nils-herrmann/clean_scirepeval huggingface dataset:
Mathematical modelling of stem cell differentiation: the PU.1–GATA-1 interaction

The transcription factors PU.1 and GATA-1 are known to be important in the development of blood progenitor cells. Specifically they are thought to regulate the differentiation of progenitor cells into the granulocyte/macrophage lineage and the erythrocyte/megakaryocite lineage. While several mathematical models have been proposed to investigate the interaction between the transcription factors in recent years, there is still debate about the nature of the progenitor state in the dynamical system, and whether the existing models adequately capture new knowledge about the interactions gleaned from experimental data. Further, the models utilise different formalisms to represent the genetic regulation, and it appears that the resulting dynamical system depends upon which formalism is adopted. In this paper we analyse the four existing models, and propose an alternative model which is shown to demonstrate a rich variety of dynamical systems behaviours found across the existing models, including both bistability and tristability required for modelling the undifferentiated progenitors.

Field of study: Biology, Mathematics
Film morphology and reaction rate for the CVD of tungsten by the WF6—SiH4 reaction

Low pressure chemical vapor deposition (LPCVD) of tungsten (W) by SiH4 reduction of WF6 on Si(100) surfaces was studied in a single-wafer, cold-wall reactor over a temperature range of 137–385°C and a pressure range of 1-10 Torr at a SiH4/WF6 ratio of 1.0. Rate data were obtained in the absence of gas-phase mass transport limitations and were measured using gravimetric techniques. The amount of tungsten that was deposited varied between 5.79 × 10−5 and 1.70 × 10−2 g/cm2 (∼300−88,000Å based on a tungsten density of 19.3 g/cm3), and the rates were between 1.02 × 10−4 and 1.74 × 10−3 g/cm2 min (∼500-9,000Å/ min). The apparent overall activation energy increased with pressure; 0.12 eV/ atom at 1 Torr, and 0.40 eV/atom at 10 Torr for short reaction times (0.5–1.5 min). The overall rate was dependent on reaction time (film thickness). Better film morphologies were obtained at higher temperatures and lower pressures. AW(110) preferential orientation was observed at the Si-W interface. Tungsten orientation switched from (110) to (100) as the films grew thicker. Higher apparent activation energies observed at higher pressures were attributed to gas phase reactions and/or by-product readsorption. The interdependence of rate and film morphology was attributed to a reconstruction of W(100) surfaces on which reactant diffusion/surface reaction is favored.

Field of study: Materials science
Altered metabolism of folates and lipids in hyperthyroid and hypothyroid rats.

Effect of excess folate on the metabolism of folate and plasma lipids in thyroid stressed animals was studied. Administration of excess dietary folate to hyperthyroid rats did not affect the decreased in vivo histidine oxidation in these animals, but it increased the hepatic tetrahydrofolate content. Hypothyroid rats had higher plasma total cholesterol (TC), high density lipoprotein cholesterol (HDLC) and trigylcerides (TG) with no change in post heparin lipolytic activity (PHLA). In hyperthyroidism both TC and HDLC were decreased in plasma and PHLA levels were elevated. On administration of excess dietary folate to hyperthyroid rats HDLC levels were not altered but PHLA and TC levels became near normal, while TG levels remained elevated.

Field of study: Biology, Chemistry, Physics
Repression of WT1-Mediated LEF1 Transcription by Mangiferin Governs β-Catenin-Independent Wnt Signalling Inactivation in Hepatocellular Carcinoma

