gebhart/patrepeval huggingface dataset:
Underlying molecular alterations in human dihydrolipoamide dehydrogenase deficiency revealed by structural analyses of disease-causing enzyme variants (2019)

Human dihydrolipoamide dehydrogenase (hLADH, hE3) deficiency (OMIM# 246900) is an often prematurely lethal genetic disease usually caused by inactive or partially inactive hE3 variants. Here we report the crystal structure of wild-type hE3 at an unprecedented high resolution of 1.75 Å and the structures of six disease-causing hE3 variants at resolutions ranging from 1.44 to 2.34 Å. P453L proved to be the most deleterious substitution in structure as aberrations extensively compromised the active site. The most prevalent G194C-hE3 variant primarily exhibited structural alterations close to the substitution site, whereas the nearby cofactor-binding residues were left unperturbed. The G426E substitution mainly interfered with the local charge distribution introducing dynamics to the substitution site in the dimer interface; G194C and G426E both led to minor structural changes. The R460G, R447G and I445M substitutions all perturbed a solvent accessible channel, the so-called H+/H2O channel, leading to the active site. Molecular pathomechanisms of enhanced reactive oxygen species (ROS) generation and impaired binding to multienzyme complexes were also addressed according to the structural data for the relevant mutations. In summary, we present here for the first time a comprehensive study that links three-dimensional structures of disease-causing hE3 variants to residual hLADH activities, altered capacities for ROS generation, compromised affinities for multienzyme complexes and eventually clinical symptoms. Our results may serve as useful starting points for future therapeutic intervention approaches.
Acoustics in granular porous media and the consolidation continuum. (2009)

One key influence on acoustic wave propagation in granular porous media is the degree to which the solid constituent grains can be treated as fully consolidated, weakly and/or partially consolidated, or entirely unconsolidated. Well-known results of Gassmann and Biot all implicitly assume that the medium is fully consolidated, with welded contacts at the grain-to-grain interfaces. Such implicit assumptions are also present in standard bounding methods for elastic behavior, such as the Hashin-Shtrikman bounds of elasticity. Influence of reductions in the degree of consolidation can be quantified for partially or weakly consolidated media, and granular media having no welded contacts can also be treated as porous media for sound waves in the Biot-Gassmann sense when grains are experiencing sufficient overall confining stress. Methods recently developed to quantify wave propagation characteristics over the full range of possible behaviors in grain packs, as well as comparisons to experiments, will be presented.
Tracing the spontaneous mixing and mobility of miscible polymer blends using differential scanning calorimetry [Cellulose acetate‐poly(styrenephosphonate ester)] (1989)

Abstract A method in which the dissolution of a miscible polymer pair is traced in a differential scanning calorimetry cell is described. The polymer blend is initially prepared as an heterogeneous system with microdomains of one component embedded in the continuous matrix of the second polymer. Annealing the system in the DSC cell above the glass‐transition temperature causes a spontaneous mixing of the polymer pair which can be observed by the progressive shift of the T g s of both components until they merge. The time scale for dissolution and aspects of mass‐transport phenomenon are thus determined for the specific blend, cellulose acetate‐poly(styronephosphonate ester). Rather sharp progressive shifts of the T g s are shown to prevail without significant broadening of the transition curve (Δ T g ). Mass‐transport analyses supported by electron microscopy observation of the blend, before and after annealing, suggest that the domain sizes remain nearly unchanged and the physicochemical makeup of the phase boundary interfaces determines the time scale of dissolution in the system. A model from which mean‐value diffusion coefficients are calculated for both components at different annealing temperatures is reported.
ARCliDS: A Clinical Decision Support System for AI-assisted Decision-Making in Response-Adaptive Radiotherapy (2022)

