gebhart/patrepeval huggingface dataset:
Instructing cells with programmable peptide DNA hybrids (2017)

Abstract The native extracellular matrix is a space in which signals can be displayed dynamically and reversibly, positioned with nanoscale precision, and combined synergistically to control cell function. Here we describe a molecular system that can be programmed to control these three characteristics. In this approach we immobilize peptide-DNA (P-DNA) molecules on a surface through complementary DNA tethers directing cells to adhere and spread reversibly over multiple cycles. The DNA can also serve as a molecular ruler to control the distance-dependent synergy between two peptides. Finally, we use two orthogonal DNA handles to regulate two different bioactive signals, with the ability to independently up- or downregulate each over time. This enabled us to discover that neural stem cells, derived from the murine spinal cord and organized as neurospheres, can be triggered to migrate out in response to an exogenous signal but then regroup into a neurosphere as the signal is removed.
Interaction of multi-functional silver nanoparticles with living cells (2010)

Silver nanoparticles (AgNPs) are widely used in household products and in medicine due to their antibacterial and to wound healing properties. In recent years, there is also an effort for their use in biomedical imaging and photothermal therapy. The primary reason behind the effort for their utility in biomedicine and therapy is their unique plasmonic properties and easy surface chemistry for a variety of functionalizations. In this study, AgNPs modified with glucose, lactose, oligonucleotides and combinations of these ligands are investigated for their cytotoxicity and cellular uptake in living non-cancer (L929) and cancer (A549) cells. It is found that the chemical nature of the ligand strongly influences the toxicity and cellular uptake into the model cells. While the lactose-and glucose-modified AgNPs enter the L929 cells at about the same rate, a significant increase in the rate of lactose-modified AgNPs into the A549 cells is observed. The binding of oligonucleotides along with the carbohydrate on the AgNP surfaces influences the differential uptake rate pattern into the cells. The cytotoxicity study with the modified AgNPs reveals that only naked AgNPs influence the viability of the A549 cells. The findings of this study may provide the key to developing effective applications in medicine such as cancer therapy.
Mechanism of anthraquinone-induced calcium release from skeletal muscle sarcoplasmic reticulum. (1988)

The anthraquinones, doxorubicin, mitoxantrone, daunorubicin and rubidazone are shown to be potent stimulators of Ca2+ release from skeletal muscle sarcoplasmic reticulum (SR) vesicles and to trigger transient contractions in chemically skinned psoas muscle fibers. These effects of anthraquinones are the direct consequence of their specific interaction with the [3H] ryanodine receptor complex, which constitutes the Ca2+ release channel from the triadic junction. In the presence of adenine nucleotides and physiological Mg2+ concentrations (approximately 1.0 mM), channel activation by doxorubicin and daunorubicin exhibits a sharp dependence on submicromolar Ca2+ which is accompanied by a selective, dose-dependent increase in the apparent affinity of the ryanodine binding sites for Ca2+, in a manner similar to that previously reported with caffeine. Unlike caffeine, however, anthraquinones increase [3H]ryanodine receptor occupancy to the level observed in the presence of adenine nucleotides. A strong interaction between the anthraquinone and the caffeine binding sites on the Ca2+ release channel is also observed when monitoring Ca2+ fluxes across the SR. Millimolar caffeine both inhibits anthraquinone-stimulated Ca2+ release, and reduces anthraquinone-stimulated [3H]ryanodine receptor occupancy, without changing the effective binding constant of the anthraquinone for its binding site. The degree of cooperativity for daunorubicin activation of Ca2+ release from SR also increases in the presence of caffeine. These results demonstrate that the mechanism by which anthraquinones stimulate Ca2+ release is caused by a direct interaction with the [3H]ryanodine receptor complex, and by sensitization of the Ca2+ activator site for Ca2+.
Mutual Understanding, The State of Attention, and the Ground for Interaction in Economic Systems (1996)

