gebhart/patrepeval huggingface dataset:
An efficient and flexible system for construction of adenovirus vectors with insertions or deletions in early regions 1 and 3. (1994)

Human adenoviruses (Ads) are attracting considerable attention because of their potential utility for gene transfer and gene therapy, for development of live viral vectored vaccines, and for protein expression in mammalian cells. Engineering Ad vectors for these applications requires a variety of reagents in the form of Ads and bacterial plasmids containing viral DNA sequences and requires different strategies for construction of vectors for different purposes. To simplify Ad vector construction and develop a procedure with maximum flexibility, efficiency, and cloning capacity, we have developed a vector system based on use of Ad5 DNA sequences cloned in bacterial plasmids. Expanded deletions in early region 1 (3180 bp) and early region 3 (2690 or 3132 bp) can be combined in a single vector that should have a capacity for inserts of up to 8.3 kb, enough to accommodate the majority of cDNAs encoding proteins with regulatory elements. Genes can be inserted into either early region 1 or 3 or both and mutations or deletions can be readily introduced elsewhere in the viral genome. To illustrate the flexibility of the system, we have introduced a wild-type early region 3 into the vectors, and to illustrate the high capacity for inserts, we have isolated a vector with two genes totaling 7.8 kb.
Generation and characterization of a competitive antagonist of human hepatocyte growth factor, HGF/NK1 (1993)

Our previous studies have suggested that a derivative of hepatocyte growth factor (HGF), HGF/NK2, containing the coding sequences for the N-terminal hairpin and first two kringle domains, is sufficient to mediate high affinity binding to the HGF receptor. Here, we wished to test directly whether HGF/NK1 (N-terminal hairpin and first kringle domains) could bind the receptor and/or mediate receptor signaling. HGF/NK1 was expressed in Escherichia coli and purified to homogeneity using heparin-affinity and fast protein liquid cation-exchange chromatography. Biological characterization of HGF/NK1 showed that it can compete for binding to the HGF receptor on human lung carcinoma A549 cells and to a soluble form of the HGF receptor. HGF/NK1 is inefficient at promoting autophosphorylation of the HGF receptor, although some activity was detected at very high concentrations. HGF/NK1 fails to exhibit mitogenic properties even at very high concentrations. However, HGF/NK1 can act as a potent competitive antagonist in this assay. Our data demonstrate directly that a receptor binding determinant of HGF is located within the N-terminal 32-212 residues of HGF. HGF/NK1 will serve as a powerful tool for (i) generating neutralizing antibodies, (ii) in determining x-ray crystallographic and nuclear magnetic resonance structures, and (iii) for in vivo studies as an HGF antagonist.
Genomic organization and chromosomal localization of the T-cell antigen 4-1BB. (1994)

4-1BB is an inducible T cell surface receptor which belongs to the nerve growth factor receptor superfamily, a group of cysteine-rich cell-surface proteins. 4-1BB is a 30-kDa glycoprotein and exists as both a monomer and a 55-kDa dimer on the T cell surface. Cross-linking 4-1BB with monoclonal antibody resulted in the 2- to 10-fold enhancement of T cell proliferation. We have isolated and characterized 4-1BB genomic clones and have found that the 4-1BB gene contains two different 5' untranslated regions, which are used alternately to form the 4-1BB mRNA. The two 5' UTRs were encoded in the same chromosome and were separated from one another by an intron of approximately 2.5 kb. The entire gene spans approximately 13 kb of mouse chromosome 4. 4-1BB gene consists of 10 exons and 9 introns, in which there are two exons for 5' untranslated regions and 8 exons for coding region. Most of the putative functional domains were encoded by separate exons. 4-1BB extracellular domain contains four potential C6 (CXn C XX C XX CXn C Xn C) motifs, of which the first motif is partial and the third is distinct from those of nerve growth factor receptor or TNF receptor 1. A comparison of exon-intron organization among the genes of the nerve growth factor receptor family indicated that most C6 motif is interrupted by an intron.
Of Minibody, Camel and Bacteriophage (2001)

