gebhart/patrepeval huggingface dataset:
A data‐driven optimization algorithm for differential algebraic equations with numerical infeasibilities (2020)

Support Vector Machines (SVMs) based optimization framework is presented for the data-driven optimization of numerically infeasible Differential Algebraic Equations (DAEs) without the full discretization of the underlying first-principles model. By formulating the stability constraint of the numerical integration of a DAE system as a supervised classification problem, we are able to demonstrate that SVMs can accurately map the boundary of numerical infeasibility. The necessity of this data-driven approach is demonstrated on a 2-dimensional motivating example, where highly accurate SVM models are trained, validated, and tested using the data collected from the numerical integration of DAEs. Furthermore, this methodology is extended and tested for a multi-dimensional case study from reaction engineering (i.e., thermal cracking of natural gas liquids). The data-driven optimization of this complex case study is explored through integrating the SVM models with a constrained global grey-box optimization algorithm, namely the ARGONAUT framework.
Intervertebral Disc Tissue Engineering I: Characterization of the Nucleus Pulposus (2003)

The characteristics of the nucleus pulposus cells from adult rabbits maintained in in vitro cultures were described in another study. Herein, the authors provide a parallel profile of adult rabbit nucleus pulposus in situ, therefore allowing direct comparisons between in vitro and in situ investigations. Nucleus pulposus specimens from adult rabbits were evaluated using biochemical and immunohistochemical morphologic techniques. The nucleus pulposus from adult rabbits contained cell clusters embedded in proteoglycan-collagen matrix. The cells exhibited a well-defined Golgi system, an extensive endoplasmic reticulum, and a complex vesicular system filled with beaded structures (proteoglycans). Neither necrotic nor apoptotic cells were evident. There was a lack of mitochondria. The extensive extracellular matrix contained amorphous, beaded, and fibrillar components. The fibrillar banding was indicative of Type VI collagen. The nucleus pulposus of adult rabbits expressed aggrecan, collagen Type I and Type II, and CD44, but not collagen Type X and displayed low alkaline phosphatase activity.
On a Source of the “Byzantine Project” by Prince Grigory Gagarin: Dominique Papety (2016)

The article is devoted to the work of the French artist Dominique Papety, whose copies of Mount Athos paintings served as one of the sources of the “Byzantine project” of Prince G.G. Gagarin, who later became vice-president of the Imperial Academy of Art and who strived to revive the “national” ecclesiasti cal art in Russia. The analysis of Papety’s works and of his views on art shows that in his religious works the art ist was inspired by the art of the remote past - in par ticular, that of Byzantium, while in his secular paintings he followed the painters of late Renaissance - Rapha el’s third manner, Titian, Michelangelo, Paolo Veronese, Bellini, Francia. Special attention is paid to the art ist’s travel to Mount Athos, undertaken by him in 1847 under the impression of the Athos manuscript with in structions for icon-painters that had been published two years earlier by A.N. Didron, an archaeologist. The cop ies of the frescoes by Panselinos, a Greek painter of the 12th century (according to Mt Athos monks), that were made by Papety at Mount Athos, show the impact of academic education on the French artist, who per fectly mastered the “plasticity” of form in pain ting. This feature of Papety’s copies allows the author of this ar ticle to conclude that, for Gagarin, they must have be come a visible demonstration of the fruitfulness of com bining the “Greek Christian thought” with the “Greek pagan form”. The idea of this combination was subse quently used by Gagarin to revive the “national style” in church paintings.
Improvement in clinical condition and thymus morphologic features associated with growth hormone treatment of immunodeficient dwarf dogs. (1984)

Immunodeficient dwarfism in Weimaraner dogs was characterized by failure to grow, emaciation, growth hormone (GH) deficiency, decreased lymphocyte blastogenic responsiveness to mitogens, lack of thymus cortex, and recurrent infections usually resulting in death. Affected pups did not respond to conventional supportive therapy, but did respond to treatment with thymosin fraction 5. Response to therapy with bovine GH was monitored by clinical observation, histopathologic examination of thymic biopsy material, lymphocyte blastogenic responsiveness to nonspecific mitogens, and radioimmunoassay of thymosin alpha 1 concentration in the serum. Growth hormone therapy (0.1 mg/kg of body weight/dose, 14 doses) during a 1-month period in 2 immunodeficient dwarf pups resulted in clinical improvement and a marked increase in the thickness and cellularity of the cortex of the thymus. Immunodeficient dwarf pups were not deficient in serum thymosin alpha 1 before GH therapy. Growth hormone therapy was not associated with a consistent increase in serum thymosin alpha 1 concentration or lymphocyte blastogenic responsiveness to mitogens.
Research and VLSI implementation on de-blocking method for MPEG (2011)

