gebhart/patrepeval huggingface dataset:
Site-specific genetic engineering of theAnopheles gambiaeY chromosome (2014)

Despite its function in sex determination and its role in driving genome evolution, the Y chromosome remains poorly understood in most species. Y chromosomes are gene-poor, repeat-rich and largely heterochromatic and therefore represent a difficult target for genetic engineering. The Y chromosome of the human malaria vector Anopheles gambiae appears to be involved in sex determination although very little is known about both its structure and function. Here, we characterize a transgenic strain of this mosquito species, obtained by transposon-mediated integration of a transgene construct onto the Y chromosome. Using meganuclease-induced homologous repair we introduce a site-specific recombination signal onto the Y chromosome and show that the resulting docking line can be used for secondary integration. To demonstrate its utility, we study the activity of a germ-line-specific promoter when located on the Y chromosome. We also show that Y-linked fluorescent transgenes allow automated sex separation of this important vector species, providing the means to generate large single-sex populations. Our findings will aid studies of sex chromosome function and enable the development of male-exclusive genetic traits for vector control.
Simultaneous Fluorescence and Raman Scattering from Single Carbon Nanotubes (2003)

Single-molecule fluorescence spectroscopy was used to determine the electronic properties of individual single-walled carbon nanotubes. Carbon nanotube structure was determined simultaneously from Raman spectroscopy. Fluorescence spectra from individual nanotubes with identical structures have different emission energies and linewidths that likely arise from defects or the local environment. Unlike most other molecules studied to date, the fluorescence intensity or spectrum from a single nanotube unexpectedly did not fluctuate.
TheTMPRSS2 gene encoding transmembrane serine protease is overexpressed in a majority of prostate cancer patients: Detection of mutatedTMPRSS2 form in a case of aggressive disease (2001)

The serine protease TMPRSS2 gene expression was studied by in situ hybridization using benign prostatic hyperplasia and prostate cancer tissue samples from 32 patients. Expression of TMPRSS2 gene was higher in cancer cells than that in benign cells in 84% of the specimens containing both benign and malignant tissues. The TMPRSS2 mRNA level was significantly increased in poorly differentiated (p = 0.014, n = 7) and untreated (p = 0.022, n = 13) primary prostate adenocarcinomas compared to benign tissues. In addition, androgen-deprivation therapy significantly decreased the expression of TMPRSS2 in benign prostate tissue (p = 0.07), which is in accordance with the androgen-inducible expression of the gene. The gene copy number of TMPRSS2, analyzed by competitively differential PCR, was duplicated in the malignant cells of about 38% of the prostate cancer patients analyzed. Thus, the increase in the gene copy number is probably not the primary reason for the detected overexpression of the TMPRSS2 gene. Mutations in the TMPRSS2 gene were screened using DNA isolated from paraffin-embedded prostate cancer tissues from 9 patients with aggressive prostate cancer and from 9 patients with nonaggressive disease. Thirteen exons covering the coding region were checked using enzymatic mutation detection and direct sequencing. One patient with aggressive prostate cancer carried a deletion and a stop codon in exon 11, leading to inactivation of the serine protease domain in TMPRSS2.
Identification of a chromosomal determinant of alpha-toxin production in Staphylococcus aureus (1980)

Production of alpha-toxin (the Hla+ phenotype, controlled by the Hla gene and scored as alpha-hemolytic activity) is a property of some isolates of Staphylococcus aureus NCTC 8325 and not of others. Genetic transformation between strains differing in the Hla phenotype revealed that the hla+ gene resides in the following sequence: purB110-bla+-hla+-ilv-129-pig-131; previously, the enterotoxin A (entA) gene of strain S-6 was shown to map very close to hla+. The hla+ mutations occurring naturally in strain Ps6 and after various mutagenic treatments in strains 8325 and 233 also mapped between bla+ and ilv-129. Among the isolates of strain 8325, the Hla+ phenotype was always associated with fibrinolytic activity, whereas Hla- isolates were non-fibrinolytic. This relationship was also observed among transformants selected for their Hla+ or Hla- phenotypes. The failure of Hla- strains and mutants to revert to hla+ at detectable frequencies, the instability of the Hla+ phenotype, and the previously observed pattern of recombination of the hla+ and entA+ determinants lend support to the view that hla+ may reside on a transposon; according to this view, Hla- mutants have lost the hla+-bearing transposon. It remains unclear whether hla+ is the structural gene for alpha-toxin.
Cordycepin/Hydroxyurea synergy allows low dosage efficacy of cordycepin in MOLT-4 leukemia cells. (2007)