This review describes the design process from conception through realisation and optimisation of a minibody'--a minimised antibody. The result was a proteinaceous molecule of novel fold and metal binding activity. We explain how combinatorial approaches, using phage display libraries, were used to randomise loop regions of the minibody. Variants were then selected for desired activities including in vitro inhibition of human interleukin-6 and the protease of the non-structural protein, NS3, of the hepatitis C virus. One such variant was successfully minimised further to produce a cyclic peptide with similar inhibition properties. Thus the work reviewed provides examples of two important processes in protein design and protein minimisation. We conclude by discussing the role of such studies in medical applications and small molecule drug discovery. We also highlight the potential of our work and similar techniques in the post-genomic era.
Slot-loaded, meandered rectangular microstrip antennawith compact dual-frequency operation (1998)

A novel single-feed compact dual-frequency design is demonstrated. The proposed design consists of a rectangular patch loaded with two parallel slots close to the radiating edges and meandered with slits at the non-radiating edges. The two operating frequencies have parallel polarisation planes and, by varying the insetting slit length, the frequency ratio of the two frequencies is tunable in the range of ~ 1.8 – 2.4. In addition, with the insetting slit, the two frequencies can be greatly lowered, which results in a large antenna size reduction for fixed dual-frequency operation.
Functional mapping and DNA sequence of an equine herpesvirus 1 origin of replication (1989)

The genome of equine herpesvirus 1 (EHV-1) defective interfering (DI) particle DNA originates from discrete regions within the standard (STD) EHV-1 genome: the left terminus (0.0 to 0.04 map units) and the inverted repeats (0.78 to 0.79 and 0.83 to 0.87 map units of the internal inverted repeat; 0.91 to 0.95 and 0.99 to 1.00 map units of the terminal inverted repeat). Since DI DNA must contain cis-acting DNA sequences, such as replication origins, which cannot be supplied in trans by the STD EHV-1 virus, regions of the EHV-1 genome shown to be in DI DNA were assayed for the presence of a viral origin of DNA replication. Specifically, STD EHV-1 DNA fragments encompassing the genomic regions present in DI particle DNA were inserted into the vector pAT153, and individual clones were tested by transfection assays for the ability to support the amplification and replication of plasmid DNA in EHV-1-infected cells. The Sma-1 subfragment of the internal inverted repeat sequence (0.83 to 0.85 map units) was shown to contain origin of replication activity. Subcloning and BAL 31 deletion analysis of the 2.35-kilobase-pair (kbp) Sma-1 fragment delineated a 200-bp fragment that contained origin activity. The origin activities of all EHV-1 clones which were positive by the transfection assay were confirmed by methylation analysis by using the methylation-sensitive restriction enzymes DpnI and MboI. DNA sequencing of the 200-bp fragment which contained an EHV-1 origin of replication indicated that this region has significant homology to previously characterized origins of replication of human herpesviruses. Furthermore, comparison of known origin sequences demonstrated that a 9-bp sequence, CGTTCGCAC, which is conserved among all origins of replication of human lytic herpesviruses and which is contained within the 18-bp region in herpes simplex virus type 1 origins shown by others to be protected by an origin-binding protein (P. Elias, M. E. O'Donnell, E. S. Mocarski, and I. R. Lehman, Proc. Natl. Acad. Sci. USA 83:6322-6326) is also conserved across species in the EHV-1 origin of replication.
Profiling of 95 MicroRNAs in Pancreatic Cancer Cell Lines and Surgical Specimens by Real‐Time PCR Analysis (2008)

Pancreatic cancer tissues or cell lines have a unique miRNA profiling pattern at the individual basis compared with relatively normal pancreatic tissues or cells as well as pancreatitis tissue. Upregulation of eight miRNAs occurs in most pancreatic cancer tissues and cell types. These miRNAs may share common pathways in pancreatic cancer pathogenesis. This study may provide useful information for further investigations of functional roles of miRNAs in pancreatic cancer development, progression, diagnosis, and prognosis.
Comparison of human alkaline phosphatase isoenzymes. Structural evidence for three protein classes (1979)

