gebhart/patrepeval huggingface dataset:
Efficient vasoactive intestinal polypeptide hydrolyzing autoantibody light chains selected by phage display (1996)

An immunoglobulin light chain (L chain) library derived from the peripheral blood lymphocytes of a patient with asthma was cloned into a phagemid vector. Phage particles displaying L chains capable of binding vasoactive intestinal polypeptide (VIP) were isolated by affinity chromatography. Two VIP binding L chains were expressed in Escherichia coli in soluble form and purified to electrophoretic homogeneity by metal chelating and protein L affinity chromatography. Both L chains catalyzed the hydrolysis of [tyr10-125I]VIP substrate. The catalytic activity eluted at the molecular mass of the monomer form of the L chain (28 kDa) from a gel filtration column. The activity was bound by immobilized anti-kappa-chain antibody. A control recombinant L chain displayed no catalytic activity. Hydrolysis of VIP by the catalytic L chains was saturable and consistent with Michaelis-Menten kinetics. The turnover of the L chains was moderate (0.22 and 2.21/min) and their Km values indicated comparatively high affinity recognition of VIP[111 and 202 nM), producing catalytic efficiencies comparable to or greater than trypsin. Unlike trypsin, the L chains did not display detectable cleavage of casein, suggesting a catalytic activity specialized for VIP. Comparisons of the nucleotide sequences of the L chain cDNA with their putative germ-line counterparts suggested the presence of several replacement mutations in the complementarity determining regions (CDRs). These observations suggest: (a) Retention or acquisition of catalytic activity by the L chains is compatible with affinity maturation of antibodies; and (b) The autoimmune L chain repertoire can serve as a source of substrate-specific and efficient catalysts.
Binary cooperative complementary nanoscale interfacial materials. Reduction of silver nanoparticles in DMF. Formation of monolayers and stable colloids (2000)

Abstract We explore in this article the reduction of Ag + ions by N,N-dimethylformamide (DMF), both in the presence and in the absence of a stabilizing agent. The reduction can lead to the formation of either thin films of silver nanoparticles electrostatically attached onto glass surfaces, or stable dispersions of silver nanoparticles if the silane coupling agent 3-aminopropyltrimethoxysilane (APS) is present. The different parameters affecting the reduction process are discussed, and the reducing ability of DMF is compared with that of ethanol, which is often used for the production of catalytically active metal colloids.
Design and implementation of a single-chip 1-d median filter (2018)

Computer Science Department
A ubiquitous factor (HF-1a) and a distinct muscle factor (HF-1b/MEF-2) form an E-box-independent pathway for cardiac muscle gene expression. (1992)

Recent studies have identified a conserved 28-bp element (HF-1) within the rat cardiac MLC-2 gene which confers cardiac muscle-specific and inducible expression during myocardial cell hypertrophy. Utilizing a combination of independent experimental approaches, this study characterizes two cardiac nuclear factors which bind to HF-1, a ubiquitous factor (HF-1a), and an A + T-rich binding factor (HF-1b) which is preferentially expressed in differentiated cardiac and skeletal muscle cells. The HF-1a binding site is located in a core region of the 28-bp conserved element, immediately upstream from the A + T-rich HF-1b site, which is homologous to the MEF-2 site found in a number of muscle genes. By a number of separate criteria (gel mobility shift, competition, and mutagenesis studies), HF-1b and MEF-2 appear to be indistinguishable and thus are either identical or closely related muscle factors. Transient assays of luciferase reporter genes containing point mutations throughout the 28-bp HF-1 regulatory element document the importance of both the HF-1a and HF-1b sites in transient assays in ventricular muscle cells. In the native 250-bp MLC-2 promoter fragment, mutations in the single E box had little effect on cardiac muscle specificity, while point mutations in either the HF-1a or HF-1b binding site significantly reduced promoter activity, underscoring the importance of both the HF-1a and HF-1b sites in the transcriptional activation of this cardiac muscle gene. Thus, this study provides evidence that a novel, ubiquitous factor (HF-1a) and a muscle factor (HF-1b/MEF-2) can form a novel, E-box-independent pathway for muscle-specific expression in ventricular cardiac muscle cells.
Viral Mutagenesis as a Means for Generating Novel Proteins (2009)

