gebhart/patrepeval huggingface dataset:
Requirements at the 3′ End of the <i>Sindbis Virus</i> Genome for Efficient Synthesis of Minus-Strand RNA (2005)

The 3'-untranslated region of the Sindbis virus genome is 0.3 kb in length with a 19-nucleotide conserved sequence element (3' CSE) immediately preceding the 3'-poly(A) tail. The 3' CSE and poly(A) tail have been assumed to constitute the core promoter for minus-strand RNA synthesis during genome replication; however, their involvement in this process has not been formally demonstrated. Utilizing both in vitro and in vivo analyses, we have examined the role of these elements in the initiation of minus-strand RNA synthesis. The major findings of this study with regard to efficient minus-strand RNA synthesis are the following: (i) the wild-type 3' CSE and the poly(A) tail are required, (ii) the poly(A) tail must be a minimum of 11 to 12 residues in length and immediately follow the 3' CSE, (iii) deletion or substitution of the 3' 13 nucleotides of the 3' CSE severely inhibits minus-strand RNA synthesis, (iv) templates possessing non-wild-type 3' sequences previously demonstrated to support virus replication do not program efficient RNA synthesis, and (v) insertion of uridylate residues between the poly(A) tail and a non-wild-type 3' sequence can restore promoter function to a limited extent. This study shows that the optimal structure of the 3' component of the minus-strand promoter is the wild-type 3' CSE followed a poly(A) tail of at least 11 residues. Our findings also show that insertion of nontemplated bases can restore function to an inactive promoter.
Antihemophilic Factor (Factor VIII) (1978)

Antihemophilic factor (Factor VIII) is an agent in normal plasma that corrects the coagulative defect of classic hemophillia. The plasma of hemophiliacs contains normal amounts of a variant of antihemophilic factor deficient in clot-promoting properties. In contrast, von Willebrand's disease is usually associated with a true deficiency of this protein. In this disorder, the platelets are poorly aggregated by ristocetin, a defect ascribed to deficiency of antihemophilic factor. Structural studies of antihemophilic factor suggest that it is composed of two dissociable subcomponents, one of high molecular weight that contains the bulk of protein and sustains ristocetin-induced platelet aggregation, and another of lower molecular weight with procoagulant activity. Both subcomponents have been identified in hemophilic plasma, as if the smaller subcomponent were qualitatively abnormal. Carriers of hemophilia can often be detected because their plasmas contain a disproportionately high concentration of antihemophilic factor, measured immunologically, compared with the titer of procoagulant antihemophilic factor.
Development of Warm-Mix Asphalt Additive and Evaluation of Performance (2012)

Several warm-mix asphalt (WMA) technologies have been developed and implemented worldwide. Because of the reduced production and compaction temperatures of WMA mixtures, WMA technology can reduce energy consumption, carbon dioxide emission, and asphalt oxidation as well as extend the paving season, increase hauling distance, and create a better working environment. A wax-based WMA additive called low-energy and low–carbon-dioxide asphalt pavement (LEADCAP), has been developed by the Korea Institute of Construction Technology and Kumho Petrochemical and is the first WMA additive developed in South Korea. This paper introduces the characteristics of this newly developed WMA additive and presents the performance evaluation of WMA with LEADCAP. To evaluate the performance of the WMA mixture with LEADCAP additive, the Superpave ® mix design, moisture susceptibility test, and mechanical test were performed. Common hot-mix asphalt and a WMA mixture with Sasobit additive were also evaluated for comparison. Sasobit is also a wax-based additive and is well-known. Mechanical tests included the dynamic modulus test, the direct tension fatigue test, and the triaxial repeated loading permanent deformation test. From the limited data obtained in this study, it was concluded that LEADCAP could be effectively used in WMA mixtures and that the performance of WMA with LEADCAP could be expected to be comparable to that of hot-mix asphalt and WMA with Sasobit additive.
Natural genetic variation in <i>Arabidopsis</i> identifies <i>BREVIS RADIX</i> , a novel regulator of cell proliferation and elongation in the root (2004)

