gebhart/patrepeval huggingface dataset:
cDNA structure and expression of bombyxin, an insulin-like brain secretory peptide of the silkmoth Bombyx mori (1989)

Bombyxin, previously referred to as 4K-prothoracicotropic hormone, is a brain peptide of the silkmoth Bombyx mori, the amino acid sequence of which shows considerable homology with vertebrate insulin family peptides. Two independent clones have been isolated from a Bombyx larval brain cDNA library by using a synthetic oligonucleotide probe, one with the complete coding region for preprobombyxin (lambda Bb360) and the other covering the coding region, possibly for bombyxin, only partially (lambda Bb204). lambda Bb360 encodes preprobombyxin in the order of prepeptide/B-chain/proteolytic cleavage signal/C-peptide/proteolytic cleavage signal/A-chain. This domain organization of preprobombyxin is the same as that of preproinsulins, suggesting that the tertiary structure and posttranslational modification mechanism are conserved through the evolution of bombyxin and insulin. Genomic Southern hybridization analyses using this cDNA as probe suggest that the Bombyx genome contains multiple copies of bombyxin gene. Northern hybridization analyses indicate that the concentration of lambda Bb360-type bombyxin mRNA in the bombyxin-producing cells is remarkably high (2.8 x 10(9) molecules/micrograms of total RNA), without undergoing appreciable change during larval-pupal development.
Analogs of ornithine as inhibitors of ornithine decarboxylase. New deductions concerning the topography of the enzyme's active site (1978)

Fourteen structural analogues of ornithine were synthesized and evaluated as inhibitors of preparations of the enzyme L-ornithine carboxylase (ODC) (E.C. 4.1.1.17) obtained from rat liver, rat hepatoma cells in culture, or bull prostate. The synthesis of these compounds was achieved either via a Bucherer type reaction or via alkylation of carbanions derived from ethyl acetamidocyanoacetate, methyl isocyanoacetate, benzyl alpha-isocyanopropionate, methylbenzaldimine alanate, and the azlactone derivative of ornithuric acid. (+)-alpha-Methylornithine, which was assigned the L configuration on the basis of rotational criteria, was found to be the most potent reversible inhibitor of ODC among the synthesized compounds. From the degree of inhibition of ODC activity in the presence of the various ornithine analogues, it has been possible to delineate some of the structural features of the substrate L-ornithine which are required for binding to the mammalian ODC active site.
A facile synthesis of novel nitrogen-sulphur heterocycles containing the amidino moiety and their antimicrobial activity—Part I (2004)

The interaction of amidinothiocarbamide 1 and 4-bromo-1,3-substituted-pyrazol-5-ones 1 afford 2-guanidino-4, 6-substituted-pyrazolo [5,4-d]thiazoles 5 on reaction with aldehydes yield the corresponding schiffs bases bases6. An alternate unambiguous one step synthesis of 6 is described. Similarly, the reaction of 1 with diethyl bromomalonate 8 to give fused ring heterocycles has been studied in detail. Certain compounds synthesized exhibit antimicrobial and antitubercular activity.
Molecular analysis of rice plants harboring an Ac/Ds transposable element‐mediated gene trapping system (1999)

In rice, limited efforts have been made to identify genes by the use of insertional mutagens, especially heterologous transposons such as the maize Ac/Ds. We constructed Ac and gene trap Ds vectors and introduced them into the rice genome by Agrobacterium-mediated transformation. In this report, rice plants that contained single and simple insertions of T-DNA were analysed in order to evaluate the gene-tagging efficiency. The 3' end of Ds was examined for putative splicing donor sites. As observed in maize, three splice donor sites were identified at the 3' end of the Ds in rice. Nearly 80% of Ds elements were excised from the original T-DNA sites, when Ac cDNA was expressed under a CaMV 35S promoter. Repetitive ratoon culturing was performed to induce new transpositions of Ds in new plants derived from cuttings. About 30% of the plants carried at least one Ds which underwent secondary transposition in the later cultures. Eight per cent of transposed Ds elements expressed GUS in various tissues of rice panicles. With cloned DNA adjacent to Ds, the genomic complexities of the insertion sites were examined by Southern hybridization. Half of the Ds insertion sites showed simple hybridization patterns which could be easily utilized to locate the Ds. Our data demonstrate that the Ac/Ds-mediated gene trap system could prove an excellent tool for the analysis of functions of genes in rice. We discuss genetic strategies that could be employed in a large scale mutagenesis using a heterologous Ac/Ds family in rice.
Stage‐specific behavioral, cognitive, and in vivo changes in community residing subjects with age‐associated memory impairment and primary degenerative dementia of the Alzheimer type (1988)

