gebhart/patrepeval huggingface dataset:
Characterization of Grapevine Rugose Wood Disease Sources from Italy (1997)

A collection of 27 sources of grapevine rugose wood (RW) disease from a viticultural region in northern Italy was analyzed by graft-inoculating vines of three selective Vitis indicators (V. rupestris cv. St. George, V. berlandieri × V. riparia cv. Kober 5BB, and hybrid cv. LN 33). On the basis of stem reactivity, different groups were identified among the selected RW inoculum sources: nine isolates induced pitting only on cv. St. George, whereas four induced grooving only on cv. Kober 5BB. These two groups were classified as isolates of rupestris stem pitting and Kober stem grooving. Three of the remaining isolates induced wood abnormalities on cvs. LN 33 and Kober 5BB, seven induced wood abnormalities on cvs. St. George and Kober 5BB, and four induced symptoms on all three indicators. These groups may represent RW sources with various disease combinations. RW-affected grapevine clones used as inoculum sources also were tested for virus infections by enzyme-linked immunosorbent assay (ELISA). ELISA revealed the presence of grapevine fleck virus, grapevine leafroll-associated closterovirus 1 and 3, and grapevine trichovirus A. These viruses infected most of the selected RW sources. However, eight of the latter were ELISA-negative. The findings are discussed, and the biological and etiological complexity of the RW phenomena in grapevine is confirmed.
Site-specific and random fragmentation of Cu,Zn-superoxide dismutase by glycation reaction. Implication of reactive oxygen species. (1992)

Site-specific and random fragmentation of human Cu,Zn-superoxide dismutase (Cu,Zn-SOD) was observed following the glycation reaction (the early stage of the Maillard reaction). The fragmentation proceeded in two steps. In the first step, Cu,Zn-SOD was cleaved at a peptide bond between Pro62 and His63, as judged by amino acid analysis and sequencing of fragment peptides, yielding a large (15 kDa) and a small (5 kDa) fragment. In the second step, random fragmentation occurred. The ESR spectrum of the glycated Cu,Zn-SOD suggested that reactive oxygen species was implicated in the both steps of fragmentation. The same fragmentations were seen upon exposure of the enzyme to an H2O2 bolus. Catalase completely blocked both steps of the fragmentation process, whereas EDTA blocked only the second step. Incubation with glucose resulted in a time-dependent release of Cu2+ from the Cu,Zn-SOD molecule. The released Cu2+ then likely participated in a Fenton's type of reaction to produce hydroxyl radical, which may cause the nonspecific fragmentation. Evidence that EDTA abolished only the second step of fragmentation induced by an H2O2 bolus supports this mechanism. This is the first report that a site-specific fragmentation of a protein is caused by reactive oxygen species formed by the Maillard reaction.
A toothless tiger? (1992)

Prep looks set to become the latest victim of the recession and the stringent restrictions on public spending that have been imposed by the government. john naish reports
Broadening of Neutralization Activity to Directly Block a Dominant Antibody-Driven SARS-Coronavirus Evolution Pathway (2008)

Phylogenetic analyses have provided strong evidence that amino acid changes in spike (S) protein of animal and human SARS coronaviruses (SARS-CoVs) during and between two zoonotic transfers (2002/03 and 2003/04) are the result of positive selection. While several studies support that some amino acid changes between animal and human viruses are the result of inter-species adaptation, the role of neutralizing antibodies (nAbs) in driving SARS-CoV evolution, particularly during intra-species transmission, is unknown. A detailed examination of SARS-CoV infected animal and human convalescent sera could provide evidence of nAb pressure which, if found, may lead to strategies to effectively block virus evolution pathways by broadening the activity of nAbs. Here we show, by focusing on a dominant neutralization epitope, that contemporaneous- and cross-strain nAb responses against SARS-CoV spike protein exist during natural infection. In vitro immune pressure on this epitope using 2002/03 strain-specific nAb 80R recapitulated a dominant escape mutation that was present in all 2003/04 animal and human viruses. Strategies to block this nAb escape/naturally occurring evolution pathway by generating broad nAbs (BnAbs) with activity against 80R escape mutants and both 2002/03 and 2003/04 strains were explored. Structure-based amino acid changes in an activation-induced cytidine deaminase (AID) "hot spot" in a light chain CDR (complementarity determining region) alone, introduced through shuffling of naturally occurring non-immune human VL chain repertoire or by targeted mutagenesis, were successful in generating these BnAbs. These results demonstrate that nAb-mediated immune pressure is likely a driving force for positive selection during intra-species transmission of SARS-CoV. Somatic hypermutation (SHM) of a single VL CDR can markedly broaden the activity of a strain-specific nAb. The strategies investigated in this study, in particular the use of structural information in combination of chain-shuffling as well as hot-spot CDR mutagenesis, can be exploited to broaden neutralization activity, to improve anti-viral nAb therapies, and directly manipulate virus evolution.
Antibodies with infinite affinity (2001)

