gebhart/patrepeval huggingface dataset:
Gut Microbial Activity, Implications for Health and Disease: The Potential Role of Metabolite Analysis (2012)

Microbial metabolism of proteins and amino acids by human gut bacteria generates a variety of compounds including phenol, indole, and sulfur compounds and branched chain fatty acids, many of which have been shown to elicit a toxic effect on the lumen. Bacterial fermentation of amino acids and proteins occurs mainly in the distal colon, a site that is often fraught with symptoms from disorders including ulcerative colitis (UC) and colorectal cancer (CRC). In contrast to carbohydrate metabolism by the gut microbiota, proteolysis is less extensively researched. Many metabolites are low molecular weight, volatile compounds. This review will summarize the use of analytical methods to detect and identify compounds in order to elucidate the relationship between specific dietary proteinaceous substrates, their corresponding metabolites, and implications for gastrointestinal health.
Kinetics and mechanism of benzoylformate decarboxylase using carbon-13 and solvent deuterium isotope effects on benzoylformate and benzoylformate analogs (1988)

Benzoylformate decarboxylase (benzoylformate carboxy-lyase, BFD; EC 4.1.1.7) from Pseudomonas putida is a thiamine pyrophosphate (TPP) dependent enzyme which converts benzoylformate to benzaldehyde and carbon dioxide. The kinetics and mechanism of the benzoylformate decarboxylase reaction were studied by solvent deuterium and 13C kinetic isotope effects with benzoylformate and a series of substituted benzoylformates (pCH3O, pCH3, pCl, and mF). The reaction was found to have two partially rate-determining steps: initial tetrahedral adduct formation (D2O sensitive) and decarboxylation (13C sensitive). Solvent deuterium and 13C isotope effects indicate that electron-withdrawing substituents (pCl and mF) reduce the rate dependence upon decarboxylation such that decreased 13(V/K) effects are observed. Conversely, electron-donating substituents increase the rate dependence upon decarboxylation such that a larger 13(V/K) is seen while the D2O effects on V and V/K are not dramatically different from those for benzoylformate. All of the data are consistent with substituent stabilization or destabilization of the carbanionic intermediate (or carbanion-like transition state) formed during decarboxylation. Additional information regarding the mechanism of the enzymic reaction was obtained from pH studies on the reaction of benzoylformate and the binding of competitive inhibitors. These studies suggest that two enzymic bases are required to be in the correct protonation state (one protonated and one unprotonated) for optimal binding of substrate (or inhibitors).
Weighted-prediction-based color gamut scalability extension for the H.265/HEVC video codec (2014)

Color gamut scalability refers to coding a video in a layered manner where the base and enhancement layers are coded in different color gamut spaces. Color gamut scalability and its relationship with spatial scalability are currently being studied for the scalable extension of HEVC (SHVC) to enable coding of ultra-high definition content having BT.2020 color gamut with 10-bit precision as an enhancement layer and high definition content having BT.709 color gamut with 8-bit precision as the base layer. In this paper, we propose to use the weighted prediction tool of the SHVC standard to map the color gamut of the base layer to the enhancement layer. In addition, we also propose a high-precision bit-depth mapping of the base layer to the enhancement layer that jointly performs upsampling with a bit-depth increase. Simulation results show that these two schemes improve the coding efficiency of the All Intra and Random Access configurations by about 6.8% and 3.6% on average, respectively, compared to a basic scheme where the bit-depth of the base layer is increased by simple bit-shifting. These gains are achieved by imposing no changes to the SHVC standard; hence make the proposed method very useful for practical use-cases as well.
DISTRIBUTION, INHERITANCE, AND PROPERTIES OF AN ANTIGEN, MUB1, AND ITS RELATION TO HEMOLYTIC COMPLEMENT (1964)