Abstract Neoclassical economic theory assumes that people pursue utility maximization within an objective framework, evident to all, that serves as the basis for the interaction. Agents are assumed to be detached observers who see the situation as it is in objective reality. It is argued in this article that there is no objective ground for interaction that exists apart from the understanding of economic agents. Agents have orientations that change over time depending on the way that the situation is currently understood. Depth of understanding and the extent of common ground depend on the quality of attention and the will to openness and honesty. Efforts to maintain connections with others make possible mutual understanding and visions of the common good that enable the coordinated pursuit of desired states of the world. Thus the understanding is … itself the lawgiver of nature. Save through it, nature, that is, synthetic unity of the manifold of appearances according to rules, would not exist at all…. Immanuel Kant, Critique of Pure Reason
Model-based design of tools for business understanding and re-engineering (2002)

Tools can provide useful assistance for business re-engineering planning. Activities such as business knowledge acquisition, business process modeling, performance, quality and impact analysis can all be done more effectively if supported by proper tools. In this paper, we describe a design scenario for business understanding and re-engineering tools that is based on the systematic modeling of business knowledge. The business knowledge model forms a conceptual schema for the tool repository. We start by building a generic business model. As both the model and required tool characteristics vary from company to company and from one business re-engineering project to another, we customize the generic model and tools to reflect needs of a given company and a business re-engineering project in hand. We achieve a required level of tool flexibility by applying meta-CASE techniques. The physical repository schema and tools themselves are automatically generated from the customized business model specifications. In this paper, we focus on tools and analysis methods that have not been extensively described in other sources. We describe an interview assistant tool, support for impact analysis, and an end-user query language in which a user can define new business analysis methods that are not supported by a generic tool environment.
Electrochemical Study of Flavins, Phenazines, Phenoxazines and Phenothiazines Immobilized on Zirconium Phosphate (1999)

Adsorption of a number of flavins, phenazines, phenoxazines, and phenothiazines on zirconium phosphate (ZP) was carried out in aqueous solution. The adsorbed organic dyes on ZP were used to prepare modified carbon paste electrodes. The electrochemical properties of the immobilized dyes were investigated and also their possible use to electrocatalytically oxidize NADH. The formal potential (E0′) of most of the adsorbed flavins, phenoxazines, and phenothiazines shifted markedly towards more positive potentials compared with their values in solution. The pH of the contacting solution did not affect their E0′-values between pH 1 and 9. The phenazines did neither present good electrochemical response nor electrocatalytic activity for NADH oxidation and their E0′-values remained pH dependent. In contrast, adsorbed flavins, phenoxazines, and phenothiazines presented good electron transfer rates between the electrode and the adsorbed molecule dye at pH 7.0.
Excessive α‐tocopherol exacerbates microglial activation and brain injury caused by acute ischemic stroke (2014)

The vitamin E family includes both tocopherols and tocotrienols, where α-tocopherol (αTOC) is the most bioavailable form. Clinical trials testing the therapeutic efficacy of high-dose αTOC against stroke have largely failed or reported negative outcomes when a "more is better" approach to supplementation (>400 IU/d) was used. This work addresses mechanisms by which supraphysiologic αTOC may contribute to stroke-induced brain injury. Ischemic stroke injury and the neuroinflammatory response were studied in tocopherol transfer protein-deficient mice maintained on a diet containing αTOC vitamin E at the equivalent human dose of 1680 IU/d. Ischemic stroke-induced brain injury was exacerbated in the presence of supraphysiologic brain αTOC levels. At 48 h after stroke, S100B and RAGE expression was increased in stroke-affected cortex of mice with elevated brain αTOC levels. Such increases were concomitant with aggravated microglial activation and neuroinflammatory signaling. A poststroke increase in markers of oxidative injury and neurodegeneration in the presence of elevated brain αTOC establish that at supraphysiologic levels, αTOC potentiates neuroinflammatory responses to acute ischemic stroke. Exacerbation of microglial activation by excessive αTOC likely depends on its unique cell signaling regulatory properties independent of antioxidant function. Against the background of clinical failure for high-dose αTOC, outcomes of this work identify risk for exacerbating stroke-induced brain injury as a result of supplementing diet with excessive levels of αTOC.
Role of Phosphoinositide 3-Kinase in Innate Immunity (2007)

