gebhart/patrepeval huggingface dataset:
Translational efficiency of poliovirus mRNA: mapping inhibitory cis-acting elements within the 5' noncoding region (1988)

Poliovirus mRNA contains a long 5' noncoding region of about 750 nucleotides (the exact number varies among the three virus serotypes), which contains several AUG codons upstream of the major initiator AUG. Unlike most eucaryotic mRNAs, poliovirus does not contain a m7GpppX (where X is any nucleotide) cap structure at its 5' end and is translated by a cap-independent mechanism. To study the manner by which poliovirus mRNA is expressed, we examined the translational efficiencies of a series of deletion mutants within the 5' noncoding region of the mRNA. In this paper we report striking translation system-specific differences in the ability of the altered mRNAs to be translated. The results suggest the existence of an inhibitory cis-acting element(s) within the 5' noncoding region of poliovirus (between nucleotides 70 and 381) which restricts mRNA translation in reticulocyte lysate, wheat germ extract, and Xenopus oocytes, but not in HeLa cell extracts. In addition, we show that HeLa cell extracts contain a trans-acting factor(s) that overcomes this restriction.
Investigating Li<sub>2</sub>NiO<sub>2</sub>–Li<sub>2</sub>CuO<sub>2</sub> Solid Solutions as High-Capacity Cathode Materials for Li-Ion Batteries (2017)

Li2Ni1–xCuxO2 solid solutions were prepared by a solid-state method to study the correlation between composition and electrochemical performance. Cu incorporation improved the phase purity of Li2Ni1–xCuxO2 with orthorhombic Immm structure, resulting in enhanced capacity. However, the electrochemical profiles suggested Cu incorporation did not prevent irreversible phase transformation during the electrochemical process, instead, it likely influenced the phase transformation upon lithium removal. By combining ex situ X-ray diffraction (XRD), X-ray absorption spectroscopy (XAS), and differential electrochemical mass spectrometry (DEMS) measurements, this study elucidates the relevant phase transformation (e.g., crystal structure, local environment, and charge compensation) and participation of electrons from lattice oxygen during the first cycle in these complex oxides.
A Convenient and Efficient Synthesis of Polyphenylmono-, di-, and -triaminobenzenes (1995)

A new convenient and efficient synthesis of polyphenylmono- and -diaminobenzenes by the palladium(0)-catalyzed cross-coupling reaction of polyhalomono- and -diaminobenzenes with phenylboronic acid is described. A synthesis of 2,4-diphenyl-1,3,5-triaminobenzene is also reported.
Living with Water: Flood Adaptive Landscapes in the Yellow River Basin of China (2008)

This paper is a report on a research project. It shows how the past experience of adaptive strategies that have evolved in the long history of survival under hazardous conditions is inspiring for us in facing future uncertainty. Based on a study of several ancient cities in the Yellow River floodplain, this paper discusses the disastrous experience of floods and waterlogging and finds three major adaptive landscape strategies: siting on high ground, constructing walls and protective dikes, and reserving or digging ponds within cities. These adaptive strategies create three types of water city: water-within-city, city-in-water, and ying-yang-city. It is argued that all these traditional experiences and landscape heritages help us to understand the vernacular cultural landscape of cities in the Yellow River floodplain, and that they have important value for landscape architecture and urban planning as universally applicable strategies in facing global warming and regional climate change as well as practical landscape strategies for better urban design in this region. It is further argued that the water-adaptive landscapes are valuable features of the cultural heritage, and should be integrated into landscape and urban planning for urban development today.
Secondary Plasmodesmata Are Specific Sites of Localization of the Tobacco Mosaic Virus Movement Protein in Transgenic Tobacco Plants (1992)

Biao Ding, James S. Haudenshield, Richard J. Hull, Shmuel Wolf, Roger N. Beachy, William J. Lucas, Secondary Plasmodesmata Are Specific Sites of Localization of the Tobacco Mosaic Virus Movement Protein in Transgenic Tobacco Plants, The Plant Cell, Vol. 4, No. 8 (Aug., 1992), pp. 915-928
Thrombopoietin induces association of Crkl with STAT5 but not STAT3 in human platelets. (1998)

