gebhart/patrepeval huggingface dataset:
Tight Binding of Bulky Fluorescent Derivatives of Adenosine to the Low Affinity E2ATP Site Leads to Inhibition of Na+/K+-ATPase (1999)

A Koshland-Némethy-Filmer model of two cooperating ATP sites has previously been shown to explain the kinetics of inhibition of Na+/K+-ATPase (EC 3.6.1.37) by dansylated ATP (Thoenges, D., and Schoner, W. (1997) J. Biol. Chem. 272, 16315-16321). The present work demonstrates that this model adequately describes all types of interactions and kinetics of a number of ATP analogs that differ in their cooperativity of the high and low affinity ATP binding sites of the enzyme. 2',3'-O(2,4,6-trinitrophenyl)ATP binds in a negative cooperative way to the E1ATP site (Kd = 0.7 microM) and to the E2ATP site (Kd = 210 microM), but 3'(2')-O-methylanthraniloyl-ATP in a positive cooperative way with a lower affinity to the E1ATP binding site (Kd = 200 microM) than to the E2ATP binding site (Kd = 80 microM). 3'(2')-O(5-Fluor-2,4-dinitrophenyl)-ATP, however, binds in a noncooperative way, with equal affinities to both ATP binding sites (Kd = 10 microM). In a research for the structural parameters determining ATP site specificity and cooperativity, we became aware that structural flexibility of ribose is necessary for catalysis. Moreover, puckering of the ring atoms in the ribose is essential for the interaction between ATP sites in Na+/K+-ATPase. A number of derivatives of 2'(3')-O-adenosine with bulky fluorescent substitutes bind with high affinity to the E2ATP site and inhibit Na+/K+-ATPase activity. Evidently, an increased number of interactions of such a bulky adenosine with the enzyme protein tightens binding to the E2ATP site.
Electrospun aligned nanofibrous composite of MWCNT/polyurethane to enhance vascular endothelium cells proliferation and function (2010)

Aligned or random nanofibrous meshes of multiwalled carbon nanotubes/polyurethane composite (MWCNT/PU) were fabricated by electrospinning and characterized by scanning electron microscopy (SEM). The regulatory effects of nanofibrous structure and MWCNT on the growth and anticoagulant function of human umbilical vein endothelial cells (HUVECs) were investigated by examining proliferation, type IV collagen secretion, tissue factor and plasminogen activator inhibitor-1 (PAI-1) release, and cytoskeleton arrangement, as well as via pull-down analysis. We show that aligned nanofibrous structure and MWCNT can function as extracellular signals to stimulate cell growth, proliferation, and extracellular collagen secretion, in addition to preserving anticoagulant function. The nanofibrous structures played important roles in the activation of Rac and Cdc42, while CNT regulated the activation of Rho. These two features synergistically activated Rho GTPases that transmitted cell-substrate signals to the cytoplasm. These signals were then relayed to the nucleus by the MAP kinase pathway to direct cytoskeletal arrangement and cell orientation.
Using hint tables to locate resources in distributed systems (2003)

The authors address the problem of determining how system parameters affect the performance of the location operations when hint tables are used. To this end they approximate a distributed system incorporating hint tables in its location strategy with an analytic model. They identify a set of parameters affecting the cost of location operations and provide a criterion to help decide whether the use of hint tables should be incorporated in the design of a given system. They give a set of examples to illustrate the usage of the analytic results. These include location using: broadcast in a broadcast network; name servers in a broadcast network; broadcast is a packet switched network and name servers in a packet switched network.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Distinct Binding Specificity of the Multiple PDZ Domains of INADL, a Human Protein with Homology to INAD from Drosophila melanogaster (2001)

