gebhart/patrepeval huggingface dataset:
Transmembrane Region of the Epidermal Growth Factor Receptor:  Behavior and Interactions <i>via</i> <sup>2</sup>H NMR (1996)

The first wide-line 2H NMR investigation of a receptor tyrosine kinase is reported. Selectively deuterated peptides from the membrane-associated portion of the human epidermal growth factor (EGF) receptor were synthesized for examination in lipid bilayers mimicking certain natural membrane features. The peptide sequence included the 23-amino acid hydrophobic stretch thought to span the membrane (Ile622-Met644 of the EGF receptor), plus the first 10 amino acids of the receptor's cytoplasmic domain (Arg645-Thr654). Dispersion of the peptide with lipid in the lipomimetic solvent, trifluoroethanol (TFE), was found to be a very useful initial step for sample preparation. TFE readily dissolved all components and was then easily removed in vacuo to yield thin films which could be subsequently hydrated to produce bilayers incorporating homogeneously dispersed peptide. Samples extensively studied consisted of 6 mol % peptide in multilamellar liposomes of 1-palmitoyl-2-oleoylphosphatidylcholine and similar liposomes containing cholesterol. 2H NMR spectra of the resulting unsonicated model membranes indicated the existence of peptide monomers undergoing rapid axially symmetric diffusion. It was possible to examine structural and behavioral effects of events often suggested as pivotal in signaling mechanisms and to consider by wide-line NMR for the first time the effect of cholesterol on hydrophobic peptides. When it was incorporated into bilayers by an alternative method involving dialysis of aqueous solutions prepared using a cationic detergent, spectra suggested that the peptide existed primarily as irreversibly aggregated oligomers which were relatively immobile on a time scale of 10(-3)-10(-4) s. For liposomes prepared by hydration of thin films, deuterated methyl groups on the peptide at locations corresponding to Ala623, Met644, and Val650 of the human EGF receptor were individually distinguishable. In highly fluid matrices, spectra suggested the presence of peptide monomers, diffusing symmetrically about axes perpendicular to the membrane. Studied as a function of temperature, 2H NMR spectra of such samples permitted independent consideration of membrane/peptide relationships at separate locations in the receptor tyrosine kinase. None of the locations probed demonstrated significant conformational sensitivity to temperature over a wide range. Effects seen at Ala623 and Met644, at opposite ends of the putative membrane-spanning domain, suggested slight increases in motional order with decreasing temperature. Addition of 33% cholesterol to the membrane caused little apparent conformational change at Val650 or Met644. However, in the presence of the sterol, Met644 and Ala623 exhibited nonaxially symmetric motion at low temperatures, perhaps as a result of peptide oligomerization. Moreover, the presence of cholesterol led to considerable change in spatial arrangement or order at Ala623. There was little evidence to support transmission of conformational changes along the peptide segment probed.
Cavity-resonator-integrated guided-mode resonance filter for aperture miniaturization (2012)

A guided-mode resonance filter integrated in a waveguide cavity resonator constructed by two distributed Bragg reflectors is designed and fabricated for miniaturization of aperture size. Reflection efficiency of >90% and wavelength selectivity of 0.4 nm are predicted in the designed SiO(2)-based filter with 50-μm aperture by a numerical calculation using the finite-difference time-domain method. A maximum reflectance of 67% with 0.5-nm bandwidth is experimentally demonstrated by the fabricated device at around 850-nm wavelength.
Pulse-Decay Method for Measuring the Thermal Conductivity of Living Tissues (1981)

