gebhart/patrepeval huggingface dataset:
The Natural Product Cyclomarin Kills Mycobacterium Tuberculosis by Targeting the ClpC1 Subunit of the Caseinolytic Protease (2011)

Die Zielstruktur des antibiotischen Cyclomarins A wurde in Mycobacterium identifiziert. Cyclomarin A (siehe Struktur) bindet hoch affin an die regulatorische Untereinheit des Clp-Protease-Komplexes und führt damit zu erhöhter Proteolyse und Apoptose. Die Eigenschaft von Cyclomarin, wachsende wie auch nichtreplizierende Mycobakterien abzutöten, macht die Clp-Protease zu einer vielversprechenden Zielstruktur für die Antituberkulose-Wirkstoffsuche. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Interdigitated Array Electrodes with Magnetic Function as a Particle-Based Biosensor (2007)

A particle-based electrochemical biosensor was developed by integrating soft magnetic material, NiFe, with interdigitated array (IDA) electrodes. The NiFe strips were embedded beneath the IDA electrodes and acted as magnetic traps to collect the enzyme labeled paramagnetic particles from a microchannel flow of particle suspension. The IDA electrodes, which overlap on top of the NiFe strips, are designed to detect in close proximity the enzyme product that is produced from the particle surface. The sensors were fabricated in such a way that the particles were positioned among IDA electrodes without blocking the active electrode surface. The theoretical prediction of the sensor response is presented. It is expected that both sensitivity and limit of detection of the biosensor would be improved significantly.
Designing Adaptive Applications Deployed on Cloud Environments (2016)

Designing an adaptive system to meet its quality constraints in the face of environmental uncertainties can be a challenging task. In a cloud environment, a designer has to consider and evaluate different control points, that is, those variables that affect the quality of the software system. This article presents a methodology for designing adaptive systems in cloud environments. The proposed methodology consists of several phases that take high-level stakeholders’ adaptation goals and transform them into lower-level MAPE-K loop control points. The MAPE-K loops are then activated at runtime using search-based algorithms. Our methodology includes the elicitation, ranking, and evaluation of control points, all meant to enable a runtime search-based adaptation. We conducted several experiments to evaluate the different phases of our methodology and to validate the runtime adaptation efficiency.
Path planning for cognitive vehicles using risk maps (2008)

This paper addresses the problem of path planning for a non-holonomic vehicle in fast changing urban environments. The developed method is flexible in utilization and generates collision-free paths with continuous curvature for a wide range of maneuvers such as regular lane-driving, rectangular or parallel parking and K-Turns. An A* algorithm is used as incremental planning method in combination with a kinematic model to follow non-holonomic constraints. A shortest-path estimate is used as optimization criteria. In the context of collision-free driving, the idea of using risk maps for representation of obstacles and other environmental influences is presented. Simulation and experiments show the applicability of this approach for lane driving as well as narrow navigation in parking spots. Further ideas of enhancements are discussed in the outlook of the paper.
Determination of Redundancy and Systems Properties of the Metabolic Network of <i>Helicobacter pylori</i> Using Genome-Scale Extreme Pathway Analysis (2002)

The capabilities of genome-scale metabolic networks can be described through the determination of a set of systemically independent and unique flux maps called extreme pathways. The first study of genome-scale extreme pathways for the simultaneous formation of all nonessential amino acids or ribonucleotides in Helicobacter pylori is presented. Three key results were obtained. First, the extreme pathways for the production of individual amino acids in H. pylori showed far fewer internal states per external state than previously found in Haemophilus influenzae, indicating a more rigid metabolic network. Second, the degree of pathway redundancy in H. pylori was essentially the same for the production of individual amino acids and linked amino acid sets, but was approximately twice that of the production of the ribonucleotides. Third, the metabolic network of H. pylori was unable to achieve extensive conversion of amino acids consumed to the set of either nonessential amino acids or ribonucleotides and thus diverted a large portion of its nitrogen to ammonia production, a potentially important result for pH regulation in its acidic habitat. Genome-scale extreme pathways elucidate emergent system-wide properties. Extreme pathway analysis is emerging as a potentially important method to analyze the link between the metabolic genotype and its phenotypes.
Flagellar Radial Spoke Protein 2 Is a Calmodulin Binding Protein Required for Motility in <i>Chlamydomonas reinhardtii</i> (2004)

