gebhart/patrepeval huggingface dataset:
Analysis of Oxidation Sensitivity of Maleate<i>cis-trans</i>Isomerase from<i>Serratia marcescens</i> (2000)

The maleate cis-trans isomerase gene (maiA) from Serratia marcescens IFO3736 was cloned and sequenced. Serratia MaiA has 62.4% amino acid identity with Alcaligenes faecalis IFO13111 MaiA and 64.9% with Bacillus stearothermophilus MI-102 MaiA. All known ten amino acid sequences of MaiA had significant conserved regions containing cysteine residues, which were previously suggested to be involved in an active site of the enzyme. The maiA gene was expressed in Escherichia coli, and expressed products MaiA was purified and characterized. The purified enzyme of strain IFO3736 showed high activity at room temperature and high heat stability. It also showed higher activity in the presence of high concentration of aspartic acid than the enzyme of A. faecalis IFO13111, but it was also sensitive to chemical oxidation. By amino acid composition analysis, cysteine, methionine, and tyrosine residues were suggested to be oxidized to inactivate the enzyme by chemical oxidation. To investigate the mechanism of chemical oxidation of the enzyme, six methionine residues in the conserved regions of S. marcescens MaiA were replaced with cysteine residues by site-directed mutagenesis. The analysis of the constructed mutants suggested that the Met201 residue near the Cys198 residue is involved in the sensitivity of the enzyme to chemical oxidation.
Study on Catalytic Pyrolysis of Manchurian Ash for Production of Bio-Oil (2010)

Pyrolysis of Manchurian ash (Fraxinus mandshurica Rupr.) sawdust with four zeolite molecular sieve catalysts was performed on a thermogravimetric analyzer coupled with a Fourier transform infrared spectrometer. Pyrolysis of pure Manchurian ash and three main components, viz. cellulose, xylan, lignin, was also carried out as reference. The four zeolite catalysts investigated in this study (viz. HZSM-5, H-β, USY and Na-Y) all catalyze the dehydration reaction, restrain the release of volatiles, and obviously promote the final residue yields. Y-type catalysts show the most evident catalytic effect, such as restraining the formation of aldehydes, acids, and ethers, and promoting that of isoalkanes and aromatics. The preferred catalyst should have both high activity for deoxygenating and selectivity for hydrocarbon production.
From Scaling Disparities to Integrated Parallelism: A Decathlon for a Decade (2017)

Based on a variety of long-term network traffic data from different geographies and applications, in addition to long-term scaling trends of key information and communication technologies, we identify fundamental scaling disparities between the technologies used to generate and process data and those used to transport data. These disparities could lead to the data transport network falling behind its required capabilities by a factor of approximately 4 every five years. By 2024, we predict the need for 10-Tb/s optical interfaces working in 1-Pb/s optical transport systems. To satisfy these needs, multiplexing in both wavelength and space in the form of a wavelength-division multiplexing × space-division multiplexing matrix will be required. We estimate the characteristics of such systems and outline their target specifications, which reveals the need for very significant research progress in multiple areas, from system and network architectures to digital signal processing to integrated arrayed device designs, in order to avoid an optical network capacity crunch.
Previous studies underestimate BMAA concentrations in cycad flour (2009)

The traditional diet of the Chamorro people of Guam has high concentrations of the neurotoxin BMAA, beta-methyl-amino-L-alanine, in cycad tortillas and from animals that feed on cycad seeds. We measured BMAA concentration in washed cycad flour and compared different extraction methods used by previous researchers in order to determine how much BMAA may have been unaccounted for in prior research. Samples were analyzed with AQC precolumn derivatization using HPLC-FD detection and verified with UPLC-UV, UPLC-MS, and triple quadrupole LC/MS/MS. Although previous workers had studied only the free amino acid component of BMAA in washed cycad flour, we detected significant levels of protein-associated BMAA in washed cycad flour. These data support a link between ALS/PDC and exposure to BMAA.
Material Balance Depletion Models for Two-Phase and Vapor-Dominated Geothermal Reservoirs (1985)

