gebhart/patrepeval huggingface dataset:
Hormone-sensitive Lipase Deficiency in Mice Causes Diglyceride Accumulation in Adipose Tissue, Muscle, and Testis (2002)

Hormone-sensitive lipase (HSL) is expressed predominantly in white and brown adipose tissue where it is believed to play a crucial role in the lipolysis of stored triglycerides (TG), thereby providing the body with energy substrate in the form of free fatty acids (FFA). From in vitro assays, HSL is known to hydrolyze TG, diglycerides (DG), cholesteryl esters, and retinyl esters. In the current study we have generated HSL knock-out mice and demonstrate three lines of evidence that HSL is instrumental in the catabolism of DG in vivo. First, HSL deficiency in mice causes the accumulation of DG in white adipose tissue, brown adipose tissue, skeletal muscle, cardiac muscle, and testis. Second, when tissue extracts were used in an in vitro lipase assay, a reduced FFA release and the accumulation of DG was observed in HSL knock-out mice which did not occur when tissue extracts from control mice were used. Third, in vitro lipolysis experiments with HSL-deficient fat pads demonstrated that the isoproterenol-stimulated release of FFA was decreased and DG accumulated intracellularly resulting in the essential absence of the isoproterenol-stimulated glycerol formation typically observed in control fat pads. Additionally, the absence of HSL in white adipose tissue caused a shift of the fatty acid composition of the TG moiety toward increased long chain fatty acids implying a substrate specificity of the enzyme in vivo. From these in vivo results we conclude that HSL is the rate-limiting enzyme for the cellular catabolism of DG in adipose tissue and muscle.
[Design of the human GM-CSF gene using the polymerase chain reaction and its expression in Pseudomonas putida cells]. (1995)

Construction of human GM-CSF gene was conducted by the PCR technique. Four exons of GM-CSF gene were synthesized on the basis of human blood DNA using thermostable Tth DNA polymerase. Synthetic oligonucleotides were used as primers. The oligonucleotides contained sequences complementary to the ends of exons. Joining of exons was conducted by reciprocal complementation of the terminal sequences, followed by filling and amplification of the joined products. In most cases the effective synthesis of exons and joined products was possible only after optimizing the polymerase reaction conditions for each primer pair. Determination of the nucleotide sequence of the synthetic gene showed complete identity with the natural one. The gene was introduced into an expression vector under control of the promoter tandem (tac+lac). Expression of the GM-CSF gene was obtained in Pseudomonas putida cells. The recombinant protein had biological activity.
Interleukin-1β costimulates interferon-γ production by human natural killer cells (2001)

Natural killer (NK) cells are an early source of immunoregulatory cytokines during the innate immune response to viruses, bacteria, and parasites. NK cells provide requisite IFN-gamma to monocytes for the elimination of obligate intracellular pathogens. IL-1beta is a pro-inflammatory cytokine produced by monocytes (i.e. a monokine) during the early immune response to infection, but its role in promoting human NK cell IFN-gamma production is unknown. The current study examines the ability of the monokine IL-1beta, plus IL-12, to costimulate IFN-gamma production by resting CD56(bright) and CD56(dim) human NK cell subsets. CD56(bright) NK cells stimulated with IL-1beta plus IL-12 produced abundant IFN-gamma protein, while little IFN-gamma was produced in identical cultures of CD56(dim) cells. In addition, upon activation with IL-1beta, CD56(bright) NK cells exhibited considerably greater phosphorylation of extracellular signal-regulated kinases p42/44 as compared to CD56(dim) NK cells. Quantitative PCR analysis showed brisk induction of IFN-gamma gene expression following costimulation with IL-1beta plus IL-12 in CD56(bright) NK cells, but intracellular flow cytometry revealed that only a fraction (42+/-2.3%) of CD56(bright) NK cells account for this high IFN-gamma production. These data suggest that the monokine IL-1beta is a potent costimulus of IFN-gamma production by a subset of NK cells following infectious insult.
Module 2: Cell Signalling Pathways (2012)

