gebhart/patrepeval huggingface dataset:
Structure and Function of DNA Methyltransferases (1995)

In prokaryotes, the major role of DNA methylation is to protect host DNA against degradation by restriction enzymes. In eukaryotes, DNA methylation has been implicated in the control of several cellular processes, including differentiation, gene regulation, and embryonic development. Structural work on HhaI DNA methyltransferase demonstrates that the substrate nucleotide is completely flipped out of the helix during the modification reaction and has provided much insight into the enzymatic properties of S-adenosyl-L-methionine (SAM)-dependent DNA-modifying enzymes. Structural comparison of three enzymes, HhaI C5-cytosine methyltransferase, TaqI N6-adenine methyltransferase, and catechol O-methyltransferase, reveals a striking similarity in protein folding and indicates that many SAM-dependent methyltransferases have a common catalytic-domain structure. This feature permits the prediction of tertiary structure for other DNA, RNA, protein, and small-molecule methyltransferases from their amino acid sequences, including the eukaryotic CpG methyltransferases.
MicroRNAs in Metabolic Disease (2013)

Alterations in the metabolic control of lipid and glucose homeostasis predispose an individual to develop cardiometabolic diseases, such as type 2-diabetes mellitus and atherosclerosis. Work over the last years has suggested that microRNAs (miRNAs) play an important role in regulating these physiological processes. The contribution of miRNAs in regulating metabolism is exemplified by miR-33, an intronic miRNA encoded in the Srebp genes. miR-33 controls cellular cholesterol export and fatty acid degradation, whereas its host genes stimulate cholesterol and fatty acid synthesis. Other miRNAs, such as miR-122, also play a critical role in regulating lipid homeostasis by controlling cholesterol synthesis and lipoprotein secretion in the liver. This review article summarizes the recent findings in the field, highlighting the contribution of miRNAs in regulating lipid and glucose metabolism. We will also discuss how the modulation of specific miRNAs may be a promising strategy to treat metabolic diseases.
Expression of the tre operon of Bacillus subtilis 168 is regulated by the repressor TreR (1996)

The tre locus from Bacillus subtilis containing the genes treP, treA, and treR has been analyzed for its regulation. We demonstrate that at least treP and treA form an operon whose expression is regulated at the transcriptional level. TreR activity has been investigated in in vivo and in vitro studies. An insertional inactivation of treR led to a constitutive expression of treP and treA. Upstream of treP we identified a 248-bp DNA fragment containing a potential sigmaA-dependent promoter and two palindromes reflecting potential tre operators which led to complex formation with TreR-containing protein extracts in DNA retardation experiments. This complex formation is abolished in the presence of trehalose-6-phosphate, which probably acts as an inducer. Therefore, we assume that treR encodes the specific Tre repressor involved in regulation of the expression of the tre operon.
Inhibition of Intracellular Growth of Salmonella enterica Serovar Typhimurium in Tissue Culture by Antisense Peptide-Phosphorodiamidate Morpholino Oligomer (2009)

Two types of phosphorodiamidate morpholino oligomers (PMOs) were tested for inhibition of growth of Salmonella enterica serovar Typhimurium. Both PMOs have the same 11-base sequence that is antisense to the region near the start codon of acpP, which is essential for lipid biosynthesis and viability. To the 3' end of each is attached the membrane-penetrating peptide (RXR)4XB (R, X, and B indicate arginine, 6-aminohexanoic acid, and beta-alanine, respectively). One peptide-PMO (AcpP PPMO) has no charge on the PMO moiety. The second PPMO has three cations (piperazine) attached to the phosphorodiamidate linkages (3+Pip-AcpP PPMO). A scrambled-sequence PPMO (Scr PPMO) was synthesized for each type of PMO. The MICs of AcpP PPMO, 3+Pip-AcpP PPMO, and either one of the Scr PPMOs were 1.25 microM (7 microg/ml), 0.156 microM (0.94 microg/ml), and >160 microM (>900 microg/ml), respectively. 3+Pip-AcpP PPMO at 1.25 or 2.5 microM significantly reduced the growth rates of pure cultures, whereas AcpP PPMO or either Scr PPMO had no effect. However, the viable cell count was significantly reduced at either concentration of 3+Pip-AcpP PPMO or AcpP PPMO, but not with either Scr PPMO. In other experiments, macrophages were infected intracellularly with S. enterica and treated with 3 microM 3+Pip-AcpP PPMO. Intracellular bacteria were reduced >99% with 3+Pip-AcpP PPMO, whereas intracellular bacteria increased 3 orders of magnitude in untreated or Scr PPMO-treated cultures. We conclude that either AcpP PPMO or 3+Pip-AcpP PPMO inhibited growth of S. enterica in pure culture and that 3+Pip-AcpP PPMO reduced intracellular viability of S. enterica in macrophages.
Ensuring robust partitioning in multicore platforms for IMA systems (2012)

