gebhart/patrepeval huggingface dataset:
Resequencing of 414 cultivated and wild watermelon accessions identifies selection for fruit quality traits (2019)

Fruit characteristics of sweet watermelon are largely the result of human selection. Here we report an improved watermelon reference genome and whole-genome resequencing of 414 accessions representing all extant species in the Citrullus genus. Population genomic analyses reveal the evolutionary history of Citrullus, suggesting independent evolutions in Citrullus amarus and the lineage containing Citrullus lanatus and Citrullus mucosospermus. Our findings indicate that different loci affecting watermelon fruit size have been under selection during speciation, domestication and improvement. A non-bitter allele, arising in the progenitor of sweet watermelon, is largely fixed in C. lanatus. Selection for flesh sweetness started in the progenitor of C. lanatus and continues through modern breeding on loci controlling raffinose catabolism and sugar transport. Fruit flesh coloration and sugar accumulation might have co-evolved through shared genetic components including a sugar transporter gene. This study provides valuable genomic resources and sheds light on watermelon speciation and breeding history.
Chemopreventive apigenin controls UVB-induced cutaneous proliferation and angiogenesis through HuR and thrombospondin-1 (2014)

Plant flavonoid apigenin prevents and inhibits UVB-induced carcinogenesis in the skin and has strong anti-proliferative and anti-angiogenic properties. Here we identify mechanisms, by which apigenin controls these oncogenic events. We show that apigenin acts, at least in part, via endogenous angiogenesis inhibitor, thrombospondin-1 (TSP1). TSP1 expression by the epidermal keratinocytes is potently inhibited by UVB. It inhibits cutaneous angiogenesis and UVB-induced carcinogenesis. We show that apigenin restores TSP1 in epidermal keratinocytes subjected to UVB and normalizes proliferation and angiogenesis in UVB-exposed skin. Importantly, reconstituting TSP1 anti-angiogenic function in UVB-irradiated skin with a short bioactive peptide mimetic representing exclusively its anti-angiogenic domain reproduced the anti-proliferative and anti-angiogenic effects of apigenin. Cox-2 and HIF-1α are important mediators of angiogenesis. Both apigenin and TSP1 peptide mimetic attenuated their induction by UVB. Finally we identified the molecular mechanism, whereby apigenin did not affect TSP1 mRNA, but increased de novo protein synthesis. Knockdown studies implicated the RNA-binding protein HuR, which controls mRNA stability and translation. Apigenin increased HuR cytoplasmic localization and physical association with TSP1 mRNA causing de novo TSP1 synthesis. HuR cytoplasmic localization was, in turn, dependent on CHK2 kinase. Together, our data provide a new mechanism, by which apigenin controls UVB-induced carcinogenesis.
Neurally Selected Embryonic Stem Cells Induce Tumor Formation after Long-Term Survival following Engraftment into the Subretinal Space (2004)

Although ES cells may provide treatment for degenerative disease in the future, their unlimited self-renewal and high differentiation potential poses the risk of tumor induction after engraftment. Thus, more care must be taken before using ES cell transplantation as a therapeutic option for patients with degenerative disease.
&lt;title&gt;Fluorescence lifetime imaging (FLIM): simulation and error analysis&lt;/title&gt; (2000)

Real-time monitoring of reorganization and molecular interactions of live cellular components on a precise spatial and temporal scale, requires a high-speed and high- sensitivity imaging system. Theoretically, excited state fluorescence lifetime imaging techniques provide high temporal resolution for dynamics studies of biological samples. In order to provide a comprehensive foundation for the development of the technique, we simulated images using the decay and normal equations for a single component with different windowing schemes. In this model we varied several parameters involved in the simulation to produce images under different theoretical conditions. To obtain a realistic result, we considered equations for noise due to readout, dark current, photon shot noises, and other factors. In addition, the simulant was validated using sample decay images with known lifetimes, which were obtained with current fluorescent decay systems. The software developed through this research is intended to create a compete tutorial describing the theory and procedures of lifetime image acquisition. This theoretical simulation is verified with experiments using known fluorophore lifetimes.© (2000) COPYRIGHT SPIE--The International Society for Optical Engineering. Downloading of the abstract is permitted for personal use only.
Resolution enhancement in nonlinear photoacoustic imaging (2015)

