gebhart/patrepeval huggingface dataset:
Isozyme‐specific inhibitors of protein kinase C translocation: effects on contractility of single permeabilized vascular muscle cells of the ferret (1999)

1. The effects on contractility of three peptides reported to inhibit protein kinase C (PKC) translocation in an isozyme-specific manner were studied: a peptide from the C2 domain of conventional PKCs (C2-2), a peptide from the N-terminal variable domain of epsilonPKC (epsilonV1-2) and a peptide (ABP) from the actin-binding domain of epsilonPKC (epsilon(223-228)). 2. Isometric force was directly recorded from individual hyperpermeable ferret portal vein or aortic smooth muscle cells. 3. Phenylephrine contracted permeabilized portal vein cells at pCa 6.7 but not at pCa 7.0. However, phenylephrine did contract aortic cells at pCa 7.0. 4. C2-2 inhibited phenylephrine-induced contraction, but did not affect resting tension, in portal vein cells at pCa 6.7. In aortic cells at either pCa 6.7 or 7.0, C2-2 had no effect on either basal tension or phenylephrine-induced contraction. 5. ABP did not evoke any changes in phenylephrine-induced contraction or baseline tension in either portal vein or aortic cells. 6. epsilonV1-2 inhibited phenylephrine-induced contraction and decreased resting tension in aortic cells at pCa 7.0, but not in portal vein cells at pCa 6.7. 7. Western blots indicated that portal vein cells contained substantially more alphaPKC than aortic cells. Portal vein cells also contained small amounts of betaPKC, which was undetectable in aortic cells. In contrast, aortic cells contained more epsilonPKC than portal vein cells. Even though epsilonPKC was expressed in portal vein and alphaPKC in aorta, imaging studies indicated that they were not translocated in these cell types. 8. These results suggest that the Ca2+-dependent isozymes of PKC (alpha and/or beta) play a major role in contraction of the portal vein but not of the aorta. In contrast, the results are consistent with epsilonPKC, but not Ca2+-dependent PKC isozymes, regulating contractility of the aorta.
Insulin-degrading Enzyme Regulates Extracellular Levels of Amyloid β-Protein by Degradation (1998)

Excessive cerebral accumulation of the 42-residue amyloid beta-protein (Abeta) is an early and invariant step in the pathogenesis of Alzheimer's disease. Many studies have examined the cellular production of Abeta from its membrane-bound precursor, including the role of the presenilin proteins therein, but almost nothing is known about how Abeta is degraded and cleared following its secretion. We previously screened neuronal and nonneuronal cell lines for the production of proteases capable of degrading naturally secreted Abeta under biologically relevant conditions and concentrations. The major such protease identified was a metalloprotease released particularly by a microglial cell line, BV-2. We have now purified and characterized the protease and find that it is indistinguishable from insulin-degrading enzyme (IDE), a thiol metalloendopeptidase that degrades small peptides such as insulin, glucagon, and atrial natriuretic peptide. Degradation of both endogenous and synthetic Abeta at picomolar to nanomolar concentrations was completely inhibited by the competitive IDE substrate, insulin, and by two other IDE inhibitors. Immunodepletion of conditioned medium with an IDE antibody removed its Abeta-degrading activity. IDE was present in BV-2 cytosol, as expected, but was also released into the medium by intact, healthy cells. To confirm the extracellular occurrence of IDE in vivo, we identified intact IDE in human cerebrospinal fluid of both normal and Alzheimer subjects. In addition to its ability to degrade Abeta, IDE activity was unexpectedly found be associated with a time-dependent oligomerization of synthetic Abeta at physiological levels in the conditioned media of cultured cells; this process, which may be initiated by IDE-generated proteolytic fragments of Abeta, was prevented by three different IDE inhibitors. We conclude that a principal protease capable of down-regulating the levels of secreted Abeta extracellularly is IDE.
Alemtuzumab for Refractory Celiac Disease in a Patient at Risk for Enteropathy-Associated T-Cell Lymphoma (2006)

