gebhart/patrepeval huggingface dataset:
Effect of Lactobacillus paracasei NCC2461 on Antigen-Specific T-Cell Mediated Immune Responses in Aged Mice (2008)

Aging is associated with a reduced capacity to mount proper immune responses, in particular to vaccines. Probiotic lactic acid bacteria may improve the immune status of the elderly; however, there is little evidence showing an effect of these bacteria on humoral and cellular immune responses. In the present study, the immunomodulatory capacity of the probiotic Lactobacillus paracasei NCC2461 combined or not with a prebiotic composition, FOS/inulin, was examined in aged mice. Male C57BL/6J mice (21-months-old) were allocated to one of three groups fed ad libitum for 44 days with different diets: a normal diet (control), a normal diet plus NCC2461 given in the drinking water, or a diet containing FOS/inulin plus NCC2461 in the drinking water. All mice were immunized on day 15 and challenged on day 22 with keyhole limpet hemocyanin (KLH). T helper (Th)1 cell-dependent immune responses (anti-KLH immunoglobulin G(2a) [IgG(2a)] levels and delayed type hypersensitivity response) were increased significantly in NCC2461-supplemented mice when compared to controls. Supplementation with FOS/inulin did not further improve the immune-enhancing effect mediated by the probiotic. Splenocyte proliferation, T cell subsets, systemic total IgG levels, and mucosal total IgA responses were not affected. Interestingly, supplementation with NCC2461 modulated the intestinal microbiota composition by increasing the numbers of bifidobacteria and lactobacilli. In conclusion, oral intake of L. paracasei NCC2461 by aged mice enhanced the specific adaptive immune response to in vivo antigenic challenge without altering other cellular and humoral immune responses. The poor responsiveness to antigenic challenge, frequently observed in elderly people, may be improved by supplementation with L. paracasei NCC2461.
Prédiction de la dynamique d'un convertisseur DC-DC piézoélectrique (2021)

International audience
Supplementary Data File from High PDGFRb Expression Predicts Resistance to Radiotherapy in DCIS within the SweDCIS Randomized Trial (2023)

&lt;p&gt;Supplementary data file with extended Materials and Methods, Supplementary Tables 1-6 and Supplementary Figures 1-3&lt;/p&gt;
Phase 3 Efficacy Trial of Modified Vaccinia Ankara as a Vaccine against Smallpox (2019)

No safety concerns associated with the MVA vaccine were identified. Immune responses and attenuation of the major cutaneous reaction suggest that this MVA vaccine protected against variola infection. (Funded by the Office of the Assistant Secretary for Preparedness and Response Biomedical Advanced Research and Development Authority of the Department of Health and Human Services and Bavarian Nordic; ClinicalTrials.gov number, NCT01913353.).
Differences in incidence and co‐occurrence of vaccine and nonvaccine human papillomavirus types in Finnish population before human papillomavirus mass vaccination suggest competitive advantage for HPV33 (2010)

To understand likelihood of type replacement after vaccination against the high-risk human papillomavirus (HPV) types, we evaluated competition of the seven most common genital HPV types in a population sample of unvaccinated, fertile-aged Finnish women. First trimester sera from two consecutive pregnancies were retrieved from 3,183 Finnish women (mean age, 23.1 years) of whom 42.3% had antibodies to at least one HPV type (6/11/16/18/31/33/45) at the baseline. Antibody positivity to more than one HPV types by the second pregnancy was common among the baseline HPV seropositives. However, compared to baseline HPV-seronegative women, significantly increased incidence rate ratios (IRRs), indicating an increased risk to seroconvert for another HPV type, were consistently noted only for HPV33 among baseline HPV16 or HPV18 antibody (ab)-positive women: HPV(16ab only) (→) (16&33ab) IRR 2.9 [95% confidence interval (CI) 1.6-5.4] and HPV(18ab only) (→) (18&33ab) IRR 2.5 (95% CI 1.1-6.0), irrespectively of the presence of antibodies to other HPV types at baseline: HPV(16ab) (→) (16&33ab) IRR 3.2 (95% CI 2.0-5.2) and HPV(18ab) (→) (18&33ab) IRR 3.6 (95% CI 2.1-5.9). Our findings suggest a possible competitive advantage for HPV33 over other genital HPV types in the unvaccinated population. HPV33 should be monitored for type replacement after HPV mass vaccination.
Binding affinities and protein ligand complex geometries of nucleotides at the F1 part of the mitochondrial ATP synthase obtained by ligand docking calculations (2002)

