gebhart/patrepeval huggingface dataset:
Thermostable β-Glucosidases (1996)

Interest in β-glucosidase has increased in recent years because of its application in the conversion of cellulose to glucose for the subsequent production of fuel alcohol. Cellulolytic enzymes in conjunction with β-glucosidase act sequentially and cooperatively to degrade cellulose to glucose. Product inhibition, thermal inactivation, low product yield and high cost of the enzyme constitute some problems to develop enzymatic hydrolysis of cellulose as a commercial process. A thermostable β-glucosidase from Aureobasidium pullulons, a yeast-like fungus, was optimally active at 75°C and pH 4.5 against p-nitrophenyl-β-D-glucoside, cellobiose and a series of higher cellooligosaccharides. Recent developments in thermostable β-glucosidase research particularly the biochemical and kinetic properties of the enzyme, mode of action and its use in the conversion of cellulose to glucose are described.
Ramaline inhibits LPS‐induced NO release in macrophages by regulating MAPK and NF‐κB activities. (2010)

Lipopolysaccharide (LPS) induces innate immune responses through TLR4 signaling and activated macrophages produce various inflammatory mediators including Nitric oxide (NO). NO produced by inducible NO synthase (iNOS) mediates a number of pathophysiological processes. Therefore, inhibiting NO production in macrophages is a potential therapeutic target in inflammatory diseases. Herein, we demonstrate that ramalin, a newly discovered antioxidant that is extracted from polar lichen, inhibits production of inflammatory mediators in macrophage‐like Raw 264.7 cell line. RT‐PCR and Western blot analysis demonstrated that ramalin suppressed the level of NO release through down‐regulating both mRNA and protein levels of iNOS. Western blot analysis also revealed that ramalin abrogated LPS‐induced phosphorylation of ERK, p38, and JNK as well as the expression of p65. Attenuated activity of NF‐κB by ramalin was also confirmed by Luciferase promoter assay. In addition, not only the surface level of LPS‐induced TLR4 but also its mRNA and protein levels were decreased by ramalin. Together, these results suggest that ramalin reduces NO release in macrophage through down‐regulation of TLR4 signaling which in turn suppresses MAPK and NF‐κB activities, and it would be a possible therapeutic approach to the treatment of inflammatory diseases.
Characterization of lignin derived from water-only and dilute acid flowthrough pretreatment of poplar wood at elevated temperatures (2015)

Elevated temperature and/or dilute acid greatly enhanced lignin removal to almost 100 % by improving G unit removal besides S unit removal in flowthrough system. Only mild lignin structural modification was caused by flowthrough pretreatment. A lignin transformation pathway was proposed to explain the complexity of the lignin structural changes during hot water and dilute acid flowthrough pretreatment.Graphical abstractLignin transformations in water-only and dilute acid flowthrough pretreatment at elevated temperatures.
Review Genetic and molecular mechanisms of aluminum tolerance in plants (2012)

Aluminum (Al) toxicity restricts root growth and agricultural yield in acid soils, which constitute approximately 40% of the potentially arable lands worldwide. The two main mechanisms of Al tolerance in plants are internal detoxification of Al and its exclusion from root cells. Genes encoding membrane transporters and accessory transcription factors, as well as cis-elements that enhance gene expression, are involved in Al tolerance in plants; thus studies of these genes and accessory factors should be the focus of molecular breeding efforts aimed at improving Al tolerance in crops. In this review, we describe the main genetic and molecular studies that led to the identification and cloning of genes associated with Al tolerance in plants. We include recent findings on the regulation of genes associated with Al tolerance. Understanding the genetic, molecular, and physiological aspects of Al tolerance in plants is important for generating cultivars adapted to acid soils, thereby contributing to food security worldwide.
<title>Real-time MPEG-1 software decoding on HP workstations</title> (1995)

