bluuebunny/crossref_metadata_2025 huggingface dataset:
Spin splitting and electric field modulated electron-hole pockets in antimonene nanoribbons
Authors: Song Yan , Wang Xiaocha , Mi Wenbo
Published: March 2017

The one-dimensional nanoribbons have great potential applications in novel multifunctional electronic devices. Herewith, we investigate the electronic structure of antimonene nanoribbons using the first-principles calculations. Four ribbon models are considered. All of them are semiconductors with appropriate band gaps. Because of the loss of inversion symmetry, spin-orbit splitting appears in the asymmetric washboard nanoribbons. Significantly, spin splittings of 62 and 44 meV are found at the valence band maximum and conduction band minimum for zigzag asymmetric washboard nanoribbon (aW-zSbNR). Further applying an in-plane electric field introduces a potential difference between the two zigzag edges. The energies for the localized edge states are modified. Eventually spin-orbit-coupling induced band inversion and electron-hole pockets with appropriately the same size could be triggered in a W-zSbNR, which is interesting for exploiting the magnetoresistance effect.
Unraveling the mystery of hearing in gerbil and other rodents with an arch-beam model of the basilar membrane
Authors: Kapuria Santosh , Steele Charles R. , Puria Sunil
Published: March 2017

The mammalian basilar membrane (BM) consists of two collagen-fiber layers responsible for the frequency-to-place tonotopic mapping in the cochlea, which together form a flat beam over at least part of the BM width. The mechanics of hearing in rodents such as gerbil pose a challenge to our understanding of the cochlea, however, because for gerbil the two layers separate to form a pronounced arch over the remaining BM width. Moreover, the thickness and total width normally thought to determine the local stiffness, and tonotopic mapping in turn, change little along the cochlear length. A nonlinear analysis of a newly developed model, incorporating flat upper and arched lower fiber layers connected by ground substance, explains the initial plateau and subsequent quadratic increase found in measured stiffness vs. deflection curves under point loading, while for pressure loading the model accurately predicts the tonotopic mapping. The model also has applicability to understanding cochlear development and to interpreting evolutionary changes in mammalian hearing.
Traumatic brain injury results in acute rarefication of the vascular network
Authors: Obenaus Andre , Ng Michelle , Orantes Amanda M. , Kinney-Lang Eli , Rashid Faisal , Hamer Mary , DeFazio Richard A. , Tang Jiping , Zhang John H. , Pearce William J.
Published: March 2017

The role of the cerebrovascular network and its acute response to TBI is poorly defined and emerging evidence suggests that cerebrovascular reactivity is altered. We explored how cortical vessels are physically altered following TBI using a newly developed technique, vessel painting. We tested our hypothesis that a focal moderate TBI results in global decrements to structural aspects of the vasculature. Rats (naïve, sham-operated, TBI) underwent a moderate controlled cortical impact. Animals underwent vessel painting perfusion to label the entire cortex at 1 day post TBI followed by whole brain axial and coronal images using a wide-field fluorescence microscope. Cortical vessel network characteristics were analyzed for classical angiographic features (junctions, lengths) wherein we observed significant global (both hemispheres) reductions in vessel junctions and vessel lengths of 33% and 22%, respectively. Biological complexity can be quantified using fractal geometric features where we observed that fractal measures were also reduced significantly by 33%, 16% and 13% for kurtosis, peak value frequency and skewness, respectively. Acutely after TBI there is a reduction in vascular network and vascular complexity that are exacerbated at the lesion site and provide structural evidence for the bilateral hemodynamic alterations that have been reported in patients after TBI.
Disentangling constraints using viability evolution principles in integrative modeling of macromolecular assemblies
Authors: Tamò Giorgio , Maesani Andrea , Träger Sylvain , Degiacomi Matteo T. , Floreano Dario , Dal Peraro Matteo
Published: March 2017

