gebhart/patrepeval huggingface dataset:
The formation of plectonemic joints by the recA protein of Escherichia coli. Requirement for ATP hydrolysis. (1985)

Formation of D-loops during the exchange of strands between a circular single-stranded DNA and a completely homologous linear duplex proceeds optimally when the duplex DNA is added to the complex of recA protein and single-stranded DNA formed in the presence of single-stranded DNA-binding protein and ATP. D-loops are undetectable when 200 microM adenosine 5'-O-(thiotriphosphate) is substituted for ATP. D-loops can be formed in the presence of adenosine 5'-O-(thiotriphosphate) if recA protein is the last component added to the reaction. However, these D-loops, which depend upon homologous sequences, are unstable upon deproteinization and are formed to a more limited extent than the structures formed with ATP. This finding indicates that D-loops formed under these conditions may be largely nonintertwined paranemic structures rather than plectonemic structures in which two of the strands are interwoven. When adenosine 5'-O-(thiotriphosphate) is added to an ongoing reaction containing ATP, formation of plectonemic structures and ATP hydrolysis is inhibited to an equivalent extent. We, therefore, conclude that ATP hydrolysis is required for the formation of plectonemic structures.
B2 and ALU retrotransposons are self-cleaving ribozymes whose activity is enhanced by EZH2 (2019)

Transposable elements make up half of the mammalian genome. One of the most abundant is the short interspersed nuclear element (SINE). Among their million copies, B2 accounts for ∼350,000 in the mouse genome and has garnered special interest because of emerging roles in epigenetic regulation. Our recent work demonstrated that B2 RNA binds stress genes to retard transcription elongation. Although epigenetically silenced, B2s become massively up-regulated during thermal and other types of stress. Specifically, an interaction between B2 RNA and the Polycomb protein, EZH2, results in cleavage of B2 RNA, release of B2 RNA from chromatin, and activation of thermal stress genes. Although an established RNA-binding protein and histone methyltransferase, EZH2 is not known to be a nuclease. Here, we provide evidence for the surprising conclusion that B2 is a self-cleaving ribozyme. Ribozyme activity depends on Mg<sup>+2</sup> and monovalent cations but is resistant to protease treatment. However, contact with EZH2 accelerates cleavage rate by >100-fold, suggesting that EZH2 promotes a cleavage-competent RNA conformation. B2 modification-interference analysis demonstrates that phosphorothioate changes at A and C nucleotides can substitute for EZH2. B2 nucleotides 45 to 55 and 100 to 101 are essential for activity. Finally, another family of SINEs, the human ALU element, also produces a self-cleaving RNA and is cleaved during T-cell activation as well as thermal and endoplasmic reticulum (ER) stress. Thus, B2/ALU SINEs may be classified as "epigenetic ribozymes" that function as transcriptional switches during stress. Given their high copy numbers, B2 and ALU may represent the predominant ribozyme activity in mammalian cells.
Plasmons in Strongly Coupled Metallic Nanostructures (2011)

ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXTPlasmons in Strongly Coupled Metallic NanostructuresNaomi J. Halas†‡§, Surbhi Lal†, Wei-Shun Chang‡, Stephan Link†‡, and Peter Nordlander*†§View Author Information† § †Department of Electrical and Computer Engineering, ‡Department of Chemistry, and §Department of Physics and Astronomy, Rice University, Houston, Texas 77005, United States*E-mail: [email protected]Cite this: Chem. Rev. 2011, 111, 6, 3913–3961Publication Date (Web):May 4, 2011Publication History Received18 February 2011Published online4 May 2011Published inissue 8 June 2011https://pubs.acs.org/doi/10.1021/cr200061khttps://doi.org/10.1021/cr200061kreview-articleACS PublicationsCopyright © 2011 American Chemical SocietyRequest reuse permissionsArticle Views55067Altmetric-Citations2614LEARN 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 InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Metal nanoparticles,Nanoparticles,Plasmonic nanoparticles,Plasmonics,Plasmons Get e-Alerts
The Globular Heads of C1q Specifically Recognize Surface Blebs of Apoptotic Vascular Endothelial Cells (2001)

