gebhart/patrepeval huggingface dataset:
Fracto-mechanoluminescent light emission of EuD4TEA-PDMS composites subjected to high strain-rate compressive loading (2017)

The objective of this study is to understand light emission characteristics of fracto-mechanoluminescent (FML) europium tetrakis(dibenzoylmethide)-triethylammonium (EuD4TEA) crystals under high strain-rate compressive loading. As a sensing material that can play a pivotal role for the self-powered impact sensor technology, it is important to understand transformative light emission characteristics of the FML EuD4TEA crystals under high strain-rate compressive loading. First, EuD4TEA crystals were synthesized and embedded into polydimethylsiloxane (PDMS) elastomer to fabricate EuD4TEA-PDMS composite test specimens. Second, the prepared EuD4TEA-PDMS composites were tested using the modified Kolsky bar setup equipped with a high-speed camera. Third, FML light emission was captured to yield 12 bit grayscale video footage, which was processed to quantify the FML light emission. Finally, quantitative parameters were generated by taking into account pixel values and population of pixels of the 12 bit grayscale images to represent FML light intensity. The FML light intensity was correlated with high strain-rate compressive strain and strain rate to understand the FML light emission characteristics under high strain-rate compressive loading that can result from impact occurrences.
Infectious Bovine Viral Diarrhea Virus (Strain NADL) RNA from Stable cDNA Clones: a Cellular Insert Determines NS3 Production and Viral Cytopathogenicity (1998)

Bovine viral diarrhea virus (BVDV), strain NADL, was originally isolated from an animal with fatal mucosal disease. This isolate is cytopathic in cell culture and produces two forms of NS3-containing proteins: uncleaved NS2-3 and mature NS3. For BVDV NADL, the production of NS3, a characteristic of cytopathic BVDV strains, is believed to be a consequence of an in-frame insertion of a 270-nucleotide cellular mRNA sequence (called cIns) in the NS2 coding region. In this study, we constructed a stable full-length cDNA copy of BVDV NADL in a low-copy-number plasmid vector. As assayed by transfection of MDBK cells, uncapped RNAs transcribed from this template were highly infectious (>10(5) PFU/microg). The recovered virus was similar in plaque morphology, growth properties, polyprotein processing, and cytopathogenicity to the BVDV NADL parent. Deletion of cIns abolished processing at the NS2/NS3 site and produced a virus that was no longer cytopathic for MDBK cells. This deletion did not affect the efficiency of infectious virus production or viral protein production, but it reduced the level of virus-specific RNA synthesis and accumulation. Thus, cIns not only modulates NS3 production but also upregulates RNA replication relative to an isogenic noncytopathic derivative lacking the insert. These results raise the possibility of a linkage between enhanced BVDV NADL RNA replication and virus-induced cytopathogenicity.
Interaction of Grb2 via its Src homology 3 domains with synaptic proteins including synapsin I. (1994)

Grb2 is a 25-kDa adaptor protein composed of a Src homology 2 (SH2) domain and two flanking Src homology 3 (SH3) domains. One function of Grb2 is to couple tyrosine-phosphorylated proteins (through its SH2 domain) to downstream effectors (through its SH3 domains). Using an overlay assay, we have identified four major Grb2-binding proteins in synaptic fractions. These proteins interact with wild-type Grb2 but not with Grb2 containing point mutations in each of its two SH3 domains corresponding to the loss of function mutants in the Caenorhabditis elegans Grb2 homologue sem-5. Two of the proteins, mSos and dynamin, were previously shown to bind Grb2. The third protein of 145 kDa is brain specific and to our knowledge has not been previously described. The fourth protein is synapsin I. Dynamin is required for synaptic vesicle endocytosis and synapsin I is thought to mediate the interaction of synaptic vesicles with the presynaptic cytomatrix. These data suggest that Grb2, or other proteins containing SH3 domains, may play a role in the regulation of the exo/endocytotic cycle of synaptic vesicles and therefore of neurotransmitter release.
RhoE is frequently down-regulated in hepatocellular carcinoma (HCC) and suppresses HCC invasion through antagonizing the Rho/Rho-Kinase/Myosin phosphatase target pathway (2012)

