gebhart/patrepeval huggingface dataset:
Characterization of High-Order Diphtheria Toxin Oligomers (2000)

In 3D domain swapping, a domain of a protein breaks its noncovalent bonds with the protein core and its place is taken by the identical domain of another molecule, creating a strongly bound dimer or higher order oligomer. For some proteins, including diphtheria toxin, 3D domain swapping may affect protein function. To explore the molecular basis of 3D domain swapping in a well-characterized protein system, domain-swapped oligomers of diphtheria toxin were produced by freezing and thawing under a variety conditions, including in various salts and buffers, and at various temperatures. Reaction yields were followed by high-performance size-exclusion chromatography. The traditional low pH pulse produced by freeze-thawing in mixed sodium phosphate buffer induces the oligomerization of DT, but the addition of alkali chloride salts was found to increase the yield in the order of Li(+) > Na(+) > K(+). Unexpectedly, oligomers also formed when DT was frozen and thawed in the presence of 1 M LiCl alone. Slower freezing and thawing of the mixture led to the production of more and larger oligomers. DT oligomers were also produced by exposure to acidic buffers, and were found by electron microscopy to adopt both linear and cyclized forms in a wide distribution of sizes. Upon the basis of these results, the model for the production of DT oligomers by freezing and thawing was expanded to include a salt-mediated pathway. We present a mechanism for the formation of high-order DT oligomers by acidification that takes into account domain swapping and hydrophobic interactions.
Clinical application of high frequency jet ventilation in stereotactic liver ablations – a methodological study (2018)

<b>Background:</b> Computer-assisted navigation during thermal ablation of liver tumours, may help to correct needle placement and improve ablation efficacy in percutaneous, laparoscopic and open interventions. The potential advantage of using high frequency jet-ventilation technique (HFJV) during the procedure is by minimising the amplitude of respiration-related upper-abdominal organs movements. The aim of this clinical methodological trial was to establish whether HFJV would give less ventilatory induced liver movements than conventional ventilation, during stereotactic navigated ablation of liver metastases under open surgery. <b>Methods:</b> Five consecutive patients scheduled for elective, open liver ablation under general propofol and remifentanil anaesthesia were included in the study protocol. During the stereotactic targeting of the tumours, HFJV was chosen for intraoperative lung ventilation. For tracking of liver movement, a rigid marker shield was placed on the liver surface and tracked with an optical position measurement system. A 4D position of the marker shield was measured for HFJV and conventional tidal volume lung ventilation (TV). At each time point the magnitude of liver displacement was calculated as an Euclidean distance between translational component of the marker shield's 3D position and previously estimated centroid of the translational motion. <b>Results:</b> The mean Euclidean liver displacement was 0.80 (0.10) mm for HFJV and 2,90 (1.03) mm for TV with maximum displacement going as far as 12 mm on standard ventilation (p=0.0001). <b>Conclusion:</b> HFJV is a valuable lung ventilation method for patients undergoing stereotactic surgical procedures in general anaesthesia when reduction of organ displacement is crucial.
Final Results of Phase III SYMMETRY Study: Randomized, Double-Blind Trial of Elesclomol Plus Paclitaxel Versus Paclitaxel Alone As Treatment for Chemotherapy-Naive Patients With Advanced Melanoma (2013)

The addition of elesclomol to paclitaxel did not significantly improve PFS in unselected patients with advanced melanoma. The association between baseline LDH and clinical outcomes suggests that LDH may be a predictive factor for treatment with this combination, consistent with recent findings on the association between elesclomol anticancer activity and cellular metabolic state.
Monumentale armenzorg, over armenzorg en gebouwen (2009)

Ter gelegenheid van de Vlaamse open monumentendag werd deze 'inspiratemodule' geschreven over monumenten en armenzorg.
Real-time Motion Control of Humanoid for Skating Motion by Foot Force Control (2016)

