gebhart/patrepeval huggingface dataset:
Automatic abstracting and indexing. II. Production of indicative abstracts by application of contextual inference and syntactic coherence criteria (1971)

Abstract Together with the increasing shortage of qualified abstractors, the factors of time, cost and value have lent impetus to a trend toward the automatic generation of abstracts and indexes. This trend has caused increased emphasis to be placed on the abstract as the locus of data for automatic retrieval systems. This necessitates the creation of high quality abstracts. It is the purpose of this paper to report on the development of techniques for the automatic production of high quality abstracts from the full text of the original document. It is necessary to analyze the conditions under which various methods of sentence selection are successful, in order to develop criteria for selecting sentences to form an abstract. But clearly, an abstract can also be produced by rejecting sentences of the original which are irrelevant to the abstract. As will be seen, it is this point which is perhaps the most significant contribution of this paper. Methods of sentence selection and rejection are discussed. These include contextual inference, intersentence reference, frequency criteria, and coherency considerations. The automatic abstracting system we have developed consists basically of a dictionary, called the Word Control List, and of a set of rules for implementing certain functions specified for each WCL entry. The abstracts we have obtained so far are of sufficiently good quality to indicate that large‐scale testing of the methods of the automatic abstracting system is warranted. This abstract was produced by the system described in this paper.
Therapeutic effect of Gag-nuclease fusion protein on retrovirus-infected cell cultures (1996)

Capsid-targeted viral inactivation is a novel protein-based strategy for the treatment of viral infections. Virus particles are inactivated by targeting toxic fusion proteins to virions, where they destroy viral components from within. We have fused Staphylococcus nuclease (SN) to the C-terminal end of Moloney murine leukemia virus Gag and demonstrated that expression of this fusion protein in chronically infected chicken embryo fibroblasts resulted in its incorporation into virions and subsequent inactivation of the virus particles by degradation of viral RNA. Release of particles incorporating Gag-SN fusion proteins into the extracellular milieu activates the nuclease and results in destruction of the virion from within. By comparing the effects of incorporated SN and SN*, an enzymatically inactive missense mutant form of SN, on the infectivity of virus particles, we have clearly demonstrated that nucleolytic activity is the antiviral mechanism. Expression of Gag-SN fusion proteins as a therapeutic agent causes a stable reduction of infectious titers by 20- to 60-fold. The antiviral effect of capsid-targeted viral inactivation in our model system, using both prophylactic and therapeutic approaches, suggests that a similar anti-human immunodeficiency virus strategy might be successful.
Conducting linear chains of sulphur inside carbon nanotubes (2013)

Despite extensive research for more than 200 years, the experimental isolation of monatomic sulphur chains, which are believed to exhibit a conducting character, has eluded scientists. Here we report the synthesis of a previously unobserved composite material of elemental sulphur, consisting of monatomic chains stabilized in the constraining volume of a carbon nanotube. This one-dimensional phase is confirmed by high-resolution transmission electron microscopy and synchrotron X-ray diffraction. Interestingly, these one-dimensional sulphur chains exhibit long domain sizes of up to 160 nm and high thermal stability (~800 K). Synchrotron X-ray diffraction shows a sharp structural transition of the one-dimensional sulphur occurring at ~450-650 K. Our observations, and corresponding electronic structure and quantum transport calculations, indicate the conducting character of the one-dimensional sulphur chains under ambient pressure. This is in stark contrast to bulk sulphur that needs ultrahigh pressures exceeding ~90 GPa to become metallic.
[A pilot study on trihalomethane formation in water treated by chlorine dioxide]. (1996)