Cells use a large number of clearly defined signalling pathways to regulate their activity. In this module, attention is focused on the On mechanisms responsible for transmitting information into the cell. These signalling pathways fall into two main groups depending on how they are activated. Most of them are activated by external stimuli and function to transfer information from the cell surface to internal effector systems. However, some of the signalling systems respond to information generated from within the cell, usually in the form of metabolic messengers. For all of these signalling pathways, information is conveyed either through protein–protein interactions or it is transmitted by diffusible elements usually referred to as second messengers. Cells often employ a number of these signalling pathways, and cross-talk between them is an important feature. In this section, attention is focused on the properties of the major intracellular signalling pathways operating in cells to regulate their cellular activity. During the processes of development, specific cell types select out those signalling systems that are suitable to control their particular functions. One of the aims of this website is to understand how these unique cell-specific signalsomes function to regulate different mammalian cell types.
A flexible graphical user interface for performance modeling (2002)

We identify three goals for the graphical user interface (GUI) of a network simulation environment: user friendliness, model re-usability, and application extensibility. We address the user friendliness issue by proposing a simple yet efficient approach to setup parameters for the simulation models. We address the application extensibility issue by a two-layer GUI architecture. The two layers are loosely-coupled, and the first layer can be easily replaced (without affecting the other components of the simulation environment). We address the model re-usability issue by subnetworks. Unlike most existing simulation packages where subnetwork is simply a method to group the nodes, the subnetwork construct in our approach is an integral part of the simulation environment (i.e., all operations for a basic node also apply to a subnetwork). The port concept is used to explicitly define the I/O relationship between a subnetwork and the outside world. Parameter dialog boxes are used to set up the parameters for a subnetwork conveniently. Finally, a simple stack mechanism is proposed to measure subnetwork-wide output statistics.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Mode isolation: A new algorithm for modal parameter identification (2001)

Multiple degree of freedom (MDOF) algorithms are the dominant methods for extracting modal parameters from measured data. These methods are founded on the notion that because the response of a linear dynamic system is the sum of many modal contributions, the extraction technique must deal with all of the modal parameters in a simultaneous fashion. The Mode Isolation Algorithm (MIA) described here is a frequency domain formulation that takes an alternative viewpoint. It extracts the modal parameters of each mode in an iterative search, and then refines the estimation of each mode by isolating its effect from the other modal contributions. The first iteration estimates modes in a hierarchy of their dominance. As each mode is estimated, its contribution is subtracted from the data set, until all that remains is noise. The second and subsequent iterations subtract the current estimates for all other modes to identify the properties of the mode under consideration. The various operations are described in detail, and then illustrated using data from a four-degree-of-freedom system that was previously used to assess the Eigensystem Realization Algorithm (ERA) and Enhanced ERA. Eigenvalues and mode shapes are compared for each algorithm. Another example analyzes simulated data for a cantilever beam with three suspended one-degree-of-freedom subsystems, in which the parameters are adjusted to bring two natural frequencies into close proximity. The results suggest that MIA is more accurate, and more robust in the treatment of noisy data, than either ERA version, and that it is able to identify modes whose bandwidth is comparable to the difference of adjacent natural frequencies.
Milk Protein Coatings Prevent Oxidative Browning of Apples and Potatoes (2001)

ABSTRACT Color analysis on apple and potato slices coated with calcium caseinate or whey protein solutions showed that the 2 coatings efficiently delayed browning by acting as oxygen barriers. The antioxidant properties of the films were realized using a model allowing the release of oxidative species by electrolysis of saline buffer. Whey proteins were a better antioxidant capacity than calcium caseinate. Furthermore, addition of carboxymethyl cellulose (CMC) to the formulations significantly improved their antioxidative power. Best scavenging of oxygen free radicals and reactive oxygen species was found for films based on whey proteins and CMC which inhibited by 75% the formation of colored compounds produced by the reaction of the oxidative species with N,N‐diethyl‐ p ‐phenylenediamine.
Nucleotide sequence of the<i>Escherichia coli</i>uridine phosphorylase (<i>udp</i>) gene (1989)

