gebhart/patrepeval huggingface dataset:
Thermodynamic analysis of the chemotactic protein from Escherichia coli, CheY (1993)

CheY, the 129 amino acid chemotactic protein from Escherichia coli, is a good model for studies of folding of parallel alpha/beta proteins. We report here the thermodynamic characterization of the wild-type CheY at different pH values and in different buffers and denaturation conditions. The denaturation of CheY by urea monitored by circular dichroism and fluorescence fits the two-state unfolding model. The stability of the protein is ionic strength dependent, probably due to the presence of three Asp residues in very close proximity in its active site. The presence of a Mg2+ ion, which seems to interact with Asp 13 in the active site, stabilizes the native structure by up to 6.9 kJ mol-1. The CheY maximum stability (31.7 +/- 2.1 kJ mol-1), without magnesium, is reached at pH 5.1. Analysis of scanning calorimetry data has shown that temperature-induced unfolding of CheY is not a two-state process and proceeds through a highly populated intermediate state, corresponding to protein dimers, as was subsequently confirmed by direct cross-linking experiments. According to circular dichroism, fluorescence, nuclear magnetic resonance, and ANS binding experiments, this "intermediate dimer" at pH 2.5 exhibits all known characteristics of the "molten globule" state. The reversible dimerization of "molten globules" might explain such peculiarities as the increased stability or the cooperative unfolding found for the molten globule state of some proteins.
Field Deployment for In-situ Metal and Radionuclide Stabilization by Microbial Metabolites (2005)

A novel biotechnology is reported here that was demonstrated at SRS that facilitates metal and actinide immobilization by incorporating the physiology and ecology of indigenous bacteria. This technology is based on our previous work with pyomelanin-producing bacteria isolated from SRS soils. Through tyrosine supplementation, overproduction of pyomelanin was achieved, which lead ultimately to metal and actinide immobilization, both in-vitro and in-situ. Pyomelanin is a recalcitrant microbial pigment and a humic type compound in the class of melanin pigments. Pyomelanin has electron shuttling and metal chelation capabilities and thus accelerates the bacterial reduction and/or immobilization of metals. Pyomelanin is produced outside the cell and either diffuses away or attaches to the cell surface. In either case, the reduced pyomelanin is capable of transferring electrons to metals as well as chelating metals. Because of its recalcitrance and redox cycling properties, pyomelanin molecules can be used over and over again for metal transformation. When produced in excess, pyomelanin produced by one bacterial species can be used by other species for metal reduction, thereby extending the utility of pyomelanin and further accelerating metal immobilization rates. Soils contaminated with Ni and U were the focus of this study in order to develop in-situ, metal bioimmobilization technologies. We have demonstrated pyomelanin production in soil from the Tims Branch area of SRS as a result of tyrosine amendments. These results were documented in laboratory soil column studies and field deployment studies. The amended soils demonstrated increased redox behavior and sequestration capacity of U and transition metals following pyomelanin production. Treatments incorporating tyrosine and lactate demonstrated the highest levels of pyomelanin production. In order to determine the potential use of this technology at other areas of SRS, pyomelanin producing bacteria were also quantified from metal contaminated soils at TNX and D areas of SRS. A bacterial culture collection from subsurface studies near P Area of SRS were also evaluated for pyomelanin production. Bacterial densities of pyomelanin producers were determined to be >10{sup 6} cells/g soil at TNX and D areas. In addition, approximately 25% of isolates from P area demonstrated pyomelanin production in the presence of tyrosine. Biogeochemical activity is an ongoing and dynamic process due, in part, to bacterial activity in the subsurface. Bacteria contribute significantly to biotransformation of metals and radionuclides. An understanding and application of the mechanisms of metal and radionuclide reduction offers tremendous potential for development into bioremedial processes and technologies. This report demonstrates the application of recent advances in bacterial physiology and soil ecology for future bioremediation activities involving metal and actinide immobilization.
THE EFFECTS OF IONS AND FREEZE–THAWING ON SUPERNATANT AND MITOCHONDRIAL MALATE DEHYDROGENASE (1967)

