gebhart/patrepeval huggingface dataset:
Complex Formation Facilitates Endocytosis of the Varicella-Zoster Virus gE:gI Fc Receptor (1998)

Open reading frames within the unique short segment of alphaherpesvirus genomes participate in egress and cell-to-cell spread. The case of varicella-zoster virus (VZV) is of particular interest not only because the virus is highly cell associated but also because its most prominent cell surface protein, gE, bears semblance to the mammalian Fc receptor Fc gammaRII. A previous study demonstrated that when expressed alone in cells, VZV gE was endocytosed from the cell surface through a tyrosine localization motif in its cytoplasmic tail (J. K. Olson and C. Grose, J. Virol. 71:4042-4054, 1997). Since VZV gE is normally found in association with gI in the infected cell, the present study was directed at defining the trafficking of the VZV gE:gI protein complex. First, VZV gI underwent endocytosis and recycling when it was expressed alone in cells, and interestingly, VZV gI contained a methionine-leucine internalization motif in its cytoplasmic tail. Second, VZV gI was found by confocal microscopy to colocalize with VZV gE during endocytosis and recycling in cells. Third, by a quantitative internalization assay, VZV gE:gI was shown to undergo endocytosis more efficiently (steady state, 55 to 60%) than either gE alone (steady state, approximately 32%) or gI alone (steady state, approximately 45%). Further, examination of endocytosis-deficient mutant proteins demonstrated that VZV gI exerted a more pronounced effect than gE on internalization of the complex. Most importantly, therefore, these studies suggest that VZV gI behaves as an accessory component by facilitating the endocytosis of the major constituent gE and thereby modulating the trafficking of the entire cell surface gE:gI Fc receptor complex.
Voice Quality Measurement (1999)

This comprehensive book explores the many facets of measuring voice quality. Voice quality is a concept that is widely recognized and applied, yet very difficult to define in a way that is universally satisfactory. A number of experts consider such topics as perceptual assessment, instrumental (objective) assessment, and various voice states and disorders. Contributors with a wide scope of experience present perspectives and ideas on how voice quality can be assessed with improved validity and reliability.
Genetic Probes Become Ever Sharper (1983)

La detection rapide d'infections a pathogenes multiples, incluant les genes majeurs de resistance aux medicaments, peut etre possible grâce a une nouvelle technique d'identification et de localisation des sequences de DNA ou de RNA
Ambidextrous transcriptional activation by SoxS: requirement for the C‐terminal domain of the RNA polymerase alpha subunit in a subset of Escherichia coli superoxide‐inducible genes (1996)

Purified MalE-SoxS fusion protein specifically stimulated in vitro transcription of the Escherichia coli zwf, fpr, fumC, micF, nfo, and sodA genes, indicating that activation of the superoxide regulon requires only SoxS. As in vivo, a 21 bp sequence adjacent to the zwf promoter was able to activate transcription of an heterologous promoter in vitro. Activation of zwf and fpr transcription required the C-terminal domain (CTD) of the RNA polymerase alpha subunit, while stimulation of fumC, micF, nfo, and sodA transcription was independent of CTD truncation. Thus, like the catabolite gene activator protein (CAP), SoxS is an 'ambidextrous' activator, activation only requiring the alpha CTD in a subset of regulated promoters. Indeed, the -35 hexamers of the zwf and fpr promoters lie downstream of the respective MalE-SoxS binding sites, while the binding sites of fumC, micF, nfo, and sodA overlap their -35 promoter hexamers.
Chiral Thiols:  The Assignment of Their Absolute Configuration by 1H NMR (2007)

A general NMR spectroscopy protocol for determination of absolute configuration of thiols, that includes the introduction of new aryl-tert-butoxyacetic acids as chiral derivatizing agents (CDAs), is described.
Involvement of endothelial PECAM-1/CD31 in angiogenesis. (1997)

