gebhart/patrepeval huggingface dataset:
Selective Detection of Deoxyribonucleic Acid at Ultralow Concentrations by SERRS (1997)

Genetic research programs such as the human genome project have demonstrated the need for selective detection of nucleic acids at ultralow concentrations (McKusik, V. A. FASEB J. 1991, 5, 12−20. Cui, X.; et al. Proc. Natl. Acad. Sci. U.S.A. 1989, 89, 9389−9393). Current detection techniques require amplification of the genetic material by the polymerase chain reaction (PCR) and detection of the amplified product by fluorescence. A new reliable method for DNA detection has been developed based on adsorption of DNA on colloidal silver and subsequent signal detection using surface-enhanced resonance Raman scattering (SERRS). It uses specifically designed primers and can be applied directly to genetic analysis. Improved surface and aggregation chemistry, utilizing modified DNA and a novel aggregating agent, has resulted in acceptable reproducibility for biological detection. DNA was detected down to 8 × 10-13 M, which equates to less than one molecule in the interrogation volume at any one time, and an RSD of 10% was obtained. The increased sensitivity compared to fluorescence circumvents the need for an amplification step, and much greater selectivity is obtained due to the sharp vibrational spectra observed, thus reducing the need for separation procedures. The method is potentially sensitive enough to eliminate the need for time-consuming amplification steps and provide a new dimension to labeling chemistry and multiplex analysis of DNA.
Design of Synthetic Peptides for Diagnostics (2003)

Due to the advantageous properties of synthetic molecules compared to biological ones biological molecules in diagnostic tests are replaced increasingly by synthetic ones, usually synthetic peptides or related molecules. The replacement of biological antigens by synthetic peptides is most advanced at present, as well as the use of site-specific antibodies induced with synthetic peptides. Moreover recent results indicate that synthetic molecules may also replace antibodies. Ultimately this will lead to diagnostic assays built of synthetic molecules only.
Cross‐species transmission of the newly identified coronavirus 2019‐nCoV (2020)

The current outbreak of viral pneumonia in the city of Wuhan, China, was caused by a novel coronavirus designated 2019-nCoV by the World Health Organization, as determined by sequencing the viral RNA genome. Many initial patients were exposed to wildlife animals at the Huanan seafood wholesale market, where poultry, snake, bats, and other farm animals were also sold. To investigate possible virus reservoir, we have carried out comprehensive sequence analysis and comparison in conjunction with relative synonymous codon usage (RSCU) bias among different animal species based on the 2019-nCoV sequence. Results obtained from our analyses suggest that the 2019-nCoV may appear to be a recombinant virus between the bat coronavirus and an origin-unknown coronavirus. The recombination may occurred within the viral spike glycoprotein, which recognizes a cell surface receptor. Additionally, our findings suggest that 2019-nCoV has most similar genetic information with bat coronovirus and most similar codon usage bias with snake. Taken together, our results suggest that homologous recombination may occur and contribute to the 2019-nCoV cross-species transmission.
Acetylcholine Receptors (1972)

Using (125)iodine-labeled alpha-bungarotoxin (alpha-BGT-(125)I) and quantitative radioautography, we have studied the time-course of the change in acetylcholine (ACh) receptor distribution and density occurring in rat diaphragm after denervation. In innervated fibers, ACh receptors are localized at the neuromuscular junction and the extrajunctional receptor density is less than five receptors per square micrometer. The extrajunctional receptor density begins to increase between 2 and 3 days after denervation and increases approximately linearly to 1695 receptors/microm(2) at 14 days, subsequently decreasing to 529 receptors/microm(2) at 45 days. We have isolated plasma membranes from rat leg muscles at various times after denervation and find that the change in concentration of ACh receptors in the membranes measured by alpha-BGT-(125)I binding and scintillation counting follows a time-course similar to the change in ACh receptor density measured radioautographically. Furthermore, we have correlated extrajunctional ACh receptor density measured by radioautography with extrajunctional ACh sensitivity measured by iontophoretic application of ACh and intracellular recording and find that the log of ACh receptor density is related to 0.53 times the log of ACh sensitivity. These results are discussed in terms of the electrophysiological experiments on the ACh receptor and the recent, more biochemical approaches to the study of ACh receptor control and function.
The Postprandial State: Mechanisms of Glucose Intolerance (1997)

