gebhart/patrepeval huggingface dataset:
Epithelial stem cells in corneal regeneration and epidermal gene therapy (2008)

Regenerative medicine refers to innovative therapies aimed at the permanent restoration of diseased tissues and organs. Regeneration of self-renewing tissues requires specific adult stem cells, which need to be genetically modified to correct inherited genetic diseases. Cultures of epithelial stem cells permanently restore severe skin and mucosal defects, and genetically corrected epidermal stem cells regenerate a normal epidermis in patients carrying junctional epidermolysis bullosa. The keratinocyte stem cell is therefore the only cultured stem cell used both in cell therapy and gene therapy clinical protocols. Epithelial stem cell identification, fate and molecular phenotype have been extensively reviewed, but not in relation to tissue regeneration. In this paper we focus on the localization and molecular characterization of human limbal stem cells in relation to corneal regeneration, and the gene therapy of genetic skin diseases by means of genetically modified epidermal stem cells.
Lateral mode control of an AlGaAs laser array in a Talbot cavity (1989)

The lateral mode thresholds of an external cavity AlGaAs laser diode array are measured as a function of cavity length. It is found that certain cavity lengths induce the array to lase in either the fundamental or highest order lateral mode. The results are explained using the theory of Talbot self-imaging in fractional Talbot planes
The shear coefficient for quartz crystal of rectangular cross section in Timoshenko's beam theory (2002)

This paper describes the shear coefficient K of transverse vibration for quartz crystal that is an anisotropic material. In this paper, we derive the shear coefficient K for quartz crystal of rectangular cross section in Timoshenko's beam theory of three dimensional elasticity. The theoretical result gives K as a function of the transformed elastic stiffness constants c'/sub 22/, c/spl circ//sub 44/, c'/sub 66/. For an isotropic material it agrees completely with that derived by G.R. Cowper (1966). In addition, a value of K and its temperature coefficient versus cut angle is calculated, so that K has a value of 0.796 to 0.867 and its temperature coefficient of the first order varies from -15.3/spl times/10/sup -6///spl deg/C to +13.2/spl times/10/sup -6///spl deg/C, when a Z-plate of quartz crystal is rotated with a cut angle /spl theta/ of 0 to 180 degrees about the x-axis. The values of K are then compared with those obtained by other authors.
Supplementary Table S5 from Pooled Genomic Screens Identify Anti-apoptotic Genes as Targetable Mediators of Chemotherapy Resistance in Ovarian Cancer (2023)

&lt;p&gt;CRISPR-Cas9 screen data&lt;/p&gt;
Practical Synthesis of Reactive Immuno-PET Linker-Chelator (1R,2R)-RESCA-TFP (2023)

We herein report the evolution of decagram syntheses of a single enantiomer of immuno-PET linker-chelator (1R,2R)-RESCA-TFP (1) from commercially available (1R,2R)-1,2-diaminocyclohexane. The syntheses feature a reductive amination, a trialkylation, a saponification followed by EDCI-promoted TFP ester formation, and finally a t-Bu ester global deprotection. While the first-generation synthesis required chromatographic purification of process intermediates and 1, the second-generation synthesis implemented salt formation and direct isolation by filtration, thus eliminating all preparative purification operations.
Quantum nanophotonic devices based on rare-earth ions (Conference Presentation) (2019)

In this talk I give an overview of our recent work on quantum nano-photonic devices based on rare-earth ions. The rare-earth ions exhibit excellent optical and spin coherence properties when embedded in nano-photonic devices. This enables on-chip optical quantum memories, single rare-earth-ion optically addressable quantum bits, and devices for quantum transduction. I will focus on our recent results based on ytterbium 171 in yttrium orthovanadate.
Simple air-tight powder x-ray diffraction cell (2003)

The design and a description of a very simple and inexpensive air-tight cell for powder x-ray diffraction analysis are discussed. The cell is designed for the Bruker AXS powder diffractometer. It is easily manipulated inside a glove box and reduces the sample preparation time to a fraction of the time required for other hermetic cells or environmental chambers.
Database search based on Bayesian alignment. (1999)

