gebhart/patrepeval huggingface dataset:
Inverse Geometric Design of Fabrication-Robust Nanophotonic Waveguides (2020)

We present an inverse design method making waveguides with high performance and high robustness to fabrication errors. As an example, we show a 1-to-4 mode converter with &gt; -1.5 dB conversion efficiency under geometric variations within fabrication tolerances.
Using Dissipative Particle Dynamics to Model Effects of Chemical Reactions Occurring within Hydrogels (2021)

Computational models that reveal the structural response of polymer gels to changing, dissolved reactive chemical species would provide useful information about dynamically evolving environments. However, it remains challenging to devise one computational approach that can capture all the interconnected chemical events and responsive structural changes involved in this multi-stage, multi-component process. Here, we augment the dissipative particle dynamics (DPD) method to simulate the reaction of a gel with diffusing, dissolved chemicals to form kinetically stable complexes, which in turn cause concentration-dependent deformation of the gel. Using this model, we also examine how the addition of new chemical stimuli and subsequent reactions cause the gel to exhibit additional concentration-dependent structural changes. Through these DPD simulations, we show that the gel forms multiple latent states (not just the "on/off") that indicate changes in the chemical composition of the fluidic environment. Hence, the gel can actuate a range of motion within the system, not just movements corresponding to the equilibrated swollen or collapsed states. Moreover, the system can be used as a sensor, since the structure of the layer effectively indicates the presence of chemical stimuli.
Fundic inhibition of acid secretion and gastrin release (2010)

Despite earlier indirect evidence that an antral chalone exists, no such inhibitor has been found in antral extract. Recently, interest in the question of an antral inhibitory mechanism has been revived by studies that showed that for a given rise in serum gastrin caused by antral distension, the response of both the innervated and denervated stomach is greatly enhanced by vagal denervation of the antrum. While this study suggested a neuro-humoral character of the antral inhibitory mechanism, it gave no indication as to the source of the inhibitor. Subsequent studies, however, suggested that neither the antrum nor the CNS was the source for this inhibitor. The initial aim of this study was to investigate the fundus as a possible source of the inhibitor by studying the effect of proximal gastric vagotomy on the antral inhibitory mechanism initiated by distension. The results gave clear indication that the inhibitor was indeed released from the fundus; indeed, the antral inhibitory mechanism was in reality a fundic one. Once the fundus was shown to be the source of the inhibitor, it was necessary to establish whether this inhibitor did in fact reside in the fundic mucosa. Four dogs were prepared with a denervated fundic pouch (or Heidenhain pouch, HP), and a fistula of the main, innervated stomach (gastric fistula, GF). The acid secretory responses of both the HP and GF to graded doses of pentagastrin and histamine was studied. In addition both the secretion of acid and the response of immunoreactive gastrin in the blood in response to a standard meal of 15% liver extract was studied. All these experiments were repeated after excision of the fundic mucosa of the main stomach. The results show that excision of the fundic mucosa reduced the GF acid secretion to the stimuli by 85-100%. By contrast, the maximal HP acid secretion increased by 247% in response to pentagastrin and 200% in response to histamine. The increase in the response to submaximal doses of these exogenous stimuli was even greater. Similarly, the peak 30 minutes HP output in response to feeding increased by 418%. Fundic mucosal excision also resulted in the increase in both basal (from 36±3 to 248±37 pg/ml) and food-stimulated response (from 168±12 preoperatively to 392±49 pg/ml postoperatively). Since the intragastric pH was held constant at 5.5 during the meal tests both before and after the operation, the augmented gastrin response could not be attributed to reduced acid secretion caused by excision of the fundic mucosa. From these studies it can be concluded that: (1) antral distension releases an inhibitor from the fundus; (2) excision of the fundic mucosa results in increased response of the HP to both submaximal and maximal doses of pentagastrin and histamine indicating that both the sensitivity of the oxyntic cell and parietal cell mass has increased; (3) excision of the fundic mucosa results in increased basal and food-stimulated gastrin response independent of the pH of the meal suggesting removal of an inhibitor of gastrin release.
Contradirectional frequency-selective couplers for guided-wave optics (1980)

Frequency-selective optical couplers in which a periodic perturbation in refractive index induces contradirectional power transfer in parallel single-mode waveguides are analyzed. Expressions for the spectral response are obtained by solving the coupled-mode equations. It is shown that by varying the amplitude of the periodic perturbation along he direction of propagation, the sidelobes present for the case of a uniform perturbation can be substantially reduced. Calculations are made of the mode propagation constants and coupling parameters for two rectangular-core waveguides with a periodic surface corrugation in the region between them. By using these results, design parameters and theoretical performance characteristics for a coupler with high transfer efficiency, low cross talk, and low reflection efficiency in the primary waveguide are determined.
CONFORMATIONAL AND ELECTRONIC INTERACTION STUDIES OF α-SUBSTITUTED CARBONYL COMPOUNDS. VI.p-SUBSTITUTED α-PHENYLTHIOACETONES (1989)