An antigen, MuB1, present in the sera of some mice, can elicit a precipitating antibody in certain other strains of mice. An antibody to the antigen MuB1 can also be elicited in rabbits. 99 strains and substrains of inbred mice were tested for the presence of MuB1; the antigen was found in the sera of 44 strains (61 per cent) and 14 DBA substrains (52 per cent). Evidence is presented indicating that mice lacking MuB1 do not make a modified antigen, corresponding to MuB1, but are genetically deficient in synthetic ability at this site. By reaction with antibody to MuB1 an antigen corresponding to MuB1 was found in 13 of the 15 orders of mammals, and in 63 of 85 mammalian species tested, including man and guinea pig. The quantity of the antigen MuB1 is always greater in the serum of male than in the serum of female mice. The concentration of MuB1 increases with age; this increase is more marked in male than in female mice. By means of backcross experiments it was shown that the inheritance of MuB1 is unifactorial, is independent of the inheritance of the gamma globulin allotype MuA2, and is qualitatively independent of the sex of the parents. The antigen MuB1 is found in the euglobulin fraction of serum; it loses its ability to precipitate with antibody after heating at 56 degrees C, but not after treatment with ammonia or hydrazine. By gel filtration, MuB1 is separated with a fraction containing molecules of molecular weight approximately 150,000. An empirical correlation was observed between the presence or absence of MuB1 in the sera from inbred mice and the presence or absence of hemolytic complement (Hc), as measured by a test using a high concentration of rabbit hemolysin. In backcross experiments also, a correlation between hemolytic complement and the presence of MuB1 was demonstrated. As with MuB1, male mice had a higher hemolytic complement level than females. The particular component of complement which may be identical with MuB1 has not been identified.
Follicular dynamics throughout the oestrous cycle in sheep. A review (1985)

Whatever the stage of the cycle, follicles of various sizes are apparent on the surface of the ovary of sheep. No evidence of waves of follicular growth at fixed-time intervals has been found during the luteal phase, and growth probably occurs at random until the follicle attains a size of 4 to 7 mm. This shows that follicles can enlarge under a wide range of hormonal levels. The recruitment of a crop of follicles, including the one which will ovulate, occurs at variable times around luteolysis due to the interaction of endocrine and follicular factors (FSH priming, sensitizing the follicle to increased LH pulsatility). All healthy follicles greater than 2 mm in diameter are recruited. Selection of the follicle due to ovulate can be defined by morphological criteria (size) or by its "killing" ability. In all cases, the timing of follicle selection is highly variable, and it is due to this variability that the mechanisms of selection are not fully known. They are presumably intraovarian, one of the follicles actively inhibiting the growth of the others. The dominant follicle is probably maintained because of its high oestradiol content, while the others undergo atresia. The main feature of terminal follicular development is its flexibility in terms of hormonal requirements, follicle size and the timing of the main events.
Bioinspired Synthesis and Characterization of Gadolinium-Labeled Magnetite Nanoparticles for Dual ContrastT1- andT2-Weighted Magnetic Resonance Imaging (2010)

Gadolinium-labeled magnetite nanoparticles (GMNPs) were synthesized via a bioinspired manner to use as dual contrast agents for T1- and T2-weighted magnetic resonance imaging. A mussel-derived adhesive moiety, 3,4-dihydroxy-l-phenylalanine (DOPA), was utilized as a robust anchor to form a mixed layer of poly(ethylene glycol) (PEG) chains and dopamine molecules on the surface of iron oxide nanoparticles. Gadolinium ions were subsequently complexed at the distal end of the dopamine molecules that were prefunctionalized with a chelating ligand for gadolinium. The resultant GMNPs exhibited high dispersion stability in aqueous solution. Crystal structure and superparamagnetic properties of magnetite nanocrystals were also maintained after the complexation of gadolinium. The potential of GMNPs as dual contrast agents for T1 and T2-weighted magnetic resonance imaging was demonstrated by conducting in vitro and in vivo imaging and relaxivity measurements.
Tunable Semiconductor Lasers: A Tutorial (2004)

Tunable semiconductor lasers have been listed in numerous critical technology lists for future optical communication and sensing systems. This paper summarizes a tutorial that was given at OFC '03. It includes some discussion of why tunable lasers might be beneficial, an outline of basic tuning mechanisms, some examples of tunable lasers that have been commercialized, and a discussion of control techniques. More extensive data is given for the widely-tunable sampled-grating distributed-Bragg-reflector (SGDBR) type of laser, including data for such lasers integrated monolithically with modulators to form complete transmitter front ends. A summary of reliability data for the SGDBR laser is also given. It is concluded that tunable lasers can reduce operational costs, that full-band tunability is desirable for many applications, that monolithic integration offers the most potential for reducing size, weight, power and cost, and that sufficient reliability for system insertion has been demonstrated.
Tensor displays (2012)

