bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analyzing synchronized clusters in neuron networks
Authors: Lodi Matteo , Della Rossa Fabio , Sorrentino Francesco , Storace Marco 
Published: October 2020

AbstractThe presence of synchronized clusters in neuron networks is a hallmark of information transmission and processing. Common approaches to study cluster synchronization in networks of coupled oscillators ground on simplifying assumptions, which often neglect key biological features of neuron networks. Here we propose a general framework to study presence and stability of synchronous clusters in more realistic models of neuron networks, characterized by the presence of delays, different kinds of neurons and synapses. Application of this framework to two examples with different size and features (the directed network of the macaque cerebral cortex and the swim central pattern generator of a mollusc) provides an interpretation key to explain known functional mechanisms emerging from the combination of anatomy and neuron dynamics. The cluster synchronization analysis is carried out also by changing parameters and studying bifurcations. Despite some modeling simplifications in one of the examples, the obtained results are in good agreement with previously reported biological data.
Quantified ischemic core’s radiological hypodensity and risk of parenchymal hematoma in > 4.5 h-window stroke thrombectomy
Authors: Chavarría-Miranda Alba , Yugueros Bárbara , Gómez-Vicente Beatriz , Schüller Miguel , Galván Jorge , Castaño Miguel , Calleja Ana I. , Cortijo Elisa , de Lera Mercedes , Reyes Javier , Coco-Martín María Begoña , Agulla Jesús , Martínez-Galdámez Mario , Arenillas Juan F. 
Published: October 2020

AbstractWe aimed to study the relationship between the ischemic core’s (IC) radiological hypodensity and the risk of parenchymal haematoma after endovascular therapy (EVT) in acute ischemic stroke (AIS) presenting > 4.5 h from onset. We studied AIS patients with a proximal anterior circulation occlusion > 4.5 h from symptoms onset treated with primary EVT. The IC regions of interest (ROI) were manually delineated on pretreatment CT within the affected hemisphere and their specular ROIs on the unaffected side. IC hypodensity ratio was calculated by dividing mean Hounsfield Unit (HU) value from all ROIs in affected/unaffected hemisphere. Primary endpoint: parenchymal hematoma (PH) type hemorrhagic transformation. Secondary: poor long-term clinical outcome. From May 2015 to November 2018, 648 consecutive AIS patients received reperfusion therapies and 107 met all inclusion criteria. PH after EVT was diagnosed in 33 (31%) patients. In bivariate analyses, IC hypodensity ratio (p < 0.001) and minimum HU value (p = 0.008) were associated with PH. A lower IC hypodensity ratio [OR < 0.001 (< 0.001–0.116) p 0.016] predicted PH but not poor clinical outcome in multivariable logistic regression models. A lower IC radiological density predicted a higher risk of PH in > 4.5 h-window AIS patients treated with primary EVT, although it was not independently associated with a worse clinical outcome.
Spatial variations in the stable isotope composition of the benthic algae, Halimeda tuna, and implications for paleothermometry
Authors: Stokes M. Dale , Leichter James J. , Wing Stephen R. 
Published: October 2020

AbstractOn Conch Reef, Florida Keys, USA we examined the effects of reef hydrography and topography on the patterns of stable isotope values (δ18O and δ13C) in the benthic green alga, Halimeda tuna. During the summer, benthic temperatures show high-frequency fluctuations (2 to 8 °C) associated with internal waves that advected cool, nutrient-rich water across the reef. The interaction between local water flow and reef morphology resulted in a highly heterogenous physical environment even within isobaths that likely influenced the growth regime of H. tuna. Variability in H. tuna isotopic values even among closely located individuals suggest biological responses to the observed environmental heterogeneity. Although isotopic composition of reef carbonate material can be used to reconstruct past temperatures (T(°C) = 14.2–3.6 (δ18OHalimeda − δ18Oseawater); r2 = 0.92), comparing the temperatures measured across the reef with that predicted by an isotopic thermometer suggests complex interactions between the environment and Halimeda carbonate formation at temporal and spatial scales not normally considered in mixed sediment samples. The divergence in estimated range between measured and predicted temperatures demonstrates the existence of species- and location-specific isotopic relationships with physical and environmental factors that should be considered in contemporary as well as ancient reef settings.
Full-length transcriptome sequencing analysis and development of EST-SSR markers for the endangered species Populus wulianensis
Authors: Wu Qichao , Zang Fengqi , Xie Xiaoman , Ma Yan , Zheng Yongqi , Zang Dekui 
Published: October 2020

