gebhart/patrepeval huggingface dataset:
Selectable One-Step PCR-Mediated Integration of a Degron for Rapid Depletion of Endogenous Human Proteins (2016)

Manipulation of protein stability with ligand-regulated degron fusions is a powerful method for investigating gene function. We developed a selectable cassette for easy C-terminal tagging of endogenous human proteins with the E. coli dihydrofolate reductase (eDHFR) degron using CRISPR/Cas9 genome editing. This cassette permits high-efficiency recovery of correct integration events using an in-frame self-cleaving 2A peptide and the puromycin resistance gene. PCR amplified donor eDHFR cassette fragments with 100 bases of homology on each end are integrated by homology-directed repair (HDR) of guide RNA (gRNA)-targeted double-stranded DNA breaks at the 3' ends of open reading frames (ORFs). As proof of principle, we generated cell lines in which three endogenous proteins were tagged with the eDHFR degron. When the antibiotic trimethoprim is removed from the media, each of the eDHFR-tagged proteins was depleted by >90% within 2-4 h, and this depletion was reversed by re-addition of trimethoprim. Since puromycin selection permits recovery of in-frame degron fusions with high efficiency using only 100-bp long regions of homology, this method should be applicable on a genome-wide scale for generating libraries of conditional mutant cell lines.
Drosophila cubitus interruptus forms a negative feedback loop with patched and regulates expression of Hedgehog target genes (1997)

The Drosophila segment polarity gene cubitus interruptus (ci) encodes a zinc finger protein that is required for the proper patterning of segments and imaginal discs. Epistasis analysis indicates that ci functions in the Hedgehog (Hh) signal transduction pathway and is required to maintain wingless expression in the embryo. In this paper, the role of the Ci protein in the Hh signaling pathway is examined in more detail. Our results show that ectopic expression of ci in imaginal discs and the embryo activates the expression of Hh target genes. One of these target genes, patched, forms a negative feedback loop with ci that is regulated by Hh signal transduction. Activation is also achieved using the Ci zinc finger domain fused to a heterologous transactivation domain. Conversely, repression of Hh target genes occurs in animals expressing the Ci zinc finger domain fused to a repression domain. To examine Ci function in more detail, regions of the Ci protein that are responsible for its ability to transactivate and its subcellular distribution have been identified.
Processing Multilevel Secure Objects (1981)

The paper describes an architecture for processing multilevel objects in a multilevel secure environment, and discusses the inherent problems involved. A multilevel intelligent terminal is proposed as a practical application for the proposed architecture.
Accuracy of Rapid Influenza Diagnostic Tests (2012)

Canadian Institutes of Health Research.
Cell adhesion molecules mediate radiation-induced leukocyte adhesion to the vascular endothelium. (1996)

The predominant early histological changes in irradiated tissues are edema and leukocyte infiltration. Cell adhesion molecules (CAMs) are required for the extravasation of leukocytes from the circulation. To study the role of CAMs in the pathogenesis of radiation-mediated inflammation, we quantified the expression of P-selectin, E-selectin, intercellular adhesion molecule-1 (ICAM-1), and vascular cell adhesion molecule-1 glycoproteins on the surface of irradiated human endothelial cells. We found that E-selectin and ICAM-1 expression increased after irradiation, whereas there was no increased expression of other cytokine-inducible adhesion molecules (P-selectin or vascular cell adhesion molecule-1). We found a dose- and time-dependent increase in radiation-induced expression of both E-selectin and ICAM-1. Furthermore, the threshold dose for E-selectin expression was 1 Gy, whereas the threshold dose for ICAM-1 synthesis was 5 Gy of X-rays. Northern blot analysis of RNA from irradiated endothelial cells demonstrated that ICAM-1 is expressed at 3-6 h following irradiation. No de novo protein synthesis was required for increased ICAM-1 mRNA expression. The 1.1-kb segment of the 5' untranslated region of the ICAM-1 gene was sufficient for X-ray induction of chloramphenicol acetyltransferase reporter gene expression. We measured whether ICAM-1 mediates adhesion of leukocyte to the irradiated endothelium and found that leukocyte adhesion occurred concurrently with ICAM-1 induction. Radiation-mediated leukocyte adhesion was prevented by anti-ICAM-1 blocking antibodies. These data indicate that ICAM-1 participates in the inflammatory response to ionizing radiation. Moreover, radiation induction of these CAMs occurs in the absence of tumor necrosis factor and interleukin 1 production.
Monocyte chemotactic protein-1 in the inflammatory pseudotumour of the lung (1998)

