gebhart/patrepeval huggingface dataset:
The Biology of Cancer Stem Cells (2007)

Cancers originally develop from normal cells that gain the ability to proliferate aberrantly and eventually turn malignant. These cancerous cells then grow clonally into tumors and eventually have the potential to metastasize. A central question in cancer biology is, which cells can be transformed to form tumors? Recent studies elucidated the presence of cancer stem cells that have the exclusive ability to regenerate tumors. These cancer stem cells share many characteristics with normal stem cells, including self-renewal and differentiation. With the growing evidence that cancer stem cells exist in a wide array of tumors, it is becoming increasingly important to understand the molecular mechanisms that regulate self-renewal and differentiation because corruption of genes involved in these pathways likely participates in tumor growth. This new paradigm of oncogenesis has been validated in a growing list of tumors. Studies of normal and cancer stem cells from the same tissue have shed light on the ontogeny of tumors. That signaling pathways such as Bmi1 and Wnt have similar effects in normal and cancer stem cell self-renewal suggests that common molecular pathways regulate both populations. Understanding the biology of cancer stem cells will contribute to the identification of molecular targets important for future therapies.
Photosensitizing compounds : their chemistry, biology and clinical use (1989)

What are the ideal properties for a photosensitizer?, A.J.MacRobert et al the chemistry, photophysics and photosensitizing properties of phthalocyanines, J.E.van Lier and J.D.Spikes comparison of haematoporphyrin derivative and new photosensitizers porphyrins as photosensitizers, R.Bonnett and M.Berenbaum photodynamic therapy - light delivery and dosage for second-generation photosensitizers, B.C.Wilson in vivo transport and pharmacokinetic behaviour of photosensitizers G.Jori intracellular localization of photosensitizers, J.Moan et al tissue localization of photosensitizers and the mechanism of photodynamic tissue destruction, B.W.Henderson and D.A.Bellnier immunosuppression in phototherapy, S.E.Ullrich et al effects of porphyrins on skin, H.W.Lim photosensitizing compounds in the treatment of psoriasis, H.Honigsmann et al extracorporeal photochemotherapy in the treatment of cutaneous T cell lymphoma and autoimmune disorders affecting the skin, A.H.Rook photodynamic therapy of early-stage lung cancer, N.Kato long-term experience with integral photodynamic therapy of TIS bladder carcinoma, D.Jocham et al photoradiation therapy of brain tumours, A.H.Kaye drug and light doses for photodynamic therapy.
Regulation of methionine synthesis in Escherichia coli : Effect of metJ gene product and S -adenosylmethionine on the expression of the metF gene (1985)

The regulation of the expression of the Escherichia coli metF gene, which codes for 5,10-methylenetet-rahydrofolate reductase (EC 1.1.99.15), has been investigated by using a simplified DNA-directed in vitro system that measures the formation of the first dipeptide (fMet-Ser) of the gene product. The synthesis of fMet-Ser directed by a plasmid containing the metF gene is specifically inhibited by metJ protein (repressor protein). S-Adenosylmethionine enhances the inhibition by the metJ protein of metF gene expression. The inhibition by the metJ protein is at the level of transcription and the results suggest that S-adenosylmethionine is functioning as an allosteric effector.
Flexural plate wave resonator excited with Lorentz forces (1998)

A flexural plate wave resonator was constructed by patterning current lines on a silicon nitride membrane suspended on a rectangular silicon frame. Eigenmodes of the rectangular membrane were excited using Lorentz forces generated between alternating surface currents and a static in-plane magnetic field. Preferential coupling to a particular membrane mode was achieved by positioning current lines along longitudinal mode antinodes. An equivalent-circuit model was derived which characterizes the input impedance of a one-port device and the transmission response of a two-port device over a range of frequencies near a single membrane resonance. Experiments were performed to characterize the device’s response to changes in dc magnetic field strength, ambient gas composition, gas pressure, and input power.
Designing a virtual access control configuration protocol for implementation over ISDN and shared-media networks (2002)