The adhesive interactions of endothelial cells with each other and the adhesion receptors that mediate these interactions are probably of fundamental importance to the process of angiogenesis. We therefore studied the effect of inhibiting the function of the endothelial cell-cell adhesion molecule, PECAM-1/ CD31, in rat and murine models of angiogenesis. A polyclonal antibody to human PECAM-1, which cross-reacts with rat PECAM-1, was found to block in vitro tube formation by rat capillary endothelial cells and cytokine-induced rat corneal neovascularization. In mice, two monoclonal antibodies against murine PECAM-1 prevented vessel growth into subcutaneously implanted gels supplemented with basic fibroblast growth factor (bFGF). Taken together these findings provide evidence that PECAM-1 is involved in angiogenesis and suggest that the interactions of endothelial cell-cell adhesion molecules are important in the formation of new vessels.
Application of space division multiple access to mobile radio (2002)

An approach is proposed to introduce a space division multiple access (SDMA) component into a frequency/time division multiple access (FTDMA) mobile radio system like the European GSM system providing higher frequency reuse and spectral efficiency. Except from signalling aspects the mobiles remain uneffected by the presented SDMA method without any need for antenna diversity or more sophisticated equalizers. Additional hard- and software-demands due to the new SDMA features are only restricted to base stations as they have to be equipped with an adaptive antenna array. This array is used to separate wavefronts in coherent multipath environments by means of a new algorithm. The number of antenna elements needed is significantly lower than the number of wavefronts impinging on the array.
NF-κB-induced KIAA1199 promotes survival through EGFR signalling (2014)

Constitutive activation of EGFR- and NF-κB-dependent pathways is a hallmark of cancer, yet signalling proteins that connect both oncogenic cascades are poorly characterized. Here we define KIAA1199 as a BCL-3- and p65-dependent gene in transformed keratinocytes. KIAA1199 expression is enhanced on human papillomavirus (HPV) infection and is aberrantly expressed in clinical cases of cervical (pre)neoplastic lesions. Mechanistically, KIAA1199 binds Plexin A2 and protects from Semaphorin 3A-mediated cell death by promoting EGFR stability and signalling. Moreover, KIAA1199 is an EGFR-binding protein and KIAA1199 deficiency impairs EGF-dependent Src, MEK1 and ERK1/2 phosphorylations. Therefore, EGFR stability and signalling to downstream kinases requires KIAA1199. As such, KIAA1199 promotes EGF-mediated epithelial-mesenchymal transition (EMT). Taken together, our data define KIAA1199 as an oncogenic protein induced by HPV infection and constitutive NF-κB activity that transmits pro-survival and invasive signals through EGFR signalling.
Nanoparticles and Catalysis (2007)

Transition-metal Nanoparticles in Catalysis: From Historical Background to the State of the Art Surfactant-stabilized Nanoparticles as Catalyst Precursors - Scientific Basis, Recent Developments and an Outlook Nanoparticle-catalysts Based on Nanostructured Polymers PAMAM-dendrimer Templated Catalysts Aerogel-supported Nanoparticles in Catalysis Transition-metal Catalysis in Imidazolium Ionic Liquids Carbon and Silicon Nanotubes-containing Catalysis Size-selective Synthesis of Nanostructured Metal- and Metal-oxide Colloids and their Use as Catalysts Multimetallic Nanoparticles Prepared by Redox Processes Applied in Catalysis The Role of Palladium Nanoparticles as Catalysts for Carbon-carbon Coupling Reactions Rhodium and Ruthenium Nanoparticles in Catalysis Supported Gold Nanoparticle as Oxidation Catalysts Gold Nanoparticle Catalyzed Oxidation in Organic Chemistry AuNP-catalyzed Propene Epoxidation by Dioxygen and Dihydrogen Gold Nanoparticles: Recent Advances in CO Oxidation NO Heterogeneous Catalysis Viewed from the Angle of Nanoparticles Hydrocarbon Catalytic Reactivity of Supported Nanometallic Particles Surface Organometallic Chemistry on Metallic NPs: Synthesis, Characterization and Application in Catalysis
Neocortical Neurofibrillary Tangles Correlate With Dementia Severity in Alzheimer's Disease (1995)

These data support the notion that neocortical neuronal degeneration, as indicated by NFT formation, is a critical determinant of the clinical progression of Alzheimer's disease and suggest that medial temporal lobe structures may represent the initial site of NFT formation. While SP density correlates with age at death, there is no correlation between SP counts and dementia severity. These results further suggest that the clinical presentation of dementia may be closely related to neurodegeneration in neocortical regions within the temporal lobe.
High glucose-induced, endothelin-dependent fibronectin synthesis is mediated via NF-κB and AP-1 (2003)

