gebhart/patrepeval huggingface dataset:
Mathematical modelling of evacuation problems: A state of art (2022)

This paper details models and algorithms which can be applied to evacuation problems. While it concentrates on building evacuation many of the results are applicable also to regional evacuation. All models consider the time as main parameter, where the travel time between components of the building is part of the input and the overall evacuation time is the output. The paper distinguishes between macroscopic and microscopic evacuation models both of which are able to capture the evacuees' movement over time. Macroscopic models are mainly used to produce good lower bounds for the evacuation time and do not consider any individual behavior during the emergency situation. These bounds can be used to analyze existing buildings or help in the design phase of planning a building. Macroscopic approaches which are based on dynamic network flow models (minimum cost dynamic flow, maximum dynamic flow, universal maximum flow, quickest path and quickest flow) are described. A special feature of the presented approach is the fact, that travel times of evacuees are not restricted to be constant, but may be density dependent. Using multicriteria optimization priority regions and blockage due to fire or smoke may be considered. It is shown how the modelling can be done using time parameter either as discrete or continuous parameter. Microscopic models are able to model the individual evacuee's characteristics and the interaction among evacuees which influence their movement. Due to the corresponding huge amount of data one uses simulation approaches. Some probabilistic laws for individual evacuee's movement are presented. Moreover ideas to model the evacuee's movement using cellular automata (CA) and resulting software are presented. In this paper we will focus on macroscopic models and only summarize some of the results of the microscopic approach. While most of the results are applicable to general evacuation situations, we concentrate on building evacuation.
Application of PCR-Based Methods To Assess the Infectivity of Enteric Viruses in Environmental Samples (2008)

The advent of the PCR has greatly enhanced our ability to detect human enteric viral pathogens in the environment, including water, municipal wastes, sewage, food, air, and fomites ([2][1], [3][2], [59][3], [69][4], [79][5]). This is especially true for those viruses which do not grow in cell
Absorptive and refractive nonlinearity of carbon nanotubes grown on Si substrate (2005)

The third-order susceptibility of multiwalled carbon nanotubes (MWCNTs) grown on Si substrate were measured using reflective Z-scan (RZ-scan) technique with femto-second laser pulses at 790 nm. The nonlinear absorption coefficient 'beta' and nonlinear refraction index 'gamma' were measured to be about 9*10^(2) cm/GW and 9.6*10^(-3) cm2/GW, respectively. This is about one order of magnitude larger than the measurement of MWCNTs on transparent quartz substrate. The enhanced optical nonlinearities are contributed by the enhanced local field and the photoinduced off-resonant absorption of the 'pi'-plamon of MWCNTs on Si.
Analysis of a tobacco mosaic virus strain capable of overcoming N gene-mediated resistance. (1993)

The genome of Ob, a tobamovirus that overcomes the N gene-mediated hypersensitive response (HR), was cloned as a cDNA, and its nucleotide sequence was determined. The genomic organization of Ob is similar to that of other tobamoviruses, consisting of 6506 nucleotides and containing at least four open reading frames. These open reading frames encode a 126-kD polypeptide with a 183-kD readthrough product, a 30.6-kD movement protein, and an 18-kD coat protein. A bacteriophage T7 promoter sequence was fused to the full-length cDNA clone to obtain infectious RNA transcripts. These transcripts, when inoculated onto tobacco plants, induced disease symptoms indistinguishable from plants inoculated with Ob viral RNA. To determine which viral factor is responsible for the resistance-breaking character of Ob, a recombinant virus was constructed in which the movement protein gene of tobacco mosaic virus was replaced with that of Ob. Cultivar Xanthi NN tobacco plants infected with this virus responded with an HR, indicating that the Ob movement protein alone does not act to overcome the N gene-mediated response. Following mutagenesis of the infectious Ob cDNA clone with hydroxylamine, populations of transcripts from the mutagenized DNA were inoculated onto Xanthi NN tobacco, and a variant that induced the HR was identified. The mutant was analyzed and found to contain a single nucleotide change in the 126-kD gene. Recreating the mutation in the Ob cDNA clone by site-directed mutagenesis resulted in a virus that caused symptoms identical to the chemically induced mutant.
Single channel optimization for an endoscopic time-of-flight positron emission tomography detector (2011)