Abstract Background Involvement of many variables, uncertainty in treatment response, and inter-patient heterogeneity challenge objective decision-making in dynamic treatment regime (DTR) in oncology. Advanced machine learning analytics in conjunction with information-rich dense multi-omics data have the ability to overcome such challenges. We have developed a comprehensive artificial intelligence (AI)-based optimal decision-making framework for assisting oncologists in DTR. In this work, we demonstrate the proposed framework to Knowledge Based Response-Adaptive Radiotherapy (KBR-ART) applications by developing an interactive software tool entitled A daptive R adiotherapy Cli nical D ecision S upport (ARCliDS). Methods ARCliDS is composed of two main components: Artificial RT Environment (ARTE) and Optimal Decision Maker (ODM). ARTE is designed as a Markov decision process and modeled via supervised learning. Given a patient’s pre- and during-treatment information, ARTE can estimate treatment outcomes for a selected daily dosage value (radiation fraction size). ODM is formulated using reinforcement learning and is trained on ARTE. ODM can recommend optimal daily dosage adjustments to maximize the tumor local control probability and minimize the side effects. Graph Neural Network (GNN) is applied to exploit the inter-feature relationships for improved modeling performance and a novel double GNN architecture is designed to avoid unphysical treatment response. Datasets of size 117 and 292 were available from two clinical trials on adaptive RT in non-small cell lung cancer (NSCLC) patients and adaptive stereotactic body RT (SBRT) in hepatocellular carcinoma (HCC) patients, respectively. For training and validation, dense data with 297 features were available for 67 NSCLC patients and 110 features for 71 HCC patients. To increase the sample size for ODM training, we applied Generative Adversarial Network to generate 10,000 synthetic patients. The ODM was trained on the synthetic patients and validated on the original dataset. Results Double GNN architecture was able to correct the unphysical dose-response trend and improve ARCliDS recommendation. The average root mean squared difference (RMSD) between ARCliDS recommendation and reported clinical decisions using double GNNs were 0.61 ± 0.03 Gy/frac (mean±sem) for adaptive RT in NSCLC patients and 2.96 ± 0.42 Gy/frac for adaptive SBRT HCC compared to the single GNN’s RMSDs of 0.97 ± 0.12 Gy/frac and 4.75 ± 0.16 Gy/frac, respectively. Overall, For NSCLC and HCC, ARCliDS with double GNNs was able to reproduce 36% and 50% of the good clinical decisions (local control and no side effects) and improve 74% and 30% of the bad clinical decisions, respectively. Conclusion ARCliDS is the first web-based software dedicated to assist KBR-ART with multi-omics data. ARCliDS can learn from the reported clinical decisions and facilitate AI-assisted clinical decision-making for improving the outcomes in DTR.
Cooperative Caching for Multimedia Streaming in Overlay Networks (2004)

Traditional data caching, such as web caching, only focuses on how to boost the hit rate of requested objects in caches, and therefore, how to reduce the initial delay for object retrieval. However, for multimedia objects, not only reducing the delay of object retrieval, but also provisioning reasonably stable network bandwidth to clients, while the fetching of the cached objects goes on, is important as well. In this paper, we propose our cooperative caching scheme for a multimedia delivery scenario, supporting a large number of peers over peer-to-peer overlay networks. In order to facilitate multimedia streaming and downloading service from servers, our caching scheme (1) determines the appropriate availability of cached stream segments in a cache community, (2) determines the appropriate peer for cache replacement, and (3) performs bandwidth-aware and availability-aware cache replacement. By doing so, it achieves (1) small delay of stream retrieval, (2) stable bandwidth provisioning during retrieval session, and (3) load balancing of clients' requests among peers.
Erratum: Fictive temperature, cooling rate, and viscosity of glasses [J. Chem. Phys. <b>120</b>, 8053 (2004)] (2004)

Udgivelsesdato: MAY 1
Experimental Investigation of the Absorption Behavior of Date Palm Fiber Reinforced Iso-Polyester Composites: Artificial Neuron Network (ANN) Modeling (2022)

