gebhart/patrepeval huggingface dataset:
Noncovalent Porphyrin–Graphene Oxide Nanohybrids: The pH-Dependent Behavior (2019)

Noncovalent nanohybrids between meso-(p-hydroxyphenyl)porphyrin (TPPH) and graphene oxide (GO) sheets were studied as a function of pH. The overall charge of the TPPH molecule changes between negative (−4), neutral, and positive (+2) depending on the pH of the solution. Results of Fourier transform infrared spectroscopy, thermogravimetric analysis, and elemental analysis confirm successful noncovalent functionalization of GO sheets with TPPH. We applied a number of methods to probe the ground-state as well as the excited-state interaction between the components of the new material. The experimental results were additionally supported by theoretical calculations that included optimizations of the ground-state structures of TPPH and TPPH2+ and their complexes with a molecular model of GO. It was demonstrated that both TPPH and TPPH2+ molecules can be assembled onto the surface of GO, but it was clearly shown that the stronger interaction with GO occurs for TPPH2+. The stronger interaction in the acidic environment can be rationalized by the electrostatic attraction between positively charged TPPH2+ and negatively charged GO, whereas the interaction between TPPH4– and GO at basic pH was largely suppressed. Our comprehensive analysis of the emission quenching led to the conclusion that it was solely attributed to static quenching of the porphyrin by GO. Surprisingly, fluorescence was not detected for the nanohybrid, which indicates that a very fast deactivation process must take place. Ultrafast time-resolved transient absorption spectroscopy demonstrated that although the singlet excited-state lifetime of TPPH2+ adsorbed on the GO sheets was decreased in the presence of GO from 1.4 ns to 12 ps, no electron-transfer products were detected. It is highly plausible that electron transfer takes place and is followed by fast back electron transfer.
Granulocyte Macrophage Colony–Stimulating Factor Expression in Human Herpetic Stromal Keratitis: Implications for the Role of Neutrophils in HSK (2006)

The data suggest that GM-CSF, expressed by cornea-resident cells such as HCFs and HCE cells, may play a role in the immunopathogenesis of HSK by prolonging the survival and modulating the effector function of corneal infiltrating neutrophils.
Watchful waiting is an Acceptable Treatment Option for Primary Ocular Adnexal Mucosa-associated Lymphoid Tissue Lymphoma: A Retrospective Study (2021)

Abstract Background: Primary ocular adnexal mucosa-associated lymphoid tissue (MALT) lymphoma (POAML) is the most common subtype of ocular adnexal lymphomas, and most patients with POAML show an indolent clinical course and achieve long-term survival. Although radiotherapy (RT) is the standard of care for localized POAML, it can occasionally lead to permanent side effects. Other treatment strategies, such as rituximab (R) monotherapy and immunochemotherapy, have been used for POAML treatment, but their long-term benefits and relative merits remain unclear. Considering that watchful waiting (WW) is a potential option for some indolent lymphomas, WW is expected to be a therapeutic option for POAML. However, the benefits of WW for POAML patients are also unclear. The aim of this study is to determine the optimal treatment strategy for POAML. Methods: We retrospectively analyzed 75 patients who were diagnosed POAML between 2008 and 2019 in the institutions of the Kyoto Clinical Hematology Study Group. Results: The median age was 68 years, and 41 patients were women. Common involved sites were conjunctiva (42.7%), orbit (36.0%), and lacrimal gland (12.0%), and most patients (92.0%) presented with Ann Arbor stage IE disease. The treatment strategy was selected at the physicians’ discretion, and more patients without subjective symptoms by tumor mass were subjected to WW (29 patients, 38.7%), while more patients with tumor-derived subjective symptoms were treated by tumor-directed therapy (24 [32.0%] received focal RT, and 19 [25.3%] received R monotherapy). Complete response rates were 79.2% and 42.1% in the RT and R groups, respectively. At 60 months’ follow-up, the estimated proportions of POAML patients not requiring new treatment were 69.4%, 85.2%, and 53.8% in the WW, RT, and R groups, respectively. There were no significant differences in the time to start of new treatment between WW and RT groups (median: both not reached [NR], p = 0.187) and between WW and R groups (median: NR vs. 69.0 months, p = 0.554). No specific predictive factor for the future need of treatment was identified in the WW group. Conclusions: WW may be an acceptable treatment option for POAML, especially in asymptomatic patients.
YODA Kinase Controls a Novel Immune Pathway of Tomato Conferring Enhanced Disease Resistance to the Bacterium Pseudomonas syringae (2020)