RhoE was frequently down-regulated in predominantly HBV-associated HCCs and this down-regulation was associated with a more aggressive HCC phenotype. RhoE regulated the cytoskeleton remodeling and suppressed HCC motility and invasiveness by way of inhibiting the Rho/ROCK axis.
Space-time block-coded multiple access through frequency-selective fading channels (2001)

Mitigation of multipath fading effects and suppression of multiuser interference (MUI) constitute major challenges in the design of wide-band third-generation wireless mobile systems. Space-time (ST) coding offers an effective transmit-antenna diversity technique to combat fading, but most existing ST coding schemes assume flat fading channels that may not be valid for wide-band communications. Single-user ST coded orthogonal frequency-division multiplexing transmissions over frequency-selective channels suffer from finite-impulse response channel nulls (fades). Especially multiuser ST block-coded transmissions through (perhaps unknown) multipath present unique challenges in suppressing not only MUI but also intersymbol/chip interference. In this paper, we design ST multiuser transceivers suitable for coping with frequency-selective multipath channels (downlink or uplink). Relying on symbol blocking and a single-receive antenna, ST block codes are derived and MUI is eliminated without destroying the orthogonality of ST block codes. The system is shown capable of providing transmit diversity while guaranteeing symbol recovery in multiuser environments, regardless of unknown multipath. Unlike existing approaches, the mobile does not need to know the channel of other users. In addition to decoding simplicity, analytic evaluation and corroborating simulations reveal its flexibility and performance merits.
On the User Performance of LTE UE Power Savings Schemes with Discontinuous Reception in LTE (2009)

The UTRAN long-term evolution (LTE) specifications provide flexible means to achieve micro-sleep operation for user equipment (UE) even though it is in active mode and running a service. By means of a discontinuous reception (DRX) framework, pauses in the transmission due to natural traffic characteristics or network prioritization can be utilized. The specifications give a number of options to optimize the performance. In this paper two of those possibilities are compared. Long DRX with the use of an inactivity timer is compared to the usage of short DRX on top of long DRX. The performance is evaluated in terms of user throughput, power consumption, and network performance, while using a realistic RF modem power consumption model for the UE. For bursty traffic, short DRX shows a gain of up to 100% over DRX with just an inactivity timer, when measuring throughput per power unit consumed in case of one or multiple users being present in the cell.
A Dynamic Metabolic Flux Analysis of Myeloid-Derived Suppressor Cells Confirms Immunosuppression-Related Metabolic Plasticity (2017)

Recent years have witnessed an increasing interest at understanding the role of myeloid-derived suppressor cells (MDSCs) in cancer-induced immunosuppression, with efforts to inhibit their maturation and/or their activity. We have thus modelled MDSCs central carbon metabolism and bioenergetics dynamic, calibrating the model using experimental data on in vitro matured mice bone marrow cells into MDSCs. The model was then used to probe the cells metabolic state and dynamics, performing a dynamic metabolic flux analysis (dMFA) study. Indeed, MDSCs maturation correlates with a high glycolytic flux contributing to up to 95% of the global ATP turnover rate, while most of the glucose-derived carbon enters the TCA cycle. Model simulations also reveal that pentose phosphate pathway and oxidative phosphorylation activities were kept at minimal levels to ensure NADPH production and anabolic precursors synthesis. Surprisingly, MDSCs immunosuppressive activity, i.e. L-arginine uptake, metabolism and endogenous synthesis, only consumes sparse quantities of energy-rich nucleotides (ATP and NADPH). Therefore, model simulations suggest that MDSCs exhibit a heterogeous metabolic profile similar to tumour cells. This behavior is probably an indirect immunosuppressive mechanism where MDSCs reduce the availability of carbon sources in the tumour periphery microenvironment, which could explain the dysfuntion and death of immune effector cells.
Aluminum nitride films on different orientations of sapphire and silicon (1996)

