gebhart/patrepeval huggingface dataset:
<title>Stationary low-coherence light imaging and spectroscopy using a CCD camera</title> (1994)

We describe a new optical low-coherence reflectometer (interferometer) for depth profiling and lateral scanning without moving parts which can also be employed as a stationary FT-IR spectrometer. The reflectometer covers a range of 0.45 mm and 1 mm in the depth and lateral dimensions, respectively. The entire depth range is recorded simultaneously in one scan using a cooled 16-bit CCD camera; the lateral dimension is covered by scanning the probe beam sequentially across the sample with an acousto- optic deflector. The frequency shift generated by this deflector and an additional one placed in the reference arm creates an AC heterodyne signal with a frequency of 2kHz. Since the CCD camera cannot record the AC signal directly, a special readout scheme is employed. Stationary imaging was demonstrated using an artificial phantom. Using the same interferometer configured as a stationary FT-IR spectrometer, we measured the emission spectrum of a LED with a resolution of 0.74 nm at a central wavelength of 820 nm. We discuss the performance of the stationary CCD imaging system and compare it to that of a single-detector system employing moving parts.
A Faceted Requirements-Driven Approach to Service Design and Composition (2008)

The Web services research community has proposed a number of approaches for service composition, ranging from manual to semi-automatic to completely automatic. However, it is often difficult to take independently developed services and compose them, since they may not work together correctly. For service composition to occur, the services in question must be designed and developed in a manner that facilitates their composition. In this paper, we propose a novel approach for service design and composition that combines top-down and bottom-up elements. Our approach is driven by faceted, tag-based functional requirements provided by end-users. These requirements describe, at a high-level, the families of compositions that end-users desire. The requirements kick off a top-down service development lifecycle, where enterprise architects and service developers design, develop and test workflows and services, possibly reusing existing flows and services in the process. At runtime, end-users can specify goals, which are satisfied through a bottom-up composition of flows from the available services. The composed flows include those explicitly designed by the architects as well as new ones that are assembled in a serendipitous manner from the available services. With examples from a case study in the financial services domain, we demonstrate our approach for designing and developing services that can be composed into myriad workflows based on end-user goals.
Functional improvement of damaged adult mouse muscle by implantation of primary myoblasts. (1997)

1. Myoblasts from expanded primary cultures were implanted into cryodamaged soleus muscles of adult BALB/c mice. One to four months later isometric tension recordings were performed in vitro, and the male donor cells implanted into female hosts were traced on histological sections using a Y-chromosome-specific probe. The muscles were either mildly or severely cryodamaged, which led to reductions in tetanic muscle force to 33% (n = 9 muscles, 9 animals) and 70% (n = 11) of normal, respectively. Reduced forces resulted from deficits in regeneration of muscle tissue as judged from the reduced desmin-positive cross-sectional areas (34 and 66% of control, respectively). 2. Implantation of 10(6) myogenic cells into severely cryodamaged muscles more than doubled muscle tetanic force (to 70% of normal, n = 14), as well as specific force (to 66% of normal). Absolute and relative amount of desmin-positive muscle cross-sectional areas were significantly increased indicating improved microarchitecture and less fibrosis. Newly formed muscle tissue was fully innervated since the tetanic forces resulting from direct and indirect (nerve-evoked) stimulation were equal. Endplates were found on numerous Y-positive muscle fibres. 3. As judged from their position under basal laminae of muscle fibres and the expression of M-cadherin, donor-derived cells contributed to the pool of satellite cells on small- and large-diameter muscle fibres. 4. Myoblast implantation after mild cryodamage and in undamaged muscles had little or no functional or structural effects; in both preparations only a few Y-positive muscle nuclei were detected. It is concluded that myoblasts from expanded primary cultures-unlike permanent cell lines-significantly contribute to muscle regeneration only when previous muscle damage is extensive and loss of host satellite cells is severe.
Detection of glycopeptide resistance genotypes and identification to the species level of clinically relevant enterococci by PCR (1995)

