gebhart/patrepeval huggingface dataset:
The VEOS Project (1994)

The Virtual Environment Operating Shell (veos) was developed at University of Washington's Human Interface Technology Laboratory as software infrastructure for the lab's research in virtual environments. veos was designed from scratch to provide a comprehensive and unified management facility to support generation of, interaction with, and maintenance of virtual environments. VEOS emphasizes rapid prototyping, heterogeneous distributed computing, and portability. We discuss the design, philosophy and implementation of veos in depth. Within the Kernel, the shared database transformations are pattern-directed, communications are asynchronous, and the programmer's interface is LISP. An entity-based metaphor extends object-oriented programming to systems-oriented programming. Entities provide first-class environments and biological programming constructs such as perceive, react, and persist. The organization, structure, and programming of entities are discussed in detail. The article concludes with a description of the applications that have contributed to the iterative refinement of the VEOS software.
Vascularized organoid engineered by modular assembly enables blood perfusion (2006)

Tissue engineering is one approach to address the donor-organ shortage, but to attain clinically significant viable cell densities in thick tissues, laboratory-constructed tissues must have an internal vascular supply. We have adopted a biomimetic approach and assembled microscale modular components, consisting of submillimeter-sized collagen gel rods seeded with endothelial cells (ECs) into a (micro)vascularized tissue; in some prototypes the gel contained HepG2 cells to illustrate the possibilities. The EC-covered modules then were assembled into a larger tube and perfused with medium or whole blood. The interstitial spaces among the modules formed interconnected channels that enabled this perfusion. Viable cell densities were high, within an order of magnitude of cell densities within tissues, and the percolating nature of the flow through the construct was evident in microcomputed tomography and Doppler ultrasound measurements. Most importantly, the ECs retained their nonthrombogenic phenotype and delayed clotting times and inhibited the loss of platelets associated with perfusion of whole blood through the construct. Unlike the conventional scaffold and cell-seeding paradigm of other tissue-engineering approaches, this modular construct has the potential to be scalable, uniform, and perfusable with whole blood, circumventing the limitations of other approaches.
Inhibition of Neointimal Smooth Muscle Accumulation After Angioplasty by an Antibody to PDGF (1991)

Approximately 30 to 40 percent of atherosclerotic coronary arteries treated by angioplasty or by bypass surgery occlude as a result of restenosis. This restenosis is due principally to the accumulation of neointimal smooth muscle cells, which is also a prominent feature of the advanced lesions of atherosclerosis. The factors responsible for the accumulation of intimal smooth muscle cells have not been identified. Platelet-derived growth factor (PDGF) is a potent smooth muscle chemoattractant and mitogen. It is present in platelets and can be formed by endothelium, smooth muscle, and monocyte-derived macrophages. The development of an intimal lesion in the carotid artery of athymic nude rats induced by intraarterial balloon catheter deendothelialization was inhibited by a polyclonal antibody to PDGF. These data demonstrate that endogenous PDGF is involved in the accumulation of neointimal smooth muscle cells associated with balloon injury and may be involved in restenosis after angioplasty, and perhaps in atherogenesis as well.
Effect of physical exercise on cartilage volume and thickness in vivo: MR imaging study. (1998)

MR imaging can be used to investigate the response of articular cartilage to physical exercise in vivo. Patients or volunteers should be allowed a sufficient period of physical rest if quantitative measurements of cartilage volume and thickness are to be undertaken in longitudinal studies.
NKT cell immune responses to viral infection (2008)

iNKT cell's versatility allows them to detect and respond to several viruses. Therapeutic approaches to specifically target iNKT cells will require additional research. Notably, the roles of non-invariant NKT cells in response to pathogens warrant further investigation.
Self-Assembled Monolayers of Alkanethiolates Presenting Mannitol Groups Are Inert to Protein Adsorption and Cell Attachment (2000)

