gebhart/patrepeval huggingface dataset:
Chitin as an indicator of the biomass of two wood-decay fungi in relation to temperature, incubation time, and media composition (1998)

Cell wall chitin was determined in the mycelia of the brown rot fungus Neolentinus lepideus (Lentinus lepideus) and an isolate of the soft rot fungus Phialophora sp. to study the correlation to mycelial dry mass. The fungi were incubated as liquid cultures for three incubation periods at three temperatures in six nutrient media with varying levels and combinations of carbon and nitrogen. The glucosamine yield was found to be maximized by hydrolysis at 90°C for 48 h. The chitin content in the studied fungi varied from 8.3 to 39.8 μg . mg -1 for N. lepideus and 7.7 to 46 μg . mg -1 for the Phialophora isolate. The chitin concentration was remarkably constant, about 10 μg . mg -1 , in mycelia growing on the low nitrogen malt extract medium. An experiment with wood blocks indicated that chitin may be a good marker for total fungal biomass production, including living and dead mycelia, in early stages of wood decay (dry weight loss &lt;6%). At higher dry weight losses, the chitin content reaches a plateau or decreases despite continuing degradation as determined by the dry weight loss. The chitin content of visible mycelia growing on wood was determined for both fungi and found to be 19.1 and 12.9 μg . mg -1 for N. lepideus and the Phialophora isolate, respectively.Key words: chitin, wood-decay fungi, utility poles, brown rot, soft rot, glucosamine, colorimetry.
Characterization of Matrigel interfaces during defined human embryonic stem cell culture (2009)

Differences in attachment, proliferation, and differentiation were measured for human embryonic stem (hES) cells cultured on various substrata coated with Matrigel, a blend of extracellular matrix proteins derived from murine tumor cells. The authors observed that hES cells attach and grow poorly on Matrigel adsorbed onto polystyrene, while they proliferate when exposed to Matrigel adsorbed onto glass or oxygen plasma treated polystyrene (e.g., "tissue culture" treated polystyrene). Furthermore, hES cells grown on the Matrigel-coated tissue culture polystyrene are less likely to differentiate than those grown on the Matrigel-coated glass. To assess the mechanism for these observations, they replicated the cell culture interface in a quartz crystal microbalance with dissipation monitoring. In addition, they used ellipsometry and scanning electron microscopy to determine the thickness and topography of Matrigel on the varying surfaces. Matrigel formed a viscoelastic multilayer with similar thickness on all three surfaces; however, the network structure was different, where the adsorbed proteins formed a globular network on polystyrene, and fibrillar networks on the hydrophilic substrates. Matrigel networks on glass were denser than on oxygen plasma treated polystyrene, suggesting that the density and structure of the Matrigel network affects stem cell differentiation, where a denser network promoted uncontrolled hES cell differentiation and did not maintain the self-renewal phenotype.
Selective Electrolytic Etching of Germanium and Silicon Junction Transistor Structures (1958)

The electrolytic dissolution of germanium and silicon has been applied to the selective etching of n‐p‐n and p‐n‐p junction transistor structures. By employing the electrical properties of p‐n junctions internal to the pellet as well as the electrolytic behavior of the n‐ and p‐type germanium or silicon, part of the emitter or collector (or both) of a transistor pellet may be etched away, leaving the rest of the pellet intact. The resulting exposure of part of the base region may be used to locate the base region and facilitate attachment of the transistor base lead.
Involvement of NADPH Oxidases in Cardiac Remodelling and Heart Failure (2007)

Cardiac remodelling occurs in response to stress, such as chronic hypertension or myocardial infarction, and forms the substrate for subsequent development of heart failure. Key pathophysiological features include ventricular hypertrophy, interstitial fibrosis, contractile dysfunction, and chamber dilatation. Although the molecular mechanisms are complex and not fully defined, substantial evidence now implicates increased oxidative stress as being important. The NADPH oxidase ('Nox') enzymes are a particularly important source of reactive oxygen species that are implicated in redox signalling. This article reviews the evidence for an involvement of NADPH oxidases in different aspects of adverse cardiac remodelling. A better understanding of the roles of this complex enzyme family may define novel therapeutic targets for the prevention of heart failure.
Progress of follicular lymphoma (2018)

Follicular lymphoma (FL) deriving from the germinal center B-cell, is the most common indolent B-cell non-Hodgkin's lymphoma (NHL) and an incurable disease. FL was reported as the most attractive subtype of NHL at the 59th American Society of Hematology Annual Meeting. The current focus includes maintenance treatment after induction therapy, new drugs combined induction therapy and maintenance therapy, chemotherapy-free for FL and the investigation of new prognostic biology markers.