Predicting the structure of large molecular assemblies remains a challenging task in structural biology when using integrative modeling approaches. One of the main issues stems from the treatment of heterogeneous experimental data used to predict the architecture of native complexes. We propose a new method, applied here for the first time to a set of symmetrical complexes, based on evolutionary computation that treats every available experimental input independently, bypassing the need to balance weight components assigned to aggregated fitness functions during optimization.
Pd/ZnO nanorods based sensor for highly selective detection of extremely low concentration hydrogen
Authors: Kumar Mohit , Singh Bhati Vijendra , Ranwa Sapana , Singh Jitendra , kumar Mahesh
Published: March 2017

We report highly hydrogen selective Pd contacted ZnO nanorods based sensor detecting low concentration even at low operating temperature of 50 °C. The sensor performance was investigated for various gases such as H2, CH4, H2S and CO2 at different operating temperatures from 50 °C to 175 °C for various gas concentrations ranging from 7 ppm to 10,000 ppm (1%). The sensor is highly efficient as it detects hydrogen even at low concentration of ~7 ppm and at operating temperature of 50 °C. The sensor’s minimum limit of detection and relative response at 175 °C were found 7 ppm with ~38.7% for H2, 110 ppm with ~6.08% for CH4, 500 ppm with ~10.06% for H2S and 1% with ~11.87% for CO2. Here, Pd exhibits dual characteristics as metal contact and excellent catalyst to hydrogen molecules. The activation energy was calculated for all the gases and found lowest ~3.658 kJ/mol for H2. Low activation energy accelerates desorption reactions and enhances the sensor’s performance.
Correction: Corrigendum: Transcriptome characterisation and simple sequence repeat marker discovery in the seagrass Posidonia oceanica
Authors: D’Esposito D. , Orrù L. , Dattolo E. , Bernardo L. , Lamontanara A. , Orsini L. , Serra I.A , Mazzuca S. , Procaccini G.
Published: March 2017

Scientific Data 3:160115 doi: 10.1038/sdata.2016.115 (2016); Published 20 December 2016; Updated 14 March 2017 The original version of this Data Descriptor contained a typographical error in the spelling of the author A. Lamontanara, which was incorrectly given as A. Lamontara. This has now been corrected in the PDF and HTML versions of the Data Descriptor.
Metazoan mitochondrial gene sequence reference datasets for taxonomic assignment of environmental samples
Authors: Machida Ryuji J. , Leray Matthieu , Ho Shian-Lei , Knowlton Nancy
Published: March 2017

Mitochondrial-encoded genes are increasingly targeted in studies using high-throughput sequencing approaches for characterizing metazoan communities from environmental samples (e.g., plankton, meiofauna, filtered water). Yet, unlike nuclear ribosomal RNA markers, there is to date no high-quality reference dataset available for taxonomic assignments. Here, we retrieved all metazoan mitochondrial gene sequences from GenBank, and then quality filtered and formatted the datasets for taxonomic assignments using taxonomic assignment tools. The reference datasets—‘Midori references’—are available for download at www.reference-midori.info. Two versions are provided: (I) Midori-UNIQUE that contains all unique haplotypes associated with each species and (II) Midori-LONGEST that contains a single sequence, the longest, for each species. Overall, the mitochondrial Cytochrome oxidase subunit I gene was the most sequence-rich gene. However, sequences of the mitochondrial large ribosomal subunit RNA and Cytochrome b apoenzyme genes were observed for a large number of species in some phyla. The Midori reference is compatible with some taxonomic assignment software. Therefore, automated high-throughput sequence taxonomic assignments can be particularly effective using these datasets.
Spatial and quantitative datasets of the pancreatic β-cell mass distribution in lean and obese mice
Authors: Parween Saba , Eriksson Maria , Nord Christoffer , Kostromina Elena , Ahlgren Ulf
Published: March 2017

