gebhart/patrepeval huggingface dataset:
Identification and characterization of a set of monocot BAHD monolignol transferases (2022)

Plant BAHD acyltransferases perform a wide range of enzymatic tasks in primary and secondary metabolism. Acyl-CoA monolignol transferases, which couple a CoA substrate to a monolignol creating an ester linkage, represent a more recent class of such acyltransferases. The resulting conjugates may be used for plant defense but are also deployed as important "monomers" for lignification, in which they are incorporated into the growing lignin polymer chain. p-Coumaroyl-CoA monolignol transferases (PMTs) increase the production of monolignol p-coumarates, and feruloyl-CoA monolignol transferases (FMTs) catalyze the production of monolignol ferulate conjugates. We identified putative FMT and PMT enzymes in sorghum (Sorghum bicolor) and switchgrass (Panicum virgatum) and have compared their activities to those of known monolignol transferases. The putative FMT enzymes produced both monolignol ferulate and monolignol p-coumarate conjugates, whereas the putative PMT enzymes produced monolignol p-coumarate conjugates. Enzyme activity measurements revealed that the putative FMT enzymes are not as efficient as the rice (Oryza sativa) control OsFMT enzyme under the conditions tested, but the SbPMT enzyme is as active as the control OsPMT enzyme. These putative FMTs and PMTs were transformed into Arabidopsis (Arabidopsis thaliana) to test their activities and abilities to biosynthesize monolignol conjugates for lignification in planta. The presence of ferulates and p-coumarates on the lignin of these transformants indicated that the putative FMTs and PMTs act as functional feruloyl-CoA and p-coumaroyl-CoA monolignol transferases within plants.
Conjugation of Camptothecins to Poly‐(l‐Glutamic Acid) (2000)

Conjugation of water-insoluble cancer chemotherapeutic drugs to macromolecular polymers can lead to improved pharmaceutical properties and improved therapeutic ratios due to accumulation of the polymer-drug conjugate in tumor tissue through the enhanced permeability and retention (EPR) to macromolecules associated with tumor vasculature. Pharmaceutical shortcomings of certain active camptothecins including difficulty in formulation and instability of the active lactone form due to interactions with human albumin might be improved by conjugation to polymers. In this report, conjugations of camptothecin (CPT), 10-hydroxy-CPT, and 9-amino-CPT to poly-(L-glutamic acid) (PG) are described; coupling was accomplished either through the 20(S)-hydroxyl or 9 and 10 substituents with and without the use of a glycine linker. Studies using a PG paclitaxel conjugate (PG-TXL), which is currently in Phase I testing, demonstrated that PG enhanced aqueous solubility, prolonged plasma residence time, and greatly increased the distribution of paclitaxel to tumor tissue in a murine model. In this report, we describe the use of similar conjugation technology for CPT derivatives and demonstrate that these difficult to formulate compounds can be rendered water soluble, that their maximum tolerated doses are increased, and that they retain substantial anti-tumor activity in syngeneic and xenogeneic tumor models. Preliminary data suggest that PG with molecular weights between 37 and 50 kDa with CPT loading between 14% and 37% with or without glycine linkers display enhanced efficacy compared with nonconjugated camptothecins administered at their maximum tolerated dose.
Visual pattern image coding (1990)

A novel framework for digital image compression called visual pattern image coding, or VPIC, is presented. In VPIC, set of visual-patterns is defined independent of the images to be coded. Each visual pattern is a subimage of limited spatial support that is visually meaningful to a normal human observer. The patterns are used as a basis for efficient image representation; since it is assumed that the images to be coded are natural optical images to be viewed by human observers, visual pattern design is developed using relevant psychophysical and physiological data. Although VPIC bears certain resemblances to block truncation (BTC) and vector quantification (VQ) image coding, there are important differences. First, there is no training phase required: the visual patterns derive from models of perceptual mechanisms; second, the assignment of patterns to image regions is not based on a standard (norm) error criterion; expensive search operations are eliminated.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Small interfering peptides as a novel way of transcriptional control (2008)

