gebhart/patrepeval huggingface dataset:
Nucleic acid (cDNA) and amino acid sequences of the maize endosperm protein glutelin-2 (1985)

The cDNA coding for a glutelin-2 protein from maize endosperm has been cloned and the complete amino acid sequence of the protein derived for the first time. An immature maize endosperm cDNA bank was screened for the expression of a beta-lactamase:glutelin-2 (G2) fusion polypeptide by using antibodies against the purified 28 kd G2 protein. A clone corresponding to the 28 kd G2 protein was sequenced and the primary structure of this protein was derived. Five regions can be defined in the protein sequence: an 11 residue N-terminal part, a repeated region formed by eight units of the sequence Pro-Pro-Pro-Val-His-Leu, an alternating Pro-X stretch 21 residues long, a Cys rich domain and a C-terminal part rich in Gln. The protein sequence is preceded by 19 residues which have the characteristics of the signal peptide found in secreted proteins. Unlike zeins, the main maize storage proteins, 28 kd glutelin-2 has several homologous sequences in common with other cereal storage proteins.
Nucleophilic Aryl Fluorination and Aryl Halide Exchange Mediated by a CuI/CuIII Catalytic Cycle (2011)

Copper-catalyzed halide exchange reactions under very mild reaction conditions are described for the first time using a family of model aryl halide substrates. All combinations of halide exchange (I, Br, Cl, F) are observed using catalytic amounts of Cu(I). Strikingly, quantitative fluorination of aryl-X substrates is also achieved catalytically at room temperature, using common F(-) sources, via the intermediacy of aryl-Cu(III)-X species. Experimental and computational data support a redox Cu(I)/Cu(III) catalytic cycle involving aryl-X oxidative addition at the Cu(I) center, followed by halide exchange and reductive elimination steps. Additionally, defluorination of the aryl-F model system can be also achieved with Cu(I) at room temperature operating under a Cu(I)/Cu(III) redox pair.
Acute Sero-positive Rheumatoid Arthritis Occurring after Hepatitis Vaccination (1994)

Acute Sero-positive Rheumatoid Arthritis Occurring after Hepatitis Vaccination G. VAUTIER, G. VAUTIER Department of Rheumatology, County HospitalGreetwell Road, Lincoln LN2 5QY Search for other works by this author on: Oxford Academic PubMed Google Scholar J. E. CARTY J. E. CARTY Department of Rheumatology, County HospitalGreetwell Road, Lincoln LN2 5QY Search for other works by this author on: Oxford Academic PubMed Google Scholar Rheumatology, Volume 33, Issue 10, October 1994, Page 991, https://doi.org/10.1093/rheumatology/33.10.991-a Published: 01 October 1994 Article history Accepted: 24 May 1994 Published: 01 October 1994
Future prevention and treatment of diabetic neuropathy. (1998)

This review orders the likely components of the pathogenesis of diabetic neuropathy into vertical (temporal) and horizontal dimensions. It is argued that the effects of hyperglycaemia are transduced to neuronal dysfunction via at least three secondary biochemical disturbances--the sorbitol (polyol) pathway, non-enzymatic glycation of proteins and oxidative stress--and that there are clear interactions between them. Because of these interactions, interference with one of these biochemical transducers could either worsen or attenuate the effects of the others. Examples of these alternatives are given. It is suggested that the prime goal for pharmacological intervention should be a combined attack on all three sources of disturbance. Interventions further on in the sequence of pathogenesis are also considered, and the arguments for the use of neurotrophic factors are persuasive because of their selectivity for different neuronal phenotypes, even though side-effects may be inevitable. Finally, a novel conjugate of gamma-linolenic acid and alpha-lipoic acid is considered as an agent with the potential to correct effects arising from more than one pathway of disorder in experimental diabetic neuropathy. The preliminary results with this agent have been encouraging.
MucoidEscherichia coliin Cystic Fibrosis (1981)

