gebhart/patrepeval huggingface dataset:
Integration of Contours Defined by Second-Order Contrast-Modulation of Texture (2019)

A BSTRACT Boundaries in the visual world can be defined by changes in luminance and texture in the input image. A “contour integration” process joins together local changes into percepts of lines or edges. A previous study tested the integration of contours defined by second-order contrast-modulation. Their contours were placed in a background of random wavelets. Subjects performed near chance. We re-visited second-order contour integration with a different task. Subjects distinguished contours with “good continuation” from distractors. We measured thresholds in different amounts of external orientation or position noise. This gave two noise-masking functions. We also measured thresholds for contours with a baseline curvature to assess performance with more curvy targets. Our subjects were able to discriminate the good continuation of second-order contours. Thresholds were higher than for first-order contours. In our modelling, we found this was due to multiple factors. There was a doubling of equivalent internal noise between first- and second-order contour integration. There was also a reduction in efficiency. The efficiency difference was only significant in our orientation noise condition. For both first- and second-order stimuli, subjects were also able to perform our task with more curved contours. We conclude that humans can integrate second-order contours, even when they are curved. There is however reduced performance compared to first-order contours. We find both an impaired input to the integrating mechanism, and reduced efficiency seem responsible. Second-order contour integration may be more affected by the noise background used in the previous study. Difficulty segregating that background may explain their result.
Nonlinear Model Predictive Control of Advanced Engines Using Discretized Nonlinear Control Oriented Models (2010)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;This paper proposes a methodology to develop a nonlinear model predictive control (NMPC) of a dual-independent variable valve timing (di-VVT) engine using discretized nonlinear engine models. In multiple-input-multiple-output (MIMO) systems, model based control methodologies are critical for realizing the full potential of complex hardware. Fast and accurate control oriented models (COM) that capture combustion physics, actuator and system dynamics are prerequisites for developing NMPC. We propose a multi-scale simulation approach to generate the non-linear combustion model, where the high-fidelity engine cycle simulation is utilized to characterize effects of turbulence, air-to-fuel ratio, residual fraction, and nitrogen oxide (NOx) emissions. The input-to-output relations are subsequently captured with artificial neural networks (ANNs). Manifold and actuator dynamics are discretized to reduce computation efforts. The discretized models are capable of handling nonlinearity of dynamics models caused by varying time steps depending on engine speeds and other inherent characteristics. The models are realized using system identification based on autoregressive ANNs. Then, NMPC is designed to achieve requested torque responses and to track the optimal actuator responses closely. The latter is important for eliminating excursions of residual and associated emissions penalty during a transient. NMPC using discretized models is capable of achieving dead-beat like control with much shorter computation time and with short prediction and control horizons.&lt;/div&gt;&lt;/div&gt;
The new advanced membrane gas exchanger (2011)

Current membrane oxygenators are constructed for patients with a body surface under 2.2 m(2). If the body surface exceeds 2.5 m(2), commercially available devices may not allow adequate oxygenation during cardiopulmonary bypass. To address this, a hollow-fiber oxygenator with an enlarged contact surface of 1.81 m(2) was tested. In an experimental set-up, six calves of mean weight 85.4 ± 3 kg were connected to cardiopulmonary bypass. They were randomly assigned to a standard oxygenator (n = 3; ADMIRAL, Euroset, Medola, Italy) with a surface of 1.35 m(2) or to an enlarged surface oxygenator (n = 3; AMG, Euroset). Blood samples were taken before bypass, after 10 min on bypass, and after 1, 2, 5 and 6 h of perfusion. Analysis of variance was used for repeated measurements. The mean flow rate was 6.5 l/min for 6 h. The total oxygen transfer at 6 h was significantly higher in the high-surface group (P < 0.05). Blood trauma, evaluated by plasma hemoglobin and lactate dehydrogenase levels, did not detect any significant hemolysis. Thrombocytes and white blood cell count profiles showed no significant differences between the two groups at 6 h of perfusion (P = 0.06 and 0.80, respectively). At the end of testing, no clot deposition was found in the oxygenator, and there was no evidence of peripheral emboli. The results suggest that the new oxygenator allows very good gas transfer and may be used for patients with a large body surface area.
A convenient synthesis of polyacetylene (1980)

