gebhart/patrepeval huggingface dataset:
STUDIES ON LIGNIN AND RELATED COMPOUNDS: XII. METHANOL LIGNIN (1935)

Methanol lignin was prepared by extracting spruce wood meal with absolute methyl alcohol, using hydrochloric acid as catalyst. In five small, bomb-tube experiments, methanol lignin preparations having the same methoxyl content (about 21.6%) were obtained, the product in each case being apparently homogeneous. The methanol lignin was acetylated, partially methylated by treatment with diazomethane, and fully methylated with dimethyl sulphate and sodium hydroxide. From the elementary analyses and the ratio of methoxyl in the original methanol lignin to that in the diazomethane-methylated compound a formula for the smallest building unit of the methanol lignin and for the native lignin can be derived. The latter is represented by the empirical formula C 47 H 52 O 16 , or, expanded, C 42 H 32 O 6 (OCH 3 ) 5 (OH) 5 .
Phase I and pharmacodynamic study of taxol in refractory acute leukemias. (1989)

Taxol, a novel antimicrotubule agent that enhances tubulin polymerization and microtubule stability, was administered to adults with refractory leukemias as a 24-h i.v. infusion in a Phase I study. The primary objectives were to determine the maximum tolerated dose of taxol administered on this schedule to patients with acute leukemias and describe the nonhematological toxicities which became dose limiting. The starting dose, 200 mg/m2, was based on the maximum tolerated dose in solid tumor trials, in which myelosuppression precluded dose escalation. Seventeen patients received 28 evaluable courses at 200, 250, 315, and 390 mg/m2. Severe mucositis limited further dose escalation. Other nonhematological effects included peripheral neuropathy, alopecia, myalgias, arthralgias, nausea, vomiting, diarrhea, and an acute pulmonary reaction that was presumptively due to taxol's Cremophor vehicle. Mean peak taxol plasma concentrations at all dose levels were in the range of concentrations that were previously demonstrated to induce microtubule bundles, a morphological effect associated with cytotoxicity, in leukemia cells in vitro. Pretreatment blasts from 12 patients were incubated with taxol ex vivo. Taxol-induced microtubule bundles were apparent in the blasts of eight patients who also had cytoreduction of tumor, and sensitivity to bundle formation was related to the magnitude of antitumor activity. In contrast, taxol did not induce microtubule bundles ex vivo in the blasts of the other four total nonresponders. Based on this study, the maximum tolerated doses and recommended Phase II doses for taxol, limited by nonhematological toxicity and administered as a 24-h i.v. infusion to patients with refractory leukemias, are 390 and 315 mg/m2. Phase II trials at these myelosuppressive doses are required to determine taxol's activity in the treatment of leukemias. In addition, further evaluation of microtubule bundle formation ex vivo in Phase II studies is necessary to determine the ultimate utility of this assay in assessing tumor sensitivity to taxol.
A Convenient Method for the Selective Esterification of Amino-Alcohols (1978)

Abstract Esters of amino-alcohols have long been considered as important biologically active compounds1 and as intermediates for the synthesis of pharmaceutically significant materials2. This ester function can also serve as protective group for the hydroxyl group of amino-alcohols. In addition, unlike other protective groups3 which do not block amines either, the ester is stable in acidic medium and can readily be removed under very mild condition4. Several examples of selective o-acetylation of amino alcohols where the maine function is protected as the salt are found in the literature5. We have attempted to use these methods to synthesize several biologically interest armatic esters of amino alcohols. None of these procedures, however, gave the desired product in reasonable yields. We now wish to describe a convenient procedure to selectively prepare amino esters from amino alcohols.
Selective Placement of Carbon Nanotubes on Metal-Oxide Surfaces (2005)

We describe a method to selectively position carbon nanotubes on Al2O3 and HfO2 surfaces. The method exploits the selective binding of alkylphosphonic acids to oxide surfaces with large isoelectric points (i.e. basic rather than acidic surfaces). We have patterned oxide surfaces with acids using both microcontact printing and conventional lithography. With proper choice of the functional end group (e.g., -CH3 or -NH2), nanotube adhesion to the surface can be either prevented or enhanced.
Trends in the Development of New Antidepressants. Is there a Light at the End of the Tunnel? (2004)

