gebhart/patrepeval huggingface dataset:
<title>Analysis of photon migration for optical diagnosis</title> (1996)

The opportunity to monitor the onset and progression of disease may be enabled by the smart implementation of biomedical optical engineering approaches to monitor tissue biochemistry. Uncorrected, these biochemical disturbances manifest themselves in microscopic structural changes which lead to gross pathophysiology and symptoms by which the disease is outwardly identified. Biomedical optical engineering techniques offer the opportunity to detect these biochemical changes and provide diagnostic information at earlier stages in the disease process, enabling greater efficacy of therapeutic intervention. In this paper, we concentrate on the fluorescence and phosphorescence lifetime spectroscopy due to advantages these techniques have to offer in tissues. The development of fluorescent and phosphorescent dyes which excite and re-emit in the near-infrared wavelength region promises the capacity for non- invasive biochemical sensing in tissues. Fluorescence intensity and fluorescence lifetime spectroscopies are established methods by which a fluorophore can provide sensing in dilute, non-scattering samples. However, fluorescence intensity or fluorescence lifetime spectroscopy in tissues or other scattering media is a complex problem. In order to extract the intrinsic fluorescence intensity for identification of the fluorophore concentration and yield, a priori information about tissue absorption and scattering must be obtained or assumed. Yet in tissues, the optical properties of absorption and scattering are highly variable. Nonetheless when successful, fluorescence intensity spectroscopy enables determination of the product of fluorescent yield and fluorophore concentration. In contrast to fluorescence intensity spectroscopy, fluorescence-lifetime tissue spectroscopy offers the ability to directly determine metabolite concentration independently of the concentration of fluorophore, whether it is endogenous or exogenous. Instead of monitoring the fluorescent intensity due to the re- emission process, the 'lifetime' or stability of the photon-activated fluorophore is measured. The lifetime of the activated state is defined as the mean time between absorption of the excitation photon and re-emission of a fluorescent photon. Typically, endogenous fluorophores have lifetimes on the order of nanoseconds while exogenous compounds have lifetimes ranging from sub nanosecond to milliseconds.
High temperature superconductor dc-SQUID microscope with a soft magnetic flux guide (2004)

A scanning SQUID microscope based on high-temperature superconductor (FITS) dc-SQUIDs was developed. An extremely soft magnetic amorphous foil was used to guide the flux from room temperature samples to the liquid-nitrogen-cooled SQUID sensor and back. The flux guide passes through the pick-up loop of the HTS SQUID, providing an improved coupling of magnetic flux of the object to the SQUID. The device measures the z component (direction perpendicular to the sample surface) of the stray field of the sample, which is rastered with submicron precision in the x-y direction by a motorized computer-controlled scanning stage. A lateral resolution better than 10 mum, with a field resolution of about 0.6 nT Hz(-1/2) was achieved for the determination of the position of the current carrying thin wires. The presence of the soft magnetic foil did not significantly increase the flux noise of the SQUID.
Method for hue plane preserving color correction (2016)

Hue plane preserving color correction (HPPCC), introduced by Andersen and Hardeberg [Proceedings of the 13th Color and Imaging Conference (CIC) (2005), pp. 141-146], maps device-dependent color values (RGB) to colorimetric color values (XYZ) using a set of linear transforms, realized by white point preserving 3×3 matrices, where each transform is learned and applied in a subregion of color space, defined by two adjacent hue planes. The hue plane delimited subregions of camera RGB values are mapped to corresponding hue plane delimited subregions of estimated colorimetric XYZ values. Hue planes are geometrical half-planes, where each is defined by the neutral axis and a chromatic color in a linear color space. The key advantage of the HPPCC method is that, while offering an estimation accuracy of higher order methods, it maintains the linear colorimetric relations of colors in hue planes. As a significant result, it therefore also renders the colorimetric estimates invariant to exposure and shading of object reflection. In this paper, we present a new flexible and robust version of HPPCC using constrained least squares in the optimization, where the subregions can be chosen freely in number and position in order to optimize the results while constraining transform continuity at the subregion boundaries. The method is compared to a selection of other state-of-the-art characterization methods, and the results show that it outperforms the original HPPCC method.
Algorithm for cellular reprogramming (2017)

