gebhart/patrepeval huggingface dataset:
Pyrolysis and Gasification Experiments of Biomass Under Elevated Pressure Condition (2007)

This paper reports on the pyrolysis and CO2-gasification of various biomass materials in a pressurized thermobalance. In particular, the primary yields of total volatiles, tar and non-condensable gases, together with the composition of non-condensable gases, are measured as a function of temperature at 1 atm and 10.8 ata. The use of a high-intensity infrared heating source, in conjunction with a non-absorbing carrier gas (viz. argon), is reported to reduce the significance of secondary gas-phase pyrolysis reactions. Linear trends with atomic H/C ratio are observed in the tar yield, total volatile yield and CH4 yield during pyrolysis. The gasification kinetics of biomass chars (pyrolysed to 700°C at a medium heating rate) have also been measured by measuring the rate of weight loss during reaction with CO2 as a function of temperature. First-order kinetic rate constants are then determined by fitting the weight loss data using a random pore model. The results indicate that the reactivity of the biomass materials is intermediate between lignin and cellulose and that they are much more reactive than a black coal char.
Quantitative Proteomics and Dynamic Imaging of the Nucleolus Reveal Distinct Responses to UV and Ionizing Radiation (2011)

The nucleolus is a nuclear organelle that coordinates rRNA transcription and ribosome subunit biogenesis. Recent proteomic analyses have shown that the nucleolus contains proteins involved in cell cycle control, DNA processing and DNA damage response and repair, in addition to the many proteins connected with ribosome subunit production. Here we study the dynamics of nucleolar protein responses in cells exposed to stress and DNA damage caused by ionizing and ultraviolet (UV) radiation in diploid human fibroblasts. We show using a combination of imaging and quantitative proteomics methods that nucleolar substructure and the nucleolar proteome undergo selective reorganization in response to UV damage. The proteomic responses to UV include alterations of functional protein complexes such as the SSU processome and exosome, and paraspeckle proteins, involving both decreases and increases in steady state protein ratios, respectively. Several nonhomologous end-joining proteins (NHEJ), such as Ku70/80, display similar fast responses to UV. In contrast, nucleolar proteomic responses to IR are both temporally and spatially distinct from those caused by UV, and more limited in terms of magnitude. With the exception of the NHEJ and paraspeckle proteins, where IR induces rapid and transient changes within 15 min of the damage, IR does not alter the ratios of most other functional nucleolar protein complexes. The rapid transient decrease of NHEJ proteins in the nucleolus indicates that it may reflect a response to DNA damage. Our results underline that the nucleolus is a specific stress response organelle that responds to different damage and stress agents in a unique, damage-specific manner.
Fully Automated 96-Well Liquid−Liquid Extraction for Analysis of Biological Samples by Liquid Chromatography with Tandem Mass Spectrometry (2000)

A fully automated high-throughput liquid−liquid extraction (LLE) methodology has been developed for preparation of biological samples using a 96-well LLE plate and a 96-channel robotic liquid handling workstation. The 96-well LLE plate is made of a 96-well filter plate filled with inert diatomaceous earth particles, allowing continuous and efficient extraction of analytes between the aqueous biological sample and the organic extraction solvent. Two carboxylic acid-based protease inhibitor compounds with high and low levels of plasma protein binding were chosen for the development and application of the automated methodology. The LLE extracts of the plasma samples of the two compounds were analyzed by high-performance liquid chromatography with electrospray (ESI) tandem mass spectrometry (LC−MS/MS). The LC−MS/MS method was developed using a rapid gradient LC separation, followed by sample introduction through an ionspray interface in the negative ion mode and tandem mass spectrometric detection with selected reaction monitoring. In the optimized LLE method, a formate buffer solution was first loaded into a 96-well filter plate packed with inert diatomaceous earth material. Then crude plasma samples and a water-immiscible organic solvent, methyl ethyl ketone, were sequentially added to the LLE plate so that LLE would occur in the interface between the two liquid phases on the surface of individual particles in each well. The organic eluate containing extracted analytes was evaporated and reconstituted for LC−MS/MS analysis. This fully automated LLE methodology avoids several disjointed steps involved in a manual or semiautomated LLE method, leading to significantly reduced sample preparation time, increased sample throughput, and clean sample extracts for improved ESI-MS/MS detection. The automated LLE methodology is universal and can be employed for sample preparation of other biological fluids. The complete bioanalytical method, based on the automated LLE and fast gradient LC−MS/MS, was validated and successfully applied to the quantitative analysis of protease inhibitors in rat plasma.
Single-photon smFRET. III. Application to pulsed illumination (2022)

