gebhart/patrepeval huggingface dataset:
Bifunctional Fe3O4–Ag Heterodimer Nanoparticles for Two‐Photon Fluorescence Imaging and Magnetic Manipulation (2008)

Fe3O4–Ag heterodimer nanocomposites of tunable sizes are synthesized with high yield under mild conditions, without the loss of high magnetic moment. A ligand-exchange scheme is devised utilizing the bifunctionality of the heterodimer system to render the nanocomposite soluble in aqueous solutions. Cells labeled with the heterodimer nanoparticles can be magnetically manipulated and imaged with two-photon fluorescence microscopy. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
12-Gene Recurrence Score Assay Stratifies the Recurrence Risk in Stage II/III Colon Cancer With Surgery Alone: The SUNRISE Study (2016)

To our knowledge, this study provides the first validation of the 12-gene Recurrence Score assay in stage III colon cancer without chemotherapy and showed the heterogeneity of recurrence risks in stage III as well as in stage II colon cancer.
Design and implementation of adoptive therapy with chimeric antigen receptor‐modified T cells (2013)

A major advance in adoptive T-cell therapy (ACT) is the ability to efficiently endow patient's T cells with reactivity for tumor antigens through the stable or regulated introduction of genes that encode high affinity tumor-targeting T-cell receptors (TCRs) or synthetic chimeric antigen receptors (CARs). Case reports and small series of patients treated with TCR- or CAR-modified T cells have shown durable responses in a subset of patients, particularly with B-cell malignancies treated with T cells modified to express a CAR that targets the CD19 molecule. However, many patients do not respond to therapy and serious on and off-target toxicities have been observed with TCR- and CAR-modified T cells. Thus, challenges remain to make ACT with gene-modified T cells a reproducibly effective and safe therapy and to expand the breadth of patients that can be treated to include those with common epithelial malignancies. This review discusses research topics in our laboratories that focus on the design and implementation of ACT with CAR-modified T cells. These include cell intrinsic properties of distinct T-cell subsets that may facilitate preparing therapeutic T-cell products of defined composition for reproducible efficacy and safety, the design of tumor targeting receptors that optimize signaling of T-cell effector functions and facilitate tracking of migration of CAR-modified T cells in vivo, and novel CAR designs that have alternative ligand binding domains or confer regulated function and/or survival of transduced T cells.
Remote Ischemic Conditioning: Evolution of the Concept, Mechanisms, and Clinical Application (2009)

Remote ischemic conditioning is a novel concept of protection against ischemia-reperfusion injury. Brief controlled episodes of intermittent ischemia of the arm or leg may confer a powerful systemic protection against prolonged ischemia in a distant organ. This conditioning phenomenon is clinically applicable and can be performed before--preconditioning, during--perconditioning, or after--postconditioning prolonged distant organ ischemia. The remote ischemic conditioning may have an immense impact on clinical practice in the near future.
The Effect of Lidocaine on the Globule Size Distribution of Propofol Emulsions (2003)

In this study, we sought to determine the globule size distribution of a propofol/lidocaine mixture as a function of lidocaine concentration and time elapsed after mixing in a standard formulation of propofol emulsion (Diprivan) and in a new formulation containing L-lysine to improve stability. The globule size was measured with a laser diffraction technique. The median diameter of the globule size in 20 mL of Diprivan immediately after the addition of 0, 10, 20, 30, 40, and 50 mg of lidocaine was similar to that of chylomicrons, ranging from 0.28 +/- 0.01 micro m to 0.30 +/- 0.02 micro m, over the whole range of lidocaine concentration. However, the maximum diameter increased slightly (from 0.97 +/- 0.01 micro m to 2.90 +/- 0.07 micro m) as the concentration of lidocaine increased. At 6 h after adding lidocaine, the maximum globule size had increased slightly (to 2.98 +/- 0.04 micro m) with 20 mg of lidocaine and increased considerably (to 51.76 +/- 0.62 micro m) when 30 mg of lidocaine was added. At 2 h after the addition of 50 mg of lidocaine, the maximum globule diameter had increased to 52.2 +/- 1.92 micro m. The maximum globule diameter in the propofol emulsion to which L-lysine was added as a stabilizer did not exceed 3.0 micro m even when the largest amount of lidocaine was added. This study demonstrated that when 30 mg of lidocaine was added to 20 mL of Diprivan and the solution was left for a period of time, the globule size increased. Its increase was minimized by the addition of L-lysine to the propofol emulsion.
c-Src Regulates the Interaction between Connexin-43 and ZO-1 in Cardiac Myocytes (2001)

