nils-herrmann/clean_scirepeval huggingface dataset:
Characterization of differentiation factor/leukaemia inhibitory factor effect on lipoprotein lipase activity and mRNA in 3T3-L1 adipocytes.

Alterations in lipid metabolism characterized in major part by a decrease in lipoprotein lipase (LPL) activity in adipose tissue are a central feature of cachexia from chronic infection or malignancy. These metabolic derangements may be mediated in large part through endogenous host proteins produced in response to various pathological stimuli. Differentiation factor/leukaemia inhibitory factor (D-factor) is a cytokine whose functions overlap those of tumour necrosis factor-alpha (TNF), IL-6 and IL-1. Recombinant murine D-factor produced a dose- and time-dependent inhibition of heparin-releasable LPL activity in differentiated 3T3-L1 adipocytes. Although 2-10 fold less potent than recombinant murine TNF, D-factor inhibited LPL activity at concentrations of 1-10 ng/ml. When added together, D-factor and TNF produced a synergistic inhibition of LPL activity. Interleukin 6 (IL-6) was 100-fold less potent than D-factor; 0.1 ng/ml of D-factor or 10 ng/ml of IL-6 caused a 50% inhibition of LPL activity. D-factor and TNF increased IL-6 production in 3T3-L1 cells. Ten ng/ml of D-factor or 1.0 ng/ml of TNF stimulated the release of < 1 ng/ml of IL-6 and inhibited LPL activity to 11 +/- 3% and 3 +/- 2% of control, respectively, whereas 50 ng/ml of recombinant IL-6 was required to decrease LPL activity to 24 +/- 19% of control. TNF produced a marked decrease in LPL mRNA, whereas D-factor had minimal or no effect at doses which inhibited LPL activity almost completely. Western blot analysis of cell extracts showed that TNF caused a greater decrease in LPL protein production than D-factor.2+ with TNF, may contribute to the manifestations of cachexia.

Field of study: Medicine
Quantum Oscillations in Hole-Doped Cuprates

One of the leading challenges of condensed matter physics in the past few decades is an understanding of the high-temperature copper-oxide superconductors. Although the d-wave character of the superconducting state is well understood, the normal state in the underdoped regime has eluded understanding. Here, we review the past few years of quantum oscillation measurements performed in the underdoped cuprates that have culminated in an understanding of the normal ground state of these materials. A nodal electron pocket created by charge order is found to characterize the normal ground state in YBa2Cu3O6+δ and is likely universal to a majority of the cuprate superconductors. An open question remains regarding the origin of the suppression of the antinodal density of states at the Fermi energy in the underdoped normal state, either from mainly charge correlations or, more likely, from mainly pairing and/or magnetic correlations that precede charge order.

Field of study: Physics
Analysis of the water-soluble products of phosphatidylcholine breakdown by ion-exchange chromatography. Bombesin and TPA (12-O-tetradecanoylphorbol 13-acetate) stimulate choline generation in Swiss 3T3 cells by a common mechanism.

A method for the rapid and quantitative separation of glycerophosphocholine, choline phosphate and choline upon ion-exchange columns is described. The method has been utilized to examine the stimulation of phosphatidylcholine breakdown in quiescent Swiss 3T3 cells in response to bombesin and 12-O-tetradecanoylphorbol 13-acetate (TPA). The stimulated generation of choline is shown to precede that of choline phosphate, with no effect upon glycerophosphocholine levels; but was attenuated in cells in which protein kinase C activity was down-regulated. The results thus suggest that stimulation of the cells with either bombesin or TPA activates phospholipase D-catalysed phosphatidylcholine breakdown by a common mechanism involving the activation of protein kinase C.

