nils-herrmann/clean_scirepeval huggingface dataset:
Transforming growth factor beta1 attenuates ceramide-induced CPP32/Yama activation and apoptosis in human leukaemic HL-60 cells.

Ceramide, a product of sphingomyelin turnover, is a novel lipid second messenger that mediates important cellular functions including proliferation, differentiation and apoptosis. This study demonstrates that the CPP32/Yama protease was activated during apoptosis induced by the membrane-permeable second messenger C2-ceramide in HL-60 cells. We also found that the addition of a specific tetrapeptide inhibitor of CPP32/Yama, Ac-DEVD-CHO, provided an effective protection against ceramide-induced cell death. These results suggested that CPP32/Yama has a central role in ceramide-mediated apoptosis. Furthermore a wide variety of cytokines were examined for their effect on ceramide-induced apoptosis. Only transforming growth factor beta1 (TGF-beta1) (1 ng/ml) exerted significant prevention of apoptosis induced by C2-ceramide, or by sphingomyelinase (increases intracellular ceramide). Consistently, TGF-beta1 abrogated the cleavage of poly(ADP-ribose) polymerase and the production of the CPP32/Yama active subunit, p17. However, TGF-beta1 treatment did not cause growth inhibition or alter the level of cyclin-dependent kinase inhibitor p27. It suggests that the preventive effect of TGF-beta1 is not mediated by growth arrest. Interestingly, we found that TGF-beta1 prevented the C2-ceramide-caused decrease of Bcl-2 protein. We thus propose that TGF-beta1 rescues ceramide-induced cell death, possibly by maintaining the constant level of Bcl-2, thereby abolishing CPP32/Yama protease activation.

Field of study: Biology, Computer science
The conversion of chicken manure to biooil by fast pyrolysis II. Analysis of chicken manure, biooils, and char by curie-point pyrolysis-gas chromatography/mass spectrometry (Cp Py-GC/MS)

The initial chicken manure and the three fractions derived from it by fast pyrolysis, that is, the two biooils Fractions I and II as well as the residual char were analyzed by Curie-point pyrolysis-gas chromatography/mass spectrometry (Cp Py-GC/MS). The individual compounds identified were grouped into the following six compound classes: (a) N-heterocyclics; (b) substituted furans; (c) phenol and substituted phenols; (d) benzene and substituted benzenes; (e) carbocyclics; and (f) aliphatics. Of special interest were the relatively high concentrations of N-heterocyclics in biooil Fraction II which was obtained in the highest yield and had the highest calorific value. Prominent N-heterocyclics in biooil Fraction II were methyl-and ethyl-substituted pyrroles, pyridines, pyrimidine, pyrazines, and pteridine. Also noteworthy was the high abundance of aliphatics in biooil Fraction I and the char. The alkanes and alkenes in biooil Fraction I ranged from n-C7 to n-C18 and C7:1 to C18:1, respectively, and those in the char from n-C7 to n-C19 and C7:1 to C19:1, respectively. The N-heterocyclics in the two biooil Fractions came from the chicken manure, from proteinaceous materials during fast pyrolysis or were formed during the fast pyrolysis manure conversion by the Maillard reaction which involved the formation of N-heterocyclics by amino acids interacting with sugars.

Field of study: Agricultural and Food sciences
Could plant diversity metrics explain climate-driven vegetation changes on mountain summits of the GLORIA network?

High-elevation habitats host a large number of plant species and are characterized by high biodiversity. The vegetation dynamics in these cold adapted ecosystems are difficult to predict, being affected by global warming, especially in the last decades. With the aim to promote a better understanding of climate-driven changes of alpine vegetation, we investigated the variation in species richness, α-diversity, β-diversity, and total cover of plant functional types over a time lapse of 15 years, relying on multiple re-surveys of mountain summit vegetation in 2001, 2008 and 2015. The study area, included in the long term global observation network GLORIA, was at the boundary between temperate and Mediterranean mountains of S-Europe (northern Apennines, Italy). We identified a trend of loss in biodiversity and signals of biotic homogenization using multiple diversity metrics, despite the overall species richness increment observed in the study area. Cold-adapted and rare species declined while dominant species like graminoids and shrubs increased. Our results highlight that long-term vegetation monitoring activities paired with multiple measures of diversity are required to properly assess biodiversity and to obtain useful indications for future conservation activities in alpine environments. The methods here presented could be applied in all GLORIA sites to quantify biodiversity changes over time, obtaining comparable results for biodiversity monitoring in high-elevation habitats from all over the world.

