gebhart/patrepeval huggingface dataset:
Characterization of the functional defect in factor IX Alabama. Evidence for a conformational change due to high affinity calcium binding in the first epidermal growth factor domain. (1990)

Factor IX Alabama is a factor IX variant in which a glycine has been substituted for Asp47 in the first epidermal growth factor (EGF) domain. The structural defect in factor IX Alabama results in a molecule with 10% of normal coagulant activity. The interactions of immunoaffinity-purified factor IX Alabama with its activator, cofactors, and substrate have been investigated to determine the functional defect in the variant. Factor IX Alabama is activated by factor XIa/calcium at near normal rates. Calcium fluorescence-quenching experiments indicate that high affinity calcium binding in the first EGF domain is not altered in factor IX Alabama. The active site of factor IXa Alabama is fully competent to activate factor X in the absence of calcium when using polylysine as a surface to catalyze the reaction. Factor IXa Alabama has only 64% of normal factor IXa activity in the presence of 300 microM CaCl2 in the polylysine-catalyzed system although apparent high affinity calcium binding constants are similar. Factor IXa Alabama has 52-60% of normal activity in a calcium/phospholipid vesicle system. The addition of factor VIIIa to the phospholipid vesicle system decreases the relative rate of factor IXa Alabama to 18-19% of normal. Three-dimensional computer-aided models of the first EGF domain of normal factor IX and factor IX Alabama indicate no major structural alterations resulting from the glycine substitution for Asp47. The model of the first EGF domain of normal factor IX predicts a calcium-binding site involving Asp47, Asp49, Asp64, and Asp65. Our binding data, however, indicate that Asp47 is not necessary to form the high affinity binding site. We conclude that Asp47 in normal factor IX coordinates to the bound calcium, inducing a conformational change in the molecule essential for proper interaction with factor X and factor VIIIa.
A bifunctional Δ6‐fatty acyl acetylenase/desaturase from the moss Ceratodon purpureus (2000)

Many plant genes have been cloned that encode regioselective desaturases catalyzing the formation of cis-unsaturated fatty acids. However, very few genes have been cloned that encode enzymes catalyzing the formation of the functional groups found in unusual fatty acids (e.g. hydroxy, epoxy or acetylenic fatty acids). Here, we describe the characterization of an acetylenase from the moss Ceratodon purpureus with a regioselectivity differing from the previously described Delta12-acetylenase. The gene encoding this protein, together with a Delta6-desaturase, was cloned by a PCR-based approach with primers derived from conserved regions in Delta5-, Delta6-fatty-acid desaturases and Delta8-sphingolipid desaturases. The proteins that are encoded by the two cloned cDNAs are likely to consist of a N-terminal extension of unknown function, a cytochrome b5-domain, and a C-terminal domain that is similar to acyl lipid desaturases with characteristic histidine boxes. The proteins were highly homologous in sequence to the Delta6-desaturase from the moss Physcomitrella patens. When these two cDNAs were expressed in Saccharomyces cerevisiae, both transgenic yeast cultures desaturated Delta9-unsaturated C16- and C18-fatty acids by inserting an additional Delta6cis-double bond. One of these transgenic yeast clones was also able to introduce a Delta6-triple bond into gamma-linolenic and stearidonic acid. This resulted in the formation of 9,12,15-(Z,Z,Z)-octadecatrien-6-ynoic acid, the main fatty acid found in C. pupureus. These results demonstrate that the Delta6-acetylenase from C. pupureus is a bifunctional enzyme, which can introduce a Delta6cis-double bond into 9,12,(15)-C18-polyenoic acids as well as converting a Delta6cis-double bond to a Delta6-triple bond.
Role of the HIV-1 envelope transmembrane domain in intracellular sorting (2018)

These results suggest that the intrinsic properties of the HIV-1 Env transmembrane domain allow the protein to escape ER-retention mechanisms, while maintaining its ability to interact with cellular proteins and to influence cellular physiology.
Absence of IL-1 signaling and reduced inflammatory response in IL-1 type I receptor-deficient mice (1997)

