gebhart/patrepeval huggingface dataset:
Aberrant methylation during cervical carcinogenesis. (2001)

We studied the pattern of aberrant methylation during the multistage pathogenesis of cervical cancers. We analyzed a total of 73 patient samples and 10 cervical cancer cell lines. In addition, tissue samples [peripheral blood lymphocytes (n = 10) and buccal epithelial cells (n = 12)] were obtained from 22 healthy volunteers. On the basis of the results of preliminary analysis, the cervical samples were grouped into three categories: (a) nondysplasia/low-grade cervical intraepithelial neoplasia (CIN; n = 37); (b) high-grade CIN (n = 17); and (c) invasive cancer (n = 19). The methylation status of six genes was determined (p16, RARbeta, FHIT, GSTP1, MGMT, and hMLH1). Our main findings are as follows: (a) methylation was completely absent in control tissues; (b) the frequencies of methylation for all of the genes except hMLH1 were >20% in cervical cancers; (c) aberrant methylation commenced early during multistage pathogenesis and methylation of at least one gene was noted in 30% of the nondysplasia/low-grade CIN group; (d) an increasing trend for methylation was seen with increasing pathological change; (e) methylation of RARbeta and GSTP1 were early events, p16 and MGMT methylation were intermediate events, and FHIT methylation was a late, tumor-associated event; and (f) methylation occurred independently of other risk factors including papillomavirus infection, smoking history, or hormone use. Although our findings need to be extended to a larger series, they suggest that the pattern of aberrant methylation in women with or without dysplasia may help identify subgroups at increased risk for histological progression or cancer development.
Sequence requirements of Escherichia coli attTn7, a specific site of transposon Tn7 insertion (1988)

Transposon Tn7 transposes at high frequency to a specific site, attTn7, in the Escherichia coli chromosome. We devised a quantitative assay for Tn7 transposition in which Tn7-end derivatives containing the cis-acting transposition sequences of Tn7 transpose from a bacteriophage lambda vector upon infection into cells containing the Tn7-encoded transposition proteins. We used this assay to identify a 68-base-pair DNA segment containing the sequences essential for attTn7 target activity. This segment is positioned asymmetrically with respect to the specific point of Tn7 insertion in attTn7 and lacks obvious homology to the sequences at the ends of Tn7 which participate directly in transposition. We also show that some sequences essential for attTn7 target activity are contained within the protein-coding sequence of a bacterial gene.
Multiple sclerosis: gadolinium enhancement in MR imaging. (1986)

Magnetic resonance (MR) images--both nonenhanced and enhanced with gadolinium DTPA/dimeglumine (Gd)--were compared with high-iodine (88.1 g I) computed tomographic (HICT) scans in demonstrating lesions in 15 patients known to have multiple sclerosis (MS). T1-weighted, mixed (T1, proton density, and T2), and T2-weighted MR pulse sequences were used. More than 20 lesions in each of 14 patients were demonstrated by pre-Gd mixed images and T2WI. Nine patients had clinical symptoms of active disease. Gd-enhanced T1WI showed at least one lesion that appeared to correspond with newly reported symptoms or signs. In addition, three clinically stable patients showed enhancement. Enhancement was best seen on 3-minute T1WI. HICT scans showed enhancement in four of the nine patients with active disease and in none of five clinically stable patients. Gd-enhanced MR imaging appears to be more sensitive than HICT in the detection of the transient abnormalities of the blood-brain barrier that occur in patients with active MS and appears capable of distinguishing active lesions that may correspond to the anatomic regions responsible for abnormal clinical findings.
Initiation of glycogen synthesis. Control of glycogenin by glycogen phosphorylase. (1993)