The present article attempts to study absorption properties of bio-composites reinforced with date palm fibers. The effect of fiber loading on water absorption at room temperature 25°C was investigated. The weight gain was measured of bio-composites immersed in distilled water, seawater and rainwater, for more than 670 hours, until reaching the saturation with a measurement interval between 24 and 48 hours. To understand absorption phenomenon, scanning electron microscopy was used. Porosity rate was determined using image J software. It was noted the water absorption rate of the bio composites reached 16.20%, 16.33%, 21.94%, 41.99% for seawater, 16.41%, 16.52%, 20.84%, 30.08% for distilled water, and 14.00%, 14.04%, 19.30%, 36.94% for rainwater, respectively. The absorption increases when increasing fiber content. The diffusion coefficient of bio-composites has minimum and maximum values of about 1.94 × 10−6mm2/s and 3.99 × 10−6mm2/s, respectively. Palm fibers are highly porous. The porosity value was higher than 51%. To predict the absorption rate, artificial neural network method was used. The ANN models obtained are very well correlated with the experimental data where the values of the correlation coefficient of the datasets are all beyond 0.99 and the average error value was estimated at 3 × 10−5.
Waxy Maize Starch Nanocrystals as Filler in Natural Rubber (2006)

Abstract Starch nanocrystals obtained from acid hydrolysis of waxy maize starch granules consist in crystalline nanoplatelets about 6–8 nm thick with a length of 20–40 nm and a width of 15–30 nm. New nanocomposite materials, i.e. natural rubber (NR) filled with waxy maize starch nanocrystals were processed by casting. Dynamic mechanical analysis has shown that starch nanocrystals were a good reinforcing agent for NR at temperatures higher than the glass transition temperature of NR. Tensile tests have shown that until a weight fraction of 20 wt%, this new filler presented the advantage to reinforce natural rubber without decreasing significantly the strain at break of the material. These properties may be due to both the morphological nature of starch nanocrystals, and the formation of a percolating starch nanocrystals network within the NR matrix, resulting from hydrogen bonding forces between starch aggregates.
In vivo application of poly-3-hydroxyoctanoate as peripheral nerve graft (2013)

Objective:This study aims to investigate the degree of biocompatibility and neuroregeneration of a polymer tube,poly-3-hydroxyoctanoate(PHO)in nerve gap repair.Methods:Forty Wistar Albino male rats were randomized into two groups:autologous nerve gap repair group and PHO tube repair group.In each group,a 10-mm right sciatic nerve defect was created and reconstructed accordingly.Neuroregeneration was studied by sciatic function index(SFI),electromyography,and immunohistochemical studies on Days 7,21,45 and 60 of implantation.Biocompatibility was analyzed by the capsule formation around the conduit.Biodegradation was analyzed by the molecular weight loss in vivo.Results:Electrophysiological and histomorphometric assessments demonstrated neuroregeneration in both groups over time.In the experimental group,a straight alignment of the Schwann cells parallel to the axons was detected.However,autologous nerve graft seems to have a superior neuroregeneration compared to PHO grafts.Minor biodegradation was observed in PHO conduit at the end of 60 d.Conclusions:Although neuroregeneration is detected in PHO grafts with minor degradation in 60 d,autologous nerve graft is found to be superior in axonal regeneration compared to PHO nerve tube grafts.PHO conduits were found to create minor inflammatory reaction in vivo,resulting in good soft tissue response.
Implementing a content-based public-oriented audio and video news retrieval system (2010)

Video is poised to largely replace both text and images as the media for transmitting information in the coming years. The challenge of the Information Processing community is how to index the information found in this voluminous and dynamic media stream. Most of the linguistic information is encoded in the audio channel of video data, which, once transcribed, can be accessed using text-based tools. This talk will describe our current research in providing an index into the content of video and audio streams, using LIMSI's state-of-the-art automatic speech transcription system for French, English, Mandarin and Arabic languages. I will also describe and demonstrate the Voxalead News system, and other results of the French-German Quaero project, that integrate results from industry and research, for the next generation of video-based information searching
Nitric oxide mediates increased P-glycoprotein activity in interferon-γ-stimulated human intestinal cells (2004)

