gebhart/patrepeval huggingface dataset:
Effect of Localized Promotion of Cytokinin Biosynthesis on Flower Morphology in Flower Buds of Torenia fournieri Lind. (2013)

To analyze the relationship between flower morphology and organ-specific promotion of cytokinin biosynthesis within flower buds, we introduced Arabidopsis isopentenyltransferase 4 (AtIPT4) into torenia (Torenia fournieri L.) under the control of APETALA1 (AP1) or APETALA3 (AP3) promoter. AP1::AtIPT4 plants had an increased number of petals, whereas AP3::AtIPT4 plants had an expanded corolla, a paracorolla, and serrated petal margins along with an increased number of petals. In AP3::AtIPT4 plants, marked receptacle enlargement was observed when the flower buds were in the early corolla development stage in which the paracorolla primordia differentiate. As expected, AtIPT4 was expressed in the sepals and petals of AP1::AtIPT4 plants, and in the petals and stamens of AP3::AtIPT4 plants. Furthermore, the type-A response regulator (TfRR1) and cytokinin oxidase (TfCKX5) genes, which were used as indices of cytokinin signal, showed the same expression patterns as the transgene. These findings indicate that expansion of the corolla and development of the paracorolla and serrated petal margins after receptacle enlargement in AP3::AtIPT4 plants are induced by localized elevated cytokinin signal in the petals and stamens. In contrast, localized elevated cytokinin signal in the sepals and petals only induced an increase in the number of petals. Therefore, an elevated cytokinin signal in the stamen may be important for inducing corolla expansion and for developing a paracorolla and serrated petal margins.
Framework and Extraframework Tin Sites in Zeolite Beta React Glucose Differently (2012)

Here, we show that framework tin sites in pure silica zeolite Beta (Sn-Beta) can isomerize glucose to fructose by a Lewis acid-mediated intramolecular hydride shift in aqueous solvent, but not in methanol solvent. Mechanistic studies using isotopically labeled (2H, 13C) glucose reactants show that in methanol, Sn-Beta instead epimerizes glucose to mannose by a Lewis acid-mediated intramolecular carbon shift mechanism known as the Bilik reaction. We also provide evidence that extraframework tin sites located within the hydrophobic channels of zeolite Beta can isomerize glucose to fructose in both water and methanol solvent, but through a base-catalyzed proton-transfer mechanism. SnO2 particles located at external zeolite crystal surfaces or supported on amorphous silica catalyze isomerization in methanol but not in water, suggesting that contact with bulk water inhibits isomerization at SnO2 surfaces. 119Sn MAS NMR spectroscopy was used to unambiguously identify framework Sn sites, which give resonances for octahedral Sn (−685 to −700 ppm) in hydrated Sn-Beta that disappear upon dehydration, with the concomitant appearance of resonances for tetrahedral Sn (−425 to −445 ppm). In sharp contrast, spectra of hydrated samples containing extraframework SnO2 show resonances for octahedral Sn centered at −604 ppm that do not change upon dehydration. These findings demonstrate that aldose–ketose isomerization reactivity on Sn-zeolite samples cannot be ascribed to the presence of framework Sn sites in the absence of isotopic labeling studies. They also indicate that any Sn-zeolite samples that initially convert glucose to fructose, instead of mannose, in methanol solvent contain Sn species that are structurally different from framework Sn centers.
Decubitus prophylaxes in surgery: A novel approach using active load controlled bedding system (2012)

Suffering from decubitus ulcer, also known as bedsore, leads to long lasting treatment of the affected region as well as it provides a significant contribution to expenditures in health care. Acquiring a decubitus ulcer during a hospital stay is often related to surgical procedures. Therefore an improvement of the intraoperative situation is eligible. In contrast to common approaches focusing on passive pressure redistribution of the mat a new approach towards an active load controlled bedding system is presented. This active support system consists of multiple elements, enabled to change height and detecting the applied load on each element. Due to lowering an overloaded region a decrease of applied load is expected while the load on the surrounding elements will increase.
Raman studies of the intermediate tin-oxide phase (2017)

