bluuebunny/crossref_metadata_2025 huggingface dataset:
Cascading lake drainage on the Greenland Ice Sheet triggered by tensile shock and fracture
Authors: Christoffersen Poul , Bougamont Marion , Hubbard Alun , Doyle Samuel H. , Grigsby Shane , Pettersson Rickard
Published: March 2018

Supraglacial lakes on the Greenland Ice Sheet are expanding inland, but the impact on ice flow is equivocal because interior surface conditions may preclude the transfer of surface water to the bed. Here we use a well-constrained 3D model to demonstrate that supraglacial lakes in Greenland drain when tensile-stress perturbations propagate fractures in areas where fractures are normally absent or closed. These melt-induced perturbations escalate when lakes as far as 80 km apart form expansive networks and drain in rapid succession. The result is a tensile shock that establishes new surface-to-bed hydraulic pathways in areas where crevasses transiently open. We show evidence for open crevasses 135 km inland from the ice margin, which is much farther inland than previously considered possible. We hypothesise that inland expansion of lakes will deliver water and heat to isolated regions of the ice sheet’s interior where the impact on ice flow is potentially large.
Compression force sensing regulates integrin αIIbβ3 adhesive function on diabetic platelets
Authors: Ju Lining , McFadyen James D. , Al-Daher Saheb , Alwis Imala , Chen Yunfeng , Tønnesen Lotte L. , Maiocchi Sophie , Coulter Brianna , Calkin Anna C. , Felner Eric I. , Cohen Neale , Yuan Yuping , Schoenwaelder Simone M. , Cooper Mark E. , Zhu Cheng , Jackson Shaun P.
Published: March 2018

Diabetes is associated with an exaggerated platelet thrombotic response at sites of vascular injury. Biomechanical forces regulate platelet activation, although the impact of diabetes on this process remains ill-defined. Using a biomembrane force probe (BFP), we demonstrate that compressive force activates integrin αIIbβ3 on discoid diabetic platelets, increasing its association rate with immobilized fibrinogen. This compressive force-induced integrin activation is calcium and PI 3-kinase dependent, resulting in enhanced integrin affinity maturation and exaggerated shear-dependent platelet adhesion. Analysis of discoid platelet aggregation in the mesenteric circulation of mice confirmed that diabetes leads to a marked enhancement in the formation and stability of discoid platelet aggregates, via a mechanism that is not inhibited by therapeutic doses of aspirin and clopidogrel, but is eliminated by PI 3-kinase inhibition. These studies demonstrate the existence of a compression force sensing mechanism linked to αIIbβ3 adhesive function that leads to a distinct prothrombotic phenotype in diabetes.
Spin-liquid-like state in a spin-1/2 square-lattice antiferromagnet perovskite induced by d10–d0 cation mixing
Authors: Mustonen O. , Vasala S. , Sadrollahi E. , Schmidt K. P. , Baines C. , Walker H. C. , Terasaki I. , Litterst F. J. , Baggio-Saitovitch E. , Karppinen M.
Published: March 2018

A quantum spin liquid state has long been predicted to arise in spin-1/2 Heisenberg square-lattice antiferromagnets at the boundary region between Néel (nearest-neighbor interaction dominates) and columnar (next-nearest-neighbor interaction dominates) antiferromagnetic order. However, there are no known compounds in this region. Here we use d10–d0 cation mixing to tune the magnetic interactions on the square lattice while simultaneously introducing disorder. We find spin-liquid-like behavior in the double perovskite Sr2Cu(Te0.5W0.5)O6, where the isostructural end phases Sr2CuTeO6 and Sr2CuWO6 are Néel and columnar type antiferromagnets, respectively. We show that magnetism in Sr2Cu(Te0.5W0.5)O6 is entirely dynamic down to 19 mK. Additionally, we observe at low temperatures for Sr2Cu(Te0.5W0.5)O6—similar to several spin liquid candidates—a plateau in muon spin relaxation rate and a strong T-linear dependence in specific heat. Our observations for Sr2Cu(Te0.5W0.5)O6 highlight the role of disorder in addition to magnetic frustration in spin liquid physics.
Crystal structure of undecaprenyl-pyrophosphate phosphatase and its role in peptidoglycan biosynthesis
Authors: El Ghachi Meriem , Howe Nicole , Huang Chia-Ying , Olieric Vincent , Warshamanage Rangana , Touzé Thierry , Weichert Dietmar , Stansfeld Phillip J. , Wang Meitian , Kerff Fred , Caffrey Martin
Published: March 2018

As a protective envelope surrounding the bacterial cell, the peptidoglycan sacculus is a site of vulnerability and an antibiotic target. Peptidoglycan components, assembled in the cytoplasm, are shuttled across the membrane in a cycle that uses undecaprenyl-phosphate. A product of peptidoglycan synthesis, undecaprenyl-pyrophosphate, is converted to undecaprenyl-phosphate for reuse in the cycle by the membrane integral pyrophosphatase, BacA. To understand how BacA functions, we determine its crystal structure at 2.6 Å resolution. The enzyme is open to the periplasm and to the periplasmic leaflet via a pocket that extends into the membrane. Conserved residues map to the pocket where pyrophosphorolysis occurs. BacA incorporates an interdigitated inverted topology repeat, a topology type thus far only reported in transporters and channels. This unique topology raises issues regarding the ancestry of BacA, the possibility that BacA has alternate active sites on either side of the membrane and its possible function as a flippase.
Publisher Correction: Identification of a peptide recognizing cerebrovascular changes in mouse models of Alzheimer’s disease
Authors: Mann Aman P. , Scodeller Pablo , Hussain Sazid , Braun Gary B. , Mölder Tarmo , Toome Kadri , Ambasudhan Rajesh , Teesalu Tambet , Lipton Stuart A. , Ruoslahti Erkki
Published: March 2018

