gebhart/patrepeval huggingface dataset:
Kinetic and Crystallographic Analysis of the Key Active Site Acid/Base Arginine in a Soluble Fumarate Reductase (2001)

There is now overwhelming evidence supporting a common mechanism for fumarate reduction in the respiratory fumarate reductases. The X-ray structures of substrate-bound forms of these enzymes indicate that the substrate is well positioned to accept a hydride from FAD and a proton from an arginine side chain. Recent work on the enzyme from Shewanella frigidimarina [Doherty, M. K., Pealing, S. L., Miles, C. S., Moysey, R., Taylor, P., Walkinshaw, M. D., Reid, G. A., and Chapman, S. K. (2000) Biochemistry 39, 10695-10701] has strengthened the assignment of an arginine (Arg402) as the proton donor in fumarate reduction. Here we describe the crystallographic and kinetic analyses of the R402A, R402K, and R402Y mutant forms of the Shewanella enzyme. The crystal structure of the R402A mutant (2.0 A resolution) shows it to be virtually identical to the wild-type enzyme, apart from the fact that a water molecule occupies the position previously taken by part of the guanidine group of R402. Although structurally similar to the wild-type enzyme, the R402A mutant is inactive under all the conditions that were studied. This implies that a water molecule, in this position in the active site, cannot function as the proton donor for fumarate reduction. In contrast to the R402A mutation, both the R402K and R402Y mutant enzymes are active. Although this activity was at a very low level (at pH 7.2 some 10(4)-fold lower than that for the wild type), it does imply that both lysine and tyrosine can fulfill the role of an active site proton donor, albeit very poorly. The crystal structures of the R402K and R402Y mutant enzymes (2.0 A resolution) show that distances from the lysine and tyrosine side chains to the nearest carbon atom of fumarate are approximately 3.5 A, clearly permitting proton transfer. The combined results from mutagenesis, crystallographic, and kinetic studies provide formidable evidence that R402 acts as both a Lewis acid (stabilizing the build-up of negative charge upon hydride transfer from FAD to fumarate) and a Brønsted acid (donating the proton to the substrate to complete the formation of succinate).
A survey of image quality measures (2009)

Image quality assessment is one of the challenging field of digital image processing system. It can be done subjectively or objectively. PSNR is the most popular and widely used objective image quality metric but it is not correlate well with the subjective assessment. Thus, there are a lot of objective image quality metrics (IQM) developed in the past few decades to replace PSNR. This paper provides a literature review of the current subjective and objective image quality measures. The purpose of this paper is to collect reported quality metrics and group them according to their strategies and techniques.
A design optimization procedure for high-speed prop-rotors (1992)

An optimization procedure has been developed to address the complex and conflicting design requirements associated with high-speed prop-rotor design. The procedure involves the couplings of aerodynamic performance and aeroelastic stability inside a closed-loop procedure. Both high-speed cruise and hover design requirements are addressed. The objective is to maximize the propulsive efficiency in axial flight while maintaining a significant figure of merit in hover. Constraints are also imposed on the aeroelastic stability in axial flight. Both structural and planform design variables are used. The optimization procedure yields significant improvements in the aerodynamic characteristics of the rotor.
Copy or Discard execution model for speculative parallelization on multicores (2008)

The advent of multicores presents a promising opportunity for speeding up sequential programs via profile-based speculative parallelization of these programs. In this paper we present a novel solution for efficiently supporting software speculation on multicore processors. We propose the Copy or Discard (CorD) execution model in which the state of speculative parallel threads is maintained separately from the nonspeculative computation state. If speculation is successful, the results of the speculative computation are committed by copying them into the non-speculative state. If misspeculation is detected, no costly state recovery mechanisms are needed as the speculative state can be simply discarded. Optimizations are proposed to reduce the cost of data copying between nonspeculative and speculative state. A lightweight mechanism that maintains version numbers for non-speculative data values enables misspeculation detection. We also present an algorithm for profile-based speculative parallelization that is effective in extracting parallelism from sequential programs. Our experiments show that the combination of CorD and our speculative parallelization algorithm achieves speedups ranging from 3.7 to 7.8 on a Dell PowerEdge 1900 server with two Intel Xeon quad-core processors.
ChemInform Abstract: A MODIFIED METHOD FOR THE SYNTHESIS OF 1,2‐BENZISOXAZOLES (1978)

