gebhart/patrepeval huggingface dataset:
Cloning and sequencing of the pheP gene, which encodes the phenylalanine-specific transport system of Escherichia coli (1991)

The phenylalanine-specific permease gene (pheP) of Escherichia coli has been cloned and sequenced. The gene was isolated on a 6-kb Sau3AI fragment from a chromosomal library, and its presence was verified by complementation of a mutant lacking the functional phenylalanine-specific permease. Subcloning from this fragment localized the pheP gene on a 2.7-kb HindIII-HindII fragment. The nucleotide sequence of this 2.7-kb region was determined. An open reading frame was identified which extends from a putative start point of translation (GTG at position 636) to a termination signal (TAA at position 2010). The assignment of the GTG as the initiation codon was verified by site-directed mutagenesis of the initiation codon and by introducing a chain termination mutation into the pheP-lacZ fusion construct. A single initiation site of transcription 30 bp upstream of the start point of translation was identified by the primer extension analysis. The pheP structural gene consists of 1,374 nucleotides specifying a protein of 458 amino acid residues. The PheP protein is very hydrophobic (71% nonpolar residues). A topological model predicted from the sequence analysis defines 12 transmembrane segments. This protein is highly homologous with the AroP (general aromatic transport) system of E. coli (59.6% identity) and to a lesser extent with the yeast permeases CAN1 (arginine), PUT4 (proline), and HIP1 (histidine) of Saccharomyces cerevisiae.
Neu differentiation factor induces ErbB2 down-regulation and apoptosis of ErbB2-overexpressing breast tumor cells. (1997)

Neu differentiation factor (NDF), a member of the epidermal growth factor (EGF)-related peptide family, activates ErbB2 via heterodimerization with the NDF receptors ErbB3 and ErbB4. In a similar fashion, EGF receptor (EGFR) agonists induce heterodimers of EGFR and ErbB2. In this paper, we show that the ErbB2-overexpressing breast tumor cells SKBR3, AU565, and MDA-MB453 are growth inhibited by NDF. Cells with elevated levels of ErbB2 but little or no NDF receptors (SKOV3 and MDA-MB361) or cells with low levels of ErbB2 (T47D and MCF7) are not growth inhibited. None of the EGFR agonists tested (EGF, beta-cellulin, or heparin-binding EGF) inhibited growth of ErbB2-overexpressing cells. These results suggest that formation of an ErbB2/NDF receptor heterodimer, but not of an ErbB2/EGFR heterodimer, promotes growth inhibition. In addition, NDF caused a down-regulation of ErbB2 but not of ErbB3. The mechanism underlying the inhibitory effect was examined further in SKBR3 cells, which are 95% growth inhibited by NDF. A G2-M arrest is seen 24 h after NDF treatment, and increased apoptosis is detectable from day 2 onward. The results demonstrate for the first time that NDF induces apoptosis of tumor cells overexpressing ErbB2.
Genetic Engineering of a Bifunctional IgG Fusion Protein with Iduronate-2-Sulfatase (2009)

Iduronate-2-sulfatase (IDS) is a lysosomal sulfatase that prevents the accumulation within the brain of glycosoaminoglycans. However, IDS does not cross the blood-brain barrier (BBB). To enable BBB transport, human IDS, minus its signal peptide, was fused to the carboxyl terminus of the heavy chain of a chimeric monoclonal antibody (mAb) to the human insulin receptor (HIR). The HIRMAb crosses the BBB on the endogenous insulin receptor and acts as a molecular Trojan horse to ferry the IDS into brain. The HIRMAb-IDS fusion protein was expressed in COS cells and purified with protein A affinity chromatography. The size of the fusion heavy chain, as measured with Western blotting and antibodies to either human IDS or human IgG, was increased about 80 kDa, relative to the size of the heavy chain of the parent HIRMAb. The HIRMAb-IDS fusion protein retained high-affinity binding for the HIR. The IDS enzyme specific activity of the fusion protein was 51 +/- 7 nmol/h per microgram of protein, which is comparable to the enzyme activity of recombinant IDS. The fusion protein was taken up by human fibroblasts, and the accumulation of glycosoaminoglycans in fibroblasts null for the sulfatase was decreased 84% by treatment with the fusion protein. The HIRMAb-IDS fusion protein is a bifunctional IgG-sulfatase fusion protein, which has been specifically engineered for targeted drug delivery across the human BBB.
Terminally functionalized polyisobutylene oligomers as soluble supports in catalysisElectronic supplementary information (ESI) available: experimental details for the synthesis and use of the PIB oligomers and catalysts. See http://www.rsc.org/suppdata/cc/b3/b312368e/ (2003)