Glycogen biosynthesis involves a specific initiation event, mediated by a specialized protein, glycogenin. Glycogenin undergoes self-glucosylation to generate an oligosaccharide primer, which, when long enough, supports the action of glycogen synthase to elongate the polysaccharide chain, leading ultimately to the formation of glycogen. We report that primed glycogenin is also a substrate for glycogen phosphorylase. Phosphorylase removed glucose from the oligosaccharide attached to glycogenin in a phosphorolysis reaction that required phosphate and produced glucose 1-phosphate. The phosphorylated form, phosphorylase a, was much more effective than the dephosphorylated phosphorylase b. However, in the presence of the allosteric effector AMP, phosphorylase b also catalyzed the phosphorolysis reaction. Glucose, an allosteric inhibitor of phosphorylase, inhibited the reaction. Glycogen, but not a short oligosaccharide (maltopentaose), also inhibited the reaction. Treatment of fully primed glycogenin with phosphorylase converted the glycogenin to a form with slightly lower apparent molecular weight, which was less effective as a substrate for glycogen synthase. These results suggest a novel role for phosphorylase in the control of glycogen biosynthesis. We propose that the glucosylation level of glycogenin would be determined by the balance between the self-glucosylation reaction and the opposing action of phosphorylase. The level of glucosylation would in turn determine whether or not glycogenin was an effective primer for glycogen synthase. In this way, several known controls of phosphorylase activity, such as epinephrine, glucagon, and insulin, could influence not only the elongation/degradation stage of glycogen metabolism but also its initiation.
Osmotic Blood-Brain Barrier Modification: Monoclonal Antibody, Albumin, and Methotrexate Delivery to Cerebrospinal Fluid and Brain (1985)

In the dog, osmotic opening of the blood-brain barrier (BBB) in the posterior circulation via the vertebral artery and in the anterior circulation via the internal carotid artery was utilized to increase the delivery of three substances of varying molecular weight to the central nervous system. The cerebrospinal fluid (CSF) concentration of all three agents dramatically increased after BBB opening. In contrast to methotrexate, Evans blue-albumin and monoclonal antibody (MAb) concentrations in CSF were 6-fold greater when given after posterior rather than anterior circulation BBB opening. Conversely, MAb delivery to brain parenchyma was optimized after osmotic BBB modification via the carotid artery. This suggests that, with higher molecular weight substances, osmotic barrier opening has a differential effect on the blood-brain vs. blood-CSF barriers.
Brillouin Lasing with aCaF2Whispering Gallery Mode Resonator (2009)

Stimulated Brillouin scattering with both pump and Stokes beams in resonance with whispering gallery modes of an ultrahigh Q calcium fluoride resonator is demonstrated for the first time. The resonator is pumped with 1064 nm light and has 3 muW Brillouin lasing threshold. The scattering is observed due to the unique morphology of the resonator reducing the phase mismatch between the optical modes and the hypersound wave.
The effect of nanoparticles on the thermal conductivity of crystalline thin films at low temperatures (2008)

This study is concerned with the prediction of the effective thermal conductivity of nanocomposite thin films consisting of nanoparticles randomly distributed in a solid matrix. Crystalline sodium chloride with embedded monodisperse silver nanoparticles is investigated as a case study for thin films where phonons are the main heat carriers. To the best of our knowledge, the equation for phonon radiative transfer is solved for the first time, with an exact scattering transport cross section of the nanoparticles as a function of frequency which was obtained from the literature. The one-dimensional equation for phonon radiative transfer based on the isotropic scaling approximation is solved on a spectral basis using the discrete ordinates method to predict the temperature profile and the heat flux across the nanocomposite thin films. The thermal conductivity is retrieved at temperatures where the effects of Umklapp and normal processes can be neglected and scattering by the particles on phonon transport dominates. The method of solution and closure laws were validated with experimental data of thermal conductivity for bulk samples at 2.53, 5.94, and 10.56 K. The effects of the film thickness (1 μm to 2.5 cm), nanoparticle diameter (5 to 100 nm) and volume fraction (0.0001 to 0.2) on the thermal conductivity of the nanocomposite thin film are investigated. The results indicate that the thermal conductivity decreases with decreasing particle radius as well as with increasing particle concentration. Finally, a dimensional analysis revealed a power-law relationship between the dimensionless thermal conductivity and a dimensionless length of the order of the acoustic thickness of the medium. These results can be used to design nanocomposite thin films for various low-temperature thermal applications by choosing optimal nanoparticle radius and volume fraction, and film thickness.
Ordered structure in blends of block copolymers. 1. Miscibility criterion for lamellar block copolymers (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTOrdered structure in blends of block copolymers. 1. Miscibility criterion for lamellar block copolymersTakeji Hashimoto, Komei Yamasaki, Satoshi Koizumi, and Hirokazu HasegawaCite this: Macromolecules 1993, 26, 11, 2895–2904Publication Date (Print):May 1, 1993Publication History Published online1 May 2002Published inissue 1 May 1993https://pubs.acs.org/doi/10.1021/ma00063a039https://doi.org/10.1021/ma00063a039research-articleACS PublicationsRequest reuse permissionsArticle Views1056Altmetric-Citations145LEARN 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
Oligonucleotide-Directed Nucleic Acid Scission by Micrococcal Nuclease (1994)