Defective carbohydrate metabolism is central to the pathogenesis of non-insulin-dependent diabetes mellitus (NIDDM) and impaired glucose tolerance (IGT). Plasma glucose concentrations are determined by a balance between glucose entry into and removal from the circulation. In non-diabetic individuals, an oral glucose load triggers a rapid insulin secretory response. Insulin suppresses hepatic glucose release and stimulates peripheral glucose uptake, thereby limiting the postprandial rise in plasma glucose concentration. In addition, the term 'glucose effectiveness' describes how glucose regulates its own metabolism. In individuals with NIDDM or IGT, the beta-cell response to glucose is impaired, the incretin effect is reduced, hepatic and peripheral tissues are resistant to insulin, and glucose effectiveness may be impaired. Furthermore, disturbances in free fatty acid metabolism may alter intracellular glucose metabolism. The relative contributions of these defects to postprandial hyperglycaemia remain to be determined. However, the defects in insulin secretion and insulin action are central to understanding diabetic and prediabetic states.
Pathophysiological concentrations of glucose promote oxidative modification of low density lipoprotein by a superoxide-dependent pathway. (1994)

Oxidized lipoproteins may be important in the pathogenesis of atherosclerosis. Because diabetic subjects are particularly prone to vascular disease, and glucose autoxidation and protein glycation generate reactive oxygen species, we explored the role of glucose in lipoprotein oxidation. Glucose enhanced low density lipoprotein (LDL) oxidation at concentrations seen in the diabetic state. Conjugated dienes, thiobarbituric acid reactive substances, electrophoretic mobility, and degradation by macrophages were increased when LDL was modified in the presence of glucose. In contrast, free lysine groups and fibroblast degradation were reduced. Although loss of reactive lysine groups could be due to either oxidative modification or nonenzymatic glycation of apolipoprotein B-100, inhibition of lipid peroxidation by the metal chelator, diethylenetriamine pentaacetic acid, blocked the changes in free lysines. Thus, glycation of lysine residues is unlikely to account for the alterations in macrophage and fibroblast uptake of LDL modified in the presence of glucose. Glucose-mediated enhancement of LDL oxidation was partially blocked by superoxide dismutase and nearly completely inhibited by butylated hydroxytoluene. These findings indicate that glucose enhances LDL lipid peroxidation by an oxidative pathway involving superoxide and raise the possibility that the chronic hyperglycemia of diabetes accelerates lipoprotein oxidation, thereby promoting diabetic vascular disease.
A Selective c-Met Inhibitor Blocks an Autocrine Hepatocyte Growth Factor Growth Loop in ANBL-6 Cells and Prevents Migration and Adhesion of Myeloma Cells (2004)

Collectively, these findings support the role of c-Met and HGF in the proliferation, migration, and adhesion of myeloma cells and identify c-Met kinase as a therapeutic target for treatment of patients with multiple myeloma.
Insertional inactivation of genes to isolate mutants of Synechococcus sp. strain PCC 7942: isolation of filamentous strains (1993)

We have developed a simple procedure for generating mutants of the cyanobacterium Synechococcus sp. strain PCC 7942 in which the site of the lesion can be readily identified. This procedure involves transforming Synechococcus sp. strain PCC 7942 with a library of its own DNA that was fully digested with Sau3A and ligated into the plasmid vector pUC8. The homologous integration of the recombinant plasmid into the genome will often result in the disruption of a gene and the loss of gene function. We have used this method to generate many mutants of Synechococcus sp. strain PCC 7942 which grow as multicellular filaments rather than as unicells. Since the gene harboring the lesion was tagged with pUC8, it was easily isolated. In this paper, we discuss the usefulness of this procedure for the generation of mutants, and we characterize one mutant in which the lesion may be in an operon involved in the assembly of lipopolysaccharides.
Differential DNA Methylation between Fetus and Mother as a Strategy for Detecting Fetal DNA in Maternal Plasma (2002)

These results represent the first use of fetal epigenetic markers in noninvasive prenatal analysis. These data may also have implications for the investigation of other types of chimerism.
A fluorescence assay to monitor vesicle fusion and lysis. (1982)