MPEG is one of the popular standards in image compression. Blocking is the most annoying artifact of encoding/decoding process. In this paper a post-processing deblocking algorithm for MPEG video stream is proposed. This method is based on the correlation of local pixels in block boundary region. It takes two 4×4 adjacent small blocks on both sides of a block boundary as a local processing region. Then the region is classified into smooth and gradual-change region, brightness step-change region, and texture region. The finally step is to eliminate blocking artifacts adaptively according to the classification. Compared with algorithm in, the proposed method offers a better result in de-blocking while preserving image details. Our design is implemented on FPGA and 0.13 μm CMOS technology.
Lifelong calorie restriction and markers of colonic health in aging mice (2018)

Diminishment of colonic health is associated with various age-related pathologies. Calorie restriction (CR) is an efficient strategy to increase healthy lifespan, although underlying mechanisms are not fully elucidated. Here we report the effects of lifelong CR on markers of colonic health in aging mice. We show that 30% energy reduction, as compared to a control (C) and moderate-fat (MF) diet, is associated with attenuated immune-related gene expression and lower levels of bile acids in the colon. Pronounced shifts in microbiota composition, together with lowered plasma levels of interleukin 6, in mice exposed to CR are in line with these findings. Furthermore, expression of genes involved in lipid metabolism was higher upon CR as compared to C and MF, pointing towards efficient regulation of energy metabolism. Switching from CR to an ad libitum MF diet at old age revealed remarkable phenotypic plasticity, although expression of a small subset of genes remained CR-associated. This research demonstrates that CR beneficially affects markers of colonic health in aging mice and as such may attenuate the progressive age-related decline in health.
Plasminogen activation in human leukemia and in normal hematopoietic cells (1999)

The active process of pericellular proteolysis is central in tumor invasion, and in particular the essential role of the urokinase-type plasminogen activator (uPA) is well established. uPA-mediated plasminogen activation facilitates cell migration and invasion through extracellular matrices by dissolving connective tissue components. uPA, its receptor (uPAR) and plasminogen activator inhibitor-1 (PAI-1) are enriched in several types of tumors. The importance of proteolysis and especially plasminogen activation is less clear in hematopoietic malignancies than in solid tumors. However, patients with leukemia have an increased tendency to bleeding, not always attributable to thrombocytopenia, and tissue infiltration by leukemic cells, processes in which plasminogen activation may be involved. Several studies have indicated that plasminogen activators (PAs) are highly expressed by cultured leukemia cells. Furthermore, differing from adherent tumor cells, leukemic cells have an enhanced capacity to activate pro-uPA and mainly the active form of uPA is released to culture medium. Ex vivo studies have shown that uPAR, uPA and its inhibitors can be found on the surface of normal blood cells and on the blast cell surfaces from patients with acute leukemia as well as from plasma samples. Elevated levels of PAs and their inhibitors have been detected in leukemic cell lysates. Few studies have tried to demonstrate a correlation between prognosis of leukemia and levels of plasminogen activators. More in vivo studies are needed to show, if any of the factors of the plasminogen activation process can be used as tools in subclassification or as markers for prognosis in leukemia. This review article will focus on the in vivo studies of plasminogen activation in leukemia and will present several in vitro findings on PAs in normal leukocytes and leukemic cell lines.
Tetraallyltin precursor for plasma enhanced atomic layer deposition of tin oxide: Growth study and material characterization (2019)

