gebhart/patrepeval huggingface dataset:
Gibberellin-responsive elements in the promoter of a barley high-pI alpha-amylase gene. (1992)

Deletion analysis has previously shown that the major gibberellic acid (GA)- and abscisic acid (ABA)-responsive elements in the promoter of a high-pI alpha-amylase gene of barley are located downstream of -174 (Jacobsen and Close, 1991). We have used transient expression assays in barley aleurone protoplasts to identify sequences between -174 and +53 that confer GA and ABA responsiveness on expression of a beta-glucuronidase reporter gene. Using alpha-amylase promoter fragments and synthetic oligonucleotides fused to minimal promoters, we have shown that the hormone-responsive region is located between -174 and -108. A single copy of this region fused to a minimal alpha-amylase promoter (-41) conferred both GA- and ABA-responsive expression on the reporter gene comparable to the positive control, Am(-174)IGN. Multiple copies of this region were able to activate even greater levels of expression. Site-directed mutagenesis was used to determine the functional importance of the conserved motifs (-169pyrimidine box, -143TAACAAA box, and -124TATCCAC box) and nonconserved intervening sequences within the region between -174 and -108. Our results showed that both the TAACAAA and TATCCAC boxes play an important role in GA-regulated expression. We propose that the TAACAAA box is a gibberellin response element, that the TATCCAC box acts cooperatively with the TAACAAA box to give a high level of GA-regulated expression, and that together these motifs form important components of a gibberellin response complex in high-pI alpha-amylase genes. The TAACAAA box also appears to be the site of action of ABA.(ABSTRACT TRUNCATED AT 250 WORDS)
Study of interleukin-6 in the spread of colorectal cancer: the diagnostic significance of IL-6. (2006)

We investigated the diagnostic significance of IL-6 for lymph node metastasis and/or hepatic metastasis from colorectal cancer in 65 patients and evaluated the contributions of 8 factors (IL-6, HGF, IL-1beta, TNF-alpha, TGF-beta1, ELAM-1, ICAM-1, VCAM-1) toward Dukes.s classification of 53 patients. We also examined IL-6 expression in tumor tissue. From the receiver operating characteristic (ROC) curve analysis, an optimal cutoff value of 5.8 pg/ml was determined to classify lymph node and/or hepatic metastasis, and that of 6.3 pg/ml was determined to classify hepatic metastasis. These values indicated sensitivities of 55.0% and 71.4%, and specifi cities of 100% and 88.6%, respectively. IL-6, HGF, and ELAM-1 were very useful for distinguishing among Dukes.s A/B group, C group, and D group. In all cases with high IL-6 values (more than 25.0 pg/ml), immunohistochemical staining was positive for IL-6 in the cytoplasm of cancer cells. IL-6 is strongly suspected to be involved in lymph node and/or hepatic metastasis by promoting it through HGF, and serum IL-6 value (pg/ml) would be useful diagnostically to estimate whether or not there is a high risk of lymph node and/or hepatic metastasis.
Yttrium-90 microspheres (TheraSphere®) treatment of unresectable hepatocellular carcinoma: Downstaging to resection, RFA and bridge to transplantation (2006)

These data suggest that intra-arterial (90)Y microspheres can be used as a bridge to transplantation, surgical resection, or RFA.
CUB-domain–containing protein 1 (CDCP1) activates Src to promote melanoma metastasis (2011)

We report the application of quantitative mass spectrometry to identify plasma membrane proteins differentially expressed in melanoma cells with high vs. low metastatic abilities. Using stable isotope labeling with amino acids in culture (SILAC) coupled with nanospray tandem mass spectrometry, we identified CUB-domain-containing protein 1 (CDCP1) as one such differentially expressed transmembrane protein. CDCP1 is not only a surface marker for cells with higher metastatic potential, but also functionally involved in enhancing tumor metastasis. Overexpression of CDCP1 also correlates with activation of Src. Pharmacological reagents, PP2 and Dasatinib, which block Src family kinase activation, blocked scattered growth of CDCP1-overexpressing cells in 3D Matrigel culture, suggesting that CDCP1 might function through the activation of Src-family kinases (SFKs). This hypothesis was further supported by mutational studies of CDCP1. Whereas wild-type CDCP1 enhances Src activation, point mutation Y734F abolishes in vitro dispersive growth in 3D culture and in vivo metastasis-enhancing activities of CDCP1. In addition, the Y734F mutation also eliminated enhanced Src activation. Thus, this work provides molecular mechanisms for the metastasis-enhancing functions of CDCP1.
Recent Trends in Catalytic Polymerizations (2019)