The original version of the Supplementary Information associated with this Article inadvertently omitted Supplementary Table 1. The HTML has now been updated to include a corrected version of the Supplementary Information.
Active cell-matrix coupling regulates cellular force landscapes of cohesive epithelial monolayers
Authors: Zhao Tiankai , Zhang Yao , Wei Qiong , Shi Xuechen , Zhao Peng , Chen Long-Qing , Zhang Sulin
Published: March 2018

Epithelial cells can assemble into cohesive monolayers with rich morphologies on substrates due to competition between elastic, edge, and interfacial effects. Here we present a molecularly based thermodynamic model, integrating monolayer and substrate elasticity, and force-mediated focal adhesion formation, to elucidate the active biochemical regulation over the cellular force landscapes in cohesive epithelial monolayers, corroborated by microscopy and immunofluorescence studies. The predicted extracellular traction and intercellular tension are both monolayer size and substrate stiffness dependent, suggestive of cross-talks between intercellular and extracellular activities. Our model sets a firm ground toward a versatile computational framework to uncover the molecular origins of morphogenesis and disease in multicellular epithelia.
Global Incidence and mortality of oesophageal cancer and their correlation with socioeconomic indicators temporal patterns and trends in 41 countries
Authors: Wong Martin C. S. , Hamilton Willie , Whiteman David C. , Jiang Johnny Y. , Qiao Youlin , Fung Franklin D. H. , Wang Harry H. X. , Chiu Philip W. Y. , Ng Enders K. W. , Wu Justin C. Y. , Yu Jun , Chan Francis K. L. , Sung Joseph J. Y.
Published: March 2018

Oesophageal cancers (adenocarcinomas [AC] and squamous cell carcinomas [SCC]) are characterized by high incidence/mortality in many countries. We aimed to delineate its global incidence and mortality, and studied whether socioeconomic development and its incidence rate were correlated. The age-standardized rates (ASRs) of incidence and mortality of this medical condition in 2012 for 184 nations from the GLOBOCAN database; national databases capturing incidence rates, and the WHO mortality database were examined. Their correlations with two indicators of socioeconomic development were evaluated. Joinpoint regression analysis was used to generate trends. The ratio between the ASR of AC and SCC was strongly correlated with HDI (r = 0.535 [men]; r = 0.661 [women]) and GDP (r = 0.594 [men]; r = 0.550 [women], both p < 0.001). Countries that reported the largest reduction in incidence in male included Poland (Average Annual Percent Change [AAPC] = −7.1, 95%C.I. = −12,−1.9) and Singapore (AAPC = −5.8, 95%C.I. = −9.5,−1.9), whereas for women the greatest decline was seen in Singapore (AAPC = −12.3, 95%C.I. = −17.3,−6.9) and China (AAPC = −5.6, 95%C.I. = −7.6,−3.4). The Philippines (AAPC = 4.3, 95%C.I. = 2,6.6) and Bulgaria (AAPC = 2.8, 95%C.I. = 0.5,5.1) had a significant mortality increase in men; whilst Columbia (AAPC = −6.1, 95%C.I. = −7.5,−4.6) and Slovenia (AAPC = −4.6, 95%C.I. = −7.9,−1.3) reported mortality decline in women. These findings inform individuals at increased risk for primary prevention.
Influence of Polymer Substrate Damage on the Time Dependent Cracking of SiNx Barrier Films
Authors: Kim Kyungjin , Luo Hao , Zhu Ting , Pierron Olivier N. , Graham Samuel
Published: March 2018

This work is concerned with the long-term behavior of environmentally-assisted subcritical cracking of PECVD SiNx barrier films on polyethylene terephthalate (PET) and polyimide (PI) substrates. While environmentally-assisted channel cracking in SiNx has been previously demonstrated, with constant crack growth rates over short periods of time (<1 hour) during which no substrate damage was observed, the present experiments over longer periods reveal a regime where cracking also develops in the polymer substrate. This time-dependent local cracking of the polymer underneath the channel crack is expected based on creep rupture or static fatigue. Our combined in-situ microscopy and finite-element modeling results highlight the combined effects of neighboring cracks and substrate cracking on the crack growth rate evolution in the film. In most cases, the subcritical crack growth rates decrease over time by up to two orders of magnitude until steady-state rates are reached. For SiNx on PI, crack growth rates were found to be more stable over time due to the lack of crack growth in the substrate as compared to SiNx on PET. These results provide a guideline to effectively improving the long-term reliability of flexible barriers by a substrate possessing high strength which limits substrate damage.
Identification of putative promoters in 48 eukaryotic genomes on the basis of DNA free energy
Authors: Yella Venkata Rajesh , Kumar Aditya , Bansal Manju
Published: March 2018

