gebhart/patrepeval huggingface dataset:
Development of porcine adenovirus-3 as an expression vector. (1999)

Porcine adenovirus-3 (PAV-3) was developed as an expression vector using homologous recombination in Escherichia coli BJ 5183. As a prerequisite, the complete genome of PAV-3 was first introduced as a PacI restriction fragment into a bacterial plasmid. The plasmid, when PacI restricted and transfected into swine testicular cells, produces an infectious virus. The potential of this procedure was demonstrated by the construction of several PAV-3 recombinants. Part of the E3 region, which is nonessential for virus replication under cell culture conditions, was identified and deleted from the virus genome. The gene for glycoprotein D (gD) of pseudorabies virus (PRV), which elicits PRV-neutralizing antibodies in pigs, was cloned and expressed from the E3 region of PAV-3. A 50 kDa polypeptide was identified in recombinant PAV-3-infected cell lysates by immunoprecipitation assays using gD-specific monoclonal antibodies. In another experiment, a region between the right inverted terminal repeat and the promoter of the E4 region was used to clone and express the chloramphenicol acetyltransferase (CAT) gene under the control of SV40 immediate early promoter. CAT gene expression was observed irrespective of the orientation of the CAT gene. These results indicate that the helper-independent recombinant PAV-3 could be used as an expression vector and has potential as a recombinant vaccine vector in pigs.
Neoplastic progression of human colorectal cancer is associated with overexpression of the stromelysin‐3 and BM‐40/SPARC genes (1995)

The interaction of neoplastic cells with the extracellular matrix is a critical event for the initiation of cancer invasion and metastasis. This study was designed to evaluate the potential implication of stromelysin-3 (ST3), a newly identified member of the matrix-degrading metalloproteinase family, and of BM-40/SPARC, a glycoprotein associated with the extracellular matrix, during the progression of human colorectal cancers. We analyzed the relative abundance of ST3 and BM-40/SPARC transcripts by Northern blot, and their distribution by in situ hybridization, in normal mucosa, benign adenomas, and primary colorectal adenocarcinomas and their liver metastases. The ST3 and BM-40/SPARC transcripts were overexpressed in primary colorectal cancers and their liver metastases compared to non-neoplastic mucosa. These transcripts were localized in stromal fibroblasts adjacent to the neoplastic foci. Overexpression of ST3 correlated with the progression of human colorectal tumors toward local invasion and liver metastasis. Induction of these genes also occurred in diverticulitis and digestive neoplasms such as gastric and esophageal carcinomas.
Regulatory region in choline acetyltransferase gene directs developmental and tissue-specific expression in transgenic mice. (1995)

Acetylcholine, one of the main neurotransmitters in the nervous system, is synthesized by the enzyme choline acetyltransferase (ChAT; acetyl-CoA:choline O-acetyltransferase, EC 2.3.1.6). The molecular mechanisms controlling the establishment, maintenance, and plasticity of the cholinergic phenotype in vivo are largely unknown. A previous report showed that a 3800-bp, but not a 1450-bp, 5' flanking segment from the rat ChAT gene promoter directed cell type-specific expression of a reporter gene in cholinergic cells in vitro. Now we have characterized a distal regulatory region of the ChAT gene that confers cholinergic specificity on a heterologous downstream promoter in a cholinergic cell line and in transgenic mice. A 2342-bp segment from the 5' flanking region of the ChAT gene behaved as an enhancer in cholinergic cells but as a repressor in noncholinergic cells in an orientation-independent manner. Combined with a heterologous basal promoter, this fragment targeted transgene expression to several cholinergic regions of the central nervous system of transgenic mice, including basal forebrain, cortex, pons, and spinal cord. In eight independent transgenic lines, the pattern of transgene expression paralleled qualitatively and quantitatively that displayed by endogenous ChAT mRNA in various regions of the rat central nervous system. In the lumbar enlargement of the spinal cord, 85-90% of the transgene expression was targeted to the ventral part of the cord, where cholinergic alpha-motor neurons are located. Transgene expression in the spinal cord was developmentally regulated and responded to nerve injury in a similar way as the endogenous ChAT gene, indicating that the 2342-bp regulatory sequence contains elements controlling the plasticity of the cholinergic phenotype in developing and injured neurons.
Prodigiosene [5-(2-pyrryl)-2,21-dipyrrylmethene] and some substituted prodigiosenes (1970)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTProdigiosene [5-(2-pyrryl)-2,21-dipyrrylmethene] and some substituted prodigiosenesWalter R. Hearn, Michael K. Elson, Robert H. Williams, and Jorge. Medina-CastroCite this: J. Org. Chem. 1970, 35, 1, 142–146Publication Date (Print):January 1, 1970Publication History Published online1 May 2002Published inissue 1 January 1970https://pubs.acs.org/doi/10.1021/jo00826a032https://doi.org/10.1021/jo00826a032research-articleACS PublicationsRequest reuse permissionsArticle Views299Altmetric-Citations50LEARN 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
Amplification of epidermal growth factor receptor gene but no evidence of ras mutations in primary human esophageal cancers. (1988)

