nils-herrmann/clean_scirepeval huggingface dataset:
Guadalupe Island: Lost paradise recovered? Overgrazing impact on extinction in a remote oceanic island as estimated through accumulation functions

Guadalupe Island, an oceanic island in the northwest of Mexico, is an outlier of the California Floristic Province that has been disturbed by introduced goats for more than a century, with dramatic effects of goats on plant communities and local species extinctions. In 2004 the island went through a successful eradication program. Since then, six previously unrecorded species have been discovered and four supposed extinct species have been found again. Quantifying the true species richness of the island at the time of eradication, to set a benchmark for the future monitoring of this large-scale natural experiment, is both a challenge and a necessity. For this purpose, we estimated (a) current and (b) accumulated historical plant species richness of the island through accumulation functions. Estimation of current species richness was based on the geographical accumulation process of species richness (80 species) obtained from sampling 110 (50 m × 2 m) transects distributed along the island in year 2004. Historical species richness was estimated through the temporal accumulation of species richness (119 species) from botanical records (1,960 specimens reviewed) between 1875 and 2000. The predicted value of historical richness (213 species) is similar to known historical records (218 species), but estimation of current richness (203 species) is significantly higher than accepted extant plant richness (187 species). Our results suggest that currently there may be more plant species living in the island than estimated through recent botanical exploration. Future monitoring of the island as it recovers will clarify this hypothesis.

Field of study: Environmental science
Combined Modalities of Compton Scattering Tomography

The requirement to scope and analyze hidden parts of the human body and the limitations of current imaging technologies is motivating the development of novel approaches. In clinical PET/CT systems, the attenuation and activity maps of the studied body region are recovered from measurements. However, the modeling of Compton scattering enables to obtain the attenuation map through the electron density directly from transmission data, thus obviating the need of a CT scan. In this context, a bimodality imaging approach (gamma-ray transmission/emission imaging) using scattered radiation referred to as Compton scattering tomography (CST) is presented. This concept is modeled by two generalized Radon transforms and proposes to reconstruct the electron density, the attenuation map, and the activity concentration of the studied body region. Simulation results demonstrate the feasibility and viability of this novel imaging concept. The present approach could be an interesting alternative to current tomographic imaging techniques.

Field of study: Physics
In situ poly(ethylene imine) coating of hollow fiber membranes used for microdialysis sampling

A method for the in situ modification of hollow fiber membranes used as sampling units for microdialysis probes is presented. The method consists of adsorption-coating, high molecular-weight poly(ethylene imine), PEI, onto membranes, already fitted on microdialysis probes. Modification of membranes was designed to specifically explore the so-called Andrade effects and thus enhance the interaction of membranes with enzyme. The performances of polysulfone, polyethersulfone, and polyamide membranes modified with PEI-enzyme complex were evaluated based on the membrane extraction fraction for maltose and maltotriose and membrane morphology as examined by scanning electron microscopy. Of the membranes tested, the PEI-enzyme complex least affected the performance of the polysulfone membranes. Conversion of maltoheptaose to maltotriose and maltose was increased reproducibly (within a 5 % relative standard deviation) by 50 % for modified membranes compared to the native hollow fiber membranes. The results demonstrate the potential to effectively modify membranes already fitted on a microdialysis probe. Such a procedure can be modified and employed to either promote or reduce membrane–protein interaction for hollow fibers used as microdialysis sampling units or other similar membrane applications.

Field of study: Chemistry
Heterosis Is a Systemic Property Emerging From Non-linear Genotype-Phenotype Relationships: Evidence From in Vitro Genetics and Computer Simulations

