gebhart/patrepeval huggingface dataset:
Use of mono Q high resolution ion exchange chromatography to obtain highly pure and active Escherichia coli RNA polymerase (1990)

A method for the purification of highly pure and active Escherichia coli RNA polymerase holoenzyme is described. This method is simple, reproducible, and can be performed at room temperature. The procedure involves the high-performance liquid chromatography of a partially purified RNA polymerase sample on a Mono Q ion-exchange column. Under the conditions used, RNA polymerase holoenzyme is well separated from the core RNA polymerase and other impurities. The purified RNA polymerase contains virtually no impurities as judged by SDS-polyacrylamide gel electrophoresis. The purified RNA polymerase holoenzyme contains the sigma 70 subunit in stoichiometric amounts and is at least 90% active.
Detecting Kernel Level Keyloggers Through Dynamic Taint Analysis (2008)

Keyloggers as invisible keystroke recorders have posed a serious threat to user privacy and security. It is difficult to detect keyloggers, especially kernel keyloggers that operate at the operating system’s kernel level, because of their inconspicuous activities and flexible interception methods. In this paper, we propose a framework using a dynamic taint analysis technique to detect kernel level keyloggers. Our design is originated from the observation that kernel keyloggers usually manipulate the data flow of a keyboard driver in order to record typed keystrokes. By tainting and monitoring the keystroke data, this framework detects and analyzes any illegitimate uses of the tainted keystroke data. Based on Argos, a system that can perform host-based intrusion detection and support dynamic taint analysis, we build a prototype of the proposed framework and evaluate its effectiveness. Our experimental results show that the proposed framework can accurately detect kernel level keylogging activities and identify their root causes.
Fast and accurate long-read alignment with Burrows–Wheeler transform (2010)

Abstract Motivation: Many programs for aligning short sequencing reads to a reference genome have been developed in the last 2 years. Most of them are very efficient for short reads but inefficient or not applicable for reads &gt;200 bp because the algorithms are heavily and specifically tuned for short queries with low sequencing error rate. However, some sequencing platforms already produce longer reads and others are expected to become available soon. For longer reads, hashing-based software such as BLAT and SSAHA2 remain the only choices. Nonetheless, these methods are substantially slower than short-read aligners in terms of aligned bases per unit time. Results: We designed and implemented a new algorithm, Burrows-Wheeler Aligner's Smith-Waterman Alignment (BWA-SW), to align long sequences up to 1 Mb against a large sequence database (e.g. the human genome) with a few gigabytes of memory. The algorithm is as accurate as SSAHA2, more accurate than BLAT, and is several to tens of times faster than both. Availability: http://bio-bwa.sourceforge.net Contact: rd@sanger.ac.uk
Direct opto-electronic synthesis of mW-level millimeter wave signals using an optical frequency comb generator and a uni-traveling-carrier photodiode (2002)

The first experimental demonstration of direct 60 GHz opto-electronic synthesis of mW-level millimeter-wave signals using an optical frequency comb generator is reported. We obtained signals from 10 to 60 GHz with a maximum power of +3 dBm at 60 GHz using a uni-traveling-carrier photodiode.
A convergent O ( n ) algorithm for off-policy temporal-difference learning with linear function approximation (2008)

