bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multivariate simulation framework reveals performance of multi-trait GWAS methods
Authors: Porter Heather F. , O’Reilly Paul F. 
Published: March 2017

AbstractBurgeoning availability of genome-wide association study (GWAS) results and national biobank data has led to growing interest in performing multi-trait genetic analyses. Numerous multi-trait GWAS methods that exploit either summary statistics or individual-level data have been developed, but their relative performance is unclear. Here we develop a simulation framework to model the complex networks underlying multivariate genetic epidemiology, enabling the vast model space of genetic effects on multiple correlated traits to be explored systematically. We perform a comprehensive comparison of the leading multi-trait GWAS methods, finding: (1) method performance is highly sensitive to the specific combination of genetic effects and phenotypic correlations, (2) most of the current multivariate methods have remarkably similar statistical power, and (3) multivariate methods may offer a substantial increase in the discovery of genetic variants over the standard univariate approach. We believe our findings offer the clearest picture to date of the relative performance of multi-trait GWAS methods and act as a guide for method selection. We provide a web application and open-source software program implementing our simulation framework, for: (i) further benchmarking of multivariate GWAS methods, (ii) power calculations for multivariate genetic studies, and (iii) generating data for testing any multivariate method in genetic epidemiology.
Ni(OH)2 nanosheets grown on porous hybrid g-C3N4/RGO network as high performance supercapacitor electrode
Authors: Li Lei , Qin Jia , Bi Huiting , Gai Shili , He Fei , Gao Peng , Dai Yunlu , Zhang Xitian , Yang Dan , Yang Piaoping 
Published: March 2017

AbstractA porous hybrid g-C3N4/RGO (CNRG) material has been fabricated through a facile hydrothermal process with the help of glucose molecules, and serves as an efficient immobilization substrate to support ultrathin Ni(OH)2 nanosheets under an easy precipitation process. It was found that the g-C3N4 flakes can uniformly coat on both sides of the RGO, forming sandwich-type composites with a hierarchical structure. It is worth noting that the introduction of the g-C3N4 can effectively achieve the high dispersion and avoid the agglomeration of the nickel hydroxide, and significantly enhance the synthetically capacitive performance. Owning to this unique combination and structure, the CNRG/Ni(OH)2 composite possesses large surface area with suitable pore size distribution, which can effectively accommodate the electrolyte ions migration and accelerate efficient electron transport. When used as electrode for supercapacitor, the hybrid material exhibits high supercapacitive performance, such as an admirable specific capacitance (1785 F/g at a current density of 2 A/g), desirable rate stability (retain 910 F/g at 20 A/g) and favorable cycling durability (maintaining 71.3% capacity after 5000 cycles at 3 A/g). Such desirable properties signify that the CNRG/Ni(OH)2 composites can be a promising electrode material in the application of the supercapacitor.
The invasive pest Drosophila suzukii uses trans-generational medication to resist parasitoid attack
Authors: Poyet M. , Eslin P. , Chabrerie O. , Prud’homme S. M. , Desouhant E. , Gibert P. 
Published: March 2017

AbstractAnimal medication is a behavioral strategy to resist enemies based on the use of substances from the environment. While it has been observed in several animals, whether invasive species can use medication to resist new enemies during its expansion is unknown. Here, we show that the worldwide invasive pest Drosophila suzukii performs trans-generational prophylactic medication by adapting its oviposition behavior in the presence of enemies. We find that flies preferentially lay their eggs on media containing atropine – an entomotoxic alkaloid – in the presence of parasitoids. We further show that flies developing on atropine more efficiently resist parasitization by parasitoids. Finally, we find that developing in hosts reared on atropine strongly impacts the life-history traits of parasitoids. This protective behavior is reported for the first time in a pest and invasive species, and suggests that animal medication may be an important driver of population dynamics during invasions.
Assessing the risk of an emerging zoonosis of worldwide concern: anisakiasis
Authors: Bao Miguel , Pierce Graham J. , Pascual Santiago , González-Muñoz Miguel , Mattiucci Simonetta , Mladineo Ivona , Cipriani Paolo , Bušelić Ivana , Strachan Norval J. C. 
Published: March 2017

