gebhart/patrepeval huggingface dataset:
Two Dimensional Mapping of SAW Propagation Constants by Using Fresnel-Phase-Plate Interdigital Transducer (1983)

The methods of measuring the acoustic properties of solids by using the acoustic beams from interdigital transducers (IDT) is described. An IDT can radiate acoustic waves into liquid in oblique directions with respect to the substrate surface, and the wave fronts can be arbitrarly controlled by designing the IDT shape. One IDT couple is used to measure the acoustic properties of a solid sample. In the present study, we show a new method for focusing the beam from an IDT and measuring the acoustic properties of solids. An interdigital electrode is divided into several sections, each of which is placed to form a one dimensional Fresnel phase plate (FPP) on a piezoelectric substrate. It has been found that the FPP IDT generates a converging beam onto a focal plane, and the present system is suitable for measuring the two dimensional variation of leaky SAW phase velocity on a sample surface.
Insulin-like growth factor I (IGF-I) and the IGF-I receptor prevent etoposide-induced apoptosis. (1995)

The interaction of insulin-like growth factors (IGF) with the IGF-I receptor promotes cell proliferation and survival. We examined the role of the IGF-I receptor as a possible direct inhibitor of apoptosis induced by the topoisomerase I inhibitor etoposide. When exposed to this agent, BALB/c 3T3 cells that constitutively overexpress the human IGF-I receptor (p6 cells) arrested in S phase and subsequently underwent apoptosis as determined by the appearance of a pre-G1 apoptotic peak when studied by flow cytometry and the characteristic internucleosomal fragmentation of DNA. The addition of IGF-I markedly inhibited etoposide-induced apoptosis in a concentration-dependent manner. IGF-I was not mitogenic in the presence of etoposide. IGF-I was less effective in preventing apoptosis in parental BALB/c 3T3 cells and had no effect on etoposide-induced cell killing of mouse embryo fibroblasts that have a targeted disruption of the IGF-I receptor gene. These results demonstrate an important role for the IGF-I receptor as an inhibitor of apoptosis, independent of its mitogenic actions.
Detection of anti-teichoic acid immunoglobulin G antibodies in experimental Staphylococcus epidermidis endocarditis (1983)

An enzyme-linked immunosorbent assay (ELISA) was developed for the detection of rabbit immunoglobulin G (IgG) antibodies to purified cell wall teichoic acids from the Staphylococcus aureus Lafferty strain and three strains of coagulase-negative staphylococci. Significant immunological cross-reactivity occurred only between the teichoic acid of S. aureus and one coagulase-negative preparation. The ELISA was used to determine the serum IgG response to Staphylococcus epidermidis in a rabbit model of aortic valve endocarditis. Blood samples were drawn before inoculation and then every 5 days until death or sacrifice at 32 to 35 days postinoculation. Valve vegetations were culture positive at autopsy in 16 (59%) of the 27 catheterized rabbits. Antibody titers in this culture-positive group and the culture-negative group began to rise as early as day 6. Although both groups demonstrated an antibody response, the culture-positive group attained a significantly higher titer on days 26 and 31. Antibodies also rose in a control group of rabbits without a heart catheter but which were inoculated with bacteria. Again, the antibody titer was significantly less than that for the culture-positive group. This ELISA may be useful for the diagnosis of coagulase-negative staphylococcal infections in humans.
Peptidoglycan derived fromStaphylococcus epidermidisinduces Connexin43 hemichannel activity with consequences on the innate immune response in endothelial cells (2010)