A PCR assay that allows simultaneous detection of glycopeptide resistance genotypes and identification to the species level of clinically relevant enterococci (Enterococcus faecium, E. faecalis, E. gallinarum, and E. casseliflavus) was developed. This assay was based on specific amplification of internal fragments of genes encoding D-alanine:D-alanine ligases and related glycopeptide resistance proteins. The specificity of the assay was tested on 5 well-characterized glycopeptide-resistant strains and on 15 susceptible enterococcal type strains. Clinical isolates of enterococci that could not be identified to the species level by conventional methods were identified by the PCR test. This assay offers a specific and rapid alternative to antibiotic susceptibility tests, in particular for detection of low-level vancomycin resistance.
The Release of Intact Oligosaccharides from Specific Glycoproteins by Endo-β-N-acetylglucosaminidase H (1974)

Abstract Endo-β-N-acetylglucosaminidase H, purified to homogeneity from cultural filtrates of Streptomyces griseus (Tarentino, A. L., and Maley, F. (1974) J. Biol. Chem. 249, 811–817) was tested for its capacity to hydrolyze oligosaccharides from various glycoproteins. A complete and rapid release of oligosaccharide was effected from sulfitolyzed ovalbumin, bovine pancreatic deoxyribonuclease A, and ribonuclease B, and an invertase from Saccharomyces cerevisiae. These glycoproteins all contain a neutral oligosaccharide that is attached to the protein by a glycosyl asparagine bond and has the following composition: Asn-(GlcNAc)2(Man)x(GlcNAc)y. Analysis of the hydrolysis products revealed that the N-acetylglucosamine residue of di-N-acetylchitobiose distal to the asparagine is on the reducing end of the oligosaccharide, whereas the proximal N-acetylglucosamine remains with the protein. Neither the enzymatic properties nor the circular dichroic patterns of ribonuclease B and deoxyribonuclease A were altered significantly by the removal of their respective oligosaccharides. However, the elution of ribonuclease B from IRC-50 was changed, as was the electrophoretic mobility of deoxyribonuclease. Treatment of proteins that contain both neutral and acidic oligosaccharides, such as thyroglobulin, immunoglobulin M, and porcine ribonuclease, resulted in the release of the neutral chains only. A marked increase in the release of oligosaccharides from immunoglobulin M was effected by 2-mercaptoethanol. Removal of the neutral oligosaccharides did not appear to affect the immunological properties of this immunoglobulin.
Surface-epitope masking and expression cloning identifies the human prostate carcinoma tumor antigen gene PCTA-1 a member of the galectin gene family. (1996)

The selective production of monoclonal antibodies (mAbs) reacting with defined cell surface-expressed molecules is now readily accomplished with an immunological subtraction approach, surface-epitope masking (SEM). Using SEM, prostate carcinoma (Pro 1.5) mAbs have been developed that react with tumor-associated antigens expressed on human prostate cancer cell lines and patient-derived carcinomas. Screening a human LNCaP prostate cancer cDNA expression library with the Pro 1.5 mAb identifies a gene, prostate carcinoma tumor antigen-1 (PCTA-1). PCTA-1 encodes a secreted protein of approximately 35 kDa that shares approximately 40% sequence homology with the N-amino terminal region of members of the S-type galactose-binding lectin (galectin) gene family. Specific galectins are found on the surface of human and marine neoplastic cells and have been implicated in tumorigenesis and metastasis. Primer pairs within the 3' untranslated region of PCTA-1 and reverse transcription-PCR demonstrate selective expression of PCTA-1 by prostate carcinomas versus normal prostate and benign prostatic hypertrophy. These findings document the use of the SEM procedure for generating mAbs reacting with tumor-associated antigens expressed on human prostate cancers. The SEM-derived mAbs have been used for expression cloning the gene encoding this human tumor antigen. The approaches described in this paper, SEM combined with expression cloning, should prove of wide utility for developing immunological reagents specific for and identifying genes relevant to human cancer.
Report of a committee convened to discuss the evaluation and staging of patients with Hodgkin's disease: Cotswolds meeting. (1989)