Journal Article Nucleotide sequence of the Escherichia coli uridine phosphorylase (udp) gene Get access Leslie Walton, Leslie Walton Search for other works by this author on: Oxford Academic PubMed Google Scholar Cynthia A. Richards, Cynthia A. Richards 1Experimental Therapy, Burroughs Wellcome Co.Research Triangle Park, NC 27709, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Lynn P. Elwell Lynn P. Elwell Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 17, Issue 16, 25 August 1989, Page 6741, https://doi.org/10.1093/nar/17.16.6741 Published: 25 August 1989 Article history Received: 05 July 1989 Published: 25 August 1989
Cellular Expression, Trafficking, and Function of Two Isoforms of Human ULBP5/RAET1G (2009)

We demonstrate that the expression patterns of ULBP5RAET1G are very similar to the well-characterised NKG2D ligand, MICA. However the two isoforms of ULBP5/RAET1G have very different cellular localisations that are likely to reflect unique functionality.
Shared books: collaborative publication management for an office information system (1988)

A Shared Book helps the users of an office information system create a multiple-part publication and manage it throughout its life cycle. The Shared Book supports simultaneous collaboration both by allowing different workers to work on different parts at the same time and by ensuring that workers use the current revision of each part. It protects publication information by providing locking and access control. The Shared Book communicates the publication's current state to each worker through a What-You-See-Is-What-I-See (WYSIWIS) display. Early users report that the Shared Books application has improved their productivity by simplifying their file management and by helping them track the production status of their publications. Shared Books will be part of the next release of the Xerox ViewPoint document processing system. In this paper we present the results of our study of publication management needs and describe how Shared Books supports them. We also describe some interesting aspects of its user interface and implementation.
The human lumbar intervertebral disc: evidence for changes in the biosynthesis and denaturation of the extracellular matrix with growth, maturation, ageing, and degeneration. (1996)

Very little is known about the turnover of extracellular matrix in the human intervertebral disc. We measured concentrations of specific molecules reflecting matrix synthesis and degradation in predetermined regions of 121 human lumbar intervertebral discs and correlated them with ageing and Thompson grade of degeneration. Synthesis in intervertebral discs, measured by immunoassay of the content of a putative aggrecan biosynthesis marker (846) and the content of types I and II procollagen markers, is highest in the neonatal and 2-5-yr age groups. The contents of these epitopes/molecules progressively diminished with increasing age. However, in the oldest age group (60-80 yr) and in highly degenerated discs, the type I procollagen epitope level increased significantly. The percentage of denatured type II collagen, assessed by the presence of an epitope that is exposed with cleavage of type II collagen, increased twofold from the neonatal discs to the young 2-5-yr age group. Thereafter, the percentage progressively decreased with increasing age; however, it increased significantly in the oldest group and in highly degenerate discs. We identified three matrix turnover phases. Phase I (growth) is characterized by active synthesis of matrix molecules and active denaturation of type II collagen. Phase II (maturation and ageing) is distinguished by a progressive drop in synthetic activity and a progressive reduction in denaturation of type 11 collagen. Phase III (degeneration and fibrotic) is illustrated by evidence for a lack of increased synthesis of aggrecan and type II procollagen, but also by an increase in collagen type II denaturation and type I procollagen synthesis, both dependent on age and grade of tissue degeneration.
Storing quantum states in bosonic dissipative networks (2008)

By considering a network of dissipative quantum harmonic oscillators, we deduce and analyse the optimum topologies which are able to store quantum superposition states, protecting them from decoherence, for the longest period of time. The storage is made dynamically, in that the states to be protected evolve through the network before being retrieved back in the oscillator where they were prepared. The decoherence time during the dynamic storage process is computed and we demonstrate that it is proportional to the number of oscillators in the network for a particular regime of parameters.
New insights from uncultivated genomes of the global human gut microbiome (2019)

