gebhart/patrepeval huggingface dataset:
Biosynthesis of a protein containing a nonprotein amino acid by Escherichia coli: L-2-aminohexanoic acid at position 21 in human epidermal growth factor. (1988)

Endeavoring to develop a method to biosynthesize proteins substituted with nonprotein amino acids, we attempted the incorporation of L-2-aminohexanoic acid (Ahx) into human epidermal growth factor (hEGF). Escherichia coli YK537 strain harboring plasmid pTA1522, which has the phoA promoter-phoA signal peptide-hEGF gene, was used. Cells were cultured first in high-phosphate medium and then, for induction of the hEGF-encoding gene, transferred to low-phosphate medium containing Ahx (0.25 mg/ml). hEGF and Ahx-substituted hEGF, [Ahx21]hEGF, secreted into the periplasm were recovered. After treatment with H2O2, [Ahx21]-hEGF was clearly separated from methionine-oxidized hEGF by one-step reverse-phase HPLC. Substitution of the methionine residue of hEGF with Ahx was confirmed by the amino acid analysis of [Ahx21]hEGF. The three biological activities of [Ahx21]hEGF were the same as those of hEGF. From the successful production of [Ahx21]hEGF, a basic strategy was established for preparing proteins substituted with nonprotein amino acid (alloprotein). Induction of the phoA promoter of pho regulon and secretion of the product to the periplasm may depress heat shock-like responses and subsequent hydrolysis of the product by cytoplasmic protease.
Parkin Regulation and Neurodegenerative Disorders (2016)

Parkin is a unique, multifunctional ubiquitin ligase whose various roles in the cell, particularly in neurons, are widely thought to be protective. The pivotal role that Parkin plays in maintaining neuronal survival is underscored by our current recognition that Parkin dysfunction represents not only a predominant cause of familial parkinsonism but also a formal risk factor for the more common, sporadic form of Parkinson's disease (PD). Accordingly, keen research on Parkin over the past decade has led to an explosion of knowledge regarding its physiological roles and its relevance to PD. However, our understanding of Parkin is far from being complete. Indeed, surprises emerge from time to time that compel us to constantly update the paradigm of Parkin function. For example, we now know that Parkin's function is not confined to mere housekeeping protein quality control (QC) roles but also includes mitochondrial homeostasis and stress-related signaling. Furthermore, emerging evidence also suggest a role for Parkin in several other major neurodegenerative diseases including Alzheimer's disease (AD) and Amyotrophic Lateral Sclerosis (ALS). Yet, it remains truly amazing to note that a single enzyme could serve such multitude of functions and cellular roles. Clearly, its activity has to be tightly regulated. In this review, we shall discuss this and how dysregulated Parkin function may precipitate neuronal demise in various neurodegenerative disorders.
Text-to-Speech Synthesis (2009)

Text-to-Speech Synthesis provides a complete, end-to-end account of the process of generating speech by computer. Giving an in-depth explanation of all aspects of current speech synthesis technology, it assumes no specialised prior knowledge. Introductory chapters on linguistics, phonetics, signal processing and speech signals lay the foundation, with subsequent material explaining how this knowledge is put to use in building practical systems that generate speech. Including coverage of the very latest techniques such as unit selection, hidden Markov model synthesis, and statistical text analysis, explanations of the more traditional techniques such as format synthesis and synthesis by rule are also provided. Weaving together the various strands of this multidisciplinary field, the book is designed for graduate students in electrical engineering, computer science, and linguistics. It is also an ideal reference for practitioners in the fields of human communication interaction and telephony.
Synthesis of a Diverse Series of Phosphacoumarins with Biological Activity. (2006)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Gamma-Glutamyl Transferase: The Silent Partner? (2010)