The present communication presents a single microprobe technique for measuring tissue thermal properties based on the dissipation of a measured amount of energy and the observation of the resulting temperature rise a given time later. An advantage of this method is that the effective sampling volume can be varied by varying the measurement time. Using a measurement time of a few seconds, the sampling volume was estimated to be several orders of magnitude greater than the probe volume. Hence artifacts due to probe-induced trauma or stress would be insignificant. Additional advantages of the technique are: the results were independent of the probe shape, size and properties, and hence represents absolute measurements without the need for calibration; the required electronics and computations are simple; the determination of thermal conductivity requires only a single measurement; and comparison of data at different measurement times yields a clear and unequivocal indication of nonconductive contributions of heat transfer, if present.
Peh Production, Flagellum Synthesis, and Virulence Reduced in <i>Erwinia carotovora</i> subsp. <i>carotovora</i> by Mutation in a Homologue of <i>cytR</i> (2003)

Erwinia carotovora subsp. carotovora is a causal agent of soft-rot diseases in a wide variety of plants. Here, we have isolated a new regulatory factor involved in the virulence of E. carotovora subsp. carotovora by in vivo insertional mutagenesis using a transposon Tn5. The gene was homologous to cytR encoding a transcriptional repressor of nucleoside uptake and catabolism genes in Escherichia coli, Salmonella typhimurium, and Vibrio cholerae. Phenotypic characterization of a nonpolar deletion mutant of the cytR homologue (delta cytR) revealed that the delta cytR mutant produced a reduced level of polygalacturonase (Peh) and lost its motility compared to that in the parental strain. With electron microscopy, the delta cytR mutant was shown to be aflagellate. Furthermore, the expression of fliA and fliC (encoding sigma28 and flagellin, respectively) was also reduced in delta cytR mutant. The virulence of delta cytR mutant was reduced in Chinese cabbage and potato compared to that of the parental strain. These results suggest that the CytR homologue of E. carotovora subsp. carotovora positively controls Peh production and flagellum synthesis and plays an important role in its pathogenicity.
Histone Deacetylase Inhibitors to Overcome Resistance to Targeted and Immuno Therapy in Metastatic Melanoma (2020)

Therapies that target oncogenes and immune checkpoint molecules constitute a major group of treatments for metastatic melanoma. A mutation in <i>BRAF</i> (BRAF V600E) affects various signaling pathways, including mitogen activated protein kinase (MAPK) and PI3K/AKT/mammalian target of rapamycin (mTOR) in melanoma. Target-specific agents, such as MAPK inhibitors improve progression-free survival. However, BRAF<sup>V600E</sup> mutant melanomas treated with BRAF kinase inhibitors develop resistance. Immune checkpoint molecules, such as programmed death-1 (PD-1) and programmed death ligand-1(PD-L1), induce immune evasion of cancer cells. MAPK inhibitor resistance results from the increased expression of PD-L1. Immune checkpoint inhibitors, such as anti-PD-L1 or anti-PD-1, are main players in immune therapies designed to target metastatic melanoma. However, melanoma patients show low response rate and resistance to these inhibitors develops within 6-8 months of treatment. Epigenetic reprogramming, such as DNA methylaion and histone modification, regulates the expression of genes involved in cellular proliferation, immune checkpoints and the response to anti-cancer drugs. Histone deacetylases (HDACs) remove acetyl groups from histone and non-histone proteins and act as transcriptional repressors. HDACs are often dysregulated in melanomas, and regulate MAPK signaling, cancer progression, and responses to various anti-cancer drugs. HDACs have been shown to regulate the expression of PD-1/PD-L1 and genes involved in immune evasion. These reports make HDACs ideal targets for the development of anti-melanoma therapeutics. We review the mechanisms of resistance to anti-melanoma therapies, including MAPK inhibitors and immune checkpoint inhibitors. We address the effects of HDAC inhibitors on the response to MAPK inhibitors and immune checkpoint inhibitors in melanoma. In addition, we discuss current progress in anti-melanoma therapies involving a combination of HDAC inhibitors, immune checkpoint inhibitors, and MAPK inhibitors.
Building Practical Self Organization Networks on Heterogeneous Wireless Modems (2011)

