bluuebunny/crossref_metadata_2025_split huggingface dataset:
Population genetics of the European rabbit along a rural-to-urban gradient
Authors: Ziege Madlen , Theodorou Panagiotis , Jüngling Hannah , Merker Stefan , Plath Martin , Streit Bruno , Lerp Hannes 
Published: February 2020

AbstractThe European rabbit (Oryctolagus cuniculus) is declining in large parts of Europe but populations in some German cities remained so far unaffected by this decline. The question arises of how urbanization affects patterns of population genetic variation and differentiation in German rabbit populations, as urban habitat fragmentation may result in altered meta-population dynamics. To address this question, we used microsatellite markers to genotype rabbit populations occurring along a rural-to-urban gradient in and around the city of Frankfurt, Germany. We found no effect of urbanization on allelic richness. However, the observed heterozygosity was significantly higher in urban than rural populations and also the inbreeding coefficients were lower, most likely reflecting the small population sizes and possibly on-going loss of genetic diversity in structurally impoverished rural areas. Global FST and G′ST-values suggest moderate but significant differentiation between populations. Multiple matrix regression with randomization ascribed this differentiation to isolation-by-environment rather than isolation-by-distance. Analyses of migration rates revealed asymmetrical gene flow, which was higher from rural into urban populations than vice versa and may again reflect intensified agricultural land-use practices in rural areas. We discuss that populations inhabiting urban areas will likely play an important role in the future distribution of European rabbits.
Novel liver fibrosis model in Macaca fascicularis induced by thioacetamide
Authors: Matsuo Megumi , Murata Soichiro , Hasegawa Shunsuke , Hatada Yumi , Ohtsuka Masayuki , Taniguchi Hideki 
Published: February 2020

AbstractAlthough transplantation is the only definitive treatment for liver cirrhosis, there remains a shortage of donors, necessitating that novel treatments be developed. We aimed to establish a liver fibrosis model in Macaca fascicularis that can help accelerate preclinical research. Liver fibrosis was induced by administering thioacetamide (TAA) and carbon tetrachloride (CCl4). Analysis of residual liver function and fibrosis progression was based on clinical indices, such as the Child–Pugh score or fibrotic markers, besides histology. TAA-induced marked fibrosis, whereas CCl4 did not induce fibrosis. Concerning residual liver function, both of TAA and CCl4 worsened the indices of the Child–Pugh score, but only the TAA model increased the retention ratio of indocyanine green. The TAA-induced fibrosis model in Macaca fascicularis worsens fibrosis and residual liver function, mimicking Child–Pugh grade B. Given that our model was evaluated by clinical indices, it could be applicable to preclinical research.
Model-based Comparisons of the Abundance Dynamics of Bacterial Communities in Two Lakes
Authors: Dam Phuongan , Rodriguez-R Luis M. , Luo Chengwei , Hatt Janet , Tsementzi Despina , Konstantinidis Konstantinos T. , Voit Eberhard O. 
Published: February 2020

AbstractLake Lanier (Georgia, USA) is home to more than 11,000 microbial Operational Taxonomic Units (OTUs), many of which exhibit clear annual abundance patterns. To assess the dynamics of this microbial community, we collected time series data of 16S and 18S rRNA gene sequences, recovered from 29 planktonic shotgun metagenomic datasets. Based on these data, we constructed a dynamic mathematical model of bacterial interactions in the lake and used it to analyze changes in the abundances of OTUs. The model accounts for interactions among 14 sub-communities (SCs), which are composed of OTUs blooming at the same time of the year, and three environmental factors. It captures the seasonal variations in abundances of the SCs quite well. Simulation results suggest that changes in water temperature affect the various SCs differentially and that the timing of perturbations is critical. We compared the model results with published results from Lake Mendota (Wisconsin, USA). These comparative analyses between lakes in two very different geographical locations revealed substantially more cooperation and less competition among species in the warmer Lake Lanier than in Lake Mendota.
EEG microstates associated with intra- and inter-subject alpha variability
Authors: Croce Pierpaolo , Quercia Angelica , Costa Sergio , Zappasodi Filippo 
Published: February 2020

