gebhart/patrepeval huggingface dataset:
Assembly of tau in transgenic animals expressing P301L tau: alteration of phosphorylation and solubility (2002)

Transgenic mice (JNPL3), which develop neurofibrillary degeneration and express four-repeat human tau with P301L missense mutation, were characterized biochemically to determine whether the development of aggregated tau from soluble tau involves an intermediate stage. Homogenates from mice of different ages were separated into buffer-soluble (S1), sarkosyl- and salt-extractable (S2) and sarkosyl-insoluble pellet (P3) fractions, and analyzed for human tau distribution, phosphorylation and filament formation. S1 and S2 fractions contained 50-60-kDa tau whereas the S2 fraction also had 64-kDa tau. The level of tau in the P3 fraction increased in an age-dependent manner and correlated positively with the soluble tau concentration. The P3 fraction from 2.5-6.5-month-old mice contained 64- and 50-60-kDa tau, whereas that from 8.5-month and older transgenic animals contained mostly 64-kDa and higher molecular weight tau. The S2 and P3 fractions contained comparable amounts of 64-kDa tau. The 64-kDa tau was predominantly human, and phosphorylated at multiple sites: Thr181, Ser202/Thr205, Thr212, Thr231, Ser262, Ser396/Ser404, Ser409 and Ser422. Most of these sites were phosphorylated to a lesser extent in S2 than in P3 fractions. Tau polymers were detected in P3 fractions from 3-month and older female JNPL3 mice, but not in non-transgenic controls. The results suggest that tau in S2 represents an intermediate from which insoluble tau is derived, and that phosphorylation may play a role in filament formation and/or stabilization.
Nuclear localization signals (NLS). (1993)

Available data strongly suggest that simple karyophilic clusters of arginines and lysines in nucleus-targeted proteins signal the anchoring of these proteins to specialized transporter molecules found on the pore complex or in the cytoplasm. These peptides have been termed nuclear localization signals (NLS). Other nuclear proteins contain "split" or "bipartite" NLS hypothesized to be reconstituted by protein folding or conformational change induced by glucocorticoids. The active NLS needs to be exposed to the protein surface, the cell has invented mechanisms to expose a hidden or cryptic NLS by protein phosphorylation, dephosphorylation, dissociation of an inhibitory subunit that masks the NLS, processing of a larger precursor, and binding of a hormone to regulate the nuclear import of a protein transcription factor at a certain stage of development, or cell cycle. It is proposed (1) that a hexapeptide with four arginines and lysines (and histidines, in some cases) is a good candidate for a "core NLS," (2) that acidic domains on proteins to be imported may participate in anchoring them to the transporter cytoplasmic or pore complex NLS-receptor, and (3) that NLS have both a cytoplasmic and a nuclear function. The interaction between nuclear proteins and transporter proteins in the pore appears to be largely electrostatic and to be disrupted by the binding of mRNA molecules to the same transporter protein, functioning also for the cytoplasmic export of RNA.
Mutation of Y407 in the CH3 domain dramatically alters glycosylation and structure of human IgG (2013)

Antibody engineering is increasingly being used to influence the properties of monoclonal antibodies to improve their biotherapeutic potential. One important aspect of this is the modulation of glycosylation as a strategy to improve efficacy. Here, we describe mutations of Y407 in the CH3 domain of IgG1 and IgG4 that significantly increase sialylation, galactosylation, and branching of the N-linked glycans in the CH2 domain. These mutations also promote the formation of monomeric assemblies (one heavy-light chain pair). Hydrogen-deuterium exchange mass spectrometry was used to probe conformational changes in IgG1-Y407E, revealing, as expected, a more exposed CH3-CH3 dimerization interface. Additionally, allosteric structural effects in the CH2 domain and in the CH2-CH3 interface were identified, providing a possible explanation for the dramatic change in glycosylation. Thus, the mutation of Y407 in the CH3 domain remarkably affects both antibody conformation and glycosylation, which not only alters our understanding of antibody structure, but also reveals possibilities for obtaining recombinant IgG with glycosylation tailored for clinical applications.
Primary structure, physicochemical properties, and chemical modification of NAD(+)-dependent D-lactate dehydrogenase. Evidence for the presence of Arg-235, His-303, Tyr-101, and Trp-19 at or near the active site. (1992)