An endoscopic time-of-flight PET detector combined with an ultrasound probe will be designed and built to develop new biomarkers for pancreas and prostate tumors. The detector will consist of a PET head mounted on an ultrasound endoscope and an external PET detector plate with small crystals individually read out via silicon photomultipliers (SiPM). A 200 ps coincidence time resolution for background rejection outside the 3 cm region of interest is required by the system. Single channel simulation and optimization regarding crystal geometry and photodetector characteristics is discussed. System integration issues are studied with the experience gained on a PET prototype.
PF-05231023, a long-acting FGF21 analogue, decreases body weight by reduction of food intake in non-human primates (2016)

PF-05231023, a long-acting FGF21 analogue, is a promising potential pharmacotherapy for the treatment of obesity and associated comorbidities. Previous studies have shown the potential of FGF21 and FGF21-like compounds to decrease body weight in mice, non-human primates, and humans; the precise mechanisms of action remain unclear. In particular, there have been conflicting reports on the degree to which FGF21-induced weight loss in non-human primates is attributable to a decrease in food intake versus an increase in energy expenditure. Here, we present a semi-mechanistic mathematical model of energy balance and body composition developed from similar work in mice. This model links PF-05231023 administration and washout to changes in food intake, which in turn drives changes in body weight. The model is calibrated to and compared with recently published data from cynomolgus macaques treated with PF-05231023, demonstrating its accuracy in describing pharmacotherapy-induced weight loss in these animals. The results are consistent with the hypothesis that PF-05231023 decreases body weight in cynomolgus macaques solely by a reduction in food intake, with no direct effect on energy expenditure.
Efficient Method for the Preparation of Peracetylated Neu5Ac2en by Flash Vacuum Pyrolysis (2009)

Peracetylated Neu5Ac2en methyl ester, an intermediate in the synthesis of the influenza neuraminidase inhibitor Relenza, has been synthesized in high yields from peracetylated Neu5Ac methyl ester by flash vacuum pyrolysis. Mechanistic evidence including deuterium labeled studies and DFT (B3LYP) calculations suggest this transformation proceeds via an intramolecular syn-elimination.
The Deoxygenation Kinetics of Hemoglobin Partially Saturated with Carbon Monoxide (1972)

Abstract The deoxygenation rate of hemoglobin solutions partially saturated with carbon monoxide, in the presence and absence of 2,3-diphosphoglycerate (2,3-DPG) at 23° and pH 7.0 and 8.0 have been measured. When the rate is calculated over the initial 30% of the reaction, solutions containing 98% HbO2 show an increase in the rate as hemoglobin deoxygenates both at neutral and alkaline pH. Partial saturation with CO severely compromises this variation at both pH values. Indeed, for a solution containing about 15% HbO2, no variation in the rate over the initial 30% of the reaction or thereafter, is observed. These results for the initial portion of the reaction are in agreement with the earlier studies of Gibson and Roughton ((1955) Proc. Roy. Soc. London B Biol. Sci. 143, 310). The values of the deoxygenation rate constant calculated between 85 and 40% saturation (k in s-1) at pH 8.0, in the absence of 2,3-DPG, are 19.5 ± 1.0 s-1 for the 98% HbO2 condition and 14.2 ± 0.7 s-1 for the 85% HbCO-15% HbO2 case. 2,3-DPG has no significant effect on k at pH 8.0. At pH 7.0, with no 2,3-DPG, the value of k for the 98% condition is 36.0 ± 1.8 s-1, and for the 85% HbCO-15% HbO2 case, it is 17.9 ± 0.9 s-1. In the presence of a 10:1 molar ratio of 2,3-DPG to hemoglobin tetramer, the effect of partial saturation with CO is even more pronounced as evidenced by a value of 52.4 ± 2.0 s-1 for 98% HbO2 and 18.0 ± 0.8 s-1 for 85% HbCO-15% HbO2. Thus solutions containing Hb4O2(CO)3 as a major initial species show no effect of 2,3-DPG at pH 7.0. The effect of this organic phosphate on k becomes significant as the concentration of the species Hb4O4(CO)2 increases. These results support the view that there is no effect of 2,3-DPG on the release of the first oxygen from the fully liganded conformation. They also suggest that 2,3-DPG exerts its influence on the rate of removal of the second and subsequent oxygen molecules. This kinetic result is consistent with the findings of MacQuarrie and Gibson ((1971) J. Biol. Chem. 246, 5832), that a 2,3-DPG analogue dissociates from its combination with hemoglobin after the binding of the third heme ligand. Since 2,3-DPG binding is thought to be dependent on the quaternary structure of hemoglobin, these results taken together would indicate that the transition from the oxy to the deoxy quaternary structure, at pH 7.0, occurs very early in the deoxygenation process, probably with the loss of the first heme ligand from fully liganded hemoglobin.
Determinants of Direct Medical Costs in Primary and Revision Total Knee Arthroplasty (2012)

