gebhart/patrepeval huggingface dataset:
Metal-activated hydrolytic cleavage of DNA (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMetal-activated hydrolytic cleavage of DNALena A. Basile, Adrienne L. Raphael, and Jacqueline K. BartonCite this: J. Am. Chem. Soc. 1987, 109, 24, 7550–7551Publication Date (Print):November 1, 1987Publication History Published online1 May 2002Published inissue 1 November 1987https://pubs.acs.org/doi/10.1021/ja00258a061https://doi.org/10.1021/ja00258a061research-articleACS PublicationsRequest reuse permissionsArticle Views758Altmetric-Citations129LEARN 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 Get e-Alerts
Where Do Web Sites Come From? Capturing and Interacting With Design (2002)

To form a deep understanding of the present; we need to construct and engage an account of the past. In this paper, we present an informal history capture and retrieval mechanism for collaborative, early-stage information design. This history system is implemented in the context of the Designers'' Outpost, a wall-scale, tangible interface for collaborative web site design. The interface elements in this history system are designed to be fluid and comfortable for early phase design. As demonstrated by an informal lab study with six professional web site designers, this history system enhances the design process itself, and provides new opportunities for reasoning about the design of complex artifacts.
APC gene mutations and extraintestinal phenotype of familial adenomatous polyposis. (1997)

Patients with the colorectal phenotype of FAP but no extraintestinal manifestations may have non-truncating mutations of the APC gene or mutation in a gene other than APC or mismatch repair genes. The site of APC gene mutation is associated with pigmented ocular fundus lesions (codons 542-1309) and predisposition to multiplicity of extraintestinal manifestations (codons 1465, 1546, and 2621).
Biomimetic amplification of nanoparticle homing to tumors (2007)

Nanoparticle-based diagnostics and therapeutics hold great promise because multiple functions can be built into the particles. One such function is an ability to home to specific sites in the body. We describe here biomimetic particles that not only home to tumors, but also amplify their own homing. The system is based on a peptide that recognizes clotted plasma proteins and selectively homes to tumors, where it binds to vessel walls and tumor stroma. Iron oxide nanoparticles and liposomes coated with this tumor-homing peptide accumulate in tumor vessels, where they induce additional local clotting, thereby producing new binding sites for more particles. The system mimics platelets, which also circulate freely but accumulate at a diseased site and amplify their own accumulation at that site. The self-amplifying homing is a novel function for nanoparticles. The clotting-based amplification greatly enhances tumor imaging, and the addition of a drug carrier function to the particles is envisioned.
Histologic factors of prognostic significance in the glioblastoma multiforme (1980)

The pretreatment biopsy specimens from 184 cases of malignant gliomas from The National Brain Tumor Study Group were reviewed in order to determine which, if any, of nine histologic factors were useful in subdividing the glioblastoma multiforme. In the smaller group of cases treated with surgery and supportive care only, there was a strong negative correlation between cellularity and survival. For those cases treated with surgery and radiation only, and for the study as a whole, there was a positive relationship between survival and the presence of a giant cell neoplasm. We have concluded, on the basis of this limited sample of this select group of patients, that this latter features offers a potential basis of subclassification of the glioblastoma multiforme.
Target specificity of the CRISPR‐Cas9 system (2014)

The CRISPR-Cas9 system, naturally a defense mechanism in prokaryotes, has been repurposed as an RNA-guided DNA targeting platform. It has been widely used for genome editing and transcriptome modulation, and has shown great promise in correcting mutations in human genetic diseases. Off-target effects are a critical issue for all of these applications. Here we review the current status on the target specificity of the CRISPR-Cas9 system.
Nanocrystal Superlattices with Thermally Degradable Hybrid Inorganic−Organic Capping Ligands (2010)

