bluuebunny/crossref_metadata_2025_split huggingface dataset:
Switchable sensitizers stepwise lighting up lanthanide emissions
Authors: Zhang Yan , Jiao Peng-Chong , Xu Hai-Bing , Tang Ming-Jing , Yang Xiao-Ping , Huang Shaoming , Deng Jian-Guo 
Published: March 2015

AbstractAnalagous to a long-ranged rocket equipped with multi-stage engines, a luminescent compound with consistent emission signals across a large range of concentrations from two stages of sensitizers can be designed. In this approach, ACQ, aggregation-caused quenching effect of sensitizers, would stimulate lanthanide emission below 10−4 M and then at concentrations higher than 10−3 M, the “aggregation-induced emission” (AIE) effect of luminophores would be activated with the next set of sensitizers for lanthanide emission. Simultaneously, the concentration of the molecules could be monitored digitally by the maximal excitation wavelengths, due to the good linear relationship between the maximal excitation wavelengths and the concentrations {lg(M)}. This model, wherein molecules are assembled with two stages (both AIE and ACQ effect) of sensitizers, may provide a practicable strategy for design and construction of smart lanthanide bioprobes, which are suitable in complicated bioassay systems in which concentration is variable.
The bacterial communities associated with fecal types and body weight of rex rabbits
Authors: Zeng Bo , Han Shushu , Wang Ping , Wen Bin , Jian Wensu , Guo Wei , Yu Zhiju , Du Dan , Fu Xiangchao , Kong Fanli , Yang Mingyao , Si Xiaohui , Zhao Jiangchao , Li Ying 
Published: March 2015

AbstractRex rabbit is an important small herbivore for fur and meat production. However, little is known about the gut microbiota in rex rabbit, especially regarding their relationship with different fecal types and growth of the hosts. We characterized the microbiota of both hard and soft feces from rex rabbits with high and low body weight by using the Illumina MiSeq platform targeting the V4 region of the 16S rDNA. High weight rex rabbits possess distinctive microbiota in hard feces, but not in soft feces, from the low weight group. We detected the overrepresentation of several genera such as YS2/Cyanobacteria and Bacteroidales and underrepresentation of genera such as Anaeroplasma spp. and Clostridiaceae in high weight hard feces. Between fecal types, several bacterial taxa such as Ruminococcaceae, and Akkermansia spp. were enriched in soft feces. PICRUSt analysis revealed that metabolic pathways such as “stilbenoid, diarylheptanoid, gingerol biosynthesis” were enriched in high weight rabbits and pathways related to “xenobiotics biodegradation” and “various types of N-glycan biosynthesis” were overrepresented in rabbit soft feces. Our study provides foundation to generate hypothesis aiming to test the roles that different bacterial taxa play in the growth and caecotrophy of rex rabbits.
Biochemical and Pharmacological Characterizations of ESI-09 Based EPAC Inhibitors: Defining the ESI-09 “Therapeutic Window”
Authors: Zhu Yingmin , Chen Haijun , Boulton Stephen , Mei Fang , Ye Na , Melacini Giuseppe , Zhou Jia , Cheng Xiaodong 
Published: March 2015

AbstractThe cAMP signaling cascade is one of the most frequently targeted pathways for the development of pharmaceutics. A plethora of recent genetic and pharmacological studies suggest that exchange proteins directly activated by cAMP (EPACs) are implicated in multiple pathologies. Selective EPAC inhibitors have been recently developed. One specific inhibitor, ESI-09, has been shown to block EPAC activity and functions, as well as to recapitulate genetic phenotypes of EPAC knockout mice when applied in vivo. However, a recent study raised concern that ESI-09 might act as a non-specific protein denaturant. Herein, we present a detailed biochemical and pharmacological characterization, as well as a structure-activity relationship (SAR) analysis of ESI-09. Our studies show that ESI-09 dose-dependently inhibits activity of both EPAC1 and EPAC2 with apparent IC50 values well below the concentrations shown to induce “protein denaturation”. Moreover, the ESI-09's action towards EPAC proteins is highly sensitive to minor modifications of the 3-chlorophenyl moiety. Taken together, these results demonstrate that ESI-09 indeed acts as an EPAC specific antagonist and does not significantly destabilize/denature proteins at pharmacological effective concentrations. This conclusion is further supported by NMR data showing that ESI-09 induces residue-dependent chemical shift changes at low concentrations, while preserving well dispersed peaks.
Complex trait architecture: the pleiotropic model revisited
Authors: North T.-L. , Beaumont M. A. 
Published: March 2015