PDZ domains are protein-protein interaction modules that typically bind to short peptide sequences at the carboxyl terminus of target proteins. Proteins containing multiple PDZ domains often bind to different trans-membrane and intracellular proteins, playing a central role as organizers of multimeric complexes. To characterize the rules underlying the binding specificity of different PDZ domains, we have assembled a novel repertoire of random peptides that are displayed at high density at the carboxyl terminus of the capsid D protein of bacteriophage lambda. We have exploited this combinatorial library to determine the peptide binding preference of the seven PDZ domains of human INADL, a multi-PDZ protein that is homologous to the INAD protein of Drosophila melanogaster. This approach has permitted the determination of the consensus ligand for each PDZ domain and the assignment to class I, class II, and to a new specificity class, class IV, characterized by the presence of an acidic residue at the carboxyl-terminal position. Homology modeling and site-directed mutagenesis experiments confirmed the involvement of specific residues at contact positions in determining the domain binding preference. However, these experiments failed to reveal simple rules that would permit the association of the chemical characteristics of any given residue in the peptide binding pocket to the preference for specific amino acid sequences in the ligand peptide. Rather, they suggested that to infer the binding preference of any PDZ domain, it is necessary to simultaneously take into account all contact positions by using computational procedures. For this purpose we extended the SPOT algorithm, originally developed for SH3 domains, to evaluate the probability that any peptide would bind to any given PDZ domain.
BORG: block-reORGanization for self-optimizing storage systems (2009)

This paper presents the design, implementation, and evaluation of BORG, a self-optimizing storage system that performs automatic block reorganization based on the observed I/O workload. BORG is motivated by three characteristics of I/O workloads: non-uniform access frequency distribution, temporal locality, and partial determinism in non-sequential accesses. To achieve its objective, BORG manages a small, dedicated partition on the disk drive, with the goal of servicing a majority of the I/O requests from within this partition with significantly reduced seek and rotational delays. BORG is transparent to the rest of the storage stack, including applications, file system(s), and I/O schedulers, thereby requiring no or minimal modification to storage stack implementations. We evaluated a Linux implementation of BORG using several real-world workloads, including individual user desktop environments, a web-server, a virtual machine monitor, and an SVN server. These experiments comprehensively demonstrate BORG’s effectiveness in improving I/O performance and its incurred resource overhead. 1
Adaptive Stream Processing using Dynamic Batch Sizing (2014)

The need for real-time processing of "big data" has led to the development of frameworks for distributed stream processing in clusters. It is important for such frameworks to be robust against variable operating conditions such as server failures, changes in data ingestion rates, and workload characteristics. To provide fault tolerance and efficient stream processing at scale, recent stream processing frameworks have proposed to treat streaming workloads as a series of batch jobs on small batches of streaming data. However, the robustness of such frameworks against variable operating conditions has not been explored.
Visual System Involvement in Patients with Newly Diagnosed Parkinson Disease (2017)

Purpose To assess intracranial visual system changes of newly diagnosed Parkinson disease in drug-naïve patients. Materials and Methods Twenty patients with newly diagnosed Parkinson disease and 20 age-matched control subjects were recruited. Magnetic resonance (MR) imaging (T1-weighted and diffusion-weighted imaging) was performed with a 3-T MR imager. White matter changes were assessed by exploring a white matter diffusion profile by means of diffusion-tensor imaging-based parameters and constrained spherical deconvolution-based connectivity analysis and by means of white matter voxel-based morphometry (VBM). Alterations in occipital gray matter were investigated by means of gray matter VBM. Morphologic analysis of the optic chiasm was based on manual measurement of regions of interest. Statistical testing included analysis of variance, t tests, and permutation tests. Results In the patients with Parkinson disease, significant alterations were found in optic radiation connectivity distribution, with decreased lateral geniculate nucleus V2 density (F, -8.28; P < .05), a significant increase in optic radiation mean diffusivity (F, 7.5; P = .014), and a significant reduction in white matter concentration. VBM analysis also showed a significant reduction in visual cortical volumes (P < .05). Moreover, the chiasmatic area and volume were significantly reduced (P < .05). Conclusion The findings show that visual system alterations can be detected in early stages of Parkinson disease and that the entire intracranial visual system can be involved. <sup>©</sup> RSNA, 2017 Online supplemental material is available for this article.
Formation and collapse of gels of sterically stabilized colloidal particles (2000)

Colloidal silica spheres (diameter 88 nm) with a thick steric stabilization layer of polystyrene (PS; Mw = 26 600 g mol-1) were prepared. In cyclohexane, a marginal solvent for PS, particle aggregation and gelation were observed on lowering the temperature. Near the gelation temperature and at particle concentrations of a few per cent by weight, the gels were sufficiently weak to slowly compact under gravity. On quenching to slightly lower temperatures, the gels still settled, but the top of the sediment did not become flat, as is usually the case. This seems to be related to an unusual mechanism for gel compaction, which starts by forming a more dense structure at the top of the sample. It is proposed that this is related to the entangled polymer chains on neighbouring particles resisting substantial rearrangement of the local structure. The transient gelation phenomenon, observed previously for mixtures of colloid and non-adsorbing polymer, has so far not been observed for our system.
Room-temperature magnetic refrigerator using permanent magnets (2000)

