gebhart/patrepeval huggingface dataset:
Evaluation of large-intestinal parameters associated with dietary treatments designed to reduce the occurrence of swine dysentery (2002)

Diets containing soluble NSP (sNSP) and resistant starch (RS) increase hindgut fermentation in pigs, which in turn increases the incidence of swine dysentery (SD) after infection with the intestinal spirochaete Brachyspira hyodysenteriae. In the present study pigs were fed diets based on either wheat or sorghum, fed either raw or treated by extrusion, and/or with the addition of dietary enzymes to reduce RS and/or sNSP content. The aim was to determine the effects of these treatments on pig performance, large intestinal fermentation and expression of SD. Weaned pigs (n 132) were fed experimental diets for 4 weeks, when half the pigs in each treatment group were euthanased and samples collected to assess the influence of the diet on hindgut fermentation. The remaining pigs then were infected with B. hyodysenteriae, and monitored for development of SD. In general, compared with pigs fed raw wheat, fermentation in all parts of the large intestine was reduced either by feeding raw sorghum-based diets, or by feeding diets that were extruded. The addition of enzymes that degrade RS or sNSP reduced fermentation only in the distal parts of the large intestine. The incidence of SD was lower in pigs fed sorghum-based diets, and some of the extruded diets, but none of the dietary treatments offered full protection against SD. Multiple regression analysis of the results from all three experiments showed that colonisation by spirochaetes was highly related to dietary sNSP concentrations, whilst development of SD was similarly influenced by RS content of the diet.
Fast Hyperparameter Tuning for Ising Machines (2022)

In this paper, we propose a novel technique to accelerate Ising machines hyperparameter tuning. Firstly, we define Ising machine performance and explain the goal of hyperparameter tuning in regard to this performance definition. Secondly, we compare well-known hyperparameter tuning techniques, namely random sampling and Tree-structured Parzen Estimator (TPE) on different combinatorial optimization problems. Thirdly, we propose a new convergence acceleration method for TPE which we call "FastConvergence".It aims at limiting the number of required TPE trials to reach best performing hyperparameter values combination. We compare FastConvergence to previously mentioned well-known hyperparameter tuning techniques to show its effectiveness. For experiments, well-known Travel Salesman Problem (TSP) and Quadratic Assignment Problem (QAP) instances are used as input. The Ising machine used is Fujitsu's third generation Digital Annealer (DA). Results show, in most cases, FastConvergence can reach similar results to TPE alone within less than half the number of trials.
Sorption Equilibrium and Thermal Regeneration of Acetone and Toluene Vapors on an Activated Carbon (2007)

Adsorption and thermal regeneration dynamics of acetone on activated carbon were compared to those of toluene. The adsorption isotherms of acetone on the activated carbon were type-II, but they approached type-III with an increase in temperature. On the other hand, those of toluene were type-I in the experimental range. Although the temperature excursion of toluene was higher than that of acetone in the activated carbon bed, the breakthrough shape of toluene was steeper due to the strong adsorption affinity. Compared to toluene, more concentrated acetone within shorter period of time could be obtained from the activated carbon bed by hot nitrogen purge regeneration because its isotherm approached type-III at high temperature. Therefore, the energy requirement and purge gas consumption for acetone desorption were significantly changed with purge gas velocity, regeneration temperature, and initial bed loading, which was different from toluene. A nonequilibrium and nonadiabatic/nonisothermal model was used to fit temperature and concentration profiles of adsorption and thermal regeneration. Even though the adsorption of acetone was performed in a low concentration range, the multilayer adsorption isotherm model should be applied for the regeneration step to design the activated carbon bed system more accurately.
Role of Prohormone Convertases in Pro-Neuropeptide Y Processing:  Coexpression and in Vitro Kinetic Investigations (1997)