Glutathione is one of the most abundant proteins in vivo involved in maintaining cellular homeostasis and is essential for the regulation of oxidant stress. Gamma-Glutamyl transferase (GGT) is the first enzyme of the gamma glutamyl cycle that regulates the antioxidant glutathione, hence it is a critical enzyme in glutathione homeostasis. Recent findings have indicated upregulation of GGT in inflammation, increasing antioxidant defence whilst potentially driving leukotriene-induced inflammation. GGT is a marker of future comorbid diseases consistent with inflammation (and oxidative stress) as a key central pathophysiological process. COPD reflects several distinct pathological phenotypes. Inflammation (and hence oxidative stress) is influenced by other factors such as bacterial colonisation and exacerbations. The increased incidence of other co-morbid conditions with systemic inflammation suggests that common pathophysiological processes are responsible. Active oxidant stress and hence the role of GGT may play a role in these processes. Future studies of systemic and local GGT function and genotypes in well characterised patients may lead to a better understanding of the processes involved and hence the development of new treatment strategies.
Human CUL1 forms an evolutionarily conserved ubiquitin ligase complex (SCF) with SKP1 and an F-box protein (1998)

The SCF ubiquitin ligase complex of budding yeast triggers DNA replication by catalyzing ubiquitination of the S phase cyclin-dependent kinase inhibitor SIC1. SCF is composed of three proteins-ySKP1, CDC53 (Cullin), and the F-box protein CDC4-that are conserved from yeast to humans. As part of an effort to identify components and substrates of a putative human SCF complex, we isolated hSKP1 in a two-hybrid screen with hCUL1, the closest human homologue of CDC53. Here, we show that hCUL1 associates with hSKP1 in vivo and directly interacts with both hSKP1 and the human F-box protein SKP2 in vitro, forming an SCF-like particle. Moreover, hCUL1 complements the growth defect of yeast cdc53(ts) mutants, associates with ubiquitination-promoting activity in human cell extracts, and can assemble into functional, chimeric ubiquitin ligase complexes with yeast SCF components. Taken together, these data suggest that hCUL1 functions as part of an SCF ubiquitin ligase complex in human cells. Further application of biochemical assays similar to those described here can now be used to identify regulators/components of hCUL1-based SCF complexes, to determine whether the hCUL2-hCUL5 proteins also are components of ubiquitin ligase complexes in human cells, and to screen for chemical compounds that modulate the activities of the hSKP1 and hCUL1 proteins.
Nε-Carboxymethyl Modification of Lysine Residues in Pathogenic Prion Isoforms (2015)

The most prominent hallmark of prion diseases is prion protein conversion and the subsequent deposition of the altered prions, PrP(Sc), at the pathological sites of affected individuals, particularly in the brain. A previous study has demonstrated that the N-terminus of the pathogenic prion isoform (PrP(Sc)) is modified with advanced glycation end products (AGEs), most likely at one or more of the three Lys residues (positions 23, 24, and 27) in the N-terminus (23KKRPKP28). The current study investigated whether N(ε)-(carboxymethyl)lysine (CML), a major AGE form specific to Lys residues produced by nonenzymatic glycation, is an AGE adduct of the N-terminus of PrP(Sc). We show that CML is linked to at least one Lys residue at the N-terminus of PrP(Sc) in 263K prion-infected hamster brains and at least one of the eight Lys residues (positions 101, 104, 106, 110, 185, 194, 204, and 220) in the proteinase K (PK)-resistant core region of PrP(Sc). The nonenzymatic glycation of the Lys residue(s) of PrP(Sc) with CML likely occurs in the widespread prion-deposit areas within infected brains, particularly in some of the numerous tyrosine hydroxylase-positive thalamic and hypothalamic nuclei. CML glycation does not occur in PrP(C) but is seen in the pathologic PrP(Sc) isoform. Furthermore, the modification of PrP(Sc) with CML may be closely involved in prion propagation and deposition in pathological brain areas.
Containers and Clusters for Edge Cloud Architectures -- A Technology Review (2015)

