gebhart/patrepeval huggingface dataset:
Massively parallel encapsulation of single cells with structured microparticles and secretion-based flow sorting (2020)

Abstract Techniques to analyze and sort single cells based on functional outputs, such as secreted products, have the potential to transform our understanding of cellular biology, as well as accelerate the development of next generation cell and antibody therapies. However, secreted molecules rapidly diffuse away from cells, and analysis of these products requires specialized equipment and expertise to compartmentalize individual cells and capture their secretions. Herein we demonstrate the use of suspendable microcontainers to sort single viable cells based on their secreted products at high-throughput using only commonly accessible laboratory infrastructure. Our microparticles act as solid supports which facilitate cell attachment, partition uniform aqueous compartments, and capture secreted proteins. Using this platform, we demonstrate high-throughput screening of stably- and transiently-transfected producer cells based on relative IgG production as well as screening of B lymphocytes and hybridomas based on antigen-specific antibody production using commercially available flow sorters. Leveraging the high-speed sorting capabilities of standard sorters, we sorted &gt;1,000,000 events in less than an hour. The reported microparticles can be easily stored, and distributed as a consumable reagent amongst researchers, democratizing access to high-throughput functional cell screening.
The Preferential Expression of the Anti-DNA Associated 8.12 Idiotype in Lupus is not Genetically Controlled (1994)

Anti-DNA antibodies are autoantibodies unique to systemic lupus erythematosus. Studies of their structure have demonstrated cross reactive idiotypes present in genetically unrelated individuals. Despite much research, it is still not clear what triggers their production and what governs the presence of particular idiotypic determinants in their structure. To study the role of genetic and environmental factors in the expression of idiotype, we analyzed sera of SLE patients, their family members and nonautoimmune individuals vaccinated with pneumococcal polysaccharide, for the presence of the 8.12 idiotype, which is present on lambda light chains of anti-DNA antibodies. Elevated titers of the 8.12 idiotype was found in the serum of 57% of SLE patients. Elevated titers were present in only 9% of family members, and always associated with the presence of high levels of IgG anti-DNA antibodies. Following vaccination with pneumococcal polysaccharide, 8.12 reactive anti-pneumococcal antibodies were produced by 7 of 10 non-autoimmune individuals and 8.12 reactive anti-DNA antibodies by one. These results suggest that 8.12 reactive antibodies are antigen driven and bind structurally related antigens, but there is no evidence that expression of this idiotype is genetically controlled.
Technology Options for Beyond-CMOS (2017)

CMOS integrated circuit technology for computation is at an inflexion point. Although this is the technology which has enabled the semiconductor industry to make vast progress over the past 30-plus years, it is expected to see challenges going beyond the ten year horizon, particularly from an energy efficiency point of view. Thus it is extremely important for the semiconductor industry to discover a new integrated circuit technology which can carry us to the beyond CMOS era, so that the power-performance of computing can continue to improve. Currently, researchers are exploring novel device concepts and new information tokens as an alternative for CMOS technology. Examples of areas being actively researched are; quantum electronic devices, such as the tunneling field-effect transistor (TFET), and devices based on electron spin and nano-magnetics (spintronics). It is clear that choices will need to be made in the next 10 years to identify viable alternatives for CMOS by 2025. To prioritize and guide the research exploration in materials, devices and circuits, benchmarking methodology and metrics are being used. This talk will give an overview of the beyond CMOS device research horizon and the benchmarking of these devices for computation. A more detailed investigation of circuits based upon some promising beyond-CMOS devices will follow.
Photoluminescence and ODMR studies of lamellar Cd2P2S6 and Zn2P2S6 lattices (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPhotoluminescence and ODMR studies of lamellar Cd2P2S6 and Zn2P2S6 latticesS. P. Sibley, A. H. Francis, and E. LifshitzCite this: J. Phys. Chem. 1994, 98, 19, 5089–5094Publication Date (Print):May 1, 1994Publication History Published online1 May 2002Published inissue 1 May 1994https://pubs.acs.org/doi/10.1021/j100070a024https://doi.org/10.1021/j100070a024research-articleACS PublicationsRequest reuse permissionsArticle Views168Altmetric-Citations13LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access options Get e-Alerts
Binding of the Wheat Germ Lectin to Cryptococcus neoformans Suggests an Association of Chitinlike Structures with Yeast Budding and Capsular Glucuronoxylomannan (2007)

