gebhart/patrepeval huggingface dataset:
Direct Chemosensitivity Monitoring <i>Ex Vivo</i> on Undissociated Melanoma Tumor Tissue by Impedance Spectroscopy (2014)

Stage III/IV melanoma remains incurable in most cases due to chemotherapeutic resistance. Thus, predicting and monitoring chemotherapeutic responses in this setting offer great interest. To overcome limitations of existing assays in evaluating the chemosensitivity of dissociated tumor cells, we developed a label-free monitoring system to directly analyze the chemosensitivity of undissociated tumor tissue. Using a preparation of tumor micro-fragments (TMF) established from melanoma biopsies, we characterized the tissue organization and biomarker expression by immunocytochemistry. Robust generation of TMF was established successfully and demonstrated on a broad range of primary melanoma tumors and tumor metastases. Organization and biomarker expression within the TMF were highly comparable with tumor tissue, in contrast to dissociated, cultivated tumor cells. Using isolated TMF, sensitivity to six clinically relevant chemotherapeutic drugs (dacarbazine, doxorubicin, paclitaxel, cisplatin, gemcitabine, and treosulfan) was determined by impedance spectroscopy in combination with a unique microcavity array technology we developed. In parallel, comparative analyses were performed on monolayer tumor cell cultures. Lastly, we determined the efficacy of chemotherapeutic agents on TMF by impedance spectroscopy to obtain individual chemosensitivity patterns. Our results demonstrated nonpredictable differences in the reaction of tumor cells to chemotherapy in TMF by comparison with dissociated, cultivated tumor cells. Our direct impedimetric analysis of melanoma biopsies offers a direct ex vivo system to more reliably predict patient-specific chemosensitivity patterns and to monitor antitumor efficacy.
Improving Distant Supervision for Information Extraction Using Label Propagation Through Lists (2015)

Because of polysemy, distant labeling for information extraction leads to noisy training data. We describe a procedure for reducing this noise by using label propagation on a graph in which the nodes are entity mentions, and mentions are coupled when they occur in coordinate list structures. We show that this labeling approach leads to good performance even when off-the-shelf classifiers are used on the distantly-labeled data.
A structural basis for drug-induced long QT syndrome (2000)

Mutations in the HERG K(+) channel gene cause inherited long QT syndrome (LQT), a disorder of cardiac repolarization that predisposes affected individuals to lethal arrhythmias [Curran, M. E. , Splawski, I., Timothy, K. W., Vincent, G. M., Green, E. D. & Keating, M. T. (1995) Cell 80, 795-804]. Acquired LQT is far more common and is most often caused by block of cardiac HERG K(+) channels by commonly used medications [Roden, D. M., Lazzara, R., Rosen, M., Schwartz, P. J., Towbin, J. & Vincent, G. M. (1996) Circulation 94, 1996-2012]. It is unclear why so many structurally diverse compounds block HERG channels, but this undesirable side effect now is recognized as a major hurdle in the development of new and safe drugs. Here we use alanine-scanning mutagenesis to determine the structural basis for high-affinity drug block of HERG channels by MK-499, a methanesulfonanilide antiarrhythmic drug. The binding site, corroborated with homology modeling, is comprised of amino acids located on the S6 transmembrane domain (G648, Y652, and F656) and pore helix (T623 and V625) of the HERG channel subunit that face the cavity of the channel. Other compounds that are structurally unrelated to MK-499, but cause LQT, also were studied. The antihistamine terfenadine and a gastrointestinal prokinetic drug, cisapride, interact with Y652 and F656, but not with V625. The aromatic residues of the S6 domain that interact with these drugs (Y652 and F656) are unique to eag/erg K(+) channels. Other voltage-gated K(+) (Kv) channels have Ile and Val (Ile) in the equivalent positions. These findings suggest a possible structural explanation for how so many commonly used medications block HERG but not other Kv channels and should facilitate the rational design of drugs devoid of HERG channel binding activity.
Melatonin and Parkinsonism (1972)