IL-1alpha and IL-1beta are potent inflammatory cytokines that contribute to a number of normal physiologic processes and to the development of a number of inflammatory diseases. Two IL-1R, the type I and type II receptors, have been identified. This work describes the derivation and characterization of mice deficient in expression of the type I IL-1R (IL-1RI). IL-1RI-deficient mice were viable and fertile, but failed to respond to IL-1 in a variety of assays, including IL-1-induced IL-6 and E-selectin expression and IL-1-induced fever. Similar to IL-1beta-deficient mice, IL-1RI-deficient mice had a reduced acute phase response to turpentine. In contrast, IL-1RI-deficient mice had a reduced delayed-type hypersensitivity response and were highly susceptible to infection by Listeria monocytogenes. These data demonstrate that the IL-1RI is essential for all IL-1-mediated signaling events examined, and that both IL-1alpha and IL-1beta are critical to the animals' response to injury and infection. These data also demonstrate that IL-1 function is not required for normal development or homeostasis.
Identification of genes regulated by an interaction between avß3 integrin and vitronectin in murine decidua (2008)

The delicate balance between embryo invasion and suppression of maternal immune rejection requires a fully functional decidua in species with haemochorial placenta. Our understanding of the decidual function is very limited due to the molecular and cellular complexity involved in decidualisation. The cell adhesion molecule alpha(v)beta(3) integrin and its ligand vitronectin are upregulated in the mouse decidua during mid-pregnancy. The implications of interactions between alpha(v)beta(3) and vitronectin in regulating decidual function are not known. In the present study, interactions between alpha(v)beta(3) and vitronectin in the decidual cells of the mouse were blocked in vitro and effects on cell fate were evaluated by studying the differentially regulated genes by cDNA array and real-time polymerase chain reaction (PCR). The results indicate that expression of various genes involved in apoptotic and cell cycle pathways, as well as cytokine receptors, was deranged. Signalling through alpha(v)beta(3) seems to be important to maintain a balance between cell proliferation and apoptosis, along with the modulation of inflammatory responses of decidual cells.
Immunoaffinity partitioning: synthesis and use of polyethylene glycol‐oxirane for coupling to bovine serum albumin and monoclonal antibodies (1991)

Polyethylene glycol (PEG)-oxirane was synthesized by reacting aminated monomethoxy-PEG 5000 (NH2-MPEG 5000) with butanediol diglycidyl ether and used to derivatize bovine serum albumin (BSA) and monoclonal antibodies (mAb) against horseradish peroxidase (HRP) and porcine lactate dehydrogenase isoenzyme 5, respectively. Determination of oxirane end groups revealed a very high number, which arise from the chain breaks of the polymer. Covalent coupling of PEG-oxirane to BSA resulted in 30-50 times higher partition coefficients under optimized conditions. The mAb investigated could be modified with PEG-oxirane while retaining its binding properties and could be used as an affinity ligand for selective extraction of Ag in immunoaffinity partitioning. However, a high degree of modification results in a lower binding constant of mAb anti-HRP and higher [mAb]/[Ag] concentration ratios in immunoaffinity partition experiments.
Greater Mortality and Morbidity in Extremely Preterm Infants Fed a Diet Containing Cow Milk Protein Products (2014)

An exclusive human milk diet, devoid of CM-containing products, was associated with lower mortality and morbidity in EP infants without compromising growth and should be considered as an approach to nutritional care of these infants.
Process for Preparing Macroscopic Quantities of Brightly Photoluminescent Silicon Nanoparticles with Emission Spanning the Visible Spectrum (2003)

