gebhart/patrepeval huggingface dataset:
Identification and characterization of genes required for post‐translational modification of Campylobacter coli VC167 flagellin (1996)

Two genes have been identified in Campylobacter coli VC167 which are required for the biosynthesis of post‐translational modifications on flagellin proteins. The ptmA gene encodes a protein of predicted M r 28 486 which shows significant homology to a family of alcohol dehydrogenases from a variety of bacteria. The ptmB gene encodes a protein of predicted M r 26 598 with significant homology to CMP‐ N ‐acetylneuraminic acid synthetase enyzmes involved in sialic acid capsular biosynthesis in Neisseria meninigitidis and Escherichia coli K1. Site‐specific mutation of either ptmA or ptmB caused loss of reactivity with antisera specific to the post‐translational modifications and a change in the isoelectric focusing fingerprints relative to the parent strains. Mutation of ptmB , but not of ptmA , caused a change in apparent M r of the flagellin subunit in SDS–PAGE gels. The ptmA and ptmB genes are present in other strains of Campylobacter . In a rabbit model the ptmA mutant showed a reduced ability to elicit protection against subsequent challenge with heterologous strains of the same Lior serotype compared to the parental wild‐type strain. This suggests that the surface‐exposed post‐translational modifications may play a significant role in the protective immune response.
Power System Dynamics as Primal-Dual Algorithm for Optimal Load Control (2013)

We formulate an optimal load control (OLC) problem in power networks where the objective is to minimize the aggregate cost of tracking an operating point subject to power balance over the network. We prove that the swing dynamics and the branch power flows, coupled with frequency-based load control, serve as a distributed primal-dual algorithm to solve OLC. Even though the system has multiple equilibrium points, we prove that it nonetheless converges to an optimal point. This result implies that the local frequency deviations at each bus convey exactly the right information about the global power imbalance for the loads to make individual decisions that turn out to be globally optimal. It allows a completely decentralized solution without explicit communication among the buses. Simulations show that the proposed OLC mechanism can resynchronize bus frequencies with significantly improved transient performance.
Developmentally restricted immunoglobulin heavy chain variable region gene expressed at high frequency in chronic lymphocytic leukemia. (1989)

During fetal development, murine and human B-lineage cells rearrange and express a highly restricted set of immunoglobulin heavy chain variable region genes (VH genes). We noted that a VH gene of the restricted human fetal repertoire, designated 51p1, potentially could encode the VH region of two human IgM rheumatoid factor proteins. These rheumatoid factors share a cross-reactive idiotype (CRI) defined by reactivity with G6, a murine monoclonal antibody that recognizes an antibody heavy chain determinant present on many human IgM autoantibodies, particularly rheumatoid factors. Recently, we found that the G6 CRI also is expressed frequently by neoplastic CD5 (Leu1) B cells from patients with chronic lymphocytic leukemia (CLL) or small lymphocytic lymphoma. However, neoplastic CD5-negative B cells from patients with lymphomas of follicular center cell origin rarely express this CRI. Here, we report that G6-reactive leukemic cells from two unrelated CLL patients express a VH gene that shares greater than 99% homology with a rearranged VH gene previously isolated from the leukemic cell DNA of another CLL patient and that is identical to VH 51p1. Using the polymerase chain reaction, we find that this VH gene is rearranged, and presumably expressed, in the genomic DNA of all examined cases of G6-reactive CLL or small lymphocytic lymphoma. Thus these data indicate that the autoantibody-associated G6 CRI is a serologic marker for a conserved and developmentally restricted VH1 gene that is expressed at high frequency in CD5 B-cell malignancies and early B-cell ontogeny.
Ir/Oxide/Cellulose Composites for Catalytic Purposes Prepared by Atomic Layer Deposition (2006)

Ir/TiO 2 /cellulose and Ir/Al 2 O 3 /cellulose composites have been prepared by atomic layer deposition of TiO 2 , Al 2 O 3 , and Ir on filter paper. Despite the aggressive conditions during Ir deposition, the cellulose fibers remain undamaged, which may be attributed to the protecting effect of the thin oxide layer. The Ir/TiO 2 /cellulose composites show enhanced photocatalytic activities as compared to TiO 2 /cellulose composites.
Solution structure of a mini IGF‐1 (1996)

