gebhart/patrepeval huggingface dataset:
Sleeping Beauty (SB) Transposon Mediated Umbilical Cord Blood (UCB) T Cell Therapy for Refractory Acute Lymphoblastic Leukemia (ALL). (2006)

Abstract UCB is a promising alternate source of hematopoietic stem cell transplantation due to a readily available graft and low risk of GVHD. However, the incidence of ALL relapse in children is relatively high (40% for high risk ALL). To test whether UCB T cells can be genetically modified as GVL effector cells, the SB transposon system was used as a delivery vehicle since we have shown that this system can mediate genomic integration and long-term reporter gene expression in 5–20% of human primary T cells without prior activation, thus reducing duration of in vitro culture and enhancing T cell function (Huang et al., Blood. 2006, 107:483). A SB bidirectional transposon was constructed to co-express a single chain chimeric antigen receptor for CD19, commonly expressed in B-ALL, and human CD20, a marker for in vitro selection of transfected T cells and a “suicide” gene for in vivo elimination by Rituxan when necessary. In preclinical studies, UCB and peripheral blood (PB) mononuclear cells were nucleofected with the bidirectional SB transposon and a SB10 transposase-expressing plasmid, and then activated and expanded by anti-CD3/CD28 beads in culture. Flow cytometric analyses confirmed the stable dual gene expression in both transfected T cell types. After sorting for the dual gene expression, engineered T cells demonstrated specific cytoxicity against CD19+ leukemia and lymphoma cell lines but not CD19− myeloid leukemia and multiple myeloma cells. Furthermore, SB engineered T cell killing was found to be CD19-specific as evidenced by killing K562 cells stably expressing CD19 but not K562 and K562 cells stably expressing eGFP. We also demonstrated that the unsorted PB T cells killed CD19+ target cells as effectively as the sorted PB T cells, suggesting that transfected T cells can be immediately infused into patients without selection and extended in vitro culture. While the mechanisms responsible for anti-leukemia cytolysis are under investigation, it is clear that both engineered CD4 and CD8 PB T cells and CD8 UCB T cells, but not engineered CD4 UCB T cells, killed CD19+ target cells. In vivo experiments are in progress to determine efficacy of CD19+ leukemia cell reduction by the engineered human T cells and the efficiency of Rituxan-mediated elimination of adoptively transferred T cells using a bioluminescent imaging technique. We conclude that the SB transposon-engineered UCB and PB T cells can stably express the therapeutic genes and mount potent anti-leukemia and lymphoma responses in vitro. Safety and therapeutic potential of engineered UCB T cells will be tested in the treatment of high risk CD19+ ALL as a strategy for reducing risk of relapse without the risk of increased acute GVHD. In addition, our approach is novel (transposon-based), simple (naked DNA), efficient (no prior T cell activation and less immunogenic), stable (integrating), and probably safe (random integration) compared to retroviral vectors and conventional plasmids.
Light manipulation with plasmonic nanoantennas (2004)

We focus on the optical response of metallic nanowires and nanowire composites. Because nanowires and their composites can act as antennas, we can use the terms "nanoantenna" and "nanowire" interchangeably. We explore the electromagnetic properties of nanostructured plasmonic antennas and show that they can be effectively used for light nano-confinement, field enhancement, and allow one to achieve left-handed response from the nanoantenna composite.
Inhibition of Peptidylglycine .alpha.-Amidating Monooxygenase by N-Substituted Homocysteine Analogs (1994)

C-terminal amidation is a posttranslational modification found in many neuropeptides. Peptidylglycine alpha-amidating monooxygenase (PAM) catalyzes the synthesis of the biologically essential C-terminal amide from a glycine-extended precursor peptide. Reported herein are the first potent inhibitors of PAM. Dipeptides containing a C-terminal homocysteine and an N-acylated hydrophobic amino acid were found to inhibit PAM with IC50s in the low nanomolar range. Inhibition potency was dependent on both the carboxylate and the thiolate functionalities of the homocysteine and on the hydrophobic groups of the second amino acid. The thiolate was postulated to produce high binding affinities through coordination with the active-site copper. The compound series also exhibited potent inhibition of PAM in rat dorsal root ganglion cells as demonstrated by a dose-dependent increase in the substance P-Gly/substance P ratio. These results indicate that the compounds have sufficient potency and intracellular bioavailability to aid future studies focused on neuropeptide function and the contributions of neuropeptides to various disease processes.
The Periodic Technique for Measuring Convective Transport and Flow Friction Characteristics of Catalytic Reactors (1997)

