gebhart/patrepeval huggingface dataset:
Excitation-Scanning Hyperspectral Imaging Microscopy to Efficiently Discriminate Fluorescence Signals (2019)

Several techniques rely on detection of fluorescence signals to identify or study phenomena or to elucidate functions. Separation of these fluorescence signals were proven cumbersome until the advent of hyperspectral imaging, in which fluorescence sources can be separated from each other as well as from background signals and autofluorescence (given knowledge of their spectral signatures). However, traditional, emission-scanning hyperspectral imaging suffers from slow acquisition times and low signal-to-noise ratios due to the necessary filtering of both excitation and emission light. It has been previously shown that excitation-scanning hyperspectral imaging reduces the necessary acquisition time while simultaneously increasing the signal-to-noise ratio of acquired data. Using commercially available equipment, this protocol describes how to assemble, calibrate, and use an excitation-scanning hyperspectral imaging microscopy system for separation of signals from several fluorescence sources in a single sample. While highly applicable to microscopic imaging of cells and tissues, this technique may also be useful for any type of experiment utilizing fluorescence in which it is possible to vary excitation wavelengths, including but not limited to: chemical imaging, environmental applications, eye care, food science, forensic science, medical science, and mineralogy.
Ion velocity distribution functions across a plasma meniscus (2023)

Here, we present laser-induced fluorescence measurements of an ion beam extraction angle and speed through a plasma-vacuum boundary as a function of plasma source parameters and bias potential applied to a wafer simulacrum outside the plasma. Ion temperature, velocity, and relative density are calculated from the measured ion velocity distribution function and are compared to a particle-in-cell model of the system. The measurements demonstrate that beam steering is feasible by varying plasma source density and extraction bias voltage. The focal point of the extracted beam, resulting from the plasma meniscus at the plasma-vacuum interface, depends on source density and extraction bias in a manner consistent with computational predictions.
High performance triangular barrier engineered NIPIN selector for bipolar RRAM (2014)

Triangular barrier has been proposed and implemented for the first time in a punch-through diode based selector by dopant profile engineering. Vertical 4F2 diodes have been fabricated on an epitaxial Si stack consists of n+ / i / delta-doped p+ / i / n+ (NIPIN) layers by low temperature (sub-520°C) Si epitaxy. We experimentally demonstrate that while conventional NPN selectors exhibit severe sub-threshold slope degradation at high voltage, NIPIN selectors produce ideal subthreshold slope of ~120mV/decade with negligible degradation. Scaled devices show on-current density of 1-2MA/cm2 below 2V. High on-off current ratio of > 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sup> is estimated from experiments. The NIPIN shows significant improvements over NPN i.e. sub-2V operation (50% improvement) and non-linearity > 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sup> (i.e. 2 orders improvement). Perimeter scaling of current due to fringing fields is demonstrated experimentally which improves current density in area scaled devices. Further, the excellent device performance indicates the high quality Si epitaxy grown at sub-520°C that enables low trap density and high in situ dopant activation.
SIEM approach for a higher level of IT security in enterprise networks (2015)

The threat of cyber-attacks grows up, as one can see by several negative security-news from companies and private persons. [7] Especially small-and-medium-sized enterprises (SME) are in focus of external attackers because they have not implemented sufficient security strategies and components for their networks yet. Additionally, tablets, smartphones, and netbooks changed the requirements of IT security rapidly. Today, there are several security components (e.g. anti-virus-system, firewall, and intrusion detection system) available to protect enterprise networks; unfortunately, they work independently from each other - isolated. But many attacks can only be recognized if logs and events of different security components are combined and correlated with each other. This possibility is offered by a security information and event management (SIEM) system. But nowadays these systems are very complex and expensive in deployment and maintenance ([12]). The SIMU project, funded by the BMBF [6] and presented in this paper, offers several features of a SIEM system with better handling and more efficient use in the SME environment.
Ultrafast Electron Diffraction of Transient [Fe(CO)4]: Determination of Molecular Structure and Reaction Pathway (2001)