Here we report an approach to the design and production of antibody/ligand pairs, to achieve functional affinity far greater than avidin/biotin. Using fundamental chemical principles, we have developed antibody/ligand pairs that retain the binding specificity of the antibody, but do not dissociate. Choosing a structurally characterized antibody/ligand pair as an example, we engineered complementary reactive groups in the antibody binding pocket and the ligand, so that they would be in close proximity in the antibody/ligand complex. Cross-reactions with other molecules in the medium are averted because of the low reactivity of these groups; however, in the antibody/ligand complex the effective local concentrations of the complementary reactive groups are very large, allowing a covalent reaction to link the two together. By eliminating the dissociation of the ligand from the antibody, we have made the affinity functionally infinite. This chemical manipulation of affinity is applicable to other biological binding pairs.
Optically sampled analog-to-digital converters (2001)

Optically sampled analog-to-digital converters (ADCs) combine optical sampling with electronic quantization to enhance the performance of electronic ADCs. In this paper, we review the prior and current work in this field, and then describe our efforts to develop and extend the bandwidth of a linearized sampling technique referred to as phase-encoded optical sampling. The technique uses a dual-output electrooptic sampling transducer to achieve both high linearity and 60-dB suppression of laser amplitude noise. The bandwidth of the technique is extended by optically distributing the post-sampling pulses to an array of time-interleaved electronic quantizers. We report on the performance of a 505-MS/s (megasample per second) optically sampled ADC that includes high-extinction LiNbO/sub 3/ 1-to-8 optical time-division demultiplexers. Initial characterization of the 505-MS/s system reveals a maximum signal-to-noise ratio of 51 dB (8.2 bits) and a spur-free dynamic range of 61 dB. The performance of the present system is limited by electronic quantizer noise, photodiode saturation, and preliminary calibration procedures. None of these fundamentally limit this sampling approach, which should enable multigigahertz converters with 12-b resolution. A signal-to-noise analysis of the phase-encoded sampling technique shows good agreement with measured data from the 505-MS/s system.
The biological activity of FasL in human and mouse lungs is determined by the structure of its stalk region (2011)

Acute lung injury (ALI) is a life-threatening condition in critically ill patients. Injury to the alveolar epithelium is a critical event in ALI, and accumulating evidence suggests that it is linked to proapoptotic Fas/FasL signals. Active soluble FasL (sFasL) is detectable in the bronchoalveolar lavage (BAL) fluid of patients with ALI, but the mechanisms controlling its bioactivity are unclear. We therefore investigated how the structure of sFasL influences cellular activation in human and mouse lungs and the role of oxidants and proteases in modifying sFasL activity. The sFasL in BAL fluid from patients with ALI was bioactive and present in high molecular weight multimers and aggregates. Oxidants generated from neutrophil myeloperoxidase in BAL fluid promoted aggregation of sFasL in vitro and in vivo. Oxidation increased the biological activity of sFasL at low concentrations but degraded sFasL at high concentrations. The amino-terminal extracellular stalk region of human sFasL was required to induce lung injury in mice, and proteolytic cleavage of the stalk region by MMP-7 reduced the bioactivity of sFasL in human cells in vitro. The sFasL recovered from the lungs of patients with ALI contained both oxidized methionine residues and the stalk region. These data provide what we believe to be new insights into the structural determinants of sFasL bioactivity in the lungs of patients with ALI.
In vitro models of pancreatic differentiation using embryonic stem or induced pluripotent stem cells (2010)

Embryonic stem (ES) cells or induced pluripotent stem (iPS) cells are expected as a surrogate cell source for regenerative medicine. Many researchers have reported the differentiation method of insulin-expressing pancreatic β cells from ES or iPS cells. However, the detailed molecular mechanisms underlying the differentiation of ES or iPS cells into pancreatic lineages are still unclear. We have established a feeder cell-based differentiation system into pancreatic progenitor cells, and revealed the signaling pathways that are involved in the differentiation of ES cells into mesendoderm, endoderm and pancreatic progenitor cells. Recently, we demonstrated that the extracellular environment, particularly the laminin-integrin signaling and heparan sulfate proteoglycan, is important for the regionalization of definitive endoderm cells into pancreatic lineages. These results provide new insights for the differentiation mechanism of pancreatic cell lineages.
A Single Vaccination with an Improved Nonspreading Rift Valley Fever Virus Vaccine Provides Sterile Immunity in Lambs (2013)

