gebhart/patrepeval huggingface dataset:
Autophagic Proteolysis of Long-Lived Proteins in Nonliver Cells (2008)

Autophagy is a cellular homeostasis pathway used to sustain cellular anabolic needs during times of nutrient or energy deprivation. Autophagosomes sequester cytoplasmic constituents, including macromolecules such as long-lived proteins. Upon fusion of autophagosomes with lysosomes, the engulfed cargo is degraded. The proteolysis of longlived proteins by macroautophagy is a standard, specific measure of autophagic degradation and represents an end-point assay for the pathway. The assay is based on a pulse-chase approach, whereby cellular proteins are radiolabeled by an isotopically marked amino acid, the short-lived, rapidly turned over, proteins are allowed to be degraded during a long chase period, and then the remaining, stable radiolabeled proteins are subjected to autophagic degradation. The classical application of this method has been in hepatocytes, but the recent growth of interest in autophagy has necessitated adaptation of this method in nonliver cells. Here we describe a protocol to quantify autophagic degradation of longlived proteins in macrophages. This chapter details the method of analyzing autophagic proteolysis in RAW264.7 mouse macrophages.
Antibacterial activity of pepsin-digested lactoferrin on foodborne pathogens in buffered broth systems and ultra-high temperature milk with EDTA (2002)

Natural preservatives that are active against Gram-negative and Gram-positive bacteria are desirable to the food industry. This study demonstrates that LFH is effective in a complex food system. Moreover, the LFH used was not purified, making its use by industry more attractive.
Increased Connective Tissue Extracellular Matrix in the <i>op/op</i> Model of Osteopetrosis (2009)

Mice that are homozygous for the recessive osteopetrosis spontaneous mutation (op/op) develop severe osteopetrosis due to a defect in the production of macrophage colony-stimulating factor (M-CSF) and a deficiency in monocyte-derived osteoclasts. Our study describes a novel soft tissue finding in an osteopetrosis (B6C3Fe a/a-Csf1(op)/J) mouse model. Tissues were obtained from B6C3Fe a/a-Csf1(op)/J mice and age-matched wild-type mice, processed for hematoxylin and eosin sections, and comprehensive light microscopic tissue evaluation was performed. Mutant mice had characteristic traits of op/op deficiency including missing incisors and domed skulls. Histologically, the bone marrow cavity was effaced by interweaving thick bony trabeculae consistent with osteopetrosis. An increase in a finely granular, basophilic interstitial extracellular matrix (ECM) was observed in the subcutaneous connective tissue of the op/op mice when compared with controls. Histochemically, the ECM was negative with periodic acid Schiff and stained dark blue with alcian blue at a pH of 2.5, indicating that it is composed primarily of nonsulfated glycosaminoglycans (GAGs). This work suggests an increased ECM that is composed mainly of GAGs located in the subcutaneous tissue in op/op mice. This increase in ECM may be related to altered matrix production or turnover because of changes in M-CSF production.
Induction of Primary,Human Antigen-Specific Cytotoxic T Lymphocytes In Vitro Using Dendritic Cells Pulsed with Peptides (1998)

Using a murine metastasis model, we have previously shown that antigen-presenting cells (APC) loaded with unfractionated peptides derived from poorly immunogenic, highly metastatic tumor cells represent a potent form of tumor vaccine. The antimetastatic effect of peptide pulsed APC could be further enhanced by pretreating the cells with antisense oligonucleotides directed against the TAP-2 gene to increase the density of specific peptide-major histocompatibility complex (MHC) class I complexes and thereby improve the APC function of the treated cells (Nair SK et al., J Immunol 1996;156:1772). In this study, we investigated whether similar strategies can be used to enhance the potency of human dendritic cells (DC) to present antigen. We show that human DC pulsed with peptides encoding known cytotoxic T-lymphocyte (CTL) epitopes stimulate both memory and primary CTL responses in vitro after two cycles of stimulation with the peptide-pulsed DC. Two approaches were used to increase the density of specific peptide-MHC complexes on the surface of DC. One approach was to inhibit transporter associated with antigen presentation (TAP) function using TAP antisense oligonucleotides. The second approach was to inhibit the endogenous generation of the peptide epitopes by pretreating the DC with a proteasome inhibitor. Treatment of DC with either TAP antisense oligonucleotides or with a proteasome inhibitor resulted in a dramatic enhancement of primary CTL induction.
Localization of a ς70 Binding Site on the N Terminus of the Escherichia coli RNA Polymerase β′ Subunit (1998)

