gebhart/patrepeval huggingface dataset:
Swine Leukocyte Antigen-&lt;italic&gt;DQA&lt;/italic&gt; Gene Variation and Its Association with Piglet Diarrhea in Large White, Landrace and Duroc (2013)

The swine leukocyte antigen class II molecules are possibly associated with the induction of protective immunity. The study described here was to investigate the relationship between polymorphisms in exon 2 of the swine DQA gene and piglet diarrhea. This study was carried out on 425 suckling piglets from three purebred pig strains (Large White, Landrace and Duroc). The genetic diversity of exon 2 in swine DQA was detected by PCR-SSCP and sequencing analysis, eight unique SSCP patterns (AB, BB, BC, CC, CD, BD, BE and DD) representing five specific allele (A to E) sequences were detected. Sequence analysis revealed 21 nucleotide variable sites and resulting in 12 amino acid substitutions in the populations. A moderate level polymorphism and significant deviations from Hardy-Weinberg equilibrium of the genotypes distribution were observed in the populations (p<0.01). The association analysis indicated that there was a statistically significant difference in the score of piglet diarrhea between different genotypes, individuals with genotype CC showed a lower diarrhea score than genotypes AB (0.98±0.09), BB (0.85±0.77) and BC (1.25±0.23) (p<0.05), and significantly low than genotype BE (1.19±0.19) (p<0.01), CC genotype may be a most resistance genotype for piglet diarrhea.
Sound Source Localization for Circular Arrays of Directional Microphones (2006)

Previous research in sound source localization has helped increase the robustness of estimates to noise and reverberation. Circular arrays are of particular interest for a number of scenarios, particularly because they can be placed in the center of the sources. First, that improves the sound capture due to the reduced distance. Second, it helps on the direction estimation, not only because of the reduced distance, but also because it increases the angle differences. Nevertheless, most research on circular arrays focused on the case of omni-directional microphones. In this paper, we present a new algorithm for sound source localization developed specifically for directional microphones. Results obtained from real meeting room setups show a typical error of less than 3 degrees.
Characterisation of Neurotrophin Dimers and Monomers (1994)

When recombinant brain-derived neurotrophic factor (BDNF) and neurotrophin-3 (NT-3) are purified by reverse-phase chromatography, these neurotrophins elute as two distinct peaks. This is also the case when naturally occurring BDNF is purified from brain tissue. As indicated by gelfiltration experiments, the peaks with shorter retention times correspond to neurotrophin dimers, those with longer retention times to monomers. In contrast, a BDNF mutant with a single amino-acid replacement (Arg-1-->Lys) in the basic processing site common to all neurotrophin precursors elutes as a single peak. This peak is shown by gel-filtration chromatography to consist of dimers with a molecular mass almost twice that of wild-type dimers. N-terminal sequencing indicates an extension of 19 amino acids, including a glycosylated asparagine residue. The biological activity of the BDNF mutant ([R-1K]BDNF) is identical with that of wild-type BDNF when tested in a neuron survival assay. Using this assay, the biological activities of guanidine-hydrochloride-denatured neurotrophin monomers were found to be much lower than that of the dimers, and experiments with NT-3 monomers and NIH3T3 cells expressing trkC suggest that such monomers exist in solution in a conformation that prevents efficient interactions with neurotrophin receptors.
Nanoliter Solvent Extraction Combined with Microspot MALDI TOF Mass Spectrometry for the Analysis of Hydrophobic Biomolecules (2001)

A nanoliter solvent extraction technique combined with microspot matrix-assisted laser desorption/ionization (MALDI) mass spectrometry is presented. This method involves the use of a nanoliter droplet containing organic solvents at the tip of a small capillary for extraction. The droplet is formed inside a microliter aqueous sample containing the analyte of interest. After extraction, the droplet is deposited onto a MALDI target precoated with a thin matrix layer. Since the nanoliter droplet never touches the sample container wall, any possible extraction of contaminants adsorbed on the plastic or glassware is avoided. In addition, there is no need to concentrate the organic phase after the extraction, thus avoiding any possible loss during the concentration step. The nanoliter volume can be readily deposited onto a MALDI target, producing a high analyte concentration within a microspot. Combined with microspot MALDI, this technique allows for very sensitive analysis of the extracted analyte. The performance of this technique is illustrated in several applications involving the detection of hydrophobic peptides or phospholipids. It is shown that very hydrophobic analytes can be extracted from small-volume samples containing a large amount of salts and/or more hydrophilic analytes, which tend to give dominant signals in conventional MALDI experiments. Nanoliter extraction of analyte from samples containing less than 100 nM hydrophobic analyte and over 1 microM easily ionized hydrophilic species is demonstrated. Finally, using the analysis of the ionophore valinomycin as an example, it is demonstrated that the technique is a more reliable tool for probing metal-peptide complexes than regular MALDI sample preparations.
Phase II study of liposomal doxorubicin in refractory ovarian cancer: antitumor activity and toxicity modification by liposomal encapsulation. (1997)

