gebhart/patrepeval huggingface dataset:
Parallelizing query optimization (2008)

Many commercial RDBMSs employ cost-based query optimization exploiting dynamic programming (DP) to efficiently generate the optimal query execution plan. However, optimization time increases rapidly for queries joining more than 10 tables. Randomized or heuristic search algorithms reduce query optimization time for large join queries by considering fewer plans, sacrificing plan optimality. Though commercial systems executing query plans in parallel have existed for over a decade, the optimization of such plans still occurs serially. While modern microprocessors employ multiple cores to accelerate computations, parallelizing query optimization to exploit multi-core parallelism is not as straightforward as it may seem. The DP used in join enumeration belongs to the challenging nonserial polyadic DP class because of its non-uniform data dependencies. In this paper, we propose a comprehensive and practical solution for parallelizing query optimization in the multi-core processor architecture, including a parallel join enumeration algorithm and several alternative ways to allocate work to threads to balance their load. We also introduce a novel data structure called skip vector array to significantly reduce the generation of join partitions that are infeasible. This solution has been prototyped in PostgreSQL. Extensive experiments using various query graph topologies confirm that our algorithms allocate the work evenly, thereby achieving almost linear speed-up. Our parallel join enumeration algorithm enhanced with our skip vector array outperforms the conventional generate-and-filter DP algorithm by up to two orders of magnitude for star queries-linear speedup due to parallelism and an order of magnitude performance improvement due to the skip vector array.
Biotransformation of Chrysin to Baicalein: Selective C6-Hydroxylation of 5,7-Dihydroxyflavone Using Whole Yeast Cells Stably Expressing Human CYP1A1 Enzyme (2017)

Naturally occurring polyphenolic compounds are of medicinal importance because of their unique antioxidant, anticancer, and chemopreventive properties. Baicalein, a naturally occurring polyhydroxy flavonoid possessing a diverse range of pharmacological activities, has been used in traditional medicines for treatment of various ailments. Apart from its isolation from natural sources, its synthesis has been reported via multistep chemical approaches. Here, we report a preparative-scale biotransformation, using whole yeast cells stably expressing human cytochrome P450 1A1 (CYP1A1) enzyme that allows regioselective C6-hydroxylation of 5,7-dihydroxyflavone (chrysin) to form 5,6,7-trihydroxyflavone (baicalein). Molecular modeling reveals why chrysin undergoes such specific hydroxylation mediated by CYP1A1. More than 92% reaction completion was obtained using a shake-flask based process that mimics fed-batch fermentation. Such highly efficient selective hydroxylation, using recombinant yeast cells, has not been reported earlier. Similar CYP-expressing yeast cell based systems are likely to have wider applications in the syntheses of medicinally important polyphenolic compounds.
DNA‐binding properties of gene‐5 protein encoded by bacteriophage M13 (1988)

The binding of gene-5 protein, encoded by bacteriophage M13, to oligodeoxynucleic acids was studied by means of fluorescence binding experiments, fluorescence depolarization measurements and irreversible dissociation kinetics of the protein.nucleotide complexes with salt. The binding properties thus obtained are compared with those of the binding to polynucleotides, especially at very low salt concentration. It appears that the binding to oligonucleotides is always characterized by a stoichiometry (n) of 2-3 nucleotides/protein, and the absence of cooperativity. In contrast the protein can bind to polynucleotides in two different modes, one with a stoichiometry of n = 3 in the absence of salt and another with n = 4 at moderate salt concentrations. Both modes have a high intramode cooperativity (omega about 500) but are non-interacting and mutually exclusive. For deoxynucleic acids with a chain length of 25-30 residues a transition from oligonucleotide to polynucleotide binding is observed at increasing nucleotide/protein ratio in the solution. The n = 3 polynucleotide binding is very sensitive to the ionic strength and is only detectable at very low salt concentrations. The ionic strength dependency per nucleotide of the n = 4 binding is much less and is comparable with the salt dependency of the oligonucleotide binding. Furthermore it appears that the influence of the salt concentration on the oligonucleotide binding constant is to about the same degree determined by the effect of salt on the association and dissociation rate constants. Model calculations indicate that the fluorescence depolarization titration curves can only be explained by a model for oligonucleotide binding in which a protein dimer binds with its two dimer halves to the same strand. In addition it is only possible to explain the observed effect of the chain length of the oligonucleotide on both the apparent binding constant and the dissociation rate by assuming the existence of interactions between protein dimers bound to different strands. This results in the formation of a complex consisting of two nucleotide strands with protein in between and stabilized by the dimer-dimer interactions.
Laser Ablation of Ventricular Tachycardia (1988)

