gebhart/patrepeval huggingface dataset:
Autoimmune encephalomyelitis (EAE) mediated or prevented by T lymphocyte lines directed against diverse antigenic determinants of myelin basic protein. Vaccination is determinant specific. (1983)

Lines of T lymphocytes reactive against the basic protein of myelin (BP) were found in previous studies to mediate experimental autoimmune encephalomyelitis (EAE) in rats. Moreover, inoculation of rats with attenuated anti-BP line cells vaccinated them against subsequent attempts to induce active EAE by injection of BP in adjuvant. In the present study, we investigated the effects of T lymphocyte lines reactive to different antigenic determinants on the BP molecule, they are the major encephalitogenic peptide (EP) determinant present on guinea pig BP (G-BP), and minor, non-EP determinants present on bovine BP (B-BP). We found that both lines of T lymphocytes could mediate EAE. Resistance to active EAE acquired by spontaneous recovery from line mediated EAE or by vaccination with attenuated cells, however, was found to be specific for the particular BP determinant. Thus, EAE may be mediated by lines of T lymphocytes reactive to different determinants on the BP molecule, but the resistance to EAE acquired by exposure to line cells is determinant specific. This suggests that acquired resistance to EAE is directed by the receptor specificity of the autoimmune anti-BP T cells.
A General Route for Post-Translational Cyclization of mRNA Display Libraries (2005)

Cyclic peptides are attractive scaffolds for the design of conformationally constrained molecular therapeutics. Previously, biological display libraries could only be cyclized via disulfide bonds, which are labile and can be reduced in an intracellular environment. In this paper, we construct high diversity, covalently cyclized mRNA display libraries (>1013 sequences) and analyze the cyclization reaction using MALDI-TOF MS and unnatural amino acid incorporation. Our route allows the extent of cyclization to be evaluated quantitatively and is broadly applicable to a variety of cyclization chemistries.
Luminescent Properties of Cerium-Activated Garnet Series Phosphor: Structure and Temperature Effects (2008)

The behaviors of Y, Tb, and Gd garnet phosphor powders activated by cerium were studied. Emission spectra with a continuous yellowish range from green-yellow to yellow-orange were produced by controlling the compositions of the solid solution. By increasing the substitution concentration of large cations in the garnet phosphor, the emission intensity tended to decrease and the temperature sensitivity of phosphors tended to increase. The redshift of the emission wavelength depended on the radius size of the substituted cation at the dodecahedral site of the garnet structure. Using a quantum mechanically based configurational coordinate diagram, the thermal quenching behavior, emission spectra, Stokes shift, nonradiative transitions in different host environments, and activator concentrations are discussed.
Investigating the target recognition of DNA cytosine-5 methyltransferase HhaI by library selection using in vitro compartmentalisation (2002)

In vitro compartmentalisation (IVC), a technique for selecting genes encoding enzymes based on compartmentalising gene translation and enzymatic reactions in emulsions, was used to investigate the interaction of the DNA cytosine-5 methyltransferase M.HhaI with its target DNA (5'-GCGC-3'). Crystallography shows that the active site loop from the large domain of M.HhaI interacts with a flipped-out cytosine (the target for methylation) and two target recognition loops (loops I and II) from the small domain make almost all the other base-specific interactions. A library of M.HhaI genes was created by randomising all the loop II residues thought to make base-specific interactions and directly determine target specificity. The library was selected for 5'-GCGC-3' methylation. Interestingly, in 11 selected active clones, 10 different sequences were found and none were wild-type. At two of the positions mutated (Ser252 and Tyr254) a number of different amino acids could be tolerated. At the third position, however, all active mutants had a glycine, as in wild-type M.HhaI, suggesting that Gly257 is crucial for DNA recognition and enzyme activity. Our results suggest that recognition of base pairs 3 and 4 of the target site either relies entirely on main chain interactions or that different residues from those identified in the crystal structure contribute to DNA recognition.
The Synthesis of Bovine Insulin by the Solid Phase Method1 (1966)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe Synthesis of Bovine Insulin by the Solid Phase Method1B. Marglin and R. B. MerrifieldCite this: J. Am. Chem. Soc. 1966, 88, 21, 5051–5052Publication Date (Print):November 1, 1966Publication History Published online1 May 2002Published inissue 1 November 1966https://pubs.acs.org/doi/10.1021/ja00973a068https://doi.org/10.1021/ja00973a068research-articleACS PublicationsRequest reuse permissionsArticle Views779Altmetric-Citations132LEARN 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
Marrow transplantation for malignant lymphoma. (1987)

