV copy-back defective interfering (DI) RNA, previously identified as a robust RIG-I activator, as the isRNA bound by multiple filovirus VP35 proteins, including the VP35 protein from the West African outbreak strain (Makona EBOV). Moreover, RNAs isolated from a VP35 RNA-binding mutant were not immunostimulatory and did not include the SeV DI RNA. Strikingly, an analysis of host RNAs bound by wild-type, but not mutant, VP35 revealed that select host RNAs are preferentially bound by VP35 in cell culture. Taken together, these data support a model in which VP35 sequesters isRNA in virus-infected cells to avert RIG-I like receptor (RLR) activation. PMID:28636653

Different Temporal Effects of Ebola Virus VP35 and VP24 Proteins on Global Gene Expression in Human Dendritic Cells.

PubMed

Ilinykh, Philipp A; Lubaki, Ndongala M; Widen, Steven G; Renn, Lynnsey A; Theisen, Terence C; Rabin, Ronald L; Wood, Thomas G; Bukreyev, Alexander

2015-08-01

Ebola virus (EBOV) causes a severe hemorrhagic fever with a deficient immune response, lymphopenia, and lymphocyte apoptosis. Dendritic cells (DC), which trigger the adaptive response, do not mature despite EBOV infection. We recently demonstrated that DC maturation is unblocked by disabling the innate response antagonizing domains (IRADs) in EBOV VP35 and VP24 by the mutations R312A and K142A, respectively. Here we analyzed the effects of VP35 and VP24 with the IRADs disabled on global gene expression in human DC. Human monocyte-derived DC were infected by wild-type (wt) EBOV or EBOVs carrying the mutation in VP35 (EBOV/VP35m), VP24 (EBOV/VP24m), or both (EBOV/VP35m/VP24m). Global gene expression at 8 and 24 h was analyzed by deep sequencing, and the expression of interferon (IFN) subtypes up to 5 days postinfection was analyzed by quantitative reverse transcription-PCR (qRT-PCR). wt EBOV induced a weak global gene expression response, including markers of DC maturation, cytokines, chemokines, chemokine receptors, and multiple IFNs. The VP35 mutation unblocked the expression, resulting in a dramatic increase in expression of these transcripts at 8 and 24 h. Surprisingly, DC infected with EBOV/VP24m expressed lower levels of many of these transcripts at 8 h after infection, compared to wt EBOV. In contrast, at 24 h, expression of the transcripts increased in DC infected with any of the three mutants, compared to wt EBOV. Moreover, sets of genes affected by the two mutations only partially overlapped. Pathway analysis demonstrated that the VP35 mutation unblocked pathways involved in antigen processing and presentation and IFN signaling. These data suggest that EBOV IRADs have profound effects on the host adaptive immune response through massive transcriptional downregulation of DC. This study shows that infection of DC with EBOV, but not its mutant forms with the VP35 IRAD and/or VP24 IRAD disabled, causes a global block in expression of host genes. The temporal effects of mutations disrupting the two IRADs differ, and the lists of affected genes only partially overlap such that VP35 and VP24 IRADs each have profound effects on antigen presentation by exposed DC. The global modulation of DC gene expression and the resulting lack of their maturation represent a major mechanism by which EBOV disables the T cell response and suggests that these suppressive pathways are a therapeutic target that may unleash the T cell responses during EBOV infection. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Manufacturing data analytics using a virtual factory representation.

PubMed

Jain, Sanjay; Shao, Guodong; Shin, Seung-Jun

2017-01-01

Large manufacturers have been using simulation to support decision-making for design and production. However, with the advancement of technologies and the emergence of big data, simulation can be utilised to perform and support data analytics for associated performance gains. This requires not only significant model development expertise, but also huge data collection and analysis efforts. This paper presents an approach within the frameworks of Design Science Research Methodology and prototyping to address the challenge of increasing the use of modelling, simulation and data analytics in manufacturing via reduction of the development effort. The use of manufacturing simulation models is presented as data analytics applications themselves and for supporting other data analytics applications by serving as data generators and as a tool for validation. The virtual factory concept is presented as the vehicle for manufacturing modelling and simulation. Virtual factory goes beyond traditional simulation models of factories to include multi-resolution modelling capabilities and thus allowing analysis at varying levels of detail. A path is proposed for implementation of the virtual factory concept that builds on developments in technologies and standards. A virtual machine prototype is provided as a demonstration of the use of a virtual representation for manufacturing data analytics.

A pragmatic approach to determine the optimal kVp in cone beam CT: balancing contrast-to-noise ratio and radiation dose

PubMed Central

Silkosessak, O; Jacobs, R; Bogaerts, R; Bosmans, H; Panmekiate, S

2014-01-01

Objectives: To determine the optimal kVp setting for a particular cone beam CT (CBCT) device by maximizing technical image quality at a fixed radiation dose. Methods: The 3D Accuitomo 170 (J. Morita Mfg. Corp., Kyoto, Japan) CBCT was used. The radiation dose as a function of kVp was measured in a cylindrical polymethyl methacrylate (PMMA) phantom using a small-volume ion chamber. Contrast-to-noise ratio (CNR) was measured using a PMMA phantom containing four materials (air, aluminium, polytetrafluoroethylene and low-density polyethylene), which was scanned using 180 combinations of kVp/mA, ranging from 60/1 to 90/8. The CNR was measured for each material using PMMA as background material. The pure effect of kVp and mAs on the CNR values was analysed. Using a polynomial fit for CNR as a function of mA for each kVp value, the optimal kVp was determined at five dose levels. Results: Absorbed doses ranged between 0.034 mGy mAs−1 (14 × 10 cm, 60 kVp) and 0.108 mGy mAs−1 (14 × 10 cm, 90 kVp). The relation between kVp and dose was quasilinear (R2 > 0.99). The effect of mA and kVp on CNR could be modelled using a second-degree polynomial. At a fixed dose, there was a tendency for higher CNR values at increasing kVp values, especially at low dose levels. A dose reduction through mA was more efficient than an equivalent reduction through kVp in terms of image quality deterioration. Conclusions: For the investigated CBCT model, the most optimal contrast at a fixed dose was found at the highest available kVp setting. There is great potential for dose reduction through mA with a minimal loss in image quality. PMID:24708447

Study of the Nankai seismogenic fault using dynamic wave propagation modelling of digital rock from the Nobeoka Fault

NASA Astrophysics Data System (ADS)

Eng, Chandoeun; Ikeda, Tatsunori; Tsuji, Takeshi

2018-10-01

To understand the characteristics of the Nankai seismogenic fault in the plate convergent margin, we calculated the P- and S-wave velocities (VP and VS) of digital rock models constructed from core samples of an ancient plate boundary fault at Nobeoka, Kyushu Island, Japan. We first constructed 3D digital rock models from microcomputed tomography images and identified their heterogeneous textures such as cracks and veins. We replaced the cracks and veins with air, water, quartz, calcite and other materials with different bulk and shear moduli. Using the Rotated Staggered Grid Finite-Difference Method, we performed dynamic wave propagation simulations and quantified the effective VP, VS and the ratio of VP to VS (VP/VS) of the 3D digital rock models with different crack-filling minerals. Our results demonstrate that the water-saturated cracks considerably decreased the seismic velocity and increased VP/VS. The VP/VS of the quartz-filled rock model was lower than that in the water-saturated case and in the calcite-filled rock model. By comparing the elastic properties derived from the digital rock models with the seismic velocities (e.g. VP and VP/VS) around the seismogenic fault estimated from field seismic data, we characterised the evolution process of the deep seismogenic fault. The high VP/VS and low VP observed at the transition from aseismic to coseismic regimes in the Nankai Trough can be explained by open cracks (or fractures), while the low VP/VS and high VP observed at the deeper coseismic fault zone suggests quartz-filled cracks. The quartz-rich fault zone characterised as low VP/VS and high VP in this study could partially relate to the coseismic behaviour as suggested by previous studies, because quartz exhibits slip-weakening behaviour (i.e. unstable coseismic slip).

[Effects of canine IL-2 and IL-7 genes on enhancing immunogenicity of canine parvovirus VP2 gene vaccine in mice].

PubMed

Chen, Huihui; Zhong, Fei; Li, Xiujin; Wang, Lu; Sun, Yan; Neng, Changai; Zhang, Kao; Li, Wenyan; Wen, Jiexia

2012-11-04

To investigate the effects of canine interleukin-2 (cIL-2) and cIL-7 genes on enhancing the immunogenicity of canine parvovirus (CPV) VP2 DNA vaccine. The bicistronic vectors of cIL-2 and cIL-7 genes were constructed using the eukaryotic expression vector containing internal ribosome entry site (IRES). The cIL-2/ cIL-7 dicistronic vector plus previously constructed vectors, including CPV VP2 DNA vaccine vector, cIL-2 vector and cIL-7 vector, were used to co-immunize mice with different combinations, consisting of VP2 alone, VP2 + cIL-2, VP2 + cIL-7 and VP2 + cIL-2/cIL-7. The VP2-specific antibody levels in immunized mice were measured by ELISA at different time post-immunization. The proliferation indices and interferon-gamma expression were measured by lymphocyte proliferation assay and ELISA, respectively. The cIL-2/cIL-7 bicistronic vector was correct and could mediate cIL-2 and cIL-7 gene expression in eukaryotic cells. Immunization results revealed that the antibody titers and the neutralizing antibody levels of the mice co-immunized with VP2 + cIL-7/cIL-2 vectors were significantly higher than that with either VP2 + cIL-2 vectors or VP2 + cIL-7 vectors (P < 0.05). The lymphocyte proliferation indices of VP2 + cIL-7/cIL-2 vector-immunized mice were also higher than that of other two groups although not statistically significant. However, the IFN-gamma expression levels of VP2 + cIL-7/cIL-2 vector-immunized mice were significantly higher than other immunized mice (P < 0.05). The cIL-2 and cIL-7 genes showed the significant synergic effects on enhancing the immunogenecity of CPV VP2 DNA vaccine.

Analysis of patient CT dose data using virtualdose

NASA Astrophysics Data System (ADS)

Bennett, Richard

X-ray computer tomography has many benefits to medical and research applications. Recently, over the last decade CT has had a large increase in usage in hospitals and medical diagnosis. In pediatric care, from 2000 to 2006, abdominal CT scans increased by 49 % and chest CT by 425 % in the emergency room (Broder 2007). Enormous amounts of effort have been performed across multiple academic and government groups to determine an accurate measure of organ dose to patients who undergo a CT scan due to the inherent risks with ionizing radiation. Considering these intrinsic risks, CT dose estimating software becomes a necessary tool that health care providers and radiologist must use to determine many metrics to base the risks versus rewards of having an x-ray CT scan. This thesis models the resultant organ dose as body mass increases for patients with all other related scan parameters fixed. In addition to this,this thesis compares a modern dose estimating software, VirtualDose CT to two other programs, CT-Expo and ImPACT CT. The comparison shows how the software's theoretical basis and the phantom they use to represent the human body affect the range of results in organ dose. CT-Expo and ImPACT CT dose estimating software uses a different model for anatomical representation of the organs in the human body and the results show how that approach dramatically changes the outcome. The results categorizes four datasets as compared to the three software types where the appropriate phantom was available. Modeling was done to simulate chest abdominal pelvis scans and whole body scans. Organ dose difference versus body mass index shows as body mass index (BMI) ranges from 23.5 kg/m 2 to 45 kg/m2 the amount of organ dose also trends a percent change from -4.58 to -176.19 %. Comparing organ dose difference with increasing x-ray tube potential from 120 kVp to 140 kVp the percent change in organ dose increases from 55 % to 65 % across all phantoms. In comparing VirtualDose to CT-Expo for organ dose difference versus age, male phantoms show percent difference of -19 % to 25 % for various organs minus bone surface and breast tissues results. Finally, for organ dose difference across all software for average adult phantom the results range from -45 % to 6 % in the comparison of ImPACT CT to VirtualDose and -27 % to 66 % for the comparison of CT-Expo to VirtualDose. In the comparison for increased BMI (done only in VirtualDose), results show that with all other parameters fixed, the organ dose goes down as BMI increases, which is due to the increase in adipose tissue and bulk of the patient model. The range of results when comparing all the three softwares have a wide range, in some cases greater than 150 %, it is evident that using a different anatomical basis for the human phantom and the theoretical basis for the dose estimation will cause fluctuation in the results. Therefore, choosing the software with the most accurate human phantom will provide a closer range to the true dose to the organ.

Purification of full-length VP22 from cells infected with HSV-1: A two-pronged approach for the solubilization and purification of viral proteins for use in biochemical studies

PubMed Central

Dewberry, Ebony J.; Dunkerley, Eric; Duffy, Carol

2012-01-01

Summary VP22, encoded by the UL49 gene, is one of the most abundant proteins of the herpes simplex virus type 1 (HSV-1) tegument and has been shown to be important for virus replication and spread. However, the exact role(s) played by VP22 in the HSV-1 replication cycle have yet to be delineated. The lack of a procedure to purify full-length VP22 has limited molecular studies on VP22 function. A procedure was developed for the purification of soluble, full-length VP22 from cells infected with HSV-1. A recombinant virus encoding His-tagged VP22 was generated and found to express VP22 at levels comparable to the wild type virus upon infection of Vero cells. By experimenting with a wide variety of cell lysis buffer conditions, several buffers that promote the solubility of full-length VP22 were identified. Buffers that gave the highest levels of solubility were then used in immobilized metal ion affinity chromatography experiments to identify conditions that provided the greatest level of VP22 binding and recovery from cobalt and nickel affinity resins. Using this strategy soluble, full-length VP22 was purified from cells infected with HSV-1. PMID:22569534

Interaction of the Mouse Polyomavirus Capsid Proteins with Importins Is Required for Efficient Import of Viral DNA into the Cell Nucleus.

PubMed

Soldatova, Irina; Prilepskaja, Terezie; Abrahamyan, Levon; Forstová, Jitka; Huérfano, Sandra

2018-03-31

The mechanism used by mouse polyomavirus (MPyV) overcomes the crowded cytosol to reach the nucleus has not been fully elucidated. Here, we investigated the involvement of importin α/β1 mediated transport in the delivery of MPyV genomes into the nucleus. Interactions of the virus with importin β1 were studied by co-immunoprecipitation and proximity ligation assay. For infectivity and nucleus delivery assays, the virus and its capsid proteins mutated in the nuclear localization signals (NLSs) were prepared and produced. We found that at early times post infection, virions bound importin β1 in a time dependent manner with a peak of interactions at 6 h post infection. Mutation analysis revealed that only when the NLSs of both VP1 and VP2/3 were disrupted, virus did not bind efficiently to importin β1 and its infectivity remarkably decreased (by 80%). Nuclear targeting of capsid proteins was improved when VP1 and VP2 were co-expressed. VP1 and VP2 were effectively delivered into the nucleus, even when one of the NLS, either VP1 or VP2, was disrupted. Altogether, our results showed that MPyV virions can use VP1 and/or VP2/VP3 NLSs in concert or individually to bind importins to deliver their genomes into the cell nucleus.

Ventral Pallidum Neurons Encode Incentive Value and Promote Cue-Elicited Instrumental Actions.

PubMed

Richard, Jocelyn M; Ambroggi, Frederic; Janak, Patricia H; Fields, Howard L

2016-06-15

The ventral pallidum (VP) is posited to contribute to reward seeking by conveying upstream signals from the nucleus accumbens (NAc). Yet, very little is known about how VP neuron responses contribute to behavioral responses to incentive cues. Here, we recorded activity of VP neurons in a cue-driven reward-seeking task previously shown to require neural activity in the NAc. We find that VP neurons encode both learned cue value and subsequent reward seeking and that activity in VP neurons is required for robust cue-elicited reward seeking. Surprisingly, the onset of VP neuron responses occurs at a shorter latency than cue-elicited responses in NAc neurons. This suggests that this VP encoding is not a passive response to signals generated in the NAc and that VP neurons integrate sensory and motivation-related information received directly from other mesocorticolimbic inputs. Copyright © 2016 Elsevier Inc. All rights reserved.

Mapping the hemagglutination domain of rotaviruses.

PubMed Central

Fuentes-Pananá, E M; López, S; Gorziglia, M; Arias, C F

1995-01-01

Most strains of animal rotaviruses are able to agglutinate erythrocytes, and the surface protein VP4 is the virus hemagglutinin. To map the hemagglutination domain on VP4 while preserving the conformation of the protein, we constructed full-length chimeras between the VP4 genes of hemagglutinating (YM) and nonhemagglutinating (KU) rotavirus strains. The parental and chimeric genes were expressed in insect cells, and the recombinant VP4 proteins were evaluated for their capacity to agglutinate human type O erythrocytes. Three chimeric genes, encoding amino acids 1 to 208 (QKU), 93 to 208 (QC), and 93 to 776 (QYM) of the YM VP4 protein in a KU VP4 background, were constructed. YM VP4 and chimeras QKU and QC were shown to specifically hemagglutinate, indicating that the region between amino acids 93 and 208 of YM VP4 is sufficient to determine the hemagglutination activity of the protein. PMID:7884915

Structure of Rotavirus Outer-Layer Protein VP7 Bound with a Neutralizing Fab

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aoki, Scott T.; Settembre, Ethan C.; Trask, Shane D.

2009-06-17

Rotavirus outer-layer protein VP7 is a principal target of protective antibodies. Removal of free calcium ions (Ca{sup 2+}) dissociates VP7 trimers into monomers, releasing VP7 from the virion, and initiates penetration-inducing conformational changes in the other outer-layer protein, VP4. We report the crystal structure at 3.4 angstrom resolution of VP7 bound with the Fab fragment of a neutralizing monoclonal antibody. The Fab binds across the outer surface of the intersubunit contact, which contains two Ca{sup 2+} sites. Mutations that escape neutralization by other antibodies suggest that the same region bears the epitopes of most neutralizing antibodies. The monovalent Fab ismore » sufficient to neutralize infectivity. We propose that neutralizing antibodies against VP7 act by stabilizing the trimer, thereby inhibiting the uncoating trigger for VP4 rearrangement. A disulfide-linked trimer is a potential subunit immunogen.« less

Imagining Tomorrow's Future Today

ERIC Educational Resources Information Center

St. George, Art

2007-01-01

Today, at the end of 2007, there are evident consolidations in wireless, storage, and virtualization and the path forward seems clearer now than previously. Trends from last year continue strongly, particularly Web 2.0 and the shift to user-driven environments and Internet sites where significant data and video processing is available to those…

Some Psychometric and Design Implications of Game-Based Learning Analytics

ERIC Educational Resources Information Center

Gibson, David; Clarke-Midura, Jody

2013-01-01

The rise of digital game and simulation-based learning applications has led to new approaches in educational measurement that take account of patterns in time, high resolution paths of action, and clusters of virtual performance artifacts. The new approaches, which depart from traditional statistical analyses, include data mining, machine…

Subsurface drainage processes and management impacts

Treesearch

Elizabeth T. Keppeler; David Brown

1998-01-01

Storm-induced streamflow in forested upland watersheds is linked to rainfall by transient, variably saturated flow through several different flow paths. In the absence of exposed bedrock, shallow flow-restrictive layers, or compacted soil surfaces, virtually all of the infiltrated rainfall reaches the stream as subsurface flow. Subsurface runoff can occur within...

Image quality and radiation dose of lower extremity CT angiography at 70 kVp on an integrated circuit detector dual-source computed tomography.

PubMed

Qi, Li; Zhao, Yan'E; Zhou, Chang Sheng; Spearman, James V; Renker, Matthias; Schoepf, U Joseph; Zhang, Long Jiang; Lu, Guang Ming

2015-06-01

Despite the well-established requirement for radiation dose reduction there are few studies examining the potential for lower extremity CT angiography (CTA) at 70 kVp. To compare the image quality and radiation dose of lower extremity CTA at 70 kVp using a dual-source CT system with an integrated circuit detector to similar studies at 120 kVp. A total of 62 patients underwent lower extremity CTA. Thirty-one patients were examined at 70 kVp using a second generation dual-source CT with an integrated circuit detector (70 kVp group) and 31 patients were evaluated at 120 kVp using a first generation dual-source CT (120 kVp group). The attenuation and image noise were measured and signal-to-noise ratio (SNR) and contrast-to-noise ratio (CNR) were calculated. Two radiologists assessed image quality. Radiation dose was compared. The mean attenuation of the 70 kVp group was higher than the 120 kVp group (575 ± 149 Hounsfield units [HU] vs. 258 ± 38 HU, respectively, P < 0.001) as was SNR (44.0 ± 22.0 vs 32.7 ± 13.3, respectively, P = 0.017), CNR (39.7 ± 20.6 vs 26.6 ± 11.7, respectively, P = 0.003) and the mean image quality score (3.7 ± 0.1 vs. 3.2 ± 0.3, respectively, P < 0.001). The inter-observer agreement was good for the 70 kVp group and moderate for the 120 kVp group. The dose-length product was lower in the 70 kVp group (264.5 ± 63.1 mGy × cm vs. 412.4 ± 81.5 mGy × cm, P < 0.001). Lower extremity CTA at 70 kVp allows for lower radiation dose with higher SNR, CNR, and image quality when compared with standard 120 kVp. © The Foundation Acta Radiologica 2014 Reprints and permissions: sagepub.co.uk/journalsPermissions.nav.

Improved image guidance technique for minimally invasive mitral valve repair using real-time tracked 3D ultrasound

NASA Astrophysics Data System (ADS)

Rankin, Adam; Moore, John; Bainbridge, Daniel; Peters, Terry

2016-03-01

In the past ten years, numerous new surgical and interventional techniques have been developed for treating heart valve disease without the need for cardiopulmonary bypass. Heart valve repair is now being performed in a blood-filled environment, reinforcing the need for accurate and intuitive imaging techniques. Previous work has demonstrated how augmenting ultrasound with virtual representations of specific anatomical landmarks can greatly simplify interventional navigation challenges and increase patient safety. These techniques often complicate interventions by requiring additional steps taken to manually define and initialize virtual models. Furthermore, overlaying virtual elements into real-time image data can also obstruct the view of salient image information. To address these limitations, a system was developed that uses real-time volumetric ultrasound alongside magnetically tracked tools presented in an augmented virtuality environment to provide a streamlined navigation guidance platform. In phantom studies simulating a beating-heart navigation task, procedure duration and tool path metrics have achieved comparable performance to previous work in augmented virtuality techniques, and considerable improvement over standard of care ultrasound guidance.

Kinematic evaluation of virtual walking trajectories.

PubMed

Cirio, Gabriel; Olivier, Anne-Hélène; Marchal, Maud; Pettré, Julien

2013-04-01

Virtual walking, a fundamental task in Virtual Reality (VR), is greatly influenced by the locomotion interface being used, by the specificities of input and output devices, and by the way the virtual environment is represented. No matter how virtual walking is controlled, the generation of realistic virtual trajectories is absolutely required for some applications, especially those dedicated to the study of walking behaviors in VR, navigation through virtual places for architecture, rehabilitation and training. Previous studies focused on evaluating the realism of locomotion trajectories have mostly considered the result of the locomotion task (efficiency, accuracy) and its subjective perception (presence, cybersickness). Few focused on the locomotion trajectory itself, but in situation of geometrically constrained task. In this paper, we study the realism of unconstrained trajectories produced during virtual walking by addressing the following question: did the user reach his destination by virtually walking along a trajectory he would have followed in similar real conditions? To this end, we propose a comprehensive evaluation framework consisting on a set of trajectographical criteria and a locomotion model to generate reference trajectories. We consider a simple locomotion task where users walk between two oriented points in space. The travel path is analyzed both geometrically and temporally in comparison to simulated reference trajectories. In addition, we demonstrate the framework over a user study which considered an initial set of common and frequent virtual walking conditions, namely different input devices, output display devices, control laws, and visualization modalities. The study provides insight into the relative contributions of each condition to the overall realism of the resulting virtual trajectories.

Identification of a nuclear localization sequence in the polyomavirus capsid protein VP2

NASA Technical Reports Server (NTRS)

Chang, D.; Haynes, J. I. 2nd; Brady, J. N.; Consigli, R. A.; Spooner, B. S. (Principal Investigator)

1992-01-01

A nuclear localization signal (NLS) has been identified in the C-terminal (Glu307-Glu-Asp-Gly-Pro-Gln-Lys-Lys-Lys-Arg-Arg-Leu318) amino acid sequence of the polyomavirus minor capsid protein VP2. The importance of this amino acid sequence for nuclear transport of newly synthesized VP2 was demonstrated by a genetic "subtractive" study using the constructs pSG5VP2 (expressing full-length VP2) and pSG5 delta 3VP2 (expressing truncated VP2, lacking amino acids Glu307-Leu318). These constructs were transfected into COS-7 cells, and the intracellular localization of the VP2 protein was determined by indirect immunofluorescence. These studies revealed that the full-length VP2 was localized in the nucleus, while the truncated VP2 protein was localized in the cytoplasm and not transported to the nucleus. A biochemical "additive" approach was also used to determine whether this sequence could target nonnuclear proteins to the nucleus. A synthetic peptide identical to VP2 amino acids Glu307-Leu318 was cross-linked to the nonnuclear proteins bovine serum albumin (BSA) or immunoglobulin G (IgG). The conjugates were then labeled with fluorescein isothiocyanate and microinjected into the cytoplasm of NIH 3T6 cells. Both conjugates localized in the nucleus of the microinjected cells, whereas unconjugated BSA and IgG remained in the cytoplasm. Taken together, these genetic subtractive and biochemical additive approaches have identified the C-terminal sequence of polyoma-virus VP2 (containing amino acids Glu307-Leu318) as the NLS of this protein.

VP24 Is a Chitin-Binding Protein Involved in White Spot Syndrome Virus Infection

PubMed Central

Li, Zaipeng; Han, Yali; Xu, Limei

2015-01-01

ABSTRACT Oral ingestion is the major route of infection for the white spot syndrome virus (WSSV). However, the mechanism by which virus particles in the digestive tract invade host cells is unknown. In the present study, we demonstrate that WSSV virions can bind to chitin through one of the major envelope proteins (VP24). Mutagenesis analysis indicated that amino acids (aa) 186 to 200 in the C terminus of VP24 were required for chitin binding. Moreover, the P-VP24186–200 peptide derived from the VP24 chitin binding region significantly inhibited the VP24-chitin interaction and the WSSV-chitin interaction, implying that VP24 participates in WSSV binding to chitin. Oral inoculation experiments showed that P-VP24186–200 treatment reduced the number of virus particles remaining in the digestive tract during the early stage of infection and greatly hindered WSSV proliferation in shrimp. These data indicate that binding of WSSV to chitin through the viral envelope protein VP24 is essential for WSSV per os infection and provide new ideas for preventing WSSV infection in shrimp farms. IMPORTANCE In this study, we show that WSSV can bind to chitin through the envelope protein VP24. The chitin-binding domain of VP24 maps to amino acids 186 to 200 in the C terminus. Binding of WSSV to chitin through the viral envelope protein VP24 is essential for WSSV per os infection. These findings not only extend our knowledge of WSSV infection but also provide new insights into strategies to prevent WSSV infection in shrimp farms. PMID:26512091

Effect of intertidal exposure on Vibrio parahaemolyticus levels in Pacific Northwest oysters.

PubMed

Nordstrom, J L; Kaysner, C A; Blackstone, G M; Vickery, M C L; Bowers, J C; DePaola, A

2004-10-01

Interest in Vibrio parahaemolyticus (Vp) increased in the United States following Vp-associated gastroenteritis outbreaks in 1997 and 1998 involving the West Coast and other areas. The present study evaluated multiple aspects of Vp ecology in the Pacific Northwest with three objectives: (i) to determine the effect of low-tide exposure on Vp levels in oysters, (ii) to determine the relationship between total and pathogenic Vp, and (iii) to examine sediments and aquatic fauna as reservoirs for pathogenic Vp. Samples were collected from intertidal reefs along Hood Canal, Wash., in August 2001. Fecal matter from marine mammals and aquatic birds as well as intestinal contents from bottom-dwelling fish were tested. Total and pathogenic Vp levels in all the samples were enumerated with colony hybridization procedures using DNA probes that targeted the thermolabile direct hemolysin (tlh) and thermostable direct hemolysin (tdh) genes, respectively. The mean Vp densities in oysters were four to eight times greater at maximum exposure than at the corresponding first exposure. While tdh-positive Vp counts were generally < or = 10 CFU/g at first exposure, counts as high as 160 CFU/g were found at maximum exposure. Vp concentrations in sediments were not significantly different from those in oysters at maximum exposure. Pathogenic (tdh positive) Vp was detected in 9 of 42 (21%) oyster samples at maximum exposure, in 5 of 19 (26%) sediment samples, but in 0 of 9 excreta samples. These results demonstrate that summer conditions permit the multiplication of Vp in oysters exposed by a receding tide.

Development of a rapid and simple immunochromatographic assay to identify Vibrio parahaemolyticus.

PubMed

Sakata, Junko; Kawatsu, Kentaro; Iwasaki, Tadashi; Kumeda, Yuko

2015-09-01

To rapidly and simply determine whether or not bacterial colonies growing on agar were Vibrio parahaemolyticus, we developed an immunochromatographic assay (VP-ICA) using two different monoclonal antibodies (designated mAb-VP34 and mAb-VP109) against the delta subunit of V. parahaemolyticus-F0F1 ATP synthase. The epitopes recognized by mAb-VP34 and mAb-VP109 were mapped to sequences of eight ((47)LLTSSFSA(54)) and six amino acid residues ((16)FDFAVD(21)), respectively. An amino acid sequence similarity search of the NCBI database using BLASTP showed that both epitopic amino acid sequences were present together only in V. parahaemolyticus. When 124 V. parahaemolyticus strains and 94 strains of 27 other Vibrio species or 35 non-Vibrio species were tested using the VP-ICA, the VP-ICA identified V. parahaemolyticus with 100% accuracy. The VP-ICA rapidly and simply identified the pathogen directly from a single agar colony within 30 min, indicating that VP-ICA will greatly reduce labor and time required to identify V. parahaemolyticus compared with conventional biochemical tests. Copyright © 2015. Published by Elsevier B.V.

Intrinsically-disordered N-termini in human parechovirus 1 capsid proteins bind encapsidated RNA.

PubMed

Shakeel, Shabih; Evans, James D; Hazelbaker, Mark; Kao, C Cheng; Vaughan, Robert C; Butcher, Sarah J

2018-04-11

Human parechoviruses (HPeV) are picornaviruses with a highly-ordered RNA genome contained within icosahedrally-symmetric capsids. Ordered RNA structures have recently been shown to interact with capsid proteins VP1 and VP3 and facilitate virus assembly in HPeV1. Using an assay that combines reversible cross-linking, RNA affinity purification and peptide mass fingerprinting (RCAP), we mapped the RNA-interacting regions of the capsid proteins from the whole HPeV1 virion in solution. The intrinsically-disordered N-termini of capsid proteins VP1 and VP3, and unexpectedly, VP0, were identified to interact with RNA. Comparing these results to those obtained using recombinantly-expressed VP0 and VP1 confirmed the virion binding regions, and revealed unique RNA binding regions in the isolated VP0 not previously observed in the crystal structure of HPeV1. We used RNA fluorescence anisotropy to confirm the RNA-binding competency of each of the capsid proteins' N-termini. These findings suggests that dynamic interactions between the viral RNA and the capsid proteins modulate virus assembly, and suggest a novel role for VP0.

Radiation dose and image conspicuity comparison between conventional 120 kVp and 150 kVp with spectral beam shaping for temporal bone CT.

PubMed

Kim, Chang Rae; Jeon, Ji Young

2018-05-01

The purpose of this article is to compare radiation doses and conspicuity of anatomic landmarks of the temporal bone between the CT technique using spectral beam shaping at 150 kVp with a dedicated tin filter (150 kVp-Sn) and the conventional protocol at 120 kVp. 25 patients (mean age, 46.8 ± 21.2 years) were examined using the 150-kVp Sn protocol (200 reference mAs using automated tube current modulation, 64 × 0.6 mm collimation, 0.6 mm slice thickness, pitch 0.8), whereas 30 patients (mean age, 54.5 ± 17.8 years) underwent the 120-kVp protocol (180 mAs, 128 × 0.6 mm collimation, 0.6 mm slice thickness, pitch 0.8). Radiation doses were compared between the two acquisition techniques, and dosimetric data from the literature were reviewed for comparison of radiation dose reduction. Subjective conspicuity of 23 anatomic landmarks of the temporal bone, expressed by 5-point rating scale and objective conspicuity by signal-to-noise ratio (SNR) which measured in 4 different regions of interest (ROI), were compared between 150-kVp Sn and 120-kVp acquisitions. The mean dose-length-product (DLP) and effective dose were significantly lower for the 150-kVp Sn scans (0.26 ± 0.26 mSv) compared with the 120-kVp scans (0.92 ± 0.10 mSv, p < 0.001). The lowest effective dose from the literature-based protocols was 0.31 ± 0.12 mSv, which proposed as a low-dose protocol in the setting of spiral multislice temporal bone CT. SNR was slightly superior for 120-kVp images, however analyzability of the 23 anatomic structures did not differ significantly between 150-kVp Sn and 120-kVp scans. Temporal bone CT performed at 150 kVp with an additional tin filter for spectral shaping markedly reduced radiation exposure when compared with conventional temporal bone CT at 120 kVp while maintaining anatomic conspicuity. The decreased radiation dose of the 150-kVp Sn was also lower in comparison to the previous literature-based low-dose temporal bone CT protocol. Copyright © 2018 Elsevier B.V. All rights reserved.

A comparison of the upper limb movement kinematics utilized by children playing virtual and real table tennis.

PubMed

Bufton, Amy; Campbell, Amity; Howie, Erin; Straker, Leon

2014-12-01

Active virtual games (AVG) may facilitate gross motor skill development, depending on their fidelity. This study compared the movement patterns of nineteen 10-12 yr old children, while playing table tennis on three AVG consoles (Nintendo Wii, Xbox Kinect, Sony Move) and as a real world task. Wrist and elbow joint angles and hand path distance and speed were captured. Children playing real table tennis had significantly smaller (e.g. Wrist Angle Forehand Real-Kinect: Mean Difference (MD): -18.2°, 95% Confidence Interval (CI): -26.15 to -10.26) and slower (e.g. Average Speed Forehand Real-Kinect: MD: -1.98 ms(-1), 95% CI: -2.35 to -1.61) movements than when using all three AVGs. Hand path distance was smaller in forehand and backhand strokes (e.g. Kinect-Wii: MD: 0.46 m, 95% CI: 0.13-0.79) during playing with Kinect than Move and Wii. The movement patterns when playing real and virtual table tennis were different and this may impede the development of real world gross motor skills. Several elements, including display, input and task characteristics, may have contributed to the differences in movement patterns observed. Understanding the interface components for AVGs may help development of higher fidelity games to potentially enhance the development of gross motor skill and thus participation in PA. Copyright © 2014 Elsevier B.V. All rights reserved.

Virtual egocenters as a function of display geometric field of view and eye station point

NASA Technical Reports Server (NTRS)

Psotka, Joseph

1993-01-01

The accurate location of one's virtual egocenter in a geometric space is of critical importance for immersion technologies. This experiment was conducted to investigate the role of field of view (FOV) and observer station points in the perception of the location of one's egocenter (the personal viewpoint) in virtual space. Rivalrous cues to the accurate location of one's egocenter may be one factor involved in simulator sickness. Fourteen subjects viewed an animated 3D model, of the room in which they sat, binocularly, from Eye Station Points (ESP) of either 300 or 800 millimeters. The display was on a 190 by 245 mm monitor, at a resolution of 320 by 200 pixels with 256 colors. They saw four models of the room designed with four geometric field of view (FOVg) conditions of 18, 48, 86, and 140 degrees. They drew the apparent paths of the camera in the room on a bitmap of the room as seen from infinity above. Large differences in the paths of the camera were seen as a function of both FOVg and ESP. Ten of the subjects were then asked to find the position for each display that minimized camera motion. The results fit well with predictions from an equation that took the ratio of human FOV (roughly 180 degrees) to FOVg times the Geometric Eye Point (GEP) of the imager: Zero Station Point = (180/FOVg)*GEP

Reference frames in virtual spatial navigation are viewpoint dependent

PubMed Central

Török, Ágoston; Nguyen, T. Peter; Kolozsvári, Orsolya; Buchanan, Robert J.; Nadasdy, Zoltan

2014-01-01

Spatial navigation in the mammalian brain relies on a cognitive map of the environment. Such cognitive maps enable us, for example, to take the optimal route from a given location to a known target. The formation of these maps is naturally influenced by our perception of the environment, meaning it is dependent on factors such as our viewpoint and choice of reference frame. Yet, it is unknown how these factors influence the construction of cognitive maps. Here, we evaluated how various combinations of viewpoints and reference frames affect subjects' performance when they navigated in a bounded virtual environment without landmarks. We measured both their path length and time efficiency and found that (1) ground perspective was associated with egocentric frame of reference, (2) aerial perspective was associated with allocentric frame of reference, (3) there was no appreciable performance difference between first and third person egocentric viewing positions and (4) while none of these effects were dependent on gender, males tended to perform better in general. Our study provides evidence that there are inherent associations between visual perspectives and cognitive reference frames. This result has implications about the mechanisms of path integration in the human brain and may also inspire designs of virtual reality applications. Lastly, we demonstrated the effective use of a tablet PC and spatial navigation tasks for studying spatial and cognitive aspects of human memory. PMID:25249956

Reference frames in virtual spatial navigation are viewpoint dependent.

PubMed

Török, Agoston; Nguyen, T Peter; Kolozsvári, Orsolya; Buchanan, Robert J; Nadasdy, Zoltan

2014-01-01

Spatial navigation in the mammalian brain relies on a cognitive map of the environment. Such cognitive maps enable us, for example, to take the optimal route from a given location to a known target. The formation of these maps is naturally influenced by our perception of the environment, meaning it is dependent on factors such as our viewpoint and choice of reference frame. Yet, it is unknown how these factors influence the construction of cognitive maps. Here, we evaluated how various combinations of viewpoints and reference frames affect subjects' performance when they navigated in a bounded virtual environment without landmarks. We measured both their path length and time efficiency and found that (1) ground perspective was associated with egocentric frame of reference, (2) aerial perspective was associated with allocentric frame of reference, (3) there was no appreciable performance difference between first and third person egocentric viewing positions and (4) while none of these effects were dependent on gender, males tended to perform better in general. Our study provides evidence that there are inherent associations between visual perspectives and cognitive reference frames. This result has implications about the mechanisms of path integration in the human brain and may also inspire designs of virtual reality applications. Lastly, we demonstrated the effective use of a tablet PC and spatial navigation tasks for studying spatial and cognitive aspects of human memory.

