gebhart/patrepeval huggingface dataset:
Discovery of Fluorescent Cyanopyridine and Deazalumazine Dyes Using Small Molecule Macroarrays (2006)

[structure: see text] Small molecule macroarrays of cyanopyridines and deazalumazines were generated in high purities via spatially addressed synthesis on planar cellulose supports. Examination of the spectral properties of the heterocycles both on and off of the planar support revealed a set of promising new fluorescent dyes that exhibit high quantum yields, low pH dependence, and high sensitivity to solvent polarity.
Advances in the Use of BiOH® Polyols in Polyurethanes (2012)

An exponential increase in the utilization of petroleum for transportation fuels, energy and industrial chemicals that has taken place over the past several decades is widely accepted as being unsustainable. Additionally, increased concerns about the environment and global warming have given rise to worldwide efforts devoted to utilizing biobased resources for fuels and industrial chemicals. Natural oils are seen as one such inexpensive, abundant renewable resource. The versatility of natural oils in industrial applications is demonstrated by the ability to introduce various functional groups, such as epoxy, hydroxyl and carboxylic acid groups, onto the fatty acid chains, which enables their use in numerous applications. The utilization of natural oils in polyurethanes is accomplished by introducing hydroxyl groups. Cargill has introduced a family of natural oil-based polyols for polyurethane foams under the BiOH® tradename. The basic technology involves epoxidation and reaction of the epoxides with nucleophiles yielding polyols that have the desired molecular weight and functionality range. BiOH® polyols have been used to partially replace petrochemical-based polyols in flexible molded foams and flexible slabstock foams, including viscoelastic foams, and to partially substitute copolymer polyols in high resilience foams.
Effects of fasting on insulin binding, glucose transport, and glucose oxidation in isolated rat adipocytes: relationships between insulin receptors and insulin action. (1976)

(a) insulin binding is increased during fasting due to an increased overall binding affinity with no change in receptor number; (b) glucose oxidation is severely impaired during fasting; (c) 2-deoxy-glucose uptake decreases with fasting due to a decrease in maximal transport capacity (Vmax) with no change in Km; (d) the decrease in glucose oxidation is much greater than the decrease in glucose transport, indicating impaired intracellular oxidative metabolism; and (e) coupling between insulin receptors and the glucose transport system is normal after 24 h of fasting but is impaired at 48 and 72 h.
Global assessment of genomic variation in cattle by genome resequencing and high-throughput genotyping (2011)

Our results provide high resolution mapping of diverse classes of genomic variation in an individual bovine genome and demonstrate that structural variation surpasses sequence variation as the main component of genomic variability. Better accuracy of SNP detection was achieved with little loss of sensitivity when algorithms that implemented mapping quality were used. IBD regions were found to be instrumental for calculating resequencing SNP accuracy, while SNP detection within CNVs tended to be less reliable. CNV discovery was affected dramatically by platform resolution and coverage biases. The combined data for this study showed that at a moderate level of sequencing coverage, an ensemble of platforms and tools can be applied together to maximize the accurate detection of sequence and structural variants.
Development of thermoplastic polyurethane vascular prostheses (2008)

Abstract In this study, the optimum electrospinning conditions for a thermoplastic polyurethane/ N,N ‐dimethylformamide solution were sought. Under these conditions, polyurethane tubes for artificial blood vessels were produced via electrospinning, and various properties of the specimen were measured. The optimum electrospinning conditions were a concentration of 16 wt %, a voltage of 13.0 kV, and a tip‐to‐collector distance of 15 cm at 27°C and 80% relative humidity. The thermal behavior from a differential scanning calorimeter showed that this polyurethane web was thermally stable in the body temperature range. Enzyme hydrolysis of the web revealed that the polyurethane vascular prostheses would perform as nondegradable blood vessels in the body system. The pore size range of the electrospun polyurethane vascular prostheses was 0–3.5 μm. With a tensile stress of about 8–9 MPa and a tensile strain of about 80%, the tensile properties were expected to be superior to those of existing vascular prostheses made of polyester and expanded polytetrafluoroethylene. In the last stage, heparin and collagen were treated on the surfaces of artificial vessels to reduce the probability of thrombi forming during the initial stage of grafting, and so the treated specimens exhibited a lower possibility of thrombi forming than untreated ones in a blood coagulation test. © 2008 Wiley Periodicals, Inc. J Appl Polym Sci, 2008
Self-aligned inkjet printing of highly conducting gold electrodes with submicron resolution (2007)