K. Soga, Y. Kobayashi, S. Ikeda and S. Kawakami, J. Chem. Soc., Chem. Commun., 1980, 931 DOI: 10.1039/C39800000931
Integrating natriuretic peptides and diastolic dysfunction to predict adverse events in high-risk asymptomatic subjects (2020)

The DAVID-Berg data suggest that we look for the quite common combination of diastolic dysfunction/high natriuretic peptides to correctly identify asymptomatic subjects at greater risk for incident heart failure/death, thus more suitable for preventive interventions.
Oligonucleotide Analogues with a Nucleobase-Including Backbone, Part 5, 2′-Deoxy-8-(hydroxymethyl)adenosine- and 2′-Deoxy-6-(hydroxymethyl)uridine-Derived Phosphoramidites: Synthesis and Incorporation into 14-Mer DNA Strands (2001)

The pairing propensity of new DNA analogues with a phosphinato group between O−C(3′) and a newly introduced OCH2 group at C(8) and C(6) of 2′-deoxyadenosine and 2′-deoxyuridine, respectively, was evaluated by force-field calculations and Maruzen model studies. These studies suggest that these analogues may form autonomous pairing systems, and that the incorporation of single modified units into DNA 14mers is compatible with duplex formation. To evaluate the incorporation, we prepared the required phosphoramidites 3 and 4 from 2′-deoxyadenosine and 2′-deoxyuridine, respectively. The phosphoramidite 5 was similarly prepared to estimate the influence of a CH2OH group at C(8) on the duplex stability. The modified 14-mers 6 – 9 were prepared by solid-phase synthesis. Pairing studies show a decrease of the melting temperature by 2.5° for the duplex 13⋅9, and of 6 – 8° for the duplexes 10⋅6, 11⋅6, 13⋅7, and 14⋅8, as compared to the unmodified duplexes.
IDENTIFICATION OF SELETIVE CLAUDIN CATION CHANNEL BLOCKERS (2021)

Abstract Compromised epithelial barrier function is known to be associated with inflammatory bowel disease (IBD) and may contribute to disease development. One mechanism of barrier dysfunction is increased expression of paracellular tight junction ion and water channels formed by claudins. Claudin-2 and -15 are two such channels. We hypothesize that blocking these channels could be a viable therapeutic approach to treat diarrhea. In an effort to develop blockers of these channels, we turn to our previously developed and validated in silico models of claudin-15 (Samanta et al. 2018). We reasoned that compounds that can bind with the interior of claudin pores can limit paracellular water and ion flux. Thus, we used docking algorithms to search for putative small molecules that bind in the claudin-15 pore. AutoDock Vina was initially used to assess rigid docking using small compound databases. The small molecules were analyzed based on binding affinity to the pore and visualized using VMD for their potential blockage of the channel. Clusters of binding modes were identified based on the prominent interacting residues of the protein with the small molecules. We initially screened 10,500 compounds from within the UIC Centre for Drug Discovery and a cross-section of 10,000 compounds from the NCI open compound repository. This initial screen allowed us to identify 2 first-in-class selective claudin-15 blockers with efficacy in MDCK monolayers induced to express claudin-15 and in wildtype duodenum. Next, we screened the entire NCI open compound repository for additional molecules structurally related to our best initially identified molecule and this has allowed us to identify 13 additional molecules that increase TER of claudin-15 expressing MDCK monolayers by 90–160%. Additionally, these molecules possess similar structural components that will be collected in a fragment library and explored through molecular dynamics simulations. We also developed a claudin-2 homology model on which we are performing docking studies and in vitro measurements, which we expect will result in similar candidate ligands for blocking claudin-2. Our study will provide important insight into the role of claudin-dependent cation permeability in fundamental physiology, which we believe will lead to the utility of claudin blockers as a novel and much needed approach to treat diseases such as IBD.
Frizzled‐7 and limb mesenchymal chondrogenesis: Effect of misexpression and involvement of N‐cadherin (2002)

