gebhart/patrepeval huggingface dataset:
La dolce vita at TOPLAS (2010)

research-article Free Access Share on La dolce vita at TOPLAS Authors: Kathryn S. Mckinley View Profile , Keshav Pingali View Profile Authors Info & Claims ACM Transactions on Programming Languages and SystemsVolume 32Issue 4April 2010 Article No.: 10pp 1–6https://doi.org/10.1145/1734206.1734207Published:22 April 2010Publication History 0citation379DownloadsMetricsTotal Citations0Total Downloads379Last 12 Months29Last 6 weeks5 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my Alerts New Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
Gene Therapy with Autologous, Interleukin 2-Secreting Tumor Cells in Patients with Malignant Melanoma (1999)

We vaccinated metastatic melanoma patients with irradiated, autologous melanoma cells genetically engineered to secrete interleukin 2 (IL-2) to investigate whether an anti-tumor immune response would be induced. Melanoma cell cultures were established from surgical specimens and were engineered to secrete IL-2 by infection with recombinant retrovirus. Twelve patients were vaccinated subcutaneously one, two, or three times with approximately 10(7) irradiated, autologous, IL-2-secreting tumor cells. Treatment was well tolerated, with local reactions at 11 of 24 injection sites and minor systemic symptoms of fever and headache after 6 injections. One patient developed anti-tumor DTH after the first vaccination and showed an increased response after the second vaccination. Anti-autologous tumor CTLs could be detected prevaccination in the peripheral blood of seven patients and their activity increased after vaccination in four patients. No UICC-defined clinical responses were seen, but three patients had stable disease for 7-15 months, one of whom has not yet progressed (15+ months). Thus, patient vaccination with autologous, genetically engineered tumor cells is feasible and safe. Anti-tumor DTH and CTLs can be induced in some patients with such a vaccine.
Magnocellular Pathway Impairment in Schizophrenia: Evidence from Functional Magnetic Resonance Imaging (2008)

Sensory processing deficits in schizophrenia have been documented for several decades, but their underlying neurophysiological substrates are still poorly understood. In the visual system, the pattern of pathophysiology reported in several studies is suggestive of dysfunction within the magnocellular visual pathway beginning in early sensory cortex or even subcortically. The present study used functional magnetic resonance imaging to investigate further the neurophysiological bases of visual processing deficits in schizophrenia and in particular the potential role of magnocellular stream dysfunction. Sinusoidal gratings systematically varying in spatial frequency content were presented to subjects at low and high levels of contrast to differentially bias activity in magnocellular and parvocellular pathways based on well established differences in neuronal response profiles. Hemodynamic responses elicited by different spatial frequencies were mapped over the occipital lobe and then over the entire brain. Retinotopic mapping was used to localize the occipital activations with respect to the boundaries of visual areas V1 and V2, which were demarcated in each subject. Relative to control subjects, schizophrenia patients showed markedly reduced activations to low, but not high, spatial frequencies in multiple regions of the occipital, parietal, and temporal lobes. These findings support the hypothesis that schizophrenia is associated with impaired functioning of the magnocellular visual pathway and further suggest that these sensory processing deficits may contribute to higher-order cognitive deficits in working memory, executive functioning, and attention.
ERK1 and ERK2 MAPK are key regulators of distinct gene sets in zebrafish embryogenesis (2008)

The gene ontology analyses showed that ERK1 and ERK2 target common and distinct gene sets, confirming the difference in knockdown phenotypes and diverse roles for these kinases during embryogenesis. For ERK1 we identified specific genes involved in dorsal-ventral patterning and subsequent embryonic cell migration. For ERK2 we identified genes involved in cell-migration, mesendoderm differentiation and patterning. The specific function of ERK2 in the initiation, maintenance and patterning of mesoderm and endoderm formation was biologically confirmed.
Isolation of an abundant 50,000-dalton actin filament bundling protein from Dictyostelium amoebae. (1990)

