gebhart/patrepeval huggingface dataset:
Characterization of fluorescence quenching in bifluorophoric protease substrates (1997)

NorFES is a relatively rigid, bent undecapeptide which contains an amino acid sequence that is recognized by the serine protease elastase (AspAlaIleProNle downward arrow SerIleProLysGlyTyr ( downward arrow indicates the primary cleavage site)). Covalent attachment of a fluorophore on each side of NorFES's elastase cleavage site enables one to use a change of fluorescence intensity as a measure of enzymatic activity. In this study two bichromophoric NorFES derivatives, D-NorFES-A and D-NorFES-D, were prepared in which D (donor) was tetramethylrhodamine and A (acceptor) was rhodamine-X, two chromophores with characteristics suitable for energy transfer. Absorption and fluorescence spectra were obtained with both the intact and cleaved homodoubly, heterodoubly and singly labeled derivatives. It was found that both the homo and hetero doubly-labeled derivatives form ground-state complexes which exhibit exciton bands. The hetero labeled derivative exhibits little or no resonance energy transfer. Spectral measurements were also done in urea, which partially disrupts ground-state dimers.
Liquid chromatographic determination of amino acids after gas-phase hydrolysis and derivatization with (dimethylamino)azobenzenesulfonyl chloride (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTLiquid chromatographic determination of amino acids after gas-phase hydrolysis and derivatization with (dimethylamino)azobenzenesulfonyl chlorideRene. Knecht and Jui Yoa. ChangCite this: Anal. Chem. 1986, 58, 12, 2375–2379Publication Date (Print):October 1, 1986Publication History Published online1 May 2002Published inissue 1 October 1986https://doi.org/10.1021/ac00125a006RIGHTS & PERMISSIONSArticle Views363Altmetric-Citations222LEARN 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 InReddit PDF (651 KB) Get e-Alerts Get e-Alerts
Regioselectivity of pyrrole synthesis from diethyl aminomalonate and 1,3-diketones: further observations (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTRegioselectivity of pyrrole synthesis from diethyl aminomalonate and 1,3-diketones: further observationsJohn B. Paine III, Jonathan R. Brough, Kathy K. Buller, and Erika E. EriksonCite this: J. Org. Chem. 1987, 52, 18, 3986–3993Publication Date (Print):September 1, 1987Publication History Published online1 May 2002Published inissue 1 September 1987https://pubs.acs.org/doi/10.1021/jo00227a009https://doi.org/10.1021/jo00227a009research-articleACS PublicationsRequest reuse permissionsArticle Views1382Altmetric-Citations30LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Release of early human hematopoietic progenitors from quiescence by antisense transforming growth factor beta 1 or Rb oligonucleotides. (1991)

We have used antisense oligonucleotides to study the roles of transforming growth factor beta (TGF-beta) and the two antioncogenes, retinoblastoma susceptibility (Rb) and p53, in the negative regulation of proliferation of early hematopoietic cells in culture. The antisense TGF-beta sequence significantly enhanced the frequency of colony formation by multi-lineage, early erythroid, and granulomonocytic progenitors, but did not affect colony formation by late progenitors. Single cell culture and limiting dilution analysis indicated that autocrine TGF-beta is produced by a subpopulation of early progenitors. Antisense Rb but not antisense p53 yielded similar results in releasing multipotential progenitors (colony-forming unit-granulocyte/erythroid/macrophage/megakaryocyte) from quiescence. Rb antisense could partially reverse the inhibitory effect of exogenous TGF-beta. Anti-TGF-beta blocking antibodies, antisense TGF-beta, or Rb oligonucleotides all had similar effects. No additive effects were observed when these reagents were combined, suggesting a common pathway of action. Our results are consistent with the model that autocrine production of TGF-beta negatively regulates the cycling status of early hematopoietic progenitors through interaction with the Rb gene product.
Gastric emptying of solid radiopaque markers: studies in healthy subjects and diabetic patients. (1984)