In this letter, the authors report on the application of tetraallyltin (TASn) as an Sn-precursor for plasma enhanced atomic layer deposition (PEALD) of tin oxide (SnO2) thin films. The selection procedure for the TASn precursor is discussed. Tin oxide PEALD growth is shown to be self-limiting with a constant growth-per-cycle of 0.046 ± 0.002 nm/cycle in the substrate temperature (Tsub) range of 50–150 °C. Optical constants, chemical bonding, and electronic properties of as-grown PEALD films were characterized to evaluate the quality of tin oxide film obtained with the TASn precursor. A 21.6 nm tin oxide film grown at Tsub = 50 °C exhibited an indirect optical bandgap (Eg) of 2.94 eV and appeared amorphous from the glancing incidence x-ray diffraction pattern. Binding energy difference ΔBE(O1s, Sn3d5/2) = 43.77 eV and valence band emission in x-ray photoelectron spectroscopy showed that these were near-stoichiometric SnO2 with the relative O:Sn atomic ratio of 1.98 (or SnO1.98). Moreover, room temperature electrical resistivity ρele = 13.1 ± 1.6 mΩ cm, with electron concentration Ne = (3.78 ± 0.79) × 1019 cm−3 and Hall mobility μe = 13.2 ± 2.0 cm2 V−1 s−1, showed that electrical characteristics of the as-grown tin oxide films with the TASn precursor are comparable to those grown using other standard Sn precursors.
Discovery of fungal surface NADases predominantly present in pathogenic species (2021)

Nicotinamide adenine dinucleotide (NAD) is a key molecule in cellular bioenergetics and signalling. Various bacterial pathogens release NADase enzymes into the host cell that deplete the host's NAD<sup>+</sup> pool, thereby causing rapid cell death. Here, we report the identification of NADases on the surface of fungi such as the pathogen Aspergillus fumigatus and the saprophyte Neurospora crassa. The enzymes harbour a tuberculosis necrotizing toxin (TNT) domain and are predominately present in pathogenic species. The 1.6 Å X-ray structure of the homodimeric A. fumigatus protein reveals unique properties including N-linked glycosylation and a Ca<sup>2+</sup>-binding site whose occupancy regulates activity. The structure in complex with a substrate analogue suggests a catalytic mechanism that is distinct from those of known NADases, ADP-ribosyl cyclases and transferases. We propose that fungal NADases may convey advantages during interaction with the host or competing microorganisms.
The shape of high molecular weight kininogen. Organization into structural domains, changes with activation, and interactions with prekallikrein, as determined by electron microscopy (1994)

Knowledge of the organization of the kininogen gene and protein structure and function correlations has allowed the development of a model of high molecular weight kininogen. Domains 1-3 on the heavy chain are evolutionarily related to cystatin and the latter two are inhibitors of cysteine proteases. Proteolytic cleavage in domain 4 to release bradykinin causes a conformational change, exposing a surface-binding region (domain 5) on the disulfide-linked light chain. The carboxyl-terminal domain 6 contains a zymogen binding sequence for factor XI and prekallikrein which, with domain 5, accounts for its cofactor activity. To explore further the domain structure, we have determined the shapes of high molecular weight kininogen and prekallikrein by electron microscopy of rotary shadowed preparations and computer image processing. High molecular weight kininogen appears to be a linear array of three linked globular regions about 16 nm long, with the two ends also connected by another thin strand. Both prekallikrein and kallikrein have a compact globular shape, with a subdivision that is sometimes visible. Different functional domains of high molecular weight kininogen were identified by monoclonal antibodies against these regions, as well as ligand binding of prekallikrein. These studies indicate that one end globular region is the prekallikrein-binding domain, the other comprises the cysteine protease inhibitor domains and the smaller central nodule is the surface-binding domain. Cleavage of high molecular weight kininogen with plasma kallikrein to yield two-chain high molecular weight kininogen results in a striking change in conformation: the central surface-binding domain swings out so that it is still adjacent to the prekallikrein-binding domain but no longer in the middle. These structural studies provide insight into the interactions of these proteins and aspects of the mechanisms of their actions.
AlGaN/GaN Microwave Switch With Hybrid Slow and Fast Gate Design (2010)

We present a novel approach to reduce the off-state capacitance of microwave transistor switches. The new design includes a “slow gate” layer, which allows for complete depletion of the channel in the source-drain region, thus reducing the gate-channel capacitance. Due to very high impedance at high frequencies, the “slow gate” shunting effect and its own capacitance contributions are negligibly small. This novel approach is validated by demonstrating an AlGaN/GaN single-pole double-throw switch with the “slow gate” layer formed by InGaN film. The new gate design decreases the insertion loss of the fabricated switch by approximately 0.5 dB and increases the isolation by approximately 5 dB.
Speed Up Bilateral Filtering via Sparse Approximation on a Learned Cosine Dictionary (2019)

