gebhart/patrepeval huggingface dataset:
Site‐directed mutagenesis of a loop at the active site of E1 (α2β2) of the pyruvate dehydrogenase complex (2003)

Limited proteolysis of the pyruvate decarboxylase (E1, alpha2beta2) component of the pyruvate dehydrogenase (PDH) multienzyme complex of Bacillus stearothermophilus has indicated the importance for catalysis of a site (Tyr281-Arg282) in the E1alpha subunit (Chauhan, H.J., Domingo, G.J., Jung, H.-I. & Perham, R.N. (2000) Eur. J. Biochem. 267, 7158-7169). This site appears to be conserved in the alpha-subunit of heterotetrameric E1s and multiple sequence alignments suggest that there are additional conserved amino-acid residues in this region, part of a common pattern with the consensus sequence -YR-H-D-YR-DE-. This region lies about 50 amino acids on the C-terminal side of a 30-residue motif previously recognized as involved in binding thiamin diphosphate (ThDP) in all ThDP-dependent enzymes. The role of individual residues in this set of conserved amino acids in the E1alpha chain was investigated by means of site-directed mutagenesis. We propose that particular residues are involved in: (a) binding the 2-oxo acid substrate, (b) decarboxylation of the 2-oxo acid and reductive acetylation of the tethered lipoyl domain in the PDH complex, (c) an "open-close" mechanism of the active site, and (d) phosphorylation by the E1-specific kinase (in eukaryotic PDH and branched chain 2-oxo acid dehydrogenase complexes).
A Membrane for the Rapid Concentration of Dilute Protein Samples in an Ultrafilter (1969)

Abstract The preparation of an anisotropic membrane which retains all proteins of a molecular weight of 25,000 and larger is described. It permits, with the help of appropriate ultrafiltration cells, the 400-fold concentration of 400 ml of a dilute protein solution within a few hours, avoiding all denaturation. Ultrafiltration with this membrane has been compared with a tannic acid precipitation method for the concentration of very dilute serum protein solutions. The ultrafiltration procedure resulted in a more representative recovery of the proteins that were present in the original undiluted sample, with quite fair yields. Some results are given on the proteins found in urine samples from normals and patients with disease.
Widespread expression of olfactory cyclic nucleotide-gated channel genes in rat brain: Implications for neuronal signalling (1999)

The cyclic nucleotides cAMP and cGMP are important intracellular messengers involved in a wide variety of signal transduction events in the nervous system. It has been proposed that cAMP/cGMP elicit some of their effects through direct gating of a novel class of Ca2+ -permeable ion channels that are termed cyclic nucleotide-gated (CNG) channels. Previous studies have identified the expression of a gene encoding one major CNG channel subtype, the olfactory receptor neuron alpha subunit, in the brain [El-Husseini et al. (1995) NeuroReport 6:1331-1335; Kingston et al. (1996a) Proc. Natl. Acad. Sci. U.S.A. 93:10440-10445; Bradley et al. (1997) J. Neurosci. 17:1993-2085]. We, therefore, proposed that the actions of cAMP/cGMP on neurons in the brain might occur through the activation of these CNG channels. To determine how widespread such a function might be, the regional and cellular distribution of the olfactory CNG channel alpha subunit has been examined in detail. Primers for multiple portions of the olfactory CNG channel were used in polymerase chain reaction (PCR) to amplify cDNA reverse-transcribed from several brain regions. The identities of PCR products were confirmed with Southern blots and by sequencing. In situ hybridization experiments demonstrated localization of CNG channel mRNA in discrete neuronal populations throughout the brain. In agreement with previous work, relatively strong hybridization signals are present in neuronal cell bodies of the cerebellum, olfactory bulb, cerebral cortex, and brainstem. Additionally, somewhat lesser signals are found in thalamus, hypothalamus, midbrain, and spinal cord while no hybridization signal was detectable in the caudate nucleus. This surprisingly wide distribution throughout the rat brain strengthens the hypothesis that CNG channels may influence numerous processes as downstream effectors of cyclic nucleotide cascades. Interestingly, the distribution of CNG channels is very similar to that of the nitric oxide/cGMP system, suggesting that one function of CNG channels in the brain could be to link diffusible messengers to elevated Ca2+ entry into neurons.
Ceftriaxone-Resistant Salmonella Infection Acquired by a Child from Cattle (2000)