The Ebola Virus VP30-NP Interaction Is a Regulator of Viral RNA Synthesis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kirchdoerfer, Robert N.; Moyer, Crystal L.; Abelson, Dafna M.

Filoviruses are capable of causing deadly hemorrhagic fevers. All nonsegmented negative-sense RNA-virus nucleocapsids are composed of a nucleoprotein (NP), a phosphoprotein (VP35) and a polymerase (L). However, the VP30 RNA-synthesis co-factor is unique to the filoviruses. The assembly, structure, and function of the filovirus RNA replication complex remain unclear. Here, we have characterized the interactions of Ebola, Sudan and Marburg virus VP30 with NP using in vitro biochemistry, structural biology and cell-based mini-replicon assays. We have found that the VP30 C-terminal domain interacts with a short peptide in the C-terminal region of NP. Further, we have solved crystal structures ofmore » the VP30-NP complex for both Ebola and Marburg viruses. These structures reveal that a conserved, proline-rich NP peptide binds a shallow hydrophobic cleft on the VP30 C-terminal domain. Structure-guided Ebola virus VP30 mutants have altered affinities for the NP peptide. Correlation of these VP30-NP affinities with the activity for each of these mutants in a cell-based mini-replicon assay suggests that the VP30-NP interaction plays both essential and inhibitory roles in Ebola virus RNA synthesis.« less

Poly(vinylidene difluoride)/poly(tetrafluoroethylene-co-vinylpyrrolidone) blend membranes with antifouling properties.

PubMed

Sun, Yuchen; Rajabzadeh, Saeid; Fang, Lifeng; Jeon, Sungil; Zhou, Zhuang; Ohmukai, Yoshikage; Miki, Jun; Wang, Xiaolin; Matsuyama, Hideto

2017-06-01

To inhibit fouling phenomenon in membrane process, a new amphiphilic copolymer, poly(tetrafluoroethylene-co-vinylpyrrolidone) (P(TFE-VP)), was blended with poly(vinylidene difluoride) (PVDF) to fabricate a series of antifouling membranes via non solvent induced phase separation (NIPS) method. The effect of copolymer blend ratios and TFE/VP ratios on membrane properties were evaluated, and the stability of P(TFE-VP) in PVDF membrane was studied. The membrane morphology was controlled by adjusting polymer concentration in dope solution, such that all membranes have similar pore size and density, as well as pure water permeability. In evaluating the effect of TFE/VP ratios, the content of VP in dope solutions was also adjusted to allow a fair comparison. We found that for P(TFE-VP) with a higher VP content, adsorption of BSA on polymer film was negligible. Higher blend ratios of this copolymer resulted in higher surface VP content and better hydrophilicity, but antifouling performance ceased to improve when blend ratio was larger than 1:9 (copolymer:PVDF). Meanwhile, a lower VP content in copolymer resulted in inferior hydrophilicity and severe fouling of the blend membranes. It was also proved that comparing with PVP homopolymer, P(TFE-VP) had satisfying stability inside PVDF membrane. Copyright © 2017 Elsevier B.V. All rights reserved.

Effect of bladder augmentation on VP shunt failure rates in spina bifida.

PubMed

Gonzalez, Dani O; Cooper, Jennifer N; McLeod, Daryl J

2017-12-11

Most patients with spina bifida require ventriculoperitoneal (VP) shunt placement. Some also require bladder augmentation, which may increase the risk of VP shunt malfunction and/or failure. The aim of this study was to assess whether bladder augmentation affects the rate of VP shunt failure in this population. Using the Pediatric Health Information System, we studied patients with spina bifida born between 1992 and 2014 who underwent VP shunt placement. Using conditional logistic regression, we compared age- and hospital-matched patients who did and did not undergo a bladder augmentation to determine their difference in rates of VP shunt failure. There were 4192 patients with spina bifida who underwent both surgical closure and VP shunt placement. Of these, 203 patients with bladder augmentation could be matched to 593 patients without bladder augmentation. VP shunt failure occurred within 2 years in 7.7% of patients, the majority of whom were in the group who underwent bladder augmentation (87%). After adjusting for confounders, undergoing bladder augmentation was independently associated with VP shunt failure (HR: 33.5, 95% CI: 13.15-85.44, p< 0.001). Bladder augmentation appears to be associated with VP shunt failure. Additional studies are necessary to better define this relationship and identify risk-reduction techniques.

Conserved differences in protein sequence determine the human pathogenicity of Ebolaviruses

PubMed Central

Pappalardo, Morena; Juliá, Miguel; Howard, Mark J.; Rossman, Jeremy S.; Michaelis, Martin; Wass, Mark N.

2016-01-01

Reston viruses are the only Ebolaviruses that are not pathogenic in humans. We analyzed 196 Ebolavirus genomes and identified specificity determining positions (SDPs) in all nine Ebolavirus proteins that distinguish Reston viruses from the four human pathogenic Ebolaviruses. A subset of these SDPs will explain the differences in human pathogenicity between Reston and the other four ebolavirus species. Structural analysis was performed to identify those SDPs that are likely to have a functional effect. This analysis revealed novel functional insights in particular for Ebolavirus proteins VP40 and VP24. The VP40 SDP P85T interferes with VP40 function by altering octamer formation. The VP40 SDP Q245P affects the structure and hydrophobic core of the protein and consequently protein function. Three VP24 SDPs (T131S, M136L, Q139R) are likely to impair VP24 binding to human karyopherin alpha5 (KPNA5) and therefore inhibition of interferon signaling. Since VP24 is critical for Ebolavirus adaptation to novel hosts, and only a few SDPs distinguish Reston virus VP24 from VP24 of other Ebolaviruses, human pathogenic Reston viruses may emerge. This is of concern since Reston viruses circulate in domestic pigs and can infect humans, possibly via airborne transmission. PMID:27009368

Conserved differences in protein sequence determine the human pathogenicity of Ebolaviruses.

PubMed

Pappalardo, Morena; Juliá, Miguel; Howard, Mark J; Rossman, Jeremy S; Michaelis, Martin; Wass, Mark N

2016-03-24

Reston viruses are the only Ebolaviruses that are not pathogenic in humans. We analyzed 196 Ebolavirus genomes and identified specificity determining positions (SDPs) in all nine Ebolavirus proteins that distinguish Reston viruses from the four human pathogenic Ebolaviruses. A subset of these SDPs will explain the differences in human pathogenicity between Reston and the other four ebolavirus species. Structural analysis was performed to identify those SDPs that are likely to have a functional effect. This analysis revealed novel functional insights in particular for Ebolavirus proteins VP40 and VP24. The VP40 SDP P85T interferes with VP40 function by altering octamer formation. The VP40 SDP Q245P affects the structure and hydrophobic core of the protein and consequently protein function. Three VP24 SDPs (T131S, M136L, Q139R) are likely to impair VP24 binding to human karyopherin alpha5 (KPNA5) and therefore inhibition of interferon signaling. Since VP24 is critical for Ebolavirus adaptation to novel hosts, and only a few SDPs distinguish Reston virus VP24 from VP24 of other Ebolaviruses, human pathogenic Reston viruses may emerge. This is of concern since Reston viruses circulate in domestic pigs and can infect humans, possibly via airborne transmission.

Heads-Up Display with Virtual Precision Approach Path Indicator as Implemented in a Real-Time Piloted Lifting-Body Simulation

NASA Technical Reports Server (NTRS)

Neuhaus, Jason R.

2018-01-01

This document describes the heads-up display (HUD) used in a piloted lifting-body entry, approach and landing simulation developed for the simulator facilities of the Simulation Development and Analysis Branch (SDAB) at NASA Langley Research Center. The HUD symbology originated with the piloted simulation evaluations of the HL-20 lifting body concept conducted in 1989 at NASA Langley. The original symbology was roughly based on Shuttle HUD symbology, as interpreted by Langley researchers. This document focuses on the addition of the precision approach path indicator (PAPI) lights to the HUD overlay.

Atmospheric radiation model for water surfaces

NASA Technical Reports Server (NTRS)

Turner, R. E.; Gaskill, D. W.; Lierzer, J. R.

1982-01-01

An atmospheric correction model was extended to account for various atmospheric radiation components in remotely sensed data. Components such as the atmospheric path radiance which results from singly scattered sky radiation specularly reflected by the water surface are considered. A component which is referred to as the virtual Sun path radiance, i.e. the singly scattered path radiance which results from the solar radiation which is specularly reflected by the water surface is also considered. These atmospheric radiation components are coded into a computer program for the analysis of multispectral remote sensor data over the Great Lakes of the United States. The user must know certain parameters, such as the visibility or spectral optical thickness of the atmosphere and the geometry of the sensor with respect to the Sun and the target elements under investigation.

Molecular cloning, expression and first antigenic characterization of human astrovirus VP26 structural protein and a C-terminal deleted form.

PubMed

Royuela, Enrique; Sánchez-Fauquier, Alicia

2010-01-01

The open reading frame 2 (ORF2) of human astrovirus (HAstV) encodes the structural VP26 protein that seems to be the main antigenic viral protein. However, its functional role remains unclear. Bioinformatic predictions revealed that VP29 and VP26 proteins could be involved in virus-cell interaction. In this study, we describe for the first time the cloning and expression in Escherichia coli (E. coli) of a recombinant VP26 (rVP26) protein and a VP26 C-terminal truncated form (VP26 Delta C), followed by purification by NTA-Ni(2+) agarose affinity chromatography. Protein expression and purification were evaluated by sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) and Western blot (WB). Then, the purified proteins were evaluated for antigenic properties in enzyme linked immunosorbent assay (ELISA) using a polyclonal antibody (PAb) and a neutralizing monoclonal antibody (nMAb) named PL2, both of them directed to HAstV. The results presented herein indicate that the C-terminal end of the VP26 protein is essential to maintain the neutralizing epitope recognized by nMAb PL2 and that the N-terminus of VP26 protein may contain antigenic lineal-epitopes recognized by PAb. Thus, these recombinant proteins can be ideal tools for further antigenic, biochemical, structural and functional VP26 protein characterization, in order to evaluate its potential role in immunodiagnosis and vaccine studies.

Production of rotavirus-like particles in tomato (Lycopersicon esculentum L.) fruit by expression of capsid proteins VP2 and VP6 and immunological studies.

PubMed

Saldaña, Sergio; Esquivel Guadarrama, Fernando; Olivera Flores, Teresa De Jesús; Arias, Nancy; López, Susana; Arias, Carlos; Ruiz-Medrano, Roberto; Mason, Hugh; Mor, Tsafrir; Richter, Liz; Arntzen, Charles J; Gómez Lim, Miguel A

2006-01-01

A number of different antigens have been successfully expressed in transgenic plants, and some are currently being evaluated as orally delivered vaccines. Here we report the successful expression of rotavirus capsid proteins VP2 and VP6 in fruits of transgenic tomato plants. By western blot analysis, using specific antibodies, we determined that the VP2 and VP6 produced in plants have molecular weights similar to those found in native rotavirus. The plant-synthesized VP6 protein retained the capacity to form trimers. We were able to recover rotavirus virus-like particles from tomato fruit (i.e., tomatoes) by centrifugation on a sucrose cushion and to visualize them by electron microscopy. This result indicated that VP2/VP6 can self-assemble into virus-like particles (VLPs) in plant cells, even though only a small proportion of VP2/VP6 assembled into VLPs. To investigate immunogenicity, adult mice were immunized intraperitoneally (i.p.) three times with a protein extract from a transgenic tomatoes in adjuvant. We found that the transgenic tomato extract induced detectable levels of anti-rotavirus antibodies in serum; however, we did not determine the contribution of either the free rotavirus proteins or the VLPs to the induction of the antibody response. These results suggest the potential of plant-based rotavirus VLPs for the development of a vaccine against rotavirus infection.

Mutations Abrogating VP35 Interaction with Double-Stranded RNA Render Ebola Virus Avirulent in Guinea Pigs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Prins, Kathleen C.; Delpeut, Sebastien; Leung, Daisy W.

2010-10-11

Ebola virus (EBOV) protein VP35 is a double-stranded RNA (dsRNA) binding inhibitor of host interferon (IFN)-{alpha}/{beta} responses that also functions as a viral polymerase cofactor. Recent structural studies identified key features, including a central basic patch, required for VP35 dsRNA binding activity. To address the functional significance of these VP35 structural features for EBOV replication and pathogenesis, two point mutations, K319A/R322A, that abrogate VP35 dsRNA binding activity and severely impair its suppression of IFN-{alpha}/{beta} production were identified. Solution nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography reveal minimal structural perturbations in the K319A/R322A VP35 double mutant and suggest that lossmore » of basic charge leads to altered function. Recombinant EBOVs encoding the mutant VP35 exhibit, relative to wild-type VP35 viruses, minimal growth attenuation in IFN-defective Vero cells but severe impairment in IFN-competent cells. In guinea pigs, the VP35 mutant virus revealed a complete loss of virulence. Strikingly, the VP35 mutant virus effectively immunized animals against subsequent wild-type EBOV challenge. These in vivo studies, using recombinant EBOV viruses, combined with the accompanying biochemical and structural analyses directly correlate VP35 dsRNA binding and IFN inhibition functions with viral pathogenesis. Moreover, these studies provide a framework for the development of antivirals targeting this critical EBOV virulence factor.« less

Accuracy of Dual-Energy Virtual Monochromatic CT Numbers: Comparison between the Single-Source Projection-Based and Dual-Source Image-Based Methods.

PubMed

Ueguchi, Takashi; Ogihara, Ryota; Yamada, Sachiko

2018-03-21

To investigate the accuracy of dual-energy virtual monochromatic computed tomography (CT) numbers obtained by two typical hardware and software implementations: the single-source projection-based method and the dual-source image-based method. A phantom with different tissue equivalent inserts was scanned with both single-source and dual-source scanners. A fast kVp-switching feature was used on the single-source scanner, whereas a tin filter was used on the dual-source scanner. Virtual monochromatic CT images of the phantom at energy levels of 60, 100, and 140 keV were obtained by both projection-based (on the single-source scanner) and image-based (on the dual-source scanner) methods. The accuracy of virtual monochromatic CT numbers for all inserts was assessed by comparing measured values to their corresponding true values. Linear regression analysis was performed to evaluate the dependency of measured CT numbers on tissue attenuation, method, and their interaction. Root mean square values of systematic error over all inserts at 60, 100, and 140 keV were approximately 53, 21, and 29 Hounsfield unit (HU) with the single-source projection-based method, and 46, 7, and 6 HU with the dual-source image-based method, respectively. Linear regression analysis revealed that the interaction between the attenuation and the method had a statistically significant effect on the measured CT numbers at 100 and 140 keV. There were attenuation-, method-, and energy level-dependent systematic errors in the measured virtual monochromatic CT numbers. CT number reproducibility was comparable between the two scanners, and CT numbers had better accuracy with the dual-source image-based method at 100 and 140 keV. Copyright © 2018 The Association of University Radiologists. Published by Elsevier Inc. All rights reserved.

New developments in digital pathology: from telepathology to virtual pathology laboratory.

PubMed

Kayser, Klaus; Kayser, Gian; Radziszowski, Dominik; Oehmann, Alexander

2004-01-01

To analyse the present status and future development of computerized diagnostic pathology in terms of work-flow integrative telepathology and virtual laboratory. Telepathology has left its childhood. The technical development of telepathology is mature, in contrast to that of virtual pathology. Two kinds of virtual pathology laboratories are emerging: a) those with distributed pathologists and distributed (>=1) laboratories associated to individual biopsy stations/surgical theatres, and b) distributed pathologists working in a centralized laboratory. Both are under technical development. Telepathology can be used for e-learning and e-training in pathology, as exemplarily demonstrated on Digital Lung Pathology Pathology (www.pathology-online.org). A virtual pathology institution (mode a) accepts a complete case with the patient's history, clinical findings, and (pre-selected) images for first diagnosis. The diagnostic responsibility is that of a conventional institution. The internet serves as platform for information transfer, and an open server such as the iPATH (http://telepath.patho.unibas.ch) for coordination and performance of the diagnostic procedure. The size of images has to be limited, and usual different magnifications have to be used. A group of pathologists is "on duty", or selects one member for a predefined duty period. The diagnostic statement of the pathologist(s) on duty is retransmitted to the sender with full responsibility. First experiences of a virtual pathology institution group working with the iPATH server (Dr. L. Banach, Dr. G. Haroske, Dr. I. Hurwitz, Dr. K. Kayser, Dr. K.D. Kunze, Dr. M. Oberholzer,) working with a small hospital of the Salomon islands are promising. A centralized virtual pathology institution (mode b) depends upon the digitalisation of a complete slide, and the transfer of large sized images to different pathologists working in one institution. The technical performance of complete slide digitalisation is still under development and does not completely fulfil the requirements of a conventional pathology institution at present. VIRTUAL PATHOLOGY AND E-LEARNING: At present, e-learning systems are "stand-alone" solutions distributed on CD or via internet. A characteristic example is the Digital Lung Pathology CD (www.pathology-online.org), which includes about 60 different rare and common lung diseases and internet access to scientific library systems (PubMed), distant measurement servers (EuroQuant), or electronic journals (Elec J Pathol Histol). A new and complete data base based upon this CD will combine e-learning and e-teaching with the actual workflow in a virtual pathology institution (mode a). The technological problems are solved and do not depend upon technical constraints such as slide scanning systems. Telepathology serves as promotor for a new landscape in diagnostic pathology, the so-called virtual pathology institution. Industrial and scientific efforts will probably allow an implementation of this technique within the next two years.

Molpher: a software framework for systematic chemical space exploration

PubMed Central

2014-01-01

Background Chemical space is virtual space occupied by all chemically meaningful organic compounds. It is an important concept in contemporary chemoinformatics research, and its systematic exploration is vital to the discovery of either novel drugs or new tools for chemical biology. Results In this paper, we describe Molpher, an open-source framework for the systematic exploration of chemical space. Through a process we term ‘molecular morphing’, Molpher produces a path of structurally-related compounds. This path is generated by the iterative application of so-called ‘morphing operators’ that represent simple structural changes, such as the addition or removal of an atom or a bond. Molpher incorporates an optimized parallel exploration algorithm, compound logging and a two-dimensional visualization of the exploration process. Its feature set can be easily extended by implementing additional morphing operators, chemical fingerprints, similarity measures and visualization methods. Molpher not only offers an intuitive graphical user interface, but also can be run in batch mode. This enables users to easily incorporate molecular morphing into their existing drug discovery pipelines. Conclusions Molpher is an open-source software framework for the design of virtual chemical libraries focused on a particular mechanistic class of compounds. These libraries, represented by a morphing path and its surroundings, provide valuable starting data for future in silico and in vitro experiments. Molpher is highly extensible and can be easily incorporated into any existing computational drug design pipeline. PMID:24655571

Molpher: a software framework for systematic chemical space exploration.

PubMed

Hoksza, David; Skoda, Petr; Voršilák, Milan; Svozil, Daniel

2014-03-21

Chemical space is virtual space occupied by all chemically meaningful organic compounds. It is an important concept in contemporary chemoinformatics research, and its systematic exploration is vital to the discovery of either novel drugs or new tools for chemical biology. In this paper, we describe Molpher, an open-source framework for the systematic exploration of chemical space. Through a process we term 'molecular morphing', Molpher produces a path of structurally-related compounds. This path is generated by the iterative application of so-called 'morphing operators' that represent simple structural changes, such as the addition or removal of an atom or a bond. Molpher incorporates an optimized parallel exploration algorithm, compound logging and a two-dimensional visualization of the exploration process. Its feature set can be easily extended by implementing additional morphing operators, chemical fingerprints, similarity measures and visualization methods. Molpher not only offers an intuitive graphical user interface, but also can be run in batch mode. This enables users to easily incorporate molecular morphing into their existing drug discovery pipelines. Molpher is an open-source software framework for the design of virtual chemical libraries focused on a particular mechanistic class of compounds. These libraries, represented by a morphing path and its surroundings, provide valuable starting data for future in silico and in vitro experiments. Molpher is highly extensible and can be easily incorporated into any existing computational drug design pipeline.

Temporal expression and immunogold localization of Plodia interpunctella granulosis virus structural proteins

NASA Technical Reports Server (NTRS)

Funk, C. J.; Consigli, R. A.; Spooner, B. S. (Principal Investigator)

1993-01-01

Monospecific antisera were produced against four structural proteins (VP12, VP17, VP31, and granulin) of the Plodia interpunctella granulosis virus using polypeptides derived by sodium dodecyl sulfate-polyacrylamide gel electrophoresis or acid extraction. The antisera were shown to be specific on immunoblots of SDS-PAGE separated granulosis virus and were further used to detect structural proteins in infected fat body lysates. Immunoblots of fat body lysates from early stages of infection indicated that VP12, VP17, VP31, and granulin were expressed by 2.5 days post-infection. Immunogold labeling of the virus using the monospecific antisera and electron microscopy confirmed earlier reports that granulin is located in the protein matrix, V17 is an envelope protein, and VP31 is a capsid protein.

The Role for Virtual Patients in the Future of Medical Education.

PubMed

Berman, Norman B; Durning, Steven J; Fischer, Martin R; Huwendiek, Soren; Triola, Marc M

2016-09-01

The medical education community is working-across disciplines and across the continuum-to address the current challenges facing the medical education system and to implement strategies to improve educational outcomes. Educational technology offers the promise of addressing these important challenges in ways not previously possible. The authors propose a role for virtual patients (VPs), which they define as multimedia, screen-based interactive patient scenarios. They believe VPs offer capabilities and benefits particularly well suited to addressing the challenges facing medical education. Well-designed, interactive VP-based learning activities can promote the deep learning that is needed to handle the rapid growth in medical knowledge. Clinically oriented learning from VPs can capture intrinsic motivation and promote mastery learning. VPs can also enhance trainees' application of foundational knowledge to promote the development of clinical reasoning, the foundation of medical practice. Although not the entire solution, VPs can support competency-based education. The data created by the use of VPs can serve as the basis for multi-institutional research that will enable the medical education community both to better understand the effectiveness of educational interventions and to measure progress toward an improved system of medical education.

C Terminus of Infectious Bursal Disease Virus Major Capsid Protein VP2 Is Involved in Definition of the T Number for Capsid Assembly

PubMed Central

Castón, José R.; Martínez-Torrecuadrada, Jorge L.; Maraver, Antonio; Lombardo, Eleuterio; Rodríguez, José F.; Casal, J. Ignacio; Carrascosa, José L.

2001-01-01

Infectious bursal disease virus (IBDV), a member of the Birnaviridae family, is a double-stranded RNA virus. The IBDV capsid is formed by two major structural proteins, VP2 and VP3, which assemble to form a T=13 markedly nonspherical capsid. During viral infection, VP2 is initially synthesized as a precursor, called VPX, whose C end is proteolytically processed to the mature form during capsid assembly. We have computed three-dimensional maps of IBDV capsid and virus-like particles built up by VP2 alone by using electron cryomicroscopy and image-processing techniques. The IBDV single-shelled capsid is characterized by the presence of 260 protruding trimers on the outer surface. Five classes of trimers can be distinguished according to their different local environments. When VP2 is expressed alone in insect cells, dodecahedral particles form spontaneously; these may be assembled into larger, fragile icosahedral capsids built up by 12 dodecahedral capsids. Each dodecahedral capsid is an empty T=1 shell composed of 20 trimeric clusters of VP2. Structural comparison between IBDV capsids and capsids consisting of VP2 alone allowed the determination of the major capsid protein locations and the interactions between them. Whereas VP2 forms the outer protruding trimers, VP3 is found as trimers on the inner surface and may be responsible for stabilizing functions. Since elimination of the C-terminal region of VPX is correlated with the assembly of T=1 capsids, this domain might be involved (either alone or in cooperation with VP3) in the induction of different conformations of VP2 during capsid morphogenesis. PMID:11602723

Phylogenetic characterization of Canine Parvovirus VP2 partial sequences from symptomatic dogs samples.

PubMed

Zienius, D; Lelešius, R; Kavaliauskis, H; Stankevičius, A; Šalomskas, A

2016-01-01

The aim of the present study was to detect canine parvovirus (CPV) from faecal samples of clinically ill domestic dogs by polymerase chain reaction (PCR) followed by VP2 gene partial sequencing and molecular characterization of circulating strains in Lithuania. Eleven clinically and antigen-tested positive dog faecal samples, collected during the period of 2014-2015, were investigated by using PCR. The phylogenetic investigations indicated that the Lithuanian CPV VP2 partial sequences (3025-3706 cds) were closely related and showed 99.0-99.9% identity. All Lithuanian sequences were associated with one phylogroup, but grouped in different clusters. Ten of investigated Lithuanian CPV VP2 sequences were closely associated with CPV 2a antigenic variant (99.4% nt identity). Five CPV VP2 sequences from Lithuania were related to CPV-2a, but were rather divergent (6.8 nt differences). Only one CPV VP2 sequence from Lithuania was associated (99.3% nt identity) with CPV-2b VP2 sequences from France, Italy, USA and Korea. The four of eleven investigated Lithuanian dogs with CPV infection symptoms were vaccinated with CPV-2 vaccine, but their VP2 sequences were phylogenetically distantly associated with CPV vaccine strains VP2 sequences (11.5-15.8 nt differences). Ten Lithuanian CPV VP2 sequences had monophyletic relations among the close geographically associated samples, but five of them were rather divergent (1.0% less sequence similarity). The one Lithuanian CPV VP2 sequence was closely related with CPV-2b antigenic variant. All the Lithuanian CPV VP2 partial sequences were conservative and phylogenetically low associated with most commonly used CPV vaccine strains.

Expression, purification and crystallization of two major envelope proteins from white spot syndrome virus

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tang, Xuhua; Hew, Choy Leong, E-mail: dbshewcl@nus.edu.sg

2007-07-01

The crystallization of the N-terminal transmembrane region-truncated VP26 and VP28 of white spot syndrome virus is described. White spot syndrome virus (WSSV) is a major virulent pathogen known to infect penaeid shrimp and other crustaceans. VP26 and VP28, two major envelope proteins from WSSV, have been identified and overexpressed in Escherichia coli. In order to facilitate purification and crystallization, predicted N-terminal transmembrane regions of approximately 35 amino acids have been truncated from both VP26 and VP28. Truncated VP26 and VP28 and their corresponding SeMet-labelled proteins were purified and the SeMet proteins were crystallized by the hanging-drop vapour-diffusion method. Crystals ofmore » SeMet-labelled VP26 were obtained using a reservoir consisting of 0.1 M citric acid pH 3.5, 3.0 M sodium chloride and 1%(w/v) polyethylene glycol 3350, whereas SeMet VP28 was crystallized using a reservoir solution consisting of 25% polyethylene glycol 8000, 0.2 M calcium acetate, 0.1 M Na HEPES pH 7.5 and 1.5%(w/v) 1,2,3-heptanetriol. Crystals of SeMet-labelled VP26 diffract to 2.2 Å resolution and belong to space group R32, with unit-cell parameters a = b = 73.92, c = 199.31 Å. SeMet-labelled VP28 crystallizes in space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 105.33, b = 106.71, c = 200.37 Å, and diffracts to 2.0 Å resolution.« less

RNA binding specificity of Ebola virus transcription factor VP30.

PubMed

Schlereth, Julia; Grünweller, Arnold; Biedenkopf, Nadine; Becker, Stephan; Hartmann, Roland K

2016-09-01

The transcription factor VP30 of the non-segmented RNA negative strand Ebola virus balances viral transcription and replication. Here, we comprehensively studied RNA binding by VP30. Using a novel VP30:RNA electrophoretic mobility shift assay, we tested truncated variants of 2 potential natural RNA substrates of VP30 - the genomic Ebola viral 3'-leader region and its complementary antigenomic counterpart (each ∼155 nt in length) - and a series of other non-viral RNAs. Based on oligonucleotide interference, the major VP30 binding region on the genomic 3'-leader substrate was assigned to the internal expanded single-stranded region (∼ nt 125-80). Best binding to VP30 was obtained with ssRNAs of optimally ∼ 40 nt and mixed base composition; underrepresentation of purines or pyrimidines was tolerated, but homopolymeric sequences impaired binding. A stem-loop structure, particularly at the 3'-end or positioned internally, supports stable binding to VP30. In contrast, dsRNA or RNAs exposing large internal loops flanked by entirely helical arms on both sides are not bound. Introduction of a 5´-Cap(0) structure impaired VP30 binding. Also, ssDNAs bind substantially weaker than isosequential ssRNAs and heparin competes with RNA for binding to VP30, indicating that ribose 2'-hydroxyls and electrostatic contacts of the phosphate groups contribute to the formation of VP30:RNA complexes. Our results indicate a rather relaxed RNA binding specificity of filoviral VP30, which largely differs from that of the functionally related transcription factor of the Paramyxoviridae which binds to ssRNAs as short as 13 nt with a preference for oligo(A) sequences.

Detection of lipid-induced structural changes of the Marburg virus matrix protein VP40 using hydrogen/deuterium exchange-mass spectrometry

PubMed Central

Wijesinghe, Kaveesha J.; Urata, Sarah; Bhattarai, Nisha; Kooijman, Edgar E.; Gerstman, Bernard S.; Chapagain, Prem P.; Li, Sheng; Stahelin, Robert V.

2017-01-01

Marburg virus (MARV) is a lipid-enveloped virus from the Filoviridae family containing a negative sense RNA genome. One of the seven MARV genes encodes the matrix protein VP40, which forms a matrix layer beneath the plasma membrane inner leaflet to facilitate budding from the host cell. MARV VP40 (mVP40) has been shown to be a dimeric peripheral protein with a broad and flat basic surface that can associate with anionic phospholipids such as phosphatidylserine. Although a number of mVP40 cationic residues have been shown to facilitate binding to membranes containing anionic lipids, much less is known on how mVP40 assembles to form the matrix layer following membrane binding. Here we have used hydrogen/deuterium exchange (HDX) mass spectrometry to determine the solvent accessibility of mVP40 residues in the absence and presence of phosphatidylserine and phosphatidylinositol 4,5-bisphosphate. HDX analysis demonstrates that two basic loops in the mVP40 C-terminal domain make important contributions to anionic membrane binding and also reveals a potential oligomerization interface in the C-terminal domain as well as a conserved oligomerization interface in the mVP40 N-terminal domain. Lipid binding assays confirm the role of the two basic patches elucidated with HD/X measurements, whereas molecular dynamics simulations and membrane insertion measurements complement these studies to demonstrate that mVP40 does not appreciably insert into the hydrocarbon region of anionic membranes in contrast to the matrix protein from Ebola virus. Taken together, we propose a model by which association of the mVP40 dimer with the anionic plasma membrane facilitates assembly of mVP40 oligomers. PMID:28167534

Detection of lipid-induced structural changes of the Marburg virus matrix protein VP40 using hydrogen/deuterium exchange-mass spectrometry.

PubMed

Wijesinghe, Kaveesha J; Urata, Sarah; Bhattarai, Nisha; Kooijman, Edgar E; Gerstman, Bernard S; Chapagain, Prem P; Li, Sheng; Stahelin, Robert V

2017-04-14

Marburg virus (MARV) is a lipid-enveloped virus from the Filoviridae family containing a negative sense RNA genome. One of the seven MARV genes encodes the matrix protein VP40, which forms a matrix layer beneath the plasma membrane inner leaflet to facilitate budding from the host cell. MARV VP40 (mVP40) has been shown to be a dimeric peripheral protein with a broad and flat basic surface that can associate with anionic phospholipids such as phosphatidylserine. Although a number of mVP40 cationic residues have been shown to facilitate binding to membranes containing anionic lipids, much less is known on how mVP40 assembles to form the matrix layer following membrane binding. Here we have used hydrogen/deuterium exchange (HDX) mass spectrometry to determine the solvent accessibility of mVP40 residues in the absence and presence of phosphatidylserine and phosphatidylinositol 4,5-bisphosphate. HDX analysis demonstrates that two basic loops in the mVP40 C-terminal domain make important contributions to anionic membrane binding and also reveals a potential oligomerization interface in the C-terminal domain as well as a conserved oligomerization interface in the mVP40 N-terminal domain. Lipid binding assays confirm the role of the two basic patches elucidated with HD/X measurements, whereas molecular dynamics simulations and membrane insertion measurements complement these studies to demonstrate that mVP40 does not appreciably insert into the hydrocarbon region of anionic membranes in contrast to the matrix protein from Ebola virus. Taken together, we propose a model by which association of the mVP40 dimer with the anionic plasma membrane facilitates assembly of mVP40 oligomers. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Rotavirus architecture at subnanometer resolution.

PubMed

Li, Zongli; Baker, Matthew L; Jiang, Wen; Estes, Mary K; Prasad, B V Venkataram

2009-02-01

Rotavirus, a nonturreted member of the Reoviridae, is the causative agent of severe infantile diarrhea. The double-stranded RNA genome encodes six structural proteins that make up the triple-layer particle. X-ray crystallography has elucidated the structure of one of these capsid proteins, VP6, and two domains from VP4, the spike protein. Complementing this work, electron cryomicroscopy (cryoEM) has provided relatively low-resolution structures for the triple-layer capsid in several biochemical states. However, a complete, high-resolution structural model of rotavirus remains unresolved. Combining new structural analysis techniques with the subnanometer-resolution cryoEM structure of rotavirus, we now provide a more detailed structural model for the major capsid proteins and their interactions within the triple-layer particle. Through a series of intersubunit interactions, the spike protein (VP4) adopts a dimeric appearance above the capsid surface, while forming a trimeric base anchored inside one of the three types of aqueous channels between VP7 and VP6 capsid layers. While the trimeric base suggests the presence of three VP4 molecules in one spike, only hints of the third molecule are observed above the capsid surface. Beyond their interactions with VP4, the interactions between VP6 and VP7 subunits could also be readily identified. In the innermost T=1 layer composed of VP2, visualization of the secondary structure elements allowed us to identify the polypeptide fold for VP2 and examine the complex network of interactions between this layer and the T=13 VP6 layer. This integrated structural approach has resulted in a relatively high-resolution structural model for the complete, infectious structure of rotavirus, as well as revealing the subtle nuances required for maintaining interactions in such a large macromolecular assembly.

Structure of the Reston ebolavirus VP30 C-terminal domain.

PubMed

Clifton, Matthew C; Kirchdoerfer, Robert N; Atkins, Kateri; Abendroth, Jan; Raymond, Amy; Grice, Rena; Barnes, Steve; Moen, Spencer; Lorimer, Don; Edwards, Thomas E; Myler, Peter J; Saphire, Erica Ollmann

2014-04-01

The ebolaviruses can cause severe hemorrhagic fever. Essential to the ebolavirus life cycle is the protein VP30, which serves as a transcriptional cofactor. Here, the crystal structure of the C-terminal, NP-binding domain of VP30 from Reston ebolavirus is presented. Reston VP30 and Ebola VP30 both form homodimers, but the dimeric interfaces are rotated relative to each other, suggesting subtle inherent differences or flexibility in the dimeric interface.

Integrin-Using Rotaviruses Bind α2β1 Integrin α2 I Domain via VP4 DGE Sequence and Recognize αXβ2 and αVβ3 by Using VP7 during Cell Entry

PubMed Central

Graham, Kate L.; Halasz, Peter; Tan, Yan; Hewish, Marilyn J.; Takada, Yoshikazu; Mackow, Erich R.; Robinson, Martyn K.; Coulson, Barbara S.

2003-01-01

Integrins α2β1, αXβ2, and αVβ3 have been implicated in rotavirus cell attachment and entry. The virus spike protein VP4 contains the α2β1 ligand sequence DGE at amino acid positions 308 to 310, and the outer capsid protein VP7 contains the αXβ2 ligand sequence GPR. To determine the viral proteins and sequences involved and to define the roles of α2β1, αXβ2, and αVβ3, we analyzed the ability of rotaviruses and their reassortants to use these integrins for cell binding and infection and the effect of peptides DGEA and GPRP on these events. Many laboratory-adapted human, monkey, and bovine viruses used integrins, whereas all porcine viruses were integrin independent. The integrin-using rotavirus strains each interacted with all three integrins. Integrin usage related to VP4 serotype independently of sialic acid usage. Analysis of rotavirus reassortants and assays of virus binding and infectivity in integrin-transfected cells showed that VP4 bound α2β1, and VP7 interacted with αXβ2 and αVβ3 at a postbinding stage. DGEA inhibited rotavirus binding to α2β1 and infectivity, whereas GPRP binding to αXβ2 inhibited infectivity but not binding. The truncated VP5* subunit of VP4, expressed as a glutathione S-transferase fusion protein, bound the expressed α2 I domain. Alanine mutagenesis of D308 and G309 in VP5* eliminated VP5* binding to the α2 I domain. In a novel process, integrin-using viruses bind the α2 I domain of α2β1 via DGE in VP4 and interact with αXβ2 (via GPR) and αVβ3 by using VP7 to facilitate cell entry and infection. PMID:12941907

Crystal Structures of Major Envelope Proteins VP26 and VP28 from White Spot Syndrome Virus Shed Light on Their Evolutionary Relationship

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tang,X.; Wu, J.; Sivaraman, J.

