gebhart/patrepeval huggingface dataset:
The plant-specific SCL30a SR protein regulates ABA-dependent seed traits and salt stress tolerance during germination (2021)

Abstract SR (serine/arginine-rich) proteins are conserved RNA-binding proteins best known as key regulators of splicing, which have also been implicated in other steps of gene expression. Despite mounting evidence for their role in plant development and stress responses, the molecular pathways underlying SR protein regulation of these processes remain elusive. Here we show that the plant-specific SCL30a SR protein negatively regulates abscisic acid (ABA) signaling to control important seed traits and salt stress responses during germination in Arabidopsis. The SCL30a gene is upregulated during seed imbibition and germination, and its loss of function results in smaller seeds displaying enhanced dormancy and elevated expression of ABA-responsive genes as well as of genes repressed during the germination process. Moreover, the knockout mutant is hypersensitive to ABA and high salinity, while transgenic plants overexpressing SCL30a exhibit reduced ABA sensitivity and enhanced tolerance to salt stress during seed germination. An ABA biosynthesis inhibitor rescues the mutant’s enhanced sensitivity to stress, and epistatic analyses confirm that this hypersensitivity requires a functional ABA pathway. Finally, seed ABA levels are unchanged by altered SCL30a expression, indicating that the SR protein positively regulates stress tolerance during seed germination by reducing sensitivity to the phytohormone. Our results reveal a new key player in ABA-mediated control of early development and stress response, and underscore the role of plant SR proteins as important regulators of the ABA signaling pathway. Author Summary Seed germination is a critical step in plant development determining the transition to aerial growth and exposure to a more challenging environment. As such, seeds have evolved mechanisms that prevent germination under adverse conditions, thereby increasing the chances of plant survival. As a general regulator of plant development and a key mediator of stress responses, the hormone abscisic acid (ABA) promotes a prolonged non-germinating state called dormancy, influences seed size and represses germination under environmental stress. Here, we show that an RNA-binding protein, SCL30a, controls seed size, dormancy, germination and tolerance to high salinity in the model plant Arabidopsis thaliana . Loss of SCL30a gene function results in smaller and more dormant seeds with reduced ability to germinate in a high-salt environment; by contrast, SCL30a overexpression produces larger seeds that germinate faster under salt stress. Using a large-scale gene expression analysis, we identify the ABA hormonal pathway as a putative target of SCL30a. We then use genetic and pharmacological tools to unequivocally demonstrate that the uncovered biological functions of SCL30a are achieved through modulation of the ABA pathway. Our study reveals a novel regulator of key seed traits and has biotechnological implications for crop improvement under adverse environments.
Stream Processing Languages in the Big Data Era (2018)

This paper is a survey of recent stream processing languages, which are programming languages for writing applications that analyze data streams. Data streams, or continuous data flows, have been around for decades. But with the advent of the big-data era, the size of data streams has increased dramatically. Analyzing big data streams yields immense advantages across all sectors of our society. To analyze streams, one needs to write a stream processing application. This paper showcases several languages designed for this purpose, articulates underlying principles, and outlines open challenges.
A New Multiparameter Approach to Computational Simulation for Fontan Assessment and Redesign (2010)

A multiparameter approach demonstrates that each parameter results in a different ranking of Fontan performance. Ranking patients using energy efficiency does not correlate with the ranking using other parameters of presumed clinical importance. As such, current simulation methods that evaluate energy dissipation alone are not sufficient for a comprehensive evaluation of new Fontan designs.
Flavin Mononucleotide-Binding Domain of the Flavoprotein Component of the Sulfite Reductase from Escherichia coli (1997)

