gebhart/patrepeval huggingface dataset:
Performance Testing of Jar Accelerators (1989)

ABSTRACT This paper presents results from a test program on jars and jar accelerators. Ten different accelerators in the range of 6.25" OD to 8" OD have been tested in a horizontal jarring rig built especially for this investigation. The test program comprises both single tool tests and full jarring tests where accelerator's are tested together with jars. Slow loading and deloading of the accelerators has revealed great differences in performance. In general hysteresis loss is higher than expected and efficiency is lower than expected from suppliers claims. Temperature tests with heated tools have shown that the temperature has a large effect, especially for accelerators using a compressible fluid as spring elements. Finally, measurements during full jarring tests where the accelerators are deloaded very fast, clearly show that dynamic friction losses are quite significant for some of the tools. The test results and their applications to real field jarring are discussed.
High-throughput oncogene mutation detection in human cancers by mass spectrometry-based genotyping (2006)

A106 Introduction: Translating tumor genetic information into therapeutic benefit remains hampered by a limited knowledge of critical alterations across the spectrum of human tumors, and the inability to identify these on a large scale in the clinical setting.Experimental Procedures: To begin to address these bottlenecks, we applied high-throughput, mass spectrometry-based genotyping (Sequenom, Inc.) to identify 250 known somatic mutations across 17 oncogenes in human cancer samples and cell lines. We then applied this approach to a panel of nearly 1,000 human tumors spanning 15 histologic types.Results: The oncogene genotyping approach enabled sensitive, rapid, and accurate oncogene mutation detection at a low cost per sample. Notably, mutation detection was largely refractory to stromal contamination, detecting somatic alterations present at a frequency of
Accurate Prediction of Complex Structure and Affinity for a Flexible Protein Receptor and Its Inhibitor (2017)

In order to predict the accurate binding configuration as well as the binding affinity for a flexible protein receptor and its inhibitor drug, enhanced sampling with multicanonical molecular dynamics (McMD) simulation and thermodynamic integration (TI) were combined as a general drug docking method. CDK2, cyclin-dependent kinase 2, is involved in the cell cycle regulation. Malfunctions in CDK2 can cause tumorigenesis, and thus it is a potential drug target. Here, we performed a long McMD simulation for docking the inhibitor CS3 to CDK2 starting from the unbound structure. Subsequently, a potential binding/unbinding pathway was given from the multicanonical ensemble, and the binding free energy was readily computed by TI along the pathway. Using this combination, the correct binding configuration of CS3 to CDK2 was obtained, and its affinity coincided well with the experimental value.
Observations on the inhibition of HIV-1 reverse transcriptase by catechins (1992)

The sensitivity and specificity of the inhibition of HIV-1 reverse transcriptase by various catechins have been examined. As previously reported, (-)epicatechin 3-gallate inhibits the viral polymerase. However, it is noted here that this inhibition is not observed in the presence of either serum albumin or Triton X-100. Other catechins behave similarly to (-)epicatechin 3-gallate in that they inhibit polymerase activity only in the absence of these reagents. Additionally, other DNA polymerases are inhibited to a similar degree by (-)epicatechin 3-gallate. Taken cumulatively, these results suggest that these catechins, and in particular (-)epicatechin 3-gallate, bind with no apparent selectivity and that the observed inhibition of HIV-1 reverse transcriptase is non-specific in nature.
Training of Small Farmers and Minority Agroforestry Landowners in Southeastern US – an Evolving Model (2022)

Traditionally, extension activities are aimed at the transferal of knowledge from professionals to small-farmers and landowners. This process is supported by the Forestry Extension Model (FEM), which posit that professionals know what small-farmers and landowners need to learn, are the most credible source of land management information, and that small-farmers’/landowners’ education leads to sustainable land management practices. Although recent studies have supported a shift to peer-to-peer landowner education, there is still a need for initial professional-to-small-farmer/landowner training. Many underserved landowners lack forestry knowledge and practice and are usually unfamiliar with the available federal and state programs and resources. Therefore, they would require training before mentoring fellow small-farmers/landowners and gaining access to available resources. This paper, based in part on the results of a questionnaire survey and small-famers/landowners training initiatives, outlines elements of an evolving ‘landowners training model’ – a model where aspects of the FEM have been applied in a setting conducive to peer-to-peer mentoring.
Open distal clavicle resection: isolated or with adjunctive acromioplasty. (2009)

