gebhart/patrepeval huggingface dataset:
Preparation of a Phage DNA Fragment Library for Whole Genome Shotgun Sequencing (2009)

The most efficient method to determine the genomic sequence of a dsDNA phage is to use a whole genome shotgun approach (WGSA). Preparation of a library where each genomic fragment has an equal chance of being represented is critical to the success of the WGSA. For many phages, there are regions of the genome likely to be under-represented in the shotgun library, which results in more gaps in the shotgun assembly than predicted by the Poisson distribution. However, as phage genomes are relatively small, this increased number of gaps does not present an insurmountable impediment to using the WGSA. This chapter will focus on construction of a high-quality random library and sequence analysis of this library in a 96-well format. Techniques are described for the mechanical fragmentation of genomic DNA into 2 kb average size fragments, preparation of the fragmented DNA for shotgun cloning, and advice on the choice of cloning vector for library preparation. Protocols for deepwell block culture, plasmid isolation, and sequencing in 96-well format are given. The rationale for determining the total number of random clones from a library to sequence for a 50 and 150 kb genome is explained. The steps involved in going from hundreds of shotgun sequencing traces to generating contigs will be outlined as well as how to close gaps in the sequence by primer walking on phage DNA and PCR-generated templates. Finally, examples will be given of how biological information about the phage genomic termini can be derived by analysis of the organization of individual clones in the shotgun sequence assembly. Specific examples are given for the circularly permuted termini of pac type phages, the direct terminal repeats found in most T7-like phages, variable host DNA at either end as in the Mu-like phages, and the 5' and 3' overhanging ends of cos type phages. The end result of these steps is the entire DNA sequence of a novel phage, ready for gene prediction.
Synthesis of polyamides by direct polycondensation with N,N'-phenylphosphonobis[2(3H)-benzothiazolone] as a new activating agent (1985)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis of polyamides by direct polycondensation with N,N'-phenylphosphonobis[2(3H)-benzothiazolone] as a new activating agentMitsuru Ueda and Amane MochizukiCite this: Macromolecules 1985, 18, 12, 2353–2356Publication Date (Print):December 1, 1985Publication History Published online1 May 2002Published inissue 1 December 1985https://pubs.acs.org/doi/10.1021/ma00154a003https://doi.org/10.1021/ma00154a003research-articleACS PublicationsRequest reuse permissionsArticle Views311Altmetric-Citations11LEARN 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
FTY720, an immunomodulatory sphingolipid mimetic: translation of a novel mechanism into clinical benefit in multiple sclerosis (2007)

FTY720 (fingolimod; 2-amino-2[2-(4-octylphenyl)ethyl]-1,3-propanediol, Novartis) is the prototype of a new generation of immunomodulators. The drug is the result of extensive chemical derivatisation based on the natural product myriocin, isolated from the ascomycete Isaria sinclairii. FTY720 bears structural similarity to sphingosine, a naturally occurring sphingolipid. As with sphingosine, FTY720 is effectively phosphorylated by sphingosine kinases in vivo and the phosphorylated drug targets G-protein-coupled receptors for sphingosine-1-phosphate (S1P). Gene deletion and reverse pharmacology studies have shown that FTY720 acts at S1P1 receptors on lymphocytes and the endothelium, thereby inhibiting the egress of T- and B cells from secondary lymphoid organs into the blood and their recirculation to inflamed tissues. Animal studies suggest that this novel mechanism translates into effective treatments for several autoimmune diseases and a recently completed Phase II clinical trial highlighted FTY720 as a potential therapy for relapsing-remitting multiple sclerosis.
Identification of Functionally Important Residues of the Epidermal Growth Factor-2 Domain of Factor IX by Alanine-scanning Mutagenesis (2002)