Recent advances in our understanding of the molecular basis of mammalian host immune responses to microbial invasion suggest that the first line of defense against microbes is the recognition of pathogen-associated molecular patterns by Toll-like receptors (TLRs). Phosphoinositide 3-kinase (PI3K) is thought to participate in the TLR signaling pathway. The activation of PI3K is commonly observed after stimulation with various TLR ligands. The resultant activation of a serine-threonine protein kinase Akt leads to the phosphorylation of glycogen synthase kinase (GSK)-3beta, which is active in resting cells but is inactivated by phosphorylation. GSK-3beta has been linked to the regulation of a multitude of transcription factors, including NF-kappaB, AP-1, NF-AT, and CREB either negatively or positively. Thus, the altered activity of GSK-3beta causes diverse effects on cytokine expression. Generally, activation of PI3K results in the inhibition of proinflammatory events such as expression of IL-12 and TNF-alpha. Thus, PI3K is a negative regulator of TLR signaling. Among the members of the Class I PI3K family, p85/p110beta appears to be the subtype activated on TLR ligation, but the molecular basis for this specificity has yet to be elucidated.
Tin-containing silicates: structure–activity relations (2012)

The selective conversion of biomass-derived substrates is one of the major challenges facing the chemical industry. Recently, stannosilicates have been employed as highly active and selective Lewis acid catalysts for a number of industrially relevant reactions. In the present work, four different stannosilicates have been investigated: Sn-BEA, Sn-MFI, Sn-MCM-41 and Sn-SBA-15. When comparing the properties of tin sites in the structures, substantial differences are observed. Sn-beta displays the highest Lewis acid strength, as measured by probe molecule studies using infrared spectroscopy, which gives it a significantly higher activity at low temperatures than the other structures investigated. Furthermore, the increased acid strength translates into large differences in selectivity between the catalysts, thus demonstrating the influence of the structure on the active site, and pointing the way forward for tailoring the active site to the desired reaction.
The HIV-1 Tat protein activates transcription from an upstream DNA-binding site: implications for Tat function. (1991)

The Tat protein of human immunodeficiency virus type 1 (HIV-1) activates transcription following binding to nascent trans-activation response (TAR) RNA downstream of the transcription start site. Because Tat functions when bound to RNA, and in a position-dependent manner, it has been proposed that Tat works by a novel mechanism. Here, we perform a series of protein fusion experiments that reveal striking similarities between Tat and conventional cellular activators. Most significantly, we demonstrate that Tat can function when bound to upstream promoter DNA. This activity depends on a region within Tat that is also required for Tat to function when bound to TAR RNA. In contrast, the arginine-rich region of Tat, which is required for binding to TAR RNA, is dispensable for the function of DNA-bound Tat. When bound either to RNA or DNA Tat activity requires cooperation with promoter-bound cellular transcription factors. Finally, we show that Tat and a strong acidic activator stimulate transcription to comparable levels. On the basis of these and other results we suggest that Tat and acidic activators act on a similar step in the transcription process.
Infrared hollow waveguides: an update (2008)

Infrared-transmissive hollow waveguides (HWGs) are enjoying resurgence as they are now being used in lengths less than 10 m for sensor and power delivery applications. HWGs are routinely fabricated with losses less than 1 dB/m from 2 to 12 μm. Most of the hollow structures involve silica or plastic tubing with an inside thin metallic film followed by a dielectric coating to enhance the reflectivity. In this paper current HWG technologies will be reviewed and several sensor and power delivery applications discussed.
The Effect of Body Posture on Brain Glymphatic Transport (2015)

