gebhart/patrepeval huggingface dataset:
Structural and Dynamic Aspects of Non-Intercalative (1:1) Binding of a Thiazole-Lexitropsin to the Decadeoxyribonucleotide d-[CGCAATTGCG] 2 : An 1 H-NMR and Molecular Modeling Study (1991)

The location, orientation and dynamics of a thiazole-containing analogue of distamycin 1 bound to the decadeoxyribonucleotide d-[CGCAATTGCG]2 have been studied by non-exchangable and imino proton NMR resonances of the 1:1 complex. Using NOE difference, COSY and NOESY experiments, lexitropsin (1) was located in the minor groove of DNA at 5'-CAAT sequence. This was concluded by an intermolecular NOE between the ligand and a minor groove A4H2 proton. The NOE cross-correlations in the NOESY map confirmed that the DNA decamer duplex in the 1:1 complex remains in a right-handed B-conformation similar to that in the free decamer. Experiments on non-exchangeable and exchangeable proton NMR resonances placed the N-formylamino terminus of drug 1 on the 5'-C3 nucleotide, while the rest of the molecule extends onto the 5'-AAT sequence. The structural evidence for sequence preferential binding at 5'CAAT rather than 5'AATT suggests this reflects an attempt on the part of the sterically demanding inward directed sulfur of the thiazole to minimize compression by moving part of the molecule to the somewhat wider CG base site. The lack of evidence for a 2:1 drug:DNA complex, in contrast to distamycin, is in accord with this interpretation. The lexitropsin 1 was found to be in an exchange between the equivalent 5'-CAAT sites at a rate of approximately 35S-1 with a delta G degree of 65 +/- 5 kJ mol-1 at 303 K. The experimental data suggests a slide-swing mechanism for this exchange process.
Physical Map and Organization of Arabidopsis thaliana Chromosome 4 (1995)

A physical map of Arabidopsis thaliana chromosome 4 was constructed in yeast artificial chromosome clones and used to analyze the organization of the chromosome. Mapping of the nucleolar organizing region and the centromere integrated the physical and cytogenetic maps. Detailed comparison of physical with genetic distances showed that the frequency of recombination varied substantially, with relative hot and cold spots occurring along the whole chromosome. Eight repeated DNA sequence families were found in a complex arrangement across the centromeric region and nowhere else on the chromosome.
Analysis of the function of two circadian‐regulated CONSTANS‐LIKE genes (2001)

The Arabidopsis genes CONSTANS-LIKE 1 (COL1) and CONSTANS-LIKE 2 (COL2) are predicted to encode zinc finger proteins with approximately 67% amino acid identity to the protein encoded by the flowering-time gene CONSTANS (CO). We show that the circadian clock regulates expression of COL1 and COL2 with a peak in transcript levels around dawn. We analyzed transgenic plants misexpressing COL1, COL2 and CO. Unlike CO, altered expression of COL1 and COL2 in transgenic plants had little effect on flowering time. However, analysis of circadian phenotypes in the transgenic plants showed that over-expression of COL1 can shorten the period of two distinct circadian rhythms. Experiments with the highest COL1 over-expressing line indicate that its circadian defects are fluence rate-dependent, suggesting an effect on a light input pathway(s).
CELLULAR MECHANISMS OF TASTE TRANSDUCTION (1999)