The effects of various ions added to the assay system for purified mitochondrial and supernatant pig-heart malate dehydrogenase have been studied. Phosphate, arsenate, and zinc ions strongly stimulate the mitochondrial enzyme. Phosphate and arsenate ions have little effect on the supernatant enzyme whereas zinc inhibits it. The stimulation by phosphate is relieved by the addition of magnesium ion, to the assay system.The effects on enzymatic activity were studied when the supernatant and mitochondrial malate dehydrogenase were subjected to freezing and thawing in various media. Freezing and thawing of the mitochondrial enzyme in Tris or citrate buffers with or without mercaptoethanol results in small activity loss. Supernatant malate dehydrogenase displays a marked loss in activity when frozen quickly in the presence of phosphate and mercaptoethanol; if mercaptoethanol is omitted, activity loss is small. NADH, oxalacetic acid (OAA), NAD, and malate protect against activity loss in the phosphate–mercaptoethanol system. Repeated freeze–thawing of mitochondrial malate dehydrogenase in the presence of both phosphate and magnesium results in extensive losses in activity. In all cases slow freezing produces little activity loss for either enzyme.
TMR film and head technologies (2006)

We have developed Al-O barrier magnetic tunnel junctions (MTJs) and obtained a magneto-resistance (MR) ratio of 27% with a resistance-area product RA of about 3 Ωμm 2 . We have also studied Ti-O and Mg-O as new low barrier energy materials for MTJs. Ti-O barrier MTJs showed a very small RA of less than 2 Ωμm 2 . We can obtain a high MR ratio of about 100% for Mg-O barrier MTJs with an RA of 2 to 3 Ωμm 2 using a CoFeB magnetic layer for the pinned and free layers. The coercivity of the free layer can be reduced using a Co 74 Fe 26 /NiFe free layer, which is suitable for head applications. An MR ratio of 40 to 50% was obtained with an RA of 2 to 3 Ωμm 2 . Mg-O barrier MTJs are the most promising for future TMR heads for recording densities over 200 Gbit/in 2 . We fabricated Al-O barrier TMR heads whose target areal recording density is around 100 Gbit/in 2 . These heads have a 25% MR ratio with an RA of 4 Ωμm 2 , and the width and height of the TMR head element are 110 nm and 100 nm, respectively. We can obtain an average output signal of about 5000 μVpp at a 150 mV bias voltage (V b ) using a synthetic ferrimagnetic medium. We have also investigated the characteristics of head noise and found that thermal magnetic noise is the dominant noise in our TMR heads. We also investigated the thermal magnetic noise as a function of the exchange coupling field H ex between the pinned and antiferromagnetic layers of TMR heads by using micromagnetic simulations. We clarified the importance of increasing not only the MR ratio but also H ex to realize ultra high density magnetic recording.
An alternative pathway for fibrinolysis. I. The cleavage of fibrinogen by leukocyte proteases at physiologic pH. (1975)

An alternative fibrinolytic system, active at physiological pH, is present in peripheral blood leukocytes. The fibrinolytic proteases localized predominantly in the leukocyte granules are capable of degrading both fibrinogen and fibrin, and plasmin activity does not contribute significantly to this proteolytic event. The specificity of the alternative fibrinolytic proteases for fibrinogen and the characteristics of the derivative cleavage fragments are clearly distinguishable from the classical plasmin system. The high molecular weight derivatives of fibrinogen, generated by the alternative system, under physiological conditions, are larger than the plasmin-generated X fragment, exhibit immunoelectrophoretic mobility comparable to native fibrinogen, and are not coagulable by thrombin. Analysis of the constituent polypeptide chains of the fragments reveals cleavage of the Aalpha, Bbeta, and gamma chains of fibrinogen. The lower molecular weight derivatives of fibrinogen, generated by the alternative system, are structurally distinct from previously described fibrinogen degradation products and exhibit potent anticoagulant activity. This anticoagulant activity can be attributed to interference with normal fibrin polymerization. The proteases of the alternative fibrinolytic systems are actively secreted by leukocytes when stimulated to undergo a nonlytic release reaction. These results provide direct evidence for a fibrinolytic system resident in leukocyte granules that is associated with the leukocyte release reaction and is capable of generating unique fibrinogen cleavage fragments.
Abatement technologies for high concentrations of NO<sub>x</sub>and SO<sub>2</sub>removal from exhaust gases: A review (2015)