AbstractAnisakiasis is an emerging zoonosis caused by the fish parasitic nematode Anisakis. Spain appears to have the highest reported incidence in Europe and marinated anchovies are recognised as the main food vehicle. Using data on fishery landings, fish infection rates and consumption habits of the Spanish population from questionnaires, we developed a quantitative risk assessment (QRA) model for the anchovy value chain. Spaniards were estimated to consume on average 0.66 Anisakis per untreated (non-frozen) raw or marinated anchovy meal. A dose-response relationship was generated and the probability of anisakiasis was calculated to be 9.56 × 10−5 per meal, and the number of annual anisakiasis cases requiring medical attention was predicted between 7,700 and 8,320. Monte Carlo simulations estimated post-mortem migration of Anisakis from viscera to flesh increases the disease burden by >1000% whilst an education campaign to freeze anchovy before consumption may reduce cases by 80%. However, most of the questionnaire respondents who ate untreated meals knew how to prevent Anisakis infection. The QRA suggests that previously reported figures of 500 anisakiasis per year in Europe is a considerable underestimate. The QRA tool can be used by policy makers and informs industry, health professionals and consumers about this underdiagnosed zoonosis.
HDL Glycoprotein Composition and Site-Specific Glycosylation Differentiates Between Clinical Groups and Affects IL-6 Secretion in Lipopolysaccharide-Stimulated Monocytes
Authors: Krishnan Sridevi , Shimoda Michiko , Sacchi Romina , Kailemia Muchena J. , Luxardi Guillaume , Kaysen George A. , Parikh Atul N. , Ngassam Viviane N. , Johansen Kirsten , Chertow Glenn M. , Grimes Barbara , Smilowitz Jennifer T. , Maverakis Emanual , Lebrilla Carlito B. , Zivkovic Angela M. 
Published: March 2017

AbstractThe goal of this pilot study was to determine whether HDL glycoprotein composition affects HDL’s immunomodulatory function. HDL were purified from healthy controls (n = 13), subjects with metabolic syndrome (MetS) (n = 13), and diabetic hemodialysis (HD) patients (n = 24). Concentrations of HDL-bound serum amyloid A (SAA), lipopolysaccharide binding protein (LBP), apolipoprotein A-I (ApoA-I), apolipoprotein C-III (ApoC-III), α-1-antitrypsin (A1AT), and α-2-HS-glycoprotein (A2HSG); and the site-specific glycovariations of ApoC-III, A1AT, and A2HSG were measured. Secretion of interleukin 6 (IL-6) in lipopolysaccharide-stimulated monocytes was used as a prototypical assay of HDL’s immunomodulatory capacity. HDL from HD patients were enriched in SAA, LBP, ApoC-III, di-sialylated ApoC-III (ApoC-III2) and desialylated A2HSG. HDL that increased IL-6 secretion were enriched in ApoC-III, di-sialylated glycans at multiple A1AT glycosylation sites and desialylated A2HSG, and depleted in mono-sialylated ApoC-III (ApoC-III1). Subgroup analysis on HD patients who experienced an infectious hospitalization event within 60 days (HD+) (n = 12), vs. those with no event (HD−) (n = 12) showed that HDL from HD+ patients were enriched in SAA but had lower levels of sialylation across glycoproteins. Our results demonstrate that HDL glycoprotein composition, including the site-specific glycosylation, differentiate between clinical groups, correlate with HDL’s immunomodulatory capacity, and may be predictive of HDL’s ability to protect from infection.
Enlightening discriminative network functional modules behind Principal Component Analysis separation in differential-omic science studies
Authors: Ciucci Sara , Ge Yan , Durán Claudio , Palladini Alessandra , Jiménez-Jiménez Víctor , Martínez-Sánchez Luisa María , Wang Yuting , Sales Susanne , Shevchenko Andrej , Poser Steven W. , Herbig Maik , Otto Oliver , Androutsellis-Theotokis Andreas , Guck Jochen , Gerl Mathias J. , Cannistraci Carlo Vittorio 
Published: March 2017