Since the introduction of tricyclic antidepressants (TCAs) and monoamine oxidase inhibitors (MAOIs) in mid-1950's, treatment of depression has been dominated by monoamine hypotheses. The well-established clinical efficacy of TCAs and MAOIs is due, at least in part, to the enhancement of noradrenergic or serotonergic mechanisms, or to both. Unfortunately, their very broad mechanisms of action also include many unwanted effects related to their potent activity on cholinergic, adrenergic and histaminergic receptors. The introduction of selective serotonin reuptake inhibitors (SSRIs) over twenty years ago had been the next major step in the evolution of antidepressants to develop drugs as effective as the TCAs but of higher safety and tolerability profile. During the past two decades SSRIs (fluoxetine, fluvoxamine, paroxetine, sertraline, citalopram) gained incredible popularity and have become the most widely prescribed medication in the psychiatric practice. The evolution of antidepressants continued resulting in introduction of selective and reversible monoamine oxidase inhibitors (eg. moclobemid), selective noradrenaline (eg. reboxetine), dual noradrenaline and serotonin reuptake inhibitors (milnacipram, venlafaxin, duloxetin) and drugs with distinct neurochemical profiles such as mirtazapine, nefazadone and tianeptine. Different novel serotonin receptor ligands have also been intensively investigated. In spite of the remarkable structural diversity, most currently introduced antidepressants are 'monoamine based'. Furthermore, these newer agents are neither more efficacious nor rapid acting than their predecessors and approximately 30% of the population do not respond to current therapies. By the turn of the new millennium, we are all witnessing a result of innovative developmental strategies based on the better understanding of pathophysiology of depressive disorder. Several truly novel concepts have emerged suggesting that the modulation of neuropeptide (substance P, corticotrophin-releasing factor, neuropeptide Y, vasopressin V1b, melanin-concentrating hormone-1), N-methyl-D-aspartate, nicotinic acetylcholine, dopaminergic, glucocorticoid, delta-opioid, cannabinoid and cytokine receptors, gamma-amino butyric acid (GABA) and intracellular messenger systems, transcription, neuroprotective and neurogenic factors, may provide an entirely new set of potential therapeutic targets, giving hope that further major advances might be anticipated in the treatment of depressive disorder soon. The goal of this review is to give a brief overview of the major advances from monoamine-based treatment strategies, and particularly focus on the new emerging approaches in the treatment of depression.
Different mechanisms underlying the stimulation of KCa channels by nitric oxide and carbon monoxide (2002)

The molecular mechanisms underlying the effects of nitric oxide (NO) and carbon monoxide (CO), individually and collectively, on large-conductance calcium-activated K+ (KCa) channels were investigated in rat vascular smooth muscle cells (SMCs). Both NO and CO increased the activity of native KCa channels. Dehydrosoyasaponin-I, a specific agonist for β subunit of KCa channels, increased the open probability of native KCa channels only when it was delivered to the cytoplasmic surface of membrane. CO, but not NO, further increased the activity of native KCa channels that had been maximally stimulated by dehydrosoyasaponin-I. After treatment of SMCs with anti–KCa,β subunit antisense oligodeoxynucleotides, the stimulatory effect of NO, but not of CO, on KCa channels was nullified. CO, but not NO, enhanced the KCa current densities of heterologously expressed cloned KCa,α subunit, showing that the presence of KCa,β subunit is not a necessity for the effect of CO but essential for that of NO. Finally, pretreatment of SMCs with NO abolished the effects of subsequently applied CO or diethyl pyrocarbonate on KCa channels. In summary, the stimulatory effects of CO and NO on KCa channels rely on the specific interactions of these gases with KCa,α and KCa,β subunits.
Strategies for the Construction of Supramolecular Compounds through Coordination Chemistry (2001)