High prosthesis costs in revision TKA represent a factor potentially amenable to cost containment efforts. Increased costs associated with demographic factors and comorbidities may put providers at financial risk and may jeopardize healthcare access for those patients in greatest need.
Planar edge terminations for high voltage 4H-SiC power MOSFETs (2017)

Several edge termination structures for high voltage 4H-SiC devices compatible with a planar power MOSFET fabrication process are analyzed in this paper. The edge terminations' efficiency has been experimentally demonstrated on PiN diodes with breakdown voltage capabilities ranging from 2 to 5 kV, fabricated within a full power MOSFET process technology. The studied edge terminations consist of typical JTEs, novel FGRs using MOSFET P-well implantation, as well as a combination of JTEs and FGRs. The experimental results have shown a good efficiency of most of the implemented edge terminations. It is also shown that P-well FGRs could be an effective cost solution for high voltage SiC based power MOSFETs. Moreover, the edge termination combining JTEs and FGRs concepts shows a better tolerance of breakdown voltage values against variations in the JTE dose. The same edge termination design allows one to obtain a good efficiency for both 1.7 and 4.5 kV PiN diodes. The optimal termination has been successfully implemented on 4.5 kV power MOSFETs.
Silicon resonant cavity enhanced photodetector based on the internal photoemission effect at 1.55μm: Fabrication and characterization (2008)

In this paper, the realization and the characterization of a resonant cavity enhanced (RCE) photodetector, completely silicon compatible and working at 1.55μm, are reported. The detector is a RCE structure incorporating a Schottky diode and its working principle is based on the internal photoemission effect. Taking advantage of a Cu∕Si Schottky diode fed on a high reflectivity Bragg mirror, an improvement in responsivity at 1.55μm is experimentally demonstrated.
Trajectory Synthesis for Air Traffic Automation (1997)

Trajectory synthesis algorithms that are key to the center ‐terminal radar approach control automation system (CTAS) developed at NASA Ames Research Center for air trafe c control automation are discussed. CTAS generates computer advisories based on synthesized trajectories that help controllers to produce a safe, efe cient, and expeditious e ow of trafe c over the extended terminal area. Trajectories are synthesized from initial aircraft positionsto ametering e x orrunway, depending on airspace.Thehorizontal pathisconstructed e rstfrom specie ed waypoints using straight lines and constant-radius turns. The vertical trajectory is divided into a series of e ight segments. Three types of e ight proe les are dee ned by connecting selected segments in a predetermined order: fast, nominal, and slow. Each proe lecan produce a certain rangeof arrivaltimes. A second-order Runge ‐Kutta scheme is used for integrating a set of simplie ed point-mass equations to generate vertical trajectories. Then, an iterative scheme is employed to determine the speed that meets a specie ed arrival time. Several special case trajectories are also explained. Two e ight scenarios are used to illustrate the use of trajectory synthesis algorithms.
The Differential Time-course of Extracellular-regulated Kinase Activity Correlates with the Macrophage Response toward Proliferation or Activation (2000)