We introduce the first temporal-difference learning algorithm that is stable with linear function approximation and off-policy training, for any finite Markov decision process, behavior policy, and target policy, and whose complexity scales linearly in the number of parameters. We consider an i.i.d. policy-evaluation setting in which the data need not come from on-policy experience. The gradient temporal-difference (GTD) algorithm estimates the expected update vector of the TD(0) algorithm and performs stochastic gradient descent on its L2 norm. We prove that this algorithm is stable and convergent under the usual stochastic approximation conditions to the same least-squares solution as found by the LSTD, but without LSTD’s quadratic computational complexity. GTD is online and incremental, and does not involve multiplying by products of likelihood ratios as in importance-sampling methods. 1 Off-policy learning methods Off-policy methods have an important role to play in the larger ambitions of modern reinforcement learning. In general, updates to a statistic of a dynamical process are said to be “off-policy ” if their distribution does not match the dynamics of the process, particularly if the mismatch is due to the way actions are chosen. The prototypical example in reinforcement learning is the learning of the value function for one policy, the target policy, using data obtained while following another policy, the behavior policy. For example, the popular Q-learning algorithm (Watkins 1989) is an offpolicy temporal-difference algorithm in which the target policy is greedy with respect to estimated action values, and the behavior policy is something more exploratory, such as a corresponding ɛ-greedy policy. Off-policy methods are also critical to reinforcement-learning-based efforts to model human-level world knowledge and state representations as predictions of option outcomes (e.g.,
An interactive audio source separation framework based on non-negative matrix factorization (2014)

Though audio source separation offers a wide range of applications in audio enhancement and post-production, its performance has yet to reach the satisfactory especially for single-channel mixtures with limited training data. In this paper we present a novel interactive source separation framework that allows end-users to provide feedback at each separation step so as to gradually improve the result. For this purpose, a prototype graphical user interface (GUI) is developed to help users annotating time-frequency regions where a source can be labeled as either active, inactive, or well-separated within the displayed spectrogram. This user feedback information, which is partially new with respect to the state-of-the-art annotations, is then taken into account in a proposed uncertainty-based learning algorithm to constraint the source estimates in next separation step. The considered framework is based on non-negative matrix factorization and is shown to be effective even without using any isolated training data.
Spinning fast iterative data flows (2012)

Parallel dataflow systems are a central part of most analytic pipelines for big data. The iterative nature of many analysis and machine learning algorithms, however, is still a challenge for current systems. While certain types of bulk iterative algorithms are supported by novel dataflow frameworks, these systems cannot exploit computational dependencies present in many algorithms, such as graph algorithms. As a result, these algorithms are inefficiently executed and have led to specialized systems based on other paradigms, such as message passing or shared memory. We propose a method to integrate incremental iterations , a form of workset iterations, with parallel dataflows. After showing how to integrate bulk iterations into a dataflow system and its optimizer, we present an extension to the programming model for incremental iterations. The extension alleviates for the lack of mutable state in dataflows and allows for exploiting the sparse computational dependencies inherent in many iterative algorithms. The evaluation of a prototypical implementation shows that those aspects lead to up to two orders of magnitude speedup in algorithm runtime, when exploited. In our experiments, the improved dataflow system is highly competitive with specialized systems while maintaining a transparent and unified dataflow abstraction.
Impact of Staphylococcus aureus on Pathogenesis in Polymicrobial Infections (2014)

Polymicrobial infections involving Staphylococcus aureus exhibit enhanced disease severity and morbidity. We reviewed the nature of polymicrobial interactions between S. aureus and other bacterial, fungal, and viral cocolonizers. Microbes that were frequently recovered from the infection site with S. aureus are Haemophilus influenzae, Enterococcus faecalis, Pseudomonas aeruginosa, Streptococcus pneumoniae, Corynebacterium sp., Lactobacillus sp., Candida albicans, and influenza virus. Detailed analyses of several in vitro and in vivo observations demonstrate that S. aureus exhibits cooperative relations with C. albicans, E. faecalis, H. influenzae, and influenza virus and competitive relations with P. aeruginosa, Streptococcus pneumoniae, Lactobacillus sp., and Corynebacterium sp. Interactions of both types influence changes in S. aureus that alter its characteristics in terms of colony formation, protein expression, pathogenicity, and antibiotic susceptibility.
Instant Handoffs for Wireless Infrastructure Meshed Networks (2008)

