bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome-wide methylation analysis identified sexually dimorphic methylated regions in hybrid tilapia
Authors: Wan Zi Yi , Xia Jun Hong , Lin Grace , Wang Le , Lin Valerie C. L. , Yue Gen Hua 
Published: October 2016

AbstractSexual dimorphism is an interesting biological phenomenon. Previous studies showed that DNA methylation might play a role in sexual dimorphism. However, the overall picture of the genome-wide methylation landscape in sexually dimorphic species remains unclear. We analyzed the DNA methylation landscape and transcriptome in hybrid tilapia (Oreochromis spp.) using whole genome bisulfite sequencing (WGBS) and RNA-sequencing (RNA-seq). We found 4,757 sexually dimorphic differentially methylated regions (DMRs), with significant clusters of DMRs located on chromosomal regions associated with sex determination. CpG methylation in promoter regions was negatively correlated with the gene expression level. MAPK/ERK pathway was upregulated in male tilapia. We also inferred active cis-regulatory regions (ACRs) in skeletal muscle tissues from WGBS datasets, revealing sexually dimorphic cis-regulatory regions. These results suggest that DNA methylation contribute to sex-specific phenotypes and serve as resources for further investigation to analyze the functions of these regions and their contributions towards sexual dimorphisms.
Broadband Focusing Acoustic Lens Based on Fractal Metamaterials
Authors: Song Gang Yong , Huang Bei , Dong Hui Yuan , Cheng Qiang , Cui Tie Jun 
Published: October 2016

AbstractAcoustic metamaterials are artificial structures which can manipulate sound waves through their unconventional effective properties. Different from the locally resonant elements proposed in earlier studies, we propose an alternate route to realize acoustic metamaterials with both low loss and large refractive indices. We describe a new kind of acoustic metamaterial element with the fractal geometry. Due to the self-similar properties of the proposed structure, broadband acoustic responses may arise within a broad frequency range, making it a good candidate for a number of applications, such as super-resolution imaging and acoustic tunneling. A flat acoustic lens is designed and experimentally verified using this approach, showing excellent focusing abilities from 2 kHz and 5 kHz in the measured results.
System analysis of gene mutations and clinical phenotype in Chinese patients with autosomal-dominant polycystic kidney disease
Authors: Jin Meiling , Xie Yuansheng , Chen Zhiqiang , Liao Yujie , Li Zuoxiang , Hu Panpan , Qi Yan , Yin Zhiwei , Li Qinggang , Fu Ping , Chen Xiangmei 
Published: October 2016

AbstractAutosomal dominant polycystic kidney disease (ADPKD) is the most common inherited kidney disorder mainly caused by mutation in PKD1/PKD2. However, ethnic differences in mutations, the association between mutation genotype/clinical phenotype, and the clinical applicable value of mutation detection are poorly understood. We made systematically analysis of Chinese ADPKD patients based on a next-generation sequencing platform. Among 148 ADPKD patients enrolled, 108 mutations were detected in 127 patients (85.8%). Compared with mutations in Caucasian published previously, the PKD2 mutation detection rate was lower, and patients carrying the PKD2 mutation invariably carried the PKD1 mutation. The definite pathogenic mutation detection rate was lower, whereas the multiple mutations detection rate was higher in Chinese patients. Then, we correlated PKD1/PKD2 mutation data and clinical data: patients with mutation exhibited a more severe phenotype; patients with >1 mutations exhibited a more severe phenotype; patients with pathogenic mutations exhibited a more severe phenotype. Thus, the PKD1/PKD2 mutation status differed by ethnicity, and the PKD1/PKD2 genotype may affect the clinical phenotype of ADPKD. Furthermore, it makes sense to detect PKD1/PKD2 mutation status for early diagnosis and prognosis, perhaps as early as the embryo/zygote stage, to facilitate early clinical intervention and family planning.
Particulate matter emissions from biochar-amended soils as a potential tradeoff to the negative emission potential
Authors: Ravi Sujith , Sharratt Brenton S. , Li Junran , Olshevski Stuart , Meng Zhongju , Zhang Jianguo 
Published: October 2016

