gebhart/patrepeval huggingface dataset:
All-Fiber System at 1750 nm Delivering 35 fs 230 kW Peak Power Pulses (2019)

Ultra-short (<; 70 fs) pulses in the short-wavelength infrared (>1.55 μm) are very attractive for many applications such as three-photon microscopy, frequency metrology, or high harmonic generation. Solitonic self-compression is an attractive effect for this purpose as compression to sub-50 fs pulses can be achieved without the need for external compressing optics, directly out of an optical fiber. Self-compression at high energy was demonstrated around 2 μm in all-solid or gas-filled hollow-core-PCFs. However, the latter demonstrations were restricted to Tm emission band in order to reach the soliton self-compression effect in low-nonlinearity media. In this communication, we present a compact monolithic all-fiber source of ultrashort (35 fs) pulses emitting outside conventional lasing bands, from 1.65 to 2 μm based on Raman-induced soliton self-frequency shift (SSFS) and soliton self-compression (SSC).
Hybrid Insulin Peptides Are Recognized by Human T Cells in the Context of DRB1*04:01 (2020)

T cells isolated from the pancreatic infiltrates of nonobese diabetic mice have been shown to recognize epitopes formed by the covalent cross-linking of proinsulin and secretory granule peptides. Formation of such hybrid insulin peptides (HIPs) was confirmed through mass spectrometry, and responses to HIPs were observed among the islet-infiltrating T cells of pancreatic organ donors and in the peripheral blood of individuals with type 1 diabetes (T1D). However, questions remain about the prevalence of HIP-specific T cells in humans, the sequences they recognize, and their role in disease. We identified six novel HIPs that are recognized in the context of DRB1*04:01, discovered by using a library of theoretical HIP sequences derived from insulin fragments covalently linked to one another or to fragments of secretory granule proteins or other islet-derived proteins. We demonstrate that T cells that recognize these HIPs are detectable in the peripheral blood of subjects with T1D and exhibit an effector memory phenotype. HIP-reactive T-cell clones produced Th1-associated cytokines and proliferated in response to human islet preparations. These results support the relevance of HIPs in human disease, further establishing a novel posttranslational modification that may contribute to the loss of peripheral tolerance in T1D.
GAL‐160 Preferentially Increases Respiratory Motor Drive to the Tongue over the Diaphragm during Unobstructed Breathing and Standardized Obstructive Apneas (OA) in Rats (2015)

GAL‐160, a carotid body (CB) stimulant, decreases spontaneous OA frequency and OA duration in a rodent model of OSA. Mechanistically, we propose that the effect of GAL‐160 on OA frequency is due to increased upper airway respiratory muscle (RM UA ) activity during eupnea, and the effect of GAL‐160 on OA duration is due to an increased response of RM UA to obstruction. We evaluated the effects of GAL‐160 on eupneic respiratory drive to the RM UA by recording hypoglossal (HN) and phrenic (PN) neurograms from urethane anesthetized, mechanically ventilated rats before and during IV infusion of vehicle and GAL‐160 (0.24 mg/kg over 30‐min). Baseline neurograms were standardized between rats by setting baseline P aCO 2 at 3 mmHg above each animal's apneic threshold to CO 2 . To evaluate the effects of GAL‐160 on the RM UA response to obstruction, the EMG GG and EMG DIA responses to standardized 10‐s tracheal obstructions were recorded from anesthetized, spontaneously breathing rats, before and during GAL‐160/vehicle infusions. GAL‐160 increased HN activity (67 ± 23% above baseline) without altering PN activity (‐13 ± 20%) during unobstructed breathing. Bilateral CB denervation abolished this effect. GAL‐160 increased the peak EMG GG response to a 10‐s obstruction (pre‐drug: 214 ± 180%; GAL‐160: 589 ± 358%; p &lt;0.01) without altering the EMG DIA response (pre‐drug: 60 ± 31%; GAL‐160: 78 ± 47%). Vehicle infusion had no effect on the neurograms or EMGs recorded. These data demonstrate that GAL‐160 preferentially increases respiratory drive to the RM UA via the CB and during both eupneic breathing and OA. This mechanism may contribute to the efficacy of GAL‐160 in our rodent model of spontaneous OSA.
The role of crop growth models in crop improvement: integrating phenomics, envirotyping and genomic prediction (2022)