The purpose of this study was to assess outcomes following open distal clavicle resection for acromioclavicular joint arthritis or distal clavicle osteolysis, with and without associated acromioplasty. Patients with painful clinical findings limited to the acromioclavicular joint had isolated distal clavicle excision (23 shoulders). Patients with acromioclavicular joint abnormalities and rotator cuff tendinopathy also underwent acromioplasty (41 shoulders). At average follow-up of 8.3 years, pain scores improved from 4.7 (1 to 5 scale) to 2.3 (p < 0.001). Patient satisfaction improved from 1.8 (1 to 10 scale) to 8.3 (p < 0.001). Postoperatively the mean Simple Shoulder Test (SST) score was 10.9. The mean American Shoulder and Elbow Surgeons (ASES) Score was 88.3. There were no statistical differences in pain, satisfaction, motion, and shoulder scores between the two groups. Results of distal clavicle resection with or without acromioplasty are favourable with a low rate of complications and seldom is further surgery required.
Carbon doping of InSb nanowires for high-performance p-channel field-effect-transistors (2013)

Due to the unique physical properties, small bandgap III-V semiconductor nanowires such as InAs and InSb have been extensively studied for the next-generation high-speed and high-frequency electronics. However, further CMOS applications are still limited by the lack of efficient p-doping in these nanowire materials for high-performance p-channel devices. Here, we demonstrate a simple and effective in situ doping technique in the solid-source chemical vapor deposition of InSb nanowires on amorphous substrates employing carbon dopants. The grown nanowires exhibit excellent crystallinity and uniform stoichiometric composition along the entire length of the nanowires. More importantly, the versatility of this doping scheme is illustrated by the fabrication of high-performance p-channel nanowire field-effect-transistors. High electrically active carbon concentrations of ~7.5 × 10(17) cm(-3) and field-effect hole mobility of ~140 cm(2) V(-1) s(-1) are achieved which are essential for compensating the electron-rich surface layers of InSb to enable heavily p-doped and high-performance device structures. All these further indicate the technological potency of this in situ doping technique as well as p-InSb nanowires for the fabrication of future CMOS electronics.
QUIC Version Aliasing (2020)

The QUIC transport protocol [QUIC-TRANSPORT] preserves its future
extensibility partly by specifying its version number. There will be a
relatively small number of published version numbers for the
foreseeable future. This document provides a method for clients and
servers to negotiate the use of other version numbers in subsequent
connections and encrypts Initial Packets using secret keys instead of
standard ones. If a sizeable subset of QUIC connections use this
mechanism, this should prevent middlebox ossification around the
current set of published version numbers and the contents of QUIC
Initial packets, as well as improving the protocol's privacy
properties.
Assembly of a Ternary Metallopeptide Complex at Specific DNA Sites Mediated by an AT‐Hook Adaptor (2020)

The nickel(II)-mediated self-assembly of a multimeric DNA binder is described. The binder is composed of two metal-chelating peptides derived from a bZIP transcription factor (brHis<sub>2</sub> ) and one short AT-hook domain equipped with two bipyridine ligands (HkBpy<sub>2</sub> ). These peptides reversibly assemble in the presence of Ni<sup>II</sup> ions at selected DNA sequences of 13 base pairs.
Modeling of Nematic Electrolytes and Nonlinear Electroosmosis (2016)