2007-01-01

White spot syndrome virus (WSSV) is a virulent pathogen known to infect various crustaceans. It has bacilliform morphology with a tail-like appendage at one end. The envelope consists of four major proteins. Envelope structural proteins play a crucial role in viral infection and are believed to be the first molecules to interact with the host. Here, we report the localization and crystal structure of major envelope proteins VP26 and VP28 from WSSV at resolutions of 2.2 and 2.0 {angstrom}, respectively. These two proteins alone account for approximately 60% of the envelope, and their structures represent the first two structural envelopemore » proteins of WSSV. Structural comparisons among VP26, VP28, and other viral proteins reveal an evolutionary relationship between WSSV envelope proteins and structural proteins from other viruses. Both proteins adopt {beta}-barrel architecture with a protruding N-terminal region. We have investigated the localization of VP26 and VP28 using immunoelectron microscopy. This study suggests that VP26 and VP28 are located on the outer surface of the virus and are observed as a surface protrusion in the WSSV envelope, and this is the first convincing observation for VP26. Based on our studies combined with the literature, we speculate that the predicted N-terminal transmembrane region of VP26 and VP28 may anchor on the viral envelope membrane, making the core {beta}-barrel protrude outside the envelope, possibly to interact with the host receptor or to fuse with the host cell membrane for effective transfer of the viral infection. Furthermore, it is tempting to extend this host interaction mode to other structural viral proteins of similar structures. Our finding has the potential to extend further toward drug and vaccine development against WSSV.« less

Effects of Human Parvovirus B19 and Bocavirus VP1 Unique Region on Tight Junction of Human Airway Epithelial A549 Cells

PubMed Central

Chiu, Chun-Ching; Shi, Ya-Fang; Yang, Jiann-Jou; Hsiao, Yuan-Chao; Tzang, Bor-Show; Hsu, Tsai-Ching

2014-01-01

As is widely recognized, human parvovirus B19 (B19) and human bocavirus (HBoV) are important human pathogens. Obviously, both VP1 unique region (VP1u) of B19 and HBoV exhibit the secreted phospholipase A2 (sPLA2)-like enzymatic activity and are recognized to participate in the pathogenesis of lower respiratory tract illnesses. However, exactly how, both VP1u from B19 and HBoV affect tight junction has seldom been addressed. Therefore, this study investigates how B19-VP1u and HBoV-VP1u may affect the tight junction of the airway epithelial A549 cells by examining phospholipase A2 activity and transepithelial electrical resistance (TEER) as well as performing immunoblotting analyses. Experimental results indicate that TEER is more significantly decreased in A549 cells by treatment with TNF-α (10 ng), two dosages of B19-VP1u and BoV-VP1u (400 ng and 4000 ng) or bee venom PLA2 (10 ng) than that of the control. Accordingly, more significantly increased claudin-1 and decreased occludin are detected in A549 cells by treatment with TNF-α or both dosages of HBoV-VP1u than that of the control. Additionally, more significantly decreased Na+/K+ ATPase is observed in A549 cells by treatment with TNF-α, high dosage of B19-VP1u or both dosages of BoV-VP1u than that of the control. Above findings suggest that HBoV-VP1u rather than B19 VP1u likely plays more important roles in the disruption of tight junction in the airway tract. Meanwhile, this discrepancy appears not to be associated with the secreted phospholipase A2 (sPLA2)-like enzymatic activity. PMID:25268969

Virtual geotechnical laboratory experiments using a simulator

NASA Astrophysics Data System (ADS)

Penumadu, Dayakar; Zhao, Rongda; Frost, David

2000-04-01

The details of a test simulator that provides a realistic environment for performing virtual laboratory experimentals in soil mechanics is presented. A computer program Geo-Sim that can be used to perform virtual experiments, and allow for real-time observations of material response is presented. The results of experiments, for a given set of input parameters, are obtained with the test simulator using well-trained artificial neural-network-based soil models for different soil types and stress paths. Multimedia capabilities are integrated in Geo-Sim, using software that links and controls a laser disc player with a real-time parallel processing ability. During the simulation of a virtual experiment, relevant portions of the video image of a previously recorded test on an actual soil specimen are dispalyed along with the graphical presentation of response from the feedforward ANN model predictions. The pilot simulator developed to date includes all aspects related to performing a triaxial test on cohesionless soil under undrained and drained conditions. The benefits of the test simulator are also presented.

Cocaine Inhibition of Synaptic Transmission in the Ventral Pallidum Is Pathway-Specific and Mediated by Serotonin.

PubMed

Matsui, Aya; Alvarez, Veronica A

2018-06-26

The ventral pallidum (VP) is part of the basal ganglia circuitry and a target of both direct and indirect pathway projections from the nucleus accumbens. VP is important in cocaine reinforcement, and the firing of VP neurons is modulated in vivo during cocaine self-administration. This modulation of firing is thought to be indirect via cocaine actions on dopamine in the accumbens. Here, we show that cocaine directly inhibits synaptic transmission evoked by selective stimulation of indirect pathway projections to VP neurons. The inhibition is independent of dopamine receptor activation, absent in 5-HT1B knockout mice, and mimicked by a serotonin transporter (SERT) blocker. SERT-expressing neurons in dorsal raphe project to the VP. Optogenetic stimulation of these projections evokes serotonin transients and effectively inhibits GABAergic transmission to VP neurons. This study shows that cocaine increases endogenous serotonin in the VP to suppress synaptic transmission selectively from indirect pathway projections to VP neurons. Published by Elsevier Inc.

Recombinant VP1 protein of duck hepatitis virus 1 expressed in Pichia pastoris and its immunogenicity in ducks.

PubMed

Wang, C; Li, X K; Wu, T C; Wang, Y; Zhang, C J; Cheng, X C; Chen, P Y

2014-01-01

The VP1 gene of duck hepatitis virus type 1 (DHV-1) strain VJ09 was amplified by reverse transcription PCR from the liver of a duckling with clinical symptoms of viral hepatitis. The resulting VP1 cDNA was 720 bp in length and encoded a 240-amino-acid protein. In VP1 gene-based phylogenetic analysis, the VJ09 strain grouped with DHV-1 genotype C. The VP1 gene was inserted into the expression vector pPICZαA and expressed in Pichia pastoris. The expressed VP1 protein was purified and identified by western blot analysis. To evaluate the recombinant VP1's immunogenic potential in ducklings, the antibodies raised in the immunized ducklings were titrated by ELISA, and lymphocyte proliferation and virus neutralization assays were performed. The results show that the recombinant VP1 protein induced a significant immune response in ducklings and this could be a candidate for the development of a subunit vaccine against DHV-1 genotype C.

Recombinant VP1 protein as a potential marker for the diagnosis of acute hepatitis A virus infection.

PubMed

da Silva Junior, Haroldo Cid; da Silva, Edimilson Domingos; Lewis-Ximenez de Souza Rodrigues, Lia Laura; Medeiros, Marco Alberto

2017-07-01

Since hepatitis A virus (HAV) production is time-consuming and expensive, the use of recombinant proteins may represent an alternative source of antigens for diagnostic purposes. The present study aimed to express, purify and evaluate the potential of recombinant VP1 protein (rVP1) as a marker for the diagnosis of acute HAV infection. The rVP1 was expressed and purified successfully from Escherichia coli. The purified rVP1 was used to establish an in-house enzyme-linked immunosorbent assay (ELISA-rVP1) for detection of IgM antibodies in sera from HAV-positive patients. For a cut-off point of 0.351, the sensitivity and specificity of ELISA-rVP1 were 100.0% and 95.0%, respectively. These results indicate that rVP1 may be a useful antigen for detection of IgM antibodies against HAV. Copyright © 2017 Elsevier B.V. All rights reserved.

Targeting of rotavirus VP6 to DEC-205 induces protection against the infection in mice.

PubMed

Badillo-Godinez, O; Gutierrez-Xicotencatl, L; Plett-Torres, T; Pedroza-Saavedra, A; Gonzalez-Jaimes, A; Chihu-Amparan, L; Maldonado-Gama, M; Espino-Solis, G; Bonifaz, L C; Esquivel-Guadarrama, F

2015-08-20

Rotavirus (RV) is the primary etiologic agent of severe gastroenteritis in human infants. Although two attenuated RV-based vaccines have been licensed to be applied worldwide, they are not so effective in low-income countries, and the induced protection mechanisms have not been clearly established. Thus, it is important to develop new generation vaccines that induce long lasting heterotypic immunity. VP6 constitutes the middle layer protein of the RV virion. It is the most conserved protein and it is the target of protective T-cells; therefore, it is a potential candidate antigen for a new generation vaccine against the RV infection. We determined whether targeting the DEC-205 present in dendritic cells (DCs) with RV VP6 could induce protection at the intestinal level. VP6 was cross-linked to a monoclonal antibody (mAb) against murine DEC-205 (αDEC-205:VP6), and BALB/c mice were inoculated subcutaneously (s.c.) twice with the conjugated containing 1.5 μg of VP6 in the presence of polyinosinic-polycytidylic acid (Poly I:C) as adjuvant. As controls and following the same protocol, mice were immunized with ovalbumin (OVA) cross-linked to the mAb anti-DEC-205 (αDEC-205:OVA), VP6 cross-linked to a control isotype mAb (Isotype:VP6), 3 μg of VP6 alone, Poly I:C or PBS. Two weeks after the last inoculation, mice were orally challenged with a murine RV. Mice immunized with α-DEC-205:VP6 and VP6 alone presented similar levels of serum Abs to VP6 previous to the virus challenge. However, after the virus challenge, only α-DEC-205:VP6 induced up to a 45% IgA-independent protection. Memory T-helper (Th) cells from the spleen and the mesenteric lymph node (MLN) showed a Th1-type response upon antigen stimulation in vitro. These results show that when VP6 is administered parenterally targeting DEC-205, it can induce protection at the intestinal level at a very low dose, and this protection may be Th1-type cell dependent. Copyright © 2015 Elsevier Ltd. All rights reserved.

Structural and Functional Characterization of Reston Ebola Virus VP35 Interferon Inhibitory Domain

DOE Office of Scientific and Technical Information (OSTI.GOV)

Leung, Daisy W.; Shabman, Reed S.; Farahbakhsh, Mina

2010-09-21

Ebolaviruses are causative agents of lethal hemorrhagic fever in humans and nonhuman primates. Among the filoviruses characterized thus far, Reston Ebola virus (REBOV) is the only Ebola virus that is nonpathogenic to humans despite the fact that REBOV can cause lethal disease in nonhuman primates. Previous studies also suggest that REBOV is less effective at inhibiting host innate immune responses than Zaire Ebola virus (ZEBOV) or Marburg virus. Virally encoded VP35 protein is critical for immune suppression, but an understanding of the relative contributions of VP35 proteins from REBOV and other filoviruses is currently lacking. In order to address thismore » question, we characterized the REBOV VP35 interferon inhibitory domain (IID) using structural, biochemical, and virological studies. These studies reveal differences in double-stranded RNA binding and interferon inhibition between the two species. These observed differences are likely due to increased stability and loss of flexibility in REBOV VP35 IID, as demonstrated by thermal shift stability assays. Consistent with this finding, the 1.71-{angstrom} crystal structure of REBOV VP35 IID reveals that it is highly similar to that of ZEBOV VP35 IID, with an overall backbone r.m.s.d. of 0.64 {angstrom}, but contains an additional helical element at the linker between the two subdomains of VP35 IID. Mutations near the linker, including swapping sequences between REBOV and ZEBOV, reveal that the linker sequence has limited tolerance for variability. Together with the previously solved ligand-free and double-stranded-RNA-bound forms of ZEBOV VP35 IID structures, our current studies on REBOV VP35 IID reinforce the importance of VP35 in immune suppression. Functional differences observed between REBOV and ZEBOV VP35 proteins may contribute to observed differences in pathogenicity, but these are unlikely to be the major determinant. However, the high level of similarity in structure and the low tolerance for sequence variability, coupled with the multiple critical roles played by Ebola virus VP35 proteins, highlight the viability of VP35 as a potential target for therapeutic development.« less

Structural and functional characterization of Reston Ebola virus VP35 interferon inhibitory domain.

PubMed

Leung, Daisy W; Shabman, Reed S; Farahbakhsh, Mina; Prins, Kathleen C; Borek, Dominika M; Wang, Tianjiao; Mühlberger, Elke; Basler, Christopher F; Amarasinghe, Gaya K

2010-06-11

Ebolaviruses are causative agents of lethal hemorrhagic fever in humans and nonhuman primates. Among the filoviruses characterized thus far, Reston Ebola virus (REBOV) is the only Ebola virus that is nonpathogenic to humans despite the fact that REBOV can cause lethal disease in nonhuman primates. Previous studies also suggest that REBOV is less effective at inhibiting host innate immune responses than Zaire Ebola virus (ZEBOV) or Marburg virus. Virally encoded VP35 protein is critical for immune suppression, but an understanding of the relative contributions of VP35 proteins from REBOV and other filoviruses is currently lacking. In order to address this question, we characterized the REBOV VP35 interferon inhibitory domain (IID) using structural, biochemical, and virological studies. These studies reveal differences in double-stranded RNA binding and interferon inhibition between the two species. These observed differences are likely due to increased stability and loss of flexibility in REBOV VP35 IID, as demonstrated by thermal shift stability assays. Consistent with this finding, the 1.71-A crystal structure of REBOV VP35 IID reveals that it is highly similar to that of ZEBOV VP35 IID, with an overall backbone r.m.s.d. of 0.64 A, but contains an additional helical element at the linker between the two subdomains of VP35 IID. Mutations near the linker, including swapping sequences between REBOV and ZEBOV, reveal that the linker sequence has limited tolerance for variability. Together with the previously solved ligand-free and double-stranded-RNA-bound forms of ZEBOV VP35 IID structures, our current studies on REBOV VP35 IID reinforce the importance of VP35 in immune suppression. Functional differences observed between REBOV and ZEBOV VP35 proteins may contribute to observed differences in pathogenicity, but these are unlikely to be the major determinant. However, the high level of similarity in structure and the low tolerance for sequence variability, coupled with the multiple critical roles played by Ebola virus VP35 proteins, highlight the viability of VP35 as a potential target for therapeutic development. Copyright 2010 Elsevier Ltd. All rights reserved.

Research on animation design of growing plant based on 3D MAX technology

NASA Astrophysics Data System (ADS)

Chen, Yineng; Fang, Kui; Bu, Weiqiong; Zhang, Xiaoling; Lei, Menglong

In view of virtual plant has practical demands on quality, image and degree of realism animation in growing process of plant, this thesis design the animation based on mechanism and regularity of plant growth, and propose the design method based on 3D MAX technology. After repeated analysis and testing, it is concluded that there are modeling, rendering, animation fabrication and other key technologies in the animation design process. Based on this, designers can subdivid the animation into seed germination animation, plant growth prophase animation, catagen animation, later animation and blossom animation. This paper compounds the animation of these five stages by VP window to realize the completed 3D animation. Experimental result shows that the animation can realized rapid, visual and realistic simulatation the plant growth process.

Isolation and characterization of two VpYABBY genes from wild Chinese Vitis pseudoreticulata.

PubMed

Xiang, J; Liu, R Q; Li, T M; Han, L J; Zou, Y; Xu, T F; Wei, J Y; Wang, Y J; Xu, Y

2013-12-01

The establishment of abaxial-adaxial polarity is an important feature of the development of lateral organs in plants. Members of the YABBY gene family may be specific to seed-plant-specific transcriptional regulators that play critical roles in promoting abaxial cell fate in the model eudicot, Arabidopsis thaliana. However, recent study has shown that the roles of YABBY genes are not conserved in the development of angiosperms. The establishment of abaxial-adaxial polarity has not been studied in perennial fruit crops. Grapes are an important fruit crop in many regions of the world. Investigating YABBY genes in grapevines should help us to discover more about the key genetic and molecular pathways in grapevine development. To understand the characterization of YABBY genes in grapevines, two YABBY genes, VpYABBY1 (GenBank accession No. KC139089) and VpYABBY2 (GenBank accession No. KC139090), were isolated from the wild Chinese species Vitis pseudoreticulata. Both of these encode YABBY proteins. Sequence characterization and phylogenetic analyses show that VpYABBY1 is group classified into the FIL subfamily while VpYABBY2 is a member of the YAB2 subfamily of Arabidopsis thaliana. Subcellular localization analysis indicates that VpYABBY1 and VpYABBY2 proteins are localized in the nucleus. Tissue specific expressional analysis reveals that VpYABBY1 is expressed strongly in young leaves of grape but only weakly in the mature leaves. Meanwhile, VpYABBY2 is expressed in grape stems, flowers, tendrils, and leaves. Transgenic Arabidopsis plants ectopically expressing VpYABBY1 caused the partial abaxialization of the adaxial epidermises of leaves, behaving similarly to those over-expressing FIL or YAB3 with abaxialized lateral organs. By contrast, ectopic expression of VpYABBY2 in Arabidopsis did not cause any alteration in the adaxial-abaxial polarity. Sequence characterization and phylogenetic analysis revealed that VpYABBY1 and VpYABBY2 are group-classified into two different subfamilies. They have diverged functionally in the control of lateral organ development. VpYABBY1 may have a function in leaf development, while VpYABBY2 may play a specific role in carpel development and grape berry morphogenesis. It is further possible that during the evolution of different species, YABBY family members have preserved different expression regulatory systems and functions.

Performance Benefits with Scene-Linked HUD Symbology: An Attentional Phenomenon?

NASA Technical Reports Server (NTRS)

Levy, Jonathan L.; Foyle, David C.; McCann, Robert S.; Null, Cynthia H. (Technical Monitor)

1999-01-01

Previous research has shown that in a simulated flight task, navigating a path defined by ground markers while maintaining a target altitude is more accurate when an altitude indicator appears in a virtual "scenelinked" format (projected symbology moving as if it were part of the out-the-window environment) compared to the fixed-location, superimposed format found on present-day HUDs (Foyle, McCann & Shelden, 1995). One explanation of the scene-linked performance advantage is that attention can be divided between scene-linked symbology and the outside world more efficiently than between standard (fixed-position) HUD symbology and the outside world. The present study tested two alternative explanations by manipulating the location of the scene-linked HUD symbology relative to the ground path markers. Scene-linked symbology yielded better ground path-following performance than standard fixed-location superimposed symbology regardless of whether the scene-linked symbology appeared directly along the ground path or at various distances off the path. The results support the explanation that the performance benefits found with scene-linked symbology are attentional.

Global Qualitative Flow-Path Modeling for Local State Determination in Simulation and Analysis

NASA Technical Reports Server (NTRS)

Malin, Jane T. (Inventor); Fleming, Land D. (Inventor)

1998-01-01

For qualitative modeling and analysis, a general qualitative abstraction of power transmission variables (flow and effort) for elements of flow paths includes information on resistance, net flow, permissible directions of flow, and qualitative potential is discussed. Each type of component model has flow-related variables and an associated internal flow map, connected into an overall flow network of the system. For storage devices, the implicit power transfer to the environment is represented by "virtual" circuits that include an environmental junction. A heterogeneous aggregation method simplifies the path structure. A method determines global flow-path changes during dynamic simulation and analysis, and identifies corresponding local flow state changes that are effects of global configuration changes. Flow-path determination is triggered by any change in a flow-related device variable in a simulation or analysis. Components (path elements) that may be affected are identified, and flow-related attributes favoring flow in the two possible directions are collected for each of them. Next, flow-related attributes are determined for each affected path element, based on possibly conflicting indications of flow direction. Spurious qualitative ambiguities are minimized by using relative magnitudes and permissible directions of flow, and by favoring flow sources over effort sources when comparing flow tendencies. The results are output to local flow states of affected components.

Interactions between the two surface proteins of rotavirus may alter the receptor-binding specificity of the virus.

PubMed Central

Méndez, E; Arias, C F; López, S

1996-01-01

The infection of target cells by most animal rotavirus strains requires the presence of sialic acids (SAs) on the cell surface. We recently isolated variants from simian rotavirus RRV whose infectivity is no longer dependent on SAs and showed that the mutant phenotype segregates with the gene coding for VP4, one of the two surface proteins of rotaviruses (the other one being VP7). The nucleotide sequence of the VP4 gene of four independently isolated variants showed three amino acid changes, at positions 37 (Leu to Pro), 187 (Lys to Arg), and 267 (Tyr to Cys), in all mutant VP4 proteins compared with RRV VP4. The characterization of revertant viruses from two independent mutants showed that the arginine residue at position 187 changed back to lysine, indicating that this amino acid is involved in the determination of the mutant phenotype. Surprisingly, sequence analysis of reassortant virus DS1XRRV, which depends on SAs to infect the cell, showed that its VP4 gene is identical to the VP4 gene of the variants. Since the only difference between DS1XRRV and the RRV variants is the parental origin of the VP7 gene (human rotavirus DS1 in the reassortant), these findings suggest that the receptor-binding specificity of rotaviruses, via VP4, may be influenced by the associated VP7 protein. PMID:8551583

Decreased LRIG1 in Human Ovarian Cancer Cell SKOV3 Upregulates MRP-1 and Contributes to the Chemoresistance of VP16.

PubMed

Yang, Hua; Yao, Jun; Yin, Jiangpin; Wei, Xuan

2016-05-01

The leucine-rich repeats and immunoglobulin-like domains (LRIG) are used as tumor suppressors in clinical applications. Although the LRIG has been identified to manipulate the cell proliferation via various oncogenic receptor tyrosine kinases in diverse cancers, its role in multidrug resistance needs to be further elucidated, especially in human ovarian cancer. We herein established that the etoposide (VP16)-resistant SKOV3 human ovarian cancer cell clones (SKOV3/VP16 cells) and mRNA expression of LRIG1 were significantly reduced by the treatment of VP16 in a concentration-dependent manner. Moreover, downregulated LRIG1 in SKOV3 could enhance the colony formation and resist the inhibition of proliferation by VP16, leading to the elevated expression of Bcl-2 and decreased apoptosis of SKOV3. Interestingly, our results uncovered that the multidrug resistance-associated protein 1 (MRP-1) was upregulated for the chemoresistance of VP16. To overcome the chemoresistance of SKOV3, SKOV3/VP16 was ectopically expressed of LRIG1. We found that the inhibition of VP16 on colony formation and proliferation was remarkably enhanced with increased apoptosis in SKOV3/VP16. Furthermore, the expression of MRP-1 and Bcl-2 was also inhibited, suggesting that the LRIG1could negatively control MRP-1 and the apoptosis to improve the sensitivity of VP16-related chemotherapy.

[Indirect ELISA for simultaneous detection of antibodies against duck hepatitis A type 1 and 3 viruses].

PubMed

Zhang, Yuyao; Ma, Xiuli; Huang, Bing; Li, Yufeng; Yu, Kexiang; Li, Jianliang; Liu, Cunxia; Han, Hongyu; Cui, Yanshun

2015-04-04

To simultaneously detect antibodies against Duck hepatitis A type 1 (DHAV-1) and type 3 (DHAV-3) viruses, we developed an indirect enzyme-linked immunosobent assay (ELISA) with bacterially expressed recombinant viral protein as antigen in Escherichia coli. We amplified the full-length VP3 gene of DHAV-1 and the full-length VP1 gene of DHAV-3 through reverse transcription-polymerase chain reaction (RT-PCR) and then cloned them into pET-32a expression vector, designated as pET-1VP3-3VP1. The fusion protein DHAV-1VP3-3VP1 expressed correctly and was subsequently used to develop an indirect ELISA assay. DHAV-1VP3-3VP1 fusion protein expressed in BL21 (DE3) cells following induction by Isopropyl-beta-D-1-thiogalactopyranoside (IPTG). The expressed protein was very antigenic and reactive to virus-specific antibodies in western blot assay. The optimal working concentration for coating antigen was 1.0 microg per well and the working concentration of serum samples was 1:200 dilution and the cut-off value that distinguished the positive from negative serum samples was OD650 > OR = 0.38. The ELISA method based on the prokaryotic expression of VP3 (DHAV-1) and VP1 proteins (DHAV-3) can be used effectively for the clinical detection antibodies against DHAV-1 and DHAV-3.

Live Attenuated Vaccine Based on Duck Enteritis Virus against Duck Hepatitis A Virus Types 1 and 3

PubMed Central

Zou, Zhong; Ma, Ji; Huang, Kun; Chen, Huanchun; Liu, Ziduo; Jin, Meilin

2016-01-01

As causative agents of duck viral hepatitis, duck hepatitis A virus type 1 (DHAV-1) and type 3 (DHAV-3) causes significant economic losses in the duck industry. However, a licensed commercial vaccine that simultaneously controls both pathogens is currently unavailable. Here, we generated duck enteritis virus recombinants (rC-KCE-2VP1) containing both VP1 from DHAV-1 (VP1/DHAV-1) and VP1 from DHAV-3 (VP1/DHAV-3) between UL27 and UL26. A self-cleaving 2A-element of FMDV was inserted between the two different types of VP1, allowing production of both proteins from a single open reading frame. Immunofluorescence and Western blot analysis results demonstrated that both VP1 proteins were robustly expressed in rC-KCE-2VP1-infected chicken embryo fibroblasts. Ducks that received a single dose of rC-KCE-2VP1 showed potent humoral and cellular immune responses and were completely protected against challenges of both pathogenic DHAV-1 and DHAV-3 strains. The protection was rapid, achieved as early as 3 days after vaccination. Moreover, viral replication was fully blocked in vaccinated ducks as early as 1 week post-vaccination. These results demonstrated, for the first time, that recombinant rC-KCE-2VP1 is potential fast-acting vaccine against DHAV-1 and DHAV-3. PMID:27777571

The VP40 protein of Marburg virus exhibits impaired budding and increased sensitivity to human tetherin following mouse adaptation.

PubMed

Feagins, Alicia R; Basler, Christopher F

2014-12-01

The Marburg virus VP40 protein is a viral matrix protein that spontaneously buds from cells. It also functions as an interferon (IFN) signaling antagonist by targeting Janus kinase 1 (JAK1). A previous study demonstrated that the VP40 protein of the Ravn strain of Marburg virus (Ravn virus [RAVV]) failed to block IFN signaling in mouse cells, whereas the mouse-adapted RAVV (maRAVV) VP40 acquired the ability to inhibit IFN responses in mouse cells. The increased IFN antagonist function of maRAVV VP40 mapped to residues 57 and 165, which were mutated during the mouse adaptation process. In the present study, we demonstrate that maRAVV VP40 lost the capacity to efficiently bud from human cell lines, despite the fact that both parental and maRAVV VP40s bud efficiently from mouse cell lines. The impaired budding in human cells corresponds with the appearance of protrusions on the surface of maRAVV VP40-expressing Huh7 cells and with an increased sensitivity of maRAVV VP40 to restriction by human tetherin but not mouse tetherin. However, transfer of the human tetherin cytoplasmic tail to mouse tetherin restored restriction of maRAVV VP40. Residues 57 and 165 were demonstrated to contribute to the failure of maRAVV VP40 to bud from human cells, and residue 57 was demonstrated to alter VP40 oligomerization, as assessed by coprecipitation assay, and to determine sensitivity to human tetherin. This suggests that RAVV VP40 acquired, during adaptation to mice, changes in its oligomerization potential that enhanced IFN antagonist function. However, this new capacity impaired RAVV VP40 budding from human cells. Filoviruses, which include Marburg viruses and Ebola viruses, are zoonotic pathogens that cause severe disease in humans and nonhuman primates but do not cause similar disease in wild-type laboratory strains of mice unless first adapted to these animals. Although mouse adaptation has been used as a method to develop small animal models of pathogenesis, the molecular determinants associated with filovirus mouse adaptation are poorly understood. Our study demonstrates how genetic changes that accrued during mouse adaptation of the Ravn strain of Marburg virus have impacted the budding function of the viral VP40 matrix protein. Strikingly, we find impairment of mouse-adapted VP40 budding function in human but not mouse cell lines, and we correlate the impairment with an increased sensitivity of VP40 to restriction by human but not mouse tetherin and with changes in VP40 oligomerization. These data suggest that there are functional costs associated with filovirus adaptation to new hosts and implicate tetherin as a filovirus host restriction factor. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Abscisic acid and stress signals induce Viviparous1 expression in seed and vegetative tissues of maize.

PubMed

Cao, Xueyuan; Costa, Liliana M; Biderre-Petit, Corinne; Kbhaya, Bouchab; Dey, Nrisingha; Perez, Pascual; McCarty, Donald R; Gutierrez-Marcos, Jose F; Becraft, Philip W

2007-02-01

Viviparous1 (Vp1) encodes a B3 domain-containing transcription factor that is a key regulator of seed maturation in maize (Zea mays). However, the mechanisms of Vp1 regulation are not well understood. To examine physiological factors that may regulate Vp1 expression, transcript levels were monitored in maturing embryos placed in culture under different conditions. Expression of Vp1 decreased after culture in hormone-free medium, but was induced by salinity or osmotic stress. Application of exogenous abscisic acid (ABA) also induced transcript levels within 1 h in a dose-dependent manner. The Vp1 promoter fused to beta-glucuronidase or green fluorescent protein reproduced the endogenous Vp1 expression patterns in transgenic maize plants and also revealed previously unknown expression domains of Vp1. The Vp1 promoter is active in the embryo and aleurone cells of developing seeds and, upon drought stress, was also found in phloem cells of vegetative tissues, including cobs, leaves, and stems. Sequence analysis of the Vp1 promoter identified a potential ABA-responsive complex, consisting of an ACGT-containing ABA response element (ABRE) and a coupling element 1-like motif. Electrophoretic mobility shift assay confirmed that the ABRE and putative coupling element 1 components specifically bound proteins in embryo nuclear protein extracts. Treatment of embryos in hormone-free Murashige and Skoog medium blocked the ABRE-protein interaction, whereas exogenous ABA or mannitol treatment restored this interaction. Our data support a model for a VP1-dependent positive feedback mechanism regulating Vp1 expression during seed maturation.

The hepatitis E virus open reading frame 3 product interacts with microtubules and interferes with their dynamics.

PubMed

Kannan, Harilakshmi; Fan, Sumin; Patel, Deendayal; Bossis, Ioannis; Zhang, Yan-Jin

2009-07-01

Hepatitis E virus (HEV) is the causative agent of hepatitis E, a major form of viral hepatitis in developing countries. The open reading frame 3 (ORF3) of HEV encodes a phosphoprotein with a molecular mass of approximately 13 kDa (hereinafter called vp13). vp13 is essential for establishing HEV infections in animals, yet its exact functions are still obscure. Our current study found evidence showing interaction between vp13 and microtubules. Live-cell confocal fluorescence microscopy revealed both filamentous and punctate distribution patterns of vp13 in cells transfected with recombinant ORF3 reporter plasmids. The filamentous pattern of vp13 was altered by a microtubule-destabilizing drug. The vp13 expression led to elevation of acetylated alpha-tubulin, indicating increased microtubule stability. Its association with microtubules was further supported by its presence in microtubule-containing pellets in microtubule isolation assays. Exposure of these pellets to a high-salt buffer caused release of the vp13 to the supernatant, suggesting an electrostatic interaction. Inclusion of ATP and GTP in the lysis buffer during microtubule isolation also disrupted the interaction, indicating its sensitivity to the nucleotides. Further assays showed that motor proteins are needed for the vp13 association with the microtubules because disruption of dynein function abolished the vp13 filamentous pattern. Analysis of ORF3 deletion constructs found that both of the N-terminal hydrophobic domains of vp13 are needed for the interaction. Thus, our findings suggest that the vp13 interaction with microtubules might be needed for establishment of an HEV infection.

Human parvovirus B19 VP1u Protein as inflammatory mediators induces liver injury in naïve mice.

PubMed

Hsu, Tsai-Ching; Chiu, Chun-Ching; Chang, Shun-Chih; Chan, Hsu-Chin; Shi, Ya-Fang; Chen, Tzy-Yen; Tzang, Bor-Show

2016-01-01

Human parvovirus B19 (B19V) is a human pathogen known to be associated with many non-erythroid diseases, including hepatitis. Although B19V VP1-unique region (B19-VP1u) has crucial roles in the pathogenesis of B19V infection, the influence of B19-VP1u proteins on hepatic injury is still obscure. This study investigated the effect and possible inflammatory signaling of B19-VP1u in livers from BALB/c mice that were subcutaneously inoculated with VP1u-expressing COS-7 cells. The in vivo effects of B19-VP1u were analyzed by using live animal imaging system (IVIS), Haematoxylin-Eosin staining, gel zymography, and immunoblotting after inoculation. Markedly hepatocyte disarray and lymphocyte infiltration, enhanced matrix metalloproteinase (MMP)-9 activity and increased phosphorylation of p38, ERK, IKK-α, IκB and NF-κB (p-p65) proteins were observed in livers from BALB/c mice receiving COS-7 cells expressing B19-VP1u as well as the significantly increased CRP, IL-1β and IL-6. Notably, IFN-γ and phosphorylated STAT1, but not STAT3, were also significantly increased in the livers of BALB/c mice that were subcutaneously inoculated with VP1u-expressing COS-7 cells. These findings revealed the effects of B19-VP1u on liver injury and suggested that B19-VP1u may have a role as mediators of inflammation in B19V infection.

Addition of six-His-tagged peptide to the C terminus of adeno-associated virus VP3 does not affect viral tropism or production.

PubMed

Zhang, Huang-Ge; Xie, Jinfu; Dmitriev, Igor; Kashentseva, Elena; Curiel, David T; Hsu, Hui-Chen; Mountz, John D

2002-12-01

Production of large quantities of recombinant adeno-associated virus (AAV) is difficult and not cost-effective. To overcome this problem, we have explored the feasibility of creating a recombinant AAV encoding a 6xHis tag on the VP3 capsid protein. We generated a plasmid vector containing a six-His (6xHis)-tagged AAV VP3. A second plasmid vector was generated that contained the full-length AAV capsid capable of producing VP1 and VP2, but not VP3 due to a mutation at position 2809 that encodes the start codon for VP3. These plasmids, necessary for production of AAV, were transfected into 293 cells to generate a 6xHis-tagged VP3mutant recombinant AAV. The 6xHis-tagged VP3 did not affect the formation of AAV virus, and the physical properties of the 6xHis-modified AAV were equivalent to those of wild-type particles. The 6xHis-tagged AAV did not affect the production titer of recombinant AAV and could be used to purify the recombinant AAV using an Ni-nitrilotriacetic acid column. Addition of the 6xHis tag did not alter the viral tropism compared to wild-type AAV. These observations demonstrate the feasibility of producing high-titer AAV containing a 6xHis-tagged AAV VP3 capsid protein and to utilize the 6xHis-tagged VP3 capsid to achieve high-affinity purification of this recombinant AAV.

Entangled Biphoton Virtual-State Spectroscopy of the A(exp 2)Sigma(sup +)-X(exp 2)Pi System of OH

NASA Technical Reports Server (NTRS)

Kojima, Jun; Nguyen, Quang-Viet

2004-01-01

This Letter describes the first application of entanglement-induced virtual-state spectroscopy to a molecular system. Non-classical, non-monotonic behavior in a two-photon absorption cross section of the OH A-X system, induced by an entangled biphoton state is theoretically demonstrated. A Fourier transform analysis of the biphoton cross section permits access to the energy eigenvalues of intermediate rovibronic states with a fixed excitation photon energy. The dependence of the Fourier spectrum on the tuning range of the entanglement time (T(sub e)) and the relative path delay (tau(sub e)) is discussed. Our analysis reveals that the implementation of molecular virtual-state spectroscopy for the OH A-X system requires the tuning of tau(sub e) over a pico-second range with femto-second resolution.

Entangled Biphoton Virtual-State Spectroscopy of the A(exp 2)Sigma(+) - X(exp 2)Pi System of OH

NASA Technical Reports Server (NTRS)

Kojima, Jun; Nguyen, Quang-Viet

2004-01-01

This Letter describes the first application of entanglement-induced virtual-state spectroscopy to a molecular system. Non-classical, non-monotonic behavior in a two-photon absorption cross section of the OH A-X system, induced by an entangled biphoton state is theoretically demonstrated. A Fourier transform analysis of the biphoton cross section permits access to the energy eigenvalues of intermediate rovibronic states with a fixed excitation photon energy. The dependence of the Fourier spectrum on the tuning range of the entanglement time T(sub e), and the relative path delay tau(sub e) is discussed. Our analysis reveals that the implementation of molecular virtual-state spectroscopy for the OH A-X system requires the tuning of tau(sub e) over a pico-second range with femto-second resolution.

Four-Dimensional Spatial Reasoning in Humans

ERIC Educational Resources Information Center

Aflalo, T. N.; Graziano, M. S. A.

2008-01-01

Human subjects practiced navigation in a virtual, computer-generated maze that contained 4 spatial dimensions rather than the usual 3. The subjects were able to learn the spatial geometry of the 4-dimensional maze as measured by their ability to perform path integration, a standard test of spatial ability. They were able to travel down a winding…

Taking a Systems View of Creativity: On the Right Path toward Understanding

ERIC Educational Resources Information Center

Hennessey, Beth A.

2017-01-01

In our 2010 "Annual Review" paper, Teresa Amabile and I argued that a virtual explosion of topics, viewpoints, and methodologies had muddied the investigative waters. Few, if any, "big" questions were being pursued by a critical mass of creativity researchers. Instead, investigators in one subfield seemed entirely unaware of…

A virtual reality oriented clinical experiment on post-stroke rehabilitation: performance and preference comparison among different stereoscopic displays­

NASA Astrophysics Data System (ADS)

Yeh, Shih-Ching; Rizzo, Albert; Sawchuk, Alexander A.

2007-02-01

We have developed a novel VR task: the Dynamic Reaching Test, that measures human forearm movement in 3D space. In this task, three different stereoscopic displays: autostereoscopic (AS), shutter glasses (SG) and head mounted display (HMD), are used in tests in which subjects must catch a virtual ball thrown at them. Parameters such as percentage of successful catches, movement efficiency (subject path length compared to minimal path length), and reaction time are measured to evaluate differences in 3D perception among the three stereoscopic displays. The SG produces the highest percentage of successful catches, though the difference between the three displays is small, implying that users can perform the VR task with any of the displays. The SG and HMD produced the best movement efficiency, while the AS was slightly less efficient. Finally, the AS and HMD produced similar reaction times that were slightly higher (by 0.1 s) than the SG. We conclude that SG and HMD displays were the most effective, but only slightly better than the AS display.

Primitive graphs with small exponent and small scrambling index

NASA Astrophysics Data System (ADS)

Surbakti, Ita Y.; Suwilo, Saib; Butar-butar, Ericha A.; Oktaviani, Helda

2018-01-01

A connected graph G is primitive provide there is a positive integer k such that for each pair of vertices u and v there is a uv-walk of length k. The smallest of such positive integer k is the exponent of G and is denoted by exp(G). The scrambling index of a primitive graph G, denoted by k(G), is the smallest positive integer k such that for each pair of vertices u and v there is a vertex w such that there is a uw-walk and a vw-walk of length k. By an n-chainring CR(n) we mean a graph obtained from an n-cycle by replacing each edge of the n-cycle by a triangle. By a (q,p)-dory, D(q,p), we mean a graph with vertex set V(D(q,p)) = V(P q × P p ) ∪ {w 1, w 2} and edge set E(D(q,p)) = E(P q × Pp ) ∪ {w 1 - (u i ,v 1) : i = 1, 2,…, q}∪{w 2 -(u i ,vp ) : i = 1, 2,…, q}, where Pn is a path on n vertices. We discus the exponent and scrambling index of an n- chainring and (q, p)-dory. We present formulae for exponent and scrambling index in terms of their diameter.