Products of the Frizzled family of tissue polarity genes have been identified as putative receptors for the Wnt family of signaling molecules. Wnt-signaling is implicated in the regulation of limb mesenchymal chondrogenesis, and our recent study indicates that N-cadherin and related activities are functionally involved in Wnt-7a-mediated inhibition of chondrogenesis. By using an in vitro high-density micromass culture system of chick limb mesenchymal cells, we have analyzed the spatiotemporal expression patterns and the effects on chondrogenesis of RCAS retroviral-mediated misexpression of Chfz-1 and Chfz-7, two Frizzled genes implicated in chondrogenic regulation. Chfz-1 expression was localized at areas surrounding the cartilaginous nodules at all time points examined, whereas Chfz-7 expression was limited to cellular aggregates during initial mesenchymal condensation, and subsequently was down-regulated from the centers toward the periphery of cartilage nodules at the time of chondrogenic differentiation, resembling the pattern of N-cadherin expression. Chondrogenesis in vitro was inhibited and limited to a smaller area of the culture upon misexpression of Chfz-7, but not affected by Chfz-1 misexpression. Analyses of cellular condensation and chondrogenic differentiation showed that the inhibitory action of Chfz-7 is unlikely to be at the chondrogenic differentiation step, but instead affects the earlier precartilage aggregate formation event. At 24 hr, expression of N-cadherin, a key component of the cellular condensation phase of chondrogenesis, was delayed/suppressed in Chfz-7 misexpressing cultures, and was limited to a significantly smaller cellular condensation area within the entire culture at 48 hr, when compared with control cultures. Chfz-1 misexpressing cultures appeared similar to control cultures at all time points. However, neither Chfz-1 nor Chfz-7 misexpression affected mesenchymal cell proliferation in vitro. These results suggest that Chfz-7 is active in regulating N-cadherin expression during the process of limb mesenchymal chondrogenesis and that Chfz-1 and Chfz-7 are involved in different Wnt-signaling pathways.
Graphene decoration with metal nanoparticles: Towards easy integration for sensing applications (2011)

A simple and versatile method for the decoration of CVD grown graphene with metal nanoparticles is presented. The mechanism of nanoparticle formation is galvanic displacement resulting in physically adsorbed clusters. The single layer graphene obtained by this method can be easily transferred. Integration onto a gas sensing transducer is presented as proof of concept.
Non-Instrumented Nucleic Acid Amplification (NINA) for Rapid Detection of Ralstonia solanacearum Race 3 Biovar 2 (2011)

We report on the use of a non-instrumented device for the implementation of a loop-mediated amplification (LAMP) based assay for the select-agent bacterial-wilt pathogen <i>Ralstonia solanacearum</i> race 3 biovar 2. Heat energy is generated within the device by the exothermic hydration of calcium oxide, and the reaction temperature is regulated by storing latent energy at the melting temperature of a renewable lipid-based engineered phase-change material. Endpoint detection of the LAMP reaction is achieved without opening the reaction tube by observing the fluorescence of an innovative FRET-based hybridization probe with a simple custom fluorometer. Non-instrumented devices could maintain reactions near the design temperature of 63°C for at least an hour. Using this approach DNA extracted from the pathogen could be detected at fewer than ten copies within a 25 μL reaction mix, illustrating the potential of these technologies for simple, powerful agricultural diagnostics in the field. Furthermore, the assay was just as reliable when implemented in a tropical environment at 31°C as it was when implemented in an air-conditioned lab maintained at 22°C, illustrating the potential value of the technology for field conditions in the tropics and subtropics.
Comparison of effect of 5 MeV proton and Co-60 gamma irradiation on silicon NPN rf power transistors and N–channel depletion MOSFETs (2017)

