gebhart/patrepeval huggingface dataset:
Comparative in Vitro Studies on Native and Recombinant Human Cationic Trypsins (2001)

Hereditary pancreatitis, an autosomal dominant disease is believed to be caused by mutation in the human trypsinogen gene. The role of mutations has been investigated by in vitro studies using recombinant rat and human trypsinogen (TG). In this study we compare the enzymatic properties and inhibition by human pancreatic secretory trypsin inhibitor (hPSTI) of the native, postsynthetically modified and recombinant cationic trypsin, and found these values practically identical. We also determined the autolytic stability of recombinant wild type (Hu1Asn21) and pancreatitis-associated (Hu1Ile21) trypsin. Both forms were equally stable. Similarly, we found no difference in the rate of activation of the two zymogens by human cationic and anionic trypsin. Mesotrypsin did not activate either form. The rate of autocatalytic activation of Hu1Asn21 TG and Hu1Ile21 TG was also identical at pH 8 both in the presence and absence of Ca2+. At pH 5 Hu1Ile21 TG autoactivated about twice as fast as Hu1Asn21 TG. The presence of physiological amount of hPSTI completely prevented autoactivation of both zymogens at pH 8 and at pH 5 as well. Cathepsin B readily activated both zymogens although Hu1Ile21 TG was activated about 2.5-3 times as fast as Hu1Asn21 TG. The presence of hPSTI did not prevent the activation of zymogens by cathepsin B. Our results underlie the central role of cathepsin B in the development of different forms of pancreatitis.
Generation of class I MHC-restricted T-T hybridomas. (1990)

In this report we describe a system for the generation of functional, class I MHC-restricted, T-T hybridomas. The BW5147 cell line was transfected with the CD8 gene. BW5147 transfectants were obtained that stably expressed CD8 and this expression was maintained after somatic cell hybridization with activated T lymphocytes. To determine whether the stable expression of CD8 would facilitate the generation of class I MHC-specific T-T hybridomas, the transfected cells were fused with alloreactive T cells and the resultant hybrids were screened for their ability to produce lymphokines in response to antigenic stimulation. Somatic cell hybridizations with BW5147-CD8 transfectants give rise to a much higher frequency of class I MHC-specific T-T hybridomas relative to parallel fusions with BW5147. To determine whether the BW5147-CD8 transfectants would also support the generation of Ag-specific, class I MHC-restricted T-T hybridomas, they were fused with OVA-specific CTL. Several T-T hybrid clones were identified that produced lymphokines after stimulation with a transfected APC that was synthesizing OVA, or with a tryptic digest of OVA in the presence of syngeneic APC. The stimulation by Ag was MHC-restricted and mapped to the Kb molecule. An anti-CD8 mAb inhibited the stimulation of these hybridomas by Ag plus APC, whereas their stimulation by mitogen was unaffected. Cytolytic activity was not detected when several of the OVA-specific or alloreactive hybridomas were tested for their ability to kill target cells bearing the appropriate Ag. These results demonstrate that the BW5147-CD8 transfectants allow the generation of class I MHC-restricted T-T hybridomas. The potential utility of this system is discussed.
Synchronization in Virtual Realities (1992)

Interactive graphics, and especially virtual reality systems, require synchronization of sight, sound, and user motion if they are to be convincing and natural. We present a solution to the synchronization problem that is based on optimal estimation methods.
Cardiolipin Is Essential for Organization of Complexes III and IV into a Supercomplex in Intact Yeast Mitochondria (2005)