In this paper, we propose a real-time control method for skating motion of humanoid. Humanoid robots have to suppress slip for acceleration in pushing the ground with one foot while keeping dynamic balance for skating. Therefore it is difficult to generate skating motions satisfying both dynamic balance and slip suppression. For solving this problem, we propose the Skating Motion Generator considering maximum frictional force and Skating Motion Stabilizer adjusting sole pressure distribution for both keeping balance and suppressing slip. We show the effectiveness of the proposed real-time controller through the experiments, in which life-sized humanoid HRP-2 skates on the skateboard.
Large raindrops against melting hail: calculation of specific differential attenuation, phase and reflectivity (2015)

The specific differential attenuation caused by large raindrops and a special form of melting hail is computed and studied. Raindrops of smoothed conical shapes and hailstones modelled by an ice sphere surrounded by a water torus are considered. For the former, scattering computation is carried out by the T‐matrix method, while the higher‐order method of moments in the surface integral equation formulation is used for the latter. Results show a much higher specific differential attenuation factor for hail particles, with the smallest hail showing values similar to the largest raindrops. This can explain the higher than expected differential attenuation observed by C‐band radars in intense storms as reported in some previous studies. Results also show that the melting hail particles exhibit higher specific differential phase factor than large raindrops, but have similar differential reflectivity.
Higher criticism for detecting sparse heterogeneous mixtures (2004)

Higher criticism, or second-level significance testing, is a multiple-comparisons concept mentioned in passing by Tukey. It concerns a situation where there are many independent tests of significance and one is interested in rejecting the joint null hypothesis. Tukey suggested comparing the fraction of observed significances at a given α-level to the expected fraction under the joint null. In fact, he suggested standardizing the difference of the two quantities and forming a z-score; the resulting z-score tests the significance of the body of significance tests. We consider a generalization, where we maximize this z-score over a range of significance levels 0<α≤α0. We are able to show that the resulting higher criticism statistic is effective at resolving a very subtle testing problem: testing whether n normal means are all zero versus the alternative that a small fraction is nonzero. The subtlety of this “sparse normal means” testing problem can be seen from work of Ingster and Jin, who studied such problems in great detail. In their studies, they identified an interesting range of cases where the small fraction of nonzero means is so small that the alternative hypothesis exhibits little noticeable effect on the distribution of the p-values either for the bulk of the tests or for the few most highly significant tests. In this range, when the amplitude of nonzero means is calibrated with the fraction of nonzero means, the likelihood ratio test for a precisely specified alternative would still succeed in separating the two hypotheses. We show that the higher criticism is successful throughout the same region of amplitude sparsity where the likelihood ratio test would succeed. Since it does not require a specification of the alternative, this shows that higher criticism is in a sense optimally adaptive to unknown sparsity and size of the nonnull effects. While our theoretical work is largely asymptotic, we provide simulations in finite samples and suggest some possible applications. We also show that higher critcism works well over a range of non-Gaussian cases.
Microfluidic device for analysis of magnetorheological fluids’ properties (2022)

The valve mode is the most common operational mode of magnetorheological fluid (MRF) devices in engineering applications. Magnetorheological (MR) valves have been studied upon their self-sensing capabilities resulting from the electro-magnetic induction phenomenon. In parallel, studies have been carried out regarding the microstructural properties and the analytical modeling of MRFs used in valves. This paper presents the design and fabrication of a microfluidic system in the form of a magnetic circuit, consisting of a MRF flow channel, with dimensions close to those of previously studied miniaturized MR valves. The channel is enclosed in ferromagnetic and transparent sheets. The sheets facilitate the magnetic field distribution, created by a coil. The channel allows the microscopical MRF particles observation and their correlation with the MRF magnetic and rheological properties when the self-sensing phenomenon occurs.
ProgXe (2010)

We demonstrate ProgXe, a practical approach to support Multi-Criteria Decision Support (MCDS) applications that need to report results as they are being generated to enable the user to make competitive decisions. ProgXe transforms the execution of MCDS queries involving skyline over joins to be non-blocking by progressively generating results early and often. The demonstration highlights key features of our progressive execution framework that optimizes for early output generation by: (1) evaluating the query at multiple levels of abstraction, (2) exploiting the skyline knowledge gained from both input as well as mapped output spaces. The audience will be able to submit MCDS queries. We provide visualization tools that enable the user to make quick decisions, compare alternative techniques, and provide capability to fine-tune the query predicates based on the early output results.
Enhanced reduction of C–N multiple bonds using sodium borohydride and an amorphous nickel catalyst (2011)