Primary esophageal squamous cell carcinomas from 41 patients were analyzed for the presence of proto-oncogene alterations associated with this malignancy. The occurrence of activating ras gene mutations in 25 tumors was determined using oligomer hybridization of target sequences amplified by polymerase chain reaction. We found no evidence for mutations in codons 12 and 61 of the H-ras, K-ras, and N-ras genes, nor in codon 13 of the K-ras and N-ras loci in any of these tumors. The apparent absence of activated ras oncogene in esophageal cancers represents a possible exception to the presence of these mutations found consistently in numerous other types of human malignancies, and is in striking contrast to the 40% prevalence of ras mutations in human colorectal cancers. Southern blot hybridization experiments with DNAs from tumors demonstrated amplification of the epidermal growth factor receptor gene (c-erbB) in two of 25 carcinomas. No amplification of the structurally related c-erbB2 (neu) gene was detected. In three out of 12 carcinomas, the level of epidermal growth factor receptor RNA was significantly higher than in normal esophageal mucosal tissue. Our results suggest that enhanced transcription of the epidermal growth factor receptor gene is associated with the development of some esophageal cancers.
The asp‐rich region at the carboxyl‐terminus of calsequestrin binds to Ca2+ and interacts with triadin (2000)

Calsequestrin (CSQ) is a high capacity Ca(2+) binding protein in the junctional sarcoplasmic reticulum of striated muscles, and has been shown to regulate the ryanodine receptor (RyR) through triadin and junctin. In order to identify the functional roles of specific regions on CSQ, several CSQ deletion mutants were prepared by molecular cloning and Escherichia coli expression. 45Ca(2+) overlay assay using a native gel system revealed that the major Ca(2+) binding motif of CSQ resides in the asp-rich region (amino acids 354-367). In an in vitro binding assay using a glutathione-S-transferase affinity column, the interaction between CSQ and triadin was found to be Ca(2+)-dependent, and the site of interaction was confined to the asp-rich region of CSQ. Our results suggest that the asp-rich region of CSQ could participate in the RyR-mediated Ca(2+) release process by offering a direct binding site to luminal Ca(2+) as well as triadin.
Four individually druggable MET hotspots mediate HGF-driven tumor progression (2014)

Activation of MET by HGF plays a key role in tumor progression. Using a recently developed llama platform that generates human-like immunoglobulins, we selected 68 different antibodies that compete with HGF for binding to MET. HGF-competing antibodies recognized 4 distinct hotspots localized in different MET domains. We identified 1 hotspot that coincides with the known HGF β chain binding site on blades 2-3 of the SEMA domain β-propeller. We determined that a second and a third hotspot lie within blade 5 of the SEMA domain and IPT domains 2-3, both of which are thought to bind to HGF α chain. Characterization of the fourth hotspot revealed a region across the PSI-IPT 1 domains not previously associated with HGF binding. Individual or combined targeting of these hotspots effectively interrupted HGF/MET signaling in multiple cell-based biochemical and biological assays. Selected antibodies directed against SEMA blades 2-3 and the PSI-IPT 1 region inhibited brain invasion and prolonged survival in a glioblastoma multiforme model, prevented metastatic disease following neoadjuvant therapy in a triple-negative mammary carcinoma model, and suppressed cancer cell dissemination to the liver in a KRAS-mutant metastatic colorectal cancer model. These results identify multiple regions of MET responsible for HGF-mediated tumor progression, unraveling the complexity of HGF-MET interaction, and provide selective molecular tools for targeting MET activity in cancer.
Periodic Microfluidic Bubbling Oscillator: Insight into the Stability of Two-Phase Microflows (2006)

