gebhart/patrepeval huggingface dataset:
Association of the Arabidopsis CTR1 Raf-like kinase with the ETR1 and ERS ethylene receptors (1998)

In Arabidopsis thaliana, signal transduction of the hormone ethylene involves at least two receptors, ETR1 and ERS, both of which are members of the two-component histidine protein kinase family that is prevalent in prokaryotes. The pathway also contains a negative regulator of ethylene responses, CTR1, which closely resembles members of the Raf protein kinase family. CTR1 is thought to act at or downstream of ETR1 and ERS based on double mutant analysis; however, the signaling mechanisms leading from ethylene perception to the regulation of CTR1 are unknown. By using the yeast two-hybrid assay, we detected a specific interaction between the CTR1 amino-terminal domain and the predicted histidine kinase domain of ETR1 and ERS. We subsequently verified these interactions by using an in vitro protein association assay(s). In addition, we determined that the amino-terminal domain of CTR1 can associate with the predicted receiver domain of ETR1 in vitro. Based on deletion analysis, the portion of CTR1 that interacts with ETR1 roughly aligns with the regulatory region of Raf kinases. These physical associations support the genetic evidence that CTR1 acts in the pathway of ETR1 and ERS and suggest that these interactions could be involved in the regulation of CTR1 activity.
An execution layer for aspect-oriented programming languages (2005)

Language mechanisms deserve language implementation effort. While this maxim has led to sophisticated support for language features specific to object-oriented, functional and logic programming languages, aspect-oriented programming languages are still mostly implemented using postprocessors. The Steamloom virtual machine, based on IBM's Jikes RVM, provides support for aspect-oriented programming at virtual machine level. A bytecode framework called BAT was integrated with the Jikes RVM to replace its bytecode management logic. While preserving the functionality needed by the VM, BAT also allows for querying application code for join point shadows, avoiding redundancy in bytecode representation. Performance measurements show that an AOP-enabled virtual machine like Steamloom does not inflict unnecessary performance penalties on a running application; when it comes to executing AOP-related operations, there even are significant performance gains compared to other approaches.
Characterization of the Tomato Cf-4 Gene for Resistance to Cladosporium fulvum Identifies Sequences That Determine Recognitional Specificity in Cf-4 and Cf-9 (1997)

Colwyn M. Thomas, David A. Jones, Martin Parniske, Kate Harrison, Peter J. Balint-Kurti, Kostas Hatzixanthis, Jonathan D. G. Jones, Characterization of the Tomato Cf-4 Gene for Resistance to Cladosporium fulvum Identifies Sequences That Determine Recognitional Specificity in Cf-4 and Cf-9, The Plant Cell, Vol. 9, No. 12 (Dec., 1997), pp. 2209-2224
Epstein-Barr virus-transformed human B lymphocytes produce natural antibodies to histones. Immunology Letters (Amsterdam, Olanda) 39, 277-282, 1994. (1994)

To study the mechanism(s) responsible for the appearance of Epstein-Barr virus (EBV)-induced anti-histone autoantibodies, peripheral blood B lymphocytes from healthy donors were infected with EBV and the resulting lymphoblastoid cell lines were tested for secretion of antibodies reacting with histones. It was found that EBV-transformed cells produce IgM antibody reactive with histones and that the frequency of EBV-inducible circulating B lymphocytes that produce antibodies to histones is at least 10(-5). Moreover, in cultures of tonsillar lymphoid cells, the enrichment in CD5+ B lymphocytes increases the percentage of EBV-transformed cultures making anti-histone IgM antibodies. EBV may therefore, also in vivo, induce natural anti-histone antibody by polyclonal B-cell activation without any requirement of antigen to trigger antibody response.
Contrasting characteristics of pulsed and sinusoidal cold atmospheric plasma jets (2006)

Pulsed excitation of cold atmospheric plasmas is commonly believed to offer valuable benefits compared to the mainstream sinusoidal excitation. However, direct comparison of pulsed and sinusoidal atmospheric plasmas remains few, if any, thus casting an uncertainty of whether pulsed excitation facilitates any significant advantage. In this letter, we report a comparison study of pulsed and sinusoidal cold atmospheric plasma jets through electrical characterization, gas temperature measurement, and optical detection of reactive plasma species. An example of pulsed excitation is shown to reduce the electrical energy consumption by a factor of 12 for producing the same amount of oxygen atoms.
DNA sequence of the herpes simplex virus type 1 gene encoding glycoprotein gH, and identification of homologues in the genomes of varicella-zoster virus and Epstein-Barr virus (1986)

