gebhart/patrepeval huggingface dataset:
Selection of Functional 5′ <i>cis</i> -Acting Elements Promoting Efficient Sindbis Virus Genome Replication (2003)

The 5' portion of the Sindbis virus (SIN) genome RNA is multifunctional. Besides initiating translation of the nonstructural polyprotein, RNA elements in the 5' 200 bases of the SIN genome RNA, or its complement at the 3' end of the negative-strand intermediate, play key roles in the synthesis of both negative- and positive-strand RNAs. We used here a combination of genetic and biochemical approaches to further dissect the functions of this sequence. Replacement of the SIN 5' end in defective-interfering (DI) and genome RNAs with sequences from a distantly related alphavirus, Semliki Forest virus (SFV), resulted in nonviable chimeras. The addition of five nucleotides from the 5' terminus of SIN restored negative-strand RNA synthesis in DI genomes but not their replication in vivo. Pseudorevertants of various SFV-SIN chimeras were isolated, and suppressor mutations were mapped to AU-rich sequences added to the 5' end of the original SFV 5' sequence or its "deleted" versions. Early pseudorevertants had heterogeneous 5' termini that were inefficient for replication relative to the parental SIN 5' sequence. In contrast, passaging of these pseudorevertant viral populations in BHK cells under competitive conditions yielded evolved, more homogeneous 5'-terminal sequences that were highly efficient for negative-strand synthesis and replication. These 5'-terminal sequences always began with 5'-AU, followed by one or more AU repeats or short stretches of oligo(A). Further analysis demonstrated a positive correlation between the number of repeat units and replication efficiency. Interestingly, some 5' modifications restored high-level viral replication in BHK-21 cells, but these viruses were impaired for replication in the cells of mosquito origin. These studies provide new information on sequence determinants required for SIN RNA replication and suggest new strategies for restricting cell tropism and optimizing the packaging of alphavirus vectors.
S-MATE: Secure Coding-based Multipath Adaptive Traffic Engineering (2010)

There have been several approaches to provisioning traffic between core network nodes in Internet Service Provider (ISP) networks. Such approaches aim to minimize network delay, increase network capacity, and enhance network security services. MATE (Multipath Adaptive Traffic Engineering) protocol has been proposed for multipath adaptive traffic engineering between an ingress node (source) and an egress node (destination). Its novel idea is to avoid network congestion and attacks that might exist in edge and node disjoint paths between two core network nodes. This paper builds an adaptive, robust, and reliable traffic engineering scheme for better performance of communication network operations. This will also provision quality of service (QoS) and protection of traffic engineering to maximize network efficiency. Specifically, we present a new approach, S-MATE (secure MATE) is developed to protect the network traffic between two core nodes (routers or switches) in a cloud network. S-MATE secures against a single link attack/failure by adding redundancy in one of the operational paths between the sender and receiver. The proposed scheme can be built to secure core networks such as optical and IP networks.
Challenges in Defining and Categorizing Falls on Diverse Unit Types (2014)

In 2012, the National Database of Nursing Quality Indicators launched a project to expand its falls indicator for use on pediatric, neonatal, and psychiatric units. We discuss challenges encountered, argue that schemes for categorizing falls by cause or supposed preventability are not suitable for large-scale efforts to track and prevent falls, express concern about the growing burden of collecting increasingly granular quality data, and discuss limitations of total and injurious fall rates as quality measures.
Bloch states of a Bloch wall (1994)

Bloch walls in mesoscopic ferromagnets can tunnel between periodically arranged pinning sites leading to a Bloch band. The quantum spin phase gives rise to a spin parity dependent shift in the dispersion. Static external magnetic fields induce magnetization oscillations and provide a magnetic analogue of the Josephson effect.
Investigation of the strain transfer for surface-attached optical fiber strain sensors (2008)

