gebhart/patrepeval huggingface dataset:
High-level expression of sperm whale myoglobin in Escherichia coli. (1987)

Sperm whale myoglobin was expressed in Escherichia coli from a totally synthetic gene inserted in the expression vector pUC19. The gene was constructed as 23 overlapping oligonucleotides encoding both strands of the DNA. Gene synthesis provides several advantages over traditional eukaryotic gene-cloning techniques, allowing the incorporation of an efficient ribosome binding site, appropriate initiation and termination sequences, restriction enzyme sites for convenient subcloning and future mutagenesis, and frequently used codons for highly expressed E. coli genes. The sperm whale myoglobin expressed from the synthetic gene constituted approximately 10% of the total soluble protein as holo-protein, indicating that iron-protoporphyrin IX biosynthesis and prosthetic-group incorporation are not limiting in the high-level expression of this heme protein in E. coli. We credit the use of frequently used E. coli codons for the observed high-level expression. The sperm whale myoglobin produced is stable, easily purified to homogeneity, and indistinguishable from commercially available sperm whale myoglobin by optical and magnetic spectroscopic methods.
The transmission of AIDS: the case of the infected cell (1988)

CURRENT approaches to preventing infection with the human immunodeficiency virus (HIV) have focused on the retrovirus itself. However, biologic and epidemiologic studies of HIV and the acquired immunodeficiency syndrome (AIDS) indicate that more emphasis should be placed on the virus-infected cell. Several groups of researchers<sup>1-10</sup>have demonstrated the presence of HIV in many different hematopoietic cells, including T and B lymphocytes and macrophages, as See also p 3023. well as in cells (macrophages and endothelial and glial cells) of the brain. These infected cells can survive and serve as reservoirs (factories) for continual virus production and spread. When found in body fluids, they can transfer the infection to other individuals. T-helper lymphocytes generally die after HIV infection,<sup>1-4</sup>but some can replicate HIV to high titer in culture without undergoing cell death.<sup>11</sup>Thus, they too could serve as a source of virus transmission. In studies from our laboratory,
Therapeutic hypothermia utilization among physicians after resuscitation from cardiac arrest* (2006)

Physician utilization of cooling after cardiac arrest remains low. For improved adoption of therapeutic hypothermia, our data suggest that development of better cooling methodology and recent incorporation into resuscitation guidelines may improve use.
Synthesis of Bridged Oligophenylenes from Fluorene. Part 1. Ter- and Quater-phenyls (1997)

Alkylation and halogenation of fluorene give halogenated 9,9-dialkylfluorenes, which are converted by Pd-catalysed coupling with aryl Grignard reagents into a series of ter- and quater-phenyls exhibiting strongly efficient fluorescence, useful solubility and photochemical stability.
Gene expression analysis of prostate cancers (2002)

Prostate cancer is a biologically heterogeneous disease with considerable variation in clinical aggressiveness. The behavior of prostate cancer can be considered a direct or indirect result of aberrant alterations of gene expression in prostate epithelial cells. Identification of the patterns of gene-expression alterations that are related to the aggressiveness of prostate cancers will greatly assist the development of tools for early detection of prostate cancers with poor clinical outcome and identification of targets for future therapeutic intervention. To detect the patterns of gene-expression alterations of prostate cancers, we performed a comprehensive gene-expression analysis on 30 prostate tissues of various levels of invasiveness (ranging from those confined to the organ to distant metastases) and Gleason grades (combined scores 4-9), using the Affymetrix chip set Hu35k (A-D) and U95a. Following three sequential selection screens, we identified 84 largely novel genes and expressed sequence tag (EST) sequences whose expression levels were altered significantly in prostate cancer samples compared with control normal tissues. In addition, the expression levels of a group of 12 genes and EST sequences was found to be altered significantly in aggressive type of prostate cancers but not in organ-confined prostate cancers. Cluster analysis using the 84-gene list showed that the highly aggressive prostate cancers contained gene-expression patterns that were distinct from organ-confined prostate cancers.
When you can't talk to customers (2003)