Amorphous nickel powder (Ni(0)) was utilised as a catalyst under mild, aqueous, basic conditions for enhancing the sodium borohydride-mediated reduction of C-N multiple bonds such as oximes, imines, hydrazones and nitriles to produce the corresponding amines in good to excellent yields.
112: Rigorous protocols using Alemtuzumab to T cell deplete stem cell products (2007)

The therapeutic effect of allogeneic peripheral stem cell transplantation (alloPSCT) is related to an immune-mediated graft-versus-tumor (GVT) effect. However, alloPSCT is limited by T-cell mediated graft-versus-host disease(GVHD). Approaches used to treat or prevent GVHD include in vitro or in vivo purging of T cells using monoclonal antibodies such as Alemtuzumab, which is directed against CD52 on B and T lymphocytes, monocytes, and some dendritic cells (DCs). Alemtuzumab has been injected systemically to treat established GVHD, and ex vivo to purge T cells from stem cell products (SCPs) to reduce GVHD induction. T-cell depletion with Alemtuzumab infusion is an effective method to treat GVHD but is also associated with relapse and infectious disease. Ex vivo purging by the addition Alemtuzumab to a SCP, shaking for 15 minutes and infusion is also effective. However, the efficacy of this T cell purging protocol can not be assessed and potentially results Alemtuzumab infusion. The present study examined the effect of Alemtuzumab co-incubation on cellular subsets and the mechanism of purging i.e. antibody dependant cellular cytotoxicity (ADCC) vs. antibody-complement toxicity. Our studies revealed that cellular concentration is critical to purging activity, such that high cellularity (10e8 cells/ml) results in a significant loss (65%) of T and B cells with only 1 hr co-incubation, raising to 85-90% at a 6 hr co-incubation. Co-incubation at a log lower cellularity results in a 20-30% T-cell loss. ADCC is the primary purging mechanism; however, serum is required to retain cellular viability as is DNAse to reduce cellular clumping. Co-incubation temperature has little effect on purging, although cellular viability is higher at 4C compared to 37C. T, B and NK cells are sensitive to Alemtuzumab ADCC. DCs have a lower sensitivity and there is a differential sensitivity of DC subsets to alemtuzumab-mediated ADCC, such that CD123+ DCs have a lower sensitivity as compared to the CD11c+ DCs. Further, immature myeloid suppressor cells (IMSCs) that are Lin-DR-CD11b+ or Lin-DR-CD14-CD11b+ cells are refractory to alemtuzumab toxicity. This novel observation is of interest as IMSCs can induce T cell tolerance and thus have the potential to control GVHD. Critically, alemtuzumab purging of a hematopoietic stem cell products has no effect on CD34+ cell numbers and their (CFU-c) as assessed in vitro.
Realizing Comprehensive User Profile as the Core Element of Adaptive and Personalized Communication Environments and Systems (2008)

Challenges today in the Web personalization and adaptation research area range from heterogeneous user needs and user environment issues such as current location and time to multi-channel delivery of applications concerning Web-based content related to services, educational multimedia, entertainment, commerce, etc. Nowadays, most Web personalization systems implement various techniques to extract the user profiles, which serve as the main component of such systems. Based on given user preferences and navigation behavior, the Web-based content returns the requested personalized result. The main scope of this paper is to present the various techniques employed by such systems with regard to extraction of user profiles and to introduce a comprehensive user profilethat includes user perceptual preference characteristics. It further analyzes the main intrinsic user characteristics such as visual, cognitive and emotional-processing parameters that are incorporated as well as the ‘traditional’ user profile characteristics that together tend to give the most optimized, adapted and personalized outcome. It finally presents a Web adaptation and personalization system that implements the proposed comprehensive user profile as well as the initial evaluation results.
Atherosclerosis--reversal with therapy. (1993)

