Optimization of RNA-based transgene expression by targeting Protein Kinase R

The aim of this thesis was to establish a method for repeated transfection of in vitro transcribed RNA (IVT-RNA) leading to a sustained protein expression lasting for days or even weeks. Once transfected cells recognize IVT-RNA as "non-self" and initiate defense pathways leading to an upregulated interferon (IFN) response and stalled translation. In this work Protein Kinase R (PKR) was identified as the main effector molecule mediating this cellular response. We assessed four strategies to inhibit PKR and the IFN response: A small molecule PKR inhibitor enhanced protein expression and hampered the induction of IFN-transcripts, but had to be excluded due to cytotoxicity. A siRNA mediated PKR knockdown and the overexpression of a kinase inactive PKR mutant elevated the protein expression, but the down-regulation of the IFN response was insufficient. The co-transfer of the viral inhibitors of PKR and the IFN response was most successful. The use of E3, K3 and B18R co-transfection enabled repeated IVT-RNA-based transfection of human fibroblasts. Thus, the developed protocol allows a continuous IVT-RNA encoded protein expression of proteins, which could be the basis for the generation of induced pluripotent stem cells (iPS) for several therapeutic applications in regenerative medicine or drug research.

An RNS based transform Architecture for H.264/AVC

This paper presents the architecture and the VHDL design of an integer 2-D DCT used in the H.264/AVC. The 2-D DCT computation is performed by exploiting it’s orthogonality and separability property. The symmetry of the forward and inverse transform is used in this implementation. To reduce the computation overhead for the addition, subtraction and multiplication operations, we analyze the suitability of carry-free position independent residue number system (RNS) for the implementation of 2-D DCT. The implementation has been carried out in VHDL for Altera FPGA. We used the negative number representation in RNS, bit width analysis of the transforms and dedicated registers present in the Logic element of the FPGA to optimize the area. The complexity and efficiency analysis show that the proposed architecture could provide higher through-put.

Performance analysis of FIR digital filter design: RNS versus traditional

Residue Number System (RNS) based Finite Impulse Response (FIR) digital filters and traditional FIR filters. This research is motivated by the importance of an efficient filter implementation for digital signal processing. The comparison is done in terms of speed and area requirement for various filter specifications. RNS based FIR filters operate more than three times faster and consumes only about 60% of the area than traditional filter when number of filter taps is more than 32. The area for RNS filter is increasing at a lesser rate than that for traditional resulting in lower power consumption. RNS is a nonweighted number system without carry propogation between different residue digits.This enables simultaneous parallel processing on all the digits resulting in high speed addition and multiplication in the RNS domain

RNS based programmable multi-mode decimation filter for WCDMA and WiMAX

The recent trends envisage multi-standard architectures as a promising solution for the future wireless transceivers to attain higher system capacities and data rates. The computationally intensive decimation filter plays an important role in channel selection for multi-mode systems. An efficient reconfigurable implementation is a key to achieve low power consumption. To this end, this paper presents a dual-mode Residue Number System (RNS) based decimation filter which can be programmed for WCDMA and 802.16e standards. Decimation is done using multistage, multirate finite impulse response (FIR) filters. These FIR filters implemented in RNS domain offers high speed because of its carry free operation on smaller residues in parallel channels. Also, the FIR filters exhibit programmability to a selected standard by reconfiguring the hardware architecture. The total area is increased only by 24% to include WiMAX compared to a single mode WCDMA transceiver. In each mode, the unused parts of the overall architecture is powered down and bypassed to attain power saving. The performance of the proposed decimation filter in terms of critical path delay and area are tabulated.

