bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reactivation of Cytomegalovirus Increases Nitric Oxide and IL-10 Levels in Sepsis and is Associated with Changes in Renal Parameters and Worse Clinical Outcome
Authors: Silva Taylon Felipe , Concato Virgínia Márcia , Tomiotto-Pellissier Fernanda , Gonçalves Manoela Daiele , Bortoleti Bruna Taciane da Silva , Tavares Eliandro Reis , Yamauchi Lucy Megumi , Grion Cintia Magalhães Carvalho , Simão Andréa Name Colado , Miranda-Sapla Milena Menegazzo , Costa Idessania Nazareth , Pavanelli Wander Rogério , Conchon-Costa Ivete 
Published: June 2019

Abstract CMV reactivation has been widely associated with bacterial sepsis and occurs in approximately 30% of these individuals, is associated with a longer ICU stay, prolongation of the need for mechanical ventilation, and over 80% increase in the mortality rate, being directly associated with severe organ dysfunction and hemodynamic imbalance. Thus, the aim of this study was to evaluate the role of CMV reactivation in sepsis progression. The overall occurrence of cytomegalovirus reactivation in the cohort was 17.58%. Was observed an increase in plasma levels of NO, reduction of percentage of free days of mechanical ventilation and arterial pH, as well as changes in coagulation parameters in the reactivated group. There was also a significant increase in IL-10, creatinine, urea levels and reduction of 24-hour urine output. These variables still correlated with viral load, demonstrating an association between the reactivation process and kidney failure present in sepsis. The reactivated group still had 2.1 times the risk of developing septic shock and an increase in the mortality rates. CMV is reactivated in sepsis and these patients presented a higher risk of developing septic shock and higher mortality rates and our data suggest that IL-10 and NO may be involved in this process.
Estimating Y-Str Mutation Rates and Tmrca Through Deep-Rooting Italian Pedigrees
Authors: Boattini Alessio , Sarno Stefania , Mazzarisi Alessandra M. , Viroli Cinzia , De Fanti Sara , Bini Carla , Larmuseau Maarten H. D. , Pelotti Susi , Luiselli Donata 
Published: June 2019

AbstractIn the population genomics era, the study of Y-chromosome variability is still of the greatest interest for several fields ranging from molecular anthropology to forensics and genetic genealogy. In particular, mutation rates of Y-chromosomal Short Tandem Repeats markers (Y-STRs) are key parameters for different interdisciplinary applications. Among them, testing the patrilineal relatedness between individuals and calculating their Time of Most Recent Common Ancestors (TMRCAs) are of the utmost importance. To provide new valuable estimates and to address these issues, we typed 47 Y-STRs (comprising Yfiler, PowerPlex23 and YfilerPlus loci, the recently defined Rapidly Mutating [RM] panel and 11 additional markers often used in genetic genealogical applications) in 135 individuals belonging to 66 deep-rooting paternal genealogies from Northern Italy. Our results confirmed that the genealogy approach is an effective way to obtain reliable Y-STR mutation rate estimates even with a limited number of samples. Moreover, they showed that the impact of multi-step mutations and backmutations is negligible within the temporal scale usually adopted by forensic and genetic genealogy analyses. We then detected a significant association between the number of mutations within genealogies and observed TMRCAs. Therefore, we compared observed and expected TMRCAs by implementing a Bayesian procedure originally designed by Walsh (2001) and showed that the method yields a good performance (up to 96.72%), especially when using the Infinite Alleles Model (IAM).
Label-free detection of nanoparticles using depth scanning correlation interferometric microscopy
Authors: Aygun Ugur , Urey Hakan , Yalcin Ozkumur Ayca 
Published: June 2019

