gebhart/patrepeval huggingface dataset:
A carbon-13 and deuterium nuclear magnetic resonance study of phosphatidylcholine/cholesterol interactions: Characterization of liquid-gel phases (1993)

A detailed study on the structure, dynamics, and thermodynamic behavior of phosphatidylcholine/cholesterol (PC/CHOL) mixtures was undertaken using differential scanning calorimetry (DSC) and solid-state nuclear magnetic resonance (NMR) spectroscopy. DSC thermograms of mixtures of cholesterol (CHOL) with 1,2-dipalmitoyl-sn-phosphatidylcholine (DPPC), 1,2-distearoyl-sn-phosphatidylcholine (DSPC), and 1,2-diarachidoyl-sn-phosphatidylcholine (DAPC) showed a broadening of the first-order gel-->liquid crystalline transition and a decrease in the transition enthalpy, indicating a gradual loss of cooperativity for high CHOL concentrations. DPPC and DSPC were labeled with 13C at the carbonyl group of the sn-2 chain and 2H was introduced into the middle of the sn-2 chain at the 6- and 12-position for DPPC and DSPC, respectively. The 13C and 2H NMR spectra of each labeled lipid were studied as a function of temperature and CHOL concentration. The residual quadrupole splitting in the 2H NMR spectra, delta nu Q perpendicular, was analyzed as a function of temperature and composition. For CHOL concentrations less than 30 mol %, a precipitous change in delta nu Q perpendicular occurs near the chain melting temperature of the phospholipid. Further increases in CHOL concentration broaden the transition and shift the midpoint to higher temperature, indicating the presence of a new phase at higher CHOL contents. Moreover, at a given temperature, delta nu Q perpendicular increases with increasing cholesterol content, which indicates a more ordered structure. The 13C NMR spectra in the gel state consisted of a superposition of two components which can be attributed to both gel-like and fluid phospholipid domains in the bilayer. This two-component spectrum can be simulated quantitatively with a two-parameter chemical exchange model, which permits the fraction of each form and the exchange rate to be determined as a function of temperature and composition. At high CHOL contents the line width of the fluid component broadens, suggesting an increase in the exchange rate between the domains. These results were interpreted in terms of a temperature composition diagram with one region L beta', two regions LGI and LGII, and one liquid crystalline region L alpha, with LG denoting "liquid-gel" type phases. Liquid-gel phases correspond to phases with increased order in the hydrocarbon chains (in comparison to that of the pure PC bilayer in the L alpha phase) combined with fast limit axial diffusion that averages the 13C NMR spectrum to a "fluidlike" line.(ABSTRACT TRUNCATED AT 400 WORDS)
Patterns of coexistence between two mesocarnivores in northern Patagonia in the presence of invasive hares and anthropogenic disturbance (2015)

Abstract We analysed coexistence patterns between two mesocarnivores, G eoffroy's cat ( L eopardus geoffroyi : F elidae) and culpeo fox ( P seudalopex culpaeus : C anidae), in northern P atagonia, A rgentina. We examined spatial distribution influenced by land cover, anthropogenic disturbance and invasive hare presence, and analysed temporal activity patterns and dietary composition. If competitive exclusion accounts for carnivore coexistence in this system, we predicted segregation would occur in one or more of these aspects as a mechanism for coexistence. We performed camera trapping in N ahuel H uapi N ational P ark, from F ebruary to M ay 2012 and J anuary to A pril 2013. Using camera detections, we analysed spatial patterns with co‐occupancy modelling and temporal patterns by fitting kernel density estimates and measuring overlap. We performed a dietary meta‐analysis using available literature and performed a discriminant function analysis of diet categories between species. We observed high spatial and temporal overlap between G eoffroy's cats and culpeo foxes. We found no evidence of segregation in relation to land cover occupancy, anthropogenic disturbance, invasive hare occurrence or activity patterns. Though both species consumed predominantly small and medium mammals, G eoffroy's cats consumed more birds, reptiles and amphibians, and culpeo foxes consumed more large mammals, carrion and plant material; coexistence between these two carnivores in this P atagonian protected area appears to be facilitated by diet segregation.
Ion Mobility Spectrometry Reveals the Mechanism of Amyloid Formation of Aβ(25–35) and Its Modulation by Inhibitors at the Molecular Level: Epigallocatechin Gallate andScyllo-inositol (2013)