A detailed understanding of pancreatic β-cell mass distribution is a key element to fully appreciate the pathophysiology of models of diabetes and metabolic stress. Commonly, such assessments have been performed by stereological approaches that rely on the extrapolation of two-dimensional data and provide very limited topological information. We present ex vivo optical tomographic data sets of the full β-cell mass distribution in cohorts of obese ob/ob mice and their lean controls, together with information about individual islet β-cell volumes, their three-dimensional coordinates and shape throughout the volume of the pancreas between 4 and 52 weeks of age. These data sets offer the currently most comprehensive public record of the β-cell mass distribution in the mouse. As such, they may serve as a quantitative and topological reference for the planning of a variety of in vivo or ex vivo experiments including computational modelling and statistical analyses. By shedding light on intra- and inter-lobular variations in β-cell mass distribution, they further provide a powerful tool for the planning of stereological sampling assessments.
T1-weighted in vivo human whole brain MRI dataset with an ultrahigh isotropic resolution of 250 μm
Authors: Lüsebrink Falk , Sciarra Alessandro , Mattern Hendrik , Yakupov Renat , Speck Oliver
Published: March 2017

We present an ultrahigh resolution in vivo human brain magnetic resonance imaging (MRI) dataset. It consists of T1-weighted whole brain anatomical data acquired at 7 Tesla with a nominal isotropic resolution of 250 μm of a single young healthy Caucasian subject and was recorded using prospective motion correction. The raw data amounts to approximately 1.2 TB and was acquired in eight hours total scan time. The resolution of this dataset is far beyond any previously published in vivo structural whole brain dataset. Its potential use is to build an in vivo MR brain atlas. Methods for image reconstruction and image restoration can be improved as the raw data is made available. Pre-processing and segmentation procedures can possibly be enhanced for high magnetic field strength and ultrahigh resolution data. Furthermore, potential resolution induced changes in quantitative data analysis can be assessed, e.g., cortical thickness or volumetric measures, as high quality images with an isotropic resolution of 1 and 0.5 mm of the same subject are included in the repository as well.
Multivariate simulation framework reveals performance of multi-trait GWAS methods
Authors: Porter Heather F. , O’Reilly Paul F.
Published: March 2017

Burgeoning 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

A 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

Animal 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

Anisakiasis 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

The 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

Omic 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

In 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

This 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

For 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

sCMOS 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

Hyaluronan 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

The 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

Human 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

α-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

Low 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

Myosin-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.
Myricitrin Alleviates Oxidative Stress-induced Inflammation and Apoptosis and Protects Mice against Diabetic Cardiomyopathy
Authors: Zhang Bin , Shen Qiang , Chen Yaping , Pan Ruile , Kuang Shihuan , Liu Guiyan , Sun Guibo , Sun Xiaobo
Published: March 2017

Diabetic cardiomyopathy (DCM) has been increasingly considered as a main cause of heart failure and death in diabetic patients. At present, no effective treatment exists to prevent its development. In the present study, we describe the potential protective effects and mechanisms of myricitrin (Myr) on the cardiac function of streptozotosin-induced diabetic mice and on advanced glycation end products (AGEs)-induced H9c2 cardiomyocytes. In vitro experiments revealed that pretreatment with Myr significantly decreased AGEs-induced inflammatory cytokine expression, limited an increase in ROS levels, and reduced cell apoptosis, fibrosis, and hypertrophy in H9c2 cells. These effects are correlated with Nrf2 activation and NF-κB inhibition. In vivo investigation demonstrated that oral administration of Myr at 300 mg/kg/day for 8 weeks remarkably decreased the expression of enzymes associated with cardiomyopathy, as well as the expression of inflammatory cytokines and apoptotic proteins. Finally, Myr improved diastolic dysfunction and attenuated histological abnormalities. Mechanistically, Myr attenuated diabetes-induced Nrf2 inhibition via the regulation of Akt and ERK phosphorylation in the diabetic heart. Collectively, these results strongly indicate that Myr exerts cardioprotective effects against DCM through the blockage of inflammation, oxidative stress, and apoptosis. This suggests that Myr might be a potential therapeutic agent for the treatment of DCM.
AKT1 and AKT2 isoforms play distinct roles during breast cancer progression through the regulation of specific downstream proteins
Authors: Riggio Marina , Perrone María C. , Polo María L. , Rodriguez María J. , May María , Abba Martín , Lanari Claudia , Novaro Virginia
Published: March 2017