Key words: 
Lymphoma, follicular; Maintenance treatment; Chemotherapy-free
Peptide Nucleic Acid Antisense Oligomer as a Therapeutic Strategy against Bacterial Infection: Proof of Principle Using Mouse Intraperitoneal Infection (2005)

Antisense oligodeoxynucleotides (ODNs) and their analogs have been successfully utilized to inhibit gene expression and bacterial growth in vitro or in cell culture. In this study, acpP-targeting antisense peptide nucleic acid (PNA) and its peptide conjugate were tested as potential antibacterial agents in two groups of experiments using a mouse model. In the first group, Escherichia coli mutant strain SM101 with a defective outer membrane was used to induce bacteremia and peritonitis in BALB/c mice by intraperitoneal (i.p.) injection. The resulting bacteremia was fatal within 48 h. A single i.p injection of 5 nmol (or more) of PNA administered 30 min before bacterial challenge significantly reduced the bacterial load in mouse blood. Reductions in serum concentrations of the proinflammatory cytokines tumor necrosis factor alpha, interleukin-1beta (IL-1beta), IL-6, and IL-12 were also observed. PNA treatment was effective in rescuing 100% of infected animals. In the second group, bacteremia in BALB/c mice was induced by i.p. injection of E. coli wild-type strain K-12. The infected mice were treated by a single intravenous injection of peptide-PNA conjugate 30 min after bacterial challenge. Treatment with the peptide-PNA conjugate significantly reduced the K-12 load, with modest reduction in cytokine concentrations. The conjugate treatment was also able to rescue up to 60% of infected animals. This report is the first demonstration of ODNs' antibacterial efficacy in an animal disease model. The ability of PNA and its peptide conjugate to inhibit bacterial growth and to prevent fatal infection demonstrates the potential for this new class of antibacterial agents.
Tumor marker concentrations in normal and malignant tissues of colorectal cancer patients and their prognostic relevance. (1997)

Tumor markers CEA, CA19-9, CA15-3, CA125, AFP, beta-HCG, SCC were measured quantitatively in serum, tumor tissue and healthy colonic mucosa of patients with colorectal cancer. We wanted to investigate whether there is a difference in concentration between patients with and without recurrence of cancer. During the follow-up period 14 of 38 patients showed tumor recurrence. Patients with cancer relapse had higher preoperative serum levels of CEA and CA19-9 and significantly higher concentrations in their histologically normal colonic mucosa of CEA, CA19-9, SCC and lower ones of CA15-3. The highest values of CEA, CA19-9, and SCC occurred in the mucosa of patients developing local cancer recurrence. Marker concentrations in tumor tissues themselves did not differ between patients with or without tumor relapse. Though this should be confirmed in a larger number of cases we conclude from these results that tumor marker concentrations in healthy colonic mucosa of patients with colorectal cancer may become valuable indicators of the risk of tumor recurrence.
Evaluation of Three Rapid Methods for the Direct Identification of Staphylococcus aureus from Positive Blood Cultures (2003)