<h3>To the Editor.—</h3> Lerner discovered melatonin (<i>N</i>-Acetyl-5-methoxytryptamine)<sup>1</sup>and showed that this pineal hormone can induce sedation in man.<sup>2</sup>This agent antagonizes the darkening of the skin and, therefore, perhaps also some other action of melanophore-stimulating hormone (βMSH).<sup>3</sup>Since injections of βMSH had aggravated the tremor of parkinsonism,<sup>4</sup>we had administered this antagonist of βMSH to a patient but induced only a diminution of tremor.<sup>3</sup>Others, however, reported impressive improvement of several symptoms of parkinsonism<sup>5</sup>at a time when we had reversed the adventitious movements caused by levodopa [3-(3, 4-dihydroxyphenyl)-L-alanine] with melatonin in experimental animals.<sup>6</sup>We conducted therefore a single-blind study in patients with parkinsonism who received either melatonin alone or melatonin plus levodopa, which had caused intermittent adventitious movements.<sup>7</sup> The inpatients listed in the Table and all of the outpatients had idiopathic parkinsonism except patient 11 who had postencephalitic disease. Among
Interferometric temperature-insensitive strain measurement with different-diameter fiber Bragg gratings (1997)

An interferometric strain-sensing system that combines an unbalanced Mach-Zehnder wavelength discriminator and spliced different-diameter fiber Bragg gratings is presented that has the capability to distinguish strain from temperature effects. Because the gratings are written in 135- and 165- microm -diameter fibers drawn from the same preform, when they are spliced they show similar temperature sensitivities but different responses to applied strain. Thus the relative Bragg wavelength difference of the two gratings is affected only by strain, and one can measure it accurately by monitoring the amplitude variation of the interference signal rather than the conventional phase variation.
Relationship between cyclic AMP production and lipolysis induced by forskolin in rat fat cells. (1992)

Forskolin (7 beta-acetoxy-8, 13-epoxy-1 alpha,6 beta,9 alpha-trihydroxy-labd-14-ene-11-one) induced both cyclic AMP production and lipolysis in intact fat cells, but stimulated lipolysis without increasing cyclic AMP at a concentration of 10(-5) M. Homogenization of fat cells elicited lipolysis without elevation of cyclic AMP. Forskolin did not stimulate lipolysis in the homogenate. Forskolin stimulated both cyclic AMP production and lipolysis in a cell-free system consisting of endogenous lipid droplets and a lipoprotein lipase-free lipase fraction prepared from fat cells. However, at a concentration of 10(-6) M, it induced lipolysis without increase in the cyclic AMP content in this cell-free system. In the cell-free system, homogenization of the lipid droplets resulted in marked increase in lipolysis to almost the same level as that with 10(-4) M forskolin without concomitant increase in cyclic AMP. Addition of forskolin to a cell-free system consisting of homogenized lipid droplets and lipase did not stimulate lipolysis further. Phosphodiesterase activities were found to be almost the same both in the presence and absence of forskolin in these reaction mixtures. Although 10(-3) M forskolin produced maximal concentrations of cyclic AMP: 6.7 x 10(-7) M in fat cells and 2.7 x 10(-7) M in the cell-free system, 10(-4) M cyclic AMP did not stimulate lipolysis in the cell-free system. In a cell-free system consisting of lipid droplets and the lipase, pyrophosphate inhibited forskolin-induced cyclic AMP production, but decreased forskolin-mediated lipolysis only slightly. Based on these results, mechanism of lipolytic action of forskolin was discussed.
Reliability of special protection systems (1999)

Special protection systems (SPS) have been widely used to increase the transfer capability of the network by assisting system operators in administering fast corrective actions. Compared with constructing new transmission facilities, SPS can be placed in service relatively quickly and inexpensively. However, increased reliance on SPS results in additional risks to system security. The purpose of this paper is to elucidate the importance of developing a systematic and comprehensive reliability framework for SPS. We review types of SPS and provide several examples of actual SPS failures. The need for SPS reliability assessment is discussed. Several reliability assessment methods are described, and efforts to deal with a similar problem in the process control industry are summarized. We also provide several recommendations.
New Yeast Species, <i>Malassezia dermatis</i> , Isolated from Patients with Atopic Dermatitis (2002)