Taste receptor cells respond to gustatory stimuli using a complex arrangement of receptor molecules, signaling cascades, and ion channels. When stimulated, these cells produce action potentials that result in the release of neurotransmitter onto an afferent nerve fiber that in turn relays the identity and intensity of the gustatory stimuli to the brain. A variety of mechanisms are used in transducing the four primary tastes. Direct interaction of the stimuli with ion channels appears to be of particular importance in transducing stimuli reported as salty or sour, whereas the second messenger systems cyclic AMP and inositol trisphosphate are important in transducing bitter and sweet stimuli. In addition to the four basic tastes, specific mechanisms exist for the amino acid glutamate, which is sometimes termed the fifth primary taste, and for fatty acids, a so-called nonconventional taste stimulus. The emerging picture is that not only do individual taste qualities use more than one mechanism, but multiple pathways are available for individual tastants as well.
Oxidation of Self-Assembled Monolayers by UV Light with a Wavelength of 254 nm (2001)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTOxidation of Self-Assembled Monolayers by UV Light with a Wavelength of 254 nmNicholas J. Brewer, Rachel E. Rawsterne, Sherry Kothari, and Graham J. LeggettView Author Information Department of Chemistry and Materials Science Centre University of Manchester Institute of Science and Technology PO Box 88, Manchester M60 1QD, UK Cite this: J. Am. Chem. Soc. 2001, 123, 17, 4089–4090Publication Date (Web):April 5, 2001Publication History Received4 January 2001Published online5 April 2001Published inissue 1 May 2001https://doi.org/10.1021/ja0155074Copyright © 2001 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views1131Altmetric-Citations103LEARN 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 InReddit Read OnlinePDF (71 KB) Get e-AlertsSUBJECTS:Electromagnetic radiation,Gold,Oxidation,Photooxidation,Silver Get e-Alerts
A vertically integrated bipolar storage cell in 6H silicon carbide for nonvolatile memory applications (1994)

A vertically integrated one transistor memory cell, in which an n-p-n bipolar access transistor is merged with a p-n-p storage capacitor, based on the wide-bandgap semiconductor silicon carbide (SiC), results in a greatly reduced thermal generation rate. Extrapolation of charge recovery data obtained at elevated temperatures suggests a room temperature recovery time of over 10/sup 6/ years.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
EVIDENCE THAT CYCLOSPORINE TREATMENT DURING PREGNANCY PREDISPOSES OFFSPRING TO DEVELOP AUTOANTIBODIES (1991)

Cyclosporine was administered (11 mg/kg/day) to pregnant mice to study the effects of passively transferred CsA on the developing immune system. Placental transfer of CsA was shown by the detection of fetal-tissue levels ranging from 400 to 1500 ng CsA/g tissue. Treatment clearly altered the developing immune system. Thymuses from the day-18 embryos exposed to CsA were partially depleted of CD4+CD8- single positive cells. Eleven of 50 offspring born to CsA-treated mothers developed significant levels of IgG autoantibodies to gastric antigens. In addition, two animals that received CsA in utero developed an extensive mononuclear cell infiltrate in the gastric mucosa resembling autoimmune gastritis. These results raise the possibility that the administration of CsA during pregnancy may result in potential long-term effects on the developing immune system. Offspring of such pregnancies may suffer an increased incidence or severity of autoimmune diseases.
Y-Ba-Cu-O/Nb Tunnel Type Josephson Junctions (1987)

Y-Ba-Cu-O/Au/AlO x /Nb tunnel type Josephson junctions were fabricated and their current-voltage relation exhibited typical characteristics of Josephson tunnel junctions such as supercurrent, hysteresis and rf-induced voltage steps at 4.2 K.
Luminal and basal subtyping of prostate cancer. (2017)

3 Background: There is a clear need to develop a clinically relevant molecular subtyping approach for prostate cancer. We hypothesized that prostate cancer can be subtyped based on luminal versus basal lineage. Methods: We applied the PAM50 classifier, which is used clinically to identify luminal and basal cancers in breast cancer, to subtype a total of 3,782 prostate cancer samples using a high-density microarray platform run in a CLIA-certified laboratory. We examined the associations of these subtypes and clinical outcomes. Results: We demonstrate that PAM50 segregates prostate cancer into three reproducible subtypes in both retrospective cohorts and on prospective validation: luminal A (33.3%-34.3%), luminal B (28.5%-32.6%), and basal (34.1%-37.1%). Luminal B prostate cancers exhibited the worst clinical prognoses, followed by basal and luminal A subtypes (10-year biochemical recurrence-free survival: 29/39/41%; distant metastasis-free survival: 53/73/73%; prostate cancer-specific survival: 78/86/89%; overall survival: 69/80/82% respectively) on both univariable and multivariable analyses accounting for standard clinicopathologic prognostic factors. Known luminal lineage markers, such as NKX3.1 and KRT18, and the basal lineage CD49f signature, were enriched in luminal- and basal-like cancers respectively, demonstrating the connection between these subtypes and established prostate cancer biology. While both luminal-like subtypes were associated with increased AR expression and signaling, only luminal B prostate cancers were significantly associated with post-operative response to androgen deprivation therapy (ADT) in a subset analysis matching patients based on clinicopathologic variables (interaction p = 0.006, luminal B 10-year metastasis: 33% (treated) vs. 55% (untreated), non-luminal B: 37% (treated) vs. 21% (untreated)). Conclusions: These findings contribute novel insight into the biology of prostate cancer, and provide translatable clinical tools for personalizing post-operative ADT for patients with prostate cancer. Similar to breast cancer, these findings suggest that luminal/basal subtyping may be useful in treatment selection in prostate cancer.
Interleukin-31 and Oncostatin-M Mediate Distinct Signaling Reactions and Response Patterns in Lung Epithelial Cells (2006)