Connexin-43 is known to interact directly with ZO-1 in cardiac myocytes, but little is known about the role of ZO-1 in connexin-43 function. In cardiac myocytes, constitutively active c-Src inhibited endogenous interaction between connexin-43 and ZO-1 by binding to connexin-43. In HEK293 cells, by contrast, a connexin-43 mutant lacking the Src phosphorylation site (Tyr265) interacted with ZO-1 despite cotransfection of a constitutively active c-Src. Moreover, in vitro binding assays using recombinant proteins synthesized from regions of connexin-43 and ZO-1 showed that the tyrosine-phosphorylated C terminus of connexin-43 interacts with the c-Src SH2 domain in parallel with the loss of its interaction with ZO-1. Cell surface biotinylation revealed that, by phosphorylating Tyr265, constitutively active c-Src reduces total and cell surface connexin-43 down to the levels seen in cells expressing a mutant connexin-43 lacking the ZO-1 binding domain. Finally, electrophysiological analysis showed that both the tyrosine phosphorylation site and the ZO-1-binding domain of connexin-43 were involved in the regulation of gap junctional function. We therefore conclude that c-Src regulates the interaction between connexin-43 and ZO-1 through tyrosine phosphorylation and through the binding of its SH2 domain to connexin-43.
Mutant CAG repeats of Huntingtin transcript fold into hairpins, form nuclear foci and are targets for RNA interference (2011)

The CAG repeat expansions that occur in translated regions of specific genes can cause human genetic disorders known as polyglutamine (poly-Q)-triggered diseases. Huntington's disease and spinobulbar muscular atrophy (SBMA) are examples of these diseases in which underlying mutations are localized near other trinucleotide repeats in the huntingtin (HTT) and androgen receptor (AR) genes, respectively. Mutant proteins that contain expanded polyglutamine tracts are well-known triggers of pathogenesis in poly-Q diseases, but a toxic role for mutant transcripts has also been proposed. To gain insight into the structural features of complex triplet repeats of HTT and AR transcripts, we determined their structures in vitro and showed the contribution of neighboring repeats to CAG repeat hairpin formation. We also demonstrated that the expanded transcript is retained in the nucleus of human HD fibroblasts and is colocalized with the MBNL1 protein. This suggests that the CAG repeats in the HTT mRNA adopt ds-like RNA conformations in vivo. The intracellular structure of the CAG repeat region of mutant HTT transcripts was not sufficiently stable to be protected from cleavage by an siRNA targeting the repeats and the silencing efficiency was higher for the mutant transcript than for its normal counterpart.
Comparison of labor induction with misoprostol vs. oxytocin/prostaglandin E2 in term pregnancy (1996)

Misoprostol is significantly more effective for labor induction than oxytocin/PGE2 gel. The maternal intrapartum and neonatal outcomes were the same for both induction regimens. From a clinical and perinatal perspective, misoprostol is an acceptable choice for labor induction.
Optimization of chemical shift selective suppression of fat (1998)

Strategies to optimize flip angles for chemical shift selective fat suppression are discussed. Mathematical models for fat suppression in spoiled gradient recalled acquisition, spin echo, and RARE, which incorporate steady state conditions and multiple spectral components of fat, are developed. The optimal suppression flip angle is found to be larger than that determined with a single fat component model by more than 10 degrees due to contributions from unflipped components such as olefinic and glycerol protons that lie outside the suppression band.
Novel biocompatible cholinium-based ionic liquids—toxicity and biodegradability (2010)