Heterosis, the superiority of hybrids over their parents for quantitative traits, represents a crucial issue in plant and animal breeding as well as evolutionary biology. Heterosis has given rise to countless genetic, genomic and molecular studies, but has rarely been investigated from the point of view of systems biology. We hypothesized that heterosis is an emergent property of living systems resulting from frequent concave relationships between genotypic variables and phenotypes, or between different phenotypic levels. We chose the enzyme-flux relationship as a model of the concave genotype-phenotype (GP) relationship, and showed that heterosis can be easily created in the laboratory. First, we reconstituted in vitro the upper part of glycolysis. We simulated genetic variability of enzyme activity by varying enzyme concentrations in test tubes. Mixing the content of “parental” tubes resulted in “hybrids,” whose fluxes were compared to the parental fluxes. Frequent heterotic fluxes were observed, under conditions that were determined analytically and confirmed by computer simulation. Second, to test this model in a more realistic situation, we modeled the glycolysis/fermentation network in yeast by considering one input flux, glucose, and two output fluxes, glycerol and acetaldehyde. We simulated genetic variability by randomly drawing parental enzyme concentrations under various conditions, and computed the parental and hybrid fluxes using a system of differential equations. Again we found that a majority of hybrids exhibited positive heterosis for metabolic fluxes. Cases of negative heterosis were due to local convexity between certain enzyme concentrations and fluxes. In both approaches, heterosis was maximized when the parents were phenotypically close and when the distributions of parental enzyme concentrations were contrasted and constrained. These conclusions are not restricted to metabolic systems: they only depend on the concavity of the GP relationship, which is commonly observed at various levels of the phenotypic hierarchy, and could account for the pervasiveness of heterosis.

Field of study: Biology
Electronic properties in quantum dots with asymmetric confining potential

N-electron eigenstates in circular, elliptical and triangular quantum dots are calculated by numerically diagonalizing the N-electron Hamiltonian. The addition energy spectrum for a circular quantum dot shows good agreement with the experimental results reported by Tarucha et al. In elliptical quantum dots, the degeneracy of the single-particle states is removed, resulting in a transition of the ground state for a quantum dot with four electrons from the spin-polarized half-filled configuration to the spin-singlet state. The states with 3, 6 and 9 electrons in a triangular quantum dot are found to be slightly more stable compared with a circular quantum dot, which is interpreted in terms of a geometrical effect.

Field of study: Materials science
Expression and analysis of recombinant human IL 18 and human IL 18 GFP fusion protein

, also known as IFN γ inducing factor, shares certain functional properties with IL 12. To study the biologic activities and receptor distribution of recombinant human IL 18 and IL 18 GFP fusion protein expressed in E. coli.  Two prokaryotic expression plasmids, pET28a/hIL 18 and pTrc99/hIL 18 GFP have been constructed to express the recombinant human IL 18 (rhIL 18) and its fusion protein with green fluorescent protein (GFP) in E. coli BL21, respectively. rhIL 18 was tagged with six histidine residues at its C terminus and was purified by nickel chelation chromatography. rhIL 18 GFP was purified with anti GFP affinity chromatography and gel filtration. Biological activities were assayed with human peripheral blood mononuclear cells (PBMC).  Preliminary studies showed that rhIL 18 GFP as well as rhIL 18 augmented T cell proliferation and IFN γ production by ConA stimulated human PBMCs, and enhanced NK cell cytotoxicity. In addition, rhIL 18,GFP has shown specific binding to P815 cells and the stained cells could be analyzed with flow cytometry.  The rhIL 18 and rhIL 18 GFP we prepared are functional and can be applied to further studies on human IL 18.

Field of study: Biology
Upcycling: converting waste plastics into paramagnetic, conducting, solid, pure carbon microspheres.

The recent tremendous increase in the volume of waste plastics (WP) will have a harmful environmental impact on the health of living beings. Hundreds of years are required to degrade WP in atmospheric conditions. Hence, in coming years, in addition to traditional recycling services, innovative "upcycling" processes are necessary. This article presents an environmentally benign, solvent-free autogenic process that converts various WP [low density polyethylene (LDPE), high density polyethylene (HDPE), polyethylene terephthalate (PET), polystyrene (PS), or their mixtures] into carbon microspheres (CMSs), an industrially significant, value-added product. The thermal dissociation of these individual or mixed WP in a closed reactor under autogenic pressure ( approximately 1000 psi) produced dry, pure powder of CMSs. In this paper, the optimization of process parameters such as the effect of mixing of WP with other materials, and the role of reaction temperature and time are reported. Employing advanced analytical techniques, the atomic structure, composition, and morphology of as-obtained CMSs were analyzed. The room-temperature paramagnetism in CMSs prepared from waste LDPE, HDPE, and PS was further studied by electron paramagnetic resonance (EPR). The conducting and paramagnetic nature of CMSs holds promise for their potential applications in toners, printers, paints, batteries, lubricants, and tires.

