gebhart/patrepeval huggingface dataset:
Elimination of intermediate species in multiscale stochastic reaction networks (2016)

We study networks of biochemical reactions modelled by continuous-time Markov processes. Such networks typically contain many molecular species and reactions and are hard to study analytically as well as by simulation. Particularly, we are interested in reaction networks with intermediate species such as the substrate-enzyme complex in the Michaelis–Menten mechanism. Such species are virtually in all real-world networks, they are typically short-lived, degraded at a fast rate and hard to observe experimentally. We provide conditions under which the Markov process of a multiscale reaction network with intermediate species is approximated by the Markov process of a simpler reduced reaction network without intermediate species. We do so by embedding the Markov processes into a one-parameter family of processes, where reaction rates and species abundances are scaled in the parameter. Further, we show that there are close links between these stochastic models and deterministic ODE models of the same networks.
Copolymerization of ethylene and propene with a TiCl4/MgCl2‐Al(C2H5)3 catalyst system using a stopped‐flow method (1993)

Abstract Copolymerization of ethylene with a small amount of propene was conducted with a TiCl 4 /MgCl 2 ‐Al(C 2 H 5 ) 3 catalyst system using a stopped‐flow method. With an increase in the polymerization time from 0,035 to 0,145 s, the copolymer yield increases linearly but the number‐average molecular weight of the copolymer showed a tendency of saturation. The rate constants of the propagation reaction as well as the concentrations of active sites were estimated using these data. On the other hand, the 1 H NMR spectra of copolymer did not display the resonances due to CC double bonds which should be formed by chain transfer with monomer and/or by β‐hydrogen elimination. It was also found that the crystallinity of the copolymer decreases to a great extent upon incorporation of even a very small quantity of propylene units. From these results, it was concluded that the apparent rate of copolymerization is not controlled by monomer diffusion through the polymer films. Rather the transfer reaction with Al(C 2 H 5 ) 3 might predominantly take place during the copolymerization.
Cold‐induced secondary dormancy and its regulatory mechanisms in Beta vulgaris (2022)

The dynamic behaviour of seeds in soil seed banks depends on their ability to act as sophisticated environmental sensors to adjust their sensitivity thresholds for germination by dormancy mechanisms. Here we show that prolonged incubation of sugar beet fruits at low temperature (chilling at 5°C, generally known to release seed dormancy of many species) can induce secondary nondeep physiological dormancy of an apparently nondormant crop species. The physiological and biophysical mechanisms underpinning this cold-induced secondary dormancy include the chilling-induced accumulation of abscisic acid in the seeds, a reduction in the embryo growth potential and a block in weakening of the endosperm covering the embryonic root. Transcriptome analysis revealed distinct gene expression patterns in the different temperature regimes and upon secondary dormancy induction and maintenance. The chilling caused reduced expression of cell wall remodelling protein genes required for embryo cell elongation growth and endosperm weakening, as well as increased expression of seed maturation genes, such as for late embryogenesis abundant proteins. A model integrating the hormonal signalling and master regulator expression with the temperature-control of seed dormancy and maturation programmes is proposed. The revealed mechanisms of the cold-induced secondary dormancy are important for climate-smart agriculture and food security.
Mison (2017)

The growing popularity of the JSON format has fueled increased interest in loading and processing JSON data within analytical data processing systems. However, in many applications, JSON parsing dominates performance and cost. In this paper, we present a new JSON parser called Mison that is particularly tailored to this class of applications, by pushing down both projection and filter operators of analytical queries into the parser. To achieve these features, we propose to deviate from the traditional approach of building parsers using finite state machines (FSMs). Instead, we follow a two-level approach that enables the parser to jump directly to the correct position of a queried field without having to perform expensive tokenizing steps to find the field. At the upper level, Mison speculatively predicts the logical locations of queried fields based on previously seen patterns in a dataset. At the lower level, Mison builds structural indices on JSON data to map logical locations to physical locations. Unlike all existing FSM-based parsers, building structural indices converts control flow into data flow, thereby largely eliminating inherently unpredictable branches in the program and exploiting the parallelism available in modern processors. We experimentally evaluate Mison using representative real-world JSON datasets and the TPC-H benchmark, and show that Mison produces significant performance benefits over the best existing JSON parsers; in some cases, the performance improvement is over one order of magnitude.
Reduced-Order Robust Superdirective Beamforming With Uniform Linear Microphone Arrays (2016)