AbstractSingle particle level visualization of biological nanoparticles such as viruses and exosomes is challenging due to their small size and low dielectric contrast. Fluorescence based methods are highly preferred, however they require labelling which may perturb the functionality of the particle of interest. On the other hand, wide-field interferometric microscopy can be used to detect sub-diffraction limited nanoparticles without using any labels. Here we demonstrate that utilization of defocused images enhances the visibility of nanoparticles in interferometric microscopy and thus improves the detectable size limit. With the proposed method termed as Depth Scanning Correlation (DSC) Interferometric Microscopy, we experimentally demonstrate the detection of sub-35nm dielectric particles without using any labels. Furthermore, we demonstrate direct detection of single exosomes. This label-free and high throughput nanoparticle detection technique can be used to sense and characterize biological particles over a range between a few tens to a few hundred nanometers, where conventional methods are insufficient.
Automated monitoring of behaviour in zebrafish after invasive procedures
Authors: Deakin Anthony G. , Buckley Jonathan , AlZu’bi Hamzah S. , Cossins Andrew R. , Spencer Joseph W. , Al’Nuaimy Waleed , Young Iain S. , Thomson Jack S. , Sneddon Lynne U. 
Published: June 2019

AbstractFish are used in a variety of experimental contexts often in high numbers. To maintain their welfare and ensure valid results during invasive procedures it is vital that we can detect subtle changes in behaviour that may allow us to intervene to provide pain-relief. Therefore, an automated method, the Fish Behaviour Index (FBI), was devised and used for testing the impact of laboratory procedures and efficacy of analgesic drugs in the model species, the zebrafish. Cameras with tracking software were used to visually track and quantify female zebrafish behaviour in real time after a number of laboratory procedures including fin clipping, PIT tagging, and nociceptor excitation via injection of acetic acid subcutaneously. The FBI was derived from activity and distance swum measured before and after these procedures compared with control and sham groups. Further, the efficacy of a range of drugs with analgesic properties to identify efficacy of these agents was explored. Lidocaine (5 mg/L), flunixin (8 mg/L) and morphine (48 mg/L) prevented the associated reduction in activity and distance swum after fin clipping. From an ethical perspective, the FBI represents a significant refinement in the use of zebrafish and could be adopted across a wide range of biological disciplines.
Seasonal development of a coastal microbial mat
Authors: Cardoso Daniela Clara , Cretoiu Mariana Silvia , Stal Lucas J. , Bolhuis Henk 
Published: June 2019

AbstractGrowth and activity of coastal microbial mats is strongly seasonal. The development of these mats starts in early spring and fully maturate during late summer, where after growth ceases and subsequently the mat deteriorates by erosion and decomposition in winter. Here, the composition of the microbial community of three different mats developing along the tidal gradient of the North Sea beach of the Dutch barrier island Schiermonnikoog was analysed. The 16S ribosomal RNA molecules and the associated gene were sequenced in order to obtain the active (RNA) and resident (DNA) community members, respectively. Proteobacteria, Cyanobacteria, and Bacteroidetes dominated the mats during the whole year but considerable differences among these groups were found along the tidal gradient and seasonally when observed at a finer taxonomic resolution. Richness and diversity increased during the year starting from a pioneering community that is gradually succeeded by a more diverse climax community. The initial pioneers consisted of the cold-adapted photoautotrophic cyanobacterium Nodularia sp. and potential cold adapted members of the alphaproteobacterial Loktanella genus. These pioneers were succeeded by, amongst others, cyanobacteria belonging to the genera Leptolyngbya, Lyngbya, and Phormidium. At the upper littoral (Dune site), which was characterized by an extensive salt marsh vegetation, the mats contained a distinct bacterial community that potentially contribute to or benefit from plant decay. This study reports in detail on the seasonal changes and succession of these coastal microbial mat communities and discusses the potential forces that drive these changes.
Broadband and Tunable RCS Reduction using High-order Reflections and Salisbury-type Absorption Mechanisms
Authors: Song Jiakun , Wu Xiaoyu , Huang Cheng , Yang Jianing , Ji Chen , Zhang Changlei , Luo Xiangang 
Published: June 2019