The temporal diffraction-difference approach of the ultrafast electron diffraction (UED) technique was used to determine the molecular structure of the transient [Fe(CO)<sub>4</sub> ] formed during the elimination of CO ligands from [Fe(CO)<sub>5</sub> ]. The results clearly show that the major product, up to 200 ps, is the transient [Fe(CO)<sub>4</sub> ] which is formed in the <sup>1</sup> A<sub>1</sub> state, rather than the ground <sup>3</sup> B<sub>2</sub> state.
Nonlinear Surface Waves at the Interface of Discrete and Continuous Media (2006)

We provide an overview of recent theoretical and experimental results in the area of surface lattice solitons. The observation of these waves in Kerr and quadratic nonlinear periodic structures is discussed
A Differential Evolution Markov Chain Monte Carlo Algorithm for Bayesian Model Updating (2018)

The use of the Bayesian tools in system identification and model updating paradigms has been increased in the last 10 years. Usually, the Bayesian techniques can be implemented to incorporate the uncertainties associated with measurements as well as the prediction made by the finite element model (FEM) into the FEM updating procedure. In this case, the posterior distribution function describes the uncertainty in the FE model prediction and the experimental data. Due to the complexity of the modeled systems, the analytical solution for the posterior distribution function may not exist. This leads to the use of numerical methods, such as Markov Chain Monte Carlo techniques, to obtain approximate solutions for the posterior distribution function. In this paper, a Differential Evolution Markov Chain Monte Carlo (DE-MC) method is used to approximate the posterior function and update FEMs. The main idea of the DE-MC approach is to combine the Differential Evolution, which is an effective global optimization algorithm over real parameter space, with Markov Chain Monte Carlo (MCMC) techniques to generate samples from the posterior distribution function. In this paper, the DE-MC method is discussed in detail while the performance and the accuracy of this algorithm are investigated by updating two structural examples.
Effect of Bifidobacterium-Monoassociation and Feeding of Fructooligosaccharides on Lethal Activity of Enterohemorrhagic Escherichia coli O157 in Germ-Free Mice (1999)

A gnotobiotic mouse study was investigated to establish a suitable experimental model for evaluating an individual bacterial role for Escherichia coli O157: H7 infection. Germ-free (GF) BALB/c mice (nu/+) were found to die after 12-14 days of E. coli O157: H7 (strain CR 7087) infection, causing rough surface, atrophy, and faded color of the kidney, while specific pathogen-free (SPF) mice survived without any damage after similar infection. Using this model, the effect of Bifidobacterium-monoassociation (BA) and feeding of fructooligosaccharides (FOS) on the lethal activity of enterohemorrhagic E. coli O157: H7 was examined to elucidate if mice inoculated with B. adolescentis strain MBL8321 showed a significantly longer survival time than original GF mice after E. coli O157: H7 (strain CR 7087) infection. An analysis of the biomarkers in the present study provided the following information: 1) B. adolescentis was successfully associated at the 109-1010 colony-forming unit (cfu) level throughout the test period, 2) the numbers of viable E. coli in feces decreased in the order of GF, BA (= BA-FOS) and SPF groups, and the amount of fecal Shiga toxin (Stx), serum creatinine and urea nitrogen also decreased in similar order, 3) the amount of cecal short-chain fatty acids (SCFAs) was found to correlate with the survival time, and 4) the feeding of FOS under this condition afforded no additional increase in either survival time or amount of cecal SCFAs. These results indicate that the study using gnotobiotic mice is suitable for an experimental model of E. coli O157: H7 infection, and suggest tha the intestinal microflora plays an important role for preventing E. coli O157 infection in mice. However, the model is not suitable for evaluating the inhibitory effect related to intestinal fermentation because the parameters for fermentation did not change.
Kullback-Leibler boosting (2003)

