nils-herrmann/clean_scirepeval huggingface dataset:
A patient infected with SARS-CoV-2 over 100 days

We recently experienced a patient with viral isolation by culture 4 months after the acute infection. an 83-year-old Japanese man visited our outpatient clinic with symptoms of upper respiratory tract infection. The patient was diagnosed with a COVID-19 infection by a quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR) test. Three months after his clinic visit, he had regained most of his pre-COVID-19 level of health. However, qRT-PCR tests continued to be positive. At day 111, specimens from a nasopharyngeal swab and sputum were inoculated into VeroE6/TMPRSS2 cells.(1) Three to five days post-inoculation, cytopathic effects were observed, and viral RNA was detected in the culture supernatant by qRT-PCR (Ct values: 29–37). The culture supernatant of the VeroE6/TMPRSS2 cells cocultured with the nasopharyngeal swab was passaged to the fresh VeroE6/TMPRSS2 cells, and after 3 days of the passage, cytopathic effect was observed again. In the supernatant of the passaged cell culture, viral RNA was detected by qRT-PCR (Ct value: 29). By sequencing the qRT-PCR product using Illumina iSEQ100, the presence of SARS-CoV-2 RNA sequence was verified. These results indicate the presence of infectious SARS-CoV-2 in the nasopharyngeal specimen even at day 111. Although SARS-CoV-2 was present, the patient developed neutralizing antibodies by a microtiter method. We tested but did not isolate SARS-CoV-2 in samples of saliva, urine, blood, or stool. Patients with ongoing symptoms of COVID-19, long-haulers, could be chronically infected with COVID-19, although they might be incapable of transmission.

Field of study: Medicine
Bacterial fossil record in whale-falls: Petrographic evidence of microbial sulfate reduction

Whale fossils from a variety of geologic ages and depositional environments were thin-sectioned and analyzed for evidence of microbial activity, comprising a combination of microborings, authigenic pyrite, botryoidal cements, and micropeloids. Borings are dense in some samples with an average diameter of 8.02 µm. Framboidal pyrite crystals with an average diameter of 61.84 µm in diameter occur within the pore spaces of the bone, in borings, and at the bone–sediment interface. The pyrite crystals are densely packed at the edges of the bone and scattered more randomly throughout the pore spaces. Aragonitic botryoidal cements line pore spaces in samples from deep bathyal settings. Potential bacterial peloids occur within pore spaces with an average size of 77.45 µm or diffuse to comprise clotted micrite. Since bacterial body fossils are extremely rare in the fossil record, recognition of past microbial ecosystems must be based on multiple lines of supporting evidence. Of the independent signatures studied, the bacterial peloids and botryoids provide the most convincing evidence of a sulfophilic stage. These fossil biosignatures suggest that a sulfophilic stage is preserved at least as far back as the Eocene.

Field of study: Environmental science, Geography
Loess-like and palaeosol sediments from Lanzarote (Canary Islands/Spain) — Indicators of palaeoenvironmental change during the Late Quaternary

On Lanzarote (Canary Islands) Quaternary Saharan dust and weathered local volcanic material were trapped in Miocence to Pliocene valleys dammed by younger volcanic edifices. These sediments show sequences of alternating reddish/clayey and loess-like yellowish/silty material. In order to investigate if reddish/clayey layers contain material derived from local pedogenesis and if so, which pedogenetic processes were active, we performed sedimentological, micromorphological and environmental magnetic analyses. The analyses demonstrate that these layers contain material derived from local soils. These soils were characterised by clay formation, rubefication and the formation of superparamagnetic particles during periods of enhanced soil moisture. Thus, they can serve as natural archives in order to reconstruct the terrestrial palaeoclimatic history of Lanzarote. The distribution of soil material in the profiles shows that cold periods of the Late Quaternary were characterised by more humid conditions than today. Using palaeontological remains and a comparison with recent soils on Tenerife, we can roughly estimate maximal palaeoprecipitation values during more humid periods.