Field of study: Biology, Computer science
Synthesis of DNA with Green Perylene Bisimides as DNA Base Substitutions

Perylene-3,4:9,10-tetracarboxylic acid bisimide represents a particularly attractive building block for DNA-based multichromophores and nanoassemblies due to its unique combination of optical and electronic properties. Despite the broad applicability of the perylene bisimide dye for DNA-based assemblies, significant fluorescence quenching by photoinduced charge-transfer processes to guanines in DNA represents a major disadvantage. In order to develop a redox actively and optically tuned perylene bisimide derivative with fluorescence that does not photooxidize guanines in DNA, we chose to attach two N-pyrrolidinyl substituents as strongly electron-donating substituents at the 1- and 7-positions of the bay area (“APBI”). The corresponding phosphoramidite 1 was synthesized and incorporated synthetically into oligonucleotides by using the automated DNA building block chemistry. The 2′-deoxyribofuranoside of natural nucleosides was replaced by (S)-1-aminopropane-2,3-diol as an acyclic linker between the phosphodiester bridges that is tethered to one of the imide nitrogen atoms of the APBI dye. Electrochemical and optical characterization of the isolated APBI dye shows that photoinduced charge transfer with guanines is indeed very unlikely. Single APBI DNA base substitutions show an exciplex-type emission with pH sensitivity. The interstrand APBI dimer in DNA could be regarded as a hydrophobically interacting base pair that stabilizes the thermal stability of the double strand. The APBI dimer behaves like an H aggregate, and the fluorescence is quenched quantitatively.

Field of study: Chemistry
In situ inflammasome activation results in severe damage to the central nervous system in fatal Zika virus microcephaly cases

HighlightsZIKV induce activation inflammasome in situ in fatal cases of microcephaly.Recognition of the ZIKV PAMPs by NLRP1, NLRP3, and AIM2 provoke release of caspase 1.Caspase 1 activation converts cytokines IL‐1&bgr;, IL‐18, and IL‐33 to bioactive form.Response induced by Caspase 1, iNOS, and cytokines enhance neuroinflammatory process.  Zika virus (ZIKV) has caused substantial concern worldwide owing to its association with severe birth defects, such as microcephaly and other congenital malformations. Inflammasomes, i.e., multi‐protein complexes that induce inflammation and pyroptosis, are predicted to contribute to the immune response to this flavivirus. Accordingly, in this study, the in situ inflammasome response was evaluated in fatal cases of ZIKV‐linked microcephaly. Brain tissue samples were collected from eight babies, including four ZIKV‐positive microcephalic neonates who died after birth and four flavivirus‐negative neonatal controls who died of other causes and whose central nervous system (CNS) architecture was preserved. In the ZIKV‐positive newborn/stillbirth babies, the major histopathological alterations included atrophy of the cortical layer, a predominance of mononuclear cell infiltration in the Virchow–Robin space, neuronal necrosis, vacuolization and neuronal degeneration, neuronophagy, and gliosis. An immunohistochemical analysis of tissues in the neural parenchyma showed significantly higher expression of the receptors NLRP1, NLRP3, and AIM2, cytokines IL‐1&bgr;, IL‐18, and IL‐33, and enzymes caspase 1, iNOS, and arginase 1 in ZIKV‐positive microcephaly cases than in flavivirus‐negative controls. These results suggest that inflammasome activation can aggravate the neuroinflammatory response and consequently increase CNS damage in neonates with fetal neural ZIKV infection and microcephaly.

Field of study: Medicine
Soil Physical Properties as Affected by Grain Cart Traffic

Changes in soil physical properties resulting from multiple passes of an 18 m3 single-axle grain cart with a 15.2 t axle load were measured one year after the traffic occurred. Air permeability, air-filled porosity, and dry density data were analyzed to determine how the soil responded to grain cart traffic and pre- and post-traffic tillage. Four repeated passes of the cart decreased air-filled porosity and permeability by as much as 50% in the 200- to 400-mm depth range when compared to the effect of a single wheel pass. With pre-traffic chisel plowing to a depth of 200 mm, most of the compaction in the 100- to 200-mm depth occurred on the first pass. However, four repeated passes had a greater effect on soil properties in the plots that received no tillage compared to the plots that were chiseled before trafficking.