A novel parallel pipeline structure of VP9 decoder

NASA Astrophysics Data System (ADS)

Qin, Huabiao; Chen, Wu; Yi, Sijun; Tan, Yunfei; Yi, Huan

2018-04-01

To improve the efficiency of VP9 decoder, a novel parallel pipeline structure of VP9 decoder is presented in this paper. According to the decoding workflow, VP9 decoder can be divided into sub-modules which include entropy decoding, inverse quantization, inverse transform, intra prediction, inter prediction, deblocking and pixel adaptive compensation. By analyzing the computing time of each module, hotspot modules are located and the causes of low efficiency of VP9 decoder can be found. Then, a novel pipeline decoder structure is designed by using mixed parallel decoding methods of data division and function division. The experimental results show that this structure can greatly improve the decoding efficiency of VP9.

Preliminary molecular detection of the somatic embryogenesis receptor-like kinase (VpSERK) and knotted-like homeobox (VpKNOX1) genes during in vitro morphogenesis of Vanilla planifolia Jacks.

PubMed

Ramírez-Mosqueda, Marco A; Iglesias-Andreu, Lourdes G; Sáenz, Luis; Córdova, Iván

2018-02-01

This work aimed to evaluate the embryogenic competence of different tissues from different stages (friable callus, bud-regenerating callus, and whole buds) of Vanilla planifolia , through the molecular detection of the somatic embryogenesis receptor-like kinase ( VpSERK ) and knotted-like homeobox ( VpKNOX1 ) genes. RNA was extracted with Trizol ® , cDNA was obtained, and the studied transcripts were amplified. Using non-specific primers, VpSERK and VpSTM gene expression was detected in the three stages evaluated. This study might contribute to providing an explanation for the recalcitrance of this Vanilla species to somatic embryogenesis.

Structural insights into the multifunctional protein VP3 of birnaviruses.

PubMed

Casañas, Arnau; Navarro, Aitor; Ferrer-Orta, Cristina; González, Dolores; Rodríguez, José F; Verdaguer, Núria

2008-01-01

Infectious bursal disease virus (IBDV), a member of the Birnaviridae family, is the causative agent of one of the most harmful poultry diseases. The IBDV genome encodes five mature proteins; of these, the multifunctional protein VP3 plays an essential role in virus morphogenesis. This protein, which interacts with the structural protein VP2, with the double-stranded RNA genome, and with the virus-encoded, RNA-dependent RNA polymerase, VP1, is involved not only in the formation of the viral capsid, but also in the recruitment of VP1 into the capsid and in the encapsidation of the viral genome. Here, we report the X-ray structure of the central region of VP3, residues 92-220, consisting of two alpha-helical domains connected by a long and flexible hinge that are organized as a dimer. Unexpectedly, the overall fold of the second VP3 domain shows significant structural similarities with different transcription regulation factors.

Comparison of two eukaryotic systems for the expression of VP6 protein of rotavirus specie A: transient gene expression in HEK293-T cells and insect cell-baculovirus system.

PubMed

da Silva Junior, Haroldo Cid; da Silva E Mouta Junior, Sérgio; de Mendonça, Marcos César Lima; de Souza Pereira, Mirian Claudia; da Rocha Nogueira, Alanderson; de Azevedo, Maria Luiza Borges; Leite, José Paulo Gagliardi; de Moraes, Márcia Terezinha Baroni

2012-09-01

The VP6 protein of rotavirus A (RVA) is a target antigen used for diagnostic assays and also for the development of new RVA vaccines. We have compared the expression of VP6 protein in human embryonic kidney (HEK293-T) cells with results obtained using a well-established insect cell-baculovirus system. The recombinant VP6 (rVP6) expressed in HEK293-T cells did not present degradation and also retained the ability to form trimers. In the insect cell-baculovirus system, rVP6 was expressed at higher levels and with protein degradation as well as partial loss of ability to form trimers was observed. Therefore, HEK293-T cells represent a less laborious alternative system than insect cells for expression of rVP6 from human RVA.

An overview of new video coding tools under consideration for VP10: the successor to VP9

NASA Astrophysics Data System (ADS)

Mukherjee, Debargha; Su, Hui; Bankoski, James; Converse, Alex; Han, Jingning; Liu, Zoe; Xu, Yaowu

2015-09-01

Google started an opensource project, entitled the WebM Project, in 2010 to develop royaltyfree video codecs for the web. The present generation codec developed in the WebM project called VP9 was finalized in mid2013 and is currently being served extensively by YouTube, resulting in billions of views per day. Even though adoption of VP9 outside Google is still in its infancy, the WebM project has already embarked on an ambitious project to develop a next edition codec VP10 that achieves at least a generational bitrate reduction over the current generation codec VP9. Although the project is still in early stages, a set of new experimental coding tools have already been added to baseline VP9 to achieve modest coding gains over a large enough test set. This paper provides a technical overview of these coding tools.

Generation of a parvovirus B19 vaccine candidate.

PubMed

Chandramouli, Sumana; Medina-Selby, Angelica; Coit, Doris; Schaefer, Mary; Spencer, Terika; Brito, Luis A; Zhang, Pu; Otten, Gillis; Mandl, Christian W; Mason, Peter W; Dormitzer, Philip R; Settembre, Ethan C

2013-08-20

Parvovirus B19 is the causative agent of fifth disease in children, aplastic crisis in those with blood dyscrasias, and hydrops fetalis. Previous parvovirus B19 virus-like-particle (VLP) vaccine candidates were produced by co-infection of insect cells with two baculoviruses, one expressing wild-type VP1 and the other expressing VP2. In humans, the VLPs were immunogenic but reactogenic. We have developed new VLP-based parvovirus B19 vaccine candidates, produced by co-expressing VP2 and either wild-type VP1 or phospholipase-negative VP1 in a regulated ratio from a single plasmid in Saccharomyces cerevisiae. These VLPs are expressed efficiently, are very homogeneous, and can be highly purified. Although VP2 alone can form VLPs, in mouse immunizations, VP1 and the adjuvant MF59 are required to elicit a neutralizing response. Wild-type VLPs and those with phospholipase-negative VP1 are equivalently potent. The purity, homogeneity, yeast origin, and lack of phospholipase activity of these VLPs address potential causes of previously observed reactogenicity. Copyright © 2013 Elsevier Ltd. All rights reserved.

Mutual antagonism between the Ebola virus VP35 protein and the RIG-I activator PACT determines infection outcome.

PubMed

Luthra, Priya; Ramanan, Parameshwaran; Mire, Chad E; Weisend, Carla; Tsuda, Yoshimi; Yen, Benjamin; Liu, Gai; Leung, Daisy W; Geisbert, Thomas W; Ebihara, Hideki; Amarasinghe, Gaya K; Basler, Christopher F

2013-07-17

The cytoplasmic pattern recognition receptor RIG-I is activated by viral RNA and induces type I IFN responses to control viral replication. The cellular dsRNA binding protein PACT can also activate RIG-I. To counteract innate antiviral responses, some viruses, including Ebola virus (EBOV), encode proteins that antagonize RIG-I signaling. Here, we show that EBOV VP35 inhibits PACT-induced RIG-I ATPase activity in a dose-dependent manner. The interaction of PACT with RIG-I is disrupted by wild-type VP35, but not by VP35 mutants that are unable to bind PACT. In addition, PACT-VP35 interaction impairs the association between VP35 and the viral polymerase, thereby diminishing viral RNA synthesis and modulating EBOV replication. PACT-deficient cells are defective in IFN induction and are insensitive to VP35 function. These data support a model in which the VP35-PACT interaction is mutually antagonistic and plays a fundamental role in determining the outcome of EBOV infection. Copyright © 2013 Elsevier Inc. All rights reserved.

Virtual Network Embedding via Monte Carlo Tree Search.

PubMed

Haeri, Soroush; Trajkovic, Ljiljana

2018-02-01

Network virtualization helps overcome shortcomings of the current Internet architecture. The virtualized network architecture enables coexistence of multiple virtual networks (VNs) on an existing physical infrastructure. VN embedding (VNE) problem, which deals with the embedding of VN components onto a physical network, is known to be -hard. In this paper, we propose two VNE algorithms: MaVEn-M and MaVEn-S. MaVEn-M employs the multicommodity flow algorithm for virtual link mapping while MaVEn-S uses the shortest-path algorithm. They formalize the virtual node mapping problem by using the Markov decision process (MDP) framework and devise action policies (node mappings) for the proposed MDP using the Monte Carlo tree search algorithm. Service providers may adjust the execution time of the MaVEn algorithms based on the traffic load of VN requests. The objective of the algorithms is to maximize the profit of infrastructure providers. We develop a discrete event VNE simulator to implement and evaluate performance of MaVEn-M, MaVEn-S, and several recently proposed VNE algorithms. We introduce profitability as a new performance metric that captures both acceptance and revenue to cost ratios. Simulation results show that the proposed algorithms find more profitable solutions than the existing algorithms. Given additional computation time, they further improve embedding solutions.

Sensorimotor Training in Virtual Reality: A Review

PubMed Central

Adamovich, Sergei V.; Fluet, Gerard G.; Tunik, Eugene; Merians, Alma S.

2010-01-01

Recent experimental evidence suggests that rapid advancement of virtual reality (VR) technologies has great potential for the development of novel strategies for sensorimotor training in neurorehabilitation. We discuss what the adaptive and engaging virtual environments can provide for massive and intensive sensorimotor stimulation needed to induce brain reorganization. Second, discrepancies between the veridical and virtual feedback can be introduced in VR to facilitate activation of targeted brain networks, which in turn can potentially speed up the recovery process. Here we review the existing experimental evidence regarding the beneficial effects of training in virtual environments on the recovery of function in the areas of gait, upper extremity function and balance, in various patient populations. We also discuss possible mechanisms underlying these effects. We feel that future research in the area of virtual rehabilitation should follow several important paths. Imaging studies to evaluate the effects of sensory manipulation on brain activation patterns and the effect of various training parameters on long term changes in brain function are needed to guide future clinical inquiry. Larger clinical studies are also needed to establish the efficacy of sensorimotor rehabilitation using VR approaches in various clinical populations and most importantly, to identify VR training parameters that are associated with optimal transfer into real-world functional improvements. PMID:19713617

Retention of heavy metal ions on comb-type hydrogels based on acrylic acid and 4-vinylpyridine, synthesized by gamma radiation

NASA Astrophysics Data System (ADS)

González-Gómez, Roberto; Ortega, Alejandra; Lazo, Luz M.; Burillo, Guillermina

2014-09-01

Two novel comb-type hydrogels based on pH-sensitive monomers (acrylic acid (AAc) and 4-vinylpyridine (4VP) were synthesized by gamma radiation. The systems were as follows: a) comb-type hydrogels of an AAc network followed by grafting of 4VP ((net-PAAc)-g-4VP) and b) comb-type hydrogels of an AAc network grafted onto polypropylene (PP) followed by grafting of 4VP (net-(PP-g-AAc)-g-4VP). The equilibrium isotherms and kinetics were evaluated for copper and zinc ions in aqueous solutions. The Zn(II) retention obtained was 480 mg g-1 and 1086 mg g-1 for (net-PAAc)-g-4VP and net-(PP-g-AAc)-g-4VP, respectively. At concentrations as low as ppm, retention efficiencies of approximately 90% were achieved for Cu(II) on (net-PAAc)-g-4VP and for Zn(II) on net-(PP-g-AAc)-g-4VP. Desorption of the hydrogels was also studied, and the results indicated that they can be used repeatedly in aqueous solutions. For both systems, the adsorption of Cu(II) and Zn(II) obeyed the Freundlich model, indicating heterogeneous sorption, and the retention process occurred by chemisorption. The sorption process follows a pseudo-second-order model.

High-yield production of the VP1 structural protein epitope from serotype O foot-and-mouth disease virus in Escherichia coli.

PubMed

Jung, Joon-Goo; Lee, Yong Jae; Velmurugan, Natarajan; Ko, Young-Joon; Lee, Hyang-Sim; Jeong, Ki Jun

2013-07-01

For effective control of foot-and-mouth disease (FMD), the development of rapid diagnostic systems and vaccines are required against its etiological agent, FMD virus (FMDV). To accomplish this, efficient large-scale expression of the FMDV VP1 protein, with high solubility, needs to be optimized. We attempted to produce high levels of a serotype O FMDV VP1 epitope in Escherichia coli. We identified the subtype-independent serotype O FMDV VP1 epitope sequence and used it to construct a glutathione S-transferase (GST) fusion protein. For efficient production of the FMDV VP1 epitope fused to GST (VP1e-GST), four E. coli strains and three temperatures were examined. The conditions yielding the greatest level of VP1e-GST with highest solubility were achieved with E. coli BL21(DE3) at 25 °C. For high-level production, fed-batch cultures were conducted in 5-l bioreactors. When cells were induced at a high density and complex feeding solutions were supplied, approximately 11 g of VP1e-GST was obtained from a 2.9-l culture. Following purification, the VP1 epitope was used to immunize rabbits, and we confirmed that it induced an immune response.

The ebola virus interferon antagonist VP24 directly binds STAT1 and has a novel, pyramidal fold.

PubMed

Zhang, Adrianna P P; Bornholdt, Zachary A; Liu, Tong; Abelson, Dafna M; Lee, David E; Li, Sheng; Woods, Virgil L; Saphire, Erica Ollmann

2012-02-01

Ebolaviruses cause hemorrhagic fever with up to 90% lethality and in fatal cases, are characterized by early suppression of the host innate immune system. One of the proteins likely responsible for this effect is VP24. VP24 is known to antagonize interferon signaling by binding host karyopherin α proteins, thereby preventing them from transporting the tyrosine-phosphorylated transcription factor STAT1 to the nucleus. Here, we report that VP24 binds STAT1 directly, suggesting that VP24 can suppress at least two distinct branches of the interferon pathway. Here, we also report the first crystal structures of VP24, derived from different species of ebolavirus that are pathogenic (Sudan) and nonpathogenic to humans (Reston). These structures reveal that VP24 has a novel, pyramidal fold. A site on a particular face of the pyramid exhibits reduced solvent exchange when in complex with STAT1. This site is above two highly conserved pockets in VP24 that contain key residues previously implicated in virulence. These crystal structures and accompanying biochemical analysis map differences between pathogenic and nonpathogenic viruses, offer templates for drug design, and provide the three-dimensional framework necessary for biological dissection of the many functions of VP24 in the virus life cycle.

Insights into the homo-oligomerization properties of N-terminal coiled-coil domain of Ebola virus VP35 protein.

PubMed

Ramaswamy, Venkata Krishnan; Di Palma, Francesco; Vargiu, Attilio V; Corona, Angela; Piano, Dario; Ruggerone, Paolo; Zinzula, Luca; Tramontano, Enzo

2018-03-02

The multifunctional Ebola virus (EBOV) VP35 protein is a key determinant of virulence. VP35 is essential for EBOV replication, is a component of the viral RNA polymerase and participates in nucleocapsid formation. Furthermore, VP35 contributes to EBOV evasion of the host innate immune response by suppressing RNA silencing and blocking RIG-I like receptors' pathways that lead to type I interferon (IFN) production. VP35 homo-oligomerization has been reported to be critical for its replicative function and to increase its IFN-antagonism properties. Moreover, homo-oligomerization is mediated by a predicted coiled-coil (CC) domain located within its N-terminal region. Here we report the homo-oligomerization profile of full-length recombinant EBOV VP35 (rVP35) assessed by size-exclusion chromatography and native polyacrylamide gel electrophoresis. Based on our biochemical results and in agreement with previous experimental observations, we have built an in silico 3D model of the so-far structurally unsolved EBOV VP35 CC domain and performed self-assembly homo-oligomerization simulations by means of molecular dynamics. Our model advances the understanding of how VP35 may associate in different homo-oligomeric species, a crucial process for EBOV replication and pathogenicity. Copyright © 2018 Elsevier B.V. All rights reserved.

Forecasting the Human Pathogen Vibrio Parahaemolyticus in Shellfish Tissue within Long Island Sound

NASA Astrophysics Data System (ADS)

Whitney, M. M.; DeRosia-Banick, K.

2016-02-01

Vibrio parahaemolyticus (Vp) is a marine bacterium that occurs naturally in brackish and saltwater environments and may be found in higher concentrations in the warmest months. Vp is a growing threat to producing safe seafood. Consumption of shellfish with high Vp levels can result in gastrointestinal human illnesses. Management response to Vp-related illness outbreaks includes closure of shellfish growing areas. Water quality observations, Vp measurements, and model forecasts are key components to effective management of shellfish growing areas. There is a clear need for observations within the growing area themselves. These areas are offshore of coastal stations and typically inshore of the observing system moorings. New field observations in Long Island Sound (LIS) shellfish growing areas are described and their agreement with high-resolution satellite sea surface temperature data is discussed. A new dataset of Vp concentrations in shellfish tissue is used to determine the LIS-specific Vp vs. temperature relationship following methods in the FDA pre-harvest Vp risk model. This information is combined with output from a high-resolution hydrodynamic model of LIS to make daily forecasts of Vp levels. The influence of river inflows, the role of heat waves, and predictions for future warmer climates are discussed. The key elements of this observational-modeling approach to pathogen forecasting are extendable to other coastal systems.

Amino Acid Residue at Position 79 of Marburg Virus VP40 Confers Interferon Antagonism in Mouse Cells.

PubMed

Feagins, Alicia R; Basler, Christopher F

2015-10-01

Marburg viruses (MARVs) cause highly lethal infections in humans and nonhuman primates. Mice are not generally susceptible to MARV infection; however, if the strain is first adapted to mice through serial passaging, it becomes able to cause disease in this animal. A previous study correlated changes accrued during mouse adaptation in the VP40 gene of a MARV strain known as Ravn virus (RAVV) with an increased capacity to inhibit interferon (IFN) signaling in mouse cell lines. The MARV strain Ci67, which belongs to a different phylogenetic clade than RAVV, has also been adapted to mice and in the process the Ci67 VP40 acquired a different collection of genetic changes than did RAVV VP40. Here, we demonstrate that the mouse-adapted Ci67 VP40 more potently antagonizes IFN-α/β-induced STAT1 and STAT2 tyrosine phosphorylation, gene expression, and antiviral activity in both mouse and human cell lines, compared with the parental Ci67 VP40. Ci67 VP40 is also demonstrated to target the activation of kinase Jak1. A single change at VP40 residue 79 was found to be sufficient for the increased VP40 IFN antagonism. These data argue that VP40 IFN-antagonist activity plays a key role in MARV pathogenesis in mice. © The Author 2015. Published by Oxford University Press on behalf of the Infectious Diseases Society of America. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Shrimp arginine kinase being a binding protein of WSSV envelope protein VP31

NASA Astrophysics Data System (ADS)

Ma, Cuiyan; Gao, Qiang; Liang, Yan; Li, Chen; Liu, Chao; Huang, Jie

2016-11-01

Viral entry into the host is the earliest stage of infection in the viral life cycle in which attachment proteins play a key role. VP31 (WSV340/WSSV396), an envelope protein of white spot syndrome virus (WSSV), contains an Arg-Gly-Asp (RGD) peptide domain known as a cellular attachment site. At present, the process of VP31 interacting with shrimp host cells has not been explored. Therefore, the VP31 gene was cloned into pET30a (+), expressed in Escherichia coli strain BL21 and purified with immobilized metal ion affinity chromatography. Four gill cellular proteins of shrimp ( Fenneropenaeus chinensis) were pulled down by an affinity column coupled with recombinant VP31 (rVP31), and the amino acid sequences were identified with MALDI-TOF/TOF mass spectrometry. Hemocyanin, beta-actin, arginine kinase (AK), and an unknown protein were suggested as the putative VP31 receptor proteins. SDS-PAGE showed that AK is the predominant binding protein of VP31. An i n vitro binding activity experiment indicated that recombinant AK's (rAK) binding activity with rVP31 is comparable to that with the same amount of WSSV. These results suggested that AK, as a member of the phosphagen kinase family, plays a role in WSSV infection. This is the first evidence showing that AK is a binding protein of VP31. Further studies on this topic will elucidate WSSV infection mechanism in the future.

Expression, Purification, Crystallization of Two Major Envelope Proteins from White Spot Syndrome Virus

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tang,X.; Hew, C.

2007-01-01

White spot syndrome virus (WSSV) is a major virulent pathogen known to infect penaeid shrimp and other crustaceans. VP26 and VP28, two major envelope proteins from WSSV, have been identified and overexpressed in Escherichia coli. In order to facilitate purification and crystallization, predicted N-terminal transmembrane regions of approximately 35 amino acids have been truncated from both VP26 and VP28. Truncated VP26 and VP28 and their corresponding SeMet-labelled proteins were purified and the SeMet proteins were crystallized by the hanging-drop vapor-diffusion method. Crystals of SeMet-labelled VP26 were obtained using a reservoir consisting of 0.1 M citric acid pH 3.5, 3.0 Mmore » sodium chloride and 1%(w/v) polyethylene glycol 3350, whereas SeMet VP28 was crystallized using a reservoir solution consisting of 25% polyethylene glycol 8000, 0.2 M calcium acetate, 0.1 M Na HEPES pH 7.5 and 1.5%(w/v) 1,2,3-heptanetriol. Crystals of SeMet-labelled VP26 diffract to 2.2 {angstrom} resolution and belong to space group R32, with unit-cell parameters a = b = 73.92, c = 199.31 {angstrom}. SeMet-labelled VP28 crystallizes in space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 105.33, b = 106.71, c = 200.37 {angstrom}, and diffracts to 2.0 {angstrom} resolution.« less

Pros and cons of VP1-specific maternal IgG for the protection of Enterovirus 71 infection.

PubMed

Kim, Young-In; Song, Jae-Hyoung; Kwon, Bo-Eun; Kim, Ha-Neul; Seo, Min-Duk; Park, KwiSung; Lee, SangWon; Yeo, Sang-Gu; Kweon, Mi-Na; Ko, Hyun-Jeong; Chang, Sun-Young

2015-11-27

Enterovirus 71 (EV71) causes hand, foot, and mouth diseases and can result in severe neurological disorders when it infects the central nervous system. Thus, there is a need for the development of effective vaccines against EV71 infection. Here we report that viral capsid protein 1 (VP1), one of the main capsid proteins of EV71, efficiently elicited VP1-specific immunoglobulin G (IgG) in the serum of mice immunized with recombinant VP1. The VP1-specific IgG produced in female mice was efficiently transferred to their offspring, conferring protection against EV71 infection immediately after birth. VP1-specific antibody can neutralize EV71 infection and protect host cells. VP1-specific maternal IgG in offspring was maintained for over 6 months. However, the pre-existence of VP1-specific maternal IgG interfered with the production of VP1-specific IgG antibody secreting cells by active immunization in offspring. Therefore, although our results showed the potential for VP1-specific maternal IgG protection against EV71 in neonatal mice, other strategies must be developed to overcome the hindrance of maternal IgG in active immunization. In this study, we developed an effective and feasible animal model to evaluate the protective efficacy of humoral immunity against EV71 infection using a maternal immunity concept. Copyright © 2015 Elsevier Ltd. All rights reserved.

VP3 is crucial for the stability of Nora virus virions.

PubMed

Sadanandan, Sajna Anand; Ekström, Jens-Ola; Jonna, Venkateswara Rao; Hofer, Anders; Hultmark, Dan

2016-09-02

Nora virus is an enteric virus that causes persistent, non-pathological infection in Drosophila melanogaster. It replicates in the fly gut and is transmitted via the fecal-oral route. Nora virus has a single-stranded positive-sense RNA genome, which is translated in four open reading frames. Reading frame three encodes the VP3 protein, the structure and function of which we have investigated in this work. We have shown that VP3 is a trimer that has an α-helical secondary structure, with a functionally important coiled-coil domain. In order to identify the role of VP3 in the Nora virus life cycle, we constructed VP3-mutants using the cDNA clone of the virus. Our results show that VP3 does not have a role in the actual assembly of the virus particles, but virions that lack VP3 or harbor VP3 with a disrupted coiled coil domain are incapable of transmission via the fecal-oral route. Removing the region downstream of the putative coiled coil appears to have an effect on the fitness of the virus but does not hamper its replication or transmission. We also found that the VP3 protein and particularly the coiled coil domain are crucial for the stability of Nora virus virions when exposed to heat or proteases. Hence, we propose that VP3 is imperative to Nora virus virions as it confers stability to the viral capsid. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

Conditional poliovirus mutants made by random deletion mutagenesis of infectious cDNA.

PubMed Central

Kirkegaard, K; Nelsen, B

1990-01-01

Small deletions were introduced into DNA plasmids bearing cDNA copies of Mahoney type 1 poliovirus RNA. The procedure used was similar to that of P. Hearing and T. Shenk (J. Mol. Biol. 167:809-822, 1983), with modifications designed to introduce only one lesion randomly into each DNA molecule. Methods to map small deletions in either large DNA or RNA molecules were employed. Two poliovirus mutants, VP1-101 and VP1-102, were selected from mutagenized populations on the basis of their host range phenotype, showing a large reduction in the relative numbers of plaques on CV1 and HeLa cells compared with wild-type virus. The deletions borne by the mutant genomes were mapped to the region encoding the amino terminus of VP1. That these lesions were responsible for the mutant phenotypes was substantiated by reintroduction of the sequenced lesions into a wild-type poliovirus cDNA by deoxyoligonucleotide-directed mutagenesis. The deletion of nucleotides encoding amino acids 8 and 9 of VP1 was responsible for the VP1-101 phenotype; the VP1-102 defect was caused by the deletion of the sequences encoding the first four amino acids of VP1. The peptide sequence at the VP1-VP3 proteolytic cleavage site was altered from glutamine-glycine to glutamine-methionine in VP1-102; this apparently did not alter the proteolytic cleavage pattern. The biochemical defects resulting from these mutations are discussed in the accompanying report. Images PMID:2152811

Development of a robotic evaluation system for the ability of proprioceptive sensation in slow hand motion.

PubMed

Tanaka, Yoshiyuki; Mizoe, Genki; Kawaguchi, Tomohiro

2015-01-01

This paper proposes a simple diagnostic methodology for checking the ability of proprioceptive/kinesthetic sensation by using a robotic device. The perception ability of virtual frictional forces is examined in operations of the robotic device by the hand at a uniform slow velocity along the virtual straight/circular path. Experimental results by healthy subjects demonstrate that percentage of correct answers for the designed perceptual tests changes in the motion direction as well as the arm configuration and the HFM (human force manipulability) measure. It can be supposed that the proposed methodology can be applied into the early detection of neuromuscular/neurological disorders.

Three-dimensional seismic velocity structure of Mauna Loa and Kilauea volcanoes in Hawaii from local seismic tomography

USGS Publications Warehouse

Lin, Guoqing; Shearer, Peter M.; Matoza, Robin S.; Okubo, Paul G.; Amelung, Falk

2016-01-01

We present a new three-dimensional seismic velocity model of the crustal and upper mantle structure for Mauna Loa and Kilauea volcanoes in Hawaii. Our model is derived from the first-arrival times of the compressional and shear waves from about 53,000 events on and near the Island of Hawaii between 1992 and 2009 recorded by the Hawaiian Volcano Observatory stations. The Vp model generally agrees with previous studies, showing high-velocity anomalies near the calderas and rift zones and low-velocity anomalies in the fault systems. The most significant difference from previous models is in Vp/Vs structure. The high-Vp and high-Vp/Vs anomalies below Mauna Loa caldera are interpreted as mafic magmatic cumulates. The observed low-Vp and high-Vp/Vs bodies in the Kaoiki seismic zone between 5 and 15 km depth are attributed to the underlying volcaniclastic sediments. The high-Vp and moderate- to low-Vp/Vs anomalies beneath Kilauea caldera can be explained by a combination of different mafic compositions, likely to be olivine-rich gabbro and dunite. The systematically low-Vp and low-Vp/Vs bodies in the southeast flank of Kilauea may be caused by the presence of volatiles. Another difference between this study and previous ones is the improved Vp model resolution in deeper layers, owing to the inclusion of events with large epicentral distances. The new velocity model is used to relocate the seismicity of Mauna Loa and Kilauea for improved absolute locations and ultimately to develop a high-precision earthquake catalog using waveform cross-correlation data.

The use of additive and subtractive approaches to examine the nuclear localization sequence of the polyomavirus major capsid protein VP1

NASA Technical Reports Server (NTRS)

Chang, D.; Haynes, J. I. 2nd; Brady, J. N.; Consigli, R. A.; Spooner, B. S. (Principal Investigator)

1992-01-01

A nuclear localization signal (NLS) has been identified in the N-terminal (Ala1-Pro-Lys-Arg-Lys-Ser-Gly-Val-Ser-Lys-Cys11) amino acid sequence of the polyomavirus major capsid protein VP1. The importance of this amino acid sequence for nuclear transport of VP1 protein was demonstrated by a genetic "subtractive" study using the constructs pSG5VP1 (full-length VP1) and pSG5 delta 5'VP1 (truncated VP1, lacking amino acids Ala1-Cys11). These constructs were used to transfect COS-7 cells, and expression and intracellular localization of the VP1 protein was visualized by indirect immunofluorescence. These studies revealed that the full-length VP1 was expressed and localized in the nucleus, while the truncated VP1 protein was localized in the cytoplasm and not transported to the nucleus. These findings were substantiated by an "additive" approach using FITC-labeled conjugates of synthetic peptides homologous to the NLS of VP1 cross-linked to bovine serum albumin or immunoglobulin G. Both conjugates localized in the nucleus after microinjection into the cytoplasm of 3T6 cells. The importance of individual amino acids found in the basic sequence (Lys3-Arg-Lys5) of the NLS was also investigated. This was accomplished by synthesizing three additional peptides in which lysine-3 was substituted with threonine, arginine-4 was substituted with threonine, or lysine-5 was substituted with threonine. It was found that lysine-3 was crucial for nuclear transport, since substitution of this amino acid with threonine prevented nuclear localization of the microinjected, FITC-labeled conjugate.

Low-tube voltage 100 kVp MDCT in screening of cocaine body packing: image quality and radiation dose compared to 120 kVp MDCT.

PubMed

Aissa, Joel; Rubbert, Christian; Boos, Johannes; Schleich, Christoph; Thomas, Christoph; Kröpil, Patric; Antoch, Gerald; Miese, Falk

2015-10-01

The aim of this study was to evaluate the impact of a reduced tube potential (100 kVp) for non-enhanced abdominal low-dose CT on radiation dose and image quality (IQ) in the detection of body packing. This retrospective study was approved by the local research ethics committee of our clinic. From March 2012 to July 2014, 99 subjects were referred to our institute with suspected body packing. 50 CT scans were performed using a 120 kVp protocol (group A), and 49 CTs were performed using a low-dose protocol with a tube voltage of 100 kVp (group B). Subjective and objective IQ were assessed. DLP and CTDIvol were analyzed. All examinations were of diagnostic IQ. Objective IQ was not significantly different between the 120 kVp and 100 kVp protocol. Mean density of solid and liquid body packets was 210 ± 60.2 HU at 120 kVp and 250.6 ± 29.7 HU at 100 kVp. Radiation dose was significantly lower in group B as compared to group A (p < 0.05). In group A, body packs were detected in 16 (32%) of the 50 patients. In group B, packets were observed in 15 (31%) of 49 patients. Laboratory analysis detected cocaine in all smuggled body packs. Low-tube voltage 100 kVp MDCT with automated tube current modulation in screening of illegal drugs leads to a diagnostic IQ and significant dose reduction compared to 120 kVp low-tube voltage protocols. Despite lower radiation dose, liquid and solid cocaine containers retain high attenuation and are easily detected.

Membrane association and localization dynamics of the Ebola virus matrix protein VP40.

PubMed

Gc, Jeevan B; Gerstman, Bernard S; Chapagain, Prem P

2017-10-01

The Ebola virus matrix protein VP40 is a major structural protein that provides the scaffolding for new Ebola virus particles. For this, VP40 is first trafficked to the lower leaflet of the plasma membrane (PM) in its dimeric form. Once associated with the PM, the VP40 dimers undergo structural rearrangements and oligomerize into hexamers and filaments that make up the virus matrix. Therefore, association of the VP40 dimers and their stabilization at the PM is a crucial step in the Ebola life-cycle. To understand the molecular details of the VP40 dimer-PM interactions, we investigated the dimer association with the inner leaflet of the PM using detailed all-atom molecular dynamics (MD) simulations. The formation of the dimer-PM complex is facilitated by the interactions of the VP40 lysine residues and the anionic lipids POPS, POPI, and PIP 2 in the PM. In contrast, the dimer fails to associate with a membrane without POPS, POPI, or PIP 2 lipids. We explored the mechanisms of the association and identified important residues and lipids involved in localization and stabilization of VP40 dimers at the PM. MD simulations elucidate the role of a C-terminal α-helix alignment parallel to the lipid bilayer surface as well as the creation of membrane defects that allow partial insertion of the hydrophobic residue V276 into the membrane to further stabilize the VP40 dimer-PM complex. Understanding the mechanisms of the VP40 dimer-PM association that facilitate oligomerization can be important for potentially targeting the VP40 for small molecules that can interfere with the virus life-cycle. Copyright © 2017 Elsevier B.V. All rights reserved.

VP40 of the Ebola Virus as a Target for EboV Therapy: Comprehensive Conformational and Inhibitor Binding Landscape from Accelerated Molecular Dynamics.

PubMed

Balmith, Marissa; Soliman, Mahmoud E S

2017-03-01

The first account of the dynamic features of the loop region of VP40 of the Ebola virus was studied using accelerated molecular dynamics simulations and reported herein. Among the proteins of the Ebola virus, the matrix protein (VP40) plays a significant role in the virus lifecycle thereby making it a promising therapeutic target. Of interest is the newly elucidated N-terminal domain loop region of VP40 comprising residues K127, T129, and N130 which when mutated to alanine have demonstrated an unrecognized role for N-terminal domain-plasma membrane interaction for efficient VP40-plasma membrane localization, oligomerization, matrix assembly, and egress. The molecular understanding of the conformational features of VP40 in complex with a known inhibitor still remains elusive. Using accelerated molecular dynamics approaches, we conducted a comparative study on VP40 apo and bound systems to understand the conformational features of VP40 at the molecular level and to determine the effect of inhibitor binding with the aid of a number of post-dynamic analytical tools. Significant features were seen in the presence of an inhibitor as per molecular mechanics/generalized born surface area binding free energy calculations. Results revealed that inhibitor binding to VP40 reduces the flexibility and mobility of the protein as supported by root mean square fluctuation and root mean square deviation calculations. The study revealed a characteristic "twisting" motion and coiling of the loop region of VP40 accompanied by conformational changes in the dimer interface upon inhibitor binding. We believe that results presented in this study will ultimately provide useful insight into the binding landscape of VP40 which could assist researchers in the discovery of potent Ebola virus inhibitors for anti-Ebola therapies.

Chaperone-Mediated Autophagy Protein BAG3 Negatively Regulates Ebola and Marburg VP40-Mediated Egress

PubMed Central

Liang, Jingjing; Sagum, Cari A.; Bedford, Mark T.; Sudol, Marius; Han, Ziying

2017-01-01

Ebola (EBOV) and Marburg (MARV) viruses are members of the Filoviridae family which cause outbreaks of hemorrhagic fever. The filovirus VP40 matrix protein is essential for virus assembly and budding, and its PPxY L-domain motif interacts with WW-domains of specific host proteins, such as Nedd4 and ITCH, to facilitate the late stage of virus-cell separation. To identify additional WW-domain-bearing host proteins that interact with VP40, we used an EBOV PPxY-containing peptide to screen an array of 115 mammalian WW-domain-bearing proteins. Using this unbiased approach, we identified BCL2 Associated Athanogene 3 (BAG3), a member of the BAG family of molecular chaperone proteins, as a specific VP40 PPxY interactor. Here, we demonstrate that the WW-domain of BAG3 interacts with the PPxY motif of both EBOV and MARV VP40 and, unexpectedly, inhibits budding of both eVP40 and mVP40 virus-like particles (VLPs), as well as infectious VSV-EBOV recombinants. BAG3 is a stress induced protein that regulates cellular protein homeostasis and cell survival through chaperone-mediated autophagy (CMA). Interestingly, our results show that BAG3 alters the intracellular localization of VP40 by sequestering VP40 away from the plasma membrane. As BAG3 is the first WW-domain interactor identified that negatively regulates budding of VP40 VLPs and infectious virus, we propose that the chaperone-mediated autophagy function of BAG3 represents a specific host defense strategy to counteract the function of VP40 in promoting efficient egress and spread of virus particles. PMID:28076420

Chaperone-Mediated Autophagy Protein BAG3 Negatively Regulates Ebola and Marburg VP40-Mediated Egress.

PubMed

Liang, Jingjing; Sagum, Cari A; Bedford, Mark T; Sidhu, Sachdev S; Sudol, Marius; Han, Ziying; Harty, Ronald N

2017-01-01

Ebola (EBOV) and Marburg (MARV) viruses are members of the Filoviridae family which cause outbreaks of hemorrhagic fever. The filovirus VP40 matrix protein is essential for virus assembly and budding, and its PPxY L-domain motif interacts with WW-domains of specific host proteins, such as Nedd4 and ITCH, to facilitate the late stage of virus-cell separation. To identify additional WW-domain-bearing host proteins that interact with VP40, we used an EBOV PPxY-containing peptide to screen an array of 115 mammalian WW-domain-bearing proteins. Using this unbiased approach, we identified BCL2 Associated Athanogene 3 (BAG3), a member of the BAG family of molecular chaperone proteins, as a specific VP40 PPxY interactor. Here, we demonstrate that the WW-domain of BAG3 interacts with the PPxY motif of both EBOV and MARV VP40 and, unexpectedly, inhibits budding of both eVP40 and mVP40 virus-like particles (VLPs), as well as infectious VSV-EBOV recombinants. BAG3 is a stress induced protein that regulates cellular protein homeostasis and cell survival through chaperone-mediated autophagy (CMA). Interestingly, our results show that BAG3 alters the intracellular localization of VP40 by sequestering VP40 away from the plasma membrane. As BAG3 is the first WW-domain interactor identified that negatively regulates budding of VP40 VLPs and infectious virus, we propose that the chaperone-mediated autophagy function of BAG3 represents a specific host defense strategy to counteract the function of VP40 in promoting efficient egress and spread of virus particles.

Crystal Structure of the Marburg Virus VP35 Oligomerization Domain.