AbstractNovel carbon sequestration strategies such as large-scale land application of biochar may provide sustainable pathways to increase the terrestrial storage of carbon. Biochar has a long residence time in the soil and hence comprehensive studies are urgently needed to quantify the environmental impacts of large-scale biochar application. In particular, black carbon emissions from soils amended with biochar may counteract the negative emission potential due to the impacts on air quality, climate, and biogeochemical cycles. We investigated, using wind tunnel experiments, the particulate matter emission potential of a sand and two agriculturally important soils amended with different concentrations of biochar, in comparison to control soils. Our results indicate that biochar application considerably increases particulate emissions possibly by two mechanisms–the accelerated emission of fine biochar particles and the generation and emission of fine biochar particles resulting from abrasion of large biochar particles by sand grains. Our study highlights the importance of considering the background soil properties (e.g., texture) and geomorphological processes (e.g., aeolian transport) for biochar-based carbon sequestration programs.
Functional kinomics establishes a critical node of volume-sensitive cation-Cl− cotransporter regulation in the mammalian brain
Authors: Zhang Jinwei , Gao Geng , Begum Gulnaz , Wang Jinhua , Khanna Arjun R. , Shmukler Boris E. , Daubner Gerrit M. , de los Heros Paola , Davies Paul , Varghese Joby , Bhuiyan Mohammad Iqbal H. , Duan Jinjing , Zhang Jin , Duran Daniel , Alper Seth L. , Sun Dandan , Elledge Stephen J. , Alessi Dario R. , Kahle Kristopher T. 
Published: October 2016

AbstractCell volume homeostasis requires the dynamically regulated transport of ions across the plasmalemma. While the ensemble of ion transport proteins involved in cell volume regulation is well established, the molecular coordinators of their activities remain poorly characterized. We utilized a functional kinomics approach including a kinome-wide siRNA-phosphoproteomic screen, a high-content kinase inhibitor screen, and a kinase trapping-Orbitrap mass spectroscopy screen to systematically identify essential kinase regulators of KCC3 Thr991/Thr1048phosphorylation – a key signaling event in cell swelling-induced regulatory volume decrease (RVD). In the mammalian brain, we found the Cl−-sensitive WNK3-SPAK kinase complex, required for cell shrinkage-induced regulatory volume decrease (RVI) via the stimulatory phosphorylation of NKCC1 (Thr203/Thr207/Thr212), is also essential for the inhibitory phosphorylation of KCC3 (Thr991/Thr1048). This is mediatedin vivoby an interaction between the CCT domain in SPAK and RFXV/I domains in WNK3 and NKCC1/KCC3. Accordingly, genetic or pharmacologic WNK3-SPAK inhibition prevents cell swelling in response to osmotic stress and ameliorates post-ischemic brain swelling through a simultaneous inhibition of NKCC1-mediated Cl−uptake and stimulation of KCC3-mediated Cl−extrusion. We conclude that WNK3-SPAK is an integral component of the long-sought “Cl−/volume-sensitive kinase” of the cation-Cl−cotransporters, and functions as a molecular rheostat of cell volume in the mammalian brain.
Mesenchymal stem cells with Sirt1 overexpression suppress breast tumor growth via chemokine-dependent natural killer cells recruitment
Authors: Yu Yang , Liu Yan , Zong Chen , Yu Qingbo , Yang Xue , Liang Lei , Ye Fei , Nong Li , Jia Yuxian , Lu Yongkui , Han Zhipeng 
Published: October 2016

AbstractMesenchymal stem cells (MSCs) are generally used in regenerative medicine, tissue engineering and therapy for immune disorder diseases. However, due to the immunosuppressive function of MSCs, the application of MSCs in breast cancer therapy remains limited. Sirt1 is the closest mammalian homologue of the yeast enzyme Sir2 which has an established capacity to influence yeast replicative lifespan. In this study, we demonstrated the effect of MSCs with Sirt1 overexpression (MSCs-Sirt1) in mice bearing 4T1 breast cancer and investigated the underlying mechanism. Firstly, we found that MSCs could accelerate breast tumor growth with promoted proliferation and inhibited apoptosis, whereas MSCs-Sirt1 significantly suppressed tumor growth with proliferation inhibition and apoptosis promotion. Moreover, we detected that NK cells were the prominent antitumor effectors for the MSCs-Sirt1-induced antitumor activity. Besides that, CXCL10 and IFN-γ showed the high level expression in MSCs-Sirt1 treatment group. The impulsive effect of MSCs-Sirt1 on 4T1 cells in vivo could be reversed by inhibition of CXCL10 and IFN-γ. Overall, our results suggest that MSCs-Sirt1 can effectively inhibit breast tumor growth via the recruitment of NK cells in tumor inflammatory microenvironment.
Maltodextrin enhances biofilm elimination by electrochemical scaffold
Authors: Sultana Sujala T. , Call Douglas R. , Beyenal Haluk 
Published: October 2016

