gebhart/patrepeval huggingface dataset:
Erratum to "Genome engineering via homologous recombination in mouse embryonic stem (ES) cells: an amazingly versatile tool for the study of mammalian biology" [An Acad Bras Cienc 73(2001): 365-383] (2001)

Reads: "...Such an interference has been demonstrated in several studies (Fiering et al. 1999) and, in some cases can lead to hypomorph mutations by the introduction the selection sequences in the 5' region of a gene."Should read: "...Such an interference has been demonstrated in several studies (Fiering et al. 1999) and, in some cases, can lead to hypomorph mutations by the introduction of the selection sequence in the 5' region of a gene."• Page 371, column 1, lines 6 to 9.
Vascular endothelial cells and smooth muscle cells mediate carbachol‐induced hepatocyte proliferation via muscarinic receptors and IP3/PKC signaling cascades (2009)

An acetylcholine (ACh) agonist, carbachol (Cch), causes hepatocytes to proliferate in the presence of hepatic nonparenchymal cells (HNPCs). To identify the HNPCs and ACh receptor subtypes involved in carbachol-induced hepatocyte proliferation (CIHP), we examined two types of vascular cells as candidates for HNPCs mediating CIHP in cocultures of hepatocytes using the Transwell filter insert. In the coculture with vascular smooth muscle cells (VSMCs) or endothelial cells (VECs), but not in the monoculture, 72 h treatment with Cch significantly increased the numbers of hepatocytes. The results suggest that both VSMCs and VECs are involved in CIHP through soluble factors secreted from these cells. Interestingly, coculture with VECs, but not with VSMCs, markedly increased the number of hepatocytes, even in the absence of Cch. Cell proliferation assays using an analogue of thymidine, bromodeoxyuridine (BrdU), demonstrated that the hepatocytes in both cocultures transiently replicated their chromosomes 12 h after Cch administration. Blocking the muscarinic type 1 ACh receptor (M1), M3/5, intracellular inositol triphosphate (IP3) receptor, or protein kinase C (PKC) pathways inhibited VSMC-mediated CIHP, whereas blocking the M3/5, IP3 receptor, or PKC pathways inhibited VEC-mediated CIHP. Co-culturing hepatocytes with both types of vascular cells markedly increased their albumin content, but addition of Cch had no effect. In conclusion, VSMCs among vascular cells mediate CIHP through M1, M3/5, and IP3/PKC signal transduction pathways, whereas VECs do so through M3/5, and IP3/PKC pathways.
The structure and function of mammalian and plant globins (2013)

Globins are haemoproteins such as haemoglobin (Hb), myoglobin (Mb), cytoglobin (Cb), neuroglobin (Nb), leghaemoglobin (LHb) and non-symbiotic Hb (NsHb).  While the monomers of these six proteins have the characteristic ‘3-on-3’ alpha-helical sandwich tertiary structure and there are similarities in their patterns of secondary structure, they have poor primary sequence homology.  Moreover, they differ in quaternary structure and in the coordination of the haem, three (Hb, Mb, LHb) being 5-coordinate and Cb, Nb and NsHb being 6-coordinate.  Despite this, each of these globins binds small ligands, such as O 2 , CO and NO, in the sixth position, which implies that it must be possible to displace the imidazole occupying that position in Cb, Nb and NsHb.  In addition to O 2 binding, globins are variously involved in O 2 sensing and NO detoxification, and act as an NO dioxygenase.   These functions can generate the oxidised (or met-) form of the globin, which may be reduced by a globin reductase.  In the case of Hb two globin reductases have been characterised: a non-enzymatic reduction by cytochrome b 5 , which is enzymatically reduced by NADH:cytochrome b 5 reductase, and an NADPH:flavin reductase.
Rethinking Reflexive Looper For Structured Pop Music (2017)

