gebhart/patrepeval huggingface dataset:
Carnosic acid, a <i>catechol‐type</i> electrophilic compound, protects neurons both <i>in vitro</i> and <i>in vivo</i> through activation of the Keap1/Nrf2 pathway via <i>S‐</i>alkylation of targeted cysteines on Keap1 (2007)

Electrophilic compounds are a newly recognized class of redox-active neuroprotective compounds with electron deficient, electrophilic carbon centers that react with specific cysteine residues on targeted proteins via thiol (S-)alkylation. Although plants produce a variety of physiologically active electrophilic compounds, the detailed mechanism of action of these compounds remains unknown. Catechol ring-containing compounds have attracted attention because they become electrophilic quinones upon oxidation, although they are not themselves electrophilic. In this study, we focused on the neuroprotective effects of one such compound, carnosic acid (CA), found in the herb rosemary obtained from Rosmarinus officinalis. We found that CA activates the Keap1/Nrf2 transcriptional pathway by binding to specific Keap1 cysteine residues, thus protecting neurons from oxidative stress and excitotoxicity. In cerebrocortical cultures, CA-biotin accumulates in non-neuronal cells at low concentrations and in neurons at higher concentrations. We present evidence that both the neuronal and non-neuronal distribution of CA may contribute to its neuroprotective effect. Furthermore, CA translocates into the brain, increases the level of reduced glutathione in vivo, and protects the brain against middle cerebral artery ischemia/reperfusion, suggesting that CA may represent a new type of neuroprotective electrophilic compound.
Contrasting effects of fish oil and safflower oil on hepatic peroxisomal and tissue lipid content (2002)

To examine the mechanism by which fish oil protects against fat-induced insulin resistance, we studied the effects of control, fish oil, and safflower oil diets on peroxisomal content, fatty acyl-CoA, diacylglycerol, and ceramide content in rat liver and muscle. We found that, in contrast to control and safflower oil-fed rats, fish oil feeding induced a 150% increase in the abundance of peroxisomal acyl-CoA oxidase and 3-ketoacyl-CoA thiolase in liver but lacked similar effects in muscle. This was paralleled by an almost twofold increase in hepatic peroxisome content (both P < 0.002 vs. control and safflower). These changes in the fish oil-fed rats were associated with a more than twofold lower hepatic triglyceride/diacylglycerol, as well as intramuscular triglyceride/fatty acyl-CoA, content. In conclusion, these data strongly support the hypothesis that n-3 fatty acids protect against fat-induced insulin resistance by serving as peroxisome proliferator-activated receptor-alpha ligands and thereby induce hepatic, but not intramuscular, peroxisome proliferation. In turn, an increased hepatic beta-oxidative capacity results in lower hepatic triglyceride/diacylglycerol and intramyocellular triglyceride/fatty acyl-CoA content.
Characterization of Calcium Alginate Beads Containing Structurally Similar Drugs (2006)

The aim of this study was to investigate the characteristics of alginate beads prepared by ionotropic gelation in which structurally similar drugs were incorporated. For this purpose theophylline and theobromine were selected as model drugs. The influence of incorporated drugs on bead characteristics such as size, shape, and morphology, as well as encapsulation efficiency, was examined. It was found that theobromine as well as theophylline content in beads significantly decreased with increasing hardening time due to drug diffusion into the hardening media. In theobromine beads the drug content was extremely improved by dropping the alginate and drug solution into an acidic calcium chloride solution, while theophylline content was to some extent improved by the hardening of beads in a calcium chloride solution saturated with the drug. The most evident difference between theophylline and theobromine beads was in their shape and morphology. Theobromine beads were round, while theophylline ones had an irregular shape with an extremely wrinkled surface. The distinction in shape was highly dependent on drug content. Additionally, it was demonstrated that beads' shape was dependent on preparation conditions as well. On the basis of x-ray powder diffraction (XRPD) and differential scanning calorimetry (DSC) analyses and scanning electron microscope (SEM) photographs it was found that the most of the drug in bead was present in an amorphous state. Therefore, it is suggested that some drug-alginate interactions could be present in beads and might be responsible for the different shape of theophylline and theobromine beads. Thus it can be concluded that the preparation of beads by ionotropic gelation cannot be generalized even though structurally similar drugs are incorporated.
Condensation Reaction Between 2,2-Diphenylthio-2,3-Dideoxyribose and Silylated Pyrimidine Bases (1992)

