gebhart/patrepeval huggingface dataset:
Circular RNA enrichment in platelets is a signature of transcriptome degradation (2015)

In platelets, splicing and translation occur in the absence of a nucleus. However, the integrity and stability of mRNAs derived from megakaryocyte progenitor cells remain poorly quantified on a transcriptome-wide level. As circular RNAs (circRNAs) are resistant to degradation by exonucleases, their abundance relative to linear RNAs can be used as a surrogate marker for mRNA stability in the absence of transcription. Here we show that circRNAs are enriched in human platelets 17- to 188-fold relative to nucleated tissues and 14- to 26-fold relative to samples digested with RNAse R to selectively remove linear RNA. We compare RNAseq read depths inside and outside circRNAs to provide in silico evidence of transcript circularity, show that exons within circRNAs are enriched on average 12.7 times in platelets relative to nucleated tissues and identify 3162 genes significantly enriched for circRNAs, including some where all RNAseq reads appear to be derived from circular molecules. We also confirm that this is a feature of other anucleate cells through transcriptome sequencing of mature erythrocytes, demonstrate that circRNAs are not enriched in cultured megakaryocytes, and demonstrate that linear RNAs decay more rapidly than circRNAs in platelet preparations. Collectively, these results suggest that circulating platelets have lost >90% of their progenitor mRNAs and that translation in platelets occurs against the backdrop of a highly degraded transcriptome. Finally, we find that transcripts previously classified as products of reverse transcriptase template switching are both enriched in platelets and resistant to decay, countering the recent suggestion that up to 50% of rearranged RNAs are artifacts.
Cloning and sequence analysis of rabbit progesterone-receptor complementary DNA. (1986)

Two lambda gt11 clones containing fragments of cDNA encoding the rabbit progesterone receptor were isolated with the aid of monoclonal and monospecific polyclonal antireceptor antibodies. RNA gel blot analysis showed that the corresponding mRNA was approximately equal to 5900 nucleotides in size and present in the uterus, where its concentration was increased by estrogen treatment, and in the vagina. This mRNA was not detected in liver, in spleen, in intestine, and in kidney where the receptor protein is known to be absent or present in very small concentration. Cross-hybridizing clones were isolated from a lambda 10 library. The DNA was sequenced, and the primary structure of the progesterone receptor was deduced. It consists of 930 amino acids and contains a basic, cysteine-rich region (residues 568-645) with extensive homology to the glucocorticoid and estrogen receptors and the v-erbA oncogene protein. This region is followed by a C-terminal domain that is similar in size to the corresponding domains of the other steroid receptors and v-erbA and shows striking amino acid homology with the glucocorticoid receptor and significant homology with the estrogen receptor. In contrast, the region extending from the cysteine-rich segment toward the N terminus differed in size and amino acid sequence from that of the other receptors and v-erbA. This region had a high proline content in the progesterone receptor.
Adhesion at the Solid-Elastomer Interface: Influence of the Interfacial Chains (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAdhesion at the Solid-Elastomer Interface: Influence of the Interfacial ChainsM. Deruelle, L. Leger, and M. TirrellCite this: Macromolecules 1995, 28, 22, 7419–7428Publication Date (Print):October 1, 1995Publication History Published online1 May 2002Published inissue 1 October 1995https://pubs.acs.org/doi/10.1021/ma00126a021https://doi.org/10.1021/ma00126a021research-articleACS PublicationsRequest reuse permissionsArticle Views1075Altmetric-Citations136LEARN 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
Endo-Selective Enyne Ring-Closing Metathesis Promoted by Stereogenic-at-Mo Monoalkoxide and Monoaryloxide Complexes. Efficient Synthesis of Cyclic Dienes Not Accessible through Reactions with Ru Carbenes (2009)

