gebhart/patrepeval huggingface dataset:
Seeking an ancient enzyme in Methanococcus jannaschii using orf , a program based on predicted secondary structure comparisons (1998)

We have developed a simple procedure to identify protein homologs in genomic databases. The program, called ORF, is based on comparisons of predicted secondary structure. Protein structure is far better conserved than amino acid sequence, and structure-based methods have been effective in exploiting this fact to find homologs, even among proteins with scant sequence identity. ORF is a secondary structure-based method that operates solely on predictions from sequence and requires no experimentally determined information about the structure. The approach is illustrated by an example: Thymidylate synthase, a highly conserved enzyme essential to thymidine biosynthesis in both prokaryotes and eukaryotes, is thought to be used by Archaea, but a corresponding gene has yet to be identified. Here, a candidate thymidylate synthase is identified as a previously unassigned open reading frame from the genome of Methanococcus jannaschii, viz., MJ0757. Using primary structure information alone, the optimally aligned sequence identity between MJ0757 and Escherichia coli thymidylate synthase is 7%, well below the threshold of sensitivity for detection by sequence-based methods.
The Transcriptional Activator Cat8p Provides a Major Contribution to the Reprogramming of Carbon Metabolism during the Diauxic Shift in Saccharomyces cerevisiae (2001)

In yeast, the transition between the fermentative and the oxidative metabolism, called the diauxic shift, is associated with major changes in gene expression and protein synthesis. The zinc cluster protein Cat8p is required for the derepression of nine genes under nonfermentative growth conditions (ACS1, FBP1, ICL1, IDP2, JEN1, MLS1, PCK1, SFC1, and SIP4). To investigate whether the transcriptional control mediated by Cat8p can be extended to other genes and whether this control is the main control for the changes in the synthesis of the respective proteins during the adaptation to growth on ethanol, we analyzed the transcriptome and the proteome of a cat8 Delta strain during the diauxic shift. In this report, we demonstrate that, in addition to the nine genes known as Cat8p-dependent, there are 25 other genes or open reading frames whose expression at the diauxic shift is altered in the absence of Cat8p. For all of the genes characterized here, the Cat8p-dependent control results in a parallel alteration in mRNA and protein synthesis. It appears that the biochemical functions of the proteins encoded by Cat8p-dependent genes are essentially related to the first steps of ethanol utilization, the glyoxylate cycle, and gluconeogenesis. Interestingly, no function involved in the tricarboxylic cycle and the oxidative phosphorylation seems to be controlled by Cat8p.
Exhaled Nitric Oxide and Acute Lung Injury in a Rat Model of Extracorporeal Circulation (2003)

Exhaled nitric oxide (NO) concentration, a marker of pulmonary inflammation, has been shown to be elevated in various models of acute lung injury (ALI). This study was undertaken to evaluate the pulmonary NO production in a rat model of postextracorporeal circulation (ECC) ALI. Wistar rats underwent either a partial femorofemoral ECC in normothermia for 3 h (n = 10) or a sham procedure (n = 10). The extracorporeal circuit consisted of a roller pump and a membrane oxygenator. Exhaled NO concentration was monitored with a chemiluminescence analyzer. After sacrifice, lungs were harvested for microscopic studies and to analyze the inducible nitric oxide synthase (iNOS) activity and expression (Western blot). ECC was responsible for an ALI characterized by a decreased arterial blood oxygen saturation (88.9% [51.7-94.2] vs. 93.7% [91.4-98.6] P = 0.005) and pulmonary histological changes (marked alveolar neutrophil infiltration; interstitial edema; intraalveolar hemorrhage). The lung injury score was significantly higher in the ECC group (n = 5; 3.0 [2-4]) in comparison to the sham group (n = 5; 1.0 [0-2]). Exhaled NO concentration remained stable throughout the experiment in all sham rats whereas it significantly increased in the ECC group from baseline (2 ppb [1-5]) until the end of experiment (33.5 ppb [1-47]). Lung iNOS activity and expression were also significantly increased in the ECC group. An increase in exhaled NO, however, did not correlate with the decrease in arterial oxygen pressure. ECC was responsible for an ALI in rats and for an elevated pulmonary NO production. Determination of the relationship between exhaled NO and the severity of the inflammatory process in ALI will require further studies.
Streaming Reduction Circuit (2009)

