gebhart/patrepeval huggingface dataset:
Phononic crystal structures for acoustically driven microfluidic manipulations (2010)

The development of microfluidic systems is often constrained both by difficulties associated with the chip interconnection to other instruments and by limitations imposed by the mechanisms that can enable fluid movement and processing. Surface acoustic wave (SAW) devices have shown promise in allowing samples to be manipulated, although designing complex fluid operations involves using multiple electrode transducers. We now demonstrate a simple interface between a piezoelectric SAW device and a disposable microfluidic chip, patterned with phononic structures to control the acoustic wave propagation. The surface wave is coupled from the piezoelectric substrate into the disposable chip where it interacts with the phononic lattice. By implementing both a phononic filter and an acoustic waveguide, we illustrate the potential of the technique by demonstrating microcentrifugation for particle and cell concentration in microlitre droplets. We show for the first time that the interaction of the fluid within this metamaterial phononic lattice is dependent upon the frequency of the acoustic wave, providing a route to programme complex fluidic functions into a microchip (in much the same way, by analogy, that a holographic element would change the phase of a light wave in optical tweezers). A practical realisation of this involves the centrifugation of blood on the chip.
Detection of influenza A and B in respiratory secretions with the polymerase chain reaction. (1992)

Influenza A and B are RNA-containing viruses that frequently infect humans. Currently, sensitive detection of these viruses requires fresh respiratory secretions and special facilities for culture. To facilitate diagnosis of influenza, the polymerase chain reaction (PCR) was used in the present studies to detect DNA produced by reverse transcription of influenzal RNA in vaccines, tissue culture fluids, and stored respiratory secretions. Primers were directed at targets on the highly conserved segment 7 (matrix gene) of influenza A (212-bp product) and B (365-bp product). The primers were completely type specific. Critical variables in the assay were the concentration of pleotropic salts used during preparation of samples, the use of carrier RNA and RNase inhibitors during sample preparation, and the use of optimum K+ and Mg2+ levels at each step. Studies of 33 patients with symptoms of viral respiratory infection whose nasal washes had been cultured and frozen for up to 1 year before assay showed that PCR provided type-specific detection of influenza with a sensitivity comparable to that of culture of the fresh secretions. The assay offers a powerful test for detection of devitalized influenza viruses and may be useful in both diagnostic work and epidemiological studies of influenza.
A β-(1,2)-Glycosynthase and an Attempted Selection Method for the Directed Evolution of Glycosynthases (2011)

Understanding how enzymes mediate catalysis is a key to their reprogramming for biotechnological applications. The family 3 retaining glycosidase postulated to be involved in erythromycin self-resistance was cloned, recombinantly expressed in Escherichia coli, purified, and characterized. Bioinformatics analysis allowed the identification of the acid/base and nucleophile residues, and mutation of these residues resulted in hydrolytically inactive proteins. One mutant was able to synthesize a glycosidic linkage using α-glucosyl fluoride as a donor and macrolide antibiotics as acceptors. This shows an unprecedented application of glycosynthase technology in accomplishing a challenging β-(1,2)-glycosylation of an amino sugar. This work also provides the first biochemical characterization of the EryBI protein and supports its role in the self-resistance mechanism involved in erythromycin biosynthesis. An in vivo selection approach was used in an attempt to spur evolution of the glycosynthase, and the results from the attempted selection method provide insight into the requirements for in vivo directed evolution of glycosynthases.
Selective expression of folate receptor ? and its possible role in methotrexate transport in synovial macrophages from patients with rheumatoid arthritis (1999)

These results demonstrate that FR-beta expression is selectively elevated in RA synovial macrophages and suggest that MTX is transported through FR-beta in RA synovial macrophages. The findings suggest that folate antagonists with higher affinity for FR-beta would be useful in the treatment of RA.
Basic Fibroblast Growth Factor Activates MEK/ERK Cell Signaling Pathway and Stimulates the Proliferation of Chicken Primordial Germ Cells (2010)

