gebhart/patrepeval huggingface dataset:
A roadmap for research on crassulacean acid metabolism (<scp>CAM</scp>) to enhance sustainable food and bioenergy production in a hotter, drier world (2015)

Crassulacean acid metabolism (CAM) is a specialized mode of photosynthesis that features nocturnal CO2 uptake, facilitates increased water-use efficiency (WUE), and enables CAM plants to inhabit water-limited environments such as semi-arid deserts or seasonally dry forests. Human population growth and global climate change now present challenges for agricultural production systems to increase food, feed, forage, fiber, and fuel production. One approach to meet these challenges is to increase reliance on CAM crops, such as Agave and Opuntia, for biomass production on semi-arid, abandoned, marginal, or degraded agricultural lands. Major research efforts are now underway to assess the productivity of CAM crop species and to harness the WUE of CAM by engineering this pathway into existing food, feed, and bioenergy crops. An improved understanding of CAM has potential for high returns on research investment. To exploit the potential of CAM crops and CAM bioengineering, it will be necessary to elucidate the evolution, genomic features, and regulatory mechanisms of CAM. Field trials and predictive models will be required to assess the productivity of CAM crops, while new synthetic biology approaches need to be developed for CAM engineering. Infrastructure will be needed for CAM model systems, field trials, mutant collections, and data management.
Supplementary site interactions are critical for the regulation of microsomal triglyceride transfer protein by microRNA-30c (2013)

Microsomal triglyceride transfer protein (MTTP) is an essential chaperone that assists in the assembly of apolipoprotein B-containing lipoproteins to transport lipids. We have shown that microRNA (miR)-30c regulates MTTP expression but other members of the same family do not. Further, we showed that interactions between miR-30c seed sequence and the 3΄-untranslated region (UTR) of the MTTP mRNA are critical for this regulation. The same seed sequence is shared by all the members of the miR-30 family. Therefore, it is unclear why only miR-30c regulates MTTP expression. Bioinformatics analysis revealed that, miR-30c interacts with MTTP mRNA involving supplementary site, besides seed sequence, forming an intervening loop. Here, we evaluated the importance of the supplementary site and the size of the intervening loop in miR-30c/MTTP mRNA interactions by cloning MTTP 3΄-UTR at the end of the luciferase gene and subjecting it to site-directed mutagenesis. Reducing the number of base pairs at the supplementary site abolished the ability of miR-30c to reduce luciferase activity. However, increasing the number of base pairs at the supplementary site, seed sequence or in the intervening loop enhanced the efficacy of miR-30c in reducing luciferase activity. These studies demonstrated that the supplementary site of miR-30c is, but the intervening loop is not, critical for binding to the MTTP mRNA. To our knowledge, this is the first demonstration that miRs might require both seed and supplementary interactions to regulate target mRNA specificity. Further, this study suggests that more potent miR-30c mimics could be synthesized by increasing base pairing in the loop region.
Recombinant single chain cardiac troponin I-C polypeptides: superior calibration and control materials for cardiac troponin I immunoassays. (2001)

There has been a need to create stable and reproducible calibration and control materials for cardiac troponin I assays. Free troponin I, native or recombinant, has been known to be unstable, while troponin CI complex can be easily dissociated in low concentrations or in the presence of chelating agents. In order to overcome these difficulties, two single chain troponin I-C polypeptides have been engineered and expressed separately in Escherichia coli. One consists of a full-length of human cardiac troponin I and C, termed as ScTnI-C and the other consists of a stable fragment (aa28-110) of human cardiac troponin I and a full-length troponin C, termed as ScTnI-C-2. Both ScTnI-C and ScTnI-C-2 were purified to homogeneity by affinity chromatography using anti-cTnI monoclonal antibodies. ScTnI-C and ScTnI-C-2 have apparent molecular weights of 45 kD and 30 kD by SDS-PAGE, respectively. Stability studies by Stratus showed that ScTn I-C and ScTnI-C-2 were stable for 4 months at 2-8 degrees C and at least one year at -20 degrees C. When incubated in human serum at 37 degrees C, ScTnI-C-2 was more resistant to proteolysis than ScTnI-C. ScTnI-C can be recognized by all commercial TnI immunoassays with excellent activity. ScTnI-C-2 can be recognized by all immunoassays that target the stable region of cardiac troponin I. Judging by their performances, ScTnI-C and ScTnI-C-2 are both superior materials to be used as calibrators and controls in clinical laboratories.
Experimental and Modeling Study of Domain Orientation in Confined Block Copolymer Thin Films (2015)