The purpose of these studies was to develop a radiologic method for assessing gastric emptying of an indigestible solid in humans and to apply this technique to the evaluation of patients with diabetes mellitus. Thirty healthy subjects ingested 10 solid radiopaque markers (small pieces of nasogastric tubing) together with a standard meal (donuts and 7-Up). Radiographs of the upper abdomen were obtained hourly for up to 6 h until all markers had emptied from the stomach. Although most of the liquid component of the meal, labeled with 111In, emptied during the first hour (as assessed simultaneously by radionuclide scintigraphy), few radiopaque markers emptied from the stomach during the first 2 h after the meal. Most markers emptied during the fourth postprandial hour, and all 10 markers had emptied by 6 h in 45 of 46 experiments. In contrast, not all of the solid radiopaque markers emptied from the stomach by 6 h in 16 of 26 experiments in patients with diabetes mellitus (p less than 0.001 vs. healthy controls). In some experiments, 99mTc-labeled scrambled eggs were added to the meal so that emptying of this digestible solid, assessed by scintigraphy, could be compared with emptying of liquids and solid radiopaque markers. In healthy subjects, the digestible solid emptied more slowly than the liquid (t 1/2 = 154 +/- 11 min vs. 30 +/- 3 min, p less than 0.001), but emptying of digestible solid was significantly faster than the emptying of the indigestible solid radiopaque markers. In diabetics, emptying rates for the digestible solid and liquid were close to normal (t 1/2 = 178 +/- 5 min and 40 +/- 3 min, respectively), whereas indigestible solid markers were retained in the stomach 6 h after the meal in 50% of the patients. Radiopaque markers proved to be a simple method for measuring gastric emptying of indigestible solids in humans. Using this technique, patients with insulin-dependent diabetes mellitus had a high incidence of abnormally slow gastric emptying of indigestible solids; the method may be a more sensitive indicator of gastric motor dysfunction than radionuclide scintigraphy.
Identification and initial characterization of a rat monoclonal antibody reactive with the murine interleukin 2 receptor-ligand complex. (1983)

Xenogeneic monoclonal antibodies were prepared to the murine interleukin 2 (IL-2)-dependent HT2 cell line. One rat IgM monoclonal antibody (7D4) was identified that inhibited proliferation of the HT2 cells and of IL-2-dependent CTLL cells in the presence of crude rat IL-2 as well as of purified human IL-2. The level of inhibition was dependent on both antibody and IL-2 concentration. Cell distribution studies using a fluorescence-activated cell sorter showed that the antigen identified by 7D4 is expressed at a high density on HT2 cells and on concanavalin A (Con A)-induced T-cell blasts and at a substantially lower density on lipopolysaccharide-induced B-cell blasts; 7D4 binding was not detected on greater than 95% of nonactivated thymocytes, T cells, or B cells. Competition binding studies indicated that 7D4 fails to inhibit the binding of 3H-labeled human IL-2 to CTLL cells. However, 7D4 specifically immunoprecipitated 3H-labeled human IL-2 from detergent extracts of HT2 cells or Con A-induced T-cell blasts that had been pulsed with [3H]IL-2; in contrast, 7D4 did not react with free [3H]IL-2. Initial biochemical analysis of immunoprecipitates with 7D4 of detergent extracts from surface-iodinated Con A-activated spleen cells showed a major band having apparent molecular weight of 48,000-62,000. Collectively, these results suggest that 7D4 detects an epitope on the IL-2 receptor distal to the ligand binding site or another molecule that physically associates with the receptor.
Implementation and evaluation of real-time Java threads (2002)

Java has many benefits such as security in distributed environments, reusability of code, and portability because it is architecture neutral. From those characteristics, Java is beginning to be used in many new environments. Even though Java provides various advantages, it still has problems which must be solved. One issue is that there are often real-time constraints that should be met in those applications. Current Java execution environment and language specification cannot satisfy those requirements. Our research focuses on the current limits of the Java language and its execution environment, and to seek the possibility for real-time using Java and the technologies we have available today. To investigate issues in real-time Java, we have implemented a prototype real-time Java environment which provides real-time Java threads and a real-time synchronization mechanism. Then we evaluated its performance. The results indicate that timing requirements are better met and unbounded priority inversion is avoided in our system.
Fabrication of 3D fractal structures using nanoscale anisotropic etching of single crystalline silicon (2013)

When it comes to high-performance filtration, separation, sunlight collection, surface charge storage or catalysis, the effective surface area is what counts. Highly regular fractal structures seem to be the perfect candidates, but manufacturing can be quite cumbersome. Here it is shown-for the first time-that complex 3D fractals can be engineered using a recursive operation in conventional micromachining of single crystalline silicon. The procedure uses the built-in capability of the crystal lattice to form self-similar octahedral structures with minimal interference of the constructor. The silicon fractal can be used directly or as a mold to transfer the shape into another material. Moreover, they can be dense, porous, or like a wireframe. We demonstrate, after four levels of processing, that the initial number of octahedral structures is increased by a factor of 625. Meanwhile the size decreases 16 times down to 300 nm. At any level, pores of less than 100 nm can be fabricated at the octahedral vertices of the fractal. The presented technique supports the design of fractals with Hausdorff dimension D free of choice and up to D = 2.322.
DigiWarp: a method for deformable mouse atlas warping to surface topographic data (2010)