The flavoprotein component (SiR-FP) of the sulfite reductase from Escherichia coli is an octamer containing one FAD and one FMN as cofactors per polypeptide chain. We have constructed an expression vector containing the DNA fragment encoding for the FMN-binding domain of SiR-FP. The overexpressed protein (SiR-FP23) was purified as a partially flavin-depleted polymer. It could incorporate FMN exclusively upon flavin reconstitution to reach a maximum flavin content of 1.2 per polypeptide chain. Moreover, the protein could stabilize a neutral air-stable semiquinone radical over a wide range of pHs. During photoreduction, the flavin radical accumulated first, followed by the fully reduced state. The redox potentials, determined at room temperature [E'1 (FMNH./FMN) = -130 +/- 10 mV and E'2 (FMNH2/FMNH.) = -335 +/- 10 mV], were very close to those previously reported for Salmonella typhimurium SiR-FP [Ostrowski, J., Barber, M. J., Rueger, D. C., Miller, B. E., Siegel, L. M., & Kredich, N. M. (1989) J. Biol. Chem. 264, 15796-15808]. Both the radical and fully reduced forms of SiR-FP23 were able to transfer their electrons to cytochrome c quantitatively. Altogether, the results presented herein demonstrate that the N-terminal end of E. coli SiR-FP forms the FMN-binding domain. It folds independently, thus retaining the chemical properties of the bound FMN, and provides a good model of the FAD-depleted form of native SiR-FP. Moreover, the FMN prosthetic group in SiR-FP23 and native SiR-FP is compared to that of cytochrome P450 reductase and bacterial cytochrome P450, which also contain one FAD and one FMN per polypeptide chain.
Discovery of Target Molecules for Cancer Immunotherapy by Genetic and Bioinformatic Approaches (2006)

It has been a long-standing vision of scientists studying tumor immunology to use the immune system’s effectors for the therapy of cancer by directing them against target molecules expressed selectively on tumor cells. Different genetic approaches for discovery of such target candidates have been developed over the last 15 yr and are being pursued. The classical approaches apply expression cloning using either cancer-reactive T-lymphocytes or autoantibodies in crude patient sera as probes to identify target molecules of spontaneous immune responses. Recent concepts utilizing high-density microarray analysis, subtractive library approaches, or in silico cloning aim at the identification of genes with cancer cell-associated expression and subsequently address the immunogenicity of such molecules with reverse immunology. This chapter summarizes the peculiarities of these approaches, reflects on rationale criteria for selection of vaccine candidates, and discusses how integrated discovery and validation strategies may assist in the delivery of suitable targets.
<title>WISE 2000 campaign: sea surface salinity and wind retrievals from L-band radiometry</title> (2000)

Sea surface salinity (SSS) has been recognized as a key parameter in climatological studies. SSS can be measured by passive microwave remote sensing at L band, where the sensitivity of the brightness temperatures shows a maximum and the atmosphere is almost transparent. To provide global coverage of this basic parameter with a 3-day revisit time, the SMOS mission was recently selected by ESA within the frame of the Earth Explorer Opportunity Missions. The SMOS mission will carry the MIRAS instrument, the first 2D L-band aperture synthesis interferometric radiometer. To address new challenges that this mission presents, such as incidence angle variation with pixel, polarization mixing, effect of wind and foam and others, a measurement campaign has been sponsored by ESA under the name of WISE 2000 and it is scheduled for October-November 2000. Two L-band radiometers, a video, a IR and a stereo-camera and four oceanographic and meteorological buoys will be installed in the oil platform 'Casablanca' located at 40 Km off the coast of Tarragona, where the sea conditions are representative of the Mediterranean open sea with periodic influence of the Ebro river fresh water plume.
Metabolic encephalopathies: inborn errors of metabolism causing encephalopathies in adults (2013)

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Critical Issues in Interaction Design (2008)

Computing technology is now so entwined with everyday life that enquiries into human computer interaction (HCI) are also studies of society and culture Cultural and Critical theory is then increasingly relevant to studies of Human Computer Interaction (HCI). It is both timely and important to develop understandings of the strengths and limitations of the various perspectives available within the fractious traditions of cultural and critical theory. This workshop will consider the challenges of making such theory relevant and accessible to HCI and interaction design.
Throughput and Effective Parameters in Crossing (2023)

In pointing, throughput TP is used as a performance metric for the input device and operator. Based on the calculation of effective parameters (width We and amplitude Ae), TP should be independent of the speed-accuracy tradeoff. To examine the validity of TP and effective parameters for crossing actions, we conducted two experiments using two established crossing tasks. Our results demonstrate that applying effective parameters to Fitts’ law model improves the fit to the data for mixed biases in both tasks. Besides, we observed that effective parameters smoothed TPs across biases. However, unlike pointing, TP was observed to be unstable across IDs in one task, while was stable across IDs in the other task. Analyzing speed profiles showed that this was likely due to the fact that one of the tasks could be completed with a ballistic movement at low IDs, whereas this was impossible for the other task.
Xylosyltransferase-1 Expression Is Refractory to Inhibition by the Inflammatory Cytokines Tumor Necrosis Factor α and IL-1β in Nucleus Pulposus Cells (2014)

