gebhart/patrepeval huggingface dataset:
Aptameric Recognition-Modulated Electroactivity of Poly(4-Styrenesolfonic Acid)-Doped Polyaniline Films for Single-Shot Detection of Tetrodotoxin (2015)

The work being reported is the first electrochemical sensor for tetrodotoxin (TTX). It was developed on a glassy carbon electrodes (C) that was modified with poly(4-styrenesolfonic acid)-doped polyaniline film (PANI/PSSA). An amine-end functionalized TTX-binding aptamer, 5'-NH₂-AAAAATTTCACACGGGTGCCTCGGCTGTCC-3' (NH₂-Apt), was grafted via covalent glutaraldehyde (glu) cross-linking. The resulting aptasensor (C//PANI⁺/PSSA-glu-NH2-Apt) was interrogated by cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS) in sodium acetate buffer (NaOAc, pH 4.8) before and after 30 min incubation in standard TTX solutions. Both CV and EIS results confirmed that the binding of the analyte to the immobilized aptamer modulated the electrochemical properties of the sensor: particularly the charge transfer resistance (Rct) of the PANI⁺/PSSA film, which served as a signal reporter. Based on the Rct calibration curve of the TTX aptasensor, the values of the dynamic linear range (DLR), sensitivity and limit of detection (LOD) of the sensor were determined to be 0.23-1.07 ng·mL(-1) TTX, 134.88 ± 11.42 Ω·ng·mL(-1) and 0.199 ng·mL(-1), respectively. Further studies are being planned to improve the DLR as well as to evaluate selectivity and matrix effects in real samples.
Pan-Genome and Comparative Genome Analyses of Propionibacterium acnes Reveal Its Genomic Diversity in the Healthy and Diseased Human Skin Microbiome (2013)

Propionibacterium acnes is a major human skin bacterium. It plays an important role in maintaining skin health. However, it has also been hypothesized to be a pathogenic factor in several diseases, including acne, a common skin disease affecting 85% of teenagers. To understand whether different strains have different virulent properties and thus play different roles in health and diseases, we compared the genomes of 82 P. acnes strains, most of which were isolated from acne or healthy skin. We identified lineage-specific genetic elements that may explain the phenotypic and functional differences of P. acnes as a commensal in health and as a pathogen in diseases. By analyzing a large number of sequenced strains, we provided an improved understanding of the genetic landscape and diversity of the organism at the strain level and at the molecular level that can be further applied in the development of new and personalized therapies.
Analysis of nuclear lamin isoprenylation in Xenopus oocytes: isoprenylation of lamin B3 precedes its uptake into the nucleus. (1995)

Protein prenylation is a posttranslational modification involving the covalent attachment of a prenyl lipid to a cysteine at or near the COOH terminus of a protein. It is required for membrane localization and efficient function of a number of cytoplasmic as well as nuclear proteins including the proto-oncogenic and activated forms of Ras. Farnesylation in conjunction with a nuclear localization signal has been shown to be necessary to target newly synthesized nuclear lamins to the inner nuclear envelope membrane. It is, however, not clear where in the cell isoprenylation of nuclear lamins takes place. In this study we describe in vivo and in vitro experiments on the isoprenylation of the Xenopus oocyte nuclear lamin B3. We show by kinetic analysis that newly synthesized lamins are isoprenylated in the cytosol of oocytes before uptake into the nucleus. From our data it can be concluded that isoprenylation of lamins in the nucleus, as it is observed under certain conditions of isoprene starvation, represents a default pathway rather than the physiological situation. We further analyzed the capacity of isolated nuclei to carry out isoprenylation of B3. Our results are in line with a dual localization of a protein farnesyltransferase in the cytosol and nuclei of amphibian oocytes. Implications for the possible functions of a nuclear protein farnesyltransferase as well as possible mechanisms of the selective inhibition of farnesylation of cytoplasmic proteins by peptidomimetics are discussed.
Isotope effect, essential diet components, and prospects of aging retardation (2010)