Self-aligned printing is a recently developed bottom-up printing technique which utilizes the unique droplet motion on heterogeneous surfaces to define sub-100-nm critical features and surpasses the resolution which can commonly be achieved by direct printing by two orders of magnitude. Here we extend this method, which was originally implemented with conductive polymer inks, to fabrication of functional conductive nanostructures with gold nanoparticle ink. We also designed a configuration where the ink was printed between two lithographically defined patterns to facilitate the study of the channel formation. Channel lengths from 4μm down to 60nm were achieved by controlling the surface tension and drying time of the ink. A fluid dynamical model is presented to explain the mechanism by which the channel forms in the self-aligned printing technique. Field-effect transistors fabricated using gold self-aligned printed source-drain electrodes exhibit significantly improved output currents than those using conducting polymers. Unambiguous evidence for the submicrometer channel dimension is obtained by imaging the potential drop along the channel using scanning Kelvin probe microscopy.
All-optical fluorescence blinking control in quantum dots with ultrafast mid-infrared pulses (2021)

Photoluminescence (PL) intermittency is a ubiquitous phenomenon detrimentally reducing the temporal emission intensity stability of single colloidal quantum dots (CQDs) and the emission quantum yield of their ensembles. Despite efforts for blinking reduction via chemical engineering of the QD architecture and its environment, blinking still poses barriers to the application of QDs, particularly in single-particle tracking in biology or in single-photon sources. Here, we demonstrate the first deterministic all-optical suppression of quantum dot blinking using a compound technique of visible and mid-infrared (MIR) excitation. We show that moderate-field ultrafast MIR pulses (5.5 $μ$m, 150 fs) can switch the emission from a charged, low quantum yield 'grey' trion state to the 'bright' exciton state in CdSe/CdS core-shell quantum dots resulting in a significant reduction of the QD intensity flicker. Quantum-tunneling simulations suggest that the MIR fields remove the excess charge from trions with reduced emission quantum yield to restore higher brightness exciton emission. Our approach can be integrated with existing single-particle tracking or super-resolution microscopy techniques without any modification to the sample and translates to other emitters presenting charging-induced PL intermittencies, such as single-photon emissive defects in diamond and two-dimensional materials.
Comparative Study of Au Modified Beta, MCM-22, Mordenite, ZSM-5, MCM-41, Ce-MCM-41 Catalysts in Piperonyl Alcohol Oxidation (2012)

Au and Au-Ce promoted catalysts supported on zeolites (Beta, H-MCM-22, H-Mordenite, ZSM-5), mesoporous material MCM-41 and metal oxides (TiO2, SiO2, Al2O3) were prepared. Catalysts were characterized by a range of methods: nitrogen physisorption, X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), diffuse reflectance infrared Fourier transformed spectroscopy (DRIFTS), transmission electron microscopy (TEM) and activity was evaluated in selective aerobic piperonyl alcohol oxidation to piperonal. The effect of such catalyst ’ s properties as Au particle size and Ce addition on the catalytic activity was highlighted. Keywords: Au catalysts, BET, XRD, XPS, DRIFT, piperonyl alcohol selective aerobic oxidation, metal, low temperature, liquid-phase oxidation of alcohols, palladium catalysts, mesoporous materials, nitrogen adsorption, hydrogen, oxygen, Gold catalysts
Titelbild: A FRET‐Based Fluorogenic Phosphine for Live‐Cell Imaging with the Staudinger Ligation (Angew. Chem. 13/2008) (2008)