Abstract The condensation reaction between 2,2-diphenylthio-2,3-dideoxyribose and silylated pyrimidine bases was examined. In the presence of TMSOTf as a catalyst, this reaction proceeded to give the nucleosides in the ratio of α: β = 2:8. Each β-anomer was converted to protected 2′,3′-dideoxynucleosides.
Aging, Stem Cells and Tissue Regeneration: Lessons from Muscle (2005)

With age, there is a gradual decline in the regenerative properties of most tissues due to a combination of age-dependent changes in tissue-specific stem cells and in the environmental cues that promote those cells to participate in tissue maintenance and repair. In adult skeletal muscle, where the resident dedicated stem cells ("satellite cells") are capable of rapid and highly effective regeneration in response to injury, there is just such a loss of regenerative potential with age. Satellite cell activation and cell fate determination are controlled by the Notch signaling pathway that is initiated by the rapid increase in expression of the Notch ligand, Delta, following injury. In old muscle, this upregulation of Delta is blunted and thus satellite cell activation is markedly diminished. However, by indirectly inducing Notch activity, the regenerative potential of aged satellite cells can be restored. Furthermore, exposure of aged satellite cells to serum from young mice, either in vivo by heterochronic parabiotic pairings or in vitro, rejuvenates the satellite cell response. This restorative potential suggests that tissue-specific stem cells do not lose their ability to participate in tissue maintenance and repair. Therefore, it may be that even very old stem cells may be capable of maintaining and repairing aged tissues if provided with optimal environmental cues.
Polyphenol-rich beverages promote a sustainable and renewable generation of energy and prevent neurotoxicity (2013)

Polyphenol-rich beverages, formulations 1 and formulation 2 composed of herbal and berry extracts were developed. Their impact on adenosine triphosphate (ATP) responses was investigated in vitro and compared to that of well-known commercial drinks (Red Bull, Coca-Cola, Antioxia, Tetley green tea). Results show that mitochondrial activity, intracellular and extracellular ATP responses are impacted upon the exposure to polyphenol-rich beverages to promote a sustainable and renewable energy supply in human oral CAL27 mucosal cells. While herbal extracts are important for the renewable energetic activity, berry extracts play a role in regulating energy conservation. Prior exposure of polyphenol-rich beverages to CAL27 cells prevented subsequent neurotoxicity of SH-SY5Y dopaminergic cells undergoing oxidative stress. Formulation 1 was best at modulating ATP and neuroprotective responses. On the other hand, Red Bull caused energy depletion, and did not prevent neurotoxicity. In summary, polyphenol-rich drinks are potential energy drinks that promote a sustainable and renewable generation of energy. In particular, Formulation 1 may be a healthy caffeine-free alternative to energy drinks with side effects, such as energy crashing and neurotoxicity.

	 

	Key words: Anthocyanins, adenosine triphosphate (ATP), conservation, dopamine, energy crashing, energy drink, mitochondria, neuroprotection, polyphenols, red bull.
New endocyclic enamine synthesis (1970)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNew endocyclic enamine synthesisDavid Albert EvansCite this: J. Am. Chem. Soc. 1970, 92, 26, 7593–7595Publication Date (Print):December 1, 1970Publication History Published online1 May 2002Published inissue 1 December 1970https://pubs.acs.org/doi/10.1021/ja00729a019https://doi.org/10.1021/ja00729a019research-articleACS PublicationsRequest reuse permissionsArticle Views586Altmetric-Citations45LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Removal of CO2 from flue gas with ammonia solution in a packed tower (2010)