This paper describes the consequences of alanine-scanning mutagenesis on 28 positions of the second epidermal growth factor (EGF-2) domain of factor IX. We identified four positions of Gln(97), Phe(98), Tyr(115), and Leu(117) that are critical for secretion of factor IX. Of the remaining mutations, 4 mutants (V86A, E113A, K122A, and S123A) are as active as wild-type factor IX (IXwt); 16 (D85A, K100A, N101A, D104A, N105A, R116A, E119A, T87A, I90A, K91A, R94A, E96A, S102A, K106A, T112A, and N120A) retain reduced but detectable activity, and 4 (N89A, N92A, G93A, and V107A) are nearly inert in the clotting assay. Both factor XIa and the factor VIIa-tissue factor complex effectively catalyzed the activation of these mutants except N89A. The mutant V107A failed to form the factor tenase complex with factor VIIIa because of a 35-fold increase in K(d). The mutants N89A and N92A did not compete with factor IXwt for factor VIIIa binding, and G93A exhibited a 6-fold increase in K(i) values in the competitive binding assay. It appears that mutations at these positions have significantly affected the interaction between factor IX and factor VIIIa, although other mutations had little effect on the binding of factor IX to factor VIIIa. Mutations in two regions, Thr(87)-Gly(93) and Asn(101)-Val(107), significantly increased the K(m) value of factor IXa (2-10-fold) in cleavage of factor X in the absence of factor VIIIa. In the presence of factor VIIIa, the catalytic efficiency of each mutant toward factor X paralleled its clotting activity. Briefly, we propose two relatively distinctive functions of factor IX for two adjacent regions in the EGF-2 domain; the first loop region (residues 89-94) is involved with the binding of its cofactor, factor VIIIa, and the third loop with connected beta-sheets (residues 102-108) is involved in the proper binding to the substrate, factor X.
Interferon-Inducible Mx Gene Expression in Cotton Rats: Cloning, Characterization, and Expression During Influenza Viral Infection (2006)

Mx proteins belong to the superfamily of large GTPases with antiviral activity against a wide range of RNA viruses. In vivo, the expression of Mx genes is tightly regulated by the presence of type I interferons (IFNs), and their induction has been described during several viral infections. However, because of the absence of functional Mx genes in most common laboratory strains of mice, in vivo studies of the expression of these genes during viral infection have been hampered. We have cloned the cDNAs for the cotton rat homologs of Mx1 and Mx2 genes that encode full-length proteins. Mx1 localized in the nucleus, whereas Mx2, as its human homolog MxA, localized in the cytoplasm. The expression of Mx genes in cotton rat cells was induced by type I IFNs (IFN-alpha and IFN-beta) but induced only marginally with type II IFN (IFN-gamma). In vivo, the expression of Mx genes was dramatically augmented in lungs of cotton rats infected with influenza virus. The expression of Mx genes and protein(s) was dependent on the dose of virus and the time postinfection for the analysis. Our data present for the first time a complete analysis of the kinetics of expression of these influenza resistant genes in vivo and underscore the fidelity and sensitivity of the cotton rat model for the study of influenza viral infection.
Utility of the methylation‐sensitive amplified polymorphism (MSAP) marker for detection of DNA methylation polymorphism and epigenetic population structure in a wild barley species ( Hordeum brevisubulatum ) (2008)

Abstract We report here that by using a modified scoring criterion, the methylation‐sensitive amplified polymorphism or MSAP marker can be used effectively to detect polymorphism in DNA methylation patterns within and among populations of a perennial wild barley species, Hordeum brevisubulatum. Twenty‐four selected individual genotypes representing four natural populations of H. brevisubulatum distributed in the Songnen Prairie in northeastern China were studied. The utility of MSAP was evidenced by its detection of high levels of polymorphism in DNA methylation patterns between individuals within a given population, and the clear inter‐population differentiation in methylation patterns (methylation‐based epigenetic population structure) revealed among the four populations. The resolving power of MSAP to detect DNA methylation polymorphism was found to be comparable with that of a retrotransposon‐based sequence‐specific amplified polymorphism marker, or SSAP, to detect genetic polymorphism in the same set of plants, suggesting that MSAP with a modified scoring criterion can be used efficiently to detect DNA methylation polymorphism and assess epigenetic population structure in natural plant populations.
ChemInform Abstract: Reaction of Diazocompounds and Hydrazines on Indolin‐2‐one Derivatives. (1986)