Field of study: Environmental science
Advances in the crystal growth and device fabrication technology of CdZnTe room temperature radiation detectors

The performance of CdZnTe room-temperature X-ray and gamma-ray detectors is determined by material and device defects that govern carrier transport trough the device. In this contribution, we review common bulk, interface, and surface defects and their effects on charge transport, charge transport uniformity, and device performance. We note that pure CdZnTe grown under Te-rich conditions has an excess of Cd-vacancies and other Te-related native defects and must be electrically compensated in order to obtain high resistivity material. Through the critical analysis of the various compensation schemes it is shown that deep level defects must be introduced with donor doping elements in order to achieve a practical compensation technique. The role of carrier trapping and limitations on detector performance with increasing crystal size are discussed. Based on typical measured carrier lifetimes and the available literature data on carrier capture cross sections, we estimate that the residual acceptor concentration in CdZnTe detector crystals is much lower than widely thought, about 10/sup 11/ cm/sup -3/ instead of 10/sup 15/ cm/sup -3/. The deleterious effects of structural defects within single crystals are also discussed. We also provide a brief overview of the progress in CdZnTe crystal growth and device fabrication technologies aiming at reducing the concentration of the detrimental defects and improving CdZnTe detector performance.

Field of study: Physics
A new standard for the analysis and design of replication studies

A new standard is proposed for the evidential assessment of replication studies. The approach combines a specific reverse-Bayes technique with prior-predictive tail probabilities to define replication success. The method gives rise to a quantitative measure for replication success, called the sceptical p-value. The sceptical p-value integrates traditional significance of both the original and replication study with a comparison of the respective effect sizes. It incorporates the uncertainty of both the original and replication effect estimates and reduces to the ordinary p-value of the replication study if the uncertainty of the original effect estimate is ignored. The proposed framework can also be used to determine the power or the required sample size to achieve replication success. Numerical calculations highlight the difficulty to achieve replication success if the evidence from the original study is only suggestive. An application to data from the Open Science Collaboration project on the replicability of psychological science illustrates the proposed methodology.

Field of study: Mathematics
Performance of PWO-II Prototype Arrays for the EMC of PANDA

The response function of a 3 times 3 matrix of 200-mm-long PWO-II crystals has been measured with energy-marked photons up to 675 MeV energy. For the first time the crystals were readout individually with one large area avalanche photo diode of the second generation operating at a temperature of 0degC. The reconstructed electromagnetic shower distributions show excellent energy resolutions down to 40 MeV. Reducing the temperature and increasing the light collection by an additional large-area avalanche photo diode can achieve further improvement.

Field of study: Physics
Epalons: Synthesis of 7-Norallopregnanolone

The title compound 2 was prepared from (20 R )-pregn-5-ene-3β,20-diyl 3-acetate 20-benzoate ( 3 ) via (20 R )-3β-acetoxy-20-benzoyloxy-5-oxo-5,6-secopregnan-6-oic acid ( 5 ) and (20 R )-3β-acetoxy-20-benzoyloxy-7-nor-5β,6α-pregnane-6,5-carbolactone ( 6 ). An intermediate 7-norpregn-5-ene derivative - (20 R )-7-norpregn-5-ene-3β,20-diyl 3-acetate 20-benzoate ( 7 ) - was hydrogenated using diimide in statu nascendi . The inversion of configuration at carbon C-3 was carried out via (20 R )-7-nor-5α-pregnane-3β,20-diyl 3-tosylate 20-benzoate ( 12 ) and (20 R )-7-nor-5α-pregnane-3α,20-diyl 20-benzoate 3-formate ( 13 ).