The chapter highlights the interplay of high throughput phenotyping with crop growth models (CGMs). The chapter shows how crop models can be used to explore knowledge of phenotype, environment and genotype to better understand and predict their complex interrelationships. It describes how CGMs have been used in envirotyping and in setting targets for phenotyping programs. It also describes current limitations in modelling, how these are being addressed as well as emerging trends.
Petite bibliographie portative (2011)

Arnauld et Lancelot, Grammaire générale et raisonnée, dite grammaire de Port-Royal, (1660), rééditée par Allia, 2010. Benveniste, Emile, Problèmes de linguistique générale, 1 et 2, Gallimard, coll. « TEL », 1967, 1974. BOLLACK, Jean, Sens contre sens. Comment lit-on ?, Entretiens avec patrick Llored, La Passe du vent, 2000. CASTANET, Hervé, avec Alain MERLET, Pourquoi écrire : Artaud, Genet, Jouhandeau, Klossowski, La différence, 2010. CESAIRE aimé, Cahier d’un retour au pays natal, 1939, in ...
H/D isotopic exchange in the fast atom bombardment of ecdysteroids (1997)

Deuterium exchange in a glycerol-O-d3 matrix affords the number of hydroxyl groups present in molecules of various types of ecdysteroids in both positive and negative ionization modes. H/D exchange also allows the easy distinguishing of isomeric and isobaric compounds. It is shown that the ecdysteroids under study exchange an additional hydrogen owing to the presence of an enol form of a C6 keto group. The high extent of enolization occurring at the C22 keto functionality was observed in the pseudomolecular ion of 22-oxo-20-hydroxyecdysone. © 1997 John Wiley & Sons, Ltd.
A Blender plug-in for comparing Structure from Motion pipelines (2018)

Structure from Motion (SfM) is a pipeline that allows three-dimensional reconstruction starting from a collection of images. A typical SfM pipeline comprises different processing steps each of which tackle a different problem in the reconstruction pipeline. Each step can exploit different algorithms to solve the problem at hand and thus many different SfM pipelines can be built. There are many SfM pipelines available in the literature. How to choose the best among them? We present a Blender plug-in that provides an easy to use tool to compare them under different conditions using both real and synthetic datasets.
Modeling contention of giga-updates per second (GUPs) in three parallel programming paradigms (2007)

In this paper we make use of the LoPC model, which is inspired by both the LogP/PG and BSP models but accounts for contention for message processing resources in parallel programming models to derive a general estimate of execution cost. We carry out this cost estimate analysis for three dominate programming models: message passing, shared memory and distributed shared memory. We analyze a typical application; GUPs written in these programming models that have irregular receiver-initiated synchronous communication. The LoPC estimate for this application is shown to be accurate when compared against measured values of runtime of actual empirical computations on an SGI O2000 multiprocessor machine.
Mesoscopic study of dynamics and gelation ability of oligomeric electrolyte gelator with dissipative particle dynamics (2011)

The poly[pyridinium-1,4-diyl-iminocarbonyl-1,4-phenylene-methylene chloride] (1-Cl) is a novel oligomeric electrolyte gelator with notable characteristics and multi-functionalities. In this study, we investigate its structural and dynamical properties by means of the dissipative particle dynamics (DPD). The structural properties of 1-Cl in aqueous solution have been analyzed with the help of the radial distribution functions for the coarse grained model of the polymer and the solvent. Diffusion coefficient and the radius of gyration for the coarse grained polymer in solution have been calculated at various concentrations. We find that both structural and dynamical quantities change significantly when the polymer concentration becomes sufficient to form the gel.
CD40 Receptor Knockout Protects against Microcystin-LR (MC-LR) Prolongation and Exacerbation of Dextran Sulfate Sodium (DSS)-Induced Colitis (2020)