Reflexive Looper (RL) is a live-looping system which allows a solo musician to incarnate the different roles of a whole rhythm section by looping rhythms, chord progressions, bassline and more. The loop pedal, is still the most used device for those types of performances, accounting for many of the cover songs performances on youtube, but not all kinds of song apply. Unlike a common loop pedal, each layer of sound in RL is produced by an intelligent looping-agent which adapts to the musician and respects given constraints, using constrained optimization. In its original form, RL worked well for jazz guitar improvisation but was unsuited to structured music such as pop songs. In order to bring the system on pop stage, we revisited the system interaction, following the guidelines of professional users who tested it extensively. We describe the revisited system which can accommodate both pop and jazz. Thanks to intuitive pedal interaction and structure-constraints, the new RL deals with pop music and has been already used in several in live concert situations.
Quasiparticle Lifetime in Macroscopically Uniform Ag/Fe(100) Quantum Wells (1998)

Epitaxial Ag(100) films have been grown on highly perfect Fe(100) substrates by deposition at low temperatures followed by annealing. Precise control of the deposition process results in film thicknesses of exactly $N$ atomic layers ( $N$ an integer up to 39) over a macroscopic distance $(\ensuremath{\sim}1\mathrm{mm})$. The elimination of atomic layer fluctuation, which has been generally believed to be impossible at such large thicknesses, allows us to observe atomic-layer resolved quantum well states. Such states exhibit extremely narrow linewidths, which provide a direct measure of the quasiparticle lifetime.
Hamsa: fast signature generation for zero-day polymorphic worms with provable attack resilience (2006)

Zero-day polymorphic worms pose a serious threat to the security of Internet infrastructures. Given their rapid propagation, it is crucial to detect them at edge networks and automatically generate signatures in the early stages of infection. Most existing approaches for automatic signature generation need host information and are thus not applicable for deployment on high-speed network links. In this paper, we propose Hamsa, a network-based automated signature generation system for polymorphic worms which is fast, noise-tolerant and attack-resilient. Essentially, we propose a realistic model to analyze the invariant content of polymorphic worms which allows us to make analytical attack-resilience guarantees for the signature generation algorithm. Evaluation based on a range of polymorphic worms and polymorphic engines demonstrates that Hamsa significantly outperforms Polygraph (J. Newsome et al., 2005) in terms of efficiency, accuracy, and attack resilience
Cloning and Characterization of Root-Specific Barley Lectin (1989)

Cereal lectins are a class of biochemically and antigenically related proteins localized in a tissue-specific manner in embryos and adult plants. To study the specificity of lectin expression, a barley (Hordeum vulgare L.) embryo cDNA library was constructed and a clone (BLc3) for barley lectin was isolated. BLc3 is 972 nucleotides long and includes an open reading frame of 212 amino acids. The deduced amino acid sequence contains a putative signal peptide of 26 amino acid residues followed by a 186 amino acid polypeptide. This polypeptide has 95% sequence identity to the antigenically indistinguishable wheat germ agglutinin isolectin-B (WGA-B) suggesting that BLc3 encodes barley lectin. Further evidence that BLc3 encodes barley lectin was obtained by immunoprecipitation of the in vitro translation products of BLc3 RNA transcripts and barley embryo poly(A(+)) RNA. In situ hybridizations with BLc3 showed that barley lectin gene expression is confined to the outermost cell layers of both embryonic and adult root tips. On Northern blots, BLc3 hybridizes to a 1.0 kilobyte mRNA in poly(A(+)) RNA from both embryos and root tips. We suggest, on the basis of immunoblot experiments, that barley lectin is synthesized as a glycosylated precursor and processed by removal of a portion of the carboxyl terminus including the single N-linked glycosylation site.
Nested chromosomal fragmentation in yeast using the meganuclease I-SceI: a new method for physical mapping of eukaryotic genomes (1992)