Colloidal metallic and semiconductor nanocrystals (NCs) functionalized with metal chalcogenide complexes (MCCs) have shown a promise for designing materials that combine high carrier mobility with the electronic structure of strongly quantum-confined solids. Here we report a simple and general methodology for switching the repulsive forces responsible for colloidal stabilization of MCC-capped NCs from long-range electrostatic to short-range steric through the formation of tight ionic pairs with cationic surfactants. This noncovalent surface modification remarkably improved the ability of MCC-capped NCs to self-assemble into long-range ordered superlattices. These NCs are highly soluble in nonpolar solvents and compatible with various technologically relevant organic molecules and polymers. The hybrid inorganic-organic coating can be thermally decomposed at significantly lower temperatures compared to those required for removal of conventional organic ligands.
Role of adenovirus E1B proteins in transformation: altered organization of intermediate filaments in transformed cells that express the 19-kilodalton protein. (1990)

Cooperation of the nuclear oncogene E1A with the E1B oncogene is required for transformation of primary cells. Expression vectors were constructed to produce the 19-kilodalton (19K) and 55K E1B proteins under the direction of heterologous promoters in order to investigate the role of individual E1B proteins in transformation. Coexpression of E1A and either the 19K or 55K E1B gene products was sufficient for the formation of transformed foci in primary rat cells at half the frequency of an intact E1B gene, suggesting that the 19K and 55K proteins function via independent pathways in transformation. Furthermore, the effects of Ha-ras and the E1B 19K gene product were additive when cotransfected with E1A, suggesting that the 19K protein functions in transformation by a mechanism independent from that of ras as well. Although expression of E1A and either E1B protein was sufficient for the subsequent growth of cells in long-term culture, the 19K protein was required to support growth in semisolid media. As the 19K protein has been shown to associate with and disrupt intermediate filaments (IFs) when transiently expressed with plasmid vectors (E. White and R. Cipriani, Proc. Natl. Acad. Sci. USA, 86:9886-9890, 1989), the organization of IFs in transformed cells was investigated. Primary rat cells transformed by plasmids encoding E1A plus the E1B 19K protein showed gross perturbations of IFs, whereas cell lines transformed by plasmids encoding E1A plus the E1B 55K protein or E1A plus Ha-ras did not. These results suggest that an intact IF cytoskeleton may inhibit anchorage-independent growth and that the E1B 19K protein can overcome this inhibition by disrupting the IF cytoskeleton.
The Knockout Mouse Project (2004)

Mouse knockout technology provides a powerful means of elucidating gene function in vivo, and a publicly available genome-wide collection of mouse knockouts would be significantly enabling for biomedical discovery. To date, published knockouts exist for only about 10% of mouse genes. Furthermore, many of these are limited in utility because they have not been made or phenotyped in standardized ways, and many are not freely available to researchers. It is time to harness new technologies and efficiencies of production to mount a high-throughput international effort to produce and phenotype knockouts for all mouse genes, and place these resources into the public domain.
Molecular self-diffusion coefficients in Fourier transform nuclear magnetic resonance spectrometric analysis of complex mixtures (1981)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMolecular self-diffusion coefficients in Fourier transform nuclear magnetic resonance spectrometric analysis of complex mixturesPeter. StilbsCite this: Anal. Chem. 1981, 53, 13, 2135–2137Publication Date (Print):November 1, 1981Publication History Published online1 May 2002Published inissue 1 November 1981https://pubs.acs.org/doi/10.1021/ac00236a044https://doi.org/10.1021/ac00236a044research-articleACS PublicationsRequest reuse permissionsArticle Views348Altmetric-Citations107LEARN 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 Get e-Alerts
Linker insertion-deletion mutagenesis of the v-src gene: isolation of host- and temperature-dependent mutants (1989)