The relation between the component strain and the strain on a surface-attached optical fiber is governed by the effectiveness of shear transfer through the adhesive and the polymeric coating(s) on the optical fiber. A classical shear lag model can predict the strain transfer through a soft layer well. However, experiments showed that the results are unsatisfactory for bare fiber with stiff adhesive case. A 3D-FEM is established to model the strain transfer of a surface-mounted strain sensor and it is verified by experiments. Then, it is used to investigate the influence of four geometric parameters of the adhesive: (1)side width, (2)top thickness, (3)bond length, (4)bottom thickness, on the strain transfer. By sensitivity analysis, it is revealed that the bond length and the bottom thickness are dominant factors. Based on finite element results, the parameter of the analytical model is modified to suit stiff layer cases. Important considerations for practical installation of surface-attached optical interferometric and FBG strain sensors will be discussed.
Silicon micromachined hollow optical waveguides for sensing applications (2002)

Novel micromachined optical waveguides useful for sensing applications are proposed. The waveguide is designed as hollow-core antiresonant reflecting optical waveguide (ARROW) and can be easily fabricated using standard silicon micromachining techniques. The hollow structure permits to use the core to confine simultaneously the light and the substance to be probed, leading to an increase of the interaction efficiency. Numerical simulations, performed using finite element method technique, show that with a suitable design these waveguides can be used in sensing applications, where the substances under test can be gases or liquids.
SPICE modeling of the transient response of irradiated MOSFETs (2000)

A new SPICE model of irradiated MOSFET taking into account the real response of the four electrodes is proposed. A comparison between SPICE-generated transient response and PISCES device simulation demonstrates the accuracy benefits when used in complex electronic architectures.
Extracellular Tropomyosin: A Novel Common Pathway Target for Anti- Angiogenic Therapy (2004)

Angiogenesis is characterized by the development of new vasculature from pre-existing vessels and plays a central role in physiological processes such as embryogenesis, wound healing and female reproductive function, as well as pathophysiologic events including cancer, rheumatoid arthritis and diabetic retinopathy. The growth and metastasis of tumors is critically dependent upon angiogenesis. Although targeting angiogenesis as a therapeutic strategy has to date met with limited success in the clinic, the recent FDA approval of the anti-VEGF antibody Avastin has validated the use of anti-angiogenic therapeutic strategies for cancer treatment. We have recently identified several plasma proteins having anti-angiogenic properties, including Histidine-Proline-Rich Glycoprotein (HPRG) and activated high-molecular-weight kininogen (HKa). Both of these proteins are able to induce apoptosis in endothelial cells in vitro and can inhibit angiogenesis in vivo. Recent studies from our laboratories have also identified a novel cell-surface binding protein for HKa that mediates its anti-angiogenic activity. This protein, tropomyosin, is normally found inside the cell and is associated with the actin cytoskeleton, where it plays a critical role in stabilizing actin filaments in a variety of cell types. However, in angiogenic endothelial cells, tropomyosin appears to have extracellular localization. Previous studies have also suggested the involvement of tropomyosin in the anti-angiogenic activity of endostatin, and our recent work indicates that tropomyosin may mediate the antiangiogenic activity of HPRG as well. In this review, we summarize data describing extracellular tropomyosin as a novel receptor for multiple anti-angiogenic proteins. Extracellular tropomyosin may therefore represent a previously undescribed central target for the development of anti-angiogenic therapy.
Comparative proteomics of cerebrospinal fluid reveals a predictive model for differential diagnosis of pneumococcal, meningococcal, and enteroviral meningitis, and novel putative therapeutic targets (2015)

Comparative proteomics of cerebrospinal fluid disclosed candidate biomarkers, which were combined in a qualitative and sequential predictive model with potential to improve the differential diagnosis of pneumococcal, meningococcal and enteroviral meningitis. Moreover, we present the first evidence of the possible implication of Kallikrein-kinin system in the pathophysiology of bacterial meningitis.
The Consistent File-Status in a User-Triggered Checkpointing Approach (1995)

The user-triggered checkpointing tool implements a non-blocking, co-ordinated (global) checkpointing method, where the programmer defines the contents and the position of the recovery-line. Within this tool, we developed and implemented file-checkpointing. This allows to include the status of files into the checkpoints and to restore this status when the application is rolled back. The file-status in the checkpoint-data is limited to those attributes of the files that are strictly needed to guarantee consistency. The developed approach is suited for files that are accessed by a single process or shared by several processes and are accessed for reading and/or for writing. Consistency is guaranteed under the fail-silent as well as under the fail-time-bounded fault-models. The programmer-involvement is compensated by the smaller time-overhead. Keywords file-checkpointing, fault-tolerance, checkpointing and rollback, backward error recovery 1. Introduction Several families of techniques...
In-situ conductivity and UV-VIS absorption monitoring of iodine doping-dedoping processes in poly(3-hexylthiophene) (P3HT) (2011)

