gebhart/patrepeval huggingface dataset:
Mouse β-Defensin 3 Is an Inducible Antimicrobial Peptide Expressed in the Epithelia of Multiple Organs (1999)

One component of host defense at mucosal surfaces is epithelium-derived peptides with antimicrobial activity called defensins. We describe in this report the isolation and characterization of a murine homologue of human beta-defensin 2 (hBD-2) called mouse beta-defensin 3 (mBD-3). The predicted amino acid sequence shows the hallmark features of other known epithelial defensins, including the ordered array of six cysteine residues. Analysis of a genomic clone of mBD-3 revealed two exons separated by a 1.7-kb intron. The mBD-3 gene is localized at the proximal portion of chromosome 8, the site where genes for mouse alpha- and beta-defensins are found. Under basal condition, mBD-3 transcripts were detected at low levels in epithelial cells of surface organs, such as the intestine and lung. After instillation of Pseudomonas aeruginosa PAO1 into mouse airways, mBD-3-specific mRNA was upregulated significantly not only in large airways but also in the small bowel and liver. Recombinant mBD-3 peptide, produced from a baculovirus expression system, showed antimicrobial activity against P. aeruginosa PAO1 (MIC of 8 micrograms/ml) and Escherichia coli D31 (MIC of 16 micrograms/ml) in a salt-dependent manner. This study demonstrates that a murine homologue of hBD-2 is present in the respiratory system and other mucosal surfaces. These similarities between murine and human host defense apparatus provide further impetus to evaluate the mouse as a model for studying the human innate host defense system.
Anomalous Increase in Carbon Capacitance at Pore Sizes Less Than 1 Nanometer (2006)

Carbon supercapacitors, which are energy storage devices that use ion adsorption on the surface of highly porous materials to store charge, have numerous advantages over other power-source technologies, but could realize further gains if their electrodes were properly optimized. Studying the effect of the pore size on capacitance could potentially improve performance by maximizing the electrode surface area accessible to electrolyte ions, but until recently, no studies had addressed the lower size limit of accessible pores. Using carbide-derived carbon, we generated pores with average sizes from 0.6 to 2.25 nanometer and studied double-layer capacitance in an organic electrolyte. The results challenge the long-held axiom that pores smaller than the size of solvated electrolyte ions are incapable of contributing to charge storage.
Prostate specific antigen. Experimental and clinical observations. (1987)

A commercially available radioimmunoassay (RIA) for prostate specific antigen (PSA) was investigated in respect to its analytical specificity and its clinical applicability for the diagnosis of prostate cancer. PSA detected in serum by RIA was immunochemically identical to PSA found in seminal plasma. PSA is not a single protein but rather a group of isoproteins with different isoelectric points (pI) in the pH range 6-8. Furthermore PSA could be split in subunits by means of denaturing electrophoresis under reducing conditions. Unlike prostatic acid phosphatase (PAP) serum PSA was stable at room temperature. In sera of patients with benign hyperplasia of the prostate (BPH) two significantly different populations were found. The lower group (0.5-5.8 ng/ml PSA) had PSA values comparable to the control group of apparently healthy males (0.5-6.3 ng/ml). The higher group between 7.7 and 12.2 ng/ml was also characteristic for early stages of prostate cancer (T0 and T1). PSA seemed to be correlated to the tumor volume and allowed to differentiate between early carcinomas of the prostate and BPH or possibly T0/1 staged prostate carcinoma. PSA may be a screening method for early cancer of the prostate.
Telomere Lengths and Telomerase Activity in Dog Tissues: A Potential Model System to Study Human Telomere and Telomerase Biology (2001)

