gebhart/patrepeval huggingface dataset:
IgA1 proteases from Haemophilus influenzae, Streptococcus pneumoniae, Neisseria meningitidis, and Streptococcus sanguis: comparative immunochemical studies. (1980)

IgA1 proteases from H. influenzae, N. meningitidis, S. pneumoniae, and S. sanguis were compared with respect to site of cleavage in the IgA1 molecule and EDTA sensitivity. Proteases from S. sanguis and S. pneumoniae cleaved the Pro (227)-Thr (228) bond within the hinge region of the alpha 1 chain and were inhibited by EDTA. H. influenzae IgA1 protease cleaved the Pro (231)-Ser (232) peptide bond. The activity of IgA1 proteases from H. influenzae and N. meningitidis was unaffected by EDTA. Purified and denatured alpha 1 chain was cleaved only in the hinge region. Other component chains of secretory IgA (secretory component, light and J chains) were not susceptible. In addition to IgA1 protease, S. pneumoniae released exo- and endoglycosidases that removed a considerable portion of carbohydrate side chains of IgA1; this activity was absent from crude IgA1 protease preparations of the other three bacterial species. Association in vitro of polymeric IgA1 with SC did not inhibit the degradation of IgA1 proteases. The considerable resistance of secretory IgA to cleavage by IgA1 proteases may be explained in part by the presence of IgA1 protease-neutralizing antibodies in secretory IgA.
Specific Activity of Polypyrrole Nanoparticulate Immunoreagents:  Comparison of Surface Chemistry and Immobilization Options (1996)

Polypyrrole-based colloids with differing surface chemistries were compared with respect to the specific activity of immobilized antibody. Monoclonal antibody to the alpha subunit of human chorionic gonadotropin (hCG) was modified by incorporation of cystamine into the Fc-carbohydrate, followed by reduction with dithiothreitol resulting in the generation of 4.5 free thiols per IgG. The reduced IgG was added to clean, unmodified and surface-modified polypyrrole colloids. Functionalized colloids included carboxylate-modified polypyrrole, poly[pyrrole-co-1-(2-carboxyethyl) pyrrole]-silica composite, and amine forms of the carboxylated colloids. The amine-functionalized colloids were subsequently treated with sulfosuccinimidyl 4-(N-maleimidomethyl)cyclohexane-1-carboxylate to provide thiol-reactive maleimide surface groups. Following the conjugation of IgG to the colloids, bound and soluble antibody activity was quantitated using a sequentially competitive immunoassay for hCG, based on an automated commercial hCG kit. The results indicated that all forms of polypyrrole retained the equivalence of between 12 and 33 micrograms of IgG activity/mg of colloidal solids, relative to the unmodified soluble IgG.
Cardiac-specific disruption of the c-raf-1 gene induces cardiac dysfunction and apoptosis (2004)

The Raf/MEK/extracellular signal-regulated kinase (ERK) signaling pathway regulates diverse cellular processes such as proliferation, differentiation, and apoptosis and is implicated as an important contributor to the pathogenesis of cardiac hypertrophy and heart failure. To examine the in vivo role of Raf-1 in the heart, we generated cardiac muscle-specific Raf-1-knockout (Raf CKO) mice with Cre-loxP-mediated recombination. The mice demonstrated left ventricular systolic dysfunction and heart dilatation without cardiac hypertrophy or lethality. The Raf CKO mice showed a significant increase in the number of apoptotic cardiomyocytes. The expression level and activation of MEK1/2 or ERK showed no difference, but the kinase activity of apoptosis signal-regulating kinase 1 (ASK1), JNK, or p38 increased significantly compared with that in controls. The ablation of ASK1 rescued heart dysfunction and dilatation as well as cardiac fibrosis. These results indicate that Raf-1 promotes cardiomyocyte survival through a MEK/ERK-independent mechanism.
Involvement of an NAD(P)H oxidase as a pO2 sensor protein in the rat carotid body (1990)

