gebhart/patrepeval huggingface dataset:
Number and location of AUUUA motifs: role in regulating transiently expressed RNAs (1994)

Many RNAs coding for either cytokines or oncogenes are unstable and have a short half-life (t1/2). The AUUUA motif is a highly conserved sequence and is repeated three or more times in the 3′ untranslated region (3′UTR) of RNAs encoding many of these short-lived cytokines and oncogenes. These sequences can confer instability. In this study, we investigated the role of number and location of AUUUA motifs in stabilization of RNA. We introduced 1xATTTA, 2xATTTA, ATTTTTTTA (second adenosine of 2xATTTA was substituted with a thymidine), 3xATTTA, 5xATTTA, 7xATTTA [AT-rich sequence from granulocyte-macrophage colony- stimulating factor [GM-CSF] gene (AT-62)], and GC-62 (GC sequences were substituted for ATTTA sequences in the 7xATTTA) into the 3′UTR of rabbit beta-globin (R beta G) gene. This construct also contained the neomycin-resistance gene. These expression vectors were transfected into human lung fibroblasts (W138), which constitutively expressed low levels of GM-CSF mRNA. Stable transfectants were selected by growth in G418. Northern blot analysis of actinomycin D-treated, stably transfected cells demonstrated that the number of AUUUA sequences correlated with rapidity of turnover of the chimeric R beta G mRNA. The rank order of stability was GC-62 = 1xATTTA = 2xATTTA (no RNA decay at 4 hours) &gt; 3xATTTA = 5xATTTA (t1/2, 4 hours) &gt; 7xATTTA (t1/2, 2 hours). Stability of mRNA of R beta G also was reduced (t1/2, 2 to 4 hours) when AT-62 was introduced into the second exon of R beta G gene. In these same cells, the t1/2 of GM-CSF RNA was approximately 10 to 15 minutes, suggesting that the AUUUA motifs cannot alone account for the rapid degradation of this cytokine mRNA. Phorbol diesters, including 12- 0-tetradecanoyl phorbol 13-acetate (TPA), stabilize a variety of transiently expressed RNAs, including GM-CSF RNA. We found that TPA markedly increased (&gt; 30-fold) the accumulation of GM-CSF RNA. In contrast, TPA was unable to stimulate the levels of the chimeric R beta G when either 1x, 2x, 3x, or 5xATTTA motifs were fused to 3′UTR, or when either AT-62 or GC-62 control sequences were fused to the second exon. The chimeric beta-globin construct with either AT-62 or ATTTTTTTA in the 3′UTR had only an approximately twofold to threefold increase in accumulation.
Observation (2001)

Observation, as the term is used here, refers to the purposeful examination of teaching and/or learning events through systematic processes of data collection and analysis. Such events may occur in untutored environments (see Chapter 12) or in formal instructional settings. This chapter focuses on observation in language classroom environments. (See also Nunan 1992: 91–114.)
Outbreak of community-acquired methicillin-resistant Staphylococcus aureus skin infections among a collegiate football team. (2007)

Outbreaks of CA-MRSA in sports teams are very serious, and recognition is crucial. Treatment includes incision for proper drainage, bacterial culture and sensitivity, and appropriate antibiotic therapy. Infection control measures include educating athletes and staff, following Centers for Disease Control and Prevention recommendations, identifying CA-MRSA carriers with nasal cultures, introducing hexachlorophene 3% soap intermittently in the showers, making alcohol-based hand sanitizers available on the field, disinfecting weight training and rehabilitation equipment, and using disposable towels on the field during practices and games.
Genetic control of IL-1β bioactivity through differential regulation of the IL-1 receptor antagonist (2002)