The existence of an intermediate phase of tin oxide was first reported in 1882. However, its stoichiometry and its crystal structure have been dubious and heavily debated ever since, despite a multitude of structural investigations. We show that Raman spectroscopy combined with ab initio theory offers a viable alternative for structure determination in cases where diffraction studies are inconclusive. We unambiguously identify the intermediate phase as ${\mathrm{Sn}}_{3}{\mathrm{O}}_{4}$ and rule out the other likely candidate, ${\mathrm{Sn}}_{2}{\mathrm{O}}_{3}$. We assign the one-phonon Raman signals of ${\mathrm{Sn}}_{3}{\mathrm{O}}_{4}$ to the mode symmetries of the corresponding point group ${C}_{2h}$ and confirm that $P{2}_{1}/c$ with 14 atoms per unit cell is the space group of ${\mathrm{Sn}}_{3}{\mathrm{O}}_{4}$.
Jahn-Teller effect in liquids: General principles and a molecular-dynamics simulation of the cupric ion in water (1992)

We discuss the general conditions under which a Jahn-Teller effect can be meaningfully associated with the solvation shell of an ion in solution. Unlike the Jahn-Teller effect in solids, no distortion of the solvation shell exists on the longest time scales. On intermediate time scales, the solvation shell exhibits cubic (${\mathit{O}}_{\mathit{h}}$) symmetry and on the shortest scales it shows the Jahn-Teller distortion (${\mathit{D}}_{4\mathit{h}}$). A molecular-dynamics simulation of a model in which the frame of reference for the Jahn-Teller potential rotates in time exhibits these features and shows how the time scales involved vary with parameters in the potential.
Efficient subculture process for adherent cells by selective collection using cultivation substrate vibration (2016)

Cell detachment and reseeding are typical operations in cell culturing, often using trypsin exposure and pipetting, even though this process is known to damage the cells. Reducing the number of detachment and reseeding steps might consequently improve the overall quality of the culture, but to date this has not been an option. This study proposes the use of resonant vibration in the cell cultivation substrate to selectively release adherent calf chondrocyte cells: Some were released from the substrate and collected while others were left upon the substrate to grow to confluence as a subculture-without requiring reseeding. An out-of-plane vibration mode with a single nodal circle was used in the custom culture substrate. At a maximum vibration amplitude of 0.6 µm, 84.9% of the cells adhering to the substrate were released after 3 min exposure, leaving a sufficient number of cells for passage and long-term cell culture, with the greatest cell concentration along the nodal circle where the vibration was relatively quiescent. The 72-h proliferation of the unreleased cells was 20% greater in number than cells handled using the traditional method of trypsin-EDTA (0.050%) release, pipette collection, and reseeding. Due to the vibration, it was possible to reduce the trypsin-EDTA used for selective release to only 0.025%, and in doing so the cell number after 72 h of proliferation was 42% greater in number than the traditional technique.
Cross-Presentation of HLA Class I Epitopes from Exogenous NY-ESO-1 Polypeptides by Nonprofessional APCs (2003)

NY-ESO-1, a germ cell Ag often detected in tumor tissues, frequently elicits Ab and CD8(+) T cell responses in cancer patients. Overlapping long peptides spanning the NY-ESO-1 sequence have been used to map HLA class I-restricted epitopes recognized by NY-ESO-1-specific CD8(+) T lymphocytes. To address the antigenicity of long peptides, we analyzed two synthetic 30-mer peptides from NY-ESO-1, polypeptides 80-109 and 145-174, for their capacity to be processed by APCs and to stimulate CD8(+) T cells. By incubating APCs with polypeptides at different temperatures or in the presence of protease inhibitors, we found that NY-ESO-1 polypeptides were rapidly internalized by B cells, T2 cells, or PBLs and submitted to cellular proteolytic action to yield nonamer epitopes presented by HLA class I. Polypeptides were also immunogenic in vitro and stimulated the expansion of CD8(+) T cells against naturally processed NY-ESO-1 epitopes in the context of three different HLA class I alleles. Polypeptides can thus serve as exogenous Ags that are cross-presented on HLA class I without requiring the action of professional APCs. These findings support innovative vaccination strategies using NY-ESO-1 polypeptides that would circumvent current limitations of HLA class I peptide vaccination, i.e., HLA eligibility criteria and knowledge of epitope, while allowing for facilitated immunogenicity in the presence of helper epitopes.
Chromosome-length genome assembly and linkage map of a critically endangered Australian bird: the helmeted honeyeater (2022)