We have determined the sequence of herpes simplex virus type 1 DNA around the previously mapped location of sequences encoding an epitope of glycoprotein gH, and have deduced the structure of the gH gene and the amino acid sequence of gH. The unprocessed polypeptide is predicted to contain 838 amino acids, and to possess an N-terminal signal sequence and a C-terminal transmembrane sequence. Temperature-sensitive mutant tsQ26 maps within the predicted gH coding sequence. Homologous genes were identified in the genomes of two other herpesviruses, namely varicella-zoster virus and Epstein-Barr virus.
Synthesis, Photophysical Properties, and Photovoltaic Devices of Oligo(p-phenylene vinylene)-fullerene Dyads (2000)

The synthesis of a homologous series of oligo(p-phenylene vinylene)-fulleropyrrolidines (OPVn-C60, n = 1−4, where n is the number of phenyl rings) is described. The photophysical properties of these donor−acceptor dyads and the corresponding model compounds, α,ω-dimethyl-2,5-bis(2-(S)-methylbutoxy)-1,4-phenylene vinylene oligomers (OPVn, n = 2−4) and N-methylfulleropyrrolidine (MP-C60), are studied as a function of the conjugation length in solvents of different polarity and as thin films. Fast singlet energy transfer occurs after photoexcitation of the OPVn moiety of the dyads toward the fullerene moiety in an apolar solvent. Photoexcitation of the dyads in a polar solvent results in electron transfer for OPV3-C60 and OPV4-C60, and to some extent for OPV2-C60, but not for OPV1-C60. These results are compared to the results obtained for mixtures of OPVn and MP-C60 in the same solvents. The solvent-dependent change in free energy for charge separation of the donor−acceptor systems is calculated from the Weller equation, and the rate constants for energy and electron transfer are derived from the fluorescence lifetime and quenching. The results show that in a polar solvent electron transfer in these dyads is likely to occur via a two-step process, that is, a very fast singlet energy transfer prior to charge separation. In thin solid films of OPV3-C60 and OPV4-C60, a long-lived charge-separated state is formed after photoexcitation. The long lifetime in the film is attributed to the migration of charges to different molecules. A flexible photovoltaic device is prepared from OPV4-C60.
Neurotrophins and hyperalgesia (1999)

Nerve growth factor (NGF), a member of the neurotrophin family, is crucial for survival of nociceptive neurons during development. Recently, it has been shown to play an important role in nociceptive function in adults. NGF is up-regulated after inflammatory injury of the skin. Administration of exogenous NGF either systemically or in the skin causes thermal hyperalgesia within minutes. Mast cells are considered important components in the action of NGF, because prior degranulation abolishes the early NGF-induced component of hyperalgesia. Substances degranulated by mast cells include serotonin, histamine, and NGF. Blockade of histamine receptors does not prevent NGF-induced hyperalgesia. The effects of blocking serotonin receptors are complex and cannot be interpretable uniquely as NGF losing its ability to induce hyperalgesia. To determine whether NGF has a direct effect on dorsal root ganglion neurons, we have begun to investigate the acute effects of NGF on capsaicin responses of small-diameter dorsal root ganglion cells in culture. NGF acutely conditions the response to capsaicin, suggesting that NGF may be important in sensitizing the response of sensory neurons to heat (a process that is thought to operate via the capsaicin receptor VR1). We also have found that ligands for the trkB receptor (brain-derived neurotrophic factor and neurotrophin-4/5) acutely sensitize nociceptive afferents and elicit hyperalgesia. Because brain-derived neurotrophic factor is up-regulated in trkA positive cells after inflammatory injury and is transported anterogradely, we consider it to be a potentially important peripheral component involved in neurotrophin-induced hyperalgesia.
The synthesis of oligonucleotides containing a primary amino group at the 5'-terminus (1987)