Robust partitioning enforcement is a mandatory requirement in IMA <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sup> systems. In this paper, we refine this requirement in the context of multicore processors and discuss a strategy to ensure it. We focus on a scenario in which several ARINC 653 partitions hosted on the same platform are executed at the same time on different cores. When this scenario is deployed on modern COTS <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> hardware, robust partitioning may be impaired by inter-core conflicts sequences. The issue with such a deployment strategy lies in the isolated parallel execution of several partitions. The approach presented here aims at identifying conditions that entail inter-core conflicts with a sufficient level of detail. This representation helps identifying robust partitioning failure causes. Such information is a first step towards an acceptation of true parallelism in partitioned systems, i.e. deployment on multicores.
Vascular image registration techniques: A living review (2016)

Registration of vascular structures is crucial for preoperative planning, intraoperative navigation, and follow-up assessment. Typical applications include, but are not limited to, Trans-catheter Aortic Valve Implantation and monitoring of tumor vasculature or aneurysm growth. In order to achieve the aforementioned goals, a large number of various registration algorithms has been developed. With this review paper we provide a comprehensive overview over the plethora of existing techniques with a particular focus on the suitable classification criteria such as the involved modalities of the employed optimization methods. However, we wish to go beyond a static literature review which is naturally doomed to be outdated after a certain period of time due to the research progress. We augment this review paper with an extendable and interactive database in order to obtain a living review whose currency goes beyond the one of a printed paper. All papers in this database are labeled with one or multiple tags according to 13 carefully defined categories. The classification of all entries can then be visualized as one or multiple trees which are presented via a web-based interactive app (http://livingreview.in.tum.de) allowing the user to choose a unique perspective for literature review. In addition, the user can search the underlying database for specific tags or publications related to vessel registration. Many applications of this framework are conceivable, including the use for getting a general overview on the topic or the utilization by physicians for deciding about the best-suited algorithm for a specific application.
Envelope Tracking or Polar—Which Is It? [Microwave Bytes] (2012)

The terms “envelope tracking” (ET), “evelope elimination and restoration” (EER), and “polar” are generally used interchangeably in the literature for any transmitter circuit built using a dynamic power supply (DPS) architecture on the RF power amplifier (PA). Indeed, these are sometimes combined together into the same category and called EER/ET or ET/EER [1]. It is my experience from more than 15 years working with these technologies that there are very distinct and major differences between these techniques. Establishing simple and clear definitions as to which is which helps us clearly understand the differences between them. More importantly, this allows much less ambiguity as the literature expands regarding these important transmitter techniques.
Platelet-derived growth factors-AA and -BB regulate collagen and collagenase gene expression differentially in human fibroblasts (1995)