We derive a mathematical model of a nematic electrolyte based on the Ericksen--Leslie theory of liquid crystal flow. Our goal is to investigate the nonlinear electrokinetic effects that occur because the nematic matrix is anisotropic, in particular, transport of ions in a direction perpendicular to the electric field as well as quadratic dependence of the induced flow velocity on the electric field. The latter effect makes it possible to generate sustained flows in the nematic electrolyte that do not reverse their direction when the polarity of the applied electric field is reversed. From a practical perspective, this enables the design of AC-driven electrophoretic and electroosmotic devices. Our study of a special flow in a thin nematic film shows good qualitative agreement with laboratory experiments.
Sphingosine-1-Phosphate and Its Receptors: Structure, Signaling, and Influence (2013)

The sphingosine-1-phosphate (S1P) receptor signaling system has biological and medical importance and is the first lipid G protein-coupled receptor (GPCR) structure to be solved to 2.8-Å resolution. S1P binds to five high-affinity GPCRs generating multiple downstream signals that play essential roles in vascular development and endothelial integrity, control of cardiac rhythm, and routine oral treatment of multiple sclerosis. Genetics, chemistry, and now structural biology have advanced this integrated biochemical system. The S1P receptors have a novel N-terminal fold that occludes access to the binding pocket from the extracellular environment as well as orthosteric and bitopic ligands with very different physicochemical properties. S1P receptors and metabolizing enzymes have been deleted, inducibly deleted, and knocked in as tagged or altered receptors in mice. An array of genetic models allows analysis of integrated receptor function in vivo. We can now directly understand causal relationships among protein expression, signal, and control points in physiology and pathology.
Design of an Os Complex‐Modified Hydrogel with Optimized Redox Potential for Biosensors and Biofuel Cells (2016)

Multistep synthesis and electrochemical characterization of an Os complex-modified redox hydrogel exhibiting a redox potential ≈+30 mV (vs. Ag/AgCl 3 M KCl) is demonstrated. The careful selection of bipyridine-based ligands bearing N,N-dimethylamino moieties and an amino-linker for the covalent attachment to the polymer backbone ensures the formation of a stable redox polymer with an envisaged redox potential close to 0 V. Most importantly, the formation of an octahedral N6-coordination sphere around the Os central atoms provides improved stability concomitantly with the low formal potential, a low reorganization energy during the Os(3+/2+) redox conversion and a negligible impact on oxygen reduction. By wiring a variety of enzymes such as pyrroloquinoline quinone (PQQ)-dependent glucose dehydrogenase, flavin adenine dinucleotide (FAD)-dependent glucose dehydrogenase and the FAD-dependent dehydrogenase domain of cellobiose dehydrogenase, low-potential glucose biosensors could be obtained with negligible co-oxidation of common interfering compounds such as uric acid or ascorbic acid. In combination with a bilirubin oxidase-based biocathode, enzymatic biofuel cells with open-circuit voltages of up to 0.54 V were obtained.
Optimization of a Thermochemical Recovery Process Using Global Optimization Methods to Enhance Heavy Oil Recovery (2018)

Abstract Thermal recovery methods are viable and commonly used to recover heavy oil reservoirs by reducing oil viscosity and improving oil displacement. However, there are many challenges associated with conventional steam injection methods. These challenges include the significant heat energy losses before steam reaches the reservoir, the high cost of steam generation and injection, as well as the emission of greenhouse gases. Therefore, it is essential to introduce a heavy oil recovery approach in which steam can be generated downhole to overcome these challenges associated with conventional steam injection methods. However, this novel heavy-oil recovery method has several designs and operational parameters that must be efficiently optimized, to achieve maximum recovery from heavy-oil reservoirs with less cost and minimum environmental impact. The objective of this work is to introduce a novel heavy-oil recovery technique using in-situ steam generated by downhole thermochemical reactions and investigate the key design and operational parameters of this complex recovery process. Modified self-adaptive differential evolution (MSaDE) and particle swarm optimization (PSO) methods are used in this work as global optimizer to find the optimum design and operation parameters to achieve the maximum net present value (NPV) and highest oil recovery (RF) of a heavy-oil reservoir after ten years of development. Comparison of the two proposed optimization methods is introduced as well. The results show that downhole thermochemical reactions can be used to generate in-situ steam, to efficiently reduce the heavy-oil viscosity and improve oil mobility. It has also shown that utilizing MSaDE and PSO methods to optimize the key components of this novel recovery process, significantly enhanced the recovery performance, in terms of higher NPV and RF. This study provides the first known in-depth optimization and uncertainty analysis to outline the significance of each design and operation parameter of the proposed novel thermochemical recovery process. This work showed and verified the concept of using downhole thermochemical reactions as an environmental-friendly solution to recover oil from heavy-oil reservoirs and is considered as a step forward to eliminate the greenhouse gases emission related to thermal recovery methods.
Process and catalyst for carbonylating olefins (2023)