Amyloid cascades leading to peptide β-sheet fibrils and plaques are central to many important diseases. Recently, intermediate assemblies of these cascades were identified as the toxic agents that interact with the cellular machinery. The relationship between the transformation from natively unstructured assembly to the β-sheet oligomers to disease is important in understanding disease onset and the development of therapeutic agents. Research on this early oligomeric region has largely been unsuccessful since traditional techniques measure only ensemble average oligomer properties. Here, ion mobility methods are utilized to deduce the modulation of peptide self-assembly pathways in the amyloid-β protein fragment Aβ(25-35) by two amyloid inhibitors (epigallocatechin gallate and scyllo-inositol) that are currently in clinical trials for Alzheimer's Disease. We provide evidence that suppression of β-extended oligomers from the onset of the conversion into β-oligomer conformations is essential for effective attenuation of β-structured amyloid oligomeric species often associated with oligomer toxicity. Furthermore, we demonstrate the ease with which ion mobility spectrometry-mass spectrometry can guide the development of therapeutic agents and drug evaluation by providing molecular level insight into the amyloid formation process and its modulation by small molecule assembly modulators.
Thermodynamic analysis of the folding of the streptococcal protein G IgG-binding domains B1 and B2: why small proteins tend to have high denaturation temperatures (1992)

We have cloned, expressed, and characterized two naturally occurring variations of the IgG-binding domain of streptococcal protein G. The domain is a stable cooperative folding unit of 56 amino acids, which maintains a unique folded structure without disulfide cross-links or tight ligand binding. We have studied the thermodynamics of the unfolding reaction for the two versions of this domain, designated B1 and B2, which differ by six amino acids. They have denaturation temperatures of 87.5 degrees C and 79.4 degrees C, respectively at pH 5.4, as determined by differential scanning calorimetry. Thermodynamic state functions for the unfolding reaction (delta G, delta H, delta S, and delta Cp) have been determined and reveal several interesting insights into the behavior of very small proteins. First, though the B1 domain has a heat denaturation point close to 90 degrees C, it is not unusually stable at physiologically relevant temperatures (delta G = 25 kJ/mol at 37 degrees C). This behavior occurs because the stability profile (delta G vs temperature) is flat and shallow due to the small delta S and delta Cp for unfolding. Related to this point is the second observation that small changes in the free energy of unfolding of the B-domain due to mutation or change in solvent conditions lead to large shifts in the heat denaturation temperature. Third, the magnitude and relative contributions of hydrophobic vs nonhydrophobic forces (per amino acid residue) to the total free energy of folding of the B-domain are remarkably typical of other globular proteins of much larger size.
Mitogenic effect of fibroblast growth factor on early passage cultures of human and murine fibroblasts. (1975)

Fibroblast growth factor (FGF), a polypeptide that has been shown to stimulate division in 3T3 cells, was tested for mitogenic effects on diploid, early-passage cells from human and murine sources. The quantitative assay of [3H]thymidine incorporation into acid-insoluble material showed that FGF at low concentrations (10 minus 9 M) was more effective than additional serum for provoking the initiation of DNA synthesis in human foreskin fibroblasts or mouse fibroblasts maintained in 5 or 10% serum, respectively. The growth of the human fibroblasts was twice as fast in the presence of FGF plus 10% calf serum as it was in the presence of 10% calf serum or 20% fetal calf serum alone. The addition of FGF to primary cultures of mouse fibroblasts in 0.4% serum resulted in a twofold increase in cell number compared to controls. In contrast to results obtained with 3T3 cells, neither insulin nor a glucocorticoid potentiated the effects of FGF on either human or mouse cells.
Analysis of Interleukin 8 Secretion by a Stem-Cell-Derived Human-Intestinal-Epithelial-Monolayer Platform (2018)

