gebhart/patrepeval huggingface dataset:
Metastatic canine mammary carcinomas can be identified by a gene expression profile that partly overlaps with human breast cancer profiles (2010)

Metastatic canine mammary carcinomas can be discriminated from non-metastatic carcinomas by their gene expression profiles. More than one third of the differentially expressed genes are also described of relevance for human breast cancer. Many of the differentially expressed genes are linked to functions and pathways which appear to be relevant for the induction and maintenance of metastatic progression and may represent new therapeutic targets. Furthermore, dogs are in some aspects suitable as a translational model for human breast tumors in order to identify prognostic molecular signatures and potential therapeutic targets.
Secondary ion mass spectrometry with cesium ion primary beam and liquid target matrix for analysis of bioorganic compounds (1982)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSecondary ion mass spectrometry with cesium ion primary beam and liquid target matrix for analysis of bioorganic compoundsWilliam. Aberth, Kenneth M. Straub, and A. L. BurlingameCite this: Anal. Chem. 1982, 54, 12, 2029–2034Publication Date (Print):October 1, 1982Publication History Published online1 May 2002Published inissue 1 October 1982https://pubs.acs.org/doi/10.1021/ac00249a028https://doi.org/10.1021/ac00249a028research-articleACS PublicationsRequest reuse permissionsArticle Views401Altmetric-Citations209LEARN 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
Adjudin Targeting Rabbit Germ Cell Adhesion as a Male Contraceptive: A Pharmacokinetics Study (2008)

Adjudin (1-(2,4-dichlorobenzyl)-1H-indazole-3-carbohydrazide; formerly called AF-2364) has been shown to inhibit spermatogenesis by disrupting anchoring junctions at the Sertoligerm cell interface. This, in turn, leads to germ cell loss from the seminiferous epithelium, and transient infertility. Adjudin's efficacyin inhibiting spermatogenesis, the recovery of spermatogenesis after cessation of the drug, and side effects were examined in adult male Japanese rabbits. The pharmacokinetics profiles of adjudin in rabbits after oral administration and after intravenous injection were compared. Rabbits received 25 mg/kg adjudin once weekly for 4 consecutive weeks either by intravenous injection or by gavage. Vehicle-treated rabbits were used as controls. At 1, 2, 3, 4, and 8 weeks after treatment, testes were removed for microscopic examination to assess the status of spermatogenesis. Four weeks after intravenous cessation of adjudin, the recovery of spermatogenesis also was monitored. Blood was withdrawn after first administration to measure plasma concentrations of adjudin by high-performance liquid chromatography. Four weeks after intravenous treatment, examination of testis sections showed rapid exfoliation of elongated/elongating spermatids and the presence of large multinucleated cells; more than 95% of germ cells were absent from the seminiferous epithelium. Intravenous treatment showed a more severe disturbance of spermatogenesis compared with gavage treatment, which was correlated with bioavailability of the drug. The areas under the curve for intravenous injection and gavage were 20.11 +/- 1.90 and 2.23 +/- 0.45 mg x h x L(-1), respectively. These results illustrate the potential of adjudin as a male contraceptive, and the efficacy is associated with the bioavailability of the drug.
The mechanism of the reaction of chymotrypsin with p-nitrophenyl acetate (1956)

5. Release of these materials from mycelium treated with fatty acid was greatest at acid pH values, but change of pH had no significant effect upon the release by detergents.
Epitopic structure of Tn glycophorin A for an anti-Tn antibody (MLS 128). (1993)

Glycophorin A was digested with glycoprotease (Pasteurella haemolytica) and the digest was fractionated by a combination of high-pressure column chromatographies to produce the glycopeptides GPA-1 to GPA-6. Sequence analysis of the glycopeptides revealed that two serine residues (Ser-14 and Ser-15) are not glycosylated, Thr-17 and Ser-19 being glycosylated instead, in disagreement with the accepted structure. The glycopeptides thus obtained were treated with sialidase and beta-galactosidase. The Tn antigenicity, as assayed by the binding to a monoclonal anti-Tn antibody (MLS 128), was found exclusively in the glycopeptides including three (cluster I) or four (cluster II) consecutive residues of GalNAc-Ser/Thr, whereas the glycopeptide (GPA-2) containing two nonconsecutive GalNAc-Ser/Thr residues had practically no Tn antigenicity. The immunoreactivities of GPA-1 and GPA-3, containing both clusters I and II, and GPA-4, containing cluster II, were 63% (calcd. 67%), 81% (calcd. 86%), and 50% (calcd. 50%), respectively, of the immunoreactivity of GPA-5 or GPA-6, containing cluster I (the average being taken as the basis), based on the reactivity per GalNAc residue. These results indicate that clusters I and II react with the antibody to the same extent. The structure consisting of three consecutive glycosylated Ser/Thr residues may be essential for Tn antigenicity in the light of previous results for ovine submaxillary mucin.
Allelic Loss in Colorectal Carcinoma (1989)