The annotated chromosome-length genome and high-density linkage map provide rich resources for evolutionary studies and will be fundamental in guiding conservation efforts for the helmeted honeyeater.
Studies of Mice Lacking Plasminogen Activator Gene Function Suggest that Plasmin Production Prior to Ovulation Exceeds the Amount Needed for Optimal Ovulation Efficiency (1997)

Many studies suggest that the plasminogen activator (PA) system plays a role in the proteolytic degradation of the follicle wall at the time of ovulation. Consistently, the ovulation efficiency is reduced by 26% in mice where both physiological PA genes have been inactivated. To reveal the mechanism behind reduced ovulation efficiency in PA-deficient mice and its effect on ovarian proteolysis. we have studied the regulation of plasmin activity in the ovaries of 25-day-old wild-type mice and mice with deficient PA gene function during gonadotropin-induced ovulation. In wild-type mice the plasmin activity was low in ovarian extracts from mice treated with pregnant mare's serum gonadotropin. However, this activity was increased between 2-8 h after an ovulatory dose of human choriogonadotropins. In mice lacking either tissue-type PA (tPA) or PA inhibitor type 1 (PAI-1) the plasmin activity levels prior to ovulation were similar to wild-type mice, while extracts prepared from urokinase-type PA (uPA) deficient mice had 10% or less of the plasmin activity. This indicates that most of the plasmin activity in the mouse ovary is generated by uPA. In addition, as the ovulation efficiency is impaired in tPA/uPA-deficient mice but appears normal in uPA-deficient mice, our data indicates that the amount of plasmin generated by PAs prior to ovulation in wild-type mice greatly exceeds the amount required for efficient ovulation.
Misspecified CRB on Parameter Estimation for a Coupled Mixture of Polynomial Phase and Sinusoidal FM Signals (2019)

This paper studies parameter estimation of a coupled mixture of polynomial phase signal (PPS) and sinusoidal frequency modulated (FM) signal, a newly introduced model motivated by industrial applications. Particularly, we analytically evaluate the estimation performance (or performance loss) via the misspecified Cramér-Rao bound (CRB) when system designers choose existing efficient estimation algorithms designed for an independent (decoupled) mixture model due to hardware limits. Our analysis provides an analytical tool to conveniently evaluate performance loss if the implemented system ignores the coupling effect. The achievability of the misspecified CRB is verified by numerical examples.
Water and Solute Movement in the Small Intestine of Patients with Sprue* (1967)

Water and electrolyte movement in the jejunum of normal subjects and patients with sprue was measured during perfusion with isotonic electrolyte solutions. Normal subjects absorbed water, sodium, and potassium. By contrast, in patients with sprue (seven with adult celiac sprue and one with tropical sprue) who had diarrhea and steatorrhea, these substances were secreted into the intestinal lumen. This indicates that the jejunal mucosa of these patients was in a secretory state with respect to water and electrolytes.A method is presented for detecting abnormalities in the effective pore size in disease states. The method is based on the principle of restrictive diffusion and involves measuring the simultaneous diffusion rates of solutes of different molecular size. Since the method does not depend on measurement of water flow in response to osmotic pressure gradients, it can be used in disease states in which absorption and secretory processes involving water may be abnormal.The ratio of urea to tritiated water diffusion in the jejunum of normal subjects averaged 0.8, compared to 0.2 in patients with sprue. This indicates a marked decrease in the effective pore size of the jejunal mucosa in sprue. This conclusion was strengthened by the finding that erythritol and L-xylose, which are somewhat larger solutes than urea, are essentially non-absorbable in small bowel involved with sprue.
Structural Basis for flg22-Induced Activation of the Arabidopsis FLS2-BAK1 Immune Complex (2013)

