gebhart/patrepeval huggingface dataset:
Biological and Structural Characterization of a Host-Adapting Amino Acid in Influenza Virus (2010)

Two amino acids (lysine at position 627 or asparagine at position 701) in the polymerase subunit PB2 protein are considered critical for the adaptation of avian influenza A viruses to mammals. However, the recently emerged pandemic H1N1 viruses lack these amino acids. Here, we report that a basic amino acid at position 591 of PB2 can compensate for the lack of lysine at position 627 and confers efficient viral replication to pandemic H1N1 viruses in mammals. Moreover, a basic amino acid at position 591 of PB2 substantially increased the lethality of an avian H5N1 virus in mice. We also present the X-ray crystallographic structure of the C-terminus of a pandemic H1N1 virus PB2 protein. Arginine at position 591 fills the cleft found in H5N1 PB2 proteins in this area, resulting in differences in surface shape and charge for H1N1 PB2 proteins. These differences may affect the protein's interaction with viral and/or cellular factors, and hence its ability to support virus replication in mammals.
BiTE: Teaching antibodies to engage T-cells for cancer therapy. (2009)

Bispecific T-cell-engager (BiTE) antibodies are designed to transiently engage cytotoxic T-cells for lysis of selected target cells. Although this therapeutic concept had been proposed more than two decades ago, BiTE, and also trispecific, antibodies did not achieve clinical proof-of-concept until the past 2 years. Their clinical activity corroborates findings that ex vivo expanded, autologous T-cells derived from tumor tissue, or transfected with specific T-cell receptors, have shown therapeutic potential in the treatment of solid tumors. While these personalized approaches prove that T-cells alone can have considerable therapeutic activity, even in late-stage cancer, they are cumbersome to perform on a broad basis. This is different for cytotoxic T-lymphocyte antigen 4 (CTLA-4) antibodies, which facilitate generation of tumor-specific T-cell clones, and also for bi- and tri-specific antibodies that directly engage a large proportion of patients' T-cells for cancer cell lysis. The potential of global T-cell engagement for human cancer therapy by T-cell-engaging antibodies has yet to be fully investigated.
Safety, efficacy and tolerability of exenatide in combination with insulin in the Association of British Clinical Diabetologists nationwide exenatide audit * (2011)

Addition of exenatide to obese, insulin-treated patients can improve glycaemia and weight. Adverse events were statistically but probably not clinically significantly higher, but combination treatment was less well tolerated. Overall, exenatide was less effective in lowering HbA1c among insulin-treated patients, although significant number of insulin-treated patients still achieved significant HbA1c, weight and insulin reductions. Further research into identifying obese, insulin-treated patients who will tolerate and benefit from exenatide treatment is urgently needed.
Design and Stability of Load-Side Primary Frequency Control in Power Systems (2014)

We present a systematic method to design ubiquitous continuous fast-acting distributed load control for primary frequency regulation in power networks, by formulating an optimal load control (OLC) problem where the objective is to minimize the aggregate cost of tracking an operating point subject to power balance over the network. We prove that the swing dynamics and the branch power flows, coupled with frequency-based load control, serve as a distributed primal-dual algorithm to solve OLC. We establish the global asymptotic stability of a multimachine network under such type of load-side primary frequency control. These results imply that the local frequency deviations on each bus convey exactly the right information about the global power imbalance for the loads to make individual decisions that turn out to be globally optimal. Simulations confirm that the proposed algorithm can rebalance power and resynchronize bus frequencies after a disturbance with significantly improved transient performance.
A Broadly Neutralizing Human Monoclonal Antibody Exhibits In Vivo Efficacy Against Both Human Metapneumovirus and Respiratory Syncytial Virus (2014)

