gebhart/patrepeval huggingface dataset:
Cp*–‐Ruthenium–Nickel‐Based H2‐Evolving Electrocatalysts as Bio‐inspired Models of NiFe Hydrogenases (2010)

Abstract Three dinuclear nickel–ruthenium complexes [Ni(xbsms)RuCp*(L)](PF 6 ) [H 2 xbsms = 1,2‐bis(4‐mercapto‐3,3‐dimethyl‐2‐thiabutyl)benzene; Cp* = pentamethylcyclopentadienyl; L = CH 3 CN, CO and O 2 ] are reported that act as bio‐inspired mimics of NiFe hydrogenases. Because of an increased electron density at the metal centres in comparison with the previously described [Ni(xbsms)RuCp(L)](PF 6 ) (Cp = cyclopentadienyl) analogues, these compounds catalyze the evolution of hydrogen from Et 3 NH + in DMF with an overpotential reduced by around 50 mV, thereby corroborating a previously established structure–function relationship [ Eur. J. Inorg. Chem. 2007 , 18 , 2613–2626; Chem. Eur. J. 2009 , 1 5, 9350–9364]. In addition, the steric protection provided by the bulky Cp* – ligand results in an increased catalytic rate and stability upon cycling.
Kinetics of hydrolysis of endocytosed substrates by mammalian cultured cells: Early introduction of lysosomal enzymes into the endocytic pathway (1990)

The kinetics of exposure of endocytosed material to two lysosomal enzymes were determined for a number of cultured cell lines using fluorogenic substrates. Hydrolysis of endocytosed substrates for cathepsin B and acid phosphatase was observed to begin within 3-10 min of substrate addition and to proceed linearly for up to 60 min thereafter. Hydrolysis of the cathepsin B substrate was not affected by inhibition of protein synthesis with cycloheximide, indicating that the enzymes present in early endosomes are not exclusively newly synthesized. As had been observed previously for a cathepsin B substrate (Roederer, M., Bowser, R., and Murphy, R. F., J. Cell. Physiol., 131:200-209, 1987), hydrolysis of the acid phosphatase substrate was not blocked at temperatures below 20 degrees C. The results suggest that the endosome is the primary site of initial exposure of endocytosed material to hydrolytic enzymes.
Trichinella spiralis: Genomic Application to Control a Zoonotic Nematode (2010)

The nematode Trichinella spiralis and related species are zoonotic food-borne pathogens of humans. The muscle larval stage of this parasite establishes a chronic infection in skeletal muscle cells of humans who acquire trichinellosis. Muscle larvae also reside in skeletal muscles of animals, swine in particular, and other food animals, including game animals. These muscle larvae are the source of zoonotic transmission to humans. Once established, muscle larvae become less susceptible to anthelmintics that are effective against other stages of the parasite. Very little information exists to guide discovery of new drug targets and improved methods of eliminating muscle larvae established in muscle cells of humans or food animals. Here we discuss progress that has been made on sequencing the genome of T. spiralis. This informational resource should prove valuable for dissecting molecular characteristics of this parasite that warrant investigation as targets for chemotherapy. The availability of the T. spiralis genome has made possible the comparison of genomes from nematodes that span the evolutionary extremes of the phylum Nematoda. We describe a pan-phylum comparison of genomes that is underway. This comparative genomics approach is expected to identify molecular characteristics that are conserved among all nematodes, and hence applicable to nematode pathogens throughout the phylum, including species from the genus Trichinella. T. spiralis expression data for muscle larvae has been integrated with genome sequences to identify specific genes and proteins with relevance to control of this stage of the parasite. Examples are discussed in which genomic information may advance understanding of T. spiralis biology and new methods for treating infections by this parasite.
Fast Quadtree Decomposition Using Histograms (1986)

Quadtree decomposition is one of the methods of representing binary image data at multiple resolutions. Such representations have found application in many areas of image processing. This paper describes a novel implementation of quadtree generation using histograms. The histogram based implementation is fast and easy to implement on any histogram generating hardware. The number of histograms to be computed depends upon the size of the original image, the size of the smallest block into which the image is to be resolved, and on the number of gray levels handled by the histogram generating hardware. The paper also describes a fast algorithm to reconstruct binary images from quadtree decomposition using video rate lookup table processing.
Detection and characterization of a high molecular weight human lung carcinoma-associated glycoprotein. (1990)