Regulation of IL-1 bioactivity by the IL-1 receptor antagonist (IL-1Ra) is critical for the preservation of normal vascular structure and function in mice. In humans, IL-1 bioactivity may be further fine-tuned by genetic polymorphisms. We recently proposed that an intronic polymorphism of the human gene encoding the IL-1R antagonist (IL1RN) is a genetic risk factor for the development of chronic cardiac allograft rejection. Here we aimed to establish a physiological basis for this susceptibility. Plasma and peripheral blood mononuclear cells (PBMC) were obtained from 55 healthy human volunteers, whose genotypes for four polymorphisms of IL1 family genes (IL1B, IL1R1 and IL1RN) were determined by PCR. IL-1beta and IL-1Ra production and release in PBMC cultures were studied by flow cytometry and ELISA. Functional and genotypic data were pooled and analyzed first by multivariate and, subsequently, by univariate statistical tests. We were able to confirm our observed association of IL1RN genotype with chronic cardiac allograft rejection using multivariate statistics. IL1RN genotype also emerged as the principal regulator of both constitutive and stimulated IL-1Ra and IL-1beta release. Allele IL1RN*2 was consistently associated with higher IL-1Ra and lower IL-1beta release, in a dosage-dependent manner. Conversely, IL1RN*2 carriage was associated with reduced production of the intracellular isoform of IL-1Ra. These genotypic effects were only observed with prolonged culture prior to stimulation and were not appreciably influenced by the presence of exogenous modulators of IL-1beta production. We conclude that IL1RN genotype is the principal determinant of IL-1beta bioactivity within theIL1 gene cluster in humans and discuss its putative role in disease.
A Novel Carbohydrate-Derived Side-Chain Polyether with Excellent Protein Resistance (2003)

A novel carbohydrate-derived side-chain polyether was synthesized as a new biomaterial by condensation polymerization of monomers derived from natural occurring carbohydrates. Surface plasmon resonance spectroscopy studies demonstrated that this side-chain polyether has excellent resistance to nonspecific protein adsorption. The protein resistant capability of the side-chain polyether is comparable to that of oligoethylene glycol, a main-chain polyether that is, to date, the best protein resistant material. In addition to the excellent biocompatibility, the new polymer also combines biodegradability and functionalizability. With these combined good properties, this side-chain polyether is envisioned as a new biomaterial for many potential biomedical applications.
Variation in Ascorbic Acid and Oxalate Levels in the Fruit of Actinidia chinensis Tissues and Genotypes (2005)

Ascorbic acid and total oxalate were measured in fruit from six genotypes of Actinidia chinensis. Ascorbic acid was separated from oxalate in fruit extracts by HPLC and quantified from absorbance at 245 nm, whereas oxalate was measured enzymatically in the HPLC eluate. Levels of whole fruit mean ascorbic acid in the different genotypes ranged from 98 to 163 mg/100 g of fresh weight (FW), whereas mean oxalate varied between 18 and 45 mg/100 g of FW. Ascorbic acid was highest in the inner and outer pericarp, whereas oxalate was concentrated in the skin, inner pericarp, and seed. Essentially no ascorbic acid was found in the seed. Each tissue clustered separately when the tissue ascorbic acid and oxalate data were normalized to the whole fruit level of ascorbic acid and oxalate in that genotype and plotted against each other, suggesting that oxalate is not a sink for excess ascorbic acid but that oxalate formation is regulated.
The Genome-Packaging Signal of the Influenza A Virus Genome Comprises a Genome Incorporation Signal and a Genome-Bundling Signal (2013)

The influenza A virus genome comprises eight single-stranded negative-sense RNA segments (vRNAs). All eight vRNAs are selectively packaged into each progeny virion via so-called segment-specific genome-packaging signal sequences that are located in the noncoding and terminal coding regions of both the 3' and the 5' ends of the vRNAs. However, it remains unclear how these signals ensure that eight different vRNAs are packaged. Here, by using a reverse genetics system, we demonstrated that, in the absence of the other seven vRNAs, a recombinant NP vRNA bearing only a reporter gene flanked by the noncoding NP regions was incorporated into virus-like particles (VLPs) as efficiently as a recombinant NP vRNA bearing the reporter gene flanked by the complete NP packaging signals (i.e., the noncoding sequences and the terminal coding regions). Viruses that comprised a recombinant NP vRNA whose packaging signal was disrupted, and the remaining seven authentic vRNAs, did not undergo multiple cycles of replication; however, a recombinant NP vRNA with only the noncoding regions was readily incorporated into VLPs, suggesting that the packaging signal as currently defined is not necessarily essential for the packaging of the vRNA in which it resides; rather, it is required for the packaging of the full set of vRNAs. We propose that the 3' and 5' noncoding regions of each vRNA bear a virion incorporation signal for that vRNA and that the terminal coding regions serve as a bundling signal that ensures the incorporation of the complete set of eight vRNAs into the virion.
Flow microfluorometric analysis of living spermatozoa stained with Hoechst 33342 (1983)

