gebhart/patrepeval huggingface dataset:
<i>Azotobacter vinelandii</i> rhodanese (2003)

Rhodanese is a sulfurtransferase which in vitro catalyzes the transfer of a sulfane sulfur from thiosulfate to cyanide. Ionic interactions of the prokaryotic rhodanese-like protein from Azotobacter vinelandii were studied by fluorescence and NMR spectroscopy. The catalytic Cys230 residue of the enzyme was selectively labelled using [15N]Cys, and changes in 1H and 15N NMR resonances on addition of different ions were monitored. The results clearly indicate that the sulfur transfer is due to a specific reaction of the persulfurated Cys residue with a sulfur acceptor such as cyanide and not to the presence of the anions. Moreover, the 1H-NMR spectrum of a defined spectral region is indicative of the status of the enzyme and can be used to directly monitor sulfur loading even at low concentrations. Selenium loading by the addition of selenodiglutathione was monitored by fluorescence and NMR spectroscopy. It was found to involve a specific interaction between the selenodiglutathione and the catalytic cysteine residue of the enzyme. These results indicate that rhodanese-like proteins may function in the delivery of reactive selenium in vivo.
The coping mechanisms of children with school refusal (2002)

There are a variety of ways in which the children of today cope with the stresses of modern life. This paper examines the mechanisms used by a sample of children who had established school refusal and found their mechanisms of coping to be quite different from those of a control group. The findings raise the question as to whether there is a connection between social isolation and poor socialisation in the aetiology of school refusal, and suggest a possible mechanism by which such problems are compounded by enmeshed family relationships. This work also indicates that some protection against the need to refuse school can be gained by establishing good social relationships, focusing upon improving coping strategies and increasing the young person's sense of belonging.
Variational Inference in Sparse Gaussian Process Regression and Latent Variable Models - a Gentle Tutorial (2014)

In this tutorial we explain the inference procedures developed for the sparse Gaussian process (GP) regression and Gaussian process latent variable model (GPLVM). Due to page limit the derivation given in Titsias (2009) and Titsias &amp; Lawrence (2010) is brief, hence getting a full picture of it requires collecting results from several different sources and a substantial amount of algebra to fill-in the gaps. Our main goal is thus to collect all the results and full derivations into one place to help speed up understanding this work. In doing so we present a re-parametrisation of the inference that allows it to be carried out in parallel. A secondary goal for this document is, therefore, to accompany our paper and open-source implementation of the parallel inference scheme for the models. We hope that this document will bridge the gap between the equations as implemented in code and those published in the original papers, in order to make it easier to extend existing work. We assume prior knowledge of Gaussian processes and variational inference, but we also include references for further reading where appropriate.
Chronic Cigarette Smoke Exposure Subdues PP2A Activity by Enhancing Expression of the Oncogene CIP2A (2018)

Phosphatase activity of the major serine threonine phosphatase, protein phosphatase 2A (PP2A), is blunted in the airways of individuals with chronic obstructive pulmonary disease (COPD), which results in heightened inflammation and proteolytic responses. The objective of this study was to investigate how PP2A activity is modulated in COPD airways. PP2A activity and endogenous inhibitors of PP2A were investigated in animal and cell models of COPD. In primary human bronchial epithelial (HBE) cells isolated from smokers and donors with COPD, we observed enhanced expression of cancerous inhibitor of PP2A (CIP2A), an oncoprotein encoded by the KIAA1524 gene, compared with cells from nonsmokers. CIP2A expression was induced by chronic cigarette smoke exposure in mice that coincided with a reduction in PP2A activity, airspace enlargements, and loss of lung function, as determined by PP2A phosphatase activity, mean linear intercept analysis, and forced expiratory volume in 0.05 second/forced vital capacity. Modulating CIP2A expression in HBE cells by silencing RNA or chemically with erlotinib enhanced PP2A activity, reduced extracellular-signal-regulated kinase phosphorylation, and reduced the responses of matrix metalloproteinases 1 and 9 in HBE cells isolated from subjects with COPD. Enhanced epithelial growth factor receptor responses in cells from subjects with COPD were observed to modulate CIP2A expression levels. Our study indicates that chronic cigarette smoke induction of epithelial growth factor receptor signaling and CIP2A expression can impair PP2A responses that are associated with loss of lung function and enhancement of proteolytic responses. Augmenting PP2A activity by manipulating CIP2A expression may represent a feasible therapeutic approach to counter smoke-induced lung disease.
Fully Blind Electromagnetic Characterization of Deep Sub-Wavelength (λ/100) Dielectric Slabs With Low Bandwidth Differential Transient Radar Technique at 10 GHz (2021)

