gebhart/patrepeval huggingface dataset:
Circular dichroic investigations of secondary structure in synthetic peptide inhibitors for cAMP-dependent protein kinase: a model for inhibitory potential (1987)

The structure of the inhibitory domain of the inhibitor protein of the cAMP-dependent protein kinase has been assessed by circular dichroism studies of synthetic inhibitory peptides. Using the inhibitory peptide PKI(5-22)amide (Thr5-Thr-Tyr-Ala-Asp-Phe-Ile-Ala-Ser-Gly-Arg-Thr-Gly-Arg-Arg-Asn- Ala-Ile22) [Cheng, H.-C., Kemp, B. E., Pearson, R. B., Smith, A. J., Misconi, L., Van Patten, S. M., & Walsh, D. A. (1986) J. Biol. Chem. 261, 989-992] and shorter peptides of this sequence, it has been estimated that this parent peptide is composed of approximately 30% alpha-helix with the remainder being random coil with one beta-turn. The pseudosubstrate arginine cluster (Arg15-Arg19) is within the suggested region of random coil and beta-turn, representing one critical region of binding recognition by the protein kinase. The alpha-helix region proposed between Thr6 and Ile11 likewise contributes to the full biological potency and specificity of the inhibitor peptide and inhibitor protein. The removal of the two N-terminal threonines, for example, causes both a marked conformational change in the peptide and a diminishment by an order of magnitude of inhibitory activity. It is proposed that this alpha-helix region could serve one of several possibilities, including that it may provide a suitable constraint on the Tyr7 such that the hydroxyl is oriented in a position proximal to the pseudosubstrate domain, and/or may allow the optimal location of other protein kinase recognition signals. These data provide an initial description of some of the structural features of the inhibitor protein that could contribute to its high biological potency.
Functional characterization of ecto-5'-nucleotidase-positive and -negative human T lymphocytes. (1989)

Functional studies were performed on human peripheral blood T lymphocytes stained with goat anti-5'-nucleotidase antibodies and separated into ecto-5'-nucleotidase (ecto-5'-NT)-positive and -negative populations using the FACSTAR fluorescence-activated cell sorter. On the average, ecto-5'-NT+ T cells contained 34 +/- 13% CD4+ and 55 +/- 15% CD8+ cells, whereas ecto-5'-NT-T cells contained 65 +/- 12% CD4+ and 23 +/- 8% CD8+ cells. Staining with anti-5'-NT antibodies did not significantly alter the ability of unseparated T cells to proliferate in response to PHA or PMA, or in a MLR. However, prior incubation with anti-5'-NT antibodies did inhibit the ability of irradiated T cells to provide help for PWM-stimulated Ig synthesis by as much as 55%. In five separate experiments, ecto-5'-NT-T cells demonstrated an equal or better ability to incorporate [3H]TdR after PHA stimulation or in a MLR, as compared with ecto-5'-NT+ T cells. Similarly, ecto-5'-NT- T cells were not diminished in their ability to provide help for autologous B cells in a PWM-driven system. Clearly, the inability of ecto-5'-NT- T cells from patients with a variety of immunodeficiency diseases to function in these assays cannot be explained solely by their lack of ecto-5'-NT activity. In contrast, ecto-5'-NT-positive and -negative T cells showed markedly different dose-response curves for proliferation in response to PMA. Ecto-5'-NT+ T cells responded to lower doses of PMA (1.0 ng/ml) than did ecto-5'-NT- T cells and showed a two- to eight-fold greater rate of [3H]TdR incorporation at 3 to 10 ng of PMA per ml. Ecto-5'-NT+ T cells may have a protein kinase C that is more accessible or more easily activated or may utilize an alternate pathway of activation when stimulated with low concentrations of PMA.
The mouse MPTP model: gene expression changes in dopaminergic neurons (2003)

