gebhart/patrepeval huggingface dataset:
Nucleic Acids for Recognition and Catalysis Landmarks, Limitations, and Looking to the Future (2000)

Combinatorial selection of nucleic acids has led to the discovery of novel ligands and catalysts that have implications for both chemistry and medicine. In the context of combinatorial chemistry, degenerate syntheses of nucleic acid libraries readily generate as many as 10(15) different molecules in which a small percentage exhibit interesting binding and/or catalytic properties. The primary advantage of nucleic acids is that library coding is an intrinsic property; sequential composition directly determines the activity. At low temperatures, the sequential composition of single stranded nucleic acids governs folding into irregular tertiary structures resulting in interesting activities. At higher temperatures, the same structures are unfolded and decoded by polymerases to reveal sequential information. The use of PCR (polymerase chain reaction) permits amplification and thus enrichment of the selected activity which is then regenerated chemi-enzymatically. Iterative selection and amplification result in one of the highest throughput screens conceivable whereby each molecule encodes its own activity permitting the ultimate in parallel sampling. Finally, sequence information, and by extension the chemical composition, is obtained by simple sequencing techniques obviating the need for mass spectrometric deconvolution, parallel tagging, and/or large volumes needed for viral and cell culture. This review begins with an introduction of general concepts and considerations. The potential for nucleic acids to generate tight-binding ligands is of interest to structural biologists and medicinal chemists. The therapeutic implications to medicine are also touched upon. Since combinatorially selected nucleic acids and antibodies share many conceptual similarities, their respective advantages and limitations are compared. Theoretical and practical limitations for catalyst discovery are discussed along with the use of other chemical and physical approaches to address some current catalytic shortcomings. Finally some future directions are suggested.
Effect of intranasal dexmedetomidine or oral midazolam premedication on sevoflurane EC50 for successful laryngeal mask airway placement in children: a randomized, double‐blind, placebo‐controlled trial (2014)

Oral midazolam and IND premedications significantly reduce the sevoflurane EC50 for laryngeal mask airway insertion in children by 17% and 21%, respectively.
Rapid, nonradioactive detection of mutations in the human genome by allele-specific amplification. (1989)

A simple, rapid, nonradioactive method has been developed to facilitate the direct detection of point mutations that cause genetic disease. The method operates on the basis of the specific amplification of a target allele by the polymerase chain reaction with extension primers designed such that their 3' end is placed at the mutation site. When this base is complementary to that of the specific allele, the DNA segment is amplified; when it is not complementary, the polymerase chain reaction cannot proceed. When alpha 1-antitrypsin (alpha 1AT) deficiency was used as a model, the technique of allele-specific amplification was capable of selective detection of five different mutations that cause the alpha 1AT deficiency state, including three different naturally occurring single-base substitution mutations (alleles Z, S, and Nullbellingham), an insertion mutation (Nullmattawa), and a deletion mutation (Nullgranite falls). Double-blind evaluation of 47 samples of genomic DNA demonstrated 100% accuracy of the method. The technique of allele-specific amplification is rapid, simple, and does not require the existence of a convenient restriction endonuclease site or the use of radioactive materials, and thus should have broad applicability for the detection of known genetic diseases in a highly sensitive and specific fashion.
Prolonged survival and tissue trafficking following adoptive transfer of CD4ζ gene-modified autologous CD4+ and CD8+ T cells in human immunodeficiency virus–infected subjects (2000)