A method is proposed that has the potential to increase the stability of lipids, proteins, nucleic acids and other cellular components towards the detrimental damages caused by reactive oxygen species (ROS). The rate-limiting step of most ROS-driven oxidation reactions is hydrogen abstraction. The oxidation-susceptible sites within these (bio)molecules can thus be made less vulnerable to ROS-driven oxidation by incorporating heavy stable isotopes, such as deuterium or/and carbon-13. Ingestion of isotopically reinforced building blocks, such as amino acids, lipids, and components of nucleic acids and their subsequent incorporation into macromolecules would make the latter more stable to ROS courtesy of the isotope effect. The suggested approach may lead to enhanced resistance toward oxidative stress and, hence, to enhanced longevity.
Expression of specific chemokines and chemokine receptors in the central nervous system of multiple sclerosis patients (1999)

Chemokines direct tissue invasion by specific leukocyte populations. Thus, chemokines may play a role in multiple sclerosis (MS), an idiopathic disorder in which the central nervous system (CNS) inflammatory reaction is largely restricted to mononuclear phagocytes and T cells. We asked whether specific chemokines were expressed in the CNS during acute demyelinating events by analyzing cerebrospinal fluid (CSF), whose composition reflects the CNS extracellular space. During MS attacks, we found elevated CSF levels of three chemokines that act toward T cells and mononuclear phagocytes: interferon-gamma-inducible protein of 10 kDa (IP-10); monokine induced by interferon-gamma (Mig); and regulated on activation, normal T-cell expressed and secreted (RANTES). We then investigated whether specific chemokine receptors were expressed by infiltrating cells in demyelinating MS brain lesions and in CSF. CXCR3, an IP-10/Mig receptor, was expressed on lymphocytic cells in virtually every perivascular inflammatory infiltrate in active MS lesions. CCR5, a RANTES receptor, was detected on lymphocytic cells, macrophages, and microglia in actively demyelinating MS brain lesions. Compared with circulating T cells, CSF T cells were significantly enriched for cells expressing CXCR3 or CCR5. Our results imply pathogenic roles for specific chemokine-chemokine receptor interactions in MS and suggest new molecular targets for therapeutic intervention.
Inhibition of in-stent restenosis by oral copper chelation in porcine coronary arteries (2006)

Stress-induced release of IL-1alpha and fibroblast growth factor-1 is dependent on intracellular copper and is a major driver of neointimal hyperplasia. Therefore, we assessed the effect of tetrathiomolybdate (TTM), a clinically proven copper chelator, on in-stent restenosis. Nine pigs were treated with TTM (5 mg/kg po) twice daily for 2 wk before stent implantation and for 4 wk thereafter, and nine pigs served as controls. In-stent restenosis was assessed by quantitative coronary angiography (QCA), intravascular ultrasound (IVUS), and histomorphometry. Serum ceruloplasmin activity was used as a surrogate marker of copper bioavailability. In TTM-treated animals, ceruloplasmin dropped 70 +/- 10% below baseline levels. Baseline characteristics were comparable in TTM-treated and control animals. At 4-wk follow-up, all parameters relevant to in-stent restenosis were significantly reduced in TTM-treated animals: minimal lumen diameter by QCA was 2.03 +/- 0.57 and 1.47 +/- 0.45 mm in TTM-treated and control animals, respectively (P < 0.05), percent stenosis diameter was 39% less in TTM-treated animals (27.1 +/- 16.6% vs. 44.5 +/- 16.1%, P < 0.05), minimal lumen area by IVUS was 60% larger in TTM-treated animals (4.27 +/- 1.56 vs. 2.67 +/- 1.19 mm(2), P < 0.05), and neointimal volume by histomorphometry was 37% less in TTM-treated animals (34.9 +/- 11.5 vs. 55.2 +/- 19.6 mm(3), P < 0.05). We conclude that systemic copper chelation with a clinically approved chelator significantly inhibits in-stent restenosis.
The 2,6-Diaminopurine Riboside.cntdot.5-Methylisocytidine Wobble Base Pair: An Isoenergetic Substitution for the Study of G.cntdot.U Pairs in RNA (1994)

