gebhart/patrepeval huggingface dataset:
Resistance of Human Hepatitis Delta Virus RNAs to Dicer Activity (2003)

The endonuclease dicer cleaves RNAs that are 100% double stranded and certain RNAs with extensive but <100% pairing to release approximately 21-nucleotide (nt) fragments. Circular 1,679-nt genomic and antigenomic RNAs of human hepatitis delta virus (HDV) can fold into a rod-like structure with 74% pairing. However, during HDV replication in hepatocytes of human, woodchuck, and mouse origin, no approximately 21-nt RNAs were detected. Likewise, in vitro, purified recombinant dicer gave <0.2% cleavage of unit-length HDV RNAs. Similarly, rod-like RNAs of potato spindle tuber viroid (PSTVd) and avocado sunblotch viroid (ASBVd) were only 0.5% cleaved. Furthermore, when a 66-nt hairpin RNA with 79% pairing, the putative precursor to miR-122, which is an abundant liver micro-RNA, replaced one end of HDV genomic RNA, it was poorly cleaved, both in vivo and in vitro. In contrast, this 66-nt hairpin, in the absence of appended HDV sequences, was >80% cleaved in vitro. Other 66-nt hairpins derived from one end of genomic HDV, PSTVd, or ASBVd RNAs were also cleaved. Apparently, for unit-length RNAs of HDV, PSTVd, and ASBVd, it is the extended structure with <100% base pairing that confers significant resistance to dicer action.
Vitamin K-dependent carboxylation and vitamin K epoxidation. Evidence that the warfarin-sensitive microsomal NAD(P)H dehydrogenase reduces vitamin K1 in these reactions (1981)

Passage of a Triton X-100-solubilized microsomal systems in vitro that are used to study these reactions is the warfarin-sensitive NAD(P)H dehydrogenase.
Bph1p, the Saccharomyces cerevisiae Homologue of CHS1/Beige, Functions in Cell Wall Formation and Protein Sorting (2004)

Mutations in the Chediak-Higashi syndrome gene (CHS1) and its murine homologue Beige result in the formation of enlarged lysosomes. BPH1 (Beige Protein Homologue 1) encodes the Saccharomyces cerevisiae homologue of CHS1/Beige. BPH1 is not essential and the encoded protein was found to be both cytosolic and peripherally bound to a membrane. Neither disruption nor overexpression of BPH1 affected vacuole morphology as assessed by fluorescence microscopy. The deltabph1 strain showed an impaired growth on defined synthetic media containing potassium acetate buffered below pH 4.25, increased sensitivity to calcofluor white, and increased agglutination in response to low pH. A library screen identified VPS9, FLO1, FLO9, BTS1 and OKP1 as high copy suppressors of the growth defect of deltabph1 on both low pH potassium acetate and calcofluor white. The deltabph1 strain demonstrated a mild defect in sorting vacuolar components, including increased secretion of carboxypeptidase Y and missorting of alkaline phosphatase. Overexpression of VPS9, BTS1 and OKP1 suppressed the carboxypeptidase Y secretion defect of deltabph1. Overexpression of BPH1 was found to suppress the calcofluor white sensitivity of a class E VPS deletion strain, deltavta1. Together, these data suggest that Bph1p associates with a membrane and is involved in protein sorting and cell wall formation.
Characterizing the LSI Yield Equation from Wafer Test Data (1984)

The results of production test on LSI wafers are analyzed to determine the parameters of the yield equation. Recognizing that a physical defect on a chip can produce several logical faults, the number of faults per defect is assumed to be a random variable with Poisson distribution. The analysis provides a relationship between the yield of the tested fraction of the chip area and the cumulative fault coverage of test patterns. The parameters of the yield equation are estimated by fitting this relation to the measured yield versus fault coverage data.
An upper bound on the cutoff rate of sequential decoding (1988)

An upper bound is given on the cutoff rate of discrete memoryless channels. This upper bound, which coincides with a known lower bound, determines the cutoff rate, and settles a long-standing open problem.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
VIRUS-INDUCED SARCOMA OF MICE: INHIBITION BY A SYNTHETIC POLYRIBONUCLEOTIDE COMPLEX (1969)

