gebhart/patrepeval huggingface dataset:
Genetic Analysis of the Chlamydomonas reinhadtii I-CreI Mobile Intron Homing System in Escherichia coli (1997)

We have developed and used a genetic selection system in Escherichia coli to study functional requirements for homing site recognition and cleavage by a representative eukaryotic mobile intron endonuclease. The homing endonuclease, I-CreI, was originally isolated from the chloroplast of the unicellular green alga Chlamydomonas reinhardtii. I-CreI homing site mutants contained base pair substitutions or single base deletions that altered the rate of homing site cleavage and/or product release. I-CreI endonuclease mutants fell into six phenotypic classes that differed in in vivo activity, toxicity or genetic dominance. Inactivating mutations clustered in the N-terminal 60% of the I-CreI amino acid sequence, and two frameshift mutations were isolated that resulted in premature translation termination though retained partial activity. These mutations indicate that the N-terminal two-thirds of the I-CreI endonuclease is sufficient for homing site recognition and cleavage. Substitution mutations altered in four potential active site residues were examined: D20N, Q47H or R70A substitutions inactivated endonuclease activity, whereas S22A did not. The genetic approach we have taken complements phylogenetic and structural studies of mobile intron endonucleases and has provided new information on the mechanistic basis of I-CreI homing site recognition and cleavage.
System Identification: Theory for the User (1987)

Das Buch behandelt die Systemidentifizierung in dem theoretischen Bereich, der direkte Auswirkungen auf Verstaendnis und praktische Anwendung der verschiedenen Verfahren zur Identifizierung hat. Da ...
Structure and Photocatalytic Activity of Ti1-xMxO2±δ (M = W, V, Ce, Zr, Fe, and Cu) Synthesized by Solution Combustion Method (2004)

The W, V, Ce, Zr, Fe, and Cu metal ion substituted nanocrystalline anatase TiO2 was prepared by solution combustion method and characterized by XRD, Raman, BET, EPR, XPS, IR TGA, UV absorption, and photoluminescence measurements. The structural studies indicate that the solid solution formation was limited to a narrow range of concentrations of the dopant ions. The photocatalytic degradation of 4-nitrophenol under UV and solar exposure was investigated with Ti1-xMxO2±δ. The degradation rates of 4-nitrophenol with these catalysts were lesser than the degradation rates of 4-nitrophenol with undoped TiO2 both with UV exposure and solar radiation. However, the photocatalytic activities of most metal ion doped TiO2 are higher than the activity of the commercial TiO2, Degussa P25. The decrease in photocatalytic activity is correlated with decrease in photoluminescence due to electron states of metal ions within the band gap of TiO2.
Targeting tumor-associated fibroblasts improves cancer chemotherapy by increasing intratumoral drug uptake (2006)

Tumor-associated fibroblasts are key regulators of tumorigenesis. In contrast to tumor cells, which are genetically unstable and mutate frequently, the presence of genetically more stable fibroblasts in the tumor-stromal compartment makes them an optimal target for cancer immunotherapy. These cells are also the primary source of collagen type I, which contributes to decreased chemotherapeutic drug uptake in tumors and plays a significant role in regulating tumor sensitivity to a variety of chemotherapies. To specifically kill tumor-associated fibroblasts, we constructed an oral DNA vaccine targeting fibroblast activation protein (FAP), which is specifically overexpressed by fibroblasts in the tumor stroma. Through CD8+ T cell-mediated killing of tumor-associated fibroblasts, our vaccine successfully suppressed primary tumor cell growth and metastasis of multidrug-resistant murine colon and breast carcinoma. Furthermore, tumor tissue of FAP-vaccinated mice revealed markedly decreased collagen type I expression and up to 70% greater uptake of chemotherapeutic drugs. Most importantly, pFap-vaccinated mice treated with chemotherapy showed a 3-fold prolongation in lifespan and marked suppression of tumor growth, with 50% of the animals completely rejecting a tumor cell challenge. This strategy opens a new venue for the combination of immuno- and chemotherapies.
Heat-shock proteins as powerful weapons in vaccine development (2008)