The details of epitaxial growth and microstrictural characteristics of AlN films grown on sapphire (0001), (101̄2) and Si (100), (111) substrates were investigated using plan-view and cross-sectional high-resolution transmission electron microscopy and x-ray diffraction techniques. The films were grown by metalorganic chemical vapor deposition using TMA1+NH3+N2 gas mixtures. Different degrees of epitaxy were observed for the films grown on α-Al2O3 and Si substrates in different orientations. The epitaxial relationship for (0001) sapphire was found to be (0001)AlN∥(0001)sap with in-plane orientation relationship of [011̄0]AlN∥[1̄21̄0]sap. This is equivalent to a 30° rotation in the basal (0001) plane. For (101̄2) sapphire substrates, the epitaxial relationship was determined to be (112̄0)AlN∥(101̄2)sap with the in-plane alignment of [0001]AlN∥[1̄011]sap. The AlN films on (0001) α-Al2O3 were found to contain inverted domain boundaries and a/3〈112̄0〉 threading dislocations with the estimated density of 1010 cm−2. The density of planar defects (stacking faults) found in AlN films was considerably higher in the case of (101̄2) compared to (0001) substrates. Films on Si substrates were found to be highly textured c axis oriented when grown on (111) Si, and c axis textured with random in-plane orientation on (100) Si. The role of thin-film defects and interfaces on device fabrication is discussed.
Methods for generating precise deletions and insertions in the genome of wild-type Escherichia coli: application to open reading frame characterization (1997)

We have developed a new system of chromosomal mutagenesis in order to study the functions of uncharacterized open reading frames (ORFs) in wild-type Escherichia coli. Because of the operon structure of this organism, traditional methods such as insertional mutagenesis run the risk of introducing polar effects on downstream genes or creating secondary mutations elsewhere in the genome. Our system uses crossover PCR to create in-frame, tagged deletions in chromosomal DNA. These deletions are placed in the E. coli chromosome by using plasmid pKO3, a gene replacement vector that contains a temperature-sensitive origin of replication and markers for positive and negative selection for chromosomal integration and excision. Using kanamycin resistance (Kn(r)) insertional alleles of the essential genes pepM and rpsB cloned into the replacement vector, we calibrated the system for the expected results when essential genes are deleted. Two poorly understood genes, hdeA and yjbJ, encoding highly abundant proteins were selected as targets for this approach. When the system was used to replace chromosomal hdeA with insertional alleles, we observed vastly different results that were dependent on the exact nature of the insertions. When a Kn(r) gene was inserted into hdeA at two different locations and orientations, both essential and nonessential phenotypes were seen. Using PCR-generated deletions, we were able to make in-frame deletion strains of both hdeA and yjbJ. The two genes proved to be nonessential in both rich and glucose-minimal media. In competition experiments using isogenic strains, the strain with the insertional allele of yjbJ showed growth rates different from those of the strain with the deletion allele of yjbJ. These results illustrate that in-frame, unmarked deletions are among the most reliable types of mutations available for wild-type E. coli. Because these strains are isogenic with the exception of their deleted ORFs, they may be used in competition with one another to reveal phenotypes not apparent when cultured singly.
Development and use of biomaterials as wound healing therapies (2019)

There is a vast number of treatments on the market for the management of wounds and burns, representing a multi-billion dollar industry worldwide. These include conventional wound dressings, dressings that incorporate growth factors to stimulate and facilitate the wound healing process, and skin substitutes that incorporate patient-derived cells. This article will review the more established, and the recent advances in the use of biomaterials for wound healing therapies, and their future direction.
Discovery of Protein Phosphatase 2C Inhibitors by Virtual Screening (2006)