Studies on telomere and telomerase biology are fundamental to the understanding of aging and age-related diseases such as cancer. However, human studies have been hindered by differences in telomere biology between humans and the classical murine animal model system. In this paper, we describe basic studies of telomere length and telomerase activity in canine normal and neoplastic tissues and propose the dog as an alternative model system. Briefly, telomere lengths were measured in normal canine peripheral blood mononuclear cells (PBMCs), a range of normal canine tissues, and in a panel of naturally occurring soft tissue tumours by terminal restriction fragment (TRF) analysis. Further, telomerase activity was measured in canine cell lines and multiple canine tissues using a combined polymerase chain reaction/enzyme-linked immunosorbent assay method. TRF analysis in canine PBMCs and tissues demonstrated mean TRF lengths to range between 12 and 23 kbp with heterogeneity in telomere lengths being observed in a range of normal somatic tissues. In soft tissue sarcomas, two subgroups were identified with mean TRFs of 22.2 and 18.2 kbp. Telomerase activity in canine tissue was present in tumour tissue and testis with little or no activity in normal somatic tissues. These results suggest that the dog telomere biology is similar to that in humans and may represent an alternative model system for studying telomere biology and telomerase-targeted anticancer therapies.
Translational initiation factor expression and ribosomal protein gene expression are repressed coordinately but by different mechanisms in murine lymphosarcoma cells treated with glucocorticoids. (1989)

P1798 murine lymphosarcoma cells cease to proliferate upon exposure to 10(-7) M dexamethasone and exhibit a dramatic inhibition of rRNA and ribosomal protein synthesis (O. Meyuhas, E. Thompson, Jr., and R. P. Perry, Mol. Cell Biol. 7:2691-2699, 1987). These workers demonstrated that ribosomal protein synthesis is regulated primarily at the level of translation, since dexamethasone did not alter mRNA levels but shifted the mRNAs from active polysomes into inactive messenger ribonucleoproteins. We have examined the effects of dexamethasone on the biosynthesis of initiation factor proteins in the same cell line. The relative protein synthesis rates of eIF-4A and eIF-2 alpha were inhibited by about 70% by the hormone, a reduction comparable to that for ribosomal proteins. The mRNA levels of eIF-4A, eIF-4D, and eIF-2 alpha also were reduced by 60 to 70%, indicating that synthesis rates are proportional to mRNA concentrations. Analysis of polysome profiles showed that the average number of ribosomes per initiation factor polysome was only slightly reduced by dexamethasone, and little or no mRNA was present in messenger ribonucleoproteins. The results indicate that initiation factor gene expression is coordinately regulated with ribosomal protein synthesis but is controlled primarily by modulating mRNA levels rather than mRNA efficiency.
Retinoid X receptor-selective ligands produce malformations in Xenopus embryos. (1996)

Retinoids exert pleiotropic effects on the development of vertebrates through the action of retinoic acid receptors (RAR) and retinoid X receptors (RXR). We have investigated the effect of synthetic retinoids selective for RXR and RAR on the development of Xenopus and zebrafish embryos. In Xenopus, both ligands selective for RAR and RXR caused striking malformations along the anterior-posterior axis, whereas in zebrafish only ligands specific for RAR caused embryonic malformations. In Xenopus, RAR- and RXR-selective ligands regulated the expression of the Xlim-1, gsc, and HoxA1 genes similarly as all-trans-retinoic acid. Nevertheless, RXR-selective ligands activated only an RXR responsive reporter but not an RAR responsive reporter introduced by microinjection into the Xenopus embryo, consistent with our failure to detect conversion of an RXR-selective ligand to different derivatives in the embryo. These results suggest that Xenopus embryos possess a unique response pathway in which liganded RXR can control gene expression. Our observations further illustrate the divergence in retinoid responsiveness between different vertebrate species.
Impulse Control Disorders in Parkinson Disease (2010)

clinicaltrials.gov Identifier: NCT00617019.
Kinetics and Mechanism of Plasma Oxidative Desulfurization in Liquid Phase (2000)