Polymers have become one of the largest and most important materials we use in daily life. Their popularity has stemmed from their wide range of material properties combined with their low cost of production. Both of these attractive traits have in part been enabled by the development of catalytic polymerizations, which provide both high levels of control while also delivering high levels of productivity. In this Perspective, we highlight recent trends and achievements made in the growing field of catalytic polymerizations.
Statistical Modelling and Phylogenetic Analysis of a Deaminase Domain (1998)

Deamination reactions are catalyzed by a variety of enzymes including those involved in nucleoside/nucleotide metabolism and cytosine to uracil (C-->U) and adenosine to inosine (A-->I) mRNA editing. The active site of the deaminase (DM) domain in these enzymes contains a conserved histidine (or rarely cysteine), two cysteines and a glutamate proposed to act as a proton shuttle during deamination. Here, a statistical model, a hidden Markov model (HMM), of the DM domain has been created which identifies currently known DM domains and suggests new DM domains in viral, bacterial and eucaryotic proteins. However, no DM domains were identified in the currently predicted proteins from the archaeon Methanococcus jannaschii and possible causes for, and a potential means to ameliorate this situation are discussed. In some of the newly identified DM domains, the glutamate is changed to a residue that could not function as a proton shuttle and in one instance (Mus musculus spermatid protein TENR) the cysteines are also changed to lysine and serine. These may be non-competent DM domains able to bind but not act upon their substrate. Phylogenetic analysis using an HMM-generated alignment of DM domains reveals three branches with clear substructure in each branch. The results suggest DM domains that are candidates for yeast, platyhelminth, plant and mammalian C-->U and A-->I mRNA editing enzymes. Some bacterial and eucaryotic DM domains form distinct branches in the phylogenetic tree suggesting the existence of common, novel substrates.
Inter-domain routing for mobile ad hoc networks (2008)

Inter-domain routing is an important component to allow interoperation among heterogeneous network domains operated by different organizations. Although inter-domain routing has been well supported in the Internet, there has been relatively little support to the Mobile Ad Hoc Networks (MANETs) space. In MANETs, the inter-domain routing problem is challenged by: (1) dynamic network topology due to mobility, and (2) diverse intra-domain ad hoc routing protocols. In this paper, we discuss how to enable inter-domain routing among MANETs, and to handle the dynamic nature of MANETs. We first present the design challenges for inter-domain routing in MANETs, and then propose a framework for inter-domain routing in MANETs.
Adaptive Communication Techniques for the Internet of Things (2013)

The vision for the Internet of Things (IoT) demands that material objects acquire communications and computation capabilities and become able to automatically identify themselves through standard protocols and open systems, using the Internet as their foundation. Yet, several challenges still must be addressed for this vision to become a reality. A core ingredient in such development is the ability of heterogeneous devices to communicate adaptively so as to make the best of limited spectrum availability and cope with competition which is inevitable as more and more objects connect to the system. This survey provides an overview of current developments in this area, placing emphasis on wireless sensor networks that can provide IoT capabilities for material objects and techniques that can be used in the context of systems employing low-power versions of the Internet Protocol (IP) stack. The survey introduces a conceptual model that facilitates the identification of opportunities for adaptation in each layer of the network stack. After a detailed discussion of specific approaches applicable to particular layers, we consider how sharing information across layers can facilitate further adaptation. We conclude with a discussion of future research directions.
Evidence for expression and function of phosphodiesterase type 5 (PDE‐V) in rat resistance arteries (2001)

