gebhart/patrepeval huggingface dataset:
Acetylpolyamine amidohydrolase from Mycoplana ramosa: gene cloning and characterization of the metal-substituted enzyme (1996)

We have cloned a gene (aphA) encoding acetylpolyamine amidohydrolase from Mycoplana ramosa ATCC 49678, (previously named Mycoplana bullata). A genomic library of M. ramosa was screened with an oligonucleotide probe designed from a N-terminal amino acid sequence of the enzyme purified from M. ramosa. Nucleotide sequence analysis revealed an open reading frame of 1,023 bp which encodes a polypeptide with a molecular mass of 36,337 Da. This is the first report of the structure of acetylpolyamine amidohydrolase. The aphA gene was subcloned under the control of the trc promoter and was expressed in Escherichia coli MM294. The recombinant enzyme was purified, and the enzymatic properties were characterized. Substrate specificities, Km values, and Vmax values were identical to those of the native enzyme purified from M. ramosa. In the analysis of the metal-substituted enzymes, we found that the acid limb of pH rate profiles shifts from 7.2 for the original zinc enzyme to 6.6 for the cobalt enzyme. This change suggests that the zinc atom is essential for the catalytic activity of the enzyme similarly to the zinc atom in carboxypeptidase A.
Antiproliferative activity to vascular smooth muscle cells and receptor binding of heparin-mimicking polyaromatic anionic compounds. (1994)

Proliferation of bovine aortic smooth muscle cells (SMCs) induced by thrombin, basic fibroblast growth factor, or serum is inhibited by anionic, nonsulfated aromatic compounds that mimic many of the effects of heparin. Among these compounds are aurintricarboxylic acid (ATA) and a newly synthesized polymer of 4-hydroxyphenoxy acetic acid (compound RG-13577). Iodinated- or 14C-labeled compound RG-13577 binds to cultured SMCs in a highly specific and saturable manner. Scatchard analysis of the binding data revealed the presence of an estimated 1 x 10(7) binding sites per cell with an apparent dissociation constant of 3 x 10(-6) mol/L. Binding of radiolabeled RG-13577 was efficiently competed for by related aromatic anionic compounds and by apolipoprotein E, but not by heparin, heparan sulfate, suramin, or various purified growth factors and extracellular matrix proteins. Receptor cross-linking of SMC-bound 125I-RG-13577 revealed a single species of high M(r) (approximately 280 kD) cell surface receptors detected in the absence but not the presence of excess unlabeled compound RG-13577. Binding was susceptible to downregulation and restoration of receptor levels in a manner similar to that of hormone and growth factor receptors. We suggest that the antiproliferative activity of compound RG-13577 and related compounds is initiated by binding to specific growth-inhibiting cell surface receptors. Heparin-mimicking compounds may be applied to inhibit SMC proliferation associated with atherosclerosis and restenosis.
Synopsis of Fungi Listed as Regulated Plant Pests by the USDA Animal and Plant Health Inspection Service: Notes on Nomenclature, Disease, Plant Hosts, and Geographic Distribution (2006)

To prevent the entry of exotic fungal pathogens, the Animal and Plant Health Inspection Service (APHIS) of the U.S. Department of Agriculture (USDA) has compiled a list of regulated plant pests of concern to the U.S., including more than 50 species of fungi that might cause serious economic or environmental damage. The fungi on the APHIS Regulated Plant Pest List represent some of the most significant threats to U.S. agriculture. For each of these fungal species, a synopsis was prepared that presents notes on nomenclature, disease, plant hosts, and geographic distribution. The following scientific names should be updated: Cercospora batatas (Pseudocercospora timorensis), Chrysomyxa ledi var. rhododendri (Chrysomyxa rhododendri), Crinipellis perniciosa (Moniliophthora perniciosa), Phacidiopycnis pseudotsugae (Allantophomopsis pseudotsugae), Pucciniastrum areolatum (Thekopsora areolata), and Stereum hiugense (Xylobolus hiugensis). Nomenclatural controversies are discussed for some species, including Diaporthe mali and Monilinia fructigena. Changes in nomenclature often reflect advances in taxonomic understanding, resulting in transfers to a different genus, modifications of lists of taxonomic synonyms, or establishing anamorph/teleomorph connections. These changes can have important implications for accurately determining the geographic distribution and host range of a fungus. Accurate information about scientific names, geographic distribution, and plant host range is essential in determining pest risk and in preventing the introduction and spread of invasive fungal pathogens. Accepted for publication 18 March 2006. Published 5 May 2006.
Carboxanilide Derivative Non-Nucleoside Inhibitors of HIV-1 Reverse Transcriptase Interact with Different Mechanistic Forms of the Enzyme (1995)