&lt;div class="htmlview paragraph"&gt;Consistent optimization of low emissions catalyst systems will require appropriate use of alternative substrate geometries. Fundamental heat transfer, mass transfer and friction characteristics provide a solid foundation for evaluating the benefits of these geometries. The purpose of this report is to validate a bench test, based on a previously reported technique, for measuring the fundamental characteristics of catalyst substrates. The sample matrix is subjected to a periodically varying inlet temperature and convective transport properties, reported as Colburn factors, are found by matching the phase shift and amplitude attenuation of the inlet and outlet temperature waves in a finite difference computer program. Flow friction attributes, reported as Fanning friction factors, are found through reduction of measured pressure loss at constant flow rate. Measured Colburn factors and Fanning friction factors for uncoated square and triangular passage monoliths agree closely with theoretical values, validating the technique. Measured results for two coated substrates are also presented.&lt;/div&gt;
Different Heparan Sulfate Proteoglycans Serve asCellular Receptors for HumanPapillomaviruses (2003)

Papillomaviruses replicate in stratified epithelia of skin and mucosa. Infection with certain human papillomavirus (HPV) types is the main cause of anogenital neoplasia, in particular cervical cancer. Early events of papillomavirus infectivity are poorly understood. While heparan sulfate proteoglycans (HSPGs) mediate initial binding to the cell surface, the class of proteins carrying heparan sulfates has not been defined. Here we examined two processes of papillomavirus infection, attachment of virus-like particles (VLP) to cells and infection with authentic HPV type 11 (HPV11) virions. Of the HSPGs, syndecan-1 is the major epithelial form and is strongly upregulated in wound edge keratinocytes. We employed K562 cells, which lack HSPGs except minor amounts of endogenous betaglycan, and stable clones that express cDNAs of syndecan-1, syndecan-4, or glypican-1. Binding of VLP correlated with levels of heparan sulfate on the cell surface. Parental K562 bound HPV16 VLP weakly, whereas all three K562 transfectants demonstrated enhanced binding, with the highest binding capacity observed for syndecan-1-transfected cells, which also expressed the most HSPG. For HPV11 infectivity assays, a high virion inoculum was required to infect K562 cells, whereas ectopic expression of syndecan-1 increased permissiveness eightfold and expression of syndecan-4 or glypican-1 fourfold. Infection of keratinocytes was eliminated by treatment with heparitinase, but not phospholipase C, further implicating the syndecan family of integral membrane proteins as receptor proteins. Human keratinocytes with a homozygous deletion of alpha6 integrin are permissive for HPV11 infection. These results indicate that several HSPGs can serve as HPV receptors and support a putative role for syndecan-1, rather than alpha6 integrin, as a primary receptor protein in natural HPV infection of keratinocytes.
Charge-Transfer Interaction and Chemical Reaction. II. Interaction of s-Triaminobenzene with Several Electron Acceptors (1970)

Abstract The charge-transfer interaction was studied for systems including s-triaminobenzene as electron donor. The formation of 1 : 1 stable outer (π,π) complexes at room temperature was observed for the systems including s-trinitrobenzene, trininitrotoluene and tetracyanobenzene as electron acceptors. From the analysis of the observed absorption intensities and peak positions of charge-transfer bands, the equilibrium constants of these complexes were determined and the ionization potential of s-triaminobenzene was estimated to be 7.3–7.4 eV. Chloranil was found to form a stable outer (π,π) complex with s-triaminobenzene only at low temperature, and to be led to a substitution reaction by raising the temperature. The spectrum of the reaction intermediate, the inner (σ) complex of s-triaminobenzene with chloranil, was observed at ∼500 mμ. A tentative reaction mechanism was proposed.
Thieno[3,2-c]chinolin-4-yl-amine - Synthese und Prüfung auf Wirksamkeit gegen Malaria (2006)