Crkl, a 39-kD SH2, SH3 domain-containing adapter protein, is constitutively tyrosine phosphorylated in hematopoietic cells from chronic myelogenous leukemia (CML) patients. We recently reported that thrombopoietin induces tyrosine phosphorylation of Crkl in normal platelets. In this study, we demonstrate that thrombopoietin induces association of Crkl with a tyrosine phosphorylated 95- to 100-kD protein in platelets and in UT7/TPO cells, a thrombopoietin-dependent megakaryocytic cell line. With specific antibodies against STAT5, we demonstrate that the 95- to 100-kD protein in Crkl immunoprecipitates is STAT5. This coimmunoprecipitation was specific in that Crkl immunoprecipitates do not contain STAT3, although STAT3 becomes tyrosine phosphorylated in thrombopoietin-stimulated platelets. The coimmunoprecipitaion of Crkl with STAT5 was inhibited by the immunizing peptide for Crkl antisera or phenyl phosphate (20 mmol/L). After denaturing of Crkl immunoprecipitates, Crkl was still immunoprecipitated by Crkl antisera. However, coimmunoprecipitation of STAT5 was not observed. Coincident with STAT5 tyrosine phosphorylation, thrombopoietin induces activation of STAT5 DNA-binding activity as demonstrated by electrophoretic mobility shift assays (EMSA). Using a beta-casein promoter STAT5 binding site as a probe, we have also demonstrated that Crkl antisera supershift the STAT5-DNA complex, suggesting that Crkl is a component of the complex in the nucleus. Furthermore, interleukin-3 (IL-3), granulocyte-macrophage colony-stimulating factor (GM-CSF), and erythropoietin also induce Crkl-STAT5 complex formation in responding cells in a stimulation-dependent manner. In vitro, glutathione S-transferase (GST)-Crkl bound to STAT5 inducibly through its SH2 domain. These results indicate that thrombopoietin, IL-3, GM-CSF, and erythropoietin commonly induce association of STAT5 and Crkl and that the complex translocates to the nucleus and binds to DNA. Interestingly, such association between STAT5 and Crkl was not observed in cytokine-stimulated murine cells, suggesting an intriguing possibility that components of the human STAT5-DNA complex may be different from those of the murine counterpart.
Spatial backoff contention resolution for wireless networks (2006)

Traditional medium access control (MAC) protocols utilize temporal mechanisms such as access probability or backoff interval adaptation for contention resolution. They typically take the set of competing nodes as a given, and address the problem of adapting each node's channel access behavior to the given channel contention level. This is a temporal approach for contention resolution, which aims to separate transmissions from different nodes in time to achieve successful transmissions. We explore an alternative approach for wireless networks-named "spatial backoff-that adapts the "space" occupied by the transmissions. Each transmission in a wireless network competes for a certain space. By adapting the space occupied by transmissions, the set of "locally" competing nodes, and thus, the channel contention level, can be adjusted to reach a suitable level. There are different ways to realize spatial backoff. In this paper, we propose a dynamic spatial backoff algorithm using the joint control of carrier sense threshold and transmission rate. Our results suggest that spatial backoff can lead to a substantial gain in channel utilization.
Cold Thermoreceptors, Unexpected Players in Tear Production and Ocular Dryness Sensations (2011)

Supported by the Spanish MICINN (Ministerio de Ciencia e Innovación): projects BFU2008-04425 (CB) and SAF2008-00529 (JG), and by Consolider-Ingenio 2010 CSD2007-00023.
EFFECT OF GAMMA RADIATION ON ANTHRACITE (1963)

The effect of gamma radiation on Pennsylvania anthracite and on reactions between anthracite and other materials was studied using a shielded, self-contained 23,000-curie cobalt 60 source. When anthracite was exposed to air at 65 deg C the reaction with oxygen was greater in the presence of radiation than in its absence. Although drop-shatter tests indicated that exposure to radiation decreased the resistance to breakage of anthracite, this evidence of structural weakening was not supported by the results of grindability or particle- size studies. Irradiation caused definite changes in the gases evolved from evacuated samples of anthracite; the percentages of hydrogen and carbon dioxide were increased, and the methane concentration remained unchanged. Carbon monoxide was evolved only from the unirradiated samples. Electron paramagnetic resonance (EPR) measurements indicated large differences between evacuated samples and those exposed to air. There was little or no difference between irradiated and unirradiated samples, except that the free-radical content of unirradiated samples of anthracite increased progressively with higher temperatures of evacuation, but in the case of irradiated samples, no such behavior was found. Attempts to produce carbon disulfide and calcium carbide by reacting anthracite with sulfur up to 120 deg C, and with calcium oxide up tomore » 400 deg C, were unsuccessful. (auth)« less
A dynamic nonlinear relationship between the static and pulsatile components of intracranial pressure in patients with subarachnoid hemorrhage (2009)