Poly(3-hexylthiophene) (P3HT) belongs to the family of conducting polymers whose conductivity can be controlled via doping. This paper is intended to study iodine doping-dedoping processes in P3HT films via in-situ measurements of the conductivity and light absorption. The film was spin-coated on ITO (indium tin oxide) patterned in the form of four-probe configuration. The sample was doped by iodine via exposure to iodine vapours in chamber and then de-doped by spontaneous release of the dopant under ambient conditions. The doping process was found to be several orders of magnitude faster than dedoping, which is attributed to the different mechanisms of diffusion. The theory of diffusion was applied to approximate the conductivity relaxation as measured experimentally. The best-fit parameters for the approximation were used to determine the dopant diffusivity D and β parameter of the semi-empirical relation between conductivity and dopant concentration (σ ∝ NβD). Their values were found to be (3.9±0.9) 10−13 cm2/s and 4.28±0.04 respectively. The latter agrees with the value known from the literature. The change of the polaron band in the absorption spectrum correlated with the conductivity changes in a complex manner and cannot be used as a measure of the concentration of free carriers contributing into the conductivity.
The New Energetic Compounds 1,5‐Diaminotetrazolium and 5‐Amino‐1‐methyltetrazolium Dinitramide – Synthesis, Characterization and Testing (Eur. J. Inorg. Chem. 26/2008) (2008)

Abstract The cover picture shows the three main topics in the research of new energetic materials: explosives, propellants and pyrotechnics. Two new highly energetic dinitramides in combination with nitrogen‐rich tetrazolium cations are also presented. Details are discussed in the article by T. M. Klapötke and J. Stierstorfer on p. 4055 ff.
Advanced insulations for refrigerator/freezers: The potential for new shell designs incorporating polymer barrier construction (1992)

The impending phase-out of chlorofluorocarbons (CFCs) used to expand foam insulation, combined with requirements for increased energy efficiency, make the use of non-CFC-based high performance insulation technologies increasingly attractive. The majority of current efforts are directed at using advanced insulations in the form of thin, flat low-conductivity gas-filled or evacuated orthogonal panels, which we refer to as Advanced Insulation Panels (AIPs). AIPs can be used in composite with blown polymer foams to improve insulation performance in refrigerator/freezers (R/Fs) of conventional design and manufacture. This AIP/foam composite approach is appealing because it appears to be a feasible, near-term method for incorporating advanced insulations into R/Fs without substantial redesign or retooling. However, the requirements for adequate flow of foam during the foam-in-place operation impose limitations on the allowable thickness and coverage area of AIPs. This report examines design alternatives which may offer a greater increase in overall thermal resistance than is possible with the use of AIP/foam composites in current R/F design. These design alternatives generally involve a basic redesign of the R/F taking into account the unique requirements of advanced insulations and the importance of minimizing thermal bridging with high thermal resistance insulations. The focus here is on R/F doors because they are relatively simple and independent R/F components and are therefore good candidates for development of alterative designs. R/F doors have significant thermal bridging problems due to the steel outer shell construction. A three dimensional finite difference computer modeling exercise of a R/F door geometry was used to compare the overall levels of thermal resistance (R-value) for various design configurations.
Enhancing Pigmented or Transparent Tissue Imaging with Laser Pulse Shaping (2015)

Enhanced control over femtosecond lasers (pulse shaping or pulse train modulation) improves contrast in tissue imaging. Pump-probe applications to melanoma diagnosis and cross phase modulation measurement in transparent tissues will be presented.
Measuring software dependability by robustness benchmarking (1997)