Transient radar method (TRM) is introduced as a novel non-destructive testing (NDT) technique that is capable of analyzing fully blindly and simultaneously the electromagnetic (EM) properties as well as geometric parameters of deep sub-wavelength thin single layer slabs. This study focuses on the minimum detectable layer thickness by means of TRM, which mainly depends on the experimental setup configuration. In this article, the complex permittivity and thickness of three polyvinyl chloride (PVC) sheets are extracted by means of a differential TRM set-up. The thickness of these PVC sheets was 1 mm, 500 μm, and 300 μm that corresponded to λ /30, λ /60, and λ /100, respectively (λ is the wavelength in free space). The carrier frequency was 10 GHz and the experiments were done in a bistatic radar setup. A differential TRM structure was used in this experiment. Some error sources, such as switch leakage and non-perpendicular illumination as well as systematic errors are considered as well. The experimentally obtained results are as follows: the thickness of these samples were 1033 ± 12, 535 ± 11, and 302 ± 9 μm with 1.18%, 0.94%, and 2.89% relative error, respectively. Additionally, the complex permittivity of these samples was found as (2.73 ± 0.02)-(0.23 ± 0.01)j, (2.70 ± 0.02)-(0.20 ± 0.02)j, and (2.65 ± 0.02)-(0.37 ± 0.01)j, respectively. This novel technique has the potential for deployment in a wide range of applications ranging from the piping, wind energy industry, and automotive to biotechnology, food industry, clinical monitoring, and pharmacy.
Content addressable memories in reproducing Kernel Hilbert spaces (2008)

Content addressable memories (CAM) are one of the few technologies that provide the capability to store and retrieve information based on content. Even more useful is their ability to recall data from noisy or incomplete inputs. However, the input data dimension limits the amount of data that CAMs can store and successfully retrieve. We propose to increase the amount of information that can be stored by implementing CAMs in a reproducing kernel Hilbert space where the input dimension is practically infinite, effectively lifting this CAM limitation. We show the advantages of kernel CAMs over CAMs by comparing their performance in information retrieval, generalization, storage, and online learning.
The remote access to IPsec-VPN gateway over mobile IPv6 (2005)

Mobile IPv6 is thought to be dominant protocol for providing mobility. In the near future, most portable communication devices will deploy mobile IPv6 mechanism. Our main concerns are that such mobile devices are going to access to their corporate network such as VPN. In this paper, we propose the efficient communication for IPsec-VPN access of mobile nodes. Our proposal is that mobile nodes use the IKEv2 CP to transfer BU. We think that our simple BU should be able to be done in IKEv2 initial exchange as well as in IKEv2 informational exchange. It is because BU can be occurred at any time before initial IPsec setup is not completed. Thus, we intend to use IKEv2 CP instead of IKEv2 notify payload (N). We consider two cases. One is the case that home agent exists in VPN domain and the other is the case that home agent is away from VPN domain. In both cases, our proposal reduces the total signals to access to VPN. Nevertheless, the security is not compromised
Curiosity in Hindsight: Intrinsic Exploration in Stochastic Environments (2022)

