bluuebunny/crossref_metadata_2025_split huggingface dataset:
Soil parameters, land use, and geographical distance drive soil bacterial communities along a European transect
Authors: Plassart Pierre , Prévost-Bouré Nicolas Chemidlin , Uroz Stéphane , Dequiedt Samuel , Stone Dorothy , Creamer Rachel , Griffiths Robert I. , Bailey Mark J. , Ranjard Lionel , Lemanceau Philippe 
Published: January 2019

AbstractTo better understand the relationship between soil bacterial communities, soil physicochemical properties, land use and geographical distance, we considered for the first time ever a European transect running from Sweden down to Portugal and from France to Slovenia. We investigated 71 sites based on their range of variation in soil properties (pH, texture and organic matter), climatic conditions (Atlantic, alpine, boreal, continental, Mediterranean) and land uses (arable, forest and grassland). 16S rRNA gene amplicon pyrosequencing revealed that bacterial communities highly varied in diversity, richness, and structure according to environmental factors. At the European scale, taxa area relationship (TAR) was significant, supporting spatial structuration of bacterial communities. Spatial variations in community diversity and structure were mainly driven by soil physicochemical parameters. Within soil clusters (k-means approach) corresponding to similar edaphic and climatic properties, but to multiple land uses, land use was a major driver of the bacterial communities. Our analyses identified specific indicators of land use (arable, forest, grasslands) or soil conditions (pH, organic C, texture). These findings provide unprecedented information on soil bacterial communities at the European scale and on the drivers involved; possible applications for sustainable soil management are discussed.
Emergence of Topological insulator and Nodal line semi-metal states in XX′Bi (X = Na, K, Rb, Cs; X′ = Ca, Sr)
Authors: Mondal Chiranjit , Barman C. K. , Kumar Sourabh , Alam Aftab , Pathak Biswarup 
Published: January 2019

AbstractIn this article, we predict the emergence of non-trivial band topology in the family of XX′Bi compounds having $$P\overline{6}2m$$
P

6

¯

2
m
(# 189) space group. Using first principles calculations within hybrid functional framework, we demonstrate that NaSrBi and NaCaBi are strong topological insulator under controlled band engineering. Here, we propose three different ways to engineer the band topology to get a non-trivial order: (i) hydrostatic pressure, (ii) biaxial strain (due to epitaxial mismatch), and (iii) doping. Non-triviality is confirmed by investigating bulk band inversion, topological Z2 invariant, surface dispersion and spin texture. Interestingly, some of these compounds also show a three dimensional topological nodal line semi-metal (NLS) state in the absence of spin orbit coupling (SOC). In these NLS phases, the closed loop of band degeneracy in the Brillouin zone lie close to the Fermi level. Moreover, a drumhead like flat surface state is observed on projecting the bulk state on the [001] surface. The inclusion of SOC opens up a small band gap making them behave like a topological insulator.
Social isolation impairs the persistence of social recognition memory by disturbing the glutamatergic tonus and the olfactory bulb-dorsal hippocampus coupling
Authors: Almeida-Santos Ana F. , Carvalho Vinícius R. , Jaimes Laura F. , de Castro Caio M. , Pinto Hyorrana P. , Oliveira Tadeu P. D. , Vieira Luciene B. , Moraes Márcio F. D. , Pereira Grace S. 
Published: January 2019

AbstractThe absence of companion may jeopardize mental health in social animals. Here, we tested the hypothesis that social isolation impairs social recognition memory by altering the excitability and the dialog between the olfactory bulb (OB) and the dorsal hippocampus (dHIP). Adult male Swiss mice were kept grouped (GH) or isolated (SI) for 7 days. Social memory (LTM) was evaluated using social recognition test. SI increased glutamate release in the OB, while decreased in the dHIP. Blocking AMPA and NMDA receptors into the OB or activating AMPA into the dHIP rescued LTM in SI mice, suggesting a cause-effect relationship between glutamate levels and LTM impairment. Additionally, during memory retrieval, phase-amplitude coupling between OB and dHIP decreased in SI mice. Our results indicate that SI impaired the glutamatergic signaling and the normal communication between OB and HIP, compromising the persistence of social memory.
Self-association and subcellular localization of Puumala hantavirus envelope proteins
Authors: Sperber Hannah Sabeth , Welke Robert-William , Petazzi Roberto Arturo , Bergmann Ronny , Schade Matthias , Shai Yechiel , Chiantia Salvatore , Herrmann Andreas , Schwarzer Roland 
Published: January 2019

