gebhart/patrepeval huggingface dataset:
Interleukin 3, granulocyte-macrophage colony-stimulating factor, and transfected erythropoietin receptors mediate tyrosine phosphorylation of a common cytosolic protein (pp100) in FDC-ER cells. (1992)

Receptors for the hematopoietic growth factors erythropoietin, interleukin 3 (IL-3), and granulocyte-macrophage colony-stimulating factor (GM-CSF) are members of a structurally related receptor superfamily. Interestingly, while none of these receptors encode tyrosine kinase activities, induced tyrosine phosphorylation has been observed in various responsive cells stimulated with each factor. Toward defining possible common transduction pathways which are activated by these three cytokines, we have studied induced protein phosphorylation in murine myeloid FDC-P1 cells stably transfected with an erythropoietin receptor cDNA (FDC-ER cells). FDC-ER cells proliferate in response to erythropoietin (Quelle, D. E., and Wojchowski, D. M. (1991) Proc. Natl. Acad. Sci. U.S.A. 88, 4801-4805), and presently are shown to rapidly phosphorylate a M(r) 100,000 cytosolic protein (pp100) at tyrosine residues in response to this factor. Phosphorylation of pp100 also is induced in FDC-P1 and FDC-ER cells in response to IL-3 or GM-CSF. Importantly, quantitative analyses showed identical concentration dependencies for factor-induced pp100 phosphorylation and induced cell proliferation. Moreover, a selective loss of proliferative responsiveness to GM-CSF in FDC-ER cells was associated with a reduced capacity of GM-CSF to induce pp100 phosphorylation. Finally, limited differences in tryptic phosphopeptide maps of pp100 as isolated following exposure to erythropoietin, IL-3, or GM-CSF were observed, suggesting that these factors also may preferentially induce phosphorylation of pp100 at distinct sites. These findings are consistent with a role for pp100 as a common cytosolic transducer in the apparently convergent pathways of erythropoietin-, IL-3-, and GM-CSF-induced proliferation of myeloid progenitor cells.
Load Reduction, Demand Response and Energy Efficient Technologies and Strategies (2008)

The Department of Energy’s (DOE’s) Pacific Northwest National Laboratory (PNNL) was tasked by the DOE Office of Electricity (OE) to recommend load reduction and grid integration strategies, and identify additional demand response (energy efficiency/conservation opportunities) and strategies at the Forest City Housing (FCH) redevelopment at Pearl Harbor and the Marine Corps Base Hawaii (MCBH) at Kaneohe Bay. The goal was to provide FCH staff a path forward to manage their electricity load and thus reduce costs at these FCH family housing developments. The initial focus of the work was at the MCBH given the MCBH has a demand-ratchet tariff, relatively high demand (~18 MW) and a commensurate high blended electricity rate (26 cents/kWh). The peak demand for MCBH occurs in July-August. And, on average, family housing at MCBH contributes ~36% to the MCBH total energy consumption. Thus, a significant load reduction in family housing can have a considerable impact on the overall site load. Based on a site visit to the MCBH and meetings with MCBH installation, FCH, and Hawaiian Electric Company (HECO) staff, recommended actions (including a "smart grid" recommendation) that can be undertaken by FCH to manage and reduce peak-demand in family housing are made. Recommendations are also made to reduce overall energy consumption, and thus reduce demand in FCH family housing.
Vascular Permeability during Antiangiogenesis Treatment: MR Imaging Assay Results as Biomarker for Subsequent Tumor Growth in Rats (2008)

The MR imaging-assayed acute change in vascular leakiness after a single dose of bevacizumab was an early, measurable predictive biomarker of tumor angiogenesis treatment response.
Enhanced osteoclastogenesis in patients with tophaceous gout: Urate crystals promote osteoclast development through interactions with stromal cells (2008)

Chronic tophaceous and erosive gout is characterized by enhanced osteoclast development. These data provide a rationale for the study of osteoclast-targeted therapies for the prevention of bone damage in chronic gout.
Video Watermarking In 3D Dct Domain (2006)

Publication in the conference proceedings of EUSIPCO, Florence, Italy, 2006
Analysis of Anti-Influenza Virus Neuraminidase Antibodies in Children, Adults, and the Elderly by ELISA and Enzyme Inhibition: Evidence for Original Antigenic Sin (2017)

