gebhart/patrepeval huggingface dataset:
Role of Acetone in the Formation of Highly Dispersed Cationic Polystyrene Nanoparticles (2017)

Abstract A modified emulsion polymerisation synthesis route for preparing highly dispersed cationic polystyrene (PS) nanoparticles is reported. The combined use of 2,2′-azobis[2-(2-imidazolin- 2-yl)propane] di-hydrochloride (VA-044) as the initiator and acetone/water as the solvent medium afforded successful synthesis of cationic PS particles as small as 31 nm in diameter. A formation mechanism for the preparation of PS nanoparticles was proposed, whereby the occurrence of rapid acetone diffusion caused spontaneous rupture of emulsion droplets into smaller droplets. Additionally, acetone helped to reduce the surface tension and increase the solubility of styrene, thus inhibiting aggregation and coagulation among the particles. In contrast, VA-044 initiator could effectively regulate the stability of the PS nanoparticles including both the surface charge and size. Other reaction parameters i.e. VA-044 concentration and reaction time were examined to establish the optimum polymerisation conditions.
Long-range surface plasmon-polariton waveguide sensors with a Bragg grating in the asymmetric double-electrode structure (2009)

We propose a Bragg grating resonance sensor based on long-range surface plasmon-polaritons (LRSPP) excited on an asymmetric double-electrode waveguide structure. The proposed LRSPP waveguide sensor utilizes spectral resonance of the asymmetric double-electrode structure by adding a Bragg grating layer on the top surface of the metal slab. We have numerically estimated the bulk index resolution and thickness detection limit of a target biomolecule layer under 30 dB total propagation loss. The sub-mum fluidic channel between the two metal layers always experiences a highly confined LRSPP mode excited by end-fire coupling with optical fibers, therefore the proposed LRSPP sensor platform can be applied to a variety of integrated sensor-chip scenarios.
Combination of genetic and quantitative serological immune markers are associated with complicated Crohnʼs disease behavior (2011)

This model combining serologic and NOD2 genetic markers may provide physicians with a tool to assess the probability of patients developing a complication over the course of CD.
Subnanometer Replica Molding of Molecular Steps on Ionic Crystals (2010)

Replica molding with elastomeric polymers has been used routinely to replicate features less than 10 nm in size. Because the theoretical limit of this technique is set by polymer-surface interactions, atomic radii, and accessible volumes, replication at subnanometer length scales should be possible. Using polydimethylsiloxane to create a mold and polyurethane to form the replica, we demonstrate replication of elementary steps 3-5 Å in height that define the minimum separation between molecular layers in the lattices of the ionic crystals potassium dihydrogen phosphate and calcite. This work establishes the operation of replica molding at the molecular scale.
Bioartificial Liver Device Based on Induced Pluripotent Stem Cell-Derived (2015)

Decompensated liver disorders require liver transplantation. However, the donor organ shortage is a limiting factor. Harnessing the power of human induced pluripotent stem cell (iPSC) technology in combination with hollow fiber-based bioartificial liver (BAL) device can be beneficial to patients with liver failure. Our goal is to develop a BAL module comprised of iPSC-derived hepatocytes (iHeps) arrayed on the extracapillary space (ECS) of hollow fiber membranous capillaries that allow the flow of blood through the intracapillary space (ICS), thus mimicking the tissue microarchitecture. For the proof-of-concept in vitro study, a cartridge having semipermeable polysulfone membrane fibers was used as an artificial liver device. As a source for human liver cells, we derived metabolically active hepatocytes from iPSCs. The iHeps on microcarrier beads were loaded into the ECS of a hollow fiber bioreactor cartridge and cultured using a closed-circuit continuous flow system. The iHeps secreted human albumin, prothrombin, and apolipoprotein B into the hollow fiber ICS media, and the continuous flow system also improved maturation of iHeps. In conclusion, the iPSC-hepatocytes in the bioartificial liver device maintained the secretory function and exhibited cell maturation. The iPSC-hepatocyte BAL has the potential to be further developed as a liver support device for the treatment of decompensated liver diseases.
Recognition and processing of a new repertoire of DNA substrates by human 3-methyladenine DNA glycosylase (AAG) (2009)

