gebhart/patrepeval huggingface dataset:
The green fluorescent protein as a marker to visualize plant mitochondria <i>in vivo</i> (1997)

To determine how to utilize the green fluorescent protein (GFP) as a marker for subcellular localization and as a label for plant mitochondria in vivo, transgenic suspension cells and tobacco plants expressing GFP with and without a mitochondrial localization signal were generated. The first GFP form used, GFP1, is easily observable in cells with low autofluorescence, such as suspension cells or trichomes, but masked in green tissue. For the visualization of GFP in cells and tissues with high autofluorescence, such as leaf, the use of a very strong promoter (35S35SAMV), a highly expressed modified mGFP4 coding region and a brighter mutant form of GFP (S65T) was necessary. Confocal or two-photon laser scanning microscopy reveal a distinct subcellular localization of the fluorescence in cells expressing GFP or coxIVGFP. In cells expressing untargeted GFP, fluorescence accumulates in the nucleoplasm but is also distributed throughout the cytoplasm. It is excluded from vacuoles, nucleoli and from round bodies that are likely to be leucoplasts. In contrast, fluorescence is localized specifically to mitochondria in cells expressing coxIVGFP fusion protein as shown by co-localization with a mitochondrial-specific dye. This permits the direct observation of mitochondria and mitochondrial movements in living plant cells and tissues throughout plant development. Three-dimensional reconstruction of individual cells can give additional information about the distribution and numbers of mitochondria.
Injection moldable ceramic-ceramic composites: Compounding behavior, whisker degradation, and orientation (1993)

During the past decade, enhanced processing has produced ceramic materials with improved mechanical properties and reliability. However, ceramic materials are still inherently brittle. Therefore, whisker-reinforced ceramic composites have recently received significant attention because of their attractive mechanical properties. In addition, the discrete nature and moderate aspect ratio of the short whiskers allow them to be processed into complex-shaped components, using automated fabrication methods, such as injection molding. Here, the compounding behavior of injection moldable silicon powder - SiC whisker formulations, for toughened reaction-bonded Si[sub 3]N[sub 4] composites, was examined as a function of the binder system. The effect on whisker degradation and orientation was also studied.
A Frame-to-Frame<i>Picturephone</i>® Coder For Signals Containing Differential Quantizing Noise (1973)

The frame-to-frame coder described in Ref. 1 used an 8-bit PCM signal for input. If, instead, the signal is obtained by digitally integrating the output of an element difference coder, the quantization noise may be misinterpreted as motion, and cause unnecessary transmission. In the particular example of the Phase I coder, <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> the quantization noise loads the frame codec to the extent that it produces an unacceptable picture. In this paper, a frame-to-frame coder for Picturephone® signals is described which is capable of coding the digital output of a Phase I codec for transmission over a 2-megabit/second channel. Improved methods are used to segment the noisy picture into moving areas and background areas. The moving areas are then transmitted using a number of data reduction techniques. During periods of slow movement, clusters of frame-to-frame differences in the moving area are transmitted. For moderate movement, frame differences are sent only in every other field, the moving areas of intervening fields being transmitted by a conditional field interpolation technique. For rapid movement, 2:1 horizontal subsampling is used, and, finally, during violent motion when the buffer fills, frame repeating is used. The picture quality obtained from a laboratory simulation of this system is believed to be satisfactory even for a very active subject. With small amounts of motion the subjective quality is actually improved because the visibility of the quantizing noise from the Phase I codec is reduced by the inherent frame repeating action of the coder.
Effect of Phase-Sensitive Environment Model and Higher Order VTS on Noisy Speech Feature Enhancement (2006)

Model-based techniques for robust speech recognition often require the statistics of noisy speech. In this paper, we propose two modifications to obtain more accurate versions of the statistics of the combined HMM (starting from a clean speech and a noise model). Usually, the phase difference between speech and noise is neglected in the acoustic environment model. However, we show how a phase-sensitive environment model can be efficiently integrated in the context of multi-stream model-based feature enhancement and gives rise to more accurate covariance matrices for the noisy speech. Also, by expanding the vector Taylor series up to the second order term, an improved noisy speech mean can be obtained. Finally, we explain how the front-end clean speech model itself can be improved by a preprocessing of the training data. Recognition results on the Aurora4 database illustrate the effect on the noise robustness for each of these modifications.
The Effects of Fatty Acids and Their Derivatives on the Intestinal Absorption of insulin in Rat (1993)