Transcription is an intricate mechanism and is orchestrated at the promoter region. The cognate motifs in the promoters are observed in only a subset of total genes across different domains of life. Hence, sequence-motif based promoter prediction may not be a holistic approach for whole genomes. Conversely, the DNA structural property, duplex stability is a characteristic of promoters and can be used to delineate them from other genomic sequences. In this study, we have used a DNA duplex stability based algorithm ‘PromPredict’ for promoter prediction in a broad range of eukaryotes, representing various species of yeast, worm, fly, fish, and mammal. Efficiency of the software has been tested in promoter regions of 48 eukaryotic systems. PromPredict achieves recall values, which range from 68 to 92% in various eukaryotes. PromPredict performs well in mammals, although their core promoter regions are GC rich. ‘PromPredict’ has also been tested for its ability to predict promoter regions for various transcript classes (coding and non-coding), TATA-containing and TATA-less promoters as well as on promoter sequences belonging to different gene expression variability categories. The results support the idea that differential DNA duplex stability is a potential predictor of promoter regions in various genomes.
Correlated Increase of High Ocean Waves and Winds in the Ice-Free Waters of the Arctic Ocean
Authors: Waseda Takuji , Webb Adrean , Sato Kazutoshi , Inoue Jun , Kohout Alison , Penrose Bill , Penrose Scott
Published: March 2018

The long-term trend of extreme ocean waves in the emerging ice-free waters of the summer Arctic is studied using ERA-Interim wave reanalysis, with validation by two drifting wave buoys deployed in summer 2016. The 38-year-long reanalysis dataset reveals an increase in the expected largest significant wave height from 2.3 m to 3.1 m in the ice-free water from the Laptev to the Beaufort Seas during October. The trend is highly correlated with the expected increase in highest wind speed from 12.0 m/s to 14.2 m/s over the ice-free ocean, and less so with the extent of the ice-free water. Since the storms in this area did not strengthen throughout the analysis period, the increase in the expected largest significant wave height follows from the enhanced probability of storms in ice-free waters, which is pertinent to the estimation of extreme sea conditions along the Northern Sea Route.
PmCBFs synthetically affect PmDAM6 by alternative promoter binding and protein complexes towards the dormancy of bud for Prunus mume
Authors: Zhao Kai , Zhou Yuzhen , Ahmad Sagheer , Yong Xue , Xie Xuehua , Han Yu , Li Yushu , Sun Lidan , Zhang Qixiang
Published: March 2018

The survival in freezing temperature for woody plants is exclusively dependent on the perception of coldness and induction of dormancy. CBF/DREB1 transcriptional factors join cold-response conduits and the DAM genes, especially PmDAM6, are well-known regulators of dormancy. Despite the immense importance, little is documented on the association between CBF proteins and the complexity of the promoter region in PmDAM6 with the function of bud dormancy in P. mume. Therefore, this study was based on the cloning of PmDAM6 and six PmCBFs to evaluate their integral roles in the process of bud development. The consistency of expressions in either vegetative or reproductive buds provided a negative control from PmCBFs to PmDAM6 during the onset of dormancy. Besides, PmCBF5 could form heteromeric complexes with PmDAM1 and PmDAM6. PmCBF1, PmCBF3, and PmDAM4 recognized the promoter of PmDAM6 by the alternative binding sites. Therefore, the interactions of these genes formulated the base of an obvious model to respond to the coldness and engendered dormancy release. Findings of this study will further help the unveil the genetic control of bud dormancy and its augmentation in P. mume and may offer an explanation for the vernalization.
Mandatory Naptimes in Childcare do not Reduce Children’s Cortisol Levels
Authors: Thorpe Karen J. , Pattinson Cassandra L. , Smith Simon S. , Staton Sally L.
Published: March 2018

The majority of preschool children (aged 3–5 years) no longer habitually nap, yet in childcare settings daily mandated naptimes in which children lie down without alternative activity remains a common practice. Mandated naptimes are associated with observed reductions in emotional climate and increased incidence of distress. While intended to be restful, mandatory naptimes may induce stress in those children unable to sleep. To examine this possibility, we applied a 2 (mandated/flexible practice) × 2 (nap/no-nap) design to test group difference in stress responses of children (N = 43, mean age 56.3 months). Salivary cortisol level was measured at 4 time-points (waking, pre-naptime, post-naptime, and bedtime) across two days at childcare. Overall our results show a significant decline in cortisol level from wake to pre-naptime and from post-naptime to bedtime. No significant change in cortisol level was observed from pre- to post- naptime. Significant group differences in cortisol patterns were observed. Notably, children under mandatory naptime conditions who did not nap showed no significant reduction in cortisol level from post-naptime to bedtime. While cortisol measurement suggests naptime is neither stressful nor restful for children in any group, implications for bedtime arousal are raised for those unable to sleep under conditions of mandated naptimes.
Bidirectional coordination of actions and habits by TrkB in mice
Authors: Pitts Elizabeth G. , Li Dan C. , Gourley Shannon L.
Published: March 2018

Specific corticostriatal structures and circuits are important for flexibly shifting between goal-oriented versus habitual behaviors. For example, the orbitofrontal cortex and dorsomedial striatum are critical for goal-directed action, while the dorsolateral striatum supports habits. To determine the role of neurotrophin signaling, we overexpressed a truncated, inactive form of tropomyosin receptor kinase B [also called tyrosine receptor kinase B (TrkB)], the high-affinity receptor for Brain-derived Neurotrophic Factor, in the orbitofrontal cortex, dorsomedial striatum and dorsolateral striatum. Overexpression of truncated TrkB interfered with phosphorylation of full-length TrkB and ERK42/44, as expected. In the orbitofrontal cortex and dorsomedial striatum, truncated trkB overexpression also occluded the ability of mice to select actions based on the likelihood that they would be reinforced. Meanwhile, in the dorsolateral striatum, truncated trkB blocked the development of habits. Thus, corticostriatal TrkB-mediated plasticity appears necessary for balancing actions and habits.
Massive shelf dense water flow influences plankton community structure and particle transport over long distance
Authors: Bernardi Aubry Fabrizio , Falcieri Francesco Marcello , Chiggiato Jacopo , Boldrin Alfredo , Luna Gian Marco , Finotto Stefania , Camatti Elisa , Acri Francesco , Sclavo Mauro , Carniel Sandro , Bongiorni Lucia
Published: March 2018