The host cell regulators and substrates of the Rous sarcoma virus transforming protein pp60v-src remain largely unknown. Viral mutants which induce a host-dependent phenotype may result from mutations which affect the interaction of pp60v-src with host cell components. To isolate such mutants and to examine the role of different regions of src in regulating pp60v-src function, we generated 46 linker insertion and 5 deletion mutations within src. The mutant src genes were expressed in chicken embryo fibroblasts and in rat-2 cells by using retrovirus expression vectors. Most linker insertions within the kinase domain (residues 260 to 512) inactivated kinase activity and transforming capacity, while most insertions in the N-terminal domain and at the extreme C terminus were tolerated. A number of mutations generated a host-dependent phenotype. Insertions after residues 225 and 227, within the N-terminal regulatory domain (SH2), produced a fusiform transformation in chicken embryo fibroblasts and abolished transformation in rat-2 cells; a similar phenotype also resulted from two deletions affecting SH2 (residues 149 to 174 and residues 77 to 225). Insertions immediately C terminal to Lys-295, which is involved in ATP binding, also produced a conditional phenotype. Insertions after residues 299 and 300 produced a temperature-sensitive phenotype, while insertions after residues 304 and 306 produced a host cell-dependent phenotype. An insertion which removed the major tyrosine autophosphorylation site (Tyr-416) greatly reduced transformation of rat-2 cells, a property not previously observed with other mutations at this site. We conclude that mutations at certain sites within src result in conditional phenotypes. These sites may represent regions important in interactions with host cell components.
E-selectin-dependent neutrophil adhesion to Rickettsia rickettsii- infected endothelial cells (1993)

Increased neutrophil or HL60 cell adhesion to Rickettsia rickettsii- infected endothelial cells (ECs) was observed at 6 to 8 hours after the initiation of infection, diminishing by 24 hours. Similar increases were observed using formaldehyde-fixed neutrophils. Cellular association and likely the intracellular presence of rickettsiae was required for enhanced neutrophil adhesion, because culture medium conditioned by infected cells or rickettsiae rendered noninfective by pretreatment with tetracycline were ineffective at inducing neutrophil adhesion. Increases in neutrophil adhesion caused by infection were blocked by pretreatment of ECs with cycloheximide, suggesting the involvement of new protein synthesis in the cells' response. Flow cytometric analysis of infected cells showed increases in cell surface expression of E-selectin compared with uninfected control cells. Furthermore, incubation of 6- to 8-hour infected cells with a blocking monoclonal antibody against E-selectin (BB11) inhibited neutrophil adhesion an average of 61%. These results suggest the involvement of E- selectin in neutrophil adhesion to infected ECs occurring early in the course of the infection process. EC-initiated recruitment of neutrophil adhesion during rickettsiae infection could contribute to the pathologic changes associated with Rocky Mountain Spotted Fever.
Distributed recognition of human actions using wearable motion sensor networks (2009)

We propose a distributed recognition framework to classify continuous human actions using a low-bandwidth wearable motion sensor network, called distributed sparsity classifier (DSC). The algorithm classifies human actions using a set of training mot
Decoherence of superconducting qubits caused by quasiparticle tunneling (2012)

In superconducting qubits, the interaction of the qubit degree of freedom with quasiparticles defines a fundamental limitation for the qubit coherence. We develop a theory of the pure dephasing rate ${\ensuremath{\Gamma}}_{\ensuremath{\phi}}$ caused by quasiparticles tunneling through a Josephson junction and of the inhomogeneous broadening due to changes in the occupations of Andreev states in the junction. To estimate ${\ensuremath{\Gamma}}_{\ensuremath{\phi}}$, we derive a master equation for the qubit dynamics. The tunneling rate of free quasiparticles is enhanced by their large density of states at energies close to the superconducting gap. Nevertheless, we find that ${\ensuremath{\Gamma}}_{\ensuremath{\phi}}$ is small compared to the rates determined by extrinsic factors in most of the current qubit designs (phase and flux qubits, transmon, fluxonium). The split transmon, in which a single junction is replaced by a SQUID loop, represents an exception that could make possible the measurement of ${\ensuremath{\Gamma}}_{\ensuremath{\phi}}$. Fluctuations of the qubit frequency leading to inhomogeneous broadening may be caused by the fluctuations in the occupation numbers of the Andreev states associated with a phase-biased Josephson junction. This mechanism may be revealed in qubits with small-area junctions, since the smallest relative change in frequency it causes is of the order of the inverse number of transmission channels in the junction.
Open: Effects of NGM282, an FGF19 variant, on colonic transit and bowel function in functional constipation: a randomized phase 2 trial (2018)