Transcription factors are key components of transcriptional regulatory networks governing virtually all aspects of plant growth and developmental processes. Their activities are regulated at various steps, including gene transcription, posttranscriptional mRNA metabolism, posttranslational modifications, nucleocytoplasmic transport, and controlled proteolytic cleavage of membrane-anchored, dormant forms. Dynamic protein dimerization also plays a critical role in this process. An exquisite regulatory scheme has recently been proposed to modulate the action of transcription factors. Small peptides possessing a protein dimerization motif but lacking the DNA-binding motif form nonfunctional heterodimers with a group of specific TFs, inhibiting their transcriptional activation activities. Extensive searches for small proteins that have a similar structural organization in the databases revealed that small peptide-mediated transcription control is not an exceptional case but would be a regulatory mechanism occurring widespread in the Arabidopsis genome.
A new FIFO for transferring data between two unrelated clock domains (2012)

A new simple-to-design FIFO that allows data transfer between two clock domains of unrelated frequencies has been developed. The fully synchronous interfaces significantly ease the system-on-chip integration process. With a relatively low gate count, the proposed FIFO allows the producer and consumer to put/get data at their respective frequencies (1 datum/clock cycle) till it gets filled, then the rates converge to the lower of the two frequencies. The maximum initial latency is three cycles of the consumer's clock. Several manifestations of the FIFO have been developed for different design cases including producer/consumer data width mismatch. Operation of the FIFO has been verified using both gate-level simulations and SPICE simulations with a 0.13 µm, 1.2 V technology. An 8-cell FIFO showed proper operation at producer and consumer clock frequencies of 2 and 3.125 GHz, respectively, with a data transfer rate of more than 2 giga datum/s and an average power of 721 µW.
CMOS Image Sensor with Watermarking Capabilities (2005)

The problem of authenticity for digital images has been helped by the development of digital watermarking. As an extension of the current state-of-the-art, a CMOS active pixel sensor (APS) imager with built-in watermarking of the output image is presented. A method for generation of watermarks specific to each chip is presented as well as simulations showing the effectiveness of the watermarking algorithm. The layout was designed in TSMC's 0.18 /spl mu/m 1.8/3.3 V process and circuit simulations indicate performance as expected.
Transflective twisted‐nematic liquid‐crystal display with double twisted‐nematic cell and twisted liquid‐crystal retarder (2007)

Abstract— Two configurations, (i) a double‐cell‐gap twisted nematic (DTN) liquid‐crystal display (LCD) and (ii) a single‐cell‐gap twisted‐nematic (TN) liquid‐crystal display (LCD) using a twisted LC retarder, were optimized for transflective liquid‐crystal displays. For the DTN configuration, both the single‐cell‐gap approach and the double‐cell‐gap approach were considered. The optimized configurations exhibit a high contrast ratio, wide viewing angles, and achromatic (black/white) switching in both the transmissive and reflective modes. They are easy to fabricate and also possess a perfect dark state. Both are suitable for high‐quality transflective TFT‐LCDs.
Homogeneity of Gd-Based Garnet Transparent Ceramic Scintillators for Gamma Spectroscopy (2012)

Abstract not provided
Use of excluded volume to increase the heterogeneity of pore size in agarose gels (1996)

When testing theoretical models that quantitatively describe the sieving of macromolecules during gel electrophoresis, investigators have been limited by absence of control of the heterogeneity of the size of pores in the gel. In a recent study performed by electron microscopy of thin sections (G. A. Griess et al., J. Struct. Biol. 1993, III, 39-47), pore size heterogeneity has been increased for agarose gels by a combination of both derivatization and molecular weight reduction of the polysaccharide chains of agarose. In the present study, pore size heterogeneity is increased by a mechanism that appears to have an origin different from the origin of this previously observed increase in heterogeneity: Pore size heterogeneity is increased by addition of a polyethylene glycol (PEG) of high molecular weight (18,500) to molten agarose before gelation. In contrast, the use of a lower molecular weight PEG (either 4,000 or 7,500) causes the formation of micron-sized precipitates within a gelled network of agarose fibers. Thus far, the PEG-induced heterogeneity of pore size occurs primarily in 100-1,000 microns scale zones separated from each other by interzone regions of decreased agarose fiber density. More uniform gels are needed for the study of sieving.
Modular Flow Structure Design for a Single-Phase Manifold Microchannel Cold Plate (2015)

