gebhart/patrepeval huggingface dataset:
Engineering of high yield production of L‐serine in <i>Escherichia coli</i> (2015)

L-serine is a widely used amino acid that has been proposed as a potential building block biochemical. The high theoretical yield from glucose makes a fermentation based production attractive. In order to achieve this goal, serine degradation to pyruvate and glycine in E. coli MG1655 was prevented by deletion of three L-serine deaminases sdaA, sdaB, and tdcG, as well as serine hydroxyl methyl transferase (SHMT) encoded by glyA. Upon overexpression of the serine production pathway, consisting of a feedback resistant version of serA along with serB and serC, this quadruple deletion strain showed a very high serine production yield (0.45 g/g glucose) during small-scale batch fermentation in minimal medium. Serine, however, was found to be highly toxic even at low concentrations to this strain, which lead to slow growth and production during fed batch fermentation, resulting in a serine production of 8.3 g/L. The production strain was therefore evolved by random mutagenesis to achieve increased tolerance towards serine. Additionally, overexpression of eamA, a cysteine/homoserine transporter was demonstrated to increase serine tolerance from 1.6 g/L to 25 g/L. During fed batch fermentation, the resulting strain lead to the serine production titer of 11.7 g/L with yield of 0.43 g/g glucose, which is the highest yield reported so far for any organism.
Conversion of d-xylose to ethanol by the yeast Pachysolen tannophilus. [Patent application] (1981)

This invention relates to a fermentation process useful in the production of ethanol from renewable plant biomass. An ever-increasing interest in the development of such process has stemmed from the current emphasis on utilizing ethanol as an alternative liquid fuel. The lack of an effective fermentation process to use D-xylose has seriously diminished the practicality of plant biomass as a source of petroleum-sparing compounds.
Methods and Applications of Multilayer Silk Fibroin Laminates Based on Spatially Controlled Welding in Protein Films (2015)

Recent use of biopolymers as interface materials between planar, inorganic electronics and biological tissues has required the adaptation of micro‐ and nanofabrication techniques for use with these nontraditional materials. In this work, a method which builds on this principle for spatial control of adhesion in multilayer silk fibroin laminates is investigated. This is accomplished through the addition of a spatially patterned amorphous silk adhesive layer in between the films to be adhered, before thermally processing them with heat (120 °C) and pressure (80 Psi) according to established procedures. A one‐step method for rapid, high‐throughput fabrication is demonstrated, which establishes a strong (1100 kPa) bond between the layers independent of the initial processing conditions of the films. The adhesive layers can be patterned using existing silk fabrication techniques, allowing for the assembly of complex geometries including bilayers and microbubbles. Additionally, the utility of this method is demonstrated for potential applications in drug delivery and transient electronics. This approach provides a versatile method for construction of complex multilayer structures in silk, which with future work may ultimately improve the utility of this material as a bridge between high technology and the biomedical sciences.
<title>Local measurement of venous saturation in tissue with noninvasive near-infrared respiratory oximetry</title> (2001)

We present preliminary results of non-invasive, near-infrared measurements of venous saturation (SvO<SUB>2</SUB>) on the leg muscle of three anesthetized piglets. We have quantified the local SvO2 by analyzing the optical spectrum of the amplitude of the absorption oscillations synchronous with breathing. To induce a variation in the muscle SvO<SUB>2</SUB>, we performed measurements during a protocol involving a cyclic change in the fraction of oxygen inspired by the piglet over the range 10-100% (by volume). In all three piglets, we have found a good agreement between the SvO<SUB>2</SUB> values measured non-invasively with near-infrared spectroscopy (NIRS) and those measured invasively by the analysis of venous blood samples.
General statistical approaches to procedural map generation (2016)

Procedural content generation (PCG) studies the algorithmic creation of content (e.g., textures, maps), typically for games. PCG has become a popular research topic in recent years, but little has been done in terms of generalized content generators: approaches that can generate content for a variety of games without hand-tuning. We are interested in exploring statistical algorithms that could lead to generalized procedural map generators.
Leptin-Replacement Therapy for Lipodystrophy (2002)