Abstract The analysis of the v co bands in the I. R. spectrum of p-substituted α-phenylthioacetones indicates a cis/gauche rotational isomerism. The slight solvent effect on the αc/αg ratios on going from a non polar solvent to a polar one, for the title compounds, as well as the minute sensitivity of the v co (cis) frequencies on going from electron-attracting to electron-donating substituents are interpreted on the grounds of the Field (F) and Inductive (I) Effects, which act in opposition in the cis rotamer, practically cancelling each other. The decreasing cis/gauche population ratio on going from electron-attracting to electron-donating substituents suggests the Occurrence of the hyperconjugative interaction in the gauche rotamers of the title compounds. The progressive shielding effect on the methylene and carbonyl carbon atoms in the 13C NMR spectra, on going from electron-donating to electron-attracting substituents is ascribed at least in part, to the “Reserve Polar Effect”.
Time-Resolved Nonclassical Photon Field Characterization (2012)

We demonstrate a new method to characterize nonclassical states that measures the temporal dependence of their statistical and coherent properties. We extract information about underlying physical processes in an InAs quantum dot in situ.
Large amplitude microwave emission and reduced nonlinear phase noise in Co2Fe(Ge0.5Ga0.5) Heusler alloy based pseudo spin valve nanopillars (2011)

We have studied microwave emission from a current-perpendicular-to-plane pseudo spin valve nanopillars with Heusler alloy Co2Fe(Ga0.5Ge0.5) electrodes. Large emission amplitude exceeding 150 nV/Hz0.5, partly owing to the large magnetoresistance, and narrow generation linewidth below 10 MHz are observed. We also find that the linewidth shows significant dependence on the applied field magnitude and its angle within the film plane. A minimum in the linewidth is observed when the slope of the frequency versus current becomes near zero. This agrees with theoretical prediction that takes into account non-linear phase noise as a source for linewidth broadening.
3D ultrasound-histology registration for validation of prostate cancer imaging methods (2013)

Several ultrasound (US) methods for localization of PCa, like contrast-enhanced US imaging [1] and elastography [2], are emerging, but any of these methods need accurate validation prior to introduction into the clinic. The current gold standard for validation is histologic analysis of the prostate after excision, which requires accurate registration between histology slices and US images. This task is complicated by misalignment between histology and US data, as well as deformation of the prostate due to pressure from the transrectal US (TRUS) probe and to the fixation process after excision. Moreover, besides the prostate contours, no reliable landmarks are present in US. In this abstract, a solution to the validation issue is proposed by means of a dedicated 3D surface-based registration algorithm. To reconstruct the prostate shape, contours are manually drawn in a 2D TRUS transversal apex-to-base video. By correlating the mid area of the video with a sagittal image, the 3D location of the contours is estimated. In addition, a 3D reconstruction of the histology, including cancer location, is realized by aligning and interpolating 4-mm-thick prostate slices. From both prostate shapes, triangulated meshes are constructed. The two meshes are registered by a combination of an affine and an elastic transformation. Volumetric deformation is estimated by interpolation of the surface displacements without use of any internal landmark. Preliminary validation was performed by an in vitro experiment with four prostate-mimicking phantoms pierced by five elastic wires. The resulting average registration error was 1.6 mm, which is far below the histology slicing resolution of 4 mm. The method’s feasibility was tested in 12 human prostates for which we were able to overlay data from histopathologic analysis onto US imaging planes. In conclusion, the presented registration algorithm shows promising performance for accurate validation of US-based PCa imaging techniques. Future employment of the method for MRI validation or fusion can also be envisaged
Novel Prefrontal Synthesis Intervention Improves Language in Children with Autism (2020)

Prefrontal synthesis (PFS) is defined as the ability to juxtapose mental visuospatial objects at will. Paralysis of PFS may be responsible for the lack of comprehension of spatial prepositions, semantically-reversible sentences, and recursive sentences observed in 30 to 40% of individuals with autism spectrum disorder (ASD). In this report we present data from a three-year-long clinical trial of 6454 ASD children age 2 to 12 years, which were administered a PFS-targeting intervention. Tablet-based verbal and nonverbal exercises emphasizing mental-juxtaposition-of-objects were organized into an application called <i>Mental Imagery Therapy for Autism</i> (MITA). The test group included participants who completed more than one thousand exercises and made no more than one error per exercise. The control group was selected from the rest of participants by a matching procedure. Each test group participant was matched to the control group participant by age, gender, expressive language, receptive language, sociability, cognitive awareness, and health score at first evaluation using propensity score analysis. The test group showed a 2.2-fold improvement in receptive language score vs. control group (<i>p</i> < 0.0001) and a 1.4-fold improvement in expressive language (<i>p</i> = 0.0144). No statistically significant change was detected in other subscales not targeted by the exercises. These findings show that language acquisition improves after training PFS and that a further investigation of the PFS-targeting intervention in a randomized controlled study is warranted.
Bimolecular Decomposition Pathways for Carboxylic Acids of Relevance to Biofuels (2014)