The synthesis, characterisation and toxicological assessment of a new group of environmentally friendly ionic liquids are presented. Focussing on the toxic effect of the anion, the ionic liquids were designed by combining the benign cholinium cation, [NMe3(CH2CH2OH)]+, with a range of linear alkanoate anions ([CnH2n+1CO2]−, n = 1-9), as well as two structural isomers (n = 3 or 4). The toxicity of these ionic liquids was evaluated using filamentous fungi as model eukaryotic organisms. Surprisingly, most of the tested species showed active growth in media containing extremely high ionic liquid concentrations, up to molar ranges in some cases. The biodegradability of these ionic liquids was assessed, and new biotechnological applications for them are proposed, e.g. as solvents for biopolymers. This study leads to the better understanding of the anion influence on the ionic liquid toxicity, but its core is the recognition that conscious design of ionic liquids can be used to deliver truly biocompatible salts without adversely affecting one of the most striking of their properties—their outstanding solvent ability.
Pre-existing AAV Capsid-specific CD8+ T Cells are Unable to Eliminate AAV-transduced Hepatocytes (2007)

The goal of these studies was to test whether adeno-associated virus (AAV) capsid-specific CD8(+) T cells cause loss of hepatic AAV-mediated gene expression in experimental animals. Mice immunized with adenoviral vectors expressing AAV capsid or with AAV vectors developed CD8(+) T cells in blood, lymphatic tissues, and liver to epitopes shared between AAV2 and AAV8, and serotype-specific neutralizing antibodies. At the height of the T cells' effector phase, mice were infused with a heterologous AAV vector expressing human factor IX under a hepatocyte-specific promoter. Despite the presence of lytic CD8(+) T cells in the liver, hepatic Factor IX expression was sustained and comparable in AAV-preimmune and naïve animals. These results suggest that, in mice, pre-existing CD8(+) T cells to AAV capsid do not affect the longevity of AAV-mediated hepatic gene transfer. These results are in contrast to the outcome of a recent gene therapy trial of hemophilia B patients who were treated by hepatic gene transfer of AAV2 vectors expressing Factor IX. The loss of Factor IX expression, accompanied by a rise in liver enzymes and detectable frequencies of circulating AAV capsid-specific T cells, suggested T-cell-mediated destruction of transduced hepatocytes following reactivation of AAV-specific T cells upon AAV transfer.
Dual Role for 1,2,4,5-Tetrazines in Polymer Networks: Combining Diels–Alder Reactions and Metal Coordination To Generate Functional Supramolecular Gels (2015)

The inverse-electron demand Diels-Alder cycloaddition of tetrazines and olefins has emerged as a powerful coupling reaction for the formation of polymer gels with diverse applications. Tetrazines are also excellent ligands for metal atoms. For example, 3,6-bis(2-pyridyl)-1,2,4,5-tetrazines (bptz) have been used to generate discrete supramolecular M<sub><i>x</i></sub>bptz<sub><i>y</i></sub> metal clusters and extended 2D grid structures. We reasoned that both the Diels-Alder and the metal-coordination modes of reactivity of bptz derivatives could be leveraged in the context of hydrogel design to yield novel hybrid materials. Here we report on the formation of supramolecular hydrogels via substoichiometric Diels-Alder functionalization of bptz ligands bound to the ends of poly(ethylene glycol) (PEG) chains followed by metal-coordination-induced gelation in the presence of Ni<sup>2+</sup> and Fe<sup>2+</sup> salts. Our results show that simple bptz-based polymers are versatile precursors to a diverse range of novel functional materials.
Theoretically informed coarse grain simulations of polymeric systems (2009)

A Monte Carlo formalism for the study of polymeric melts is described. The model is particle-based, but the interaction is derived from a local density functional that appears in the field-based model. The method enables Monte Carlo simulations in the nVT, nPT, semigrandcanonical and Gibbs ensembles, and direct calculation of free energies. The approach is illustrated in the context of two examples. In the first, we consider the phase separation of a binary homopolymer blend and present results for the phase diagram and the critical point. In the second, we address the microphase separation of a symmetric diblock copolymer, examine the distribution of local stresses in lamellae, and determine the order-disorder transition temperature.
The use of HLA class I tetramers to design a vaccination strategy for melanoma patients (2002)