Abstract Es wird die Cyclisierung von o‐Hydroxyarylketoximacetaten durch Sieden mit trockenem Pyridin zu 1,2‐Benzisoxazolen beschrieben.
Ligand Adsorption/Desorption on Sterically Stabilized InP Colloidal Nanocrystals: Observation and Thermodynamic Analysis (2006)

Macroscopic characterisation: The adsorption/desorption equilibrium of trioctylphosphine oxide ligands at colloidal InP nanocrystals (see picture) is investigated with quantitative, one-dimensional 1H NMR spectroscopy. Thermodynamic analysis of the isotherm demonstrates that formation of the capping is driven by favorable adsorbate–substrate interactions and is strengthened by adsorbate–adsorbate interactions. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2267/2006/z500659_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Electrochemical Generation of Free Nitric Oxide from Nitrite Catalyzed by Iron meso-Tetrakis(4-N-methylpyridiniumyl)porphyrin (2004)

Electrochemical generation of free nitric oxide (NO) from nitrite (NO(2)(-)) catalyzed by iron meso-tetrakis(4-N-methylpyridiniumyl)porphyrin, [Fe(III)(TMPyP)](5+), has been developed in this study. To obtain free NO, a cathodic electrolysis and an anodic electrolysis were performed in two connected flow electrolytic cells in sequence. The flow electrolytic cell upstream was used for cathodic electrolysis, where the solution of [Fe(III)(TMPyP)](5+) and NO(2)(-) was reduced at -0.25 V (vs Ag/AgCl) into [Fe(II)(NO(2)(-))(2)(TMPyP)](2+) and [Fe(II)(NO)(TMPyP)](4+) in sequence. The flow electrolytic cell downstream was utilized for anodic electrolysis, where [Fe(II)(NO)(TMPyP)](4+) formed from the upstream cell was oxidized at +0.40 V (vs Ag/AgCl) into [Fe(III)(TMPyP)](5+) and free NO. Finally, NO was bubbled out from anodic electrolyte by argon gas. The mechanism and the optimum conditions for electrochemical generation of NO from NO(2)(-) catalyzed by [Fe(III)(TMPyP)](5+) were studied in detail by voltammetric and spectroelectrochemical methods.
SC3 and SC4 hydrophobins have distinct roles in formation of aerial structures in dikaryons of Schizophyllum commune (2000)

Two monokaryons of Schizophyllum commune can form a fertile dikaryon when the mating-type genes differ. Monokaryons form sterile aerial hyphae, while dikaryons also form fruiting bodies that function in sexual reproduction. The SC3 hydrophobin gene is expressed both in monokaryons and in dikaryons. The SC4 hydrophobin is dikaryon specific. In the monokaryon, SC3 lowers the water surface tension, coats aerial hyphae with a hydrophobic layer and mediates attachment of hyphae to hydrophobic surfaces. The SC4 protein lines gas channels within fruiting bodies with a hydrophobic membrane. Using gene disruptions, in this study, we show that in dikaryons SC3 fulfils the same roles as in monokaryons. SC4, on the other hand, has a role within fruiting bodies. In contrast to gas channels in fruiting bodies of the wild type, those of a DeltaSC4 strain easily filled with water. Thus, SC4 prevents gas channels filling with water under wet conditions, probably serving uninterrupted gas exchange. Other dikaryon-specific hydrophobin genes, SC1 and SC6, apparently do not substitute for the SC4 gene. In addition, by expressing the SC4 gene behind the SC3 promoter in a DeltaSC3 monokaryon, it was shown that SC4 cannot fully substitute for SC3, indicating that both hydrophobins evolved to fulfil specific functions.
Long-term persistence of monotypic dengue transmission in small size isolated populations, French Polynesia, 1978-2014 (2020)