Abstract Material balance calculations often referred to as "zero-dimensional" reservoir evaluations have been used extensively in petroleum and geothermal engineering. This paper presents a Havlena and Odeh-type1 material balance depletion model for two-phase reservoirs incorporating adsorption phenomena. A straight line, formed between groups of thermodynamic and adsorption properties of water and the cumulative production history provides the initial-fluid-in-place and the size of the vapor-dominated "steam cap". Adsorption phenomena were found by Economides and Hiller as the controlling mechanism in the depletion of vapor-dominated geothermal reservoirs. A material balance for vapor-dominated geothermal reservoirs, demonstrating the importance of adsorption phenomena is also presented. A straight line provides the initial-fluid-in-place.
Multimodal multiphoton and vibrational microscopy reveals early therapy-induced senescence in human tumors: a non-invasive tool to prevent the risk of cancer relapse (2023)

Recent studies have shown that common anticancer treatments can induce cell senescence rather than death, a critical phenotype governing tumor recurrence. This calls for the urgent development of safe, precise, and quick tools to unveil critical Therapy-Induced Senescence (TIS). Merging different coherent Raman and multiphoton techniques, we present label-free multimodal nonlinear optical (NLO) microscopy as a powerful tool to spot early TIS. We home-built a microscope including different NLO modalities: Stimulated Raman Scattering (SRS), forward and epi-detected Coherent Anti-Stokes Raman Scattering (CARS and E-CARS), and Two-Photon Excited Fluorescence (TPEF). The infrared laser source outputs synchronized narrowband 780 nm pump pulses and 950-1050 nm tunable Stokes pulses, so to match the CH-stretching region of the Raman spectrum. Thanks to the co-registration of these diverse techniques applied on label-free TIS cells and controls, we exposed quantitative hallmarks of early TIS, confirmed by comparing different optical signals monitored over 72 hours of treatment. TPEF from metabolic coenzymes combined with E-CARS from cardiolipin and cytochrome C indicated an early shrinking of mitochondria. CARS and SRS revealed lipid vesicles overproduction and accumulation. Nuclei enlarged irregularly, visualized via subtraction of SRS signals of proteins and lipids, and CARS from deoxyribose. We consider our results will strongly influence anticancer pre-clinical studies and translated clinical applications, helping to identify quickly, non-invasively, and quantitatively TIS in human tumors.
Assessing an ASCO Decision Aid for Improving the Accuracy and Attribution of Serious Adverse Event Reporting From Investigators to Sponsors (2019)

The Decision Aid shows promise as a method to improve the quality of SAE attribution, which may improve the detection of valid safety signals and reduce the administrative burden of uninformative investigational new drug safety reports. Study of the Decision Aid in a larger sample with analysis stratified by participant role and SAE reporting experience would further assess the tool's impact.
Powering the next industrial revolution: transitioning from nonrenewable energy to solar fuels<i>via</i>CO<sub>2</sub>reduction (2020)

Solar energy has been used for decades for the direct production of electricity in various industries and devices; however, harnessing and storing this energy in the form of chemical bonds has emerged as a promising alternative to fossil fuel combustion. The common feedstocks for producing such solar fuels are carbon dioxide and water, yet only the photoconversion of carbon dioxide presents the opportunity to generate liquid fuels capable of integrating into our existing infrastructure, while simultaneously removing atmospheric greenhouse gas pollution. This review presents recent advances in photochemical solar fuel production technology. Although efforts in this field have created an incredible number of methods to convert carbon dioxide into gaseous and liquid fuels, these can generally be classified under one of four categories based on how incident sunlight is utilised: solar concentration for thermoconversion (Category 1), transformation toward electroconversion (Category 2), natural photosynthesis for bioconversion (Category 3), and artificial photosynthesis for direct photoconversion (Category 4). Select examples of developments within each of these categories is presented, showing the state-of-the-art in the use of carbon dioxide as a suitable feedstock for solar fuel production.
DAMAD: Database, Attack, and Model Agnostic Adversarial Perturbation Detector (2021)

