gebhart/patrepeval huggingface dataset:
Adenoviral Infections in Pediatric Liver Transplant Recipients (1987)

Over a 5 1/2-year period, 22 of 262 children receiving liver transplants developed adenoviral infections. Five had adenoviral hepatitis in the allograft, caused by serotype 5. All five were treated for rejection, either just before or at the time of infection. Liver biopsy specimens had characteristic histological appearance, and diagnosis of adenoviral infection was confirmed with monoclonal antiadenoviral antibodies, electron microscopy, and by culture of liver tissue. In the remaining 17 patients, adenovirus was isolated from urine, stool, throat secretions, and/or blood samples, but none had any detectable visceral infection. Serotypes 1 and 2 predominated, similar to children not receiving transplants during the same time period. Three of the patients with hepatitis are alive and well; two died of liver failure. Adenoviral hepatitis did not recur in the second allograft of a patient who underwent retransplantation for combined rejection and adenoviral hepatitis, and appears, therefore, not to be a contraindication to retransplantation when liver failure ensues.
The wheat and barley vernalization gene VRN3 is an orthologue of FT (2006)

Winter wheat and barley varieties require an extended exposure to low temperatures to accelerate flowering (vernalization), whereas spring varieties do not have this requirement. In this study, we show that in these species, the vernalization gene VRN3 is linked completely to a gene similar to Arabidopsis FLOWERING LOCUS T (FT). FT induction in the leaves results in a transmissible signal that promotes flowering. Transcript levels of the barley and wheat orthologues, designated as HvFT and TaFT, respectively, are significantly higher in plants homozygous for the dominant Vrn3 alleles (early flowering) than in plants homozygous for the recessive vrn3 alleles (late flowering). In wheat, the dominant Vrn3 allele is associated with the insertion of a retroelement in the TaFT promoter, whereas in barley, mutations in the HvFT first intron differentiate plants with dominant and recessive VRN3 alleles. Winter wheat plants transformed with the TaFT allele carrying the promoter retroelement insertion flowered significantly earlier than nontransgenic plants, supporting the identity between TaFT and VRN-B3. Statistical analyses of flowering times confirmed the presence of significant interactions between vernalization and FT allelic classes in both wheat and barley (P < 0.0001). These interactions were supported further by the observed up-regulation of HvFT transcript levels by vernalization in barley winter plants (P = 0.002). These results confirmed that the wheat and barley FT genes are responsible for natural allelic variation in vernalization requirement, providing additional sources of adaptive diversity to these economically important crops.
DNA damage by mycotoxins (1999)

Mycotoxins are toxic fungal metabolites which are structurally diverse, common contaminants of the ingredients of animal feed and human food. To date, mycotoxins with carcinogenic potency in experimental animal models include aflatoxins, sterigmatocystin, ochratoxin, fumonisins, zearalenone, and some Penicillium toxins. Most of these carcinogenic mycotoxins are genotoxic agents with the exception of fumonisins, which is currently believed to act by disrupting the signal transduction pathways of the target cells. Aflatoxin B1 (AFB1), a category I known human carcinogen and the most potent genotoxic agent, is mutagenic in many model systems and produces chromosomal aberrations, micronuclei, sister chromatid exchange, unscheduled DNA synthesis, and chromosomal strand breaks, as well as forms adducts in rodent and human cells. The predominant AFB1-DNA adduct was identified as 8, 9-dihydro-8-(N7-guanyl)-9-hydroxy-AFB1 (AFB1-N7-Gua), which derives from covalent bond formation between C8 of AFB1-8,9-epoxides and N7 of guanine bases in DNA. Initial AFB1-N7-guanine adduct can convert to a ring-opened formamidopyrimidine derivative, AFB1-FAPY. The formation of AFB1-N7-guanine adduct was linear over the low-dose range in all species examined, and liver, the primary target organ, had the highest level of the adduct. Formation of initial AFB1-N7-guanine adduct was correlated with the incidence of hepatic tumor in trout and rats. The AFB1-N7-guanine adduct was removed from DNA rapidly and was excreted exclusively in urine of exposed rats. Several human studies have validated the similar correlation between dietary exposure to AFB1 and excretion of AFB1-N7-guanine in urine. Replication of DNA containing AFB1-N7-guanine adduct-induced G-->T mutations in an experimental model. Activation of ras protooncogene has been found in AFB1-induced tumors in mouse, rat, and fish. More strikingly, the relationship between aflatoxin exposure and development of human hepatocellular carcinoma (HHC) was demonstrated by the studies on the p53 tumor suppressor gene. High frequency of p53 mutations (G-->T transversion at codon 249) was found to occur in HHC collected from populations exposed to high levels of dietary aflatoxin in China and Southern Africa. Furthermore, AFB1-induced DNA damage and hepatocarcinogenesis in experimental models can be modulated by a variety of factors including nutrients, chemopreventive agents, and other factors such as food restriction and viral infection, as well as genetic polymorphisms.
Monoclonal antibody exposure in rat and cynomolgus monkey cerebrospinal fluid following systemic administration (2018)

