nils-herrmann/clean_scirepeval huggingface dataset:
From colloidal dispersions to colloidal pastes through solid-liquid separation processes

Solid-liquid separation is an operation that starts with a dispersion of solid particles in a liquid and removes some of the liquid from the particles, producing a concentrated solid paste and a clean liquid phase. It is similar to thermodynamic processes where pressure is applied to a system in order to reduce its volume. In dispersions, the resistance to this osmotic compression depends on interactions between the dispersed particles. The first part of this work deals with dispersions of repelling particles, which are either silica nanoparticles or synthetic clay platelets, dispersed in aqueous solutions. In these conditions, each particle is surrounded by an ionic layer, which repels other ionic layers. This results in a structure with strong short-range order. At high particle volume fractions, the overlap of ionic layers generates large osmotic pressures; these pressures may be calculated, through the cell model, as the cost of reducing the volume of each cell. The variation of osmotic pressure with volume fraction is the equation of state of the dispersion. The second part of this work deals with dispersions of aggregated particles, which are silica nanoparticles, dispersed in water and flocculated by multivalent cations. This produces large bushy aggregates, with fractal structures that are maintained through interparticle surface-surface bonds. As the paste is submitted to osmotic pressures, small relative displacements of the aggregated particles lead to structural collapse. The final structure is made of a dense skeleton immersed in a nearly homogeneous matrix of aggregated particles. The variation of osmotic resistance with volume fraction is the compression law of the paste; it may be calculated through a numerical model that takes into account the noncentral interparticle forces. According to this model, the response of aggregated pastes to applied stress may be controlled through the manipulation of interparticle adhesion.

Field of study: Chemistry
Computational framework for coupling compressible and low Mach number codes

A hybrid multicode computational method is developed that allows combining compressible and low Mach number codes into a single computational solver. The proposed methodology can be used for integrated simulations of multicomponent engineering problems. The unsteady coupling between the two codes is performed via exchanging time-dependent state information through the interfaces using overlapping meshes. The proposed coupling procedure is validated on laminar steady and unsteady test problems. Both constant-density and variable-density regimes of the low Mach number code are investigated. Results of the test cases performed in frameworks of one-way coupling and two-way coupling are documented. Several methods of implementation of interface conditions for the compressible code are compared by looking at the levels of dilatation, as well as numerical errors. The injection method (when all the variables are simply transformed from one code to another through an interpolation procedure) is chosen for its superior stability, accuracy, and simplicity of implementation. Numerical results for the coupled calculations obtained with the injection method show good agreement with both standalone calculations and analytical solutions.

Field of study: Physics
Corrosion studies through open circuit potential determination of Zinc-Aluminium alloy in 1M NaCl solution by using Schiff base

The corrosion behavior of ZINC-ALUMINIUM alloy in the presence of Schiffs Base derivative has been investigated in 1M NaCl solution using Open Circuit Potential techniques. Inhibition efficiency of this compound has been found to vary with concentration of the inhibitor derivative and temperature. The results obtained from OCP measurements were in good agreement.

Field of study: Materials science
Efficiencies of Aloof-Scattered Electron Beam Excitation of Metal and Graphene Plasmons

We assessed the efficiencies of surface plasmon excitation by an aloof-scattered electron beam on metals and graphene. Graphene is shown to exhibit high energy transfer efficiencies at very low electron kinetic energy requirements. We show that the exceptional performance of graphene is due to its unique plasmon dispersion, low electronic density, and thin-film structure. The potential applications of these aloof-scattered graphene plasmons are discussed in the aspects of coherent radiation.

Field of study: Physics
Performance of the SMLR deconvolution algorithm

A performance analysis is presented for false alarms, correct detections, and the resolution of the suboptimal maximum-likelihood deconvolution (MLD) algorithm, called the single most likely replacement (SMLR) algorithm. It is assumed that the source wavelet and statistical parameters are given a priori. It is shown analytically that the performance improves as the signal-to-noise ratio (SNR) increases and as the mainlobe width of the normalized autocorrelation function of the source wavelet decreases. For the same performance, a higher SNR is required as the mainlobe width of the normalized autocorrelation function increases. Some simulation results which are consistent with the analytic results are presented.