Ammonia was used for the major absorbent while sodium hydroxide was used as a reference in either a bubble column (semi-batch reaction) or a packed tower (continuous reaction) to absorb CO2 in this study. In the bubble column, bubbling time as a function of temperature, pH, and dissolved inorganic carbon concentration in the solution was measured to see the characteristics of the reaction and the capacity of ammonia with regard to CO2 absorption. Its CO2 removal efficiency (RE) and/or absorbent utilization (AU) in the packed tower were quantified as a function of packing type, concentration/pH of absorbent, concentration of simulated flue gas (CO2, O2, SO2, NO), gas flow rate, and liquid/gas ratio. Additionally, an empirical formula obtained, via the analysis of a multiple regression, was used to relate CO2 RE and the major operation parameters. In the bubble column, the capacity of ammonia on CO2 absorption is 1.4 kg CO2 kg -1 NH3 in an exothermic reaction. In the packed tower, the optimum number of packing layers is 21 layers in an orderly arrangement with a reaction length of 220 mm. In addition, the optimum CO2 RE and AU are 93 and 19%, respectively, at a given condition. After a multiple regression, the empirical formula indicates four major parameters responsible for CO2 removal, namely ammonia concentration, CO2 concentration, gas flow rate, and initial pH of ammonia solution. The results of this work are feasible for practical application with regard to CO2 absorption with ammonia in a packed tower.
A randomized Web-cache replacement scheme (2002)

The problem of document replacement in Web caches has received much attention in the literature research, and it has been shown that the eviction rule "replace the least recently used document" performs poorly in Web caches. Instead, it has been shown that using a combination of several criteria, such as the recentness and frequency of use, the size, and the cost of fetching a document, leads to a sizeable improvement in hit rate and latency reduction. However, in order to implement these novel schemes, one needs to maintain complicated data structures. We propose randomized algorithms for approximating any existing Web-cache replacement scheme and thereby avoid the need for any data structures. At document-replacement times, the randomized algorithm samples N documents from the cache and replaces the least useful document from the sample, where usefulness is determined according to the criteria mentioned above. The next M<N least useful documents are retained for the succeeding iteration. When the next replacement is to be performed, the algorithm obtains N-M new samples from the cache, and replaces the least useful document from the N-M new samples and the M previously retained. Using theory and simulations, we analyze the algorithm and find that it matches the performance of existing document replacement schemes for values of N and M as low as 8 and 2 respectively. Rather surprisingly, we find that retaining a small number of samples from one iteration to the next leads to an exponential improvement in performance as compared to retaining no samples at all.
Specific phosphorothioate substitutions probe the active site of Bacillus subtilis ribonuclease P (2002)

Ribonuclease P (RNase P) is a ribonucleoprotein that requires magnesium ions to catalyze the 5' maturation of transfer RNA. To identify interactions essential for catalysis, the properties of RNase P containing single sulfur substitutions for nonbridging phosphodiester oxygens in helix P4 of Bacillus subtilis RNase P were analyzed using transient kinetic experiments. Sulfur substitution at the nonbridging oxygens of the phosphodiester bond of nucleotide U51 only modestly affects catalysis. However, phosphorothioate substitutions at A49 and G50 decrease the cleavage rate constant enormously (300-4,000-fold for P RNA and 500-15,000-fold for RNase P holoenzyme) in magnesium without affecting the affinity of pre-tRNA(Asp), highlighting the importance of this region for catalysis. Furthermore, addition of manganese enhances pre-tRNA cleavage catalyzed by B. subtilis RNase P RNA containing an Sp phosphorothioate modification at A49, as observed for Escherichia coli P RNA [Christian et al., RNA, 2000, 6:511-519], suggesting that an essential metal ion may be coordinated at this site. In contrast, no manganese rescue is observed for the A49 Sp phosphorothioate modification in RNase P holoenzyme. These differential manganese rescue effects, along with affinity cleavage, suggest that the protein component may interact with a metal ion bound near A49 in helix P4 of P RNA.
Regulation of metallothionein genes by heavy metalsappears to be mediated by a zinc-sensitive inhibitor that interacts with aconstitutively active transcription factor, MTF-1. (1994)

