gebhart/patrepeval huggingface dataset:
Stimulation of bone formation by intraosseous application of recombinant basic fibroblast growth factor in normal and ovariectomized rabbits (1997)

The effect on intraosseous bone formation of a single local injection of recombinant human basic fibroblast growth factor into the distal femur was examined in normal and ovariectomized rabbits. In normal rabbits, basic fibroblast growth factor increased bone mineral density around the injected site in a dose-dependent manner at 4 weeks, with significant effects at concentrations of 400 micrograms and greater. Doses of 400 and 1,600 micrograms of basic fibroblast growth factor increased bone mineral density by 8 and 9%, respectively, compared with the opposite control femur. Histological examination showed that basic fibroblast growth factor (400 micrograms) induced the proliferation or recruitment of undifferentiated mesenchymal cells around the existing trabeculae at 3 days after the injection. For the first 2 weeks, osteoid formation was strongly stimulated, and this was followed by mineral apposition for another 2 weeks, at which time the femurs were harvested. Consequently, basic fibroblast growth factor stimulated intraosseous bone formation at 4 weeks. We speculate that the direct action of basic fibroblast growth factor on bone formation may be to stimulate proliferation or recruitment of minimally differentiated mesenchymal cells and to initiate the cascade of events in later stages of bone formation. In ovariectomized rabbits, basic fibroblast growth factor (400 micrograms) also increased bone mineral density, histomorphometrical bone formation markers, and trabecular connectivity to levels similar to those in rabbits who had received sham operations.
Nanomaterials for In Vivo Imaging (2017)

In vivo imaging, which enables us to peer deeply within living subjects, is producing tremendous opportunities both for clinical diagnostics and as a research tool. Contrast material is often required to clearly visualize the functional architecture of physiological structures. Recent advances in nanomaterials are becoming pivotal to generate the high-resolution, high-contrast images needed for accurate, precision diagnostics. Nanomaterials are playing major roles in imaging by delivering large imaging payloads, yielding improved sensitivity, multiplexing capacity, and modularity of design. Indeed, for several imaging modalities, nanomaterials are now not simply ancillary contrast entities, but are instead the original and sole source of image signal that make possible the modality's existence. We address the physicochemical makeup/design of nanomaterials through the lens of the physical properties that produce contrast signal for the cognate imaging modality-we stratify nanomaterials on the basis of their (i) magnetic, (ii) optical, (iii) acoustic, and/or (iv) nuclear properties. We evaluate them for their ability to provide relevant information under preclinical and clinical circumstances, their in vivo safety profiles (which are being incorporated into their chemical design), their modularity in being fused to create multimodal nanomaterials (spanning multiple different physical imaging modalities and therapeutic/theranostic capabilities), their key properties, and critically their likelihood to be clinically translated.
An intelligent tool for re-engineering software modularity (1991)

The author describes a software tool that provides heuristic modularization advice for improving existing code. A heuristic design similarity measure is defined, based on the Parna information hiding principle. The measure supports two services: clustering, which identifies groups of related procedures, and maverick analysis, which identifies individual procedures that appear to be in the wrong module. The tool has already provided useful advice in several real programming projects. The tool will soon incorporate an automatic tuning method, which allows the tool to learn from its mistakes, adapting its advice to the architect's preferences. A preliminary experiment demonstrates that the automatically tuned similarity function can assign procedures to modules very accurately. >
Maximal exponential growth rate and yield of E. coli obtainable in a bench‐scale fermentor (1974)

Abstract Oxygen supply is one of the main factors which influences aerobic cell growth in a fermentor. Maximal rates at which E. coli can grow on glucose as carbon source under various limiting oxygen‐supply conditions were determined in a bench‐scale fermentor. Culture conditions are described which gave yields of about 38 g dry cells per liter medium.
The Evolution of Advanced Mechanical Defenses and Potential Technological Applications of Diatom Shells (2005)