This study provides additional evidence that antibiotic-resistant strains of salmonella in the United States evolve primarily in livestock. Resistance to ceftriaxone, the drug of choice for invasive salmonella disease, is a public health concern, especially with respect to children, since fluoroquinolones, which can also be used to treat this disease, are not approved for use in children.
The Influence of Telephonic Nursing Care Coordination on Patient Satisfaction in a Predominantly Low-income, High-risk Pregnancy Population (2002)

The effect of telephonic nursing case management on patient satisfaction in a predominantly non-Caucasian low-income, high-risk pregnancy population was studied. Patient satisfaction of care was significantly higher for treatment group participants than for controls on 9 of 10 items measuring satisfaction. The satisfaction score of the treatment patients, constructed by summing scores for each item, averaged 8 points higher than the control group’s score. Demographics made little difference. Telephonic case management was the strongest predictor of satisfaction in a multiple regression analysis. Satisfaction was unrelated to mode of delivery, infant birth weight, or gestational age. The satisfaction levels of treatment patients were high, whether or not they had outpatient charges. Participants rated the program highly for the nurses’ ability to answer questions, overall program experience, the opportunity to ask the nurses questions, health teachings and instructions received, and confidence in the nurse coordinating their care or their child’s care.
A new era in idiopathic pulmonary fibrosis: considerations for future clinical trials (2015)

The past decade has seen substantial progress in understanding the pathobiology, natural history, and clinical significance of idiopathic pulmonary fibrosis (IPF), culminating in the establishment of two effective medical therapies. Now seems an important time to reconsider the design and conduct of future IPF clinical trials. Building on lessons learned over the past decade, we use this perspective to lay out four key considerations for moving forward effectively and efficiently with the next generation of clinical trials in IPF. These are: development of a coordinated IPF clinical trials network; establishment of expectations for early phase proof of concept studies; adaptation of late-phase efficacy trial designs to the emergence of approved therapies, and; agreement on primary end-points for late phase clinical trials. Continued progress in the field of IPF will require creativity and collaboration on the part of all stakeholders. We believe that addressing these four considerations will encourage and enable investment in this new era of drug development in IPF, and will lead to more rapid development of effective therapies.
Amino acids of the recombinant kringle 1 domain of human plasminogen that stabilize its interaction with .omega.-amino acids (1993)

A series of strategically designed recombinant (r) mutants of the kringle 1 region of human plasminogen ([K1HPg]) have been constructed and the resulting gene products employed to reveal the identities of the residues that contribute to stabilization of the binding of omega-amino acid ligands to this domain. On the basis of determinations of the binding constants of the ligands, 6-aminohexanoic acid and trans-4-(aminomethyl)cyclohexane-1-carboxylic acid, to a variety of these mutants, we find that the anionic site of the polypeptide responsible for stabilization of the amino group of the ligands consists of both D54 and D56 and the cationic site of the polypeptide that interacts with the carboxylate group of the ligand is composed solely of R70. The main hydrophobic interactions that stabilize binding of these ligands, likely by interactions with the ligand hydrophobic regions, are principally due to W61, Y63, and Y71. The results obtained are consistent with conclusions that could be made from analysis of the X-ray crystal structure of r-[K1HPg] and from previous studies from this laboratory regarding the binding of ligands of this type to the kringle 2 region of tissue-type plasminogen activator ([K2tPA]). It thus appears as though a common ligand binding site has evolved in different kringles with ligand specificity differences between r-[K2tPA] and r-[K1HPg] perhaps explainable by the different nature of the cationic sites on these polypeptides that are involved in coordination to the ligand carboxylate groups.
Specificity of HLA class I antigen recognition by human NK clones: evidence for clonal heterogeneity, protection by self and non-self alleles, and influence of the target cell type. (1993)