Mini insulin-like growth factor 1, an inactive insulin-like growth factor 1 mutant lacking the C region, was studied by 2D NMR spectroscopy. Resonances were assigned for almost all protons of the 57 amino acid residues. The 3D structure of the protein was determined by distance geometry methods. Three helical segments; Ala 8-Cys 18, Gly 42-Phe 49, and Leu 54-Cys 61, were identified, corresponding to those present in wild-type insulin-like growth factor 1 and in single-chain insulin. Their relative orientation, however, was found to be changed. This change is connected with a displacement of the Phe 23-Tyr 24-Phe 25-Asn 26 beta-strand-like segment, i.e., of aromatic side chains known to be important for receptor binding. Thus, deletion of the C region of IGF-1 results in a substantial tertiary structural rearrangement that accounts for the loss of receptor affinity.
Analysis of the site in CD4 that binds to the HIV envelope glycoprotein. (1990)

The first step in infection of human mononuclear cells with HIV involves the high affinity binding of the viral envelope glycoprotein, gp120, to the cell-surface receptor, CD4. To gain a better understanding of the molecular basis of this interaction, we have analyzed the ability of gp120 to bind to a panel of 40 mutant CD4 proteins containing single or double amino acid substitutions. In addition, the binding of several anti-CD4 mAb to the mutant CD4 proteins was measured. These mAb were chosen on the basis of the previous demonstration that they bind to epitopes in CD4 adjacent to the gp120-binding site. This analysis permits discrimination between mutations that probably cause localized conformational changes and those that alter residues likely to make direct contact with gp120 and with the mAb. Our results indicate that gp120 from two different strains of HIV binds to a larger region of the CD4 protein than previously described. The data has also been used to map the epitopes of mAb previously identified as anti-idiotype vaccine candidates. The results have important implications for the development of CD4-based therapies for AIDS.
Cytomegalovirus antigenemia assay or PCR can be used to monitor ganciclovir treatment in bone marrow transplant recipients. (1992)

The antigenemia assay, polymerase chain reaction (PCR) and rapid culture technique on buffy coat cells (DEAFF test) were used to monitor 37 cytomegalovirus (CMV) seropositive bone marrow transplant (BMT) recipients for active CMV infection during the first 3 months after BMT. The antigen assay and PCR demonstrated a comparable sensitivity for the detection of CMV in blood: discordant results were only obtained in the early or late phase of infection when the viral load was low. The antigen assay was more sensitive than the DEAFF test. Only 12 out of 40 antigen-positive samples yielded a positive result with DEAFF test, whereas viremia without antigenemia was never found. The discordance between these two tests increased further during antiviral therapy with ganciclovir. A correlation was observed between the duration of antigenemia during treatment and the recurrence of systemic CMV reactivation. Ten out of 11 patients with antigen-positive leukocytes present for more than 1 week after starting the treatment subsequently exhibited a relapse of active infection, whereas only three out of nine patients who resolved their antigenemia within 1 week did so. In conclusion, the antigen assay and PCR are useful techniques for detection of CMV infection in BMT patients. Test results obtained during therapy give reliable information regarding the viral load and the possibility of recurrence of antigenemia, and can be taken into account when prolonged administration of ganciclovir is considered.
The incorporation of various porphyrins into blood cells measured via flow cytometry, absorption and emission spectroscopy. (1998)