Rift Valley fever virus (RVFV) is an important pathogen that affects ruminants and humans. Recently we developed a vaccine based on nonspreading RVFV (NSR) and showed that a single vaccination with this vaccine protects lambs from viremia and clinical signs. However, low levels of viral RNA were detected in the blood of vaccinated lambs shortly after challenge infection. These low levels of virus, when present in a pregnant ewe, could potentially infect the highly susceptible fetus. We therefore aimed to further improve the efficacy of the NSR vaccine. Here we report the expression of Gn, the major immunogenic protein of the virus, from the NSR genome. The resulting NSR-Gn vaccine was shown to elicit superior CD8 and CD4-restricted memory responses and improved virus neutralization titers in mice. A dose titration study in lambs revealed that the highest vaccination dose of 10(6.3) TCID50/ml protected all lambs from clinical signs and viremia. The lambs developed neutralizing antibodies within three weeks after vaccination and no anamnestic responses were observed following challenge. The combined results suggest that sterile immunity was achieved by a single vaccination with the NSR-Gn vaccine.
Comparison of myristoyl-CoA:protein N-myristoyltransferases from three pathogenic fungi: Cryptococcus neoformans, Histoplasma capsulatum, and Candida albicans. (1994)

Myristoyl-CoA:protein N-myristoyltransferase (Nmt) transfers myristate from CoA to the N-terminal Gly residue of cellular proteins in an ordered reaction mechanism that first involves binding of myristoyl-CoA to the apoenzyme. The gene encoding Saccharomyces cerevisiae Nmt1p (NMT1) is essential for vegetative growth. Candida albicans, Cryptococcus neoformans var. neoformans, and Histoplasma capsulatum are the principal causes of systemic fungal infections in immunocompromised humans. Metabolic labeling studies indicate that they synthesize a small set of cellular N-myristoylproteins during exponential growth on rich media, the most prominent of which co-migrate with two essential functionally interchangeable S. cerevisiae N-myristoylproteins, ADP ribosylation factor-1 (Arf1p) and Arf2p. NMT and ARF genes have been recovered from C. neoformans and H. capsulatum using the polymerase chain reaction. They are single copy genes, interrupted by multiple introns. C. neoformans and H. capsulatum Nmts have approximately 50% amino acid sequence identity with the orthologous S. cerevisiae, C. albicans, and Homo sapiens N-myristoyltransferases, whereas C. neoformans and H. capsulatum Arfs are approximately 80% identical with C. albicans Arf and S. cerevisiae Arf1p and Arf2p. Functional studies of C. neoformans and C. albicans Nmts conducted in Escherichia coli reveal that (i) both efficiently acylate S. cerevisiae Arf2p; (ii) C. neoformans Arf is a substrate for C. neoformans Nmt; and (iii) substitution of an Asp for a Gly located 5 residues from the C terminus of these two enzymes causes marked temperature-dependent reductions in their catalytic efficiency, just as it does with S. cerevisiae and H. sapiens Nmts. Wild type C. neoformans, C. albicans, and H. sapiens NMTs can fully complement the lethal phenotype of a S. cerevisiae nmt1 null allele at 24 and 37 degrees C when the GAL1-10 promoter controlling their expression is induced by galactose. Only the C. albicans enzyme is able to do so when the promoter is repressed with glucose. This complementation profile likely arises, at least in part, from differences in the protein substrate specificities of the orthologous Nmts. A Gly-->Asp mutation in S. cerevisiae, C. neoformans, C. albicans, and H. sapiens Nmts produces temperature-sensitive growth arrest in isogenic S. cerevisiae strains with a nmt1 null allele. Growth of strains producing the mutant C. albicans or H. sapiens, but not the C. neoformans, enzyme can be rescued by myristate at the non-permissive temperature (37 degrees C) even in the presence of cerulenin, an inhibitor of fatty acid synthetase.(ABSTRACT TRUNCATED AT 400 WORDS)
Model Substrates for an RNA Enzyme (1987)

M1 RNA, the catalytic RNA subunit of Escherichia coli ribonuclease P, can cleave novel transfer RNA (tRNA) precursors that lack specific domains of the normal tRNA sequence. The smallest tRNA precursor that was cleaved efficiently retained only the domain of the amino acid acceptor stem and the T stem and loop. The importance of the 3' terminal CCA nucleotide residues in the processing of both novel and normal tRNA precursors implies that the same enzymatic function of M1 RNA is involved.
X-ray photoelectron spectroscopy analysis of whole cells and isolated cell walls of gram-positive bacteria: comparison with biochemical analysis (1997)