Oligonucleotides containing a primary amino group at their 5'-termini have been prepared and further derivatised with amino specific probes. The sequence required is prepared using standard solid phase phosphoramidite techniques and an extra round of synthesis is then performed with N-monomethoxytrityl-0-methoxydiisopropylaminophosphinyl 3-aminopropan(1)ol. After cleavage from the resin, removal of the phosphate and base protecting groups and purification gives a monomethoxytrityl-NH(CH2)3PO4-oligomer. The monomethoxytrityl group can be removed with acetic acid to give the desired amino containing oligomer. The amino group can be further derivatised with amino specific probes yielding fluorescent or biotinylated oligonucleotide products.
Calpastatin Exon 1B-Derived Peptide, a Selective Inhibitor of Calpain: Enhancing Cell Permeability by Conjugation with Penetratin (2003)

The ubiquitous calpains, mu- and m-calpain, have been implicated in essential physiological processes and various pathologies. Cell-permeable specific inhibitors are important tools to elucidate the roles of calpains in cultivated cells and animal models. The synthetic N-acetylated 27-mer peptide derived from exon B of the inhibitory domain 1 of human calpastatin (CP1B) is unique as a potent and highly selective reversible calpain inhibitor, but is poorly cell-permeant. By addition of N-terminal cysteine residues we have generated a disulfide-conjugated CP1B with the cell-penetrating 16-mer peptide penetratin derived from the third helix of the Antennapedia homeodomain protein. The inhibitory potency and selectivity of CP1B for calpain versus cathepsin B and L, caspase 3 and the proteasome was not affected by the conjugation with penetratin. The conjugate was shown to efficiently penetrate into living LCLC 103H cells, since it prevents ionomycin-induced calpain activation at 200-fold lower concentration than the non-conjugated inhibitor and is able to reduce calpain-triggered apoptosis of these cells. Penetratin-conjugated CP1B seems to be a promising alternative to the widely used cell-permeable peptide aldehydes (e.g. calpain inhibitor 1) which inhibit the lysosomal cathepsins and partially the proteasome as well or even better than the calpains.
Reduced apoptotic levels in squamous but not basal cell carcinomas correlates with detection of cutaneous human papillomavirus (2002)

We have investigated the apoptotic levels and expression of the apoptotic inducer Bak in non-melanoma skin cancers. Squamous cell carcinomas of known human papillomavirus status from immunocompetent patients were analysed for the expression of the Bak protein, and the expression profile was compared both to the presence of apoptotic cells and the proliferation marker Ki-67. We demonstrate an inverse correlation between human papillomavirus positivity and Bak expression in squamous cell carcinomas, with concomitantly fewer apoptoic cells being detected in the human papillomavirus positive tumours. Bak expression was not observed in basal cell carcinomas irrespective of human papillomavirus status, suggesting that Bak only plays a role in signalling apoptosis in squamous, but not basal, cell cancers. No differences were observed in the proliferation rates between papillomavirus positive and negative squamous cell tumours. However, a significant decrease in the number of apoptotic cells was observed in human papillomavirus-positive squamous cell carcinomas which suggests that the virus may have significantly altered the relationship between proliferation and apoptosis in a proportion of these tumours.
Molecular and Clinical Evaluation of Atypical Hemolytic Uremic Syndrome (2006)

Familial hemolytic uremic syndrome (HUS) was first described in 1956; both autosomal dominant and recessive forms of inheritance have been reported. The chapter discusses three pieces of evidence which suggested that complement genes apart from the gene for factor H were involved in the pathogenesis of atypical HUS. Structurally, membrane cofactor protein (MCP) consists of four alternatively spliced isoforms that coexist on most cells. The extracellular domain is composed of four control protein modules (CCPs). Western blot, flow cytometry, cell surface labeling, and pulse-chase analysis all showed that the mutant protein was retained intracellularly. Noris et al. described a family in which two siblings were affected by HUS. Mutation screening in both revealed a heterozygous 2-bp deletion in MCP exon 7, which encodes CCP4. The functional effect of this mutation is similar to the deletion mutation and results in half of the normal level of cell surface expression of MCP. The two techniques most frequently used for mutation scanning are denaturing high-performance liquid chromatography (DHPLC) and single-strand conformation polymorphism (SSCP). DHPLC is based on heteroduplex analysis in which mutant and wild-type sequences present in a PCR product are heated and allowed to reanneal slowly. This results in the formation of two heteroduplexes and two homoduplexes. MLPA (multiplex ligationdependent probe amplification) is a relatively new method for detecting deletions and duplications in a simple two-stage procedure and gives dosage information for up to 45 exons in one test.
Redirection of T cell-mediated cytotoxicity by a recombinant single-chain Fv molecule. (1994)