Antibody responses to influenza virus hemagglutinin provide protection against infection and are well studied. Less is known about the human antibody responses to the second surface glycoprotein, neuraminidase. Here, we assessed human antibody reactivity to a panel of N1, N2, and influenza B virus neuraminidases in different age groups, including children, adults, and the elderly. Using enzyme-linked immunosorbent assays (ELISA), we determined the breadth, magnitude, and isotype distribution of neuraminidase antibody responses to historic, current, and avian strains, as well as to recent isolates to which these individuals have not been exposed. It appears that antibody levels against N1 neuraminidases were lower than those against N2 or B neuraminidases. The anti-neuraminidase antibody levels increased with age and were, in general, highest against strains that circulated during the childhood of the tested individuals, providing evidence for "original antigenic sin." Titers measured by ELISA correlated well with titers measured by the neuraminidase inhibition assays. However, in the case of the 2009 pandemic H1N1 virus, we found evidence of interference from antibodies binding to the conserved stalk domain of the hemagglutinin. In conclusion, we found that antibodies against the neuraminidase differ in magnitude and breadth between subtypes and age groups in the human population. (This study has been registered at ClinicalTrials.gov under registration no. NCT00336453, NCT00539981, and NCT00395174.)<b>IMPORTANCE</b> Anti-neuraminidase antibodies can afford broad protection from influenza virus infection in animal models and humans. However, little is known about the breadth and magnitude of the anti-neuraminidase response in the human population. Here we assessed antibody levels of children, adults, and the elderly against a panel of N1, N2, and type B influenza virus neuraminidases. We demonstrated that antibody levels measured by ELISA correlate well with functional neuraminidase inhibition titers. This is an important finding since ELISA is a simpler method than functional assays and can be implemented in high-throughput settings to analyze large numbers of samples. Furthermore, we showed that low titers of broadly cross-reactive antibodies against neuraminidase are prevalent in humans. By the use of an appropriate vaccination strategy, these titers could potentially be boosted to levels that might provide broad protection from influenza virus infection.
Anisotropy of selective epitaxy in nanoscale-patterned growth: GaAs nanowires selectively grown on a SiO2-patterned (001) substrate by molecular-beam epitaxy (2005)

Anisotropic selective epitaxy in nanoscale-patterned growth (NPG) by molecular-beam epitaxy is investigated on a 355nm period two-dimensional array of circular holes fabricated in a 30-nm-thick SiO2 film on a GaAs(001) substrate. The hole diameter ranged from 70to150nm. The small hole diameter and the very thin masking layer stimulated lateral growth over the SiO2 surface at an early stage of selective epitaxy on this patterned substrate. Lateral overgrowth associated with selective epitaxy, however, did not proceed isotropically along the circular boundary between the open substrate surface and the SiO2 mask. There was preferential growth direction parallel to ⟨111⟩B. This anisotropy in the selective epitaxy resulted in the formation of a nanoscale, nontapered, straight-wire-type epitaxial layer (GaAs nanowires), which had a length of up to 1.8μm for a nominal 200nm deposition. Every GaAs nanowire had a hexagonal prismatic shape directed along ⟨111⟩B and was surrounded by six (110) sidewalls. The anisotropy of selective epitaxy and faceting in NPG were affected by the profile of the SiO2 mask and are interpreted using a minimization of the total surface energy for equilibrium crystal shape.
Identification of high excision capacity for 5-hydroxymethyluracil mispaired with guanine in DNA of Escherichia coli MutM, Nei and Nth DNA glycosylases (2003)

The oxidation and deamination of 5-methylcytosine (5mC) in DNA generates a base-pair between 5-hydroxymethyluracil (5hmU) and guanine. 5hmU normally forms a base-pair with adenine. Therefore, the conversion of 5mC to 5hmU is a potential pathway for the generation of 5mC to T transitions. Mammalian cells have high levels of activity of 5hmU-DNA glycosylase, which excises 5hmU from DNA. However, glycosylases that similarly excise 5hmU have not been observed in yeast or Escherichia coli. Recently, we found that E.coli MutM, Nei and Nth have DNA glycosylase activity for 5-formyluracil, which is another type of oxidation product of the thymine methyl group. In this study, we examined whether or not E.coli MutM, Nei and Nth have also DNA glycosylase activity that acts on 5hmU in vitro. When incubated with synthetic duplex oligonucleotides containing 5hmU:G or 5hmU:A, purified MutM, Nei and Nth cleaved the 5hmU:G oligonucleotide 58, 5 and 37 times, respectively, more efficiently than the 5hmU:A oligonucleotide. In E.coli, the 5hmU-DNA glycosylase activities of MutM, Nei and Nth may play critical roles in the repair of 5hmU:G mispairs to avoid 5mC to T transitions.
Failing the Public Health — Rofecoxib, Merck, and the FDA (2004)