Förster resonance energy transfer (FRET) using pulsed illumination has been pivotal in leveraging lifetime information in FRET analysis. However, there remain major challenges in quantitative single-photon, single-molecule FRET (smFRET) data analysis under pulsed illumination including 1) simultaneously deducing kinetics and number of system states; 2) providing uncertainties over estimates, particularly uncertainty over the number of system states; and 3) taking into account detector noise sources such as cross talk and the instrument response function contributing to uncertainty; in addition to 4) other experimental noise sources such as background. Here, we implement the Bayesian nonparametric framework described in the first companion article that addresses all aforementioned issues in smFRET data analysis specialized for the case of pulsed illumination. Furthermore, we apply our method to both synthetic as well as experimental data acquired using Holliday junctions.
A Novel Piezoactuated XY Stage With Parallel, Decoupled, and Stacked Flexure Structure for Micro-/Nanopositioning (2010)

This paper presents the design and manufacturing processes of a new piezoactuated XY stage with integrated parallel, decoupled, and stacked kinematics structure for micro-/nanopositioning application. The flexure-based XY stage is composed of two decoupled prismatic-prismatic limbs which are constructed by compound parallelogram flexures and compound bridge-type displacement amplifiers. The two limbs are assembled in a parallel and stacked manner to achieve a compact stage with the merits of parallel kinematics. Analytical models for the mechanical performance assessment of the stage in terms of kinematics, statics, stiffness, load capacity, and dynamics are derived and verified with finite element analysis. A prototype of the XY stage is then fabricated, and its decoupling property is tested. Moreover, the Bouc-Wen hysteresis model of the system is identified by resorting to particle swarm optimization, and a control scheme combining the inverse hysteresis model-based feedforward with feedback control is employed to compensate for the plant nonlinearity and uncertainty. Experimental results reveal that a submicrometer accuracy single-axis motion tracking and biaxial contouring can be achieved by the micropositioning system, which validate the effectiveness of the proposed mechanism and controller designs as well.
An efficient anti-occlusion depth estimation using generalized EPI representation in light field (2016)

Light field cameras have been rapidly developed and are likely to appear in mobile devices in near future. It is essential to develop efficient and robust depth estimation algorithm for mobile applications. However, existing methods are either slow or lack of adaptability to occlusion such that they are not suitable to mobile computing platform. In this paper, we present the generalized EPI representation in light field and formulate it using two linear functions. By combining it with the light field occlusion theory, a highly efficient and anti-occlusion depth estimation algorithm is proposed. Our algorithm outperforms the previous local method, especially in occlusion areas. Experimental results on public light field datasets have demonstrated the effectiveness and efficiency of the proposed algorithm.
Preparation of cycloalkylated benzothiadiazine derivatives and their use as AMPA receptor modulators (2005)

publication date: 2009-07-07; filing date: 2008
Heuristic algorithm of the multiple-choice multidimensional knapsack problem (MMKP) for cluster computing (2009)