AbstractIn this paper, a broadband and tunable radar cross section (RCS) reduction structure is proposed by using the hybrid physical mechanism that is based on high-order reflections and Salisbury-type absorption. Our design combines the high-index grating structure with a traditional Salisbury screen in which the lossy sheet is made of a graphene structure. When it is illuminated by a plane wave with normal incidence, the Salisbury screen can absorb the incoming wave, and the introducing high-index grating structure could further reduce the backward scattering wave by generating high-order reflection beams, which broadens the RCS reduction bandwidth. In addition, the RCS reduction level can be dynamically controlled by tuning the surface resistance of the graphene layer. Simulated results show that the proposed structure can realize tunable RCS reduction between 4.1 and 18 GHz under normal incidence with different graphene resistances. Experimental results are in accordance with those of the simulation results. In addition, the scattering field distributions and the plots of surface power loss density have been illustrated to analyze the RCS-reduction mechanism of our structure.
An in vitro pressure model towards studying the response of primary retinal ganglion cells to elevated hydrostatic pressures
Authors: Wu Jing , Mak Heather Kayew , Chan Yau Kei , Lin Chen , Kong Cihang , Leung Christopher Kai Shun , Shum Ho Cheung 
Published: June 2019

AbstractGlaucoma is a leading cause of blindness characterized by progressive degeneration of retinal ganglion cells (RGCs). A well-established risk factor for the development and progression of glaucoma is elevation of intraocular pressure (IOP). However, how elevated IOP leads to RGC degeneration remains poorly understood. Here, we fabricate a facile, tunable hydrostatic pressure platform to study the effect of increased hydrostatic pressure on RGC axon and total neurite length, cell body area, dendritic branching, and cell survival. The hydrostatic pressure can be adjusted by varying the height of a liquid reservoir attached to a three-dimensional (3D)-printed adapter. The proposed platform enables long-term monitoring of primary RGCs in response to various pressure levels. Our results showed pressure-dependent changes in the axon length, and the total neurite length. The proportion of RGCs with neurite extensions significantly decreased by an average of 38 ± 2% (mean ± SEM) at pressures 30 mmHg and above (p < 0.05). The axon length and total neurite length decreased at a rate of 1.65 ± 0.18 μm and 4.07 ± 0.34 μm, respectively (p < 0.001), for each mmHg increase in pressure after 72 hours pressure treatment. Dendritic branching increased by 0.20 ± 0.05 intersections/day at pressures below 25 mmHg, and decreased by 0.07 ± 0.01 intersections/day at pressures above 25 mmHg (p < 0.001). There were no significant changes in cell body area under different levels of hydrostatic pressure (p ≥ 0.05). Application of this model will facilitate studies on the biophysical mechanisms that contribute to the pathophysiology of glaucoma and provide a channel for the screening of potential pharmacological agents for neuroprotection.
Core regulon of the global anaerobic regulator Anr targets central metabolism functions in Pseudomonas species
Authors: Tribelli Paula M. , Lujan Adela M. , Pardo Agustín , Ibarra José G. , Fernández Do Porto Darío , Smania Andrea , López Nancy I. 
Published: June 2019

AbstractA comparative genome analysis of the global anaerobic regulator Anr regulon in five species of Pseudomonas with different life style was performed. Expression of this regulator was detected in all analyzed Pseudomonas. The predicted Anr regulon (pan-regulon) consisted of 253 genes. However, only 11 Anr-boxes located upstream of qor/hemF, hemN, cioA/PA3931, azu, rpsL, gltP, orthologous to PA2867, cspD, tyrZ, slyD and oprG, were common to all species. Whole genome in silico prediction of metabolic pathways identified genes belonging to heme biosynthesis, cytochromes and Entner-Doudoroff pathway as members of Anr regulon in all strains. Extending genome analysis to 28 Pseudomonas spp. spanning all phylogenetic groups showed Anr-boxes conservation in genes related to these functions. When present, genes related to anaerobic metabolism were predicted to hold Anr-boxes. Focused on the genomes of eight P. aeruginosa isolates of diverse origins, we observed a conserved regulon, sharing nearly 80% of the genes, indicating its key role in this opportunistic pathogen. The results suggest that the core Anr regulon comprises genes involved in central metabolism and aerobic electron transport chain, whereas those genes related to anaerobic metabolism and other functions constitute the accessory Anr-regulon, thereby differentially contributing to the ecological fitness of each Pseudomonas species.
Geometrically designed domain wall trap in tri-segmented nickel magnetic nanowires for spintronics devices
Authors: Nasirpouri Farzad , Peighambari-Sattari Seyed-Majid , Bran Cristina , Palmero Ester M. , Berganza Eguiarte Eider , Vazquez Manuel , Patsopoulos Aristotelis , Kechrakos Dimitris 
Published: June 2019

