nils-herrmann/clean_scirepeval huggingface dataset:
Questions of mass extinction

Earth's biodiversity is being overtaken by a mass extinction which, if allowed to proceed unchecked, could well eliminate between one quarter and one half of all species. Our conservation responses must be science-based if we are to address the problem in its full scope and with most productive use of conservation resources. Yet our scientific understanding of the impending mass extinction is inadequate in many salient respects. We have only a rudimentary grasp of the number of species at risk, of biodiversity depletion processes, of island biogeography in practice, and of evolutionary consequences, to cite but a few leading questions. The same applies to the issue of the most efficient strategies to confront the conservation challenge. Worse, there is scant evidence (due in part to gross lack of funding) of a comprehensive and coordinated campaign to mount a research effort of scope to match the problem. The paper broaches ten key questions that warrant urgent attention.

Field of study: Environmental science
Two trans-acting rat-brain proteins, MARTA1 and MARTA2, interact specifically with the dendritic targeting element in MAP2 mRNAs.

Different isoforms of the microtubule-associated protein 2 (MAP2) are somatodendritic components of neurons that seem to regulate the stability of the dendritic cytoskeleton. MAP2 localization into dendrites appears to be a complex multicausal mechanism that involves the specific recruitment of MAP2 mRNAs into dendritic compartments. Recently, we have functionally characterized a 640-nucleotide dendritic targeting element (DTE) in the 3' untranslated region (3' UTR) of MAP2 transcripts that mediates extrasomatic mRNA localization in primary neurons (Blichenberg et al. , 1999). In analogy to molecular mechanisms regulating cytoplasmic RNA translocation in other cell systems, we propose that, in vivo, the cis-acting MAP2-DTE interacts with specific protein factors present in neurons. To identify putative trans-acting DTE-binding proteins, we performed in vitro ultraviolet crosslinking assays. Using this experimental system, two 90-kDa and 65-kDa MAP2-RNA trans-acting proteins, MARTA1 and MARTA2, were identified in rat-brain extracts. Both MARTAs bind with high affinity to the MAP2-DTE, but not to other investigated regions of MAP2 transcripts or the somatically restricted alpha-tubulin mRNA. Moreover, MARTA1 and MARTA2 do not bind significantly to other dendritically localized transcripts encoding vasopressin and arg3.1, nor to a dendritic trafficking element from the mRNA encoding the alpha-subunit of the Ca(2+)/calmodulin-dependent protein kinase II. Binding of MARTA1 and MARTA2 to the MAP2-DTE occurs with an affinity in the nanomolar range. Whereas MARTA1 is clearly detectable in crude lysates, cytosolic and ribosomal salt-wash fractions, and in nuclear extracts, MARTA2 is preferentially found in the ribosomal salt-wash preparation. Neither MARTA is restricted to rat brain, and both are present in a number of other rat tissues. Thus, both proteins may be involved in a variety of nuclear and cytoplasmic events that regulate RNA metabolism in different cell types.

Field of study: Biology
Quantitative capabilities of STXM to measure spatially resolved organic volume fractions of mixed organic ∕ inorganic particles

Scanning transmission X-ray microscopy coupled with near-edge X-ray
absorption and fine structure (STXM-NEXAFS) spectroscopy can be used to
characterize the morphology and composition of aerosol particles. Here, two
inorganic  ∕  organic systems are used to validate the calculation of
organic volume fraction (OVF) and determine the level of associated error by
using carbon K-edge STXM data at 278, 285.4, 288.6, and 320 eV. Using the
mixture of sodium chloride and sucrose as one system and ammonium sulfate and
sucrose as another, three solutions were made with 10:1 , 1:1 , and 1:10 
mass ratios (inorganic to organic). The OVFs of the organic-rich aerosols of
both systems deviated from the bulk OVF by less than 1%, while the
inorganic-rich aerosols deviated by approximately 1 %. Aerosols from the
equal mass mixture deviated more (about 4 %) due to thick inorganic
regions exceeding the linear range of Beer's law. These calculations were
performed after checking the data for poor image alignment, defocusing issues, and
particles too thick to be analyzed. The potential for systematic error in the
OVF calculation was also tested by assuming the incorrect composition. There
is a small (about 0.5 %) OVF difference if the organic is erroneously
assumed to be adipic acid rather than the known organic, sucrose. A much
larger difference (up to 25 %) is seen if sodium chloride is assumed
instead of ammonium sulfate. These results show that the OVF calculations are
fairly insensitive to the organic while being much more sensitive to the
choice of inorganic.