A monomeric actin bundling protein with a native molecular weight of approximately 50,000 (ABP-50) has been isolated from amoebae of Dictyostelium discoideum. ABP-50 cross-links F-actin to form tightly packed bundles, some of which are highly ordered. It exhibits a Kd of 2.1 microM and a molar ratio to actin of 1:1 in bundles. Calcium and ATP at physiological concentrations have no effect on these activities. ABP-50 is immunologically unrelated to 30-kDa protein, a previously described bundling protein from Dictyostelium. Immunofluorescence with affinity-purified polyclonal antibodies indicates that ABP-50 is localized in regions of the amoeboid cell cortex containing actin bundles. The molar ratio of ABP-50 to actin is approximately 1:5 in vivo. Therefore, the abundance of ABP-50 suggests that it may be responsible for the majority of the bundling activity in these cells.
Double optical feedback and PT-symmetry breaking induced nonlinear dynamics in semiconductor lasers (2016)

A central aim of this research is to probe the nonlinear dynamics that arise in a semiconductor laser due to optical feedback. We investigate two schemes of optical feedback. The first scheme subjects the laser to optical feedback from two external cavities (or two loops), wherein each cavity contains a spectral filter. Using two filtered optical feedbacks, we experimentally demonstrate the ability to elicit and control unique dynamics in the optical emission frequency (wavelength) of the laser. These results are compared to a deterministic model describing the evolution of the complex electric field and carrier density of the laser. As the feedback rate from one cavity is increased, we observe a period doubling route in the frequency dynamics. To determine the influence of quantum noise on the period doubling route, we examine an augmented model of the rate equations which includes the effects of spontaneous emission and shot noise. One of the more surprising results is that in the presence of noise a larger feedback strength is required to induce chaotic dynamics. We find that noise drives the system toward stable attractors and the effects of the time-delay on the periodic dynamics are more pronounced. The second scheme we use is a system consisting of two time-delayed, optically coupled semiconductor lasers. We show that coupled lasers are an excellent test-bed to study parity (P) and time-reversal (T) symmetry breaking. Not only do optically coupled SCLs capture many of the characteristic signatures of PT symmetry breaking, but the time-delay between the lasers introduces novel and surprising features. We develop a simple PT model (analogous to a 2x2 Hamiltonian) that includes the effects of the time-delay. By examining the eigenvalues of the PT model, we can predict the intensity fluctuations by scanning the PT parameter, i.e. the frequency difference between the lasers. We experimentally observe the intensity fluctuations and find excellent agreement with the rate equation model which includes the dynamics of the carrier inversion and optical field.
Rock slope risk analysis based on non-linear failure criterion (2011)

The probability of failure of a rock slope is generally estimated by using the Limit Equilibrium Method (LEM) in conjunction with a reliability analysis. Although the LEM is relatively simple and time efficient, recent studies have indicated that using the LEM may overestimate the factor of safety by 21%, when based on a non-linear failure criterion. Fortunately, the solutions presented by Li et al. (2008, 2009) can provide more accurate evaluations for rock slope stability as the numerical upper and lower bound limit analysis methods (2002a, 2002b, 2005) were employed. The advantages of these methods are used in this study to assess the rock slope probability of failure. The motivation is that with more accurate methods to evaluate the factor of safety, more economic designs can be performed.
Rous sarcoma virus-transformed cells develop peculiar adhesive structures along the cell periphery (1993)

Alteration of the cell/substratum adhesive structures of rat fibroblasts (3Y1 cells) upon transformation by Rous sarcoma virus (RSV) was investigated by immunofluorescence microscopy. In serum-containing culture medium, 3Y1 cells developed focal adhesions as their main adhesive structures, while BY1 cells expressed peculiar close contacts along the cell periphery with the vitronectin receptor integrin, in addition to podosomes. These peripheral close contacts are referred to as the peripheral adhesions. The peripheral adhesions were observed as a darker region than podosomes by interference reflection microscopy. They were more easily destroyed by incubating the cells with RGD-containing peptide than were the focal adhesions. In contrast to focal adhesions and podosomes, actin bundles were not detected within the peripheral adhesions, where pp60v-src and tyrosine-phosphorylated proteins accumulated. Expression of the integrin was determined by the substratum composition when BY1 cells were cultured in serum-free culture medium. Under such conditions, BY1 cells expressed the peripheral adhesions within 3 hours on adhesion molecule-coated glass. On the other hand, in serum-containing medium, they first developed focal adhesions transiently at their early stage of adhesion, and then the peripheral adhesions were predominantly expressed within 12 hours. Podosomes were formed in a time course similar to that of the peripheral adhesions. These findings suggest that the peripheral adhesion is a class of stable adhesive structure distinct from the focal adhesion or podosome of BY1 cells. Similar close contact-type peripheral adhesions with the integrin were also observed in a variety of cultured cells such as normal fibroblasts at their logarithmic growth phase, phorbol ester-treated fibroblasts, and several malignant tumor cells, with poorly organized focal adhesions and stress fibers. These findings further suggest that the peripheral adhesions may be widely involved in the adhesion of cells that inadequately develop stress fibers and focal adhesions.
Pepsinogen secretion from dispersed chief cells from guinea pig stomach (1984)