Consider the problem of exploration in sparse-reward or reward-free environments, such as in Montezuma's Revenge. In the curiosity-driven paradigm, the agent is rewarded for how much each realized outcome differs from their predicted outcome. But using predictive error as intrinsic motivation is fragile in stochastic environments, as the agent may become trapped by high-entropy areas of the state-action space, such as a "noisy TV". In this work, we study a natural solution derived from structural causal models of the world: Our key idea is to learn representations of the future that capture precisely the unpredictable aspects of each outcome -- which we use as additional input for predictions, such that intrinsic rewards only reflect the predictable aspects of world dynamics. First, we propose incorporating such hindsight representations into models to disentangle "noise" from "novelty", yielding Curiosity in Hindsight: a simple and scalable generalization of curiosity that is robust to stochasticity. Second, we instantiate this framework for the recently introduced BYOL-Explore algorithm as our prime example, resulting in the noise-robust BYOL-Hindsight. Third, we illustrate its behavior under a variety of different stochasticities in a grid world, and find improvements over BYOL-Explore in hard-exploration Atari games with sticky actions. Notably, we show state-of-the-art results in exploring Montezuma's Revenge with sticky actions, while preserving performance in the non-sticky setting.
Thermoelectric properties of the Zintl phases Yb_5M_2Sb_6 (M = Al, Ga, In) (2015)

Zintl compounds with chemical formula Yb_5M_2Sb_6 (M = Al, Ga, and In) form one of two known A_5M_2Pn_6 structure types characterized by double chains of corner-linked MPn_4 tetrahedra bridged by Pn_2 dumbbells. High temperature electronic and thermal transport measurements were used to characterize the thermoelectric properties of Yb_5M_2Sb_6 compounds. All samples were found to exhibit similar high p-type carrier concentrations, low resistivity and low Seebeck coefficients in agreement with the band structure calculations. These results, combined with previous studies, suggest that Yb_5M_2Sb_6 compounds are semimetals (i.e., they lack an energy gap between the valence and conduction bands), in contrast to the semiconducting alkaline earth (Ca, Sr, Ba) and Eu based A_5M_2Sb_6 compounds. Yb_5M_2Sb_6 compounds have very low lattice thermal conductivity, comparable to other closely related A_5M_2Sb_6 and A_3MSb_3 phases. However, due to the semimetallic behaviour, the figure of merit of investigated samples remains low (zT < 0.15).
Novel O/W Emulsions by Utilizing a Vesicle/Disc Transformation of Polyether Modified Silicone (2023)

Emulsification is an important technology in the field of cosmetics and household products. Emulsions are in non-equilibrium state; therefore, the products vary depending on the preparation process, and their state changes with time. Furthermore, it is known empirically that different types of oils have different emulsification properties (preparation and stability). For these reasons, the variables in emulsification research are numerous and complicated to analyze. As a result, many industrial applications have had to rely on empirical rules. In this study, emulsions with a lamellar liquid crystalline phase as an adsorption layer at the emulsion interface were investigated. The characteristics of O/W emulsions formed with the excess solvent phases (aqueous and oil phases) separated from the lamellar liquid crystalline phase were investigated based on the phase equilibrium of the ternary system.As a result, it was found that by agitating the aqueous phase containing dispersed vesicles of emulsifier (polyether modified silicone) together with the oil phase, an emulsion with a uniform interfacial membrane of lamellar liquid crystalline phase could be obtained. The emulsions prepared by this method were found to have good stability against coalescence. The process of transformation from vesicles to the uniform liquid crystal interfacial membrane during the emulsification process was clarified by a freeze-fracture transmission electron micrograph and the calculation of interfacial membrane thickness based on precise particle size analysis. Furthermore, the emulsification properties of polyether-modified silicones were clarified using polar oils and silicone oils, which are a combination of high/low and low/high compatibility with hydrophilic (polyethylene glycol) and lipophilic (polydimethylsiloxane) groups of polyether modified silicone, respectively. It is expected that this research will lead to the evolution of various functionalities in products in the fields of cosmetics, household products, food, pharmaceuticals, paint and others.
Influence of paper properties on streamers creeping in mineral oil (2017)