AbstractOmic science is rapidly growing and one of the most employed techniques to explore differential patterns in omic datasets is principal component analysis (PCA). However, a method to enlighten the network of omic features that mostly contribute to the sample separation obtained by PCA is missing. An alternative is to build correlation networks between univariately-selected significant omic features, but this neglects the multivariate unsupervised feature compression responsible for the PCA sample segregation. Biologists and medical researchers often prefer effective methods that offer an immediate interpretation to complicated algorithms that in principle promise an improvement but in practice are difficult to be applied and interpreted. Here we present PC-corr: a simple algorithm that associates to any PCA segregation a discriminative network of features. Such network can be inspected in search of functional modules useful in the definition of combinatorial and multiscale biomarkers from multifaceted omic data in systems and precision biomedicine. We offer proofs of PC-corr efficacy on lipidomic, metagenomic, developmental genomic, population genetic, cancer promoteromic and cancer stem-cell mechanomic data. Finally, PC-corr is a general functional network inference approach that can be easily adopted for big data exploration in computer science and analysis of complex systems in physics.
Chitosan nerve conduits seeded with autologous bone marrow mononuclear cells for 30 mm goat peroneal nerve defect
Authors: Muheremu Aikeremujiang , Chen Lin , Wang Xiyuan , Wei Yujun , Gong Kai , Ao Qiang 
Published: March 2017

AbstractIn the current research, to find if the combination of chitosan nerve conduits seeded with autologous bone marrow mononuclear cells (BM-MNCs) can be used to bridge 30 mm long peroneal nerve defects in goats, 15 animals were separated into BM-MNC group (n = 5), vehicle group (n = 5), and autologous nerve graft group (n = 5). 12 months after the surgery, animals were evaluated by behavioral observation, magnetic resonance imaging tests, histomorphological and electrophysiological analysis. Results revealed that animals in BM-MNC group and autologous nerve graft group achieved fine functional recovery; magnetic resonance imaging tests and histomorphometry analysis showed that the nerve defect was bridged by myelinated nerve axons in those animals. No significant difference was found between the two groups concerning myelinated axon density, axon diameter, myelin sheath thickness and peroneal nerve action potential. Animals in vehicle group failed to achieve significant functional recovery. The results indicated that chitosan nerve conduits seeded with autologous bone marrow mononuclear cells have strong potential in bridging long peripheral nerve defects and could be applied in future clinical trials.
A Novel Microwave-Induced Plasma Ionization Source for Ion Mobility Spectrometry
Authors: Dai Jianxiong , Zhao Zhongjun , Liang Gaoling , Duan Yixiang 
Published: March 2017

AbstractThis work demonstrates the application of a novel microwave induced plasma ionization (MIPI) source to ion mobility spectrometry (IMS). The MIPI source, called Surfatron, is composed of a copper cavity and a hollow quartz discharge tube. The ion mobility spectrum of synthetics air has a main peak with reduced mobility of 2.14 cm2V−1s−1 for positive ion mode and 2.29 cm2V−1s−1 for negative ion mode. The relative standard deviations (RSD) are 0.7% and 1.2% for positive and negative ion mode, respectively. The total ion current measured was more than 3.5 nA, which is much higher than that of the conventional 63Ni source. This indicates that a better signal-to-noise ratio (SNR) can be acquired from the MIPI source. The SNR was 110 in the analysis of 500 pptv methyl tert-butyl ether (MTBE), resulting in the limit of detection (SNR = 3) of 14 pptv. The linear range covers close to 2.5 orders of magnitude in the detection of triethylamine with a concentration range from 500 pptv to 80 ppbv. Finally, this new MIPI-IMS was used to detect some volatile organic compounds, which demonstrated that the MIPI-IMS has great potential in monitoring pollutants in air.
Tool use for corpse cleaning in chimpanzees
Authors: van Leeuwen Edwin J. C. , Cronin Katherine A. , Haun Daniel B. M. 
Published: March 2017

AbstractFor the first time, chimpanzees have been observed using tools to clean the corpse of a deceased group member. A female chimpanzee sat down at the dead body of a young male, selected a firm stem of grass, and started to intently remove debris from his teeth. This report contributes novel behaviour to the chimpanzee’s ethogram, and highlights how crucial information for reconstructing the evolutionary origins of human mortuary practices may be missed by refraining from developing adequate observation techniques to capture non-human animals’ death responses.
SPAD imagers for super resolution localization microscopy enable analysis of fast fluorophore blinking
Authors: Antolovic Ivan Michel , Burri Samuel , Bruschini Claudio , Hoebe Ron A. , Charbon Edoardo 
Published: March 2017