Field of study: Environmental science, Geography
On the transcendency of function

iThe main goal of the paper is to prove the transcendency of functions by means o{ functional equations. AMS ClMsirication 1980<39B20.Secondar3r 26A30. 1. It is well known that a function / iD »R with D C R is called an algebraic function if it satisfies the equaüon (1 ) P ( x , / ( x ) ) = 0 , x C D . where is a polynomial in two variables and where all ^ i i ( x ) ( k = 0 , l , " , n ) are polynomials in x. All the other functions are called transcendental functions. In other words.if the function /|D-»R is not the Solution of any algebraic equation ( l ) , i n its dotnain of definition or partial domain of definition.then /iD-^R is a transcendental function. REMARK. If /|D»R is an algebraic function. then the Solution set of the equation f(.x) = c (where c is any constant) is finite. In this paper.we present a rule which can be used to teil whether a function is transcendental. This criterion is built on the base of certain functional equations. 2. We put R ' =R'^\A.where R'*' is the set of all positive real numbers and A is an enumerable set contained in R"*". We shall prove the following THEOREM 1. Suppose that / is a nonconstant function with its domain of definition DZ)R ' .and / iD »R satisfies the Poincari functional equation (2 ) / ( < u : ) G ( / ( x ) ) . x 6 D where a > l , G « E — R and E 3 / ( D ) . I f /and G fulfil the conditions. ( i ) there exists a fixed point f e E f l / C D ) of G , i . e . G ( ( ) = ^ . ( i i ) there exists a xo€R* such that / ( x o ) = l t ( iü) o * x , 6 R ' f o r n 1 , 2 , . then / is a transcendental function.

Field of study: Philosophy
The Transcription Factors NFAT and CREB Have Different Susceptibilities to the Reduced Ca2+ Responses Caused by the Knock Down of Inositol Trisphosphate Receptor in HEK 293A Cells

The inositol 1,4,5-trisphosphate receptor (IP<sub>3</sub>R), a ligand-gated Ca<sup>2+</sup> channel, plays an important role in the control of intracellular Ca<sup>2+</sup>. Three isoforms of IP<sub>3</sub>R have been identified and most cell types express different proportions of these isoforms. The purpose of this study was to investigate how IP<sub>3</sub>R signalling is involved in the activation of the Ca<sup>2+</sup>-sensitive transcription factors NFAT and CREB.  Each IP<sub>3</sub>R isoform expressed in HEK 293A cells was knocked down using selective siRNA. Free intracellular Ca<sup>2+</sup> was monitored spectrofluometrically. NFAT and CREB activities were measured with luciferase reporter constructs.  IP<sub>3</sub>R-2-knocked down HEK 293A cells showed a deficient CCh-induced Ca<sup>2+</sup> response that could be rescued by co-stimulation with VIP, a cAMP increasing agonist. NFAT transcriptional activity, but not CREB transcriptional activity, was significantly reduced in IP<sub>3</sub>R-2-knocked down HEK 293A cells. Overexpression of IP<sub>3</sub>R-1 could fully compensate for IP<sub>3</sub>R-2 knock down to mobilize Ca<sup>2+</sup> and to activate NFAT.  Our results show that the knock down of IP<sub>3</sub>R-2 significantly reduced the intracellular Ca<sup>2+</sup> response of HEK 293 cells. This reduced Ca<sup>2+</sup> response did not affect the activation of CREB but significantly decreased the activation of NFAT, suggesting that the Ca<sup>2+</sup> signals required for the activation of NFAT are stronger than those required for the activation of CREB.

Field of study: Biology, Chemistry
Outcast London: A Study in the Relationship Between Classes in Victorian Society

In the second half of the nineteenth century, Victorian middle and upper classes felt increasingly threatened by the masses of "outcast London." Gareth Stedman Jones, working from a mass of statistical and documentary evidence, argues that after 1850 London passed through a crisis of social and economic development. Outcast London is a fascinating and important study of the problem at the center of the crisis: the casual poor and their fraught relations with the labor market, with housing and with middle-class London.