Clinical and pathological associations with molecular genetic alterations were studied in colorectal carcinomas from 83 patients. Fractional allelic loss, a measure of allelic deletions throughout the genome, and allelic deletions of specific chromosomal arms (the short arm of 17 and long arm of 18) each provided independent prognostic information by multivariate analysis when considered individually with Dukes'classification. Distant metastasis was significantly associated with high fractional allelic loss and with deletions of 17p and 18q. Mutations of ras proto-oncogenes and deletions of 5q had no prognostic importance. Statistically significant associations were also found between allelic losses and a family history of cancer, left-sided tumor location, and absence of extracellular tumor mucin. Allelic deletion analysis thus identified subsets of colorectal carcinoma with increased predilection for distant metastasis and cancer-related death. Further studies may define a subset of genetic alterations that can be used clinically to help assess prognosis. (<i>JAMA</i>. 1989;261:3099-3103)
DNA polymerase accuracy and spontaneous mutation rates: frequencies of purine.purine, purine.pyrimidine, and pyrimidine.pyrimidine mismatches during DNA replication. (1981)

DNA from the am16 mutant of bacteriophage phi X174 may be replicated in vitro and expressed in vivo to give five classes of revertants. Each class may be specifically induced by the appropriate biasing of the concentrations of deoxynucleoside triphosphates in a predictable manner. The frequency of each reversion follows a kinetic rate equation relating it to the concentrations of the triphosphates involved in the substitution. The reversions corresponding to TAG leads to GAG, AAG, CAG, TGG, and TCG are calculated to occur with frequencies of 5 X 10(-7), 4 X 10(-7), 4 X 10(-7), approximately 2 X 10(-7), and approximately 5 X 10(-9), respectively, at the concentration of triphosphates found in vivo. The frequencies are in the range found for the reversion of the phage in vivo and so are consistent with errors in nucleotide selection by DNA polymerase (deoxynucleosidetriphosphate:DNA deoxynucleotidyltransferase, EC 2.7.7.7) III being largely responsible for the rate of spontaneous mutation in vivo. The relative frequency of mispairing leading to misincorporation is: purine.purine approximately purine.pyrimidine much greater than pyrimidine.pyrimidine, confirming predictions from model-building studies that transversions arise through purine.purine mismatches.
Submicrometer Intracellular Chemical Optical Fiber Sensors (1992)

A thousandfold miniaturization of immobilized optical fiber sensors, a millionfold or more sample reduction, and at least a hundredfold shorter response time, all simultaneously, were achieved by combining nanofabricated optical fiber tips with near-field photopolymerization. Specifically, pH optical fiber sensors were prepared with internal calibration, making use of the differences in both fluorescence and absorption of the acidic and basic dye species. The submicrometer sensors have excellent detection limits, as well as photostability, reversibility, and millisecond response times. Successful applications include intracellular and intraembryonic measurements. Potential applications include spatially and temporally resolved chemical analysis and kinetics inside single biological cells and their substructures.
Assembly and role of pili in group B streptococci (2006)