The day we understand the time evolution of subcellular events at a level of detail comparable to physical systems governed by Newton's laws of motion seems far away. Even so, quantitative approaches to cellular dynamics add to our understanding of cell biology. With data-guided frameworks we can develop better predictions about, and methods for, control over specific biological processes and system-wide cell behavior. Here we describe an approach for optimizing the use of transcription factors (TFs) in cellular reprogramming, based on a device commonly used in optimal control. We construct an approximate model for the natural evolution of a cell-cycle-synchronized population of human fibroblasts, based on data obtained by sampling the expression of 22,083 genes at several time points during the cell cycle. To arrive at a model of moderate complexity, we cluster gene expression based on division of the genome into topologically associating domains (TADs) and then model the dynamics of TAD expression levels. Based on this dynamical model and additional data, such as known TF binding sites and activity, we develop a methodology for identifying the top TF candidates for a specific cellular reprogramming task. Our data-guided methodology identifies a number of TFs previously validated for reprogramming and/or natural differentiation and predicts some potentially useful combinations of TFs. Our findings highlight the immense potential of dynamical models, mathematics, and data-guided methodologies for improving strategies for control over biological processes.
Network congestion avoidance through Speculative Reservation (2012)

Congestion caused by hot-spot traffic can significantly degrade the performance of a computer network. In this study, we present the Speculative Reservation Protocol (SRP), a new network congestion control mechanism that relieves the effect of hot-spot traffic in high bandwidth, low latency, lossless computer networks. Compared to existing congestion control approaches like Explicit Congestion Notification (ECN), which react to network congestion through packet marking and rate throttling, SRP takes a proactive approach of congestion avoidance. Using a light-weight endpoint reservation scheme and speculative packet transmission, SRP avoids hot-spot congestion while incurring minimal overhead. Our simulation results show that SRP responds more rapidly to the onset of severe hot-spots than ECN and has a higher network throughput on bursty network traffic. SRP also performs comparably to networks without congestion control on benign traffic patterns by reducing the latency and throughput overhead commonly associated with reservation protocols.
The Specular Array Radiometric Calibration (SPARC) method: a new approach for absolute vicarious calibration in the solar reflective spectrum (2010)

Physics-based exploitation of image data from Earth observing sensors requires knowledge of the accuracy, stability and repeatability of a sensor's radiometric response within its in-flight environment. Vicarious radiometric calibration techniques, using terrestrial targets, provide an effective approach to obtaining this knowledge by measuring system performance under actual operational conditions. This paper introduces a new capability for performing the vicarious radiometric calibration of high spatial resolution sensors. The SPecular Array Radiometric Calibration (SPARC) method employs convex mirrors to create two arrays of calibration targets for deriving absolute calibration coefficients of Earth remote sensing systems in the solar reflective spectrum. The first is an array of single mirrors used to oversample the sensor's point spread function (PSF) providing necessary spatial quality information needed to perform the radiometric calibration of a sensor when viewing small targets. The second is a set of panels consisting of multiple mirrors designed to stimulate detector response with known at-sensor irradiance traceable to the exo-atmospheric solar spectral constant. The outcome is improved radiometric performance knowledge compared to other in-flight vicarious techniques through reduced uncertainties in target reflectance, atmospheric effects, and temporal variability. The only ground truth needed is the measurement of atmospheric transmittance. In addition, the simplification of calibration targets and ground truth collection in the SPARC method makes the deployment more cost effective and portable, thus creating the opportunity to imbed spectral, spatial and radiometric targets at a study site providing references that improve a sensor's interactivity as a phenomenological tool. A demonstration of the SPARC method is presented based on data collected with the IKONOS satellite operated by GeoEye. A SPARC measurement of absolute calibration coefficients for the IKONOS multispectral bands is compared to coefficients derived from the established reflectance-based vicarious calibration method.
A novel adhesion pathway that regulates dendritic cell trafficking and T cell interactions (2002)