Digitonin extracts of mitochondria from cardiolipin-containing (wild type) and cardiolipin-lacking (crd1Delta mutant) Saccharomyces cerevisiae subjected to colorless native polyacrylamide gel electrophoresis in the presence of 0.003% digitonin displayed a supercomplex composed of homodimers of complexes III and IV in the former case but only the individual homodimers in the latter case. To avoid treatment with any detergent or dye, we compared organization of the respiratory chain in intact mitochondria from wild type and cardiolipin-lacking cells by using a functional analysis developed previously for the study of the organization of the respiratory chain of S. cerevisiae (Boumans, H., Grivell, L. A., and Berden, J. A. (1998) J. Biol. Chem. 273, 4872-4877). Dependence of the kinetics of NADH oxidation via complexes III, IV, and cytochrome c on the concentration of the complex III-specific inhibitor antimycin A was studied. A linear relationship between respiratory activity and saturation of complex III with antimycin A was obtained for wild type mitochondria consistent with single functional unit kinetics of the respiratory chain. Under the same conditions, cardiolipin-lacking mitochondria displayed a hyperbolic relationship indicating cytochrome c pool behavior. No release of cytochrome c from cardiolipin-lacking mitochondria or mitoplasts under our standard experimental conditions was detected. Identical cytochrome c pool behavior was observed for both wild type and cardiolipin-lacking mitochondria in the presence of a chaotropic agent, which disrupts the interaction between respiratory complexes. The results demonstrate that cardiolipin is essential for association of complexes III and IV into a supercomplex in intact yeast mitochondria.
A low-gate-leakage-current GaAs MESFET with a thin epitaxial silicon layer (1991)

An n-channel depletion-mode GaAs MESFET with an Al gate and a 6-A epitaxial Si layer between the metal and the GaAs, grown in situ by molecular beam epitaxy, is described. Its DC electrical characteristics are compared with a similar control structure grown without the Si layer. The gate leakage current in the Al/Si/GaAs MESFETs was three to four orders of magnitude lower than in the control structure, due to all increased barrier height in the Al/Si/n-GaAs Schottky gate of 1.04 eV, versus 0.78 eV for the Al/n-GaAs structure. The differences in threshold voltages, I-V characteristics, and transconductances between the two devices are consistent with an enhanced effective barrier height for the Al/Si/GaAs MESFET.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Crystal Structure of Protein Farnesyltransferase at 2.25 Angstrom Resolution (1997)

Protein farnesyltransferase (FTase) catalyzes the carboxyl-terminal lipidation of Ras and several other cellular signal transduction proteins. The essential nature of this modification for proper function of these proteins has led to the emergence of FTase as a target for the development of new anticancer therapy. Inhibition of this enzyme suppresses the transformed phenotype in cultured cells and causes tumor regression in animal models. The crystal structure of heterodimeric mammalian FTase was determined at 2.25 angstrom resolution. The structure shows a combination of two unusual domains: a crescent-shaped seven-helical hairpin domain and an alpha-alpha barrel domain. The active site is formed by two clefts that intersect at a bound zinc ion. One cleft contains a nine-residue peptide that may mimic the binding of the Ras substrate; the other cleft is lined with highly conserved aromatic residues appropriate for binding the farnesyl isoprenoid with required specificity.
Inactivation of enveloped virus by laser-driven protein aggregation (2012)

Ultrafast lasers in the visible and near-infrared range have emerged as a potential new method for pathogen reduction of blood products and pharmaceuticals. However, the mechanism of enveloped virus inactivation by this method is unknown. We report the inactivation as well as the molecular and structural effects caused by visible (425 nm) femtosecond laser irradiation on murine cytomegalovirus (MCMV), an enveloped, double-stranded DNA virus. Our results show that laser irradiation (1) caused a 5-log reduction in MCMV titer, (2) did not cause significant changes to the global structure of MCMV virions including membrane and capsid, as assessed by electron microscopy, (3) produced no evidence of double-strand breaks or crosslinking in MCMV genomic DNA, and (4) caused selective aggregation of viral capsid and tegument proteins. We propose a model in which ultrafast laser irradiation induces partial unfolding of viral proteins by disrupting hydrogen bonds and/or hydrophobic interactions, leading to aggregation of closely associated viral proteins and inactivation of the virus. These results provide new insight into the inactivation of enveloped viruses by visible femtosecond lasers at the molecular level, and help pave the way for the development of a new ultrafast laser technology for pathogen reduction.
Testosterone Receptor Blockade After Hemorrhage in Males (1997)