Evidence for atherosclerosis reversal comes from studies in animals wherein atherosclerosis is induced and then allowed to regress, autopsy studies of starved humans, and angiographic studies testing antiatherosclerosis treatment. Animal models and autopsy studies have provided detailed histologic and biochemical descriptions of regression. Cellular and subcellular information exists on what can occur, but because the same lesions are not re-examined, what actually does occur is unknown. Studies of isolated arterial cell systems and intact lesions indicate that atherogenesis involves at least the following: Increased permeability of the endothelium to macromolecules such as low-density lipoprotein; platelet adherence to areas of functional endothelial injury or denudation; the entrance of monocytes or macrophages and lymphocytes into the subintimal space; and the secretion of growth factors by platelets, injured endothelium, and macrophages. These processes can be initiated or enhanced by various vasoactive agents that induce endothelial cell constriction with the opening of endothelial junctions. These processes also can recruit smooth muscle cells from the media to the subintima where they proliferate. Proliferating smooth muscle cells, along with macrophages, can internalize lipids and lipoproteins to form foam cells. Subintimal smooth muscle cells can also synthesize collagen, elastin, glycosaminoglycans, and other connective tissue elements that trap lipoproteins. Peroxidative injury increases the atherogenic potential of both cholesteryl ester-rich (low-density) and triglyceride-rich (very-low-density and intermediate-density) lipoproteins. Steep oxygen gradients within the arterial wall create local conditions for free radical generation, and any increase in residence time of lipoprotein particles can be atherogenic. In summary, there are many areas where treatment may retard or reverse atherogenesis. Angiographic trials that identify and track individual human lesions have shown that reducing known atherogenic risk factors can lessen coronary and femoral atherosclerosis. But they provide no information on events within arterial wall cells or the intracellular matrix. They deal only with lesions that intrude into the vessel lumen and obtain measurements at infrequent intervals. The weight of evidence is that regression is possible, but there is no consensus on the most effective therapy. The challenge for future trials is to select optimal targets for intervention among the known atherogenic processes.
Influence de l'intensité du champ magnétique sur l'imagerie RMN des poumons à l'aide d'hélium-3 hyperpolarisé (2003)

Les maladies pulmonaires obstructives chroniques sont la quatrieme cause de mortalite en Europe. Les techniques disponibles pour les suivre ne permettent de diagnostiquer la maladie que tardivement. Une nouvelle methode a ete proposee en 1994 : l'imagerie par resonance magnetique (IRM) avec des gaz hyperpolarises (HP). Les poumons constituent un immense interface entre le gaz et le tissu. Dans un champ magnetique (B0), la difference de susceptibilite magnetique entre les deux milieux a pour consequence de deteriorer le signal. Cet effet est d'autant plus fort que B0 est eleve. Ayant a notre disposition deux appareils a deux B0 differents (0,1 T et 1,5 T) ainsi qu'un systeme de pompage optique pour produire de l'helium 3 (3He) HP, nous avons etudie quantitativement l'influence de B0 sur le signal de l'3He HP dans les poumons. Dans un premier temps les bases theoriques et la liste exhaustive des materiels necessaires pour cette etude ont ete presentees. Puis nous avons mis en evidence que le temps de relaxation transversale de l'3He HP lors de l'application d'un train d'echos de spins, T2cpmg, s'allonge lorsque B0 decroit. Une variation de deux ordres de grandeur a ete observee entre 0,1 et 1,5 T. Des etudes sur modele animal (rat) ont montre que d'une part T2cpmg a une sensibilite au remplissage pulmonaire equivalente a celle du coefficient apparent de diffusion, et d'autre part l'ajout d'un agent super paramagnetique provoque la compensation de l'effet de susceptibilite. Nous avons ensuite mis en evidence le rallongement du temps de vie du signal de l'helium-3 HP dans les poumons, T2*, a faible B0. Enfin une comparaison du rapport signal sur bruit mesure sur les deux appareils a ete entreprise. En conclusion bien que le rallongement de T2* a faible B0 soit benefique pour l'IRM, cet effet est limite et l'utilisation d'appareil classique haut champ ne represente pas un inconvenient determinant pour cette application.
Genome‐Wide Meta‐Analysis of Cerebrospinal Fluid Biomarkers in Alzheimer's Disease and Parkinson's Disease Cohorts (2023)