NPN transistors and N-channel depletion metal oxide semiconductor field effect transistors (MOSFETs) were irradiated with 5 MeV protons and 60Co gamma radiation in the dose ranging from 1 Mrad(Si) to 100 Mrad(Si). The different electrical characteristics of the NPN transistor such as Gummel characteristics, excess base current (ΔIB), dc current gain (hFE), transconductance (gm), displacement damage factor (K) and output characteristics were studied as a function of total dose. The different electrical characteristics of N-channel MOSFETs such as threshold voltage (Vth), density of interface trapped charges (ΔNit), density of oxide trapped charges (ΔNot), transconductance (gm), mobility (µ) and drain saturation current (IDSat) were studied systematically before and after irradiation in the same dose ranges. A considerable increase in the base current (IB) and decrease in the hFE, gm and collector saturation current (ICSat) were observed after irradiation in the case of the NPN transistor. In the N-channel MOSFETs, the ΔNit and ΔNot were found to increase and Vth, gm, µ and IDSat were found to decrease with increase in the radiation dose. The 5 MeV proton irradiation results of both the NPN transistor and N-channel MOSFETs were compared with 60Co gamma-irradiated devices in the same dose ranges. It was observed that the degradation in 5 MeV proton-irradiated devices is more when compared with the 60Co gamma-irradiated devices at higher total doses.
Methotrexate polymer implant for the treatment of head and neck cancer (1994)

Abstract A biodegradable polymeric device releasing methotrexate (MTX) for the treatment of cancer of the head and neck was evaluated in vitro and in vivo . The polymer used for the preparation of the device was a copolyanhydride based on dimer erucic acid and sebacic acid loaded with 2–20% MTX. The drug was released constantly for about two weeks from small discs (1 × 3 mm) with complete degradation of the polymer when placed in phosphate buffer pH 7.4 at 37°C. The release and degradation rate was similar for all drug loading. MTX‐loaded discs implanted subcutaneously in mice released the drug for about ten days with about 50% elimination of the device from the implantation site. The drug concentration was the highest in the tissue in contact with the device and decreased at distance from the device following a first order kinetics. The LD50 of MTX in polymer when implanted in mice was between 20 and 40 mg per kg. (1994)
Sparsity-Driven Statistical Inference for Inverse Problems (2015)

This thesis addresses statistical inference for the resolution of inverse problems. Our work is motivated by the recent trend whereby classical linear methods are being replaced by nonlinear alternatives that rely on the sparsity of naturally occurring signals. We adopt a statistical perspective and model the signal as a realization of a stochastic process that exhibits sparsity as its central property. Our general strategy for solving inverse problems then lies in the development of novel iterative solutions for performing the statistical estimation. The thesis is organized in five main parts. In the first part, we provide a general overview of statistical inference in the context of inverse problems. We discuss wavelet--based and gradient--based algorithms for linear and nonlinear forward models. In the second part, we present an in-depth discussion of cycle spinning, which is a technique used to improve the quality of signals recovered with wavelet--based methods. Our main contribution here is its proof of convergence; we also introduce a novel consistent cycle-spinning algorithm for denoising statistical signals. In the third part, we introduce a stochastic signal model based on L\'evy processes and investigate popular gradient--based algorithms such as those that deploy total-variation regularization. We develop a novel algorithm based on belief propagation for computing the minimum mean-square error estimator and use it to benchmark several popular methods that recover signals with sparse derivatives. In the fourth part, we propose and analyze a novel adaptive generalized approximate message passing (adaptive GAMP) algorithm that reconstructs signals with independent wavelet-coefficients from generalized linear measurements. Our algorithm is an extension of the standard GAMP algorithm and allows for the joint learning of unknown statistical parameters. We prove that, when the measurement matrix is independent and identically distributed Gaussian, our algorithm is asymptotically consistent. This means that it performs as well as the oracle algorithm, which knows the parameters exactly. In the fifth and final part, we apply our methodology to an inverse problem in optical tomographic microscopy. In particular, we propose a novel nonlinear forward model and a corresponding algorithm for the quantitative estimation of the refractive index distribution of an object.
Carrier Mobilities in Organic Electron Transport Materials Determined from Space Charge Limited Current (2002)