Upon systemic administration, average antibodies CSF-to-serum concentration ratios in rats and monkeys were 0.1-0.2%. The <sup>CSF</sup> t <sub>½</sub> of the antibodies was largely determined by their long systemic t <sub>½</sub> ( <sup>systemic</sup> t <sub>½</sub> ).
Patent Review of Manufacturing Routes to Oncology Drugs: Carfilzomib, Osimertinib, and Venetoclax (2016)

Synthetic routes and final forms for three recently approved oncology drugs are reviewed: carfilzomib (Kyprolis), osimertinib (Tagrisso), and venetoclax (Venclexta). Several patent applications have been filed for the major synthetic challenge for carfilzomib, installation of the chiral epoxide. The apparent manufacturing route to osimertinib involves seven steps and a longest linear sequence of six steps with a yield of 56%. The apparent manufacturing route to venetoclax is a ten-step convergent synthesis with a seven-step longest linear sequence that proceeds in 52% yield.
A Single-stranded DNA-binding Protein Is Needed for Efficient Presynaptic Complex Formation by the Saccharomyces cerevisiae Rad51 Protein (1997)

Protein-promoted DNA strand exchange requires formation of an active presynaptic complex between the DNA-pairing protein and single-stranded DNA (ssDNA). Formation of such a contiguous filament is stimulated by a ssDNA-binding protein. Here, the effects of replication protein A (RPA) on presynaptic complex formation and DNA strand exchange activities of Rad51 protein were examined. Presynaptic complex formation was assessed by measuring ATP hydrolysis. With phiX174 ssDNA, the ATPase activity of Rad51 protein is stimulated approximately 1.4-fold by RPA, provided that Rad51 protein is in excess of the ssDNA concentration; otherwise, RPA inhibits ATPase activity. In contrast, with ssDNA devoid of secondary structure (poly(dT), poly(dA), poly(dI), and etheno-M13 DNA), RPA does not stimulate the already elevated ATPase activity of Rad51 protein, but inhibits activity at low Rad51 protein concentrations. These results suggest that Rad51 protein and RPA exclude one another from ssDNA by competing for the same binding sites and that RPA exerts its effect on presynaptic complex formation by eliminating secondary structure to which Rad51 protein is bound nonproductively. DNA strand exchange catalyzed by Rad51 protein is also greatly stimulated by RPA. The optimal stoichiometry for stimulation is approximately 20-30 nucleotides of ssDNA/RPA heterotrimer. The ssDNA-binding protein of Escherichia coli can substitute for RPA, showing that the role of RPA is not specific. We conclude that RPA affects both presynaptic complex formation and DNA strand exchange via changes in DNA structure, employing the same mechanism used by the ssDNA-binding protein to effect change in E. coli RecA protein activity.
DRUG TARGETING BY RETROMETABOLIC DESIGN: SOFT DRUGS AND CHEMICAL DELIVERY SYSTEMS (2001)