AbstractVariation of the magnitude of posterior alpha rhythm (8–12 Hz) has functional and behavioural effects in sensory processing and cognitive performances. Electrical brain activity, as revealed by electroencephalography (EEG), can be represented by a sequence of microstates of about 40–120 ms duration, in which distributed neural pools are synchronously active and generate stable spatial potential topographies on the scalp. Microstate dynamics may reflect transitions between global states characterized by selective inhibition of specific intra-cortical regions, mediated by alpha activity. We investigated the intra-subject and inter-subject relationship between microstate features and alpha band. High-density EEG signals were acquired in 29 healthy subjects during ten minutes of eyes closed rest. Individual EEG signal epochs were classified into four groups depending on the amount of occipital alpha power, and microstate metrics (duration, coverage and frequency of occurrence) were calculated and compared across groups. Correlations between alpha power and microstate metrics between individuals were also performed. To assess if microstate parameter variations are specific for the alpha band, the same analysis was also performed for theta and beta bands, as well as for global field power. We observed an increase in the metrics of microstate, previously associated to the visual system, with the level of intra-subject amplitude alpha oscillations, together with lower coverage of microstate associated with executive attention network and a higher frequency of microstate associated with task negative network. Other modulation effects of broad-band EEG power level on microstate metrics were observed. These effects are not specific for the alpha band, since they can equally be attributed to fluctuations in other frequency bands. We can interpret our results as a regulation mechanism mediated by posterior alpha level, dynamically interacting with other frequency bands, responsible for the switching between active areas.
Poor resolution at the back of the tongue is the bottleneck for spatial pattern recognition
Authors: Pamir Zahide , Canoluk M. Umut , Jung Jae-Hyun , Peli Eli 
Published: February 2020

AbstractSpatial patterns presented on the tongue using electro-tactile sensory substitution devices (SSDs) have been suggested to be recognized better by tracing the pattern with the tip of the tongue. We examined if the functional benefit of tracing is overcoming the poor sensitivity or low spatial resolution at the back of the tongue or alternatively compensating for limited information processing capacity by fixating on a segment of the spatial pattern at a time. Using a commercially available SSD, the BrainPort, we compared letter recognition performance in three presentation modes; tracing, static, and drawing. Stimulation intensity was either constant or increased from the tip to the back of the tongue to partially compensate for the decreasing sensitivity. Recognition was significantly better for tracing, compared to static and drawing conditions. Confusion analyses showed that letters were confused based on their characteristics presented near the tip in static and drawing conditions. The results suggest that recognition performance is limited by the poor spatial resolution at the back of the tongue, and tracing seems to be an effective strategy to overcome this. Compensating for limited information processing capacity or poor sensitivity by drawing or increasing intensity at the back, respectively, does not improve the performance.
Identification and evaluation of reliable reference genes for quantitative real-time PCR analysis in tea plants under differential biotic stresses
Authors: Xu Wei , Dong Yanan , Yu Yongchen , Xing Yuxian , Li Xiwang , Zhang Xin , Hou Xiangjie , Sun Xiaoling 
Published: February 2020

AbstractThe selection of reliable reference genes (RGs) for normalization under given experimental conditions is necessary to develop an accurate qRT-PCR assay. To the best of our knowledge, only a small number of RGs have been rigorously identified and used in tea plants (Camellia sinensis (L.) O. Kuntze) under abiotic stresses, but no critical RG identification has been performed for tea plants under any biotic stresses till now. In the present study, we measured the mRNA transcriptional levels of ten candidate RGs under five experimental conditions; these genes have been identified as stable RGs in tea plants. By using the ΔCt method, geNorm, NormFinder and BestKeeper, CLATHRIN1 and UBC1, TUA1 and SAND1, or SAND1 and UBC1 were identified as the best combination for normalizing diurnal gene expression in leaves, stems and roots individually; CLATHRIN1 and GAPDH1 were identified as the best combination for jasmonic acid treatment; ACTIN1 and UBC1 were identified as the best combination for Toxoptera aurantii-infested leaves; UBC1 and GAPDH1 were identified as the best combination for Empoasca onukii-infested leaves; and SAND1 and TBP1 were identified as the best combination for Ectropis obliqua regurgitant-treated leaves. Furthermore, our results suggest that if the processing time of the treatment was long, the best RGs for normalization should be recommended according to the stability of the proposed RGs in different time intervals when intragroup differences were compared, which would strongly increase the accuracy and sensitivity of target gene expression in tea plants under biotic stresses. However, when the differences of intergroup were compared, the RGs for normalization should keep consistent across different time points. The results of this study provide a technical guidance for further study of the molecular mechanisms of tea plants under different biotic stresses.
Improvement of the mechanical property and thermal stability of polypropylene/recycled rubber composite by chemical modification and physical blending
Authors: Chiang Tai-Chin , Liu Huan-Li , Tsai Lung-Chang , Jiang Tao , Ma Ning , Tsai Fang-Chang 
Published: February 2020

