nils-herrmann/clean_scirepeval huggingface dataset:
Multiscale behavior analysis and molar behaviorism: An overview.

In the context of evolutionary theory, behavior is the interaction between the organism and its environment. Two implications follow: (a) behavior takes time; and (b) behavior is defined by its function. That behavior takes time implies that behavioral units are temporally extended patterns or activities. An activity functions as an integrated whole composed of parts that are themselves smaller-scale activities. That behavior is defined by its function implies that behavior functions to change the environment in ways that promote reproductive success. Phylogenetically important events (PIEs) are enhanced or mitigated by activities they induce as a result of natural selection. Induction explains all the phenomena that have traditionally been explained by reinforcement. This multiscale view replaces discrete responses and contiguity with multiscale activities and covariance. A PIE induces operant activity as a result of covariance in the form of a feedback relation between the activity and the PIE. A signal (conditional inducer) induces PIE-induced activities as a result of covariance between the PIE and the signal. In an ontological perspective, behavior is a process, and an activity is a process individual. For example, ontological considerations clarify the status of delay and probability discounting. A true natural science of behavior is possible.

Field of study: Biology, Psychology
Stereoelectroencephalography in children: a review.

Stereoelectroencephalography (SEEG) is an intracranial diagnostic measure that has grown in popularity in the United States as outcomes data have demonstrated its benefits and safety. The main uses of SEEG include 1) exploration of deep cortical/sulcal structures; 2) bilateral recordings; and 3) 3D mapping of epileptogenic zones. While SEEG has gradually been accepted for treatment in adults, there is less consensus on its utility in children. In this literature review, the authors seek to describe the current state of SEEG with a focus on the more recent technology-enabled surgical techniques and demonstrate its efficacy in the pediatric epilepsy population.

Field of study: Medicine
Progress of intense heavy ion beam driven high energy density physics

Intense ion beams can quasi-isometrically heat any high-density sample and generate warm dense matter (WDM) with large scale, uniform state distribution without any shock wave inside. This kind of driver provides a new opportunity for the laboratory high energy density physics (HEDP) research. The typical intense ion beam accelerators around the world, as well as their critical parameters and research plans of HEDP study are introduced.The progress of ion driven WDM generation and evolution using PIC and hydrodynamic simulations is shown. The high energy electron beam radiography technique with high spatial resolution, high temporal evolution, and high penetrating ability is also introduced. The collisional and charge transfer processes of the interaction between low-to-medium energy ion and plasma are analyzed. The nonlinear effect during the intense ion beam stopping and transportation process are presented.

Field of study: Physics
The Brassica napus extA extensin gene negative regulatory region controls expression in response to mechanical stresses.

In the present study the hypothesis that the -433 to -664 bp negative regulatory region (NRR) of the Brassica napus extA extensin promoter controls extA activation in response to externally applied weight loads was tested. When weight loads were applied to the nodal regions of transgenic tobacco plants containing extA promoter deletions fused to GUS, repression controlled by the NRR was overcome and GUS expression was induced only in the transgenics carrying the NRR. This proves that extensin expression in nodal regions is not developmentally controlled, but is induced in response to mechanical stresses, and is controlled by the NRR. It was also shown that the activation of the extA promoter during the development of lateral roots is a stress-related response that is also under the control of the NRR but that the constitutive expression of extensin mRNA in the phloem of roots is not due to the mechanical forces the root experiences as it forces it way through the soil. Electrophoretic mobility shift assays using a 25 bp oligonucleotide have been used to show that an 8 bp consensus sequence from the NRR binds nuclear proteins. Wound-induced signals regulating extensin gene expression are shown to travel bi-directionally through the plant, from root to leaf and vice versa.

Field of study: Environmental science
NON-PROBABILITY RELIABILITY OPTIMIZATION DESIGN FOR STRUCTURES WITH FUZZY AND INTERVAL VARIABLES

The reliability method is one of effective ways to deal with the uncertainty existing in engineering structures.Due to the existence of hybrid uncertainties in many engineering structures,a reliability method of hybrid uncertainties is proposed,and it is suitable for engineering application.Based on the interval reliability model of the volume ratio,a non-probabilistic reliability model for the structure with fuzzy-interval hybrid variables is established by transforming the fuzzy variables into the interval variables.The presented hybrid reliability model can be used as a supplement to the previous methods,as it has a clearer meaning and it is reasonable to deal with the fuzzy information.The proposed model was used in the optimization design of an airfoil,and the numerical example shows that the method is effective and feasible.