In vitro models of the human intestinal epithelium derived from primary stem cells are much needed for the study of intestinal immunology in health and disease. Here, we describe an intestinal monolayer cultured on a porous membrane with accessible basal and apical surfaces for assay of intestinal cytokine production in response to stimuli. The system was composed of a differentiated, confluent epithelial monolayer derived from human primary stem cells obtained from small or large intestine. Interleukin 8 (IL-8) and monocyte chemoattractant protein 1 (MCP-1) were the most abundant inflammatory cytokines produced by the intestinal epithelium. The epithelium from all five tested regions of the intestine preferentially secreted into the apical reservoir of the monolayer, with a 26-fold greater concentration of IL-8 present in the apical reservoir of the colonic monolayer relative to that in the basal reservoir. Upon application of tumor-necrosis factor α (TNF-α) to the basal surface of the colonic monolayer, the IL-8 concentration significantly increased in the basal, but not the apical, reservoir. A dose-dependent elevation of IL-8 in the basal reservoir was observed for TNF-α-stimulation of the monolayer but not for an organoid-based platform. To demonstrate the utility of the monolayer system, 88 types of dietary metabolites or compounds were screened for their ability to modulate IL-8 production in the basal reservoir of the intestinal monolayer in the absence or presence of TNF-α. No dietary metabolite or compound caused an increase in IL-8 in the basal reservoir in the absence of TNF-α. After addition of TNF-α to the monolayer, two compounds (butyrate and gallic acid) suppressed IL-8 production, suggesting their potential anti-inflammatory effects, whereas the dietary factor forskolin significantly increased IL-8 production. These results demonstrate that the described human-intestinal-monolayer platform has the potential for assays and screening of metabolites and compounds that alter the inflammatory response of the intestine.
Futile cycles in Saccharomyces cerevisiae strains expressing the gluconeogenic enzymes during growth on glucose. (1993)

The systems which control the levels of the gluconeogenic enzymes in Saccharomyces cerevisiae have been bypassed to ascertain their physiological significance. The coding regions of the genes FBP1 and PCK1, which encode fructose-1,6-bisphosphatase and phosphoenolpyruvate carboxykinase, have been put under the control of the promoter of ADC1 (alcohol dehydrogenase I), a gene not repressed by glucose, and introduced into yeast in multicopy plasmids. The transformed yeast cells show high levels of the gluconeogenic enzymes during growth on glucose. Generation time and growth yield of yeast expressing either fructose-1,6-bisphosphatase or phosphoenolpyruvate carboxykinase are not significantly different from those of the wild-type strain. For a strain expressing both enzymes the increase in generation time is about 20% and the decrease in growth yield around 30%. The concentration of ATP is about 1.5 mM in the growing cells of the different strains. The extent of in vivo cycling was measured by 13C NMR in cell-free extracts from yeast growing on [6-13C]glucose. Cycling between fructose-6-phosphate and fructose-1,6-bisphosphate is < 2%, most likely due to the very strong inhibition of fructose-1,6-bisphosphatase by fructose 2,6-bisphosphate. Cycling between phosphoenolpyruvate and pyruvate is low, but a precise figure could not be obtained due to poor equilibration of label between carbons 2 and 3 of oxaloacetate.
Designing and realizing an information-centric internet (2012)

Information-centric networking has been attracting increasing attention within the networking community. Technological solutions as well as entire architectures have been proposed with subtle but seemingly important differences. In this article, we define a set of design tenets for an information-centric architecture together with a demonstration of its feasibility. For the latter, we present an early prototype of an artifact that is directly based on our design framework. This prototype is available under open source, deployed in a European-wide testbed, and can be used for Planetlab-scale experiments. Early indications of its performance show promising results for our future work.
Can single-electron integrated circuits and quantum computers be fabricated in silicon? (2000)

Single-electronics and quantum computers have tremendous potential, but obstacles to fabricating them are enormous. Here we consider the physical difficulties in terms of both circuit architecture and plausible future advancements in silicon technology. Our discussion will focus on a set of recent proposals which involve tunnelling between 2D arrays of Coulomb islands or ‘quantum dots’. Planar architectures of this type can potentially be realized through in situ e-beam patterning of self-ordered dopant precursor molecules on hydrogen-terminated silicon surfaces. Low-temperature molecular beam epitaxy would then be used to overgrow them into Si/SiGe heterolayers. Epitaxial structures of this kind could potentially eliminate the random polarization offsets which plague all single-electron devices today, hopefully to levels permitting large-scale (fault-tolerant) integration. Individual donor atoms might be incorporated via STM lithography to fabricate the critical elements of a quantum computer. This approach offers many potential advantages, but the degree of material perfection it requires will be very challenging. Copyright © 2000 John Wiley & Sons, Ltd.
Reversion of autoimmune lymphoproliferative syndrome with an antimalarial drug: preliminary results of a clinical cohort study and molecular observations (2002)

