gebhart/patrepeval huggingface dataset:
Homogeneous Ignition Delay, Flame Propagation Rate and End-Gas Autoignition Fraction Measurements of Natural Gas and Exhaust Gas Recirculation Blends in a Rapid Compression Machine (2020)

Abstract To evaluate the effect of exhaust gas recirculation (EGR) and variable fuel reactivity on knock and misfire in spark ignited national gas engines, experiments were conducted in a rapid compression machine to measure homogeneous ignition delay, flame propagation rate, and end-gas autoignition fraction for stoichiometric natural gas/oxidizer/EGR blends. Natural gas with a range of chemical reactivity was simulated using mixtures of CH4, C2H6, and C3H8. Reactive exhaust gas recirculation (R-EGR) gases were simulated with mixtures of Ar, CO2, CO, and NO and non-reactive exhaust gas recirculation gases (NR-EGR) were simulated with mixtures of AR and CO2. Homogeneous ignition delay period, flame propagation rate and end-gas autoignition fraction were measured at compressed pressures and temperatures of 30.2 to 34.0 bar and 667 to 980 K, respectively. Flame propagation rate decreased with both R-EGR and NR-EGR substitution. The substitution of R-EGR increased the end-gas autoignition fraction, whereas NR-EGR substitution decreased the end-gas autoignition fraction. The results indicate that the presence of the reactive species NO in the R-EGR has a strong impact on end-gas autoignition fraction. An 82-species reduced chemical kinetic mechanism was also developed that reproduces measured homogeneous ignition delay period with a total average relative error of 11.0%.
Resonant gratings with an etch-stop layer and a fabrication-error tolerant design (2018)

Sub-wavelength gratings (SWG) have shown much promise for applications such as lightweight high bandwidth reflectors, polarising filters and focusing lenses. Unfortunately, grating performance may be rapidly degraded through variability in grating dimensions. We demonstrate, in particular, how an error in depth of etch can be detrimental to the performance of zero contrast grating reflectors. We mitigate the impact of this fabrication error through the introduction of an etch stop layer and in so doing we experimentally realise a high bandwidth reflector based on this modified structure. Another common fabrication error is variation in the duty-cycle of fabricated gratings. This duty-cycle variation can weaken grating performance, however we demonstrate that grating designs that exhibit tolerance to duty-cycle fluctuation can be identified through simulation. Finally, we discuss the impact of lateral etching and the resulting sidewall concavity. We present our approach for numerically predicting the spectral response from such a grating and also for convenience we outline an approach for quickly approximating grating performance. Good agreement is observed between these numerical predictions and measurements made on a HCG with concave sidewalls.
Untersuchung von HCV Resistenzen in Verbindung mit dem Therapieansprechen bei Patienten mit einer chronischen Hepatitis C Genotyp 4 Infektion (2017)

Aktuell steigt die Zahl der Patienten mit einer Hepatitis C Virus (HCV) Genotyp (GT) 4 Infektion in Europa. Zur Behandlung stehen verschiedene direkt antiviral wirksame Substanzen (DAAs) zur Verfügung, welche aus Kombinationen eines NS5A-Inhibitors mit einem nukleotidischen NS5B-Inhibitor oder mit einem NS3 Protease-Inhibitor bestehen. Die Anzahl an Studien mit Resistenzdaten zum GT4 ist bisher gering. In dieser Arbeit wurden Resistenz-assoziierte Substitutionen (RASs) bei DAA-naiven und -erfahren Patienten in Verbindung mit dem Therapieansprechen analysiert.
Sialidases and Fucosidases of <i>Akkermansia muciniphila</i> are crucial for growth on mucin and nutrient sharing with mucus-associated gut bacteria (2022)

