gebhart/patrepeval huggingface dataset:
Removal of B-domain Sequences from Factor V Rather than Specific Proteolysis Underlies the Mechanism by Which Cofactor Function Is Realized (2004)

Factor V, the precursor of factor Va, circulates in plasma with little or no procoagulant activity. Activity is generated following limited proteolysis indicating that the conversion of factor V to factor Va results in appropriate structural changes, which impart cofactor function. We have produced recombinant partial B-domain-truncated derivatives of factor V (FV(des811-1491) and FV(des811-1491) with Arg(709) and Arg(1545) mutated to Gln) to investigate whether discrete proteolysis within the B-domain followed by a conformational transition is responsible for activation. Direct binding fluorescence measurements as well as steady-state kinetic assays were employed to assess the ability of these factor V derivatives to assemble and function in prothrombinase. In contrast to human factor V, single-chain B-domain-truncated factor V bound to FXa membranes with an affinity that was identical to factor Va. Additionally, it was found that, once this modified derivative was assembled in prothrombinase, it functioned in an equivalent manner to factor Va. Taken together these data support the hypothesis that proteolysis within the B-domain of factor V, although necessary, is incidental to the mechanism by which cofactor function is realized. Instead, our results are more consistent with the interpretation that proteolytic activation of factor V simply eliminates steric and/or conformational constraints contributed by the B-domain that otherwise interfere with discrete binding interactions that govern the eventual function of factor Va.
Intestinal Electrolyte Transport and Diarrheal Disease (1989)

(Second of Two Parts)The Pathophysiology of Diarrheal DiseasesInfectious DiarrheasEnteric organisms cause diarrhea in several ways. Some are noninvasive but secrete toxins that interact with intestinal epithelial cells to stimulate fluid secretion (e.g., cholera). Others invade and destroy intestinal epithelial cells, thereby altering fluid transport. Selective destruction of small-intestinal villus cells by enteric viruses, for example, leaves the crypt portion of the epithelium unimpaired, so that its secretory activity is unopposed by the absorptive activity of villus cells.79 Some enteric organisms are both enteroinvasive and toxicogenic (shigella,80 for example). Others penetrate the epithelium, largely bypassing the enterocytes, and . . .
The Second Generation of Cholinesterase Inhibitors: Pharmacological Aspects (1991)

Present genetic findings do not point to a rapid therapeutic solution. In 1987, genetic linkage studies (St. George-Hyslop et al., 1987; Goate et al., 1989) revealed co-segregation of a familial form of Alzheimer disease (AD) with the D21S1/S11 and D21S16 loci on chromosome 21. The discovery of a gene mapped to chromosome 21 encoding for the β-amyloid precursor protein (APP) and the identification of the closely located gene locus segregating with a familial form raised strong hopes for a rapid development of a cure. However, the AAP gene and the gene for AD are not always inherited together. Recent genetic linkage studies suggest that AD may not be a single homogeneous disorder but rather result from several genetic defects as well as from non-genetic factors (St. George-Hyslop et al., 1990). Genetic analysis performed in a large number of AD families demonstrates that the disease is genetically heterogeneous involving two or more genes (St. George-Hyslop, 1990). The segregation of a missense mutation in the APP gene with familial AD is probably rare (Goate et al., 1991). It was not present in most of the families screened by Goate et al. (1991) and Tanzi et al. (1988) did not find it in any of their 21 AD families.
Reactions of VX, GD, and HD with Nanosize CaO:  Autocatalytic Dehydrohalogenation of HD (2000)

Room-temperature reactions of the chemical warfare agents VX, GD, and HD with nanosize CaO (AP-CaO), and HD with commercial CaO have been studied using solid-state MAS NMR. VX and GD hydrolyze to yield surface-bound complexes of nontoxic ethyl methylphosphonate and pinacolyl methylphosphonate, respectively. The kinetics are characterized by an initial fast reaction followed by a slower, diffusion-limited reaction. Similar behavior is observed for HD on either dried or hydrated AP-CaO and CaO. On partially hydrated AP-CaO (but not CaO), a rather fast steady-state elimination of HCl occurs after an induction period. This behavior is attributed to acid-catalyzed surface reconstruction (to regenerate fresh surface) and the formation of CaCl2, which is known to be more reactive than CaO. The product distribution for HD is about 80% divinyl sulfide and 20% thiodiglycol and/or sulfonium ions, which apparently reside as surface alkoxides. Such kinetic behavior was not evident for the common mustard simulant 2-chloroethyl ethyl sulfide (CEES) on partially hydrated AP-CaO, which exhibited only the typical fast/diffusion-limited reaction.
Recent Advances and Applications of Transgenic Animal Technology (2012)

