gebhart/patrepeval huggingface dataset:
Hydrophobic Organization of Membrane Proteins (1989)

Membrane-exposed residues are more hydrophobic than buried interior residues in the transmembrane regions of the photosynthetic reaction center from Rhodobacter sphaeroides. This hydrophobic organization is opposite to that of water-soluble proteins. The relative polarities of interior and surface residues of membrane and water soluble proteins are not simply reversed, however. The hydrophobicities of interior residues of both membrane and water-soluble proteins are comparable, whereas the bilayer-exposed residues of membrane proteins are more hydrophobic than the interior residues, and the aqueous-exposed residues of water-soluble proteins are more hydrophilic than the interior residues. A method of sequence analysis is described, based on the periodicity of residue replacement in homologous sequences, that extends conclusions derived from the known atomic structure of the reaction center to the more extensive database of putative transmembrane helical sequences.
“Nano Lab” Advanced Characterization Platform for Studying Electrocatalytic Iridium Nanoparticles Dispersed on TiOxNy Supports Prepared on Ti Transmission Electron Microscopy Grids (2023)

Aiming at speeding up the discovery and understanding of promising electrocatalysts, a novel experimental platform, <i>i.e.</i>, the <i>Nano Lab</i>, is introduced. It is based on state-of-the-art physicochemical characterization and atomic-scale tracking of individual synthesis steps as well as subsequent electrochemical treatments targeting nanostructured composites. This is provided by having the entire experimental setup on a transmission electron microscopy (TEM) grid. Herein, the oxygen evolution reaction nanocomposite electrocatalyst, i.e., iridium nanoparticles dispersed on a high-surface-area TiO<sub><i>x</i></sub>N<sub><i>y</i></sub> support prepared on the Ti TEM grid, is investigated. By combining electrochemical concepts such as anodic oxidation of TEM grids, floating electrode-based electrochemical characterization, and identical location TEM analysis, relevant information from the entire composite's cycle, <i>i.e.</i>, from the initial synthesis step to electrochemical operation, can be studied. We reveal that Ir nanoparticles as well as the TiO<sub><i>x</i></sub>N<sub><i>y</i></sub> support undergo dynamic changes during all steps. The most interesting findings made possible by the <i>Nano Lab</i> concept are the formation of Ir single atoms and only a small decrease in the N/O ratio of the TiO<sub><i>x</i></sub>N<sub><i>y</i></sub>-Ir catalyst during the electrochemical treatment. In this way, we show that the precise influence of the nanoscale structure, composition, morphology, and electrocatalyst's locally resolved surface sites can be deciphered on the atomic level. Furthermore, the <i>Nano Lab</i>'s experimental setup is compatible with <i>ex situ</i> characterization and other analytical methods, such as Raman spectroscopy, X-ray photoelectron spectroscopy, and identical location scanning electron microscopy, hence providing a comprehensive understanding of structural changes and their effects. Overall, an experimental toolbox for the systematic development of supported electrocatalysts is now at hand.
Quantification of Neutralizing Antibodies to Human Type I Interferons Using Division-Arrested Frozen Cells Carrying an Interferon-Regulated Reporter-Gene (2008)

Development of neutralizing antibodies (NAbs) to interferons (IFNs) can reduce the clinical response to IFN therapy. As current cell-based assays for quantifying NAbs have limitations, a highly sensitive and reproducible assay was developed, using division-arrested frozen human U937 cells transfected with the luciferase reportergene controlled by an IFN-responsive chimeric promoter, which allows IFN activity to be determined with precision within hours. Assay-ready PIL5 cells can be stored frozen for >3 years without loss of IFN sensitivity or the need for cell propagation. The assay is highly IFN sensitive (detecting <1.0 IU/mL), reproducible (SE +/- 15%) over concentrations from <1.0 to 100 IU/mL and able to measure different IFN subtypes and their pegylated variants. The use of this assay has shown that NAbs from patients treated with IFN-alpha2 exhibited markedly lower titers against 10 LU/mL of low specific activity IFNs, namely, IFN-alpha1, PEG-Intron(TM) (Schering-Plough, Levallois-Perret,France), or Pegasys(TM) (Hoffmann-La Roche, Neuilly-sur-Seine, France, than against 10 LU/mL IFN-alpha2. Similarly, NAbs from patients treated with IFN-beta1a exhibit lower titers against 10 LU/mL of low specific activity IFN-beta1b than against IFN-beta1a. The combination of the use of division-arrested, IFN-responsive human cells transfected with the luciferase reporter-gene makes the rapid PIL5 assay for NAbs highly advantageous.
On the oscillation mode of gas-filled micropores (1985)