This paper reports on a model surface that is inert in biological fluids and that is important for studies in biointerfacial science. A self-assembled monolayer (SAM) terminated in the mannitol group was found to prevent the adsorption of proteins and the attachment of cells. Surface plasmon resonance spectroscopy showed that the mannitol-terminated SAM prevented the adsorption of several proteins and was indistinguishable from a SAM presenting tri(ethylene glycol)groups. In a second set of experiments, monolayers were patterned into circular regions of hexadecanethiolate with the surrounding area terminated in the mannitol group in order to evaluate the inert surface for patterning cell attachment. 3T3 fibroblasts, attached to the circular regions, proliferated to occupy these regions completely and remained patterned on these regions for 25 days. The use of oligo(ethylene glycol)-terminated SAMs, by contrast, showed a loss in fidelity of the pattern after one week in culture. The mannitol-terminated monolayers significantly extend the time course for maintaining patterned cells and will have immediate utility in fundamental and applied biology.
[The effect of new quaternary ammonium compounds on bacteria and fungi. 5: Synthesis of 3-methyl-n-alkylthiomethylpyridinium-, 1-methyl-3-n-alkylthiomethylimidazolium- and 1-ethyl-3-n-alkylthioimidazolinium chloride]. (1983)

Synthesis of some chlorides indicated in headline and their antibacterial properties was described. Synthesis of quaternary pyridine and imidazoline chlorides was performed by reaction of chloromethyl-n-alkylthioether with 3-methylpyridine or 1-methyl- and 1-ethylimidazole. Antibacterial properties of obtained compounds was tested on 13 strains of bacteria and fungi. Chlorides with dodecyl radical indicated the best antibacterial activity.
Monoamine Oxidase B Inhibitors in Parkinson's Disease (2017)

Due to the efficacy shown in clinical trials and their favorable side-effect profile, MAO-B inhibitors are valuable drugs in the treatment of PD. They are recommended as monotherapy in the early stages of the disease and as add-on therapy to levodopa in advanced PD.
The Michelson Interferometer for Global High-resolution Thermospheric Imaging (MIGHTI): Wind and Temperature Observations from the Ionospheric Connection Explorer (ICON) (2013)

We describe the Michelson Interferometer for Global High-resolution Thermospheric Imaging (MIGHTI), an instrument designed to measure thermospheric wind and temperature as part of the Ionospheric Connection (ICON) Explorer mission proposal to the NASA Explorer program.
Upregulation of a T-Type Ca2+Channel Causes a Long-Lasting Modification of Neuronal Firing Mode after Status Epilepticus (2002)

A single episode of status epilepticus (SE) causes numerous structural and functional changes in the brain that can lead to the development of a chronic epileptic condition. Most studies of this plasticity have focused on changes in excitatory and inhibitory synaptic properties. However, the intrinsic firing properties that shape the output of the neuron to a given synaptic input may also be persistently affected by SE. Thus, 54% of CA1 pyramidal cells, which normally fire in a regular mode, are persistently converted to a bursting mode after an episode of SE induced by the convulsant pilocarpine. In this model, intrinsic bursts evoked by threshold-straddling depolarizations, and their underlying spike afterdepolarizations (ADPs), were resistant to antagonists of N-, P/Q-, or L-type Ca2+ channels but were readily suppressed by low (30-100 microm) concentrations of Ni2+ known to block T- and R-type Ca2+ channels. The density of T-type Ca2+ currents, but not of other pharmacologically isolated Ca2+ current types, was upregulated in CA1 pyramidal neurons after SE. The augmented T-type currents were sensitive to Ni2+ in the same concentration range that blocked the novel intrinsic bursting in these neurons (IC50 = 27 microm). These data suggest that SE may persistently convert regular firing cells to intrinsic bursters by selectively increasing the density of a Ni2+-sensitive T-type Ca2+ current. This nonsynaptic plasticity considerably amplifies the output of CA1 pyramidal neurons to synaptic inputs and most probably contributes to the development and expression of an epileptic condition after SE.
VRML: Browsing and Building Cyberspace (1995)

Written by the creator of the VRML graphical standard, this book shows users how to create, display, view and manipulate VRML objects on the Internet. An accompanying CD-ROM includes a collection of VRML objects, VRML converter and object-viewing software.
Quantitative Multicolor Subdiffraction Imaging of Bacterial Protein Ultrastructures in Three Dimensions (2013)

We demonstrate quantitative multicolor three-dimensional (3D) subdiffraction imaging of the structural arrangement of fluorescent protein fusions in living Caulobacter crescentus bacteria. Given single-molecule localization precisions of 20-40 nm, a flexible locally weighted image registration algorithm is critical to accurately combine the super-resolution data with <10 nm error. Surface-relief dielectric phase masks implement a double-helix response at two wavelengths to distinguish two different fluorescent labels and to quantitatively and precisely localize them relative to each other in 3D.
Plasma Melatonin Rhythms In Young and Older Humans During Sleep, Sleep Deprivation, and Wake (2007)