Our study identified a novel association at the intronic region of DNAAF5 associated with increased levels of p-tau across all diseases. We also observed some disease-specific genetic associations with these biomarkers. Published 2023. This article is a U.S. Government work and is in the public domain in the USA.
Multi-resolution error analysis of predicted absorption coefficients. Method and computer implementation. Application to the IR spectrum of methane at high temperature. (2009)

A general method for the estimation of the confidence interval of molecular absorption coefficients is presented. It combines statistical numerical experiments with analytical calculations. The method uses line parameter predictions (position and intensity) with known estimated uncertainties. The propagation of errors from line parameters to absorption coefficients or cross-sections are analyzed in detail as a function of the resolution. This work is especially intended to provide expert information for applications requiring theoretical predictions for which the present state of the art of line by line high-resolution modeling is not accurate enough to meet the experimental precision. As an illustration, it is applied to predict the absorption coefficient of methane at high temperature involving simultaneously well known lower energy levels (cold bands) and higher energy levels with much lower precisions (hot bands). Potential extensions to applications for atmospheric remote sensing of astrophysical objects are discussed.
Targeted monitoring in offshore windfarms — the need to understand cause–effect relationshipsin the marine benthos (2012)

In many European countries offshore windfarm projects are accompanied by obligatory
environmental impact assessments, including baseline monitoring of the marine benthos and
demersal fish. The effects of offshore windfarm developments on the benthic system are complex.
However, legal baseline monitoring merely allows for net effect descriptions but not for identifying
and understanding the underlying processes. Instead, key processes should be identified and
become subject to hypotheses‐based target monitoring and/or experimental studies in order to
make environmental impact assessments more efficient and reduce duplication internationally. We
compiled an overview over the anthropogenic activities associated with the construction and
operation of offshore windfarms and identified cause–effect relationship to facilitate the
development of specific hypotheses. We expect offshore windfarming activities to modify the geomorphological
and hydrodynamic environment at different temporal and spatial scales. The
environmental effects will have consequences for the behaviour and physiology of benthic
organisms, including demersal fish, restructuring natural local populations and communities.
Major effects on biological production, biogeochemical processes, as well as on structure and
function related to biodiversity, are expected from the massive colonization of the artificial
underwater constructions by a specific hard‐bottom fauna which is naturally missing in soft
sedimentary habitats. Understanding the mechanisms behind these changes is a priority for
assessing and predicting the ecological implications for the benthic system. Such predictions may
help to develop science‐based mitigation actions.
Limitations of Microresonators as Heralded Single Photon Sources (2016)

We demonstrate a fundamental limitation of the use of microresonators as heralded single photon sources. Such sources suffer from a tradeoff between heralding efficiency and heralding rate, which depend sensitively on the resonator-channel coupling.
Dielectric and thermal properties of Polyamide-imide (PAI) films (2009)

Polyamide-imide (PAI) materials appear as potential candidates for the encapsulation of wide band gap semiconductor power devices operating at high temperature (>200°C). However, electrical properties of PAIs are under-known compared to those of polyimides (Pis). We propose to evaluate the dielectric properties of two PAI materials with two different glass transition temperatures Tg. The aim is to observe the benefit of increasing T <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">g</sub> , from 280 up to 335°C for a novel kind of PAIs. So, the broadband dielectric relaxation spectroscopy has been used for measuring the dielectric parameters versus temperature. This paper highlights the role of the glass transition phenomenon in the dielectric properties evolution of PAIs at high temperature. It appears that the glass transition temperature has a strong influence in both the increase of the permittivity, the loss factor and the dc conductivity of several orders of magnitude, and in the characteristic temperature shift when these increases occur.