Abstract Die Indolinone (Ia) bzw. (Ib) reagieren mit den Diazoverbindungen (IIa) bzw. (IIb) unter N 2 ‐Abspaltung und Ringerweiterung zu den Chinolinonen (IIIa) bzw. (IIIb).
Insulin-like growth factor-II (IGF-II) inhibits both the cellular uptake of β-galactosidase and the binding of β-galactosidase to purified IGF-II/mannose 6-phosphate receptor (1989)

The insulin-like growth factor-II/mannose 6-phosphate receptor which targets acid hydrolases to lysosomes, has two different binding sites, one for the mannose 6-phosphate (Man-6-P) recognition marker on lysosomal enzymes and the other for insulin-like growth factor-II (IGF-II). We have asked whether IGF-II can regulate the cellular uptake of the lysosomal enzyme 125I-beta-galactosidase by modulating the binding of 125I-beta-galactosidase to the IGF-II/Man-6-P receptor. We first isolated high affinity 125I-beta-galactosidase by affinity chromatography on an IGF-II/Man-6-P receptor-Sepharose column. Specific uptake (mannose 6-phosphate-inhibitable) of 125I-beta-galactosidase in BRL 3A2 rat liver cells and in rat C6 glial cells was 3.7-4.8 and 4.0-8.0% of added tracer, respectively. The cell-associated 125I-beta-galactosidase in the uptake experiments largely represented internalized radioligand as measured by acid or mannose 6-phosphate washing. The uptake of 125I-beta-galactosidase was inhibited by an antiserum (No. 3637) specific for the IGF-II/Man-6-P receptor. Low concentrations of IGF-II also inhibited the uptake of 125I-beta-galactosidase. Maximal concentrations of IGF-II inhibited uptake by 73 +/- 8% (mean +/- S.D.) in C6 cells and by 77 +/- 6% in BRL 3A2 cells compared to the level of inhibition by mannose 6-phosphate. The relative potency of IGF-II, IGF-I, and insulin (IGF-II much greater than IGF-I; insulin, inactive) were characteristic of the relative affinities of the ligands for the IGF-II/Man-6-P receptor. IGF-II also partially inhibited the binding of 125I-beta-galactosidase to C6 and BRL 3A2 cells at 4 degrees C and inhibited the binding to highly purified IGF-II/Man-6-P receptor by 58 +/- 14%. We conclude that IGF-II inhibits the cellular uptake of 125I-beta-galactosidase and that this inhibition is partly explained by the ability of IGF-II to inhibit binding of 125I-beta-galactosidase to the IGF-II/Man-6-P receptor.
Heterogeneous Catalysis Using a Nanostructured Solid Acid Resin Based on Lyotropic Liquid Crystals (2004)

The catalytic reactivity and selectivity of the first example of a nanostructured solid acid resin (1) are described. This new type of solid acid catalyst is formed by the self-assembly and copolymerization of two acidic lyotropic liquid crystals (LLCs), affording a columnar hexagonal polymer network with monodisperse nanochannels lined with sulfonic acid groups. The performance of this material as a heterogeneous catalyst was compared against that of two commercially available, amorphous sulfonic acid resins: Amberlyst-15 and Nafion NR50. Using the acid-catalyzed esterification of benzyl alcohol with 1-hexanoic acid in dry toluene as a test reaction, it was found that resin 1 displayed only slightly lower overall reactivity as compared to Amberlyst-15 and Nafion NR50 but more than an order of magnitude higher selectivity for the desired ester product over dibenzyl ether side-product. Control experiments revealed that the higher product selectivity is not due to differences in relative acidity between the nanostructured acid resin and the two amorphous resins. Instead, it appears that a large component of the enhanced selectivity is due to the regular nanostructure present in the LLC resin, which affords a much more uniform local acid microenvironment for reactions to occur. Resin 1 can also be recycled with almost complete recovery of catalytic activity and selectivity, and with essentially no leaching of reactive groups into the solution phase.
Accelerated age-related CpG island methylation in ulcerative colitis. (2001)