An assay based on the fluorescent compound 2',7'-([bis(carboxymethyl)amino]methyl) fluorescein (calcein) has been developed to investigate vesicle fusion and lysis. The assay involves encapsulating the nonfluorescent Co2+ complex of calcein in one set of vesicles and EDTA in a second set. If fusion occurs, EDTA chelates Co2+, releasing calcein which may be assayed by means of its intense fluorescence. Leakage of either component of the reaction can be directly quantitated by titrating the external medium with the other component. This assay was used to investigate the effects of calcium ion on small phosphatidylserine vesicles, a system reported to undergo fusion. It revealed immediate and extensive leakage of the encapsulated contents; membrane fusion must, therefore, be simultaneously with or subsequent to, loss of vesicle integrity. This assay is convenient and flexible; it should be useful in a variety of investigations of membrane-bounded compartments.
Mechanism of Interaction of Different Classes of Cationic Antimicrobial Peptides with Planar Bilayers and with the Cytoplasmic Membrane ofEscherichia coli (1999)

Antimicrobial cationic peptides are prevalent throughout nature as part of the intrinsic defenses of most organisms, and have been proposed as a blueprint for the design of novel antimicrobial agents. They are known to interact with membranes, and it has been frequently proposed that this represents their antibacterial target. To see if this was a general mechanism of action, we studied the interaction, with model membranes and the cytoplasmic membrane of Escherichia coli, of 12 peptides representing all 4 structural classes of antimicrobial peptides. Planar lipid bilayer studies indicated that there was considerable variance in the interactions of the peptides with model phospholipid membranes, but generally both high concentrations of peptide and high transmembrane voltages (usually -180 mV) were required to observe conductance events (channels). The channels observed for most peptides varied widely in magnitude and duration. An assay was developed to measure the interaction with the Escherichia coli cytoplasmic membrane employing the membrane potential sensitive dye 3,5-dipropylthiacarbocyanine in the outer membrane barrier-defective E. coli strain DC2. It was demonstrated that individual peptides varied widely in their ability to depolarize the cytoplasmic membrane potential of E. coli, with certain peptides such as the loop peptide bactenecin and the alpha-helical peptide CP26 being unable to cause depolarization at the minimal inhibitory concentration (MIC), and others like gramicidin S causing maximal depolarization below the MIC. We discuss the mechanism of interaction with the cytoplasmic membrane in terms of the model of Matsuzaki et al. [(1998) Biochemistry 37, 15144-15153] and the possibility that the cytoplasmic membrane is not the target for some or even most cationic antimicrobial peptides.
McGraw-Hill encyclopedia of chemistry (1993)

This resource includes 900 alphabetically arranged articles - 110 new to this edition - in all fields of chemistry (analytical, physical, organic, inorganic) and covers theory, laboratory methods and instruments, classes of compounds and reactions, materials, elements, and more. Also included are related subjects essential to the understanding of chemistry, such as atomic physics, quantum theory, statistical mechanics, and thermodynamics. The text is thoroughly cross-referenced and supplemented by numerous structural formulas and other illustrations.
Receptor for Advanced Glycation End Products Is Subjected to Protein Ectodomain Shedding by Metalloproteinases (2008)

The receptor for advanced glycation end products (RAGE) is a 55-kDa type I membrane glycoprotein of the immunoglobulin superfamily. Ligand-induced up-regulation of RAGE is involved in various pathophysiological processes, including late diabetic complications and Alzheimer disease. Application of recombinant soluble RAGE has been shown to block RAGE-mediated pathophysiological conditions. After expression of full-length RAGE in HEK cells we identified a 48-kDa soluble RAGE form (sRAGE) in the culture medium. This variant of RAGE is smaller than a 51-kDa soluble version derived from alternative splicing. The release of sRAGE can be induced by the phorbol ester PMA and the calcium ionophore calcimycin via calcium-dependent protein kinase C subtypes. Hydroxamic acid-based metalloproteinase inhibitors block the release of sRAGE, and by RNA interference experiments we identified ADAM10 and MMP9 to be involved in RAGE shedding. In protein biotinylation experiments we show that membrane-anchored full-length RAGE is the precursor of sRAGE and that sRAGE is efficiently released from the cell surface. We identified cleavage of RAGE to occur close to the cell membrane. Ectodomain shedding of RAGE simultaneously generates sRAGE and a membrane-anchored C-terminal RAGE fragment (RAGE-CTF). The amount of RAGE-CTF increases when RAGE-expressing cells are treated with a gamma-secretase inhibitor, suggesting that RAGE-CTF is normally further processed by gamma-secretase. Identification of these novel mechanisms involved in regulating the availability of cell surface-located RAGE and its soluble ectodomain may influence further research in RAGE-mediated processes in cell biology and pathophysiology.
Optical and channeling studies of ion-bombarded GaP (1974)

