gebhart/patrepeval huggingface dataset:
In vitro selection of ribozymes dependent on peptides for activity (2003)

A peptide-dependent ribozyme ligase (aptazyme ligase) has been selected from a random sequence population based on the small L1 ligase. The aptazyme ligase is activated > 18,000-fold by its cognate peptide effector, the HIV-1 Rev arginine-rich motif (ARM), and specifically recognizes the Rev ARM relative to other peptides containing arginine-rich motifs. Moreover, the aptazyme ligase can preferentially recognize the Rev ARM in the context of the full-length HIV-1 Rev protein. The only cross-reactivity exhibited by the aptazyme is toward the Tat ARM. Reselection of peptide- and protein-dependent aptazymes from a partially randomized population yielded aptazymes that could readily discriminate against the Tat ARM. These results have important implications for the development of aptazymes that can be used in arrays for the detection and quantitation of multiple cellular proteins (proteome arrays).
Research on Prevention of Bilirubin-Induced Brain Injury and Kernicterus: National Institute of Child Health and Human Development Conference Executive Summary (2004)

In July 2003, the National Institute of Child Health and Human Development convened a conference, "Research on Prevention of Bilirubin-Induced Brain Injury and Kernicterus: Bench-to-Bedside." This article will provide a summary of presentations and discussions from this conference. The summary will focus on the identified knowledge gaps in 5 areas related to bilirubin-induced brain injury and kernicterus: 1) neurobiology and neuroimaging; 2) epidemiology and issues of clinical management; 3) methodologies for assessing clinical jaundice and direct and noninvasive measurement of serum bilirubin and hemolysis; 4) therapies for management of neonatal hyperbilirubinemia; and 5) public health surveillance and systems-based approaches to prevention.
Pattern Generation on Semiconductor Surfaces by a Scanning Tunneling Microscope Operating in Air (1991)

Recent results employing scanning tunneling microscope‐based techniques for the generation of nanometer‐scale patterns on passivated semiconductor surfaces are presented. Preparation and characterization of hydrogen‐passivated silicon and sulfur‐passivated gallium arsenide surfaces are described and the determination of the chemical and morphological properties of the patterned regions by scanning electron microscopy and time‐of‐flight secondary ion mass spectrometry are discussed. Our recent demonstration that ultrashallow, oxide features written by scanning tunneling microscope (STM) can serve as an effective mask for selective‐area GaAs heteroepitaxy on silicon is used to illustrate key requirements necessary for the realization of a unique, STM‐based nanotechnology.
Different Domains of the Mitogen-activated Protein Kinases ERK3 and ERK2 Direct Subcellular Localization and Upstream Specificityin Vivo (2002)

Extracellular signal-regulated kinase 3 (ERK3) is a member of the mitogen-activated protein (MAP) kinase family. ERK3 is most similar in its kinase catalytic domain to ERK2, yet it displays many unique properties. Among these, unlike ERK2, which translocates to the nucleus following activation, ERK3 is constitutively localized to the nucleus, despite the lack of a defined nuclear localization sequence. We created two chimeras between ERK2 and the catalytic domain of ERK3 (ERK3DeltaC), and some mutants of these chimeras, to examine the basis for the different behaviors of these two MAP kinase family members. We find the following: 1) the N-terminal folding domain of ERK3 functions in phosphoryl transfer reactions with the C-terminal folding domain of ERK2; 2) the C-terminal halves of ERK2 and ERK3DeltaC are primarily responsible for their subcellular localization in resting cells; and 3) the N-terminal folding domain of ERK2 is required for its activation in cells, its interaction with MEK1, and its accumulation in the nucleus.
11.beta.-Methoxy-, 11.beta.-ethyl, and 17.alpha.-ethynyl-substituted 16.alpha.-fluoroestradiols: receptor-based imaging agents with enhanced uptake efficiency and selectivity (1990)