Heat-shock proteins (HSPs) have been known as multifunctional proteins. They facilitate the folding and unfolding of proteins, participate in vesicular transport processes, prevent protein aggregation in the densely packed cytosol and are involved in signaling processes. HSPs have been involved in different fields, including autoimmunity, immunity to infections and tumor immunology. Although there are many different kinds of HSPs, only some HSPs, including HSP70 and Gp96, have immunological properties. HSP molecules have been applied into DNA- or protein (peptide)-based vaccines as antigens, chaperones or adjuvants. HSP-based vaccines have been shown to immunize against cancer and infectious diseases in both prophylactic and therapeutic protocols. The immunogenicity of HSPs results from two different properties: a peptide-dependent capacity to chaperone and elicit adaptive cytotoxic T-lymphocyte responses against antigenic peptides and a peptide-independent immunomodulatory capacity. Furthermore, HSPs could be immunoregulatory agents with potent and widely applicable therapeutic uses. Accordingly, certain HSPs, such as HSP70 and Gp96, are highly effective carrier molecules for cross-presentation. Their ability in eliciting immune responses against different pathogens (parasite and virus) and their role in cancer immunity will be discussed in this review.
Structural and Functional Characterization of Tick Anticoagulant Peptide (TAP): A Potent and Selective Inhibitor of Blood Coagulation Factor Xa (1993)

The discovery of rTAP has provided a wealth of important scientific information ranging from the structural and kinetic characterization of a novel serine protease inhibitor to the importance of factor Xa in the thrombotic process. The results obtained with this inhibitor thus far have broadened our understanding of hemostasis and thrombosis and ultimately may result in the development of newer and more efficient therapeutic agents to combat one of the leading causes of morbidity and mortality in man today.
Lessons Learnt From Root Cause Analysis of Gulf of Mexico Oil Spill 2010 (2012)

Abstract Root cause analysis (RCA) is a class of problem solving methods aimed at identifying the root causes of problems/ incidents. By directing corrective measures at core causes, it is hoped that the chances of problem recurrence will be minimized. Thus, RCA is frequently considered to be an iterative process, and is frequently viewed as a tool of continuous improvement. RCA, initially is a reactive method of problem detection &amp; solving. This means that, the analysis is done after an incident has occurred. By gaining proficiency in RCA it becomes a pro-active method. This means that RCA is able to estimate the possibility of an incident even before it could occur. Root cause analysis mainly consists of three steps A): Define the problem. B): Analyze the problem. C): Find the solutions for the problem. In view of the accident which took place recently i.e. Gulf of Mexico oil spill 2010, there were eight catastrophic failures which led to the explosion that destroyed the Deepwater Horizon drilling rig in the Gulf of Mexico. These failures included the sending of unofficial cement by specialist cementing services, no indications of testing done on the surface by drilling rig provider company before deploying it, pressure test which would have revealed problems in the drill was incorrectly deemed as a success by operator company and drilling rig provider company rig personnel. A complex and interlinked succession of mechanical failures, human judgments, engineering design, operational implementation and team interfaces caused this tragedy. Consequences of these plain errors were quite hazardous. It affected the humanity, environment, economy and also the settlements. The core objective of the paper is to bring about a detailed analysis so as to throw light on new techniques and how they can be utilised to prevent such disasters. To achieve this objective we acknowledged all the possible solutions for this issue so that the most excellent solutions can be selected and the challenges that are to be faced are studied thoroughly and examined to prevent future errors. However, it is recognized that complete prevention of reappearance by a single intrusion is not always possible. On the belief that problems are best solved by attempting to correct or eliminate root causes, as opposed to merely addressing the immediately obvious symptoms.
A Reflection Based, Pulsed THz Imaging System with 1 mm Spatial Resolution (2007)