Field of study: Agricultural and Food sciences
Late Neogene paleoclimate and paleoenvironment reconstructions from the Pipe Creek Sinkhole, Indiana, USA

The Late Neogene represents warm Earth conditions immediately prior to the development of extensive northern hemisphere glaciation, and this period in Earth history may therefore provide the best available analog for the projected outcome of continued global warming. There are few interior continental sites of Late Neogene age from the eastern half of North America and subsequently very little is known about the conditions characterizing climate. The Early Pliocene (~ 5 Ma) Pipe Creek Sinkhole (PCS) includes the sediment fill of a complex karst environment that developed in north-central Indiana, USA (Lat. 40° 27′ 25.4″, Long. 85° 47′ 37.2″). The site includes more than 3 m of high-chroma, red-colored silty-clay sediment interpreted to be terra rossa. The terra rossa δ13C values average − 20 ± 0.7‰ PDB and are interpreted to represent sediment deposited in a closed cave system under high summer temperatures and with well-drained soils. An in-situ paleosol at the top of the terra rossa represents a transition from a closed cave to an open environment that eventually flooded, thereby becoming a small pond. δ13C values from lacustrine sediments with organic matter derived dominantly from algae average − 20.6‰ and suggest the pond was stagnant and enriched with bicarbonate from the underlying limestones or via aquifers. Pond sediments include abundant vertebrate fossils, which are broadly consistent with those inhabiting an open ecosystem such as a savannah or parkland. However, the PCS pollen includes low taxonomic diversity that is dominated by pine with some hickory and flowering plants, but no grass pollen. We propose two hypotheses to explain the PCS stratigraphic record: (1) The pollen assemblage may represent a local pine dominated ecosystem associated with the pond paleoenvironment, such as a riparian community, and that the greater landscape was drier and open; (2) Alternatively, the climate may have became wetter raising the elevation of the groundwater table and initiating the formation of the pond. Then in response to the wetter conditions an early succession forest ecosystem developed.

Field of study: Environmental science, Geography
Effects of copper on early developmental stages of Lessonia nigrescens Bory (Phaeophyceae).

Copper effects on the early developmental gametophytic and sporophytic stages of the kelp Lessonia nigrescens were tested in gradients of increasing concentrations of ASV-labile copper. The results demonstrated a high sensitivity to copper of all life-history stages of the alga, where even the lowest tested concentration affected spore release as well as their subsequent settlement. More significant, concentrations higher than 7.87 microg L(-1) totally interrupted the development of the spores after they settle. This effect led to a failure in the formation of male and female gametophytes and, as a consequence, to a complete disruption of the normal life cycle of the kelp. Thus, we suggest that the absence of L. nigrescens from copper-enriched environments results from the high sensitivity of its early life cycle stages, which limits growth and maturation of the gametophytic microscopic phase and, as a consequence, prevents development of the macroscopic sporophytic phase.

Field of study: Environmental science
The role of verbal behavior in the establishment of comparative relations.

Twelve college students received conditional discrimination training with nonarbitrary and arbitrary stimuli, and derived comparative and transformation of function tests with a think-aloud condition across 2 experiments. Participants who failed these tests received remedial verbal operant training. Four control participants received verbal operant training alone. Across both experiments, only 1 participant passed the derived comparative test after conditional discrimination training. However, all participants passed derived comparative tests and 11 out of 12 participants passed transformation of function tests following verbal operant training, including the 4 control participants. Participants who passed derived comparative tests engaged in a high percentage of correct vocalizations during the think-aloud condition, while participants who failed did not. These results suggest that mediating verbal behavior could have played a crucial role in participants' responses during derived stimulus relations tests.

Field of study: Biology, Psychology
Language and meaning making: Register choices in seventh- and ninth-grade students' factual writing

Register refers to functional variation in language use across contexts. Developing a repertoire of lexical and grammatical choices for instantiating academic registers is key to literacy success in school. This study examined register choices adolescent learners made in factual writing, a key genre of schooling that is also highly valued in the workplace and society. A total of 93 seventh- and ninth-grade students from an American public school were asked to write about crocodilians based on a “wordless” picture book. Their writing was coded for presence of a range of academic and everyday register features, as well as content quality. Statistical and qualitative analyses revealed that (a) the students juxtaposed features of academic and everyday registers in ways that prevented them from presenting knowledge precisely, densely, authoritatively, and logically; (b) academic register use and content quality were significantly impacted by social class but not grade level or gender; and (c) register choices and content quality were positively correlated, with academic register associated with more scientific content. These findings suggest that adolescents need considerable support to develop linguistic tools and awareness that enable them to cope with the literacy demands of academic learning in secondary schooling.

