gebhart/patrepeval huggingface dataset:
Bioconjugation: Protein Coupling Techniques for the Biomedical Sciences (1998)

Introduction - Applications - Protein Chemistry - Enzymes - Antibodies - Protein-Protein Coupling - Protein-Small Molecule Coupling - Protein-DNA Coupling - Protein-Solid Phase & others - Molecular Biology Approaches - Purification and Characterisation - Stability of Protein Reagents - Manufacturability of Processes - Index
Combined enzymatic modification of stevioside and rebaudioside A (2006)

Cyclodextrin glucanotransferases (CGTases, EC 2.4.1.19) produced by mesophilic, thermophilic, alkaliphilic, and halophilic bacilli were used for transglycosylating stevioside and rebaudiosides A with the use of starch as a donor. CGTases produced by B. stearothermophilus B-5076 B. macerans BIO-4m were the most effective biocatalysts. This method can be successfully used for direct transglycosylation of stevia extract without purification of its individual components.
Cytokine control of parasite-specific anergy in human urinary schistosomiasis. IL-10 modulates lymphocyte reactivity (1996)

Humans chronically infected with schistosomiasis usually have impaired parasite Ag-specific lymphocyte proliferation and IFN-gamma production that may facilitate persistence of the parasite while producing little clinical disease. The mechanisms that contribute to the immunologic hyporesponsiveness in these patients remain undefined. IL-10 has been shown to exert an inhibitory effect on cell-mediated immunity. To determine whether endogenous IL-10 has a role in regulating parasite-specific anergy in schistosomiasis, neutralizing anti-IL-10 added to PBMC from Schistosoma haematobium patients' enhanced adult worm (SWAP)- or egg Ag (SEA)-driven lymphocyte proliferation and/or IFN-gamma production by 2- to >100-fold in 32 of 38 subjects. In contrast, anti-IL-10 failed to significantly augment the mycobacterial Ag, purified protein derivative (PPD)-driven lymphocyte proliferation, or IFN-gamma production in 9 or 10 of 14 individuals, respectively. SWAP or SEA triggered IL-10 release from PBMC of both patients and healthy individuals; however, CD4+ cells were a significant source of IL-10 only in infected subjects. PPD relative to SWAP induced fivefold less IL-10 release by CD4+ cells (p < 0.01). A possible mechanism whereby IL-10 suppressed Ag-specific T cell responses was demonstrated by the ability of SWAP and not PPD to suppress B7 expression on PBMC. Anti-IL-10 completely inhibited the parasite Ag-induced down-regulation of B7 expression. These studies indicate that IL-10 contributes to parasite Ag-induced T cell hyporesponsiveness observed in patients with chronic schistosomiasis hematobia.
Tryptase Inhibitors Block Allergen-Induced Airway and Inflammatory Responses in Allergic Sheep (1995)

Tryptase, a mast cell serine protease, has been implicated in the pathophysiology of allergic asthma, but formal evidence to support this hypothesis has been limited by the lack of specific inhibitors for use in vivo. Therefore, in this study we examined the effects of two inhibitors of tryptase, APC 366 [N-(1-hydroxy-2-naphthoyl)-L-arginyl-L-prolinamide hydrochloride] and BABIM [bis(5-amidino-2-benzimidazolyl)methane] on antigen-induced early and late responses, airway responsiveness as measured by carbachol provocation, microvascular permeability as measured by bronchoalveolar lavage (BAL) albumin concentrations, and tissue eosinophilia from biopsies in allergic sheep. APC 366 and BABIM were administered by aerosol in all experiments. In vehicle control trials, antigen challenge resulted in peak early and late increases in specific lung resistance (SRL) of (mean +/- SE, n = 6) 259 +/- 30% and 183 +/- 27% over baseline, respectively. Treatment with APC 366 (9 mg/3 ml H2O given 0.5 h before, 4 h after, and 24 h after antigen challenge) slightly reduced the peak early response (194 +/- 41%), but significantly inhibited the late response (38 +/- 6%, p < 0.05 versus control trials). Twenty-four hours after challenge, APC 366 also completely blocked the antigen-induced airway hyperresponsiveness to inhaled carbachol observed in the control trial.(ABSTRACT TRUNCATED AT 250 WORDS)
Rapid vacuolar sequestration: the horseweed glyphosate resistance mechanism (2010)