Malassezia species are considered to be one of the exacerbating factors in atopic dermatitis (AD). During examination of the cutaneous colonization of Malassezia species in AD patients, we found a new species on the surface of the patients' skin. Analysis of ribosomal DNA sequences suggested that the isolates belonged to the genus MALASSEZIA: They did not grow in Sabouraud dextrose agar but utilized specific concentrations of Tween 20, 40, 60, and 80 as a lipid source. Thus, we concluded that our isolates were new members of the genus Malassezia and propose the name Malassezia dermatis sp. nov. for these isolates.
Minimum Detectable Power of a Pyroelectric Thermal Receiver (1962)

For a ferroelectric crystal, the rate of change of polarization with temperature is large, especially close to the Curie point where a phase transition occurs. Thus, a change of polarization due to an incident radiation flux gives rise to a large pyroelectric voltage output. The ``minimum detectable power'' Wm is calculated. For barium titanate, the value of Wm thus obtained is found to be much better than other uncooled thermal receivers and comparable with a superconducting bolometer, if dielectric noise at the transition is small. In certain cases, Wm is limited only by temperature noise, so that the receiver may be thought of as a true thermal receiver.
Altered regulation of collagen metabolism in scleroderma fibroblasts grown within three‐dimensional collagen gels (1992)

In systemic scleroderma (SSc) excessive deposition of collagen leads to fibrosis of various tissues including the skin. Previous studies have demonstrated that scleroderma fibroblasts in explant monolayer cultures are heterogeneous with respect to their levels of collagen synthesis. The critical role played by the extracellular matrix (ECM) in the modulation of fibroblast metabolism prompted us to study the regulation of collagen synthesis in scleroderma fibroblasts grown within three-dimensional collagen gels, a culture system representing more physiological conditions than monolayer cultures. Normal fibroblasts grown in this system dramatically reduce their collagen synthesis as compared to monolayer cultures. Quantification of total protein and collagen synthesis showed that scleroderma fibroblasts did not demonstrate the down regulation of collagen synthesis as observed in control fibroblasts, resulting in a much higher collagen synthesis in scleroderma fibroblasts compared to controls. However, also in this system scleroderma fibroblasts were heterogeneous in their response to the collagenous lattice. Ten strains were investigated, of which 3 were indistinguishable from controls, while 7 maintained higher levels of collagen production. In addition, our data showed that the changes in collagen synthesis on the protein level were accompanied by respective up- or downregulation on the mRNA level. These results indicate that an altered response to the surrounding ECM is an important factor in the disturbed regulation of connective tissue synthesis in scleroderma fibroblasts observed in vivo.
A DNA Polymerase with Increased Reactivity for Ribonucleotides and C5‐Modified Deoxyribonucleotides (2010)

Just do it: Directed evolution enables efficient enzymatic synthesis of catalytically active RNA as well as highly functionalized C5-modified DNA. The DNA polymerase variant that is proficient in incorporating nucleobase and sugar-modified nucleotides was identified by a chip-based protein library screening assay. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
An efficient locking and unlocking method of sequential systems (2012)

In this paper, we propose an efficient locking and unlocking method for sequential systems. The method is based on extracting and utilizing an inherent property of synchronicity directly from the original sequential system without modifying the system. We analyze the synchronicity property in the context of sequential locking and unlocking function. We address the advantages and limitations of proposed method. The feasibility of proposed method is also demonstrated.
Involvement of Heparanase in the Pathogenesis of Mesothelioma: Basic Aspects and Clinical Applications (2018)

Our results imply that heparanase is clinically relevant in mesothelioma development. Given these preclinical and clinical data, heparanase appears to be an important mediator of mesothelioma, and heparanase inhibitors are worthy of investigation as a new therapeutic modality in mesothelioma clinical trials.
Vector quantization of LSP parameters by split (2002)

An important problem in speech coding is the quantization of the linear predictive coefficients (LPC) with the smallest possible number of bits. Since the direct quantization of LPC coefficients is known to be unsatisfactory, we consider this problem for an equivalent representation namely the line spectrum pairs (LSPs). The performance of two algorithms for the quantization of the LSP parameters is studied. For the first algorithm, the well-known ordering property of LSP parameters is exploited in quantizing the frequency differences of consecutive LSP parameters. Vector quantizers are more efficient than scalar quantizers, their use for accurate quantization of LSP parameters is impeded due to their prohibitively high complexity problem. A split vector quantizer is used to overcome the complexity problem. The LPC vector consisting of 10 LSPs is split into three parts. For the spectral distortion measure, appropriate performance comparisons between the two quantization schemes are rendered.
The <i>Caenorhabditis elegans</i> gene <i>unc-76</i> and its human homologs define a new gene family involved in axonal outgrowth and fasciculation (1997)