The bimolecular thermal reactions of carboxylic acids were studied using quantum mechanical molecular modeling. Previous work1 investigated the unimolecular decomposition of a variety of organic acids, including saturated, α,β-unsaturated, and β,γ-unsaturated acids, and showed that the type and position of the unsaturation resulted in unique branching ratios between dehydration and decarboxylation, [H2O]/[CO2]. In this work, the effect of bimolecular chemistry (water-acid and acid-acid) is considered with a representative of each acid class. In both cases, the strained 4-centered, unimolecular transition state, typical of most organic acids, is opened up to 6- or 8-centered bimolecular geometries. These larger structures lead to a reduction in the barrier heights (20-45%) of the thermal decomposition pathways for organic acids and an increase in the decomposition kinetics. In some cases, they even cause a shift in the branching ratio of the corresponding product slates.
Supplementary Figure 1 from <i>CMTM3</i>, Located at the Critical Tumor Suppressor Locus 16q22.1, Is Silenced by CpG Methylation in Carcinomas and Inhibits Tumor Cell Growth through Inducing Apoptosis (2023)

Supplementary Figure 1 from &lt;i&gt;CMTM3&lt;/i&gt;, Located at the Critical Tumor Suppressor Locus 16q22.1, Is Silenced by CpG Methylation in Carcinomas and Inhibits Tumor Cell Growth through Inducing Apoptosis
Catalysis by Ribonuclease A Is Limited by the Rate of Substrate Association (2003)

The value of k(cat)/K(M) for catalysis of RNA cleavage by ribonuclease (RNase) A can exceed 10(9) M(-1) s(-1) in a solution of low salt concentration. This value approaches that expected for the diffusional encounter of the enzyme and its substrate. To reveal the physicochemical constraints upon catalysis by RNase A, the effects of salt concentration, pH, solvent isotope, and solvent viscosity on catalysis were determined with synthetic substrates that bind to all of the enzymic subsites and thereby enable a meaningful analysis. The pK(a) values determined from pH-k(cat)/K(M) profiles at 0.010, 0.20, and 1.0 M NaCl are inconsistent with the known macroscopic pK(a) values of RNase A. This incongruity indicates that catalysis of RNA cleavage by RNase A is limited by the rate of substrate association, even at 1.0 M NaCl. The effect of solvent isotope and solvent viscosity on catalysis support this conclusion. The data are consistent with a mechanism in which RNase A associates with RNA in an intermediate complex, which is stabilized by Coulombic interactions, prior to the formation of a Michaelis complex. Thus, RNase A has evolved to become an enzyme limited by physics rather than chemistry, a requisite attribute of a perfect catalyst.
An alternative method for determination of the carpal height ratio. (1994)

Radiographs of the wrist often do not include the entire third metacarpal, so the standard method for measurement of the carpal height ratio (the carpal height divided by the length of the third metacarpal) cannot be used. In this study, the ratio of the carpal height relative to the length of the capitate was evaluated for its suitability as a reproducible alternative. The revised carpal height ratio (the carpal height divided by the capitate length) was evaluated for reproducibility and clinical utility in both in vitro and in vivo studies: it was determined from the radiographs of ten cadaveric wrists; those of 100 wrists (fifty pairs) of normal volunteers, made with controlled positioning; those of 100 wrists, drawn at random from radiographs that had been previously interpreted as showing normal findings; and those of fifty wrists of twenty-nine patients who had documented rheumatoid arthritis. The new ratio was found to be constant in the normal population, consistent bilaterally, decreased in patients who had carpal collapse, and reproducible.
Effect of Phosphodiesterase-5 Inhibition on Exercise Capacity and Clinical Status in Heart Failure With Preserved Ejection Fraction (2013)

clinicaltrials.gov Identifier: NCT00763867.
Functional characterization of the ectopically expressed olfactory receptor 2AT4 in human myelogenous leukemia (2016)