The capsule of Cryptococcus neoformans is a complex structure whose assembly requires intermolecular interactions to connect its components into an organized structure. In this study, we demonstrated that the wheat germ agglutinin (WGA), which binds to sialic acids and beta-1,4-N-acetylglucosamine (GlcNAc) oligomers, can also bind to cryptococcal capsular structures. Confocal microscopy demonstrated that these structures form round or hooklike projections linking the capsule to the cell wall, as well as capsule-associated structures during yeast budding. Chemical analysis of capsular extracts by gas chromatography coupled to mass spectrometry and high-pH anion-exchange chromatography suggested that the molecules recognized by WGA were firmly associated with the cell wall. Enzymatic treatment, competition assays, and staining with chemically modified WGA revealed that GlcNAc oligomers, but not sialic acids, were the molecules recognized by the lectin. Accordingly, treatment of C. neoformans cells with chitinase released glucuronoxylomannan (GXM) from the cell surface and reduced the capsule size. Chitinase-treated acapsular cells bound soluble GXM in a modified pattern. These results indicate an association of chitin-derived structures with GXM and budding in C. neoformans, which may represent a new mechanism by which the capsular polysaccharide interacts with the cell wall and is rearranged during replication.
Steady-State and Transient Performance of Ion-Sensitive Electrodes Suitable for Wearable and Implantable Electro-Chemical Sensing (2021)

Traditional Potentiometric Ion-selective Electrodes (ISE) are widely used in industrial and clinical settings. The simplicity and small footprint of ISE have encouraged their recent adoption as wearable/implantable sensors for personalized healthcare and precision agriculture, creating a new set of unique challenges absent in traditional ISE. In this paper, we develop a fundamental physics-based model to describe both steady-state and transient responses of ISE relevant for wearable/implantable sensors. The model is encapsulated in a "generalized Nernst formula" that explicitly accounts for the analyte density, time-dynamics of signal transduction, ion-selective membrane thickness, and other sensor parameters. The formula is validated numerically by self-consistent modeling of multispecies ion-transport and experimentally by interpreting the time dynamics and thickness dependence of thin-film solid-contact and graphene-based ISE sensors for measuring soil nitrate concentration. These fundamental results will support the accelerated development of ISE for wearable/implantable applications.
Geometrical Isomerism of RuII Dye‐Sensitized Solar Cell Sensitizers and Effects on Photophysical Properties and Device Performances (2014)

To supplement our study on thiocyanate-free ruthenium sensitizers (TFRS) for dye-sensitized solar cells (DSSCs), which belong to a class of Ru(II)-based complexes coordinated by a single 4,4'-dicarboxylic acid-2,2'-bipyridine and two symmetrically arranged functionalized trans-azolate chelates, we carefully isolated and characterized the second and less-abundant stereoisomer, in which the two pyridyl azolate ancillaries are asymetrically cis-arranged to each other. Two distinctive ancillaries, namely: 5-[4-(5-hexyl-2-thienyl)-2-pyridinyl]-3-trifluoromethyl pyrazole and 5-(6-tert-butyl-1-isoquinolinyl)-3-trifluoromethyl pyrazole, were employed in this study, giving a total of four sensitizers, that is, thienyl substituted TFRS-2 a and 2 b, and isoquinolinyl substituted TFRS-52 a and 52 b, in which the suffix b indicates the cis-stereoisomers. To gain insight into their fundamental properties their photophysical, electrochemical, and spectroelectrochemical behavior was investigated by density functional theory. Upon comparison of the correspondingly fabricated DSSCs, the sensitizers TFRS-2 a and 52 a yielded significantly higher conversion efficiencies than their asymmetrical cis-counterparts, TFRS-2 b and 52 b. To rationalize the cell performances charge extraction/photovoltage decay and impedance spectroscopic measurements were carried out to compare the rates of interfacial electron recombination from the TiO2 conduction band to the electrolyte.
<title>Fiber optic and portable instruments for ammonia sensing in field operating conditions</title> (1993)