The present work is generally related to the design of a manifold microchannel heat sink with high modularity and performance for electronics cooling, utilizing two well established (i.e., jet impingement and channel flow) cooling technologies. The present cold plate design provides flexibility to assemble manifold sections in five different configurations to reach different flow structures, and thus different cooling performance, without redesign. The details of the modular manifold and possible configurations of a cold plate comprising three manifold sections are shown herein. A conjugate flow and heat transfer 3-D model is developed for each configuration of the cold plate to demonstrate the merits of each modular design. Parallel flow configurations are used to satisfy a uniform cooling requirement from each module, but a “U-shape” parallel flow “base” configuration cools the modules more uniformly than a “Z-shape” flow pattern due to intrinsic pressure distribution characteristics. A serial fluid flow configuration requires the minimum coolant flow rate with a gradually increasing device temperature along the flow direction. Two mixed (i.e., parallel + serial flow) configurations achieve either cooling performance similar to the “U-shape” configuration with slightly more than half of the coolant flow rate, or cooling of a specific module to a much lower temperature level. Generally speaking, the current cold plate design significantly extends its application to different situations with different cooling requirements.
A Method to Prevent Iron Contamination during Manufacture of Incandescent Filaments (1973)

Tungsten wire for incandescent lamp filaments is manufactured with rigorous control of trace impurities known to be detrimental to lamp performance. The finished coiled filaments, however, do not always retain the original purity of the tungsten wire throughout the coil-making process. It has been found that an appreciable amount of iron can diffuse into the tungsten coil on a steel mandrel during annealing and can cause embrittlement of the filaments. That iron diffuses into the filament from the steel mandrel has been determined by electron microprobe analysis and Auger electron spectroscopy. Filaments having localized iron contamination suffer drastic reductions in ductility and fracture stress and are responsible for rejects during coil mounting. Results are presented showing that iron contamination during annealing can be prevented by using steel mandrel coated with a thin layer of copper which serves as a barrier against iron atoms diffusing into tungsten.
Rh-Catalyzed Anti-Markovnikov Hydrocyanation of Terminal Alkynes (2017)

We report the first highly stereo- and regioselective hydrocyanation of terminal alkynes to furnish E-configured alkenyl nitriles. Acrylonitriles can be accessed on gram scale with broad substrate scope and functional group tolerance. The hydrocyanation reaction employs acetone cyanohydrin as a practical alternative to HCN gas.
Analytical- and Process-Scale Cell Separation with Bioreceptor Ferrofluids and High-Gradient Magnetic Separation (1991)

The development of small colloidal magnetic particles (< 0.1u) and their application to cell separations via high gradient magnetic methods is reviewed. An analysis of the properties of these particles contrasted to large magnetic particles (1-5u) argues for the superiority of the former even though their use has been plagued by non-specific binding issues and the use of crude high gradient magnetic separators. The development of a BioReceptor (antibody, enzyme, lectin) coated Ferrofluid and two novel high gradient magnetic separators are described. Both separators can be used for analytical scale cell separations (200 - 300 ul volumes) and one of them can easily be adapted for process scale separations. Performance data on separations done in simple and complex matrices is given.
An electron optical theory of beam blanking (1993)

Trajectory equations are derived in closed form for electrons in time-dependent electric fields produced by beam blankers. Simple parallel plate and double-deflection blankers with transmission delay lines are evaluated. Lens imaging of the apparent beam motion is analyzed by developing the virtual electron trajectories obtained from linear extrapolation back into the blanker region. Lens excitation effects and conjugate blanking optics can then be described. The blanker voltage is represented by a damped exponential cosine term, which satisfies a typical circuit equation for the driver-amplifier. The form of the trajectory equation is written as a 3×3 matrix, which comprises a set of conditional solutions that are determined by blanker geometry. The optimum delay line length of any double-deflection blanker can then be determined. The blanker-induced beam jitter is shown to be significantly reduced by using this configuration. The effect of the blanker beam stop on the motion at the target plane is given by combining results on the real and apparent beam trajectories.
LC‐polyimides, 32. Characterization of the Mitsui‐Toatsu LC‐polyimide and related polyimides (1997)

