gebhart/patrepeval huggingface dataset:
Physiological actions of diacylglycerol outcome (2004)

The stimulation of enzyme activities responsible for beta-oxidation and regulation of lipid metabolism-related gene expression in the small intestine may contribute to reduced postprandial hyperlipidemia as well as to increased energy expenditure, which result in suppression of diet-induced obesity. Further analysis is required to elucidate the chemical and biological properties of diacylglycerol, especially of 1,3-diacylglycerol, on digestion, absorption and metabolic processes that may provide new insights for managing a lifestyle-related chronic disease such as the metabolic syndrome.
Characterization of human anti-high molecular weight-melanoma-associated antigen single-chain Fv fragments isolated from a phage display antibody library. (1998)

The human high molecular weight-melanoma-associated antigen (HMW-MAA) meets the criteria to be used as an immunogen for immunotherapy of malignant melanoma, because it is expressed by a large percentage of melanoma lesions with limited heterogeneity and has a restricted distribution in normal tissues. The high immunogenicity of the HMW-MAA in BALB/c mice has resulted in the development of a large number of anti-HMW-MAA monoclonal antibodies (mAbs). In contrast, no human anti-HMW-MAA mAbs have been described. Because the latter may serve as useful probes to characterize the antigenic profile of the HMW-MAA, human anti-HMW-MAA single-chain fragments of the variable region (scFvs) were isolated by panning synthetic scFv library 1 on purified HMW-MAA. Colony hybridization studies and nucleotide sequence analysis revealed that scFv 19, 44, 56, and 61 belong to the V(H)3 gene family and use the DP-38 germ-line gene segment but have a diverse third complementarity-determining region. The human scFvs share some characteristics with mouse anti-HMW-MAA mAb but also display some distinct features. Like mouse mAbs, human scFvs recognize determinants of HMW-MAA with a heterogeneous cellular and molecular distribution in human melanoma cells. Furthermore, like some mouse mAbs, human scFvs react with rat neural cells expressing the chondroitin sulfate proteoglycan NG2, which shows 81% homology to the HMW-MAA. However, at variance with mouse mAbs, the human scFvs show poor reactivity with guinea pig melanoma cells. Lastly, human scFv 61 stains both benign and malignant lesions of melanocytic origin, although with a lower frequency than mouse mAbs. Analysis of the clinical significance of the differential expression of the scFv 61-defined determinant in melanoma lesions will be facilitated by its reactivity with formalin-fixed melanoma lesions. In contrast to mouse mAb, scFv 61 immunoprecipitates the >450-kDa chondroitin sulfate proteoglycan component of the HMW-MAA, but not its 250-kDa subunit from melanoma cells. Thus, contrary to the current view about the structure of HMW-MAA, our results demonstrate that the two components are not associated. The described scFv antibodies, which represent the first example of human anti-HMW-MAA antibodies, have provided novel information about the structure of this antigen. Future studies will assess the impact of these in vitro-assembled antibody fragments on the identification of antigenic determinants of the HMW-MAA that can be recognized by the human immune system.
Two Regions of the Mouse Mammary Tumor Virus Long Terminal Repeat Regulate the Activity of Its Promoter in Mammary Cell Lines (1991)

In vivo expression of the mouse mammary tumor virus (MMTV) is restricted to a few organs, with the highest rate of transcription found in the mammary gland. Using a series of mammary and nonmammary murine cell lines, we have identified two regulatory elements, located upstream of the hormone responsive element, that specifically regulate the MMTV promoter. The first element displays an enhancerlike activity and is coincident with the binding of a nuclear factor (designated MP4; position -1078 to -1052 in the long terminal repeat) whose presence is apparently restricted to mammary cell lines. The second regulatory region mediates a repressive activity and is mapped to the long terminal repeat segment from -415 to -483. This repression is specific for a particular subtype of mammary cells (RAC cells) able to grow under two differentiation states (A. Sonnenberg, H. Daams, J. Calafat, and J. Hilgers, Cancer Res. 46:5913-5922, 1986). The MMTV promoter in mammary cell lines thus appears to be modulated by two cis-acting elements that are likely to be involved in tissue-specific expression in vivo.
Histamine and its receptors (2006)