Die Staudinger-Ligation bietet eine nichttoxische Methode zur Markierung von Azid-funktionalisierten Biomolekülen in lebenden Zellen und in Organismen. C. R. Bertozzi und M. J. Hangauer beschreiben in ihrer Zuschrift auf S. 2428 ff. ein fluorogenes Phosphan mit resonantem Förster-Energietransfer, das zur direkten Fluorenzenzmarkierung von Azidobiomolekülen in lebenden Zellen bei minimaler Hintergrundfluoreszenz geeignet ist. Das Titelbild zeigt lebende HeLa-Zellen, die durch Markierung von Azidosialinsäure mit dem fluorogenen Phosphan visualisiert sind.
Temporal Dissection of Tumorigenesis in Primary Cancers (2011)

Timely intervention for cancer requires knowledge of its earliest genetic aberrations. Sequencing of tumors and their metastases reveals numerous abnormalities occurring late in progression. A means to temporally order aberrations in a single cancer, rather than inferring them from serially acquired samples, would define changes preceding even clinically evident disease. We integrate DNA sequence and copy number information to reconstruct the order of abnormalities as individual tumors evolve for 2 separate cancer types. We detect vast, unreported expansion of simple mutations sharply demarcated by recombinative loss of the second copy of TP53 in cutaneous squamous cell carcinomas (cSCC) and serous ovarian adenocarcinomas, in the former surpassing 50 mutations per megabase. In cSCCs, we also report diverse secondary mutations in known and novel oncogenic pathways, illustrating how such expanded mutagenesis directly promotes malignant progression. These results reframe paradigms in which TP53 mutation is required later, to bypass senescence induced by driver oncogenes.
Robustness and reliability achievements for direct hybrid bonding integration: a review (2019)

The paper reviews the robustness/reliability achievements and include previously published data related to the hybrid bonding module for W2W and D2W bonding techniques.
A high-content imaging assay for the quantification of the Burkholderia pseudomallei induced multinucleated giant cell (MNGC) phenotype in murine macrophages (2014)

We have successfully developed an automated HCI assay to quantitate MNGCs induced by Bp in macrophages. This assay was then used to characterize the phenotype of the Bp mutants for their ability to induce MNGC formation and identify small molecules that interfere with this process. Successful application of chemical genetics and functional reverse genetics siRNA approaches in the MNGC assay will help gain a better understanding of the molecular targets and cellular mechanisms responsible for the MNGC phenotype induced by Bp, by other bacteria such as Mycobacterium tuberculosis, or by exogenously added cytokines.
Microscope-Cockpit: Python-based bespoke microscopy for bio-medical science (2021)

Abstract We have developed “Microscope-Cockpit” (Cockpit), a highly adaptable open source user-friendly Python-based GUI environment for precision control of both simple and elaborate bespoke microscope systems. The user environment allows next-generation near-instantaneous navigation of the entire slide landscape for efficient selection of specimens of interest and automated acquisition without the use of eyepieces. Cockpit uses “Python-Microscope” (Microscope) for high-performance coordinated control of a wide range of hardware devices using open source software. Microscope also controls complex hardware devices such as deformable mirrors for aberration correction and spatial light modulators for structured illumination via abstracted device models. We demonstrate the advantages of the Cockpit platform using several bespoke microscopes, including a simple widefield system and a complex system with adaptive optics and structured illumination. A key strength of Cockpit is its use of Python, which means that any microscope built with Cockpit is ready for future customisation by simply adding new libraries, for example machine learning algorithms to enable automated microscopy decision making while imaging. Highlights User-friendly setup and use for simple to complex bespoke microscopes. Facilitates collaborations between biomedical scientists and microscope technologists. Touchscreen for near-instantaneous navigation of specimen landscape. Uses Python-Microscope, for abstracted open source hardware device control. Well-suited for user training of AI-algorithms for automated microscopy.
Lipidomics biomarkers in women with polycystic ovary syndrome (PCOS) using ultra-high performance liquid chromatography–quadrupole time of flight electrospray in a positive ionization mode mass spectrometry (2019)