We have genetically engineered CD4(+) and CD8(+) T cells with human immunodeficiency virus (HIV) specificity by inserting a gene, CD4zeta, containing the extracellular domain of human CD4 (which binds HIV env) linked to the zeta (zeta) chain of the T-cell receptor (which mediates T-cell activation). Twenty-four HIV-positive subjects received a single infusion of 2 to 3 x 10(10) autologous CD4zeta-modified CD4(+) and CD8(+) T cells administered with (n = 11) or without (n = 13) interleukin-2 (IL-2). Subjects had CD4 counts greater than 50/microL and viral loads of at least 1000 copies/mL at entry. T cells were costimulated ex vivo through CD3 and CD28 and expanded for approximately 2 weeks. CD4zeta was detected in 1% to 3% of blood mononuclear cells at 8 weeks and 0.1% at 1 year after infusion, and survival was not enhanced by IL-2. Trafficking of gene-modified T cells to bulk rectal tissue and/or isolated lamina propria lymphocytes was documented in a subset of 5 of 5 patients at 14 days and 2 of 3 at 1 year. A greater than 0.5 log mean decrease in rectal tissue-associated HIV RNA was observed for at least 14 days, suggesting compartmental antiviral activity of CD4zeta T cells. CD4(+) counts increased by 73/microL at 8 weeks in the group receiving IL-2. There was no significant mean change in plasma HIV RNA or blood proviral DNA in either treatment arm. This sustained, high-level persistence of gene-modified T cells demonstrates the feasibility of ex vivo T-cell gene therapy in HIV-infected adults and suggests the importance of providing HIV-specific T-helper function.
A novel application of ADC/K-foaming agent-loaded NBR rubber composites as pressure sensor (2006)

Nitrile butadiene rubber (NBR) structure foam of different apparent densities was obtained by using different concentrations of foaming agent, azodicarbonamide, ADC/K. The true stress–strain characteristics, in case of compression, of foamed samples were measured. It was found that the theoretical values predicted from the simple blending model are in more agreement with the experimental results than those from the square-relationship model. The effect of cyclic loading–unloading and dissipation energy of rubber foams was studied. The results also indicated that foams with low density exhibited a small hysteresis. The electrical properties were found dependent on the foaming agent concentration. This study was assisted by Mott and Gurney equation. The effect of compressive strain on the electrical conductivity of rubber foams was studied. The free current carrier mobility and the equilibrium concentration of charge carrier in the conduction band were produced as functions of compressive strain. The results also indicate that there is a linear variation between pressure and conductivity for all samples, which means that these samples can be used as a pressure sensor. At a certain concentration of foaming agent (7.5 phr) a change of electrical conductivity by more than three orders is observed at 20% compression strain.
OX40-OX40L expression in idiopathic inflammatory myopathies. (2013)

The simultaneous expression of both OX40 and its ligand OX40L in idiopathic inflammatory myopathies suggests that they might participate in disease pathogenesis. Expression of OX40L by different types of cells within the inflamed muscle implies that OX40-OX40L interaction may contribute in disease mechanisms through different pathways.
Stat3 mediates myeloid cell–dependent tumor angiogenesis in mice (2008)

The underlying molecular mechanisms that cause immune cells, mediators of our defense system, to promote tumor invasion and angiogenesis remain incompletely understood. Constitutively activated Stat3 in tumor cells has been shown to promote tumor invasion and angiogenesis. Therefore, we sought to determine whether Stat3 activation in tumor-associated inflammatory cells has a similar function. We found that Stat3 signaling mediates multidirectional crosstalk among tumor cells, myeloid cells in the tumor stroma, and ECs that contributes to tumor angiogenesis in mice. Myeloid-derived suppressor cells and macrophages isolated from mouse tumors displayed activated Stat3 and induced angiogenesis in an in vitro tube formation assay via Stat3 induction of angiogenic factors, including VEGF and bFGF. Stat3-regulated factors produced by both tumor cells and tumor-derived myeloid cells also induced constitutive activation of Stat3 in tumor endothelium, and inhibiting Stat3 in ECs substantially reduced in vitro tumor factor-induced endothelial migration and tube formation. In vivo assays demonstrated the requirement for Stat3 signaling in tumor-associated myeloid cells for tumor angiogenesis. Our results indicate that, by virtue of the ability of Stat3 in tumor cells and tumor-derived myeloid cells to upregulate expression of factors that activate Stat3 in ECs, Stat3 mediates multidirectional crosstalk among tumor cells, tumor-associated myeloid cells, and ECs that contributes to tumor angiogenesis.
Nitric Oxide Scavenging by Red Blood Cell Microparticles and Cell-Free Hemoglobin as a Mechanism for the Red Cell Storage Lesion (2011)

The results of these studies suggest new mechanisms for endothelial injury and impaired vascular function associated with the most fundamental of storage lesions, hemolysis.
Azole Endothelin Antagonists. 2. Structure−Activity Studies (1996)