AbstractThe binary blend materials containing the modified recycled rubber powder with maleic a hydride modified polypropylene thermoplastic elastomer were prepared by dynamic vulcanization and blended with a variety of additives such as activated agent, accelerator, solubilizer, and the crosslinking agent. The thermal properties and mechanical properties including tensile strengths and impact strengths of pristine rubber, polypropylene and their corresponding binary blends were investigated. Besides, the effects of the amount of rubber powder, polypropylene, crosslinking agent, accelerator, activator, and solvent were studied and the microstructures of the pristine rubber, pristine polypropylene, and their corresponding binary blends were observed by scanning electron microscopy. It was found that the compatibilizer could effectively disperse the size of 120 mesh of recycled rubber powder into the polypropylene in the same manner and the homogeneous tear section of the rubber/polypropylene thermoplastic elastomer was obtained. The results on the effects of additives on mechanical and morphological properties of recycled rubber/polypropylene binary blends guide the rational design of novel polymeric composites from recycled polymeric materials.
Characterization of HIV-1 diversity in various compartments at the time of primary infection by ultradeep sequencing
Authors: Gaube Géraldine , Armero Alix , Salmona Maud , Néré Marie-Laure , Mahjoub Nadia , Lascoux-Combe Caroline , Gabassi Audrey , Gallien Sébastien , Amara Ali , Molina Jean Michel , Delaugerre Constance , Chaix Marie-Laure 
Published: February 2020

AbstractWe used next-generation sequencing to evaluate the quantity and genetic diversity of the HIV envelope gene in various compartments in eight patients with acute infection. Plasma (PL) and seminal fluid (SF) were available for all patients, whole blood (WB) for seven, non-spermatozoid cells (NSC) for four, and saliva (SAL) for three. Median HIV-1 RNA was 6.2 log10 copies/mL [IQR: 5.5–6.95] in PL, 4.9 log10 copies/mL [IQR: 4.25–5.29] in SF, and 4.9 log10 copies/mL [IQR: 4.46–5.09] in SAL. Median HIV-1 DNA was 4.1 log10 copies/106 PBMCs [IQR: 3.15–4.15] in WB and 2.6 log10 copies /106 Cells [IQR: 2.23–2.75] in NSC. The median overall diversity per patient varied from 0.0005 to 0.0232, suggesting very low diversity, confirmed by the clonal aspect of most of the phylogenetic trees. One single haplotype was present in all compartments for five patients in the earliest stage of infection. Evidence of higher diversity was established for two patients in PL and WB, suggesting compartmentalization. Our study shows low diversity of the env gene in the first stages of infection followed by the rapid establishment of cellular reservoirs of the virus. Such clonality could be exploited in the search for early patient-specific therapeutic solutions.
Dysregulated metabolic pathways in age-related macular degeneration
Authors: Zhang Meng , Jiang Nisi , Chu Yi , Postnikova Olga , Varghese Rency , Horvath Anelia , Cheema Amrita K. , Golestaneh Nady 
Published: February 2020