Patients with cystic fibrosis commonly harbor in their lungs strains of Pseudomonas aeruginosa that have a mucoid coating considered virtually pathognomonic for the disease. We found that strains of Escherichia coli with a morphologically similar mucoid coating were present in the respiratory tracts of eight (11.8 per cent) of 68 patients with cystic fibrosis whose sputum cultures yielded Esch. coli, as compared with none of 89 patients without cystic fibrosis who had Esch. coli in sputum. Mucoid strains of Esch. coli were also recovered from the stools of five (11.1 per cent) of 45 patients with cystic fibrosis, as compared with one (0.7 per cent) of 150 patients without cystic fibrosis. The mucoid substances purified from Esch. coli were biochemically and antigenically distinct from those of P. aeruginosa. We conclude that the respiratory tract in cystic fibrosis offers an environment conducive to the production of a mucoid coating not only by P. aeruginosa but by other gram-negative bacilli as well. (N Engl J Med. 1981; 304:1445–9).
Towards a content-based aggregation network (2002)

We present an architecture for content-based aggregation in peer-to-peer filesharing networks. It is designed to significantly reduce the amount of nodes that have to be queried, by introducing a distributed index into the system. This index allows content to be located in a peer-to-peer network without using broadcast-style techniques. We also show how this index can be created and maintained in a decentralized self-organizing fashion.
Insertion of new sequences into the catalytic domain of an enzyme (1989)

Activities of enzymes can be modified by the replacement of active-site amino acids with residues that strengthen specific interactions with substrates or that alter the specificity. The scope for engineered enzymes would be broadened if additional, new sequences could be inserted into a catalytic domain. Properly designed, these sequences could encode new ligand binding sites, be intermediates in the construction of chimeric enzymes, or alter the internal flexibility and "breathing" modes of the active-site region. As a first step toward this objective, we inserted oligopeptides of up to 14 amino acids into various locations within an 82 amino acid region of the adenylate synthesis domain of Escherichia coli methionyl-tRNA synthetase. These sites include ones that are flanked by sequences that are conserved between the proteins from E. coli and the yeast Saccharomyces cerevisiae and those that are essential for activity and stability. We found that all of the insertional mutants are stable and some have catalytic parameters for adenylate synthesis that are comparable to those of the wild-type enzyme. Thus, such an approach may provide for a variety of novel applications.
Therapy for colon carcinoma xenografts with bispecific antibody-targeted, iodine-131-labeled bivalent hapten (1997)

The long term tumor regression consecutive to AES RIT represents a very significant improvement over the use of directly labeled IgG. Toxicity consecutive to AES or IgG RIT were similar despite an administered activity nearly ten times higher with the AES. However, given the efficacy of the AES treatment, a lower dose may afford lower toxicity and significant antitumor effect.
SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSMILES, a chemical language and information system. 1. Introduction to methodology and encoding rulesDavid WeiningerCite this: J. Chem. Inf. Comput. Sci. 1988, 28, 1, 31–36Publication Date (Print):February 1, 1988Publication History Published online1 May 2002Published inissue 1 February 1988https://pubs.acs.org/doi/10.1021/ci00057a005https://doi.org/10.1021/ci00057a005research-articleACS PublicationsRequest reuse permissionsArticle Views12790Altmetric-Citations4077LEARN 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 options Get e-Alerts
Molecular cloning of two DNA-binding proteins of maize that are structurally different but interact with the same sequence motif (1993)

Nuclear extracts from maize leaves have been shown previously to contain a factor, MNF1, that interacts with both the cauliflower mosaic virus 35S promoter and the promoter of the maize gene for phosphoenolpyruvate carboxylase, which is involved in C4 photosynthesis. We have isolated two cDNA clones encoding proteins (MNB1a and MNB1b), that bind to an MNF1-binding site in a sequence-specific manner, by screening of a maize cDNA expression library with synthetic oligonucleotides. Using various mutated oligonucleotides, we showed that both proteins recognize an AAGG motif at the MNF1-binding site as important bases for binding, as does MNF1 in maize nuclear extracts. However, the binding specificities of MNB1a and MNB1b are similar but not identical to that of MNF1. The deduced amino acid sequences of these proteins are completely different from each other. The basic region of MNB1b exhibits homology to the high mobility group (HMG) box of the vertebrate HMG1 family, whereas MNB1a exhibits no homology to any known proteins. Southern blot analysis of genomic DNA revealed that the cDNA for MNB1a is derived from a multigene family whose members have highly homologous N-terminal basic domain, whereas the gene for MNB1b exhibits only limited homology to a few other genes. These results suggest that the MNF1-binding site on the 35S promoter is a target of multiple DNA-binding proteins.
CD3 antibody-induced dominant self tolerance in overtly diabetic NOD mice (1997)

