gebhart/patrepeval huggingface dataset:
Characterization of the Effects of Oxygen on Xanthine Oxidase-mediated Nitric Oxide Formation (2004)

Under anaerobic conditions, xanthine oxidase (XO)-catalyzed nitrite reduction can be an important source of nitric oxide (NO). However, questions remain regarding whether significant XO-mediated NO generation also occurs under aerobic conditions. Therefore, electron paramagnetic resonance, chemiluminescence NO-analyzer, and NO-electrode studies were performed to characterize the kinetics and magnitude of XO-mediated nitrite reduction as a function of oxygen tension. With substrates xanthine or 2,3-dihydroxybenz-aldehyde that provide electrons to XO at the molybdenum site, the rate of NO production followed Michaelis-Menten kinetics, and oxygen functioned as a competitive inhibitor of nitrite reduction. However, with flavin-adenine dinucleotide site-binding substrate NADH as electron donor, aerobic NO production was maintained at more than 70% of anaerobic levels, and binding of NADH to the flavin-adenine dinucleotide site seemed to prevent oxygen binding. Therefore, under aerobic conditions, NADH would be the main electron donor for XO-catalyzed NO production in tissues. Studies of the pH dependence of NO formation indicated that lower pH values decrease oxygen reduction but greatly increase nitrite reduction, facilitating NO generation. Isotope tracer studies demonstrated that XO-mediated NO formation occurs in normoxic and hypoxic heart tissue. Thus, XO-mediated NO generation occurs under aerobic conditions and is regulated by oxygen tension, pH, nitrite, and reducing substrate concentrations.
Interleukin 6 levels in synovial fluids of patients with different arthritides: correlation with local IgM rheumatoid factor and systemic acute phase protein production. (1992)

Interleukin 6 (IL-6), a multifunctional cytokine particularly active in regulation of the acute phase response, governs the terminal maturation of B lymphocytes and participates in early activation of T cells. IL-6 levels of synovial fluids of 153 patients with different arthritides were measured by a simple sandwich enzyme immunoassay. Highest IL-6 concentrations were detected in patients with rheumatoid arthritis (RA), particularly in those characterized by very active general symptoms and severe joint pain. High IL-6 levels were detected in patients with juvenile RA with polyarticular onset of disease and in gout. Corresponding to the suggested in vivo relevance of IL-6, dose correlation of IL-6 levels with the synovial IgM rheumatoid factor accumulation was demonstrated. The rate of the correlation between synovial IL-6 level and concentration of serum C-reactive protein in RA was inversely proportional to the dose of steroid treatment in patients with RA.
Essential fatty acid deficiency and renewal of rod outer segments in the albino rat. (1976)

Biochemical studies in albino rats fed a lab chow diet (control) showed a 9 to 10 day turnover time for rhodopsin in rod photoreceptor membranes, whereas the turnover time in animals raised on a fat-free diet (experimental) was not easily measurable. The number of phagosomes in the pigment epithelium of the control group was three times that found in the experimetals. These studies support earlier autoradiographic data which suggested that the renewal of new photoreceptor discs in the rat retina is controlled by the availability of polyunsaturated fatty acids.
A 95mV-startup step-up converter with V<inf>th</inf>-tuned oscillator by fixed-charge programming and capacitor pass-on scheme (2011)

Harvesting energy from the environment by using a thermoelectric generator (TEG) or photovoltaic cells provides a solution for battery-free sensor networks or electronic healthcare systems. In these systems, the harvested energy is supplied at a very low voltages, requiring a low-startup-voltage power circuit for kick-start from low voltage. A previous sub-100mV-startup-voltage boost converter was implemented by using a mechanically assisted step-up process that needs vibration at startup and the application is rather limited. In this paper, a 95mV startup voltage step-up converter without any mechanical stimulus extends the applicability of energy harvesting. The circuit converts a 100mV input to a 0.9V output with 72% conversion efficiency without any external clocks or mechanical switches. A capacitor pass-on scheme eliminates an additional external output capacitor that functions only at the startup.
Dopaminergic mechanisms in the pathogenesis of schizophrenia 1 (1992)