Dense waters (DW) formation in shelf areas and their cascading off the shelf break play a major role in ventilating deep waters, thus potentially affecting ecosystem functioning and biogeochemical cycles. However, whether DW flow across shelves may affect the composition and structure of plankton communities down to the seafloor and the particles transport over long distances has not been fully investigated. Following the 2012 north Adriatic Sea cold outbreak, DW masses were intercepted at ca. 460 km south the area of origin and compared to resident ones in term of plankton biomass partitioning (pico to micro size) and phytoplankton species composition. Results indicated a relatively higher contribution of heterotrophs in DW than in deep resident water masses, probably as result of DW-mediated advection of fresh organic matter available to consumers. DWs showed unusual high abundances of Skeletonema sp., a diatom that bloomed in the north Adriatic during DW formation. The Lagrangian numerical model set up on this diatom confirmed that DW flow could be an important mechanism for plankton/particles export to deep waters. We conclude that the predicted climate-induced variability in DW formation events could have the potential to affect the ecosystem functioning of the deeper part of the Mediterranean basin, even at significant distance from generation sites.
Analysis of generic coupling between EEG activity and PETCO2 in free breathing and breath-hold tasks using Maximal Information Coefficient (MIC)
Authors: Morelli Maria Sole , Greco Alberto , Valenza Gaetano , Giannoni Alberto , Emdin Michele , Scilingo Enzo Pasquale , Vanello Nicola
Published: March 2018

Brain activations related to the control of breathing are not completely known. The respiratory system is a non-linear system. However, the relationship between neural and respiratory dynamics is usually estimated through linear correlation measures, completely neglecting possible underlying nonlinear interactions. This study evaluate the linear and nonlinear coupling between electroencephalographic (EEG) signal and variations in carbon dioxide (CO2) signal related to different breathing task. During a free breathing and a voluntary breath hold tasks, the coupling between EEG power in nine different brain regions in delta (1–3 Hz) and alpha (8–13 Hz) bands and end-tidal CO2 (PET CO2) was evaluated. Specifically, the generic associations (i.e. linear and nonlinear correlations) and a “pure” nonlinear correlations were evaluated using the maximum information coefficient (MIC) and MIC-ρ2 between the two signals, respectively (where ρ2 represents the Pearson’s correlation coefficient). Our results show that in delta band, MIC indexes discriminate the two tasks in several regions, while in alpha band the same behaviour is observed for MIC-ρ2, suggesting a generic coupling between delta EEG power and PETCO2 and a pure nonlinear interaction between alpha EEG power and PETCO2. Moreover, higher indexes values were found for breath hold task respect to free breathing.
A benzene-degrading nitrate-reducing microbial consortium displays aerobic and anaerobic benzene degradation pathways
Authors: Atashgahi Siavash , Hornung Bastian , van der Waals Marcelle J. , da Rocha Ulisses Nunes , Hugenholtz Floor , Nijsse Bart , Molenaar Douwe , van Spanning Rob , Stams Alfons J. M. , Gerritse Jan , Smidt Hauke
Published: March 2018

In this study, we report transcription of genes involved in aerobic and anaerobic benzene degradation pathways in a benzene-degrading denitrifying continuous culture. Transcripts associated with the familyPeptococcaceaedominated all samples (21–36% relative abundance) indicating their key role in the community. We found a highly transcribed gene cluster encoding a presumed anaerobic benzene carboxylase (AbcA and AbcD) and a benzoate-coenzyme A ligase (BzlA). Predicted gene products showed >96% amino acid identity and similar gene order to the corresponding benzene degradation gene cluster described previously, providing further evidence for anaerobic benzene activation via carboxylation. For subsequent benzoyl-CoA dearomatization,bam-like genes analogous to the ones found in other strict anaerobes were transcribed, whereas gene transcripts involved in downstream benzoyl-CoA degradation were mostly analogous to the ones described in facultative anaerobes. The concurrent transcription of genes encoding enzymes involved in oxygenase-mediated aerobic benzene degradation suggested oxygen presence in the culture, possibly formed via a recently identified nitric oxide dismutase (Nod). Although we were unable to detect transcription of Nod-encoding genes, addition of nitrite and formate to the continuous culture showed indication for oxygen production. Such an oxygen production would enable aerobic microbes to thrive in oxygen-depleted and nitrate-containing subsurface environments contaminated with hydrocarbons.
Electrolytic copper as cheap and effective catalyst for one-pot triazole synthesis
Authors: Mularski Jacek , Czaplińska Barbara , Cieślik Wioleta , Bebłot Jakub , Bartczak Piotr , Sitko Rafał , Polański Jarosław , Musiol Robert
Published: March 2018

Electrolytic copper is a well-known form of pure, oxygen free copper that is used for industrial applications. In this work, the catalytic potential of this relatively cheap material was studied. The addition of less than 0.015 mol equivalent of copper powder effectively catalysed the one-pot synthesis of triazoles from a diverse range of organic halides and alkynes. Quantitative conversions in aqueous solvents can be achieved within minutes. The heterogenous nature of the catalyst afforded a low level of copper contamination in the products, thus meeting the rigorous criteria of the pharmaceutical industry.
Microvillar and ciliary defects in zebrafish lacking an actin-binding bioactive peptide amidating enzyme
Authors: Kumar Dhivya , Thomason Rebecca T. , Yankova Maya , Gitlin Jonathan D. , Mains Richard E. , Eipper Betty A. , King Stephen M.
Published: March 2018