We demonstrate that a mutation-prone virus engineered to express a foreign gene is an expedient means for generating novel mutant nonviral proteins in mammalian cells. Using vesicular stomatitis virus to express a gene coding for a fluorescent DsRed protein, a number of green mutant variants including a new variant not previously described were rapidly isolated from infected cells, sequenced, and cloned. Similar methods may be useful in the development of physiologically sensitive fluorescent reporter proteins and directed evolution or mutagenesis of proteins in general.
Chemical Reactions and Stability of Riboflavin in Foods (2005)

ABSTRACT: Riboflavin is relatively stable during thermal and nonthermal food processing and storage but is very sensitive to light. It can accept or donate a pair of hydrogen atoms. It can act as a photosensitizer (through either Type I or Type II mechanism) or a prooxidant for food components under light. Photosensitization of riboflavin causes production of reactive oxygen species such as superoxide anion, singlet oxygen, hydroxy radical, and hydrogen peroxide. Radicals and reactive oxygen species accelerate the decomposition of proteins, lipids, carbohydrates, and vitamins, and could cause significant nutrient loss in foods. Carbohydrates are less sensitive to riboflavinphotosensitized oxidation than proteins, lipids, or vitamins. Riboflavin is an excellent photosensitizer for singlet oxygen formation and a superb reactant for singlet oxygen, with the reaction rate of 1.01 ± 10 10 /M/s.
Optical and electrical characterization of α-InGaZnO thin film fabricated by pulsed laser deposition for thin film transistor applications (2009)

Highly transparent and amorphous InGaZnO thin films with high mobility were deposited on fused silica by pulsed laser deposition. The films remained amorphous after annealing at 700 °C and had bandgaps in the range 3.50–3.62 eV. The film deposited at 5 Pa and room temperature exhibits a Hall mobility of 54 cm2 V−1 s−1. An α-InGaZnO thin film transistor with high-k Ba0.6Sr0.4TiO3 as a dielectric layer and operating in enhanced mode with a saturation mobility of 5.8 cm2 V−1 s−1 and on/off ratio of 2 × 105 is demonstrated.
Retinal uptake of intravitreally injected Hsc/Hsp70 and its effect on susceptibility to light damage. (2001)

Intravitreally injected Hsc/Hsp70 is taken up by retinal cells and, when administered after an acute injury like light damage, increased the number of surviving photoreceptors.
Successful treatment of severe recalcitrant psoriasis with combination infliximab and methotrexate (2001)

Plaques of psoriasis contain increased levels of cytokines, including tumour necrosis factor-alpha (TNF-alpha), which are thought to be essential to the maintenance of the psoriatic process. We report the successful treatment of severe, recalcitrant psoriasis when infliximab (a monoclonal antibody to TNF-alpha) was used in combination with methotrexate.
Channelrhodopsins: directly light-gated cation channels (2005)

Phototaxis and photophobic responses of green algae are mediated by rhodopsins with microbial type chromophores, i.e. all-trans-retinal in the ground state. The green alga Chlamydomonas reinhardtii was recently completely sequenced and the EST (expressed sequence tag) database was made public. We and others detected overlapping partial cDNA sequences that encode two proteins which we termed channelopsins (Chops). The N-terminal half of chop1 (approximately 300 of 712 amino acids) comprises hypothetical seven-transmembrane segments with sequence similarity to the proton pump bacteriorhodopsin and the chloride pump halorhodopsin. Even though the overall sequence homology is low, several amino acids are conserved that define the retinal-binding site and the H+-transporting network in BR (bacteriorhodopsin). Expression of Chop1, or only the hydrophobic core, in Xenopus laevis oocytes, enriched with retinal, produced a light-gated conductance (maximum at approx. 500 nm), which shows characteristics of a channel [ChR1 (channelrhodopsin-1)] that is selectively permeable for protons. Also ChR2 (737 amino acids) is an ion channel that is switched directly by light and also here the hydrophobic N-terminal half of the protein is sufficient to enable light-sensitive channel activity. The action spectrum is blue-shifted (maximum at approx. 460 nm) with respect to ChR1. In addition to protons, ChR2 is permeable to univalent and bivalent cations. We suggest that ChRs are involved in phototaxis of green algae. We show that heterologous expression of ChR2 is useful to manipulate intracellular pCa or membrane potential of animal cells, simply by illumination.
Amino acid sequence of CAP37, a human neutrophil granule‐derived antibacterial and monocyte‐specific chemotactic glycoprotein structurally similar to neutrophil elastase (1990)