Inflammatory Bowel Disease (IBD) is one of the most common gastrointestinal (GI) disorders around the world, and includes diagnoses such as Crohn's disease and ulcerative colitis. The etiology of IBD is influenced by genetic and environmental factors. One environmental perturbagen that is not well studied within the intestines is microcystin-leucine arginine (MC-LR), which is a toxin produced by cyanobacteria in freshwater environments around the world. We recently reported that MC-LR has limited effects within the intestines of healthy mice, yet interestingly has significant toxicity within the intestines of mice with pre-existing colitis induced by dextran sulfate sodium (DSS). MC-LR was found to prolong DSS-induced weight loss, prolong DSS-induced bloody stools, exacerbate DSS-induced colonic shortening, exacerbate DSS-induced colonic ulceration, and exacerbate DSS-induced inflammatory cytokine upregulation. In addition, we previously reported a significant increase in expression of the pro-inflammatory receptor CD40 in the colons of these mice, along with downstream products of CD40 activation, including plasminogen activator inhibitor-1 (PAI-1) and monocyte chemoattractant protein-1 (MCP-1). In the current study, we demonstrate that knocking out CD40 attenuates the effects of MC-LR in mice with pre-existing colitis by decreasing the severity of weight loss, allowing a full recovery in bloody stools, preventing the exacerbation of colonic shortening, preventing the exacerbation of colonic ulceration, and preventing the upregulation of the pro-inflammatory and pro-fibrotic cytokines IL-1β, MCP-1, and PAI-1. We also demonstrate the promising efficacy of a CD40 receptor blocking peptide to ameliorate the effects of MC-LR exposure in a proof-of-concept study. Our findings suggest for the first time that MC-LR acts through a CD40-dependent mechanism to exacerbate colitis.
Analysis of recorded image noise in nuclear medicine (1981)

The concepts of autocovariance function and Wiener spectrum have been applied to describe the recorded image noise in nuclear medicine. They were derived as functions of the expected detected count density and the detector and exposure point spread functions. It was shown that the detector system affects only the noise magnitude, whereas the recorder system affects both noise magnitude and texture. In experimental studies, the autocovariance function and Wiener spectrum of recorded image noise were measured by one-dimensional time-series analysis. Due to the non-linearity of the recording film, the best agreement between the theoretical predictions and the experimental results is found when the detected count density is sufficiently high and the size of the exposure spot is sufficiently large for the density fluctuations in the recorded noise image to be relatively low.
Microbial Coculture and OSMAC Approach as Strategies to Induce Cryptic Fungal Biogenetic Gene Clusters (2017)

This chapter provides an overview of successful examples that highlight the power of the one strain many compounds (OSMAC) approach or of microbial cocultivation for an elicitation of bioactive fungal natural products that resulted either in an enhanced accumulation of constitutively present compounds, and/or in an accumulation of new natural compounds missing in axenic control cultures. The OSMAC concept is applied to explore changes of microbial metabolite profiles influenced by changing fermentation conditions, such as different media, different temperature regimes, different culture vessels, and other factors. Another approach that has proven highly successful in triggering the activation of silent biosynthetic gene clusters is the cocultivation of two or more different microbes together in one culture vessel rather than maintaining pure cultures. This strategy mimics the natural microbial ecosystem, defined as microbiome, where the microorganisms interact with each other in synergistic and/or antagonistic relationships, which are the driving ecological forces for triggering secondary metabolite biosynthesis.
The Role of Immunotherapy in a Tolerogenic Environment: Current and Future Perspectives for Hepatocellular Carcinoma (2021)

In contrast to several tumors whose prognoses are radically affected by novel immunotherapeutic approaches and/or targeted therapies, the outcomes of advanced hepatocellular carcinoma (HCC) remain poor. The underlying cirrhosis that is frequently associated with it complicates medical treatment and often determines survival. The landscape of HCC treatment had included sorafenib as the only drug available for ten years, until 2018, when lenvatinib was approved for treatment. The second-line systemic treatments available for hepatocellular carcinoma include regorafenib, cabozantinib, ramucirumab, and, more recently, immune checkpoint inhibitors. However, the median survival remains below 15 months. The results obtained in clinics should be interpreted whilst considering the peculiar role of the liver as an immune organ. A healthy liver microenvironment ordinarily experiences stimulation by gut-derived antigens. This setup elucidates the response to chronic inflammation and the altered balance between tolerance and immune response in HCC development. This paper provides an overview of the mechanisms involved in HCC pathogenesis, with a special focus on the immune implications, along with current and future clinical perspectives.
Laboratory Toxicity of Three Mosquito Oviposition Repellents to Six Nontarget Aquatic Invertebrates (2000)