The NAD(+)-dependent D-lactate dehydrogenase was purified to apparent homogeneity from Lactobacillus bulgaricus and its complete amino acid sequence determined. Two gaps in the polypeptide chain (10 residues) were filled by the deduced amino acid sequence of the polymerase chain reaction amplified D-lactate dehydrogenase gene sequence. The enzyme is a dimer of identical subunits (specific activity 2800 +/- 100 units/min at 25 degrees C). Each subunit contains 332 amino acid residues; the calculated subunit M(r) being 36,831. Isoelectric focusing showed at least four protein bands between pH 4.0 and 4.7; the subunit M(r) of each subform is 36,000. The pH dependence of the kinetic parameters, Km, Vm, and kcat/Km, suggested an enzymic residue with a pKa value of about 7 to be involved in substrate binding as well as in the catalytic mechanism. Treatment of the enzyme with group-specific reagents 2,3-butanedione, diethylpyrocarbonate, tetranitromethane, or N-bromosuccinimide resulted in complete loss of enzyme activity. In each case, inactivation followed pseudo first-order kinetics. Inclusion of pyruvate and/or NADH reduced the inactivation rates manyfold, indicating the presence of arginine, histidine, tyrosine, and tryptophan residues at or near the active site. Spectral properties of chemically modified enzymes and analysis of kinetics of inactivation showed that the loss of enzyme activity was due to modification of a single arginine, histidine, tryptophan, or tyrosine residue. Peptide mapping in conjunction with peptide purification and amino acid sequence determination showed that Arg-235, His-303, Tyr-101, and Trp-19 were the sites of chemical modification. Arg-235 and His-303 are involved in the binding of 2-oxo acid substrate whereas other residues are involved in binding of the cofactor.
Frequency offset and symbol timing recovery in flat-fading channels: a cyclostationary approach (1998)

Two open-loop algorithms are developed for estimating jointly frequency offset and symbol timing of a linearly modulated waveform transmitted through a frequency-flat fading channel. The methods exploit the received signal's second-order cyclostationarity and, with respect to existing solutions: (1) they take into account the presence of time-selective fading effects; (2) they do not need training data; (3) they do not rely on the Gaussian assumption of the complex equivalent low-pass channel process; and (4) they are tolerant to additive stationary noise of any color or distribution. Performance analysis of the proposed methods using Monte Carlo simulations, unifications, and comparisons with existing approaches are also reported.
Structure and Functionality of Barley Starches (1998)

ABSTRACT Amylose contents of prime starches from nonwaxy and high‐amylose barley, determined by colorimetric method, were 24.6 and 48.7%, respectively, whereas waxy starch contained only a trace (0.04%) of amylose. There was little difference in isoamylase‐debranched amylopectin between nonwaxy and high‐amylose barley, whereas amylopectin from waxy barley had a significantly higher percentage of fraction with degree of polymerization &lt; 15 (45%). The X‐ray diffraction pattern of waxy starch differed from nonwaxy and high‐amylose starches. Waxy starch had sharper peaks at 0.58, 0.51, 0.49, and 0.38 nm than nonwaxy and high‐amylose starches. The d ‐spacing at 0.44 nm, characterizing the amylose‐lipids complex, was most evident for high‐amylose starch and was not observed in waxy starch. Differential scanning calorimetry (DSC) thermograms of prime starch from nonwaxy and high‐amylose barley exhibited two prominent transition peaks: the first was &gt;60°C and corresponded to starch gelatinization; the second was &gt;100°C and corresponded to the amylose‐lipid complex. Starch from waxy barley had only one endothermic gelatinization peak of amylopectin with an enthalpy value of 16.0 J/g. The retrogradation of gelatinized starch of three types of barley stored at 4°C showed that amylopectin recrystallization rates of nonwaxy and high‐amylose barley were comparable when recrystallization enthalpy was calculated based on the percentage of amylopectin. No amylopectin recrystallization peak was observed in waxy barley. Storage time had a strong influence on recrystallization of amylopectin. The enthalpy value for nonwaxy barley increased from 1.93 J/g after 24 hr of storage to 3.74 J/g after 120 hr. When gel was rescanned every 24 hr, a significant decrease in enthalpy was recorded. A highly statistically significant correlation ( r = 0.991) between DSC values of retrograded starch of nonwaxy barley and gel hardness was obtained. The correlation between starch enthalpy value and gel hardness of starch concentrate indicates that gel texture is due mainly to its starch structure and functionality. The relationship between the properties of starch and starch concentrate may favor the application of barley starch concentrate without the necessity of using the wet fractionation process.
Introduction: The conservative revolutionaries (2016)

