bluuebunny/crossref_metadata_2025_split huggingface dataset:
The contribution of ancient admixture to reproductive isolation between European sea bass lineages
Authors: Duranton Maud , Allal François , Valière Sophie , Bouchez Olivier , Bonhomme François , Gagnaire Pierre-Alexandre 
Published: April 2020

AbstractUnderstanding how new species arise through the progressive establishment of reproductive isolation (RI) barriers between diverging populations is a major goal in Evolutionary Biology. An important result of speciation genomics studies is that genomic regions involved in RI frequently harbor anciently diverged haplotypes that predate the reconstructed history of species divergence. The possible origins of these old alleles remain much debated, as they relate to contrasting mechanisms of speciation that are not yet fully understood. In the European sea bass (Dicentrarchus labrax), the genomic regions involved in RI between Atlantic and Mediterranean lineages are enriched for anciently diverged alleles of unknown origin. Here, we used haplotype-resolved whole-genome sequences to test whether divergent haplotypes could have originated from a closely related species, the spotted sea bass (Dicentrarchus punctatus). We found that an ancient admixture event between D. labrax and D. punctatus is responsible for the presence of shared derived alleles that segregate at low frequencies in both lineages of D. labrax. An exception to this was found within regions involved in RI between the two D. labrax lineages. In those regions, archaic tracts originating from D. punctatus locally reached high frequencies or even fixation in Atlantic genomes but were almost absent in the Mediterranean. We showed that the ancient admixture event most likely occurred between D. punctatus and the D. labrax Atlantic lineage, while Atlantic and Mediterranean D. labrax lineages were experiencing allopatric isolation. Our results suggest that local adaptive introgression and/or the resolution of genomic conflicts provoked by ancient admixture have probably contributed to the establishment of RI between the two D. labrax lineages.
Wide‐scale evaluation of Origanum munzurense Kit Tan & Sorger using different extraction techniques: Antioxidant capacity, chemical compounds, trace element content, total phenolic content, antibacterial activity and genotoxic effect
Authors: Yabalak Erdal , Emire Zuhal , Adıgüzel Ali Osman , Könen Adıgüzel Serpil , Gizir A. Murat 
Published: April 2020

AbstractThis aim of this work was to investigate the various properties of Origanum munzurense Kit Tan & Sorger that are previously unknown. In this context, chemical compound, antioxidant activity, total polyphenol content, mineral and trace element composition, antibacterial activity and genotoxicity effects of its extracts and essential oil were widely analysed. The extracts and essential oil of Origanum munzurense were obtained by three different extraction methods. All contents of extracts and essential oil were analysed by GC‐MS and evaluated according to mass spectral libraries of GC‐MS. The identified compounds were evaluated according to literature to put forward their benefits on human health. The phenolic content analysis of Origanum munzurense was performed using the Folin‐Ciocalteu method. 178.59, 184.20, 231.17, 319.28 and 1051.94 mg GAE/100 g dry weight were determined for methanol, water, acetonitrile, ethanol and subcritical water extracts, respectively. DPPH and CUPRAC methods were used to determine antioxidant activity. The highest half‐maximal inhibitory concentration and Trolox equivalent antioxidant capacity values were found as 0.110 mg mL−1 and 2.197 using water and tetrahydrofuran extracts, respectively. A total of 21 mineral and trace elements were detected in the ICP‐MS analysis of O munzurense using the wet digestion procedure. The effects of the extracts and essential oil on Klebsiella pneumoniae, Escherichia coli, Pseudomonas aeruginosa and S aureus were examined using disc diffusion and microdilution methods. Essential oil exhibited the highest antibacterial activity. The essential oil was found to cause less DNA damage using the comet assay in Hep G2 cells compared with tetrahydrofuran extract.
Optimal futures hedging for energy commodities: An application of the GAS model
Authors: Xu Yingying , Lien Donald 
Published: April 2020

AbstractThis paper applies generalized autoregressive score‐driven (GAS) models to futures hedging of crude oil and natural gas. For both commodities, the GAS framework captures the marginal distributions of spot and futures returns and corresponding dynamic copula correlations. We compare within‐sample and out‐of‐sample hedging effectiveness of GAS models against constant ordinary least square (OLS) strategy and time‐varying copula‐based GARCH models in terms of volatility reduction and Value at Risk reduction. We show that the constant OLS hedge ratio is not inherently inferior to the time‐varying alternatives. Nonetheless, GAS models tend to exhibit better hedging effectiveness than other strategies, particularly for natural gas.
Redating the formation of Lake Bafa, western Turkey: Integrative geoarchaeological methods and new environmental and dating evidence
Authors: Akçer‐Ön Sena , Greaves Alan M. , Manning Sturt W. , Ön Z. Bora , Çağatay M. Namık , Sakınç Mehmet , Oflaz Aslı , Tunoğlu Cemal , Salihoğlu Rana 
Published: April 2020