Dendritic cells (DC) are present in essentially every tissue, where they operate at the interface of innate and acquired immunity by recognizing pathogens and presenting pathogen-derived peptides to T cells. Cell-cell interactions between DC, T cells and endothelial cells are crucial to all immunological processes. Recently, several C-type lectin receptors have been characterized that are abundantly expressed on the surface of DC. It is now becoming clear that these lectin receptors serve not only as antigen-receptors recognizing pathogens, but they may also function as adhesion receptors and/or signaling molecules. In particular the DC specific C-type lectin DC-SIGN (CD209) regulates adhesion processes, such as DC trafficking by interacting with ICAM-2 and T cell synapse formation, upon binding of ICAM-3. C-type lectins such as DC-SIGN contain a lectin domain that recognizes in a Ca2+-dependent manner carbohydrates such as mannose-containing structures presented on the glycoproteins ICAM-2 and ICAM-3. Although the integrin LFA-1 is a counter-receptor for both ICAM-2 and ICAM-3, on DC, DC-SIGN is the high affinity adhesion receptor for ICAM-2/-3. Here we discuss how the heterogeneity of mannose-residues exposed on cellular proteins and pathogens regulates specific binding of a repertoire of DC-expressed C-type lectins that contribute to the diversity of immune responses created by DC.
Herpes Simplex Virus 1 ICP0 Phosphorylation Site Mutants Are Attenuated for Viral Replication and Impaired for Explant-Induced Reactivation (2011)

In cell culture experiments, phosphorylation appears to be a critical regulator of the herpes simplex virus 1 (HSV-1) immediate-early (IE) protein, ICP0, which is an E3 ubiquitin ligase that transactivates viral gene expression. Three major regions of phosphorylation in ICP0 (amino acids 224 to 232, 365 to 371, and 508 to 518) have been identified, and mutant viruses that block phosphorylation sites within each region (termed Phos 1, 2, and 3, respectively) have been constructed. Previous studies indicated that replication of Phos 1 is significantly reduced compared to that of wild-type virus in cell culture (C. Boutell, et al., J. Virol. 82:10647-10656, 2008). To determine the effects these phosphorylation site mutations have on the viral life cycle in vivo, mice were ocularly infected with wild-type HSV-1, the Phos mutants, or their marker rescue counterparts. Subsequently, viral replication, establishment of latency, and viral explant-induced reactivation of these viruses were examined. Relative to wild-type virus, Phos 1 eye titers were reduced as much as 7- and 18-fold on days 1 and 5 postinfection, respectively. Phos 2 eye titers showed a decrease of 6-fold on day 1 postinfection. Titers of Phos 1 and 2 trigeminal ganglia were reduced as much as 16- and 20-fold, respectively, on day 5 postinfection. Additionally, the reactivation efficiencies of Phos 1 and 2 were impaired relative to wild-type HSV-1, although both viruses established wild-type levels of latency in vivo. The acute replication, latency, and reactivation phenotypes of Phos 3 were similar to those of wild-type HSV-1. We conclude from these studies that phosphorylation is likely a key modulator of ICP0's biological activities in a mouse ocular model of HSV-1 infection.
The Developing Technology of Gas Separating Membranes (1983)

The background of and commercial needs leading to the development of practical membrane systems for the separation of industrial gases are presented. The critical issues and fundamental technical limitations that delayed earlier development of such systems and the solutions of some of the major problems in the field are discussed. Particular attention is given to the methods by which high gas fluxes and high selectivities have been achieved in hollow fibers. The performance characteristics of various practical gas separation methods are compared, and the effects of parameters such as pressure and contaminant levels are illustrated with representative examples.
Criblage d’une banque de glycoclusters sur DDI-glycoarray : Application à Pseudomonas aeruginosa. (2014)