Complement protein C1q is required to maintain immune tolerance. The molecular mechanism responsible for this link has not been determined. We have previously demonstrated that C1q binds directly and specifically to surface blebs of apoptotic human keratinocytes, suggesting that it may participate in clearance of self Ags generated during programmed cell death. Here, we demonstrate that C1q also binds directly to apoptotic blebs of vascular endothelial cells and PBMC. These apoptotic cells are recognized by the globular heads of C1q, which bind specifically to the surface blebs, and deposition increases as the blebs mature on the cell surface. These observations suggest that C1q may participate in the clearance of apoptotic cells from the circulation and from the walls of the vascular lumen. The interaction of surface blebs with the globular heads of C1q suggests that surface blebs may be capable of directly activating the classical pathway of complement under certain circumstances, generating C4- and C3-derived ligands for receptors such as CR1, CR2, CR3, and CR4. Appropriate recognition of apoptotic cells by C1q and targeted clearance of the molecular contents of surface blebs to complement receptors may be critical for the maintenance of immune tolerance.
Large-scale synthesis of highly dispersed layered double hydroxide powders containing delaminated single layer nanosheets (2013)

A facile method for the synthesis of Zn2Al-borate and Mg3Al-borate layered double hydroxides (LDHs) with extremely high specific surface areas of 458.6 and 263 m(2) g(-1) and containing delaminated nanosheets is reported. To the best of our knowledge, this is the first report of LDH powders that still remain exfoliated on drying.
Practical Data Hiding in TCP/IP (2002)

This work relates the areas of steganography, network protocols and security for practical data hiding in communication networks employing TCP/IP. Two approaches are proposed based on packet header manipulation and packet ordering within the IPSec framework. For the former the Internet protocol IPv4 header is analyzed to identify covert channels by exploiting redundancy and multiple interpretations of protocol strategies; by passing supplementary information through IPv4 headers we demonstrate how security mechanisms can be enhanced in routers, firewalls, and for services such as authentication, audit and logging without considerable additions to software or hardware. For the latter approach, we show the use of packet sorting for steganographic embedding with IPSec can allow for enhanced network security.
Progress in Adeno-Associated Virus Type 2 Vector Production: Promises and Prospects for Clinical Use (1999)

Vectors derived from the human parvovirus AAV-2 (adeno-associated virus type 2) are among the most promising gene delivery vehicles currently being developed. These vectors are not only capable of transducing a large variety of human cell types in vitro and in vivo, but in immunocompetent animal models can establish long-term gene expression without being pathogenic to the recipient. However, a limitation of this vector system with respect to its clinical application has long been the laborious work needed to prepare high-titer and pure AAV-2 vector stocks. A number of improvements to the basic manufacturing protocol have recently been reported that now allow the production of AAV-2 vectors of significantly higher quality and quantity. This article considers the most relevant approaches taken so far, which include modifications to the conventional transfection/infection protocol as well as the development of helper virus-free packaging methods and the establishment of vector producer cell lines. The various novel protocols are discussed, including their advantages and drawbacks, with a particular focus being put on their prospects for clinical use. Despite these advancements, the development of an ideal AAV-2 vector production method fully suiting clinical requirements obviously remains a challenging issue.
Genetically fluorescent melanoma bone and organ metastasis models. (1999)

We report here the establishment and metastatic properties of bright, highly stable, green fluorescent protein (GFP) expression transductants of the B16 mouse malignant melanoma cell line and the LOX human melanoma line. The highly fluorescent malignant melanoma cell lines allowed the visualization of skeletal and multiorgan metastases after i.v. injection of B16 cells in C57BL/6 mice and intradermal injection of LOX cells in nude mice. The melanoma cell lines were transduced with the pLEIN expression retroviral vector containing the GFP and neomycin resistance genes. Stable B16F0 and LOX clones expressing high levels of GFP were selected stepwise in vitro in levels of G418 of up to 800 microg/ml. Extensive bone and bone marrow metastases of B16F0 were visualized by GFP expression when the animals were sacrificed 3 weeks after cell implantation. Metastases for both cell lines were visualized in many organs, including the brain, lung, pleural membrane, liver, kidney, adrenal gland, lymph nodes, skeleton, muscle, and skin by GFP fluorescence. This is the first observation of experimental skeletal metastases of melanoma, which was made possible by GFP expression. These models should facilitate future studies of the mechanism and therapy of bone and multiorgan metastasis of melanoma.
Communications flow considerations in vehicle navigation and information systems (2003)