Phylogenetically invariant G.U wobble pairs are present in a wide variety of RNA's. As a means to study the contribution of individual chemical groups within a G.U pair, we have synthesized and thermodynamically characterized oligoribonucleotides containing the unnatural nucleosides 2,6-diaminopurine riboside (DAP) and 5-methylisocytidine (MeiC). The DAP.MeiC pair at the end of an RNA duplex is as stable as a G.U pair, consistent with formation of a wobble base pair with two hydrogen bonds. DAP.MeiC is a valuable substitution for the study of G.U wobble pairs because it is conformationally similar to the G.U pair, but has a different array of functional groups in the major and minor grooves of the duplex and a reversed hydrogen bonding polarity between the bases. We also report the stability of several other terminal pairs proposed to be in a wobble configuration including inosine.U (I.U), A.MeiC, DAP.C, A.C, G.5-methyl-U,2'-deoxyguanosine.U, and 2'-deoxy-7-deazaguanosine.U. These pairs present a diversity of functional group substitutions in the context of a wobble conformation. Comparison of wobble pairs with and without the N2 exocyclic amine, i.e., G.U vs I.U, DAP.MeiC vs A.MeiC, and DAP.C vs A.C, demonstrates that the amine does not contribute to base pairing stability when the pair is located at the terminal position of the RNA duplex. However, at a position internal to the duplex, the exocyclic amine does improve helix stability. An internal I.U pair is less stable (approximately 1 kcal.mol-1) than an internal G.U pair, and substantially less stable (approximately 2 kcal.mol-1) than an internal A-U pair. These data provide quantitation for the reduced duplex stability observed upon conversion of A-U to I.U pairs by double-stranded RNA adenosine deaminase (dsRAD). This collection of wobble pairs will help identify the contribution made by individual functional groups in RNA/protein interactions and in the tertiary folding of RNA.
Use of bioluminescent Salmonella for assessing the efficiency of constructed phage-based biosorbent (2000)

A bacteriophage-based biosorbent for Salmonella enteritidis was constructed, and bacterial bioluminescence was used for assessment of the efficiency of cell capture. A strain of S. enteritidis with bioluminescent phenotype was constructed by transformation with plasmid pT7 carrying the entire lux operon from Photorhabdus luminescens. The relation between relative light output (RLU) and colony-forming units (CFU/ml) of the bioluminescent strain was established. The bacteriophage specific to S. enteritidis was biotinylated, and the biotinylation procedure was optimized based on the maximum retention of phage infectivity. The biotinylated phages were then coated onto streptavidin-labeled magnetic beads, and were used to capture the bioluminescent S. enteritidis cells. Our preliminary results showed that the number of cells captured by constructed biosorbent was five times higher than that of the control, magnetic beads coated with nonbiotinylated phage, indicating the capture is specific. Journal of Industrial Microbiology & Biotechnology (2000) 25, 273–275.
Gold Nanocages: Synthesis, Properties, and Applications (2008)

Noble-metal nanocages comprise a novel class of nanostructures possessing hollow interiors and porous walls. They are prepared using a remarkably simple galvanic replacement reaction between solutions containing metal precursor salts and Ag nanostructures prepared through polyol reduction. The electrochemical potential difference between the two species drives the reaction, with the reduced metal depositing on the surface of the Ag nanostructure. In our most studied example, involving HAuCl(4) as the metal precursor, the resultant Au is deposited epitaxially on the surface of the Ag nanocubes, adopting their underlying cubic form. Concurrent with this deposition, the interior Ag is oxidized and removed, together with alloying and dealloying, to produce hollow and, eventually, porous structures that we commonly refer to as Au nanocages. This approach is versatile, with a wide range of morphologies (e.g., nanorings, prism-shaped nanoboxes, nanotubes, and multiple-walled nanoshells or nanotubes) available upon changing the shape of the initial Ag template. In addition to Au-based structures, switching the metal salt precursors to Na(2)PtCl(4) and Na(2)PdCl(4) allows for the preparation of Pt- and Pd-containing hollow nanostructures, respectively. We have found that changing the amount of metal precursor added to the suspension of Ag nanocubes is a simple means of tuning both the composition and the localized surface plasmon resonance (LSPR) of the metal nanocages. Using this approach, we are developing structures for biomedical and catalytic applications. Because discrete dipole approximations predicted that the Au nanocages would have large absorption cross-sections and because their LSPR can be tuned into the near-infrared (where the attenuation of light by blood and soft tissue is greatly reduced), they are attractive materials for biomedical applications in which the selective absorption of light at great depths is desirable. For example, we have explored their use as contrast enhancement agents for both optical coherence tomography and photoacoustic tomography, with improved performance observed in each case. Because the Au nanocages have large absorption cross-sections, they are also effective photothermal transducers; thus, they might provide a therapeutic effect through selective hyperthermia-induced killing of targeted cancer cells. Our studies in vitro have illustrated the feasibility of applying this technique as a less-invasive form of cancer treatment.
Acute kidney injury is associated with early cytokine changes after trauma (2013)

