gebhart/patrepeval huggingface dataset:
Crystal structure of RNase T1 complexed with the product nucleotide 3'-GMP. Structural evidence for direct interaction of histidine 40 and glutamic acid 58 with the 2'-hydroxyl group of the ribose. (1994)

The crystal structure of RNase T1 complexed with 3'-GMP has been determined. The glycosyl conformation of 3'-GMP is in the syn conformation, and the ribose adopts the O4'-endo pucker. This observed pucker is different from that in any complex structures of RNase T1. In the present complex, this energetically unfavorable conformation is stabilized by the water molecule with the bridged hydrogen bonds between the O2' and the O3' atoms of the ribose. The guanine base is recognized in the same manner as observed in the complex of 2'-GMP. The 2'-hydroxyl group of the ribose shows a tight hydrogen bond to both His-40 and Glu-58 with the suitable geometry for the proton transfer. These hydrogen bonds suggest that the two residues can participate directly in the proton transfer. His-92 is hydrogen bonded to two the proton transfer. His-92 is hydrogen bonded to two oxygen atoms of the phosphate group. Based on the geometry in the active site, the O1P atom may correspond to the O5' atom of the leaving nucleotide in the phosphoryl transfer or a water molecule as a nucleophile in the hydrolysis reaction. In the present complex, the conformations of the 3'-GMP molecule and the side chains of the catalytic residues would be represented as the conformation before the phosphoryl transfer reaction and/or after the hydrolysis reaction.
Aspectos socioeconômicos da produção orgânica de hortaliças nas Várzeas de Sousa - Paraíba (2016)

O consumo de hortalicas de origem orgânica apresentam atraentes perspectivas no mercado mundial. Estando atrelada a um paradigma sustentavel e a crescente demanda da populacao por alimentos mais saudaveis. Os produtos cultivados em sistema de cultivo orgânico, geralmente sao comercializados em supermercados locais e feiras livres, chegando a custar cerca de 30% a mais, quando comparado aos produtos de cultivo convencional. Outra via de distribuicao e de comercializacao sao os mercados institucionais de programas governamentais como PAA, doacao simultânea e PNAE, que permite o escoamento de parte desta producao. O Projeto de Irrigacao Varzeas de Sousa (PIVAS) capta, conduz e distribui a agua proveniente de Coremas – Mae d’agua, irrigando cerca de 4.390 hectares de propriedades agricolas localizadas entre os municipios de Sousa e Aparecida. Foram estudados aspectos socio economicos da producao de hortalicas orgânica, em um Lote com uma area de 5,0 ha, localizado no Perimetro Irrigado das Varzeas de Sousa, Setor 6, Lote 5, cerca de 15 Km da cidade de Sousa, mesorregiao do Sertao da Paraiba. Com o objetivo de buscar identificar os aspectos sociais e economicos da producao orgânica de hortalicas, em uma propriedade rural das varzeas de Sousa.
MicroRNA-21: A novel therapeutic target in human cancer (2010)

Resistance to anticancer agents is the major clinical obstacle to the successful treatment of cancer, yet the mechanisms underlying drug resistance have not been fully characterized. MicroRNAs (miRNAs) are endogenous, small (19-25 nucleotides in length) noncoding RNAs, which function by base pairing with messenger RNAs, thereby regulating protein expression. Emerging evidence shows that alteration of miRNAs is involved in cancer initiation and progression. MiR-21 is a miRNA that is overexpressed in most tumor types, and acts as an oncogene by targeting many tumor suppressor genes related to proliferation, apoptosis, and invasion. In vivo and in vitro studies suggest that miR-21 may serve as a diagnostic and prognostic marker for human malignancies. More recently, studies have identified an important role for miR-21 in anticancer drug resistance. Here, we review the mechanisms underlying miR-21-mediated chemoresistance and the potential use of miR-21 as a novel molecular target for cancer chemotherapy.
Basic SiGe ICs for optical-fiber links with maximum operating speeds between 40 and 60 Gb/s (2000)