Field of study: Environmental science
A model for fragment excitation and kinetic energy in nuclear fission

We present a model which allows for the calculation of fragment excitation and kinetic energy in nuclear fission. The model assumes that fission products are excited independently according to an exponential distribution function, which depends on the Q-value of the reaction and the level density parameter in the single fragment. We develop the model description and compare the results for different fissioning systems from actinium to fermium, and for different compound reactions, namely spontaneous fission, fission following thermal neutron capture, and high-energetic reactions with experimental data.

Field of study: Physics
Structural changes in the German pharmaceutical market: price setting mechanisms based on the early benefit evaluation.

In the past, free price setting mechanisms in Germany led to high prices of patented pharmaceuticals and to increasing expenditures in the pharmaceutical sector. In order to control patented pharmaceutical prices and to curb increasing pharmaceutical spending, the Act for Restructuring the Pharmaceutical Market in Statutory Health Insurance (AMNOG) came into effect on 1st January 2011. In a structured dossier, pharmaceutical manufacturers have to demonstrate the additional therapeutic benefit of the newly approved pharmaceutical compared to its appropriate comparator. According to the level of additional benefit, pharmaceuticals will be subject to price negotiations between the Federal Association of Statutory Health Insurance Funds and the pharmaceutical company concerned (or assigned to a reference price group in case of no additional benefit). Therefore, the health care reform is a first step to decision making based on "value for money". The process of price setting based on early benefit evaluation has an impact on the German as well as the European pharmaceutical markets. Therefore, these structural changes in Germany are of importance for pricing decisions in many European countries both from a political point of view and for strategic planning for pharmaceutical manufacturers, which may have an effect on insured patients' access to pharmaceuticals.

Field of study: Medicine, Political science
Binding sites of cholinesterases. Alkylation by an aziridinium derivative.

1. Alkylation of acetylcholinesterase and butyrylcholinesterase by 2-chloro-N-(chloroethyl)-N-methyl-2-phenylethylamine was observed. This alkylating agent was more potent than related compounds previously described, and less stable (half-life 8.5min. at 23 degrees ). 2. Alkylation had effects on hydrolysis of substrates varying from activation for indophenyl acetate to inhibition for acetylcholine, and intermediate effects with five other substrates. The effects were on V(max.) and not K(m). 3. Alkylation caused a variety of changes in sensitivity to inhibition by five carbamates, five organophosphates and four other inhibitors, varying from total protection against tetraethylammonium to mildly enhanced sensitivity to urea. 4. The findings suggested the existence of three binding sites, one of which was anionic and another hydrophobic, in addition to the esteratic site.

Field of study: Biology, Computer science
Cancellation of Quantum Anomalies and Bosonization of the 3D Time-Reversal Symmetric Topological Insulator

The strong time-reversal symmetric (TRS) topological insulator (TI) in three space dimensions features gapless surface states in the form of massless Dirac fermions. We study these surface states with the method of bosonization, and find that the resulting bosonic theory has a topological contribution due to the parity anomaly of the surface Dirac fermions. We argue that the presence of a quantum anomaly is, in fact, the main reason for the existence of a surface state, by the principle that anomalies of a surface and bulk must cancel. Inspecting other classes of topological insulators, we argue that this principle holds in general. Moving beyond purely topological considerations, we incorporate the dynamics of the surface electron states into the bosonic theory. Additionally, we discuss the thermodynamics of the bosonic theory and propose a representation of the surface Dirac fermions in terms of the bosonic fields.

