gebhart/patrepeval huggingface dataset:
Polyisobutylene‐based polyurethanes. II. Polyureas containing mixed PIB/PTMO soft segments (2009)

Abstract The design, synthesis, characterization, and structure–property behavior of polyureas containing novel soft segments of mixed polyisobutylene (PIB)/poly(tetramethylene oxide) (PTMO) chains and conventional hard segments is presented. Modest amounts (12%) of PTMO in the soft PIB phase significantly increase both the tensile strength and elongation of the polyureas. These polyureas exhibit not only oxidative/hydrolytic stabilities far superior to Bionate® and Elast‐Eon® considered the most oxidatively stable polyurethanes on the market but also display mechanical properties (29 MPa tensile strength and 200% elongation) approaching those of conventional thermoplastic polyurethanes. The surfaces of these polyureas are covered/protected by PIB segments, which will lead to excellent biocompatibility. Our results demonstrate that the PTMO segments facilitate stress transfer from the continuous mixed soft phase to the dispersed hard phase, which strengthens and flexibilizes PIB‐based polyureas and thus significantly improves elastomeric properties without compromising oxidative and hydrolytic stability. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 2787–2797, 2009
Development of the S-303 Pathogen Inactivation Technology for Red Blood Cell Concentrates (2011)

Pathogen inactivation systems are in use in many European countries as routine procedures. However, a pathogen inactivation system for erythrocytes is currently not available. Although significant improvements have been made to decrease the incidence of transfusion-transmitted infections, risks remain for infectious disease agents specific to red blood cell concentrates, such as parasitic infections resulting in babesiosis and malaria. The pathogen inactivation system for erythrocytes utilizes S-303 and glutathione for the treatment of red blood cell concentrates. Preclinical studies to assess the pathogen inactivation efficacy and toxicology as well as preliminary clinical studies have been completed. Preclinical studies have shown log reduction for leukocytes, several viruses and bacteria in excess of 4 to 6 logs. Preclinical toxicology studies were conducted to enable the initiation of two phase III clinical studies in the USA for support of acute and chronic anemia. A second-generation system was developed after observation of an unexpected immune response in two chronic anemia patients. Preclinical pathogen inactivation studies, serological evaluations and a clinical study to evaluate survival of S-303-treated erythrocytes have been completed to support advanced development of the S-303 pathogen inactivation system. A functional system for the inactivation of red blood cell concentrates has been completed and is reaching clinical application.
Structural basis for the enhancement of virulence by viral spindles and their in vivo crystallization (2015)

The great benefits that chemical pesticides have brought to agriculture are partly offset by widespread environmental damage to nontarget species and threats to human health. Microbial bioinsecticides are considered safe and highly specific alternatives but generally lack potency. Spindles produced by insect poxviruses are crystals of the fusolin protein that considerably boost not only the virulence of these viruses but also, in cofeeding experiments, the insecticidal activity of unrelated pathogens. However, the mechanisms by which spindles assemble into ultra-stable crystals and enhance virulence are unknown. Here we describe the structure of viral spindles determined by X-ray microcrystallography from in vivo crystals purified from infected insects. We found that a C-terminal molecular arm of fusolin mediates the assembly of a globular domain, which has the hallmarks of lytic polysaccharide monooxygenases of chitinovorous bacteria. Explaining their unique stability, a 3D network of disulfide bonds between fusolin dimers covalently crosslinks the entire crystalline matrix of spindles. However, upon ingestion by a new host, removal of the molecular arm abolishes this stabilizing network leading to the dissolution of spindles. The released monooxygenase domain is then free to disrupt the chitin-rich peritrophic matrix that protects insects against oral infections. The mode of action revealed here may guide the design of potent spindles as synergetic additives to bioinsecticides.
Elevated levels of protein kinase C activity and alpha-isoenzyme expression in murine peritoneal B cells (1991)