Trihalomethane (THM) formation was determined by gas chromatography in water disinfected with chlorine dioxide (ClO2) only or ClO2 combined with chlorine (Cl2), to lay a basis for water disinfected with ClO2. Results showed no THM was produced in water disinfected with ClO2 only if without existence of bromine (Br) ion in it; certain amount of bromoform could be formed with existence of bromine ion, and THM formation could be inhibited by ClO2 and Cl2, with a ratio of greater than 1 between them. Light irradiation could decrease the amount of THM produced whether in disinfection with ClO2 or combination with ClO2 and Cl2. No significant effect of pH value of water on THM formation was observed, but pH should be controlled under neutral or slightly acidic to ensure the concentration of ClO2 in water.
Alkyl Hydroperoxide Reductases C and D Are Major Antigens Constitutively Expressed by Mycobacterium avium subsp. paratuberculosis (2000)

Antigens characteristic for Mycobacterium avium subspecies paratuberculosis were identified by crossed immunoelectrophoresis (CIE) and by absorbing out cross-reactive antigens by using a polyclonal and polyvalent Mycobacterium avium subspecies avium antiserum. Two antigens were present in M. avium subsp. paratuberculosis and not detected in Mycobacterium avium subsp. avium. They were identified as antigens 17 and 20 in a CIE reference system for M. avium subsp. paratuberculosis antigens. Purified antigen 20 was identified as alkyl hydroperoxide reductase C (AhpC) while the N-terminal part of purified antigen 17 showed 80% homology with alkyl hydroperoxide reductase D (AhpD) of Mycobacterium tuberculosis. AhpC had a nonreduced mobility in sodium dodecyl sulfate-polyacrylamide gel electrophoresis corresponding to a molecular mass of 45 kDa and is probably a homodimer linked with disulfide bridges in its native form. AhpD had a mobility corresponding to 19 kDa. Monospecific rabbit antiserum against AhpC and AhpD reacted with 9 strains of M. avium subsp. paratuberculosis but not with 20 other mycobacterial strains except for a Mycobacterium gordonae strain, against which a weak cross-reactive band was produced. Goats experimentally infected with M. avium subsp. paratuberculosis had strong gamma interferon (IFN-gamma) responses toward both AhpC and AhpD, and they also had antibodies against AhpC. The ability of AhpC and AhpD to induce IFN-gamma production shows that these proteins potentially could be used in future vaccines or in diagnostic assays. These results further show that AhpC and AhpD are immunologically important proteins which are constitutively and highly expressed in M. avium subsp. paratuberculosis without the bacteria being submitted to oxidative stress and that the specificities of antigens can be a matter of different levels of protein expression in various species as well as distinct structural differences.
Proteomics computational analyses suggest that baculovirus GP64 superfamily proteins are class III penetrenes (2008)

These results suggest that proteins in the GP64 superfamily are class III penetrenes.
An Innovative Unit Cell Guide to Multimodal Frequency-Selective Surfaces (2006)

A number of multimodal frequency-selective surfaces (FSS) have been fabricated from arrays of unit cells containing two or four, triangular or square, split-ring resonators. In this paper, the underlying physics of the modulation of the spectral intensities in these surfaces is examined
Malignant Activation of a K- ras Oncogene in Lung Carcinoma But Not in Normal Tissue of the Same Patient (1984)

A single genetic alteration, a guanine-to-cytosine transversion, is responsible for the acquisition of malignant properties by K-ras genes of two human tumor cell lines established from carcinomas of the bladder (A1698) and lung (A2182). As a consequence, arginine instead of the normal glycine is incorporated into the K-ras-coded p21 proteins at amino acid position 12. This mutation creates a restriction enzyme polymorphism that can be used to screen human cells for transforming K-ras genes. This approach was used to identify the mutational event responsible for the malignant activation of a K-ras oncogene in a squamous cell lung carcinoma of a 66-year-old man; this point mutation was not present in either the normal bronchial or parenchymal tissue or in the blood lymphocytes. Hence, malignant activation of a ras oncogene appears to be specifically associated with the development of a human neoplasm.
Antitumor effects of ricin A chain immunotoxins prepared from intact antibodies and Fab' fragments on solid human Hodgkin's disease tumors in mice. (1990)