This Letter describes a periodically oscillating foam flow in a microfluidic device. For constant input parameters, both the produced bubble volume and the flow rate vary over a factor of two. We make explicit the link between the foam topology alternance and flow rate changes, and construct a retroaction model where bubbles still present downstream determine the volume of new bubbles, in agreement with experiment. This gives insight into the various parameters important to maintain monodispersity and at the same time shows a method to achieve controlled polydispersity.
Vaccination with Heat-killed Leishmania Antigen or Recombinant Leishmanial Protein and CpG Oligodeoxynucleotides Induces Long-Term Memory CD4+and CD8+T Cell Responses and Protection Against Leishmania major Infection (2002)

CpG oligodeoxynucleotides (ODN) have potent effects on innate and adaptive cellular immune responses. In this report, the ability of CpG ODN to confer long-term immunity and protection when used as a vaccine adjuvant with a clinical grade of leishmanial antigen, autoclaved Leishmania major (ALM), or a recombinant leishmanial protein was studied. In two different mouse models of L. major infection, vaccination with ALM plus CpG ODN was able to control infection and markedly reduce lesion development in susceptible BALB/c and resistant C57BL/6 (B6) mice, respectively, up to 12 wk after immunization. Moreover, B6 mice immunized with ALM plus CpG ODNs were still protected against infectious challenge even 6 mo after vaccination. In terms of immune correlates of protection, ALM plus CpG ODN-vaccinated mice displayed L. major-specific T helper cell 1 and CD8+ responses. In addition, complete protection was markedly abrogated in mice depleted of CD8+ T cells at the time of vaccination. Similarly, mice vaccinated with a recombinant leishmanial protein plus CpG ODN also had long-term protection that was dependent on CD8+ T cells in vivo. Together, these data demonstrate that CpG ODN, when used as a vaccine adjuvant with either a recombinant protein or heat-killed leishmanial antigen, can induce long-term protection against an intracellular infection in a CD8-dependent manner.
Mechanisms of acquired resistance to tyrosine kinase inhibitors (2011)

In recent years, structural and functional studies reveal that tyrosine kinases (TKs) act as the essential components of signal transduction pathways that regulate cancer cell proliferation, apoptosis and angiogenesis, and therefore become potential targets for anticancer therapy. Most of TK inhibitors (TKIs) are small molecular and hydrophobic compounds, thus they can rapidly reach their specific intracellular targets and inhibit the activation of the related TKs. Unfortunately, accompanied with patients who gain great benefit of TKIs therapy, increasing evidences of acquired resistance to these agents have been documented. The unveiling point mutations within the kinase domain, gene amplification or overexpression, or modification of signaling pathway have been implicated in drug resistance. Additionally, overexpression of ABC transporters is likely to set stage for resistant development. In this review, we focus on the discussion of the molecular mechanisms of acquired resistance to TKIs therapy. The mechanistic understanding may help to put forward new hypotheses on drug development and design better therapies to overcome TKIs resistance.
Molecular and functional analysis of nicotinate catabolism in Eubacterium barkeri (2006)

