gebhart/patrepeval huggingface dataset:
Kalman filter based calibration of precision motion control (2002)

A method is described and validated for the automatic calibration of analog sine-wave quadrature sensors, such as optical encoders, embedded in a functioning system. The algorithm uses a Kalman filter to estimate the true position of the direct-drive actuator joint using a model of it's dynamics, an applied actuator command and measurements from the uncalibrated sensor. From the estimated true position, a lookup table is constructed which corrects sensor errors. Our results indicate that this method achieves accuracies typical of interferometric calibration, without requiring an external measurement device. The accuracy is surprisingly robust to modeling errors.
Rapid identification of mycobacteria to the species level by polymerase chain reaction and restriction enzyme analysis (1993)

A method for the rapid identification of mycobacteria to the species level was developed on the basis of evaluation by the polymerase chain reaction (PCR) of the gene encoding for the 65-kDa protein. The method involves restriction enzyme analysis of PCR products obtained with primers common to all mycobacteria. Using two restriction enzymes, BstEII and HaeIII, medically relevant and other frequent laboratory isolates were differentiated to the species or subspecies level by PCR-restriction enzyme pattern analysis. PCR-restriction enzyme pattern analysis was performed on isolates (n = 330) from solid and fluid culture media, including BACTEC, or from frozen and lyophilized stocks. The procedure does not involve hybridization steps or the use of radioactivity and can be completed within 1 working day.
Dual effect of meningococcal antigens on a T cell dependent immune response (1983)

Meningococcal antigens (MA) showed adjuvant activity when administered to mice at the same time as antigen (sheep erythrocyte (SE], by increasing the splenocyte plaque-forming response in a dose-related manner. However, when SE were given 1 day after MA administration, the subsequent plaque formation was diminished from normal in proportion to the dose of MA injected. Splenocytes taken from mice up to 5 days after MA injection actively inhibited plaque formation when mixed with splenocytes immunized with SE 4 days earlier. Two days after MA injection the nonspecific inhibition of plaque formation was mainly due to adherent spleen cells, while at 5 days nonadherent cells had acquired the inhibitory activity. It appears that it is the degree of activation of adherent cells resulting from the timing and dosage of MA which modulates the subsequent development and secretion of antibody-forming cells.
Expressed Protein Ligation: A New Tool for the Biosynthesis of Cyclic Polypeptides (2005)

The present paper reviews the use of expressed protein ligation for the biosynthesis of backbone cyclized polypeptides. This general method allows the in vivo and in vitro biosynthesis of cyclic polypeptides using recombinant DNA expression techniques. Biosynthetic access to backbone cyclic peptides opens the possibility to generate cell-based combinatorial libraries that can be screened inside living cells for their ability to attenuate or inhibit cellular processes.
Evidence for two different active sites on human beta-hexosaminidase A. Interaction of GM2 activator protein with beta-hexosaminidase A. (1985)

Competition experiments were carried out on the hydrolysis of different substrates by beta-hexosaminidase A isolated from human liver. The results show that ganglioside GM2 in the presence of the GM2 activator protein and a new synthetic substrate, 4-methylumbelliferyl-beta-N-acetylglucosaminide 6-sulfate, are hydrolyzed at the same active site on the alpha subunit of beta-hexosaminidase A, whereas 4-methylumbelliferyl-beta-N-acetylglucosaminide is degraded predominantly by a different active site on the beta-subunit. This finding provides for the first time a possible molecular basis for the observation that, in variant B1 of the GM2 gangliosidoses, beta-hexosaminidase A has lost its activity toward GM2 ganglioside and the sulfated artificial substrate while being still able to hydrolyze the unsulfated artificial substrate at a normal rate. Furthermore, the finding that the GM2 activator protein inhibits the degradation of the sulfated substrate by beta-hexosaminidases A and S indicates that the alpha subunit common to both isoenzymes might provide a binding site for the activator protein.
Systems metabolic engineering of Escherichia coli for L ‐threonine production (2007)