Use of block copolymer thin films in lithographic applications requires orientation of domains perpendicular to a substrate. Algebraic models were used to predict conditions that are favorable for perpendicular versus parallel domain orientation in films confined between two interfaces. The free energy of each orientation was evaluated, yielding response surface plots as a function of film thickness and the preferential interaction strength at each interface. The model predicts that perpendicular orientation is generally favored for thinner films and at thicknesses incommensurate with the bulk periodicity, L0. If either the top or bottom interfaces are preferential for one block, the favorable thickness windows shift depending on the interface wetting behavior. An extensive body of thin film experimental work corroborated the analytical predictions. The algebraic model has predictive value, and it demonstrates the complexity of the dependence of block copolymer orientation on the wetting behavior of the interfaces and the film thickness.
Monolithically integrated external-cavity tunable laser (2005)

We propose a novel external-cavity tunable laser realized by monolithically integrating a semiconductor optical amplifier, a phase-control section, a dispersive element, and an etched diffraction grating in InP. The tuning operation is based on electrically controlled deflection of the propagating beam through the dispersive element while the grating offers to select a specific wavelength. With the electrical control, the continuous wavelength tuning of 11 nm with a side mode suppression ratio of more than 35 dB has been successfully achieved. (2 pages)
Mycobacterium tuberculosis Malate Synthase Structures with Fragments Reveal a Portal for Substrate/Product Exchange (2016)

Fragment screening and high throughput screening are complementary approaches that combine with structural biology to explore the binding capabilities of an active site. We have used a fragment-based approach on malate synthase (GlcB) from Mycobacterium tuberculosis and discovered several novel binding chemotypes. In addition, the crystal structures of GlcB in complex with these fragments indicated conformational changes in the active site that represent the enzyme conformations during catalysis. Additional structures of the complex with malate and of the apo form of GlcB supported that hypothesis. Comparative analysis of GlcB structures in complex with 18 fragments allowed us to characterize the preferred chemotypes and their binding modes. The fragment structures showed a hydrogen bond to the backbone carbonyl of Met-631. We successfully incorporated an indole group from a fragment into an existing phenyl-diketo acid series. The resulting indole-containing inhibitor was 100-fold more potent than the parent phenyl-diketo acid with an IC<sub>50</sub> value of 20 nm.
A Novel Phenolate “Constrained Geometry” Catalyst System. Efficient Synthesis, Structural Characterization, and α-Olefin Polymerization Catalysis (1997)

This paper reports the convenient “one-pot” synthesis of a bifunctional -Me4Cp⌒phenolate- ligand and the efficient “one-step” synthesis of the corresponding TiIV and ZrIV complexes. The reaction of 2-bromo-4-methylphenol with 2 equiv of nBuLi followed by addition of 2,3,4,5-tetramethyl-2-cyclopentenone produces the bifunctional mono-Cp phenol ligand precursor 2-(tetramethylcyclopentadienyl)-4-methylphenol ((TCP)H2, 1). Reaction of 1 with Ti(CH2Ph)4 at 60 °C in toluene cleanly generates (TCP)Ti(CH2Ph)2 (2), while the corresponding reaction with Zr(CH2Ph)4 at higher temperatures affords the chelated C2-symmetric zirconocene (TCP)2Zr (3). In solution at room temperature, the two benzyl groups of 2 are magnetically equivalent, however, in the solid state, X-ray diffraction reveals that one benzyl group is coordinated in a normal η1-fashion and the other in an η2-mode. The small Cp(centroid)−Ti−O angle of 107.7(2)° in 2 indicates sterically open features in common with amido-based “constrained geometry” polymerization catalysts. Low-temperature NMR-scale reactions of 2 with B(C6F5)3 and Ph3C+B(C6F5)4- indicate the formation of the corresponding cationic complexes (TCP)TiCH2Ph+ PhCH2B(C6F5)3- (4) and (TCP)TiCH2Ph+B(C6F5)4- (5). Upon activation with Ph3C+B(C6F5)4-, complex 2 is highly active for ethylene, propylene, and styrene polymerization.
Experimental Study of Co-Flow Jet Airfoil Performance Enhancement Using Discreet Jets (2011)