Small pores in hydrophobic membranes trap gas when the membrane is immersed in aqueous media, and the resulting "gas bodies" may be used for studying biophysical effects of ultrasonic cavitation. In a previous study [D. L. Miller and W. L. Nyborg, J. Acoust. Soc. Am. 73, 1537-1544 (1983)], two modes of oscillation, a "pistonlike" and a "membranelike" mode, were described theoretically, and either model appears capable of qualitatively explaining observations of the linear behavior of the gas-filled micropores. In this study, low-amplitude nonlinear theory is employed with observations of second harmonic emissions to show that the membranelike model is the more appropriate model for the 3.4- and 4.0-microns-diam micropores tested at 0.81 and 1.62 MHz. In addition, this model is expanded to include the case for which the gas is asymmetrically situated in a pore, to discuss the motion of the three-phase line at the periphery of an air-water interface in a pore, and to suggest an explanation of the phenomenon of gas loss from the pores when the incident field intensity is raised. Knowledge of the behavior of the gas-filled micropores in an ultrasonic field should allow a more complete understanding of biological effects on cells exposed to this form of cavitation activity.
Cluster Adaptive Training for Deep Neural Network Based Acoustic Model (2015)

Although context-dependent DNN-HMM systems have achieved significant improvements over GMM-HMM systems, significant performance degradation has been observed if the acoustic condition of the test data mismatches that of the training data. Hence, adaptation and adaptive training of DNN are of great research interest. Previous DNN adaptation works mainly focus on adapting parameters of a single DNN by applying linear transformations to feature or hidden-layer output; introducing vector representation of non-speech variability into the input. In these methods, large number of parameters are required to be estimated during adaptation. In this paper, the cluster adaptive training (CAT) framework is employed for DNN adaptive training. Here, multiple weight matrices are constructed to form the basis of a canonical parametric space. During adaptation, for a new acoustic condition, an interpolation vector is estimated to combine the weight basis into a single adapted weight matrix. Since only the interpolation vector need to be estimated during adaptation, the number of updated parameters is much smaller than existing DNN adaptation methods. The CAT-DNN approach was evaluated on an English switchboard task in unsupervised adaptation mode. It achieved significant WER reductions over the unadapted DNN-HMM, relative 7.6% to 10.6%, with only 10 parameters.
Enhanced plasma IL-6 and IL-1ra responses to repeated vs. single bouts of prolonged cycling in elite athletes (2002)

The impact of repeated bouts of exercise on plasma levels of interleukin (IL)-6 and IL-1 receptor antagonist (IL-1ra) was examined. Nine well-trained men participated in four different 24-h trials: Long [two bouts of exercise, at 0800-0915 and afternoon exercise (Ex-A), separated by 6 h]; Short (two bouts, at 1100-1215 and Ex-A, separated by 3 h); One (single bout performed at the same Ex-A as second bout in prior trials); and Rest (no exercise). All exercise bouts were performed on a cycle ergometer at 75% of maximal O(2) uptake and lasted 75 min. Peak IL-6 observed at the end of Ex-A was significantly higher in Short (8.8 +/- 1.3 pg/ml) than One (5.2 +/- 0.7 pg/ml) but not compared with Long (5.9 +/- 1.2 pg/ml). Peak IL-1ra observed 1 h postexercise was significantly higher in Short (1,774 +/- 373 pg/ml) than One (302 +/- 53 pg/ml) but not compared with Long (1,276 +/- 451 pg/ml). We conclude that, when a second bout of endurance exercise is performed after only 3 h of recovery, IL-6 and IL-1ra responses are elevated. This may be linked to muscle glycogen depletion.
Error Analysis of the Rapid Lifetime Determination Method for Double-Exponential Decays and New Windowing Schemes (1999)