Bovine spermatozoa were stained with Hoechst 33342. The fluorescence distribution of stained spermatozoa was complex. Non-motile spermatozoa displayed a higher fluorescence than did motile spermatozoa. The fluorescence profile of the motile spermatozoa was bimodal. Sort and reanalysis, and orientation experiments suggested that there are two distinct populations of motile spermatozoa.
Effects of feeding level of milk replacer on body growth, plasma metabolite and insulin concentrations, and visceral organ growth of suckling calves (2009)

ABSTRACT The objective was to evaluate effects of feeding level of milk replacer on body growth, plasma metabolite and insulin concentrations, and allometric growth of visceral organs in suckling calves. Holstein bull calves ( n = 8; 3–4 days of age) were fed either a low amount (average 0.63 kgDM/day, LM) or high amount (average 1.15 kgDM/day, HM) of high protein milk replacer until they were slaughtered at 6 weeks of age. Body weight (BW) at 4, 5, and 6 weeks of age, feed intake, average daily gain, and feed efficiency were higher in the HM than LM calves. The HM group had higher plasma glucose at 3 and 4 weeks of age and insulin levels after the age of 4 weeks compared with LM calves whereas no effect was detected on plasma nonesterified fatty acid or urea nitrogen concentrations. The HM calves had greater empty body weight (EBW), viscera‐free BW and most of the organs dissected than LM calves. Relative weights (% of EBW) of liver, spleen, kidneys, and internal fat were higher, whereas head and large intestine was lower in HM than LM calves. The results suggest that increased milk feeding levels would accelerate the growth of the body and specific organs.
Statistical Methods in Cancer Research (1980)

Statistical methods in cancer research , Statistical methods in cancer research , کتابخانه مرکزی دانشگاه علوم پزشکی تهران
SYNOPSIS:  SYNthesize and OPtimize System in Silico (2003)

We present a de novo design program called SYNOPSIS, that includes a synthesis route for each generated molecule. SYNOPSIS designs novel molecules by starting from a database of available molecules and simulating organic synthesis steps. This way of generating molecules imposes synthetic accessibility on the molecules. In addition to a starting database, a fitness function is needed that calculates the value of a desired property for an arbitrary molecule. The values obtained from this function guide the design process in optimizing the molecules toward an optimal value of the calculated property. Two applications are described. The first uses an electric dipole moment calculation to generate molecules possessing a strong dipole moment. The second makes use of the three-dimensional structure of a viral enzyme in order to generate high affinity ligands. Twenty eight compounds designed with the program resulted in 18 synthesized and tested compounds, 10 of which showed HIV inhibitory activity in vitro.
Aptamers as a Sensitive Tool to Detect Subtle Modifications in Therapeutic Proteins (2012)

Therapeutic proteins are derived from complex expression/production systems, which can result in minor conformational changes due to preferential codon usage in different organisms, post-translational modifications, etc. Subtle conformational differences are often undetectable by bioanalytical methods but can sometimes profoundly impact the safety, efficacy and stability of products. Numerous bioanalytical methods exist to characterize the primary structure of proteins, post translational modifications; protein-substrate/protein/protein interactions and functional bioassays are available for most proteins that are developed as products. There are however few analytical techniques to detect changes in the tertiary structure of proteins suitable for use during drug development and quality control. For example, x-ray crystallography and NMR are impractical for routine use and do not capture the heterogeneity of the product. Conformation-sensitive antibodies can be used to map proteins. However the development of antibodies to represent sufficient epitopes can be challenging. Other limitations of antibodies include limited supply, high costs, heterogeneity and batch to batch variations in titer. Here we provide proof-of-principle that DNA aptamers to thrombin can be used as surrogate antibodies to characterize conformational changes. We show that aptamers can be used in assays using either an ELISA or a label-free platform to characterize different thrombin products. In addition we replicated a heat-treatment procedure that has previously been shown to not affect protein activity but can result in conformational changes that have serious adverse consequences. We demonstrate that a panel of aptamers (but not an antibody) can detect changes in the proteins even when specific activity is unaffected. Our results indicate a novel approach to monitor even small changes in the conformation of proteins which can be used in a routine drug-development and quality control setting. The technique can provide an early warning of structural changes during the manufacturing process that could have consequential outcomes downstream.
Targeting apoptosis in neurological disease using the herpes simplex virus (2002)