Reduction circuits are used to reduce rows of floating point values to single values. Binary floating point operators often have deep pipelines, which may cause hazards when many consecutive rows have to be reduced. We present an algorithm by which any number of consecutive rows of arbitrary lengths can be reduced by a pipelined commutative and associative binary operator in an efficient manner. The algorithm is simple to implement, has a low latency, produces results in-order, and requires only small buffers. Besides, it uses only a single pipeline for the involved operation. The complexity of the algorithm depends on the depth of the pipeline, not on the length of the input rows. In this paper we discuss an implementation of this algorithm and we prove its correctness.
Reactions of 2-acyloxyisobutyryl halides with nucleosides. 7. Synthesis and biological evaluation of some 2,2'-anhydro-1-(3',5'-di-O-acyl-.beta.-D-arabinofuranosyl)cytosine hydrochlorides (1976)

The direct acylation of 2,2'-anhydro-1(beta-D-arabinofuranosyl)cytosine hydrochloride (cycloC) with a homologous series of saturated and unsaturated acyl chlorides in dimethylacetamide has been investigated. Such acylation reactions have made available a considerable number of 3',5'-diesters of cycloC that have been examined for biological activities. The compounds all show cytotoxicity against HeLa cells in tissue culture, and with the exception of the highly insoluble long-chain diesters (C16--C22), show pronounced activity against vaccinia and Herpes simplex viruses. Against L1210 leukemia in mice the compounds show varied activities, the C12--C14 saturated diesters and the C18--C22 unsaturated diesters being highly effective. Other diesters, varying by only a few methylene groups, show dramatically different results.
Relation between Reactive Surface Sites and Precursor Choice for Area-Selective Atomic Layer Deposition Using Small Molecule Inhibitors (2022)

Implementation of vapor/phase dosing of small molecule inhibitors (SMIs) in advanced atomic layer deposition (ALD) cycles is currently being considered for bottom-up fabrication by area-selective ALD. When SMIs are used, it can be challenging to completely block precursor adsorption due to the inhibitor size and the relatively short vapor/phase exposures. Two strategies for precursor blocking are explored: (i) physically covering precursor adsorption sites, i.e., steric shielding, and (ii) eliminating precursor adsorption sites from the surface, i.e., chemical passivation. In this work, it is determined whether steric shielding is enough for effective precursor blocking during area-selective ALD or whether chemical passivation is required as well. At the same time, we address why some ALD precursors are more difficult to block than others. To this end, the blocking of the Al precursor molecules trimethylaluminum (TMA), dimethylaluminum isopropoxide (DMAI), and tris(dimethylamino)aluminum (TDMAA) was studied by using acetylacetone (Hacac) as inhibitor. It was found that DMAI and TDMAA are more easily blocked than TMA because they adsorb on the same surface sites as Hacac, while TMA is also reactive with other surface sites. This work shows that chemical passivation plays a crucial role for precursor blocking in concert with steric shielding. Moreover, the reactivity of the precursor with the surface groups on the non-growth area dictates the effectiveness of blocking precursor adsorption.
Development of continuously frequency tunable gyrotron and its application to 200 MHz DNP-NMR spectroscopy as a radiation source (2009)

The gyrotron, Gyrotron FU CW IV continues to produce output radiation in the wide range of magnetic fields from 4.9 T to 5.2 T, and continuous frequency tuning in 6 GHz interval from 134 GHz to 140 GHz can be realized. This type of gyrotron will play an important role as a high power radiation source with the function of continuous frequency tuning to the applications in the fields of millimeter to sub-millimeter wavelength range. A sensitive NMR spectroscopy using a dynamic nuclear polarization (DNP-NMR) is the versatile analytical technique to enhance the sensitivity of the NMR spectroscopy. It is well known that the enhancement of the NMR sensitivity depends strongly on the frequency of the irradiating electromagnetic wave. This gyrotron will be applied to 200 MHz DNP-NMR spectroscopy for analysis of polymer surface. Another continuous frequency tuning range (131 GHz-132.5 GHz) realized by this gyrotron covers that of the DNP-NMR spectroscopy with high performance.
INTRAVENOUS REGIONAL ANESTHESIA (1987)

