bluuebunny/crossref_metadata_2025_split huggingface dataset:
Acoustic analog computing system based on labyrinthine metasurfaces
Authors: Zuo Shuyu , Wei Qi , Tian Ye , Cheng Ying , Liu Xiaojun 
Published: June 2018

AbstractAcoustic computing devices, including switches, logic gates, differentiator and integrator, have attracted extensive attentions in both academic research and engineering. However, no scheme of acoustic computing device with more complex functionality has been proposed, such as ordinary differential equation (ODE) solver. Here, we propose an acoustic analog computing (AAC) system based on three cascaded metasurfaces to solve the nth-order ODEs. The metasurfaces are constructed with layered labyrinthine units featuring broad amplitude and phase modulation ranges. The simulated transmitted pressure of the AAC system agrees well with the theoretical solution of ODE, demonstrating the excellent functionality. Unlike the optical ODE solver based on differentiator or integrator, whose geometry becomes more complicated for solving higher order ODE, the proposed AAC system with fixed geometry can be designed for arbitrary nth-order ODE in principle. The proposal may find applications in various scenarios such as acoustic communication, analog computing and signal processing.
Exploiting sorghum genetic diversity for enhanced aluminum tolerance: Allele mining based on the AltSB locus
Authors: Hufnagel Barbara , Guimaraes Claudia T. , Craft Eric J. , Shaff Jon E. , Schaffert Robert E. , Kochian Leon V. , Magalhaes Jurandir V. 
Published: June 2018

AbstractRoot damage due to aluminum (Al) toxicity restricts crop production on acidic soils, which are extensive in the tropics. The sorghum root Al-activated citrate transporter, SbMATE, underlies the Al tolerance locus,AltSB, and increases grain yield under Al toxicity. Here,AltSBloci associated with Al tolerance were converted intoAmplification Refractory Mutation System(ARMS) markers, which are cost effective and easy to use. A DNA pooling strategy allowed us to identify accessions harboring rare favorableAltSBalleles in three germplasm sets while greatly reducing genotyping needs. Population structure analysis revealed that favorableAltSBalleles are predominantly found in subpopulations enriched with guinea sorghums, supporting a possible Western African origin ofAltSB. The efficiency of allele mining in recovering Al tolerance accessions was the highest in the largest and highly diverse germplasm set, with a 10-fold reduction in the number of accessions that would need to be phenotyped in the absence of marker information. Finally, Al tolerant accessions were found to rely onSbMATEto exclude Al3+from sensitive sites in the root apex. This study emphasizes gene-specific markers as important tools for efficiently mining useful rare alleles in diverse germplasm, bridging genetic resource conservation efforts and pre-breeding for Al tolerance.
Dissecting Distinct Roles of NEDDylation E1 Ligase Heterodimer APPBP1 and UBA3 Reveals Potential Evolution Process for Activation of Ubiquitin-related Pathways
Authors: Malik-Chaudhry Harbani Kaur , Gaieb Zied , Saavedra Amanda , Reyes Michael , Kung Raphael , Le Frank , Morikis Dimitrios , Liao Jiayu 
Published: June 2018

AbstractDespite the similar enzyme cascade in the Ubiquitin and Ubiquitin-like peptide(Ubl) conjugation, the involvement of single or heterodimer E1 activating enzyme has been a mystery. Here, by using a quantitative Förster Resonance Energy Transfer (FRET) technology, aided with Analysis of Electrostatic Similarities Of Proteins (AESOP) computational framework, we elucidate in detail the functional properties of each subunit of the E1 heterodimer activating-enzyme for NEDD8, UBA3 and APPBP1. In contrast to SUMO activation, which requires both subunits of its E1 heterodimer AOS1-Uba2 for its activation, NEDD8 activation requires only one of two E1 subunits, UBA3. The other subunit, APPBP1, only contributes by accelerating the activation reaction rate. This discovery implies that APPBP1 functions mainly as a scaffold protein to enhance molecular interactions and facilitate catalytic reaction. These findings for the first time reveal critical new mechanisms and a potential evolutionary pathway for Ubl activations. Furthermore, this quantitative FRET approach can be used for other general biochemical pathway analysis in a dynamic mode.
Fossilized Melts in Mantle Wedge Peridotites
Authors: Naemura Kosuke , Hirajima Takao , Svojtka Martin , Shimizu Ichiko , Iizuka Tsuyosi 
Published: June 2018