The Escherichia coli genome encodes genes for seven different sigma subunit species while only having single genes for the alpha, beta, and beta' subunits that make up the RNA polymerase core enzyme. The various sigma factors compete for binding to the core enzyme, upon which they confer promoter DNA-specific transcription initiation to the polymerase. We have mapped a major interaction site between one of the sigma species, sigma70, and beta'. Using far-Western blotting analysis of chemically cleaved and genetically engineered protein fragments, we have identified a N-terminal fragment of beta' (residues 60-309) that could bind sigma70. We were able to more precisely map the interaction domain to amino acid residues 260-309 of beta' using nickel nitrilotriacetic acid co-immobilization assays.
Elevated serum levels in human pregnancy of a molecule immunochemically similar to eosinophil granule major basic protein. (1983)

We have shown that serum levels of a molecule immunochemically similar to eosinophil granule major basic protein (MBP) are elevated in pregnant women throughout gestation. MBP levels increase during gestation and plateau at approximately 7,500 ng/ml by the 20th wk (greater than 10-fold above normal). Levels return to normal after delivery, with a T1/2 of 13.7 d. The MBP in pregnancy serum is remarkably similar to the eosinophil granule MBP in that: (a) pregnancy MBP fully inhibits the binding of radiolabeled MBP standard in a double antibody radioimmunoassay; (b) this inhibition reaction is specific for human MBP because pregnancy serum produces no inhibition of the binding of radiolabeled guinea pig MBP in the guinea pig MBP radioimmunoassay; (c) in a two-site immunoradiometric assay for MBP, slopes of dose-response curves for pregnancy serum, purified MBP, and serum from a patient with hypereosinophilic syndrome are identical, and maximal binding is comparable; (d) reduction and alkylation of pregnancy sera increases measured MBP 100-fold, as previously shown for eosinophil granule MBP in serum; and (e) the MBP in pregnancy serum demonstrates the same pattern of heat lability as has been previously reported for MBP. Four observations have raised the possibility that the eosinophil is not the source of the MBP in pregnancy serum: (a) no correlation between serum MBP level and peripheral blood eosinophil count exists in pregnant women, in contrast to previous studies of patients with eosinophilia; (b) levels of three other eosinophil-associated proteins are normal or low in pregnancy sera, whereas the serum levels of these proteins are elevated in patients with eosinophilia; (c) the slopes of dose-response curves for pregnancy sera and MBP standards differ in the double antibody radioimmunoassay; and (d) the molecule in pregnancy serum elutes from Sephadex G-50 columns at the void volume, while eosinophil granule MBP and the MBP in serum of patients with eosinophilia elute at a volume consistent with the previously established molecular weight of 9,300. These findings suggest that the MBP in pregnancy serum is derived from a source other than the eosinophil.
Gaze correction for home video conferencing (2012)

Effective communication using current video conferencing systems is severely hindered by the lack of eye contact caused by the disparity between the locations of the subject and the camera. While this problem has been partially solved for high-end expensive video conferencing systems, it has not been convincingly solved for consumer-level setups. We present a gaze correction approach based on a single Kinect sensor that preserves both the integrity and expressiveness of the face as well as the fidelity of the scene as a whole, producing nearly artifact-free imagery. Our method is suitable for mainstream home video conferencing: it uses inexpensive consumer hardware, achieves real-time performance and requires just a simple and short setup. Our approach is based on the observation that for our application it is sufficient to synthesize only the corrected face. Thus we render a gaze-corrected 3D model of the scene and, with the aid of a face tracker, transfer the gaze-corrected facial portion in a seamless manner onto the original image.
In vitro elucidation of substrate specificity and bioassay of proprotein convertase 4 using intramolecularly quenched fluorogenic peptides (2004)