Abstract The gut mucolytic specialist Akkermansia muciniphila is strongly associated with the integrity of the mucus layer. Mucin glycan utilization requires the removal of diverse protective caps, notably, fucose and sialic acid, but the enzymatic details of this process remain largely unknown. Here, we describe the specificities of ten A. muciniphila glycoside hydrolases, which collectively remove all known sialyl and fucosyl mucin caps including those with double sulphated epitopes. Structural analyses revealed an unprecedented fucosidase modular arrangement and explained the exclusive sialyl T-antigen specificity of a sialidase of a previously unknown family and catalytic apparatus. Key cell attached sialidases and fucosidases conferred mucin-binding and their inhibition abolished growth of A. muciniphila on mucin. Remarkably, the sialic acid fucose did not contribute to A. muciniphila growth, but instead promoted butyrate production by co-cultured Clostridia. This study brings unique mechanistic insight into the initiation of mucin O -glycan degradation by A. muciniphila and the nutrient sharing between key mucus-associated bacteria.
Input of multidimensional phenotyping in the metabolic syndrome stratification (2017)

Metabolic syndrome (MetS) is defined by a cluster of cardio-metabolic factors including obesity, hypertension, dysglycemia, and dyslipidemia. It affects a growing number of persons, in particular older adults often suffering from multiple chronic diseases, and its prevalence is now a public health challenge. In the context of personalized medicine/nutrition, new tools are necessary to bring additional knowledge about MetS etiology, better stratify populations and customise strategies for prevention.
A nested case-control study on MetS was designed within the Quebec Longitudinal Study on Nutrition and Successful Aging (NuAge). It includes 61 cases and 62 controls of similar age (68-82 y.o.), selected among the 853 men. Both targeted and untargeted metabolomic/lipidomic approaches, available within the MetaboHUB French infrastructure [1], will be performed on serum samples collected at recruitment 2003-2005 (T1) and three years later (T4). Data analysis will be performed using reproducible online Galaxy workflows [2].
The metabolomic/lipidomic data will be processed to identify specific signatures of MetS and its components, and study their stability over time. Then, these data will be analysed for evaluation of a molecular reclassification of the MetS phenotype. Finally, they will be integrated with phenotypic and detailed nutritional data available to better characterize sub-phenotypes.
The approach developed here will open a door for a more comprehensive understanding of the metabolic phenotype resulting from the complex interplay between intrinsic and extrinsic factors. Thus, this project will allow an improved description of MetS associated characteristics and will offer new tools for better patient stratification in elderly populations.
Novel staircase array antenna configuration using stacked Butler matrix for low profile base station (2022)

Massive MIMO is a promising wireless communication technology that realizes large capacity. However, it has the problem that circuit mounting becomes difficult due to the narrow antenna spacing and increased loss and phase deviation of connectors and wiring, especially in the millimeter-wave band. To solve these problems, we propose a novel Massive MIMO device configuration using a stacked Butler matrix and a staircase array antenna. From the simulation results, the radiation patterns are the same between the proposed and conventional antenna at stairs up to about 0.1λ.
An approach to define Very High Capacity Networks with improved quality\n at an affordable cost (2020)

This paper aims to propose one possible approach in the setting of VHCNs\n(Very High Capacity Networks) performance targets that should be capable of\npromoting efficient investments for operators and, at the same time, improving\nthe benefits for end-users. To this aim, we suggest relying on some specific\nKPIs (Key Performance Indicators), especially throughput - i.e., the bandwidth\nas perceived by the customer - valid at the application layer, instead of the\nphysical layer data-rate. In this regard, the paper underlines that the\nbandwidth perceived is strictly linked to the latency. The most important\nimplication is that some of the most demanding services envisaged for the\nfuture (e.g., mobile virtual and augmented reality, tactile internet) cannot be\nmet by merely increasing the low-level protocol data-rate. Therefore, for the\nVHCNs reducing latency through Edge Cloud Computing (ECC) is a mandatory\npre-requisite.\n
Conditions to Control Furan Ring Opening during Furfuryl Alcohol Polymerization (2022)