Both sleep and sleep deprivation likely influence melatonin amplitude, and the effect of sleep on melatonin appears to be age dependent.
Combining Musical And Cultural Features For Intelligent Style Detection. (2002)

[TODO] Add abstract here.
Thresher (2005)

We describe Thresher, a system that lets non-technical users teach their browsers how to extract semantic web content from HTML documents on the World Wide Web. Users specify examples of semantic content by highlighting them in a web browser and describing their meaning. We then use the tree edit distance between the DOM subtrees of these examples to create a general pattern, or wrapper, for the content, and allow the user to bind RDF classes and predicates to the nodes of these wrappers. By overlaying matches to these patterns on standard documents inside the Haystack semantic web browser, we enable a rich semantic interaction with existing web pages, "unwrapping" semantic data buried in the pages' HTML. By allowing end-users to create, modify, and utilize their own patterns, we hope to speed adoption and use of the Semantic Web and its applications.
Aging of the Liver: Age–Associated Mitochondrial Damage in Intact Hepatocytes (1996)

Mitochondrial damage may be a major cause of cellular aging. So far, this hypothesis had only been tested using isolated mitochondria. The aim of this study was to investigate the involvement of mitochondria in aging using whole liver cells and not isolated mitochondria only. Using flow cytometry, we found that age is associated with a decrease in mitochondrial membrane potential (30%), an increase in mitochondrial size, and an increase in mitochondrial peroxide generation (23%). Intracellular peroxide levels were also increased. The number of mitochondria per cell and inner mitochondrial membrane mass did not change. Gluconeogenesis from glycerol or fructose (mitochondrial-independent) did not change with age, whereas it did from lactate (mitochondrial-dependent). The change in the rate of gluconeogenesis was not accompanied by changes in any of the following parameters: phosphoenolpyruvate carboxykinase or pyruvate carboxylase activities or mitochondrial ATP/ADP or cytosolic NADH/NAD+ ratios. This was caused by a decreased rate of malate export (to 20% of the controls) from mitochondria. The impairment of the mitochondrial malate transporter is posttranscriptional because its expression in Xenopus oocytes using polyadenylated RNA from livers of young or old animals did not change. Ketogenesis from oleate also fell in hepatocytes from old rats. Our results show, for the first time in intact cells, a correlation between age-associated impairment of cell metabolism and specific changes in mitochondrial function and morphology, supporting the hypothesis that mitochondrial damage plays a key role in aging.
Cloning and characterization of a unique elastolytic metalloproteinase produced by human alveolar macrophages. (1993)

Human alveolar macrophages have the capacity to degrade elastin. As an approach to define proteinases responsible for this activity, we recently cloned a murine macrophage elastase cDNA and demonstrated that it is a member of the matrix metalloproteinase gene family (Shapiro, S. D., Griffin, G. L., Gilbert, D. J., Jenkins, N. A., Copeland, N. G., Welgus, H. G., Senior, R. M., and Ley, T. J. (1992) J. Biol. Chem. 267, 4664-4671). We now report that there is a human orthologue of murine macrophage metalloelastase that we call human macrophage metalloelastase (HME). The full-length HME cDNA spans 1.8 kilobases and contains an open reading frame of 1410 base pairs; the predicted molecular mass of the HME proenzyme is 54 kDa. HME mRNA and protein were detected in human alveolar macrophages. Similar to murine macrophage metalloelastase, HME readily undergoes NH2- and COOH-terminal processing to a mature 22-kDa form. Both recombinant HME expressed in Escherichia coli and native HME derived from human alveolar macrophage-conditioned media degraded insoluble elastin. HME is a unique human metalloproteinase that possesses elastolytic activity and is expressed in alveolar macrophages; it is therefore a candidate molecule for the causation of diseases characterized by damage to the extracellular matrix.
Synthesis and Thermal Behavior of Esterified Aliphatic Hyperbranched Polyether Polyols (2000)