Abstract“Domain wall traps” have been engineered and well-exploited in nanostrips by creating a geometrical trapping site, e.g. a single notch along a stripe, compared to diameter-modulated (DM) cylindrical magnetic nanowires (NWs) where multi-segmented DM-NWs have been generally studied. Here, we report our systematic study on the magnetization behavior, domain wall structure and its nucleation/propagation in tri-segmented diameter-modulated Ni nanowires, a simple system to investigate the magnetization reversal as function of segment geometry and lay-out order. We find out that the magnetization behavior of single Ni DM-NWs exhibits the significance of positional ordering of thick and thin segments, distinguished by two distinct geometries including: dumbbell-type (type I) and rolling pin-type (type II). Based on experimental and theoretical simulations, it was evidenced that the wide-narrow junctions create trap sites for domain walls where the narrow segment restricts their motion. This type of geometrically engineered nanowires exhibit potential efficiency for future novel spintronic devices in particular when assembled in arrays of DM-NWs as a practical three-dimensional memory device.
Rapid population transfer of a two-level system by a polychromatic driving field
Authors: Li D. X. , Shao X. Q. 
Published: June 2019

AbstractWe propose a simple exact analytical solution for a model consisting of a two-level system and a polychromatic driving field. It helps us to realize a rapid complete population transfer from the ground state to the excited state, and the system can be stable at the excited state for an extremely long time. A combination of the mechanism and the Rydberg atoms successfully prepares the Bell state and multipartite W state, and the experimental feasibility is discussed via the current experimental parameters. Finally, the simple exact analytical solution is generalized into a three-level system, which leads to a significant enhancement of the robustness against dissipation.
Gene expression profiling suggests differences in molecular mechanisms of fin elongation between cichlid species
Authors: Ahi Ehsan Pashay , Richter Florian , Lecaudey Laurène Alicia , Sefc Kristina M. 
Published: June 2019

AbstractComparative analyses of gene regulation inform about the molecular basis of phenotypic trait evolution. Here, we address a fin shape phenotype that evolved multiple times independently across teleost fish, including several species within the family Cichlidae. In a previous study, we proposed a gene regulatory network (GRN) involved in the formation and regeneration of conspicuous filamentous elongations adorning the unpaired fins of theNeolamprologus brichardi. Here, we tested the members of this network in the blockhead cichlid,Steatocranus casuarius, which displays conspicuously elongated dorsal and moderately elongated anal fins. Our study provided evidence for differences in the anatomy of fin elongation and suggested gene regulatory divergence between the two cichlid species. Only a subset of the 20 genes tested inS. casuariusshowed the qPCR expression patterns predicted from the GRN identified inN. brichardi, and several of the gene-by-gene expression correlations differed between the two cichlid species. In comparison toN. brichardi, gene expression patterns inS. casuariuswere in better (but not full) agreement with gene regulatory interactions inferred in zebrafish. WithinS. casuarius, the dorsoventral asymmetry in ornament expression was accompanied by differences in gene expression patterns, including potential regulatory differentiation, between the anal and dorsal fin.
Marker-trait associations and genomic predictions of interspecific pear (Pyrus) fruit characteristics
Authors: Kumar Satish , Kirk Chris , Deng Cecilia Hong , Shirtliff Angela , Wiedow Claudia , Qin Mengfan , Wu Jun , Brewer Lester 
Published: June 2019