Three monoclonal antibodies which strongly bind to Hodgkin and Reed-Sternberg cells and two corresponding Fab' fragments were linked to deglycosylated ricin A chain (dg A) to evaluate their potential as immunotoxins for the treatment of Hodgkin's disease. Two of the antibodies, Ber-H2 and HRS-3, were shown to bind to the same epitope on the CD30 antigen, whereas the third antibody, IRac, bound to a different antigen. None of the antibodies significantly cross-reacted with normal human tissues as judged by indirect immunofluorescence and immunoperoxidase analyses on frozen sections from 28 normal tissues. All three antibodies formed potent and specific immunotoxins. They inhibited protein synthesis of the L540 Hodgkin's disease cell line in vitro by 50% at concentrations of 1 x 10(-11) M for IRac.dgA, 9 x 10(-11) M for HRS-3.dgA, and 2 x 10(-10) M for Ber-H2.dgA. HRS-3 Fab' and IRac Fab' immunotoxins were 7.8- and 60-fold less cytotoxic, respectively, than their intact counterparts in vitro. In vivo, a single i.v. injection of a dose of Ber-H2.dgA, HRS-3.dgA, or IRac.dgA corresponding to 40% of the LD50 induced lasting complete remissions in 38, 44, and 50%, respectively, of mice with solid s.c. L540 tumors of 60 to 80 mm3 size (0.5-cm diameter). At equivalent dosage (40% of the LD50), the HRS-3 Fab'.dgA and the IRac Fab'.dgA both induced lasting complete remissions in 25% of the mice, although the HRS-3 Fab'.dgA was significantly superior to IRac Fab'.dgA at retarding tumor growth in the remaining animals. The effectiveness of the immunotoxins depended on the size of the tumor at the time of injection, since IRac.dgA treatment induced complete remissions in 100% of mice with small tumors (10 to 20 mm3, approximately 0.3 cm in diameter) but only 13% of mice with larger tumors of 400 to 600 mm3 (approximately 1 cm in diameter). Tumors which regrew after IRac.dgA treatment mainly consisted of antigen-deficient mutants having reduced sensitivity to IRac.dgA but normal sensitivity to HRS-3.dgA. It is concluded that HRS-3.dgA, HRS-3 Fab'.dgA, and IRac.dgA are candidates for the treatment of Hodgkin's disease in humans.
The Met Proto-Oncogene Mesenchymal to Epithelial Cell Conversion (1994)

Coexpression of the human Met receptor and its ligand, hepatocyte growth factor/scatter factor (HGF/SF), in NIH 3T3 fibroblasts causes the cells to become tumorigenic in nude mice. The resultant tumors display lumen-like morphology, contain carcinoma-like focal areas with intercellular junctions resembling desmosomes, and coexpress epithelial (cytokeratin) and mesenchymal (vimentin) cytoskeletal markers. The tumor cells also display enhanced expression of desmosomal and tight-junction proteins. The apparent mesenchymal to epithelial conversion of the tumor cells mimics the conversion that occurs during embryonic kidney development, suggesting that Met-HGF/SF signaling plays a role in this process as well as in tumors that express both epithelial and mesenchymal markers.
Application of a modification of the Polonovski reaction to the synthesis of vinblastine-type alkaloids (1976)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTApplication of a modification of the Polonovski reaction to the synthesis of vinblastine-type alkaloidsNicole Langlois, Francoise Gueritte, Yves Langlois, and Pierre PotierCite this: J. Am. Chem. Soc. 1976, 98, 22, 7017–7024Publication Date (Print):October 1, 1976Publication History Published online1 May 2002Published inissue 1 October 1976https://pubs.acs.org/doi/10.1021/ja00438a046https://doi.org/10.1021/ja00438a046research-articleACS PublicationsRequest reuse permissionsArticle Views1471Altmetric-Citations198LEARN 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
Clinical significance of the expression of epidermal growth factor and its receptor in esophageal cancer (1991)