Factors affecting the plasma oxidative desulfurization of organic sulfides in the liquid phase were investigated. The organic sulfides, including mercaptan, thioether, and thiophene, are mixed with n-heptane severally or jointly. The plasma power load, i.e., the ratio of oxygen flow to plasma power, and the reaction time are the primary factors affecting the desulfurization reaction when the reaction temperature was controlled at about −85 °C. Under suitable conditions, the degree of desulfurization for mercaptan, thioether, thiophene, and/or their mixtures can exceed 99%, 80%, 79%, and 88%, respectively. On the basis of the conception that the electron energy function f(ε) and the molar ratio of the reactants R control the reaction rate and the product composition, a kinetic model was developed to describe the plasma oxidative desulfurization reaction in the liquid phase using macroscopic test parameters. The good agreement of the calculated results with the experimental data indicates that the plasma reaction in the liquid phase is essentially the gaseous reaction occurring under special conditions. The normal viewpoint that the reaction takes place between energetic electrons and the surface molecule of the liquid may be incorrect. The reaction mechanism for plasma oxidative desulfurization of mercaptan, thioether, and thiophene in the liquid phase is discussed.
Expression of Hepatitis C Virus Proteins Induces Distinct Membrane Alterations Including a Candidate Viral Replication Complex (2002)

Plus-strand RNA viruses characteristically replicate their genome in association with altered cellular membranes. In the present study, the capacity of hepatitis C virus (HCV) proteins to elicit intracellular membrane alterations was investigated by expressing, in tetracycline-regulated cell lines, a comprehensive panel of HCV proteins individually as well as in the context of the entire HCV polyprotein. As visualized by electron microscopy (EM), expression of the combined structural proteins core-E1-E2-p7, the NS3-4A complex, and protein NS4B induced distinct membrane alterations. By immunogold EM (IEM), the membrane-altering proteins were always found to localize to the respective altered membranes. NS4B, a protein of hitherto unknown function, induced a tight structure, designated membranous web, consisting of vesicles in a membranous matrix. Expression of the entire HCV polyprotein gave rise to membrane budding into rough endoplasmic reticulum vacuoles, to the membranous web, and to tightly associated vesicles often surrounding the membranous web. By IEM, all HCV proteins were found to be associated with the NS4B-induced membranous web, forming a membrane-associated multiprotein complex. A similar web-like structure in livers of HCV-infected chimpanzees was previously described (Pfeifer et al., Virchows Arch. B., 33:233-243, 1980). In view of this finding and the observation that all HCV proteins accumulate on the membranous web, we propose that the membranous web forms the viral replication complex in HCV-infected cells.
Total Synthesis of (+)-Seimatopolide A (2014)

Total synthesis of 10-membered lactone (+)-seimatopolide A is presented from furfural. Key reactions in the present strategy include the effective use of furan as a E-but-2-ene-1,4-dione surrogate, Nagao acetate aldol reaction, and Shiina lactonization.
A new approach to spectral estimation: a tunable high-resolution spectral estimator (2000)

Traditional maximum entropy spectral estimation determines a power spectrum from covariance estimates. Here, we present a new approach to spectral estimation, which is based on the use of filter banks as a means of obtaining spectral interpolation data. Such data replaces standard covariance estimates. A computational procedure for obtaining suitable pole-zero (ARMA) models from such data is presented. The choice of the zeros (MA-part) of the model is completely arbitrary. By suitable choices of filter bank poles and spectral zeros, the estimator can be tuned to exhibit high resolution in targeted regions of the spectrum.
Temporal Summation of Loudness: An Analysis (1969)

A quantitative psychophysiological theory is developed for loudness level and loudness as a function of stimulus duration. It is based on the psychophysical as well as neurophysiological evidence that the apparent temporal summation of acoustic energy is a result of neural summation at a high level of the auditory system. The theory shows how this can be achieved in spite of a nonlinear relationship between sound intensity and neural excitation. The temporal decay of neural firing preceding the final stage of temporal summation seems to be responsible for overcoming the nonlinearity.
Characterization of a Novel CC Chemokine, HCC-4, Whose Expression Is Increased by Interleukin-10 (1998)