This work presents an experimental study of second mode positive streamers propagating along mineral oilpaper interfaces. A point-plane arrangement immersed in mineral oil with the paper inclined 60 degrees to the plane electrode is used to create the liquid-solid interface. Kraft paper and a kraft fibril paper, made from cellulosic micro and nano fibrils, with higher density and lower surface roughness are used as the solid materials. High speed shadowgraphy and charge recordings are used to compare the propagation of second mode positive streamers along the mineral oil-kraft paper and mineral oil-kraft fibril paper. Streamers creeping along the mineral oil-kraft paper interface propagate mainly into the liquid, with one or two main filaments. In comparison, the streamers propagating along the kraft fibril paper show a strong reduction of the branching; these streamers consist of a single filament that propagates exactly on the solid surface. Streamers along the kraft fibril paper also have longer propagation time than for the case with kraft paper. Mutual electrostatic shielding between filaments is observed for the streamers creeping on the kraft paper. An electrostatic analysis of the influence of permittivity, density and surface roughness of the solid in the electrical properties of the streamer filaments is also performed.
Optimisation de la production de méthane en codigestion par l'ajout de résidus issus du raffinage des huiles végétales (2011)

National audience
Tunable higher-order orbital angular momentum using polarization-maintaining fiber (2017)

For the first time, to the best of our knowledge, light with orbital angular momentum (OAM) of ±2ℏ per photon is produced using commercially available polarization-maintaining fiber with modal purity of 96%. Twist measurements demonstrate that the average orbital angular momentum can be continuously tuned between ±2ℏ. The authors consider beams of non-integer OAM, created using the presented method, as superpositions of integer OAM states.
Clarification Regarding “Phase II Trials Published in 2002: A Cross-Specialty Comparison Showing Significant Design Differences between Oncology Trials and Other Medical Specialties” and the Accompanying Commentary, “Phase II Cancer Trials: Out of Control?” (2007)

To the Editors: We would like to clarify our comments about the use of placebos in phase II cancer clinical trials, as discussed in the article by Michaelis and Ratain, “Phase II Trials Published in 2002: A Cross-Specialty Comparison Showing Significant Design Differences between Oncology Trials and Other Medical Specialties” (1), and the accompanying commentary, “Phase II Cancer Trials: Out of Control” by Chabner (2).In particular, the commentary addressed the “problematic” inclusion of a control group treated only with placebo as one arm of a randomized phase II evaluation of an experimental compound. Although many oncologists would find it difficult to offer such a trial to patients with progressive and potentially fatal disease, we both strongly endorse certain “innovative” trial designs that use placebos. Such designs might include either a limited period of placebo treatment versus initial therapy with experimental drug, a trial of a standard agent plus placebo versus the same standard agent plus an experimental agent, or a randomized discontinuation design in which all patients receive experimental drug, and, thereafter, stable patients receive either continued experimental drug or placebo, until disease progression. These and other designs might provide valuable information regarding the effect of the experimental drug on disease progression, and at the same time provide an opportunity to assess the effect of drug on biomarkers. In these and other trial designs, periods of placebo treatment are not likely to adversely affect patient outcomes compared with “standard” treatment. Other novel designs using placebos are certainly possible.
Response Characteristics and Mechanisms of Dynamic Fluid Field for Well Interference of Coal Bed Methane Group Wells in Production Block (2014)