Liposomal doxorubicin has substantial activity against ovarian cancer refractory to platinum and paclitaxel. The responses achieved with liposomal doxorubicin were durable and maintained with minimal toxicity. This liposomal formulation should be evaluated further in combination with other drugs in less refractory patients.
Loss of EphB4 receptor tyrosine kinase protein expression during carcinogenesis of the human breast (2002)

Members of the Eph family of receptor tyrosine kinase have been implicated in cell-cell communication and tissue integrity during embryogenesis. We have previously demonstrated cell type specific and hormone dependent EphB4 expression in the mouse mammary parenchyma suggesting involvement in the homeostasis of this organ. Since disruption of tissue organization is crucial for metastatic dissemination, we have investigated the expression of EphB4 during carcinogenesis of the human breast. Immunohistochemical analysis of 24 normal human breast samples and 124 consecutive breast carcinomas was correlated with tumor characteristics (stage, histology, grade, lymph node involvement) and the expression of ER, PR, Ki-67, p53 and HER2. In normal breast tissue, the EphB4 protein was expressed exclusively in parenchymal cells. Strikingly, a drastic reduction in the number of EphB4 protein expressing cells was observed in almost all invasive carcinomas analyzed, irrespective of the tumor type (p<0.0001). Furthermore, we found a highly significant correlation between EphB4 positivity and low histological grading of the tumor cells (p=0.002) suggesting that in breast cancer, EphB4 expression is not compatible with tumor progression. This raises the possibility that EphB4 could represent a potent tool for therapeutic intervention.
A cascade of tyrosine autophosphorylation in the beta-subunit activates the phosphotransferase of the insulin receptor. (1988)

We identified the major autophosphorylation sites in the insulin receptor and correlated their phosphorylation with the phosphotransferase activity of the receptor on synthetic peptides. The receptor, purified from Fao hepatoma cells on immobilized wheat germ agglutinin, undergoes autophosphorylation at several tyrosine residues in its beta-subunit; however, anti-phosphotyrosine antibody (alpha-PY) inhibited most of the phosphorylation by trapping the initial sites in an inactive complex. Exhaustive trypsin digestion of the inhibited beta-subunit yielded two peptides derived from the Tyr-1150 domain (Ullrich, A, Bell, J. R., Chen, E. Y., Herrera, R., Petruzzelli, L. M., Dull, T. J., Gray, A., Coussens, L., Liao, Y.-C., Tsubokawa, M., Mason, A., Seeburg, P. H., Grunfeld, C., Rosen, O. M., and Ramachandran, J. (1985) Nature 313, 756-761) called pY4 and pY5. Both peptides contained 2 phosphotyrosyl residues (2Tyr(P], one corresponding to Tyr-1146 and the other to Tyr-1150 or Tyr-1151. In the absence of the alpha-PY additional sites were phosphorylated. The C-terminal domain of the beta-subunit contained phosphotyrosine at Tyr-1316 and Tyr-1322. Removal of the C-terminal domain by mild trypsinolysis did not affect the phosphotransferase activity of the beta-subunit suggesting that these sites did not play a regulatory role. Full activation of the insulin receptor during in vitro assay correlated with the appearance of two phosphopeptides in the tryptic digest of the beta-subunit, pY1 and pY1a, that were inhibited by the alpha-PY. Structural analysis suggested that pY1 and pY1a were derived from the Tyr-1150 domain and contained 3 phosphotyrosyl residues (3Tyr(P] corresponding to Tyr-1146, Tyr-1150, and Tyr-1151. The phosphotransferase of the receptor that was phosphorylated in the presence of alpha-PY at 2 tyrosyl residues in the Tyr-1150 domain was not fully activated during kinase assays carried out with saturating substrate concentrations which inhibited further autophosphorylation. During insulin stimulation of the intact cell, the 3Tyr(P) form of the Tyr-1150 domain was barely detected, whereas the 2Tyr(P) form predominated. We conclude that 1) autophosphorylation of the insulin receptor begins by phosphorylation of Tyr-1146 and either Tyr-1150 or Tyr-1151; 2) progression of the cascade to phosphorylation of the third tyrosyl residue fully activates the phosphotransferase during in vitro assay; 3) in vivo, the 2Tyr(P) form predominates, suggesting that progression of the autophosphorylation cascade to the 3Tyr(P) form is regulated during insulin stimulation.(ABSTRACT TRUNCATED AT 400 WORDS)
Electron- and Hole-Capture Reactions on Pt/TiO2 Photocatalyst Exposed to Methanol Vapor Studied with Time-Resolved Infrared Absorption Spectroscopy (2002)