AbstractAge-related macular degeneration is a major cause of vision impairment in the Western world among people of 55 years and older. Recently we have shown that autophagy is dysfunctional in the retinal pigment epithelium (RPE) of the AMD donor eyes (AMD RPE). We also showed increased reactive oxygen (ROS) production, increased cytoplasmic glycogen accumulation, mitochondrial dysfunction and disintegration, and enlarged and annular LAMP-1-positive organelles in AMD RPE. However, the underlying mechanisms inducing these abnormalities remain to be elucidated. Here, by performing a comprehensive study, we show increased PAPR2 expression, deceased NAD+, and SIRT1, increased PGC-1α acetylation (inactive form), lower AMPK activity, and overactive mTOR pathway in AMD RPE as compared to normal RPE. Metabolomics and lipidomics revealed dysregulated metabolites in AMD RPE as compared to normal RPE, including glycerophospholipid metabolism, involved in autophagy, lipid, and protein metabolisms, glutathione, guanosine, and L-glutamic acid, which are implicated in protection against oxidative stress and neurotoxicity, further supporting our observations. Our data show dysregulated metabolic pathways as important contributors to AMD pathophysiology, and facilitate the development of new treatment strategies for this debilitating disease of the visual system.
A data-driven approach to decompose motion data into task-relevant and task-irrelevant components in categorical outcome
Authors: Furuki Daisuke , Takiyama Ken 
Published: February 2020

AbstractDecomposition of motion data into task-relevant and task-irrelevant components is an effective way to clarify the diverse features involved in motor control and learning. Several previous methods have succeeded in this type of decomposition while focusing on the clear relation of motion to both a specific goal and a continuous outcome, such as a 10 mm deviation from a target or 1 m/s hand velocity. In daily life, it is vital to quantify not only continuous but also categorical outcomes. For example, in baseball, batters must judge whether the opposing pitcher will throw a fastball or a breaking ball; tennis players must decide whether an opposing player will serve out wide or down the middle. However, few methods have focused on quantifying categorical outcome; thus, how to decompose motion data into task-relevant and task-irrelevant components when the outcome is categorical rather than continuous remains unclear. Here, we propose a data-driven method to decompose motion data into task-relevant and task-irrelevant components when the outcome takes categorical values. We applied our method to experimental data where subjects were required to throw fastballs or breaking balls with a similar form. Our data-driven approach can be applied to the unclear relation between motion and outcome, and the relation can be estimated in a data-driven manner. Furthermore, our method can successfully evaluate how the task-relevant components are modulated depending on the task requirements.
Reactive Extraction of Malic Acid using Trioctylamine in 1–Decanol: Equilibrium Studies by Response Surface Methodology Using Box Behnken Optimization Technique
Authors: Inyang Victoria , Lokhat David 
Published: February 2020

AbstractReactive extraction is a significant technique employed for the removal of organic acids such as carboxylic acid which are usually present in low concentrations in aqueous solutions. This technique was explored by applying Response Surface Methodology (RSM) in process parameter optimization for malic acid recovery from aqueous streams using Trioctylamine as extractant and 1-decanol as organic diluent. Malic acid, a C4 dicarboxylic acid has a wide variety of applications in the polymer, food, chemical and pharmaceutical industries. The optimization of the response function: extraction efficiency was systematically carried out using three process parameters for reactive extraction: temperature, initial malic acid concentration and extractant (Trioctylamine) composition. Response Surface Methodology in combination with Box-Behnken design involving seventeen experimental runs was employed for malic acid reactive extraction in this study. A statistical second-order polynomial predicted an extraction efficiency of 97.53%. The optimum conditions of the process variables were found to be: temperature: 304.73 K, acid concentration: 0.25 kmol/m3, Trioctylamine composition: 23.54% (v/v). Under these optimum conditions, the experimental response of extraction efficiency of 93.25% was obtained. The experimental results obtained was in close conformity with the predicted values by numerical optimization using Response Surface Methodology. These findings can pave the way for the reactive separation process design for recovery of carboxylic acids from dilute aqueous waste streams as well as a fermentation broth.
Mantle cloaking due to ideal magnetic dipole scattering
Authors: Cappello Barbara , Ospanova Anar K. , Matekovits Ladislau , Basharin Alexey A. 
Published: February 2020

