gebhart/patrepeval huggingface dataset:
Single Photon Ionization Orthogonal Acceleration Time-of-Flight Mass Spectrometry and Resonance Enhanced Multiphoton Ionization Time-of-Flight Mass Spectrometry for Evolved Gas Analysis in Thermogravimetry: Comparative Analysis of Crude Oils (2009)

Coupling thermal analysis (TA) with a subsequent analytical method in order to investigate evolved gaseous products from the thermal analysis is a well established method. A popular practice to analyze the gaseous products evolving from thermal analysis is mass spectrometry using electron impact ionization (EI).(1-4) As the kinetic energy of the electrons thereby is typically far beyond the ionization energies of the assayed samples, the electron impact effects fragmentation particularly of organic compounds, hampering the correlation of the ion signals to the gaseous compounds. This applies for complex mixtures in particular. Fragmentation can be reduced using so-called soft ionization techniques. In the course of the presented setup, single photon ionization (SPI) using electron beam pumped excimer lamps (EBEL) emitting vacuum ultraviolet (VUV) light (lambda = 126 nm) is employed. For the instrumentation, a TA system has been coupled to an EBEL-SPI-oaTOFMS (oaTOFMS: orthogonal acceleration time-of-flight mass spectrometry) system using a heated transfer capillary in order to detect semivolatile organic substances from the gas flow of a thermobalance with high temporal resolution. Presented measurements focus on crude oils of different origins. In-depth analysis demonstrates that it is possible to tell apart different crude oil samples on the basis of temperature resolved mass spectra gained from the described setup. TA allows for the assay of crude oils without sample preparation via a distillation process which precedes the thermal decomposition of nonvolatile oil components, i.e., resins and asphaltenes. The gases that evolve during thermal analysis are a complex mixture of organic compounds. These can be analyzed without losing molecular information using mass spectrometry with a soft ionization technique, such as SPI.
Multi-layer and Multi-domain Network Orchestration by ODENOS (2016)

We propose a network orchestrator based on ODENOS for orchestrating multi-layer and multi-domain networks. The network orchestrator can dynamically provide end-to-end paths according to requests of network services.
Boosting engineered T cells (2019)

Vaccines augment the antitumor activity of cellular therapy
Expression, cross-linking and characterization of recombinant chitin binding resilin (2010)

Resilin is a polymeric rubber-like protein secreted by insects to specialized cuticle regions, in areas where high resilience and low stiffness are required. Resilin binds to the cuticle polysaccharide chitin via a chitin binding domain and is further polymerized through oxidation of the tyrosine residues resulting in the formation of dityrosine bridges and assembly of a high-performance protein-carbohydrate composite material. We describe for the first time a comprehensive study on the mechanical, structural and biochemical function of chitin binding recombinant Drosophila melanogaster resilin. Various resilin constructs were cloned including the full length gene enabling Ni-NTA purification, as well as heat and salt precipitation for rapid and efficient purification. The binding isotherms and constants (K <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">d</inf> , B <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">max</inf> ) of resilin to chitin via its chitin binding domain were determined and displayed high affinity to chitin, implying its important role in the assembly of the resilin-chitin composite. The structural and elastic properties were investigated using Fourier Transform Infrared Spectroscopy (FTIR), Circular Dichroism (CD) and Atomic Force Microscopy (AFM) with peroxidase crosslinked solid resilin materials. Generally, little structural organization was found by these biophysical methods, suggesting structural order was not induced by the dityrosine crosslinks. Further, the elastomeric properties found from the full length protein compared favorably with the shorter resilin generated previously from exon 1. The unusual elastomeric behavior of this protein suggests possible utility in biomaterials applications.
Integrative analysis of DNA methylation and mRNA expression during differentiation of umbilical cord blood derived mononuclear cells to endothelial cells (2017)