Proneuropeptide Y (ProNPY) undergoes cleavage at a single dibasic site Lys38-Arg39 resulting in the formation of 1-39 amino acid NPY which is further processed successively by carboxypeptidase-like and peptidylglycine alpha-amidating monooxygenase enzymes. To investigate whether prohormone convertases are involved in ProNPY processing, a vaccinia virus derived expression system was used to coexpress recombinant ProNPY with each of the prohormone convertases PC1/3, PC2, furin, and PACE4 in Neuro2A and NIH 3T3 cell lines as regulated neuroendocrine and constitutive prototype cell lines, respectively. The analysis of processed products shows that only PC1/3 generates NPY in NIH 3T3 cells while both PC1/3 and PC2 are able to generate NPY in Neuro2A cells. The convertases furin and PACE4 are unable to process ProNPY in either cell line. Moreover, comparative in vitro cleavage of recombinant NPY precursor by the enzymes PC1/3, PC2 and furin shows that only PC1/3 and PC2 are involved in specific cleavage of the dibasic site. Kinetic studies demonstrate that PC1/3 cleaves ProNPY more efficiently than PC2. The main difference between the cleavage efficiency is observed in the Vmax values whereas no major difference is observed in Km values. In addition the cleavage by PC1/3 and PC2 of two peptides reproducing the dibasic cleavage site with different amino acid sequence lengths namely (20-49)-ProNPY and (28-43)-ProNPY was studied. These shortened ProNPY substrates, when recognized by the enzymes, are more efficiently cleaved than ProNPY itself. The shortest peptide is not cleaved by PC2 while it is by PC1/3. On the basis of these observations it is proposed, first, that the constitutive secreted NPY does not result from the cleavage carried out by ubiquitously expressed enzymes furin and PACE4; second, that PC1/3 and PC2 are not equipotent in the cleavage of ProNPY; and third, substrate peptide length might discriminate PC1/3 and PC2 processing activity.
Segmental Dynamics of Ethylene Oxide-Containing Polymers with Diverse Backbone Chemistries (2016)

The dielectric response of seven nonionic ethylene oxide-containing polymers are investigated. Four different backbone chemistries are considered, including polymethacrylate, polyester ether, polyphosphazene, and polysiloxane. The chemistry of the backbone and the linking chemistry to incorporate ether oxygen (EO) groups dramatically affect polymer segmental dynamics. The Tg of the inorganic backbone polymers is ∼15 °C lower than that of the PEO homopolymer. Polysiloxanes exhibit the lowest Tg of −86 °C when attached with pendent −(CH2–CH2–O)4–CH3 groups. The strength of the alpha relaxation is the same for the hydrocarbon backbone polymers (Δε = 10), whereas the dielectric constants of inorganic polymers with short pendent groups is lower (Δε = 3). The difference in relaxation strengths is due to restricted motion of ether oxygens close to the backbone. This effect diminishes as the relative backbone concentration is decreased by increasing the pendent EO length. As pendent EO chain length is increased, the segmental relaxation broadens due to ether oxygens experiencing different local environments.
Highly valley-polarized singlet and triplet interlayer excitons in van der Waals heterostructure (2019)

Two-dimensional semiconductors feature valleytronics phenomena due to locking of the spin and momentum valley of the electrons. However, the valley polarization is intrinsically limited in monolayer crystals by the fast intervalley electron-hole exchange. Heterobilayer crystals have been shown to have a longer exciton lifetime and valley depolarization time. Yet most reported valley polarization was low; the valley selection rules and mechanisms of valley depolarization remain controversial. Here, we show that nearly pure valley polarizations are achievable in high-quality heterostructures with precise momentum-valley alignment. Together with time-resolved and temperature dependence measurements, we furthermore identify both singlet and brightened triplet interlayer excitons with opposite valley polarizations, which originate from direct band-gap transitions and are localized at the ${H}_{h}^{h}$ atomic registry---corresponding to the band minima of the heterostructure. Our results also reveal ultrafast interlayer electron transfer and strongly suppressed interlayer exciton valley depolarization. Our results pave the way for using semiconductor heterobilayers to control valley selection rules for valleytronic applications.
Memristors: Direct Observation of Localized Radial Oxygen Migration in Functioning Tantalum Oxide Memristors (Adv. Mater. 14/2016) (2016)