BACKGROUND: Human metapneumovirus (HMPV) is a leading cause of acute respiratory tract infection, with significant morbidity and mortality. No licensed vaccines or therapeutic agents exist. Monoclonal antibodies (mAbs) are effective at preventing other infectious diseases and could be used against HMPV in high-risk hosts. METHODS: In vitro assays were performed to assess the neutralizing activity and affinity kinetics of human mAb 54G10. A new mouse model was developed to assess prophylactic and therapeutic efficacy in vivo. The epitope of 54G10 was identified by generating mAb-resistant mutants (MARMs). RESULTS: At low concentrations, 54G10 neutralized all 4 subgroups of HMPV in vitro and had subnanomolar affinity for the fusion protein. DBA/2 mice were permissive for all 4 HMPV subgroups, and 54G10 was effective both prophylactically and therapeutically against HMPV in vivo. Sequencing of HMPV MARMs identified the 54G10 epitope, which was similar to an antigenic site on respiratory syncytial virus (RSV). 54G10 also exhibited in vitro neutralizing activity and in vivo protective and therapeutic efficacy against RSV. CONCLUSIONS: Human mAb 54G10 has broad neutralizing activity against HMPV and could have prophylactic and therapeutic utility clinically. The conserved epitope could represent a structural vaccine target for HMPV and RSV.
Panopticon: A Parallel Video Overview Technique (2012)

Panopticon is a novel method of arranging a moving video sequence that displays multiple sub-sequences in parallel. The technique provides a consistent spatio-temporal layout for context, while presenting a rapid overview of the entire sequence to the user, and yet does so in a way that allows any sub-sequence to be followed without interruption. Furthermore, this output can be generated offline as a highly efficient repeated animation loop. Panopticon can be used directly on source video as a new form of video abstract. Moreover it could be used to augment existing video skims with additional context. About the authors Dan Jackson works as a Senior Research Associate for the School of Computing Science at Newcastle University. He studied an MEng Computer Systems and Software Engineering Degree with the Department of Computer Science at The University of York. Patrick Olivier is based in Culture Lab and leads the Cultural Technologies theme in which computer scientists and electronic engineers are engaging with researchers in the arts and humanities both in the development of new technology and research methods. He is also a member of the Informatics Research Institute and the Institute of Ageing and Health. His research interests spans aspects of human computer interaction (especially for pervasive computing and computing of older people and the cognitively impaired), computer graphics, and artificial intelligence. Patrick has an undergraduate degree in Physics (Natural Sciences, Cantab, 1989) and a PhD is in computational linguistics (UMIST, 1998). Prior to coming to Newcastle (2004), he was a lecturer at the University of Wales, Aberystywth and the University of York. In York he founded Lexicle Limited where he led the development of the world's first commercial 3D embodied conversational agent. Suggested keywords PARALLEL VIDEO VIDEO ABSTRACTION VIDEO SUMMARIZATION VIDEO BROWSING
Time-lapse monitoring as a tool for clinical embryo assessment (2012)

As elective transfer of a single embryo (eSET) becomes increasingly accepted, the need to improve implantation rates becomes crucial. Selecting the most competent embryo therefore constitutes a major challenge in assisted reproductive technology. Embryo morphology and developmental stage at given time points are closely correlated with developmental competence and assessment of morphological parameters at discrete inspection points thus remains the preferred way of evaluating embryonic potential. Lately, more attention has been given to the assessment of dynamic embryo development as a tool for evaluating embryonic potential. The introduction of time-lapse equipment approved for use on human embryos offers novel clinical opportunities for continuous monitoring of embryos, enabling flexible evaluation of known morphological parameters and potentially introducing new dynamic markers of viability. Due to lack of larger, randomized clinical studies it remains to be elucidated whether embryo selection using dynamic parameters improves clinical outcome and which parameters are of significance. Before such randomized controlled studies are organized, the most promising parameters to evaluate must be identified. This mini-review summarizes the current knowledge about dynamic markers of viability and discusses the potential clinical role of time-lapse analysis in embryo assessment and selection.
Butyl acrylate/methyl methacrylate latexes: adhesive properties (2004)