AbstractPopulus wulianensis is an endangered species endemic to Shandong Province, China. Despite the economic and ornamental value of this species, few genomics and genetic studies have been performed. In this study, we performed a relevant analysis of the full-length transcriptome sequencing data of P. wulianensis and obtained expressed sequence tag (EST)-simple sequence repeat (SSR) markers with polymorphisms that can be used for further genetic research. In total, 8.18 Gb (3,521,665) clean reads with an average GC content of 42.12% were obtained. From the corrected 64,737 high-quality isoforms, 42,323 transcript sequences were obtained after redundancy analysis with CD-HIT. Among these transcript sequences, 41,876 sequences were annotated successfully. A total of 23,539 potential EST-SSRs were identified from 16,057 sequences. Excluding mononucleotides, the most abundant motifs were trinucleotide SSRs (47.80%), followed by di- (46.80%), tetra- (2.98%), hexa- (1.58%) and pentanucleotide SSRs (0.84%). Among the 100 designed EST-SSRs, 18 were polymorphic with high PIC values (0.721 and 0.683) and could be used for analyses of the genetic diversity and population structure of P. wulianensis. These full-length transcriptome sequencing data will facilitate gene discovery and functional genomics research in P. wulianensis, and the novel EST-SSRs developed in our study will promote molecular-assisted breeding, genetic diversity and conservation biology research in this species.
A novel MRI compatible mouse fracture model to characterize and monitor bone regeneration and tissue composition
Authors: Schmitz Nina , Timmen Melanie , Kostka Katharina , Hoerr Verena , Schwarz Christian , Faber Cornelius , Hansen Uwe , Matthys Romano , Raschke Michael J. , Stange Richard 
Published: October 2020

AbstractOver the last years, murine in vivo magnetic resonance imaging (MRI) contributed to a new understanding of tissue composition, regeneration and diseases. Due to artefacts generated by the currently used metal implants, MRI is limited in fracture healing research so far. In this study, we investigated a novel MRI-compatible, ceramic intramedullary fracture implant during bone regeneration in mice. Three-point-bending revealed a higher stiffness of the ceramic material compared to the metal implants. Electron microscopy displayed a rough surface of the ceramic implant that was comparable to standard metal devices and allowed cell attachment and growth of osteoblastic cells. MicroCT-imaging illustrated the development of the callus around the fracture site indicating a regular progressing healing process when using the novel implant. In MRI, different callus tissues and the implant could clearly be distinguished from each other without any artefacts. Monitoring fracture healing using MRI-compatible implants will improve our knowledge of callus tissue regeneration by 3D insights longitudinal in the same living organism, which might also help to reduce the consumption of animals for future fracture healing studies, significantly. Finally, this study may be translated into clinical application to improve our knowledge about human bone regeneration.
Progressive optic atrophy in a retinal ganglion cell-specific mouse model of complex I deficiency
Authors: Wang Luyu , Klingeborn Mikael , Travis Amanda M. , Hao Ying , Arshavsky Vadim Y. , Gospe Sidney M. 
Published: October 2020

AbstractOptic atrophy resulting from retinal ganglion cell (RGC) degeneration is a prominent ocular manifestation of mitochondrial dysfunction. Although transgenic mice lacking the mitochondrial complex I accessory subunit NDUFS4 develop early-onset optic atrophy, severe systemic mitochondrial dysfunction leads to very early death and makes this mouse line impractical for studying the pathobiology of mitochondrial optic neuropathies. Theoretically, RGC-specific inactivation of ndufs4 would allow characterization of RGC degeneration over a longer time course, provided that RGC death from mitochondrial dysfunction is a cell-autonomous process. We demonstrate that the vesicular glutamate transporter VGLUT2 may be exploited to drive robust Cre recombinase expression in RGCs without any expression observed in directly neighboring retinal cell types. Deletion of ndufs4 in RGCs resulted in reduced expression of NDUFS4 protein within the optic nerves of Vglut2-Cre;ndufs4loxP/loxP mice. RGC degeneration in Vglut2-Cre;ndufs4loxP/loxP retinas commenced around postnatal day 45 (P45) and progressed to loss of two-thirds of RGCs by P90, confirming that intrinsic complex I dysfunction is sufficient to induce RGC death. The rapidly-developing optic atrophy makes the Vglut2-Cre;ndufs4loxP/loxP mouse line a promising preclinical model for testing therapies for currently untreatable mitochondrial optic neuropathies such as Leber Hereditary Optic Neuropathy.
Long-term outcomes of omentum-preserving versus resecting gastrectomy for locally advanced gastric cancer with propensity score analysis
Authors: Sakimura Yusuke , Inaki Noriyuki , Tsuji Toshikatsu , Kadoya Shinichi , Bando Hiroyuki 
Published: October 2020