Low doses of the CD3 mAb 145 2C11 restored self tolerance to beta cell Ags in adult overtly diabetic NOD mice. Within 2 to 4 wk after treatment, complete and permanent remission of diabetes was observed. Autoreactive T cells were not deleted in CD3 Ab-protected animals as evidenced first, by the persistence of peripheral insulitis and, second, by the capacity of spleen cells from CD3 Ab-treated mice to transfer diabetes to adult irradiated syngeneic recipients. Moreover, the conferred tolerance was reproducibly reversed by a single injection of cyclophosphamide. For 5 to 7 wk after treatment, IFN-gamma production by stimulated spleen cells was significantly decreased in treated animals. One unique feature was that the CD3 Ab-induced tolerance ensued only from treatment of overtly diabetic NOD mice. Durable protection was exclusively observed when treating mice with recent onset disease (14-20 wk old). At variance with this finding, treatment of 4- and 8-wk-old mice was without effect, and complete but transient protection followed the treatment of 12-wk-old NOD mice. The tolerogenic properties of 145 2C11 did not depend on its mitogenic capacity, since nonmitogenic F(ab')2 fragments also appeared potent at inducing durable remission in overtly diabetic NOD, although nonmitogenic CD3 F(ab')2 fragments could mediate T cell signaling, as evidenced by cytokine gene transcription (IL-2, IFN-gamma, IL-4, and IL-10) assessed by PCR on splenocytes from treated mice. A concomitant cyclosporine treatment abrogated the CD3 mAb-induced protection, further pointing to the crucial role of T cell signaling in the effect observed.
Murine hybridomas secreting monoclonal antibodies reacting with Mlsa antigens. (1993)

Murine monoclonal antibodies have been developed from spleens of AKR mice hyperimmunised with the monoclonal antibody against TCR-V beta 6. Two new monoclonal antibodies called AL-12-3 and AL-32-7 were able to specifically block Mlsa-induced but not MHC-induced mixed lymphocyte responses in a dose-dependent manner. Both antibodies are mouse IgG3 lambda chain isotype and bind to Mlsa-bearing lymphocytes from different strains of mice. The availability of such antibodies may well facilitate future research aimed at immunochemical and molecular characterization of Mls determinants.
α-1,4-Glucosidase–albumin polymers : in vitro properties and advantages for enzyme replacement therapy (1980)

Soluble polymers of rat (or human) albumin and alpha-1,4-glucosidase are prepared using the cross-linking agent glutaraldehyde. The resulting polymer has an average molecular weight of 800 000 indicating an average composition of 12 albumin molecules for each enzyme molecule. Compared with an equivalent amount of free enzyme, the enzyme-albumin polymer has an increased resistance to heat denaturation (half-life of 15 h compared with 1 h for free enzyme at 37 degrees C) and to proteolysis by trypsin (half-life of 180 min compared with 10 min). The high degree of resistance to bioinactivation of the enzyme-albumin polymer is discussed in relation to requirements for enzyme replacement therapy in a range of metabolic diseases including type II glycogenosis (Pompe's disease) where alpha-1,4-glucosidase is the defective enzyme.
Sequence-Dependent Pausing of Single Lambda Exonuclease Molecules (2003)

Lambda exonuclease processively degrades one strand of duplex DNA, moving 5'-to-3' in an ATP-independent fashion. When examined at the single-molecule level, the speeds of digestion were nearly constant at 4 nanometers per second (12 nucleotides per second), interspersed with pauses of variable duration. Long pauses, occurring at stereotypical locations, were strand-specific and sequence-dependent. Pause duration and probability varied widely. The strongest pause, GGCGAT TCT, was identified by gel electrophoresis. Correlating single-molecule dwell positions with sequence independently identified the motif GGCGA. This sequence is found in the left lambda cohesive end, where exonuclease inhibition may contribute to the reduced recombination efficiency at that end.
Reliable test for prenatal prediction of fetal RhD type using maternal plasma from RhD negative women (2005)