AbstractInterspecific pear (Pyrusspp.) hybrid populations are often used to develop novel cultivars. Pear cultivar breeding is a lengthy process because of long juvenility and the subsequent time required for reliable fruit phenotyping. Molecular techniques such as genome-wide association (GWA) and genomic selection (GS) provide an opportunity to fast-forward the development of high-value cultivars. We evaluated the genetic architecture of 10 pear fruit phenotypes (including sensory traits) and the potential of GS using genotyping-by-sequencing of 550 hybrid seedlings from nine interrelated full-sib families. Results from GWA suggested a complex polygenic nature of all 10 traits as the maximum variance explained by each marker was less than 4% of the phenotypic variance. The effect-size of SNPs for each trait suggested many genes of small effect and few of moderate effect. Some genomic regions associated with pear sensory traits were similar to those reported for apple – possibly a result of high synteny between the apple and pear genomes. The average (across nine families) GS accuracy varied from 0.32 (for crispness) to 0.62 (for sweetness), with an across-trait average of 0.42. Further efforts are needed to develop larger genotype-phenotype datasets in order to predict fruit phenotypes of untested seedlings with sufficient efficiency.
Cotton plant defence against a fungal pathogen is enhanced by expanding BLADE-ON-PETIOLE1 expression beyond lateral-organ boundaries
Authors: Zhang Zhennan , Wang Peng , Luo Xiaoli , Yang Chunlin , Tang Ye , Wang Zhian , Hu Guang , Ge Xiaoyang , Xia Guixian , Wu Jiahe 
Published: June 2019

AbstractIn the plant response to pathogen infection, many genes’ expression is temporally induced, while few spatially induced expression genes have been reported. Here, we show that GhBOP1 can autonomously expand expression from restrained tissue when Gossypium hirsutum plants are attacked by Verticillium dahliae, which is considered to be spatially induced expression. Loss- and gain-of-function analyses show that GhBOP1 is a positive regulator in the modulation of plant resistance to V. dahliae. Yeast two-hybrid assays, luciferase complementation imaging and GUS reporting show that GhBOP1 interaction with GhTGA3 promotes its activation activity, regulating the expression of down-stream defence-related genes. Moreover, the induced spatial expression of GhBOP1 is accompanied by GhBP1 repression. Both antagonistically regulate the lignin biosynthesis, conferring cotton plants enhanced resistance to V. dahliae. Taken together, these results demonstrate that GhBOP1 is an economic positive regulator participating in plant defence through both the GhBOP1-GhTGA3 module and lignin accumulation.
Ancient duplications and grass-specific transposition influenced the evolution of LEAFY transcription factor genes
Authors: Gao Bei , Chen Moxian , Li Xiaoshuang , Zhang Jianhua 
Published: June 2019

AbstractThe LFY transcription factor gene family are important in the promotion of cell proliferation and floral development. Understanding their evolution offers an insight into floral development in plant evolution. Though a promiscuous transition intermediate and a gene duplication event within the LFY family had been identified previously, the early evolutionary path of this family remained elusive. Here, we reconstructed the LFY family phylogeny using maximum-likelihood and Bayesian inference methods incorporating LFY genes from all major lineages of streptophytes. The well-resolved phylogeny unveiled a high-confidence duplication event before the functional divergence of types I and II LFY genes in the ancestry of liverworts, mosses and tracheophytes, supporting sub-functionalization of an ancestral promiscuous gene. The identification of promiscuous genes in Osmunda suggested promiscuous LFY genes experienced an ancient transient duplication. Genomic synteny comparisons demonstrated a deep genomic positional conservation of LFY genes and an ancestral lineage-specific transposition activity in grasses.
GABA in the suprachiasmatic nucleus refines circadian output rhythms in mice
Authors: Ono Daisuke , Honma Ken-ichi , Yanagawa Yuchio , Yamanaka Akihiro , Honma Sato 
Published: June 2019

AbstractIn mammals, the circadian rhythms are regulated by the central clock located in the hypothalamic suprachiasmatic nucleus (SCN), which is composed of heterogeneous neurons with various neurotransmitters. Among them an inhibitory neurotransmitter, γ-Amino-Butyric-Acid (GABA), is expressed in almost all SCN neurons, however, its role in the circadian physiology is still unclear. Here, we show that the SCN of fetal mice lacking vesicular GABA transporter (VGAT−/−) or GABA synthesizing enzyme, glutamate decarboxylase (GAD65−/−/67−/−), shows burst firings associated with large Ca2+ spikes throughout 24 hours, which spread over the entire SCN slice in synchrony. By contrast, circadian PER2 rhythms in VGAT−/− and GAD65−/−/67−/− SCN remain intact. SCN-specific VGAT deletion in adult mice dampens circadian behavior rhythm. These findings indicate that GABA in the fetal SCN is necessary for refinement of the circadian firing rhythm and, possibly, for stabilizing the output signals, but not for circadian integration of multiple cellular oscillations.