We have identified and characterized a human β (CC) chemokine, designated HCC-4, that is most closely related to HCC-1 and which demonstrates chemotactic activity for monocytes. Northern analysis of multiple tissue blots and of activated monocytes mRNA shows expression of a 500-bp mRNA. A 1,500-bp mRNA was highly expressed in monocytes activated 12 hours in the presence of interleukin-10 (IL-10) but was absent in monocytes activated for only 1 hour regardless of the presence or absence of IL-10. The upregulation of expression in the presence of IL-10 is in contrast to the downregulatory effects of IL-10 on expression of most other chemokines. Recombinant HCC-4 demonstrated chemotactic activity for human monocytes and THP-1 monocyte cells but not for resting lymphocytes or neutrophils. HCC-4 also induced a Ca2+ flux in THP-1 cells that was desensitized by prior exposure to RANTES. Taken together, these data indicate that HCC-4 is a novel chemokine whose expression is uniquely upregulated by IL-10.
Field cancerization, clonality, and epithelial stem cells: the spread of mutated clones in epithelial sheets (1999)

There has been considerable debate about the origin of human tumours, whether they arise from a single cell and are clonal populations or whether there needs to be some sort of co-operativity between cells for the neoplastic process to begin. Current theories subscribe to the clonal view, where a series of mutations in one cell begins a process of selection and clonal evolution leading to the development of the malignant phenotype. This review approaches this problem by asking how mutated clones, once established, spread through tissues before becoming overtly invasive. While there is substantial evidence in favour of independent origins of each tumour from a unique mutated clone, there are instances where such clones expand and remain cohesive, often involving a large area of tissue. The main example is the movement of mutated clonal crypts through the colorectal epithelium, by the process of crypt fission. In passing, the clonal architecture of early, pre-invasive lesions is examined, often with some surprising results.
Genome sequence of Streptomyces mangrovisoli MUSC 149 T isolated from intertidal sediments (2017)

As the largest genus in Actinobacteria family, Streptomyces species have the ability to synthesize numerous compounds of diverse structures with bioactivities. Streptomyces mangrovisoli MUSC 149<sup>T</sup> was previously isolated as a novel streptomycete from mangrove forest in east coast of Peninsular Malaysia. The high quality draft genome of MUSC 149<sup>T</sup> comprises 9,165,825bp with G+C content of 72.5%. Through bioinformatics analysis, 21 gene clusters identified in the genome were associated with the production of bioactive secondary metabolites. The presence of these biosynthetic gene clusters in MUSC 149<sup>T</sup> suggests the potential exploitation of the strain for production of medically important compounds.
Polarisation independent 8×8 waveguide grating multiplexer on InP (1993)

A polarisation independent InP-based 8×8 multiplexer is realised by designing the free spectral range to exactly match the TM-TE shift. The device exhibits a channel spacing of 88.4 GHz (0.71 nm), a crosstalk of −20 dB and a channel bandwidth of 39 GHz (0.31 nm). The insertion loss is below 5 dB for all eight channels.
Anticancer Agents, 15. Squaric Acid Diethyl Ester: A New Coupling Reagent for the Formation of Drug Biopolymer Conjugates. Synthesis of Squaric Acid Ester Amides and Diamides (1991)

Abstract Reaction of squaric acid diethyl ester ( 1 ) with a slight excess of a primary or secondary amine 2 in ethanol, dichloromethane or aqueous buffer (pH 7) at 20°C for 0.3–12 h gives the squaric acid amide esters 3 in mostly excellent yields. Treatment of 3 with amines 2 or 4 in organic solvents in the presence of triethylamine or in aqueous buffer (pH 9) leads to the corresponding symmetrical and unsymmetrical squaric acid diamides 5 , respectively. The reaction can be followed by UV spectroscopy.
A new glycopeptide antibiotic, OA-7653, produced by Streptomyces hygroscopicu subsp. hiwasaensis. (1983)

A new glycopeptide antibiotic, OA-7653, was isolated and purified from the culture broth of an actinomycete, designated as Streptomyces hygroscopicus subsp. hiwasaensis subsp. nov. OA-7653 appears to be most analogous to vancomycin in that it is a water-soluble compound with an ultraviolet absorption maximum at around 280 nm, containing only glucose as a neutral carbohydrate component and active against Gram-positive bacteria. The antibiotic exhibited moderate antimicrobial activities against Gram-positive bacteria including Mycobacterium and showed very low toxicity. It inhibited specifically the synthesis of cell wall peptidoglycan in bacteria.
The thermodynamics of calcite nucleation at organic interfaces: Classical vs. non-classical pathways (2012)