On May 21, 1999, Merck was granted approval by the Food and Drug Administration (FDA) to market rofecoxib (Vioxx). On September 30, 2004, after more than 80 million patients had taken this medicine and annual sales had topped $2.5 billion, the company withdrew the drug because of an excess risk of myocardial infarctions and strokes. This represents the largest prescription-drug withdrawal in history, but had the many warning signs along the way been heeded, such a debacle could have been prevented. Neither of the two major forces in this five-and-a-half-year affair — neither Merck nor the FDA — fulfilled its . . .
Transcription Activation by the Ecdysone Receptor (EcR/USP): Identification of Activation Functions (2003)

The ecdysone receptor is a heterodimer of the two nuclear receptors EcR and ultraspiracle (USP). We have identified the regions of Drosophila EcR and USP responsible for transcriptional activation of a semisynthetic Eip71CD promoter in Kc cells. The isoform-specific A/B domains of EcR-B1 and B2, but not those of EcR-A or USP, exhibit strong activation activity [activation function 1 (AF1)], both in isolation and in the context of the intact receptor. AF1 activity in isoform B1 derives from dispersed elements; the B2-specific AF1 consists of a 17-residue amphipathic helix. AF2 function was studied using a two-hybrid assay in Kc cells, based on the observation that potent hormone-dependent activation by the EcR/USP ligand-binding domain heterodimer requires the participation of both partners. Mutagenesis reveals that AF2 function depends on EcR helix 12, but not on the cognate USP region. EcR helix 12 mutants (F645A and W650A) exhibit a dominant negative phenotype. Thus, in the setting tested, the ecdysone receptor can activate transcription using the AF1 regions of EcR-B1 or -B2 and the AF2 region of EcR. USP acts as an allosteric effector for EcR, but does not contribute any intrinsic function.
A Mechanism for Conductance Switching in Carbon-Based Molecular Electronic Junctions (2002)

A molecular junction formed by a 10-15 Å organic monolayer between carbon and mercury contacts exhibited conductance switching for several monolayer structures. When the carbon potential was scanned to a sufficiently negative voltage relative to the mercury, the junction resistance suddenly decreased by at least an order of magnitude, and high resistance could be restored by a positive voltage scan. The high and low conductance states were persistent, and conductance switching was repeatable at least 100 cycles for the case of a terphenyl junction. The switching behavior is consistent with phenyl ring rotation and formation of a planar, quinoid structure as a consequence of electron injection into the monolayer. A unique feature of the junction structure is the strong electronic coupling between the monolayer π system and the graphitic carbon through a quinoid double bond. Not only does this interaction lead to high conductivity and possible practical applications as a molecular switch, it also combines the electronic properties of the conjugated monolayer with those of the graphitic substrate. The switching mechanism reported here is an example of "dry electrochemistry" in which a redox process appears to occur under the influence of a high electric field in the absence of solvent or electrolyte. © 2002 The Electrochemical Society.
Risk factors in early pregnancy complications. (2010)

Abortion was found as the most frequent early pregnancy complication and the most frequent underlying risk factor was hypertension. Outcome included anaemia, psychological upset and infection.
Investigating dielectric properties of different stages of syngeneic murine ovarian cancer cells (2013)

In this study, the electrical properties of four different stages of mouse ovarian surface epithelial (MOSE) cells were investigated using contactless dielectrophoresis (cDEP). This study expands the work from our previous report describing for the first time the crossover frequency and cell specific membrane capacitance of different stages of cancer cells that are derived from the same cell line. The specific membrane capacitance increased as the stage of malignancy advanced from 15.39 ± 1.54 mF m(-2) for a non-malignant benign stage to 26.42 ± 1.22 mF m(-2) for the most aggressive stage. These differences could be the result of morphological variations due to changes in the cytoskeleton structure, specifically the decrease of the level of actin filaments in the cytoskeleton structure of the transformed MOSE cells. Studying the electrical properties of MOSE cells provides important information as a first step to develop cancer-treatment techniques which could partially reverse the cytoskeleton disorganization of malignant cells to a morphology more similar to that of benign cells.
Relationship of Serum Antibody to Risk of Respiratory Syncytial Virus Infection in Elderly Adults (1998)