Field of study: Environmental science
INTERACTION OF VISCOELASTIC SATURATED SOIL AND TUNNEL LINING SUBJECT TO ININER WATER PRESSURE

The concrete lining has viscoelastic properties and permeability.The inner water pressure is partly undertaken by the lining and partly balanced by pore water pressure;it depends on the stress coefficient related to the volume fraction of pore fluid.According to the fluid velocity equality at the interface of lining and soil,and continuity condition of the stress and displacement,the boundary conditions of partially permeability are established.Treating the lining and soil as porous viscoelastic material and two phase medium for liquid-solid respectively,adopting saturated porous medium and viscoelastic theory,this paper developed the analytical expressions for the displacement,stress and pore water pressure of saturated viscoelastic soil subjected to the inner water pressure in the frequency domain,as well as the displacement and stress of lining under the interaction of saturated viscoelastic soil and lining.Parametric study shows that,the stress coefficient and the relative permeability coefficient of the lining and soil have remarkable influence on the system dynamic response.In addition,the inner water pressure undertaken by the boundary lining and pore water can be determined by the stress coefficient.

Field of study: Engineering
Pillow shelves: determination of bedding direction and structural facing direction from shelves in deformed pillow lavas

Des structures etagees se forment dans les parties superieures des coussins de lave ou des tunnels de coulee de lave, et marquent une pause de leur drainage. Donc, l'identification de ces structures dans des coussins de lave tectoniquement deformes permet de determiner la direction paleohorizontale (i.e., le litage) et la direction approximative de la polarite. Nous presentons un exemple choisi dans la zone de plissement de Cape Smith dans la nord du Quebec, ou la polarite et le litage furent determines separement. La mesure dans des sequences de coussins de lave fortement deformees permet de definir la position de la partie superieure des coulees, ce qui constitue une etape cruciale pour reconstituer l'evolution structurale de terrains ou predominenet des laves en coussins, par exemple, dans les zones de roches vertes.

Field of study: Environmental science
Indications of superconductivity in doped highly oriented pyrolytic graphite

We have observed possible superconductivity using standard resistance versus temperature techniques in phosphorous ion implanted highly oriented pyrolytic graphite. The onset appears to be above 100?K and quenching by an applied magnetic field has been observed. The four initial boron implanted samples showed no signs of becoming superconductive whereas all four initial and eight subsequent samples that were implanted with phosphorous showed at least some sign of the existence of small amounts of the possibly superconducting phases. The observed onset temperature is dependent on both the number of electron donors present and the amount of damage done to the graphene sub-layers in the highly oriented pyrolytic graphite samples. As a result the data appears to suggest that the potential for far higher onset temperatures in undamaged doped graphite exists.

Field of study: Physics
Thromboembolic ischemic stroke changes red blood cell morphology.

Stroke is one of the most debilitating diseases causing morbidity and mortality worldwide. During ischemic stroke, erythrocytes undergo oxidative and proteolytic changes resulting not only in inflammation but also in changes in cellular rheology. During the event, fibrin fibers, which are typically a fine net, clot abnormally to form a clot of dense matted deposits (DMDs). This atypical coagulum causes blood cells to be trapped in the mesh.



Here we study red blood cell (RBC) ultrastructure in thromboembolic ischemic stroke using high resolution scanning electron microscopy.



We show that RBCs in patients change shape, with membrane extensions that form close interactions with the DMDs.



We suggest that the RBC membrane changes and resulting DMD interactions play a pivotal role in the persistent presence of thrombi. This ultrastructural observation might open a renewed debate regarding possible additional structural and biochemical roles of RBCs in the circulatory system.