We introduce tensor displays: a family of compressive light field displays comprising all architectures employing a stack of time-multiplexed, light-attenuating layers illuminated by uniform or directional backlighting (i.e., any low-resolution light field emitter). We show that the light field emitted by an N -layer, M -frame tensor display can be represented by an N th -order, rank- M tensor. Using this representation we introduce a unified optimization framework, based on nonnegative tensor factorization (NTF), encompassing all tensor display architectures. This framework is the first to allow joint multilayer, multiframe light field decompositions, significantly reducing artifacts observed with prior multilayer-only and multiframe-only decompositions; it is also the first optimization method for designs combining multiple layers with directional backlighting. We verify the benefits and limitations of tensor displays by constructing a prototype using modified LCD panels and a custom integral imaging backlight. Our efficient, GPU-based NTF implementation enables interactive applications. Through simulations and experiments we show that tensor displays reveal practical architectures with greater depths of field, wider fields of view, and thinner form factors, compared to prior automultiscopic displays.
Growth Factor Receptor-bound Protein 2 SH2/SH3 Domain Binding to CD28 and Its Role in Co-signaling (1998)

The co-stimulatory antigen CD28 has been shown to bind to several intracellular proteins including phosphatidylinositol 3-kinase, growth factor receptor-bound protein 2 (Grb2), and ITK. Paradoxically, Grb2 and phosphatidylinositol 3-kinase binding has been mapped to a similar pYMNM motif within the CD28 cytoplasmic tail. Given the importance of CD28 co-signaling to T cell function, questions exist regarding the mechanism by which Grb2 binds to CD28, and whether the interaction plays a role in co-stimulation. To biochemically characterize Grb2/CD28 binding, we initially utilized glutathione S-transferase-Grb2 fusion proteins carrying inactivating mutations within the SH2 and SH3 domains of Grb2, and assessed their ability to bind to CD28. In vitro binding experiments indicated that the Grb2 SH2 domain is critical for the association, while the SH3 domain plays an additional role in facilitating optimal binding. Enhanced binding via the SH3 domains was not observed when the C-terminal PXXP motif within CD28 was disrupted, thereby indicating that both SH2 and SH3 domains contribute to CD28 binding. Mutations that alter Grb2 binding were found to block the CD28-dependent interleukin-2 production. Further, tyrosine phosphorylation of Vav and the costimulation-dependent activation of Jun N-terminal kinase was blocked in cells defective in CD28/Grb2 binding. These results provide evidence for an alternate CD28-mediated signaling process involving Grb2 binding to the co-receptor.
Predicting distortions and overlay errors due to wafer deformation during chucking on lithography scanners (2009)

Chucking of substrates with wafer shape and thickness variations results in elastic deformation that can cause significant in-plane distortions that lead to overlay errors in lithographic patterning. As feature sizes shrink, overlay errors due to the combination of wafer geometry and chucking become a larger fraction of the error budget and must be controlled. We use a finite element model and a lithographic correction postprocessing scheme to predict in-plane distortions that result from chucking wafers with shape variations. We then use the predictions of in-plane distortions at two different patterning steps to calculate the component of overlay error that arises from localized shape variations. Using the model, in-plane distortion and overlay errors due to chucking are examined for multiple wafers with different geometries. The results show that long spatial wavelength shape variations cause significant distortion, but can largely be mitigated through the use of simple first-order corrections that are applied in typical lithography scanners. In contrast, high-frequency spatial variations cause distortions that cannot be corrected and hence lead to meaningful overlay errors. The results provide fundamental insight into chucking-induced overlay errors and can serve as a basis for the development of higher order scanner correction schemes that explicitly account for the wafer geometry through high-density wafer shape measurements.
Detection of choroidal neovascularization in age-related macular degeneration using subtraction methods in indocyanine green angiography. (1995)