AbstractThere is currently much debate about how much the genetic heritability of complex traits is due to very rare alleles. This issue is important because it determines sampling strategies for genetic association studies. Several recent theoretical papers based on a pleiotropic model for trait evolution suggest that it is possible that a large proportion of the genetic variance could be explained by rare alleles. This model assumes that mutations with a large effect on fitness also tend to have large positive or negative effects on phenotypic traits. We show that conclusions based on standard diffusion results are generally applicable to simulations of whole genomes with overlapping generations in a finite population, although the variance contribution of rare alleles is somewhat smaller than theoretical predictions. We show that under many scenarios the pleiotropic model predicts trait distributions that are unrealistically leptokurtic. We argue that this imposes a limit on the relationship between fitness and trait effects.
The mealybug Phenacoccus solenopsis suppresses plant defense responses by manipulating JA-SA crosstalk
Authors: Zhang Peng-Jun , Huang Fang , Zhang Jin-Ming , Wei Jia-Ning , Lu Yao-Bin 
Published: March 2015

AbstractInduced plant defenses against herbivores are modulated by jasmonic acid-, salicylic acid- and ethylene-signaling pathways. Although there is evidence that some pathogens suppress plant defenses by interfering with the crosstalk between different signaling pathways, such evidence is scarce for herbivores. Here, we demonstrate that the mealybug Phenacoccus solenopsis suppresses the induced defenses in tomato. We found that exogenous JA, but not SA, significantly decreased mealybug feeding time and reduced nymphal performance. In addition, constitutive activation of JA signaling in 35s::prosys plants reduced mealybug survival. These data indicate that the JA signaling pathway plays a key role in mediating the defense responses against P. solenopsis. We also found that mealybug feeding decreased JA production and JA-dependent defense gene expression, but increased SA accumulation and SA-dependent gene expression. In SA-deficient plants, mealybug feeding did not suppress but activated JA accumulation, indicating that the suppression of JA-regulated defenses depends on the SA signaling pathway. Mealybugs benefit from suppression of JA-regulated defenses by exhibiting enhanced nymphal performance. These findings confirm that P. solenopsis manipulates plants for its own benefits by modulating the JA-SA crosstalk and thereby suppressing induced defenses.
MicroRNA-derived Fragment Length Polymorphism Assay
Authors: Xie Xiaoping , Tang Fang , Yang Zhao , Zhang Yaoyi , Feng Zihao , Yang Yu , Wu Xiujin , Zhang Feifei , Zhu Jie , Xu Kai 
Published: March 2015

AbstractMicroRNA (miRNA) studies are experiencing a transition from basic research applications to clinical applications. However, the lack of reliable and sensitive miRNA detection methods has become a bottleneck in the process. Here, we report an absolute quantification method based on the competitive PCR amplification of specific miRNAs and synthetic RNA spike-ins in a single reaction. RNA spike-ins are quantified as dynamic RNA copy number standards and are used to measure selected miRNAs free from the effects of intra-assay variables, including those from individual sample sources. Combined with the size differentiation power of capillary electrophoresis, the content of miRNAs was reproducibly measured, with verifiable detection limits of 10–46 copies over 5-log detection ranges. The direct measurements of miRNAs from 168 human serum samples and their considerable value as a diagnostic for bronchopneumonia and bronchiolitis demonstrate the potential of the assay in clinical applications.
Light-Emitting Devices Based on Top-down Fabricated GaAs Quantum Nanodisks
Authors: Higo Akio , Kiba Takayuki , Tamura Yosuke , Thomas Cedric , Takayama Junichi , Wang Yunpeng , Sodabanlu Hassanet , Sugiyama Masakazu , Nakano Yoshiaki , Yamashita Ichiro , Murayama Akihiro , Samukawa Seiji 
Published: March 2015