Field of study: Biology, Medicine
Supporting emergent bilinguals’ argumentation: Evaluating evidence in informational science texts

Much of the research on teaching argumentation has focused on the genre, its features, and ways to support students in orally constructing or writing an argument, but far less is known about what students need to do as readers in preparation for writing an argument. The case study presented here explores how close attention to language features commonly found in informational science texts can support fourth-grade emergent bilinguals in identifying and evaluating evidence. It illustrates how, with functional grammar metalanguage of usuality and likelihood, a teacher can facilitate discussions about words in science texts that indicate authors’ degrees of uncertainty and in turn support students’ evaluations of evidence. Analysis of the instructional discourse also reveals potential pitfalls in this approach, as degrees of uncertainty expressed by an author do not make evidence inherently strong or weak. The strength of evidence must be determined through considering its relationship to the claim.

Field of study: Education, Linguistics
Which are, what is their status and what can we expect from ecosystem services provided by Spanish rivers and riparian areas?

By applying the framework proposed by Millennium Ecosystem Assessment, we analysed the current state and trends of 20 ecosystem services provided by Spanish rivers and riparian areas using 139 indicators. We compared the obtained results with the Europe and UK assessment. It is the first document that attempts to analyse the importance of services provided by Spanish rivers and riparian areas, and it forms part of the evaluation carried out for the Spanish Millennium Ecosystem Assessment. Among the provisioning services, freshwater, hydropower energy and genetic resources were classified as high importance, and water regulation and self-purification capacity, and natural hazard mitigation are among the regulating services, with landscape-aesthetic values and recreation and ecotourism featuring among the cultural services. About 61 % of the assessed ecosystem services are currently declining or degrading, but are higher than the percentage calculated for Europe (45 %) or for the UK (53 %). All regulating services are degrading, especially water regulation, natural hazard mitigation, soil formation and fertility and biological control, and the cultural services related to rural populations. Likewise, the biodiversity of Spanish aquatic ecosystems is decreasing rapidly. Land use changes and overexploitation of biological and mineral raw materials have been the main direct drivers of change in Spanish rivers and riparian zones, and relate directly to increase urbanised areas and irrigated agriculture. Finally, we draw some considerations on alternative models for aquatic ecosystems management which maintain aquatic ecosystem services and their biodiversity.

Field of study: Environmental science
Genome Wide Assessment of Genetic Variation and Population Distinctiveness of the Pig Family in South Africa

Genetic diversity is of great importance and a prerequisite for genetic improvement and conservation programs in pigs and other livestock populations. The present study provides a genome wide analysis of the genetic variability and population structure of pig populations from different production systems in South Africa relative to global populations. A total of 234 pigs sampled in South Africa and consisting of village (n = 91), commercial (n = 60), indigenous (n = 40), Asian (n = 5) and wild (n = 38) populations were genotyped using Porcine SNP60K BeadChip. In addition, 389 genotypes representing village and commercial pigs from America, Europe, and Asia were accessed from a previous study and used to compare population clustering and relationships of South African pigs with global populations. Moderate heterozygosity levels, ranging from 0.204 for Warthogs to 0.371 for village pigs sampled from Capricorn municipality in Eastern Cape province of South Africa were observed. Principal Component Analysis of the South African pigs resulted in four distinct clusters of (i) Duroc; (ii) Vietnamese; (iii) Bush pig and Warthog and (iv) a cluster with the rest of the commercial (SA Large White and Landrace), village, Wild Boar and indigenous breeds of Koelbroek and Windsnyer. The clustering demonstrated alignment with genetic similarities, geographic location and production systems. The PCA with the global populations also resulted in four clusters that where populated with (i) all the village populations, wild boars, SA indigenous and the large white and landraces; (ii) Durocs (iii) Chinese and Vietnamese pigs and (iv) Warthog and Bush pig. K = 10 (The number of population units) was the most probable ADMIXTURE based clustering, which grouped animals according to their populations with the exception of the village pigs that showed presence of admixture. AMOVA reported 19.92%–98.62% of the genetic variation to be within populations. Sub structuring was observed between South African commercial populations as well as between Indigenous and commercial breeds. Population pairwise FST analysis showed genetic differentiation (P ≤ 0.05) between the village, commercial and wild populations. A per marker per population pairwise FST analysis revealed SNPs associated with QTLs for traits such as meat quality, cytoskeletal and muscle development, glucose metabolism processes and growth factors between both domestic populations as well as between wild and domestic breeds. Overall, the study provided a baseline understanding of porcine diversity and an important foundation for porcine genomics of South African populations.