We have produced two single-chain Fv (sFv) proteins by bacterial periplasmic secretion, one sFv with specificity for the hapten DNP, and the other for the human transferrin receptor. After solubilization and refolding, we recovered several mg of active sFv per liter of bacterial culture. Each sFv bound to cells bearing the appropriate Ag and could be used to direct targeted cellular cytotoxicity. Targeting relied on a universal bispecific antibody designed to cross-link CD3 on the cytotoxic T cell with a peptide fused to the sFv carboxyl-terminus. The universal bispecific antibody was used in combination with the Ag-specific sFv to redirect human cytotoxic T cells to kill a variety of target cells. Such an approach has a number of advantages that may make it useful for the immunotherapy of cancer and other diseases.
The chemical and biological properties of methoxyfenozide, a new insecticidal ecdysteroid agonist (2001)

Methoxyfenozide [N-tert-butyl-N'-(3-methoxy-o-toluoyl)-3,5-xylohydrazide; RH-2485] is the newest diacylhydrazine insecticide to reach the marketplace. It binds with very high affinity to the ecdysone receptor complex (EcR:USP) in lepidopteran insects [Kd = 0.5 nM (Plodia)], where it functions as a potent agonist, or mimic, of the insect molting hormone, 20-hydroxyecdysone (20E). Methoxyfenozide exhibits high insecticidal efficacy against a wide range of important caterpillar pests, including many members of the family Pyralidae, Pieridae, Tortricidae and Noctuidae. It is most effective when ingested by the target caterpillar, but it also has some topical and ovicidal properties. It is modestly root systemic, but not significantly leaf-systemic. Evidence collected to date indicates that methoxyfenozide has an excellent margin of safety to non-target organisms, including a wide range of non-target and beneficial insects.
Antineoplastic agents 322. synthesis of combretastatin A-4 prodrugs. (1995)

Combretastatin A-4 (1a), the principal cancer cell growth-inhibitory constituent of the Zulu medicinal plant Combretum caffrum, has been undergoing preclinical development. However, the very limited water solubility of this phenol has complicated drug formation. Hence, derivatives of the combretastatin A-4 (1a) 3'-phenol group were prepared for evaluation as possible water-soluble prodrugs. As observed for combretastatin A-4, the sodium salt (1b), potassium salt (1c) and hemisuccinic acid ester (1e) derivatives of phenol 1a were essentially insoluble in water. Indeed, these substances regenerated combretastatin A-4 upon reaction with water. A series of other simple derivatives (1d, 1f-j) proved unsatisfactory in terms of water solubility or stability, or both. The most soluble derivatives evaluated included the ammonium (1l), potassium (1m) and sodium (1n) phosphate salts, where the latter two proved most stable and suitable. Both the potassium (1m) and sodium (1n) phosphate derivatives of combretastatin A-4 were also found to exhibit the requisite biological properties necessary for a useful prodrug. Sodium salt 1n was selected for drug formulation and further pre-clinical development.
Dose- and Route-Dependent Teratogenicity, Toxicity, and Pharmacokinetic Profiles of the Hedgehog Signaling Antagonist Cyclopamine in the Mouse (2008)

The Hedgehog (Hh) signaling pathway is an essential regulator of embryonic development and appears to play important roles in postnatal repair and cancer progression and metastasis. The teratogenic Veratrum alkaloid cyclopamine is a potent Hh antagonist and is used experimentally both in vitro and in vivo to investigate the role of Hh signaling in diverse biological processes. Here, we set out to establish an administration regimen for cyclopamine-induced teratogenicity in the mouse. The dysmorphogenic concentration of cyclopamine was determined in vitro via mouse whole-embryo culture assays to be 2.0 microM. We administered cyclopamine to female C57BL/6J mice at varied doses by oral gavage, ip injection, or osmotic pump infusion and assessed toxicity and pharmacokinetic (PK) models. Bolus administration was limited by toxicity and rapid clearance. In vivo cyclopamine infusion at 160 mg/kg/day yielded a dam serum steady-state concentration of approximately 2 microM with a corresponding amniotic fluid concentration of approximately 1.5 microM. Gross facial defects were induced in 30% of cyclopamine-exposed litters, with affected embryos exhibiting cleft lip and palate. This is the first report describing the PKs and teratogenic potential of cyclopamine in the mouse and demonstrates that transient Hh signaling inhibition induces facial clefting anomalies in the mouse that mimic common human birth defects.
Method for Label-Free Detection of Femtogram Quantities of Biologics in Flowing Liquid Samples (2007)