Field of study: Economics, History
Quantitative measurement of calretinin and β-actin mRNAIN rat brain micropunches without prior isolation of RNA

A microdissection technique for quantitation of neurochemicals in discrete brain nuclei has been applied to quantitative measurement of mRNA. The method permits quantitation of low abundance mRNA from submilligram amounts of tissue (10–500 μ protein). Discrete nuclei and other regions of the brain are solubilized in concentrated guanidine thiocyanate solution, mRNA is directly hybridized with riboprobes, and detected with a ribonuclease protection assay. This method eliminates the necessity for RNA isolation from solid tissue. No assumptions regarding RNA recovery are necessary since tissue specimens are solubilized, hybridized and treated with ribonuclease in a single tube. We have determined the mRNA levels of calretinin, a predominantly neuron-specific calcium binding protein in microdissected nuclei and other regions of rat brain. For interassay comparison, measurement of sample protein and β-actin mRNA permits normalization and quantitation in terms of these internal controls. The quantity of calretinin mRNA ranged from 281 ± 35 fg/μg protein in the thalamic paraventricular nucleus to 2.3 ± 0.5 fg/μg protein for the cerebral cortex. The calretinin/β-actin ratios ranged from 79.9 ± 9.3% to 1.3 ± 0.1%, respectively. The combination of microdissection techniques with a lysate RNase protection assay: (1) establishes this technique as quantitative for detection of high and low abundance mRNAs from microdissected brain specimens; (2) bypasses the inefficiencies and uncertainties associated with isolating RNA; and (3) enables large numbers of determinations from discrete brain nuclei to be analyzed in 2 to 3 days.

Field of study: Biology
Modeling Australian twin data using shared positive stable frailty models based on reversed hazard rate

Unobserved heterogeneity, also called frailty, is a major concern in the application of survival analysis. The shared frailty models allow for the statistical dependence between the observed survival data. In this paper, we consider shared positive stable frailty model with the reversed hazard rate (RHR) with three different baseline distributions, namely the exponentiated Gumbel, the generalized Rayleigh, and the generalized inverse Rayleigh distributions. With these three baseline distributions we propose three different shared frailty models. We develop the Bayesian estimation procedure using Markov Chain Monte Carlo technique to estimate the parameters involved in these models. We present a simulation study to compare the true values of the parameters with the estimated values. A search of the literature suggests that currently no work has been done for these three baseline distributions with a shared positive stable frailty with the RHR so far. We also apply these three models by using a real-life bivariate survival data set of Australian twin data given by Duffy et a1. (1990) and a better model is suggested for the data.

Field of study: Mathematics
A review of the electronic structure of CaFe(2)As(2) and FeTe(0.6)Se(0.4)

Fe-based superconductors have drawn much attention during the last decade due to the finding of superconductivity in materials containing the magnetic element, Fe, and the coexistence of superconductivity & magnetism. Extensive study of the electronic structure of these systems suggested dominant role of d states in their electronic properties, whereas the cuprate superconductors show major role of the ligand derived states. In this article, we review some of our results on the electronic structure of these fascinating systems employing high resolution photoemission spectroscopy. The combined effect of electron correlation and covalency reveal an interesting scenario in their electronic structure. The ligand p states contribution at the Fermi level is found to be much more significant than that indicated in earlier studies. Temperature evolution of the energy bands reveals signature of transition akin to Lifshitz transition in these systems.

Field of study: Physics
Graph Spectral Feature Learning for Mixed Data of Categorical and Numerical Type

Feature learning in the presence of a mixed type of variables, numerical and categorical types, is important for related modeling problems. In this work, we propose a novel strategy to explicitly model the probabilistic dependence structure among the mixed type of variables by an undirected graph. The dependence structure among different pairs of variables are encoded by a suitable mapping function to estimate the edges of the graph. Spectral decomposition of the graph Laplacian provides the desired feature transformation. We numerically validate the implications of the feature learning strategy on various datasets in terms of data clustering.

Field of study: Computer science
Crustal contamination in the petrogenesis of a calc-alkalic rock series: Josephine Mountain intrusion, California

The Josephine Mountain intrusion is a Cretaceous calc-alkalictonalite-granite pluton emplaced at 22 km depth in a continental margin arc. Variable uplift of adjacent terranes in southern California since mid-Cretaceous time allows us to reconstruct the local crustal column and evaluate its role as a contaminant of mantle-derived arc magmas in this region. The parental magma of the intrusion was high-alumina basalt whose isotopic signature ( 87 Sr/ 86 Sr = 0.7087; δ 18 O = 7.5; ϵ Nd = −10) cannot have been generated by intracrustal assimilation of known or inferred rock types in the middle or lower crust. Such a signature could have resulted from high-pressure fractionation of primary low-alumina basalt coupled with assimilation of felsic/pelitic lower crust, partial melting of enriched subcontinental mantle followed by high-pressure fractionation, or a combination of these processes. Tonalite of the intrusion was formed by fractionation of the parent magma coupled with assimilation of local felsic wall rocks or by crustal melts similar to slightly younger granite. Assessment of the magnitude of crustal contamination is hampered by uncertainty regarding the existence and role of partial melting of previously enriched subcontinental mantle in generating the parental basaltic magma, leading to concomitant uncertainty in the fraction of new continental crust created by such arc plutonism.