Field of study: Biology
Lift of the trivial representation to a nonlinear double cover

Let $\widetilde G$ be the nonlinear double cover of the real points of a connected, simply connected, semisimple complex group. In [Ts], we introduce a set of genuine small representations of $\widetilde G$ with infinitesimal character $\lambda$, denoted $\prod _\lambda ^s (\widetilde G)$. In this paper, we show that $\prod _{\rho/2} ^s (\widetilde G)$ is precisely the set of genuine irreducible representations arising from the Kazhdan-Patterson lifting of the trivial representation, when $\widetilde G$ is simply laced and split.

Field of study: Mathematics
Preferred Orientation Contribution to the Anisotropic Normal State Resistivity in Superconducting Melt-Cast Processed Bi2Sr2CaCu2O8+δ

We describe how the contribution of crystallographic texture to the anisotropy of the resistivity of polycrystalline samples can be estimated by averaging over crystallographic orientations through a geometric mean approach. The calculation takes into account the orientation distribution refined from neutron diffraction data and literature values for the single crystal resistivity tensor. The example discussed here is a melt-cast processed Bi2Sr2CaCu2O8+δ (Bi-2212) polycrystalline tube in which the main texture component is a <010> fiber texture with relatively low texture strength. Experimentally-measured resistivities along the longitudinal, radial, and tangential directions of the Bi-2212 tube were compared to calculated values and found to be of the same order of magnitude. Calculations for this example and additional simulations for various texture strengths and single crystal resistivity anisotropies confirm that in the case of highly anisotropic phases such as Bi-2212, even low texture strengths have a significant effect on the anisotropy of the resistivity in polycrystalline samples.

Field of study: Materials science
Relevance of exotic pine plantations as a surrogate habitat for ground beetles (Carabidae) where native forest is rare

Plantation forests are of increasing importance worldwide for wood and fibre production, and in some areas they are the only forest cover. Here we investigate the potential role of exotic plantations in supporting native forest-dwelling carabid beetles in regions that have experienced extensive deforestation. On the Canterbury Plains of New Zealand, more than 99% of the previous native forest cover has been lost, and today exotic pine (Pinus radiata) plantations are the only forest habitat of substantial area. Carabids were caught with pitfall traps in native kanuka (Kunzea ericoides) forest remnants and in a neighbouring pine plantation, grassland and gorse (Ulex europaeus) shrubland. A total of 2,700 individuals were caught, with significantly greater abundance in traps in young pine, grassland and gorse habitats than in kanuka and older pine. Rarefied species richness was greatest in kanuka, a habitat that supported two forest specialist species not present in other habitat types. A critically endangered species was found only in the exotic plantation forest, which also acts as a surrogate habitat for most carabids associated with kanuka forest. The few remaining native forest patches are of critical importance to conservation on the Canterbury Plains, but in the absence of larger native forest areas plantation forests are more valuable for carabid conservation than the exotic grassland that dominates the region.

Field of study: Environmental science
The cloning of a rat peptidoglycan recognition protein (PGRP) and its induction in brain by sleep deprivation.

Peptidoglycan recognition protein (PGRP) binds to peptidoglycan (PG) or live bacteria and is upregulated by PG. PGRP is a ubiquitous protein involved in innate immunity. Tag7, a novel cytokine, is also induced by bacterial products; tag7 is apoptotic to murine L929 cells in a NF-kappaB-independent manner. Both of these genes are expressed in brain, lymphatic and haematopoietic tissues. We provide evidence that murine PGRP and tag7 encode identical transcripts and have structural relationships to lysozymes. Further, we have cloned the cDNA of rat PGRP and analyzed its expression in brains of sleep-deprived and control rats. The mRNA levels of PGRP/tag7 were measured by RT-PCR and compared to the housekeeping gene porphobilinogen deaminase (PBD). PGRP was constitutively expressed in rat brain. PGRP mRNA was increased by 43% and 17% in the brainstem and hypothalamus, respectively, in sleep-deprived rats compared to controls. The upregulation of PGRP expression by sleep deprivation suggests a role for PGRP in a homeostatic regulation of sleep.