Field of study: Engineering
New method for the synthesis of the 1,3-thiazine system. 2-phenylamino-5,6-dihydro-4H-1,3-thiazin-5-ones

Treatment of N-phenylthioureidoalkyl-α-diazo ketones with acids leads to 2-phenyl-amino-5,6-dihydro-4H-1,3-thiazin-5-ones.

Field of study: Chemistry
Prostaglandins but not nitric oxide are endothelium-derived relaxing factors in the trout aorta.

To identify the type of prostanoids produced by endothelial cells of trout aorta and to determine whether or not the smooth muscle responds to nitric oxide.



Ventral aortas, with and without endothelium from rainbow trout (S gairdneri), were incubated in a buffered salt solution.



Addition of the calcium ionophore A23187 caused a significant increase in prostaglandin E's and a consistent increase in the stable metabolite of prostacyclin (6-keto-prostaglandin F1 alpha) in the incubation media only when the endothelium was present. This production was inhibited by methylene blue (10 mumol/L). In rings of trout aorta without endothelium suspended for the measurement of isometric force in organ chambers, prostacyclin and prostaglandin E1 but not prostaglandin E2 caused concentration-dependent decreases in tension when the rings were contracted with acetylcholine. The smooth muscle did not relax to nitric oxide but did so to sodium nitroprusside. Relaxations to the latter nitrovasodilator were not inhibited by methylene blue. Descending aorta without endothelium from frogs relaxed in a concentration-dependent manner to nitric oxide.



Predominant endothelium-derived relaxing factors in trout aorta are prostaglandins, the synthesis of which can be inhibited by methylene blue. A phylogenetic appearance of nitric-oxide sensitive mechanism for vasodilatation, perhaps is associated with the transition from water to air respiration.

Field of study: Biology, Chemistry, Medicine
The Ni-rich Part of the Ni-P-Sn System: Isothermal Sections

Due to the use of phosphorus-containing nickel substrates in microelectronics, understanding of their reaction with Sn-based solders and knowledge of the corresponding reaction products is highly important. Therefore the ternary Ni-P-Sn system was investigated experimentally using x-ray diffraction (XRD), scanning electron microscopy (SEM) + energy dispersive x-ray spectroscopy (EDX)/wavelength-dispersive x-ray spectroscopy (WDS), and differential thermal analysis (DTA). Sample preparation was done by alloying powders of the starting components contained in alumina crucibles in evacuated quartz tubes. In this study the phase equilibria in the Ni-rich part of the ternary Ni-P-Sn system are described in the form of three partial isothermal sections at 550°C, 700°C, and 850°C. A total of five ternary compounds exist in the Ni-rich part, and the binary Ni3Sn2 HT phase was found to dissolve 17.6 at.% P at 850°C. This well agrees with literature reports, while a different extent and shape of the large homogeneity range of this phase were found. Between 850°C and 700°C phase equilibria change significantly due to the formation of the ternary phases Ni10P3Sn5 (T3), Ni13P3Sn8 (T4), and Ni2PSn (T5).

Field of study: Materials science
Isothiafludine, a novel non-nucleoside compound, inhibits hepatitis B virus replication through blocking pregenomic RNA encapsidation