Although an essential part of customer-centered design is the customers themselves, in some circumstances, talking with them is not always an option. What can designers do in such situations to better understand peoples' physical, cognitive, and emotional needs? In this paper, we discuss our attempts to elicit customers' needs and emotions without talking with them. We discuss how we: 1) used customer surrogates (in the form of direct-experience storyboarding, personas and narratives) to understand customers' frustrating and pleasurable experiences with a national, public library; 2) communicated the customer experience to stakeholders and helped them empathize with customers; and 3) relied on the personas and narratives to develop design recommendations.
De novo Assembly of a 40 Mb Eukaryotic Genome from Short Sequence Reads: Sordaria macrospora, a Model Organism for Fungal Morphogenesis (2010)

Filamentous fungi are of great importance in ecology, agriculture, medicine, and biotechnology. Thus, it is not surprising that genomes for more than 100 filamentous fungi have been sequenced, most of them by Sanger sequencing. While next-generation sequencing techniques have revolutionized genome resequencing, e.g. for strain comparisons, genetic mapping, or transcriptome and ChIP analyses, de novo assembly of eukaryotic genomes still presents significant hurdles, because of their large size and stretches of repetitive sequences. Filamentous fungi contain few repetitive regions in their 30-90 Mb genomes and thus are suitable candidates to test de novo genome assembly from short sequence reads. Here, we present a high-quality draft sequence of the Sordaria macrospora genome that was obtained by a combination of Illumina/Solexa and Roche/454 sequencing. Paired-end Solexa sequencing of genomic DNA to 85-fold coverage and an additional 10-fold coverage by single-end 454 sequencing resulted in approximately 4 Gb of DNA sequence. Reads were assembled to a 40 Mb draft version (N50 of 117 kb) with the Velvet assembler. Comparative analysis with Neurospora genomes increased the N50 to 498 kb. The S. macrospora genome contains even fewer repeat regions than its closest sequenced relative, Neurospora crassa. Comparison with genomes of other fungi showed that S. macrospora, a model organism for morphogenesis and meiosis, harbors duplications of several genes involved in self/nonself-recognition. Furthermore, S. macrospora contains more polyketide biosynthesis genes than N. crassa. Phylogenetic analyses suggest that some of these genes may have been acquired by horizontal gene transfer from a distantly related ascomycete group. Our study shows that, for typical filamentous fungi, de novo assembly of genomes from short sequence reads alone is feasible, that a mixture of Solexa and 454 sequencing substantially improves the assembly, and that the resulting data can be used for comparative studies to address basic questions of fungal biology.
What Constitutes Dental Caries? Histopathology of Carious Enamel and Dentin Related to the Action of Cariogenic Biofilms (2004)

Substantial pH fluctuations within the biofilm on the tooth surface are a ubiquitous and natural phenomenon, taking place at any time during the day and night. The result may be recordable in the dental tissues at only a chemical and/or ultrastructural level (subclinical level). Alternatively, a net loss of mineral leading to dissolution of dental hard tissues may result in a caries lesion that can be seen clinically. Thus, the appearance of the lesion may vary from an initial loss of mineral, seen only in the very surface layers at the ultrastructural level, to total tooth destruction. Regular removal of the biofilm, preferably with a toothpaste containing fluoride, delays or even arrests lesion progression. This can occur at any stage of lesion progression, because it is the biofilm at the tooth or cavity surface that drives the caries process. Active enamel lesions involve surface erosion and subsurface porosity. Inactive or arrested lesions have an abraded surface, but subsurface mineral loss remains, and a true subsurface remineralization is rarely achievable, because the surface zone acts as a diffusion barrier. The dentin reacts to the stimulus in the biofilm by tubular sclerosis and reactionary dentin.
Chromosomal site-specific double-strand breaks are efficiently targeted for repair by oligonucleotides in yeast (2003)

