gebhart/patrepeval huggingface dataset:
Structural effects in the recognition of DNA by circular oligonucleotides (1992)

It was recently reported that certain pyrimidine-rich circular DNA oligomers can bind strongly and specifically to purine-rich DNA or RNA strands by forming bimolecular triple helical complexes.<sup>1-3</sup> In this study are investigated the effects of structural variations on the strength of binding for this new class of nucleotide-binding ligand. The number of loop nucleotides (nt) which is optimum for bridging the two binding domains of a circle is examined. Comparing loop sizes of 3, 4, 5, 6, and 10 nt, the optimum number of nucleotides in a loop is found to be five for the sequences studied. In order to test the method of construction and the ability of these compounds to bind sites of varied length, we attempted to synthesize circles of varied size. Circles over the size range 24-46 nt were successfully constructed. Varying the target site length shows that oligomers of four, eight, twelve, and eighteen nucleotides can be complexed strongly by circles, with melting temperatures (<i>T</i><sub>m</sub>) 17° to >33 °C higher at pH 7.0 than the corresponding Watson-Crick duplexes of the same length. Also studied is the effect of the covalently closed circular structure in comparison to linear oligomers having the same sequence; it is shown that a covalently closed circle has considerably higher binding affinity than do three different "nicked" circles (linear oligomers) which contain the same bases. The high binding affinities of these circles are thus attributed to the entropic benefit of preorganization. Finally, the ability of such circles to bind to complementary sites within longer oligomers, the ends of which must pass beyond the loops of a circle, is confirmed by melting studies with synthetic target strands 36 bases in length.
Angiogenic activity of the K-fgf/hst oncogene in neural transplants. (1992)

Using retrovirus-mediated gene transfer into neural transplants, we have expressed the human K-fgf/hst oncogene in the central nervous system. Single-cell suspensions of fetal rat brains were removed at embryonic days 13 and 14, exposed to a retroviral vector encoding the K-fgf oncogene and stereotaxically implanted into the caudate putamen of syngenic adult Fisher rats. Recipient animals were sacrificed at intervals of 6-16 months without evidence of neurological impairment. Mock-infected grafts showed the characteristic histopathological appearance of organotypically differentiated neural transplants. In contrast, grafts exposed to the K-fgf gene exhibited abundant capillary proliferation and capillary angiomas. By in situ hybridization analysis and immunohistochemistry, expression of K-fgf was detected in neural cells adjacent to vascular proliferations. Neurons and glia with abundant K-fgf transcripts were morphologically unaffected. In order to examine the transforming potential of the K-fgf gene in the nervous system, we combined retrovirus-mediated transfer of the K-fgf oncogene with a single transplacental exposure of the donor animals to the neurotropic carcinogen N-ethyl-N-nitrosourea (NEU). However, this combination of transforming agents did not result in tumor formation in the grafts. These results provide evidence for a powerful angiogenic effect of K-fgf on the developing brain in vivo.
Acetaminophen (paracetamol) is a selective cyclooxygenase‐2 inhibitor in man (2007)

For more than three decades, acetaminophen (INN, paracetamol) has been claimed to be devoid of significant inhibition of peripheral prostanoids. Meanwhile, attempts to explain its action by inhibition of a central cyclooxygenase (COX)-3 have been rejected. The fact that acetaminophen acts functionally as a selective COX-2 inhibitor led us to investigate the hypothesis of whether it works via preferential COX-2 blockade. Ex vivo COX inhibition and pharmacokinetics of acetaminophen were assessed in 5 volunteers receiving single 1000 mg doses orally. Coagulation-induced thromboxane B(2) and lipopolysaccharide-induced prostaglandin E(2) were measured ex vivo and in vitro in human whole blood as indices of COX-1 and COX-2 activity. In vitro, acetaminophen elicited a 4.4-fold selectivity toward COX-2 inhibition (IC(50)=113.7 micromol/L for COX-1; IC(50)=25.8 micromol/L for COX-2). Following oral administration of the drug, maximal ex vivo inhibitions were 56% (COX-1) and 83% (COX-2). Acetaminophen plasma concentrations remained above the in vitro IC(50) for COX-2 for at least 5 h postadministration. Ex vivo IC(50) values (COX-1: 105.2 micromol/L; COX-2: 26.3 micromol/L) of acetaminophen compared favorably with its in vitro IC(50) values. In contrast to previous concepts, acetaminophen inhibited COX-2 by more than 80%, i.e., to a degree comparable to nonsteroidal antiinflammatory drugs (NSAIDs) and selective COX-2 inhibitors. However, a >95% COX-1 blockade relevant for suppression of platelet function was not achieved. Our data may explain acetaminophen's analgesic and antiinflammatory action as well as its superior overall gastrointestinal safety profile compared with NSAIDs. In view of its substantial COX-2 inhibition, recently defined cardiovascular warnings for use of COX-2 inhibitors should also be considered for acetaminophen.
Genome Engineering with TAL-Effector Nucleases and Alternative Modular Nuclease Technologies (2013)

