gebhart/patrepeval huggingface dataset:
Complete protective immunity induced in mice by immunization with the 19-kilodalton carboxyl-terminal fragment of the merozoite surface protein-1 (MSP1[19]) of Plasmodium yoelii expressed in Saccharomyces cerevisiae: correlation of protection with antigen-specific antibody titer, but not with effector CD4+ T cells (1997)

The 19-kDa carboxyl-terminal fragment of the merozoite surface protein-1 (MSP1) is a leading malaria vaccine candidate but is unable to induce immunity in all monkeys or all strains of mice. The mechanism of immunity is unclear, although data show that cell-mediated immunity plays a critical role following immunization with the larger mature MSP1 protein. We optimized a vaccine protocol using the MSP1(19) fragment of Plasmodium yoelii expressed in Saccharomyces cerevisiae, such that following exposure of mice to parasites, they remained undetectable in peripheral blood, whereas control animals all died at very high parasitemia within 10 days. We then depleted the vaccinated mice of >99% of CD4+ T cells by anti-CD4 mAb treatment and could show that infections in most animals remained subpatent following challenge. Furthermore, mice in which the gene for the mu-chain of Ig had been disrupted could not be immunized with MSP1(19). Immunity in normal mice did not depend on the presence of an intact spleen nor production of nitric oxide, persisting unabated when >70% of splenic macrophages were depleted. Thus, while effector CD4+ T cells may contribute to immunity, neither they nor factors associated with a Th1-type cell mediated immune response appeared to play the major role in MSP1(19)-induced protection in normal mice. Furthermore, T cells were not sufficient for immunity in mice lacking B cells. In normal mice, protection correlated with a very high titer of MSP1(19)-specific Abs (>6,400,000), predominantly G1 and G2b, which may function by merozoite neutralization.
CFD simulation for the analysis of a contaminated environment with chemical war: influence of flow profiles and determination of risk areas over a reservoir for water distribution (2020)

Brazil is in evidence, because of global events held in the last decade as Rio + 20, the World Cup and the 2016 Olympics. Therefore, the real threats posed to the defense of the country by terrorist acts should be considered seriously. This work proposes to analyze an attack on a reservoir for distribution of water for terrorist contamination, in order to identify performance times and contamination mode. It is shown that the characteristic diffusion time is very large, so that the contaminant in water distribution system is controlled by convection. Thus, it is proposed to use a continuous drainage system for removal of contaminants denser and less dense than water.
Molecular Dissection of the Mechanism of Protein Import into Chloroplasts (1995)

The chloroplasts of green plants have evolved an intricate, yet exquisitely organized, architecture to house such essential metabolic processes as fatty acid and amino acid synthesis and the reactions of photosynthesis. Although chloroplasts contain their own genome, it encodes only a small specialized group of proteins and RNAs: primarily components of the DNA replication, transcription, translation, and electron transport systems of the organelle. The vast majority of chloroplast polypeptides—approximately 90% of the soluble and membrane components—re encoded in the nucleus and synthesized as precursors on cytoplasmic ribosomes. These polypeptides are posttranslationally imported into the organelle, sorted to one of at least six suborganellar compartments, and assembled into their functional native proteins.
Thermal stability of arc evaporated high aluminum-content Ti1−xAlxN thin films (2002)

The thermal stability of Ti1−xAlxN films deposited by arc evaporation from Ti–Al cathodes with 67 and 75 at. % aluminum, respectively, has been investigated. The microstructure of as-deposited and isothermally annealed samples were studied using scanning electron microscopy, transmission electron microscopy, and x-ray diffraction. The chemical composition and elemental distribution were determined by energy dispersive x ray (EDX), Rutherford backscattering spectrometry, and EDX mapping. Transmission electron micrographs revealed a dense and columnar microstructure in the as-deposited condition. Films deposited from the 67 at. % cathodes were of cubic NaCl-structure phase, whereas films deposited from the 75 at. % cathodes exhibited nanocrystallites of wurzite-structure hexagonal-phase AlN in a cubic (c)-(Ti,Al)N matrix. Both films were stable during annealing at 900 °C/120 min with respect to phase composition and grain size. Annealing at 1100 °C of films deposited from the 67 at. % cathodes resulted in phase separation of c-TiN and h-AlN, via spinodal decomposition of c-TiN and c-AlN. (Ti,Al)N films undergo extensive stress relaxation and defect annihilation at relatively high temperatures, and aspects of these microstructural transformations are discussed.
Current Concepts in Orthopaedic Biomaterials and Implant Fixation (1993)