Amino-acid producers have traditionally been developed by repeated random mutagenesis owing to the difficulty in rationally engineering the complex and highly regulated metabolic network. Here, we report the development of the genetically defined L-threonine overproducing Escherichia coli strain by systems metabolic engineering. Feedback inhibitions of aspartokinase I and III (encoded by thrA and lysC, respectively) and transcriptional attenuation regulations (located in thrL) were removed. Pathways for Thr degradation were removed by deleting tdh and mutating ilvA. The metA and lysA genes were deleted to make more precursors available for Thr biosynthesis. Further target genes to be engineered were identified by transcriptome profiling combined with in silico flux response analysis, and their expression levels were manipulated accordingly. The final engineered E. coli strain was able to produce Thr with a high yield of 0.393 g per gram of glucose, and 82.4 g/l Thr by fed-batch culture. The systems metabolic engineering strategy reported here may be broadly employed for developing genetically defined organisms for the efficient production of various bioproducts.
H2O enhanced focused ion beam micromachining (1995)

The use of H2O vapor as a chemical adjunct for focused ion beam micromachining has been investigated. The presence of H2O vapor during micromachining with a 25 keV Ga+ beam increases the removal rate of carbon-containing materials such as polyimide, PMMA, and other resists by a factor of 20 (relative to physical sputtering), and that of diamond by a factor of 10. In addition, H2O causes a decrease in the removal rate of some other materials (e.g., Si and Al) by as much as a factor of 10, effectively increasing the selectivity of polymers over these other materials by as much as a factor of 200. The dependence of the removal rate on H2O pressure at the sample, pixel dwell time, pixel size, pattern frame time (corresponding to pattern size), and current density has been investigated utilizing PMMA. PMMA removal rates were calculated by measuring the depth of rectangular pits micromachined into PMMA films under the various experimental conditions. In addition to investigating the effect of H2O on material removal rates, the change in removal rate of PMMA in the presence of selected gases including O2, H2, and CH3OH, has been measured.
Identification, purification and properties of clone-specific glycoprotein antigens constituting the surface coat ofTrypanosoma brucei (1975)

Soluble glycoproteins have been purified from a series of clones of Trypanosoma brucei 427. Each clone yielded a characteristic predominant glycoprotein which induced clone-specific immunity to trypanosome infection in mice. These glycoproteins were shown by specific labelling and enzyme digestion of cells to be the major components of the trypanosome surface coat. Each glycoprotein consisted of a single polypeptide chain having an apparent molecular weight of 65 000 (as measured by SDS-polyacrylamide gel electrophoresis) and containing around 600 amino acid and 20 monosaccharide residues. Preliminary structural studies indicated large changes in amino acid sequence dispersed over a considerable length of the polypeptide chain. Proteolytic activity was demonstrated in semi-purified trypanosome extracts, providing one reason for the heterogeneity sometimes observed in surface glycoprotein antigen preparations.
Cell-Type-Specific Function of BCL9 Involves a Transcriptional Activation Domain That Synergizes with β-Catenin (2008)

Transcriptional regulation by the canonical Wnt pathway involves the stabilization and nuclear accumulation of beta-catenin, which assembles with LEF1/TCF transcription factors and cofactors to activate Wnt target genes. Recently, the nuclear beta-catenin complex has been shown to contain BCL9, which interacts with beta-catenin and recruits Pygopus as a transcriptional coactivator. However, the presumed general functions of Pygopus and BCL9, which has been proposed to act as a scaffolding protein for Pygopus, have been challenged by the rather specific and modest developmental defects of targeted inactivations of both the Pygo1 and the Pygo2 genes. Here, we analyze the function of BCL9 in transcriptional activation by beta-catenin. We find that BCL9 acts in a cell-type-specific manner and, in part, independent of Pygopus. We show that BCL9 itself contains a transcriptional activation domain in the C terminus, which functionally synergizes in lymphoid cells with the C-terminal transactivation domain of beta-catenin. Finally, we identify amino acids in the transactivation domain of beta-catenin that are important for its function and association with the histone acetyltransferases CBP/p300 and TRRAP/GCN5. Thus, BCL9 may serve to modulate and diversify the transcriptional responses to Wnt signaling in a cell-type-specific manner.
Contribution of respiratory syncytial virus G antigenicity to vaccine-enhanced illness and the implications for severe disease during primary respiratory syncytial virus infection (2004)