Inflammatory pseudotumour of the lung is a lesion mainly composed of histiocytes. Histiocyte accumulation may arise from local proliferation of migratory cells, from cytokine induced recruitment of monocytes from the systemic circulation, or both. Cell proliferation was investigated with Ki-67 immunostaining and cytokine production with reverse transcriptase-polymerase chain reaction in two cases of inflammatory pseudotumour of the lung. It was found that the two lesions were composed mainly of non-proliferating (Ki-67 non-binding) macrophages that stained positive for CD68, CD14, CD4, and mannose receptor. Both cases contained mRNA transcripts for monocyte chemotactic protein-1 (MCP-1), a monocyte chemoattractant, and for interleukin 6 (IL-6), an inducer of plasma cell differentiation. One of the two cases also contained mRNA transcripts for IL-8, a neutrophil chemoattractant. These findings are consistent with the possibility that accumulation of non-proliferating histiocytes induced by MCP-1 is one of the pathogenic events occurring in inflammatory pseudotumour of the lung.
Role of dopamine D3 receptors in the addictive properties ofethanol (2004)

After the cloning of the dopamine D(1) and D(2) receptors (1-3), several additional dopamine receptors were identified. These new subtypes included the D(3) and D(4) receptors, which are similar to D(2), and the D(5) receptor, which is similar to D(1) (4-6). Although most studies have focused on the role of dopamine D(1) and D(2) receptors in mediating the addictive liability of drugs, the lack of selective pharmacological tools has significantly hampered this particular field of research. In contrast, recent studies using selective competitive antagonists have shown that the dopamine D(3) receptor is involved in drug-seeking behavior. The present review is intended to highlight a new, promising area in alcohol research that focuses on the role of the dopamine D(3) receptor in the addictive properties of ethanol.
Expression and control of the natural autoreactive IgG repertoire in normal human serum (1993)

We have investigated the autoreactive repertoire expressed by serum IgG of healthy individuals of various age groups using a large panel of self antigens. Natural IgG autoantibodies against all self antigens of the panel were found in the purified IgG fraction of the serum of all donors that were tested. The mean binding activity to self antigens of IgG of pregnant women was higher than that of IgG purified from the serum of infants, young adults and aged individuals. No increase in IgG autoreactivity was observed with aging neither in the purified IgG fraction of serum nor in whole serum. Whereas autoantibody activity was easily detectable in purified IgG, it was low in serum. No difference was observed, however, between the binding activity of purified IgG and of IgG in serum in the case of foreign antigens nor in the case of anti-thyroglobulin autoantibodies of patients with hashimoto's thyroiditis. Purified IgM from normal serum bound to F(ab')2 fragments of autologous IgG in a dose-dependent fashion and inhibited the binding of autologous IgG to self antigens. Our results thus indicate that autologous IgM contributes to regulate expression of the natural IgG autoreactive repertoire through V region-dependent interactions, resulting in low levels of IgG autoreactivity in serum under physiological conditions.
Receptor-mediated endocytosis: insights from the lipoprotein receptor system. (1979)