Streptococcus agalactiae[group B streptococcus (GBS)] is the leading cause of neonatal pneumonia, sepsis and meningitis. An in silico genome analysis indicated that GBS strain NEM316 encodes five putative sortases, including the major class A sortase enzyme and four class C sortases. The genes encoding the class C sortases are tandemly arranged in two different loci, srtC1-C2 and srtC3-C4, with a similar genetic organization and are thought to be involved in pilus biosynthesis. Each pair of sortase genes is flanked by LPXTG protein encoding genes, two upstream and one downstream, and a divergently transcribed regulatory gene located upstream from this locus. We demonstrated that strain NEM316 expresses only the srtC3-C4 locus, which encodes three surface proteins (Gbs1474, Gbs1477 and Gbs1478) that polymerize to form appendages resembling pili. Structural and functional analysis of this locus revealed that: (i) the transcriptional activator RogB is required for expression of the srtC3-C4 operon; (ii) Gbs1477, and either SrtC3 or SrtC4 are absolutely required for pilus biogenesis; and (iii) GBS NEM316 pili are composed of three surface proteins, Gbs1477, the bona fide pilin which is the major component, Gbs1474, a minor associated component, and Gbs1478, a pilus-associated adhesin. Surprisingly, pilus-like structures can be formed in the absence of the two minor components, i.e. the putative anchor Gbs1474 or the adhesin Gbs1478. Adherence assays showed that Gbs1478 confers adhesive capacity to the pilus. This study provides the first evidence that adhesive pili are also present in Gram-positive pathogens.
Glycolipid-anchored IL-12 expressed on tumor cell surface induces antitumor immune response. (2002)

Systemic or local administration of cytokine has been used as a mode to enhance the antitumor immune response induced by many cancer vaccines. We have investigated whether the expression of cytokines on the tumor cell surface as a glycolipid (GPI)-anchored form will be effective in inducing antitumor immune response using a GPI-anchored interleukin (IL)-12 (GPI-IL-12) as a model. GPI-IL-12-induced the proliferation of concanavalin A-activated T cells and induced IFN-gamma secretion by activated and allogeneic T cells, indicating that the membrane-expressed IL-12 can stimulate T cells. GPI-IL-12 expressed on the tumor cell surface prevented tumor growth in mice in a highly tumorigenic murine mastocytoma model. These results suggest that the cell surface-expressed GPI-IL-12 can be effective in inducing antitumor immune response, and GPI-anchored cytokines expressed on the tumor cell surface may be a novel approach to deliver cytokines at the immunization site during vaccination against cancer. Furthermore, purified GPI-anchored cytokines can be used to quickly modify tumor membranes by the protein transfer method to express the desired cytokines for vaccine development.
Structure-Based Design and Synthesis of Macroheterocyclic Peptidomimetic Inhibitors of the Aspartic Protease β-Site Amyloid Precursor Protein Cleaving Enzyme (BACE) (2006)

Based on the X-ray cocrystal structure of the Tang-Ghosh heptapeptide inhibitor 1 (OM00-3), a series of macroheterocyclic analogues were designed and synthesized. Analogues containing dithia, dioxa, oxathia, and carbathia macrocycles were synthesized by methods relying on ring-closing olefin metathesis for the dioxa analogues and by alkylation of thiolates or bisthiolates for the others. Molecular modeling suggested that the incorporation of piperidine units appended to the macrocycles improved interactions through additional H-bonds and introduced further rigidity. These were synthesized in enantiomerically pure form using enzyme-catalyzed desymmetrization and diastereomer separation. Inhibitory activity on beta-site amyloid precursor protein cleaving enzyme (BACE) was observed with several macroheterocyclic inhibitors and structure-activity relationship (SAR) correlations were deduced. Cocrystal structures of two synthetic analogues revealed interesting and unexpected binding interactions.
Highly Selective End-Tagged Antimicrobial Peptides Derived from PRELP (2011)

Hydrophobic C-terminal end-tagging of the cationic sequence RRPRPRPRP generates highly selective AMPs with potent activity against multiresistant bacteria and efficiency in ex vivo wound infection models. A precise "tuning" of toxicity and proteolytic stability may be achieved by changing tag-length and adding W- or F-amino acid tags.
Galactosylserine in extensin (1973)

Cell walls obtained from tomato suspension cultures were treated at pH1 for 1h at 100 degrees C to remove arabinose oligosaccharide substituents from the hydroxyproline residues of extensin. Tryptic attack of these acid-stripped walls yielded glycopeptides containing galactose. When one of these glycopeptides (designated S(2)A(6); sequence NH(2)-Ser-Hyp-Hyp-Hyp-Hyp-Ser-Hyp-Lys-CO(2)H) was treated with (a) NaOH-NaBH(4) or (b) NaOH-Na(2)SO(3) some of the serine was converted into (a) alanine or (b) cysteic acid, and the peptide lost galactose. Maleylation or 3-carboxypropionylation of N-terminal serine was necessary for conversion of this residue and for complete loss of galactose. These results indicate that a single galactose residue is attached O-glycosidically to each of the two serine residues. Hydrazinolysis of peptide S(2)A(6) or of isolated cell walls also led to destruction of serine. In control experiments non-glycosylated serine was not destroyed during hydrazinolysis. Thus the galactosylserine linkage is sensitive to N(2)H(4).
Antitumor agents. 100. Inhibition of human DNA topoisomerase II by cytotoxic ether and ester derivatives of podophyllotoxin and .alpha.-peltatin (1989)