FI-RSV vaccine-enhanced illness is not attributable to RSV G. Furthermore formulation of a safe and effective RSV vaccine must ensure RSV antigen production, processing and presentation via the endogenous pathways. Thus gene delivery by vector, by DNA or by live attenuated virus are attractive vaccine approaches.
Hepatic clearance of arterially infused ferromagnetic particles (2003)

This study has shown that, although arterially infused ferromagnetic particles were extensively phagocytosed, there was no significant hepatic clearance 28 days after infusion. It also determined that the suspension of 150 nm ferromagnetic particles in lipiodol was too vaso-occlusive for use in hepatic tissue. However, the suspension of 32 microm microspheres containing ferromagnetic particles in tween-water was safe and well tolerated.
De Novo Initiation of RNA Synthesis by Hepatitis C Virus Nonstructural Protein 5B Polymerase (2000)

RNA-dependent RNA polymerase (RdRp) encoded by positive-strand RNA viruses is critical to the replication of viral RNA genome. Like other positive-strand RNA viruses, replication of hepatitis C virus (HCV) RNA is mediated through a negative-strand intermediate, which is generated through copying the positive-strand genomic RNA. Although it has been demonstrated that HCV NS5B alone can direct RNA replication through a copy-back primer at the 3' end, de novo initiation of RNA synthesis is likely to be the mode of RNA replication in infected cells. In this study, we demonstrate that a recombinant HCV NS5B protein has the ability to initiate de novo RNA synthesis in vitro. The NS5B used HCV 3' X-tail RNA (98 nucleotides) as the template to synthesize an RNA product of monomer size, which can be labeled by ¿gamma-(32)Pnucleoside triphosphate. The de novo initiation activity was further confirmed by using small synthetic RNAs ending with dideoxynucleotides at the 3' termini. In addition, HCV NS5B preferred GTP as the initiation nucleotide. The optimal conditions for the de novo initiation activity have been determined. Identification and characterization of the de novo priming or initiation activity by HCV NS5B provides an opportunity to screen for inhibitors that specifically target the initiation step.
Monoclonal antibodies and peptide therapy in autoimmune diseases (1993)

Part 1 Basis for monoclonal antibody and peptide therapy: the nature of B- and T-cell determinants, Akio Ametani and Eli E. Sercarz molecular dissection of the T-cell receptor/CD3 complex, Bernard Malissen et al CD4, CD8 and other surface molecules regulating T-cell activation, Jean-Pierre Revillard and Nathalie Berard-Bonnefoy MHC proteins and MHC peptide interactions, Dominique J. Charron and Vincent Lotteau monoclonal antibodies for the therapeutic induction of tolerance, Herman Waldmann et al T-cell receptor-based immunointervention in autoimmune diseases - therapeutic use of monoclonal antibodies, Lucienne Chatenoud and Jean-Francois Bach. Part 2 Mechanisms of autoimmune diseases: the role of autoantigens in the driving of autoimmune diseases, Ivan M. Roitt T-cell receptors in autoimmune disease, Hans Acha-Orbea MHC and autoimmune diseases, Gerald T. Nepom. Part 3 T-cell receptor-based immunointervention in autoimmune diseases: anti-TcR antibodies in autoimmune diseases, Christian Boitard and Jean-Francois Bach anti-CD3 antibodies, Lucienne Chatenoud and Jean-Francois Bach anti-T-cell receptor V8 antibodies in autoimmunity, Hans Acha-Orbea vaccination with T-cell receptor peptides, Steven Brostoff. Part 4 Anti-CD4 antibodies: treatment of murine lupus with anti-CD4 monoclonal antibodies, David Wofsky anti-CD4 antibodies in diabetes, Judith A. Shizuru and C. Garrison Fathman from treatment of experimental allergic encephalomyelitis to clinical trials in multiple sclerosis, Lawrence Steinman et al human-murine chimeric CD4 monoclonal antibodies - a modern panacea for autoimmune disease, Gert Riethmuller et al CD4 antibody therapy in chronic inflammatory dermatological diseases, P. Morel et al. Part 5 Other monoclonal antibodies: anti-class II antibody treatment in autoimmune diseases, Christian Boitard interleukin-2 receptor-targeted immune therapy, T. Diamantstein and Hans Juergen Hahn anti-gamma interferon (IFN-gamma) monoclonal antibodies, Jean-Francois Bach. Part 6 Autoantigens: suppression of T-cell activation by administration of MHC class II-binding peptides, Luciano Adorini and Jean-Charles Guery autoantigenic peptide therapy in experimental autoimmune encephalomyelitis, David C. Wraith thyroglobulin as autoantigen and tolerogen, David C. Rayner et al prevention of myosin-induced autoimmune myocarditis with competitor peptides, Stacy C. Smith and Paul M. Allen. Part 7 Summary: summary of monoclonal antibody and peptide therapy, Jean-Francois Bach.
Variations in Cyclotide Expression in Viola Species (2004)