The olfactory receptor (OR) family was found to be expressed mainly in the nasal epithelium. In the last two decades members of the OR family were detected to be functional expressed in different parts of the human body such as in liver, prostate or intestine cancer cells. Here, we detected the expression of several ORs in the human chronic myelogenous leukemia (CML) cell line K562 and in white blood cells of clinically diagnosed acute myeloid leukemia (AML) patients by RT-PCR and next-generation sequencing. With calcium-imaging, we characterized in greater detail the cell biological role of one OR (OR2AT4) in leukemia. In both cell systems, the OR2AT4 agonist Sandalore-evoked strong Ca(2+) influx via the adenylate cyclase-cAMP-mediated pathway. The OR2AT4 antagonist Phenirat prevented the Sandalore-induced intracellular Ca(2+) increase. Western blot and flow cytometric experiments revealed that stimulation of OR2AT4 reduced the proliferation by decreasing p38-MAPK phosphorylation and induced apoptosis via phosphorylation of p44/42-MAPK. Furthermore, Sandalore increased the number of hemoglobin-containing cells in culture. We described for the first time an OR-mediated pathway in CML and AML that can regulate proliferation, apoptosis and differentiation after activation. This mechanism offers novel therapeutic options for the treatment of AML.
Stocator: Providing High Performance and Fault Tolerance for Apache Spark Over Object Storage (2018)

Until now object storage has not been a first-class citizen of the Apache Hadoop ecosystem including Apache Spark. Hadoop connectors to object storage have been based on file semantics, an impedance mismatch, which leads to low performance and the need for an additional consistent storage system to achieve fault tolerance. In particular, Hadoop depends on its underlying storage system and its associated connector for fault tolerance and allowing speculative execution. However, these characteristics are obtained through file operations that are not native for object storage, and are both costly and not atomic. As a result these connectors are not efficient and more importantly they cannot help with fault tolerance for object storage. We introduce Stocator, whose novel algorithm achieves both high performance and fault tolerance by taking advantage of object storage semantics. This greatly decreases the number of operations on object storage as well as enabling a much simpler approach to dealing with the eventually consistent semantics typical of object storage. We have implemented Stocator and shared it in open source. Performance testing with Apache Spark shows that it can be 18 times faster for write intensive workloads and can perform 30 times fewer operations on object storage than the legacy Hadoop connectors, reducing costs both for the client and the object storage service provider.
Discrete-time cross-term forwarding design of robust controllers for HCCI engines (2010)

This paper presents a model-based nonlinear feedback controller designed to regulate the crank angle at 50% fuel burned (θ <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">CA50</inf> ) for a gasoline homogeneous charge compression ignition (HCCI) engine with high dilution during load transitions and charge temperature variations. Discrete-time version of cross-term forwarding, which has not been presented in the literature to the best of the authors' knowledge, is developed in this example based on a positive definite Lyapunov function with set-point for the temperature at intake valve closing (IVC). The nonlinear feedback controller depends on measurement of the combustion timing θ <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">CA50</inf> and estimation of the temperature at IVC. Closed-loop simulation of the full order engine model shows that the nonlinear feedback controller, along with a nonlinear observer, is able to regulate the combustion timing θ <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">CA50</inf> by stabilizing the temperature dynamics during load transitions and intake temperature variations despite the existence of model uncertainties and measurement noise.
On Using Blockchain Based Workflows (2019)

We have been involved in the development of several blockchain-based solutions that largely utilize workflows. Workflows are used to guide users from independent organizations to process and manage transactions, data and documents in a trusted, immutable, and transparent manner for all relevant entities on a given blockchain network. This work discusses our approach to automate the process of creating, updating, and using workflows for blockchain-based solutions. In particular, we present a workflow definition schema using existing templates. We also show how the workflow definition is used to automate the generation of graphical user interfaces and the possibility of generating associated blockchain smart contracts in the future.
Improved High Temperature Oxidation Behaviour of AISI 347 Grade Stainless Steel by Superficial Coating of CeO2. (1995)

Influence of superficially applied CeO,coating on the high temperature oxidation behaviour of AISI 347 grade stainless steel under different rates of heating followed by isothermal holding at 1 273 K in dry air is reported. The reactive oxide coating not only reduced the oxidation rate but also facilitated improved oxide scale adherenceto the alloy substrate. The coated steel could withstand a number of thermal cyclings with- out scale rupture and exhibited further reduction in rate in sequential exposures. Reducedreaction rate has been attributed mainly to a change over in the rate controlling process from outward migration of cations to the ingress of oxidant species, Improved scale adhesion is due to change in chemical composition and grain size of the resultant oxide scale promoted by the formation of silicon-oxide stringers into the base al]oy favouring pegging mechanism. Scale growth mechanismhas been substantiated by post oxidation analyses using SEM,EDS, EPMA and XRD which could illustrate the role of reactive oxide coating and the formation of various complex oxide phases a]ong with NiNb,O*.