The rodent brain removes waste better during sleep or anesthesia compared with the awake state. Animals exhibit different body posture during the awake and sleep states, which might affect the brain's waste removal efficiency. We investigated the influence of body posture on brainwide transport of inert tracers of anesthetized rodents. The major finding of our study was that waste, including Aβ, removal was most efficient in the lateral position (compared with the prone position), which mimics the natural resting/sleeping position of rodents. Although our finding awaits testing in humans, we speculate that the lateral position during sleep has advantage with regard to the removal of waste products including Aβ, because clinical studies have shown that sleep drives Aβ clearance from the brain.
Thermal stability and frying performance of genetically modified sunflower seed (Helianthus annuus L.) oils (1993)

High-oleic sunflower seed oils containing varying levels of oleic acid were evaluated in comparison to\nconventional sunflower and olive oils, under both thermoxidative and frying conditions. Analytical \ndeterminations included quantitation of triglyceride species and polar compound level and distribution. Total polar compounds were significantly lower in high-oleic sunflower oils as compared to conventional sunflower oil. This was essentially attributable to oxidized and polymeric compounds. No differences were found between high-oleic sunflower oils and olive oil, which could not be anticipated on the basis of fatty acid composition but might be otherwise related to differences in triglyceride distribution. After drying, oils and lipids extracted from fried potatoes did not differ significantly in polar compounds. Overall, results showed an excellent behavior of high-oleic sunflower oils with regard to thermoxidation and frying.
Gradient-based global features for seam carving (2016)

We propose a gradient-based global feature and its application to seam carving. We focus on areas, rather than points and lines, to be assigned as important elements for expressing the rough location of salient objects in an image. The proposed feature is calculated with a low computational load based on gray-scale intensity. The superior performance of the proposed gradient-based global feature, as compared to state-of-the-art salient features for seam carving, is demonstrated experimentally.
Relation between D‐Glucose and L‐ and D‐Alanine in the Initiation of Germination of <i>Bacillus subtilis</i> Spore (1984)

The rate of L-alanine-initiated germination of Bacillus subtilis spore was measured by both loss of heat resistance and loss of turbidity, and the effect of glucose on the germination response to a wide range of concentrations of the germinant was analyzed in the presence and absence of D-alanine, an inhibitor. Glucose stimulated L-alanine germination by means of a cooperative effect: glucose increased the affinity of L-alanine by about 3-fold and the rate of germination by about 1.3-fold. However, glucose had little effect on the binding affinity of D-alanine. The apparent binding constant of L-alanine to the spore, which was determined by the next measurable event in the trigger reaction, was 1.2 X 10(-5), that of D-alanine was 6 X 10(-6), and that of glucose was 5 X 10(-5). The relation between the binding site for glucose and those for L- and D-alanine on the spore is discussed. Effect of glucose analogs was also examined.
Generative Topographic Mapping (GTM): Universal Tool for Data Visualization, Structure‐Activity Modeling and Dataset Comparison (2012)

Here, the utility of Generative Topographic Maps (GTM) for data visualization, structure-activity modeling and database comparison is evaluated, on hand of subsets of the Database of Useful Decoys (DUD). Unlike other popular dimensionality reduction approaches like Principal Component Analysis, Sammon Mapping or Self-Organizing Maps, the great advantage of GTMs is providing data probability distribution functions (PDF), both in the high-dimensional space defined by molecular descriptors and in 2D latent space. PDFs for the molecules of different activity classes were successfully used to build classification models in the framework of the Bayesian approach. Because PDFs are represented by a mixture of Gaussian functions, the Bhattacharyya kernel has been proposed as a measure of the overlap of datasets, which leads to an elegant method of global comparison of chemical libraries.
Entwerfen und Gestalten im Maschinenbau (2016)