Cyclotides, a family of approximately 50 mini-proteins isolated from various Violaceae and Rubiaceae plants, are characterized by their circular peptide backbone and six conserved cysteine residues arranged in a cystine knot motif. Cyclotides show a wide range of biological activities, making them interesting targets for both pharmaceutical and agrochemical research, but little is known about their natural function and the events that trigger their expression. An investigation of the geographical and seasonal variations of cyclotide profiles has been performed, using the native Australian violet, Viola hederacea, and the Swedish sweet violet, Viola odorata, as model plants. The results showed that in the Australian violet the relative peptide levels of some cyclotides remained almost constant throughout the year, while other cyclotides were present only at certain times of the year. Therefore, it appears that V. hederacea expresses a basic armory of cyclotides as well as special "add-ons" whose levels are influenced by external factors. In the Swedish violet, cyclotide levels were increased up to 14 times during the warmest period of the year. The larger variation in expression levels of the Swedish plants may be a reflection of a greater climatic variation.
Neutralizing Human Fab Fragments against Measles Virus Recovered by Phage Display (2002)

Five human recombinant Fab fragments (Fabs) specific for measles virus (MV) proteins were isolated from three antibody phage display libraries generated from RNAs derived from bone marrow or splenic lymphocytes from three MV-immune individuals. All Fabs reacted in an enzyme-linked immunosorbent assay with MV antigens. In radioimmunoprecipitation assays two of the Fabs, MV12 and MT14, precipitated an approximately equal 80-kDa protein band corresponding to the hemagglutinin (H) protein from MV-infected Vero cell cultures, while two other Fabs, MT64 and GL29, precipitated an approximately equal 60-kDa protein corresponding the nucleocapsid (N) protein. In competition studies with MV fusion, H- and N protein-specific monoclonal antibodies (MAbs), the H-specific Fabs predominantly blocked the binding of H-specific MAbs, while the N-specific Fabs blocked MAbs to N. In addition, N-specific Fabs bound to denatured MV N protein in Western blotting. The specificity of the fifth Fab, MV4, could not be determined. By plaque reduction assays, three of the five Fabs, MV4, MV12, and MT14, exhibited neutralizing activity (80% cutoff) against MV (LEC-KI strain) at concentrations ranging between approximately 2 and 7 microg x ml(-1). Neutralization capacity against MV strains Edmonston and Schwarz was also detected, albeit at somewhat higher Fab concentrations. In conclusion, three neutralizing Fabs were isolated, two of them reactive against the H glycoprotein of MV and another reactive against an undefined epitope. This is the first study in which MV-neutralizing human recombinant Fab antibodies have been isolated from phage display libraries.
Use of human papillomavirus type 11 virions in an ELISA to detect specific antibodies in humans with condylomata acuminata (1991)

Human papillomavirus types 6 and 11 (HPV-6 and HPV-11) are the major aetiological agents of condylomata acuminata. Serological studies of this disease have been difficult to perform and interpret because native, type-specific antigens have not been available. In particular, since these viruses have not been propagated in vitro and sufficient quantities of virions are not present in lesions, virus particles have been difficult to obtain. In the present study, we used HPV-11 particles, obtained from human tumours produced in athymic mice, as antigen in an ELISA to compare antibody responses between 46 patients with biopsyproven condylomata acuminata and 44 controls. The median [interquartile range] of the absorbance values for the condylomata acuminata and the control groups were respectively 0.324 [0.183, 1.029] and 0.118 [0.047, 0.286] (P = 0.0001). Thirty-three per cent of the absorbance values in the condylomata acuminata group were higher than any of those of the control group. Sera from patients whose biopsies contained the papillomavirus common antigen were more reactive than sera from patients whose biopsies did not contain it (P = 0.0014). This study demonstrates the presence of specific antibodies directed at native HPV-11 viral particles in the sera of patients with condylomata acuminata, and describes a test which can be used in future serological studies of this common sexually transmitted disease.
Science and Statistics (1976)