The rapid lifetime determination method (RLD) is a mathematical technique for extremely rapid evaluations of lifetimes in exponential decays. It has been applied in luminescence microscopy and single-molecule lifetime evaluation. To date, the primary application has been in single-exponential evaluations. We present extensions of the method to double exponentials. Using Monte Carlo simulations, we assess the performance of both the double-exponential decay with known lifetimes and the double-exponential decay with unknown preexponential factors and lifetimes. Precision is evaluated as a function of the noise level (Poisson statistics), the ratios of the lifetimes, the ratios of their preexponential factors, and the fitting window. Optimum measurement conditions are determined. RLD is shown to work well over a wide range of practical experimental conditions. If the lifetimes are known, the preexponential factors can be determined with good precision even at low total counts (10(4)). With unknown preexponential factors and lifetimes, precisions decrease but are still acceptable. A new gating scheme (overlapped gating) is shown to offer improved precision for the case of a single-exponential decay. Theoretical predictions are tested against actual experimental data from a laser-based lifetime instrument.
Automatic Differentiation of C++ Codes for Large-Scale Scientific Computing (2006)

We discuss computing first derivatives for models based on elements, such as large-scale finite-element PDE discretizations, implemented in the C++ programming language. We use a hybrid technique of automatic differentiation (AD) and manual assembly, with local elementlevel derivatives computed via AD and manually summed into the global derivative. C++ templating and operator overloading work well for both forward-and reverse-mode derivative computations. We found that AD derivative computations compared favorably in time to finite differencing for a scalable finite-element discretization of a convection-diffusion problem in two dimensions.
Growth of epitaxial semiconductor alloys and superlattices with continuously variable composition by pulsed-laser ablation (1993)

We describe a new method to grow epitaxial semiconductor alloys with continuously variable composition, while using a single pulsed laser ablation target of fixed composition. Expitaxial ZnSe1−xSx films with continuously variable sulfur content ‘‘x’’ were grown by ablating a ZnSe target through low‐pressure ambient H2S gas. The sulfur content was easily controlled by varying the H2S partial pressure. The composition of ZnSe1−xSx films differs by as much as x=0.52 from the pure ZnSe target. We have used this method to grow heteroepitaxial structures with either continuously graded or periodically repeating, abrupt compositional changes (compositional superlattices). Structures that simultaneously incorporate both types of compositional modulation also have been grown. This development removes the principal barrier to convenient PLA growth of compositionally graded semiconductor thin‐film materials, namely that the film and target normally have the same composition. The method appears to have broad application for PLA growth of other compound semiconductor films and heterostructures, as well as for doping individual layers.
Molecular Locking with All‐Organic Surface Modifiers Enables Stable and Efficient Slot‐Die‐Coated Methyl‐Ammonium‐Free Perovskite Solar Modules (2023)

The power conversion efficiency (PCE) of the state-of-the-art large-area slot-die-coated perovskite solar cells (PSCs) is now over 19%, but issues with their stability persist owing to significant intrinsic point defects and a mass of surface imperfections introduced during the fabrication process. Herein, the utilization of a hydrophobic all-organic salt is reported to modify the top surface of large-area slot-die-coated methylammonium (MA)-free halide perovskite layers. Bearing two molecules, each of which is endowed with anchoring groups capable of exhibiting secondary interactions with the perovskite surfaces, the organic salt acts as a molecular lock by effectively binding to both anion and cation vacancies, substantially enhancing the materials' intrinsic stability against different stimuli. It not only reduces the ingression of external species such as oxygen and moisture, but also suppresses the egress of volatile organic components during the thermal stability testing. The treated PSCs demonstrate efficiency of 19.28% (active area of 58.5 cm<sup>2</sup> ) and 17.62% (aperture area of 64 cm<sup>2</sup> ) for the corresponding mini-module. More importantly, unencapsulated slot-die-coated mini-modules incorporating the all-organic surface modifier show ≈80% efficiency retention after 7500 h (313 days) of storage under 30% relative humidity (RH). They also remarkably retain more than 90% of the initial efficiency for over 850 h while being measured continuously.
KVM/ARM (2014)