The dopamine hypothesis of schizophrenia has been the dominant theoretical construction guiding research and treatment of the schizophrenic disorders over the past generation. This hypothesis, in its simplest guise, posits the presence of a functional alteration in central dopaminergic systems in the brains of schizophrenic patients. Recent findings have resulted in a greater understanding of the complexity of the central dopaminergic systems and have led to revisions of the hypothesis of a simple functional hyperactivity of central dopaminergic systems. These recent data suggest that there may be regionally restricted changes in the function of the mesotelencephalic dopamine system, and that these changes may be in opposite directions. Such changes may be associated with dysfunctions of interactions between distinct dopaminergic terminal field regions, and may be subserved by functional derangements in other transmitter systems or reflect regionally restricted changes in expression or function of distinct dopamine receptors or catecholamine synthetic enzymes. A recent FASEB symposium reviewed new advances in molecular biology, biochemistry, pharmacology, anatomy, and systems neuroscience as they relate to schizophrenia, and discussed the implications of these data for guiding future research and treatment strategies.
Ionic polymer-metal composites (IPMCs) as biomimetic sensors, actuators and artificial muscles - a review (1998)

This paper presents an introduction to ionic polymer-metal composites and some mathematical modeling pertaining to them. It further discusses a number of recent findings in connection with ion-exchange polymer-metal composites (IPMCs) as biomimetic sensors and actuators. Strips of these composites can undergo large bending and flapping displacement if an electric field is imposed across their thickness. Thus, in this sense they are large motion actuators. Conversely by bending the composite strip, either quasi-statically or dynamically, a voltage is produced across the thickness of the strip. Thus, they are also large motion sensors. The output voltage can be calibrated for a standard size sensor and correlated to the applied loads or stresses. They can be manufactured and cut in any size and shape. In this paper first the sensing capability of these materials is reported. The preliminary results show the existence of a linear relationship between the output voltage and the imposed displacement for almost all cases. Furthermore, the ability of these IPMCs as large motion actuators and robotic manipulators is presented. Several muscle configurations are constructed to demonstrate the capabilities of these IPMC actuators. This paper further identifies key parameters involving the vibrational and resonance characteristics of sensors and actuators made with IPMCs. When the applied signal frequency varies, so does the displacement up to a critical frequency called the resonant frequency where maximum deformation is observed, beyond which the actuator response is diminished. A data acquisition system was used to measure the parameters involved and record the results in real time basis. Also the load characterizations of the IPMCs were measured and it was shown that these actuators exhibit good force to weight characteristics in the presence of low applied voltages. Finally reported are the cryogenic properties of these muscles for potential utilization in an outer space environment of a few Torrs and temperatures of the order of -140 degrees Celsius. These muscles are shown to work quite well in such harsh cryogenic environments and thus present a great potential as sensors and actuators that can operate at cryogenic temperatures.
Low density lipoprotein subclasses and response to a low-fat diet in healthy men (1994)

Lipid and lipoprotein response to reduced dietary fat intake was investigated in relation to differences in distribution of LDL subclasses among 105 healthy men consuming high-fat (46%) and low-fat (24%) diets in random order for six weeks each. On high-fat, 87 subjects had predominantly large, buoyant LDL as measured by gradient gel electrophoresis and confirmed by analytic ultracentrifugation (pattern A), while the remainder had primarily smaller, denser LDL (pattern B). On low-fat, 36 men changed from pattern A to B. Compared with the 51 men in the stable A group, men in the stable B group (n = 18) had a three-fold greater reduction in LDL cholesterol and significantly greater reductions in plasma apoB and mass of intermediate (LDL II) and small (LDL III) LDL subtractions measured by analytic ultracentrifugation. In both stable A and change groups, reductions in LDL-cholesterol were not accompanied by reduced plasma apoB, consistent with the observation of a shift in LDL particle mass from larger, lipid-enriched (LDL I and II) to smaller, lipid-depleted (LDL III and IV) subfractions, without significant change in particle number. Genetic and environmental factors influencing LDL subclass distributions thus may also contribute substantially to interindividual variation in response to a low-fat diet.
DNA polymerase active site is highly mutable: Evolutionary consequences (2000)