Researchers at the National Cancer Institute first recognized the anti-HIV potential of the carboxanilide compound oxathiin carboxanilide (UC84) [Bader, J. P., et al. (1991) Proc. Natl. Acad. Sci. U.S.A. 88, 6740-6744]. We have compared the inhibitory effect of UC84 and a second-generation thiocarboxanilide derivative, UC38, on HIV-1 reverse transcriptase (RT) RNA-dependent DNA polymerase activity. UC38 was a much better inhibitor (IC50 = 0.8 microM) than UC84 (IC50 = 4.3 microM). Inhibition by UC84 was competitive with respect to primer/template (P/T), whereas that by UC38 was uncompetitive. Both compounds were mixed noncompetitive inhibitors with respect to deoxynucleoside triphosphate (dNTP). Both compounds protected RT from irreversible photoinactivation by an azido derivative of nevirapine, implying that UC84 and UC38 bind to the same region of RT as nevirapine. UC84 photoprotected both free RT and the RT-P/T binary complex, but did not protect the RT-P/T-dNTP ternary complex. In contrast, UC38 completely photoprotected the RT-P/T-dNTP ternary complex, but not free RT or the RT-P/T binary complex. UC84 and UC38 thus appear to bind to different mechanistic forms of RT in the polymerase reaction sequence.
Unique site of IgG2a and rheumatoid factor production in MRL/lpr mice (1997)

MRL/lpr (Fas-deficient) mice develop an autoimmune syndrome associated with excessive production of autoantibodies. A significant portion of these autoantibodies are IgG2a molecules specific for many of the autoantigens recognized by the sera of patients with systemic lupus erythematosus. In addition, MRL/lpr mice make exceedingly high titers of IgG or IgA rheumatoid factors (RF) specific for autologous IgG2a. The microenvironment of the IgG2a-producing B cells as well as the prototypic RF autoantibodies was determined by a combination of immunohistochemical and in situ hybridization techniques. In contrast to the antibody-producing cells present in mice responding to conventional foreign antigens, both IgG2a+ and RF+ B cells were found to be densely clustered in the T-cell-rich inner periarteriolar lymphatic sheath of the spleen. These results suggest that conventional antibody and autoantibody production in MRL/lpr mice may be mechanistically distinct processes.
Upper bounds of rates of space-time block codes from complex orthogonal designs (2002)

Derives some upper bounds on the rates R of (generalized) COST block codes (or complex orthogonal designs) when the number of transmit antennas is more than 2.
Thermodynamic Fluctuations in a Reacting System—Measurement by Fluorescence Correlation Spectroscopy (1972)

The temporal correlations of thermodynamic concentration fluctuations have been measured in a chemically reactive system at equilibrium by observing fluctuations of the fluorescence of a reaction product. The experiment yields the chemical rate constants and diffusion coefficients and shows the coupling among them. Data are reported for binding of ethidium bromide to DNA.
The Phosphorylation Status of a Cyclic AMP-Responsive Activator Is Modulated via a Chromatin-Dependent Mechanism (2000)