A construct, MRE-beta Geo, with five metal response elements fused to a selectable reporter gene was transfected into BHK cells and a stable clone that could be induced up to 100-fold by zinc, cadmium, bismuth, silver, cobalt, copper, mercury, or nickle was isolated. Some, and perhaps all, of these metals induce MRE-beta Geo by displacing zinc. Transfection of these cells with a construct encoding the transcriptional activator MTF-1 resulted in constitutive expression of MRE-beta Geo, whereas expression of an antisense MTF-1 construct in these cells prevented induction by all of the metals. A variant cell line with high constitutive expression in the absence of added metals was isolated; normal regulation was restored by cell fusion. These results suggest that regulation of metallothionein genes by metals is mediated by MTF-1 interacting with metal response elements and that zinc functions to release MTF-1 from an inhibitor.
Tissue- and age-specific expression patterns of alternatively spliced agrin mRNA transcripts in embryonic rat suggest novel developmental roles (1995)

Agrin is an extracellular matrix protein that mediates the nerve-induced clustering of nicotinic acetylcholine receptors on target muscle cells, and thus plays a key role in development of the neuromuscular synapse. Alternative exon usage within the rat agrin gene predicts numerous protein isoforms, which differ by the inclusion or exclusion of small inserts at three sites in the C-terminal half of the molecule; the insert status at two of these sites, termed Y and Z, profoundly influences the acetylcholine receptor clustering activity. We have examined the cellular expression patterns of agrin messenger RNA transcripts during rat embryogenesis by in situ hybridization with isoform-specific probes. Six 36-mer oligonucleotide probes were designed to distinguish between mRNA isoforms at either the Y site: the encoded protein contains either no insert (Y0) or a 4-amino acid insert (Y4), or the Z site: the encoded protein contains either no insert or one of 8 (Z8), 11 (Z11), or 19 (Z19) amino acids. Strikingly different expression patterns were observed for the individual Y- and Z-site encoding messages. While optional exon usage predicts the possibility of eight different agrin isoforms at the two splice sites, we detected only four isoforms in vivo: Y4Z0, Y0Z0, Y4Z8, and Y4Z19. The Y4Z0 transcript, which comprised the majority of the agrin expressed, was localized exclusively to nervous tissue and exhibited a distribution profile suggestive of a potential role in neurogenesis and/or neural differentiation. From embryonic day 13 to birth, Y4Z0 was found in mitotic ventricular zones, spinal, cranial, and sympathetic ganglia, and diffusely throughout the brain. In contrast, Y0Z0 was not expressed in neurons, but specifically labeled capillary endothelial cells within the developing nervous system. Y4Z8 and Y4Z19, the forms most active in acetylcholine receptor aggregation, were expressed at low levels only in spinal and brainstem motor neurons; Z19 expression declined from embryonic day 15 to adulthood, whereas Z8 expression increased slightly during this period. Transcripts encoding the Z11 insert could not be detected. These data suggest potential novel biological roles for agrin beyond that originally proposed in synapse formation.
Home and Work Place Prediction for Urban Planning Using Mobile Network Data (2014)

We present methods to predict and validate home and work places of anonymized users using their mobile network data. Knowledge of home and work place of a user is essential in order to find his (and overall population) mobility profiles. There are many methods that predict home and work places using GPS data. But unlike GPS data, mobile network data using GSM do not provide the exact location of a phone event. We use a novel criterion that combines an extracted feature from mobile data (i.e., Inactivity - no phone event for a given period of time) with open source data about location category % (i.e., Streetdirectory.com) to predict home location. Results show that the new criterion gives better prediction accuracy than inactivity alone. We predict work place using the idea that one goes to her work place on most of the weekdays but rarely on weekends. We validate our methods by comparing against the ground truth obtained from open source data. Validation results show that our proposed methods are about 25% more accurate than existing methods both for home and work place predictions.
Identification in gelada baboons (Theropithecus gelada) of a distinct simian T-cell lymphotropic virus type 3 with a broad range of Western blot reactivity (2004)