To the Editor: A 56-year-old woman had a two-year history of refractory celiac disease for which she had taken prednisone (20 mg per day) for the previous six months, during which time her condition had worsened despite a gluten-free diet. Duodenal biopsy showed severe atrophy with crypt hyperplasia and increased intraepithelial lymphocyte counts. On immunohistochemical analysis, the cytoplasm was positive for CD3 and negative for CD4 and CD8 (Figure 1). Flow-cytometric analysis of intraepithelial lymphocytes showed that more than 50 percent of the cells expressed T-cell receptor γδ (TCRγδ). In addition, we identified a second aberrant population of intraepithelial lymphocytes, . . .
Kinetic vs Thermodynamic Self-Sorting of Cucurbit[6]uril, Cucurbit[7]uril, and a Spermine Derivative (2009)

Cucurbit[6]-, cucurbit[7]-, and cucurbit[6]uril cavitands can be aligned along a spermine derivative axle in a well-defined, kinetically favored sequence at room temperature, and can undergo a reorganization toward a more stable [4]pseudorotaxane bearing three cucurbit[6]uril units upon thermally induced scrambling.
RNA interference of influenza virus production by directly targeting mRNA for degradation and indirectly inhibiting all viral RNA transcription (2003)

Influenza A virus causes widespread infection in the human respiratory tract, but existing vaccines and drug therapy are of limited value. Here we show that short interfering RNAs (siRNAs) specific for conserved regions of the viral genome can potently inhibit influenza virus production in both cell lines and embryonated chicken eggs. The inhibition depends on the presence of a functional antisense strand in the siRNA duplex, suggesting that viral mRNA is the target of RNA interference. However, siRNA specific for nucleocapsid (NP) or a component of the RNA transcriptase (PA) abolished the accumulation of not only the corresponding mRNA but also virion RNA and its complementary RNA. These siRNAs also broadly inhibited the accumulation of other viral, but not cellular, RNAs. The findings reveal that newly synthesized NP and PA proteins are required for influenza virus transcription and replication and provide a basis for the development of siRNAs as prophylaxis and therapy for influenza infection in humans.
Evaluation of Pectoralis Major Muscle in Patients with Posterior Breast Tumors on Breast MR Images: Early Experience (2000)

Extension of adjacent tumor into underlying musculature was indicated by abnormal enhancement within these structures. Violation of the fat plane between tumor and muscle, without other findings, did not indicate tumor involvement of these deep structures.
A small size microstrip antenna having a partial short circuit (1995)

Two special configurations of partially shorted microstrip antennas are studied experimentally. In the first configuration, the shorted portion of the partially shorted edge is formed in one continuous section centered around the central line of the antenna, on which the feed point is located. The different widths of the shorted section and the corresponding resonant frequencies and the feed locations that provide 50 ohms input impedance are shown. In order to satisfy the required input impedance of 50 ohms, the feed point should be moved closer to the partially shorted edge as the width of the shorted section of that edge decreases. In the second configuration the short circuited portion comprises two equal sections at the outer ends of the partially shorted edge. In such a case, any point on the central line of the antenna, including the feed point, will always be far enough from the shorted sections of the partially shorted edge. Hence, the variation of the input impedance along the central line of the antenna is much smaller than the first configuration.
Evaluation of the Structure of the Polysaccharides from Chondria macrocarpa and Ceramium rubrum as Determined by 13C NMR Spectroscopy (2002)

The polysaccharides from Chondria macrocarpa and Ceramium rubrum were examined by 13 C NMR spectroscopy and their spectra were analysed bymeans of set theory. The spectra of the polysaccharides from Chondria macrocarpa collected in autumn were in accord with previous chemical analysis but polysaccharides from seaweed collected in spring comprise a higher level of agar precursors, much lower levels of galactose 2-sulfate, and the polysaccharide is separable into two components, the predominant one of which is essentially free of anhydrogalactose. The signal subset due to the xylosyl unit substituted at the 3-position of 4-linked l-galactose could be assigned from the spectrum of desulfated polysaccharide from Chondria macrocarpa . The extract from Ceramium rubrum consisted of a backbone of 3-linked d-galactosyl units alternating with the 4-linked units 3, 6- anhydro-l-galactosyl and l-galactosyl in a ratio of 2:1 respectively, to which substitution by xylose occurred at approximately 8% of the total sugar units. The natural polymer had moderate levels of sulfate ester, with galactose-6-sulfate being the predominant unit, some of which survives alkaline treatment and was consistent with being 3-linked. There is also evidence of low levels of 3-linked galactose-2-sulfate.
Cyclopropane Fatty Acids in Relation to Earliness in Spring and Drought Tolerance in Plants (1972)