F(0)F(1) ATP synthases utilize a transmembrane electrochemical potential difference to synthesize ATP from ADP and phosphate. In this work, the binding modes of ADP, ATP and ATP analogues to the catalytic sites of the F(1) part of the mitochondrial ATP synthase were investigated with ligand docking calculations. Binding geometries of ATP and ADP at the three catalytic sites agree with X-ray crystal data; their binding free energies suggest an assignment to the 'tight', 'open' and 'loose' states. The rates of multi-site hydrolysis for two fluorescent ATP derivatives were measured using a fluorescence assay. Reduced hydrolysis rates compared to ATP can be explained by the ligand docking calculations.
High-gain, polarization-preserving, Yb-doped fiber amplifier for low-duty-cycle pulse amplification (2006)

Amplified spontaneous emission (ASE) suppression techniques were utilized to fabricate a double-pass, Yb-doped amplifier with the noise properties of a single-pass amplifier. Simulations based on a rate equation model were used to analyze the ASE and the effectiveness of the suppression techniques. These techniques were implemented in an alignment-free, double-pass, Yb-doped fiber amplifier with a 26 dB gain at a wavelength 23 nm off the gain peak and a -48 dB noise floor while amplifying linearly polarized optical pulses with a low-duty cycle.
Cloud Deployment and Management of Dataflow Engines (2017)

Maxeler Technologies successfully commercialises high-performance computing systems based on dataflow technology. Maxeler dataflow computers have been deployed in a wide range of application domains including financial data analytics, geoscience and low-latency transaction processing. In the context of cloud computing steadily growing acceptance in new domains, we illustrate how Maxeler dataflow systems can be integrated and employed in a self-organising self-managing heterogeneous cloud environment.
Compounds containing meta-biphenylenedioxy moieties and polymers therefrom (1993)

Two monomers containing meta-biphenylenedioxy moieties were prepared. One monomer, a diamine, is used to prepare polyimide, polyamide, and epoxy polymers. The other monomer, a dianhydride, was used to prepare polyimide polymers. These polymers are used to make films, coatings, and selective membranes.
Proton in a Confined Space: Structural Studies of H+⊂Crypt‐111 Iodide and Some Halogen‐Bonded Derivatives (2017)

Experimental observations and modeling data are reported on the solid-state structural features of crypt- 111⋅HI (1) and the three-component co-crystals that 1 forms with α,ω-diiodoperfluoroalkanes 2 a-d. X-ray analyses indicate that, in all five systems and at low temperature, the caged proton is covalently bonded to a single nitrogen atom and is involved in a network of intramolecular hydrogen bonds. In contrast, room-temperature, solid-state <sup>15</sup> N NMR spectroscopy suggests magnetic equivalency of the two N atoms of crypt-111 in both 1 and co-crystals of 1 with diiodoperfluoroalkanes. Computational modelling confirms that the acidic hydrogen inside the cavity preferentially sits along the internitrogen axis and is covalently bonded to one nitrogen. The computed energy barriers suggest that the hopping of the encapsulated proton between the two N atoms of the cage can occur in the halogen-bonded co-crystals of 1⋅2, but it is hardly possible in the pure H<sup>+</sup> ⊂crypt-111 iodide 1. These different pictures of the proton position and dynamics obtained by using different techniques and conditions confirm the unique characteristics of the confined space within the cavity of crypr-111 and the distinctive features of processes occurring therein.
Biotransformation of fluorophenyl pyridine carboxylic acids by the model fungusCunninghamella elegans (2016)

1. Fluorine plays a key role in the design of new drugs and recent FDA approvals included two fluorinated drugs, tedizolid phosphate and vorapaxar, both of which contain the fluorophenyl pyridyl moiety. 2. To investigate the likely phase-I (oxidative) metabolic fate of this group, various fluorinated phenyl pyridine carboxylic acids were incubated with the fungus Cunninghamella elegans, which is an established model of mammalian drug metabolism. 3. <sup>19</sup>F NMR spectroscopy established the degree of biotransformation, which varied depending on the position of fluorine substitution, and gas chromatography-mass spectrometry (GC-MS) identified alcohols and hydroxylated carboxylic acids as metabolites. The hydroxylated metabolites were further structurally characterised by nuclear magnetic resonance spectroscopy (NMR), which demonstrated that hydroxylation occurred on the 4' position; fluorine in that position blocked the hydroxylation. 4. The fluorophenyl pyridine carboxylic acids were not biotransformed by rat liver microsomes and this was a consequence of inhibitory action, and thus, the fungal model was crucial in obtaining metabolites to establish the mechanism of catabolism.
Preliminary design and techno-economic assessment of a trigeneration system integrated with compressed air and chemical energy storage (2023)