This article reviews the development of our knowledge of the actions of histamine which have taken place during the course of the 20th century. Histamine has been shown to have a key physiological role in the control of gastric acid secretion and a pathophysiological role in a range of allergic disorders. The synthesis of, and pharmacological studies on, selective agonists and antagonists has established the existence of four types of histamine receptor and histamine receptor antagonists have found very important therapeutic applications. Thus, in the 1940s, H(1)-receptor antagonists ('the antihistamines') yielded and still provide valuable treatment for allergic conditions such as hay fever and rhinitis. In the late 1970s and 1980s, H(2)-receptor antagonists (in the discovery of which the two authors were personally involved) revolutionised the treatment of peptic ulcer and other gastric acid-related diseases. The H(3)-receptor antagonists, although available since 1987, have been slower to find a therapeutic role. However, the discovery of nonimidazole derivatives such as brain-penetrating H(3) antagonists has provided drugs that are in early-phase clinical trials, possibly for application in obesity, and a variety of central nervous system disorders, such as memory, learning deficits and epilepsy. Finally, the most recently (1999) discovered H(4) receptor promises the potential to provide drugs acting on the immunological system with possible applications in asthma and inflammation.
Reduction in noise-induced temporary threshold shift in humans following oral magnesium intake (2004)

A previous study demonstrated the prophylactic effects of magnesium on noise-induced permanent threshold shift in humans. For the first time, this study explores the effects of magnesium on temporary threshold shift in 20 human subjects, all men (16-37 years, mean age 21 years). The study was conducted in a double-blind manner on the same subjects tested in three different phases (placebo, magnesium, no-drug). The cochlear changes were assessed using both behavioural (audiograms) and objective (otoacoustic emission) measures. Blood samples were collected at the beginning and end of each phase. Amongst subjects and phases, magnesium intake was associated with significantly lower temporary threshold shift, compared with the other two phases, which were reflected both by the behavioural and cochlear measures. A correlation was found between the blood magnesium levels and temporary threshold shift reduction. No side-effects were associated with the oral ingestion of the magnesium. Magnesium provides significant protection against temporary threshold shift, complementing the previous permanent threshold shift human study. Both human noise-induced hearing loss studies introduced a novel, biological, natural agent for prevention and possible treatment of noise-induced cochlear damage in humans.
The Gla Domain of Factor IXa Binds to Factor VIIIa in the Tenase Complex (2003)

During blood coagulation factor IXa binds to factor VIIIa on phospholipid membranes to form an enzymatic complex, the tenase complex. To test whether there is a protein-protein contact site between the gamma-carboxyglutamic acid (Gla) domain of factor IXa and factor VIIIa, we demonstrated that an antibody to the Gla domain of factor IXa inhibited factor VIIIa-dependent factor IXa activity, suggesting an interaction of the factor IXa Gla domain with factor VIIIa. To study this interaction, we synthesized three analogs of the factor IXa Gla domain (FIX1-47) with Phe-9, Phe-25, or Val-46 replaced, respectively, with benzoylphenylalanine (BPA), a photoactivatable cross-linking reagent. These factor IX Gla domain analogs maintain native tertiary structure, as demonstrated by calcium-induced fluorescence quenching and phospholipid binding studies. In the absence of phospholipid membranes, FIX1-47 was able to inhibit factor IXa activity. This inhibition is dependent on the presence of factor VIIIa, suggesting a contact site between the factor IXa Gla domain and factor VIIIa. To demonstrate a direct interaction we did cross-linking experiments with FIX1-479BPA, FIX1-4725BPA, and FIX1-4746BPA. Covalent cross-linking to factor VIIIa was observed primarily with FIX1-4725BPA and to a much lesser degree with FIX1-4746BPA. Immunoprecipitation experiments with an antibody to the C2 domain of factor VIIIa indicate that the factor IX Gla domain cross-links to the A3-C1-C2 domain of factor VIIIa. These results suggest that the factor IXa Gla domain contacts factor VIIIa in the tenase complex through a contact site that includes phenylalanine 25 and perhaps valine 46.
Characterization of the Relationship between Polysaccharide Intercellular Adhesin and Hemagglutination inStaphylococcus epidermidis (1999)