The availability of a potent inducer of interferon, the synthetic double-stranded RNA (poly I.poly C), prompted us to determine its possible prophylactic and/or therapeutic effect on virus-induced sarcomas of mice. When treatment was begun prior to virus inoculation and repeated on alternate days, the majority of NIH Swiss mice inoculated with Moloney or Friend pseudotypes of Moloney murine sarcoma virus failed to develop tumors. Other experiments suggested that repeated injections initiated even after the establishment of tumor nodules were also effective. Mice injected on the day of birth with poly I.poly C develop high titers of interferon. The evidence favors, but does not establish, the interpretation that the observed tumor inhibition is mediated through the induction of endogenous interferon. These experiments demonstrate that treatment with poly I.poly C is followed by a regression of established murine sarcoma infection in mice.
Vocal Folds Disorder Detection using Pattern Recognition Methods (2007)

Diagnosis of pathological voice is one of the most important issues in biomedical applications of speech technology. This study focuses on the classification of pathological voice using the HMM(Hidden Markov Model), the GMM(Gaussian Mixture Model) and a SVM (Support Vector Machine), and then compares the results to work done previously using an ANN (Artificial Neural Network). Speech data were collected from those without and those with vocal disorders. Normal and pathological speech data were mixed in out experiment. Six characteristic parameters (Jitter, Shimmer, NHR, SPI, APQ and RAP) were chosen. Then the pattern recognition methods (HMM, GMM and SVM) were used to distinguish the mixed data into categories of normal and pathological speech. We found that the GMM-based method can give us superior classification rates compared to the other classification methods.
Syntheses and activities of new single-component, ruthenium-based olefin metathesis catalysts (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSyntheses and activities of new single-component, ruthenium-based olefin metathesis catalystsSonBinh T. Nguyen, Robert H. Grubbs, and Joseph W. ZillerCite this: J. Am. Chem. Soc. 1993, 115, 21, 9858–9859Publication Date (Print):October 1, 1993Publication History Published online1 May 2002Published inissue 1 October 1993https://pubs.acs.org/doi/10.1021/ja00074a086https://doi.org/10.1021/ja00074a086research-articleACS PublicationsRequest reuse permissionsArticle Views4544Altmetric-Citations628LEARN 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 (3)»Supporting Information Supporting Information Get e-Alerts
Chiral, Porous, Hybrid Solids for Highly Enantioselective Heterogeneous Asymmetric Hydrogenation of β‐Keto Esters (2003)

Catalytic building blocks: Chiral porous zirconium phosphonates containing Ru-binap moieties are synthesized by a molecular building-block approach, and characterized by a variety of techniques. These hybrid solids are used for enantioselective heterogeneous asymmetric hydrogenation of β-keto esters with ee values of up to 95 % (see picture). Ready tunability of such a molecular building-block approach promises to lead to useful heterogeneous asymmetric catalysts. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2003/z51264_s.pdf or from the author. 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.
Discussion—Differential Earnings Behavior and the Security Market Assessment of Variation in Seasonal Earnings Patterns (2004)

Soffer and Lys (1999) investigate the fraction of predictable positive serial autocorrelation in seasonally differenced earnings reflected in stock prices and find no appreciation of serial correlation immediately after quarterly earnings announcements. Bathke, Lorek, and Willinger (2004) reexamine this result by separating firms with earnings that appear to follow a seasonal random walk (good-fit firms) from the remainder (bad-fit firms). They find that the Soffer and Lys result of zero autocorrelation implied by stock prices represents the combination of a negative implied autocorrelation for good-fit firms and a positive implied autocorrelation for bad-fit firms. This discussion considers different interpretations of that finding.
Activation of LANCL2 by BT-11 Ameliorates IBD by Supporting Regulatory T Cell Stability Through Immunometabolic Mechanisms (2018)