Diatoms are unicellular algae with silicified cell walls, which exhibit a high degree of symmetry and complexity. Their diversity is extraordinarily high; estimates suggest that about 10(5) marine and limnic species may exist. Recently, it was shown that diatom frustules are mechanically resilient, statically sophisticated structures made of a tough glass-like composite. Consequently, to break the frustules, predators have to generate large forces and invest large amounts of energy. In addition, they need feeding tools (e.g., mandibles or gastric mills) which are hard, tough, and resilient enough to resist high stress and wear, which are bound to occur when they feed on biomineralized objects such as diatoms or other biomineralized protists. Indeed, many copepods feeding on diatoms possess, in analogy to the enamelcoated teeth of mammals, amazingly complex, silica-laced mandibles. The highly developed adaptations both to protect and to break diatoms indicate that selection pressure is high to optimize material properties and the geometry of the shells to achieve mechanical strength of the overall structure. This paper discusses the mechanical challenges which force the development of mechanical defenses, and the structural components of the diatom frustules which indicate that evolutionary optimization has led to mechanically sophisticated structures. Understanding the diatom frustule from the nanometer scale up to the whole shell will provide new insights to advanced combinations of nanostructured composite ceramic materials and lightweight architecture for technological applications.
The regulation of the expression of human interleukin-2 gene. (1993)

Interleukin-2 (IL-2) is a glycoprotein produced by CD4$\sp{+}$ T lymphocytes after mitogenic or antigenic stimulation. IL-2 is required for the proliferation, differentiation and function of both T and B cells, and the IL-2 gene expression is restricted to activated T cells. This work investigates the functions of the cis-acting regulatory sites within the IL-2 enhancer region and the mechanism(s) that control the cell-specific expression of the IL-2 gene. Our results indicate that the IL-2 gene expression is regulated by the cell-specific derepression of its promoter and the positive and negative regulatory effects of the cis-acting sites in the enhancer. The functions of the IL-2 gene regulatory sites have been analyzed in the native IL-2 enhancer and promoter sequences by investigating the transient expression of site-specific mutants of an IL2-CAT plasmid in human or mouse T cells. Different functions have been observed for these regulatory sites in T cells. The NFAT, the distal octamer and the proximal octamer sites have a silencing effect on IL-2 transcription in resting cells, and act as enhancers in the presence of stimulation; the distal and proximal purine box sites display disparate effects on IL-2 gene expression in different T cells; the $\kappa$B and the AP-1 sites respond to IL-1 or PMA stimulation, respectively. The mechanism(s) of the restricted and inducible IL-2 gene expression have been investigated by analyzing the transactivation of the IL-2 gene by the infected cell protein 0 (ICP0) of the herpes simplex virus type 1. We have found that the IL-2 gene expression is controlled in part by the derepression of its promoter between the $-$51 to +18 region in a cell-specific fashion. This derepression requires both an intact TATA box sequence and the transcription initiation site of IL-2 and is sensitive to an immunosuppressant, cyclosporin A. In electrophoretic mobility shift assays, protein complexes have been found to bind to this IL-2 promoter region and correlate with the cell-specific depression effect(s). No cyclosporin A effect has been observed on these DNA-protein complexes. These observations suggest that the IL-2 promoter is regulated in part by derepression, and the lineage specific gene expression can be regulated by factors that regulate the derepression in a cell-specific fashion.
Differentiation of infectious laryngotracheitis virus strains using restriction endonucleases. (1983)

Strains of infectious laryngotracheitis virus (ILTV) were examined using an indirect immunofluorescent test (IIF) and with restriction endonucleases for detecting intratypic differences. Electrophoretic analysis of ILTV DNA fragments cleaved with restriction endonuclease Hind 111 clearly distinguished between strains. The IIF test did not discriminate between strains. A molecular weight estimate of ILTV DNA was made by summation of restriction endonuclease fragments cleaved with BamH1 (102.1 X 10(6)) and Hind111 (97.35 X 10(6)). Differences between the estimates may indicate the presence of submolar fragments.
Abstract 2459: A Potentially Novel Role Of The Follistatin-activin Pathway In Heart Failure And Myocardial Recovery Following Lvad Combination Therapy (2007)