Understanding the transition of epidemic to endemic dengue transmission remains a challenge in regions where serotypes co-circulate and there is extensive human mobility. French Polynesia, an isolated group of 117 islands of which 72 are inhabited, distributed among five geographically separated subdivisions, has recorded mono-serotype epidemics since 1944, with long inter-epidemic periods of circulation. Laboratory confirmed cases have been recorded since 1978, enabling exploration of dengue epidemiology under monotypic conditions in an isolated, spatially structured geographical location. A database was constructed of confirmed dengue cases, geolocated to island for a 35-year period. Statistical analyses of viral establishment, persistence and fade-out as well as synchrony among subdivisions were performed. Seven monotypic and one heterotypic dengue epidemic occurred, followed by low-level viral circulation with a recrudescent epidemic occurring on one occasion. Incidence was asynchronous among the subdivisions. Complete viral die-out occurred on several occasions with invasion of a new serotype. Competitive serotype replacement has been observed previously and seems to be characteristic of the South Pacific. Island population size had a strong impact on the establishment, persistence and fade-out of dengue cases and endemicity was estimated achievable only at a population size in excess of 175 000. Despite island remoteness and low population size, dengue cases were observed somewhere in French Polynesia almost constantly, in part due to the spatial structuration generating asynchrony among subdivisions. Long-term persistence of dengue virus in this group of island populations may be enabled by island hopping, although could equally be explained by a reservoir of sub-clinical infections on the most populated island, Tahiti.
Phytoestrogens and bone health at different reproductive stages (2013)

The present review suggests that isoflavone increase bone mineral density and decrease the bone turnover resorption markers. The effect of soy isoflavones on BMD is mediated by equol production, reproductive status, supplement type, isoflavone dose and intervention duration.
REAL-TIME ANORMALY DETECTION OF RIVER WATER LEVEL OBSERVATION BASED ON PROBABILITY DISTRIBUTION OF WATER LEVEL ESTIMATION ERROR (2019)

水位計による河川水位のオリジナル観測データには，各種の異常値が含まれる．観測水位の異常値は，防災対応の判断や洪水予測システムに致命的なエラーを引き起こす可能性があるが，リアルタイムでの異常検知は十分に行われていない．本研究では，10分毎に観測所から配信される河川水位データを対象として，リアルタイムに異常値を検出する技術を開発した．機械学習による水位推定手法の技術を用いて，周辺の水位・雨量状況から対象とする観測地点の現時刻の水位を推定し，実観測データとの乖離度合いから異常度を算出した．さらにルールベースによる異常検知と組み合わせ，検知性能の向上を図った．九州管内の実データを用いて提案手法の精度検証を行い，既存手法と比較して高い検知性能を確認した．
Dlouhodobé výsledky alogenních transplantací krvetvorných buněk u 533 pacientů s různými hematologickými malignitami – zkušenost jednoho centra (2018)

Dlouhodobe výsledky alogennich transplantaci krvetvorných buněk u 533 pacientů s různými hematologickými malignitami – zkusenost jednoho centra, Dlouhodobe výsledky alogennich transplantaci krvetvorných buněk u 533 pacientů s různými hematologickými malignitami – zkusenost jednoho centra.
Optical fibers for communication (1973)

The transparency of glass fibers in the visible and near infrared—improved beyond all expectations by recent breakthroughs—seems now sufficient to transmit optical signals unprocessed over miles. No wonder that efforts have intensified all over the world to utilize fibers in future communication systems. Materials research and fabrication are the fields where present progress is most rapid. New ways of preform preparation by deposition, doping, or diffusion are being studied and found to offer improvements and versatility. As far as materials are concerned, fused silica has shown the lowest bulk losses and hence receives the most interest, but many glasses are being studied as well. As new processes become available and record lows in fiber loss are being reached, propagation theory is finding new challenges as well. On the one hand, multimode fibers seem desirable with respect to transmitter compatibility, splicing, and fabrication tolerances. On the other hand, the signal distortion caused by mode delay differences in multimode fibers can be considerable and requires equalization—inherent in the fiber or at the fiber end. Beyond that, the wavelength dependence of the refractive index produces dispersion effects serious enough to be of importance. Thinking ahead, one is confronted with the question of fiber handling, strength, and life. The technology of making cables and splices from a brittle material like glass is in its infancy, and we can only indicate the extent of these difficult problems ahead.
Mid-scale biocemented soil columns via enzyme-induced carbonate precipitation (EICP) (2021)