The rat carotid body tissue reveals a photometrically measurable haem signal with absorbance maxima at 560 nm, 518 nm and 425 nm, suggesting the presence of a b-type cytochrome; this was confirmed by pyridine haemochrome and CO spectra. The quantity of cytochrome b was estimated to be 310 pmol.mg of protein-1. This haem is capable of H2O2 formation, which can be inhibited by 10 microM-diphenyliodonium (DPI). The hypoxia-induced increase in nervous chemoreceptor discharge and the reduction of FAD and NAD(P)+ were also inhibited by DPI (10 microM). These results suggest that an oxidase such as the NAD(P)H oxidase of neutrophils may act as a pO2 sensor protein in the rat carotid body, probably inducing the pO2 chemoreceptor process by H2O2 formation.
Ultra-Thin Flexible Ceramic Membranes for Electronic Applications (2013)

In 2010, ENrG Incorporated commercialized 40 microns thick, flexible zirconia based ceramic membranes as shown in Figure 1. Even though so thin, the membranes are gas-tight, fully dense, strong, thermal shock tolerant and chemically inert. Historically, zirconia membranes are used mainly for applications such as solid oxide fuel cells and oxygen sensors, making use of the ionic property of partially stabilized zirconia at elevated temperatures.
User-controllable polycube map for manifold spline construction (2008)

Polycube T-spline has been formulated elegantly that can unify T-splines and manifold splines to define a new class of shape representations for surfaces of arbitrary topology by using polycube map as its parametric domain. In essense, The data fitting quality using polycube T-splines hinges upon the construction of underlying polycube maps. Yet, existing methods for polycube map construction exhibit some disadvantages. For example, existing approaches for polycube map construction either require projection of points from a 3D surface to its polycube approximation, which is therefore very difficult to handle the cases when two shapes differ significantly; or compute the map by conformally deforming the surfaces and polycubes to the common canonical domain and then construct the map using function composition, which is challenging to control the location of singularities and makes it hard for the data-fitting and hole-filling processes later on.
Tungstate Uptake by a Highly Specific ABC Transporter inEubacterium acidaminophilum (2001)

The Gram-positive anaerobe Eubacterium acidaminophilum contains at least two tungsten-dependent enzymes: viologen-dependent formate dehydrogenase and aldehyde dehydrogenase. (185)W-Labeled tungstate was taken up by this organism with a maximum rate of 0.53 pmol min(-)1 mg(-)1 of protein at 36 degrees C. The uptake was not affected by equimolar amounts of molybdate. The genes tupABC coding for an ABC transporter specific for tungstate were cloned in the downstream region of genes encoding a tungsten-containing formate dehydrogenase. The substrate-binding protein, TupA, of this putative transporter was overexpressed in Escherichia coli, and its binding properties toward oxyanions were determined by a native polyacrylamide gel retardation assay. Only tungstate induced a shift of TupA mobility, suggesting that only this anion was specifically bound by TupA. If molybdate and sulfate were added in high molar excess (>1000-fold), they were also slightly bound by TupA. The K(d) value for tungstate was determined to be 0.5 microm. The genes encoding the tungstate-specific ABC transporter exhibited highest similarities to putative transporters from Methanobacterium thermoautotrophicum, Haloferax volcanii, Vibrio cholerae, and Campylobacter jejuni. These five transporters represent a separate phylogenetic group of oxyanion ABC transporters as evident from analysis of the deduced amino acid sequences of the binding proteins. Downstream of the tupABC genes, the genes moeA, moeA-1, moaA, and a truncated moaC have been identified by sequence comparison of the deduced amino acid sequences. They should participate in the biosynthesis of the pterin cofactor that is present in molybdenum- and tungsten-containing enzymes except nitrogenase.
Acute Anti-Ischemic Effect of Testosterone in Men With Coronary Artery Disease (1999)

Short-term administration of testosterone induces a beneficial effect on exercise-induced myocardial ischemia in men with coronary artery disease. This effect may be related to a direct coronary-relaxing effect.
Complement component C3 fixes selectively to the major outer membrane protein (MOMP) of Legionella pneumophila and mediates phagocytosis of liposome-MOMP complexes by human monocytes. (1990)