Nonlinear processes can be exploited to gain access to more information than is possible in the linear regime. Nonlinearity modifies the spectra of the excitation signals through harmonic generation, frequency mixing, and spectral shifting, so that features originally outside the detector range can be detected. Here, we present an experimental study of resolution enhancement for photoacoustic imaging of thin metal layers immersed in water. In this case, there is a threshold in the excitation below which no acoustic signal is detected. Above threshold, the nonlinearity reduces the width of the active area of the excitation beam, resulting in a narrower absorption region and thus improved spatial resolution. This gain is limited only by noise, as the active area of the excitation can be arbitrarily reduced when the fluence becomes closer to the threshold. Here, we demonstrate a two-fold improvement in resolution and quantify the image quality as the excitation fluence goes through threshold.
Platform for patient-specific finite-element modeling and application for radiofrequency ablation (2012)

Finite element (FE) simulation is frequently used in biophysics problems, but applications using patient-specific geometry have been limited since generating patient-specific meshes is tedious and requires use of multiple software tools. We present a research tool as well as a workflow to generate patient-specific finite element models and demonstrate this tool for simulation of radiofrequency (RF) ablation−a commonly used clinical procedure for localized thermal cancer treatment where patient-specific simulation would allow computer-aided treatment planning. Our research tool allows pre- and post-processing of patient-specific models and provides integration with commercial FE software. Based on a liver cancer patient's CT data set, 3D geometry of bone, liver, tumor, and vessels was derived following tissue segmentation. A RF electrode was placed interactively within the tumor via our tool, and surfaces, as well as volumes, were meshed with triangular and tetrahedral meshes, respectively. Subsequently, tissue heating surrounding the RF electrode and vascular cooling were simulated via commercial FE software, and tissue temperature at the end of a 12-min ablation procedure was visualized as overlay over the patient's CT data with our tool. Simulations such as the one presented may provide additional information for the treating physician for more effective pretreatment planning of procedures. The presented tool may have additional applications in other areas where biophysical simulation of biomedical problems (e.g., biomechanical, bioelectrics) on patient-specific geometry is of interest.
Real free space antenna factors for validating completely absorber lined chambers? (2002)

The validation of a completely absorber lined chamber (CALC) turned out to be difficult. The first attempt was made with antennas calibrated on an open area test site (OATS). In this case a correction factor was necessary, this factor is related to the ground reflection and thus to the antennas. The validation started with determining the real free space antenna factors (AF/sub FS/). These real free space antenna factors were used for new site attenuation measurements in the CALC. The goal has been to validate the CALC by means of practical measurements. As a result the CALC can meet the normalized site attenuation (NSA) requirements. Because of near field effects and mutual coupling a minor problem area below 80 MHz remains, this problem was not dealt with. In our opinion the CALC should replace the OATS as the reference site. In conclusion, a CALC is the best test site for compliance testing for both immunity and emission, and all radiated EMC-measurements should be normalized to free space.
The role of impact in the stability of bipedal locomotion (1986)

A mathematical model of a simple inverted double-pendulum locomotion system was developed. The stability of the nonlinear model was analysed. Periodic impact of the system with the ground plays a major role in the achievement of stable locomotion. Phase-plane portraits of the generalized coordinates and velocities were utilized to study the behaviour of the system.
eDoS Mitigation for Autonomic Management on Multi-Tier IoT (2018)

In this age of the Internet of Things and ubiquitous computing, autonomic management has become a critical component in cloud platforms. Autonomic management helps systems adapt seamlessly and efficiently to rapidly fluctuating workloads. However, economic Denial of Sustainability (eDoS) attacks can directly target the autonomic management to waste resources. In this paper, we propose an eDoS mitigation framework that incorporates online anomaly detection with our Elascale autonomic management system to thwart eDoS attacks in real-time. This allows the detection system to be application-agnostic as this framework utilizes only resource statistics of the monitoring applications. We present the design and implementation of our anomaly detection framework with Elascale. We evaluate Hierarchical Temporal Memory (HTM) and Tukey with Relative Entropy against spatial and temporal anomalies. Our results prove that the HTM-based anomaly detection method outperforms with significant accuracy.
Derivation of logarithmic integrals expressed in teams of the Hurwitz zeta function (2020)