Herpes Simplex Viruses type 1 (HSV-1) and 2 (HSV-2) cause central nervous system (CNS) disease ranging from benign aseptic meningitis to fatal encephalitis. In adults, CNS infection with HSV-2 is most often associated with aseptic meningitis while HSV-1 frequently produces severe, focal encephalitis associated with high mortality and morbidity. Recent studies suggested that the distinct neurological outcome of CNS infection with the two viruses may be due to their distinct modulation of apoptotic cell death: HSV-1 triggers neuronal apoptosis, while HSV-2 is neuroprotective. Apoptosis also occurs in the etiology of neurodegenerative disorders such as Alzheimer's disease, Parkinson's disease and Down's syndrome, and determines the loss of specific neuronal populations and the decline in cognitive functions. Notwithstanding, the therapy of these disorders may rely on the use of replication-defective HSV-1 vectors to deliver anti-apoptotic transgenes to the CNS. However, the recent discovery of a neuroprotective activity innate to the HSV-2 genome (the ICP10 PK gene) suggests that: i) ICP10 PK may constitute a novel therapeutic approach by targeting both the apoptotic cell death and the cognitive decline, and ii) HSV-2 may be more suitable than HSV-1 as a vector for targeting neuronal disease.
Cleavage of Fibrinogen by Proteinases Elicits Allergic Responses Through Toll-Like Receptor 4 (2013)

Proteinases and the innate immune receptor Toll-like receptor 4 (TLR4) are essential for expression of allergic inflammation and diseases such as asthma. A mechanism that links these inflammatory mediators is essential for explaining the fundamental basis of allergic disease but has been elusive. Here, we demonstrate that TLR4 is activated by airway proteinase activity to initiate both allergic airway disease and antifungal immunity. These outcomes were induced by proteinase cleavage of the clotting protein fibrinogen, yielding fibrinogen cleavage products that acted as TLR4 ligands on airway epithelial cells and macrophages. Thus, allergic airway inflammation represents an antifungal defensive strategy that is driven by fibrinogen cleavage and TLR4 activation. These findings clarify the molecular basis of allergic disease and suggest new therapeutic strategies.
Intestinal stem cells (2005)

The intestinal tract has a rapid epithelial cell turnover, which continues throughout life. The process is regulated and maintained by a population of stem cells, which give rise to all the intestinal epithelial cell lineages. Studies in both the mouse and the human show that these cells are capable of forming clonal crypt populations. Stem cells remain hard to identify, however it is thought that they reside in a 'niche' towards the base of the crypt and their activity is regulated by the paracrine secretion of growth factors and cytokines from surrounding mesenchymal cells. Stem cell division is usually asymmetric with the formation of an identical daughter stem cell and committed progenitor cells. Progenitor cells retain the ability to divide until they terminally differentiate. Occasional symmetric division produces either 2 daughter cells with stem cell loss, or 2 stem cells and eventual clone dominance. This stochastic extinction of stem cell lines with eventual dominance of one cell line is called 'niche succession'. The discovery of plasticity, the ability of stem cells to engraft into, and in some cases replace the function of damaged host tissues has generated a large amount of scientific and clinical interest: however the concept remains controversial and is still a subject of hot debate. Studies are beginning to identify the complex molecular, genetic and cellular pathways underlying stem cell function such as Wnt signalling, bone morphogenetic protein (BMP) and Notch/Delta pathways. The derangement of these pathways within stem cells plays an integral part in the development of malignancy within the intestinal tract.
Protein Kinase C Overactivity Impairs Prefrontal Cortical Regulation of Working Memory (2004)

The prefrontal cortex is a higher brain region that regulates thought, behavior, and emotion using representational knowledge, operations often referred to as working memory. We tested the influence of protein kinase C (PKC) intracellular signaling on prefrontal cortical cognitive function and showed that high levels of PKC activity in prefrontal cortex, as seen for example during stress exposure, markedly impair behavioral and electrophysiological measures of working memory. These data suggest that excessive PKC activation can disrupt prefrontal cortical regulation of behavior and thought, possibly contributing to signs of prefrontal cortical dysfunction such as distractibility, impaired judgment, impulsivity, and thought disorder.
Darstellung und Reaktionen von 2‐Acetyl‐3‐amino‐5‐hydroxy‐2‐cyclohexenonen; Benzol‐Derivate aus Pyronen (1985)