Selective sequestration of glyphosate into the vacuole confers the observed horseweed resistance to glyphosate. This observation represents the first clear evidence for the glyphosate resistance mechanism in C. canadensis.
The structure and signalling functions of the invariant T cell receptor components. (1990)

The T cell antigen receptor (TCR) is a multisubunit surface molecule on T cells which recognizes foreign antigens. In addition to the clone-specific alpha beta or gamma delta heterodimer antigen recognition element, each TCR has five invariant chains--the CD3-gamma, -delta, and -epsilon chains and a zeta zeta or zeta eta disulfide dimer. Receptor assembly and surface expression requires the presence of all chains except eta. Targetting of partial complexes, however, is determined differently by specific chains with the zeta chain in murine T cells providing safe transport of assembled pentamers from the Golgi complex to the cell surface. TCR signalling involves activation of two kinase pathways--protein kinase C and a non-receptor protein tyrosine kinase. zeta eta-containing TCRs couple preferentially to the PKC pathway by mediating phosphoinositide hydrolysis. We have evidence that the activated protein tyrosine kinase may be fyn, a member of the src family. While specific signalling roles for all invariant chains are not yet defined, we have implicated the zeta chain as uniquely coupling TCR antigen engagement to distal IL-2 signalling, perhaps via activation of the tyrosine kinase pathway.
Detection and Analysis of Interferon-α Receptors on Plasma Membranes and in Detergent Extracts (1990)

The binding of interferons-alpha (IFN-alpha) to various cells is well characterized, but fewer studies have reported on the interaction of IFN-alpha with receptors on plasma membranes or in detergent-solubilized form. We describe a simple, sensitive, and semiquantitative assay procedure to detect the presence of IFN-alpha receptors on bovine spleen plasma membrane preparations or in detergent-solubilized extracts. The procedure involves spotting the sample on hydrophobic polyvinylidene difluoride (PVDF; Immobilon P) membranes, blocking the filter with milk, and binding radiolabeled IFN-alpha A to the membrane filter, with detection by either autoradiography or scintillation counting. This assay procedure has been applied for the identification of IFN-alpha receptors in crude and affinity-purified fractions. The partially purified IFN-alpha receptors have been further characterized by SDS-polyacrylamide gel electrophoresis (PAGE). The separated IFN-alpha receptor protein on the SDS-PAGE gel has been electrophoretically transferred to Immobilon membrane and visualized by ligand blotting. This provides an estimate of 95-110 kD for the apparent molecular weight and a tool for further studies of the receptor protein.
CDw50 and ICAM‐3: Two names for the same molecule (1993)

CDw50 differentiation antigen is a molecule broadly expressed on hematopoetic cells but not on other cells. Previous experiments showed that CDw50 monoclonal antibodies (mAb) inhibited primary mixed lymphocyte culture (MLC). To understand the function of CDw50 better, we purified it and obtained peptide sequence. At the same time, intercellular adhesion molecule (ICAM)-3, the third ligand of lymphocyte function-associated molecule 1, was described by mAb and subsequent cDNA cloning. Immunochemical, functional, and protein sequencing studies show that ICAM-3 and CDw50 are the same glycoprotein, a 120-kDa surface molecule with presumably an important role in the immune responses.
Ectopic Pregnancy-Derived Human Trophoblastic Stem Cells Regenerate Dopaminergic Nigrostriatal Pathway to Treat Parkinsonian Rats (2012)

We successfully isolated and characterized the unique ectopic pregnancy-derived hTS cells. hTS cells are pluripotent stem cells that can be efficiently induced to tNSCs with positive results in PD rat models. Our data suggest that the hTS cell is a dynamic stem cell platform that is potentially suitable for use in disease models, drug discovery, and cell therapy such as PD.
Forskolin, a hedgehog signalling inhibitor, attenuates carbon tetrachloride‐induced liver fibrosis in rats (2016)

In our model, forskolin exerted promising antifibrotic effects which could be partly attributed to its antioxidant and anti-inflammatory effects, as well as to its inhibition of Hh signalling, mediated by cAMP-dependent activation of PKA.
Studies on the syntheses of N-heterocyclic compounds. XXVI. Syntheses of pyrido(3,4-d)pyridazine derivatives. III. (1975)