We investigated whether expression of xylosyltransferase-1 (XT-1), a key enzyme in glycosaminoglycan biosynthesis, is responsive to disk degeneration and to inhibition by the inflammatory cytokines tumor necrosis factor α and IL-1β in nucleus pulposus (NP) cells. Analysis of human NP tissues showed that XT-1 expression is unaffected by degeneration severity; XT-1 and Jun, Fos, and Sp1 mRNA were positively correlated. Cytokines failed to inhibit XT-1 promoter activity and expression. However, cytokines decreased activity of XT-1 promoters containing deletion and mutation of the -730/-723 bp AP-1 motif, prompting us to investigate the role of AP-1 and Sp1/Sp3 in the regulation of XT-1 in healthy NP cells. Overexpression and suppression of AP-1 modulated XT-1 promoter activity. Likewise, treatment with the Sp1 inhibitors WP631 and mithramycin A or cotransfection with the plasmid DN-Sp1 decreased XT-1 promoter activity. Inhibitors of AP-1 and Sp1 and stable knockdown of Sp1 and Sp3 resulted in decreased XT-1 expression in NP cells. Genomic chromatin immunoprecipitation analysis showed AP-1 binding to motifs located at -730/-723 bp and -684/-677 bp and Sp1 binding to -227/-217 bp and -124/-114 bp in XT-1 promoter. These results suggest that XT-1 expression is refractory to the disease process and to inhibition by inflammatory cytokines and that signaling through AP-1, Sp1, and Sp3 is important in the maintenance of XT-1 levels in NP cells.
Comparison of privacy‐protecting analytic and data‐sharing methods: A simulation study (2018)

Overall, we found that we can avoid sharing individual-level data and obtain valid results in many settings, although care must be taken with meta-analysis approach in infrequent exposure and rare outcome scenarios, particularly when confounding adjustment is performed with IPTW.
Critical current density in wire drawn and hydrostatically extruded Nb-Ti superconductors (1979)

Critical current studies have been made on copper-clad Nb-Ti composite wire prepared under area reductions of 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> :1 and 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sup> :1 by hydrostatic extrusion (HE), wire drawing and HE plus drawing, in a comparative evaluation of the thermomechanical processing equivalent of HE.
Ultrafine Grain Structure and Thermal Stability of Al-Fe Alloys Processed by Severe Plastic Deformation (2017)

International audience
Potentiometric urea biosensor utilizing nanobiocomposite of chitosan-iron oxide magnetic nanoparticles (2013)

The iron oxide (Fe3O4) magnetic nanoparticles have been fabricated through a simple, cheap and reproducible approach. Scanning electron microscope, x-rays powder diffraction of the fabricated nanoparticles. Furthermore, the fabrication of potentiometric urea biosensor is carried out through drop casting the initially prepared isopropanol and chitosan solution, containing Fe3O4 nanoparticles, on the glass fiber filter with a diameter of 2 cm and a copper wire (of thickness −500 μm) has been utilized to extract the voltage signal from the functionalized nanoparticles. The functionalization of surface of the Fe3O4 nanoparticles is obtained by the electrostatically immobilization of urease onto the nanobiocomposite of the chitosan- Fe3O4 in order to enhance the sensitivity, specificity, stability and reusability of urea biosensor. Electrochemical detection procedure has been adopted to measure the potentiometric response over the wide logarithmic concentration range of the 0.1 mM to 80 mM. The Fe3O4 nanoparticles based urea biosensor depicts good sensitivity with ~42 mV per decade at room temperature. Durability of the biosensor could be considerably enhanced by applying a thin layer of the nafion. In addition, the reasonably stable output response of the biosensor has been found to be around 12 sec.
Cellules souches et médecine régénératrice (2002)