AbstractInsulin solution (25 U/ml/kg, pH 8.0) was administered with 50 mM of various C8-Cl8 fatty acid and derivative absorption enhancers to the duodenum, colon and rectum of fasted normal rats under sodium pentobarbital anesthesia. Solutions were administered directly into ligated or sealed intestinal segments. Blood was sampled periodically from the jugular vein and blood glucose levels determined. The maximum decrease in blood glucose level and area under the depression curve were used to estimate bioavailability. Enhancing effects rectally were further investigated in streptozotocin-induced diabetic rats in both the fasted and non-fasted states. Blood glucose levels and serum insulin concentrations were determined.
Sputum viscoelasticity in chronic bronchitis. (1971)

A recently developed, simple method for simultaneously measuring viscosity and elasticity of sputum was used to follow the clinical changes in 16 patients with bronchitis and to relate the bronchial fluid dynamics to the physical properties of sputum. During periods of clinical stability, the elastic recoil of sputum ranged within the narrow limits of less than 6 units; although the viscosity covered a larger range, it usually measured less than 400 poises. During acute exacerbations, great difficulty in raising sputum was experienced, and the viscosity invariably increased, sometimes to as much as 2,000 poises. Viscosity was measured at shear rates of 1 sec−1 to 1.5 sec−1, a value calculated to be most representative of the actual rates in these patients. In each patient, purulent sputum had greater viscosity and less elastic recoil than mucoid sputum, correlating closely with difficulty in expectoration. In accordance with viscoelastic theory, this behavior indicates the presence of varying quantities o...
Learning from bug-introducing changes to prevent fault prone code (2007)

A version control system, such as CVS/SVN, can provide the history of software changes performed during the evolution of a software project. Among all the changes performed there are some which cause the introduction of bugs, often resolved later with other changes.
Nonsurgical Treatment of Gallstones (1989)

During the past 18 years, three approaches have been introduced as alternatives to surgical treatment of gallbladder stones,1 2 3 4 a condition known since antiquity. All have as their objective the dissolution of the stones, leaving the gallbladder intact and stone-free. Elimination of the stones should be accompanied by relief of symptoms and should prevent the development of more serious complications — e.g., cholecystitis, pancreatitis, cholangitis, or obstructive jaundice.In contrast to cholecystectomy, for which prior knowledge of the composition of the stones is unnecessary, dissolution therapy is effective only for cholesterol stones. Gallstones composed predominantly of pigment (bilirubin polymers) or calcium . . .
On the convergence of spherical harmonic expansion of topographic and atmospheric biases in gradiometry (2009)

On the convergence of spherical harmonic expansion of topographic and atmospheric biases in gradiometry The gravity gradiometric data are affected by the topographic and atmospheric masses. In order to fulfill Laplace-Poisson's equation and to simplify the downward continuation process, these effects should be removed from the data. However, if the analytical downward continuation is considered, the gravity gradients can be continued downward disregarding such effects but the result will be biased. The topographic and atmospheric biases can be expressed in terms of spherical harmonics and studying these biases gives some ideas about analytical downward continuation of these quantities to sea level. In formulation of harmonic coefficients of the topographic and atmospheric biases, a truncated binomial expansion of topographic height is used. In this paper, we show that the harmonics are convergent to the third term of this binomial expansion. The harmonics of the biases on V zz are convergent to the first term and they are convergent in V xy for all the terms. The harmonics of the other components of the gravity gradient tensor are convergent to the second terms, while the third terms are only asymptotically convergent. This means that in terrestrial and airborne gradiometry the biases should be computed just to the second order term, while in satellite gravity gradiometry, e.g. GOCE, the third term can also be considered.
The Metal Binding Site of the Hepatitis C Virus NS3 Protease (1998)