"Sequence-dictated" scission of DNA can be achieved by tethering a fusion protein composed of glutathione S-transferase and attenuated micrococcal nuclease (MN) to a targeting oligonucleotide using Cibacron blue (CB) F3G-A. Deoxyoligonucleotides derivatized with this dye bind to the fusion protein in gel mobility shift assays. This binding scheme was successfully used to achieve site-specific scission of a single-stranded DNA substrate after hybridization with a CB-derivatized complementary oligonucleotide. Although covalently cross-linked hybrids of MN and oligonucleotides have been successfully used in the past to target nucleolytic activity, this novel scheme opens new possibilities for targeting and probing both DNA and RNA sequences by allowing the addition of the nuclease subsequent to hybridization.
IntentNet: Learning to Predict Intention from Raw Sensor Data (2021)

In order to plan a safe maneuver, self-driving vehicles need to understand the intent of other traffic participants. We define intent as a combination of discrete high-level behaviors as well as continuous trajectories describing future motion. In this paper, we develop a one-stage detector and forecaster that exploits both 3D point clouds produced by a LiDAR sensor as well as dynamic maps of the environment. Our multi-task model achieves better accuracy than the respective separate modules while saving computation, which is critical to reducing reaction time in self-driving applications.
Distributed source coding using syndromes (DISCUS): design and construction (1999)

We address the problem of distributed source coding, i.e. compression of correlated sources that are not co-located and/or cannot communicate with each other to minimize their joint description cost. In this work we tackle the related problem of compressing a source that is correlated with another source which is available only at the decoder. In contrast to prior information-theoretic approaches, we introduce a new construction and practical framework for tackling the problem based on the judicious incorporation of channel coding principles into this source coding problem. We dub our approach as distributed source coding using syndromes (DISCUS). We focus in this paper on trellis-structured constructions of the framework to illustrate its utility. Simulation results confirm the power of DISCUS, opening up a new and exciting constructive playing-ground for the distributed source coding problem. For the distributed coding of correlated i.i.d. Gaussian sources that are noisy versions of each other with "correlation-SNR" in the range of 12 to 20 dB, the DISCUS method attains gains of 7-15 dB in SNR over the Shannon-bound using "naive" independent coding of the sources.
Slow- and tight-binding inhibitors of the 85-kDa human phospholipase A2 (1993)