A principal mechanism of action of the clinical antitumor drugs etoposide (1) and teniposide (2) is the inhibition of catalytic activity of type II DNA topoisomerase and concurrent enzyme-mediated production of lethal DNA strand breaks. Substitution of the glycosidic moiety of 1 or 2 by ester and ethers, as well as the esterification and etherification of alpha-peltatin (4) including its glucosidic ethylidene and thenylidene cyclic acetals (25 and 26), has afforded compounds of much less activity than that of 1. The in vitro cytotoxicity (KB) appears to have no correlation with the inhibitory activity of the human DNA topoisomerase II.
Allelotyping of ductal carcinoma in situ of the breast: deletion of loci on 8p, 13q, 16q, 17p and 17q. (1995)

In order to determine which tumor suppressor loci are involved in preinvasive breast cancer, we have assayed for loss of heterozygosity (LOH) in ductal carcinoma in situ (DCIS). Areas of DCIS were microdissected from archival paraffin-embedded tissue. DNA was extracted, and LOH was determined by PCR of microsatellite markers that map to 39 autosomal arms. Either uninvolved lymph node or white cell DNA was used as normal control. A total of 61 samples of DCIS were assayed. The average number of informative tumors examined for each marker was 19 (range, 8-48). The median fractional allelic loss was 0.037. The highest percentage of LOH was shown for loci on 8p (18.7%), 13q (18%), 16q (28.6%), 17p (37.5%), and 17q (15.9%). LOH on 18q was found in 10.7% of informative tumors. Fractional allelic loss was associated with LOH on 17p, with high nuclear grade and with the comedo subtype of DCIS. LOH on 17p correlated with LOH on 17q and on 13q. Additional markers were used for 16q and 17p to determine the smallest common region of deletion. These data provide evidence that tumor suppressor loci that map to these regions are involved in the oncogenesis of breast cancer before progression to the invasive phenotype. Our findings provide additional support that multiple loci on 17p and 16q are involved in the development of breast cancer.
Inhibition of Class I Phosphoinositide 3-Kinase Activity Impairs Proliferation and Triggers Apoptosis in Acute Promyelocytic Leukemia without Affecting Atra-Induced Differentiation (2009)

We have investigated the role of phosphoinositide 3-kinases (PI3Ks) in the in vitro pathophysiology of acute promyelocytic leukemia (APL) and in the response to treatment with all-trans-retinoic-acid (ATRA), utilizing a range of novel inhibitors that target individual or all catalytic class I isoforms of PI3K (p110alpha, p110beta, p110delta, and p110gamma). ATRA-induced phosphorylation of the Akt kinase and ribosomal S6 protein in APL cells was sensitive to class I PI3K, and p110beta or p110delta inhibitors, and to the mammalian target of rapamycin (mTOR) inhibitor rapamycin. In primary APL, inhibition of p110beta or p110delta triggered apoptosis in the absence or presence of ATRA. Class I PI3K inhibition could also reverse ATRA-induced protection of these cells against doxorubicin and arsenic trioxide, correlating with impaired induction of the antiapoptotic MCL-1 protein. The differentiation-inducing effects of ATRA were not dependent on class I PI3K/mTOR. In summary, class I PI3K signaling, mediated by p110beta and p110delta, plays an important role in basal and ATRA-induced cell survival mechanisms in APL. Addition of PI3K inhibitors to induction treatment regimens may provide therapeutic benefit.
Enrichment of large-diameter semiconducting SWCNTs by polyfluorene extraction for high network density thin film transistors (2014)

