gebhart/patrepeval huggingface dataset:
Isolation of a cDNA Encoding a Novel Member of the Transglutaminase Gene Family from Human Keratinocytes (1998)

We developed a method using a single set of degenerate oligonucleotide primers for amplification of the conserved active site of transglutaminases by reverse transcription-polymerase chain reaction (RT-PCR) and identification of the PCR products by cleavage with diagnostic restriction enzymes. We demonstrate amplification of tissue transglutaminase (TGC), keratinocyte transglutaminase (TGK), prostate transglutaminase (TGP), the a-subunit of factor XIII, and band 4.2 protein from different human cells or tissues. Analysis of normal human keratinocytes revealed expression of a transglutaminase different from the expected and characterized transglutaminase gene products. A full-length cDNA for the novel transglutaminase (TGX) was obtained by anchored PCR. The deduced amino acid sequence encoded a protein with 720 amino acids and a molecular mass of approximately 81 kDa. A comparison of TGX to the other members of the gene family revealed that the domain structure and the residues required for enzymatic activity and Ca2+ binding are conserved and showed an overall sequence identity of about 35%. Two transcripts with an apparent size of 2.2 and 2.8 kilobases were detected with a specific probe for TGX on Northern blots of human foreskin keratinocyte mRNA, indicating the presence of alternatively spliced mRNAs. cDNA sequencing revealed a shorter TGX transcript lacking the sequence homologous to that encoded by exon III of other transglutaminase genes. TGX expression increased severalfold when keratinocyte cultures were induced to differentiate by suspension or growth to postconfluency, suggesting that TGX contributes to the formation of the cornified envelope.
PPAC: A Versatile In-Memory Accelerator for Matrix-Vector-Product-Like\n Operations (2019)

Processing in memory (PIM) moves computation into memories with the goal of\nimproving throughput and energy-efficiency compared to traditional von\nNeumann-based architectures. Most existing PIM architectures are either\ngeneral-purpose but only support atomistic operations, or are specialized to\naccelerate a single task. We propose the Parallel Processor in Associative\nContent-addressable memory (PPAC), a novel in-memory accelerator that supports\na range of matrix-vector-product (MVP)-like operations that find use in\ntraditional and emerging applications. PPAC is, for example, able to accelerate\nlow-precision neural networks, exact/approximate hash lookups, cryptography,\nand forward error correction. The fully-digital nature of PPAC enables its\nimplementation with standard-cell-based CMOS, which facilitates automated\ndesign and portability among technology nodes. To demonstrate the efficacy of\nPPAC, we provide post-layout implementation results in 28nm CMOS for different\narray sizes. A comparison with recent digital and mixed-signal PIM accelerators\nreveals that PPAC is competitive in terms of throughput and energy-efficiency,\nwhile accelerating a wide range of applications and simplifying development.\n
A <i>Solanum lycopersicum</i> catechol‐<i>O</i>‐methyltransferase involved in synthesis of the flavor molecule guaiacol (2011)

O-methyltransferases (OMT) are important enzymes that are responsible for the synthesis of many small molecules, which include lignin monomers, flavonoids, alkaloids, and aroma compounds. One such compound is guaiacol, a small volatile molecule with a smoky aroma that contributes to tomato flavor. Little information is known about the pathway and regulation of synthesis of guaiacol. One possible route for synthesis is via catechol methylation. We identified a tomato O-methyltransferase (CTOMT1) with homology to a Nicotiana tabacum catechol OMT. CTOMT1 was cloned from Solanum lycopersicum cv. M82 and expressed in Escherichia coli. Recombinant CTOMT1 enzyme preferentially methylated catechol, producing guaiacol. To validate the in vivo function of CTOMT1, gene expression was either decreased or increased in transgenic S. lycopersicum plants. Knockdown of CTOMT1 resulted in significantly reduced fruit guaiacol emissions. CTOMT1 overexpression resulted in slightly increased fruit guaiacol emission, which suggested that catechol availability might limit guaiacol production. To test this hypothesis, wild type (WT) and CTOMT1 that overexpress tomato pericarp discs were supplied with exogenously applied catechol. Guaiacol production increased in both WT and transgenic fruit discs, although to a much greater extent in CTOMT1 overexpressing discs. Finally, we identified S. pennellii introgression lines with increased guaiacol content and higher expression of CTOMT1. These lines also showed a trend toward lower catechol levels. Taken together, we concluded that CTOMT1 is a catechol-O-methyltransferase that produces guaiacol in tomato fruit.
Resource-sensitive profile-directed data flow analysis for code optimization (1997)