Hyperbranched polyglycerols (DPn = 23−83; Mw/Mn = 1.2−1.5) as well as their propoxylated derivatives were esterified to different extents (23%−100%) with various carboxylic acids (C2 to C18, benzoic, biphenylcarboxylic, and benzoic acid). Composition and molecular weight of the hyperbranched polyether scaffolds were varied with absolute molecular weights (NMR) ranging from Mn = 1800 to 12 400 g/mol. Complete or partial esterification did not affect the narrow polydispersities of the hyperbranched polymers, which were in the range 1.2−1.5 for the esterified polyglycerol samples and 1.2−1.9 for the esterified propoxylated polyether polyols. The parameter a (fractional molecular weight increase) was introduced, which permitted to demonstrate that SEC separates the branched polymers according to hydrodynamic volume. Because of the narrow polydispersity, the samples could be studied systematically by DSC, showing that the flexibility, i.e., Tg, of the hyperbranched polymers is controlled mainly by two factors: (i) the extent of hydrogen bonding and (ii) the formation of order (mesophases, crystallization), which raises the Tg. Tg's of the esterified polyether polyols were in the range −58 to −22 °C, showing the scope and limitations of tailoring the thermal properties of hyperbranched polymers by means of derivatization.
Raised cortisol:DHEAS ratios in the elderly after injury: potential impact upon neutrophil function and immunity (2005)

The detrimental effect of stress on the immune response increases with age, though the mechanisms responsible are not fully understood. The physiological response to stress is regulated in part by the adrenocortical system. Adrenal hormones dehydroepiandrosterone sulphate (DHEAS) and cortisol have opposing effects on the innate immune system, DHEAS enhances while cortisol suppresses immunity and the molar ratio of cortisol to DHEAS increases with age. We found that elderly hip fracture patients produced a robust neutrophilia after injury, but circulating neutrophils showed an impaired antibacterial response. We therefore proposed that adrenocortical hormones mediate the heightened immunosuppression seen in the elderly after injury. We examined neutrophil function and adrenocortical hormone levels in elderly (> 65 years) hip fracture patients and age-matched healthy controls. Thirteen out of 35 elderly patients acquired infections following hip fracture. Neutrophil superoxide production was lower in elderly hip fracture patients compared with controls (P < 0.005) and lower in patients who acquired infection following injury compared with those who did not (P < 0.05). Serum cortisol:DHEAS ratio was higher in elderly hip fracture patients (0.56 +/- 0.38) compared with either age-matched controls (0.36 +/- 0.21; P < 0.05) or young fracture patients (0.087 +/- 0.033; P < 0.0001). Moreover, cortisol: DHEAS was increased in elderly patients who succumbed to infection compared with those who did not (0.803 +/- 0.42 vs. 0.467 +/- 0.28; P < 0.02). In vitro cortisol significantly decreased neutrophil superoxide generation (P < 0.05) and this was prevented by coincubation with DHEAS. We propose that increased cortisol:DHEAS ratios may contribute to reduced immunity following physical stress in the elderly.
Cardiac Surgery in Germany during 2006: A Report on Behalf of the German Society for Thoracic and Cardiovascular Surgery (2007)

All cardiac surgical procedures performed in 81 German cardiac surgical units throughout the year 2006 are presented in this report, based on a voluntary registry which is organized by the German Society for Thoracic and Cardiovascular Surgery. In 2006 a total of 97,123 cardiac surgical procedures (ICD and pacemakers procedures excluded) have been collected in this registry. More than 9.6 % of the patients were older than 80 years compared to 8.4 % in 2005. Hospital mortality in 51,273 isolated CABG procedures (10.1 % off-pump) was 3.1 %. In 20,028 isolated valve procedures a mortality of 4.9 % has been observed. This registry will continue to be an important tool of the German Society for Thoracic and Cardiovascular Surgery enabling a continuous and voluntary quality assurance and illustrating the development of cardiac surgery in Germany.
Book of Abstracts, 4th International Conference on Plasma Medicine (ICPM4) (2012)

International audience
Zygotically Activated Genes Are Suppressed in Mouse Nuclear Transferred Embryos (2006)