The fourth member of Ca2+-dependent mammalian secretory subtilase, PC4 (proprotein convertase 4), is primarily expressed in testicular germ cell and ovarian macrophage. Its role in sperm fertilization and in early embryonic development has been demonstrated earlier through several studies, including those with PC4 null mice. A number of physiological substrates found in reproductive tissues have been postulated or identified for PC4 by various biochemical studies. These include growth factors IGF-1 (insulin-like growth factor-1) and IGF-2, hormonal polypeptide proPACAP (where PACAP stands for pituitary adenylate cyclase-activating polypeptide) and a number of surface proteins of ADAM (ADisintegrin And Metalloproteinase-like) family such as ADAM-1 (fertilin a), ADAM-2 (fertilin b), ADAM-3 (procyritestin) and ADAM-5. To provide further evidence in support of this notion and also to study the substrate specificity and bioassay of PC4, a series of intramolecularly quenched fluorogenic peptides containing the cleavage sites and several mutants were prepared. A comparative kinetic analysis and measurement of Vmax (app)/Km (app) ratio of these fluorogenic substrates against PC4 and PC7 revealed that the mutant variants of h (human) proPACAP and m (mouse) ADAM-5 derived peptides Q-PACAP141-151-mutant [Abz-141RVKNKGRRI150P151SY(NO2)-A-CONH2] (150A151Y replaced by PS) and Q-ADAM-5380-388-mutant [Abz-380E381PKPARRP388RY(NO2)A-CONH2] (381R replaced by P) are most efficiently and selectively cleaved by PC4. Using these two and Q-IGF-263-71 peptides, we showed that the sperm extract of normal adult mice is much higher when compared with that of PC4-null mice. This suggests that these fluorogenic peptides are useful for specific bioassay of PC4 activity. In addition, kinetic studies with various peptidyl-MCA indicate that the hexapeptide Ac-KTKQLR-MCA (where MCA stands for 4-methyl coumaryl-7-amide) is most efficiently and selectively cleaved by PC4 at RMCA, making it another effective agent for bioassay of PC4 activity. The study concludes that the most probable sequence motif for recognition by PC4 is KXKXXR or KXXR, where X is any amino acid other than cysteine and that it prefers proline at P3, P5 and/or P2' positions. It was also revealed that PC4 is a good candidate processing enzyme for growth factors IGF-1 and -2, neuropeptide proPACAP and several ADAM proteins such as ADAM-1, -2, -3 and -5.
Site-specific intracoronary thrombolysis with urokinase-coated hydrogel balloons: Acute and follow-up studies in 95 patients (1997)

Conventional balloon angioplasty in the presence of intracoronary thrombus is associated with an elevated risk for acute myocardial infarction, emergency bypass surgery, and death. The purpose of this study was to assess the safety and efficacy of a new technique to treat thrombus-containing stenoses consisting of the local delivery of urokinase directly to the site of intraluminal clot with hydrogel-coated balloons. Ninety-five patients with angiographically apparent intracoronary thrombus were treated with urokinase-coated hydrogel balloons either prior to (n = 74) or following (n = 21) conventional balloon angioplasty. Clinical diagnoses for the study group included acute myocardial infarction in 50 patients, postinfarction angina in 23 patients, and unstable angina in 22 patients. All hydrogel balloons were initially coated with urokinase by immersing the inflated balloon in a concentrated Abbokinase solution (50,000 units/ml) for 60 s. All patients were subsequently treated with drug-coated balloons using a balloon:artery ratio of 1:1, a mean of 2.2 +/- 1.2 inflations, and a mean total inflation time of 7.5 +/- 4.9 min. Use of urokinase-coated balloons resulted in angiographic disappearance of intracoronary thrombus in 78 patients, improvement in 14, and no change in the remaining 3 patients. Following hydrogel balloon use for the entire 95 patients, TIMI flow increased from 1.4 +/- 1.2 to 2.9 +/- 0.4, minimal lumen diameter increased from 0.4 +/- 0.4 to 2.0 +/- 0.6 mm, and thrombus score decreased from 2.0 +/- 0.9 to 0.2 +/- 0.6 (all P < 0.01). Procedural and early in-hospital complications were noted in 7 of the 95 patients (7.4%) and included abrupt closure in 3 patients, distal embolization in 1 patient, no reflow in 1 patient, sidebranch occlusion in 1 patient, and late closure in 1 patient. Two of the 3 patients with abrupt closure and the single patient with late closure required intracoronary stenting to maintain vessel patency. Two of these 7 patients sustained small myocardial infarctions, although no patient required emergency bypass surgery or experienced a procedural death. Late clinical follow-up (mean = 8.3 +/- 6.6 months; range = 2 wk to 29 mo) demonstrated adverse recurrent events in 29 of the 95 patients (30.5%), including death (n = 5), myocardial infarction (n = 2), and recurrence of angina (n = 22). The results of this study suggest that intracoronary thrombolysis can be safely and rapidly achieved by using limited quantities of urokinase delivered directly to the site of intraluminal clot with hydrogel balloons. Use of this technique may result in improved acute outcomes in comparison with conventional techniques currently being used to treat thrombus-containing stenoses.
Structural and Functional Roles of the Surface-Exposed Loops of the β-Barrel Membrane Protein OmpA from Escherichia coli (1999)