Abstract Toxicity of three mosquito oviposition repellents, N,N-diethyl-3-methylbenzamide (AI3-22542 or deet), AI3-35765, and AI3-37220 to 6 aquatic nontarget invertebrates, was evaluated in the laboratory. The 24-h LC50 values for Cypricercus sp. (Ostracoda), Moina sp. (Cladocera), Eucyclops agilis Koch (Copepoda), Strelkovimermis spiculatus Poinar &amp; Camino (Nematoda), first- and fourth-instar Toxorhynchites amboinensis Doleschall larvae (Diptera), and fourth-instar Chironomus decorus Johannsen larvae (Diptera) ranged from 0.012 to 0.127% or 120 to 1,270 ppm. Cypricercus sp., Moina sp., E. agilis, first-instar Tx. amboinensis and fourth-instar C. decorus were generally more sensitive to the test repellents than male and female S. spiculatus and fourth-instar Tx. amboinensis. Male S. spiculatus was more sensitive to the repellents than its female and this was probably because of the smaller body size of the male. All invertebrates were generally more sensitive to AI3-37220 than to deet and AI3-35765. The experimental repellents were considered safe to the aquatic nontarget organisms when employed as oviposition repellents for Aedes albopicus (Skuse) mosquitoes.
Aortic hyporeactivity to norepinephrine induced by lipopolysaccharide in cirrhotic rats: Beneficial effects of a non‐steroidal anti‐inflammatory drug coupled with a nitric oxide donor (2001)

These findings suggest that NO-flurbiprofen has a beneficial hemodynamic effect in cirrhotic rats and may help to prevent LPS aortic hyporeactivity.
Influence of Template Geometry on Polymer Micro-Structure Duplication in Electrohydrodynamics Patterning Process (2012)

Electrohydrodynamics patterning is a process for electrically duplicating micro–nano patterns on polymer films by applying an electrical field. An investigation into the hydraulic behavior of the polymer as affected by the template-modulated electrical field is critical for understanding the process capability and template design. A coupling model is presented to characterize the influence of template geometry on the pattern duplication. The transient simulation is carried out to study the formation of a pattern. It is proposed that the electrical field modulated by the template can be divided into a spatially nonhomogeneous component which generates the periodic pillars undesirably and a spatially nonhomogeneous component which generates a duplication of the template pattern as desired. We find that the template geometry has a significant effect on the template-modulated electrohydrodynamics. A high-fidelity duplication of pattern is better suited to a low projection ratio, a decreased template spacer height, and an increased pattern aspect ratio.
Kinetic properties of crystalline enzymes. Carboxypeptidase A (1977)

Spectrochemical probes have demonstrated that the conformations of carboxypeptidase A differ in solution and in the crystalline state. Detailed kinetic studies of carboxypeptidase A crystals and solutions now show that the physical state of the enzyme is also a critical parameter that affects this enzyme's function. Thus, for all substrates examined, crystallization of the enzyme markedly reduces catalytic efficiency, kcat, from 20- to 1000-fold. In addition, substrate inhibition, apparent in solution for some di- and depsipeptides, is abolished with crystals, while longer substrates with normal kinetics in solution may exhibit activation with the crystals. The physical state of the enzyme also affects the mode of action of known modifiers of peptidase activity of the enzyme. In solution, addition of benzoylglycine or cinnamic acid markedly increases the rate of hydrolysis of CbzGly-Phe, but, with the crystalline enzyme, their addition hardly alters the activity. This is in accord with the weakening or absence of inhibitory enzyme-substrate binding modes. Kinetic studies on crystals were carried out over a range of enzyme concentrations, substrate concentrations, and crystal sizes, and in all instances the results are in good agreement with the theory developed by Katchalski for enzymes insolubilized by other means. Importantly, these kinetic parameters are determined under conditions which obviate artifacts due to diffusion limitation of substrates or products. The differences in the kinetic behavior of carboxypeptidase crystals, on the one hand, and of their solutions, on the other hand, bear importantly on efforts to interpret the function of the enzyme in structural terms. Hypothetical modes of substrate-enzyme interaction, generated by superimposing substrate models on the crystal structure of carboxypeptidase to stimulate kinetics in solution, have failed to detect all of these changes which affect inhibitory or activating binding modes.
Development of the Wheat Practical Haplotype Graph Database as a Resource for Genotyping Data Storage and Genotype Imputation (2021)