HU was identified as a promising potential alternative for anti-cancer therapy with cordycepin, thus eliminating the need for the toxic deoxycoformycin.
Transcatheter closure of patent foramen ovale (PFO) in patients with paradoxical embolism Periprocedural safety and mid-term follow-up results of three different device occluder systems (2004)

Interventional PFO closure appears to be safe and a promising technique in symptomatic PFO patients with a low incidence of periinterventional complications and recurrent thromboembolic events using three different devices (PFO-Star, Amplatzer PFO occluder or the CardioSeal/Starflex).
Novel Membrane-Interactive Ether Lipid Analogs That Inhibit Infectious HIV-1 Production and Induce Defective Virus Formation (1990)

A new class of membrane-active ether lipid (EL) analogs of platelet-activating factor were studied for in vitro anti-HIV-1 activity. Human T-cell (CEM-ss) monolayers or suspension cultures were used to determine effects of structural modifications of Type A phosphorus-containing and Type B nonphosphorus EL analogs on (a) the inhibitory concentration50 (IC50) for HIV-1 syncytial plaque formation and cell growth, and, (b) virus budding at the cell plasma membrane. Results indicate that representative Type A and Type B EL inhibit HIV-1 but not herpes simplex virus type 2 plaque formation when added before or up to 2 days after viral infection. Anti-HIV-1 activity does not involve direct inactivation of virus infectivity. Type A EL (IC50 range = 0.2-1.4 microM) with alkyoxy, alkylthio, or alkyamido substitution at glycerol position 1 and ethoxy or methoxy substitution at position 2, and Type B compounds (IC50 range = 0.33-0.63 microM) with an inverse choline or nitrogen heterocyclic substitution at position 3 have selective activity against HIV-1-infected T-cells. EL treatment of HIV-1-infected cells is associated with subsequent release of reverse transcriptase activity, but infectious virus production is inhibited with time after infection. Electron microscopic examination of HIV-1-infected and EL-treated cells revealed absence of detectable budding virus at the plasma membrane but presence of intracytoplasmic vacuolar virus particles. In summary, these data suggest that EL analogs are a novel class of agents that induce defective intracytoplasmic vacuolar HIV-1 formation in T-cells. Being membrane interactive, EL are ideally suited for combination chemotherapy with DNA-interactive anti-HIV nucleoside analogs.
NUTRITIONAL CONTROL OF CELL PIGMENTATION IN CHLORELLA PROTOTHECOIDES WITH SPECIAL REFERENCE TO THE DEGENERATION OF CHLOROPLAST INDUCED BY GLUCOSE1 (1964)

1. Measuring the chlorophyll contents and growth of the algal cells grown in media containing different amounts of glucose (G) and urea fas a nitrogen source, N), it was found that the ratio N/G determines pigmentation of the cells (colourless, yellow, yellowish green and green) under the experimental conditions used, and thus a sort of colour map of the differently pigmented cells was obtained. 2. The bleached cells produced at lower N/G ratios and the green cells obtained at higher ratios could he cultured successively under heterotrophic and photoautotrophic conditions, respectively, and both forms were interconvertible on transferring each cell type into a new medium having appropriate N/G ratio. 3. Studies on these bleaching and greening processes under different experimental conditions revealed that the greening requires essentially the supply of N-sources—no strict specificity was observed with different N-sources tested—as well as light, but can take place independently of growth, while the bleaching is caused most strongly by glucose (and fructose) among the carbon sources examined and proceeds essentially independent of light. 4. The bleaching effect of glucose at its higher concentrations is primarily due to its degradation effect on chloroplast structures including lamellae. This effect of glucose is markedly diminished at its decreasing concentrations and is also counteracted by the supply of N-source (urea) of higher concentrations.
Wireless Communication Technology in the 21st Century (1999)

Wireless communication is expected to be a dominant mode of access technology in the next century. Besides voice, a new range of services such asmultimedia, highspeed data, etc. are being offered for delivery over wireless networks. This paper introduces some concepts of the third international mobile communications IMT 2000 and wireless asynchronous transfer mode WATM, summarizes their key technologies, and expounds their perspective of the next millennium.
Highly Antimalaria‐Active Artemisinin Derivatives: Biological Activity Does Not Correlate with Chemical Reactivity (2004)

New leads for antimalarial drugs? 10-Alkylaminoartemisinin derivatives like that shown display in vivo antimalarial activities greater than those of the parent artemisinin. Previous conclusions regarding the chemical basis for the antimalarial activity of these compounds must be reconsidered.
Molecular mechanism of dysfunctional factor VII associated with the homozygous missense mutation 331Gly to Ser (2005)