The N-terminal domain of the OmpA protein from Escherichia coli, consisting of 170 amino acid residues, is embedded in the outer membrane, in the form of an antiparallel beta-barrel whose eight transmembrane beta-strands are connected by three short periplasmic turns and four relatively large surface-exposed hydrophilic loops. This protein domain serves as a paradigm for the study of membrane assembly of integral beta-structured membrane proteins. In order to dissect the structural and functional roles of the surface-exposed loops, they were shortened separately and in all possible combinations. All 16 loop deletion mutants assembled into the outer membrane with high efficiency and adopted the wild-type membrane topology. This systematic approach proves the absence of topogenic signals (e.g., in the form of loop sizes or charge distributions) in these loops. The shortening of surface-exposed loops did not reduce the thermal stability of the protein. However, none of the mutant proteins, with the exception of the variant with the fourth loop shortened, served as a receptor for the OmpA-specific bacteriophage K3. Furthermore, all loops were necessary for the OmpA protein to function in the stabilization of mating aggregates during F conjugation. An OmpA deletion variant with all four loops shortened, consisting of only 135 amino acid residues, constitutes the smallest beta-structured integral membrane protein known to date. These results represent a further step toward the development of artificial outer membrane proteins.
Contrast agents and cerebral hemodynamics (1991)

Contrast-enhanced magnetic resonance imaging of regional cerebral hemodynamics is discussed. Techniques for measuring cerebral blood volume (CBV) have been validated in animal models and have recently been applied to human studies. Factors affecting CBV measurement in pathologic tissue are addressed. Extension of these techniques to the measurement of cerebral blood flow is presented.
New Syntheses of E7389 C14−C35 and Halichondrin C14−C38 Building Blocks: Reductive Cyclization and Oxy-Michael Cyclization Approaches (2009)

Cr-mediated coupling reactions are usually achieved with a slight excess of a given nucleophile. To develop a cost-effective use of this process, two different approaches have been studied. The first approach depends on two consecutive catalytic asymmetric Cr-mediated couplings, with use of coupling partners purposely being of unbalanced molecular size and complexity. The second approach rests on the success in identifying the nucleophile, which allows us to achieve the coupling satisfactorily with a 1:1 molar ratio of the coupling partners. The C23-O bond is stereospecifically constructed via reductive cyclization of the oxonium ion, or oxy-Michael cyclization. Both syntheses have a high overall efficiency: E7389 C14-C35 and halichondrin C14-C38 building blocks have been synthesized from the corresponding C27-C35 and C27-C38 aldehydes, respectively, in high overall yields with an excellent stereoselectivity. Because of operational simplicity, the synthesis outlined herein appears to be well suited for scaling.
347 ARTIFICIAL INSEMINATION OF LACTATING HOLSTEIN COWS WITH SEXED SPERM (2005)