Lung epithelial cells are primary targets of oncostatin M (OSM) and, to a lower degree, of interleukin (IL)-6 and IL-31, all members of the IL-6 cytokine family. The OSM receptor (OSMR) signals through activation of STAT and mitogen-activated protein kinase pathways to induce genes encoding differentiated cell functions, reduce cell-cell interaction, and suppress cell proliferation. IL-31 functions through the heteromeric IL-31 receptor, which shares with OSMR the OSMRbeta subunit, but does not engage gp130, the common subunit of all other IL-6 cytokine receptors. Because the response of epithelial cells to IL-31 is unknown, the action of IL-31 was characterized in the human alveolar epithelial cell line A549 in which the expression of the ligand-binding IL-31Ralpha subunit was increased. IL-31 initiated signaling that differed from other IL-6 cytokines by the particularly strong recruitment of the STAT3, ERK, JNK, and Akt pathways. IL-31 was highly effective in suppressing proliferation by altering expression of cell cycle proteins, including up-regulation of p27(Kip1) and down-regulation of cyclin B1, CDC2, CDK6, MCM4, and retinoblastoma. A single STAT3 recruitment site (Tyr-721) in the cytoplasmic domain of IL-31Ralpha exerts a dominant function in the entire receptor complex and is critical for gene induction, morphological changes, and growth inhibition. The data suggest that inflammatory and immune reactions involving activated T-cells regulate functions of epithelial cells by IL-6 cytokines through receptor-defined signaling reactions.
Effects of intrauterine inflammation on developing rat brain (2002)

Damage to the white matter in the brain during development can lead to cerebral palsy (CP), a heterogeneous group of clinical syndromes that results in life-long disorders of movement and posture. Periventricular leukomalacia (PVL) is a pathological process within the white matter characterized by oligodendrocyte loss and is associated with the development of CP. Clinically, CP and PVL are associated with intrauterine infection and inflammation, but mechanisms involved are not well understood. We developed a model of intrauterine inflammation in Lewis and Fischer 344 rats to study the effects of intrauterine inflammation on developing glia. Pregnant rats were intracervically injected with lipopolysaccharide (LPS) at 15 days of gestation (E15) and a dose of LPS that caused low fetal mortality was determined. At E20, treated fetuses had increased TUNEL(+) nuclei and tumor necrosis factor (TNF)-alpha-immunoreactive areas within the brains. In a second series of animals allowed to survive until postnatal day 21 (PND 21), immunostaining was performed against several glial markers. Staining for the oligodendrocyte-specific proteins 2', 3'-cyclic nucleotide phosphodiesterase (CNP) and myelin proteolipid protein (PLP) was decreased in treated pups compared to shams within the corpus callosum, a white matter structure used as a representative area of developing white matter. Treated pups had activated astrocytes lining cerebral blood vessels, as observed by glial fibrillary acidic protein (GFAP) staining, while sham pups did not. Activated microglia were not detected using OX42 as a cell marker. Our model of intrauterine inflammation causes increased TUNEL and TNF-alpha staining early after injury, suggesting increased apoptotic cell death, possibly by cytokine-related mechanisms.
Dextran enhances calcium-induced aggregation of phosphatidylserine liposomes: possible implications for exocytosis. (1999)

We have studied the calcium-induced aggregation of phosphatidylserine liposomes in the presence of various concentration of a high-molecular water-soluble polysaccharide dextran. It has been shown that threshold concentrations of calcium necessary to induce liposome aggregation in the presence of approximately 1 mM concentration of dextran is about one order lower than in the absence of dextran. Soluble intracellular polymers may thus play an important role in the process of exocytosis.
Stroma-supported immunocytometric assay (SIA): a novel method for testing the sensitivity of acute lymphoblastic leukemia cells to cytotoxic drugs. (1993)