Autoimmune lymphoproliferative syndrome (ALPS) is a paediatric disease characterized by lymphoproliferation and autoimmunity. Most patients are known to carry heterozygous mutations of the TNFRSF6 gene leading to diminished Fas-mediated apoptosis and failure of activated lymphocytes to undergo apoptosis. A subgroup of patients without the TNFRSF6 gene mutation has similar defective apoptosis and clinical features. No effective treatment has been reported so far. Glucocorticoids, intravenous immunoglobulin and/or immunosuppressive drugs have usually led to only transient clinical improvement. Seven ALPS patients (two type Ia and five type III) were treated with the antimalarial drug Fansidar. No toxicity was observed. An objective response was seen in six of them and, in two, the treatment was stopped without reappearance of the symptoms. Moreover, a marked decrease in interleukin-10 levels was observed in two patients during the treatment. We found that the drug induced apoptosis in activated lymphocytes through activation of the mitochondrial apoptotic pathway.
Poder y comunicación: una segunda revisión crítica (2009)

Las tecnologías de la información y la comunicación (TICs) suele ser la dimensión más recurrente en los exámenes acerca del nuevo lugar y espesor de lo comunicativo en las sociedades contemporáneas. Sin embargo, una perspectiva únicamente tecnológica de la cuestión, obvia la complejidad de la inserción de la comunicación en el entramado de las relaciones sociales. Tomando como punto de partida un análisis conceptual de las interrelaciones de lo comunicativo con otras esferas de la realidad social –política, económica, cultural y militar-, se realiza una indagación teórica crítica acerca de las múltiples conexiones entre comunicación y relaciones de poder, así como la funcionalidad de una representación social del poder de lo mediático.
The problem with and benefit of ventilations: should our approach be the same in cardiac and respiratory arrest? (2006)

The fundamental hemodynamic principle of intrathoracic pressure defines cardio-cerebral-pulmonary interactions during cardiopulmonary resuscitation. Further research is essential to optimize these interactions during treatment of profound shock.
Future research directions for mastering end-to-end semiconductor supply chains (2012)

The supply chain operational excellence has become a key competitive advantage in the globalized world economy. Since all manufactured technology products contain and depend on semiconductor components, an efficient semiconductor industry is crucially important for the broad manufacturing sector. Due to the high complexity of semiconductor manufacturing combined with the extreme volatility of the market, a deep understanding of its mechanisms and influencing parameters is essential in order to minimize the costs and to increase the customer satisfaction. There is a need for Agile, Adaptable, and Aligned end-to-end semiconductor supply chains. Over the last decades supply chain management problems have gained increasing popularity in industrial and academic environments. Even though numerous problems have been solved, we identify three areas of improvement. In this position paper, we address three research directions, which we intent on tackling within future research activities. We focus on contract clauses, gambling in collaborative supply chain planning, and simulation approaches for evaluating supply chain models. For each research direction we describe the underlying motivation, the objectives, the methodology, and the modelling approaches.
Target Regulation of Axotomy‐Sensitive Proteins (1990)

Large changes in the production of certain proteins often follow axotomy. How the cell body is signaled to make these changes, or terminate them after regeneration is finished, is unclear. This issue was addressed by studying an axotomized giant identified neuron, the giant cerebral neuron of the sea slug Aplysia, both in vivo and in culture. One week after axon crush in vivo, there were increases of 1.5-18-fold in the 5-h incorporation of [35S]methionine into seven proteins identified by two-dimensional gel electrophoresis. There were decreases of five- to 28-fold in the labeling of four other proteins. An axotomized giant cerebral neuron grows vigorously when placed in culture and forms chemical synapses with appropriate target cells while continuing unabated growth. The labeling of two of the proteins that up-regulate after axotomy in vivo was suppressed by the presence of target cells in culture. For one of the proteins, this effect was also produced by membranes of target cells, but not by medium conditioned by exposure to target cells. These results are consistent with the idea that loss of membrane-membrane contact with target cells (or its restoration) is involved in the initiation (or termination) of the up-regulation of certain proteins after axotomy.
Compact Model of a pH Sensor with Depletion-Mode Silicon-Nanowire Field-Effect Transistor (2014)