The encroachment of digital technology into our lifestyle and corporate environment has given rise to the need for individuals to safeguard personal information, and for organizations to protect trade-secret information either stored in computers or transmitted over LANs and WANs. A secure network and communication environment requires the services of encryption mechanisms, user password authentication, and network and user-interface based access control schemes that prevent unauthorised access to application programs and operating systems. While various encryption and authentication security mechanisms have garnered a lot of development effort, access control schemes using a virtual dedicated-media network system have not been fully developed. A dedicated-media network enables the authorization of access based on non-repudiate authenticity of the source. This capability presently cannot be implemented in shared-media networks. The paper introduces a a virtual access control configuration protocol (VACCP) which provides a dynamic security access authorization mechanism. The VACCP performs token-basad access security control to an application's user-interface resources. The VACCP security program is designed to control remote access for both the shared-media and dedicated-media mode of communication. The VACCP security measures are implemented as a network session-layer protocol which governs the access capability and assigns access authorization to each application program on a per-user-basis.
Site-specific Genome Editing in PBMCs With PLGA Nanoparticle-delivered PNAs Confers HIV-1 Resistance in Humanized Mice (2013)

Biodegradable poly (lactic-co-glycolic acid) (PLGA) nanoparticles (NPs) encapsulating triplex-forming peptide nucleic acids (PNAs) and donor DNAs for recombination-mediated editing of the CCR5 gene were synthesized for delivery into human peripheral blood mononuclear cells (PBMCs). NPs containing the CCR5-targeting molecules efficiently entered PBMCs with low cytotoxicity. Deep sequencing revealed that a single treatment with the formulation resulted in a targeting frequency of 0.97% in the CCR5 gene and a low off-target frequency of 0.004% in the CCR2 gene, a 216-fold difference. NP-treated PBMCs efficiently engrafted immunodeficient NOD-scid IL-2rγ(-/-) mice, and the targeted CCR5 modification was detected in splenic lymphocytes 4 weeks posttransplantation. After infection with an R5-tropic strain of HIV-1, humanized mice with CCR5-NP-treated PBMCs displayed significantly higher levels of CD4(+) T cells and significantly reduced plasma viral RNA loads compared with control mice engrafted with mock-treated PBMCs. This work demonstrates the feasibility of PLGA-NP-encapsulated PNA-based gene-editing molecules for the targeted modification of CCR5 in human PBMCs as a platform for conferring HIV-1 resistance.Molecular Therapy-Nucleic Acids (2013) 2, e135; doi:10.1038/mtna.2013.59; published online 19 November 2013.
Combinatorial interactions between positive and negative cis‐acting elements control spatial patterns of 4CL‐1 expression in transgenic tobacco (1993)

The phenylpropanoid enzyme 4-coumarate:coenzyme A ligase (4CL) plays a key role in linking general phenylpropanoid metabolism to end-product specific biosynthetic pathways. During vascular system and floral organ differentiation, the parsley 4CL-1 gene is expressed in a restricted set of tissues and cell types where 4CL activity is required to supply precursors for the synthesis of diverse phenylpropanoid-derived products such as lignin and flavonoids. In order to localize cis-acting elements which specify complex patterns of 4CL-1 expression, we analyzed the expression of internally deleted promoter fragment-GUS fusions in tobacco plants and parsley protoplasts. Elements located between -244 and -78 were required for most aspects of developmentally regulated expression. Within this region, three separate promotor domains containing partially redundant cis-elements directed vascular-specific expression when combined with a TATA-proximal domain. A negative cis-acting element which represses phloem expression was revealed in one of the domains and appears to be responsible for restricting vascular expression to the xylem. Distinct but overlapping promoter domain combinations were required for expression in floral organs, suggesting that different combinations of cis-acting elements may direct expression in different organs. Gel retardation assays were used to demonstrate the formation of DNA-protein complexes between factors present in nuclear extracts of parsley tissue culture cells and various tobacco organs and a 4CL-1 promoter fragment. Competition experiments showed that complex formation required the presence of a 42 bp promoter domain shown to be critical for 4CL-1 expression in vascular and floral tissues. The results are discussed in light of the coordinate expression of 4CL and other phenylpropanoid genes.
Targeted Single Primer Enrichment Sequencing with Single End Duplex-UMI (2019)