Mitogen-activated protein kinases (MAPK) play pivotal roles in transducing developmental cues and environmental signals into cellular responses through pathways initiated by MAPK kinase kinases (MAP3K). AtYODA is a MAP3K of <i>Arabidopsis thaliana</i> that controls stomatal development and non-canonical immune responses. <i>Arabidopsis</i> plants overexpressing a constitutively active YODA protein (<i>AtCA-YDA</i>) show broad-spectrum disease resistance and constitutive expression of defensive genes. We tested YDA function in crops immunity by heterologously overexpressing <i>AtCA-YDA</i> in <i>Solanum lycopersicum</i>. We found that these tomato <i>AtCA-YDA</i> plants do not show developmental phenotypes and fitness alterations, except a reduction in stomatal index, as reported in <i>Arabidopsis AtCA-YDA</i> plants. Notably, <i>AtCA-YDA</i> tomato plants show enhanced resistance to the bacterial pathogen <i>Pseudomonas syringae</i> pv. <i>tomato</i> DC3000 and constitutive upregulation of defense-associated genes, corroborating the functionality of YDA in tomato immunity. This function was further supported by generating CRISPR/Cas9-edited tomato mutants impaired in the closest orthologs of <i>AtYDA</i> [<i>Solyc08g081210</i> (<i>SlYDA1</i>) and <i>Solyc03g025360</i> (<i>SlYDA2</i>)]. <i>Slyda1</i> and <i>Slyda2</i> mutants are highly susceptible to <i>P. syringae</i> pv. <i>tomato</i> DC3000 in comparison to wild-type plants but only <i>Slyda2</i> shows altered stomatal index. These results indicate that tomato orthologs have specialized functions and support that YDA also regulates immune responses in tomato and may be a trait for breeding disease resistance.
Particularites du métabolisme des lipides et du métabolisme énergetique chez le dromadaire (1989)

National audience
Broadband Velocity Model Building and Imaging Using Reflections, Refractions and Multiples from Dual-sensor Streamer Data (2014)

Summary We demonstrate a novel workflow using reflections, refractions and multiples for building highly accurate PSDM velocity models for a complex geological setting. By combining wavelet shift tomography, full waveform inversion and separated wavefield imaging, we are able to produce high-resolution velocity models that are ideally suited for imaging of broadband data. Leveraging dual sensor streamer technology and the wavefield separation that comes with it, we are using up- and down-going wavefields in imaging and tomography to improve resolution and illumination. Further, we utilize the refracted, low-frequency energy for FWI. As the streamer is towed deep, we preserve the low frequencies that are so important for the success of FWI, but without sacrificing a broadband signal that is key for producing high-resolution reflection images of the shallow overburden and deep reservoir sections.
Dopant profiling on semiconducting sample by scanning capacitance force microscopy (2002)

Scanning capacitance force microscopy (SCFM) capable of mapping differential capacitance (∂C/∂V) on semiconducting sample based on atomic force microscopy (AFM) without an external capacitance sensor is introduced. While an electric field alternating at an angular frequency ω is applied between the tip and the sample, an induced electrostatic force (ESF) oscillating at its third harmonic frequency (3ω) is detected by a lock-in amplifier. Owing to the fact that the magnitude of the induced ESF is proportional to the square of the magnitude of the applied electric field and the fact that the capacitance of the semiconducting sample is also modulated at ω, the amplitude and the phase of the induced ESF oscillating at 3ω contain information on ∂C/∂V. We present ∂C/∂V images on a Si test sample obtained by SCFM using both contact-mode AFM and dynamic-mode AFM, showing clear contrasts depending on species and density of dopants.
Activation of human cancer/testis antigen gene, XAGE‐1, in tumor cells is correlated with CpG island hypomethylation (2005)