The decay kinetics of photogenerated electrons in a Pt/TiO2 catalyst has been studied by time-resolved infrared absorption (TR-IR) spectroscopy. The electron decay was drastically affected by exposure to methanol vapor, and the electron−hole pair recombination was prevented. A certain fraction of the electrons remained beyond 1 s and slowly decayed from ∼1−9 s. The prevented recombination was interpreted with the effective capture of the holes. The extent of the hole capture was insensitive to the pressure of methanol vapor. An irreversibly adsorbed methoxy groups was proposed to capture the holes on the basis of the steady-state FT-IR spectra of the catalyst exposed to methanol vapor of different pressures. However, the slow decay of the electrons exhibited a positive-order response to the methanol pressure. Undissociated methanol physisorbed and equilibrated with the gas phase, which was identified in the steady-state spectra, should play a key role in the electron capture process. Possible mechanisms of the process are discussed.
The regulatory role of heat shock protein 70-reactive CD4+ T cells during rat listeriosis. (1998)

Protection against infection with Listeria monocytogenes depends primarily on Listeria-specific T cells. We show here that CD4+ TCR alphabeta+ T cells are capable of recognizing the mycobacterial heat shock protein (HSP) 70, that appears in the peritoneal cavity of F344 rats infected i.p. with L. monocytogenes. The HSP70-reactive CD4+ T cells recognized a peptide comprising 234-252 residues as present in the 70 kDa HSP of Mycobacterium tuberculosis in the context of RT1.B MHC class II molecules. Analysis of TCR Vbeta gene expression with RT-PCR revealed that the HSP70-reactive CD4+ T cells predominantly used the Vbeta16 gene segment, whereas the heat-killed Listeria (HKL)-specific T cells expressed a diverse set of Vbeta gene segments. In contrast to the HKL-specific T cells producing IFN-gamma, the HSP70-reactive CD4+ T cells produced TGF-beta1 and IL-10 but neither Th1- or Th2-type cytokines. Adoptive transfer with HSP70-reactive T cells rendered rats susceptible to listerial infection. Collectively, these results proposed that the HSP70-reactive CD4+ T cells appearing during rat listeriosis may be involved in termination of Th1 cell-mediated excessive inflammation after the battle against L. monocytogenes has been won.
The role of oncology clinical practice guidelines in the managed care era. (1995)

The development of clinical practice guidelines in oncology presents unique problems and challenges due to the heterogeneity of disease presentations and the complexity of therapeutic decisions. Guidelines should incorporate not only standard outcomes measures such as survival but, if feasible, quality of life measures, patient preferences, and cost-effectiveness analyses. Although clinical guidelines are being promulgated as a means of assisting physicians in making therapeutic decisions, another purpose of guidelines implementation reflects the goals of managed care, ie, to promote practice conformity and reduce the cost of care. Methods to monitor physicians' adherence to guidelines are expected to increase as a means of ensuring compliance. This article reviews the process of developing two common types of guidelines used in oncology: path guidelines (using stage II breast cancer as a paradigm) and boundary guidelines (such as the ASCO growth factor guidelines).
PRINCIPLES AND APPLICATION OF MAXIMUM KURTOSIS PHASE ESTIMATION1 (1988)