Leptin-replacement therapy improved glycemic control and decreased triglyceride levels in patients with lipodystrophy and leptin deficiency. Leptin deficiency contributes to the insulin resistance and other metabolic abnormalities associated with severe lipodystrophy.
A comparison of some gradient‐encoded volume‐selection techniques for <i>in vivo</i> NMR spectroscopy (1987)

Four of the techniques proposed for in vivo volume-selected NMR spectroscopy have been compared using a simple phantom with a large background water signal which was outside the region of interest. The methods VSE, SPACE, SPARS, and DIGGER all use pulsed field gradients for spatial encoding and were tested with a symmetric and an asymmetric phantom. SPACE was used to obtain volume-selected 1H NMR spectra of a human leg, demonstrating excellent discrimination between bone marrow and muscle.
SARS Vaccine Development (2005)

Developing effective and safe vaccines is urgently needed to prevent infection by severe acute respiratory syndrome (SARS)-associated coronavirus (SARS-CoV). The inactivated SARS-CoV vaccine may be the first one available for clinical use because it is easy to generate; however, safety is the main concern. The spike (S) protein of SARS-CoV is the major inducer of neutralizing antibodies, and the receptor-binding domain (RBD) in the S1 subunit of S protein contains multiple conformational neutralizing epitopes. This suggests that recombinant proteins containing RBD and vectors encoding the RBD sequence can be used to develop safe and effective SARS vaccines.
Ribozyme-mediated reversal of the multidrug-resistant phenotype. (1994)

This study examined the effects of suppressing c-fos oncogene expression on multidrug resistance (MDR). A2780S human ovarian carcinoma cells with resistance to actinomycin D were isolated and the resultant A2780AD cells exhibited the MDR phenotype. A hammerhead ribozyme designed to cleave fos RNA cloned into the pMAMneo plasmid was transfected into A2780AD cells. Induction of the ribozyme resulted in decreased expression of c-fos, as well as that of the MDR gene (mdr-1), c-jun, and mutant p53. The transformants displayed altered morphology and restored sensitivity to chemotherapeutic agents comprising the MDR phenotype. An anti-mdr ribozyme separately expressed in A2780AD cells efficiently degraded mdr-1 mRNA. However, reversal of the MDR phenotype by the anti-mdr ribozyme occurred one-fourth as rapidly as that induced by the anti-fos ribozyme. These results reinforce the central role played by c-fos in drug resistance through its participation in signal transduction pathways.
Cell‐free synthesis of proteins that require disulfide bonds using glucose as an energy source (2006)

The primary objective of this work was to create a cell-free protein synthesis extract that produces proteins requiring disulfide bonds while using glucose as an energy source. We attempted to avoid using iodoacetamide (IAM) to stabilize the required oxidizing thiol redox potential, since previous IAM pretreatments prevented glucose utilization apparently by inactivating glyceraldehyde 3-phosphate dehydrogenase (G-3PDH). Instead, the glutathione reductase (Gor)-mediated disulfide reductase system was disabled by deleting the gor gene from the KC6 cell-extract source strain. The thioredoxin reductase (TrxB)-mediated system was disabled by first adding a purification tag to the trxB gene in the chromosome to create strain KGK10 and then by affinity removal of the tagged TrxB. This was expected to result in a cell extract devoid of all disulfide reductase activity, but this was not the case. Although the concentration of IAM required to stabilize oxidized glutathione in the KGK10 extract could be reduced 20-fold, IAM pretreatment was still required to avoid disulfide reduction. Nonetheless, active urokinase and murine granulocyte macrophage-colony stimulating factor (mGM-CSF) were produced in reactions with KGK10 extract either with affinity removal of TrxB or with 50 microM IAM pretreatment. With the less intensive IAM pretreatment, glucose could be used as an energy source in a production system that promotes oxidative protein folding. This new protocol offers an economically feasible cell-free system for the production of secreted mammalian proteins as human therapeutics or vaccines.
An Attention-based Recurrent Convolutional Network for Vehicle Taillight\n Recognition (2019)