We have identified a Japanese homozygous FVII deficiency associated with the mutation G331S (c184 [in chymotrypsin numbering]), and have determined the mechanisms responsible for the dysfunctional FVII variant by expressing the mutant recombinant FVII protein. In addition, the recombinant proteins FVIIG331D, G331W and G331F were expressed. The purified recombinant FVII proteins ran as a single chain form on SDS-PAGE having a molecular mass of approximately 50 Kda. The recombinant FVIIG331S expressed the level of the recombinant wild type FVII at 2.0%, and this mutant form was also similar to FVII in the patient's plasma. However, the amidolytic activity of FVIIa using peptidyl substrate S-2288 differed little between the wild type and the four mutant FVII molecules. We suggest that the functional defect found in these mutants is not directly associated with peptidyl substrate recognition or catalysis. The Km values of FX and FIX for the mutant proteins were approximately 7.6- to 15-fold and 13- to 19-fold higher than those for the wild-type protein, respectively. Molecular modelling indicated that the side chain of the S331 mutant is oriented close to the side chain of D338 (c189) at the bottom of the specificity pocket of FVIIa. We show that the replacement of G331 with a serine likely results in a steric hindrance of macromolecular substrate binding, leading to a loss of FVIIa enzymatic activity.
Restriction of the Conformational Dynamics of the Cyclic Acyldepsipeptide Antibiotics Improves Their Antibacterial Activity (2014)

The cyclic acyldepsipeptide (ADEP) antibiotics are a new class of antibacterial agents that kill bacteria via a mechanism that is distinct from all clinically used drugs. These molecules bind and dysregulate the activity of the ClpP peptidase. The potential of these antibiotics as antibacterial drugs has been enhanced by the elimination of pharmacological liabilities through medicinal chemistry efforts. Here, we demonstrate that the ADEP conformation observed in the ADEP-ClpP crystal structure is fortified by transannular hydrogen bonding and can be further stabilized by judicious replacement of constituent amino acids within the peptidolactone core structure with more conformationally constrained counterparts. Evidence supporting constraint of the molecule into the bioactive conformer was obtained by measurements of deuterium-exchange kinetics of hydrogens that were proposed to be engaged in transannular hydrogen bonds. We show that the rigidified ADEP analogs bind and activate ClpP at lower concentrations in vitro. Remarkably, these compounds have up to 1200-fold enhanced antibacterial activity when compared to those with the peptidolactone core structure common to two ADEP natural products. This study compellingly demonstrates how rational modulation of conformational dynamics may be used to improve the bioactivities of natural products.
Design and Synthesis of a Long-Wavelength Latent Fluorogenic Substrate for Salicylate Hydroxylase: A Useful Fluorimetric Indicator for Analyte Determination by Dehydrogenase-Coupled Biosensors (2010)

Salicylate hydroxylase (SHL) catalyzes the production of catechol (plus CO(2) and H(2)O) from salicylate, NADH, and O(2). Coimmobilization of SHL with a NAD(P)(+)-dependent dehydrogenase in front of a Clark-type oxygen electrode has been investigated in the development of a general type of dehydrogenase-based biosensors that can detect various biological analytes; however, currently, no fluorophores are available for these applications. We synthesized the first new long-wavelength latent fluorogenic substrate SHLF (3) for SHL. In the presence of NADH and under aerobic conditions, SHL catalyzes the decarboxylative hydroxylation of SHLF followed by a quinone-methide-type rearrangement reaction concomitant with the ejection of a fluorescence coumarin 2, which is spontaneous and irreversible at physiological temperatures in aqueous media. The fluorescence signal generated by this process is specific and, in the near red spectral region with an emission maximum at 595 nm, is suppressed by salicylic acid. The fluorescence response of SHLF is insensitive to various biological reactive oxygen species (ROS) and reductants. Furthermore, SHLF is a sensitive fluorimetric indicator for analyte determination in the SHL-coupled dehydrogenase assay in which NAD(+) is converted to NADH. This novel fluorescence assay detected 3-hydroxybutyrate and cholesterol in the nanomolar range and is more sensitive than the current SHL-dehydrogenase amperometric sensors, making it applicable to the construction of a fiber-optic fluorescence biosensor for clinical diagnostic uses.
Activation of Metabotropic Glutamate 2/3 Receptors Reverses the Effects of NMDA Receptor Hypofunction on Prefrontal Cortex Unit Activity in Awake Rats (2005)