We used image subtraction to analyze the findings of ICG angiography in choroidal neovascularization associated with age related macular degeneration. This method was useful in clear determination of the extent and location of CNV and in evaluating the degree and exact location of ICG leakage.
Distinct and Overlapping Functions of Insulin and IGF-I Receptors (2001)

Targeted gene mutations have established distinct, yet overlapping, developmental roles for receptors of the insulin/IGF family. IGF-I receptor mediates IGF-I and IGF-II action on prenatal growth and IGF-I action on postnatal growth. Insulin receptor mediates prenatal growth in response to IGF-II and postnatal metabolism in response to insulin. In rodents, unlike humans, insulin does not participate in embryonic growth until late gestation. The ability of the insulin receptor to act as a bona fide IGF-II-dependent growth promoter is underscored by its rescue of double knockout Igf1r/Igf2r mice. Thus, IGF-II is a true bifunctional ligand that is able to stimulate both insulin and IGF-I receptor signaling, although with different potencies. In contrast, the IGF-II/cation-independent mannose-6-phosphate receptor regulates IGF-II clearance. The growth retardation of mice lacking IGF-I and/or insulin receptors is due to reduced cell number, resulting from decreased proliferation. Evidence from genetically engineered mice does not support the view that insulin and IGF receptors promote cellular differentiation in vivo or that they are required for early embryonic development. The phenotypes of insulin receptor gene mutations in humans and in mice indicate important differences between the developmental roles of insulin and its receptor in the two species.
Disordered Eating Or Disordered Education? Refocusing the Analysis of Gender, Eating Disorders and Education (2002)

Eating disorders, especially anorexia nervosa and bulimia, have received a good deal of attention recently in a range of disciplines. In this paper we highlight how much of the aetiology of eating disorders centres largely on media images and the "cult of slenderness" as the base element of its production. We argue that this influential, if reductionist, and overly deterministic discursive tendency, has had a powerful impact on the way in which eating disorders have been conceptualised in relation to education and schools. Essentially, formal education has been viewed largely as an ameliorative, "corrective" or intervention agency, a potential "cure" to disorder, rather than as a set of processes which may, themselves, have a problematic, damaging and "disordering" effect on young people's lives. We suggest that the focus on the cult of slenderness may have deviated attention from the analysis of more complex and immediate negative effects of education, inherent in the form, organisation and content of schooling that erode young women's sense of competence, responsibility and control. The possible twist in all of this is that "achieving slenderness" may well become a resource and support structure, even a solution (albeit a bad one) to the other "problems of schooling". In this vein we again need ask, what are the cultural toxins in education that may be at work in pressing young people toward corporeal disorder, if body image alone is not to blame. Until we do so, simply dismantling the emphasis on slenderness, may not, ironically, be what these young women need (author abstract)
Risk Factors for Acute Wheezing in Infants and Children: Viruses, Passive Smoke, and IgE Antibodies to Inhalant Allergens (1993)

Wheezing children younger than 2 years of age had a high rate of viral infection and a low rate of IgE antibody to inhalant allergens. When these children were exposed to passive smoke, salivary cotinine levels were elevated suggesting heavy exposure. After 2 years of age, sensitization to inhaled allergens became increasingly important and viruses remained a significant risk factor for wheezing. These data support recommendations to reduce tobacco smoke exposure at home, especially for young patients, and to consider sensitization to inhaled allergens and allergen avoidance in wheezing children at an early age, particularly after age 2 years.
A new prognostic system for hepatocellular carcinoma: A retrospective study of 435 patients (1998)