Praxisgerechte Gestaltungslehre für das Maschinenbaustudium und den Einstieg in die Konstruktionspraxis In diesem Lehrbuch wird diejenige Phase des Konstruktionsprozess behandelt, in der ein Maschinenteil unter Berücksichtigung eines zweckmäßigen Werkstoffs und wesentlicher Fertigungsverfahren seine grobgeometrische Gestalt erhält. Die Gestaltungsphase endet mit der Festlegung der Feingeometrie, d. h. mit Aussagen zu Maßtoleranzen, Form- und Lageabweichungen und Angaben zur Feingestalt der Oberflächen. Insbesondere soll das Lehrbuch dazu beitragen, den Erfahrungsschatz des Konstrukteurs herauszubilden, um das nicht allein den praktikums- und einsatzbedingten Zufällen zu überlassen. Verständlich aufbereitet und anschaulich durch: • viele erklärende Bilder mit Gegenüberstellungen • Tabellen mit Erläuterungen • kritische Hinweise Für Studierende wie Ingenieure in der Praxis als Begleitbuch gleichermaßen geeignet.
Beneficial effects of omega‐3 fatty acids in cardiovascular disease (2010)

There is a large body of evidence supporting beneficial effects of omega-3 fatty acids for both primary and secondary prevention of cardiac disease in people. However, evidence is increasing for the use of omega-3 fatty acids in dogs with cardiac disease as well. Omega-3 fatty acids' anti-inflammatory and anti-arrhythmic effects may be beneficial in managing the loss of lean body mass and arrhythmias that are common in heart failure. However, omega-3 fatty acids also may have positive effects on myocardial energy metabolism, endothelial function, heart rate and blood pressure, and immune function. Additional research is needed to determine optimal indications, doses and formulations for dogs and cats with cardiac disease.
Bluecache (2016)

A key-value store (KVS), such as memcached and Redis, is widely used as a caching layer to augment the slower persistent backend storage in data centers. DRAM-based KVS provides fast key-value access, but its scalability is limited by the cost, power and space needed by the machine cluster to support a large amount of DRAM. This paper offers a 10X to 100X cheaper solution based on flash storage and hardware accelerators. In BlueCache key-value pairs are stored in flash storage and all KVS operations, including the flash controller are directly implemented in hardware. Furthermore, BlueCache includes a fast interconnect between flash controllers to provide a scalable solution. We show that BlueCache has 4.18X higher throughput and consumes 25X less power than a flash-backed KVS software implementation on x86 servers. We further show that BlueCache can outperform DRAM-based KVS when the latter has more than 7.4% misses for a read-intensive aplication. BlueCache is an attractive solution for both rack-level appliances and data-center-scale key-value cache.
Quorum Sensing Communication Modules for Microbial Consortia (2016)

The power of a single engineered organism is limited by its capacity for genetic modification. To circumvent the constraints of any singular microbe, a new frontier in synthetic biology is emerging: synthetic ecology, or the engineering of microbial consortia. Here we develop communication systems for such consortia in an effort to allow for complex social behavior across different members of a community. We posit that such communities will outpace monocultures in their ability to perform complicated tasks if communication among and between members of the community is well regulated. Quorum sensing was identified as the most promising candidate for precise control of engineered microbial ecosystems, due to its large diversity and established utility in synthetic biology. Through promoter and protein modification, we engineered two quorum sensing systems (rpa and tra) to add to the extensively used lux and las systems. By testing the cross-talk between all systems, we thoroughly characterized many new inducible systems for versatile control of engineered communities. Furthermore, we've identified several system pairs that exhibit useful types of orthogonality. Most notably, the tra and rpa systems were shown to have neither signal crosstalk nor promoter crosstalk for each other, making them completely orthogonal in operation. Overall, by characterizing the interactions between all four systems and their components, these circuits should lend themselves to higher-level genetic circuitry for use in microbial consortia.