Department of Anesthesia, Wake Forest University Medical Center, Bowman Gray School of Medicine, Winston-Salem, North Carolina, 27103.
Editor's Preface (1932)

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Programmable active droplet generation enabled by integrated pneumatic micropumps (2012)

In this work we have investigated the integrated diaphragm micropump as an active fluidic control approach for the on-demand generation of droplets with precisely defined size, frequency and timing. In contrast to valve-actuated devices that only modulate the flow of the dispersed phase being continuously injected, this integrated micropump allows the combination of fluidic transport and modulation to achieve active control of droplet generation. A distinct characteristic of this method compared to the valve modulated droplet formation processes is that it enables independent control of droplet generation frequency by adjusting the pumping frequency and droplet size by flow conditions. We also demonstrated the generation of complex droplet patterns through programming the pumping configurations and the application to multi-volume digital PCR for precise and quantitative detection of genetic targets. Overall, our results suggest that the pump-based droplet microfluidics provide a robust platform for programmable active droplet generation which could facilitate the development of high-performance chemical and biological assays.
Evaluation of Bond Performance of FastTack® Emulsion for Tack Coat Applications (2008)

The purpose of this study was to evaluate the bond performance of FastTack® relative to that of AET through a host of laboratory tests. FastTack® is a proprietary, rapid-setting emulsion used as a bituminous tack coat for pavement applications. The product, produced by Whitaker Roads Corporation, is touted to exhibit a very fast set time feature that distinguishes it from regular rapid-setting emulsions. This is achieved by the introduction of certain additives, a process referred to as Colnet®. The rapid set time is beneficial for fast-track paving projects and hence could prove to be highly cost effective. However, the adoption of FastTack® as an approved replacement to typical tack coats used by PennDOT is contingent on it exhibiting bond characteristics similar to those exhibited by other rapid-setting emulsions such as AET.
Contention-based performance evaluation of multidimensional range search in peer-to-peer networks (2007)

Performance evaluation of peer-to-peer search techniques has been based on simple performance metrics, such as message hop counts and total network traffic, mostly disregarding their inherent concurrent nature, where contention may arise. This paper is concerned with the effect of contention in complex P2P network search, focusing on techniques for multidimensional range search. We evaluate peer-to-peer networks derived from recently proposed works, introducing two novel metrics related to concurrency and contention, namely responsiveness and throughput. Our results highlight the impact of contention on these networks, and demonstrate that some studied networks do not scale in the presence of contention. Also, our results indicate that certain network properties believed to be desirable (e.g. uniform data distribution or peer accesses) may not be as critical as previously believed.
503 Small Intestinal Bacterial Overgrowth (SIBO) in Functional Dyspepsia (FD): Does Dyspeptic Symptom Pattern Make a Difference? (2019)

INTRODUCTION: FD is a common gastrointestinal disorder with poorly understood pathophysiology. Patients with FD and SIBO frequently overlap symptomatically. The prevalence of SIBO in patients with FD is not well studied, particularly in relation to the predominant FD symptom profile. We aimed to evaluate the prevalence of SIBO diagnosed by glucose breath test (GBT) in patients with FD and compare the SIBO prevalence in FD subtypes - Postprandial Distress Syndrome (PDS), Epigastric Pain Syndrome (EPS) or both (PDS+EPS). METHODS: Retrospective, tertiary center, study of patients fulfilling Rome criteria for FD, who completed GBT (2018-2019). Demographics, history, medications, and GBT findings were reviewed. Patients with documented structural disease (eg. neoplasm) were excluded. GI symptoms (including mid upper abdominal pain or burning, early satiety and postprandial fullness) were prospectively collected from all patients at the time of their GBT. Based on these responses, patients were classified into: 1. FD-PDS, 2. FD-EPS and 3. FD-PDS+EPS. A priori variables associated with SIBO were analyzed including: presence of diabetes, GERD, and gastroparesis; history of small bowel surgery or gastric bypass; use of opioids or proton pump inhibitors. Prior to GBT, patients had low carbohydrate diet (2 days), no antibiotics (30 days) and no tobacco (12 hrs). Positive GBT for SIBO was defined by ≥20 ppm H2 increase over basal within 90 min and/or ≥10 ppm CH4 increase at any time. Statistical methods included chi-square and t test. RESULTS: 737 consecutive patients were studied (mean age=51.6±17.6 years, 70% female, 88% Caucasian, mean BMI=28.4±7.1). No differences in demographic or a priori SIBO-associated variables were found between the 3 subgroups of FD patients ( P = NS). 31.4% of patients fulfilling criteria for FD had a GBT positive for SIBO. Individual gas (H2, CH4, or both) excretion responsible for a positive glucose HBT in each of the FD subgroups is shown on Table 1. There was no statistically significant difference in the prevalence of SIBO (by either H2, CH4 or both) between the three FD patient subtypes. There was borderline significant difference for slower H2 peak depicting a positive GBT in FD-PDS compared to FD-EPS and FD-EPS+PDS (83.8 vs. 70.7 vs. 65.7 minutes, P = 0.05). CONCLUSION: SIBO diagnosed by GBT is common in patients with FD regardless of the predominant symptomatic pattern. The prevalence of SIBO was similar in the three FD subtypes.
A Survey on I/O Virtualization and Optimization (2010)