The development of hepatocellular carcinoma (HCC) is a complex process which involves deregulation of multiple signalling pathways. The hyper-activation of Wnt signalling promotes sustained expansion, invasion, and neovascularization of HCC. Mangiferin, a natural small molecule present in Mangifera indica L. has been shown to inactivate β-catenin, which is an indispensable regulator in Wnt pathway. Our study aimed to determine whether mangiferin has any inhibitory effect on HCC and examine how it modulates Wnt signalling.  The tumour inhibitory effect of mangiferin was examined by in vitro cellular models and an in vivo orthotopic HCC implantation model. The genes responsible for mangiferin-mediated anti-HCC were delineated by polymerase chain reaction (PCR) microarray. The expression of target genes was further determined by quantitative PCR and immuno-blotting assays. The binding capacity of Wilms’ tumour 1 (WT1) to the lymphoid enhancer-binding factor 1 (LEF1) promoter was confirmed by chromatin immunoprecipitation-qPCR.  Oral administration of mangiferin inhibited orthotopic tumour growth. Cellular investigations confirmed the dose-dependent inhibition of mangiferin on HCC expansion and invasion. PCR array combined with Gene Ontology analysis revealed that the Wnt pathway was the predominant target of mangiferin and LEF1 was the most reduced gene in the Wnt pathway. Overexpression of LEF1 diminished repression of Wnt signalling and reduced proliferation activity in mangiferin-treated HCC cells. The mangiferin-mediated down-regulation of LEF1 was independent of β-catenin but associated with WT1 protein. WT1 knock-in in HCC cells further enhanced LEF1 expression. Chromatin immunoprecipitation assays revealed that the mangiferin induced repression of LEF1 was associated with decreased occupancy of WT1 on the LEF1 promoter.  Our study identifies a novel mechanism of hepatocellular carcinoma inhibition through β-catenin-independent Wnt signalling, which is regulated by WT1-associated LEF1 repression. The study also highlights mangiferin as a promising Wnt inhibitor for HCC treatment.

Field of study: Biology, Chemistry
Double impact of sterilizing pathogens: added value of increased life expectancy on pest control effectiveness

Sterilizing pathogens are commonly assumed not to affect longevity of infected individuals, and if they do then negatively. Examples abound, however, of species in which the absence of reproduction actually increases life expectancy. This happens because by decreasing the energy outlay on reproduction individuals with lowered reproduction can live longer. Alternatively, fertile individuals are more susceptible to predators or parasitoids if the latter can capitalize on mating signals of the former. Here we develop and analyze an SI epidemiological model to explore whether and to what extent does such a life expectancy prolongation due to sterilizing pathogens affect host dynamics. In particular, we are interested in an added value of increased life expectancy on the possibility of successful pest control, that is, the effect of increased lifespan and hence increased potential of the infected individuals to spread the disease on pest control effectiveness. We show that although the parameter range in which we observe an effect of increased lifespan of the sterilized individuals is not large, the effect itself can be significant. In particular, the increase in pest control effectiveness can be very dramatic when disease transmission efficiency is close to birth rate, mortality rate of susceptibles is relatively high (i.e., the species is relatively short-lived), and sterilization efficiency is relatively high. Our results thus characterize pathogens that are promising candidates for an effective pest control and that might possibly be engineered if not occurring naturally.

Field of study: Biology, Mathematics
Acidosis-induced p38 MAPK activation and its implication in regulation of cardiac contractility.

To determine the possible role of pH in mediating activation of p38 mitogen-activated protein kinase (MAPK) and the consequent function of activated p38 MAPK in regulating cardiac contractility.



Adult rat cardiomyocytes were isolated and cultured. Low pH media was used to induce intracellular acidosis and contraction of single cardiomyocyte was measured.



Phosphorylation of p38 MAPK was increased during ischemia, and pHi was decreased. Intracellular acidosis activated p38 MAPK to a similar level as ischemia. Inhibition of p38 MAPK activation by SB203580, a specific inhibitor of p38 MAPK, reversed acidosis-mediated reduction of myocyte contractility.



In adult rat cardiomyocytes, intracellular acidification activated p38 MAPK and decreased cardiac contractility. Pretreatment of cardiomyocytes with SB203580 completely blocked p38 MAPK activation and partially reversed acidosis-mediated decline of cardiac contractility.

Field of study: Biology, Chemistry, Medicine
Fast Edge Detection Algorithm

Edge detection,which measures,checks and captures discontinuity in pixel values in an image,is a basic problem in image analysis.The Inclined plane Decomposition based Non-symmetry and Anti-packing image representation Method(IDNAM),inspired by the concepts of the inclined plane fitting and anti-packing,uses a set of instances of the Rectangular Inclined Plane sub-pattern(RIP sub-pattern) to represent an image.On the basis of IDNAM,and ideal edge model within a RIP sub-pattern is presented.In the ideal edge model,edges within a RIP sub-pattern are divided into five types,and the methods for computing the edge strength and direction of the edges.The criterions for the existence of an edge within a RIP sub-pattern are presented,to separate between edge and noise.An edge detection algorithm is proposed based on IDNAM,according to the ideal edge model and the criterions.The theoretical analyses and experimental results show that the edge detection algorithm using IDNAM performs faster than the classical ones.

