gebhart/patrepeval huggingface dataset:
Control of tumor cell biology through regulation of peptide hormone processing. (1992)

Control of the biology of individual cells, organs, and organisms is achieved through an interplay of a host of specific interactions, many involving peptide hormones as modulators or effectors. In tumor cells these processes may result in uncontrolled growth as a consequence of autocrine and/or paracrine growth effects. Most peptide hormones are bioactive only after processing of the precursor prohormone by posttranslational processing enzymes. The enzymes involved with the production of bioactive peptides, in particular those associated with peptide alpha-amidation, provide potential targets for disruption of posttranslational processing mechanisms as a means of regulation of the progression of tumor cells. This information provides a rational basis for consideration of inhibition of autocrine neuropeptide synthesis as a strategy for chemointervention.
Class II (IIa)-Selective Histone Deacetylase Inhibitors. 1. Synthesis and Biological Evaluation of Novel (Aryloxopropenyl)pyrrolyl Hydroxyamides (2005)

Chemical manipulations performed on aroyl-pyrrolyl-hydroxyamides (APHAs) led to (aryloxopropenyl)pyrrolyl hydroxamates 2a-w, and their inhibition against maize HDACs and their class I or class II HDAC selectivity were determined. In particular, from these studies some benzene meta-substituted compounds emerged as highly class II (IIa)-selective HDAC inhibitors, the most selective being the 3-chloro- and 3-fluoro-substituted compounds 2c (SI = 71.4) and2f (SI = 176.4). The replacement of benzene with a 1-naphthyl ring afforded 2s, highly active against the class II homologue HD1-A (IC(50) = 10 nM) but less class II-selective than 2c,f. When tested against human HDAC1 and HDAC4, 2f showed no inhibitory activity against HDAC1 but was able to inhibit HDAC4. Moreover, in human U937 acute myeloid leukaemia cells 2f did not produce any effect on apoptosis, granulocytic differentiation, and the cell cycle, whereas 2s (that retain class I HDAC inhibitory activity) was 2-fold less potent than SAHA used as reference.
Cloning and expression of an Î±-amylase encoding gene from the hyperthermophilic archaebacteriumThermococcus hydrothermalisand biochemical characterisation of the recombinant enzyme (2000)

An alpha-amylase encoding gene from the extremely thermophilic Archaea Thermococcus hydrothermalis was cloned and expressed in Escherichia coli. The encoded alpha-amylase possesses molecular characteristics specific to the Archaea, especially from Pyrococcus species, with biochemical characteristics of the alpha-amylases from Thermococcus. The gene is 1374 bp long and encodes a protein of 457 amino acids composed of a 22 amino acid putative signal peptide and a 435 amino acid mature protein (calculated molecular mass 49236 Da). The T. hydrothermalis recombinant alpha-amylase is optimally active at 75-85 degrees C and at pH 5.0-5.5.
Current Density Distribution Under Surface Electrode on Posterior Tibial Nerve Electrical Stimulation (2005)

Electrical stimulation on the posterior tibial nerve is commonly used in the measurement of somatosensory evoked potential (SEP). To improve the efficiency of stimulation, the potential field and current density distributions under the surface electrodes were simulated with a three layer theoretical model. The mirror method was used to analyze the potential field of point charge. Integration of the field and the stimulus area provide the potential field for one surface electric pole. Potential field distribution of the bipolar electrodes was calculated by superimposition of two unipolar fields. Finally, the current density distribution was calculated by Laplace equation. An analytical solution of the potential field was obtained; thereafter the numerical solution of the current density distribution was calculated. The potential field and current density distribution were simulated by 2-D plot. From the model and simulation, the potential and current density distributions were not found to be evenly distributed under transcutaneous stimulation electrode and the maximum current density is located under the poles. The result suggests that bipolar stimulator should be applied axially along the stimulated nerve course.
Antineoplastic agents 337. Synthesis of dolastatin 10 structural modifications. (1995)