Abstract Stage‐specific relationships between the seven‐stage Global Deterioration Scale (GDS) for age‐associated memory impairment and primary degenerative dementia of the Alzheimerapos;s type and behavioral, cognitive, and neuroradiologic changes were examined in community residing subjects with normal aging or Alzheimerapos;s disease (AD). The results revealed significant decrements between GDS stages 2 and 3; 3 and 4; 4 and 5; and 5 and 6 for most behavioral measures. No decrements were noted between GDS stages 1 and 2. Consequently, the subjective complaints of cognitive decrement, which characterize GDS 2 subjects and which commonly accompany aging, do not appear to be accompanied by objective behavioral or cognitive change. Floor effects for most behavioral and cognitive measures occurred by GDS 6, with nearly uniform bottom scores by GDS stage 7. Computerized tomographic (CT) assessments of brain change revealed significant relationships with global severity on the GDS, but few significant consecutive stage decrements were noted. The magnitude of the relationship between CT assessments of brain change and GDS scores was notably less than the magnitude of the relationship noted between various behavioral measures and GDS. Although behavioral and neurcradiologic measures studied did not reveal decrements in the GDS 2 subjects in comparison with age‐matched GDS 1 subjects who do not have subjective decrements, previous studies of a neuroimmunologic measure (brain reactive antibody levels) do appear to have indicated significant differences between these groups. Consequently, there is some current preliminary evidence for the hypothesis of a physiologic substrate for the subjective deficits characteristic of the GDS 2 stage, as well as clear‐cut behavioral data distinguishing each of the subsequent GDS stages of aging and AD.
Optimization of an optically pumped 1.3-μm GaInNAs vertical-cavity surface-emitting laser (2002)

Numerical model predictions are used to optimize the design of an 980-nm-pumped 1.3-μm GaInNAs vertical-cavity surface-emitting laser. The optimum architecture utilizes pumping through the substrate and a double-band mirror to obtain double-pass pumping. We compare the results obtained with this approach to those with conventional architectures. These results are of general relevance to GaInNAs optically pumped surface-emitting or amplifying structures.
Signal Transduction Pathways Coupled to a P<sub>2U</sub> Receptor in Neuroblastoma × Glioma (NG108‐15) Cells (1993)