Abstract Aspects of scientific method are discussed: In particular, its representation as a motivated iteration in which, in succession, practice confronts theory, and theory, practice. Rapid progress requires sufficient flexibility to profit from such confrontations, and the ability to devise parsimonious but effective models, to worry selectively about model inadequacies and to employ mathematics skillfully but appropriately. The development of statistical methods at Rothamsted Experimental Station by Sir Ronald Fisher is used to illustrate these themes.
Fundamental differences in the equilibrium considerations for siRNA and antisense oligodeoxynucleotide design (2008)

Both siRNA and antisense oligodeoxynucleotides (ODNs) inhibit the expression of a complementary gene. In this study, fundamental differences in the considerations for RNA interference and antisense ODNs are reported. In siRNA and antisense ODN databases, positive correlations are observed between the cost to open the mRNA target self-structure and the stability of the duplex to be formed, meaning the sites along the mRNA target with highest potential to form strong duplexes with antisense strands also have the greatest tendency to be involved in pre-existing structure. Efficient siRNA have less stable siRNA-target duplex stability than inefficient siRNA, but the opposite is true for antisense ODNs. It is, therefore, more difficult to avoid target self-structure in antisense ODN design. Self-structure stabilities of oligonucleotide and target correlate to the silencing efficacy of siRNA. Oligonucleotide self-structure correlations to efficacy of antisense ODNs, conversely, are insignificant. Furthermore, self-structure in the target appears to correlate with antisense ODN efficacy, but such that more effective antisense ODNs appear to target mRNA regions with greater self-structure. Therefore, different criteria are suggested for the design of efficient siRNA and antisense ODNs and the design of antisense ODNs is more challenging.
In-Cell NMR Study of Tau and MARK2 Phosphorylated Tau (2018)

The intrinsically disordered protein, Tau, is abundant in neurons and contributes to the regulation of the microtubule (MT) and actin network, while its intracellular abnormal aggregation is closely associated with Alzheimer's disease. Here, using in-cell Nuclear Magnetic Resonance (NMR) spectroscopy, we investigated the conformations of two different isoforms of Tau, Tau40 and k19, in mammalian cells. Combined with immunofluorescence imaging and western blot analyses, we found that the isotope-enriched Tau, which was delivered into the cultured mammalian cells by electroporation, is partially colocalized with MT and actin filaments (F-actin). We acquired the NMR spectrum of Tau in human embryonic kidney 293 (HEK-293T) cells, and compared it with the NMR spectra of Tau added with MT, F-actin, and a variety of crowding agents, respectively. We found that the NMR spectrum of Tau in complex with MT best recapitulates the in-cell NMR spectrum of Tau, suggesting that Tau predominantly binds to MT at its MT-binding repeats in HEK-293T cells. Moreover, we found that disease-associated phosphorylation of Tau was immediately eliminated once phosphorylated Tau was delivered into HEK-293T cells, implying a potential cellular protection mechanism under stressful conditions. Collectively, the results of our study reveal that Tau utilizes its MT-binding repeats to bind MT in mammalian cells and highlight the potential of using in-cell NMR to study protein structures at the residue level in mammalian cells.
Localizing in unstructured environments: dealing with the errors (1994)

A robot navigating in an unstructured outdoor environment must determine its own location in spite of problems due to environmental conditions, sensor limitations and map inaccuracies, exact measurements are seldom known, and the combination of approximate measures can lead to large errors in self-localization. The conventional approach to this problem has been to deal with the errors either during processing or after they occur. The authors maintain that it is possible to limit the errors before they occur. The authors analyze how measurement errors affect errors in localization and propose that a simple algorithm can be used to exploit the geometric properties of landmarks in the environment in order to decrease errors in localization. The authors' goal is to choose landmarks that will provide the best localization regardless of measurement error, determine the best areas in which to identify new landmarks to be used for further localization and choose paths that will provide the least chance of "straying". The authors show the result of implementing this concept in experiments run in simulation with USGS 30 m DEM data for a robot statically locating, following a path and identifying new landmarks.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>