The relationship between the static and pulsatile components of ICPs changes over time. It evolves, even in individual patients, over a number of hours. This can be one reason the observation of high pulsatile ICP (indicative of reduced intracranial compliance) despite normal mean ICP that is seen in some patients with SAH. The meaning and potential clinical usefulness of such changes in the curves is uncertain, but it implies that clinical events result not only from moving further out on a compliance curve; in practice, the curve, and the biological system that underlies the curve, may itself change.
Nanoscale geometry assisted proximity effect correction for electron beam direct write nanolithography (2009)

Nanoscale geometry assisted proximity effect correction is presented for nanoscale structures and the results clearly show improvements in feature sharpness down to 20 nm structures. The design rule is simple to implement onto existing PEC software and enables implementation of PEC down to the resolution limits of electron beam lithography.
Evaluating Mapping Repair Systems with Large Biomedical Ontologies (2013)

Abstract. In this paper we provide empirical evidence of the necessity of integrating mapping repair techniques within the ontology matching process, an aspect that is neglected in many ontology matching systems. We also evaluate the feasibility of using state-of-the-art mapping repair techniques in practice, such as those implemented in Alcomo and LogMap. A preliminary evaluation was conducted in the context of the Ontology Alignment Evaluation Initiative (OAEI) 2012. We extend this evaluation and report about the results in detail. 1
Automated 360° profilometry of 3-D diffuse objects (1985)

A novel approach to 360° measurement and reconstruction of the surface topography of 3-D diffuse objects is presented. The method is fully automated and based on the principle of phase-measuring profilometry with a projected sinusoidal grating. A complete 3-D shape is reconstructed from a series of line-section profiles corresponding to discrete angular positions of the object. The system consists simply of a slide projector with a translatable grating, a linear detector array, and a microcomputer for control and processing. Experimental results for a general 3-D object and a performance analysis are presented.
Effect of FGF-BP on angiogenesis in squamous cell carcinoma. (2004)

OBJECTIVE To localize fibroblast growth factors binding protein (FGF-BP) mRNA in squamous cell carcinoma (SCC) and study the FGF-BP association with vascularity. METHODS Thirty-five primary squamous cell carcinoma specimens, 8 metastatic squamous cell carcinoma specimens and 7 histologically adjacent tissues were studied. The localization of FGF-BP mRNA expression was performed using in situ hybridization with 35 S-labeled human FGF-BP. Microvessels in tumor specimens were identified by von Willebrand Factor-specific immunohistochemical staining for endothelial cells. RESULTS In situ hybridization demonstrated that FGF-BP mRNA was overexpressed in SCC. But a specific hybridization signal for FGF-BP mRNA was not detected in normal adult muscle, larynx, tongue, and lymph node. The highest density of microvessels was observed at the invasive edge of the tumor. The mean microvessel count in FGF-BP positive SCC was significantly higher than that in FGF-BP negative tumors (P < 0.001). CONCLUSION The results demonstrated that FGF-BP is present in SCC of the head and neck. The association of FGF-BP expression with angiogenesis suggests that FGF-BP may be an angiogenic factor in SCC.
A combined interfacial and in-situ polymerization strategy to construct well-defined core-shell epoxy-containing SiO <sub>2</sub> -based microcapsules with high encapsulation loading, super thermal stability and nonpolar solvent tolerance (2016)