Operating in reflection and using single pixel, whiskbroom scanning to generate images, we report on a THz imaging system with a spatial resolution of 1 mm and a post detection SNR of 67 dB. The source in the system is an ErAs:GaAs photoconductive switch, , and the detector is a waveguide mounted, zero-bias Schottky diode operating at a center frequency of 600 GHz and a 3 dB bandwidth of 200 GHz. The high output power of the photoconductive switch and large instantaneous bandwidth of both switch and detector allow the system to achieve this high post detection SNR in a 60 Hz bandwidth when reflecting off a specular metal target at a standoff of 4 cm. The spatial resolution is superior to that predicted by the standard Rayleigh criterion as expected from the systems' Gaussian (non uniform) illumination, but is inferior to the Sparrow Criterion due to the presence of system noise, and discrete rounding of sample amplitudes.
Rituximab in the treatment of autoimmune haematological disorders (2008)

Current treatment regimens for haematological autoimmune diseases are relatively non-selective and are often associated with considerable toxicity. Recently, it has become clear that B cells play a key role in both the development and perpetuation of autoimmunity, suggesting that B-cell depletion could be a valuable treatment approach for patients with autoimmune diseases. This article reviews data supporting the use of rituximab--an anti-CD20 monoclonal antibody that specifically depletes B cells--in four key autoimmune haematological disorders: idiopathic thrombocytopenic purpura (ITP); autoimmune haemolytic anaemia (AIHA); acquired haemophilia; and thrombotic thrombocytopenic purpura (TTP). Although treatment of ITP, AIHA, acquired haemophilia and TTP with rituximab is still relatively uncommon, results from case series and small phase II trials indicate that patients of all ages can respond to rituximab, irrespective of the number or type of prior treatments that they have received. Moreover, patients with these diseases receiving rituximab experienced predominantly mild adverse events, with only a few serious adverse events reported. These data suggest that rituximab provides an effective and well-tolerated alternative treatment option for patients with ITP, AIHA, acquired haemophilia and TTP, many of whom have limited treatment choices.
Noninvasive evaluation of oral lesions using depth‐sensitive optical spectroscopy (2009)

The ability to selectively target epithelial and shallow stromal depth regions appeared to be diagnostically useful. For nonkeratinized oral sites, the sensitivity and specificity of this objective diagnostic technique were comparable to that of clinical diagnosis by expert observers. Thus, DSOS has potential to augment oral cancer screening efforts in community settings.
Prediction of Distribution Coefficient from Structure. 1. Estimation Method (1997)

A method has been developed for the estimation of the distribution coefficient (D), which considers the microspecies of a compound. D is calculated from the microscopic dissociation constants (microconstants), the partition coefficients of the microspecies, and the counterion concentration. A general equation for the calculation of D at a given pH is presented. The microconstants are calculated from the structure using Hammett and Taft equations. The partition coefficients of the ionic microspecies are predicted by empirical equations using the dissociation constants and the partition coefficient of the uncharged species, which are estimated from the structure by a Linear Free Energy Relationship method. The algorithm is implemented in a program module called PrologD.
Recombinase‐mediated Gene Stacking as a Transformation Operating SystemF (2011)

The current method for combining transgenes into a genome is through the assortment of independent loci, a classical operating system compatible with transgenic traits created by different developers, at different times and/or through different transformation techniques. However, as the number of transgenic loci increases over time, increasingly larger populations are needed to find the rare individual with the desired assortment of transgenic loci along with the non-transgenic elite traits. Introducing a transgene directly into a field cultivar would bypass the need to introgress the engineered trait. However, this necessitates separate transformations into numerous field cultivars, along with the characterization and regulatory approval of each independent transformation event. Reducing the number of segregating transgenic loci could be achieved if multiple traits are introduced at the same time, a preferred option if each of the many traits is new or requires re-engineering. If re-engineering of previously introduced traits is not needed, then appending a new trait to an existing locus would be a rational strategy. The insertion of new DNA at a known locus can be accomplished by site-specific integration, through a host-dependent homology-based process, or a heterologous site-specific recombination system. Here, we discuss gene stacking through the use of site-specific recombinases.
Trap densities in amorphous-InGaZnO4 thin-film transistors (2008)