The size of protein sequence database is getting larger each day. One common challenge is to predict protein structures or functions of the sequences in databases. It is easy when a sequence shares direct similarity to a well-characterized protein. If there is no direct similarity, we have to rely on a third sequence or a model as intermediate to link two proteins together. We developed a new model based method, called Bayesian search, as a means to connect two distantly related proteins. We compared this Bayesian search model with pairwise and multiple sequence comparison methods on structural databases using structural similarity as the criteria for relationship. The results show that the Bayesian search can link more distantly related sequence pairs than other methods, collectively and consistently over large protein families. If each query made one error on average against SCOP database PDB40D-B, Bayesian search found 36.5% of related pairs, PSI-Blast found 32.6%, and Smith-Waterman method found 25%. Examples are presented to show that the alignments predicted by the Bayesian search agree well with structural alignments. Also false positives found by Bayesian search at low cutoff values are analyzed.
On the mechanism of selective inhibition of herpesvirus replication by (E)-5-(2-bromovinyl)-2'-deoxyuridine. (1981)

Bromovinyldeoxyuridine (BVdUrd) is a potent antiherpesvirus compound with low cytotoxicity. To gain an insight into its selectivity and mechanism of inhibition, we chemically synthesized the 5'-triphosphate of BVdUrd, BVdUTP, and tested its effect on the activities of DNA polymerases [DNA nucleotidyltransferase (DNA directed), EC 2.7.7.7] of two herpesviruses--i.e., herpes simplex virus type 1 (HSV-1) and Epstein-Barr virus (EBV)--as well as cellular DNA polymerases alpha, beta, and gamma. The effects on the DNA polymerases were determined under assay conditions optimal for the individual polymerases. We found that the BVdUTP was considerably more inhibityory to the utilization of dTTP by the HSV-1 DNA polymerase then by the cellular DNA polymerases. For instance, as little as 1 microM BVdUTP inhibited the utilization of dTTP by HSV-1 DNA polymerase 50%, whereas the same concentration inhibited the DNA polymerase alpha and the DNA polymerase beta activities only 9% and 3%, respectively. The BVdUTP inhibited DNA synthesis by competing with the natural substrate, dTTP. The Km for dTTP and the Ki for the BVdUTP of the HSV-1 DNA polymerase were 0.66 and 0.25 microM, respectively. Kinetic analyses with the DNA polymerases alpha and beta and the EBV DNA polymerase also reflected a similar difference in sensitivity between the HSV-1 enzyme and other enzymes. Increasing the concentration of either the DNA template or the enzyme in the reaction mixture did not bring about a significant change in the extent of inhibition. Preincubation of the inhibitor with the enzyme was not necessary for inhibition. Studies on time course of inhibition revealed that the compound is inhibitory even after the initiation of DNA synthesis. These studies indicate that the ability of BVdUTP to preferentially inhibit the HSV-1 DNA polymerase may contribute towards its selective inhibition of the viral DNA replication in infected cells.
Redundant Backscattering Modulation from UHF Passive RFID Tags (2013)

International audience
Cryogenic magnetic properties of iron garnets diluted with Al-In and Ca-V-In combinations (2001)

Investigations of magnetic dilution in Y/sub 3/Fe/sub 5/O/sub 12/ (YIG) indicate that magnetic and dielectric parameters suitable for microwave applications can be obtained at cryogenic temperatures. For simultaneous dilutions of 35% into the octahedral (a) sublattice and 27% into the tetrahedral (d) sublattice, there were no apparent degrading effects on the dielectric loss tangents. At low temperatures, a-site substitutions of In caused the expected large increases in saturation magnetization and corresponding decreases in Curie temperatures. Moreover, measurements of hysteresis loops showed that coercive fields /spl sim/0.5 Oe could be obtained at T<77 K despite the likely sharp rise in anisotropy. Dilution by In also lowered anisotropy fields by a factor greater than five from that of Y/sub 3/(Fe,Al)/sub 5/O/sub 12/ in both {Y,Ca}/sub 3/(Fe,V,In)/sub 5/O/sub 12/ and Y/sub 3/(Fe,Al,In)/sub 5/O/sub 12/ compounds.
The antigenicity and cholesteroid nature of mycolic acids determined by recombinant chicken antibodies (2018)