Gram-positive bacterial cell wall components including PGN (peptidoglycan) elicit a potent pro-inflammatory response in diverse cell types, including endothelial cells, by activating TLR2 (Toll-like receptor 2) signalling. The functional integrity of the endothelium is under the influence of a network of gap junction intercellular communication channels composed of Cxs (connexins) that also form hemichannels, signalling conduits that are implicated in ATP release and purinergic signalling. PGN modulates Cx expression in a variety of cell types, yet effects in endothelial cells remain unresolved. Using the endothelial cell line b.End5, a 6 h challenge with PGN induced IL-6 (interleukin 6), TLR2 and Cx43 mRNA expression that was associated with enhanced Cx43 protein expression and gap junction coupling. Cx43 hemichannel activity, measured by ATP release from the cells, was induced following 15 min of exposure to PGN. Inhibition of hemichannel activity with carbenoxolone or apyrase prevented induction of IL-6 and TLR2 mRNA expression by PGN, but had no effect on Cx43 mRNA expression levels. In contrast, knockdown of TLR2 expression had no effect on PGN-induced hemichannel activity, but reduced the level of TLR2 and Cx43 mRNA expression following 6 h of PGN challenge. PGN also acutely induced hemichannel activity in HeLa cells transfected to express Cx43, but had no effect in Cx43-deficient HeLa OHIO cells. All ATP responses were blocked with Cx-specific channel blockers. We conclude that acute Cx43 hemichannel signalling plays a role in the initiation of early innate immune responses in the endothelium.
Fluorescent labeling of a DNA sequencing primer (1993)

Several oligonucleotides containing one to four fluorescein labels in various positions were synthesized and the fluorescence intensity and thermal stability of the duplex forms with their complementary sequences were measured. Oligomers that contain two fluorescein molecules, one attached at the 5' terminus and the other at an internal phosphate, were hybridized with less stability than that containing fluorescein at only the 5' terminus, but it formed more efficient primers for dideoxy sequencing with an automated sequencer.
Strain stiffening in collagen I networks (2012)

Abstract Biopolymer gels exhibit strain stiffening that is generally not seen in synthetic gels. Here, we investigate the strain‐stiffening behavior in collagen I gels that demonstrate elasticity derived from a variety of sources including crosslinking through telopeptides, bundling through low‐temperature gelation, and exogenous crosslinking with genipin. In all cases, it is found that these gels exhibit strain stiffening; in general, onset of strain stiffening occurs earlier, yield strain is lower, and degree of strain stiffening is smaller in higher concentration gels and in those displaying thick fibril bundles. Recovery after exposure to high strains is substantial and similar in all gels, suggesting that much of the stiffening comes from reversible network deformations. A key finding of this study is that collagen I gels of identical storage and loss moduli may display different nonlinear responses and different capacities to recover from high strain. © 2012 Wiley Periodicals, Inc.
Nucleotide sequence and corresponding amino acid sequence of the gene for the major antigen of foot and mouth disease virus (1981)

A segment of 1160 nucleotides of the FMDV genome has been sequenced using three overlapping fragments of cloned cDNA from FMDV strain O1K. This sequence contains the coding sequence for the viral capsid protein VP1 as shown by its homology to known and newly determined amino acid sequences from this man antigenic polypeptide of the FMDV virion. The structural gene for VP1 comprises 639 nucleotides which specify a sequence of 213 amino acids for the VP1 protein. The coding sequence is not flanked by start and stop codons which is consistent with the mode of biosynthesis of VP1 by post-translational processing of a polyprotein precursor.
Transcriptional regulation in cardiac muscle. Coordinate expression of Id with a neonatal phenotype during development and following a hypertrophic stimulus in adult rat ventricular myocytes in vitro. (1992)

The transcriptional regulatory mechanisms in heart muscle that direct cardiac development and allow for a flexible, adaptive response to physiologic stress are not well understood. We demonstrate that a negative regulator of gene transcription termed Id that has been described predominantly in proliferating cell lines and in undifferentiated tissue during growth, is expressed in freshly isolated terminally differentiated adult rat ventricular myocytes, in contrast to most other tissues in the adult rat. Id mRNA expression is regulated in ventricular myocytes during post-natal development, peaking at the transition from hyperplastic to hypertrophic growth at day 17 in the rat, declining subsequently to lower, stable levels in adult myocytes. Although Id mRNA becomes undetectable in adult ventricular myocytes 48 h following isolation in the absence of serum, it can be rapidly reinduced by an alpha-adrenergic agonist, accompanied by increased protein synthesis and the reexpression, in defined media, of the neonatal genes prepro-ANP and skeletal muscle alpha-actin. Thus, the differential regulation of Id during cardiac development, the presence of Id mRNA in normal cardiac myocytes, and its increased expression following a hypertrophic stimulus all suggest a role for this transcriptional regulator in the control of cardiac muscle cell phenotype.
ACCURACY ANALYSIS OF KINECT DEPTH DATA (2011)