The NS3 region of the hepatitis C virus encodes for a serine protease activity, which is necessary for the processing of the nonstructural region of the viral polyprotein. The minimal domain with proteolytic activity resides in the N terminus, where a structural tetradentate zinc binding site is located. The ligands being been identified by x-ray crystallography as being three cysteines (Cys97, Cys99, and Cys145) and one histidine residue (His149), which is postulated to coordinate the metal through a water molecule. In this article, we present an analysis of the role of metal coordination with respect to enzyme activity and folding. Using NMR spectroscopy, the resonances of His149 were assigned based on their isotropic shift in a Co(II)-substituted protein. Data obtained with 15N-labeled NS3 protease were compatible with the involvement of the delta-N of His149 in metal coordination. pH titration experiments showed that the cooperative association of at least two protons is required in the protonation process of His149. Changes in the NMR signals of this residue between pH 7 and 5 are interpreted as evidence for a structural change at the metal binding site, which switches from a "closed" to an "open" conformation. Site-directed mutagenesis of His149 has shown the importance of this residue in the metal incorporation pathway and for achieving an active fold. The metal coordination of the protease was also investigated by circular dichroism and electronic absorption spectroscopies using a Co(II)-substituted enzyme. We show evidence for rearrangements of the metal coordination geometry induced by complex formation with an NS4A peptide cofactor. No such changes were observed upon binding to a substrate peptide. Also, CN- and N3- induced Co(II) ligand field perturbations, which went along with an 1.5-fold enhancement of protease activity.
Increased susceptibility of aged hearts to ventricular fibrillation during oxidative stress (2009)

Oxidative stress with hydrogen peroxide (H(2)O(2)) readily promotes early afterdepolarizations (EADs) and triggered activity (TA) in isolated rat and rabbit ventricular myocytes. Here we examined the effects of H(2)O(2) on arrhythmias in intact Langendorff rat and rabbit hearts using dual-membrane voltage and intracellular calcium optical mapping and glass microelectrode recordings. Young adult rat (3-5 mo, N = 25) and rabbit (3-5 mo, N = 6) hearts exhibited no arrhythmias when perfused with H(2)O(2) (0.1-2 mM) for up to 3 h. However, in 33 out of 35 (94%) aged (24-26 mo) rat hearts, 0.1 mM H(2)O(2) caused EAD-mediated TA, leading to ventricular tachycardia (VT) and fibrillation (VF). Aged rabbits (life span, 8-12 yr) were not available, but 4 of 10 middle-aged rabbits (3-5 yr) developed EADs, TA, VT, and VF. These arrhythmias were suppressed by the reducing agent N-acetylcysteine (2 mM) and CaMKII inhibitor KN-93 (1 microM) but not by its inactive form (KN-92, 1 microM). There were no significant differences between action potential duration (APD) or APD restitution slope before or after H(2)O(2) in aged or young adult rat hearts. In histological sections, however, trichrome staining revealed that aged rat hearts exhibited extensive fibrosis, ranging from 10-90%; middle-aged rabbit hearts had less fibrosis (5-35%), whereas young adult rat and rabbit hearts had <4% fibrosis. In aged rat hearts, EADs and TA arose most frequently (70%) from the left ventricular base where fibrosis was intermediate ( approximately 30%). Computer simulations in two-dimensional tissue incorporating variable degrees of fibrosis showed that intermediate (but not mild or severe) fibrosis promoted EADs and TA. We conclude that in aged ventricles exposed to oxidative stress, fibrosis facilitates the ability of cellular EADs to emerge and generate TA, VT, and VF at the tissue level.
A class of optical receivers using optical feedback (1976)

Thesis. 1976. Ph.D.--Massachusetts Institute of Technology. Dept. of Electrical Engineering and Computer Science.
Investigations of Rat Mast Cell Heterogeneity (1987)