A new synthetic route to 1, 4-dimorpholino-7-phenylpyrido [3, 4-d] pyridazine (1), a potent diuretic, has been investigated. Chlorination and the subsequent dechlorination by catalytic hydrogenation of ethyl 3-cyano-2-oxo-6-phenyl-4 (1H)-pyridinecarboxylate (2) gave ethyl 3-cyano-6-phenyl-4-pyridinecarboxylate (6), which was also obtained by desulfurization of ethyl 3-cyano-6-phenyl-2-thioxo-4 (1H)-pyridinecarboxylate (3). 6 was led to 7-phenylpyrido [3, 4-d] pyridazine-1, 4 (2H, 3H)-dione (12), a key intermediate in the synthesis of 1, by way of cyclic imide (10) or anhydride (11). Several homologs of 1 could also be prepared by employing these procedures. Reactivity of the three chloro groups in 1, 4, 5-trichloro-7-phenylpyrido [3, 4-d] pyridazine (18) towards nucleophilic substitution with morpholine is discussed.
Isolation, Synthesis, and Antiplatelet Aggregation Activity of Resveratrol 3-O-β-d-Glucopyranoside and Related Compounds (1997)

Resveratrol 3-O-beta-D-glucopyranoside (1) has been isolated from the seeds of Erythrophleum lasianthum (Caesalpinioidae, Leguminosae), a South African plant used in traditional medicine, and has shown antiplatelet aggregation activity. The synthesis of 1, related hydroxystilbenes, and their glucosides has been undertaken to provide larger quantities, for further biological evaluation, and has been accomplished via Wittig reactions followed by glucosylation under phase transfer catalysis.
End-Cretaceous Brachiopod Extinctions in the Chalk of Denmark (1984)

The results of a detailed study of the brachiopods of the most complete Cretaceous-Tertiary boundary in Denmark, Nye Klslashed circlev, show an extinction pattern for this marine invertebrate group compatible with that reported for pelagic foraminifera and coccoliths and with the impact scenario. The extinction is abrupt, coinciding with the Maastrichtian-Danian boundary. There is no warning in the form of decreasing density, decreasing diversity, or early extinction of specialized groups. The basal few meters of the Danian are almost devoid of brachiopods, and a Danian brachiopod fauna starts almost as abruptly as the Maastrichtian fauna disappeared. The new fauna is similar to the Maastrichtian as regards density and diversity, and at maximum six species are common to both stages. The northwest European Masstrichtian chalk is composed mainly of the remains of coccoliths and pelagic foraminifera. The mass extinction of these groups led to a total cessation of chalk production. The chalk is overlain by a thin clay bed deposited partly under anoxic conditions. This combination of anoxia and clay deposition coupled with a cessation of productivity led to the extinction of specialized groups such as the chalk brachiopods. The surviving species included forms that could survive in well-aerated shallow marine waters on substrates other than chalk.
LRP in Alzheimer’s disease: friend or foe? (2000)

Alzheimer's disease (AD) is a neurodegenerative disorder and the leading cause of senile dementia. The brains of AD patients show two major pathological hallmarks: amyloid or senile plaques (SPs) and neurofibrillary tangles (NFTs). While NFTs are bundles of protein filaments found in the cytoplasm of neurons, SPs are extracellular aggregates of insoluble protein fibrils. The major component of SPs is a small, hydrophobic peptide termed amyloid peptide (A), which is derived from a ubiquitous type I transmembrane protein of unknown function named amyloid precursor protein (APP) (1).
Cellular senescence and protein degradation (2014)

Autophagy and the ubiquitin-proteasome pathway (UPP) are the major protein degradation systems in eukaryotic cells. Whereas the former mediate a bulk nonspecific degradation, the UPP allows a rapid degradation of specific proteins. Both systems have been shown to play a role in tumorigenesis, and the interest in developing therapeutic agents inhibiting protein degradation is steadily growing. However, emerging data point to a critical role for autophagy in cellular senescence, an established tumor suppressor mechanism. Recently, a selective protein degradation process mediated by the UPP was also shown to contribute to the senescence phenotype. This process is tightly regulated by E3 ubiquitin ligases, deubiquitinases, and several post-translational modifications of target proteins. Illustrating the complexity of UPP, more than 600 human genes have been shown to encode E3 ubiquitin ligases, a number which exceeds that of the protein kinases. Nevertheless, our knowledge of proteasome-dependent protein degradation as a regulated process in cellular contexts such as cancer and senescence remains very limited. Here we discuss the implications of protein degradation in senescence and attempt to relate this function to the protein degradation pattern observed in cancer cells.
Angiotensin-converting Enzyme Inhibitors, Inhibition of Brain and Peripheral Angiotensin-converting Enzymes, and Left Ventricular Dysfunction in Rats After Myocardial Infarction (2008)