The findings that flutamide not only markedly improves the depressed immune functions but also the survival of animals after hemorrhage and the induction of sepsis suggest that the short-term administration of androgen receptor blocker in males after trauma represents a safe and novel approach for preventing immune deficiency and decreasing the mortality rate from subsequent sepsis.
Identification of Internalizing Human Single-Chain Antibodies Targeting Brain Tumor Sphere Cells (2010)

Glioblastoma multiforme (GBM) is the most common and aggressive form of primary brain tumor for which there is no curative treatment to date. Resistance to conventional therapies and tumor recurrence pose major challenges to treatment and management of this disease, and therefore new therapeutic strategies need to be developed. Previous studies by other investigators have shown that a subpopulation of GBM cells can grow as neurosphere-like cells when cultured in restrictive medium and exhibits enhanced tumor-initiating ability and resistance to therapy. We report here the identification of internalizing human single-chain antibodies (scFv) targeting GBM tumor sphere cells. We selected a large naive phage antibody display library on the glycosylation-dependent CD133 epitope-positive subpopulation of GBM cells grown as tumor spheres and identified internalizing scFvs that target tumor sphere cells broadly, as well as scFvs that target the CD133-positive subpopulation. These scFvs were found to be efficiently internalized by GBM tumor sphere cells. One scFv GC4 inhibited self-renewal of GBM tumor sphere cells in vitro. We have further developed a full-length human IgG1 based on this scFv, and found that it potently inhibits proliferation of GBM tumor sphere cells and GBM cells grown in regular nonselective medium. Taken together, these results show that internalizing human scFvs targeting brain tumor sphere cells can be readily identified from a phage antibody display library, which could be useful for further development of novel therapies that target subpopulations of GBM cells to combat recurrence and resistance to treatment.
Solution Phase Synthesis of Glu-Abu(P)-Leu by Using Z-Abu(PO3Et2)-OH (1992)

This paper describes the synthesis of the 2-amino-4-(phosphono)butanoyl-containing peptide H-Glu-Abu(P)-Leu-OH.CF3CO2H by the use of Z-Abu(PO3Et2)-OH for the solution phase synthesis of Boc-Glu(Obut)-Abu(PO3Et2)-Leu-Obut (mixed-anhydride method) followed by acidolytic cleavage of the t-butyl groups, and final removal of the ethyl groups from Glu- Abu(PO3Et2)-Leu by treatment with 10% bromotrimethylsilane in acetonitrile. Although silylitic cleavage of the peptide was facile, the slow dissolution of the peptide in the reaction solvent suggests that deprotection of the Abu(PO3.Et2) residue has not yet been optimized.
Neutral Amino Acid Transport Characterization of Isolated Luminal and Abluminal Membranes of the Blood-Brain Barrier (1995)

The neutral amino acid carrier composition of luminal and abluminal membranes of the blood-brain barrier has been studied using isolated membrane vesicles. Phenylalanine was carried almost exclusively by a high affinity (Km = 10 +/- 2 microM), Na(+)-independent amino acid transport system, presumably L1 system, that was found to be symmetrically distributed between luminal and abluminal membranes. Inhibition of phenylalanine uptake was used to determine the affinities (Ki values) toward leucine (17 +/- 3 microM), tryptophan (8 +/- 1), 2-aminobicyclo(2,2,1)-heptane-2-carboxylic acid (BCH) (11 +/- 2), alanine (628 +/- 117), and glutamine (228 +/- 51). Alanine was found to be transported by two Na(+)-dependent transport systems that were located exclusively on the abluminal membrane. Kinetic and inhibition experiments indicated that one of these activities was due to system A, which is probably the main route for Na(+)-dependent alanine transport (Km = 0.6 +/- 0.2 mM) under physiological conditions. The other Na(+)-dependent activity was attributed to a B(o,+)-like system based on its sensitivity toward BCH. This latter system showed greater affinity for large neutral amino acids. The affinities of these two transport systems for several other amino acids were also studied.
Biochemical and genetic characterization of multiple splice variants of the Flt3 ligand (1996)