Field of study: Physics
Rapamycin can restore the negative regulatory function of transforming growth factor beta 1 in high grade lymphomas.

TGF-β1 (transforming growth factor beta 1) is a negative regulator of lymphocytes, inhibiting proliferation and switching on the apoptotic program in normal lymphoid cells. Lymphoma cells often lose their sensitivity to proapoptotic/anti-proliferative regulators such as TGF-β1. Rapamycin can influence both mTOR (mammalian target of rapamycin) and TGF-β signaling, and through these pathways it is able to enhance TGF-β induced anti-proliferative and apoptotic responses. In the present work we investigated the effect of rapamycin and TGF-β1 combination on cell growth and on TGF-β and mTOR signalling events in lymphoma cells. Rapamycin, an inhibitor of mTORC1 (mTOR complex 1) did not elicit apoptosis in lymphoma cells; however, the combination of rapamycin with exogenous TGF-β1 induced apoptosis and restored TGF-β1 dependent apoptotic machinery in several lymphoma cell lines with reduced TGF-β sensitivity in vitro. In parallel, the phosphorylation of p70 ribosomal S6 kinase (p70S6K) and ribosomal S6 protein, targets of mTORC1, was completely eliminated. Knockdown of Smad signalling by Smad4 siRNA had no influence on apoptosis induced by the rapamycin+TGF-β1, suggesting that this effect is independent of Smad signalling. However, apoptosis induction was dependent on early protein phosphatase 2A (PP2A) activity, and in part on caspases. Rapamycin+TGF-β1 induced apoptosis was not completely eliminated by a caspase inhibitor. These results suggest that high mTOR activity contributes to TGF-β resistance and lowering mTORC1 kinase activity may provide a tool in high grade B-cell lymphoma therapy by restoring the sensitivity to normally available regulators such as TGF-β1.

Field of study: Medicine
The singularity category of an algebra with radical square zero

To an artin algebra with radical square zero, a regular algebra in the sense of von Neumann and a family of invertible bimodules over the regular algebra are associated. These data describe completely, as a triangulated category, the singularity category of the artin algebra. A criterion on the Hom-finiteness of the singularity category is given in terms of the valued quiver of the artin algebra.

Field of study: Mathematics
Trends and Progress in Nuclear and Hadron Physics: A Straight or Winding Road

Quantitative calculations of the properties of hadrons and nuclei, with assessed uncertainties, have emerged as competitive with experimental measurements in a number of major cases. We may well be entering an era where theoretical predictions are critical for experimental progress. Cross-fertilization between the fields of relativistic hadronic structure and non-relativistic nuclear structure is readily apparent. Non-perturbative renormalization methods such as similarity renormalization group and Okubo–Lee–Suzuki schemes as well as many-body methods such as coupled cluster, configuration interaction and lattice simulation methods are now employed and advancing in both major areas of physics. New algorithms to apply these approaches on supercomputers are shared among these areas of physics. The roads to success have intertwined with each community taking the lead at various times in the recent past. We briefly sketch these fascinating paths and comment on some symbiotic relationships. We also overview some recent results from the Hamiltonian basis light-front quantization approach.

Field of study: Physics
A learning-based module extraction method for object-oriented systems

We propose a novel learning-based module extraction approach for OO systems.The approach is based on common OO design characteristics and design principles.We train our model with data obtained from a real modular reference-system.Experimental results show that it outperforms existing methods for OO systems.Extracting modules can help in software comprehension and architecture recovery. Developers apply object-oriented (OO) design principles to produce modular, reusable software. Therefore, service-specific groups of related software classes called modules arise in OO systems. Extracting the modules is critical for better software comprehension, efficient architecture recovery, determination of service candidates to migrate legacy software to a service-oriented architecture, and transportation of such services to cloud-based distributed systems. In this study, we propose a novel approach to automatic module extraction to identify services in OO software systems. In our approach, first we create a weighted and directed graph of the software system in which vertices and edges represent the classes and their relations, respectively. Then, we apply a clustering algorithm over the graph to extract the modules. We calculate the weight of an edge by considering its probability of being within a module or between modules. To estimate these positional probabilities, we propose a machine-learning-based classification system that we train with data gathered from a real-world OO reference system. We have implemented an automatic module extraction tool and evaluated the proposed approach on several open-source and industrial projects. The experimental results show that the proposed approach generates highly accurate decompositions that are close to authoritative module structures and outperforms existing methods.