Long chain cyclopropane fatty acids were observed in the sulfolipid fraction extracted from leaves of the early spring plants Galanthus nivalis L. and Anthriscus silvestris L. (Hoffm.). The content of cyclopropane fatty acids with 25 carbon atoms appeared to be clearly correlated with earliness in spring, and it ranged from 68% (G. nivalis L., snow drop) to 0.5% (wheat). Several long chain cyclopropane fatty acids were found in the drought-tolerant Corynephorus canescens (L.) P.B., exclusively in the phosphatidyl choline fraction.
Induction of human interleukin-1 by a product of Staphylococcus aureus associated with toxic shock syndrome. (1984)

Certain strains of Staphylococcus aureus associated with toxic shock syndrome elaborate material that induces human blood monocytes to secrete interleukin-1 (IL-1). IL-1 was detected both by its ability to cause fever in rabbits using the leukocytic pyrogen (LP) assay and by its mitogenic activity towards thymocytes in the so-called lymphocyte-activating factor (LAF) assay. Anti-human IL-1 prevents the manifestation of both activities. Filtrates of control strains of S. aureus manifest neither activity. Thus, culture filtrates derived from toxic shock syndrome (TSS)-associated strains cause biphasic fever in rabbits when injected intravenously. The fever lasts several hours. Plasma taken at the peak of the fever and injected into a second set of rabbits produces a brief monophasic fever typical of LP. Further, human monocytes release LP when incubated with TSS filtrates in vitro. The monocyte products also stimulate the proliferation of mouse thymocytes in the presence of phytohemagglutinin in a manner characteristic of LAF. A bacterial filtrate is much less effective without an intermediate incubation with monocytes. The stimulation of monocyte IL-1 production is easily quantified, provides a simple method of assaying the TSS toxin, and since it involves human cells, is directly relevant to the human disease. The assay was used to monitor the purification of TSS toxin. Only 0.1 ng/ml of the purified material is required to induce monocyte IL-1 production. It is thus more potent than endotoxin. In contrast to endotoxin, its effect is not blocked by polymyxin B. We conclude that in TSS the sudden fever and probably other components of the acute phase response may be attributed to a massive release of IL-1.
Modified Reagents for Determination of Urea and Ammonia (1962)

Abstract Combinations of reagents are described for the catalyzed indophenol reaction for the determination of ammonia, which produces a stable blue color. The procedure is adapted to the determination of urea after hydrolysis with urease.
Evidence That the Autoimmune Regulator Gene Influences Thymic Production of Ovarian Antigens and Prevents Autoimmune-Mediated Premature Reproductive Senescence1 (2012)

The importance of the ovarian reserve, defined as the supply of primordial follicles in the mammalian ovary, to women’s health [1, 2], mammalian fertility [3, 4], and mammalian assisted reproductive technologies [5, 6] has been the subject of much research. Depletion of the ovarian reserve is considered to be a major factor influencing reproductive senescence in female mammals, and menopause is associated with a number of health risks in women [2, 7]. Premature ovarian failure (POF; also known as premature ovarian dysfunction or primary ovarian insufficiency) causes premature menopause (also known as premature reproductive senescence), defined as menopause before age 40 in women [8]. Recent research has demonstrated both genetic predisposition [9] and autoimmune disorders [10] to be major factors contributing to the occurrence of POF.\nThe thymus is the organ responsible for T cell development and establishment of central tolerance, the process that allows the immune system to recognize self and prevent autoimmune disorders. T cells are derived from hematopoietic precursors that arise in the bone marrow and migrate to the thymus, where central tolerance is promoted by both positive and negative selection [11]. Positive selection sets the baseline T cell receptor (TCR) signaling threshold; negative selection occurs when the T cells migrate to the thymic medulla, where thymocytes with strong self-reactive TCRs undergo apoptosis, preventing them from initiating an autoimmune response in the peripheral tissues.
SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information (2014)