This paper presents two heuristic algorithms of the MMKP (a variant of 0-1 knapsack problem) for cluster computing. We present an architecture of a cluster, such that algorithm requires small message passing. The algorithms divide the problem among computational nodes. Each node solves its sub problem using a sequential heuristic. This nai¿ve divide and conquer approach cannot achieve good revenue. The revenue is the value achieved by the solution of MMKP. To improve the revenue, it accumulates the unused resources from every node, and assigns to the node, which gives maximum revenue over all nodes. This is the residue exploitation (RE) strategy. The solution quality can be improved by a novel resource-division policy rather than equal division. The policy divides the resource among all nodes such that total revenue increases. A sequential heuristic calculates the solution incrementally for different amounts of resource capacity, and the best combination is taken as the solution. This is the resource adjustment (RA) strategy. We experiment the algorithm using MPI (Message Passing Interface). The proposed algorithms show encouraging results.
The measurement of KNN and KLL in p[downward right arrow]p → n[downward right arrow]X at 800 MeV (1981)

The spin transfer parameters, KNN and KLL have been measured in p↘p → n↘X at 0° and 800 MeV for neutron momenta between 700 and 1200 MeV/c. Peak values of KNN and KLL are −.3±.05 and −.5±.1 respectively.
On the signal-to-noise ratio and short-term stability of passive rubidium frequency standards (1981)

Results are presented on theoretical calculations of the signal-to-noise ratio and of the short-term stability realizable in passive rubidium frequency standards. Measurements made on systems using either the separate hyperfine filter or the integrated hyperfine filter approach are reported. It is concluded that shot noise produced by the lamp at the photodetector is responsible for the observed white frequency noise spectrum limiting the stability in the short-term region.
On variations in the propagation of positive discharges between transformer oil and silicone fluids (1980)

The propagation of the positive discharge in transformer oil is compared with that in silicone oils of two different viscosities. Once initiated, in transformer oil, the discharge propagates readily, being little influenced by variations in the applied voltage or by the position of the tip within the gap. In the case of the silicone fluids the tip velocity is a strong function of its position within the gap and of the applied voltage. The discharges have characteristic forms; a bush-like structure in transformer oils and a tree-like structure in silicone fluids. The results presented support a model of discharge propagation based on a field ionisation process at the tip leading to heating and dissociation with the discharge filament.
[Effects of sodium diethyldithiocarbamate on ischemia-reperfusion-induced brain injury in Mongolian gerbil]. (1994)

Brain injury in Mongolian gerbil (Merisones unguiculatus) was induced by occluding bilateral common carotid arteries for 60 min followed by reperfusion for 5 or 30 min. Oxygen free radicals in brain tissue were measured by electron spin resonance (ESR) technique, malondialdehyde (MDA) was measured by fluorescence spectrometry, and superoxide dismutase (SOD) was measured by nitrite kit. Oxygen free radicals and MDA were not significantly increased, but activities of T-SOD and Mn-SOD were decreased after 60 min of cerebral ischemia. The free radicals were increased at 5-min reperfusion, and then reduced to the level of ischemia group after 30-min reperfusion. MDA was increased remarkably after reperfusion of 30 min, whereas the activity of SOD continued to decrease. Sodium diethyldithiocarbamate (DTC), i.v. 5-100 mg.kg-1 15 min before occlusion, decreased the production of MDA and increased the activities of T-SOD and Mn-SOD. The formation of oxygen free radicals was depressed by i.v. DTC 50 mg.kg-1. The result suggested that the protective effects of DTC on ischemia-reperfusion-induced brain injury might be induced by scavenging the oxygen free radicals, increasing the Mn-SOD activity and decreasing the production of MDA.
Robust Differential Beamforming with Rectangular Arrays (2021)

In this paper, we introduce a robust approach for rectangular differential beamforming. We present a 2-D multistage spatial mean operator which operates independently on the columns and rows of the observation signals of a uniform rectangular array (URA). The multistage approach enables high flexibility: two design parameters, <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">$Q_{c}$</tex> and <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">$Q_{r}$</tex> , set the number of mean stages in the array columns and rows, respectively. Then, we design a rectangular differential beamformer and apply it to the output of the spatial operator. We demonstrate that the first mean operation improves the white noise robustness of the resulting beamformer. We focus on the maximum directivity factor (MDF) and null-constrained maximum directivity factor (NCMDF) differential beamformers and analyze their performances in terms of both the white noise gain (WNG) and directivity factor (DF) measures. We show that the configuration <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">$(Q_{c}, Q_{r})$</tex> constitutes a useful mean to mitigate the white noise amplification of differential beamformers in low frequencies.
The Role of Mineral in the Storage of Elastic Energy in Turkey Tendons (2000)