This paper presents an investigation of the geometric quality of depth data obtained by the Kinect sensor. Based on the mathematical model of depth measurement by the sensor a theoretical error analysis is presented, which provides an insight into the factors influencing the accuracy of the data. Experimental results show that the random error of depth measurement increases with increasing distance to the sensor, and ranges from a few millimetres up to about 4 cm at the maximum range of the sensor. The accuracy of the data is also found to be influenced by the low resolution of the depth measurements. 1.
Influence of SHIP on the NK Repertoire and Allogeneic Bone Marrow Transplantation (2002)

Natural killer cell (NK) receptors for major histocompatibility complex (MHC) class I influence engraftment and graft-versus-tumor effects after allogeneic bone marrow transplantation. We find that SH2-containing inositol phosphatase (SHIP) influences the repertoire of NK receptors. In adult SHIP-/- mice, the NK compartment is dominated by cells that express two inhibitory receptors capable of binding either self or allogeneic MHC ligands. This promiscuous repertoire has significant functional consequences, because SHIP-/- mice fail to reject fully mismatched allogeneic marrow grafts and show enhanced survival after such transplants. Thus, SHIP plays an important role in two processes that limit the success of allogeneic marrow transplantation: graft rejection and graft-versus-host disease.
Insertion mutagenesis of the gene encoding the ferrichrome-iron receptor of Escherichia coli K-12 (1990)

The ferrichrome-iron receptor of Escherichia coli K-12 encoded by the fhuA gene is a multifunctional outer membrane receptor with an Mr of 78,000. It is required for the binding and uptake of ferrichrome and is the receptor for bacteriophages T5, T1, phi 80, and UC-1 as well as for colicin M. The fhuA gene was cloned into pBR322, and the recombinant plasmid pGC01 was mutagenized by the insertion of 6-base-pair TAB (two amino acid Barany) linkers into CfoI and HpaII restriction sites distributed throughout the coding region. A library of 18 TAB linker insertions in fhuA was generated; 8 of the mutations were at CfoI sites and 10 were at HpaII sites. All mutations inserted a hexamer that encoded a unique SacI site. A large deletion in fhuA was also isolated by TAB linker mutagenesis. Except for the deletion mutant, all of the linker insertion mutant FhuA proteins were found in the outer membrane in amounts similar to those found in the wild type. Five of the linker insertion mutants were susceptible to cleavage by endogenous proteolytic activity: a second FhuA-related band that migrated at approximately 72 kilodaltons could be detected on Coomassie blue-stained gels and on Western blots (immunoblots) by using a carboxy terminus-specific anti-peptide antibody. Receptor functions were measured with the mutated genes present in a single copy on the chromosome. Some of the receptors conferred wild-type phenotypes: they demonstrated growth promotion by ferrichrome and the same efficiency of plating as that of wild-type FhuA; killing by colicin M was also unaffected. Several mutants were altered in their sensitivities to the lethal agents. TAB linker insertions after amino acids 69 and 128 abolished all receptor functions. Phage T5 id not bind to these mutant FhuA proteins in detergent extracts. The deletion mutant was also defective in all FhuA functions. Sensitivity to the lethal agents of cellsl that expressed mutant FhuAs with insertions after amino acids 59 and 135 was reduced by several orders of magnitude. Insertion at other selected sites decreased some or all receptor functions only slightly. An insertion after amino acid 321 selectively eliminated ferrichrome growth promotion. Finally, a strain carrying a mutant fhuA gene on the chromosome in which the linker insertion occurred after amino acid 82 showed a tonB phenotype. These subtle perturbations that were introduced into the FhuA protein resulted in changes in its stability and in the binding and uptake of its cognate ligands.
Unmet need: what justifies the search for a new antidepressant? (2002)