Platelet-derived growth factor (PDGF) is a mitogen associated with tissue repair, a process involving collagen synthesis and remodelling by interstitial collagenase. This study examines and compares the regulation of interstitial collagenase and collagen gene expression by PDGF-AA and -BB in human fibroblasts. Time-course analysis showed that neither PDGF-AA or -BB had a consistent effect on the expression of pro-alpha 1(I) or pro-alpha 2(I) type-I collagen genes. In contrast, interstitial collagenase gene expression was found to be consistently up-regulated severalfold by PDGF-BB. Enhanced expression of the collagenase gene was not apparently due to up-regulation of its promoter activity in human dermal fibroblasts, as indicated by transient and stable transfection experiments. Unlike PDGF-BB, PDGF-AA did not alter collagenase mRNA levels under low-serum culture conditions. Thus, the biological activities of the PDGF homodimers are different, with PDGF-BB being clearly more potent than PDGF-AA in its regulation of collagenase gene expression.
Role of sublingual asenapine in treatment of schizophrenia (2011)

Asenapine tablets are a new option for the treatment of schizophrenia. Sublingual administration is essential because bioavailability if ingested is less than 2%. Efficacy is supported by acute and long-term randomized controlled studies conducted by the manufacturer, with asenapine 5 mg twice daily evidencing superiority over placebo in six-week studies of acute schizophrenia, and flexibly-dosed asenapine (modal dose 10 mg twice daily) superior to placebo in a 26-week maintenance of response study. Tolerability advantages over some second-generation antipsychotics, such as olanzapine, include a relatively favorable weight and metabolic profile, as demonstrated in a 52-week randomized, head-to-head, double-blind clinical trial. Although dose-related extrapyramidal symptoms and akathisia can be present, the frequency of these effects is lower than that for haloperidol and risperidone. Somnolence may also occur, and appears to be somewhat dose-dependent when examining rates of this among patients receiving asenapine for schizophrenia and bipolar disorder. Prolactin elevation can occur, but at a rate lower than that observed for haloperidol or risperidone. Unique to asenapine is the possibility of oral hypoesthesia, occurring in about 5% of participants in the clinical trials. Obstacles to the use of asenapine are the recommendations for twice-daily dosing and the need to avoid food or liquids for 10 minutes after administration, although the bioavailability is only minimally reduced if food or liquids are avoided for only two minutes.
Absolute quantitation of regional myocardial blood flow of rats using dynamic pinhole SPECT (2004)

PET and SPECT have been widely used to investigate the physiological function of animals in vivo. However, little efforts have been done to estimate absolute physiological parameters, i.e. blood flow of small animals. The present study was aimed at the absolute quantitation of myocardial blood flow of rats by means of the dynamic SPECT fitted with a pinhole collimator with a careful determination of the arterial input function (IF). The center-of-rotation was carefully aligned to the center of the field-of-view of a fixed gamma camera with the accuracy < 0.05 mm. A rat was placed on a rotating device that fixes the rat in a stand position. The arterial blood samples were frequently collected and their radioactivity concentration was measured using a well counter cross-calibrated to the SPECT images. Dynamic SPECT (the step-and-shoot mode) was initiated at 5 min after the injection of 201TlCl into the tail vein. Acquisition period was 10 sec at each rotation angle, and 120 view projection data were obtained. The 360-degree complete data sets were obtained at approximately 20 min interval for 5 time frames. Images were reconstructed by filtered-back projection technique with Feldkamp algorithm. The cross-calibration factor was determined using a cylindrical phantom of 5 cm diameter filled with the 201TlCl solution. Regions-of-interest were placed on the left ventricular wall to generate the tissue time activity curve (TTAC). TTAC and IF were fitted to the previously validated single-tissue compartment model to estimate the regional myocardial blood flow (rMBF) and volume of distribution (Vd) of thallium. The present system provided clear images of myocardial uptake of 201TlCl, and the time-dependent change of the tissue radioactivity concentration in regional basis, which was statistically sufficient for applying the compartment model analysis. The kinetic analysis yielded the rMBF of approximately 0.77 ml/min/g, which appeared to be an acceptable value with a consideration of contribution of partial volume effect and other error sources. Vd of approximately 91.9 ml/ml was also consistent with the know value of the potassium potential across the cell membrane. These results strongly suggested the potential of the dynamic pinhole SPECT as a tool for absolute quantitation of physiological parameters in small animals.
Modifications in the binding domain of avian retrovirus envelope protein to redirect the host range of retroviral vectors (1994)