Below-gap optical absorption, above-gap reflectivity, photoluminescence, and He ion channeling backscattering measurements are reported for ion-bombarded GaP. Each of the four experiments provides a measure of disorder. A one-to-one correspondence exists between the absorption, reflectivity, and backscattering measurements, and all three exhibit comparable sensitivity to damage. Photoluminescence is ∼ 100 times more sensitive. The absorption results suggest that every implanted ion species produces amorphous regions associated with each projectile and that these regions have properties very much like those of cold-deposited amorphous films. The results are interpreted in terms of a model which ascribes these amorphous regions to localized melting followed by rapid quenching to a glassy (amorphous) state in which short-range tetrahedral order remains intact. The damaged volume per bombarding ion as determined from absorption data is ∼6 times larger than that determined from channeling measurements. Although the annealing experiments show considerable scatter, the damage-induced changes in absorption and reflectivity can be largely removed by annealing at ∼600°C for 30 min. Some anomalies are observed in the photoluminescence annealing results.
Extraction of chromophoric humic substances from seawater (1990)

Chromophoric humic substances were extracted from seawater using hydrophobic solid-phase extraction, ultrafiltration, and a hydrophobic macroreticular resin (XAD-2). Four criteria were used to evaluate the efficiency of extraction: (1) UV-visible absorbance, (2) dissolved organic matter fluorescence, (3) capacity for photoproduction of H2O2, and (4) retention of total organic carbon. Extraction efficiencies for solid-phase media followed the order C18 > C8 > cyclohexyl (CH) > phenyl (PH)=C2. The extent of removal of humic substances from seawater decreased between 70 and 40% with volume extracted and varied with the source of water. Using our criteria, extraction of humic substances with C18 solid phase was between 22 and 84% more effective than with XAD-2. Concentration of humic substances by ultrafiltration was more efficient with membranes of molecular weight cut-off values of 500 than 5000. C18 solid-phase extraction of humic substances was as effective as ultrafiltration. Seawater reconstituted with humic substances extracted by C18 solid-phase extraction and by ultrafiltration had properties that were between 90 and 101% of those of the original water samples. Our results indicate that extraction of humic substances from seawater is most conveniently achieved by using C18 solid-phase extraction. A scaled-up version of this procedure has been used for the extraction of chromophoric humic substances from large volumes (1001) of coastal and open-ocean water.
Automatic modeling for adding new words to a large-vocabulary continuous speech recognition system (1991)

The authors report on the detection of new words for the speaker-dependent and speaker-independent paradigms. A useful operating point in a speaker-dependent paradigm is defined at 71% detection rate and 1% false alarm rate. The authors present a novel technique for obtaining a phonetic transcription for a new word, which is needed to add the new word to the system. The technique utilizes DECtalk's text-to-sound rules to obtain an initial phonetic transcription for the new word. Since these text-to-sound rules are imperfect, a probabilistic transformation technique is used that produces a phonetic pronunciation network of all possible pronunciations given DECtalk's transcription. The network is used to constrain a phonetic recognition process that results in an improved phonetic transcription for the new word. The resulting transcriptions are sufficient for speech recognition purposes.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Low Molecular Weight Hydroxyethyl Chitosan-Prednisolone Conjugate for Renal Targeting Therapy: Synthesis, Characterization and In Vivo Studies (2012)