The burden of major depressive disorder is huge, as is clearly documented by World Health Organization data. A major component of this burden is the episodic nature of depression. Depressive episodes may be precipitated by stress and if left untreated can become episodic, recurrent, and chronic. Hippocampal atrophy may be a consequence of chronic depression, but antidepressants and mood stabilizers have been suggested to prevent or reverse this damage. Adequate treatment is essential for preventing depression from becoming chronic. Unfortunately, current antidepressant treatments fall short of being adequate for many patients. Shortcomings such as low remission/high treatment-resistance rates, slow onset of action, side effects, and drug-drug interactions influence patient adherence, which may be as low as 56% after the first 3 months of treatment. Since many patients may need long-term antidepressant treatment, new antidepressants need to be developed that are effective, tolerable, and safe and that improve maintenance of wellness.
That one there! Pointing to establish device identity (2002)

Computing devices within current work and play environments are relatively static. As the number of 'networked' devices grows, and as people and their devices become more dynamic, situations will commonly arise where users will wish to use 'that device there' instead of navigating through traditional user interface widgets such as lists. This paper describes a process for identifying devices through a pointing gesture using custom tags and a custom stylus called the gesturePen. Implementation details for this system are provided along with qualitative and quantitative results from a formal user study. As ubiquitous computing environments become more pervasive, people will rapidly switch their focus between many computing devices. The results of our work demonstrate that our gesturePen method can improve the user experience in ubiquitous environments by facilitating significantly faster interactions between computing devices.
Metabolic and cardiovascular traits: an abundance of recently identified common genetic variants (2008)

Genome-wide association studies are providing new insights into the genetic basis of metabolic and cardiovascular traits. In the past 3 years, common variants in approximately 50 loci have been strongly associated with metabolic and cardiovascular traits. Several of these loci have implicated genes without a previously known connection with metabolism. Further studies will be required to characterize the full impact of these loci on metabolism. Many of the identified loci include multiple independent variants that influence the same metabolic or cardiovascular trait and a few loci harbor independent variants that each influence distinct traits. The total proportion of trait heritability explained by variants identified so far is still modest (typically <10%). Future studies will build on these successes by identifying additional common and rare variants and by determining the functional impact of the underlying alleles and genes.
Specific modulation of ectodermal cell fates in Xenopus embryos by glycogen synthase kinase (1995)

Shaggy is a downstream component of the wingless and Notch signaling pathways which operate during Drosophila development. To address the role of glycogen synthase kinase 3 beta (GSK3 beta), a mammalian homologue of Shaggy, in vertebrate embryogenesis, it was overexpressed in Xenopus embryos. Microinjection of rat GSK3 beta mRNA into animal ventral blastomeres of 8-cell-stage embryos triggered development of ectopic cement glands with an adjacent anterior neural tissue as evidenced by in situ hybridization with Xotx2, a fore/midbrain marker, and NCAM, a pan-neural marker. In contrast, animal dorsal injection of the same dose of GSK3 beta mRNA caused eye deficiencies, whereas vegetal injections had no pronounced effects on normal development. Using several mutated forms of rat GSK3 beta, we demonstrate that the observed phenotypes are dose-dependent and tightly correlate with GSK3 beta enzymatic activity. Lineage tracing experiments showed that the effects of GSK3 beta are cell autonomous and that ectopic cement glands and eye deficiencies arose directly from cells containing GSK3 beta mRNA. Molecular marker analysis of ectodermal explants overexpressing GSK3 beta has revealed activation of Xotx2 and of cement gland marker XAG-1, but expression of NCAM and XIF-3 was not detected. Phenotypic effects of mRNA encoding a Xenopus homologue of GSK3 beta were identical to those of rat GSK3 beta mRNA. We hypothesize that GSK3 beta mediates the initial steps of neural tissue specification and modulates anteroposterior ectodermal patterning via activation of Otx2 transcription. Our observations implicate GSK3 beta in signaling pathways operating during neural tissue development and during specification of anterior ectodermal cell fates.
Way-predicting set-associative cache for high performance and low energy consumption (1999)