Bone marrow-derived macrophages proliferate in response to specific growth factors, including macrophage colony-stimulating factor (M-CSF). When stimulated with activating factors, such as lipopolysaccharide (LPS), macrophages stop proliferating and produce proinflammatory cytokines. Although triggering opposed responses, both M-CSF and LPS induce the activation of extracellular-regulated kinases (ERKs) 1 and 2. However, the time-course of ERK activation is different; maximal activation by M-CSF and LPS occurred after 5 and 15 min of stimulation, respectively. Granulocyte/macrophage colony-stimulating factor, interleukin 3, and TPA, all of which induced macrophage proliferation, also induced ERK activity, which was maximal at 5 min poststimulation. The use of PD98059, which specifically blocks ERK 1 and 2 activation, demonstrated that ERK activity was necessary for macrophage proliferation in response to these factors. The treatment with phosphatidylcholine-specific phospholipase C (PC-PLC) inhibited macrophage proliferation, induced the expression of cytokines, and triggered a pattern of ERK activation equivalent to that induced by LPS. Moreover, PD98059 inhibited the expression of cytokines induced by LPS or PC-PLC, thus suggesting that ERK activity is also required for macrophage activation by these two agents. Activation of the JNK pathway did not discriminate between proliferative and activating stimuli. In conclusion, our results allow to correlate the differences in the time-course of ERK activity with the macrophagic response toward proliferation or activation.
A novel lateral field emitter triode with insitu vacuum encapsulation (2002)

We have designed and fabricated a novel lateral field emitter triode, which is in-situ vacuum encapsulated so that any troublesome additional vacuum sealing process is not required. The device exhibits low turn-on voltage of 7 V, stable current density of 2 /spl mu/A/tip at V/sub AC/=30 V, and high transconductance of 1.7 /spl mu/S at V/sub AC/=22 V. An in-situ vacuum encapsulation employing recessed cavities by isotropic RIE (Reactive Ion Etch) method and an electron beam evaporated molybdenum vacuum seals is implemented to fabricate a new field emitter triode.
Acoustic Wattmeter (1956)

The author has constructed a device which gives pointer indications of acoustic intensity over a 50-db range at frequencies up to 10 000 c/sec. The signals from a pair of pressure-sensitive condenser microphones, mounted back to back in a space roughly the size of a dime, are treated electronically to provide pressure and velocity signals which are then multiplied and averaged in a specially designed moving-coil dynamometer to give precise pointer readings. The theory of operation of the apparatus is discussed and the paper concludes with a brief account of the test results of the acoustic wattmeter.
A randomised prospective study on treatment of central retinal vein occlusion by isovolaemic haemodilution and photocoagulation. (1985)

Thirty eight patients with ischaemic and non-ischaemic central retinal vein occlusion were evaluated for the effect of isovolaemic haemodilution. They were allocated at random to a haemodilution group (19 patients, panretinal photocoagulation and isovolaemic haemodilution) and a control group (19 patients, panretinal photocoagulation). Haematocrit was lowered in steps to 30 to 35% in the haemodilution group by repeated exchanges of whole blood for plasma and dextran (MW 40 000) and kept at this level for a period of six weeks. The haemodilution did not lead to serious complications. Three months after starting the treatment eight of 19 patients with haemodilution showed a better visual acuity, whereas only one of 19 control patients had improved. Seven of 17 patients with haemodilution, but only one of 17 control patients, retained a better visual acuity after one year. In the haemodilution group there were fewer patients with macular fibrosis and more with only minor foveal changes. The haemodilution seems to be more effective in patients with ischaemic than with non-ischaemic central retinal vein occlusion. It is concluded that isovolaemic haemodilution improves the visual outcome of patients with central retinal vein occlusion, probably mediated by enhanced retinal blood flow.
Active Sites of Spinoxin, a Potassium Channel Scorpion Toxin, Elucidated by Systematic Alanine Scanning (2016)