Field of study: Education, Linguistics
Research on 1, 2, 4-triazoles

Alkylation of 4-phenyl-1, 2, 4-triazolinethione-3 with halogen compounds gives sulfides, which oxidize to sulfones. Unlike the corresponding tetrazole derivatives they do not exhibit antitubercular activity. The oxidation of 4-phenyl-3-carboxymethylthio-1, 2, 4-triazole is investigated. Permanganate oxidation is accompanied by decarboxylation and formation of 4-phenyl-1, 2, 4-triazolylmethylsulfone-3, while oxidation with hydrogen peroxide gives 4-phenyl-1, 2, 4-triazolinone-3. It is found that treatment of 4-phenyl-3-carboxymethylthio-1, 2, 4-triazole with acetic anhydride gives di(4-phenyl-3-methylenethio-1, 2, 4-triazoline)ketone, possibly via formation of an anhydro- derivative.

Field of study: Chemistry
Early Cretaceous gabbroic complex from Yinan, Shandong Province: petrogenesis and mantle domains beneath the North China Craton

Sensitive high resolution ion microprobe (SHRIMP) zircon U–Pb ages, geochemical and Sr-Nd-Pb isotopic data are reported for the gabbroic complex from Yinan (Shandong Province) with the aims of characterizing the nature of the Mesozoic mantle beneath the North China Craton. The Yinan gabbros contain alkali feldspar and biotite, and are characterized by moderate Mg#, high SiO2, low FeO and TiO2 contents and a strong enrichment of light rare earth elements [(La/Yb)n=11–50], but no Eu anomaly. They have low Nb/La (0.07–0.29), radiogenic 87Sr/86Sr (0.710) and unradiogenic εNd(t) (−15 to −13). These “crustal fingerprints” cannot be attributed to crustal contamination, given the lack of correlation between isotopic ratios and differentiation indices and the unreasonably high proportion of crustal contaminant (>20%) required in modeling. Instead, compositional similarities to contemporaneous basalts from nearby regions imply that the Yinan gabbros were not significantly affected by crystal cumulation. Isotopic data available for the Mesozoic mafic magmas reveal two distinct mantle domains beneath Shandong. While the EM1-like domain (with low 87Sr/86Sr) is confined to western Shandong, the mantle beneath eastern Shandong is dominated by EM2-type (with high 87Sr/86Sr) affinities. This aerial distinction suggests that the EM2-like signature of the Yinan gabbros may have been inherited from westerly-subducted Yangtze crust during the Triassic North China-South China collision. Emplacement of the Yinan gabbros (127 Ma) is likely affiliated with the widespread and protracted extension during the late Mesozoic in this region.

Field of study: Environmental science
Two-dimensional Wide-Angle X-ray Scattering on a Cm-doped borosilicate glass in a beryllium container.

The two-dimensional wide-angle X-ray diffraction technique was applied to a Cm-doped borosilicate glass in a beryllium container. The experiment involved a high-energy X-ray beam and an image plate. It is shown that it is possible to extract the structure factor of the radioactive glass successfully from diffraction patterns and compare it with that of the pristine one. Striking differences appear under the first diffraction peak, revealing new sub-structures for the radioactive glass. It is suggested that they could be related to structural changes in the medium-range order, in particular the size distribution of rings or chains under the influence of mixed interactions between the glass network, α-particles and recoil nuclei.