Progress in human tumor immunology has recently been accelerated by new assays for antigen-specific cytotoxic T lymphocytes (CTLs). We have used tetrameric MHC class I complexes (tetramers) to study melanoma-specific CTLs both in vivo and in vitro, and have utilized the results to optimize vaccination strategies for patients. Tetramers have provided some of the best evidence to date that CTL responses against melanoma antigens arise spontaneously in patients. However, CTL responses to common (nonmutated) melanoma epitopes are generally weak or localized, and occur mostly in advanced metastatic disease, hence justifying early immunotherapeutic approaches. These observations led us to design a polyvalent vaccine construct for early administration to melanoma patients at high risk of progression. To compare possible vaccination protocols, we encoded this construct in several different vectors, and developed novel tetramers to track responses to the human melanoma epitopes in transgenic mice. Priming and boosting with the same poly-epitope construct encoded in heterologous vectors led to the expansion of CTLs with a single dominant specificity. Separating the antigens for independent presentation by antigen-presenting cells reversed the effect of immunodominance and induced a powerful polyvalent CTL response. These results provide important pointers for future vaccination trials, and tetramers will form an important tool in the immunomonitoring of these clinical studies.
View maintenance in a warehousing environment (1995)

A warehouse is a repository of integrated information drawn from remote data sources. Since a warehouse effectively implements materialized views, we must maintain the views as the data sources are updated. This view maintenance problem differs from the traditional one in that the view definition and the base data are now decoupled. We show that this decoupling can result in anomalies if traditional algorithms are applied. We introduce a new algorithm, ECA (for Eager Compensating Algorithm), that eliminates the anomalies. ECA is based on previous incremental view maintenance algorithms, but extra compensating queries are used to eliminate anomalies. We also introduce two streamlined versions of ECA for special cases of views and updates, and we present an initial performance study that compares ECA to a view recomputation algorithm in terms of messages transmitted, data transferred, and I/O costs.
Synthesis of crafted optical pulses by time domain modulation in a fiber-grating compressor (1988)

We report a method for direct generation of voltage programmable, arbitrarily shaped laser pulses of subpicosecond duration and roughly 100 fs resolution. A waveguide intensity modulator was fabricated and incorporated into a fiber-grating pulse compressor to shape temporally the chirped pulse before compression. Optical pulses with sin(x)/x and square envelopes are synthesized to demonstrate the technique.
Surfactant Control of Phases in the Synthesis of Mesoporous Silica-Based Materials (1996)

The low-temperature formation of liquid-crystal-like arrays made up of molecular complexes formed between molecular inorganic species and amphiphilic organic molecules is a convenient approach for the synthesis of mesostructure materials. This paper examines how the molecular shapes of covalent organosilanes, quaternary ammonium surfactants, and mixed surfactants in various reaction conditions can be used to synthesize silica-based mesophase configurations, MCM-41 (2d hexagonal, p6m), MCM-48 (cubic Ia3d), MCM-50 (lamellar), SBA-1 (cubic Pm3n), SBA-2 (3d hexagonal P63/mmc), and SBA-3 (hexagonal p6m from acidic synthesis media). The structural function of surfactants in mesophase formation can to a first approximation be related to that of classical surfactants in water or other solvents with parallel roles for organic additives. The effective surfactant ion pair packing parameter, g = V/a0l, remains a useful molecular structure-directing index to characterize the geometry of the mesophase products, and phase transitions may be viewed as a variation of g in the liquid-crystal-like solid phase. Solvent and cosolvent structure direction can be effectively used by varying polarity, hydrophobic/hydrophilic properties and functionalizing the surfactant molecule, for example with hydroxy group or variable charge. Surfactants and synthesis conditions can be chosen and controlled to obtain predicted silica-based mesophase products. A room-temperature synthesis of the bicontinuous cubic phase, MCM-48, is presented. A low-temperature (100 °C) and low-pH (7−10) treatment approach that can be used to give MCM-41 with high-quality, large pores (up to 60 Å), and pore volumes as large as 1.6 cm3/g is described.
Structural and Initial Biological Analysis of Synthetic Arylomycin A2 (2007)