Patients with refractory inflammatory bowel disease (IBD) exhibit increased expression of intestinal P-glycoprotein (P-gp) as well as elevated luminal IFN-gamma and nitric oxide (NO) levels. Using the in vitro Caco-2 cell culture model, we investigated whether these pathological mediators associated with the etiology of IBD affect functional activity of intestinal efflux systems. IFN-gamma reduced cellular uptake of cyclosporin A (CysA) but not methotrexate (MTX) in a time- and concentration-dependent manner. Simultaneously, P-gp expression increased by approximately twofold. Coincubation with the inducible NO synthase inhibitor l-N(6)-(1-iminoethyl)lysine (l-NIL) dramatically reduced production of intracellular NO in response to IFN-gamma stimulus. The presence of l-NIL also abrogated the cytokine-mediated increase in P-gp expression and function suggesting that NO is required for IFN-gamma-mediated activation of this efflux system. Exposure of Caco-2 cells to the chemical NO donor S-nitroso-N-acetylpenicillamine (SNAP) produced a concentration-dependent decrease in intracellular CysA accumulation that was paralleled by an increase in P-gp expression. Both IFN-gamma and SNAP enhanced DNA binding of NF-kappaB, whereas inclusion of l-NIL dramatically decreased this cytokine-induced effect on NF-kappaB binding. These results suggest that NO mediates IFN-gamma-induced increase in expression and function of intestinal P-gp in the human Caco-2 cell culture model by altering DNA binding of NF-kappaB, which may enhance transcription of the ABCB1 gene encoding for this efflux system.
Heavy–ion particle identification for the transfer reaction channels for the system <sup>18</sup>O + <sup>116</sup>Sn under the NUMEN Project (2018)

International audience
Language-Guided Face Animation by Recurrent StyleGAN-based Generator (2022)

Recent works on language-guided image manipulation have shown great power of language in providing rich semantics, especially for face images. However, the other natural information, motions, in language is less explored. In this paper, we leverage the motion information and study a novel task, language-guided face animation, that aims to animate a static face image with the help of languages. To better utilize both semantics and motions from languages, we propose a simple yet effective framework. Specifically, we propose a recurrent motion generator to extract a series of semantic and motion information from the language and feed it along with visual information to a pre-trained StyleGAN to generate high-quality frames. To optimize the proposed framework, three carefully designed loss functions are proposed including a regularization loss to keep the face identity, a path length regularization loss to ensure motion smoothness, and a contrastive loss to enable video synthesis with various language guidance in one single model. Extensive experiments with both qualitative and quantitative evaluations on diverse domains (\textit{e.g.,} human face, anime face, and dog face) demonstrate the superiority of our model in generating high-quality and realistic videos from one still image with the guidance of language. Code will be available at https://github.com/TiankaiHang/language-guided-animation.git.
Variation of coupling coefficients by sampled gratings in complex coupled distributed-feedback lasers (1995)

We present an efficient method for an almost arbitrary variation of the complex coupling coefficient of distributed feedback lasers by using superstructure gratings, As shown by detailed transfer matrix model calculations the coupling coefficient can be reduced locally according to the duty cycle of a sampled grating. The additional supermodes caused by the superstructure can be strongly suppressed by choosing a small superperiod so that the supermodes are shifted apart from the gain curve. This novel approach for the realization of nonuniform coupling coefficients is applied to analyze experimentally the influence of the complex coupling strength on the performance of loss coupled InGaAs-InGaAlAs-InP-DFB lasers.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Genome engineering of Stx1-and Stx2-converting bacteriophages unveils the virulence of the dairy isolate Escherichia coli O174:H2 strain UC4224 (2023)