Inability to identify weaknesses or to quantify advancements in software system robustness frequently hinders the development of robust software systems. Efforts have been made to develop benchmarks of software robustness to address this problem, but they all suffer from significant shortcomings. The paper presents the various features that are desirable in a benchmark of system robustness, and evaluates some existing benchmarks according to these features. A new hierarchically structured approach to building robustness benchmarks, which overcomes many deficiencies of past efforts, is also presented. This approach has been applied to building a hierarchically structured benchmark that tests part of the Unix file and virtual memory systems. The resultant benchmark has successfully been used to identify new response class structures that were not detected in a similar situation by other less organized techniques.
Characterization of neuraminidases produced by various serotypes of Pasteurella multocida (1996)

Neuraminidases produced by 16 strains of Pasteurella multocida (serotypes 1 to 16) were characterized by molecular weight, substrate specificity, and antigenic identity. After growth in a chemically defined medium, stage I (lyophilized) culture supernatants were assayed for activity with N-acetylneuramin lactose, human alpha-1-acid glycoprotein, fetuin, colominic acid, and bovine submaxillary mucin. Neuraminidase produced by P. multocida A:3 was purified by a combination of salt fractionation, ion-exchange chromatography on DEAE-Sephacel, and gel filtration on Sephadex G-200. Purified P. multocida A:3 neuraminidase was employed to immunize rabbits, and the resulting antiserum reduced the activity of the P. multocida A:3 enzyme by 40.3%. This antiserum also reduced the activities of the neuraminidases produced by other serotypes by between 30.8 and 59.6%. Molecular weight estimates of the neuraminidases produced by the various serotypes were obtained by gel filtration chromatography on Sephadex G-200. Each of the 16 serotypes examined produced a neuraminidase with a molecular weight of approximately 500,000. In addition, all 16 high-molecular-weight neuraminidases showed similar substrate specificities. On the basis of these data, it appears that the high-molecular-weight neuraminidases produced by different P. multocida serotypes are quite similar.
Safety and Efficacy of Chlorine Dioxide for <i>Legionella</i> Control in a Hospital Water System (2007)

In a 30-month prospective study, we evaluated the efficacy of chlorine dioxide to control Legionella organisms in a water distribution system of a hospital with 364 patient beds and 74 skilled nursing beds. The number of hot water specimens positive for Legionella organisms decreased from 12 (60%) of 20 to 2 (10%) of 20. An extended time (18 months) was needed to achieve a significant reduction in the rate of Legionella positivity among hot water specimens. At the time of writing, no cases of hospital-acquired Legionnaires disease have been detected at the hospital since the chlorine dioxide system was installed in January 2003. Use of chlorine dioxide was safe, based on Environmental Protection Agency limits regarding maximum concentrations of chlorine dioxide and chlorite.
Crystal data for two enkephaline peptides (1978)

The two enkephaline Tyr-Gly-Gly (I) and Phe-Met (II) peptides have been crystallized with the following crystal data: (I) space group P21212 or P2221 (Z = 4); a = 9.549 (3), b = 8.073 (2), c = 18.424 (5) Å; (II) space group I41 (Z = 8); a = b = 23.891 (4), c = 5.589 (3) Å.
Nickel Enrichment at the Interface between Oxide Layer and Matrix in Iron-Nickel Alloys (2002)

GD-OES has been used for characterizing the behavior of nickel during oxidation in Fe-Ni alloys. GD-OES depth profiles show that nickel is enriched at the interface between the oxide layer and matrix, and nickel is almost depleted in the oxide layer. Based on the relationship between the amount of nickel and the oxide thickness, characteristic features of nickel in the oxidation of Fe-Ni alloys is discussed.
U.S. Phase I Preliminary Results of Use of the Otologics MET Fully‐Implantable Ossicular Stimulator (2007)

Although monaural word scores and aided thresholds favored the walk-in-aided condition, preliminary results indicate that the Otologics MET Fully-Implantable Ossicular Stimulator is an alternative to currently available hearing aids in patients with sensorineural hearing loss.
Results and relevance of critical temperature threshold testing in patients with acquired cold urticaria (2009)