Expression of the XAGE-1 antigen is restricted to germ cells of the testis and a variety of neoplastic tissues. To date, the molecular mechanism for regulating expression of this cancer/testis antigen gene has been unknown. To evaluate methylation as a potential mechanism for regulating expression of this gene, we first correlated gene methylation status (measured by sequencing of bisulfide-modified DNA and COBRA) to expression of XAGE-1 mRNA in normal and cancerous cells. This analysis revealed dense methylation of the CpG island in the XAGE-1 gene promoter for the normal and cancerous cells that do not express this gene but loss of this methylation in normal testis, cancer cell lines and the primary gastric cancers where the gene is highly expressed. Further supporting the role of methylation in regulating expression of XAGE-1 were observations that treatment of 2 heavily methylated cell lines, SNU620 and HT29, with 5'-aza-deoxycytidine resulted in demethylation of XAGE-1 promoter and corresponding expression of this gene. Finally, we cloned various segments of the CpG-rich XAGE-1 gene promoter linked to a luciferase reporter construct and transiently transfected this construct into HCT116 cells. These experiments confirmed transcriptional regulatory activity for the promoter region that incorporates the CpG island and demonstrated that in vitro methylation of this island results in loss of promoter activity. Collectively, these studies indicate that XAGE-1 expression in normal and cancerous tissues is regulated by methylation of the CpG island in the gene promoter.
Characterizing Dimensional Form Surface Texture and Feature Resolution in Additive Manufacturing. (2017)

Abstract not provided.
Concomitant Latent Pulmonary Vascular Disease Leads to Impaired Global Cardiac Performance in Heart Failure with Preserved Ejection Fraction (2023)

Latent PVD is a feature of HFpEF and is associated with impaired RV functional reserve, global diastolic filling and LV-CI. This can be quantified by CMR and used to identify patients likely to benefit from IASD implantation.
Synthèse et application au piégeage radicalaire de nitrones de type DEPMPO (2005)

Le premier objectif de ce travail etait d'etudier l'effet de la substitution en position 4 de nitrones de type DEPMPO sur la geometrie des adduits superoxyde, sur leur persistance et sur l'allure de leurs spectres RPE. Le deuxieme objectif etait de fournir des precurseurs pour la synthese de nitrones plus specifiques. Mon travail de doctorat a consiste en la synthese et l'etude RPE de deux series de nitrones fonctionnalisees par un groupement phenyl en position 4. Les deux diastereoisomeres : la 4 PhDEPMPOt et la 4 PhDEPMPOc furent prepares et utilises pour le piegeage de plusieurs especes radicalaires. L'adduit de spin forme par reaction de la 4 PhDEPMPOc avec le superoxyde a presente un signal compose de 8 raies montrant seulement un leger phenomene de largeur de raie alternee. Les temps de demi-vie de la 4PhDEPMPOc-OOH sont similaire ( ~15mm). La deuxieme serie de molecules, ce sont les nitrones derivees de la 4HMDEPMPO. Cette molecule fut obtenu en trois etapes et utilisee comme precurseur pour la preparation de nitrones vectorisees. L'adduit de spin forme par reaction de la 4HMDEPMPOc avec le superoxyde a presente un signal compose de 8 raies montrant seulement un phenomene de largeur de raie alternee residuel. Le temps de demi-vie de la 4HMDEPMPO-cOOH est plus grand (21mn) que celui de la DEPMPO-OOH. Un premier test de vectorisation par une molecule presentant une activite biologique a ete concluant puisque la 4BIODEPMPOc fut synthetisee et l'etude RPE a demontre que l'introduction du motif biotine est compatible avec le piegeage de radicaux libres et a presente un adduit du superoxyde dont le signal fut facilement attribuable
Association of Skin Wetness and pH With Diaper Dermatitis (1994)

The strength of the association between diaper dermatitis and measurements of skin wetness and skin pH was evaluated by statistical analysis of four diaper trials involving 1601 infants. Although the strength of the association between skin wetness and diaper dermatitis was greater than that between skin pH and diaper dermatitis, increases in wetness and pH were both significantly associated with elevated mean grades for diaper dermatitis. The skin environment least likely to be associated with diaper dermatitis is one in which increases in both skin wetness and skin pH are minimized.
Positive Reinforcement Mediated by Midbrain Dopamine Neurons Requires D1 and D2 Receptor Activation in the Nucleus Accumbens (2014)