Background - Recent evidence suggests that the activin pathway may play an important role in the pathogenesis of heart failure. Follistatins are potent inhibitors of activin signalling but their role in the heart is unknown. The purpose of this study was to investigate myocardial expression of follistatin (FST) and follistatin-like (FSTL1 and FSTL3) in heart failure and following recovery in patients who received combined mechanical unloading using left ventricular assist device (LVAD) and pharmacologic therapy. Methods and results - Real time quantitative PCR was used to examine gene expression in myocardial samples from donors (n=9), end-stage heart failure patients (n=27) and patients who recovered from heart failure sampled at the time of LVAD implant, at the time of LVAD removal following recovery, and one year post explant. Both FSTL1 and FSTL3 were elevated in heart failure (1.51 and 2.50 fold respectively p&lt;0.005) with expression returning to normal following recovery. Whereas FSTL3 correlated with molecular markers of disease severity, FSTL1 showed negative correlation with skeletal α-actin and positive correlation with the endothelial cell marker CD31, suggesting a potential link with extent of vascularization. FSTL1 expression levels at LVAD implant also correlated with significantly higher ejection fraction following recovery suggesting initial levels may have an influence on long term outcome. Immunohistochemical analysis showed that FST was localised in fibroblasts and endothelium, FSTL1 in myocytes, endothelium and smooth muscle cells, and FSLT3 in myocytes and endothelium. Microarray analysis showed that FST and FSTL1 expression correlate with extracellular matrix-related and calcium binding proteins, whereas FSTL3 is associated with cell signalling and transcription. Conclusion - These data show for the first time that elevated myocardial expression of follistatin-like genes is a feature of heart failure and that this may be linked both to disease severity and to mechanisms underlying recovery thereby revealing new insight into the pathogenesis of heart failure and offering novel therapeutic targets.
Hyaluronan synthase expression in bovine eyes. (1999)

Hyaluronan synthase isoforms were expressed in the ocular anterior segment and are speculated to be involved in HA production in situ.
Functional role of periostin in development and wound repair: implications for connective tissue disease (2008)

Integrity of the extracellular matrix (ECM) is essential for maintaining the normal structure and function of connective tissues. ECM is secreted locally by cells and organized into a complex meshwork providing physical support to cells, tissues, and organs. Initially thought to act only as a scaffold, the ECM is now known to provide a myriad of signals to cells regulating all aspects of their phenotype from morphology to differentiation. Matricellular proteins are a class of ECM related molecules defined through their ability to modulate cell-matrix interactions. Matricellular proteins are expressed at high levels during development, but typically only appear in postnatal tissue in wound repair or disease, where their levels increase substantially. Members of the CCN family, tenascin-C, osteopontin, secreted protein acidic rich in cysteine (SPARC), bone sialoprotein, thrombospondins, and galectins have all been classed as matricellular proteins. Periostin, a 90 kDa secreted homophilic cell adhesion protein, was recently added to matricellular class of proteins based on its expression pattern and function during development as well as in wound repair. Periostin is expressed in connective tissues including the periodontal ligament, tendons, skin and bone, and is also prominent in neoplastic tissues, cardiovascular disease, as well as in connective tissue wound repair. This review will focus on the functional role of periostin in tissue physiology. Fundamentally, it appears that periostin influences cell behaviour as well as collagen fibrillogenesis, and therefore exerts control over the structural and functional properties of connective tissues in both health and disease. Periostin is a novel matricellular protein with close homology to Drosophila fasciclin 1. In this review, the functional role of periostin is discussed in the context of connective tissue physiology, in development, disease, and wound repair.
Intravenous Immunoglobulins in Autoimmune and Inflammatory Diseases (2007)

Initially used for the treatment of immunodeficiencies, intravenous immunoglobulins (IVIg) have increasingly been used as immunomodulatory agents in autoimmune and inflammatory disorders. The mode of action of IVIg is enigmatic, probably involving Fc-dependent and/or F(ab')2-dependent nonexclusive mechanisms of action. IVIg broadly interacts with the different components of the immune system: cytokines, complement, Fc receptors, and several cell surface immunocompetent molecules. IVIg has also an impact on effector functions of immune cells. These mechanisms of action of IVIg reflect the importance of natural antibodies in the maintenance of immune homeostasis. We discuss here the recent advances in the understanding of immunoregulatory effects of IVIg, and we pointed out the need for new strategies to overcome the predicted increasing worldwide shortage of IVIg.
Activities of Synthetic Hybrid Peptides against Anaerobic Bacteria: Aspects of Methodology and Stability (2000)