The clinical outcome of cirrhotic patients with hepatocellular carcinoma (HCC) depends both on the residual liver function and tumor characteristics. However, the relative prognostic weight of these variables is not well defined. The aims of this study were to verify the value of known prognostic factors and to devise a prognostic index more sensitive than the commonly used Okuda stage. A retrospective analysis of the cases of HCC diagnosed at 16 Italian institutions from 1990 to 1992 was performed. Overall survival was the only end point used in the analysis. The Cox model, stratified by locoregional treatment, was used for multivariate analyses. The final model was derived from 10 randomly chosen training samples, and the prognostic validity of the Cancer of the Liver Italian Program (CLIP) score was assessed on the corresponding testing samples. Four hundred thirty-five cases of HCC were collected. As of January 1997, 313 patients (72%) were deceased. Overall median survival was 20 months. At multivariate analysis, independent predictive factors of survival were Child-Pugh stage, tumor morphology, alpha-fetoprotein (AFP), and portal vein thrombosis. A simple scoring system (CLIP score) was thus produced, assigning linear scores (0/1/2) to the covariates. Compared with Okuda stage, the CLIP score, structured as a six-category tool, has a greater discriminant ability, revealing a class of patients with an impressively more favorable prognosis and another class with a relatively shorter life expectancy. The CLIP score is a new prognostic system that accounts for both liver function and tumor characteristics. It is easy to calculate and appears to give more precise information than the Okuda stage.
Immunochemical and functional characterization of an agonist‐like monoclonal antibody against the M2 acetylcholine receptor (1998)

Monoclonal antibodies were raised against a peptide corresponding to the second extracellular loop of the M2 acetylcholine receptor. One of the monoclonal antibodies, B8E5, was selected for further characterization on the basis of its high yield, its isotype (IgG2a), its dissociation kinetics and its agonist-like activity. The epitope recognized by B8E5 corresponded to the N-terminal part of the second extracellular loop of the receptor (V-R-T-V-E-) as determined by competition immunoassays and epitope scanning. The KA of B8E5 for the target peptide was assessed by surface plasmon resonance (SPR) to be 6.5x10(7) M(-1) by equilibrium and 3.7x10(7) M(-1) by kinetic analysis. B8E5 recognized the M2 acetylcholine receptor on rat cardiac tissue. It only recognized the non-reduced receptor in immunoblots. The antibody had no effect on antagonist binding but decreased the affinity for the agonist carbachol. B8E5 decreased the beating frequency of neonatal rat cardiomyocytes. The effect was specific since it was blocked by the target peptide and the antagonist atropine. The EC50 of the antibody corresponded to the KA measured by surface plasmon resonance. The physiological effect of the antibody did not lead to desensitization. The Fab fragments had no physiological effect; subsequent addition of anti-mouse IgG however restored the physiological effect. These results confirm that the N-terminus of the second extracellular loop is a functional target for antibodies against the M2 acetylcholine receptor. They suggest that the functional epitope is only accessible in the non-reduced receptor. The antibodies act through a functional dimerization of the receptor.
Thrombospondin interaction with plasminogen. Evidence for binding to a specific region of the kringle structure of plasminogen (1989)

Platelet thrombospondin interacts with plasminogen in a specific and saturable manner. Thrombospondin was found to specifically bind to plasminogen and the nonenzyme chain of plasmin. Preincubation of 125I- labeled thrombospondin with 30 mmol/L lysine was without effect in the binding of thrombospondin to immobilized plasminogen; preincubation of 125I-labeled plasminogen with 30 mmol/L lysine, on the other hand, significantly reduced the binding of plasminogen to immobilized thrombospondin, suggesting that the interaction of thrombospondin with plasminogen is not the direct result of the lysine binding sites of plasminogen. Arginine and benzamidine, ligands known to specifically bind to the kringle 5 domain of plasminogen, blocked the binding of thrombospondin to plasminogen. Limited elastase proteolysis of plasminogen and plasmin resulted in the generation of two distinct thrombospondin binding domains, one of which was retained on lysine- agarose. The isolation and amino-terminal analysis of these domains following elastase proteolysis of plasminogen identified them, respectively, as a domain containing kringle structures 4 and 5 and plasmin and the other domain consisting of kringle 5-plasmin. A 16- residue synthetic peptide, which represents the amino acids linking kringle 4 to kringle 5 (residues 435–450 of native plasminogen), was without effect in either binding to thrombospondin or blocking the binding of thrombospondin to plasminogen. Plasminogen, therefore, possesses a single thrombospondin interactive site that is independent of, but influenced by, the lysine binding site containing kringle structures and most likely is located within the kringle 5 domain.