gebhart/patrepeval huggingface dataset:
Inactivation of Caspase-8 on Mitochondria of Bcl-xL-expressing MCF7-Fas Cells (2002)

Apoptosis induction through CD95 (APO-1/Fas) critically depends on generation of active caspase-8 at the death-inducing signaling complex (DISC). Depending on the cell type, active caspase-8 either directly activates caspase-3 (type I cells) or relies on mitochondrial signal amplification (type II cells). In MCF7-Fas cells that are deficient for pro-caspase-3, even high amounts of caspase-8 produced at the DISC cannot directly activate downstream effector caspases without mitochondrial help. Overexpression of Bcl-x(L) in these cells renders them resistant to CD95-mediated apoptosis. However, activation of caspase-8 in control (vector) and Bcl-x(L) transfectants of MCF7-Fas cells proceeds with similar kinetics, resulting in a complete processing of cellular caspase-8. Most of the cytosolic caspase-8 substrates are not cleaved in the Bcl-x(L) protected cells, raising the question of how Bcl-x(L)-expressing MCF7-Fas cells survive large amounts of potentially cytotoxic caspase-8. We now demonstrate that active caspase-8 is initially generated at the DISC of both MCF7-Fas-Vec and MCF7-Fas-Bcl-x(L) cells and that the early steps of CD95 signaling such as caspase-8-dependent cleavage of DISC bound c-FLIP(L), caspase-8-dependent clustering, and internalization of CD95, as well as processing of pro-caspase-8 bound to mitochondria are very similar in both transfectants. However, events downstream of mitochondria, such as release of cytochrome c, only occur in the vector-transfected MCF7-Fas cells, and no in vivo caspase-8 activity can be detected in the Bcl-x(L)-expressing cells. Our data suggest that, in Bcl-x(L)-expressing MCF7-Fas cells, active caspase-8 is sequestered on the outer mitochondrial surface presumably by association with the protein "bifunctional apoptosis regulator" in a way that does not allow substrates to be cleaved, identifying a novel mechanism of regulation of apoptosis sensitivity by mitochondrial Bcl-x(L).
Can Negligible Cooperation Increase Network Capacity? The Average-Error\n Case (2018)

In communication networks, cooperative strategies are coding schemes where\nnetwork nodes work together to improve network performance metrics such as\nsum-rate. This work studies encoder cooperation in the setting of a discrete\nmultiple access channel with two encoders and a single decoder. A node in the\nnetwork that is connected to both encoders via rate-limited links, referred to\nas the cooperation facilitator (CF), enables the cooperation strategy.\nPreviously, the authors presented a class of multiple access channels where the\naverage-error sum-capacity has an infinite derivative in the limit where CF\noutput link capacities approach zero. The authors also demonstrated that for\nsome channels, the maximal-error sum-capacity is not continuous at the point\nwhere the output link capacities of the CF equal zero. This work shows that the\nthe average-error sum-capacity is continuous when CF output link capacities\nconverge to zero; that is, the infinite derivative of the average-error\nsum-capacity is not a result of its discontinuity as in the maximal-error case.\n
Fluorescence energy transfer between ligand binding sites on chloroplast coupling factor 1 (1975)

The method of fluorescence energy transfer is used to measure the distance from the tight nucleotide binding sites to the 7-chloro-4-nitrobenzo-2-oxa-1,3-diazole reactive sites on solubilized spinach chloroplast coupling factor 1 (CF1). The fluorescent adenine nucleotide analogs 1,N-6-ethenoadenosine diphosphate and 1,N-6-ethenoadenylyl imidodiphosphate were used as donors and 4-nitrobenzo-2-oxa-1,3-diazole bound to a tyrosine group and to an amino group were used as acceptors of energy transfer. Using three different donor-acceptor pairs, the distance measured varied from 38 to 43 A assuming both donor sites are equidistant from the acceptor site. A model is proposed for the location of the tight nucleotide binding sites and the active site on the alpha and beta subunits of CF1.
High-power 200 fs Kerr-lens mode-locked Yb:YAG thin-disk oscillator (2011)