AbstractThe ancient Gulf of Latmos is an iconic example of a dynamic landscape and humankind's historical relationship with it. Using extensive new primary data and original models for calibrating radiocarbon dates in transitional lagoon environments, we demonstrate that Lake Bafa (or Bafa Gölü, in Turkish) formed at a much earlier date than previously thought. In questioning the logical process by which previous dates were achieved, we re‐examine the relationship between sedimentological data, archaeology and written history. We reassert the need to establish independently dated environmental data sets as the foundation of regional studies as distinct from archaeological and historical interpretive processes. We conclude that Lake Bafa slowly transitioned to become an isolated lagoon sometime between the end of the second millennium B.C. and end of the first millennium B.C.; becoming a fully closed brackish lake during the second millennium A.D. This marks a major shift in our understanding of the nature of human occupation and activity here during the last four millennia but also in the way we date ancient lagoons and integrate historical and environmental data in general.
Letting the stones speak: An interdisciplinary survey of stone collection and construction at Liangzhu City, prehistoric Lower Yangtze River
Authors: Wang Ningyuan , Dong Chuanwan , Xu Honggen , Zhuang Yijie 
Published: April 2020

AbstractOur interdisciplinary investigation of the stone collection and construction process of Liangzhu City walls offers important evidence to understand the engineering and organization behind the construction. We examined spatial distributions, physical and petrological characteristics of the stones discovered from our excavations of representative wall sections. These results were compared with similar aspects as well as sedimentation contexts and availability of the surveyed stones from the surrounding regions to identify the source areas for the stone collection. We developed criteria based on physical and petrological characteristics and spatial distribution of stones for the identification of construction units and estimated the volume of stones for each unit. We concluded that even though the overall scale of stonework construction was enormous, the actual tasks of stone collection and construction were likely completed by small individual working groups. Liangzhu workers preferred to collect directly available, hand‐portable stones from source areas. However, some areas with suitable stone sources were neglected by Liangzhu workers. The total workforce may have followed a central organization, and many groups likely worked simultaneously. Through the repeated efforts of numerous small working groups, Liangzhu society constructed a massive, multicomponent infrastructure. Our study holds implications for wider archaeological research of ancient stone architecture.
Milk Fat Globule–Epidermal Growth Factor–Factor 8 Improves Hepatic Steatosis and Inflammation
Authors: Zhang Lei , Tian Ruifeng , Yao Xinxin , Zhang Xiao‐Jing , Zhang Peng , Huang Yongping , She Zhi‐Gang , Li Hongliang , Ji Yan‐Xiao , Cai Jingjing 
Published: April 2020

Background and Aims
Milk fat globule–epidermal growth factor–factor 8 (MFGE8) has been shown to be a critical extracellular molecule that mediates apoptotic signaling in the pathological process of nonalcoholic fatty liver disease (NAFLD). MFGE8 is abundantly expressed in hepatocytes, but its function in the pathogenesis of NAFLD has not been characterized.

Approach and Results
In our current study, hepatic MFGE8 showed a protective role in the pathogenesis of NAFLD. Hepatic MFGE8 deletion largely exacerbated lipid accumulation and inflammatory responses in the liver in response to overnutrition. Mechanistically, intercellular MFGE8 was shown to directly bind to apoptosis signal‐regulating kinase 1 (ASK1) and to inhibit its dimerization and phosphorylation under a normal diet. However, under metabolic challenges, decreased cytoplasmic MFGE8 facilitated the dimerization and phosphorylation of ASK1 and subsequent mitogen‐activated protein kinase signaling in hepatocytes.