Mammals elastically store energy in leg and foot tendons during locomotion. In the turkey, much of the force generated by the gastrocnemius muscle is stored as elastic energy during tendon deformation and not within the muscle. During growth, avian tendons mineralize in the portions distal to the muscle and show increased tensile strength and modulus as a result. The purpose of this study was to evaluate the viscoelastic behavior of turkey tendons and self-assembled collagen fiber models to determine the molecular basis for tendon deformation. The stress-strain behavior of tendons and self-assembled collagen fibers was broken into elastic and viscous components. The elastic component was found to be to a first approximation independent of source of the collagen and to depend only on the extent of cross-linking. In the absence of cross-links the elastic component of the stress was found to be negligible for self-assembled type I collagen fibers. In the presence of cross-links the behavior approached that found for mineralized turkey tendons. The elastic constant for turkey tendon was shown to be between 5 and 7.75 GPa while it was about 6.43 GPa for self-assembled collagen fibers aged for 6 months at 22 degrees C. The viscous component for mineralized turkey tendons was about the same as that of self-assembled collagen fibers aged for 6 months, a result suggesting that addition of mineral does not alter the viscous properties of tendon. It is concluded that elastic energy storage in tendons involves direct stretching of the collagen triple-helix, nonhelical ends, and cross-links between the molecules and is unaffected by mineralization. Furthermore, it is hypothesized that mineralization of turkey tendons is an efficient means of preserving elastic energy storage while providing for increased load-bearing ability required for locomotion of adult birds.
Stepwise Injection of Energetic Electrons and Holes in Plasmon-Induced Charge Separation (2019)

Although there are many mechanistic studies for plasmon-induced charge separation (PICS), most of them have been devoted to energetic electron injection (or hot electron injection) from plasmonic metal nanoparticles into electron transport materials (ETMs) including n-type semiconductors. Here we also studied energetic hole injection (or hot hole injection) into five different organic hole transport materials (HTMs) with different ionization energies, by using solid-state photovoltaic cells fabricated by introducing gold nanoparticles (AuNPs) in between TiO₂, which is an ETM, and a HTM. As a result, photocurrents based on PICS are obtained even if the height of the energy barrier at the Au–HTM interface is 0.9 eV. Therefore, the present PICS processes involve both energetic electron injection from AuNPs to TiO₂ and hole injection from AuNPs to the HTMs. In this case, simultaneous electron–hole injection, in which one electron–hole pair gives simultaneous electron injection into TiO₂ and hole injection into a HTM, is often postulated. However, there is another possibility of stepwise electron–hole injection, in which one electron–hole pair leads to electron injection into TiO₂ and another pair gives hole injection into a HTM. The stepwise injection process is accompanied by recombination of the residual hole of the former pair and the electron of the latter. The present cells generated the photocurrents even if the incident photon energy was lower than the sum of the TiO₂–Au and Au–HTM barrier energies (≤2.1 eV). In addition, experimentally obtained photocurrent action spectra of the cells can be reproduced on the basis of plasmonic light absorption and theoretically analyzed carrier injection efficiencies, when the stepwise injection is assumed. It was therefore concluded that the stepwise carrier injection chiefly contributes to the present PICS processes.
Neural recordings from a benzocyclobutene (BCB) based intra-cortical neural implant in an acute animal model (2004)

