gebhart/patrepeval huggingface dataset:
Modular simulation environments: an object manager based architecture (2003)

To perform a simulation project, simulationists employ simulation specific software tools, general purpose software tools, and perhaps software developed to meet the needs of a particular project. Ideally, these divergent tools would work together in a seamless simulation environment. Modular simulation environments are one way of meeting this goal. Software tools can be added to or deleted from a modular simulation as needed. Thus, the simulation environment can be configured on a project by project basis or even dynamically during the course of a project. The flow of data between the tools in the environment is also a primary concern. An object manager based architecture provides the capabilities to add and delete software tools as necessary as well as to control the flow of data between the software tools. Each software tool and each data set can be viewed as an object with certain attributes. The object manager controls the invocation of the software tools as well as meeting input data requirements and organizing and managing the results of each operation. The design of such an object manager is presented. An example modular simulation environment is given and its configuration and operation illustrated.
Heuristic search based on Petri net structures for FMS scheduling (1999)

A heuristic search method using Petri net structures for flexible manufacturing system (FMS) scheduling is presented. To minimize makespan, an FMS scheduling problem is formulated as finding a firing sequence from the initial state to the final state of a timed Petri net model, such that the sequence reveals the minimal cost. The reachability graph is partially generated and searched. The search process is guided by a heuristic function based on firing count vectors of the state equation, predicting the total cost. Since this heuristic search exploits the linear characteristics of the state equation, which contains sufficient global information, it can efficiently generate a near-optimal or optimal solution. To deal with large systems, the proposed algorithm exploits the concurrency information to reduce the searched state space.
Why are mammalian alkaline phosphatases much more active than bacterial alkaline phosphatases? (1994)

Mammalian alkaline phosphatases are 20-30-fold more active than the corresponding bacterial enzymes even though their amino acid sequences are 25-30% absolutely conserved. In the active-site region there are two noticeable differences between the sequences of the bacterial and mammalian enzymes. In the Escherichia coli enzyme positions 153 and 328 are Asp and Lys, respectively, but in the mammalian enzymes His is observed at both of these positions. Site-specific mutagenesis, genetic and X-ray crystallographic data, which will be summarized here, suggest that the His substitutions at positions 153 and 328 are primarily responsible for the differences in properties between the bacterial and mammalian alkaline phosphatases.
AKT induces senescence in human cells via mTORC1 and p53 in the absence of DNA damage: implications for targeting mTOR during malignancy (2011)

The phosphatidylinositol 3-kinase (PI3K)/AKT and RAS oncogenic signalling modules are frequently mutated in sporadic human cancer. Although each of these pathways has been shown to play critical roles in driving tumour growth and proliferation, their activation in normal human cells can also promote cell senescence. Although the mechanisms mediating RAS-induced senescence have been well characterised, those controlling PI3K/AKT-induced senescence are poorly understood. Here we show that PI3K/AKT pathway activation in response to phosphatase and tensin homolog (PTEN) knockdown, mutant PI3K, catalytic, α polypeptide (PIK3CA) or activated AKT expression, promotes accumulation of p53 and p21, increases cell size and induces senescence-associated β-galactosidase activity. We demonstrate that AKT-induced senescence is p53-dependent and is characterised by mTORC1-dependent regulation of p53 translation and stabilisation of p53 protein following nucleolar localisation and inactivation of MDM2. The underlying mechanisms of RAS and AKT-induced senescence appear to be distinct, demonstrating that different mediators of senescence may be deregulated during transformation by specific oncogenes. Unlike RAS, AKT promotes rapid proliferative arrest in the absence of a hyperproliferative phase or DNA damage, indicating that inactivation of the senescence response is critical at the early stages of PI3K/AKT-driven tumourigenesis. Furthermore, our data imply that chronic activation of AKT signalling provides selective pressure for the loss of p53 function, consistent with observations that PTEN or PIK3CA mutations are significantly associated with p53 mutation in a number of human tumour types. Importantly, the demonstration that mTORC1 is an essential mediator of AKT-induced senescence raises the possibility that targeting mTORC1 in tumours with activated PI3K/AKT signalling may exert unexpected detrimental effects due to inactivation of a senescence brake on potential cancer-initiating cells.
Corruption tactics: outrage management in a local government scandal (2012)