To investigate the action of isothiafludine (NZ-4), a derivative of bis-heterocycle tandem pairs from the natural product leucamide A, on the replication cycle of hepatitis B virus (HBV) in vitro and in vivo.HBV replication cycle was monitored in HepG2.2.15 cells using qPCR, qRT-PCR, and Southern and Northern blotting. HBV protein expression and capsid assembly were detected using Western blotting and native agarose gel electrophoresis analysis. The interaction of pregenomic RNA (pgRNA) and the core protein was investigated by RNA immunoprecipitation. To evaluate the anti-HBV effect of NZ-4 in vivo, DHBV-infected ducks were orally administered NZ-4 (25, 50 or 100 mg·kg−1·d−1) for 15 d.NZ-4 suppressed intracellular HBV replication in HepG2.2.15 cells with an IC50 value of 1.33 μmol/L, whereas the compound inhibited the cell viability with an IC50 value of 50.4 μmol/L. Furthermore, NZ-4 was active against the replication of various drug-resistant HBV mutants, including 3TC/ETV-dual-resistant and ADV-resistant HBV mutants. NZ-4 (5, 10, 20 μmol/L) concentration-dependently reduced the encapsidated HBV pgRNA, resulting in the assembly of replication-deficient capsids in HepG2.2.15 cells. Oral administration of NZ-4 dose-dependently inhibited DHBV DNA replication in the DHBV-infected ducks.NZ-4 inhibits HBV replication by interfering with the interaction between pgRNA and HBcAg in the capsid assembly process, thus increasing the replication-deficient HBV capsids. Such mechanism of action might provide a new therapeutic strategy to combat HBV infection.

Field of study: Biology, Chemistry, Medicine
In vitro evaluation of the mutagenic and cytostatic effect of Tamaron, Lannate and Manzate alone and in mixture

Pesticides are often used in agriculture, especially in floriculture. They are frequently applied in binary or ternary mixtures. Nevertheless, their impact on the genetic material has been scarcely explored. In this study, the mutagenic and cytostatic effect of three widely used pesticides, alone and combined, were analyzed. Briefly, lymphocytes cultures were obtained from peripheral blood samples of five healthy donors to determine the sister chromatid exchange and the replicative index (RI). Then, lymphocytes were exposed to Tamaron (100 ppm), Lannate (200 ppm) and Manzate (300 ppm) alone and combined. For the binary mixtures, the concentrations used were 50 ppm of Tamaron, 100 ppm of Lannate and 150 ppm of Manzate. For the ternary mixtures the following concentrations were used: Tamaron (33 ppm), Lannate (70 ppm) and Manzate (100 ppm). Finally, differential staining was performed. It was found that the frequency of SCE/cell showed a significant difference (P ≤ 0.05) between the control (2.66) and the individual treatments of Tamaron (4.87), Lannate: (5.12) and Manzate (4.23). Also, the values of the SCE in the binary mixture of Tamaron+Lannate (5.57), Tamaron+Manzate (6.06) and Lannate+Manzate (6.22) and the ternary mixture (6.63) were statistically different compared to the control. In the RI there was a significant difference between the control (1.98) and the Manzate (1.87). RI differences were also statistically significant (P ≤ 0.05) in mixtures of Tamaron+Lannate (1.64), Tamaron+Manzate (1.63), Lannate+Manzate (1.69) and total mixture (1.53). Therefore, it is suggested that these pesticides alone and in mixtures have both mutagenic and cytostatic synergistic effect in human lymphocytes in vitro.

Field of study: Agricultural and Food sciences
Thrust-top lacustrine-lagoonal basin development in accretionary wedges: late Messinian (Lago-Mare) episode in the central Apennines (Italy)

We analysed in detail the geometry, sedimentology and palaeontology (both mollusc and ostracod assemblages) of a small lacustrine–lagoonal basin located at about 1100 m a.s.l. in the Marsica region of the Apennines, at Le Vicenne locality (L'Aquila, Abruzzo, central Italy). The structure of the basin infill deposits outlines an open syncline with an E–W axis. Polygenic conglomerates interbedded with clay levels and sandy marls, which constitute roughly coarsening-upward progradational sequences, are the dominant lithologies. These sequences are interpreted as lacustrine to coastal lagoon deposits with episodic fan delta supplies. This sedimentological interpretation is also supported by mollusc and ostracod assemblages, which suggest that the sedimentary environment was characterized by a mesohaline closed water body, with salinity probably ranging from 10‰ to 13‰. Both mollusc and ostracod assemblages show a clear Paratethyan influence. In the ostracod assemblage ten species out of the fourteen collected forms belong to the Loxoconcha djaffarovi Zone as defined by Carbonnel (1978) . Thus, it is possible to refer the siltitic–clayey intercalations of Le Vicenne to the top of the Messinian (post-salinity crisis). The presence of a strong angular unconformity at the base of the basin, together with the structural setting of its deposits, suggesting a light compressive deformation, are common features in all the thrust-top basins recognized in the central Apennines. Taking into account the regional data, the age of the youngest deposit involved in the substratum (siliciclastic turbidites which recorded the Messinian salinity crisis) and the palaeobiological indications given by the mollusc and ostracod assemblages, it is possible to constrain the origin of the Le Vicenne basin to the Messinian Lago-Mare–Early Pliocene tectono-sedimentary event of the Apennines. The recognition in the Marsica range of this thrust-top basin allows us to attempt a palinspastic reconstruction locating the Marsica region in the latest Miocene–Early Pliocene active thrust zone of the Apennine accretionary wedge.