The relationship of serum antibody to respiratory syncytial virus (RSV) and risk of RSV infection was prospectively evaluated in frail elderly persons. Baseline blood samples from 22 subjects who developed symptomatic RSV infection during the 26-month study and from 22 control subjects who did not become infected with RSV were compared. The mean serum IgG titer to RSV fusion protein was significantly lower in the RSV-infected group than in the controls (15.4 +/- 1.6 vs. 16.4 +/- 1.8, P = .05), as were the neutralizing titers to group A RSV (12.4 +/- 2.2 vs. 14.2 +/- 2.2, P = .008) and group B virus (9.1 +/- 2.1, vs. 10.3 +/- 1.5, P = .01). These results suggest that older adults with low titers of serum neutralizing antibody may be at greater risk of developing symptomatic RSV infection than those who have high antibody titers.
The Ciliary Neurotrophic Factor/Leukemia Inhibitory Factor/gp130 Receptor Complex Operates in the Maintenance of Mammalian Forebrain Neural Stem Cells (2001)

The cytokines that signal through the common receptor subunit gp130, including ciliary neurotrophic factor (CNTF), interleukin-6, leukemia inhibitory factor (LIF) and oncostatin M, have pleiotropic functions in CNS development. Given the restricted expression domain of the CNTF receptor alpha (CNTFR) in the developing forebrain germinal zone and adult forebrain periventricular area, we have examined the putative role of CNTFR/LIFR/gp130-mediated signaling in regulating forebrain neural stem cell fate in vivo and in vitro. Analysis of LIFR-deficient mice revealed that a decreased level of LIFR expression results in a reduction in the number of adult neural stem cells. In adult LIFR heterozygote (+/-) mice, the number of neural stem cells and their progeny in the forebrain subependyma and TH-immunoreactive neurons in the olfactory bulb were significantly reduced. Intraventricular infusion of CNTF into the adult mouse forebrain, in the absence or presence of epidermal growth factor (EGF), enhanced self-renewal of neural stem cells in vivo. Analyses of EGF-responsive neural stem cells proliferating in vitro found that CNTF inhibits lineage restriction of neural stem cells to glial progenitors, which in turn results in enhanced expansion of stem cell number. These results suggest that CNTFR/LIFR/gp130-mediated signaling supports the maintenance of forebrain neural stem cells, likely by suppressing restriction to a glial progenitor cell fate.
Stereodependent Inhibition of Plasminogen Activator Inhibitor Type 1 by Phosphorothioate Oligonucleotides: Proof of Sequence Specificity in Cell Culture and In Vivo Rat Experiments (1997)

Hexadecadeoxyribonucleotides complementary to a fragment of human PAI-1 mRNA located upstream of the start codon and their phosphorothioate analogs were studied in cultured HUVECs as sequence-dependent inhibitors of PAI-1 expression. The activity of the random mixture of diastereomers of phosphorothioate hexadecanucleotide PS-16H has been compared with that of isosequential, stereoregular [All-Sp] and [All-Rp] isomers. The highest inhibitory effect on PAI-1 synthesis was observed with the [All-Sp] diastereomer. Stereorandom phosphorothioate oligonucleotide PS-16R complementary to the same region of rat PAI-1 mRNA, when injected into tail vein of rats, substantially decreased the level of PAI-1 in blood plasma.
Dynamic Coupling of the Putative Coiled-coil Domain of ORAI1 with STIM1 Mediates ORAI1 Channel Activation (2008)