Field of study: Engineering
The Critical Role of PTEN/PI3K/AKT Signaling Pathway in Shikonin-Induced Apoptosis and Proliferation Inhibition of Chronic Myeloid Leukemia

Chronic myeloid leukemia (CML) is a myeloproliferative neoplasm. Tyrosine kinase inhibitors (TKIs) are commonly used to treat CML; however, drug resistance of CML cells to TKIs has limited their clinical application. Shikonin, a traditional Chinese herb, has long been used to treat leukemia in China, but the roles and related molecular mechanisms of shikonin treatment in CML remain unclear. Here, we aimed to evaluate the effects of shikonin on the proliferation, apoptosis, and migration of K562 cells, a CML cell line.  Firstly, K562 cell proliferation and apoptosis were tested by CCK8 assay and flow cytometry with Annexin V-FITC/PI staining. Cell migration was measured by Transwell migration assay. In addition, western blot was performed to determine the proteins (PI3K, Bax, Bcl-2, cleaved caspase-3, PTEN, p-AKT, AKT, CXCR4, SDF-1, CD44) involved in the mechanism of action of shikonin. Finally, neutrophils from peripheral blood of CML patients were obtained, and cell proliferation and apoptosis were tested by CCK8 assay and flow cytometry.  Shikonin reduced the proliferation of K562 cells in a time- and dose-dependent manner and promoted the apoptosis of K562 cells. Moreover, shikonin increased the PTEN level and inactivated the PI3K/AKT signaling pathway, subsequently upregulating BAX in K562 cells. In addition, shikonin could block K562 cell migration via the CXCR4/SDF-1 axis. Finally, shikonin significantly inhibited the proliferation and promoted the apoptosis of neutrophils from CML patients.  These results demonstrated that shikonin inhibits CML proliferation and migration and induces apoptosis by the PTEN/PI3K/AKT pathway, revealing the effects of shikonin therapy on CML.

Field of study: Biology, Chemistry
Online Cooperation in English Language Learning

The purpose of this study aimed at examining the results of cooperative online activities in English Language Learning.  This study is a quantitative study with experimental design. Random sampling method was used to determine learners and classes. Participants of this study were 229 English language learners in B1 level, 113 of whom are experimental group in 5 classes and 116 of whom are control group in 5 classes. Learners in experimental group followed a course design based on cooperative online activities and tasks for fifteen weeks. For data collection, a proficiency test named ALCPT was administered to learners at the beginning and end of the term as a pre-test and post-test. Cronbach alpha level of the test was found to be, 98. Reading, writing, listening, speaking, vocabulary and grammar achievement tests were implemented at the end of the semester. Data were analyzed with the help of SPSS 20 by employing descriptive and inferential statistics. Test of normality and homogeneity were calculated by applying Kolmogorov-Smirnova and Levene Statistic respectively. Results showed experimental group were significantly different in their proficiency test scores although there was no significant difference between control group and experimental group at the beginning of the semester in their pre- test proficiency test scores. Achievement test scores revealed that learners in experimental group did significantly better in listening, reading, writing and vocabulary achievement tests. However, there weren’t significant differences in speaking and grammar achievement tests between two groups.  cooperation, language learning, proficiency, achievement DOI : 10.7176/JEP/10-36-09 Publication date: December 31 st 2019

Field of study: Education
Transthyretin is a metallopeptidase with an inducible active site.