The epidermal growth factor receptor (EGFR) level in 56 esophageal cancer tissues was measured by 125I-EGF binding assay to elucidate its role in tumor progression. The survival rate of patients with high EGFR level (more than 50 fmol/mg protein) was significantly lower than that of patients with low EGFR level (less than 50 fmol/mg protein, P less than 0.01), although a correlation between EGFR level and the pathologic findings was not observed. The expression of EGF was examined immunohistochemically using anti-EGF monoclonal antibody in 100 esophageal cancer tissues; EGF-positive tumor cells were detected in 92.0%. The immunoreactivity of EGF was classified arbitrarily into four grades according to the number of stained tumor cells. The expression of EGF significantly correlated with the differentiation of esophageal squamous cell carcinoma (P less than 0.01, by chi-square test). The survival rate of patients with high EGF immunoreactivity (Grade 2 or 3) was much lower than in those with lower grade (0 or 1) tumors, (P less than 0.01). Patients with both high EGFR level and EGF immunoreactivity had a much worse prognosis than if both were low. Furthermore, the mitotic index was higher in groups with both high EGFR and EGF than if both were low (16.39 +/- 5.35 versus 6.90 +/- 3.31). These results suggest that EGF and EGFR in the autocrine system may play an important role in tumor progression in esophageal cancer and their expression could be of prognostic significance.
Protein purification applications : a practical approach (1990)

J. Asenjo: Large scale purification A. F. Bristow: Purification of proteins for therapeutic use S. P. Wood: Purification for crystallography J. B. C. Findlay: Purification of membrane proteins J. B. C. Findlay: Purification of proteins for sequencing S. J. Brewer & H. M. Sassenfeld: Engineering proteins for purification
From atoms and bonds to three-dimensional atomic coordinates: automatic model builders (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleFrom atoms and bonds to three-dimensional atomic coordinates: automatic model buildersJens. Sadowski and Johann. GasteigerCite this: Chem. Rev. 1993, 93, 7, 2567–2581Publication Date (Print):November 1, 1993Publication History Published online1 May 2002Published inissue 1 November 1993https://pubs.acs.org/doi/10.1021/cr00023a012https://doi.org/10.1021/cr00023a012research-articleACS PublicationsRequest reuse permissionsArticle Views938Altmetric-Citations356LEARN 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
To Tune or Not to Tune? Adapting Pretrained Representations to Diverse Tasks (2019)

While most previous work has focused on different pretraining objectives and architectures for transfer learning, we ask how to best adapt the pretrained model to a given target task. We focus on the two most common forms of adaptation, feature extraction (where the pretrained weights are frozen), and directly finetuning the pretrained model. Our empirical results across diverse NLP tasks with two stateof-the-art models show that the relative performance of fine-tuning vs. feature extraction depends on the similarity of the pretraining and target tasks. We explore possible explanations for this finding and provide a set of adaptation guidelines for the NLP practitioner.
Structure of a single-chain antibody variable domain (Fv) fragment complexed with a carbohydrate antigen at 1.7-A resolution. (1994)

We describe here the 1.7-A resolution structure of a single-chain antibody variable domain (scFv) molecule, based on the carbohydrate-binding antibody Se155-4, complexed with the trisaccharide ligand alpha-D-Gal(1-->2)[alpha-D-Abe(1-->3)]alpha-D-Manp1-->OMe, where Abe is abequose. The scFv expressed in Escherichia coli has the variable region light chain to heavy chain polarity with the domains connected by a 19-residue linker. Although the linker is partially disordered in the crystal, the packing of the molecules suggests a monomeric state of the scFv. The carbohydrate adopts a different conformation about the Man-Gal linkage than was observed previously in the Fab-trisaccharide complex. Instead of a direct hydrogen bond between O2Abe and O2Gal, these two atoms are bridged by a water molecule in the present complex.
Biclustering of expression data. (2000)