Infrastructure meshed networks provide access to wireless clients that do not participate in traffic forwarding. This paper proposes minimalist instant handoff for wireless access networks (MIHAN), allowing for seamless movement of nodes in coverage areas, while maintaining connectivity. The approach of MIHAN is that all client frames, send in radio range of an access node, are received and forwarded to a central gateway. The node removes duplicate packets and tracks the network attachment of wireless clients. MIHAN relies on standard medium access control and a TCP/IP protocol stack. It is transparent to and does not require any special support, in the clients. Only limited configuration changes are necessary in the access nodes; all routing and tracking is handled by the gateway. Advantages include instant handoffs, no changes to access points and protocols and the simplicity of the solution. The paper introduces the scheme, provides details on various implementation options and gives simulation results that show the operation. Proof of concept implementation and some test results are presented.
Adenoassociated Virus-Mediated Transfer of a Functional Water Channel into Salivary Epithelial Cells <i>In Vitro</i> and <i>In Vivo</i> (1998)

Aquaporin 1 (AQP1) is the archetypal member of a family of integral membrane proteins that function as water channels. Previously we have shown that this protein can be expressed transiently from a recombinant adenovirus (AdhAQP1) in vitro in different epithelial cell lines, and in vivo in rat submandibular glands. In the present study we have constructed a recombinant adenoassociated virus (rAAV) containing the human aquaporin 1 gene (rAAVhAQP1). rAAVhAQP1 was produced at relatively high titers. Approximately 10(11)-10(12) particles/ml and approximately 10(8)-10(9) transducing units/ml. We show that the rAAVhAQP1 can transduce in vitro four epithelial cell lines of different origins, at a level sufficient to detect the recombinant hAQP1 protein by either Western blot or confocal microscopic analysis. The recombinant hAQP1 was correctly targeted to the plasma membranes in all cell lines. Function of the recombinant hAQP1 was measured as fluid flow, in response to an osmotic gradient, across a monolayer of transduced epithelial cells. The data show that even at a low level of transduction, typically approximately 10% of the cells in the monolayer, transepithelial fluid movement is enhanced about threefold above basal levels. In addition, we report that rAAVhAQP1 can transduce epithelial cells in the salivary glands and liver of mice in vivo. These results suggest that rAAVs may be useful gene transfer vectors to direct the production of functional transgenes in salivary epithelial cell types.
THE PENN STATE ROAD FRICTION TESTER AS ADAPTED TO ROUTINE MEASUREMENT OF PAVEMENT SKID RESISTANCE (1963)

THE SKID RESISTANCE PROBLEM IS RESTATED AND THE NEED FOR MODERN AND EFFICIENT SKID TESTING EQUIPMENT FOR ROUTINE FIELD TESTS IS DERIVED. THE DESIGN AND OPERATION REQUIREMENTS FOR A ROUTINE TESTER ARE DEFINED IN TERMS OF PRECISION, RUGGEDNESS, COMPACTNESS, TRAFFIC INTERFERENCE, AND COST OF OPERATION. THE DESIGN CONCEPT OF THE PENN STATE ROAD FRICTION TESTER IS SHOWN TO FULFILL THESE REQUIREMENTS. THE TRAILER AND TOWING VEHICLE, INSTRUMENTATION AND CONTROLS, THE CALIBRATION EQUIPMENT AND METHOD OF CALIBRATION ARE DESCRIBED. DIMENSIONS AND SPECIFICATIONS OF THE ROAD FRICTION TESTER, PERFORMANCE DATA AND SELECTED RESULTS OF RECENT TESTS ARE GIVEN. ALSO DESCRIBED IS THE PROTOTYPE OF A NEW PORTABLE TESTER DEVELOPED ESPECIALLY FOR FIELD USE TO SUPPLEMENT THE LARGE UNIT. THE NEED FOR FURTHER WORK ON THE OVERALL SKID RESISTANCE PROBLEM IS OUTLINED AND SPECIFIC PROBLEMS ARE SHOWN TO DEMAND EARLY SOLUTIONS. /AUTHOR/
A pen-based tool for efficient labeling of 2D sketches (2007)