Genetic and morphological studies have revealed that the radial spokes regulate ciliary and flagellar bending. Functional and biochemical analysis and the discovery of calmodulin in the radial spokes suggest that the regulatory mechanism involves control of axonemal protein phosphorylation and calcium binding to spoke proteins. To identify potential regulatory proteins in the radial spoke, in-gel kinase assays were performed on isolated axonemes and radial spoke fractions. The results indicated that radial spoke protein 2 (RSP2) can bind ATP and transfer phosphate in vitro. RSP2 was cloned and mapped to the PF24 locus, a gene required for motility. Sequencing revealed that pf24 contains a point mutation converting the first ATG to ATA, resulting in only trace amounts of RSP2 and confirming the RSP2 mapping. Surprisingly, the sequence does not include signature domains for conventional kinases, indicating that RSP2 may not perform as a protein kinase in vivo. However, the predicted RSP2 protein sequence contains Ca2+-dependent calmodulin binding motifs and a GAF domain, a domain found in diverse signaling proteins for binding small ligands including cyclic nucleotides. As predicted from the sequence, recombinant RSP2 binds calmodulin in a calcium-dependent manner. We postulate that RSP2 is a regulatory subunit of the radial spoke involved in localization of calmodulin for control of motility.
Kainic acid-induced neuronal death is associated with DNA damage and a unique immediate-early gene response in c-fos-lacZ transgenic rats (1995)

Previously, we established that persistent upregulation of c-fos expression preceded kainic acid (KA)-induced neuronal death in mice. To discriminate between events that are products of the seizures elicited by KA and those that are specifically associated with its neurotoxic actions, we have examined the expression of cellular immediate-early genes (cIEGs) following KA or pentylenetetrazol (PTZ) treatment in c-fos-lacZ transgenic rats. While both chemoconvulsants elicit seizures, only KA causes selective neuronal death. Following treatment of transgenic rats with KA there was a protracted expression of Fos-lacZ that lasted for 2-3 d. In contrast, PTZ elicited a transient increase in the transgene product that lasted about 6 hr. Normally, Fos and Fos-lacZ were detected only in neuronal nuclei. However, 6 hr following kainic acid (but not PTZ) administration, beta-galactosidase activity appeared in the cytoplasm of neurons within vulnerable regions (as determined by the terminal transferase biotinylated-UTP nick end labeling (TUNEL) procedure). Like c-fos, transcripts for other cIEGs were elevated for longer periods in the KA-treated rat hippocampus. In addition, fra-1 and fra-2 were only induced in the KA-treated rat. These changes in mRNA levels were paralleled by a sustained increase in AP-1 DNA binding activity. Thus, quantitative and qualitative changes in AP-1 DNA binding complexes accompany neurotoxic cell death that are not observed following seizures.
Transcriptional enhancer factor-1 in cardiac myocytes interacts with an alpha 1-adrenergic- and beta-protein kinase C-inducible element in the rat beta-myosin heavy chain promoter. (1993)

In cultured rat cardiac myocytes, a 20-base pair sequence (-215/-196) of the rat beta-myosin heavy chain (MHC) promoter mediates induction by both alpha 1-adrenergic stimulation and a constitutively activated beta-protein kinase C (PKC), and binds cardiac myocyte nuclear factor(s) through an "enhancer core" element (5'-TGTGG-TATG-3') (Kariya, K., Karns, L. R., and Simpson, P. C. (1994) J. Biol. Chem. 269, in press). Here, we report identification of this enhancer core binding factor as the rat homologue of transcriptional enhancer factor-1 (TEF-1), a human transcription factor for viral enhancers. In gel mobility shift and immunoblot analyses, the myocyte factor and human TEF-1 were indistinguishable in terms of sequence recognition, mobility, and immunoreactivity. Furthermore, DNA binding activity for the beta-MHC enhancer core and TEF-1 immunoreactivity correlated closely. These results are the first to suggest a role for TEF-1 in transcriptional regulation by PKC. The data also provide direct evidence for interaction of TEF-1 with the beta-MHC promoter, supporting a function for TEF-1 in regulation of cellular gene expression, as well as viral, and outline a pathway for alpha 1-adrenergic regulation of beta-MHC gene transcription in cardiac myocytes.
ErAs:GaAs photomixer with two-decade tunability and 12μW peak output power (2004)