Sensor arrays for audio and speech signal acquisition are generally required to have frequency-invariant beampatterns to avoid adding spectral distortion to the broadband signals of interest. One way to obtain frequency-invariant beampatterns is via superdirective beamforming. However, traditional superdirective beamformers may cause significant white noise amplification (particularly at low frequencies), making them sensitive to uncorrelated white noise. To circumvent the problem of white noise amplification, a method was developed to find the superdirective beamforming filter with a constraint on the white noise gain (WNG), leading to the so-called WNG-constrained superdirective beamformer. But this method damages the frequency invariance of the beampattern. In this paper, we develop a flatness-constrained robust superdirective beamformer. We divide the overall beamformer into two subbeamformers, which are convolved together: one subbeamformer forms a lower order superdirective beampattern while the other attempts to improve the WNG. We show that this robust approach can improve the WNG while limiting the frequency dependency of the beampattern at the same time.
Monkeypox (Mpox) requires continued surveillance, vaccines, therapeutics and mitigating strategies (2023)

The widespread outbreak of the monkeypox virus (MPXV) recognized in 2022 poses new challenges for public healthcare systems worldwide. With more than 86,000 people infected, there is concern that MPXV may become endemic outside of its original geographical area leading to repeated human spillover infections or continue to be spread person-to-person. Fortunately, classical public health measures (e.g., isolation, contact tracing and quarantine) and vaccination have blunted the spread of the virus, but cases are continuing to be reported in 28 countries in March 2023. We describe here the vaccines and drugs available for the prevention and treatment of MPXV infections. However, although their efficacy against monkeypox (mpox) has been established in animal models, little is known about their efficacy in the current outbreak setting. The continuing opportunity for transmission raises concerns about the potential for evolution of the virus and for expansion beyond the current risk groups. The priorities for action are clear: 1) more data on the efficacy of vaccines and drugs in infected humans must be gathered; 2) global collaborations are necessary to ensure that government authorities work with the private sector in developed and low and middle income countries (LMICs) to provide the availability of treatments and vaccines, especially in historically endemic/enzootic areas; 3) diagnostic and surveillance capacity must be increased to identify areas and populations where the virus is present and may seed resurgence; 4) those at high risk of severe outcomes (e.g., immunocompromised, untreated HIV, pregnant women, and inflammatory skin conditions) must be informed of the risk of infection and be protected from community transmission of MPXV; 5) engagement with the hardest hit communities in a non-stigmatizing way is needed to increase the understanding and acceptance of public health measures; and 6) repositories of monkeypox clinical samples, including blood, fluids, tissues and lesion material must be established for researchers. This MPXV outbreak is a warning that pandemic preparedness plans need additional coordination and resources. We must prepare for continuing transmission, resurgence, and repeated spillovers of MPXV.
Piston and bowl for gasoline direct injection compression ignition (GDCI) (2023)

A piston for use in a GDCI engine cooperates with the wall of a cylinder defined in the engine and with a cylinder head to define a combustion chamber. The surface of the piston that faces the cylinder head defines a bowl that is configured to receive fuel that is dispensed from a fuel injector that is located in the cylinder head substantially along the central axis of the cylinder. The bowl is configured such that substantially all of the injected fuel associated with a combustion event reaches a localized equivalence ratio greater than 0.0 and less than or equal to 1.2 at a time immediately preceding initiation of the combustion event.
Attentive Neural Processes and Batch Bayesian Optimization for Scalable Calibration of Physics-Informed Digital Twins (2021)