The advent of numerous intelligent vehicle/highway system projects has brought to the forefront issues that must be decided before an integrated approach can proceed. The author discusses possible methods of transferring information to and from the vehicle navigation system, outlining some of the advantages and disadvantages of each method, and presents some of the types of information that may be communicated in future vehicle navigation and traffic control systems. He concludes, from knowledge of the minimum desired functionality of a vehicle navigation system, that the need for some type of two-way infrastructure to facilitate data transfer is apparent. He points out that a thorough investigation of the alternative uses for the vehicle navigation system and its communications network must be conducted, and expansion must be taken into account in all standards for vehicle navigation systems and their infrastructures.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Disability, mortality, and incidence of cancer among Geneva painters and electricians: a historical prospective study. (1989)

The 1916 painters and the 1948 electricians who resided in the Canton of Geneva at the time of the 1970 census were identified and followed up to 1984. During the study period 121 disability pensions were awarded to painters and 59 to electricians. Age standardised incidence of disability per 1000 man-years at risk was higher among painters than among electricians for all neuropsychiatric causes (1.23/1000 and 0.68/1000, respectively) and for all other causes (5.50/1000 and 3.41/1000, respectively). No case of presenile dementia was diagnosed among painters. There was inadequate evidence to indicate that the higher risk of neuropsychiatric disability for painters might have been due to their occupational exposure to organic solvents. A possible toxic effect of these substances on the central nervous system was confounded with alcoholism which was associated with disability from neuropsychiatric disease in 12 of 20 painters and in only one of 10 electricians. Mortality and incidence of cancer were assessed among both cohorts and compared with the expected figures calculated from Geneva rates. Among painters there was a significant increase in overall mortality (O = 254, E = 218.5), in mortality from all cancers (O = 96, E = 75.4), and in incidence from all cancers (O = 159, E = 132.0). For the specific cancer sites, there was a significant excess risk for lung cancer (mortality: O = 40, E = 23.0), which was possibly related to occupational exposure to asbestos and to zinc chromate, although cigarette smoking was not controlled. The significant excesses of biliary tract cancer and of bladder cancer were in accordance with previous observations among painters from other countries. There was also a significant increase in incidence from testicular cancer (O=5, E=1.6), which has not been reported before. For causes of death other than cancer the excesses for alcoholism (O=5, E=0.8). for liver cirrhosis (O=14, E=8.8), for motor vehicle accidents (O=12, E=5.9), and for cerebrovascular disease when allowing for ten years of latency (O=8, E=4.0), were consistent with a probable increased risk of alcohol abuse. Among electricians overall mortality was similar to that expected (O=137, E=139.0). No significant excess risk was found for all cancers or for any specific cancer site. Because of the small number of expected deaths the statistical power was low for the assessment of a possible risk for leukaemia or for brain tumour.
<title>Phase-shifting mask design tool</title> (1992)