This letter reports the fabrication and demonstration of an ErAs:GaAs interdigitated photomixer as a tunable THz source ranging from ∼20GHzto∼2THz, with 12μW maximum power typically around ∼90GHz. Each photomixer is coupled to a composite dipole-spiral planar antenna that emits a Gaussian-type beam into free space. The beam switches from dipole to spiral antenna behavior as the frequency increases. A distributed Bragg reflector is embedded in the device beneath the photomixer to increase its external quantum efficiency. The photomixer has a 900Å thick silicon nitride coating which serves as an antireflection and passivation layer, and also improves the reliability and heat tolerance of the device.
Effects of Hydrogen Partial Pressure in the Annealing Process on Graphene Growth (2014)

Graphene domains with different sizes and densities were successfully grown on Cu foils with use of a chemical vapor deposition method. We investigated the effects of volume ratios of argon to hydrogen during the annealing process on graphene growth, especially as a function of hydrogen partial pressure. The mean size and density of graphene domains increased with an increase in hydrogen partial pressure during the annealing time. In addition, we found that annealing with use of only hydrogen gas resulted in snowflake-shaped carbon aggregates. Energy-dispersive X-ray spectroscopy (EDX) and high-resolution photoemission spectroscopy (HRPES) revealed that the snowflake-shaped carbon aggregates have stacked sp2 carbon configuration. With these observations, we demonstrate the key reaction details for each growth process and a proposed growth mechanism as a function of the partial pressure of H2 during the annealing process.
Reforming Republicanism: Alexander Hamilton's Theory of Republican Citizenship and Press Liberty (2005)

During his life and ever since, Alexander Hamilton has been criticized as an opponent of republicanism, even a closet monarchist. Recent scholarly efforts to rescue Hamilton from these interpretations have succeeded perhaps too well, making him out to be a moderate, mainstream republican of his day. This essay assesses Hamilton's public performance during the late 1780s and 1790s as a defender of a particular federalist vision of republicanism. Drawing on a central conceptual divide over the proper virtue of republican citizenshipÑshould citizens have "confidence" in their elected leaders or maintain a "vigilant" scrutiny of them?Ñthe essay explores Hamilton's stress on confidence in his vision of republican citizenship and freedom of the press. The theory he publicly developed and defended is judged less moderate than others have suggested, but Hamilton's philosophy is best understood as an energetic, elitist reformulation of republicanism.
Establishment of a Human Keratinocyte Cell Line Carrying Complete Human Papillomavirus Type 1 Genomes: Lack of Vegetative Viral DNA Synthesis upon Keratinization (1983)

A human papillomavirus type 1 (HPV-1)/pBR322 recombinant plasmid was constructed consisting of two complete HPV-1 genomes in a head-to-tail arrangement, inserted into the BamHI site of pBR322. To obtain established human keratinocytes keratinocytes carrying dimeric HPV-1, origin-minus simian virus 40 (SV40) DNA was used as a dominant transforming marker in co-transfection experiments performed with cultured human foetal keratinocytes. Using the Southern blotting technique, HPV-1 DNA was detected in one out of five SV40-transformed human keratinocyte cell lines which were obtained in this way. Further blotting experiments using SV40, pBR322 and HPV-1 DNA as probes revealed patterns of hybridization which were consistent with co-integration of SV40 DNA with between two and four copies of the HPV-1 genome. The HPV-1 sequences in this cell line were virtually non-methylated and were transcribed at a lower level than SV40 mRNAs in the same cultured cells. A low level of monomeric HPV form I DNA was detected by blotting of undigested total cellular DNA. No evidence for a stimulation of form I HPV DNA replication could be obtained by blotting analysis of total DNA extracted from keratinizing cysts, which were formed by subcutaneous inoculation of these cells into nude mice.
Flow behaviour of entangled surfactant micelles (1996)