The purpose of this study was to elucidate the mechanisms associated with the specific effects of AKT1 and AKT2 isoforms in breast cancer progression. We modulated the abundance of specific AKT isoforms in IBH-6 and T47D human breast cancer cell lines and showed that AKT1 promoted cell proliferation, through S6 and cyclin D1 upregulation, but it inhibited cell migration and invasion through β1-integrin and focal adhesion kinase (FAK) downregulation. In contrast, AKT2 promoted cell migration and invasion through F-actin and vimentin induction. Thus, while overexpression of AKT1 promoted local tumor growth, downregulation of AKT1 or overexpression of AKT2 promoted peritumoral invasion and lung metastasis. Furthermore, we evaluated The Cancer Genome Atlas (TCGA) dataset for invasive breast carcinomas and found that increased AKT2 but not AKT1 mRNA levels correlated with a worse clinical outcome. We conclude that AKT isoforms play specific roles in different steps of breast cancer progression, with AKT1 involved in the local tumor growth and AKT2 involved in the distant tumor dissemination, having AKT2 a poorer prognostic value and consequently being a worthwhile target for therapy.
Uptake and biotransformation of 2,2′,4,4′-tetrabromodiphenyl ether (BDE-47) in four marine microalgae species
Authors: Po Beverly H. K. , Ho Ka-Lok , Lam Michael H. W. , Giesy John P. , Chiu Jill M. Y.
Published: March 2017

Hydroxylated- and methoxylated- polybrominated diphenyl ethers (OH-PBDEs and MeO-PBDEs) are more toxic than PBDEs and occur widely in the marine environment, and yet their origins remain controversial. In this study, four species of microalgae (Isochrysis galbana, Prorocentrum minimum, Skeletonema grethae and Thalassiosira pseudonana) were exposed to BDE-47, which is synthetic and is the predominant congener of PBDEs in the environment. By chemical analysis after incubation of 2 to 6 days, the efficiency of uptake of BDE-47 and, more importantly, the potential of undergoing biotransformation to form OH-PBDEs and MeO-PBDEs by the microalgae were investigated. Growth rates of these axenic microalgae were not affected upon exposure to environmentally relevant concentrations (0.2–20 μg BDE-47 L−1), and accumulation ranged from 0.772 ± 0.092 μg BDE-47 g−1 lipid to 215 ± 54 μg BDE-47 g−1 lipid within 2 days. Debromination of BDE-47 and formation of BDE-28 occurred in all microalgae species (0.01 to 0.87%), but biotransformation to OH-PBDEs was only found in I. galbana upon exposure to extremely high concentration. The results of this study showed that biotransformation of microalgae species is unlikely an explanation for the OH-PBDEs and MeO-PBDEs found in the marine environment.
Pitch discrimination associated with phonological awareness: Evidence from congenital amusia
Authors: Sun Yanan , Lu Xuejing , Ho Hao Tam , Thompson William Forde
Published: March 2017

Research suggests that musical skills are associated with phonological abilities. To further investigate this association, we examined whether phonological impairments are evident in individuals with poor music abilities. Twenty individuals with congenital amusia and 20 matched controls were assessed on a pure-tone pitch discrimination task, a rhythm discrimination task, and four phonological tests. Amusic participants showed deficits in discriminating pitch and discriminating rhythmic patterns that involve a regular beat. At a group level, these individuals performed similarly to controls on all phonological tests. However, eight amusics with severe pitch impairment, as identified by the pitch discrimination task, exhibited significantly worse performance than all other participants in phonological awareness. A hierarchical regression analysis indicated that pitch discrimination thresholds predicted phonological awareness beyond that predicted by phonological short-term memory and rhythm discrimination. In contrast, our rhythm discrimination task did not predict phonological awareness beyond that predicted by pitch discrimination thresholds. These findings suggest that accurate pitch discrimination is critical for phonological processing. We propose that deficits in early-stage pitch discrimination may be associated with impaired phonological awareness and we discuss the shared role of pitch discrimination for processing music and speech.
Targeted mutagenesis in cotton (Gossypium hirsutum L.) using the CRISPR/Cas9 system
Authors: Chen Xiugui , Lu Xuke , Shu Na , Wang Shuai , Wang Junjuan , Wang Delong , Guo Lixue , Ye Wuwei
Published: March 2017

The CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)/Cas9 system has been widely used for genome editing in various plants because of its simplicity, high efficiency and design flexibility. However, to our knowledge, there is no report on the application of CRISPR/Cas9-mediated targeted mutagenesis in cotton. Here, we report the genome editing and targeted mutagenesis in upland cotton (Gossypium hirsutum L., hereafter cotton) using the CRISPR/Cas9 system. We designed two guide RNAs to target distinct sites of the cotton Cloroplastos alterados 1 (GhCLA1) and vacuolar H+-pyrophosphatase (GhVP) genes. Mutations in these two genes were detected in cotton protoplasts. Most of the mutations were nucleotide substitutions, with one nucleotide insertion and one substitution found in GhCLA1 and one deletion found in GhVP in cotton protoplasts. Subsequently, the two vectors were transformed into cotton shoot apexes through Agrobacterium-mediated transformation, resulting in efficient target gene editing. Most of the mutations were nucleotide deletions, and the mutation efficiencies were 47.6–81.8% in transgenic cotton plants. Evaluation using restriction-enzyme-PCR assay and sequence analysis detected no off-target mutations. Our results indicated that the CRISPR/Cas9 system was an efficient and specific tool for targeted mutagenesis of the cotton genome.
Fluorogenic Peptide Substrate for Quantification of Bacterial Enzyme Activities
Authors: Al-Abdullah Ismail H. , Bagramyan Karine , Bilbao Shiela , Qi Meirigeng , Kalkum Markus
Published: March 2017

A novel peptide substrate (A G G P L G P P G P G G) was developed for quantifying the activities of bacterial enzymes using a highly sensitive Fluorescence Resonance Energy Transfer (FRET) based assay. The peptide substrate was cleaved by collagenase class I, II, Liberase MTF C/T, collagenase NB1, and thermolysin/neutral protease, which was significantly enhanced in the presence of CaCl2. However, the activities of these enzymes were significantly decreased in the presence of ZnSO4 or ZnCl2. Collagenase I, II, Liberase MTF C/T, thermolysin/neutral protease share similar cleavage sites, L↓G and P↓G. However, collagenase NB1 cleaves the peptide substrate at G↓P and P↓L, in addition to P↓G. The enzyme activity is pH dependent, within a range of 6.8 to 7.5, but was significantly diminished at pH 8.0. Interestingly, the peptide substrate was not cleaved by endogenous pancreatic protease such as trypsin, chymotrypsin, and elastase. In conclusion, the novel peptide substrate is collagenase, thermolysin/neutral protease specific and can be applied to quantify enzyme activities from different microbes. Furthermore, the assay can be used for fine-tuning reaction mixtures of various agents to enhance the overall activity of a cocktail of multiple enzymes and achieve optimal organ/tissue digestion, while protecting the integrity of the target cells.
Cooperative growth of Geobacter sulfurreducens and Clostridium pasteurianum with subsequent metabolic shift in glycerol fermentation
Authors: Moscoviz Roman , de Fouchécour Florence , Santa-Catalina Gaëlle , Bernet Nicolas , Trably Eric
Published: March 2017