The human 3-methyladenine DNA glycosylase (AAG) recognizes and excises a broad range of purines damaged by alkylation and oxidative damage, including 3-methyladenine, 7-methylguanine, hypoxanthine (Hx), and 1,N[superscript 6]-ethenoadenine (εA). The crystal structures of AAG bound to εA have provided insights into the structural basis for substrate recognition, base excision, and exclusion of normal purines and pyrimidines from its substrate recognition pocket. In this study, we explore the substrate specificity of full-length and truncated Δ80AAG on a library of oligonucleotides containing structurally diverse base modifications. Substrate binding and base excision kinetics of AAG with 13 damaged oligonucleotides were examined. We found that AAG bound to a wide variety of purine and pyrimidine lesions but excised only a few of them. Single-turnover excision kinetics showed that in addition to the well-known εA and Hx substrates, 1-methylguanine (m1G) was also excised efficiently by AAG. Thus, along with εA and ethanoadenine (EA), m1G is another substrate that is shared between AAG and the direct repair protein AlkB. In addition, we found that both the full-length and truncated AAG excised 1,N[superscript 2]-ethenoguanine (1,N[superscript 2]-εG), albeit weakly, from duplex DNA. Uracil was excised from both single- and double-stranded DNA, but only by full-length AAG, indicating that the N-terminus of AAG may influence glycosylase activity for some substrates. Although AAG has been primarily shown to act on double-stranded DNA, AAG excised both εA and Hx from single-stranded DNA, suggesting the possible significance of repair of these frequent lesions in single-stranded DNA transiently generated during replication and transcription.
TiN thin film on stainless steel for extremely high vacuum material (1995)

We have shown that titanium nitride (TiN) coating by activated reactive evaporation using the hollow cathode discharge method is a good surface treatment for stainless steel used in extremely high vacuum (XHV) applications. The TiN film blocks hydrogen diffusion because it has a much lower hydrogen permeation coefficient than stainless steel. By varying the coating and film parameters (e.g., thickness, composition, and substrate bias voltage Vb) the barrier effects on hydrogen permeation of the TiN films were evaluated using small membrane samples. The parameters were varied to optimize the properties of the TiN coating for vacuum materials. The structure of the TiN films was analyzed by an x-ray diffractometry and transmission electron microscopy to clarify the dependence of the barrier effect on the film structure. Stoichiometric TiN films with few defects were shown to have high barrier effects. To demonstrate the use of TiN coatings for XHV applications, the outgassing rates of a stainless steel chamber with and without a TiN film were measured by a modified throughput type apparatus that had a bakeable cryopump for obtaining XHV. The outgassing rates for the chambers were measured using a method which completely eliminated the outgassing contribution of the vacuum gauges. The nitrogen equivalent outgassing rates of the stainless steel chamber with and without a TiN film were 7×10−12 and 9.7×10−10 Pa m s−1, respectively.
Foreword SNAPI 2008 (2008)

The Workshop on Storage Network Architecture and Parallel I/Os (SNAPI) brings together experts from academia and industry to discuss cutting edge research on parallel and distributed data storage technologies, storage interconnects, and storage management. These topics gain importance based on the tremendous need for storage capacity and I/O performance, which have become critical factors for computing systems, generally, from enterprise systems to computational science and everything in between. As a result, disk I/O and data storage on which data reside have clearly become first class citizens in the modern information world. In addition, parallelism is now ubiquitous in computing, from multi-core processors within a single enclosure to massively parallel I/O systems that span many racks of equipment. This volume consists of nine papers that were presented at the 5th IEEE Workshop on Storage Network Architecture and Parallel I/Os, held on September 25th, 2008, in Baltimore, Maryland, USA. Three independent reviewers, ensuring high evidence of the scientific contributions, have reviewed each of the presented papers. The IEEE Mass Storage Systems Technical Committee has sponsored SNAPI. We would like to especially thank exegy, Inc. and BECS technology, Inc for additional financial support. Based on last year’s great success, IEEE SNAPI has been held together with the 25th IEEE Symposium on Massive Storage Systems and Technologies (MSST). The cooperation between MSST and affiliated workshops, like SNAPI, ensures that storage experts from all over the world are able to meet at a single event, ensuring fruitful discussions and information exchange. The organizers and the program committee want to thank all authors who have submitted papers and all external reviewers. As co-chairs of this workshop, we would like to additional thank the members of the program committee, who have made an excellent job and provided their very helpful comments in time. The names of the program committee appear later in this proceedings.
Novel AMP surface treatment for improving optical fiber strength and laser gain (Conference Presentation) (2018)