High quality labeled data is essential for developing and evaluating sketch recognition algorithms. Unfortunately, labeling freely-drawn sketches is time-consuming and difficult, if not impossible, using current technologies. These difficulties and the resulting lack of labeled data fundamentally limit the development of recognition algorithms. We present an intuitive, direct manipulation pen-based application for labeling sketch data in any two-dimensional domain. Our labeling tool supports the three essential sketch recognition labeling tasks: stroke fragmentation, stroke grouping and label application. Our interface integrates standard and novel interaction techniques to make each task efficient and natural. In a user study, all users felt that labeling data with our tool was quick and efficient.
Treatment for Lupus, First in 50 Years, Offers Modest Benefits, Hope to Patients (2011)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA HomeNew OnlineCurrent IssueFor Authors Publications JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) Podcasts Clinical Reviews Editors' Summary Medical News Author Interviews More JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA journal
A secure and privacy-preserving communication scheme for Advanced Metering Infrastructure (2012)

Smart grid is the modernization of the existing nation-wide power grid. As a core component of the smart grid, Advanced Metering Infrastructure (AMI) integrates a two-way communications network which enables customers and utilities to actively monitor and manage their energy use. While the deployment of AMI brings enormous social and industrial benefits, some incurred security and privacy issues need to be properly addressed. In this paper, we propose a data communication scheme for AMI with particular considerations on these issues. In our approach, we require strong device authentication before a smart meter joins AMI network. Data confidentiality as well as customer privacy associated with sensitive data are protected by taking advantage of homomorphic encryption. Each in-network message is digitally signed for data integrity. Security analysis is provided to justify our scheme.
A novel, lower cost, thermally enhanced exposed silicon plastic package (ESPP) (2002)

The plastic Quad Flat Package has evolved into a large, high pin count package, however higher reliability and thermal dissipation requirements constitute the boundary conditions it must overcome to evolve as a viable high density package. The present mold compounds used as encapsulants have poor thermal conductivities and represent a large portion of the thermal resistance in the plastic package. Existing thermally enhanced plastic packages are prone to delamination, and higher costs. A new plastic package is proposed herein that achieves a new level of reliability and performance, all at a cost lower than the standard plastic package. The ESPP package integrity is analyzed and compared to other thermally enhanced packages. Thermal performance is measured and compared to other packages.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Bismuth Triflate Catalyzed [1,3] Rearrangement of Aryl 3-Methylbut-2-enyl Ethers (2006)

An efficient bismuth triflate catalyzed [1,3] rearrangement of aryl 3-methylbut-2-enyl ethers has been developed. The reaction proceeds rapidly and affords the corresponding para- and ortho-prenylated phenols and naphthols in moderate to good yields (up to 86%). ortho-Prenylphenols are immediately cyclized under the reaction conditions to the corresponding chroman derivatives.
High‐resolution MR imaging of mouse brain microvasculature using the relaxation rate shift index <i>Q</i> (2004)

Magnetic resonance imaging (MRI) is a powerful method for in vivo quantification of tissue properties. It has been previously proposed that the index Q identical with Delta R2/(Delta R2*)2/3, where Delta R2 and Delta R2* are the spin echo and gradient echo relaxation rate shifts caused by the injection of an intravascular contrast agent, may be useful for characterizing microvasculature. In particular, Q is expected to correlate well with the density of microvessels. This study presents high-resolution in vivo Q-maps of normal mouse brain obtained with a superparamagnetic iron oxide contrast agent at a field of level of 9.4 T. Normative Q values are derived for several regions of interest and significant interregional variations are observed. Microvessel densities estimated from the Q-maps are found to be in reasonable accord with histologically determined values. A possible application of Q-maps is the assessment of angiogenic activity in tumors.
Review of oral appliances for treatment of sleep-disordered breathing (2006)