Abstract The introduction sets the scene and argument of the book. It begins by describing how the Irish people in 2011 elected a government of Fine Gael and Labour who themselves had presided over a severe recession in the 1980s leading to their rejection by the people in the 1987 general election. It shows how decision made by Irish politicians and voters alike resulted in the boom to bust scenario that characterised Irish politics since 1987. In that context the introduction sets out how this is a book which seeks to explain how political agency and clientelist relationships in modern Ireland have shaped political competition within the Irish state
A molecularly-imprinted electrochemical sensor based on a graphene–Prussian blue composite-modified glassy carbon electrode for the detection of butylated hydroxyanisole in foodstuffs (2013)

In this study, we developed a novel molecularly-imprinted electrochemical sensor based on a glassy carbon electrode (GCE) decorated by graphene-Prussian blue (GR-PB) composites for the selective and sensitive determination of butylated hydroxyanisole (BHA). The molecularly-imprinted polymers (MIPs) were synthesized by BHA and pyrrole as the template molecule and functional monomer, respectively. Also, the MIPs were assembled on the surface of the GR-PB/GCE by electropolymerization. The sensor was characterized by cyclic voltammetry (CV), scanning electron microscopy (SEM), electrochemical impedance spectroscopy (EIS) and chronoamperometry. It was confirmed that the synergistic effects of GR and PB could improve the electrochemical response and the sensitivity of the sensor. The linear range of the sensor was from 9 × 10(-8) mol L(-1) to 7 × 10(-5) mol L(-1), with a limit of detection (LOD) of 7.63 × 10(-8) mol L(-1) (S/N = 3). The proposed sensor displayed high selectivity, excellent stability and good reproducibility for the determination of BHA. It was successfully applied to the determination of BHA in real samples.
Clinical Monitoring During Carbamazepine Slow‐Release, Once‐Daily Monotherapy (1988)

Forty-eight patients with complex partial and/or tonic-clonic seizures were treated with an 8 p.m. single dose of carbamazepine slow release (CBZ-SR) monotherapy. The steady-state serum level profiles of carbamazepine (CBZ) and its metabolites CBZ-10,11-epoxide (CBZE) and 10,11-dihydro-CBZ-10,11-diole (CBZD) during 24 h in 21 of 48 patients treated with daily single doses of 8.4 (+/- 2.4) mg/kg body weight CBZ-SR were determined by a high-performance liquid chromatography procedure. The 8 a.m. CBZ levels correlated very well with the mean CBZ levels of the 24-h profile. Unlike CBZD, the individual 24-h mean CBZE levels also correlated well with the respective CBZ levels (CBZE = 14.2% +/- 2.9 of CBZ). Increasing CBZ-SR doses does not result in a proportional increase of CBZ levels. Clinical efficacy of changing from CBZ standard tablets under mono- or combination therapy or from therapy with other antiepileptic drugs to once-daily evening CBZ-SR monotherapy or commencement CBZ-SR therapy in previously untreated patients was monitored in 35 of 48 patients for a period of 8 months to 2 years. Complete seizure control was observed in 51% of patients and more than 75% reduction of seizure frequency in 14%. Eight of 11 previously untreated patients became seizure free. With change from CBZ monotherapy to CBZ-SR single-dose therapy, five of six patients became seizure free. Changing from other therapeutic regimens to CBZ-SR once-daily evening monotherapy was less successful.
High Resolution Dissection of Reactive Glial Nets in Alzheimer’s Disease (2016)