TTR (transthyretin) was found recently to possess proteolytic competency besides its well-known transport capabilities. It was described as a cryptic serine peptidase cleaving multiple natural substrates (including β-amyloid and apolipoprotein A-I) involved in diseases such as Alzheimer's disease and atherosclerosis. In the present study, we aimed to elucidate the catalytic machinery of TTR. All attempts to identify a catalytic serine residue were unsuccessful. However, metal chelators abolished TTR activity. Proteolytic inhibition by EDTA or 1,10-phenanthroline could be reversed with Zn2+ and Mn2+. These observations, supported by analysis of three-dimensional structures of TTR complexed with Zn2+, led to the hypothesis that TTR is a metallopeptidase. Site-directed mutagenesis of selected amino acids unambiguously confirmed this hypothesis. The TTR active site is inducible and constituted via a protein rearrangement resulting in ~7% of proteolytically active TTR at pH 7.4. The side chain of His88 is shifted near His90 and Glu92 establishing a Zn2+-chelating pattern HXHXE not found previously in any metallopeptidase and only conserved in TTR of humans and some other primates. Point mutations of these three residues yielded proteins devoid of proteolytic activity. Glu72 was identified as the general base involved in activation of the catalytic water. Our results unveil TTR as a metallopeptidase and define its catalytic machinery.

Field of study: Biology, Computer science
Long-term monitoring of the succession of a microbial community in activated sludge from a circulation flush toilet as a closed system.

The microbial diversity and community succession of a circulation flush toilet were investigated by terminal restriction fragment length polymorphism and cloning analyses. Clonal libraries of 16S rRNA gene on day 3 and day 127 were constructed. On day 3, 102 clones were sequenced; Proteobacteria and Bacteroidetes accounted for 27% and 45%, respectively. On day 127, Proteobacteria had increased to 43% and Bacteroidetes had decreased to 26% of a total of 100 clones. Terminal restriction fragment length polymorphism peaks were identified by in silico analysis of clone libraries. The relative abundances of Nitrosomonas increased from 1% to 6% with commencement of nitrification and denitrification. Similarly, the relative abundance of terminal restriction fragments generated from Xanthomonas increased from 3% to 10%. Therefore, these bacteria could play a prominent role in this process. To reveal the relationship between stability of the microbial community and performance of the system, microbial community succession was visualized by multidimensional scaling analysis. The microbial community structure changed markedly, particularly during the start-up period of the system. The plots then became stable after the start of nitrification and denitrification. This result suggests that the succession of microbial community structure had a correlation with the performance of the system.

Field of study: Biology, Environmental science
Identification of a 251-bp fragment of the PAI-1 gene promoter that mediates the ethanol-induced suppression of PAI-1 expression.

Moderate alcohol consumption reduces the risk for coronary heart disease. This cardioprotection may be due to ethanol enhancement of fibrinolysis. Fibrinolysis involves the interaction of plasminogen activators (PAs) and the plasminogen activator inhibitor type-1 (PAI-1). Factor(s) that decrease endothelial cell (EC) PAI-1 expression increase fibrinolysis and may decrease the risk for cardiovascular disease.



Five promoter deletion fragments were generated from a 1.1-kb PAI-1 promoter fragment and ligated to a luciferase reporter gene. Cultured human umbilical vein endothelial cells (HUVECs) were transiently transfected with these PAI-1 deletion constructs. A 251-base pair (bp) fragment of the PAI-1 promoter, positions -800 to -549, was cloned upstream of a heterologous promoter/enhancer. ECs luciferase activity was measured in the absence/presence of 20 mM ethanol. Electrophoresis mobility shift assays were performed with nuclear extracts from untreated and ethanol-treated ECs using this 251-bp fragment.



Deletion analysis showed a region between position -800 and -549 mediated ethanol repression of luciferase activity. This 251-bp promoter fragment also repressed the activity of a heterologous promoter/enhancer in the presence of ethanol. Using the labeled 251-bp fragment, nuclear extracts from ethanol-treated ECs contained two inducible bands and one enhanced band. Non-ethanol treated nuclear extracts also contained a band that was not observed in ethanol-treated samples. Competition using 100-fold molar excess of unlabeled probe abolished these four bands.



Repression of PAI-I gene transcription in cultured HUVECs exposed to ethanol may involve the interaction of several transcription factors with binding sites localized between positions -800 and -549 of the PAI-1 gene promoter.

Field of study: Medicine
Formation and Occurrence of N-Chloro-2,2-dichloroacetamide, a Previously Overlooked Nitrogenous Disinfection Byproduct in Chlorinated Drinking Waters.