In the rat, two distinct mast cell subsets have been identified. One, represented by the easily accessible and purified peritoneal mast cell, differs from the other, the intestinal mucosal mast cell, in staining properties, fixation sensitivity, mediator content, and responsiveness to various secretagogues and antiallergic drugs. To investigate the molecular basis and control mechanisms of mast cell heterogeneity, we have initiated sodium dodecylsulfate polyacrylamide gel electrophoretic analysis of the constituents of rat peritoneal and intestinal mucosal mast cells; developed subcellular fractionation protocols to facilitate these comparisons; produced a mast cell specific rabbit antiserum, and established methods to isolate mast cell RNA. These approaches require refinement, but will prove to be useful in further investigations of mast cell biology.
Dissecting the role of the mitochondrial chaperone mortalin in Parkinson's disease: functional impact of disease-related variants on mitochondrial homeostasis (2010)

The mitochondrial chaperone mortalin has been linked to neurodegeneration in Parkinson's disease (PD) based on reduced protein levels in affected brain regions of PD patients and its interaction with the PD-associated protein DJ-1. Recently, two amino acid exchanges in the ATPase domain (R126W) and the substrate-binding domain (P509S) of mortalin were identified in Spanish PD patients. Here, we identified a separate and novel variant (A476T) in the substrate-binding domain of mortalin in German PD patients. To define a potential role as a susceptibility factor in PD, we characterized the functions of all three variants in different cellular models. In vitro import assays revealed normal targeting of all mortalin variants. In neuronal and non-neuronal human cell lines, the disease-associated variants caused a mitochondrial phenotype of increased reactive oxygen species and reduced mitochondrial membrane potential, which were exacerbated upon proteolytic stress. These functional impairments correspond with characteristic alterations of the mitochondrial network in cells overexpressing mutant mortalin compared with wild-type (wt), which were confirmed in fibroblasts from a carrier of the A476T variant. In line with a loss of function hypothesis, knockdown of mortalin in human cells caused impaired mitochondrial function that was rescued by wt mortalin, but not by the variants. Our genetic and functional studies of novel disease-associated variants in the mortalin gene define a loss of mortalin function, which causes impaired mitochondrial function and dynamics. Our results support the role of this mitochondrial chaperone in neurodegeneration and underscore the concept of impaired mitochondrial protein quality control in PD.
Cloning and expression of a cDNA coding for a human monocyte-derived plasminogen activator inhibitor. (1988)

Human monocyte-derived plasminogen activator inhibitor (mPAI-2) was purified to homogeneity from the U937 cell line and partially sequenced. Oligonucleotide probes derived from this sequence were used to screen a cDNA library prepared from U937 cells. One positive clone was sequenced and contained most of the coding sequence as well as a long incomplete 3' untranslated region (1112 base pairs). This cDNA sequence was shown to encode mPAI-2 by hybrid-select translation. A cDNA clone encoding the remainder of the mPAI-2 mRNA was obtained by primer extension of U937 poly(A)+ RNA using a probe complementary to the mPAI-2 coding region. The coding sequence for mPAI-2 was placed under the control of the lambda PL promoter, and the protein expressed in Escherichia coli formed a complex with urokinase that could be detected immunologically. By nucleotide sequence analysis, mPAI-2 cDNA encodes a protein containing 415 amino acids with a predicted unglycosylated Mr of 46,543. The predicted amino acid sequence of mPAI-2 is very similar to placental PAI-2 (3 amino acid differences) and shows extensive homology with members of the serine protease inhibitor (serpin) superfamily. mPAI-2 was found to be more homologous to ovalbumin (37%) than the endothelial plasminogen activator inhibitor, PAI-1 (26%). Like ovalbumin, mPAI-2 appears to have no typical amino-terminal signal sequence. The 3' untranslated region of the mPAI-2 cDNA contains a putative regulatory sequence that has been associated with the inflammatory mediators.
A sterically controlled recyclable system: reversible photoredox reactions between anthraquinone and hindered tertiary amines (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA sterically controlled recyclable system: reversible photoredox reactions between anthraquinone and hindered tertiary aminesHong Gan and David G. WhittenCite this: J. Am. Chem. Soc. 1993, 115, 18, 8031–8037Publication Date (Print):September 1, 1993Publication History Published online1 May 2002Published inissue 1 September 1993https://pubs.acs.org/doi/10.1021/ja00071a014https://doi.org/10.1021/ja00071a014research-articleACS PublicationsRequest reuse permissionsArticle Views580Altmetric-Citations23LEARN 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
Asymmetric Primaquine and Halogenaniline Fumardiamides as Novel Biologically Active Michael Acceptors (2018)