Protein structure homology modelling has become a routine technique to generate 3D models for proteins when experimental structures are not available. Fully automated servers such as SWISS-MODEL with user-friendly web interfaces generate reliable models without the need for complex software packages or downloading large databases. Here, we describe the latest version of the SWISS-MODEL expert system for protein structure modelling. The SWISS-MODEL template library provides annotation of quaternary structure and essential ligands and co-factors to allow for building of complete structural models, including their oligomeric structure. The improved SWISS-MODEL pipeline makes extensive use of model quality estimation for selection of the most suitable templates and provides estimates of the expected accuracy of the resulting models. The accuracy of the models generated by SWISS-MODEL is continuously evaluated by the CAMEO system. The new web site allows users to interactively search for templates, cluster them by sequence similarity, structurally compare alternative templates and select the ones to be used for model building. In cases where multiple alternative template structures are available for a protein of interest, a user-guided template selection step allows building models in different functional states. SWISS-MODEL is available at http://swissmodel.expasy.org/.
Capsule Retentions and Incomplete Capsule Endoscopy Examinations: An Analysis of 2300 Examinations (2011)

Capsule endoscopy is considered a safe procedure, although obstructive symptoms and serious complications due to capsule retention can be found in a large series of patients.
Contamination and Sensitivity Issues with a Real-Time Universal 16S rRNA PCR (2000)

A set of universal oligonucleotide primers specific for the conserved regions of the eubacterial 16S rRNA gene was designed for use with the real-time PCR Applied Biosystems 7700 (TaqMan) system. During the development of this PCR, problems were noted with the use of this gene as an amplification target. Contamination of reagents with bacterial DNA was a major problem exacerbated by the highly sensitive nature of the real-time PCR chemistry. This was compounded by the use of a small amplicon of approximately 100 bases, as is necessary with TaqMan chemistry. In an attempt to overcome this problem, several methodologies were applied. Certain treatments were more effective than others in eliminating the contaminating DNA; however, to achieve this there was a decrease in sensitivity. With UV irradiation there was a 4-log reduction in PCR sensitivity, with 8-methoxypsoralen activity facilitated by UV there was between a 5- and a 7-log reduction, and with DNase alone and in combination with restriction digestion there was a 1.66-log reduction. Restriction endonuclease treatment singly and together did not reduce the level of contaminating DNA. Without the development of ultrapure Taq DNA polymerase, ultrapure reagents, and plasticware guaranteed to be free of DNA, the implementation of a PCR for detection of eubacterial 16S rRNA with the TaqMan system will continue to be problematical.
Plasmid Interleukin-23 (IL-23), but Not Plasmid IL-27, Enhances the Protective Efficacy of a DNA Vaccine againstMycobacterium tuberculosisInfection (2005)

Protection against intracellular pathogens such as Mycobacterium tuberculosis requires the development of Th1-like T-cell responses. This in turn is dependent on the pattern of cytokine produced from dendritic cells (DCs) after infection. Three heterodimeric cytokines, interleukin-12 (IL-12), IL-23, and IL-27, as well as IL-18, contribute to the differentiation and expansion of naive CD4(+) T cells. In this study we compared the effects of plasmids expressing both chains of IL-12, IL-23, or IL-27 as adjuvants for DNA immunization against M. tuberculosis infection. The genes encoding p19 and p40 chains of IL-23 or EBI3 and p28 chains of IL-27 were cloned on either side of a self-cleaving peptide from the FMDV2A protein. The secretion of functional cytokines from transfected cells was detected with bioassays. Supernatant from p2AIL-23-transfected cells induced the release of IL-17 from activated lymphocytes, confirming the presence of bioactive IL-23. Further, supernatant from p2AIL-27-transfected cells stimulated a significant increase in the proliferation of peptide-stimulated transgenic CD4(+) T cells. In initial experiments, M. tuberculosis infection of DCs was more potent at inducing IL-12 and IL-23 secretion than infection with the vaccine strain Mycobacterium bovis bacille Calmette-Guérin (BCG), and no significant upregulation of IL-27 was observed. Coimmunization of C57BL/6 mice with DNA expressing M. tuberculosis antigen 85B (Ag85B; DNA85B) and plasmids expressing IL-23 or IL-12 stimulated stronger Ag85B-specific T-cell proliferative and IFN-gamma responses than DNA85B alone, whereas the addition of p2AIL-27 had no effect. Interestingly, DNA85B codelivered with p2AIL-12, but not p2AIL-23, reduced the immunoglobulin G antibody response. Both p2AIL-23 and p2AIL-12, but not p2AIL-27, enhanced the protective efficacy of DNA85B against aerosol M. tuberculosis challenge. Therefore, both p2AIL-23 and p2AIL-12 are valuable as cytokine adjuvants for increasing the protective antituberculosis immunity induced by DNA vaccines.
Quinazolines. Part IX. Covalent hydration in the neutral species of substituted quinazolines (1967)