Despite marked differences in the extent of peripheral blockade, all three treatments similarly affected sympathetic activity and decreased cardiac Ang II, preload and remodeling after MI. One may speculate that central and peripheral ACE-mediated mechanisms are sequential and therefore only minor additional effects of peripheral ACE blockade are noted.
Molecular targets of oxidative stress (2011)

Aerobic life requires organisms to resist the damaging effects of ROS (reactive oxygen species), particularly during stress. Extensive research has established a detailed picture of how cells respond to oxidative stress. Attention is now focusing on identifying the key molecular targets of ROS, which cause killing when resistance is overwhelmed. Experimental criteria used to establish such targets have differing merits. Depending on the nature of the stress, ROS cause loss of essential cellular functions or gain of toxic functions. Essential targets on which life pivots during ROS stress include membrane lipid integrity and activity of ROS-susceptible proteins, including proteins required for faithful translation of mRNA. Protein oxidation also triggers accumulation of toxic protein aggregates or induction of apoptotic cell death. This burgeoning understanding of the principal ROS targets will offer new possibilities for therapy of ROS related diseases.
Coronary Vessel Wall Contrast Enhancement Imaging as a Potential Direct Marker of Coronary Involvement (2014)

We demonstrate that quantification of coronary CE by CNR and total CE area is feasible for detection of subclinical and clinical uptake of gadolinium within the coronary vessel wall. Coronary vessel wall CE may become an instrumental novel direct marker of vessel wall injury and remodeling in subpopulations at risk.
Partitioned instruction cache architecture for energy efficiency (2003)

The demand for high-performance architectures and powerful battery-operated mobile devices has accentuated the need for low-power systems. In many media and embedded applications, the memory system can consume more than 50% of the overall system energy, making it a ripe candidate for optimization. To address this increasingly important problem, this article studies energy-efficient cache architectures in the memory hierarchy that can have a significant impact on the overall system energy consumption.Existing cache optimization approaches have looked at partitioning the caches at the circuit level and enabling/disabling these cache partitions (subbanks) at the architectural level for both performance and energy. In contrast, this article focuses on partitioning the cache resources architecturally for energy and energy-delay optimizations. Specifically, we investigate ways of splitting the cache into several smaller units, each of which is a cache by itself (called a subcache ). Subcache architectures not only reduce the per-access energy costs, but can potentially improve the locality behavior as well.The proposed subcache architecture employs a page-based placement strategy, a dynamic page remapping policy, and a subcache prediction policy in order to improve the memory system energy behavior, especially on-chip cache energy. Using applications from the SPECjvm98 and SPEC CPU2000 benchmarks, the proposed subcache architecture is shown to be very effective in improving both the energy and energy-delay metrics. It is more beneficial in larger caches as well.
Epitope mapping with a recombinant human 68-kDa (U1) ribonucleoprotein antigen reveals heterogeneous autoantibody profiles in human autoimmune sera. (1988)

Several cDNA fragments encoding parts of the (U1)RNP specific 68-kDa autoantigen were expressed in Escherichia coli and the fusion proteins were used as substrate for localization of the autoreactive epitopes. We have identified a region of approximately 30 amino acids reacting with more than 90% (16 of 17) of all human anti-p68 sera tested, regions which carry only a few and a region with no autoepitopes. Comparative analysis of epitopes recognized on partially degraded fusion proteins indicated that the anti-p68 autoimmune response is polyclonal. It involves generation of antibodies to several epitopes including one in a region with retroviral gag protein homology speculated to play a role in the initiation of the autoimmune response. Each of the 17 sera tested contained a different set of autoantibody specificities. These data are not consistent with random mutation as a sole mechanism of anti-p68 autoantibody induction and argue for an Ag-driven autoimmune response.
A robust and efficient cobalt molecular catalyst for CO2 reduction (2015)