The advantages of compressed air energy storage (CAES) have been demonstrated by the trigeneration system with the characteristic of high penetration of renewable energy. However, since the irreversible loss of compression heat occurs during the overall operation processes of CAES, the development of CAES with high energy efficiency has been hindered by the conventional conversion pathway of compression heat. Therefore, a trigeneration system integrated with compressed air and chemical energy storage is proposed in this study to improve energy utilization efficiency. The compression heat is converted into H2 and CO via the endothermic methanol decomposition reaction to improve its energy level during the charging process, and then the syngas production can be used for air preheating during the discharging process. The parametric analysis is first performed to investigate the technical and economic feasibility of the system. Subsequently, the multi-objective optimization is conducted to identify the tradeoffs in the thermo-economic performance of the system and acquire the optimal values of operating parameters. Notably, the proposed system with a computed exergy efficiency of 43.31% and levelized cost of energy (LCOE) of 97.53 $/MWh is selected as the most compromise solution by the decision maker of Technique for Order Preference by Similarity to an Ideal Solution among the Pareto optimum fronts, which are 8.47% higher than the exergy efficiency and 7.39 $/MWh lower than the LCOE under the design conditions.
Design and Fabrication of Thin-Film Diarylethene Recording Layer and Its Reflective Reproduction for Super-Multilayered Optical Memories (2007)

We studied the feasibility of two-photon absorption recording and reflective reproduction for three-dimensional (3D) optical memories by comparison between bulk and super-multilayered media. The basic design of such a super-multilayered structure for achieving a high reflectance from a pit and for reducing layer thickness was described. To evaluate basic optical characteristics, two types of sample with a 100% diarylethene recording layer were fabricated. It was experimentally confirmed that reflective reproduction can be possible in the super-multilayered structure, whereas reflective signals were not obtained in the bulk structure as indicated by the results of theoretical analysis. Therefore, 3D recording and reproducing in a super-multilayered medium would be promising for a future high-capacity memory system.
Material Flow Analysis and Life Cycle Assessment of Polyethylene Terephthalate and Polyolefin Plastics Supply Chains in the United States (2022)

Plastics are useful and beneficial materials that contribute to an improved quality of life, yet they generate significant solid wastes and emissions and consume significant energy resources. Systems analysis is incomplete on current linear production systems of plastics supply chains and their associated processes. Our study combines material flow and life cycle assessment data sets of polyethylene terephthalate (PET) and the main polyolefin polymers in the United States, comprising over 70% of plastics flows. This study estimates the total greenhouse gas (GHG) emissions and energy consumption of these supply chains, including transportation and end-of-life processes, lacking in prior studies. We calculate annual GHG emissions and energy consumption of these plastic supply chains to be 101 MMT CO2-eq and 3248 PJ in 2019, respectively. The GHG emissions of these supply chains represented 1.5% of the total U.S. emissions and 5% of the total U.S. industry-related GHG emissions. The total energy consumption of these supply chains represented 3.1% of the total U.S. energy consumption in 2019. Transportation of PET and polyolefin plastic materials contributes 5% and 2% to the total supply chain GHG emissions and energy consumption, respectively. This baseline study provides a benchmark and enables a comparison to future circular production systems for plastics in the United States.
SARS-CoV-2 Variants in Immunocompromised Patient Given Antibody Monotherapy (2021)

A 72-year-old immunocompromised man infected with severe acute respiratory syndrome coronavirus 2 received bamlanivimab monotherapy. Viral evolution was monitored in nasopharyngeal and blood samples by melting curve analysis of single-nucleotide polymorphisms and whole-genome sequencing. Rapid emergence of spike receptor binding domain mutations was found, associated with a compartmentalization of viral populations.
Identification in the yeast Pichia stipitis of the first l‐rhamnose‐1‐dehydrogenase gene (2008)