Polymer dye films incorporating a pH indicator, immobilized on a polymer support, can be used for ammonia gas (NH<SUB>3</SUB>) sensing in fiber optic and portable instruments in the field operating conditions with changing temperature and humidity. Experimental results on the NH<SUB>3</SUB> detection in the range 0 - 100 mg/m<SUP>3</SUP> are reported for the range of temperature 25 - 45 degree(s)C and 60 - 80% relative humidity. A model of steady-state instrument response in the field has been developed with four adjustable parameters to describe the coupling of ambient NH<SUB>3</SUB> concentration to absorbance change of the sensing element. Practical problems associated with the applications of such sensing chemistry for NH<SUB>3</SUB> monitoring in the field are discussed.
A new oxygen-regulated promoter for the expression of proteins in Escherichia coli. (1989)

Several properties of a new oxygen-regulated promoter, OXYPRO, were tested in small-scale Escherichia coli cultures. Using OXYPRO, maximal activity of a reporter gene encoding chloramphenicol acetyltransferase (CAT) occurred in cultures that were tightly capped immediately after inoculation. This is probably a result of the reduced oxygen concentration attained in capped cultures, a condition known to be required for OXYPRO induction. CAT levels were significantly higher when the cells were grown in a glycerol-based medium. Similar levels of CAT expression were obtained when OXYPRO was compared to the trp-lac (tac) promoter. In addition, regulated expression of CAT occurred in a wild type strain of E. coli, suggesting that OXYPRO will be useful in most E. coli strains. Thus, OXYPRO provides a simple, inexpensive, and unobtrusive method to achieve high levels of cloned protein expression in most strains of E. coli. OXYPRO is available in a high copy plasmid with a convenient multiple cloning site for the insertion of genes for direct expression in E. coli.
Polarized observations for advanced atmosphere-ocean algorithms using airborne multi-spectral hyper-angular polarimetric imager (2021)

Airborne measurements of the linear polarization state of light were carried out over coastal and open ocean conditions to study aerosol and water column properties and investigate the possibility of using a multi-spectral, hyper-angular imaging polarimeter for retrieving aerosol and hydrosol optical properties. The instrument, the Versatile Imager for the Coastal Ocean (VICO), is used to support the analysis of ocean color polarized observations and their implication for future space-borne polarimetry such as the polarimeters planned to be deployed with the NASA Plankton, Aerosol, Cloud, and ocean Ecosystem (PACE) mission. Several sets of images at different viewing angles from the visible to the near-infrared spectrum were collected and compared with simulations using a vector radiative transfer (VRT) code. The simulations were obtained based on measured seawater inherent optical properties from shipborne instruments and measured atmospheric parameters from the Aerosol Robotic Network (AERONET) and a shipborne sunphotometer at different locations. An uncertainty method has been derived by propagating uncertainties from the measured polarized radiances. The method demonstrates practicable uncertainty formulations that can be used to construct a measurement uncertainty budget for the polarized data products. Results from VICO and the VRT simulation are consistent for both radiance and polarization spectrum at all the measured viewing angles. The total and polarized water-leaving reflectances are retrieved at four bands and varied geometries. It is also shown that the polarized remote sensing reflectance measured at various angles could be used to distinguish between the aerosols’ and hydrosols’ optical signatures by exploiting the fact that the polarized reflectance is fairly insensitive to hydrosols for given acquisition geometries. This study thus provides an opportunity to investigate various relationships between the microphysical properties of the oceanic and atmospheric particulates such as refractive index and particle size properties. It also contributes to the development of polarization-based inverse ocean color algorithms. Finally, the provided analysis gives insights for the validation of the ocean color parameters that will be retrieved from the forthcoming polarimetric satellite missions.
Extracellular Vesicles from Cryptococcus neoformans Modulate Macrophage Functions (2010)