AbstractOmentectomy is conducted for advanced gastric cancer (AGC) patients as radical surgery without an adequate discussion of the effect. This study was conducted to reveal the impact of omentum-preserving gastrectomy on postoperative outcomes. AGC patients with cT3 and 4 disease who underwent total or distal gastrectomy with R0 resection were identified retrospectively. They were divided into the omentum-preserved group (OPG) and the omentum-resected group (ORG) and matched with propensity score matching with multiple imputation for missing values. Three-year overall survival (OS) and 3-year relapse-free survival (RFS) were compared, and the first recurrence site and complications were analysed. The numbers of eligible patients were 94 in the OPG and 144 in the ORG, and after matching, the number was 73 in each group. No significant difference was found in the 3-year OS rate (OPG: 78.9 vs. ORG: 78.9, P = 0.54) or the 3-year RFS rate (OPG: 77.8 vs. ORG: 68.2, P = 0.24). The proportions of peritoneal carcinomatosis and peritoneal dissemination as the first recurrence site and the rate and severity of complications were similar in the two groups. Omentectomy is not required for radical gastrectomy for AGC.
Wide-angle, wide-band, polarization-insensitive metamaterial absorber for thermal energy harvesting
Authors: Elsharabasy Ahmed , Bakr Mohamed , Deen M. Jamal 
Published: October 2020

AbstractWe propose a wide-band metamaterial perfect absorber (MPA), using the coupling in the near-field of a quadruple split-ring resonator concentric with crossed ellipses. We designed the MPA with a metal–insulator-metal (MIM) structure for use in thermal energy harvesting. A gradient-based optimization approach was carried out to maximize the absorption of infrared (IR) radiation around 10 μm. Owing to the near-field coupling of resonators with optimal design parameters, the peaks of the absorption responses approach each other, thus broadening the overall bandwidth with almost unity absorptivity. The proposed design has a resonance at 10 μm resulting from magnetic polaritons (MPs) and thus maintains high absorption above 99% up to a range of incident-angles greater than 60° and exhibits a polarization-free behavior due to symmetry. When the optimal design was numerically examined to fabrication tolerances, it showed negligible sensitivities in the absorptivity with respect to design parameters. The strong electric field enhancement inside the split-ring gaps and between the ends of the cross arms and the surrounding ring enables designing MIM diodes to rectify the harvested thermal radiations at 288 K. MIM diodes can be built by the deposition of thin insulators to sit in these gaps. The MIM diode and MPA work together to harvest and rectify the incident IR radiation in a manner similar to the operation of rectennas. The MPA outperforms the traditional nano-antennas in impedance matching efficiency because of its higher resistance. Also, its dual-polarization reception capability doubles the rectenna efficiency. Our proposed MPA retained absorptivity more than 99% when coupled with MIM diodes whose resistances are in the range of 500 Ω–1 MΩ.
Construction of a dense genetic map of the Malus fusca fire blight resistant accession MAL0045 using tunable genotyping-by-sequencing SNPs and microsatellites
Authors: Emeriewen Ofere Francis , Richter Klaus , Berner Thomas , Keilwagen Jens , Schnable Patrick S. , Malnoy Mickael , Peil Andreas 
Published: October 2020