Parkinson's disease (PD) is a common neurodegenerative disorder, characterized by the progressive loss of dopaminergic neurons in the substantia nigra. Although valuable animal models have been developed, our knowledge of the aetiology and pathogenic factors implicated in PD is still insufficient to develop causal therapeutic strategies aimed at halting its progression. The neurotoxicity induced by 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) is one of the most valuable models for analysing pathological aspects of PD. In this paper we studied the gene expression patterns underlying the pathogenesis of MPTP-induced neurodegeneration. We treated young and old C57BL/6 mice with different schedules of MPTP to induce degenerative processes that vary in intensity and time-course. During the first week after intoxication we used nonradioactive in situ-hybridization to investigate the expression patterns of genes associated with (i) dopamine metabolism and signalling; (ii) familial forms of PD; (iii) protein folding and (iv) energy metabolism. MPTP injections induced different severities of neuronal injury depending on the age of the animals and the schedule of administration as well as a significant degeneration in the striatum. In situ hybridization showed that MPTP intoxication initiated a number of gene expression changes that (i) were restricted to the neurons of the substantia nigra pars compacta; (ii) were correlated in intensity and number of changes with the age of the animals and the severity of histopathological disturbances; (iii) displayed in each a significant down-regulation by the end of one week after the last MPTP injection, but (iv) varied within one MPTP regimen in expression levels during the observation period. The subacute injection of MPTP into one-year-old mice induced the most severe changes in gene expression. All genes investigated were affected. However, alpha-synuclein was the only gene that was exclusively up-regulated in MPTP-treated animals displaying cell death.
The Effect of Vertical Fractures on Well Productivity (1960)

Introduction Several years ago, we used an electric analogue computer to study the effect of vertical fractures on the productivity of wells in expanding fluid-drive reservoirs. The results of this work were used both as a guide to research and as a basis for the design of actual fracturing operations. In 1958, Dyes, Kemp and Caudle published portions of the data from this study. The results were released in 1959 to service companies for use in fracturing guides. The purpose of this note is to discuss the experimental conditions and assumptions which were made to derive the information which is already partially a matter of public record. Assumptions This study applies to fractures which extend in a vertical plane symmetrically from the well. For simplicity, we chose to study the case of a well in a square drainage area with its fractures extending toward two of its nearest neighbors. We have assumed no migration of fluid across the boundary of this area. The quadrant shown in Fig. 1 models this system. We made the usual assumptions that the reservoir is homogeneous and isotropic, that the fluid is homogeneous and that production is effected by fluid-expansion drive. We also assumed that the fracture extends from top to bottom of the reservoir. Of more practical interest is our assumption that the fracture does not change the size of the drainage area. This premise is appropriate if all the wells in the reservoir are fractured in the same way. But where a single well is fractured, its drainage area may be enlarged at the expense of its neighbors. This could be of economic importance. The assumption that the fracture will not extend beyond the established drainage area of the well also limits the application of the results. Such long fractures will yield benefits in excess of those predicted here. When we assume homogeneity, we disregard the frequently observed zone of damage in the vicinity of the well. Where damage is severe, the benefits resulting from by-passing it will far exceed those predicted by this study. All comparisons were made of systems producing in the semi-steady state. By this we mean that equal volumes contributed equally to flow (pressure was dropping at a uniform rate throughout the system) when the rate of flow was observed.
Purification and Properties of Fatty Acid Hydroperoxide Lyase from Green Bell Pepper Fruits (1995)

Fatty acid hydroperoxide lyase (HPO lyase) was purified to apparently homogeneity state from immature fruits of green bell pepper (Capsicum annuum L.) by differential centrifugation, ion-exchange chromatography, hydroxylapatite chromatography and gel filtration. The enzymatic activity was separated into two fractions (HPO lyases I and II) during the chromatography on hydroxylapatite. Both the isoforms were deduced to be trimers of 55-kDa subunits and have similar enzymatic properties. Peptide maps revealed only slight differences between them. Furthermore, immunoblot analysis showed that an antibody raised against HPO lyase I reacted with HPO lyase II as strongly as with the original antigen. These results indicate that there is only limited heterogeneity in terms of amino acid sequence and/or post-translational modification. The activities of both HPO lyases were considerably inhibited by lipophilic antioxidants, such as nordihydroguaiaretic acid and α-tocopherol. The activities with 13-hydroperoxy-(9Z,11E,15Z)-octadecatrienoic acid as substrate were about 12 times higher than those with 13-hydroperoxy-(9Z, 11E)-octadecadienoic acid. By contrast, no reactivity was detectable against the geometrical isomer, 13-hydroperoxy-(9E,11E)-octadecadienoic acid or against the positional isomer, 9-hydroperoxy-(10E,12Z)-octadecadienoic acid. Tissue-print immunoblot analyses using antiserum against HPO lyase indicated that HPO lyase was most abundant in the outer parenchymal cells of the pericarp.
Large fragment of the probasin promoter targets high levels of transgene expression to the prostate of transgenic mice (1997)