The incorporation of the five following porphyrins: meso-tetra(4-phenyl)porphyrin (TPP); meso-tetra(4-sulfonato-phenyl)porphyrin (TPPS4); meso-tetra(4-naphthyl)porphyrin (TNP); tri-sulfo-tetra-phenyl porphyrin (TPPS3) and tetra-sulfonato-naphthyl porphyrin (TNPS4) into human blood cells was investigated using flow cytometry, and absorption and emission spectroscopy. The percentage of stained cells, measured in a fluorescence cytometer, provided information on the efficiency of incorporation of fluorescent dye molecules into different types of cells. The yield of the incorporation of a dye was dependent on the type of dye and the solvent used for cell incubation. The degree of dye aggregation and ionization varied with the incubation medium, but dye molecules incorporated into cells seemed to be restricted to those in the monomeric state, exhibiting similar fluorescence yield. Of the three sulfonated porphyrins investigated only TPPS4 was efficiently incorporated into leukocytes. In the incubation solvent, this dye was in monomeric and neutral form. TPPS3 which was also in monomeric form, practically was not incorporated into cells. TPP and TNP dissolved in 5% aqueous dimethyl sulfoxide were present mostly in aggregated forms but they penetrated the cells with a high efficiency.
Matrix Metalloproteinase-Mediated Disruption of Tight Junction Proteins in Cerebral Vessels is Reversed by Synthetic Matrix Metalloproteinase Inhibitor in Focal Ischemia in Rat (2006)

Matrix metalloproteinases (MMPs) disrupt the blood-brain barrier (BBB) during reperfusion. Occludin and claudins are recently described tight junction proteins (TJPs) that form the BBB. We hypothesized that the opening of the BBB was because of the degradation of TJPs by the MMPs. Spontaneously hypertensive rats had a 90 mins middle cerebral artery occlusion with reperfusion for 2, 3, or 24 h. Matrix metalloproteinases were measured by immunohistochemistry and in situ and gel zymography. Real-time polymerase chain reaction (PCR) measured mRNAs of MMP-2 and -9, furin, membrane-type MMP (MT1-MMP), occludin, and claudin-5. There was opening of the BBB in the piriform cortex after 3 h of reperfusion, and an MMP inhibitor, BB-1101 (30 mg/kg), prevented the opening. At 3 h, in situ zymograms showed gelatinase activity. Zymography and PCR showed greater increases in MMP-2 than in MMP-9. There were increased mRNA and immunohistochemistry for MT1-MMP and furin, which activate MMP-2. Claudin-5 and occludin mRNA expression decreased at 2 h in both hemispheres with fragments of both proteins seen on Western blot by 3 h on the ischemic side; treatment with BB-1101 reversed the degradation of the TJPs. Immunohistochemistry at 3 h showed fragmented TJPs within the endothelial cell clefts. By 24 h, in situ zymography showed gelatinase activity and gel zymography showed elevated levels of MMP-9. Disrupted TJPs previously seen in endothelial cells appeared in the surrounding astrocytes. Our results provide direct evidence that MMPs open the BBB by degrading TJPs and that an MMP inhibitor prevents degradation of the TJPs by MMPs.
Physiology of Female Sexual Function: Animal Models (2004)

More research is needed in animal models in the physiology of female sexual function.
Non‐linear mapping for structure‐activity and structure‐property modelling (1993)

Abstract From a review of the theoretical aspects of non‐linear mapping and the different algorithms available in the literature, the methodological and practical problems linked to the use of this multivariate method in structure‐activity and structure‐property relationship studies are underlined. Useful tools for the graphical display of the outputs and the interpretation of the obtained clusters are presented. Statistical parameters estimating the quality of the graphical representation of each individual are also introduced. An example of application on a data matrix of 37 acaricides described by four physicochemical descriptors (π, F, R, MR ) is presented.
Simvastatin induces Foxp3+ T regulatory cells by modulation of transforming growth factor‐β signal transduction (2010)

Summary Statins are widely used drugs for the treatment of hypercholesterolaemia. A number of recent studies have suggested that statins also have pleiotropic effects on immune responses and statins have proven to be effective in the treatment of autoimmune diseases in animal models. Foxp3 + T regulatory cells are a unique subset of CD4 + T cells that mediate immunosuppression. Foxp3 + T cells develop in the thymus, but can also be induced in peripheral sites in the presence of transforming growth factor‐β (TGF‐β). We demonstrate here that simvastatin blockade of the mevalonate pathway can mediate induction of mouse Foxp3 + T cells and that simvastatin can synergize with low levels of TGF‐β to induce Foxp3 + T cells. The effects of simvastatin are secondary to a blockade of protein geranylgeranylation, are mediated at late time‐points after T‐cell activation, and are associated with demethylation of the Foxp3 promoter. One major effect of simvastatin was inhibition of the induction of Smad6 and Smad7, inhibitory Smads that inhibit TGF‐β signalling. Our results suggest that one mechanism responsible for the immunosuppressive effects of statins is the ability to promote the generation of Foxp3 + T regulatory cells.
In vitro myelopoiesis stimulated by rapid medium exchange and supplementation with hematopoietic growth factors (1991)