BT-11 is a safe, efficacious oral therapeutic for IBD with a human translatable mechanism of action that involves activation of LANCL2, immunometabolic modulation of CD4+ T cell subsets leading to stable regulatory phenotypes in the colonic LP.
Isolation of genes by complementation in yeast: molecular cloning of a cell-cycle gene. (1980)

cdc28, one of several genes required for cell division in the yeast Saccharomyces cerevisiae, has been isolated on recombinant plasmids. A recombinant plasmid pool containing the entire yeast genome was constructed by partial digestion of yeast DNA with the four-base recognition restriction endonuclease Sau3A to give the equivalent of random fragments, size selection on sucrose gradients, and introduction of the fragments into the yeast vector YRp7 by use of the homology of Sau3A ends with those generated in the vector by cleavage with BamHI. Recombinant plasmids capable of complementing cdc28 mutations were isolated by transformation of a cdc28ts strain and selection for clones capable of growth at the restrictive temperature. Plasmids responsible for complementing the cdc28ts phenotype were shown to recombine specifically with the chromosomal cdc28 locus, confirming the identity of the cloned sequences. In addition, one of the recombinant plasmids was capable of complementing a mutation in tyr1, a gene genetically linked to cdc28. This method of gene isolation and identification should be applicable to all yeast genes for which there are readily scorable mutants.
Ablation of PRC1 by Small Interfering RNA Demonstrates that Cytokinetic Abscission Requires a Central Spindle Bundle in Mammalian Cells, whereas Completion of Furrowing Does Not (2004)

The temporal and spatial regulation of cytokinesis requires an interaction between the anaphase mitotic spindle and the cell cortex. However, the relative roles of the spindle asters or the central spindle bundle are not clear in mammalian cells. The central spindle normally serves as a platform to localize key regulators of cell cleavage, including passenger proteins. Using time-lapse and immunofluorescence analysis, we have addressed the consequences of eliminating the central spindle by ablation of PRC1, a microtubule bundling protein that is critical to the formation of the central spindle. Without a central spindle, the asters guide the equatorial cortical accumulation of anillin and actin, and of the passenger proteins, which organize into a subcortical ring in anaphase. Furrowing goes to completion, but abscission to create two daughter cells fails. We conclude the central spindle bundle is required for abscission but not for furrowing in mammalian cells.
Scalable Production of Genetically Engineered Nanofibrous Macroscopic Materials via Filtration (2016)

As interest in using proteins to assemble functional, biocompatible, and environmentally friendly materials is growing, developing scalable protocols for producing recombinant proteins with customized functions coupled to straightforward fabrication processes is becoming crucial. Here, we use <i>E. coli</i> bacteria to produce amyloid protein nanofibers that are key constituents of the biofilm extracellular matrix and show that protein nanofiber aggregates can be purified using a fast and easily accessible vacuum filtration procedure. With their extreme resistance to heat, detergents, solvents, and denaturing agents, engineered curli nanofibers remain functional throughout the rigorous processing and can be used to assemble macroscopic materials directly from broth culture. As a demonstration, we show that engineered curli nanofibers can be fabricated into self-standing films while maintaining the functionality of various fused domains that confer new specific binding activity to the material. We also demonstrate that purified curli fibers can be disassembled, reassembled into thin films, and recycled for further materials processing. Our scalable approach, which combines established purification techniques for amyloid fibers, is applicable to a new class of recombinant amyloid proteins whose sequence can be easily tailored for diverse applications through genetic engineering.
Stepwise “Click” Chemistry for the Template Independent Construction of a Broad Variety of Cross-Linked Oligonucleotides: Influence of Linker Length, Position, and Linking Number on DNA Duplex Stability (2011)