Multi-channel micro-electrode arrays provide unmatched spatio-temporal resolution for assessing the activity of populations of neurons. These neural implants provide a powerful tool for developing a better understanding of cortical processing, as well as provide an intimate interface for neuroprosthetic applications. Over the years, micro-wire based devices that are manufactured by hand, have allowed researchers to record for several months, and in rare cases up to a year or more. Devices based on microelectro-mechanical systems (MEMs) offer more controlled designs with the added benefit of batch fabrication. Polymer-based MEMs interfaces offer exciting promise over traditional silicon arrays due to their mechanical flexibility and excellent biocompatibility. In this paper we microfabricated a neural interface using a new class of polymer known as benzocyclobutene (BCB), developed for microelectronics under the trade name Cyclotene/spl trade/. This polymer has properties that we believe make it an attractive candidate for chronic implant applications. We provide for the first time a quantitative assessment of its recording capability in an acute animal model. Continuous recordings of neural signals (100 /spl mu/V) from barrel cortex of a rat were successfully demonstrated. These results are encouraging for further development of a long term implant based on BCB.
Echolocation calls of free-flying Himalayan swiftlets ( Aerodramus brevirostris ) (2013)

Here, we present our findings of free-flying echolocation calls of Himalayan swiftlets (Aerodramus brevirostris), which were recorded in Shenjing Cave, Hupingshan National Reserve, Shimen County, Hunan Province in June 2012, using Avisoft-UltraSoundGate 116(e). We noted that after foraging at dusk, the Himalayan swiftlets flew fast into the cave without clicks, and then slowed down in dark area in the cave, but with sounds. The echolocation sounds of Himalayan swiftlets are broadband, double noise burst clicks, separated by a short pause. The inter-pulse intervals between double clicks (99.3±3.86 ms)were longer than those within double clicks (6.6±0.42 ms) (P<0.01). With the exception of peak frequency, between 6.2±0.08 kHz and 6.2±0.10 kHz, (P>0.05) and pulse duration 2.9±0.12 ms, 3.2±0.17 ms, (P>0.05) between the first and second, other factors-maximum frequency, minimum frequency, frequency bandwidth, and power-were significantly different between the clicks. The maximum frequency of the first pulse (20.1±1.10 kHz) was higher than that of second (15.4±0.98 kHz) (P<0.01), while the minimum frequency of the first pulse (3.7±0.12 kHz) was lower than that of second (4.0±0.09 kHz) (P<0.05); resulting in the frequency bandwidth of the first pulse (16.5±1.17 kHz) longer than that of second (11.4±1.01 kHz) (P<0.01). The power of the first pulse (-32.5±0.60 dB) was higher than that of second (-35.2±0.94 dB) (P<0.05). More importantly, we found that Himalayan swiftlets emitted echolocation pulses including ultrasonic sound, with a maximum frequency reaching 33.2 kHz.
Unit Test Generation During Software Development: EvoSuite Plugins for Maven, IntelliJ and Jenkins (2016)

Different techniques to automatically generate unit tests for object oriented classes have been proposed, but how to integrate these tools into the daily activities of software development is a little investigated question. In this paper, we report on our experience in supporting industrial partners in introducing the EvoSuite automated JUnit test generation tool in their software development processes. The first step consisted of providing a plugin to the Apache Maven build infrastructure. The move from a research-oriented point-and-click tool to an automated step of the build process has implications on how developers interact with the tool and generated tests, and therefore, we produced a plugin for the popular IntelliJ Integrated Development Environment (IDE). As build automation is a core component of Continuous Integration (CI), we provide a further plugin to the Jenkins CI system, which allows developers to monitor the results of EvoSuite and integrate generated tests in their source tree. In this paper, we discuss the resulting architecture of the plugins, and the challenges arising when building such plugins. Although the plugins described are targeted for the EvoSuite tool, they can be adapted and their architecture can be reused for other test generation tools as well.
Differences in Vulnerability to Permanent Focal Cerebral Ischemia Among 3 Common Mouse Strains (2000)

The extent of ischemic injury differed markedly between the 3 strains. The presence and patency of posterior communicating arteries, although variable among strains, did not affect preischemic or postischemic cortical blood flow or bear any relationship to ischemic injury. Therefore, intrinsic factors, other than hemodynamic variability, may contribute to the differences in ischemic vulnerability among strains. These findings underscore the importance of selecting genetically matched wild-type controls.