PubMed

Bruhn, Jessica F; Kirchdoerfer, Robert N; Urata, Sarah M; Li, Sheng; Tickle, Ian J; Bricogne, Gérard; Saphire, Erica Ollmann

2017-01-15

Marburg virus (MARV) is a highly pathogenic filovirus that is classified in a genus distinct from that of Ebola virus (EBOV) (genera Marburgvirus and Ebolavirus, respectively). Both viruses produce a multifunctional protein termed VP35, which acts as a polymerase cofactor, a viral protein chaperone, and an antagonist of the innate immune response. VP35 contains a central oligomerization domain with a predicted coiled-coil motif. This domain has been shown to be essential for RNA polymerase function. Here we present crystal structures of the MARV VP35 oligomerization domain. These structures and accompanying biophysical characterization suggest that MARV VP35 is a trimer. In contrast, EBOV VP35 is likely a tetramer in solution. Differences in the oligomeric state of this protein may explain mechanistic differences in replication and immune evasion observed for MARV and EBOV. Marburg virus can cause severe disease, with up to 90% human lethality. Its genome is concise, only producing seven proteins. One of the proteins, VP35, is essential for replication of the viral genome and for evasion of host immune responses. VP35 oligomerizes (self-assembles) in order to function, yet the structure by which it assembles has not been visualized. Here we present two crystal structures of this oligomerization domain. In both structures, three copies of VP35 twist about each other to form a coiled coil. This trimeric assembly is in contrast to tetrameric predictions for VP35 of Ebola virus and to known structures of homologous proteins in the measles, mumps, and Nipah viruses. Distinct oligomeric states of the Marburg and Ebola virus VP35 proteins may explain differences between them in polymerase function and immune evasion. These findings may provide a more accurate understanding of the mechanisms governing VP35's functions and inform the design of therapeutics. Copyright © 2017 American Society for Microbiology.

Investigation of the Lipid Binding Properties of the Marburg Virus Matrix Protein VP40.

PubMed

Wijesinghe, Kaveesha J; Stahelin, Robert V

2015-12-30

Marburg virus (MARV), which belongs to the virus family Filoviridae, causes hemorrhagic fever in humans and nonhuman primates that is often fatal. MARV is a lipid-enveloped virus that during the replication process extracts its lipid coat from the plasma membrane of the host cell it infects. MARV carries seven genes, one of which encodes its matrix protein VP40 (mVP40), which regulates the assembly and budding of the virions. Currently, little information is available on mVP40 lipid binding properties. Here, we have investigated the in vitro and cellular mechanisms by which mVP40 associates with lipid membranes. mVP40 associates with anionic membranes in a nonspecific manner that is dependent upon the anionic charge density of the membrane. These results are consistent with recent structural determination of mVP40, which elucidated an mVP40 dimer with a flat and extensive cationic lipid binding interface. Marburg virus (MARV) is a lipid-enveloped filamentous virus from the family Filoviridae. MARV was discovered in 1967, and yet little is known about how its seven genes are used to assemble and form a new viral particle in the host cell it infects. The MARV matrix protein VP40 (mVP40) underlies the inner leaflet of the virus and regulates budding from the host cell plasma membrane. In vitro and cellular assays in this study investigated the mechanism by which mVP40 associates with lipids. The results demonstrate that mVP40 interactions with lipid vesicles or the inner leaflet of the plasma membrane are electrostatic but nonspecific in nature and are dependent on the anionic charge density of the membrane surface. Small molecules that can disrupt lipid trafficking or reduce the anionic charge of the plasma membrane interface may be useful in inhibiting assembly and budding of MARV. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Acutely elevated vasopressin increases circulating concentrations of cortisol and aldosterone in fasting northern elephant seal (Mirounga angustirostris) pups

NASA Technical Reports Server (NTRS)

Ortiz, Rudy M.; Wade, Charles E.; Ortiz, C. Leo; Talamantes, Frank

2003-01-01

The physiological actions of vasopressin (VP) in marine mammals are not well defined. To help elucidate its hormonal and renal effects in this group of mammals, northern elephant seal (Mirounga angustirostris) pups (N=7; 99+/-4 kg) were first infused with 0.9% saline (control; 220 ml), followed 24 h later with VP (as a 20 ng kg(-1) bolus, then 2 ng kg(-1) min(-1) for approximately 35 min in 225+/-16 ml saline). During both control and VP periods, blood samples were collected prior to infusion, and 15, 30, 60, 120 min and 24 h after infusion to examine the hormonal responses of the pups to VP. Renal responses were quantified from 24 h urine samples obtained prior to infusion (control) and 24 h post-infusion. Compared to the control period, infusion of VP increased plasma concentrations of cortisol over a 120 min period and aldosterone over 30 min, while plasma renin activity (PRA) was decreased for a 120 min period. The plasma urea:creatinine ratio was elevated following infusion of VP. Urine output and osmotic clearance were increased by 69+/-18% (mean +/- S.E.M.) and 36+/-10%, respectively, but free water clearance and glomerular filtration rate were not significantly altered 24 h post-infusion of VP. Solute (osmolality, Na(+), K(+) and Cl(-)) excretion and fractional excretion of electrolytes were also increased when compared to control values. The increase in cortisol concentration suggests that VP may possess corticotropin releasing hormone-like activity in elephant seals. If osmotic diuresis and natriuresis are typical consequences of elevated [VP] in fasting pups, then not increasing VP normally during the fast may serve as a protective mechanism to avoid the potential loss of Na(+) induced by elevated [VP]. Therefore, under natural fasting conditions, pups may be highly sensitive to small changes in [VP], resulting in the maintenance of water and electrolyte balance.

An interference account of the missing-VP effect

PubMed Central

Häussler, Jana; Bader, Markus

2015-01-01

Sentences with doubly center-embedded relative clauses in which a verb phrase (VP) is missing are sometimes perceived as grammatical, thus giving rise to an illusion of grammaticality. In this paper, we provide a new account of why missing-VP sentences, which are both complex and ungrammatical, lead to an illusion of grammaticality, the so-called missing-VP effect. We propose that the missing-VP effect in particular, and processing difficulties with multiply center-embedded clauses more generally, are best understood as resulting from interference during cue-based retrieval. When processing a sentence with double center-embedding, a retrieval error due to interference can cause the verb of an embedded clause to be erroneously attached into a higher clause. This can lead to an illusion of grammaticality in the case of missing-VP sentences and to processing complexity in the case of complete sentences with double center-embedding. Evidence for an interference account of the missing-VP effect comes from experiments that have investigated the missing-VP effect in German using a speeded grammaticality judgments procedure. We review this evidence and then present two new experiments that show that the missing-VP effect can be found in German also with less restricting procedures. One experiment was a questionnaire study which required grammaticality judgments from participants without imposing any time constraints. The second experiment used a self-paced reading procedure and did not require any judgments. Both experiments confirm the prior findings of missing-VP effects in German and also show that the missing-VP effect is subject to a primacy effect as known from the memory literature. Based on this evidence, we argue that an account of missing-VP effects in terms of interference during cue-based retrieval is superior to accounts in terms of limited memory resources or in terms of experience with embedded structures. PMID:26136698

Production and characterization of egg yolk antibody (IgY) against recombinant VP8-S2 antigen.

PubMed

Nasiri, K; Nassiri, M R; Tahmoorespur, M; Haghparast, A; Zibaee, S

2016-01-01

Bovine Rotavirus and Bovine Coronavirus are the most important causes of diarrhea in newborn calves and in some other species such as pigs and sheep. VP8 subunit of rotavirus is the major determinant of the viral infectivity and neutralization. Spike glycoprotein of coronavirus is responsible for induction of neutralizing antibody response. Studies showed that immunoglobulin of egg yolk (IgY) from immunized hens has been identified to be a convenient source for specific antibodies for using in immunotherapy and immunodiagnostic to limit the infections. In this study, chimeric VP8-S2 gene was designed using by computational techniques. The chimeric VP8-S2 gene was cloned and sub-cloned into pGH and pET32a (+) vectors. Then, recombinant pET32a-VP8-S2 vector was transferred into E. coli BL21 CodonPlus (DE3). The expressed protein was purified by Ni-NTA chromatography column. Hens were immunized with the purified VP8-S2 protein three times. IgY was purified from egg yolks using polyethylene glycol precipitation method. Activity and specificity of anti-VP8-S2 IgY were detected by dot-blotting, Western-blotting and indirect ELISA. We obtained anti-VP8-S2 IgY by immunizing hens with the recombinant VP8-S2 protein. The anti-VP8-S2 IgY was showed to bind specifically to the chimeric VP8-S2 protein by dot-blotting, Western-blotting analyses and indirect ELISA. The result of this study indicated that such construction can be useful to investigate as candidates for development of detection methods for simultaneous diagnosis of both infections. Specific IgY against the recombinant VP8-S2 could be recommended as a candidate for passive immunization against bovine rotavirus and bovine coronavirus.

Crystal Structure of the Marburg Virus VP35 Oligomerization Domain

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bruhn, Jessica F.; Kirchdoerfer, Robert N.; Urata, Sarah M.

ABSTRACT Marburg virus (MARV) is a highly pathogenic filovirus that is classified in a genus distinct from that of Ebola virus (EBOV) (generaMarburgvirusandEbolavirus, respectively). Both viruses produce a multifunctional protein termed VP35, which acts as a polymerase cofactor, a viral protein chaperone, and an antagonist of the innate immune response. VP35 contains a central oligomerization domain with a predicted coiled-coil motif. This domain has been shown to be essential for RNA polymerase function. Here we present crystal structures of the MARV VP35 oligomerization domain. These structures and accompanying biophysical characterization suggest that MARV VP35 is a trimer. In contrast, EBOVmore » VP35 is likely a tetramer in solution. Differences in the oligomeric state of this protein may explain mechanistic differences in replication and immune evasion observed for MARV and EBOV. IMPORTANCEMarburg virus can cause severe disease, with up to 90% human lethality. Its genome is concise, only producing seven proteins. One of the proteins, VP35, is essential for replication of the viral genome and for evasion of host immune responses. VP35 oligomerizes (self-assembles) in order to function, yet the structure by which it assembles has not been visualized. Here we present two crystal structures of this oligomerization domain. In both structures, three copies of VP35 twist about each other to form a coiled coil. This trimeric assembly is in contrast to tetrameric predictions for VP35 of Ebola virus and to known structures of homologous proteins in the measles, mumps, and Nipah viruses. Distinct oligomeric states of the Marburg and Ebola virus VP35 proteins may explain differences between them in polymerase function and immune evasion. These findings may provide a more accurate understanding of the mechanisms governing VP35's functions and inform the design of therapeutics.« less

dsRNA binding characterization of full length recombinant wild type and mutants Zaire ebolavirus VP35.

PubMed

Zinzula, Luca; Esposito, Francesca; Pala, Daniela; Tramontano, Enzo

2012-03-01

The Ebola viruses (EBOVs) VP35 protein is a multifunctional major virulence factor involved in EBOVs replication and evasion of the host immune system. EBOV VP35 is an essential component of the viral RNA polymerase, it is a key participant of the nucleocapsid assembly and it inhibits the innate immune response by antagonizing RIG-I like receptors through its dsRNA binding function and, hence, by suppressing the host type I interferon (IFN) production. Insights into the VP35 dsRNA recognition have been recently revealed by structural and functional analysis performed on its C-terminus protein. We report the biochemical characterization of the Zaire ebolavirus (ZEBOV) full-length recombinant VP35 (rVP35)-dsRNA binding function. We established a novel in vitro magnetic dsRNA binding pull down assay, determined the rVP35 optimal dsRNA binding parameters, measured the rVP35 equilibrium dissociation constant for heterologous in vitro transcribed dsRNA of different length and short synthetic dsRNA of 8bp, and validated the assay for compound screening by assessing the inhibitory ability of auryntricarboxylic acid (IC(50) value of 50μg/mL). Furthermore, we compared the dsRNA binding properties of full length wt rVP35 with those of R305A, K309A and R312A rVP35 mutants, which were previously reported to be defective in dsRNA binding-mediated IFN inhibition, showing that the latter have measurably increased K(d) values for dsRNA binding and modified migration patterns in mobility shift assays with respect to wt rVP35. Overall, these results provide the first characterization of the full-length wt and mutants VP35-dsRNA binding functions. Copyright © 2012 Elsevier B.V. All rights reserved.

Application of bluetongue Disabled Infectious Single Animal (DISA) vaccine for different serotypes by VP2 exchange or incorporation of chimeric VP2.

PubMed

Feenstra, Femke; Pap, Janny S; van Rijn, Piet A

2015-02-04

Bluetongue is a disease of ruminants caused by the bluetongue virus (BTV). Bluetongue outbreaks can be controlled by vaccination, however, currently available vaccines have several drawbacks. Further, there are at least 26 BTV serotypes, with low cross protection. A next-generation vaccine based on live-attenuated BTV without expression of non-structural proteins NS3/NS3a, named Disabled Infectious Single Animal (DISA) vaccine, was recently developed for serotype 8 by exchange of the serotype determining outer capsid protein VP2. DISA vaccines are replicating vaccines but do not cause detectable viremia, and induce serotype specific protection. Here, we exchanged VP2 of laboratory strain BTV1 for VP2 of European serotypes 2, 4, 8 and 9 using reverse genetics, without observing large effects on virus growth. Exchange of VP2 from serotype 16 and 25 was however not possible. Therefore, chimeric VP2 proteins of BTV1 containing possible immunogenic regions of these serotypes were studied. BTV1, expressing 1/16 chimeric VP2 proteins was functional in virus replication in vitro and contained neutralizing epitopes of both serotype 1 and 16. For serotype 25 this approach failed. We combined VP2 exchange with the NS3/NS3a negative phenotype in BTV1 as previously described for serotype 8 DISA vaccine. DISA vaccine with 1/16 chimeric VP2 containing amino acid region 249-398 of serotype 16 raised antibodies in sheep neutralizing both BTV1 and BTV16. This suggests that DISA vaccine could be protective for both parental serotypes present in chimeric VP2. We here demonstrate the application of the BT DISA vaccine platform for several serotypes and further extend the application for serotypes that are unsuccessful in single VP2 exchange. Copyright © 2014 Elsevier Ltd. All rights reserved.

Recombinant VP1, an Akt Inhibitor, Suppresses Progression of Hepatocellular Carcinoma by Inducing Apoptosis and Modulation of CCL2 Production

PubMed Central

Chen, Tai-An; Wang, Jui-Ling; Hung, Shao-Wen; Chu, Chiao-Li; Cheng, Yung-Chih; Liang, Shu-Mei

2011-01-01

Background The application of viral elements in tumor therapy is one facet of cancer research. Recombinant capsid protein VP1 (rVP1) of foot-and-mouth disease virus has previously been demonstrated to induce apoptosis in cancer cell lines. Here, we aim to further investigate its apoptotic mechanism and possible anti-metastatic effect in murine models of hepatocellular carcinoma (HCC), one of the most common human cancers worldwide. Methodology/Principal Findings Treatment with rVP1 inhibited cell proliferation in two murine HCC cell lines, BNL and Hepa1-6, with IC50 values in the range of 0.1–0.2 µM. rVP1 also induced apoptosis in these cells, which was mediated by Akt deactivation and dissociation of Ku70-Bax, and resulted in conformational changes and mitochondrial translocation of Bax, leading to the activation of caspases-9, -3 and -7. Treatment with 0.025 µM rVP1, which did not affect the viability of normal hepatocytes, suppressed cell migration and invasion via attenuating CCL2 production. The production of CCL2 was modulated by Akt-dependent NF-κB activation that was decreased after rVP1 treatment. The in vivo antitumor effects of rVP1 were assessed in both subcutaneous and orthotopic mouse models of HCC in immune-competent BALB/c mice. Intratumoral delivery of rVP1 inhibited subcutaneous tumor growth as a result of increased apoptosis. Intravenous administration of rVP1 in an orthotopic HCC model suppressed tumor growth, inhibited intra-hepatic metastasis, and prolonged survival. Furthermore, a decrease in the serum level of CCL2 was observed in rVP1-treated mice. Conclusions/Significance The data presented herein suggest that, via inhibiting Akt phosphorylation, rVP1 suppresses the growth, migration, and invasion of murine HCC cells by inducing apoptosis and attenuating CCL2 production both in vitro and in vivo. Recombinant protein VP1 thus has the potential to be developed as a new therapeutic agent for HCC. PMID:21826248

Evasion of interferon responses by Ebola and Marburg viruses.

PubMed

Basler, Christopher F; Amarasinghe, Gaya K

2009-09-01

The filoviruses, Ebola virus (EBOV) and Marburg virus (MARV), cause frequently lethal viral hemorrhagic fever. These infections induce potent cytokine production, yet these host responses fail to prevent systemic virus replication. Consistent with this, filoviruses have been found to encode proteins VP35 and VP24 that block host interferon (IFN)-alpha/beta production and inhibit signaling downstream of the IFN-alpha/beta and the IFN-gamma receptors, respectively. VP35, which is a component of the viral nucleocapsid complex and plays an essential role in viral RNA synthesis, acts as a pseudosubstrate for the cellular kinases IKK-epsilon and TBK-1, which phosphorylate and activate interferon regulatory factor 3 (IRF-3) and interferon regulatory factor 7 (IRF-7). VP35 also promotes SUMOylation of IRF-7, repressing IFN gene transcription. In addition, VP35 is a dsRNA-binding protein, and mutations that disrupt dsRNA binding impair VP35 IFN-antagonist activity while leaving its RNA replication functions intact. The phenotypes of recombinant EBOV bearing mutant VP35s unable to inhibit IFN-alpha/beta demonstrate that VP35 IFN-antagonist activity is critical for full virulence of these lethal pathogens. The structure of the VP35 dsRNA-binding domain, which has recently become available, is expected to provide insight into how VP35 IFN-antagonist and dsRNA-binding functions are related. The EBOV VP24 protein inhibits IFN signaling through an interaction with select host cell karyopherin-alpha proteins, preventing the nuclear import of otherwise activated STAT1. It remains to be determined to what extent VP24 may also modulate the nuclear import of other host cell factors and to what extent this may influence the outcome of infection. Notably, the Marburg virus VP24 protein does not detectably block STAT1 nuclear import, and, unlike EBOV, MARV infection inhibits STAT1 and STAT2 phosphorylation. Thus, despite their similarities, there are fundamental differences by which these deadly viruses counteract the IFN system. It will be of interest to determine how these differences influence pathogenesis.

A Single Amino Acid Change in the Marburg Virus Matrix Protein VP40 Provides a Replicative Advantage in a Species-Specific Manner

PubMed Central

Koehler, Alexander; Kolesnikova, Larissa; Welzel, Ulla; Schudt, Gordian; Herwig, Astrid

2015-01-01

ABSTRACT Marburg virus (MARV) induces severe hemorrhagic fever in humans and nonhuman primates but only transient nonlethal disease in rodents. However, sequential passages of MARV in rodents boosts infection leading to lethal disease. Guinea pig-adapted MARV contains one mutation in the viral matrix protein VP40 at position 184 (VP40D184N). The contribution of the D184N mutation to the efficacy of replication in a new host is unknown. In the present study, we demonstrated that recombinant MARV containing the D184N mutation in VP40 [rMARVVP40(D184N)] grew to higher titers than wild-type recombinant MARV (rMARVWT) in guinea pig cells. Moreover, rMARVVP40(D184N) displayed higher infectivity in guinea pig cells. Comparative analysis of VP40 functions indicated that neither the interferon (IFN)-antagonistic function nor the membrane binding capabilities of VP40 were affected by the D184N mutation. However, the production of VP40-induced virus-like particles (VLPs) and the recruitment of other viral proteins to the budding site was improved by the D184N mutation in guinea pig cells, which resulted in the higher infectivity of VP40D184N-induced infectious VLPs (iVLPs) compared to that of VP40-induced iVLPs. In addition, the function of VP40 in suppressing viral RNA synthesis was influenced by the D184N mutation specifically in guinea pig cells, thus allowing greater rates of transcription and replication. Our results showed that the improved viral fitness of rMARVVP40(D184N) in guinea pig cells was due to the better viral assembly function of VP40D184N and its lower inhibitory effect on viral transcription and replication rather than modulation of the VP40-mediated suppression of IFN signaling. IMPORTANCE The increased virulence achieved by virus passaging in a new host was accompanied by mutations in the viral genome. Analyzing how these mutations affect the functions of viral proteins and the ability of the virus to grow within new host cells helps in the understanding of the molecular mechanisms increasing virulence. Using a reverse genetics approach, we demonstrated that a single mutation in MARV VP40 detected in a guinea pig-adapted MARV provided a replicative advantage of rMARVVP40(D184N) in guinea pig cells. Our studies show that this replicative advantage of rMARV VP40D184N was based on the improved functions of VP40 in iVLP assembly and in the regulation of transcription and replication rather than on the ability of VP40 to combat the host innate immunity. PMID:26581998

Information spread of emergency events: path searching on social networks.

PubMed

Dai, Weihui; Hu, Hongzhi; Wu, Tunan; Dai, Yonghui

2014-01-01

Emergency has attracted global attentions of government and the public, and it will easily trigger a series of serious social problems if it is not supervised effectively in the dissemination process. In the Internet world, people communicate with each other and form various virtual communities based on social networks, which lead to a complex and fast information spread pattern of emergency events. This paper collects Internet data based on data acquisition and topic detection technology, analyzes the process of information spread on social networks, describes the diffusions and impacts of that information from the perspective of random graph, and finally seeks the key paths through an improved IBF algorithm. Application cases have shown that this algorithm can search the shortest spread paths efficiently, which may help us to guide and control the information dissemination of emergency events on early warning.

Heat Shock Protein 70 Enhances Mucosal Immunity against Human Norovirus When Coexpressed from a Vesicular Stomatitis Virus Vector

PubMed Central

Ma, Yuanmei; Duan, Yue; Wei, Yongwei; Liang, Xueya; Niewiesk, Stefan; Oglesbee, Michael

2014-01-01

ABSTRACT Human norovirus (NoV) accounts for 95% of nonbacterial gastroenteritis worldwide. Currently, there is no vaccine available to combat human NoV as it is not cultivable and lacks a small-animal model. Recently, we demonstrated that recombinant vesicular stomatitis virus (rVSV) expressing human NoV capsid protein (rVSV-VP1) induced strong immunities in mice (Y. Ma and J. Li, J. Virol. 85:2942–2952, 2011). To further improve the safety and efficacy of the vaccine candidate, heat shock protein 70 (HSP70) was inserted into the rVSV-VP1 backbone vector. A second construct was generated in which the firefly luciferase (Luc) gene was inserted in place of HSP70 as a control for the double insertion. The resultant recombinant viruses (rVSV-HSP70-VP1 and rVSV-Luc-VP1) were significantly more attenuated in cell culture and viral spread in mice than rVSV-VP1. At the inoculation dose of 1.0 × 106 PFU, rVSV-HSP70-VP1 triggered significantly higher vaginal IgA than rVSV-VP1 and significantly higher fecal and vaginal IgA responses than rVSV-Luc-VP1, although serum IgG and T cell responses were similar. At the inoculation dose of 5.0 × 106 PFU, rVSV-HSP70-VP1 stimulated significantly higher T cell, fecal, and vaginal IgA responses than rVSV-VP1. Fecal and vaginal IgA responses were also significantly increased when combined vaccination of rVSV-VP1 and rVSV-HSP70 was used. Collectively, these data indicate that (i) insertion of an additional gene (HSP70 or Luc) into the rVSV-VP1 backbone further attenuates the VSV-based vaccine in vitro and in vivo, thus improving the safety of the vaccine candidate, and (ii) HSP70 enhances the human NoV-specific mucosal and T cell immunities triggered by a VSV-based human NoV vaccine. IMPORTANCE Human norovirus (NoV) is responsible for more than 95% of acute nonbacterial gastroenteritis worldwide. Currently, there is no vaccine for this virus. Development of a live attenuated vaccine for human NoV has not been possible because it is uncultivable. Thus, a live vector-based vaccine may provide an alternative vaccine strategy. In this study, we developed a vesicular stomatitis virus (VSV)-based human NoV vaccine candidate. We constructed rVSV-HSP70-VP1, coexpressing heat shock protein (HSP70) and capsid (VP1) genes of human NoV, and rVSV-Luc-VP1, coexpressing firefly luciferase (Luc) and VP1 genes. We found that VSVs with a double gene insertion were significantly more attenuated than VSV with a single VP1 insertion (rVSV-VP1). Furthermore, we found that coexpression or coadministration of HSP70 from VSV vector significantly enhanced human NoV-specific mucosal immunity. Collectively, we developed an improved live vectored vaccine candidate for human NoV which will be useful for future clinical studies. PMID:24574391

TH-CD-202-04: Evaluation of Virtual Non-Contrast Images From a Novel Split-Filter Dual-Energy CT Technique

DOE Office of Scientific and Technical Information (OSTI.GOV)

Huang, J; Szczykutowicz, T; Bayouth, J

Purpose: To compare the ability of two dual-energy CT techniques, a novel split-filter single-source technique of superior temporal resolution against an established sequential-scan technique, to remove iodine contrast from images with minimal impact on CT number accuracy. Methods: A phantom containing 8 tissue substitute materials and vials of varying iodine concentrations (1.7–20.1 mg I /mL) was imaged using a Siemens Edge CT scanner. Dual-energy virtual non-contrast (VNC) images were generated using the novel split-filter technique, in which a 120kVp spectrum is filtered by tin and gold to create high- and low-energy spectra with < 1 second temporal separation between themore » acquisition of low- and high-energy data. Additionally, VNC images were generated with the sequential-scan technique (80 and 140kVp) for comparison. CT number accuracy was evaluated for all materials at 15, 25, and 35mGy CTDIvol. Results: The spectral separation was greater for the sequential-scan technique than the split-filter technique with dual-energy ratios of 2.18 and 1.26, respectively. Both techniques successfully removed iodine contrast, resulting in mean CT numbers within 60HU of 0HU (split-filter) and 40HU of 0HU (sequential-scan) for all iodine concentrations. Additionally, for iodine vials of varying diameter (2–20 mm) with the same concentration (9.9 mg I /mL), the system accurately detected iodine for all sizes investigated. Both dual-energy techniques resulted in reduced CT numbers for bone materials (by >400HU for the densest bone). Increasing the imaging dose did not improve the CT number accuracy for bone in VNC images. Conclusion: VNC images from the split-filter technique successfully removed iodine contrast. These results demonstrate a potential for improving dose calculation accuracy and reducing patient imaging dose, while achieving superior temporal resolution in comparison sequential scans. For both techniques, inaccuracies in CT numbers for bone materials necessitate consideration for radiation therapy treatment planning.« less

WE-FG-207B-12: Quantitative Evaluation of a Spectral CT Scanner in a Phantom Study: Results of Spectral Reconstructions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Duan, X; Arbique, G; Guild, J

Purpose: To evaluate the quantitative image quality of spectral reconstructions of phantom data from a spectral CT scanner. Methods: The spectral CT scanner (IQon Spectral CT, Philips Healthcare) is equipped with a dual-layer detector and generates conventional 80-140 kVp images and variety of spectral reconstructions, e.g., virtual monochromatic (VM) images, virtual non-contrast (VNC) images, iodine maps, and effective atomic number (Z) images. A cylindrical solid water phantom (Gammex 472, 33 cm diameter and 5 cm thick) with iodine (2.0-20.0 mg I/ml) and calcium (50-600 mg/ml) rod inserts was scanned at 120 kVp and 27 mGy CTDIvol. Spectral reconstructions were evaluatedmore » by comparing image measurements with theoretical values calculated from nominal rod compositions provided by the phantom manufacturer. The theoretical VNC was calculated using water and iodine basis material decomposition, and the theoretical Z was calculated using two common methods, the chemical formula method (Z1) and the dual-energy ratio method (Z2). Results: Beam-hardening-like artifacts between high-attenuation calcium rods (≥300 mg/ml, >800 HU) influenced quantitative measurements, so the quantitative analysis was only performed on iodine rods using the images from the scan with all the calcium rods removed. The CT numbers of the iodine rods in the VM images (50∼150 keV) were close to theoretical values with average difference of 2.4±6.9 HU. Compared with theoretical values, the average difference for iodine concentration, VNC CT number and effective Z of iodine rods were −0.10±0.38 mg/ml, −0.1±8.2 HU, 0.25±0.06 (Z1) and −0.23±0.07 (Z2). Conclusion: The results indicate that the spectral CT scanner generates quantitatively accurate spectral reconstructions at clinically relevant iodine concentrations. Beam-hardening-like artifacts still exist when high-attenuation objects are present and their impact on patient images needs further investigation. YY is an employee of Philips Healthcare.« less

Ebola Virus VP35 Interaction with Dynein LC8 Regulates Viral RNA Synthesis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Luthra, Priya; Jordan, David S.; Leung, Daisy W.

2015-03-04

Ebola virus VP35 inhibits alpha/beta interferon production and functions as a viral polymerase cofactor. Previously, the 8-kDa cytoplasmic dynein light chain (LC8) was demonstrated to interact with VP35, but the functional consequences were unclear. Here we demonstrate that the interaction is direct and of high affinity and that binding stabilizes the VP35 N-terminal oligomerization domain and enhances viral RNA synthesis. Mutational analysis demonstrates that VP35 interaction is required for the functional effects of LC8.

Identification of a novel NLS of herpes simplex virus type 1 (HSV-1) VP19C and its nuclear localization is required for efficient production of HSV-1.

PubMed

Li, You; Zhao, Lei; Wang, Shuai; Xing, Junji; Zheng, Chunfu

2012-09-01

Herpes simplex virus type 1 (HSV-1) triplex is a complex of three protein subunits, consisting of two copies of VP23 and one copy of VP19C. Here, we identified a non-classical NLS of VP19C between aa 50 and 61, and the nuclear import of VP19C was mediated by RanGTP and importin β1-, but not importin α5-, dependent pathway. Additionally, recombinant virus harbouring this NLS mutation (NLSm) replicates less efficiently as wild-type. These data strongly suggested that the nuclear import of VP19C is required for efficient HSV-1 production.

Using a virtual world for robot planning

NASA Astrophysics Data System (ADS)

Benjamin, D. Paul; Monaco, John V.; Lin, Yixia; Funk, Christopher; Lyons, Damian

2012-06-01

We are building a robot cognitive architecture that constructs a real-time virtual copy of itself and its environment, including people, and uses the model to process perceptual information and to plan its movements. This paper describes the structure of this architecture. The software components of this architecture include PhysX for the virtual world, OpenCV and the Point Cloud Library for visual processing, and the Soar cognitive architecture that controls the perceptual processing and task planning. The RS (Robot Schemas) language is implemented in Soar, providing the ability to reason about concurrency and time. This Soar/RS component controls visual processing, deciding which objects and dynamics to render into PhysX, and the degree of detail required for the task. As the robot runs, its virtual model diverges from physical reality, and errors grow. The Match-Mediated Difference component monitors these errors by comparing the visual data with corresponding data from virtual cameras, and notifies Soar/RS of significant differences, e.g. a new object that appears, or an object that changes direction unexpectedly. Soar/RS can then run PhysX much faster than real-time and search among possible future world paths to plan the robot's actions. We report experimental results in indoor environments.

Research on axisymmetric aspheric surface numerical design and manufacturing technology

NASA Astrophysics Data System (ADS)

Wang, Zhen-zhong; Guo, Yin-biao; Lin, Zheng

2006-02-01

The key technology for aspheric machining offers exact machining path and machining aspheric lens with high accuracy and efficiency, in spite of the development of traditional manual manufacturing into nowadays numerical control (NC) machining. This paper presents a mathematical model between virtual cone and aspheric surface equations, and discusses the technology of uniform wear of grinding wheel and error compensation in aspheric machining. Finally, a software system for high precision aspheric surface manufacturing is designed and realized, based on the mentioned above. This software system can work out grinding wheel path according to input parameters and generate machining NC programs of aspheric surfaces.

Training on a virtual reality simulator--is it really possible a correct evaluation of the surgeons' experience?

PubMed

Moldovanu, R; Târcoveanu, E; Lupaşcu, C; Dimofte, G; Filip, V; Vlad, N; Vasilescu, A

2009-01-01

Laparoscopic simulators provide a safe and efficient means of acquiring surgical skills. It is well known that virtual reality training improves the performance of young surgeons. Most of the virtual reality simulators have construct validity and can differentiate between novice and expert surgeons. However, for some training modules and trainees categories the possibility to distinguish the real surgeon's experience is still discussed. A total of 14 young surgeons were evaluated during a 5 days postgraduate laparoscopic course using a LapSim Basic Skills, v. 3.0 simulator and a Virtual Laparoscopic Interface (VLI) hardware. The best performances of the surgeons were included in a MS Access database and statistical analyzed. There were 6 males and 8 women with a mean age of 30.21 +/- 1.01 years old (range 26-38). Nine surgeons (64.28%) were young residents without any laparoscopic surgical experience (group I), and the other 5, had some laparoscopic surgical experience (10 to 30 laparoscopic procedures) (group II). During the instrument navigation task we found that both hands performances were significant better in group II--the navigation time was 12.43 +/- 1.31 vs 19.01 +/- 1.40 seconds for the left hand--p = 0.006 and 13.57 +/- 1.47 vs 22.18 +/- 3.16 seconds for the right hand--p = 0.032); the right instrument angular path degree was also shorter for experienced surgeons (153.17 +/- 16.72 vs 230.88 +/- 22.6 - p = 0.017). The same data were noted for the lifting and grasping module. However, the suturing module tasks revealed contradictory results: the group I residents recorded better performances then the group II surgeons: total time--677.06 +/- 111.48 vs 1122.65 +/- 166.62 seconds; p = 0.043; right instrument path (m)--15.62 +/- 2.47 vs 25.73 +/- 3.13; p = 0.028; right instrument angular path (degree)--3940.43 +/- 572.54 vs 6595.5597 +/- 753.26; p = 0.017. Laparoscopic simulators are useful to evaluate the surgeons' experience; the parameters of the instrument navigation and lifting and grasping modules, which require a higher degree of eye-hand coordination, were better for residents with previous surgical experience and revealed a good transfer of training (TOT). The suturing module is less influenced by surgeons' experience. This result is probably explained by a lack of TOT.

Knee, Shoulder, and Fundamentals of Arthroscopic Surgery Training: Validation of a Virtual Arthroscopy Simulator.

PubMed

Tofte, Josef N; Westerlind, Brian O; Martin, Kevin D; Guetschow, Brian L; Uribe-Echevarria, Bastián; Rungprai, Chamnanni; Phisitkul, Phinit

2017-03-01

To validate the knee, shoulder, and virtual Fundamentals of Arthroscopic Training (FAST) modules on a virtual arthroscopy simulator via correlations with arthroscopy case experience and postgraduate year. Orthopaedic residents and faculty from one institution performed a standardized sequence of knee, shoulder, and FAST modules to evaluate baseline arthroscopy skills. Total operation time, camera path length, and composite total score (metric derived from multiple simulator measurements) were compared with case experience and postgraduate level. Values reported are Pearson r; alpha = 0.05. 35 orthopaedic residents (6 per postgraduate year), 2 fellows, and 3 faculty members (2 sports, 1 foot and ankle), including 30 male and 5 female residents, were voluntarily enrolled March to June 2015. Knee: training year correlated significantly with year-averaged knee composite score, r = 0.92, P = .004, 95% confidence interval (CI) = 0.84, 0.96; operation time, r = -0.92, P = .004, 95% CI = -0.96, -0.84; and camera path length, r = -0.97, P = .0004, 95% CI = -0.98, -0.93. Knee arthroscopy case experience correlated significantly with composite score, r = 0.58, P = .0008, 95% CI = 0.27, 0.77; operation time, r = -0.54, P = .002, 95% CI = -0.75, -0.22; and camera path length, r = -0.62, P = .0003, 95% CI = -0.8, -0.33. Shoulder: training year correlated strongly with average shoulder composite score, r = 0.90, P = .006, 95% CI = 0.81, 0.95; operation time, r = -0.94, P = .001, 95% CI = -0.97, -0.89; and camera path length, r = -0.89, P = .007, 95% CI = -0.95, -0.80. Shoulder arthroscopy case experience correlated significantly with average composite score, r = 0.52, P = .003, 95% CI = 0.2, 0.74; strongly with operation time, r = -0.62, P = .0002, 95% CI = -0.8, -0.33; and camera path length, r = -0.37, P = .044, 95% CI = -0.64, -0.01, by training year. FAST: training year correlated significantly with 3 combined FAST activity average composite scores, r = 0.81, P = .0279, 95% CI = 0.65, 0.90; operation times, r = -0.86, P = .012, 95% CI = -0.93, -0.74; and camera path lengths, r = -0.85, P = .015, 95% CI = -0.92, -0.72. Total arthroscopy cases performed did not correlate significantly with overall FAST performance. We found significant correlations between both training year and knee and shoulder arthroscopy experience when compared with performance as measured by composite score, camera path length, and operation time during a simulated diagnostic knee and shoulder arthroscopy, respectively. Three FAST activities demonstrated significant correlations with training year but not arthroscopy case experience as measured by composite score, camera path length, and operation time. We attempt to validate an arthroscopy simulator that could be used to supplement arthroscopy skills training for orthopaedic residents. Copyright © 2016 Arthroscopy Association of North America. Published by Elsevier Inc. All rights reserved.

Simulating Navigation with Virtual 3d Geovisualizations - a Focus on Memory Related Factors

NASA Astrophysics Data System (ADS)

Lokka, I.; Çöltekin, A.

2016-06-01

The use of virtual environments (VE) for navigation-related studies, such as spatial cognition and path retrieval has been widely adopted in cognitive psychology and related fields. What motivates the use of VEs for such studies is that, as opposed to real-world, we can control for the confounding variables in simulated VEs. When simulating a geographic environment as a virtual world with the intention to train navigational memory in humans, an effective and efficient visual design is important to facilitate the amount of recall. However, it is not yet clear what amount of information should be included in such visual designs intended to facilitate remembering: there can be too little or too much of it. Besides the amount of information or level of detail, the types of visual features (`elements' in a visual scene) that should be included in the representations to create memorable scenes and paths must be defined. We analyzed the literature in cognitive psychology, geovisualization and information visualization, and identified the key factors for studying and evaluating geovisualization designs for their function to support and strengthen human navigational memory. The key factors we identified are: i) the individual abilities and age of the users, ii) the level of realism (LOR) included in the representations and iii) the context in which the navigation is performed, thus specific tasks within a case scenario. Here we present a concise literature review and our conceptual development for follow-up experiments.