Vehicle taillight recognition is an important application for automated\ndriving, especially for intent prediction of ado vehicles and trajectory\nplanning of the ego vehicle. In this work, we propose an end-to-end deep\nlearning framework to recognize taillights, i.e. rear turn and brake signals,\nfrom a sequence of images. The proposed method starts with a Convolutional\nNeural Network (CNN) to extract spatial features, and then applies a Long\nShort-Term Memory network (LSTM) to learn temporal dependencies. Furthermore,\nwe integrate attention models in both spatial and temporal domains, where the\nattention models learn to selectively focus on both spatial and temporal\nfeatures. Our method is able to outperform the state of the art in terms of\naccuracy on the UC Merced Vehicle Rear Signal Dataset, demonstrating the\neffectiveness of attention models for vehicle taillight recognition.\n
Synthesis of surface controlled nickel/palladium hydride nanodendrites with high performance in benzyl alcohol oxidation (2019)

Benzaldehyde byproduct is an imperative intermediate in the production of fine chemicals and additives. Tuning selectivity to benzaldehyde is therefore critical in alcohol oxidation reactions at the industrial level. Herein, we report a simple but innovative method for the synthesis of palladium hydride and nickel palladium hydride nanodendrites with controllable morphology, high stability, and excellent catalytic activity. The synthesized dendrites can maintain the palladium hydride phase even after their use in the chosen catalytic reaction. Remarkably, the high surface area morphology and unique interaction between nickel-rich surface and palladium hydride (β-phase) of these nanodendrites are translated in an enhanced catalytic activity for benzyl alcohol oxidation reaction. Our Ni/PdH0.43 nanodendrites demonstrated a high selectivity towards benzaldehyde of about 92.0% with a conversion rate of 95.4%, showing higher catalytic selectivity than their PdH0.43 counterparts and commercial Pd/C. The present study opens the door for further exploration of metal/metal-hydride nanostructures as next-generation catalytic materials.
Measurement of the Intensity and Phase of Ultrashort Pulses from a Ti:Sapphire Laser Using Second-Harmonic-Generation Frequency-Resolved Optical Gating (1994)

Recently, we developed a simple and general technique, which we call Frequency-Resolved Optical Gating (FROG), that succeeds in measuring the full intensity and phase evolution of an individual, arbitrary ultrashort pulse. 1 - 3 In brief, FROG involves measuring the pulse spectrogram, i.e., the spectrum of the signal pulse in an auto- or cross-correlation using any instantaneous nonlinearity, yielding signal intensity vs. delay and frequency. This trace can then be shown to fully and uniquely characterize the pulse—the pulse extraction problem is equivalent to two-dimensional phase retrieval, a solved problem from image science.
Optimized MIMO transmission and compression for interference mitigation with cooperative relay (2015)

This paper considers a novel use of device-to-device link for cooperative communication wherein a nearby user terminal acts as a relay in enabling both signal enhancement and common interference rejection at the intended destination. Assuming Gaussian transmission and Gaussian compress-and-forward relaying strategy for the multiple-input multiple-output (MIMO) relay channel with a finite-capacity out-of-band relay-destination link and with arbitrarily correlated noises, this paper proposes a coordinate ascent approach for iteratively optimizing the transmit covariance matrix at the source and the quantization noise covariance matrix at the relay. We show that the optimization of quantization noise covariance matrix under fixed input can be solved in closed form using a simultaneous diagonalization approach, while the optimization of transmit covariance matrix under fixed quantization can be cast as a convex optimization problem. This paper further introduces the concept of antenna pooling and illustrates the importance of accounting for the noise correlation across the user terminals due to common interference. We show that the optimized transmission and device-to-device relaying strategies that take advantage of the noise correlation can significantly improve the user throughput in a cellular environment by enabling interference rejection across the user terminals.
An Application-Level Approach for Privacy-Preserving Virtual Machine Checkpointing (2013)