International audience
Novel Cylindrical, Conical, and Macrocyclic Peptides from the Cyclooligomerization of Functionalized Thiazole Amino Acids (2000)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTNovel Cylindrical, Conical, and Macrocyclic Peptides from the Cyclooligomerization of Functionalized Thiazole Amino AcidsYogendra Singh, Nikolai Sokolenko, Michael J. Kelso, Lawrence R. Gahan, Giovanni Abbenante, and David P. FairlieView Author Information Centre for Drug Design and Development Institute for Molecular Bioscience and Department of Chemistry University of Queensland Brisbane, Qld 4072, Australia Cite this: J. Am. Chem. Soc. 2001, 123, 2, 333–334Publication Date (Web):December 19, 2000Publication History Received21 July 2000Published online19 December 2000Published inissue 1 January 2001https://pubs.acs.org/doi/10.1021/ja002666zhttps://doi.org/10.1021/ja002666zrapid-communicationACS PublicationsCopyright © 2001 American Chemical SocietyRequest reuse permissionsArticle Views828Altmetric-Citations56LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Group theory,Macrocycles,Monomers,Organic compounds,Peptides and proteins Get e-Alerts
Fuzzy and possibilistic shell clustering algorithms and their application to boundary detection and surface approximation. I (1995)

Traditionally, prototype-based fuzzy clustering algorithms such as the Fuzzy C Means (FCM) algorithm have been used to find "compact" or "filled" clusters. Recently, there have been attempts to generalize such algorithms to the case of hollow or "shell-like" clusters, i.e., clusters that lie in subspaces of feature space. The shell clustering approach provides a powerful means to solve the hitherto unsolved problem of simultaneously fitting multiple curves/surfaces to unsegmented, scattered and sparse data. In this paper, we present several fuzzy and possibilistic algorithms to detect linear and quadric shell clusters. We also introduce generalizations of these algorithms in which the prototypes represent sets of higher-order polynomial functions. The suggested algorithms provide a good trade-off between computational complexity and performance, since the objective function used in these algorithms is the sum of squared distances, and the clustering is sensitive to noise and outliers. We show that by using a possibilistic approach to clustering, one can make the proposed algorithms robust.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Evidence for the chylomicron origin of lipids accumulating in diabetic eruptive xanthomas: a correlative lipid biochemical, histochemical, and electron microscopic study (1970)

Plasma lipoprotein alterations in nine insulin-dependent diabetics with hyperlipemia have been related to the lipid accumulating in eruptive xanthomas evolving in these patients. Histochemical and electron microscopic examination of xanthomas have been correlated with the lipid analyses in order to obtain additional evidence regarding the lipoprotein origin of lipids accumulating in the lesions. Both analytical and morphologic evidence suggested that circulating chylomicrons significantly contribute to the xanthoma lipids. All the patients had large quantities of circulating triglyceriderich chylomicrons which carried approximately 70% of the triglyceride found in the plasma. The fatty acid pattern of chylomicron and xanthoma triglycerides were similar. Triglyceride constituted the major lipid found in the xanthomas when they were sampled during their eruption. These findings, take in conjunction with histochemical and electron microscopic evidence of chylomicron particles in the dermal capillary walls, support the theory that blood lipoproteins, and particularly chylomicrons, permeated the vascular walls and the triglycerides carried by these lipoproteins apparently accumulated in tissue macrophages and perithelial cells which evolved into foam cells. Initiation of appropriate therapy resulted in clearance of the chylomicronemia and a concomitant resolution of the xanthomas as reflected by a decrease in total xanthoma lipid. Sequential studies of resolving xanthomas in five patients revealed that xanthoma triglyceride was mobilized more rapidly than cholesterol, resulting in a redistribution of the xanthoma lipids, so that the resolving lesions were cholesterol rich. Consistent with this change in lipid composition, correlative electron microscopy revealed loss of amorphous material from many of the foam cell vacuoles.
Realizability conditions and bounds on synthesis of switched-capacitor DC-DC voltage multiplier circuits (1997)