Cyclic AMP (cAMP) stimulates the expression of numerous genes via the protein kinase A (PKA)-mediated phosphorylation of CREB at Ser133. Ser133 phosphorylation, in turn, promotes recruitment of the coactivator CREB binding protein and its paralog p300, histone acetyltransferases (HATs) that have been proposed to mediate target gene activation, in part, by destabilizing promoter bound nucleosomes and thereby allowing assembly of the transcriptional apparatus. Here we show that although histone deacetylase (HDAC) inhibitors potentiate target gene activation via cAMP, they do not stimulate transcription over the early burst phase, during which CREB phosphorylation and CBP/p300 recruitment are maximal. Rather, HDAC inhibitors augment CREB activity during the late attenuation phase by prolonging CREB phosphorylation on chromosomal but, remarkably, not on extrachromosomal templates. In reconstitution studies, assembly of periodic nucleosomal arrays on a cAMP-responsive promoter template potently inhibited CREB phosphorylation by PKA, and acetylation of these template-bound nucleosomes by p300 partially rescued CREB phosphorylation by PKA. Our results suggest a novel regulatory mechanism by which cellular HATs and HDACs modulate the phosphorylation status of nuclear activators in response to cellular signals.
Growth, Sporulation, and Enzyme Defects of Glucosamine Mutants of Bacillus subtilis (1970)

Two glucosamine (GCA)-requiring mutants have been isolated which grow on glucose minimal or nutrient sporulation medium only in the presence of either GCA or acetyl-GCA. They lack the l-glutamine-d-fructose-6-phosphate aminotransferase (EC 2.6.1.13), which is repressible by GCA and whose activity in the standard strain decreases after cessation of growth. But the mutants can grow on GCA as sole carbon and ammonia source, because GCA induces the synthesis of 2-amino-2-deoxy-d-glucose-6-phosphate ketol-isomerase (deaminating) (EC 5.3.1.10). With respect to sporulation, the GCA-requiring mutants are in a serious dilemma, as GCA represses the onset of massive sporulation and yet a small amount of GCA-6-phosphate derivatives is necessary to allow sporulation. When GCA is continuously provided in small quantities, sporelike particles are produced which contain little or no spore cortex but a normal spore coat. Apparently, GCA derivatives are needed especially for cortex formation. Many of the sporelike particles can produce colonies after octanol, but not after heat treatment. When they are purified by treatment with lysozyme and sodium dodecylsulfate, they do not show the decrease in optical density at 600 nm typical of germination nor do they produce offspring.
Glucose deprivation and acute cycloheximide treatment stimulate system L amino acid transport in cultured vascular smooth muscle cells. (1994)

The effect of glucose deprivation on the uptake of leucine has been examined in cultured vascular smooth muscle cells isolated from rat aortae. Equimolar substitution of sucrose or fructose for glucose in the culture medium enhanced the uptake of leucine in a time- and concentration-dependent manner. The effect was first detectable after 12 h and reached the maximum, 2-fold, after 48 h with an apparent half-maximal effect at 1 mM glucose and could be reversed after 48 h of glucose refeeding. The enhanced leucine uptake was completely inhibited by 2-amino-2-norbornane-carboxylic acid, a specific substrate for System L, but not by alpha-(methylamino)isobutyric acid or lysine. Kinetic analyses indicated that this stimulation was mediated via a homogenous system with a 1.7-fold increase in the Vmax without any change in the Km (0.15 mM). Prolonged treatments with cycloheximide (10 micrograms/ml) or actinomycin D (10 micrograms/ml) blocked this glucose deprivation effect and its reversal. However, cycloheximide also very rapidly stimulated leucine uptake, reaching the maximum, 2.5-fold over the basal at 1 h. This effect occurred at concentrations that matched its inhibition on protein synthesis (half-maximal at 0.1 micrograms/ml) and could be reproduced with puromycin as well as actinomycin D. The stimulatory effect of cycloheximide was also accompanied by an increase in the Vmax but not in the Km, being sensitive to 2-amino-2-norbornane-carboxylic acid inhibition only, and appeared to occur in an additive manner to that of glucose deprivation. Although the uptake of leucine was stimulated by glucose deprivation and brief exposure to cycloheximide, these treatments had no effect on the efflux of the substrate. These results are all consistent with the System L amino acids transport activity in cultured rat vascular smooth muscle cells being under the control of at least two non-hormonal regulatory mechanisms, one that is likely to involve a labile repressor molecule and the other involving de novo protein synthesis as a result of chronic glucose deprivation.
Efficient run-length encodings (1982)