Field of study: Physics
Interaction of NH$_3$ gas on $\alpha$-MoO$_3$ nanostructures $-$ a DFT investigation

The structural stability, electronic properties and NH$_3$ adsorption properties of pristine, Ti, Zr and F substituted $\alpha$-MoO$_3$ nanostructures are successfully studied using density functional theory with B3LYP/LanL2DZ basis set. The structural stability of $\alpha$-MoO$_3$ nanostructures is discussed in terms of formation energy. The electronic properties of pristine, Ti, Zr and F incorporated $\alpha$-MoO$_3$ nanostructures are discussed in terms of HOMO-LUMO gap, ionization potential and electron affinity. $\alpha$-MoO$_3$ nanostructures can be fine-tuned with suitable substitution impurity to improve the adsorption characteristics of ammonia, which can be used to detect NH$_3$ in a mixed environment. The present work gives an insight into tailoring $\alpha$-MoO$_3$ nanostructures for NH$_3$ detection.

Field of study: Physics
Hnbue property in a shock model with cumulative damage threshold

A device subjected to shocks occurring randomly according to a general counting process and that fails when the cu~nulative damage exceeds a fixed threshold is considered. Sufficient conditions for the lifetime of an HNBTJE class device are given and it is shown that the HNBUE property for the shock model depends only on the arrival process. A means of obtaining distribution functions of the HNBUE class in parametric form is given and the characteristic function of the accumulated damage process is obtained.

Field of study: Mathematics
Biological and sedimentary facies of Australian salt lakes

Four main types of salt lakes are recognized in Australian: (1) large playa lakes, (2) small closed lakes, or pans, (3) crater lakes, and (4) coastal lakes (not connected to the sea). Basically all have an NaCl chemistry. Biological and sedimentary facies characteristic of these salt lakes can be arranged into three basic groups which relate to particular phases in lake regimes. These phases are: (1) wet phases of ephemeral shallow lakes, (2) dry lakes, and (3) deep water lakes. All elements of the salt lake biota with fossilizable remains are discussed, with a detailed account of the (palaeo)ecological information they offer. Elements of the nonaquatic biota associated with salt lake sediments are also analysed. Sedimentary features of Australian salt lakes pertinent to palaeoecology are discussed in the context of their association with the biota, using numerous illustrations. The distribution of the biota on lake floors, for example, its concentration in particular areas of the lake, or its destruction during particular episodes such as lake filling and drying, is mentioned in the context of recognizing different facies. Three major lake regime phases are presented with emphasis on the biological and sedimentary facies which characterize them. The paper concludes with a brief discussion of the relevance of recognizing particular salt lake facies and changes in lake histories for the study of palaeoclimates and for mineral and oil exploration.

Field of study: Environmental science, Geography
Understanding and treating moyamoya disease in children.

Moyamoya disease, a known cause of pediatric stroke, is an unremitting cerebrovascular occlusive disorder of unknown etiology that can lead to devastating, permanent neurological disability if left untreated. It is characterized by progressive stenosis of the intracranial internal carotid arteries and their distal branches and the nearly simultaneous appearance of basal arterial collateral vessels that vascularize hypoperfused brain distal to the occluded vessels. Moyamoya disease may be idiopathic or may occur in association with other syndromes. Most children with moyamoya disease present with recurrent transient ischemic attacks or strokes. Although there is no definitive medical treatment, numerous direct and indirect revascularization procedures have been used to improve the compromised cerebral circulation, with outcomes varying according to procedure type. Such techniques improve the long-term outcome of patients with both idiopathic and syndrome-associated moyamoya disease. This review provides a comprehensive discussion of moyamoya disease in children, with an emphasis on the most effective surgical treatment options.

Field of study: Medicine
Large-amplitude driving of a superconducting artificial atom

Superconducting persistent-current qubits are quantum-coherent artificial atoms with multiple, tunable energy levels. In the presence of large-amplitude harmonic excitation, the qubit state can be driven through one or more of the constituent energy-level avoided crossings. The resulting Landau–Zener–Stückelberg (LZS) transitions mediate a rich array of quantum-coherent phenomena. We review here three experimental works based on LZS transitions: Mach–Zehnder-type interferometry between repeated LZS transitions, microwave-induced cooling, and amplitude spectroscopy. These experiments exhibit a remarkable agreement with theory, and are extensible to other solid-state and atomic qubit modalities. We anticipate they will find application to qubit state-preparation and control methods for quantum information science and technology.

Field of study: Physics