Our results demonstrate that chicken PGCs can be maintained in vitro without any differentiation or dedifferentiation in feeder free culture conditions, and subsequent analysis revealed that bFGF is one of the key factors that enable proliferation of chicken PGCs via MEK/ERK signaling regulating downstream genes that may be important for PGC proliferation and survival.
Strain‐ and torsion‐induced resonance energy tuning of Raman scattering in single‐wall carbon nanotubes (2016)

Abstract Raman excitation profiles for homogeneously deformed single‐walled carbon nanotubes are calculated and systematically analyzed. A number of attractive and apparent effects significant in designing electromechanical devices are caused by torsion and uniaxial strain. The shift of radial breathing mode (RBM) phonon energies due to deformation is negligible. The linear dependence of electronic transition energy shift on deformation is confirmed and it is found that the slope of it is strongly related to the chiral angle of the tube. It is also shown that for some tubes the transition energy shift covers the entire visible‐light interval, making them perfectly tunable light absorbers. Two types of deformation are compared, a relaxed (slow) deformation and an adiabatic (fast) one. It is found that transition energies are more sensitive to adiabatic deformation, which can be useful for optomechanical device designing. Raman excitation profile of a (9,9) nanotube under torsion.
Inhibition of fungal spore germination by gramicidin S and its potential use as a biocontrol against fungal plant pathogens (1986)

Journal Article Inhibition of fungal spore germination by gramicidin S and its potential use as a biocontrol against fungal plant pathogens Get access THELMA MURRAY, THELMA MURRAY Division of Bacteriology, Department of Agriculture, School of Agriculture Building, University of Aberdeen, Aberdeen AB9 WD, UK Search for other works by this author on: Oxford Academic Google Scholar FIONA C. LEIGHTON, FIONA C. LEIGHTON Division of Bacteriology, Department of Agriculture, School of Agriculture Building, University of Aberdeen, Aberdeen AB9 WD, UK Search for other works by this author on: Oxford Academic Google Scholar B. SEDDON B. SEDDON Division of Bacteriology, Department of Agriculture, School of Agriculture Building, University of Aberdeen, Aberdeen AB9 WD, UK Search for other works by this author on: Oxford Academic Google Scholar Letters in Applied Microbiology, Volume 3, Issue 1, 1 January 1986, Pages 5–7, https://doi.org/10.1111/j.1472-765X.1986.tb01534.x Published: 01 January 1986 Article history Published: 01 January 1986 Received: 10 April 1986 Accepted: 21 April 1986
236. Some reactions of 2-(3-oxindolyl)ethylamines (1964)

P. J. Islip and A. C. White, J. Chem. Soc., 1964, 1201 DOI: 10.1039/JR9640001201
Requirement of dendritic calcium spikes for induction of spike‐timing‐dependent synaptic plasticity (2006)

Spike-timing-dependent synaptic plasticity (STDP) by definition requires the temporal association of pre- and postsynaptic action potentials (APs). Yet, in cortical pyramidal neurons pairing unitary EPSPs with single APs at low frequencies is ineffective at generating plasticity. Using recordings from synaptically coupled layer 5 pyramidal neurons, we show here that high-frequency (200 Hz) postsynaptic AP bursts, rather than single APs, are required for both long-term potentiation (LTP) induction and NMDA channel activation during EPSP-AP pairing at low frequencies. Furthermore, we find that AP bursts can lead to LTP induction and NMDA channel activation during EPSP-AP pairing at both positive and negative times. High-frequency AP bursts generated supralinear calcium signals in basal dendrites suggesting the generation of dendritic calcium spikes, as has been observed previously in apical dendrites during AP burst firing at frequencies greater than 100 Hz. Consistent with a role of these dendritic calcium spikes in LTP induction, pairing EPSPs with low frequency (50 Hz) AP bursts was ineffective in generating LTP. Furthermore, supralinear calcium signals in basal dendrites during AP bursts were blocked by low concentrations of the T- and R-type calcium channel antagonist nickel, which also blocked LTP and NMDA channel activation. These data suggest an important role of dendritic calcium spikes during AP bursts in determining both the efficacy and time window for STDP induction.
The Origin and Function of the Pituitary Adenylate Cyclase-Activating Polypeptide (PACAP)/Glucagon Superfamily* (2000)