We demonstrate a power-scalable Kerr-lens mode-locked Yb:YAG thin-disk oscillator. It delivers 200 fs pulses at an average power of 17 W and a repetition rate of 40 MHz. At an increased (180 W) pump power level, the laser produces 270 fs 1.1 μJ pulses at an average power of 45 W (optical-to-optical efficiency of 25%). Semiconductor-saturable-absorber-mirror-assisted Kerr-lens mode locking (KLM) and pure KLM with a hard aperture show similar performance. To our knowledge, these are the shortest pulses achieved from a mode-locked Yb:YAG disk oscillator and this is the first demonstration of a Kerr-lens mode-locked thin-disk laser.
Association of High Serum Interleukin‐6 Levels With Severe Progression of Rheumatoid Arthritis and Increased Treatment Response Differentiating Sarilumab From Adalimumab or Methotrexate in a Post Hoc Analysis (2020)

IL-6 may be a prognostic marker of disease progression and severity, and patients with high IL-6 levels may be likely to benefit from sarilumab compared to adalimumab or MTX. Prospective validation is warranted to confirm the results of these post hoc analyses.
Potent Anti-Cancer Effect of 3′-Hydroxypterostilbene in Human Colon Xenograft Tumors (2014)

Here we report that 3'-hydroxypterostilbene (HPSB), a natural pterostilbene analogue, was more potent than pterostilbene against the growth of human cancer cells (COLO 205, HCT-116, and HT-29) with measured IC50 values of 9.0, 40.2, and 70.9 µM, respectively. We found that HPSB effectively inhibited the growth of human colon cancer cells by inducing apoptosis and autophagy. Autophagy occurred at an early stage and was observed through the formation of acidic vesicular organelles and microtubule-associated protein 1 light chain 3-II production. At the molecular levels, the results from western blot analysis showed that HPSB significantly down-regulated phosphatidylinositol 3-kinase (PI3K)/Akt and mitogen-activated protein kinases (MAPKs) signalings including decreased the phosphorylation of mammalian target of rapamycin (mTOR). Significant therapeutic effects were demonstrated in vivo by treating nude mice bearing COLO 205 tumor xenografts with HPSB (10 mg/kg i.p.). These inhibitory effects were accompanied by mechanistic down-regulation of the protein levels of cyclooxygenase-2 (COX-2), matrix metallopeptidase-9 (MMP-9), vascular endothelial growth factor (VEGF), and cyclin D1, as well as by the induction of apoptosis in colon tumors. Our findings suggest that HPSB could serve as a novel promising agent for colon cancer treatment.
An Automotive Communication Bus Using OFDMA (2023)

Today’s automotive communication systems use baseband pulse modulation and time-division or carrier-sense multiple access. In future in-vehicle networks, more devices need to be connected in a multipoint-to-multipoint topology. We have developed a new automotive bus system based on orthogonal frequency division multiple access (OFDMA) enabling better channel adaptation and fine-granular multi-user access. We highlight the advantages of OFDMA in automotive and industrial applications, introduce our system concept and demonstrate its feasibility by means of a prototype. Finally, we discuss the use of electrical and optical media.
Glucagon amino groups. Evaluation of modifications leading to antagonism and agonism. (1980)

Using native glucagon and [12-homoarginine]glucagon (analogue A), prepared in high yield and purity by new procedures, we have synthesized the following glucagon analogues by semisynthetic methods: [1-deshistidine][12-homoarginine]glucagon (analogue B); N alpha-carbamoylglucagon (analogue C); N alpha, N epsilon-dicarbamoylglucagon (analogue D); [1-N alpha-carbamoylhistidine, 12-N epsilon-trinitrophenyllsyine]glucagon (analogue II); [1-deshistidine] [2-N alpha-trinitrophenylserine, 12-homoarginine]glucagon (analogue III); and [1-N alpha-trinitrophenylhistidine, 12-homoarginine]glucagon (analogue IV). The introduction of hydrophylic groups at the alpha- and epsilon-amino positions of glucagon results in a reduction in potency. The alpha-position is also involved in biological activity. Carbamylation of the alpha-position results in a partial agonist (analogues C and D). The introduction of hydrophobic groups and the neutralization of the positive charge at the alpha- and epsilon-amino positions result in glucagon antagonists (analogues II, III, and IV). [1-N alpha-Trinitrophenylhistidine, 12-homoarginine]glucagon (analogue IV) is the most potent inhibitor tested. Based on its competitive inhibitory action, this analogue appears to have about one-third the affinity of glucagon for the receptor site. These modifications at the epsilon-amino position cause an increase in the secondary structure of the peptide (as shown by circular dichroism studies) which may be related to their biological activities.
Cost-Effectiveness of Emissions Reduction through Vehicle Repair Compared to CNG Conversion (1996)