Structure-activity studies have been performed in an attempt to improve the potency of a novel series of azole-based endothelin-A (ET(A)) selective antagonists. Modifications of the hydrophobic group on the terminal urea produced substantial effects on receptor affinity; in particular, the choice of cyclohexyl- or arylureas led to substantial improvements in activity. Conformational restriction of these groups provides an additional benefit. N-Methylation of the indole moiety which is part of the heterocyclic dipeptide surrogate also improves potency. The effects of these two modifications appear to be synergistic, with the best of the resultant doubly modified analogs (e.g. 14q, 15y, and 15ff) exhibiting an 80-200-fold improvement over the original leads.
Effects of Insulin in Relatives of Patients with Type 1 Diabetes Mellitus (2002)

In persons at high risk for diabetes, insulin at the dosage used in this study does not delay or prevent type 1 diabetes.
Exploring the proton pump mechanism of cytochrome c oxidase in real time (2007)

Cytochrome c oxidase catalyzes most of the biological oxygen consumption on Earth, a process responsible for energy supply in aerobic organisms. This remarkable membrane-bound enzyme also converts free energy from O(2) reduction to an electrochemical proton gradient by functioning as a redox-linked proton pump. Although the structures of several oxidases are known, the molecular mechanism of redox-linked proton translocation has remained elusive. Here, correlated internal electron and proton transfer reactions were tracked in real time by spectroscopic and electrometric techniques after laser-activated electron injection into the oxidized enzyme. The observed kinetics establish the long-sought reaction sequence of the proton pump mechanism and describe some of its thermodynamic properties. The 10-micros electron transfer to heme a raises the pK(a) of a "pump site," which is loaded by a proton from the inside of the membrane in 150 micros. This loading increases the redox potentials of both hemes a and a(3), which allows electron equilibration between them at the same rate. Then, in 0.8 ms, another proton is transferred from the inside to the heme a(3)/Cu(B) center, and the electron is transferred to Cu(B). Finally, in 2.6 ms, the preloaded proton is released from the pump site to the opposite side of the membrane.
Phase III Randomized Trial Comparing Three Platinum-Based Doublets in Advanced Non–Small-Cell Lung Cancer (2002)

Efficacy end points were not significantly different between experimental and reference arms, although toxicities showed differences. These findings suggest that chemotherapy in NSCLC has reached a therapeutic plateau.
Single primer amplification (SPA) of cDNA for microarray expression analysis (2003)

The potential of expression analysis using cDNA microarrays to address complex problems in a wide variety of biological contexts is now being realised. A limiting factor in such analyses is often the amount of RNA required, usually tens of micrograms. To address this problem researchers have turned to methods of improving detection sensitivity, either through increasing fluorescent signal output per mRNA molecule or increasing the amount of target available for labelling by use of an amplification procedure. We present a novel DNA-based method in which an oligonucleotide is incorporated into the 3' end of cDNA during second-strand cDNA synthesis. This sequence provides an annealing site for a single complementary heel primer that directs Taq DNA polymerase amplification of cDNA following multiple cycles of denaturation, annealing and extension. The utility of this technique for transcriptome-wide screening of relative expression levels was compared to two alternative methodologies for production of labelled cDNA target, namely incorporation of fluorescent nucleotides by reverse transcriptase or the Klenow fragment. Labelled targets from two distinct mouse tissues, adult liver and kidney, were compared by hybridisation to a set of cDNA microarrays containing 6500 mouse cDNA probes. Here we demonstrate, through a dilution series of cDNA derived from 10 micro g of total RNA, that it is possible to produce datasets comparable to those produced with unamplified targets with the equivalent of 30 ng of total RNA. The utility of this technique for microarray analysis in cases where sample is limited is discussed.
Intravitreal Injection of Normal Saline Induces Retinal Degeneration in the C57BL/6J Mouse (2014)