The gene unc-76 (unc, uncoordinated) is necessary for normal axonal bundling and elongation within axon bundles in the nematode Caenorhabditis elegans. The UNC-76 protein and two human homologs identified as expressed sequence tags are not similar to previously characterized proteins and thus represent a new protein family. At least one of these human homologs can function in C. elegans, suggesting that it, like UNC-76, acts in axonal outgrowth. We propose that the UNC-76 protein, which is found in cell bodies and processes of all neurons throughout development, either has a structural role in the formation and maintenance of axonal bundles or transduces signals to the intracellular machinery that regulates axonal extension and adhesion.
Predictors of Transcutaneous Oxygen Tension in the Lower Limbs of Diabetic Subjects (1996)

We examined neuropathy, ankle pressure index (API), and other factors as predictors of transcutaneous oxygen (TcPO2) in the lower limbs of 657 diabetic subjects. Eligible subjects underwent a clinical assessment that included three standard measures of autonomic neuropathy. TcPO2 measurements were performed at 37 °C and 44 °C at four lower limb locations. Associations between potential predictors and TcPO2 were tested using univariate and multivariate statistics. Mean TcPO2 at any site did not differ by presence of autonomic neuropathy at either temperature, except for a significantly lower value at 44 °C below the knee (56.5 versus 59.2 mmHg, p = 0.021). In multivariate analysis, autonomic neuropathy was significantly and independently related to leg 44 °C TcPO2 only (coefficient = −2.6734, p= 0.0182). Much stronger associations were seen between TcPO2 and age, ankle blood pressure, and relative body weight on the plantar foot; and between API, glycosylated haemoglobin, ankle blood pressure, and pedal oedema on the dorsal foot and leg. We conclude that factors related to lower limb TcPO2 vary depending on measurement site. Autonomic neuropathy is not an important determinant of TcPO2 in the feet of diabetic subjects. Although several predictors of TcPO2 were identified, most of the variance of this measurement remains unexplained.
Growth of high-<i><i>T<sub>c</sub></i></i>thin films (1999)

An overview of the deposition and deposition techniques (with the emphasis on PVD techniques) of high-Tc material is presented. The major technologies are discussed and compared, and advantages and problems of various substrate materials are illustrated. The consequences connected with lattice mismatch are discussed, and film nucleation and growth modes of ceramic superconducting material are sketched. Finally, remaining areas for further research are listed.
Analytical solutions to eddy-current testing problems for a layered medium with varying properties (1997)

A one-parameter family of analytical solutions is found for the case where a single-turn coil is located above a two-layer conducting medium. The conductivity /spl sigma/ and the relative magnetic permeability /spl mu/ of the upper conducting layer are constants, while for the lower conducting half-space, these are of the form /spl sigma/(z)=Az/sup b/ and /spl mu/(z)=Bz/sup a/, where A and B are constants and a+b=-2 or a+b=0. The change in impedance is computed, and the results of numerical simulation are presented.
Theoretical Study of the Adsorption of Acetylene on the (111) Surfaces of Pd, Pt, Ni, and Rh (2002)

Plane-wave density functional theory and extended Hückel calculations have been used to study the adsorption of acetylene and hydrogen on the (111) surface planes of Pd, Pt, Ni, and Rh. In agreement with previous experimental and computational studies, atomic hydrogen is found to preferentially adsorb in a 3-fold hollow site on each metal surface, although the potential-energy surface for hydrogen binding is apparently rather flat. Differences in the adsorption behavior of acetylene on the four surfaces are more pronounced. An adsorption structure in which C2H2 is oriented above a 3-fold hollow, with its axis parallel to but tilted away from a metal−metal bond, is computed to be most stable on Pd, Pt, and Rh. On Ni(111), acetylene is found to strongly adsorb above two contiguous hollow sites, with its molecular plane perpendicular to the surface and bisecting a Ni−Ni bond. The anomalous adsorption behavior on Ni is explained using the crystal orbital Hamilton population formalism. Calculated C2H2 adsorption behavior is compared with experimental studies of acetylene decomposition and hydrogenation on single-crystal surfaces. Implications for the mechanism of acetylene hydrogenation on supported metal catalysts are also discussed.
Diastereomer-specific quantification of bioactive hexosylceramides from bacteria and mammals (2017)