In this paper, we develop a general classification framework called Kullback-Leibler Boosting, or KLBoosting. KLBoosting has following properties. First, classification is based on the sum of histogram divergences along corresponding global and discriminating linear features. Second, these linear features, called KL features, are iteratively learnt by maximizing the projected Kullback-Leibler divergence in a boosting manner. Third, the coefficients to combine the histogram divergences are learnt by minimizing the recognition error once a new feature is added to the classifier. This contrasts conventional AdaBoost where the coefficients are empirically set. Because of these properties, KLBoosting classifier generalizes very well. Moreover, to apply KLBoosting to high-dimensional image space, we propose a data-driven Kullback-Leibler Analysis (KLA) approach to find KL features for image objects (e.g., face patches). Promising experimental results on face detection demonstrate the effectiveness of KLBoosting.
Expression and modulation of cellular receptors for interferon‐γ, tumour necrosis factor, and Fas on human bone marrow CD34+ cells (1997)

Interferon-gamma (IFN-gamma), tumour necrosis factor-alpha (TNF-alpha) and Fas-ligand can mediate potent inhibitory signals in haemopoietic cells. Clinical and laboratory studies have suggested the involvement of these cytokines in the regulation of normal haemopoiesis and in the pathophysiology of bone marrow (BM) failure syndromes. As the effects of cytokines may also be regulated at the cellular receptor level, we studied the expression and modulation of TNF receptor (TNFR), IFN-gammaR and Fas-R on haemopoietic progenitor cells. In freshly isolated BM, using flow cytometry, TNFR1 (p55), TNFR2 (p75), IFN-gammaR, and Fas-R were detected on 5-12% of mononuclear cells. Two-colour staining showed comparable receptor expression on a CD34+ population, which includes haemopoietic progenitor and stem cells. Using reverse transcriptase-PCR (RT-PCR) transcription of mRNA coding for these receptors was demonstrated in fresh, highly purified CD34+ cells. These findings indicate that the effects of these factors on progenitor cells may be directly mediated. In cultured BM cells, expression of TNFR1 was not influenced by IFN-gamma, TNF-alpha or apoptosis-inducing anti-Fas monoclonal antibody (mAb). IFN-gamma decreased CD34+ cell TNFR2 expression. CD34+ cell Fas-R expression was increased by IFN-gamma and TNF-alpha. IFN-gammaR expression was enhanced by anti-Fas mAb and to lesser degree with TNF-alpha. Similar results were obtained with RT-PCR analysis in cultured CD34+ cells. Potentiation of anti-Fas mAb-mediated inhibition of haemopoietic colony formation by IFN-gamma and TNF-alpha was observed. Similarly, anti-Fas mAb enhanced the inhibitory effects of IFN-gamma. These results suggest that, in addition to interacting at the level of intracellular signalling pathways, IFN-gamma, TNF-alpha or Fas-ligand may potentiate or antagonize their effects through modulation of cytokine receptor expression.
Program Size, Halting Probabilities, Randomness, & Metamathematics (1987)

Having done the bulk of the work necessary to encode the halting probability Ω as an exponential diophantine equation, we now turn to theory. In Chapter 5 we trace the evolution of the concepts of program-size complexity. In Chapter 6 we define these concepts formally and develop their basic properties. In Chapter 7 we study the notion of a random real and show that Ω is a random real. And in Chapter 8 we develop incompleteness theorems for random reals.
Resting functional connectivity in patients with brain tumors in eloquent areas (2011)

Preoperative resting state MEG connectivity analysis is a useful noninvasive tool to evaluate the functionality of the tissue surrounding tumors within eloquent areas, and could potentially contribute to surgical planning and patient counseling.
Modeling of a Bacterial Cellulose-based Composite in Bending Configuration (2022)

Composites obtained by bio-derived polymers are promising materials for the realization of green sensors. Bio-derived composites consisting of a sheet of bacterial cellulose, covered on both faces by two layers of conducting polymers and infused by ionic liquids have been demonstrated to have generating properties when used as deformation sensor. In the paper, the frequency analysis of the composite is investigated in order to experimentally determine the dependence of the transduction property on the frequency of the applied mechanical deformation. A model has been proposed to fit experimental data.
From inventory to functional mechanisms (2013)