A Computer Aided Design tool is being developed to automatically produce design graphs that will facilitate the layout of phase-shift masks. This tool is a design interface which utilizes SPLAT1 for the aerial image simulations. The program accepts a user specified geometry and the mask parameter space to be explored. It then automatically extracts information such as intensity, contrast, space width, line width, and intensity slope from the SPLAT results for each iteration. In this paper, we apply the design system to a number of phase-shift mask patterns to explore design rule tradeoffs. For dark field masks with isolated spaces and Levenson arrays of spaces, we determine that a shrink of the mask combined with a bloat of open areas shows promise as a means of designing phase-shift masks if one is willing to sacrifice distance between light areas. By examining several typical mask patterns, we also show that an overall shrink of the mask does not require special design rules for each type of feature, but better scaling could result by appropriately developing new rules for different patterns. Since printing clear field masks is also important, we further probe the scalability of phase transitions. We show that a phase transition of 0.6 A/NA is the optimum length to achieve the highest intensity throughout the phase transition region. For 90 degree transitions, a length of 0.6 A/NA is needed while for 60-120 degree transitions, each step transition region must be at least 0.6 A/NA long. Finally, we present a new mask pattern for chains of contacts that has high intensity slope for a pitch of 1.2 A/NA and below.
Endocytosis and Lysosomal Targeting of Epidermal Growth Factor Receptors Are Mediated by Distinct Sequences Independent of the Tyrosine Kinase Domain (1995)

Ligand-induced internalization of the epidermal growth factor receptor (EGFR) leads to accelerated receptor degradation. Two models have been proposed to explain this. In the first model, induced internalization expands the intracellular pool of receptors, leading to enhanced lysosomal targeting. The second model proposes that activation of intrinsic receptor kinase activity induces inward vesiculation of endosomes, thus interrupting receptor recycling. To test these models, we created EGFR mutants that lack the conserved tyrosine kinase domain, but retain different parts of the distal carboxyl terminus regulatory region. Mutants lacking all distal regulatory sequences underwent slow internalization (0.02 min-1) and turnover (t1/2 approximately 24 h), similar to unoccupied, holo-EGFR. Mutant receptors that lacked the kinase domain, but retained the entire distal regulatory domain, were constitutively internalized and targeted to lysosomes, even in the absence of EGF. The turnover of these receptors (t1/2 approximately 11 h) was similar to that of occupied, kinase-active holo-EGFR (t1/2 approximately 9.5 h). These results show that receptor tyrosine kinase activity is not required for the targeting of EGFR to lysosomes. Receptor mutants which expressed previously identified endocytic sequences underwent rapid internalization. Unexpectedly, enhanced turnover of EGFR mutants required additional sequences located between residues 945 and 991 in the holo-EGFR. Thus, internalization and lysosomal targeting of EGFR are separate processes mediated by distinct sequences. Our results indicate that induced internalization is necessary, but not sufficient, for enhanced EGFR degradation. Instead, down-regulation requires exposure of previously cryptic internalization and lysosomal targeting sequences. Occupied EGFR thus appear to be handled by the endocytic machinery in the same fashion as other constitutively internalized or lysosomally targeted receptors.
Incorporation of caged cysteine and caged tyrosine into a transmembrane segment of the nicotinic ACh receptor (2001)

The nonsense codon suppression technique was used to incorporate o-nitrobenzyl cysteine or o-nitrobenzyl tyrosine (caged Cys or Tyr) into the 9' position of the M2 transmembrane segment of the gamma-subunit of the muscle nicotinic ACh receptor expressed in Xenopus oocytes. The caged amino acids replaced an endogenous Leu residue that has been implicated in channel gating. ACh-induced current increased substantially after ultraviolet (UV) irradiation to remove the caging group. This represents the first successful incorporation of caged Cys into a protein in vivo and the first incorporation of caged amino acids within a transmembrane segment of a membrane protein. The bulky nitrobenzyl group does not prevent the synthesis, assembly, or trafficking of the ACh receptor. When side chains were decaged using 1-ms UV light flashes, the channels with caged Cys or caged Tyr responded with strikingly different kinetics. The increase in current upon photolysis of caged Cys was too rapid for resolution by the voltage-clamp circuit [time constant (tau) <10 ms], whereas the increase in current upon photolysis of caged Tyr was dominated by a phase with tau approximately 500 ms. Apparently, the presence of a bulky o-nitrobenzyl Tyr residue distorts the receptor into an abnormal conformation. Upon release of the caging group, the receptor relaxes, with tau approximately 500 ms, into a conformation that allows the channel to open. Tyr at the 9' position of the gamma-subunit greatly increases the ability of ACh to block the channel by binding within the channel pore. This is manifested in two ways. 1) A "rebound," or increase in current, occurs upon removal of ACh from the bathing medium; and 2) at ACh concentrations >400 microM, inward currents are decreased through the mutated channel. The ability to incorporate caged amino acids into proteins should have widespread utility.
PD-L1 expression in squamous-cell carcinoma and adenocarcinoma of the lung (2017)