We have performed a comprehensive analysis of cell lines and tissues to compare and contrast the expression patterns of Flt3 ligand (FL), c-Kit ligand (KL), and macrophage colony-stimulating factor as well as their receptors, Flt3, c-Kit, and c-Fms. The message for FL is unusually ubiquitous, whereas that of its receptor is quite restricted, apparently limiting the function of the ligand to fetal development and early hematopoiesis. We have also sequenced a mouse FL genomic clone, revealing how the three splice variant FL mRNAs that we have isolated arise. The chromosomal location of the FL gene has been mapped, by in situ hybridization, to chromosome 7 in mouse and chromosome 19 in human. Natural FL protein has been purified from a stromal cell line and shown to be a 65 kD nondisulfide-linked homodimeric glycoprotein comprised of 30 kD subunits, each containing 12 kD of N- and O-linked sugars. Pulse-chase experiments show that one of the splice variants (T110) is responsible for producing the bulk of soluble FL, but only after it has first been expressed at the cell surface as a membrane-bound form. The other splice-variant forms produce molecules that are either obligatorily soluble (T169) or membrane-bound but released only very slowly (T118). Finally, even though most cell lines express some amount of FL mRNA, we found that very little FL protein is actually made, with T cells and stromal cells being the major producers. The data suggests that FL plays its roles over very short distances, perhaps requiring cell-cell contact.
Development of a vaccine of cross-linked heat-stable and heat-labile enterotoxins that protects against Escherichia coli producing either enterotoxin (1982)

A vaccine of cross-linked heat-stable (ST) and heat-labile (LT) toxins that protects against heterologous serotypes of strains of Escherichia coli which produce either the LT or ST enterotoxin was developed by conjugating ST to LT by the carbodiimide reaction. Three interrelated factors were found to affect the composition and properties of the final conjugate: (i) the amount of carbodiimide added to the toxins, (ii) the initial ratio of ST to LT, and (iii) the duration of the conjugation reaction. Optimal conjugation conditions were identified as a carbodiimide-to-toxin ratio of 10:1 by weight, an initial molar ratio of ST to LT of 100:1, and a conjugation reaction time of 96 h. This approach yielded a conjugate that contained 96% by moles and 36% by weight pure ST, determined with radioiodinated pure ST, and 34% by weight semi-pure ST, determined by the Lowry protein method. The retained antigenicities of the conjugated toxins, as determined by enzyme-linked immunosorbent assays, was greater than or equal to 82%, and their toxicities, as determined by the Y1 adrenal cell assay for LT and by the suckling mouse assay for ST, were reduced to less than or equal to 0.15%. Immunization of rats with this cross-linked ST-LT vaccine provided strong protection against challenge with either the LT or the ST toxin or with viable heterologous strains which produce these toxins, either singly or together. These observations indicate that conjugation of ST to LT results in a unique new immunogen in that ST acquires immunogenicity as a function of the reaction, LT retains most of its antigenicity, and the toxic properties of each individual toxin are greatly reduced.
Incorporation of 2‘-Deoxy-2‘-mercaptocytidine into Oligonucleotides via Phosphoramidite Chemistry (1997)

ADVERTISEMENT RETURN TO ISSUEPREVNoteIncorporation of 2'-Deoxy-2'-mercaptocytidine into Oligonucleotides via Phosphoramidite ChemistryMichelle L. Hamm and Joseph A. PiccirilliView Author Information Howard Hughes Medical Institute, Department of Biochemistry and Molecular Biology, and Department of Chemistry, The University of Chicago, 5841 South Maryland Avenue, Room N104, Chicago, Illinois 60637 Cite this: J. Org. Chem. 1997, 62, 10, 3415–3420Publication Date (Web):May 16, 1997Publication History Received17 January 1997Published online16 May 1997Published inissue 1 May 1997https://doi.org/10.1021/jo970096oCopyright © 1997 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views385Altmetric-Citations24LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit Read OnlinePDF (265 KB) Get e-AlertsSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Anions,Biopolymers,Disulfides,Reaction products,Silver Get e-Alerts
Template-based modeling and free modeling by I-TASSER in CASP7 (2007)