Flagellin perception in Arabidopsis is through recognition of its highly conserved N-terminal epitope (flg22) by flagellin-sensitive 2 (FLS2). Flg22 binding induces FLS2 heteromerization with BRASSINOSTEROID INSENSITIVE 1-associated kinase 1 (BAK1) and their reciprocal activation followed by plant immunity. Here, we report the crystal structure of FLS2 and BAK1 ectodomains complexed with flg22 at 3.06 angstroms. A conserved and a nonconserved site from the inner surface of the FLS2 solenoid recognize the C- and N-terminal segment of flg22, respectively, without oligomerization or conformational changes in the FLS2 ectodomain. Besides directly interacting with FLS2, BAK1 acts as a co-receptor by recognizing the C terminus of the FLS2-bound flg22. Our data reveal the molecular mechanisms underlying FLS2-BAK1 complex recognition of flg22 and provide insight into the immune receptor complex activation.
ChemInform Abstract: 2,3‐Dimethylene‐2,3‐dihydrothiophene: The Thiophene Analogue of ortho‐Xylylene. (1988)

Abstract Thiophene‐2‐carboxylic acid (I) is converted to the disubstituted derivatives (III).
mGlu5positive allosteric modulation normalizes synaptic plasticity defects and motor phenotypes in a mouse model of Rett syndrome (2016)

Rett syndrome (RS) is a neurodevelopmental disorder that shares many symptomatic and pathological commonalities with idiopathic autism. Alterations in protein synthesis-dependent synaptic plasticity (PSDSP) are a hallmark of a number of syndromic forms of autism; in the present work, we explore the consequences of disruption and rescue of PSDSP in a mouse model of RS. We report that expression of a key regulator of synaptic protein synthesis, the metabotropic glutamate receptor 5 (mGlu<sub>5</sub>) protein, is significantly reduced in both the brains of RS model mice and in the motor cortex of human RS autopsy samples. Furthermore, we demonstrate that reduced mGlu<sub>5</sub> expression correlates with attenuated DHPG-induced long-term depression in the hippocampus of RS model mice, and that administration of a novel mGlu<sub>5</sub> positive allosteric modulator (PAM), termed VU0462807, can rescue synaptic plasticity defects. Additionally, treatment of Mecp2-deficient mice with VU0462807 improves motor performance (open-field behavior and gait dynamics), corrects repetitive clasping behavior, as well as normalizes cued fear-conditioning defects. Importantly, due to the rationale drug discovery approach used in its development, our novel mGlu<sub>5</sub> PAM improves RS phenotypes and synaptic plasticity defects without evoking the overt adverse effects commonly associated with potentiation of mGlu<sub>5</sub> signaling (i.e. seizures), or affecting cardiorespiratory defects in RS model mice. These findings provide strong support for the continued development of mGlu<sub>5</sub> PAMs as potential therapeutic agents for use in RS, and, more broadly, for utility in idiopathic autism.
Etat de l'art sur les microcapteurs de gaz pour la qualité de l'air (2016)

National audience
Correlating Nitrogen Accumulation With Temporal Fuel Cell Performance (2008)

The permeability or crossover characteristics of a typical polymeric perfluorosulfonic acid membrane are used for the temporal and spatial estimation of nitrogen concentration along the anode channels of a fuel cell stack. The predicted nitrogen accumulation is then used to estimate the impact of local fuel starvation on stack voltage through the notion of apparent current density. Despite simplifying assumptions on membrane hydration levels, the calibrated model reasonably predicts the response of a 20-cell stack whenever there is no significant liquid water accumulation in the dead-ended anode. Specifically, the predicted voltage decay and estimated anode outlet gas composition are experimentally validated using stack-averaged voltage and a mass spectrometer. This work shows that the crossover of nitrogen and its accumulation in the anode can cause a considerable stack voltage decay and should be considered under high hydrogen utilization conditions.
Immunostimulatory Polymers as Adjuvants, Immunotherapies, and Delivery Systems (2022)

Activating innate immunity in a controlled manner is necessary for the development of next-generation therapeutics. Adjuvants, or molecules that modulate the immune response, are critical components of vaccines and immunotherapies. While small molecules and biologics dominate the adjuvant market, emerging evidence supports the use of immunostimulatory polymers in therapeutics. Such polymers can stabilize and deliver cargo while stimulating the immune system by functioning as pattern recognition receptor (PRR) agonists. At the same time, in designing polymers that engage the immune system, it is important to consider any unintended initiation of an immune response that results in adverse immune-related events. Here, we highlight biologically derived and synthetic polymer scaffolds, as well as polymer-adjuvant systems and stimuli-responsive polymers loaded with adjuvants, that can invoke an immune response. We present synthetic considerations for the design of such immunostimulatory polymers, outline methods to target their delivery, and discuss their application in therapeutics. Finally, we conclude with our opinions on the design of next-generation immunostimulatory polymers, new applications of immunostimulatory polymers, and the development of improved preclinical immunocompatibility tests for new polymers.
Ensembles of GANs for synthetic training data generation (2021)