Field of study: Computer science
Phase-matching properties of BaGa2GeSe6 for three-wave interactions in the 0.778-10.5910 μm spectral range.

We present new experimental results for the phase-matching properties of the recently discovered BaGa2GeSe6 crystal for harmonic generation of a Nd:YAG laser-pumped KTP OPO and a CO2 laser in the 0.778-10.5910 μm spectral range. In addition, we present new Sellmeier equations that provide a good reproduction of the present experimental results as well as the published data points for SHG of a CO2 laser at 10.5910 μm and a 1.85 μm-pumped OPO in the 2.156-3.220 μm and 4.348-13.035 μm spectral ranges.

Field of study: Physics
[Corticosterone-induced changes in the inhibitory neurotransmission in hippocampal CA1 synapses depending on the activity of inhibitory synapses that express cannabinoid receptors].

To study an effect of corticosterone (100 nM) on spontaneous inhibitory postsynaptic currents (sIPSC) in pyramidal neurons of CA1 area and a role of inhibitory CB1-expressing synapses in the development of corticosterone-induced effects.



The experiments were performed on acute slices of the rat ventral hippocampus using whole-cell configuration of the patch-clamp technique.



The addition of corticosterone resulted in a small, but significant, increase in the frequency of sIPSCs during the first 10 minutes and then this parameter returned to the basal level. Corticosterone treatment resulted in a considerable decrease in the sIPSC amplitude 40 minutes after the beginning of treatment. The activation of CB1 receptors weakly affected sIPSC characteristics, however, the addition of corticosterone did not induce the rapid elevation in the sIPSC frequency, which occurred on the 10th minute in the control, as well as a decrease in the sIPSC amplitude, which was observed in the control on the 40th min after the beginning of corticosterone treatment. The data obtained suggest that both rapid and slow effects of corticosterone are associated with the activity of CB1-expressing inhibitory synapses of the hippocampus.

Field of study: Medicine, Psychology
Colleges take advantage of Cray time grants for students

From terminals at their college campuses, undergraduate and graduate students can access the CRAY Y-MP8/864 at the National Center for Atmospheric Research in Boulder, Colorado, to run models as part of their classroom assignments. Professors in a variety of disciplines have incorporated hands-on supercomputing experience into their classes, thanks to special grants of computing time from Cray Research, Inc.

Field of study: Environmental science
Intrinsic electron doping in nominal “nondoped” superconducting (La,Y)2CuO4 thin films grown by magnetron sputtering

The superconducting nominal “nondoped” La1.85Y0.15CuO4 (LYCO) thin films are prepared by magnetron sputtering. The best TC0 of more than 13K is achieved in the optimal films with highly pure c-axis oriented T′-type structure. The quasiquadratic temperature dependence of resistivity and the negative Hall coefficient in the normal state, effect of oxygen content are all quite similar to the known Ce-doped n-type cuprate superconductors, suggesting the electron-doping nature in T′-LYCO. The charge carriers are considered to arise from oxygen deficiency.

Field of study: Physics
Distributed Gradient Descent Algorithm Robust to an Arbitrary Number of Byzantine Attackers

Due to the growth of modern dataset size and the desire to harness computing power of multiple machines, there is a recent surge of interest in the design of distributed machine learning algorithms. However, distributed algorithms are sensitive to Byzantine attackers who can send falsified data to prevent the convergence of algorithms or lead the algorithms to converge to value of the attackers’ choice. Some recent work proposed interesting algorithms that can deal with the scenario when up to half of the workers are compromised. In this paper, we propose a novel algorithm that can deal with an arbitrary number of Byzantine attackers. The main idea is to ask the parameter server to randomly select a small clean dataset and compute noisy gradient using this small dataset. This noisy gradient will then be used as a ground truth to filter out information sent by compromised workers. We show that the proposed algorithm converges to the neighborhood of the population minimizer regardless the number of Byzantine attackers. We further provide numerical examples to show that the proposed algorithm can benefit from the presence of good workers and achieve better performance than existing algorithms.