Adversarial perturbations have demonstrated the vulnerabilities of deep learning algorithms to adversarial attacks. Existing adversary detection algorithms attempt to detect the singularities; however, they are in general, loss-function, database, or model dependent. To mitigate this limitation, we propose DAMAD-a generalized perturbation detection algorithm which is agnostic to model architecture, training data set, and loss function used during training. The proposed adversarial perturbation detection algorithm is based on the fusion of autoencoder embedding and statistical texture features extracted from convolutional neural networks. The performance of DAMAD is evaluated on the challenging scenarios of cross-database, cross-attack, and cross-architecture training and testing along with traditional evaluation of testing on the same database with known attack and model. Comparison with state-of-the-art perturbation detection algorithms showcase the effectiveness of the proposed algorithm on six databases: ImageNet, CIFAR-10, Multi-PIE, MEDS, point and shoot challenge (PaSC), and MNIST. Performance evaluation with nearly a quarter of a million adversarial and original images and comparison with recent algorithms show the effectiveness of the proposed algorithm.
1Relay-assisted Multiple Access with Full-duplex Multi-Packet Reception (2016)

The effect of full-duplex cooperative relaying in a random access multiuser network is investigated here. First, we model the self-interference incurred due to full-duplex operation, assuming multi-packet reception capabilities for both the relay and the destination node. Traffic at the source nodes is considered saturated and the cooperative relay, which does not have packets of its own, stores a source packet that it receives successfully in its queue when the transmission to the destination has failed. We obtain analytical expressions for key performance metrics at the relay, such as arrival and service rates, stability conditions, and average queue length, as functions of the transmission probabilities, the self interference coefficient, and the links ’ outage probabilities. Furthermore, we study the impact of the relay node and the self-interference coefficient on the per-user and aggregate throughput, and the average delay per packet. We show that perfect self-interference cancelation plays a crucial role when the SINR threshold is small, since it may result to worse performance in throughput and delay comparing with the half-duplex case. This is because perfect self-interference cancelation can cause an unstable queue at the relay under some conditions.
Development of kinetic energy harvesting systems for vehicle applications (2011)

This work demonstrates the implementation of a functional kinetic energy harvester designed to power wireless sensor electronics used in vehicular applications. The design, fabrication, and experimental characterization of a complete electrodynamic (magnetic) energy harvesting system capable of delivering in excess of 10 mW from 100 milli-g's of acceleration is presented. Unlike previous energy harvesting research, which typically focuses on individual components for proof-of-concept testing, the system implemented for this work includes the integration of a low-frequency transducer, power electronics circuitry, and a rechargeable storage element, all of which are required for a functional system. The design trade-offs, which result from the integration of these system components are examined and design rules for maximizing efficiency are given. Finally, field testing is presented, which demonstrates the ability of the system to operate over a range of different vehicle speeds.
Observation of a Resonant Structure near the <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:msubsup><mml:mi>D</mml:mi><mml:mi>s</mml:mi><mml:mo>+</mml:mo></mml:msubsup><mml:msubsup><mml:mi>D</mml:mi><mml:mi>s</mml:mi><mml:mo>−</mml:mo></mml:msubsup></mml:math> Threshold in the <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msup><mml:mrow><mml:mi>B</mml:mi></mml:mrow><mml:mrow><mml:mo>+</mml:mo></mml:mrow></mml:msup><mml:mo stretchy="false">→</mml:mo><mml:msubsup><mml:mrow><mml:mi>D</mml:mi></mml:mrow><mml:mrow><mml:mi>s</mml:mi></mml:mrow><mml:mrow><mml:mo>+</mml:mo></mml:mrow></mml:msubsup><mml:msubsup><mml:mrow><mml:mi>D</mml:mi></mml:mrow><mml:mrow><mml:mi>s</mml:mi></mml:mrow><mml:mrow><mml:mo>−</mml:mo></mml:mrow></mml:msubsup><mml:msup><mml:mrow><mml:mi>K</mml:mi></mml:mrow><mml:mrow><mml:mo>+</mml:mo></mml:mrow></mml:msup></mml:mrow></mml:math> Decay (2023)