Legionella pneumophila is a facultative intracellular bacterial pathogen that parasitizes human monocytes and alveolar macrophages. Previous studies from this laboratory have shown that monocyte complement receptors CR1 and CR3 and complement component C3 in serum mediate L. pneumophila phagocytosis. In this study, we have explored C3 fixation to L. pneumophila. We developed a whole-cell enzyme-linked immunosorbent assay (ELISA) to measure C3 fixation to the bacterial surface. By this assay, C3 fixes to L. pneumophila that are opsonized in fresh nonimmune serum, and C3 fixation takes place via the alternative pathway of complement activation. Immunoblot analysis of opsonized L. pneumophila indicated that C3 fixes selectively to specific acceptor molecules of L. pneumophila. Consistent with this, when nitrocellulose blots of whole L. pneumophila or bacterial components are incubated in fresh nonimmune serum, C3 fixes exclusively to the major outer membrane protein (MOMP) of L. pneumophila, a porin; C3 does not fix to L. pneumophila LPS on these blots. To further explore the role of MOMP in C3 fixation and phagocytosis, we reconstituted purified MOMP into liposomes. By the ELISA, MOMP-liposomes, but not plain liposomes lacking MOMP, avidly fix C3. Consistent with a dominant role for MOMP in C3 fixation, MOMP-liposomes form a C3 complex of the same apparent molecular weight as whole L. pneumophila in nonimmune serum. Opsonized radioiodinated MOMP-liposomes avidly adhere to monocytes, and adherence is dose dependent upon serum. By electron microscopy, opsonized MOMP-liposomes are efficiently phagocytized by human monocytes, and phagocytosis takes place by a conventional appearing form of phagocytosis. This study demonstrates that C3 fixes selectively to the MOMP of L. pneumophila, and that, in the presence of nonimmune serum, MOMP can mediate phagocytosis of liposomes and, potentially, phagocytosis of intact L. pneumophila by human monocytes.
Velocity field of the “La Clapière” landslide measured by the correlation of aerial and QuickBird satellite images (2004)

Two displacement maps of the “La Clapière” landslide (France) have been derived over two periods of 4 years (1995–1999 and 1999–2003) by correlation of aerial photographs and a QuickBird satellite image. The movement of the landslide ranges from 2.5 m to 20 m per year. Those values have been validated over 13 points monitored by conventional tacheometric measurements. Three areas with significant differences in velocity field have been mapped. Limits of those areas are in good agreement with in situ observations. Velocity maps show the low long term temporal variability of the landslide movement and its spatial variability. The optical correlation method using images derived from various sensors (airborne and spatial) is a promising technique for improving the spatial resolution of velocity field observation of landslides over several years.
Analysis of a tunable single mode optical fiber coupler (1982)

We report the operation and the theoretical modeling of an efficient, tunable, and low-loss single mode fiber coupler. The coupler design follows a scheme previously reported, in which two optical fibers mounted in curved grooves in separate quartz substrates are polished until sufficient cladding material has been removed to permit optical coupling between the mated polished faces of the fibers. The results of a computer analysis of the distributed coupling taking place between the fibers are discussed, emphasizing the intuitive dependences of the coupling coefficient and effective interaction length of the device on its geometrical parameters. A detailed experimental analysis of fiber couplers follows in which we characterize two types of couplers made with different brands of single-mode fibers. Operation up to 100 percent coupling ratio and 50 dB extinction ratio between coupled and direct branch as well as operation in overcoupling regimes are demonstrated, both at visible and infrared signal wavelengths. Tuning curves are shown that emphasize the excellent tunability properties of such couplers in which the coupling ratio can be smoothly and continuously tuned between 0 and 100 percent. Experimental evidence of the relatively low loss level and very low polarization dependence of the fiber couplers are also presented. All experimental results, including an analysis of the influence of the refractive index of the intermediate layer of index-matching liquid between the polished faces of the fibers, are found to be very well predicted by our theoretical model.
Mutation of the Maturase Lipoprotein Attenuates the Virulence ofStreptococcus equito a Greater Extent than Does Loss of General Lipoprotein Lipidation (2006)