DNA polymerases contain active sites that are structurally superimposable and highly conserved in sequence. To assess the significance of this preservation and to determine the mutational burden that active sites can tolerate, we randomly mutated a stretch of 13 amino acids within the polymerase catalytic site (motif A) of Thermus aquaticus DNA polymerase I. After selection, by using genetic complementation, we obtained a library of approximately 8, 000 active mutant DNA polymerases, of which 350 were sequenced and analyzed. This is the largest collection of physiologically active polymerase mutants. We find that all residues of motif A, except one (Asp-610), are mutable while preserving wild-type activity. A wide variety of amino acid substitutions were obtained at sites that are evolutionarily maintained, and conservative substitutions predominate at regions that stabilize tertiary structures. Several mutants exhibit unique properties, including DNA polymerase activity higher than the wild-type enzyme or the ability to incorporate ribonucleotide analogs. Bacteria dependent on these mutated polymerases for survival are fit to replicate repetitively. The high mutability of the polymerase active site in vivo and the ability to evolve altered enzymes may be required for survival in environments that demand increased mutagenesis. The inherent substitutability of the polymerase active site must be addressed relative to the constancy of nucleotide sequence found in nature.
Profiles of prostaglandin biosynthesis in normal lung and tumor tissue from lung cancer patients. (1988)

prostaglandin (PG) biosynthetic profiles from endogenous arachidonic acid were determined by capillary gas chromatography-mass spectrometry in matched fresh normal lung (NL) and lung cancer (LC) tissue fragments obtained from 42 individual LC patients at the time of diagnostic thoracotomy. The histological diagnoses represented were squamous cell carcinoma (N = 20), adenocarcinoma (N = 7), small cell carcinoma (N = 4), mixed cell carcinoma (N = 2), bronchioloalveolar cell carcinoma (N = 2), large cell undifferentiated carcinoma (N = 3), bronchial carcinoid (N = 1), and metastatic tumors (N = 3). When PG biosynthesis was determined in NL tissue separately, low mean levels of PGE2 and PGF2 alpha (less than 2 pmol/mg protein/15 min), intermediate levels of PGD2 and 6-keto-PGF1 alpha (6KPGF1 alpha) (2-7 pmol/mg protein/15 min), and high levels of thromboxane B2 (TXB2) (greater than 7 pmol/mg protein/15 min) were observed. There was no particular correlation with cigarette smoking history and PG biosynthesis in NL. When PG production in LC tissue was evaluated separately, high levels of PGE2, PGF2 alpha, and 6KPGF1 alpha as well as TXB2 and low levels of PGD2 were noted. In addition, LC tissue from cigarette smokers demonstrated elevated levels of PGE2, 6KPGF1 alpha, and TXB2 when compared to current nonsmokers with LC (P less than 0.05 in all instances). Simultaneous comparison of PG production in matched LC and NL tissue from individual patients indicated increased biosynthesis of PGE2 and PGF2 alpha and low levels of PGD2 in LC compared to NL tissue (P less than 0.05 in all instances; paired, two-tailed, Student's t test). Individual comparison of PG biosynthesis according to LC histological cell type revealed that PGE2 and PGF2 alpha were consistently elevated in all four common primary LC histological cell types, the only exception being large cell undifferentiated carcinoma. Interestingly, this latter LC histological cell type presented a unique profile with lower levels of PGE2 and PGD2 in LC than in NL tissue (P less than 0.05 in both instances). In addition, the biosynthesis of all 5 PGs studied was consistently higher in primary than metastatic adenocarcinomas of the lung (P less than 0.05 in all instances). No differences were observed in NL and LC tissue for the major LC histological cell types when PGD2, TXB2, or 6KPGF1 alpha biosyntheses were compared. These findings indicate that the profiles of PG biosynthesis in LC and NL tissue from individual patients may differ substantially. These differences may reflect, in part, contributions to the PG biosynthetic profile unique to malignant cells.
Neuroprotective effects of resveratrol against β‐amyloid‐induced neurotoxicity in rat hippocampal neurons: involvement of protein kinase C (2004)