Abstract In this study, butyl acrylate/methyl methacrylate (BA/MMA) latexes of bimodal molecular weight and particle size distribution were prepared in a multi‐step process by seeded conventional emulsion and seeded miniemulsion polymerization. For the conventional emulsion case, a BA/MMA batch copolymerization was conducted as a first step (seed generation) and was followed by a monomer addition step to ensure particle growth. In a third step, a BA/MMA pre‐emulsified mixture was added to generate a second particle population. For the miniemulsion case, a BA/MMA copolymerization was carried out as a first step (seed generation) and was followed by a monomer addition step. The addition of a BA/MMA miniemulsion served to generate a bimodal particle size and molecular weight distribution. The final latexes were coated onto a polyethylene terephthalate carrier, dried and their performance as pressure‐sensitive adhesives was evaluated using tack, peel and shear adhesion measurements. Structure‐property relationships between the adhesive properties and the weight‐average molecular weight and average particle size were examined. Even though the polymers obtained by miniemulsion showed better shear resistance, their shear resistance was low. There was no statistically significant difference in peel resistance of the polymers obtained by the two reactions. While a significant difference in tackiness between the two emulsion procedures was found when the adhesives were tested using the less sensitive, rolling ball test, no differences were found when they were tested using a loop tack test.
Electron Transfer in Chemistry and Biology: An Introduction to the Theory (1999)

Some Theoretical Prerequisites. The Tunnel Effect in Physical, Chemical and Biological Processes. Elements of Dielectric Theory. Charge Transfer in Solids. The Simplest Chemical Process: Electron Transfer. Some Selected Experimental Data for Simple Electron Transfer Reactions. Towards More Precise Electron Transfer Theory. Optical Charge Transfer in Allowed and Forbidden Transitions. Elements of Proton and Other Light-Atom Transfer Theory. The Electrochemical Process. Elements of Long-Range and Multi-Level Electron Transfer. Stochastic Views in Chemical Rate Theory. Elements of Charge Transfer in Biological Systems. Perspectives and Outlook. Appendices. Index.
A wireless power receiver with an on-chip antenna for millimeter-size biomedical implants in 180 nm SOI CMOS (2017)

In this paper, we present a biphasic RF power harvesting system for biomedical wireless implantable applications that operates in low-GHz frequency range. The design includes an on-chip loop antenna, a six-stage voltage rectifier, a low dropout voltage regulator, a power management unit (PMU), and an array of low-noise differential amplifiers for sensing bio potentials. The system is fabricated in a 180 nm SOI CMOS technology with a total area of 1.6×1.6 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> including a 1.2 nF on-chip storage capacitor. A power management unit with an average current consumption of 10 nA, which is 8x smaller than the state-of-the-art, divides the operation of the system into two different phases. The system is capable of delivering 1.21 mW to an external load that is fed by an on-chip voltage regulator.
Evidence for Frequent Recombination within SpeciesHuman Enterovirus BBased on Complete Genomic Sequences of All Thirty-Seven Serotypes (2003)

The species Human enterovirus B (HEV-B) in the family Picornaviridae consists of coxsackievirus A9; coxsackieviruses B1 to B6; echoviruses 1 to 7, 9, 11 to 21, 24 to 27, and 29 to 33; and enteroviruses 69 and 73. We have determined complete genome sequences for the remaining 22 HEV-B serotypes whose sequences were not represented in public databases and analyzed these in conjunction with previously available complete sequences in GenBank. Members of HEV-B were monophyletic relative to all other human enterovirus species in all regions of the genome except in the 5'-nontranslated region (NTR), where they are known to cluster with members of HEV-A. Within HEV-B, phylogenies constructed from the structural (P1) and nonstructural regions of the genome (P2 and P3) are incongruent, suggesting that recombination had occurred. Similarity plots and bootscanning analysis across the complete genome identified multiple sites at which the phylogeny of a given strain's sequence shifted, indicating potential recombination points. These points are distributed in the 5'-NTR and throughout P2 and P3, but no sites with >80% bootstrap support were identified within the capsid. Individual sequence comparisons and phylogenetic analyses suggest that members of HEV-B have recombined with one another on multiple occasions, resulting in a complex mosaic of sequences derived from multiple parental viruses in the nonstructural regions of the genome. We conclude that RNA recombination is a common mechanism for enterovirus evolution and that recombination within the nonstructural regions of the genome (P2 and P3) has been observed only among members of the same species.
Modfit: A pharmacokinetics computer program (1990)