For pre-clinical bioluminescence or fluorescence optical tomography, the animal's surface topography and internal anatomy need to be estimated for improving the quantitative accuracy of reconstructed images. The animal's surface profile can be measured by all-optical systems, but estimation of the internal anatomy using optical techniques is non-trivial. A 3D anatomical mouse atlas may be warped to the estimated surface. However, fitting an atlas to surface topography data is challenging because of variations in the posture and morphology of imaged mice. In addition, acquisition of partial data (for example, from limited views or with limited sampling) can make the warping problem ill-conditioned. Here, we present a method for fitting a deformable mouse atlas to surface topographic range data acquired by an optical system. As an initialization procedure, we match the posture of the atlas to the posture of the mouse being imaged using landmark constraints. The asymmetric L(2) pseudo-distance between the atlas surface and the mouse surface is then minimized in order to register two data sets. A Laplacian prior is used to ensure smoothness of the surface warping field. Once the atlas surface is normalized to match the range data, the internal anatomy is transformed using elastic energy minimization. We present results from performance evaluation studies of our method where we have measured the volumetric overlap between the internal organs delineated directly from MRI or CT and those estimated by our proposed warping scheme. Computed Dice coefficients indicate excellent overlap in the brain and the heart, with fair agreement in the kidneys and the bladder.
An enhanced method for post-embedding immunocytochemical staining which preserves cell membranes. (1990)

We have devised a method for immunogold staining of unosmicated, plastic-embedded tissue which gives high levels of specific staining without scrificing cell ultrastructure. The key to this method is a combination of several standard techniques optimized to preserve cell membranes as well as antigen. Important conditions include (a) a combination primary fixative, (b) post-fixation with uranyl acetate to preserve membrane phospholipids, (c) dehydration with acetone to minimize extraction of phospholipids, (d) low-temperature embedding in LR Gold resin, and (e) use of osmium tetroxide to stain thin sections after immunogold labeling. We have developed this method specifically to localize the membrane receptor for immunoglobulin G in the jejunal epithelium of the neonatal rat. Ultra-thin sections of embedded tissue were stained with a monoclonal primary antibody and colloidal gold-labeled secondary antibody, followed by 2% osmium tetroxide and lead citrate. The receptor was resolved in the well-preserved network of tubules, endosomes, and other membrane compartments involved in immunoglobulin transport. In several other tissues processed by this method, cell ultrastructure resembled that seen after conventional osmium post-fixation and epoxy embedding. In addition to its usefulness in these studies, this general method should be applicable to many other immunocytochemical problems.
Midazolam: an effective intravenous agent for seizure control. (1987)

Midazolam meleate, a water soluble 1,4 benzodiazepine, was used intravenously in 20 patients suffering seizures, of whom 12 were in status epilepticus. In all cases, midazolam in a dose of 2.5-15 mg rapidly terminated the seizure. There were no complications from the use of midazolam. The causes of the seizures were varied but alcohol-withdrawal seizures were the single largest cause. Thirteen patients were taking some form of anticonvulsant medication but only three were in the therapeutic range. Midazolam is seen to be an effective agent in the emergency treatment of seizures.
Urinary tract infection in spinal cord injury. (1989)

Loss of normal bladder function results in increased risk of developing urinary tract infection. Recurrent bacteriuria continues to be a problem in most spinal cord injured persons regardless of the bladder emptying method used. Lower urinary tract complications have decreased with intermittent catheterization, but the effect of increased intravesical pressure and presence of bacteriuria on renal function are still undetermined. Current methods of neurogenic bladder management are often based on professional or institutional presuppositions rather than scientific data. Although there are many unanswered questions about the role of urinary tract infection in spinal cord injury patients, treatment should be based on scientific knowledge, even though the knowledge base is still limited. Preservation of renal function is the ultimate goal of any method of neurogenic bladder management. Although a person with spinal cord injury is described, the material covered is applicable to other neurogenic bladder disturbances.
Isotope Effects on Acidity of Deuterated Formic, Acetic, Pivalic, and Benzoic Acids (1963)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTIsotope Effects on Acidity of Deuterated Formic, Acetic, Pivalic, and Benzoic AcidsA. Streitwieser and H. S. KleinCite this: J. Am. Chem. Soc. 1963, 85, 18, 2759–2763Publication Date (Print):September 1, 1963Publication History Published online1 May 2002Published inissue 1 September 1963https://pubs.acs.org/doi/10.1021/ja00901a019https://doi.org/10.1021/ja00901a019research-articleACS PublicationsRequest reuse permissionsArticle Views627Altmetric-Citations38LEARN 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
A homeodomain gene Ptx 3 has highly restricted brain expression in mesencephalic dopaminergic neurons (1997)