1. Resveratrol, an active ingredient of red wine extracts, has been shown to exhibit neuroprotective effects in several experimental models. 2. The present study evaluated the neuroprotective effects of resveratrol against amyloid beta(Abeta)-induced toxicity in cultured rat hippocampal cells and examined the role of the protein kinase C (PKC) pathway in this effect. 3. Pre-, co- and post-treatment with resveratrol significantly attenuated Abeta-induced cell death in a concentration-dependent manner, with a concentration of 25 microm being maximally effective. 4. Pretreatment (1 h) of hippocampal cells with phorbol-12-myristate-13-acetate, a PKC activator, at increasing concentrations (1-100 ng x ml(-1)), resulted in a dose-dependent reduction in Abeta-induced toxicity, whereas the inactive 4alpha-phorbol had no effect. 5. Pretreatment (30 min) of hippocampal cells with GF 109203X (1 microm), a general PKC inhibitor, significantly attenuated the neuroprotective effect of resveratrol against Abeta-induced cell death. 6. Treatment of hippocampal cells with resveratrol (20 microm) also induced the phosphorylation of various isoforms of PKC leading to activation. 7. Taken together, the present results indicate that PKC is involved in the neuroprotective action of resveratrol against Abeta-induced toxicity.
Fabrication of the Funnel-Shaped Three-Dimensional Plasmonic Tip Arrays by Directional Photofluidization Lithography (2010)

Plasmonics allow localization of an electromagnetic (EM) field into nanoscale "hotspots", a feature that is of technological significance due to potential applications related to spectroscopic sensing and nanofocusing. In relation to this, many researchers have sought to fabricate metallic nanostructures with sharp edges, as they provide much higher EM field enhancement compared with rounded structures. However, a fabrication method satisfying stringent requirements for the efficient EM field enhancement including three-dimensionality, vertical orientation, large-area fabrication, and tunability of structural features, which are of practical importance for efficient plasmonic light enhancement at hotspots, has yet to be achieved. Herein, we fabricate large-area, vertically aligned three-dimensional plasmonic tip (i.e., nanofunnel) arrays with unprecedented flexibility in the control of the structural features by directional photofluidization lithography. Using this approach, the structural features of nanofunnel tips including the sharpness, shape, and orientation were precisely controlled in a scalable and deterministic manner. The effects of the structural features of the nanofunnel on the EM field enhancement were systematically investigated and analyzed, and the optimum tip features for maximum EM field enhancement were thereupon identified. The suggested nanofabrication technique and resulting structures will be of practical importance in spectroscopic and nanophotonic applications.
Molecular Expression Analysis of Restrictive Receptor for Interleukin 13, a Brain Tumor-associated Cancer/Testis Antigen (2000)

The results strongly support a need to redirect IL13 towards its more restrictive, IL4-independent, receptor for glioma diagnosis and therapies. Moreover, the gene for IL13R alpha resides on chromosome X. Since IL13R alpha is (1) a cancer-associated protein, (2) virtually restricted to testes among normal tissues, and (3) its gene is on chromosome X, IL13R alpha is unexpectedly categorized as a cancer/testis antigen. Our findings make IL13R alpha even more attractive as a target for variety of approaches in glioma molecular management.
Abrogation of p27 by cDNA Antisense Suppresses Quiescence (G0 State) in Fibroblasts (1996)

Progression of eukaryotic cells through the cell cycle is governed by the sequential formation, activation, and subsequent inactivation of a series of cyclin-dependent kinase (Cdk) complexes. p27(Kip1) (p27) is a Cdk inhibitor that blocks, in vitro, the activity of cyclin D-Cdk4, cyclin D-Cdk6, cyclin E-Cdk2 as well as cyclin A-Cdk2, a complex active during S phase. The level of p27 protein expression, usually high in G0/G1 resting cells, declines as cells progress toward S phase and enforced expression of p27 in fibroblasts causes G1 arrest. This situation prevails in CCL39, a Chinese hamster lung fibroblast cell line (this report). However, in addition to p27, several other Cdk inhibitors known to alter G1 progression coexist in most mammalian cells. To investigate the specific contribution of p27 in the control of the mitogen-sensitive G0/G1 arrest, we specifically reduced its synthesis by expressing a full-length p27 antisense cDNA in CCL39 cells. Interestingly, reduction of up to 90% of p27 protein expression increased both basal and serum-stimulated gene transcription of cyclin D1, cyclin A, dihydrofolate reductase, and DNA synthesis reinitiation. Moreover, overexpression of this antisense allows cells to grow for several generations in a serum-free medium supplemented with insulin and transferrin only, thus suggesting that p27-depleted cells cannot exit the cell cycle. These effects were fully reversed by coexpression of a plasmid encoding p27 sense. We conclude that p27, by setting the level of growth factor requirement, plays a pivotal role in controlling cell cycle exit, a fundamental step in growth control.
Evidence for a fatty acid reductase catalyzing the synthesis of aldehydes for the bacterial bioluminescent reaction. Resolution from luciferase and dependence on fatty acids. (1979)