As ARM CPUs become increasingly common in mobile devices and servers, there is a growing demand for providing the benefits of virtualization for ARM-based devices. We present our experiences building the Linux ARM hypervisor, KVM/ARM, the first full system ARM virtualization solution that can run unmodified guest operating systems on ARM multicore hardware. KVM/ARM introduces split-mode virtualization, allowing a hypervisor to split its execution across CPU modes and be integrated into the Linux kernel. This allows KVM/ARM to leverage existing Linux hardware support and functionality to simplify hypervisor development and maintainability while utilizing recent ARM hardware virtualization extensions to run virtual machines with comparable performance to native execution. KVM/ARM has been successfully merged into the mainline Linux kernel, ensuring that it will gain wide adoption as the virtualization platform of choice for ARM. We provide the first measurements on real hardware of a complete hypervisor using ARM hardware virtualization support. Our results demonstrate that KVM/ARM has modest virtualization performance and power costs, and can achieve lower performance and power costs compared to x86-based Linux virtualization on multicore hardware.
1,3‐Diphosphacyclobutadienecobalt(I) Complexes from Phosphaalkynes (1986)

The first diphosphacyclobutadiene with three-coordinate phosphorus could be stabilized as cobalt-complexed compound 3 by dimerization of the phosphaalkyne 1 in the presence of the cobalt complex 2. If 2 is present in excess, di- and tri-nuclear cobalt complexes are also formed, by coordination of the fragment [(C5H5)(C2H4)Co] to the P atoms of 3.
<em>Ex vivo</em> Culture of Mouse Embryonic Skin and Live-imaging of Melanoblast Migration (2014)

Melanoblasts are the neural crest derived precursors of melanocytes; the cells responsible for producing the pigment in skin and hair. Melanoblasts migrate through the epidermis of the embryo where they subsequently colonize the developing hair follicles(1,2). Neural crest cell migration is extensively studied in vitro but in vivo methods are still not well developed, especially in mammalian systems. One alternative is to use ex vivo organotypic culture(3-6). Culture of mouse embryonic skin requires the maintenance of an air-liquid interface (ALI) across the surface of the tissue(3,6). High resolution live-imaging of mouse embryonic skin has been hampered by the lack of a good method that not only maintains this ALI but also allows the culture to be inverted and therefore compatible with short working distance objective lenses and most confocal microscopes. This article describes recent improvements to a method that uses a gas permeable membrane to overcome these problems and allow high-resolution confocal imaging of embryonic skin in ex vivo culture(6). By using a melanoblast specific Cre-recombinase expressing mouse line combined with the R26YFPR reporter line we are able to fluorescently label the melanoblast population within these skin cultures. The technique allows live-imaging of melanoblasts and observation of their behavior and interactions with the tissue in which they develop. Representative results are included to demonstrate the capability to live-image 6 cultures in parallel.
Fine‐needle aspiration of low grade adenosquamous carcinoma of the breast (1996)

Low-grade adenosquamous carcinoma is an unusual variant of mammary carcinoma. This malignancy generally presents as a palpable mass without mammographic microcalcifications, and fine-needle aspiration may be the initial technique selected for diagnosis. To our knowledge, the cytologic findings associated with this neoplasm have not been reported. We report a case of low-grade adenosquamous carcinoma of the breast in a 57-yr-old woman, initially studied by fine-needle aspiration cytology and confirmed by excisional biopsy. The aspiration biopsy smears were characterized by low cellularity and small disoriented clusters containing uniform cells of small to medium size. Bipolar cells were not seen in the background. The diagnostic features and differential diagnosis of this unusual neoplasm are reviewed. Diagn Cytopathol 1996;14:321–324. © 1996 Wiley-Liss, Inc.
Online-trajectory planning for state- and input-constrained linear SISO systems using a switched state variable filter (2017)

The problem of online-trajectory generation for flat feedforward controllers of linear single input single output systems with polytopic state and input constraints is discussed for servo-tracking problems, i.e. for a-priori unknown command reference signals. Such problems occur for example in the context of a joystick or gas pedal operation. For the generation of smooth reference trajectories, required for the realization of a flatness-based feedforward controller, a switched state variable filter is designed in such a way that an optimal trajectory tracking is realized in accordance to the feasible dynamics in the case of state and input constraints. Therefore, a flatness-based relation is derived such that the highest derivative is linked with the respective constraints. In order to obtain a switching law for the selection of the actual active constraint and the adjustment of the admissible dynamics of the filter, an optimization problem with respect to the tracking behavior is solved. The performance of the algorithm is finally discussed by means of simulation studies of example systems.
Interleukin-33 inhibits glucose uptake in human adipocytes and its expression in adipose tissue is elevated in insulin resistance and type 2 diabetes (2022)