FRIEDMAN, RICHARD J.; BLACK, JONATHAN; GALANTE, JORGE O.; JACOBS, JOSHUA J.; SKINNER, HARRY B. Author Information
Microbial life at −13 °C in the brine of an ice-sealed Antarctic lake (2012)

The permanent ice cover of Lake Vida (Antarctica) encapsulates an extreme cryogenic brine ecosystem (-13 °C; salinity, 200). This aphotic ecosystem is anoxic and consists of a slightly acidic (pH 6.2) sodium chloride-dominated brine. Expeditions in 2005 and 2010 were conducted to investigate the biogeochemistry of Lake Vida's brine system. A phylogenetically diverse and metabolically active Bacteria dominated microbial assemblage was observed in the brine. These bacteria live under very high levels of reduced metals, ammonia, molecular hydrogen (H(2)), and dissolved organic carbon, as well as high concentrations of oxidized species of nitrogen (i.e., supersaturated nitrous oxide and ∼1 mmol⋅L(-1) nitrate) and sulfur (as sulfate). The existence of this system, with active biota, and a suite of reduced as well as oxidized compounds, is unusual given the millennial scale of its isolation from external sources of energy. The geochemistry of the brine suggests that abiotic brine-rock reactions may occur in this system and that the rich sources of dissolved electron acceptors prevent sulfate reduction and methanogenesis from being energetically favorable. The discovery of this ecosystem and the in situ biotic and abiotic processes occurring at low temperature provides a tractable system to study habitability of isolated terrestrial cryoenvironments (e.g., permafrost cryopegs and subglacial ecosystems), and is a potential analog for habitats on other icy worlds where water-rock reactions may cooccur with saline deposits and subsurface oceans.
Novel efficiency-Optimal Frequency Modulation for high power density DC/AC converter systems (2017)

State-of-the-art high power density AC/DC and DC/AC converter systems typically employ Triangular Current Mode (TCM) modulation or conventional PWM. TCM is characterized by a wide variation of switching frequency over the mains period and ensures soft-switching in all operating points, but results in increased conduction and high-frequency losses due to the necessary large current ripple. In contrast, PWM with constant switching frequency features a lower RMS current and thus reduced conduction losses, but cannot achieve soft-switching over the entire mains period and suffers from turn-on losses. In this paper it is investigated if an optimal combination of these two operating modes, i. e. an optimal adjustment of switching frequency and/or current ripple amplitude throughout the mains period, can lead to an increase in conversion efficiency and how such an Optimal Frequency Modulation (OFM) control scheme can be implemented in practice. The presented analysis is based on an ultra compact 2kW, 400V DC/AC converter system designed to overcome the GOOGLE Little Box Challenge.
Determination of jet energy calibration and transverse momentum resolution in CMS (2011)

Americanae nace como un proyecto conjunto que surge dentro de la Red Europea de Información y Documentación sobre América Latina (REDIAL), y que ha afrontado la Biblioteca de la Agencia Española de Cooperación Internacional para el Desarrollo (AECID). Esta nueva biblioteca virtual hace más accesibles los libros digitales de tema americanista a los investigadores y usuarios interesados de cualquier parte del mundo.
Transcriptome Spectral Analysis using Hyperspectral Imaging for Hepatocellular Carcinoma Detection (2021)

Abstract Hepatocellular carcinoma (HCC) is a noteworthy health problem with a poor diagnosis due to limited detection techniques. Transcriptome studies can be used to classify cancer further away from anatomical location and histopathology. Recent studies demonstrated the novelty of numerous types of specific RNA biomarkers that differentially expressed both the normal liver and the HCC tissues, but those specific types overlapped with the detection of other types of cancers. In this study, total RNA was used to ensure the existence of differences between different cancer types. A multispectral light source (340-1000 nm) interacted with the sample. Multi-wavelengths images were captured using a hyperspectral camera (wavelength 380-1000 nm). The optimum wavelength to discriminate between the normal and HCC samples was selected by calculating the optical properties (transmission, absorption and scattered light). Results showed specific spectral signatures for total RNA within the red-band (633-700 nm) that discriminate HCC from control. The amount of light scattering, transmission and absorption relatively changed due to the variations of size, shape, and concentration of total RNA. The spectral RNA signature that is dependent on the shape and size of total RNA may be utilized as the gold standard for HCC detection.
Evaluation of spectroscopic properties ofYb3+-doped glasses (1995)