It was demonstrated that all ICs in the high-speed electronics of a 40 Gb/s optical-fiber TDM system can be realized in Si-based technologies (possibly apart from the modulator driver). The measures taken to reach this goal are: use of an advanced SiGe bipolar technology; application of advanced modeling tools and careful mounting techniques; elimination of the speed-critical ICs in the link (as far as possible) and relaxation of circuit specifications for the remaining ones (compared to 10 and 20 Gb/s systems); use of advanced optoelectronic components. The results and statements were focussed on long-distance transmission systems, but they also might help to comment on potential use of very high data rates in future short-distance links. (19 pages)
Defective expression of Tamm-Horsfall protein/uromodulin in COX-2-deficient mice increases their susceptibility to urinary tract infections (2005)

Mice lacking a functional cyclooxygenase-2 (COX-2) gene develop abnormal kidneys that contain hypoplastic glomeruli and reduced proximal tubular mass, and they often die of renal failure. A comparison of kidney-specific gene expression between wild-type and COX-2-deficient mice by cDNA microarrays revealed that although more than 500 mRNAs were differentially expressed between the two strains of mice depending on their ages, the genes encoding pre-pro-epidermal growth factor (pre-pro-EGF) and Tamm-Horsfall protein (THP)/uromodulin were aberrantly expressed in the kidneys of COX-2 -/- mice at all stages of their development. Downregulation of EGF could potentially affect renal development, and THP/uromodulin gene has been implicated in abnormal kidney development and end-stage renal failure in humans. We assessed in detail mechanism of defective THP/uromodulin gene expression and its potential consequences in COX-2-deficient mice. Consistent with the microarray data, the steady-state levels of THP/uromodulin mRNA were severely reduced in the COX-2 -/- kidney. Furthermore, reduced expression of renal THP/uromodulin, as assessed by Western blot and immunohistological methods, was closely corroborated by a corresponding decline in the urinary secretion of THP/uromodulin in COX-2 -/- mice. Finally, we demonstrate that the bladders of COX-2 -/- mice, in contrast to those of the wild-type mice, are highly susceptible to colonization by uropathogenic Escherichia coli.
Immunoblotting Techniques (2005)

Immunoblotting techniques use antibodies (or other specific ligands in related techniques) to identify target proteins among a number of unrelated protein species. They involve identification of protein target via antigen-antibody (or protein-ligand) specific reactions. Proteins are typically separated by electrophoresis and transferred onto membranes (usually nitrocellulose). The membrane is overlaid with a primary antibody for a specific target and then with a secondary antibody labeled, for example, with enzymes or with radioisotopes. When the ligand is not an antibody, the reaction can be visualized using a ligand that is directly labeled. Dot blot is a simplified procedure in which protein samples are not separated by electrophoresis but are spotted directly onto membrane. Immunoblotting is now widely used in conjunction with two-dimensional polyacrylamide gel electrophoresis, not only for traditional goals, such as the immunoaffinity identification of proteins and analysis of immune responses but also as a genome-proteome interface technique.
Long‐lasting bladder overactivity and bladder afferent hyperexcitability in rats with chemically‐induced prostatic inflammation (2019)

Formalin-induced prostatic inflammation can lead to long-lasting bladder overactivity in association with bladder afferent neuron hyperexcitability. This long-lasting model could be a useful tool for the study of inflammation-related aspects of male LUTS pathophysiology.
A comparison of three strategies for withdrawal of noninvasive ventilation in chronic obstructive pulmonary disease with acute respiratory failure: Randomized trial (2019)

Immediate withdrawal of the NIV after recovery of respiratory failure among patients with exacerbation of COPD is feasible. Immediate withdrawal did not increase the risk of weaning failure from the NIV.
Mapping of key horticultural traits related to fruit quality, plant architecture and plant development in pepper (Capsicum annuum L.) (2007)

International audience
Hyperpolarizing DNA Nucleobases via NMR Signal Amplification by Reversible Exchange (2023)