AbstractAlthough, the Pacific crabapple,Malus fusca, is a hardy and disease resistant species, studies relating to the genetics of its unique traits are very limited partly due to the lack of a genetic map of this interesting wild apple. An accession ofM. fusca(MAL0045) of Julius Kühn-Institut collection in Germany is highly resistant to fire blight disease, incited by different strains of the causative pathogen—Erwinia amylovora. This is the most destructive bacterial disease ofMalusof which most of the domesticated apples (Malus domestica) are susceptible. Using a scarcely dense genetic map derived from a population of 134 individuals of MAL0045 × ‘Idared’, the locus (Mfu10) controlling fire blight resistance mapped on linkage group 10 (LG10) and explained up to 66% of the phenotypic variance with different strains. Although the development of robust and tightly linked molecular markers on LG10 through chromosome walking approach led to the identification of a major candidate gene, any minor effect locus remained elusive possibly due to the lack of marker density of the entire genetic map. Therefore, we have developed a dense genetic map ofM. fuscausing tunable genotyping-by-sequencing (tGBS) approach. Of thousands of de novo SNPs identified, 2677 were informative inM. fuscaand 90.5% of these successfully mapped. In addition, integration of SNP data and microsatellite (SSR) data resulted in a final map comprising 17 LGs with 613 loci spanning 1081.35 centi Morgan (cM). This map will serve as a template for mapping using different strains of the pathogen.
Deficits in hippocampal neurogenesis in obesity-dependent and -independent type-2 diabetes mellitus mouse models
Authors: Bonds Jacqueline A. , Shetti Aashutosh , Stephen Terilyn K. L. , Bonini Marcelo G. , Minshall Richard D. , Lazarov Orly 
Published: October 2020

AbstractHippocampal neurogenesis plays an important role in learning and memory function throughout life. Declines in this process have been observed in both aging and Alzheimer’s disease (AD). Type 2 Diabetes mellitus (T2DM) is a disorder characterized by insulin resistance and impaired glucose metabolism. T2DM often results in cognitive decline in adults, and significantly increases the risk of AD development. The pathways underlying T2DM-induced cognitive deficits are not known. Some studies suggest that alterations in hippocampal neurogenesis may contribute to cognitive deterioration, however, the fate of neurogenesis in these studies is highly controversial. To address this problem, we utilized two models of T2DM: (1) obesity-independent MKR transgenic mice expressing a mutated form of the human insulin-like growth factor 1 receptor (IGF-1R) in skeletal muscle, and (2) Obesity-dependent db/db mice harboring a mutation in the leptin receptor. Our results show that both models of T2DM display compromised hippocampal neurogenesis. We show that the number of new neurons in the hippocampus of these mice is reduced. Clone formation capacity of neural progenitor cells isolated from the db/db mice is deficient. Expression of insulin receptor and epidermal growth factor receptor was reduced in hippocampal neurospheres isolated from db/db mice. Results from this study warrant further investigation into the mechanisms underlying decreased neurogenesis in T2DM and its link to the cognitive decline observed in this disorder.
Validation of stable reference genes in Staphylococcus aureus to study gene expression under photodynamic treatment: a case study of SEB virulence factor analysis
Authors: Ogonowska Patrycja , Nakonieczna Joanna 
Published: October 2020

AbstractStaphylococcal enterotoxin B (SEB), encoded by the seb gene, is a virulence factor produced by Staphylococcus aureus that is involved mainly in food poisoning and is known to act as an aggravating factor in patients with atopic dermatitis. Research results in animal infection models support the concept that superantigens, including SEB contribute to sepsis and skin and soft tissue infections. In contrast to antibiotics, antimicrobial photodynamic inactivation (aPDI) is a promising method to combat both bacterial cells and virulence factors. The main aims of this research were to (1) select the most stable reference genes under sublethal aPDI treatments and (2) evaluate the impact of aPDI on seb. Two aPDI combinations were applied under sublethal conditions: rose bengal (RB) and green light (λmax = 515 nm) and new methylene blue (NMB) and red light (λmax = 632 nm). The stability of ten candidate reference genes (16S rRNA, fabD, ftsZ, gmk, gyrB, proC, pyk, rho, rpoB and tpiA) was evaluated upon aPDI using four software packages—BestKeeper, geNorm, NormFinder and RefFinder. Statistical analyses ranked ftsZ and gmk (RB + green light) and ftsZ, proC, and fabD (NMB + red light) as the most stable reference genes upon photodynamic treatment. Our studies showed downregulation of seb under both aPDI conditions, suggesting that aPDI could decrease the level of virulence factors.
Experimental measurements and modelling of viscosity and density of calcium and potassium chlorides ternary solutions
Authors: Arshad Mohammad , Easa Ahmed , Qiblawey Hazim , Nasser Mustafa , Benamor Abdelbaki , Bhosale Rahul , Al-Ghouti Mohammad 
Published: October 2020