The repair of chromosomal double-strand breaks (DSBs) can be accomplished through homologous recombination in most organisms. We report here that exogenous oligonucleotides can efficiently target for repair a single DSB induced in a chromosome of yeast. The efficiency of recombinational targeting leading to a desired DNA change can be as high as 20% of cells. The DSB was generated either by a regulatable I-SceI endonuclease just before transformation or appeared spontaneously at the site of a long inverted repeat composed of human Alu sequences. The approach used features of our previously described delitto perfetto system for selecting transformants with integrative recombinant oligonucleotides. The DSB repair mediated by pairs of complementary integrative recombinant oligonucleotides was efficient for targeting to homologous sequences that were close to or distant from the DSB and in the presence of a competing homologous chromosome in diploid cells. We also demonstrate that a DSB can strongly stimulate recombination with single-stranded DNA, without strand bias. These findings expand current models of DSB repair. In addition, we establish a high-throughput system for rapid genome-wide modification with oligonucleotides.
Opportunistic Autoimmune Disorders Potentiated by Immune-Checkpoint Inhibitors Anti-CTLA-4 and Anti-PD-1 (2014)

To improve the efficacy of immunotherapy for cancer and autoimmune diseases, recent ongoing and completed clinical trials have focused on specific targets to redirect the immune network toward eradicating a variety of tumors and ameliorating the self-destructive process. In a previous review, both systemic immunomodulators and monoclonal antibodies (mAbs), anti-CTLA-4, and anti-CD52, were discussed regarding therapeutics and autoimmune sequelae, as well as predisposing factors known to exacerbate immune-related adverse events (irAEs). This review will focus on immune-checkpoint inhibitors, and the data from most clinical trials involve blockade with anti-CTLA-4 such as ipilimumab. However, despite the mild to severe irAEs observed with ipilimumab in ~60% of patients, overall survival (OS) averaged ~22-25% at 3-5 years. To boost OS, other mAbs targeting programed death-1 and its ligand are undergoing clinical trials as monotherapy or dual therapy with anti-CTLA-4. Therapeutic combinations may generate different spectrum of opportunistic autoimmune disorders. To simulate clinical scenarios, we have applied regulatory T cell perturbation to murine models combined to examine the balance between thyroid autoimmunity and tumor-specific immunity.
Infectious cDNA clones of tick-borne encephalitis virus European subtype prototypic strain Neudoerfl and high virulence strain Hypr. (1997)

Infectious cDNA clones of two strains of tick-borne encephalitis (TBE) virus, i.e. European subtype prototypic strain Neudoerfl and the closely related but more virulent strain Hypr, were constructed. The recombinant constructs consisted of cDNAs stably inserted into the bacterial plasmid pBR322 under the control of T7 promoter elements. The genome of TBE virus strain Neudoerfl was successfully cloned, both as a full-length cDNA and as two partial cDNAs. In the case of strain Hypr, the genome is represented by two cDNA clones corresponding to the 5'- and 3'-terminal halves of the genome. Highly infectious RNAs can be produced from the full-length cDNA clone or from the partial clones ligated in vitro to form full-length cDNA templates prior to T7 transcription. The biological properties of the recombinant progeny viruses, including virulence characteristics, were indistinguishable from the corresponding parent virus strains. Thus, the described infectious cDNA clones represent a useful and reliable experimental system for the specific mutagenesis of TBE virus.
Comparative Kinetic Studies of the Copolymerization of Cyclohexene Oxide and Propylene Oxide with Carbon Dioxide in the Presence of Chromium Salen Derivatives. In Situ FTIR Measurements of Copolymer vs Cyclic Carbonate Production (2003)