The structural relationships among human alkaline phosphatase isoenzymes from placenta, bone, kidney, liver and intestine were investigated by using three criteria. 1. Immunochemical characterization by using monospecific antisera prepared against either the placental isoenzyme or the liver isoenzyme distinguishes two antigenic groups: bone, kidney and liver isoenzymes cross-react with anti-(liver isoenzyme) serum, and the intestinal and placental isoenzymes cross-react with the anti-(placental isoenzyme) antiserum. 2. High-resolution two-dimensional electrophoresis of the 32P-labelled denatured subunits of each enzyme distinguishes three groups of alkaline phosphatase: (a) the liver, bone and kidney isoenzymes, each with a unique isoelectric point in the native form, can be converted into a single form by treatment with neuraminidase; (b) the placental isoenzyme, whose position also shifts after removal of sialic acid; and (c) the intestinal isoenzyme, which is distinct from all other phosphatases and is unaffected by neuraminidase digestion. 3. Finally, we compare the primary structure of each enzyme by partial proteolytic-peptide 'mapping' in dodecyl sulphate/polyacrylamide gels. These results confirm the primary structural identity of liver and kidney isoenzymes and the non-identity of the placental and intestinal forms. These data provide direct experimental support for the existence of at least three alkaline phosphatase genes.
Principles of Instrumental Analysis (2001)

Introduction. Section I: Measurement Basics. Electrical Components and Circuits. Operational Amplifiers in Chemical Instrumentation. Digital Electronics and Microcomputers. Signals and Noise. Section II: Atomic Spectroscopy. An Introduction to Spectrometric Methods. Components of Optical Instruments. An Introduction to Optical Atomic Spectrometry. Atomic Absorption and Atomic Fluorescence Spectrometry. Atomic Emission Spectrometry. Atomic Mass Spectrometry. Atomic X-Ray Spectrometry. Section III: Molecular Spectroscopy. An Introduction to Ultraviolet/Visible Molecular Absorption Spectrometry. Applications of Ultraviolet/Visible Molecular Absorption Spectrometry. Molecular Luminescence Spectrometry. An Introduction to Infrared Spectrometry Applications of Infrared Spectrometry. Raman Spectroscopy. Nuclear Magnetic Resonance Spectroscopy. Molecular Mass Spectrometry. Surface Characterisation by Spectroscopy and Microscopy. Section IV: Electroanalytical Chemistry. Introduction to Electroanalytical Chemistry. Potentiometry. Coulometry. Voltammetry. Section V: Separation Methods. An Introduction to Chromatographic Separations. Gas Chromatography. High-Performance Liquid Chromatography. Supercritical Fluid Chromatography and Extraction. Capillary Electrophoresis and Capillary Electrochromatography. Section VI: Miscellaneous Methods. Thermal Methods. Radiochemical Methods. Automated Methods of Analysis. Appendices.
Transcranial magnetic stimulation (1990)

<h3>Abstract</h3> SARS-CoV-2, the etiological agent of COVID-19 was first described in Wuhan in December 2019 and has now spread globally. Ecuador was the second country in South America to report confirmed cases. The first case reported in Quito, the capital city of Ecuador, was a tourist who came from the Netherlands and presented symptoms on March 10th, 2020 (index case). In this work we used the MinION platform (Oxford Nanopore Technologies) to sequence the metagenome of the bronchoalveolar lavage (BAL) from this case reported, and subsequently we sequenced the whole genome of the index case and other three patients using the ARTIC network protocols. Our data from the metagenomic approach confirmed the presence of SARS-CoV-2 coexisting with pathogenic bacteria suggesting coinfection. Relevant bacteria found in the BAL metagenome were <i>Streptococcus pneumoniae, Mycobacterium tuberculosis, Staphylococcus aureus</i> and <i>Chlamydia</i> spp. Lineage assignment of the four whole genomes revealed three different origins. The variant HEE-01 was imported from the Netherlands and was assigned to B lineage, HGSQ-USFQ-018, belongs to the B.1 lineage showing nine nucleotide differences with the reference strain and grouped with sequences from the United Kingdom, and HGSQ-USFQ-007 and HGSQ-USFQ-010 belong to the B lineage and grouped with sequences from Scotland. All genomes show mutations in their genomes compared to the reference strain, which could be important to understand the virulence, severity and transmissibility of the virus. Our findings also suggest that there were at least three independent introductions of SARS-CoV-2 to Ecuador. <h3>IMPORTANCE</h3> COVID-19, an infectious disease caused by SARS-CoV-2, has spread globally including Latin American countries including Ecuador. The first strain of SARS-CoV-2 sequenced was from Wuhan, which is considered as the reference strain. There were no data about the SARS-CoV-2 lineages in Ecuador, and the purpose of this study was to find out the origin of the different lineages circulating in the population. We also were interested in the mutations present in these genomes as they can influence virulence, transmission and infectivity.
Holographic lithography with thick photoresist (1983)