Trap densities in amorphous-InGaZnO4 (α-IGZO) are extracted directly from the capacitance-voltage characteristics of thin-film transistors at low frequencies. It is found that the trap densities are flat in the energy gap, and are 1.7×1016cm−3eV−1 in the deep energy far from the conduction band edge (Ec), but become larger near Ec. Moreover, postannealing reduces the trap density near Ec, which is associated with the reduction of the hysteresis in the current-voltage characteristics. The annealed α-IGZO does not have a Gaussian-type state and has fewer tail states than amorphous Si.
Fusion of multiple clues for photo-attack detection in face recognition systems (2011)

We faced the problem of detecting 2-D face spoofing attacks performed by placing a printed photo of a real user in front of the camera. For this type of attack it is not possible to relay just on the face movements as a clue of vitality because the attacker can easily simulate such a case, and also because real users often show a “low vitality” during the authentication session. In this paper, we perform both video and static analysis in order to employ complementary information about motion, texture and liveness and consequently to obtain a more robust classification.
Distinct Roles for Mammalian Target of Rapamycin Complexes in the Fibroblast Response to Transforming Growth Factor-β (2008)

Transforming growth factor-beta (TGF-beta) promotes a multitude of diverse biological processes, including growth arrest of epithelial cells and proliferation of fibroblasts. Although the TGF-beta signaling pathways that promote inhibition of epithelial cell growth are well characterized, less is known about the mechanisms mediating the positive response to this growth factor. Given that TGF-beta has been shown to promote fibrotic diseases and desmoplasia, identifying the fibroblast-specific TGF-beta signaling pathways is critical. Here, we investigate the role of mammalian target of rapamycin (mTOR), a known effector of phosphatidylinositol 3-kinase (PI3K) and promoter of cell growth, in the fibroblast response to TGF-beta. We show that TGF-beta activates mTOR complex 1 (mTORC1) in fibroblasts but not epithelial cells via a PI3K-Akt-TSC2-dependent pathway. Rapamycin, the pharmacologic inhibitor of mTOR, prevents TGF-beta-mediated anchorage-independent growth without affecting TGF-beta transcriptional responses or extracellular matrix protein induction. In addition to mTORC1, we also examined the role of mTORC2 in TGF-beta action. mTORC2 promotes TGF-beta-induced morphologic transformation and is required for TGF-beta-induced Akt S473 phosphorylation but not mTORC1 activation. Interestingly, both mTOR complexes are necessary for TGF-beta-mediated growth in soft agar. These results define distinct and overlapping roles for mTORC1 and mTORC2 in the fibroblast response to TGF-beta and suggest that inhibitors of mTOR signaling may be useful in treating fibrotic processes, such as desmoplasia.
Neurotrophin Receptor-Based Strategies for Alzheimers Disease (2005)

The traditional perspective of applying neurotrophins in the context of Alzheimer's disease is based on the premise that neurotrophins are capable of upregulating cholinergic function and of rendering neurons less vulnerable to certain processes causing degeneration. Factors limiting the therapeutic application of neurotrophin proteins include their poor pharmacological properties and their pleiotropic effects mediated by interaction with Trk, p75NTR and sortilin receptors. Recent studies suggesting and that pro-forms of neurotrophins accumulating in Alzheimer's and other pathological states cause cell death, that p75NTR modulates amyloid beta- and injury-induced neurodegeneration and that small molecules can be created that bind specifically to individual neurotrophin receptors point to novel strategies by which neurotrophin receptors might be targeted in Alzheimer's and other neuropathological states.
Gene Transfer to Plants: Assessment of Published Approaches and Results (1991)

Crop loss due to soil salinization is an increasing threat to agriculture worldwide. This review provides an overview of cellular and physiological mechanisms in plant responses to salt. We place cellular responses in a time- and tissue-dependent context ...Read More
Peptides related to the antigenic determinant block T cell recognition of the native protein as processed by antigen‐presenting cells (1986)