AbstractThe shallow oxidized asthenosphere may contain a small fraction of potassic silicate melts that are enriched in incompatible trace elements and volatiles. Here, to determine the chemical composition of such melt, we analysed fossilized melt inclusions, preserved as multiphase solid inclusions, from an orogenic garnet peridotite in the Bohemian Massif. Garnet-poor (2 vol.%) peridotite preserves inclusions of carbonated potassic silicate melt within Zn-poor chromite (<400 ppm) in the clinopyroxene-free harzburgite assemblage that equilibrated within the hot mantle wedge (Stage 1, > 1180 °C at 3 GPa). The carbonated potassic silicate melt, which has a major element oxide chemical composition of K2O = 5.2 wt.%, CaO = 17 wt.%, MgO = 18 wt.%, CO2 = 22 wt.%, and SiO2 = 20 wt.%, contains extremely high concentrations of large ion lithophile elements, similar to kimberlite melts. Peridotites cooled down to ≅800 °C during Stage 2, resulted in the growth of garnet relatively poor in pyrope content, molar Mg/(Mg + Fe + Ca + Mn), (ca. 67 mol.%). This garnet displays a sinusoidal REE pattern that formed in equilibrium with carbonatitic fluid. Subsequently, subduction of the peridotite resulted in the formation of garnet with a slightly higher pyrope content (70 mol.%) during the Variscan subduction Stage 3 (950 °C, 2.9 GPa). These data suggest the following scenario for the generation of melt in the mantle wedge. Primarily, infiltration of sediment-derived potassic carbonatite melt into the deep mantle wedge resulted in the growth of phlogopite and carbonate/diamond. Formation of volatile-bearing minerals lowered the density and strength of the peridotite. Finally, phlogopite-bearing carbonated peridotite rose as diapirs in the mantle wedge to form carbonated potassic silicate melts at the base of the overriding lithosphere.
Genotype-Corrector: improved genotype calls for genetic mapping in F2 and RIL populations
Authors: Miao Chenyong , Fang Jingping , Li Delin , Liang Pingping , Zhang Xingtan , Yang Jinliang , Schnable James C. , Tang Haibao 
Published: June 2018

AbstractF2 and recombinant inbred lines (RILs) populations are very commonly used in plant genetic mapping studies. Although genome-wide genetic markers like single nucleotide polymorphisms (SNPs) can be readily identified by a wide array of methods, accurate genotype calling remains challenging, especially for heterozygous loci and missing data due to low sequencing coverage per individual. Therefore, we developed Genotype-Corrector, a program that corrects genotype calls and imputes missing data to improve the accuracy of genetic mapping. Genotype-Corrector can be applied in a wide variety of genetic mapping studies that are based on low coverage whole genome sequencing (WGS) or Genotyping-by-Sequencing (GBS) related techniques. Our results show that Genotype-Corrector achieves high accuracy when applied to both synthetic and real genotype data. Compared with using raw or only imputed genotype calls, the linkage groups built by corrected genotype data show much less noise and significant distortions can be corrected. Additionally, Genotype-Corrector compares favorably to the popular imputation software LinkImpute and Beagle in both F2 and RIL populations. Genotype-Corrector is publicly available on GitHub at https://github.com/freemao/Genotype-Corrector.
Electrophysiological evidence of RML12 mosquito cell line towards neuronal differentiation by 20-hydroxyecdysdone
Authors: Gaburro Julie , Duchemin Jean-Bernard , Paradkar Prasad N. , Nahavandi Saeid , Bhatti Asim 
Published: June 2018

AbstractContinuous cell lines from insect larval tissues are widely used in different research domains, such as virology, insect immunity, gene expression, and bio pharmacology. Previous study showed that introduction of 20-hydroxyecdysone to Spodoptera cell line induced a neuron-like morphology with neurite extensions. Despite some results suggesting potential presence of neuro-receptors, no study so far has shown that these neuron-induced cells were functional. Here, using microelectrode arrays, we showed that the mosquito cell line, RML12, differentiated with 20-hydroxyecdysone, displays spontaneous electrophysiological activity. Results showed that these cells can be stimulated by GABAergic antagonist as well as nicotinic agonist. These results provide new evidence of neuron-like functionality of 20-hydroxyecdysone induced differentiated mosquito cell line. Finally, we used this new model to test the effects of two insecticides, temephos and permethrin. Our analysis revealed significant changes in the spiking activity after the introduction of these insecticides with prolonged effect on the neuronal activity. We believe that this differentiated mosquito neuronal cell model can be used for high-throughput screening of new pesticides on insect nervous system instead of primary neurons or in vivo studies.
Assessment of the key regulatory genes and their Interologs for Turner Syndrome employing network approach
Authors: Farooqui Anam , Tazyeen Safia , Ahmed Mohd. Murshad , Alam Aftab , Ali Shahnawaz , Malik Md. Zubbair , Ali Sher , Ishrat Romana 
Published: June 2018