Disclosed is an improved catalyst system and process for preparing aliphatic carbonyl compounds such as aliphatic carboxylic acids, alkyl esters of aliphatic carboxylic acids and anhydrides of aliphatic carboxylic acids by carbonylating olefins in the presence of a catalyst system comprising (1) a first component selected from at least one Group 6 metal, i.e., chromium, molybdenum, and/or tungsten and (2) a second component selected from at least one of certain halides and tertiary and quaternary compounds of a Group 15 element, i.e., nitrogen, phosphorus and/or arsenic, and (3) as a third component, a polar, aprotic solvent. The process employing the improved catalyst system is carried out under carbonylating conditions of pressure and temperature discussed herein. The process constitutes and improvement over known processes since it can be carried out at moderate carbonylation conditions without the necessity of using an expensive noble metal catalyst, volatile, toxic materials such as nickel tetracarbonyl, formic acid or a formate ester. Further, the addition of a polar, aprotic solvent to the catalyst system significantly increases, or accelerates, the rate at which the carbonylation takes place.
A Behavior-Based Approach for Analyzing Knowledge-Process Dynamics (2013)

Understanding and managing knowledge processes have been recognized as critical issues in regard to knowledge management. However, no practical methodology for understanding and managing the knowledge process has been devised because of the tacit nature of the process. This research work proposes a new methodology called “knowledge-process dynamics (KPD)” analysis featuring objective behavioral measurement. KPD analysis utilizes interaction data between workers (collected from wearable sensors) and update history of documents to clarify workers’ behavioral dynamics in the form of a causal-loop diagram. To demonstrate the effectiveness of KPD analysis, it was applied to product-design organizations. The resulting understanding of behavioral dynamics successfully helped a junior manager to idenfity problems and measures related to knowledge processes.
Experimental Characterization of Cold Plates used in Cooling Multi Chip Server Modules (MCM) (2018)

Miniaturization of microelectronic components comes at a price of high heat flux density. By adopting liquid cooling, the rising demand of high heat flux devices can be met while the reliability of the microelectronic devices can also be improved to a greater extent. Liquid cooled cold plates are largely replacing air based heat sinks for electronics in data center applications, thanks to its large heat carrying capacity. A bench level study was carried out to characterize the thermohydraulic performance of two microchannel cold plates which uses warm DI water for cooling Multi Chip Server Modules (MCM). A laboratory built mock package housing mock dies and a heat spreader was employed while assessing the thermal performance of two different cold plate designs at varying coolant flow rate and temperature. The case temperature measured at the heat spreader for varying flow rates and input power were essential in identifying the convective resistance. The flow performance was evaluated by measuring the pressure drop across cold plate module at varying flow rates. Cold plate with the enhanced microchannel design yielded better results compared to a traditional parallel microchannel design. The study conducted at higher coolant temperatures yielded lower pressure drop values with no apparent change in the thermal behavior using different cold plates. The tests conducted after reversing the flow direction in microchannels provide an insight at the effect of neighboring dies on each other and reveal the importance of package specific cold plate designs for top performance. The experimental results were validated using a numerical model which are further optimized for improved geometric designs.
The “String Sign” for Diagnosis of Mucinous Pancreatic Cysts (2013)