Field of study: Chemistry
Modified profile likelihood estimation for the Weibull regression models in survival analysis

In this study, adjustment of profile likelihood function of parameter of interest in presence of many nuisance parameters is investigated for survival regression models. Our objective is to extend the Barndorff–Nielsen’s technique to Weibull regression models for estimation of shape parameter in presence of many nuisance and regression parameters. We conducted Monte-Carlo simulation studies and a real data analysis, all of which demonstrate and suggest that the modified profile likelihood estimators outperform the profile likelihood estimators in terms of three comparison criterion: mean squared errors, bias and standard errors.

Field of study: Mathematics
Strontium and Carbon Isotope Stratigraphy of the Llandovery (Early Silurian): Implications for Tectonics and Weathering

A high-resolution 87Sr/86Sr curve and paired δ13C carbonate-organic data set is generated for the Llandovery Series from the Ikla drill core in Estonia. A δ13C carbonate curve is also presented from the Pancake Range in Nevada. Observed 87Sr/86Sr values in the Ikla drill core are at a minimum in the early Llandovery Rhuddanian Stage (∼ 0.7079 to 0.7080), and then trend to more radiogenic ratios in the basal part of the Telychian Stage. An 87Sr/86Sr high near ∼ 0.7084 is observed in the Telychian at the top of the studied section. The range of values is in general agreement with the data from previous sample sets of brachiopods and conodonts recovered from localities in North America and Europe that record a rising trend in the 87Sr/86Sr ratio throughout the Llandovery from approximately 0.7080 to 0.7084. The major increase in the 87Sr/86Sr ratio during the late Llandovery may be due to weathering of radiogenic source rocks that were uplifted during early Silurian continent–continent collisions. The Sr rise potentially coincides with the occurrence of an unusually thick sequence of K-bentonite beds representing large-magnitude ash falls in the early Telychian. A previously documented negative δ13C excursion in marine carbonates in the lower Telychian interval of the Ikla core is quasi-synchronous with the increase in 87Sr/86Sr. Our new organic matter δ13C data from the Ikla core confirm that this negative δ13C carbonate excursion is not a result of diagenesis. Furthermore, a negative δ13C excursion in carbonates from the early Telychian portion of the Pancake Range section in Nevada seems to confirm the global scope of this carbon cycle perturbation.

Field of study: Environmental science, Geography
The Future of Literary Scholarship

O NE might summarily describe literary scholarship in the nineteenth century as a continuous struggle between the philologists and the historians. In the one corner, we had the philologists. They were influenced by the new discoveries in chemistry and geology. They tried to break literature also into its elements-words. Each word they subjected to analysis, studying its roots and variations. As the chemists postulated undiscovered elements in their table and the astronomers undiscovered planets, they could formulate a Sanskrit word that they had not yet found. In their studies the beauties of literature, the rhythms of poetry, the structure of drama were lost in the pursuit of each separate word. Such was philology, scholarship made in Germany, the science of language. In the other corner were the historians. They sought not for elements but for links in the great chain of being. Darwin was their hero; they applied evolution not merely to horses and men but to the drama, the ode, the novel. Under their scrutiny the once Dark Ages became the Middle Ages. Sources, parallels, influences were their concern. The masterpieces were not broken up into separate words by them, but were hidden under webs of cross reference. After their analyses, the finest literary tapestry looked like a patchwork quilt. Through the late nineteenth century the warfare between the schools continued. Literary history was the easier task, but each university needed also its philologist, born or trained in Germany, as a sign of real scholarship. But the twentieth century saw a change in this warfare one side undermined, the other victorious. The study of the history and origin of words may be dying slowly-but it is dying surely. Ancient languages, and some modern ones, have gone out of the high schools and almost out of the colleges. In i900 a student might enter college with four years of Latin, two of Greek, two of German, and two of French. In I94i he would be unlikely to enter the graduate school with that equipment. The linguistic teacher may discover in each graduate class a student with the gift of tongues but never a whole class. The study of comparative philology may still have a few disciples, in phonetic laboratories or dialectic excursions, but most of its followers have turned to other fields. On the other hand, the historians have flourished. Sources, parallels,