We report the amino acid sequence of CAP37, a human neutrophil granule protein with antibacterial and monocyte-specific chemotactic activity. CAP37 is a single-chain protein consisting of 222 amino acid residues. It has three N-glycosylation sites, at Asn residues 100, 114 and 145. Some species of CAP37 are glycosylated at all three sites; some at Asn-114 alone, others at Asn-114 and Asn-110 or Asn-145. CAP37 has 45% sequence identity to human neutrophil elastase, and 30-37% identity to several other granule serine proteinases. Despite these similarities, CAP37 is not a serine proteinase because the active site residues serine and histidine are replaced.
Toxicity Analysis of N- and C-Terminus-Deleted Vegetative Insecticidal Protein from Bacillus thuringiensis (2001)

A vegetative insecticidal protein (VIP)-encoding gene from a local isolate of Bacillus thuringiensis has been cloned, sequenced, and expressed in Escherichia coli. The expressed protein shows insecticidal activity against several lepidopteran pests but is ineffective against Agrotis ipsilon. Comparison of the amino acid sequence with those of reported VIPs revealed a few differences. Analysis of insecticidal activity with N- and C-terminus deletion mutants suggests a differential mode of action of VIP against different pests.
A 51-Year-Old Woman With Acute Onset of Facial Pressure, Rhinorrhea, and Tooth Pain (2009)

Acute rhinosinusitis is a common ailment accounting for millions of office visits annually, including that of Mrs D, a 51-year-old woman presenting with 5 days of upper respiratory illness and facial pain. Her case is used to review the diagnosis and treatment of acute rhinosinusitis. Acute viral rhinosinusitis can be difficult to distinguish from acute bacterial rhinosinusitis, especially during the first 10 days of symptoms. Evidence-based clinical practice guidelines developed to guide diagnosis and treatment of acute viral and bacterial rhinosinusitis recommend that the diagnosis of acute rhinosinusitis be based on the presence of "cardinal symptoms" of purulent rhinorrhea and either facial pressure or nasal obstruction of less than 4 weeks' duration. Antibiotic treatment generally can be withheld during the first 10 days of symptoms for mild to moderate cases, given the likelihood of acute viral rhinosinusitis or of spontaneously resolving acute bacterial rhinosinusitis. After 10 days, the likelihood of acute bacterial rhinosinusitis increases, and initiation of antibiotic therapy is supported by practice guidelines. Complications of sinusitis, though rare, can be serious and require early recognition and treatment.
Expression of P2X7 Receptor Increases In Vivo Tumor Growth (2012)

The P2X7 receptor is an ATP-gated ion channel known for its cytotoxic activity. However, recent evidence suggests a role for P2X7 in cell proliferation. Here, we found that P2X7 exhibits significant growth-promoting effects in vivo. Human embryonic kidney cells expressing P2X7 exhibited a more tumorigenic and anaplastic phenotype than control cells in vivo, and the growth rate and size of these tumors were significantly reduced by intratumoral injection of the P2X7 inhibitor-oxidized ATP. The accelerated growth of P2X7-expressing tumors was characterized by increased proliferation, reduced apoptosis, and a high level of activated transcription factor NFATc1. These tumors also showed a more developed vascular network than control tumors and secreted elevated amounts of VEGF. The growth and neoangiogenesis of P2X7-expressing tumors was blocked by intratumoral injection of the VEGF-blocking antibody Avastin (bevacizumab), pharmacologic P2X7 blockade, or P2X7 silencing in vivo. Immunohistochemistry revealed strong P2X7 positivity in several human cancers. Together, our findings provide direct evidence that P2X7 promotes tumor growth in vivo.
Dynamic history-length fitting: a third level of adaptivity for branch prediction (1998)

Accurate branch prediction is essential for obtaining high performance in pipelined superscalar processors that execute instructions speculatively. Some of the best current predictors combine a part of the branch address with a fixed amount of global history of branch outcomes in order to make a prediction. These predictors cannot perform uniformly well across all workloads because the best amount of history to be used depends on the code, the input data and the frequency of context switches. Consequently, all predictors that use a fixed history length are therefore unable to perform up to their maximum potential.We introduce a method---called DHLF---that dynamically determines the optimum history length during execution, adapting to the specific requirements of any code, input data and system workload. Our proposal adds an extra level of adaptivity to two-level adaptive branch predictors. The DHLF method can be applied to any one of the predictors that combine global branch history with the branch address. We apply the DHLF method to gshare (dhlf-gshare) and obtain near-optimal results for all SPECint95 benchmarks, with and without context switches. Some results are also presented for gskewed (dhlf-gskewed), confirming that other predictors can benefit from our proposal.
FRET microscopy: from principle to routine technology in cell biology (2010)