Prior studies using polyclonal populations of natural killer (NK) cells have revealed that expression of certain major histocompatibility complex (MHC) class I molecules on the membrane of normal and transformed hematopoietic target cells can prevent NK cell-mediated cytotoxicity. However, the extent of clonal heterogeneity within the NK cell population and the effect of self versus non-self MHC alleles has not been clearly established. In the present study, we have generated more than 200 independently derived human NK cell clones from four individuals of known human histocompatibility leukocyte antigens (HLA) type. NK clones were analyzed for cytolytic activity against MHC class I-deficient Epstein Barr virus (EBV) transformed B lymphoblastoid cell lines (B-LCL) stably transfected with several HLA-A, -B, or -C genes representing either self or non-self alleles. All NK clones killed the prototypic HLA-negative erythroleukemia K562 and most lysed the MHC class I-deficient C1R and 721.221 B-LCL. Analysis of the panel of HLA-A, -B, and -C transfectants supported the following general conclusions. (a) Whereas recent studies have suggested that HLA-C antigens may be preferentially recognized by NK cells, our findings indicate that 70% or more of all NK clones are able to recognize certain HLA-B alleles and many also recognize HLA-A alleles. Moreover, a single NK clone has the potential to recognize multiple alleles of HLA-A, HLA-B, and HLA-C antigens. Thus, HLA-C is not unique in conferring protection against NK lysis. (b) No simple patterns of HLA specificity emerged. Examination of a large number of NK clones from a single donor revealed overlapping, yet distinct, patterns of reactivity when a sufficiently broad panel of HLA transfectants was examined. (c) Both autologous and allogeneic HLA antigens were recognized by NK clones. There was neither evidence for deletion of NK clones reactive with self alleles nor any indication for an increased frequency of NK clones recognizing self alleles. (d) With only a few exceptions, protection conferred by transfection of HLA alleles into B-LCL was usually not absolute. Rather a continuum from essentially no protection for certain alleles (HLA-A*0201) to very striking protection for other alleles (HLA-B*5801), with a wide range of intermediate effects, was observed. (e) Whereas most NK clones retained a relatively stable HLA specificity, some NK clones demonstrated variable and heterogeneous activity over time. (f) NK cell recognition and specificity cannot be explained entirely by the presence or absence of HLA class I antigens on the target cell.(ABSTRACT TRUNCATED AT 400 WORDS)
Efficient production of a bioactive, multiple disulfide‐bonded protein using modified extracts of Escherichia coli (2003)

In this report, we demonstrate that a complex mammalian protein containing multiple disulfide bonds is successfully expressed in an E.coli-based cell-free protein synthesis system. Initially, disulfide-reducing activities in the cell extract prevented the formation of disulfide bonds. However, a simple pretreatment of the cell extract with iodoacetamide abolished the reducing activity. This extract was still active for protein synthesis even under oxidizing conditions. The use of a glutathione redox buffer coupled with the DsbC disulfide isomerase and pH optimization produced 40 microg/mL of active urokinase protease in a simple batch reaction. This result not only demonstrates efficient production of complex proteins, it also emphasizes the control and flexibility offered by the cell-free approach.
"Patriotic" Traitors: Dutch National Socialists in Peace and War (1991)

Fat reduction by cryolipolysis was successfully achieved in our porcine model. Thus, our findings indicate that CRYOLIPO II(™) may be a promising fat reduction device for body contouring and fat reduction in humans, and that cryolipolysis exerts its effects, at least partly, by targeting the PPARδ signaling pathway. These results show that both investigative and diagnostic potentials capacity.
Hyperthermia-induced Nuclear Translocation of Transcription Factor YB-1 Leads to Enhanced Expression of Multidrug Resistance-related ABC Transporters (2001)

Genotoxic stress leads to nuclear translocation of the Y-box transcription factor YB-1 and enhanced expression of the multidrug resistance gene MDR1. Because hyperthermia is used for the treatment of colon cancer in combination with chemoradiotherapy, we investigated the influence of hyperthermia on YB-1 activity and the expression of multidrug resistance-related genes. Here we report that hyperthermia causes YB-1 translocation from the cytoplasm into the nucleus of human colon carcinoma cells HCT15 and HCT116. Nuclear translocation of YB-1 was associated with increased MDR1 and MRP1 gene activity, which is reflected in strong efflux pump activity. However, a combination of hyperthermia and drug treatment effectively reduced cell survival of the HCT15 and HCT116 cells. These results demonstrate that activation of MDR1 and MRP1 gene expression and increased efflux pump activity after hyperthermia were insufficient to cause an increase in drug resistance in colon cancer cell lines. The ability of hyperthermia to abrogate drug resistance in the presence of an increase in functional MDR proteins may provide an explanation for the efficacious results seen in the clinic in colon cancer patients treated with a combination of hyperthermia and chemotherapy.
Predictions versus high-throughput experiments in T-cell epitope discovery: competition or synergy? (2011)