Cryptococcus neoformans and distantly related fungal species release extracellular vesicles that traverse the cell wall and contain a varied assortment of components, some of which have been associated with virulence. Previous studies have suggested that these extracellular vesicles are produced in vitro and during animal infection, but the role of vesicular secretion during the interaction of fungi with host cells remains unknown. In this report, we demonstrate by fluorescence microscopy that mammalian macrophages can incorporate extracellular vesicles produced by C. neoformans. Incubation of cryptococcal vesicles with murine macrophages resulted in increased levels of extracellular tumor necrosis factor alpha (TNF-alpha), interleukin-10 (IL-10), and transforming growth factor beta (TGF-beta). Vesicle preparations also resulted in a dose-dependent stimulation of nitric oxide production by phagocytes, suggesting that vesicle components stimulate macrophages to produce antimicrobial compounds. Treated macrophages were more effective at killing C. neoformans yeast. Our results indicate that the extracellular vesicles of C. neoformans can stimulate macrophage function, apparently activating these phagocytic cells to enhance their antimicrobial activity. These results establish that cryptococcal vesicles are biologically active.
A conditional mouse model to study murine hemochromatosis (2005)

Aims: Hereditary hemochromatosis (HH) is a common iron overload disorder that is most frequently caused by mutations in the HFE gene. Work from our lab and others demonstrates that HFE is required for appropriate hepatic expression of the iron hormone and anti-microbial peptide hepcidin: expression of this negative regulator of duodenal iron absorption is decreased and cannot be adjusted in response to elevated hepatic iron levels in Hfe-deficient mice and HH patients. These findings further our understanding of the molecular mechanism of HFE function and suggest that the primary locus of HFE function is the liver and not the duodenum, as was previously hypothesized. It is currently not understood in which cell type HFE functions to direct appropriate hepcidin expression. Methods: Based on a mouse line with generalized Hfe deficiency [1] we generated a mouse line with a „floxed“, functionally active Hfe allele. This mouse line was crossed with transgenic mouse lines with Cre expression restricted to duodenal enterocytes, macrophages, and hepatocytes, respectively. Results and Conclusions: We have established a mouse line with a floxed Hfe allele. Based on this mouse line, we generated mouse lines with Hfe deletions in duodenal enterocytes, macrophages (incl. Kupffer cells), and hepatocytes, respectively. Experiments are ongoing to assess the efficiency and specificity of Hfe recombination in the targeted cells, the effect of Hfe deletion on hepatic iron content and hepcidin expression as well as cell type specific gene regulation elicited by the specific Hfe deletions.
Generation of twin photon beams in 1D microcavities (2011)

Communication orale
Discovering and using groups to improve personalized search (2009)

Personalized Web search takes advantage of information about an individual to identify the most relevant results for that person. A challenge for personalization lies in collecting user profiles that are rich enough to do this successfully. One way an individual's profile can be augmented is by using data from other people. To better understand whether groups of people can be used to benefit personalized search, we explore the similarity of query selection, desktop information, and explicit relevance judgments across people grouped in different ways. The groupings we explore fall along two dimensions: the longevity of the group members' relationship, and how explicitly the group is formed. We find that some groupings provide valuable insight into what members consider relevant to queries related to the group focus, but that it can be difficult to identify valuable groups implicitly. Building on these findings, we explore an algorithm to "groupize" (versus "personalize") Web search results that leads to a significant improvement in result ranking on group-relevant queries.
Characterization of acute myocardial infarction by pre-contrast T1 mapping (2012)