Abstract Two polyimides were prepared from 1,3‐bis[4′‐(4″‐aminophenoxy)cumyl]benzene and 1,2:4,5‐benzenetetracarboxylic dianhydride (PMDA) or 1,8:4,5‐naphthalenetetracarboxylic dianhydride. A poly(amide‐imide) was prepared from the same diamine and trimellitic anhydride. Furthermore, two polyimides were prepared from 1,4‐bis‐[4′‐(4″‐aminophenoxy)cumyl]benzene or a mixture of the 1,3‐ and 1,4‐diamines. Moreover, one polyimide was synthesized from PMDA and 1,3‐(4‐aminocumyl)benzene. All polyimides were characterized by elemental analyses, optical microscopy, DSC and various X‐ray measurements. Only the polyimide of PMDA and the 1,3‐amine proved to be thermotropic. SAXS and WAXS measurements between 25 and 350°C, along with a fiber pattern suggest that this LC‐polyimide forms a smectic‐A phase in the melt and a disordered smectic‐B phase in the solid state. Also most other polyimides formed a disordered smectic‐B or a smectic‐A glass in the solid state. However, the polyimide derived from 1,3‐(4‐aminocumyl)benzene crystallized in the form of a smectic‐H phase with tilted mesogens. All results together underline the high potential of polyimides of form layer structures.
Can We Localize an Autonomous Vehicle From a Single Image? Deep-Geometric Six Degrees-of-Freedom Localization in Topo-Metric Maps (2021)

Abstract We describe a deep-geometric localizer that is able to estimate the full six degrees-of-freedom (DOF) global pose of the camera from a single image in a previously mapped environment. Our map is a topo-metric one, with discrete topological nodes whose 6DOF poses are known. Each topo-node in our map also comprises of a set of points, whose 2D features and 3D locations are stored as part of the mapping process. For the mapping phase, we utilize a stereo camera and a regular stereo visual SLAM pipeline. During the localization phase, we take a single camera image, localize it to a topological node using deep learning, and use a geometric algorithm (perspective-n-point (PnP)) on the matched 2D features (and their 3D positions in the topo map) to determine the full 6DOF globally consistent pose of the camera. Our method divorces the mapping and the localization algorithms and sensors (stereo and mono) and allows accurate 6DOF pose estimation in a previously mapped environment using a single camera. With results in simulated and real environments, our hybrid algorithm is particularly useful for autonomous vehicles (AVs) and shuttles that might repeatedly traverse the same route.
The use of tandem mass spectrometry as a problem‐solving tool in the industrial environment (1990)

Abstract This paper deals with a number of the benefits associated with a variety of tandem mass spectrometer geometries and the way in which these configurations have been applied to the solution of real problems. It discusses the use made of a variety of tandem mass spectrometry approaches to the study of analytical problems of industrial relevance. ICIs utilization of tandem mass spectrometry has grown substantially from an initial involvement in the early 1980s to a point where a number of instruments have been installed and used predominantly for trace analysis, structural studies and in the characterization of complex mixtures. We have selected a small number of examples of the use of the various tandem mass spectrometry approaches emphasizing the unique features of the technique.
Spontaneous Neutrophil Migration Patterns during Sepsis after Major Burns (2014)

Finely tuned to respond quickly to infections, neutrophils have amazing abilities to migrate fast and efficiently towards sites of infection and inflammation. Although neutrophils ability to migrate is perturbed in patients after major burns, no correlations have yet been demonstrated between altered migration and higher rate of infections and sepsis in these patients when compared to healthy individuals. To probe if such correlations exist, we designed microfluidic devices to quantify the neutrophil migration phenotype with high precision. Inside these devices, moving neutrophils are confined in channels smaller than the neutrophils and forced to make directional decisions at bifurcations and around posts. We employed these devices to quantify neutrophil migration across 18 independent parameters in 74 blood samples from 13 patients with major burns and 3 healthy subjects. Blinded, retrospective analysis of clinical data and neutrophil migration parameters revealed that neutrophils isolated from blood samples collected during sepsis migrate spontaneously inside the microfluidic channels. The spontaneous neutrophil migration is a unique phenotype, typical for patients with major burns during sepsis and often observed one or two days before the diagnosis of sepsis is confirmed. The spontaneous neutrophil migration phenotype is rare in patients with major burns in the absence of sepsis, and is not encountered in healthy individuals. Our findings warrant further studies of neutrophils and their utility for early diagnosing and monitoring sepsis in patients after major burns.
Scalable Auto-Tuning of Synthesis Parameters for Optimizing High-Performance Processors (2016)