The ratios of hydrated to anhydrous neutral species of twenty-eight quinazolines are found to be in the range 10–2–10–5. The effects of substituents on this ratio in the neutral species are shown to be comparable to those observed in the respective cations, and suggest that the factors influencing the amount of hydration in these two species are similar. The ionisation constants of the hydrated species of thirty-two quinazolines have been measured and the effects of substituents on these constants are discussed.
Starch Division and Partitioning. A Mechanism for Granule Propagation and Maintenance in the Picophytoplanktonic Green Alga Ostreococcus tauri (2004)

Whereas Glc is stored in small-sized hydrosoluble glycogen particles in archaea, eubacteria, fungi, and animal cells, photosynthetic eukaryotes have resorted to building starch, which is composed of several distinct polysaccharide fractions packed into a highly organized semicrystalline granule. In plants, both the initiation of polysaccharide synthesis and the nucleation mechanism leading to formation of new starch granules are currently not understood. Ostreococcus tauri, a unicellular green alga of the Prasinophyceae family, defines the tiniest eukaryote with one of the smallest genomes. We show that it accumulates a single starch granule at the chloroplast center by using the same pathway as higher plants. At the time of plastid division, we observe elongation of the starch and division into two daughter structures that are partitioned in each newly formed chloroplast. These observations suggest that in this system the information required to initiate crystalline polysaccharide growth of a new granule is contained within the preexisting polysaccharide structure and the design of the plastid division machinery.
A c- myb Antisense Oligodeoxynucleotide Inhibits Normal Human Hematopoiesis in Vitro (1988)

The nuclear protein encoded by the proto-oncogene c-myb has been hypothesized to play an important role in the process of hematopoiesis, but direct proof of this function has been lacking. To address this issue, normal human bone marrow mononuclear cells were exposed to c-myb sense and antisense synthetic oligodeoxynucleotides, and the effects on hematopoietic colony formation and maturation were examined. Exposure of these cells to c-myb antisense, oligodeoxynucleotides resulted in a decrease in both colony size and number, without apparent effect on the maturation of residual colony cells. Exposure to c-myb sense, or irrelevant antisense, oligonucleotides had no such effect. These results show that (i) c-myb plays a critical role in regulating normal human hematopoiesis and (ii) the combined use of antisense oligodeoxynucleotides and hematopoietic cell culture techniques will provide a powerful tool for studying the role of proteins encoded by proto-oncogenes, or other specific genes, in normal human hematopoiesis.
Application of the Four-Parameter Logistic Model to Bioassay: Comparison with Slope Ratio and Parallel Line Models (1978)

In systems consisting of multiple clusters of processors which employ space sharing for scheduling jobs, such as our distributed ASCI supercomputer (DAS), co-allocation, i.e., the simultaneous allocation of processors to single jobs in multiple clusters, may be required. In studies of scheduling in single clusters it has been shown that the achievable (maximal) utilization may be much less than 100%, a problem that may be aggravated in multicluster systems. In this paper we study the maximal utilization when co-allocating jobs in multicluster systems, both with analytic means (we derive exact and approximate formulas when the service-time distribution is exponential), and with simulations with synthetic workloads and with workloads derived from the logs of actual systems.