Abstract To improve the efficiency of high-density genotype data storage and imputation in bread wheat ( Triticum aestivum L.), we applied the Practical Haplotype Graph (PHG) tool. The wheat PHG database was built using whole-exome capture sequencing data from a diverse set of 65 wheat accessions. Population haplotypes were inferred for the reference genome intervals defined by the boundaries of the high-quality gene models. Missing genotypes in the inference panels, composed of wheat cultivars or recombinant inbred lines genotyped by exome capture, genotyping-by-sequencing (GBS), or whole-genome skim-seq sequencing approaches, were imputed using the wheat PHG database. Though imputation accuracy varied depending on the method of sequencing and coverage depth, we found 93% imputation accuracy with 0.01x sequence coverage, which was only slightly lower than the accuracy obtained using the 0.5x sequence coverage (96.9%). Compared to Beagle, on average, PHG imputation was ~4% ( p-value = 0.00027) more accurate, and showed 27% higher accuracy at imputing a rare haplotype introgressed from a wild relative into wheat. The reduced accuracy of imputation with GBS data (90.4%) is likely associated with the small overlap between GBS markers and the exome capture dataset, which was used for constructing PHG. The highest imputation accuracy was obtained with exome capture for the wheat D genome, which also showed the highest levels of linkage disequlibrium and proportion of identity-by-descent regions among accessions in our reference panel. We demonstrate that genetic mapping based on genotypes imputed using PHG identifies SNPs with a broader range of effect sizes that together explain a higher proportion of genetic variance for heading date and meiotic crossover rate compared to previous studies.
Public Road Signs as Intermediate Interaction (2008)

This article reports a study of the abundant practice among people who live along roads to communicate with passing drivers by making and mounting public road signs. These signs can be seen as a complement, parallel, or second to official signs posted by road authorities. The article focuses specifically on how public road signs support different forms of communities, the practical work of enhancing readability for passing drivers, and the adoption to road inspectors' work of removing public road signs. The authors argue that public road signs are important, enabling intermediate interaction between communities. Furthermore, people posting signs adopt different tactics so that their messages are detected by passing drivers, while not being deleted by road authorities. However, road inspectors' work of removing signs is also vital for the success of public road signs, seeing their maintenance work as editing the road.
Contribution of Ferroptosis to Aging and Frailty (2020)

Ferroptosis is a recently characterized cell death phenotype resulting from iron-catalyzed peroxidation of polyunsaturated fatty acid phospholipids. Increased dysfunctional iron metabolism is thought to lead to increased levels of iron and ferroptosis, which in turn leads to cell and organismal death at least in the nematode <i>Caenorhabditis elegans</i>. Drugs that block lipid peroxidation or scavenge intracellular iron extend healthspan and lifespan in <i>C. elegans</i> independently of other mechanisms such as the <i>daf-1/daf-16</i> (insulin/insulin-like growth factor 1 [IGF-1]) pathway, but unlike many aging mechanisms do not alter temporal scaling across the life cycle of <i>C. elegans</i>, but rather act at specific late points in the organism's life history, temporarily blocking execution of critical dysfunction that results in listless worms. As such, inhibition of ferroptosis may be a means to extend healthspan and treat frailty and possibly neurodegenerative diseases that have a reported role for iron dyshomeostasis. However, a significant effort to understand ferroptosis in the context of mammalian and human biology is necessary. For example, some tumors block ferroptosis to survive. The constraints of balancing iron metabolism are significant and will require careful consideration in any drug development program.