AbstractElectrochemical scaffolds (e-scaffolds) continuously generate low concentrations of H2O2 suitable for damaging wound biofilms without damaging host tissue. Nevertheless, retarded diffusion combined with H2O2 degradation can limit the efficacy of this potentially important clinical tool. H2O2 diffusion into biofilms and bacterial cells can be increased by damaging the biofilm structure or by activating membrane transportation channels by exposure to hyperosmotic agents. We hypothesized that e-scaffolds would be more effective against Acinetobacter baumannii and Staphylococcus aureus biofilms in the presence of a hyperosmotic agent. E-scaffolds polarized at −600 mVAg/AgCl were overlaid onto preformed biofilms in media containing various maltodextrin concentrations. E-scaffold alone decreased A. baumannii and S. aureus biofilm cell densities by (3.92 ± 0.15) log and (2.31 ± 0.12) log, respectively. Compared to untreated biofilms, the efficacy of the e-scaffold increased to a maximum (8.27 ± 0.05) log reduction in A. baumannii and (4.71 ± 0.12) log reduction in S. aureus biofilm cell densities upon 10 mM and 30 mM maltodextrin addition, respectively. Overall ~55% decrease in relative biofilm surface coverage was achieved for both species. We conclude that combined treatment with electrochemically generated H2O2 from an e-scaffold and maltodextrin is more effective in decreasing viable biofilm cell density.
Integrated presentation of ecological risk from multiple stressors
Authors: Goussen Benoit , Price Oliver R. , Rendal Cecilie , Ashauer Roman 
Published: October 2016

AbstractCurrent environmental risk assessments (ERA) do not account explicitly for ecological factors (e.g. species composition, temperature or food availability) and multiple stressors. Assessing mixtures of chemical and ecological stressors is needed as well as accounting for variability in environmental conditions and uncertainty of data and models. Here we propose a novel probabilistic ERA framework to overcome these limitations, which focusses on visualising assessment outcomes by construct-ing and interpreting prevalence plots as a quantitative prediction of risk. Key components include environmental scenarios that integrate exposure and ecology, and ecological modelling of relevant endpoints to assess the effect of a combination of stressors. Our illustrative results demonstrate the importance of regional differences in environmental conditions and the confounding interactions of stressors. Using this framework and prevalence plots provides a risk-based approach that combines risk assessment and risk management in a meaningful way and presents a truly mechanistic alternative to the threshold approach. Even whilst research continues to improve the underlying models and data, regulators and decision makers can already use the framework and prevalence plots. The integration of multiple stressors, environmental conditions and variability makes ERA more relevant and realistic.
Oocyte aging-induced Neuronatin (NNAT) hypermethylation affects oocyte quality by impairing glucose transport in porcine
Authors: Gao Ying-Ying , Chen Li , Wang Tao , Nie Zheng-Wen , Zhang Xia , Miao Yi-Liang 
Published: October 2016

AbstractDNA methylation plays important roles in regulating many physiological behaviors; however, few studies were focused on the changes of DNA methylation during oocyte aging. Early studies showed that some imprinted genes’ DNA methylation had been changed in aged mouse oocytes. In this study, we used porcine oocytes to test the hypothesis that oocyte aging would alter DNA methylation pattern of genes and disturb their expression in age oocytes, which affected the developmental potential of oocytes. We compared several different types of genes and found that the expression and DNA methylation of Neuronatin (NNAT) were disturbed in aged oocytes significantly. Additional experiments demonstrated that glucose transport was impaired in aged oocytes and injection of NNAT antibody into fresh oocytes led to the same effects on glucose transport. These results suggest that the expression of NNAT was declined by elevating DNA methylation, which affected oocyte quality by decreasing the ability of glucose transport in aged oocytes.
Collective Influence of Multiple Spreaders Evaluated by Tracing Real Information Flow in Large-Scale Social Networks
Authors: Teng Xian , Pei Sen , Morone Flaviano , Makse Hernán A. 
Published: October 2016