Virtualization has been widely adopted in recent years in the cloud computing platform to improve server consolidation and reduce operating cost. Virtual Machine (VM) checkpointing refers to the act of saving a persistent snapshot (or checkpoint) of a VM's state at any instant. VM checkpointing can drastically prolong the lifetime and vulnerability of confidential or private user data in applications that execute within VMs. Simply encrypting the checkpoint does not reduce the lifetime of confidential data that should be quickly discarded after its use. In this paper, we present an application-level approach, called Privacy-preserving Checkpointing (PPC), which excludes confidential data from VM checkpoints, instead of encrypting such data. PPC enables an application programmer to register memory locations that represent the origins of confidential data. During the VM's execution, PPC performs information flow analysis to automatically track the propagation of confidential data through the application and various components of the VM, including the guest operating system. During VM checkpointing, the locations identified during the information flow analysis are excluded from the persistent checkpoint. We present the design and implementation of the PPC system in VirtualBox VMs running the commodity Linux operating system. We demonstrate the use of our system using the vim and gedit text editors. We also show that PPC introduces acceptable performance overhead.
Molecular thin film transistors with a subthreshold swing of 100 mV/decade (2004)

We have developed a molecular thin film transistor concept based on a high-mobility organic semiconductor (pentacene) and an ultra-thin, molecular self-assembling monolayer (SAM) gate dielectric. These transistors operate at voltages between 1 and 3 V, with a subthreshold swing as low as 100 mV/decade. For a transistor with a channel length of 5 /spl mu/m, we have measured a transconductance of 0.01 /spl mu/S//spl mu/m, to our knowledge the largest transconductance reported for an organic semiconductor device.
Private Data Objects: an Overview (2018)

We present Private Data Objects (PDOs), a technology that enables mutually untrusted parties to run smart contracts over private data. PDOs result from the integration of a distributed ledger and Intel Secure Guard Extensions (SGX). In particular, contracts run off-ledger in secure enclaves using Intel SGX, which preserves data confidentiality, execution integrity and enforces data access policies (as opposed to raw data access). A distributed ledger verifies and records transactions produced by PDOs, in order to provide a single authoritative instance of such objects. This allows contracting parties to retrieve and check data related to contract and enclave instances, as well as to serialize and commit contract state updates. The design and the development of PDOs is an ongoing research effort, and open source code is available and hosted by Hyperledger Labs [5, 7].
Terahertz polarization-division multiplexing within a four-wire waveguide (2022)

We demonstrate a new metal-wire waveguide topology, namely a four-wire waveguide, which simultaneously acts as a broadband terahertz polarization-division multiplexer and as a novel platform to realize the independent manipulation of polarization-division multiplexed terahertz signals.
Composite multilayer insulations for thermal protection of aerospace vehicles (1989)

Composite flexible multilayer insulation systems (MLI), consisting of alternating layers of metal foil and scrim cloth or insulation quilted together using ceramic thread, were evaluated for thermal performance and compared with a silica fibrous (baseline) insulation system. The systems studied included: (1) alternating layers of aluminoborosilicate (ABS) scrim cloth and stainless steel foil, with silica, ABS, or alumina insulation; (2) alternating layers of scrim cloth and aluminum foil, with silica or ABS insulation; (3) alternating layers of alumininum foil and silica or ABS insulation; and (4) alternating layers of aluminum-coated polyimide placed on the bottom of the silica insulation. The MLIs containing aluminum were the most efficient, measuring as little as half the backface temperature increase of the baseline system.
A Versatile Approach for Synthesis of 2,3-Dimethyl Chroman-4-ones, Intermediate for Calanolide Anti-HIV Agents,<i>VIA</i>Aldol/Mitsunobu Reactions (1996)

Abstract Combined aldol/Mitsunobu reactions have been employed for the first time for synthesis of 2,3-dimethyl chroman-4-ones, intermediates for calanolide anti-HIV agents. Thus, the lithium enolate of chromene 1 reacted with acetaldehyde at -78°C to afford the aldol products 4 and 5. Under Mitsunobu conditions (Ph3P/DEAD), the syn aldol product 4 led to the formation of trans-2,3-dimethyl chroman-4-one 2 while the anti aldol product 5 yielded both trans and cis derivatives (2 and 3). The use of other phosphorous and azo compounds in this reaction has also been investigated.
Aqueous Processing and Fiber Spinning of Recombinant Spider Silks (2002)