Mycolic acids (MA) are major, species-specific lipid components of Mycobacteria and related genera. In Mycobacterium tuberculosis, it is made up of alpha-, methoxy- and keto-MA, each with specific biological functions and conformational characteristics. Antibodies in tuberculosis (TB) patient sera respond differently towards the three MA classes and were reported to cross-react with cholesterol. To understand the antigenicity and cholesterol cross-reactivity of MA, we generated three different chicken -derived phage-displayed single-chain variable fragments (scFv) that reacted similarly towards the natural mixture of MA, but the first recognized all three classes of chemically synthetic MAs, the second only the two oxygenated types of MAs and the third only methoxy MA. The cholesterol cross-reactivity was investigated after grafting each of the three scFv types onto two configurations of constant chain domains-CH1-4 and CH2-4. Weak but significant cross-reactivity with cholesterol was found only with CH2-4 versions, notably those two that were also able to recognize the trans-keto MA. The cholesteroid nature of mycobacterial mycolic acids therefore seems to be determined by the trans-keto MA subclass. The significantly weaker binding to cholesterol in comparison to MA confirms the potential TB diagnostic application of these antibodies.
Results from solvophobic theory applied to methylene selectivity in reversed-phase HPLC (2018)

A significant amount of work has been previously dedicated to the understanding of methylene selectivity parameter. The conventional theory applied for this understanding was mostly based on the assumption that the difference in the Gibbs free energy of transfer from the mobile phase to the stationary phase is a constant for any two compounds in a homologous series that differ by a CH2 group. In the present study, it is shown based on solvophobic theory that this assumption is indeed correct, but it provides a theoretical justification for it. Exemplification of the results of theory was obtained using the values for methylene selectivity (α(CH2)) measured experimentally for seven different C18 chromatographic columns including two core–shell columns and using water and either methanol or acetonitrile as an organic component. Four different homologous series of compounds were used for evaluation. The study proved the theoretical prediction that the values for α(CH2) obtained using different homologous series of compounds are only slightly different from those obtained using the toluene–butylbenzene series. Even using different homologous series, the same type of information regarding the columns comparison, and the changes in log α(CH2) with the solvent composition was obtained.
Connecting the dots with related notes (2009)

During visual analysis, users must often connect insights discovered at various points of time to understand implicit relations within their analysis. This process is often called "connecting the dots." In this paper, we describe an algorithm to recommend related notes from a user's past analysis based on his/her current line of inquiry during an interactive visual exploration process. We have implemented the related notes algorithm in HARVEST, a web based visual analytic system.
Immunologic effects of prophylactic donor lymphocyte infusion after allogeneic marrow transplantation for multiple myeloma (2002)

Reconstitution of T-cell immunity after bone marrow transplantation (BMT) is often delayed, resulting in a prolonged period of immunodeficiency. Donor lymphocyte infusion (DLI) has been used to enhance graft-versus-leukemia activity after BMT, but the effects of DLI on immune reconstitution have not been established. We studied 9 patients with multiple myeloma who received myeloablative therapy and T-cell-depleted allogeneic BMT followed 6 months later by infusion of lymphocytes from the same donor. DLI consisted of 3 x 10(7) CD4(+) donor T cells per kilogram obtained after in vitro depletion of CD8(+) cells. Cell surface phenotype of peripheral lymphocytes, T-cell receptor (TCR) V beta repertoire, TCR rearrangement excision circles (TRECs), and hematopoietic chimerism were studied in the first 6 months after BMT and for 1 year after DLI. These studies were also performed in 7 patients who received similar myeloablative therapy and BMT but without DLI. Phenotypic reconstitution of T and natural killer cells was similar in both groups, but patients who received CD4(+) DLI developed increased numbers of CD20(+) B cells. TCR V beta repertoire complexity was decreased at 3 and 6 months after BMT but improved more rapidly in patients who received DLI (P =.01). CD4(+) DLI was also associated with increased numbers of TRECs in CD3(+) T cells (P <.001) and with conversion to complete donor hematopoiesis (P =.05). These results provide evidence that prophylactic infusion of CD4(+) donor lymphocytes 6 months after BMT enhances reconstitution of donor T cells and conversion to donor hematopoiesis as well as promoting antitumor immunity.
Interpretable Clustering via Multi-Polytope Machines (2022)