Evidence is provided for expression and a functional role for phosphodiesterase type V (PDE-V) in the rat isolated small mesenteric artery. The reverse transcription polymerase chain reaction (RT--PCR) demonstrated mRNA for PDE-V, while Western blotting and immunocytochemical studies showed corresponding protein expression. Smooth muscle relaxation to the nitric oxide donor, diethylamine NONOate (DEA NONOate; 1 nM - 10 microM; pEC(50)=6.7+/-0.3) was potentiated significantly by the specific inhibitor of PDE-V, 4-[[3,4-(methylenedioxy)benzyl]amino]-6-chloroquinazoline (MBCQ; 1 microM; pEC(50)=10.5+/-0.04). These data show that PDE-V is expressed in both the smooth muscle and endothelial cells of a resistance artery, and the enzyme can significantly influence nitric oxide-evoked vasorelaxation.
Genes governing swarming in <i>Bacillus subtilis</i> and evidence for a phase variation mechanism controlling surface motility (2004)

Undomesticated strains of Bacillus subtilis, but not laboratory strains, exhibit robust swarming motility on solid surfaces. The failure of laboratory strains to swarm is caused by a mutation in a gene (sfp) needed for surfactin synthesis and a mutation(s) in an additional unknown gene(s). Insertional mutagenesis of the undomesticated 3610 strain with the transposon mini-Tn10 was carried out to discover genes needed for swarming but not swimming motility. Four such newly identified swarming genes are reported, three of which (swrA, swrB, and efp) had not been previously characterized and one of which (swrC) was known to play a role in resistance to the antibacterial effect of surfactin. Laboratory strains were found to harbour a frameshift mutation in the swrA gene. When corrected for the swrA mutation, as well as the mutation in sfp, laboratory strains regained the capacity to swarm and did so as robustly as the wild strain. The swrA mutation was an insertion of an A:T base pair in a homopolymeric stretch of eight A:T base pairs, and readily reverted to the wild type. These findings suggest that the swrA insertion and its reversion take place by slipped-strand mispairing during DNA replication and that swarming motility is subject to phase variation.
Low temperature stabilization of cubic (Li7−xAlx/3)La3Zr2O12: role of aluminum during formation (2013)

The lithium lanthanum zirconium oxide garnet, Li7La3Zr2O12 (LLZ), has received significant attention in recent years due to its high room temperature lithium ion conductivity and its stability against lithium metal. Together these features make it a promising electrolyte candidate for a high energy all solid-state battery. Previous studies have shown that incorporation of aluminum cations during the synthesis stabilizes the higher conductivity cubic phase of LLZ; however the incorporation process and its effect on the phase transition are still unclear. In the present study, we have combined powder X-ray diffraction (XRD), 27Al and 7Li MAS NMR and high-resolution X-ray diffraction (HRXRD) to determine the disposition of Al cations during the formation of low temperature cubic LLZ. At temperatures as low as 700 °C, the aluminum is incorporated into amorphous or nanocrystalline grain boundary phases. Above 700 °C, the Al cations are associated with a poorly crystalline anti-fluorite phase Li5AlO4, composed of molecular [AlO4]5− anions. This phase then reacts with tetragonal LLZ to form cubic LLZ over a 25 hour period at 850 °C. Although the reaction appears complete by powder X-ray diffraction, 27Al NMR spectra showed overlapping resonances suggesting multiple Al environments due to uneven substitution of the 24d Li(1) site. This was confirmed by high-resolution XRD and was consistent with a series of closely related cubic LLZ phases with slightly different Al concentrations, indicating the slower Al(III) diffusion within the lattice has not reached equilibrium in the time allotted. The disorder over the two crystallographic tetrahedral sites by lithium and aluminum cations at this temperature contributes to the observed lattice enlargement associated with the low temperature cubic phase.
Refractometers (1968)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTRefractometersL. E. Maley Cite this: J. Chem. Educ. 1968, 45, 6, A467Publication Date (Print):June 1, 1968Publication History Received3 August 2009Published online1 June 1968Published inissue 1 June 1968https://doi.org/10.1021/ed045pA467Request reuse permissionsArticle Views255Altmetric-Citations2LEARN 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 InReddit PDF (7 MB) Get e-Alertsclose Get e-Alerts
Novel Cross-Linking Reagents Based on 3,3-Dimethyl-1-phenylenetriazene (1993)