Mammalian oocytes have the ability to confer totipotency to terminally differentiated somatic cell nuclei. Viable cloned animals have been produced by somatic cell nuclear transfer (NT) into oocytes in many mammalian species including mouse. However, the success rates of the production were quite low in all species. Many studies have measured differences in gene expression between NT and fertilized embryos in relatively advanced stages of development such as pre- and post-natal stages or the blastocyst stage. In the present study, we compared gene expression patterns using differential display RT-PCR (DDRT-PCR) between the NT and IVF embryos at the 2-cell stage to detect some abnormalities affecting later development of NT embryos. Aberrant gene expression was detected in NT embryos compared with IVF embryos, and MuERV-L and Dnaja2 genes were down-regulated and Inpp5b and Chst12 genes were up-regulated in the NT embryos. Further analysis showed that the expression of zygotically activated genes such as Interferon-gamma, Dub-1, Spz1, DD2106 (unknown gene), and DD2111 (unknown gene) were suppressed in NT embryos, suggesting that the cellular process involved in the nuclear reprogramming of somatic nucleus is not appropriately regulated.
Cathodoluminescence study of Zn doped Gan (1978)

The luminescence properties of GaN doped with Zn are reported. As the Zn concentration increases four different emissions are found using cathodoluminescence : blue (2.85 eV), green (2.5 eV), yellow (2.2 eV) and sometimes red (1.9 eV). Through the analysis of the influence of temperature, injection and time dependence, the blue, green and yellow emissions are found to fit a pair transition model, with a strong phonon coupling. The recombination model is discussed in view of the observed variation of the emission intensities versus injection level.
Interaction of Plasminogen Activator Inhibitor (PAI-1) with Vitronectin (1989)

Immobilized vitronectin was found to bind both purified plasminogen activator inhibitor type 1 (PAI-1) and the PAI-1 in conditioned culture medium of human sarcoma cells. Similarly, immobilized PAI-1 bound both purified vitronectin and vitronectin from normal human serum. These interactions were demonstrated using both enzyme immunoassay and radioiodinated proteins. Solid-phase vitronectin bound PAI-1 with Kd 1.9 x 10(-7) M, and the reverse interaction gave a Kd 5.5 x 10(-8) M. Evidence was also found for a second type of binding with a Kd below 10(-10) M. The molar ratios of the two proteins in the complex at the saturation levels were approximately one molecule of soluble PAI-1 bound per three molecules of immobilized vitronectin and approximately one molecule of soluble vitronectin being bound per one molecule of immobilized PAI-1. Binding of PAI-1 to vitronectin did not lead to an irreversible loss of the ability of PAI-1 to inhibit urokinase (u-PA) and tissue-type plasminogen activator (t-PA). Active u-PA released vitronectin-bound 125I-labeled PAI-1 radioactivity, suggesting that u-PA interacts with the complex. The Mr 50,000 urokinase cleavage product of PAI-1 also bound to vitronectin, but this bound fragment did not inhibit u-PA. Binding of PAI-1 to vitronectin did not interfere with the ability of vitronectin to promote the adhesion and spreading of cells. These results suggest that the interaction between vitronectin and PAI-1 may serve to confine pericellular u-PA activity to focal contact sites where cells use proteolysis in regional detachment.
Molecular hyperpolarizabilities determined from conjugated and nonconjugated organic liquids (1974)

The magnitude and sign (positive) of the molecular hyperpolarizability γ has been determined for several mixtures of nitrobenzene and benzene. This has allowed the testing of the adequacy of Onsager's local field factors, which are found to be valid. By comparing γ of nitrobenzene with that of nitromethane, we find that the delocalized conjugated electrons are an order of magnitude more effective in contributing to γ than are the localized nonconjugated electrons.
HOW CELLS RESPOND TO INTERFERONS (1998)

Interferons play key roles in mediating antiviral and antigrowth responses and in modulating immune response. The main signaling pathways are rapid and direct. They involve tyrosine phosphorylation and activation of signal transducers and activators of transcription factors by Janus tyrosine kinases at the cell membrane, followed by release of signal transducers and activators of transcription and their migration to the nucleus, where they induce the expression of the many gene products that determine the responses. Ancillary pathways are also activated by the interferons, but their effects on cell physiology are less clear. The Janus kinases and signal transducers and activators of transcription, and many of the interferon-induced proteins, play important alternative roles in cells, raising interesting questions as to how the responses to the interferons intersect with more general aspects of cellular physiology and how the specificity of cytokine responses is maintained.