Instruction schedulers employ code motion as a means of instruction reordering to enable scheduling of instructions at points where the resources required for their execution are available. In addition, driven by the profiling data, schedulers take advantage of predication and speculation for aggressive code motion across conditional branches. Optimization algorithms for partial dead code elimination (PDE) and partial redundancy elimination (PRE) employ code sinking and hoisting to enable optimization. However, unlike instruction scheduling, these optimization algorithms are unaware of resource availability and are incapable of exploiting profiling information, speculation, and predication. In this paper we develop data flow algorithms for performing the above optimizations with the following characteristics: (i) opportunities for PRE and PDE enabled by hoisting and sinking are exploited; (ii) hoisting and sinking of a code statement is driven by availability of functional unit resources; (iii) predication and speculation is incorporated to allow aggressive hoisting and sinking; and (iv) path profile information guides predication and speculation to enable optimization.
Characterisation of the Diagnostic Window of Serum Glial Fibrillary Acidic Protein for the Differentiation of Intracerebral Haemorrhage and Ischaemic Stroke (2008)

The time window between 2 and 6 h after stroke onset is best for using GFAP to differentiate between ICH and IS. In the very early phase (i.e. <2 h), sensitivity for detecting ICH is low, thus hampering the application of GFAP as a near-patient test in the prehospital phase.
Reversible Chain Transfer Catalyzed Polymerization of Methyl Methacrylate with In-Situ Formed Alkyl Iodide Initiator (2009)

A method utilizing generation of an alkyl iodide (low-mass dormant species) in situ formed in polymerization was adopted to reversible chain transfer catalyzed polymerizations (RTCP) (living radical polymerizations) with several nitrogen and phosphorus catalysts. The polymerization of methyl methacrylate afforded low-polydispersity polymers (Mw/Mn ~1.2–1.4), with Mn values predicted to high conversions; where Mn and Mw are the number- and weight-average molecular weights respectively. This method is robust and would enhance the utility of RTCP.
Coherent Viterbi and threshold demodulators for pulse-driven GMSK signals (2003)

Pulse-driven Gaussian minimum shift keying (PDGMSK) was introduced to facilitate a trade between bandwidth efficiency and receiver complexity when using the classical GMSK waveform. The waveform was purposely devised to converge, as the data rate decreases, to SDPSK or DPSK without expanding the absolute bandwidth. This paper studies the optimal coherent demodulation of the PDGMSK waveform, and provides simulation results of a near-optimal Viterbi demodulator and a low-complexity threshold demodulator in both single and multiple carrier settings. Trade-off among the signal-to-noise ratio (SNR), adjacent channel interference (ACI) level and carrier frequency spacing is also provided.
Conservation of Mannan Synthesis in Fungi of the Zygomycota and Ascomycota Reveals a Broad Diagnostic Target (2018)

A key question asked when faced with an infection, an infestation, or environmental damage is whether it is a fungus. Identification of fungi as the cause of the problem can lead to remediation or treatment. Zygomycetes and ascomycetes account for the vast majority of fungal causes of human, animal, and plant disease, large-scale biodiversity loss, agricultural spoilage, and contamination of water-damaged buildings. These studies revealed the conservation of a common cell wall structural component of zygomycetes and ascomycetes to be a diagnostic target applicable to multiple pathogenic fungi and have leveraged that insight for practical use. Monoclonal antibodies reactive with this pan-fungal structure were produced and used to construct immunoassays (including ELISA and lateral flow assay) for detection of a broad range of pathogenic fungi.
Design and dynamic analysis of a Transformable Hovering Rotorcraft (THOR) (2017)