Over three years following the discovery of the TAL code, artificial TAL effector DNA binding domains have emerged as the premier platform for building site-specific DNA binding polypeptides for use in biological research. Here, we provide an overview of TAL effector and alternative modular DNA binding domain (mDBD) technologies, focusing on their use in established and emerging architectures for building site-specific endonucleases for genome engineering applications. We also discuss considerations for choosing TAL effector/mDBD or alternative nuclease technologies for genome engineering projects ranging from basic laboratory gene editing of cultured cell lines to therapeutics. Finally, we highlight how the rapid pace of development of mDBD-based, such as monomeric TALENs (I-TevI-TAL), and more recently RNA-guided nucleases (CRISPR-Cas9) has led to a transition in the field of genome engineering towards development of the next generation of technologies aimed at controlling events that occur after targeted DNA breaks are made.
Selective Oxidation of Methane to Methanol Catalyzed, with CH Activation, by Homogeneous, Cationic Gold (2004)

Cationic gold catalyzes the title reaction in strong acid solvents with SeVI as the stoichiometric oxidant. At 180 oC and 27 bar of CH4 turnover numbers of about 30 and methanol concentrations of 0.6 M have been observed with selectivities >90%. DFT calculations indicate that cationic AuI and AuIII are both viable catalysts that operate by electrophilic CH activation and oxidative functionalization (see picture).
Management of acute renal failure (2006)

Acute renal failure is a common condition, frequently encountered in both community practice and hospital inpatients. While it remains a heterologous condition, following basic principles makes investigation straightforward, and initial management follows a standard pathway in most patients. This article shows this, advises on therapeutic strategies, including those in special situations, and should help the clinician in deciding when to refer to a nephrologist, and when to consider renal replacement therapy.
Sustained release intraocular drug delivery devices for treatment of uveitis. (2011)

Corticosteroids have been the mainstay of uveitis therapy. When intraocular inflammation is unresponsive to steroids, or steroid related side effects become a concern, steroid-sparing medications may be administered which can be classified into immunosuppressive and immunomodulatory agents. Uveitis treatment can be delivered systemically, topically, periocularly or intraocularly. All of the above mentioned medications can entail significant systemic side effects, particularly if administered for prolonged durations, which may become treatment-limiting. Some medications, particularly hydrophobic compounds, may poorly cross the blood-retinal barrier. Topical medications, which have the least side effects, do not penetrate well into the posterior segment and are unsuitable for posterior uveitis which is often sight-threatening. Intraocular or periocular injections can deliver relatively high doses of drug to the eye with few or no systemic side effects. However, such injections are associated with significant complications and must often be repeated at regular intervals. Compliance with any form of regular medication can be a problem, particularly if its administration is associated with discomfort or if side effects are unpleasant. To overcome the above-mentioned limitations, an increasing number of sustained-release drug delivery devices using different mechanisms and containing a variety of agents have been developed to treat uveitis. This review discusses various current and future sustained-release ophthalmic drug delivery systems for treatment of uveitis.
Theoretical Analysis of Diamond Mechanosynthesis. Part II. C<SUB>2</SUB> Mediated Growth of Diamond C(110) Surface via Si/Ge-Triadamantane Dimer Placement Tools (2004)