Streptococcus equi is the causative agent of strangles, a prevalent and highly contagious disease of horses. Despite the animal suffering and economic burden associated with strangles, little is known about the molecular basis of S. equi virulence. Here we have investigated the contributions of a specific lipoprotein and the general lipoprotein processing pathway to the abilities of S. equi to colonize equine epithelial tissues in vitro and to cause disease in both a mouse model and the natural host in vivo. Colonization of air interface organ cultures after they were inoculated with a mutant strain deficient in the maturase lipoprotein (DeltaprtM(138-213), with a deletion of nucleotides 138 to 213) was significantly less than that for cultures infected with wild-type S. equi strain 4047 or a mutant strain that was unable to lipidate preprolipoproteins (Deltalgt(190-685)). Moreover, mucus production was significantly greater in both wild-type-infected and Deltalgt(190-685)-infected organ cultures. Both mutants were significantly attenuated compared with the wild-type strain in a mouse model of strangles, although 2 of 30 mice infected with the Deltalgt(190-685) mutant did still exhibit signs of disease. In contrast, only the DeltaprtM(138-213) mutant was significantly attenuated in a pony infection study, with 0 of 5 infected ponies exhibiting pathological signs of strangles compared with 4 of 4 infected with the wild-type and 3 of 5 infected with the Deltalgt(190-685) mutant. We believe that this is the first study to evaluate the contribution of lipoproteins to the virulence of a gram-positive pathogen in its natural host. These data suggest that the PrtM lipoprotein is a potential vaccine candidate, and further investigation of its activity and its substrate(s) are warranted.
Regulation of the immune response. V. An analysis of the function of the Fc portion of antibody in suppression of an immune response with respect to interaction with components of the lymphoid system. (1971)

Pepsin digested, F(ab')(2) antibody has less ability to inhibit an antibody response than has intact IgG antibody, when the antibodies were given one day after antigen. F(ab')(2) antibody has to be given with antigen to attain maximal suppression, while IgG antibody, administered after antigen, is still highly immunosuppressive. The IgG antibody was able to terminate established immune responses, whereas F(ab')(2) antibody could not do so. We interpret these findings to indicate that F(ab')(2) antibody suppresses immune responses by simple masking of antigen, whereas IgG antibody alters the immune response through a further activity which takes place after antibody has combined with antigen. This further activity involves the Fc portion of antibody. Two alterations in immune mechanism are suggested: (1) increased destruction of antigen and (2) inactivation of the antibody forming cell precursor population by antigen—antibody complexes. This latter possibility is considered in detail. The tripartite inactivation model has been constructed to explain the presently known observations concerning immunosuppression by antibody and to make a prediction which has been verified. A further prediction concerning the affinities of antibodies produced under IgG or F(ab')(2) antibody-mediated immunosuppression is put forward. Thymus-bone marrow cell synergism does not give a simple thymus cell dose-response relationship but a multi-phasic relationship where the response increases once the dose of thymus cells is decreased to a sufficiently low level. Such a dose-response relationship is not explainable in terms of the usual mechanisms proposed for thymus-bone marrow cell interaction and this deviation from a simple dose-response relationship is interpreted in terms of the proposed function of thymus-derived cells in controlling antibody feedback regulation.
Identification and characterization of a new conserved motif within the presequence of proteins targeted into complex diatom plastids (2004)

Several groups of algae evolved by secondary endocytobiosis, which is defined as the uptake of a eukaryotic alga into a eukaryotic host cell and the subsequent transformation of the endosymbiont into an organelle. Due to this explicit evolutionary history such algae possess plastids that are surrounded by either three or four membranes. Protein targeting into plastids of these organisms depends on N-terminal bipartite presequences consisting of a signal and a transit peptide domain. This suggests that different protein targeting systems may have been combined during establishment of secondary endocytobiosis to enable the transport of proteins into the plastids. Here we demonstrate the presence of an apparently new type of transport into diatom plastids. We analyzed protein targeting into the plastids of diatoms and identified a conserved amino acid sequence motif within plastid preprotein targeting sequences. We expressed several diatom plastid presequence:GFP fusion proteins with or without modifications within that motif in the diatom Phaeodactylum tricornutum and found that a single conserved phenylalanine is crucial for protein transport into the diatom plastids in vivo, thus indicating the presence of a so far unknown new type of targeting signal. We also provide experimental data about the minimal requirements of a diatom plastid targeting presequence and demonstrate that the signal peptides of plastid preproteins and of endoplasmic reticulum-targeted preproteins in diatoms are functionally equivalent. Furthermore we show that treatment of the cells with Brefeldin A arrests protein transport into the diatom plastids suggesting that a vesicular transport step within the plastid membranes may occur.
Lane-Level Integrity Provision for Navigation and Map Matching With GNSS, Dead Reckoning, and Enhanced Maps (2009)