We have defined a human lung carcinoma antigen using murine monoclonal antibodies (DF-L1 and DF-L2) prepared against a primary adenocarcinoma of the lung. This antigen is expressed on the surface of human lung carcinoma cell lines and has an apparent Mr of 350,000-420,000. Immunoperoxidase staining has demonstrated expression of the antigen in the cytoplasm and membranes of adenocarcinomas and squamous cell carcinomas but not small cell tumors of the lung. Immunoprecipitation of the antigen following radiolabeling has demonstrated the presence of both protein and carbohydrate. Antigen purified by immunoaffinity was used to study the epitopes defined by monoclonal antibodies DF-L1 and DF-L2. The results indicate that the DF-L1 epitope primarily involves a peptide structure, while the DF-L2 epitope is comprised in part by peptide and O-linked carbohydrate. In contrast, there was no detectable evidence for the presence of N-linked glycosylation. The results also demonstrate that this antigen circulates at elevated levels in patients with carcinoma of the lung. These findings are similar to previous reports of high molecular weight glycoproteins in breast and ovarian carcinomas. Indeed, the present results in lung cancer identify another member of this heterogeneous family of human carcinoma-associated glycoproteins.
P4–012: Allopregnanolone as a regenerative therapeutic for Alzheimer's disease, 1: From discovery to phase I multiple‐ascending‐dose clinical trial (2013)

Regenerative therapeutics hold the promise of self-renewal and repair. Aging and Alzheimer's are marked by a decline in self-renewal and repair, but a capacity for regeneration is retained. Allopregnanolone (Allo) is a pleiotropic regenerative therapeutic that promotes neurogenesis and restores cognitive function in both a pre-clinical AD model and wild type aged mice while also reducing AD pathology in AD mouse brain. Further, Allo promoted regeneration of human neural stem cells. Allo is a neurosteroid endogenous to the brain of low molecular weight and blood brain barrier penetrant with abundant existing safety data in animals and humans. Its mechanisms of neural stem cell proliferation, restoration of cognitive function and AD pathology reduction are well characterized and unlikely to induce amyloid related imaging abnormalities (ARIA). Based on a foundation of pre-clinical discovery, translational research, clinical development with NIA USC ADRC and FDA assessment and IND approval, we designed a Phase 1 multiple ascending dose clinical trial of Allo doses administered in a regenerative regimen of once-per-week for twelve weeks to establish a safe and tolerated dose of Allo necessary to advance to a Phase 2 efficacy trial. A Phase 1 multiple ascending dose trial of Allo in participants diagnosed with MCI due to AD and early AD was designed. Primary safety objectives are to determine: maximally tolerated dose; incidence and severity of treatment emergent adverse events; designated medical events; clinically important changes in safety assessments including ARIA. Secondary objectives are to: assess potential short-term effects of Allo dosing on cognition and MRI indicators of AD; inform subsequent phase 2 proof of concept trial with MRI-based biomarkers of regenerative efficacy. Allopregnanolone is a first in class regenerative therapeutic for MCI and AD that targets endogenous neural stem cells and disease modifying mechanisms. Trial outcomes will provide: 1) an estimated safe and well-tolerated dose of Allo; 2) parameter estimates for cognitive efficacy to advance to a Phase 2 proof of concept trial of Allo; and 3) parameter estimates for MRI-based biomarkers.
ITQ-15: The first ultralarge pore zeolite with a bi-directional pore system formed by intersecting 14- and 12-ring channels, and its catalytic implications (2004)

The pore topology of ITQ-15 zeolite consists of an ultra-large 14-ring channel that is intersected perpendicularly by a 12-ring pore; acid sites have been introduced in its framework and this unique structure shows advantages over unidirectional ultralarge pore zeolites for diffusing and reacting large molecules.
Effective Contact Resistivity Reduction for Mo/Pd/n-In0.53Ga0.47 as Contact (2019)