AbstractQuantum dots photonic devices based on the III–V compound semiconductor technology offer low power consumption, temperature stability and high-speed modulation. We fabricated GaAs nanodisks (NDs) of sub-20-nm diameters by a top-down process using a biotemplate and neutral beam etching (NBE). The GaAs NDs were embedded in an AlGaAs barrier regrown by metalorganic vapor phase epitaxy (MOVPE). The temperature dependence of photoluminescence emission energies and the transient behavior were strongly affected by the quantum confinement effects of the embedded NDs. Therefore, the quantum levels of the NDs may be tuned by controlling their dimensions. We combined NBE and MOVPE in a high-throughput process compatible with industrial production systems to produce GaAs NDs with tunable optical characteristics. ND light emitting diode exhibited a narrow spectral width of 38 nm of high-intensity emission as a result of small deviation of ND sizes and superior crystallographic quality of the etched GaAs/AlGaAs layer.
Enhanced photocurrent production by bio-dyes of photosynthetic macromolecules on designed TiO2 film
Authors: Yu Daoyong , Wang Mengfei , Zhu Guoliang , Ge Baosheng , Liu Shuang , Huang Fang 
Published: March 2015

AbstractThe macromolecular pigment-protein complex has the merit of high efficiency for light-energy capture and transfer after long-term photosynthetic evolution. Here bio-dyes of A.platensis photosystem I (PSI) and spinach light-harvesting complex II (LHCII) are spontaneously sensitized on three types of designed TiO2 films, to assess the effects of pigment-protein complex on the performance of bio-dye sensitized solar cells (SSC). Adsorption models of bio-dyes are proposed based on the 3D structures of PSI and LHCII and the size of particles and inner pores in the TiO2 film. PSI shows its merit of high efficiency for captured energy transfer, charge separation and transfer in the electron transfer chain (ETC) and electron injection from FB to the TiO2 conducting band. After optimization, the best short current (JSC) and photoelectric conversion efficiency (η) of PSI-SSC and LHCII-SSC are 1.31 mA cm-2 and 0.47% and 1.51 mA cm-2 and 0.52%, respectively. The potential for further improvement of this PSI based SSC is significant and could lead to better utilization of solar energy.
Broadband Lamb Wave Trapping in Cellular Metamaterial Plates with Multiple Local Resonances
Authors: Zhao De-Gang , Li Yong , Zhu Xue-Feng 
Published: March 2015

AbstractWe have investigated the Lamb wave propagation in cellular metamaterial plates constructed by bending-dominated and stretch-dominated unit-cells with the stiffness differed by orders of magnitude at an ultralow density. The simulation results show that ultralight metamaterial plates with textured stubs deposited on the surface can support strong local resonances for both symmetric and anti-symmetric modes at low frequencies, where Lamb waves at the resonance frequencies are highly localized in the vibrating stubs. The resonance frequency is very sensitive to the geometry of textured stubs. By reasonable design of the geometry of resonant elements, we establish a simple loaded-bar model with the array of oscillators having a gradient relative density (or weight) that can support multiple local resonances, which permits the feasibility of a broadband Lamb wave trapping. Our study could be potentially significant in designing ingenious weight-efficient acoustic devices for practical applications, such as shock absorption, cushioning and vibrations traffic, etc.
A stable RNA G-quadruplex within the 5′-UTR of Arabidopsis thaliana ATR mRNA inhibits translation
Authors: Kwok Chun Kit , Ding Yiliang , Shahid Saima , Assmann Sarah M. , Bevilacqua Philip C. 
Published: March 2015

Guanine quadruplex structures (GQSs) play important roles in the regulation of gene expression and cellular processes. Recent studies provide strong evidence for the formation and function of DNA and RNA GQSs in human cells. However, whether GQSs form and are functional in plants remains essentially unexplored. On the basis of circular dichroism (CD)-detected titration, UV-detected melting, in-line probing (ILP) and reporter gene assay studies, we report the first example of a plant RNA GQS that inhibits translation. This GQS is located within the 5′-UTR of the ATAXIA TELANGIECTASIA-MUTATED AND RAD3-RELATED (ATR) mRNA of Arabidopsis thaliana (mouse-ear cress). We show that this GQS is highly stable and is thermodynamically favoured over a competing hairpin structure in the 5′-UTR at physiological K+ and Mg2+ concentrations. Results from ILP reveal the secondary structure of the RNA and support formation of the GQS in vitro in the context of the complete 5′-UTR. Transient reporter gene assays performed in living plants reveal that the GQS inhibits translation but not transcription, implicating this GQS as a translational repressor in vivo. Our results provide the first complete demonstration of the formation and function of a regulatory RNA GQS in plants and open new avenues to explore potential functional roles of GQS in the plant kingdom.
Determinants of oligosaccharide specificity of the carbohydrate-binding modules of AMP-activated protein kinase
Authors: Mobbs Jesse I. , Koay Ann , Di Paolo Alex , Bieri Michael , Petrie Emma J. , Gorman Michael A. , Doughty Larissa , Parker Michael W. , Stapleton David I. , Griffin Michael D.W. , Gooley Paul R. 
Published: March 2015