In this paper by means of contour integration we will evaluate definite integrals of the form $ \begin{equation*} \int_{0}^{1}\left(\ln^k(ay)-\ln^k\left(\frac{a}{y}\right)\right)R(y)dy \end{equation*} $ in terms of a special function, where $R(y)$ is a general function and $k$ and $a$ are arbitrary complex numbers. These evaluations can be expressed in terms of famous mathematical constants such as the Euler's constant $\gamma$ and Catalan's constant $C$. Using derivatives, we will also derive new integral representations for some Polygamma functions such as the Digamma and Trigamma functions along with others.
Studies on syntheses and permeabilities of special polymer membranes. 22. Ultrafiltration characteristics and membrane structure of cellulose nitrate membranes (1981)

Abstract The formation mechanism of anisotropic polymer membranes formed by a system of cellulose nitrate (CN)/n‐propyl alcohol (n‐PrOH)/N,N‐dimethyl formamide (DMF) was investigated. The ultrafiltration characteristics and the membrane structure were influenced significantly by the casting solvents (ratio of n‐PrOH to DMF) and the evaporation period during the membrane formation process. The finger‐like structure in the sponge layer was observed in all systems except that of n‐PrOH/DMF = 2/1 and increased with the evaporation period, after 2 min in the system of pure DMF and after 5 min in the system of n‐PrOH/DMF = 1/3. The formation mechanism of the anisotropic CN membranes and the ultrafiltration characteristics were discussed in detail.
Photoinduced Ratchet‐Like Rotational Motion of Branched Molecular Crystals (2016)

Photomechanical molecular crystals can undergo a variety of light-induced motions, including expansion, bending, twisting, and jumping. The use of more complex crystal shapes may provide ways to turn these motions into useful work. To generate such shapes, pH-driven reprecipitation has been used to grow branched microcrystals of the anthracene derivative 4-fluoroanthracenecarboxylic acid. When these microcrystals are illuminated with light of λ=405 nm, an intermolecular [4+4] photodimerization reaction drives twisting and bending of the individual branches. These deformations drive a rotation of the overall crystal that can be repeated over multiple exposures to light. The magnitude and direction of this rotation vary because of differences in the crystal shape, but a typical branched crystal undergoes a 50° net rotation after 25 consecutive irradiations for 1 s. The ability of these crystals to undergo ratchet-like rotation is attributed to their chiral shape.
Dynamic probabilistic networks for modelling and identifying dynamic systems: a MCMC approach (1997)

In this article we deal with the problem of interpreting data coming from a dynamic system by using causal probabilistic (CPN), a probabilistic graphical model particularly appealing in Intelligent Data Analysis. We discuss the different approaches presented in the literature, outlining their pros and cons through a simple training example. Then, we present a new method for reconstructing the state of the dynamic system, based on Markov Chain Monte Carlo algorithms, called dynamic probabilistic network smoothing (DPN-smoothing). Finally, we present an example of the application of DPN-smoothing in the field of signal deconvolution.
&lt;title&gt;Electronic noise in nanoelectronic building elements for nanoMEMS and bioMEMS&lt;/title&gt; (2002)

One of the most widely known effects in nano electronics is the Coulomb-blocked effect which reduces the shot noise in a device. However, the effect of shrinking of the size is not always so beneficial, shot noise can even increase, because of other effects. Moreover, other types of noises and new effects can set strong limits for device performance. From classical knowledge on device noise, an increased 1/f noise and increased effective thermal noise voltage and quantum uncertainty noises are expected which imply performance limitations at the low frequency and high frequency ends, respectively. The results is a reduced long-term stability an increased frequency of false-bit-switching or false alarm events. These considerations can help us to understand why biology is using neural spikes. From the research-and- development side, the original and engineering of conductance noise is often an unsolved problem. For example, in carbon nanotubes, the published experimental results are contradictory and it is not possible to draw a final conclusion about the nature and possible ways of engineering this crucial kind of noise source. It is important to realize that more active noise sources do not always mean limitation of performance. In chemical sensing applications, the measurement of noise can be used to detect chemical agents and their composition with a great selectivity and sensitivity, because the chemical fragments dynamically interact with the current transport in the device. This is the situation when the noise in nano-sensors has a great advantage as compared to the noise in classical devices. The increased specific surface of nanostructures and the large number of possible structural combinations have a great potential for both gas and fluid sensing application s via noise analysis.
Grapevine fanleaf virus detection in various grapevine organs using polyclonal and monoclonal antibodies (2015)