A magnetic refrigerator device based on adiabatic magnetic refrigeration is described. The magnetic material is cyclically magnetized and demagnetized by permanent magnets in an adiabatic process. A temperature difference of 1.6 K between the hot and cold regions was obtained under a low magnetic field (0.3 T). Gadolinium was the magnetic material used in experiments at room temperature. The range of working temperatures is between 70 and 300 K for a variety of active magnetic materials. The optimized experimental setup increased the device efficiency by achieving a temperature difference between hot and cold sources up to 5 K.
DNA Interaction and Phosphotransfer of the C 4 -Dicarboxylate- Responsive DcuS-DcuR Two-Component Regulatory System from Escherichia coli (2004)

The DcuS-DcuR system of Escherichia coli is a two-component sensor-regulator that controls gene expression in response to external C(4)-dicarboxylates and citrate. The DcuS protein is particularly interesting since it contains two PAS domains, namely a periplasmic C(4)-dicarboxylate-sensing PAS domain (PASp) and a cytosolic PAS domain (PASc) of uncertain function. For a study of the role of the PASc domain, three different fragments of DcuS were overproduced and examined: they were PASc-kinase, PASc, and kinase. The two kinase-domain-containing fragments were autophosphorylated by [gamma-(32)P]ATP. The rate was not affected by fumarate or succinate, supporting the role of the PASp domain in C(4)-dicarboxylate sensing. Both of the phosphorylated DcuS constructs were able to rapidly pass their phosphoryl groups to DcuR, and after phosphorylation, DcuR dephosphorylated rapidly. No prosthetic group or significant quantity of metal was found associated with either of the PASc-containing proteins. The DNA-binding specificity of DcuR was studied by use of the pure protein. It was found to be converted from a monomer to a dimer upon acetylphosphate treatment, and native polyacrylamide gel electrophoresis suggested that it can oligomerize. DcuR specifically bound to the promoters of the three known DcuSR-regulated genes (dctA, dcuB, and frdA), with apparent K(D)s of 6 to 32 micro M for untreated DcuR and < or =1 to 2 microM for the acetylphosphate-treated form. The binding sites were located by DNase I footprinting, allowing a putative DcuR-binding motif [tandemly repeated (T/A)(A/T)(T/C)(A/T)AA sequences] to be identified. The DcuR-binding sites of the dcuB, dctA, and frdA genes were located 27, 94, and 86 bp, respectively, upstream of the corresponding +1 sites, and a new promoter was identified for dcuB that responds to DcuR.
Compliance, quality of life and quantitative voice quality aspects of hands-free speech (2005)

After 6 months, 19% of patients used the new ASV on a daily basis (mean 5 h/day), while 57% used it on an irregular basis as an additional rehabilitation tool for special occasions. Two-thirds of the study group indicated that they would continue to use the new ASV after the study period. With respect to the objective parameters, statistically significantly better maximum phonation times and dynamic loudness ranges were observed with the new ASV compared to the Blom-Singer ASV. However, the best results for all the objective parameters were obtained with digital occlusion via the Provox HME.
Anti-GBM disease following CTLA4 blockade in a patient with metastatic melanoma (2009)

Cytotoxic T-lymphocyte-associated antigen-4 (CTLA4) antagonists are currently being investigated in patients with metastatic malignant melanoma. It is proposed that this therapy will upregulate T-cell responses to melanoma cells while simultaneously targeting regulatory T lymphocytes (Tregs) which are known to suppress the host's immune response to cancer cells. In some of these patients, immune-mediated adverse events such as enterocolitis, dermatitis, uveitis and hepatitis have been observed. We report a case of a 50-year-old man presenting with cough, fever, macroscopic haematuria and oligoanuric kidney failure following treatment with the CTLA4 antagonist tremelimumab for metastatic malignant melanoma. Kidney biopsy demonstrated crescentic glomerulonephritis and strong linear glomerular basement membrane (GBM) staining for IgG and C3; serum anti-GBM antibody level was markedly elevated (>200 U/ml).
Transmission Study of Andes Hantavirus Infection in Wild Sigmodontine Rodents (2004)