A systematic study on the use of 9,9-dialkylfluorene homopolymers (PFs) for large-diameter semiconducting (sc-) single-walled carbon nanotube (SWCNT) enrichment is the focus of this report. The enrichment is based on a simple three-step extraction process: (1) dispersion of as-produced SWCNTs in a PF solution; (2) centrifugation at a low speed to separate the enriched sc-tubes; (3) filtration to collect the enriched sc-SWCNTs and remove excess polymer. The effect of the extraction conditions on the purity and yield including molecular weight and alkyl side-chain length of the polymers, SWCNT concentration, and polymer/SWCNT ratio have been examined. It was observed that PFs with alkyl chain lengths of C10, C12, C14, and C18, all have an excellent capability to enrich laser-ablation sc-SWCNTs when their molecular weight is larger than ∼10 000 Da. More detailed studies were therefore carried out with the C12 polymer, poly(9,9-di-n-dodecylfluorene), PFDD. It was found that a high polymer/SWCNT ratio leads to an enhanced yield but a reduced sc-purity. A ratio of 0.5-1.0 gives an excellent sc-purity and a yield of 5-10% in a single extraction as assessed by UV-vis-NIR absorption spectra. The yield can also be promoted by multiple extractions while maintaining high sc-purity. Mechanistic experiments involving time-lapse dispersion studies reveal that m-SWCNTs have a lower propensity to be dispersed, yielding a sc-SWCNT enriched material in the supernatant. Dispersion stability studies with partially enriched sc-SWCNT material further reveal that m-SWCNTs : PFDD complexes will re-aggregate faster than sc-SWCNTs : PFDD complexes, providing further sc-SWCNT enrichment. This result confirms that the enrichment was due to the much tighter bundles in raw materials and the more rapid bundling in dispersion of the m-SWCNTs. The sc-purity is also confirmed by Raman spectroscopy and photoluminescence excitation (PLE) mapping. The latter shows that the enriched sc-SWCNT sample has a narrow chirality and diameter distribution dominated by the (10,9) species with d = 1.29 nm. The enriched sc-SWCNTs allow a simple drop-casting method to form a dense nanotube network on SiO2/Si substrates, leading to thin film transistors (TFTs) with an average mobility of 27 cm(2) V(-1) s(-1) and an average on/off current ratio of 1.8 × 10(6) when considering all 25 devices having 25 μm channel length prepared on a single chip. The results presented herein demonstrate how an easily scalable technique provides large-diameter sc-SWCNTs with high purity, further enabling the best TFT performance reported to date for conjugated polymer enriched sc-SWCNTs.
Analysis of human hematopoietic stem cell populations. (1994)

Purification of human hematopoietic stem cells (HSC) may be useful clinically for preparation of tumor-free grafts to be used for autologous transplantation and as targets for gene therapy. To analyze the phenotype of the human HSC, assays were used that measure the unique properties of stem cells, i.e., their long-term repopulating ability and their multilineage potential. These assays include: (1) an in vitro long-term hematopoietic culture system, using the murine bone marrow stromal cell line SyS1, which supports both B lymphopoiesis and myelopoiesis; (2) fetal human bone grafts implanted in SCID-hu mice, in which maintenance of CD34+ cells and B and myeloid differentiative capacity of candidate stem cell populations may be measured; (3) fetal human thymus grafts in SCID-hu mice, which allow the analysis of in vivo T-cell potential of a candidate stem cell population. Stem cells in adult bone marrow (ABM) or cytokine-mobilized peripheral blood (MPB) are thought to express CD34 but lack expression of markers indicating lineage commitment. This CD34+ Lineage- (Lin-) subpopulation has been isolated by fluorescence-activated cell sorting and tested for activity in the assays described here. CD34+ Lin- cells from both ABM and MPB demonstrated long-term engraftment in the SCID-hu bone model. This CD34+ Lin- population can be subfractionated further using an antibody to Thy-1. The Thy-1+ subset of CD34+Lin- cells is enriched for both long-term culture-initiating cells (LTC-1C) and has the ability to engraft in vivo.
Female sexual dysfunction: anatomy, physiology, evaluation and treatment options (1999)

It has been estimated that up to 76% of women, depending upon their age, have complaints of sexual dysfunction, including decreased libido, vaginal dryness, pain with intercourse, decreased genital sensation and difficulty or inability to achieve orgasm. Female sexual dysfunction is a significant problem that affects the quality of life of many women. This review addresses the etiologies and incidence of female sexual complaints, as well as new findings in the evaluation and treatment of female sexual dysfunction.