The assembly of membranous extensions such as microvilli and cilia in polarized cells is a tightly regulated, yet poorly understood, process. Peptidylglycine α-amidating monooxygenase (PAM), a membrane enzyme essential for the synthesis of amidated bioactive peptides, was recently identified in motile and non-motile (primary) cilia and has an essential role in ciliogenesis in Chlamydomonas, Schmidtea and mouse. In mammalian cells, changes in PAM levels alter secretion and organization of the actin cytoskeleton. Here we show that lack of Pam in zebrafish recapitulates the lethal edematous phenotype observed in Pam
−/−
mice and reveals additional defects. The pam
−/−
zebrafish embryos display an initial striking loss of microvilli and subsequently impaired ciliogenesis in the pronephros. In multiciliated mouse tracheal epithelial cells, vesicular PAM staining colocalizes with apical actin, below the microvilli. In PAM-deficient Chlamydomonas, the actin cytoskeleton is dramatically reorganized, and expression of an actin paralogue is upregulated. Biochemical assays reveal that the cytosolic PAM C-terminal domain interacts directly with filamentous actin but does not alter the rate of actin polymerization or disassembly. Our results point to a critical role for PAM in organizing the actin cytoskeleton during development, which could in turn impact both microvillus formation and ciliogenesis.
Interconnected Microphysiological Systems for Quantitative Biology and Pharmacology Studies
Authors: Edington Collin D. , Chen Wen Li Kelly , Geishecker Emily , Kassis Timothy , Soenksen Luis R. , Bhushan Brij M. , Freake Duncan , Kirschner Jared , Maass Christian , Tsamandouras Nikolaos , Valdez Jorge , Cook Christi D. , Parent Tom , Snyder Stephen , Yu Jiajie , Suter Emily , Shockley Michael , Velazquez Jason , Velazquez Jeremy J. , Stockdale Linda , Papps Julia P. , Lee Iris , Vann Nicholas , Gamboa Mario , LaBarge Matthew E. , Zhong Zhe , Wang Xin , Boyer Laurie A. , Lauffenburger Douglas A. , Carrier Rebecca L. , Communal Catherine , Tannenbaum Steven R. , Stokes Cynthia L. , Hughes David J. , Rohatgi Gaurav , Trumper David L. , Cirit Murat , Griffith Linda G.
Published: March 2018

Microphysiological systems (MPSs) are in vitro models that capture facets of in vivo organ function through use of specialized culture microenvironments, including 3D matrices and microperfusion. Here, we report an approach to co-culture multiple different MPSs linked together physiologically on re-useable, open-system microfluidic platforms that are compatible with the quantitative study of a range of compounds, including lipophilic drugs. We describe three different platform designs – “4-way”, “7-way”, and “10-way” – each accommodating a mixing chamber and up to 4, 7, or 10 MPSs. Platforms accommodate multiple different MPS flow configurations, each with internal re-circulation to enhance molecular exchange, and feature on-board pneumatically-driven pumps with independently programmable flow rates to provide precise control over both intra- and inter-MPS flow partitioning and drug distribution. We first developed a 4-MPS system, showing accurate prediction of secreted liver protein distribution and 2-week maintenance of phenotypic markers. We then developed 7-MPS and 10-MPS platforms, demonstrating reliable, robust operation and maintenance of MPS phenotypic function for 3 weeks (7-way) and 4 weeks (10-way) of continuous interaction, as well as PK analysis of diclofenac metabolism. This study illustrates several generalizable design and operational principles for implementing multi-MPS “physiome-on-a-chip” approaches in drug discovery.
The Cannabinoid Content of Legal Cannabis in Washington State Varies Systematically Across Testing Facilities and Popular Consumer Products
Authors: Jikomes Nick , Zoorob Michael
Published: March 2018

The majority of adults in the U.S. now have state-legal access to medical or recreational cannabis products, despite their federal prohibition. Given the wide array of pharmacologically active compounds in these products, it is essential that their biochemical profile is measured and reported to consumers, which requires accurate laboratory testing. However, no universal standards for laboratory testing protocols currently exist, and there is controversy as to whether all reported results are legitimate. To investigate these concerns, we analyzed a publicly available seed-to-sale traceability dataset from Washington state containing measurements of the cannabinoid content of legal cannabis products from state-certified laboratories. Consistent with previous work, we found that commercial Cannabis strains fall into three broad chemotypes defined by the THC:CBD ratio. Moreover, we documented systematic differences in the cannabinoid content reported by different laboratories, relative stability in cannabinoid levels of commercial flower and concentrates over time, and differences between popular commercial strains. Importantly, interlab differences in cannabinoid reporting persisted even after controlling for plausible confounds. Our results underscore the need for standardized laboratory methodologies in the legal cannabis industry and provide a framework for quantitatively assessing laboratory quality.
Characteristic and optimization of the effective perspective images’ segmentation and mosaicking (EPISM) based holographic stereogram: an optical transfer function approach
Authors: Su Jian , Yan Xingpeng , Jiang Xiaoyu , Huang Yingqing , Chen Yibei , Zhang Teng
Published: March 2018

