bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prevalence of isomeric plastomes and effectiveness of plastome super-barcodes in yews (Taxus) worldwide
Authors: Fu Chao-Nan , Wu Chung-Shien , Ye Lin-Jiang , Mo Zhi-Qiong , Liu Jie , Chang Yu-Wen , Li De-Zhu , Chaw Shu-Miaw , Gao Lian-Ming 
Published: February 2019

AbstractTaxus (yew) is both the most species-rich and taxonomically difficult genus in Taxaceae. To date, no study has elucidated the complexities of the plastid genome (plastome) or examined the possibility of whole plastomes as super-barcodes across yew species worldwide. In this study, we sequenced plastomes from two to three individuals for each of the 16 recognized yew species (including three potential cryptics) and Pseudotaxus chienii. Our comparative analyses uncovered several gene loss events that independently occurred in yews, resulting in a lower plastid gene number than other Taxaceous genera. In Pseudotaxus and Taxus, we found two isomeric arrangements that differ by the orientation of a 35 kb fragment flanked by “trnQ-IRs”. These two arrangements exist in different ratios within each sampled individual, and intraspecific shifts in major isomeric arrangements are first reported here in Taxus. Moreover, we demonstrate that entire plastomes can be used to successfully discriminate all Taxus species with 100% support, suggesting that they are useful as super-barcodes for species identification. We also propose that accD and rrn16-rrn23 are promising special barcodes to discriminate yew species. Our newly developed Taxus plastomic sequences provide a resource for super-barcodes and conservation genetics of several endangered yews and serve as comprehensive data to improve models of plastome complexity in Taxaceae as a whole and authenticate Taxus species.
Analytic framework for understanding the competing multiple light scattering processes
Authors: Lee Ye-Ryoung , Choi Wonjun , Jeong Seungwon , Choi Wonshik 
Published: February 2019

AbstractIn many complex physical phenomena such as wave propagation in scattering media, the process of interest often cannot be easily distinguished from other processes because only the total combined process is accessible. This makes it difficult to extract the precise knowledge of each subprocess. Here, we derive an analytic expression describing the way the eigenchannel coupling of the total process distributes its energy to the individual subprocesses, with only partial information on each subprocess such as the average eigenvalue 〈τ〉 and enhancement factor η. We found that the ratio of (η − 1)〈τ〉 between two subprocesses is a critical parameter determining the preferable subprocess in the energy coupling. This work provides a new analytic framework for understanding the effect of wavefront shaping in the control of wave propagation in disordered media.
Repeated neonatal isoflurane exposures in the mouse induce apoptotic degenerative changes in the brain and relatively mild long-term behavioral deficits
Authors: Maloney Susan E. , Yuede Carla M. , Creeley Catherine E. , Williams Sasha L. , Huffman Jacob N. , Taylor George T. , Noguchi Kevin N. , Wozniak David F. 
Published: February 2019

AbstractEpidemiological studies suggest exposures to anesthetic agents and/or sedative drugs (AASDs) in children under three years old, or pregnant women during the third trimester, may adversely affect brain development. Evidence suggests lengthy or repeated AASD exposures are associated with increased risk of neurobehavioral deficits. Animal models have been valuable in determining the type of acute damage in the developing brain induced by AASD exposures, as well as in elucidating long-term functional consequences. Few studies examining very early exposure to AASDs suggest this may be a critical period for inducing long-term functional consequences, but the impact of repeated exposures at these ages has not yet been assessed. To address this, we exposed mouse pups to a prototypical general anesthetic, isoflurane (ISO, 1.5% for 3 hr), at three early postnatal ages (P3, P5 and P7). We quantified the acute neuroapoptotic response to a single versus repeated exposure, and found age- and brain region-specific effects. We also found that repeated early exposures to ISO induced subtle, sex-specific disruptions to activity levels, motor coordination, anxiety-related behavior and social preference. Our findings provide evidence that repeated ISO exposures may induce behavioral disturbances that are subtle in nature following early repeated exposures to a single AASD.
Quantitative hydro-geophysical analysis of a complex structural karst aquifer in Eastern Saudi Arabia
Authors: Alfy Mohamed El , Lashin Aref , Faraj Turki , Alataway Abed , Tarawneh Qassem , Al-Bassam Abdelaziz 
Published: February 2019