Monoclonal antibodies prepared with grapevine fanleaf virus (GFV) are useful for detecting the virus in plant extracts. In this paper we describe comparisons between different ELISA techniques using rabbit and chicken immunoglobulins as weil as monoclonal antibodies (MCA). The technique using chicken immunoglobulins for coating the plates followed by MCA and goat anti-mouse phosphatase conjugate was the best one for detecting GFV in plant sap. In this technique, ascitic fluids containing MCA could be diluted up to 10-6. Our experiments clearly demonstrate that the detection of GFV is possible in grapevine not only from leaves or rootlets, but also from wood shavings, without grinding them. We replaced the classical nicotine containing extraction medium by a harmless phosphate or Tris-HCl buffer. To detect GFV with these media it is essential that the buffer should contain polyvinylpyrrolidone and that its molarity should not be less than 0.1 M.
Repolarization of tumor infiltrating macrophages and increased survival in mouse primary CNS lymphomas after XPO1 and BTK inhibition (2020)

These data highlight the pathogenic role of the innate immune microenvironment in PCNSL and provide pre-clinical evidence for the development of selinexor and ibrutinib as a new promising therapeutic option with cytotoxic and immunomodulatory potential.
Impact of dexamethasone on the incidence of ventilator-associated pneumonia in mechanically ventilated COVID-19 patients: a propensity-matched cohort study (2022)

NCT04388670, retrospectively registered May 14, 2020.
Structures of New Sesquiterpenes from Curcuma comosa (2008)

From the methanolic extract of the rhizomes of Curcuma comosa cultivated in Thailand, six new sesquiterpenes, (+)- and (-)-comosols (1, 2), comosones I (3), II (4), and III (5), and dimethoxycurcumenone (6), were isolated. Their structures were elucidated on the basis of chemical and physicochemical evidence.
Fabrication of a Portable Electrochemiluminescence-induced Fluorescence Detection Chip with Microfluidic Excitation Source for Point-of-care Diagnostics (2015)

In this study, we propose an electrochemiluminescence (ECL)-induced fluorescence detection chip toward portable point-of-care diagnostics. A prototype chip consists of polydimethylsiloxane (PDMS)-based flow channels for target samples and on-demand multi-color microfluidic excitation sources. The microfluidic ECL cells were fabricated via a heterogeneous bonding technique through the use of self-assembled monolayers. The flow channels for target samples, which were formed by soft lithography, were combined with the excitation source. A pink fluorescence of resorufin was successfully detected with yellow ECL emission of 5,6,11,12-tetraphenyltetracene (rubrene). The proposed principle can open a new possibility for on-onsite multiple fluorescence detections.
Effective Perforating and Gravel Placement: Key to Low Skin, Sand-Free Production in Gravel Packs (2009)

Abstract Cased-hole gravel packing is commonly utilized to control sand production from oil and gas wells. The success of a cased-hole gravel-pack job depends on the ability to effectively pack perforation tunnels, which act as conduits between the reservoir and the wellbore for hydrocarbon production. This project presents a system approach for removal of perforation damage, effective gravel placement, and packing of the perforation tunnels. It was found that surging the perforations greatly increased the ability to pack the perforation tunnels and improved the connectivity to the reservoir. Guidelines to surging the formation and executing the perforation packing job are presented. This study also discusses the current practices commonly employed in cased-hole gravel packing to pack perforation tunnels and the potential limitations of these practices. Incomplete packing of perforation tunnels is mostly encountered in gravel-pack jobs completed with brine as the carrier fluid (water packs). The proposed technique involves surging the perforations prior to the gravel-pack operation, followed by pumping the gravel slugs in a nondamaging carrier fluid in concentrations ranging from 1 to 3 ppa. These slugs range from 5 to 7 bbl and are pumped intermittently between stages of the completion fluid to minimize cost. The carrier fluid, by virtue of its viscosity and mechanical suspension capability, ensures that the gravel enters the perforations. This technique was successfully implemented at the Abu Cluster field in west Malaysia. This reservoir had extremely high permeability (1.5 to 3 Darcy), with sand production a major concern. Several jobs were completed with the above mentioned technique and perforation packing factors improved from 10 to 40 lb of gravel per foot of perforations. Discussion of the placement and production data is presented. Sand-free production has been achieved with reduced drawdown across the sandface and production rates as high as 5,000 BOPD.
Aufbau von Subskriptionssystemen (2002)