Contaminants can severely limit the efficiency, laser damage threshold, and strength of photonic crystal fiber-based lasers. Such contamination can occur due to environmental exposure during the pulling or stacking of rods and tubes or improper handling and storage of these glass components. A preform made by the “stack and draw” process is susceptible to incorporating surface contaminants into the bulk laser glass. We have adapted cleaning and handling protocols originally developed for processing large fused silica optics for the National Ignition Facility. The etch cleaning process reported here mimics the “AMP” or “Advanced Mitigation Process” developed for NIF optics that see high fluence 351nm light. In addition, all cleaning, fixturing and assembly processes used to prep a stack for pulling into a fiber are done in a Class 100 cleanroom. Glass rods (1-3mm in diameter and 10” long) are assembled into a Teflon fixture that only contacts the rods at each end. The loaded fixture receives 120kHz ultrasonic cleaning in 10% sodium hydroxide at 45C and 3% Brulin 1696 detergent at 55C. Parts are thoroughly rinsed using ultrasonicated ultrapure water and spray rinses. A 200nm etch in buffered hydrofluoric acid (6:1 BOE diluted 2:1 in DI water) is followed by additional ultasonicated (120kHz-270kHz) ultrapure water and spray rinse. Finally, the components are allowed to fully dry inside the Teflon frame. The rods are cleaned, stacked, and assembled into a fused silica tube. The preform stack is then returned to a non-cleanroom area to be pulled into fiber using standard telecom fiber-based draw tower equipment and without clean air filters around the draw area. Four fibers were made to test independently the damage threshold and the background loss, two Yb core active fibers and two silica core (F clad) fibers. One of each was cleaned with the AMP process, and one of each with a methanol wipe cleaning process. The active fiber was coated with a dual acrylate coating, first with a low-index inner coating to provide a pump cladding, and then with a relatively hard coating to protect the relatively soft primary coating. The active fibers were pumped at 980nm in a double Fresnel cavity configuration and the power increased until the fiber was damaged up to 1kW. The passive fiber background loss was measured using a standard cut-back technique. Replacing the former methanol wipe clean process with this aqueous cleaning process improved the 1060nm damage threshold of a fiber laser by >30x to above the kW level in the laboratory and reduced the background attenuation by >18x. Early indications are that the acid etching also makes the tensile strength of the fiber consistently high. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.
Extremely High Power Efficiency Solution‐Processed Orange‐Red TADF OLEDs via a Synergistic Strategy of Molecular and Device Engineering (2022)

Abstract The development of high‐performance, solution‐processed, orange‐red organic light‐emitting diodes (OLEDs) based on thermally activated delayed fluorescence (TADF) emitters is a challenging endeavor. In this study, two orange‐red TADF emitters, namely 2DMAC‐DBP‐2 t BuCz and 2SPAC‐DBP‐2 t BuCz , are developed by a novel donor–acceptor–functional‐group (D‐A‐R) molecular design strategy. This design makes the molecules highly soluble and inhibits concentration quenching of excitons, rendering the emitter suitable for use in devices with high concentration to boost their performance. The solution‐processed, orange‐red OLEDs manufactured in this study achieve a state‐of‐the‐art maximum external quantum efficiency ( EQE max ) value of 23.7% and an extremely high maximum power efficiency ( PE max ) of 48.8 lm W −1 , which is nearly twice higher than the previously reported best value (27.1 lm W −1 ). Therefore, the collaboration of molecular engineering and sophisticated device design provides a novel method for extremely low power consumption solution‐processed OLEDs.
DELAY OF GERMINATION1 ( DOG1 ) regulates both seed dormancy and flowering time through microRNA pathways (2016)