Field of study: Engineering
Expression of various cellular markers in genitourinary rhabdomyosarcoma: immunohistochemical study using tma methodology

Immunohistochemical analysis of the expression of various cellular markers in rhabdomyosarcoma (RMS) may improve the design of therapeutic schedules according to individualized risk-based data and may even define specific therapeutic targets in RMS. The aim of this study was to evaluate the extent of the expression of various cellular markers in RMS, using tissue microarray (TMA) technique. Material and methods TMA paraffin embedded block was constructed of 8 samples of RMS from different patients. Each tumour sample was presented in the block by several cores, 2 mm in diameter, containing tumour tissue with adjacent transitional epithelium and normal detrusor which served as positive and negative controls. After serial slicing of 4 μm thickness, the histological slides were stained with hematoxylin & eosin (H&E) and immunostained with antibodies against Erb-B2, p53, c-kit, Ki 67, Caspase 3, EGFR, N-CAM, TOPO-II and BCL-10. The immunostaining was graded semi quantitatively by the percent of positively staining cells and the intensity of stain.  Four cellular markers were expressed in RMS including Erb-B2, Ki 67, EGFR and N-CAM. Significant positive staining (grades 2-3), for at least one of these markers, was noted in 5 of the cases.  The expression of Erb-B2, Ki 67, EGFR and N-CAM in genitourinary RMS may have potential therapeutic implications. Our preliminary results may promote further studies to assess the potential role of these markers to serve as therapeutic targets for specific therapeutic agents and thus decrease the overall treatment burden in children suffering from genitourinary RMS.

Field of study: Medicine
Climate Science: An Empirical Example of Postnormal Science

This paper addresses the views regarding the certainty and uncertainty of climate science knowledge held by contemporary climate scientists. More precisely, it addresses the extension of this knowledge into the social and political realms as per the definition of postnormal science. The data for the analysis is drawn from a response rate of approximately 40% from a survey questionnaire mailed to 1000 scientists in Germany, the United States, and Canada, and from a series of in-depth interviews with leading scientists in each country. The international nature of the sample allows for cross-cultural comparisons. With respect to the relative scientific discourse, similar assessments of the current state of knowledge are held by the respondents of each country. Almost all scientists agreed that the skill of contemporary models is limited. Minor differences were notable. Scientists from the United States were less convinced of the skills of the models than their German counterparts and, as would be expected un...

Field of study: Environmental science
Preparation and structural properties of layer-type oxides NaxNix/2Ti1−x/2O2 (0.60≤x≤1.0)

Layer-type oxides NaxNix/2Ti1−x/2O2 (0.60≤x≤1.0) have been successfully prepared through solid-state reactions at 1223–1423 K under inert argon atmosphere. XRD measurements showed that they crystallize in α-NaFeO2 type (space group R 3 m) for 0.72 0.72) to trigonal prism (x≤0.72). Rietveld refinement results for x=0.90 and 0.67 suggest that the covalency is strengthened in (Ni,Ti)–O and weakened in Na–O through the competition (Ni,Ti)–O–Na as x decreases, and consequently the lattice becomes more two-dimensional. In Na0.67Ni0.33Ti0.67O2 sodium ions have been found to be distributed at two different prismatic sites, having the occupation ratios, 0.198 at (0, 0, 1/4) and 0.472 at (1/3, 2/3, 1/4), respectively. The occurrence of structural transition is considered to be correlated with the composition parameters such as x, the bond natures and the positive charge distribution. Comparison of lattice energies of two structure types suggests that the entropy change should also play an important role in the transition.