In-depth proteomic analysis of Varroa destructor: Detection of DWV-complex, ABPV, VdMLV and honeybee proteins in the mite.

PubMed

Erban, Tomas; Harant, Karel; Hubalek, Martin; Vitamvas, Pavel; Kamler, Martin; Poltronieri, Palmiro; Tyl, Jan; Markovic, Martin; Titera, Dalibor

2015-09-11

We investigated pathogens in the parasitic honeybee mite Varroa destructor using nanoLC-MS/MS (TripleTOF) and 2D-E-MS/MS proteomics approaches supplemented with affinity-chromatography to concentrate trace target proteins. Peptides were detected from the currently uncharacterized Varroa destructor Macula-like virus (VdMLV), the deformed wing virus (DWV)-complex and the acute bee paralysis virus (ABPV). Peptide alignments revealed detection of complete structural DWV-complex block VP2-VP1-VP3, VDV-1 helicase and single-amino-acid substitution A/K/Q in VP1, the ABPV structural block VP1-VP4-VP2-VP3 including uncleaved VP4/VP2, and VdMLV coat protein. Isoforms of viral structural proteins of highest abundance were localized via 2D-E. The presence of all types of capsid/coat proteins of a particular virus suggested the presence of virions in Varroa. Also, matches between the MWs of viral structural proteins on 2D-E and their theoretical MWs indicated that viruses were not digested. The absence/scarce detection of non-structural proteins compared with high-abundance structural proteins suggest that the viruses did not replicate in the mite; hence, virions accumulate in the Varroa gut via hemolymph feeding. Hemolymph feeding also resulted in the detection of a variety of honeybee proteins. The advantages of MS-based proteomics for pathogen detection, false-positive pathogen detection, virus replication, posttranslational modifications, and the presence of honeybee proteins in Varroa are discussed.

In-depth proteomic analysis of Varroa destructor: Detection of DWV-complex, ABPV, VdMLV and honeybee proteins in the mite

PubMed Central

Erban, Tomas; Harant, Karel; Hubalek, Martin; Vitamvas, Pavel; Kamler, Martin; Poltronieri, Palmiro; Tyl, Jan; Markovic, Martin; Titera, Dalibor

2015-01-01

We investigated pathogens in the parasitic honeybee mite Varroa destructor using nanoLC-MS/MS (TripleTOF) and 2D-E-MS/MS proteomics approaches supplemented with affinity-chromatography to concentrate trace target proteins. Peptides were detected from the currently uncharacterized Varroa destructor Macula-like virus (VdMLV), the deformed wing virus (DWV)-complex and the acute bee paralysis virus (ABPV). Peptide alignments revealed detection of complete structural DWV-complex block VP2-VP1-VP3, VDV-1 helicase and single-amino-acid substitution A/K/Q in VP1, the ABPV structural block VP1-VP4-VP2-VP3 including uncleaved VP4/VP2, and VdMLV coat protein. Isoforms of viral structural proteins of highest abundance were localized via 2D-E. The presence of all types of capsid/coat proteins of a particular virus suggested the presence of virions in Varroa. Also, matches between the MWs of viral structural proteins on 2D-E and their theoretical MWs indicated that viruses were not digested. The absence/scarce detection of non-structural proteins compared with high-abundance structural proteins suggest that the viruses did not replicate in the mite; hence, virions accumulate in the Varroa gut via hemolymph feeding. Hemolymph feeding also resulted in the detection of a variety of honeybee proteins. The advantages of MS-based proteomics for pathogen detection, false-positive pathogen detection, virus replication, posttranslational modifications, and the presence of honeybee proteins in Varroa are discussed. PMID:26358842

Role and mechanism of the maturation cleavage of VP0 in poliovirus assembly: structure of the empty capsid assembly intermediate at 2.9 A resolution.

PubMed Central

Basavappa, R.; Syed, R.; Flore, O.; Icenogle, J. P.; Filman, D. J.; Hogle, J. M.

1994-01-01

The crystal structure of the P1/Mahoney poliovirus empty capsid has been determined at 2.9 A resolution. The empty capsids differ from mature virions in that they lack the viral RNA and have yet to undergo a stabilizing maturation cleavage of VP0 to yield the mature capsid proteins VP4 and VP2. The outer surface and the bulk of the protein shell are very similar to those of the mature virion. The major differences between the 2 structures are focused in a network formed by the N-terminal extensions of the capsid proteins on the inner surface of the shell. In the empty capsids, the entire N-terminal extension of VP1, as well as portions corresponding to VP4 and the N-terminal extension of VP2, are disordered, and many stabilizing interactions that are present in the mature virion are missing. In the empty capsid, the VP0 scissile bond is located some 20 A away from the positions in the mature virion of the termini generated by VP0 cleavage. The scissile bond is located on the rim of a trefoil-shaped depression in the inner surface of the shell that is highly reminiscent of an RNA binding site in bean pod mottle virus. The structure suggests plausible (and ultimately testable) models for the initiation of encapsidation, for the RNA-dependent autocatalytic cleavage of VP0, and for the role of the cleavage in establishing the ordered N-terminal network and in generating stable virions. PMID:7849583

Immunogenicity and efficacy in mice of an adenovirus-based bicistronic rotavirus vaccine expressing NSP4 and VP7.

PubMed

Xie, Li; Yan, Min; Wang, Xiaonan; Ye, Jing; Mi, Kai; Yan, Shanshan; Niu, Xianglian; Li, Hongjun; Sun, Maosheng

2015-12-02

NSP4 and VP7 are important functional proteins of rotavirus. Proper combination of viral gene expression is favorable to improving the protection effect of subunit vaccine. In the present study, We evaluated the immunogenicity and efficacy of the bicistronic recombinant adenovirus (rAd-NSP4-VP7) and two single-gene expressing adenoviruses (rAd-NSP4, rAd-VP7). The three adenovirus vaccines were used to immunize mice by intramuscular or intranasal administration. The data showed significant increases in serum antibodies, T lymphocyte subpopulations proliferation, and cytokine secretions of splenocyte in all immunized groups. However, the serum IgA and neutralizing antibody levels of the rAd-NSP4-VP7 or rAd-VP7 groups were significantly higher than those of the rAd-NSP4, while the splenocyte numbers of IFN-γ secretion in the rAd-NSP4-VP7 or rAd-NSP4 groups was greater than that of the rAd-VP7. Furthermore, the efficacy evaluation in a suckling mice model indicated that only rAd-NSP4-VP7 conferred significant protection against rotavirus shedding challenge. These results suggest that the co-expression of NSP4 and VP7 in an adenovirus vector induce both humoral and cell-mediated immune responses efficiently, and provide potential efficacy for protection against rotavirus disease. It is possible to represent an efficacious subunits vaccine strategy for control of rotavirus infection and transmission. Copyright © 2015 Elsevier B.V. All rights reserved.

The Research Path to the Virtual Class. ZIFF Papiere 105.

ERIC Educational Resources Information Center

Rajasingham, Lalita

This paper describes a project conducted in 1991-92, based on research conducted in 1986-87 that demonstrated the need for a telecommunications system with the capacity of integrated services digital networks (ISDN) that would allow for sound, vision, and integrated computer services. Called the Tri-Centre Project, it set out to explore, from the…

A Tale of Three Cases: Examining Accuracy, Efficiency, and Process Differences in Diagnosing Virtual Patient Cases

ERIC Educational Resources Information Center

Doleck, Tenzin; Jarrell, Amanda; Poitras, Eric G.; Chaouachi, Maher; Lajoie, Susanne P.

2016-01-01

Clinical reasoning is a central skill in diagnosing cases. However, diagnosing a clinical case poses several challenges that are inherent to solving multifaceted ill-structured problems. In particular, when solving such problems, the complexity stems from the existence of multiple paths to arriving at the correct solution (Lajoie, 2003). Moreover,…

A Dynamic Programming Approach to Identifying the Shortest Path in Virtual Learning Environments

ERIC Educational Resources Information Center

Fazlollahtabar, Hamed

2008-01-01

E-learning has been widely adopted as a promising solution by many organizations to offer learning-on-demand opportunities to individual employees (learners) in order to reduce training time and cost. While successful information systems models have received much attention among researchers, little research has been conducted to assess the success…

Fluid-filled porosity of magmatic underplates from joint inversion of P and S receiver functions

NASA Astrophysics Data System (ADS)

Vinnik, Lev; Oreshin, Sergey; Makeyeva, Larissa; Dündar, Süleyman

2017-05-01

Vp/Vs ratio where Vp and Vs are P- and S-wave velocities is an indicator of rock composition, but estimates of Vp/Vs for the lower continental crust remain sparse. We present estimates of Vs, Vp and Vp/Vs in the crust of the Archean-Paleoproterozoic Siberian craton that are obtained by simultaneous inversion of P and S receiver functions from GSN seismograph stations NRIL, YAK and TIXI. These stations are located in the region of the Siberian traps (NRIL), close to the Laptev Sea Rift (TIXI) and the Viluy rift system (YAK). The most conspicuous result of our analysis is a high Vp/Vs ratio (≥2.0) at depths from 20-30 to 40 km. A very high Vp in this layer (from 7 to 8 km s-1) is indicative of magmatic underplating. We find broadly similar data in the western Mediterranean and in India. In a dry lower crust the Vp/Vs ratio is ∼1.8, which is hard to reconcile with the estimates >2.0. A coincidence in depths of zones of high electric conductivity and of anomalously high Vp/Vs in Siberia suggests that both may have the same origin: fluid-filled porosity. The porosity which is required by our seismic observations is on the order of 1 per cent. Origins of the fluids may be linked with processes of magmatic underplating.

Fluid-filled porosity of magmatic underplates from joint inversion of P and S receiver functions

NASA Astrophysics Data System (ADS)

Vinnik, Lev; Oreshin, Sergey; Makeyeva, Larissa; Dündar, Süleyman

2017-04-01

Vp/Vs ratio where Vp and Vs are P- and S-wave velocities is an indicator of rock composition, but estimates of Vp/Vs for the lower continental crust remain sparse. We present estimates of Vs, Vp and Vp/Vs in the crust of the Archean-Paleoproterozoic Siberian craton that are obtained by simultaneous inversion of P and S receiver functions from GSN seismograph stations NRIL, YAK and TIXI. These stations are located in the region of the Siberian traps (NRIL), close to the Laptev Sea Rift (TIXI) and the Viluy rift system (YAK). The most conspicuous result of our analysis is a high Vp/Vs ratio (≥2.0) at depths from 20-30 km to 40 km. A very high Vp in this layer (from 7 to 8 km/s) is indicative of magmatic underplating. We find broadly similar data in the western Mediterranean and in India. In a dry lower crust the Vp/Vs ratio is 1.8, which is hard to reconcile with the estimates > 2.0. A coincidence in depths of zones of high electric conductivity and of anomalously high Vp/Vs in Siberia suggests that both may have the same origin: fluid-filled porosity. The porosity which is required by our seismic observations is on the order of 1%. Origins of the fluids may be linked with processes of magmatic underplating.

Oral immunization with recombinant enterovirus 71 VP1 formulated with chitosan protects mice against lethal challenge

PubMed Central

2014-01-01

Background Enterovirus 71 (EV71) is the etiologic agent of hand-foot-and-mouth disease (HFMD) in the Asia-Pacific region, Many strategies have been applied to develop EV71 vaccines but no vaccines are currently available. Mucosal immunization of the VP1, a major immunogenic capsid protein of EV71, may be an alternative way to prevent EV71 infection. Results In this study, mucosal immunogenicity and protect function of recombinant VP1 protein (rVP1) in formulation with chitosan were tested and assessed in female ICR mouse model. The results showed that the oral immunization with rVP1 induced VP1-specific IgA antibodies in intestine, feces, vagina, and the respiratory tract and serum-specific IgG and neutralization antibodies in vaccinated mice. Splenocytes from rVP1-immunized mice induced high levels of Th1 (cytokine IFN-γ), Th2 (cytokine IL-4) and Th3 (cytokine TGF-β) type immune responses after stimulation. Moreover, rVP1-immunized mother mice conferred protection (survival rate up to 30%) on neonatal mice against a lethal challenge of 103 plaque-forming units (PFU) EV71. Conclusions These data indicated that oral immunization with rVP1 in formulation with chitosan was effective in inducing broad-spectrum immune responses and might be a promising subunit vaccine candidate for preventing EV71 infection. PMID:24885121

VP7: an attachment protein of bluetongue virus for cellular receptors in Culicoides variipennis.

PubMed

Xu, G; Wilson, W; Mecham, J; Murphy, K; Zhou, E M; Tabachnick, W

1997-07-01

The importance of VP7 of bluetongue virus (BTV) in the binding of BTV to membrane proteins of the BTV vector Culicoides variipennis was investigated. Core BTV particles, prepared from whole viruses, lacked outer proteins VP2 and VP5 and had VP7 exposed. More core particles and whole viruses bound to membrane preparations of adults of C. variipennis and KC cells, which were cultured from this vector insect, than to membrane preparations of Manduca sexta larvae. More core particles than whole viruses bound to membrane preparations of adults of C. variipennis and KC cells. Polyclonal anti-idiotypic antibodies (anti-Id), which were made against an antigen-combining region of an anti-BTV-10 VP7 antibody and functionally mimicked VP7, bound more to the membrane preparations of adults of C. variipennis and KC cells, and less to cytosol preparations. In Western overalay analysis, the Culicoides plasma membrane preparation reduced binding of an anti-VP7 monoclonal antibody to VP7. Whole and core BTV particles and the anti-Id bound to a membrane protein with a molecular mass of 23 kDa that was present predominantly in membrane preparations of adults of C. variipennis and KC cells. This protein was present in much lower concentrations in membrane preparations of C6/36 and DM-2 insect cells.

Effects of water saturation on P-wave propagation in fractured coals: An experimental perspective

NASA Astrophysics Data System (ADS)

Liu, Jie; Liu, Dameng; Cai, Yidong; Gan, Quan; Yao, Yanbin

2017-09-01

Internal structure of coalbed methane (CBM) reservoirs can be evaluated through ultrasonic measurements. The compressional wave that propagates in a fractured coal reservoir may indicate the internal coal structure and fluid characteristics. The P-wave propagation was proposed to study the relations between petrophysical parameters (including water saturation, fractures, porosity and permeability) of coals and the P-wave velocity (Vp), using a KON-NM-4A ultrasonic velocity meter. In this study, the relations between Vps and water saturations were established: Type I is mainly controlled by capillary of developed seepage pores. The controlling factors on Type II and Type III are internal homogeneity of pores/fractures and developed micro-fractures, respectively. Micro-fractures density linearly correlates with the Vp due to the fracture volume and dispersion of P-wave; and micro-fractures of types C and D have a priority in Vp. For dry coals, no clear relation exists between porosity, permeability and the Vp. However, as for water-saturated coals, the correlation coefficients of porosity, permeability and Vp are slightly improved. The Vp of saturated coals could be predicted with the equation of Vp-saturated = 1.4952Vp-dry-26.742 m/s. The relation between petrophysical parameters of coals and Vp under various water saturations can be used to evaluate the internal structure in fractured coals. Therefore, these relations have significant implications for coalbed methane (CBM) exploration.

Coinfection with recombinant vaccinia viruses expressing poliovirus P1 and P3 proteins results in polyprotein processing and formation of empty capsid structures.

PubMed

Ansardi, D C; Porter, D C; Morrow, C D

1991-04-01

The assembly process of poliovirus occurs via an ordered proteolytic processing of the capsid precursor protein, P1, by the virus-encoded proteinase 3CD. To further delineate this process, we have isolated a recombinant vaccinia virus which expresses, upon infection, the poliovirus P1 capsid precursor polyprotein with an authentic carboxy terminus. Coinfection of HeLa cells with the P1-expressing vaccinia virus and with a second recombinant vaccinia virus which expresses the poliovirus proteinase 3CD resulted in the correct processing of P1 to yield the three individual capsid proteins VP0, VP3, and VP1. When extracts from coinfected cells were fractionated on sucrose density gradients, the VP0, VP3, and VP1 capsid proteins were immunoprecipitated with type 1 poliovirus antisera from fractions corresponding to a sedimentation consistent for poliovirus 75S procapsids. Examination of these fractions by electron microscopy revealed structures which lacked electron-dense cores and which corresponded in size and shape to those expected for poliovirus empty capsids. We conclude that the expression of the two poliovirus proteins P1 and 3CD in coinfected cells is sufficient for the correct processing of the capsid precursor to VP0, VP3, and VP1 as well as for the assembly of poliovirus empty capsid-like structures.

First genetic characterization of rotavirus C in Russia.

PubMed

Zhirakovskaia, Elena; Tikunov, Artem; Klemesheva, Vera; Loginovskikh, Natalia; Netesov, Sergey; Tikunova, Nina

2016-04-01

Rotaviruses C (RVC) cause sporadic cases and outbreaks of diarrhea in humans and animals worldwide. The aim of this study was to monitor RVC during a surveillance study of sporadic cases of viral gastroenteritis in the Novosibirsk and Omsk regions of Russia from 2006 to 2011. A total of 2144 stool samples from children and adults hospitalized with acute gastroenteritis were tested for RVC by RT-PCR. Sixteen RVC-positive stool samples were detected at a rate of 0.6% (13/2037) in children and 2.8% (3/107) in adults. The low detection rate suggested that RVC infection was an uncommon cause of hospitalization in Russia. The complete VP7, VP4, VP6, and NSP4 gene sequences were determined. It was found that RVCs with at least two different genome backgrounds circulated in Siberia. VP4, VP6, and NSP4 gene sequences of most Russian RVC strains clustered with South Asian strains, while the VP7 gene showed a closer relationship to European strains. Meanwhile, only VP4 and NSP4 sequences of the strain Omsk08-386 clustered with South Asian strains, while its VP6 and VP7 sequences clustered with European strains. This is the first genetic characterization of Russian RVC strains and the first report on the prevalence of RVC in the Asian part of Russia. Copyright © 2016 Elsevier B.V. All rights reserved.

Supramolecular Assembly of Gold Nanoparticles in PS-b-P2VP Diblock Copolymers via Hydrogen Bonding

NASA Astrophysics Data System (ADS)

Jang, Se Gyu; Hawker, Craig J.; Kramer, Edward J.

2011-03-01

We report a simple route to control the spatial distribution of Au nanoparticles (Au-NPs) in PS- b -P2VP diblock copolymers using hydrogen bonding between P2VP and the hydroxyl-containing (PI-OH) units in PS- b -PIOH thiol-terminated ligands on Au-NP. End-functional thiol ligands of poly(styrene- b -1,2&3,4-isoprene-SH) are synthesized by anionic polymerization. After synthesis of Au-NPs, the inner PI block is hydroxylated by hydroboration and the resulting micelle-like Au-NPs consist of a hydrophobic PS outer brush and a hydrophilic inner PI-OH block. The influence of the hydroxyl groups is significant with strong segregation being observed to the PS/P2VP interface and then to the P2VP domain of lamellar-forming PS-b-P2VP diblock copolymers as the length of the PI-OH block is increased. The strong hydrogen bonding between nanoparticle block copolymer ligands and the P2VP block allows the Au-NPs to be incorporated within the P2VP domain to high Au--NP volume fractions ϕp without macrophase separation, driving transitions from lamellar to bicontinuous morphologies as ϕp increases.

Essential role of the unordered VP2 n-terminal domain of the parvovirus MVM capsid in nuclear assembly and endosomal enlargement of the virion fivefold channel for cell entry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sanchez-Martinez, Cristina; Grueso, Esther; Carroll, Miles

The unordered N-termini of parvovirus capsid proteins (Nt) are translocated through a channel at the icosahedral five-fold axis to serve for virus traffick. Heterologous peptides were genetically inserted at the Nt of MVM to study their functional tolerance to manipulations. Insertion of a 5T4-single-chain antibody at VP2-Nt (2Nt) yielded chimeric capsid subunits failing to enter the nucleus. The VEGFR2-binding peptide (V1) inserted at both 2Nt and VP1-Nt efficiently assembled in virions, but V1 disrupted VP1 and VP2 entry functions. The VP2 defect correlated with restricted externalization of V1-2Nt out of the coat. The specific infectivity of MVM and wtVP-pseudotyped mosaicmore » MVM-V1 virions, upon heating and/or partial 2Nt cleavage, demonstrated that some 2Nt domains become intracellularly translocated out of the virus shell and cleaved to initiate entry. The V1 insertion defines a VP2-driven endosomal enlargement of the channel as an essential structural rearrangement performed by the MVM virion to infect.« less

Antigenic and Genomic Diversity of Human Rotavirus VP4 in Two Consecutive Epidemic Seasons in Mexico

PubMed Central

Padilla-Noriega, Luis; Méndez-Toss, Martha; Menchaca, Griselda; Contreras, Juan F.; Romero-Guido, Pedro; Puerto, Fernando I.; Guiscafré, Héctor; Mota, Felipe; Herrera, Ismael; Cedillo, Roberto; Muñoz, Onofre; Calva, Juan; Guerrero, María de Lourdes; Coulson, Barbara S.; Greenberg, Harry B.; López, Susana; Arias, Carlos F.

1998-01-01

In the present investigation we characterized the antigenic diversity of the VP4 and VP7 proteins in 309 and 261 human rotavirus strains isolated during two consecutive epidemic seasons, respectively, in three different regions of Mexico. G3 was found to be the prevalent VP7 serotype during the first year, being superseded by serotype G1 strains during the second season. To antigenically characterize the VP4 protein of the strains isolated, we used five neutralizing monoclonal antibodies (MAbs) which showed specificity for VP4 serotypes P1A, P1B, and P2 in earlier studies. Eight different patterns of reactivity with these MAbs were found, and the prevalence of three of these patterns varied from one season to the next. The P genotype of a subset of 52 samples was determined by PCR. Among the strains characterized as genotype P[4] and P[8] there were three and five different VP4 MAb reactivity patterns, respectively, indicating that the diversity of neutralization epitopes in VP4 is greater than that previously appreciated by the genomic typing methods. PMID:9620401

Quantification of systemic and local immune responses to individual rotavirus proteins during rotavirus infection in mice.

PubMed Central

Ishida, S; Feng, N; Tang, B; Gilbert, J M; Greenberg, H B

1996-01-01

The purpose of the present study was to develop a quantitative assay that could be used to measure the local and systemic immune responses to specific rotavirus proteins following rotavirus infection of adult mice. To measure these responses, we used an immunocytochemical staining assay of Spodoptera frugiperda (Sf-9) cells which were infected with recombinant baculovirus expressing selected rotavirus proteins. The specificity of the assay was documented by using a series of monoclonal antibodies to individual rotavirus proteins. We observed that the assay had high levels of sensitivity and specificity for a series of VP7- and VP4-specific neutralizing monoclonal antibodies which recognized conformation-dependent epitopes on their target proteins. We also studied immunoglobulin G (IgG) immune responses in serum and IgA immune responses in the stools of mice infected with wild-type murine rotavirus strain EHPw. In both sera and stools, the most immunogenic proteins were VP6 and VP4. VP2 was less immunogenic than VP6 or VP4, and the immune responses to VP7, NSP2, and NSP4 were very low in serum and undetectable in stools. PMID:8784572

Controlling pore morphology and properties of nanoporous silica films using the different architecture PS-b-P2VP as a template.

PubMed

Yu, Yang-Yen; Chien, Wen-Chen; Chen, Shih-Ting

2010-07-01

Nanoporous silica films were prepared through the templating of amphiphilic block copolymer, poly(styrene-2-vinyl pyridine) (PS-b-P2VP), and monodispersed colloidal silica nanoparticles. The experimental and theoretical studies suggested that the intermolecular hydrogen bonding existes between the colloidal silica nanoparticles and PS-b-P2VP. The effects of the loading ratio and P2VP chain length on the morphology and properties of the prepared nanoporous silica films were investigated. TEM and AFM studies showed that the uniform pore size could be achieved and the pore size increased with increasing porogen loading. The refractive index and dielectric constant of the prepared nanoporous films decreased with an increase in PS-b-P2VP loading. On the other hand, the porosity increased with an increasing PS-b-P2VP loading. This study demonstrated a methodology to control pore morphology and properties of the nanoporous silica films through the templating of PS-b-P2VP.

Structural basis for dsRNA recognition and interferon antagonism by Ebola VP35

DOE Office of Scientific and Technical Information (OSTI.GOV)

Leung, Daisy W.; Prins, Kathleen C.; Borek, Dominika M.

2010-03-12

Ebola viral protein 35 (VP35), encoded by the highly pathogenic Ebola virus, facilitates host immune evasion by antagonizing antiviral signaling pathways, including those initiated by RIG-I-like receptors. Here we report the crystal structure of the Ebola VP35 interferon inhibitory domain (IID) bound to short double-stranded RNA (dsRNA), which together with in vivo results reveals how VP35-dsRNA interactions contribute to immune evasion. Conserved basic residues in VP35 IID recognize the dsRNA backbone, whereas the dsRNA blunt ends are 'end-capped' by a pocket of hydrophobic residues that mimic RIG-I-like receptor recognition of blunt-end dsRNA. Residues critical for RNA binding are also importantmore » for interferon inhibition in vivo but not for viral polymerase cofactor function of VP35. These results suggest that simultaneous recognition of dsRNA backbone and blunt ends provides a mechanism by which Ebola VP35 antagonizes host dsRNA sensors and immune responses.« less

Serum and Wound Vancomycin Levels After Intrawound Administration in Primary Total Joint Arthroplasty.

PubMed

Johnson, Jeremiah D; Nessler, Joseph M; Horazdovsky, Ryan D; Vang, Sandy; Thomas, Avis J; Marston, Scott B

2017-03-01

Periprosthetic joint infection is the most common cause of readmissions after total joint arthroplasty (TJA). Intrawound vancomycin powder (VP) has reduced infection rates in spine surgery; however, there are no data regarding VP in primary TJA. Thirty-four TJA patients received 2 g of VP intraoperatively to investigate VP's pharmacokinetics. Serum and wound concentrations were measured at multiple intervals over 24 hours after closure. All serum concentrations were subtherapeutic (<15μg/mL) and peaked 12 hours after closure (4.7μg/mL; standard deviation [SD], 3.2). Wound concentrations were 922 μg/mL (SD, 523) 3 hours after closure and 207 μg/mL (SD, 317) at 24 hours. VP had a half-life of 7.2 hours (95% confidence interval, 7.0-9.3) in TJA wounds. VP produced highly therapeutic intrawound concentrations while yielding low systemic levels in TJA. VP may serve as a safe adjunct in the prevention of periprosthetic joint infection. Copyright © 2015 Elsevier Inc. All rights reserved.

Mechanism for Coordinated RNA Packaging and Genome Replication by Rotavirus Polymerase VP1

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lu, Xiaohui; McDonald, Sarah M.; Tortorici, M. Alejandra

2009-04-08

Rotavirus RNA-dependent RNA polymerase VP1 catalyzes RNA synthesis within a subviral particle. This activity depends on core shell protein VP2. A conserved sequence at the 3' end of plus-strand RNA templates is important for polymerase association and genome replication. We have determined the structure of VP1 at 2.9 {angstrom} resolution, as apoenzyme and in complex with RNA. The cage-like enzyme is similar to reovirus {lambda}3, with four tunnels leading to or from a central, catalytic cavity. A distinguishing characteristic of VP1 is specific recognition, by conserved features of the template-entry channel, of four bases, UGUG, in the conserved 3' sequence.more » Well-defined interactions with these bases position the RNA so that its 3' end overshoots the initiating register, producing a stable but catalytically inactive complex. We propose that specific 3' end recognition selects rotavirus RNA for packaging and that VP2 activates the autoinhibited VP1/RNA complex to coordinate packaging and genome replication.« less

The Ebola Virus Nucleoprotein Recruits the Host PP2A-B56 Phosphatase to Activate Transcriptional Support Activity of VP30.

PubMed

Kruse, Thomas; Biedenkopf, Nadine; Hertz, Emil Peter Thrane; Dietzel, Erik; Stalmann, Gertrud; López-Méndez, Blanca; Davey, Norman E; Nilsson, Jakob; Becker, Stephan

2018-01-04

Transcription of the Ebola virus genome depends on the viral transcription factor VP30 in its unphosphorylated form, but the underlying molecular mechanism of VP30 dephosphorylation is unknown. Here we show that the Ebola virus nucleoprotein (NP) recruits the host PP2A-B56 protein phosphatase through a B56-binding LxxIxE motif and that this motif is essential for VP30 dephosphorylation and viral transcription. The LxxIxE motif and the binding site of VP30 in NP are in close proximity, and both binding sites are required for the dephosphorylation of VP30. We generate a specific inhibitor of PP2A-B56 and show that it suppresses Ebola virus transcription and infection. This work dissects the molecular mechanism of VP30 dephosphorylation by PP2A-B56, and it pinpoints this phosphatase as a potential target for therapeutic intervention. Copyright © 2017 Elsevier Inc. All rights reserved.

Cracking the egg: virtual embryogenesis of real robots.

PubMed

Cussat-Blanc, Sylvain; Pollack, Jordan

2014-01-01

All multicellular living beings are created from a single cell. A developmental process, called embryogenesis, takes this first fertilized cell down a complex path of reproduction, migration, and specialization into a complex organism adapted to its environment. In most cases, the first steps of the embryogenesis take place in a protected environment such as in an egg or in utero. Starting from this observation, we propose a new approach to the generation of real robots, strongly inspired by living systems. Our robots are composed of tens of specialized cells, grown from a single cell using a bio-inspired virtual developmental process. Virtual cells, controlled by gene regulatory networks, divide, migrate, and specialize to produce the robot's body plan (morphology), and then the robot is manually built from this plan. Because the robot is as easy to assemble as Lego, the building process could be easily automated.

Training of goal directed arm movements with motion interactive video games in children with cerebral palsy - a kinematic evaluation.

PubMed

Sandlund, Marlene; Domellöf, Erik; Grip, Helena; Rönnqvist, Louise; Häger, Charlotte K

2014-10-01

The main aim of this study was to evaluate the quality of goal-directed arm movements in 15 children with cerebral palsy (CP) following four weeks of home-based training with motion interactive video games. A further aim was to investigate the applicability and characteristics of kinematic parameters in a virtual context in comparison to a physical context. Kinematics and kinetics were captured while the children performed arm movements directed towards both virtual and physical targets. The children's movement precision improved, their centre of pressure paths decreased, as did the variability in maximal shoulder angles when reaching for virtual objects. Transfer to a situation with physical targets was mainly indicated by increased movement smoothness. Training with motion interactive games seems to improve arm motor control in children with CP. The results highlight the importance of considering both the context and the task itself when investigating kinematic parameters.

Interactive analysis of geographically distributed population imaging data collections over light-path data networks

NASA Astrophysics Data System (ADS)

van Lew, Baldur; Botha, Charl P.; Milles, Julien R.; Vrooman, Henri A.; van de Giessen, Martijn; Lelieveldt, Boudewijn P. F.

2015-03-01

The cohort size required in epidemiological imaging genetics studies often mandates the pooling of data from multiple hospitals. Patient data, however, is subject to strict privacy protection regimes, and physical data storage may be legally restricted to a hospital network. To enable biomarker discovery, fast data access and interactive data exploration must be combined with high-performance computing resources, while respecting privacy regulations. We present a system using fast and inherently secure light-paths to access distributed data, thereby obviating the need for a central data repository. A secure private cloud computing framework facilitates interactive, computationally intensive exploration of this geographically distributed, privacy sensitive data. As a proof of concept, MRI brain imaging data hosted at two remote sites were processed in response to a user command at a third site. The system was able to automatically start virtual machines, run a selected processing pipeline and write results to a user accessible database, while keeping data locally stored in the hospitals. Individual tasks took approximately 50% longer compared to a locally hosted blade server but the cloud infrastructure reduced the total elapsed time by a factor of 40 using 70 virtual machines in the cloud. We demonstrated that the combination light-path and private cloud is a viable means of building an analysis infrastructure for secure data analysis. The system requires further work in the areas of error handling, load balancing and secure support of multiple users.

Serologic markers in early stages of African horse sickness virus infection.

PubMed

Martínez-Torrecuadrada, J L; Díaz-Laviada, M; Roy, P; Sánchez, C; Vela, C; Sánchez-Vizcaíno, J M; Casal, J I

1997-02-01

Fifteen horses were experimentally infected with African horse sickness virus (AHSV) serotype 4. To learn more about the time course of production and specificity of AHSV-specific antibodies, sera were analyzed by immunoblot analysis. Only animals that survived for more than 9 days were able to develop a humoral immune response detectable by immunoblotting. The earliest serological markers corresponded mainly to VP5, VP6, and NS2 and to a lesser extent to VP3, NS1, and NS3. Neutralizing antibodies to VP2 were not detected by immunoblotting, suggesting that they are mostly conformation dependent. VP7-specific antibodies were detected later in infection. These results make NS2 and VP6 the most attractive candidates for the rapid diagnosis of the infection.

Serologic markers in early stages of African horse sickness virus infection.

PubMed Central

Martínez-Torrecuadrada, J L; Díaz-Laviada, M; Roy, P; Sánchez, C; Vela, C; Sánchez-Vizcaíno, J M; Casal, J I

1997-01-01

Fifteen horses were experimentally infected with African horse sickness virus (AHSV) serotype 4. To learn more about the time course of production and specificity of AHSV-specific antibodies, sera were analyzed by immunoblot analysis. Only animals that survived for more than 9 days were able to develop a humoral immune response detectable by immunoblotting. The earliest serological markers corresponded mainly to VP5, VP6, and NS2 and to a lesser extent to VP3, NS1, and NS3. Neutralizing antibodies to VP2 were not detected by immunoblotting, suggesting that they are mostly conformation dependent. VP7-specific antibodies were detected later in infection. These results make NS2 and VP6 the most attractive candidates for the rapid diagnosis of the infection. PMID:9003637

A collaborative network middleware project by Lambda Station, TeraPaths, and Phoebus

NASA Astrophysics Data System (ADS)

Bobyshev, A.; Bradley, S.; Crawford, M.; DeMar, P.; Katramatos, D.; Shroff, K.; Swany, M.; Yu, D.

2010-04-01

The TeraPaths, Lambda Station, and Phoebus projects, funded by the US Department of Energy, have successfully developed network middleware services that establish on-demand and manage true end-to-end, Quality-of-Service (QoS) aware, virtual network paths across multiple administrative network domains, select network paths and gracefully reroute traffic over these dynamic paths, and streamline traffic between packet and circuit networks using transparent gateways. These services improve network QoS and performance for applications, playing a critical role in the effective use of emerging dynamic circuit network services. They provide interfaces to applications, such as dCache SRM, translate network service requests into network device configurations, and coordinate with each other to setup up end-to-end network paths. The End Site Control Plane Subsystem (ESCPS) builds upon the success of the three projects by combining their individual capabilities into the next generation of network middleware. ESCPS addresses challenges such as cross-domain control plane signalling and interoperability, authentication and authorization in a Grid environment, topology discovery, and dynamic status tracking. The new network middleware will take full advantage of the perfSONAR monitoring infrastructure and the Inter-Domain Control plane efforts and will be deployed and fully vetted in the Large Hadron Collider data movement environment.

VP08R from Infectious Spleen and Kidney Necrosis Virus Is a Novel Component of the Virus-Mock Basement Membrane

PubMed Central

Xu, Xiaopeng; Yan, Muting; Wang, Rui; Lin, Ting; Tang, Junliang; Li, Chaozheng; Weng, Shaoping

2014-01-01

ABSTRACT Infectious spleen and kidney necrosis virus (ISKNV), the type species of the genus Megalocytivirus, family Iridoviridae, brings great harm to fish farming. In infected tissues, ISKNV infection is characterized by a unique phenomenon, in that the infected cells are attached by lymphatic endothelial cells (LECs), which are speculated to wall off the infected cells from host immune attack. A viral membrane protein, VP23R, binds and recruits the host nidogen-1 protein to construct a basement membrane (BM)-like structure, termed virus-mock basement membrane (VMBM), on the surface of infected cells to provide attaching sites for LECs. VMBMs do not contain collagen IV protein, which is essential for maintenance of BM integrity and functions. In this study, we identified the VP08R protein encoded by ISKNV. VP08R was predicted to be a secreted protein with a signal peptide but without a transmembrane domain. However, immunofluorescence assays demonstrated that VP08R is located on the plasma membrane of infected cells and shows an expression profile similar to that of VP23R. Coimmunoprecipitation showed that VP08R interacts with both VP23R and nidogen-1, indicating that VP08R is a component of VMBM and is present on the cell membrane by binding to VP23R. Through formation of intermolecular disulfide bonds, VP08R molecules self-organized into a multimer, which may play a role in the maintenance of VMBM integrity and stability. Moreover, the VP08R multimer was easily degraded when the ISKNV-infected cells were lysed, which may be a mechanism for VMBM disassembly when necessary to free LECs and release the mature virions. IMPORTANCE Infectious spleen and kidney necrosis virus (ISKNV; genus Megalocytivirus, family Iridovirus) is most harmful to cultured fishes. In tissues, the ISKNV-infected cells are attached by lymphatic endothelial cells (LECs), which are speculated to segregate the host immune system. A viral membrane protein, VP23R, binds and recruits the host nidogen-1 protein to construct virus-mock basement membranes (VMBMs) on the surface of infected cells to provide attaching sites for LECs. Although VMBMs lack the collagen IV network, which is an essential structural part of true BMs, VMBMs still show an intact structure. An ISKNV-encoded VP08R protein can self-assemble into a multimer and bind both VP23R and nidogen-1 to maintain the integrity and stability of VMBMs. On the basis of these facts, we redrew the putative schematic illustration of the VMBM structure. Our study suggests that the virus adopts a strategy to remodel the cellular matrix and may provide an important reference to elucidate BM functions and the mechanisms of lymphangiogenesis. PMID:24599992

Cellular Action of Vasopressin in Medullary Tubules of Mice with Hereditary Nephrogenic Diabetes Insipidus

PubMed Central

Jackson, Brian A.; Edwards, Richard M.; Valtin, Heinz; Dousa, Thomas P.