The 4-aryl derivative 3, obtained by Suzuki cross coupling of the methyl 4-bromothiophene-3-carboxylate (2) with 2-nitrophenylboronic acid cyclizes under reductive conditions pH-dependant to yield the tricyclic hydroxamic acid 4 or the lactam 5. The chlorothieno[3,4-c]quinoline 6 was formed by reaction of the lactam 5 with P,P-dichlorophenylphosphinoxide. The amines 7-14 were synthesized from the chloroimine 6. Compounds 7a,b, 8, 9, 10b, 11, 12 and 14a, b were tested for in vitro antimalarial activity using the chloroquine sensitive 3D7 and the chloroquine resistant Plasmodium falciparum strain Dd2. The highest activity were shown by 10b with IC 50 values of 130 nM and 50 nM, respectively and by 11 with IC 50 values of 190 nM and 44 nM, respectively.
Synthesis and Optimization of Fractional-Order Elements Using a Genetic Algorithm (2019)

This study proposes a new approach for the optimization of phase and magnitude responses of fractional-order capacitive and inductive elements based on the mixed integer-order genetic algorithm (GA), over a bandwidth of four-decade, and operating up to 1 GHz with a low phase error of approximately ±1°. It provides a phase optimization in the desired bandwidth with minimal branch number and avoids the use of negative component values, and any complex mathematical analysis. Standardized, IEC 60063 compliant commercially available passive component values are used; hence, no correction on passive elements is required. To the best knowledge of the authors, this approach is proposed for the first time in the literature. As validation, we present numerical simulations using MATLAB <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">®</sup> and experimental measurement results, in particular, the Foster-II and Valsa structures with five branches for precise and/or high-frequency applications. Indeed, the results demonstrate excellent performance and significant improvements over the Oustaloup approximation, the Valsa recursive algorithm, and the continued fraction expansion and the adaptability of the GA-based design with five different types of distributed RC/RL network.
Designer Nanoparticle-Liposome Hybrid Capsules for Drug Delivery (2015)

Journal Article Designer Nanoparticle-Liposome Hybrid Capsules for Drug Delivery Get access Joseph A Zasadzinski, Joseph A Zasadzinski Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota 55455 Search for other works by this author on: Oxford Academic Google Scholar Jeong Eun Shin, Jeong Eun Shin Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota 55455 Search for other works by this author on: Oxford Academic Google Scholar Natalie Forbes, Natalie Forbes Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota 55455 Search for other works by this author on: Oxford Academic Google Scholar Maria Ogunyankin Maria Ogunyankin Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota 55455 Search for other works by this author on: Oxford Academic Google Scholar Microscopy and Microanalysis, Volume 21, Issue S3, 1 August 2015, Pages 2285–2286, https://doi.org/10.1017/S1431927615012209 Published: 23 September 2015
LCMC2-Suppl_Fig_Legends from The Impact of Smoking and TP53 Mutations in Lung Adenocarcinoma Patients with Targetable Mutations—The Lung Cancer Mutation Consortium (LCMC2) (2023)

&lt;p&gt;Supplemental Figure Legends&lt;/p&gt;
Spectral and spatial mode engineering of plasmonic nanocavities: Subradiant modes and tunable Fano resonances (2009)

Plasmonic nanostructures can serve as unit cells of new types of optical metamaterials with carefully engineered optical properties. For example, hybridized plasmonic systems consisting of several metallic subunits separated by nanoscale gaps can exhibit superradient and subradient modes due to dipolar coupling between the individual units. Additionally, in nanostructures with broken symmetry, Fano resonances can arise due to the interaction of narrow dark modes with broad bright modes. We have recently identified non-concentric ring/disk cavities as a system with a highly tunable Fano resonance and exceptionally large refractive index sensitivity and localized surface plasmon resonance figure of merit [1]. Here we present an experimental demonstration of Fano resonances in two plasmonic systems: firstly a dimer/monomer slab slab structure (“dolmen”), first proposed by Zhang et al [2], and secondly for a side-by-side arrangement of a Au ring and a Au disk (ring near disk cavity, RNDC), both fabricated using e-beam lithography. We analyze the dependence of the Fano lineshapes on the polarization of the incident light, and of the strength of the feature on the separation between individual nanoscale sub-units. We further show that for significantly broad dipolar modes, multiple Fano resonances can arise. The observed Fano-type dispersive features constitute a classical analogue [3] to the well-known phenomenon of electromagnetically induced transparency (EIT).
Protein Kinase D1 Is Essential for Bone Acquisition during Pubertal Growth (2013)