We have prepared three analogues of 16 alpha-fluoroestradiol (FES) substituted either with an 11 beta-methoxy group (1, 11 beta-MeO-FES), an 11 beta-ethyl group (2, 11 beta-Et-FES), or a 17 alpha-ethynyl group (3, 17 alpha-ethynyl-FES). These substituents all lower the binding of FES to the serum proteins alphafetoprotein and sex steroid binding protein, but their effect on estrogen receptor binding varies: Receptor binding is increased by the 11 beta-ethyl and 17 alpha-ethynyl groups, but decreased by the 11 beta-methoxy group. These substituents also have a parallel effect on the lipophilicity, and hence the nonspecific binding estimated for these compounds. All three compounds were prepared in fluorine-18 labeled form, at effective specific activities of 90-1600 Ci/mmol, by fluoride ion displacement reactions as done previously with FES. Tissue distribution studies in immature rats show high uptake selectivity by target tissue (uterus) and effective competition by an excess of unlabeled estradiol. Percent injected dose per gram values (% ID/g) at 1 h are 6% for 11 beta-MeO-FES and 11-13% for 11 beta-Et-FES and 17 alpha-ethynyl-FES (FES itself has a % ID/g of 9%). Uptake selectivity in terms of uterus to blood or muscle ratios at 1 h is highest for 11 beta-MeO-FES and 17 alpha-ethynyl-FES (43-149). Metabolic consumption studies show that most activity in uterus is unmetabolized and in blood is rapidly and nearly completely metabolized. In muscle, FES and the substituted estrogens show intermediate levels of metabolic consumption; in some cases activity in muscle extracts is nearly unmetabolized. Thus, the substituents on FES cause major alterations in receptor and nonreceptor binding affinity, uptake efficiency and selectivity, and extent of metabolism. It is not readily clear, however, whether the alterations in uptake efficiency and selectivity are the result of differences in receptor or nonreceptor binding or lipophilicity, or altered patterns of metabolism. Nevertheless, these compounds should be useful in providing a spectrum of uptake properties that could be used for imaging different estrogen-receptor-containing structures.
Nitric oxide inhibits endothelin-1 production through the suppression of nuclear factor κB (2002)

We have reported previously that the nitric oxide (NO) donor FK409 [(+/-)-(E)-4-ethyl-2-[(E)-hydroxyimino]-5-nitro-3-hexanamide] improved renal dysfunction as well as renal lesions in rats with ischaemia/reperfusion injury. We also found that FK409 substantially reduced endothelin-1 (ET-1) production in cultured vascular endothelial cells (ECs). Nuclear factor kappa B (NF-kappa B) is known to play a key role in the development of ischaemic disorders through regulation of the expression of a variety of genes. In the present study, we examined the effects of FK409 on ET-1 production in cultured pig aortic ECs, and the possible involvement of NF-kappa B in the inhibitory effect of NO on ET-1 production. FK409 significantly attenuated basal and tumour necrosis factor-alpha (TNF-alpha)-induced preproET-1 mRNA expression in ECs. In addition, FK409 diminished basal and TNF-alpha-stimulated NF-kappa B activation in ECs. Pretreatment with N-benzyloxycarbonyl-Ile-Glu(O-t-Bu)-Ala-leucinal or BAY 11-7082, both of which are suppressors of NF-kappa B activation, effectively attenuated basal and TNF-alpha-induced ET-1 mRNA expression. These findings suggest that the suppression of NF-kappa B activation is at least partly involved in the FK409-induced inhibition of ET-1 production in ECs. We propose that NF-kappa B activation plays an important role in ET-1 production.
Biomolecular Materials (1994)

The second half of the 20th century has witnessed a productive interplay between chemistry and materials science—in fields as varied as polymers, catalysis, interface science, ceramics, and electronic materials. Society also has enjoyed the spectacular results-most notably in information and communications technologies—achieved by merging condensed matter physics and materials research. In contrast, connections between materials science and biology have been relatively weak. To be sure, materials research has made important contributions to medicine, but the discipline has yet to draw on biology in the same way that it has absorbed people, ideas, and skills from chemistry and physics.&#13;\n&#13;\nThis is beginning to change. With increasing frequency, new materials or processing strategies are emerging, inspired by biological examples or developed directly from biological systems. Already, researchers are engineering bacteria or other organisms to synthesize monomers for polymer production. They are synthesizing and expressing artificial genes to produce proteinlike materials with the mechanical properties of silk, collagen, or other materials containing elastic fibers. They are beginning to use phospholipids as templates for electronic materials; make synthetic phospholipid vesicles that, like proteins, respond to signals; use stereoselective catalyses to produce optically active polymers from racernic starting materials; and develop protein- and lipid-based sensors.&#13;\n&#13;\nChemists are playing a vital role in these developments, providing synthetic skills as well as insights into the behavior of complex molecular systems.
Mutations of theAPC adenomatous polyposis coli) gene (1993)