A new phase selective hydrocarbon soluble polymer support is described.
Structure-Based Design, Synthesis, and Biological Evaluation of Irreversible Human Rhinovirus 3C Protease Inhibitors. 3. Structure−Activity Studies of Ketomethylene-Containing Peptidomimetics (1999)

The structure-based design, chemical synthesis, and biological evaluation of various ketomethylene-containing human rhinovirus (HRV) 3C protease (3CP) inhibitors are described. These compounds are comprised of a peptidomimetic binding determinant and an ethyl propenoate Michael acceptor moiety which forms an irreversible covalent adduct with the active site cysteine residue of the 3C enzyme. The ketomethylene-containing inhibitors typically display slightly reduced 3CP inhibition activity relative to the corresponding peptide-derived molecules, but they also exhibit significantly improved antiviral properties. Optimization of the ketomethylene-containing compounds is shown to provide several highly active 3C protease inhibitors which function as potent antirhinoviral agents (EC90 = <1 microM) against multiple virus serotypes in cell culture.
AUTOLOGOUS STEM CELL TRANSPLANTATION USING PERIPHERAL BLOOD STEM CELLS (1987)

Section of Hematology-Oncology Department of Medicine Loyola University Stritch School of Medicine Maywood, Illinois 60153 Department of Medicine Southern Illinois University School of Medicine Central Illinois Community Blood Bank Department of Pathology Memorial Medical Center Springfield, Illinois 62708
Nanostructures in Diatom Frustules: Functional Morphology of Valvocopulae in Cocconeidacean Monoraphid Taxa (2005)

Nanopositioning is one of the most intriguing challenges in nanoelectronics and photonics. As the optoelectronic circuit components become more and more complex, the importance of nanopositioning becomes critical. For example, in single-mode fiber telecommunications it is easy to show that an alignment deviation as small as a few tens of nanometers can yield to 50 percent of loss performance. Diatoms are unicellular plants occurring in almost every aquatic environment. Their main morphological character is the frustule, a silica cell wall that consists of two valves, encasing the protoplasm, joined together by a girdle. The girdle is composed of a series of silica bands (copulae) linked together along their margins. In several diatom species, the first girdle bands (valvocopulae), which associate the valves with the rest of the girdle, appear different in shape and bring specific nanostructures devoted to facilitate this linkage. The species of the diatom family Cocconeidaceae show elaborate linkage systems between the valves in which functionally complex valvocopulae are involved. Different levels of complexity and functional efficiency are recognizable in the valve-valvocopula and valvocopula-valvocopula linkages of different cocconeidacean taxa. This work briefly reviews the morphological characteristics and the functional role of the nanostructures involved in the linkages; in fact, we firmly believe that they are stimulating models for design and manufacturing engineers working in the technological nanoworld.
Biologically and Mechanically Biocompatible Titanium Alloys (2008)

Nb, Ta, and Zr are the favorable nontoxic and allergy-free alloying elements suitable for use in titanium alloys for biomedical applications. Low-rigidity titanium alloys composed of nontoxic and allergy-free elements are receiving considerable attention. The advantage of low-rigidity titanium alloys in the healing of bone fracture and bone remodeling is successfully proven by using tibia of rabbit as a fracture model. Ni-free superelastic and shape memory titanium alloys for biomedical applications are being actively developed. The mechanical properties such as fatigue and fretting fatigue are important from the viewpoint of mechanical properties, which may be collectively referred to as mechanical biocompatibilities in the broad sense, in addition to the rigidity, i.e. Young’s modulus. Bioactive surface modifications of titanium alloys for biomedical applications are very important for achieving further biocompatibility.
Carbamyl phosphate synthetase I deficiency. One base substitution in an exon of the CPS I gene causes a 9-basepair deletion due to aberrant splicing. (1993)