Differentiation of umbilical cord blood derived mononuclear cells to endothelial cells is accompanied by massive changes in gene expression. Although methylation and demethylation of DNA likely play crucial roles in regulating gene expression, their interplay during differentiation remains elusive. To address this question, we performed deep sequencing of DNA methylation and mRNA expression to profile global changes in promoter methylation and gene expression during differentiation from mononuclear cells to outgrowing cells. We identified 61 downregulated genes with hypermethylation, including CD74, VAV1, TLR8, and NCF4, as well as 21 upregulated genes with hypomethylation, including ECSCR, MCAM, PGF, and ARHGEF15. Interestingly, gene ontology analysis showed that downregulated genes with hypermethylation were enriched in immune-related functions, and upregulated genes with hypomethylation were enriched in the developmental process and angiogenesis, indicating the important roles of DNA methylation in regulating differentiation. We performed polymerase chain reaction analyses and bisulfite sequencing of representative genes (CD74, VAV1, ECSCR, and MCAM) to verify the negative correlation between DNA methylation and gene expression. Further, inhibition of DNA methyltransferase and demethylase activities using 5'-aza-dc and shRNAs, specific for TET1 and TET2 mRNAs, respectively, revealed that DNA methylation was the main regulator of the reversible expression of functionally important genes. Collectively, our findings implicate DNA methylation as a critical regulator of gene expression during umbilical cord blood derived mononuclear cells to endothelial cell differentiation.
ChemInform Abstract: SYNTHESE VON 1,2,3,4‐TETRAKIS‐(PERFLUOROALKYL)‐BUTADIENEN‐(1,3) DURCH VERDOPPELUNG VON 1,2‐BIS‐(PERFLUOROALKYL)‐JODAETHYLENEN IN GEGENWART VON KUPFER, NEUE VERBINDUNGEN ALS TRAEGER FUER GELOESTE GASE IN BIOLOGISCHEN SYSTEMEN (1975)

Abstract Die thermische Kondensation der 1‐J od‐perfluoralkane (I) mit den Perfluoralkylacetylenen (II) ergibt die Telomeren (III) und die erwarteten Derivate (IV); die AR Bildung der Nebenprodukte (III) läßt sich auf ein Minimum reduzieren, wenn man die Jodide (I) in einem 100%igen Überschuß einsetzt.
Patterning Vascular Networks In Vivo for Tissue Engineering Applications (2014)

The ultimate design of functionally therapeutic engineered tissues and organs will rely on our ability to engineer vasculature that can meet tissue-specific metabolic needs. We recently introduced an approach for patterning the formation of functional spatially organized vascular architectures within engineered tissues in vivo. Here, we now explore the design parameters of this approach and how they impact the vascularization of an engineered tissue construct after implantation. We used micropatterning techniques to organize endothelial cells (ECs) into geometrically defined "cords," which in turn acted as a template after implantation for the guided formation of patterned capillaries integrated with the host tissue. We demonstrated that the diameter of the cords before implantation impacts the location and density of the resultant capillary network. Inclusion of mural cells to the vascularization response appears primarily to impact the dynamics of vascularization. We established that clinically relevant endothelial sources such as induced pluripotent stem cell-derived ECs and human microvascular endothelial cells can drive vascularization within this system. Finally, we demonstrated the ability to control the juxtaposition of parenchyma with perfused vasculature by implanting cords containing a mixture of both a parenchymal cell type (hepatocytes) and ECs. These findings define important characteristics that will ultimately impact the design of vasculature structures that meet tissue-specific needs.
S054041 Stability against Disturbances of Liquid Lithium Flows for the Target and Coolant of BNCT using Accelerators (2011)

We discussed the stability against disturbances of liquid lithium flows for the target and coolant of BNCT (Boron 4eutron Capture Therapy) using accelerators, which makes cancers and tumors curable with cell-level selections. The )bject of our research is the thin and high-speed plane sheet jet / film flow (on a guide plate) of liquid lithium in a sighvacuum because of the ambience using accelerators, and it serves both as a target of accelerators and as a coolant or the target itself. In this paper, we made the linear stability analysis suitable to the physical features of thin plane ,heet jets of liquid lithium in a high-vacuum. As the results, we proved that the anti-symmetric sinusoidal wave has no lispersion and the symmetric dilatational wave has a strong dispersion in which the very slow phase velocity is )roportional to the wave number, when the thickness of a plane sheet jet of liquid lithium is sufficiently thinner than the vave length.
Oxygen and Erbium related donor centers in Czochralski grown silicon implanted with erbium (1999)