Several investigators have reported germline mutations of the APC gene in patients with familial adenomatous polyposis (FAP) as well as somatic mutations in tumors developed in digestive organs (stomach, pancreas, colon, and rectum). Those results provide evidence that inactivation of the APC gene plays a significant role in FAP and in sporadic tumors of these tissues. APC mutations have led to some interesting observations. First, the great majority of the mutations found to date would result in truncation of the APC product. Second, almost all the mutations have occurred within the first half of the coding sequence, and somatic mutations in colorectal tumors are further clustered in a particular region called MCR (mutation cluster region). Third, most identified point mutations in the APC gene are transitions from cytosine to other nucleotides. Fourth, the location of germ-line mutations tends to correlate with the number of colorectal polyps in FAP patients. Furthermore, inactivation of both alleles of the APC gene seems to be required as an early event to develop most of adenomas and carcinomas in the colon and rectum as well as some of those in the stomach.
Invited Review: Nutrition for Adult Burn Patients: A Review (1991)

Adequate nutritional support is an important aspect of burn therapy. To accomplish this goal, nutrition assessment must be conducted, with particular attention given to the determination of energy and macronutrient needs. Providing these nutrients by the enteral route is recommended.
X-Ray Emission and Absorption Spectroscopy with Binary Amorphous Alloys from the B-Co-, B-Ni-, Co-P-, Co-Ti-, Cu-Mg-, Cu-Ti-, Mg-Zn-, Ni-P-, and Ni-Ti-Systems (1984)

X-ray emission and absorption spectroscopy has been used to determine the partial density of occupied and unoccupied states in various metallic glasses. The X-ray emission spectra also indicate a possible electronic charge transfer between the alloyed atoms. The experiments were done by means of an electron microprobe. Amorphous Mg2Cu was prepared by ionic sputtering, the glasses of the Mg-Cu-, Mg-Zn-, Cu-Ti-, Co-Ti-, Co-B-, Co-P-, Ni-Ti-, Ni-B-, and Ni-Psystems by the melt-spinning method. From the measurements it is concluded that the amorphous phase is stabilized by compound formation. A combination with results of X-ray diffraction measurements on amorphous Mg 2 Cu indicates that the glassy structures should be favoured by a correlation between the atoms of higher electronegativity. The shape of the density of unoccupied states vs. energy curve shows that the local symmetry around the Zn- and Cu-atoms in the amorphous phases differs from that in the corresponding crystalline phases. For the transition-metalloid glasses evidence for a fcc-like local short range order is found.
Quantitative and qualitative analysis of a microfluidic DNA extraction system using a nanoporous AlOx membrane (2008)

A nanoporous aluminium oxide membrane was integrated into a microfluidic system designed to extract hgDNA (human genomic DNA) from lysed whole blood. The effectiveness of this extraction system was determined by passing known concentrations of purified hgDNA through nanoporous membranes with varying pore sizes and measuring the amount of hgDNA deposited on the membrane while also varying salt concentration in the solution. DNA extraction efficiency increased as the salt concentration increased and nanopore size decreased. Based on these results, hgDNA was extracted from whole blood while varying salt concentration, nanopore size and elution buffer to find the conditions that yield the maximum concentration of hgDNA. The optimal conditions were found to be using a low-salt lysis solution, 100 nm pores, and a cationic elution buffer. Under these conditions the combination of flow and ionic disruption were sufficient to elute the hgDNA from the membrane. The extracted hgDNA sample was analysed and evaluated using PCR (polymerase chain reaction) to determine whether the eluted sample contained PCR inhibition factors. Eluted samples from the microfluidic system were amplified without any inhibition effects. PCR using extracted samples was demonstrated for several genes of interest. This microfluidic DNA extraction system based on embedded membranes will reduce the time, space and reagents needed for DNA analysis in microfluidic systems and will prove valuable for sample preparation in lab-on-a-chip applications.
Volumetric Aerobiological Survey of Conidial Fungi in the North‐East Netherlands (1985)