Based on our proposed method for holographic stereogram printing using effective perspective images’ segmentation and mosaicking (EPISM), we analyze the reconstructed wavefront errors, and establish the exit pupil function model of proposed printing system. To evaluate the imaging quality, the optical transfer function (OTF) of the holographic stereogram is modelled from the aspect of frequency response. The characteristic of the OTF with respect to the exit pupil size and the aberration are investigated in detail. We also consider the flipping effect in spatial domain. The optimization of hogel sizes, i.e., the sampling interval of original perspective images and the printing interval of synthetic effective perspective images, are given for the optimized reconstruction. Numerical simulations and optical experiments are implemented, and the results demonstrate the validity of our analysis, and the optimized parameters of hogel sizes can improve the imaging quality of full parallax holographic stereogram effectively.
Chain Breakage in the Supercooled Liquid - Liquid Transition and Re-entry of the λ-transition in Sulfur
Authors: Zhang Linji , Ren Yang , Liu Xiuru , Han Fei , Evans-Lutterodt Kenneth , Wang Hongyan , He Yali , Wang Junlong , Zhao Yong , Yang Wenge
Published: March 2018

Amorphous sulfur was prepared by rapid compression of liquid sulfur at temperatures above the λ-transition for to preserve the high-temperature liquid structure. We conducted synchrotron high-energy X-ray diffraction and Raman spectroscopy to diagnose the structural evolution of amorphous sulfur from room temperature to post-λ-transition temperature. Discontinuous changes of the first and second peaks in atomic pair-distribution-function, g(r), were observed during the transition from amorphous to liquid sulfur. The average first-neighbor coordination numbers showed an abrupt drop from 1.92 to 1.81. The evolution of the chain length clearly shows that the transition was accompanied by polymeric chains breaking. Furthermore, a re-entry of the λ-transition structure was involved in the heating process. The amorphous sulfur, which inherits the post-λ-transition structure from its parent melts, transformed to the pre-λ-transition liquid structure at around 391 K. Upon further heating, the pre-λ-transition liquid transformed to a post-λ-transition structure through the well-known λ-transition process. This discovery offers a new perspective on amorphous sulfur’s structural inheritance from its parent liquid and has implications for understanding the structure, evolution and properties of amorphous sulfur and its liquids.
Hsc70-2 is required for Beet black scorch virus infection through interaction with replication and capsid proteins
Authors: Wang Xiaoling , Cao Xiuling , Liu Min , Zhang Ruiqi , Zhang Xin , Gao Zongyu , Zhao Xiaofei , Xu Kai , Li Dawei , Zhang Yongliang
Published: March 2018

Dissecting the complex molecular interplay between the host plant and invading virus improves our understanding of the mechanisms underlying viral pathogenesis. In this study, immunoprecipitation together with the mass spectrometry analysis revealed that the heat shock protein 70 (Hsp70) family homolog, Hsc70-2, was co-purified with beet black scorch virus (BBSV) replication protein p23 and coat protein (CP), respectively. Further experiments demonstrated that Hsc70-2 interacts directly with both p23 and CP, whereas there is no interaction between p23 and CP. Hsc70-2 expression is induced slightly during BBSV infection of Nicotiana benthamiana, and overexpression of Hsc70-2 promotes BBSV accumulation, while knockdown of Hsc70-2 in N. benthamiana leads to drastic reduction of BBSV accumulation. Infection experiments revealed that CP negatively regulates BBSV replication, which can be mitigated by overexpression of Hsc70-2. Further experiments indicate that CP impairs the interaction between Hsc70-2 and p23 in a dose-dependent manner. Altogether, we provide evidence that besides specific functions of Hsp70 family proteins in certain aspects of viral infection, they can serve as a mediator for the orchestration of virus infection by interacting with different viral components. Our results provide new insight into the role of Hsp70 family proteins in virus infection.
Author Correction: Prevalence and risk factors associated with stroke in middle-aged and older Chinese: A community-based cross-sectional study
Authors: Gan Yong , Wu Jiang , Zhang Shengchao , Li Liqing , Yin Xiaoxv , Gong Yanhong , Herath Chulani , Mkandawire Naomie , Zhou Yanfeng , Song Xingyue , Zeng Xiaozhou , Li Wenzhen , Liu Qiaoyan , Shu Chang , Wang Zhihong , Lu Zuxun
Published: March 2018

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper.
Soil pH is equally important as salinity in shaping bacterial communities in saline soils under halophytic vegetation
Authors: Zhao Shuai , Liu Jun-Jie , Banerjee Samiran , Zhou Na , Zhao Zhen-Yong , Zhang Ke , Tian Chang-Yan
Published: March 2018

While saline soils account for 6.5% of the total land area globally, it comprises about 70% of the area in northwestern China. Microbiota in these saline soils are particularly important because they are critical to maintaining ecosystem services. However, little is known about the microbial diversity and community composition in saline soils. To investigate the distribution patterns and edaphic determinants of bacterial communities in saline soils, we collected soil samples across the hypersaline Ebinur Lake shoreline in northwestern China and assessed soil bacterial communities using bar-coded pyrosequencing. Bacterial communities were diverse, and the dominant phyla (>5% of all sequences) across all soil samples were Gammaproteobacteria, Actinobacteria, Firmicutes, Alphaproteobacteria, Bacteroidetes and Betaproteobacteria. These dominant phyla made a significant (P < 0.05) contribution to community structure variations between soils. Halomonas, Smithella, Pseudomonas and Comamonas were the indicator taxa across the salinity gradient. Bacterial community composition showed significant (P < 0.05) correlations with salt content and soil pH. Indeed, bacterial phylotype richness and phylogenetic diversity were also higher in soils with middle-level salt rates, and were significantly (P < 0.05) correlated with salt content and soil pH. Overall, our results show that both salinity and pH are the determinants of bacterial communities in saline soils in northwest China.
Selection of trilateral continuums of life history strategies under food web interactions
Authors: Fujiwara Masami
Published: March 2018