A MPEG1 codec that is capable of real-time playback of video and audio on HP's RISC-based workstations has been developed. Real-time playback is achieved by examining the complete MPEG1 decoding pipeline and optimizing the algorithms used for the various stages of the video and audio decompression process. For video decompression, efficient implementations are derived by examining the huffman decoder, inverse quantizer and inverse DCT as a single system. For audio decompression, by viewing the subband synthesis function in MPEG1 layer I and layer II decoding as a DCT, a fast 32-point DCT suitable for use in MPEG1 audio decompression has been developed. Besides algorithmic enhancements, in order to achieve real-time performance, minor changes to the CPU architecture and the display pipeline architecture were needed. The integration of algorithmic and architectural enhancements results in real-time playback of MPEG1 video and audio on HP's RISC based workstations.
Promises and challenges for the development of<i>Listeria monocytogenes</i>-based immunotherapies (2008)

Active immunotherapy has shown great promise in preclinical models for the treatment of infectious and malignant disease. Yet, these promising results have not translated into approved therapies. One of the major deficits of active immunotherapies tested to date in advanced clinical studies has been their inability to stimulate both arms of the immune system appropriately. The interest in using recombinant bacteria as vaccine vectors for active immunotherapy derives in part from their ability to stimulate multiple innate immune pathways and, at the same time, to deliver antigen for presentation to the adaptive immune system. This review will focus on the development of live-attenuated and killed strains of the intracellular bacterium Listeria monocytogenes for treatment of chronic infections and cancer. Early clinical trials intended to demonstrate safety as well as proof of concept have recently been initiated in several indications. Advances in molecular engineering as well as successes and challenges for clinical development of L. monocytogenes-based vaccines will be discussed.
An 11 $\mu{\rm W}$ Sub-pJ/bit Reconfigurable Transceiver for mm-Sized Wireless Implants (2015)

A wirelessly powered 11 μW transceiver for implantable devices has been designed and demonstrated through 35 mm of porcine heart tissue. The prototype was implemented in 65 nm CMOS occupying 1 mm × 1 mm with a 2 mm × 2 mm off-chip antenna. The IC consists of a rectifier, regulator, demodulator, modulator, controller, and sensor interface. The forward link transfers power and data on a 1.32 GHz carrier using low-depth ASK modulation that minimizes impact on power delivery and achieves from 4 to 20 Mbps with 0.3 pJ/bit at 4 Mbps. The backscattering link modulates the antenna impedance with a configurable load for operation in diverse biological environments and achieves up to 2 Mbps at 0.7 pJ/bit. The device supports TDMA, allowing for operation of multiple devices from a single external transceiver.
CAD-CAP: une base de données française à vocation internationale, pour le développement et la validation d'outils de diagnostic assisté par ordinateur en vidéocapsule endoscopique du grêle (2018)

La vidéocapsule endoscopique du grêle (VCE-G) est un examen de première ligne dans l'exploration non-invasive de l'intestin grêle. Avec un nombre moyen de 50000 images du grêle par examen, l'interprétation d'un enregistrement reste fastidieux et chronophage (en moyenne 30 à 40 minutes par vidéo), et source potentielle de lésions manquées. Aussi, le développement de programmes de détection assisté par ordinateur (DAO) est un enjeu majeur de recherche en VCE-G. La création d'une banque d'images et de vidéo de VCE-G, ouvertes à la communauté des chercheurs dans ce domaine, est indispensable d'une part aux processus d'apprentissage par ordinateur (machine learning) et d'autre part aux comparaisons valides de différents algorithmes.
A Two Step Stain for Normal and Leukemic Monocytes Using Two Different Dyes Applied in Sequence (1992)

A staining procedure for monocytes in specimens of blood and bone marrow was developed. The technique was a two step procedure in which unfixed cells were exposed first to a methanolic solution of C.I. basic blue 54. Next, an aqueous alkaline buffered solution of C.I. basic blue 141 was added to the first staining solution. After staining for 10 min in the solution with two stains, slides or coverslips were washed for 5 sec in pH 5.6 phosphate buffer and drained dry. The cytoplasm of monocytes stained intensely deep purple and frequently nuclei were stained red. Similar staining was not found in other types of normal or abnormal blood and bone marrow cells.
Thermal analysis of magnetron sputtering designs (1992)