Prognostic study, level III.
Arabidopsis TCP20 links regulation of growth and cell division control pathways (2005)

During postembryonic plant development, cell division is coupled to cell growth. There is a stringent requirement to couple these processes in shoot and root meristems. As cells pass through meristems, they transit through zones with high rates of cell growth and proliferation during organogenesis. This transition implies a need for coordinate regulation of genes underpinning these two fundamental cell functions. Here, we report a mechanism for coregulation of cell division control genes and cell growth effectors. We identified a GCCCR motif necessary and sufficient for high-level cyclin CYCB1;1 expression at G2/M. This motif is overrepresented in many ribosomal protein gene promoters and is required for high-level expression of the S27 and L24 ribosomal subunit genes we examined. p33(TCP20), encoded by the Arabidopsis TCP20 gene, binds to the GCCCR element in the promoters of cyclin CYCB1;1 and ribosomal protein genes in vitro and in vivo. We propose a model in which organ growth rates, and possibly shape in aerial organs, are regulated by the balance of positively and negatively acting teosinte-branched, cycloidea, PCNA factor (TCP) genes in the distal meristem boundary zone where cells become mitotically quiescent before expansion and differentiation.
Laser “cross‐hair” sidelight (1978)

A technique is described for forming an optical laser cross-hair image for use as a radiotherapy sidelight. The technique is developed from a concept introduced earlier by which a line image is formed from a laser beam using a cylindrical lens. By using two cylindrical lenses and appropriate reflectors, two line images can be made to form a cross.
Pharmacology and Pharmacodynamics of Bevacizumab as Monotherapy or in Combination with Cytotoxic Therapy in Preclinical Studies (2005)

Preclinical models have examined the pharmacologic and pharmacodynamic activities of an anti-vascular endothelial growth factor (VEGF) humanized, monoclonal antibody, bevacizumab, and/or its murine equivalent A4.6.1. These studies found that single-agent therapy with bevacizumab/A4.6.1 resulted in tumor growth inhibition of 20 different human tumor cell lines (13 tumor types) implanted into nude mice irrespective of the route of administration or tumor location. Several of these studies also observed significant inhibition of tumor metastases. Various studies have examined the feasibility of combining anti-VEGF therapy with cytotoxic or biological agents. Combining bevacizumab/A4.6.1 with doxorubicin, topotecan, paclitaxel, docetaxel, or radiotherapy resulted in additive or synergistic tumor growth inhibition. Changes in vascular functions were frequently reported, including decreased vessel diameter, density, and permeability in response to treatment. A reduction in interstitial fluid pressure was also observed. In some studies, these improvements resulted in an increase in intratumoral uptake of chemotherapy, implying that the most effective use of anti-VEGF therapy is in combination with chemotherapy. Alternatively, combination treatment with radiation increased tumor oxygenation and tumor growth inhibition. Interestingly, anti-VEGF therapy has also been reported to reduce the development of ascites in ovarian mouse models. Finally, safety pharmacology studies with bevacizumab in cynomolgus monkeys showed that this agent is generally well tolerated with no unexpected adverse events.
The testis-specific double bromodomain-containing protein BRDT forms a complex with multiple spliceosome components and is required for mRNA splicing and 3′-UTR truncation in round spermatids (2012)

Members of the BET (bromodomain and extra terminal motif) family of proteins have been shown to be chromatin-interacting regulators of transcription. We previously generated a mutation in the testis-specific mammalian BET gene Brdt (bromodomain, testis-specific) that yields protein lacking the first bromodomain (BRDT(ΔBD1)) and observed disrupted spermiogenesis and male sterility. To determine whether BRDT(ΔBD1) protein results in altered transcription, we analyzed the transcriptomes of control versus Brdt(ΔBD1/ΔBD1) round spermatids. Over 400 genes showed statistically significant differential expression, and among the up-regulated genes, there was an enrichment of RNA splicing genes. Over 60% of these splicing genes had transcripts that lacked truncation of their 3'-untranslated region (UTR) typical of round spermatids. We selected four of these genes to characterize: Srsf2, Ddx5, Hnrnpk and Tardbp. The 3'-UTRs of Srsf2, Ddx5 and Hnrnpk mRNAs were longer in mutant round spermatids and resulted in reduced protein levels. Tardbp was transcriptionally up-regulated and a splicing shift toward the longer variant was observed. All four splicing proteins were found to complex with BRDT in control and mutant testes. We thus suggest that, along with modulating transcription, BRDT modulates gene expression as part of the splicing machinery. These modulations alter 3'-UTR processing in round spermatids; importantly, the BD1 is essential for these functions.
bcl-2/bax mRNA expression ratio as prognostic factor in low-grade urinary bladder cancer (1996)