The low density lipoprotein (LDL) receptor system coordinates the metabolism of cholesterol, an essential component of the plasma membrane of all mammalian cells. Study of this system has led to an enhanced understanding of the cellular basis of cholesterol homeostasis. It has also brought into focus an important mechanism of metabolic regulation--the process of receptor-mediated endocytosis. In this article, we first describe the receptor-mediated endocytosis of LDL, a sequence of events in which receptor binding and internalization are coupled in specialized regions of the plasma membrane called coated pits. Second, we trace the cellular functions of the cholesterol derived from internalized LDL. Third, genetic evidence is presented to indicate that both the binding and internalization of LDL are mediated by a single receptor molecule that contains two active sites, one mediating binding and the other internalization. Finally, the characteristics of the LDL receptor system are used to suggest models for receptor systems in general.
APPROPRIATION OF THE KNOWLEDGE IN A PUBLIC RESEARCH INSTITUTE (2010)

The National Institute for Space Research - INPE is a Research Unit of the Ministry of Science and Technology - MCT and turns 50 in 2011. During this period, it gave several solutions for the company and now offers unique products such as satellites of the series and SCD-series satellites, programs PRODES and DETER, the weather, among others. It happens that, for the development of these products, INPE has a set of human knowledge that has differentiated. It should be noted also that the knowledge generated in the Institute comes from internal research and international cooperation, as is the case of cooperation between Brazil and China. In this context, this paper aims to point out the current opportunities that the Institute has to appropriate the knowledge generated at home and abroad, and in conclusion makes some suggestions to improve the appropriation of their tacit and explicit.
The role of topical antifungal therapy for onychomycosis and the emergence of newer agents. (2014)

Onychomycosis is a common infection of the nail unit that is usually caused by a dermatophyte (tinea unguium) and most frequently affects toenails in adults. In most cases, onychomycosis is associated with limited treatment options that are effective in achieving complete clearance in many cases. In addition, recurrence rates are high in the subset of treated patients who have been effectively cleared, usually with an oral antifungal agent. There has been a conspicuous absence of medical therapies approved in the United States since the introduction of topical ciclopirox (8% nail lacquer), with no new effective agents introduced for more than 10 years. Fortunately, newer agents and formulations have been under formal development. While patients might prefer a topical therapy, efficacy with ciclopirox 8% nail lacquer, the only available agent until the very recent approval of efinaconazole 10% solution, has been disappointing. The poor therapeutic outcomes achieved with ciclopirox 8% nail lacquer were not unexpected as the cure rates achieved in the clinical trials were unimpressive, despite concomitant nail debridement, which was an integral part of the pivotal trials with ciclopirox 8% nail lacquer. Efinaconazole 10% solution and tavaborole 5% solution are new topical antifungals specifically developed for the treatment of dermatophyte onychomycosis. In Phase 3 clinical trials, both newer agents were applied once daily for 48 weeks without concomitant nail debridement. Mycologic cure rates with efinaconazole 10% solution are markedly superior to what was achieved with ciclopirox 8% nail lacquer. To add, they appear to be nearly comparable to those achieved with oral itraconazole in pivotal clinical trials. However, it is important to remember that direct comparisons between different studies are not conclusive, are not generally considered to be scientifically sound, and may not be entirely accurate due to differences in study design and other factors. Well-designed and properly powered head-to-head studies are needed in order to draw definitive conclusions about efficacy comparisons between therapies, at least based on academic and regulatory standards. Although tavaborole 5% solution is in an earlier phase of development for onychomycosis, treatment success rates reported thus far for both efinaconazole 10% solution and tavaborole 5% solution are superior to ciclopirox 8% nail lacquer. As a result, a new era of onychomycosis appears to be upon us that incorporates topical therapy more effectively than in the past. Not only may these newer topical agents provide viable monotherapy alternatives to oral therapy for onychomycosis, topical therapy for onychomycosis that is effective, well tolerated, and easy to use may also find a role in combination therapy, and/or as continued therapy after initial clearance to reduce recurrence or re-infection.
Immunotherapy in ovarian cancer (2012)