The accuracy of drug-sensitivity assays for neoplastic cells depends on the ability to sustain cell survival in vitro, but cells in most cases of acute lymphoblastic leukemia (ALL) rapidly die by apoptosis in culture. We recently reported that allogeneic bone marrow stromal layers support long-term culture of ALL cells. We now describe the standardization of a novel drug-sensitivity assay for ALL lymphoblasts maintained on stromal layers, in which the viability of treated and untreated cells is compared using flow cytometry. Cultures were performed in U-bottomed 96-well plates: 2 x 10(4) stromal cells per well produced rapidly confluent layers which supported the survival of ALL blasts. In four ALL cases studied, 68.8-106% (median 94.8%) of the lymphoblasts originally seeded were recovered after 7 days of culture, in contrast to < 5% recovered in the absence of stroma. Sensitivity to five antileukemic drugs was tested at the indicated concentrations: vincristine (0.001-1 microgram/ml); dexamethasone (0.001-100 microM); 6-thioguanine (0.078-20 micrograms/ml); teniposide (0.001-10 microM); cytosine arabinoside (0.039-10 microM). After 4 days of culture, cells were labeled with CD19 monoclonal antibody and analyzed by flow cytometry. The concentration of each antileukemic agent producing 50% cytotoxicity (LC50) was determined for each patient by fitting a sigmoid model to the drug concentrations versus percentage viability data. Clinically relevant drug concentrations produced cytotoxic effects, and ALL blast sensitivity varied considerably among patients. We conclude that this is an informative method of systematically evaluating drug sensitivity in ALL patients.
Membrane-bound Secreted Forms of Human Asialoglycoprotein Receptor Subunits (1996)

The H2a alternatively spliced variant of the human asialoglycoprotein receptor H2 subunit differs from the H2b variant by an extra pentapeptide, EGHRG, present in the ectodomain next to the membrane-span. This difference causes retention and degradation in the endoplasmic reticulum (ER) of H2a when expressed without the H1 subunit in 3T3 cells. In contrast, a significant portion of singly expressed H2b is Golgi-processed and reaches the cell surface. Using a new specific anti-H2a antibody, we found that in HepG2 cells, H2a is rapidly cleaved to a 35-kDa fragment, comprising the entire ectodomain, most of which is secreted into the medium. The cleavage site for the secreted fragment was located at the lumenal end of the membrane span. No membrane-bound H2a exits the ER, indicating that the pentapeptide is a signal for ER retention and degradation of the membrane form but does not hinder secretion of the cleaved soluble form. H2a does not form a membrane receptor complex with H1 as H2b does. H2a is therefore not a subunit of the receptor but a precursor for a secreted form of the protein; signal peptidase is probably responsible for the cleavage to the soluble fragment. Therefore, the juxtamembrane sequence regulates the function of the transmembrane domain of a type II membrane protein as either a signal-anchor sequence (H2b) or as a cleaved signal sequence, which generates a secreted product (H2a).
Comparing sub-survival functions in a competing risks model. (2000)

In the competing risks literature, one usually compares whether two risks are equal or whether one is "more serious." In this paper, we propose tests for the equality of two competing risks against an ordered alternative specified by their sub-survival functions. These tests are naturally developed as extensions of those based on hazard rates and cumulative incidence functions. We note that the interpretation of the new test results is more direct compared to the situation when the hypotheses are framed in terms of their cumulative incidence functions. The proposed tests are of the Kolmogrov-Smirnov type, based on maximum differences between sub-survival functions. Our simulation studies indicate that they are excellent competitors of the existing tests, that are based mainly on differences between cumulative incidence functions. A numerical example will demonstrate the advantages of the proposed tests.
Rapid estimation of camera motion from compressed video with application to video annotation (2000)