Lane-level positioning and map matching are some of the biggest challenges for navigation systems. Additionally, in safety applications or in those with critical performance requirements (such as satellite-based electronic fee collection), integrity becomes a key word for the navigation community. In this scenario, it is clear that a navigation system that can operate at the lane level while providing integrity parameters that are capable of monitoring the quality of the solution can bring important benefits to these applications. This paper presents a pioneering novel solution to the problem of combined positioning and map matching with integrity provision at the lane level. The system under consideration hybridizes measurements from a global navigation satellite system (GNSS) receiver, an odometer, and a gyroscope, along with the road information stored in enhanced digital maps, by means of a multiple-hypothesis particle-filter-based algorithm. A set of experiments in real environments in France and Germany shows the very good results obtained in terms of positioning, map matching, and integrity consistency, proving the feasibility of our proposal.
Reconstitution of Hematopoiesis after High-Dose Chemotherapy by Autologous Progenitor Cells Generated ex Vivo (1995)

A small number of peripheral-blood CD34+ cells, when grown ex vivo, can supply a population of hematopoietic precursors that have the ability to restore blood formation in patients treated with high doses of chemotherapy. This method, which requires only a small volume of the patient's blood, may reduce the risk of tumor-cell contamination, circumvent the need for leukapheresis, and allow repeated cycles of high-dose chemotherapy.
UCbase & miRfunc: a database of ultraconserved sequences and microRNA function (2008)

Four hundred and eighty-one ultraconserved sequences (UCRs) longer than 200 bases were discovered in the genomes of human, mouse and rat. These are DNA sequences showing 100% identity among the three species. UCRs are frequently located at genomic regions involved in cancer, differentially expressed in human leukemias and carcinomas and in some instances regulated by microRNAs (miRNAs). Here we present UCbase & miRfunc, the first database which provides ultraconserved sequences data and shows miRNA function. Also, it links UCRs and miRNAs with the related human disorders and genomic properties. The current release contains over 2000 sequences from three species (human, mouse and rat). As a web application, UCbase & miRfunc is platform independent and it is accessible at http://microrna.osu.edu/.UCbase4.
Design and Properties of NCCG-gp41, a Chimeric gp41 Molecule with Nanomolar HIV Fusion Inhibitory Activity (2001)

The abbreviations used are: HIV, human immunodeficiency virus; Env, viral envelope glycoproteins; HIV-I, HIV, type I; HPLC, high pressure liquid chromatography; N34, N35, and N36 are segments derived from the N-terminal helix of gp41 and comprise residues 546 -579, 546 -580, and 546 -581, respectively, of HIV-I Env; C28 and C34 are segments derived from the C-terminal helix of gp41 and comprise residues 628 -655 and 628 -661, respectively, of HIV-I Env; N34-(L6)-C28 is a construct comprising peptides N34 and C28 connecting by a six-residue linker (L6).
Results of a Phase 1 Study of AME-133v (LY2469298), an Fc-Engineered Humanized Monoclonal Anti-CD20 Antibody, in FcγRIIIa-Genotyped Patients with Previously Treated Follicular Lymphoma (2012)

AME-133v was safe and well tolerated at the doses tested. AME-133v showed encouraging results as an anti-CD20 therapy in heavily pretreated FL patients with the less favorable FcγRIIIa F-carrier genotype.
Sequence requirements for the biotinylation of carboxyl-terminal fragments of human propionyl-CoA carboxylase alpha subunit expressed in Escherichia coli. (1994)

Biotin-dependent enzymes play an essential role in the metabolism of all organisms. Their biotinylation is catalyzed by holoenzyme synthetases, which attach a biotin molecule to a specific lysine residue on the apoenzymes. The sequence flanking the biotin binding site is highly conserved among biotin-dependent enzymes. This sequence conservation might be related to the extensive cross-species activity showed by holoenzyme synthetases. In this study, we have expressed carboxyl-terminal fragments of the alpha subunit of human propionyl-CoA carboxylase (PCC-alpha) in Escherichia coli and used site-directed mutagenesis to determine the sequence requirements for biotinylation by the bacterial holoenzyme synthetase. We show that the carboxyl-terminal 67 amino acids of PCC-alpha act as an independent domain in the biotinylation reaction. Mutations that affect several conserved Gly residues and a Pro-Met-Pro sequence near the biotin binding site are critical for biotinylation. Substitution of the amino acids that flank the biotin acceptor Lys residue or elimination of the last 3 amino acids of the PCC-alpha peptides had little or no effect on their biotinylation despite their high conservation in biotin enzymes.