The past decade witnessed the emergence in Shiga toxin-producing <i>Escherichia coli</i> (STEC) infections linked to the consumption of unpasteurized milk and raw milk cheese. The virulence of STEC is primarily attributed to the presence of Shiga toxin genes (<i>stx1</i> and <i>stx2</i>) carried by Stx-converting bacteriophages, along with the intimin gene <i>eae</i>. Most of the available information pertains to the "Top 7" serotypes associated with STEC infections. The objectives of this study were to characterize and investigate the pathogenicity potential of <i>E. coli</i> UC4224, a STEC O174:H2 strain isolated from semi-hard raw milk cheese and to develop surrogate strains with reduced virulence for use in food-related studies. Complete genome sequence analysis of <i>E. coli</i> UC4224 unveiled the presence of a Stx1a bacteriophage, a Stx2a bacteriophage, the Locus of Adhesion and Autoaggregation (LAA) pathogenicity island, plasmid-encoded virulence genes, and other colonization facilitators. In the <i>Galleria mellonella</i> animal model, <i>E. coli</i> UC4224 demonstrated high pathogenicity potential with an LD<sub>50</sub> of 6 CFU/10 μL. Upon engineering <i>E. coli</i> UC4224 to generate single and double mutant derivatives by inactivating <i>stx1a</i> and/or <i>stx2a</i> genes, the LD<sub>50</sub> increased by approximately 1 Log-dose in the single mutants and 2 Log-doses in the double mutants. However, infectivity was not completely abolished, suggesting the involvement of other virulence factors contributing to the pathogenicity of STEC O174:H2. Considering the possibility of raw milk cheese serving as a reservoir for STEC, cheesemaking model was developed to evaluate the survival of UC4224 and the adequacy of the respective mutants as reduced-virulence surrogates. All tested strains exhibited the ability to survive the curd cooking step at 48°C and multiplied (3.4 Log CFU) in cheese within the subsequent 24 h. These findings indicate that genomic engineering did not exert any unintended effect on the double <i>stx1</i>-<i>stx2</i> mutant behaviour, making it as a suitable less-virulent surrogate for conducting studies during food processing.
Optimal Scheduling Control in Fluid Models of General $n\times n$ Input-Queued Switches (2019)

Most of the early input-queued switch research focused on establishing throughput optimality of the max-weight scheduling policy, with some recent research showing that max-weight scheduling is optimal with respect to total expected delay asymptotically in the heavy-traffic regime. However, the question of delay-optimal scheduling in input-queued switches remains open in general, as does the question of delay-optimal scheduling under more general objective functions. To gain fundamental insights into these very difficult problems, we consider a fluid model of $n \times n$ input-queued switches with associated fluid-flow costs, and we derive an optimal scheduling control policy to an infinite horizon discounted control problem with a general linear objective function of fluid cost. Our optimal policy coincides with the $cμ$-rule in certain parameter domains. More generally, due to the input-queued switch constraints, the optimal policy takes the form of the solution to a flow maximization problem, after we identify the Lagrangian multipliers of some key constraints through carefully designed algorithms. Computational experiments demonstrate the benefits of our optimal scheduling policy over variants of max-weight scheduling within fluid models of input-queued switches.
Development of Membrane Technology for CO2 Removal and H2 Purification:A Techno-Economic, Lab-Scale, and Pilot-Scale Study (2016)

Membrane technology is a cost-and energy-efficient process for gas separation.Polymer membranes for CO 2 removal offer the advantage of desirable performance along with adequate robustness, handling and ease of scale-up.Facilitated transport-type of CO 2 -selective polymer membranes, offer reasonably high CO 2 permeance, and a remarkably high CO 2 /H 2 and CO 2 /N 2 selectivity at 57 -102 o C.This work focusses the on the development facilitated transport membranes for CO 2 removal and H 2 purification.Novel membrane materials were developed in the lab-scale for high temperature H 2 purification application.A 2-Stage membrane process was proposed for integrating the membrane process to the Integrated Gasification Combined Cycle (IGCC)-based power plant for syngas purification.The experimentally obtained transport performances (of the lab-synthesized amine-containing facilitated transport membranes) were used for the techno-economic analysis of the 2-Stage process.A comprehensive cost-sensitivity study was performed to obtain the optimum operating condition for membrane process in an IGCC power plant for syngas purification.The proposed 2-Stage membrane process for syngas purification at > 100 o C was demonstrated to be economically feasible.Based on the cost sensitivity study, the 2-Stage membrane process resulted in an impressive 14 -18% increase in the cost of electricity (COE).
Supplementary Data from Radium-223 Treatment Increases Immune Checkpoint Expression in Extracellular Vesicles from the Metastatic Prostate Cancer Bone Microenvironment (2023)

&lt;p&gt;Supplementary Figures&lt;/p&gt;