Synthetic organic chemists enjoy the luxury of having a large collection of reliable reactions at their disposal for preparing small molecules, mesoscopic structures, and polymers. Coordination chemists, on the other hand, are faced with the fact that transition metal chemistry, when normalized for the number of transition metals, has relatively few high-yielding reactions, when compared to the chemistry of carbon, for preparing even small molecule structures. This lack of control is manifested, in large part, in the weak metal-ligand interactions found in coordination complexes as compared with the strong covalent bonds in organic compounds. Weak bonding often translates into many reaction pathways that are not substantially different from an energetic point of view, and therefore, results in poor selectivity. As a result, many coordination chemists in recent years have come to the realization that it may be easier and more productive to develop straightforward and reliable routes to mesoscopic supramolecular structures by capitalizing on the modest collection of high-yielding reactions in coordination chemistry, the directional bonding afforded by metal centers, and strategies aimed at taking advantage of the weak metal bonds found in coordination complexes. Three emerging synthetic strategies, the symmetry-interaction, directional-bonding, and weak-link synthetic approaches, all use metal centers as structural building blocks to rationally assemble molecular components into supramolecular metallocyclophanes. These three approaches are discussed herein, and the fundamental principles underlying each as well as their capabilities are compared and contrasted.
Advancing Understanding of Knowledge's Role in Lay Risk Perception (1993)

Emphasizing how knowledge affects lay Risk perception, summarizing studies and suggesting further research, the author differentiates between knowledge production, knowledge dissemination and information processing as affected by, e.g., heuristics and Risk aversion. He also suggests that better understanding of lay knowledge can also illuminate experts' hazard knowledge.
Metal-free Synthesis of Ynones from Acyl Chlorides and Potassium Alkynyltrifluoroborate Salts (2015)

Ynones are a valuable functional group and building block in organic synthesis. Ynones serve as a precursor to many important organic functional groups and scaffolds. Traditional methods for the preparation of ynones are associated with drawbacks including harsh conditions, multiple purification steps, and the presence of unwanted byproducts. An alternative method for the straightforward preparation of ynones from acyl chlorides and potassium alkynyltrifluoroborate salts is described herein. The adoption of organotrifluoroborate salts as an alternative to organometallic reagents for the formation of new carbon-carbon bonds has a number of advantages. Potassium organotrifluoroborate salts are shelf stable, have good functional group tolerance, low toxicity, and a wide variety are straightforward to prepare. The title reaction proceeds rapidly at ambient temperature in the presence of a Lewis acid without the exclusion of air and moisture. Fair to excellent yields may be obtained via reaction of various aryl and alkyl acid chlorides with alkynyltrifluoroborate salts in the presence of boron trichloride.
Nifedipine prevents hepatic fibrosis in a non-alcoholic steatohepatitis model induced by an L-methionine-and choline-deficient diet (2011)

Recent reports have shown that nifedipine, a calcium channel blocker, increases peroxisome proliferator-activated receptor-γ (PPARγ) activity. Since PPARγ agonists, such as pioglitazone and rosiglitazone, are effective in reducing non-alcoholic steatohepatitis (NASH) and cirrhosis in animal models, we examined the protective effects of nifedipine, as compared with bezafibrate, a PPARα agonist, in a NASH model induced by an L-methionine- and choline-deficient (MCD) diet. An MCD diet for 20 weeks changed the color of the rat liver to yellow with an irregular surface, whereas the color of the liver in both the bezafibrate and nifedipine treatment groups was markedly changed to yellow-brown with a smooth surface. Furthermore, nifedipine, as well as bezafibrate, significantly prevented liver fibrosis induced by an MCD diet, as assessed by Masson's trichrome staining, accompanied by a significant decrease in serum AST. Overall, nifedipine treatment resulted in an improvement in NASH, similar to bezafibrate, in a rat model. In hypertensive patients with metabolic syndrome, nifedipine may provide additional benefits, beyond its blood pressure-lowering effects, to prevent NASH and fatty liver disease.
Detection of homeobox genes in development and evolution. (1991)

The homeobox genes encode a family of DNA-binding regulatory proteins whose function and genomic organization make them an important model system for the study of development and differentiation. Oligonucleotide primers corresponding to highly conserved regions of Antennapediaclass homeodomains were designed to detect and identify homeobox sequences in populations of DNA or RNA by means of the polymerase chain reaction (PCR). Here we present a survey of sequences detected by PCR using an initial set of primers (HoxA and HoxB) based on an early nucleotide consensus for vertebrate Antennapedia-class homeodomains. Several novel sequences are reported from both mouse genomic DNA and RNA from the developing mouse telencephalon. Forebrain-derived clones are similar to the chicken CHox7, Drosophila H2.0, and mouse Hlx genes. PCR also proved to be a rapid method for identifying homeobox sequences from diverse metazoan species. Cloning of three Antennapedia-related sequences from cnidarians provides evidence of ancient roles for homeobox genes early in metazoan evolution.
ALPS: The Age-Layered Population Structure for Reducing the Problem of Premature Convergence (Genetic Programming Track) (2006)