Staphylococci represent the most commonly encountered blood culture isolates. Differentiating Staphylococcus aureus from coagulase-negative staphylococci (CoNS) is important in guiding empirical therapy, especially since the majority of CoNS are contaminants. This study evaluated three rapid methods for the direct identification of S. aureus from blood cultures. A total of 157 patient blood cultures with gram stains showing gram-positive cocci in clusters were included. The following assays were evaluated: API RAPIDEC staph (API) (bioMerieux, Durham, N.C.), the tube coagulase test (TCT) read at 4 h, and peptide nucleic acid (PNA) fluorescence in situ hybridization (FISH) (AdvanDx, Woburn, Mass.). All assays yielded results of S. aureus or non-S. aureus. The direct rapid results were compared to results obtained with isolated colonies using the AccuProbe Staphylococcus aureus Culture Identification Test (Gen-Probe, San Diego, Calif.). API, TCT, and PNA FISH exhibited sensitivities of 96, 84, and 99% and specificities of 99, 100, and 100%, respectively. Direct identification testing by any of these three assays yielded acceptable performance and timely results. This ability to accurately detect S. aureus in blood cultures gives the physician information with which to initiate or tailor antimicrobial therapy. Coupled with direct susceptibility testing of positive blood culture broths, the patient and institution may experience improved outcomes.
A Universal System for Highly Efficient Cardiac Differentiation of Human Induced Pluripotent Stem Cells That Eliminates Interline Variability (2011)

This efficient and cost-effective universal system for cardiac differentiation of hiPSC allows a potentially unlimited production of functional cardiomyocytes suitable for application to hPSC-based drug development, cardiac disease modeling, and the future generation of clinically-safe nonviral human cardiac cells for regenerative medicine.
Proteomics of Protein Secretion by Bacillus subtilis : Separating the “Secrets” of the Secretome (2004)

Secretory proteins perform a variety of important "remote-control" functions for bacterial survival in the environment. The availability of complete genome sequences has allowed us to make predictions about the composition of bacterial machinery for protein secretion as well as the extracellular complement of bacterial proteomes. Recently, the power of proteomics was successfully employed to evaluate genome-based models of these so-called secretomes. Progress in this field is well illustrated by the proteomic analysis of protein secretion by the gram-positive bacterium Bacillus subtilis, for which approximately 90 extracellular proteins were identified. Analysis of these proteins disclosed various "secrets of the secretome," such as the residence of cytoplasmic and predicted cell envelope proteins in the extracellular proteome. This showed that genome-based predictions reflect only approximately 50% of the actual composition of the extracellular proteome of B. subtilis. Importantly, proteomics allowed the first verification of the impact of individual secretion machinery components on the total flow of proteins from the cytoplasm to the extracellular environment. In conclusion, proteomics has yielded a variety of novel leads for the analysis of protein traffic in B. subtilis and other gram-positive bacteria. Ultimately, such leads will serve to increase our understanding of virulence factor biogenesis in gram-positive pathogens, which is likely to be of high medical relevance.
High-speed Atomic Force Microscopy for Capturing Dynamic Behavior of Protein Molecules at Work (2005)

It seems that only the atomic force microscope (AFM) has a potential to trace a protein in action with high spatial and temporal resolution. To realize that potential, we have been developing a high-speed AFM. We have made efforts not only to enhance the scan speed but also to reduce the tip-sample interaction force as much as possible. The high-speed AFM can capture moving protein molecules and weakly interacting protein molecules on video without disturbing their physiological function. Here we review our studies carried out over the past 10 years, and our preliminary work toward the next generation of the instrument. [DOI: 10.1380/ejssnt.2005.384]
Effect of Ice-Induced Cross-Polarization on Digital Earth- Space Links (1984)

Among the techniques proposed to increase the capacity of the allocated frequency bands, reuse of the same channel twice with orthogonal polarizations seems to be very promising. However, imperfect isolation between the two orthogonal channels, arising, for example, from nonspherical scatterers encountered by the transmitted waves during propagation, is likely to limit the possibilities of this frequency reuse technique. While rain-induced cross-polarization is relatively well understood, the impact of cross-polarization coupling due to ice crystals on communication systems has to be thoroughly investigated. In this paper a statistical analysis of depolarization events observed at 20 GHz from the linearly polarized beacon of ATS-6 is carried out. It shows that ice depolarization events occur as frequently and are as significant as rain depolarization events, and also that ice crystals are typically canted within <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">\pm10\deg</tex> of the vertical. From the results obtained, the effect of ice cross-polarization on a dual-polarized microwave link utilizing <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">M</tex> -ary PSK transmission is investigated. These results point out the necessity of implementing cross-polarization cancellation devices.
Latency: the hidden HIV-1 challenge (2006)