AMP-activated protein kinase (AMPK) is an αβγ heterotrimer that is important in regulating energy metabolism in all eukaryotes. The β-subunit exists in two isoforms (β1 and β2) and contains a carbohydrate-binding module (CBM) that interacts with glycogen. The two CBM isoforms (β1- and β2-CBM) are near identical in sequence and structure, yet show differences in carbohydrate-binding affinity. β2-CBM binds linear carbohydrates with 4-fold greater affinity than β1-CBM and binds single α1,6-branched carbohydrates up to 30-fold tighter. To understand these affinity differences, especially for branched carbohydrates, we determined the NMR solution structure of β2-CBM in complex with the single α1,6-branched carbohydrate glucosyl-β-cyclodextrin (gBCD) which supported the dynamic nature of the binding site, but resonance broadening prevented defining where the α1,6 branch bound. We therefore solved the X-ray crystal structures of β1- and β2-CBM, in complex with gBCD, to 1.7 and 2.0 Å (1 Å=0.1 nm) respectively. The additional threonine (Thr101) of β2-CBM expands the size of the surrounding loop, creating a pocket that accommodates the α1,6 branch. Hydrogen bonds are formed between the α1,6 branch and the backbone of Trp99 and Lys102 side chain of β2-CBM. In contrast, the α1,6 branch could not be observed in the β1-CBM structure, suggesting that it does not form a specific interaction. The orientation of gBCD bound to β1- and β2-CBM is supported by thermodynamic and kinetic data obtained through isothermal titration calorimetry (ITC) and NMR. These results suggest that AMPK containing the muscle-specific β2-isoform may have greater affinity for partially degraded glycogen.
SRY gene transferred by extracellular vesicles accelerates atherosclerosis by promotion of leucocyte adherence to endothelial cells
Authors: Cai Jin , Guan Weiwei , Tan Xiaorong , Chen Caiyu , Li Liangpeng , Wang Na , Zou Xue , Zhou Faying , Wang Jialiang , Pei Fang , Chen Xinjian , Luo Hao , Wang Xinquan , He Duofen , Zhou Lin , Jose Pedro A. , Zeng Chunyu 
Published: March 2015

We set out to investigate whether and how SRY (sex-determining region, Y) DNAs in plasma EVs (extracellular vesicles) is involved in the pathogenesis of atherosclerosis. PCR and gene sequencing found the SRY gene fragment in plasma EVs from male, but not female, patients; EVs from male patients with CAD (coronary artery disease) had a higher SRY GCN (gene copy number) than healthy subjects. Additional studies found that leucocytes, the major source of plasma EVs, had higher SRY GCN and mRNA and protein expression in male CAD patients than controls. After incubation with EVs from SRY-transfected HEK (human embryonic kidney)-293 cells, monocytes (THP-1) and HUVECs (human umbilical vein endothelial cells), which do not endogenously express SRY protein, were found to express newly synthesized SRY protein. This resulted in an increase in the adherence factors CD11-a in THP-1 cells and ICAM-1 (intercellular adhesion molecule 1) in HUVECs. EMSA showed that SRY protein increased the promoter activity of CD11-a in THP-1 cells and ICAM-1 in HUVECs. There was an increase in THP-1 cells adherent to HUVECs after incubation with SRY-EVs. SRY DNAs transferred from EVs have pathophysiological significance in vivo; injection of SRY EVs into ApoE−/− (apolipoprotein-knockout) mice accelerated atherosclerosis. The SRY gene in plasma EVs transferred to vascular endothelial cells may play an important role in the pathogenesis of atherosclerosis; this mechanism provides a new approach to the understanding of inheritable CAD in men.
Global trends in antimicrobial use in food animals
Authors: Van Boeckel Thomas P. , Brower Charles , Gilbert Marius , Grenfell Bryan T. , Levin Simon A. , Robinson Timothy P. , Teillant Aude , Laxminarayan Ramanan 
Published: March 2015