Our results suggest a significantly higher PD-L1 expression in TC of SCC compared to AC, regardless of the cut-off value. PD-L1 expression in IC is high in both histological subtypes of NSCLC, and adds significantly to the overall positivity of AC but not SCC.
Luminescent conjugated poly- and oligo-thiophenes: optical ligands for spectral assignment of a plethora of protein aggregates (2012)

The deposition of protein aggregates in various parts of our body gives rise to several devastating diseases, and the development of probes for the selective detection of aggregated proteins is crucial to advance our understanding of the pathogenesis underlying these diseases. LCPs (luminescent conjugated polythiophenes) are fluorescent probes that bind selectively to protein aggregates. The conjugated thiophene backbone is flexible and offers a connection between the conformation and the emission properties, hence binding of LCPs gives the molecule a spectral fingerprint. The present review covers the utilization of LCPs to study the heterogeneity of protein aggregates. It emphasizes specifically the introduction of well-defined probes called LCOs (luminescent conjugated oligothiophenes) and reports how these molecules can be used for real-time in vivo imaging of cerebral plaques as well as for spectral discrimination of protein aggregates and detection of early species in the fibrillation pathway of amyloid β-peptide.
Implementation of Multichannel Sensors for Remote Biomedical Measurements in a Microsystems Format (2004)

A novel microelectronic "pill" has been developed for in situ studies of the gastro-intestinal tract, combining microsensors and integrated circuits with system-level integration technology. The measurement parameters include real-time remote recording of temperature, pH, conductivity, and dissolved oxygen. The unit comprises an outer biocompatible capsule encasing four microsensors, a control chip, a discrete component radio transmitter, and two silver oxide cells (the latter providing an operating time of 40 h at the rated power consumption of 12.1 mW). The sensors were fabricated on two separate silicon chips located at the front end of the capsule. The robust nature of the pill makes it adaptable for use in a variety of environments related to biomedical and industrial applications.
Low-dislocation-density GaAs epilayers grown on Ge-coated Si substrates by means of lateral epitaxial overgrowth (1982)

Single-crystal GaAs layers have been obtained by means of lateral epitaxial overgrowth seeded within stripe openings in a SiO2 mask over GaAs layers grown on Ge-coated Si substrates. Transmission electron microscope and scanning cathodoluminescence studies indicate that the laterally overgrown GaAs layers have a dislocation density of less than 104 cm−2, compared to 107–108 cm−2 for the GaAs layers grown directly on the Ge/Si substrates. Initial experiments indicate that the electrical properties of the laterally overgrown layers are comparable to those of conventional GaAs epilayers grown on single-crystal GaAs substrates.
AFM of Poly(vinyl alcohol) Crystals Next to an Inorganic Surface (2001)

Crystallization of poly(vinyl alcohol) in the presence of an inorganic filler surface (sodium montmorillonite, MMT) was observed and compared to the crystallization of the neat polymer. For this purpose, several atomic force microscopy modes, providing spatial resolution between amorphous and crystalline polymer, are employed to observe filled and unfilled PVA films. The various AFM modes utilized are detailed, with the emphasis on how they can contrast stiff (crystalline) and softer (amorphous) domains on a polymer surface. The study revealed changes in the PVA crystal morphology, with bulk crystallites growing to sizes of more than 5 μm, whereas next to the inorganic surfaces grow to only 1−2 μm in size. Moreover, complementary X-ray diffraction and DSC investigations indicate a new crystal structure formed next to the MMT surfaces, at the expense of the bulklike crystal.