1980-01-01

Our previous studies (1974. J. Clin. Invest.54: 753-762.) suggested that impaired metabolism of cyclic AMP (cAMP) may be involved in the renal unresponsiveness to vasopressin (VP) in mice with hereditary nephrogenic diabetes insipidus (NDI). To localize such a defect to specific segments of the nephron, we studied the activities of VP-sensitive adenylate cyclase, cAMP phosphodiesterase (cAMP-PDIE), as well as accumulation of cAMP in medullary collecting tubules (MCT) and in medullary thick ascending limbs of Henle's loop (MAL) microdissected from control mice with normal concentrating ability and from mice with hereditary NDI. Adenylate cyclase activity stimulated by VP or by NaF was only slightly lower (−24%) in MCT from NDI mice, compared with controls. In MAL of NDI mice, basal, VP-sensitive, and NaF-sensitive adenylate cyclase was markedly (> −60%) lower compared with MAL of controls. The specific activity of cAMP-PDIE was markedly higher in MCT of NDI mice compared with controls, but was not different between MAL of control and NDI mice. Under present in vitro conditions, incubation of intact MCT from control mice with VP caused a striking increase in cAMP levels (>10), but VP failed to elicit a change in cAMP levels in MCT from NDI mice. When the cAMP-PDIE inhibitor 1-methyl-3-isobutyl xanthine (MIX) was added to the above incubation, VP caused a significant increase in cAMP levels in MCT from both NDI mice and control mice. Under all tested conditions, cAMP levels in MCT of NDI mice were lower than corresponding values in control MCT. Under the present experimental setting, VP and other stimulating factors (MIX, cholera toxin) did not change cAMP levels in MAL from either control mice or from NDI mice. The results of the present in vitro experiments suggest that the functional unresponsiveness of NDI mice to VP is perhaps mainly the result of the inability of collecting tubules to increase intracellular cAMP levels in response to VP. In turn, this inability to increase cAMP in response to VP is at least partly the result of abnormally high activity of cAMP-PDIE, a somewhat lower activity of VP-sensitive adenylate cyclase in MCT of NDI mice, and perhaps to a deficiency of some other as yet unidentified factors. The possible contribution of low VP-sensitive adenylate cyclase activity in MAL of NDI mice to the renal resistance to VP remains to be defined. PMID:6249843

VpRFP1, a novel C4C4-type RING finger protein gene from Chinese wild Vitis pseudoreticulata, functions as a transcriptional activator in defence response of grapevine

PubMed Central

Yu, Yihe; Xu, Weirong; Wang, Shengyi; Xu, Yan; Li, Hui'e; Wang, Yuejin; Li, Shuxiu

2011-01-01

RING finger proteins comprise a large family and play important roles in regulation of growth and development, hormone signalling, and responses to biotic and abiotic stresses in plants. In this study, the identification and functional characterization of a C4C4-type RING finger protein gene from the Chinese wild grapevine Vitis pseudoreticulata (designated VpRFP1) are reported. VpRFP1 was initially identified as an expressed sequence tag (EST) from a cDNA library constructed from leaves of V. pseudoreticulata inoculated with the grapevine powdery mildew Uncinula necator. Sequence analysis of the deduced VpRFP1 protein based on the full-length cDNA revealed an N-terminal nuclear localization signal (NLS) and a C-terminal C4C4-type RING finger motif with the consensus sequence Cys-X2-Cys-X13-Cys-X1-Cys-X4-Cys-X2-Cys-X10-Cys-X2-Cys. Upon inoculation with U. necator, expression of VpRFP1 was rapidly induced to higher levels in mildew-resistant V. pseudoreticulata plants. In contrast, expression of VpRFP1 was down-regulated in mildew-susceptible V. vinifera plants. Western blotting using an antibody raised against VpRFP1 showed that VpRFP1 was also induced to higher levels in V. pseudoreticulata plants at 12–48 hours post-inoculation (hpi). However, there was only slight increase in VpRFP in V. vinifera plants in the same time frame, even though a more significant increase was observed at 96–144 hpi in these plants. Results from transactivation assays in yeast showed that the RING finger motif of VpRFP1 exhibited some activity of transcriptional activation; however, no activity was seen with the full-length VpRFP1. Overexpression of VpRFP1 in Arabidopsis plants was found to enhance resistance to Arabidopsis powdery mildew Golovinomyces cichoracearum, which seemed to be correlated with increased transcript levels of AtPR1 and AtPR2 in the pathogen-infected tissues. In addition, the Arabidopsis transgenic lines showed enhanced resistance to a virulent bacterial pathogen Pseudomonas syringae pv. tomato DC3000. Taken together, the results suggested that VpRFP1 may be a transcriptional activator of defence-related genes in grapevines. PMID:21862480

Fbis report. Science and technology: China, October 18, 1995

DOE Office of Scientific and Technical Information (OSTI.GOV)

NONE

1995-10-18

;Partial Contents: Nanomaterials Fabrication, Applications Research Advances Noted; CAST Announces World`s First Space-Grown Large-Diameter GaAs Monocrystal; Assay of Antiviral Activity of Antisense Phosphorothioate Oligodeoxynucleotide Against Dengue Virus; Expression and Antigenicity of Chimeric Proteins of Cholera Toxin B Subunit With Hepatitis C Virus; CNCOFIEC Signs Agreement With IBM for New Intelligent Building; Latest Reports on Optical Computing, Memory; BIDC To Introduce S3 Company`s Multimedia Accelerator Chipset; Virtual Private PCN Ring Network Based on ATM VP Cross-Connection; Beijing Gets Nation`s First Frame Relay Network; Situation of Power Industry Development and International Cooperation; Diagrams of China`s Nuclear Waste Containment Vessels; Chinese-Developed Containment Vesselmore » Material Reaches World Standards; Second Fuel Elements for Qinshan Plant Passes Inspection; and Geothermal Deep-Well Electric Pump Technology Developed.« less

Quantitative Evaluation of Protein Heterogeneity within Herpes Simplex Virus 1 Particles.

PubMed

El Bilali, Nabil; Duron, Johanne; Gingras, Diane; Lippé, Roger

2017-05-15

Several virulence genes have been identified thus far in the herpes simplex virus 1 genome. It is also generally accepted that protein heterogeneity among virions further impacts viral fitness. However, linking this variability directly with infectivity has been challenging at the individual viral particle level. To address this issue, we resorted to flow cytometry (flow virometry), a powerful approach we recently employed to analyze individual viral particles, to identify which tegument proteins vary and directly address if such variability is biologically relevant. We found that the stoichiometry of the U L 37, ICP0, and VP11/12 tegument proteins in virions is more stable than the VP16 and VP22 tegument proteins, which varied significantly among viral particles. Most interestingly, viruses sorted for their high VP16 or VP22 content yielded modest but reproducible increases in infectivity compared to their corresponding counterparts containing low VP16 or VP22 content. These findings were corroborated for VP16 in short interfering RNA experiments but proved intriguingly more complex for VP22. An analysis by quantitative Western blotting revealed substantial alterations of virion composition upon manipulation of individual tegument proteins and suggests that VP22 protein levels acted indirectly on viral fitness. These findings reaffirm the interdependence of the virion components and corroborate that viral fitness is influenced not only by the genome of viruses but also by the stoichiometry of proteins within each virion. IMPORTANCE The ability of viruses to spread in animals has been mapped to several viral genes, but other factors are clearly involved, including virion heterogeneity. To directly probe whether the latter influences viral fitness, we analyzed the protein content of individual herpes simplex virus 1 particles using an innovative flow cytometry approach. The data confirm that some viral proteins are incorporated in more controlled amounts, while others vary substantially. Interestingly, this correlates with the VP16 trans -activating viral protein and indirectly with VP22, a second virion component whose modulation profoundly alters virion composition. This reaffirms that not only the presence but also the amount of specific tegument proteins is an important determinant of viral fitness. Copyright © 2017 American Society for Microbiology.

Assembly/disassembly of a complex icosahedral virus to incorporate heterologous nucleic acids

NASA Astrophysics Data System (ADS)

Pascual, Elena; Mata, Carlos P.; Carrascosa, José L.; Castón, José R.

2017-12-01

Hollow protein containers are widespread in nature, and include virus capsids as well as eukaryotic and bacterial complexes. Protein cages are studied extensively for applications in nanotechnology, nanomedicine and materials science. Their inner and outer surfaces can be modified chemically or genetically, and the internal cavity can be used to template, store and/or arrange molecular cargos. Virus capsids and virus-like particles (VLP, noninfectious particles) provide versatile platforms for nanoscale bioengineering. Study of capsid protein self-assembly into monodispersed particles, and of VLP structure and biophysics is necessary not only to understand natural processes, but also to infer how these platforms can be redesigned to furnish novel functional VLP. Here we address the assembly dynamics of infectious bursal disease virus (IBDV), a complex icosahedral virus. IBDV has a ~70 nm-diameter T  =  13 capsid with VP2 trimers as the only structural subunits. During capsid assembly, VP2 is synthesized as a precursor (pVP2) whose C terminus is cleaved. The pVP2 C terminus has an amphipathic helix that controls VP2 polymorphism. In the absence of the VP3 scaffolding protein, necessary for control of assembly, 466/456-residue pVP2 intermediates bearing this helix assemble into VLP only when expressed with an N-terminal His6 tag (the HT-VP2-466 protein). HT-VP2-466 capsids are optimal for genetic insertion of proteins (cargo space ~78 000 nm3). We established an in vitro assembly/disassembly system of HT-VP2-466-based VLP for heterologous nucleic acid packaging and/or encapsulation of drugs and other molecules. HT-VP2-466 (empty) capsids were disassembled and reassembled by dialysis against low-salt/basic pH and high-salt/acid pH buffers, respectively, thus illustrating the reversibility in vitro of IBDV capsid assembly. HT-VP2-466 VLP also packed heterologous DNA by non-specific confinement during assembly. These and previous results establish the bases for biotechnological applications based on the IBDV capsid and its ability to incorporate exogenous proteins and nucleic acids.

Quantitative Evaluation of Protein Heterogeneity within Herpes Simplex Virus 1 Particles

PubMed Central

El Bilali, Nabil; Duron, Johanne; Gingras, Diane

2017-01-01

ABSTRACT Several virulence genes have been identified thus far in the herpes simplex virus 1 genome. It is also generally accepted that protein heterogeneity among virions further impacts viral fitness. However, linking this variability directly with infectivity has been challenging at the individual viral particle level. To address this issue, we resorted to flow cytometry (flow virometry), a powerful approach we recently employed to analyze individual viral particles, to identify which tegument proteins vary and directly address if such variability is biologically relevant. We found that the stoichiometry of the UL37, ICP0, and VP11/12 tegument proteins in virions is more stable than the VP16 and VP22 tegument proteins, which varied significantly among viral particles. Most interestingly, viruses sorted for their high VP16 or VP22 content yielded modest but reproducible increases in infectivity compared to their corresponding counterparts containing low VP16 or VP22 content. These findings were corroborated for VP16 in short interfering RNA experiments but proved intriguingly more complex for VP22. An analysis by quantitative Western blotting revealed substantial alterations of virion composition upon manipulation of individual tegument proteins and suggests that VP22 protein levels acted indirectly on viral fitness. These findings reaffirm the interdependence of the virion components and corroborate that viral fitness is influenced not only by the genome of viruses but also by the stoichiometry of proteins within each virion. IMPORTANCE The ability of viruses to spread in animals has been mapped to several viral genes, but other factors are clearly involved, including virion heterogeneity. To directly probe whether the latter influences viral fitness, we analyzed the protein content of individual herpes simplex virus 1 particles using an innovative flow cytometry approach. The data confirm that some viral proteins are incorporated in more controlled amounts, while others vary substantially. Interestingly, this correlates with the VP16 trans-activating viral protein and indirectly with VP22, a second virion component whose modulation profoundly alters virion composition. This reaffirms that not only the presence but also the amount of specific tegument proteins is an important determinant of viral fitness. PMID:28275191

Genetic relatedness among human rotavirus genes coding for VP7, a major neutralization protein, and its application to serotype identification.

PubMed Central

Midthun, K; Flores, J; Taniguchi, K; Urasawa, S; Kapikian, A Z; Chanock, R M

1987-01-01

Antigenic characterization of human rotaviruses by plaque reduction neutralization assay has revealed four distinct serotypes. The outer capsid protein VP7, coded for by gene 8 or 9, is a major neutralization protein; however, studies of rotaviruses derived from genetic reassortment between two strains have confirmed that another outer capsid protein, VP3, is in some cases equally important in neutralization. In this study, the genetic relatedness of the genes coding for VP7 of human rotaviruses belonging to serotypes 1 through 4 was examined by hybridization of their denatured double-stranded genomic RNAs to labeled single-stranded mRNA probes derived from human-animal rotavirus reassortants containing only the VP7 gene of their human rotavirus parent. A high degree of homology was demonstrated between the VP7 genes of strain D and other serotype 1 human rotaviruses, strain DS-1 and other serotype 2 human rotaviruses, strain P and other serotype 3 human rotaviruses, and strain ST3 and other serotype 4 human rotaviruses. Hybrid bands could not be demonstrated between the VP7 gene of D, DS-1, P, or ST3 and the corresponding gene of human rotaviruses belonging to a different serotype. RNA specimens extracted from the stools of 15 Venezuelan children hospitalized with rotavirus diarrhea were hybridized to each of the reassortant probes representing the four human serotypes. All five viruses with short RNA patterns showed homology with the DS-1 strain VP7 gene; two of these were previously adapted to tissue culture and shown to be serotype 2 strains by tissue culture neutralization. Of the remaining 10 viruses with long RNA patterns, 2 hybridized only to the D strain VP7 gene, 6 hybridized only to the P strain VP7 gene, and 2 hybridized only to the ST3 strain VP7 gene. Hybridization using single human rotavirus gene substitution reassortants as probes may provide an alternative method for identifying the VP7 serotype of field isolates that would circumvent the need for tissue culture adaptation. Images PMID:3038948

Accuracy of iodine quantification using dual energy CT in latest generation dual source and dual layer CT.

PubMed

Pelgrim, Gert Jan; van Hamersvelt, Robbert W; Willemink, Martin J; Schmidt, Bernhard T; Flohr, Thomas; Schilham, Arnold; Milles, Julien; Oudkerk, Matthijs; Leiner, Tim; Vliegenthart, Rozemarijn

2017-09-01

To determine the accuracy of iodine quantification with dual energy computed tomography (DECT) in two high-end CT systems with different spectral imaging techniques. Five tubes with different iodine concentrations (0, 5, 10, 15, 20 mg/ml) were analysed in an anthropomorphic thoracic phantom. Adding two phantom rings simulated increased patient size. For third-generation dual source CT (DSCT), tube voltage combinations of 150Sn and 70, 80, 90, 100 kVp were analysed. For dual layer CT (DLCT), 120 and 140 kVp were used. Scans were repeated three times. Median normalized values and interquartile ranges (IQRs) were calculated for all kVp settings and phantom sizes. Correlation between measured and known iodine concentrations was excellent for both systems (R = 0.999-1.000, p < 0.0001). For DSCT, median measurement errors ranged from -0.5% (IQR -2.0, 2.0%) at 150Sn/70 kVp and -2.3% (IQR -4.0, -0.1%) at 150Sn/80 kVp to -4.0% (IQR -6.0, -2.8%) at 150Sn/90 kVp. For DLCT, median measurement errors ranged from -3.3% (IQR -4.9, -1.5%) at 140 kVp to -4.6% (IQR -6.0, -3.6%) at 120 kVp. Larger phantom sizes increased variability of iodine measurements (p < 0.05). Iodine concentration can be accurately quantified with state-of-the-art DECT systems from two vendors. The lowest absolute errors were found for DSCT using the 150Sn/70 kVp or 150Sn/80 kVp combinations, which was slightly more accurate than 140 kVp in DLCT. • High-end CT scanners allow accurate iodine quantification using different DECT techniques. • Lowest measurement error was found in scans with largest photon energy separation. • Dual-source CT quantified iodine slightly more accurately than dual layer CT.

Structural basis for Marburg virus VP35-mediated immune evasion mechanisms

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ramanan, Parameshwaran; Edwards, Megan R.; Shabman, Reed S.

2013-07-22

Filoviruses, marburgvirus (MARV) and ebolavirus (EBOV), are causative agents of highly lethal hemorrhagic fever in humans. MARV and EBOV share a common genome organization but show important differences in replication complex formation, cell entry, host tropism, transcriptional regulation, and immune evasion. Multifunctional filoviral viral protein (VP) 35 proteins inhibit innate immune responses. Recent studies suggest double-stranded (ds)RNA sequestration is a potential mechanism that allows EBOV VP35 to antagonize retinoic-acid inducible gene-I (RIG-I) like receptors (RLRs) that are activated by viral pathogen–associated molecular patterns (PAMPs), such as double-strandedness and dsRNA blunt ends. Here, we show that MARV VP35 can inhibit IFNmore » production at multiple steps in the signaling pathways downstream of RLRs. The crystal structure of MARV VP35 IID in complex with 18-bp dsRNA reveals that despite the similar protein fold as EBOV VP35 IID, MARV VP35 IID interacts with the dsRNA backbone and not with blunt ends. Functional studies show that MARV VP35 can inhibit dsRNA-dependent RLR activation and interferon (IFN) regulatory factor 3 (IRF3) phosphorylation by IFN kinases TRAF family member-associated NFkb activator (TANK) binding kinase-1 (TBK-1) and IFN kB kinase e (IKKe) in cell-based studies. We also show that MARV VP35 can only inhibit RIG-I and melanoma differentiation associated gene 5 (MDA5) activation by double strandedness of RNA PAMPs (coating backbone) but is unable to inhibit activation of RLRs by dsRNA blunt ends (end capping). In contrast, EBOV VP35 can inhibit activation by both PAMPs. Insights on differential PAMP recognition and inhibition of IFN induction by a similar filoviral VP35 fold, as shown here, reveal the structural and functional plasticity of a highly conserved virulence factor.« less

Identification of three PPV1 VP2 protein-specific B cell linear epitopes using monoclonal antibodies against baculovirus-expressed recombinant VP2 protein.

PubMed

Sun, Jianhui; Huang, Liping; Wei, Yanwu; Wang, Yiping; Chen, Dongjie; Du, Wenjuan; Wu, Hongli; Feng, Li; Liu, Changming

2015-11-01

Porcine parvovirus type 1 (PPV1) is a major causative agent of embryonic and fetal death in swine. The PPV1 VP2 protein is closely associated with viral immunogenicity for eliciting neutralizing antibodies, but its antigenic structures have been largely unknown. We generated three monoclonal antibodies (MAbs) against baculovirus-expressed recombinant PPV1 VP2 protein. A PEPSCAN analysis identified the minimal B cell linear epitopes of PPV1 VP2 based on these MAbs. Three core epitopes, (228)QQITDA(233), (284)RSLGLPPK(291), and (344)FEYSNGGPFLTPI(356), were defined and mapped onto three-dimensional models of the PPV1 virion and VP2 monomer. The epitope (228)QQITDA(233) is exposed on the virion surface, and the other two are located inside the protein. An alignment of the PPV1 VP2 amino acid sequences showed that (284)RSLGLPPK(291) and (344)FEYSNGGPFLTPI(356) are absolutely conserved, whereas (228)QQITDA(233) has a single substitution at residue 233 in some (S → A or T). We developed a VP2 epitope-based indirect enzyme-linked immunosorbent assay (iELISA) to test for anti-PPV1 antibodies. In a comparative analysis with an immunoperoxidase monolayer assay using 135 guinea pig sera, the VP2-epitope-based iELISA had a concordance rate of 85.19 %, sensitivity of 83.33 %, and specificity of 85.47 %. MAb 8H6 was used to monitor VP2 during the PPV1 replication cycle in vitro with an indirect immunofluorescence assay, which indicated that newly encapsulated virions are released from the nucleus at 24 h postinfection and the PPV1 replication cycle takes less than 24 h. This study provides valuable information clarifying the antigenic structure of PPV1 VP2 and lays the foundations for PPV1 serodiagnosis and antigen detection.

Low-Contrast and Low-Radiation Dose Protocol in Cardiac Computed Tomography: Usefulness of Low Tube Voltage and Knowledge-Based Iterative Model Reconstruction Algorithm.

PubMed

Iyama, Yuji; Nakaura, Takeshi; Yokoyama, Koichi; Kidoh, Masafumi; Harada, Kazunori; Oda, Seitaro; Tokuyasu, Shinichi; Yamashita, Yasuyuki

This study aimed to evaluate the feasibility of a low contrast, low-radiation dose protocol of 80-peak kilovoltage (kVp) with prospective electrocardiography-gated cardiac computed tomography (CT) using knowledge-based iterative model reconstruction (IMR). Thirty patients underwent an 80-kVp prospective electrocardiography-gated cardiac CT with low-contrast agent (222-mg iodine per kilogram of body weight) dose. We also enrolled 30 consecutive patients who were scanned with a 120-kVp cardiac CT with filtered back projection using the standard contrast agent dose (370-mg iodine per kilogram of body weight) as a historical control group. We evaluated the radiation dose for the 2 groups. The 80-kVp images were reconstructed with filtered back projection (protocol A), hybrid iterative reconstruction (HIR, protocol B), and IMR (protocol C). We compared CT numbers, image noise, and contrast-to-noise ratio among 120-kVp protocol, protocol A, protocol B, and protocol C. In addition, we compared the noise reduction rate between HIR and IMR. Two independent readers compared image contrast, image noise, image sharpness, unfamiliar image texture, and overall image quality among the 4 protocols. The estimated effective dose (ED) of the 80-kVp protocol was 74% lower than that of the 120-kVp protocol (1.4 vs 5.4 mSv). The contrast-to-noise ratio of protocol C was significantly higher than that of protocol A. The noise reduction rate of IMR was significantly higher than that of HIR (P < 0.01). There was no significant difference in almost all qualitative image quality between 120-kVp protocol and protocol C except for image contrast. A 80-kVp protocol with IMR yields higher image quality with 74% decreased radiation dose and 40% decreased contrast agent dose as compared with a 120-kVp protocol, while decreasing more image noise compared with the 80-kVp protocol with HIR.

Evaluation of ToxA and Vibrio parahaemolyticus lysate on humoral immune response and immune-related genes in Pacific red snapper.

PubMed

Reyes-Becerril, Martha; Maldonado-García, Minerva; Guluarte, Crystal; León-Gallo, Amalia; Rosales-Mendoza, Sergio; Ascencio, Felipe; Hirono, Ikuo; Angulo, Carlos

2016-09-01

Immunogenicity of ToxA and Vibrio parahaemolyticus lysate was evaluated in a double immunostimulation scheme in Pacific red snapper after V. parahaemolyticus infection. Three groups of Pacific red snapper were intraperitonealy (i.p.) injected with phosphate-buffered saline (PBS group), ToxA of V. parahaemolyticus (ToxA-Vp group) or V. parahaemolyticus lysate (lysate-Vp group) (first injection, day 1; second injection, day 7). Fish were subsequently infected with live V. parahaemolyticus. Humoral immune parameters in skin mucus and serum were evaluated on days 1, 7, 8 and 14 days post-immunostimulation and 7 days post-infection. Moreover expression of immune-related genes was quantified by real time PCR in head-kidney leukocytes, spleen, liver, and intestine. The ToxA-Vp-treated group showed a higher anti-protease and catalase activity in skin mucus when compared with the PBS group. Measurements of SOD and CAT activities showed an increment in both activities a day after the second boost with ToxA-Vp or lysate-Vp. Interestingly, IgM levels in mucus and transcripts were enhanced followed the ToxA-Vp treatment even after challenge. Furthermore, IL-1β was strongly expressed in all analyzed cell or tissues followed ToxA-Vp or Vp-lysate treatments. Finally, SOD and CAT gene expression was up-regulated in fish immunostimulated with either treatment ToxA-Vp or lysate-Vp, mainly after infection in head-kidney leukocytes and intestine. This is the first study where the effects of ToxA from V. parahaemolyticus in the immune system of Pacific red snapper was evaluated. These results suggest that ToxA-Vp would positively affect humoral immune response and up-regulate expression of genes involved in the immune system function; and could help in the control of V. parahaemolyticus infection in Pacific red snapper Lutjanus peru, an economic important fish in Mexico. Copyright © 2016 Elsevier Ltd. All rights reserved.

Composition of the crust in the Grenville and Appalachian Provinces of North America inferred from VP/VS ratios

USGS Publications Warehouse

Musacchio, G.; Mooney, W.D.; Luetgert, J.H.; Christensen, N.I.

1997-01-01

We use the ratios between P and S wave velocities (VP/VS), derived from seismic refraction data, to infer the composition of the crust in the Grenville and the Appalachian Provinces of North America. The crust exhibits VP/VS increasing with depth from 1.64 to 1.84; there is a clear distinction between the Grenville Province (average VP/VS=1.81) and the Appalachian Province (average VP/VS=1.73) which persists at all depths. The boundary between these provinces is east dipping extending for 100 km east of the Champlain thrust. In the Appalachian Province the increase in VP/VS ratios with depth from 1.67 to 1.74 ?? 0.02 may reflect a normal decrease of silica content in the continental crust. In the Grenville Province beneath the Central Granulite Terrane, an anomalous VP/VS ratio of 1.82 ?? 0.02 is observed extending to a depth of 10 km; this correlates with the abundance of Ca-plagioclase in the Marcy Anorthosite. At greater depth (15-20 km), where seismic lamination and high electrical conductivity is observed, VP/VS is 1-84 ?? 0.02 and correlates with the Tahawus Complex, a layered mafic intrusion. Within the 25-km-thick lower crust of the Grenville Province the VP/VS is 1-84 ?? 0.02 and P-velocity is 7.0 ?? 0.1 km/s, which are typical for plagioclase-bearing rocks (gabbro-norite). The high VP/VS ratio in the Grenville Province has not been reported in crust of any other age. Since the Grenville Province contains 75% of the world's known anorthosites, high VP/VS ratio is related to high plagioclase. We suggest that the composition of the Grenville lower crust was significantly modified by the emplacement of the anorthosites in the mid-Proterozoic. Copyright 1997 by the American Geophysical Union.

Reducing the Radiation Dose for CT Colonography: Effect of Low Tube Voltage and Iterative Reconstruction.

PubMed

Yamamura, Sadahiro; Oda, Seitaro; Imuta, Masanori; Utsunomiya, Daisuke; Yoshida, Morikatsu; Namimoto, Tomohiro; Yuki, Hideaki; Kidoh, Masafumi; Funama, Yoshinori; Baba, Hideo; Yamashita, Yasuyuki

2016-02-01

The purpose of this study was to assess the effect of a low-tube-voltage technique and iterative reconstruction (IR) on the radiation dose and image quality of computed tomography colonography (CTC). We studied 30 patients (14 women and 16 men; mean age, 64.5 ± 13.1 years; range, 39-90 years) with colorectal cancer referred for surgical treatment. All underwent CTC with fecal tagging under a standard 120-kVp protocol in the supine position and a 100-kVp protocol in the prone position. The 120-kVp images were reconstructed with filtered back projection (FBP). The 100-kVp images were postprocessed using FBP and a hybrid type of IR (adaptive iterative dose reduction 3D). The effective radiation dose (ED), image noise, and contrast-to-noise ratio (CNR) were compared among the three protocols. The visual image quality was scored on a four-point scale. The mean ED was significantly lower under the 100-kVp protocol than the 120-kVp protocol, resulting in a 27% radiation dose decrease (3.5 ± 2.0 vs 2.5 ± 1.5 mSv; P < .01). Image noise decreased by 48%, and the mean attenuation of tagged fluid increased from 452 to 558 HU on images acquired at 100 kVp with IR compared to that in the 120-kVp protocol; these differences were significant. The mean CNR was significantly higher under the 100 kVp with IR than the other two protocols. We found no significant differences in the visual scores for diagnostic utility between the 100 kVp with IR and the 120 kVp with FBP protocol (P = .10). Low-tube-voltage CTC reduced the radiation dose by approximately 27% while maintaining the image quality. Copyright © 2016 AUR. Published by Elsevier Inc. All rights reserved.

Processing of the VP1/2A junction is not necessary for production of foot-and-mouth disease virus empty capsids and infectious viruses: characterization of "self-tagged" particles.

PubMed

Gullberg, Maria; Polacek, Charlotta; Bøtner, Anette; Belsham, Graham J

2013-11-01

The foot-and-mouth disease virus (FMDV) capsid protein precursor, P1-2A, is cleaved by 3C(pro) to generate VP0, VP3, VP1, and the peptide 2A. The capsid proteins self-assemble into empty capsid particles or viruses which do not contain 2A. In a cell culture-adapted strain of FMDV (O1 Manisa [Lindholm]), three different amino acid substitutions (E83K, S134C, and K210E) were identified within the VP1 region of the P1-2A precursor compared to the field strain (wild type [wt]). Expression of the O1 Manisa P1-2A (wt or with the S134C substitution in VP1) plus 3C(pro), using a transient expression system, resulted in efficient capsid protein production and self-assembly of empty capsid particles. Removal of the 2A peptide from the capsid protein precursor had no effect on capsid protein processing or particle assembly. However, modification of E83K alone abrogated particle assembly with no apparent effect on protein processing. Interestingly, the K210E substitution, close to the VP1/2A junction, completely blocked processing by 3C(pro) at this cleavage site, but efficient assembly of "self-tagged" empty capsid particles, containing the uncleaved VP1-2A, was observed. These self-tagged particles behaved like the unmodified empty capsids in antigen enzyme-linked immunosorbent assays and integrin receptor binding assays. Furthermore, mutant viruses with uncleaved VP1-2A could be rescued in cells from full-length FMDV RNA transcripts encoding the K210E substitution in VP1. Thus, cleavage of the VP1/2A junction is not essential for virus viability. The production of such engineered self-tagged empty capsid particles may facilitate their purification for use as diagnostic reagents and vaccines.

One-year neurodevelopmental outcome of very and late preterm infants: Risk factors and correlation with maternal stress.

PubMed

Coletti, Maria Franca; Caravale, Barbara; Gasparini, Corinna; Franco, Francesco; Campi, Francesca; Dotta, Andrea

2015-05-01

Although "late preterm" (LP) newborns (33-36 weeks of gestational age) represent more than 70% of all preterm labors, little is known about the relation between certain risk factors and developmental outcomes in LP compared to "very preterm" (≤32 weeks) children (VP). This study investigates: (1) LP and VP infants' development at 12 months of corrected age (CA) using the Bayley Scales of Infant Development - 3rd Edition (BSID-III); (2) correlation between BSID-III performances and maternal stress (using Parenting Stress Index-Short Form, PSI-SF) among LP and VP at 12 months CA; and (3) the link between known neonatal and demographic risk factors and developmental outcomes of LP and VP infants. For both LP and VP infants the Mean Cognitive (LP: 102.69±7.68; VP: 103.63±10.68), Language (LP: 96.23±10.08; VP: 99.10±10.37) and Motor (LP: 91.11±10.33; VP: 93.85±10.17) composite scores were in the normal range, without significant differences between the groups. Correlations between PSI-SF and BSID-III showed that in the VP group (but not LP), Language score was negatively related to the PSI-SF 'Difficult Child' scale (r=-.34, p<.05). Regression models revealed that cognitive performance was significantly predicted by physical therapy in LP and by cesarean section in VP infants. For VP only maternal education and length of stay predicted Language score, whereas physical therapy predicted Motor score. Results of the study underline the importance of considering cognitive, language and motor developments separately when assessing a preterm child's development. Prediction models of developmental performance confirm the influence of some known neonatal risk factors and indicate the need for further research on the role of sociodemographic risk factors. Copyright © 2015 Elsevier Inc. All rights reserved.

A Conserved Epitope Mapped with a Monoclonal Antibody against the VP3 Protein of Goose Parvovirus by Using Peptide Screening and Phage Display Approaches.

PubMed

Li, Chenxi; Liu, Hongyu; Li, Jinzhe; Liu, Dafei; Meng, Runze; Zhang, Qingshan; Shaozhou, Wulin; Bai, Xiaofei; Zhang, Tingting; Liu, Ming; Zhang, Yun

2016-01-01

Waterfowl parvovirus (WPV) infection causes high mortality and morbidity in both geese (Anser anser) and Muscovy ducks (Cairina moschata), resulting in significant losses to the waterfowl industries. The VP3 protein of WPV is a major structural protein that induces neutralizing antibodies in the waterfowl. However, B-cell epitopes on the VP3 protein of WPV have not been characterized. To understand the antigenic determinants of the VP3 protein, we used the monoclonal antibody (mAb) 4A6 to screen a set of eight partially expressed overlapping peptides spanning VP3. Using western blotting and an enzyme-linked immunosorbent assay (ELISA), we localized the VP3 epitope between amino acids (aa) 57 and 112. To identify the essential epitope residues, a phage library displaying 12-mer random peptides was screened with mAb 4A6. Phage clone peptides displayed a consensus sequence of YxRFHxH that mimicked the sequence 82Y/FNRFHCH88, which corresponded to amino acid residues 82 to 88 of VP3 protein of WPVs. mAb 4A6 binding to biotinylated fragments corresponding to amino acid residues 82 to 88 of the VP3 protein verified that the 82FxRFHxH88 was the VP3 epitope and that amino acids 82F is necessary to retain maximal binding to mAb 4A6. Parvovirus-positive goose and duck sera reacted with the epitope peptide by dot blotting assay, revealing the importance of these amino acids of the epitope in antibody-epitope binding reactivity. We identified the motif FxRFHxH as a VP3-specific B-cell epitope that is recognized by the neutralizing mAb 4A6. This finding might be valuable in understanding of the antigenic topology of VP3 of WPV.

Interaction of monomeric Ebola VP40 protein with a plasma membrane: A coarse-grained molecular dynamics (CGMD) simulation study.

PubMed

Mohamad Yusoff, Mohamad Ariff; Abdul Hamid, Azzmer Azzar; Mohammad Bunori, Noraslinda; Abd Halim, Khairul Bariyyah

2018-06-01

Ebola virus is a lipid-enveloped filamentous virus that affects human and non-human primates and consists of several types of protein: nucleoprotein, VP30, VP35, L protein, VP40, VP24, and transmembrane glycoprotein. Among the Ebola virus proteins, its matrix protein VP40 is abundantly expressed during infection and plays a number of critical roles in oligomerization, budding and egress from the host cell. VP40 exists predominantly as a monomer at the inner leaflet of the plasma membrane, and has been suggested to interact with negatively charged lipids such as phosphatidylinositol 4,5-bisphosphate (PIP 2 ) and phosphatidylserine (PS) via its cationic patch. The hydrophobic loop at the C-terminal domain has also been shown to be important in the interaction between the VP40 and the membrane. However, details of the molecular mechanisms underpinning their interactions are not fully understood. This study aimed at investigating the effects of mutation in the cationic patch and hydrophobic loop on the interaction between the VP40 monomer and the plasma membrane using coarse-grained molecular dynamics simulation (CGMD). Our simulations revealed that the interaction between VP40 and the plasma membrane is mediated by the cationic patch residues. This led to the clustering of PIP 2 around the protein in the inner leaflet as a result of interactions between some cationic residues including R52, K127, K221, K224, K225, K256, K270, K274, K275 and K279 and PIP 2 lipids via electrostatic interactions. Mutation of the cationic patch or hydrophobic loop amino acids caused the protein to bind at the inner leaflet of the plasma membrane in a different orientation, where no significant clustering of PIP 2 was observed around the mutated protein. This study provides basic understanding of the interaction of the VP40 monomer and its mutants with the plasma membrane. Copyright © 2018 Elsevier Inc. All rights reserved.

Deciphering the role of multiple betaine-carnitine-choline transporters in the Halophile Vibrio parahaemolyticus.

PubMed

Ongagna-Yhombi, Serge Y; McDonald, Nathan D; Boyd, E Fidelma

2015-01-01

Vibrio parahaemolyticus is a halophile that is the predominant cause of bacterial seafood-related gastroenteritis worldwide. To survive in the marine environment, V. parahaemolyticus must have adaptive strategies to cope with salinity changes. Six putative compatible solute (CS) transport systems were previously predicted from the genome sequence of V. parahaemolyticus RIMD2210633. In this study, we determined the role of the four putative betaine-carnitine-choline transporter (BCCT) homologues VP1456, VP1723, VP1905, and VPA0356 in the NaCl stress response. Expression analysis of the four BCCTs subjected to NaCl upshock showed that VP1456, VP1905, and VPA0356, but not VP1723, were induced. We constructed in-frame single-deletion mutant strains for all four BCCTs, all of which behaved similarly to the wild-type strain, demonstrating a redundancy of the systems. Growth analysis of a quadruple mutant and four BCCT triple mutants demonstrated the requirement for at least one BCCT for efficient CS uptake. We complemented Escherichia coli MHK13, a CS synthesis- and transporter-negative strain, with each BCCT and examined CS uptake by growth analysis and (1)H nuclear magnetic resonance (NMR) spectroscopy analyses. These data demonstrated that VP1456 had the most diverse substrate transport ability, taking up glycine betaine (GB), proline, choline, and ectoine. VP1456 was the sole ectoine transporter. In addition, the data demonstrated that VP1723 can transport GB, proline, and choline, whereas VP1905 and VPA0356 transported only GB. Overall, the data showed that the BCCTs are functional and that there is redundancy among them. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Dimerization Controls Marburg Virus VP24-dependent Modulation of Host Antioxidative Stress Responses.

PubMed

Johnson, Britney; Li, Jing; Adhikari, Jagat; Edwards, Megan R; Zhang, Hao; Schwarz, Toni; Leung, Daisy W; Basler, Christopher F; Gross, Michael L; Amarasinghe, Gaya K

2016-08-28

Marburg virus (MARV), a member of the Filoviridae family that also includes Ebola virus (EBOV), causes lethal hemorrhagic fever with case fatality rates that have exceeded 50% in some outbreaks. Within an infected cell, there are numerous host-viral interactions that contribute to the outcome of infection. Recent studies identified MARV protein 24 (mVP24) as a modulator of the host antioxidative responses, but the molecular mechanism remains unclear. Using a combination of biochemical and mass spectrometry studies, we show that mVP24 is a dimer in solution that directly binds to the Kelch domain of Kelch-like ECH-associated protein 1 (Keap1) to regulate nuclear factor (erythroid-derived 2)-like 2 (Nrf2). This interaction between Keap1 and mVP24 occurs through the Kelch interaction loop (K-Loop) of mVP24 leading to upregulation of antioxidant response element transcription, which is distinct from other Kelch binders that regulate Nrf2 activity. N-terminal truncations disrupt mVP24 dimerization, allowing monomeric mVP24 to bind Kelch with higher affinity and stimulate higher antioxidative stress response element (ARE) reporter activity. Mass spectrometry-based mapping of the interface revealed overlapping binding sites on Kelch for mVP24 and the Nrf2 proteins. Substitution of conserved cysteines, C209 and C210, to alanine in the mVP24 K-Loop abrogates Kelch binding and ARE activation. Our studies identify a shift in the monomer-dimer equilibrium of MARV VP24, driven by its interaction with Keap1 Kelch domain, as a critical determinant that modulates host responses to pathogenic Marburg viral infections. Copyright © 2016 Elsevier Ltd. All rights reserved.