Field of study: Medicine
Adiponectin is required for enhancement of CCL2 expression in adipose tissue during Listeria monocytogenes infection.

Obesity is an important background of metabolic syndrome progression. Our previous study demonstrated that chemokine CCL2 expression was suppressed in liver of obese mice that were highly susceptible to Listeria monocytogenes infection. We investigated the role of adiponectin in CCL2 expression in obese mice after L. monocytogenes infection. When leptin-deficient obese ob/ob mice were infected intraperitoneally with L. monocytogenes, the elimination of bacteria from spleen, liver, mesenteric lymph nodes and adipose tissue was inhibited in ob/ob mice compared with their heterozygote littermates, ob/? mice. CCL2 expression in the adipose tissue of ob/? mice was enhanced by L. monocytogenes infection, different from ob/ob mice. Similarly, adiponectin expression was not observed in the adipose tissue of ob/ob mice. When mouse adipocyte 3T3-F442A-derived adipocytes were infected with L. monocytogenes, CCL2 expression was transiently up-regulated, following up-regulation of adiponectin expression. Up-regulation of CCL2 in adipocytes by L. monocytogenes infection was suppressed by knocked-down of adiponectin expression and supplementation of recombinant adiponectin partially recovered CCL2 expression. These results suggest that adiponectin is required for appropriate expression of CCL2 that is important for macrophage recruitment in response to bacterial infection.

Field of study: Medicine
Production and loss of N2+, Ne+ and Ne2+ during the decay period of plasmas produced in neon-nitrogen mixtures

Studies of the time dependencies of the number density of N2+, Ne+ and Ne2+ ions have been made during the decay period of plasmas produced in neon containing various concentrations of nitrogen molecules. Reaction rate constants were obtained for N2++N2+Ne→N4++Ne((1.2±0.2)×10−29 cm6 sec−1) and Ne++N2→N2++ Ne ((2.9±0.3) × 10−12 cm3 sec−1). The ambipolar diffusion coefficient of N2+ in neon was found to beDapo=350±20 cm2 sec−1 Torr.

Field of study: Physics
Effect of substrate temperature on the properties of LiNbO3 nanocrystalline films during pulsed laser deposition

The results are presented from studying the effect substrate temperature has on the morphological, electrophysical, and optical parameters of LiNbO3 films obtained via pulsed laser deposition. It is established that films formed at temperatures of 300 to 600°C have a nanocrystalline structure with crystallites predominantly oriented in planes (110), (1010), and (220). The refractive index of the obtained films in the wavelength range of 500–800 nm varies from 2.13 to 2.26.

Field of study: Physics
ST. PAUL GROUP: A REVISION OF THE “STONES RIVER” GROUP OF MARYLAND AND ADJACENT STATES

The “Stones River” group of Maryland and adjacent States has been studied in light of recent classifications of the Middle Ordovician. The term St. Paul group (new), proposed as a substitute for the erroneously applied “Stones River” group, contains two formations, a lower, Row Park limestone (new), and the overlying New Market limestone. The Row Park limestone forms a wedge whose thin edge lies in West Virginia, thickening to an observable maximum in southern Pennsylvania. The formation includes dark, granular limestone bordering dove vaughanites on the south, east, and north. The New Market limestone was traced from Virginia, through West Virginia and Maryland, to southern Pennsylvania; it thickens in Maryland and southern Pennsylvania at the same rate and in the same direction as the Row Park limestone. The New Market is primarily dove vaughanite in southern areas, but considerable amounts of darker and magnesian limestones form the lower part of the formation north of the Potomac River.

The Row Park limestone fauna suggests correlation with type Lenoir limestone of northeastern Tennessee, and its equivalents in Virginia, and with the Chazy limestone of New York.

Corals dominate the fauna of the New Market; this fauna suggests correlation with the Pamelia limestone of New York and Ontario and with the Five Oaks limestone of the southern Appalachians.

Field of study: Geology