AbstractHantavirus assembly and budding are governed by the surface glycoproteins Gn and Gc. In this study, we investigated the glycoproteins of Puumala, the most abundant Hantavirus species in Europe, using fluorescently labeled wild-type constructs and cytoplasmic tail (CT) mutants. We analyzed their intracellular distribution, co-localization and oligomerization, applying comprehensive live, single-cell fluorescence techniques, including confocal microscopy, imaging flow cytometry, anisotropy imaging and Number&Brightness analysis. We demonstrate that Gc is significantly enriched in the Golgi apparatus in absence of other viral components, while Gn is mainly restricted to the endoplasmic reticulum (ER). Importantly, upon co-expression both glycoproteins were found in the Golgi apparatus. Furthermore, we show that an intact CT of Gc is necessary for efficient Golgi localization, while the CT of Gn influences protein stability. Finally, we found that Gn assembles into higher-order homo-oligomers, mainly dimers and tetramers, in the ER while Gc was present as mixture of monomers and dimers within the Golgi apparatus. Our findings suggest that PUUV Gc is the driving factor of the targeting of Gc and Gn to the Golgi region, while Gn possesses a significantly stronger self-association potential.
3D vessel-wall virtual histology of whole-body perfused mice using a novel heavy element stain
Authors: Dunmore-Buyze P. Joy , Cruje Charmainne , Nong Zengxuan , Lee Jason J. , Kiernan John A. , Pickering J. Geoffrey , Drangova Maria 
Published: January 2019

AbstractVirtual histology – utilizing high-resolution three-dimensional imaging – is becoming readily available. Micro-computed tomography (micro-CT) is widely available and is often coupled with x-ray attenuating histological stains that mark specific tissue components for 3D virtual histology. In this study we describe a new tri-element x-ray attenuating stain and perfusion protocol that provides micro-CT contrast of the entire vasculature of an intact mouse. The stain – derived from an established histology stain (Verhoeff’s) – is modified to enable perfusion through the vasculature; the attenuating elements of the stain are iodine, aluminum, and iron. After a 30-minute perfusion through the vasculature (10-minute flushing with detergent-containing saline followed by 15-minute perfusion with the stain and a final 5-minute saline flush), animals are scanned using micro-CT. We demonstrate that the new staining protocol enables sharp delineation of the vessel walls in three dimensions over the whole body; corresponding histological analysis verified that the CT stain is localized primarily in the endothelial cells and media of large arteries and the endothelium of smaller vessels, such as the coronaries. The rapid perfusion and scanning protocol ensured that all tissues are available for further analysis via higher resolution CT of smaller sections or traditional histological sectioning.
The Impact of Cardiac Lipotoxicity on Cardiac Function and Mirnas Signature in Obese and Non-Obese Rats with Myocardial Infarction
Authors: Marín-Royo Gema , Ortega-Hernández Adriana , Martínez-Martínez Ernesto , Jurado-López Raquel , Luaces María , Islas Fabián , Gómez-Garre Dulcenombre , Delgado-Valero Beatriz , Lagunas Esther , Ramchandani Bunty , García-Bouza Mónica , Nieto María Luisa , Cachofeiro Victoria 
Published: January 2019