We studied the effect of the combination of rapid culture medium exchange with the addition of the human hematopoietic growth factors interleukin-3 (IL-3), granulocyte-macrophage colony-stimulating factor (GM-CSF), and erythropoietin (Epo) on the proliferation and differentiation of human long-term bone marrow cultures (LTBMCs). Individually and in combinations, IL-3, GM-CSF, and Epo were added to the culture medium of LTBMCs that were maintained with 50% medium volume exchange per day. The combination of IL-3 + GM-CSF + Epo generated the most prolific cultures with an order of magnitude increase in nonadherent cell production from weeks 2 through 8 in culture as compared with unsupplemented controls. Under these conditions, the cultures produced as many cells as were inoculated every 2 weeks and led to a greater than 2.5-fold expansion in terms of the number of nonadherent cells produced over a 6- to 8-week period. Furthermore, the LTBMCs produced nonadherent colony-forming unit-GM (CFU-GM) for more than 20 weeks. The rapid medium exchange combined with the addition of human hematopoietic CSFs significantly enhances the proliferation and differentiation of LTBMCs. These results indicate that addition of combinations of hematopoietic CSFs, together with a rapid medium exchange rate, can provide culture conditions that are suitable for the expansion of the progenitor cell pool and perhaps for the increased survival of hematopoietic stem cells in culture. Although these culture conditions still fall short of full reconstitution of functional human bone marrow, they provide an improved approach to hematopoietic cell culture that may permit the expansion and manipulation of progenitor cells in vitro.
Origin of low Gilbert damping in half metals (2009)

Using a combination of first-principles calculations and an extended Hückel tight binding model this letter reports on the origin of the low Gilbert damping in half metals. This approach enables the prediction of the lower limit for the magnetization relaxation in a wide variety of material systems relevant for future spintronic applications. For the two model systems Co2MnGe and Co2MnSi minimal damping parameters of 1.9×10−4 and 0.6×10−4 are predicted.
Non-race concurrency bug detection through order-sensitive critical sections (2013)

This paper introduces a new heuristic condition for non-race concurrency bugs, named order-sensitive critical sections, and proposes a run-time bug detection scheme based on the condition. The order-sensitive critical sections are defined as a pair of critical sections that can lead to non-deterministic shared memory state depending on the order in which they execute. In a sense, the order-sensitive critical sections can be seen as extending the intuition in using data races as a potential bug condition to capture non-race bugs. Experiments show that the proposed scheme provides a good coverage for multiple types of non-race bugs, with a small number of false positives. For example, the scheme detected all 9 real-world non-race bugs that were tested as well as over 90% of injected non-race bugs. Additionally, this paper presents an efficient hardware architecture that supports the proposed scheme with minor hardware changes and a small amount of additional state - a 9-KB buffer per core and a 1-bit tag per data cache block. The hardware-based scheme could still detect all 9 real-world bugs that were tested and more than 84% of the injected non-race bugs. Moreover, the hardware supported scheme has a negligible impact on performance, with a 0.23% slowdown on average.
Adenosine 3',5'-monophosphate formation by preparations of rat liver soluble guanylate cyclase activated with nitric oxide, nitrosyI ferroheme, S-nitrosothiols, and other nitroso compounds (1980)