The pituitary adenylate cyclase-activating polypeptide (PACAP)/ glucagon superfamily includes nine hormones in humans that are related by structure, distribution (especially the brain and gut), function (often by activation of cAMP), and receptors (a subset of seven-transmembrane receptors). The nine hormones include glucagon, glucagon-like peptide-1 (GLP-1), GLP-2, glucose-dependent insulinotropic polypeptide (GIP), GH-releasing hormone (GRF), peptide histidine-methionine (PHM), PACAP, secretin, and vasoactive intestinal polypeptide (VIP). The origin of the ancestral superfamily members is at least as old as the invertebrates; the most ancient and tightly conserved members are PACAP and glucagon. Evidence to date suggests the superfamily began with a gene or exon duplication and then continued to diverge with some gene duplications in vertebrates. The function of PACAP is considered in detail because it is newly (1989) discovered; it is tightly conserved (96% over 700 million years); and it is probably the ancestral molecule. The diverse functions of PACAP include regulation of proliferation, differentiation, and apoptosis in some cell populations. In addition, PACAP regulates metabolism and the cardiovascular, endocrine, and immune systems, although the physiological event(s) that coordinates PACAP responses remains to be identified.
In Praise of the Hyperglycemic Clamp: A method for assessment of β-cell sensitivity and insulin resistance (1996)

The most widely used methods for the assessment of beta-cell response and peripheral tissue sensitivity to insulin include the oral glucose tolerance test (OGTT), the frequently sampled intravenous glucose tolerance test, and the hyperinsulinemiceuglycemic clamp technique. During an OGTT, glucose levels increase after a variable lag period, then reach a peak and fall variably among individuals. The response even varies in the same subject upon repeat testing. A more reproducible glucose curve is achieved with an intravenous glucose tolerance test in which the plasma glucose levels rise rapidly to a very high level and fall exponentially. In neither of the two methods is a steady-state glucose level achieved. In the hyperinsulinemic-euglycemic clamp technique, a steady-state glucose level can be maintained at any level of hyperinsulinemia. However, an assessment of beta-cell sensitivity is not obtained. The less used hyperglycemic clamp technique can assess beta-cell sensitivity as well as peripheral tissue sensitivity. Moreover, a measure of glucose effectiveness or non-insulin-mediated glucose uptake can also be determined. With this technique the beta-cells of all subjects are stimulated with the same arterial glucose concentration, thus enabling assessment of beta-cell response to identical plasma glucose levels. Comparison of responses to stable hyperglycemic stimuli can be made in glucose-tolerant and -intolerant states with the addition of various substances, either alone or in combination. The use of the hyperglycemic clamp and several of its variant forms is reviewed as an alternative method for assessment of glucose homeostasis.
Prevention of Preterm Delivery (2007)

Although preterm birth (at <37 weeks' gestation) is sometimes indicated for the health of the mother or her fetus, spontaneous preterm births occur as a consequence of spontaneous preterm labor or preterm rupture of fetal membranes before the onset of labor. This review focuses on therapeutic strategies for the prevention and treatment of spontaneous preterm labor and delivery.
Several Log Increase in Therapeutic Transgene Delivery by Distinct Adeno-Associated Viral Serotype Vectors (2000)