Our study was designed to contribute to an understanding of the timing and conditions under which transmission of Andes hantavirus in Oligoryzomys longicaudatus reservoir populations takes place. Mice were caged in test habitats consisting of steel drums containing holding cages, where seronegative rodents were exposed to wild seropositive individuals by freely sharing the same cage or being separated by a wire mesh. Tests were also performed for potential viral transmission to mice from excrement-tainted bedding in the cages. Andes virus transmitted efficiently; from 130 attempts with direct contact, 12.3% resulted in virus transmission. However, if we consider only those rodents that proved to be infectious, from 93 attempts we obtained 16 infected animals (17.2%). Twelve of them resulted from intraspecies O. longicaudatus encounters where male mice were differentially affected and 4 resulted from O. longicaudatus to Abrothrix olivaceus. Experiments using Abrothrix longipilis as receptors were not successful. Transmission was not observed between wire mesh-separated animals, and mice were not infected from excrement-tainted bedding. Bites seemed not to be a requisite for oral transmission. Genomic viral RNA was amplified in two out of three saliva samples from seropositive rodents, but it was not detected in urine samples obtained by vesicle puncture from two other infected rodents. Immunohistochemistry, using antibodies against Andes (AND) hantavirus proteins, revealed strong reactions in the lung and salivary glands, supporting the possibility of oral transmission. Our study suggests that AND hantavirus may be principally transmitted via saliva or saliva aerosols rather than via feces and urine.
Bile acid sequestrants: their use in combination with other lipid-lowering agents. (1999)

Several potent drugs are currently available for the treatment of hyperlipidemia. These pharmacotherapies include bile acid sequestrants, HMG-CoA reductase inhibitors (commonly referred to as 'statins'), fibrates and nicotinic acid. Combination therapy to reduce plasma cholesterol levels in hyperlipidemic patients is becoming more popular, as concerns about toxicity resulting from the long-term used of systemically acting drugs are raised. One of the more widespread combinations used to reduce plasma cholesterol levels is that of a bile acid sequestrant and a statin. Combinations of bile acid sequestrants with either niacin or fibrates have been found to be very effective in patients with mixed hyperlipidemia, since the triglyceride-lowering effect of niacin or a fibrate complements the cholesterol-lowering effect of the sequestrant. One major advantage of combination therapy is the ability to reduce the dose of each component to more tolerable levels for the patient. An additional advantage is the reduced cost to achieve the cholesterol reduction goal, as the dose response is relatively good at greatly reduced doses for each component.
Emerging memories: resistive switching mechanisms and current status (2012)

The resistance switching behaviour of several materials has recently attracted considerable attention for its application in non-volatile memory (NVM) devices, popularly described as resistive random access memories (RRAMs). RRAM is a type of NVM that uses a material(s) that changes the resistance when a voltage is applied. Resistive switching phenomena have been observed in many oxides: (i) binary transition metal oxides (TMOs), e.g. TiO(2), Cr(2)O(3), FeO(x) and NiO; (ii) perovskite-type complex TMOs that are variously functional, paraelectric, ferroelectric, multiferroic and magnetic, e.g. (Ba,Sr)TiO(3), Pb(Zr(x) Ti(1-x))O(3), BiFeO(3) and Pr(x)Ca(1-x)MnO(3); (iii) large band gap high-k dielectrics, e.g. Al(2)O(3) and Gd(2)O(3); (iv) graphene oxides. In the non-oxide category, higher chalcogenides are front runners, e.g. In(2)Se(3) and In(2)Te(3). Hence, the number of materials showing this technologically interesting behaviour for information storage is enormous. Resistive switching in these materials can form the basis for the next generation of NVM, i.e. RRAM, when current semiconductor memory technology reaches its limit in terms of density. RRAMs may be the high-density and low-cost NVMs of the future. A review on this topic is of importance to focus concentration on the most promising materials to accelerate application into the semiconductor industry. This review is a small effort to realize the ambitious goal of RRAMs. Its basic focus is on resistive switching in various materials with particular emphasis on binary TMOs. It also addresses the current understanding of resistive switching behaviour. Moreover, a brief comparison between RRAMs and memristors is included. The review ends with the current status of RRAMs in terms of stability, scalability and switching speed, which are three important aspects of integration onto semiconductors.
Different 3' end regions strongly influence the level of gene expression in plant cells. (1989)