The present work investigates the potential for enhancing the NMR signals of DNA nucleobases by parahydrogen-based hyperpolarization. Signal amplification by reversible exchange (SABRE) and SABRE in Shield Enables Alignment Transfer to Heteronuclei (SABRE-SHEATH) of selected DNA nucleobases is demonstrated with the enhancement (<i>ε</i>) of <sup>1</sup>H, <sup>15</sup>N, and/or <sup>13</sup>C spins in 3-methyladenine, cytosine, and 6-O-guanine. Solutions of the standard SABRE homogenous catalyst Ir(1,5-cyclooctadeine)(1,3-bis(2,4,6-trimethylphenyl)imidazolium)Cl ("IrIMes") and a given nucleobase in deuterated ethanol/water solutions yielded low <sup>1</sup>H <i>ε</i> values (≤10), likely reflecting weak catalyst binding. However, we achieved natural-abundance enhancement of <sup>15</sup>N signals for 3-methyladenine of ~3300 and ~1900 for the imidazole ring nitrogen atoms. <sup>1</sup>H and <sup>15</sup>N 3-methyladenine studies revealed that methylation of adenine affords preferential binding of the imidazole ring over the pyrimidine ring. Interestingly, signal enhancements (<i>ε</i>~240) of both <sup>15</sup>N atoms for doubly labelled cytosine reveal the preferential binding of specific tautomer(s), thus giving insight into the matching of polarization-transfer and tautomerization time scales. <sup>13</sup>C enhancements of up to nearly 50-fold were also obtained for this cytosine isotopomer. These efforts may enable the future investigation of processes underlying cellular function and/or dysfunction, including how DNA nucleobase tautomerization influences mismatching in base-pairing.
The UCLA abutment (1993)

The UCLA abutment concept has found many uses in implant dentistry. The authors recommend the UCLA abutment for the following situations: limited interocclusal space, to improve esthetics, for improperly angled abutments, for abutments placed too close to each other, and in patients with chronic gingival hyperplasia adjacent to conventional titanium abutment cylinders. With the UCLA abutment, the fixed prosthesis is fabricated directly on the superior surface of a Brånemark implant fixture without the use of an abutment cylinder. Forty-six patients were treated using the UCLA abutment in a variety of treatment situations over a 4-year period. They were restored with 59 restorations using 118 UCLA abutments. Twelve of the restorations were overdenture tissue bars, 2 were fixed complete dentures, and 46 were fixed partial dentures. Success rates of 92.3 percent for the maxillary and 100 percent for the mandibular UCLA abutments were reported for a combined success rate of 96.8 percent There was no breakage of the UCLA abutment screws. The authors conclude that the use of the UCLA abutment has no apparent adverse effect on the short-term success rates of the Brånemark implant system.
Residual image coding for stereo image compression (2003)

One main focus of research in stereo image coding has been disparity estimation, a technique used to reduce the coding rate by taking advantage of the redundancy in a stereo image pair. Significantly less effort has been put into the coding of the residual image. These images display characteristics that are different from that of natural images. We propose a new method for the coding of residual images that takes into account the properties of residual images. Particular attention is paid to the effects of occlusion and the correlation properties of residual images that result from block-based disparity estimation. The embedded, progressive nature of our coder enables one to stop decoding at any time. We demonstrate that it is possible to achieve good results with a computationally simple method.
Narrow-band filters for ocean colour imager (2017)

During the last few years, the evolution of deposition technologies of optical thin films coatings and associated in-situ monitoring methods enables us today to successfully answer the increasingly request of space systems for Earth observation. Geostationary satellite COMS-1 (Communication, Ocean, Meteorological Satellite-1) of Astrium has the role of ensuring meteorological observation as well as monitoring of the oceans. It is equipped with a colour imager to observe the marine ecosystem through 8 bands in the visible spectrum with a ground resolution of 500m. For that, this very high technology instrument is constituted with a filters wheel in front of the oceanic colour imager with 8 narrow band filters carried out and qualified by Cilas.
High Fidelity Physics Simulation of 128 Channel MIMO Sensor for 77GHz Automotive Radar (2020)

Automotive radar is one of the enabling technologies for advanced driver assistance systems (ADAS) and subsequently fully autonomous vehicles. Along with determining the range and velocity of targets with fairly high resolution, autonomous vehicles navigating complex urban environments need radar sensors with high azimuth and elevation resolution. Size and cost constraints limit the physical number of antennas that can be used to achieve high resolution direction-of-arrival (DoA) estimation. Multiple-input/multiple-output (MIMO) schemes achieve larger virtual arrays using fewer physical antennas than would be needed for a single-input/multiple-output (SIMO) system. This paper presents a high-fidelity physics simulation of a 77GHz, frequency-modulated continuous-waveform (FMCW)-based 128 channel (8 transmitters (T <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</sub> ), 16 receivers (R <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</sub> )) MIMO radar sensor. The 77GHz synthetic radar returns from full scale traffic scenes are obtained using a high-fidelity physics, shooting and bouncing ray electromagnetics solver. A fast Fourier transform (FFT) based signal processing scheme is used across slow-time (chirp) and space (channel) to obtain range-Doppler and DoA maps, respectively. Detection and angular separation performance comparisons of 16, 64 and 128 channel MIMO radar sensors are made for two complex driving scenarios.
Anatomical-image aided PET reconstruction by the kernel method (2014)