Human endothelial cells cultured under high glucose (HG) conditions were shown before to upregulate several basement membrane proteins, including fibronectin (FN), thus mimicking effects of diabetes. Using human macrovascular (HUVEC) and microvascular (HMEC) endothelial cell lines, we evaluated in the present study some of the key molecular signaling events involved in HG-induced FN overexpression. This expression was shown to be dependent on endogenous endothelin (ET) receptor-mediated signaling. We also examined the roles played by protein kinase C (PKC) and the transcription factors nuclear factor kappaB (NF-kappaB) and activating protein (AP)-1 with respect to such changes. HG, PKC activators, and ETs (ET-1 and ET-3) that increased FN expression also caused activation of NF-kappaB and AP-1. Inhibitors of both NF-kappaB and AP-1 prevented HG- and ET-induced FN production. ET receptor blockade also prevented these HG- and ET-mediated changes. The results of this study indicate that glucose-induced increased FN production in diabetes may be mediated via ET-dependent NF-kappaB and AP-1 activation.
Second harmonic generation in polymeric channelwaveguides using modal dispersion (1996)

The authors report phase-matched second harmonic generation using the modal dispersion of a polymeric channel waveguide. An internal figure of merit of 1%/W cm2 was obtained for TM00ω to TM202ω conversion. Phase matching was maintained for 2 mm using multilayer spincoating technology.
Rodent models of cerebral ischemia. (1989)

The use of physiologically regulated, reproducible animal models is crucial to the study of ischemic brain injury--both the mechanisms governing its occurrence and potential therapeutic strategies. Several laboratory rodent species (notably rats and gerbils), which are readily available at relatively low cost, are highly suitable for the investigation of cerebral ischemia and have been widely employed for this purpose. We critically examine and summarize several rodent models of transient global ischemia, resulting in selective neuronal injury within vulnerable brain regions, and focal ischemia, typically giving rise to localized brain infarction. We explore the utility of individual models and emphasize the necessity for meticulous experimental control of those variables that modulate the severity of ischemic brain injury.
Carcinogenicity predictions for a group of 30 chemicals undergoing rodent cancer bioassays based on rules derived from subchronic organ toxicities. (1996)

Rodent carcinogenicities for a group of 30 chemicals which form the subject of the Second NIEHS Predictive-Toxicology Evaluation Experiment are predicted based on their subchronic organ toxicities. Predictions are made by rules learned by the rule learning (RL) induction program.
Segment-directed mutagenesis: construction in vitro of point mutations limited to a small predetermined region of a circular DNA molecule. (1980)

A general method for efficiently mutagenizing a predetermined segment of a closed circular duplex DNA molecule was used to construct mutations in two specific regions of the beta-lactamase (bla) gene carried by the small plasmid pBR322. The principle of segment-directed mutagenesis is the use of a single-stranded homologous DNA fragment to direct the nicking of circular duplex DNA within a segment defined by the DNA fragment in a two-step reaction. First, Escherichia coli recA protein is used to catalyze assimilation of the homologous single-stranded DNA, producing a displacement loop ("D-loop") in the circular DNA. Second, a small amount of the single-strand-specific S1 nuclease is used to nick the displaced DNA. The segment-directed nicks are converted to small gaps, which are then mutagenized specifically with sodium bisulfite. A short (128-base pair) restriction endonuclease fragment from the center of the bla gene was used to direct mutagenesis with the result that 7.5% of the recovered plasmids were bla- mutants and 49/51 of these mutants, mapped genetically, were found to lie in a deletion interval whose endpoints approximate those of the restriction fragment. Similar results were obtained when another short fragment covering the beginning of the gene was used; many of these mutations map in the region coding the "signal" sequence thought to be involved in secretion of beta-lactamase.
Identification of the genes responsive to etoposide‐induced apoptosis: application of DNA chip technology (1999)