A study was undertaken to see whether the principal airborne fungi in the North-East Netherlands were also found to be the most reactive in skin testing. Atmospheric samples were taken weekly with the Andersen sampler, from April 1981, up to and including, June 1983. At the same time skin tests of 833 patients referred to the outpatient Departments of Pulmonology and Allergology, because of recurrent bronchial obstructive complaints and a suspected allergy, were studied for strongly positive skin reactivity to fungi. 4.6% of the patients reacted with a wheal of 10 mm diameter or more to one or more of the tested fungi. Almost three-quarters of the airborne fungal "flora" was composed of seven genera, namely (in order of occurrence): Cladosporium (42.6%), Botrytis (8.6%), Yeasts (7%), Penicillium (5.8%), Basidiomycetes (5.7%), Aspergillus (3.7%), and Alternaria (0.9%). In skin-testing, however, a different order of occurrence existed: namely: Beauveria (6.8%), Botrytis (6.1%), Aspergillus (4.7%), Mucor (3.8%), Epicoccum (3%), Cladosporium (2.3%), and Alternaria (1.1%). It is concluded that the most prevailing airborne moulds are not necessarily the most potent allergens, at least in skin testing. Aspergillus and Botrytis showed a high sensitization rate, while Cladosporium and Alternaria did not. Botrytis deserves further study because of its frequent airborne occurrence and marked allergenic properties.
H-ras but Not K-ras Traffics to the Plasma Membrane through the Exocytic Pathway (2000)

Ras proteins must be localized to the inner surface of the plasma membrane to be biologically active. The motifs that effect Ras plasma membrane targeting consist of a C-terminal CAAX motif plus a second signal comprising palmitoylation of adjacent cysteine residues or the presence of a polybasic domain. In this study, we examined how Ras proteins access the cell surface after processing of the CAAX motif is completed in the endoplasmic reticulum (ER). We show that palmitoylated CAAX proteins, in addition to being localized at the plasma membrane, are found throughout the exocytic pathway and accumulate in the Golgi region when cells are incubated at 15 degrees C. In contrast, polybasic CAAX proteins are found only at the cell surface and not in the exocytic pathway. CAAX proteins which lack a second signal for plasma membrane targeting accumulate in the ER and Golgi. Brefeldin A (BFA) significantly inhibits the plasma membrane accumulation of newly synthesized, palmitoylated CAAX proteins without inhibiting their palmitoylation. BFA has no effect on the trafficking of polybasic CAAX proteins. We conclude that H-ras and K-ras traffic to the cell surface through different routes and that the polybasic domain is a sorting signal diverting K-Ras out of the classical exocytic pathway proximal to the Golgi. Farnesylated Ras proteins that lack a polybasic domain reach the Golgi but require palmitoylation in order to traffic further to the cell surface. These data also indicate that a Ras palmitoyltransferase is present in an early compartment of the exocytic pathway.
ATP Increases the Affinity between MutS ATPase Domains (2004)