With a large number of patients treated, some more than a decade ago, it is now clear that the use of high-dose therapy combined with marrow transplantation can cure some patients of malignant lymphoma who are otherwise incurable. Two major questions which are considered in this review are: (1) how can currently available transplant techniques be best applied, and (2) how do we go about developing more effective transplant regimens?
Cloning of RNA moleculesin vitro (1993)

A method for RNA amplification in an immobilized medium is described. The medium contains a complete set of nucleotide substrates and purified Q beta replicase, an enzyme capable of exponentially amplifying RNAs under isothermal conditions. RNA amplification in the immobilized medium results in the formation of separate 'colonies', each comprising the progeny of a single RNA molecule (a clone). The colonies were visualized by staining with ethidium bromide, by utilizing radioactive substrates, and by hybridization with sequence-specific labeled probes. The number and identity of the RNA colonies corresponded to that of the RNAs seeded. When a mixture of different RNA species was seeded, these species were found in different colonies. Possible implementations of this technique include a search for recombinant RNAs, very sensitive nucleic acid diagnostics, and gene cloning in vitro.
Asymptotic Dipole Radiation Formulas (1929)

The analysis of the radiation from dipoles as given hy Sommerfeld and by von Hoerschelmann is deficient in one respect: it does not give the true <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sup> asymptotic expressions for the radiation leaving at a considerable angle from the horizontal. The correct asymptotic formulas have already heen easily supplied by an appeal to the Reciprocal Theorem; lately M. J. O. Strutt <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> has got them directly from the boundary conditions and H. Weyl <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> has derived the correct asymptotic formula for a vertical dipole at the surface of the earth by a method quite different from Sommerfeld's. In the present paper it is shown how they can be got by merely improving the rigor of Sommerfeld's analysis.
Imaging and Tracking of Tat Peptide-Conjugated Quantum Dots in Living Cells:  New Insights into Nanoparticle Uptake, Intracellular Transport, and Vesicle Shedding (2007)

We report the use of Tat peptide-conjugated quantum dots (Tat-QDs) to examine the complex behavior of nanoparticle probes in live cells, a topic that is of considerable current interest in developing advanced nanoparticle agents for molecular and cellular imaging. Dynamic confocal imaging studies indicate that the peptide-conjugated QDs are internalized by macropinocytosis, a fluid-phase endocytosis process triggered by Tat-QD binding to negatively charged cell membranes. The internalized Tat-QDs are tethered to the inner vesicle surfaces and are trapped in cytoplasmic organelles. The QD loaded vesicles are found to be actively transported by molecular machines (such as dyneins) along microtubule tracks. The destination of this active transport is an asymmetric perinuclear region (outside the cell nucleus) known as the microtubule organizing center (MTOC). We also find that Tat-QDs strongly bind to cellular membrane structures such as filopodia and that large QD-containing vesicles are released from the tips of filopodia by vesicle shedding. These results provide new insights into the mechanisms of Tat peptide-mediated delivery as well as toward the design of functionalized nanoparticles for molecular imaging and targeted therapy.
NMR studies of DNA duplexes singly cross-linked by different synthetic linkers (1995)

Molecular modelling studies resulted in the design of a variety of non-nucleotidic covalent linkers to bridge the 3'-end of the (+)-strand and the 5'-end of the (-)-strand in DNA duplexes. Three of these linkers were synthesized and used to prepare singly cross-linked duplexes d(GTGGAATTC)-linker-d(GAATTCCAC). Linker I is an assembly of a propylene-, a phosphate- and a second propylene-group and is thought to mimic the backbone of two nucleotides. Linkers II and III consist of five and six ethyleneglycol units, respectively. The melting temperatures of the cross-linked duplexes are 65 degrees C for I and 73 degrees C for II and III, as compared with 36 degrees C for the corresponding non-linked nonadeoxynucleotide duplex. The three cross-linked duplexes were structurally characterized by nuclear magnetic resonance spectroscopy. The 1H and 31P resonance assignments in the DNA stem were obtained using standard methods. For the resonance assignment of the linker protons, two-dimensional 1H-31P heteronuclear COSY and two-quantum-experiments were used. Distance geometry calculations with NOE-derived distance constraints were performed and the resulting structures were energy-minimized. In duplex I, the nucleotides flanking the propylene-phosphate-propylene-linker do not form a Watson-Crick base pair, whereas in duplexes II and III the entire DNA stem is in a B-type double helix conformation.
Inference of Population Structure Using Multilocus Genotype Data (2000)