This paper presents a computer program, MODFIT, written in FORTRAN, primarily for use on the Digital Equipment Company VAX series computers for the mathematical analysis of concentration-time data. Drug data generated from biological fluids and tissues may be fitted by a variety of different models. For many models, parameter starting estimates are program generated prior to automatic nonlinear regression analysis using a modified Davidon-Fletcher-Powell algorithm. The output of results is extensive and plotting facilities are available. Explicit and differential equation models may be fitted to single dose data and simulations using all models (single or repeat dose) may be employed to generate drug concentration-time data with plotting output. The package has been tested on numerous data with no problems regarding local function minima. Some comparisons with existing programs have been made and MODFIT compares well with respect to robustness, efficiency, and ease of use.
A NAND Flash Memory Controller for SD/MMC Flash Memory Card (2006)

In this paper, a novel NAND Flash Memory Controller was designed. A t-EC w-bit parallel BCH ECC code was designed for correcting the random bit errors of the flash memory chip, which is suitable for the randomly bit errors property and parallel I/O interface of the NAND type Flash memory. A Code-Banking mechanism was designed for the trade-offs between the controller cost and the ISP (in system programmability) support. With the ISP functionality and the Flash Parameters programmed in the reserved area of the Flash Memory chip during the card production stage, the function for supporting various kinds of NAND Flash memory could be provided by a single controller. In addition, built-in defect management and wear-leveling algorithm enhanced the product life cycle and reliability. Dual Channel accessing of the Flash memory provided the good performance in data transfer rate. With respect to the proposed controller architecture, a real SD/MMC flash memory card controller chip was designed and implemented with UMC 0.18mum CMOS process. Experimental results show the designed circuit can fully comply with the system specifications and shows the good performances.
Demonstration of a GaAs-based compliant substrate using wafer bonding and substrate removal techniques (1997)

A GaAs-based compliant substrate that uses an intermediate AlGaAs-oxide layer to separate thin 150 /spl Aring/-1000 A GaAs compliant layers from a GaAs host substrate is described. The compliant substrates and epitaxial layers of lattice-mismatched In/sub 0.15/Ga/sub 0.85/As were studied using atomic force microscopy and double-crystal X-ray diffraction. The surface morphology of the 1000 A compliant substrate prior to growth had an RMS and peak-to-peak roughness of 10 /spl Aring/ and 100 /spl Aring/. Following growth of 3000 /spl Aring/ In/sub 0.15/Ga/sub 0.85/ the root mean square (RMS) roughness increased to 50 /spl Aring/, and slip lines were observed in the [110] direction. A comparison of lattice-matched p/sup +/-n junction diodes grown on a substrate with a 1000 /spl Aring/ compliant layer and a standard GaAs substrate revealed similar dark current-voltage characteristics, which demonstrate the high quality of the compliant substrate.
Ptychographic transmission microscopy in three dimensions using a multi-slice approach (2012)

Generally, methods of three-dimensional imaging such as confocal microscopy and computed tomography rely on two essentials: multiple measurements (at a range of focus positions or rotations) and a weakly scattering specimen (to avoid distortion of the focal spot in the confocal microscope or to satisfy the projection approximation in tomography). Here we show that an alternative form of multi-measurement imaging, ptychography, can be extended to three dimensions and can successfully recover images in the presence of multiple scattering and when the projection approximation is not applicable. We demonstrate our technique experimentally using visible light, where it has applications in imaging thick samples such as biological tissues; however the results also have important implications for x ray and electron imaging.
Retrofitting network security to third-party applications: the secureBase experience (1993)