La thérapie cellulaire au service d’une médecine régénératrice trouvera certainement une place croissante dans la médecine des décennies prochaines. Elle profitera des progrès considérables réalisés ces dernières années dans le domaine de la biologie des cellules souches et progénitrices, qu’elles soient isolées d’embryons au stade blas-tocyste ou de tissus différenciés, adultes ou fœtaux. Chacun de ces matériels cellulaires présente des avantages et des inconvénients de principe, si bien qu’il semble raisonnable de développer parallèlement la recherche dans les deux directions. Quant à l’isolement des cellules souches embryonnaires à partir des blastocystes résultant d’un transfert de noyaux somatiques dans des ovules énucléés (aussi désigné sous le nom de «clonage thérapeutique »), il n’est pas encore maîtrisé chez l’homme. De plus,la stratégie apparaît à l’examen peu réaliste en médecine humaine, et continue de soulever de difficiles problèmes éthiques.
Retroviral-Mediated Gene Transfer and Expression of Human Lipoprotein Lipase in Somatic Cells (1995)

Lipoprotein lipase (LPL) is an enzyme responsible for the hydrolysis of triglyceride-rich circulating lipoproteins. Humans with complete defects in LPL activity present from infancy with failure to thrive, eruptive xanthomas, pancreatitis, and lactescent plasma. In addition, heterozygous carriers for this disorder may be at increased risk for the development of coronary artery disease. In view of a potential strategy for correcting complete or partial LPL deficiency, a 1.56-kb human LPL cDNA was inserted into a series of recombinant myeloproliferative sarcoma virus (MPSV)-based retroviral vectors under transcriptional control of the constitutive MPSV long terminal repeat (LTR). Stable gene transfer and enhanced expression of human LPL was observed at both the RNA and protein level in a variety of somatic cell types in vitro. Genetically modified cell populations included mouse NIH-3T3 fibroblasts and C2C12 myoblasts, primary human fibroblasts, and established human hematopoietic cell lines of erythroid (K562), myelocytic (HL60), and monocytic (U937,THP-1) type. The achieved levels of bioactive human LPL were found to vary widely between the different transduced cell lines, which may be critical to an approach to gene therapy. Transduced primary human fibroblasts yielded maximal elevation of LPL immunoreactive mass and activity of at least 24- and 50-fold, respectively, above constitutively expressed levels for this cell type. Human fibroblasts, therefore, appear to accommodate in vitro the complex processes readily leading to the maturation and secretion of bioactive human LPL and may serve as an effective cellular vehicle for LPL gene delivery and expression in human LPL deficiency.
Local electronic structure of dilute hydrogen in β−Ga2O3 probed by muons (2023)

The local electronic structure of muons (Mu) as dilute pseudohydrogen in single-crystalline $\ensuremath{\beta}\text{\ensuremath{-}}{\mathrm{Ga}}_{2}{\mathrm{O}}_{3}$ has been studied by the muon spin rotation/relaxation $(\ensuremath{\mu}\mathrm{SR})$. High-precision measurements over a long time range of $\ensuremath{\sim}25\phantom{\rule{4pt}{0ex}}\textmu{}\mathrm{s}$ have clearly identified two distinct Mu states: a quasistatic Mu $({\mathrm{Mu}}_{1})$ and fast-moving Mu $({\mathrm{Mu}}_{2})$. By comparing this result with predictions from the recently established ambipolarity model, these two states are respectively attributed to the relaxed-excited states associated with the donor $({E}^{+/0})$ and acceptor $({E}^{\ensuremath{-}/0})$ levels predicted by density functional theory (DFT) calculations for the interstitial H. Furthermore, the local electronic structure of ${\mathrm{Mu}}_{1}$ is found to be an OMu-bonded state with three-coordinated oxygen. The structure is almost identical with the thermal equilibrium state of H, and it is found to function as an electron donor. The other ${\mathrm{Mu}}_{2}$ is considered to be in the hydride state $({\mathrm{Mu}}^{\ensuremath{-}})$ from the ambipolarity model, suggesting that it is in fast diffusion motion through the short-lived neutral state due to the charge exchange reaction with conduction electrons $({\mathrm{Mu}}^{\ensuremath{-}}\ensuremath{\rightleftarrows}{\mathrm{Mu}}^{0}+{e}^{\ensuremath{-}})$.
High spin-filter efficiency in a Co ferrite fabricated by a thermal oxidation (2010)