opened on cell membranes are conducive to the entry of foreign gene; on the other hand, the shock is also an injury to cells that causes irreversible damage to sperm motility. 4) Adenoviral vector mediated gene transfer. Exposure of spermatozoa to adenovirus bearing the E. coli lacZ gene resulted in the transfer of the gene to the head of the spermatozoa. Of the 2-to 8-cell embryos obtained after in vitro fertilization with adenovirus-exposed sperm, 21.7% expressed the LacZ product. Four out of 56 piglets (about 7%) obtained foreign gene in PCR analyses after artificial insemination with adenovirusexposed spermatozoa. SMGT is based on the intrinsic ability of sperm cells to bind and internalise exogenous DNA and to transfer it into the egg at fertilisation as illustrated in Fig.
Successful prevention and treatment of autoimmune encephalomyelitis by short-term administration of anti-T-cell receptor alpha beta antibody. (1994)

To identify an effective immunotherapy for T-cell-mediated autoimmune diseases, prevention and treatment of experimental autoimmune encephalomyelitis (EAE) induced in Lewis rats was attempted by administering a monoclonal antibody (mAb), R73, which is specific for rat T-cell receptor (TcR) alpha beta. Short-term administration of R73 at relatively low doses before immunization with encephalitogenic antigen, myelin basic protein (MBP), prevented the development of EAE. However, treatment with anti-CD4 and anti-Ia mAb in the same protocol was ineffective. Flow cytometric analysis demonstrated that short-term administration of R73 resulted in transient down-regulation of the TcR molecules, whereas the number of CD2-expressing T cells was well preserved. Furthermore, the response to MBP of T cells isolated from rats that were pretreated with R73 and then immunized with MBP was strongly suppressed. On the other hand, the T-cell response of R73-pretreated rats to a third-party antigen which was immunized at a later period was not inhibited. These findings suggest that in vivo administration of a low dose of R73 protects rats from EAE by inducing anergy of MBP-reactive encephalitogenic T cells. Furthermore, R73 treatment which started on day 10 of the immunization (shortly before the day of onset of clinical signs) completely suppressed the induction of EAE and that which started on day 11 (the day of onset) hastened recovery. Since the phenotypes of the TcR V beta chain of encephalitogenic T cells are not so limited as previously believed, immunotherapy with mAb against the TcR alpha beta framework may be one of the best methods for treatment of T-cell-mediated autoimmune diseases.
Purification and characterization of the 210‐amino acid recombinant basic fibroblast growth factor form (FGF‐2) (1994)

Four forms of basic fibroblast-growth factor (bFGF or FGF-2) using one AUG (155 amino acids) and three upstream CUG (210, 201 and 196 amino acids) start codons, were synthesized through an alternative use of initiation codons. The 210-amino acid form of FGF-2 (210FGF-2) was expressed in a plasmid vector under the control of a bacteriophage T7 RNA polymerase promoter system in Escherichia coli. Characterization of the purified protein was performed by electrospray mass spectrometry and Edman degradation. The recombinant 210FGF-2 produced in E. coli had a mitogenic activity similar to the 146-amino acid form extracted from tissues.
Nearly Chromatography-Free Synthesis of the A3B-Porphyrin 5-(4-Hydroxymethylphenyl)-10,15,20-tri-p-tolylporphinatozinc(II) (2006)