Mutant analysis has been tremendously successful in deciphering the genetics of plant development. However, less is known about the molecular basis of morphological variation within species, which is caused by naturally occurring alleles. In this study, we succeeded in isolating a novel regulator of root growth by exploiting natural genetic variation in the model plant Arabidopsis. Quantitative trait locus analysis of a cross between isogenized accessions revealed that a single locus is responsible for approximately 80% of the variance of the observed difference in root length. This gene, named BREVIS RADIX (BRX), controls the extent of cell proliferation and elongation in the growth zone of the root tip. We isolated BRX by positional cloning. BRX is a member of a small group of highly conserved genes, the BRX gene family, which is only found in multicellular plants. Analyses of Arabidopsis single and double mutants suggest that BRX is the only gene of this family with a role in root development. The BRX protein is nuclear localized and activates transcription in a heterologous yeast system, indicating that BRX family proteins represent a novel class of transcription factors. Thus, we have identified a novel regulatory factor controlling quantitative aspects of root growth.
Theory for equilibrium 180° stripe domains in PbTiO3 films (2006)

A thermodynamic theory is developed for equilibrium 180° stripe domains in ferroelectric thin films on insulating substrates. Such stripe domains form to minimize the energy of the depolarizing field, and lead to a suppression of TC in thin films. Expressions including depolarizing field and domain wall energy are developed and applied to coherently strained PbTiO3 films on SrTiO3 substrates, with an upper boundary condition of either a dielectric (SrTiO3), a conductor, or vacuum. An elastic solution appropriate for epitaxially strained stripe domains and 180° domain walls is presented. We minimize the full nonlinear free energy using a numerical technique to obtain equilibrium polarization and field distributions, and determine the equilibrium stripe period as a function of temperature and film thickness for each upper boundary condition. While the stripe periods found agree reasonably well with the existing analytical solution using a linearized free energy, the suppression of TC as film thickness decreases is as much as a factor of 10 smaller than that given by the linear solution.
Aerodynamic Shape Optimization of a Three-Dimensional Wing by Genetic Algorithm. (1998)

A Genetic Algorithm (GA) has been applied to optimize a wing aerodynamic shape for generic subsonic transportation aircraft. A three-dimensional compressible Navier-Stokes (N-S) solver is used to evaluate aerodynamic performance of a wing. Although a GA has proved its ability to solve hard optimization problems, a GA coupled with a three-dimensional N-S solver has not been done yet because it needs large computational time even on the latest supercomputer. To overcome this difficulty, Numerical Wind Tunnel at National Aerospace Laboratory, a parallel vector machine with 166 processing elements, was used. In the optimum design obtained from the present GA, the design principles for the wing developed by existing theory and experience are found to be realized. This indicates feasibility of the present approach for the aerodynamic optimization in advanced computational environment.
Abstract 2159: Genomic characterization of benign and malignant thyroid tumors (2010)

Abstract Background: Thyroid cancer cells typically harbor multiple genomic aberrations that drive malignant transformation. The goal of this study was to identify novel genetic markers to improve preoperative discrimination between benign and malignant thyroid neoplasms. Methods: Using Illumina HumanHap550 BeadChip with 561,446 single-nucleotide polymorphism (SNP) mark¬ers, we estimated copy number (CN) across the genome on 39 thyroid tumors with matched normal tissue, which included 14 benign tumors (follicular adenomas, FAs) and 25 malignant tumors (13 follicular variant papillary thyroid cancers, FVPTCs, and 12 papillary thyroid cancers, PTCs). The Cir¬cu¬lar Binary Seg¬men¬ta¬tion (CBS) algo¬rithm was applied to calculate copy number variation (CNV) based on Log R Ratio (LRR) values. Loss of heterozygosity (LOH) analysis was performed by using LOH Score plug-in in BeadStudio program. Within the regions showing CNV, candidate genes were further examined by real-time PCR. Results: The comprehensive genetic profile of 39 thyroid tumors was defined, and tumor -specific somatic change assessed using matched normal thyroid tissue as reference. With strict control of the false discovery rate, significant alterations averaged 32 CNVs in benign FAs, and 8 in malignant thyroid cancer (PTCs and FVPTCs), including 17 gains in FAs and 3 gains in cancers, and 2.9 losses in FAs and 4.4 losses in cancers. Additionally, an average of 12 copy-neutral LOHs per FA and 1 LOH per cancer were detected. Among the CNVs, we found 60 focal alterations that were specific either for benign FAs, or for thyroid cancers. We used empirical Bayes modified ANOVA to identify genes for which copy number was associated with tumor type. Increases in copy number on chromosome 12 were much more common in FAs than in cancers. GDF3, a candidate gene located in 12p13.31, was further validated by quantitative real time PCR, which showed results consistent with our SNP array results. Overall, follicular adenomas showed considerably higher levels of copy number variation than the two malignant tumor subtypes studied, i.e. PTCs and FVPTCs. Conclusions: Benign and malignant thyroid tumors may possess characteristic and distinguishable genomic profiles. The genetic changes identified in this study may allow the development of biomarkers for differentiation of benign and malignant thyroid nodules. In the next phase of this study, we will perform a transcriptome-wide expression analysis on the same tissue sample set used for the SNP array study, and perform an integrated analysis combining DNA genetic alterations and differential gene expression to further refine the identification of candidate molecular changes that may be used in differentiating benign from malignant thyroid lesions. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2159.
The influence of temperature and humidity on stratum corneum and its relation to skin chapping (1973)