The Ann Arbor classification for describing the stage of Hodgkin's disease at initial presentation has formed the basis upon which treatment is selected and has allowed comparison of results achieved by different investigators for almost two decades. A meeting was convened to review the classification and modify it in the light of experience gained in its use and new techniques for evaluating disease. It was concluded that the structure of the classification be maintained. It was particularly recommended: (1) that computed tomography (CT) be included as a technique for evaluating intrathoracic and infradiaphragmatic lymph nodes; (2) that the criteria for clinical involvement of the spleen and liver be modified to include evidence of focal defects with two imaging techniques and that abnormalities of liver function be ignored; (3) that the suffix 'X' to designate bulky disease (greater than 10 cm maximum dimension) be introduced; and (4) that a new category of response to therapy, unconfirmed/uncertain complete remission (CR[u]), be introduced to accommodate the difficulty of persistent radiological abnormalities of uncertain significance.
Transparent and conductive Ga-doped ZnO films grown by low pressure metal organic chemical vapor deposition (1997)

Highly transparent conductive Ga-doped zinc oxide (ZnO:Ga) has been deposited on 3 in.×4 in. Corning 7059 glass and other substrates using a high speed rotating disk reactor low pressure metal organic chemical vapor deposition system. Diethylzinc, oxygen, and triethylgallium were used as precursors. The films exhibit low resistivity, ∼2.6×10−4 Ω cm, high optical transparency (&amp;gt;85%) in the visible range, good adhesion, and are highly stable. The film properties were correlated with the growth conditions, including flow rate, temperature, pressure, and doping concentrations. The microstructural properties of the films, such as surface and interface morphology, crystallinity, and composition were studied using scanning electron microscopy, x-ray diffraction, and secondary ion mass spectroscopy. The resistivity and transmittance of the films were investigated by four-point probe measurements, photoluminescence spectroscopy, and optical absorption spectroscopy. In order to meet the needs for application to flat panel displays, the thermal stability of the Ga-doped ZnO films have been tested by a dc biased heater. The feasibility of film processing was also investigated through patterning and wet chemical etching.
Neurobehavioral changes following caudate infarct: a case report with literature review. (1991)

A case of left caudate infarct with its associated neurobehavioral changes is reported with review of literature. The patient showed apathy, decreased problem solving ability, impaired memory and abstract thinking, especially the verbal memory. Such behavioral and cognitive changes correspond to disturbances of specific prefrontal-caudate circuits, either dorsolateral prefrontal or lateral orbitofrontal circuits. From review of literature, it is known that patients with dorsolateral caudate involvement may show apathy, reduced spontaneity and initiative; Patients with ventromedial caudate involvement will exhibit disinhibition, disorganization and impulsiveness, and patients with larger caudate lesion may show affective symptoms with psychotic features.
Induction of Hepatocyte Stimulating Activity by T3and Appearance of the Activity despite Inhibition of DNA Synthesis by Adriamycin (1984)

A hepatocyte stimulating activity (HSA) has been extracted from rats that had received an injection of a pharmacological dose of T3 20 hours earlier. The injection of HSA from T3-treated rats into different recipient rats that had previously had 40% of their liver removed resulted in a significant increase in hepatic DNA synthesis. The injection of saline or HSA from normal rat liver had little or no effect on hepatic DNA synthesis in recipient rats. HSA from the T3-treated rats also stimulated DNA synthesis in Novikoff hepatoma cells and primary hepatocytes in culture, and in isolated normal rat liver nuclei in a nuclear incorporating system. In further experiments in which the increased DNA synthesis that follows partial hepatectomy was blocked by adriamycin, HSA appeared in these non-regenerating livers. This latter observation had indicated that the development of HSA is not merely an accompaniment of DNA synthesis.
Proto-Oncogenes and Human Cancers (1987)

The idea that specific genes or groups of genes are responsible for the induction or maintenance of cancer is by no means new. Recent research efforts to understand such genetic sequences have focused on the study of cellular oncogenes or proto-oncogenes. Much of what we have learned about proto-oncogenes has its basis in studies of the rapidly transforming retroviruses. These viruses are known to cause cancer in a variety of vertebrate species, including primates.The molecular characterization of the genome of the rapidly transforming retroviruses first led to the identification of oncogenic sequences. All of the rapidly transforming retroviruses carry . . .
Density of newly synthesized plasma membrane proteins in intracellular membranes II. Biochemical studies. (1984)