Dual-mode RNS based programmable decimation filter for WCDMA and WLANa

The recent trends envisage multi-standard architectures as a promising solution for the future wireless transceivers. The computationally intensive decimation filter plays an important role in channel selection for multi-mode systems. An efficient reconfigurable implementation is a key to achieve low power consumption. To this end, this paper presents a dual-mode Residue Number System (RNS) based decimation filter which can be programmed for WCDMA and 802.11a standards. Decimation is done using multistage, multirate finite impulse response (FIR) filters. These FIR filters implemented in RNS domain offers high speed because of its carry free operation on smaller residues in parallel channels. Also, the FIR filters exhibit programmability to a selected standard by reconfiguring the hardware architecture. The total area is increased only by 33% to include WLANa compared to a single mode WCDMA transceiver. In each mode, the unused parts of the overall architecture is powered down and bypassed to attain power saving. The performance of the proposed decimation filter in terms of critical path delay and area are tabulated

Relating the RNS and pure spinor formalisms for the superstring

Recently, the superstring was covariantly quantized using the BRST-like operator Q = ∮ λαdα where λα is a pure spinor and dα are the fermionic Green-Schwarz constraints. By performing a field redefinition and a similarity transformation, this BRST-like operator is mapped to the sum of the Ramond-Neveu-Schwarz BRST operator and η0 ghost. This map is then used to relate physical vertex operators and tree amplitudes in the two formalisms. Furthermore, the map implies the existence of a b ghost in the pure spinor formalism which might be useful for loop amplitude computations.

RNS derivation of N-point disk amplitudes from the revisited S-matrix approach

Recently, in [7] we proposed a revisited S-matrix approach to efficiently find the bosonic terms of the open superstring low energy effective lagrangian (OSLEEL). This approach allows to compute the alpha'(N) terms of the OSLEEL using open superstring n-point amplitudes in which n is considerably lower than (N + 2) (which is the order of the required amplitude to obtain those alpha'(N) terms by means of the conventional S-matrix approach). In this work we use our revisited S-matrix approach to examine the structure of the scattering amplitudes, arriving at a closed form for them. This is a RNS derivation of the formula first found by Mafra, Schlotterer and Stieberger [21], using the pure spinor formalism. We have succeeded doing this for the 5, 6 and 7-point amplitudes. In order to achieve these results we have done a careful analysis of the kinematical structure of the amplitudes, finding as a by-product a purely kinematical derivation of the BCJ relations (for N = 4, 5, 6 and 7). Also, following the spirit of the revisited S-matrix approach, we have found the alpha' expansions for these amplitudes up to alpha'(6) order in some cases, by only using the well known open superstring 4-point amplitude, cyclic symmetry and tree level unitarity: we have not needed to compute any numerical series or any integral involving polylogarithms, at any moment. (C) 2014 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/3.0/).

The viral RNase E(rns) prevents IFN type-I triggering by pestiviral single- and double-stranded RNAs

Interferon (IFN) type-I is of utmost importance in the innate antiviral defence of eukaryotic cells. The cells express intra- and extracellular receptors that monitor their surroundings for the presence of viral genomes. Bovine viral diarrhoea virus (BVDV), a Pestivirus of the family Flaviviridae, is able to prevent IFN synthesis induced by poly(IC), a synthetic dsRNA. The evasion of innate immunity might be a decisive ability of BVDV to establish persistent infection in its host. We report that ds- as well as ssRNA fragments of viral origin are able to trigger IFN synthesis, and that the viral envelope glycoprotein E(rns), that is also secreted from infected cells, is able to inhibit IFN expression induced by these extracellular viral RNAs. The RNase activity of E(rns) is required for this inhibition, and E(rns) degrades ds- and ssRNA at neutral pH. In addition, cells infected with a cytopathogenic strain of BVDV contain more dsRNA than cells infected with the homologous non-cytopathogenic strain, and the intracellular viral RNA was able to excite the IFN system in a 5'-triphosphate-, i.e. RIG-I-, independent manner. Functionally, E(rns) might represent a decoy receptor that binds and enzymatically degrades viral RNA that otherwise might activate the IFN defence by binding to Toll-like receptors of uninfected cells. Thus, the pestiviral RNase efficiently manipulates the host's self-nonself discrimination to successfully establish and maintain persistence and immunotolerance.