Nitrogen oxides (NOx) and sulfur dioxide (SO2) are the main air pollutants. Both of them are mostly formed during the process of fossil fuels combustion, while some processes generate very high concentrations of NOx and SO2. In this review the authors describe and summarize the currently used methods and the new techniques that are under investigation. They also give a detailed description of the regulations and sources of SO2 and NOx emissions, as well as their impact on human health and the environment. The authors focus primarily on the environmental protection technologies used in power plants, vehicles, ships, and the chemical industry.
Diabetic-like retinopathy ameliorated with the aldose reductase inhibitor WAY-121,509. (1996)

A dose of WAY-121,509 sufficient to reduce retinal polyol levels by 95% ameliorated the development of galactose-induced cataracts and diabetic-like retinopathy but was insufficient to prevent early lens opacifications or all the diabetic-like retinal microangiopathies.
A new antithrombogenic heparinized polymer (1977)

A new antithrombogenic polymer was synthesized by photoinduced graft copolymerization of both a hydrophilic polymer and a cationic polymer to hydrophobic poly (vinyl chloride) copolymer, and by quarternizing and heparinizing the obtained graft copolymer. For polymers of various compositions obtained by the method described above, chemical composition, water absorption, membrane potential, and quantity of adsorbed heparin were determined and antithrombogenicity evaluated in vivo. Thus, it has been found that the polymer of excellent antithrombogenicity has a negative membrane potential, a moderate elution rate of heparin, adsorbs heparin in a quantity of approximately 15 wt-%, and has a degree of water adsorption of about 30 wt-%. Also, measurement of membrane potential was very useful for the estimation of the quantity of the adsorbed heparin and its change with time.
Data flow graphs: system specification with the most unrestricted semantics (1991)

A new data flow graph concept is defined to be used for architectural synthesis as well as verification of a system. The graph contains only the explicit data dependencies, but any other constraints can also be described. The semantics of this graph does not impose any restriction on the scheduler, except for the explicit data dependencies. For instance, the scheduler is not forced to work on certain blocks in the graph, like loop bodies but may work also across these borders. It is also proved that an optimal schedule can be found efficiently. >
Promoters and serotypes: targeting of adeno‐associated virus vectors for gene transfer in the rat central nervous system <i>in vitro</i> and <i>in vivo</i> (2004)

The brain parenchyma consists of several different cell types, such as neurones, astrocytes, microglia, oligodendroglia and epithelial cells, which are morphologically and functionally intermingled in highly complex three-dimensional structures. These different cell types are also present in cultures of brain cells prepared to serve as model systems of CNS physiology. Gene transfer, either in a therapeutic attempt or in basic research, is a fascinating and promising tool to manipulate both the complex physiology of the brain and that of isolated neuronal cells. Viral vectors based on the parvovirus, adeno-associated virus (AAV), have emerged as powerful transgene delivery vehicles. Here we describe highly efficient targeting of AAV vectors to either neurones or astrocytes in cultured primary brain cell cultures. We also show that transcriptional targeting can be achieved by the use of small promoters, significantly boosting the transgene capacity of the recombinant viral genome. However, we also demonstrate that successful targeting of a vector in vitro does not necessarily imply that the same targeting works in the adult brain. Cross-packaging the AAV-2 genome in capsids of other serotypes adds additional benefits to this vector system. In the brain, the serotype-5 capsid allows for drastically increased spread of the recombinant vector as compared to the serotype-2 capsid. Finally, we emphasize the optimal targeting approach, in which the natural tropism of a vector for a specific cell type is employed. Taken together, these data demonstrate the flexibility which AAV-based vector systems offer in physiological research.
The hearing aid feedback path: Mathematical simulations and experimental verification (1985)