As information bits of 0's and 1's are stored in crosspoint tantalum oxide memristors, or resistive random access memory (RRAM) cells, nanoscale-resolution in operando X-ray transmission spectromicroscopy is used by J. P. Strachan and co-workers, as reported on page 2772, to directly observe oxygen migration and clustering, revealing an important operation and failure mechanism of RRAM, a frontrunner technology for next-generation computer memory.
AN OBJECT-ORIENTED COMPONENT-BASED FRAMEWORK FOR ON-BOARD SOFTWARE (2001)

This paper will advocate the use of component-based software frameworks for on-board systems. Software frameworks are a reuse technology that makes architectural (as opposed to code) reuse possible. They have been successfully applied in the desktop and commercial arena. The sudden expansion in on-board memory and CPU resources subsequent to the space qualification of the ERC32 processor means that they can now be applied to space systems. This new technology was tested in a study done for ESA that resulted in the development of a prototype component-based framework for the AOCS software. The framework was developed in C++ and tested on an ERC32 simulator. The experience of this study is that advanced software technologies can be safely applied to space systems bringing to them the same benefits as already seen in other fields.
PRIMARY STRUCTURE OF EQUINE GROWTH HORMONE (1976)

The study of the structure of the peptides arising from native, oxidized, reduced and alkylated or citraconylated equine growth hormone on incubation with trypsin and chymotrypsin is reported. The data obtained, combined with results already published, support the assembly of a unique sequence of amino acids for the polypeptide chain of the protein.
Genotoxic effects of zinc oxide nanoparticles (2015)

The potential toxicity of nanoparticles has currently provoked public and scientific discussions, and attempts to develop generally accepted handling procedures for nanoparticles are under way. The investigation of the impact of nanoparticles on human health is overdue and reliable test systems accounting for the special properties of nanomaterials must be developed. Nanoparticular zinc oxide (ZnO) may be internalised through ambient air or the topical application of cosmetics, only to name a few, with unpredictable health effects. Therefore, we analysed the determinants of ZnO nanoparticle (NP) genotoxicity. ZnO NPs (15-18 nm in diameter) were investigated at concentrations of 0.1, 10 and 100 μg mL(-1) using the cell line A549. Internalised NPs were only infrequently detectable by TEM, but strongly increased Zn(2+) levels in the cytoplasm and even more in the nuclear fraction, as measured by atom absorption spectroscopy, indicative of an internalised zinc and nuclear accumulation. We observed a time and dosage dependent reduction of cellular viability after ZnO NP exposure. ZnCl2 exposure to cells induced similar impairments of cellular viability. Complexation of Zn(2+) with diethylene triamine pentaacetic acid (DTPA) resulted in the loss of toxicity of NPs, indicating the relevant role of Zn(2+) for ZnO NP toxicity. Foci analyses showed the induction of DNA double strand breaks (DSBs) by ZnO NPs and increased intracellular reactive oxygen species (ROS) levels. Treatment of the cells with the ROS scavenger N-acetyl-l-cysteine (NAC) resulted in strongly decreased intracellular ROS levels and reduced DNA damage. However, a slow increase of ROS after ZnO NP exposure and reduced but not quashed DSBs after NAC-treatment suggest that Zn(2+) may exert genotoxic activities without the necessity of preceding ROS-induction. Our data indicate that ZnO NP toxicity is a result of cellular Zn(2+) intake. Subsequently increased ROS-levels cause DNA damage. However, we found evidence for the assumption that DNA-DSBs could be caused by Zn(2+) without the involvement of ROS.
Impact of Probiotics on Risk Factors for Cardiovascular Diseases. A Review (2012)