The enzyme responsible for the stimulation by ATP AND NADPH of light emission catalyzed by bacterial luciferase has been partially purified from extracts of the luminescent bacterium, Photobacterium phosphoreum. The stimulatory activity was found to be stabilized by high concentrations of mercaptoethanol, permitting it to be separated from luciferase into an active and stable form and enabling further characterization of its functional properties. The activity of the enzyme was shown to be dependent not only on ATP and NADPH but also on the presence of a long chain fatty acid, and was inhibited by the addition of NADH and horse liver alcohol dehydrogenase. The specificity for fatty acids, as measured by the stimulation of luciferase activity, had a very limited range, with maximal luminescence being obtained with myristic acid and lower responses being observed only with tridecanoic and pentadecanoic acid. These results provide evidence in vitro for an enzyme in bioluminescent bacteria that functions as a fatty acid reductase converting fatty acids to aldehydes which in turn can be utilized by luciferase in the light-emitting reaction.
Selective Lysis of Bacteria but Not Mammalian Cells by Diastereomers of Melittin:  Structure−Function Study (1997)

Studies on lipid-peptide interactions of cytolytic polypeptides tend to emphasize the importance of the amphipathic alpha-helical structure for their cytolytic activity. In this study, diasetereomers of the bee venom melittin (26 a.a.), a non-cell-selective cytolysin, were synthesized and investigated for their structure and cytolytic activity toward bacteria and mammalian cells. Similarly to the findings with the diastereomers of the less cytolytic peptide pardaxin (33 a.a.) (Shai & Oren. 1996), the melittin diastereomer, lest their alpha-helical structure, which abrogated their hemolytic activity toward human erythrocytes. However, they retained their antibacterial activity and completely lysed both Gram-positive and Gram-negative bacteria, as revealed by transmission electron microscopy. To understand the molecular mechanism underlying this selectivity, binding experiments utilizing the intrinsic tryptophan of melittin, tryptophan quenching experiments using brominated phospholipids, and membrane destabilization studies were done. The data revealed that the melittin diastereomers bound to and destabilized only negatively-charged phospholipid vesicles, in contrast to native melittin, which binds strongly to both negatively-charged and zwitterionic phospholipids. However, the partition coefficient, the depth of penetration into the membrane, and the membrane-permeating activity of the diastereomers with negatively-charged phospholipids were similar to those obtained with melittin. The results obtained do not support the formation of transmembrane pores as the mode of action of the diastereomers, but rather suggest that these peptides bind to the surface of the bacterial membrane, cover it in a "carpet-like" manner, and dissolve it like a detergent. The results presented here together with those obtained with the cytolytic peptide pardaxin suggest that the combination of hydrophobicity and net positive charge may be sufficient in the design of potent diastereomers of antibacterial polypeptides for the treatment of infectious diseases.
Distinct Early Serological Signatures Track with SARS-CoV-2 Survival (2020)

As SARS-CoV-2 infections and death counts continue to rise, it remains unclear why some individuals recover from infection, whereas others rapidly progress and die. Although the immunological mechanisms that underlie different clinical trajectories remain poorly defined, pathogen-specific antibodies often point to immunological mechanisms of protection. Here, we profiled SARS-CoV-2-specific humoral responses in a cohort of 22 hospitalized individuals. Despite inter-individual heterogeneity, distinct antibody signatures resolved individuals with different outcomes. Although no differences in SARS-CoV-2-specific IgG levels were observed, spike-specific humoral responses were enriched among convalescent individuals, whereas functional antibody responses to the nucleocapsid were elevated in deceased individuals. Furthermore, this enriched immunodominant spike-specific antibody profile in convalescents was confirmed in a larger validation cohort. These results demonstrate that early antigen-specific and qualitative features of SARS-CoV-2-specific antibodies point to differences in disease trajectory, highlighting the potential importance of functional antigen-specific humoral immunity to guide patient care and vaccine development.