This paper demonstrates a new performance enhancement methodology for Co-Flow Jet (CFJ) airfoils using discrete injection jets. This research is motivated by the hypothesis that a discrete CFJ (DCFJ) airfoil will generate both streamwise and spanwise vortex structures to achieve more effective turbulent mixing than an open slot CFJ airfoil. Aerodynamic forces and DPIV measurements show that the DCFJ airfoil can achieve up to a 250% increase of maximum lift, and simultaneously generates a tremendous thrust. Nearly 80% of the injection momentum is converted to drag reduction, which indicates that CFJ airfoils are highly energy efficient. The stall angle of attack is also significantly increased. In other words, a DCFJ airfoil is a high lift system and at the same time is also a high thrust propulsion system with low energy expenditure. Best performances are achieved with small discrete holes and large obstruction factor. Power consumption is analyzed and is found to be low compared with the performance gain. Thus, the DCFJ airfoil concept appears to be very promising for the development of integrated airframe-propulsion systems and rotorcraft systems with high performance and high efficiency.
Purified Scatter Factor Stimulates Epithelial and Vascular Endothelial Cell Migration (1990)

Fibroblasts and smooth muscle cells release a protein activity which causes epithelial sheets to "scatter" into isolated cells. Purification of scatter factor (SF) activity from ras-transformed 3T3 cells was reported recently. We purified ras-3T3 SF by a slightly different method with essentially similar findings. Purified factor showed a single band at 77 +/- 3 kDa on sodium dodecyl sulfate-polyacrylamide gel electrophoresis under nonreducing conditions. Scatter activity was eluted from gel slices at this molecular size. Reduction with mercaptoethanol caused the loss of activity and the appearance of two bands (58 and 31 kDa). We report the amino acid composition of ras-3T3 SF and sequences of several tryptic peptides. These sequences were not similar to the known proteins in the Protein Database. We have shown previously that partially purified ras-3T3 scatter activity stimulates migration of epithelial and vascular endothelial cells in a new migration assay utilizing microcarrier beads. We now demonstrate that the same purified ras-3T3 protein scatters epithelial cells and stimulates epithelial and endothelial migration in microcarrier bead and Boyden chamber assays. Partially purified human smooth muscle scatter activity shares these activities, but the protein(s) responsible has not been isolated. Migration-stimulating activity was maximal at ras-3T3 protein concentrations less than 10 ng/ml (0.13 nM). ras-3T3 SF had no collagenolytic activity and did not stimulate DNA synthesis in fibroblast growth factor-responsive human melanocytes. ras-3T3 SF appears to be a new protein which regulates endothelial and epithelial mobility; and, therefore, it may be involved in vascular repair and wound healing.
A performance prediction framework for protection and control applications in substation automation (2009)

Protection and control is critical in substation automation in order to safely operate and manage the expensive primary equipment. Protection and control can be developed as a composition of function blocks which are executed periodically on processing devices. To ease the architectural design of substation automation by evaluating the feasibilty of the mapping of protection and control functions on processing devices, this paper presents a performance prediction framework. Instead of a classical time consuming worst case execution time analysis, the proposed framework relies on a pragmatic approach by evaluating the probability of the CPU utilization prediction. The framework takes advantages of the composability property of the protection and control functions by analyzing the performance of each function block individually and then combining them into various configurations. The paper's contribution is the definition of the performance prediction framework as well as its empirical validation against a real-world case study.
Dioxane Treatment to Improve Microbial Digestibility of Cellulosic Fibers (1975)

The hemicelluloses of grass seed straws can be extracted rather completely by acid detergent, but the treated residue (acid-detergent fiber) is normally not digested by rumen microorganisms. This residue can be made digestible if it is treated with acidic dioxane.
Analysis and design the bell-shaped vibratory gyroscope under parabolic coordinates system (2016)