AbstractThe Umm er Radhuma (UER) Formation is a major karst aquifer in Saudi Arabia. This study investigated the hydraulic and petrophysical characteristics of the folded UER carbonate aquifer using integrated hydrological and geophysical logging datasets to understand its complex hydraulic setting as well as detect possible water flow. Petrophysical analysis showed that the UER aquifer has three zones with different lithologic and hydraulic properties. The upper zone attains the best properties with average values of 20%, >100 mD, 3.30 × 10−5–1.34 × 10−3 m/s, and 1.49 × 10−3–6.04 × 10−2 m2/s, with respect to effective porosity, permeability, hydraulic conductivity and transmissivity. The gamma-ray logs indicate a good fracture system near the upper zone of the UER Formation. Pumping test measurements of transmissivity, hydraulic conductivity and storage coefficients were matched with those from geophysical logs and found to be within the expected range for confined and leaky aquifers. Hydrogeological properties were mapped to detect possible groundwater flow in relation to the dominant structure. The underground water of the folded UER aquifer was forced along meandering flow patterns from W-E to SW-NE through the anticlinal axes. The integrated approach can be further used to enhance local aquifer models and improve strategies for identifying the most productive zones in similar aquifer systems.
A complex interaction between pre-harvest and post-harvest factors determines fresh-cut melon quality and aroma
Authors: Spadafora Natasha D. , Cocetta Giacomo , Cavaiuolo Marina , Bulgari Roberta , Dhorajiwala Rakhee , Ferrante Antonio , Spinardi Anna , Rogers Hilary J. , Müller Carsten T. 
Published: February 2019

AbstractMelons are prized for their characteristic aroma, however, pre-harvest growth, stage of ripening at harvest, post-harvest processing and storage conditions lead to quality changes in fresh-cut fruit. We considered changes in metabolites and gene expression over 14 days storage to assess underlying mechanisms and identify potential quality markers. Overall, 99 volatile organic compounds (VOCs) were detected and VOC profiles discriminated between two melon seasons, cut-size, storage temperatures and storage time, although season affected their discriminatory power. Abundance of two VOCs fell rapidly and was not associated with cut size, indicating their use as markers for early changes post-processing. Non-acetate to acetate ester ratio differed between the seasons and correlated with changes in alcohol acyl-transferase (CmAAT1) gene expression. Furthermore, CmAAT1 expression clustered with two ester VOCs that may be potential new products of this enzyme. Season also strongly affected post-harvest sugar content, most likely attributable to meteorological differences during growth. Storage temperature and cut size affected expression of transcription factors ERF71, ERF106, and TINY, whose expression generally rose during storage, probably related to increased stress. Thus, although time × temperature of storage are key factors, pre-harvest conditions and fruit processing impact significantly gene expression and aroma loss post-harvest.
Survival, growth and physiology of marine bivalve (Sinonovacula constricta) in long-term low-salt culture
Authors: Maoxiao Peng , Xiaojun Liu , Donghong Niu , Bo Ye , Tianyi Lan , Zhiguo Dong , Jiale Li 
Published: February 2019

AbstractIn this study, we investigated the possibility of rearing and breeding the razor clam (Sinonovacula constricta) in inland low salinity water or freshwater. Long-term low salinity (LS) rearing was performed for 3 months to determine the effects of LS on the survival rate, growth rate, and the activities of critical enzymes in juvenile S. constricta (JSC). The survival rate in the LS group was only 15.67% at the end of the LS rearing test. In the first month, the survival rate in the LS group was significantly lower than that in the control group (P < 0.001). The growth rate (shell length growth rate and weight gain rate) was significantly lower in the LS group than the control group in the first month (P < 0.001 for length and weight). However, the growth rates in the two groups differed little during the second and third months. The oxygen consumption and ammonia excretion rates by JSCs were significantly higher in the LS group than the control group during the first month, but they decreased gradually during the following 2 months. The Na+/K+ ATPase and superoxide dismutase activities were significantly higher in the LS group than the control group during the first month, but they then decreased gradually until there were no significant differences between the groups. However, the aspartate aminotransferase activity was higher in the LS group than the control group during all 3 months. Most of the JSCs died due to LS but the survival of some JSCs suggests the possibility of breeding LS resistant or freshwater S. constricta.
Quasiparticle Properties under Interactions in Weyl and Nodal Line Semimetals
Authors: Kang Jing , Zou Jianfei , Li Kai , Yu Shun-Li , Shao Lu-Bing 
Published: February 2019