Seed germination and flowering, two critical developmental transitions in plant life cycles, are coordinately regulated by genetic and environmental factors to match plant establishment and reproduction to seasonal cues. The DELAY OF GERMINATION1 (DOG1) gene is involved in regulating seed dormancy in response to temperature and has also been associated genetically with pleiotropic flowering phenotypes across diverse Arabidopsis thaliana accessions and locations. Here we show that DOG1 can regulate seed dormancy and flowering times in lettuce (Lactuca sativa, Ls) and Arabidopsis through an influence on levels of microRNAs (miRNAs) miR156 and miR172. In lettuce, suppression of LsDOG1 expression enabled seed germination at high temperature and promoted early flowering in association with reduced miR156 and increased miR172 levels. In Arabidopsis, higher miR156 levels resulting from overexpression of the MIR156 gene enhanced seed dormancy and delayed flowering. These phenotypic effects, as well as conversion of MIR156 transcripts to miR156, were compromised in DOG1 loss-of-function mutant plants, especially in seeds. Overexpression of MIR172 reduced seed dormancy and promoted early flowering in Arabidopsis, and the effect on flowering required functional DOG1 Transcript levels of several genes associated with miRNA processing were consistently lower in dry seeds of Arabidopsis and lettuce when DOG1 was mutated or its expression was reduced; in contrast, transcript levels of these genes were elevated in a DOG1 gain-of-function mutant. Our results reveal a previously unknown linkage between two critical developmental phase transitions in the plant life cycle through a DOG1-miR156-miR172 interaction.
Processing of eukaryotic tRNA precursors: secondary structure of the precursor specific sequences affects the rate but not the accuracy of processing reactions (1982)

The primary transcriptional product of eukaryotic tRNA genes is a precursor molecule with extranucleotides at the 5' and at the 3' end. We show that the 5' and 3' sequences, uniquely present in the RNA precursor molecule do not play any role in the efficiency and accuracy of processing reactions. If, however, as a consequence of in vitro manipulation, these extranucleotides form a base-paired extension of the aminoacid acceptor stem, the rate of processing is slowed down. The rate of processing is brought back to normal in a single base-pair deletion mutant probably as a consequence of a destabilization of the base-paired extension of the aminoacid acceptor stem.
Mapping Epitopes Recognised by Autoantibodies Shows Potential for the Diagnosis of High-Grade Serous Ovarian Cancer and Monitoring Response to Therapy for This Malignancy (2021)

Autoantibodies recognising phosphorylated heat shock factor 1 (HSF1-PO4) protein are suggested as potential new diagnostic biomarkers for early-stage high-grade serous ovarian cancer (HGSOC). We predicted in silico B-cell epitopes in human and murine HSF1. Three epitope regions were synthesised as peptides. Circulating immunoglobulin A (cIgA) against the predicted peptide epitopes or HSF1-PO4 was measured using ELISA, across two small human clinical trials of HGSOC patients at diagnosis. To determine whether chemotherapy would promote changes in reactivity to either HSF1-PO4 or the HSF-1 peptide epitopes, IgA responses were further assessed in a sample of patients after a full cycle of chemotherapy. Anti-HSF1-PO4 responses correlated with antibody responses to the three selected epitope regions, regardless of phosphorylation, with substantial cross-recognition of the corresponding human and murine peptide epitope variants. Assessing reactivity to individual peptide epitopes, compared to HSF1-PO4, improved assay sensitivity. IgA responses to HSF1-PO4 further increased significantly post treatment, indicating that HSF1-PO4 is a target for immunity in response to chemotherapy. Although performed in a small cohort, these results offer potential insights into the interplay between autoimmunity and ovarian cancer and offer new peptide biomarkers for early-stage HGSOC diagnosis, to monitor responses to chemotherapy, and widely for pre-clinical HGSOC research.
Targeting Intracellular Pathogenic Bacteria with Unnatural Proline‐Rich Peptides: Coupling Antibacterial Activity with Macrophage Penetration (2013)

Das De-novo-Design nichtnatürlicher prolinreicher Peptide führt zu einem Wirkstoff gegen sowohl Gram-positive als auch Gram-negative Bakterien. Dieses Peptid löst weder bakterielle Membranen auf, noch bewirkt es eine Hämolyse; überdies ist es über längere Zeit gegen Trypsin stabil. Das leichte Eindringen in Makrophagen führt zu einer gründlichen Beseitigung pathogener Bakterien in diesen Zellen.
Charge-sign dependent solar modulation for everyone (2016)