Cyclic AMP formation from ATP was stimulated by unpurified and partially purified soluble hepatic guanylate cyclase in the presence of nitric oxide (NO) or compounds containing a nitroso moiety such as nitroprusside, N-methyl-N-nitro-N-nitrosoguanidine (MNNG), nitrosyl ferroheme, and S-nitrosothiols. Cyclic AMP formation was undetectable in the absence of NO or nitroso compounds and was not stimulated by fluoride or glucagon, indicating the absence of adenylate cyclase activity. The nitroso compounds failed to activate, whereas fluoride or glucagon activated, adenylate cyclase in washed rat liver membrane fractions. Cyclic GMP formation from GTP was markedly stimulated by the soluble hepatic fraction in the presence of NO or nitroso compounds. Cyclic AMP formation by partially purified guanylate cyclase was competitively inhibited by GTP and cyclic GMP formation is well-known to be competitively inhibited by ATP. Therefore, it appears that activated guanylate cyclase, rather than adenylate cyclase, was responsible for the formation of cyclic AMP from ATP. Formation of cyclic AMP of cyclic GMP was enhanced by thiols, inhibited by hemoproteins and oxidants, and required the addition of either Mg2+ or Mn2+. Further, several nitrosyl ferroheme compounds and S-nitrosothiols stimulated the formation of both cyclic AMP and cyclic GMP by the soluble hepatic fraction. These observations support the view that soluble guanylate cyclase is capable, under certain well-defined conditions, of catalyzing the conversion of ATP to cyclic AMP.
Uptake and transport of exogenous proteins by respiratory epithelium. (1976)

The tracer proteins, horseradish peroxidase and ferritin, placed in the trachea of guinea pigs were taken up by epithelial cells and transported to the extracellular space. The interval between the introduction of the tracer proteins into the lumen of the trachea and the morphologic demonstration of the porteins in the extracellular space or within the basal portion of the cells was between 30 and 60 minutes. The proteins were transported in vesicles and no penetration of the epithelial intercellular tight junctions was found. The intercellular tight junctions were made permeable to horseradish peroxidase by anesthetic ether and this permeable epithelium was compared to the vesicle type transport. Transepithelial transport of proteins is a possible mechanism for the introduction of antigenic material into the subepithelial lymphoid tissue and this transport may also be of importance in the late onset type of asthma.
Primary Structure of Human Fibrinogen and Fibrin (1979)

The cyanogen bromide fragment, N-DSK, containing the NH2-terminal portions of the three chains of fibrinogen, was found to exist in dimeric and polymeric forms. These different forms gave rise to identical chain fragments on reduction and alkylation. The B beta chain of N-DSK from fibrinogen and the beta chain of N-DSK from fibrin were isolated and characterized. The B beta chain fragment has a blocked NH2-terminal residue, and fibrinopeptide B is released on digestion with thrombin. The beta chain fragment has glycine as NH2-terminal residue. The molecular weight of the B beta chain fragment is 12200 as determined by ultracentrifugal analysis. Gel electrophoresis in sodium dodecyl sulphate gave the molecular weights of 14000 and 13000 for the B beta chain and beta chain fragments, respectively. The NH2-terminal B beta chain fragment consists of 118 amino acid residues and the beta chain fragment of 104 residues. The amino acid sequence of beta chain fragment is identical to B beta chain fragment except for the fibrinopeptide B portion. The isolation of a B beta-related fragment (B beta +), with a molecular weight of 30000, is also reported. The presence of B beta + was explained on the basis of incomplete cleavage at the Met-118 residue during treatment with cyanogen bromide. Some functional aspects of the B beta chain fragment are discussed.
Synthesis and Biological Activity of Folic Acid and Methotrexate Analogues Containing l-threo-(2S,4S)-4-Fluoroglutamic Acid and dl-3,3-Difluoroglutamic Acid (1996)

The stereospecific syntheses of L-threo-gamma-fluoromethotrexate (1t) and L-threo-gamma-fluorofolic acid (3t) are reported. Compounds 1t and 3t have no substrate activity with folylpoly-gamma-glutamate synthetase isolated from CCRF-CEM human leukemia cells, and compound 1t inhibits human dihydrofolate reductase at similar levels as methotrexate. The synthesis of DL-3,3-difluoroglutamic acid (6) and its incorporation into DL-beta,beta-difluorofolic acid (4) are also reported. Compound 4 acts as a better substrate for human CCRF-CEM folylpoly-gamma-glutamate synthetase than folic acid (V/K = ca. 7-fold greater). Thus, replacement of the glutamate moiety of methotrexate and folic acid with 4-fluoroglutamic acid and 3,3-difluoroglutamic acid results in folates and antifolates with altered polyglutamylation activity.