44 Objectives We study a new approach to incorporating anatomical prior information into PET reconstruction using the kernel method. This method was originally developed for dynamic PET and is readily applicable to anatomical-image aided PET image reconstruction. Methods The kernel method computes a kernel matrix from an anatomical prior image, and represents the unknown PET image as a linear combination of the kernels. The linear model is incorporated into the maximum likelihood (ML) expectation-maximization (EM) algorithm to obtain an ML estimate. We conducted computer simulation studies to compare the kernel method with the conventional ML EM algorithm without anatomical prior and the Bowsher method utilizing the same anatomical prior image. A BrainWeb MRI phantom was used to simulate PET data as well as to provide anatomical prior information. One hundred noisy realizations were reconstructed to compute the bias-variance tradeoff and contrast recovery coefficient (CRC) for region-of-interest (ROI) quantification. Uncertainty in the estimates was computed by bootstrapping. Two sets of prior information with and without the lesion were simulated. For all methods studied, the reconstruction parameters were tuned to yield the best performance. Results Both anatomical-prior aided methods resulted in increased accuracy in ROI quantification when provided the lesion-present prior. Compared with the ML EM algorithm and the Bowsher method, the kernel method demonstrated a 9.8±3.0% and 6.0±3.8% reduction in ensemble noise standard deviation, respectively, at a matched bias of -9%, and a 18.4±3.2% and 7.0±5.8% reduction in CRC standard deviation, respectively, at a matched CRC of 0.9. In the case of the lesion-absent prior, the kernel method displayed similar performance to the ML EM algorithm in the lesion ROI quantification and outperformed the Bowsher method. Conclusions The kernel method shows improvement for ROI quantification compared to both the MLEM algorithm and the Bowsher method. It requires the same amount of preprocessing as the Bowsher method and is a promising method for MR/PET brain imaging. Research Support This work is supported by NIBIB under grant number R01EB014894.
Prospects for a T-cell receptor vaccination against myasthenia gravis (2005)

T-cell receptor (TCR) vaccination has been proposed as a specific therapy against autoimmune diseases. It is already used in clinical trials, which are supported by pharmaceutical companies for the treatment of multiple sclerosis, rheumatoid arthritis and psoriasis. Current vaccine developments are focusing on enhancement of immunogenicity as well as selecting the best route of immunization and adjuvant to favor the therapeutic effect. In the meantime, academic laboratories are tackling the regulatory mechanisms involved in the beneficial effect of the vaccines to further understand how to control the therapeutic tool. Indeed, several examples in experimental models of autoimmune diseases indicate that any specific therapy may rely on a delicate balance between the pathogenic and regulatory mechanisms. This review presents a critical analysis of the potential of such therapy in myasthenia gravis, a prototype antibody-mediated disease. Indeed, a specific pathogenic T-cell target population and a TCR-specific regulatory mechanism mediated by anti-TCR antibodies and involved in protection from the disease have recently been identified in a patient subgroup. The presence of spontaneous anti-TCR antibodies directed against the pathogenic T-cells that may be boosted by a TCR vaccine provides a rationale for such therapy in myasthenia gravis. The development of this vaccine may well benefit from experience gained in the other autoimmune diseases in which clinical trials are ongoing.
Producción y evaluación inmunoquímica de extractos alergénicos del ácaro del polvo doméstico Blomia tropicalis (Acari: Echymyopodidae) (2018)