Thermal flow characteristics of a new type of magnetron sputtering source design have been analyzed for various materials, heat rates and geometries using TOPAZ2D code. Thermal conduction has been assumed to be the only mechanism for transporting heat through the apparatus. Solutions compare well with experiments and demonstrate the usefulness (and cost savings) of performing experimental parameter variations with the model rather than the hardware. Optimal designs based on the present analysis are also discussed.
Self-propagating high-temperature synthesis of boron phosphide (2013)

A new method of producing boron phosphide (BP) submicron powders by a self-propagating high-temperature reaction between boron phosphate and magnesium in the presence of an inert diluent (sodium chloride) has been proposed. Bulk polycrystalline BP with microhardness of H V = 28(2) GPa has been prepared by sintering the above powders at 7.7 GPa and 2600 K.
Photonic multilayer sensors from photo-crosslinkable polymer films (2012)

Colorimetric temperature sensors are prepared from photo-crosslinkable polymers by sequentially spin-coating and crosslinking alternating layers of poly(N-isopropylacrylamide) and poly(para-methyl styrene). Layer thicknesses and copolymer chemistries are chosen to provide robust colorimetric temperature sensors that cover nearly the full visible spectrum.
Resource provisioning framework for mapreduce jobs with performance goals (2011)

Many companies are increasingly using MapReduce for efficient large scale data processing such as personalized advertising, spam detection, and different data mining tasks. Cloud computing offers an attractive option for businesses to rent a suitable size Hadoop cluster, consume resources as a service, and pay only for resources that were utilized. One of the open questions in such environments is the amount of resources that a user should lease from the service provider. Often, a user targets specific performance goals and the application needs to complete data processing by a certain time deadline. However, currently, the task of estimating required resources to meet application performance goals is solely the users' responsibility. In this work, we introduce a novel framework and technique to address this problem and to offer a new resource sizing and provisioning service in MapReduce environments. For a MapReduce job that needs to be completed within a certain time, the job profile is built from the job past executions or by executing the application on a smaller data set using an automated profiling tool. Then, by applying scaling rules combined with a fast and efficient capacity planning model, we generate a set of resource provisioning options. Moreover, we design a model for estimating the impact of node failures on a job completion time to evaluate worst case scenarios. We validate the accuracy of our models using a set of realistic applications. The predicted completion times of generated resource provisioning options are within 10% of the measured times in our 66-node Hadoop cluster.
Canine Distemper Virus Strains Circulating among North American Dogs (2008)

Canine distemper virus (CDV) is a highly contagious virus that causes multisystemic disease in dogs. We received seven samples from dogs with CD from the United States during 2007. CDV isolates from these samples formed large, multinucleated syncytia in a Vero cell line expressing canine signaling lymphocyte activation molecule (SLAM). Based on the hemagglutinin gene sequences, the CDV isolates from three states (California, Missouri, and Oklahoma) formed two CDV genetic groups: group I (major; six of seven isolates) consisted of CDV isolates closely related to the European wildlife lineage of CDV, and group II (minor; one of seven isolates) was genetically related to the Arctic-like lineage of CDV. However, both CDV groups were genetically different from the current vaccine strains that belong to the American-1 lineage of the old (1930 to 1950) CDV isolates.
Controlled sp<sup>2</sup> Functionalization of Boron Doped Diamond as a Route for the Fabrication of Robust and Nernstian pH Electrodes (2015)