MAC protocols are very essential to build real networks. So far, although several protocols are proposed for MAC layer, in real world systems, we always deploy heterogeneous modems. In this paper, we propose a novel wireless ad hoc MAC protocol for the master-slave heterogeneous modems, based on this kind of modems' work mode and topology structure. The protocol is of great robustness, flexibility and bandwidth utilization, improving the survival ability of ad hoc network in adverse environment. We implement this protocol in an embedded system with existing master-slave heterogeneous modems, to validate the protocol's robustness and the stability. And the related parameter values are measured. We have deployed our system in outdoors, and thereafter, we conducted several experiments on our protocol. As a result, our experimental results show that, our proposed protocol gained high performance.
ALTERNATING AUTOENCODERS FOR MATRIX COMPLETION (2018)

We consider autoencoders (AEs) for matrix completion (MC) with application to collaborative filtering (CF) for recommendation systems. It is observed that for a given sparse user-item rating matrix, denoted as M, an AE performs matrix factorization so that the recovered matrix is represented as a product of user and item feature matrices. Such an AE sequentially estimates user and item feature matrices: for the item-based AE (I-AE) that uses columns of M as its input vectors, the AE's encoder first estimates an item feature matrix and then the decoder estimates a user feature matrix based on the output of the encoder. Similarly, the user-based AE (U-AE) that uses the columns of MT as its input vectors first estimates a user feature matrix and then an item feature matrix. This sequential estimation can degrade the performance of the MC/CF, because the decoder depends on the output of the encoder. To enhance MC/CF performance, we propose alternating AEs (AAEs), a parallel algorithm employing both I-AE and U-AE and alternatively use them. We apply the AAE to synthetic, MovieLens 100k and 1M data sets. The results demonstrate that AAE can outperform all existing MC/CF methods.
Detection of microcystins, a blue-green algal hepatotoxin, in drinking water sampled in Haimen and Fusui, endemic areas of primary liver cancer in China, by highly sensitive immunoassay (1996)

An epidemiological survey for the causes of a high incidence of primary liver cancer (PLC) in Haimen city, Jian-Su province and Fusui county, Guangxi province in China, found a close correlation between the incidence of PLC and the drinking of pond and ditch water. With an aim to clarify whether microcystins (MC), a hepatotoxic peptide produced by water bloom algae, contaminate the drinking water in the endemic areas of PLC in China, a highly sensitive enzyme-linked immunosorbent assay with a detection limit of 50 pg/ml, was introduced to monitor the MC. Three trials to survey the drinking water were carried out in 1993-1994. Samples, 1135 in total, were collected from different sources such as: ponds, ditches, rivers, shallow wells and deep wells in Haimen city. The first survey in September 1993 found that three out of 14 ditch water specimens were positive for MC, with a range of 90-460 pg/ml. Several toxic algae such as Oscillatoria agardhii were present in some of the ditches. In the second trial, samples were collected from five ponds/ditches, two rivers, two shallow wells and two deep wells monthly for the whole year of 1994. These data showed that MC was highest in June to September, with a range of 62-296 pg/ml. A third trial on the 989 different water samples collected from the different types of water sources in July 1994 revealed that 17% of the pond/ditch water, 32% of the river water, and 4% of the shallow-well water were positive for MC, with averages of 101, 160 and 68 pg/ml respectively. No MC was detected in deep well water. A similar survey on 26 drinking water samples in Fusui, Guangxi province, demonstrated a high contamination frequency of MC in the water of ponds/ditches and rivers but no MC in shallow and deep wells. These data support a hypothesis that the blue-green algal toxin MC in the drinking water of ponds/ditches and rivers, or both, is one of the risk factors for the high incidence of PLC in China. Based on previous findings on the epidemiology of PLC and the present results from the mass screening of MC in the drinking water, an advisory level of MC in drinking water was proposed to below 0.01 microg/l. The combined effect of a potent hepatocarcinogen AFB1 and an intermittent intake of MC in drinking water in the summer season was discussed as an etiology of PLC.
Nuclear receptor-mediated repression of human cholesterol 7α-hydroxylase gene transcription by bile acids (2001)