Fixed human brain samples in tissue repositories hold great potential for unlocking complexities of the brain and its alteration with disease. However, current methodology for simultaneously resolving complex three-dimensional (3D) cellular anatomy and organization, as well as, intricate details of human brain cells in tissue has been limited due to weak labeling characteristics of the tissue and high background levels. To expose the potential of these samples, we developed a method to overcome these major limitations. This approach offers an unprecedented view of cytoarchitecture and subcellular detail of human brain cells, from cellular networks to individual synapses. Applying the method to AD samples, we expose complex features of microglial cells and astrocytes in the disease. Through this methodology, we show that these cells form specialized 3D structures in AD that we refer to as reactive glial nets (RGNs). RGNs are areas of concentrated neuronal injury, inflammation, and tauopathy and display unique features around β-amyloid plaque types. RGNs have conserved properties in an AD mouse model and display a developmental pattern coinciding with the progressive accumulation of neuropathology. The method provided here will help reveal novel features of the healthy and diseased human brain, and aid experimental design in translational brain research.
Elastin-derived peptides enhance angiogenesis by promoting endothelial cell migration and tubulogenesis through upregulation of MT1-MMP (2005)

Elastin-derived peptides display a wide range of biological activities in a number of normal and transformed cells but their involvement in angiogenesis has not been reported. In the present study, we show that kappa-elastin and VGVAPG hexapeptide elastin motif accelerated angiogenesis in the chick chorio-allantoic membrane in an in vivo model. They also stimulated pseudotube formation from human vascular and microvascular endothelial cells in the matrigel and collagen models as well as cell migration in an in vitro wound healing assay. Confocal and scanning electron microscopy analyses revealed the main reorganization of actin filaments mediated by elastin-derived peptides and changes in cell shape that correlated with a decrease of the cell form factor determined by computerized image analysis. Such elastin-derived peptide effects were attributed to upregulation of proMT1-MMP and proMMP-2 expression and activation at both the mRNA and protein levels. Batimastat, an inhibitor of furin convertase and TIMP-2, but not TIMP-1, totally abolished the influence of elastin-derived peptides (EDPs) on cell migration and tubulogenesis, thus favoring the involvement of MT1-MMP in such processes. To assess its contribution to EDP-mediated angiogenesis further, we used a small interfering RNA (siRNA) approach for specifically silencing MT1-MMP in human microvascular endothelial cells. Four sets of 21 bp siRNA duplexes targeting MT1-MMP mRNA were synthesized by in vitro transcription. Two of them proved to inhibit MT1-MMP expression efficiently but did not affect MT2-, MT3- and MT5-MMP expression. Seventy-two hours after transfection with 25 nM siRNAs EDP-induced MT1-MMP expression at the mRNA and protein levels was decreased fourfold. In parallel, proMMP-2 activation was inhibited. A scrambled siRNA, used as a negative control, had no effect. Finally, the effect of elastin peptides on pseudotube formation in MT1-MMP-siRNA transfected cells was totally abolished. These data emphasise the crucial role of MT1-MMP in the elastin-induced angiogenic phenotype of endothelial cells.
Expression of mRNAs for collagens and other matrix components in dedifferentiating and redifferentiating human chondrocytes in culture (1989)

Cell cultures were initiated from epiphyseal cartilages, diaphyseal periosteum, and muscle of 16-week human fetuses. Total RNAs isolated from these cultures were analyzed for the levels of mRNAs for major fibrillar collagens, two proteoglycan core proteins and osteonectin. In standard monolayer cultures the differentiated chondrocyte phenotype was replaced by a dedifferentiated one: the mRNA levels of cartilage-specific type II collagen decreased upon subculturing, while those of types I and III collagen, and the core proteins increased. When the cells were transferred to grow in agarose, redifferentiation (reappearance of type II collagen mRNA) occurred. Fibroblasts grown from periosteum and muscle were found to contain mRNAs for types I and III collagen and proteoglycan cores. When these cells were transferred to agarose they acquired a shape indistinguishable from chondrocytes, but no type II collagen mRNA was observed.
Isolation of Human Oncogene Sequences (v- fes Homolog) from a Cosmid Library (1982)