This paper describes the Transformable HOvering Rotorcraft (THOR), a prototype Unmanned Aerial Vehicle (UAV) that explores a novel approach in combining the range and speed of a horizontal flying platform with the hovering and maneuverability of a rotor-wing. This is achieved by integrating a tailless flying wing configuration with a single-axis rotor, or monocopter. By maintaining full utilization of all aerodynamic surfaces and propulsion sources in both flight modes, this method represents the most structurally efficient approach to achieving a cruising mode and a hovering mode on the same frame. Using a dual servo and motor configuration, we propose an under-actuated system that is able to achieve controllability in 4 degrees of freedom while in its horizontal cruising mode and in 5 degrees of freedom while in its hovering mode. In both indoor and outdoor experiments, the UAV is able to transition between either flight modes seamlessly and repeatedly without the need for any additional mechanisms and actuators.
Silicon/metal silicide heterostructures grown by molecular beam epitaxy (1980)

Epitaxial NiSi2 and CoSi2 layers have been grown on crystalline silicon by molecular beam epitaxy (MBE). Stoichiometric, highly crystalline films can be grown by either silicon-metal codeposition or by pure metal deposition on substrates heated to 550–800 °C. Crystalline quality is relatively insensitive to deposition conditions. Film smoothness is maximized by codeposition at temperatures near 600 °C. Both silicides have been epitaxially overgrown with silicon producing a fully crystalline silicon/metal silicide/silicon heterostructure.
Insitu (2011)

Architecture is design in spatial context. The only current methods for representing context involve designing in a heavyweight computer-aided design system, using a full model of existing buildings and landscape, or sketching on a panoramic photo. The former is too cumbersome; the latter is too restrictive in viewpoint and in the handling of occlusions and topography. We introduce a novel approach to presenting context such that it is an integral component in a lightweight conceptual design system. We represent sites through a fusion of data available from different sources. We derive a site model from geographic elevation data, on-site point-to-point distance measurements, and images of the site. To acquire and process the data, we use publicly available data sources, multidimensional scaling techniques and refinements of recent bundle adjustment techniques. We offer a suite of interactive tools to acquire, process, and combine the data into a lightweight stroke and image-billboard representation. We create multiple and linked pop-ups derived from images, forming a lightweight representation of a three-dimensional environment. We implemented our techniques in a stroke-based conceptual design system we call Insitu. We developed our work through continuous interaction with professional designers. We present designs created with our new techniques integrated in a conceptual design system.
Synthesis of ammonium cyanate and urea from NO (reacting with CO and hydrogen via cyanate species) over noble metal and base metal catalysts (ruthenium or platinum on alumina) (1983)

Synthesis of ammonium cyanate and urea from NO reacting with CO and hydrogen via cyanate species over noble metal and base metal catalysts (ruthenium or platinum on alumina) is discussed.
Selective Process for Efficient Isolation of Soil <i>Bacillus</i> spp (1987)

We were able to isolate Bacillus thuringiensis from environmental samples with a background of 10 bacteria per g of soil. Our selection process differed significantly from classical selection methods which permit only the desired organism to grow. In our process, germination of B. thuringiensis spores was selectively inhibited by sodium acetate, while most of the undesired sporeformers germinated. Next, all of the nonsporulated microbes were eliminated by heat treatment at 80 degrees C for 3 min. The surviving spores were then plated on a rich agar medium and allowed to grow until they sporulated. Of random colonies picked from agar, 20 to 96% were crystal-forming Bacillus species. B. thuringiensis and B. sphaericus were routinely selected by this method.
A Motion-Compensated Interframe Coding Scheme for Television Pictures (1982)

A motion-compensated prediction system for interframe coding is proposed. An interframe coding system is developed using this prediction method and second-order temporal prediction. Real-time hardware of reasonable circuit size using this coding system for monochrome TV pictures has been constructed. Assessments have been made of the picture quality of coded/decoded pictures from a variety of broadcast television programs. Quality was good for almost all such programs. A subjective test of picture quality was performed under stringent conditions, using some of the most difficult scenes selected in earlier experiments.
Optimal Distance Bounds on Time-Series Data (2009)