Stereogenic-at-Mo monoalkoxide and monoaryloxide complexes promote enyne ring-closing metathesis (RCM) reactions, affording the corresponding endo products with high selectivity (typically >98:<2 endo:exo). All catalysts can be prepared and used in situ. Five-, six-, and seven-membered rings are obtained through reactions with enyne substrates that bear all-carbon tethers as well as those that contain heteroatom substituents. The newly developed catalytic protocols complement the related exo-selective Ru-catalyzed processes. In cases where Ru-based complexes deliver exo and endo products nondiscriminately, such as when tetrasubstituted cyclic alkenes are generated, Mo-catalyzed reactions afford the endo product exclusively. The efficiency of synthesis of N- and O-containing endo diene heterocycles can be improved significantly through structural modification of Mo catalysts. The modularity of Mo-based monopyrrolides is thus exploited in the identification of the most effective catalyst variants. Through alteration of O-based monodentate ligands, catalysts have been identified that promote enyne RCM with improved efficiency. The structural attributes of three Mo complexes are elucidated through X-ray crystallography. The first examples of catalytic enantioselective enyne RCM reactions are reported (up to 98:2 enantiomer ratio and >98% endo).
Interleukin-6–dependent survival of multiple myeloma cells involves the Stat3-mediated induction of microRNA-21 through a highly conserved enhancer (2007)

Signal transducer and activator of transcription 3 (Stat3) is implicated in the pathogenesis of many malignancies and essential for IL-6-dependent survival and growth of multiple myeloma cells. Here, we demonstrate that the gene encoding oncogenic microRNA-21 (miR-21) is controlled by an upstream enhancer containing 2 Stat3 binding sites strictly conserved since the first observed evolutionary appearance of miR-21 and Stat3. MiR-21 induction by IL-6 was strictly Stat3 dependent. Ectopically raising miR-21 expression in myeloma cells in the absence of IL-6 significantly reduced their apoptosis levels. These data provide strong evidence that miR-21 induction contributes to the oncogenic potential of Stat3.
The relationship between tissue factor and cancer progression: insights from bench and bedside (2011)

It is now widely recognized that a strong correlation exists between cancer and aberrant hemostasis. Patients with various types of cancers, including pancreatic, colorectal, and gastric cancer, often develop thrombosis, a phenomenon commonly referred to as Trousseau syndrome. Reciprocally, components from the coagulation cascade also influence cancer progression. The primary initiator of coagulation, the transmembrane receptor tissue factor (TF), has gained considerable attention as a determinant of tumor progression. On complex formation with its ligand, coagulation factor VIIa, TF influences protease-activated receptor-dependent tumor cell behavior, and regulates integrin function, which facilitate tumor angiogenesis both in vitro and in mouse models. Furthermore, evidence exists that an alternatively spliced isoform of TF also affects tumor growth and tumor angiogenesis. In patient material, TF expression and TF cytoplasmic domain phosphorylation correlate with disease outcome in many, but not in all, cancer subtypes, suggesting that TF-dependent signal transduction events are a potential target for therapeutic intervention in selected types of cancer. In this review, we summarize our current understanding of the role of TF in tumor growth and metastasis, and speculate on anticancer therapy by targeting TF.
Function of Escherichia coli MsbA, an Essential ABC Family Transporter, in Lipid A and Phospholipid Biosynthesis (1998)

The Escherichia coli msbA gene, first identified as a multicopy suppressor of htrB mutations, has been proposed to transport nascent core-lipid A molecules across the inner membrane (Polissi, A., and Georgopoulos, C. (1996) Mol. Microbiol. 20, 1221-1233). msbA is an essential E. coli gene with high sequence similarity to mammalian Mdr proteins and certain types of bacterial ABC transporters. htrB is required for growth above 32 degreesC and encodes the lauroyltransferase that acts after Kdo addition during lipid A biosynthesis (Clementz, T., Bednarski, J., and Raetz, C. R. H. (1996) J. Biol. Chem. 271, 12095-12102). By using a quantitative new 32Pi labeling technique, we demonstrate that hexa-acylated species of lipid A predominate in the outer membranes of wild type E. coli labeled for several generations at 42 degreesC. In contrast, in htrB mutants shifted to 42 degreesC for 3 h, tetra-acylated lipid A species and glycerophospholipids accumulate in the inner membrane. Extra copies of the cloned msbA gene restore the ability of htrB mutants to grow at 42 degreesC, but they do not increase the extent of lipid A acylation. However, a significant fraction of the tetra-acylated lipid A species that accumulate in htrB mutants are transported to the outer membrane in the presence of extra copies of msbA. E. coli strains in which msbA synthesis is selectively shut off at 42 degreesC accumulate hexa-acylated lipid A and glycerophospholipids in their inner membranes. Our results support the view that MsbA plays a role in lipid A and possibly glycerophospholipid transport. The tetra-acylated lipid A precursors that accumulate in htrB mutants may not be transported as efficiently by MsbA as are penta- or hexa-acylated lipid A species.
Radio over Fiber Transport for the Support of Wireless Broadband Services (2009)