Bone formation and maintenance represents the summation of the balance of local and endocrine hormonal stimuli within a complex organ. Protein kinase D (PKD) is a member of the Ca(2+)/calmodulin-dependent kinase superfamily of serine/threonine kinases and has been described as the crossroads for the bone morphogenetic protein (BMP)-IGF-I signaling axis, which plays a major role in bone formation. The current study exploits the PKD1-deficient mouse model to examine the role of PKD in vivo in the skeleton. Dual-energy x-ray absorptiometry scan analysis of male and female pubescent mice demonstrated significantly decreased bone mineral density in the whole body and femoral bone compartments of PKD1 (+/-) mice, compared with their wild-type littermates. The body weight, nasal-anal length, and percentage body fat of the mice were not significantly different from their wild-type littermates. Cultured bone marrow stromal cells from PKD1 (+/-) mice demonstrated lower alkaline phosphatase activity in early differentiating osteoblasts and decreased mineralized nodule formation in mature osteoblasts. Quantitative RT-PCR analysis of osteoblast differentiation markers and osteoclast markers exhibited lower levels of expression in PKD1 (+/-) male mice than wild type. In female mice, however, only markers of osteoblast differentiation were reduced. PKD1 (+/-) mice also demonstrated a profound reduction in mRNA expression levels of BMP type II receptor and IGF-I receptor and in BMP-7 responsiveness in vitro. Together these data suggest that in mice, PKD1 action contributes to the regulation of osteoblastogenesis by altering gene expression with gender-specific effects on osteoclastogenesis, subsequently affecting skeletal matrix acquisition during puberty.
Numerical Methods for Calculating Component Modes for Geometric Mistuning Reduced-Order Models (2021)

Abstract Geometric mistuning models formulated from a component mode synthesis methods often require the calculation of component modes, particularly constraint and fixed interface normal modes, during substructuring. For Integrally Bladed Rotors, these calculations are required for each sector. This paper proposes methods that reuse information garnered from solving the constraint modes of a single sector on the remaining sectors to reduce memory requirements and solution times. A mesh metamorphosis tool is used to ensure finite element models match geometry obtained from a 3D optical scanner. This tool also produces a common mesh pattern from sector-to-sector. This is exploited to produce common permutation matrices and symbolic factorizations of sector stiffness matrices that are proposed for reuse in solving subsequent constraint modes. Furthermore, a drop tolerance is introduced to remove small values during constraint mode calculation to reduce memory requirements. It is proposed to reuse this dropping pattern produced from a single sector on the remaining sectors. Approaches are then extended to a parallel processing scheme to propose effective matrix partitioning methods. Finally, information gathered during the constraint mode calculations are reused during the solution of the fixed interface normal modes to improve solution time. Results show reusing permutation matrices and symbolic factorizations from sector-to-sector improves solution time and introduces no error. Using a drop tolerance is shown to reduce storage requirements of a constraint mode matrix. Additionally, it is shown that reusing the same dropping pattern introduces minimal error without degradation in solution times. Similarly, reusing the information from constraint modes for calculating fixed interface normal modes greatly improves the performance in a shift-and-invert technique for solving eigenvalue problems.
Nanomaterials : synthesis, processing and characterization (2007)

In this project, three classes of polymer nanocomposites were developed and their processing-structure-property relationships were systematically studied. Polymethylmethacrylate (PMMA)/expanded graphite (EG) and PMMA/untreated graphite (UG) composites were prepared by direct solution blending of PMMA with EG and UG fillers. A four-point resistivity probe system was used to measure the electrical conductivity of the composites. With the increase of filler content, the electrical conductivity of the composites showed the transition from an insulator to a semiconductor.
A Bifunctional Pd/MgO Solid Catalyst for the One‐Pot Selective N‐Monoalkylation of Amines with Alcohols (2009)