The surface chemical composition of whole cells and isolated cell walls of four coryneform bacteria and of a Bacillus brevis strain has been determined by X-ray photoelectron spectroscopy (XPS). The XPS data were converted into concentrations of model compounds: peptides, polysaccharides, and hydrocarbonlike compounds. The composition of the surface of B. brevis differed markedly from that of coryneforms: the peptide concentration was about twice higher in the former case, which is attributed to the presence of an S-layer at the cell surface; in contrast, the surface of coryneforms was rich in hydrocarbonlike compounds (about 40%), which was concomitant with a high water contact angle. The peptide surface concentration of the isolated cell walls of the five strains deduced from XPS data fitted well with the total peptide content determined by biochemical analysis, which supports the validity of XPS to determine the overall macromolecular composition of the bacterial cell surface. Compared to biochemical analysis of isolated cell walls, XPS analysis of whole cells provides information which concerns directly the cell surface (2- to 5-nm-thick layer) and is less subject to alteration via losses of cell wall constituents or contamination by intracellular compounds.
Structure-activity relations in the vitamin E series. II. Derivatives of .alpha.-tocopherol substituted at the 5-methyl group (1969)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStructure-activity relations in the vitamin E series. II. Derivatives of .alpha.-tocopherol substituted at the 5-methyl groupWilfred A. Skinner, R. M. Parkhurst, Jean Scholler, and Klaus SchwarzCite this: J. Med. Chem. 1969, 12, 1, 64–66Publication Date (Print):January 1, 1969Publication History Published online1 May 2002Published inissue 1 January 1969https://pubs.acs.org/doi/10.1021/jm00301a017https://doi.org/10.1021/jm00301a017research-articleACS PublicationsRequest reuse permissionsArticle Views72Altmetric-Citations13LEARN 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
Inhibition of Angiotensin-Converting Enzyme by Contrast Media I. In Vitro Findings (1990)

There is increasing evidence that activation of the plasma contact system that results in the production of bradykinin plays an important role in contrast material systemic reactions. The effects of bradykinin in anaphylaxis depend on its rate of destruction and its rate of production. The highest percentage of contrast material reactions occur after intravenous injections, and the major enzyme hydrolyzing bradykinin (kininase II; angiotensin-converting enzyme) is found on pulmonary vascular endothelial surfaces. The inhibitory effects of numerous ionic and nonionic contrast material solutions on the enzyme have been determined. Additionally, the role in this inhibition of the chelators found in all commercial contrast material vials has been studied. In vitro, all such preparations combined with their chelators inhibit angiotensin-converting enzyme. Whether this inhibition plays a role in vivo remains to be established.
High-mobility Si and Ge structures (1997)

Silicon-based heterostructures have come a long way from the discovery of strain as a new and essential parameter for band structure engineering to the present state of electron and hole mobilities, which surpass those achieved in the traditional material combination by more than an order of magnitude and are rapidly approaching the best III - V heteromaterials. It is the purpose of this article to report on the most recent developments, and the performance level achieved to date in this material system, in a concise and critical manner. The first part of this review is concerned with the structural and electronic properties of the lattice-mismatched Si/SiGe heterostructure. Emphases are put on the effects of strain both on the band structure and on the band offsets, as well as on means to actually control the strain in a stack of heteroepitaxial layers. The second part is dedicated to the transport properties of low-dimensional carrier systems in Si/SiGe and Ge/SiGe heterostructures. The prospects and limitations of the different layer concepts are discussed in terms of scattering mechanisms and experimental results. This part also reviews the most recent magneto-transport experiments on quantum wires and quantum point contacts, which became possible by the enhanced mean free paths in these materials. The third part covers the device aspects of these high-mobility materials, which is of special interest, because silicon-based heterostructures can significantly enhance the performance level of contemporary Si devices without sacrificing the essential compatibility with standard Si technologies. The recent achievements in this application-driven research field, but also the foreseeable problems and limitations, are discussed, and an assessment of the possible role of such heterodevices in future microelectronic circuits is given.
Open-vocabulary speech indexing for voice and video mail retrieval (1996)

Article Free Access Share on Open-vocabulary speech indexing for voice and video mail retrieval Authors: M. G. Brown Olivetti Research Limited, 24a Trumpington St., Cambridge, CB2 1QA, UK Olivetti Research Limited, 24a Trumpington St., Cambridge, CB2 1QA, UKView Profile , J. T. Foote Cambridge University Engineering Department, Cambridge, CB2 1PZ, UK Cambridge University Engineering Department, Cambridge, CB2 1PZ, UKView Profile , G. J. F. Jones Cambridge University Computer Laboratory, Cambridge, CB2 3QG, UK Cambridge University Computer Laboratory, Cambridge, CB2 3QG, UKView Profile , K. Spärck Jones View Profile , S. J. Young Cambridge University Engineering Department, Cambridge, CB2 1PZ, UK Cambridge University Engineering Department, Cambridge, CB2 1PZ, UKView Profile Authors Info & Claims MULTIMEDIA '96: Proceedings of the fourth ACM international conference on MultimediaFebruary 1997 Pages 307–316https://doi.org/10.1145/244130.244232Published:01 February 1997Publication History 39citation794DownloadsMetricsTotal Citations39Total Downloads794Last 12 Months13Last 6 weeks2 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF