gebhart/patrepeval huggingface dataset:
cis-Antisense RNA, Another Level of Gene Regulation in Bacteria (2011)

A substantial amount of antisense transcription is a hallmark of gene expression in eukaryotes. However, antisense transcription was first demonstrated in bacteria almost 50 years ago. The transcriptomes of bacteria as different as Helicobacter pylori, Bacillus subtilis, Escherichia coli, Synechocystis sp. strain PCC6803, Mycoplasma pneumoniae, Sinorhizobium meliloti, Geobacter sulfurreducens, Vibrio cholerae, Chlamydia trachomatis, Pseudomonas syringae, and Staphylococcus aureus have now been reported to contain antisense RNA (asRNA) transcripts for a high percentage of genes. Bacterial asRNAs share functional similarities with trans-acting regulatory RNAs, but in addition, they use their own distinct mechanisms. Among their confirmed functional roles are transcription termination, codegradation, control of translation, transcriptional interference, and enhanced stability of their respective target transcripts. Here, we review recent publications indicating that asRNAs occur as frequently in simple unicellular bacteria as they do in higher organisms, and we provide a comprehensive overview of the experimentally confirmed characteristics of asRNA actions and intimately linked quantitative aspects. Emerging functional data suggest that asRNAs in bacteria mediate a plethora of effects and are involved in far more processes than were previously anticipated. Thus, the functional impact of asRNAs should be considered when developing new strategies against pathogenic bacteria and when optimizing bacterial strains for biotechnology.
什么是平等？第二部分：资源平等（续） (2002)

二、计划 既然平等拍卖这一手段(device这个词在本文第一部分译作装置,似嫌不妥,现改译为手段.--译者),作为一种用以达到对于诸如荒岛这样简单情形下资源平等的富有魅力的解释的方法(technique),似乎是有希望的,因此就出现这样一个问题:它在发展一种对于资源平等这个理想的更一般说明上是否将证明是有用的.
Analysis of inhibitory action of modified U1 snRNAs on target gene expression: discrimination of two RNA targets differing by a 1 bp mismatch (2002)

The modified U1 snRNA gene can suppress expression of a target transgene. In the present study, its potential utility to inhibit a dominant negative/gain of function mutation is explored. Using a green fluorescent protein (GFP) target gene, inhibition was achieved in all cells transduced with U1antiGFP directed at multiple sites within GFP. Using a chloramphenicol acetyltransferase (CAT) target gene, inhibition was not increased by increasing the hybridization domain from 10 to 16 bp or when a site in an upstream exon or intron was targeted. To determine if a U1 anti-target design could discriminate between two transcripts that differ by a 1-2 bp mismatch, GFPtpz and GFPsaph were chosen as targets because they share sequence homology except for three regions where a 1, 2 or 3 bp mismatch exists. The results demonstrated that U1antiGFP correctly reduced its cognate GFP expression by >90% and therefore U1 anti-target constructs are able to discriminate a 1 or 2 bp mismatch in their target mRNA. Thus, these U1 anti-target constructs may be effective in a strategy of somatic gene therapy for a dominant negative/gain of function mutation due to the discreteness of its discrimination. It may complement other anti-target strategies to reduce the cellular load of a mutant transcript.
Structural determinants of human APOBEC3A enzymatic and nucleic acid binding properties (2013)

Human APOBEC3A (A3A) is a single-domain cytidine deaminase that converts deoxycytidine residues to deoxyuridine in single-stranded DNA (ssDNA). It inhibits a wide range of viruses and endogenous retroelements such as LINE-1, but it can also edit genomic DNA, which may play a role in carcinogenesis. Here, we extend our recent findings on the NMR structure of A3A and report structural, biochemical and cell-based mutagenesis studies to further characterize A3A's deaminase and nucleic acid binding activities. We find that A3A binds ssRNA, but the RNA and DNA binding interfaces differ and no deamination of ssRNA is detected. Surprisingly, with only one exception (G105A), alanine substitution mutants with changes in residues affected by specific ssDNA binding retain deaminase activity. Furthermore, A3A binds and deaminates ssDNA in a length-dependent manner. Using catalytically active and inactive A3A mutants, we show that the determinants of A3A deaminase activity and anti-LINE-1 activity are not the same. Finally, we demonstrate A3A's potential to mutate genomic DNA during transient strand separation and show that this process could be counteracted by ssDNA binding proteins. Taken together, our studies provide new insights into the molecular properties of A3A and its role in multiple cellular and antiviral functions.
Coexpression of the c-kit and stem cell factor genes in breast carcinomas. (1995)

Expression of the c-kit tyrosine kinase growth factor receptor has been reported in some breast tumors; however, no data exist concerning expression of its ligand, stem cell factor. The aim of this study was to determine how frequently the c-kit and stem cell factor genes were coexpressed in breast tumors and tumor-derived cell lines and to determine whether coexpression of c-kit and stem cell factor could result in growth stimulation of breast tumor cells. Expression of the c-kit and stem cell factor genes in tissue specimens and cell lines was determined using an RNase protection assay, with confirmation of c-kit protein expression by immunohistochemistry and Western blotting in tumor tissue and cell lines, respectively. Of 11 tumor specimens studied, 9 expressed variable but detectable quantities of c-kit; 7 of 13 tumor-derived cell lines also expressed c-kit. All tumor specimens and cell lines expressed detectable stem cell factor mRNA, suggesting that an autocrine growth loop could exist in the majority of breast carcinomas. To determine the biological effects of coexpression of c-kit and stem cell factor, the MCF-7 cell line, which expresses only stem cell factor, was transfected with a c-kit expression vector. Coexpression of c-kit and stem cell factor in MCF-7 cells resulted in an enhanced growth rate and cloning efficiency but not a loss of the dependence of this cell line upon estrogen. Analysis of subclones expressing different amounts of c-kit protein revealed that, although they all showed enhanced growth relative to control transfectants in serum-free medium containing IGF-1, only the highest c-kit expressor responded with additional growth to exogenous soluble stem cell factor. However, all c-kit-expressing clones, but not control clones, showed growth inhibition when exposed to a blocking anti-c-kit antibody. This blocking antibody also significantly inhibited the growth of the established ZR75-1 cell line in serum-free medium containing IGF-1. Taken together, these data suggest that coexpression of stem cell factor and c-kit could be responsible for growth deregulation in a significant number of breast carcinomas.
The Pomeranz-Fritsch reaction, isoquinoline vs. oxazoles (1977)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe Pomeranz-Fritsch reaction, isoquinoline vs. oxazolesEllis V. BrownCite this: J. Org. Chem. 1977, 42, 19, 3208–3209Publication Date (Print):September 1, 1977Publication History Published online1 May 2002Published inissue 1 September 1977https://pubs.acs.org/doi/10.1021/jo00439a025https://doi.org/10.1021/jo00439a025research-articleACS PublicationsRequest reuse permissionsArticle Views1114Altmetric-Citations37LEARN 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
Channels with block interference (1984)

A new class of channel models with memory is presented in order to study various kinds of interference phenomena. It is shown, among other things, that when all other parameters are held fixed, channel capacity <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">C</tex> is an {\em increasing} function of the memory length, while the cutoff rate <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">R_{0}</tex> generally is a {\em decreasing} function. Calculations with various explicit coding schemes indicate that <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">C</tex> is better than <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">R_{0}</tex> as a performance measure for these channel models. As a partial resolution of this <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">C</tex> versus <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">R_{0}</tex> paradox, the conjecture is offered that <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">R_{0}</tex> is more properly a measure of coding delay rather than of coding complexity.
Trading structure for randomness in wireless opportunistic routing (2007)

Opportunistic routing is a recent technique that achieves high throughput in the face of lossy wireless links. The current opportunistic routing protocol, ExOR, ties the MAC with routing, imposing a strict schedule on routers' access to the medium. Although the scheduler delivers opportunistic gains, it misses some of the inherent features of the 802.11 MAC. For example, it prevents spatial reuse and thus may underutilize the wireless medium. It also eliminates the layering abstraction, making the protocol less amenable to extensions to alternate traffic types such as multicast.
Increased nm23-H1 and nm23-H2 Messenger RNA Expression and Absence of Mutations in Colon Carcinomas of Low and High Metastatic Potential (1993)

These findings also contrast with the demonstration of nm23 metastasis suppressor activity in murine melanoma and with the correlation of loss of nm23 expression in breast cancer with poor prognosis. It may be that metastasis suppression by the nm23 gene is a tissue-specific phenomenon.
High-performance 1-Gb-NAND flash memory with 0.12-μm technology (2002)

A 1.8-V, 1-Gb NAND flash memory is fabricated with 0.12-/spl mu/m CMOS STI process technology. For higher integration, a 32-cell NAND structure, which enables row decoder layout in one block pitch, is applied for the first time. Resulting cell and die sizes are 0.076 /spl mu/m/sup 2/ and 129.6 mm/sup 2/, respectively. A pseudo-4-phase charge pump circuit can generate up to 20 V even under the supply voltage of 1.6 V. A newly applied cache program function and expanded page size of (2 k + 64) byte lead to program throughput of 7 MB/s. The page copy-back function is provided for on-chip garbage collection. The read throughput of 27 MB/s is achieved by simply expanding I/O width and page size. A measured disturbance free-window of 3.5 V at 1.5 V-V/sub DD/ is obtained.
Viral Resistance and the Selection of Antiretroviral Combinations (1995)

Mounting scientific evidence suggests that viral replication and evolution of diversification, with the resulting emergence of variants including drug-resistant strains, is responsible for the gradual destruction of the immune system and is the mechanism of disease progression in HIV-infected patients. Monotherapy does not give long-term suppression of viral replication and evolution, and combination therapy is viewed as a potentially more effective long-term approach based on increased and more durable suppression of HIV replication. Because of the large number of drugs that could be used in combination therapy regimens, it is important to investigate, in clinical studies, only those combinations likely to be most effective. In vitro studies are therefore critical in the selection of such combinations. Resistance mutations to many antiretroviral agents have been documented and their patterns of emergence elucidated. A number of studies have since demonstrated the phenomenon of cross-resistance, in which resistant virus emerging under the selective pressure of one therapy is also cross-resistant to a second antiviral agent. This information can be used to avoid combining agents to which cross-resistance can occur. Suppression or "phenotypic reversal" of zidovudine resistance by the lamivudine-resistance mutation at codon 184 has been demonstrated in in vitro studies. It is encouraging that this finding has led to the clinical evaluation of these two agents with promising results. Moreover, in vitro scientific data are critical in facilitating the identification of potentially effective combination therapies.
Geschichten: Der Kleine und der Grobe Mann (1989)

Veröffentlicht zuerst unter dem Titel L’Homme Statue (1937), entworfen schon 1929, doch erst 1935 niedergeschrieben, zählt diese Geschichte zu den wenigen Prosaarbeiten Brechts, die nach Anlaß und Aussage im engeren Sinne seiner Faschismuskritik zuzurechnen sind. Als auslösendes Moment der ersten Niederschrift erwähnt Brecht Zeitungsmeldungen über die Kriegsbegeisterung italienischer Truppen in Eritrea, die zur Eroberung Abessiniens eingesetzt werden. Der italienische Faschismus führt den ersten Kriegszug zur Gründung eines Imperiums. Brecht leitet mit diesem Hinweis die frühe Fassung der Geschichte ein und fährt fort: Vor meinen Augen stand wieder, wie oft in letzter Zeit, ein merkwürdiges Bild, das ich vor Jahren gesehen habe: der Poilu von La Ciotat.
Developing Learning Skills (1984)

The aim of the Youth Training Scheme [1] is to provide young people entering the labour market with a broad‐based and integrated training programme which will:
Structure of the bovine pancreatic ribonuclease gene: the unique intervening sequence in the 5′ untranslated region contains a promoter-like element (1988)

Although pancreatic ribonucleases are extensively studied proteins, little information is available on nucleic acids coding for these enzymes. Here, for the first time, the structure of a gene coding for such an enzyme, the well known bovine pancreatic ribonuclease, is reported. The coding region of this gene is devoid of introns, whereas the 5' untranslated sequence of the pancreatic transcript contains an intron of 735 nucleotides. This intervening sequence is endowed with signals (CAAT and TATA boxes) which might act as regulatory elements. The structural organization of this gene suggests that the sequence coding for the bovine pancreatic ribonuclease might be expressed under the control of two different promoters.
Second-Order Nonlinear Optical Imaging of Chiral Crystals (2011)

Second-order nonlinear optical imaging of chiral crystals (SONICC) is an emerging technique for crystal imaging and characterization. We provide a brief overview of the origin of second harmonic generation signals in SONICC and discuss recent studies using SONICC for biological applications. Given that they provide near-complete suppression of any background, SONICC images can be used to determine the presence or absence of protein crystals through both manual inspection and automated analysis. Because SONICC creates high-resolution images, nucleation and growth kinetics can also be observed. SONICC can detect metastable, homochiral crystalline forms of amino acids crystallizing from racemic solutions, which confirms Ostwald's rule of stages for crystal growth. SONICC's selectivity, based on order, and sensitivity, based on background suppression, make it a promising technique for numerous fields concerned with chiral crystal formation.
Targeted Treatment of Metastatic Breast Cancer by PLK1 siRNA Delivered by an Antioxidant Nanoparticle Platform (2017)

Metastatic breast cancer is developed in about 20% to 30% of newly diagnosed patients with early-stage breast cancer despite treatments. Herein, we report a novel nanoparticle platform with intrinsic antimetastatic properties for the targeted delivery of Polo-like kinase 1 siRNA (siPLK1). We first evaluated it in a triple-negative breast cancer (TNBC) model, which shows high metastatic potential. PLK1 was identified as the top therapeutic target for TNBC cells and tumor-initiating cells in a kinome-wide screen. The platform consists of a 50-nm mesoporous silica nanoparticle (MSNP) core coated layer-by-layer with bioreducible cross-linked PEI and PEG polymers, conjugated with an antibody for selective uptake into cancer cells. siRNA is loaded last and fully protected under the PEG layer from blood enzymatic degradation. The material has net neutral charge and low nonspecific cytotoxicity. We have also shown for the first time that the MSNP itself inhibited cancer migration and invasion in TNBC cells owing to its ROS- and NOX4-modulating properties. <i>In vivo</i>, siPLK1 nanoconstructs (six doses of 0.5 mg/kg) knocked down about 80% of human <i>PLK1</i> mRNA expression in metastatic breast cancer cells residing in mouse lungs and reduced tumor incidence and burden in lungs and other organs of an experimental metastasis mouse model. Long-term treatment significantly delayed the onset of death in mice and improved the overall survival. The platform capable of simultaneously inhibiting the proliferative and metastatic hallmarks of cancer progression is unique and has great therapeutic potential to also target other metastatic cancers beyond TNBC. <i>Mol Cancer Ther; 16(4); 763-72. ©2017 AACR</i>.
Synthesis and Characterization of Stacked and Quenched Uridine Nucleotide Fluorophores (1999)