Conclusions
Hepatic MFGE8 is an endogenous inhibitor that halts the progression of hepatic steatosis and inflammation. Metabolic challenge–induced loss of intracellular MFGE8 facilitates ASK1 dimerization and phosphorylation. Therefore, maintaining hepatic MFGE8 levels may serve as an alternative strategy for the treatment of NAFLD.
PPARγ Coactivator‐1α Suppresses Metastasis of Hepatocellular Carcinoma by Inhibiting Warburg Effect by PPARγ–Dependent WNT/β‐Catenin/Pyruvate Dehydrogenase Kinase Isozyme 1 Axis
Authors: Zuo Qiaozhu , He Jia , Zhang Shu , Wang Hui , Jin Guangzhi , Jin Haojie , Cheng Zhuoan , Tao Xuemei , Yu Chengtao , Li Botai , Yang Chen , Wang Siying , Lv Yuanyuan , Zhao Fangyu , Yao Ming , Cong Wenming , Wang Cun , Qin Wenxin 
Published: April 2020

Background and Aims
Peroxisome proliferator‐activated receptor‐gamma (PPARγ) coactivator‐1α (PGC1α) is a key regulator of mitochondrial biogenesis and respiration. PGC1α is involved in the carcinogenesis, progression, and metabolic state of cancer. However, its role in the progression of hepatocellular carcinoma (HCC) remains unclear.

Approach and Results
In this study, we observed that PGC1α was down‐regulated in human HCC. A clinical study showed that low levels of PGC1α expression were correlated with poor survival, vascular invasion, and larger tumor size. PGC1α inhibited the migration and invasion of HCC cells with both in vitro experiments and in vivo mouse models. Mechanistically, PGC1α suppressed the Warburg effect through down‐regulation of pyruvate dehydrogenase kinase isozyme 1 (PDK1) mediated by the WNT/β‐catenin pathway, and inhibition of the WNT/β‐catenin pathway was induced by activation of PPARγ.

Conclusions
Low levels of PGC1α expression indicate a poor prognosis for HCC patients. PGC1α suppresses HCC metastasis by inhibiting aerobic glycolysis through regulating the WNT/β‐catenin/PDK1 axis, which depends on PPARγ. PGC1α is a potential factor for predicting prognosis and a therapeutic target for HCC patients.
Double hybrid DFT calculations with Slater type orbitals
Authors: Förster Arno , Visscher Lucas 
Published: April 2020

AbstractOn a comprehensive database with 1,644 datapoints, covering several aspects of main‐group as well as of transition metal chemistry, we assess the performance of 60 density functional approximations (DFA), among them 36 double hybrids (DH). All calculations are performed using a Slater type orbital (STO) basis set of triple‐ζ (TZ) quality and the highly efficient pair atomic resolution of the identity approach for the exchange‐ and Coulomb‐term of the KS matrix (PARI‐K and PARI‐J, respectively) and for the evaluation of the MP2 energy correction (PARI‐MP2). Employing the quadratic scaling SOS‐AO‐PARI‐MP2 algorithm, DHs based on the spin‐opposite‐scaled (SOS) MP2 approximation are benchmarked against a database of large molecules. We evaluate the accuracy of STO/PARI calculations for B3LYP as well as for the DH B2GP‐PLYP and show that the combined basis set and PARI‐error is comparable to the one obtained using the well‐known def2‐TZVPP Gaussian‐type basis set in conjunction with global density fitting. While quadruple‐ζ (QZ) calculations are currently not feasible for PARI‐MP2 due to numerical issues, we show that, on the TZ level, Jacob's ladder for classifying DFAs is reproduced. However, while the best DHs are more accurate than the best hybrids, the improvements are less pronounced than the ones commonly found on the QZ level. For conformers of organic molecules and noncovalent interactions where very high accuracy is required for qualitatively correct results, DHs provide only small improvements over hybrids, while they still excel in thermochemistry, kinetics, transition metal chemistry and the description of strained organic systems.
Thermal sensitivity of lizard embryos indicates a mismatch between oxygen supply and demand at near‐lethal temperatures
Authors: Hall Joshua M. , Warner Daniel A. 
Published: April 2020