Gratings with periods as fine as 199 nm and height-to-width ratios ∼5:1 have been produced directly in photoresist by holographic lithography using a technique that reduces ‘‘orthogonal standing wave’’ problems. The technique uses a single layer of photoresist to attenuate the ‘‘orthogonal standing wave,’’ as well as record the grating pattern. The technique is tolerant of process variations and produces structures suitable for further processing steps such as liftoff and etching.
A phased approach to network intrusion detection (1991)

This paper describes the design and development of a prototype intrusion detection system for the Los Alamos National Laboratory's Integrated Computing Network (ICN). The development of this system is based on three basic assumptions: (1) that statistical analysis of computer system and user activates may be used to characterize normal system and user behavior, and that given the resulting statistical profiles, behavior which deviates beyond certain bounds can be detected, (2) that expert system techniques can be applied to security auditing and intrusion detection, and (3) that successful intrusion detection may take place while monitoring a limited set of network activities. The Network Anomaly Detection and Intrusion Reporter (NADIR) design intent was to duplicate and improve the audit record review activities which had previously been undertaken by security personnel, to replace the manual review of audit logs with a near realtime expert system.
NK cell–mediated cytotoxicity contributes to tumor control by a cytostatic drug combination (2018)

Molecularly targeted therapies aim to obstruct cell autonomous programs required for tumor growth. We show that mitogen-activated protein kinase (MAPK) and cyclin-dependent kinase 4/6 inhibitors act in combination to suppress the proliferation of KRAS-mutant lung cancer cells while simultaneously provoking a natural killer (NK) cell surveillance program leading to tumor cell death. The drug combination, but neither agent alone, promotes retinoblastoma (RB) protein-mediated cellular senescence and activation of the immunomodulatory senescence-associated secretory phenotype (SASP). SASP components tumor necrosis factor-α and intercellular adhesion molecule-1 are required for NK cell surveillance of drug-treated tumor cells, which contributes to tumor regressions and prolonged survival in a KRAS-mutant lung cancer mouse model. Therefore, molecularly targeted agents capable of inducing senescence can produce tumor control through non-cell autonomous mechanisms involving NK cell surveillance.
The genomic structure of the human UBE1L gene. (1995)

The human UBE1L gene, for which the product may well play a role in the ubiquitin system because of its high degree of identity to the ubiquitin activating enzyme, is located at 3p21, a chromosomal region consistently showing loss of heterozygosity in lung cancer. The finding that UBE1L is well expressed in normal lung tissue, but hardly or not in lung cancer-derived cell lines, prompted us to investigate its genomic structure to find an explanation for the lack of expression in lung cancer. The gene has 22 exons distributed over 8.4 kb. Both anchored PCR experiments and mapping of DNase I-hypersensitive sites point to the region immediately upstream of exon 1 as the promoter site. Three moderately to well-informative polymorphisms were found, of which one is easily directly detectable. Cancer-specific mutations were not detected. The lack of expression in lung cancer cell lines correlated with a highly decreased sensitivity towards DNAse I of the promoter region and with an almost complete methylation of the HhaI site in the first exon. 5'-Azacytidine-induced demethylation did not result in a marked increase of the UBE1L mRNA level in the tumor cell lines. This leaves the possibility that mutation or absence of yet unknown transcription factors causes a regulatory block of the UBE1L gene.
Synergism between paracetamol and nonsteroidal anti-inflammatory drugs in experimental acute pain (2006)

The antinociception induced by the intraperitoneal coadministration of combinations of paracetamol with the nonsteroidal anti-inflammatory drugs (NSAIDs) diclofenac, ibuprofen, ketoprofen, meloxicam, metamizol, naproxen, nimesulide, parecoxib and piroxicam was studied by isobolographic analysis in the acetic acid abdominal constriction test of mice (writhing test). The effective dose that produced 50% antinociception (ED50) was calculated from the log dose-response curves of fixed ratio combinations of paracetamol with each NSAID. By isobolographic analysis, this ED50 was compared to the theoretical additive ED50 calculated from the ED(50) of paracetamol and of each NSAID alone obtained from ED50 dose-response curves. As shown by isobolographic analysis, all the combinations were synergistic, the experimental ED50s being significantly smaller than the theoretically calculated ED50s. The results of this study demonstrate potent interactions between paracetamol and NSAIDs and validate the clinical use of combinations of these drugs in the treatment of pain conditions.
Commercial considerations in tissue engineering (2006)