NGM282 significantly impacts GE and colonic transit, consistent with the observed clinical symptoms. The specific mechanism of prokinetic activity requires further research.
Si-Ca-P xerogels and bone morphogenetic protein act synergistically on rat stromal marrow cell differentiationin vitro (1998)

This study describes a novel bioactive xerogel glass as a carrier for bone morphogenetic protein (BMP) and the value of this carrier in terms of stimulating osteogenic activity of rat stromal marrow cells in vitro. These cells were seeded onto the surface of xerogel glass disks with BMP either incorporated in the glass, adsorbed to the surface of the glass, or added to the culture media and then compared to cells on glass with no added BMP or to cells on tissue culture plastic (TCP) with and without BMP. Cells were cultured for 6 and 10 days and examined for total DNA, alkaline phosphatase activity, and osteocalcin and total protein production. Stromal cell differentiation, as measured by alkaline phosphatase activity and osteocalcin synthesis was most increased when the BMP was incorporated or adsorbed onto the xerogel glass. Cells on xerogel glass without BMP were more differentiated than cells grown on plastic with BMP, thereby demonstrating the additive effect of a bioactive substrate and BMP on osteoblastic cell differentiation. These data indicate that xerogel glass effects differentiation of cells with osteogenic potential and that it can serve as a delivery vehicle for BMP.
Sperm Morphology, Motility, and Concentration in Fertile and Infertile Men (2001)

Threshold values for sperm concentration, motility, and morphology can be used to classify men as subfertile, of indeterminate fertility, or fertile. None of the measures, however, are diagnostic of infertility.
Introduction and Expression of the Human Insulin Gene in Adult Rat Liver (1989)

Liposomes associated with gangliosides and loaded with the human insulin gene were incubated with HVJ (Sendai virus) and red blood cell membranes containing non-histone chromosomal protein, high mobility group 1 (HMG-1), or bovine serum albumin (BSA) to form vesicle complexes. These vesicle complexes were then injected into the portal vein of adult rats. The insulin gene co-introduced with HMG-1 was transported into the nuclei of liver cells much more efficiently than the gene co-introduced with BSA. Moreover, the amount of transcript of the insulin gene co-introduced with HMG-1 was more than 10 times greater than that of the gene co-introduced with BSA. Similar amounts of DNA and RNA of human insulin were found in the liver within 7 days after injection of the gene, and then the amounts of both decreased rapidly. The level of human insulin in rat serum gradually increased to a maximum (20-30 microunits/ml) after 7 or 8 days and then decreased rapidly.
Profiling Bovine Antibody Responses to Mycobacterium avium subsp. paratuberculosis Infection by Using Protein Arrays (2007)

With the genome sequence of Mycobacterium avium subsp. paratuberculosis determined, technologies are now being developed for construction of protein arrays to detect the presence of antibodies against M. avium subsp. paratuberculosis in host serum. The power of this approach is that it enables a direct comparison of M. avium subsp. paratuberculosis proteins to each other in relation to their immunostimulatory capabilities. In this study, 93 recombinant proteins, produced in Escherichia coli, were arrayed and spotted onto nitrocellulose. These proteins include unknown hypothetical proteins and cell surface proteins as well as proteins encoded by large sequence polymorphisms present uniquely in M. avium subsp. paratuberculosis. Also included were previously reported or known M. avium subsp. paratuberculosis antigens to serve as a frame of reference. Sera from healthy control cattle (n = 3) and cattle infected with either M. avium subsp. avium and Mycobacterium bovis were exposed to the array to identify nonspecific or cross-reactive epitopes. These data demonstrated a degree of cross-reactivity with the M. avium subsp. avium proteins that was higher than the degree of cross-reactivity with the more distantly related M. bovis proteins. Finally, sera from naturally infected cattle (n = 3) as well as cattle experimentally infected with M. avium subsp. paratuberculosis (n = 3) were used to probe the array to identify antigens in the context of Johne's disease. Three membrane proteins were the most strongly detected in all serum samples, and they included an invasion protein, an ABC peptide transport permease, and a putative GTPase protein. This powerful combination of genomic information, molecular tools, and immunological assays has enabled the identification of previously unknown antigens of M. avium subsp. paratuberculosis.
Imaging of Prostate Cancer with Immuno-PET and Immuno-SPECT Using a Radiolabeled Anti-EGP-1 Monoclonal Antibody (2011)