Interruptions in Workflow for RNs in a Level One Trauma Center

An understanding of interruptions in healthcare is important for the design, implementation, and evaluation of health information systems and for the management of clinical workflow and medical errors. The purpose of this study is to identify and classify the types of interruptions experienced by Emergency Department(ED) nurses working in a Level One Trauma Center. This was an observational field study of Registered Nurses (RNs) employed in a Level One Trauma Center using the shadowing method. Results of the study indicate that nurses were both recipients and initiators of interruptions. Telephones, pagers, and face-to-face conversations were the most common sources of interruptions. Unlike other industries, the healthcare community has not systematically studied interruptions in clinical settings to determine and weigh the necessity of the interruption against their sometimes negative results such as medical errors, decreased efficiency, and increased costs. Our study presented here is an initial step to understand the nature, causes, and effects of interruptions, thereby improving both the quality of healthcare and patient safety. We developed an ethnographic data collection technique and a data coding method for the capturing and analysis of interruptions. The interruption data we collected are systematic, comprehensive, and close to exhaustive. They confirmed the findings from earlier studies by other researchers that interruptions are frequent events in critical care and other healthcare settings. We are currently using these data to analyze the workflow dynamics of ED clinicians, to identify the bottlenecks of information flow, and to develop interventions to improve the efficiency of emergency care through the management of interruptions.

Interruptions in workflow for RNs in a Level One Trauma Center.

An understanding of interruptions in healthcare is important for the design, implementation, and evaluation of health information systems and for the management of clinical workflow and medical errors. The purpose of this study is to identify and classify the types of interruptions experienced by ED nurses working in a Level One Trauma Center. This was an observational field study of Registered Nurses employed in a Level One Trauma Center using the shadowing method. Results of the study indicate that nurses were both recipients and initiators of interruptions. Telephone, pagers, and face-to-face conversations were the most common sources of interruptions. Unlike other industries, the outcomes caused by interruptions resulting in medical errors, decreased efficiency and increased cost have not been systematically studied in healthcare. Our study presented here is an initial step to understand the nature, causes, and effects of interruptions, and to develop interventions to manage interruptions to improve healthcare quality and patient safety. We developed an ethnographic data collection technique and a data coding method for the capturing and analysis of interruptions. The interruption data we collected are systematic, comprehensive, and close to exhaustive. They confirmed the findings from early studies by other researchers that interruptions are frequent events in critical care and other healthcare settings. We are currently using these data to analyze the workflow dynamics of ED clinicians, identify the bottlenecks of information flow, and develop interventions to improve the efficiency of emergency care through the management of interruptions.

An analysis of the shortage of registered nurses (RNs) in acute care hospitals in El Paso, Texas

The purpose of this analysis of the shortage of Registered Nurses (RNs) in acute care hospitals in El Paso, Texas, was to evaluate twenty-two specific organizational and/or patient care unit (nursing unit) characteristics that effect the retention and turnover of professional nurses. Vacancy Rates were used to measure the level of the shortage in each hospital and nursing unit in the study. Vacancy Rates are a function of both RN retention and RN turnover. Seventy-three patient care units in five acute care hospitals were included in the study population.^ Fredrick Herzberg's motivational - hygiene theory was used to explain the types of characteristics or factors that can effect worker dissatisfaction. Dissatisfiers (hygiene factors) are those work place characteristics that influence workers to leave the job. The twenty-two potentially dissatisfying work place characteristics were either organizational or patient care unit specific in nature. The focus of the study was to evaluate high vacancy rates caused by both low retention of RNs and high turnover rates. Retention and turnover are a function of workers (RNs) not staying in their jobs, therefore hygiene factors were appropriate characteristics to study.^ Various multivariate analysis techniques were used to assess both the individual and combined effects of the hygiene factors on Vacancy Rates, Retention and Turnover. Results suggest that certain organizational and patient care unit characteristics are associated with and have a statistically significant effect on vacancy rates, and the retention and turnover of RNs. The type of Hospital was of particular interest in this regards. For-Profit facilities were less effected by most of the study variables than the Not-for-Profits. ^

Individual Video Training iVT and Annotating Academic Videos AAV: two complementing technologies