23/03/2014 au 27/03/2014
Extending the UML Metamodel for Sequence Diagram to Enhance Model Traceability (2010)

Specification of object-oriented systems by UML models has become an eminent practice among software practitioners. UML Sequence diagrams are used to model the dynamic behavior of the software system depicting how objects interact by passing messages. The UML Metamodel, which is contained in the UML Specification Version 2, has undergone a significant change with respect to sequence diagrams. Complex logic that allows message exchange between objects in a non-sequential manner was made possible through the use of combined fragments. The UML metamodel is used by design tools to verify the correctness of the constructed models. Ensuring well-formedness of these models still remains a challenging task mainly due to unavailability of a formal description for some rules listed in the UML specification. In this paper, we propose an extension to the UML metamodel that eliminates some well-formedness rules defined over combined fragments in UML sequence diagrams. This is achieved by introducing new metaclasses in the UML metamodel. The proposed solution also provides ease for future metamodel extensions and a better mapping framework between the UML metamodel and program code assisting in enhanced reverse engineering.
Design and Processing of Structural Composite Batteries (2007)

This report is a reprint from the Proceedings of Society for the Advancement of Materiel and Process Engineering (SAMPE) 2007 Symposium and Exhibition held in Baltimore, MD, on 3-7 June 2007. Multifunctional structural composites are being developed to simultaneously bear mechanical loads and store electrochemical energy. These composite batteries can replace inert structural components and concurrently provide supplementary power for light load applications. Significant weight savings can be achieved by designing composite battery components, packaging, electrolyte, separator, and/or electrodes with built-in structural and energy efficiency. Prior efforts have focused only on utilizing structural packaging with traditional battery components. In this approach, novel electrolyte and electrode materials are being developed to optimize both electrochemical and mechanical proper properties. Solvent-free structural vinyl ester polymer electrolytes are being formulated to achieve necessary mechanical strength while enabling ion conductivity. Structural carbon anodes and cathode materials deposited on metal substrates are being developed as electrode components. Charge/discharge cycling is used to evaluate electrochemical capacity of the electrode materials, and tensile tests are used to evaluate their mechanical properties. Several different structural separator materials are being investigated as well. All of these components allow the use of moldable, scalable, and cost-effective composite processing techniques.
Multi-Component, Multi-Point Interferometric Rayleigh/Mie Doppler Velocimeter (2012)

An interferometric Rayleigh scattering system was developed to enable the measurement of multiple, orthogonal velocity components at several points within very-high-speed or high-temperature flows. The velocity of a gaseous flow can be optically measured by sending laser light into the gas flow, and then measuring the scattered light signal that is returned from matter within the flow. Scattering can arise from either gas molecules within the flow itself, known as Rayleigh scattering, or from particles within the flow, known as Mie scattering. Measuring Mie scattering is the basis of all commercial laser Doppler and particle imaging velocimetry systems, but particle seeding is problematic when measuring high-speed and high-temperature flows. The velocimeter is designed to measure the Doppler shift from only Rayleigh scattering, and does not require, but can also measure, particles within the flow. The system combines a direct-view, large-optic interferometric setup that calculates the Doppler shift from fringe patterns collected with a digital camera, and a subsystem to capture and re-circulate scattered light to maximize signal density. By measuring two orthogonal components of the velocity at multiple positions in the flow volume, the accuracy and usefulness of the flow measurement increase significantly over single or nonorthogonal component approaches.
Tuning of whispering gallery modes of spherical resonators using an external electric field (2009)