AbstractCardiac lipotoxicity is involved in the cardiac functional consequences associated with obesity. Therefore, the aim of this study was to explore whether changes in the mitochondrial lipid cardiac profile could reflect differences in cardiac function and structure in obese and non-obese rats with myocardial infarction (MI). Whether these changes can also be reflected in a specific plasma miRNA signature as markers of cardiac damage was also evaluated. Rats were fed with either standard (3.5% fat) or high fat diet (35% fat) for 6 weeks before the induction of MI and sacrificed 4 weeks later. MI showed cardiac lipotoxicity independently of the presence of obesity, although obese and non-obese rats did not present the same cardiac lipid profile at mitochondrial level. Several cardiac lipid species in mitochondria, including cardiolipins and triglycerides, were associated with myocardial fibrosis, with mitochondrial triglyceride levels being independently associated with it; this supports that lipotoxicity can affect cardiac function. MI down-regulated plasma levels of miRNA 15b-5p and 194-5p in obese and non-obese animals, which were associated with cardiac function, mitochondrial lipids and myocardial fibrosis, with miRNA 15b-5p levels being independently associated with cardiac fibrosis. This could support that lipotoxicity could affect heart function by modulating plasma miRNAs.
Identification of epileptic brain states by dynamic functional connectivity analysis of simultaneous EEG-fMRI: a dictionary learning approach
Authors: Abreu Rodolfo , Leal Alberto , Figueiredo Patrícia 
Published: January 2019

AbstractMost fMRI studies of the brain’s intrinsic functional connectivity (FC) have assumed that this is static; however, it is now clear that it changes over time. This is particularly relevant in epilepsy, which is characterized by a continuous interchange between epileptic and normal brain states associated with the occurrence of epileptic activity. Interestingly, recurrent states of dynamic FC (dFC) have been found in fMRI data using unsupervised learning techniques, assuming either their sparse or non-sparse combination. Here, we propose an l1-norm regularized dictionary learning (l1-DL) approach for dFC state estimation, which allows an intermediate and flexible degree of sparsity in time, and demonstrate its application in the identification of epilepsy-related dFC states using simultaneous EEG-fMRI data. With this l1-DL approach, we aim to accommodate a potentially varying degree of sparsity upon the interchange between epileptic and non-epileptic dFC states. The simultaneous recording of the EEG is used to extract time courses representative of epileptic activity, which are incorporated into the fMRI dFC state analysis to inform the selection of epilepsy-related dFC states. We found that the proposed l1-DL method performed best at identifying epilepsy-related dFC states, when compared with two alternative methods of extreme sparsity (k-means clustering, maximum; and principal component analysis, minimum), as well as an l0-norm regularization framework (l0-DL), with a fixed amount of temporal sparsity. We further showed that epilepsy-related dFC states provide novel insights into the dynamics of epileptic networks, which go beyond the information provided by more conventional EEG-correlated fMRI analysis, and which were concordant with the clinical profile of each patient. In addition to its application in epilepsy, our study provides a new dFC state identification method of potential relevance for studying brain functional connectivity dynamics in general.
Influence of accuracy, repeatability and detection probability in the reliability of species-specific eDNA based approaches
Authors: Mauvisseau Quentin , Burian Alfred , Gibson Ceri , Brys Rein , Ramsey Andrew , Sweet Michael 
Published: January 2019

AbstractEnvironmental DNA (eDNA) barcoding has a high potential to increase the cost-efficiency of species detection and monitoring in aquatic habitats. However, despite vast developments in the field, many published assays often lack detailed validation and there is little to no commonly (agreed upon) standardization of protocols. In this study, we evaluated the reliability of eDNA detection and quantification using published primers and assays targeting the Freshwater Pearl Mussel as a model organism. We first assessed limits of detection for two different target genes (COI and 16S) following the MIQE guidelines, and then tested the reliability of quantification in a double-blind mesocosm experiment. Our results reveal that different methodological indicators, namely accuracy, repeatability and detection probability affected the reliability of eDNA measurement at the different levels tested. The selection of the optimal analytical method was mainly determined by detection probability. Both the COI and 16S assays were highly specific for the targeted organism and showed similar accuracy and repeatability, whilst the limit of detection was clearly lower for the COI based approach. In contrast, the reliability of eDNA quantification hinged on repeatability, reflected by the scattering (r2 = 0.87) around the relationship between eDNA and mussel density in mesocosms. A bootstrapping approach, which allowed for the assignment of measures associated with repeatability of samples, revealed that variability between natural replicates (i.e. accuracy) strongly influenced the number of replicates required for a reliable species detection and quantification in the field.
Exosomes Cause Preterm Birth in Mice: Evidence for Paracrine Signaling in Pregnancy
Authors: Sheller-Miller Samantha , Trivedi Jayshil , Yellon Steven M. , Menon Ramkumar 
Published: January 2019