Mammals synthesize, cell-type specifically, the diastereomeric hexosylceramides, β-galactosylceramide (GalCer) and β-glucosylceramide (GlcCer), which are involved in several diseases, such as sphingolipidosis, diabetes, chronic kidney diseases, or cancer. In contrast, <i>Bacteroides fragilis</i>, a member of the human gut microbiome, and the marine sponge, <i>Agelas mauritianus</i>, produce α-GalCer, one of the most potent stimulators for invariant natural killer T cells. To dissect the contribution of these individual stereoisomers to pathologies, we established a novel hydrophilic interaction chromatography-based LC-MS<sup>2</sup> method and separated (<i>R</i> > 1.5) corresponding diastereomers from each other, independent of their lipid anchors. Testing various bacterial and mammalian samples, we could separate, identify (including the lipid anchor composition), and quantify endogenous β-GlcCer, β-GalCer, and α-GalCer isomers without additional derivatization steps. Thereby, we show a selective decrease of β-GlcCers versus β-GalCers in cell-specific models of GlcCer synthase-deficiency and an increase of specific β-GlcCers due to loss of β-glucoceramidase 2 activity. Vice versa, β-GalCer increased specifically when cerebroside sulfotransferase (<i>Gal3st1</i>) was deleted. We further confirm β-GalCer as substrate of globotriaosylceramide synthase for galabiaosylceramide synthesis and identify additional members of the human gut microbiome to contain immunogenic α-GalCers. Finally, this method is shown to separate corresponding hexosylsphingosine standards, promoting its applicability in further investigations.
Identification of bacteria contaminating pulp and a paper machine in a Canadian paper mill (2003)

Over 100 bacteria from pulp and slime samples in a Canadian paper mill were identified by partial sequencing of their 16S rDNAs. Seventy-one percent of the isolates could be assigned to a bacterial genus with a high level of confidence. Another 12% exhibited at least 95% similarity within their 16S rDNA sequence with unidentified organisms that originate from warm or wet environments. Pseudomonas, Bacillus, and Pseudoxanthomonas isolates were represented at a relatively high proportion in both pulp and slime samples. This is the first time that Pseudoxanthomonas strains have been isolated from pulp and slime samples on a paper machine.
Chaotic synchronization in small assemblies of driven Chua's circuits (2000)

Chaotic synchronization is studied in experiments performed on dynamic arrays of Chua's circuits that are connected by using a recently introduced driving method especially suited for the design of such arrays. Namely, the driven circuit has the same number of energy storage elements as the driving circuit. The experimental results, which are supported by theoretical analysis, are different depending on the geometric arrangement of the array. In the case of linear arrays, the first circuit always imposes its behavior on the rest of the chain at a finite velocity. Instead, in the case of ring geometries, the chaotic synchronized state is only stable up to a certain size of the ring. Beyond this critical size a desynchronizing bifurcation occurs, leading to a chaotic rotating wave that travels through the array. This instability is explained by performing an analysis in terms of modes.
Selection of regularization parameter in total variation image restoration (2009)

We consider and study total variation (TV) image restoration. In the literature there are several regularization parameter selection methods for Tikhonov regularization problems (e.g., the discrepancy principle and the generalized cross-validation method). However, to our knowledge, these selection methods have not been applied to TV regularization problems. The main aim of this paper is to develop a fast TV image restoration method with an automatic selection of the regularization parameter scheme to restore blurred and noisy images. The method exploits the generalized cross-validation (GCV) technique to determine inexpensively how much regularization to use in each restoration step. By updating the regularization parameter in each iteration, the restored image can be obtained. Our experimental results for testing different kinds of noise show that the visual quality and SNRs of images restored by the proposed method is promising. We also demonstrate that the method is efficient, as it can restore images of size 256 x 256 in approximately 20 s in the MATLAB computing environment.