CpG island hypermethylation is a mechanism of gene silencing that can be usurped by neoplastic cells to inactivate undesirable genes. In the colon, hypermethylation often starts in normal mucosa as a function of age and is markedly increased in cancer. To test the hypothesis that subjects at increased risk of colon cancer have higher levels of methylation in their nonneoplastic mucosa, we studied methylation patterns of five genes in the normal and dysplastic mucosa of patients with ulcerative colitis (UC), a condition associated with a marked increased risk of colon cancer. One gene (Mlh1) was unmethylated in all tissues examined. All four remaining genes had low but detectable levels of methylation in the epithelium of UC patients without evidence of dysplasia, and this methylation was not different from non-UC controls. By contrast, all four genes were highly methylated in dysplastic epithelium from high-grade dysplasia (HGD)/cancer patients with UC; methylation in HGD versus controls averaged 40.0% versus 7.4% (P = 0.00003) for ER, 44.0% versus 3.0% (P < 0.00003) for MYOD, 9.4% versus 2.4% (P = 0.03) for p16 exon 1, and 57.5% versus 30.6% (P = 0.01) for CSPG2. Importantly, three of the four genes were also highly methylated in the normal appearing (nondysplastic) epithelium from these same HGD/cancer patients, indicating that methylation precedes dysplasia and is widespread in these patients. Compared with controls, methylation averaged 20.1% versus 7.2% (P = 0.07) for ER, 18.4% versus 3.0% (P < 0.008) for MYOD, and 7.9% versus 2.4% (P = 0.007) for p16 exon 1. These results are consistent with the hypothesis that age-related methylation marks (and may lead to) the field defect that reflects acquired predisposition to colorectal neoplasia. Furthermore, the data suggest that chronic inflammation is associated with high levels of methylation, perhaps as a result of increased cell turnover, and that UC can be viewed as resulting in premature aging of colorectal epithelial cells.
Learning Category-Specific Mesh Reconstruction from Image Collections (2018)

We present a learning framework for recovering the 3D shape, camera, and texture of an object from a single image. The shape is represented as a deformable 3D mesh model of an object category where a shape is parameterized by a learned mean shape and per-instance predicted deformation. Our approach allows leveraging an annotated image collection for training, where the deformable model and the 3D prediction mechanism are learned without relying on ground-truth 3D or multi-view supervision. Our representation enables us to go beyond existing 3D prediction approaches by incorporating texture inference as prediction of an image in a canonical appearance space. Additionally, we show that semantic keypoints can be easily associated with the predicted shapes. We present qualitative and quantitative results of our approach on CUB and PASCAL3D datasets and show that we can learn to predict diverse shapes and textures across objects using only annotated image collections. The project website can be found at https://akanazawa.github.io/cmr/.
p53 protein, EGF receptor, and anti-p53 antibodies in serum from patients with occupationally derived lung cancer (1999)