AbstractOne of the most exciting applications of metaparticles and metasurfaces consists in the magnetic light excitation. However, the principal limitation is due to parasitic extra multipoles of electric family excited in magnetic dipole meta-particles characterized by a radiating nature and corresponding radiating losses. In this paper, we propose the “ideal magnetic dipole” with suppressed additional multipoles except of magnetic dipole moment in the scattered field from a cylindrical object by using mantle cloaking based on metasurface and on anapole concept. The considered metasurface consists of a periodic width modulated microstrip line, with a sinusoidally shaped profile unit cell printed on a dielectric substrate.
The Effects of Leukocyte-Platelet Rich Fibrin (L-PRF) on Suppression of the Expressions of the Pro-Inflammatory Cytokines, and Proliferation of Schwann Cell, and Neurotrophic Factors
Authors: Wang Zhanqi , Mudalal Mahmoud , Sun Yue , Liu Yiping , Wang Jia , Wang Yao , Sun Xiaolin , Zhou Yanmin 
Published: February 2020

AbstractThis study evaluates the use of L-PRF as an autologous scaffold in nerve regeneration, and Schwann cells (SCs) proliferation and secretion of neurotrophic factors and its anti-inflammatory effect on SC Porphyromonas Gingivalis-Lipopolysaccharide (PG-LPS)-induced inflammatory responses in vitro. SEM was done to investigate various features of L-PRF. L-PRF-extracts was used to investigate the release of growth factors and treatment of SCs line. ELISA was applied to examine the release of IGF-1. The proliferative effect of L-PRF on SCs was assessed with CCK-8 assay. The effect of L-PRF on the mRNA and protein expression of SC neurotrophic factors were analyzed by RT-qPCR and ELISA. CCK-8 assay and RT-qPCR were used to determine the required concentration and the action time of PG-LPS before the anti-inflammatory effect of L-PRF was determined by measuring the changes in IL-1β, IL-6, and TNF-a with RT-qPCR and ELISA. There are different features in L-PRF. Fourteen days was sufficient to release adequate GF. The mRNA expressions of the pro-inflammatory cytokines were notably raised by PG-LPS in 3-hours treatment. L-PRF can increase SC proliferation, neurotrophic factors secretion, and suppress SC PG-LPS-induced inflammatory responses in vitro. L-PRF has the potential as an autologous biological additive for peripheral nerve regeneration in the event of nerve inflammation and injuries.
MorbiNet: multimorbidity networks in adult general population. Analysis of type 2 diabetes mellitus comorbidity
Authors: Aguado Alba , Moratalla-Navarro Ferran , López-Simarro Flora , Moreno Victor 
Published: February 2020

AbstractMultimorbidity has great impact on health care. We constructed multimorbidity networks in the general population, extracted subnets focused on common chronic conditions and analysed type 2 diabetes mellitus (T2DM) comorbidity network. We used electronic records from 3,135,948 adult people in Catalonia, Spain (539,909 with T2DM), with at least 2 coexistent chronic conditions within the study period (2006–2017). We constructed networks from odds-ratio estimates adjusted by age and sex and considered connections with OR > 1.2 and p-value < 1e-5. Directed networks and trajectories were derived from temporal associations. Interactive networks are freely available in a website with the option to customize characteristics and subnets. The more connected conditions in T2DM undirected network were: complicated hypertension and atherosclerosis/peripheral vascular disease (degree: 32), cholecystitis/cholelithiasis, retinopathy and peripheral neuritis/neuropathy (degree: 31). T2DM has moderate number of connections and centrality but is associated with conditions with high scores in the multimorbidity network (neuropathy, anaemia and digestive diseases), and severe conditions with poor prognosis. The strongest associations from T2DM directed networks were to retinopathy (OR: 23.8), glomerulonephritis/nephrosis (OR: 3.4), peripheral neuritis/neuropathy (OR: 2.7) and pancreas cancer (OR: 2.4). Temporal associations showed the relevance of retinopathy in the progression to complicated hypertension, cerebrovascular disease, ischemic heart disease and organ failure.