AbstractEndocrine factors and signals of fetal organ maturation are reported determinants of birth timing. To test the hypothesis that paracrine signaling by exosomes are key regulators of parturition, maternal plasma exosomes from CD-1 mice were isolated and characterized throughout gestation and the biological pathways associated with differentially-expressed cargo proteins were determined. Results indicate that the shape and size of exosomes remained constant throughout gestation; however, a progressive increase in the quantity of exosomes carrying inflammatory mediators was observed from gestation day (E)5 to E19. In addition, the effects of late-gestation (E18) plasma exosomes derived from feto-maternal uterine tissues on parturition was determined. Intraperitoneal injection of E18 exosomes into E15 mice localized in maternal reproductive tract tissues and in intrauterine fetal compartments. Compared to controls that delivered at term, preterm birth occurred in exosome-treated mice on E18 and was preceded by increased inflammatory mediators on E17 in the cervix, uterus, and fetal membranes but not in the placenta. This effect was not observed in mice injected with early-gestation (E9) exosomes. This study provides evidence that exosomes function as paracrine mediators of labor and delivery.
Molecular structure and function of myelin protein P0 in membrane stacking
Authors: Raasakka Arne , Ruskamo Salla , Kowal Julia , Han Huijong , Baumann Anne , Myllykoski Matti , Fasano Anna , Rossano Rocco , Riccio Paolo , Bürck Jochen , Ulrich Anne S. , Stahlberg Henning , Kursula Petri 
Published: January 2019

AbstractCompact myelin forms the basis of nerve insulation essential for higher vertebrates. Dozens of myelin membrane bilayers undergo tight stacking, and in the peripheral nervous system, this is partially enabled by myelin protein zero (P0). Consisting of an immunoglobulin (Ig)-like extracellular domain, a single transmembrane helix, and a cytoplasmic extension (P0ct), P0 harbours an important task in ensuring the integrity of compact myelin in the extracellular compartment, referred to as the intraperiod line. Several disease mutations resulting in peripheral neuropathies have been identified for P0, reflecting its physiological importance, but the arrangement of P0 within the myelin ultrastructure remains obscure. We performed a biophysical characterization of recombinant P0ct. P0ct contributes to the binding affinity between apposed cytoplasmic myelin membrane leaflets, which not only results in changes of the bilayer properties, but also potentially involves the arrangement of the Ig-like domains in a manner that stabilizes the intraperiod line. Transmission electron cryomicroscopy of native full-length P0 showed that P0 stacks lipid membranes by forming antiparallel dimers between the extracellular Ig-like domains. The zipper-like arrangement of the P0 extracellular domains between two membranes explains the double structure of the myelin intraperiod line. Our results contribute to the understanding of PNS myelin, the role of P0 therein, and the underlying molecular foundation of compact myelin stability in health and disease.
The relationship between oxidant levels and gut physiology in a litter-feeding termite
Authors: Sousa Gessica , Gandara Ana Caroline P. , Oliveira Pedro L. , Gomes Fabio M. , Bahia Ana Cristina , Machado Ednildo A. 
Published: January 2019

AbstractThe termite gut is an efficient decomposer of polyphenol-rich diets, such as lignocellulosic biomasses, and it has been proposed that non-enzymatic oxidative mechanisms could be involved with the digestive process in these animals. However, oxidant levels are completely unknown in termites, as well as protective mechanisms against oxidative damage to the termite gut and its microbiota. As the first step in investigating the role oxidants plays in termite gut physiology, this work presents oxidant levels, antioxidant enzymatic defenses, cell renewal and microbiota abundance along the litter-feeding termite Cornitermes cumulans gut compartments (foregut, midgut, mixed segment and hindgut p1, p3, p4, and p5 segments) and salivary glands. The results show variable levels of oxidants along the C. cumulans gut, the production of antioxidant enzymes, gut cell renewal as potential defenses against oxidative injuries and the profile of microbiota distribution (being predominantly inverse to oxidant levels). In this fashion, the oxidative challenges imposed by polyphenol-rich diet seem to be circumvented by the C. cumulans gut, ensuring efficiency of the digestive process together with preservation of tissue homoeostasis and microbiota growth. These results present new insights into the physicochemical properties of the gut in a litter-feeding termite, expanding our view in relation to termites’ digestive physiology.
Finding and analysing the minimum set of driver nodes required to control multilayer networks
Authors: Nacher Jose C. , Ishitsuka Masayuki , Miyazaki Shuichi , Akutsu Tatsuya 
Published: January 2019