Interspecies electron transfer is a common way to couple metabolic energy balances between different species in mixed culture consortia. Direct interspecies electron transfer (DIET) mechanism has been recently characterised with Geobacter species which couple the electron balance with other species through physical contacts. Using this mechanism could be an efficient and cost-effective way to directly control redox balances in co-culture fermentation. The present study deals with a co-culture of Geobacter sulfurreducens and Clostridium pasteurianum during glycerol fermentation. As a result, it was shown that Geobacter sulfurreducens was able to grow using Clostridium pasteurianum as sole electron acceptor. C. pasteurianum metabolic pattern was significantly altered towards improved 1,3-propanediol and butyrate production (+37% and +38% resp.) at the expense of butanol and ethanol production (−16% and −20% resp.). This metabolic shift was clearly induced by a small electron uptake that represented less than 0.6% of the electrons consumed by C. pasteurianum. A non-linear relationship was found between G. sulfurreducens growth (i.e the electrons transferred between the two species) and the changes in C. pasteurianum metabolite distribution. This study opens up new possibilities for controlling and increasing specificity in mixed culture fermentation.
Efficient Photocatalytic Bilirubin Removal over the Biocompatible Core/Shell P25/g-C3N4 Heterojunctions with Metal-free Exposed Surfaces under Moderate Green Light Irradiation
Authors: Kang Shifei , Qin Hengfei , Zhang Lu , Huang Yongkui , Bai Xia , Li Xi , Sun Di , Wang Yangang , Cui Lifeng
Published: March 2017

Highly-monodispersed g-C3N4/TiO2 hybrids with a core/shell structure were synthesized from a simple room temperature impregnation method, in which g-C3N4 was coated through self-assembly on the commercially available Degussa P25 TiO2 nanoparticles. Structural and surface characterizations showed that the presence of g-C3N4 notably affected the light absorption characteristics of TiO2. The g-C3N4/TiO2 heterojunctions with metal-free exposed surfaces were directly used as biocompatible photocatalysts for simulated jaundice phototherapy under low-power green-light irradiation. The photocatalytic activity and stability of g-C3N4/TiO2 were enhanced relative to pure P25 or g-C3N4, which could be ascribed to the effective Z-scheme separation of photo-induced charge carriers in g-C3N4/TiO2 heterojunction. The photoactivity was maximized in the 4 wt.% g-C3N4-coated P25, as the bilirubin removal rate under green light irradiation was more than 5-fold higher than that under the clinically-used blue light without any photocatalyst. This study approves the future applications of the photocatalyst-assisted bilirubin removal in jaundice treatment under moderate green light which is more tolerable by humans.
A ‘Disease Severity Index’ to identify individuals with Subjective Memory Decline who will progress to mild cognitive impairment or dementia
Authors: Ferreira Daniel , Falahati Farshad , Linden Cecilia , Buckley Rachel F. , Ellis Kathryn A. , Savage Greg , Villemagne Victor L. , Rowe Christopher C. , Ames David , Simmons Andrew , Westman Eric
Published: March 2017

Subjective memory decline (SMD) is a heterogeneous condition. While SMD might be the earliest sign of Alzheimer’s disease (AD), it also occurs in aging and various neurological, medical, and psychiatric conditions. Identifying those with higher risk to develop dementia is thus a major challenge. We tested a novel disease severity index generated by multivariate data analysis with numerous structural MRI measures as input. The index was used to identify SMD individuals with high risk of progression to mild cognitive impairment (MCI) or AD. A total of 69 healthy controls, 86 SMD, 45 MCI, and 38 AD patients were included. Subjects were followed up for 7.5 years. Clinical, cognitive, PET amyloid imaging and APOE ε4 data were used as outcome variables. The results showed that SMD evidenced cognitive performance intermediate between healthy controls and MCI. The disease severity index identified eleven (13%) SMD individuals with an AD-like pattern of brain atrophy. These individuals showed lower cognitive performance, increased CDR-SOB, higher amyloid burden and worse clinical progression (6.2 times higher likelihood to develop MCI, dementia or die than healthy controls). The current disease severity index may have relevance for clinical practice, as well as for selecting appropriate individuals for clinical trials.