Ovarian cancer is the most deadly gynecologic malignancy, with more than 15,000 deaths anticipated in 2012. While approximately 80% of patients will respond to frontline chemotherapy, more than 60% of patients will experience disease recurrence and only 44% will be alive at 5 y. Host anti-tumor immune responses are associated with a significant improvement in overall survival for women with ovarian cancer. By bolstering these responses, it may therefore be possible to significantly influence the prognosis of women with this lethal disease. In this review, we will focus on innovative immune-based strategies which are currently being investigated in the treatment of ovarian cancer.
Isodideoxynucleosides: a conceptually new class of nucleoside antiviral agents. (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTIsodideoxynucleosides: a conceptually new class of nucleoside antiviral agents.Vasu Nair and Zoraida M. NuescaCite this: J. Am. Chem. Soc. 1992, 114, 20, 7951–7953Publication Date (Print):September 1, 1992Publication History Published online1 May 2002Published inissue 1 September 1992https://pubs.acs.org/doi/10.1021/ja00046a074https://doi.org/10.1021/ja00046a074research-articleACS PublicationsRequest reuse permissionsArticle Views278Altmetric-Citations103LEARN 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
Megalencephalic leukoencephalopathy with subcortical cysts: an update and extended mutation analysis ofMLC1 (2006)

Megalencephalic leukoencephalopathy with subcortical cysts (MLC) is an autosomal recessive cerebral white matter disorder in children. This disease is histopathologically characterized by myelin splitting and intramyelinic vacuole formation. MLC is caused by mutations in the gene MLC1, which encodes a novel protein, MLC1. Since the first report, 50 mutations in this gene have been found. Mutations occur throughout the entire coding region and include all different types: 11 splice-site mutations; one nonsense mutation; 24 missense mutations; and 14 deletions and insertions. Until now, six polymorphisms within the coding sequence of MLC1 had been reported. In about 20% of the patients with a typical clinical and MRI picture, no mutations in the MLC1 gene are found. Several of the families, in which no mutations are found, also do not show linkage with the MLC1 locus, which suggests a second gene involved in MLC. The absence of mutations may also be the consequence of performing standard mutation analysis that can miss heterozygous deletions, mutations in the promoter, 3' and 5' untranslated regions (UTRs), and intron mutations, which may influence the amino acid composition of the end product. In this work we describe 13 novel mutations, including those found with extended mutation analysis on MLC patients. This study shows that extended mutation analysis is a valuable tool to identify at least some of the missing mutations. Therefore, we suggest extended mutation analysis for the MLC1 gene, if no mutations are found during standard analysis.
Evidence to Use Botulinum Toxin Injections in Tension-Type Headache Management: A Systematic Review (2017)

Tension-type headache (TTH) is the most common type of chronic recurring head pain. It can occur twice as often in women as in men. It is the most common type of headache. Its lifetime prevalence is 30% to 78% in the general population. TTH treatment should be multilevel. It often consists of taking pain medication, muscle relaxants, antidepressants, using biofeedback therapy, acupuncture, and attending behavioral therapy. Several clinical trials also suggest that botulinum toxin (BTX) may be an effective treatment option for such patients. The aim of this study was to evaluate if BTX can be used as a treatment method in TTH in the light of current medical literature. The authors searched the PubMed, EBSCOhost, OVID, Web of Knowledge, Cochrane Library and CINAHL databases to identify relevant publications. The authors finally included 11 papers-prospective and retrospective cohort studies. Among most of the selected studies, there was a significant correlation between using BTX and reduction of TTH pain intensity and severity. By analyzing qualified studies, it can be concluded that botulinum toxin seems to be effective in TTH management.
Nutritional Assessment of Processing Effects on Major and Trace Element Content in Sea Buckthorn Juice ( Hippophaë rhamnoides L. ssp . rhamnoides ) (2008)