The Hall effect measurements were conducted on Czochralski-grown silicon after implantation of erbium and two-step annealing at 700 °C and 900 °C. After the first step the formation of oxygen-related shallow donors was observed at E c in the range 20–40 meV and erbium-related donor centers at ≈E c -70 meV and ≈E c -120 meV. Along with the same oxygen-related shallow thermal donors and donor centers at ≈E c -70 meV, other donor centers at ≈E c -150 meV are formed following the 900°C anneal, instead of those at ≈E c -120 meV. The new donor states are of particular interest because of their possible involvement in the photoluminescence process. The obtained results for erbium-implanted silicon are compared with some fragmentary DLTS data found in the current literature on the donors with ionization energies less than 0.2 eV.
A Novel ATR‐FTIR Approach for Characterisation and Identification of Ex Situ Immobilised Species (2007)

We demonstrate a novel method to analyse ex situ prepared protein chips by attenuated total reflection Fourier IR spectroscopy (ATR-FTIR), which circumvents tedious functionalisation steps of internal reflection elements (IREs), and simultaneously allows for complementary measurements by other analytical techniques. This concept is proven by utilising immobilised metal affinity capture (IMAC) chips containing about 10 mum thick films of copolymers coated with nitrilotriacetic acid (NTA) groups, which originally was manufactured for surface enhanced laser desorption ionisation (SELDI) spectrometry. Three immobilisation steps were analysed by ATR-FTIR spectroscopy: 1) NTA complexation with nickel(II) ions 2) binding of two histidine (His)-tagged synthetic peptides of 25 (25-His6) and 48 (48-His6) amino acids to the NTA-groups and 3) attachment of a ligand, mesyl amide, to the surface-bound 48-His6. Despite interference from H(2)O, both amide I and II were well resolved. Utilising peptide adsorption in the thick copolymer matrix yields a high saturation peptide concentration of approximately 100 mg mL(-1) and a dissociation constant of 116+/-11 muM, as determined by a detailed analysis of the Langmuir adsorption isotherm. The mesyl amide ligand was directly seen in the raw ATR-FTIR spectrum with specific peaks in the fingerprint region at 1172 and 1350 cm(-1). Several aspects of the fine structure of the amide I band of the peptide were analysed: influences from secondary structure, amino side chains and competing contamination product. We believe that this approach has great potential as a stand-alone or complementary analytical tool for determination of the chemical composition of functionalised surfaces. We emphasise further that with this approach no chemical treatment of IREs is needed; the chips can be regenerated and reused, and applied in other experimental set-ups.
Aspiration ratio of a double-shrouded probe under low pressure conditions in troposphere (2020)

Particulate matter forecasting is based on data measured at several monitoring stations fixed on the ground. The most effective way to improve forecast accuracy is to obtain measurements over a wider range. To this end, research is being conducted into data improvement methods using three-dimensional measurements over a large area using unmanned aerial vehicles (UAVs) such as drones. The environment of the troposphere, where atmospheric aerosol measurements are made using UAVs, is characterized by high velocity airflow and low pressure, and these conditions hinder representative sampling, which is the first step to accurately measure atmospheric aerosol concentrations. We evaluated the aspiration ratio using a double-shrouded probe designed to be mounted on a UAV at a high speed of up to 300 km/h and at a low pressure of 0.3 atm, the pressure in the upper troposphere. The aspiration ratio of the double-shrouded probe was predicted through simulation, and a low pressure high-speed wind tunnel that can implement an airflow velocity over 300 km/h was developed and verified through experiments. The results showed that as the pressure was lowered from 1 atm to 0.3 atm, the drag force of the air on particles decreased and the aspiration ratio of the double-shrouded probe was overestimated to some extent. However, representative sampling could be implemented with an error of 10% or less, even at speeds below 300 km/h for PM2.5. Therefore, the double-shrouded probe developed in this study enables representative sampling over much wider speed and pressure ranges than the existing sampling probes.Copyright © 2020 American Association for Aerosol Research
RS2G: Data-Driven Scene-Graph Extraction and Embedding for Robust Autonomous Perception and Scenario Understanding (2023)