Hydrophobic bile acids strongly repressed transcription of the human cholesterol 7alpha-hydroxylase gene (CYP7A1) in the bile acid biosynthetic pathway in the liver. Farnesoid X receptor (FXR) repressed CYP7A1/Luc reporter activity in a transfection assay in human liver-derived HepG2 cells, but not in human embryonic kidney (HEK) 293 cells. FXR-binding activity was required for bile acid repression of CYP7A1 transcription despite the fact that FXR did not bind to the CYP7A1 promoter. FXR-induced liver-specific factors must be required for mediating bile acid repression. Bile acids and FXR repressed endogenous CYP7A1 but stimulated alpha-fetoprotein transcription factor (FTF) and small heterodimer partner (SHP) mRNA expression in HepG2 cells. Feeding of rats with chenodeoxycholic acid repressed CYP7A1, induced FTF, but had no effect on SHP mRNA expression in the liver. FTF strongly repressed CYP7A1 transcription in a dose-dependent manner, and SHP further inhibited CYP7A1 in HepG2 cells, but not in HEK 293 cells. FXR only moderately stimulated SHP transcription, whereas FTF strongly inhibited SHP transcription in HepG2 cells. Results revealed that FTF was a dominant negative factor that was induced by bile acid-activated FXR to inhibit both CYP7A1 and SHP transcription. Differential regulation of FTF and SHP expression by bile acids may explain the wide variation in CYP7A1 expression and the rate of bile acid synthesis and regulation in different species.
A Unified Theory on Residual Oil Saturation and Irreducible Water Saturation (2002)

Abstract In many mature fields, there is a growing debate as to how much of the remaining oil is mobile in the unswept regions versus immobile in the swept regions. Log measured oil saturations behind the flood front are substantially lower than the residual oil saturations measured from special core analysis. In order to explain this contradiction, data from several fields is analyzed with special emphasis on capillary pressure. The concept of irreducible water saturation, connate water saturation, residual oil saturation and "critical water saturation" are discussed. The conclusions which are supported by experiment and theory, have substantial commercial implications concerning the location of remaining reserves – in the immobile region or the unswept region. Based on these results, entirely different depletion strategies should be recommended. The concepts presented in this paper help to explain, in part, why reservoirs continue to produce past their forecasted abandonment, and why perfectly "history-matched" reservoir simulation models tend to grossly under-estimate incremental reserves through improved sweep efficiency. These issues are critical in optimizing the depletion strategy of oil and gas reservoirs. The discussion throughout this paper refers to an oil-water system in a water-wet or mixed-wet reservoir; however, these basic concepts can be applied to gas-water systems, three-phase systems, or other immiscible displacement systems and and oil-wet reservoirs.
Te Iwi Maori, a New Zealand Population, Past, Present and Projected (1991)

This important new book gives a thorough and very interesting survey of the history of the Maori population from earliest times to the present, concentrating particularly on the demographic impact of European colonization. It also considers present and future population trends, many of which have major implications for social and resource policy. Among questions explored are the marked fertility decline of the 1970s, urbanization, emigration, especially to Australia, and regional population patterns.
RELATIONS BETWEEN DISTRIBUTION RATIO, TEMPERATURE AND CONCENTRATION IN SYSTEM: WATER, ETHER, SUCCINIC ACID. (1919)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTRELATIONS BETWEEN DISTRIBUTION RATIO, TEMPERATURE AND CONCENTRATION IN SYSTEM: WATER, ETHER, SUCCINIC ACID.George Shannon Forbes and Albert Sprague CoolidgeCite this: J. Am. Chem. Soc. 1919, 41, 2, 150–167Publication Date (Print):February 1, 1919Publication History Published online1 May 2002Published inissue 1 February 1919https://pubs.acs.org/doi/10.1021/ja01459a004https://doi.org/10.1021/ja01459a004research-articleACS PublicationsRequest reuse permissionsArticle Views211Altmetric-Citations13LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
MEMS Packaging - Current Issues and Approaches (2000)