AbstractTurner Syndrome (TS) is a condition where several genes are affected but the molecular mechanism remains unknown. Identifying the genes that regulate the TS network is one of the main challenges in understanding its aetiology. Here, we studied the regulatory network from manually curated genes reported in the literature and identified essential proteins involved in TS. The power-law distribution analysis showed that TS network carries scale-free hierarchical fractal attributes. This organization of the network maintained the self-ruled constitution of nodes at various levels without having centrality–lethality control systems. Out of twenty-seven genes culminating into leading hubs in the network, we identified two key regulators (KRs) i.e. KDM6A and BDNF. These KRs serve as the backbone for all the network activities. Removal of KRs does not cause its breakdown, rather a change in the topological properties was observed. Since essential proteins are evolutionarily conserved, the orthologs of selected interacting proteins in C. elegans, cat and macaque monkey (lower to higher level organisms) were identified. We deciphered three important interologs i.e. KDM6A-WDR5, KDM6A-ASH2L and WDR5-ASH2L that form a triangular motif. In conclusion, these KRs and identified interologs are expected to regulate the TS network signifying their biological importance.
Development of outbred CD1 mouse colonies with distinct standardized gut microbiota profiles for use in complex microbiota targeted studies
Authors: Hart Marcia L. , Ericsson Aaron C. , Lloyd K. C. Kent , Grimsrud Kristin N. , Rogala Allison R. , Godfrey Virginia L. , Nielsen Judith N. , Franklin Craig L. 
Published: June 2018

AbstractStudies indicate that the gut microbiota (GM) can significantly influence both local and systemic host physiologic processes. With rising concern for optimization of experimental reproducibility and translatability, it is essential to consider the GM in study design. However, GM profiles can vary between rodent producers making consistency between models challenging. To circumvent this, we developed outbred CD1 mouse colonies with stable, complex GM profiles that can be used as donors for a variety of GM transfer techniques including rederivation, co-housing, cross-foster, and fecal microbiota transfer (FMT). CD1 embryos were surgically transferred into CD1 or C57BL/6 surrogate dams that varied by GM composition and complexity to establish four separate mouse colonies harboring GM profiles representative of contemporary mouse producers. Using targeted 16S rRNA amplicon sequencing, subsequent female offspring were found to have similar GM profiles to surrogate dams. Furthermore, breeding colonies of CD1 mice with distinct GM profiles were maintained for nine generations, demonstrating GM stability within these colonies. To confirm GM stability, we shipped cohorts of these four colonies to collaborating institutions and found no significant variation in GM composition. These mice are an invaluable experimental resource that can be used to investigate GM effects on mouse model phenotype.
Interaction between hydrogen and gallium vacancies in β-Ga2O3
Authors: Wei Yidan , Li Xingji , Yang Jianqun , Liu Chaoming , Zhao Jinyu , Liu Yong , Dong Shangli 
Published: June 2018

AbstractIn this paper, the revised Heyd-Scuseria-Ernzerhof screened hybrid functional (HSE06) is used to investigate the interaction between hydrogen with different concentrations and gallium vacancies in β-Ga2O3. The hydrogen can compensate a gallium vacancy by forming hydrogen-vacancy complex. A gallium vacancy can bind up to four hydrogen atoms, and formation energies decrease as the number of hydrogen atoms increases. Hydrogen prefers to bind with three coordinated oxygen. The bonding energy and annealing temperatures of complexes containing more than two hydrogen atoms are computed, and show relatively high stability. In addition, vacancy concentrations increase with the increasing vapor pressures. This paper can effectively explain the hydrogen impact in β-Ga2O3.
Application of conicity index adjusted total body fat in young adults-a novel method to assess metabolic diseases risk
Authors: Zhang Yujie , Zeng Qiang , Li Xiaoying , Zhu Pengli , Huang Feng 
Published: June 2018