AbstractThe quasiparticle spectra of interacting Weyl and nodal-line semimetals on a cubic lattice are studied using the cluster perturbation theory. By tracking the spectral functions under interaction, we find that the Weyl points will move to and meet at a specific point in one Weyl semimetal model, while in the other Weyl semimetal model they are immobile. In the nodal-line semimetals, we find that the nodal line shrinks to a point and then disappears under interaction in one-nodal-line system. When we add another nodal line to this system, we find that the two nodal lines both shrink to specific points, but the disappearing processes of the two nodal lines are not synchronized. We argue that the nontrivial evolution of Weyl points and nodal lines under interaction is due to the presence of symmetry breaking order, e.g., a ferromagnetic moment, in the framework of mean field theory, whereas the stability of Weyl points under interaction is protected by symmetry. Among all these models, the spectral gap is finally opened when the interaction is strong enough.
Facile Surface Modification of Polyethylene Film via Spray-Assisted Layer-by-Layer Self-Assembly of Graphene Oxide for Oxygen Barrier Properties
Authors: Heo Jiwoong , Choi Moonhyun , Hong Jinkee 
Published: February 2019

AbstractThe oxygen barrier properties are essential for the food packaging systems that preserve perishable food. In this research, the facile surface modification method for oxygen barrier properties is introduced by using spray assisted layer-by-layer (LbL) self-assembly. The nano-sized graphene oxide (GO−) multilayer films were developed and characterized. Positively charged amine-functionalized GO+ was synthesized using the negatively charged GO− dispersion, ethylenediamine, and 1-(3-dimethylaminopropyl)-3-ethylcarbodiimide methiodide (EDC). Alternating layers of GO− and GO+ were deposited onto the flexible polyethylene (PE) substrate which has no intrinsic gas barrier properties. This method is able to modify surfaces which are challenging for the conventional dipping LbL method. The oxygen transmittance rate of coated PE film (3511.5 cc/m2·day) decreased significantly to 1091 cc/m2·day after a GO film with a thickness of only 60 nm was deposited. The light transmittance in the visible light range was not significantly decreased after coating of GO films, thus ensuring transparency for PE packaging applications.
Phylogeography of plastid DNA sequences suggests post-glacial southward demographic expansion and the existence of several glacial refugia for Araucaria angustifolia
Authors: Stefenon Valdir Marcos , Klabunde Gustavo , Lemos Rafael Plá Matielo , Rogalski Marcelo , Nodari Rubens Onofre 
Published: February 2019

AbstractDespite the high diversity of the Southern South American environments, the patterns and processes driving both their species diversity and demographic history are still poorly known and are a challenging task. In this study, we evaluate plastid DNA sequences of the conifer species Araucaria angustifolia aiming to (i) assess the species genetic structure within its main range of occurrence, (ii) infer its population demographic history, looking for evidence of southward expansion, (iii) search for evidence of glacial refugia within the species distribution area and (iv) discuss some conservation and management strategies for this species. Twenty haplotypes were identified, revealing the presence of three distinct genetic groups across the geographic range of the species and structuring the populations into Northern, Central and Southern groups. Our results suggest the occurrence of post-glacial expansion of A. angustifolia towards the south, as well as the existence of at least three refugia within the species occurrence area. Testing the occurrence of historical demographic expansion, we suggest that genetic groups experienced fluctuations in effective size, associated to a structured distribution of populations. The identification of three genetic groups in this study corroborates the proposition of using the geographic distribution of A. angustifolia for selecting in situ conservation areas, for planning seed collection for ex situ conservation, as well as for the delineation of seed zones.
Microstructural damage sensitivity prediction using spatial statistics
Authors: Cameron B. C. , Tasan C. C. 
Published: February 2019