For specific detection of somatic variants at very low levels, artifacts from the NGS workflow have to be eliminated. Various approaches using unique molecular identifiers (UMI) to analytically remove NGS artifacts have been described. Among them, Duplex-seq was shown to be highly effective, by leveraging the sequence complementarity of two DNA strands. However, all of the published Duplex-seq implementations so far required pair-end sequencing and in the case of combining duplex sequencing with target enrichment, lengthy hybridization enrichment was required. We developed a simple protocol, which enabled the retrieval of duplex UMI in multiplex PCR based enrichment and sequencing. Using this protocol and reference materials, we demonstrated the accurate detection of known SNVs at 0.1-0.2% allele fractions, aided by duplex UMI. We also observed that low level base substitution artifacts could be introduced when preparing in vitro DNA reference materials, which could limit their utility as a benchmarking tool for variant detection at very low levels. Our new targeted sequencing method offers the benefit of using duplex UMI to remove NGS artifacts in a much more simplified workflow than existing targeted duplex sequencing methods.
An On-line Occlusio-Culling Algorithm for FastWalkthrough in Urban Areas (2001)

We describe a fast algorithm to speed up rendering of scenes for walkthroughs in urban environments. Our occlusion culling algorithm takes advantage of temporal coherence in image space. As such, occlusion calculation is performed online only when needed. This enables us to employ intelligent occluder-selection and culling algorithms. We do not preprocess visibility information or pre-select occluders. Therefore, we can update scenes dynamically at a little cost. The algorithm features a tradeoff between accuracy and efficiency. While it approximates visibility testing, our experiments show that errors occur rarely.
A high-sensitivity electrochemiluminescence-based detection system for automated PCR product quantitation. (1993)

A high-sensitivity nonisotopic system has been developed for post-PCR product detection. The probe-based detection system exploits a chemiluminescent reaction that takes place on the electrode surface in an electrochemical cell. The detection system incorporates a biotin-streptavidin capture reaction onto a solid support that permits fast post-PCR product detection at the attomole level. The system precision is within 5% relative standard deviation over a linear dynamic range of greater than three orders of magnitude. In this paper, the principles and features of the electrochemiluminescent-based detection system, together with its application to PCR product quantitation, are described in detail.
Evidence for Mono- and Bisdentate Boronate Complexes of Glucose in the Furanose Form. Application of 1JC-C Coupling Constants as a Structural Probe (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTEvidence for Mono- and Bisdentate Boronate Complexes of Glucose in the Furanose Form. Application of 1JC-C Coupling Constants as a Structural ProbeJens C. Norrild and Hanne EggertCite this: J. Am. Chem. Soc. 1995, 117, 5, 1479–1484Publication Date (Print):February 1, 1995Publication History Published online1 May 2002Published inissue 1 February 1995https://doi.org/10.1021/ja00110a003RIGHTS & PERMISSIONSArticle Views2016Altmetric-Citations233LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (758 KB) Get e-Alerts Get e-Alerts
Identification and characterization of a Mycoplasma hyopneumoniae adhesin (1995)

An adhesin of Mycoplasma hyopneumoniae was identified and characterized in this study. A monoclonal antibody (MAb), F2G5, and its F(ab')2 fragments inhibited the adherence of M. hyopneumoniae to porcine tracheal cilia, the natural targets to which the mycoplasma binds during infection. MAb F2G5 detected multiple bands, but predominantly recognized a 97-kDa (P97) protein of M. hyopneumoniae on immunoblots. Affinity chromatography, conducted with immobilized MAb F2G5, mainly purified P97. The purified proteins were able to bind to cilia and blocked the adherence of intact M. hyopneumoniae cells to cilia. Immunolabeling of mycoplasmas with MAb F2G5 under electron microscopy demonstrated that the proteins recognized by MAb F2G5 were located at the surface of the mycoplasma, predominantly on a surface fuzzy layer. These results indicate that P97 functions as an adhesin of M. hyopneumoniae. The N-terminal amino acid sequence of P97 did not have significant homology with any known bacterial or mycoplasmal adhesins, suggesting that P97 is a novel protein. The predominant proteins detected by MAb F2G5 in different strains varied in size, indicating that the antigen bearing the epitope for MAb F2G5 undergo intraspecies size variation. Antigenic variation of adhesins may be a pathogenic mechanism utilized by M. hyopneumoniae to evade the porcine immune system.
Sur1 Knockout Mice (2000)