Co ferrites fabricated by a thermal oxidation have been tested as a spin filter. Spin-filter efficiencies of 44% and 4.3% were confirmed at 10 K and RT, respectively, using a magnetic tunnel junction of Pt/CoFe2O4/MgO/Co. By increasing the bias voltage, the tunneling magnetoresistance (TMR) at 10 K increases then decreases. This is interpreted as a tunneling via spin-down conduction band in the Co ferrite. Since the electron at RT is attributed to a hopping conduction on the defect states in the Co ferrite, the reduction of the defects will be the key to achieving a higher spin-filter effect.
Inside-Out of Complement in Cancer (2022)

The role of complement in cancer has received increasing attention over the last decade. Recent studies provide compelling evidence that complement accelerates cancer progression. Despite the pivotal role of complement in fighting microbes, complement seems to suppress antitumor immunity <i>via</i> regulation of host cell in the tumor microenvironment. Although most studies link complement in cancer to complement activation in the extracellular space, the discovery of intracellular activation of complement, raises the question: what is the relevance of this process for malignancy? Intracellular activation is pivotal for the survival of immune cells. Therefore, complement can be important for tumor cell survival and growth regardless of the role in immunosuppression. On the other hand, because intracellular complement (the complosome) is indispensable for activation of T cells, these functions will be essential for priming antitumor T cell responses. Here, we review functions of complement in cancer with the consideration of extra and intracellular pathways of complement activation and spatial distribution of complement proteins in tumors and periphery and provide our take on potential significance of complement as biomarker and target for cancer therapy.
<title>Matching pursuit of images</title> (1995)

A crucial problem in image analysis is to construct efficient low-level representations of an image, providing precise characterization of features which compose it, such as edges and texture components. An image usually contains very different types of features, which have been successfully modeled by the very redundant family of 2D Gabor oriented wavelets, describing the local properties of the image: localization, scale, preferred orientation, amplitude and phase of the discontinuity. However, this model generates representations of very large size. Instead of decomposing a given image over this whole set of Gabor functions, we use an adaptive algorithm (called matching pursuit) to select the Gabor elements which approximate at best the image, corresponding to the main features of the image. This produces compact representation in terms of few features that reveal the local image properties. Results prove that the elements are precisely localized on the edges of the images, and give a local decomposition as linear combinations of `textons' in the textured regions. We introduce a fast algorithm to compute the matching pursuit decomposition for images with a complexity of (Omicron) (N log<SUP>2</SUP> N) per iteration for an image of N<SUP>2</SUP> pixels.
High-responsivity high-gain In/sub 0.53/Ga/sub 0.47/As-InP quantum-well infrared photodetectors grown using metal-organic vapor phase epitaxy (2005)

We report the growth and fabrication of bound-to-bound In/sub 0.53/Ga/sub 0.47/As-InP quantum-well infrared photodetectors using metal-organic vapor phase epitaxy. These detectors have a peak detection wavelength of 8.5 /spl mu/m. The peak responsivities are extremely large with R/sub pk/=6.9 A/W at bias voltage V/sub b/=3.4 V and temperature T=10 K. These large responsivities arise from large detector gain that was found to be g/sub n/=82 at V/sub b/=3.8 V from dark current noise measurements at T=77 K and g/sub p/=18.4 at V/sub b/=3.4 V from photoresponse data at T=10 K. The background-limited temperature with F/1.2 optics is T/sub BLIP/=65 K for 0<V/sub b//spl les/3.4 V. The highest value of peak detectivity is D/sub /spl lambda///sup */=5.4/spl times/10/sup 9/ cm/spl radic/Hz/W at V/sub b/=2.9 V and T=77 K, while for T<T/sub BLIP/=65 K, the background-limited detectivity, which exhibits negligible bias dependence, is D/sub BLIP//sup */=3/spl times/10/sup 10/ cm/spl radic/Hz/W.
Factors associated with study protocol adherence and bio banking participation in reproductive medicine clinical trials and their relationship to live birth (2020)

ClinicalTrials.gov number: NCT00719186; NCT01044862.