Extracellular ATP has neurotransmitter-like properties in the CNS and PNS that are mediated by a cell-surface P2 purinergic receptor. In the present study, we have extensively characterized the signal transduction pathways that are associated with activation of a P2U receptor in a cultured neuroblastoma x glioma hybrid cell line (NG108-15 cells). The addition of > or = 1 microM ATP to NG108-15 cells caused a transient increase in [Ca2+]i that was inhibited by 40% when extracellular calcium was chelated by EGTA. ATP concentrations > or = 500 microM also elicited a sustained increase in [Ca2+]i that was inhibited when extracellular calcium was chelated by EGTA. The increase in [Ca2+]i elicited by ATP occurred concomitantly with the hydrolysis of [32P]-phosphatidylinositol 4,5-bisphosphates and an increase in the level of inositol 1,4,5-trisphosphate. ATP also caused a time- and dose-dependent increase in levels of [3H]inositol monophosphates in lithium-treated cells. Separation of the inositol monophosphate isomers by ion chromatography revealed a specific increase in the level of inositol 4-monophosphate. The magnitude of the increase in [Ca2+]i elicited by ATP correlated with the concentration of the fully ionized form of ATP (ATP4-) in the medium and not with the concentration of magnesium-ATP (MgATP2-). Similar to ATP, UTP also induced polyphosphoinositide breakdown, inositol phosphate formation, and an increase in [Ca2+]i. ADP, ITP, TTP, GTP, ATP gamma S, 2-methylthio ATP, beta, gamma-imidoATP or 3'-O-(4-benzoyl)benzoylATP, but not CTP, AMP, beta, gamma-methylene ATP, or adenosine, also caused an increase in [Ca2+]i. In cells labeled with [32P]P(i) or [14C]-arachidonic acid, ATP caused a transient increase in levels of labeled phosphatidic acids, but had no effect on levels of arachidonic acid. The increase in phosphatidic acid levels elicited by ATP apparently was not due to activation of a phospholipase D because ATP did not induce the formation of phosphatidylethanol in [14C]myristic acid-labeled cells incubated in the presence of ethanol. These findings support the hypothesis that a P2 nucleotide receptor in NG108-15 cells is coupled to a signal transduction pathway involving the activation of a phospholipase C and a plasma membrane calcium channel, but not the activation of phospholipases A2 and D.
Relative channel reciprocity calibration in MIMO/TDD systems (2010)

Abstract: Channel state information at the transmitter (CSIT) can greatly improve the capacity of a wireless MIMO communication system. In a time division duplex (TDD) system CSIT can be obtained by exploiting the reciprocity of the wireless channel. This however requires calibration of the radio frequency (RF) chains of the receiver and the transmitter, which are in general not reciprocal. In this paper we in-vestigate different methods for relative calibration in the presence of frequency offsets between transmitter and receiver. We show results of theses calibration methods with real two-directional channel measurements, which were performed using the Eure-com MIMO Openair Sounder (EMOS). We demonstrate that in a single-user MIMO channel and for low signal-to-noise (SNR) ratios, the relative calibration method can increase the capacity close to the theoretical limit. 1.
Structure refinement of trigonal zinc-chlorine boracite, Zn<sub>3</sub>B<sub>7</sub>O<sub>13</sub>Cl, from single-crystal and powder X-ray diffraction (1991)

Abstract Zn3B7O13Cl: R3c, a hex = 8.53725(7) Å, c hex = 20.96849(25) Å. V hex = 1323.53(3) Å,3 a rh = 8.5527(1) Å, αrh = 59.8809(1)°, Dx = 3.8931Mg/m3, Rp = 0.081 and RB = 0.047 for 35 reflections and 44 parameters from powder profile refinement (T = 298 K); R = 0.051 for 1568 reflections and 74 parameters from single-crystal refinement (T = 298 K). A comparison with isostructural iron-chlorine boracite, Fe3B7O13Cl, suggests that the magnitude of the rhombohedral lattice shear in trigonal boracites depends in a complex manner on the bonding requirement of the five-coordinate metal ions, and the space requirement of an oxygen-boron framework that is relatively rigid with respect to changes of O—B bondlengths and O—O contact distances, but more flexible with respect to changes of bond angles and torsion angles.
Integration of ZnO Nanotubes with Well-Ordered Nanorods through Two-Step Thermal Evaporation Approach (2007)

We have successfully realized the integration of ZnO nanotubes and well-ordered nanorods through a simple two-step thermal evaporation of Zn powder without any metal catalyst. Detailed structural analysis shows that the step-one prepared samples at the low substrate temperature are composed of hexagonal-shaped Zn/Zn suboxide nanowires dominated by Zn with little oxidation via the layer-by-layer growth mechanism. In the second step, by heating the step-one deposited samples and Zn powder at high temperature, highly ordered single-crystalline ZnO nanorods were epitaxially grown on the surface of nanowires through the screw dislocation growth mode. Simultaneously, Zn inside the nanowires sublimates to form hollow ZnO nanotubes, which finally results in the formation of ZnO nanotubes surrounded by well-ordered nanorods (ZNSWN). The field-emission scanning electron microscopy images of samples with different heating times indicate that the length of ZnO nanorods in the tube walls can be well controlled by changing the reaction time with a growth rate of ∼3 nm/min. We also further present the comparative X-ray diffraction, Raman, and photoluminescence investigation for the growth process and structural information of the fabricated ZNSWN nanostructures.
Impact of target mRNA structure on siRNA silencing efficiency: A large‐scale study (2008)