Physics-informed dynamical system models form critical components of digital twins of the built environment. These digital twins enable the design of energy-efficient infrastructure, but must be properly calibrated to accurately reflect system behavior for downstream prediction and analysis. Dynamical system models of modern buildings are typically described by a large number of parameters and incur significant computational expenditure during simulations. To handle large-scale calibration of digital twins without exorbitant simulations, we propose ANP-BBO: a scalable and parallelizable batch-wise Bayesian optimization (BBO) methodology that leverages attentive neural processes (ANPs).
Survey Results of the Expert Meeting on Laparoscopic Living Donor Hepatectomy and Literature Review (2017)

This survey and literature review show that laparoscopic donor hepatectomy is performed by experienced surgeons in selected cases, and that its incidence is increasing worldwide.
High-order Galerkin method for Helmholtz and Laplace problems on multiple open arcs (2020)

We present a spectral Galerkin numerical scheme for solving Helmholtz and Laplace problems with Dirichlet boundary conditions on a finite collection of open arcs in two-dimensional space. A boundary integral method is employed, giving rise to a first kind Fredholm equation whose variational form is discretized using weighted Chebyshev polynomials. Well-posedness of the discrete problems is established as well as algebraic or even exponential convergence rates depending on the regularities of both arcs and excitations. Our numerical experiments show the robustness of the method with respect to number of arcs and large wavenumber range. Moreover, we present a suitable compression algorithm that further accelerates computational times.
The farnesoid X receptor induces fetuin-B gene expression in human hepatocytes (2007)

FXR (farnesoid X receptor), a nuclear receptor activated by BAs (bile acids), is a key factor in the regulation of BA, lipid and carbohydrate metabolism. The recent development of synthetic FXR agonists and knockout mouse models has accelerated the discovery of FXR target genes. In the present study, we identify human fetuin-B as a novel FXR target gene. Treatment with FXR agonists increased fetuin-B expression in human primary hepatocytes and in the human hepatoma HepG2 cell line. In contrast, fetuin-B expression was not responsive to FXR agonist treatment in murine primary hepatocytes. Fetuin-B induction by FXR agonist was abolished upon FXR knockdown by siRNA (small interfering RNA). In addition to the previously described P1 promoter, we show that the human fetuin-B gene is also transcribed from an alternative promoter, termed P2. Transcription via the P2 promoter was induced by FXR agonist treatment, whereas P1 promoter activity was not sensitive to FXR agonist treatment. Two putative FXR-response elements [IR-1 (inverted repeat-1)] were identified in the region -1.6 kb upstream of the predicted P2 transcriptional start site. Both motifs bound FXR-RXR (retinoid X receptor) complexes in vitro and were activated by FXR in transient transfection reporter assays. Mutations in the IR-1 sites abolished FXR-RXR binding and activation. Taken together, these results identify human fetuin-B as a new FXR target gene in human hepatocytes.
Search for resonant WZ production in the fully leptonic final state in proton–proton collisions at $$\mathbf {\sqrt{s} = 13}$$ TeV with the ATLAS detector (2023)

Abstract A search for a WZ resonance, in the fully leptonic final state (electrons or muons), is performed using 139 fb $$^{-1}$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msup> <mml:mrow/> <mml:mrow> <mml:mo>-</mml:mo> <mml:mn>1</mml:mn> </mml:mrow> </mml:msup> </mml:math> of data collected at a centre-of-mass energy of 13 TeV by the ATLAS detector at the Large Hadron Collider. The results are interpreted in terms of a singly charged Higgs boson of the Georgi–Machacek model, produced by WZ fusion, and of a Heavy Vector Triplet, with the resonance produced by WZ fusion or the Drell–Yan process. No significant excess over the Standard Model prediction is observed and limits are set on the production cross-section times branching ratio as a function of the resonance mass for these processes.
ChemInform Abstract: Chemistry, Pharmacology, and Clinical Efficacy of the Chinese Nootropic Agent Huperzine A (1999)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Identifying The True Echo Path Impulse Responses In Stereophonic Acoustic Echo Cancellation (1996)