Most data mining operations include an integral search component at their core. For example, the performance of similarity search or classification based on Nearest Neighbors is largely dependent on the underlying compression and distance estimation techniques. As data repositories grow larger, there is an explicit need not only for storing the data in a compressed form, but also for facilitating mining operations directly on the compressed data. Naturally, the quality or tightness of the estimated distances on the compressed objects directly affects the search performance. We motivate our work within the setting of search engine weblog repositories, where keyword demand trends over time are represented and stored as compressed time-series data. Search and analysis over such sequence data has important applications for the search engines, including discovery of important news events, keyword recommendation and efficient keyword-to-advertisement mapping. We present new mechanisms for very fast search operations over the compressed time-series data, with specific focus on weblog data. An important contribution of this work is the derivation of optimally tight bounds on the Euclidean distance estimation between compressed sequences. Since our methodology is applicable to sequential data in general, the proposed technique is of independent interest. Additionally, our distance estimation strategy is not tied to a specific compression methodology, but can be applied on top of any orthonormal based compression technique (Fourier, Wavelet, PCA, etc). The experimental results indicate that the new optimal bounds lead to a significant improvement in the pruning power of search compared to previous state-of-the-art, in many cases eliminating more than 80% of the candidate search sequences.
Preliminary Design of the Hybrid Air-launching Rocket for Nanosat (2007)

Air-Launching is an effective method that can launch the 'Nanosat' for low launching cost. In this study, the preliminary design of the air-launching micro rocket was performed. Mission and trajectory optimization was performed and the propulsion system was designed based on the mission design. A supersonic air launching rocket with total weight of 830.95 kg, the payload weight of 3.56 kg and the propulsion system length of 5.89 m has been designed.
Pharmacokinetics and Pharmacodynamics of Recombinant FGF‐2 in a Phase I Trial in Coronary Artery Disease (2001)

Fibroblast growth factor-2 (FGF-2) is a heparin-binding protein capable of inducing angiogenesis in multiple animal models of chronic ischemia. The pharmacokinetics and pharmacodynamics of a single dose of recombinant FGF-2 (rFGF-2) administered by intracoronary or intravenous infusion were evaluated in a Phase I trial in 66 patients with severe coronary artery disease. rFGF-2 displayed biphasic elimination with a mean studywide distribution t1/2 of 21 minutes and a mean apparent terminal elimination t1/2 of 7.6 hours. Systemic exposure to rFGF-2 was comparable following intracoronary or intravenous administration. Peak plasma concentration and area under the concentration-time curve increased proportionally with dose, indicating linear pharmacokinetics over the dose range examined (0.33 to 48.0 micrograms/kg). Greater systemic exposure was observed when heparin was administered closer to rFGF-2 infusion, consistent with slower clearance of heparin/rFGF-2 complexes. Infusion of rFGF-2 was associated with changes in acute hemodynamics. While a clear PK/PD dose-response relationship was not established, a trend toward hypotension and tachycardia with higher rFGF-2 doses was observed.
A 2-element reconfigurable MIMO antenna consisting of miniaturized patch elements (2016)

In this paper, a frequency reconfigurable multiple-input-multiple-output (MIMO) antenna is presented. The proposed antenna consists of miniaturized patch antenna elements, loaded with varactor diodes to achieve frequency reconfigurability. The antenna has a bandwidth of 50 MHz with frequency reconfigurability range from 2.1 GHz to 2.4 GHz. The antenna is designed on an FR4 substrate and occupying a space of 50×100×0.8 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> . The antenna is analyzed from far-field characteristics as well as for MIMO performance parameters.
Peptide-based cationic liposome-mediated gene delivery (2011)

As peptide-based cationic liposomes still hold some limitations, future research needs to select suitable peptide heads and investigate the surface modification of peptide cationic liposomes, in order to facilitate targeting and reduce cytotoxicity.
Scalable nanomanufacturing of millimetre-length 2D NaxCoO2 nanosheets (2012)