The recommended use of sexed sperm has been limited to heifers. The objective of this field trial was to determine pregnancy rates in lactating dairy cows following artificial insemination of 2 or 10 × 106 sexed or 10 × 106 unsexed frozen/thawed sperm. Sperm were separated into X chromosome-bearing populations at rates of 3000-5000/s, on the basis of DNA content, with a flow cytometer/sperm sorter operating at 40 psi and using 150 mW of laser intensity. Sperm were sorted, collected and cryopreserved in a Tris-based medium. Holstein cows, averaging 2.4 lactations (range: 1-9), were presynchronized with prostaglandin F2± (PGF)2±; (25 mg) i.m. at 40-58 days in milk (DIM) (average, 44 days). A second dose of PGF2± (25 mg) i.m. was administered 14 days later. All cows were screened with ultrasound 14 days later, and those with normal ovarian and uterine status were used for this study. Qualifying cows received 100 µg gonadotropin-releasing hormone (GnRH) i.m. (average, 72 DIM) and 25 mg PGF2± i.m. 7 days later, and then 100 ¼g GnRH i.m. 2 days after the prostaglandin. Cows ( n = 172) were fixed-timed inseminated 16-19 h after the last GnRH treatment, balanced over three sperm insemination treatments, two Holstein bulls, and two inseminators. Both 32-day pregnancy and 60-day fetal sex were determined using ultrasound. Cows carrying fetuses identified as dying at the 32-day ultrasound check were considered not pregnant. Data were subjected to ANOVA. Effects of sperm treatment, bulls, inseminators, and subsequent interactions on pregnancy rate were not significant ( P &amp;gt; 0.05). The 32-day pregnancy rate and 95% confidence interval for 10 × 106 unsexed, 10 × 106 sexed, and 2 × 106 sexed inseminates were 55.6 (42.5-68.6), 43.9 (31.6-57.0), and 40.4% (28.4-53.6), respectively. Additionally, DIM or cow parity did not affect pregnancy rate ( P &amp;gt; 0.05). Fetal death (&amp;lt;32 days) for unsexed inseminates was 5.5% (two pregnancies) compared to 9.5% (four pregnancies) for pooled sexed inseminates ( P &amp;gt; 0.05). There were four confirmed pregnancies of sexed sperm that also aborted between Days 32-60. Fetal sex ratio was significantly altered ( P &amp;lt; 0.05) for sexed (93% female fetuses) compared to unsexed (52% female fetuses) inseminates. Pregnancy rate in these selected lactating cows inseminated with sexed sperm was not significantly lower ( P &amp;gt; 0.05) than that for unsexed sperm. However, these results should be viewed cautiously due to the limited numbers of cows used. Successful use of sexed sperm in dairy cows, which approached an elective waiting period of 80 DIM, was achieved with cows that were selected for reproductive status prior to insemination.
Ischemic Ventricular Tachycardia Presenting as a Narrow Complex Tachycardia (2014)

This report describes a patient presenting with a narrow complex tachycardia in the context of prior myocardial infarction and impaired ventricular function. Electrophysiological studies confirmed ventricular tachycardia and activation and entrainment mapping demonstrated a critical isthmus within an area of scar involving the His-Purkinje system accounting for the narrow QRS morphology. This very rare case shares some similarities with upper septal ventricular tachycardia seen in patients with structurally normal hearts, but to our knowledge has not been seen previously in patients with ischemic heart disease.
Proanthocyanidin-Accumulating Cells in Arabidopsis Testa: Regulation of Differentiation and Role in Seed Development (2003)

Anthocyanidin reductase encoded by the BANYULS (BAN) gene is the core enzyme in proanthocyanidin (PA) biosynthesis. Here, we analyzed the developmental mechanisms that regulate the spatiotemporal expression of BAN in the developing Arabidopsis seed coat. PA-accumulating cells were localized histochemically in the inner integument (seed body and micropyle) and pigment strand (chalaza). BAN promoter activity was detected specifically in these cells. Gain-of-function experiments showed that an 86-bp promoter fragment functioned as an enhancer specific for PA-accumulating cells. Mutations in regulatory genes of PA biosynthesis abolished BAN promoter activity (transparent testa2 [tt2], tt8, and transparent testa glabra1 [ttg1]), modified its spatial pattern (tt1 and tt16), or had no influence (ttg2), thus revealing complex regulatory interactions at several developmental levels. Genetic ablation of PA-accumulating cells targeted by the BAN promoter fused to BARNASE led to the formation of normal plants that produced viable yellow seeds. Importantly, these seeds had no obvious defects in endosperm and embryo development.