Insufficient training data is a major bottleneck for most deep learning practices, not least in medical imaging where data is difficult to collect and publicly available datasets are scarce due to ethics and privacy. This work investigates the use of synthetic images, created by generative adversarial networks (GANs), as the only source of training data. We demonstrate that for this application, it is of great importance to make use of multiple GANs to improve the diversity of the generated data, i.e. to sufficiently cover the data distribution. While a single GAN can generate seemingly diverse image content, training on this data in most cases lead to severe over-fitting. We test the impact of ensembled GANs on synthetic 2D data as well as common image datasets (SVHN and CIFAR-10), and using both DCGANs and progressively growing GANs. As a specific use case, we focus on synthesizing digital pathology patches to provide anonymized training data.
Influence of Motor Operating Parameters on Discharge Bearing Current Activity (2011)

While the cause-and-effect chains of inverter-induced bearing currents have been well understood today, not much is known about the damage mechanism inside the bearings. Research has suggested that the bearing degradation is approximately proportional to the frequency of occurrence of the bearing currents. For bearing currents that occur statistically distributed-such as discharge bearing currents-this parameter has not been thoroughly researched yet. In this paper, we present an analysis of the influence of different motor operating parameters on the frequency of occurrence (“discharge activity”) of discharge bearing currents, using a non-intrusive detection method. When analyzed individually, the motor speed, motor shaft temperature, inverter switching frequency, and inverter dc-link voltage influence the discharge activity. However, the overall running time of the motor, the state-steady-state versus instantaneous-and the “operating history” on the time-scale of several days have the strongest effect on the frequency of the discharge bearing current occurrence.
Manga109Dialog: A Large-scale Dialogue Dataset for Comics Speaker Detection (2023)

The expanding market for e-comics has spurred interest in the development of automated methods to analyze comics. For further understanding of comics, an automated approach is needed to link text in comics to characters speaking the words. Comics speaker detection research has practical applications, such as automatic character assignment for audiobooks, automatic translation according to characters' personalities, and inference of character relationships and stories. To deal with the problem of insufficient speaker-to-text annotations, we created a new annotation dataset Manga109Dialog based on Manga109. Manga109Dialog is the world's largest comics speaker annotation dataset, containing 132,692 speaker-to-text pairs. We further divided our dataset into different levels by prediction difficulties to evaluate speaker detection methods more appropriately. Unlike existing methods mainly based on distances, we propose a deep learning-based method using scene graph generation models. Due to the unique features of comics, we enhance the performance of our proposed model by considering the frame reading order. We conducted experiments using Manga109Dialog and other datasets. Experimental results demonstrate that our scene-graph-based approach outperforms existing methods, achieving a prediction accuracy of over 75%.
Radar detection for non-stationary Doppler signal in one burst based on information geometry: Distance between paths on covariance matrices manifold (2015)

Classical Radar processing for non-stationary signal, corresponding to fast time variation of Doppler Spectrum in one burst, is no longer optimal. This phenomenon could be observed for high speed or abrupt Doppler variations of clutter or target signal but also in case of target migration during the burst duration due to high range resolution. We propose new Radar Doppler processing assuming that each non-stationary signal in one burst can be split into several short signals with less Doppler resolution but locally stationary, represented by time series of Toeplitz covariance matrices. In Information Geometry (IG) framework, these time series could be defined as a geodesic path (or geodesic polygon in discrete case) on covariance Toeplitz Hermitian Positive Definite matrix manifold. For this micro-Doppler analysis, we generalize the Fréchet distance between two curves in the plane to geodesic paths in abstract IG metric spaces of covariance matrix manifold. This approach is used for robust detection of target in case of non-stationary Time-Doppler spectrum (NS-OS-HDR-CFAR).