Abstract Das 3‐Acetylpyron 2 reagiert mit den sek. Aminen 3a–3k zu den Aminocyclohexenonen 5a–5g und 8 bzw. den Aminophenolen 7h und 7i ; Ammoniak und o‐Phenylendiamin dagegen bilden die Tetrahydropyridinone 11a und 11b bzw. das Dihydropyridin 12 . In 5a läßt sich die Aminogruppe durch Ammoniak, Amine, Aminosäuren bzw. Hydrazin‐Derivate austauschen, wobei 14a, 14c, 14e–14g entstehen; mit Benzamidin bzw. Hydrazinen reagiert 5a zum Tetrahydrochinazolin 21 bzw. den Tetrahydroindazolen 24a und 24b . Die Cyclohexenon‐Derivate 5, 8, 14, 21 und 24 werden bei Einwirkung von Kaliumhydroxid in Ethanol dehydratisiert, wobei die Phenol‐Derivate 7a–7h, 9, 15a, 15c, 15e und 15g, 22, 25a und 25b entstehen.
Characterization of an RNase P activity from HeLa cell mitochondria. Comparison with the cytosol RNase P activity. (1985)

A ribonuclease P-like activity was partially purified from HeLa cell mitochondria by DEAE-cellulose and octyl-Sepharose chromatography. RNase P-like activity can be quantitatively recovered from intact mitochondrial preparations treated with micrococcal nuclease, strongly suggesting that the enzyme is localized within the organelles. Mitochondrial RNase P (mtRNase P) cleaves the precursor to Escherichia coli suppressor tRNATyr at the same site as E. coli RNase P, producing the mature 5'-end of tRNATyr. The sensitivity of mtRNase P to pretreatment with nucleases or Pronase indicates that the enzyme has essential RNA and protein components. Although the ionic requirements of mtRNase P are similar to those of the RNase P activity isolated from the post-mitochondrial cytosol fraction, the chromatographic properties of mtRNase P are distinct. Mitochondrial RNase P is probably a part of the mitochondrial RNA processing machinery of mammalian mitochondria, being responsible for the endonucleolytic cleavage of the RNA transcripts at the 5'-side of the tRNA sequences.
A new flash-erase EEPROM cell with a sidewall select-gate on its source side (2003)

A novel flash-erase EEPROM (electrically erasable PROM) cell is described. It consists of a stacked-gate MOSFET with a sidewall select gate on the source side of the FET (SISOS cell). Three layers of polysilicon are used. The cell has a self-aligned structure which makes it possible to realize a small cell area of 4.0*3.5 mu m/sup 2/ with 1.0- mu m technology. It also has a select gate which prevents undesirable leakage current due to overerasing. The cell is programmed by channel hot electron injection at the source side and erased by Fowler-Nordheim tunneling of electrons from the floating gate to the drain. The programming by source-side injection makes it possible for the drain junction to be optimized independently of hot electron generation and for the erasure to be achieved with no degradation in programmability.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Chromosome aberration, sister‐chromatid exchange, proliferative rate index, and serum thiocyanate concentration in smokers exposed to low‐dose benzene (1994)

Cytogenetical endpoints, i.e., chromosome aberration (CA), sister-chromatid exchange (SCE), and proliferative rate indexes (PRI), were measured in peripheral blood lymphocytes (PBL) of 42 workers exposed occupationally to low-dose benzene, and of 42 controls. The role of smoking habit as a confounding factor of genotoxic effects caused by occupational low-dose benzene exposure was also studied. The benzene concentrations in the ambient air samples varied from 3 to 20 mg/m3 (mean: 7 mg/m3). The continuous low-dose benzene exposure significantly increased the CA and SCE frequencies, but did not influence PRI. Smoking levels were characterized by subjective accounts and by serum thiocyanate concentrations (SCN). CA and SCE were not significantly increased in smokers compared to nonsmokers, but the differences were expressed to a greater extent in the case of measurement of SCN concentrations. Determination of SCN proved to be more objective in the assessment of genotoxic effects of smoking as a confounding factor of occupational low-dose benzene exposure.