This paper presents a computational and theoretical investigation of the vacuum mechanosynthesis of di- amond on the clean C(110) surface from carbon dimer (C2) precursors positionally constrained throughout the reaction pathway by silicon- or germanium-doped triadamantane derivatives mounted on a scanning probe tip. Interactions between the dimer placement tools and the bare diamond C(110) surface are inves- tigated using Density Functional Theory (DFT) with generalized gradient approximation (GGA) by con- structing the reaction path potential energy profiles and analyzing ab initio molecular dynamics simulations. Similar methods are applied to study the energetics and kinetics of recharging the tool with acetylene. Molecular mechanics simulations on extended tool tips are carried out to elucidate the positional uncer- tainty of the carbon dimer due to thermal fluctuations, and the possibility of intermolecular dimerization and dehydrogenation of the dimer placement tools is explored.
Ultrahigh vacuum instrument that combines variable-temperature scanning tunneling microscopy with Fourier transform infrared reflection-absorption spectroscopy for studies of chemical reactions at surfaces (2002)

We describe the construction of an ultrahigh vacuum chamber that incorporates variable-temperature scanning tunneling microscopy (STM), Fourier transform infrared reflection-absorption spectroscopy (FT-IRAS), Auger electron spectroscopy, low-energy electron diffraction, and temperature programmed desorption, for studying structure and reactivity at surfaces. The chamber and manipulator design enables in situ sample preparation and analysis, and rapid access to several surface-analytical techniques by rotation only. This eliminates sample inconsistencies due to ex situ preparation or the necessity to run parallel experiments. Inclusion of FT-IRAS allows us to characterize surface species and identify adsorbates during studies using STM.
Mise au Point d`une Méthde de Quantification Visuelle du Développement du Blé (2005)

La quantification quotidienne des variations de la morphologie de la plante est primordiale. Ces variation sont, en fait, utilisees pour effectuer un suivi precis des cultures et evaluer leur reponse aux divers traitements et/ou aux conditions du milieu. L`echelle de Haun permet de quantifier visuellement ces variations de maniere a fournir une expression numerique continue du developpement. Le systeme de notation se base sur l`apparition reguliere des feuilles. Chaque feuille represente une unite de (...)
Dislocation Velocities and Mechanical Strength of Bulk GeSi Crystals (1999)

The dislocation velocities and mechanical strength of bulk crystals of Ge1—xSix alloys have been investigated by the etch pit technique and compressive deformation tests, respectively. The velocity of dislocations has been determined as a function of stress and temperature in the composition ranges 0 < x < 0.08 and 0.94 < x < 1. In the composition range 0 < x < 1 the yield stress showed a maximum around x = 0.5 and was dependent on the composition as being proportional to x(1—x). Built-in long-range internal stress fields in GeSi alloy caused by local fluctuations of the alloy composition together with dynamic development of the solute atmosphere around dislocations were thought to result in the strengthening of GeSi as a unique alloying effect.
Non-covalent double functionalization of carbon nanotubes with a NADH oxidation Ru(ii)-based molecular catalyst and a NAD-dependent glucose dehydrogenase (2014)

We report the double functionalization of multiwalled carbon nanotube electrodes by two functional pyrene molecules. In combination, an immobilized Ru(II)-based NADH oxidation catalyst and glucose dehydrogenase achieve highly efficient glucose oxidation with low overpotential of -0.10 V and high current densities of 6 mA cm(-2).
Monitoring inflammatory bowel disease activity: Clinical activity is judged to be more relevant than endoscopic severity or biomarkers (2011)

Clinical activity is judged to be more relevant for monitoring IBD activity and guiding therapeutic decisions than endoscopic severity and biomarkers. As such, the accumulating scientific evidence on the clinical impact of mucosal healing does not yet seem to influence the management of IBD in daily gastroenterologic practice.
Intracellular Functions of N-Linked Glycans (2001)

N-linked oligosaccharides arise when blocks of 14 sugars are added cotranslationally to newly synthesized polypeptides in the endoplasmic reticulum (ER). These glycans are then subjected to extensive modification as the glycoproteins mature and move through the ER via the Golgi complex to their final destinations inside and outside the cell. In the ER and in the early secretory pathway, where the repertoire of oligosaccharide structures is still rather small, the glycans play a pivotal role in protein folding, oligomerization, quality control, sorting, and transport. They are used as universal "tags" that allow specific lectins and modifying enzymes to establish order among the diversity of maturing glycoproteins. In the Golgi complex, the glycans acquire more complex structures and a new set of functions. The division of synthesis and processing between the ER and the Golgi complex represents an evolutionary adaptation that allows efficient exploitation of the potential of oligosaccharides.
Repair of Oxidized Iron-Sulfur Clusters in Escherichia coli (2004)