AbstractAspects of global change create stressful thermal environments that threaten biodiversity. Oviparous, non‐avian reptiles have received considerable attention because eggs are left to develop under prevailing conditions, leaving developing embryos vulnerable to increases in temperature. Though many studies assess embryo responses to long‐term (i.e., chronic), constant incubation temperatures, few assess responses to acute exposures which are more relevant for many species. We subjected brown anole (Anolis sagrei) eggs to heat shocks, thermal ramps, and extreme diurnal fluctuations to determine the lethal temperature of embryos, measure the thermal sensitivity of embryo heart rate and metabolism, and quantify the effects of sublethal but stressful temperatures on development and hatchling phenotypes and survival. Most embryos died at heat shocks of 45°C or 46°C, which is ~12°C warmer than the highest constant temperatures suitable for successful development. Heart rate and O2 consumption increased with temperature; however, as embryos approached the lethal temperature, heart rate and CO2 production continued rising while O2 consumption plateaued. These data indicate a mismatch between oxygen supply and demand at high temperatures. Exposure to extreme, diurnal fluctuations depressed embryo developmental rates and heart rates, and resulted in hatchlings with smaller body size, reduced growth rates, and lower survival in the laboratory. Thus, even brief exposure to extreme temperatures can have important effects on embryo development, and our study highlights the role of both immediate and cumulative effects of high temperatures on egg survival. Such effects must be considered to predict how populations will respond to global change.
Combined nitrogen input from legume residues and fertilizer improves early nitrogen supply and uptake by wheat
Authors: Muschietti-Piana Pilar , McBeath Therese M. , McNeill Ann M. , Cipriotti Pablo A. , Gupta Vadakattu V. S. R. 
Published: April 2020

AbstractSoil nitrogen (N) supply for wheat N uptake can be manipulated through legume and fertilizer N inputs to achieve yield potential in low‐rainfall sandy soil environments. Field experiments over 2 years (2015–2016) were conducted at 2 different sites in a low‐rainfall sandy soil to determine the soil N supply capacity relative to wheat N uptake at key growth stages, after a combination of crop residue (removed, wheat or lupin) and fertilizer N (nil, low or high N) treatments were manipulated to improve wheat yield. We measured the temporal patterns of the soil profile mineral N and PAW to 100 cm depth, wheat aerial biomass and N uptake in both years. In 2016 we also measured the disease incidence as a key environmental variable. There was 35 kg ha−1 more soil mineral N to 100 cm depth following lupin than wheat residues at the end of the fallow on average in both years. In a below average rainfall season, wheat biomass produced on lupin residues was responsive to N input with soil profile mineral N depleted by increased crop N uptake early in the season. In an above average rainfall season, a higher soil mineral N supply increased actual and potential grain yield, total biomass, N uptake, harvest index and water use efficiency of wheat, regardless of the source of N. Our study showed that the combination of lupin residues with high N rate increased soil profile mineral N at early growth stages, providing a greater soil N supply at the time of high wheat N demand, and the inclusion of a legume in the rotation is critical for improving the N supply to wheat, with added disease break benefits in a low‐rainfall sandy soil environment.
Influences of high‐molecular‐weight glutenin subunits and rye translocations on dough‐mixing properties and sugar‐snap cookie‐baking quality of soft winter wheat
Authors: Ma Fengyun , Kim Jieun , Baik Byung‐Kee 
Published: April 2020

AbstractBACKGROUNDThe significance of high‐molecular‐weight glutenin subunits (HMW‐GSs) and rye translocations, and their associations with gluten strength for hard wheat used for making bread has been understood well, but remains poorly understood for soft wheat used for making cookies. The influences of HMW‐GSs and rye translocations on the dough‐mixing properties and cookie‐baking quality of soft wheat were investigated using 50 US eastern soft winter (ESW) wheat varieties possessing 14 predominant HMW‐GS profiles.RESULTSGlu‐A1 and Glu‐B1 loci only influenced dough‐mixing properties significantly, whereas the Glu‐D1 locus influenced both dough‐mixing properties and cookie‐baking quality significantly. The subunits 1, 7* + 8 and 5 + 10 at the Glu‐A1, Glu‐B1 and Glu‐D1 loci, respectively, were associated with a long midline peak time, whereas only the rare subunits 2 + 121 at the Glu‐D1 locus exhibited significant associations with improved cookie‐baking quality of ESW wheat. The contributions of rye translocations to dough‐mixing properties and cookie‐baking quality depended on HMW‐GS profiles. Three HMW‐GS profiles (2*, 7 + 9, 2 + 121), (2*, 7 + 8, 2 + 121) and (1, 7 + 8, 2 + 121) were identified as being desirable for making large‐diameter cookies. Flour protein content, lactic acid (LA), and sodium carbonate (SC) solvent retention capacities and softness equivalence were identified as effective predictors of cookie diameter and accounted for 79% of the variation in cookie diameter.CONCLUSIONSubunits 2 + 121 have significant associations with the protein characteristics and cookie‐baking quality of soft wheat. The determination of HMW‐GS composition would be an effective tool in soft‐wheat breeding programs for quickly identifying and selecting acceptable breeding lines possessing desirable cookie‐baking potential. Published 2020. This article is a U.S. Government work and is in the public domain in the USA.
Strong Interface Construction of Carbon Fiber–reinforced PEEK Composites: An Efficient Method for Modifying Carbon Fiber with Crystalline PEEK
Authors: Yang Yanchao , Wang Tianjiao , Wang Shengdao , Cong Xin , Zhang Shuling , Zhang Mei , Luan Jiashuang , Wang Guibin 
Published: April 2020