In the present study we examined the actions of various secretagogues on pepsinogen secretion from freshly dispersed chief cells prepared from guinea pig stomach. Chief cells were obtained by preparing dispersed gastric glands, subjecting the glands to mechanical disruption in the presence of EGTA, and fractionating the resulting mucosal cells on a Percoll density gradient. Chief cells constituted 90% of the final cell suspension and cell viability was 99%. In these cells, pepsinogen secretion was stimulated by agents whose actions are probably mediated by calcium: carbachol, cholecystokinin, and A23187. Pepsinogen secretion was also stimulated by agents whose actions are probably mediated by cAMP: secretin, vasoactive intestinal peptide, and 8-bromo-cAMP. Reducing the incubation temperature from 37 degrees to 4 degrees C or adding carbonyl cyanide m-chlorophenylhydrazone abolished secretagogue-induced pepsinogen secretion. These results indicate that freshly dispersed chief cells from guinea pig stomach are responsive to secretagogues and provide a suitable model for investigating cellular mechanisms of secretagogue-induced pepsinogen secretion.
The prostaglandin E<sub>2</sub> EP2 receptor accelerates disease progression and inflammation in a model of amyotrophic lateral sclerosis (2008)

These data suggest that prostaglandin E(2) signaling via the EP2 receptor functions in the mutant SOD model and more broadly in inflammatory neurodegeneration to regulate expression of a cassette of proinflammatory genes. Inhibition of EP2 signaling may represent a novel strategy to downregulate the inflammatory response in neurodegenerative disease.
Distinct subtypes of group I metabotropic glutamate receptors on rat spinal neurons mediate complex facilitatory and inhibitory effects (2003)

While group I glutamate metabotropic (mGlu) receptors show discrete neuronal distribution in the neonatal rat spinal cord, the functional role of their distinct receptor subtypes remains uncertain. Intracellular recording from lumbar motoneurons together with extracellular recording of ventral root (VR) responses was used to investigate the differential contribution by mGlu receptor subtypes to cell excitability and network activity. The group I agonist DHPG evoked motoneuron depolarization (via the AIDA or CPCCOEt-sensitive mGlu receptor subtype 1) mainly at network level and generated sustained, network-dependent oscillations (via the MPEP-sensitive mGlu receptor subtype 5). DHPG also decreased the peak amplitude of synaptic responses induced by dorsal root stimuli, an effect unrelated to depolarization and dependent on glycinergic transmission. Synaptic responses were insensitive to AIDA or MPEP. The present results can be explained by assuming excitation of discrete classes of interneurons by group I mGlu receptor activity. Thus, the cellular distribution of those mGlu receptors at strategic circuit connections may determine the functional outcome of the network in terms of excitation or inhibition. Even if there was insufficient activation by endogenous glutamate of mGlu receptors during synaptic activity evoked by DR stimuli, it is apparent that such receptors are important pharmacological targets for powerful and rapid up- or down-regulation of spinal signal processing at network level, providing a rationale for the proposed use of mGlu receptor agonists in a variety of spinal pathological conditions.
Non-Brownian particle gel (2009)

Particle gels are usually formed by density matching or Brownian motion against gravity. However, the suspended state of non-Brownian particles is essential in applications, such as Si-wafer wire sawing. By the addition of alkyl amine, micron-sized SiC suspensions are shown to form particle gel in ethylene glycol. The ratio of storage to loss modulus is about 3, indicating a weak gel. The structure by particle-particle attraction is demonstrated through existing yield stress. With increasing surfactant concentration, the gel forms easier, the sediment layer swells more significantly, and the yield stress is greater accordingly. A gelling mechanism has been proposed and examined.
Titelbild (2001)