One of the most important goals of pharmaceutical research and development is
targeted drug delivery, deﬁned as optimization of the therapeutic index by localizing the pharmacological activity of the drug to the site of action. It is important
to distinguish this broad deﬁnition as the ability to achieve a desired pharmacological response at a selected site without undesired interaction at other sites
from a narrower deﬁnition of the basic targeting concept. Within this narrower
deﬁnition, a speciﬁc drug receptor is considered as target, and the objective is
to improve ﬁt, afﬁnity, and binding to this receptor that ultimately will trigger
the pharmacological activity.
A Distinct Sequence (ATAAA) Separates Methylated and Unmethylated Domains at the 5′-End of theGSTP1 CpG Island* (2000)

What defines the boundaries between methylated and unmethylated domains in the genome is unclear. In this study we used bisulfite genomic sequencing to map the boundaries of methylation that flank the 5'- and 3'-ends of the CpG island spanning the promoter region of the glutathione S-transferase (GSTP1) gene. We show that GSTP1 is expressed in a wide range of tissues including brain, lung, skeletal muscle, spleen, pancreas, bone marrow, prostate, heart, and blood and that this expression is associated with the CpG island being unmethylated. In these normal tissues a marked boundary was found to separate the methylated and unmethylated regions of the gene at the 5'-flank of the CpG island, and this boundary correlated with an (ATAAA)(19-24) repeated sequence. In contrast, the 3'-end of the CpG island was not marked by a sharp transition in methylation but by a gradual change in methylation density over about 500 base pairs. In normal tissue the sequences on either side of the 5'-boundary appear to lie in separate domains in which CpG methylation is independently controlled. These separate methylation domains are lost in all prostate cancer where GSTP1 expression is silenced and methylation extends throughout the island and spans across both the 5'- and 3'-boundary regions.
Human GLUT4/Muscle-Fat Glucose-Transporter Gene: Characterization and Genetic Variation (1992)

Four overlapping DNA fragments spanning 32 kb containing the human GLUT4 facilitative glucose-transporter gene were isolated and characterized. The sequence of the GLUT4 gene (∼6.3 kb) and 2.0 kb of the promoter region was determined. The sequence of the promoter revealed potential binding sites for transcription factors known to regulate gene expression in muscle cells and adipocytes. However, transfection of constructs including 2 kb of the GLUT4 promoter fused to the bacterial CAT gene into 3T3-L1 adipocytes displayed only weak promoter activity. Because insulin resistance plays a prominent role in the development of NIDDM, genetic variation in the sequence of GLUT4 also was evaluated. Oligonucleotide primer pairs were selected that allowed the protein-coding region of the human GLUT4 gene to be amplified by PCR. The sequence of the protein-coding region of the GLUT4 gene and all intron-exon junctions was determined for a single diabetic Pima Indian and was identical to that of the cloned gene and cDNA. SSCP analysis was used to screen patients with diabetes mellitus and normal, healthy nondiabetic individuals for mutations at the GLUT4 locus. In addition to the silent substitution in the codon for Asn130 (AAC or AAT) and a Val383(GTC)→IIe(ATC) replacement described previously, two new variants were identified. One was a T→A substitution in intron 1 that was found in 1 of 36 NIDDM patients who were typed for this variant. The second was a lle385(ATT)→Thr(ACT) replacement that occurred in 1 normal individual and was not found in any of 676 other normal and diabetic subjects. A large and racially diverse group of normal and diabetic individuals also was screened for the lle383 polymorphism. It occurred in both diabetic and nondiabetic subjects. There is no indication from our data that these polymorphisms are associated with NIDDM.
Eicosapentaenoic acid and docosahexaenoic acid have distinct membrane locations and lipid interactions as determined by X-ray diffraction (2018)

Eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) differentially influence lipid oxidation, signal transduction, fluidity, and cholesterol domain formation, potentially due in part to distinct membrane interactions. We used small angle X-ray diffraction to evaluate the EPA and DHA effects on membrane structure. Membrane vesicles composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and cholesterol (C) (0.3C:POPC mole ratio) were prepared and treated with vehicle, EPA, or DHA (1:10 mol ratio to POPC). Electron density profiles generated from the diffraction data showed that EPA increased membrane hydrocarbon core electron density over a broad area, up to ± 20 Å from the membrane center, indicating an energetically favorable extended orientation for EPA likely stabilized by van der Waals interactions. By contrast, DHA increased electron density in the phospholipid head group region starting at ± 12 Å from the membrane center, presumably due to DHA-surface interactions, with coincident reduction in electron density in the membrane hydrocarbon core centered ± 7-9 Å from the membrane center. The membrane width (d-space) decreased by 5 Å in the presence of vehicle as the temperature increased from 10 °C to 30 °C due to increased acyl chain trans-gauche isomerizations, which was unaffected by addition of EPA or DHA. The influence of DHA on membrane structure was modulated by temperature changes while the interactions of EPA were unaffected. The contrasting EPA and DHA effects on membrane structure indicate distinct molecular locations and orientations that may contribute to observed differences in biological activity.
The use of micronized cellulose disintegrants as insoluble swellable matrices for sustained-release tablets. (1991)

Five cellulose disintegrants--low-substituted hydroxypropylcellulose (L-HPC), microcrystalline cellulose (MCC), carboxymethylcellulose (CMC), cross-linked NaCMC (C.L.NaCMC), and CaCMC-were evaluated as directly compressed matrices for sustained-release (SR) tablets in vitro, using procainamide hydrochloride as a model drug. Coarser particles (14-19 microns) of the jet mill ground disintegrants, as well as intact disintegrants, provided rapidly disintegrating tablets with fast drug release but finer particles (2.5-3.5 microns) provided matrix-type SR tablets. The SR tablets based on non-ionic polymers (L-HPC and MCC) did not disintegrate at any pH; those based on anionic polymers (C.L.NaCMC and CaCMC) did not disintegrate at pH 1.2, but they disintegrated gradually from the exterior in water and in a pH 6.8 medium. We conclude that the particle size and concentration of the cellulose disintegrants are determinant factors in the formulation of SR matrices.
A Scanning Spherical Mirror Interferometer for Spectral Analysis of Laser Radiation (1964)

The results of a theoretical and experimental investigation of a scanning spherical mirror interferometer designed specifically for analysis of laser radiation are given. It is shown that the high degree of spatial coherence and monochromaticity of laser radiation makes it possible to excite individual interferometer modes selectively. A theory of single-mode excitation is presented, and a specific example treated. The mechanical construction of the instrument and the dynamics of the scanning system are described. The capability of the instrument for observation of laser mode separation, amplitudes, and frequency shifts is illustrated by specific experiments. It is shown that the instrument can easily be used in both the visible and infrared. Results of simultaneous observation of beats between laser modes with an rf spectrum analyzer and of the laser optical field with the scanning interferometer are given, and it is shown that the combined system, in certain cases, will permit determination of the relative phases of the laser modes. Experiments illustrating the use of the scanning interferometer for observation of mode competition and the effects of magnetic fields on laser output are recounted, as is also the operation of an active scanning interferometer with which resolving powers of 2.5 × 109 and finesses of 1040 were obtained. Effects of coupling between laser and interferometer are shown, and a polarization isolator for decoupling is described.
Resistance to Radiation (1995)

The bacterium Deinococcus radiodurans can survive extremely large doses of radiation without mutagenesis. Daly and Minton suggest how this organism repairs its radiation-damaged DNA so efficiently and why such a system may have evolved.
Dissociation of progeny vaccinia virus from the cell membrane is regulated by a viral envelope glycoprotein: effect of a point mutation in the lectin homology domain of the A34R gene (1993)