Background Acquired cold urticaria (ACU) is a physical urticaria characterized by local skin reactions after cold exposure. Objective markers of disease severity and activity would be helpful. Unfortunately, such markers are not yet available, even though stimulation time and temperature thresholds are promising candidates. Objectives We assessed and correlated critical temperature thresholds (CTTs) with disease severity and activity in patients with ACU. Methods CTTs were determined in 45 patients with ACU by TempTest-based cold contact stimulation tests (Emo Systems GmbH, Berlin, Germany), and ACU severity and activity were assessed using Likert scales. Results Patients with ACU exhibited mean +/- SEM CTTs of 17 +/- 6 degrees C (range 4-27 degrees C). These thresholds and their changes correlated with the severity (r = 0.53, P < 0.05) and activity of disease (r = 0.64, P < 0.05), respectively. Conclusions These findings indicate that temperature threshold measurements may be used for assessing disease severity and activity as well as the efficacy of therapeutic measures including novel treatment approaches for cold urticaria.
Improvement of Steering Feel of Electric Power Steering System with Variable Gear Transmission System Using Decoupling Control (2009)

In this paper a new control method of Electric Power Steering (EPS) system with Variable Gear Transmission System (VGTS) is proposed. The control purpose is to achieve the desired steering gear ratio and the desired power assist with good steering feel. The basic idea of controller design is to apply decoupling control to this system and to separately design controllers for two decoupled systems. The angle control system and the torque control system are designed for the decoupled systems. In the angle control system the PID control is used for the desired gear ratio. In the torque control system the PID control is used for the desired assist torque designed so as to achieve good steering feel. In order to evaluate steering feel the Lissajous curve between the steering torque and steering angle is used. The effectiveness of the proposed controller is verified experimentally.
Pilot trial of cisplatin, radiation, and WR2721 in carcinoma of the uterine cervix: a New York Gynecologic Oncology Group study. (1993)

PURPOSE A phase I trial of WR2721 was initiated to determine the maximal safe dose for incorporation into a consecutive 5-day schedule of cisplatin administered concurrently with radiation therapy in patients with cervical cancer. PATIENTS AND METHODS WR2721 was administered at 340 to 910 mg/m2/d immediately before cisplatin. Cisplatin was administered at 20 mg/m2/d for 5 days every 3 weeks in combination with external-beam radiation therapy and at 100 mg/m2 after each brachytherapy treatment. Pelvic radiation consisted of external-beam therapy to a dose of 39.6 Gy, followed by brachytherapy with cesium 137 tandem and ovoid insertions to deliver 80 Gy to point A and 55 Gy to point B. RESULTS Twenty patients were enrolled; 19 were assessable. The dose-limiting toxicity of WR2721 was hypotension. No patients developed serious sequelae, but hypotension required a reduction in the dose of WR2721 at the highest dose level tested. The major grade 3 or 4 toxicities included transient azotemia (five of 19), leukopenia (nine of 19), vomiting (four of 19), and neurotoxicity (two of 19). One patient experienced an anaphylactic reaction to cisplatin. CONCLUSION The recommended dose of WR2721 administered in conjunction with cisplatin on a daily x 5 schedule plus radiation therapy is 825 mg/m2/d for 5 days.
Cryo-EM structure and rRNA model of a translating eukaryotic 80S ribosome at 5.5-Å resolution (2010)

Protein biosynthesis, the translation of the genetic code into polypeptides, occurs on ribonucleoprotein particles called ribosomes. Although X-ray structures of bacterial ribosomes are available, high-resolution structures of eukaryotic 80S ribosomes are lacking. Using cryoelectron microscopy and single-particle reconstruction, we have determined the structure of a translating plant (Triticum aestivum) 80S ribosome at 5.5-Å resolution. This map, together with a 6.1-Å map of a Saccharomyces cerevisiae 80S ribosome, has enabled us to model ∼98% of the rRNA. Accurate assignment of the rRNA expansion segments (ES) and variable regions has revealed unique ES-ES and r-protein-ES interactions, providing insight into the structure and evolution of the eukaryotic ribosome.
Clinical Outcomes of Breast Cancer in Carriers of <i>BRCA1</i> and <i>BRCA2</i> Mutations (2007)

Breast cancer-specific rates of death among Israeli women are similar for carriers of a BRCA founder mutation and noncarriers.