The edge-preserving bilateral filter (BF) is a widely used smoothing tool in many applications. However, its brute-force implementation depends on the size of the box window. The shortcoming causes BF time-consuming for the image processing task with a large window. To make the computational complexity irrelevant to the window size, sparse approximations of the filtering kernels are calculated on a learned cosine dictionary by two steps. First, all possible frequencies are learned (estimated) from the filtering kernel to compose a cosine dictionary. Then, the sparse approximation is conducted on the learned dictionary to seek the optimal cosine approximation for both the range and spatial kernels. By making use of the one-dimensional cosine approximation for the range kernel, the BF is transformed into spatial convolutions. Subsequently, by employing the two-dimensional cosine approximation for the spatial kernel, spatial convolutions are decomposed into box filters of which the computational complexity is O(1). To the best of our knowledge, our approach is the first method that adaptively constructs a cosine dictionary according to the input kernel. This merit guarantees the best filtering accuracy and efficiency. These advantages are corroborated by several carefully designed experiments.
Sn delta-doping in GaAs (1999)

We have prepared a number of GaAs structures d-doped by Sn using the well known molecular beam epitaxy growth technique. The samples obtained for a wide range of Sn doping densities were characterized by magnetotransport experiments at low temperatures and in high magnetic fields up to 38 T. Hall-effect and Shubnikov-de Haas measurements show that the electron densities reached are higher than for other d dopants, like Si and Be. The maximum carrier density determined by the Hall effect equals 8.4 × 1013 cm-2. For all samples several Shubnikov-de Haas frequencies were observed, indicating the population of multiple subbands. The depopulation fields of the subbands were determined by measuring the magnetoresistance with the magnetic field in the plane of the d-layer. The experimental results are in good agreement with selfconsistent bandstructure calculations. This calculation shows that in the sample with the highest electron density also the conduction band at the L point is populated.
Dopant‐Free Pyrrolopyrrole‐Based (PPr) Polymeric Hole‐Transporting Materials for Efficient Tin‐Based Perovskite Solar Cells with Stability Over 6000 h (2023)

A new set of pyrrolopyrrole-based (PPr) polymers incorporated with thioalkylated/alkylated bithiophene (SBT/BT) is synthesized and explored as hole-transporting materials (HTMs) for Sn-based perovskite solar cells (TPSCs). Three bithiophenyl spacers bearing the thioalkylated hexyl (SBT-6), thioalkylated tetradecyl (SBT-14), and tetradecyl (BT-14) chains are utilized to examine the effect of the alkyl chain lengths. Among them, the TPSCs are fabricated using PPr-SBT-14 as HTMs through a two-step approach by attaining a power conversion efficiency (PCE) of 7.6% with a remarkable long-term stability beyond 6000 h, which has not been reported elsewhere for a non-PEDOT:PSS-based TPSC. The PPr-SBT-14 device is stable under light irradiation for 5 h in air (50% relative humidity) at the maximum power point (MPP). The highly planar structure, strong intramolecular S(alkyl)···S(thiophene) interactions, and extended π-conjugation of SBT enable the PPr-SBT-14 device to outperform the standard poly(3-hexylthiophene,-2,5-diyl (P3HT) and other devices. The longer thio-tetradecyl chain in SBT-14 restricts molecular rotation and strongly affects the molecular conformation, solubility, and film wettability over other polymers. Thus, the present study makes a promising dopant-free polymeric HTM model for the future design of highly efficient and stable TPSCs.
Correlation between the antisite pair and theDIcenter in SiC (2003)

The ${D}_{\mathrm{I}}$ low temperature photoluminescence center is a well-known defect stable up to $1700\ifmmode^\circ\else\textdegree\fi{}\mathrm{C}$ annealing in SiC, still its structure is not yet known. Combining experimental and theoretical studies, in this paper we will show that the properties of an antisite pair can reproduce the measured one-electron level position and local vibration modes of the ${D}_{\mathrm{I}}$ center, and are consistent with other experimental findings as well. We give theoretical values of the hyperfine constants of the antisite pair in its paramagnetic state as a means to confirm a model.
Developing a "responsible assessment" system to improve research impact: a case study from Catalonia (2018)