New structural modifications of the marine shell-less mollusk peptide constituent dolastatin 10 (1) have been synthesized, and evaluated against a variety of cancer cell lines and for their ability to inhibit tubulin polymerization. A number of useful structure-activity relationships were uncovered. The most important observation was that the dolaphenine unit of dolastatin 10 could be satisfactorily replaced with a phenethylamine. Peptide 11C, designated auristatin PE, was found to exhibit inhibition of cancer cell growth and tubulin assembly comparable to that of dolastatin 10.
Secretion of staphylococcal nuclease by Bacillus subtilis (1985)

The staphylococcal nuclease (nuc) gene from Staphylococcus aureus has been cloned and expressed in Bacillus subtilis. The nuclease protein was expressed either from its own promoter and translation start signals, or from a combination of a B. subtilis promoter, ribosome binding site, and a signal peptide sequence. Greater than 80% of the active gene product was secreted into the medium, whereas, when a signal peptide sequence was absent, as little as 4% of the nuclease activity was found in the culture medium. Intracellular (or cell-bound) nuclease, as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and Western blotting, was shown to have the molecular weight of the predicted precursor protein with the signal peptide. Levels of nuclease reached 50 mg per liter in the culture medium, depending on the growth medium and the strain used. These findings indicate the prospective use of nuclease as a model system for studying secretion of heterologous proteins in B. subtilis.
Serum levels of interleukin 1β, interleukin 8 and tumour necrosis factor α as markers of gastric cancer (2006)

Despite the efforts made, a serum marker reliable for the screening and follow-up of patients with gastric cancer has not yet been identified. The aim of this preliminary study was to test the role of pro-inflammatory cytokines interleukin 1beta, interleukin 8 and tumour necrosis factor alpha in patients with gastric cancer and in control groups. The statistical analysis of cytokines serum levels in the group with gastric cancer versus control groups has shown considerable differences (p < 0.001) in their mean rates. The results indicate that the cytokines interleukin 1beta, interleukin 8 and tumour necrosis factor alpha might perhaps act as diagnostic markers in patients with gastric cancer. Therefore, it is hypothesized that after more extended trials, their use in the screening and prognostic assessment of these patients could be a possibility.
A Software Technique to Improve Yield of Processor Chips in Presence of Ultra-Leaky SRAM Cells Caused by Process Variation (2007)

Exceptionally leaky transistors are increasingly more frequent in nano-scale technologies due to lower threshold voltage and its increased variation. Such leaky transistors may even change position with changes in the operating voltage and temperature, and hence, redundancy at circuit-level is not sufficient to tolerate such threats to yield. We show that in SRAM cells this leakage depends on the cell value and propose a first software-based runtime technique that suppresses such abnormal leakages by storing safe values in the corresponding cache lines before going to standby mode. Analysis shows the performance penalty is, in the worst case, linearly dependent to the number of so-cured cache lines while the energy saving linearly increases by the time spent in standby mode. Analysis and experimental results on commercial processors confirm that the technique is viable if the standby duration is more than a small fraction of a second.
Extensive phosphorothioate substitution yields highly active and nuclease-resistant hairpin ribozymes (1992)

The catalytic function of the hairpin ribozyme has been investigated by modification-interference analysis of both ribozyme and substrate, using ribonucleoside phosphorothioates. Thiophosphate substitutions in two ribozyme domains were examined by using a novel and highly efficient two-piece ribozyme assembled from two independently synthesized oligoribonucleotides. The catalytic proficiency of the two-piece construct (KM = 48 nM, kcat = 2.3 min-1) is nearly identical to that of the one-piece ribozyme. The two-piece ribozyme is essentially unaffected by substitution with thiophosphates 5' to all guanosines, cytidines, and uridines. In contrast, incorporation of multiple adenosine phosphorothioates in the 5' domain of the ribozyme decreases ribozyme activity by a factor of 25. Modification-interference experiments using ribozymes partially substituted with adenosine phosphorothioate suggest that thiophosphates 5' to A7, A9 and A10 interfere with cleavage to a greater extent than substitutions at other sites within the molecule, but the effect is modest. Within the substrate, phosphorothioate substitution does not directly interfere with cleavage, rather, increasing thiophosphate content decreases the stability of the ribozyme-substrate complex. We describe the construction of a hairpin ribozyme containing dinucleotide extensions at its 5' and 3' ends. Full substitution of this molecule with G and C phosphorothioates results in a ribozyme with greatly enhanced stability against cellular ribonucleases without significant loss of catalytic efficiency.
Static and dynamic properties of polymers in random media (1989)