Probiotic microorganisms have historically been used to rebalance disturbed intestinal microbiota and to diminish gastrointestinal disorders, such as diarrhea or inflammatory bowel diseases (e.g., Crohn's disease and ulcerative colitis). Recent studies explore the potential for expanded uses of probiotics on medical disorders that increase the risk of developing cardiovascular diseases and diabetes, such as obesity, hypercholesterolemia, arterial hypertension, and metabolic disturbances such as hyperhomocysteinemia and oxidative stress. This review aims at summarizing the proposed molecular and cellular mechanisms involved in probiotic-host interactions and to identify the nature of the resulting beneficial effects. Specific probiotic strains can act by modulating immune response, by producing particular molecules or releasing biopeptides, and by modulating nervous system activity. To date, the majority of studies have been conducted in animal models. New investigations on the related mechanisms in humans need to be carried out to better enable targeted and effective use of the broad variety of probiotic strains.
Special Section Guest Editorial: Tandem Junction Solar Cells (2018)

The <i>Journal of Photonics for Energy</i> (JPE) covers fundamental and applied research areas focused on the applications of photonics for renewable energy harvesting, conversion, storage, distribution, monitoring, consumption, and efficient usage.
Endoscopic ultrasound criteria to predict the need for intervention in pancreatic necrosis (2012)

Pancreatic necrotic cavities with high liquid content are associated with a high risk of complications. Therefore, close clinical monitoring is needed and early elective intervention might be considered in these patients.
On the solenoidal heat-flux in quasi-ballistic thermal conduction (2015)

The Boltzmann transport equation for phonons is recast directly in terms of the heat-flux by means of iteration followed by truncation at the second order in the spherical harmonic expansion of the distribution function. This procedure displays the heat-flux in an explicitly coordinate-invariant form, and leads to a natural decomposition into two components, namely, the solenoidal component in addition to the usual irrotational component. The solenoidal heat-flux is explicitly shown to arise by applying the heat-flux equation to a right-circular cylinder. These findings are important in the context of phonon resonators that utilize the strong quasi-ballistic thermal transport reported recently in silicon membranes at room temperature.
Multiplexed and millimeter-scale fluorescence nanoscopy of cells and tissue sections via prism-illumination and microfluidics-enhanced DNA-PAINT (2022)

Abstract Fluorescence nanoscopy has become increasingly powerful for biomedical research, but it has historically afforded a small field-of-view (FOV) around 50 µm x 50 µm at once and more recently up to ~200 µm x 200 µm. Efforts to further increase the FOV in fluorescence nanoscopy have thus far relied on the use of fabricated waveguide substrates, adding cost and sample constraints on the applications. Here we report PRism-Illumination and Microfluidics-Enhanced DNA-PAINT (PRIME-PAINT) for multiplexed fluorescence nanoscopy across millimeter-scale FOVs. Built upon the well-established prism-type total internal reflection microscopy, PRIME-PAINT achieves robust single-molecule localization with up to ~520 µm x 520 µm single FOVs and 25-40 nm lateral resolutions. Through stitching, nanoscopic imaging over mm 2 sample areas can be completed in as little as 40 minutes per target. An on-stage microfluidics chamber facilitates probe exchange for multiplexing and enhances image quality particularly for formalin-fixed paraffin-embedded (FFPE) tissue sections. We demonstrate the utility of PRIME-PAINT by analyzing ~10 6 caveolae structures in ~1,000 cells and imaging entire pancreatic cancer lesions from patient tissue biopsies. By imaging from nanometers to millimeters with multiplexity and broad sample compatibility, PRIME-PAINT will be useful for building multiscale, Google-Earth-like views of biological systems.
Supplementary Figure 9 from Immortalization of Human Bronchial Epithelial Cells in the Absence of Viral Oncoproteins (2023)

Supplementary Figure 9 from Immortalization of Human Bronchial Epithelial Cells in the Absence of Viral Oncoproteins
Origami-Inspired Folding of Thick, Rigid Panels (2014)