Cross-linked DNA was constructed by a "stepwise click" reaction using a bis-azide. The reaction is performed in the absence of a template, and a monofunctionalized oligonucleotide bearing an azido-function is formed as intermediate. For this, an excess of the bis-azide has to be used compared to the alkynylated oligonucleotide. The cross-linking can be carried out with any alkynylated DNA having a terminal triple bond at any position of the oligonucleotide, independent of chain length or sequence with identical or nonidentical chains. Short and long linkers with terminal triple bonds were introduced in the 7-position of 8-aza-7-deaza-2'-deoxyguanosine (1 or 2), and the outcome of the "stepwise" click and the "bis-click" reaction was compared. The cross-linked DNAs form cross-linked duplexes when hybridized with single-stranded complementary oligonucleotides. The stability of these cross-linked duplexes is as high as respective individual duplexes when they were ligated at terminal positions with linkers of sufficient length. The stability decreases when the linkers are incorporated at central positions. The highest duplex stability was reached when two complementary cross-linked oligonucleotides were hybridized.
Experimental and simulation studies of thermal flow of borophosphosilicate and phosphosilicate glasses (1995)

We use EVOLVE−FLOW, a thin film thermal flow process simulator, to simulate the thermal flow of borophosphosilicate glass (BPSG) and phosphosilicate glass (PSG) thin films in trenches on patterned wafers, where two-dimensional surface evolution is appropriate. For a fixed anneal time, two parameters control the thin film flow processes: surface tension and viscosity. We demonstrate our simulator by reproducing flowed BPSG film profiles after a 15 min furnace annealing cycle. Digitized as-deposited BPSG film and substrate profiles from experimental scanning electron micrographs are used as initial profiles in the simulations. We then predict flowed phosphosilicate film profiles, and combine experiments and simulations to estimate the surface tension of PSG films in a rapid thermal annealing process. The viscosity of the PSG films is modeled as a function of temperature and phosphorus pentoxide concentration using an Arrhenius type equation. The estimated values of the viscosity and surface tension are used to simulate the PSG film profiles at different annealing times. The simulation results are in good agreement with experimental observations.
Development of a ceramic membrane for upgrading methane to high-value-added clean fuels (1996)

The upgrading of natural gas (which consists mostly of methane) to high-value-added clean-burning fuels such as dimethyl ether, alcohols, and pollution-fighting fuel additives is driven by the abundance of natural gas discovered in remote areas. Recently, extensive efforts have focused on both direct and indirect conversion of methane to these value-added products. The direct-conversion route is the most difficult approach because the products are more reactive than the starting reactant, methane. Indirect routes require the partial oxidation of methane to synthesis gas (syngas, CO + H{sub 2}) in a first stage. The syngas is then converted to upgraded products in a second stage. The most significant cost associated with partial oxidation of methane to syngas is that of the oxygen plant. In this paper, we offer a technology that is based on dense ceramic membranes and that uses air as the oxidant for methane-conversion reaction; thus eliminating tile need for the costly oxygen plant. Certain ceramic materials exhibit both electronic and oxide-ionic conductivities. These mixed-conductor materials transport not only oxygen ions (functioning as selective oxygen separators), but also electrons. No external electrodes are required and such a system will operate without an externally applied potential. Oxygen is transported across the ceramic material in the form of oxygen anions, not oxygen molecules.
”Another world is plantable” : Urban activist gardeners’ communicative action (2013)

Urban activist gardening can take many forms and is practiced in cities all over the world from community gardens on vacant lots, that is, the cultivation of what is considered to be neglected land ...
Combined penetrating keratoplasty and keratolimbal allograft transplantation in comparison with corneoscleral transplantation in the treatment of severe eye burns (2008)

PK combined with KLAL transplantation may reduce the risk of postoperative complications. Long-term prognosis appears better than corneoscleral transplantation in the treatment of severe eye burns.
Adenocarcinoma Cells Are Targeted by the New GnRH-PE66 Chimeric Toxin through Specific Gonadotropin-releasing Hormone Binding Sites (1997)