Polycystic ovary syndrome (PCOS), characterized by oligo-anovulation and androgen excess is considered a high-risk condition for metabolic disorders. Herein, untargeted metabolomics analysis was applied to women with PCOS, aiming to provide deeper insights into lipidomics biomarkers signature of PCOS, for better diagnosis and management. This was a cross-sectional study in which 15 Caucasian women with PCOS and 15 Caucasian healthy, age-matched women were enrolled. Lipidomics analysis was performed using Ultra-High Performance Liquid Chromatography-Quadrupole Time of Flight Electrospray Mass Spectrometry. Partial Least Squares Discriminant Analysis retrieved the most important discriminative metabolites. Significantly increased levels of triacylglycerol (18:2/18:2/0-18:0) in addition to cholestane-3beta, 5alpha, 6beta-triol (18:0/0:0) and cholestane-5alpha (18:1/0:0) appeared as valuable variables to differentiate subjects with PCOS from controls. Acyl-carnitine 2-hydroxylauroylcarnitine was significantly elevated in PCOS in opposition to decreased phosphocholines metabolites (18:1/18:4, 18:3/18:2), to suggest a metabolic pattern linked to lipid peroxidation. A high fat intake or reduced fat energy consumption during nighttime due to diminished ability to switch to lipid oxidation during fasting time possibly contribute to hypertriglyceridemia found in PCOS. Furthermore, inflammatory mediators including metabolites of the prostaglandin (PG) E2 pathway and oxo-leukotrienes (LT) were increased in patients with PCOS. Potential lipidomics biomarkers were identified that could stratify between women with PCOS and healthy controls. The results show particular alterations in acylglycerols, PGs and LTs and phosphocholines and carnitine metabolites. The lipidomics profiles of PCOS indicate a higher risk of developing metabolic diseases.
Advanced Sensors & Controls FWP Overview (2021)

Fossil energy power generation is needed now and in the future, but its role is shifting from baseload operation to fulfilling dispatchable power needs in regions of the United States.&amp;#160;Novel sensors and controls will help to increase efficiency, minimize emissions, and reduce operating costs of existing power generation technologies under this increased load following role; and help enable next generation power systems with high efficiency and greater operational flexibility.&amp;lt;br&amp;gt;
Waveguiding in planar photonic crystals (2001)

Photonic crystal planar circuits designed and fabricated in silicon on silicon dioxide are demonstrated. Our structures are based on two-dimensional confinement by photonic crystals in the plane of propagation, and total internal reflection to achieve confinement in the third dimension. These circuits are shown to guide light at 1550 nm around sharp corners where the radius of curvature is similar to the wavelength of light.
Science at LLNL with IBM Blue Gene/Q (2013)

Lawrence Livermore National Laboratory (LLNL) has a long history of working with IBM on Blue Gene® supercomputers. Beginning in November 2001 with the joint announcement of a partnership to expand the Blue Gene research project (including Blue Gene®/L and Blue Gene®/P), the collaboration extends to this day with LLNL planning for the installation of a 96-rack Blue Gene®/Q (called Sequoia) supercomputer. As with previous machines, we envision Blue Gene/Q will be used for a wide array of applications at LLNL, ranging from meeting programmatic requirements for certification to increasing our understanding of basic physical processes. We briefly describe a representative sample of mature codes that span this application space and scale well on Blue Gene hardware. Finally, we describe advances in multi-scale whole-organ modeling of the human heart as an example of breakthrough science that will be enabled with the Blue Gene/Q architecture.
Advances in Electrolytes for Lithium-Ion Batteries: A Mechanistic Understanding (2010)

Abstract not Available.
A system level design approach to UWB localization (2009)

We have developed a novel UWB positioning system with millimeter range 3D accuracy. It is difficult to comprehensively simulate a system of this nature since many disparate components must be simulated including the analog front end, digital backend, UWB channel, 3D tag and base station positions, etc. Only through a novel simulation framework where Agilent advanced design system (ADS) is used, combining its analog/RF and Ptolemy digital simulators and also its Matlab cosimulation is it possible to accurately simulate the positioning system. Experimental results from our UWB positioning system are compared to simulated results to validate the accuracy of our simulation framework. Simulated results show how one stage of automatic gain control can significantly increase operating range while analog-to-digital converter specifications do not significantly affect our overall system performance due to the use of a sub-sampling mixer.
miRPathDB: a new dictionary on microRNAs and target pathways (2016)