Conventional murine splenic B cells are stimulated to initiate DNA synthesis by the combination of a phorbol ester protein kinase C (PKC) agonist, and a calcium ionophore; in contrast, recent work from this laboratory has shown that peritoneal B cells, enriched for the Ly-1+ B cell subset, differ in that they proliferate in response to the single signal provided by phorbol ester, acting alone. To elucidate the mechanism responsible for the abbreviated signaling requirement of peritoneal B cells, studies of intracellular Ca2+ and PKC were carried out. Measurements using the calcium sensitive dye, Indo-1, showed that base line levels of intracellular Ca2+ in peritoneal B cells were similar to those of splenic B cells, and that there was no change as a result of phorbol ester treatment. However, measurements of PKC based on the phosphorylation of histone showed enzymatic activity in peritoneal B cells to be about 60% greater than that of splenic B cells on a per microgram protein basis. Furthermore, this difference was accentuated by phorbol ester treatment, so that after 4 h, membrane and cytosol fractions from peritoneal B cells contained more than 5 times the PKC activity of the corresponding splenic B cell fractions because the down-regulation of PKC was relatively delayed in peritoneal B cells. This could not be accounted for by the onset of new PKC synthesis, but may relate to the finding that peritoneal B cells express more of the alpha-isoenzyme of PKC than splenic B cells, as shown by immunoblot analysis. Together with data from experiments using the PKC inhibitor 1-(5-isoquinolinesulfonyl)-2-methylpiperazine dihydrochloride(H7), these results suggest that PKC activity remaining hours after phorbol ester treatment may contribute to the unusual phorbol ester responsiveness of peritoneal B cells, and indicate that B cells from separate anatomic locations differ in terms of several parameters relating to the activity and behavior of PKC.
Synthetic lethality between CCNE1 amplification and loss of BRCA1 (2013)

High-grade serous ovarian cancers (HGSCs) are characterized by a high frequency of TP53 mutations, BRCA1/2 inactivation, homologous recombination dysfunction, and widespread copy number changes. Cyclin E1 (CCNE1) gene amplification has been reported to occur independently of BRCA1/2 mutation, and it is associated with primary treatment failure and reduced patient survival. Insensitivity of CCNE1-amplified tumors to platinum cross-linking agents may be partly because of an intact BRCA1/2 pathway. Both BRCA1/2 dysfunction and CCNE1 amplification are known to promote genomic instability and tumor progression. These events may be mutually exclusive, because either change provides a path to tumor development, with no selective advantage to having both mutations. Using data from a genome-wide shRNA synthetic lethal screen, we show that BRCA1 and members of the ubiquitin pathway are selectively required in cancers that harbor CCNE1 amplification. Furthermore, we show specific sensitivity of CCNE1-amplified tumor cells to the proteasome inhibitor bortezomib. These findings provide an explanation for the observed mutual exclusivity of CCNE1 amplification and BRCA1/2 loss in HGSC and suggest a unique therapeutic approach for treatment-resistant CCNE1-amplified tumors.
Coordinated assembly of multisubunit proteins: oligomerization of bacterial enterotoxins in vivo and in vitro. (1988)

In this paper we study the assembly, in vivo and in vitro, of a family of hexameric, heat-labile enterotoxins produced by diarrheagenic bacteria. The toxins, which consist of an A subunit and five B subunits, are assembled by a highly coordinated process that ensures secretion of the holotoxin complex. We show that (i) oxidation of cysteine residues in the B subunits is a prerequisite step for in vivo formation of B-subunit pentamers, (ii) reduction of dissociated B subunits in vitro abolishes their ability to reassemble, (iii) the kinetics of B-pentamer assembly in vivo can be mimicked under defined conditions in vitro, (iv) A subunits cannot associate with fully assembled B pentamers in vitro, and (v) A subunits cause an approximately 3-fold acceleration in the rate of B-subunit pentamerization in vivo, implying that A subunits play a coordinating role in the pathway of holotoxin assembly. The last finding is likely to be of general significance, since it provides a mechanism for preferentially excluding or favoring certain intermediates in the assembly of multisubunit proteins.
In vitro measurements with electrocatalytic glucose sensor in blood. (1989)