Cloud technology is moving towards more distribution across multi-clouds and the inclusion of various devices, as evident through IoT and network integration in the context of edge cloud and fog computing. Generally, lightweight virtualisation solutions are beneficial for this architectural setting with smaller, but still virtualised devices to host application and platform services, and the logistics required to manage this. Containerisation is currently discussed as a lightweight virtualisation solution. In addition to having benefits over traditional virtual machines in the cloud in terms of size and flexibility, containers are specifically relevant for platform concerns typically dealt with Platform-as-a-Service (PaaS) clouds such as application packaging and orchestration. For the edge cloud environment, application and service orchestration can help to manage and orchestrate applications through containers as an application packaging mechanism. We review edge cloud requirements and discuss the suitability container and cluster technology of that arise from having to facilitate applications through distributed multi-cloud platforms build from a range of networked nodes ranging from data centres to small devices, which we refer to here as edge cloud.
Effect of calcium on in vitro activity of LY146032 against Clostridium difficile (1987)

The in vitro MICs of LY146032 against 63 isolates of Clostridium difficile tested in Wilkins-Chalgren broth ranged from 0.5 to greater than 32 micrograms/ml, with MICs of 4 and 8 micrograms/ml for 50 and 90% of the isolates, respectively. However, when the test medium was supplemented with physiologic concentrations of calcium, the MIC for 90% of the isolates was reduced to less than or equal to 0.12 microgram/ml.
Postweaning mulstisystemic wasting syndrome (PMWS) in pigs. A review (2002)

Postweaning multisystemic wasting syndrome, caused by porcine circovirus type 2 (PCV2), is a recently described clinical condition which affects nursery and growing pigs. PMWS was initially recognized in Canada in 1991 and nowadays is considered to be worldwide distributed. Clinically, PMWS most representative symptoms include wasting, unthriftness, paleness of the skin, respiratory distress, diarrhea and sometimes icterus. PCV2 infection occurs in both PMWS affected and non-affected farms, and viral seroconversion shows a typical pattern, with declining of colostral antibodies during the lactating and nursery periods, with the lowest levels at the end of the nursery period, and active seroconversion of almost all pigs during the grower period. Although antibodies to PCV2 have been detected as early as 1969, no explanation for the emergence of this disease in the 90s has been established. Macroscopic lesions associated with PMWS are quite unspecific, but histopathological lesions in lymphoid tissues (lymphocyte depletion with histiocytic infiltration) are almost unique for this disease. These lesions together with other clinical and laboratorial findings suggest that severely affected pigs may be immunosuppressed. The criteria used for the diagnosis of PMWS include the existence of compatible clinical signs, presence of characteristic microscopic lesions and detection of PCV2 within these lesions. Because of the lack of appropriate treatment or vaccination against PCV2, zootechnical changes have been proposed in affected farms to reduce the so-called "infection pressure" due to PCV2 as well as to any other pathogen.
Initiation of Repair of DNA−Polypeptide Cross-Links by the UvrABC Nuclease (2005)

Although the biochemical pathways that repair DNA-protein cross-links have not been clearly elucidated, it has been proposed that the partial proteolysis of cross-linked proteins into smaller oligopeptides constitutes an initial step in removal of these lesions by nucleotide excision repair (NER). To test the validity of this repair model, several site-specific DNA-peptide and DNA-protein cross-links were engineered via linkage at (1) an acrolein-derived gamma-hydroxypropanodeoxyguanosine adduct and (2) an apurinic/apyrimidinic site, and the initiation of repair was examined in vitro using recombinant proteins UvrA and UvrB from Bacillus caldotenax and UvrC from Thermotoga maritima. The polypeptides cross-linked to DNA were Lys-Trp-Lys-Lys, Lys-Phe-His-Glu-Lys-His-His-Ser-His-Arg-Gly-Tyr, and the 16 kDa protein, T4 pyrimidine dimer glycosylase/apurinic/apyrimidinic site lyase. For the substrates examined, DNA incision required the coordinated action of all three proteins and occurred at the eighth phosphodiester bond 5' to the lesion. The incision rates for DNA-peptide cross-links were comparable to or greater than that measured on fluorescein-adducted DNA, an excellent substrate for UvrABC. Incision rates were dependent on both the site of covalent attachment on the DNA and the size of the bound peptide. Importantly, incision of a DNA-protein cross-link occurred at a rate approximately 3.5-8-fold slower than the rates observed for DNA-peptide cross-links. Thus, direct evidence has been obtained indicating that (1) DNA-peptide cross-links can be efficiently incised by the NER proteins and (2) DNA-peptide cross-links are preferable substrates for this system relative to DNA-protein cross-links. These data suggest that proteolytic degradation of DNA-protein cross-links may be an important processing step in facilitating NER.
STIR - Synthesis and Characterization of Nanotube-Elastomer Damping Composites (2003)