SiO2-based microcapsules containing hydrophobic molecules exhibited potential applications such as extrinsic self-healing, drug delivery, due to outstanding thermal and chemical stability of SiO2. However, to construct SiO2-based microcapsules with both high encapsulation loading and long-term structural stability is still a troublesome issue, limiting their further utilization. We herein design a single-batch route, a combined interfacial and in-situ polymerization strategy, to fabricate epoxy-containing SiO2-based microcapsules with both high encapsulation loading and long-term structural stability. The final SiO2-based microcapsules preserve high encapsulation loading of 85.7 wt% by controlling exclusively hydrolysis and condensed polymerization at oil/water interface in the initial interfacial polymerization step. In the subsequent in-situ polymerization step, the initial SiO2-based microcapsules as seeds could efficiently harvest SiO2 precursors and primary SiO2 particles to finely tune the SiO2 wall thickness, thereby enhancing long-term structural stability of the final SiO2-based microcapsules including high thermal stability with almost no any weight loss until 250°C, and strong tolerance against nonpolar solvents such as CCl4 with almost unchanged core-shell structure and unchanged core weight after immersing into strong solvents for up to 5 days. These SiO2-based microcapsules are extremely suited for processing them into anticorrosive coating in the presence of nonpolar solvents for self-healing application.
DIRECT IN VIVO GENE TRANSFER TO UROLOGICAL ORGANS (1999)

This study demonstrates that direct in vivo electrotransfection is a feasible method of transient gene delivery into intact urological organs. Its apparent safety and relative simplicity suggest that direct in vivo electrotransfection may be useful clinically.
Organocatalytic Synthesis of Spiro[pyrrolidin-3,3′-oxindoles] with High Enantiopurity and Structural Diversity (2009)

The privileged spiro[pyrrolidin-3,3'-oxindole] derivatives exhibit important biological activities. An enantioselective organocatalytic approach to the rapid synthesis of spiro[pyrrolidin-3,3'-oxindole] derivatives with high enantiopurity and structural diversity is described. The asymmetric catalytic three-component 1,3-dipolar cycloaddition of a broad range of methyleneindolinones with aldehydes and amino esters in the presence of chiral phosphoric acid provides spirooxindole derivatives in high yield with unusual regiochemistry and excellent stereoselectivities (up to 98% ee) under mild conditions. The straightforward construction of spirooxindole skeletons with high stereo- and regioselectivity suggests a new avenue to medicinal chemistry and diversity-oriented synthesis. Theoretical calculations disclosed that both the azomethine ylide and the methyleneindolinone are hydrogen-bonded with the phosphoric acid, which accounted for the high enantio- and regioselectivity and indicated that the unusual regioselectivity results from the stabilization stemming from the favorable pi-pi stacking interaction between the oxo-indole ring and the conjugated esters.
Relationship of <i>Pneumocystis jiroveci</i> Humoral Immunity to Prevention of Colonization and Chronic Obstructive Pulmonary Disease in a Primate Model of HIV Infection (2010)

Pulmonary colonization by the opportunistic pathogen Pneumocystis jiroveci is common in HIV(+) subjects and has been associated with development of chronic obstructive pulmonary disease (COPD). Host and environmental factors associated with colonization susceptibility are undefined. Using a simian-human immunodeficiency virus (SHIV) model of HIV infection, the immunologic parameters associated with natural Pneumocystis jiroveci transmission were evaluated. SHIV-infected macaques were exposed to P. jiroveci by cohousing with immunosuppressed, P. jiroveci-colonized macaques in two independent experiments. Serial plasma and bronchoalveolar lavage (BAL) fluid samples were examined for changes in antibody titers to recombinant Pneumocystis-kexin protein (KEX1) and evidence of Pneumocystis colonization by nested PCR of BAL fluid. In experiment 1, 10 of 14 monkeys became Pneumocystis colonized (Pc(+)) by 8 weeks post-SHIV infection, while 4 animals remained Pneumocystis colonization negative (Pc(-)) throughout the study. In experiment 2, 11 of 17 animals became Pneumocystis colonized by 16 weeks post-SHIV infection, while 6 monkeys remained Pc(-). Baseline plasma KEX1-IgG titers were significantly higher in monkeys that remained Pc(-), compared to Pc(+) monkeys, in experiments 1 (P = 0.013) and 2 (P = 0.022). Pc(-) monkeys had greater percentages of Pneumocystis-specific memory B cells after SHIV infection compared to Pc(+) monkeys (P = 0.037). After SHIV infection, Pc(+) monkeys developed progressive obstructive pulmonary disease, whereas Pc(-) monkeys maintained normal lung function throughout the study. These results demonstrate a correlation between the KEX1 humoral response and the prevention of Pneumocystis colonization and obstructive lung disease in the SHIV model. In addition, these results indicate that an effective Pneumocystis-specific memory B-cell response is maintained despite progressive loss of CD4(+) T cells during SHIV infection.
El Cabildo, los vecinos y la utilización de la ‘‘otra banda’’ como territorio alternativo en la economía rural colonial. Buenos Aires y Santa Fe durante la extinción del ganado cimarrón y las vaquerías tradicionales (1720-1750) (2015)