hRS7 is a humanized IgG1 monoclonal antibody directed against the epithelial glycoprotein-1 (EGP-1; also known as TROP2). This antigen is found in many epithelial cancers, including prostate cancer, and therefore this antibody could be suitable for targeting this cancer. In this study, the characteristics of hRS7 for targeting prostate cancer were examined. The potential for immuno-PET with <sup>89</sup>Zr-hRS7 and immuno-SPECT with <sup>111</sup>In-hRS7 was assessed using nude mice with human prostate cancer xenografts. <b>Methods:</b> EGP-1 expression was assessed by immunohistology in human primary and metastatic prostate cancer samples and in PC3 xenografts. The optimal antibody protein dose for prostate cancer targeting was examined in nude mice with subcutaneous PC3 xenografts, and then the biodistribution of <sup>111</sup>In-, <sup>125</sup>I-, and <sup>89</sup>Zr-labeled hRS7 was determined in subcutaneous PC3 xenografts at 1, 3, and 7 d after injection. Immuno-PET and immuno-SPECT were performed with <sup>89</sup>Zr-hRS7 and <sup>111</sup>In-hRS7 in mice with subcutaneous and intraprostatic PC3 xenografts, respectively. <b>Results:</b> Immunohistochemical analysis showed abundant EGP-1 expression in human primary and metastatic prostate cancers and in PC3 xenografts. <sup>111</sup>In-hRS7 and <sup>89</sup>Zr-hRS7 preferentially and specifically accumulated in PC3 xenografts, with tumor uptake as high as 60% injected dose per gram at a protein dose of 0.1 μg per mouse. PC3 tumors in nude mice were clearly visualized with both tracers with immuno-PET and immuno-SPECT. <b>Conclusion:</b> hRS7 shows excellent in vivo tumor targeting in human prostate cancer xenografts. Therefore, hRS7 is a potential vehicle for targeting prostate cancer.
Cooperative translocation enhances the unwinding of duplex DNA by SARS coronavirus helicase nsP13 (2010)

SARS coronavirus encodes non-structural protein 13 (nsP13), a nucleic acid helicase/NTPase belonging to superfamily 1 helicase, which efficiently unwinds both partial-duplex RNA and DNA. In this study, unwinding of DNA substrates that had different duplex lengths and 5'-overhangs was examined under single-turnover reaction conditions in the presence of excess enzyme. The amount of DNA unwound decreased significantly as the length of the duplex increased, indicating a poor in vitro processivity. However, the quantity of duplex DNA unwound increased as the length of the single-stranded 5'-tail increased for the 50-bp duplex. This enhanced processivity was also observed for duplex DNA that had a longer single-stranded gap in between. These results demonstrate that nsP13 requires the presence of a long 5'-overhang to unwind longer DNA duplexes. In addition, enhanced DNA unwinding was observed for gapped DNA substrates that had a 5'-overhang, indicating that the translocated nsP13 molecules pile up and the preceding helicase facilitate DNA unwinding. Together with the propensity of oligomer formation of nsP13 molecules, we propose that the cooperative translocation by the functionally interacting oligomers of the helicase molecules loaded onto the 5'-overhang account for the observed enhanced processivity of DNA unwinding.