Using two independent methods, incorporation of radioactive amino-acid and quantitative immunoblotting, we have determined that the rate of synthesis of each of the Semliki Forest virus (SFV) proteins in infected baby hamster kidney (BHK) cells is 1.2 X 10(5) copies/cell/min. Given the absolute surface areas of the endoplasmic reticulum and Golgi complex presented in the companion paper (Griffiths, G., G. Warren, P. Quinn , O. Mathieu - Costello , and A. Hoppeler , 1984, J. Cell Biol. 98:2133-2141), and the approximate time spent in these organelles during their passage to the plasma membrane (Green J., G. Griffiths, D. Louvard , P. Quinn , and G. Warren 1981, J. Mol. Biol. 152:663-698), the mean density of each viral protein in these organelles can be calculated to be 90 and 750 molecules/micron 2 membrane, respectively. In contrast, we have determined that the density of total endogenous integral membrane proteins in these organelles is approximately 30,000 molecules/micron 2 so that the spike proteins constitute only 0.28 and 2.3% of total membrane protein in the endoplasmic reticulum and Golgi, respectively. Quantitative immunoblotting was used to give direct estimates of the concentrations of one of the viral membrane protein precursors (E1) in subcellular fractions; these agreed closely with the calculated values. The data are discussed with respect to the sorting of transported proteins from those endogenous to the intracellular membranes.
S-nitrosylation of proteins with nitric oxide: synthesis and characterization of biologically active compounds. (1992)

Endothelium-derived relaxing factor (EDRF) activity has been attributed to the highly labile nitric oxide radical (NO). In view of the fact that the plasma and cellular milieux contain reactive species that can rapidly inactivate NO, it has been postulated that NO is stabilized by a carrier molecule that preserves its biological activity. Reduced thiol species are candidates for this role, reacting readily in the presence of NO to yield biologically active S-nitrosothiols that are more stable than NO itself. Because sulfhydryl groups in proteins represent an abundant source of reduced thiol in biologic systems, we examined the reaction of several sulfhydryl-containing proteins of diverse nature and function upon exposure to authentic NO and EDRF. We demonstrate that S-nitroso proteins form readily under physiologic conditions and possess EDRF-like effects of vasodilation and platelet inhibition. These observations suggest that S-nitrosothiol groups in proteins may serve as intermediates in the cellular metabolism of NO and raise the possibility of an additional type of cellular regulatory mechanism.
Low‐dose naltrexone for the treatment of fibromyalgia: Findings of a small, randomized, double‐blind, placebo‐controlled, counterbalanced, crossover trial assessing daily pain levels (2013)

The preliminary evidence continues to show that low-dose naltrexone has a specific and clinically beneficial impact on fibromyalgia pain. The medication is widely available, inexpensive, safe, and well-tolerated. Parallel-group randomized controlled trials are needed to fully determine the efficacy of the medication.
Proto-value functions (2005)

This paper presents a novel framework called proto-reinforcement learning (PRL), based on a mathematical model of a proto-value function: these are task-independent basis functions that form the building blocks of all value functions on a given state space manifold. Proto-value functions are learned not from rewards, but instead from analyzing the topology of the state space. Formally, proto-value functions are Fourier eigenfunctions of the Laplace-Beltrami diffusion operator on the state space manifold. Proto-value functions facilitate structural decomposition of large state spaces, and form geodesically smooth orthonormal basis functions for approximating any value function. The theoretical basis for proto-value functions combines insights from spectral graph theory, harmonic analysis, and Riemannian manifolds. Proto-value functions enable a novel generation of algorithms called representation policy iteration, unifying the learning of representation and behavior.
Methotrexate-Modified Superparamagnetic Nanoparticles and Their Intracellular Uptake into Human Cancer Cells (2005)