We describe a model-based clustering method for using multilocus genotype data to infer population structure and assign individuals to populations. We assume a model in which there are K populations (where K may be unknown), each of which is characterized by a set of allele frequencies at each locus. Individuals in the sample are assigned (probabilistically) to populations, or jointly to two or more populations if their genotypes indicate that they are admixed. Our model does not assume a particular mutation process, and it can be applied to most of the commonly used genetic markers, provided that they are not closely linked. Applications of our method include demonstrating the presence of population structure, assigning individuals to populations, studying hybrid zones, and identifying migrants and admixed individuals. We show that the method can produce highly accurate assignments using modest numbers of loci-e.g. , seven microsatellite loci in an example using genotype data from an endangered bird species. The software used for this article is available from http://www.stats.ox.ac.uk/ approximately pritch/home. html.
Combining High Level Symptom Descriptions and Low Level State Information for Configuration Fault Diagnosis (2004)

Automatic fault diagnosis is an important problem for system management. In this paper, we combine high level symptom descriptions and low level state information to solve the system fault diagnosis problem. We extract state-symptom correlation information from knowledge sources in text format, and then use symptom similarity to rank the candidate system states. We apply the method to Windows Registry problems to help Product Support Service (PSS) engineers. Promising results with two different knowledge sources show the robustness of our method. Finally, we explain why this combination is successful and also discuss its limitations.
Context preserving dynamic word cloud visualization (2010)

In this paper, we introduce a visualization method that couples a trend chart with word clouds to illustrate temporal content evolutions in a set of documents. Specifically, we use a trend chart to encode the overall semantic evolution of document content over time. In our work, semantic evolution of a document collection is modeled by varied significance of document content, represented by a set of representative keywords, at different time points. At each time point, we also use a word cloud to depict the representative keywords. Since the words in a word cloud may vary one from another over time (e.g., words with increased importance), we use geometry meshes and an adaptive force-directed model to lay out word clouds to highlight the word differences between any two subsequent word clouds. Our method also ensures semantic coherence and spatial stability of word clouds over time. Our work is embodied in an interactive visual analysis system that helps users to perform text analysis and derive insights from a large collection of documents. Our preliminary evaluation demonstrates the usefulness and usability of our work.
Small noncleaved cell lymphoma and leukemia in adults. A retrospective study of 65 adults treated with the LMB pediatric protocols (1995)

In France, more than 80% of children with Burkitt's lymphoma or Burkitt's leukemia (ALL3) are now cured with the LMB (B-cell non-Hodgkin's lymphoma and B-ALL) protocols of the Société Française d'Oncologie Pédiatrique, but so far, poor results have been obtained in the few adult studies available. We have analyzed the experience with LMB protocols in adult patients. This retrospective study involved 65 adult patients with small noncleaved cell lymphoma or ALL3 treated with the LMB protocols. They were 17 to 65 years old and not previously treated. Human immunodeficiency virus-infected patients were excluded. The diagnoses were made between September 1984 and August 1991. According to the Murphy classification, 12 patients (18%) had stage I or II disease, 25 (38%), stage III disease; 4 (6%), stage IV disease; and 24 (37%), ALL3 (> or = 25% blasts). According to the Ann Arbor classification, 9 patients had stage I disease; 8 patients, stage II; 5 patients, stage III; 21 patients, stage IV disease; and 22 patients, ALL (> or = 30% blasts). Twelve patients had central nervous system (CNS) involvement before treatment. Thirty-nine patients were treated according to the LMB 84 protocol scheme; 14 according to the LMB 86 protocol, and 12 patients received the LMB 84 induction courses followed by the LMB 86 consolidation courses. Three patients underwent bone marrow transplantation (BMT) while in second complete remission (CR) and 3 others had refractory disease. There were some protocol violations caused by empirical medical decisions: local irradiation was performed in 4 patients, 2 patients received prophylactic radiation to the brain that was not specified in the protocol, 13 patients underwent BMT in first CR, and methotrexate doses were modified in 10 patients. Fifty-eight patients (89%) achieved a CR. There were four (6%) primary induction treatment failures, and three (4%) early treatment-related deaths. Eight patients relapsed between 2 and 30 months after CR (median, 4.7 months). Forty-seven patients are alive in CR (45 first CR, 2 second CR) with a median follow-up of 57 months (24 to 93 months). There were five toxicity-related deaths among patients in CR including four BMT-related deaths and five deaths caused by refractory relapses. One patient died in CR at 62 months of rectal cancer. The 3-year overall survival rate is 74% (SE = 5). According to the stages in the Murphy classification, the 3-year survival rates are stages I and II, 100%; stage III, 80% (SE = 7); and stage IV and ALL, 57% (SE = 8). Seven of 12 patients with initial CNS disease are alive with a median survival of 56 months.(ABSTRACT TRUNCATED AT 400 WORDS)
Distinct Protein Targets for Signals Acting at the c- fos Serum Response Element (1991)