The properties of polymers in a disordered environment are studied with emphasis on the effect of trapping due to fluctuations in the porosity of the environment. Results are obtained for ${Z}_{N}$, the number of self-avoiding walks of length N starting at the origin, and D, the diffusion coefficient for the center of mass of the polymer. The two most important new results are that 〈ln${Z}_{N}$〉\ensuremath{\approxeq}N-${a}_{1}$${N}^{\ensuremath{\alpha}}$, with \ensuremath{\alpha}=2-d\ensuremath{\nu} and \ensuremath{\nu} the Flory exponent, and that the leading behavior of the diffusion coefficient is D\ensuremath{\approxeq}exp(-${a}_{2}$${N}^{\ensuremath{\alpha}}$).
A General and Efficient Method for the Suzuki–Miyaura Coupling of 2‐Pyridyl Nucleophiles (2008)

One of the most general systems for the cross-coupling of aryl and heteroaryl bromides and chlorides with 2-pyridyl-derived nucleophiles has been developed, for which catalysts comprising [Pd2(dba)3] and either diaryl (1) or dialkyl phosphine oxide (2) supporting ligands were found to be ideal (see scheme). Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2008/z801465_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
AUA-Cleaving Hammerhead Ribozymes: Attempted Selection for Improved Cleavage (1994)

In order to find a ribozyme which can cleave the AUA triplet efficiently, the specificities and rates of intermolecular cleavage by the ribozyme of the satellite RNA of the barley yellow dwarf virus have been determined. Although it cleaves the AUA triplet in the plus strand of the viroid RNA, cleavage of AUC and AUU is more efficient, and AUG is essentially not cleaved. Attempts were made to increase cleavage efficiency by in vitro selection with randomization at positions 7, 10.1, and 11.1 in the core region. Fifteen clones were analyzed, two of which showed increased AUA cleavage efficiency. They have a G10.1.C11.1 base pair and a pyrimidine at position 7. This corresponds to the sequence of the consensus hammerhead ribozyme. Attempts to further increase cleavage efficiency by in vitro selection of the consensus hammerhead ribozyme with randomization of the 10 nucleotides in the core region or of the sBYDV ribozyme with 12 core nucleotides randomized were not successful.
Localization of cells from the winter flounder gill expressing a skin type antifreeze protein gene (2002)

In situ hybridization on whole mounts and paraffin-sectioned winter flounder (Pleuronectes americanus) gill, using riboprobes specific to a skin type antifreeze protein (AFP) gene, showed a mRNA distribution associated with cells throughout the filament and the lamellae. Immunohistochemistry using antibodies for a skin-type AFP identified cells corresponding to those detected using in situ hybridization. Parallel experiments with antibodies for chloride-cell markers showed that these cells were not involved in antifreeze-protein expression. Similarly, goblet cells did not show cross-reactivity with the AFP antibodies. This general distribution suggested that pavement cells were likely involved. Reverse transcription polymerase chain reaction using gill cDNA templates and subsequent sequencing of the products confirmed the presence of skin type AFP transcripts in this tissue. Expression of a AFP in this area may act as a first line of defence against ice-crystal migration into peripheral tissues.
PLOD2 induced under hypoxia is a novel prognostic factor for hepatocellular carcinoma after curative resection (2011)

PLOD2 is a potential novel prognostic factor for HCC patients following surgery.
Spectral shaping for non-Gaussian source spectra in optical coherence tomography (2002)

We present a digital spectral shaping technique to reduce the sidelobes (ringing) of the axial point-spread function in optical coherence tomography for non-Gaussian-shaped source spectra. The spectra of two superluminescent diodes were combined to generate a spectrum with significant modulation. Images of onion cells demonstrate the improved image quality in a turbid biological sample. A quantitative analysis of the accompanying penalty in signal-to-noise ratio is given.
Comparison of two different methods for inactivation of viruses in serum (1997)