AbstractThe aim of the study was to evaluate the usefulness of conicity index (CI) adjusted total body fat (TBF), which was defined as TBF/CI, in various metabolic diseases in young adults. A cross-sectional study was carried out in Chinese PLA General Hospital and a total of 1365 young adults (age 20–40 years) who underwent a health check-up examination were finally included in the analysis from February 2016 to 2017. Linear Regression and logistic regression were used to further examine relationship between the index and metabolic diseases. The average age was 34.5 years. Odds Ratios (ORs) for the risk of metabolic diseases increased from the lowest to highest TBF/CI quartile (all P trends < 0.001). Young adults with increased TBF/CI had higher risk of hyperhomocysteinemia (Hhcy) (OR = 1.528, 95% confidence interval = 1.057–2.209). There was a 1.407 increase in the odds of obesity, a 1.112 increase in the odds of hyperlipidemia (HLP) and a 1.094 increase in the odds of diabetes mellitus (DM) per standard deviation (SD) increase in TBF/CI (all P < 0.001). TBF/CI showed higher predictive values for obesity, HLP, DM and Hhcy than weight adjusted total body fat (all P < 0.001). Young adults with increased TBF/CI had higher ratios of metabolic diseases, which suggested that TBF/CI can be a good indicator and had a close relationship with metabolic diseases.
Cold weather increases respiratory symptoms and functional disability especially among patients with asthma and allergic rhinitis
Authors: Hyrkäs-Palmu Henna , Ikäheimo Tiina M. , Laatikainen Tiina , Jousilahti Pekka , Jaakkola Maritta S. , Jaakkola Jouni J. K. 
Published: June 2018

AbstractCold weather affects the respiratory epithelium and induces bronchial hyperresponsiveness. We hypothesized that individuals with allergic rhinitis or/and asthma experience cold weather-related functional disability (FD) and exacerbation of health problems (EH) more commonly than individuals without these. This was a population-based study of 7330 adults aged 25–74 years. The determinants of interest, including doctor-diagnosed asthma and allergic rhinitis, and the outcomes, including cold weather-related FD and EH, were measured using a self-administered questionnaire. The prevalences of cold-related FD and EH were 20.3% and 10.3%, respectively. In Poisson regression, the risk of FD increased in relation to both allergic rhinitis (adjusted prevalence ratio (PR) 1.19, 95% CI 1.04–1.37 among men; 1.26, 95% CI 1.08–1.46 among women), asthma (1.29, 0.93–1.80; 1.36, 0.92–2.02, respectively) and their combination (1.16, 0.90–1.50; 1.40, 1.12–1.76, respectively). Also the risk of cold weather-related EH was related to both allergic rhinitis (1.53, 1.15,−2.04 among men; 1.78, 1.43–2.21 among women), asthma (4.28, 2.88–6.36; 3.77, 2.67–5.34, respectively) and their combination (4.02, 2.89–5.59; 4.60, 3.69–5.73, respectively). We provide new evidence that subjects with allergic rhinitis or/and asthma are more susceptible to cold weather-related FD and EH than those without pre-existing respiratory diseases.
Optimization of sample preparation and green color imaging using the mNeonGreen fluorescent protein in bacterial cells for photoactivated localization microscopy
Authors: Stockmar Iris , Feddersen Helge , Cramer Kimberly , Gruber Stephan , Jung Kirsten , Bramkamp Marc , Shin Jae Yen 
Published: June 2018

AbstractmNeonGreen fluorescent protein is capable of photo-switching, hence in principle applicable for super-resolution imaging. However, difficult-to-control blinking kinetics that lead to simultaneous emission of multiple nearby mNeonGreen molecules impedes its use for PALM. Here, we determined the on- and off- switching rate and the influence of illumination power on the simultaneous emission. Increasing illumination power reduces the probability of simultaneous emission, but not enough to generate high quality PALM images. Therefore, we introduce a simple data post-processing step that uses temporal and spatial information of molecule localizations to further reduce artifacts arising from simultaneous emission of nearby emitters. We also systematically evaluated various sample preparation steps to establish an optimized protocol to preserve cellular morphology and fluorescence signal. In summary, we propose a workflow for super-resolution imaging with mNeonGreen based on optimization of sample preparation, data acquisition and simple post-acquisition data processing. Application of our protocol enabled us to resolve the expected double band of bacterial cell division protein DivIVA, and to visualize that the chromosome organization protein ParB organized into sub-clusters instead of the typically observed diffraction-limited foci. We expect that our workflow allows a broad use of mNeonGreen for super-resolution microscopy, which is so far difficult to achieve.
Discordance between self-report and clinical diagnosis of Internet gaming disorder in adolescents
Authors: Jeong Hyunsuk , Yim Hyeon Woo , Lee Seung-Yup , Lee Hae Kook , Potenza Marc N. , Kwon Jung-Hye , Koo Hoon Jung , Kweon Yong-Sil , Bhang Soo-young , Choi Jung-Seok 
Published: June 2018