Peptide toxins from scorpion venoms constitute the largest group of toxins that target the voltage-gated potassium channel (Kv). Spinoxin (SPX) isolated from the venom of scorpion Heterometrus spinifer is a 34-residue peptide neurotoxin cross-linked by four disulfide bridges. SPX is a potent inhibitor of Kv1.3 potassium channels (IC50 = 63 nM), which are considered to be valid molecular targets in the diagnostics and therapy of various autoimmune disorders and cancers. Here we synthesized 25 analogues of SPX and analyzed the role of each amino acid in SPX using alanine scanning to study its structure-function relationships. All synthetic analogues showed similar disulfide bond pairings and secondary structures as native SPX. Alanine replacements at Lys(23), Asn(26), and Lys(30) resulted in loss of activity against Kv1.3 potassium channels, whereas replacements at Arg(7), Met(14), Lys(27), and Tyr(32) also largely reduced inhibitory activity. These results suggest that the side chains of these amino acids in SPX play an important role in its interaction with Kv1.3 channels. In particular, Lys(23) appears to be a key residue that underpins Kv1.3 channel inhibition. Of these seven amino acid residues, four are basic amino acids, suggesting that the positive electrostatic potential on the surface of SPX is likely required for high affinity interaction with Kv1.3 channels. This study provides insight into the structure-function relationships of SPX with implications for the rational design of new lead compounds targeting potassium channels with high potency.
Area, Age and Gender Dependence of the Nucleoside System in the Brain: a Review of Current Literature (2011)

Nucleosides, such as uridine, inosine, guanosine and adenosine, may participate in the regulation of sleep, cognition, memory and nociception, the suppression of seizures, and have also been suggested to play a role in the pathophysiology of some neurodegenerative and neuropsychiatric diseases. Under pathological conditions, levels of nucleosides change extremely in the brain, indicating their participation in the pathophysiology of disorders like Alzheimer's disease, Parkinson's disease and schizophrenia. These findings have resulted in an increasing attention to the roles of nucleosides in the central nervous system. The specific effects of nucleosides depend on the expression of their receptors and transporters in neuronal and glial cells, as well as their extracellular concentrations in the brain. A complex interlinked metabolic network and transporters of nucleosides may balance nucleoside levels in the brain tissue under normal conditions and enable the fine modulation of neuronal and glial processes via nucleoside receptor signaling mechanisms. Brain levels of nucleosides were found to vary when measured in a variety of different brain regions. In addition, nucleoside levels also depend on age and gender. Furthermore, distributions of nucleoside transporters and receptors as well as nucleoside metabolic enzyme activities demonstrate the area, age and gender dependence of the nucleoside system, suggesting different roles of nucleosides in functionally different brain areas. The aim of this review article is to summarize our present knowledge of the area-, age- and gender-dependent distribution of nucleoside levels, nucleoside metabolic enzyme activity, nucleoside receptors and nucleoside transporters in the brain.
Parvoviruses: Structure and Infection (2012)

Parvoviruses package a ssDNA genome. Both nonpathogenic and pathogenic members exist, including those that cause fetal infections, encompassing the entire spectrum of virus phenotypes. Their small genomes and simple coding strategy has enabled functional annotation of many steps in the infectious life cycle. They assemble a multifunctional capsid responsible for cell recognition and the transport of the packaged genome to the nucleus for replication and progeny virus production. It is also the target of the host immune response. Understanding how the capsid structure relates to the function of parvoviruses provides a platform for recombinant engineering of viral gene delivery vectors for the treatment of clinical diseases, and is fundamental for dissecting the viral determinants of pathogenicity. This review focuses on our current understanding of parvovirus capsid structure and function with respect to the infectious life cycle.
Goal-Directed Reasoning for Specification-Based Data Structure Repair (2006)

Software errors and hardware failures can cause data structures in running programs to violate key data structure consistency properties. As a result of this violation, the program may produce unacceptable results or even fail. We present a new data structure repair system. This system accepts a specification of data structure consistency properties stated in terms of an abstract set-and relation-based model of the data structures in the running program. It then automatically generates a repair algorithm that, during the execution of the program, detects and repairs any violations of these constraints. The goal is to enable the program to continue to execute acceptably in the face of otherwise crippling data structure corruption errors. We have applied our system to repair inconsistent data structures in five applications: CTAS (an air traffic control system), AbiWord (an open source word processing program), Freeciv (an interactive multiplayer game), a parallel x86 emulator, and a simplified Linux file system. Our results indicate that the generated repair algorithms can effectively repair inconsistent data structures in these applications to enable the applications to continue to operate successfully in cases where the original application would have failed. Without repair, all of the applications fail