AbstractIdentifying the most influential spreaders that maximize information flow is a central question in network theory. Recently, a scalable method called “Collective Influence (CI)” has been put forward through collective influence maximization. In contrast to heuristic methods evaluating nodes’ significance separately, CI method inspects the collective influence of multiple spreaders. Despite that CI applies to the influence maximization problem in percolation model, it is still important to examine its efficacy in realistic information spreading. Here, we examine real-world information flow in various social and scientific platforms including American Physical Society, Facebook, Twitter and LiveJournal. Since empirical data cannot be directly mapped to ideal multi-source spreading, we leverage the behavioral patterns of users extracted from data to construct “virtual” information spreading processes. Our results demonstrate that the set of spreaders selected by CI can induce larger scale of information propagation. Moreover, local measures as the number of connections or citations are not necessarily the deterministic factors of nodes’ importance in realistic information spreading. This result has significance for rankings scientists in scientific networks like the APS, where the commonly used number of citations can be a poor indicator of the collective influence of authors in the community.
HULC cooperates with MALAT1 to aggravate liver cancer stem cells growth through telomere repeat-binding factor 2
Authors: Wu Mengying , Lin Zhuojia , Li Xiaonan , Xin Xiaoru , An Jiahui , Zheng Qidi , Yang Yuxin , Lu Dongdong 
Published: October 2016

AbstractThe dysregulation of lncRNAs has increasingly been linked to many human diseases, especially in cancers. Our results demonstrate HULC, MALAT1 and TRF2 are highly expressed in human hepatocellular carcinoma tissues, and HULC plus MALAT1 overexpression drastically promotes the growth of liver cancer stem cells. Mechanistically, both HULC and MALAT1 overexpression enhanced RNA polII, P300, CREPT to load on the promoter region of telomere repeat-binding factor 2(TRF2), triggering the overexpression, phosphorylation and SUMOylation of TRF2. Strikingly, the excessive TRF2 interacts with HULC or MALAT1 to form the complex that loads on the telomeric region, replacing the CST/AAF and recruiting POT1, pPOT1, ExoI, SNM1B, HP1 α. Accordingly, the telomere is greatly protected and enlonged. Furthermore, the excessive HULC plus MALAT1 reduced the methylation of the TERC promoter dependent on TRF2, increasing the TERC expression that causes the increase of interplay between TRET and TERC. Ultimately, the interaction between RFC and PCNA or between CDK2 and CyclinE, the telomerase activity and the microsatellite instability (MSI) are significantly increased in the liver cancer stem cells. Our demonstrations suggest that haploinsufficiency of HULC/MALAT1 plays an important role in malignant growth of liver cancer stem cell.
Opposite-sex attraction in male mice requires testosterone-dependent regulation of adult olfactory bulb neurogenesis
Authors: Schellino Roberta , Trova Sara , Cimino Irene , Farinetti Alice , Jongbloets Bart C. , Pasterkamp R. Jeroen , Panzica Giancarlo , Giacobini Paolo , De Marchis Silvia , Peretto Paolo 
Published: October 2016

AbstractOpposite-sex attraction in most mammals depends on the fine-tuned integration of pheromonal stimuli with gonadal hormones in the brain circuits underlying sexual behaviour. Neural activity in these circuits is regulated by sensory processing in the accessory olfactory bulb (AOB), the first central station of the vomeronasal system. Recent evidence indicates adult neurogenesis in the AOB is involved in sex behaviour; however, the mechanisms underlying this function are unknown. By using Semaphorin 7A knockout (Sema7A ko) mice, which show a reduced number of gonadotropin-releasing-hormone neurons, small testicles and subfertility, and wild-type males castrated during adulthood, we demonstrate that the level of circulating testosterone regulates the sex-specific control of AOB neurogenesis and the vomeronasal system activation, which influences opposite-sex cue preference/attraction in mice. Overall, these data highlight adult neurogenesis as a hub for the integration of pheromonal and hormonal cues that control sex-specific responses in brain circuits.
Pure spin current devices based on ferromagnetic topological insulators
Authors: Götte Matthias , Joppe Michael , Dahm Thomas 
Published: October 2016

AbstractTwo-dimensional topological insulators possess two counter propagating edge channels with opposite spin direction. Recent experimental progress allowed to create ferromagnetic topological insulators realizing a quantum anomalous Hall (QAH) state. In the QAH state one of the two edge channels disappears due to the strong ferromagnetic exchange field. We investigate heterostructures of topological insulators and ferromagnetic topological insulators by means of numerical transport calculations. We show that spin current flow in such heterostructures can be controlled with high fidelity. Specifically, we propose spintronic devices that are capable of creating, switching and detecting pure spin currents using the same technology. In these devices electrical currents are directly converted into spin currents, allowing a high conversion efficiency. Energy independent transport properties in combination with large bulk gaps in some topological insulator materials may allow operation even at room temperature.
Visceral Adiposity and Anthropometric Indicators as Screening Tools of Metabolic Syndrome among Low Income Rural Adults in Xinjiang
Authors: Guo Shu-xia , Zhang Xiang-hui , Zhang Jing-yu , He Jia , Yan Yi-zhong , Ma Jiao-long , Ma Ru-lin , Guo Heng , Mu La-ti , Li Shu-gang , Niu Qiang , Rui Dong-sheng , Zhang Mei , Liu Jia-ming , Wang Kui , Xu Shang-zhi , Gao Xiang , Ding Yu-song 
Published: October 2016