Acoustic feedback in hearing aids has received little attention in the literature. Feedback occurs when stability conditions of the open-loop transfer function of an in situ hearing aid are violated. Solving the feedback problem will first require knowledge of the open-loop transfer function. Included in the open-loop transfer function is the acoustical path by which sound emanating from the earmold vent returns to the microphone (i.e., the feedback path). Reported herein are two different mathematical procedures for simulating transfer functions of the feedback path of an eyeglass-type hearing aid. In one procedure the vent exit was modeled as a point source of sound located on a flat plane, while it was treated as a point source on a sphere in the other. Results of laboratory experiments indicate that the mathematical models accurately predict those acoustic phenomena for which they were intended: point sources on plane and spherical baffles. Results of manikin experiments showed both models to be less accurate for simulating the feedback path around the human head. The maximum difference between experiment and theory was 6 dB at one frequency. Surprisingly, the flat-baffle model produced better agreement with experimental results than did the sphere model.
Performance analysis of interference averaging for link adaptation in LTE/LTE-A downlink (2013)

In LTE/LTE-A system, Link Adaptation (LA) is a crucial procedure. One key factor is to have precious interference estimation considered in the LA, since the accuracy of interference estimation has a significant impact on the Channel Quality Indicator (CQI). In this paper we pay our attention to the CQI mismatch problem in Link Adaptation procedure, which is mainly caused by rapid fluctuation of inter-cell interference depending heavily on traffic load. Obvious performance loss has been observed in system level simulation due to this problem, thus we propose an interference averaging scheme for CQI calculation by considering not only the instantaneous interference level, but also the interference level in the past when UEs doing CQI calculation. Based on intensive system level simulations, it can be observed that the proposed scheme can improve the system performance both for average throughput and cell-edge throughput.
Protease-Activated G Protein-Coupled Receptors on Human Platelets and Endothelial Cells (1997)

Extracellular proteases can trigger intracellular events via at least two members of the super-family of G protein coupled receptors: the thrombin receptor and PAR-2. The two receptors have a similar structure, share a common mechanism of activation and may have arisen by gene duplication, but there are differences as well as similarities in their tissue distribution, the proteases by which they are activated and potentially in the consequences of their activation. Human platelets express the thrombin receptor, but not PAR-2, while at least some types of human endothelial cells express both. This review briefly summarizes current information about the two receptors and considers their roles in platelet and endothelial cell biology, their interactions with proteases, and the known mechanisms for receptor redistribution and replacement.
All-optical format conversion using an ultrafast polarization bistable vertical-cavity surface-emitting laser (2000)

Summary form only given.Ultrafast polarization bistable switching with a 7 ps switching-time in a vertical-cavity surface-emitting laser (VCSEL) has been demonstrated. We propose and experimentally demonstrate an all-optical format conversion (both RZ to NRZ and vice versa) using an ultrafast polarization bistable VCSEL. Our numerical simulation predicts that 20 Gbit/s signals can be converted. For many systems, particularly those in which dispersion plays a consequential role, the NRZ transmission format may be prefer able. Using the memory function and thresholding function of the polarization bistable VCSEL, the all-optical format conversion from RZ to NRZ can be accomplished.
Dispersive Mixing Effects on the Sloss Field Micellar System (1982)

Abstract This paper presents results of laboratory experiments and computer simulation studies of the micellar/polymer fluids injected in the Sloss field, NE. The paper shows that the dispersion coefficient for the partitioned sulfonate in the oil phase can be an order of magnitude larger than the dispersion coefficient in the water phase. The results show that the two principal components of the micellar fluid (sulfonate and polymer) propagate at different rates because of partitioning and dispersive mixing effects. Sulfonate is produced much earlier than polymer and is concentrated in the produced oil. Sulfonate partitions into the oil phase as a consequence of ion exchange, and the polymer remains in the water phase. The oil phase that contains the partitioned sulfonate—i.e., upper-phase microemulsion—has high mobility. The increased dispersion coefficient for a component in the nonwetting phase, in this case the partitioned sulfonate into the oil phase, is supported by an independent study. These mechanisms contribute to early sulfonate breakthrough and a larger sulfonate requirement per barrel of oil displaced than anticipated for a nondispersive displacement. The results of this paper can be beneficial for design of other micellar fluids and performance predictions and interpretation of micellar floods in other fields.
Molecular basis of gynecological oncology – TopBP1 protein as the guardian of genome integrity (2013)