This study demonstrates that important regulatory DNA sequences located in the LPB fragment contribute to tissue-specific expression and greatly increase levels of transgene expression induced by androgens and zinc.
Strategies for the multiplex mapping of genes to traits (2013)

Rewiring and optimization of metabolic networks to enable the production of commercially valuable chemicals is a central goal of metabolic engineering. This prospect is challenged by the complexity of metabolic networks, lack of complete knowledge of gene function(s), and the vast combinatorial genotype space that is available for exploration and optimization. Various approaches have thus been developed to aid in the efficient identification of genes that contribute to a variety of different phenotypes, allowing more rapid design and engineering of traits desired for industrial applications. This review will highlight recent technologies that have enhanced capabilities to map genotype-phenotype relationships on a genome wide scale and emphasize how such approaches enable more efficient design and engineering of complex phenotypes.
Microbiology : A Laboratory Manual (1991)

I: Basic Laboratory Techniques for Isolation, Cultivation, and Cultural Characterization of Microorganisms. II: Microscopy. III: Bacterial Staining. IV: Cultivation of Microorganisms: Nutritional and Physical Requirements, and Enumeration of Microbial Populations. V: Biochemical Activities of Microorganisms. VI: The Protozoa. VII: The Fungi. VIII: The Viruses. IX: Physical and Chemical Agents for the Control of Microbial Growth. X: Microbiology of Food. XI: Microbiology of Water. XII: Microbiology of Soil. XIII: Bacterial Genetics. XIV: Medical Microbiology. XV: Immunology. Appendices.
Human platelet glycoprotein V: characterization of the polypeptide and the related Ib-V-IX receptor system of adhesive, leucine-rich glycoproteins. (1993)

Human platelet glycoprotein (GP) V (M(r) 83,300), whose primary structure is reported here, is a part of the Ib-V-IX system of surface glycoproteins (GPs Ib alpha, Ib beta, V, IX) that constitute the receptor for von Willebrand factor (vWf) and mediate the adhesion of platelets to injured vascular surfaces in the arterial circulation, a critical initiating event in hemostasis. System members share physical associations, leucine-rich glycoprotein (LRG) structures, and a congenital deficiency state, Bernard-Soulier syndrome. With PCR techniques and platelet cDNA templates, 1.4 kb of GP V cDNA sequence was obtained that encodes 469 GP V amino acids. A genomic 3.5-kb BamHI fragment was then isolated that includes 3.46 kb of GP V cDNA sequence: the 1.7-kb open reading frame plus 2 bases of the 5' and 1.8 kb of the 3' untranslated regions. Northern blot analysis reveals three GP V platelet transcripts of 3.8, 4.2, and 5.2 kb. A 16-amino acid signal peptide is present. Mature GP V is a 544-amino acid transmembrane protein with a 504-amino acid extracellular domain that encompasses a set of 15 tandem LRG repeats in a "flank-LRG center-flank" array [Roth, G. J. (1991) Blood 77, 5-19] along with eight putative N-linked glycosylation sites and cleavage sites for thrombin and calpain. GP V is a transmembrane, adhesive LRG protein that plays an undefined, but potentially critical, role in the expression and/or function of the Ib-V-IX receptor for vWf/shear-dependent platelet adhesion in arteries.
Immunocytochemical Identification of VPAC1, VPAC2, and PAC1 Receptors in Normal and Neoplastic Human Tissues with Subtype-Specific Antibodies (2004)