Arylene ethers containing two or three 3,3-dimethyl-1-phenylenetriazene (-C6H4-N = N-NMe2) reactive end-groups have been prepared. Differential scanning calorimetry (DSC) of these triazene functionalized arylene ethers exhibits exothermal decomposition peak temperature ranging from 263 °C to 285 °C. These arylene ethers crosslink a fluorinated polyimide at 300 °C to give high gel contents, and exert little influence on the dielectric constants of the crosslinked polymers. The crosslinked polymers exhibit improved thermal stability and resistance to organic solvents.
The Haar+ Tree: A Refined Synopsis Data Structure (2007)

We introduce the Haar <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> tree: a refined, wavelet-inspired data structure for synopsis construction. The advantages of this structure are twofold: First, it achieves higher synopsis quality at the task of summarizing data sets with sharp discontinuities than state-of-the-art histogram and Haar wavelet techniques. Second, thanks to its search space delimitation capacity, Haar <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> synopsis construction operates in time linear to the size of the data set for any monotonic distributive error metric. Through experimentation, we demonstrate the superiority of Haar <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> synopses over histogram and Haar wavelet methods in both construction time and achieved quality for representative error metrics.
Transcriptome of the Lymantria dispar (Gypsy Moth) Larval Midgut in Response to Infection by Bacillus thuringiensis (2013)

Transcriptomic profiles of the serious lepidopteran insect pest Lymantria dispar (gypsy moth) were characterized in the larval midgut in response to infection by Bacillus thuringiensis kurstaki, a biopesticide commonly used for its control. RNA-Seq approaches were used to define a set of 49,613 assembled transcript sequences, of which 838, 1,248 and 3,305 were respectively partitioned into high-, mid- and low-quality tiers on the basis of homology information. Digital gene expression profiles suggested genes differentially expressed at 24 hours post infection, and qRT-PCR analyses were performed for verification. The differentially expressed genes primarily associated with digestive function, including α-amylase, lipase and carboxypeptidase; immune response, including C-type lectin 4; developmental genes such as arylphorin; as well as a variety of binding proteins: cellular retinoic acid binding protein (lipid-binding), insulin-related peptide binding protein (protein-binding) and ovary C/EBPg transcription factor (nucleic acid-binding). This is the first study conducted to specifically investigate gypsy moth response to a bacterial infection challenge using large-scale sequencing technologies, and the results highlight important genes that could be involved in biopesticide resistance development or could serve as targets for biologically-based control mechanisms of this insect pest.
CCL3-CCR5 Axis Regulates Intratumoral Accumulation of Leukocytes and Fibroblasts and Promotes Angiogenesis in Murine Lung Metastasis Process (2008)

Metastasis proceeds through interaction between cancer cells and resident cells such as leukocytes and fibroblasts. An i.v. injection of a mouse renal cell carcinoma, Renca, into wild-type mice resulted in multiple metastasis foci in lungs and was associated with intratumoral accumulation of macrophages, granulocytes, and fibroblasts. A chemokine, CCL3, was detected in infiltrating cells and, to a lesser degree, tumor cells, together with an infiltration of leukocytes expressing CCR5, a specific receptor for CCL3. A deficiency of the CCL3 or CCR5 gene markedly reduced the number of metastasis foci in the lung, and the analysis using bone marrow chimeric mice revealed that both bone marrow- and non-bone marrow-derived cells contributed to metastasis formation. CCL3- and CCR5-deficient mice exhibited a reduction in intratumoral accumulation of macrophages, granulocytes, and fibroblasts. Moreover, intratumoral neovascularization, an indispensable process for metastasis, was attenuated in these gene-deficient mice. Intrapulmonary expression of matrix metalloproteinase (MMP)-9 and hepatocyte growth factor (HGF) was enhanced in wild-type mice, and the increases were markedly diminished in CCL3- and CCR5-deficient mice. Furthermore, MMP-9 protein was detected in macrophages and granulocytes, the cells that also express CCR5 and in vitro stimulation by CCL3-induced macrophages to express MMP-9. Intratumoral fibroblasts expressed CCR5 and HGF protein. In vitro CCL3 stimulated fibroblasts to express HGF. Collectively, the CCL3-CCR5 axis appears to regulate intratumoral trafficking of leukocytes and fibroblasts, as well as MMP-9 and HGF expression, and as a consequence to accelerate neovascularization and subsequent metastasis formation.
PitchPerfect (2014)