About 5-10% of patients after myocardial infarction experience sustained ventricular tachycardias. Drug therapy is successful only in 60% of these patients, so that a number of them is on a high risk of a sudden cardiac death. Indirect surgical approaches like myocardial revascularization, or aneurysm resection have proven to be ineffective in the treatment of these malignant tachycardias. By the development of electrophysiologic techniques a mechanism of the ventricular tachycardias could be identified as a micro-reentry at the border of myocardial infarction. On this base different direct surgical approaches were advocated by Guiraudon, proposing an encircling endocardial ventriculotomy and by Josephson and Harken recommending a subendocardial resection technique. The results of these direct procedures were much better than those of the prior indirect techniques. The mortality in this series was around 10% and there still was a postoperative recurrence of the tachycardia in about 20-30%. Our group started a study in which a Nd:YAG laser was used to photocoagulate areas of myocardium responsible for the initiation of ventricular tachycardia. By its deeper penetration depth the Nd:YAG laser was preferrable to other laser systems like CO2 and Argon-laser. In contrast to cryothermy the Nd:YAG showed three special advantages: First, it was more effective in the normothermic myocardium, it showed not peripheral zone of temporary myocardial injury, potentially causing late failures, and third equal ablation of tissue could be achieved in much shorter time. Patients were considered operative candidates when drug therapy failed. Preoperative investigations included formal cardiac catheterization and an electrophysiologic testing with induction and mapping of the ventricular tachycardia.(ABSTRACT TRUNCATED AT 250 WORDS)
Subjektive Aufstiegskarrieren (2010)

Die Analyse der subjektiven Karriere bedeutet einen Perspektivenwechsel. Ich definiere die Dimensionen des Aufstiegs, die Regelmäßigkeit oder die Loyalität nicht mehr selber. Stattdessen höre ich jenen zu, die eine Karriere machen und versuche zu verstehen in welchen Begriffen, Phasen und Bildern sie ihren Aufstieg wahrnehmen und denken. Es handelt sich also in diesem Kapitel um eine theoretische Verdichtung des Karriereverständnisses. Zudem hoffe ich gewisse Erklärungslücken zu schließen, die die Analyse der objektiven Karriere offen gelassen hat: wieso, zum Beispiel, sind technische Karrieren weniger erfolgreich als andere Karrieren? Welche Entscheidungen liegen den Karrierevariationen zu Grunde? Zu welchen biographischen Zeitpunkten fallen sie?
Ligand Cooperative Iridium PCP Complexes for Small Molecule Activation (2017)

Simple small molecules are perhaps the most fundamental components to synthetic chemistry, acting as the building blocks from which larger, more complex compounds are made. These simple molecules are also important in of themselves, sometimes as fuels, greenhouse gases, the water we drink, or the air we breathe. Studying the way in which these molecules behave and react is therefore of great importance. Organometallic chemistry has had considerable success in using transition metal complexes to manipulate small molecules and perform otherwise difficult transformations such as the splitting of water into H2 and O2 or the decomposition of harmful emissions such as CO2 or N2O. This thesis presents the synthesis of a new PCP pincer ligand framework bearing benzo[b]thiophene linking groups as an alternative to the parent ortho-phenylene linkers. This ligand was installed onto an iridium center via double C-H activation at the central carbon atom, resulting in a carbene donor which can be used in favorable metal-ligand cooperative processes. This design feature was used for the activation of N2O, where a series of “iridaepoxide” complexes were made through oxygen atom transfer to the iridium-carbon bond with the release of N2 gas. The formal hydrogenation of N2O to H2O was accomplished by reaction of the iridaepoxide species with H2. The mechanistic details of these processes were studied extensively and reveal a unique ligand cooperative system. Halide abstraction from several neutral iridium complexes was then performed to explore the reactivity of their cationic counterparts. This allowed for the use of milder conditions in previous reactions and for the formation of highly reactive species capable of numerous bond activations including the strong O-H bonds of water and alcohols.
Analysis of TRU waste for RCRA-listed elements (1996)