STIM1 and ORAI1 (also termed CRACM1) are essential components of the classical calcium release-activated calcium current; however, the mechanism of the transmission of information of STIM1 to the calcium release-activated calcium/ORAI1 channel is as yet unknown. Here we demonstrate by Förster resonance energy transfer microscopy a dynamic coupling of STIM1 and ORAI1 that culminates in the activation of Ca(2+) entry. Förster resonance energy transfer imaging of living cells provided insight into the time dependence of crucial events of this signaling pathway comprising Ca(2+) store depletion, STIM1 multimerization, and STIM1-ORAI1 interaction. Accelerated store depletion allowed resolving a significant time lag between STIM1-STIM1 and STIM1-ORAI1 interactions. Store refilling reversed both STIM1 multimerization and STIM1-ORAI1 interaction. The cytosolic STIM1 C terminus itself was able, in vitro as well as in vivo, to associate with ORAI1 and to stimulate channel function, yet without ORAI1-STIM1 cluster formation. The dynamic interaction occurred via the C terminus of ORAI1 that includes a putative coiled-coil domain structure. An ORAI1 C terminus deletion mutant as well as a mutant (L273S) with impeded coiled-coil domain formation lacked both interaction as well as functional communication with STIM1 and failed to generate Ca(2+) inward currents. An N-terminal deletion mutant of ORAI1 as well as the ORAI1 R91W mutant linked to severe combined immune deficiency syndrome was similarly impaired in terms of current activation despite being able to interact with STIM1. Hence, the C-terminal coiled-coil motif of ORAI1 represents a key domain for dynamic coupling to STIM1.
Transition jitter estimates in tilted and conventional perpendicular recording media at 1 tb/in2 (2003)

The recent proposal of tilted perpendicular recording for Tb/in <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> densities is extended here to examine the effects of intergranular exchange and anisotropy distributions on signal-to-noise ratio. This new recording system includes the single pole head, the medium and the soft underlayer as in perpendicular recording, but the medium anisotropy axes are titled at about 45°, optimally in the crosstrack direction. Both analytical formulas and micromagnetic simulations are utilized and both tilted and conventional perpendicular media are considered. At 1.2 Tb/in <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> exchange optimization and suitable anisotropy distribution limits give percentage transition jitter of 10% and 30% for tilted and conventional perpendicular media, respectively.
Ease.ml: Towards Multi-tenant Resource Sharing for Machine Learning Workloads (2017)

We present ease.ml, a declarative machine learning service platform we built to support more than ten research groups outside the computer science departments at ETH Zurich for their machine learning needs. With ease.ml, a user defines the high-level schema of a machine learning application and submits the task via a Web interface. The system automatically deals with the rest, such as model selection and data movement. In this paper, we describe the ease.ml architecture and focus on a novel technical problem introduced by ease.ml regarding resource allocation. We ask, as a "service provider" that manages a shared cluster of machines among all our users running machine learning workloads, what is the resource allocation strategy that maximizes the global satisfaction of all our users? Resource allocation is a critical yet subtle issue in this multi-tenant scenario, as we have to balance between efficiency and fairness. We first formalize the problem that we call multi-tenant model selection, aiming for minimizing the total regret of all users running automatic model selection tasks. We then develop a novel algorithm that combines multi-armed bandits with Bayesian optimization and prove a regret bound under the multi-tenant setting. Finally, we report our evaluation of ease.ml on synthetic data and on one service we are providing to our users, namely, image classification with deep neural networks. Our experimental evaluation results show that our proposed solution can be up to 9.8x faster in achieving the same global quality for all users as the two popular heuristics used by our users before ease.ml.
Development of a pericardial acellular matrix biomaterial: Biochemical and mechanical effects of cell extraction (1994)

There is evidence to suggest that the cellular components of homografts and bioprosthetic xenografts may contribute to calcification or immunogenic reactions. A four-step detergent and enzymatic extraction process has been developed to remove cellular components from bovine pericardial tissue. The process results in an acellular matrix material consisting primarily of elastin, insoluble collagen, and tightly bound glycosaminoglycans. Light and electron microscopy confirmed that nearly all cellular constituents are removed without ultrastructural evidence of damage to fibrous components. Collagen denaturation temperatures remained unaltered. Biochemical analysis confirmed the retention of collagen and elastin and some differential extraction of glycosaminoglycans. Low strain rate fracture testing and high strain rate viscoelastic characterization showed that, with the exception of slightly increased stress relaxation, the mechanical properties of the fresh tissue were preserved in the pericardial acellular matrix. Crosslinking of the material in glutaraldehyde or poly(glycidyl ether) produced mechanical changes consistent with the same treatments of fresh tissue. The pericardial acellular matrix is a promising approach to the production of biomaterials for heart valve or cardiovascular patching applications.