The [4Fe-4S]2+ clusters of dehydratases are rapidly damaged by univalent oxidants, including hydrogen peroxide, superoxide, and peroxynitrite. The loss of an electron destabilizes the cluster, causing it to release its catalytic iron atom and converting the cluster initially to an inactive [3Fe-4S]1+ form. Continued exposure to oxidants in vitro leads to further iron release. Experiments have shown that these clusters are repaired in vivo. We sought to determine whether repair is mediated by either the Isc or Suf cluster-assembly systems that have been identified in Escherichia coli. We found that all the proteins encoded by the isc operon were critical for de novo assembly, but most of these were unnecessary for cluster repair. IscS, a cysteine desulfurase, appeared to be an exception: although iscS mutants repaired damaged clusters, they did so substantially more slowly than did wild-type cells. Because sulfur mobilization should be required only if clusters degrade beyond the [3Fe-4S]1+ state, we used whole cell EPR to visualize the fate of oxidized enzymes in vivo. Fumarase A was overproduced. Brief exposure of cells to hydrogen peroxide resulted in the appearance of the characteristic [3Fe-4S]1+ signal of the oxidized enzyme. When hydrogen peroxide was then scavenged, the enzyme activity reappeared within minutes, in concert with the disappearance of the EPR signal. Thus it is unclear why IscS is required for efficient repair. The iscS mutants grew poorly, allowing the possibility that metabolic defects indirectly slow the repair process. Our data did indicate that damaged clusters decompose beyond the [3Fe-4S]1+ state in vivo when stress is prolonged. Under the conditions of our experiments, mutants that lacked other repair candidates--Suf proteins, glutathione, and NADPH: ferredoxin reductase--all repaired clusters at normal rates. We conclude that the mechanism of cluster repair is distinct from that of de novo assembly and that this is true because mild oxidative stress does not degrade clusters in vivo to the point of presenting an apoenzyme to the de novo cluster-assembly systems.
Characteristics of nerve growth factor induced hyperalgesia in adult rats: dependence on enhanced bradykinin-1 receptor activity but not neurokinin-1 receptor activation (1996)

Treatment of adult rats with a single dose of nerve growth factor (NGF, 1 mg/kg, i.p.) results in a prolonged hypersensitivity to noxious thermal stimulation which becomes noticeable within 30 min of administration and lasts for several days. A significant mechanical hyperalgesia develops within 7 h following injection of NGF and persists for up to 7 days. In the present set of experiments we describe certain quantitative features of this hyperalgesia. The initial thermal hyperalgesia can be highly variable and is associated to some degree with the presence of an overt immunologic reaction. The mechanical hyperalgesia is reproducible enough to reveal a clear dependency on the dose of NGF. We also examined the pharmacological properties of the NGF-induced hyperalgesia. The bradykinin BK1 receptor antagonist des-Arg9[Leu8]BK transiently blocked the thermal hyperalgesia when injected 1 day after NGF administration whereas mechanical thresholds were further reduced under this protocol. The BK2 antagonist HOE 140 had no effect on this late NGF-induced hyperalgesia. Injection of the neurokinin NK1 receptor antagonist CP-96345 or its inactive enantiomer CP-96344 one day after NGF both induced a transient block of NGF-induced thermal hyperalgesia indicating a non-specific effect rather than an action at NK1 receptors. This was confirmed by finding no reversal of NGF-induced hyperalgesia by RP67580, another NK1 receptor blocker. These results suggest upregulation and activation of BK1 but not NK1 receptors as an additional, probably peripheral, mechanism for the late phase of NGF-induced thermal hyperalgesia.
Impact of Common Epidermal Growth Factor Receptor and HER2 Variants on Receptor Activity and Inhibition by Lapatinib (2008)