International audience
Polymer Gel Light‐Modulation Materials Imitating Pigment Cells (2002)

Novel light‐modulation materials composed of stimuli‐responsive gel particles with an added high concentration of colorants, which can modulate light due to an induced volume phase transition, have been obtained (see Figure). The light‐modulation mechanism and constitution of this material are similar to those of pigment cells existing in cephalopods, and the light absorption change is based on diffusion and aggregation of the colorants.
Adenoviral-mediated gene transfer in lymphocytes (1998)

Although adenovirus can infect a wide range of cell types, lymphocytes are not generally susceptible to adenovirus infection, in part because of the absence of the expression of the cellular receptor for the adenoviral fiber protein. The cellular receptor for adenovirus and coxsackievirus (CAR) recently was cloned and shown to mediate adenoviral entry by interaction with the viral fiber protein. We show that the ectopic expression of CAR in various lymphocyte cell lines, which are almost completely resistant to adenovirus infection, is sufficient to facilitate the efficient transduction of these cells by recombinant adenoviruses. Furthermore, this property of CAR does not require its cytoplasmic domain, consistent with the idea that CAR primarily serves as a high affinity binding site for the adenoviral fiber protein, and that viral entry is mediated by interaction of the viral penton base proteins with cellular integrins. As a demonstration of their functional utility, we used CAR-expressing lymphocytes transduced with an adenovirus expressing Fas ligand to efficiently kill Fas receptor-expressing tumor cells. The ability to efficiently manipulate gene expression in lymphocyte cells by using adenovirus vectors should facilitate the functional characterization of pathways affecting lymphocyte physiology.
Fast semianalytical Monte Carlo simulation for time-resolved light propagation in turbid media (1996)

The statistical estimator concept, created in the nuclear engineering field, has been adapted to the elaboration of a new and fast semianalytical Monte Carlo numerical simulation for time-resolved light-scattering problems. This concept has also been generalized to the case of unmatched boundaries. The model, discussed in detail in this paper, contains two stages. The first stage is the information generator in which, for each scattering event, the contribution to the total reflectance and transmittance is evaluated and subtracted from the photon current energy. This procedure reduces the number of photons required to produce a given accuracy, which makes it possible to store all event positions and energies. In the second stage, called the information processor, the results of the first stage are used to calculate analytically any desired result. Examples are given for scattering slabs of isotropic or anisotropic scatterers when collimated-beam incidence is used. Reflections at the boundaries are taken into account. The results obtained either with this new method or with classical Monte Carlo methods are very similar. However, the convergence of our new model is much better and, because of the separation into two stages, any quantity related to the problem can be easily calculated afterward without recomputing the simulation.
한국영화에 나타난 가족,모성 윤리의 변화에 관한 연구 (2007)

본 연구는 한국영화에 재현된 가족과 모성의 윤리 변화를 탐색하되, 2000년대 전후를 중심으로 해서 그 변화의 특징과 양상을 살피고 있다. 1990년대와 2000년대를 구분하는 주된 특징은 바로 2000년대에서 들어와서 가족과 모성이 강화되고 있다는 것이다. 1990년대의 경우 전통적 가족윤리가 약화되고 양성평등을 추구하면서 모성역할의 갈등과 가족 부재의 개인주의적 양상이 많이 나타났다. 하지만 2000년대에 이르러 가족주의가 강화되면서도 가족주의 문제점을 살피는 성찰적 시각들이 나타나고 있으며 가족해체의 위기를 재현하면서도 새로운 부성의 모습이 나타나고 있다. 한편 가족과 모성의 역할이 강조되면서도 보다 복수적이고 다양한 가족과 모성의 모습으로 변화되고 있다. 결국 2000년대에는 보다 가족과 모성에 대해 관심을 가지면서도 가족과 모성에 대해 다층적 재구성의 윤리가 시도되고 있다고 하겠다. 영화에 재현된 이러한 변화는 가족과 모성의 타자성과 복잡성에 민감한 공동체윤리의 필요성을 보여준다.
Semi-Nested PCR Detection of Bartonella henselae in Ixodes persulcatus Ticks from Western Siberia, Russia (2004)