A novel, scalable nanomanufacturing technique is reported for batch fabrication of nanoscale-thick Na0.7CoO2 nanosheets. The nanomanufacturing technique is a high-yield, bottom-up process that is capable of producing tens of thousands of nanosheets stacked into a macro-scale pellet. The nanosheets are uniform in length and shape with very high crystal anisotropy. The nanosheet thicknesses can be 10–100 nm while their lengths can measure up to 1.8 mm long. The typical dimension ratios are highly anisotropic, at 10−5:1 : 1 (thickness:length:width). X-ray synchrotron studies indicate that the 2D crystals are stacked in a turbostratic arrangement with rotational misalignment with respect to the stacking axis. The stacked nanosheets are readily delaminated into very large (350 μm × 150 μm × 100 nm) free-standing 2D crystals. The novel nanomanufacturing technique is based on sol–gel and electric-field induced kinetic-demixing followed by a brief high temperature treatment, thus providing an efficient means of large scale crystal growth requiring only a simple furnace and power supply. Evidence shows that the demixing process increases the concentration of Na ions and that demixing is necessary to produce the millimetre-length nanosheets. Electric field induced kinetic-demixing is successfully performed at low temperatures (<300 °C), which is more than three times lower than past kinetic-demixing temperatures.
New opioid peptides, peptidomimetics, and heterocyclic compounds from combinatorial libraries (1999)

Abstract: Here we review the use of combinatorial libraries in opioid receptor assays. Following a brief description of the history of the combinatorial field, methods for the generation of synthetic libraries and the deconvolution of mixture-based libraries are presented. Case studies involving opioid assays used to demonstrate the viability of combinatorial libraries are described. The identification of new opioid peptides from combinatorial libraries is reviewed. The peptides found are composed of L-amino acids, D-amino acids, or L-, D-, and unnatural amino acids, and range from tetrapeptides to decapeptides. Likewise, new opioid compounds identified from peptidomimetic libraries, such as peptoids and alkylated dipeptides, and those identified from acyclic (e.g., polyamine, urea) and heterocyclic (e.g., bicyclic guanidine) libraries, are reviewed. © 2000 John Wiley & Sons, Inc. Biopoly 51: 379–390, 1999
A Rational Approach to the Design and Synthesis of a New Bradykinin B<sub>1</sub> Receptor Antagonist (2000)

We have previously synthesized a potent and selective B(1) bradykinin receptor antagonist, JMV1645 (H-Lys-Arg-Pro-Hyp-Gly-Igl-Ser-D-BT-OH), containing a dipeptide mimetic ((3S)-amino-5-carbonylmethyl-2,3-dihydro-1, 5-benzothiazepin-4(5H)-one (D-BT) moiety) at the C-terminal. Analogues of this potent B(1) bradykinin receptor antagonist in which the central Pro(2)-Hyp(3)-Gly(4)-Igl(5) tetrapeptide has been replaced by constrained N-1-substituted-1,3,8-triazaspiro¿4. 5decan-4-one ring system were synthesized. Among these analogues, compound JMV1640 (1) was found to have an affinity of 24.10 +/- 9.48 nM for the human cloned B(1) receptor. It antagonized the ¿des-Arg(10)-kallidin-induced contraction of the human umbilical vein (pA(2) = 6.1 +/- 0.1). Compound 1 was devoid of agonist activity at the kinin B(1) receptor. Moreover, it did not bind to the human cloned B(2) receptor. Therefore, JMV1640 constitutes a lead compound for the rational search of nonpeptide B(1) receptor analogues based on the BK sequence.
Performance of Automated Calibration for Water Distribution Systems (2004)

Use of optimization to calibrate a water distribution model has been the subject of considerable research. Such models have not been systematically studied on realistic sized systems to any great extent. This paper presents an evaluation of Darwin Calibrator, a genetic algorithm approach to achieving optimal calibration. It shows that the Calibrator works well when given a sufficient amount of good quality data and examines the relationship between the quality of the data and the quality of results.
Optical and near infrared plasmonic filters integrated with terahertz metamaterials (2014)

We have designed, simulated and fabricated multi-spectral materials operating in visible, near infrared and terahertz wavebands by combining plasmonic filters with metamaterials. Multi-spectral materials offer a path to the creation of co-axial multi-spectral imagers.