In the last decade, miRNAs and their regulatory mechanisms have been intensively studied and many tools for the analysis of miRNAs and their targets have been developed. We previously presented a dictionary on single miRNAs and their putative target pathways. Since then, the number of miRNAs has tripled and the knowledge on miRNAs and targets has grown substantially. This, along with changes in pathway resources such as KEGG, leads to an improved understanding of miRNAs, their target genes and related pathways. Here, we introduce the miRNA Pathway Dictionary Database (miRPathDB), freely accessible at https://mpd.bioinf.uni-sb.de/ With the database we aim to complement available target pathway web-servers by providing researchers easy access to the information which pathways are regulated by a miRNA, which miRNAs target a pathway and how specific these regulations are. The database contains a large number of miRNAs (2595 human miRNAs), different miRNA target sets (14 773 experimentally validated target genes as well as 19 281 predicted targets genes) and a broad selection of functional biochemical categories (KEGG-, WikiPathways-, BioCarta-, SMPDB-, PID-, Reactome pathways, functional categories from gene ontology (GO), protein families from Pfam and chromosomal locations totaling 12 875 categories). In addition to Homo sapiens, also Mus musculus data are stored and can be compared to human target pathways.
Carrier Frequency Offset Estimation in Multiantenna Transmission Systems Based on Single-Carrier Modulation (2008)

The implementation challenges in building compact and low-cost radios for future wireless systems are continuously growing. This is partially due to the introduction of multiantenna transmission techniques, calling for several parallel radio implementations in a single terminal, with considerably reduced implementation resources (size and cost) for individual radios. In this context, one important aspect is the so-called "dirty RF" theme stemming from the unavoidable physical limitations of the used analog electronics. This has started to draw wide attention in both academic and industrial communities. One concrete example is the carrier frequency offset (CFO) problem, caused by frequency instability of the used oscillators and the mobility of the terminals, which can severely degrade the system performance. In this paper, we consider the CFO estimation problem in multi-antenna system context utilizing single-carrier modulation. One efficient pilot based algorithm with built-in diversity against fading channel state is proposed and a lower bound for the estimation error variance is derived analytically. This analysis reveals additional elements for further improving the estimator performance, in terms of pilot structure design. Extensive computer simulations are then used to further assess the estimator performance and to verify the analysis results.
Antimicrobial resistance: the role of aquatic environments (2014)

Antimicrobial resistance is a major concern worldwide. Antibiotics are one of the most used drugs in humans and animals. The intensive use of antimicrobial agents is one of the main factors for the generation of resistant bacteria. Infections with resistant organisms and the emergence of multi-drug resistant pathogenic and non-pathogenic bacteria, represents an urgent global challenge since increases the incidence of morbidity and mortality and decreases the effectiveness of infectious diseases treatments. Many of the encoding antimicrobial resistant genes from human pathogens have originated in natural environments. Anthropogenic activities on aquatic environments, sediments and soils, such as hospital, pharmaceuticals and municipals discharges into rivers and lakes increase the generation of new resistance genes and the spread of resistant bacteria in the environment as well as in public health. This highlights the importance of the environment as a reservoir of resistance genes and dispersal vector. It is necessary to take measures to reduce the introduction and spread of resistant bacteria and its determinants in the environment, which could contain diverse chemicals, antibiotic residues or quaternary ammonium compounds. These measures include the management of wastewater treatment.
Verknüpfung von Mikrokristallen durch kooperative koordinative Wechselwirkungen (2007)

Chemischer Kleber: Koordinative Wechselwirkungen zwischen Zinkionen und Terpyridinliganden wurden genutzt, um selbstorganisierte eindimensionale Anordnungen von Zeolith-L-Kristallen aufzubauen. Durch Verknüpfen von fluorophorhaltigen Zeolithkristallen, in deren Kanälen entweder Pyronin (grün) oder Oxonin (rot) eingelagert war, wurden mehrfarbige, heterochrome Emittersysteme erhalten (siehe Bild).