Haloacetamides (HAMs) are a class of newly identified nitrogenous disinfection byproducts (N-DBPs) whose occurrence in drinking waters has recently been reported in several DBP surveys. As the most prominent HAM species, it is commonly acknowledged that 2,2-dichloroacetamide (DCAM) is mainly generated from dichloroacetonitrile (DCAN) hydrolysis because the concentrations of these two compounds are often well correlated. Instead of DCAM, a previously unreported N-DBP, N-chloro-2,2-dichloroacetamide (N-Cl-DCAM), was confirmed in this study as the actual DCAN degradation product in chlorinated drinking waters. It is suspected that N-Cl-DCAM has been erroneously identified as DCAM, because its nitrogen-bound chlorine is readily reduced by most commonly used quenching agents. This hypothesis is supported by kinetic studies that indicate almost instantaneous N-chlorination of DCAM even at low chlorine residuals. Therefore, it is unlikely that DCAM can persist as a long-lived DCAN decomposition product in systems using free chlorine as a residual disinfectant. Instead, chlorination of DCAM will lead to the formation of an equal amount of N-Cl-DCAM by forming a hydrogen bond between hypochlorite oxygen and amino hydrogen. Alternatively, N-Cl-DCAM can be produced directly from DCAN chlorination via nucleophilic addition of hypochlorite on the nitrile carbon. Due to its relatively low pKa value, N-Cl-DCAM tends to deprotonate under typical drinking water pH conditions, and the anionic form of N-Cl-DCAM was found to be very stable in the absence of chlorine. N-Cl-DCAM can, however, undergo acid-catalyzed decomposition to form the corresponding dichloroacetic acid (DCAA) when chlorine is present, although those acidic conditions that favor N-Cl-DCAM degradation are generally atypical for finished drinking waters. For these reasons, N-Cl-DCAM is predicted to have very long half-lives in most distribution systems that use free chlorine. Furthermore, an analytical method using ultra performance liquid chromatography (UPLC)/negative electrospray ionization (ESI-)/quadrupole time-of-flight mass spectrometry (qTOF) was developed for the detection of a family of seven N-chloro-haloacetamides (N-Cl-HAMs). Combined with solid phase extraction (SPE), the occurrence of N-Cl-DCAM and its two brominated analogues (i.e., N-chloro-2,2-bromochloroacetamide and N-chloro-2,2-dibromoacetamide) was quantitatively determined for the first time in 11 real tap water samples. The discovery of N-Cl-DCAM or, more broadly speaking, N-Cl-HAMs in chlorinated drinking waters is of significance because they are organic chloramines, a family of compounds that is perceived to be more toxicologically potent than halonitriles (e.g., DCAN) and haloamides (e.g., DCAM), and therefore they may pose greater risks to drinking water consumers given their widespread occurrence and high stability.

Field of study: Environmental science
Computer Model for Moisture Distribution in Stratified Soils Under a Trickle Source

THIS research was conducted to: (1) develop a computer simulation model—or use an existing one—to simulate irrigation in stratified soils, (2) study the moisture distribution under a trickle source in a Lakeland sand, and (3) compare results of the computer model with field measurements. Field tests were conducted at various application rates and volumes, a CSMP model was modified for use in stratified soils, and this modified program was used to simulate irrigation in the Lakeland soil. The neutron scattering method was used to measure the moisture distribution to a depth of 150 cm and to a radius of 105 cm from the trickle emitter. For each test, measurements were made before and after irrigation and again after some redistribution period. Also, tensiometers were placed at specified depths at a radius of 45 cm to help locate the wetting front during application and redistribution. Input data for the CSMP simulation model (in-situ tension vs. water content and hydraulic conductivity vs. water content for each soil horizon) were obtained using the instantaneous profile method. Field measurements showed that the shape and size of the wetted zone is more a function of the volume of water applied than of the rate of application. When more than 32 L were applied, the additional water did not greatly increase the horizontal dimension of the wetted zone, but moved vertically through the profile. The CSMP simulation compared favorably with the field measurements in the Lakeland sand.