Protein phosphatase 2C (PP2C) is an archetype of the PPM Ser/Thr phosphatases, characterized by dependence on divalent magnesium or manganese cofactors, absence of known regulatory proteins, and resistance to all known Ser/Thr phosphatase inhibitors. We have used virtual ligand screening with the AutoDock method and the National Cancer Institute Diversity Set to identify small-molecule inhibitors of PP2Calpha activity at a protein substrate. These inhibitors are active in the micromolar range and represent the first non-phosphate-based molecules found to inhibit a type 2C phosphatase. The compounds docked to three recurrent binding sites near the PP2Calpha active site and displayed novel Ser/Thr phosphatase selectivity profiles. Common chemical features of these compounds may form the basis for development of a PP2C inhibitor pharmacophore and may facilitate investigation of PP2C control and cellular function.
Molecular cloning, sequence analysis and expression of human pituitary glutaminyl cyclase (1994)

A cDNA clone for glutaminyl cyclase was isolated from a human pituitary cDNA library and the complete DNA sequence determined. The cDNA clone had 1573 bp and contained an open reading frame of 1086 bases, coding for a protein of 361 amino acids and molecular mass of 40,876 Da. The predicted amino acid sequence of the human cDNA showed 86% sequence identity to the previously reported bovine glutaminyl cyclase sequence. A comparison of the amino acid sequences derived from the human and bovine cDNAs showed that several glycosylation and phosphorylation sites as well as two cysteine residues (Cys139, Cys164) were conserved. The human cDNA was cloned into the Escherichia coli expression vectors pMALc2 and pET19b. Expression of this cDNA in either vector resulted in the production of a glutaminyl cyclase fusion protein which was enzymatically active and reacted with anti-bovine glutaminyl cyclase antisera. Substrate specificity studies with the recombinant enzyme suggested a bias against acidic and tryptophan residues adjacent to the N-terminal glutaminyl residue and a lack of importance of chain length after the second residue.
Systemic Acquired Resistance: Turning Local Infection into Global Defense (2013)

Systemic acquired resistance (SAR) is an induced immune mechanism in plants. Unlike vertebrate adaptive immunity, SAR is broad spectrum, with no specificity to the initial infection. An avirulent pathogen causing local programmed cell death can induce SAR through generation of mobile signals, accumulation of the defense hormone salicylic acid, and secretion of the antimicrobial PR (pathogenesis-related) proteins. Consequently, the rest of the plant is protected from secondary infection for a period of weeks to months. SAR can even be passed on to progeny through epigenetic regulation. The Arabidopsis NPR1 (nonexpresser of PR genes 1) protein is a master regulator of SAR. Recent study has shown that salicylic acid directly binds to the NPR1 adaptor proteins NPR3 and NPR4, regulates their interactions with NPR1, and controls NPR1 protein stability. However, how NPR1 interacts with TGA transcription factors to activate defense gene expression is still not well understood. In addition, redox regulators, the mediator complex, WRKY transcription factors, endoplasmic reticulum-resident proteins, and DNA repair proteins play critical roles in SAR.
Remote Sensing of Salinity in the Coastal Zone (1995)

MAJOR PROBLEM in coastal oceanography is the lack of knowledge of the spatial and temporal scales at which water masses of various origins interact within the coastal zone. While their gross characteristics may be known, the smallscale, two-dimensional, horizontal variability of water mass properties cannot be adequately determined using conventional oceanographic measurement methods. Typically, these small-scale variations are measured in one dimension, if at all, using conventional techniques and usually at great expense. Thus many key parameters necessary for the characterization and quantification of important physical, chemical, and biological processes in the coastal and estuarine regions remain unknown. A prototype instrument that promises to remedy this situation for the parameter which most influences
PEGylation: An Approach for Drug Delivery. A Review (2008)