Sur1 knockout mouse beta-cells lack K(ATP) channels and show spontaneous Ca(2+) action potentials equivalent to those seen in patients with persistent hyperinsulinemic hypoglycemia of infancy, but the mice are normoglycemic unless stressed. Sur1(-/-) islets lack first phase insulin secretion and exhibit an attenuated glucose-stimulated second phase secretion. Loss of the first phase leads to mild glucose intolerance, whereas reduced insulin output is consistent with observed neonatal hyperglycemia. Loss of K(ATP) channels impairs the rate of return to a basal secretory level after a fall in glucose concentration. This leads to increased hypoglycemia upon fasting and contributes to a very early, transient neonatal hypoglycemia. Whereas persistent hyperinsulinemic hypoglycemia of infancy underscores the importance of the K(ATP)-dependent ionic pathway in control of insulin release, the Sur1(-/-) animals provide a novel model for study of K(ATP)-independent pathways that regulate insulin secretion.
Preparation of Single-Walled Carbon Nanotube Reinforced Polystyrene and Polyurethane Nanofibers and Membranes by Electrospinning (2004)

Single-walled carbon nanotube (SWNT) reinforced polymer composite membranes have been fabricated using the electrospinning technique. Nanofibers with a diameter in the range 50−100 nm were obtained by electrospinning SWNT-filled polystyrene composites. TEM observations revealed incorporation of small SWNT bundles oriented parallel to the nanofiber axis. As-prepared (AP) and ester (EST) functionalized SWNTs have been electrospun with polyurethane (PU) to demonstrate the effect of the chemical functionalization of SWNTs on the mechanical properties of SWNT-reinforced composites. The tensile strength of EST-SWNT-PU membranes is enhanced by 104% as compared to electrospun pure polyurethane membranes, while an increase of only 46% was achieved incorporating AP−SWNT in the polyurethane matrix. The tangent moduli of AP- and EST-SWNT-PU membranes were found to be respectively 215% and 250% higher than the control polyurethane membranes.
Photonic time-stretched analog-to-digital converter: fundamental concepts and practical considerations (2003)

Ultra-wide-band analog-to-digital (A/D) conversion is one of the most critical problems faced in communication, instrumentation, and radar systems. This paper presents a comprehensive analysis of the recently proposed time-stretched A/D converter. By reducing the signal bandwidth prior to digitization, this technique offers revolutionary enhancements in the performance of electronic converters. The paper starts with a fundamental-physics analysis of the time-wavelength transformation and the implication of time dilation on the signal-to-noise ratio. A detailed mathematical description of the time-stretch process is then constructed. It elucidates the influence of linear and nonlinear optical dispersion on the fidelity of the electrical signal. Design issues of a single-sideband time-stretch system, as they relate to broad-band operation, are examined. Problems arising from the nonuniform optical power spectral density are explained, and two methods for overcoming them are described. As proof of the concept, 120 GSa/s real-time digitization of a 20-GHz signal is demonstrated. Finally, design issues and performance features of a continuous-time time-stretch system are discussed.
Dysfunction of astrocytes in senescence‐accelerated mice SAMP8 reduces their neuroprotective capacity (2008)