Our findings suggest that T2D subjects have higher IL-33 gene and protein expressionin SATthan control subjects, which is associated with insulin resistance and reduced gene expression of lipid storage and adipogenesis markers. IL-33 may reduce adipocyte glucose uptake. This opens up a potential pharmacological route for reversing insulin resistance in T2D and prediabetes.
Antimicrobial properties of plant secondary metabolites (2004)

Increasing awareness of hazards associated with the use of antibiotic and chemical feed additives has accelerated investigations into plants and their extracts as feed additives. The present review mainly discusses two classes of plant secondary compounds in this context, i.e. essential oils and saponins. The broader potential of plants and their extracts is illustrated by the progress of an EC Framework 5 project, 'Rumen-up'. Dietary inclusion of a commercial blend of essential oils causes markedly decreased NH3 production from amino acids in rumen fluid taken from sheep and cattle. This effect is mediated partly by the effects on hyper-NH3-producing bacteria and the protein- and starch-fermenting rumen bacterium, Ruminobacter amylophilus. Saponin-containing plants and their extracts suppress the bacteriolytic activity of rumen ciliate protozoa and thereby enhance total microbial protein flow from the rumen. The effects of some saponins are transient, because saponins are hydrolysed by bacteria to their corresponding sapogenin aglycones, which are much less toxic to protozoa. Saponins also have selective antibacterial effects that may prove useful in, for example, controlling starch digestion. The 'Rumen-up' project began with a targetted collection of European plants and their extracts, which partners have tested for their effects on rumen proteolysis, protozoa, methanogenesis and lactate production. A success rate of about 5% in terms of positive hits illustrates that plant secondary compounds, of which essential oils and saponins comprise a small proportion, have great potential as 'natural' manipulators of rumen fermentation to benefit the farmer and the environment in the future.
A Silica-Supported Double-Decker Silsesquioxane Provides a Second Skin for the Selective Generation of Bipodal Surface Organometallic Complexes (2012)

A well-defined silica-based material with a homogeneous nanolayer presenting identical pairs of vicinal silanols has been prepared by reaction of the surface organometallic species [≡SiOZr(CH2CMe3)3], obtained on a silica dehydroxylated at 900 °C, with the double-decker-shaped silsesquioxane (OH)2DD(OH)2. The surface structure has been established using extensive NMR characterization (1H, 13C, 29Si, HETCOR, double-quantum, triple-quantum). Treatment with Zr(CH2CMe3)4 leads to the first well-defined single-site bipodal grafted bis-neopentyl zirconium complex.
Misfolded amyloid-β-42 impairs the endosomal–lysosomal pathway (2020)

Misfolding and aggregation of proteins is strongly linked to several neurodegenerative diseases, but how such species bring about their cytotoxic actions remains poorly understood. Here we used specifically-designed optical reporter probes and live fluorescence imaging in primary hippocampal neurons to characterise the mechanism by which prefibrillar, oligomeric forms of the Alzheimer's-associated peptide, Aβ42, exert their detrimental effects. We used a pH-sensitive reporter, Aβ42-CypHer, to track Aβ internalisation in real-time, demonstrating that oligomers are rapidly taken up into cells in a dynamin-dependent manner, and trafficked via the endo-lysosomal pathway resulting in accumulation in lysosomes. In contrast, a non-assembling variant of Aβ42 (vAβ42) assayed in the same way is not internalised. Tracking ovalbumin uptake into cells using CypHer or Alexa Fluor tags shows that preincubation with Aβ42 disrupts protein uptake. Our results identify a potential mechanism by which amyloidogenic aggregates impair cellular function through disruption of the endosomal-lysosomal pathway.
Passive Foot Design and Contact Area Analysis for Climbing Mini-Whegs (2007)

Mini-Whegstrade, a power-autonomous vehicle that uses multi-spoke wheel-legs for locomotion, is able to climb vertical glass surfaces with several different wheel-leg designs. Adhesion to the glass is achieved using pressure sensitive adhesives. In this paper, high-speed video is used to compare the performance and contact area during steps of five passive foot designs. The contact area, when normalized by the leg length, may help explain the differences in performance between several designs.