An efficient node-deletion algorithm is introduced to find submatrices in expression data that have low mean squared residue scores and it is shown to perform well in finding co-regulation patterns in yeast and human. This introduces "biclustering", or simultaneous clustering of both genes and conditions, to knowledge discovery from expression data. This approach overcomes some problems associated with traditional clustering methods, by allowing automatic discovery of similarity based on a subset of attributes, simultaneous clustering of genes and conditions, and overlapped grouping that provides a better representation for genes with multiple functions or regulated by many factors.
Transmembrane Protein Structure: Spin Labeling of Bacteriorhodopsin Mutants (1990)

Transmembrane proteins serve important biological functions, yet precise information on their secondary and tertiary structure is very limited. The boundaries and structures of membrane-embedded domains in integral membrane proteins can be determined by a method based on a combination of site-specific mutagenesis and nitroxide spin labeling. The application to one polypeptide segment in bacteriorhodopsin, a transmembrane chromoprotein that functions as a light-driven proton pump is described. Single cysteine residues were introduced at 18 consecutive positions (residues 125 to 142). Each mutant was reacted with a specific spin label and reconstituted into vesicles that were shown to be functional. The relative collision frequency of each spin label with freely diffusing oxygen and membrane-impermeant chromium oxalate was estimated with power saturation EPR (electron paramagnetic resonance) spectroscopy. The results indicate that residues 129 to 131 form a short water-exposed loop, while residues 132 to 142 are membrane-embedded. The oxygen accessibility for positions 131 to 138 varies with a periodicity of 3.6 residues, thereby providing a striking demonstration of an alpha helix. The orientation of this helical segment with respect to the remainder of the protein was determined.
Asymptotic variance expressions for identified black-box transfer function models (1985)

Identification of black-box transfer function models is considered. It is assumed that the transfer function models possess a certain shift-property, which is satisfied for example by all polynomial-type models. Expressions for the variances of the transfer function estimates are derived, that are asymptotic both in the number of observed data and in the model orders. The result is that the joint covariance matrix of the transfer functions from input to output and from driving white noise source to the additive output disturbance, respectively, is proportional to the inverse of the joint spectrum matrix for the input and driving noise multiplied by the spectrum of the additive output noise. The factor of proportionality is the ratio of model order to number of data. This result is independent of the particular model structure used. The result is applied to evaluate the performance degradation due to variance for a number of typical model uses. Some consequences for input design are also drawn.
Suppression of immune responses by nonimmunogenic oligodeoxynucleotides with high affinity for high-mobility group box proteins (HMGBs) (2011)

The activation of innate immune responses by nucleic acids is central to the generation of host responses against pathogens; however, nucleic acids can also trigger the development and/or exacerbation of pathogenic responses such as autoimmunity. We previously demonstrated that the selective activation of nucleic acid-sensing cytosolic and Toll-like receptors is contingent on the promiscuous sensing of nucleic acids by high-mobility group box proteins (HMGBs). From this, we reasoned that nonimmunogenic nucleotides with high-affinity HMGB binding may function as suppressing agents for HMGB-mediated diseases, particularly those initiated and/or exacerbated by nucleic acids. Here we characterize an array of HMGB-binding, nonimmunogenic oligodeoxynucleotides (ni-ODNs). Interestingly, we find that binding affinity is rather independent of nucleotide sequence, but is instead dependent on length and structure of the deoxyribose backbone. We further show that these ni-ODNs can strongly suppress the activation of innate immune responses induced by both classes of nucleic acid-sensing receptors. We also provide evidence for the suppressive effect of an ni-ODN, termed ISM ODN, on the induction of adaptive immune responses and in mouse models of sepsis and autoimmunity. We discuss our findings in relation to the critical role of HMGBs in initiating immune responses and the possible use of these ni-ODNs in therapeutic interventions.