In return for a temporary waiver from converting five vehicles to operate on compressed natural gas (CNG) for the Denver Clean Fuels program, the University of Denver identified, tested, repaired, and retested nine employee commuter vehicles. The results of the study validated the concept that employer-based identification and repair programs can be carried out in a cost-effective way. On average, each repaired vehicle removed fifty times more carbon monoxide (CO) emissions from Denver air than each CNG conversion. The average cost of each repair was eight times less than the average cost of each conversion. The average fuel economy benefit from the repairs was enough to pay for the average cost of repairs in less than three years of normal driving. When the expected lifetimes of repairs and conversions are included, the targeted repair program appears to be over sixty times more cost-effective as a CO emissions reduction strategy than CNG conversion.
Intracerebral Transplantation of Adult Mouse Neural Progenitor Cells into the Niemann-Pick-A Mouse Leads to a Marked Decrease in Lysosomal Storage Pathology (2004)

Niemann-Pick disease is caused by a genetic deficiency in acid sphingomyelinase (ASM) leading to the intracellular accumulation of sphingomyelin and cholesterol in lysosomes. In the present study, we evaluated the effects of direct intracerebral transplantation of neural progenitor cells (NPCs) on the brain storage pathology in the ASM knock-out (ASMKO) mouse model of Type A Niemann-Pick disease. NPCs derived from adult mouse brain were genetically modified to express human ASM (hASM) and were transplanted into multiple regions of the ASMKO mouse brain. Transplanted NPCs survived, migrated, and showed region-specific differentiation in the host brain up to 10 weeks after transplantation (the longest time point examined). In vitro, gene-modified NPCs expressed up to 10 times more and released five times more ASM activity into the culture media compared with nontransduced NPCs. In vivo, transplanted cells expressed hASM at levels that were barely detectable by immunostaining but were sufficient for uptake and cross-correction of host cells, leading to reversal of distended lysosomal pathology and regional clearance of sphingomyelin and cholesterol storage. Within the host brain, the area of correction closely overlapped with the distribution of the hASM-modified NPCs. No correction of pathology occurred in brain regions that received transplants of nontransduced NPCs. These results indicate that the presence of transduced NPCs releasing low levels of hASM within the ASMKO mouse brain is necessary and sufficient to reverse lysosomal storage pathology. Potentially, NPCs may serve as a useful gene transfer vehicle for the treatment of CNS pathology in other lysosomal storage diseases and neurodegenerative disorders.
Implémentation asynchrone d'un algorithme de marché de l'électricité décentralisé (2021)

International audience
Investigation of Coupling Mechanism of Multidisciplinary Sub-models of Electric Machines for Multi-physics optimization (2020)

Electric machine design, by nature, involves the knowledge of multiple physics. The sub-models in each physics domain of an electric machine are coupled with each other in one way or another. Physical couplings are the way of sharing input and/or output data between sub-models of different physics. This paper investigates the coupling mechanism of the multidisciplinary sub-models of electric machines. Attempts proposed in literature to decouple or partially decouple these sub-models in order to reduce computing time and to yield effective Pareto front for large scale multi-physics optimization of electric machines are reviewed.
Synthesis and Solubility of Linear Poly(tetrafluoroethylene-co-vinyl acetate) in Dense CO2:  Experimental and Molecular Modeling Results (2004)

Supercritical carbon dioxide was used as a reaction medium to synthesize statistically random (i.e., no specific correlation between the location of the monomers on the polymer) copolymers of tetrafluoroethylene (TFE) and vinyl acetate (VAc) with similar molar mass and 11.6−63.3 mol % TFE content. The solubility of the copolymers at 25 °C in CO2 reduced after reaching a maximum value at a TFE molar concentration of 19.3 mol %. The 46.7 mol % TFE copolymer only dissolved in CO2 at elevated temperatures, whereas the 63.3 mol % TFE copolymer did not dissolve in CO2 even at temperatures in excess of 144 °C and pressures of 210 MPa. The molecular modeling results show that the interaction of CO2 with acetate side group was not affected by presence of fluorine in the polymer backbone; therefore, the enhanced solubility of the semifluorinated copolymers is attributable to the enhanced binding between CO2 and the semifluorinated backbone of the copolymer when the CO2 molecule can access both the fluorinated (Lewis base) and hydrogenated (Lewis acid) parts of the backbone simultaneously.
Efficient spectrum coding for super-wideband speech and its application to 7/10/15 kHz bandwidth scalable coders (2004)