Silicon nanoparticles with bright visible photoluminescence have been prepared by a new combined vapor phase and solution phase process, using only inexpensive commodity chemicals. CO2 laser induced pyrolysis of silane was used to produce Si nanoparticles at high rates (20−200 mg/h). Particles with an average diameter as small as 5 nm were prepared directly by this vapor phase (aerosol) synthesis. Etching these particles with mixtures of hydrofluoric acid (HF) and nitric acid (HNO3) reduced the size and passivated the surface of these particles such that after etching they exhibited bright visible luminescence at room temperature. The wavelength of maximum photoluminescence (PL) intensity was controlled from above 800 nm to below 500 nm by controlling the etching time and conditions. Particles with blue emission (maximum PL intensity at 420 nm) were prepared by rapid thermal oxidation of orange-emitting particles. The particle synthesis methods; steady-state photoluminescence spectra; results of their characterization using TEM, XRD, FTIR absorption spectroscopy, and XPS; and preliminary assessments of the stability of the photoluminescence properties with time are presented here. Preparation of macroscopic quantities by the methods described here opens the door to chemical studies of free silicon nanoparticles that could previously be carried out only on porous silicon wafers, as well as to potential commercial applications of silicon nanoparticles.
Selection and Characterization of Interferon-sensitive Cells Derived from an Interferon-resistant NIH 3T3 Line (1987)

We have developed a selection protocol to isolate interferon (IFN)-sensitive subclones directly from an IFN-resistant cell population. The protocol uses encephalomyocarditis virus (EMCV) as a selection agent in combination with pretreatment with low doses of IFN and subsequent growth in the presence of virus-neutralizing antiserum. We have applied this protocol to the partially IFN-resistant NIH 3T3 clone 1 line and have obtained a number of IFN-sensitive subclones. Sensitivity to IFN was restricted to protection against EMCV. Replication of vesicular stomatitis virus as well as cell growth were resistant to IFN treatment as in the original clone 1 line. We have compared levels of 2',5'-oligoadenylate (2-5A) synthetase, dsRNA-activated protein kinase and 2-5A-dependent RNase in some IFN-sensitive subclones and found no difference from the resistant clone 1 cells. Markedly decreased levels of 2-5A-dependent RNase and thus a defective 2-5A pathway have been implicated as a possible cause for the partial resistance of clone 1 cells to IFN. Since the selected IFN-sensitive subclones are of the same phenotype in this respect as the clone 1 line we suggest that inhibition of EMCV in these lines occurs through a mechanism independent of the 2-5A system.
Source Code Revision History Visualization Tools: Do They Work and What Would it Take to Put Them to Work? (2014)

Source code revision history visualization tools have been around for over two decades. Yet, they have not become a mainstream tool in a typical programmer's toolbox and are not typically available in intergraded development environments. So, do they really work? And if they do, what would it take to put them to work? This paper seeks to answer these two questions through experiments, surveys, and interviews. A source code history visualization tool named TeamWATCH was implemented to visualize subversion code repositories. Two comparative controlled experiments were conducted to evaluate the effectiveness of TeamWATCH. The experimental results showed that the subjects using TeamWATCH spent less time than subjects using the command-line subversion client and TortoiseSVN in answering the same set of questions regarding source code revision history. In addition, surveys and interviews were conducted to identify obstacles in adopting source code history visualization tools. Collectively, the results show that source code history visualization tools do bring value to programmers. Key obstacles to wider adoption in practice include nontrivial overhead in using the tools and perceived complexity in visualization.
A miniature position and orientation locator for three dimensional echocardiography (2002)

The accuracy of a new miniature prototype (6 mm/spl times/6 mm/spl times/9 mm) six dimensional (6D) locator sensor for three dimensional (3D) echocardiography was investigated. This new sensor identifies its 3D position and 3D orientation in space with respect to the position of a magnetic field generator. The sensor when attached to an ultrasound imaging transducer allows identifying and tracking the position and orientation in space of the ultrasonic imaging plane. The accuracy of this new miniature sensor was tested by rotating it on a lever arm apparatus which maintained a constant distance (R) from the sensor to the fixed point of rotation. At each rotational spatial position the sensor's readings were used to calculate the fixed point's position in space. The mean (MRE) and standard deviation (STDRE) of the radial error in this determination were calculated for N trials. The results with the apparatus: for R=10.6 cm were MRE=1.3 mm, STDRE=0.06 mm, N=500; and for R=18 cm they were MRE=1.8 mm, STDR=0.7 mm, N=500. It was then tested with a transcutaneous 5 MHz echo probe on 3D imaging a fixed position string target. The results in locating the position of the target was MRE=2.2 mm and STDRE=1.5 mm for N=45.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Apoptosis and ovarian function (1996)