The selection of active siRNAs is generally based on identifying siRNAs with certain sequence and structural properties. However, the efficiency of RNA interference has also been shown to depend on the structure of the target mRNA, primarily through studies using exogenous transcripts with well-defined secondary structures in the vicinity of the target sequence. While these studies provide a means for examining the impact of target sequence and structure independently, the predicted secondary structures for these transcripts are often not reflective of structures that form in full-length, native mRNAs where interactions can occur between relatively remote segments of the mRNAs. Here, using a combination of experimental results and analysis of a large dataset, we demonstrate that the accessibility of certain local target structures on the mRNA is an important determinant in the gene silencing ability of siRNAs. siRNAs targeting the enhanced green fluorescent protein were chosen using a minimal siRNA selection algorithm followed by classification based on the predicted minimum free energy structures of the target transcripts. Transfection into HeLa and HepG2 cells revealed that siRNAs targeting regions of the mRNA predicted to have unpaired 5'- and 3'-ends resulted in greater gene silencing than regions predicted to have other types of secondary structure. These results were confirmed by analysis of gene silencing data from previously published siRNAs, which showed that mRNA target regions unpaired at either the 5'-end or 3'-end were silenced, on average, approximately 10% more strongly than target regions unpaired in the center or primarily paired throughout. We found this effect to be independent of the structure of the siRNA guide strand. Taken together, these results suggest minimal requirements for nucleation of hybridization between the siRNA guide strand and mRNA and that both mRNA and guide strand structure should be considered when choosing candidate siRNAs.
A Record Black Bear (1939)

A Record Black Bear Get access Hartley H. T. Jackson Hartley H. T. Jackson U. S. Biological Survey, Washington, D. C. Search for other works by this author on: Oxford Academic Google Scholar Journal of Mammalogy, Volume 20, Issue 2, 14 May 1939, Pages 252–253, https://doi.org/10.1093/jmammal/20.2.252b Published: 14 May 1939
Azelastine hydrochloride, a dual-acting anti-inflammatory ophthalmic solution, for treatment of allergic conjunctivitis (2010)

Over 50% of patients who seek treatment for allergies present with ocular symptoms. Our current ability to control ocular allergic symptoms is greater than ever before. Newer dual-acting topical eyedrops attack multiple facets of the allergic cascade. Azelastine has antihistaminic effects providing immediate relief, mast cell stabilization providing early-phase intervention, and inhibition of expression and activation of anti-inflammatory mediators which characterize the late phase of the immune reaction. The ophthalmic eyedrop formulation is approved for treatment of allergic conjunctivitis in adults and children aged over 3 years. In clinical trials comparing azelastine with other dual-acting eyedrops, such as levocabastine and olopatadine, azelastine was reported to be slightly less efficacious and to sting briefly upon administration. Even so, many patients experienced the full benefit of symptom relief, and preferred azelastine. As a broad-spectrum drug, azelastine offers many desirable properties for management of ocular allergies. Because it can often produce maximal effect with just twice-daily dosing, azelastine is a particularly good choice for the allergic population in whom minimizing exposure to topical products and preservatives is a key concern.
Space/Time/Sovereignty (1996)

In an unusually interesting conference held in Kadoma, Zimbabwe, early in 1993, in a post-Cold War era desperately searching for directions amidst crumpled signposts and snakeoil prophets, conversation centred, predictably enough, upon the fate of claims about state sovereignty under contemporary conditions. They focussed especially on the status of sovereignty under those conditions that have been ascribed to something called the Third World.1 Only slightly less predictably, conversation became especially heated around questions about language (in the broadest sense implied by terms like 'ideology' and 'discourse') and around the sharply diverging readings of contemporary trajectories offered by analysts deemed to be representative of North and South.KeywordsInternational RelationSovereign StateState SovereigntyModem WorldWorld Capitalist EconomyThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
Palladium-Catalyzed, Modular Synthesis of Highly Functionalized Indoles and Tryptophans by Direct Annulation of Substituted <i>o</i>-Haloanilines and Aldehydes (2006)