The increasing problem of antibiotic resistance among pathogenic bacteria requires development of new antimicrobial agents. One line of investigation is the synthesis of antimicrobial hybrid peptides. The aim of the present investigation was to determine the in vitro activities of 16 cecropin-melittin hybrid peptides (CAMEL analogues) against 60 anaerobic bacterial strains, to compare their activities with those of seven clinically used antimicrobial agents, and to compare different methods for anaerobic susceptibility testing of these peptides. The stability of one of the peptides, temporin B, with different stereoisomeric configurations was investigated in a fecal milieu. The CAMEL analogues showed antimicrobial activity against the anaerobic bacteria, with MICs ranging from 0.125 to 32 microg/ml. The overall activities (the MICs at which 90% of isolates are inhibited) of the CAMEL analogues against anaerobic bacteria were mainly inferior to those of imipenem, clindamycin, and piperacillin but were equal to or superior to those of metronidazole, cefoxitin, ciprofloxacin, and chloramphenicol. The agarose dilution method was found to be an accurate method for the testing of large numbers of bacterial strains. The D isomer of temporin B was inactivated more slowly in feces than the L isomer. This study shows that the CAMEL analogues are potential agents for the treatment of anaerobic infections.
Bayesian Theory (2001)

Within metrology the evaluation of measurement uncertainty plays a special and very important role. In the past the generally accepted procedure for establishing the uncertainty was the so-called error analysis. Within this procedure probability is interpreted strictly in the statistical (frequentist) sense. Since the available information needed to infer the measurand almost never consists of only observed statistical data, the inference on the basis of error analysis showed difficulties that in 1993 were overcome by an international recommendation to apply, at least within the various branches of metrology, Bayesian Statistics to measurement data. But the price to pay for the resulting consistent and satisfying evaluation procedure is to change one's view of probability and to accept the consequences. This needs guidance, particularly for those educated in frequency-based statistics.
Characterization of the diacylglycerol acyltransferase activity in the membrane fraction from a fungus (1993)

In an attempt to clarify the mechanism of lipid accumulation inMortierella ramanniana var.angulispora, diacylglycerol acyltransferase (DGAT) in the membrane fraction from this fungus was characterized. The enzyme had an optimum pH of 7.0-7.5, and enzyme activity was blocked by SH-reagents. Metal ions were not essential for maintaining DGAT activity.n-Octyl-β-D-glucoside, 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate and Tween 80 were found to preserve activity, while Triton X-100 and sucrose monolaurate inhibited it. As the inhibition of DGAT activity by Triton X-100 was overcome by the addition of diacylglycerol (DG), the dependency of DGAT activity on exogenous DG was determined in the presence of 0.1% Triton X-100. DGAT activity in the membrane fraction was traced in fungi cultured for different time periods or in media at different carbon to nitrogen (C/N) ratios. Although the increase in total lipid content with culture time was accompanied by an increase in DGAT activity, total lipid changes related to changes in C/N ratio did not correlate with DGAT activity. Factors other than DGAT activity in the membrane fraction would appear to be involved in the regulation of total lipid content in this fungus.
Mitochondrial dysfunction, persistently elevated levels of reactive oxygen species and radiation-induced genomic instability: a review (2006)

Radiation-induced genomic instability (RIGI) challenges the long-standing notion that radiation's effects derive solely from nuclear impact. In RIGI it is the unirradiated progeny that can display phenotypic changes at delayed times after irradiation of the parental cell. RIGI might well provide the driving force behind the development of radiation-induced tumorigenesis as most cancer cells even in pre-neoplastic states display multiple genetic alterations. Thus, understanding RIGI may help elucidate the mechanisms underlying radiation-induced carcinogenesis. One characteristic of clones of genetically unstable cells is that many exhibit persistently increased levels of reactive oxygen species (ROS). Furthermore, oxidants enhance and antioxidants diminish radiation-induced instability. However, much about the mechanisms behind the initiation and perpetuation of RIGI remains unknown and we examine the evidence for the hypothesis that oxidative stress and mitochondrial dysfunction may be involved in perpetuating the unstable phenotype in some cell clones surviving ionizing radiation.
CF3 Oxonium Salts, O-(Trifluoromethyl)dibenzofuranium Salts:  In Situ Synthesis, Properties, and Application as a Real CF3+ Species Reagent (2007)