Analytical methods for RCRA listed elements on Portland cement type waste have been employed using both microwave and open hot plate digestions with subsequent analysis by inductively coupled plasma atomic emission spectroscopy (ICP-AES), inductively coupled plasma mass spectrometry (ICP-AES), inductively coupled plasma mass spectrometry (ICP-MS), graphite furnace atomic absorption (GFAA) and cold vapor atomic absorption and fluorescence (CVAA/CVAFS). Four different digestion procedures were evaluated including an open hot plate nitric acid digestion, EPA SW-846 Method 3051, and 2 methods using modifications to Method 3051. The open hot plate and the modified Method 3051, which used aqua regia for dissolution, were the only methods which resulted in acceptable data quality for all 14 RCRA-listed elements. Results for the nitric acid open hot plate digestion were used to qualify the analytical methods for TRU waste characterization, and resulted in a 99% passing score. Direct chemical analysis of TRU waste is being developed at Los Alamos National Laboratory in an attempt to circumvent the problems associated with strong acid digestion methods. Technology development includes laser induced breakdown spectroscopy (LIBS), laser ablation inductively coupled plasma mass spectrometry (LA-ICPMS), dc arc CID atomic emission spectroscopy (DC-AES), and glow discharge mass spectrometry (GDMS). Analytical methods using the Portland cement matrix are currently being developed for each of the listed techniques. Upon completion of the development stage, blind samples will be distributed to each of the technology developers for RCRA metals characterization.
Which insights can gas diffusion electrode half-cell experiments give into activity trends and transport phenomena of membrane electrode assemblies? (2023)

This work highlights how the different environment of the catalyst in GDE and MEA evaluation results in different trends of catalyst layer activity towards the oxygen reduction reaction being observed with both techniques.
Surface-acoustic-wave delay-line controlled low-frequency oscillators (1975)

Surface-acoustic-wave delay line is used as the frequency controling element of a low-frequency oscillator, operating at a fundamental frequency of a few kilohertz. Some salient properties of such oscillators are discussed. Initial experimental results indicate that high-frequency stability can be obtained.
Natural capsaicinoids improve swallow response in older patients with oropharyngeal dysphagia (2012)

Stimulation of TRPV1 by capsaicinoids strongly improved safety and efficacy of swallow and shortened the swallow response in older patients with OD. Stimulation of TRPV1 might become a pharmacologic strategy to treat OD.
Deformable mirror-based photoacoustic remote sensing (PARS) microscopy for depth scanning (2022)

Optically shifting the focal plane to allow depth scanning of delicate biological structures and processes in their natural environment offers an appealing alternative to conventional mechanical scanning. Our technique uses a deformable mirror-based photoacoustic remote sensing microscopy (PARS) with a focus shifting of Δz ∼ 240 µm. We achieve this by integrating a deformable mirror that functions as a varifocal mirror for axial scanning. First, the system's focal shift capability was demonstrated with USAF resolution targets and carbon fiber phantoms, followed by <i>in-vivo</i> visualizations of blood vessels in chicken embryo chorioallantoic membrane (CAM). This work represents an initial step toward developing a non-contact, label-free, and aberration-free PARS imaging system with axial scanning capability.
A possible world approach to uncertain relational data (2004)