Carbamyl phosphate synthetase I (CPS I; EC6,3,4,16) is an autosomal recessive disorder characterized by hyperammonemia. We studied the molecular bases of CPS I deficiency in a newborn Japanese girl with consanguineous parents. Northern and Western blots revealed a marked decrease in CPS I mRNA and enzyme protein but with a size similar to that of the control, respectively. Sequencing of the patient's cDNA revealed a nine-nucleotide deletion at position 832-840. Sequencing analysis of the genomic DNA revealed a G to C transversion at position 840, the last nucleotide of an exon in the splice donor site. This substitution altered the consensus sequence of the splice donor site and the newly cryptical donor site in the exon caused the 9-bp in-frame deletion. This report seems to be the first complete definition of CPS I deficiency, at the molecular level.
[3H]Dihydrorotenone Binding to NADH: Ubiquinone Reductase (Complex I) of the Electron Transport Chain: An Autoradiographic Study (1996)

Abnormalities of mitochondrial energy metabolism may play a role in normal aging and certain neurodegenerative disorders. In this regard, complex I of the electron transport chain has received substantial attention, especially in Parkinson's disease. The conventional method for studying complex I has been quantitation of enzyme activity in homogenized tissue samples. To enhance the anatomic precision with which complex I can be examined, we developed an autoradiographic assay for the rotenone site of this enzyme. [3H]dihydrorotenone ([3H]DHR) binding is saturable (KD = 15-55 nM) and specific, and Hill slopes of 1 suggest a single population of binding sites. Nicotinamide adenine dinucleotide (NADH) enhances binding 4- to 80-fold in different brain regions (EC50 = 20-40 microM) by increasing the density of recognition sites (Bmax). Nicotinamide adenine dinucleotide phosphate also increases binding, but NAD+ does not. In skeletal muscle, heart, and kidney, binding was less affected by NADH. [3H]DHR binding is inhibited by rotenone (IC50 = 8-20 nM), meperidine (IC50 = 34-57 microM), amobarbitol (IC50 = 375-425 microM), and MPP+ (IC50 = 4-5 mM), consistent with the potencies of these compounds in inhibiting complex I activity. Binding is heterogeneously distributed in brain with the density in gray matter structures varying more than 10-fold. Lesion studies suggest that a substantial portion of binding is associated with nerve terminals. [3H]DHR autoradiography is the first quantitative method to examine complex I with a high degree of anatomic precision. This technique may help to clarify the potential role of complex I dysfunction in normal aging and disease.
Liquid Egg as an Alternative Protein Source in Calf Milk Replacers (2003)

The use of alternative proteins in milk replacer has been evaluated for their ability to decrease the cost of milk replacers without negatively impacting performance of the calf. Three studies were conducted to evaluate the performance of calves fed milk replacer utilizing liquid egg as an alternative protein and to determine the optimal concentration of liquid egg to include in milk replacers. Calves in trials 1 and 2 were assigned to a control diet of all milk protein replacer (MILK) or a diet formulated to contain 5% of the diet (13.5% of the protein) from liquid egg (5% EGG). Calves in trial 3 were assigned to one of four diets: the control (MILK) and 5% EGG diets fed in trials 1 and 2, or diets formulated to contain either 10 or 15% of the diet (27 or 40.5% of the protein) from liquid egg (10% EGG, 15% EGG). For all experiments, milk replacers were formulated to contain 20% protein, 20% fat and were fed at 454 g/d reconstituted to 12% DM. Production of the diets containing egg protein utilized breaker eggs that were pasteurized during manufacturing. Holstein bull calves (n = 44 for experiment 1, n = 38 for experiment 2, and n = 120 for experiment 3), were purchased from an area sale barn. Calves were housed in individual hutches with water available free choice starting on d 0. A commercially available calf starter was offered free choice beginning on d 7 for experiments 1 and 2 and on d 1 for experiment 3. Feed intake, scour scores, and antibiotic treatments were recorded daily. For experiment 1, calves fed 5% EGG had greater weight gains than calves fed MILK. No differences in average daily feed intake were observed. For experiment 2, weight gains tended to be lower with 5% EGG, whereas feed intakes and gain to feed ratios were similar between calves fed MILK or 5% EGG. For experiment 3, as the amount of egg in the diet increased, weight gain decreased in a linear fashion during the milk replacer feeding period, but the decrease in gain was significant only with the 15% EGG diet. These results indicate that egg is an effective alternative protein source to milk protein in calf milk replacers when fed at levels up to 10% of the diet in a conventional feeding program of 0.45 kg per head per day.
Variable expression of Toll-like receptor in murine innate and adaptive immune cell lines (2002)