The study of life history strategies has a long history in ecology and evolution, but determining the underlying mechanisms driving the evolution of life history variation and its consequences for population regulation remains a major challenge. In this study, a food web model with constant environmental conditions was used to demonstrate how multi-species consumer–resource interactions (food-web interactions) can create variation in the duration of the adult stage, age of maturation, and fecundity among species. The model included three key ecological processes: size-dependent species interactions, energetics, and transition among developmental stages. Resultant patterns of life history variation were consistent with previous empirical observations of the life history strategies of aquatic organisms referred to as periodic, equilibrium, and opportunistic strategies (trilateral continuums of life history strategies). Results from the simulation model suggest that these three life history strategies can emerge from food web interactions even when abiotic environmental conditions are held constant.
Feasibility and resolution limits of opto-magnetic imaging of neural network activity in brain slices using color centers in diamond
Authors: Karadas Mürsel , Wojciechowski Adam M. , Huck Alexander , Dalby Nils Ole , Andersen Ulrik Lund , Thielscher Axel
Published: March 2018

We suggest a novel approach for wide-field imaging of the neural network dynamics of brain slices that uses highly sensitivity magnetometry based on nitrogen-vacancy (NV) centers in diamond. In-vitro recordings in brain slices is a proven method for the characterization of electrical neural activity and has strongly contributed to our understanding of the mechanisms that govern neural information processing. However, this traditional approach only acquires signals from a few positions, which severely limits its ability to characterize the dynamics of the underlying neural networks. We suggest to extend its scope using NV magnetometry-based imaging of the neural magnetic fields across the slice. Employing comprehensive computational simulations and theoretical analyses, we determine the spatiotemporal characteristics of the neural fields and the required key performance parameters of an NV magnetometry-based imaging setup. We investigate how the technical parameters determine the achievable spatial resolution for an optimal 2D reconstruction of neural currents from the measured field distributions. Finally, we compare the imaging of neural slice activity with that of a single planar pyramidal cell. Our results suggest that imaging of slice activity will be possible with the upcoming generation of NV magnetic field sensors, while single-shot imaging of planar cell activity remains challenging.
The Transpolar Drift conveys methane from the Siberian Shelf to the central Arctic Ocean
Authors: Damm E. , Bauch D. , Krumpen T. , Rabe B. , Korhonen M. , Vinogradova E. , Uhlig C.
Published: March 2018

Methane sources and sinks in the Arctic are poorly quantified. In particular, methane emissions from the Arctic Ocean and the potential sink capacity are still under debate. In this context sea ice impact on and the intense cycling of methane between sea ice and Polar surface water (PSW) becomes pivotal. We report on methane super- and under-saturation in PSW in the Eurasian Basin (EB), strongly linked to sea ice-ocean interactions. In the southern EB under-saturation in PSW is caused by both inflow of warm Atlantic water and short-time contact with sea ice. By comparison in the northern EB long-time sea ice-PSW contact triggered by freezing and melting events induces a methane excess. We reveal the Ttranspolar Drift Stream as crucial for methane transport and show that inter-annual shifts in sea ice drift patterns generate inter-annually patchy methane excess in PSW. Using backward trajectories combined with δ18O signatures of sea ice cores we determine the sea ice source regions to be in the Laptev Sea Polynyas and the off shelf regime in 2011 and 2015, respectively. We denote the Transpolar Drift regime as decisive for the fate of methane released on the Siberian shelves.
Demonstration of the potential of environmental DNA as a tool for the detection of avian species
Authors: Ushio Masayuki , Murata Koichi , Sado Tetsuya , Nishiumi Isao , Takeshita Masamichi , Iwasaki Wataru , Miya Masaki
Published: March 2018

Birds play unique functional roles in the maintenance of ecosystems, such as pollination and seed dispersal, and thus monitoring bird species diversity is a first step towards avoiding undesirable consequences of anthropogenic impacts on bird communities. In the present study, we hypothesized that birds, regardless of their main habitats, must have frequent contact with water and that tissues that contain their DNA that persists in the environment (environmental DNA; eDNA) could be used to detect the presence of avian species. To this end, we applied a set of universal PCR primers (MiBird, a modified version of fish/mammal universal primers) for metabarcoding avian eDNA. We confirmed the versatility of MiBird primers by performing in silico analyses and by amplifying DNAs extracted from bird tissues. Analyses of water samples from zoo cages of birds with known species composition suggested that the use of MiBird primers combined with Illumina MiSeq could successfully detect avian species from water samples. Additionally, analysis of water samples collected from a natural pond detected five avian species common to the sampling areas. The present findings suggest that avian eDNA metabarcoding would be a complementary detection/identification tool in cases where visual census of bird species is difficult.
Structural characterisation of the catalytic domain of botulinum neurotoxin X - high activity and unique substrate specificity
Authors: Masuyer Geoffrey , Zhang Sicai , Barkho Sulyman , Shen Yi , Henriksson Linda , Košenina Sara , Dong Min , Stenmark Pål
Published: March 2018