AbstractThe vast compositional space of metallic materials provides ample opportunity to design stronger, more ductile and cheaper alloys. However, the substantial complexity of deformation micro-mechanisms makes simulation-based prediction of microstructural performance exceedingly difficult. In absence of predictive tools, tedious experiments have to be conducted to screen properties. Here, we develop a purely empirical model to forecast microstructural performance in advance, bypassing these challenges. This is achieved by combining in situ deformation experiments with a novel methodology that utilizes n-point statistics and principle component analysis to extract key microstructural features. We demonstrate this approach by predicting crack nucleation in a complex dual-phase steel, achieving substantial predictive ability (84.8% of microstructures predicted to crack, actually crack), a substantial improvement upon the alternate simulation-based approaches. This significant accuracy illustrates the utility of this alternate approach and opens the door to a wide range of alloy design tools.
Protective effect of oxytocin on LPS-induced acute lung injury in mice
Authors: An Xiaona , Sun Xiaotong , Hou Yonghao , Yang Xiaomei , Chen Hongli , Zhang Peng , Wu Jianbo 
Published: February 2019

AbstractOxytocin (OT), a neurohypophyseal hormone synthesized in the paraventricular and supraoptic nuclei of the hypothalamus, has been reported to have an anti- inflammatory effect. However, its role in acute lung injury (ALI) has never been investigated. The aim of this study was to explore the therapeutic effects and potential mechanism action of OT on lipopolysaccharide (LPS)-induced ALI. Mice were treated with OT 30 min before the intraperitoneal injection of LPS. After 2 h, the effects of OT on lung histopathological changes, lung wet/dry (W/D) ratio, myeloperoxidase (MPO) activity, levels of inflammatory cytokines in the bronchoalveolar lavage fluid (BALF), and expression of inflammation proteins were detected. The results showed that OT significantly reduced LPS-induced pathological injury, W/D ratio, MPO activity, and the levels of interleukin (IL)-1β, IL-18 and IL-6. Further, OT also inhibited LPS-induced Toll-like receptor 4 expression and NLR family pyrin domain containing 3 inflammasome activation. OT receptor antagonist (L-368,899) was given 90 min before injecting OT to further demonstrate the role of OT in LPS-induced ALI. The results showed OT could not alleviate the aforementioned inflammatory reactions after administering L-368,899. In conclusion, the present results indicated that OT could reduce inflammatory responses of LPS-induced ALI.
A novel mechanism for the protection of embryonic stem cell derived tenocytes from inflammatory cytokine interleukin 1 beta
Authors: McClellan Alyce , Evans Richard , Sze Cheryl , Kan Shohei , Paterson Yasmin , Guest Deborah 
Published: February 2019

AbstractInterleukin 1β (IL-1β) is upregulated following tendon injury. Here we demonstrate that in adult and fetal tenocytes IL-1β increases the expression of matrix metalloproteinases, tenascin-C and Sox9 and decreases the expression of scleraxis and cartilage oligomeric matrix protein. When cultured in 3-dimensional collagen gels adult and fetal tenocytes exposed to IL-1β have reduced contraction ability and generate tendon-like constructs with a lower storage modulus. In contrast, equine embryonic stem cell (ESC) derived tenocytes exposed to IL-1β exhibit no changes in gene expression and generate identical tendon-like constructs. We propose that ESC-derived tenocytes do not respond to IL-1β due to their low expression of interleukin 1 (IL-1) receptor 1 and high expression of the decoy receptor IL-1 receptor 2 and IL-1 receptor antagonist protein (IL1Ra). This may make ESC-derived tenocytes an advantageous source of cells for tissue regeneration and allow the development of novel pharmaceutical interventions to protect endogenous cells from inflammation.
Land carbon models underestimate the severity and duration of drought’s impact on plant productivity
Authors: Kolus Hannah R. , Huntzinger Deborah N. , Schwalm Christopher R. , Fisher Joshua B. , McKay Nicholas , Fang Yuanyuan , Michalak Anna M. , Schaefer Kevin , Wei Yaxing , Poulter Benjamin , Mao Jiafu , Parazoo Nicholas C. , Shi Xiaoying 
Published: February 2019