DNA chip technology was used in an attempt to identify target genes responsible for apoptosis induced by etoposide, a p53 activating topoisomerase II inhibitor used clinically as an antitumor agent. 62 Individual mRNAs whose mass changed significantly were identified after screening oligonucleotide arrays capable of detecting 6591 unique human mRNA species. 12 (Nine induced and three repressed) of the etoposide-responsive genes were further studied by Northern analysis and an agreement rate of 92%, was reached. Among the 12 genes studied, two (WAF1/p21 and PCNA) are known p53 regulatory genes, two (glutathione peroxidase and S100A2 calcium-binding protein) appear to be the novel p53 target genes and the others appear to be p53-independent. Based upon these findings, the signalling pathways that possibly mediate etoposide-induced apoptosis are proposed.
Energy Expenditure and Water Turnover Assessed by Doubly Labeled Water during Manual Work in a Dry and Warm Environment (2004)

Objective: During training and other strenuous physical activity in the mountains, deserts, and other wilderness areas, those consuming pre-packaged rations or take-along-food often have difficulty maintaining adequate energy, water and electrolytes, and carbohydrate intakes. This study assessed the effects of ad libitum consumption of a carbohydrate beverage supplement (8% maltodextrin sweetened with aspartame) on energy and carbohydrate intakes of physically active test volunteers. Methods: Energy and carbohydrate intakes of volunteers randomly assigned to receive either a carbohydrate beverage supplement (CHO) (n=32) or a non-caloric placebo beverage (PLACEBO) (n=31) during an 11-day field training exercise were assessed. Mean total energy expenditure (TEE), water turnover (RH2O), and total body water (TBW) were measured in a sub-group of volunteers (CHO: n=10, PLACEBO: n=9) using the stable isotopes 2H2O and H218O. Results: The CHO group had greater daily energy intake (EICHO: 12.8±0.6 MJ/day; EIPLACEBO: 11.0±0.8 MJ/day; p<0.05) and carbohydrate intake (CHO: 470±139 g/day; PLACEBO: 317±68 g/day; p<0.05). No differences were observed in TEE (TEECHO: 18.41±4.40 MJ/day; TEEPLACEBO: 16.12±2.70 MJ/day), TBW (TBWCHO: 46.9±5.5 L; TBWPLACEBO: 44.5±3.3 L) or water turnover (RH2O–CHO: 5.6±1.1 L/day; RH2O–PLACEBO: 5.1±0.7 L/day) between groups. Discussion: Providing a carbohydrate beverage may reduce energy and CHO deficits that commonly occur during recreational treks or in those working for extended periods in wilderness environments.
Frontotemporal Dementia (2007)

Frontotemporal dementia (FTD) is an uncommon but important form of degenerative disease. It may make up 50% of dementia cases presenting before age 60. The symptoms are related to the anatomic areas affected. Neary divided the clinical syndromes into "frontotemporal dementia," "progressive nonfluent aphasia," and "semantic dementia." However, the pathology may extend beyond the frontal and temporal lobes and additional symptoms may be found. Although most cases are sporadic, some cases are genetic. The best-known genetic mutation causing FTD is frontotemporal dementia with parkinsonism, linked to the microtubule-associated protein tau on chromosome 17. There are other known genes and chromosome loci related to FTD. The most common pathology found is frontotemporal degeneration with ubiquitin inclusions. In contrast, FTD with Pick bodies is rare. Although there are strategies to help patients and their families, there is no known treatment for the disease.
PolyUnpack: Automating the Hidden-Code Extraction of Unpack-Executing Malware (2006)

Modern malware often hide the malicious portion of their program code by making it appear as data at compile-time and transforming it back into executable code at runtime. This obfuscation technique poses obstacles to researchers who want to understand the malicious behavior of new or unknown malware and to practitioners who want to create models of detection and methods of recovery. In this paper we propose a technique for automating the process of extracting the hidden-code bodies of this class of malware. Our approach is based on the observation that sequences of packed or hidden code in a malware instance can be made self-identifying when its runtime execution is checked against its static code model. In deriving our technique, we formally define the unpack-executing behavior that such malware exhibits and devise an algorithm for identifying and extracting its hidden-code. We also provide details of the implementation and evaluation of our extraction technique; the results from our experiments on several thousand malware binaries show our approach can be used to significantly reduce the time required to analyze such malware, and to improve the performance of malware detection tools.
Can Quantum-Mechanical Description of Physical Reality Be Considered Complete? (1935)