Tissue engineering is a field with immense promise. Using the example of an early tissue-engineered skin implant, Dermagraft, factors involved in the successful commercial development of devices of this type are explored. Tissue engineering has to strike a balance between tissue culture, which is a resource-intensive activity, and business considerations that are concerned with minimizing cost and maximizing customer convenience. Bioreactor design takes place in a highly regulated environment, so factors to be incorporated into the concept include not only tissue culture considerations but also matters related to asepsis, scaleup, automation and ease of use by the final customer. Dermagraft is an allogeneic tissue. Stasis preservation, in this case cryopreservation, is essential in allogeneic tissue engineering, allowing sterility testing, inventory control and, in the case of Dermagraft, a cellular stress that may be important for hormesis following implantation. Although the use of allogeneic cells provides advantages in manufacturing under suitable conditions, it raises the spectre of immunological rejection. Such rejection has not been experienced with Dermagraft. Possible reasons for this and the vision of further application of allogeneic tissues are important considerations in future tissue-engineered cellular devices. This review illustrates approaches that indicate some of the criteria that may provide a basis for further developments. Marketing is a further requirement for success, which entails understanding of the mechanism of action of the procedure, and is illustrated for Dermagraft. The success of a tissue-engineered product is dependent on many interacting operations, some discussed here, each of which must be performed simultaneously and well.
Inhibition of PDGF-induced c-jun and c-fos expression by a tyrosine protein kinase inhibitor. (1991)

The expression of the proto-oncogenes c-fos, c-jun, jun B and jun D was monitored in quiescent C3H10T1/2 fibroblasts after stimulation with PDGF. The mRNA level of c-fos, c-jun and jun B, but not of jun D, was stimulated by PDGF. The inductions were abolished when genistein, a specific tyrosine protein kinase inhibitor, was added concomitantly with PDGF, a condition in which DNA synthesis is known to be inhibited. As already shown previously, treatment with PDGF and genistein for 4h followed by the replacement with fresh medium induces the progression of the cells through the G1 phase of their growth-division cycle, without phospholipase C activation. The removal of PDGF and genistein was accompanied by an important increase in c-fos, c-jun and jun B mRNA expression, which correlated with the entrance of cells into G1 phase. Thus, the proto-oncogene expressions induced by PDGF are also obtained in the absence of phospholipase C activation. This result also suggests that the mRNA levels of c-jun, jun B and to a lesser degree c-fos are positively regulated by tyrosine protein kinase activity, whereas jun D is negatively regulated.
Modulation of Insulin Receptor Substrate-1 Tyrosine Phosphorylation by an Akt/Phosphatidylinositol 3-Kinase Pathway (1999)

Serine/threonine phosphorylation of insulin receptor substrate 1 (IRS-1) has been implicated as a negative regulator of insulin signaling. Prior studies have indicated that this negative regulation by protein kinase C involves the mitogen-activated protein kinase and phosphorylation of serine 612 in IRS-1. In the present studies, the negative regulation by platelet-derived growth factor (PDGF) was compared with that induced by endothelin-1, an activator of protein kinase C. In contrast to endothelin-1, the inhibitory effects of PDGF did not require mitogen-activated protein kinase or the phosphorylation of serine 612. Instead, three other serines in the phosphorylation domain of IRS-1 (serines 632, 662, and 731) were required for the negative regulation by PDGF. In addition, the PDGF-activated serine/threonine kinase called Akt was found to inhibit insulin signaling. Moreover, this inhibition required the same IRS-1 serine residues as the inhibition by PDGF. Finally, the negative regulatory effects of PDGF and Akt were inhibited by rapamycin, an inhibitor of the mammalian target of rapamycin (mTOR), one of the downstream targets of Akt. These studies implicate the phosphatidylinositol 3-kinase/Akt kinase cascade as an additional negative regulatory pathway for the insulin signaling cascade.