Rational routes to synthetic porphyrins bearing distinct meso-substituents have typically been implemented at modest scale (<1 g quantities). The A3B-porphyrin 5-(4-hydroxymethylphenyl)-10,15,20-tri-p-tolylporphinatozinc(II) (Zn-1) is required in multigram quantities for possible commercial use in information storage applications. The synthesis of Zn-1 has been carried out by reaction of 5-(4-hydroxymethylphenyl)dipyrromethane and the dicarbinol derived from 1,9-di-p-toluoyl-5-p-tolyldipyrromethane. Four improvements have been made to the steps leading to the dipyrromethane and dipyrromethane−dicarbinol: (i) use of 50 equiv of pyrrole in the condensation of an aldehyde to give the dipyrromethane (versus 100 equiv previously), (ii) 1,9-diacylation of a dipyrromethane using the hindered Grignard reagent 2,6-dimethylphenylmagnesium bromide and p-toluoyl chloride to give the 1,9-diacyl versus 1-acyl products in >10:1 ratio (versus 4:1 using EtMgBr), (iii) isolation of the dibutyltin complex of the 1,9-diacyldipyrromethane from the crude reaction mixture by direct crystallization using methanol/methyl tert-butyl ether (MTBE) (versus silica chromatography), and (iv) reduction of the dibutyltin complex of the 1,9-diacyldipyrromethane (250 mM) with ∼10−15 mol equiv of NaBH4 (versus 25 mM and 40 mol equiv). The procedures have been carried out with no chromatography at large scale, affording the dipyrromethane (31, 59, or 79 g), the dibutyltin complex of a 1,9-diacyldipyrromethane (361 g), and reduction of the latter (45 g). The porphyrin-forming reaction has been performed (25 mM reactants at 50-mmol scale, or 10 mM at 64-mmol scale) in a two-step process of condensation and oxidation to give the free base porphyrin 1 in 3.7- or 5.8-g quantities. Metalation with zinc acetate afforded Zn-1, which was isolated by direct crystallization. Taken together, the various improvements facilitate synthesis of the target porphyrin Zn-1 and may have broad applicability.
Glucocorticoids transform CD40-triggering of dendritic cells into an alternative activation pathway resulting in antigen-presenting cells that secrete IL-10 (2000)

Dendritic cell (DC) activation through CD40-CD40 ligand interactions is a key regulatory step for the development of protective T-cell immunity and also plays an important role in the initiation of T-cell responses involved in autoimmune diseases and allograft rejection. In contrast to previous reports, we show that the immunosuppressive drug dexamethasone (DEX) redirects rather than simply blocks this DC activation process. We found that DCs triggered through CD40 in the presence of DEX were unable to acquire high levels of costimulatory, adhesion, and major histocompatibility complex class I and II molecules and failed to express the maturation marker CD83, whereas antigen uptake was not affected. Moreover, DEX strikingly modified the CD40-activated DC cytokine secretion profile by suppressing the production of the proinflammatory cytokine interleukin (IL)-12 and potentiating the secretion of the anti-inflammatory cytokine IL-10. Accordingly, DEX-exposed CD40-triggered DCs displayed a decreased T-cell allostimulatory potential and a dramatically impaired ability to activate cloned CD4(+) T helper 1 (Th1) cells. Moreover, interaction between Th1 cells and these DCs rendered the T cells hyporesponsive to further antigen-specific restimulation. Collectively, our results demonstrate that DEX profoundly modulates CD40-dependent DC activation and suggest that the resulting alternatively activated DCs can be exploited for suppression of unwanted T-cell responses in vivo.
In Vivo and In Vitro Studies on γ-Aminobutyric Acid Metabolism with the Radish Plant (Raphanus sativus, L.) (1972)

Labeled glutamate was rapidly converted to gamma-aminobutyrate in intact, excised radish (Raphanus sativus L., var. Champion) leaves. Labeled gamma-aminobutyrate was metabolized via succinate and the Krebs cycle and was not carboxylated to form glutamate. Administration of carbon-14 and tritium-labeled succinate indicated that less than 10% of the gamma-aminobutyrate formation occurs by amination of succinic semialdehyde. Therefore, most gamma-aminobutyrate formation must be via glutamate decarboxylation.Radish leaf extracts were more active in catalyzing transamination between gamma-aminobutyrate and pyruvate than that between gamma-aminobutyrate and alpha-ketoglutarate. Glutamate decarboxylase was approximately 20 times more active than gamma-aminobutyrate: pyruvate transaminase. Succinic semialdehyde dehydrogenase was found in the extracts, and NAD was much more active as a hydrogen acceptor than NADP. No reduction of succinate to succinic semialdehyde by the NAD-linked dehydrogenase could be demonstrated. The following pH optima were determined: glutamate decarboxylase, 5.9; gamma-aminobutyrate: pyruvate transaminase, 8.9; succinic semialdehyde: NAD dehydrogenase, about 9.0.
Process monitoring and optimization for power systems applications (1994)