Many lessons can be drawn from the burgeoning discourse on research impact assessment. Paula Adam, Maite Solans-Domènech, Núria Radó-Trilla, Toni Dedeu and Albert Barberà explain how they have applied these to the design of a health research assessment system in Catalonia, one that helps to embed impact from the early stages of a research programme. Emphasising the importance of values, leadership, culture, and empowerment, the SARIS system is focused on all research stakeholders and promotes the idea of “responsible” assessment, underpinned by openness, analysis, and engagement.
Identification and characterization of suppressor mutants of stop1 (2017)

We have identified and characterized nine strong stop1 suppressor mutants. Candidate loci for two tps mutations that partially rescue the hypersensitive phenotypes of stop1 to low pH and Al stresses were identified by mapping-by-sequencing approaches. Further studies could provide insights into the structure and function of TPSs and the regulatory networks underlying the STOP1-mediated processes that lead to resistance to low pH and Al stresses in Arabidopsis.
Enhanced Binding of Antibodies to Neutralization Epitopes following Thermal and Chemical Inactivation of Human Immunodeficiency Virus Type 1 (2000)

Inactivation of viral particles is the basis for several vaccines currently in use. Initial attempts to use simian immunodeficiency virus to model a killed human immunodeficiency virus type 1 (HIV-1) vaccine were unsuccessful, and limited subsequent effort has been directed toward a systematic study of the requirements for a protective killed HIV-1 vaccine. Recent insights into HIV-1 virion and glycoprotein structure and neutralization epitopes led us to revisit whether inactivated HIV-1 particles could serve as the basis for an HIV-1 vaccine. Our results indicate that relatively simple processes involving thermal and chemical inactivation can inactivate HIV-1 by at least 7 logs. For some HIV-1 strains, significant amounts of envelope glycoproteins are retained in high-molecular-weight fractions. Importantly, we demonstrate retention of each of three conformation-dependent neutralization epitopes. Moreover, reactivity of monoclonal antibodies directed toward these epitopes is increased following treatment, suggesting greater exposure of the epitopes. In contrast, treatment of free envelope under the same conditions leads only to decreased antibody recognition. These inactivated virions can also be presented by human dendritic cells to direct a cell-mediated immune response in vitro. These data indicate that a systematic study of HIV-1 inactivation, gp120 retention, and epitope reactivity with conformation-specific neutralizing antibodies can provide important insights for the development of an effective killed HIV-1 vaccine.
Image-based numerical evaluation techniques in volume holographic memory systems (2007)

A simulation technique for a volume holographic memory system based on binary page data is proposed to evaluate quantitative diffraction efficiency, bit error rate, and signal-to-noise ratio. In this simulator, propagation of a signal and reference beams and diffraction at gratings are calculated quantitatively by use of numerical Fresnel propagation and Kogelnik's coupled-wave theory. To apply Kogelnik's wave theory to arbitrary signal and reference beams, both beams at the hologram plane are decomposed into plane waves. Numerical results show good agreement with the exact solution under the Born approximation in a transmission-type volume hologram. We also apply the simulator to reflection-type holographic memory.
Supplementary Figure 1 from Detection, Characterization, and Inhibition of FGFR–TACC Fusions in IDH Wild-type Glioma (2023)

&lt;p&gt;Supplementary Figure 1. Genomic PCR images and Sanger sequences of FGFR3-TACC3 genomic breakpoints.&lt;/p&gt;
NMR relaxation and pulsed-gradient diffusion study of polyethylene nanocomposites (2005)

We performed pulsed-gradient spin-echo nuclear-magnetic-resonance (NMR) experiments on zinc oxide filled polyethylene. The molecular weights of the polyethylene samples ranged between 808 and 33,000 gmol, and four different zinc oxide samples were used: 27-, 33-, 51-, and 2500-nm-diameter particles. The results of these experiments showed that the diffusion coefficients of the polyethylene chains did not change with nanofiller content, but a drastic change is observed in the NMR relaxation spectrum in spin-spin-relaxation experiments. At fixed zinc oxide content and polyethylene molecular weight (close to entanglement), the system with the smallest zinc oxide showed the most rigid environment. At high polyethylene molecular weights, this effect was still observable but the difference between the three investigated systems was very small, suggesting that the system was dominated by entanglements.