gebhart/patrepeval huggingface dataset:
Immunoaffinity purification and neutralization of scrapie prion infectivity. (1988)

Prions are unusual infectious pathogens causing scrapie of sheep and goats as well as Creutzfeldt-Jakob disease of humans. Biochemical and genetic studies contend that the scrapie isoform of the prion protein (PrPSc) is a major component of the prion. Limited proteinase K digestion of PrPSc produced a protein of 27-30 kDa. After dispersion of brain microsomes isolated from scrapie-infected hamsters into detergent-lipid-protein complexes, copurification of PrPSc and scrapie infectivity was obtained with scrapie prion protein of 27-30 kDa monoclonal antibody-affinity columns. PrPSc was enriched approximately equal to 5700-fold with respect to total brain protein, whereas scrapie prion infectivity was enriched approximately equal to 4000-fold. The ratio of prion titer to PrPSc remained constant throughout purification. Heterologous monoclonal antibody columns failed to bind either PrPSc or scrapie infectivity. Polyclonal rabbit prion protein antiserum raised against NaDodSO4/PAGE-purified scrapie prion protein of 27-30 kDa reduced scrapie infectivity dispersed into detergent-lipid-protein complexes by a factor of 100. These results represent direct immunologic and chromatographic demonstrations of a relationship between PrPSc and prion infectivity as well as providing additional support for the contention that PrPSc is a major component of the infectious scrapie particle. That PrPSc is a host-encoded protein is an important feature distinguishing prions from viruses.
Mutation in an intervening sequence splice junction in man. (1981)

The alpha 2-globin gene of an individual with alpha-thalassemia associated with the absence of alpha 2 mRNA was cloned in bacteriophage. This mutant globin gene was normally active in transcription in vitro. The DNA sequence of the gene, however, revealed a pentanucleotide deletion within the 5' splice junction of the first intervening sequence. Following the G of the invariant G-T dinucleotide normally located within such junctions, a deletion of T-G-A-G-G was found. No other sequence abnormalities within the mutant gene were present. We speculate therefore that this deletion within the splice junction is the primary genetic defect in this individual with thalassemia and that loss of a functional splice junction results in failure of stable mRNA formation.
Human CD3−CD16+ natural killer cells express the hGATA‐3 T cell transcription factor and an unrearranged 2.3‐kb TcR δ transcript (1993)

In this study we analyzed the T cell receptor(TcR) delta transcripts expressed by CD3-CD16+ cells and we investigated whether these cells expressed the hGATA-3 T cell transcription factor and the recombination-activating gene (RAG)-1. Multiple TcR delta transcripts deriving from an unrearranged TcR delta gene were detected in both polyclonal and clonal CD3-CD16+ natural killer(NK) cell lines. Two unrearranged TcR delta transcripts had a size similar to that of the functional TcR delta mRNA (2.3 and 1.3 kb) found in TcR gamma/delta+ T lymphocytes. Sequence analysis of nine different 2.3-kb cDNA clones obtained from NK-derived polyA+ RNA confirmed that they corresponded to an unrearranged TcR delta gene. These cDNA were 2343 bp long and their transcription initiation site was located 814 bp upstream from the J delta 1 segment. The sequence located upstream of the J delta 1 segment corresponded to the previously reported germ-line sequence. The J delta 1 segment was correctly spliced to C delta; in addition the four C delta exons were found to be already assembled. Two polyadenylation sites were present in the fourth C delta exon. However, only that located at the 3' end appeared to be utilized in the 2.3-kb cDNA. The expression of hGATA-3, a T cell-specific factor known to be involved in the regulation of the transcription of TcR delta locus, was analyzed by Northern blot, in cultured NK cell population and clones (but not in freshly derived cell populations). All NK clones and cell lines studied were found to express hGATA-3-specific mRNA, suggesting that hGATA-3 may be involved in the regulation of the unrearranged TcR delta gene expression in NK cells. Finally, no transcription of the RAG-1 gene could be detected in all NK cell lines or clones analyzed.
Photoremovable Protecting Groups in Chemistry and Biology: Reaction Mechanisms and Efficacy (2012)

ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXTPhotoremovable Protecting Groups in Chemistry and Biology: Reaction Mechanisms and EfficacyPetr Klán*†‡, Tomáš Šolomek†‡, Christian G. Bochet§, Aurélien Blanc∥, Richard Givens⊥, Marina Rubina⊥, Vladimir Popik#, Alexey Kostikov#, and Jakob Wirz∇View Author Information† Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic‡ Research Centre for Toxic Compounds in the Environment, Faculty of Science, Masaryk University, Kamenice 3, 625 00 Brno, Czech Republic§ Department of Chemistry, University of Fribourg, Chemin du Musée 9, CH-1700 Fribourg, Switzerland∥ Institut de Chimie, University of Strasbourg, 4 rue Blaise Pascal, 67000 Strasbourg, France⊥ Department of Chemistry, University of Kansas, 1251 Wescoe Hall Drive, 5010 Malott Hall, Lawrence, Kansas 66045, United States# Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States∇ Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland*E-mail: [email protected]. Phone: +420-54949-4856. Fax: +420-54949-2443.Cite this: Chem. Rev. 2013, 113, 1, 119–191Publication Date (Web):December 21, 2012Publication History Received29 April 2012Published online21 December 2012Published inissue 9 January 2013https://doi.org/10.1021/cr300177kCopyright © 2012 American Chemical SocietyRIGHTS & PERMISSIONSACS AuthorChoiceArticle Views77851Altmetric-Citations1248LEARN 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 (17 MB) Get e-AlertscloseSUBJECTS:Alcohols,Fluorescence,Irradiation,Organic compounds,Reaction products Get e-Alerts
Structure of the Clostridium thermocellum gene licB and the encoded β‐1,3‐1,4‐glucanase (1992)

The nucleotide sequence of the Clostridium thermocellum gene licB, coding for a thermoactive beta-1,3-1,4-glucanase, has been determined. The gene is located downstream, but in opposite orientation to the beta-glucosidase gene bglA. A coding region of 1002 bp is flanked by canonical promoter and transcription terminator sequences. The primary translation product of the licB gene has a predicted molecular mass of 37,896 Da. The protein sequence can be divided into several discrete segments: an N-terminal signal peptide, a catalytic region, a segment rich in Pro and Thr residues and a C-terminal reiterated domain. The catalytic region shows close similarity to lichenases of bacilli (52-58% identity) and Fibrobacter succinogenes (35% identity), but is unrelated to barley beta-1,3-1,4-glucanases. It consists of two domains, which in the case of the F. succinogenes lichenase are arranged in reversed order to that of C. thermocellum and Bacillus lichenases. The C-terminal reiterated domain of C. thermocellum lichenase is homologous to the duplicated non-catalytic domain of endo-beta-1,4-glucanases and xylanase Z from the same organism. This domain is considered a characteristic feature of clostridial cellulases organized as multienzyme complex (cellulosome). The beta-1,3-1,4-glucanase encoded by the licB gene might therefore be an additional enzyme component of the C. thermocellum cellulosome.
DNA Mapping Using Microfluidic Stretching and Single-Molecule Detection of Fluorescent Site-Specific Tags (2004)

We have developed a rapid molecular mapping technology--Direct Linear Analysis (DLA)--on the basis of the analysis of individual DNA molecules bound with sequence-specific fluorescent tags. The apparatus includes a microfluidic device for stretching DNA molecules in elongational flow that is coupled to a multicolor detection system capable of single-fluorophore sensitivity. Double-stranded DNA molecules were tagged at sequence-specific motif sites with fluorescent bisPNA (Peptide Nucleic Acid) tags. The DNA molecules were then stretched in the microfluidic device and driven in a flow stream past confocal fluorescence detectors. DLA provided the spatial locations of multiple specific sequence motifs along individual DNA molecules, and thousands of individual molecules could be analyzed per minute. We validated this technology using the 48.5 kb lambda phage genome with different 8-base and 7-base sequence motif tags. The distance between the sequence motifs was determined with an accuracy of +/-0.8 kb, and these tags could be localized on the DNA with an accuracy of +/-2 kb. Thus, DLA is a rapid mapping technology, suitable for analysis of long DNA molecules.
Evolution of Oncolytic Viruses: Novel Strategies for Cancer Treatment (2013)