For decades, the mechanisms responsible for germ cell depletion from the ovary, either directly during the perinatal period or indirectly via follicular atresia during postnatal life, have remained relatively obscure. The recent application of sensitive biochemical techniques for the study of cell death to the analysis of ovarian function has revealed that these two events, as well as a third instance of ovarian cell degeneration (luteolysis), are dependent upon the activation of physiological cell death mechanisms. It is therefore hypothesized that the controlled deletion of ovarian cell populations is accomplished via activation of a 'universal' pathway of cellular suicide involving altered expression of a conserved cohort of genes. The identity of the hormonal and intracellular effectors responsible for the coordination of life and death decisions made by ovarian cells during development as well as the biological and clinical implications of gene-directed cell death in the ovary are explored in this review.
Differential Macrophage Polarization in Male and Female BALB/c Mice Infected With Coxsackievirus B3 Defines Susceptibility to Viral Myocarditis (2009)

Rational: Myocardial infiltrating macrophages play an important role in the pathogenesis of viral myocarditis in male BALB/c mice following coxsackievirus B3 (CVB3) infection. Interestingly, comparable macrophage numbers were observed in the myocardium of female mice during acute myocarditis. Objective: Given CVB3 infection causes severe myocarditis in male but not female mice, we postulated that macrophages infiltrating the myocardium of female mice may display distinct functional properties that contribute to differential susceptibility to CVB3 myocarditis. Methods and Results: Here, we found that myocardial infiltrating macrophages from CVB3-infected male mice expressed high levels of classically activated macrophages (M1) markers, including inducible nitric oxide synthase, interleukin-12, tumor necrosis factor-α, and CD16/32, whereas those of females showed enhanced expression of arginase 1, interleukin-10, macrophage mannose receptor (MMR) and macrophage galactose type C-type lectin (MGL) that were associated with alternatively activated macrophage (M2) phenotype. Moreover, distinct myocardial-derived cytokines were found to play a critical role in differential macrophage polarization between sexes after CVB3 infection. Adoptive transfer of ex vivo programmed M1 macrophages, as expectedly, significantly increased myocarditis in both male and female mice. Strikingly, transfer of M2 macrophages into susceptible male mice remarkably alleviated myocardial inflammation by modulating local cytokine profile and promoting peripheral regulatory T cell (Treg) differentiation. Conclusions: Taken together, this study may facilitate the understanding of the mechanism underlying gender bias in susceptibility to CVB3 myocarditis and the development of therapeutic strategies based on macrophage polarization for inflammatory heart disease.
Changes in Peripheral Blood Level of Regulatory T cells in Patients with Malignant Melanoma During Treatment with Dendritic Cell Vaccination and Low‐dose IL‐2 (2010)

In this study, changes in peripheral blood regulatory T cell (Treg) levels were evaluated in 46 progressive patients with melanoma treated with a dendritic cell-based vaccine and concomitant low-dose IFN-α and IL-2. The regulatory subset of CD4 T cells, characterized by CD25(high) , was prospectively analysed in fresh blood, and treatment-associated quantitative and qualitative changes were analysed. By the 4th vaccine, patients showed a marked increase in CD4+ CD25(high) T cell subset from 6% to 22% (P<0.001). At the 6th vaccine, a general decline was observed and a significantly (P=0.01) lower level of CD4+ CD25(high) Treg cells was reached in the group of patients who attained disease stabilization (9.5%) compared to patients with continued progressive disease (14.5%). However, when FoxP3 was employed for retrospective analysis of Tregs on frozen blood, this difference did not reach significance (P=0.09). The vast majority of the Treg produced IL-10 and, to a varying extent, TGF-β. In addition, sorted CD4+ CD25(high) CD127⁻ Tregs were able to suppress proliferation of peripheral blood mononuclear cells in a dose-dependent manner, thus suggesting a regulatory functionality. These findings emphasize the need for strategies to effectively eliminate Treg cells to optimize the clinical effectiveness of cancer immunotherapy.
Measurement of the scrapie agent using an incubation time interval assay (1982)