Processing effects on the mineral content were investigated during juice production from sea buckthorn (Hippophaë rhamnoides L. ssp. rhamnoides, Elaeagnaceae) using berries from 2 different growing areas. The major and trace elements of sea buckthorn berries and juices were determined by atomic absorption spectroscopy (AAS)--(calcium, iron, magnesium, potassium, sodium) and inductively coupled plasma-mass spectrometry (ICP-MS)--(arsenic, boron, chromium, copper, manganese, molybdenum, nickel, selenium, zinc). Potassium is the most abundant major element in sea buckthorn berries and juices. The production process increased the potassium content in the juice by about 20%. Moreover, the processing of juice increased the value of manganese up to 32% compared to the content in berries. During industrial juice production, the technological steps caused a loss of about 53% to 77% of the chromium concentration, 50% of the copper content, 64% to 75% of the molybdenum amount, and up to 45% of the iron concentration in the final juice product. Consumption of sea buckthorn juice represents a beneficial source of chromium, copper, manganese, molybdenum, iron, and potassium for the achievement of the respective dietary requirements.
Adam Smith: Desire, History and Value (2006)

The fragment, reproduced from my Reading ‘Adam Smith’ (Shapiro 1993), which begins ‘Smith and the Problem of Value,’ is predicated on the central argument of the book: Smith’s Wealth of Nations is best read as a spatio-temporal story. And insofar as the Wealth’s narrativity shapes its perspective, what I refer to as Smith’s ‘theory of value’ is located more in the way he develops a historical plot than in his explicit economic concepts. In Smith’s writing, value emerges in the interface between his larger historical plot and his smaller, epistemological one. The former (elaborated in Smith’s Wealth) treats his narrative of expanding exchange, while the latter (developed in many of his other writings) comprises his sensationalist account of how the world becomes intelligible to individual, perceiving subjects, as bodies encounter objects. Ultimately, after analyzing the failure of Smith’s theory to account for how things become valued, I suggest, that an appreciation of the way value is deployed in the dynamics of political economy cannot be derived from an inspection of the way an object’s materiality satisfies a need or want, even when, à la Smith, one focuses on the productive processes that make that object available. Rather, it is necessary to locate a drive towards satisfaction — this is, desire — within a complex set of evolving cultural codes. Among the implications of this argument is a shift in the intellectual terrain within which political economy is to be thought.
2,4,6‐Trifluoropyrimidine. Reactions with nitrogen nucleophiles (2004)

Abstract In a continuation of our studies involving the nucleophilic displacement of one of the chlorines from 2,4,6‐trichloropyrimidine, we now report the initial displacement of one of the fluorine atoms from 2,4,6‐trifluoropyrimidine using both aliphatic and aromatic amines. The monosubstitution products favor 2‐substitution with ammonia and ethanolamine while aniline gave the 4‐substituted derivative as the preferred product.
Low Serum Medium for CH07E02 Hybridoma (1993)

하이브리도마 배양을 위해 첨가한 기존의 혈 청농도는 10% FBS였으나, 이 농도는 3%까지 줄여도 세포의 비성장속도와 최고세포농도에 차이가 없었다. 세포성장을 촉진한다고 알려진 물 질들을 1% FBS 배지에 첨가하였을 때 insulin, pyruvate, oxaloacetate, pluronic F-68 등에 의해 세포성장이 촉진되었다. 3% FBS는 2% CS로 대치할 수 있었고, 혈청의 농도는 IPOP의 첨가시 0.5 % CS에서도 active proliferation을 보였다. 최종 조성의 배지가격은 기존의 10 % FBS 배지의 1/10 정도였으며 배지조성을 cell line에 따라 달리 결정함으로써 배지의 가격은 현저히 낮출 수 있음을 알았다.
The Development of L2X2RuCHR Olefin Metathesis Catalysts:  An Organometallic Success Story (2000)

In recent years, the olefin metathesis reaction has attracted widespread attention as a versatile carbon-carbon bond-forming method. Many new applications have become possible because of major advances in catalyst design. State-of-the-art ruthenium catalysts are not only highly active but also compatible with most functional groups and easy to use. This Account traces the ideas and discoveries that were instrumental in the development of these catalysts, with particular emphasis on (PCy3)2Cl2Ru=CHPh and its derivatives. The discussion includes an analysis of trends in catalyst activity, a description of catalysts coordinated with N-heterocyclic carbene ligands, and an overview of ongoing work to improve the activity, stability, and selectivity of this family of L2X2Ru=CHR complexes.