AbstractMeasured viscosity and density data for ternary aqueous solutions of CaCl2 and KCl are presented at temperatures between 293 and 323 K with 5 K increment. A modified Jones–Dole was introduced by adding extra terms and proved to be suitable for modelling of the viscosity data. Goldsack and Franchetto, Hu and Exponential models are used to correlate the viscosity data, too. Al models are correlated as a function of temperature and concentration. All models had successfully predicted the viscosity with high precision reaching a maximum average absolute deviation (AAD) of less than 2.3%. The modified Jones–Dole showed the best results among other models. Viscosity of the ternary solution is higher than the viscosity of water by about 15% at low concentrations and reaches about 270% at the highest concentrations. The amount of CaCl2 has more significant effect on the ternary mixture viscosity compared to KCl. This has created difficulty in measuring the viscosity and consequently the challenge in finding the different models parameters. Ternary solution densities were successfully correlate with Kumar’s model with AAD of less than 0.4%. Comparison of the ternary solution density and viscosity with the few available data literature showed a good agreement.
Gravitational models explain shifts on human visual attention
Authors: Zanca Dario , Gori Marco , Melacci Stefano , Rufa Alessandra 
Published: October 2020

AbstractVisual attention refers to the human brain’s ability to select relevant sensory information for preferential processing, improving performance in visual and cognitive tasks. It proceeds in two phases. One in which visual feature maps are acquired and processed in parallel. Another where the information from these maps is merged in order to select a single location to be attended for further and more complex computations and reasoning. Its computational description is challenging, especially if the temporal dynamics of the process are taken into account. Numerous methods to estimate saliency have been proposed in the last 3 decades. They achieve almost perfect performance in estimating saliency at the pixel level, but the way they generate shifts in visual attention fully depends on winner-take-all (WTA) circuitry. WTA is implemented by the biological hardware in order to select a location with maximum saliency, towards which to direct overt attention. In this paper we propose a gravitational model to describe the attentional shifts. Every single feature acts as an attractor and the shifts are the result of the joint effects of the attractors. In the current framework, the assumption of a single, centralized saliency map is no longer necessary, though still plausible. Quantitative results on two large image datasets show that this model predicts shifts more accurately than winner-take-all.
CT features and disease spread patterns in ROS1-rearranged lung adenocarcinomas: comparison with those of EGFR-mutant or ALK-rearranged lung adenocarcinomas
Authors: Woo Jung Han , Kim Tae Jung , Kim Tae Sung , Han Joungho 
Published: October 2020

AbstractThe purpose of this study was to investigate the differences in CT characteristics and disease spread patterns between ROS1-rearranged adenocarcinomas and epidermal growth factor receptor (EGFR)-mutant or anaplastic lymphoma kinase (ALK)-rearranged adenocarcinomas. Patients with stage IIIb/IV adenocarcinoma with ROS1 rearrangement, EGFR mutations, or ALK rearrangement were retrospectively identified. Two radiologists evaluated CT features and disease spread patterns. A multivariable logistic regression model was applied to determine the clinical and CT characteristics that can discriminate between ROS1-rearranged and EGFR-mutant or ALK-rearranged adenocarcinomas. A cohort of 169 patients was identified (ROS1 = 23, EGFR = 120, and ALK = 26). Compared to EGFR-mutant adenocarcinomas, ROS1-rearranged adenocarcinomas were less likely to have air-bronchogram (p = 0.011) and pleural retraction (p = 0.048) and more likely to have pleural effusion (p = 0.025), pericardial metastases (p < 0.001), intrathoracic and extrathoracic nodal metastases (p = 0.047 and 0.023, respectively), and brain metastases (p = 0.017). Following multivariable analysis, age (OR = 1.06; 95% CI: 1.01, 1.12; p = 0.024), pericardial metastases (OR = 10.50; 95% CI: 2.10, 52.60; p = 0.005), and nodal metastases (OR = 8.55; 95% CI: 1.14, 62.52; p = 0.037) were found to be more common in ROS1-rearranged tumors than in non-ROS1-rearranged tumors. ROS1-rearranged adenocarcinomas appeared as solid tumors and were associated with young age, pericardial metastases and advanced nodal metastases relative to tumors with EGFR mutations or ALK rearrangement.