Significance
Antimicrobials are used in livestock production to maintain health and productivity. These practices contribute to the spread of drug-resistant pathogens in both livestock and humans, posing a significant public health threat. We present the first global map (228 countries) of antibiotic consumption in livestock and conservatively estimate the total consumption in 2010 at 63,151 tons. We project that antimicrobial consumption will rise by 67% by 2030, and nearly double in Brazil, Russia, India, China, and South Africa. This rise is likely to be driven by the growth in consumer demand for livestock products in middle-income countries and a shift to large-scale farms where antimicrobials are used routinely. Our findings call for initiatives to preserve antibiotic effectiveness while simultaneously ensuring food security in low- and lower-middle-income countries.
Automatic determination of NET (neutrophil extracellular traps) coverage in fluorescent microscopy images
Authors: Coelho Luis Pedro , Pato Catarina , Friães Ana , Neumann Ariane , von Köckritz-Blickwede Maren , Ramirez Mário , Carriço João André 
Published: March 2015

Abstract
Motivation: Neutrophil extracellular traps (NETs) are believed to be essential in controlling several bacterial pathogens. Quantification of NETs in vitro is an important tool in studies aiming to clarify the biological and chemical factors contributing to NET production, stabilization and degradation. This estimation can be performed on the basis of fluorescent microscopy images using appropriate labelings. In this context, it is desirable to automate the analysis to eliminate both the tedious process of manual annotation and possible operator-specific biases.
Results: We propose a framework for the automated determination of NET content, based on visually annotated images which are used to train a supervised machine-learning method. We derive several methods in this framework. The best results are obtained by combining these into a single prediction. The overall Q2 of the combined method is 93%. By having two experts label part of the image set, we were able to compare the performance of the algorithms to the human interoperator variability. We find that the two operators exhibited a very high correlation on their overall assessment of the NET coverage area in the images (R2 is 97%), although there were consistent differences in labeling at pixel level (Q2, which unlike R2 does not correct for additive and multiplicative biases, was only 89%).
Availability and implementation: Open source software (under the MIT license) is available at https://github.com/luispedro/Coelho2015_NetsDetermination for both reproducibility and application to new data.
Contact: luis@luispedro.org
Supplementary information : Supplementary data are available at Bioinformatics online.
MAGNA++: Maximizing Accuracy in Global Network Alignment via both node and edge conservation
Authors: Vijayan V. , Saraph V. , Milenković T. 
Published: March 2015

Abstract
Motivation: Network alignment aims to find conserved regions between different networks. Existing methods aim to maximize total similarity over all aligned nodes (i.e. node conservation). Then, they evaluate alignment quality by measuring the amount of conserved edges, but only after the alignment is constructed. Thus, we recently introduced MAGNA (Maximizing Accuracy in Global Network Alignment) to directly maximize edge conservation while producing alignments and showed its superiority over the existing methods. Here, we extend the original MAGNA with several important algorithmic advances into a new MAGNA++ framework.
Results: MAGNA++ introduces several novelties: (i) it simultaneously maximizes any one of three different measures of edge conservation (including our recent superior S3 measure) and any desired node conservation measure, which further improves alignment quality compared with maximizing only node conservation or only edge conservation; (ii) it speeds up the original MAGNA algorithm by parallelizing it to automatically use all available resources, as well as by reimplementing the edge conservation measures more efficiently; (iii) it provides a friendly graphical user interface for easy use by domain (e.g. biological) scientists; and (iv) at the same time, MAGNA++ offers source code for easy extensibility by computational scientists.
Availability and implementation: http://www.nd.edu/∼cone/MAGNA++/
Contact: tmilenko@nd.edu
Solubis: optimize your protein
Authors: De Baets Greet , Van Durme Joost , van der Kant Rob , Schymkowitz Joost , Rousseau Frederic 
Published: March 2015

Abstract
Motivation: Protein aggregation is associated with a number of protein misfolding diseases and is a major concern for therapeutic proteins. Aggregation is caused by the presence of aggregation-prone regions (APRs) in the amino acid sequence of the protein. The lower the aggregation propensity of APRs and the better they are protected by native interactions within the folded structure of the protein, the more aggregation is prevented. Therefore, both the local thermodynamic stability of APRs in the native structure and their intrinsic aggregation propensity are a key parameter that needs to be optimized to prevent protein aggregation.
Results: The Solubis method presented here automates the process of carefully selecting point mutations that minimize the intrinsic aggregation propensity while improving local protein stability.
Availability and implementation: All information about the Solubis plugin is available at http://solubisyasara.switchlab.org/.
Contact: joost.schymkowitz@switch.vib-kuleuven.be or Frederic.Rousseau@switch.vib-kuleuven.be
Supplementary information: Supplementary data are available at Bioinformatics online.