A method for the noiseless coding of binary memoryless sources when the symbol probabilities are unknown is investigated. Codes of long block length are constructed from truncated run-length codes. Though not universal, the codes are shown to achieve high efficiencies over a wide range of symbol probabilities. Several generalizations of the basic scheme are also presented. The schemes presented in this paper are particularly well-suited for facsimile coding.
Association of Epstein–Barr Virus with Leiomyosarcomas in Young People with AIDS (1995)

EBV can infect smooth-muscle cells, at least in patients with AIDS, and it may contribute to the pathogenesis of leiomyomas and leiomyosarcomas in children with AIDS. EBV seems to play no part in smooth-muscle tumors in HIV-negative children.
An analysis of latent sector errors in disk drives (2007)

The reliability measures in today's disk drive-based storage systems focus predominantly on protecting against complete disk failures. Previous disk reliability studies have analyzed empirical data in an attempt to better understand and predict disk failure rates. Yet, very little is known about the incidence of latent sector errors i.e., errors that go undetected until the corresponding disk sectors are accessed.
Antiviral immune responses in gene-targeted mice expressing the immunoglobulin heavy chain of virus-neutralizing antibodies (2003)

Two gene-targeted immunoglobulin heavy chain transgenic mouse strains, TgH(KL25) and TgH(VI10), expressing neutralizing specificities for lymphocytic choriomeningitis virus and vesicular stomatitis virus, respectively, have been generated. Three days after lymphocytic choriomeningitis virus infection, TgH(KL25) mice showed a thymus-independent neutralizing IgM response followed by thymus-dependent (TD) IgG. In contrast, WT mice mounted only a TD IgG response around day 80. These observations indicated that not only structural properties of the virus but also immunological parameters such as the frequency of B cells were indicative for the induction of thymus-independent versus TD Ig responses. Naïve vesicular stomatitis virusspecific Ig heavy chain transgenic mice displayed greatly elevated natural antibody titers. However, despite these high naïve titers, de novo activation of naïve CD4+ T and B cells was not blocked. Therefore, B cells giving rise to natural antibodies do not participate in virus-induced antibody responses.
Transposase mediated construction of RNA-seq libraries (2011)

RNA-seq has been widely adopted as a gene-expression measurement tool due to the detail, resolution, and sensitivity of transcript characterization that the technique provides. Here we present two transposon-based methods that efficiently construct high-quality RNA-seq libraries. We first describe a method that creates RNA-seq libraries for Illumina sequencing from double-stranded cDNA with only two enzymatic reactions. We generated high-quality RNA-seq libraries from as little as 10 pg of mRNA (∼1 ng of total RNA) with this approach. We also present a strand-specific RNA-seq library construction protocol that combines transposon-based library construction with uracil DNA glycosylase and endonuclease VIII to specifically degrade the second strand constructed during cDNA synthesis. The directional RNA-seq libraries maintain the same quality as the nondirectional libraries, while showing a high degree of strand specificity, such that 99.5% of reads map to the expected genomic strand. Each transposon-based library construction method performed well when compared with standard RNA-seq library construction methods with regard to complexity of the libraries, correlation between biological replicates, and the percentage of reads that align to the genome as well as exons. Our results show that high-quality RNA-seq libraries can be constructed efficiently and in an automatable fashion using transposition technology.
Entwicklungstendenzen photonischer Nachrichtennetze (1996)

Photonic networks will be the base of a future broadband Internet that permits easy access to a variety of multimedia services. Optical frequency and time division multiplexing techniques enable an optimum matching of the photonic network's capacity to the increasing communications demand, thereby reacting to the requirements of new services in a flexible way. Flexibility and reliability with high profitability are the crucial characteristics of future photonic networks.
Oxygen sensors and energy sensors act synergistically to achieve a graded alteration in gene expression: consequences for assessing the level of neuroprotection in response to stressors (2004)