Many viruses have documented oncolytic activity, with the first evidence observed clinically over a decade ago. In recent years, there has been a resurgence of interest in the field of oncolytic viruses. Viruses may be innately oncotropic, lacking the ability to cause disease in people or they may require engineering to allow selective tumor targeting and attenuation of pathogenicity. Following infection of a neoplastic cell, several events may occur, including direct viral oncolysis, apoptosis, necrotic cell death and autophagic cellular demise. Of late, a large body of work has recognized the ability of oncolytic viruses (OVs) to activate the innate and adaptive immune system, as well as directly killing tumors. The production of viruses expressing transgenes encoding for cytokines, colony-stimulating factors, costimulatory molecules and tumor-associated antigens has been able to further incite immune responses against target tumors. Multiple OVs are now in the advanced stages of clinical trials, with several individual viruses having completed their respective trials with positive results. This review introduces the multiple mechanisms by which OVs are able to act as an antineoplastic therapy, either on their own or in combination with other more traditional treatment modalities. The full benefit and the place where OVs will be integrated into standard-of-care therapies will be determined with ongoing studies ranging from the laboratory to the patient. With various different viruses now in the clinic this therapeutic option is beginning to prove its worth, and the versatility of these agents means further innovative and novel applications will continue to be developed.
Novel Bioconjugates of Aminolevulinic Acid with Vitamins (2008)

5-Aminolevulinic acid (ALA) and derivatives thereof have been successfully used in photodynamic cancer therapy (PDT). The synthesis of novel bioconjugates combining ALA with two lipophilic and one hydrophilic vitamins is reported. The new bioconjugates allow studying the potential synergies between the two components in PDT. The synthetic methodology is robust giving the bioconjugates in good to satisfactory yield.
Expression and Immune Response to Hepatitis C Virus Core Dna-Based Vaccine Constructs (1996)

Hepatitis C virus (HCV) is a major worldwide cause of acute and chronic hepatitis, cirrhosis, and hepatocellular carcinoma. The development of vaccines against HCV have been complicated by the high variability of the envelope region, and it is likely that the cellular immune responses to viral structural proteins may be important for eradicating persistent viral infection. Recently, it was reported that the injection into muscle cells of plasmids encoding viral genes resulted in the generation of strong cellular immune responses. We constructed vectors that express the highly conserved HCV core gene. In this regard, the pHCV 2-2 construct contained the entire HCV core region and pHCV 4-2 contained both the 5' noncoding region and the core gene. Cellular expression of HCV core protein was assessed following transfection into human and murine cell lines, and higher intracellular levels of the 21-kd core protein were observed with pHCV 2-2. These HCV core DNA constructs were used to immunize BALB/c mice and produced low-level anti-HCV core humoral immune responses. To assess cytotoxic T-lymphocyte (CTL) activity generated in vivo, a cloned syngeneic SP2/O myeloma cell line constitutively expressing HCV core protein was established and inoculated into BALB/c mice to produce growth of plasmacytomas. Strong CTL activity was generated because the tumor size and weight in pHCV 2-2-immunized mice were remarkably reduced compared with mice injected with mock DNA. Spontaneous CTL activity was also exhibited by splenocytes in an in vitro cytotoxicity assay. These investigations demonstrate that plasmid constructs expressing HCV core protein generate strong CTL activity, as assessed both in vivo and in vitro, and are promising candidates as antiviral agents.
Serum and Plasma Metabolomic Biomarkers for Lung Cancer (2017)

In drug invention and early disease prediction of lung cancer, metabolomic biomarker detection is very important. Mortality rate can be decreased, if cancer is predicted at the earlier stage. Recent diagnostic techniques for lung cancer are not prognosis diagnostic techniques. However, if we know the name of the metabolites, whose intensity levels are considerably changing between cancer subject and control subject, then it will be easy to early diagnosis the disease as well as to discover the drug. Therefore, in this paper we have identified the influential plasma and serum blood sample metabolites for lung cancer and also identified the biomarkers that will be helpful for early disease prediction as well as for drug invention. To identify the influential metabolites, we considered a parametric and a nonparametric test namely student׳s t-test as parametric and Kruskal-Wallis test as non-parametric test. We also categorized the up-regulated and down-regulated metabolites by the heatmap plot and identified the biomarkers by support vector machine (SVM) classifier and pathway analysis. From our analysis, we got 27 influential (p-value<0.05) metabolites from plasma sample and 13 influential (p-value<0.05) metabolites from serum sample. According to the importance plot through SVM classifier, pathway analysis and correlation network analysis, we declared 4 metabolites (taurine, aspertic acid, glutamine and pyruvic acid) as plasma biomarker and 3 metabolites (aspartic acid, taurine and inosine) as serum biomarker.
Biomedical applications of degradable polyphosphazenes (1996)