Rehearsal is a critical component of preparing to give an oral presentation, yet it is frequently abbreviated, performed in ways that are inefficient or ineffective, or simply omitted. We conducted an exploratory study to understand the relationship between the theory and practice of presentation rehearsal, classifying our qualitative results into five themes to motivate more structured rehearsal support deeply integrated in slide presentation software. In a within-subject study (N=12) comparing against participants' existing rehearsal practices, we found that our resulting PitchPerfect system significantly improved overall presentation quality and content coverage as well as provided greater support for content mastery, time management, and confidence building.
The CDK5 repressor CDK5RAP1 is a methylthiotransferase acting on nuclear and mitochondrial RNA (2012)

The unusual cyclin-dependent protein kinase 5 (CDK5) was discovered based on its sequence homology to cell cycle regulating CDKs. CDK5 was found to be active in brain tissues, where it is not involved in cell cycle regulation but in the regulation of neuronal cell differentiation and neurocytoskeleton dynamics. An aberrant regulation of CDK5 leads to the development of various neurodegenerative diseases including Alzheimer's disease. Although CDK5 is not regulated by cyclins, its activity does depend on the association with a protein activator and the presence or absence of further inhibitory factors. Recently, CDK5RAP1 was discovered to inhibit the active CDK5 kinase. Here, we show that CDK5RAP1 is a radical SAM enzyme, which postsynthetically converts the RNA modification N6-isopentenyladenosine (i(6)A) into 2-methylthio-N6-isopentenyladenosine (ms(2)i(6)A). This conversion is surprisingly not limited to mitochondrial tRNA, where the modification was known to exist. Instead, CDK5RAP1 introduces the modification also into nuclear RNA species establishing a link between postsynthetic kinase-based protein modification and postsynthetic RNA modification.
Full soft-switching capability of the dual-active bridge by using the auxiliary-resonant commutated-pole technique (2017)

Many publications present the extension of the soft-switching range of the dual-active bridge (DAB). Unfortunately soft-switching over the entire operating area of the DAB is hard to realize. In this paper, the loss reduction of a 5 MW dual-active bridge using the auxilary-resonant commutated pole technique are derived by simulation. The aim of this technique is to improve the converter's efficiency. To reach that goal each phase is extended with an auxiliary-resonant pole to force a soft-switched commutation of the converter legs to prevent switching losses. Basic control algorithms are presented and proper controllability is demonstrated by a small-scale setup.
<i>In vitro</i>effects of three woody plant and sainfoin extracts on 3rd-stage larvae and adult worms of three gastrointestinal nematodes (2004)

Most studies on the effects of tanniferous plants on nematodes have examined forages but have neglected the woody plants. Therefore, in vitro effects of extracts from 3 woody plants (Rubus fructicosus, Quercus robur, Corylus avellana) have been tested on trichostrongyles and compared to sainfoin, a legume forage. Because some in vivo results indicated that the effects of tannins differed depending on the parasitic species and/or stages, the effects were measured on 3rd-stage larvae (L3) and adult worms of Teladorsagia circumcincta, Haemonchlus contortus and Trichostrongylus colubriformis. The effects of plant extracts varied according to the plant sources, the parasite species and stages. For the woody plants, significant inhibitory effects were obtained on both stages of abomasal species. Results for T. colubriformis were more variable. Effects of sainfoin extracts were significant on T. colubriformis and H. contortus L3, and on abomasal adult worms. In order to assess the implications of tannins, polyethylene glycol (PEG), an inhibitor of tannins, was added to hazel tree, oak and sainfoin extracts. Without PEG, significant inhibitory effects on L3 and adult worms were confirmed. After addition of PEG, the larval migration and motility of adult worms were restored in most cases. These results confirm variations in effects depending on factors related to plants or parasites and suggest that tannins are partly responsible for the effects.