To achieve power of 250 kW or greater, a large compression ratio of stowed-to-deployed area is needed. Origami folding patterns were used to inspire the folding of a solar array to achieve synchronous deployment; however, origami models are generally created for near-zero-thickness material. Panel thickness is one of the main challenges of origami-inspired design. Three origami-inspired folding techniques (flasher, square twist, and map fold) were created with rigid panels and hinges. Hinge components are added to the model to enable folding of thick, rigid materials. Origami models are created assuming zero (or near zero) thickness. When a material with finite thickness is used, the panels are required to bend around an increasingly thick fold as they move away from the center of the model. The two approaches for dealing with material thickness are to use membrane hinges to connect the panels, or to add panel hinges, or hinges of the same thickness, at an appropriate width to enable folding.
Cryogenic Ion Mobility-Mass Spectrometry: Tracking Ion Structure from Solution to the Gas Phase (2016)

Electrospray ionization (ESI) combined with ion mobility-mass spectrometry (IM-MS) is adding new dimensions, that is, structure and dynamics, to the field of biological mass spectrometry. There is increasing evidence that gas-phase ions produced by ESI can closely resemble their solution-phase structures, but correlating these structures can be complicated owing to the number of competing effects contributing to structural preferences, including both inter- and intramolecular interactions. Ions encounter unique hydration environments during the transition from solution to the gas phase that will likely affect their structure(s), but many of these structural changes will go undetected because ESI-IM-MS analysis is typically performed on solvent-free ions. Cryogenic ion mobility-mass spectrometry (cryo-IM-MS) takes advantage of the freeze-drying capabilities of ESI and a cryogenically cooled IM drift cell (80 K) to preserve extensively solvated ions of the type [M + xH](x+)(H2O)n, where n can vary from zero to several hundred. This affords an experimental approach for tracking the structural evolution of hydrated biomolecules en route to forming solvent-free gas-phase ions. The studies highlighted in this Account illustrate the varying extent to which dehydration can alter ion structure and the overall impact of cryo-IM-MS on structural studies of hydrated biomolecules. Studies of small ions, including protonated water clusters and alkyl diammonium cations, reveal structural transitions associated with the development of the H-bond network of water molecules surrounding the charge carrier(s). For peptide ions, results show that water networks are highly dependent on the charge-carrying species within the cluster. Specifically, hydrated peptide ions containing lysine display specific hydration behavior around the ammonium ion, that is, magic number clusters with enhanced stability, whereas peptides containing arginine do not display specific hydration around the guanidinium ion. Studies on the neuropeptide substance P illustrate the ability of cryo-IM-MS to elucidate information about heterogeneous ion populations. Results show that a kinetically trapped conformer is stabilized by a combination of hydration and specific intramolecular interactions, but upon dehydration, this conformer rearranges to form a thermodynamically favored gas-phase ion conformation. Finally, recent studies on hydration of the protein ubiquitin reveal water-mediated dimerization, thereby illustrating the extension of this approach to studies of large biomolecules. Collectively, these studies illustrate a new dimension to studies of biomolecules, resulting from the ability to monitor snapshots of the structural evolution of ions during the transition from solution to gas phase and provide unparalleled insights into the intricate interplay between competing effects that dictate conformational preferences.
Individual QoS versus aggregate QoS: a loss performance study (2005)

This paper explores the differences that can exist between individual and aggregate loss guarantees in an environment where guarantees are only provided at the aggregate level. The focus is on understanding which traffic parameters are responsible for inducing possible deviations and to what extent. In addition, we seek to evaluate the level of additional resources, e.g., bandwidth or buffer, required to ensure that all individual loss measures remain below their desired target. This paper's contributions are in developing analytical models that enable the evaluation of individual loss probabilities in settings where only aggregate losses are controlled, and in identifying traffic parameters that have a major influence on the differences between individual and aggregate losses. The latter allows us to further construct practical tools and guidelines for rapidly assessing if specific traffic sources can be safely multiplexed into a common service class.
Heterostructure collinear graded index polymer waveguide modulator (1991)

We are reporting a novel graded index (GRIN) collinear asymmetrical polymer waveguide modulator. Disparity of the waveguide pair provides us with a much larger dynamic range of phase matching condition suitable for single-mode waveguide to multi-mode waveguide coupling. Formation of a universal polymer waveguide was made possible by tuning the guiding layer index profile from stepped index to graded index through a mass perturbation method.