The development of a voltammetric boron doped diamond (BDD) pH sensor is described. To obtain pH sensitivity, laser micromachining (ablation) is utilized to introduce controlled regions of sp(2) carbon into a high quality polycrystalline BDD electrode. The resulting sp(2) carbon is activated to produce electrochemically reducible quinone groups using a high temperature acid treatment, followed by anodic polarization. Once activated, no further treatment is required. The quinone groups show a linear (R(2) = 0.999) and Nernstian (59 mV/(pH unit)) pH-dependent reductive current-voltage response over a large analyzable pH range, from pH 2 to pH 12. Using the laser approach, it is possible to optimize sp(2) coverage on the BDD surface, such that a measurable pH response is recorded, while minimizing background currents arising from oxygen reduction reactions on sp(2) carbon in the potential region of interest. This enables the sensor to be used in aerated solutions, boding well for in situ analysis. The voltammetric response of the electrode is not compromised by the presence of excess metal ions such as Pb(2+), Cd(2+), Cu(2+), and Zn(2+). Furthermore, the pH sensor is stable over a 3 month period (the current time period of testing), can be stored in air between measurements, requires no reactivation of the surface between measurements, and can be reproducibly fabricated using the proposed approach. The efficacy of this pH sensor in a real-world sample is demonstrated with pH measurements in U.K. seawater.
Design and performance of a reflectron based time-of-flight secondary ion mass spectrometer with electrodynamic primary ion mass separation (1987)

In many secondary ion mass spectrometry (SIMS) investigations, the total number of generated secondary ions is limited by the amount of sample material available. This is the case in surface reaction studies as well as in organic and inorganic trace analysis or imaging SIMS. In such cases a time-of-flight mass spectrometer has some considerable advantages: quasisimultaneous detection of all masses, unlimited mass range, and very high transmission. We have developed a high-resolution reflectron based time-of-flight secondary ion mass spectrometer with a new electrodynamic mass separation and beam chopping technique based on a pulsed 90° deflection of the primary ion beam. A primary ion pulse width of less than 1.5 ns has been obtained. Second-order energy focusing in the flight path of the secondary ions is achieved by a two-stage reflectron. A mass resolution m/Δm=13 000 and a dynamic range of five orders of magnitude have been obtained with this instrument.
Multi-object detection and behavior recognition from motion 3D data (2011)

This paper presents methods for 3D object detection and multi-object (or multi-agent) behavior recognition using a sequence of 3D point clouds of a scene taken over time. This motion 3D data can be collected using different sensors and techniques such as flash LIDAR (Light Detection And Ranging), stereo cameras, time-of-flight cameras, or spatial phase imaging sensors. Our goal is to segment objects from the 3D point cloud data in order to construct tracks of multiple objects (i.e., persons and vehicles) and then classify the multi-object tracks as one of a set of known behaviors, such as “A person drives a car and gets out”. A track is a sequence of object locations changing over time and is the compact object-level information we use and obtain from the motion 3D data. Leveraging the rich structure of dynamic 3D data makes many visual learning problems better posed and more tractable. Our behavior recognition method is based on combining the Dynamic Time Warping-based behavior distances from the multiple object-level tracks using a normalized car-centric coordinate system to recognize the interactive behavior of those multiple objects. We apply our techniques for behavior recognition on data collected using a LIDAR sensor, with promising results.
A new controllable CMOS impedance scaler (2016)

This paper presents a new compact CMOS capacitance multiplier. The multiplier is based on using the trnaslinear principle. Only four MOSFETs operating in subthreshold region are used. The multiplication factor is controllable to meet the designer requirements. Tanner TSPICE simulator is used to confirm the functionality of the design in 0.18μm CMOS Technology. The circuit operates from ±0.75 supply voltage. Simulation results indicate that the multiplication factor is large compared to existing designs. The functionality of the proposed capacitance multiplier is demonstrated by using it in designing relaxation oscillator.
<i>In situ</i> ultrasonic monitoring of photoresist development (1998)