The anaerobic soil bacterium Eubacterium barkeri catabolizes nicotinate to pyruvate and propionate via a unique fermentation. A full molecular characterization of nicotinate fermentation in this organism was accomplished by the following results: (i) A 23.2-kb DNA segment with a gene cluster encoding all nine enzymes was cloned and sequenced, (ii) two chiral intermediates were discovered, and (iii) three enzymes were found, completing the hitherto unknown part of the pathway. Nicotinate dehydrogenase, a (nonselenocysteine) selenium-containing four-subunit enzyme, is encoded by ndhF (FAD subunit), ndhS (2 x [2Fe-2S] subunit), and by the ndhL/ndhM genes. In contrast to all enzymes of the xanthine dehydrogenase family, the latter two encode a two-subunit molybdopterin protein. The 6-hydroxynicotinate reductase, catalyzing reduction of 6-hydroxynicotinate to 1,4,5,6-tetrahydro-6-oxonicotinate, was purified and shown to contain a covalently bound flavin cofactor, one [2Fe-2S](2+/1+) and two [4Fe-4S](2+/1+) clusters. Enamidase, a bifunctional Fe-Zn enzyme belonging to the amidohydrolase family, mediates hydrolysis of 1,4,5,6-tetrahydro-6-oxonicotinate to ammonia and (S)-2-formylglutarate. NADH-dependent reduction of the latter to (S)-2-(hydroxymethyl)glutarate is catalyzed by a member of the 3-hydroxyisobutyrate/phosphogluconate dehydrogenase family. A [4Fe-4S]-containing serine dehydratase-like enzyme is predicted to form 2-methyleneglutarate. After the action of the coenzyme B(12)-dependent 2-methyleneglutarate mutase and 3-methylitaconate isomerase, an aconitase and isocitrate lyase family pair of enzymes, (2R,3S)-dimethylmalate dehydratase and lyase, completes the pathway. Genes corresponding to the first three enzymes of the E. barkeri nicotinate catabolism were identified in nine Proteobacteria.
RNAi: A Guide to Gene Silencing (2003)

The ability of double stranded RNA to inhibit the expression of genes with an appropriate sequence can be harnessed to silence target genes in vitro in a new and powerful way. This volume combines reliable RNAi protocols for a variety of species with discussion of strategies for the effective design of experiments using this important new technique that is changing the way experimental science is done.
Single- and dual-polarized slot and patch antennas with wide tuning ranges (2008)

Frequency- and polarization-agile antennas are of great interest for multi-function, software-defined, and cognitive radios. Frequency tuning over an octave is challenging because the radiation conductance changes as the antennas are tuned. In this work, single- and dual-polarized antennas are tuned over frequency ranges of up to 2:1 and 1.7:1, respectively, while remaining impedance matched. The impedance match over tuning is maintained by a properly chosen reactive element in series with the antenna. Both polarizations of the dual-polarized antennas are tuned independently—enabling either simultaneous frequency- and polarization-agility, or operation at two independent frequencies on orthogonal polarizations. First, the tunability of the slot-ring antenna is demonstrated with fixed-capacitor loading, and then, single and dual-polarized slot-ring antennas are tuned from 0.95 – 1.8 GHz and 0.93 – 1.6 GHz, respectively, using varactor diodes. Microstrip reactive loads are developed to maintain >20 dB port-to-port isolation over most of the tuning range of the dual-polarized antenna. This may be the first dual-polarized tunable antenna with independent control of both polarizations over a 1.7:1 frequency range. Single-sided radiation is desirable for many applications, and varactor-tuned cavity-backed slots are investigated for this purpose. A shallow cavity-backed slot is tuned from 1.0 to 1.9 GHz with <-20 dB return loss. The antenna operates either in free-space or conformally mounted with minimal change in input impedance. Finally, a dual-polarized cavity-backed patch antenna is tuned from 0.6 – 1 GHz. Differential feeds are employed to achieve >30 dB port-to-port isolation (differential-differential mode) over the tuning range, and the measured cross-polarization level at 0.65, 0.8, and 0.95 GHz is <-25 dB. This may be the first demonstration of dual-polarized independent tuning over a 1.7:1 frequency range with single-sided radiation.
DNA Damage Signaling Is Required for Replication of Human Bocavirus 1 DNA in Dividing HEK293 Cells (2016)

The parvovirus human bocavirus 1 (HBoV1) is an emerging respiratory virus that causes lower respiratory tract infections in young children worldwide. HEK293 cells are the only dividing cells tested that fully support the replication of the duplex genome of this virus and allow the production of progeny virions. In this study, we demonstrate that HBoV1 induces a DDR that plays significant roles in the replication of the viral DNA and the production of progeny virions in HEK293 cells. We also show that both cellular DNA replication factors and DNA repair DNA polymerases colocalize within centers of viral DNA replication and that Pol η and Pol κ play an important role in HBoV1 DNA replication. Whereas the DDR that leads to the replication of the DNA of other parvoviruses is facilitated by the cell cycle, the DDR triggered by HBoV1 DNA replication or NS1 is not. HBoV1 is the first parvovirus whose NS1 has been shown to be able to activate all three PI3KKs (ATM, ATR, and DNA-PKcs).
Low complexity turbo equalization with binary precoding (2002)