Changes in gene expression are associated with switching to an autoprotected phenotype in response to environmental and physiological stress. Ubiquitous molecular chaperones from the heat shock protein (HSP) superfamily confer neuronal protection that can be blocked by antibodies. Recent research has focused on the interactions between the molecular sensors that affect the increased expression of neuroprotective HSPs above constitutive levels. An examination of the conditions under which the expression of heat shock protein 70 (Hsp70) was up regulated in a hypoxia and anoxia tolerant tropical species, the epaulette shark (Hemiscyllium ocellatum), revealed that up-regulation was dependent on exceeding a stimulus threshold for an oxidative stressor. While hypoxic-preconditioning confers neuroprotective changes, there was no increase in the level of Hsp70 indicating that its increased expression was not associated with achieving a neuroprotected state in response to hypoxia in the epaulette shark. Conversely, there was a significant increase in Hsp70 in response to anoxic-preconditioning, highlighting the presence of a stimulus threshold barrier and raising the possibility that, in this species, Hsp70 contributes to the neuroprotective response to extreme crises, such as oxidative stress. Interestingly, there was a synergistic effect of coincident stressors on Hsp70 expression, which was revealed when metabolic stress was superimposed upon oxidative stress. Brain energy charge was significantly lower when adenosine receptor blockade, provided by treatment with aminophylline, was present prior to the final anoxic episode, under these circumstances, the level of Hsp70 induced was significantly higher than in the pair-matched saline treated controls. An understanding of the molecular and metabolic basis for neuroprotective switches, which result in an up-regulation of neuroprotective Hsp70 expression in the brain, is needed so that intervention strategies can be devised to manage CNS pathologies and minimise damage caused by ischemia and trauma. In addition, the current findings indicate that measurements of HSP expression per se may provide a useful correlate of the level of neuroprotection achieved in the switch to an autoprotected phenotype.
Polytronics for biotronics: unique possibilities of polymers in biosensors and bioMEMS ? (2003)

In recent years, sensing polymeric materials have gained a wide theoretical interest and practical application in biomedicine both in sensors and in bio-MEMS. They can be used for very different purposes and may offer unique possibilities. The paper give a broad summary of the polymer films used in these type applications. Polymers offer a lot of advantages for medical and biosensor technologies: they are relatively low cost materials, their fabrication techniques are quite simple, they can be deposited on various types of substrates using methods compatible with all microelectronic and micro fabrication technologies, as well as the wide choice of their molecular structure and the possibility to build in side chains, charged or neutral particles or even grains of specific behavior into the bulk material or on its surface region enables producing films with various physical and chemical properties including also sensing behavior.
Enzyme-Free Sugar Sensing in Microfluidic Channels with an Affinity-Based Single-Wall Carbon Nanotube Sensor (2010)

We present a novel nonenzymatic carbon nanotube sensor integrated in a microfluidic channel for the detection of sugars. The sensor is assembled as a liquid-gated field-effect transistor, with the transistor channel composed of 1 to 10 nanotubes, which are controllably functionalized with boronic acid receptors. The devices show sensitivity to glucose in a concentration range of 5 to 30 mM. Furthermore, by controlling the type of nanotube-receptor coupling (as covalent or noncovalent) and by deploying a sensitive impedance-based detection technique, we corroborate in detail the transduction mechanism of our affinity-based sensor. In the case of covalent coupling, charge carrier scattering along the nanotubes is the dominant mechanism. While in the noncovalent case, surface charge effects dominate. The identification of the mechanism along with the tunability of the chemical coupling and the cost-effective integration in microchannels constitute a solid basis for the entry of nanotube-based sensors in lab-on-a-chip applications.
A Novel and Efficient Total Synthesis of Cephalotaxine (2003)

[reaction: see text] Total synthesis of cephalotaxine (CET), the parent member of a class of structurally unique antileukemia Cephalotaxus alkaloids, was accomplished on the basis of a conceptually novel strategy featuring transannular reductive skeletal rearrangements as the key transformations for the construction of the pentacyclic ring skeleton of CET. The synthetic potential of the designated Clemmensen-Clemo-Prelog-Leonard reductive rearrangement was demonstrated for the first time in a facile synthesis of the benzazepine subunit of CET. A novel endocyclic enamine (cyclopentenone) annulation was discovered and rationalized as an unusual azo-Nazarov-type cyclization.