As digital video becomes more pervasive, efficient ways of searching and annotating video according to content will be increasingly important. Such tasks arise, for example, in the management of digital video libraries for content-based retrieval and browsing. We develop tools based on camera motion for analyzing and annotating a class of structured video using the low-level information available directly from MPEG-compressed video. In particular, we show that in certain structured settings, it is possible to obtain reliable estimates of camera motion by directly processing data easily obtained from the MPEG format. Working directly with the compressed video greatly reduces the processing time and enhances storage efficiency. As an illustration of this idea, we have developed a simple basketball annotation system which combines the low-level information extracted from an MPEG stream with the prior knowledge of basketball structure to provide high-level content analysis, annotation, and browsing for events such as wide-angle and close-up views, fast breaks, probable shots at the basket, etc. The methods used in this example should also be useful in the analysis of high-level content of structured video in other domains.
Inhibition of Tumor Growth by Direct Intratumoral Gene Transfer of Herpes Simplex Virus Thymidine Kinase Gene with DNA–Liposome Complexes (1996)

To establish the expression of the herpes simplex virus thymidine kinase (HSV-TK) gene in tumor cells, we analyzed the promoter function of the SV40 promoter and the nucleotide sequence (CACGTG) to which Myc-Max heterodimers (Myc/Max) were capable of binding in four kinds of cell lines: COLO320 DM, A-431, KF, and Nakajima. When luciferase reporter plasmid under the control of SV40 promoter was transfected into tumor cells in vitro, a high level of luciferase activity was observed in all kinds of cell lines. However, by transfection of the luciferase gene promoted by the Myc/Max binding sequence, accelerated luciferase expression was observed in COLO320 DM and A-431 cells with high expression of c-myc, but not in KF and Nakajima cells, which showed low expression of c-myc. The repeated transfection of the liposome-conjugated HSV-TK gene regulated by the SV40 promoter and cultivation in 100 micrograms/ml of aciclovir for 5 days in vitro demonstrated growth inhibition for all four kinds of cell lines. However, cell toxicity was observed only in COLO320 DM and A-431 cells when the HSV-TK gene promoted by the Myc/Max binding sequence was introduced. (The survival rate to 100 micrograms/ml of aciclovir concentration in COLO320 DM, A-431, KF, and Nakajima cells was 59%, 53%, 74%, and 79%, respectively.) In vivo direct injection of the liposome-conjugated HSV-TK gene regulated by the SV40 promoter into established tumors and aciclovir administration for 10 days into the mice resulted in significant tumor volume reduction in three tested tumor cells. However, injection of the HSV-TK gene promoted by the Myc/Max binding sequence and aciclovir administration into mice could achieve significant tumor regression only in COLO320 DM and A-431 cells. These results suggest that gene therapy using the HSV-TK gene promoted by the Myc/Max binding sequence can be an attractive approach for treatment against tumor cells expressing high levels of c-myc.
Co-expression of the Hepatitis B Surface and Core Antigens Using Baculovirus Multiple Expression Vectors (1988)

The hepatitis B (HB) virus DNA sequences coding for the pre-core (preC) or C antigens (HBpcAg, HBcAg) have been inserted into the baculovirus plasmid transfer vector, pAcYM1, such that the HB viral sequences are under the control of the polyhedrin promoter of Autographa californica nuclear polyhedrosis virus (AcNPV). Spodoptera frugiperda cells infected with either of the derived recombinant plasmids in the presence of infectious AcNPV DNA yielded recombinant, polyhedrin-negative viruses that expressed high levels of the respective HBpcAg or HBcAg (representing approx. 5 to 10% and approx. 40% of the stained cellular proteins, respectively). The particulate 27 nm HBcAgs have been purified to homogeneity from infected cell extracts by density gradient centrifugation. Dual expression transfer vectors containing the HBcAg gene sequences and the coding sequences of the HB viral S antigen (HBsAg), each gene under the control of its own copy of the polyhedrin promoter, have also been constructed and used to derive recombinant viruses. The recombinant with the HB C and S genes expressed high levels of the HBcAg (approx. 40% of the cellular proteins) and low levels of the HBsAg (approx. 2% of the stained cellular proteins). Dual expression, occluded, recombinant baculoviruses that make HBsAg, as well as the AcNPV polyhedrin protein, have been prepared that are highly infectious for Trichoplusia ni caterpillars, allowing reproducible preparation of the antigen in larvae. Using radioimmunoassays (RIAs) and ELISAs, the recombinant HBcAg (RIA) and HBsAg (ELISA) have been used to identify human antibodies to HB virus with results that compare favourably with the data obtained with non-recombinant antigens.