It has been found that a bifunctional metal Pd/base (MgO) catalyst performs the selective monoalkylation of amines with alcohols. The reaction goes through a series of consecutive steps in a cascade mode that involves: 1) the abstraction of hydrogen from the alcohol that produces the metal hydride and the carbonyl compound; 2) condensation of the carbonyl with the amine to give an imine, and 3) hydrogenation of the imine with the surface hydrogen atoms from the metal hydride. Based on isotopic and spectroscopic studies and on the rate of each elementary step, a global reaction mechanism has been proposed. The controlling step of the process is the hydride transfer from the metal to the imine. By changing the crystallite size of the Pd, it is demonstrated that this is a structure-sensitive reaction, whereas the competing processes that lead to subproducts are not. On these bases, a highly selective catalyst has been obtained with Pd crystallite size below 2.5 nm in diameter. The high efficiency of the catalytic system has allowed us to extend the process to the one-pot synthesis of piperazines.
Emission and capture measurements on deep levels in InP (1983)

DLTS measurements have been made on a large number of InP samples. Eight different electron traps are observed in this material, and their emission characteristics are reported. For three of these levels, detailed capture cross section measurements were possible, leading to an accurate description of their thermodynamic properties.
ChemInform Abstract: The Influence of Oxygen Variation on the Crystal Structure and Phase Composition of the Superconductor YBa2Cu3O7‐x. (1988)

Abstract In attempts to prepare a material with an O7.00 (x = 0 in the title compound) composition, the highest oxygen content achieved by annealing in an O 2 stream at 440 °C for 24 h is 6.96 (iodometric determination).
Application of PDV towards Determination of Constituent Materials Properties (2009)

Slides presented at the 4th Annual Photonic Doppler Velocimetry (PDV) Workshop held at the University of Texas, Austin, Texas, November 5-6, 2009.
Tumorigenesis and male sterility in transgenic mice expressing a MMTV/N-ras oncogene. (1990)

Transgenic mice carrying the activated N-ras oncogene under the transcriptional control of the mouse mammary tumor virus (MMTV) long terminal repeat were produced. The transgene is expressed in a tissue distribution consistent with the fact that it is driven by the MMTV-LTR, and similarly to MMTV/H-ras constructs, its presence elicits tumors in Harderian, mammary and salivary glands. In addition it appears to compromise male reproductive function, which has not been described with the other ras transgenes. This finding is consistent with the existence of distinct physiological actions for each of the ras family members.
A Visual Language for Robot Control and Programming: A Human-Interface Study (2007)

We describe an interaction paradigm for controlling a robot using hand gestures. In particular, we are interested in the control of an underwater robot by an on-site human operator. Under this context, vision-based control is very attractive, and we propose a robot control and programming mechanism based on visual symbols. A human operator presents engineered visual targets to the robotic system, which recognizes and interprets them. This paper describes the approach and proposes a specific gesture language called "RoboChat". RoboChat allows an operator to control a robot and even express complex programming concepts, using a sequence of visually presented symbols, encoded into fiducial markers. We evaluate the efficiency and robustness of this symbolic communication scheme by comparing it to traditional gesture-based interaction involving a remote human operator
ChemInform Abstract: Solid‐Phase Synthesis of Oligosaccharides (2001)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Matching and grokking: approaches to personalized crowdsourcing (2015)

Personalization in computing helps tailor content to a person’s individual tastes. As a result, the tasks that benefit from personalization are inherently subjective. Many of the most robust approaches to personalization rely on large sets of other people’s preferences. However, existing preference data is not always available. In these cases we propose leveraging online crowds to provide on-demand personalization. We introduce and evaluate two methods for personalized crowdsourcing: taste-matching for finding crowd workers that are similar to a personalization target, and taste-grokking, where crowd workers explicitly predict the requester’s tastes. Both approaches show improvement over a non-personalized baseline, and have various benefits and drawbacks that are discussed.