This article describes the synthesis of biodegradable polyphosphazenes. The rate of degradation can be varied in a controllable manner by the introduction of hydrolysis-sensitive amino acid ester side groups or by blending of polymers. Biodegradable polyphosphazenes can be used for the preparation of drug-containing implants and this is illustrated for devices containing the cytostatic agent mitomycin C. This article reviews data about the degradation characteristics of poly[(amino acid ester)phosphazene] derivatives that have been discussed previously. Some new data about MMC-containing poly[(organo)phosphazene] devices are discussed as well. © 1996 John Wiley & Sons, Inc.
NT Network Plumbing: Routers, Proxies, and Web Services (1998)

From the Publisher:
Sort through the maze of bridges, routers, and gateways to design and manage an efficient NT 4.0 internetwork. Networking authority Anthony Northrup provides straightforward, step-by-step guidelines for assessing your current and future networking needs, acquiring the best hardware and software for your LAN or WAN, and implementing Internet connectivity that is reliable, secure, and requires minimal maintenance.
Wearing‐off scales in Parkinson's disease: Critique and recommendations (2011)

Wearing-off occurs in the majority of patients with Parkinson's disease after a few years of dopaminergic therapy. Because a variety of scales have been used to estimate wearing-off, the Movement Disorder Society commissioned a task force to assess their clinimetric properties. A systematic review was conducted to identify wearing-off scales that have either been validated or used in Parkinson's patients. A scale was designated "Recommended" if it had been used in clinical studies beyond the group that developed it, if it had been specifically used in Parkinson's disease reports, and if clinimetric studies had established that it is valid, reliable, and sensitive. "Suggested" scales met 2 of the above criteria, and those meeting 1 were "Listed." We identified 3 diagnostic and 4 severity rating scales for wearing-off quantification. Two questionnaires met the criteria to be Recommended for diagnostic screening (questionnaires for 19 and 9 items), and 1 was Suggested (questionnaire for 32 items). Only the patient diaries were Recommended to assess wearing-off severity, with the caveat of relatively limited knowledge of validity. Among the other severity assessment tools, the Unified Parkinson Disease Rating Scale version 3 and the version revised from the Movement Disorders Society were classified as Suggested, whereas the Treatment Response Scale was Listed.
Site-specific recombination of yeast 2-micron DNA in vitro. (1983)

Most strains of the yeast Saccharomyces cerevisiae harbor several copies of a 2-micron plasmid circle DNA termed "2 micron." This circular plasmid contains two 599-base-pair precise inverted repeats across which a site-specific inversion event occurs in vivo. This inversion is promoted by a plasmid-encoded function called "FLP." We have cloned the FLP gene of 2-micron DNA under control of a strong yeast promoter and transformed yeast cells with a plasmid containing the cloned FLP gene. Cell-free extracts from such a transformant promote highly efficient inversion of 2-micron DNA in vitro. The reaction requires a cation and works efficiently on supercoiled, relaxed circular, or linear DNA. The FLP activity bears certain similarities to the cre protein, a site-specific recombinase encoded by bacteriophage P1.
Interrelationships Among Circulating Interleukin-6, C-Reactive Protein, and Traditional Cardiovascular Risk Factors in Women (2002)

Plasma levels of IL-6 and CRP are independently related to several clinical cardiovascular risk factors in women.
Neuropeptide Y and peptide YY: major modulators of gastrointestinal blood flow and function (1991)