Effectively capturing intricate interactions among road users is of critical importance to achieving safe navigation for autonomous vehicles. While graph learning (GL) has emerged as a promising approach to tackle this challenge, existing GL models rely on predefined domain-specific graph extraction rules that often fail in real-world drastically changing scenarios. Additionally, these graph extraction rules severely impede the capability of existing GL methods to generalize knowledge across domains. To address this issue, we propose RoadScene2Graph (RS2G), an innovative autonomous scenario understanding framework with a novel data-driven graph extraction and modeling approach that dynamically captures the diverse relations among road users. Our evaluations demonstrate that on average RS2G outperforms the state-of-the-art (SOTA) rule-based graph extraction method by 4.47% and the SOTA deep learning model by 22.19% in subjective risk assessment. More importantly, RS2G delivers notably better performance in transferring knowledge gained from simulation environments to unseen real-world scenarios.
Supplementary Figure from INK4 Tumor Suppressor Proteins Mediate Resistance to CDK4/6 Kinase Inhibitors (2023)

Supplementary Figure from INK4 Tumor Suppressor Proteins Mediate Resistance to CDK4/6 Kinase Inhibitors
Electrooptically tunable narrowband Fabry-Perot/Solc filter design (1987)

Tunable narrowband spectral filters are useful in many applications. A new electrooptically tunable narrowband (0.01 nm in some cases) spectral filter which combines the characteristics of a Fabry-Perot filter and a folded Sole filter, called the Fabry-Perot/Solc filter, is described. The design is based on the three-layer multiple-pass filter proposed by Williamson. 1
Impurity centers in silicon doped with rare-earth impurities of dysprosium, holmium, erbium, and ytterbium (1999)

The results of an investigation of the donor centers in Czochralski-grown silicon ion-implanted with rare-earth impurities of Dy, Ho, Er, and Yb are presented. The formation of three groups of dominant donors with ionization energies less than 0.2 eV in silicon after annealing at 700 and 900 °C is discussed. The shallow donors at ≈E c −40 meV are interpreted as thermal donors containing oxygen and intrinsic defects. The two other groups of donor states are identified as centers containing rare-earth ions.
Mathematical Model for a Standing Wave Acoustic Parametric Source (1973)

A standing wave acoustic parametric source (SWAPS) has been proposed as a small, efficient, low-frequency, nearly omni-directional underwater sound source. SWAPS is envisioned to be a cylindrical tube driven on one end by a piston transducer and terminated on the other end by a thin plug of pressure release material to form a resonant cavity. When the piston is driven at two neighboring resonance frequencies, the resulting large amplitude primary sound waves mix non-linearly to produce secondary sound waves. The secondary wave at the difference frequency is of low frequency so that it passes easily through the relatively thin tube walls and radiates to the farfield. The farfield radiation at the difference frequency is calculated by use of the virtual source density method. The results are expressed in terms of a quality factor which represents the resonance properties of the cavity. Comparison is made to a traveling wave acoustic parametric source using the same piston transducer.
Glycogen Content Regulates Peroxisome Proliferator Activated Receptor-∂ (PPAR-∂) Activity in Rat Skeletal Muscle (2013)