AbstractThe ability to accurately predict ecosystem drought response and recovery is necessary to produce reliable forecasts of land carbon uptake and future climate. Using a suite of models from the Multi-scale Synthesis and Terrestrial Model Intercomparison Project (MsTMIP), we assessed modeled net primary productivity (NPP) response to, and recovery from, drought events against a benchmark derived from tree ring observations between 1948 and 2008 across forested regions of the US and Europe. We find short lag times (0–6 months) between climate anomalies and modeled NPP response. Although models accurately simulate the direction of drought legacy effects (i.e. NPP decreases), projected effects are approximately four times shorter and four times weaker than observations suggest. This discrepancy between observed and simulated vegetation recovery from drought reveals a potential critical model deficiency. Since productivity is a crucial component of the land carbon balance, models that underestimate drought recovery time could overestimate predictions of future land carbon sink strength and, consequently, underestimate forecasts of atmospheric CO2.
Extensive epigenomic integration of the glucocorticoid response in primary human monocytes and in vitro derived macrophages
Authors: Wang Cheng , Nanni Luca , Novakovic Boris , Megchelenbrink Wout , Kuznetsova Tatyana , Stunnenberg Hendrik G. , Ceri Stefano , Logie Colin 
Published: February 2019

AbstractGlucocorticoid receptor is a transcription factor that is ubiquitously expressed. Glucocorticoids are circadian steroids that regulate a wide range of bodily functions, including immunity. Here we report that synthetic glucocorticoids affect 1035 mRNAs in isolated healthy human blood monocytes but only 165 in the respective six day-old monocyte-derived macrophages. The majority of the glucocorticoid response in monocytes concerns genes that are dynamic upon monocyte to macrophage differentiation, whereby macrophage-like mRNA levels are often reached in monocytes within four hours of treatment. Concomitantly, over 5000 chromosomal H3K27ac regions undergo remodelling, of which 60% involve increased H3K27ac signal. We find that chromosomal glucocorticoid receptor binding sites correlate with positive but not with negative local epigenomic effects. To investigate further we assigned our data to topologically associating domains (TADs). This shows that about 10% of macrophage TADs harbour at least one GR binding site and that half of all the glucocorticoid-induced H3K27ac regions are confined to these TADs. Our analyses are therefore consistent with the notion that TADs naturally accommodate information from sets of distal glucocorticoid response elements.
Native mass spectrometry identifies an alternative DNA-binding pathway for BirA from Staphylococcus aureus
Authors: Satiaputra Jiulia , Sternicki Louise M. , Hayes Andrew J. , Pukala Tara L. , Booker Grant W. , Shearwin Keith E. , Polyak Steven W. 
Published: February 2019

AbstractAn adequate supply of biotin is vital for the survival and pathogenesis of Staphylococcus aureus. The key protein responsible for maintaining biotin homeostasis in bacteria is the biotin retention protein A (BirA, also known as biotin protein ligase). BirA is a bi-functional protein that serves both as a ligase to catalyse the biotinylation of important metabolic enzymes, as well as a transcriptional repressor that regulates biotin biosynthesis, biotin transport and fatty acid elongation. The mechanism of BirA regulated transcription has been extensively characterized in Escherichia coli, but less so in other bacteria. Biotin-induced homodimerization of E. coli BirA (EcBirA) is a necessary prerequisite for stable DNA binding and transcriptional repression. Here, we employ a combination of native mass spectrometry, in vivo gene expression assays, site-directed mutagenesis and electrophoretic mobility shift assays to elucidate the DNA binding pathway for S. aureus BirA (SaBirA). We identify a mechanism that differs from that of EcBirA, wherein SaBirA is competent to bind DNA as a monomer both in the presence and absence of biotin and/or MgATP, allowing homodimerization on the DNA. Bioinformatic analysis demonstrated the SaBirA sequence used here is highly conserved amongst other S. aureus strains, implying this DNA-binding mechanism is widely employed.