The principle of measurement with electrocatalytic glucose sensor is based on the direct electrochemical oxidation of glucose at an active and membrane-covered noble metal electrode. The objective is to measure glucose in the range of diffusion limiting current, since the glucose concentration in front of the membrane is proportional to the oxidative current. The determination of glucose concentration is realized by considering the electrode processes taking place at different potentials, and by measuring the impedance of the electrode/membrane system using the conventional three-electrode arrangement. Performance and long-term stability of the sensor are mainly dependent on the properties of the membrane and on the poisoning reactions at the electrode. Using this method, measurements were carried out in defibrinated sheep blood at 37 degrees C. After reproducible in vitro measurements could be made with the sensor over up to 3 weeks with an error of 20%, experiments were conducted in sheep using an extracorporeal circulation system. The correlation between the electrode signal and the glucose concentration in blood could be confirmed during glucose tolerance tests.
Inhibition of IL-6 and IL-10 Signaling and Stat Activation by Inflammatory and Stress Pathways (2000)

The development and resolution of an inflammatory process are regulated by a complex interplay among cytokines that have pro- and anti-inflammatory effects. Effective and sustained action of a proinflammatory cytokine depends on synergy with other inflammatory cytokines and antagonism of opposing cytokines that are often highly expressed at inflammatory sites. We analyzed the effects of the inflammatory and stress agents, IL-1, TNF-alpha, LPS, sorbitol, and H(2)O(2), on signaling by IL-6 and IL-10, pleiotropic cytokines that activate the Jak-Stat signaling pathway and have both pro- and anti-inflammatory actions. IL-1, TNF-alpha, and LPS blocked the activation of Stat DNA binding and tyrosine phosphorylation by IL-6 and IL-10, but not by IFN-gamma, in primary macrophages. Inhibition of Stat activation correlated with inhibition of expression of IL-6-inducible genes. The inhibition was rapid and independent of de novo gene induction and occurred when the expression of suppressor of cytokine synthesis-3 was blocked. Inhibition of IL-6 signaling was mediated by the p38 subfamily of stress-activated protein kinases. Jak1 was inhibited at the level of tyrosine phosphorylation, indicating that inhibition occurred at least in part upstream of Stats in the Jak-Stat pathway. Experiments using Stat3 mutated at serine 727 and using truncated IL-6Rs suggested that the target of inhibition is contained within the membrane-proximal region of the cytoplasmic domain of the gp130 subunit of the IL-6 receptor and is different from the SH2 domain-containing protein-tyrosine phosphatase/suppressor of cytokine synthesis-3 docking site. These results identify a new level at which IL-1 and TNF-alpha modulate signaling by pleiotropic cytokines such as IL-6 and IL-10 and provide a molecular basis for the previously described antagonism of certain IL-6 actions by IL-1.
Protein abundancy and mRNA levels of the adipocyte-type fatty acid binding protein correlate in non-invasive and invasive bladder transitional cell carcinomas. (1998)

The adipocyte type fatty acid-binding protein (A-FABP) is a small molecular weight fatty acid-binding protein whose expression correlates both with the grade of atypia and the stage of bladder transitional cell carcinomas (TCCs). To determine if the protein abundancy correlates with the mRNA levels in non-invasive and invasive lesions, we have analysed fresh TCCs (grade II, Ta; grade III, T2-4) by two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and measured the mRNA levels using the reverse transcription linked polymerase chain reaction (RT-PCR). Overall, the results showed a good correlation between protein abundancy and mRNA levels, indicating that the lack of expression of the protein observed in some lesions reflects low levels of transcription of the A-FABP gene rather than translational regulation. In addition, our studies showed that the loss of A-FABP protein observed in some tumors is not compensated by an increase in the skin fatty acid-binding protein PA-FABP, as is the case in the A-FABP knockout mice.
Involvement of ERK1/2, p38 MAPK, and PI3K/Akt signaling pathways in the regulation of cell cycle progression by PTHrP in colon adenocarcinoma cells (2014)