Many viscoelastic surfactant solutions contain giant, self-assembled micelles. These can be described as `living polymers', whose chains are subject to reversible scission and recombination. Their dynamics in the entangled regime is accordingly modified from the reptation picture for conventional polymer chains. For rapid scission kinetics, the linear viscoelastic spectrum approaches a single-exponential (Maxwell) behaviour: small departures from this can be measured, and the model used to deduce information both on the micellar kinetics (the lifetime of a typical micelle before breaking) and on the structure (the mean micelle length). These ideas work for several systems, but for others, unreasonable trends for these quantities are found. The most likely reason for this is micellar branching effects, which (as far as the reptation - reaction model is concerned) introduce an effective micellar length equal to the mean distance between branch points. Another possible discrepancy comes from the breakdown of mean-field averaging for the micellar reactions. The reptation - reaction model yields a non-linear constitutive equation which shows a non-monotonic dependence of stress on strain rate, in simple steady shear. This leads one to expect flow instabilities, and (with further assumptions) suggests that steady shear-banded flows should arise, in which macroscopic layers of fluid of different shear rates coexist. Several experimental observations support this general picture, although the same instability could instead lead to wall slip, or unsteady flows.
Judging the East Timor Dispute: Self-Determination at the International Court of Justice (1994)

In this Article, the author discusses the likely approach of the International Court of Justice to the issue of self-determination for East Timor in the forthcoming case between Portugal and Australia. To this end, the substantive jurisprudence of the Court will be outlined in the area of self-determination. Initially, the existence of a right to selfdetermination is established at international law (and in the work of the Court). Next the application of this principle to East Timor is considered. Third, potential qualifications on this right are discussed. Finally, an inquiry is made into the legal relationship between the people claiming the right of self-determination and certain third parties. The author introduces the discussion with some remarks about the function of the Court in the international community and, in particular, how the political debate about this function affects its decision-making.
Continuous-mode dielectrophoretic gating for highly efficient separation of analytes in surface micromachined microfluidic devices (2008)

Here, we describe a dielectrophoretic (DEP) gating technique for preconcentrating and separating biological and non-biological particles in a microfluidic device. The microfluidic devices are surface-micromachined on silicon substrates and are fully encapsulated without substrate bonding procedures. DEP gates in the devices consist of embedded microelectrodes that are coupled to the fluid channels for analyte manipulation with electric fields. We consider several different microelectrode designs such as low and high radius-of-curvature edges, and we detail the time- and frequency-dependent preconcentration of particles. Simulations of the particle motion under the manipulation of DEP forces are found to be in good agreement with the experimental results. Experimental results show that bioparticles such as Penicillium brevicompactum (PBC), T-cells and Escherichia coli (E. coli) undergo positive DEP and are trapped in regions of large electric-field gradient adjacent to the DEP gate. In contrast to our previous demonstration of batch-mode separation of particles with different dielectric properties, here we perform a continuous-mode separation of latex particles and E. coli from a mixture.
Preferential Oxidation of Carbon Monoxide Catalyzed by Platinum Nanoparticles in Mesoporous Silica (2007)

Preferential oxidation (PROX) of CO is an important practical process to purify H2 for use in polymer electrolyte fuel cells. Although many supported noble metal catalysts have been reported so far, their catalytic performances remain insufficient for operation at low temperature. We found that Pt nanoparticles in mesoporous silica give unprecedented activity, selectivity, and durability in the PROX reaction below 353 K. We also studied the promotional effect of mesoporous silica in the Pt-catalyzed PROX reaction by infrared spectroscopy using the isotopic tracer technique. Gas-phase O2 is not directly used for CO oxidation, but the oxygen of mesoporous silica is incorporated into CO2. These results suggest that CO oxidation is promoted by the attack of the surface OH groups to CO on Pt without forming water.
New results on robustness of secure steganography (2006)