To further evaluate the potential renal targeting profile of low molecular weight hydroxyethyl chitosan (LMWHC) we developed before, prednisolone (Pre) was conjugated with LMWHC by EDC/NHS chemistry to improve the therapeutic effect of glucocorticoids in vivo. The conjugate was denoted as LMWHC-Pre. The prednisolone content of the conjugate was determined by reversed-phase high-performance liquid chromatography (HPLC) with Kromasil C18 column. The results showed that the average coupling degree of prednisolone to LMWHC was 76.7±3.2 μg·mg(-1). The stability and physicochemical characterization of LMWHC-Pre under various conditions were also investigated. To study the fate of LMWHC-Pre after intravenous (i.v.) administration, fluorescein isothiocyanate (FITC) was coupled to the conjugate to explore the renal targeting efficacy. The in vivo results showed that significant amount of the conjugate was accumulated into the kidneys while negligible signal could be detected when the mixture of FITC-LMWHC and prednisolone was co-administered. The preliminary pharmacodynamics study of LMWHC-Pre showed that the conjugate could effectively alleviate the nephrotic syndrome of rats induced by minimal change nephrosis (MCN) model. Toxicity study also revealed that there was little glucocorticoid-induced osteoporosis by LMWHC-Pre upon 20 days of treatment. From this study, LMWHC-Pre may be employed as an effective potential drug candidate for the treatment of chronic renal disease.
A dynamic reaction cell for inductively coupled plasma mass spectrometry (ICP-DRC-MS) (1999)

The existing vast database of ion-molecule reaction kinetics may, with advantage, be used to overcome spectral interference in ICP-MS. To be directly applicable to an rf multipole reactor, it must be shown that the multipole provides a controlled thermal environment. The contribution of the rf field energy to the ion energy is modeled for a quadrupole reaction cell. It is shown that the rf field contribution increases with increasing rf amplitude and decreasing rf frequency (i.e., towards the high-q side of the quadrupole stability region). A thermodynamic ladder is proposed as a convenient measure of the thermal characteristics of the reactor, and should serve as a benchmark for comparison of various reaction cell designs. Experimental results for charge transfer reactions are presented. These indicate that the configuration reported is near-thermal, with an rf field energy contribution less than about 0.4 eV. The rich variety of ion-molecule processes which might be studied is demonstrated by examples of condensation, simple association and complex ligation reactions.
Smooth Function Approximation Using Neural Networks (2005)

An algebraic approach for representing multidimensional nonlinear functions by feedforward neural networks is presented. In this paper, the approach is implemented for the approximation of smooth batch data containing the function's input, output, and possibly, gradient information. The training set is associated to the network adjustable parameters by nonlinear weight equations. The cascade structure of these equations reveals that they can be treated as sets of linear systems. Hence, the training process and the network approximation properties can be investigated via linear algebra. Four algorithms are developed to achieve exact or approximate matching of input-output and/or gradient-based training sets. Their application to the design of forward and feedback neurocontrollers shows that algebraic training is characterized by faster execution speeds and better generalization properties than contemporary optimization techniques.
National, Regional, State, and Selected Local Area Vaccination Coverage Among Adolescents Aged 13–17 Years — United States, 2015 (2016)

The Advisory Committee on Immunization Practices (ACIP) recommends that adolescents aged 11-12 years routinely receive vaccines to prevent diseases, including human papillomavirus (HPV)-associated cancers, pertussis, and meningococcal disease (1). To assess vaccination coverage among adolescents in the United States, CDC analyzed data collected regarding 21,875 adolescents through the 2015 National Immunization Survey-Teen (NIS-Teen).* During 2014-2015, coverage among adolescents aged 13-17 years increased for each HPV vaccine dose among males, including ≥1 HPV vaccine dose (from 41.7% to 49.8%), and increased modestly for ≥1 HPV vaccine dose among females (from 60.0% to 62.8%) and ≥1 quadrivalent meningococcal conjugate vaccine (MenACWY) dose (from 79.3% to 81.3%). Coverage with ≥1 HPV vaccine dose was higher among adolescents living in households below the poverty level, compared with adolescents in households at or above the poverty level.(†) HPV vaccination coverage (≥1, ≥2, or ≥3 doses) increased in 28 states/local areas among males and in seven states among females. Despite limited progress, HPV vaccination coverage remained lower than MenACWY and tetanus, diphtheria, and acellular pertussis vaccine (Tdap) coverage, indicating continued missed opportunities for HPV-associated cancer prevention.