Nucleation in the natural world often occurs in the presence of organic interfaces. In mineralized tissues, a range of macromolecular matrices are found in contact with inorganic phases and are believed to direct mineral formation. In geochemical settings, mineral surfaces, which are often covered with organic or biological films, surround the volume within which nucleation occurs. In the classical picture of nucleation, the presence of such interfaces is expected to have a profound effect on nucleation rates, simply because they can reduce the interfacial free energy, which controls the height of the thermodynamic barrier to nucleation of the solid phase. However, the recent discovery of a nearly monodisperse population of calcium carbonate clusters—so called pre-nucleation clusters—and the many observations of amorphous precursor phases have called into question the applicability of classical descriptions. Here we use in situ observations of nucleation on organothiol self-assembled monolayers (SAMs) to explore the energetics and pathways of calcite nucleation at organic interfaces. We find that carboxyl SAM-directed nucleation is described well in purely classical terms through a reduction in the thermodynamic barrier due to decreased interfacial free energy. Moreover, the differences in nucleation kinetics on odd and even chain-length carboxyl SAMs are attributable to relative differences in these energies. These differences arise from varying degrees of SAM order related to oxygen-oxygen interactions between SAM headgroups. In addition, amorphous particles formed prior to or during crystal nucleation do not grow and are not observed to act as precursors to the crystalline phase. Instead, calcite appears to nucleate independently. These results imply that the recently proposed model of calcite formation as a non-classical process, one which proceeds via aggregation of stable pre-nucleation clusters that form an amorphous precursor from which the crystalline phase emerges, is not applicable to template-directed nucleation on carboxyl SAMs and does not provide a universal description of calcite formation.
Correlated line broadening in multidimensional vibrational spectroscopy (2002)

The third-order optical response of two coupled anharmonic vibrations interacting with a Brownian oscillator bath that induces energy level fluctuations with arbitrary time scales and degree of correlation is calculated. Two-dimensional correlation plots show distinct signatures of these fluctuations in the various possible three pulse, infrared, femtosecond techniques.
Gastric Electrical Stimulation with the TANTALUS® System in Obese Type 2 Diabetes Patients: Effect on Weight and Glycemic Control (2009)

Short-term therapy with the TANTALUS System improves glucose control, induces weight loss, and improves blood pressure and lipids in obese T2DM subjects on oral antidiabetes therapy.
Immobilization of sorghum leaf oxalate oxidase onto alkylamine and arylamine glass. (1999)

An oxalate oxidase (EC 1.2.3.4) purified from grain sorghum leaves was immobilized onto alkylamine and arylamine glass beads through glutaraldehyde coupling and diazotization with a conjugation yield of 10.8 mg/g support and 9.2 mg/g support, respectively. The enzyme retained 67.5% and 34.1% of its initial specific activity after immobilization onto alkylamine and arylamine glass, respectively. The enzyme exhibited an increase in optimum pH, temperature for maximum activity, energy of activation (Ea) and time for linearity but decrease in thermal stability at 60 degrees C after immobilization on both types of beads. The K(m) value for oxalate was increased by 9- to 10-fold but Vmax remained unaltered after immobilization. Both alkyl and arylamine glass bound enzyme was unaffected by physiological concentrations of Cl- and NO3-. The analytic importance of this work is demonstrated.
Electronic Momentary Assessment of Weather Changes as a Trigger of Headaches in Children (2009)

Results of the present study lend some support to the belief commonly held by children with recurrent headaches that weather changes may contribute to headache onset. Although electronic momentary assessment methodology was found to be feasible in this population and to have the potential to identify specific headache triggers for children, it remains to be determined how best (or even whether) to incorporate this information into treatment recommendations.