We compare the contact characteristics for Mo, Pd, and Ti on n-InGaAs layer with a range of active donor concentration from 1.6×10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">18</sup> cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-3</sup> to 4.8×10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">19</sup> cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-3</sup> . The Fermi level pinning of 0.18 eV lower than the bottom of n-InGaAs conduction band is experimentally manifested. It is also revealed that the contact resistivity (ρ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">c</sub> ) of Mo/nInGaAs contact clearly outperforms after annealing. However, for the first time, we demonstrate that the Mo/Pd (2nm)/n-InGaAs contact can achieve a ρ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">c</sub> 35% and 20% lower than a single Mo/n-InGaAs contact after annealing at 400 °C and 450 °C for 1min, respectively.
Consideration of feed-through voltage in amorphous-Si TFT's (1993)

Feedthrough voltage is an important factor in designing integrated data drive circuits and display area in thin-film-transistor liquid-crystal displays (TFT LCDs). With respect to feedthrough voltage, only the gate-source overlay capacitance has been considered in amorphous-Si (a-Si) TFTs, because of their staggered structure with overlap area. It is pointed out that, in a-Si TFTs designed as active elements, feedthrough voltage is mainly due to the carrier redistribution. The main reason is that, since the field-effect mobility is low (W/L>1), the leakage current must be kept low (L>or=10 mu m), and an active layer is inserted in the overlap area (unlike the case with MOS device structures), the area of the active layer is large. Taking the carrier redistribution into account, the maximum difference between the voltage obtained using the modified model and the experimental voltage is within 20%. By comparison, the results obtained using the previous model for TFTs are approximately three times smaller than the experimental results.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Quantum message-passing algorithm for optimal and efficient decoding (2021)

Recently, Renes proposed a quantum algorithm called belief propagation with quantum messages (BPQM) for decoding classical data encoded using a binary linear code with tree Tanner graph that is transmitted over a pure-state CQ channel [Renes, NJP 19 072001 (2017)]. The algorithm presents a genuine quantum counterpart to decoding based on the classical belief propagation algorithm, which has found wide success in classical coding theory when used in conjunction with LDPC or Turbo codes. More recently Rengaswamy et al. [npj Quantum Information 7 97 (2021)] observed that BPQM implements the optimal decoder on a small example code. Here we significantly expand the understanding, formalism, and applicability of the BPQM algorithm with the following contributions. First, we prove analytically that BPQM realizes optimal decoding for any binary linear code with tree Tanner graph. We also provide the first formal description of the BPQM algorithm in full detail and without any ambiguity. In so doing, we identify a key flaw overlooked in the original algorithm and subsequent works which implies quantum circuit realizations will be exponentially large in the code dimension. Although BPQM passes quantum messages, other information required by the algorithm is processed globally. We remedy this problem by formulating a truly message-passing algorithm which approximates BPQM and has quantum circuit complexity $\mathcal{O}(\text{poly } n, \text{polylog } \frac{1}ε)$, where $n$ is the code length and $ε$ is the approximation error. Finally, we also propose a novel method for extending BPQM to factor graphs containing cycles by making use of approximate cloning. We show some promising numerical results that indicate that BPQM on factor graphs with cycles can significantly outperform the best possible classical decoder.
READY: Completeness is in the Eye of the Beholder (2017)

Modern database systems support one set of integrity constraints per database.Imagine you could specify multiple sets of integrity constraints per database, one for each type of application.This paper argues why this might be a good idea and introduces a system that implements this idea.
Performance of block‐coded land mobile satellite systems (2008)

Abstract Although various measurements have indicated that mobile satellite channels are not memoryless, most related coded system performance analysis assumes perfect interleaving is in place so that the effect of channel memory can be completely ignored. This paper presents a systematic method to accurately and efficiently predict the performance of errors‐and‐erasures or errors‐only decoders for block‐coded systems in general mobile satellite channels. Numerical results are provided to validate our analytic results. Copyright © 2008 John Wiley &amp; Sons, Ltd.
Design of Four Small-Molecule-Inducible Systems in the Yeast Chromosome, Applied to Optimize Terpene Biosynthesis (2023)