ABSTRACT Methods of minimum entropy deconvolution (MED) try to take advantage of the non‐Gaussian distribution of primary reflectivities in the design of deconvolution operators. Of these, Wiggins’(1978) original method performs as well as any in practice. However, we present examples to show that it does not provide a reliable means of deconvolving seismic data: its operators are not stable and, instead of whitening the data, they often band‐pass filter it severely. The method could be more appropriately called maximum kurtosis deconvolution since the varimax norm it employs is really an estimate of kurtosis. Its poor performance is explained in terms of the relation between the kurtosis of a noisy band‐limited seismic trace and the kurtosis of the underlying reflectivity sequence, and between the estimation errors in a maximum kurtosis operator and the data and design parameters. The scheme put forward by Fourmann in 1984, whereby the data are corrected by the phase rotation that maximizes their kurtosis, is a more practical method. This preserves the main attraction of MED, its potential for phase control, and leaves trace whitening and noise control to proven conventional methods. The correction can be determined without actually applying a whole series of phase shifts to the data. The application of the method is illustrated by means of practical and synthetic examples, and summarized by rules derived from theory. In particular, the signal‐dominated bandwidth must exceed a threshold for the method to work at all and estimation of the phase correction requires a considerable amount of data. Kurtosis can estimate phase better than other norms that are misleadingly declared to be more efficient by theory based on full‐band, noise‐free data.
Synthetic Malaria Peptide Vaccine Elicits High Levels of Antibodies in Vaccinees of Defined HLA Genotypes (2000)

A multiple antigen peptide (MAP) malaria vaccine containing minimal Plasmodium falciparum circumsporozoite protein repeat epitopes was assessed for safety and immunogenicity in volunteers of known class II genotypes. The MAP/alum/QS-21 vaccine formulation elicited high levels of parasite-specific antibodies in 10 of 12 volunteers expressing DQB1*0603, DRB1*0401, or DRB1*1101 class II molecules. In contrast, volunteers of other HLA genotypes were low responders or nonresponders. A second study of 7 volunteers confirmed the correlation of class II genotype and high responder phenotype. This is the first demonstration in humans that a peptide vaccine containing minimal T and B cell epitopes composed of only 5 amino acids (N, A, V, D, and P) can elicit antibody titers comparable to multiple exposures to irradiated P. falciparum—infected mosquitoes. Moreover, the high-responder phenotypes were predicted by analysis of peptide/HLA interactions in vitro, thus facilitating the rational design of epitope-based peptide vaccines for malaria, as well as for other pathogens.
Optical-fiber-based Mueller optical coherence tomography (2003)

An optical-fiber-based multichannel polarization-sensitive Mueller optical coherence tomography (OCT) system was built to acquire the Jones or Mueller matrix of a scattering medium, such as biological tissue. For the first time to our knowledge, fiber-based polarization-sensitive OCT was dynamically calibrated to eliminate the polarization distortion caused by the single-mode optical fiber in the sample arm, thereby overcoming a key technical impediment to the application of optical fibers in this technology. The round-trip Jones matrix of the sampling fiber was acquired from the reflecting surface of the sample for each depth scan (A scan) with our OCT system. A new rigorous algorithm was then used to retrieve the calibrated polarization properties of the sample. This algorithm was validated with experimental data. The skin of a rat was imaged with this fiber-based system.
Sleep Loss Results in an Elevation of Cortisol Levels the Next Evening (1997)

Sleep curtailment constitutes an increasingly common condition in industrialized societies and is thought to affect mood and performance rather than physiological functions. There is no evidence for prolonged or delayed effects of sleep loss on the hypothalamo-pituitary-adrenal (HPA) axis. We evaluated the effects of acute partial or total sleep deprivation on the nighttime and daytime profile of cortisol levels. Plasma cortisol profiles were determined during a 32-hour period (from 1800 hours on day 1 until 0200 hours on day 3) in normal young men submitted to three different protocols: normal sleep schedule (2300-0700 hours), partial sleep deprivation (0400-0800 hours), and total sleep deprivation. Alterations in cortisol levels could only be demonstrated in the evening following the night of sleep deprivation. After normal sleep, plasma cortisol levels over the 1800-2300-hour period were similar on days 1 and 2. After partial and total sleep deprivation, plasma cortisol levels over the 1800-2300-hour period were higher on day 2 than on day 1 (37 and 45% increases, p = 0.03 and 0.003, respectively), and the onset of the quiescent period of cortisol secretion was delayed by at least 1 hour. We conclude that even partial acute sleep loss delays the recovery of the HPA from early morning circadian stimulation and is thus likely to involve an alteration in negative glucocorticoid feedback regulation. Sleep loss could thus affect the resiliency of the stress response and may accelerate the development of metabolic and cognitive consequences of glucocorticoid excess.
A Design Verification Methodology Based on Concurrent Simulation and Clock Suppression (1983)