Data exchange between embedded systems and other small or large computing device increases. Since data in different data sources may refer to the same real world objects, data cannot simply be merged. Furthermore, in many situations, conflicts in data about the same real world objects need to be resolved without interference from a user. We report on an attempt to make a RDBMS probabilistic, i.e., data in a relation represents all possible views on the real world, in order to achieve unattended data integration. We define a probabilistic relational data model and review standard SQL query primitives in the light of probabilistic data. It appears that thinking in terms of 'possible worlds' is powerful in determining the proper semantics of these query primitives.
A wireless recharging system for electrical agriculture robots with autonomous docking (2014)

In this work we present a system for the autonomous recharge of the batteries of an electric powered mobile robot, developed in the context of agricultural robotics. The system is composed of a wireless charging station at high power which can provide up to 4 kW and an autonomous docking algorithm exploiting a camera and a laser range nder. The wireless charging station consists of a power supply and two coils for the wireless power transfer, one attached to the docking station and one attached at the bottom of the robot. Since a mechanical plug is not used to establish the electrical connection a high precision alignment docking is not required. However, the better the two coils are aligned, the more power is transferred and the eciency of the recharging system increases. The robot navigation module is based on the standard navigation stack of Robot Operating System (ROS). This is used to get close to the docking station, while a ne grain motion planner was specically developed for the docking task. It generates a precise alignment of the robot's coil with the ground coil by fusing the sensory information from the camera and the laser range nder. A detailed description of the wireless charging station and of the motion planner is reported together experiments on a real robot showing the good performances of the complete system.
Performance evaluation of dual tuned knee coil (23Na/1H) for articular cartilage imaging on 1.5Tesla MRI (2012)

Recent advancements in MRI hardware such as radio frequency (RF) coils and high field magnetic strength have played an increasingly important role to enhance the diagnostic capabilities in musculoskeletal imaging. However, in clinical practices, 1.5Tesla field strength is commonly available in most of the hospitals. In this work, the performance of a dual tuned knee coil (23Na/1H) that has the capability to excite sodium and proton nuclei for morphological and physiological assessment of articular cartilage (AC) at 1.5Tesla field strength has been evaluated. Experiments are conducted on phantoms and in vivo human knee without the use of contrasting agents. Sodium and proton images of in vivo human knee in the same plane are obtained with adequate signal-to-noise ratios, enabling the assessment of morphology and physiology of AC. Sodium and proton images acquired using 23Na/1H coil without changing the position of subject are analysed to enhance diagnostic capabilities for assessment of degenerative AC at early stages.
Study on carbon dioxide gas cooler heat transfer process under supercritical pressures (2002)

In carbon dioxide transcritical air-conditioning and heat pump systems, the high-pressure-side heat exchanger operating at supercritical pressures is usually called as gas cooler. The carbon dioxide gas cooler displays much difference from the traditional heat exchangers employing constant property fluids. The commonly used logarithmic mean temperature difference (LMTD) and effectiveness—heat transfer unit (ε-NTU) fail for the gas cooler design calculation as the carbon dioxide properties change sharply near the critical or pseudo-critical point in the heat transfer processes. The new effective heat transfer temperature difference expression for variable fluid property derived by the authors is verified by numeric simulation of the carbon dioxide gas cooler. Moreover, the available correlated models for the cooled carbon dioxide supercritical heat transfer are used to simulate the gas cooler. Detail analysis is made for the deviations among the different models, and for the distributions of local convective coefficient, heat flux, and local temperature of carbon dioxide along the flow path in the gas cooler. Copyright © 2002 John Wiley & Sons, Ltd.
Network enhancement of web rendering time (2015)

The demonstrated system gathers browser rendering status information at the client side and transfers it toward the cellular network. The network can do the traffic scheduling/boosting accordingly achieving enhanced Quality of Experience (QoE) for the user in a congested radio cell. The realized gain in web rendering time by the demonstrated system is in the range of 7-60% depending on the page structure.
Identifying Key Residues That Drive Strong Electrostatic Attractions between Therapeutic Antibodies (2019)