Intramolecular aromatic interactions in aqueous solution often lead to stacked conformation for model organic molecules. This designing principle was used to develop stacked and folded uridine nucleotide analogs that showed highly quenched fluoroscence in aqueous solution by attaching the fluorophore 1-aminonaphthalene-5-sulfonate (AmNS) to the terminal phosphate via a phosphoramidate bond. Severalfold enhancement of fluorescence could be observed by destacking the molecules in organic solvents, such as isopropanol and dimethylsulfoxide or by enzymatic cleavage of the pyrophosphate bond. Stacking and destacking were confirmed by 1-H NMR spectroscopy. The extent of quenching of the uridine derivatives correlated very well with the extent of stacking. Taking 5-H as the monitor, temperature-variable NMR studies demonstrated the presence of a rapid interconversionary equilibrium between the stacked and open forms for uridine-5'-diphosphoro-beta-1-(5-sulfonic acid) naphthylamidate (UDPAmNS) in aqueous solution. DeltaH was calculated to be -2.3 Kcal/mol, with 43-50% of the population in stacked conformation. Fluorescence lifetime for UDPAmNS in water was determined to be 2.5 ns as against 11 ns in dimethyl sulfoxide or 15 ns for the pyrophosphate adduct of AmNS in water. Such a greatly reduced lifetime for UDPAmNS in water suggests collisional interaction between the pyrimidine and thefluorophore moieties to be responsible for quenching. The potential usefulness of such stacked and quenched nucleotide fluorophores as probes for protein-ligand interaction studies has been briefly discussed.
Efficient Algorithms for Pattern Matching on Directed Acyclic Graphs (2005)

Recently graph data models have become increasingly popular in many scientific fields. Efficient query processing over such data is critical. Existing works often rely on index structures that store pre-computed transitive relations to achieve efficient graph matching. In this paper, we present a family of stack-based algorithms to handle path and twig pattern queries for directed acyclic graphs (DAGs) in particular. With the worst-case space cost linearly bounded by the number of edges in the graph, our algorithms achieve a quadratic runtime complexity in the average size of the query variable bindings. This is optimal among the navigation-based graph matching algorithms.
Process Variable Classification and Data Reconciliation (1992)

Process data are used in chemical plants for the purpose of control, performance evaluation, optimization, etc. Measurements usually have some degree of error, therefore it is necessary to adjust them through a reconciliation procedure in order to obtain a reliable process knowledge. In this work a computer package (PLADAT) is described which performs an output set assignment of the process balance equations to classify the measured and unmeasured operational variables of a complete chemical plant. The results of this procedure are used to reduce the size of the reconciliation problem and obtain the minimum amount of instruments required for the determinability of all unmeasured process variables in order to develop the complete mass and energy balances. Results are presented corresponding to a section of an existing ethylene plant with 150 streams and 45 units.
Cellular and molecular mechanisms for rapid regression of atherosclerosis: from bench top to potentially achievable clinical goal (2007)

Purpose of review Decades of literature have unambiguously demonstrated regression and remodeling of atherosclerotic lesions, including advanced plaques. Recent insights into underlying mechanisms are reviewed. Recent findings Factors promoting regression include decreased apolipoprotein B-lipoprotein retention within the arterial wall, efflux of cholesterol and other harmful lipids from plaques, and emigration of lesional foam cells followed by entry of healthy phagocytes that remove necrotic debris and other plaque components. Cellular lipid efflux and foam cell emigration can occur surprisingly rapidly once the plaque milieu is improved. Lipid efflux and foam cell emigration each involve specific molecular mediators, many of which have been identified. Necrotic debris removal can be surprisingly comprehensive, with essentially full disappearance documented in animal models. Summary The essential prerequisite for regression is robust improvement in plaque milieu, meaning large plasma reductions in atherogenic apolipoprotein B-lipoproteins or brisk enhancements in ‘reverse’ lipid transport from plaque into liver. Importantly, the processes of regression are consistent with rapid correction of features characteristic of the rupture-prone, vulnerable plaques responsible for acute coronary syndromes. New interventions to lower apolipoprotein B-lipoprotein levels and enhance reverse lipid transport may allow regression to become a widespread clinical goal. Strategies based on recent mechanistic insights may facilitate further therapeutic progress.
Pharmacotherapy of adult attention deficit/hyperactivity disorder: review of evidence-based practices and future directions (2008)

The reviewed body of evidence strongly supports the use of pharmacotherapy as a first-line therapeutic option for the treatment of adults with ADHD.