Early onset increases in oxidative stress and tau pathology are present in the brain of senescence-accelerated mice prone (SAMP8). Astrocytes play an essential role, both in determining the brain's susceptibility to oxidative damage and in protecting neurons. In this study, we examine changes in tau phosphorylation, oxidative stress and glutamate uptake in primary cultures of cortical astrocytes from neonatal SAMP8 mice and senescence-accelerated-resistant mice (SAMR1). We demonstrated an enhancement of abnormally phosphorylated tau in Ser(199) and Ser(396) in SAMP8 astrocytes compared with that of SAMR1 control mice. Gsk3beta and Cdk5 kinase activity, which regulate tau phosphorylation, was also increased in SAMP8 astrocytes. Inhibition of Gsk3beta by lithium or Cdk5 by roscovitine reduced tau phosphorylation at Ser(396). Moreover, we detected an increase in radical superoxide generation, which may be responsible for the corresponding increase in lipoperoxidation and protein oxidation. We also observed a reduced mitochondrial membrane potential in SAMP8 mouse astrocytes. Glutamate uptake in astrocytes is a critical neuroprotective mechanism. SAMP8 astrocytes showed a decreased glutamate uptake compared with those of SAMR1 controls. Interestingly, survival of SAMP8 or SAMR1 neurons cocultured with SAMP8 astrocytes was significantly reduced. Our results indicate that alterations in astrocyte cultures from SAMP8 mice are similar to those detected in whole brains of SAMP8 mice at 1-5 months. Moreover, our findings suggest that this in vitro preparation is suitable for studying the molecular and cellular processes underlying early aging in this murine model. In addition, our study supports the contention that astrocytes play a key role in neurodegeneration during the aging process.
Increased anterior corpus callosum size associated positively with hypnotizability and the ability to control pain (2004)

This is the first MRI study to report differences in brain structure size between low and highly hypnotizable, healthy, right-handed young adults. Participants were stringently screened for hypnotic susceptibility with two standardized scales, and then exposed to hypnotic analgesia training to control cold pressor pain. Only the highly hypnotizable subjects (HHs) who eliminated pain perception were included in the present study. These HHs, who demonstrated more effective attentional and inhibitory capabilities, had a significantly (P < 0.003) larger (31.8%) rostrum, a corpus callosum area involved in the allocation of attention and transfer of information between prefrontal cortices, than low hypnotizable subjects (LHs). These results provide support to the neuropsychophysiological model that HHs have more effective frontal attentional systems implementing control, monitoring performance and inhibiting unwanted stimuli from conscious awareness, than LHs.
Roles of Pseudomonas aeruginosa las and rhl quorum-sensing systems in control of elastase and rhamnolipid biosynthesis genes (1997)

Two quorum-sensing systems (las and rhl) regulate virulence gene expression in Pseudomonas aeruginosa. The las system consists of a transcriptional activator, LasR, and LasI, which directs the synthesis of the autoinducer N-(3-oxododecanoyl) homoserine lactone (PAI-1). Induction of lasB (encoding elastase) and other virulence genes requires LasR and PAI-1. The rhl system consists of a putative transcriptional activator, RhlR, and RhlI, which directs the synthesis of N-butyryl homoserine lactone (PAI-2). Rhamnolipid production in P. aeruginosa has been reported to require both the rhl system and rhlAB (encoding a rhamnosyltransferase). Here we report the generation of a delta lasI mutant and both delta lasI delta rhlI and delta lasR rhlR::Tn501 double mutants of strain PAO1. Rhamnolipid production and elastolysis were reduced in the delta lasI single mutant and abolished in the double-mutant strains. rhlAB mRNA was not detected in these strains at mid-logarithmic phase but was abundant in the parental strain. Further RNA analysis of the wild-type strain revealed that rhlAB is organized as an operon. The rhlAB transcriptional start was mapped, and putative sigma 54 and sigma 70 promoters were identified upstream. To define components required for rhlAB expression, we developed a bioassay in Escherichia coli and demonstrated that PAI-2 and RhlR are required and sufficient for expression of rhlA. To characterize the putative interaction between PAI-2 and RhlR, we demonstrated that [3H]PAI-2 binds to E. coli cells expressing RhlR and not to those expressing LasR. Finally, the specificity of the las and rhl systems was examined in E. coli bioassays. The las system was capable of mildly activating rhlA, and similarly, the rhl system partly activated lasB. However; these effects were much less than the activation of rhlA by the rhl system and lasB by the las system. The results presented here further characterize the roles of the rhl and las quorum-sensing systems in virulence gene expression.