The current review presents an update on polyethylene glycol (PEG), which is widely used as a covalent modifier of macromolecules. This review discusses the polymers suitable for conjugation, their conjugation methods, and their properties. Proteins and bioactive substances can be chemically modified by binding synthetic macromolecules of PEG to the surface of these biomolecules. Protein and peptide PEGylation improves the biopharmaceutical properties of drugs-that is, increased stability, increased resistance to proteolytic inactivation, decreased to nonexistent immunogenicity, increased circulatory lives, and low toxicity. These altered properties improve the delivery and efficacy of proteins.
Thermoresponsive Block Copolymer–Protein Conjugates Prepared by Grafting‐from via RAFT Polymerization (2011)

Well-defined "smart" block copolymer-protein conjugates were prepared by two consecutive "grafting-from" reactions via reversible addition-fragmentation chain transfer (RAFT) polymerization. The initiating portion (R-group) of the RAFT agent was anchored to a model protein such that the thiocarbonylthio moiety was readily accessible for chain transfer with propagating chains in solution. Well-defined polymer-protein conjugates of poly(N-isopropylacrylamide) (PNIPAM) and bovine serum albumin (BSA) were prepared at room temperature in aqueous media. The retained trithiocarbonate moiety on the free end group of the immobilized polymer allowed the homopolymer conjugate to be extended by polymerization of N,N-dimethylacrylamide. Polyacrylamide gel electrophoresis, size exclusion chromatography, and NMR spectroscopy confirmed the synthesis of the various conjugates and revealed that the polymerizations were well controlled. As expected, the resulting block copolymer-protein conjugates demonstrated thermoresponsive behavior due to the temperature-sensitivity of the PNIPAM block, as evidenced by turbidity measurements and dynamic light scattering analysis.
Parameters affecting the immunogenicity of a liposome‐associated synthetic hexapeptide antigen (1991)

The effect of liposome association on the immunogenicity of the hexapeptide IRGERA was investigated. When administered in the absence of a carrier and adjuvant this peptide, which corresponds to a linear epitope located at the C-terminus of histone H3, was not immunogenic. When mice were immunized with the peptide covalently linked to the surface of small unilamellar vesicles containing monophosphoryl lipid A as adjuvant, a relatively long-lasting response with memory cell induction was observed. The anti-peptide antibodies raised in this way reacted with the cognate sequence in the native histone. In contrast, coupling of the peptide to the surface of large vesicles yielded both an IgM and IgG response of short duration whereas encapsulation of the free peptide in large vesicles was ineffective. These results indicate that with short synthetic peptides, liposomes provide a substitute for a carrier protein. However, an adjuvant has to be incorporated in the vesicles in order to obtain an efficient immune response. Such an approach may be useful for designing synthetic vaccines.
Assessment of fungicide resistance and pathogen diversity in Erysiphe necator using quantitative real‐time PCR assays (2010)

The real-time PCR assay developed in this study provides a potentially useful tool for efficient quantification of different alleles of interest for fungicide monitoring and for population structure of E. necator.
Impact of biophysical parameters on the biological assessment of peptide nucleic acids, antisense inhibitors of gene expression (1995)

Abstract Peptide nucleic acids (PNA) are oligodeoxynucleotide (ODN) analogs in which the sugar phosphate backbone of the ODN has been replaced by one derived from units of N‐ethylaminoglycine. PNAs recognize DNA and RNA in a sequence specific manner and form complexes that can be characterized by biophysical methods. The binding motif is context dependent; homopyrimidine PNAs combine with complementary polypurine targets to form stoichiometric 2:1 complexes, whereas PNAs containing both purine and pyrimidine bases afford a 1:1 heteroduplex with mis‐match sensitivity comparable to that found in dsDNA. These complexes mediate the antigene and antisense effects of PNAs via the steric blockade of enzyme complexes responsible for DNA transcription, cDNA synthesis, and RNA translation. PNAs, like ODNs, are taken up by cells via endocytosis leading to their entrapment within intracytoplasmic vesicles. Under circumstances where agent delivery is solved by cell microinjection, PNAs can effect selective inhibition of endogenous and exogenous genes. The impact of biophysical parameters on the biological assessment of PNAs as antisense inhibitors of gene expression is presented and discussed. © 1995 Wiley‐Liss, Inc.