A trifluoromethyl ketone analogue of arachidonic acid in which the COOH group is replaced with COCF3 (AACOCF3) was prepared and found to be a tight- and slow-binding inhibitor of the 85-kDa cytosolic human phospholipase A2 (cPLA2). Enzyme inhibition was observed when AACOCF3 was tested in assays using either phospholipid vesicles or phospholipid/Triton X-100 mixed micelles. The fact that the inhibition developed over several minutes in both assays establishes that AACOCF3 inhibits by direct binding to the enzyme rather than by decreasing the fraction of enzyme bound to the substrate interface. From the measured values of the inhibitor association and dissociation rate constants, an upper limit of the equilibrium dissociation constant for the Ca(2+).AACOCF3.PLA2 complex of 5 x 10(-5) mole fraction was obtained. Thus, detectable inhibition of cPLA2 by AACOCF3 occurs when this compound is present in the assay at a level of one inhibitor per several thousand substrates. Arachidonic acid analogues in which the COOH group is replaced by COCH3, CH(OH)CF3, CHO, or CONH2 did not detectably inhibit the cPLA2. The arachidonyl ketones AACOCF2CF3 and AACOCF2Cl were found by 19F NMR to be less hydrated than AACOCF3 in phospholipid/Triton X-100 mixed micelles, and compared to AACOCF3 these compounds are also weaker inhibitors of cPLA2. In keeping with the fact that cPLA2 displays substrate specificity for arachidonyl-containing phospholipids, the arachidic acid analogue C19H39COCF3 is a considerably less potent inhibitor compared to AACOCF3.(ABSTRACT TRUNCATED AT 250 WORDS)
Complexes of Silicic Acid Polymer-Inorganic Compounds as Wood-preserving Agents. (1996)

木材への注入時点では液体で注入後常温で高分子化して木材中に固定される,コロイド状ケイ酸溶液あるいはケイ酸モノマー溶液と無機化合物との複合薬剤溶液の木材用難燃化剤あるいは防腐剤としての性能を,検討した。その結果は,次のようであった。1)木材中への固定量は,コロイド状ケイ酸溶液を用いた場合に高く,ケイ酸モノマー溶液を用いた場合にはその濃度に依存した。銅,鉄などの金属と複合化した場合には,添加する金属化合物の割合に至適濃度が存在すると考えられ,金属化合物の過剰の添加は溶脱割合が高くなる。しかし,ホウ素を混合した場合には良好に固定され,ケイ酸－ホウ素系化合物によるこの方法はホウ素を木材に固定する方法として優れていることがわかった。2)ケイ酸とホウ酸などの難燃化性能付与薬剤との複合薬剤で処理した木材は,燃焼試験において,加熱開始から着火までの時間が延長され,着火後300秒間の発熱速度(RHR300)は薬剤注入固定割合(WI)の高かったスギ材で低下した。さらに,燃焼時の発煙量も減少すると共に,燃焼試験のデータから算出した見かけのフラッシュオーバーまでの時間も延長された。3)ケイ酸のみでの処理では,大きな耐朽性は付与されない。しかし,ケイ酸と金属化合物との複合薬剤は,防腐性能を木材に付与する。4)ケイ酸モノマー溶液とホウ酸との複合薬剤は,高い防腐性能を有し,処理木材からの薬剤の溶脱もほとんどない良好な薬剤である。すなわち,ケイ酸溶液に,ホウ素化合物を添加して調製した木材用保存剤としてのケイ酸―ホウ素化合物複合薬剤溶液は,木材中で常温で高分子量の複合体となり,木材中に固定され,処理木材からの薬剤の溶脱が抑えられ,木材に難燃性および高い防腐性能を付与する低毒性の木材用保存剤であるといえる。
Identification of protein‐protein interactions using in vivo cross‐linking and mass spectrometry (2004)