This paper outlines a methodology for design verification of very large networks based on Concurrent Simulation and Clock Suppression. Concurrent Simulation is expected to yield a 30:1 to 600:1 speed advantage over conventional (serial) simulation when roughly 5,000 "good machines" are simulated concurrently. This speed advantage increases with the number of concurrent machines. Clock Suppression is an auxiliary technique to avoid simulation slowdowns if very large networks with very large clock fanouts must be simulated. The methodology proposed here for design verification is "Concurrent Case Simulation", i.e., the simultaneous simulation of distinct sets of input patterns. Advantages of this method are (1) speed, (2) the fundamental ability to simulate cases concurrently, (3) to observe differences between cases in a more economic, simpler, and more natural style than with serial simulation, (4) to run many more cases than would be possible with serial simulation, (5) and the fact that running cases against each other establishes a powerful design verification philosophy.
BLOCKADE OF CD4 MOLECULES BY NONDEPLETING ANTI-CD4 MONOCLONAL ANTIBODIES PREVENTS XENOGENEIC PIG ISLET GRAFT REJECTION AND RECURRENCE OF AUTOIMMUNE DIABETES (1999)

29 CD4+ T cells play a major role in xenogeneic islet graft rejection and recurrence of autoimmune diabetes after islet transplantation. CD4 molecule is required as a co-receptor of TCR for CD4+ T cell activation and function. Non-depleting anti-CD4 monoclonal antibody (mAb) which blocks association of CD4 with TCR for signal transduction and disrupts CD4+ T cell function without significantly reducing circulating CD4+ T cells has been developed for transplantation. In this study we investigated whether blockade of CD4 molecules by non-depleting CD4 mAbs (YTS177.9.6) prevents pig islet graft rejection in STZ-induced and autoimmune diabetic mice; and whether it prevents recurrence of autoimmune diabetes. Five hundred islets from pig or NOR which is a MHC-matched control strain for NOD mouse were transplanted under the left kidney capsule of each STZ-induced diabetic Balb/c mouse or autoimmune diabetic NOD mouse, respectively. Islet graft survival was monitored by blood glucose measurement. YTS177 at 250 μg were given i.p. on days −1, 0 and then once every two days until 14 days post-transplantation. Islet graft survival is shown as follows: (Table)TableNOD mice marked with * were transplanted with allogeneic Balb/c mouse skin graft at 50 or 60 days post-transplantation. Skin grafts in these mice were rejected between 10 to 13 days. Removal of the kidney bearing the islet grafts at 64 or 72 days post-transplantation resulted in a return of hyperglycemia. Pathological examination revealed intact islets with well-expressed insulin granules and mild lymphocyte infiltration in these islet grafts. However, only a few insulin granules and a massive lymphocyte infiltration were noted in all rejected islet grafts. Our results demonstrate that transient blockade of CD4 molecules by nondepleting CD4 mAbs can significantly prolong pig islet graft survival in STZ-induced and autoimmune diabetic mice. Recurrence of autoimmune diabetes can be prevented and self-tolerance to islet autoantigen in NOD mice may be restored after MHC-matched islet transplantation and transient blockade of CD4 molecules.
Monoclonal antibodies inhibit in vitro fibrillar aggregation of the Alzheimer beta-amyloid peptide. (1996)

The beta-amyloid peptide, the hallmark of Alzheimer disease, forms fibrillar toxic aggregates in brain tissue that can be dissolved only by strong denaturing agents. To study beta-amyloid formation and its inhibition, we prepared immune complexes with two monoclonal antibodies (mAbs), AMY-33 and 6F/3D, raised against beta-amyloid fragments spanning amino acid residues 1-28 and 8-17 of the beta-amyloid peptide chain, respectively. In vitro aggregation of beta-amyloid peptide was induced by incubation for 3 h at 37 degrees C and monitored by ELISA, negative staining electron microscopy, and fluorimetric studies. We found that the mAs prevent the aggregation of beta-amyloid peptide and that the inhibitory effect appears to be related to the localization of the antibody-binding sites and the nature of the aggregating agents. Preparation of mAbs against "aggregating epitopes," defined as sequences related to the sites where protein aggregation is initiated, may lead to the understanding and prevention of protein aggregation. The results of this study may provide a foundation for using mAbs in vivo to prevent the beta-amyloid peptide aggregation that is associated with Alzheimer disease.