We report the mobility in organic electron transport materials determined from current–voltage characteristics in the regime of space charge limited current. The electron mobilities obtained are highly dependent on applied electric field, similar to the cases using a conventional time-of-flight method. The electron mobilities of phenanthroline derivatives are high and comparable to hole mobilities of conventional hole transport materials. Two parameters, zero-field mobility and electric field activation parameter are discussed from the viewpoint of oxidation and reduction reactions. The electric field activation parameter increases gradually with the increase of ionization potential. These facts suggest that there is a good possibility for realizing low driving voltage in organic light-emitting diodes (OLEDs).
Jacobus Henricus van 't Hoff und sein Einfluss auf die Stereochemie in den Niederlanden in den letzten hundert Jahren (2001)

Vom Tetraeder bis zur Thermodynamik reichten die Konzepte des niederländischen Physikochemikers Jacobus Henricus van 't Hoff, der einen einmaligen Einfluss auf die Chemie ausübte und vor nunmehr hundert Jahren der erste Träger des Chemie-Nobelpreises wurde. In seinen jungen Jahren gab er der Chemie als Wissenschaftsdisziplin ein ganz neues Gesicht. Van 't Hoff inspirierte über die Jahre hinweg viele niederländische Naturwissenschaftler zur Beschäftigung mit neuartigen stereochemischen Konzepten. Das Bild zeigt zeitgenössische stereochemische Modelle, die Van 't Hoff selbst hergestellt hat.
Modeling of MMC-HVDC for grid integration applications (2017)

The large number of constitutive elements of modular multilevel converters requires a complex model for control and modulation simulation which usually requires a small step time in the range of microseconds. However, to study the interaction of the MMC-HVDC station with the electrical DC and AC systems, which dynamical response is in the range of seconds, requires a model more simple but without losing the main dynamical characteristics. This paper presents a simplified model which allows longer step time simulation retaining the main features of the modular multilevel converter. The complete model of MMC is introduced and sequentially simplified in order to achieve a given simulation step time. Simulation results of the different stages of simplification are given.
A GAMOS plug-in for GEANT4 based Monte Carlo simulation of radiation-induced light transport in biological media (2013)

We describe a tissue optics plug-in that interfaces with the GEANT4/GAMOS Monte Carlo (MC) architecture, providing a means of simulating radiation-induced light transport in biological media for the first time. Specifically, we focus on the simulation of light transport due to the Čerenkov effect (light emission from charged particle's traveling faster than the local speed of light in a given medium), a phenomenon which requires accurate modeling of both the high energy particle and subsequent optical photon transport, a dynamic coupled process that is not well-described by any current MC framework. The results of validation simulations show excellent agreement with currently employed biomedical optics MC codes, [i.e., Monte Carlo for Multi-Layered media (MCML), Mesh-based Monte Carlo (MMC), and diffusion theory], and examples relevant to recent studies into detection of Čerenkov light from an external radiation beam or radionuclide are presented. While the work presented within this paper focuses on radiation-induced light transport, the core features and robust flexibility of the plug-in modified package make it also extensible to more conventional biomedical optics simulations. The plug-in, user guide, example files, as well as the necessary files to reproduce the validation simulations described within this paper are available online at http://www.dartmouth.edu/optmed/research-projects/monte-carlo-software.