The c-fos serum response element (SRE) is a primary nuclear target for intracellular signal transduction pathways triggered by growth factors. It is the target for both protein kinase C (PKC)-dependent and -independent signals. Function of the SRE requires binding of a cellular protein, termed serum response factor (SRF). A second protein, p62TCF, recognizes the SRE-SRF complex to form a ternary complex. A mutated SRE that bound SRF but failed to form the ternary complex selectively lost response to PKC activators, but retained response to PKC-independent signals. Thus, two different signaling pathways act through discrete nuclear targets at the SRE. At least one of these pathways functions by recruitment of a pathway-specific accessory factor (p62TCF). These results offer a molecular mechanism to account for the biological specificity of signals that appear to act through common DNA sequence elements.
Is bone a target-tissue for the nervous system? New advances on the understanding of their interactions. (2000)

Bone cells respond in specific ways to various hormones and growth factors, but the biology of skeletal innervation and its physiologic significance in bone metabolism is poorly understood. With the introduction of immunohistochemical staining techniques and new molecular biology tools, the knowledge in this field has significantly improved. In this review, we update current understanding of the effects of neuropeptides on bone metabolism, specifically vasoactive intestinal peptide (VIP) and calcitonin-gene related peptide (CGRP). In addition, new information concerning the role of growth factors, such as neurotrophins, is also discussed. There is strong evidence to suggest that bone can be a target of the nervous system. Further investigations in this field will allow us to answer questions related to pre-natal development, bone growth, fracture healing, osteoporosis, osteoarthritis or neoplasias of mesoderm origin.
CELL WALL COMPOSITION AND VIRULENCE IN ESCHERICHIA COLI (1968)

Uridine diphosphate galactose 4-epimerase and phosphomannose isomerase-deficient mutants of Escherichia coli O111:B4 were studied to test the hypothesis that in E. coli a specific relationship exists between O antigenicity, virulence, and capacity to resist phagocytosis. The first mutant, designated J-5, produces a cell wall lipopolysaccharide, the side chains of which do not contain galactose, glucose, N-acetylglucosamine, or colitose. The second mutant produces a cell wall lipopolysaccharide which lacks only colitose. The capacity of these various organisms to kill mice was strikingly different. E. coli O111 was 1000 times as virulent as J-5, and 100 times as virulent as L-2. The capacity of the organisms to kill mice was correlated with their ability to resist phagocytosis and to persist in the peritoneal cavity. The parent strain of O111 resisted phagocytosis by macrophages in vivo and polymorphonuclear leukocytes in vitro. The mutants did not, and the organism most deficient in the saccharide component of its LPS was most susceptible to phagocytosis and least virulent. These results were corroborated by growing the mutants in appropriately supplemented media which permitted the synthesis of complete LPS, reversed the susceptibility to phagocytosis, and restored virulence. Finally, serological reactivity was consistent with previous observations which had demonstrated that the O antigenicity of E. coli is determined by the saccharide composition of its cell wall lipopolysaccharide. Despite the difference in the capacity of the various log-phase organisms to kill mice when injected intraperitoneally, purified lipopolysaccharides extracted from them did not differ significantly in their capacity to kill or produce fever. Thus virulence was shown to be independent of endotoxin activity which in turn seemed to be unrelated to the saccharide composition of the cell wall LPS. Collectively, these data provide at least a partial molecular definition of virulence in E. coli by demonstrating that the presence or absence of specific sugars in its cell wall lipopolysaccharide is a determinant of its antiphagocytic capacity and its virulence.
Type inference for spreadsheets (2006)

Spreadsheets are the most popular programming systems in use today. Since spreadsheets are visual, first-order functional languages, research into the foundations of spreadsheets is therefore a highly relevant topic for the principles and, in particular, the practice, of declarative programming.Since the error rate in spreadsheets is very high and since those errors have significant impact, methods and tools that can help detect and remove errors from spreadsheets are very much needed. Type systems have traditionally played a strong role in detecting errors in programming languages, and it is therefore reasonable to ask whether type systems could not be helpful in improving the current situation of spreadsheet programming.In this paper we introduce a type system and a type inference algorithm for spreadsheets and demonstrate how this algorithm and the underlying typing concept can identify programming errors in spreadsheets. In addition, we also demonstrate how the type inference algorithm can be employed to infer models, or specifications, for spreadsheets, which can be used to prevent future errors in spreadsheets.