espanolEste articulo tiene como eje la ganaderia rioplatense durante la primera mitad del siglo XVIII, caracterizada por los importantes cambios sobre la vida economica, tales como la extincion del ganado cimarron (primero en la campana bonaerense, mas tarde en Santa Fe), y a partir de eso la consolidacion de nuevas formas de explotacion como las recogidas de ganado alzado, la estancia colonial y la busqueda de animales salvajes en otros puntos de dichas jurisdicciones. En este contexto, la utilizacion de las tierras y los recursos de ‘‘la otra banda’’, entendida como los campos abiertos que se encontraban mas alla de los limites senalados por importantes rios, fueron importantes para el desarrollo productivo, fundamentalmente por la disponibilidad de cimarron y demas recursos. Analizamos en este trabajo las jurisdicciones capitulares de Santa Fe y Buenos Aires entre 1720-1750, donde se agudizo la desaparicion de cimarrones y se dio una intensa explotacion de los recursos disponibles en aquellas tierras. Para analizar las problematicas socioeconomicas vinculadas, se analizaron las actas del Cabildo de Santa Fe (ACSF), los acuerdos del extinguido Cabildo de Buenos Aires (AECBA), el archivo de dicha institucion (AC) y datos obtenidos en los padrones de Buenos Aires EnglishThe purpose of this article is the River Plate shaft livestock during the first half of the eighteenth century, characterized by major changes on economic life, such as the extinction of wild cattle (first in Buenos Aires, later in Santa Fe), and from that the consolidation of new forms of exploitation as the sum collected from cattle, the colonial stay and search for wild animals elsewhere in those jurisdictions. In this context, the use of land and resources '' the other side '', understood as open fields that were beyond the limits set by major rivers were important for productive development, mainly by availability bighorn and other resources. In this paper we analyze the Chapter jurisdictions Santa Fe and Buenos Aires between 1720-1750, where the disappearance of runaway deepened and given a thorough exploitation of the resources available in those lands. To analyze the socio-economic problems related, the minutes of the Santa Fe Council (ACSF) were analyzed, the agreements of the Buenos Aires Council (AECBA), the file of the institution (AC) and data on the pattern of Buenos Aires
The deconvolution problem: Fast algorithms including the preconditioned conjugate-gradient to compute a MAP estimator (1984)

Different aspects of the deconvolution problem are discussed and a solution by the MAP estimator using the a priori knowledge of smoothness and nonnegativity of the unknown signal is proposed. Several fast algorithms are examined and the conjugate-gradient (CG) method is show to have several advantages: it allows computation of a constrained solution and when used with a preconditioning technique it can be faster than other algorithms for general near-to-Toeplitz systems, in particular, for Toeplitz-block-Toeplitz systems.
A potentiostat circuit for multiple implantable electrochemical sensors (2010)

This work proposes a potentiostat circuit for multiple implantable sensor applications. Implantable sensors play a vital role in continuous in situ monitoring of biological phenomena in a real-time health care monitoring system. In the proposed work a three-electrode based electrochemical sensing system has been employed. In this system a fixed potential difference between the working and the reference electrodes is maintained using a potentiostat to generate a current signal in the counter electrode which is proportional to the concentration of the analyte. This potential difference between the working and the reference electrodes can be changed to detect different analytes. The designed low power potentiostat consumes only 66 μW with 2.5 volt power supply which is highly suitable for low-power implantable sensor applications. All the circuits are designed and fabricated in a 0.35-micron standard CMOS process.