Steganographic embedding is generally guided by two performance constraints at the encoder. Firstly, as is typical in the field of watermarking, all the transmission codewords must conform to an average power constraint. Secondly, for the embedding to be statistically undetectable (secure), it is required that the density of the watermarked signal must be equal to the density of the host signal. Assuming that this is not the case, statistical steganalysis will have a probability of detection error less than 1/2 and the communication may be terminated. Recent work has shown that some common watermarking algorithms can be modified such that both constraints are met. In particular, spread spectrum (SS) communication can be secured by a specific scaling of the host before embedding. Also, a side informed scheme called stochastic quantization index modulation (SQIM), maintains security with the use of an additive stochastic element during the embedding. In this work the performance of both techniques is analysed under the AWGN channel assumption. It will be seen that the robustness of both schemes is lessened by the steganographic constraints, when compared to the standard algorithms on which they are based. Specifically, the probability of decoding error in the SS technique increases when security is required, and the achievable rate of SQIM is shown to be lower than that of dither modulation (on which the scheme is based) for a finite alphabet size.
(200) Influence of Planting Density on Yield and Quality of Confectionery Seed Pumpkins (2005)

Afield study evaluated the influence of planting density on the yield and quality of confectionery seed pumpkins grown near Hatton, N.D. An open-pollinated selection of Chinese snow-white seeds (CS) and a hull-less (HL) seed cultivar (`Takai', Johnny's Selected Seeds) were grown at three different planting densities (1-, 2-, or 3-ft plant spacing on rows 5 ft apart) from 5 May to 7 Oct. The total number of plants at high, medium, and low densities was 8712, 4356, and 2904 per acre (21,529, 10,764, and 7176 plants per ha, respectively). The average number of fruits harvested at high, medium, and low densities, respectively, was 0.93, 1.2, and 1.4 per plant for CS and 1.2, 1.7, and 2.5 per plant for HL. Total seed yields were estimated at 1011, 599, and 466 kg/acre (2498, 1480, and 1151 kg·ha -1 ) for CS and 661, 500, and 498 kg/acre (1633, 1235, and 1231 kg·ha -1 ) for HL, respectively, at high, medium, and low planting densities. While the average weight of fruits decreased as planting density increased, the total number and weight of seeds produced per fruit were unaffected by changing plant density in either cultivar.
A Modular Sensor Fusion Approach for Agricultural Machines (2012)

Today’s architectures for sensor data handling in agricultural equipment are static and single vehicle-centric. This means that they assume a static system configuration over time while ignoring data contributed by other sources like implements and other machines that they currently interact with. Therefore, it can be stated that the inability to adapt to machine reconfiguration can be identified as a significant bottleneck. The approach presented in this paper is designed to overcome this shortcoming. For this purpose, a data handling system was designed that combines solutions for management of distributed knowledge and data fusion algorithms especially designed for the demanding application field at hand. Besides supporting the user, this modular approach enables engineers to design future systems in a holistic manner with reduced complexity. Furthermore it can help to reduce hardware costs due to elimination of redundant sensing systems and pushes the limit of applications to open up new opportunities in the future. Key words: modular architecture, sensor fusion, reconfiguration, vehicle state estimation
Some properties of the metallic state II—Metallic hydrogen and deuterium (1937)

Abstract The heat of formation of 1 g. atom of metal from the atoms has been calcu­lated to differ by about 1·6 kcal. for hydrogen and deuterium (Wigner and Huntingdon 1935). Allowing for the difference in the zero point energies of molecular hydrogen and deuterium (1·8 kcal. /mol. according to Rideal and Melville (1935)), the heat of formation of the metal from molecular hydrogen is smaller by 0·7 kcal./g. atom than from molecular deuterium. The difference in zero point energy between H and D in the α-phase is 0·5 kcal. /g. atom (Rideal and Melville). No data are available for the β-phase. This difference is about 6 % of the heat of solution in forming the β-phase, and since the expansion of the palladium lattice is sensitive to small energy changes (cf. Part I), an appreciable difference in expansions may be expected in the two alloys (cf. the discussion of other types of chemical linkage, Ubbelohde (1936). Measurements of the lattice expansion, and change of resistance on alloying with the two metals were undertaken to test this.