The neural basis of positive reinforcement is often studied in the laboratory using intracranial self-stimulation (ICSS), a simple behavioral model in which subjects perform an action in order to obtain exogenous stimulation of a specific brain area. Recently we showed that activation of ventral tegmental area (VTA) dopamine neurons supports ICSS behavior, consistent with proposed roles of this neural population in reinforcement learning. However, VTA dopamine neurons make connections with diverse brain regions, and the specific efferent target(s) that mediate the ability of dopamine neuron activation to support ICSS have not been definitively demonstrated. Here, we examine in transgenic rats whether dopamine neuron-specific ICSS relies on the connection between the VTA and the nucleus accumbens (NAc), a brain region also implicated in positive reinforcement. We find that optogenetic activation of dopaminergic terminals innervating the NAc is sufficient to drive ICSS, and that ICSS driven by optical activation of dopamine neuron somata in the VTA is significantly attenuated by intra-NAc injections of D1 or D2 receptor antagonists. These data demonstrate that the NAc is a critical efferent target sustaining dopamine neuron-specific ICSS, identify receptor subtypes through which dopamine acts to promote this behavior, and ultimately help to refine our understanding of the neural circuitry mediating positive reinforcement.
Characterization of curved composite structure using laser infrared photothermal radiometry (2007)

The effects of curved-surface of both cylindrical and spherical samples with either a 2-layer structure (thin-film coating) or a continuous gradient structure (case hardened surface) are investigated. By appropriate signal processing, it is found theoretically that the curvature effect of both cylindrical and spherical samples can be eliminated under certain conditions and the PTR signal from the curved composite sample can be equivalent to a flat surface with same structure.
Application of Living Free Radical Polymerization for Nucleic Acid Delivery (2012)

Therapeutic gene delivery can alter protein function either through the replacement of nonfunctional genes to restore cellular health or through RNA interference (RNAi) to mask mutated and harmful genes. Researchers have investigated a range of nucleic acid-based therapeutics as potential treatments for hereditary, acquired, and infectious diseases. Candidate drugs include plasmids that induce gene expression and small, interfering RNAs (siRNAs) that silence target genes. Because of their self-assembly with nucleic acids into virus-sized nanoparticles and high transfection efficiency in vitro, cationic polymers have been extensively studied for nucleic acid delivery applications, but toxicity and particle stability have limited the clinical applications of these systems. The advent of living free radical polymerization has improved the quality, control, and reproducibility of these synthesized materials. This process yields well-defined, narrowly disperse materials with designed architectures and molecular weights. As a result, researchers can study the effects of polymer architecture and molecular weight on transfection efficiency and cytotoxicity, which will improve the design of next-generation vectors. In this Account, we review findings from structure-function studies that have elucidated key design motifs necessary for the development of effective nucleic acid vectors. Researchers have used robust methods such as atom transfer radical polymerization (ATRP), reverse addition-fragmentation chain transfer polymerization (RAFT), and ring-opening metastasis polymerization (ROMP) to engineer materials that enhance extracellular stability and cellular specificity and decrease toxicity. In addition, we discuss polymers that are biodegradable, form supramolecular structures, target specific cells, or facilitate endosomal release. Finally, we describe promising materials with a range of in vivo applications from pulmonary gene delivery to DNA vaccines.
Characterization of Auger Recombination and Its Contribution to the Efficiency Droop in III-Nitride Quantum Wells (2015)

Tailored (AlGaIn)N multi-quantum well structures are characterized using low temperature photoluminescence spectroscopy. The results show that Auger recombination plays a key role in the efficiency droop in (AlGaIn)N based LEDs at high carrier densities.
Retina implant adjustment with reinforcement learning (2002)

A tuning method with reinforcement learning (RL) for the retina encoder (RE) of a retina implant (RI) as a visual prosthesis for blind subjects with retinal degenerations is proposed. The RE simulates retinal information processing in real time by means of spatio-temporal receptive field (RF) filters and generates electrical signals for stimulation of several hundreds of ganglion cells (GC) to regain a modest amount of vision. For each contacted GC, the RE has to be optimized with regard to the patient's perception. The patient's (for the present simulated) evaluative feedback is applied here in a dialog module as a reinforcement signal to train several RL agents in a neural network learning process.
Structure Investigation of TiIV‐BODOLates Involved in the Catalytic Asymmetric Reduction of Ketones Using Catecholborane (2003)