The assembly and packaging of MEMS (Microelectromechanical Systems) devices raise a number of issues over and above those normally associated with the assembly of standard microelectronic circuits. MEMS components include a variety of sensors, microengines, optical components, and other devices. They often have exposed mechanical structures which during assembly require particulate control, space in the package, non-contact handling procedures, low-stress die attach, precision die placement, unique process schedules, hermetic sealing in controlled environments (including vacuum), and other special constraints. These constraints force changes in the techniques used to separate die on a wafer, in the types of packages which can be used in the assembly processes and materials, and in the sealing environment and process. This paper discusses a number of these issues and provides information on approaches being taken or proposed to address them.
On Schedulability Bounds of Static Priority Schedulers (2005)

While utilization bound based schedulability test is simple and effective, it is often difficult to derive the bound itself. For its analytical complexity, utilization bound results are usually obtained on a case-by-case basis. In this paper, we develop a general framework that allows one to effectively derive schedulability bounds for a wide range of real-time systems with different workload patterns and schedulers. Our analytical model is capable of describing a wide range of tasks and schedulers' behaviors. We propose a new definition of utilization, called workload rate. While similar to utilization, workload rate enables flexible representation of different scheduling and workload scenarios and leads to uniform derivation of schedulability bounds. We derive a parameterized schedulability bound for static priority schedulers with arbitrary priority assignment. Existing utilization bounds for different priority assignments and task releasing patterns can be derived from our closed-form formula by simple assignments of proper parameters.
Comparison of 2% hydroxypropyl methylcellulose and 1% sodium hyaluronate in implant surgery. (1988)

We conducted a prospective randomized clinical trial of 2% hydroxypropyl methylcellulose and 1% sodium hyaluronate (Healon) in routine extracapsular cataract surgery with implantation of a posterior chamber intraocular lens. Of the 84 patients 40 received methylcellulose and 44 received sodium hyaluronate. There was no statistically significant difference in endothelial-cell loss or induced cellular polymegathism between the two groups. The intraocular pressure before and after surgery was similar in the two groups, as was the visual acuity 8 weeks after surgery. The results suggest that 2% hydroxypropyl methylcellulose is a safe and effective alternative to 1% sodium hyaluronate in routine implant surgery.
Carrier to envelope and dispersion control in a cavity with prism pairs (2007)

Continuously mode-locked lasers combine a broad bandwidth with a fine comb structure that enables high resolution spectroscopy. Independent control of the pulse duration, center of gravity of the spectrum, the mode position, and spacing are essential for spectral applications and metrology. Exact analytical expressions are derived for the first, second, and third order dispersion in a cavity with a pair of intracavity prisms. The influence of cavity controls such as tilt and translation of the end mirror on the frequency comb parameters are analyzed and calculated.
Robust solving of optical motion capture data by denoising (2018)

Raw optical motion capture data often includes errors such as occluded markers, mislabeled markers, and high frequency noise or jitter. Typically these errors must be fixed by hand - an extremely time-consuming and tedious task. Due to this, there is a large demand for tools or techniques which can alleviate this burden. In this research we present a tool that sidesteps this problem, and produces joint transforms directly from raw marker data (a task commonly called "solving") in a way that is extremely robust to errors in the input data using the machine learning technique of denoising. Starting with a set of marker configurations, and a large database of skeletal motion data such as the CMU motion capture database [CMU 2013b], we synthetically reconstruct marker locations using linear blend skinning and apply a unique noise function for corrupting this marker data - randomly removing and shifting markers to dynamically produce billions of examples of poses with errors similar to those found in real motion capture data. We then train a deep denoising feed-forward neural network to learn a mapping from this corrupted marker data to the corresponding transforms of the joints. Once trained, our neural network can be used as a replacement for the solving part of the motion capture pipeline, and, as it is very robust to errors, it completely removes the need for any manual clean-up of data. Our system is accurate enough to be used in production, generally achieving precision to within a few millimeters, while additionally being extremely fast to compute with low memory requirements.