The optimization of cellular functions often requires the balancing of gene expression, but the physical construction and screening of alternative designs are costly and time-consuming. Here, we construct a strain of <i>Saccharomyces cerevisiae</i> that contains a "sensor array" containing bacterial regulators that respond to four small-molecule inducers (vanillic acid, xylose, aTc, IPTG). Four promoters can be independently controlled with low background and a 40- to 5000-fold dynamic range. These systems can be used to study the impact of changing the level and timing of gene expression without requiring the construction of multiple strains. We apply this approach to the optimization of a four-gene heterologous pathway to the terpene linalool, which is a flavor and precursor to energetic materials. Using this approach, we identify bottlenecks in the metabolic pathway. This work can aid the rapid automated strain development of yeasts for the bio-manufacturing of diverse products, including chemicals, materials, fuels, and food ingredients.
Outgassing Measurement for Vacuum Engineering (2015)

In this article, two common methods to evaluate the outgassing properties of vacuum system materials, thermal desorption spectroscopy (TDS) and the method of switching between two pumping paths (SPP), are discussed. TDS can evaluate the outgassing properties of small samples, while SPP method can measure low outgassing rate, such as the case after baking. Ion gauges and/or quadrupole mass spectrometers (QMS) consist of the TDS and SPP setups. In these cases, QMS are typically calibrated using a standard conductance element (SCE). The calibration using the SCE enables the direct conversion of the QMS ion current into the gas flow rate.
Respiratory Syncytial Virus (RSV) Infection in Elderly Mice Results in Altered Antiviral Gene Expression and Enhanced Pathology (2014)

Elderly persons are more susceptible to RSV-induced pneumonia than young people, but the molecular mechanism underlying this susceptibility is not well understood. In this study, we used an aged mouse model of RSV-induced pneumonia to examine how aging alters the lung pathology, modulates antiviral gene expressions, and the production of inflammatory cytokines in response to RSV infection. Young (2-3 months) and aged (19-21 months) mice were intranasally infected with mucogenic or non-mucogenic RSV strains, lung histology was examined, and gene expression was analyzed. Upon infection with mucogenic strains of RSV, leukocyte infiltration in the airways was elevated and prolonged in aged mice compared to young mice. Minitab factorial analysis identified several antiviral genes that are influenced by age, infection, and a combination of both factors. The expression of five antiviral genes, including pro-inflammatory cytokines IL-1β and osteopontin (OPN), was altered by both age and infection, while age was associated with the expression of 15 antiviral genes. Both kinetics and magnitude of antiviral gene expression were diminished as a result of older age. In addition to delays in cytokine signaling and pattern recognition receptor induction, we found TLR7/8 signaling to be impaired in alveolar macrophages in aged mice. In vivo, induction of IL-1β and OPN were delayed but prolonged in aged mice upon RSV infection compared to young. In conclusion, this study demonstrates inherent differences in response to RSV infection in young vs. aged mice, accompanied by delayed antiviral gene induction and cytokine signaling.
H+/e- stoichiometry for NADH dehydrogenase I and dimethyl sulfoxide reductase in anaerobically grown Escherichia coli cells (1996)

Anaerobically grown Escherichia coli cells were shown to acidify the reaction medium in response to oxygen or dimethyl sulfoxide (DMSO) pulses, with the H+/e- stoichiometry being close to 2.5 and 1.5, respectively. In the presence of the NADH dehydrogenase I (NDH-I) inhibitor 8-methyl-N-vanillyl-6-nonenamide (capsaicin) or in mutants lacking NDH-I, this ratio decreased to 1 for O2 and to 0 for DMSO. These data suggest that (i) the H+/e- stoichiometry for E. coli NDH-I is at least 1.5 and (ii) the DMSO reductase does not generate a proton motive force.
Retinex based Reflectance Decomposition Using Convolutional Sparse Coding (2020)