The absorption and emission properties of numerous glasses doped with ${\mathrm{Yb}}^{3+}$ ions have been investigated. The emission cross sections have been evaluated using the measured absorption spectra and principle of reciprocity, and again using the Fuchtbauer-Ladenburg formula. Agreement between the two methods is typically within 25% for most materials. The spectroscopic properties of the $^{2}F_{\frac{7}{2}}\ensuremath{-}^{2}F_{\frac{5}{2}}$ transition have been found to be very sensitive to the ${\mathrm{Yb}}^{3+}$ site environment as well as an hypersensitive transition, and their values increase as the asymmetry of the ${\mathrm{Yb}}^{3+}$ site becomes higher. High asymmetry of the ${\mathrm{Yb}}^{3+}$ site is essentially caused not only by large difference in the cationic field strengths between network formers around the [Yb${\mathrm{O}}_{6}$] coordination sphere, but also by difference in the coordination numbers of oxygens surrounding network formers that are associated with the ${\mathrm{Yb}}^{3+}$ through the oxygens. A system of $\mathrm{Yb}:(15\ensuremath{-}25){\mathrm{P}}_{2}{\mathrm{O}}_{5}\ensuremath{-}(10\ensuremath{-}20){\mathrm{Nb}}_{2}{\mathrm{O}}_{5}\ensuremath{-}(0\ensuremath{-}15){\mathrm{B}}_{2}{\mathrm{O}}_{3}\ensuremath{-}(48\ensuremath{-}55)R\mathrm{O}$ ($R=\mathrm{M}\mathrm{g},\phantom{\rule{0ex}{0ex}}\mathrm{C}\mathrm{a},\phantom{\rule{0ex}{0ex}}\mathrm{S}\mathrm{r},\phantom{\rule{0ex}{0ex}}\mathrm{B}\mathrm{a},\phantom{\rule{0ex}{0ex}}\mathrm{a}\mathrm{n}\mathrm{d}\phantom{\rule{0ex}{0ex}}\mathrm{Z}\mathrm{n}$) glasses which possess higher asymmetry of ${\mathrm{Yb}}^{3+}$ ligands has been developed. These glasses exhibit the most useful laser properties, and are expected to be substantially superior to Yb: Si${\mathrm{O}}_{2}$ and Yb: ZBLAN glass fiber lasers in many key spectroscopic parameter values.
Altered hydroxymethylation is seen at regulatory regions in pancreatic cancer and regulates oncogenic pathways (2017)

Transcriptional deregulation of oncogenic pathways is a hallmark of cancer and can be due to epigenetic alterations. 5-Hydroxymethylcytosine (5-hmC) is an epigenetic modification that has not been studied in pancreatic cancer. Genome-wide analysis of 5-hmC-enriched loci with hmC-seal was conducted in a cohort of low-passage pancreatic cancer cell lines, primary patient-derived xenografts, and pancreatic controls and revealed strikingly altered patterns in neoplastic tissues. Differentially hydroxymethylated regions preferentially affected known regulatory regions of the genome, specifically overlapping with known H3K4me1 enhancers. Furthermore, base pair resolution analysis of cytosine methylation and hydroxymethylation with oxidative bisulfite sequencing was conducted and correlated with chromatin accessibility by ATAC-seq and gene expression by RNA-seq in pancreatic cancer and control samples. 5-hmC was specifically enriched at open regions of chromatin, and gain of 5-hmC was correlated with up-regulation of the cognate transcripts, including many oncogenic pathways implicated in pancreatic neoplasia, such as <i>MYC</i>, <i>KRAS</i>, <i>VEGFA</i>, and <i>BRD4</i> Specifically, <i>BRD4</i> was overexpressed and acquired 5-hmC at enhancer regions in the majority of neoplastic samples. Functionally, acquisition of 5-hmC at <i>BRD4</i> promoter was associated with increase in transcript expression in reporter assays and primary samples. Furthermore, blockade of BRD4 inhibited pancreatic cancer growth in vivo. In summary, redistribution of 5-hmC and preferential enrichment at oncogenic enhancers is a novel regulatory mechanism in human pancreatic cancer.
In situ resistance measurement of the p-type contact in InP–InGaAsP coolerless ridge waveguide lasers (2005)