Pattern recognition receptors (PRR) play an important roll in immediate responses to different conserved molecules produced by microbes. In this paper we describe the cloning of the mouse homolog of Toll-like receptor (TLR) 3, and present an analysis of the expression of this gene in innate and adaptive immune cell lines. We also performed a broad expression study on these cells of other TLR, including TLR family members whose expression pattern is not known, i.e. TLR7. The analysis was done in order to understand, and possibly predict, how innate and adaptive immune cells respond to microbial pattern antigens. This first large-scale analysis of immune cell TLR expression in the mouse reveals that cells of the innate immune system express a broader number of TLR than cells of the adaptive immune system, supporting preconceptions concerning the hierarchy of immune cells involved in direct pathogen recognition. Additionally, the expression of TLR transcripts by mast cells, neutrophils and microglial cells observed here suggests that pathogen-associated molecular pattern molecules could induce activation of these cells through TLR. Finally, the mouse homolog of human TLR3 identified here may, like its human counterpart, be an exceptional TLR molecule due to its lack of a conserved proline residue seen to be involved in existing TLR signaling capabilities found in other TLR family members.
Developing a Peptide-Based Near-Infrared Molecular Probe for Protease Sensing (2004)

Recently near-infrared (NIR) molecular probes have become important reporter molecules for a number of types of in vivo biomedical imaging. A peptide-based NIR fluorescence probe consisting of a NIR fluorescence emitter (Cy5.5), a NIR fluorescence absorber (NIRQ820), and a protease selective peptide sequence was designed to sense protease activity. Using a MMP-7 model, we showed that NIRQ820 efficiently absorbs the emission energy of Cy5.5 resulting in a low initial signal. Upon reacting with its target, MMP-7, the fluorescence signal of the designed probe was increased by 7-fold with a K(cat)/K(m) of 100 000 M(-)(1) s(-)(1). The described synthetic strategy should have wide application for other NIR probe preparations.
Synthesis of Nanocrystalline Indium Arsenide and Indium Phosphide from Indium(III) Halides and Tris(trimethylsilyl)pnicogens. Synthesis, Characterization, and Decomposition Behavior of I3In.cntdot.P(SiMe3)3 (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis of Nanocrystalline Indium Arsenide and Indium Phosphide from Indium(III) Halides and Tris(trimethylsilyl)pnicogens. Synthesis, Characterization, and Decomposition Behavior of I3In.cntdot.P(SiMe3)3Richard L. Wells, Steven R. Aubuchon, Shreyas S. Kher, Michael S. Lube, and Peter S. WhiteCite this: Chem. Mater. 1995, 7, 4, 793–800Publication Date (Print):April 1, 1995Publication History Published online1 May 2002Published inissue 1 April 1995https://pubs.acs.org/doi/10.1021/cm00052a027https://doi.org/10.1021/cm00052a027research-articleACS PublicationsRequest reuse permissionsArticle Views1135Altmetric-Citations112LEARN 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-AlertscloseSupporting Info (3)»Supporting Information Supporting Information Get e-Alerts
Interleukin 1 alpha and interleukin 1 beta bind to the same receptor on T cells. (1986)