Questing adult Ixodes persulcatus ticks from Western Siberia, Russia were tested for infections with Bartonella spp. using seminested PCR assay with primers specific to the groEL gene. The proportion of ticks infected with Bartonella spp. was 44% in 2002 (n = 50) and 38% in 2003 (n = 50). Nucleotide sequences of a portion of the PCR products corresponded to Bartonella henselae species.
Tandem dosing of samarium‐153 ethylenediamine tetramethylene phosphoric acid with stem cell support for patients with high‐risk osteosarcoma (2010)

Tandem doses of 153Sm-EDTMP were safe for this cohort of heavily pretreated patients with very high-risk disease. The strong correlation between absorbed dose and administered activity within each evaluable patient provides a methodology to individually tailor tandem doses of this agent.
Metal‐Catalyzed One‐Pot Synthesis of Tetrazines Directly from Aliphatic Nitriles and Hydrazine (2012)

Paving the way: The lack of convenient synthetic methods is a significant roadblock to the broader use of 1,2,4,5-tetrazines in bioorthogonal chemistry and functional materials. Lewis acid metal catalysts—most notably divalent nickel and zinc salts—are described to catalyze the one-pot synthesis of 1,2,4,5-tetrazines directly from aliphatic nitriles (see scheme). Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
On the Capacity Achieving Covariance Matrix for Rician MIMO Channels: An Asymptotic Approach (2010)

In this paper, the capacity-achieving input covariance matrices for coherent block-fading correlated multiple input multiple output (MIMO) Rician channels are determined. In contrast with the Rayleigh and uncorrelated Rician cases, no closed-form expressions for the eigenvectors of the optimum input covariance matrix are available. Classically, both the eigenvectors and eigenvalues are computed numerically and the corresponding optimization algorithms remain computationally very demanding. In the asymptotic regime where the number of transmit and receive antennas converge to infinity at the same rate, new results related to the accuracy of the approximation of the average mutual information are provided. Based on the accuracy of this approximation, an attractive optimization algorithm is proposed and analyzed. This algorithm is shown to yield an effective way to compute the capacity achieving matrix for the average mutual information and numerical simulation results show that, even for a moderate number of transmit and receive antennas, the new approach provides the same results as direct maximization approaches of the average mutual information.
BIOCHEMISTRY OF SULFUR-CONTAINING AMINO ACIDS (1983)

The literature on sulfur amino acid metabolism is too vast for a short chapter to cover in great depth. I attempt here a brief overview with references to many specialized review articles. This review emphasizes aspects of sulfur amino acid metabolism elucidated in the last ten years, in particular aspects not generally covered in biochemistry texts, e.g. transaminative pathways of methionine metabolism. A selected list of reviews is given in references 1-15. References to reviews on glutathione are covered in the chapter by A. Meister in this volume (1a).
Sequential Steps in Human Immunodeficiency Virus Particle Maturation Revealed by Alterations of Individual Gag Polyprotein Cleavage Sites (1998)