Abstract Eradication of HIV-1 from an infected individual cannot be achieved by current regimens. Viral reservoirs established early during the infection remain unaffected by anti-retroviral therapy for a long time and are able to replenish systemic infection upon interruption of the treatment. Therapeutic targeting of viral latency will require a better understanding of the basic mechanisms underlying the establishment and long-term maintenance of HIV-1 in resting memory CD4 T cells, the most prominent reservoir of transcriptionally silent provirus. Since the molecular mechanisms that permit long term transcriptional control of proviral gene expression in these cells are still obscure, this review aims at summarizing the various aspects of the problem that need to be considered. In particular, this review will focus the attention on the control of transcription imposed by chromatin through various epigenetic mechanisms. Exploring the molecular details of viral latency will provide new insights for eventual future therapeutics that aim at viral eradication.
Pulse Shape Discrimination in a Plastic Scintillator (1960)

A plastic scintillator has been developed which shows a decay time dependent upon energy loss per unit distance, and hence is suitable for use with pulse shape discrimination methods. This scintillator was employed in conjunction with an improved discrimination system and the data were analyzed on a two-dimensional analyzer which provided a matrix of 72 × 64 channels. At a bias level where 99 per cent of the electron scintillations were eliminated, it was possible to obtain almost 100 per cent counting efficiency for recoil protons of 2 mev, and the scintillator was useful for protons down to 0.5 mev. The influence of various monomers, polymerization conditions, scintillating solutes, and secondary solvents was investigated, and a preliminary survey of the effects of these variables on pulse shape discrimination is presented.
Systemic capsaicin and olvanil reduce the acute algogenic and the late inflammatory phase following formalin injection into rodent paw (1991)

Systemic capsaicin and an analogue, olvanil (NE-19550, 4-hydroxy-3-methoxyphenyl methyl-9Z-octadecenamide), were tested for antinociceptive activity in a model of persistent pain produced by the subcutaneous injection of formalin into the rodent hind paw. Formalin induced a biphasic nociceptive response in mice and rats which was measured (a) by the time spent licking the injected paw in mice and (b) by making electrophysiological recordings of single nociceptive neurone discharges in L1-L3 of the spinal dorsal horn of halothane-anaesthetised rats. In mice the initial phase of the response was reduced by systemic administration of morphine, capsaicin and olvanil but not by indomethacin. The second, more prolonged, inflammatory phase of the response was reduced by each agent. In rats, similar concentrations of capsaicin and olvanil reduced both the first and second components of the formalin response. These data show that capsaicin and a non-pungent analogue, olvanil, are efficacious antinociceptive agents in a model of prolonged chemical nociception induced by formalin. Their activity compares favourably with that of morphine and appears superior to that of indomethacin.
A structure-activity analysis of chemical and biological parameters of chloroethylnitrosoureas in mice. (1977)

Summary Linear regression analysis was performed to study the correlation of in vitro carbamoylating activities, alkylating activities, and chemical half-lives with the biological activities of six chloroethylnitrosoureas in mice. The biological parameters included the dose resulting in the death of 10% of normal mice (LD 10 ), antitumor activity for the L1210 leukemia system, and myelotoxicity as expressed by the nadir of the peripheral blood neutrophil count following an LD 10 dose. There was a highly significant inverse linear relationship between alkylating activity and the chemical half-life of the chloroethylnitrosoureas. A significant linear relationship was found between the molar LD 10 and alkylating activity or the chemical half-life; the greater the alkylating activity or the shorter the half-life, the lower the molar LD 10 . In contrast, carbamoylating activity did not demonstrate a significant correlation with the molar LD 10 . None of the three chemical parameters demonstrated a significant linear correlation with antitumor activity or myelotoxicity. Water solubility did not function as an independent variable for either of these biological activities. Two agents in this series, chlorozotocin and 1-(2-chloroethyl)-3-(β-d-glucopyranosyl)-1-nitrosourea, produced no suppression of the peripheral blood neutrophil count at an LD 10 dose; both have a glucose carrier that may be responsible for their reduced myelotoxicity.
Structural Basis of a Flavivirus Recognized by Its Neutralizing Antibody (2003)