Publication in the conference proceedings of EUSIPCO, Trieste, Italy, 1996
HF oder UHF – Welche Frequenz darf es sein? : Vor- und Nachteile der gängigen RFID-Technologien (2016)

Die Frage nach der Funkfrequenz eines Radio-Frequency-Identification-Systems (RFID-Systems) ist in etwa wie die Frage nach der PS-Zahl eines Autos: Eigentlich keine primäre Kennzahl für den Anwender wie Höchstgeschwindigkeit oder Beschleunigungsverhalten, aber aufgrund ihrer technischen Bedeutung trotzdem maßgeblich. Ähnlich verhält es sich bei RFID: Zwar stehen eigentlich Eckdaten wie Reichweite, Speicherkapazität oder auch Kosten im Vordergrund. Doch die verwendete Frequenz ist so bedeutend für die Eigenschaften eines RFID-Systems, dass man auch als reiner Anwender kaum an der Frage »HF oder UHF?« vorbei kommt.
Molecular genetics of the fibrinolytic and coagulation systems in haemostasis, thrombogenesis, restenosis and atherosclerosis (1997)

The plasminogen and coagulation systems have been extensively characterized at the biochemical level. Recent gene targeting and gene transfer studies have provided novel insights into their role in the formation of blood vessels and in the pathogenesis of blood vessel disorders including thrombosis, restenosis and atherosclerosis.
Real-Time Colour Doppler Imaging for HIFU Therapy Guidance (2005)

This study is an investigation of interference and blooming artifacts in real‐time color Doppler imaging during High‐Intensity Focused Ultrasound (HIFU) therapy to improve the field of view (FOV) and distinguish blood vessels from the artifacts. It is hypothesized that the interference and blooming artifacts are caused by incoherent interference between HIFU and imaging signals and inertial cavitation/boiling, respectively. The incoherent interference shifts the tissue velocity estimates toward the Nyquist limits in standard autocorrelation‐based estimation. The interference artifact is removed by applying a threshold according to the acceleration in tissue velocity estimation. The effects of inertial cavitation and/or boiling (i.e., broadband spectrum and high amplitude) in the blooming artifact are analyzed by measuring the standard deviation of phase differences, the average difference between adjacent eigenvalues and the average power. From in vivo rabbit experiments, due to its broadband spectrum, while the standard deviation of phase differences in the blooming artifact (0.0959 ± 0.0368 PRF) is significantly increased compared to the normal blood vessels (0.0078 ± 0.0013 PRF), the average difference between adjacent eigenvalues in the blooming artifact (−35.0 ± 8.6 dB) is moderately changed compared to those in the normal blood vessels (i.e., −58.6 ± 4.6 dB). The average power in the blooming artifact (i.e., 48.0 ± 12.7) is also increased compared to the normal blood vessels (i.e., 6.2 ± 1.2). This broadband and high amplitude signature could be utilized to remove this blooming artifact by thresholding after further investigation to distinguish the target blood vessel from the artifact.
Analysis of In Vitro Migration Patterns of Human Spermatozoa by a Petri Dish-Based Horizontal Column1 (1999)