To determine whether a relationship exists between biofilm formation and hemagglutination in Staphylococcus epidermidis, 20 skin isolates and 19 prosthetic valve endocarditis isolates were characterized for biofilm formation, hemagglutination, and the presence of a 357-bp polymerase chain reaction product within icaA. A strong association existed between biofilm formation, which has been linked to strains that produce polysaccharide intercellular adhesin (PIA), and hemagglutination. Strains that produced biofilm were significantly (P<.001) more likely to mediate hemagglutination (16 biofilm-positive/hemagglutination-positive strains and 19 biofilm-negative/hemagglutination-negative strains) within the 39 clinical strains tested. In addition, Staphylococcus carnosus TM300, a biofilm-negative, hemagglutination-negative strain, carrying the ica operon-containing plasmid pCN27, produced significant biofilm on glass and mediated hemagglutination (>/=1/128). It was concluded that production of PIA and hemagglutination are strongly associated and that PIA, at least in part, mediates hemagglutination in S. epidermidis.
Asymmetric Autocatalysis Triggered by Carbon Isotope ( 13 C/ 12 C) Chirality (2009)

Many apparently achiral organic molecules on Earth may be chiral because of random substitution of the 1.11% naturally abundant 13C for 12C in an enantiotopic moiety within the structure. However, chirality from this source is experimentally difficult to discern because of the very small difference between 13C and 12C. We have demonstrated that this small difference can be amplified to an easily seen experimental outcome using asymmetric autocatalysis. In the reaction between pyrimidine-5-carbaldehyde and diisopropylzinc, addition of chiral molecules in large enantiomeric excess that are, however, chiral only by virtue of isotope substitution causes a slight enantiomeric excess in the zinc alkoxide of the produced pyrimidyl alkanol. Asymmetric autocatalysis then leads to pyrimidyl alcohol with a large enantiomeric excess. The sense of enantiomeric excess of the product alcohol varies consistently with the sense of the excess enantiomer of the carbon isotopically chiral compound.
Electron microscopy in molecular biology : a practical approach (1987)

Abbreviations Preparation of nucleic acids for electron microscopy Denaturation and hybridization of nucleic acids Binding of protein to nucleic acids Chromatin spreading Visualizing active genes Negative staining of protein molecules and filaments Rotary metal shadowing for visualizing rod-shaped proteins Em immunolabelling Autoradiography of spread molecular complexes Hybridization to chromatin and whole chromosome mounts Appendix
High quality epitaxial GaAs and InP wafers by isoelectronic doping (1985)

It is shown that strained isoelectronically doped buffer layers grown on GaAs and InP wafers allow one to reduce the dislocation density drastically by a factor greater than 20. Correspondingly, the photoluminescence efficiency of near-band-edge emission is enhanced by about the same factor. By deep level transient spectroscopy measurements practically no deep levels can be detected in contrast to uncoated wafers. Applied to device fabrication a great improvement is found in comparison to conventionally fabricated optoelectronic and electronic devices.
Dendrimer−Drug Conjugates for Tailored Intracellular Drug Release Based on Glutathione Levels (2008)