We previously demonstrated that rAAV vectors carrying human and canine factor IX (FIX) cDNA can infect, stably persist, and secrete functional human and canine FIX following direct intramuscular injection. In an attempt to improve FIX protein secretion for eventual therapeutic use, we set out to determine if alteration of the AAV capsid would affect skeletal muscle transduction and factor IX secretion. Two reasons to pursue this question were (1) the persistence of high-titer neutralizing antibody (NAB) to AAV2 and (2) our previous study that supported a restricted tropism of muscle fiber types to AAV2 transduction. Using an identical CMV/canine factor IX (cFIX) expression cassette, we cross-packaged this genome into virions generated from each of the five AAV serotypes. In a dose-response assay, equivalent amounts of rAAV/cFIX serotypes were tested in vitro and in vivo. In tissue culture cells, FIX antigen levels secreted into the supernatant varied depending on the AAV serotype used; type 2 transduced maximally, with serotypes 3, 1, 5, and 4, respectively, expressing lower levels. However, when the same viruses were tested in vivo using immunodeficient NOD/SCID animals, we obtained surprisingly different results. While the time to onset of detectable serum levels appeared the same for all serotypes, types 1, 3, and 5 produced 100- to 1000-fold more cFIX than type 2. In fact, 12 weeks after transduction, type 1 continued to express levels of cFIX on average at 80 microg/ml followed by type 5 (6.52 microg/ml), type 3 (3.27 microg/ml), type 4 (258 ng/ml), and finally type 2 (90 ng/ml). Coagulant activity of cFIX as measured by aPTT supported the circulating levels measured by ELISA demonstrating the secreted protein was functional, and RT-PCR of injected tissue correlated with the serotype-specific transduction data. In summary, we found significant differences in cFIX expression upon introducing various rAAV serotypes into mouse muscle. These data have direct bearing on the design of AAV gene therapy clinical trials for hemophilia and should also extend to most therapeutic transgenes.
Gauge color codes: optimal transversal gates and gauge fixing in topological stabilizer codes (2015)

Color codes are topological stabilizer codes with unusual transversality properties. Here I show that their group of transversal gates is optimal and only depends on the spatial dimension, not the local geometry. I also introduce a generalized, subsystem version of color codes. In 3D they allow the transversal implementation of a universal set of gates by gauge fixing, while error-dectecting measurements involve only four or six qubits.
Starburst/Cascade Dendrimers: Fundamental building blocks for a new nanoscopic chemistry set (1994)

That dendrimer structures act as fundamental chemical building blocks (see Figure), forming a “nanoscopic chemistry set” analogous to the “picoscopic chemistry set” formed by atoms, is discussed in this review. Following the logic used by 19th century chemists while defining the atomic “chemistry set”, it is shown that the ability to preface directionality in dendrimer systems validates this approach. magnified image
The Carboxyl-Terminal Region Is a Determinant for the Intracellular Behavior of the Chorionic Gonadotropin β Subunit: Effects on the Processing of the Asn-Linked Oligosaccharides (1998)

The placental hormone human CG (hCG) consists of two noncovalently linked alpha- and beta-subunits similar to the other glycoprotein hormones LH, FSH, and TSH. These heterodimers share a common alpha subunit but differ in their structurally distinct beta subunits. The CGbeta subunit is distinguished among the beta subunits by the presence of a C-terminal extension with four serine-linked oligosaccharides (carboxyl terminal peptide or CTP). In previous studies we observed that deleting this sequence decreased assembly of the truncated CGbeta subunit (CGbeta114) with the alpha-subunit and increased the heterogeneity of the secreted forms of the uncombined subunit synthesized in transfected Chinese hamster ovary (CHO) cells. The latter result was attributed to alterations in the processing of the two N-linked oligosaccharides. To examine at what step this heterogeneity occurs, the CGbeta and CGbeta114 genes were transfected into wild-type and mutant CHO cell lines that are defective in the late steps of the N-linked carbohydrate-processing pathway. We show here that removal of the CTP alters the processing of the core mannosyl unit of the subunit to complex forms at both glycosylation sites and that the oligosaccharides contain polylactosamine. Although it has been presumed that there is little intramolecular interaction between the CTP and the proximal domains of the subunit, our data suggest that the CTP sequence participates in the folding of the newly synthesized subunit, which is manifest by the posttranslational changes observed here.
A Second Conserved GAF Domain Cysteine Is Required for the Blue/Green Photoreversibility of Cyanobacteriochrome Tlr0924 from Thermosynechococcus elongatus (2008)