The bell-shaped vibratory angular rate gyro (abbreviated as BVG) which is inspired by the Chinese traditional bell is a novel shell vibratory gyroscope. It sensitizes angular rate by the standing wave precession effects. This work presents the gyroscopic effect of paraboloidal bell-shaped resonator under rotating condition and analyzes the feasibility of it to make axisymmetric shell resonator gyroscopes. Firstly, based on the vibratory characteristics of bell-shaped resonator, it derives the transformation matrix that transforms from parabolic coordinates to rectangular coordinates with tensor analysis theory, by which it solves the elastic field equations under the parabolic coordinates, establishes the dynamic equations of bell-shaped resonator. It analyzes the gyroscopic effect of bell-shaped resonator due to coriolis force, proves the equivalency between bell-shaped vibratory gyro and traditional coriolis vibratory gyro, gets the formulas of natural frequency and Bryan's factor. Compared to traditional analysis methods, it simplify the analysis process and is more intuitive to describe the vibratory process of paraboloidal bell-shaped resonator. Then, It analyzes how the bell-shaped resonator vibrates under parabolic coordinates using finite element analysis method and investigates the relationship between the coordinates parameters and nature frequency. It demonstrates the correctness about the analysis method.
<title>Eye-position tracking stereoscopic display using image-shifting optics</title> (1996)

We have developed an eye-position tracking stereoscopic projector which employs image shifting optics. The display allows 3D images to be viewed without special glasses from any position along a lateral axis. Its image shifting device contains a plane parallel glass plate and is installed in a liquid crystal projector. Refraction produced by inclination of the glass plate shifts the optical axis of the projected image. Since the only moving part in the optics is the lightweight glass plate, the response of the image shifting device is both fast and precise enough for interactive 3D-CAD and virtual reality applications. To improve the system's interactive response, we have widened the stereoscopic viewing area by adding a device which causes the image to vibrate laterally. Also we use a new tracking algorithm which reduces the tracking error that would ordinarily be created by delay time. Experimental results confirm the success of these improvements.
Audio-visual synchrony for detection of monologues in video archives (2004)

We present our approach to detecting monologues in video shots. A monologue shot is defined as a shot containing a talking person in the video channel with the corresponding speech in the audio channel. Whilst motivated by the TREC 2002 Video Retrieval Track (VT02), the underlying approach of synchrony between audio and video signals is also applicable for voice and face-based biometrics, assessing lip-synchronization quality in movie editing, and for speaker localization in video. Our approach is envisioned as a two part scheme. We first detect the occurrence of speech and face in a video shot. In shots containing both speech and a face, we distinguish monologue shots as those shots where the speech and facial movements are synchronized. To measure the synchrony between speech and facial movements we use a mutual-information based measure. Experiments with the VT02 corpus indicate that using synchrony, the average precision improves by more than 50% relative compared to using face and speech information alone. Our synchrony based monologue detector submission had the best average precision performance (in VT02) amongst 18 different submissions.
Fragment-Based and Structure-Guided Discovery and Optimization of Rho Kinase Inhibitors (2012)

Using high concentration biochemical assays and fragment-based screening assisted by structure-guided design, we discovered a novel class of Rho-kinase inhibitors. Compound 18 was equipotent for ROCK1 (IC(50) = 650 nM) and ROCK2 (IC(50) = 670 nM), whereas compound 24 was more selective for ROCK2 (IC(50) = 100 nM) over ROCK1 (IC(50) = 1690 nM). The crystal structure of the compound 18-ROCK1 complex revealed that 18 is a type 1 inhibitor that binds the hinge region in the ATP binding site. Compounds 18 and 24 inhibited potently the phosphorylation of the ROCK substrate MLC2 in intact human breast cancer cells.
Directional light output from photonic-wire microcavity semiconductor lasers (1996)

We have obtained directional light output from a recently realized InGaAsP photonic-wire microcavity ring lasers. The output was achieved by fabricating a 0.45-μm-wide U-shape waveguide next to a 10-μm diameter microcavity ring laser. The laser has a threshold pump power of around 124 μW when optically pumped at 514 nm. It is comparable to the former structure without output coupling. The output coupling efficiency can be controlled carefully by choosing the spacing between the laser cavity and the waveguide.
Gas desulfurization. [17 claims] (1977)