The flavivirus envelope protein is the dominant antigen in eliciting neutralizing antibodies and plays an important role in inducing immunologic responses in the infected host. We have determined the solution structure of the major antigenic domain (domain III) of the Japanese encephalitis virus (JEV) envelope protein. The JEV domain III forms a beta-barrel type structure composed of six antiparallel beta-strands resembling the immunoglobulin constant domain. We have also identified epitopes of the JEV domain III to its neutralizing antibody by chemical shift perturbation measurements. Site-directed mutagenesis experiments are performed to confirm the NMR results. Our study provides a structural basis for understanding the mechanism of immunologic protection and for rational design of vaccines effective against flaviviruses.
Suppression of recA deficiency in plasmid recombination by bacteriophage lambda beta protein in RecBCD- ExoI- Escherichia coli cells (1989)

Plasmid recombination, like other homologous recombination in Escherichia coli, requires RecA protein in most conditions. We have found that the plasmid recombination defect in a recA mutant can be efficiently suppressed by the beta protein of bacteriophage lambda. beta protein is required for homologous recombination of lambda chromosomes during lytic phage growth in a recA host and is known to have a strand-annealing activity resembling that of RecA protein. The bioluminescence recombination assay was used for genetic analysis of beta-protein-mediated plasmid recombination. Efficient suppression of the recA mutation by beta protein required the absence of the E. coli nucleases exonuclease I and RecBCD nuclease. These nucleases inhibit a RecA-mediated plasmid recombination pathway that is more efficient than the pathway functioning in wild-type cells. Like RecA-mediated plasmid recombination in RecBCD- ExoI- cells, beta-protein-mediated plasmid recombination depended on concurrent DNA replication and on the activity of the recQ gene. However, unlike RecA-mediated plasmid recombination, beta-protein-mediated recombination in RecBCD- ExoI- cells was independent of recF and recJ activities. We propose that inactivation of exonuclease I and RecBCD nuclease stabilizes a recombination intermediate that is involved in RecA- and beta-protein-catalyzed homologous pairing reactions. We suggest that the intermediate may be linear plasmid DNA with a protruding 3' end, since these nucleases are known to interfere with the synthesis of such linear forms. The different recF and recJ requirements for beta-protein-dependent and RecA-dependent recombinations imply that the mechanisms of formation or processing of the putative intermediate differ in the two cases.
Cellular Uptake of Functional Nanogels Prepared by Inverse Miniemulsion ATRP with Encapsulated Proteins, Carbohydrates, and Gold Nanoparticles (2009)

Atom transfer radical polymerization (ATRP) was used to produce a versatile drug delivery system capable of encapsulating a range of molecules. Inverse miniemulsion ATRP permitted the synthesis of biocompatible and uniformly cross-linked poly(ethylene oxide)-based nanogels entrapping gold nanoparticles, bovine serum albumin, rhodamine B isothiocyanate-dextran, or fluoresceine isothiocyanate-dextran. These moieties were entrapped to validate several biological outcomes and to model delivery of range of molecules. Cellular uptake of nanogels was verified by transmission electron microscopy, gel electrophoresis, Western blotting, confocal microscopy, and flow cytometry. Fluorescent colocalization of nanogels with a fluorophore-conjugated antibody for clathrin indicated clathrin-mediated endocytosis. Furthermore, internalization of nanogels either with or without GRGDS cell attachment-mediating peptides was quantified using flow cytometry. After 45 min of incubation, the uptake of unmodified FITC-Dx-loaded nanogels was 62%, whereas cellular uptake increased to >95% with the same concentration of GRGDS-modified FITC-Dx nanogels. In addition, a spheroidal coculture of human umbilical vascular endothelial cells (HUVECs) and human mesenchymal stem cells (hMSCs) validated cell endocytosis. Application of ATRP enabled the synthesis of a functionalized drug delivery system with a uniform network that is capable of encapsulating and delivering inorganic, organic, and biological molecules.