Field of study: Agricultural and Food sciences
Vibration Reduction of Rotor Supported by Superconducting Magnetic Bearing Utilizing Electromagnetic Shunt Damper

A superconducting magnetic bearing can levitate a rotor without control and is expected to be applied to flywheel energy storage systems. However, because the levitation force has nonlinearity, the rotor can show nonlinear vibrations such as subharmonic resonance and superharmonic resonance. Therefore, it is necessary to suppress the amplitude of nonlinear vibration of the rotor. Recently, an “electromagnetic shunt damper,” which can replace a dynamic vibration absorber, has been researched. The purpose of this study is to investigate whether an electromagnetic shunt damper can suppress the nonlinear vibration of a rotor supported by a superconducting magnetic bearing. We obtained the system's governing equations via an analytical model and nondimensionalized the equations. Linear analysis was performed, and we confirmed that an electromagnetic shunt damper is effective against linear systems. Furthermore, numerical calculations via the Rung-Kutta method were carried out. The obtained results show that an electromagnetic shunt damper can suppress the vibration amplitude of primary resonance and subharmonic resonance of order 1/2.

Field of study: Physics
A new method to deduce high-order compact difference schemes for two-dimensional Poisson equation

This paper introduces a novel method for deducing high-order compact difference schemes for the two-dimensional (2D) Poisson equation. Like finite volume method, a dual partition is introduced. Combining Simpson integral formula and parabolic interpolation, a family of fourth-order and sixth-order compact difference schemes are obtained based on three different types of dual partitions. Moreover, several new fourth-order compact schemes are gained and numerical experiments are shown two of them are much better than almost any other fourth-order schemes which have been presented in others’ work. The outline for the nonlinear Poisson equation is also given. Numerical experiments are presented to verify the feasibility of this new method and the high accuracy of these fourth-order and sixth-order compact difference schemes.

Field of study: Mathematics
Magmatic processes associated with caldera collapse at Ossipee ring dyke, New Hampshire

A detailed textural and chemical study of a section through the 121 Ma Ossipee ring dyke in New Hampshire provides a comprehensive record of magmatic and volcanic events during caldera formation. Phenocryst-rich quartz syenite is the main rock type; syenite, rhyolite, and basalt form small mingled dykes, xenoliths, and magmatic enclaves. Enclaves of fine-grained syenite have positive Eu anomalies, are more mafic, and are depleted in crystals relative to host quartz syenite. Anorthoclase phenocrysts in enclaves have compositions similar to the bulk enclave; high CaO contents in the crystals indicate magmatic temperatures up to 1050 °C. Rhyolite in the ring dyke is texturally and chemically equivalent to ignimbrite inside the caldera. Basalt occurs both as xenoliths and megabreccias from earlier volcanoes and as dykes that mixed and mingled with rhyolitic dykes during eruption. We suggest the following sequence of events: (1) Convection, crystal settling, and filtration of melt away from solidification fronts formed a zoned magma chamber containing voluminous rhyolite overlying crystal-rich quartz syenite and cumulate syenite. (2) Basalt partially melted the anorthoclase syenite cumulate at the base of the chamber to form a hot mobile syenitic liquid, now represented by enclaves in the ring dyke. (3) Continued intrusion of basalt replenished and rejuvenated the Ossipee chamber, driving large eruptions of rhyolitic ignimbrite that ponded in the caldera as the chamber roof collapsed. (4) Caldera collapse stirred the chamber, mingling and mixing rhyolitic, quartz syenitic, and syenitic magma. Vortices around subsiding blocks during caldera collapse caused the mixing and mingling. (5) Quartz syenite, rhyolite, and small volumes of basalt magma were intruded simultaneously into the ring dyke, causing the basalt and rhyolite to mingle explosively. The rejuvenation of the magma chamber and subsequent subsidence of the caldera produced a mixed and mingled crystal mush now preserved in the ring dyke. The ring dyke represents residual magma from a caldera-forming eruption.

Field of study: Geology