Das Titelbild zeigt, wie sich eine Thrombose in tief liegenden Venen des Oberschenkels entwickelt: Ein Blutstau infolge einer langsamen, turbulenten Blutströmung kann in Verbindung mit einer übermäßig starken Gerinnung, wie sie z. B. bei Operationen auftritt, zu einem Thrombus führen. Das synthetische sulfatierte Pentasaccharid, von dem ein Abschnitt gezeigt ist, wirkt durch Aktivierung des Plasmaproteins Antithrombin III antithrombotisch. Konformativ fixierte Monosaccharide wurden nun synthetisiert, anhand derer nachgewiesen wurde, dass L-Iduronsäure, ein Bestandteil des Pentasaccharids, eine ungewöhnliche verzerrte Konformation annehmen muss, um Antithrombin III zu aktivieren. Derartige konformative Effekte sind möglicherweise auch zur Erklärung der einzigartigen biologischen Eigenschaften von Glycosaminglycanen heranzuziehen, die ebenfalls L-Iduronsäure enthalten. Im Hintergrund des Bildes ist ein Schwarm Vampire gezeigt, die vom Pentasaccharid angezogen werden. Die Bezeichnung Vampir stammt vom französischen Naturforscher Georges Louis Leclerc Comte de Buffon (1707–1788), der diesen Namen 1761 südamerikanischen, Blut saugenden Fledermäusen (lateinischer Name desmodus rotundus) gab. Diese Fledermäuse greifen bisweilen Vieh und vereinzelt auch schlafende Menschen an. Zwar enthält die Speichelflüssigkeit der Vampire ein Antikoagulans, doch würden sie auch das oben erwähnte Pentasaccharid gut nutzen können, um das Blut leichter aus den Venen zu saugen. Mehr über diese für Vampire nützliche Verbindung finden Sie in der Zuschrift von Petitou, Sinaÿ et al. auf S. 1723 ff.
Neurocalcin-immunoreactive neurons in the mammalian dorsal root ganglia, including humans (2000)

Neurocalcin (NC) is a recently characterized EF-hand calcium-binding protein present in a discrete population of sensory neurons and their peripheral mechanoreceptors, but its presence in peripheral nervous system neurons other than in the rat is still unknown. The present study was designed to investigate the occurrence of NC in the dorsal root ganglia (DRG) of several mammalian species (horse, buffalo, cow, sheep, pig, dog, and rat), including humans. DRG were fixed, embedded in paraffin, and processed for immunohistochemistry using a polyclonal antibody against NC. The size of the immunoreactive neurons was measured. In all species examined, NC immunoreactivity (IR) was restricted to neurons but the percentage, as well as the size of the immunoreactive neurons, varied among different species. As a rule, small neurons (diameter <20 microm) lack NC IR. In some species (pig, dog, buffalo, cow), only the largest neurons showed IR, whereas in others (sheep, horse, rat, and humans) they covered the entire range of neuron sizes. The pattern of immunostaining was cytoplasmic, although in some species (cow and buffalo), it formed a peripheral "ring." The present results demonstrate that mammalian DRG contain a subpopulation of NC-positive neurons, which varies from one species to another. Based on the neuron size, the possible function of the NC-containing neurons is discussed.
Accurate modeling of line-defect photonic crystal waveguides (2003)

An accurate three-dimensional method to calculate the Bloch modes of photonic crystal (PhC) waveguides is proposed. Good agreement with available experimental and numerical data is obtained. The originality of the method lies in the fact that the Bloch modes are seen as the electromagnetic fields associated to the complex poles of an in-plane transversal scattering matrix. In comparison with previous approaches, the computational domain discretized is smaller and a higher accuracy for the losses of PhC waveguides is achieved.
Overexpression of manganese superoxide dismutase ameliorates high-fat diet-induced insulin resistance in rat skeletal muscle (2012)