The complexes formed by the reaction of [Ti(OiPr)(4)] and bicyclo-octanediols (BODOLs) 1 and 2 (1:1) are useful as chiral catalysts in asymmetric reductions and were investigated by (1)H NMR spectroscopy and computational methods. A consistent picture emerged of head-to-tail dimers being kept together via a Ti-O-Ti-O micro-oxo bridge similar to the Ti-tartrates but different from the corresponding Ti-BINOLates and Ti-TADDOLates.
Review Heterogeneity of human effector CD4 + T cells (2009)

For many years the heterogeneity of CD4 + T-helper (Th) cells has been limited to Th1 and Th2 cells, which have been considered not only to be responsible for different types of protective responses, but also for the pathogenesis of many disorders. Th1 cells are indeed protective against intracellular microbes and they are thought to play a pathogenic role in organ-specific autoimmune and other chronic inflammatory disorders. Th2 cells provide protection against helminths, but are also responsible for the pathogenesis of allergic diseases. The identification and cloning of new cytokines has allowed one to enlarge the series of functional subsets of CD4 + Th effector cells. In particular, CD4 + Th cells producing IL-17 and IL-22, named Th17, have been initially implicated in the pathogenesis of many chronic inflammatory disorders instead of Th1 cells. However, the more recent studies in both humans and mice suggest that Th17 cells exhibit a high plasticity toward Th1 cells and that both Th17 and Th1 cells may be pathogenic. More recently, another two subsets of effector CD4 + Th cells, named Th9 and Th22 cells, have been described, even if their pathophysiological meaning is still unclear. Despite the heterogeneity of CD4 + effector Th cells being higher than previously thought and some of their subsets exhibiting high plasticity, the Th1/Th2 paradigm still maintains a strong validity.
Tissue-Expressed B7-H1 Critically Controls Intestinal Inflammation (2014)

B7-H1 (PD-L1) on immune cells plays an important role in T cell coinhibition by binding its receptor PD-1. Here, we show that both human and mouse intestinal epithelium express B7-H1 and that B7-H1-deficient mice are highly susceptible to dextran sodium sulfate (DSS)- or trinitrobenzenesulfonic acid (TNBS)-induced gut injury. B7-H1 deficiency during intestinal inflammation leads to high mortality and morbidity, which are associated with severe pathological manifestations in the colon, including loss of epithelial integrity and overgrowth of commensal bacteria. Results from bone marrow chimeric and knockout mice show that B7-H1 expressed on intestinal parenchyma, but not on hematopoietic cells, controls intestinal inflammation in an adaptive immunity-independent fashion. Finally, we demonstrate that B7-H1 dampened intestinal inflammation by inhibiting tumor necrosis factor α (TNF-α) production and by stimulating interleukin 22 secretion from CD11c(+)CD11b(+) lamina propria cells. Thus, our data uncover a mechanism through which intestinal tissue-expressed B7-H1 functions as an essential ligand for innate immune cells to prevent gut inflammation.
Anaphylaxis (2019)

The dramatic and unexpected fatal response was the opposite of protection. Anaphylaxis is the syndrome elicited in a hypersensitive subject upon subsequent exposure to the sensitizing antigen. Immunoglobulin E-mediated anaphylaxis has been implicated in untoward reactions elicited by many foods as well as drugs, chemicals, insect stings, preservatives, and environmental factors. Sulfiting agents are added to foods as preservatives, to prevent discoloration. Strenuous exercise may lead to anaphylaxis in susceptible subjects. The response resembles anaphylaxis in every respect, including elevated urine and plasma histamine levels. The primary anaphylactic shock organs in humans are the cutaneous, gastrointestinal, respiratory, and cardiovascular systems. Involvement of the respiratory and cardiovascular systems is most significant as regards mortality. When mast cells degranulate, preformed and rapidly generated mediators are released into the connective tissue along with the molecules that constitute the granular matrix. The correct diagnosis is much more difficult to determine in a syncopal or sedated patient.