In order to compare protocols for inactivation of viruses potentially present in biological specimens, three different model viruses were treated in bovine serum by two different inactivation methods: samples were subjected either to chemical inactivation with ethylenimine (El) at concentrations of 5 and 10 mM at 37 degrees C for periods up to 72 h or to electron-beam irradiation in frozen and liquid form with doses varying between 11 and 46 kGy. The chemical inactivation resulted in nonlinear tailing curves in a semilogarithmic plot of virus titer versus inactivation time showing non-first-order kinetics with respect to virus titer. The time for inactivation of 7 log10 units of porcine parvovirus (PPV) was about 24 h for both El concentrations, whereas 5 log10 units of bovine viral diarrhea virus (BVDV) was inactivated in 2 h for both El concentrations and 6 log10 units of porcine enterovirus (PEV) was inactivated within 3 h. The inactivation with electron-beam irradiation resulted in almost linear curves in a semilogarithmic plot of virus titer versus irradiation dose, reflecting a first-order inactivation. The rate of inactivation was almost twice as fast in the liquid samples compared to the rate in frozen ones, giving values of the doses needed to reduce virus infectivity 1 log10 unit for inactivation of PPV of 11.8 and 7.7 kGy for frozen and liquid samples, respectively, whereas the corresponding values for BVDV were 4.9 and 2.5 kGy, respectively, and those for PEV were 6.4 and 4.4 kGy, respectively. The nonlinear inactivation with El makes it impossible to extrapolate the curves beyond the virus detection limit and thereby predict the necessary time for complete inactivation, i.e., to a level beyond the detection limit, of virus in a given sample. The first-order inactivation obtained with electron-beam irradiation makes such a prediction possible and justifiable. The two methods are discussed with respect to their different kinetics and applicability under different circumstances and criteria for inactivation, and considerations for choice of method are discussed.
Assembly Factor Omp85 Recognizes Its Outer Membrane Protein Substrates by a Species-Specific C-Terminal Motif (2006)

Integral beta-barrel proteins are found in the outer membranes of Gram-negative bacteria, mitochondria, and chloroplasts. The assembly of these proteins requires a proteinaceous apparatus of which Omp85 is an evolutionary conserved central component. To study its molecular mechanism, we have produced Omp85 from Escherichia coli in inclusion bodies and refolded it in vitro. The interaction of Omp85 with its substrate proteins was studied in lipid-bilayer experiments, where it formed channels. The properties of these channels were affected upon addition of unfolded outer-membrane proteins (OMPs) or synthetic peptides corresponding to their C-terminal signature sequences. The interaction exhibited species specificity, explaining the inefficient assembly of OMPs from Neisseria in E. coli. Accordingly, the in vivo assembly of the neisserial porin PorA into the E. coli outer membrane was accomplished after adapting its signature sequence. These results demonstrate that the Omp85 assembly machinery recognizes OMPs by virtue of their C-terminal signature sequence.
Protein A is the von Willebrand factor binding protein on Staphylococcus aureus. (2000)

Endovascular infection is a highly critical complication of invasive Staphylococcus aureus disease. For colonization, staphylococci must first adhere to adhesive endovascular foci. Von Willebrand factor (vWF) is a large, multimeric glycoprotein mediating platelet adhesion at sites of endothelial damage. Earlier it was demonstrated that vWF binds to and promotes the surface adhesion of S. aureus, prompting this effort to identify the vWF adhesin. In Western ligand assays of S. aureus lysates, staphylococcal protein A (SPA) was recognized by purified vWF. Surface plasmon resonance demonstrated the binding of soluble vWF to immobilized recombinant protein A with a K(d) of 1.49 x 10(-8) mol/L. Using flow cytometry, the binding of fluorescein isothiocyanate-labeled vWF to S. aureus was found to be saturable and inhibitable by unlabeled vWF, antiprotein-A antibodies, or IgG. Isogenic Deltaspa::Tc(r) mutants were constructed by the insertion of a tetracycline resistance cassette into spa using allelic replacement, and it exhibited decreased binding of soluble vWF and decreased adhesion to vWF-adsorbed surfaces. The interaction was restored on complementation of the mutants with spa-containing plasmid pSPA7235. In conclusion, protein A confers interaction of S. aureus with soluble and immobilized vWF in a newly discovered function characterizing protein A as a novel member of the staphylococcal surface protein adhesin superfamily and suggesting its potential role in the pathogenesis of endovascular staphylococcal disease.
Vitamin C Inhibits Endothelial Cell Apoptosis in Congestive Heart Failure (2001)