Datenbanksysteme bilden einen zentralen Baustein moderner IT-Infrastruktur. Neben klassischen Aufgaben, wie die Erbringung transaktionaler Dienste (OLTP, ’Online Transaction Processing’; [GrRe93]), werden Datenbanksysteme immer mehr in auswertungsorientierten Anwendungsgebieten eingesetzt. Schlagworte wie ’Data Warehouse Systeme’ ([BaGü0l], [Inmo92], [Kimb96]), ‘Online Analytical Processing’ (OLAP; [CoCS93]) oder ’Decision Support Systeme’ (DSS; [TuAr00]) haben sich in den letzten Jahren einen festen Platz sowohl in der Forschungsgemeinschaft als auch im kommerziellen Bereich gesichert. Nachfragegetriebene Informationsbereitstellung erscheint jedoch, wie bereits in der Einleitung zu diesem Buch argumentiert, mit Blick auf die Entwicklungstendenzen von Einsatzbereichen für Datenbanksysteme (Tabelle 1.1 auf Seite 49), durch eine angebotsgetriebene und auf dem Subskriptionsmodell beruhende Informationsversorgung ergänzungsbedürftig ([Rade97]). Ein Versuch, eine derartige Ergänzung datenbankbasierter Informationssysteme zu vollziehen, wird in diesem Kapitel vorgenommen, so dass aus allgemeiner Perspektive nach der ablauforientierten Aufarbeitung im vorangegangenen Kapitel die datenzentrierte Sichtweise in den folgenden Ausführungen im Vordergrund steht.
Long-term outcome of congenital aortic valve stenosis: predictors of reintervention (2014)

Aortic valve intervention is a safe and effective procedure for congenital aortic stenosis with excellent survival results. However, rate of reintervention is high and influenced by increased left ventricular posterior wall thickness pre-intervention, prior balloon valvuloplasty, higher residual peak systolic valve gradient, and more than mild regurgitation post-intervention. The study highlights that long-term follow-up is recommended for these patients.
Influence of Ionic Liquids on the Viscoelastic Properties of Crude Oil Emulsions (2017)

Thermochemical treatments are traditionally employed to perform the separation between the oil and water phases in the petroleum industry. The chemical agents have the function of reducing the barrier rigidity formed by natural surfactants present in the emulsion, thus favoring destabilization. The main objective of this study was to analyze the viscoelastic properties of samples composed of water and a crude oil with the addition of distinct ionic liquids. The methodology used to obtain the interfacial properties was the pedant drop technique. The results showed that the addition of the ionic liquids induced a reduction in the interfacial elasticity and an increase in the compressibility of interfacial films. It was also observed that an enhancement in the alkyl chain length has a positive effect on changing the interfacial properties. The ionic liquid with the highest alkyl chain length investigated ([C12min]+[NTf2]−) showed the ability to produce the more elastic films for the crude oil investigated.
Cyber physical attacks with control objectives and detection constraints (2016)

This paper studies attackers with control objectives and explicit detection constraints against cyber-physical systems. The cyber-physical system is equipped with a Kalman filter and an attack detector that uses the innovations process of the Kalman filter. The attacker performs an integrity attack on the actuators and sensors of the system with the aim of moving the system to a target state under the constraint that the probability of him or her being detected is equal to the false alarm probability of the attack detector. We formulate and solve a constrained optimization problem that gives the optimal sequence of attacks and demonstrate our attack strategy in a numerical example.