The chemistry of biomass-derived furans is particularly sensitive to ring openings. These side reactions occur during furfuryl alcohol polymerization. In this work, the furan ring-opening was controlled by changing polymerization conditions, such as varying the type of acidic initiator or the water content. The degree of open structures (DOS) was determined by quantifying the formed carbonyl species by means of quantitative <sup>19</sup>F NMR and potentiometric titration. The progress of polymerization and ring opening were monitored by DSC and FT-IR spectroscopy. The presence of additional water is more determining on ring opening than the nature of the acidic initiator. Qualitative structural assessment by means of <sup>13</sup>C NMR and FT-IR shows that, depending on the employed conditions, poly(furfuryl alcohol) samples can be classified in two groups. Indeed, either more ester or more ketone side groups are formed as a result of side ring opening reactions. The absence of additional water during FA polymerization preferentially leads to opened structures in the PFA bearing more ester moieties.
Interaction with PALB2 Is Essential for Maintenance of Genomic Integrity by BRCA2 (2016)

Human breast cancer susceptibility gene, BRCA2, encodes a 3418-amino acid protein that is essential for maintaining genomic integrity. Among the proteins that physically interact with BRCA2, Partner and Localizer of BRCA2 (PALB2), which binds to the N-terminal region of BRCA2, is vital for its function by facilitating its subnuclear localization. A functional redundancy has been reported between this N-terminal PALB2-binding domain and the C-terminal DNA-binding domain of BRCA2, which undermines the relevance of the interaction between these two proteins. Here, we describe a genetic approach to examine the functional significance of the interaction between BRCA2 and PALB2 by generating a knock-in mouse model of Brca2 carrying a single amino acid change (Gly25Arg, Brca2G25R) that disrupts this interaction. In addition, we have combined Brca2G25R homozygosity as well as hemizygosity with Palb2 and Trp53 heterozygosity to generate an array of genotypically and phenotypically distinct mouse models. Our findings reveal defects in body size, fertility, meiotic progression, and genome stability, as well as increased tumor susceptibility in these mice. The severity of the phenotype increased with a decrease in the interaction between BRCA2 and PALB2, highlighting the significance of this interaction. In addition, our findings also demonstrate that hypomorphic mutations such as Brca2G25R have the potential to be more detrimental than the functionally null alleles by increasing genomic instability to a level that induces tumorigenesis, rather than apoptosis.
Unsupervised image translation with distributional semantics awareness (2023)

Unsupervised image translation (UIT) studies the mapping between two image domains. Since such mappings are under-constrained, existing research has pursued various desirable properties such as distributional matching or two-way consistency. In this paper, we re-examine UIT from a new perspective: distributional semantics consistency, based on the observation that data variations contain semantics, e.g., shoes varying in colors. Further, the semantics can be multi-dimensional, e.g., shoes also varying in style, functionality, etc. Given two image domains, matching these semantic dimensions during UIT will produce mappings with explicable correspondences, which has not been investigated previously. We propose distributional semantics mapping (DSM), the first UIT method which explicitly matches semantics between two domains. We show that distributional semantics has been rarely considered within and beyond UIT, even though it is a common problem in deep learning. We evaluate DSM on several benchmark datasets, demonstrating its general ability to capture distributional semantics. Extensive comparisons show that DSM not only produces explicable mappings, but also improves image quality in general.
Rapid Self‐healing Film From Novel Photo Polymerization Additive. (2018)

Abstract Self‐healing materials have ability to repair damage by themselves. Their properties have been developed to increase the reliability of materials. Generally, self‐healing polymers have been developed by thermal polymerization. Especially, hydrogel materials showed relatively rapid recovery and goodhealing efficiency. However, it is very difficult to restore their properties without the self‐healing mediator such as water. Herein, we report the novel type of self‐healing polymer using photo‐polymerization. This is achieved through an unprecedented concept of an additive of photopolymerization, named as ‘healer’ which can act as a physical crosslinker between main chains and a self‐healing mediator in hydrogel materials. This transparent, easily fabricated self‐healing polymer healed scratch in 40 seconds as well as restored the mechanical properties to 82%.
Supplemental Figures from Aberrant Activation of Notch Signaling Inhibits PROX1 Activity to Enhance the Malignant Behavior of Thyroid Cancer Cells (2023)