Field of study: Computer science, Engineering
Thermomechanical characteristics of KM2PLUSKevlar nanocomposites

Woven fabric laminates have proved to have grander properties compared to those of laminates made of unidirectional prepregs. Through control/ alteration of certain additives at the nanoscale level, it is possible to maximize property enhancement of selected polymer systems to meet or exceed the requirements of current applications. The current paper studies the thermal and mechanical properties of newly developed KM2PLUS woven Kevlar composites and the effect of mixing three different types of nanomaterials, namely SiC, Al2O3 and Carbone nanotubes to the composite. The mechanical properties for the composite materials samples were tested using three-point bending and nano-indentation tests. Thermal properties of the laminated samples were investigated using Thermal GravimetricAnalysis (TGA) and Differential Scanning Calorimetry (DSC). The results showed that 0.5% CNT added to the laminate system increased the stiffness and the load carrying capacity significantly. Thermal analysis showed that there was no major change in the thermal properties due to the addition of the nano fillers.

Field of study: Materials science
Meta-Analysis of SNP-Environment Interaction With Overlapping Data

Meta-analysis, which combines the results of multiple studies, is an important analytical method in genome-wide association studies. In genome-wide association studies practice, studies employing meta-analysis may have overlapping data, which could yield false positive results. Recent studies have proposed models to handle the issue of overlapping data when testing the genetic main effect of single nucleotide polymorphism. However, there is still no meta-analysis method for testing gene-environment interaction when overlapping data exist. Inspired by the methods of testing the main effect of gene with overlapping data, we proposed an overlapping meta-regulation method to address the issue in testing the gene-environment interaction. We generalized the covariance matrices of the regular meta-regression model by employing Lin’s and Han’s correlation structures to incorporate the correlations introduced by the overlapping data. Based on our proposed models, we further provided statistical significance tests of the gene-environment interaction as well as joint effects of the gene main effect and the interaction. Through simulations, we examined type I errors and statistical powers of our proposed methods at different levels of data overlap among studies. We demonstrated that our method well controls the type I error and simultaneously achieves statistical power comparable with the method that removes overlapping samples a priori before the meta-analysis, i.e., the splitting method. On the other hand, ignoring overlapping data will inflate the type I error. Unlike the splitting method that requires individual-level genotype and phenotype data, our proposed method for testing gene-environment interaction handles the issue of overlapping data effectively and statistically efficiently at the meta-analysis level.

Field of study: Biology
Trust and Rejection Sensitivity in Personality Disorders

of ReviewWe review recent empirical investigations about two core processes subtending impairments in interpersonal functioning and, more precisely, cooperative behaviors in personality disorders: Trust toward others and rejection sensitivity. The main contributions are about borderline and narcissistic personality disorders but we report a little evidence about other personality disorders too (i.e., avoidant, antisocial, and paranoid personality disorders).Recent FindingsRegarding borderline personality disorder, a misinterpretation of situations as threatening seems to be relevant for both trust and rejection sensitivity. With specific regard to narcissistic personality disorder, results suggest rejection sensitivity and distrust to be plausible risk factors for aggressive outbursts.SummaryEmpirical findings display specific patterns of disturbances in rejection sensitivity and trust dynamics across different personality disorders. Nonetheless, further studies on personality disorders other than borderline or narcissistic personality disorder are needed. A deeper understanding may provide insight for better clinical management of such impairments among patients with personality disorders.