For decades, the pyruvate dehydrogenase complex in the mitochondrial matrix was considered as a rare example of how protein kinases and phosphatases can regulate important functions within this organelle. During the last decade, several proteomic studies revealed that a large fraction of mitochondrial proteins are indeed phosphorylated. A surprisingly high number of phosphorylation sites was found at the preprotein import machinery, TOM, in the outer membrane that provides the central protein import gate for most mitochondrial precursors synthesized in the cytosol. This review describes current knowledge of the mitochondrial phosphoproteome and introduces the first regulatory mechanisms of protein import dynamics by reversible phosphorylation, which have been uncovered mainly in the model organism Saccharomyces cerevisiae.
Experimental industrial robotics (2002)

Robot control systems and other manufacturing equipment are traditionally closed. This circumstance has hampered system integration of manipulators, sensors and other equipment and such system integration has often been made at an unsuitably high hierarchical level. The purpose of the present project is to show how to organize open robot control systems and to verify these ideas by means of experimental verification. As a part of this research, we have developed an experimental robot control system. The system is built around industrially available robots that have been reconfigured for experimental purposes. The developed specific robot interfaces and the integration of the robots into a complete system forms a unique environment for testing and development of algorithms for improvement of performance, programming and autonomous operation.
Local Area Networks (2004)

Abstract Local area networks (LANs) have become ubiquitous, not only in businesses and academia, but in homes. As more and more locations need access to the Internet and shared resources, LANs are being installed as a cheap alternative. Where once computer users worked in isolation on personal computers, local area networks allow computer users to share hardware, software, and data as well as enhance communications. This chapter summarizes the variety of local area network configurations, looks briefly at the importance of local area networks to the Internet, and explores the emerging wireless technology. The chapter also provides an outline for readers who are interested in setting up their own local area networks.
The Acquired Immune Response to the Mucosal Adjuvant LTK63 Imprints the Mouse Lung with a Protective Signature (2007)

LTK63, a nontoxic mutant of Escherichia coli heat labile enterotoxin (LT), is a potent and safe mucosal adjuvant that has also been shown to confer generic protection to several respiratory pathogens. To understand the mechanisms of action underlying the LTK63 protective effect, we analyzed the molecular and cellular events triggered by its administration in vivo. We show here that LTK63 intrapulmonary administration induced in the mouse lung a specific gene expression signature characterized by the up-regulation of cell cycle genes, several host defense genes, chemokines, chemokine receptors, and immune cell-associated genes. Such a transcriptional profile reflected the activation of alveolar macrophages and the recruitment to the lung of T and B cells and innate immune cells such as granulocytes, NK, and dendritic cells. All of these events were T cell dependent and specific for LTK63 because they were absent in SCID and nude mice. Additionally, we showed that LTK63 induces a potent adaptive immune response against itself directed to the lung. We propose that acquired response to LTK63 is the driving force for the local recruitment of both adaptive and innate immune cells. Our data suggest that LTK63 acts as an airway infection mimic that establishes a generic protective environment limiting respiratory infection by innate immune mechanisms and by improving adaptive responses to invading pathogens.
Dynamics of antigen re-exposure to CD8+ T cells during Toxoplasma gondii infection (2019)