Biocemented soil columns were created at a reduced scale (mid-scale) using enzyme-induced carbonate precipitation (EICP) as a prelude to field scale deployment. Approximately 0.3 m diameter × 0.75 m long columns were created using a tube-à-manchette grouting technique in 0.6 m × 0.6 m × 1.2 m boxes filled with a dry washed quarry sand. Treatment solution composition and treatment protocol, including number of cycles of treatment and time interval between cycles, were established based upon laboratory testing. The urease enzyme used in the treatment solution was extracted from jack beans in a just-in-time manner on site. The biocemented soil columns were characterized in situ using shear wave velocity, needle penetrometer and pocket penetrometer testing, dimensional measurements, and by unconfined compression strength (UCS) and carbonate content measurements on specimens recovered from the columns. The in situ measurements indicated the target UCS of 500 kPa was achieved. However, the UCS tests on recovered specimens had inconsistent results, which may be attributed to sample disturbance. Overall, the results demonstrate that EICP is a viable method for creating biocemented soil columns for ground improvement.
Interleukin-17 Induces Hyperresponsive Interleukin-8 and Interleukin-6 Production to Tumor Necrosis Factor-α in Structural Lung Cells (2005)

Lung epithelial cells contribute to local inflammation by the production of pro-inflammatory mediators like interleukin (IL)-8 and IL-6. Although their production depends on gene transcription, previous studies showed that post-transcriptional mechanisms modulate IL-8 and IL-6 production. Human lung epithelial cells turn from normoresponsive into hyperresponsive IL-8- and IL-6-producing cells when their IL-8 and IL-6 mRNA degradation is reduced. We hypothesized that IL-17, a mediator predominantly released by memory T cells and present in airways of individuals with asthma, would modulate rather than induce IL-8 and IL-6 production by both human lung epithelial cells and fibroblasts. We show here for both cell types that IL-17 was a weak stimulus of IL-8 and IL-6 production, but markedly enhanced IL-8 and IL-6 responses to another stimulus, such as tumor necrosis factor-alpha. This modulatory effect of IL-17 was paralleled by a reduced IL-8 and IL-6 mRNA degradation, with no effect on IL-8 and IL-6 gene transcription. In conclusion, IL-17 particularly affects post-transcriptional regulation of IL-8 and IL-6 expression leading to enhanced IL-8 and IL-6 responses to secondary stimuli, and is only a weak proinflammatory stimulus by itself. This poses the interesting concept that by releasing IL-17 from memory T cells, the adaptive immune system instructs lung structural cells as part of the innate immune system to respond more vigorously.
Lipopolysaccharide-Induced Suppression of Airway Th2 Responses Does Not Require IL-12 Production by Dendritic Cells (2003)

The prevalence of atopic asthma, a Th2-dependent disease, is reaching epidemic proportions partly due to improved hygiene in industrialized countries. There is an inverse correlation between the level of environmental endotoxin exposure and the prevalence of atopic sensitization. As dendritic cells (DC) have been implicated in causing sensitization to inhaled Ag, we studied the effect of endotoxin on Th2 development induced by bone marrow DC in vitro and by intratracheal injection in vivo, with particular emphasis on the role played by the polarizing cytokine IL-12. Bone marrow-derived DC stimulated with Escherichia coli O26:B6 LPS produced IL-12p70 for a limited period of time, after which production became refractory to further stimulation with CD40 ligand, a phenomenon previously called "exhaustion." The level of IL-12 production of DC did not correlate with Th1 development, as exhausted OVA-pulsed DC were still capable of shifting the cytokine pattern of responding OVA-specific Th cells toward Th1 in vitro and in vivo. When mice were first immunized by intratracheal injection of OVA-DC and subsequently challenged with OVA aerosol, prior in vitro stimulation of DC with LPS reduced the development of airway eosinophilia and Th2 cytokine production. Most surprisingly, the capacity of LPS to reduce Th2-dependent eosinophilic airway inflammation was IL-12-independent altogether, as IL-12p40 knockout DC had a similar reduced capacity to prime for Th2 responses. These results suggest that LPS reduces sensitization to inhaled Ag by reducing DC-driven Th2 development, but that IL-12 is not necessary for this effect.
Novel zero-current-transition PWM converters (1994)

A new family of zero-current-transition (ZCT) pulsewidth-modulated (PWM) converters is proposed. The new family of converters implements zero-current turn-off for power transistor(s) without increasing voltage/current stresses and operates at a fixed frequency. The proposed converters are deemed most suitable for high-power applications where the minority-carrier semiconductor devices (such as IGBTs, BJTs, and MCTs) are predominantly used as the power switches. Theoretical analysis is verified on a 100 kHz, 1 kW ZCT-PWM boost converter using an IGBT.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Dual energy x-ray laser measurement of calcaneal bone mineral density (2003)