A mobilised citizenry is a threat to corrupt operations. Therefore, those involved in behaviours potentially labelled as corrupt have an interest in minimising public outrage. Five ways of doing this are to hide the activity, denigrate opponents, reinterpret actions as legitimate, use official channels to give an appearance of justice, and intimidate or bribe people involved. A local government scandal in Wollongong, Australia, illustrates all these tactics, with public hearings and media coverage providing volumes of revealing information. The implication of this analysis is that anti-corruption efforts should emphasise ways of increasing public outrage.
Phthaloyl Strategy—A New Approach Towards Oligodeoxyribonucleotide Synthesis (1997)

Abstract A new rapid strategy for machine-aided oligodeoxyribonucleotide synthesis has been established utilizing phthaloyl groups for protection of the heterocyclic amino functions within the phosphoramidite approach. A large number of DNA-sequences has been synthesized. Due to high purity and speed of performance this strategy offers an excellent alternative to the common used acyl approach.
Analysis of a Hydroxystilbene Glucoside in Several Softwood Barks (1989)

Abstract A method has been developed for determination of isorhapontin in softwood barks. The barks are extracted with aqueous acetone, the dried extracts re-extracted with butan-2-one, and the final extract analysed by liquid chromatography. Of seven softwood barks from five genera, only Engelmann spruce, with 13%, contained more than 1% of the stilbene glucoside.
Prophylactic Cranial Irradiation for Patients with Small-Cell Lung Cancer in Complete Remission (1999)

Prophylactic cranial irradiation improves both overall survival and disease-free survival among patients with small-cell lung cancer in complete remission.
Estrogen Control of Uterine Glucose Metabolism (1968)

During incubation in vitro, uterine tissue readily converts the nonutilizable sugar, Z-deoxyglucose-lJ4C, to P-deoxyglucose-6-PJ4C.This process appears to be analogous to transport and phosphorylation of glucose and is a sensitive measure of the activity in the early steps of uterine sugar metabolism.Nonradioactive 2-deoxyglucose-lJ4C and Dglucose show similar inhibition of 2-deoxyglucose-lJ4C phosphorylation at equimolar concentrations, but %-O-methylglucose does not inhibit this reaction.Conversion of 2deoxyglucose-1-W to 2-deoxyglucose-6-PJ4C by uteri from rats treated for 1 hour with 5 pg of estradiol-178 showed a 135% increase above control values, and this conversion rate continues to increase with longer periods of hormone treatment.The results show that e&radio1 accelerates either the transport or phosphorylation steps in early uterine sugar metabolism.Kinetic analyses indicate that estradiol increases the tissue V,,, for 2-deoxyglucose-lJ4C phosphorylation without changing the tissue &.Cycloheximide injected 30 min prior to estradiol abolishes the effect of the hormone, implying that the development of this metabolic response is dependent on protein synthesis.
Is it genomic imprinting or preferential expression? (2007)

Imprinted genes are monoallelically expressed in a parent-of-origin-specific manner, but for many genes reported to be imprinted, the occurrence of preferential expression--where both alleles are expressed but one is expressed more strongly than the other in a parent-of-origin-specific way--has been reported. This preferential expression found in genes described as imprinted has not been thoroughly addressed in genomic imprinting studies. To study this phenomenon, 50 genes, reported to be imprinted in the mouse, were chosen for investigation. Preferential expression was observed for 21 of 27 maternally expressed genes. However, only 5 of 23 paternally expressed genes showed preferential expression. Recently, it has been reported that a remarkable proportion of non-imprinted genes show differential allelic expression. If there is overlap between non-imprinted genes that are differentially expressed and imprinted genes that are preferentially expressed, we need to set new definitions of imprinted genes that, in turn, would probably lead to reassessments of the total number of imprinted genes in mammalian species.
Tomato Defense to <i>Oldium neolycopersici</i>: Dominant <i>OI</i> Genes Confer Isolate-Dependent Resistance Via a Different Mechanism Than Recessive <i>oI-2</i> (2005)