: An amplitude analysis of the B^{+}→D_{s}^{+}D_{s}^{-}K^{+} decay is carried out to study for the first time its intermediate resonant contributions, using proton-proton collision data collected with the LHCb detector at center-of-mass energies of 7, 8, and 13 TeV. A near-threshold peaking structure, referred to as X(3960), is observed in the D_{s}^{+}D_{s}^{-} invariant-mass spectrum with significance greater than 12 standard deviations. The mass, width, and the quantum numbers of the structure are measured to be 3956±5±10 MeV, 43±13±8 MeV, and J^{PC}=0^{++}, respectively, where the first uncertainties are statistical and the second systematic. The properties of the new structure are consistent with recent theoretical predictions for a state composed of cc[over ̄]ss[over ̄] quarks. Evidence for an additional structure is found around 4140 MeV in the D_{s}^{+}D_{s}^{-} invariant mass, which might be caused either by a new resonance with the 0^{++} assignment or by a J/ψφ↔D_{s}^{+}D_{s}^{-} coupled-channel effect.
Effects of adjuvant exemestane versus anastrozole on bone mineral density for women with early breast cancer (MA.27B): a companion analysis of a randomised controlled trial (2020)

Treatment of breast cancer with aromatase inhibitors is associated with damage to bones. NCIC CTG MA.27 was an open-label, phase 3, randomised controlled trial in which women with breast cancer were assigned to one of two adjuvant oral aromatase inhibitors—exemestane or anastrozole. We postulated that exemestane—a mildly androgenic steroid—might have a less detrimental effect on bone than non-steroidal anastrozole. In this companion study to MA.27, we compared changes in bone mineral density (BMD) in the lumbar spine and total hip between patients treated with exemestane and patients treated with anastrozole.
CALCIUM ALTERATIONS IN ALZHEIMER'S DISEASE: PATHOPHYSIOLOGY, MODELS AND THERAPEUTIC OPPORTUNITIES (1999)

Calcium plays a pivotal role in mediating many important biological functions. The intracellular calcium concentration is tightly regulated by a variety of systems and mechanisms. Calcium is sequestered by various organelles such as mitochondria and/or endoplasmic reticulum and extruded across the plasma membrane by energy-dependent transport systems. Different Ca2+-binding proteins are also involved in these processes. Alterations in calcium homeostasis might be critically implicated in brain aging and in the neuropathology of Alzheimer's disease (AD). In fact, one of the postulated mechanisms of beta-amyloid toxicity seems to involve a Ca2+ dysregulation accompanied with enhanced vulnerability to excitotoxic stimuli. Although brain characteristic lesions-plaques and tangles-constitute the hallmarks of AD, accumulated evidence suggests the systemic feature of this disease. Therefore peripheral cell lines may represent a useful approach to explore the cellular pathophysiology of AD, including calcium alterations and associated phenomena.
Non-covalent double functionalization of carbon nanotubes with a NADH oxidation Ru(<scp>ii</scp>)-based molecular catalyst and a NAD-dependent glucose dehydrogenase (2014)

We report the double functionalization of multiwalled carbon nanotube electrodes by two functional pyrene molecules. In combination, an immobilized Ru(II)-based NADH oxidation catalyst and glucose dehydrogenase achieve highly efficient glucose oxidation with low overpotential of -0.10 V and high current densities of 6 mA cm(-2).
Introduction to CYBERLEGs: Hardware and Control (2014)

There is a growing need to assist those who have suffered an amputation due to vascular diseases, especially in those who have general lower limb weakness and need additional assistance to retain independence and overall quality of life. The CYBERLEGs system is a new artificial physical and cognitive lower-limb replacement system for dysvascular transfemoral amputees intended for assistance in activities of daily living. By lowering the cognitive and metabolic effort of using a prosthetic system, CYBERLEGs is intended to increase the number of amputees using prosthetic systems as well as expand the capabilities of those who use currently available technology.
DNA Vaccination (2003)

This unit details some of the key methods for setting up and testing DNA vaccines in animal models. The basic procedures are discussed, as well as alternative methods that have been developed over the past several years. The Basic Protocol gives step-by-step instructions for administering the DNA vaccine via intramuscular injection of the quadriceps muscle, while an alternate procedure details injection of the anterior tibialis.
Novel Palladium-Catalyzed Biaryl Synthesis with Haloarenes (1991)