Synopsis The susceptibility of the STRATUM CORNEUM to CHAPPING depends upon its mechanical properties such as extensibility. It has previously been shown that at constant temperature, extensibility of isolated corneum is related to RELATIVE HUMIDITY and that at constant relative humidity, extensibility increases when the temperature is raised above 25oC. In this report extensibility of isolated animal corneum has been determined at 5oC where skin chapping occurs more frequently. EXTENSIBILITY was found to be lower at reduced temperatures although the corneum water content did not decrease. It was concluded that skin chapping is the result of a low corneum TEMPERATURE and WATER CONTENT and that greater flaking and chapping of the surface corneum is a result of a gradient of temperature or water content across the corneum in a cold or dry ENVIRONMENT.
Fermentation of 1,2-Propanediol and 1,2-Ethanediol by Some Genera of <i>Enterobacteriaceae</i> , Involving Coenzyme B <sub>12</sub> -Dependent Diol Dehydratase (1979)

Klebsiella pneumoniae (Aerobacter aerogenes) ATCC 8724 was able to grow anaerobically on 1,2-propanediol and 1,2-ethanediol as carbon and energy sources. Whole cells of the bacterium grown anaerobically on 1,2-propanediol or on glycerol catalyzed conversion of 1,2-diols and aldehydes to the corresponding acids and alcohols. Glucose-grown cells also converted aldehydes, but not 1,2-diols, to acids and alcohols. The presence of activities of coenzyme B(12)-dependent diol dehydratase, alcohol dehydrogenase, coenzyme-A-dependent aldehyde dehydrogenase, phosphotransacetylase, and acetate kinase was demonstrated with crude extracts of 1,2-propanediol-grown cells. The dependence of the levels of these enzymes on growth substrates, together with cofactor requirements in in vitro conversion of these substrates, indicates that 1,2-diols are fermented to the corresponding acids and alcohols via aldehydes, acyl-coenzyme A, and acyl phosphates. This metabolic pathway for 1,2-diol fermentation was also suggested in some other genera of Enterobacteriaceae which were able to grow anaerobically on 1,2-propanediol. When the bacteria were cultivated in a 1,2-propanediol medium not supplemented with cobalt ion, the coenzyme B(12)-dependent conversion of 1,2-diols to aldehydes was the rate-limiting step in this fermentation. This was because the intracellular concentration of coenzyme B(12) was very low in the cells grown in cobalt-deficient medium, since the apoprotein of diol dehydratase was markedly induced in the cells grown in the 1,2-propanediol medium. Better cell yields were obtained when the bacteria were grown anaerobically on 1,2-propanediol. Evidence is presented that aerobically grown cells have a different metabolic pathway for utilizing 1,2-propanediol.
A highly sensitive model for quantification of in vivo tumor angiogenesis induced by alginate-encapsulated tumor cells. (1997)