&lt;p&gt;Supplemental Figures. Fig S1:Expression of HEY1 and HEY2 in thyroid cancers vs. normal thyroid tissues. Fig S2:PROX1 mislocalization in TPC-1 cells does not depend on CRM1, energy or temperature. Fig S3: T3 promotes PROX1 nuclear exclusion in a dose-dependent manner. Fig S4: Engineered BCPAP cells conditionally express FLAG-tagged PROX1 by doxycycline administration. Fig S5: Wnt/β-catenin signaling is suppressed in PTC cells. Fig S6: PROX1-mediated regulation of thyroid cancer-associated genes in TPC1 and 8505c cells. Fig S7: Single cell motility assay. Fig S8: Reinstatement of PROX1 expression in TPC1 and 8505c thyroid cancer cells. Fig S9: Dox-induced expression of PROX1 in BCPAP tumor cells in mouse. Fig S10: PROX1 re-expression inhibits tumor growth and aggressive tumor cell morphology of TPC1 thyroid carcinoma cells. Fig S11: PROX1 re-expression suppressed tumor growth and aggressive morphology of 8505c thyroid cancer cells. Fig S12: Cytoplasmic localization of PROX1 in other cancer cells.&lt;/p&gt;
Factors Associated with Stroke Misdiagnosis in the Emergency Department: A Retrospective Case-Control Study (2018)

Patients with stroke misdiagnosis were commonly FAST-negative with nonspecific symptoms including altered mental status, dizziness and nausea/vomiting often associated with PCS. Improved diagnostic accuracy may increase access to acute therapies.
Platelets Apoptosis and Clearance in The Presence of Sodium Octanoate during Storage of Platelet Concentrate at 4˚C. (2020)

SO could partially moderate the effects of cold temperature on apoptosis and viability of platelets. It also decreases the ingestion rate of long-time refrigerated PLTs in vitro. Further studies using higher numbers of samples are required to demonstrate the effect of SO on reducing the clearance rate of PLTs.
The Analysis of Sulfur-35 as a Young Groundwater Tracer at E-Tunnel, Rainier Mesa, Nevada National Security Site (2017)

Analysis of the relatively short-lived radionuclide sulfur-35 (t1/2 = 87 days) provides useful insight into groundwater discharge from E-Tunnel at the Nevada National Security Site (NNSS). Discharge rates at E-Tunnel vary with precipitation, potentially as the result of short or fast flowpaths between recharge and discharge. The presence of sulfur-35 in groundwater would indicate a significant component of young (< 2-year-old) groundwater. We collected two large volume (20 L) samples of discharge water in November 2016. The samples were sent to Lawrence Livermore National Laboratory (LLNL), where they were processed and analyzed by Liquid Scintillation Counting (LSC). Sulfur-35 was not detected in either the sample or field duplicate, a finding consistent with E-Tunnel discharge containing no significant component of groundwater with age less than six months.
Coming out of the Shell: Building the Molecular Infrastructure for Research on Parasite-Harbouring Snails (2013)

&lt;p&gt;Coming out of the Shell: Building the Molecular Infrastructure for Research on Parasite-Harbouring Snails&lt;/p&gt;
Isolated ostial left main coronary artery stenosis causing ischemic cardiomyopathy in a child with bicuspid aortic valve (2022)

Bicuspid aortic valve (BAV) is the most common congenital cardiac defect, commonly associated with valve dysfunction and coarctation of aorta. Rarely, BAV can be associated with abnormalities of the coronary arteries, the most common of which are ectopic coronary origins. In this report, we present a case of a 2-year-old child with BAV, without coexisting supravalvular aortic stenosis, who was found to have a left main coronary ostio-proximal stenosis, leading to ischemic cardiomyopathy and congestive heart failure.
Disposition, profiling and identification of emixustat and its metabolites in humans (2017)