Novel primaquine (PQ) and halogenaniline asymmetric fumardiamides <b>4a</b>⁻<b>f</b>, potential Michael acceptors, and their reduced analogues succindiamides <b>5a</b>⁻<b>f</b> were prepared by simple three-step reactions: coupling reaction between PQ and mono-ethyl fumarate (<b>1a</b>) or mono-methyl succinate (<b>1b</b>), hydrolysis of PQ-dicarboxylic acid mono-ester conjugates <b>2a</b>,<b>b</b> to corresponding acids <b>3a</b>,<b>b</b>, and a coupling reaction with halogenanilines. 1-[bis(Dimethylamino)methylene]-1<i>H</i>-1,2,3-triazolo[4,5-<i>b</i>]pyridinium 3-oxide hexafluorophosphate (HATU) was used as a coupling reagent along with Hünig's base. Compounds <b>4</b> and <b>5</b> were evaluated against a panel of bacteria, several <i>Mycobacterium</i> strains, fungi, a set of viruses, and nine different human tumor cell lines. <i>p</i>-Chlorofumardiamide <b>4d</b> showed significant activity against <i>Staphylococcus aureus,</i><i>Streptococcus pneumoniae</i> and <i>Acinetobacter baumannii</i>, but also against <i>Candida albicans</i> (minimum inhibitory concentration (MIC) 6.1⁻12.5 µg/mL). Together with <i>p</i>-fluoro and <i>p</i>-CF₃ fumardiamides <b>4b</b>,<b>f</b>, compound <b>4d</b> showed activity against <i>Mycobacterium marinum</i> and <b>4b</b>,<b>f</b> against <i>M. tuberculosis</i>. In biofilm eradication assay, most of the bacteria, particularly <i>S. aureus</i>, showed susceptibility to fumardiamides. <i>m</i>-CF₃ and <i>m</i>-chloroaniline fumardiamides <b>4e</b> and <b>4c</b> showed significant antiviral activity against reovirus-1, sindbis virus and Punta Toro virus (EC<sub>50</sub> = 3.1⁻5.5 µM), while <b>4e</b> was active against coxsackie virus B4 (EC<sub>50</sub> = 3.1 µM). <i>m</i>-Fluoro derivative <b>4a</b> exerted significant cytostatic activity (IC<sub>50</sub> = 5.7⁻31.2 μM). Acute lymphoblastic leukemia cells were highly susceptible towards <i>m</i>-substituted derivatives <b>4a</b>,<b>c</b>,<b>e</b> (IC<sub>50</sub> = 6.7⁻8.9 μM). Biological evaluations revealed that fumardiamides <b>4</b> were more active than succindiamides <b>5</b> indicating importance of Michael conjugated system.
A direct, general approach based on isobolograms for assessing the joint action of drugs in pre‐clinical experiments (1994)

Pharmacologists and other biologists frequently use methods based on the interpretation of isobolograms to quantify the extent of synergy or antagonism between drugs used in combination in pre-clinical studies. Most methods have been unsatisfactory from a statistical viewpoint, many because they have relied solely on visual evaluation, others because the methods have not taken into account the variability of the measurements. We describe a direct approach for quantifying the joint potency of two drugs, a central feature being the use of simple isobole models that lead directly to response surface models for the expected experimental outcomes. The approach is general in the sense that one can use it for discrete or continuous responses, different underlying probability distributions, linear or non-linear dose-response functions of the drugs used singly, and a variety of experimental designs. Our approach extends the suggestions made by Hewlett for measuring the joint potency of drugs, and is similar in spirit to the approaches proposed by Greco et al. and Weinstein et al. We describe the analysis of data from an in vitro experiment conducted to evaluate the efficacy of the antiviral drugs AZT and ddI used in combination.