Clustering is a popular unsupervised learning tool often used to discover groups within a larger population such as customer segments, or patient subtypes. However, despite its use as a tool for subgroup discovery and description few state-of-the-art algorithms provide any rationale or description behind the clusters found. We propose a novel approach for interpretable clustering that both clusters data points and constructs polytopes around the discovered clusters to explain them. Our framework allows for additional constraints on the polytopes including ensuring that the hyperplanes constructing the polytope are axis-parallel or sparse with integer coefficients. We formulate the problem of constructing clusters via polytopes as a Mixed-Integer Non-Linear Program (MINLP). To solve our formulation we propose a two phase approach where we first initialize clusters and polytopes using alternating minimization, and then use coordinate descent to boost clustering performance. We benchmark our approach on a suite of synthetic and real world clustering problems, where our algorithm outperforms state of the art interpretable and non-interpretable clustering algorithms.
MIRAS Functional Test Results for the SMOS Mission (2006)

MIRAS (Microwave Imaging Radiometer with Aperture Synthesis) is the single payload on board ESA's Soil Moisture and Ocean Salinity (SMOS) second Earth Explorer Opportunity Mission. Although MIRAS is a complex 69 element L-band interferometer with full on-board calibration capability, end-to-end performance tests have been possible on a reduced but yet representative part of the instrument, built to engineering model (EM) space standards. This paper presents the most relevant results obtained during the testing of the EM model of MIRAS including explanations for any deviations from expectations, and from them, the best estimation of the achievable performance by the SMOS mission. This is the first measurement campaign of MIRAS, which shall be followed in the future by further verification tests of the full flight model when this be completed
Primary frequency regulation with Li-ion battery energy storage system: A case study for Denmark (2013)

Meeting ambitious goals of transition to distributed and environmentally-friendly renewable energy generation can be difficult to achieve without energy storage systems due to technical and economical challenges. Moreover, energy storage systems have a high potential of not only smoothing and improving the predictability of the intermittent renewables but also of providing the ancillary services in the future energy markets. However, this is currently difficult to achieve due to high prices of the energy storage systems and difficulties with accurate prediction of the energy storage systems lifetime, which introduces significant risk into the business model. This paper deals with the investigation of the lifetime of LiFePO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sub> /C battery systems when they are used to provide primary frequency regulation service. A semi-empirical lifetime model for these battery cells was developed based on the results obtained from accelerated lifetime testing. The developed Li-ion battery lifetime model is later a base for the analyses of the economic profitability of the investment in the Li-ion battery energy storage system (BESS), which delivers the primary frequency regulation service on the Danish electricity market. Moreover, in this paper a possible improvement of the Li-ion BESS energy management strategy is shown, which allows for obtaining the higher NPV.
Microfluidic emulsification with a surfactant and a particulate emulsifier: Dripping-to-jetting transitions and drop size scaling (2022)

We report an experimental investigation on the effect of emulsifiers on the dripping-to-jetting transition and droplet size scaling in a co-flow microcapillary device. The emulsifiers studied include an oil-soluble surfactant Span 80, a water-soluble nanosheet, and their combination. We characterize the dispersed phase behaviors in the state space comprising the Weber number of the inner phase Wein and the capillary number of the outer phase Caout. Results show that the dripping-to-jetting (D-J) transition occurs at Wein ≈ O(1) for the no-emulsifier case and Wein ≈ 65 for the Span 80 system. In the case of the nanosheet, the D-J transition is dependent on concentration with Wein ≈ 0.08–5.6. For the combination system, depending on the nanosheet concentration, the critical Wein varies from 0.3 to 21. We explain that these emulsifier-dependent critical Wein result in terms of additional interfacial stresses arising due to surfactant transport and adsorbed nanosheets. Combining droplet size data from this study and literature, we find that in the dripping regime, the droplet diameter decreases with increasing Caout, yielding a scaling exponent of ≈−0.33 and a pre-factor that could be dependent on the type of emulsifier. In the jetting regime, the droplet diameter increases with the flow rate ratio of the two phases, with a scaling exponent of ≈ 0.37 that is independent of the type of emulsifier. The results from this work help to better understand the influence of surfactants and particulate emulsifiers in microfluidic emulsification.
Role of Intracellular Ca2+Levels in the Regulation of CD11a/CD18 Mediated Cell Adhesion (1993)