Human tumors frequently overexpress receptors for vasoactive intestinal peptide (VIP) and pituitary adenylate cyclase-activating peptide (PACAP). However, none of the VIP/PACAP receptor proteins has been visualized individually in human tumors. Here, we developed and characterized a panel of antipeptide antibodies to the carboxyl-terminal regions of the VIP/PACAP receptor subtypes vasoactive intestinal peptide receptor (VPAC)1, VPAC2, and pituitary adenylate cyclase-activating peptide receptor (PAC)1. Specificity of the antisera was shown by the following: (1) detection of broad bands migrating at Mr 50,000 to 70,000 in Western blots of membranes from receptor-expressing tumors and receptor-transfected cells; (2) cell surface staining of VIP/PACAP receptor-transfected cells; (3) translocation of VIP/PACAP receptor immunostaining in transfected cells after agonist exposure; and (4) abolition of tissue immunostaining by preadsorbtion of the antibodies with their immunizing peptides. The distribution of VIP/PACAP receptors was investigated in 98 human tumors and their tissues of origin. VPAC1, VPAC2, and PAC1 receptors were clearly located at the plasma membrane of the tumor cells in a variety of human neoplasms. In the gastrointestinal tract, VPAC1 receptor immunoreactivity was abundant in the mucosa and myenteric neurons; VPAC2 receptor immunoreactivity was detected in neuroendocrine cells, blood vessels, and smooth muscle; and PAC1 receptor immunoreactivity was found in myenteric neurons. This is the first localization of all of the VIP/PACAP receptor subtypes in human formalin-fixed, paraffin-embedded tissues. VIP/PACAP receptor visualization with this simple and rapid immunohistochemical method will facilitate identification of tumors with a sufficient receptor overexpression for diagnostic or therapeutic intervention.
The design for the wall street journal-based CSR corpus (1992)

The DARPA Spoken Language System (SLS) community has long taken a leadership position in designing, implementing, and globally distributing significant speech corpora widely used for advancing speech recognition research. The Wall Street Journal (WSJ) CSR Corpus described here is the newest addition to this valuable set of resources. In contrast to previous corpora, the WSJ corpus will provide DARPA its first general-purpose English, large vocabulary, natural language, high perplexity, corpus containing significant quantities of both speech data (400 hrs.) and text data (47M words), thereby providing a means to integrate speech recognition and natural language processing in application domains with high potential practical value. This paper presents the motivating goals, acoustic data design, text processing steps, lexicons, and testing paradigms incorporated into the multi-faceted WSJ CSR Corpus.
Monoclonal antibodies inhibitory to human plasmin (1986)

Four monoclonal antibodies raised against purified human plasminogen were characterized for their effects on the activation of plasminogen and on three enzymic properties of plasmin: (a) thioesterolysis, (b) fibrinolysis, (c) conversion of high-Mr urokinase to its low-Mr form. None of the monoclonal antibodies inhibited plasminogen (plg) activation by urokinase. The monoclonal antibodies characterized in this study fell into three groups. Anti-plg 1 inhibited (a), (b) and (c), while anti-plg 2 inhibited activities (a), (b) and (c) to varying degrees but also formed complexes with plasmin that were stable to sodium dodecyl sulphate. Anti-plg 3 and anti-plg 4 inhibited only activity (c). Selective use of these monoclonal antibodies demonstrated unequivocally that plasmin mediates the activation of the proenzyme form of urokinase-type plasminogen activator. Besides their use in affinity chromatography, therefore, these antibodies are valuable for defining the role of plasmin in the mechanisms of extracellular matrix degradation.
A lipid-coated lipase as a new catalyst for triglyceride synthesis in organic solvents (1988)

Lipid-coated enzyme (lipase) was prepared by mixing aqueous solutions of enzyme and synthetic dialkyl amphiphiles; it was insoluble in water but soluble in most organic solvents and showed a high activity for the synthesis of di- and tri-glycerides from monoglycerides and aliphatic acids in non-aqueous and homogeneous organic solvents.
Biological Control of Leafy Spurge: An Emerging Success Story (1999)