Competitive quenching: a possible novel approach in protecting RPE cells from damage during PDT.

PubMed

Weinberger, Dov; Ron, Yonina; Lusky, Moshe; Gaaton, Dan; Orenstein, Arie; Blank, Michael; Mandel, Mathilda; Livnat, Tamar; Barliya, Tilda; Lavie, Gad

2005-04-01

The purpose of this study is to demonstrate feasibility of using our novel concept, termed competitive quenching, for protecting the choroidal extravascular compartment and retinal pigment epithelium (RPE) from verteporfin (VP)-induced phototoxicity using hypericin. Furthermore, we aim to achieve partitioning of the quencher, hypericin, in the extravascular space and VP within the microvascular compartment of the chorio-retinal complex in vivo. We protect RPE cells from damage inflicted by photoactivated VP by introducing hypericin into these cells prior to photosensitization to quench the photosensitizing activity of VP. Cell protection levels were measured by MTT and Hemacolor viability assays. Wavelength range used for VP photoexcitation (700 +/- 40 nm) excludes the absorption range of hypericin, preventing the latter from photoactivation. Pharmacokinetic conditions, in which hypericin spreads throughout the choroidal and retinal extravascular space while VP is confined to the vasculature, are delineated using double-fluorescence imaging. Cell viability increased 3- to 5-fold when 10-20 microM hypericin were present in RPE cells during photosensitization with 0.1-0.5 microM VP. VP fluorescence intensity was unchanged by the presence of hypericin in the cells. Hypericin administered intravenously to rats was confined to the choroidal vasculature after 15 min to 2 hr. Subsequently, hypericin partitioned to the choroidal and retinal extravascular space. VP administered at this time was confined to the microvasculature. RPE and choroid may potentially be protected by compartmentalizing hypericin to the extravascular compartment while VP administered shortly before photosensitization is confined to the microvasculature. Adverse photodynamic therapy (PDT) damage to choroidal tissues adjacent to neovasculature targeted for photoablation have the potential of being prevented by competitive quenching with hypericin.

Rotavirus capsid VP6 tubular and spherical nanostructures act as local adjuvants when co-delivered with norovirus VLPs.

PubMed

Malm, M; Heinimäki, S; Vesikari, T; Blazevic, V

2017-09-01

A subunit protein vaccine candidate based on norovirus (NoV) virus-like particles (VLPs) and rotavirus (RV) VP6 protein against acute childhood gastroenteritis has been proposed recently. RV VP6 forms different oligomeric nanostructures, including tubes and spheres when expressed in vitro, which are highly immunogenic in different animal models. We have shown recently that recombinant VP6 nanotubes have an adjuvant effect on immunogenicity of NoV VLPs in mice. In this study, we investigated if the adjuvant effect is dependent upon a VP6 dose or different VP6 structural assemblies. In addition, local and systemic adjuvant effects as well as requirements for antigen co-delivery and co-localization were studied. The magnitude and functionality of NoV GII.4-specific antibodies and T cell responses were tested in mice immunized with GII.4 VLPs alone or different combinations of VLPs and VP6. A VP6 dose-dependent adjuvant effect on GII.4-specific antibody responses was observed. The adjuvant effect was found to be strictly dependent upon co-administration of NoV GII.4 VLPs and VP6 at the same anatomic site and at the same time. However, the adjuvant effect was not dependent on the types of oligomers used, as both nanotubes and nanospheres exerted adjuvant effect on GII.4-specific antibody generation and, for the first time, T cell immunity. These findings elucidate the mechanisms of VP6 adjuvant effect in vivo and support its use as an adjuvant in a combination NoV and RV vaccine. © 2017 The Authors. Clinical & Experimental Immunology published by John Wiley & Sons Ltd on behalf of British Society for Immunology.

Dimerization Controls Marburg Virus VP24-dependent Modulation of Host Antioxidative Stress Responses

DOE Office of Scientific and Technical Information (OSTI.GOV)

Johnson, Britney; Li, Jing; Adhikari, Jagat

Marburg virus (MARV), a member of the Filoviridae family that also includes Ebola virus (EBOV), causes lethal hemorrhagic fever with case fatality rates that have exceeded 50% in some outbreaks. Within an infected cell, there are numerous host-viral interactions that contribute to the outcome of infection. Recent studies identified MARV protein 24 (mVP24) as a modulator of the host antioxidative responses, but the molecular mechanism remains unclear. Using a combination of biochemical and mass spectrometry studies, we show that mVP24 is a dimer in solution that directly binds to the Kelch domain of Kelch-like ECH-associated protein 1 (Keap1) to regulatemore » nuclear factor (erythroid-derived 2)-like 2 (Nrf2). This interaction between Keap1 and mVP24 occurs through the Kelch interaction loop (K-Loop) of mVP24 leading to upregulation of antioxidant response element transcription, which is distinct from other Kelch binders that regulate Nrf2 activity. N-terminal truncations disrupt mVP24 dimerization, allowing monomeric mVP24 to bind Kelch with higher affinity and stimulate higher antioxidative stress response element (ARE) reporter activity. Mass spectrometry-based mapping of the interface revealed overlapping binding sites on Kelch for mVP24 and the Nrf2 proteins. Substitution of conserved cysteines, C209 and C210, to alanine in the mVP24 K-Loop abrogates Kelch binding and ARE activation. Our studies identify a shift in the monomer-dimer equilibrium of MARV VP24, driven by its interaction with Keap1 Kelch domain, as a critical determinant that modulates host responses to pathogenic Marburg viral infections.« less

Altered brainstem auditory evoked potentials in a rat central sensitization model are similar to those in migraine

PubMed Central

Arakaki, Xianghong; Galbraith, Gary; Pikov, Victor; Fonteh, Alfred N.; Harrington, Michael G.

2014-01-01

Migraine symptoms often include auditory discomfort. Nitroglycerin (NTG)-triggered central sensitization (CS) provides a rodent model of migraine, but auditory brainstem pathways have not yet been studied in this example. Our objective was to examine brainstem auditory evoked potentials (BAEPs) in rat CS as a measure of possible auditory abnormalities. We used four subdermal electrodes to record horizontal (h) and vertical (v) dipole channel BAEPs before and after injection of NTG or saline. We measured the peak latencies (PLs), interpeak latencies (IPLs), and amplitudes for detectable waveforms evoked by 8, 16, or 32 KHz auditory stimulation. At 8 KHz stimulation, vertical channel positive PLs of waves 4, 5, and 6 (vP4, vP5, and vP6), and related IPLs from earlier negative or positive peaks (vN1-vP4, vN1-vP5, vN1-vP6; vP3-vP4, vP3-vP6) increased significantly 2 hours after NTG injection compared to the saline group. However, BAEP peak amplitudes at all frequencies, PLs and IPLs from the horizontal channel at all frequencies, and the vertical channel stimulated at 16 and 32 KHz showed no significant/consistent change. For the first time in the rat CS model, we show that BAEP PLs and IPLs ranging from putative bilateral medial superior olivary nuclei (P4) to the more rostral structures such as the medial geniculate body (P6) were prolonged 2 hours after NTG administration. These BAEP alterations could reflect changes in neurotransmitters and/or hypoperfusion in the midbrain. The similarity of our results with previous human studies further validates the rodent CS model for future migraine research. PMID:24680742

Vaccination with vascular progenitor cells derived from induced pluripotent stem cells elicits antitumor immunity targeting vascular and tumor cells.

PubMed

Koido, Shigeo; Ito, Masaki; Sagawa, Yukiko; Okamoto, Masato; Hayashi, Kazumi; Nagasaki, Eijiro; Kan, Shin; Komita, Hideo; Kamata, Yuko; Homma, Sadamu

2014-05-01

Vaccination of BALB/c mice with dendritic cells (DCs) loaded with the lysate of induced vascular progenitor (iVP) cells derived from murine-induced pluripotent stem (iPS) cells significantly suppressed the tumor of CMS-4 fibrosarcomas and prolonged the survival of CMS-4-inoculated mice. This prophylactic antitumor activity was more potent than that of immunization with DCs loaded with iPS cells or CMS-4 tumor cells. Tumors developed slowly in mice vaccinated with DCs loaded with iVP cells (DC/iVP) and exhibited a limited vascular bed. Immunohistochemistry and a tomato-lectin perfusion study demonstrated that the tumors that developed in the iVP-immunized mice showed a marked decrease in tumor vasculature. Immunization with DC/iVP induced a potent suppressive effect on vascular-rich CMS-4 tumors, a weaker effect on BNL tumors with moderate vasculature, and nearly no effect on C26 tumors with poor vasculature. Treatment of DC/iVP-immunized mice with a monoclonal antibody against CD4 or CD8, but not anti-asialo GM1, inhibited the antitumor activity. CD8(+) T cells from DC/iVP-vaccinated mice showed significant cytotoxic activity against murine endothelial cells and CMS-4 cells, whereas CD8(+) T cells from DC/iPS-vaccinated mice did not. DNA microarray analysis showed that the products of 29 vasculature-associated genes shared between genes upregulated by differentiation from iPS cells into iVP cells and genes shared by iVP cells and isolated Flk-1(+) vascular cells in CMS-4 tumor tissue might be possible targets in the immune response. These results suggest that iVP cells from iPS cells could be used as a cancer vaccine targeting tumor vascular cells and tumor cells.

Nematicidal fluorescent pseudomonads for the in vitro and in vivo suppression of root knot (Meloidogyne incognita) of Capsicum annuum L.

PubMed

Wahla, Verinder; Maheshwari, Dinesh K; Bajpai, Vivek K

2012-08-01

Considerable attention has been paid to plant-growth-promoting rhizobacteria (PGPR), especially the fluorescent group of Pseudomonas species, as the best alternatives to chemicals for facilitating ecofriendly biological control of soil- and seedborne microorganisms. On the basis of their novel plant-growth-promoting attributes, two rhizobacteria Pseudomonas aeruginosa VP1 and VP2 selected out of over 63 isolates from the rhizosphere of chilli (Capsicum annuum) were identified as potential candidates for biocontrol of the root-knot nematode Meloidogyne incognita on chilli. The nematicidal activity of both strains was evaluated in vitro and in vivo for their efficacy against M. incognita. P. aeruginosa VP2 exhibited strong nematicidal activity in comparison with VP1, based on the in vitro killing of the second-stage juveniles (J2) of M. incognita. Seed bacterisation with both strains VP1 and VP2 was able to manage root-knot M. incognita on chilli (C. annuum) in a pot trial study. Increase in root and shoot length and in fresh and dry weight of root and shoot and reduction in the root-knot index over the control were attained. In overall performance, VP2 was 29.5% more effective than VP1, and about 30% more effective than the control (non-bacterised). The application of P. aeruginosa VP1 and P. aeruginosa VP2 controls the development of M. incognita in C. annuum, and hence they are recommended as efficient plant growth promotors and biocontrolling agents for raising healthy crop of C. annuum that can promote the growth of plants and reduce the nematode (M. incognita) population. Copyright © 2012 Society of Chemical Industry.

Identification of Short Hairpin RNA Targeting Foot-And-Mouth Disease Virus with Transgenic Bovine Fetal Epithelium Cells

PubMed Central

He, Hongbin; Ding, Fangrong; Yang, Hongjun; Cheng, Lei; Liu, Wenhao; Zhong, Jifeng; Dai, Yunping; Li, Guangpeng; He, Chengqiang; Yu, Li; Li, Jianbin

2012-01-01

Background Although it is known that RNA interference (RNAi) targeting viral genes protects experimental animals, such as mice, from the challenge of Foot-and-mouth disease virus (FMDV), it has not been previously investigated whether shRNAs targeting FMDV in transgenic dairy cattle or primary transgenic bovine epithelium cells will confer resistance against FMDV challenge. Principal Finding Here we constructed three recombinant lentiviral vectors containing shRNA against VP2 (RNAi-VP2), VP3 (RNAi-VP3), or VP4 (RNAi-VP4) of FMDV, and found that all of them strongly suppressed the transient expression of a FLAG-tagged viral gene fusion protein in 293T cells. In BHK-21 cells, RNAi-VP4 was found to be more potent in inhibition of viral replication than the others with over 98% inhibition of viral replication. Therefore, recombinant lentiviral vector RNAi-VP4 was transfected into bovine fetal fibroblast cells to generate transgenic nuclear donor cells. With subsequent somatic cell cloning, we generated forty transgenic blastocysts, and then transferred them to 20 synchronized recipient cows. Three transgenic bovine fetuses were obtained after pregnant period of 4 months, and integration into chromosome in cloned fetuses was confirmed by Southern hybridization. The primary tongue epithelium cells of transgenic fetuses were isolated and inoculated with 100 TCID50 of FMDV, and it was observed that shRNA significantly suppressed viral RNA synthesis and inhibited over 91% of viral replication after inoculation of FMDV for 48 h. Conclusion RNAi-VP4 targeting viral VP4 gene appears to prevent primary epithelium cells of transgenic bovine fetus from FMDV infection, and it could be a candidate shRNA used for cultivation of transgenic cattle against FMDV. PMID:22905125

Acoustic velocity in rift basin mudstones: effects of in situ stress and sample lithology, and its relation to formation strength

NASA Astrophysics Data System (ADS)

Zakharova, N. V.; Goldberg, D.

2017-12-01

Acoustic/sonic velocity (Vp) provides one of the best proxies for formation strength, which is essential for geomechanical modeling and formation evaluation. Vp-strength relations need to be built empirically for specific basins and/or rock types. Since velocity is stress- and frequency-dependent, such relations can be very sensitive to experimental conditions; therefore, it is important to quantify their effect on velocity values. In this study, we present confined velocity and strength measurements for over 70 samples from the Newark Rift basin, a candidate site for carbon sequestration, and one of the largest in a series of the Mesozoic rift basins on the eastern North-American coast. Acoustic velocity measurements were obtained for a range of confining pressures from 0 to 6,000 psi, roughly corresponding to in situ confining pressure range. Although, overall, Vp values tend to increase with increasing pressure, the degree of Vp response to stress varies dramatically from sample to sample, and does not appear to correlate directly to lithology or porosity. Select samples exhibit near-zero change in Vp with increasing confining pressure, while others are characterized by up to 15% Vp change with 3,000 psi increase in confining pressure. Compared to sonic logs, the low-stress Vp values usually underestimate sonic velocities, while high-stress values tend to overestimate them. Therefore, a systematic frequency-dependent core-log difference is not observed in these rift basin formations, but accounting for Vp dependence on confining pressure is important. We quantify the Vp-pressure dependence using laboratory acoustic measurements, and develop depth-dependent Vp-strength relation, which could be used with sonic logs for geomechanical analysis in similar Mesozoic rift basin formations.

Autocatalytic Activity of the Ubiquitin-Specific Protease Domain of Herpes Simplex Virus 1 VP1-2▿†

PubMed Central

Bolstad, M.; Abaitua, F.; Crump, C. M.; O'Hare, P.

2011-01-01

The herpes simplex virus (HSV) tegument protein VP1-2 is essential for virus entry and assembly. VP1-2 also contains a highly conserved ubiquitin-specific protease (USP) domain within its N-terminal region. Despite conservation of the USP and the demonstration that it can act on artificial substrates such as polyubiquitin chains, identification of the relevance of the USP in vivo to levels or function of any substrate remains limited. Here we show that HSV VP1-2 USP can act on itself and is important for stability. VP1-2 N-terminal variants encompassing the core USP domain itself were not affected by mutation of the catalytic cysteine residue (C65). However, extending the N-terminal region resulted in protein species requiring USP activity for accumulation. In this context, C65A mutation resulted in a drastic reduction in protein levels which could be stabilized by proteosomal inhibition or by the presence of normal C65. The functional USP domain could increase abundance of unstable variants, indicating action at least in part, in trans. Interestingly, full-length variants containing the inactive USP, although unstable when expressed in isolation, were stabilized by virus infection. The catalytically inactive VP1-2 retained complementation activity of a VP1-2-negative virus. Furthermore, a recombinant virus expressing a C65A mutant VP1-2 exhibited little difference in single-step growth curves and the kinetics and abundance of VP1-2 or a number of test proteins. Despite the absence of a phenotype for these replication parameters, the USP activity of VP1-2 may be required for function, including its own stability, under certain circumstances. PMID:21715485

Joint inversion for Vp, Vs, and Vp/Vs at SAFOD, Parkfield, California

USGS Publications Warehouse

Zhang, H.; Thurber, C.; Bedrosian, P.

2009-01-01

We refined the three-dimensional (3-D) Vp, Vs and Vp/Vs models around the San Andreas Fault Observatory at Depth (SAFOD) site using a new double-difference (DD) seismic tomography code (tomoDDPS) that simultaneously solves for earthquake locations and all three velocity models using both absolute and differential P, S, and S-P times. This new method is able to provide a more robust Vp/Vs model than that from the original DD tomography code (tomoDD), obtained simply by dividing Vp by Vs. For the new inversion, waveform cross-correlation times for earthquakes from 2001 to 2002 were also used, in addition to arrival times from earthquakes and explosions in the region. The Vp values extracted from the model along the SAFOD trajectory match well with the borehole log data, providing in situ confirmation of our results. Similar to previous tomographic studies, the 3-D structure around Parkfield is dominated by the velocity contrast across the San Andreas Fault (SAF). In both the Vp and Vs models, there is a clear low-velocity zone as deep as 7 km along the SAF trace, compatible with the findings from fault zone guided waves. There is a high Vp/Vs anomaly zone on the southwest side of the SAF trace that is about 1-2 km wide and extends as deep as 4 km, which is interpreted to be due to fluids and fractures in the package of sedimentary rocks abutting the Salinian basement rock to the southwest. The relocated earthquakes align beneath the northeast edge of this high Vp/Vs zone. We carried out a 2-D correlation analysis for an existing resistivity model and the corresponding profiles through our model, yielding a classification that distinguishes several major lithologies. ?? 2009 by the American Geophysical Union.

Characterization of the RNA silencing suppression activity of the Ebola virus VP35 protein in plants and mammalian cells.

PubMed

Zhu, Yali; Cherukuri, Nil Celebi; Jackel, Jamie N; Wu, Zetang; Crary, Monica; Buckley, Kenneth J; Bisaro, David M; Parris, Deborah S

2012-03-01

Ebola virus (EBOV) causes a lethal hemorrhagic fever for which there is no approved effective treatment or prevention strategy. EBOV VP35 is a virulence factor that blocks innate antiviral host responses, including the induction of and response to alpha/beta interferon. VP35 is also an RNA silencing suppressor (RSS). By inhibiting microRNA-directed silencing, mammalian virus RSSs have the capacity to alter the cellular environment to benefit replication. A reporter gene containing specific microRNA target sequences was used to demonstrate that prior expression of wild-type VP35 was able to block establishment of microRNA silencing in mammalian cells. In addition, wild-type VP35 C-terminal domain (CTD) protein fusions were shown to bind small interfering RNA (siRNA). Analysis of mutant proteins demonstrated that reporter activity in RSS assays did not correlate with their ability to antagonize double-stranded RNA (dsRNA)-activated protein kinase R (PKR) or bind siRNA. The results suggest that enhanced reporter activity in the presence of VP35 is a composite of nonspecific translational enhancement and silencing suppression. Moreover, most of the specific RSS activity in mammalian cells is RNA binding independent, consistent with VP35's proposed role in sequestering one or more silencing complex proteins. To examine RSS activity in a system without interferon, VP35 was tested in well-characterized plant silencing suppression assays. VP35 was shown to possess potent plant RSS activity, and the activities of mutant proteins correlated strongly, but not exclusively, with RNA binding ability. The results suggest the importance of VP35-protein interactions in blocking silencing in a system (mammalian) that cannot amplify dsRNA.

Role of protein phosphatase 1 in dephosphorylation of Ebola virus VP30 protein and its targeting for the inhibition of viral transcription.

PubMed

Ilinykh, Philipp A; Tigabu, Bersabeh; Ivanov, Andrey; Ammosova, Tatiana; Obukhov, Yuri; Garron, Tania; Kumari, Namita; Kovalskyy, Dmytro; Platonov, Maxim O; Naumchik, Vasiliy S; Freiberg, Alexander N; Nekhai, Sergei; Bukreyev, Alexander

2014-08-15

The filovirus Ebola (EBOV) causes the most severe hemorrhagic fever known. The EBOV RNA-dependent polymerase complex includes a filovirus-specific VP30, which is critical for the transcriptional but not replication activity of EBOV polymerase; to support transcription, VP30 must be in a dephosphorylated form. Here we show that EBOV VP30 is phosphorylated not only at the N-terminal serine clusters identified previously but also at the threonine residues at positions 143 and 146. We also show that host cell protein phosphatase 1 (PP1) controls VP30 dephosphorylation because expression of a PP1-binding peptide cdNIPP1 increased VP30 phosphorylation. Moreover, targeting PP1 mRNA by shRNA resulted in the overexpression of SIPP1, a cytoplasm-shuttling regulatory subunit of PP1, and increased EBOV transcription, suggesting that cytoplasmic accumulation of PP1 induces EBOV transcription. Furthermore, we developed a small molecule compound, 1E7-03, that targeted a non-catalytic site of PP1 and increased VP30 dephosphorylation. The compound inhibited the transcription but increased replication of the viral genome and completely suppressed replication of EBOV in cultured cells. Finally, mutations of Thr(143) and Thr(146) of VP30 significantly inhibited EBOV transcription and strongly induced VP30 phosphorylation in the N-terminal Ser residues 29-46, suggesting a novel mechanism of regulation of VP30 phosphorylation. Our findings suggest that targeting PP1 with small molecules is a feasible approach to achieve dysregulation of the EBOV polymerase activity. This novel approach may be used for the development of antivirals against EBOV and other filovirus species. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Resection plane-dependent error in computed tomography volumetry of the right hepatic lobe in living liver donors

PubMed Central

Kwon, Heon-Ju; Kim, Bohyun; Kim, So Yeon; Lee, Chul Seung; Lee, Jeongjin; Song, Gi Won; Lee, Sung Gyu

2018-01-01

Background/Aims Computed tomography (CT) hepatic volumetry is currently accepted as the most reliable method for preoperative estimation of graft weight in living donor liver transplantation (LDLT). However, several factors can cause inaccuracies in CT volumetry compared to real graft weight. The purpose of this study was to determine the frequency and degree of resection plane-dependent error in CT volumetry of the right hepatic lobe in LDLT. Methods Forty-six living liver donors underwent CT before donor surgery and on postoperative day 7. Prospective CT volumetry (VP) was measured via the assumptive hepatectomy plane. Retrospective liver volume (VR) was measured using the actual plane by comparing preoperative and postoperative CT. Compared with intraoperatively measured weight (W), errors in percentage (%) VP and VR were evaluated. Plane-dependent error in VP was defined as the absolute difference between VP and VR. % plane-dependent error was defined as follows: |VP–VR|/W∙100. Results Mean VP, VR, and W were 761.9 mL, 755.0 mL, and 696.9 g. Mean and % errors in VP were 73.3 mL and 10.7%. Mean error and % error in VR were 64.4 mL and 9.3%. Mean plane-dependent error in VP was 32.4 mL. Mean % plane-dependent error was 4.7%. Plane-dependent error in VP exceeded 10% of W in approximately 10% of the subjects in our study. Conclusions There was approximately 5% plane-dependent error in liver VP on CT volumetry. Plane-dependent error in VP exceeded 10% of W in approximately 10% of LDLT donors in our study. This error should be considered, especially when CT volumetry is performed by a less experienced operator who is not well acquainted with the donor hepatectomy plane. PMID:28759989

Fault diagnosis of sensor networked structures with multiple faults using a virtual beam based approach

NASA Astrophysics Data System (ADS)

Wang, H.; Jing, X. J.

2017-07-01

This paper presents a virtual beam based approach suitable for conducting diagnosis of multiple faults in complex structures with limited prior knowledge of the faults involved. The "virtual beam", a recently-proposed concept for fault detection in complex structures, is applied, which consists of a chain of sensors representing a vibration energy transmission path embedded in the complex structure. Statistical tests and adaptive threshold are particularly adopted for fault detection due to limited prior knowledge of normal operational conditions and fault conditions. To isolate the multiple faults within a specific structure or substructure of a more complex one, a 'biased running' strategy is developed and embedded within the bacterial-based optimization method to construct effective virtual beams and thus to improve the accuracy of localization. The proposed method is easy and efficient to implement for multiple fault localization with limited prior knowledge of normal conditions and faults. With extensive experimental results, it is validated that the proposed method can localize both single fault and multiple faults more effectively than the classical trust index subtract on negative add on positive (TI-SNAP) method.

Ebolavirus VP35 is a multifunctional virulence factor.

PubMed

Leung, Daisy W; Prins, Kathleen C; Basler, Christopher F; Amarasinghe, Gaya K

2010-01-01

Ebola virus (EBOV) is a member of the filoviridae family that causes severe hemorrhagic fever during sporadic outbreaks, and no approved treatments are currently available. The multifunctional EBOV VP35 protein facilitates immune evasion by antagonizing antiviral signaling pathways and is important for viral RNA synthesis. In order to elucidate regulatory mechanisms and to develop countermeasures, we recently solved the structures of the Zaire and Reston EBOV VP35 interferon inhibitory domain (IID) in the free form and of the Zaire EBOV VP35 IID bound to dsRNA. Together with biochemical, cell biological, and virological studies, our structural work revealed that distinct regions within EBOV VP35 IID contribute to virulence through host immune evasion and viral RNA synthesis. Here we summarize our recent structural and functional studies and discuss the potential of multifunctional Ebola VP35 as a therapeutic target.

Revealing the role of phospholipase Cβ3 in the regulation of VEGF-induced vascular permeability

PubMed Central

Hoeppner, Luke H.; Phoenix, Kathryn N.; Clark, Karl J.; Bhattacharya, Resham; Gong, Xun; Sciuto, Tracey E.; Vohra, Pawan; Suresh, Sandip; Bhattacharya, Santanu; Dvorak, Ann M.; Ekker, Stephen C.; Dvorak, Harold F.; Claffey, Kevin P.

2012-01-01

VEGF induces vascular permeability (VP) in ischemic diseases and cancer, leading to many pathophysiological consequences. The molecular mechanisms by which VEGF acts to induce hyperpermeability are poorly understood and in vivo models that easily facilitate real-time, genetic studies of VP do not exist. In the present study, we report a heat-inducible VEGF transgenic zebrafish (Danio rerio) model through which VP can be monitored in real time. Using this approach with morpholino-mediated gene knock-down and knockout mice, we describe a novel role of phospholipase Cβ3 as a negative regulator of VEGF-mediated VP by regulating intracellular Ca2+ release. Our results suggest an important effect of PLCβ3 on VP and provide a new model with which to identify genetic regulators of VP crucial to several disease processes. PMID:22674805

Controlled supramolecular assembly of micelle-like gold nanoparticles in PS-b-P2VP diblock copolymers via hydrogen bonding.

PubMed

Jang, Se Gyu; Kramer, Edward J; Hawker, Craig J

2011-10-26

We report a facile strategy to synthesize amphiphilic gold (Au) nanoparticles functionalized with a multilayer, micelle-like structure consisting of a Au core, an inner hydroxylated polyisoprene (PIOH) layer, and an outer polystyrene shell (PS). Careful control of enthalpic interactions via a systematic variation of structural parameters, such as number of hydroxyl groups per ligand (N(OH)) and styrene repeating units (N(PS)) as well as areal chain density of ligands on the Au-core surface (Σ), enables precise control of the spatial distribution of these nanoparticles. This control was demonstrated in a lamellae-forming poly(styrene-b-2-vinylpyridine) (PS-b-P2VP) diblock copolymer matrix, where the favorable hydrogen-bonding interaction between hydroxyl groups in the PIOH inner shell and P2VP chains in the PS-b-P2VP diblock copolymer matrix, driving the nanoparticles to be segregated in P2VP domains, could be counter balanced by the enthalphic penalty of mixing of the PS outer brush with the P2VP domains. By varying N(OH), N(PS), and Σ, the nanoparticles could be positioned in the PS or P2VP domains or at the PS/P2VP interface. In addition, the effect of additives interfering with the hydrogen-bond formation between hydroxyl groups on Au nanoparticles and P2VP chains in a diblock copolymer matrix was investigated, and an interesting pea-pod-like segregation of Au nanoparticles in PS domains was observed.

Non-active site mutations disturb the loop dynamics, dimerization, viral budding and egress of VP40 of the Ebola virus.

PubMed

Balmith, Marissa; Soliman, Mahmoud E S

2017-02-28

The first account of the dynamic features of the loop region of VP40 of the Ebola virus (EboV) using accelerated molecular dynamics (aMD) simulations is reported herein. Due to its major role in the Ebola life cycle, VP40 is considered a promising therapeutic target. The available experimental data on the N-terminal domain (NTD) loop indicates that mutations K127A, T129A and N130A demonstrate an unrecognized role for NTD-plasma membrane (PM) interaction for efficient VP40-PM localization, oligomerization, matrix assembly and egress. Despite experimental results, the molecular description of VP40 and the information it can provide still remain vague. Therefore, to gain further molecular insight into the effect of mutations on the loop region of VP40 and its effects on the overall protein conformation and VP40 dimerization, aMD simulations and post-dynamic analyses were employed for wildtype (WT) and mutant systems. The results showed significant variations in the presence of mutations as per RMSF, RMSD, R g , PCA and distance calculations in comparison to the WT. These results could provide researchers with insight with regards to the conformational aspects concerning VP40 and its close relation to the experimental data. We believe that the results presented in this study will ultimately provide a useful understanding of the structural landscape of the loop region of VP40, which would contribute towards the discovery of novel EboV inhibitors.

Immunogenicity of porcine P[6], P[7]-specific △VP8* rotavirus subunit vaccines with a tetanus toxoid universal T cell epitope.

PubMed

Wen, Xiaobo; Wei, Xiaoman; Ran, Xuhua; Ni, Hongbo; Cao, Si; Zhang, Yao

2015-08-26

Currently, commercial porcine rotavirus vaccines remain varied limitations. The objective of this study is to develop an alternative porcine rotavirus subunit vaccine candidate by parenteral administration, which enables to elicit robust immune responses against most prevalence porcine rotavirus strains. The bacterially-expressed porcine rotavirus P[6]- or P[7]-specific truncated VP8* (aa 64-223) recombinant protein with or without a universal tetanus toxoid CD4(+) T cell epitope P2 was generated. All the recombinant subunit proteins △VP8*s or P2-△VP8*s were of high solubility and high yields. The immunogenicity of each purified △VP8* and P2-△VP8* was evaluated in mice (10 μg/dose) or guinea pigs (20 μg/dose) immunized IM with 600 μg aluminum hydroxide three times at 2-week interval. The introduction of P2T cell epitope to P[7]-△VP8* elicited significantly higher IgG titer in mice than its absence. Comparatively, P2 epitope slightly enhanced the immunogenicity of P[6]-△VP8*. P2-P[7]△VP8* elicited high titer of neutralizing antibody against heterotypic P[7]-specific rotaviruses with varied G type combination. Our data indicated that two subunit vaccines could be plausible bivalent rotavirus vaccine candidate to provide antigenic coverage of porcine rotavirus strains of global or regional importance. Copyright © 2015 Elsevier Ltd. All rights reserved.

Expression and immunogenicity of novel subunit enterovirus 71 VP1 antigens

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xu, Juan; Department of Microbiology and Immunology, Nanjing Medical University; Wang, Shixia

Highlights: Black-Right-Pointing-Pointer EV71 is a major emerging infectious disease in many Asian countries. Black-Right-Pointing-Pointer Inactivated EV71 vaccines are in clinical studies but their safety and efficacy are unknown. Black-Right-Pointing-Pointer Developing subunit based EV71 vaccines is significant and novel antigen design is needed. Black-Right-Pointing-Pointer DNA immunization is an efficient tool to test the immunogenicity of VP1 based EV71 vaccines. Black-Right-Pointing-Pointer Multiple VP1 antigens are developed showing immunogenic potential. -- Abstract: Hand, foot, and mouth disease (HFMD) is a common viral illness in young children. HFMD is caused by viruses belonging to the enterovirus genus of the picornavirus family. Recently, enterovirus 71more » (EV71) has emerged as a virulent agent for HFMD with severe clinical outcomes. In the current report, we conducted a pilot antigen engineering study to optimize the expression and immunogenicity of subunit VP1 antigen for the design of EV71 vaccines. DNA immunization was adopted as a simple technical approach to test different designs of VP1 antigens without the need to express VP1 protein in vitro first. Our studies indicated that the expression and immunogenicity of VP1 protein can be improved with alternated VP1 antigen designs. Data presented in the current report revealed novel pathways to optimize the design of VP1 antigen-based EV71 vaccines.« less

A novel recombinant pseudorabies virus expressing parvovirus VP2 gene: Immunogenicity and protective efficacy in swine.

PubMed

Chen, Yang; Guo, Wanzhu; Xu, Zhiwen; Yan, Qigui; Luo, Yan; Shi, Qian; Chen, Dishi; Zhu, Ling; Wang, Xiaoyu

2011-06-16

Porcine parvovirus (PPV) VP2 gene has been successfully expressed in many expression systems resulting in self-assembly of virus-like particles (VLPs) with similar morphology to the native capsid. Here, a pseudorabies virus (PRV) system was adopted to express the PPV VP2 gene. A recombinant PRV SA215/VP2 was obtained by homologous recombination between the vector PRV viral DNA and a transfer plasmid. Then recombinant virus was purified with plaque purification, and its identity confirmed by PCR amplification, Western blot and indirect immunofluorescence (IFA) analyses. Electronic microscopy of PRV SA215/VP2 confirmed self-assembly of both pseudorabies virus and VLPs from VP2 protein. Immunization of piglets with recombinant virus elicited PRV-specific and PPV-specific humoral immune responses and provided complete protection against a lethal dose of PRV challenges. Gilts immunized with recombinant viruses induced PPV-specific antibodies, and significantly reduced the mortality rate of (1 of 28) following virulent PPV challenge compared with the control (7 of 31). Furthermore, PPV virus DNA was not detected in the fetuses of recombinant virus immunized gilts. In this study, a recombinant PRV SA215/VP2 virus expressing PPV VP2 protein was constructed using PRV SA215 vector. The safety, immunogenicity, and protective efficacy of the recombinant virus were demonstrated in piglets and primiparous gilts. This recombinant PRV SA215/VP2 represents a suitable candidate for the development of a bivalent vaccine against both PRV and PPV infection.

The Ebola virus matrix protein penetrates into the plasma membrane: a key step in viral protein 40 (VP40) oligomerization and viral egress.

PubMed

Adu-Gyamfi, Emmanuel; Soni, Smita P; Xue, Yi; Digman, Michelle A; Gratton, Enrico; Stahelin, Robert V

2013-02-22

Ebola, a fatal virus in humans and non-human primates, has no Food and Drug Administration-approved vaccines or therapeutics. The virus from the Filoviridae family causes hemorrhagic fever, which rapidly progresses and in some cases has a fatality rate near 90%. The Ebola genome encodes seven genes, the most abundantly expressed of which is viral protein 40 (VP40), the major Ebola matrix protein that regulates assembly and egress of the virus. It is well established that VP40 assembles on the inner leaflet of the plasma membrane; however, the mechanistic details of plasma membrane association by VP40 are not well understood. In this study, we used an array of biophysical experiments and cellular assays along with mutagenesis of VP40 to investigate the role of membrane penetration in VP40 assembly and egress. Here we demonstrate that VP40 is able to penetrate specifically into the plasma membrane through an interface enriched in hydrophobic residues in its C-terminal domain. Mutagenesis of this hydrophobic region consisting of Leu(213), Ile(293), Leu(295), and Val(298) demonstrated that membrane penetration is critical to plasma membrane localization, VP40 oligomerization, and viral particle egress. Taken together, VP40 membrane penetration is an important step in the plasma membrane localization of the matrix protein where oligomerization and budding are defective in the absence of key hydrophobic interactions with the membrane.

Association of manual or engine-driven glide path preparation with canal centring and apical transportation: a systematic review.

PubMed

Hartmann, R C; Peters, O A; de Figueiredo, J A P; Rossi-Fedele, G

2018-04-28

The role and effect of glide path preparation in root canal treatment remain controversial. This systematic review aims to compare apical transportation and canal centring of different glide path preparation techniques, with or without subsequent engine-driven root canal preparation. A database search in PubMed, PubMed Central, Embase, Scopus, EBSCO Dentistry & Oral Sciences Source and Virtual Health Library was conducted, using appropriate key words to identify the effect of glide path preparation (or its absence) on apical transportation and canal centring. An assessment for the risk of bias in included studies was carried out. Amongst 2146 studies, 18 satisfied the inclusion criteria. Nine studies assessed glide path preparation per se, comparing apical transportation and canal centring of rotary systems and/or manual files; eleven further investigations examined the efficacy of the glide path prior to final canal preparation with different engine-driven systems. Risk of bias and other study design features with potential influence on study outcomes and clinical implications were assessed. Based on the available evidence, and within the limitation of the studies included, preparation of a glide path using rotary sequences performs similarly (in most of the component studies) or significantly better than manual preparation when assessing apical transportation or canal centring. When compared to the absence of a glide path, canal shaping following glide path preparation was of similar, or significantly better quality, in regard to apical transportation or canal centring. © 2018 International Endodontic Journal. Published by John Wiley & Sons Ltd.

Information Spread of Emergency Events: Path Searching on Social Networks

PubMed Central

Hu, Hongzhi; Wu, Tunan

2014-01-01

Emergency has attracted global attentions of government and the public, and it will easily trigger a series of serious social problems if it is not supervised effectively in the dissemination process. In the Internet world, people communicate with each other and form various virtual communities based on social networks, which lead to a complex and fast information spread pattern of emergency events. This paper collects Internet data based on data acquisition and topic detection technology, analyzes the process of information spread on social networks, describes the diffusions and impacts of that information from the perspective of random graph, and finally seeks the key paths through an improved IBF algorithm. Application cases have shown that this algorithm can search the shortest spread paths efficiently, which may help us to guide and control the information dissemination of emergency events on early warning. PMID:24600323