MutS is the key protein of the Escherichia coli DNA mismatch repair system. It recognizes mispaired and unpaired bases and has intrinsic ATPase activity. ATP binding after mismatch recognition by MutS serves as a switch that enables MutL binding and the subsequent initiation of mismatch repair. However, the mechanism of this switch is poorly understood. We have investigated the effects of ATP binding on the MutS structure. Crystallographic studies of ATP-soaked crystals of MutS show a trapped intermediate, with ATP in the nucleotide-binding site. Local rearrangements of several residues around the nucleotide-binding site suggest a movement of the two ATPase domains of the MutS dimer toward each other. Analytical ultracentrifugation experiments confirm such a rearrangement, showing increased affinity between the ATPase domains upon ATP binding and decreased affinity in the presence of ADP. Mutations of specific residues in the nucleotide-binding domain reduce the dimer affinity of the ATPase domains. In addition, ATP-induced release of DNA is strongly reduced in these mutants, suggesting that the two activities are coupled. Hence, it seems plausible that modulation of the affinity between ATPase domains is the driving force for conformational changes in the MutS dimer. These changes are driven by distinct amino acids in the nucleotide-binding site and form the basis for long-range interactions between the ATPase domains and DNA-binding domains and subsequent binding of MutL and initiation of mismatch repair.
Small interference RNA modulation of IL‐10 in human monocyte‐derived dendritic cells enhances the Th1 response (2004)

RNA interference technology has been used to modulate dendritic cell (DC) function by targeting the expression of genes such as IL-12 and NF-kappa B. In this paper, we demonstrate that transfection of DC with IL-10-specific double strands of small interference RNA (siRNA) resulted in potent suppression of IL-10 gene expression without inducing DC apoptosis or blocking DC maturation. Inhibition of IL-10 by siRNA was accompanied by increased CD40 expression and IL-12 production after maturation, which endowed DC with the ability to significantly enhance allogeneic T cell proliferation. IL-10 siRNA transfection did not affect MHC class II, CD86, CD83, or CD54 expression in mature DC. To further test the ability of IL-10 siRNA-treated DC to induce a T cell response, naive CD4 T cells were stimulated by autologous DC pulsed with KLH. The results indicated that IL-10 siRNA-transfected DC enhanced Th1 responses by increasing IFN-gamma and decreasing IL-4 production. These findings suggest the potential for a novel immunotherapeutic strategy of using IL-10 siRNA-transfected antigen-presenting cells as vaccine delivery agents to boost the Th1 response against pathogens and tumors that are controlled by Th1 immunity.
Chronic Inflammation: A Common and Important Factor in the Pathogenesis of Neoplasia (2006)

A causal link between chronic inflammation and carcinogenesis is explored by reviewing illustrative examples of specific cancers and causal agents and mechanisms. The causal agents or pathologic conditions include microbial agents, gastroesophageal reflux, chronic cholecystitis and cholelithiasis, inflammatory bowel disease, and specific agents that cause chronic obstructive or diffuse interstitial lung disease. The proportion of total cancer deaths attributable to infectious agents is estimated to be about 20% to 25% in developing countries and 7% to 10% in more industrialized countries. Recurrent or persistent inflammation may induce, promote, or influence susceptibility to carcinogenesis by causing DNA damage, inciting tissue reparative proliferation, and/or creating a stromal "soil" that is enriched with cytokines and growth factors. Future research on the complex cascade of cellular and humoral factors participating in the chronic inflammatory process will further understanding of the pathogenesis of various cancers and potentially provide a rationale for targeted chemopreventive interventions.
Carbamates and Ureas Derived from Amino- and Oxopyrimidines1,2 (1962)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCarbamates and Ureas Derived from Amino- and Oxopyrimidines1,2ELIZABETH DYER, MARTIN L. GLUNTZ, and ELINOR J. TANCKCite this: J. Org. Chem. 1962, 27, 3, 982–985Publication Date (Print):March 1, 1962Publication History Published online1 May 2002Published inissue 1 March 1962https://pubs.acs.org/doi/10.1021/jo01050a071https://doi.org/10.1021/jo01050a071research-articleACS PublicationsRequest reuse permissionsArticle Views262Altmetric-Citations10LEARN 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
The PageRank Citation Ranking : Bringing Order to the Web (1999)

The importance of a Web page is an inherently subjective matter, which depends on the readers interests, knowledge and attitudes. But there is still much that can be said objectively about the relative importance of Web pages. This paper describes PageRank, a method for rating Web pages objectively and mechanically, efectively measuring the human interest and attention devoted to them. We compare PageRank to an idealized random Web surfer. We show how to efficiently compute PageRank for large numbers of pages. And, we show how to apply PageRank to search and to user navigation.