According to production data and reservoir data of 16 coal bed methane (CBM) wells in southern Qinshui Basin, this paper draws the contour map of groundwater fluid potential at 8 moments in the production monitoring area and establishes three-dimensional visualization model of superimposed pressure drop funnel in CBM well with Matlab mathematical software; discusses the response relationship between well interference and dynamic fluid field on the basis of analyzing dynamic change features of groundwater fluid potential and evolution features of superimposed pressure drop funnel and puts forward an evaluation program of dynamic fluid field for well interference. The research result shows that dynamic fluid field has a good response relationship with well interference of CBM well and is manifested by the corresponding relation between evolutionary phase and space distribution. Evolution features of dynamic fluid field can be used to judge the phase and degree of well interference. The stage when well interference does not form is corresponding to the failure stage of original groundwater fluid potential and evolutionary phase of single-well pressure drop funnel. CBM wells do not have well interference and pressure drop funnel exists in the form of independent funnel. The space distribution of groundwater fluid potential is balanced. Due to the influence of groundwater fluid potential distribution, formation water flows to the shaft from the scope of pressure drop funnel. The stage when well interference forms preliminarily is corresponding to the stage of differentiation and reconstruction of groundwater fluid potential and formation stage of local superimposed pressure drop funnel. CBM wells start to have well interference and the degree of superposition of pressure drop funnel increases in local areas. “Low-lying” collecting area of groundwater fluid potential forms in superimposed area. Coal bed water flows to this area. The stabilization stage of well interference is corresponding to the formation and stabilization stage of new groundwater fluid potential and formation stage of regional superimposed pressure drop funnel. Regional superimposed pressure drop funnel is basically mature. New groundwater fluid potential centering on superimposed pressure drop funnel basically forms and coal bed water flows to the center of well network from surrounding areas.
Optimizing Hydraulic Fracturing Treatment Integrating Geomechanical Analysis and Reservoir Simulation for a Fractured Tight Gas Reservoir, Tarim Basin, China (2013)

A comprehensive geomechanical study was carried out to optimize stimulation for a fractured tight gas reservoir in the northwest Tarim Basin. Conventional gel fracturing and acidizing operations carried out in the field previously failed to yield the expected productivity. The objective of this study was to assess the effectiveness of slickwater or low-viscosity stimulation of natural fractures by shear slippage, creating a conductive, complex fracture network. This type of stimulation is proven to successfully exploit shale gas resources in many fields in the United States.
Automated blood vessel extraction using local features on retinal images (2016)

An automated blood vessel extraction using high-order local autocorrelation (HLAC) on retinal images is presented. Although many blood vessel extraction methods based on contrast have been proposed, a technique based on the relation of neighbor pixels has not been published. HLAC features are shift-invariant; therefore, we applied HLAC features to retinal images. However, HLAC features are weak to turned image, thus a method was improved by the addition of HLAC features to a polar transformed image. The blood vessels were classified using an artificial neural network (ANN) with HLAC features using 105 mask patterns as input. To improve performance, the second ANN (ANN2) was constructed by using the green component of the color retinal image and the four output values of ANN, Gabor filter, double-ring filter and black-top-hat transformation. The retinal images used in this study were obtained from the "Digital Retinal Images for Vessel Extraction" (DRIVE) database. The ANN using HLAC output apparent white values in the blood vessel regions and could also extract blood vessels with low contrast. The outputs were evaluated using the area under the curve (AUC) based on receiver operating characteristics (ROC) analysis. The AUC of ANN2 was 0.960 as a result of our study. The result can be used for the quantitative analysis of the blood vessels.
A High‐Throughput Screen for Chemical Inhibitors of Exocytic Transport in Yeast (2010)

Most of the components of the membrane and protein traffic machinery were discovered by perturbing their functions, either with bioactive compounds or by mutations. However, the mechanisms responsible for exocytic transport vesicle formation at the Golgi and endosomes are still largely unknown. Both the exocytic traffic routes and the signaling pathways that regulate these routes are highly complex and robust, so that defects can be overcome by alternate pathways or mechanisms. A classical yeast genetic screen designed to account for the robustness of the exocytic pathway identified a novel conserved gene, AVL9, which functions in late exocytic transport. We now describe a chemical-genetic version of the mutant screen, in which we performed a high-throughput phenotypic screen of a large compound library and identified novel small-molecule secretory inhibitors. To maximize the number and diversity of our hits, the screen was performed in a pdr5Delta snq2Delta mutant background, which lacks two transporters responsible for pleiotropic drug resistance. However, we found that deletion of both transporters reduced the fitness of our screen strain, whereas the pdr5Delta mutation had a relatively small effect on growth and was also the more important transporter mutation for conferring sensitivity to our hits. In this and similar chemical-genetic yeast screens, using just a single pump mutation might be sufficient for increasing hit diversity while minimizing the physiological effects of transporter mutations.