The growing threat of untreatable bacterial infections has refocused efforts to identify new antibiotics, especially those acting by novel mechanisms. While the inhibition of pathogen proteases has proven to be a successful strategy for drug development, such inhibitors are often limited by toxicity due to their promiscuous inhibition of homologous and mechanistically related human enzymes. Unlike many protease inhibitors, inhibitors of the essential type I bacterial signal peptidase (SPase) may be more specific and thus less toxic due to the enzyme's unique structure and catalytic mechanism. Recently, the arylomycins and related lipoglycopeptide natural products were isolated and shown to inhibit SPase. The core structure of the arylomycins and lipoglycopeptides consists of a biaryl-linked, N-methylated peptide macrocycle attached to a lipopeptide tail, and in the case of the lipoglycopeptides, a deoxymannose moiety. Herein, we report the first total synthesis of a member of this group of antibiotics, arylomycin A2. The synthesis relies on Suzuki-Miyaura-mediated biaryl coupling, which model studies suggested would be more efficient than a lactamization-based route. Biological studies demonstrate that these compounds are promising antibiotics, especially against Gram-positive pathogens, with activity against S. epidermidis that equals that of the currently prescribed antibiotics. Structural and biological studies suggest that both N-methylation and lipidation may contribute to antibiotic activity, whereas glycosylation appears to be generally less critical. Thus, these studies help identify the determinants of the biological activity of arylomycin A2 and should aid in the design of analogs to further explore and develop this novel class of antibiotic.
Glow discharge plasma treatment of polyethylene tubing with tetraglyme results in ultralow fibrinogen adsorption and greatly reduced platelet adhesion (2006)

Previous studies from our lab have shown that fibrinogen adsorption (Gamma(Fg)) must be reduced below 10 ng/cm(2) to significantly reduce platelet adhesion, and that radio frequency glow discharge (RFGD) treatment of polymeric films in the presence of tetraethylene glycol dimethyl ether (tetraglyme) can reduce Gamma(Fg) to the desired ultralow value. In this report, the effects of RFGD coatings of tetraglyme on the lumenal surface of PE tubing on Gamma(Fg) and on blood interactions both in vitro and ex vivo are described. Gamma(Fg) on the tetraglyme-coated PE tubing was reduced to the desired ultralow level (<10 ng/cm(2)), and we also observed a significant decrease in adsorption of von Willebrand's factor. In vitro platelet adhesion from washed platelet suspensions, platelet rich plasma, or whole blood to tetraglyme-coated PE tubing was decreased compared to PE, polyurethane, or silicone rubber tubes. In addition, thrombin generation by platelets adherent to tetraglyme-coated PE was also much less than by platelets adherent to PE. When inserted in an ex vivo carotid artery-carotid artery shunt in sheep, the RFGD tetraglyme-coated PE exhibited a very low number of adherent platelets compared to heparin-coated, chromic acid-etched, or plain PE. The RFGD tetraglyme-coated PE tubes exhibited high protein and platelet resistance in vitro, and high platelet resistance ex vivo. The improved hemocompatibility is attributed to the unique chemical structure of RFGD tetraglyme that makes it highly protein resistant.
Cost Allocation in Power Grids (2012)

We consider a set of agents, each of them able to produce and demand a
service, like power. Agents can send and receive power through a tree. This tree
has associated a cost (the maintenance cost, for instance) that should be paid by
the agents. In this paper we propose, and characterize axiomatically, two rules
for sharing the cost of the tree.
One step assembly of multiple DNA fragments with a designed order and orientation in Bacillus subtilis plasmid (2003)

A universal method to reconstitute sets of genes was developed. Owing to the intrinsic nature of the plasmid establishment mechanism in Bacillus subtilis, the assembly of five antibiotic resistance genes with a defined order and orientation was achieved. These five fragments and the plasmid have three-base protruding sequences at both ends. The protruding sequences are designed so that each fragment is ligated once in a row according to the pairing. Ligation by T4 DNA ligase in the presence of 150 mM NaCl and 10% polyethylene glycol at 37 degrees C yielded high molecular tandem repeat linear form DNA. This multimeric form of DNA was preferentially used for plasmid establishment in B.subtilis. The method, referred to as Ordered Gene Assembly in B.subtilis (OGAB), allows for the design of multiple fragments with very high efficiency and great fidelity.