Field of study: Medicine, Psychology
Isotopic provenance of sandstones from the Eocene Tyee Formation, Oregon Coast Range

The Tyee Formation of Eocene age in the Oregon Coast Range has been studied by a variety of isotopic techniques in order to determine its provenance. Traditional basin analyses including paleocurrent measurements, lithofacies mapping, and study of sandstone compositions made previously suggest derivation from the Klamath Mountains, which lie to the south. In contrast, the isotopic compositions of whole-rock sandstone samples, white mica, and potassium feldspar separates preclude derivation solely from this local source area. Nd-Sm, Rb-Sr, K-Ar, 18 O/ 16 O, and D/H analyses of sandstones from the Tyee and related formations yield the following information about their source areas. (1) Whole-rock ϵ Nd values between −7.1 and −7.3 at the time of deposition indicate that an old crustal component (∼700 Ma) was incorporated in the source rocks. (2) Whole-rock Rb-Sr systematics implies an older age than those of sandstones clearly derived from the Klamath Mountains. These Rb-Sr values are similar to those of modern sands of the Columbia River that were derived from eastern source areas. (3) Either apparent Rb-Sr ages of potassium feldspars are too old or their initial 87 Sr/ 86 Sr ratios are too high to have been derived from plutonic rocks of the Klamath Mountains or Sierra Nevada. (4) White micas have a fairly consistent Late Jurassic Rb-Sr isochron but have K-Ar ages of 68 Ma, an overprint not recognized in the Klamath terranes. (5) White micas have δ 18 O values of ∼9.5, a value typical of S-type granges such as are found in the Idaho batholith, but too high for normal I-type granites such as in the northern Sierra Nevada and too low for metamorphic rocks in the Klamath Mountains. (6) White micas have δD values consistent with those observed for plutonic white mica in the Idaho batholith, but markedly lower than those of white mica from schist in the Klamath Mountains. (7) Potassium feldspars have δ 18 O values that vary widely and that mainly are not in oxygen-isotope equilibrium with coexisting white mica, suggesting that these minerals were not derived from the same source area. These results indicate that the provenance of these sandstones included S-type (two-mica) granites that formed in Late Jurassic time from sources that included an old crustal component. Minerals in the granites underwent subsequent thermotectonic age resetting in Late Cretaceous time. Rocks in the Klamath Mountains and northern Sierra Nevada do not possess these features and consequently are precluded from being major source areas for the Tyee Formation. The sandstones most likely were derived from the Idaho batholith. Abundant detritus from that source area is consistent with a model in which the Oregon Coast Range basin lay much farther east, closer to Idaho, during deposition and subsequently moved westward to its present position. Such major displacement is compatible with the tectonic-rotation history documented for the Oregon Coast Range that began during the time of deposition of the Tyee Formation.

Field of study: Geology
Perceived Versus Actual Transparency of Goals in Negotiation

Participants in Study 1 either engaged in a negotiation with a '"phantom "second negotiator or observed the negotiation. Negotiators judged whether the observer would be able to accurately discern their goals from their behavior; observers judged the negotiator's goals. Results indicated that negotiators overestimated the transparency of their objectives. An interaction between goal salience and constraints on communication was also evident: When communication was highly constrained, negotiators overestimated their transparency only when they were led to focus on their goals; when communication was less constrained, negotiators overestimated their transparency regardless of goal salience. Study 2 revealed that motivational forces are not necessary for transparency overestimation to occur: Observers informed about a negotiator's goals also overestimated the extent to which his or her goals would be transparent to an uninformed observer.

Field of study: Psychology
Direct study of the proximity effect in the normal layer inside of the stacked SINIS device.

We have observed a striking anisotropy in the electrical transport of layered multiterminal SINIS structures [where S, I, and N denote a superconductor (Nb), an insulator (AlOx), and a normal metal (Al), respectively]. We find that the lateral conductivity of the N layer is dissipative, but a superconducting current can flow normal to the structure, suggesting a direct Josephson coupling between the external S electrodes. A small coherent contribution to the lateral conductivity of the N layer is observed near zero voltage.

Field of study: Physics