Field of study: Geology
Berberine Sensitizes Human Ovarian Cancer Cells to Cisplatin Through miR-93/PTEN/Akt Signaling Pathway

Berberine, a well-known component of the Chinese herbal medicine Huanglian, has wide range of biochemical and pharmacological effects, including antineoplastic effect, but the exact mechanisms remain unclear. The aim of the present study was to evaluate the potential chemo-sensitization effect of berberine in ovarian cancer cell line A2780.  The expression of miR-93 was measure by RT-PCR. The target of miR-93 was confirmed by luciferase activity assay. Hoechst 33258 staining, Annexin V and PI double staining were used for apoptosis analysis.  In this study, we found A2780/DDP cells that were incubated with berberine combined with cisplatin had a significantly lower survival than the control group. Berberine enhanced cisplatin induced apoptosis and induced G0/G1 cell cycle arrest in A2780 cells. Next, we observed that the miR-93 levels in cisplatin resistant cell lines were higher than that in cisplatin sensitive cell lines. Furthermore, our study found berberine could inhibit miR-93 expression and function in ovarian cancer, as shown by an increase of its target PTEN, an important tumor suppressor in ovarian cancer. A2780 cells that were treated with PTEN siRNA had increased survival compared to NC group and this could be partly alleviated by the AKT inhibitor Triciribine. More importantly, A2780 cells that were treated with PTEN siRNA had a survival pattern that is similar to cells with miR-93 overexpression.  The results suggested that berberine modulated the sensitivity of cisplatin through miR-93/PTEN/AKT signaling pathway in the ovarian cancer cells.

Field of study: Biology, Chemistry
Locus of Control and Mathematics Instruction: Three Exploratory Studies.

The relationship between locus of control and three dimensions of discovery learning was investigated in a series of studies. Mathematics students were randomly assigned to treatments that differed in level of guidance, inductive or deductive sequencing, or use of small groups. A significant aptitude-treatment interaction occurred between locus of control and small-group instruction on the topic of networks. The other studies did not produce significant interactions, although varying the level of guidance did produce a trend in the predicted direction. Using inductive or deductive sequences of instruction did not appear to interact with locus of control.

Field of study: Education
Magnetic Impurities on Superconducting Surfaces: Phase Transitions and the Role of Impurity-Substrate Hybridization

Spin-dependent scattering from magnetic impurities inside a superconductor gives rise to Yu-Shiba-Rusinov (YSR) states within the superconducting gap. As such, YSR states have been very successfully modeled with an effective scattering potential (Kondo impurity model). Using a scanning tunneling microscope, we exploit the proximity of the tip to a surface impurity and its influence on the YSR state to make a quantitative connection between the YSR state energy and the impurity-substrate hybridization. We corroborate the coupling between impurity and substrate as a key energy scale for surface derived YSR states using the Anderson impurity model in the mean field approximation, which accurately explains our observations. The model allows to decide on which side of the quantum phase transition the system resides based on additional conductance measurements. We propose that the Anderson impurity model is much more appropriate to describe YSR states from impurities on a superconducting surface than the Kondo impurity model, which is more appropriate for impurities inside a superconductor. We thus provide a first step towards a more quantitative comparison of experimental data with fully correlated calculations based on the Anderson impurity model.