There are two distinctly different pathways for the catabolism of l ‐rhamnose in microorganisms. One pathway with phosphorylated intermediates was described in bacteria; here the enzymes and the corresponding gene sequences are known. The other pathway has no phosphorylated intermediates and has only been described in eukaryotic microorganisms. For this pathway, the enzyme activities have been described but not the corresponding gene sequences. The first enzyme in this catabolic pathway is the NAD‐utilizing l ‐rhamnose 1‐dehydrogenase. The enzyme was purified from the yeast Pichia stipitis , and the mass of its tryptic peptides was determined using MALDI‐TOF MS. This enabled the identification of the corresponding gene, RHA1 . It codes for a protein with 258 amino acids belonging to the protein family of short‐chain alcohol dehydrogenases. The ORF was expressed in Saccharomyces cerevisiae . As the gene contained a CUG codon that codes for serine in P. stipitis but for leucine in S. cerevisiae , this codon has changed so that the same amino acid was expressed in S. cerevisiae . The heterologous protein showed the highest activity and affinity with l ‐rhamnose and a lower activity and affinity with l ‐mannose and l ‐lyxose. The enzyme was specific for NAD. A northern blot analysis revealed that transcription in P. stipitis is induced during growth on l ‐rhamnose but not on other carbon sources.
Humidity rise after purge in micro-environments (2012)

The mass transport properties of four micro-environment (ME) materials were tested: polycarbonate (PC), poly(ether imide) (PEI), poly(ether ether ketone) (PEEK) and the Entegris barrier material (EBM). Permeation, diffusion and solubility coefficients of water vapor were measured at room temperature with 45% and 100% relative humidity (RH). These mass transport coefficients were used to estimate the humidity rise after purge in a 300 mm front opening unified pod (FOUP) constructed of these materials. PC was estimated to show 20% humidity rise two hours after purge. PEI was comparable to PC. PEEK showed better performance than PC or PEI. EBM showed the best water permeation resistance and the slowest and lowest humidity rise.
3.1 An Integrated BAW Oscillator with <±30ppm Frequency Stability Over Temperature, Package Stress, and Aging Suitable for High-Volume Production (2020)

Wireless sensor nodes with low power and small form factor are desirable for emerging IoT applications. These nodes usually consist of a processor, memory, radio, sensors, battery, and two quartz crystals: one at 32kHz to synchronize data transmission and the other in the MHz range to synthesize RF signals. SoC integration of the memory, processor, and radio is common; however the MHz crystal remains external, which makes up a significant portion of the entire wireless node size.
Delivery of methoxymorpholinyl doxorubicin by interleukin 2-activated NK cells: effect in mice bearing hepatic metastases (1999)

The possibility of using interleukin 2 (IL-2)-activated natural killer cells (A-NK) to carry methoxymorpholinyl doxorubicin (MMDX; PNU 152243) to liver-infiltrating tumours was explored in mice bearing 2-day established M5076 reticulum cell sarcoma hepatic metastases. In vitro, MMDX was 5.5-fold more potent than doxorubicin against M5076 tumour cells. MMDX uptake by A-NK cells correlated linearly with drug concentration in the incubation medium [correlation coefficient (r) = 0.999]; furthermore, as MMDX incorporation was readily reproducible in different experiments, the amount of drug delivered by A-NK cells could be modulated. In vivo experiments showed that intravenous (i.v.) injection of MMDX-loaded A-NK cells exerted a greater therapeutic effect than equivalent or even higher doses of free drug. The increase in lifespan (ILS) following A-NK cell delivery of 53 microg kg(-1) MMDX, a dosage that is ineffective when administered in free form, was similar to that observed in response to 92 microg kg(-1) free drug, a dosage close to the 10% lethal dose (ILS 42% vs. 38% respectively). These results correlated with pharmacokinetic studies showing that MMDX encapsulation in A-NK cells strongly modifies its organ distribution and targets it to tissues in which IL-2 activated lymphocytes are preferentially entrapped after i.v. injection.
An Inference-based Prognostic Framework for Health Management of Automotive Systems (2020)