N-Acetyl-L-cysteine (NAC) is an antioxidant and anti-inflammatory agent with significant potential in clinical applications including stroke and neuroinflammation. The drug shows high plasma binding upon IV administration, requiring high doses and associated side effects. Through the use of an appropriate delivery vehicle, the stability and efficacy of NAC can be significantly improved. Dendrimers are an emerging class of nanoscale drug delivery vehicles, which enable high drug payloads and intracellular delivery. Poly(amidoamine) (PAMAM) dendrimer-NAC conjugates having cleavable disulfide linkages are designed for intracellular delivery based on glutathione levels. We have successfully synthesized two conjugates with a cationic G4-NH(2) and an anionic G3.5-COOH PAMAM dendrimer with NAC payloads of 16 and 18 per dendrimer, respectively, as confirmed by (1)H NMR and MALDI-TOF analysis. NAC release from the conjugates at intracellular and extracellular glutathione (GSH) concentrations were evaluated by reverse phase HPLC (RP-HPLC) analysis, and approximately 70% of NAC payload was released within one hour at intracellular GSH concentrations (approximately 10 mM), whereas negligible NAC release was observed at extracellular GSH levels (2 microM). FITC-labeled conjugates showed that they enter cells rapidly and localize in the cytoplasm of lipopolysaccharide (LPS)-activated microglial cells (the target cells in vivo). The significantly improved efficacies of dendrimer-NAC conjugates in activated microglial cells was confirmed by measuring the nitrite inhibition in the cell culture medium, which is an indication of the antioxidative property of the drug. Both G4-NH(2) and G3.5-COOH conjugates showed significantly better nitrite inhibition both at 24 and 72 h compared to free NAC, by as much as a factor of 16. The results indicate that PAMAM dendrimer conjugates produce higher local NAC concentration inside the cells, with GSH-sensitive disulfide linker enabling efficient and rapid cellular release of the drug.
Cholecystokinin receptors and vagal nerves in control of food intake in rats (1990)

This study was designed to determine the specificity and physiological nature of short-term satiety effects of cholecystokinin (CCK) in rats with intact and transected vagal nerves. Rats with-the gastric fistulas, closed or open, were used for normal feeding or sham feeding of liquid meal offered for 30 min. CCK-8 (0.5-10 nmol/kg) injected intraperitoneally (ip) 15 min before feeding inhibited food intake dose dependently in both normal-fed and sham-fed rats at a minimal inhibitory dose of 1 nmol/kg. CCK-8 at the same doses caused a potent stimulation of pancreatic protein secretion, reaching maximum at a dose of approximately 0.5 nmol/kg. Pretreatment with a potent CCK receptor antagonist, L-364,718 (2.5 mg/kg ip), increased food intake during normal feeding (but not sham feeding) and almost completely blocked the satiety and pancreatic stimulatory effects of CCK. When feeding was preceded by intragastric administration of proteinase inhibitor (Foy-305, 200 mg/kg), food preload, or diversion of bile-pancreatic secretion to the exterior, there was a significant increase in the plasma level of CCK and an inhibition of food intake by about 36, 78, and 25%, respectively. Pretreatment with L-364,718 completely abolished this inhibition by Foy-305 and bile-pancreatic diversion and reduced that caused by food preload. Among other gut peptides given ip (10 nmol/kg) only bombesin reduced food intake, whereas gastrin, secretin, gastric inhibitory polypeptide (GIP), pancreatic polypeptide (PP), and peptide YY (PYY) were ineffective.(ABSTRACT TRUNCATED AT 250 WORDS)
Modeling View and Posture Manifolds for Tracking (2007)

In this paper we consider modeling data lying on multiple continuous manifolds. In particular, we model the shape manifold of a person performing a motion observed from different view points along a view circle at fixed camera height. We introduce a model that ties together the body configuration (kinematics) manifold and the visual manifold (observations) in a way that facilitates tracking the 3D configuration with continuous relative view variability. The model exploits the low dimensionality nature of both the body configuration manifold and the view manifold where each of them are represented separately.
Sonic Hedgehog Regulates Early Human Thymocyte Differentiation by Counteracting the IL-7-Induced Development of CD34+ Precursor Cells (2004)

The Hedgehog (Hh) family of signaling molecules normally functions in the development of numerous tissues by regulating cellular differentiation and proliferation. Recent results have demonstrated that the different components of the Hh signaling pathway are expressed in the human thymus. In this study, we investigate the potential role of Sonic hedgehog (Shh) in human intrathymic T cell maturation. Results show that the expression of the two components of the Hh receptor, Patched and Smoothened, is mostly restricted to CD34+ precursor cells that are committing to the T cell lineage. Shh significantly increased the viability of CD34+ T cell precursors modulating bcl-2 and bax protein expression, and also inhibited their proliferation. The treatment of chimeric human-mouse fetal thymus organ cultures with Shh resulted in an arrested thymocyte differentiation and an accumulation of CD34+ progenitor cells. This effect was mainly attributed to the ability of Shh to counteract the IL-7-induced proliferation and differentiation of CD34+ cells. Shh down-regulated in the precursor cell population the expression of IL-7R as well as stromal-derived factor-1 chemokine receptor, CXCR4, and inhibited IL-7-dependent STAT5 phosphorylation. Therefore, Shh may function as a maintenance factor for intrathymic CD34+ precursor cells.
Level set methods : evolving interfaces in geometry, fluid mechanics, computer vision, and materials science (1996)