Parathyroid hormone-related peptide (PTHrP) is distributed in most fetal and adult tissues, and its expression correlates with the severity of colon carcinoma. Recently we obtained evidence that in Caco-2 cells, a cell line from human colorectal adenocarcinoma, exogenous PTHrP increases the number of live cells, via ERK1/2, p38 MAPK, and PI3-kinase and induces the expression of cyclin D1, a cell cycle regulatory protein. In this study, we further investigated the role of PTHrP in the regulation of the cell cycle progression in these intestinal cells. Flow cytometry analysis revealed that PTHrP treatment diminishes the number of cells in the G0/G1 phase and increases the number in both S and G2/M phases. The hormone increases the expression of CDK6 and diminishes the amount of negative cell cycle regulators p27Kip1, p15INK4B, and p53. However, PTHrP does not modify the expression of cyclin D3, CDK4, and p16INK4A. In addition, inhibitors of ERK1/2 (PD98059), p38 MAPK (SB203580), and PI3Kinase (LY294002) reversed PTHrP response in Caco-2 cells. Taken together, our results suggest that PTHrP positively modulates cell cycle progression and changes the expression of proteins involved in cell cycle regulation via ERK1/2, p38 MAPK, and PI3K signaling pathways in Caco-2 cells.
Superantigen‐Like Effects of aCandida albicansPolypeptide (2008)

The amino terminal sequence of the Candida albicans cell wall protein Int1 exhibited partial identity with the major histocompatibility complex (MHC) class II binding site of the Mycoplasma arthritidis superantigen MAM. Int1-positive C. albicans blastospores activated human T lymphocytes and expanded Vbeta subsets 2, 3, and/or 14; Int1-negative strains were inactive. Release of interferon-gamma (IFN-gamma) but not of tumor necrosis factor-alpha or interleukin-6 was Int1 dependent; interleukin-4 and interleukin-10 were not detected. T lymphocyte activation, Vbeta expansion, and IFN-gamma release were associated with a soluble polypeptide that encompassed the first 263 amino acids of Int1 (Pep(263)). Monoclonal antibody 163.5, which recognizes an Int1 epitope that overlaps the region of identity with MAM, significantly inhibited these activities when triggered by Int1-positive blastospores or Pep(263) but not by staphylococcal enterotoxin B. Histidine(263) was required. Pep(263) bound to T lymphocytes and MHC class II and was detected in the urine of a patient with C. albicans fungemia. These studies identify a candidal protein that displays superantigen-like activities.
Development of Class III Antiarrhythmic Agents (1992)

Summary: Currently available antiarrhythmic agents that act by lengthening the action potential duration and refractory period exert most of their effect during bradycardia (class IIIB). Unfortunately, when these agents are most needed, i.e., during tachycardia, they lose most of their effect. In my opinion, ideally, antiarrhythmic agents need not change the electrophysiology of the normal sinus beat, but should lengthen refractoriness upon acceleration (class IIIA) of the heart until the refractory period exceeds the cycle length of the tachycardia. Three examples of how such class IIIA effects can be achieved are: (i) an upstroke-dependent activator of inward currents could form a universal class IIIA agent, (ii) a usedependent blocker of i To could be a great class IIIA agent in the atria, and (iii) a frequency-dependent blocker of late repolarizing currents (e.g., iks) could be a good target for a ventricular agent.
Overexpression and Properties of Wild-Type and Tyr437His Mutated Myocilin in the Eyes of Transgenic Mice (2004)

The results do not support the concept that increasing amounts of myocilin in the outflow tissues obstruct the system and directly cause an increase in outflow resistance. Mutated Tyr437His myocilin is not secreted in vivo and causes severe alterations of cellular structure and function. A comparable mechanism may cause POAG in patients with myocilin mutations.
Nutritional Influences on Biofilm Development (1997)