We have developed a new method for the physical mapping of genomes and the rapid sorting of genomic libraries which is based on chromosome fragmentation by the meganuclease I-Sce I, the first available member of a new class of endonucleases with very long recognition sequences. I-Sce I allows complete cleavage at a single artificially inserted site in an entire genome. Sites can be inserted by homologous recombination using specific cassettes containing selectable markers or, at random, using transposons. This method has been applied to the physical mapping of chromosome XI (620 kb) of Saccharomyces cerevisi and to the sorting of a cosmid library. Our strategy has potential applications to various genome mapping projects. A set of transgenic yeast strains carrying the I-Sce I sites at various locations along a chromosome defines physical intervals against which new genes, DNA fragments or clones can be mapped directly by simple hybridizations.
Multiple divergent mRNAs code for a single human calmodulin. (1988)

The isolation of a novel complementary DNA (cDNA) clone coding for human calmodulin (CaM) is reported. Although it encodes a protein indistinguishable from the only known higher vertebrate calmodulin, its nucleotide sequence varies extensively from that of two previously reported human CaM cDNAs (Wawrzynczak and Perham, 1984; SenGupta et al., 1987). Only 82 and 81% identity, respectively, is found between the newly isolated and the two known human mRNAs in their coding regions. No striking homology is present in their noncoding regions. Codon usage in the three CaM mRNAs is also surprisingly divergent. A 2.3-kilobase mRNA corresponding to the newly isolated clone is expressed to varying extents in several human tissues, together with an approximately 0.8-kilobase mRNA species presumably arising from alternative polyadenylation of the same primary transcript. The results indicate that the human genome contains at least three divergent CaM genes that are under selective pressure to encode an identical protein while maintaining maximally divergent nucleotide sequences. Partial characterization of a genomic clone specifying the 3' portion of the newly identified CaM mRNA shows that this gene contains introns at identical positions as the previously characterized bona fide vertebrate CaM genes. Evolutionary implications of the presence of a CaM multigene family are discussed.
Mucosal FOXP3 -Expressing CD4 + CD25 high Regulatory T Cells in Helicobacter pylori -Infected Patients (2004)

Helicobacter pylori chronically colonizes the stomach and duodenum and causes peptic ulcers or gastric adenocarcinoma in 10 to 20% of infected individuals. We hypothesize that the inability of patients to clear H. pylori infections is a consequence of active suppression of the immune response. Here we show that H. pylori-infected individuals have increased frequencies of CD4(+) CD25(high) T cells in both the stomach and duodenal mucosa compared to uninfected controls. These cells have the phenotype of regulatory T cells, as they express FOXP3, a key gene for the development and function of regulatory T cells, as well as high levels of the cytotoxic T lymphocyte-associated antigen 4 (CTLA-4) protein. In contrast, mucosal CD4(+) CD25(low) and CD4(+) CD25(-) cells express little FOXP3 mRNA and low levels of the CTLA-4 protein. Mucosal CD4(+) CD25(high) T cells are present in individuals with asymptomatic H. pylori infections as well as in duodenal ulcer patients. The frequencies of CD4(+) CD25(high) cells are also increased in the stomachs of H. pylori-infected patients with gastric adenocarcinoma, particularly in cancer-affected tissues. These findings suggest that regulatory T cells may suppress mucosal immune responses and thereby contribute to the persistence of H. pylori infections.
Surface grafting of polymers onto glass plate: Polymerization of vinyl monomers initiated by initiating groups introduced onto the surface (1997)

The surface grafting of polymers onto a glass plate surface was achieved by the polymerization of vinyl monomers initiated by initiating groups introduced onto the surface. Azo groups were introduced onto the glass plate surface by the reaction of 4,4′-azobis(4-cyanopentanoic acid) with isocyanate groups, which were introduced by the treatment with tolylene-2,4-diisocyanate. The radical polymerization of various vinyl monomers was initiated by azo groups introduced onto the glass plate surface and the corresponding polymers were grafted from the surface: The surface grafting of polymers was confirmed by IR spectra, and the contact angle of surface, with water. The contact angle of the glass plate increased by the grafting of hydrophobic polymers, but decreased by the grafting of hydrophilic polymers. The radical postpolymerization was successfully initiated by the pendant peroxycarbonate groups of grafted polymer on the surface to give branched polymer-grafted glass plate. The cationic polymerization of vinyl monomers was also successfully initiated by benzylium perchlorate groups introduced onto the glass plate surface and the corresponding polymers were grafted onto the surface. The contact angle of the glass plate surface obtained from the cationic polymerization of styrene was larger than that obtained from the radical polymerization. © 1997 John Wiley & Sons, Inc. J Appl Polym Sci 65: 2165–2172, 1997
Intestinal Methanobrevibacter smithii but not total bacteria is related to diet‐induced weight gain in rats (2013)