Scanning voltage microscopy (SVM) is employed to measure the voltage division—and resulting contact resistance and power loss—at the p-In0.53Ga0.47As–p-InP heterojunction in a working InP–InGaAsP laser diode. This heterojunction is observed to dissipate ∼35% of the total power applied to the laser over the operating bias range. This in situ experimental study of the parasitic voltage division (and resulting power loss and series contact resistance) highlights the need for a good p-type contact strategy. SVM technique provides a direct, fast and in situ measurement of specific contact resistance, an important device parameter.
A global atlas of substrate specificities for the human serine/threonine kinome (2022)

ABSTRACT Protein phosphorylation is one of the most widespread post-translational modifications in biology. With the advent of mass spectrometry-based phosphoproteomics, more than 200,000 sites of serine and threonine phosphorylation have been reported, of which several thousand have been associated with human diseases and biological processes. For the vast majority of phosphorylation events, it is not yet known which of the more than 300 protein Ser/Thr kinases encoded in the human genome is responsible. Here, we utilize synthetic peptide libraries to profile the substrate sequence specificity of nearly every functional human Ser/Thr kinase. Viewed in its entirety, the substrate specificity of the kinome was substantially more diverse than expected and was driven extensively by negative selectivity. Our kinome-wide dataset was used to computationally annotate and identify the most likely protein kinases for every reported phosphorylation site in the human Ser/Thr phosphoproteome. For the small minority of phosphosites where the protein kinases involved have been previously identified, our predictions were in excellent agreement. When this approach was applied to examine the signaling response of tissues and cell lines to hormones, growth factors, targeted inhibitors, and environmental or genetic perturbations, it revealed unexpected insights into pathway complexity and compensation. Overall, these studies reveal the full extent of substrate specificity of the human Ser/Thr kinome, illuminate cellular signaling responses, and provide a rich resource to link unannotated phosphorylation events to biological pathways.
Measurement of optical binding force between two colloidal particles (2009)

Optical binding has been proposed to be responsible for the cluster formation of micron size dielectric spheres in coherent light fields. However, a direct measurement of the forces involved in binding is missing. We report an experimental study of optical binding forces between two optically trapped dielectric spheres. Results for optical forces are presented as a function of three parameters: inter particle separation, particle size, and respective polarizations. A comprehensive calculation based on the generalized Mie scattering theory for the experiment has also been conducted. This paper will present a comparison between experimental and theoretical results.
Least-squares estimation of the common acoustical poles in room acoustics and head related transfer functions (2017)

Accurate and stable estimation of common acoustical poles is required in many applications such as speech dereverberation, acoustic feedback cancellation, sound field equalization, and virtual auditory display. In this paper, an algorithm for the least-squares estimation of the acoustical poles is presented. In contrast to previous methods, which may have limited accuracy and/or limitations imposed by nonlinear optimization, our method precisely estimates the acoustical poles after a low number of iterations. The proposed method unconditionally guarantees stability of the estimated poles. The method is examined using measured head related and room transfer functions. Experimental results show that estimated common acoustical poles accurately match the resonance frequencies of the ear canal and precisely agree with theoretical poles for a room acoustic response.
Immune Requirements of Post-Exposure Immunization with Modified Vaccinia Ankara of Lethally Infected Mice (2010)

Current prophylactic vaccines work via the induction of B and T cell mediated memory that effectively control further replication of the pathogen after entry. In the case of therapeutic or post-exposure vaccinations the situation is far more complex, because the pathogen has time to establish itself in the host, start producing immune-inhibitory molecules and spread into distant organs. So far it is unclear which immune parameters have to be activated in order to thwart an existing lethal infection. Using the mousepox model, we investigated the immunological mechanisms responsible for a successful post-exposure immunization with modified vaccinia Ankara (MVA). In contrast to intranasal application of MVA, we found that intravenous immunization fully protected mice infected with ectromelia virus (ECTV) when applied three days after infection. Intravenous MVA immunization induced strong innate and adaptive immune responses in lethally infected mice. By using various gene-targeted and transgenic mouse strains we show that NK cells, CD4 T cells, CD8 T cells and antibodies are essential for the clearance of ECTV after post-exposure immunization. Post-exposure immunization with MVA is an effective measure in a murine model of human smallpox. MVA activates innate and adaptive immune parameters and only a combination thereof is able to purge ECTV from its host. These data not only provide a basis for therapeutic vaccinations in the case of the deliberate release of pathogenic poxviruses but possibly also for the treatment of chronic infections and cancer.
Automatic Steering Control for Agricultural Tractors in Vineyards (2021)