Spermatozoa are required to travel a considerable distance in vivo to meet the oocyte at the fertilization site. However, none of the existing in vitro tests critically evaluates migration of sperm to assess their potential of reaching the oocyte. On the other hand, an in vivo model is not suitable for this type of study because of ethical and technical constraints. In the present study we utilized a horizontal column technique to analyze sperm migration. Migratory characteristics of fresh, unwashed semen sperm and sperm undergoing various treatments were examined in vitro using a Petri dish-based horizontal fluid column. The procedure involved loading a sperm sample into the column and determining sperm concentration, motility, and viability at different column segments for different migration durations (6, 12, 24, 48, and 72 h). All sperm samples produced an exponential migration pattern in all durations of migration. Propagation along the column edge, tendency to exit from the column, and hiding in the blind pouches were some of the important characteristic features exhibited by the migratory sperm. Variations in migration patterns were documented among semen donors, between fresh and frozen semen, and between washed and unwashed sperm. Prolonged postejaculation time diminished migratory potential. The recovery of sperm in the column end was independent of seminal variables with the exception of oligozoospermia. These observations suggest that the Petri dish-based horizontal column is effective for analyzing sperm migration characteristics for prolonged periods. The potential of this migration assay in predicting the in vivo potential of spermatozoa to reach the fertilization site will be worth exploring.
Photochromism of 4-cyanophenylazobenzene in liquid crystalline-coil AB diblock copolymers: the influence of microstructure (2000)

The UV and V spectral features of an AB diblock copolymer composed of polystyrene and a poly(1,2 & 3,4)isoprene-based polymer with a pendant liquid crystalline 4-cyanophenylazobenzene (Az) group in comparison with those of a corresponding LC polyisoprene homopolymer are reported. The orientational and photochromic behavior of an AB diblock copolymer in thin films shows distinct differences from that of a corresponding Az homopolymer. This can be attributed to the influence of the phase separated polymer coil microdomain of polystyrene in the AB block copolymer film.
Substrate Modulation of the Activity of an Artificial Nanoesterase Made of Peptide‐Functionalized Gold Nanoparticles (2006)

Nanozyme mit einem Herz aus Gold: Durch das Aufpfropfen eines Dodecapeptids auf die Oberfläche von Goldnanopartikeln (siehe Bild) ließ sich ein funktionelles künstliches Protein herstellen. Dieses System katalysiert die Hydrolyse von Carbonsäureestern und zeigt enzymartige Eigenschaften.
Mn x Pt 1−x : A new exchange bias material for Permalloy (1997)

We report exchange biasing of Permalloy in as-grown MnxPt1−x/Permalloy structures grown by coevaporation in ultra-high vacuum. Polycrystalline and epitaxial structures with x between 0.35 and 0.75 were studied. X-ray diffraction confirms the presence of chemical ordering in the MnxPt1−x films (grown at 200 °C) in as-grown polycrystalline and epitaxial structures. An interfacial coupling energy of 0.032 erg/cm2 is found for structures where the MnxPt1−x (x=0.56) is grown at 200 °C onto epitaxial Permalloy (001). Polycrystalline structures have a smaller (0.027 erg/cm2) interfacial coupling energy. No exchange bias is observed for films with x≲0.4. The blocking temperature, for a sample with x=0.56, is &amp;gt;500 K.
Therapeutic Antibodies—Protein Engineering to InfluenceADME,PK, and Efficacy (2015)

Abstract This chapter focuses on protein engineering strategies to reduce nonspecific uptake. One of those strategies tries to reduce the isoelectric point (pI) of the antibody by protein engineering, which can be an effective way to reduce nonspecific cellular uptake as well as improve various pharmacokinetic properties of the antibody. The authors have developed a technology to reduce target‐mediated clearance by adding a pH‐dependent antigen binding property to the therapeutic antibody, thereby increasing its chances of being recycled. For antibodies targeting soluble antigens, conventional antibodies still face significant drawbacks even if their pharmacokinetic profile is in the acceptable range. In some cases, higher concentrations of the therapeutic antibody are needed due to this accumulation of antigen, which may require substantially higher dose levels. The authors have also developed a technology to reduce antigen accumulation by optimized pH‐dependent antigen binding and increased affinity to neonatal Fc receptor (FcRn) or Fcγ receptors (FcγRs).