We present a tool to compute the influence of charge-sign dependent solar modulation for cosmic ray spectra. The code is publicly available, easy to use and offers an extended view on solar modulation compared to the force-field approximation. We present some examples for proton and antiproton fluxes in the light of recent experimental data.
Iodinated Analogs of Trimetoquinol as Highly Potent and Selective β2-Adrenoceptor Ligands (1996)

A series of trimetoquinol (1, TMQ) analogs were designed and synthesized based on the lead compound 2, a diiodinated analog of trimetoquinol which exhibits improved selectivity for beta 2-versus beta 1-adrenoceptors (AR). To determine the influence of 1-benzyl substituents of trimetoquinol on beta 2-AR binding affinity and selectivity, we replaced and/or removed the 3'-, 4'-, and 5'-methoxy substituents of trimetoquinol. Replacement of the 4'-methoxy group of 2 with an amino (21c) or acetamido (15) moiety did not significantly alter beta 2-AR and thromboxane A2/prostaglandin H2 (TP) receptor affinity. Substitution with a 4'-hydroxy (18) or -iodo (21b) group did not significantly alter beta 2-AR affinity, but greatly reduced TP receptor affinity (380- and 1200-fold, respectively). Further, the beta 2-AR can accommodate larger substituents such as a benzamide at the 4'-position (26b). Other monoiodo derivatives (24, 26a) have similar or slightly lower affinity to both beta 2-AR and TP receptor compared to their diiodo analogs. Interestingly, removal of the 4'-substituent of 3',5'-diiodo analogs increased beta 2-AR affinity with little or no effect on beta 1-AR and TP binding. Thus, analog 21a displayed highly potent (pKi 9.52) and selective (beta 2/beta 1 = 600) binding affinity for beta 2-AR. On the other hand, trifluoromethyl substituents at the 3'- and 5'-positions (27) essentially abolished binding affinity at beta 2-AR and TP receptors. The differential binding effects of the aforementioned trimetoquinol modifications on the receptor systems may reflect differences in the binding pocket that interacts with the benzyl portion of trimetoquinol analogs. Thus, manipulation of the 1-benzyl moiety of trimetoquinol (1) has resulted in analogs that exhibit potent beta 2-AR binding affinity and significantly lower beta 1-AR and TP receptor affinities.
IC‐P‐024: A novel positron emission tomography contrast agent targeting cathepsin d shows preferential in vivo retention in an Alzheimer's disease mouse model (2015)

Early detection of Alzheimer's disease (AD) pathology remains a serious challenge for both diagnosis and development of treatment. Cathepsin D (CatD), a lysosomal aspartyl protease, is over-expressed in AD and therefore is a potential biomarker. Previously, we introduced a novel Contrast Agent (CA) that was preferentially taken up by CatD over-expressing cells (in-vitro) and able to transverse the BBB in mice (ex-vivo). We have also found that a Near-Infrared-labeled version of this CA demonstrates prolonged in-vivo retention in the brain of a transgenic (Tg) mouse model of AD at 12 months compared to age matched wild type controls. Here, we present the performance of a CA labeled with 68Ga evaluated by micro Positron Emission Tomography (microPET). The CA consists of a Cell Penetrating Peptide (CPP; the Tat peptide from HIV-1), attached to a CatD cleavage sequence followed by a 68Ga labeled DOTA chelator flanked by a fluorescent dye. The CPP allows the agent to cross the blood brain barrier bidirectionally. In the presence of elevated levels of CatD, cleavage of the CatD site removes the CPP resulting in prolonged retention of the imaging moeity. For this study, Tg AD mice (N=8, 5XFAD model) and non-Tg age matched littermates (N=8) at 2 and 4.5 months of age received an intravenous tail vein CA injection of ∼12 MBq of CA under isofluorane anesthesia. Mice were scanned for 3 hours using the Inveon preclinical microPET system (Siemens Medical Solutions, Knoxville TN, USA). Regions of interest were identified in reconstructed images and were used to measure the uptake and washout of the CA in the brain, liver, kidneys and bladder. The Tg mice demonstrated significantly greater uptake (p<0.05) of the CA in the brain in the first two hours following injection at 4.5 months but not 2 months of age compared to controls. No differences in uptake were observed in other organs. This preliminary work further supports the capacity of this CatD targeted CA to help differentiate between AD mice and controls.