Tomato powdery mildew caused by Oidium neolycopersici has become a globally important disease of tomato (Lycopersicon esculentum). To study the defense responses of tomato triggered by tomato powdery mildew, we first mapped a set of resistance genes to O. neolycopersici from related Lycopersicon species. An integrated genetic map was generated showing that all the dominant resistance genes (Ol-1, Ol-3, Ol-4, Ol-5, and Ol-6) are located on tomato chromosome 6 and are organized in three genetic loci. Then, near-isogenic lines (NIL) were produced that contain the different dominant Ol genes in a L. esculentum genetic background. These NIL were used in disease tests with local isolates of O. neolycopersici in different geographic locations, demonstrating that the resistance conferred by different Ol genes was isolate-dependent and, hence, may be race-specific. In addition, the resistance mechanism was analyzed histologically. The mechanism of resistance conferred by the dominant Ol genes was associated with hypersensitive response, which varies in details depending on the Ol-gene in the NIL, while the mechanism of resistance governed by the recessive gene ol-2 on tomato chromosome 4 was associated with papillae formation.
The visual display of parallel performance data (1995)

Several performance visualization tools have demonstrated that helpful insights into parallel performance can be gained through graphical displays. However, much of this work has been experimental, specialized, and ad hoc. Evolving performance visualization into an integral, productive tool for evaluating parallel performance requires a more systematic, formal methodology that relates behavior abstractions to visual representations in a more structured way. We propose a high-level abstract model for the performance visualization process, explain its relationship to the most important concepts and principles of effective visualization practice, and illustrate the relationship between these concepts and our abstract model through specific case studies. We also discuss the relationship of performance visualization to general scientific visualization.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
A Monocular Vision Sensor-Based Obstacle Detection Algorithm for Autonomous Robots (2016)

This paper presents a monocular vision sensor-based obstacle detection algorithm for autonomous robots. Each individual image pixel at the bottom region of interest is labeled as belonging either to an obstacle or the floor. While conventional methods depend on point tracking for geometric cues for obstacle detection, the proposed algorithm uses the inverse perspective mapping (IPM) method. This method is much more advantageous when the camera is not high off the floor, which makes point tracking near the floor difficult. Markov random field-based obstacle segmentation is then performed using the IPM results and a floor appearance model. Next, the shortest distance between the robot and the obstacle is calculated. The algorithm is tested by applying it to 70 datasets, 20 of which include nonobstacle images where considerable changes in floor appearance occur. The obstacle segmentation accuracies and the distance estimation error are quantitatively analyzed. For obstacle datasets, the segmentation precision and the average distance estimation error of the proposed method are 81.4% and 1.6 cm, respectively, whereas those for a conventional method are 57.5% and 9.9 cm, respectively. For nonobstacle datasets, the proposed method gives 0.0% false positive rates, while the conventional method gives 17.6%.
Biomolecules as nanomaterials: interface characterization for sensor development (2006)

Extensive research is underway to understand and exploit the interface between biological materials and integrated systems Today, "nanotechnology" can be defined as a group of emerging technologies in which the structure of matter is controlled at the nanometer scale, the scale of small numbers of atoms, to produce novel materials and devices having useful and unique properties. An ideal biological candidate for use in nanoscale devices is the microtubule, an essential component of the eukaryotic cytoskeleton, which, unlike most proteins, has been shown to be electrically conductive. Due to the presence of an intrinsic dipole in the protein polymer, RF reflectance spectroscopy was chosen as an interrogation method. RF reflectance spectroscopy measures the electrical response of a sample in response to sinusoidally alternating currents as a function of frequency By interrogating the protein electrically, we are able to detect the polymerization state of the system, track any associated conductivity changes, and monitor binding of microtubule-associated proteins. We demonstrate manipulation of the microtubule system through the use of low-frequency electric fields, and discuss implications for sensor development.
SLC46A3 Is Required to Transport Catabolites of Noncleavable Antibody Maytansine Conjugates from the Lysosome to the Cytoplasm (2015)

