bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bidirectional coordination of actions and habits by TrkB in mice
Authors: Pitts Elizabeth G. , Li Dan C. , Gourley Shannon L. 
Published: March 2018

AbstractSpecific 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

AbstractDense 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

AbstractBrain 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

AbstractIn 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

AbstractElectrolytic 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

AbstractThe 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

AbstractMicrophysiological 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

AbstractThe 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

AbstractBased 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

AbstractAmorphous 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

AbstractDissecting 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.
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

AbstractWhile 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

AbstractThe 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

AbstractWe 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

AbstractMethane 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.