In dual energy x-ray absorptiometry (DXA) the photon attenuation is assumed to be similar in soft tissue overlying, adjacent to and inside the measured bone. In the calcaneal dual energy x-ray laser (DXL) technique, this assumption is not needed as attenuation by soft tissues at the local bone site is determined by combining DXA and heel thickness measurements. In the present study, 38 subjects were measured with DXL Calscan, Lunar PIXI and Lunar DPX-IQ DXA instruments and Hologic Sahara ultrasound instrument, and the performance and agreement of the instruments were analysed. Furthermore, numerical simulations on the effect of non-uniform fat-to-lean tissue ratio within soft tissue in heel were conducted. In vivo short-term precision (CV%, sCV%) of DXL Calscan (1.24%, 1.48%) was similar to that of Lunar PIXI (1.28%, 1.60%). Calcaneal areal bone mineral densities (BMD, g cm(-2)) measured using DXL Calscan and Lunar PIXI predicted equally well variations in BMD of femoral neck (r2 = 0.63 and 0.52, respectively) or lumbar spine (r2 = 0.61 and 0.64, respectively), determined with Lunar DPX-IQ. BMD values measured with DXL Calscan were, on average, 19% lower (p < 0.01) than those determined with Lunar PIXI. Interestingly, the difference in BMD values between instruments increased as a function of body mass index (BMI) (r2 = 0.17, p < 0.02) or heel thickness (r2 = 0.37, p < 0.01). Numerical simulations suggested that the spatial variation of soft tissue composition in heel can induce incontrollable inaccuracy in BMD when measured with the DXA technique. Theoretically, in contrast to DXA instruments, elimination of the effect of non-uniform soft tissue is possible with DXL Calscan.
Challenges in Understanding and Predictive Modeling of Plasma Assisted Combustion (2015)

Key challenges to quantitative insight into fuel-air plasma kinetics, as well as plasma assisted ignition and flameholding, are identified and assessed based on the results of recent experimental and kinetic modeling studies. Experimental and modeling approaches to address these critical issues are discussed. The results have major implications for fundamental understanding of pulsed electric discharge dynamics, molecular energy transfer in reacting flows, plasma chemical reactions, and development of low-temperature plasma assisted combustion technologies.
A Representation for Error Detection and Recovery in Robot Task Plans (1990)

A flexible robotic assembly cell will have to deal with error detection, diagnosis and recovery. Much of the literature in this area to date has concentrated on devising specific algorithms for detection and recovery, and has largely ignored the central issues of (1) determining what needs to be represented in order to deal with the problem of detecting and recovering from errors and (2) building an appropriate general representation. We begin our work by defining the components of the error detection and recovery problem and by defining what kinds of errors can reasonably be detected. We then construct a generally applicable representation for error detection and recovery information that supports these definitions. The representation, which is based on our previous work on task grammars16, is similar to Donald&apos;s3 notation of an EDR plan. We use RS, a process-based model for representing task plans11, as the underlying &apos;vocabulary&apos; to describe our representation concisely. We evaluate our representation by applying it to the following problems: 1. Distinguishing between planned decision-making and error detection so that the two are not intermixed arbitrarily in a plan. 2. Developing a hierarchical structuring to allow localized error detection and recovery. 3. Gracefully handling errors that cannot be diagnosed. 4. Performing error monitoring on the error monitoring system. Although some formal material is included here, the main emphasis in this paper will be on the representational advantages of our approach.
Generating Sentences by Editing Prototypes (2018)

We propose a new generative language model for sentences that first samples a prototype sentence from the training corpus and then edits it into a new sentence. Compared to traditional language models that generate from scratch either left-to-right or by first sampling a latent sentence vector, our prototype-then-edit model improves perplexity on language modeling and generates higher quality outputs according to human evaluation. Furthermore, the model gives rise to a latent edit vector that captures interpretable semantics such as sentence similarity and sentence-level analogies.
Mixed reality holograms for heart surgery planning: first user experience in congenital heart disease (2018)

This preliminary study demonstrates that MR holograms as surgical planning tool for congenital heart disease may have a high diagnostic value and contribute to understanding complex morphology. The first users experience of the hologram presentation was found to be very positive, with a preference among the female and the younger users. There is potential for improvement of the hologram manipulation tools.