The amounts and types of nutrients in the environment influence the development and final bacterial and chemical composition of biofilms. In oligotrophic environments, organisms respond to nutrient stress by alterations in their cell morphology and cell surfaces, which enhance adherence. Little is known of the responses to stress by bacteria in the animal oral cavity. The environment in the oral cavity is less extreme, and saliva provides a constant source of nutrients. Catabolic cooperation among oral bacteria allow carbon and nitrogen from salivary glycoproteins to be utilized. Modification of growth environments of oral bacteria can influence their cell surfaces and adhesion. Studies in experimental animals have shown that feeding either glucose or sucrose diets or fasting has little effect on the initial stages of development of oral biofilms. However, diet can influence the proportions of different bacterial species later in biofilm development. Studies of competition among populations in communities of oral bacteria in vitro and in vivo have shown the significance of carbon limitation and excess and changes in environmental pH. Relatively few studies have been made of the role of a nitrogen metabolism in bacterial competition in biofilms. In keeping with biofilms in nature, oral biofilms provide a sequestered habitat, where organisms are protected from removal by saliva and where interactions among cells generate a biofilm environment, distinct from that of saliva. Oral biofilms are an essential component in the etiologies of caries and periodontal disease, and understanding the biology of oral biofilms has aided and will continue to aid in the prevention and treatment of these diseases.
Dual Roles for Ste24p in Yeast a-Factor Maturation: NH2-terminal Proteolysis and COOH-terminal CAAX Processing (1998)

Maturation of the Saccharomyces cerevisiae a-factor precursor involves COOH-terminal CAAX processing (prenylation, AAX tripeptide proteolysis, and carboxyl methylation) followed by cleavage of an NH2-terminal extension (two sequential proteolytic processing steps). The aim of this study is to clarify the precise role of Ste24p, a membrane-spanning zinc metalloprotease, in the proteolytic processing of the a-factor precursor. We demonstrated previously that Ste24p is necessary for the first NH2-terminal processing step by analysis of radiolabeled a-factor intermediates in vivo (Fujimura-Kamada, K., F.J. Nouvet, and S. Michaelis. 1997. J. Cell Biol. 136:271-285). In contrast, using an in vitro protease assay, others showed that Ste24p (Afc1p) and another gene product, Rce1p, share partial overlapping function as COOH-terminal CAAX proteases (Boyartchuk, V.L., M.N. Ashby, and J. Rine. 1997. Science. 275:1796-1800). Here we resolve these apparently conflicting results and provide compelling in vivo evidence that Ste24p indeed functions at two steps of a-factor maturation using two methods. First, direct analysis of a-factor biosynthetic intermediates in the double mutant (ste24Delta rce1Delta) reveals a previously undetected species (P0*) that fails to be COOH terminally processed, consistent with redundant roles for Ste24p and Rce1p in COOH-terminal CAAX processing. Whereas a-factor maturation appears relatively normal in the rce1Delta single mutant, the ste24Delta single mutant accumulates an intermediate that is correctly COOH terminally processed but is defective in cleavage of the NH2-terminal extension, demonstrating that Ste24p is also involved in NH2-terminal processing. Together, these data indicate dual roles for Ste24p and a single role for Rce1p in a-factor processing. Second, by using a novel set of ubiquitin-a-factor fusions to separate the NH2- and COOH-terminal processing events of a-factor maturation, we provide independent evidence for the dual roles of Ste24p. We also report here the isolation of the human (Hs) Ste24p homologue, representing the first human CAAX protease to be cloned. We show that Hs Ste24p complements the mating defect of the yeast double mutant (ste24Delta rce1Delta) strain, implying that like yeast Ste24p, Hs Ste24p can mediate multiple types of proteolytic events.
Computing the internet checksum (1989)

This memo discusses methods for efficiently computing the Internet checksum that is used by the standard Internet protocols IP, UDP, and TCP.An efficient checksum implementation is critical to good performance. As advances in implementation techniques streamline the rest of the protocol processing, the checksum computation becomes one of the limiting factors on TCP performance, for example. It is usually approapriate to carefully hand-craft the checksum routine, exploiting every machine-dependent trick possible; a fraction of a microsecond per TCP data byte can add up to significant CPU time savings overall.