Field of study: Environmental science, Geography
Production and partial characterization of hybridoma clones secreting monoclonal antibodies against Francisella tularensis.

Hybridomas secreting monoclonal antibodies against Francisella tularensis cellular antigens were produced and characterized. These monoclonal antibodies reacted with F. tularensis in ELISA but not by immunoblot, indicating that the antibodies are directed against conformational epitopes. One of these monoclonal antibodies was directed against outer membrane protein (OMP) components, and the remainder are likely directed against capsular components. The OMP-specific monoclonal antibodies are F. tularensis-specific in contrast to the others which cross-react with a number of other bacterial species. These OMP-specific monoclonal antibodies are of the IgG1 subclass, and may prove to be a useful diagnostic tool for detection and identification of F. tularensis in clinical materials.

Field of study: Biology
Effect of Magnetite Nanoparticle Morphology on the Parameters of MRI Relaxivity

Results are presented from synthesizing and characterizing magnetite nanoparticles with spherical, cubic and octahedral geometry. Magnetic properties (saturation magnetization, residual magnetization, and coercive force), cytotoxicity, and T2 relaxivity are measured for the synthesized nanoparticles. They are characterized via X-ray diffraction and dynamic light scattering (hydrodynamic size and zeta potential). The effect the shape of the nanoparticles have on the values of T2 relaxivity is analyzed. Nontoxic magnetite nanoparticles coated with copolymer are excellent contrast agents for magnetic resonance imaging (MRI) and show better contrast properties than their commercial analogs (Rezovist, Ferumoxytol, Feridex).

Field of study: Physics
Numerical Analysis of Eddy Viscosity Models in Supersonic Turbulent Boundary Layers

Three multilayer eddy viscosity models by Herring-Mellor, Cebeci-Smith-Mosinskis, and Maise-McDonald are compared in this investigation. The aforementioned models were incorporated into an implicit finite difference numerical scheme for compressible turbulent boundary layers. Calculations were performed over Mach number ranges of approximately 0 to 4.55 with the Reynolds number spanning the range of 4 x 106 to 1.41 x 109 for zero pressure gradient and adiabatic wall. All selected viscosity models produced comparable results and provided excellent agreement with the experimental measurements. The calculated results revealed the dominant nature of the viscous sublayer while modifications in the law of the wake region exhibited a relatively mild influence on the numerical solutions.

Field of study: Physics
Cross-cultural Pedagogy: Practical Strategies for a Successful Interprofessional Study Abroad Course

This article discusses some practical strategies for designing and implementing a cross-cultural interprofessional study abroad course, including pre-departure preparation, facilitating small groups with local students, establishing a weekly theme, utilizing role-play and reflective assignments, and implementing meaningful evaluation strategies. These strategies were based on three years of experience and were found to effectively increase students’ cultural competence and self-confidence, as evidenced by student evaluations and results from a focus group conducted one year after the course. Short term study abroad courses with appropriate pedagogical design are significant strategies for health profession programs in the face of growing diversity and globalization.

Field of study: Education
The "Underside" of the Mexican Revolution: El Paso, 1912

The Mexican Revolution was predominantly a Northern movement. In part this was a logical continuation of what had occurred during the Diaz regime, namely, the rapid development of the northern tier of Mexican states. But in large measure the rise to prominence of leaders such as Francisco Madero, Pascual Orozco, Francisco Villa, Venustiano Carranza, Alvaro Obregon, and Pablo Gonzalez reflected the advantage they enjoyed over revolutionaries in other parts of Mexico—access to the American border. Arms and ammunition could be imported, loot to pay for these munitions could be exported, United States territory could be used as a base of operations, and the United States provided a sanctuary for the members of defeated factions. Moreover, since the majority of the population along the border were of Mexican extraction, they inevitably became caught up in the factional struggle, as, for that matter, did many of the Anglos, either out of sympathy or because the Revolution became a lucrative business. Yet despite the extent to which the Revolution spilled over into the United States, we still have but a sketchy knowledge of this phenomenon. Precisely how did Mexican juntas function, how were munitions acquired, how was recruiting conducted, and how was revolutionary activity financed? To understand this critical aspect of the Revolution we need much more work along the lines of David N. Johnson's admirable study of Maderista activities in San Antonio in 1910–1911.