AbstractIn order to improve the poor solvent resistance and poor temperature resistance caused by traditional sizing agents, crystalline poly(ether ether ketone) (PEEK) is introduced to the interfacial phases of carbon fiber (CF) reinforced PEEK composites by a soluble precursor named PEEK‐1,3‐dioxolane. By changing the soluble precursor molecular weight and concentration in the sizing solution, the content of PEEK coated on the CF fiber surface can be controlled and the different interfacial properties of the PEEK composites can be obtained. The results shows that, with this method, crystalline PEEK can be completely coated on the CF surface, and the interfacial shear strength of the PEEK composites increases from 43.42 to 83.13 MPa. Due to none of any soluble compounds in the PEEK composites, the interfacial layer is well preserved under organic solvents and hygrothermal conditions, and the interfacial shear strength (IFSS) of the PEEK composites maintained above 85.4% and 90.44%, respectively. Scanning electron microscope clarifies that the mechanism of interface enhancement comes from a better wetting of crystalline PEEK on the fiber surface. Additionally, the sizing system of this investagation has the potential commercial value because of no toxic reagent (such as 2,4,5‐trichloro‐1‐hydroxy‐benzene or concentrated sulfuric acid) is required during sizing.
Optically stimulated luminescent dosimeters stable response to dose after repeated bleaching
Authors: Jursinic Paul A. 
Published: April 2020

PurposeTo investigate the dose response of optically stimulated luminescent dosimeters (OSLDs), and how this response changes with repeated use, increased accumulated dose, and bleaching light with or without a UV component. To devise a method to stabilize dose response characteristics of OSLDs that are used repeatedly. To decrease measurement uncertainty.MethodsOptically stimulated luminescent dosimeters irradiations were made using a linear accelerator and Ir‐192. The OSLDs (InLight nanoDots) dose response was characterized for these various irradiations under the batch, single use, method and the repeated irradiation method. Some nanoDots were preirradiated with hundreds of Gray of dose with Ir‐192 gamma rays. Repeated use OSLDs were bleached with lights that had different UV content. A special bleaching light was fabricated and used that had the same spectrum as the light in the OSLD reader.ResultsNew, never irradiated, nanoDots had their characteristics altered by illumination with bleaching light that had a UV component. Each new nanoDot had unique sensitivity to dose as well as a unique linearity factor, which was supra‐linear. NanoDots that were irradiated and bleached repeatedly had changes in low and high dose sensitivity that was altered if the bleaching light had UV in its spectrum. For nanoDots that have been preirradiated with up to 1500 Gy of dose, their dose response was supra‐linear for bleaching light without UV content and infra‐linear for light with UV content. Preirradiated nanoDots that were bleached with light without UV content had stable dose sensitivity (±1.5%), stable linearity factor (±3.5%) for over 10 bleaching cycles, nonlinear response that was quadratic in dose, and dose measurement uncertainty of ±1.4% for 277 measurements.ConclusionsThe UV component in bleaching light has an impact on the dose sensitivity characteristics shown by new or repeatedly irradiated nanoDots. Each new nanoDot has a unique sensitivity to dose as well as a unique linearity factor, which was supra‐linear. As nanoDots accumulate dose with repeated use they change sensitivity to low and high dose very differently based on the UV content of the bleaching light. For nanoDots that have been preirradiated with hundreds of Gray of dose their dose response was supra‐linear for bleaching light without UV content and infra‐linear for light that has UV content. NanoDots can be used repeatedly and have stable dose response characteristics if they are preirradiated and bleached with light without UV content. Dose can be measured with an uncertainty of 1.4%, which is a threefold reduction of the uncertainty found with the single use batch method recommended by the manufacturer.