The catalysis of the reaction of carbon dioxide with epoxides (cyclohexene oxide or propylene oxide) using the (salen)Cr(III)Cl complex as catalyst, where H(2)salen = N,N'-bis(3,5-di-tert-butylsalicylidene)-1,2-cyclohexenediimine (1), to provide copolymer and cyclic carbonate has been investigated by in situ infrared spectroscopy. As previously demonstrated for the cyclohexene oxide/CO(2) reaction in the presence of complex 1, coupling of propylene oxide and carbon dioxide was found to occur by way of a pathway first-order in catalyst concentration. Unlike the cyclohexene oxide/carbon dioxide reaction catalyzed by complex 1, which affords completely alternating copolymer and only small quantities of trans-cyclic cyclohexyl carbonate, under similar conditions propylene oxide/carbon dioxide produces mostly cyclic propylene carbonate. Comparative kinetic measurements were performed as a function of reaction temperature to assess the activation barrier for production of cyclic carbonates and polycarbonates for the two different classes of epoxides, i.e., alicyclic (cyclohexene oxide) and aliphatic (propylene oxide). As anticipated in both instances the unimolecular pathway for cyclic carbonate formation has a larger energy of activation than the bimolecular enchainment pathway. That is, the energies of activation determined for cyclic propylene carbonate and poly(propylene carbonate) formation were 100.5 and 67.6 kJ.mol(-1), respectively, compared to the corresponding values for cyclic cyclohexyl carbonate and poly(cyclohexylene carbonate) production of 133 and 46.9 kJ.mol(-1). The small energy difference in the two concurrent reactions for the propylene oxide/CO(2) process (33 kJ.mol(-1)) accounts for the large quantity of cyclic carbonate produced at elevated temperatures in this instance.
Design of Chimeric Histone Deacetylase- and Tyrosine Kinase-Inhibitors: A Series of Imatinib Hybrides as Potent Inhibitors of Wild-Type and Mutant BCR-ABL, PDGF-Rβ, and Histone Deacetylases (2009)

Inhibitors of histone deacetylases are a new class of cancer therapeutics with possibly broad applicability. Combinations of HDAC inhibitors with the kinase inhibitor 1 (Imatinib) in recent studies showed additive and synergistic effects. Here we present a new concept by combining inhibition of protein kinases and HDACs, two independent pharmacological activities, in one synthetic small molecule. In general, the HDAC inhibition profile, the potencies, and the probable binding modes to HDAC1 and HDAC6 were similar as for 6 (SAHA). Inhibition of Abl kinase in biochemical assays was maintained for most compounds, but in general the kinase selectivity profile differed from that of 1 with nearly equipotent inhibition of the wild-type and the Imatinib resistant Abl T(315)I mutant. A potent cellular inhibition of PDGFR and cytotoxicity toward EOL-1 cells, a model for idiopathic hypereosinophilic syndrome (HES), are restored or enhanced for selected analogues (12b, 14b, and 18b). Cytotoxicity was evaluated by using a broad panel of tumor cell lines, with selected analogues displaying mean IC(50) values between 3.6 and 7.1 muM.
A Human Antibody That Inhibits Factor IX/IXa Function Potently Inhibits Arterial Thrombosis Without Increasing Bleeding (2002)

10C12, a human antibody F(ab')2, which specifically binds to the gamma-carboxyglutamic acid domain of factor IX/factor IXa (F.IX/IXa), interferes with all known coagulation processes in which F.IX/IXa is involved. In a rabbit model of carotid artery injury, intravenous administration of 10C12 or heparin decreased thrombosis dose dependently. The dose that resulted in a 90% reduction of thrombus mass (ED90) was a 30-microg/kg bolus of 10C12 or a 100-U/kg bolus plus 1.0 U x kg(-1) x min(-1) infusion of heparin. Heparin, at and below the ED90, significantly prolonged coagulation times and cuticle bleeding times. In contrast, 10C12 had no effect on coagulation or bleeding times at doses up to 4 times the ED90. To further evaluate the effect of 10C12 on bleeding, it was compared with heparin in a novel model of blood loss. At the ED90 of heparin, blood loss induced by a standardized injury to the vasculature of the rabbit tibia increased to more than 2 times that of saline controls. In contrast, the dose of 10C12 required to produce a similar increase in blood loss was more than 30 times the ED90. The antithrombotic potency and relative safety of this fully human antibody suggests that it may have therapeutic value for treatment of thrombotic disorders.
Basic fibroblast growth factor-like activity and receptors are expressed in a human glioma cell line. (1990)