Los alérgenos de Blomia tropicalis son un factor de riesgo para el desarrollo de alergias en países tropicales. Los extractos alergénicos son reactantes valiosos para el diagnóstico de la hipersensibilidad alérgica a los ácaros y su control biológico. El objetivo fue evaluar las propiedades inmunoquímicas de extractos de B. tropicalis producidos desde cultivos in vitro. Este trabajo no tuvo como propósito producir extractos de aplicación clínica. Los ejemplares de B. tropicalis se establecieron a partir de ácaros aislados del polvo doméstico en la ciudad de Barranquilla, Colombia. Los ácaros libres de medio de cultivo se usaron para la obtención de los extractos. El rendimiento de la extracción se determinó mediante ensayo Bradford y el perfil electroforético por SDS-PAGE. La presencia de enzimas hidrolasas se determinó por Api® Zym y la inmunogenicidad se evaluó mediante Western blot donde se identificaron proteínas de unión a IgE sérica. La producción máxima de ácaros en los cultivos fue de 0,9 g/300 g medio. El rendimiento de extracción de proteínas fue de 3,61 % (± 0,42). Todos los extractos presentaron actividad enzimática tripsina, alfa-amilasa y quimotripsina. Western blot confirmó la presencia de proteínas de unión a IgE sérica. Presentamos un método sencillo para obtener extractos del ácaro B. tropicalis con actividad enzimática y alergénica.
Halogen‐Incorporated Sn Catalysts for Selective Electrochemical CO2 Reduction to Formate (2022)

Electrochemically reducing CO<sub>2</sub> to valuable fuels or feedstocks is recognized as a promising strategy to simultaneously tackle the crises of fossil fuel shortage and carbon emission. Sn-based catalysts have been widely studied for electrochemical CO<sub>2</sub> reduction reaction (CO<sub>2</sub> RR) to make formic acid/formate, which unfortunately still suffer from low activity, selectivity and stability. In this work, halogen (F, Cl, Br or I) was introduced into the Sn catalyst by a facile hydrolysis method. The presence of halogen was confirmed by a collection of ex situ and in situ characterizations, which rendered a more positive valence state of Sn in halogen-incorporated Sn catalyst as compared to unmodified Sn under cathodic potentials in CO<sub>2</sub> RR and therefore tuned the adsorption strength of the key intermediate (*OCHO) toward formate formation. As a result, the halogen-incorporated Sn catalyst exhibited greatly enhanced catalytic performance in electrochemical CO<sub>2</sub> RR to produce formate.
The importance of authentic human epidermal growth factor in offering effective treatments for hard-to-heal wounds (2019)

Skin regeneration and repair of wounds in a timely and effective manner could highly reduce the risk of infection. Authentic human epidermal growth factor (aEGF) consisting of 53 amino acids is a functionally versatile protein, which is able to stimulate the proliferation of epidermal cells. However, due to the availability of unauthentic EGF derivatives (EGF isoforms) in the market, the identity of aEGF is mystified by the presence of these isoforms. Although aEGF has been shown to be safe and effective in promoting wound healing, it is suspicious that EGF isoforms could offer the same level of performance. In this communication, we present results to support that aEGF, which was derived from the extracellular production of a recombinant Escherichia coli excretion system, is highly effective in treating different kinds of wounds, including chronic disorders such as diabetic foot ulcers, bedsores, and various hard-to-heal wounds such as scalds and surgical injuries. In many cases, difficulties were encountered in initial treatments using other methods before aEGF was employed to result in successful healing.
The role of service areas in the optimization of FSS orbital and frequency assignments (1988)

A relationship is derived, on a single-entry interference basis, for the minimum allowable spacing between two satellites as a function of electrical parameters and service-area geometries for fixed-satellite service (FSS). For circular beams, universal curves relate the topocentric satellite spacing angle to the service-area separation angle measured at the satellite. The corresponding geocentric spacing depends only weakly on the mean longitude of the two satellites, and this is true also for elliptical antenna beams. As a consequence, if frequency channels are preassigned, the orbital assignment synthesis of a satellite system can be formulated as a mixed-integer programming (MIP) problem or approximated by a linear programming (LP) problem, with interference protection requirements enforced by constraints while some linear function is optimized. Numerical results are given for three ideal location prescriptions for both the MIP and LP formations. The resulting scenarios also satisfy reasonable aggregate interference protection requirements.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Epithelial–Mesenchymal Transition Predicts Polo-Like Kinase 1 Inhibitor–Mediated Apoptosis in Non–Small Cell Lung Cancer (2015)

In this first reported large-scale integrated analysis of PLK1 inhibitor sensitivity, we demonstrated that EMT leads to PLK1 inhibition sensitivity of NSCLC cells. Our findings have important clinical implications for mesenchymal NSCLC, a significant subtype of the disease that is associated with resistance to currently approved targeted therapies.