Systemic exposure to N-methyl-d-aspartate (NMDA) receptor antagonists can lead to psychosis and prefrontal cortex (PFC)-dependent behavioral impairments. Agonists of metabotropic glutamate 2/3 (mGlu2/3) receptors ameliorate the adverse behavioral effects of NMDA antagonists in humans and laboratory animals, and are being considered as a novel treatment for some symptoms of schizophrenia. Despite the compelling behavioral data, the cellular mechanisms by which potentiation of mGlu2/3 receptor function attenuates the effects of NMDA receptor hypofunction remain unclear. In freely moving rats, we recorded the response of medial PFC (prelimbic) single units to treatment with the NMDA antagonist MK801 and assessed the dose-dependent effects of pre- or posttreatment with the mGlu2/3 receptor agonist LY354740 on this response. NMDA receptor antagonist-induced behavioral stereotypy was measured during recording because it may relate to the psychotomimetic properties of this treatment and is dependent on the functional integrity of the PFC. In most PFC neurons, systemic administration of MK801 increased the spontaneous firing rate, decreased the variability of spike trains, and disrupted patterns of spontaneous bursts. Given alone, LY354740 (1, 3, and 10 mg/kg) decreased spontaneous activity of PFC neurons at the highest dose. Pre- or posttreatment with LY354740 blocked MK801-induced changes on firing rate, burst activity, and variability of spike activity. These physiological changes coincided with a reduction in MK801-induced behavioral stereotypy by LY354740. These data indicate that activation of mGlu2/3 receptors reduces the disruptive effects of NMDA receptor hypofunction on the spontaneous spike activity and bursting of PFC neurons. This mechanism may provide a physiological basis for reversal of NMDA antagonist-induced behaviors by mGlu2/3 agonists.
Initial Use of Ambrisentan plus Tadalafil in Pulmonary Arterial Hypertension (2015)

Among participants with pulmonary arterial hypertension who had not received previous treatment, initial combination therapy with ambrisentan and tadalafil resulted in a significantly lower risk of clinical-failure events than the risk with ambrisentan or tadalafil monotherapy. (Funded by Gilead Sciences and GlaxoSmithKline; AMBITION ClinicalTrials.gov number, NCT01178073.).
Automatic method to quantify starter activity based on pH measurement (1989)

Summary A new method for measuring the activity of mesophilic and thermophilic lactic acid bacteria is proposed based on measuring the pH of cultures at extremely short intervals (30–90 s) during growth and calculating several kinetic parameters, i.e. the maximum acidification rate (V m ), the time and pH at which V m occurred, the time or pH range during which the observed rates were greater than V m /2. These were easily calculated by coupling the pH meter to a microcomputer.
Progress in high-power fiber lasers (2004)

We review current work on fiber laser systems at Corning. In particular, we describe design and performance of all-glass double-clad laser fibers, broad-area laser pumps, and pump coupling optics. We discuss our approaches using single-polarization fiber and low-nonlinearity photonic band gap fiber as technologies for developing the next generation of high-power fiber lasers.
Inflammatory reaction in experimental autoimmune encephalomyelitis (EAE) is accompanied by a microglial expression of the βA4‐amyloid precursor protein (APP) (1995)

Neuropathological studies of the amyloid depositions and senile plaques in the brains of elderly patients or patients diagnosed with Alzheimer's disease reveal the conspicuous presence of numerous proteins which are usually expressed during reactions of the immune system. This has led to speculations that the pathomechanism of neurodegenerative diseases might involve inflammatory processes. These considerations constitute the theoretical basis for therapeutic intervention with antiinflammatory drugs in neurodegenerative diseases. Here, we show that the beta A4-amyloid precursor (APP) is rapidly induced in microglia in a model of experimental autoimmune encephalomyelitis (EAE). Using specific monoclonal antibodies against APP, the first glial cells newly expressing APP immunoreactivity were found at an early preclinical stage, i.e., 24 h after T-cell transfer. At the peak of clinical disease (6 days after T-cell transfer), numerous characteristically ramified cells were strongly positive for APP. Based on morphology and double-labeling, most of the de novo APP-expressing cells were identified as microglia. Additionally, APP-immunoreactive round cells were detected in and around perivascular infiltrates. Reflecting the course of the clinical disease, the induction of APP immunoreactivity terminated in the postclinical stage, i.e., 14 days after T-cell transfer. These results support earlier work demonstrating that microglia can rapidly de novo synthesise APP not only in response to direct nerve injury (Banati et al: Glia 9:199, 1993a) but also in immune-mediated disease. Apart from its possible therapeutic relevance, such a production of APP--reminiscent of an acute phase protein-suggests a role of APP in immune and repair mechanisms of the central nervous system.
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