Attractive electrostatic protein-protein interactions (PPI) necessarily involve identifying oppositely charged regions of the protein surface that interact favorably. This cannot be done reliably if one only considers a single protein in isolation unless there are obvious charge "patches" that result in extreme molecular dipoles. Prior work [ <i>J. Pharm. Sci.</i> 2019 , 108 , 120 - 132 ] identified three monoclonal antibodies (MAbs) that displayed experimental behavior ranging from net repulsive to strongly attractive electrostatic interactions. The present work provides a systematic computational approach for identifying the origin of diverse PPI, in terms of which sets of amino acids or individual amino acids are most influential, and determining if there are different patterns of pairwise amino acid interaction "maps" that result in different behaviors. The charge was eliminated computationally, one by one, for each charged residue in the wild-type sequences, which resulted in predicted changes in the second osmotic virial coefficient. The results highlight interaction "maps" that correspond to cases with qualitatively different net electrostatic PPI for the different MAbs and solution conditions, as well as key sets of residues that contribute to strongly attractive PPI. A more computationally efficient method is also proposed to identify key amino acids based on Mayer-weighted interaction energies.
Optimal management of oropharyngeal and esophageal candidiasis in patients living with HIV infection (2010)

Mucocutaneous candidiasis is frequently one of the first signs of human immunodeficiency virus (HIV) infection. Over 90% of patients with AIDS will develop oropharyngeal candidiasis (OPC) at some time during their illness. Although numerous antifungal agents are available, azoles, both topical (clotrimazole) and systemic (fluconazole, itraconazole, voriconazole, posaconazole) have replaced older topical antifungals (gentian violet and nystatin) in the management of oropharyngeal candidiasis in these patients. The systemic azoles, are generally safe and effective agents in HIV-infected patients with oropharyngeal candidiasis. A constant concern in these patients is relapse, which is dependent on the degree of immunosuppression commonly seen after topical therapy, rather than with systemic azole therapy. Candida esophagitis (CE) is also an important concern since it occurs in more than 10% of patients with AIDS and can lead to a decrease in oral intake and associated weight loss. Fluconazole has become the most widely used antifungal in the management of mucosal candidiasis. However, itraconazole and posaconazole have similar clinical response rates as fluconazole and are also effective alternative agents. In patients with fluconazole-refractory mucosal candidiasis, treatment options now include itraconazole solution, voriconazole, posaconazole, and the newer echinocandins (caspofungin, micafungin, and anidulafungin).
Distributed Coordination with Deaf Neighbors: Efficient Medium Access for 60 GHz Mesh Networks (2010)

Multi-gigabit outdoor mesh networks operating in the unlicensed 60 GHz "millimeter (mm) wave" band, offer the possibility of a quickly deployable broadband extension of the Internet. We consider mesh nodes with electronically steerable antenna arrays, with both the transmitter and receiver synthesizing narrow beams that compensate for the higher path loss at mm-wave frequencies, achieving ranges on the order of 100 meters using the relatively low transmit powers attainable with low-cost silicon implementations. Such highly directional networking differs from WiFi networks at lower carrier frequencies in two ways that have a crucial impact on protocol design: (1) directionality drastically reduces spatial interference, so that pseudowired link abstractions form an excellent basis for protocol design; (2) directionality induces deafness, which makes medium access control (MAC) based on carrier sensing infeasible. Interference analysis in our prior work shows that, in such a setting, coordination between transmitters and receivers, rather than interference management, becomes the key MAC performance bottleneck. However, the question of whether such coordination can be achieved in a distributed fashion while achieving high medium utilization, was left open. In this paper, we answer this question in the affirmative, presenting a distributed MAC protocol that employs memory to achieve approximate time division multiplexed (TDM) schedules without explicit coordination or resource allocation. The efficacy of the protocol is demonstrated via packet level simulations, while a Markov chain fixed-point analysis provides insight into the effect of parameter choices.
Development of the Estimation System of the Equivalent Dielectric Constant of Dielectric Materials (2006)

In this research, the relative dielectric constant for the liquid materials with no contact between a sensor and the materials are estimated. SE is first measured using a shield box. Then, the shield box with a multi-layered model is modeled with Sommerfeld integral, and the electromagnetic field is calculated at the observation point. Finally, the SE is calculated to be fitted to the measured value of SE, in order to estimate the electric parameters as an inverse problem