Our set-up was very reliable for determination of fetal RhD genotype, and thus will be of value in prenatal Rh prophylaxis and in the management of immunized women.
Wall Teichoic Acids of Gram-Positive Bacteria (2013)

The peptidoglycan layers of many gram-positive bacteria are densely functionalized with anionic glycopolymers known as wall teichoic acids (WTAs). These polymers play crucial roles in cell shape determination, regulation of cell division, and other fundamental aspects of gram-positive bacterial physiology. Additionally, WTAs are important in pathogenesis and play key roles in antibiotic resistance. We provide an overview of WTA structure and biosynthesis, review recent studies on the biological roles of these polymers, and highlight remaining questions. We also discuss prospects for exploiting WTA biosynthesis as a target for new therapies to overcome resistant infections.
Bendamustine-bortezomib-dexamethasone is an active and well-tolerated regimen in patients with relapsed or refractory multiple myeloma (2013)

Bendamustine with bortezomib and dexamethasone was evaluated in 79 patients with relapsed/refractory multiple myeloma. Median age was 64 years, and patients had a median of 2 prior treatment lines (range, 1 to 6 lines). Bendamustine 70 mg/m(2) days 1 and 4; bortezomib 1.3 mg/m(2) intravenously days 1, 4, 8, and 11; and dexamethasone 20 mg days 1, 4, 8, and 11 once every 28 days was given for up to 8 cycles. Primary end point was overall response rate (ORR). Secondary end points were progression-free survival (PFS), overall survival, time to response, and toxicity. ORR was 60.8%, and when minor responses were included, 75.9%. Median time to response was 31 days. ORR rate was similar in patients previously exposed to bortezomib, lenalidomide, and bortezomib plus lenalidomide. PFS was 9.7 and OS was 25.6 months. Multivariate analysis showed high lactate dehydrogenase, ≥3 prior treatment lines, and low platelet counts correlating with short survival. Grade 3/4 thrombocytopenia was noted in 38%, and grade 3/4/5 infections were noted in 23%. Grade ≤2 polyneuropathy increased from 19% at baseline to 52% at cycle 8 and grade 4, from 0% to 7%. Bendamustine-bortezomib-dexamethasone is active and well tolerated in patients with relapsed/refractory myeloma. This trial was registered in the EudraCT database as No. 2008-006421-13.
PATHFINDER system design (2003)

The authors describe an experimental project designed to test the feasibility of using the latest technological devices to aid the motorist in avoiding urban traffic congestion. The basic objectives are to design, install, and operate a system that will provide real-time information to motorists in their vehicles; to evaluate the driver's response to the information provided; to evaluate the utility of using vehicles as a source of information on traffic conditions; and to evaluate a computer-assisted method of combining real-time traffic information from various sources. The experiment is taking place in the Smart Corridor, a 13-mile (20 km) stretch along the Freeway between Santa Monica and downtown Los Angeles. Twenty-five vehicles, equipped with an in-vehicle navigation system using a modified Etak map display to show traffic congestion information, will be used. After a system overview, descriptions are given of the vehicle system, the central system, and the communication system, and details of the experimental evaluation are given.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A Defect in DNA Ligase4 Enhances the Frequency of TALEN-Mediated Targeted Mutagenesis in Rice (2015)

We have established methods for site-directed mutagenesis via transcription activator-like effector nucleases (TALENs) in the endogenous rice (Oryza sativa) waxy gene and demonstrated stable inheritance of TALEN-induced somatic mutations to the progeny. To analyze the role of classical nonhomologous end joining (cNHEJ) and alternative nonhomologous end joining (altNHEJ) pathways in TALEN-induced mutagenesis in plant cells, we investigated whether a lack of DNA Ligase4 (Lig4) affects the kinetics of TALEN-induced double-strand break repair in rice cells. Deep-sequencing analysis revealed that the frequency of all types of mutations, namely deletion, insertion, combination of insertion with deletion, and substitution, in lig4 null mutant calli was higher than that in a lig4 heterozygous mutant or the wild type. In addition, the ratio of large deletions (greater than 10 bp) and deletions repaired by microhomology-mediated end joining (MMEJ) to total deletion mutations in lig4 null mutant calli was higher than that in the lig4 heterozygous mutant or wild type. Furthermore, almost all insertions (2 bp or greater) were shown to be processed via copy and paste of one or more regions around the TALENs cleavage site and rejoined via MMEJ regardless of genetic background. Taken together, our findings indicate that the dysfunction of cNHEJ leads to a shift in the repair pathway from cNHEJ to altNHEJ or synthesis-dependent strand annealing.
α-Synuclein in filamentous inclusions of Lewy bodies from Parkinson’s disease and dementia with Lewy bodies (1998)