Three distinct computational intelligence paradigms combine to support the task of process monitoring and optimization. These are neural-net computing, evolutionary programming and fuzzy-logic. We describe briefly some of our contributions to these paradigms and outline how they function in process monitoring and optimization. Four different types of monitoring tasks are considered. This type of combined computational intelligence is being applied successfully to optimal process planning in electric power utilities. Examples of these include heat rate improvement and NO/sub x/ minimization at some Western Pennsylvania and Western New York State utilities.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Fibroblast Growth Factor-2 Activates a Latent Neurogenic Program in Neural Stem Cells from Diverse Regions of the Adult CNS (1999)

During development of the mammalian brain, both neurons and glia are generated from multipotent neural stem cells. Although neurogenesis ceases in most areas at birth, stem cells continue to generate neurons within the subventricular zone and hippocampal dentate gyrus throughout adult life. In this work, we provide the first demonstration that precursors native to regions of the adult brain that generate only glia can also generate neurons after exposure to FGF-2 in vitro. When progenitors isolated from hippocampal tissue were directly compared with cells isolated from the neocortex, both populations were able to initiate a program of proliferative neurogenesis. Genetic marking and lineage analysis showed that a majority of the cells able to generate neurons were multipotent precursors; however, progeny from these precursors acquired the competence to differentiate into neurons only after exposure to FGF-2. The recruitment of similar FGF-2-responsive cells from the adult optic nerve, a structure well isolated from the neurogenic zones within the brain, confirmed that neuron-competent precursors naturally exist in widely divergent tissues of the adult brain.
Networks for Computer Scientists and Engineers (2001)

Networks for Computer Scientists and Engineers is a data communications and networks textbook with a unique software-projects and laboratory-based approach. Due to its innovative and distinctive features, it has won unanimous recommendation and partial sponsorship by the curriculum development committee of the National Science Foundation. Designed for undergraduate students, it covers both fundamental theory and modern technologies. The Instructor's Manual and CD (available to adopters) provide step-by-step instructions for configuring client/server computers, hubs, routers, and switches to construct a cost-effective prototype network lab with implementation of web (http), email, VPN and other servers. This prototype lab is based on Linux and other popular platforms, demonstrates how different protocols and components are integrated into a heterogeneous network, and provides an ideal environment for troubleshooting and experimental network management. The book's accompanying software projects-included on the instructor's CD-are not merely samples but complete software packages with real applications and utilities written in Java, C, C++, assembly language, and thoroughly tested by professors and students at several universities. Used together, Networks for Computer Scientists and Engineers and the accompanying laboratory projects actively engage students in the learning process and provide opportunities for critical thinking, problem solving, and creativity in a controlled real-world setting.
Ribosomal RNA is the target for oxazolidinones, a novel class of translational inhibitors (1999)

Oxazolidinones are antibacterial agents that act primarily against gram-positive bacteria by inhibiting protein synthesis. The binding of oxazolidinones to 70S ribosomes from Escherichia coli was studied by both UV-induced cross-linking using an azido derivative of oxazolidinone and chemical footprinting using dimethyl sulphate. Oxazolidinone binding sites were found on both 30S and 50S subunits, rRNA being the only target. On 16S rRNA, an oxazolidinone footprint was found at A864 in the central domain. 23S rRNA residues involved in oxazolidinone binding were U2113, A2114, U2118, A2119, and C2153, all in domain V. This region is close to the binding site of protein L1 and of the 3' end of tRNA in the E site. The mechanism of action of oxazolidinones in vitro was examined in a purified translation system from E. coli using natural mRNA. The rate of elongation reaction of translation was decreased, most probably because of an inhibition of tRNA translocation, and the length of nascent peptide chains was strongly reduced. Both binding sites and mode of action of oxazolidinones are unique among the antibiotics known to act on the ribosome.
Hrp pilus: An hrp -dependent bacterial surface appendage produced by Pseudomonas syringae pv. tomato  DC3000 (1997)