A mouse T cell hybrid specific for pigeon cytochrome c in the context of I-Ek responds by secreting interleukin 2 when co-cultured with the native antigen and the B cell lymphoma, LK-35.2, or naive splenic B cells as antigen-presenting cells (APC). Cytochromes c and their corresponding C-terminal fragments which are not capable of stimulating the TPc9.1 cells, including the autologous mouse cytochrome c, block the T cells' response to pigeon cytochrome c. In contrast, nonstimulatory N-terminal peptides of cytochrome c, which share no homology with the antigenic peptide, do not block. Blocking is observed when the nonstimulatory cytochromes c or peptides are present in culture with the live APC and nonsaturating concentrations of pigeon cytochrome c. With tobacco hornworm moth cytochrome c as antigen, a protein for which the T cell has a higher functional affinity, the response of TPc9.1 cannot be blocked by the nonstimulatory cytochromes c or by peptides, even when limiting concentrations of the tobacco hornworm moth cytochrome c are used. When paraformaldehyde-fixed APC are employed, no native cytochrome c can stimulate the T cells, including the tobacco hornworm moth protein which with the live APC is effective at 50 to 100-fold lower concentrations than pigeon cytochrome c. However, with fixed APC the T cells are stimulated by the C-terminal fragments containing residues 81-104 of the pigeon protein or residues 81-103 of the tobacco hornworm moth protein as readily and with the same relative efficiencies as the native protein, presented by live APC. The nonstimulatory peptides, but not the native cytochromes c, block T cell activation by pigeon cytochrome c pulsed-fixed APC, indicating that the nonstimulatory peptides compete with the stimulatory pigeon cytochrome c peptides produced by the APC. This competition appears to be due to nonstimulatory peptides which associate at the APC surface and not to those acting from solution because the APC which have been incubated with pigeon cytochrome c and nonstimulatory peptides and washed free of excess antigen and peptides are not stimulatory to the T cell hybrid. It was concluded that the activation of a pigeon cytochrome c-specific T cell, which recognizes a peptide fragment of the native protein on the surface of an APC, can be blocked by an excess of nonstimulatory homologous peptides when these are also associated on the surface of the APC.(ABSTRACT TRUNCATED AT 400 WORDS)
ChemInform Abstract: Unsupported Nanoporous Gold for Heterogeneous Catalysis (2013)

Abstract Review: 60 refs.
Characterization of Globular Protein Solutions by Dynamic Light Scattering, Electrophoretic Mobility, and Viscosity Measurements (2008)

In this work, physicochemical properties of two globular proteinsbovine serum albumin (BSA) having a molecular weight of 67 kDa and human serum albumin (HSA) having a molecular weight of 69 kDawere characterized. The bulk characteristics of these proteins involved the diffusion coefficient (hydrodynamic radius), electrophoretic mobility, and dynamic viscosity as a function of protein solution concentration for various pH values. The hydrodynamic radius data suggested an association of protein molecules, most probably forming compact dimers. Using the hydrodynamic diameter and the electropheretic mobility data allowed the determination of the number of uncompensated (electrokinetic) charges on protein surfaces. The electrophoretic mobility data were converted to zeta potential values, which allowed one to determine the isoelectric point (iep) of these proteins. It was found to be at pH 5.1 for both proteins, in accordance with previous experimental data and theoretical estimations derived from amino acid composition and p K values. To determine further the stability of protein solutions, dynamic viscosity measurements were carried out as a function of their bulk volume concentration for various pH values. The intrinsic viscosity derived from these measurements was interpreted in terms of the Brenner model, which is applicable to hard spheroidal particles. It was found that the experimental values of the intrinsic viscosity of these proteins were in good agreement with this model when assuming protein dimensions of 9.5 x 5 x 5 nm3 (prolate spheroid). The possibility of forming linear aggregates of association degree higher than 2 was excluded by these measurements. It was concluded that the combination of dynamic viscosity and dynamic light scattering can be exploited as a convenient tool for detecting not only the onset of protein aggregation in suspensions but also the form and composition of these aggregates.