Rapid (approximately 10 min) measurement of very low concentration of pathogens (approximately 10 cells/mL) and protein (approximately fg/mL) has widespread use in medical diagnostics, monitoring biothreat agents, and in a broader context as a research method. For low-level pathogen, we currently use culture enrichment methods and, thus, rapid analysis is not possible. For low protein concentration, no direct method is currently available. We report here a novel macrocantilever design whose high-order resonant mode near 1 MHz exhibits mass detection sensitivity of 10 cells/mL for cells and 100 fg/mL for protein. The sensor is 1x3 mm and uses a piezoelectric layer for both actuation and sensing resonance. Sample is flowed (approximately 1 mL/min) past the antibody-immobilized sensor, and as antigen binds to the sensor, resonance frequency decreases in proportion to antigen concentration. The sensor showed selectivity to the pathogen even though copious nonpathogenic variant was simultaneously present.
Profiles in cyber courage #1: Fred Cohen (2007)

Dario Forte and Richard Power have identified a number of security gurus who have made a difference in the IT security field. Every second month our authors will interview an established expert. The first profile focuses on Fred Cohen, a pioneer who first described a computer virus.
Electron transport in strained Si inversion layers grown on SiGe-on-insulator substrates (2002)

We show by simulation that electron mobility and velocity overshoot are greater when strained inversion layers are grown on SiGe-On-insulator substrates (strained Si/SiGe-OI) than when unstrained silicon-on-insulator (SOI) devices are employed. In addition, mobility in these strained inversion layers is only slightly degraded compared with strained bulk Si/SiGe inversion layers, due to the phonon scattering increase produced by greater carrier confinement. Poisson and Schroedinger equations are self-consistently solved to evaluate the carrier distribution in this structure. A Monte Carlo simulator is used to solve the Boltzmann transport equation. Electron mobility in these devices is compared to that in SOI inversion layers and in bulk Si/SiGe inversion layers. The effect of the germanium mole fraction x, the strained-silicon layer thickness, TSi, and the total width of semiconductor (Si+SiGe) slab sandwiched between the two oxide layers, Tw were carefully analyzed. We observed strong dependence of the electron mobility on TSi, due to the increase in the phonon scattering rate as the silicon layer thickness is reduced, a consequence of the greater confinement of the carriers. This effect is less important as the germanium mole fraction, x, is reduced, and as the value of TSi increases. For TSi&amp;gt;20 nm, mobility does not depend on TSi, and maximum mobility values are obtained.
Blockade of HIV-1 Infection of New World Monkey Cells Occurs Primarily at the Stage of Virus Entry (2002)

HIV-1 naturally infects chimpanzees and humans, but does not infect Old World monkeys because of replication blocks that occur after virus entry into the cell. To understand the species-specific restrictions operating on HIV-1 infection, the ability of HIV-1 to infect the cells of New World monkeys was examined. Primary cells derived from common marmosets and squirrel monkeys support every phase of HIV-1 replication with the exception of virus entry. Efficient HIV-1 entry typically requires binding of the viral envelope glycoproteins and host cell receptors, CD4 and either CCR5 or CXCR4 chemokine receptors. HIV-1 did not detectably bind or utilize squirrel monkey CD4 for entry, and marmoset CD4 was also very inefficient compared with human CD4. A marmoset CD4 variant, in which residues 48 and 59 were altered to the amino acids found in human CD4, supported HIV-1 entry efficiently. The CXCR4 molecules of both marmosets and squirrel monkeys supported HIV-1 infection, but the CCR5 proteins of both species were only marginally functional. These results demonstrate that the CD4 and CCR5 proteins of New World monkeys represent the major restriction against HIV-1 replication in these primates. Directed adaptation of the HIV-1 envelope glycoproteins to common marmoset receptors might allow the development of New World monkey models of HIV-1 infection.