Novel CMR techniques are needed to assess reversible myocardial injury in acute MI. Our results show that pre-contrast T1 mapping CMR could be such a technique: increasingly higher T1 values are associated with larger extent of acute myocardial injury and with reduced functional recovery at 6 months.
Simultaneous Dual Living Polymerizations: A Novel One-Step Approach to Block and Graft Copolymers (1998)

Just one step is required for the synthesis of block copolymers by simultaneous “living”/controlled ring-opening and radical polymerization initiated by a difunctional (A–B) compound (shown schematically on the right).
A Rapid Throughput System for Shock and Impact Characterization: Design and Examples in Compaction, Spallation, and Impact Welding (2020)

Many important physical phenomena are governed by intense mechanical shock and impulse. These can be used in material processing and manufacturing. Examples include the compaction or shearing of materials in ballistic, meteor, or other impacts, spallation in armor and impact to induce phase and residual stress changes. The traditional methods for measuring very high strain rate behavior usually include gas-guns that accelerate flyers up to km/s speeds over a distance of meters. The throughput of such experiments is usually limited to a few experiments per day and the equipment is usually large, requiring specialized laboratories. Here, a much more compact method based on the Vaporizing Foil Actuator (VFA) is used that can accelerate flyers to over 1 km/s over a few mm of travel is proposed for high throughput testing in a compact system. A system with this primary driver coupled with Photonic Doppler Velocimetry (PDV) is demonstrated to give insightful data in powder compaction allowing measurements of shock speed, spall testing giving fast and reasonable estimates of spall strength, and impact welding providing interface microstructure as a function of impact angle and speed. The essential features of the system are outlined, and it is noted that this approach can be extended to other dynamic tests as well.
A Monte-Carlo study on the fluorescent nuclear track detector (FNTD) response to fast neutrons: Which information can be obtained by single layer and 3D track reconstruction analyses? (2021)

Fluorescence Nuclear Track Detectors (FNTDs) are part of a new technology developed for particle detection and applicable to personal neutron dosimetry. The objective of this study is to simulate the FNTD fast neutron response to: (i) assess and understand the performance of the existing neutron dosimeter design (Landauer Inc.) and its associated single layer track-spots analysis; and (ii) evaluate the potential information that can be obtained by the analysis of the 3D reconstructed recoil proton trajectories. To achieve that, a FLUKA Monte Carlo (MC) model of the current FNTD design was developed and the FNTD response was investigated for mono-energetic neutrons and the 252Cf and 241AmBe neutron sources. The investigation of the recoil proton densities behind the different converters showed that the single layer analysis and dose calculation algorithm, based on the comparison and subtraction of the track densities behind the different converters, works properly only up to neutron energies ~13 MeV. Above this neutron energies, recoil protons generated in the detector housing (PE) have a range larger than the thickness of the PTFE and 6Li-enriched glass, reaching the FTND and, therefore, adding to the signal in these detection regions and influencing the secondary electron discrimination and the energy determination algorithm. MC simulations show that the FNTD 3D reconstructed recoil proton tracks can provide estimates of the irradiation angles and average neutron energy. The results show that the angle or displacement (dX/dZ or dY/dZ) distributions of the recoil proton tracks can be used to obtain information on irradiation angle; the angle with the detector's normal (polar angle), the most important because of its influences on the FTND sensitivity, can be determined in laboratory and for irradiation angles < 60° with an 4° uncertainty already for doses > 4.5 mSv in the case of a214AmBe neutron irradiation. The neutron field mean energy can also be determined for normal irradiation by analysing the depth distribution of the recoil proton tracks already for a minimum of 150 tracks, or 2.5 mSv for 241AmBe, assuming a scanned area is ~2.0 mm2. Therefore, the present study contributes to understanding the performance of the current FNTD design and analysis for neutron dosimetry and investigates a new detector evaluation approach to gain additional information on the irradiation conditions.