One-pot synthesis of indoles by a palladium-catalyzed annulation of ortho-haloanilines and aldehydes has been developed. Coupling of ortho-iodoaniline with aldehyde is realized under mild ligandless conditions [Pd(OAc)2, DABCO, DMF, 85 degrees C], whereas X-Phos is found to be the ligand of choice for coupling reactions involving ortho-chloroanilines/ortho-bromoanilines and aldehydes. A variety of ortho-haloanilines with different electronic properties are suitable substrates, and aldehydes including chiral ones participated in this reaction without racemization. Coupling of (S)-2-N,N-di-tert-butoxycarbonyl-5-oxopentanoate, derived from L-glutamic acid, with ortho-haloanilines provides a rapid access to the ring-A-substituted tryptophans in good to excellent yields.
Inline control of an ultra low-k ILD layer using Broadband Spectroscopic Ellipsometry (2011)

As chip dimensions are scaling down new challenges develop in the back-end-of-line. In order to keep the capacitance small while decreasing the volume of the inter-layer dielectric (ILD), new materials and processes have been introduced over the past years to lower the dielectric constant of the ILD layers. For design rules of 45 nm and below porous Ultra low-k materials are widely used in today's semiconductor process flows. Beside process challenges this introduces stringent requirements for metrology not only to monitor film thickness but other properties of the material as well. This paper discusses the development and implementation of a Broadband Spectroscopic Ellipsometer for inline process control of a SiCOH based porous ultra low-k film. After deposition the material is cured with UV light to introduce the porosity. The challenge for the metrology is to measure both the thickness and an adequate metric for the chemical properties which do no longer correlate with optical properties. In addition the chemical properties vary as a gradient from top to bottom of the film. We discuss the methodology to develop a metrology recipe resulting in the thickness of a metric layer and the percentaged thickness shrink being the best parameters to sense and track the process adequately. Results demonstrate the sensitivity of the technique to process variations. Short term precision, long term stability and tool-to-tool matching results prove that the technique enables routine process monitoring in a high volume automated semiconductor fab.
A New Type of Bacteriophytochrome Acts in Tandem with a Classical Bacteriophytochrome to Control the Antennae Synthesis in Rhodopseudomonas palustris (2005)

Phytochromes are chromoproteins found in plants and bacteria that switch between two photointerconvertible forms via the photoisomerization of their chromophore. These two forms, Pr and Pfr, absorb red and far-red light, respectively. We have characterized the biophysical and biochemical properties of two bacteriophytochromes, RpBphP2 and RpBphP3, from the photosynthetic bacterium Rhodopseudomonas palustris. Their genes are contiguous and localized near the pucBAd genes encoding the polypeptides of the light harvesting complexes LH4, whose synthesis depends on the light intensity. At variance with all (bacterio)phytochromes studied so far, the light-induced isomerization of the chromophore of RpBphP3 converts the Pr form to a form absorbing at shorter wavelength around 645 nm, designated as Pnr for near red. The quantum yield for the transformation of Pr into Pnr is about 6-fold smaller than for the reverse reaction. Both RpBphP2 and RpBphP3 autophosphorylate in their dark-adapted Pr forms and transfer their phosphate to a common response regulator Rpa3017. Under semiaerobic conditions, LH4 complexes replace specifically the LH2 complexes in wild-type cells illuminated by wavelengths comprised between 680 and 730 nm. In contrast, mutants deleted in each of these two bacteriophytochromes display no variation in the composition of their light harvesting complexes whatever the light intensity. From both the peculiar properties of these bacteriophytochromes and the phenotypes of their deletion mutants, we propose that they operate in tandem to control the synthesis of LH4 complexes by measuring the relative intensities of 645 and 710 nm lights.