We consider the design of convolutionally coded systems and low complexity receivers for communicating through intersymbol interference (ISI) channels when iterative equalization and decoding is employed in the receiver. We first introduce a binary precoding technique that makes a non-recursive ISI channel 'appear' recursive to the outer code and, hence, provides excellent bit error rate (BER) performance. Then, a low complexity soft output algorithm based on the M and T-algorithms is proposed for soft-output equalization of channels with long memory.
Zinc Deficiency in Surgical Patients: A Clinical Study (1985)

Four stressed surgical patients who had different diseases are presented. They had dermatitis associated with low serum zinc levels but were not on total parenteral nutrition. The range of serum zinc varied between 25 and 56 mu/dl when first seen. All but one had hypoalbuminemia and anemia; one patient had diarrhea. When measured, other microelements were normal. These patients were thought to have zinc deficiency and all their symptoms responded favorably to oral zinc and nutritional support. A highlight of previous reported cases of zinc deficiency is presented along with a brief review of the subject. Acute stress including major operations will decrease the serum zinc level temporarily. Zinc deficiency may be the result of chronic zinc depletion caused by other conditions. Chronic leg ulcers are associated with low serum zinc levels and might precipitate zinc selectively. A zinc supplement will help in the healing of these ulcers and wounds in general. The possibility of an interrelationship of zinc and other microelements is raised but is not clear.
Complete physical map of the human immunoglobulin heavy chain constant region gene complex. (1989)

We have found by pulsed-field gel electrophoresis that the human immunoglobulin heavy chain constant region gene complex maps entirely to a 350-kilobase (kb) Mlu I fragment. The enzyme Eag I was used with pulsed-field gel electrophoresis alone and in double digests with Spe I to map the region. C gamma 3, of the C gamma 3-C gamma 1-C psi epsilon 1-C alpha 1 cluster, maps 60 kb to the 3' side of C delta; C gamma 2 of the C gamma 2-C gamma 4-C epsilon-C alpha 2 cluster maps 80 kb to the 3' side of C alpha 1, where C gamma 3 encodes the constant region of the immunoglobulin gamma 3 chain, C gamma 1 encodes the constant region of the immunoglobulin gamma 1 chain, etc. C psi gamma maps 35 kb to the 3' side of C alpha 1 and is in the same transcriptional orientation as the other genes. Although in the cloned DNA many CpG-containing restriction sites were identified, most of these were methylated in peripheral blood leukocytes. The sites that were not methylated were predominantly found in three clusters, or Hpa I tiny fragment islands. One was found on the 5' side of C mu; the other two lie 30 kb to the 3' side of each of the C alpha genes and could indicate the presence of regulatory sequences or genes. A region showing strong linkage disequilibrium between all C gamma genes spans at least 160 kb. The 70-kb C mu-C gamma 3 region, however, shows no linkage disequilibrium, possibly indicating a recombination hot spot. The immunoglobulin heavy chain constant region has been almost entirely cloned and mapped, and thus most rearrangements occurring in this region should be detectable.
Visualization of cutaneous hemoglobin oxygenation and skin hydration using near‐infrared spectroscopic imaging (2001)

Near-infrared reflectance spectroscopic imaging is demonstrated to be a powerful augmentation to the standard clinical assessment of skin.
Analysis of the role of the COL1 domain and its adjacent cysteine‐containing sequence in the chain assembly of type IX collagen (1993)

The mechanisms of chain selection and assembly of type IX collagen, a heterotrimer alpha 1(IX)alpha 2(IX)alpha 3(IX), must differ from that of fibrillar collagens since it lacks the characteristic C-propeptide of these latter molecules. We have tested the hypothesis that the information required for this process is contained within the C-terminal triple helical disulfide-bonded region (LMW). The reassociations of the purified LMW fragments of pepsinized bovine type IX collagen were followed by the formation of disulfide-bonded multimers. Our data demonstrate that only three triple helical assemblies form readily, (alpha 1)3, (alpha 2)3 and alpha 1 alpha 2 alpha 3. The information required for chain selection and assembly is thus, at least in part, contained in the studied fragments. Molecular stoichiometries different from the classical heterotrimer may thus also form under certain conditions.