We have developed an in situ method to measure the change in thickness of photoresist during development. The phase of a high frequency ultrasound signal is monitored as it is reflected from the silicon/photoresist interface during resist development. The method was tested using a 1.5 μm film of Shipley 1811 resist. The total phase change during development of 19° was consistent with theoretical calculations at 280 MHz, and this change was used to obtain the resist thickness during development. The method was used to find the development rate of this positive-tone resist as a function of exposure dose in the 20–68 mJ/cm2 range. As expected, there was an increase in development rate as the exposure time increased; this continued up to about 40 s of exposure, beyond which the rates were essentially unchanged. Measurements on a wafer with microelectronic devices ranging in topography from 0.10 to 1.0 μm show that the method is applicable to wafers with typical circuit topography.
Fine-Tuning the Selectivity of Aldosterone Synthase Inhibitors: Structure−Activity and Structure−Selectivity Insights from Studies of Heteroaryl Substituted 1,2,5,6-Tetrahydropyrrolo[3,2,1-<i>ij</i>]quinolin-4-one Derivatives (2011)

Pyridine substituted 3,4-dihydro-1H-quinolin-2-ones (e.g., 1-3) constitute a class of highly potent and selective inhibitors of aldosterone synthase (CYP11B2), a promising target for the treatment of hyperaldosteronism, congestive heart failure, and myocardial fibrosis. Among these, ethyl-substituted 3 possesses high selectivity against CYP1A2. Rigidification of 3 by incorporation of the ethyl group into a 5- or 6-membered ring affords compounds with a pyrroloquinolinone or pyridoquinolinone molecular scaffold (e.g., 4 and 5). It was found that these molecules are even more potent and selective CYP11B2 inhibitors than their corresponding open-chain analogues. Moreover, pyrroloquinolinone 4 exhibits no inhibition of the six most important hepatic CYP enzymes as well as a bioavailability in the range of the marketed drug fadrozole. The SAR studies disclose that subtle changes in the heterocyclic moiety are responsible for either a strong or a weak inhibition of the highly homologous 11β-hydroxylase (CYP11B1). These results are not only important for fine-tuning the selectivity of CYP11B2 inhibitors but also for the development of selective CYP11B1 inhibitors that are of interest for the treatment of Cushing's syndrome and metabolic syndrome.
Chirped-Pulse Inverse Free Electron Laser: A Tabletop, High-Gradient Vacuum Laser Accelerator (2001)

The inverse free-electron laser (IFEL) interaction is studied both theoretically and numerically in the case where the drive laser intensity approaches the relativistic regime, and the pulse duration is only a few optical cycles long. We show that by using an ultrashort, ultrahigh-intensity drive laser pulse, the IFEL interaction bandwidth and accelerating gradient are increased considerably, thus yielding large energy gains. Using a chirped pulse and negative dispersion focusing optics allows one to take further advantage of the laser optical bandwidth and produce a chromatic line focus maximizing the gradient. The combination of these novel ideas results in a compact vacuum laser accelerator capable of accelerating picosecond electron bunches with a high gradient (GeV/m) and very low energy spread. A computer code which takes into account the three-dimensional nature of the interaction is currently in development and results are expected this Spring.
Percutaneous, in vivo excimer laser angioplasty: Results in two experimental animal models (1988)

Pulsed ultraviolet light from an excimer laser was successfully transmitted via conventional fused silica optical fibers and used to accomplish recanalization of stenotic or totally occluded arteries in an intact, flowing blood field of two atherosclerotic animal models. The fibers, 300-600 micron in diameter, were delivered percutaneously in wire-guided multilumen catheters and then used to transmit wavelengths of 308 or 351 nm from excimer lasers with pulse durations of 12 nsec or less. Lesions from 70-100% diameter narrowing, and 0.6 to 5.5 cm in length were successfully recanalized (less than 50% residual diameter narrowing) in eight animals, using 3-4 J/cm2/pulse, 10-50 Hz, and 48-370-sec cumulative exposure. Necropsy examination in six of the eight animals disclosed no signs of thermal injury. Perforations were observed in four of eight animals. Thus, while use of an excimer laser power source did not obviate vascular perforation as a complication of laser angioplasty, these preliminary results indicate that energies of pulsed ultraviolet light sufficient to ablate atherosclerotic plaque can be both transmitted via conventional fused silica optical fibers and used successfully within an intact, flowing blood field. It may therefore be possible to use pulsed ultraviolet light from an excimer laser to accomplish percutaneous ablation of atherosclerotic arterial obstructions in humans.