AbstractMost previous studies on metabolic syndrome (MetS) examined urban and high income settings. We thus investigated the prevalence of MetS among a multi-ethnic population living in a low income rural area and explored the use of visceral adiposity and anthropometric indicators to identify men and women with MetS. We recruited 10,029 individuals of nomadic Kazakhs, rural Uyghur and Han residents in Xinjiang, China. MetS was defined by the Joint Interim Statement criteria. The receiver operating characteristic curve (ROC) was used to compare the area under the ROC curve (AUC) of each index. The age-adjusted prevalence of MetS was 21.8%. The visceral adiposity index (VAI), lipid accumulation product (LAP), body adiposity index (BAI) and the waist-to-height ratio (WHtR) were significantly associated with MetS, independent of ethnic, age, and other covariates. The AUC of VAI, LAP and WHtR were all greater than 0.7, and the LAP was the index that most accurately identified MetS status in men (AUC = 0.853) and women (AUC = 0.817), with the optimal cut-offs of 34.7 and 27.3, respectively. In conclusion, the prevalence of MetS in low income rural adults of Xinjiang was high and the LAP was an effective indicator for the screening of MetS.
Improvement of Terahertz Wave Radiation for InAs Nanowires by Simple Dipping into Tap Water
Authors: Park Dong Woo , Bin Ji Young , Hwang Jehwan , Lee Cheul-Ro , Lee Sang Jun , Kim Jun Oh , Noh Sam Kyu , Oh Seung Jae , Kim Sang-Hoon , Jeon Tae-In , Jeong Kwang-Un , Kim Jin Soo 
Published: October 2016

AbstractWe report improvement of terahertz (THz) wave radiation for Si-based catalyst-free InAs nanowires (NWs) by simple dipping into tap water (DTW). In addition, the possibility of using InAs NWs as a cost-effective method for biomedical applications is discussed by comparison to bulk InAs. The peak-to-peak current signals (PPCSs) of InAs NWs measured from THz time-domain spectroscopy increased with increasing NW height. For example, the PPCS of 10 μm-long InAs NWs was 2.86 times stronger than that of 2.1 μm-long NWs. The THz spectra of the InAs NWs obtained by applying a fast Fourier transformation to the current signals showed a main frequency of 0.5 THz, which can be applied to a variety of medical imaging systems. After the DTW process, structural variation was not observed for 2.1 μm-long InAs NWs. However, the top region of several InAs NWs with heights of 4.6 and 5.8 μm merged into a conical structure. InAs NWs with a height of 10 μm resulted in a bundle feature forming above the conical shape, where the length of bundle region was 4 μm. After the DTW process, the PPCS for 10 μm-long InAs NWs increased by 15 percent compared to that of the as-grown case.
Dynamics of soil organic and inorganic carbon in the cropland of upper Yellow River Delta, China
Authors: Guo Yang , Wang Xiujun , Li Xianglan , Wang Jiaping , Xu Minggang , Li Dongwei 
Published: October 2016

AbstractSoil inorganic carbon (SIC) and organic carbon (SOC) are important carbon reservoirs in terrestrial ecosystems. However, little attention was paid to SIC dynamics in cropland. We conducted a survey in the upper Yellow River Delta of North China Plain. We collected 155 soil samples from 31 profiles, and measured SOC, SIC and soluble Ca2+ and Mg2+ contents. Our results showed that mean SOC content decreased from 9.30 g kg−1 near the surface to 2.36 g kg−1 in 80–100 cm whereas mean SIC content increased from 10.48 to 12.72 g kg−1. On average, SOC and SIC stocks over 0–100 cm were 5.73 kg C m−2 and 16.89 kg C m−2, respectively. There was a significantly positive correlation (r = 0.88, P < 0.001) between SOC and SIC in the cropland. We also found that SIC had a significantly positive correlation with both soluble Ca2+ (r = 0.57, P < 0.01) and Mg2+ (r = 0.43, P < 0.05). Our study suggested that increasing SOC might lead to an increase in SIC stocks in the cropland of North China Plain. This study highlights the importance of SIC in the carbon cycle of China’s semi-arid region.