The paper presents an efficient spectrum coding method for super-wideband (beyond 7 kHz, e.g. 10 kHz or 15 kHz bandwidth) speech signals based on a bandwidth expansion technique. By using a 7 kHz bandwidth speech signal, its frequency band over 7 kHz is generated by the expansion technique without violating the harmonics structure of the speech signal. The bandwidth expansion is performed by pitch filtering in a frequency domain. A 7 kHz bandwidth spectrum is used as a pitch filter state, and pitch filtering is performed toward a frequency band over 7 kHz. We adopted this pitch filtering based spectrum coding (PFSC) to our proposing 7/10/15 kHz bandwidth scalable coder. The scalable coder consists of an existing standard wideband coder as a base-layer and two PFSC coders as an enhancement-layer. One PFSC coder encodes a 7-10 kHz band spectrum at 4.4 kbit/s and the other a 10-15 kHz band spectrum at 2.2 kbit/s. When the AMR-WB coder at 15.85 kbit/s is used as the base-layer, the total bitrate of the scalable coder is 22.45 kbit/s and the total algorithmic delay is 30 ms. We conducted degradation category rating (DCR) tests for both 10 kHz and 15 kHz bandwidth signals. The results show that the DMOS score of the proposed coder is better than that of the 7 kHz bandwidth original signals in both bandwidth clean speech conditions. In addition, when G.722 at 56 kbit/s is used as the base-layer instead of the AMR-WB coder, the DMOS score of this scalable coder is close to that of the 7 kHz bandwidth original signals in both bandwidth audio conditions.
Lipoidal Derivative of Estradiol: The Biosynthesis of a Nonpolar Estrogen Metabolite* (1981)

The incubation of estradiol with human breast tumors as well as several estrogen-responsive tissues of the rat, including dimethylbenzanthracene-induced mammary tumors, leads to the formation of a nonpolar metabolite. This compound has been called a lipoidal derivative of estradiol because of its nonpolar characteristics and because it is converted back into estradiol with alkali. The properties of this metabolite are similar to those of the endogenous lipoidal derivatives of the delta 5-3 beta-hydroxysteroids, pregnenolone, 17-hydroxypregnenolone, and dehydroisoandrosterone, that were found in the adrenal. When estrone was incubated in a similar manner, a nonpolar metabolite was formed, but it was the lipoidal derivative of estradiol, not estrone. The lipoidal derivative of estradiol was not oxidized by treatment with CrO3, which showed that the lipoidal moiety is linked to the C-17 of the steroid nucleus. Unlike other estrogen metabolites, the lipoidal derivative of estradiol is found only within the tissue and cannot be detected in the incubation medium.
Motion-Adaptive Depth Superresolution (2017)

Multi-modal sensing is increasingly becoming important in a number of applications, providing new capabilities and processing challenges. In this paper, we explore the benefit of combining a low-resolution depth sensor with a high-resolution optical video sensor, in order to provide a high-resolution depth map of the scene. We propose a new formulation that is able to incorporate temporal information and exploit the motion of objects in the video to significantly improve the results over existing methods. In particular, our approach exploits the space-time redundancy in the depth and intensity using motion-adaptive low-rank regularization. We provide experiments to validate our approach and confirm that the quality of the estimated high-resolution depth is improved substantially. Our approach can be a first component in systems using vision techniques that rely on high-resolution depth information.
LARC-TPI: A multi-purpose thermoplastic polyimide (1982)

A linear thermoplastic polyimide, LARC-TPI, was characterized and developed for a variety of high temperature applications. In its fully imidized form, this material can be used as an adhesive for bonding metals such as titanium, aluminum, copper, brass, and stainless steel. LARC-TPI was evaluated as a thermoplastic for bonding large pieces of polyimide film to produce flexible, 100 void-free laminates for flexible circuit applications. The development of LARC-TPI as a potential molding powder, composite matrix resin, high temperature film and fiber is also discussed.
Abstract 5293: A method to identify somatic mutations from tumor samples in the absence of matched normal tissue (2018)