Field of study: History
Validation of photosynthetic-fluorescence parameters as biomarkers for isoproturon toxic effect on alga Scenedesmus obliquus.

Photosynthetic-fluorescence parameters were investigated to be used as valid biomarkers of toxicity when alga Scenedesmus obliquus was exposed to isoproturon [3-(4-isopropylphenyl)-1,1-dimethylurea] effect. Chlorophyll fluorescence induction of algal cells treated with isoproturon showed inactivation of photosystem II (PSII) reaction centers and strong inhibition of PSII electron transport. A linear correlation was found (R2>or=0.861) between the change of cells density affected by isoproturon and the change of effective PSII quantum yield (PhiM'), photochemical quenching (qP) and relative photochemical quenching (qP(rel)) values. The cells density was also linearly dependent (R2=0.838) on the relative unquenched fluorescence parameter (UQF(rel)). Non-linear correlation was found (R2=0.937) only between cells density and the energy transfer efficiency from absorbed light to PSII reaction center (ABS/RC). The order of sensitivity determined by the EC-50% was: UQF(rel)>PhiM'>qP>qP(rel)>ABS/RC. Correlations between cells density and those photosynthetic-fluorescence parameters provide supporting evidence to use them as biomarkers of toxicity for environmental pollutants.

Field of study: Environmental science
The Anisotropic Noise in Stochastic Gradient Descent: Its Behavior of Escaping from Sharp Minima and Regularization Effects

Understanding the behavior of stochastic gradient descent (SGD) in the context of deep neural networks has raised lots of concerns recently. Along this line, we study a general form of gradient based optimization dynamics with unbiased noise, which unifies SGD and standard Langevin dynamics. Through investigating this general optimization dynamics, we analyze the behavior of SGD on escaping from minima and its regularization effects. A novel indicator is derived to characterize the efficiency of escaping from minima through measuring the alignment of noise covariance and the curvature of loss function. Based on this indicator, two conditions are established to show which type of noise structure is superior to isotropic noise in term of escaping efficiency. We further show that the anisotropic noise in SGD satisfies the two conditions, and thus helps to escape from sharp and poor minima effectively, towards more stable and flat minima that typically generalize well. We systematically design various experiments to verify the benefits of the anisotropic noise, compared with full gradient descent plus isotropic diffusion (i.e. Langevin dynamics).

Field of study: Computer science
Evaluation of Pathway Activation for a Single Sample Toward Inflammatory Bowel Disease Classification

Since similar complex diseases are much alike in clinical symptoms, patients are easily misdiagnosed and mistreated. It is crucial to accurately predict the disease status and identify markers with high sensitivity and specificity for classifying similar complex diseases. Many approaches incorporating network information have been put forward to predict outcomes, but they are not robust because of their low reproducibility. Several pathway-based methods are robust and functionally interpretable. However, few methods characterize the disease-specific states of single samples from the perspective of pathways. In this study, we propose a novel framework, Pathway Activation for Single Sample (PASS), which utilizes the pathway information in a single sample way to better recognize the differences between two similar complex diseases. PASS can mainly be divided into two parts: for each pathway, the extent of perturbation of edges and the statistic difference of genes caused by a single disease sample are quantified; then, a novel method, named as an AUCpath, is applied to evaluate the pathway activation for single samples from the perspective of genes and their interactions. We have applied PASS to two main types of inflammatory bowel disease (IBD) and widely verified the characteristics of PASS. For a new patient, PASS features can be used as the indicators or potential pathway biomarkers to precisely diagnose complex diseases, discover significant features with interpretability and explore changes in the biological mechanisms of diseases.

Field of study: Biology