Antibody-drug conjugates (ADC) target cytotoxic drugs to antigen-positive cells for treating cancer. After internalization, ADCs with noncleavable linkers are catabolized to amino acid-linker-warheads within the lysosome, which then enter the cytoplasm by an unknown mechanism. We hypothesized that a lysosomal transporter was responsible for delivering noncleavable ADC catabolites into the cytoplasm. To identify candidate transporters, we performed a phenotypic shRNA screen with an anti-CD70 maytansine-based ADC. This screen revealed the lysosomal membrane protein SLC46A3, the genetic attenuation of which inhibited the potency of multiple noncleavable antibody-maytansine ADCs, including ado-trastuzumab emtansine. In contrast, the potencies of noncleavable ADCs carrying the structurally distinct monomethyl auristatin F were unaffected by SLC46A3 attenuation. Structure-activity experiments suggested that maytansine is a substrate for SLC46A3. Notably, SLC46A3 silencing led to relative increases in catabolite concentrations in the lysosome. Taken together, our results establish SLC46A3 as a direct transporter of maytansine-based catabolites from the lysosome to the cytoplasm, prompting further investigation of SLC46A3 as a predictive response marker in breast cancer specimens.
TRON HMI design analysis by the semiotic approach (2002)

In order to evaluate and design the cognitive elements of HMI (human-machine interface) the authors propose an original method, semiotic analysis, which aims to reframe the knowledge gained through cognitive science by taking a semiotic approach. They describe three aspects of semiotic analysis: semantic structure analysis, sequential analysis, and expression-function analysis. Secondly, they present reviews of the TRON HMI specifications and home appliances developed by using this application. As a result the authors confirm that the concept of TRON HMI is based on language structure and has a good interface with cognitive science.
Highly Efficient Production of Laccase by the Basidiomycete <i>Pycnoporus cinnabarinus</i> (2004)

An efficient transformation and expression system was developed for the industrially relevant basidiomycete Pycnoporus cinnabarinus. This was used to transform a laccase-deficient monokaryotic strain with the homologous lac1 laccase gene placed under the regulation of its own promoter or that of the SC3 hydrophobin gene or the glyceraldehyde-3-phosphate dehydrogenase (GPD) gene of Schizophyllum commune. SC3-driven expression resulted in a maximal laccase activity of 107 nkat ml(-1) in liquid shaken cultures. This value was about 1.4 and 1.6 times higher in the cases of the GPD and lac1 promoters, respectively. lac1-driven expression strongly increased when 25 g of ethanol liter(-1) was added to the medium. Accordingly, laccase activity increased to 1,223 nkat ml(-1). These findings agree with the fact that ethanol induces laccase gene expression in some fungi. Remarkably, lac1 mRNA accumulation and laccase activity also strongly increased in the presence of 25 g of ethanol liter(-1) when lac1 was expressed behind the SC3 or GPD promoter. In the latter case, a maximal laccase activity of 1,393 nkat ml(-1) (i.e., 360 mg liter(-1)) was obtained. Laccase production was further increased in transformants expressing lac1 behind its own promoter or that of GPD by growth in the presence of 40 g of ethanol liter(-1). In this case, maximal activities were 3,900 and 4,660 nkat ml(-1), respectively, corresponding to 1 and 1.2 g of laccase per liter and thus representing the highest laccase activities reported for recombinant fungal strains. These results suggest that P. cinnabarinus may be a host of choice for the production of other proteins as well.
A 65-kV insulated gate bipolar transistor switch applied in damped AC voltages partial discharge detection system (2014)