This paper proposes a new approach using way prediction for achieving high performance and low energy consumption of set-associative caches. By accessing only a single cache way predicted, instead of accessing all the ways in a set, the energy consumption can be reduced. This paper shows that the way-predicting set-associative cache improves the ED (energy-delay) product by SO-70% compared to a conventional set-associative cache.
Hyperthermia enables tumor-specific nanoparticle delivery: effect of particle size. (2000)

The efficacy of novel cancer therapeutics has been hampered by the ability to deliver these agents to the tumor at effective concentrations. Liposomes have been used as a method to overcome some delivery issues and, in combination with hyperthermia, have been shown to increase drug delivery to tumors. Particle size has been shown to affect the delivery of liposomes, but it is not known how hyperthermia affects size dependence. This study investigates the effect of hyperthermia (42 degrees C) on the extravasation of different sized nanoparticles (albumin; 100-, 200-, and 400-nm liposomes) from tumor microvasculature in a human tumor (SKOV-3 ovarian carcinoma) xenograft grown in mouse window chambers. In this model (at 34 degrees C), no liposomes were able to extravasate into the tumor interstitium. Hyperthermia enabled liposome extravasation of all sizes. The magnitude of hyperthermia-induced extravasation was inversely proportional to particle size. Thus, at normothermia (34 degrees C), the pore cutoff size for this model was between 7 and 100 nm (e.g., liposomes did not extravasate). At 42 degrees C, the pore cutoff size was increased to >400 nm, allowing all nanoparticles tested to be delivered to the tumor interstitium to some degree. With hyperthermia, the 100-nm liposome experienced the largest relative increase in extravasation from tumor vasculature. Hyperthermia did not enable extravasation of 100-nm liposomes from normal vasculature, potentially allowing for tumor-specific delivery. These experiments indicate that hyperthermia can enable and augment liposomal drug delivery to tumors and potentially help target liposomes specifically to tumors.
Transduction of the MPG-tagged fusion protein into mammalian cells and oocytes depends on amiloride-sensitive endocytic pathway (2009)

The results show that the transduction of MPG fusion protein utilizes endocytic pathway(s) which is amiloride-sensitive and partially dynamin-dependent. Collectively, the MPG fusion protein could be further developed as a novel tool of "protein therapeutics", with potentials to be used in various cell systems including mammalian oocytes.
Holographically Directed Assembly of Polymer Nanocomposites (2010)

Layered polymer/nanoparticle composites have been created through the one-step two-beam interference lithographic exposure of a dispersion of 25 and 50 nm silica particles within a photopolymerizable mixture at a wavelength of 532 nm. The polymerizable mixture is composed of pentaerythritol triacrylate (monomer), 1-vinyl-2-pyrrolidinone (monomer), and photoinitiator. In the areas of constructive interference, the monomer begins to polymerize via a free-radical process and concurrently the nanoparticles move into the regions of destructive interference. The effects of exposure time, power density, nanoparticle size, and periodicity on the final nanocomposite structure were measured with transmission electron microscopy to determine the mechanism for particle segregation. Diffraction from the sample was monitored as well, though its magnitude was not a good predictor of nanostructure in this relatively low index contrast system. Exposure time did not have a strong effect on the final structure. The best nanoparticle sequestration was observed at reduced laser power density, smaller interferogram periodicity, and decreased nanoparticle size, indicating that particle segregation is dominated by diffusion-limited nanoparticle transport directed by a matrix containing a gradient of polymerization kinetics.
Angiogenesis-Dependent and Independent Phases of Intimal Hyperplasia (2004)

Our findings indicate that adventitial angiogenesis stimulates intimal thickening but does not initiate it.