This paper surveys virtualization of I/O devices, which is one of the most difficult parts in system virtualization. Current technologies of virtualizing I/O devices include full virtualization, paravirtualization, software emulation and VMM-bypass direct I/O. Optimizations are also done to improve the performance of each technology. Most optimizations used paravirtualization technology for reference. VMM-bypass direct I/O performs the best performance, but the VM direct-access I/O devices is difficult to be migrated, for it is hard to capture the states of the devices without VMM interference. An ideal approach is still required, and all the optimizations to the other approaches can be used for reference. We evaluated I/O performance in KVM and proposed some optimizations to improve KVM.
Clinical Utility of Cytomegalovirus Viral Load Testing for Predicting CMV Disease in D+/R- Solid Organ Transplant Recipients (2004)

Despite prophylaxis, cytomegalovirus (CMV) disease is common in donor seropositive (D+)/recipient seronegative (R-) transplant patients after cessation of prophylaxis. Early detection of CMV may allow for pre-emptive therapy to prevent active disease. The clinical utility of quantitative plasma viral load measurements for predicting CMV disease was determined in 364 D+/R- organ transplant patients receiving prophylaxis (100 d of valganciclovir or oral ganciclovir). Measurements were performed every 2 weeks until day 100 and at months 4, 4.5, 5, 6, 8 and 12 post-transplant. CMV disease occurred in 64 (17.6%) patients by 12 months. Using a positive cut-off value of >400 copies/mL, sensitivity was 38%, specificity 60%, positive predictive value 17%, and negative predictive value 82% for prediction of CMV disease. Therefore, routine monitoring would have predicted disease in only 24/64 (38%) patients. The test characteristics were not improved by changing the viral load cut-off point for defining a positive result. Similarly, single time point measures at the end of prophylaxis or month 4 had low sensitivity for disease prediction. Overall, regular CMV plasma viral load measurements were only of modest value in predicting CMV disease.
Simple partial purification of d‐pinitol from soybean leaves (2001)

There is growing interest in the use of D‐pinitol (D‐3‐ O ‐methyl‐ chiro ‐inositol) as a food supplement because of its reported efficacy in lowering blood glucose levels. Pinitol is a common constituent of legume plants and is a major component of soybean [ Glycine max (L.) Merr.] leaves. The objective of the studies was to identify a combination of simple methods that would result in the purification of pinitol from soybean leaves. Ethanolic extracts of soybean leaves following solvent partitioning to remove lipids, passage of the aqueous fraction through ion exchange resins, and treatment of the effluent with activated charcoal yielded a white crystalline product that was 85.5% pinitol by weight. Other components in the product included D‐ chiro ‐inositol (5.2%), myo‐inositol (3.4%), and ononitol (D‐4‐ O ‐methyl‐ myo ‐inositol; 1.9%). Thus, 96% of the crystalline product was cyclitols following the simple purification protocol.
Triarylamine‐Pyridine‐Carbonitriles for Organic Light‐Emitting Devices with EQE Nearly 40% (2021)