Systems such as Kerberos, designed to provide secure user and service authentication over insecure open networks, continue to gain acceptance in the UNIX world. There are both freely available and commercial products which reduce the vulnerabilities inherent in trusting traditional UNIX security in a distributed environment. However, such products generally do not provide similar protection for third-party applications which have their own network security paradigms. This paper show how such protection can be extended to encompass SYBASE, a widely-used distributed database system. The experience with SYBASE is generalized to other network applications.
An object-oriented approach to nested data parallelism (2002)

This paper describes an implementation technique for integrating nested data parallelism into an object-oriented language. Data-parallel programming employs data aggregates called "collections" and expresses parallelism as operations performed over the elements of a collection. When the elements of a collection are also collections, then there is the possibility for "nested data parallelism." Few current programming languages support nested data parallelism however. In an object-oriented framework, a collection is a single object. Its type defines the parallel operations that may be applied to it. Our goal is to design and build an object-oriented data-parallel programming environment supporting nested data parallelism. Our initial approach is built upon three fundamental additions to C++. We add new parallel base types by implementing them as classes, and add a new parallel collection type called a "vector" that is implemented as a template. Only one new language feature is introduced: the foreach construct, which is the basis for exploiting elementwise parallelism over collections. The strength of the method lies in the compilation strategy, which translates nested data-parallel C++ into ordinary C++. Extracting the potential parallelism in nested foreach constructs is called "flattening" nested parallelism. We show how to flatten foreach constructs using a simple program transformation. Our prototype system produces vector code which has been successfully run on workstations, a CM-2 and a CM-5.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The ErbB-2/HER2 oncoprotein of human carcinomas may function solely as a shared coreceptor for multiple stroma-derived growth factors (1999)

The erbB-2/HER2 oncogene is overexpressed in a significant fraction of human carcinomas of the breast, ovary, and lung in a manner that correlates with poor prognosis. Although the encoded protein resembles several receptors for growth factors, no high affinity ligand of ErbB-2 has so far been fully characterized. However, several lines of evidence have raised the possibility that ErbB-2 can augment signal transduction initiated by binding of certain growth factors to their direct receptors. Here, we contrasted these two models of ErbB-2 function: First, examination of a large series of epidermal growth factor (EGF)-like ligands and neuregulins, including virus-encoded ligands as well as related motifs derived from the precursor of EGF, failed to detect interactions with ErbB-2 when this protein was singly expressed. Second, by using antibodies that block inter-ErbB interactions and cells devoid of surface ErbB-2, we learned that signaling by all ligands examined, except those derived from the precursor of EGF, was enhanced by the oncoprotein. These results imply that ErbB-2 evolved as a shared receptor subunit of all ErbB-specific growth factors. Thus, oncogenicity of ErbB-2 in human epithelia may not rely on the existence of a specific ligand but rather on its ability to act as a coreceptor for multiple stroma-derived growth factors.
Reduction of inrush current in single-phase transformer using virtual air gap technique (1998)

In this paper the authors present a technique based on the use of a virtual air gap in which equivalent thickness varies as a function of controllable parameters adapted to the configuration of the magnetic circuit and the associated control system. The principle is presented using a magnetic circuit similar to the transformer one. Among the numerous applications, this technique can be applied to reduce inrush current in single-phase transformers.
Mobile media metadata for mobile imaging (2005)

Camera phones offer a new platform for digital imaging that integrates capture, programmable processing, networking, and rich user interaction capabilities. This platform can support software that leverages the spatio-temporal context and social community of image capture and (re)use to infer media content. Our mobile media metadata prototype (MMM) uses a small custom client on the camera phone and its XHTML browser along with a metadata server to enable annotation at the time of image capture, leverage contextual metadata and networked metadata resources, and use iterative metadata refinement on the mobile imaging device.