1. Emixustat is a small molecule that potently inhibits retinal pigment epithelium 65 isomerohydrolase. Emixustat is in clinical development for the treatment of various retinopathies (i.e. Stargardt disease and diabetic retinopathy). 2. A human absorption, distribution, metabolism, and excretion (ADME) study was conducted with a single dose of [<sup>14</sup>C]-emixustat in healthy male subjects. Total <sup>14</sup>C content in plasma, urine, and faeces was determined using accelerator mass spectrometry (AMS), and metabolic profiles in pooled plasma and urine were investigated by both HPLC-AMS and 2D LC-MS/MS. 3. After a single, oral 40-mg dose of [<sup>14</sup>C]-emixustat, recovery of total <sup>14</sup>C was nearly complete within 24 h. Urine was the major route of <sup>14</sup>C elimination; accounting for > 90% of the administered dose. 4. Biotransformation of emixustat occurred primarily at two structural moieties; oxidation of the cyclohexyl moiety and oxidative deamination of the 3R-hydroxypropylamine, both independently and in combination to produce secondary metabolites. Metabolite profiling in pooled plasma samples identified 3 major metabolites: ACU-5124, ACU-5116 and ACU-5149, accounting for 29.0%, 11.5%, and 10.6% of total <sup>14</sup>C, respectively. Emixustat was metabolized in human hepatocytes with unchanged emixustat accounting for 33.7% of sample radioactivity and predominantly cyclohexanol metabolites observed.
Censure et religion : le juge judiciaire, gardien de la liberté d'expression artistique (2020)

International audience
Emergent dynamics of underlying regulatory network links EMT and androgen receptor-dependent resistance in prostate cancer (2023)

Advanced prostate cancer patients initially respond to hormone therapy, be it in the form of androgen deprivation therapy or second-generation hormone therapies, such as abiraterone acetate or enzalutamide. However, most men with prostate cancer eventually develop hormone therapy resistance. This resistance can arise through multiple mechanisms, such as through genetic mutations, epigenetic mechanisms, or through non-genetic pathways, such as lineage plasticity along epithelial-mesenchymal or neuroendocrine-like axes. These mechanisms of hormone therapy resistance often co-exist within a single patient's tumor and can overlap within a single cell. There exists a growing need to better understand how phenotypic heterogeneity and plasticity results from emergent dynamics of the regulatory networks governing androgen independence. Here, we investigated the dynamics of a regulatory network connecting the drivers of androgen receptor (AR) splice variant-mediated androgen independence and those of epithelial-mesenchymal transition. Model simulations for this network revealed four possible phenotypes: epithelial-sensitive (ES), epithelial-resistant (ER), mesenchymal-resistant (MR) and mesenchymal-sensitive (MS), with the latter phenotype occurring rarely. We observed that well-coordinated "teams" of regulators working antagonistically within the network enable these phenotypes. These model predictions are supported by multiple transcriptomic datasets both at single-cell and bulk levels, including in vitro EMT induction models and clinical samples. Further, our simulations reveal spontaneous stochastic switching between the ES and MR states. Addition of the immune checkpoint molecule, PD-L1, to the network was able to capture the interactions between AR, PD-L1, and the mesenchymal marker SNAIL, which was also confirmed through quantitative experiments. This systems-level understanding of the driver of androgen independence and EMT could aid in understanding non-genetic transitions and progression of such cancers and help in identifying novel therapeutic strategies or targets.
SDN-Controlled Routing of Elephants and Mice over a Hybrid Optical/Electrical DCN Testbed (2015)

We propose an SDN-controlled hybrid optical/electrical intra-DCN framework allowing differentiated routing of diverse flow types. Experimental results demonstrate flow completion time reduction of up to 60% and 40% for elephants and mice respectively.
Monitoring electrically-evoked hemodynamic responses in the squirrel monkey brain using photoacoustic computed tomography and photoacoustic microscopy (2022)

The feasibility of using photoacoustic imaging (PAI) to measure electrically-evoked hemodynamic responses in a squirrel monkey brain in vivo was examined. A linear-array photoacoustic computed tomography (PACT) system and a high-resolution photoacoustic microscopy (PAM) system were built for imaging subcortical and cortical brain regions, respectively. The hemodynamic responses at multiple cortices, including premotor, primary motor, and primary somatosensory cortices, were monitored. The variations could be observed in all cortices and their underlying cortical and subcortical brain regions. The results from this study validated the potential of PAI technique for multiscale and multi-resolution functional brain mapping for non-human primates.