We developed and tested the I-TASSER protein structure prediction algorithm in the CASP7 experiment, where targets are first threaded through the PDB library and continuous fragments in the threading alignments are exploited to assemble the global structure. The final models are obtained from the progressive refinements started from the last round structure clusters. A majority of the targets in the template-based modeling (TBM) category have the templates drawn closer to the native structure by more than 1 A within the aligned regions. For the free-modeling (FM) targets, I-TASSER builds correct topology for 7/19 cases with sequence up to 155 residues long. For the first time, the automated server prediction generates models as good as the human-expert does in all the categories, which shows the robustness of the method and the potential of the application to genome-wide structure prediction. Despite the success, the accuracy of I-TASSER modeling is still dominated by the similarity of the template and target structures with a strong correlation coefficient ( approximately 0.9) between the root-mean-squared deviation (RMSD) to native of the templates and the final models. Especially, there is no high-resolution model below 2 A for the FM targets. These problems highlight the issues that need to be addressed in the next generation of atomic-level I-TASSER development especially for the FM target modeling.
A CMOS multichannel electrical stimulation prototype system (2011)

SUMMARY We developed an inductively powered integrated electronic prosthesis, allowing for the trade‐offs among implant functionality, circuit complexity, power consumption, hardware cost, and integrity of data recovery, for a multichannel microstimulation circuitry. The proposed prosthesis features energy efficiency and is capable of up to 40 scan/s with 240 stimulus channels in mode I and three times resolution at the same scan rate in mode II under a carrier frequency of 2 MHz. In order to satisfy future upgrade demands, the prototype has been constructed with a 16‐channel‐based stimulation scheme so that the spatial resolution of the design can be extended toward various experimental purposes. The circuit techniques used in the system are detailed. Results from fabricated chips using a 0.18‐µm CMOS process are given as proof of concept. Copyright © 2011 John Wiley &amp; Sons, Ltd.
Efficient SNP analysis enabled by joint application of the muTGGE and heteroduplex methods. (2005)

Gene science-based diagnoses have become an increasingly realistic option as the state of knowledge has improved regarding the genetic basis of disease. To facilitate the creation of this potential diagnostic tool, researchers have made large-scale detection of point mutations a key issue. Here, we propose an inexpensive and convenient method with a high performance level for this purpose: micro temperature gradient gel electrophoresis (muTGGE)-empowered heteroduplex analysis (muTG-HD). First, muTGGE was shown to separate double-stranded DNA containing single nucleotide polymorphism (SNP) with sufficiently high resolution when used in the mode of perpendicular TGGE. Using human c-Ki-ras and rat p53 DNA, point mutations could be unequivocally detected by muTG-HD when parallel TGGE was employed. The mutation type (such as G/C to A/T), the position of the point mutation (centre or not) and the DNA size (around 100 or 200 bp) were examined and found to be detectable. Thus, muTG-HD could detect point mutations efficiently at a much lower cost by having multiple lanes per gel.
Advanced SVC control for damping power system oscillations (1991)

A new SVC (static VAR compensation) control for damping of power system oscillations has been developed. To increase system damping an SVC uses a phase angle signal estimated from the measurement of voltage and power at the SVC location. By means of an optimization and identification procedure, optimized design of the damping control with various control concepts can be determined, taking into account nonlinear power systems. As a result of this method it is possible to increase power system damping considerably, in particular in critical situations close to the stability limit, using only locally measured state variables at the SVC, thus leading to an increase in the transmission capability of the power system.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>