Botulinum neurotoxins (BoNTs) are among the most potent toxins known and are also used to treat an increasing number of medical disorders. There are seven well-established serotypes (BoNT/A-G), which all act as zinc-dependent endopeptidases targeting specific members of the SNARE proteins required for synaptic vesicle exocytosis in neurons. A new toxin serotype, BoNT/X, was recently identified. It cleaves not only the canonical targets, vesicle associated membrane proteins (VAMP) 1/2/3 at a unique site, but also has the unique ability to cleave VAMP4/5 and Ykt6. Here we report the 1.35 Å X-ray crystal structure of the light chain of BoNT/X (LC/X). LC/X shares the core fold common to all other BoNTs, demonstrating that LC/X is a bona fide member of BoNT-LCs. We found that access to the catalytic pocket of LC/X is more restricted, and the regions lining the catalytic pocket are not conserved compared to other BoNTs. Kinetic studies revealed that LC/X cleaves VAMP1 with a ten times higher efficiency than BoNT/B and the tetanus neurotoxin. The structural information provides a molecular basis to understand the convergence/divergence between BoNT/X and other BoNTs, to develop effective LC inhibitors, and to engineer new scientific tools and therapeutic toxins targeting distinct SNARE proteins in cells.
Early direct competition does not determine the community structure in a desert riparian forest
Authors: Wu Guilin , Jiang Shaowei , Liu Hui , Zhu Shidan , Zhou Duoduo , Zhang Ying , Luo Qi , Li Jun
Published: March 2018

In riparian zones along the Tarim River in northeastern China, the co-dominance by Populus euphratica and Tamarix ramosissima at the early succession stage shifts to P. euphratica dominance in the late stages. However, little is known about how this shift is mediated by the highly variable water conditions in riparian zones. Here we conducted a mesocosm experiment in which we measured the physiological and morphological traits of these two co-occuring species grown in mixtures under simulated favorable groundwater condition and no groundwater availability. Results indicated that T. ramosissima, in comparison to P. euphratica, had much lower WUE, less proportion of root biomass under favorable groundwater condition. Under no groundwater condition, T. ramosissima also showed higher maximal quantum yield of PSII which allowed it to accumulate higher aboveground and total biomass. Therefore, regardless of groundwater conditions, T. ramosissima exhibited superior competitive advantages against P. euphratica under direct competition condition, which demonstrates that the dominance shift was not resulted from the direct competition at seedling stage. Our findings further imply that a strategy of “sit and wait” in P. euphratica might favor its growth and survival when suffered flooding disturbances, thus allowing P. euphratica not being excluded through competition at early successional stage.
Directly converting carbon dioxide to linear α-olefins on bio-promoted catalysts
Authors: Guo Lisheng , Sun Jian , Ji Xuewei , Wei Jian , Wen Zhiyong , Yao Ruwei , Xu Hengyong , Ge Qingjie
Published: March 2018

Although considerable efforts have been made in converting carbon dioxide to hydrocarbons via hydrogenation processes, precise control of C–C coupling towards heavy olefins remains a challenge. Here we report a carbon dioxide hydrogenation to olefin process that achieves 72% selectivity for alkenes and 50.3% selectivity for C4–18 alkenes, of which formation of linear α-olefins accounts for 80%. The process is catalyzed by carbon-supported iron, commonly used in C–C coupling reactions, with multiple alkali promoters extracted from corncob. The design is based on the synergistic catalysis of mineral elements in biomass enzyme on which carbon dioxide can be directly converted into carbohydrate. The mineral elements from corncob may promote the surface enrichment of potassium, suppressing the secondary hydrogenation of alkenes on active sites. Furthermore, carburization of iron species is enhanced to form more Fe5C2 species, promoting both the reverse water–gas shift reaction and subsequent C–C coupling.
CRISPR Highlights and Transition of Cas9 into a Genome Editing Tool
Authors: Bentin Thomas
Published: March 2018

CRISPR–cas systems provide microbial immunity to invasive genetic elements in many bacteria and most investigated archea. This chapter highlights important advances following the discovery of CRISPR–cas, its function in immunity and the biochemical characterisation of a subset of immune-effector components, which together target and cleave foreign genomes in a sequence-specific manner. These advances encouraged transplantation of engineered CRISPRS–cas components into human cells to induce sequence-targeted double-strand breaks followed by cell-mediated repair, thereby effectively repurposing CRISPR effectors into efficient genome-editing tools exploiting the different eukaryotic repair pathways. The challenges of genome-wide specific targeting versus potentially harmful off-target activity and efforts to improve target specificity using protein engineering are discussed. The chapter concludes with a brief summary of current ongoing human trials involving CRISPR–cas and the challenges facing clinical development of the technology.
Melting proteins confined in nanodroplets with 10.6 μm light provides clues about early steps of denaturation
Authors: El-Baba Tarick J. , Fuller Daniel R. , Woodall Daniel W. , Raab Shannon A. , Conant Christopher R. , Dilger Jonathan M. , Toker Yoni , Williams Evan R. , Russell David H. , Clemmer David E.
Published: March 2018

Irradiation of protein molecules in nanodroplets with 10.6 μm laser light reveals details of conformer stabilities and unfolding pathways.
A novel strategy to motivate the luminescence efficiency of a phosphor: drilling nanoholes on the surface
Authors: Yin Liang-Jun , Liang Ying-Lin , Zhang Sheng-Hui , Wang Meng , Li Langkai , Xie Wen-Jie , Zhong Hao , Jian Xian , Xu Xin , Wang Xin , Deng Long-Jiang
Published: March 2018

Drilling nanoholes is shown to enhance excitation light absorption of phosphors and consequently increase the quantum efficiency.
Enthalpic interactions in aqueous strong electrolytes upon addition of ionic liquids
Authors: Jain Preeti , Kumar Anil
Published: March 2018

The present study deals with the inter-ionic interactions between strong electrolytes and ionic liquids based on the thermodynamic properties such as excess partial molar enthalpy, HEIL, relative apparent molar enthalpy, ϕL, and the enthalpic interaction parameters.