To reduce the problem of premature convergence we dene a new attribute of an individual, its age, and propose the Age-Layered Population Structure (ALPS), in which age is used to restrict competition and breeding between members of the population. ALPS diers from a typical EA by segregating individuals into dieren t age-layers by their \age { a measure of how long the genetic material has been in the population { and by regularly replacing all individuals in the bottom layer with randomly generated ones. The introduction of new, randomly generated individuals at regular intervals results in an EA that is never completely converged and is always looking at new parts of the tness landscape. By using age to restrict competition and breeding search is able to develop promising young individuals without them being dominated by older ones. We demonstrate the eectiveness of the ALPS algorithm on an antenna design problem in which evolution with ALPS produces antennas more than twice as good as does evolution with two other types of EAs. Further analysis shows that the ALPS model does allow the ospring of newly generated individuals to move the population out of mediocre local-optima to better parts of the tness landscape.
Insulinomimetic effect on glucose transport by epidermal growth factor when combined with a major histocompatibility complex class I-derived peptide. (1993)

Peptides derived from the alpha 1-region of the murine H-2Dk molecule enhance glucose uptake in rat adipose cells above the maximum obtained with insulin stimulation alone (Stagsted, J., Reaven, G. M., Hansen, T., Goldstein, A., and Olsson, L. (1990) Cell 62, 297-307). We now describe that epidermal growth factor (EGF) in combination with the same peptides, Dk-(61-85) and Dk-(62-85), stimulates cellular glucose uptake 5-7 times over the basal level, i.e. to 30-50% of the maximal insulin effect. EGF alone increased glucose uptake by only approximately 50% above basal and the peptide alone by 100% above basal. Maximal effect of EGF and peptide was reached in 10-20 min with 30 microM peptide (EC50 10-15 microM) and 50 nM EGF (EC50 1-2 nM). The effect of EGF and peptide on glucose uptake was additive to that of insulin and peptide until the maximal level attained with insulin and peptide was reached. The combined effect of EGF plus peptide on glucose transport was associated with a recruitment of GLUT4 molecules to the plasma membrane. However, the phosphatidylinositol (PI) kinase which is activated by insulin was not activated by EGF plus peptide. Thus, the effect of EGF plus peptide on glucose uptake seems independent of the activity status of the insulin receptor. 125I-Labeled EGF bound specifically to rat adipose cells with an apparent affinity of approximately 2 nM and Bmax approximately 5 x 10(3). However, the major histocompatibility complex (MHC) peptides did not affect EGF-stimulated internalization of EGF receptor, in contrast to their effect on the insulin receptors. Transforming growth factor alpha had an effect similar to EGF on glucose uptake. Three other peptides derived from other parts of murine MHC class I had no effect on glucose uptake in combination with EGF. Thus, EGF in combination with certain MHC class I-derived peptides is insulinomimetic concerning glucose transport and this effect is independent of the insulin receptor activity.
International Workshop on Lessons From Animal Models for Human Type 1 Diabetes (2001)