In this paper we investigate the electrostriction effect on the whispering gallery modes (WGM) of polymeric microspheres and the feasibility of a WGM-based microsensor for electric field measurement. The electrostriction is the elastic deformation (strain) of a dielectric material under the force exerted by an electrostatic field. The deformation is accompanied by mechanical stress which perturbs the refractive index distribution in the sphere. Both strain and stress induce a shift in the WGM of the microsphere. In the present, we develop analytical expressions for the WGM shift due to electrostriction for solid and thin-walled hollow microspheres. Our analysis indicates that detection of electric fields as small as ~500V/m may be possible using water filled, hollow solid polydimethylsiloxane (PDMS) microspheres. The electric field sensitivities for solid spheres, on the other hand, are significantly smaller. Results of experiments carried out using solid PDMS spheres agree well with the analytical prediction.
Stem cell-paved biobridge facilitates neural repair in traumatic brain injury (2014)

Modified mesenchymal stromal cells (MSCs) display a unique mechanism of action during the repair phase of traumatic brain injury by exhibiting the ability to build a biobridge between the neurogenic niche and the site of injury. Immunohistochemistry and laser capture assay have visualized this biobridge in the area between the neurogenic subventricular zone and the injured cortex. This biobridge expresses high levels of extracellular matrix metalloproteinases (MMPs), which are initially co-localized with a stream of transplanted MSCs, but later this region contains only few to non-detectable grafts and becomes overgrown by newly recruited host cells. We have reported that long-distance migration of host cells from the neurogenic niche to the injured brain site can be attained via these transplanted stem cell-paved biobridges, which serve as a key regenerative process for the initiation of endogenous repair mechanisms. Thus, far the two major schools of discipline in stem cell repair mechanisms support the idea of "cell replacement" and the bystander effects of "trophic factor secretion." Our novel observation of stem cell-paved biobridges as pathways for directed migration of host cells from neurogenic niche toward the injured brain site adds another mode of action underlying stem cell therapy. More in-depth investigations on graft-host interaction will likely aid translational research focused on advancing this stem cell-paved biobridge from its current place, as an equally potent repair mechanism as cell replacement and trophic factor secretion, into a new treatment strategy for traumatic brain injury and other neurological disorders.
First steps of an interdisciplinary approach towards miniaturised cryopreservation for cellular nanobiotechnology (2004)

The only widely used and accepted method for long-term cell preservation is storage below -130 degrees C. The biosciences will make increasing use of preservation and place new demands on it. Currently, cells are frozen in volumes greater than 1 ml but the new cell and implantation therapies (particularly those using stem cells) will require accurately defined freezing and storage conditions for each single cell. Broadly-based, routine freezing of biological samples allows the advantage of retrospective analysis and the possibility of saving genetic rights. For such applications, one billion is a modest estimation for the number of samples. Current cryotechniques cannot handle so many samples in an efficient and economic way, and the need for new cryotechnology is evident. The interdisciplinary approach presented here should lead to a new sample storage and operating strategy that fulfils the needs mentioned above. Fundamental principles of this new kind of smart sample storage are: (i) miniaturisation; (ii) modularisation; (iii) informationsample integration, i.e. freezing memory chips with samples; and (iv) physical and logical access to samples and information without thawing the samples. In contrast to current sample systems, the prototyped family of intelligent cryosubstrates allows the recovery of single wells (parts) of the substrate without thawing the rest of the sample. The development of intelligent cryosubstrates is linked to developments in high throughput freezing, high packing density storage and minimisation of cytotoxic protective agents.
Per panel photovoltaic energy extraction with multilevel output DC-DC switched capacitor converters (2011)

Switched capacitor multilevel output DC-DC converters are evaluated as panel integrated modules in a solar maximum power point tracking system. The recommended system includes a central input current-controlled ripple port inverter. Potential benefits include per panel MPPT without inter-panel communication, electrolytic capacitors or per panel magnetics. Statistical methods are used to predict average tracking and conversion efficiencies. A particular implementation of the switched capacitor module is studied - the Marx converter. Average total efficiencies (tracking × conversion) greater than 93% are predicted for a simulated 510 W, 3 panel, DC-DC system.