Novel palladium-catalyzed couplings of bromo- and iodoarenes to give biaryls were accomplished in the presence of equimolar amounts of trialkylamine. Bromoarenes require triphenylarsine as cocatalyst. The trialkylamine was found to cause dehalogenation of haloarenes as a side reaction.
&lt;title&gt;Relating binary and continuous problem entropy to backpropagation network architecture&lt;/title&gt; (1991)

The research presented focuses on characterization of problems, with emphasis on process control data, as they relate to backpropagation neural network architectures, particularly contrasting one and two hidden layers networks. The effects of architecture alterations on network convergence, performance, and stability are empirically examined for continuous and binary domains. Shannon entropy for binary sets and statistical complexity for continuous sets are calculated and related to optimal architecture.© (1991) COPYRIGHT SPIE--The International Society for Optical Engineering. Downloading of the abstract is permitted for personal use only.
An Improved Non-Regression Coefficients Method in Finding Sea Surface Temperature With a VHRR Data (2001)

Yu and Barton proposed a non-regression-coefficient method in improving the accuracy of routine sea surface temperature retrievals through satellite data, which are then applied to sea surface temperature estimation models such as MCSST or CPSST algorithms. Their method involves a parameter called R54(=∆T5/∆T4), which is derived from the ratio of neighborhood temperature variances from two window channels in the thermal IR region. Due to the fact that statistical calculations were used in the derivation for the value of R54, the method is not applicable in various real cases. The aim of this study is to retain the advantage of their method in terms of its physical considerations and derivations, while providing an alternative in improving the calculations of R54. In this study, a spatial coherence method is also used to mask cloudy areas, and an improved three-point method was brought in to determine the clear-sky brightness temperature. A NOAA-12 AVHRR data set partially covered with clouds was used to estimate a 100 × 100 longitude-latitude SST map of the Taiwan area, which were compared with 61 ship-measured SSTs, as well as SST retrievals estimated by Chen, MCSST and CPSST. The results reveal improvements in the 0.8K RMSE and 0.1K bias SST map. The accuracy levels also grew higher, especially for partially cloud-contaminated cases. Moreover, this study can further produce maps regarding the amount of clouds present, or the temperature distribution of the cloud-tops for related research.
Single-camera PTV within interfacially sheared drops in microgravity (2023)

Abstract Development of experimental methods for in situ particle tracking velocimetry (PTV) is fundamental for allowing measurement of moving systems non-tailored for velocimetry. This investigation focuses on the development of a post-processing methodology for single-camera PTV, without laser-sheet illumination, tracking native air-bubbles as tracer particles within a liquid drop of human insulin in microgravity. This PTV scenario was facilitated by microgravity technology known as the ring-sheared drop (RSD), aboard the International Space Station, which produced an optical imaging scenario and fluid flow geometry suitable as a testbed for PTV research. The post processing methodology performed included five steps: (i) physical system characterization and native air-bubble tracer identification, (ii) image projection and single-camera calibration, (iii) depth determination and 3D particle position determination, (iv) ray tracing and refraction correction, and (v) particle history and data expansion for suboptimal particles. Overall, this post processing methodology successfully allowed for a total of 1,085 particle measurements in a scenario where none were previously possible. Such post processing methodologies have promise for application to other in situ PTV scenarios allowing better understanding of physical systems whose flow is difficult to measure and or where PTV-specific optical elements (such as laser lights sheets and dual camera setups) are not permissible due to physical or safety constraints.
Closing the gap between stochastic and rule-based LFG grammars (2010)

Developing large-scale deep grammars in a constraint-based framework such as Lexical Functional Grammar (LFG) is time-consuming and requires significant linguistic insight. Recently, treebank-based constraint-grammar acquisition
approaches have been developed as an alternative to hand-crafting such resources. While treebank-based approaches are wide coverage and robust and achieve competitive evaluation results for many languages, the granularity of the linguistic analyses provided by treebank-based resources
tends to be less fine-grained than what is offered by state-of-the-art handcrafted grammars. This paper presents an approach to extend the English DCU LFG annotation algorithm with more detailed f-structure information to provide probabilistic treebank-based LFG grammars with rich feature information comparable to that implemented by the hand-crafted English XLE grammar, while maintaining the robustness and the coverage of treebankbased stochastic grammars.