Individual Video Training iVT and Annotating Academic Videos AAV: two complementing technologies 1. Recording communication skills training sessions and reviewing them by oneself, with peers, and with tutors has become standard in medical education. Increasing numbers of students paired with restrictions of financial and human resources create a big obstacle to this important teaching method. 2. Everybody who wants to increase efficiency and effectiveness of communication training can get new ideas from our technical solution. 3. Our goal was to increase the effectiveness of communication skills training by supporting self, peer and tutor assessment over the Internet. Two technologies of SWITCH, the national foundation to support IT solutions for Swiss universities, came handy for our project. The first is the authentication and authorization infrastructure providing all Swiss students with a nationwide single login. The second is SWITCHcast which allows automated recording, upload and publication of videos in the Internet. Students start the recording system by entering their single login. This automatically links the video with their password. Within a few hours, they find their video password protected on the Internet. They now can give access to peers and tutors. Additionally, an annotation interface was developed. This software has free text as well as checklist annotations capabilities. Tutors as well as students can create checklists. Tutor’s checklists are not editable by students. Annotations are linked to tracks. Tracks can be private or public. Public means visible to all who have access to the video. Annotation data can be exported for statistical evaluation. 4. The system was well received by students and tutors. Big numbers of videos were processed simultaneously without any problems. 5. iVT http://www.switch.ch/aaa/projects/detail/UNIBE.7 AAV http://www.switch.ch/aaa/projects/detail/ETHZ.9

Individual Video Training iVT - Development of a National Infrastructure for Video-Supported Learning

Introduction: Video‐Supported Learning is particularly effective when it comes to skills and behaviors. Video registration of patient‐physician interviews, class room instruction or practical skills allow it to learners themselves, their peers, and their tutors to assess the quality of the learner's performance, to give specific feedback, and to make suggestions for improvement. Methods: In Switzerland, four pedagogical universities and two medical faculties joined to initiate the development of a national infrastructure for Video Supported Learning. The goal was to have a system that is simple to use, has most steps automated, provides the videos over the Internet, and has a sophisticated access control. Together with SWITCH, the national IT‐Support‐Organisation for Swiss Universities, the program iVT (Individual Video Training) was developed by integrating two preexisting technologies. The first technology is SWITCHcast, a podcast system. With SWITCHcast, videos are automatically uploaded to a server as soon as the registration is over. There the videos are processed and converted to different formats. The second technology is the national Single Logon System AAI (Authentification and Authorization Infrastructure) that enables iVT to link each video with the corresponding learner. The learner starts the registration with his Single Logon. Thus, the video can unambiguously be assigned. Via his institution's Learning Management System (LMS), the learner can access his video and give access to his video to peers and tutors. Results: iVT is now used at all involved institutions. The system works flawlessly. In Bern, we use iVT for the communications skills training in the forth and sixth year. Since students meet with patient actors alone, iVT is also used to certify attendance. Students are encouraged to watch the videos of the interview and the feedback of the patient actor. The offer to discuss a video with a tutor was not used by the students. Discussion: We plan to expand the use of iVT by making peer assessment compulsory. To support this, annotation capabilities are currently added to iVT. We also want to use iVT in training of practical skills, again for self as well as for peer assessment.  At present, we use iVT for quality control of patient actor's performance.

Pestiviral E(rns) blocks TLR-3-dependent IFN synthesis by LL37 complexed RNA

The ribonuclease activity of the soluble glycoprotein E(rns) of pestiviruses represents a unique mechanism to circumvent the host's innate immune system by blocking interferon type-I synthesis in response to extracellularly added single- (ss) and double-stranded (ds) RNA. However, the reason why pestiviruses encode a ribonuclease in addition to the abundant serum RNases remained elusive. Here, we show that the 5' UTR and NS5B regions of various strains of the RNA genome of the pestivirus bovine viral diarrhea virus (BVDV) are resistant to serum RNases and are potent TLR-3 agonists. Inhibitory activity of E(rns) was restricted to cleavable RNA products, and did not extend to the synthetic TLR-7/8 agonist R-848. RNA complexed with the antimicrobial peptide LL37 was protected from degradation by E(rns)in vitro but was fully inhibited by E(rns) in its ability to induce IFN in cell cultures, suggesting that the viral protein is mainly active in cleaving RNA in an intracellular compartment. We propose that secreted E(rns) represents a potent IFN antagonist, which degrades viral RNA that is resistant to the ubiquitous host RNases in the extracellular space. Thus, the viral RNase prevents its own pathogen-associated molecular pattern (PAMP) to inadvertently activate the IFN response that might break innate immunotolerance required for persistent pestivirus infections.