Purpose: : To investigate the adverse effect of intravitreal injection of normal saline (NS) and phosphate buffered saline (PBS) in mouse eyes. Methods: : NS or PBS was injected intravitreally into C57BL/6J mouse eyes. Retinal lesions were monitored by fundus imaging, spectral-domain optical coherence tomography (SD-OCT), and histological investigations. Retinal immune gene expression was determined by real-time polymerase chain reaction (PCR). The toxic effect of NS and PBS or retinal protein from NS- or PBS-injected eyes on retinal pigment epithelium (RPE) was tested in B6-RPE-07 mouse RPE cell cultures. Results: : Intravitreal injection of NS dose-dependently induced localized retinal lesion in mice. Histological investigations revealed multiple vacuoles in photoreceptor outer segments and RPE cells. The lesions recovered over time and by 3 weeks post injection the majority of lesions vanished in eyes receiving 1 μl NS. Inflammatory genes, including TNF- α, IL-1β, IL-6, iNOS, and VEGF were upregulated in NS injected eyes. Intravitreal injection of PBS did not cause any pathology. The treatment of B6-RPE07 cells with 30% PBS or 30% NS did not affect RPE viability. However, incubation of 1-μg/ml retinal protein from NS-injected eyes, but not PBS-injected eyes induced RPE cell death. Conclusion: : NS is toxic to the C57BL/6J mouse retina and should not be used as a vehicle for intraocular injection. PBS is not toxic to the retina and is a preferred vehicle. Translational Relevance: : NS is not a physiological solution for intraocular injection in the C57BL/6J mice and questions its suitability for intraocular injection in other species, including human.
Mechanisms of RNA-induced toxicity in CAG repeat disorders (2013)

Several inherited neurodegenerative disorders are caused by CAG trinucleotide repeat expansions, which can be located either in the coding region or in the untranslated region (UTR) of the respective genes. Polyglutamine diseases (polyQ diseases) are caused by an expansion of a stretch of CAG repeats within the coding region, translating into a polyQ tract. The polyQ tract expansions result in conformational changes, eventually leading to aggregate formation. It is widely believed that the aggregation of polyQ proteins is linked with disease development. In addition, in the last couple of years, it has been shown that RNA-mediated mechanisms also have a profound role in neurotoxicity in both polyQ diseases and diseases caused by elongated CAG repeat motifs in their UTRs. Here, we review the different molecular mechanisms assigned to mRNAs with expanded CAG repeats. One aspect is the mRNA folding of CAG repeats. Furthermore, pathogenic mechanisms assigned to CAG repeat mRNAs are discussed. First, we discuss mechanisms that involve the sequestration of the diverse proteins to the expanded CAG repeat mRNA molecules. As a result of this, several cellular mechanisms are aberrantly regulated. These include the sequestration of MBNL1, leading to misregulated splicing; sequestration of nucleolin, leading to reduced cellular rRNA; and sequestration of proteins of the siRNA machinery, resulting in the production of short silencing RNAs that affect gene expression. Second, we discuss the effect of expanded CAG repeats on the subcellular localization, transcription and translation of the CAG repeat mRNA itself. Here we focus on the MID1 protein complex that triggers an increased translation of expanded CAG repeat mRNAs and a mechanism called repeat-associated non-ATG translation, which leads to proteins aberrantly translated from CAG repeat mRNAs. In addition, therapeutic approaches for CAG repeat disorders are discussed. Together, all the findings summarized here show that mutant mRNA has a fundamental role in the pathogenesis of CAG repeat diseases.
Animal models of hypertension and effect of drugs (2003)

Hypertension, the most common cardiovascular disease is the primary cause of stroke, coronary artery disease and sudden cardiac death. Many factors are believed to be involved in the pathogenesis of hypertension and its complications. Experimental models of human disease are used to study pathophysiological factors involved in hypertension and assess antihypertensive agents. Today different strains of rats with genetic hypertension are available and in most laboratories, therapeutic studies on hypertension are carried out on these models. As new insights in to the pathogenesis of hypertension are revealed, new models are being developed to produce hypertension in animals. This article reviews experimental models of hypertension. Both conventional and genetic models of hypertension are discussed.
Effect of 1-chloro-2,4-dinitrobenzene on K+ transport in normal and sickle human red blood cells (2003)