Field of study: Physics
Low voltage stress-induced leakage current and traps in ultrathin oxide (1.2–2.5 nm) after constant voltage stresses

It has been shown that the low voltage gate current in ultrathin oxide metal?oxide?semiconductor devices is very sensitive to electrical stresses. Therefore, it can be used as a reliability monitor when the oxide thickness becomes too small for traditional electrical measurements to be used. In this work, we present a study on n-MOSCAP devices at negative gate bias in the direct tunneling (DT) regime. If the low voltage stress-induced leakage current (LVSILC) depends strongly on the low sense voltages, it also depends strongly on the stress voltage magnitude. We show that two LVSILC peaks appear as a function of the sense voltage in the LVSILC region and that their magnitude, one compared to the other, depends strongly on the stress voltage magnitude. One is larger than the other at low stress voltage and smaller at high stress voltage. From our experimental results, different conduction mechanisms are analyzed. To explain LVSILC variations, we propose a model of the conduction through the ultrathin gate oxide based on two distinctly different trap-assisted tunneling mechanisms: inelastic of gate electron (INE) and trap-assisted electron (ETAT).

Field of study: Materials science
[Effect of potassium and magnesium aspartate on experimental myocardial ischemia and infarction].

Following occlusion of the lower 1/3 of left anterior descending coronary artery (LAD) in cats the epicardial ST-segment elevation was depressed obviously by iv paverine 2 or 4 mg/kg as well as K-Mg-aspartate (K-Mg-ASP) 100 mg/kg. But iv K-ASP 100 mg/kg showed no effect. Hence K-Mg-ASP manifested a beneficial effect against myocardial ischemia injury, and the effect of K-ASP was enhanced by the Mg-ASP. The size of myocardial infarction (SMI) caused by occlusion of the upper LAD in rabbits after 24 h was 21±5%, ∑ST 18±8 mV. However, the SMI and ST decreased to 4±3%, 10±4 mV by iv K-Mg-ASP 100mg/kg qid and to 6±3%, 99±6 mV by iv propranolol 0.5 mg/kg qid. It indicated that K-Mg-ASP was as effective as propranolol in diminishing SMI.

Field of study: Biology, Chemistry, Medicine
Induced innovation in energy technologies and systems: a review of evidence and potential implications for CO2 mitigation

We conduct a systematic and interdisciplinary review of empirical literature assessing evidence on induced innovation in energy and related technologies. We explore links between demand-drivers (both market-wide and targeted); indicators of innovation (principally, patents); and outcomes (cost reduction, efficiency, and multi-sector/macro consequences). We build on existing reviews in different fields and assess over 200 papers containing original data analysis. Papers linking drivers to patents, and indicators of cumulative capacity to cost reductions (experience curves), dominate the literature. The former does not directly link patents to outcomes; the latter does not directly test for the causal impact of on cost reductions. Diverse other literatures provide additional evidence concerning the links between deployment, innovation activities, and outcomes. We derive three main conclusions. (a) Demand-pull forces enhance patenting; econometric studies find positive impacts in industry, electricity and transport sectors in all but a few specific cases. This applies to all drivers—general energy prices, carbon prices, and targeted interventions that build markets. (b) Technology costs decline with cumulative investment for almost every technology studied across all time periods, when controlled for other factors. Numerous lines of evidence point to dominant causality from at-scale deployment (prior to self-sustaining diffusion) to cost reduction in this relationship. (c) Overall innovation is cumulative, multi-faceted, and self-reinforcing in its direction (path-dependent). We conclude with brief observations on implications for modelling and policy. In interpreting these results, we suggest distinguishing the economics of active deployment, from more passive diffusion processes, and draw the following implications. There is a role for policy diversity and experimentation, with evaluation of potential gains from innovation in the broadest sense. Consequently, endogenising innovation in large-scale models is important for deriving policy-relevant conclusions. Finally, seeking to relate quantitative economic evaluation to the qualitative socio-technical transitions literatures could be a fruitful area for future research.

Field of study: Environmental science
Gamma-gamma density measurements

The basic response of a gamma-gamma density logging tool and the environmental corrections to that response have been determined. This has been accomplished through the use of test formation data and Monte Carlo modeling. The basic response has been determined for formation densities of 1.6 g/cc to 3.1 g/cc. Environmental corrections have been obtained for a full range of borehole conditions. Mudcake corrections in light mud, barite mud, and hematite mud have been obtained for simulated mudcake thicknesses of up to 0.75 inches. Borehole size corrections have been obtained for mudcake thicknesses of up to 0.75 inches. Borehole size corrections have been obtained for air filled, water filled, and mud filled boreholes with diameters ranging from 6 to 14 inches. The response and corrections have been verified downhole through extensive comparisons with core and gravinometer data.

Field of study: Physics