Hydrogen sulfide and its precursors can be selectively sorbed from gas streams containing the same by contacting the gas stream at elevated temperatures with a regenerable sorbent comprising a steam-treated support composited with a rare earth metal component. Presteaming the support lowers the amount of rare earth metal component needed to achieve a given activity level for hydrogen sulfide removal. Subsequent to sorption, the sorbent composite may be desorbed and regenerated by treatment with steam (desorption) and an oxidizing gas (regeneration). The sorbent capacity may be increased by the use of alkali or alkaline earth metal components as promoters. A preferred sorbent comprises lanthanum composited with presteamed alumina. 17 claims, 1 drawing figure.
A New Method for the Synthesis of Nonsymmetrical Sulfamides Using Burgess-Type Reagents (2002)

Unsymmetrisch N,N-substituierte Sulfamide sind mithilfe von Reagentien vom Burgess-Typ in hoher Ausbeute in einer Eintopfsynthese ausgehend von Aminoalkoholen (siehe Schema) oder einfachen Aminen zugänglich. Diese Methode ermöglicht bei den cyclischen Produkten eine beliebige Differenzierung an beiden „Seiten“.
N-Terminal Phosphorylation Sites of Herpes Simplex Virus 1 ICP0 Differentially Regulate Its Activities and Enhance Viral Replication (2012)

The herpes simplex virus 1 (HSV-1) infected cell protein 0 (ICP0) is an immediate-early phosphoprotein that transactivates viral gene expression. Evidence suggests that phosphorylation regulates the functions of ICP0, and three regions (termed regions I, II, and III) in the protein are known to be phosphorylated. Mutation of the putative phosphorylation sites within region I, termed Phos 1, which lies in the N-terminal portion of ICP0, impairs the E3 ubiquitin (Ub) ligase and ND10-disrupting activities of ICP0 in cell culture and diminishes viral replication. To identify the specific phosphorylation site(s) or residues responsible for the phenotypes observed with Phos 1, individual residues within region I were mutated to alanine (S224A, T226A, T231A, and T232A) and one double mutant S224A/T226A was constructed. Tissue culture studies demonstrated that the S224A, S224A/T226A, T231A, and T232A mutants were unable to dissociate the cellular protein PML from ND10 and that the S224/T226A mutant was defective in its ability to dissociate the cellular protein Sp100 from ND10. Additionally, the transactivation activity of ICP0 was impaired in the S224A and S224A/T226A mutants. The S224A and S224A/T226A mutant forms were more stable than wild-type ICP0, suggesting that their ability to autoubiquitinate was limited. Moreover, one ICP0 ubiquitination target, USP-7, was also more stable after infection with these two mutants. Lastly, the replication of the S224A and S224A/T226A mutant viruses was reduced in cell culture and in vivo. Overall, our data suggest that specific phosphorylation sites within region I differentially regulate the activities of ICP0, which are required for efficient viral replication.
High temperature CW operation of interband cascade lasers at &#x003BB;&#x002DC;4.0 &#x003BC;m (2007)

The mid-infrared spectral band encompasses a variety of important applications, including chemical sensing, free-space optical communication, and IR countermeasures. Currently, however, most of the wavelength range between 3 and 4 μm is not accessible with semiconductor sources operating in continuous mode at room temperature. We believe that the most promising structure for bridging this gap is the interband cascade laser (ICL).
Spatial conductivity mapping of carbon nanotube composite thin films by electrical impedance tomography for sensing applications (2007)

This paper describes the application of electrical impedance tomography (EIT) to demonstrate the multifunctionality of carbon nanocomposite thin films under various types of environmental stimuli. Carbon nanotube (CNT) thin films are fabricated by a layer-by-layer (LbL) technique and mounted with electrodes along their boundaries. The response of the thin films to various stimuli is investigated by relying on electric current excitation and corresponding boundary potential measurements. The spatial conductivity variations are reconstructed based on a mathematical model for the EIT technique. Here, the ability of the EIT method to provide two-dimensional mapping of the conductivity of CNT thin films is validated by (1) electrically imaging intentional structural defects in the thin films and (2) mapping the film's response to various pH environments. The ability to spatially image the conductivity of CNT thin films holds many promises for developing multifunctional CNT-based sensing skins.