Abstract Tumor-specific molecular profiling by next-generation sequencing (NGS) from tissue or blood (liquid biopsy) can have a tremendous potential to guide personalized healthcare for cancer treatments. However, based on the current clinical practices1, often tumor or blood may be sequenced without the matched germline normal tissue or buffy coat. Since the tumor cell content of the specimens can vary widely, as well as the fact that sequencing will identify both germline and somatic variations, confident identification of somatic mutations becomes very challenging in the absence of a matched normal. Identification of somatic variations in cell-free DNA becomes even more difficult due especially to the low yields of tumor-derived DNA in plasma samples. An ensemble tree-based machine learning method was developed to classify tumor-specific somatic mutations in the absence of matched normal (CSMutan). This algorithm leverages multiple public databases and variant allele frequencies as features to classify somatic mutations and germline variants. Using The Cancer Genome Atlas (TCGA) and in-house datasets, models were built for each of the three different types of tumor specimens: i.e., fresh frozen, formalin-fixed, paraffin-embedded (FFPE), and plasma samples. The performance of the models was evaluated using cross-validation and/or testing on independent sets of samples. Lung adenocarcinoma samples from TCGA were used to build the fresh frozen model, which achieved an area under the ROC curve (AUC) of 0.9968 on an independent data set of lung squamous cell carcinoma samples, also from TCGA. In-house sample sets were used to build the FFPE model and the plasma model. The FFPE model achieved an ROC AUC of 0.993, while the model trained on plasma samples was able to classify with an AUC of 0.997 based on ten-fold cross-validation. Although sequencing matched normal tissue is the most preferred and accurate method for identifying high-confidence somatic mutations, this work demonstrates that it is possible to identify somatic mutations in tissue or blood with high accuracy when the matched normal samples may not be available. The future directions for this method are to add additional, and more diverse, cancer samples for both the training and independent validation so that potentially higher accuracy and generalizability can be obtained. 1. Meyerson, M., Gabriel, S. &amp; Getz, G. Advances in understanding cancer genomes through second-generation sequencing. Nature Reviews Genetics 11, 685-696 (2010) Citation Format: Lijing Yao, Preeti Lal, Li-Tai Fang, John Lee, John Palma, Andre Rosenthal, Bernd Hinzmann, Alex Lovejoy, Hugo Y. K. Lam. A method to identify somatic mutations from tumor samples in the absence of matched normal tissue [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5293.
Meshfree Approximation Methods for Surface Representation of Free-Form Optical Surfaces (2008)

This paper summarizes the impact of a change of basis from polynomials to radial basis functions for describing free-form optical surfaces. © 2008 Optical Society of America.
Using Meta-Cognition for Regulating Explanatory Quality Through a Cognitive Architecture. (2014)

Abstract. Recent years have seen a renewed interest in cognitive systems with the ability to explain either external phenomena or their own internal reason-ing processes while solving problems. Some successful models of explanation-generation have made use of structured representations, reasoned over using ana-logical or deductive mechanisms. But before such models can be adapted for use in real-world situations, they need to incorporate additional features associ-ated with explanation-generation. For example, generated explanations may dif-fer qualitatively based on the explanandum’s domain; e.g., explanations rooted in physical causality to explain physical phenomena vs. folk-psychology expla-nations that rely on propositional attitudes (believes, knows, intends,...). This may affect the generated explanations in both explicit and implicit ways. We tackle both the explicit and implicit effects of this cognitive feature and incor-porate them into a comprehensive cognitive architecture: CLARION (especially its meta-cognitive and non-action-centered subsystems).
Kontrollierte biochemische Synthese auf Metall/Halbleiter-Nanostrukturen (Controlled Biochemical Synthesis on Metal/Semiconductor Nanostructures) (2004)

Abstract Die Antennenwirkung von metallischen oder halbleitenden Nanostrukturen in elektromagnetischen Feldern soll eingesetzt werden, um chemische Reaktionen an deren Oberflächen zu optimieren. Das Ziel ist die spezifische Synthese von Oligonukleinsäuresequenzen zum Aufbau von hochdichten “DNA-Arrays” mit nanotechnologischen Methoden. Die Nanostrukturen werden für die Untersuchungen von einerseits Photonen-Transfer-Reaktionen und andererseits für Elektronen-Transfer-Reaktionen durch die Wahl geeigneter Geometrien und Materialien angepasst.