A formal study of the theoretical performance of switched-capacitor (SC) dc-dc voltage multiplier circuits is given. A question concerning the necessary number of circuit elements to realize a given conversion ratio is addressed. In response to the question the bound on attainable voltage ratio for a given number of capacitors k and the bound on the number of switches required in any circuit configuration have been established. The maximum step-up or step-down ratio is given by the kth Fibonacci number, while the bound on the number of switches required in any SC circuit is 3k-2. The complete set of attainable DC conversion ratios is found. A canonical circuit realization of the maximum voltage ratio is discussed and illustrative examples are included. Necessary and sufficient conditions for the realizability of a dc conversion ratio are determined and formal proofs are given.
The effect of acute phase proteins on clearance of chromatin from the circulation of normal mice (1996)

The clearance of nucleosome core particles and H1-stripped chromatin from the circulation of mice was examined. Radiolabeled chromatin preparations were injected into mice, and blood samples were obtained over 60 min. The animals were then killed, and the selected organs were collected and radioactivity was measured. The acute phase response (APR) was induced by i.p. injections of casein before some clearance studies. Serum amyloid P component, the major acute phase protein in mice, increased from 27 microg/ml to 339 microg/ml during the acute phase. The rate of chromatin clearance decreased during the acute phase in C57BL/10J mice. At 5 min, 18% +/- 3% of the originally measured radioactivity remained in control animals compared with 49% +/- 2% in acute phase animals (p < 0.001). Co-injection of either serum amyloid P component or C-reactive protein, the major acute phase protein in humans, caused a decrease in the rate of chromatin clearance similar to that observed following the induction of the APR. APR induction also caused a higher percentage of the chromatin to localize in the liver compared with the spleen, with the ratio changing from 10.2 +/- 0.7 to 16.1 +/- 1.9 (p < 0.004). In addition, the APR caused a decrease in the percentage of chromatin localized in the kidney. The lack of radioactivity associated with cells in the circulation indicates that complement is not a major factor in the clearance mechanism of chromatin. These findings suggest that the APR produces major changes in the rate and path of chromatin clearance. These changes may protect against deposition of chromatin in target organs of systemic lupus erythematosus.
Simple method for quantitation of viable mycoplasmas (1982)

A rapid, simple, and inexpensive method for quantitation of viable mycoplasmas is described. Serial dilutions were made in sterile microtiter plates with standard microtiter equipment. The results were multiplied by a factor of 2.38 to obtain colony-forming units comparable to those obtained with the laborious glass pipette-tube dilution method.
Evidence of a Role for LytB in the Nonmevalonate Pathway of Isoprenoid Biosynthesis (2000)

It is proposed that the lytB gene encodes an enzyme of the deoxyxylulose-5-phosphate (DOXP) pathway that catalyzes a step at or subsequent to the point at which the pathway branches to form isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). A mutant of the cyanobacterium Synechocystis strain PCC 6803 with an insertion in the promoter region of lytB grew slowly and produced greenish-yellow, easily bleached colonies. Insertions in the coding region of lytB were lethal. Supplementation of the culture medium with the alcohol analogues of IPP and DMAPP (3-methyl-3-buten-1-ol and 3-methyl-2-buten-1-ol) completely alleviated the growth impairment of the mutant. The Synechocystis lytB gene and a lytB cDNA from the flowering plant Adonis aestivalis were each found to significantly enhance accumulation of carotenoids in Escherichia coli engineered to produce these colored isoprenoid compounds. When combined with a cDNA encoding deoxyxylulose-5-phosphate synthase (dxs), the initial enzyme of the DOXP pathway, the individual salutary effects of lytB and dxs were multiplied. In contrast, the combination of lytB and a cDNA encoding IPP isomerase (ipi) was no more effective in enhancing carotenoid accumulation than ipi alone, indicating that the ratio of IPP and DMAPP produced via the DOXP pathway is influenced by LytB.