Leafy spurge (Euphorbia esula L.) is a deep-rooted, perennial weed with erect stems 40 to 80 cm tall. The weed reproduces by both vegetative buds and the production of large quantities of seeds. A native of Eurasia, leafy spurge was first reported in the state of Massachusetts in 1827. Leafy spurge now occurs abundantly on the northern Great Plains of the United States and the prairie provinces of Canada, where it often forms stands dense enough to displace native plants and restrict cattle grazing. Biological control of leafy spurge in the United States began in the 1960s with the introduction of Hyles euphorbia. Fifteen nonindigenous insect species have been approved for release in the United States for the control of leafy spurge. Different biological control agents affect the leafy spurge plant in different ways. Primary methods of attack include consumption of above-ground plant material, consumption of root material, and blocking seed production. Aphthona sp. flea beetles have produced the greatest impact on leafy spurge. A. nigriscutis and A czwalinae/lacertosa impact the plant by ovipositing eggs at the base of the plant. The resulting larvae feed on leafy spurge roots, increasing plant morbidity, reducing plant
Prolonged poststimulation inhibition of bladder activity induced by tibial nerve stimulation in cats (2010)

Inhibition of bladder activity by tibial nerve stimulation was investigated in α-chloralose-anesthetized cats with an intact spinal cord. Short-duration (3-5 min) tibial nerve stimulation at both low (5 Hz) and high (30 Hz) frequencies applied repeatedly during rhythmic isovolumetric bladder contractions was effective in inhibiting reflex bladder activity. Both frequencies of stimulation were also effective in inducing inhibition that persisted after the termination of the stimulation. The poststimulation inhibitory effect induced by the short-duration stimulation significantly increased bladder capacity to 181.6 ± 24.36% of the control capacity measured before applying the stimulation. Thirty-minute continuous stimulation induced prolonged poststimulation inhibition of bladder activity, which lasted for more than 2 h and significantly increased bladder capacity to 161.1 ± 2.9% of the control capacity. During the poststimulation periods, 5-Hz stimulation applied during the cystometrogram elicited a further increase (~30% on average) in bladder capacity, but 30-Hz stimulation was ineffective. These results in cats support the clinical observation that tibial nerve neuromodulation induces a long-lasting poststimulation inhibitory effect that is useful in treating overactive bladder symptoms.
Deficiency in l‐serine deaminase results in abnormal growth and cell division of Escherichia coli K‐12 (2008)

The loss of the ability to deaminate l-serine severely impairs growth and cell division in Escherichia coli K-12. A strain from which the three genes (sdaA, sdaB, tdcG) coding for this organism's three l-serine deaminases had been deleted grows well in glucose minimal medium but, on subculture into minimal medium with glucose and casamino acids, it makes very large, abnormally shaped cells, many of which lyse. When inoculated into Luria-Bertani (LB) broth with or without glucose, it makes very long filaments. Provision of S-adenosylmethionine restores cell division in LB broth with glucose, and repairs much of the difficulty in growth in medium with casamino acids. We suggest that replication of E. coli is regulated by methylation, that an unusually high intracellular l-serine concentration, in the presence of other amino acids, starves the cell for S-adenosylmethionine and that it is the absence of S-adenosylmethionine and/or of C1-tetrahydrofolate derivatives that prevents normal cell division.
The amino‐terminal part of ActA is critical for the actin‐based motility of Listeria monocytogenes; the central proline‐rich region acts as a stimulator (1995)

The intracellular bacterial pathogen Listeria monocytogenes moves inside the host-cell cytoplasm propelled by continuous actin assembly at one pole of the bacterium. This process requires expression of the bacterial surface protein ActA. Recently, in order to identify the regions of ActA which are required for actin assembly, we and others have expressed different domains of ActA by transfection in eukaryotic cells. As this type of approach cannot address the role of ActA in the actin-driven bacterial propulsion, we have now generated several L. monocytogenes strains expressing different domains of ActA and analysed the ability of the different domains to trigger actin assembly and bacterial movement in both infected cells and cytoplasmic extracts. We show here that the amino-terminal part is critical for F-actin assembly and movement. The internal proline-rich repeats and the carboxy-terminal domains are not essential. However, in vitro motility assays have demonstrated that mutants lacking the proline-rich repeats domain of ActA moved two times slower (6+/-2 micrometers min(-1)) than the wild type (13 +/-3 micrometers min(-1)). In addition, phosphatase treatment of protein extracts of cells infected with the L. monocytogenes strains expressing the ActA variants suggested that phosphorylation may not be essential for ActA activity.