We have investigated the functional role of a 3' end region on the expression of a reporter gene in plant cells. In stably transformed plants, expression of the reporter gene without a plant gene 3' end is variable and depends on the fortuitous presence of polyadenylation signals in the downstream sequences. When the reporter gene is flanked by pBR322 DNA, 3'-processing and polyadenylation occurs at (a) cryptic site(s) within these vector sequences. Using a transient gene expression system, we present a deletion analysis of the 3' end of the octopine synthase gene showing that the most proximal polyadenylation signal per se is not sufficient to ensure expression but that a downstream (G)T-rich sequence is also required. Optimal expression of the fusion gene requires more than 98 base pairs and at most 142 base pairs downstream from the most distal polyadenylation site. We analyzed the expression of chimeric genes with 3' end sequences originating from different plant genes. In the transient expression assay, all constructs direct similar neomycin phosphotransferase II activities. However, in stably transformed tissue, the gene constructs displayed characteristic expression levels which varied as much as 60-fold. This result suggests a role for 3' end sequences in post-transcriptional processes such as efficiency of 3'-processing and/or mRNA stability.
Lignin peroxidase oxidation of manganese(2+) in the presence of veratryl alcohol, malonic or oxalic acid, and oxygen (1990)

Veratryl alcohol (3,4-dimethoxybenzyl alcohol) appears to have multiple roles in lignin degradation by Phanerochaete chrysosporium. It is synthesized de novo by the fungus. It apparently induces expression of lignin peroxidase (LiP), and it protects LiP from inactivation by H2O2. In addition, veratryl alcohol has been shown to potentiate LiP oxidation of compounds that are not good LiP substrates. We have now observed the formation of Mn3+ in reaction mixtures containing LiP, Mn2+, veratryl alcohol, malonate buffer, H2O2, and O2. No Mn3+ was formed if veratryl alcohol or H2O2 was omitted. Mn3+ formation also showed an absolute requirement for oxygen, and oxygen consumption was observed in the reactions. This suggests involvement of active oxygen species. In experiments using oxalate (a metabolite of P. chrysosporium) instead of malonate, similar results were obtained. However, in this case, we detected (by ESR spin-trapping) the production of carbon dioxide anion radical (CO2.-) and perhydroxyl radical (.OOH) in reaction mixtures containing LiP, oxalate, veratryl alcohol, H2O2, and O2. Our data indicate the formation of oxalate radical, which decays to CO2 and CO2.-. The latter reacts with O2 to form O2.-, which then oxidizes Mn2+ to Mn3+. No radicals were detected in the absence of veratryl alcohol. These results indicate that LiP can indirectly oxidize Mn2+ and that veratryl alcohol is probably a radical mediator in this system.
High power, single mode, all-fiber source of femtosecond pulses at 1550 nm and its use in supercontinuum generation (2004)

We present a source of high power femtosecond pulses at 1550 nm with compressed pulses at the end of a single mode fiber (SMF) pigtail. The system generates 34 femtosecond pulses at a repetition rate of 46 MHz, with average powers greater than 400 mW. The pulses are generated in a passively modelocked, erbium-doped fiber laser, and amplified in a short, erbium-doped fiber amplifier. The output of the fiber amplifier consists of highly chirped picosecond pulses. These picosecond pulses are then compressed in standard single mode fiber. While the compressed pulses in the SMF pigtail do show a low pedestal that could be avoided with the use of bulk-optic compression, the desire to compress the pulses in SMF is motivated by the ability to splice the single mode fiber to a nonlinear fiber, for continuum generation applications. We demonstrate that with highly nonlinear dispersion shifted fiber (HNLF) fusion spliced directly to the amplifier output, we generate a supercontinuum spectrum that spans more than an octave, with an average power 400 mW. Such a high power, all-fiber supercontinuum source has many important applications including frequency metrology and bio-medical imaging.