AbstractThis study aimed to estimate overreporting (the false positive) and underreporting (false negative) rates in self-reported IGD assessment compared with clinical diagnosed IGD. The study population consisted of 45 with IGD and 228 without IGD based on clinical diagnosis from the Internet User Cohort for Unbiased Recognition of Gaming Disorder in Early Adolescence (iCURE) study. All participants completed self-reported IGD assessments. Clinical interviews were conducted blindly by trained mental health professionals based on DSM-5 IGD criteria. Self-assessed average daily amount of gaming time and game genre were measured. Psychological characteristics, including anxiety, suicidality, aggression, self-control, self-esteem, and family support, were obtained from the baseline survey. The false-negative rate for self-reported IGD assessment was 44%. The false-negative group reported less time playing online games than the IGD group, though their psychological characteristics were similar to those of the IGD group. The false-positive rate was 9.6%. They reported more time playing online games than non-IGD group, though their psychological characteristics were similar to those of non-IGD group except self-control. The discrepancy of IGD diagnoses between self-reports and clinical diagnosis revealed limitations of self-measurements. Various strategies are required to overcome the methodological shortfalls of self-reports for the assessment of IGD.
Floquet Weyl Magnons in Three-Dimensional Quantum Magnets
Authors: Owerre S. A. 
Published: June 2018

AbstractIn three-dimensional (3D) quantum magnets, magnonic Weyl points (WPs) featuring linear band crossing of two non-degenerate magnon branches can emerge in certain lattice geometry when time-reversal symmetry is broken macroscopically. Unfortunately, there are very limited 3D quantum magnets that host magnonic WPs, and they are yet to be observed experimentally because the intrinsic perturbative interactions that break time-reversal symmetry macroscopically can be very negligible. Here, we present an alternative means via photo-irradiation, in which magnonic WPs can emerge in 3D quantum magnets without relying on intrinsic perturbative interactions to break time-reversal symmetry. By utilizing the magnonic Floquet-Bloch theory, we put forward the general theory of magnonic Floquet WPs in 3D quantum magnets. We show that periodically driven 3D magnonic Dirac nodal-line (DNL) and 3D magnonic gapped trivial insulators can generate 3D magnonic Floquet WPs, which can be tuned by the incident circularly-polarized light. We demonstrate the existence of magnonic Floquet WPs by combining the study of the magnon dispersions, Berry curvatures, and the anomalous thermal Hall effect. The general theoretical formalism can be applied to different magnetic insulators, and thus extending the concept of magnonic WPs to a broader class of 3D magnetically ordered systems.
The functional and inflammatory response of brain endothelial cells to Toll-Like Receptor agonists
Authors: Johnson Rebecca H. , Kho Dan T. , O’ Carroll Simon J. , Angel Catherine E. , Graham E. Scott 
Published: June 2018

AbstractToll-Like receptors (TLRs) represent an important early warning mechanism for the immune system to detect infection or tissue damage. The focus of this research was to determine the neuroinflammatory responses to commercial TLR ligands and their effects on brain endothelial barrier strength. Using biosensor technology we screened TLR ligands to all human TLRs and found that the brain endothelial hCMVECs cell line only responded to Poly(I:C) (TLR3-ligand), LPS (TLR4-ligand) and Imiquimod (TLR7 ligand). Both Poly(I:C) and LPS induced pronounced pro-inflammatory cytokine secretion as expected, whereas Imiquimod did not induce secretion of any pro-inflammatory cytokines. Using ECIS technology to measure endothelial barrier function, LPS and Poly(I:C) both acutely reduced barrier-strength, whereas Imiquimod caused immediate and sustained strengthening of the barrier. Further cytokine and ECIS studies showed that Imiquimod could abrogate some of the pro-inflammatory responses to Poly(I:C) and LPS. Most surprisingly, PCR revealed that the hCMVECs lacked TLR7 but expressed both TLR3 and TLR4 and did not respond to other structurally different TLR7 ligands. These data demonstrate that brain endothelial cells can be regulated by TLR 3 and TLR4 ligands in a pro-inflammatory manner and have receptors to Imiquimod, distinct to the classical TLR7, that function in an anti-inflammatory manner.