Apoptotic cell death represents an important mechanism for the precise regulation of cell numbers, and a defence mechanism against tumoral cell. bcl-2 and bax genes are known to be involved in the control of apoptotic pathways; in particular, the ratio between bcl-2 and bax represents a cell rheostat that is able to predict a cell's response toward life or death to an apoptotic stimulus. In the present study we investigated the role of bcl-2 and bax gene expression in a panel of 37 low-grade tumours of the urinary bladder, and correlated the expression of these genes to the prognosis of patients in a follow-up of more than one year. We found that levels of bax expression higher than bcl-2 in bladder tumours well correlates to a better outcome for patients. Early relapses are much more frequently observed in those patients whose tumours express more bcl-2 than bax mRNA. We conclude that the bcl-2/bax expression ratio may be considered as a marker for disease progression in low grade bladder tumours, independently of clinical staging and histological grading.
Metabolism of low-density lipoprotein-free cholesterol by human plasma lecithin-cholesterol acyltransferase (1991)

The metabolism of cholesterol derived from [3H]cholesterol-labeled low-density lipoprotein (LDL) was determined in human blood plasma. LDL-derived free cholesterol first appeared in large alpha-migrating HDL (HDL2) and was then transferred to small alpha-HDL (HDL3) for esterification. The major part of such esters was retained within HDL of increasing size in the course of lecithin-cholesterol acyltransferase (LCAT) activity; the balance was recovered in LDL. Transfer of preformed cholesteryl esters within HDL contributed little to the labeled cholesteryl ester accumulating in HDL2. When cholesterol for esterification was derived instead from cell membranes, a significantly smaller proportion of this cholesteryl ester was subsequently recovered in LDL. These data suggest compartmentation of cholesteryl esters within plasma that have been formed from cell membrane or LDL free cholesterol, and the role for HDL2 as a relatively unreactive sink for LCAT-derived cholesteryl esters.
Analysis of Some Italian Lemon Liquors (Limoncello) (2003)

The chemical composition of several commercial Italian Limoncellos, lemon-peel-based alcoholic beverages, was studied by chromatographic techniques. These methods allowed a rapid monitoring of Limoncello, giving information on quality markers and possible adulteration of the product. Quantitative data for more than 60 compounds are reported. Limoncellos were characterized by the presence of selected volatile (terpenes, aldehydes, alcohols) and nonvolatile compounds (psoralens, coumarins, phenolics, carbohydrates and acids). On the basis of their composition, the samples were grouped by PCA analysis in two sets; the first group showed a composition similar to lemon essential oils, with a high content of b-pinene, myrcene, trans-a-bergamottene, and b-bisabolene, and a low content in neral and geranial. The composition of the second group suggested the occurrence of oxidative phenomena and/or the addition of flavors. The presence of ethyl acetate, acetaldehyde, 2-methyl-1-propanol and glycerol showed that a fermentation probably occurred in the sugar syrup used to dilute the Limoncello after the extraction process.
Impact of sugar stereochemistry on natural killer T cell stimulation by bacterial glycolipids (2011)

Natural killer T (NKT) cells recognize glycolipids produced by Sphingomonas bacteria, and these glycolipids contain C6-oxidized sugars, either glucuronic acid or galacturonic acid, linked to ceramides. Glycolipids with gluco stereochemistry are the most prevalent. Multiple studies have demonstrated that galactosylceramides are more potent stimulators of NKT cells than their glucose isomers. To determine if this stereoselectivity is retained in the context of the C6-oxidized sugars found in bacterial glycolipids, we prepared two sets of gluco and galacto-glycolipids oxidized at their C6 positions and compared their NKT stimulatory properties. In the context of carboxylic acid groups at C6, gluco stereochemistry gave the more potent responses. We also prepared bacterial glycolipids containing more complex ceramide groups to determine if these chains impact NKT cell responses.