Luteinizing hormone-releasing hormone, also termed gonadotropin-releasing hormone (GnRH), accounts for the hypothalamic-pituitary gonadal control of human reproduction. The involvement of GnRH has been demonstrated in several carcinomas of hormone-responsive tissues. Exploiting this common feature, we constructed a Pseudomonas exotoxin (PE)-based chimeric toxin (GnRH-PE66) aimed at targeting those cancer cells bearing GnRH binding sites. We report here the strong growth inhibition and killing of a surprisingly wide variety of cancers, confined to the adenocarcinoma type. These cancer cells arising from hormone-responsive tissues, as well as non-responsive ones, express specific GnRH binding sites as indicated by the marked killing of ovarian, breast, endometrial, cervical, colon, lung, hepatic, and renal adenocarcinoma. This cytotoxicity is specific as it could be blocked upon addition of excess GnRH. The specificity of GnRH-PE66 chimeric toxin was also confirmed by GnRH binding assays, and its ability to prevent the formation of colon cancer xenografts in nude mice is presented. Although the functional role of specific GnRH binding sites in human carcinomas remains obscure, GnRH-PE66 displays considerable targeting potential and its use as a therapeutic agent for cancer should be considered.
Molecular therapies for systemic lupus erythematosus: clinical trials and future prospects (2009)

The prognosis of patients with systemic lupus erythematosus has greatly improved since treatment regimens combining corticosteroids and immunosuppressive medications have been widely adopted in therapeutic strategies given to these patients. Immune suppression is evidently efficient but also leads to higher susceptibility to infectious and malignant diseases. Toxic effects and sometimes unexpectedly dramatic complications of current therapies have been progressively reported. Identifying novel molecular targets therefore remains an important issue in the treatment of lupus. The aim of this review article is to highlight emerging pharmacological options and new therapeutic avenues for lupus with a particular focus on non-antibody molecular strategies.
Two-photon volume information storage in doped polymer systems (1990)

Volume information writing and reading is demonstrated for two photochromic materials doped in polymer systems that may be utilized in a 3D optical memory. Writing and reading in volume is achieved by means of two-photon processes and a means of erasing by two-photon processes is discussed. Some of the advantages and problems associated with the two-photon 3D memory device are discussed.
Challenges in industrial applications of technical lignins (2011)

The primary aim of modern biorefineries is the efficient conversion of lignocellulosic materials into valuable products. Sugars and oils can be converted into valuable chemicals, but processing of lignin is still a challenge. A vast amount of lignin is incinerated to produce process steam and energy, and only a very small part is used for the production of value-added products. Technical lignins are isolated as by-streams in lignocellulosic refineries, e.g., as kraft, soda, organosolv, and hydrolysis lignins, as well as lignosulphonates. They have a modified structure and contain impurities that are dependent on the processing method. The structure and the composition of technical lignins restrict their subsequent applications. This paper reviews limiting factors in utilization of technical lignins. Four major classes of problems are identified, and approaches to overcoming these problems are suggested.
Adenosine diphosphate glucose pyrophosphatase: A plastidial phosphodiesterase that prevents starch biosynthesis (2000)

A distinct phosphodiesterasic activity (EC 3.1.4) was found in both mono- and dicotyledonous plants that catalyzes the hydrolytic breakdown of ADPglucose (ADPG) to produce equimolar amounts of glucose-1-phosphate and AMP. The enzyme responsible for this activity, referred to as ADPG pyrophosphatase (AGPPase), was purified over 1,100-fold from barley leaves and subjected to biochemical characterization. The calculated K(eq)' (modified equilibrium constant) value for the ADPG hydrolytic reaction at pH 7.0 and 25 degrees C is 110, and its standard-state free-energy change value (DeltaG') is -2.9 kcal/mol (1 kcal = 4.18 kJ). Kinetic analyses showed that, although AGPPase can hydrolyze several low-molecular weight phosphodiester bond-containing compounds, ADPG proved to be the best substrate (K(m) = 0.5 mM). P(i) and phosphorylated compounds such as 3-phosphoglycerate, PP(i), ATP, ADP, NADP(+), and AMP are inhibitors of AGPPase. Subcellular localization studies revealed that AGPPase is localized exclusively in the plastidial compartment of cultured cells of sycamore (Acer pseudoplatanus L.), whereas it occurs both inside and outside the plastid in barley endosperm. In this paper, evidence is presented that shows that AGPPase, whose activity declines concomitantly with the accumulation of starch during development of sink organs, competes with starch synthase (ADPG:1,4-alpha-d-glucan 4-alpha-d-glucosyltransferase; EC) for ADPG, thus markedly blocking the starch biosynthesis.