The goal of this study was to characterize the effects of non-small cell lung carcinoma (NSCLC)-associated mutations in epidermal growth factor receptor (EGFR/ErbB1) and HER2 (ErbB2) on interactions with the dual tyrosine kinase inhibitor lapatinib. Biochemical studies show that commonly observed variants of EGFR [G719C, G719S, L858R, L861Q, and Delta746-750 (del15)] are enzyme activating, increasing the tyrosine kinase V(max) and increasing the K(m)((app)) for ATP. The point mutations G719C and L861Q had minor effects on lapatinib K(i)s, whereas EGFR mutations L858R and del15 had a higher K(i) for lapatinib than wild-type EGFR. Structural analysis of wild-type EGFR-lapatinib complexes and modeling of the EGFR mutants were consistent with these data, suggesting that loss of structural flexibility and possible stabilization of the active-like conformation could interfere with lapatinib binding, particularly to the EGFR deletion mutants. Furthermore, EGFR deletion mutants were relatively resistant to lapatinib-mediated inhibition of receptor autophosphorylation in recombinant cells expressing the variants, whereas EGFR point mutations had a modest or no effect. Of note, EGFR T790M, a receptor variant found in patients with gefitinib-resistant NSCLC, was also resistant to lapatinib-mediated inhibition of receptor autophosphorylation. Two HER2 insertional variants found in NSCLC were less sensitive to lapatinib inhibition than two HER2 point mutants. The effects of lapatinib on the proliferation of human NSCLC tumor cell lines expressing wild-type or variant EGFR and HER2 cannot be explained solely on the basis of the biochemical activity or receptor autophosphorylation in recombinant cells. These data suggest that cell line genetic heterogeneity and/or multiple determinants modulate the role played by EGFR/HER2 in regulating cell proliferation.
Structural Basis for the Interaction between Tankyrase-2 and a Potent Wnt-Signaling Inhibitor (2010)

We report two crystal structures of the PARP domain of human tankyrase-2 (TNKS2). Tankyrases are involved in fundamental cellular processes such as telomere homeostasis and Wnt signaling. The complex of TNKS2 with the potent inhibitor XAV939 provides insights into the molecular basis of the strong interaction and suggests routes for further development of tankyrase inhibitors.
A General and Fast Scoring Function for Protein−Ligand Interactions:  A Simplified Potential Approach (1999)

A fast, simplified potential-based approach is presented that estimates the protein-ligand binding affinity based on the given 3D structure of a protein-ligand complex. This general, knowledge-based approach exploits structural information of known protein-ligand complexes extracted from the Brookhaven Protein Data Bank and converts it into distance-dependent Helmholtz free interaction energies of protein-ligand atom pairs (potentials of mean force, PMF). The definition of an appropriate reference state and the introduction of a correction term accounting for the volume taken by the ligand were found to be crucial for deriving the relevant interaction potentials that treat solvation and entropic contributions implicitly. A significant correlation between experimental binding affinities and computed score was found for sets of diverse protein-ligand complexes and for sets of different ligands bound to the same target. For 77 protein-ligand complexes taken from the Brookhaven Protein Data Bank, the calculated score showed a standard deviation from observed binding affinities of 1.8 log Ki units and an R2 value of 0.61. The best results were obtained for the subset of 16 serine protease complexes with a standard deviation of 1.0 log Ki unit and an R2 value of 0.86. A set of 33 inhibitors modeled into a crystal structure of HIV-1 protease yielded a standard deviation of 0.8 log Ki units from measured inhibition constants and an R2 value of 0.74. In contrast to empirical scoring functions that show similar or sometimes better correlation with observed binding affinities, our method does not involve deriving specific parameters that fit the observed binding affinities of protein-ligand complexes of a given training set. We compared the performance of the PMF score, Böhm's score (LUDI), and the SMOG score for eight different test sets of protein-ligand complexes. It was found that for the majority of test sets the PMF score performs best. The strength of the new approach presented here lies in its generality as no knowledge about measured binding affinities is needed to derive atomic interaction potentials. The use of the new scoring function in docking studies is outlined.
Major Depression Is Associated with Significant Diurnal Elevations in Plasma Interleukin-6 Levels, a Shift of Its Circadian Rhythm, and Loss of Physiological Complexity in Its Secretion: Clinical Implications (2005)

We report profound morning elevations of plasma IL-6 and a reversal of its circadian rhythm in MDD patients, in the absence of hypercortisolism. These findings may be relevant to the increased risk for coronary heart disease and bone loss in MDD.