Modern logic and physical synthesis tools provide numerous options and parameters that can drastically impact design quality; however, the large number of options leads to a complex design space difficult for human designers to navigate. By employing intelligent search strategies and parallel computing we can tackle this parameter tuning problem, thus automating one of the key design tasks conventionally performed by a human designer. In this paper we present a novel learning-based algorithm for synthesis parameter optimization. This new algorithm has been integrated into our existing autonomous parameter-tuning system, which was used to design multiple 22nm industrial chips and is currently being used for 14nm chips. These techniques show, on average, over 40% reduction in total negative slack and over 10% power reduction across hundreds of 14nm industrial processor macros while reducing overall human design effort. We also present a new higher-level system that manages parameter tuning of multiple designs in a scalable way. This new system addresses the needs of large design teams by prioritizing the tuning effort to maximize returns given the available compute resources.
High-affinity monoclonal antibodies to cell surface tumor antigen glypican-3 generated through a combination of peptide immunization and flow cytometry screening (2012)

Isolating high-affinity antibodies against native tumor antigens on the cell surface is not straightforward using standard hybridoma procedures. Here, we describe a combination method of synthetic peptide immunization and high-throughput flow cytometry screening to efficiently isolate hybridomas for cell binding. Using this method, we identified high-affinity monoclonal antibodies specific for the native form of glypcian-3 (GPC3), a target heterogeneously expressed in hepatocellular carcinoma (HCC) and other cancers. We isolated a panel of monoclonal antibodies (YP6, YP7, YP8, YP9 and YP9.1) for cell surface binding. The antibodies were used to characterize GPC3 protein expression in human liver cancer cell lines and tissues by flow cytometry, immunoblotting and immunohistochemistry. The best antibody (YP7) bound cell surface-associated GPC3 with equilibrium dissociation constant, KD = 0.3 nmol/L and was highly specific for HCC, not normal tissues or other forms of primary liver cancers (such as cholangiocarcinoma). Interestingly, the new antibody was highly sensitive in that it detected GPC3 in low expression ovarian clear cell carcinoma and melanoma cells. The YP7 antibody exhibited significant HCC xenograft tumor growth inhibition in nude mice. These results describe an improved method for producing high-affinity monoclonal antibodies to cell surface tumor antigens and represent a general approach to isolate therapeutic antibodies against cancer. The new high-affinity antibodies described here have significant potential for GPC3-expressing cancer diagnostics and therapy.
Mapping Quantitative Trait Loci in Plant Breeding Populations (2003)

Applied breeding programs evaluate large numbers of progeny derived from multiple related crosses for a wide range of agronomic traits and for tens to hundreds of molecular markers. This study was conducted to determine how these phenotypic and genetic data could be used for routinely mapping quantitative trait loci (QTLs). With dense maps, haplotype sharing of parents in a certain region is a good indicator for QTL-allele sharing, albeit not 100% perfect. With this in mind, an approximate and simple method has been developed where ancestral genome blocks in the parents of the crosses can be identified via haplotype analysis and where the effect of a putative QTL is then modeled and estimated per ancestral genome block. A simulation of an early-generation maize breeding scheme demonstrates the potential of the present approach for QTL detection in existing breeding programs. With this new QTL mapping strategy, the power, precision, and accuracy associated with large numbers of progeny may be attained, inferences about QTLs can be drawn across the breeding program rather than being limited to the sample of progeny from a single cross, and results may be much more valuable for marker-assisted breeding because the QTLs apply to agronomically challenging situations in the field.