Pure, E. coli-derived recombinant murine interleukin 1 alpha (IL 1 alpha) was labeled with 125I and used for receptor binding studies. The 125I-IL 1 binds to murine EL-4 thymoma cells in a specific and saturable manner. Scatchard plot analysis for binding studies carried out at 4 degrees C reveals a single type of high affinity binding site with an apparent dissociation constant of approximately 2.6 X 10(-10) M and the presence of approximately 1200 binding sites per cell. The rate of association of the 125I-IL 1 with EL-4 cells is slow, requiring more than 3 h to reach apparent steady state at 4 degrees C. Cell-bound 125I-IL 1 cannot be dissociated from EL-4 cells upon removal of unbound 125I-IL 1 and incubation of the cells at 4 degrees C in the presence or absence of unlabeled IL 1. Unlabeled recombinant murine IL 1 competes for 125I-IL 1 binding in a dose-dependent manner, whereas interferon-alpha A, interleukin 2 (IL 2), epidermal growth factor, and nerve growth factor have no effect. The 125I-IL 1 binding site is sensitive to trypsin, suggesting that it is localized on the cell surface. We have also examined the ability of purified recombinant human IL 1 alpha and IL 1 beta to compete for binding of the radiolabeled murine IL 1 to its receptor and to stimulate IL 2 production by EL-4 cells. Previous reports have shown that human IL 1 alpha is approximately 60% homologous in amino acid sequence with murine IL 1, but that human IL 1 beta is only about 25% homologous with either murine IL 1 or human IL 1 alpha. Despite these marked differences, however, we report here that both human IL 1 proteins are able to recognize the same binding site as mouse IL 1. In addition, murine as well as both human IL 1 proteins stimulate IL 2 production by EL-4 cells.
Transcriptional profiling of the effects of 25-hydroxycholesterol on human hepatocyte metabolism and the antiviral state it conveys against the hepatitis C virus (2009)

Treatment of Huh-7 cells bearing HCV replicons with 25-HC leads to the downregulation of many key genes involved in the mevalonate pathway leading to an antiviral state within the host cell. Furthermore, dysregulation of a larger subset of genes not directly related to the mevalonate pathway occurs both in 25-HC-treated HCV replicon harbouring cells as well as during the initial rise in viremia in infected chimpanzees. Functional studies of 3 of these genes demonstrates that they do not directly act as antiviral gene products but that they indirectly contribute to the antiviral state in the host cell. These genes may also represent novel biomarkers for HCV infection, since they demonstrate an outcome-specific expression profile.
Synthesis and Characterization of a Cationic Poly(β-hydroxyalkanoate) (2008)

Poly(beta-hydroxyalkanoates) (PHAs) are biodegradable polyesters produced by a wide range of bacteria. The structures of these polymers may be tuned by controlling the carbon source composition in the feed stock, but the range of functional groups accessible in this manner is limited to those that the organism is able to metabolize. Much effort has been made to chemically modify the side chains of these polymers to achieve new materials. Here, we report the synthesis of the first cationic PHA, poly(beta-hydroxy-octanoate)- co-(beta-hydroxy-11-(bis(2-hydroxyethyl)-amino)-10-hydroxyundecanoate) (PHON). Pseudomonas putida Gpo1 was used to produce poly(beta-hydroxy-octanoate)- co-(beta-hydroxy-10-undecenoate) (PHOU), whose vinyl-terminated side chains were first converted to terminal epoxides and then modified with diethanolamine. The modification of PHOU was examined using (1)H, COSY, and HSQC NMR and GPC and resulted in a loss of molecular weight due to aminolysis and also in the introduction of side chains terminated with tertiary amine groups, which are protonated at physiological pH. The polycationic PHA is soluble in polar solvents such as DMSO, DMF, and water. The new biodegradable cationic polymers are envisioned as nucleic acid delivery systems.
Preparation of azido derivatives from amino acids and peptides by diazo transfer (1981)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPreparation of azido derivatives from amino acids and peptides by diazo transferJeffrey Zaloom and David C. RobertsCite this: J. Org. Chem. 1981, 46, 25, 5173–5176Publication Date (Print):December 1, 1981Publication History Published online1 May 2002Published inissue 1 December 1981https://pubs.acs.org/doi/10.1021/jo00338a022https://doi.org/10.1021/jo00338a022research-articleACS PublicationsRequest reuse permissionsArticle Views1790Altmetric-Citations74LEARN 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