A compact model of a depletion-mode silicon-nanowire (Si-NW) pH sensor is proposed. This drain current model is obtained from the Pao-Sah integral and the continuous charge-based model, which is derived by applying the parabolic potential approximation to the Poisson's equation in the cylindrical coordinate system. The threshold-voltage shift in the drain-current model is obtained by solving the nonlinear Poisson-Boltzmann equation for the electrolyte. The simulation results obtained from the proposed drain-current model for the Si-NW field-effect transistor (SiNWFET) agree well with those of the three-dimensional (3D) device simulation, and those from the Si-NW pH sensor model also agree with the experimental data.
Cnr interferes with dimerization of the replication protein alpha in phage-plasmid P4 (2001)

DNA replication of phage-plasmid P4 in its host Escherichia coli depends on its replication protein alpha. In the plasmid state, P4 copy number is controlled by the regulator protein Cnr (copy number regulation). Mutations in alpha (alpha(cr)) that prevent regulation by Cnr cause P4 over-replication and cell death. Using the two-hybrid system in Saccharomyces cerevisiae and a system based on lambda immunity in E.coli for in vivo detection of protein-protein interactions, we found that (i) alpha protein interacts with Cnr, whereas alpha(cr) proteins do not; (ii) both alpha-alpha and alpha(cr)-alpha(cr) interactions occur and the interaction domain is located within the C-terminal of alpha; (iii) Cnr-Cnr interaction also occurs. Using an in vivo competition assay, we found that Cnr interferes with both alpha-alpha and alpha(cr)-alpha(cr) dimerization. Our data suggest that Cnr and alpha interact in at least two ways, which may have different functional roles in P4 replication control.
Fractional Synchrosqueezing Transformation and its Application in the Estimation of the Instantaneous Frequency of a Rolling Bearing (2020)

The time-frequency energy distribution processed by a short-time Fourier transform can be compressed to the real instantaneous frequency by the synchrosqueezing transformation (SST), which improves the time-frequency energy concentration of the signal. However, there is a large error in the instantaneous frequency estimation of a multicomponent nonpure harmonic signal by the SST. Therefore, a method for determining the instantaneous frequency (IF) of a rolling bearing based on a fractional synchrosqueezing transformation (FRSST) is proposed. First, the theoretical derivation of the FRSST algorithm as a signal processing technique is given and the steps of the IF estimation are presented. Second, the main advantages of the proposed FRSST algorithm are proved. In the comparison of simulation signals, it is verified that the FRSST algorithm has a high time-frequency concentration, is non-fragile to the frequency modulation rate, has noise robustness and has nonsensitivity to the cross-frequency signal. Finally, the FRSST algorithm is applied to the IF estimation of a rolling bearing under rising speed and fluctuated speed, and is compared with the SST based on variational mode decomposition (VMD-SST), the generalized parametric SST (PSST) and polynomial chirplet transform (PCT). The test results show that the estimation error of IF based on the FRSST method is the least for a rolling bearing with the four fault types under rising speed. On average, the estimation error is 2.2180 Hz less than the corresponding error of the VMD-SST and 1.1862 Hz less than the corresponding error of the PSST method.
Plasma and Urine Concentrations of Atropine After the Ingestion of Cooked Deadly Nightshade Berries (1996)

Background: Adult intoxications due to ingestion of deadly nightshade berries is uncommon. Case Reports: Collective intoxication of eight persons occurred after accidental ingestion of ripened Atropa belladonna berries. Three of the four adults displayed delirious states with visual hallucinations; one patient fell into a coma and required mechanical ventilation. Four children and one adult exhibited mild peripheral anticholinergic symptoms. Kinetic data were obtained on the three hospitalized adults. Discussion: The optimal intensive care for such patients is discussed.