Retroviruses are produced as immature particles containing structural polyproteins, which are subsequently cleaved by the viral proteinase (PR). Extracellular maturation leads to condensation of the spherical core to a capsid shell formed by the capsid (CA) protein, which encases the genomic RNA complexed with nucleocapsid (NC) proteins. CA and NC are separated by a short spacer peptide (spacer peptide 1 [SP1]) on the human immunodeficiency virus type 1 (HIV-1) Gag polyprotein and released by sequential PR-mediated cleavages. To assess the role of individual cleavages in maturation, we constructed point mutations abolishing cleavage at these sites, either alone or in combination. When all three sites between CA and NC were mutated, immature particles containing stable CA-NC were observed, with no apparent effect on other cleavages. Delayed maturation with irregular morphology of the ribonucleoprotein core was observed when cleavage of SP1 from NC was prevented. Blocking the release of SP1 from CA, on the other hand, yielded normal condensation of the ribonucleoprotein core but prevented capsid condensation. A thin, electron-dense layer near the viral membrane was observed in this case, and mutant capsids were significantly less stable against detergent treatment than wild-type HIV-1. We suggest that HIV maturation is a sequential process controlled by the rate of cleavage at individual sites. Initial rapid cleavage at the C terminus of SP1 releases the RNA-binding NC protein and leads to condensation of the ribonucleoprotein core. Subsequently, CA is separated from the membrane by cleavage between the matrix protein and CA, and late release of SP1 from CA is required for capsid condensation.
Incorporation of a stabilizing calcium-binding loop into subtilisin BPN' (1992)

A rational approach was taken to improve the stability of subtilisin BPN' to autoproteolysis. Two sites of autoproteolysis were identified by isolation of early autolysis products and amino-terminal sequence analysis. These studies showed that subtilisin rapidly cleaves Ala48-Ser49 and Ser163-Thr164 peptide bonds at elevated temperatures. These two sites appear in regions of high mobility as estimated from crystallographic B-factors and are in extended surface loops. To improve the resistance to thermal-induced autolysis, we replaced sequences around these two sites with sequences derived from a thermophilic homologue of subtilisin, thermitase. Thermitase contains a Ca(2+)-binding site in the region surrounding Ser49. When the Ca(2+)-binding segment of thermitase corresponding to residues 45-63 of subtilisin BPN' was installed into subtilisin BPN', the chimeric protein gained the ability to bind another Ca2+ with moderate affinity (Kd approximately 100 microM). This enzyme had the same kcat as wild-type, had a KM value 8-fold larger than wild-type, and was slightly less stable to thermal inactivation in EDTA. However, in 10 mM CaCl2, the mutant subtilisin BPN' was 10-fold more stable to irreversible inactivation at 60 degrees C than wild-type subtilisin BPN' as measured by residual activity against the substrate sAAPF-pna. Next, mutations and deletions derived from thermitase were introduced near the second autolysis loop in subtilisin BPN' (residues 158-165). However, all of these mutants were less stable than wild-type subtilisin. Thus, some (but not all) mutations derived from a thermophilic homologue near sites of autolysis can be stabilizing to a mesophilic protease.
Translocation of p21 Cip1/WAF1 from the nucleus to the cytoplasm correlates with pancreatic myofibroblast to fibroblast cell conversion (2005)

The results indicate that pancreatic MFBs are transient and suggest that intracellular localisation of p21(Cip1/WAF1) can contribute to the phenotype conversion of these cells to fibroblasts in culture and experimental injury.
Ethylammonium nitrate: a protein crystallization reagent (1999)

Ethylammonium nitrate (EAN) is a liquid organic salt that has many potential applications in protein chemistry. Because this solvent has hydrophobic and ionic character as well as the ability to hydrogen bond, it is especially well suited for broad use in protein crystallography. For example, EAN may be used as an additive, a detergent, a precipitating agent or to deliver ligands into protein crystals. A discussion of the crystallization of lysozyme using EAN as a precipitating agent is given here.
Nanoscale CuO solid-electrolyte-based conductive-bridging-random-access-memory cell operating multi-level-cell and 1selector1resistor (2015)

Nanoscale non-volatile CBRAM-cells are developed by using a CuO solid-electrolyte, providing a ∼10<sup>2</sup>memory margin, ∼3 × 10<sup>6</sup>endurance cycles, ∼6.63-years retention time at 85 °C, ∼100 ns writing speed, and MLC operation.
Effects of rivastigmine on the quantitative EEG in demented Parkinsonian patients (2003)

qEEG may serve as an objective tool to monitor the effects of antidementia drug therapy. The changes characterized by increased faster frequencies and decreased slower frequencies that were observed may indicate increased arousal or improvement in the cognitive state of the patients as a consequence of the treatment with rivastigmine.