A remarkable approach to a specific tumor angiogenesis model in vivo is the use of alginate implants encapsulating tumor cells. However, this previously reported approach has often been questioned because of doubts regarding the relevance of hemoglobin at the alginate implant as a parameter of vascularization. In the present investigation, we examined whether or not the use of the blood pool agents FITC-dextran of high molecular weight would significantly improve the determination of vascularization at the alginate implant. In our experiments, we found a rapid distribution of FITC-dextran within the blood circulation of mice after i.v. bolus injection. The amount of FITC-dextran within alginate implants strongly correlated with the number of LL2 carcinoma cells or B16/F10 cells encapsulated. Even a low number of 10(3) cells per alginate implant led to a significantly increased accumulation of FITC-dextran. A more than 10-fold stimulation above that of controls was found with alginate implants containing 10(4) LL2 or B16/F10 tumor cells. Using the investigational compound AGM-1470 in different treatment schedules, we found that quantification of alginate implant anglogenesis with FITC-dextran is a sensitive method for the determination of angiogenesis inhibition. In conclusion, our results demonstrated that the use of FITC-dextran enables highly sensitive, quantitative measurement of blood vessel formation by alginate implants.
Interaction of novel cationic meso-tetraphenylporphyrins in the ground and excited states with DNA and nucleotides (2000)

The syntheses and aggregation properties of novel cationic meso-tetraphenylporphyrins substituted in the para-positions with -CH2(pyridinio)+ (P11), -CH2N+(CH3)3 (P22), -CH2P+(n-butyl)3 (P33), -CH2P+(phenyl)3 (P44), -CH2S+(CH3)2 (P55) and -CH2SC(NH2)2+ (P66) groups are described. Their use as photosensitizers and their interactions with DNA and nucleotides were studied by optical methods and their properties were compared with those of anionic meso-tetrakis(4-sulfonatophenyl)porphyrin (TPPS) and cationic meso-tetrakis(4-N-methylpyridyl)porphyrin (TMPyP). P11 and P22 formed stable complexes with calf thymus DNA in phosphate buffer (Ka ≈ 106 M−1; outside stacking binding mode) and with some nucleotides in methanol (Ka ≈ 103–104 M−1). P33–P66 aggregated readily in aqueous solution due to their more hydrophobic nature. The cationic porphyrins TMPyP and P11–P66 sensitized the decomposition of guanosine 5′-monophosphate (GMP). The rates of GMP decomposition were found to be greater with cationic porphyrins P11–P66 than with anionic TPPS, presumably because of Coulombic attraction between the positively charged porphyrins P11–P66 and the anionic GMP. In oxygen-free conditions, GMP decomposition was initiated by interaction of the singlet (P11, P22) or triplet (P11–P66) excited states of the porphyrins with GMP. In the presence of oxygen, GMP is decomposed predominantly via singlet oxygen mechanism.
Resolution characteristics of a novel silicone-based positive photoresist (1989)

A novel silicone-based positive photoresist (SPP) is developed for a two-layer resist system. SPP is composed of an alkali-soluble silicone polymer (APSQ) and a diazonaphthoquinone compound as a sensitizer. APSQ is newly synthesized by means of acetylation of polyphenylsilsesquioxane (PSQ). A fine SPP pattern below 0.5 μm can be fabricated with a g-line stepper (NA=0.6) using a two-layer resist system. Moreover, a 0.4 μm line/space pattern is successfully fabricated at a defocus of ±0.4 μm. The high oxygen reactive ion etching (O2RIE) resistance of SPP makes possible the fabrication of a submicron pattern with a high aspect ratio in a two-layer system. Pattern width loss can be negligible during O2RIE of a 2 μm thick bottom resist when a 0.6 μm thick SPP is used as the top imaging layer.
Multi-Grained Reconfigurable Datapath Structures for Online-Adaptive Reconfigurable Hardware Architectures (2005)

Modern application scenarios out of multimedia and mobile communication domains demand more and more performant data processing architectures, which cannot be achieved by using current DSP or microprocessor approaches. This paper describes a new multi-grained architecture approach out of the reconfigurable array field which offers a set of new features to increase the flexibility and usability of reconfigurable array architectures by increasing the performance benefit concurrently and decreasing the management effort caused by the system controller. Multi-grained support allows execution of multi-grained application as well as realization of flexible control mechanisms for control-based applications. The main focus of this publication is the introduction of the developed datapath structure where the authors discuss the concepts and features in detail.
Cone rod dystrophies (2007)