Prediction methods as well as experimental methods for T-cell epitope discovery have developed significantly in recent years. High-throughput experimental methods have made it possible to perform full-length protein scans for epitopes restricted to a limited number of MHC alleles. The high costs and limitations regarding the number of proteins and MHC alleles that are feasibly handled by such experimental methods have made in silico prediction models of high interest. MHC binding prediction methods are today of a very high quality and can predict MHC binding peptides with high accuracy. This is possible for a large range of MHC alleles and relevant length of binding peptides. The predictions can easily be performed for complete proteomes of any size. Prediction methods are still, however, dependent on good experimental methods for validation, and should merely be used as a guide for rational epitope discovery. We expect prediction methods as well as experimental validation methods to continue to develop and that we will soon see clinical trials of products whose development has been guided by prediction methods.
Fluorotyrosine Alkaline Phosphatase from Escherichia coli : Preparation, Properties, and Fluorine-19 Nuclear Magnetic Resonance Spectrum (1974)

Alkaline phosphatase (EC 3.1.3.1) containing m-flurotyrosine has been prepared from E. coli grown in the presence of m-flurotyrosine. The kinetic properties of the m-fluorotyrosine enzyme measured with p-nitrophenylphosphate at pH 8.0 and dinitrophenylphosphate at pH 5.5 are essentially the same as those of normal alkaline phosphatase. However, the ability of the m-fluorotyrosine protein to refold active enzyme after acid denaturation, while unchanged at pH 5.8, was markedly decreased at pH 7.6. This result implies that the tyrosines must be in their protonated form for the protein to refold, reassociate, and take on zinc. The (19)F nuclear magnetic resonance spectrum of m-fluorotyrosine alkaline phosphatase contains resolved resonances corresponding to different chemical environments for each m-fluorotyrosine in the folded protein. This demonstrates that (19)F nuclear magnetic resonance spectroscopy of enzymes specifically labeled with (19)F, even with enzymes as large as alkaline phosphatase (molecular weight, 86,000), will provide a very valuable probe for conformational changes in proteins.
Effect of mouse interferon on growth and differentiation of mouse bone marrow cells stimulated by two different types of colony-stimulating factor (1983)

The effects of mouse L-cell interferon (IFN) on growth of mouse bone marrow cells and their differentiation into macrophages and granulocytes were investigated in a liquid suspension culture system with two different types of colony-stimulating factor (CSF). Within 7 days, most bone marrow cells differentiated into macrophages in the presence of macrophage colony-stimulating factor (M-CSF) derived from mouse fibroblast L929 cells, but into both granulocytes (40%) and macrophages (23%) in the presence of a granulocyte-macrophage colony-stimulating factor (GM-CSF) from mouse lung tissue. IFN inhibited growth of bone marrow cells with both M-CSF and GM-CSF, but had 20 times more effect on bone marrow cells stimulated with M-CSF than on those stimulated with GM-CSF. A low concentration of IFN (50 IU/ml) stimulated production of macrophages by GM-CSF in liquid culture medium, whereas it selectively inhibited colony formation of macrophages in semisolid agar culture. IFN caused no detectable block of late stages of differentiation; mature macrophages and granulocytes were produced even when cell proliferation was inhibited by IFN. These results indicate that IFN preferentially affects growth and differentiation of the cell lineage of macrophages among mouse bone marrow cells.
MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets (2016)

We present the latest version of the Molecular Evolutionary Genetics Analysis (Mega) software, which contains many sophisticated methods and tools for phylogenomics and phylomedicine. In this major upgrade, Mega has been optimized for use on 64-bit computing systems for analyzing larger datasets. Researchers can now explore and analyze tens of thousands of sequences in Mega The new version also provides an advanced wizard for building timetrees and includes a new functionality to automatically predict gene duplication events in gene family trees. The 64-bit Mega is made available in two interfaces: graphical and command line. The graphical user interface (GUI) is a native Microsoft Windows application that can also be used on Mac OS X. The command line Mega is available as native applications for Windows, Linux, and Mac OS X. They are intended for use in high-throughput and scripted analysis. Both versions are available from www.megasoftware.net free of charge.
Repression of the interleukin 6 gene promoter by p53 and the retinoblastoma susceptibility gene product. (1991)