Lewy bodies and Lewy neurites are the defining neuropathological characteristics of Parkinson's disease and dementia with Lewy bodies. They are made of abnormal filamentous assemblies of unknown composition. We show here that Lewy bodies and Lewy neurites from Parkinson's disease and dementia with Lewy bodies are stained strongly by antibodies directed against amino-terminal and carboxyl-terminal sequences of alpha-synuclein, showing the presence of full-length or close to full-length alpha-synuclein. The number of alpha-synuclein-stained structures exceeded that immunoreactive for ubiquitin, which is currently the most sensitive marker of Lewy bodies and Lewy neurites. Staining for alpha-synuclein thus will replace staining for ubiquitin as the preferred method for detecting Lewy bodies and Lewy neurites. We have isolated Lewy body filaments by a method used for the extraction of paired helical filaments from Alzheimer's disease brain. By immunoelectron microscopy, extracted filaments were labeled strongly by anti-alpha-synuclein antibodies. The morphologies of the 5- to 10-nm filaments and their staining characteristics suggest that extended alpha-synuclein molecules run parallel to the filament axis and that the filaments are polar structures. These findings indicate that alpha-synuclein forms the major filamentous component of Lewy bodies and Lewy neurites.
Post-meiotic transcription in Drosophila testes (2008)

Post-meiotic transcription was accepted to be essentially absent from Drosophila spermatogenesis. We identify 24 Drosophila genes whose mRNAs are most abundant in elongating spermatids. By single-cyst quantitative RT-PCR, we demonstrate post-meiotic transcription of these genes. We conclude that transcription stops in Drosophila late primary spermatocytes, then is reactivated by two pathways for a few loci just before histone-to-transition protein-to-protamine chromatin remodelling in spermiogenesis. These mRNAs localise to a small region at the distal elongating end of the spermatid bundles, thus they represent a new class of sub-cellularly localised mRNAs. Mutants for a post-meiotically transcribed gene (scotti), are male sterile, and show spermatid individualisation defects, indicating a function in late spermiogenesis.
Genetic Polymorphisms of Tobacco- and Alcohol-Related Metabolizing Enzymes and Human Esophageal Squamous Cell Carcinoma Susceptibility (1997)

Many human cancers are caused by synthetic or natural chemical compounds in the environment. Esophageal squamous cell carcinoma has been reported to be epidemiologically associated with tobacco and alcohol consumption. We studied the association between genetic polymorphisms of tobacco- and alcohol-related metabolizing enzymes and esophageal squamous cell carcinoma susceptibility. We examined genetic polymorphisms of the CYPIA1, GSTM1, CYPIIE1, ADH2, and ALDH2 genes in 94 Japanese patients with esophageal squamous cell carcinoma and 70 unrelated healthy Japanese persons. There were no significant differences between healthy controls and patients with esophageal cancer in the polymorphisms of the CYPIA1, GSTM1, and CYPIIE1 genes. On the other hand, there were significant differences in the ADH2 and ALDH2 polymorphisms between healthy controls and esophageal cancer patients. The ADH2(1)/ADH2(1) and ALDH2(1)/ALDH2(2) genotypes were independently and significantly higher in esophageal cancer patients than in healthy controls. Furthermore, persons with the combined genotypes ADH2(1)/ADH2(1) and ALDH2(1)/ALDH2(2) were at extraordinarily high risk for esophageal squamous cell carcinoma, with an odds ratio of 17.9 (p < 0.001). Thus polymorphisms of alcohol-metabolizing enzymes, that is, ADH2 and ALDH2, may be useful for screening patients at high risk for esophageal cancer, which might facilitate clarification of esophageal tumorigenesis and prevention of esophageal cancer.