Abstract : The objectives of this research are: (a) to develop novel polymeric damping composites through distributing carbon nanotubes (CNTs) within the host polymer, and (b) to investigate the damping characteristics of such new composites. We aim to obtain good understanding and insight of this innovative approach and provide guidelines for future research possibilities. In this study, the system is modeled using a four-phase composite, composed of a resin, voids, and bonded and debonded nanotubes. To address damping effects, the concept of interfacial stick-slip frictional motion between the nanotubes and the resin is proposed. The analytical results show that the critical bonding stress, nanotube weight ratio and structure deformation are the factors affecting the damping characteristic. Experimental efforts are also performed to verify the trends predicted by the analysis. Through comparing with neat resin specimens, the study shows that one can indeed enhance damping by adding CNT fillers into polymeric resins. The test results also show that the damping ratio of specimens with nanotubes depends on the strain (deformation) of the composite, with trends similar to those predicted by the analytical model, showing the validity of the model and the analytical predictions.
Dynamic Targeting of the Agonist-stimulated m2 Muscarinic Acetylcholine Receptor to Caveolae in Cardiac Myocytes (1997)

In cardiac myocytes, as well as specialized conduction and pacemaker cells, agonist binding to muscarinic acetylcholine receptors (mAchRs) results in the activation of several signal transduction cascades including the endothelial isoform of nitric-oxide synthase (eNOS) expressed in these cells. Recent evidence indicates that, as in endothelial cells, eNOS in cardiac myocytes is localized to plasmalemma caveolae, specialized lipid microdomains that contain caveolin-3, a muscle-specific isoform of the scaffolding protein caveolin. In this report, using a detergent-free method for isolation of sarcolemmal caveolae from primary cultures of adult rat ventricular myocytes, we demonstrated that the muscarinic cholinergic agonist carbachol promotes the translocation of mAchR into low density gradient fractions containing most myocyte caveolin-3 and eNOS. Following isopycnic centrifugation, the different gradient fractions were exposed to the muscarinic radioligand [3H]quinuclidinyl benzilate (QNB), and binding was determined after membrane filtration or immunoprecipitation. In a direct radioligand binding assay, we found that [3H]QNB binding can be detected in caveolin-enriched fractions only when cardiac myocytes have been previously exposed to carbachol. Furthermore, most of this [3H]QNB binding can be specifically immunoprecipitated by an antibody to the m2 mAchR, indicating that the translocation of this receptor subtype is responsible for the [3H]QNB binding detected in the low density fractions. Moreover, the [3H]QNB binding could be quantitatively immunoprecipitated from the light membrane fractions with a caveolin-3 antibody (but not a control IgG1 antibody), confirming that the m2 mAchR is targeted to caveolae after carbachol treatment. Importantly, atropine, a muscarinic cholinergic antagonist, did not induce translocation of m2 mAchR to caveolae and prevented receptor translocation in response to the agonist carbachol. Thus, dynamic targeting of sarcolemmal m2 mAchR to caveolae following agonist binding may be essential to initiate specific downstream signaling cascades in these cells.
Elastic Properties of Lipid Bilayers: Theory and Possible Experiments (1973)

Abstract A theory of the elasticity of lipid bilayers is proposed. Three types of strain, i. e. stretching, tilt and curvature, are distinguished and the associated stresses are identified. It is argued that in the case of vesicles (= closed bilayer films) the only elasticity controlling nonspherical shapes is that of curvature. Euler-Lagrange equations are derived for the shape in magnetic fields and under excess outside pressure. It is shown that magnetic fields can deform spherical vesicles into ellipsoids of revolution. Under excess outside pressure the spherical shape becomes unstable at a certain threshold pressure. Both effects can be influenced by a spontaneous curvature of the bilayer. Some possible experiments to determine the elastic properties are also discussed
Response : Unraveling the Structure of IL-2 (1992)

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Performance Evaluation of Thermal Cyclers for PCR in a Rapid Cycling Condition (2008)

The performance of thermal cyclers for polymerase chain reactions (PCR) is of great concern in terms of the reliability of PCR-based assays, particularly when rapid cycling conditions are applied to small volume reactions. In this work, the precision of the temperature controls during rapid thermal cycling was measured in 19 commercial thermal cyclers of 8 different models. The temperatures of test solutions in specific locations in each thermal block were simultaneously monitored at 1 s intervals during thermal cycling. A temperature-sensitive multiplex PCR was run in parallel to assess undesirable PCR results caused by poor temperature control. Under the given conditions (20 s of annealing time and 20 microL reaction volume), a majority of the tested instruments showed prominent curving, undershooting, and/or overshooting in their temperature profiles, which substantially influenced the results of the temperature-sensitive multiplex PCR. Variations between wells were also observed in most instruments. It is strongly hoped that these problems will be addressed by manufacturers and that they will make substantial improvements in the precision and efficiency of thermal cyclers. In the meantime, users of thermal cyclers might be able to avoid unexpected poor outcomes of sensitive PCR-based assays by designing their PCR protocols with these findings in mind.
Control of Graphene's Properties by Reversible Hydrogenation: Evidence for Graphane (2009)

Although graphite is known as one of the most chemically inert materials, we have found that graphene, a single atomic plane of graphite, can react with atomic hydrogen, which transforms this highly conductive zero-overlap semimetal into an insulator. Transmission electron microscopy reveals that the obtained graphene derivative (graphane) is crystalline and retains the hexagonal lattice, but its period becomes markedly shorter than that of graphene. The reaction with hydrogen is reversible, so that the original metallic state, the lattice spacing, and even the quantum Hall effect can be restored by annealing. Our work illustrates the concept of graphene as a robust atomic-scale scaffold on the basis of which new two-dimensional crystals with designed electronic and other properties can be created by attaching other atoms and molecules.
Binge Eating as a Major Phenotype of Melanocortin 4 Receptor Gene Mutations (2003)

Binge eating is a major phenotypic characteristic of subjects with a mutation in MC4R, a candidate gene for the control of eating behavior.
The Option-Critic Architecture (2017)

Temporal abstraction is key to scaling up learning and planning in reinforcement learning. While planning with temporally extended actions is well understood, creating such abstractions autonomously from data has remained challenging.We tackle this problem in the framework of options [Sutton,Precup and Singh, 1999; Precup, 2000]. We derive policy gradient theorems for options and propose a new option-critic architecture capable of learning both the internal policies and the termination conditions of options, in tandem with the policy over options, and without the need to provide any additional rewards or subgoals. Experimental results in both discrete and continuous environments showcase the flexibility and efficiency of the framework.
Design of an in vivo Cleavable Disulfide Linker in Recombinant Fusion Proteins (2010)

In order to achieve optimal biological activity and desired pharmacokinetic profiles, a dithiocyclopeptide linker was designed for in vivo release of protein domains from a recombinant fusion protein. This novel in vivo cleavable disulfide linker, based on a dithiocyclopeptide containing a thrombin-sensitive sequence and an intramolecular disulfide bond, was inserted between transferrin and granulocyte colony-stimulating factor (G-CSF) recombinant fusion protein domains. After expression of the fusion protein, G-C-T, from HEK293 cells, thrombin treatment in vitro generated a fusion protein linked via a reversible disulfide bond that was quickly cleaved in vivo, separating the protein domains. After release from the fusion protein, free G-CSF exhibited an improved biological activity in a cell proliferation assay. Although reversible disulfide bonds are commonly used in protein chemical conjugation methods, to our knowledge this report is the first example of the construction of a recombinant fusion protein with a disulfide linkage for the release of the functional domain. This linker design can be adapted to diverse recombinant fusion proteins in which in vivo separation of protein domains is required to achieve an improved therapeutic effect and a desirable pharmacokinetic profile and biodistribution of the functional domain.