We conclude that M. smithii colonization occurs in the small bowel as well as in the colon, and that the level and extent of M. smithii colonization is predictive of degree of weight gain in this animal model.
Paclitaxel Inhibits Arterial Smooth Muscle Cell Proliferation and Migration In Vitro and In Vivo Using Local Drug Delivery (1997)

Our data show that paclitaxel inhibits haSMC proliferation and migration in a dose-dependent manner in monocultures and cocultures even in the presence of mitogens. Furthermore, paclitaxel prevents neointima formation in rabbits after balloon angioplasty. The long-lasting effect after just several minutes' exposure time makes this lipophilic substance a promising candidate for local antiproliferative therapy of restenosis.
Solubilization of the Cytoplasmic Membrane of Escherichia coli by Triton X-100 (1971)

Treatment of a partially purified preparation of cell walls of Escherichia coli with Triton X-100 at 23 C resulted in a solubilization of 15 to 25% of the protein. Examination of the Triton-insoluble material by electron microscopy indicated that the characteristic morphology of the cell wall was not affected by the Triton extraction. Contaminating fragments of the cytoplasmic membrane were removed by Triton X-100, including the fragments of the cytoplasmic membrane which were normally observed attached to the cell wall. Treatment of a partially purified cytoplasmic membrane fraction with Triton X-100 resulted in the solubilization of 60 to 80% of the protein of this fraction. Comparison of the Triton-soluble and Triton-insoluble proteins from the cell wall and cytoplasmic membrane fractions by polyacrylamide gel electrophoresis after removal of the Triton by gel filtration in acidified dimethyl formamide indicated that the detergent specifically solubilized proteins of the cytoplasmic membrane. The proteins solubilized from the cell wall fraction were qualitatively identical to those solubilized from the cytoplasmic membrane fraction, but were present in different proportions, suggesting that the fragments of cytoplasmic membrane which are attached to the cell wall are different in composition from the remainder of the cytoplasmic membrane of the cell. Treatment of unfractionated envelope preparations with Triton X-100 resulted in the solubilization of 40% of the protein, and only proteins of the cytoplasmic membrane were solubilized. Extraction with Triton thus provides a rapid and specific means of separating the proteins of the cell wall and cytoplasmic membrane of E. coli.
Monte Carlo Simulation of Cu−Ni Nanoclusters: Surface Segregation Studies (2001)

ADVERTISEMENT RETURN TO ISSUEPREVNoteMonte Carlo Simulation of Cu−Ni Nanoclusters: Surface Segregation StudiesDaniela S. Mainardi and Perla B. BalbuenaView Author Information Department of Chemical Engineering, University of South Carolina, Columbia, South Carolina 29208 Cite this: Langmuir 2001, 17, 6, 2047–2050Publication Date (Web):February 21, 2001Publication History Received10 October 2000Revised11 January 2001Published online21 February 2001Published inissue 1 March 2001https://pubs.acs.org/doi/10.1021/la0014306https://doi.org/10.1021/la0014306brief-reportACS PublicationsCopyright © 2001 American Chemical SocietyRequest reuse permissionsArticle Views542Altmetric-Citations52LEARN 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 SUBJECTS:Colloids,Metal clusters,Nanoclusters,Surface energy,Surface segregation Get e-Alerts
MicroRNA: A new player in stem cells (2006)

microRNAs (miRNAs) are an abundant class of endogenous non-protein-coding small RNAs, which negatively regulate gene expression at the posttranscriptional level in many developmental and metabolic processes. miRNAs regulate a variety of biological processes, including developmental timing, signal transduction, tissue differentiation and maintenance, disease, and carcinogenesis. Emerging evidence demonstrates that miRNAs also play an essential role in stem cell self-renewal and differentiation. Some miRNAs are specifically expressed in stem cells, control stem cell self-renewal, and differentiation through negatively regulating the expression of certain key genes in stem cells.
Is there hope to treat glioblastoma effectively? (2015)