The purification of protein complexes can be accomplished by different types of affinity chromatography. In a typical immunoaffinity experiment, protein complexes are captured from a cell lysate by an immobilized antibody that recognizes an epitope on one of the known components of the complex. After extensive washing to remove unspecifically bound proteins, the complexes are eluted and analyzed by mass spectrometry (MS). Transient complexes, which are characterized by high dissociation constants, are typically lost by this approach. In the present study, we describe a novel method for identifying transient protein-protein interactions using in vivo cross-linking and MS-based protein identification. Live cells are treated with formaldehyde, which rapidly permeates the cell membrane and generates protein-protein cross-links. Proteins cross-linked to a Myc-tagged protein of interest are copurified by immunoaffinity chromatography and subjected to a procedure which dissociates the cross-linked complexes. After separation by SDS-PAGE, proteins are identified by tandem mass spectrometry. Application of this method enabled the identification of numerous proteins that copurified with a constitutively active form of M-Ras (M-Ras(Q71L)). Among these, we identified the RasGAP-related protein IQGAP1 to be a novel interaction partner of M-Ras(Q71L). This method is applicable to many proteins and will aid in the study of protein-protein interactions.
Enzymatic Polymerization (2001)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTEnzymatic PolymerizationShiro Kobayashi, Hiroshi Uyama, and Shunsaku KimuraView Author Information Department of Materials Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 606-8501, Japan Cite this: Chem. Rev. 2001, 101, 12, 3793–3818Publication Date (Web):November 7, 2001Publication History Received8 February 2001Published online7 November 2001Published inissue 1 December 2001https://pubs.acs.org/doi/10.1021/cr990121lhttps://doi.org/10.1021/cr990121lresearch-articleACS PublicationsCopyright © 2001 American Chemical SocietyRequest reuse permissionsArticle Views9328Altmetric-Citations831LEARN 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 SUBJECTS:Catalysts,Organic polymers,Peptides and proteins,Polymerization,Polymers Get e-Alerts
Molecular biological approaches to neurological disorders including knockout and transgenic mouse models (2002)

Advances of molecular biology have provided a great variety of new approaches to research on human disorders. This article gives an outline of molecular biological approaches to analysis of neurological disorders such as giant cell glioblastoma (GGBM) and amyotrophic lateral sclerosis (ALS), and their respective animal models: p53 knockout mice for GGBM and mutant superoxide dismutase-1 transgenic mice for ALS. Genomic DNA extracted from fresh-frozen tissue is examined by Southern blotting for screening mutations in a certain gene. Polymerase chain reaction (PCR) products of a gene in genomic DNA are examined by single-stranded conformation polymorphism, sequencing and agarose gel electrophoresis for identifying mutations, and for preparing and evaluating DNA probes used in Southern blotting and DNA in situ hybridization (ISH). Total RNA from tissue is examined by northern blotting for quantifying and verifying a certain mRNA. Reverse transcription-PCR products of a certain mRNA in total RNA are examined by sequencing and agarose gel electrophoresis for preparing and evaluating cDNA probes used in northern blotting and mRNA ISH. Tissue total protein is immunoblotted for quantifying and verifying a certain protein, and for evaluating the specificity of antibodies used in western blotting and immunohistochemistry. Immunoprecipitates are immunoblotted for evaluating a profile of protein or other substances. Enzyme-linked immunosorbent assay is used for measuring tissue concentration of protein or other substances, and for determining titers of specific antibodies. By these procedures, chronological analysis of animal models for human diseases contribute to elucidating pathogenic mechanisms and exploiting new therapies. Noticing both the similarity and difference between human and animal disorders will help understand the nature of disease.
Avidity of IgG forStreptococcus pneumoniaeType 6B and 23F Polysaccharides in Infants Primed with Pneumococcal Conjugates and Boosted with Polysaccharide or Conjugate Vaccines (1998)

Relative avidity of IgG to Streptococcus pneumoniae type 6B and 23F polysaccharides (PSs) was measured in sera of children immunized with pneumococcal vaccines, using an EIA and the chaotropic agent thiocyanate. Infants were immunized at 2, 4, and 6 months of age with pneumococcal PS-diphtheria toxoid conjugate vaccine, and boosted at 14 months with the homologous conjugate or a pneumococcal PS vaccine. The concentrations of antibodies to 6B and 23F PSs increased significantly after the booster with both vaccines. A significant increase in the avidity of anti-6B and anti-23F antibodies was seen after the booster with conjugate but not with PS vaccine. Avidity also increased in another group of infants primed and boosted with pneumococcal PS-meningococcal protein conjugate but not in a group boosted with PS vaccine after priming with pneumococcal PS-tetanus toxoid conjugate. In the latter group, however, the avidity of anti-6B was high before boosting.