We report in situ synthesis of the first CF(3) oxonium salts, thermally unstable O-(trifluoromethyl)dibenzofuranium salts, which furthermore have different counteranions (BF(4)-, PF(6)-, SbF(6)-, and Sb(2)F(11)-) and ring substituents (tert-butyl, F, and OCH(3)), by photochemical decomposition of the corresponding 2-(trifluoromethoxy)biphenylyl-2'-diazonium salts at -90 to -100 degrees C. The yields markedly increased in the order of BF(4)- < PF(6)- < SbF(6)- < Sb(2)F(11)-. The CF(3) oxonium salts were fully assigned by means of (1)H and (19)F NMR spectroscopy at low temperature. The CF(3) salts decomposed to form CF(4) and dibenzofurans. The half-life times at -60 degrees C of the 2-tert-butyl salts having different counteranions were 29 min for BF(4)- salt 2d, 36 min for PF(6)- salt 2c, 270 min for SbF(6)- salt 2a, and 415 min for Sb(2)F(11)- salt 2b. Those at -60 degrees C of the Sb(2)F(11)- salts having different 2-substituents were 13 min for F salt 3b, 63 min for H (unsubstituted) salt 1b, and 415 min for tert-butyl salt 2b. Thus, the stability of the CF(3) oxonium salts increased in the order of BF(4)- < PF(6)- < SbF(6)- < Sb(2)F(11)- and F < H < tert-butyl, which is in accord with the increasing orders of the non-nucleophilicity of counteranions and the electron-donating effect of ring substituents. 2-tert-Butyl-O-(trifluoromethyl)dibenzofuranium hexafluoroantimonate (2a) was thus chosen and successfully applied as a real CF(3)+ species source to the direct O- and N-trifluoromethylations of alcohols, phenols, amines, anilines, and pyridines under very mild conditions. The thermal decomposition method with a mixture of diazonium salt 17a and aryl- or alkylsulfonic acids, pyridine, or pyridines having an electron-withdrawing group also afforded CF(3)O or CF(3)N products. The trifluoromethylation mechanism is discussed and an S(N)2 mechanism containing the transient formation of free CF(3)+ is proposed. Thus, the present study has demonstrated that the exceedingly reactive CF(3)+ species can be generated much easier than the CH(3)+ species, contrary to the common sense that CF(3)+ is extremely difficult to generate in solution.
Inhibitory control of excitable dendrites in neocortex (1995)

1. Many dendrites of pyramidal cells in mature neocortex express active Na+ and Ca2+ conductances. Dendrites are also the target of numerous inhibitory synapses. We examined the interactions between the intrinsic excitability of dendrites and synaptic inhibition using whole cell recordings from the apical dendrites of layer 5 pyramidal cells. Experiments were performed on slices of somatosensory cortex from mature rats. Slices were bathed in the glutamate receptor antagonists 2-amino-5-phosphonopentanoic acid and 6,7-dinitroquinoxaline-2,3-dione, and maintained at 32-36 degrees C. 2. In agreement with previous findings, intradendritic current injection evoked two distinct types of dendritic firing. Type I dendrites generated monophasic fast spikes, whereas type II dendrites showed more complex firing patterns, consisting of fast and slow spike components. 3. Stimulation of cortical layers 2/3 evoked fast inhibitory postsynaptic potentials (IPSPs) in all dendrites tested. IPSP reversal potentials were bimodally distributed, with means of about -53 and -85 mV when recorded with high-Cl(-)-concentration-filled electrodes. Interestingly, IPSP reversal potentials were correlated with the type of dendritic spiking pattern. 4. IPSPs were able to delay, completely block, or partially block spiking in dendrites, depending on the relative timing between inhibition and dendritic spiking. Slow, Ca(2+)-dependent spike components could be blocked selectively by IPSPs. Furthermore, inhibition could either phase advance or phase delay repetitive patterns of dendritic spiking, depending on the timing of the IPSP.