Damped AC voltages detection system (DAC) is a productive way to detect the faults in power cables. To solve the problems of large volume, complicated structure and electromagnetic interference in existing switches, this paper developed a compact solid state switch based on electromagnetic trigger, which is suitable for DAC test system. Synchronous electromagnetic trigger of 32 Insulated Gate Bipolar Transistors (IGBTs) in series was realized by the topological structure of single line based on pulse width modulation control technology. In this way, external extension was easily achieved. Electromagnetic trigger and resistor-capacitor-diode snubber circuit were optimized to reduce the switch turn-on time and circular layout. Epoxy encapsulating was chosen to enhance the level of partial discharge initial voltage (PDIV). The combination of synchronous trigger and power supply is proposed to reduce the switch volume. Moreover, we have overcome the drawback of the electromagnetic interference and improved the detection sensitivity of DAC by using capacitor storage energy to maintain IGBT gate driving voltage. The experimental results demonstrated that the solid-state switch, with compact size, whose turn-on time was less than 400 ns and PDIV was more than 65 kV, was able to meet the actual demands of 35 kV DAC test system.
Deglycyrrhizinized liquorice in the treatment of chronic duodenal ulcer. A retrospective endoscopic survey of 32 patients. (1975)

Endoscopic examination in 32 cases of chronic duodenal ulceration treated with deglycyrrhizinized liquorice tablets showed that healing of the ulceration had occurred and in the majority the mucosa appeared normal. For optimum effect it appears to be important that the preparation in adequate dosage should be well chewed and swallowed on an empty stomach in the ambulant patient.
Defined medium for Moraxella bovis (1986)

A defined medium (medium MB) for Moraxella bovis was formulated. Nineteen strains grew well on medium MB. One strain was auxotrophic for asparagine, and another was auxotrophic for methionine. Strains of M. equi and M. lacunata also grew on medium MB. All strains had an absolute requirement for thiamine and were stimulated by or actually required the other growth factors in the medium.
C2′-Pyrene-Functionalized Triazole-Linked DNA: Universal DNA/RNA Hybridization Probes (2011)

Development of universal hybridization probes, that is, oligonucleotides displaying identical affinity toward matched and mismatched DNA/RNA targets, has been a longstanding goal due to potential applications as degenerate PCR primers and microarray probes. The classic approach toward this end has been the use of "universal bases" that either are based on hydrogen-bonding purine derivatives or aromatic base analogues without hydrogen-bonding capabilities. However, development of probes that result in truly universal hybridization without compromising duplex thermostability has proven challenging. Here we have used the "click reaction" to synthesize four C2'-pyrene-functionalized triazole-linked 2'-deoxyuridine phosphoramidites. We demonstrate that oligodeoxyribonucleotides modified with the corresponding monomers display (a) minimally decreased thermal affinity toward DNA/RNA complements relative to reference strands, (b) highly robust universal hybridization characteristics (average differences in thermal denaturation temperatures of matched vs mismatched duplexes involving monomer W are <1.7 °C), and (c) exceptional affinity toward DNA targets containing abasic sites opposite of the modification site (ΔT(m) up to +25 °C). The latter observation, along with results from absorption and fluorescence spectroscopy, suggests that the pyrene moiety is intercalating into the duplex whereby the opposing nucleotide is pushed into an extrahelical position. These properties render C2'-pyrene-functionalized triazole-linked DNA as promising universal hybridization probes for applications in nucleic acid chemistry and biotechnology.
A glutathione amperometric biosensor based on an amphiphilic fullerene redox mediator immobilised within an amphiphilic polypyrrole film (2002)

A novel biosensor for the amperometric detection of glutathione is proposed in which glutathione reductase is coupled to a pyrrolofullerene bis-adduct playing the role of redox mediator between electrode and enzyme. The adoption of a simple procedure for realizing the immobilization of the redox mediator, together with the enzyme, within a polypyrrole film cast onto a glassy carbon electrode, was made possible by the amphiphilic properties of the fullerene derivative. The biosensor showed a fast and reproducible response to glutathione and, because of its lower sensitivity, a wider linear range with respect to a similar device based on a diffusional redox mediator.
A study of serum nitric oxide levels in psoriasis (2005)

Nitric oxide levels were significantly increased in patients with psoriasis and these levels showed a positive correlation with severity and duration in the chronic plaque type group.