A magnetic nanoparticle conjugate was developed that can potentially serve both as a contrast enhancement agent in magnetic resonance imaging and as a drug carrier in controlled drug delivery, targeted at cancer diagnostics and therapeutics. The conjugate is made of iron oxide nanoparticles covalently bound with methotrexate (MTX), a chemotherapeutic drug that can target many cancer cells whose surfaces are overexpressed by folate receptors. The nanoparticles were first surface-modified with (3-aminopropyl)trimethoxysilane to form a self-assembled monolayer and subsequently conjugated with MTX through amidation between the carboxylic acid end groups on MTX and the amine groups on the particle surface. Drug release experiments demonstrated that MTX was cleaved from the nanoparticles under low pH conditions mimicking the intracellular conditions in the lysosome. Cellular viability studies in human breast cancer cells (MCF-7) and human cervical cancer cells (HeLa) further demonstrated the effectiveness of such chemical cleavage of MTX inside the target cells through the action of intracellular enzymes. The intracellular trafficking model proposed was supported through nanoparticle uptake studies which demonstrated that cells expressing the human folate receptor internalized a higher level of nanoparticles than negative control cells.
Flow Cytometry - Recent Perspectives (2012)

"Flow Cytometry - Recent Perspectives" is a compendium of comprehensive reviews and original scientific papers. The contents illustrate the constantly evolving application of flow cytometry to a multitude of scientific fields and technologies as well as its broad use as demonstrated by the international composition of the contributing author group. The book focuses on the utilization of the technology in basic sciences and covers such diverse areas as marine and plant biology, microbiology, immunology, and biotechnology. It is hoped that it will give novices a valuable introduction to the field, but will also provide experienced flow cytometrists with novel insights and a better understanding of the subject.
The envA Permeability/Cell Division Gene of Escherichia coli Encodes the Second Enzyme of Lipid A Biosynthesis (1995)

The envA gene of Escherichia coli has been shown previously to be essential for cell viability (Beall, B. and Lutkenhaus, J. (1987) J. Bacteriol. 169, 5408-5415), yet it encodes a protein of unknown function. Extracts of strains harboring the mutant envA1 allele display 3.5-18-fold reductions in UDP-3-O-acyl-N-acetylglucosamine deacetylase specific activity. The deacetylase is the second enzymatic step of lipid A biosynthesis. The structural gene coding for the deacetylase has not been assigned. In order to determine if the envA gene encodes the deacetylase, envA was cloned into an isopropyl-1-thio-beta-D-galactopyranoside-inducible T7-based expression system. Upon induction, a protein of the size of envA was highly overproduced, as judged by SDS-PAGE. Direct deacetylase assays of cell lysates revealed a concomitant approximately 5,000-fold overproduction of activity. Assays of the purified, overproduced EnvA protein demonstrated a further approximately 5-fold increase in specific activity. N-terminal amino acid sequencing of the purified protein showed that the first 20 amino acids matched the predicted envA nucleotide sequence. Contaminating species were present at less than 1% of the level of the EnvA protein. Thus, envA is the structural gene for UDP-3-O-acyl-GlcNAc deacetylase. Based on its function in lipid A biosynthesis, we propose the new designation lpxC for this gene.
Rejuvenating cellular respiration for optimizing respiratory function: targeting mitochondria (2015)

Altered bioenergetics with increased mitochondrial reactive oxygen species production and degradation of epithelial function are key aspects of pathogenesis in asthma and chronic obstructive pulmonary disease (COPD). This motif is not unique to obstructive airway disease, reported in related airway diseases such as bronchopulmonary dysplasia and parenchymal diseases such as pulmonary fibrosis. Similarly, mitochondrial dysfunction in vascular endothelium or skeletal muscles contributes to the development of pulmonary hypertension and systemic manifestations of lung disease. In experimental models of COPD or asthma, the use of mitochondria-targeted antioxidants, such as MitoQ, has substantially improved mitochondrial health and restored respiratory function. Modulation of noncoding RNA or protein regulators of mitochondrial biogenesis, dynamics, or degradation has been found to be effective in models of fibrosis, emphysema, asthma, and pulmonary hypertension. Transfer of healthy mitochondria to epithelial cells has been associated with remarkable therapeutic efficacy in models of acute lung injury and asthma. Together, these form a 3R model--repair, reprogramming, and replacement--for mitochondria-targeted therapies in lung disease. This review highlights the key role of mitochondrial function in lung health and disease, with a focus on asthma and COPD, and provides an overview of mitochondria-targeted strategies for rejuvenating cellular respiration and optimizing respiratory function in lung diseases.