Several self-antigens have been reported as targets of the autoimmune response in nonobese diabetic (NOD) mice. The aim of this workshop was to identify autoantibody assays that could provide useful markers of autoimmunity in this animal model for type 1 diabetes. More than 400 serum samples from NOD (4, 8, and 12 weeks of age and at diabetes onset), BALB/c, and B6 mice were collected from six separate animal facilities, coded, and distributed to five laboratories for autoantibody measurement. Insulin autoantibodies (IAA) were measured by radiobinding assay (RBA) by four laboratories and by enzyme-linked immunosorbent assay (ELISA) in one laboratory. Using the 99th percentile of BALB/c and B6 control mice as the threshold definition of positivity, IAA by RBA were detected in NOD mice at frequencies ranging from 10 to 30% at age 4 weeks, from 26 to 56% at 8 weeks, from 42 to 56% at 12 weeks, and from 15 to 75% at diabetes onset. With ELISA, IAA signals differed significantly between control mouse strains and increased with age in both control and NOD mice, with frequencies in NOD animals being 0% at 4 weeks, 14% at 8 weeks, 19% at 12 weeks, and 42% at diabetes onset. For IAA, the ELISA results were relatively discordant with those of RBA. GAD autoantibody (GADA) and IA-2 autoantibody (IA-2A) signals obtained by RBA were low (maximum 2.5% of total) but were increased in NOD mice compared with control mice at diabetes onset (GADA 29-50%; IA-2A 36-47%). ELISA also detected GADA (42%) and IA-2A (50%) at diabetes onset, with results concordant with those of RBA. Remarkably, GADA and IA-2A frequencies varied significantly with respect to the source colony of NOD mice. Furthermore, whereas neither GADA nor IA-2A correlated with IAA, there was strong concordance between GADA and IA-2A in individual mice. Sera with increased binding to GAD and IA-2 also had increased binding to the unrelated antigen myelin oligodendrocyte glycoprotein, and binding to GAD could not be inhibited with excess unlabeled antigen, suggesting nonspecific interactions. In sum, this workshop demonstrated that IAA measured by sensitive RBA are a marker of autoimmunity in NOD mice and draw into question the true nature of GADA and IA-2A in this animal model.
Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data (2011)

The application of established drug compounds to new therapeutic indications, known as drug repositioning, offers several advantages over traditional drug development, including reduced development costs and shorter paths to approval. Recent approaches to drug repositioning use high-throughput experimental approaches to assess a compound's potential therapeutic qualities. Here, we present a systematic computational approach to predict novel therapeutic indications on the basis of comprehensive testing of molecular signatures in drug-disease pairs. We integrated gene expression measurements from 100 diseases and gene expression measurements on 164 drug compounds, yielding predicted therapeutic potentials for these drugs. We recovered many known drug and disease relationships using computationally derived therapeutic potentials and also predict many new indications for these 164 drugs. We experimentally validated a prediction for the antiulcer drug cimetidine as a candidate therapeutic in the treatment of lung adenocarcinoma, and demonstrate its efficacy both in vitro and in vivo using mouse xenograft models. This computational method provides a systematic approach for repositioning established drugs to treat a wide range of human diseases.
Nonnatural deoxyribonucleoside D3 incorporated in an intramolecular DNA triplex binds sequence-specifically by intercalation (1993)

Oligonucleotide-directed triple helix formation is one of the&#13;\nmost powerful methods for the sequence-specific recognition of&#13;\ndouble-helical DNA. Pyrimidine oligonucleotides bind purine&#13;\ntracts in the major groove of DNA parallel to the purine Watson-Crick&#13;\nstrand through the formation of specific Hoogsteen-type&#13;\nhydrogen bonds. Specificity is derived from thymine (T)&#13;\nrecognition of adenine·thymine (A·T) base pairs (T·A·T triplet)&#13;\nand N3-protonated cytosine (C+) recognition of guanine-cytosine&#13;\n(G·C) base pairs (C + G·C triplets). The sequence-specific&#13;\nrecognition of double-helical DNA by a third strand to form a&#13;\ntriple helix is limited to mostly purine tracts. Although G in the&#13;\nthird strand has been found to specifically bind to T·A, the lower&#13;\nstability of the G·T·A triplet and its dependence on the sequence&#13;\nof the neigh boring triplets reveals that this will have limitations.&#13;\nIn an attempt to extend the recognition code to all four Watson-Crick&#13;\nbase pairs, the nonnatural deoxyribonucleoside 1-(2-deoxy/&#13;\nβ-D-ribofuranosyl)-4-(3-benzamido)phenylimidazole [D_3] was&#13;\nsynthesized and incorporated into pyrimidine DNA oligonucleotides&#13;\n(Figure 1a). It was found that D_3 selectively recognizes&#13;\nboth T·A and C·G Watson-Crick base pairs within the&#13;\npyrimidine·purine·pyrimidine triple-helix motif. This was also&#13;\nfound to have a nearest neighbor dependence.