Antibodies to simian T-cell lymphotropic virus (STLV) were found in serum or plasma from 12 of 23 (52.2 %) gelada baboons (Theropithecus gelada) captive in US zoos. A variety of Western blot (WB) profiles was seen in the 12 seroreactive samples, including human T-cell lymphotropic virus (HTLV)-1-like (n=5, 41.7 %), HTLV-2-like (n=1, 8.3 %), HTLV-untypable (n=4, 33.3 %) and indeterminate (n=2, 16.6 %) profiles. Phylogenetic analysis of tax or env sequences that had been PCR amplified from peripheral blood lymphocyte DNA available from nine seropositive geladas showed that four were infected with identical STLV-1s; these sequences clustered with STLV-1 from Celebes macaques and probably represent recent cross-species infections. The tax sequences from the five remaining geladas were also identical and clustered with STLV-3. Analysis of the complete STLV-3 genome (8917 bp) from one gelada, TGE-2117, revealed that it is unique, sharing only 62 % similarity with HTLV-1/ATK and HTLV-2/Mo. STLV-3/TGE-2117 was closest genetically to STLV-3 from an Eritrean baboon (STLV-3/PH969, 95.6 %) but more distant from STLV-3s from red-capped mangabeys from Cameroon and Nigeria (STLV-3/CTO-604, 87.7 %, and STLV-3/CTO-NG409, 87.2 %, respectively) and Senegalese baboons (STLV-3/PPA-F3, 88.4 %). The genetic relatedness of STLV-3/TGE-2117 to STLV-3 was confirmed by phylogenetic analysis of a concatenated gag-pol-env-tax sequence (6795 bp). An ancient origin of 73 628-109 809 years ago for STLV-3 was estimated by molecular clock analysis of third-codon positions of gag-pol-env-tax sequences. LTR sequences from five STLV-3-positive geladas were >99 % identical and clustered with that from a Papio anubisxP. hamadryas hybrid Ethiopian baboon, suggesting a common source of STLV-3 in these sympatric animals. LTR sequences obtained 20 years apart from a mother-infant pair were identical, providing evidence of both mother-to-offspring transmission and a high genetic stability of STLV-3. Since STLV-3-infected primates show a range of HTLV-like WB profiles and have an ancient origin, further studies using STLV-3-specific testing are required to determine whether STLV-3 infects humans, especially in regions of Africa where STLV-3 is endemic.
Retinal pigment epithelium segmentation by polarization sensitive optical coherence tomography (2008)

We present a new method for identifying and segmenting the retinal pigment epithelium (RPE) in polarization sensitive optical coherence tomography (PS-OCT) images of the human retina. Contrary to previous, intensity based segmentation algorithms, our method uses an intrinsic tissue property of the RPE: its depolarizing, or polarization scrambling effect on backscattered light. Two different segmentation algorithms are presented and discussed: a simpler algorithm based on retardation data, and a more sophisticated algorithm based on local variations of the polarization state calculated from averaged Stokes vector elements. By using a state of the art spectral domain PS-OCT instrument, we demonstrate the method in healthy and diseased eyes.
Detection of deletions and cryptic translocations in Miller-Dieker syndrome by in situ hybridization. (1991)

Fluorescence in situ hybridization (FISH) using two cosmid probes (41A and P13) from the Miller-Dieker syndrome (MDS) critical region in 17p13.3 was performed in a blinded comparison of three MDS patients with submicroscopic deletions and in four normal relatives used as controls. The controls showed both chromosome 17 homologues labeled in 85%-95% of cells, while each patient showed only one homologue labeled in 75%-80% of cells. Two MDS patients with cryptic translocations were also studied. In one case, a patient and her mother had the same der(17) (p+), but the reciprocal product of the translocation could not be identified in the mother by G-banding (i.e., it was a "half-cryptic" translocation). FISH revealed a 3q;17p translocation. The other case involved a patient with apparently normal karyotype. Because a large molecular deletion was found, a translocation involving two G-negative telomeres (i.e., a "full-cryptic" translocation) was postulated. FISH studies on her father and normal brother showed an 8q;17p translocation. These studies demonstrate that in situ hybridization is an efficient method for deletion detection in Miller-Dieker syndrome. More important, parental studies by FISH on patients demonstrating molecular deletions and a normal karyotype may identify cryptic translocation events, which cannot be detected by other molecular genetic strategies. Similar in situ strategies for deletion detection can be developed for other microdeletion syndromes, such as Prader-Willi/Angelman syndrome or DiGeorge syndrome.