Abstract The role of T cell Receptor (TCR) stimulation in activation, expansion, and eventual exhaustion of CD8+ T cells has been well characterized in multiple mouse models of disease. What has not been well characterized is the dynamics of antigen re-exposure to CD8+ T cells in non-lymphoid tissues throughout disease progression, and what proportion of CD8+ T cells have been re-stimulated by antigen at any given time. To answer this question, Nur77-GFP reporter OT-I mice were utilized, which provides a sensitive fluorescent reporter for recent TCR stimulation. In mice infected with a transgenic version of the parasite Toxoplasma gondii expressing OVA, the response of Nur77-GFP OT-I to this stimulus was assessed during the acute and chronic phases of infection. Data from these experiments showed that TCR stimulation varies between infected tissues, but largely correlated with infectious burden. For example, during acute infection, up to 50% of the OT-I in the brain had recently re-encountered antigen whereas during the chronic phase approximately 15% of the OT-I expressed Nur77-GFP. Furthermore, characterization of Nur77GFP+ versus Nur77-GFP− OT-I revealed a role of TCR stimulation in co-expression of the inhibitory receptors Tim3 and PD-1. This model system provides a better understanding of how frequently pathogen specific T cells re-encounter cognate antigen and future studies will focus on the role antigen re-exposure plays in CD8+ T cell effector function and memory formation.
The start‐up of anaerobic sequencing batch reactors at 20 °C and 25 °C for the treatment of slaughterhouse wastewater (2001)

Abstract The objective of this research was to evaluate the feasibility, the stability and the efficiency of a start‐up at 20 °C and 25 °C of anaerobic sequencing batch reactors (ASBRs) treating slaughterhouse wastewater. Influent chemical oxygen demand (COD) and suspended solids concentrations averaged 7500 and 1700 mg dm −3 , respectively. Reactor start‐up was completed in 168 and 136 days at 20 °C, and 25 °C, respectively. The start‐up process was stable at both temperatures, except for a short period at 20 °C, when effluent volatile fatty acid (VFA) concentrations increased from an average of 40 to 400 mg dm −3 . Effluent quality varied throughout start‐up, but in the last 25 days of the experiment, as the ASBRs were operated under organic loading rates of 2.25 ± 0.21 and 2.86 ± 0.24 kg m −3 d −1 at 20 °C and 25 °C, respectively, total COD was reduced by 90.3% ± 1.3%. Methanogenesis was not a limiting factor during start‐up. At 20 °C, the limiting factor was the acidification of the soluble organics and, to a smaller extent, the reduction of propionic, isobutyric and isovaleric acids into lower VFAs. At 25 °C, the limiting factor was the hydrolysis of particulate organics. To minimize biomass loss during the start‐up period, the organic loading rate should be increased only when 75 –80% of the COD fed has been transformed into methane within the design hydraulic retention time. © 2001 Society of Chemical Industry
Les oméga-conotoxines : des ligants hautement spécifiques des canaux Ca++ qui représentent une source potentielle d'agents thérapeutiques [Omega-conotoxins : specific ligands for Ca2+ channels representing a potential source of therapeutic agents] (2004)

12èmes Rencontres en toxinologie, Paris, 2 et 3 décembre 2004, organisées par la SFET, Société française pour l'étude des toxines
Morphological properties of mouse retinal ganglion cells during postnatal development (2007)

Quantitative methods were used to assess dendritic stratification and other structural features of developing mouse retinal ganglion cells from birth to after eye opening. Cells were labeled by transgenic expression of yellow fluorescent protein, DiOlistics or diffusion of DiI, and subsequently imaged in three dimensions on a confocal microscope followed by morphometric analysis of 13 different structural properties. At postnatal day 1 (P1), the dendrites of all cells ramified across the vertical extent of the inner plexiform layer (IPL). By P3/4, dendrites were largely confined to different strata of the IPL. The stratification of dendrites initially reflected a retraction of widely ramifying dendritic processes, but for the most part this was due to the subsequent vertical expansion of the IPL. By P8, distinct cell classes could be recognized, although these had not yet attained adult-like properties. The structural features differentiating cell classes were found to follow three different developmental trends. The mean values of one set of morphological parameters were essentially unchanged throughout postnatal development; another set of measures showed a rapid rise with age to adult values; and a third set of measures first increased with age and later decreased, with the regressive events initiated around the time of eye opening. These findings suggest that the morphological development of retinal ganglion cells is regulated by diverse factors operating during different but overlapping time periods. Our results also suggest that dendritic stratification may be more highly specified in the developing mammalian retina than has been previously realized.