In a complete theory there is an element corresponding to each element of reality. A sufficient condition for the reality of a physical quantity is the possibility of predicting it with certainty, without disturbing the system. In quantum mechanics in the case of two physical quantities described by non-commuting operators, the knowledge of one precludes the knowledge of the other. Then either (1) the description of reality given by the wave function in quantum mechanics is not complete or (2) these two quantities cannot have simultaneous reality. Consideration of the problem of making predictions concerning a system on the basis of measurements made on another system that had previously interacted with it leads to the result that if (1) is false then (2) is also false. One is thus led to conclude that the description of reality as given by a wave function is not complete.
CYP3A4-mediated Pharmacokinetic Interactions in Cancer Therapy (2015)

Cytochromes P450 enzymes, especially CYP3A4, are responsible for metabolizing a broad range of anticancer drugs. Combination therapy is common in patients with cancer, which may cause potential drug drug interactions (DDIs) leading to increased risk of side-effects/toxicity or decreased effectiveness. The review summarizes CYP3A4-mediated DDIs, with anticancer drugs as CYP3A4 substrates or modulators, in clinical trials during cancer therapy and aims to increase clinicians' awareness to take caution to reduce the risk.
Recombinant Factor VIII for the Treatment of Previously Untreated Patients with Hemophilia A -- Safety, Efficacy, and Development of Inhibitors (1993)

Transient or low levels of inhibitor, as observed in this study, may represent part of the natural history of hemophilia in infants. In view of the transient nature and lower concentration of the inhibitors detected and the generally satisfactory response to treatment, the benefits of recombinant factor VIII for the treatment of hemophilia seem to outweigh the risks.
The Application of Next Generation Sequencing in DNA Methylation Analysis (2010)

DNA methylation is a major form of epigenetic modification and plays essential roles in physiology and disease processes. In the human genome, about 80% of cytosines in the 56 million CpG sites are methylated to 5-methylcytosines. The methylation pattern of DNA is highly variable among cells types and developmental stages and influenced by disease processes and genetic factors, which brings considerable theoretical and technological challenges for its comprehensive mapping. Recently various high-throughput approaches based on bisulfite conversion combined with next generation sequencing have been developed and applied for the genome wide analysis of DNA methylation. These methods provide single base pair resolution, quantitative DNA methylation data with genome wide coverage. We review these methods here and discuss some technical points of special interest like the sequence depth necessary to reach conclusions, the identification of clonal DNA amplification after bisulfite conversion and the detection of non-CpG methylation. Future application of these methods will greatly facilitate the profiling of the DNA methylation in the genomes of different species, individuals and cell types under healthy and disease states.
CTLA-4 Blockage Increases Resistance to Infection with the Intracellular Protozoan Trypanosoma cruzi (2004)

Recent studies have revealed an important role for CTLA-4 as a negative regulator of T cell activation. In the present study, we evaluated the importance of CTLA-4 to the immune response against the intracellular protozoan, Trypanosoma cruzi, the causative agent of Chagas' disease. We observed that the expression of CTLA-4 in spleen cells from naive mice cultured in the presence of live trypomastigote forms of T. cruzi increases over time of exposure. Furthermore, spleen cells harvested from recently infected mice showed a significant increase in the expression of CTLA-4 when compared with spleen cells from noninfected mice. Blockage of CTLA-4 in vitro and/or in vivo did not restore the lymphoproliferative response decreased during the acute phase of infection, but it resulted in a significant increase of NO production in vivo and in vitro. Moreover, the production of IFN-gamma in response to parasite Ags was significantly increased in spleen cells from anti-CTLA-4-treated infected mice when compared with the production found in cells from IgG-treated infected mice. CTLA-4 blockade in vivo also resulted in increased resistance to infection with the Y and Colombian strains of T. cruzi. Taken together these results indicate that CTLA-4 engagement is implicated in the modulation of the immune response against T. cruzi by acting in the mechanisms that control IFN-gamma and NO production during the acute phase of the infection.