The present paper reviews the chemistry, distribution, and release of neuropeptide Y (NPY) and peptide YY (PYY) and evaluates their role as neuronal and hormonal regulators in gastrointestinal physiology. In addition, the current concepts of receptors for NPY and PYY, the Y1 and Y2 receptor subtypes and their localization, characterization by ligand binding studies, and structural analysis by affinity-labeling experiments, are presented and discussed. NPY is present in both central and peripheral neurons, whereas PYY is mainly expressed in endocrine cells in the lower bowel. PYY and NPY inhibit gut motility, gastric emptying and acid secretion, and pancreatic exocrine secretion and are potent vasoconstrictors in many vascular beds. It is suggested that these peptides regulate gastrointestinal function by effects on blood flow, by modulating neural control mechanism, and in some cases by direct effects on differential functional cells such as enterocytes. Multiple receptors for NPY and PYY probably exist, and these appear to fall into Y1 and Y2 types by their specificity for a long COOH-terminal fragment, NPY-(13-36) and an NPY analogue, [Leu31,Pro34]NPY. The latter is specific for Y1 receptors, whereas the COOH-terminal fragment preferentially binds to Y2 receptors. Furthermore, affinity-labeling experiments have shown that the Y1 and Y2 receptors are structurally distinct glycoproteins. It is concluded that the herein characterized Y1 and Y2 receptors may be the structural proteins that mediate the physiological actions of NPY and PYY.
Theory of Complex Spectra. I (1942)

This paper gives a closed formula which entirely replaces for the two-electron spectra the previous lengthy calculations with the diagonal-sum method. Applications are also made to some configurations with three or more electrons and to the ${p}^{\ensuremath{'}\ensuremath{'}}$ configurations of the nuclei.
Isolation and characterization of a high-molecular-weight polysaccharide from the slime of Pseudomonas aeruginosa (1978)

A procedure is described for isolating a high-molecular-weight polysaccharide (PS) from the slime of Pseudomonas aeruginosa immunotype 1. The resultant material, obtained from the void volume of a Sephadex G-100 column, was composed of carbohydrate and water. No lipopolysaccharide (LPS), 2-keto-3-deoxyoctonoate, heptose, phosphate, or protein was detectable, and nucleic acid contamination was generally below 1%. The carbohydrate composition of the PS was glucose, rhamnose, galactose, arabinose, and mannose. PS had a molecular weight of between 100,000 and 350,000 and did not disaggregate when chromatographed in the presence of sodium deoxycholate. An antigen immunologically indistinguishable from PS could be obtained from LPS by either acetic acid hydrolysis and column chromatography or by allowing solutions of LPS to stand at room temperature for 3 days. Some of this LPS-associated polysaccharide eluted as the void volume of a G-100 column but differed from PS by its lack of galactose and arabinose. LPS also contained an immunodeterminant not shared with PS that was detected by its stability to dilute alkali treatment (0.1 N NaOH, 37 degrees C, 2 h). PS was destroyed by alkali treatment. PS appeared to represent a form of LPS polysaccharide side chain that contains galactose and arabinose and is of a high molecular weight.
A Practical Guide to Supramolecular Chemistry (2005)

The origins of supramolecular chemistry are intimately linked to Pedersen's pioneering work on crown ethers.
Electron-Transport Rates in an Enzyme Electrode for Glucose (1994)

We describe here the kinetics and mechanism of electron transport in an enzyme electrode where glucose oxidase is connected to the electrode surface with an electron transfer relay consisting of an osmium polypyridyl complex pendent on a polypyridine backbone. The effective electron diffusion coefficient in this polymer hydrogel was measured in films containing various loadings of enzyme using a steady-state-method involving interdigitated array electrodes and was found to range between 1.6x10-9 and <1.5x10-10 cm2 s-1. The behavior of this parameter as a function of enzyme loading was related to the mechanism proposed to be operating in these sensors.
Screening of Protein Crystallization Conditions on a Microfluidic Chip Using Nanoliter-Size Droplets (2003)

Protein crystallization is a major bottleneck in determining tertiary protein structures from genomic sequence data. This paper describes a microfluidic system for screening hundreds of protein crystallization conditions using less than 4 nL of protein solution for each crystallization droplet. The droplets are formed by mixing protein, precipitant, and additive stock solutions in variable ratios in a flow of water-immiscible fluids inside microchannels. Each droplet represents a discrete trial testing different conditions. The system has been validated by crystallization of several water-soluble proteins.