Thomas Mehrling was appointed Managing Director of Mundipharma EDO GmbH, Basel, in January 2013 and brings extensive experience with more than 17 years in the industry to this role. During his career, he has held various senior positions in different companies across almost all functions in drug development and commercialization. Most recently, he held the position of International Director Oncology Strategy (2011-2013). From 2004 to 2011 he served as European Director Oncology at Mundipharma International Ltd. During his tenure the oncology business of the European Mundipharma network of independent associated companies was set up and two major products were launched in Europe, DepoCyte® and Levact® (Ribomustin®, Treanda®). He joined Mundipharma in 2000 as Head of Business Development. Prior to Mundipharma, he was Senior Vice President of the global CRO Medical Affairs at Staticon International, and prior to this he acted as Medical Leader at Takeda European R&D center. Dr. Mehrling is a certified Pharmacist with a PhD in pharmacology and a certified Physician trained in haemato-oncology. He obtained his PhD from Frankfurt University following work on developing a new 5-HT3 antagonist to treat nausea and vomiting and developed a particular interest in mechanisms of multidrug resistance into chemotherapy. Dr. Mehrling earned his MD degree through his work in the Department of Internal medicine at Frankfurt University (Hemato-oncology and Cardiology) where he worked for several years before starting his career in the pharmaceutical industry.
The “Silent” Global Burden of Congenital Cytomegalovirus (2013)

Human cytomegalovirus (CMV) is a leading cause of congenital infections worldwide. In the developed world, following the virtual elimination of circulating rubella, it is the commonest nongenetic cause of childhood hearing loss and an important cause of neurodevelopmental delay. The seroprevalence of CMV in adults and the incidence of congenital CMV infection are highest in developing countries (1 to 5% of births) and are most likely driven by nonprimary maternal infections. However, reliable estimates of prevalence and outcome from developing countries are not available. This is largely due to the dogma that maternal preexisting seroimmunity virtually eliminates the risk for sequelae. However, recent data demonstrating similar rates of sequelae, especially hearing loss, following primary and nonprimary maternal infection have underscored the importance of congenital CMV infection in resource-poor settings. Although a significant proportion of congenital CMV infections are attributable to maternal primary infection in well-resourced settings, the absence of specific interventions for seronegative mothers and uncertainty about fetal prognosis have discouraged routine maternal antibody screening. Despite these challenges, encouraging results from prototype vaccines have been reported, and the first randomized phase III trials of prenatal interventions and prolonged postnatal antiviral therapy are under way. Successful implementation of strategies to prevent or reduce the burden of congenital CMV infection will require heightened global awareness among clinicians and the general population. In this review, we highlight the global epidemiology of congenital CMV and the implications of growing knowledge in areas of prevention, diagnosis, prognosis, and management for both low (50 to 70%)- and high (>70%)-seroprevalence settings.
Microbial Degradation ofcis-1, 4-Polyisoprene (1979)

An organism isolated from soil grew well on isoprene oligomers and degraded 60 percent of a sample of synthetic cis-1,4-polyisoprene (Mn=940) in 4 days. The organism hardly degraded synthetic polyisoprene with higher average molecular weight of 2,500. From gel permeation chromatography, oligomers with molecular weight as high as 1,000 were shown to be attacked. The residual substrate after degradation was shown by infrared spectroscopy to have a relatively higher amount of 3,4-structure than the original. From these results, it was supposed that 3,4-linkages in synthetic polymers prevent biodegradation of higher oligomers.