Basic fibroblast growth factor (bFGF), a potent mitogen and angiogenic peptide, has been examined as an autocrine regulator of glioma cell growth. The addition of purified bovine pituitary bFGF to an established human glioma cell line, SNB-19, doubled the density of these cells in chemically defined medium. Half-maximal stimulation occurred at 8.2 ng/ml (480 pM). Also, human recombinant bFGF (hr-bFGF) significantly enhanced the growth of SNB-19 cells in soft agar. SNB-19 cells expressed both high and low affinity binding sites for hr-bFGF. These cells expressed approximately 13,000 high affinity sites/cell (Kd = 16.6 +/- 1.7 pM) and 9.5 x 10(6) low affinity sites/cell (Kd = 61.2 +/- 4.1 nM). The results of cross-linking experiments with iodinated hr-bFGF demonstrated the presence of two bands with molecular masses of 145 and 130 kDa. High affinity receptors were also demonstrated in SNB-19 tumors grown in nude mice. SNB-19 cell extracts contained mitogenic activity that eluted from heparin-agarose with high salt (1.2-2 M NaCl) and exhibited many properties normally associated with authentic bFGF. This material cross-reacted with a monoclonal antibody to hr-bFGF, comigrated with hr-bFGF by Western blot analysis, competed with 125I-hr-bFGF in a radioreceptor assay, and stimulated SNB-19 cell growth. These results indicate that a human glioma cell line both expresses and utilizes a bFGF-like growth factor. Such a factor may be an important autocrine regulator of glioma cell growth and may also facilitate its neoplastic progression.
Sentiment Analysis: Mining Opinions, Sentiments, and Emotions (2015)

Sentiment analysis is the computational study of people's opinions, sentiments, emotions, and attitudes. This fascinating problem is increasingly important in business and society. It offers numerous research challenges but promises insight useful to anyone interested in opinion analysis and social media analysis. This book gives a comprehensive introduction to the topic from a primarily natural-language-processing point of view to help readers understand the underlying structure of the problem and the language constructs that are commonly used to express opinions and sentiments. It covers all core areas of sentiment analysis, includes many emerging themes, such as debate analysis, intention mining, and fake-opinion detection, and presents computational methods to analyze and summarize opinions. It will be a valuable resource for researchers and practitioners in natural language processing, computer science, management sciences, and the social sciences
Synthetic studies on antitumor antibiotic, bleomycin. 27. Man-designed bleomycin with altered sequence specificity in DNA cleavage (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthetic studies on antitumor antibiotic, bleomycin. 27. Man-designed bleomycin with altered sequence specificity in DNA cleavageMasami Otsuka, Takeshi Masuda, Andreas Haupt, Masaji Ohno, Takashi Shiraki, Yukio Sugiura, and Kenji MaedaCite this: J. Am. Chem. Soc. 1990, 112, 2, 838–845Publication Date (Print):January 1, 1990Publication History Published online1 May 2002Published inissue 1 January 1990https://doi.org/10.1021/ja00158a052RIGHTS & PERMISSIONSArticle Views1791Altmetric-Citations95LEARN 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 PDF (2 MB) Get e-Alerts Get e-Alerts
Efficient synthesis of narrowly dispersed amphiphilic double-brush copolymers through the polymerization reaction of macromonomer micelle emulsifiers at the oil–water interface (2016)

Narrowly dispersed amphiphilic PMA-<italic>g</italic>-PMMA/PDMA DBCs with high molecular weight were efficiently synthesized by Pickering emulsion template directed radical polymerization of macromonomer micelles.
Testosterone (2001)

This book provides information on testosterone and other androgens, and their role in human physiology and pathology. It covers biosynthesis and mechanisms of action and reviews their effects on brain and behaviour, spermatogenesis, hair growth, bones, muscles, erythropoiesis, the cardiovascular system and lipids, erection, and the prostate. Therapeutic uses of testosterone preparations are carefully evaluated, including use in women, the aging male, and its abuse and detection in sport. The book reviews applications in male contraception, the role of 5a-reductase inhibitors and the controversial use of DHEA. For this book the editors have assembled the world leaders in testosterone research and clinical andrology and endocrinology. A special feature of the book is the fact that its 24 chapters were submitted simultaneously to insure rapid publication. This revised and significantly expanded edition will serve as the standard source of reference for many years.
Catching a Moving Target (2011)

Broadly neutralizing antibodies could help create an influenza vaccine that would not have to be updated.