Administration of vitamin C to CHF patients suppresses EC apoptosis in vivo, which might contribute to the established functional benefit of vitamin C supplementation on endothelial function.
White organic light-emitting devices with a bipolar transport layer between blue fluorescent and orange phosphorescent emitting layers (2007)

White organic light-emitting devices based on an orange phosphorescent iridium complex, bis(2-(2-fluorphenyl)-1,3-benzothiozolato-N,C2′) iridium (acetylacetonate) [(F-BT)2Ir(acac)] and blue fluorescent 4,4′-bis(2,2′-diphenylvinyl)-1,1′-biphenyl are reported. By introducing a bipolar transport 4,4′N,N′-dicarbazole-biphenyl layer between the fluorescent and the phosphorescent emission layers, additional light emission from (F-BT)2Ir(acac) is observed. The authors attributed it to the elimination of the Dexter energy transfer between the two emitters. Pure white emission with Commission Internationale de I’Eclairage coordinates of (0.33, 0.34) and a maximum luminance of 40960cd∕m2 were obtained. The maximum current efficiency and the color rendering index of the device are 13.4cd∕A and 71, respectively.
Differential effect of adenosine on tumor and normal cell growth: Focus on the A3 adenosine receptor (2000)

Adenosine is an ubiquitous nucleoside present in all body cells. It is released from metabolically active or stressed cells and subsequently acts as a regulatory molecule through binding to specific A1, A2A, A2B and A3 cell surface receptors. The synthesis of agonists and antagonists to the adenosine receptors and their cloning enabled the exploration of their physiological functions. As nearly all cells express specific adenosine receptors, adenosine serves as a physiological regulator and acts as a cardioprotector, neuroprotector, chemoprotector, and as an immunomodulator. At the cellular level, activation of the receptors by adenosine initiates signal transduction mechanisms through G-protein associated receptors. Adenosine's unique characteristic is to differentially modulate normal and transformed cell growth, depending upon its extracellular concentration, the expression of adenosine cell surface receptors, and the physiological state of the target cell. Stimulation of cell proliferation following incubation with adenosine has been demonstrated in a variety of normal cells in the range of low micromolar concentrations, including mesangial and thymocyte cells, Swiss mouse 3T3 fibroblasts, and bone marrow cells. Induction of apoptosis in tumor or normal cells was shown at higher adenosine concentrations (>100 microM) such as in leukemia HL-60, lymphoma U-937, A431 epidermoid cells, and GH3 tumor pituitary cell lines. It was further noted that the A3 adenosine receptor (A3AR) plays a key role in the inhibitory and stimulatory growth activities of adenosine. Modulation of the A3AR was found to affect cell growth either positively or negatively depending on the concentration of the agonist, similar to the effect described for adenosine. At nanomolar concentrations, the A3AR agonists possess dual activity, i.e., antiproliferative activity toward tumor cells and stimulatory effect on bone marrow cells. In vivo, these agonists exerted anti-cancer effects, and when given in combination with chemotherapy, they enhanced the chemotherapeutic index and acted as chemoprotective agents. Taken together, activation of the A3AR, by minute concentrations of its natural ligand or synthetic agonists, may serve as a new approach for cancer therapy.
Error rates and resource overheads of repetition cat qubits (2021)

We estimate and analyze the error rates and the resource overheads of the repetition cat qubit approach to universal and fault-tolerant quantum computation. The cat qubits stabilized by two-photon dissipation exhibit an extremely biased noise where the bit-flip error rate is exponentially suppressed with the mean number of photons. In a recent work we suggested that the remaining phase-flip error channel could be suppressed using a one-dimensional repetition code. Indeed, using only bias-preserving gates on the cat qubits, it is possible to build a universal set of fault-tolerant logical gates at the level of the repetition cat qubit. In this paper we perform Monte Carlo simulations of all the circuits implementing the protected logical gates, using a circuit-level error model. Furthermore, we analyze two different approaches to implement a fault-tolerant Toffoli gate on repetition cat qubits. These numerical simulations indicate that very low logical error rates could be achieved with a reasonable resource overhead, and with parameters that are within the reach of near-term circuit QED experiments.