Color constancy is a feature of the human visual system, which detects the relative inconsistency of the perceived color of an object so that the perceived color may not be changed under various illumination conditions, even when the conditions for observing color are changed. Thus, the Retinex theory was designed in consideration of this color constancy. The physics based Retinex algorithms have been popularly used to effectively decompose the illumination and reflectance of the object. However, if there are many detail areas in the image or the illumination changes rapidly, the illumination and reflectance may not be decomposed properly, because of the violation of the smoothness constraint on illumination. In this paper, we use the convolutional sparse coding model to represent the reflectance in more detail. This allows the reflectance component to provide improved visual quality over conventional methods, as shown in experimental results. Consequently, we can decompose Retinex based illumination and reflectance more precisely, then, reduce the perception gap between humans and machines.
Effects of Surface and Morphological Properties of Zeolite on Impedance Spectroscopy-Based Sensing Performance (2012)

Measurement by impedance spectroscopy of the changes in intrazeolitic cation motion of pressed pellets of zeolite particles upon adsorption of dimethylmethylphosphonate (DMMP) provides a strategy for sensing DMMP, a commonly used simulant for highly toxic organophosphate nerve agents. In this work, two strategies for improving the impedance spectroscopy based sensing of DMMP on zeolites were investigated. The first one is the use of cerium oxide (CeO(2)) coated on the zeolite surface to neutralize acidic groups that may cause the decomposition of DMMP, and results in better sensor recovery. The second strategy was to explore the use of zeolite Y membrane. Compared to pressed pellets, the membranes have connected supercages of much longer length scales. The zeolite membranes resulted in higher sensitivity to DMMP, but recovery of the device was significantly slower as compared to pressed zeolite pellets.
Two-wheeled vehicles black-box sideslip angle estimation (2017)

This paper deals with sideslip angle estimation of powered two-wheeled vehicles. Since available sensors used to directly measure this variable are bulky and expensive, estimation algorithms based on on-board measurements have been developed. These algorithms are mainly devoted to four-wheeled vehicles whereas the sideslip estimation for two-wheeled vehicles is still an open topic. This paper presents a Neural Network estimation algorithm that uses on-board standard measures available in modern motorbikes and studies the role of the most significant signals for the estimation. The employed black-box approach does not require the derivation of any physics-based model of the motorcycle dynamics and thus is meant as a valid tool for a preliminary insight in such estimation problem. The experimental data collected cover a rich amount of manoeuvres that are used to train the network and several other manoeuvres have been used to analyse its performances.
Formation and metabolism of histone mRNAs with mutant 3' ends formed by snRNA termination signals. (1995)

Histone mRNAs are the only non-polyadenylated mRNAs, ending in a conserved 26 nt sequence which can form a stem-loop. It has not been possible to make histone mRNAs with mutant stem-loops since most mutations in the stem-loop interfere with the 3' processing reaction. The snRNA genes transcribed by RNA polymerase II form their 3' ends by transcription termination directed by a signal which is located entirely 3' of the snRNA coding sequence. Chimeric genes which express RNAs ending in a histone 3' end or in mutant histone 3' ends formed by snRNA termination signals were constructed. The mRNAs from these genes were efficiently transported from the nucleus after injection of the genes into frog oocytes. This was true even for RNAs which end in mutant stem-loops suggesting that the snRNA termination signals promote transport of the transcripts.
Mixed-kinematic body sideslip angle estimator for high performance cars (2018)

Body sideslip angle estimation is a well-known issue in the automotive field. Many vehicle dynamic control systems are based on the control or monitoring of the sideslip angle. Unfortunately, measurement of this quantity requires expensive instrumentation that commercial cars can not be equipped with. This paper further develops the so-called hybrid dynamic-kinematic approach to the problem providing an automated tuning approach. A state observer merges a kinematic model with a lateral dynamic one, so that they can compensate each other shortcomings. The resulting estimator depends on a number of parameters whose manual tuning require expertise. The paper proposes a grey-box approach for the tuning of the algorithm. The optimization-based approach requires only standard track tests and no special vehicle characterization. The approach is validated on a large experimental dataset from a high performance car.