The phenomenon of resonance energy transfer first described by Theodor Förster presents the opportunity of retrieving information on molecular proximity, orientation and conformation on the nanometre scale from (living) samples with conventional fluorescence microscopes (or even macroscopic devices). During the past 10 years Förster (or fluorescence) resonance energy transfer (FRET) microscopy has been revolutionized by the vast progress in fluorescent protein and in situ fluorescent labelling technology as well as by the commercial availability of advanced quantitative microscopy instrumentation. FRET microscopy is now routinely used in modern cell biology research. This short review will guide the reader through the most established FRET microscopy techniques, their inherent strengths and limitations, potential pitfalls, and assist the reader in making an educated choice on the FRET microscopy method most suited for their specific application.
Dephosphorylation of simian virus 40 large-T antigen and p53 protein by protein phosphatase 2A: inhibition by small-t antigen. (1991)

Simian virus 40 (SV40) large-T antigen and the cellular protein p53 were phosphorylated in vivo by growing cells in the presence of 32Pi. The large-T/p53 complex was isolated by immunoprecipitation and used as a substrate for protein phosphatase 2A (PP2A) consisting of the catalytic subunit (C) and the two regulatory subunits, A and B. Three different purified forms of PP2A, including free C, the AC form, and the ABC form, could readily dephosphorylate both proteins. With both large-T and p53, the C subunit was most active, followed by the AC form, which was more active than the ABC form. The activity of all three forms of PP2A toward these proteins was strongly stimulated by manganese ions and to a lesser extent by magnesium ions. The presence of complexed p53 did not affect the dephosphorylation of large-T antigen by PP2A. The dephosphorylation of individual phosphorylation sites of large-T and p53 were determined by two-dimensional peptide mapping. Individual sites within large-T and p53 were dephosphorylated at different rates by all three forms of PP2A. The phosphates at Ser-120 and Ser-123 of large-T, which affect binding to the origin of SV40 DNA, were removed most rapidly. Three of the six major phosphopeptides of p53 were readily dephosphorylated, while the remaining three were relatively resistant to PP2A. Dephosphorylation of most of the sites in large-T and p53 by the AC form was inhibited by SV40 small-t antigen. The inhibition was most apparent for those sites which were preferentially dephosphorylated. Inhibition was specific for the AC form; no effect was observed on the dephosphorylation of either protein by the free C subunit or the ABC form. The inhibitory effect of small-t on dephosphorylation by PP2A could explain its role in transformation.
Magnetic stimulation of muscle evokes cerebral potentials by direct activation of nerve afferents: A study during muscle paralysis (1996)

We tested the hypothesis that magnetic stimulation of muscle evokes cerebral potentials by causing a muscle contraction that then activates muscle receptors. We measured cerebral evoked potentials accompanying magnetic stimulation of muscle in 3 patients during surgery both before and after muscle paralysis with succinylcholine, a depolarizing agent. The magnetic stimulation was at low intensity (30%) and at a 2/s rate. The administration of succinylcholine sufficient to produce muscle paralysis did not alter cerebral potentials evoked by either low-intensity magnetic stimulation of muscle (gastrocnemius/soleus) or electrical stimulation of peripheral nerve (tibial nerve). In 1 normal subject, the S1 nerve root action potentials conducting at rapid velocity (> 60 m/s) were detected at the S1 foramen with a needle electrode using electrical stimulation of the tibial nerve. However, no S1 nerve root potentials could be identified to magnetic stimulation of muscle that evoked a cerebral potential. We conclude that magnetic stimulation of muscle activates terminal afferents in the muscle to provide the afferent drive for the cerebral potentials independent of muscle contraction. The failure to detect the afferent volley in S1 nerve root to magnetic stimulation suggests that only a few afferents are activated or that the activation of afferents is temporally dispersed.
Thiazolides inhibit growth and induce glutathione‐S‐transferase Pi (GSTP1)‐dependent cell death in human colon cancer cells (2008)