Phytochromes are widely occurring red/far-red photoreceptors that utilize a linear tetrapyrrole (bilin) chromophore covalently bound within a knotted PAS-GAF domain pair. Cyanobacteria also contain more distant relatives of phytochromes that lack this knot, such as the phytochrome-related cyanobacteriochromes implicated to function as blue/green switchable photoreceptors. In this study, we characterize the cyanobacteriochrome Tlr0924 from the thermophilic cyanobacterium Thermosynechococcus elongatus. Full-length Tlr0924 exhibits blue/green photoconversion across a broad range of temperatures, including physiologically relevant temperatures for this organism. Spectroscopic characterization of Tlr0924 demonstrates that its green-absorbing state is in equilibrium with a labile, spectrally distinct blue-absorbing species. The photochemically generated blue-absorbing state is in equilibrium with another species absorbing at longer wavelengths, giving a total of 4 states. Cys499 is essential for this behavior, because mutagenesis of this residue results in red-absorbing mutant biliproteins. Characterization of the C 499D mutant protein by absorbance and CD spectroscopy supports the conclusion that its bilin chromophore adopts a similar conformation to the red-light-absorbing P r form of phytochrome. We propose a model photocycle in which Z/ E photoisomerization of the 15/16 bond modulates formation of a reversible thioether linkage between Cys499 and C10 of the chromophore, providing the basis for the blue/green switching of cyanobacteriochromes.
Biomarkers of Endothelial Cell Activation in Early Sepsis (2013)

This multicenter validation study confirms that markers of endothelial activation are associated with sepsis severity, organ dysfunction, and mortality in sepsis. This supports the hypothesis that the endothelium plays a central role in the pathophysiology of sepsis and may serve as a more accurate prediction tool and a target for therapies aimed at ameliorating endothelial cell dysfunction. In addition, sFLT-1 holds promise as a novel sepsis severity biomarker.
Dispersion polymerization of methyl methacrylate: Mechanism of particle formation (1994)

Abstract The mechanism for the formation of micron‐size polymer particles in the dispersion polymerization of methyl methacrylate was investigated by applying dynamic light scattering to monitor the evolution of the average particle size in the early stages of the polymerization. In addition, the contributions of physically adsorbed stabilizer and graft copolymer were evaluated by measuring the bound, unbound (adsorbed), and free stabilizer, and by determining the amount of added stabilizer required in seeded dispersion polymerizations. Twenty nanometer particles (termed nuclei) were the smallest particles detected and are considered to be formed by aggregation of growing polymer chains precipitating from solution as they exceed their critical chain length. Aggregation of these nuclei with themselves and their aggregates continues until mature and stable particles are formed. This occurs when sufficient stabilizer occupies the particle surface which includes both the polymeric stabilizer [poly(vinylpyrrolidone)] and its graft copolymer which is created in situ . The effects of process variables are discussed based on this mechanistic picture of the dispersion polymerization process. © 1994 John Wiley &amp; Sons, Inc.
The vision of autonomic computing (2003)

A 2001 IBM manifesto observed that a looming software complexity crisis -caused by applications and environments that number into the tens of millions of lines of code - threatened to halt progress in computing. The manifesto noted the almost impossible difficulty of managing current and planned computing systems, which require integrating several heterogeneous environments into corporate-wide computing systems that extend into the Internet. Autonomic computing, perhaps the most attractive approach to solving this problem, creates systems that can manage themselves when given high-level objectives from administrators. Systems manage themselves according to an administrator's goals. New components integrate as effortlessly as a new cell establishes itself in the human body. These ideas are not science fiction, but elements of the grand challenge to create self-managing computing systems.