The aberrant overexpression of interleukin 6 (IL-6) is implicated as an autocrine mechanism in the enhanced proliferation of the neoplastic cell elements in various B- and T-cell malignancies and in some carcinomas and sarcomas; many of these neoplasms have been shown to be associated with a mutated p53 gene. The possibility that wild-type (wt) p53, a nuclear tumor-suppressor protein, but not its transforming mutants might serve to repress IL-6 gene expression was investigated in HeLa cells. We transiently cotransfected these cells with constitutive cytomegalovirus (CMV) enhancer/promoter expression plasmids overproducing wt or mutant human or murine p53 and with appropriate chloramphenicol acetyltransferase (CAT) reporter plasmids containing the promoter elements of human IL-6, c-fos, or beta-actin genes or of porcine major histocompatibility complex (MHC) class I gene in pN-38 to evaluate the effect of the various p53 species on these promoters. Murine and human wt p53 derived from pCMVNc9 and pC53-SN3, respectively, strongly repressed the IL-6 (promoter position -225 to +13), c-fos (-711 to +42), beta-actin (-3400 to +912), and MHC (-528 to -38) promoters in serum-induced HeLa cells; additionally, IL-6 promoter/CAT transcription unit constructs induced by IL-1, phorbol ester, or pseudorabies virus were also repressed by wt human and murine p53. The murine transforming mutant p53 (pCMVc5) was less active in repressing the IL-6, c-fos, beta-actin, and MHC promoter constructs. The human p53 mutant derived from pC53-SCX3 was also less active than the wt protein in repressing the IL-6, c-fos, beta-actin, and MHC promoters, except that serum-induced IL-6/CAT expression was equally repressed by both human wt and mutant p53. In similar transient transfection experiments in HeLa cells, overexpression of the wt human retinoblastoma susceptibility gene product, RB, was found to repress the serum-induced IL-6 (-225 to +13), c-fos (-711 to +42), and beta-actin (-3400 to +912) promoters but not the PRV-induced IL-6 (-110 to +13) or the serum-induced MHC (-528 to -38) promoters. These observations identify transcriptional repression as a property of p53 and suggest that p53 and RB may be involved as transcriptional repressors in modulating IL-6 gene expression during cellular differentiation and oncogenesis.
Blood–brain barrier drug delivery of IgG fusion proteins with a transferrin receptor monoclonal antibody (2014)

The BBB delivery of biologic drugs is possible following re-engineering as a fusion protein with a molecular Trojan horse such as a TfRMAb. The efficacy of this technology will be determined by the outcome of future clinical trials.
Use of Ionic Liquids for π-Conjugated Polymer Electrochemical Devices (2002)

pi-Conjugated polymers that are electrochemically cycled in ionic liquids have enhanced lifetimes without failure (up to 1 million cycles) and fast cycle switching speeds (100 ms). We report results for electrochemical mechanical actuators, electrochromic windows, and numeric displays made from three types of pi-conjugated polymers: polyaniline, polypyrrole, and polythiophene. Experiments were performed under ambient conditions, yet the polymers showed negligible loss in electroactivity. These performance advantages were obtained by using environmentally stable, room-temperature ionic liquids composed of 1-butyl-3-methyl imidazolium cations together with anions such as tetrafluoroborate or hexafluorophosphate.
Isolation and culture of gymnosperm root protoplasts (Pinus pinaster) (1983)

Various factors affecting the yield and isolation of axenic protoplast cultures originating from Pinus pinaster root segments (in which most cells are differentiating) were studied. In spite of the use of plant material collected from germinating seeds under aseptic conditions, an additional sterilization with 0.1 % w/v mercuric chloride in 50% ethanol was a prerequisite for obtaining an axenic protoplast culture. A pretreatment with 30 mM cysteine in 0.7 M sorbitol for I h tripled the yield. Cen‐trifugation at lOOg instead of 40 g further increased the yield to 6 × 103 protoplasts per cm of root segment. Viability ranged from 80 to 91%. Cell divisions occurred after a minimum of 7 days of culture.