The genome sequences of many species of the human gut microbiome remain unknown, largely owing to challenges in cultivating microorganisms under laboratory conditions. Here we address this problem by reconstructing 60,664 draft prokaryotic genomes from 3,810 faecal metagenomes, from geographically and phenotypically diverse humans. These genomes provide reference points for 2,058 newly identified species-level operational taxonomic units (OTUs), which represents a 50% increase over the previously known phylogenetic diversity of sequenced gut bacteria. On average, the newly identified OTUs comprise 33% of richness and 28% of species abundance per individual, and are enriched in humans from rural populations. A meta-analysis of clinical gut-microbiome studies pinpointed numerous disease associations for the newly identified OTUs, which have the potential to improve predictive models. Finally, our analysis revealed that uncultured gut species have undergone genome reduction that has resulted in the loss of certain biosynthetic pathways, which may offer clues for improving cultivation strategies in the future.
A control method for voltage source inverter without dc link capacitor (2008)

Voltage source inverter plays an important role in modern industry. Conventional voltage source inverter has a large electrolytic capacitor as energy store element in order to keep the dc link voltage constant. However, a large electrolytic capacitor increases the input current distortion. Replacing the large electrolytic capacitor by a small film capacitor the input current quality is improved but the output currents are distorted by low order harmonics. This paper proposes a simple current control method for a voltage source inverter without the use of a large electrolytic capacitor in the dc link in order to compensate the low order harmonics in the output currents. The proposed current control scheme employs just one PI regulator and since that the space vector modulation is used in this control the switching frequency of the converter is kept constant.
Amrinone metabolism (1981)

High-performance liquid chromatographic methods for the analysis of amrinone in plasma and for both amrinone and its N-acetyl metabolite in urine were developed and applied to measure specimens obtained from a number of healthy men who had received intravenous or oral amrinone. The intravenous doses ranged from 0.8 to 2.2 mg/kg. Terminal elimination of amrinone from the bloodstream followed apparent first-order kinetics. Half-life, after the drug had distributed to the tissues, was estimated by a log-linear least-squares regression; mean half-life was 2.6 +/- 1.4 hr. During the first 24 hr after medication, unchanged amrinone excreted in the urine of these subjects represented 10% to 40% of the dose. N-Acetyl metabolite in the urine represented less than 2% of the dose. In the oral study, doses ranged from 25 to 250 mg (0.31 to 3.5 mg/kg) and the maximum plasma concentration attained was proportional to the dose. The first order terminal elimination half-life was possibly dose-related. In only one subject were there unequivocal amounts of the N-acetyl metabolite in the plasma.
Sequence-selective binding of phleomycin to DNA (1987)

The binding of phleomycin and bleomycin to DNA has been investigated by studying their effects on cleavage by DNAase I and micrococcal nuclease. In the presence of cobalt, cleavage of DNA by the antibiotics is suppressed, yet they still provide protection from nuclease attack in regions surrounding the drug cleavage sites. We conclude that cleavage by phleomycin occurs at bonds around which the antibiotic is already selectively bound.
Regulating Bone Formation <i>via</i> Controlled Scaffold Degradation (2003)

It is widely assumed that coupling the degradation rate of polymers used as cell transplantation carriers to the growth rate of the developing tissue will improve its quantity or quality. To test this hypothesis, we developed alginate hydrogels with a range of degradation rates by gamma-irradiating high-molecular-weight alginate to yield polymers of various molecular weights and structures. Decreasing the size of the polymer chains increased the degradation rate in vivo, as measured by implant retrieval rates, masses, and elastic moduli. Rapidly and slowly degrading alginates, covalently modified with RGD-containing peptides to control cell behavior, were then used to investigate the effect of biodegradation rate on bone tissue development in vivo. The more rapidly degrading gels led to dramatic increases in the extent and quality of bone formation. These results indicate that biomaterial degradability is a critical design criterion for achieving optimal tissue regeneration with cell transplantation.
Example-based dynamic skinning in real time (2008)