1-Chloro-2,4-dinitrobenzene (CDNB), which causes oxidative stress through depletion of reduced glutathione (GSH), increases the passive K+ permeability of red cells. In this paper, we investigated the effects of CDNB (1 mM) on the activities of the K+-Cl- cotransporter (KCC; measured as Cl--dependent K+ influx) and the Gardos channel (taken as clotrimazole-sensitive K+ influx, 5 microM) in human red cells, using 86Rb+ as a K+ congener. 45Ca2+ was used to study passive Ca2+ entry and active Ca2+ efflux via the plasma membrane Ca2+ pump. Both the Gardos channel and KCC were stimulated in both normal and sickle red cells. In sickle cells, stimulation of KCC was similar in oxygenated and deoxygenated cells; that of the Gardos channel was greater in deoxygenated cells. In normal red cells, stimulation of both pathways was greater in oxygenated cells (by 4 +/- 1-fold; all means +/- S.E.M., n = 3). The effects on the Gardos channel were dependent on extracellular Ca2+ and were associated with inhibition of the plasma membrane Ca2+ pump (by 29 +/- 3 %, P < 0.01) and increased Ca2+ sensitivity of the channel (EC50 for [Ca2+]i reduced from 260 +/- 26 to 175 +/- 15 nM; P < 0.05). Cell volume, pHi, ATP levels and passive Ca2+ entry were not affected by CDNB. The effects on KCC were inhibited (93 +/- 6 %) by prior treatment with the protein phosphatase inhibitor calyculin A (100 nM) and were not additive with stimulation by N-ethylmaleimide (1 mM), regardless of the order of addition. These findings are therefore consistent with inhibition of a regulatory protein kinase, although stimulation of the conjugate protein phosphatase(s) may also occur. KCC stimulation was also Ca2+ dependent. These findings are important for understanding how GSH depletion alters membrane permeability and how to protect against red cell dehydration.
Isolation and Characterization of Chicken Insulin (1968)

A method is described for isolation of insulin from chicken pancreas which makes use of modifications of established procedures to deal with the low insulin content of the tissue and permits isolation of significant quantities of the hormone. The insulin isolated is essentially homogeneous by paper chromatography and polyacrylamide gel electrophoresis. The amino acid composition of the insulin and of the separated A and B chains is consistent with the known amino acid sequence of chicken insulin. (Endocrinology 83: 1323, 1968)
Microfabricated Polycarbonate CE Devices for DNA Analysis (2001)

The microchip capillary electrophoresis (CE) devices were fabricated in polycarbonate (PC) plastic material by compression molding. The molded devices were enclosed utilizing thermal bonding to another PC wafer. These thermal bonds do not yield up to an applied force equivalent to 150 psi. Aqueous fluid transport inside the plastic CE devices was enhanced by UV irradiation treatment of the hydrophobic polycarbonate plastic surfaces prior to thermal bonding. In comparison to glass microchannels, electroosmotic flow (EOF) in native PC channels is low and is independent of buffer pH at pH 7 and 9. UV irradiation of PC surfaces increases surface hydrophilicity and increases EOF. CE DNA separation was demonstrated in these PC CE devices with good resolution and run-to-run reproducibility. The on-chip PCR/CE analysis of a 500-bp region of bacteriophage lambda DNA was also demonstrated.
Molecular cloning and expression of the human homologue of the murine gene encoding myeloid leukemia-inhibitory factor. (1988)

A human homologue of the recently cloned murine leukemia-inhibitory factor (LIF) gene was isolated from a genomic library by using the murine cDNA as a hybridization probe. The nucleotide sequence of the human gene indicated that human LIF has 78% amino acid sequence identity with murine LIF, with no insertions or deletions, and that the region of the human gene encoding the mature protein has one intervening sequence. After oligonucleotide-mediated mutagenesis, the mature protein-coding region of the LIF gene was introduced into the yeast expression vector YEpsec1. Yeast cells transformed with the resulting recombinant could be induced with galactose to produce high levels of a factor that induced the differentiation of murine M1 leukemic cells in a manner analogous to murine LIF. This factor competed with 125I-labeled native murine LIF for binding to specific cellular receptors on murine cells, compatible with a high degree of structural similarity between the murine and human factors.
Reversal of type 1 diabetes via islet β cell regeneration following immune modulation by cord blood-derived multipotent stem cells (2012)

ClinicalTrials.gov number, NCT01350219.
The Determinants of Residential Property Values with Special Reference to Air Pollution (1967)

Ronald G. Ridker, John A. Henning, The Determinants of Residential Property Values with Special Reference to Air Pollution, The Review of Economics and Statistics, Vol. 49, No. 2 (May, 1967), pp. 246-257