To define the human homolog (or homologs) of transforming sequences (v-fes gene) common to Gardner (GA) and Snyder Theilen (ST) isolates of feline sarcoma virus (FeSV), a representative library of human lung carcinoma DNA in a cosmid vector system was constructed. Three cosmid clones were isolated containing GA/ST FeSV v-fes homologous cellular sequences, within 32- to 42-kilobase cellular inserts representing 56 kilobases of contiguous human cellular DNA. Sequences both homologous to, and colinear with, GA or ST FeSV v-fes are distributed discontinuously over a region of up to 9.5 kilobases and contain a minimum of three regions of nonhomology representing probable introns. A thymidine kinase selection system was used to show that, upon transfection to RAT-2 cells, the human c-fes sequence lacked detectable transforming activity.
A20 zinc finger protein inhibits TNF and IL-1 signaling (1996)

A20 zinc finger protein is a product of a cytokine-induced primary response gene. In this report, we demonstrate that A20 specifically inhibits signal transduction pathways induced by TNF and IL-1, suggesting that it functions as a negative regulator of the cytokine response. Overexpression of A20 in MCF7 breast carcinoma cells or in WEHI-S fibrosarcoma cells inhibits apoptosis induced by TNF, whereas cytotoxicity induced by anti-Fas (anti-CD95); lymphokine-activated killer (LAK) cells, serum starvation, oxidative stress, or okadaic acid is not inhibited. Overexpression of A20 also inhibits TNF-induced activation of phospholipase A2 in a similar dose-dependent manner as it inhibits TNF-mediated apoptosis, whereas it does not affect the activation of phospholipase A2 by anti-Fas. Interestingly, A20 also blocks TNF-induced signal transduction pathways not directly related to the cytotoxicity, namely activation of NF-kappa B and AP-1 transcription factors. Activation of these transcription factors by a functionally related cytokine, IL-1, is also inhibited by A20, whereas activation induced by hydrogen peroxide or phorbol ester is unaffected. Overexpression of A20 does not affect the binding of TNF to its cell surface receptors. These data suggest that A20 functions as a negative regulator of TNF and IL-1, interfering with signal transduction pathways at an early point following receptor binding but before the activation of various second messengers, leading to the wide variety of effects induced by these cytokines.
The sulfate activation locus of Escherichia coli K12: cloning, genetic, and enzymatic characterization. (1988)

The sulfate activation locus of Escherichia coli K12 has been cloned by complementation. The genes and gene products of this locus have been characterized by correlating the enzyme activity, complementation patterns, and polypeptides associated with subclones of the cloned DNA. The enzymes of the sulfate activation pathway, ATP sulfurylase (ATP:sulfate adenylyltransferase, EC 2.7.7.4) and APS kinase (ATP:adenosine-5'-phosphosulfate 3'-phosphotransferase, EC 2.7.1.25) have been overproduced approximately 100-fold. Overproduction of ATP sulfurylase requires the expression of both the cysD gene, encoding a 27-kDa polypeptide, and a previously unidentified gene, denoted cysN, which encodes a 62-kDa polypeptide. Purification of ATP sulfurylase to homogeneity reveals that the enzyme is composed of two types of subunits which are encoded by cysD and cysN. Insertion of a kanamycin resistance gene into plasmid or chromosomal cysN prevents sulfate activation and decreases expression of the downstream cysC gene. cysC appears to be the APS kinase structural gene and encodes a 21-kDa polypeptide. The genes are adjacent and are transcribed counterclockwise on the E. coli chromosome in the order cysDNC. cysN and cysC are within the same operon and cysDNC are not in an operon containing cysHIJ.
Spiderplots versus Tornado Diagrams for Sensitivity Analysis (1992)

Sensitivity analysis, supported by computer hardware and software, can easily overwhelm an analyst or decision maker with data. However, this data can be organized in a readily understandable way using well-designed graphs. Two graphical techniques, spiderplots and tornado diagrams, are commonly used respectively by engineering economists and decision analysts. Their advantages are complementary. Management scientists should often use both to convey their results to decision makers succinctly and clearly. The simpler tornado diagram can summarize the total impact of many independent variables. An individual spiderplot displays more information about a smaller number of variables. This includes the limits for each independent variable, the impact of each on the dependent outcome, and the amount of change required to reach a break-even point.