AbstractsCMOS imagers are currently utilized (replacing EMCCD imagers) to increase the acquisition speed in super resolution localization microscopy. Single-photon avalanche diode (SPAD) imagers feature frame rates per bit depth comparable to or higher than sCMOS imagers, while generating microsecond 1-bit-frames without readout noise, thus paving the way to in-depth time-resolved image analysis. High timing resolution can also be exploited to explore fluorescent dye blinking and other photophysical properties, which can be used for dye optimization. We present the methodology for the blinking analysis of fluorescent dyes on experimental data. Furthermore, the recent use of microlenses has enabled a substantial increase of SPAD imager overall sensitivity (12-fold in our case), reaching satisfactory values for sensitivity-critical applications. This has allowed us to record the first super resolution localization microscopy results obtained with a SPAD imager, with a localization uncertainty of 20 nm and a resolution of 80 nm.
Hyaluronan synthesis by developing cortical neurons in vitro
Authors: Fowke Tania M. , Karunasinghe Rashika N. , Bai Ji-Zhong , Jordan Shawn , Gunn Alistair J. , Dean Justin M. 
Published: March 2017

AbstractHyaluronan is a linear glycosaminoglycan that forms the backbone of perineuronal nets around neurons in the cerebral cortex. However, it remains controversial whether neurons are capable of independent hyaluronan synthesis. Herein, we examined the expression of hyaluronan and hyaluronan synthases (HASs) throughout cortical neuron developmentin vitro. Enriched cultures of cortical neurons were established from E16 rats. Neurons were collected at daysin vitro(DIV) 0 (4 h), 1, 3, 7, 14, and 21 for qPCR or immunocytochemistry. In the relative absence of glia, neurons exhibited HAS1–3 mRNA at all time-points. By immunocytochemistry, puncta of HAS2–3 protein and hyaluronan were located on neuronal cell bodies, neurites, and lamellipodia/growth cones from as early as 4 h in culture. As neurons matured, hyaluronan was also detected on dendrites, filopodia, and axons, and around synapses. Percentages of hyaluronan-positive neurons increased with culture time to ~93% by DIV21, while only half of neurons at DIV21 expressed the perineuronal net markerWisteria floribundaagglutinin. These data clearly demonstrate that neuronsin vitrocan independently synthesise hyaluronan throughout all maturational stages, and that hyaluronan production is not limited to neurons expressing perineuronal nets. The specific structural localisation of hyaluronan suggests potential roles in neuronal development and function.
Visual detection and differentiation of Classic Swine Fever Virus strains using nucleic acid sequence-based amplification (NASBA) and G-quadruplex DNAzyme assay
Authors: Lu Xiaolu , Shi Xueyao , Wu Gege , Wu Tiantian , Qin Rui , Wang Yi 
Published: March 2017

AbstractThe split G-quadruplex DNAzyme has emerged as a valuable tool for visual DNA detection. Here, we successfully integrated colorimetric split G-quadruplex DNAzyme assay with nucleic acid sequence-based amplification to generate a novel detection approach, allowing visual and rapid detection for the RNA of Shimen and HCLV strains of Classic Swine Fever Virus (CSFV). CSFV is a RNA virus that causes a highly contagious disease in domestic pigs and wild boar. With this method, we were able to detect as little as 10 copies/ml of CSF viral RNA within 3 h in serum samples taken from the field. No interference was encountered in the amplification and detection of Classic Swine Fever Virus in the presence of non-target RNA or DNA. Moreover, Shimen and HCLV strains of Classic Swine Fever Virus could be easily differentiated using the NASBA-DNAzyme system. These findings indicate the NASBA-DNAzyme system is a rapid and practical technique for detecting and discriminating CSFV strains and may be applied to the detection of other RNA viruses.
Subjective experience of difficulty depends on multiple cues
Authors: Desender Kobe , Van Opstal Filip , Van den Bussche Eva 
Published: March 2017

AbstractHuman cognition is characterized by subjective experiences that go along with our actions, but the nature and stability of these experiences remain largely unclear. In the current report, the subjective experience of difficulty is studied and it is proposed that this experience is constructed by integrating information from multiple cues. Such an account can explain the tight relationship between primary task performance and subjective difficulty, while allowing for dissociations between both to occur. Confirming this hypothesis, response conflict, reaction time and response repetition were identified as variables that contribute to the experience of difficulty. Trials that were congruent, fast or required the same response as the previous trial were more frequently rated as easy than trials that were incongruent, slow or required a different response as the previous trial. Furthermore, in line with theoretical accounts that relate metacognition to learning, a three day training procedure showed that the influence of these variables on subjective difficulty judgments can be changed. Results of the current study are discussed in relation to work on meta-memory and to recent theoretical advancements in the understanding of subjective confidence.
A new group of glycoside hydrolase family 13 α-amylases with an aberrant catalytic triad
Authors: Sarian Fean D. , Janeček Štefan , Pijning Tjaard , Ihsanawati  , Nurachman Zeily , Radjasa Ocky K. , Dijkhuizen Lubbert , Natalia Dessy , van der Maarel Marc J. E. C. 
Published: March 2017