Abstract The titer of the scrapie agent was determined by measurements of time intervals from inoculation to onset of illness and from inoculation to death. Both intervals were found to be inversely proportional to the size of the dose injected intracerebrally into random‐bred weanling Syrian hamsters. The logarithms of the time intervals minus a time factor were linear functions of the logarithm of the inoculum size. The time factors were determined by regression analysis in order to maximize these linear relationships. An equation relating the titer of the inoculum to the dilution of the sample and the length of the time intervals was developed. This equation facilitates the use of a computerized data base. Validation of these relationships was provided by comparing samples for which the agent was measured both by end‐point titration and by time interval assay. Agreement between the two methods was generally within ±0.5 log 10 median infective dose units. No differences between the molecular properties of the agents from hamster and murine sources were observed using primarily the incubation time interval method with the former and end‐point titration with the latter. The advantages of this new approach based on time interval measurements are considerable with respect to time and resources.
[The impact of autologous stem cell transplantation on the prognosis in multiple myeloma]. (2008)

ASCT can further enhance the response, prolong the DOR and TTP and probably OS, and therefore improve the quality of life in MM. MM patients not achieved good response by non-ASCT therapy may benefit from ASCT.
Interactions between protein 4.1 and band 3. An alternative binding site for an element of the membrane skeleton. (1985)

Protein 4.1 from human erythrocytes formed a complex with band 3 in inside-out erythrocyte membrane vesicles and with soluble peptides derived from the cytoplasmic domain of band 3. Protein 4.1 labeled metabolically with 32P bound saturably to vesicles depleted of endogenous protein 4.1. The soluble cytoplasmic domain of band 3 (43K) competitively displaced approximately 60% of bound 32P-protein 4.1 from reconstituted membrane vesicles. Pretreatment of vesicles with anti-43K similarly inhibited the rebinding of protein 4.1. In solution, 125I-43K formed a complex with protein 4.1 that saturated at 1:1 stoichiometry and migrated as a discrete band when analyzed by nondenaturing polyacrylamide gel electrophoresis. In rate-zonal sedimentation in isotonic salt solutions, protein 4.1 and 43K sedimented as a sharp peak at 4.4 S. In experiments aimed at exploring the role of the protein 4.1-band 3 interaction in the organization of the membrane skeleton, the effect of spectrin was investigated. Spectrin and protein 4.1 formed a complex which co-sedimented in sucrose gradients, but the addition of 43K to preformed spectrin-protein 4.1 complexes resulted in disruption of the complex and co-sedimentation of most of the protein 4.1 with 43K. These results suggest that protein 4.1 can associate with band 3 in the erythrocyte membrane and that this association may modulate the attachment of the membrane skeleton to the membrane.
Comparative proteomics based on stable isotope labeling and affinity selection (2002)

Disease, external stimuli (such as drugs and toxins), and mutations cause changes in the rate of protein synthesis, post-translational modification, inter-compartmental transport, and degradation of proteins in living systems. Recognizing and identifying the small number of proteins involved is complicated by the complexity of biological extracts and the fact that post-translational alterations of proteins can occur at many sites in multiple ways. It is shown here that a variety of new tools and methods based on internal standard technology are now being developed to code globally all peptides in control and experimental samples for quantification. The great advantage of these stable isotope-labeling strategies is that mass spectrometers can rapidly target those proteins that have changed in concentration for further analysis. When coupled to stable isotope quantification, targeting can be further focused through chromatographic selection of peptide classes on the basis of specific structural features. Targeting structural features is particularly useful when they are unique to types of regulation or disease. Differential displays of targeted peptides show that stimulus-specific markers are relatively easy to identify and will probably be diagnostically valuable tools.