Highly efficient thermally activated delayed fluorescence (TADF) molecules are in urgent demand for solid-state lighting and full-color displays. Here, the design and synthesis of three triarylamine-pyridine-carbonitrile-based TADF compounds, TPAPPC, TPAmPPC, and tTPAmPPC, are shown. They exhibit excellent photoluminescence quantum yields of 79-100% with small ΔE<sub>ST</sub> values, fast reverse intersystem crossing (RISC), and high horizontal dipole ratios (Θ<sub>//</sub> = 86-88%) in the thin films leading to the enhancement of device light outcoupling. Consequently, a green organic light-emitting diode (OLED) based on TPAmPPC shows a high average external quantum efficiency of 38.8 ± 0.6%, a current efficiency of 130.1 ± 2.1 cd A<sup>-1</sup> , and a power efficiency of 136.3 ± 2.2 lm W<sup>-1</sup> . The highest device efficiency of 39.8% appears to be record-breaking among TADF-based OLEDs to date. In addition, the TPAmPPC-based device shows superior operation lifetime and high-temperature resistance. It is worth noting that the TPA-PPC-based materials have excellent optical properties and the potential for making them strong candidates for TADF practical application.
Modular interleaved carrier generator using a straightforward implementation method (2013)

This article presents a modular approach to generate the interleaved carriers of a parallel converters. Compared with previous solutions requiring accurate analog computations, a straightforward implementation of the generator is proposed here. By using only comparators and logical gates dedicated to the tuning of the carrier phase, a correct interleaving of the carriers is obtained in steady-state. The simplicity of the circuit offers the opportunity to implement it in a digital system. Connected together in a daisy-chain topology, the carrier generators communicate with its neighboring modules. This solution presents a complete modularity and allows reconfiguring the converter from a given number of legs to another without any additional consideration. In order to guarantee a proper start-up, some special cares on the setup of the carrier generators have to be considered. A study of the start-up is presented which ensure the system convergence for any number of legs.
InP Monolithically Integrated 1×8 Broadcast and Select Polarization Insensitive Switch for optical switching systems (2021)

For the first time we have designed and demonstrated polarization insensitive, high gain and broadband 1×8 broadcast and select switch suitable for optical packet switching system based on bulk SOAs integrated with passive elements.
Effect of Body Mass Index on Outcomes after Prepectoral Breast Reconstruction (2019)

Risk, II.
Summary of AH-1G flight vibration data for validation of coupled rotor-fuselage analyses (1986)

Under a NASA research program designated DAMVIBS (Design Analysis Methods for VIBrationS), four U. S. helicopter industry participants (Bell Helicopter, Boeing Vertol, McDonnell Douglas Helicopter, and Sikorsky Aircraft) are to apply existing analytical methods for calculating coupled rotor-fuselage vibrations of the AH-1G helicopter for correlation with flight test data from an AH-1G Operational Load Survey (OLS) test program. Bell Helicopter, as the manufacturer of the AH-1G, was asked to provide pertinent rotor data and to collect the OLS flight vibration data needed to perform the correlations. The analytical representation of the fuselage structure is based on a NASTRAN finite element model (FEM) developed by Bell which has been extensively documented and correlated with ground vibration tests.The AH-1G FEM was provided to each of the participants for use in their coupled rotor-fuselage analyses. This report describes the AH-1G OLS flight test program and provides the flight conditions and measured vibration data to be used by each participant in their correlation effort. In addition, the mechanical, structural, inertial and aerodynamic data for the AH-1G two-bladed teetering main rotor system are presented. Furthermore, modifications to the NASTRAN FEM of the fuselage structure that are necessary to make it compatible with the OLS test article are described. The AH-1G OLS flight test data was found to be well documented and provide a sound basis for evaluating currently existing analysis methods used for calculation of coupled rotor-fuselage vibrations.
Nonlinear ultrasound: Potential of the cross-correlation method for osseointegration monitoring (2012)

Recently the concept of probing nonlinear elasticity at an interface prosthesis/bone has been proposed as a promising method to monitor the osseointegration/sealing of a prosthesis. However, the most suitable method to achieve this goal is a point of debate. To this purpose, two approaches termed the scaling subtraction method and the cross-correlation method are compared here. One nonlinear parameter derived from the cross-correlation method is as sensitive as a clinical device based on linear elasticity measurement. Further, this study shows that cross-correlation based methods are more sensitive than those based on subtraction/addition, such like pulse inversion and similar methods.