Field of study: Education
A miniature SQUID magnetometer with direct read-out electronics

A novel miniature SQUID magnetometer with direct read-out electronics has been developed. A high flux-to-voltage transfer factor of up to 2500 mV//spl Phi//sub 0/ is achieved without additional positive feedback (/spl Phi//sub 0/ is the flux quantum). A flux resolution of 8/spl times/10/sup -7/ /spl Phi//sub 0//Hz/sup 1/2 /, corresponding to a magnetic moment sensitivity of approximately 2/spl times/10/sup -2/0 Am/sup 2//Hz/sup 1/2 / has been measured. This magnetometer can be used to study the dynamic magnetization properties (including NMR and MRI) of micron and sub-micron size particles and for high-resolution surface magnetometry.

Field of study: Physics
Common problems in pediatric ophthalmology.

Because in children the neurological connections of sight are still plastic, any condition that is able to cause a reduction of visual acuity will also cause cortical suppression of the input from that eye. Early management of amblyopia is essential to its effective treatment. Prompt recognition of strabismus, nystagmus, dyslexia, retinoblastoma and albinism will also lead to an improved visual prognosis for the affected child. In the child with retinoblastoma, it will also vastly improve the prognosis for life.

Field of study: Medicine
The Structure and Tectonic History of the Eastern Aleutian Trench

The tectonic character of the eastern Aleutian Trench and some major events in its geologic history can be estimated from nine continuous seismic reflection records. A section of pre-trench, deep oceanic sediments rests on the down-warped crust that forms the trench. Nearly horizontal undeformed strata that unconformably overlie this deep oceanic section partially fill the trench. The trench fill is thickest near present sediment sources. A Pliocene age for development of the eastern Aleutian Trench is estimated from the thickness of deep oceanic sediment that accumulated after the trench began to fill. The eastern Aleutian Trench thus appears younger than the central Aleutian Trench—a relation which helps to explain the distribution of sediment along the two trench segments.

Depression of the eastern Aleutian Trench diminished or virtually ended soon after the trench began to fill. The undeformed fill provides no evidence for a large thrust fault zone at the base of the continental slope. Nor is there any evidence that oceanic sediments have disappeared beneath the continents in late Tertiary time. These observations are difficult to reconcile with the simple model of a continental margin advanced in the hypothesis of plate tectonics.

Field of study: Geology
Poor Consumers as Global Consumers: The Diffusion of Tea and Coffee Drinking in the Eighteenth Century

This paper challenges the prevailing view among economic historians that tea and coffee were luxury articles of consumption prior to the nineteenth century. It reviews an array of available evidence, including national trade statistics and probate inventory studies. In particular, it examines the surprisingly wide social and economic diffusion of tea and coffee drinking among Amsterdam citizens of lower to middling economic status during the period of that city's ascendency and subsequent decline at the centre of global trade networks. Using the distribution of tea and coffee wares of both local and exotic manufacture across households of the artisanal and labouring classes, it seeks to map both the economic reach of the East Indian trade into the poorer parts of the city, as well as to locate the cultural meanings associated with the consumption of these new goods. New data to address this issue have been derived from a substantial collection of after-death inventories drawn up on the estates of middling and poor Amsterdam citizens in the middle decades of the eighteenth century by the Regents of the Municipal Orphanage.

Field of study: Economics, History
Phase locking high-order lateral modes of laser diode array with an external cavity

The possibility of phase locking high-order lateral modes of broad-stripe laser diode array(LDA) with a short external cavity is analyzed theoretically.The far field pattern of multi-lateral modes,which comprises a main lobe and side lobes,is observed for a LDA positioned in a short external cavity.From the experimental records,structures composed of peaks and valleys,symbolizing phase locking,can be observed within the side lobes.Moreover,the modulation depth of this structure is considerably larger than that in the main lobe.From these results,it can be concluded that the phase-locking between high-order lateral modes of emitters of the LDA is realized when the external cavity is short enough.

Field of study: Physics