Advanced Driver Assistance Systems (ADAS) and autonomous driving systems are relevant in the agricultural field, since they can ease personnel of demanding and repetitive tasks while increasing precision and productivity. This is particularly true in constrained environments represented by intensive and high value cultivations, like vineyards and orchards. Anyway, these contexts present numerous challenges: positioning accuracy in the range of centimeters is required in an environment with continuously-changing vegetation, reduced maneuvering space and unstable terrain. This paper presents an ADAS of level 3 for an agricultural tractor in a vineyard, focusing on its control system. The goal of the developed controller is to bring the vehicle at a desired distance from the crop rows and keep it aligned to them, so that the operator only has to set the tractor advancement speed and can focus on the ongoing agricultural procedures. This is achieved through a Linear Quadratic Integral (LQI) controller that relies on a control-oriented model of the system describing the dynamics of the vehicle position with respect to the vines. The system proves to be effective and easily tunable in order to obtain the desired behavior. An extensive experimental campaign validates the closed-loop system performance. In particular, the controller attains a steady state error of 5 cm, using a steering angle with Root Mean Square (RMS) of 1.05 deg.
Passivity-Preserving Parametric Macromodeling for Highly Dynamic Tabulated Data Based on Lur'e Equations (2010)

We present a new method for the construction of parametric macromodels for admittance and impedance input- output representations starting from multivariate data samples that depend on frequency and additional design variables such as geometric and material parameters. Poles and residues are parameterized indirectly, while stability and passivity of the parametric macromodel are guaranteed over a user defined range of design parameter values. Pertinent numerical examples validate the proposed parametric macromodeling approach.
The Biopolitics of Numbers (2020)

Victor Li shares this essay in response to the 2020 COVID-19 / coronavirus pandemic. Numbers have always counted in our everyday lives. But, in this time of the Covid-19 pandemic, numbers count for even more as they display their full biopolitical character. Every day the entire mediascape bombards us with numbers of confirmed coronavirus cases and of those who have died from the disease.
ChemInform Abstract: ORGANOPHOSPHORUS PEPTIDE‐COUPLING REAGENTS. PART 7. TERTIARY PHOSPHINE/HEXACHLOROETHANE AS A CONDENSING REAGENT IN PEPTIDE SYNTHESIS (1979)

Abstract Mit den Dehydratisierungsreagenzien (III), die aus dem Phosphoran (I) mit Hexachlorethan gebildet werden, lassen sich N‐geschützte Aminosäuren, z.B. (IV), und Aminosäureester wie z.B. (V) in hohen Ausb. zu Peptiden, z.B. (VI) [analoge Darstellung von (VII)] kondensieren [(IIIa) ist am vorteilhaftesten].
The M Segment of the 2009 New Pandemic H1N1 Influenza Virus Is Critical for Its High Transmission Efficiency in the Guinea Pig Model (2011)

A remarkable feature of the 2009 pandemic H1N1 influenza virus is its efficient transmissibility in humans compared to that of precursor strains from the triple-reassortant swine influenza virus lineage, which cause only sporadic infections in humans. The viral components essential for this phenotype have not been fully elucidated. In this study, we aimed to determine the viral factors critical for aerosol transmission of the 2009 pandemic virus. Single or multiple segment reassortments were made between the pandemic A/California/04/09 (H1N1) (Cal/09) virus and another H1N1 strain, A/Puerto Rico/8/34 (H1N1) (PR8). These viruses were then tested in the guinea pig model to understand which segment of Cal/09 virus conferred transmissibility to the poorly transmissible PR8 virus. We confirmed our findings by generating recombinant A/swine/Texas/1998 (H3N2) (sw/Tx/98) virus, a representative triple-reassortant swine virus, containing segments of the Cal/09 virus. The data showed that the M segment of the Cal/09 virus promoted aerosol transmissibility to recombinant viruses with PR8 and sw/Tx/98 virus backgrounds, suggesting that the M segment is a critical factor supporting the transmission of the 2009 pandemic virus.