The mesencephalic dopaminergic (mesDA) system regulates behavior and movement control and has been implicated in psychiatric and affective disorders. We have identified a bicoid-related homeobox gene, Ptx3, a member of the Ptx-subfamily, that is uniquely expressed in these neurons. Its expression starting at E11.5 in the developing mouse midbrain correlates with the appearance of mesDA neurons. The number of Ptx3-expressing neurons is reduced in Parkinson patients, and these neurons are absent from 6-hydroxydopamine-lesioned rats, an animal model for this disease. Thus, Ptx3 is a unique transcription factor marking the mesDA neurons at the exclusion of other dopaminergic neurons, and it may be involved in developmental determination of this neuronal lineage.
Mechanism of thermoinactivation of immobilized glucose isomerase (1989)

Irreversible thermoinactivation of immobilized glucose isomerase from Streptomyces olivochromogenes has been mechanistically investigated at the pH-optimum of enzymatic activity (pH 8.0). Ligands (high fructose corn syrup and the competitive inhibitor xylitol) greatly stabilize the immobilized enzyme at high temperatures. At 90 degrees C in the presence of 2M xylitol, irreversible inactivation of immobilized glucose isomerase is caused by deamidation of its asparagine/glutamine residues. On the basis of the data obtained, it appears that the time-dependent decay of glucose isomerase activity in industrial bioreactors is brought about by oxidation of the enzyme's cysteine residue and/or heat-induced deleterious reactions with high fructose corn syrup or its impurities.
Quantitation and characterization of plasma DNA in normals and patients with systemic lupus erythematosus. (1980)

Using the in vitro DNA labeling technique of nick translation on purified plasma DNA, we have estimated the plasma DNA concentration in three normal individuals to be 266 +/- 57 ng/ml (mean +/- SD). This was not significantly different in three patients with a chronic inflammatory disease (209 +/- 14 ng/ml) or in five patients with steroid-inactivated systemic lupus erythematosus (SLE) (293 +/- 57 ng/ml). In two untreated, newly diagnosed, active SLE patients, however, the plasma DNA concentration was considerably higher (4,024 and 2,437 ng/ml, respectively). Characterization of these in vitro labeled DNA preparations by neutral sucrose-gradient sedimentation analysis showed a sedimentation coefficient of 6-8S, corresponding to a molecular weight of similar to or approximately 0.2-0.45 x 10(6). No difference was observed between normal subjects or patients. In addition, the relative size uniformity of these DNA molecules might suggest some form of specific protection of the DNA from blood DNAases. Further characterization in terms of buoyant density in cesium chloride did not reveal a difference between normal or SLE plasma and the human (HEp-2 cell) DNA used as marker. Taking into account the limitations of the method, no indication of a possible exogenous origin of the DNA circulating in SLE patients could be found. The physiological or pathophysiological role of this plasma DNA remains to be determined.
Segment spanning residues 727-768 of the complement C3 sequence contains a neoantigenic site and accommodates the binding of CR1, factor H, and factor B (1992)

CR1, CR2, DAF, MCP, factor H, C4bp, factor B, and C3 are members of a family of structurally related molecules, the majority of which belong to the complement system. Several of these molecules also share functional features such as cofactor and decay/dissociation activity and compete with one another in binding to C3b. Since factor H appears to bind to multiple sites in C3, we investigated the relationship between the factor H- and CR1-binding sites in C3b. Factor H binding to C3b is inhibited by either the C3c or C3d fragments, and addition of both fragments together augments this inhibition. One monoclonal anti-C3c antibody, anti-C3-9, which recognizes a neoantigenic epitope expressed upon cleavage to C3 to C3b, inhibited both factor H and CR1 binding to EC3b cells. This monoclonal antibody (MoAb) also inhibited factor B binding to EC3b. Two observations further supported our hypothesis that these molecules bind to proximal sites in C3b. First, a synthetic peptide spanning this region of C3b (C3(727-768)) inhibited factor H binding. Second, antibodies raised against this peptide inhibited binding to CR1, factor H, and factor B to C3b. These data show that H binds to at least two sites in C3b: the site in the C3c fragment is within the identified CR1-binding domain while the site in the C3d fragment surrounds the CR2-binding site.(ABSTRACT TRUNCATED AT 250 WORDS)