Thiazolides are a novel class of broad-spectrum anti-infective drugs with promising in vitro and in vivo activities against intracellular and extracellular protozoan parasites. The nitrothiazole-analogue nitazoxanide (NTZ; 2-acetolyloxy-N-(5-nitro 2-thiazolyl) benzamide) represents the thiazolide parent compound, and a number of bromo- and carboxy-derivatives with differing activities have been synthesized. Here we report that NTZ and the bromo-thiazolide RM4819, but not the carboxy-thiazolide RM4825, inhibited proliferation of the colon cancer cell line Caco2 and nontransformed human foreskin fibroblasts (HFF) at or below concentrations the compounds normally exhibit anti-parasitic activity. Thiazolides induced typical signs of apoptosis, such as nuclear condensation, DNA fragmentation and phosphatidylserine exposure. Interestingly, the apoptosis-inducing effect of thiazolides appeared to be cell cycle-dependent and induction of cell cycle arrest substantially inhibited the cell death-inducing activity of these compounds. Using affinity chromatography and mass spectrometry glutathione-S-transferase P1 (GSTP1) from the GST class Pi was identified as a major thiazolide-binding protein. GSTP1 expression was more than 10 times higher in the thiazolide-sensitive Caco2 cells than in the less sensitive HFF cells. The enzymatic activity of recombinant GSTP1 was strongly inhibited by thiazolides. Silencing of GSTP1 using siRNA rendered cells insensitive to RM4819, while overexpression of GSTP1 increased sensitivity to RM4819-induced cell death. Thiazolides may thus represent an interesting novel class of future cancer therapeutics.
Mouse endosialin, a C-type lectin-like cell surface receptor: expression during embryonic development and induction in experimental cancer neoangiogenesis. (2006)

Endosialin is a C-type lectin-like cell surface receptor of unknown function, with a distinctive pattern of endothelial expression in newly formed blood vessels in human cancers. The murine orthologue of endosialin has been identified, opening up the analysis of developmental regulation in the embryo and in aberrant tissue remodeling, notably cancer angiogenesis. To advance these studies we have generated an antibody to the extracellular domain of mouse endosialin and mapped protein expression from embryonic day E10.0 to the adult stage, complemented by mRNA quantification and co-typing for standard endothelial markers. Four main findings emerged. First, endosialin protein is restricted to vascular endothelium and fibroblast-like cells in developing organs, and largely disappears in the adult. Second, endothelial expression varies markedly between organs regarding spatial and temporal patterns. For instance, in the E10.0 embryo, endosialin is prominent in the endothelium of the dorsal aorta and, from E11.0 to E14.5, in vessels sprouting from the dorsal aorta, in perineural vascular plexuses, and in brain capillaries. Third, circumscribed mesenchymal expression in fibroblast-like cells was evident throughout development, most pronounced adjacent to certain budding epithelia, as exemplified by the lung and kidney glomeruli, but unrelated to the endothelial expression. The endosialin protein persists in the stromal fibroblasts of the adult uterus. Finally, in subcutaneous cancer xenograft models endosialin re-appears in the host-derived tumor stroma, both in neo-angiogenic vascular endothelium and in activated stromal fibroblasts. In future studies, the search for intrinsic or extrinsic signals contributing to endosialin induction in cancer stroma will be of interest.
Conditional expression of N-myc in human neuroblastoma cells increases expression of alpha-prothymosin and ornithine decarboxylase and accelerates progression into S-phase early after mitogenic stimulation of quiescent cells. (1996)

To elucidate the contribution of the N-Myc protein to neuroblastomas we have used a synthetic inducible expression system on the basis of the tetracycline repressor of E coli to reversibly express N-myc in a human neuroblastoma cell line in which expression of endogenous N-myc is barely detectable. Like the c-Myc protein, N-Myc up-regulates the expression of both alpha-prothymosin and ornithine decarboxylase. Induction of N-myc increases both the rate of DNA-synthesis and the proliferation rate, and shortens the G1 phase of the cell cycle. A comparison of cell populations in which the presence of N-Myc protein was restricted to different parts of G(zero)/G1 revealed that N-Myc is rate-limiting for cell cycle progression during the first 5 h after serum stimulation of quiescent cells providing direct evidence that Myc-proteins act early after mitogenic stimulation of quiescent cells.