Performing exercise in a glycogen depleted state increases skeletal muscle lipid utilization and the transcription of genes regulating mitochondrial β-oxidation. Potential candidates for glycogen-mediated metabolic adaptation are the peroxisome proliferator activated receptor (PPAR) coactivator-1α (PGC-1α) and the transcription factor/nuclear receptor PPAR-∂. It was therefore the aim of the present study to examine whether acute exercise with or without glycogen manipulation affects PGC-1α and PPAR-∂ function in rodent skeletal muscle. Twenty female Wistar rats were randomly assigned to 5 experimental groups (n = 4): control [CON]; normal glycogen control [NG-C]; normal glycogen exercise [NG-E]; low glycogen control [LG-C]; and low glycogen exercise [LG-E]). Gastrocnemius (GTN) muscles were collected immediately following exercise and analyzed for glycogen content, PPAR-∂ activity via chromatin immunoprecipitation (ChIP) assays, AMPK α1/α2 kinase activity, and the localization of AMPK and PGC-1α. Exercise reduced muscle glycogen by 47 and 75% relative to CON in the NG-E and LG-E groups, respectively. Exercise that started with low glycogen (LG-E) finished with higher AMPK-α2 activity (147%, p<0.05), nuclear AMPK-α2 and PGC-1α, but no difference in AMPK-α1 activity compared to CON. In addition, PPAR-∂ binding to the CPT1 promoter was significantly increased only in the LG-E group. Finally, cell reporter studies in contracting C2C12 myotubes indicated that PPAR-∂ activity following contraction is sensitive to glucose availability, providing mechanistic insight into the association between PPAR-∂ and glycogen content/substrate availability. The present study is the first to examine PPAR-∂ activity in skeletal muscle in response to an acute bout of endurance exercise. Our data would suggest that a factor associated with muscle contraction and/or glycogen depletion activates PPAR-∂ and initiates AMPK translocation in skeletal muscle in response to exercise.
Mechanistic Studies of Palladium Thin Film Growth from Palladium(II) β-Diketonates. 1. Spectroscopic Studies of the Reactions of Bis(hexafluoroacetylacetonato)palladium(II) on Copper Surfaces (1996)

The reactions of bis(hexafluoroacetylacetonato)palladium(II), Pd(hfac)2, on copper have been studied. Whereas multilayers of Pd(hfac)2 desorb molecularly from copper surfaces between 200 and 270 K, submonolayer coverages of Pd(hfac)2 react in a multistep sequence. At temperatures below 120 K, Pd(hfac)2 transfers its hfac ligands to the copper surface and the metal center is reduced to Pd0. The hfac groups adopt a variety of molecular orientations on the surface at 120 K but undergo an apparent ordering transition near 300 K that re-orients the hfac groups to an upright geometry (perpendicular to the surface plane). At low coverages on clean surfaces, further annealing results in the decomposition of the surface-bound hfac ligands to give adsorbed Pd atoms and COCF3, CF3, and fluoride species. These intermediates ultimately yield a partial monolayer of Pd atoms, a carbon (possibly graphitic) deposit, and a variety of organic products that desorb between 500 and 650 K; the desorbing flux after ionization consists of CF3COF, COCF3, CF3, and CO fragments. The activation parameters for the decomposition of hfac groups on copper foils have been determined to be A = 1.3 × 1013 s-1 and Ea = 36.8 kcal mol-1. When Pd(hfac)2 is dosed onto copper surfaces bearing submonolayer coverages of carbon, a new reaction channel is evident: some of the hfac ligands abstract copper atoms from the surface and generate Cu(hfac)2, which desorbs when the surface is heated. The palladium atoms remain behind and diffuse into the bulk of the Cu crystal. This redox transmetalation reaction (PdII(hfac)2 + Cu0 → Pd0 + CuII(hfac)2) is the same one that is responsible for the ability of Pd(hfac)2 to effect the chemical vapor deposition of palladium selectively on copper at higher pressures. This redox transmetalation reaction is the first example of the simultaneous etching of copper and deposition of palladium.
Practical Route to a New Class of LTD4 Receptor Antagonists (1996)

A general approach to the synthesis of a new class of LTD4 antagonists is presented. The key diarylpropane framework was prepared by Claisen−Schmidt condensation and selective reduction of the enone. Depending on the bridge to the 7-chloroquinaldine moiety, alkylation or Heck coupling methodology was developed. The chiral sulfides were introduced by asymmetric reduction of the diarylpropanone intermediates and subsequent inversion of the chiral center.