The oncogene product epidermal growth factor receptor (EGF-R), the tumour suppressor gene product p53 and anti-p53 antibodies are detectable in the serum of certain cancer patients. Increased levels of some of these products were reported in lung cancer patients after occupational asbestos exposure and after exposure to polycyclic aromatic hydrocarbons or vinylchloride. In the first step, this study investigated the possible diagnostic value of serum EGF-R, p53-protein and anti-p53 antibodies, measured by an enzyme-linked immunosorbent assay, in lung tumour patients. In addition to being investigated on a molecular epidemiological basis, these parameters were examined as biomarkers of carcinogenesis, especially with regard to asbestos incorporation effects or of radon-induced lung cancers. Also, a possible effect of cigarette smoking and age dependence were studied. A total of 116 male patients with lung or pleural tumours were examined. The histological classification was four small-cell cancers, six large-cell cancers, 32 adenocarcinomas, 47 squamous carcinomas, 12 mixed lung carcinomas, five diffuse malignant mesotheliomas and ten lung metastasis of extrapulmonary tumours. Twenty-two lung cancers and all mesotheliomas were related to asbestos, 22 lung cancers were related to ionizing radiation and 61 patients had cigarette smoke-related lung cancer. Besides these patients 50 male patients with non-malignant lung or pleural diseases were included; of the latter eight subjects suffered from asbestosis. Controls were 129 male subjects without any lung disease. No significantly elevated or decreased serum values for p53 protein, EGF-R, or anti-p53 antibodies as a function of histological tumour type, age, or degree and type of exposure (asbestos, smoking, ionizing radiation) could be found. The utility of p53-protein, EGF-R and anti-p53 antibodies as routine biomarkers for screening occupationally derived lung cancers is limited.
Tylonolide hemiacetal, the aglycone of tylosin and its partial synthesis (1976)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTylonolide hemiacetal, the aglycone of tylosin and its partial synthesisSatoru Masamune, Yoshio Hayase, Wan Kit Chan, and Ronald L. SobczakCite this: J. Am. Chem. Soc. 1976, 98, 24, 7874–7875Publication Date (Print):November 1, 1976Publication History Published online1 May 2002Published inissue 1 November 1976https://pubs.acs.org/doi/10.1021/ja00440a096https://doi.org/10.1021/ja00440a096research-articleACS PublicationsRequest reuse permissionsArticle Views216Altmetric-Citations35LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Specific contact resistivity of metal-semiconductor contacts-a new, accurate method linked to spreading resistance (1988)

A method to determine the specific contact resistivity of metal-semiconductor contacts has been developed. It allows the separation of the total series resistance between two contacts into the contributing component resistances. The principle of the method is the subtraction of the semiconductor spreading resistance from the total two-contact resistance. This requires geometrically well-defined small contacts that are fabricated precisely by lithographic methods. Using this method, accurate values were obtained for the specific contract resistivity of an aluminium-1.5% silicon alloy to p-type silicon wafers having dopant densities from 5*10/sup 14/ to 2*10/sup 20/ cm/sup -3/. The specific contact resistivity values are lower than previously published values obtained using earlier methods in which parasitic and nonideal effects could not be quantified or eliminated. The lower values indicate that contact resistance has a less-limiting effect on the performance of integrated circuits than presently believed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Histopathologic prognostic factors in adenocarcinomas of the peripheral lung less than 2 CM in diameter (1988)

The histologic prognostic factors of pulmonary adenocarcinomas of the lung less than 2 cm in diameter were analyzed in 75 patients who had undergone surgical resection. The pathologic stage, lymph node involvement, and pleural involvement were found to be the major determinants of prognosis (P less than 0.01). In addition, other single factors, such as tumor differentiation (P less than 0.01), vascular invasion (P less than 0.01), the degree of collagenization in the fibrotic focus (P less than 0.01), the standard deviation (SD) of nuclear areas (P less than 0.05), and mitotic index (P less than 0.05) correlated significantly with prognosis by the log-rank test on the Kaplan-Meier survival curves of these factors. Patients with dense infiltration of "T-zone histiocytes" survived significantly longer than those with less infiltration (P less than 0.05). Cox's proportional hazard general linear model analysis showed the importance of factors, such as lymph node or pleural involvement and the SD of nuclear area, when the pathologic stage was excluded, and of the mitotic index when all four factors were excluded to emphasize the cellular characteristics. It is possible to predict the postoperative prognosis of patients with small pulmonary adenocarcinoma more precisely by combination of the above histopathologic factors.