Part I. The Theory of Moving Interfaces: 1. Theory of front evolution 2. Level set formulation Part II. Algorithms, Analysis, and Implementations of Level Set Methods: 3. Traditional techniques for tracking interfaces 4. Hyperbolic conservation laws 5. Approximating the level set equation 6. Viscosity solutions and Hamilton-Jacobi equations 7. A hierarchy of fast level set methods 8. A fast marching level set method 9. Extensions to the basic method Part III. Applications: 10. Geometry: curve/surface shrinkage and self-similar surfaces 11. Grid generation 12. Image enhancement and noise removal 13. Minimal surfaces and surfaces of prescribed curvature 14. Combustion, crystal growth, and two-fluid flow 15. Computer vision: shape detection and recognition 16. Applications of the fast marching level set method 17. Etching and deposition in microchip fabrication 18. New areas.
Identification of a Streptococcus agalactiae protein antigen associated with bovine mastitis isolates (1987)

Immunoblotting was used to analyze the immune response of cows to Streptococcus agalactiae. Antibody from the milk of cows immunized (via the superficial inguinal lymph node) with formalinized S. agalactiae cells or from the milk of cows with S. agalactiae mastitis reacted strongly with a group of high-molecular-weight proteinaceous antigens. The two most predominant antigenic polypeptides in this group had apparent molecular weights of 97,000 and 104,000. Because the data indicated that these two antigens, as well as several minor antigens sometimes observed in the 70- to 100-kilodalton size range, seemed to be different forms of the same protein, we refer to the entire group as Sas97/104. A monoclonal antibody that was reactive with Sas97/104 was derived and was used to purify the antigen by affinity chromatography. Whole-cell and colony blot enzyme-linked immunoassays with either the monoclonal antibody or a polyclonal serum sample raised against the affinity-purified antigen indicated that this antigen (or cross-reactive proteins with higher molecular weights) is present on the S. agalactiae strains that were freshly isolated from mastitic cows. However, the antigen was not detected in S. agalactiae of human origin, bovine strains of S. agalactiae maintained for a prolonged period in the laboratory, or other streptococci. The data are consistent with the notion that Sas97/104 is a surface antigen and does not correspond to previously described type-specific antigens of group B streptococci.
Transactional memory with strong atomicity using off-the-shelf memory protection hardware (2009)

This paper introduces a new way to provide strong atomicity in an implementation of transactional memory. Strong atomicity lets us offer clear semantics to programs, even if they access the same locations inside and outside transactions. It also avoids differences between hardware-implemented transactions and software-implemented ones. Our approach is to use off-the-shelf page-level memory protection hardware to detect conflicts between normal memory accesses and transactional ones. This page-level mechanism ensures correctness but gives poor performance because of the costs of manipulating memory protection settings and receiving notifications of access violations. However, in practice, we show how a combination of careful object placement and dynamic code update allows us to eliminate almost all of the protection changes. Existing implementations of strong atomicity in software rely on detecting conflicts by conservatively treating some non-transactional accesses as short transactions. In contrast, our page-level mechanism lets us be less conservative about how non-transactional accesses are treated; we avoid changes to non-transactional code until a possible conflict is detected dynamically, and we can respond to phase changes where a given instruction sometimes generates conflicts and sometimes does not. We evaluate our implementation with C# versions of many of the STAMP benchmarks, and show how it performs within 25% of an implementation with weak atomicity on all the benchmarks we have studied. It avoids pathological cases in which other implementations of strong atomicity perform poorly.