CD2, CD3, and MHC class II have been demonstrated to stimulate lymphocyte function-associated antigen (LFA)-1 (CD11a/CD18) mediated adhesion (Van Kooyk et al., 1989, Dustin and Springer, 1989; Mourad et al., 1990). Activation of LFA-1 may be mediated by different intracellular signals generated from these stimuli, since previous findings suggest that triggering of LFA-1 through CD2 or CD3 leads to sustained and transient cell adhesion respectively (Van Kooyk et al., 1989). We investigated the role of intracellular signalling pathways in more detail. The results demonstrate that, in addition to protein tyrosine kinase (PTK) and protein kinase C (PKC) mediated signalling, increase in cytosolic-free calcium ([Ca2+]i) levels play a major role in the activation of LFA-1. The calcium ionophore Ionomycin, which increases [Ca2+]i is capable of directly activating LFA-1. Furthermore, activation of LFA-1 by triggering through CD2, CD3 or MHC class II is associated with an increase in [Ca2+]i levels, with kinetics that directly correlate with cell adhesiveness. Moreover, entry of extracellular Ca2+ via Ca-channels is involved in both the CD3- and MHC class II, as well as part of the CD2 induced LFA-1 activation. Depletion of intracellular calcium results in unresponsiveness of LFA-1 to these stimuli, further demonstrating a regulatory role for [Ca2+]i in LFA-1 mediated adhesion.
Magnetic Resonance Imaging of PSMA-Positive Prostate Cancer by a Targeted and Activatable Gd(III) MR Contrast Agent (2021)

Prostate-specific membrane antigen (PSMA) is a transmembrane protein that is highly expressed in aggressive prostate cancer (PCa) and has been extensively studied as a PCa diagnostic imaging biomarker. Multiple imaging modalities have exploited PSMA as a biomarker including magnetic resonance (MR), Optical, and PET imaging. Of all the imaging MR imaging provides the most detailed information, concurrently providing anatomical, functional, and potentially molecular information. However, the lower sensitivity of MR requires development of molecular MR contrast agents that provides high signal-to-noise ratios. Herein, we report the first targeted and activatable Gd(III)-based MR contrast agents prostate cancer probe 1 and 2 (PCP-1 and -2). We successfully used PCP-2 to differentiate between PSMA+ and PSMA- prostate cancer cells with both in vitro fluorescence imaging and in vivo MR imaging. The in vivo MR imaging results were further supported by ex vivo fluorescence imaging studies, showcasing the unique bimodal feature of PCP-2. Furthermore, PCP-2 highlights a unique molecular MR probe design strategy that improved the sensitivity of traditional biomarker-targeted MR imaging, addressing a critical unmet need in molecular MR imaging field. This work represents the first example of a targeted and activatable MR contrast agent that can be systemically administered <i>in vivo</i> to highlight PSMA+ prostate tumors, paving the way for the clinical translation of MR PSMA imaging.
Computer Simulations of Continuous 3-D Printing (2017)

3-D printing is a revolutionary manufacturing technique which makes it possible to fabricate objects of any shape and size that are hard to reproduce by traditional methods. We develop a coarse-grained molecular dynamics simulation approach to model the continuous liquid interface production (CLIP) 3-D printing technique. This technique utilizes a continuous polymerization and cross-linking of the liquid monomeric precursor by the UV light within a thin layer while pulling the cross-linked polymeric object out of a pool of monomers. Simulations show that the quality of the shape of the 3-D printed objects is determined by a fine interplay between elastic, capillary, and friction forces. Using simulation results, we identify the source of the object shape deformations and develop a set of rules for calibration of the parameters to meet the accuracy requirements. Comparison between different continuous 3-D printing setups shows that proposed modifications of the printing process could improve quality and accuracy of the printed parts.
Modular Polynomials for Genus 2 (2009)

Modular polynomials are an important tool in many algorithms involving elliptic curves. In this article we investigate their generalization to the genus 2 case following pioneering work by Gaudry and Dupont. We prove various properties of these genus 2 modular polynomials and give an improved way to explicitly compute them.