Visible-light driven CO2 reduction is considered to be a sustainable energy source. However, earth-abundant molecular catalysts with high efficiency and robustness towards solar-driven CO2 reduction are limited. Herein, we report a cobalt complex supported by a tetradentate tripodal ligand, which demonstrates catalytic solar-driven CO2 reduction with TON(CO) > 900 over 70 h in the presence of a photosensitizer.
Autonomous expression of a noncatalytic domain of the focal adhesion-associated protein tyrosine kinase pp125FAK. (1993)

Integrins play a central role in cellular adhesion and anchorage of the cytoskeleton and participate in the generation of intracellular signals, including tyrosine phosphorylation. We have recently isolated a cDNA encoding a unique, focal adhesion-associated protein tyrosine kinase (FAK) that is a component of an integrin-mediated signal transduction pathway. Here we report the isolation of cDNAs encoding the C-terminal, noncatalytic domain of the FAK kinase, termed FRNK (FAK-related nonkinase). Both the FAK- and FRNK-encoded polypeptides, pp125FAK and p41/p43FRNK, are expressed in normal chicken embryo cells. pp125FAK and p41/p43FRNK were localized to focal adhesions, suggesting that pp125FAK is directed to the focal adhesions by sequences within its C-terminal domain. We also show that the fibronectin-dependent increase in tyrosine phosphorylation of pp125FAK is accompanied by a concomitant posttranslational modification of p41FRNK.
Endothelium-derived contracting factors. (1992)

The endothelium not only mediates relaxation but is a source of contracting factors. Endothelium-dependent contractions are elicited by physical and chemical stimuli (i.e., hypoxia, pressure, and stretch) and autacoids, local and circulating hormones. The mechanism of endothelium-dependent contractions to hypoxia involves withdrawal of nitric oxide. The endothelial cyclooxygenase pathway can produce thromboxane A2, prostaglandin H2, and superoxide anions. The peptide endothelin is a potent contracting factor; its production is stimulated by vasopressor hormones, platelet-derived factors, coagulation products, and cytokines, whereas endothelium-derived nitric oxide, prostacyclin, and a smooth muscle cell-derived inhibitory factor reduce endothelin production. In hypertension, the release of cyclooxygenase-dependent endothelium-derived contracting factors to stretch, acetylcholine, and platelet-derived products is augmented. Vascular endothelin production in hypertension remains controversial but appears mostly normal; it is augmented in the presence of vascular disease or renal insufficiency. The endothelium-dependent inhibition of endothelin-induced contractions is reduced in hypertension while the reactivity of vascular smooth muscle may be normal, increased, or reduced. The potentiating effects of low concentrations of endothelin on contractions to norepinephrine are augmented with aging and hypertension. In atherosclerosis, the production of the cyclooxygenase-dependent endothelium-derived contracting factors and endothelin is enhanced. Thus, endothelium-derived contracting factors can profoundly affect vascular tone and counteract relaxing factors produced within the endothelium. In hypertension and atherosclerosis, the role of contracting factors appears to become more dominant, leading to an imbalance of endothelium-dependent vascular regulation.
A cylindrical-section ultrasound phased-array applicator for hyperthermia cancer therapy (1988)

A phased-array applicator geometry for deep localized hyperthermia is presented. The array consists of rectangular transducer elements forming a section of a cylinder that conforms to the body portals in the abdominal and pelvic regions. Focusing and scanning properties of the cylindrical-section array are investigated in homogeneous lossy media using appropriate computer simulations. The characteristic focus of this array is shown to be spatially limited in both transverse and longitudinal directions with intensity gain values suitable for deep hyperthermia applications. The ability of the cylindrical-section phased array to generate multiple foci using the field conjugation method is examined. The effect of the grating lobes on the power deposition pattern of the scanned field is shown to be minimal. Steady-state temperature distributions are simulated using a three-dimensional thermal model of the normal tissue layers surrounding a tumor of typical volume. The advantages and the limitations of this array configuration are discussed.
Suppression of Magnetic Flux Trapping by Moats formed in NbN Ground Planes (2010)

We have investigated the effect of moats in NbN ground planes on magnetic flux trapping by using series arrays of 1000 Josephson junctions fabricated on Nb and NbN ground planes. The junctions on the NbN ground plane exhibited no trapping for external magnetic fields in the range of -2.2 to 1.2 µT, which was twice the range over which no flux trapping occurred for junctions on the Nb ground plane. This advantage of the NbN ground plane can be explained using a Bean–Livingston model with a longer penetration depth and higher critical temperature of NbN than those of Nb.