Vaccinia virus strains vary considerably in the amounts of extracellular enveloped virus (EEV) that they release from infected cells. The IHD-J strain produces up to 40 times more EEV than does the related WR strain and consequently generates elongated comet-shaped virus plaques instead of sharply defined round ones in susceptible monolayer cells under liquid medium. The difference in EEV formation is due to the retention of enveloped WR virions on the cell surface (R. Blasco and B. Moss, J. Virol. 66:4170-4179, 1992). By using WR and IHD-J DNA fragments for marker transfer and analyzing the progeny virus by the comet formation assay, we determined that gene A34R and at least one other gene regulate the release of cell-associated virions. Replacement of the A34R gene of WR with the corresponding gene from IHD-J increased the amount of EEV produced by 10-fold and conferred the ability to form distinctive comet-shaped plaques. Gene A34R encodes an EEV-specific glycoprotein with homology to C-type animal lectins (S.A. Duncan and G.L. Smith, J. Virol. 66:1610-1621, 1992). The nucleotide sequences of the A34R genes of WR and IHD-J strains differed in six positions, of which four were silent. One of the codon mutations (Lys-151--&gt;Glu), which is located in the putative carbohydrate recognition domain, was sufficient to transfer a comet-forming phenotype to WR virus. These data indicate that the A34R-encoded glycoprotein is involved, through its lectin homology domain, in the retention of progeny virus on the surface of parental cells and raise the possibility that the protein also has a role in virus attachment to uninfected cells.
Deamination cytosine derivatives by bisulfite. Mechanism of the reaction (1974)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDeamination cytosine derivatives by bisulfite. Mechanism of the reactionRobert Shapiro, Victor DeFate, and Marvin WelcherCite this: J. Am. Chem. Soc. 1974, 96, 3, 906–912Publication Date (Print):February 1, 1974Publication History Published online1 May 2002Published inissue 1 February 1974https://pubs.acs.org/doi/10.1021/ja00810a043https://doi.org/10.1021/ja00810a043research-articleACS PublicationsRequest reuse permissionsArticle Views851Altmetric-Citations88LEARN 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
An Essential Component of a Novel Bacterial Protein Export System with Homologues in Plastids and Mitochondria (1998)

Proteins are transported across the bacterial plasma membrane and the chloroplast thylakoid membrane by means of protein translocases that recognize N-terminal targeting signals in their cognate substrates. Transport of many of these proteins involves the well defined Sec apparatus that operates in both membranes. We describe here the identification of a novel component of a bacterial Sec-independent translocase. The system probably functions in a similar manner to a Sec-independent translocase in the thylakoid membrane, and substrates for both systems bear a characteristic twin-arginine motif in the targeting peptide. The translocase component is encoded in Escherichia coli by an unassigned reading frame, yigU, disruption of which blocks the export of at least five twin-Arg-containing precursor proteins that are predicted to bind redox cofactors, and hence fold, prior to translocation. The Sec pathway remains unaffected in the deletion strain. The gene has been designated tatC (for twin-arginine translocation), and we show that homologous genes are present in a range of bacteria, plastids, and mitochondria. These findings suggest a central role for TatC-type proteins in the translocation of tightly folded proteins across a spectrum of biological membranes.
Xenogeneic expression of human stem cell factor in transgenic mice mimics codominant c-kit mutations (1996)

Mutations of c-kit, which encodes a transmembrane receptor tyrosine kinase, have been identified in mice by abnormal coat color, anemia, and germ cell defects. Mice heterozygous for mutations of c-kit have a white forehead blaze and a white ventral spot, leading these mutants to be termed dominant White spotting (W). We have previously demonstrated that the membrane-associated isoform of human stem cell factor (hSCF220, the ligand for c-kit) is inefficiently processed in murine stromal cell transfectants. Thus, in murine cell lines analyzed in vitro, hSCF220 transfectants present SCF as a membrane restricted protein in contrast to the murine SCF220 cDNA protein product, which is slowly cleaved and secreted. We show here that transgenic mice expressing the human SCF220 isoform in vivo display a phenotype indistinguishable from some alleles of W. Specifically, hSCF220-expressing transgenic mice display a prominent forehead blaze and a white ventral spot. Generations of doubly heterozygous animals that carry both a mutated c-kit allele and the hSCF220 transgene display a more severe coat color abnormality. This phenotype appears to be due to occupancy of murine c-kit by human SCF and diminished cell surface expression of endogenous murine SCF. Normal signaling events that lead to cell survival or proliferation appear to be disrupted in vivo in these transgenic mice.