In this paper we present an approach to enrich skeleton-driven animations with physically-based secondary deformation in real time. To achieve this goal, we propose a novel, surface-based deformable model that can interactively emulate the dynamics of both low-and high-frequency volumetric effects. Given a surface mesh and a few sample sequences of its physical behavior, a set of motion parameters of the material are learned during an off-line preprocessing step. The deformable model is then applicable to any given skeleton-driven animation of the surface mesh. Additionally, our dynamic skinning technique can be entirely implemented on GPUs and executed with great efficiency. Thus, with minimal changes to the conventional graphics pipeline, our approach can drastically enhance the visual experience of skeleton-driven animations by adding secondary deformation in real time.
Microencapsulated Palladium Catalysts: Allylic Substitution and Suzuki Coupling Using a Recoverable and Reusable Polymer-Supported Palladium Catalyst (2001)

Buried alive! A triphenylphosphane palladium catalyst was immobilized onto/into a polymer by microencapsulation and the polymer-supported catalyst (MC [Pd(PPh3)]) successfully used in several palladium-catalyzed reactions (one example is shown). The reactions proceeded in high yields, and the catalyst was recovered by filtration and reused. The air-sensitivity of the palladium complex is substantially suppressed by this immobilization.
Plasma donor-derived cell-free DNA kinetics after kidney transplantation using a single tube multiplex PCR assay (2018)

In conclusion, plasma ddcfDNA fractions decreased exponentially within 10 days after transplantation to a ddcfDNA threshold value of 0.88% or less. To investigate the role of ddcfDNA for rejection monitoring of the graft, future research is needed to determine causes of ddcfDNA% increases above this threshold value.
Modification of hemoglobin - tetrameric stabilization. (1983)

Advantage has been taken of the unique affinity of DBBF for hemoglobin to stabilize the T state and crosslink tetrameric hemoglobin. The oxygen affinity has been further decreased by using PLP to produce a chemically unique molecule with a P50 of 32 under physiologic conditions. Furthermore, the modification is specific, requires only reagents that are commercially available or easily synthesized, and can be prepared in large quantities with up to 80% yield. The unique modified hemoglobin was purified by HPLC and the crosslink was found between the beta chains. This derivative, pyridoxalated-fumarate hemoglobin, sustained life in five rats that were 95% exchanged-transfused with the solution. Preliminary in vivo tests support this derivative as a desirable oxygen-transporting resuscitation fluid.
Temperature Dependence of Up-Conversion Luminescence and Photoluminescence of Mn&lt;SUP&gt;2+&lt;/SUP&gt; in ZnS:Mn&lt;SUP&gt;2+&lt;/SUP&gt; Nanoparticles (2001)

The photoluminescence (excited at both 300 nm and 383.5 nm) and up-conversion luminescence (excited at 767 nm) of the Mn2+ 4T1-->6A1 transition in both bulk and ZnS:Mn2+ nanoparticles have been measured as a function of temperature. The Mn2+ emission spectra shift monotonically to longer wavelengths at lower temperatures, whereas the intensity change of the luminescence is more complex. The complicated temperature behavior is explained by considering the processes of nonradiation relaxation via phonon coupling, exciton thermal dissociation (binding energy), energy transfer, carrier trapping, and the temperature change of the absorption spectra. The fact that the temperature dependence of the 767 nm excited up-conversion luminescence is the same as the 383.5 nm excited photoluminescence in both bulk and nanoparticles supports the conclusion that the up-conversion luminescence is due to two-photon absorption.
Multiplexed Parallel Single Transport Recordings on Nanopore Arrays (2010)

We introduce a nanofabricated silicon chip for massively multiplexed analysis of membrane channels and transporters in suspended lipid membranes that does not require any surface modification or organic solvent. Transport processes through single membrane complexes are monitored by fluorescence. The chip consists of an array of well-defined nanopores, addressing an individual pyramidal back-reflecting 30-fL compartment. The setup allows simultaneous analyses of ∼1000 single transmembrane events in one field of view, observing translocation kinetics of transmembrane complexes.