Hypersensitive response and pathogenicity (hrp) genes control the ability of major groups of plant pathogenic bacteria to elicit the hypersensitive response (HR) in resistant plants and to cause disease in susceptible plants. A number of Hrp proteins share significant similarities with components of the type III secretion apparatus and flagellar assembly apparatus in animal pathogenic bacteria. Here we report that Pseudomonas syringae pv. tomato strain DC3000 (race 0) produces a filamentous surface appendage (Hrp pilus) of 6-8 nm in diameter in a solid minimal medium that induces hrp genes. Formation of the Hrp pilus is dependent on at least two hrp genes, hrpS and hrpH (recently renamed hrcC), which are involved in gene regulation and protein secretion, respectively. Our finding of the Hrp pilus, together with recent reports of Salmonella typhimurium surface appendages that are involved in bacterial invasion into the animal cell and of the Agrobacterium tumefaciens virB-dependent pilus that is involved in the transfer of T-DNA into plant cells, suggests that surface appendage formation is a common feature of animal and plant pathogenic bacteria in the infection of eukaryotic cells. Furthermore, we have identified HrpA as a major structural protein of the Hrp pilus. Finally, we show that a nonpolar hrpA mutant of P. syringae pv. tomato DC3000 is unable to form the Hrp pilus or to cause either an HR or disease in plants.
Dicistronic targeting constructs: reporters and modifiers of mammalian gene expression. (1994)

To investigate the activity of candidate regulatory molecules in mammalian embryogenesis, we have developed a general strategy for modifying and reporting resident chromosomal gene expression. The picornaviral internal ribosome-entry site was incorporated into gene targeting constructs to provide cap-independent translation of a selectable marker from fusion transcripts generated following homologous recombination. These promoterless constructs were highly efficient and have been used both to inactivate the stem-cell-specific transcription factor Oct-4 and to introduce a quantitative regulatory modification into the gene for a stem-cell maintenance factor, differentiation-inhibiting activity. In addition, the inclusion of a beta-galactosidase reporter gene in the constructs enabled accurate and sensitive detection of cellular sites of transcription. This has allowed visualization of putative "stem-cell niches" in which sources of elevated expression of differentiation-inhibiting activity were localized to the differentiated cells surrounding colonies of stem cells.
Surface-Induced Dissociation on a MALDI-Ion Mobility-Orthogonal Time-of-Flight Mass Spectrometer:  Sequencing Peptides from an “In-Solution” Protein Digest (2001)

Peptide sequencing by surface-induced dissociation (SID) on a MALDI-ion mobility-orthogonal TOF mass spectrometer is demonstrated. SID of approximately 100-fmol amounts of model peptides HLGLAR (m/z 666.8), gramicidin S (m/z 1142.5), and bovine insulin b chain (m/z 3495.5) was accomplished using hydrocarbon-coated gold grids and approximately 20-eV collision energies. The current version of the instrument achieves a mobility resolution of approximately 20 and TOF mass resolution better than 200. Peptide sequences of four peptides from a tryptic digest of cytochrome c (approximately 1 pmol deposited) were obtained. The advantage of IM-SID-o-TOF-MS is that a single experiment can be used to simultaneously measure the molecular weights of the tryptic peptide fragments (e.g., peptide mass mapping) and partial sequence analysis, (e.g., real-time tandem mass spectrometry.)
High Insulin–Like Growth Factor Binding Protein 1 Levels in Cirrhosis: Link With Insulin Resistance (1996)

Hyperinsulinemic euglycemic clamps were performed on six patients with compensated alcoholic cirrhosis and on six normal comparison subjects. As in previous studies, glucose uptake in the cirrhotic patients was only 21% of the comparison value. The cirrhotic patients had high growth hormone (GH) and low insulin-like growth factor-I (IGF-I) levels, with low insulin-like growth factor-binding protein (IGFBP)-3 levels, but surprisingly high IGFBP-I levels (26.8 +/- 8.4 microgH vs. 3.2 +/- 0.2 microm/L, P < .001). The log IGFBP-1 level was inversely correlated with the log insulin sensitivity (r = -.95). The clamps were repeated with a somatostatin infusion to suppress GH secretion. IGFBP-1 increased in both groups, especially in the cirrhotic subjects. Insulin sensitivity increased in the normal subjects but was unchanged in the cirrhotic patients. Following GH treatment (0.13 U/kg/d for 5 days), the clamps were repeated. GH, IGF-1, and IGFBP-3 levels were now similar in the two groups; IGFBP-1 levels decreased in the cirrhotic patients but remained fivefold higher than the comparison value (10.6 +/- 3.7 vs. 2.1 +/- 0.4, P < .05). Glucose uptake in the cirrhotic patients remained only 29% of the comparison value, but the change in their insulin sensitivity was inversely correlated with the change in their IGFB-1 levels (r = -.84). These results suggests an important role for IGFBP-1 in modulating insulin sensitivity in cirrhosis.