AbstractIt is difficult to control multilayer networks in situations with real-world complexity. Here, we first define the multilayer control problem in terms of the minimum dominating set (MDS) controllability framework and mathematically demonstrate that simple formulas can be used to estimate the size of the minimum dominating set in multilayer (MDSM) complex networks. Second, we develop a new algorithm that efficiently identifies the MDSM in up to 6 layers, with several thousand nodes in each layer network. Interestingly, the findings reveal that the MDSM size for similar networks does not significantly differ from that required to control a single network. This result opens future directions for controlling, for example, multiple species by identifying a common set of enzymes or proteins for drug targeting. We apply our methods to 70 genome-wide metabolic networks across major plant lineages, unveiling some relationships between controllability in multilayer networks and metabolic functions at the genome scale.
Geoarchaeological Evidence of Middle-Age Tsunamis at Stromboli and Consequences for the Tsunami Hazard in the Southern Tyrrhenian Sea
Authors: Rosi M. , Levi S. T. , Pistolesi M. , Bertagnini A. , Brunelli D. , Cannavò V. , Di Renzoni A. , Ferranti F. , Renzulli A. , Yoon D. 
Published: January 2019

AbstractLarge-scale landslides at volcanic islands are one of the most dangerous geological phenomena, able to generate tsunamis whose effects can propagate far from the source. However, related deposits are scarcely preserved on-land in the geologic records, and are often difficult to be interpreted. Here we show the discovery of three unprecedented well-preserved tsunami deposits related to repeated flank collapses of the volcanic island of Stromboli (Southern Italy) occurred during the Late Middle Ages. Based on carbon datings, on stratigraphic, volcanological and archaeological evidence, we link the oldest, highest-magnitude investigated tsunami to the following rapid abandonment of the island which was inhabited at that time, contrary than previously thought. The destructive power of this event is also possibly related to a huge marine storm that devastated the ports of Naples in 1343 (200 km north of Stromboli) described by the famous writer Petrarch. The portrayed devastation can be potentially attributed to the arrival of multiple tsunami waves generated by a major landslide in Stromboli island, confirming the hypothetical hazard of these phenomena at a regional scale.
High Serum Uric Acid is Highly Associated with a Reduced Left Ventricular Ejection Fraction Rather than Increased Plasma B-type Natriuretic Peptide in Patients with Cardiovascular Diseases
Authors: Oki Yoshitsugu , Kawai Makoto , Minai Kosuke , Ogawa Kazuo , Inoue Yasunori , Morimoto Satoshi , Tanaka Toshikazu , Nagoshi Tomohisa , Ogawa Takayuki , Yoshimura Michihiro 
Published: January 2019

AbstractHigh serum uric acid (UA) has been reported to be associated with left ventricular (LV) dysfunction; however, the relationship between UA and plasma B-type natriuretic peptide (BNP), a sensitive biomarker of heart failure, is still unclear. This study investigated their relationship to provide an accurate assessment of high UA. The study patients consisted of 3,077 subjects who underwent cardiac catheterization because of various cardiovascular disorders. Since the explanatory factors of multiple regression analysis were mostly confounding with each other, subgroup analysis was performed by quartering the study population using the respective risk factors and by covariance structure analysis. This analysis revealed that UA was almost always well associated with a reduced LV ejection fraction (LVEF), but generally not with BNP. UA was significantly associated with BNP in lean aged females, but not in obese adolescent males, although LVEF was significantly reduced in response to a high UA in both groups. A high UA is a direct risk factor for cardiac dysfunction from the perspective of BNP; however, augmentation of BNP in response to a high UA would likely be restricted among obese adolescent males. On the other hand, the observed LV systolic dysfunction, such as LVEF, reflects a high UA on an almost constant basis.