Abstractα-Amylases are glycoside hydrolase enzymes that act on the α(1→4) glycosidic linkages in glycogen, starch, and related α-glucans, and are ubiquitously present in Nature. Most α-amylases have been classified in glycoside hydrolase family 13 with a typical (β/α)8-barrel containing two aspartic acid and one glutamic acid residue that play an essential role in catalysis. An atypical α-amylase (BmaN1) with only two of the three invariant catalytic residues present was isolated from Bacillus megaterium strain NL3, a bacterial isolate from a sea anemone of Kakaban landlocked marine lake, Derawan Island, Indonesia. In BmaN1 the third residue, the aspartic acid that acts as the transition state stabilizer, was replaced by a histidine. Three-dimensional structure modeling of the BmaN1 amino acid sequence confirmed the aberrant catalytic triad. Glucose and maltose were found as products of the action of the novel α-amylase on soluble starch, demonstrating that it is active in spite of the peculiar catalytic triad. This novel BmaN1 α-amylase is part of a group of α-amylases that all have this atypical catalytic triad, consisting of aspartic acid, glutamic acid and histidine. Phylogenetic analysis showed that this group of α-amylases comprises a new subfamily of the glycoside hydrolase family 13.
Hydrogel increases localized transport regions and skin permeability during low frequency ultrasound treatment
Authors: Pereira Tatiana Aparecida , Ramos Danielle Nishida , Lopez Renata F. V. 
Published: March 2017

AbstractLow frequency ultrasound (LFU) enhances skin permeability via the formation of heterogeneous localized transport regions (LTRs). In this work, hydrogels with different zeta potentials were used as the coupling medium for LFU to investigate their contribution to LTR patterns and to the skin penetration of two model drugs, calcein and doxorubicin (DOX). When hydrogels were used, LTRs covering at least a 3-fold greater skin area were observed compared to those resulting from traditional LFU treatment and sodium lauryl sulfate. More LTRs resulted in an enhancement of calcein skin permeation. The zeta potential of the hydrogels affected the skin penetration of the positively charged DOX; the cationic coupling medium decreased the DOX recovered from the viable epidermis by 2.8-fold, whereas the anionic coupling medium increased the DOX accumulation in the stratum corneum by 4.4-fold. Therefore, LFU/hydrogel treatment increases LTRs areas and can target ionized drugs to specific skin layers depending on the zeta potential of the coupling medium.
Activated full-length myosin-X moves processively on filopodia with large steps toward diverse two-dimensional directions
Authors: Sato Osamu , Jung Hyun Suk , Komatsu Satoshi , Tsukasaki Yoshikazu , Watanabe Tomonobu M. , Homma Kazuaki , Ikebe Mitsuo 
Published: March 2017

AbstractMyosin-X, (Myo 10), is an unconventional myosin that transports the specific cargos to filopodial tips, and is associated with the mechanism underlying filopodia formation and extension. To clarify the innate motor characteristic, we studied the single molecule movement of a full-length myosin-X construct with leucine zipper at the C-terminal end of the tail (M10FullLZ) and the tail-truncated myosin-X without artificial dimerization motif (BAP-M101–979HMM). M10FullLZ localizes at the tip of filopodia like myosin-X full-length (M10Full). M10FullLZ moves on actin filaments in the presence of PI(3,4,5)P3, an activator of myosin-X. Single molecule motility analysis revealed that the step sizes of both M10FullLZ and BAP-M101–979HMM are widely distributed on single actin filaments that is consistent with electron microscopy observation. M10FullLZ moves on filopodial actin bundles of cells with a mean step size (~36 nm), similar to the step size on single actin filaments (~38 nm). Cartesian plot analysis revealed that M10FullLZ meandered on filopodial actin bundles to both x- and y- directions. These results suggest that the lever-arm of full-length myosin-X is flexible enough to processively steps on different actin filaments within the actin bundles of filopodia. This characteristic of myosin-X may facilitate actin filament convergence for filopodia production.