Purpose: To assess the performance characteristics of the “string sign” in pancreatic cyst fluid for the diagnosis of mucinous cysts, and the utility of a novel sequential interpretation model for cyst fluid tests. Methods: Medical records of all patients undergoing EUS FNA (fine needle aspiration) of pancreatic cystic lesions at one institution from 2003 to 2012 were reviewed. String sign was performed prospectively, and results were obtained from EUS reports. The string sign was performed at the time of EUS FNA by placing a drop of fluid between two gloved fingers, or watching the fluid drip from the FNA needle. A positive sign was defined as formation of a string at least 1 cm in length and lasting for at least 1 second. Diagnosis for each cystic lesion was independently determined using standardized criteria including histology results. A sequential cyst fluid test interpretation model was created, in which the string sign was interpreted first, followed by additional tests interpreted sequentially. Results: String sign results were available for 318 cystic lesions, of which 232 had an independent basis for diagnosis, including 118 mucinous lesions. For 98 histologically proven cases the sensitivity, specificity, PPV, NPV, +LR, and -LR of the string sign for diagnosis of mucinous cysts was 58%, 95%, 94%, 60%, 11.3, and 0.45 respectively. Results were similar for all 232 lesions. String sign performance was comparable to cyst fluid CEA at a diagnostic threshold of 800 ng/ml. The string sign had a superior sensitivity to mucin staining (p=0.029) and cytology (p=0.002). In 10 cases the string sign was positive and cyst fluid CEA was < 200 ng/ml; 6 of these were IPMN. The remaining 4, which were not mucinous, all had cyst fluid CEA < 5 ng/ml. The sequential testing model is shown in the table. When the string sign was positive, specificity was high without further cyst fluid test interpretation. When the string sign was negative, additional stepwise test interpretation improved the sensitivity for diagnosis of a mucinous lesion from 58% to 96%.Table: Table. Performance of a sequential test interpretation modelConclusion: The string sign is highly specific for mucinous pancreatic cysts, and improves overall diagnostic accuracy of pancreatic cyst fluid analysis. A sequential test interpretation model incorporating the string sign yields high diagnostic specificity and sensitivity for mucinous pancreatic lesions.
High-fidelity estimates of spikes and subthreshold waveforms from 1-photon voltage imaging in vivo (2021)

The ability to probe the membrane potential of multiple genetically defined neurons simultaneously would have a profound impact on neuroscience research. Genetically encoded voltage indicators are a promising tool for this purpose, and recent developments have achieved a high signal-to-noise ratio in vivo with 1-photon fluorescence imaging. However, these recordings exhibit several sources of noise and signal extraction remains a challenge. We present an improved signal extraction pipeline, spike-guided penalized matrix decomposition-nonnegative matrix factorization (SGPMD-NMF), which resolves supra- and subthreshold voltages in vivo. The method incorporates biophysical and optical constraints. We validate the pipeline with simultaneous patch-clamp and optical recordings from mouse layer 1 in vivo and with simulated and composite datasets with realistic noise. We demonstrate applications to mouse hippocampus expressing paQuasAr3-s or SomArchon1, mouse cortex expressing SomArchon1 or Voltron, and zebrafish spines expressing zArchon1.
Electronic Structure and Conformational Properties of Polybenzimidazole-Based Ionenes—A Density Functional Theory Investigation (2020)

Polybenzimidazole-based ionenes are explored for use in both alkaline anion-exchange membrane fuel cells and alkaline polymer electrolyzers. Poly-(hexamethyl-<i>p</i>-terphenylbenzimidazolium) (HMT-PMBI), the material of interest in this article, is exceptionally hydroxide-stable and water-insoluble. The impact of the degree of methylation on conformations and electronic structure properties of HMT-PMBI oligomers, from the monomer to the pentamer, is studied with density functional theory calculations. Optimization studies are presented for both the gas phase and in the presence of implicit water. In addition, time-dependent density functional theory is employed to generate the UV-vis absorption spectra of the studied systems. Results are insightful for experimentalists and theorists investigating the impact of synthetic and environmental conditions on the conformation and electronic properties of polybenzimidazole-based membranes.