Elevated mitochondrial reactive oxygen species have been suggested to play a causative role in some forms of muscle insulin resistance. However, the extent of their involvement in the development of diet-induced insulin resistance remains unclear. To investigate, manganese superoxide dismutase (MnSOD), a key mitochondrial-specific enzyme with antioxidant modality, was overexpressed, and the effect on in vivo muscle insulin resistance induced by a high-fat (HF) diet in rats was evaluated. Male Wistar rats were maintained on chow or HF diet. After 3 wk, in vivo electroporation (IVE) of MnSOD expression and empty vectors was undertaken in right and left tibialis cranialis (TC) muscles, respectively. After one more week, insulin action was evaluated using hyperinsulinemic euglycemic clamp, and tissues were subsequently analyzed for antioxidant enzyme capacity and markers of oxidative stress. MnSOD mRNA was overexpressed 4.5-fold, and protein levels were increased by 70%, with protein detected primarily in the mitochondrial fraction of muscle fibers. This was associated with elevated MnSOD and glutathione peroxidase activity, indicating that the overexpressed MnSOD was functionally active. The HF diet significantly reduced whole body and TC muscle insulin action, whereas overexpression of MnSOD in HF diet animals ameliorated this reduction in TC muscle glucose uptake by 50% (P < 0.05). Decreased protein carbonylation was seen in MnSOD overexpressing TC muscle in HF-treated animals (20% vs. contralateral control leg, P < 0.05), suggesting that this effect was mediated through an altered redox state. Thus interventions causing elevation of mitochondrial antioxidant activity may offer protection against diet-induced insulin resistance in skeletal muscle.
CH4 oxidation potential measurements for a warm-dry to cold-wet environmental gradient using the C. Hart Merriam Elevation Gradient (2005)

We determined the response of terrestrial methane (CH4) uptake to 4 years of full-factorial manipulations of precipitation and temperature in four ecosystems along a 50 km warm and dry to cold and wet climatic gradient (desert grassland, pinyon-juniper woodland, ponderosa pine forest, and mixed conifer forest). Our goals were to determine whether ecosystem-specific, intraannual, and interactive responses to altered precipitation and warming are quantitatively important. Passive collectors and interceptors increased (+50% per event) and reduced (-30% per event) the quantity of precipitation delivered to experimental plant-soil mesocosms, and downward transfer along the elevation gradient warmed mesocosms by 1.8_C on average. Methane uptake in the colder and wetter ecosystems along the gradient decreased with increasing precipitation, especially during the wet season. The warmer and drier ecosystems, however, responded more strongly to warming, exhibiting less CH4 uptake with increasing temperature. We found no interaction between altered precipitation and warming in any ecosystem. Soil CH4 consumption in the laboratory was a strong predictor of ecosystem differences in field CH4 consumption, but was a poor predictor of the effects of climatic change observed in the field. Based on our results, future climate scenarios that are wet and warm will cause the largest reduction in terrestrial CH4 uptake across ecosystem types.
Transcriptional activation of matrix genes by transforming growth factor beta 1 in mesangial cells. (1994)

The accumulation of mesangial matrix is a common histologic abnormality observed over the course of various glomerular diseases. To examine the role of transforming growth factor beta 1 (TGF-beta 1), a well-known regulator of extracellular matrix metabolism, in such processes, we studied the effects of this peptide on the gene expression of extracellular matrix components in cultured rat mesangial cells. TGF-beta 1 increased the mRNA levels for alpha 1 (I) and alpha 1 (IV) collagens and fibronectin. The increase in these mRNA levels was detectable 6 h after stimulation by TGF-beta 1. At 24 h, the mRNA levels for alpha 1 (I) and alpha 1 (IV) collagens and fibronectin increased 1.9-, 2.8- and 2.6-fold, respectively, above their basal levels. Concomitant treatment with cycloheximide did not prevent the stimulation by TGF-beta 1 and resulted in exceptional superinduction for the fibronectin gene. Concomitant treatment with actinomycin D completely inhibited the increase in the mRNA levels induced by TGF-beta 1. Furthermore, TGF-beta 1 showed no stabilizing effect on the transcripts. These results suggest that TGF-beta 1, which is released in glomerular injury, induces an increase in the transcription of the alpha 1 (I) and alpha 1 (IV) collagen and fibronectin genes in mesangial cells and may mediate the accumulation of the extracellular matrix in the mesangium.
Element analysis of solid samples by laser ablation and optical spectroscopy (1993)

The requirements for quantitative, matrix independent element analysis of solid samples by laser ablation and optical spectroscopy are discussed. In particular, the methods of direct optical emission spectrometry of laser produced plasmas and by re‐excitation of the laser ablated vapor plume are described.