Field of study: Materials science
Self-Reinforcement, Locus of Reward and Task Maintenance, and Alcoholism

Groups of 44 hospitalized alcoholics and 31 psychiatric patients were compared with 40 nonclinical controls on their self-reinforcement behaviors. The groups did not differ on self-reward but the psychiatric group self-punished more than the other two groups, while the alcoholics tended to self-punish the least. On a second task, 30 alcoholic subjects were assigned to either one of two reward conditions, self- or externally (other-) administered reward for task maintenance. Those alcoholics receiving rewards from others did significantly better on the task than those rewarding themselves. Results are discussed in light of the externality hypotheses of alcoholism.

Field of study: Psychology
Monitoring and managing pollution load in Bohai Sea, PR China

Bohai Sea, China's only inland sea, became seriously polluted because of rapid economic development. The pollution monitoring system of Bohai Sea started in 1978, and has grown to have 215 monitoring stations today. The Chinese government recently increased efforts to improve the environmental quality of Bohai Sea in an effort to achieve the sustainable development of the Wider Bohai Sea Area. This paper presents the current pollution situation and its environmental impacts. It also discusses the existing pollution management mechanisms and pollution abatement programs for Bohai Sea.

Field of study: Environmental science
Determination of Hg and diet identification in otter (Lontra longicaudis) feces.

An analytical procedure for the determination of Hg in otter (Lontra longicaudis) feces was developed, to separate fish scales for the identification of the animal diet. Samples were washed with ultra-pure water and the suspension was sampled and transferred for digestion. The solubilization was performed with nitric-perchloric acid mixture, and detection carried out by the atomic fluorescence spectrometry (AFS). The quality of the analytical procedure was assessed by analyzing in-house standard solutions and certified reference materials. Total Hg concentrations were in the range of 7.6-156 ng g(-1) (July 2004), 25.6-277 ng g(-1) (January 2005) and 14.6-744 ng g(-1) (May 2005) that is approximately the same order of magnitude for all samples collected in two reservoirs at the Tiete River, Brazil. Although Hg concentrations varied with sampling periods and diet, high levels were correlated to the percentage of carnivorous fish scales present in the otter feces.

Field of study: Environmental science
Management of paroxysmal atrial fibrillation.

Paroxysmal atrial fibrillation is a common, poorly understood and difficult-to-treat arrhythmia. Although it tends to be treated in a similar fashion to chronic atrial fibrillation, its pathophysiology is different, and drugs commonly used for chronic atrial fibrillation may have only limited value in treating paroxysmal atrial fibrillation. A broad range of presenting clinical symptoms may be associated with this arrhythmia, and even in the asymptomatic patient, there may be a risk of serious thromboembolic events. In symptomatic patients, effective control of paroxysms with antiarrhythmic therapy can often be difficult, and the role of anticoagulation remains controversial. This review attempts to clarify these issues, by surveying the range of therapies available.

Field of study: Medicine
CHARACTERIZATION OF SURFACE OXIDATION OF Nd FILM X-RAY LASER TARGET

Quartz crystal oscillation technique was applied to measure the increase of oxide scale on Nd film targets and Auger electron spectroscopy was used to analyze the depth distribution of oxygen and neodymium. Scanning electron microscopy, X-ray diffraction and X-ray photonelectron spectroscopy were used to characterize oxide scale. Results show that the environment where Nd films were stored plays a great role in the oxidation behavior of the Nd films. Water contained in the atmosphere is the key factor for the rapid oxidation of the Nd film. The scale is amorphous and shows steamed bread like surface. The small ratio of the oxide volumn to the metal volumn may be the cause of the Nd inclining to oxidation. The scale is covered by a layer of hydroxide. the thickness of the hydroxide is the least for the films in vacuum, the second in dry air and the greatest in humid air.

Field of study: Physics
The effect of trust crisis on China Professional Soccer League Games and countermeasures therein

Trust is an important social capital in economic activities. Trust crisis has seriously affected the development of China Professional Soccer League Games. Trust crisis in China Professional Soccer Games shows mainly in the following aspects: The loss of authority of referees; sharp decrement of sponsoring funds,abortion of local soccer lottery, mutual suspects between the clubs and the lack of audiences. The authors offered the following suggestions: The punishment on trust violators should be reinforced; the act of governmental participation should be standardized; steady and clear enough property right system should be established; legal system should be perfected; public supervision should be strengthened; a professional soccer league should be established.

Field of study: Education