Cone rod dystrophies (CRDs) (prevalence 1/40,000) are inherited retinal dystrophies that belong to the group of pigmentary retinopathies. CRDs are characterized by retinal pigment deposits visible on fundus examination, predominantly localized to the macular region. In contrast to typical retinitis pigmentosa (RP), also called the rod cone dystrophies (RCDs) resulting from the primary loss in rod photoreceptors and later followed by the secondary loss in cone photoreceptors, CRDs reflect the opposite sequence of events. CRD is characterized by primary cone involvement, or, sometimes, by concomitant loss of both cones and rods that explains the predominant symptoms of CRDs: decreased visual acuity, color vision defects, photoaversion and decreased sensitivity in the central visual field, later followed by progressive loss in peripheral vision and night blindness. The clinical course of CRDs is generally more severe and rapid than that of RCDs, leading to earlier legal blindness and disability. At end stage, however, CRDs do not differ from RCDs. CRDs are most frequently non syndromic, but they may also be part of several syndromes, such as Bardet Biedl syndrome and Spinocerebellar Ataxia Type 7 (SCA7). Non syndromic CRDs are genetically heterogeneous (ten cloned genes and three loci have been identified so far). The four major causative genes involved in the pathogenesis of CRDs are ABCA4 (which causes Stargardt disease and also 30 to 60% of autosomal recessive CRDs), CRX and GUCY2D (which are responsible for many reported cases of autosomal dominant CRDs), and RPGR (which causes about 2/3 of X-linked RP and also an undetermined percentage of X-linked CRDs). It is likely that highly deleterious mutations in genes that otherwise cause RP or macular dystrophy may also lead to CRDs. The diagnosis of CRDs is based on clinical history, fundus examination and electroretinogram. Molecular diagnosis can be made for some genes, genetic counseling is always advised. Currently, there is no therapy that stops the evolution of the disease or restores the vision, and the visual prognosis is poor. Management aims at slowing down the degenerative process, treating the complications and helping patients to cope with the social and psychological impact of blindness.
Intermittent exposure of medulloblastoma cells to topotecan produces growth inhibition equivalent to continuous exposure. (1997)

Camptothecin analogues such as topotecan increase the number of covalent topoisomerase I-DNA complexes, which, in turn, have been proposed to initiate apoptosis. If induction of apoptosis by the camptothecins is, in fact, dependent on the formation of topoisomerase I-DNA complexes, then it would be of clinical relevance to identify schedules of exposure to the camptothecins that maximize the formation of these complexes but minimize the total amount of the drug administered. The time and dose dependence of topoisomerase I-DNA complex formation was determined by incubating Daoy pediatric medulloblastoma cells in vitro with topotecan at concentrations equivalent to those achievable in the plasma clinically (10, 50, or 200 nM) and measuring the number of complexes present in cells incubated for 15 min to 48 h with the drug. Regardless of the concentration of topotecan used, covalent topoisomerase I-DNA complexes were maximal within 15 min following addition of the lactone form of topotecan to the tissue culture medium. After 2 h of exposure to topotecan, complexes had decreased from maximum to approximately half of that value. Few, if any, complexes were detectable with topotecan incubations of 24-48 h. Growth inhibition studies showed that the IC50s of topotecan for the Daoy cell line (2.2 x 10(-9) M) and also for a second pediatric medulloblastoma cell line, SJ-Med3 (3.6 x 10(-9) M), exposed to topotecan 8 h daily for 5 days or continuous exposure were equivalent. The decrease in topoisomerase I-DNA complexes between 15 min and 1 h was consistent with a pH-dependent re-equilibration of topotecan to the less active hydroxyacid form of the drug. The decrease in complexes after a 2-48-h incubation with the drug was attributable neither to biological inactivation of topotecan as shown by sequential growth inhibition studies nor to a decrease in amount of topoisomerase I in the drug-treated cells. Indirect immunofluorescence labeling of topoisomerase I in Daoy cells incubated for 48 h with 10 nM topotecan showed a redistribution of nucleolar topoisomerase I. We are currently evaluating the antitumor effect of intermittent repetitive exposures to topotecan in mice bearing Daoy cells as a xenograft. The clinical utility of each effective schedule of exposure will depend on whether the therapeutic index of repetitive intermittent exposure to the drug is more or less favorable than the therapeutic index of continuous exposure.