Between 1982 and 2006, there were 89 distinct publications dealing with oral appliance therapy involving a total of 3,027 patients, which reported results of sleep studies performed with and without the appliance. These studies, which constitute a very heterogeneous group in terms of methodology and patient population, are reviewed and the results summarized. This review focused on the following outcomes: sleep apnea (i.e. reduction in the apnea/hypopnea index or respiratory disturbance index), ability of oral appliances to reduce snoring, effect of oral appliances on daytime function, comparison of oral appliances with other treatments (continuous positive airway pressure and surgery), side effects, dental changes (overbite and overjet), and long-term compliance. We found that the success rate, defined as the ability of the oral appliances to reduce apnea/hypopnea index to less than 10, is 54%. The response rate, defined as at least 50% reduction in the initial apnea/hypopnea index (although it still remained above 10), is 21%. When only the results of randomized, crossover, placebo-controlled studies are considered, the success and response rates are 50% and 14%, respectively. Snoring was reduced by 45%. In the studies comparing oral appliances to continuous positive airway pressure (CPAP) or to uvulopalatopharyngoplasty (UPPP), an appliance reduced initial AHI by 42%, CPAP reduced it by 75%, and UPPP by 30%. The majority of patients prefer using oral appliance than CPAP. Use of oral appliances improves daytime function somewhat; the Epworth sleepiness score (ESS) dropped from 11.2 to 7.8 in 854 patients. A summary of the follow-up compliance data shows that at 30 months, 56-68% of patients continue to use oral appliance. Side effects are relatively minor but frequent. The most common ones are excessive salivation and teeth discomfort. Efficacy and side effects depend on the type of appliance, degree of protrusion, vertical opening, and other settings. We conclude that oral appliances, although not as effective as CPAP in reducing sleep apnea, snoring, and improving daytime function, have a definite role in the treatment of snoring and sleep apnea.
A Rheometer for Evaluating Drilling Fluids at Elevated Temperatures (1970)

Abstract The trend toward deeper wells with subsequent higher bore-hole temperatures has increased the need for data on drilling fluid properties at elevated temperatures and pressures. Equipment presently available does not allow direct presently available does not allow direct determination of fluid properties from lower laminar to fully turbulent flow with precision. This paper presents the design precision. This paper presents the design considerations that led to the construction of equipment at the University of Oklahoma to provide high temperature data for drilling fluids and cement slurries and examples of such data for three drilling mud systems. The equipment will operate up to 350 degrees F through flow ranges from lower laminar to turbulent flow with sufficient precision for extrapolation to other precision for extrapolation to other pipe sizes and other geometries of flow pipe sizes and other geometries of flow conduit. It was determined that the equipment was adequate and that the fluid properties of at least some fluid systems properties of at least some fluid systems are highly dependent on temperatures and should be examined by this procedure for critical design programs. Introduction Several investigators have recently been interested in the high temperature behavior of drilling fluids due to the increasing numbers of deep wells and the need to critically control drilling fluid rheology in these wells. The experimental methods and the chosen form of data presentation vary considerably among the presentation vary considerably among the various investigators but all have indicated a deleterious effect on drilling fluid caused by a high temperature environment. Many of the investigators have tried to relate the deleterious effects to measurable chemical or physical changes that occur in clay drilling fluids at elevated temperatures. Most of the previous investigators have chosen to study the rheological properties of drilling fluids at elevated properties of drilling fluids at elevated temperatures with a modified rotational viscometer and report the data considering the fluids as Bingham Plastics.
A new wavelet-based algorithm for filtering low SRN signals (2002)

In this work we present a new algorithm suitable for detecting and filtering radar or sonar pulses in presence of strong noise, jamming signals and Doppler frequency shift in the received signal. The novel algorithm is based on the multiresolution wavelet analysis, a powerful tool right to analyze non stationary signals. We exploit the Wavelet-based time-frequency domain analysis to detect and reconstruct radar or sonar pulses, obtaining very good matching between transmitted and received signals up to a signal-to-noise level of -11 dB.