Breast cancer is the most common malignancy in women. Its estimated annual incidence is about one million cases worldwide. A number of risk factor have been identified, among them early menarche, late menopause, nulliparity and positive family history Moreover a number of highly penetrant breast and ovarian cancer susceptibility genes, such as BRCA 1 and BRCA2, have been identified. Recent findings suggest TopBP1 to be a breast and ovarian cancer susceptibility gene. Moreover; TopBPI protein may be an important prognostic marker of breast cancer TopBP1 protein is involved in DNA replication, mitosis and meiosis, as well as DNA repair Deregulation of these processes may have pathological implications in cancer
Mutational removal of the Thr669 and Ser671 phosphorylation sites alters substrate specificity and ligand-induced internalization of the epidermal growth factor receptor. (1990)

The epidermal growth factor (EGF) receptor contains multiple sites of phosphorylation on serine, threonine, and tyrosine residues. Because the biological responsiveness of the EGF receptor is regulated by phosphorylation at several of these sites, we studied the functional consequences of removal of the Thr669 and Ser671 phosphorylation sites using site-directed mutagenesis. The mutant EGF receptor expressed in mouse B82 cells displayed normal EGF binding and in vivo autophosphorylation and was fully active in biological signal transduction as measured by EGF-stimulated gene transcription. However, the EGF-dependent phosphorylation of an 85-kDa cellular substrate by the mutant receptor was impaired relative to the wild type receptor, indicating that the mutated region may specifically interact with this substrate. Endocytosis of the mutant receptor was also impaired as measured by both receptor down-regulation and ligand internalization studies. This was due to impaired uptake of the mutant receptor by the saturable, high affinity endocytic system. Several aspects of mutant receptor function were regulated normally by TPA, indicating a lack of interaction between the mutated phosphorylation sites and the nearby protein kinase C phosphorylation site Thr654. These results suggest that phosphorylation of the EGF receptor at Thr669 and Ser671 mediates interaction of the receptor with a specific tyrosine kinase substrate and is required for efficient ligand-induced receptor internalization.
Dikationether, 11. Ambidoselektive Reaktionen von β‐Ketoenolaten mit Dikationethern (1986)

Abstract Die elektrophile Übertragung einer Tetramethylformamidinum‐Gruppe aus dem Bis‐( N , N , N ′, N ′‐tetramethylformamidinio)ether‐Salz 5a auf die ambidenten β‐Ketoenolate 7a – h, j und das β‐Ketonitril‐Anion 7i erfolgt in Acetonitril ausschileßlich am Enolatsauerstoff, wobei man die Uronium‐Salze 8a – j erhält. Aus den acyclischen β‐Ketoenolaten 7a – f entstehen diastereoselektiv die β‐Acylenolether‐Salze ( E )‐ 8a – f . Das Diimidazolinioether‐Salz 5b und die Dipyridinioether‐Salze 5c, d reagieren mit dem Anion von Dimedon ebenfalls ausschließlich am Sauerstoff ( 8k, 15, 18 ). Aus 5c und dem Anion von Meldrumsäure erhält man unter C/C‐Verknüpfung das Olefin 16 . – Eine Röntgenstrukturanalyse von ( E )‐ 8f wurde ausgeführt.
The association constants of triethyloxonium salts and their solvation by diethyl ether (1970)

From conductimetric measurements we have obtained the association constants of two tertiary oxonium salts in methylene dichloride solution, and also direct evidence for solvation of the cation by diethyl ether.
Analysis of optimal velocity model with explicit delay (1998)

We analyze the optimal velocity model (OVM) with explicit delay. The properties of congestion and the delay time of car motion are investigated by analytical and numerical methods. It is shown that the small explicit delay time has almost no effects. In the case of the large explicit delay time, a new phase of congestion pattern of OVM seems to appear.