Spiders have captured the interest of scientists for many years because spider silks are among the toughest materials, having properties that surpass some man-made synthetic materials. Spinning recombinant silk to duplicate those properties has proved to be extremely difficult. This is the first known report of spinning recombinant silk fibers in an aqueous environment. The method seeks to keep the protein soluble throughout the process, not unlike the way the spider stores and spins silk. Recombinant silk proteins were produced by bacterial fermentation in which the cell pellets were lyophilized and lysed with organic acid. Silk protein was purified from the lysate by chromatography and processed in dilute denaturing buffer into a fiber spinning solution. Circular dichroism measurements of the silk solutions revealed an increase in β-sheet content as a function of time. Time-dependent self-association of silk protein was monitored in solution by dynamic light scattering. Furthermore, the observed increase in β-sheet content and self-association appear to be required for fiber formation. Recombinant silk fibers were 10−60 μm in diameter, water insoluble, and birefringent, indicating molecular orientation within the fiber.
A New Class of Biodegradable Thermosensitive Polymers. 2. Hydrolytic Properties and Salt Effect on the Lower Critical Solution Temperature of Poly(organophosphazenes) with Methoxypoly(ethylene glycol) and Amino Acid Esters as Side Groups (1999)

The hydrolytic properties of the novel biodegradable thermosensitive poly(organophosphazenes) with methoxypoly(ethylene glycol) (MPEG) and amino acid esters as side groups have been studied by means of gel permeation chromatography and 31P and 1H NMR spectroscopy and by identification of the hydrolysis products. The polymers substituted with α-amino acid esters were hydrolyzed faster than that with β-amino acid ester. The higher content of the amino acid ester in the polymer backbone caused enhanced hydrolysis. The rate of the polymer degradation decreased in the order of methyl > ethyl > benzyl esters. The polymer hydrolysis occurred more rapidly in both acidic and basic buffer solutions than in the neutral solution. The 31P NMR spectra of the polymers with high content of glycine ethyl ester showed that the polyphosphazene backbone underwent fragmentation mostly to small molecules after incubation in the buffer solution of pH 10 for 26 days. Phosphates and ammonia were formed as hydrolysis products in most cases. The hydrolytic behaviors of the present thermosensitive polyphosphazenes are consistent with the conventional acid-catalyzed degradation mechanism, and a detailed pathway to their hydrolytic degradation is proposed. The salt and pH effects on the thermosensitivity of the polymers were also examined by measuring their lower critical solution temperature (LCST) in aqueous solutions containing various inorganic and organic salts. When various inorganic salts were added to aqueous solutions of the polymers, their salting-in and salting-out effects were found to be mainly dependent on the anions of the salts. On the other hand, in the case of tetraalkylammonium halides which are organic salts, cations seem to play an important role: the salting-in effect is stronger with increasing alkyl chain of the ammonium salt. The aqueous solutions of the polymers showed higher LCST in the acidic solution than in the neutral and basic buffer solutions.
Overcoming Fundamental Limitations in Adsorbent Design: Alkene Adsorption by Non‐porous Copper(I) Complexes (2020)

Purifying alkenes from alkanes requires cryogenic distillation. This consumes energy equivalent to countries of ca. 5 million people. Replacing distillation with adsorption processes would significantly increase energy efficiency. Trade-offs between kinetics, selectivity, capacity, and heat of adsorption have prevented production of an optimal adsorbent. We report adsorbents that overcome these trade-offs. [Cu-Br]<sub>3</sub> and [Cu-H]<sub>3</sub> are air-stable trinuclear complexes that undergo reversible solid-state inter-molecular rearrangements to produce dinuclear [Cu-Br⋅(alkene)]<sub>2</sub> and [Cu-H⋅(alkene)]<sub>2</sub> . The reversible solid-state rearrangement, confirmed in situ using powder X-ray diffraction, allows adsorbent design trade-offs to be overcome, coupling low heat of adsorption (-10 to -17 kJ mol<sup>-1</sup><sub>alkene</sub> ), high alkene:alkane selectivity (47; 29), and uptake capacity (>2.5 mol<sub>alkene</sub> mol<sup>-1</sup><sub>Cu3</sub> ). Most remarkably, [Cu-H]<sub>3</sub> displays fast uptake and regenerates capacity within 10 minutes.