This paper presents a unified data-driven prognostic framework that combines failure time data, static parameter data and dynamic time-series data. The framework employs proportional hazards model and a soft dynamic multiple fault diagnosis algorithm for inferring the degraded state trajectories of components and to estimate their remaining useful life times. The framework takes into account the cross-subsystem fault propagation, a case prevalent in any networked and embedded system. The key idea is to use Cox proportional hazards model to estimate the survival functions of error codes and symptoms (probabilistic test outcomes/prognostic indicators) from failure time data and static parameter data, and use them to infer the survival functions of components via soft dynamic multiple fault diagnosis algorithm. The average remaining useful life and its higher-order central moments (e.g., variance, skewness, kurtosis) can be estimated from these component survival functions. The framework is demonstrated on datasets derived from two automotive systems, namely hybrid electric vehicle regenerative braking system, and an electronic throttle control subsystem simulator. Although the proposed framework is validated on automotive systems, it has the potential to be applicable to a wide variety of systems, ranging from aerospace systems to buildings to power grids.
In Situ Microscopic Studies on the Interaction of Multi-Principal Element Nanoparticles and Bacteria (2023)

Multi-principal element nanoparticles are an emerging class of materials with potential applications in medicine and biology. However, it is not known how such nanoparticles interact with bacteria at nanoscale. In the present work, we evaluated the interaction of multi-principal elemental alloy (FeNiCu) nanoparticles with <i>Escherichia coli</i> (<i>E. coli</i>) bacteria using the <i>in situ</i> graphene liquid cell (GLC) scanning transmission electron microscopy (STEM) approach. The imaging revealed the details of bacteria wall damage in the vicinity of nanoparticles. The chemical mappings of S, P, O, N, C, and Cl elements confirmed the cytoplasmic leakage of the bacteria. Our results show that there is selective release of metal ions from the nanoparticles. The release of copper ions was much higher than that for nickel while the iron release was the lowest. In addition, the binding affinity of bacterial cell membrane protein functional groups with Cu, Ni, and Fe cations is found to be the driving force behind the selective metal cations' release from the multi-principal element nanoparticles. The protein functional groups driven dissolution of multielement nanoparticles was evaluated using the density functional theory (DFT) computational method, which confirmed that the energy required to remove Cu atoms from the nanoparticle surface was the least in comparison with those for Ni and Fe atoms. The DFT results support the experimental data, indicating that the energy to dissolve metal atoms exposed to oxidation and/or the to presence of oxygen atoms at the surface of the nanoparticle catalyzes metal removal from the multielement nanoparticle. The study shows the potential of compositional design of multi-principal element nanoparticles for the controlled release of metal ions to develop antibacterial strategies. In addition, GLC-STEM is a promising approach for understanding the nanoscale interaction of metallic nanoparticles with biological structures.
Electrostatic Control of Polymorphism in Charged Amphiphile Assemblies (2017)

Stimuli-induced structural transformations of molecular assemblies in aqueous solutions are integral to nanotechnological applications and biological processes. In particular, pH responsive amphiphiles as well as proteins with various degrees of ionization can reconfigure in response to pH variations. Here, we use in situ small and wide-angle X-ray scattering (SAXS/WAXS), transmission electron microscopy (TEM), and Monte Carlo simulations to show how charge regulation via pH induces morphological changes in the assembly of a positively charged peptide amphiphile (PA). Monte Carlo simulations and pH titration measurements reveal that ionic correlations in the PA assemblies shift the ionizable amine pK ∼ 8 from pK ∼ 10 in the lysine headgroup. SAXS and TEM show that with increasing pH, the assembly undergoes spherical micelle to cylindrical nanofiber to planar bilayer transitions. SAXS/WAXS reveal that the bilayer leaflets are interdigitated with the tilted PA lipid tails crystallized on a rectangular lattice. The details of the molecular packing in the membrane result from interplay between steric and van der Waals interactions. We speculate that this packing motif is a general feature of bilayers comprised of amphiphilic lipids with large ionic headgroups. Overall, our studies correlate the molecular charge and the morphology for a pH-responsive PA system and provide insights into the Å-scale molecular packing in such assemblies.
Primary Structure (2016)

In the past, aggregation and self-assembly have been associated principally with micellar and colloidal systems of molecules; however, with the advent of supramolecular chemistry, molecular self-assembly has been opened to a much wider understanding that has facilitated access to a variety of different shapes and sizes, along with the construction of new and fascinating molecular topologies. This document aims at defining more than 150 terms related to aggregation and self-assembly in the particular case of macromolecules. The list is restricted to the most commonly encountered terms.