bluuebunny/crossref_metadata_2025 huggingface dataset:
Horizontal mantle flow controls subduction dynamics
Authors: Ficini E. , Dal Zilio L. , Doglioni C. , Gerya T. V.
Published: August 2017

It is generally accepted that subduction is driven by downgoing-plate negative buoyancy. Yet plate age –the main control on buoyancy– exhibits little correlation with most of the present-day subduction velocities and slab dips. “West”-directed subduction zones are on average steeper (~65°) than “East”-directed (~27°). Also, a “westerly”-directed net rotation of the lithosphere relative to the mantle has been detected in the hotspot reference frame. Thus, the existence of an “easterly”-directed horizontal mantle wind could explain this subduction asymmetry, favouring steepening or lifting of slab dip angles. Here we test this hypothesis using high-resolution two-dimensional numerical thermomechanical models of oceanic plate subduction interacting with a mantle flow. Results show that when subduction polarity is opposite to that of the mantle flow, the descending slab dips subvertically and the hinge retreats, thus leading to the development of a back-arc basin. In contrast, concordance between mantle flow and subduction polarity results in shallow dipping subduction, hinge advance and pronounced topography of the overriding plate, regardless of their age-dependent negative buoyancy. Our results are consistent with seismicity data and tomographic images of subduction zones. Thus, our models may explain why subduction asymmetry is a common feature of convergent margins on Earth.
Fabrication of Water Jet Resistant and Thermally Stable Superhydrophobic Surfaces by Spray Coating of Candle Soot Dispersion
Authors: Qahtan Talal F. , Gondal Mohammed A. , Alade Ibrahim O. , Dastageer Mohammed A.
Published: August 2017

A facile synthesis method for highly stable carbon nanoparticle (CNP) dispersion in acetone by incomplete combustion of paraffin candle flame is presented. The synthesized CNP dispersion is the mixture of graphitic and amorphous carbon nanoparticles of the size range of 20–50 nm and manifested the mesoporosity with an average pore size of 7 nm and a BET surface area of 366 m2g−1. As an application of this material, the carbon nanoparticle dispersion was spray coated (spray-based coating) on a glass surface to fabricate superhydrophobic (water contact angle > 150° and sliding angle < 10 °) surfaces. The spray coated surfaces were found to exhibit much improved water jet resistance and thermal stability up to 400 °C compared to the surfaces fabricated from direct candle flame soot deposition (candle-based coating). This study proved that water jet resistant and thermally stable superhydrophobic surfaces can be easily fabricated by simple spray coating of CNP dispersion gathered from incomplete combustion of paraffin candle flame and this technique can be used for different applications with the potential for the large scale fabrication.
Gender difference in spontaneous deception: A hyperscanning study using functional near-infrared spectroscopy
Authors: Zhang Mingming , Liu Tao , Pelowski Matthew , Yu Dongchuan
Published: August 2017

Previous studies have demonstrated that the neural basis of deception involves a network of regions including the medial frontal cortex (MFC), superior temporal sulcus (STS), temporo-parietal junction (TPJ), etc. However, to test the actual activity of the brain in the act of deceptive practice itself, existing studies have mainly adopted paradigms of passive deception, where participants are told to lie in certain conditions, and have focused on intra-brain mechanisms in single participants. In order to examine the neural substrates underlying more natural, spontaneous deception in real social interactions, the present study employed a functional near-infrared spectroscopy (fNIRS) hyperscanning technique to simultaneously measure pairs of participants’ fronto-temporal activations in a two-person gambling card-game. We demonstrated higher TPJ activation in deceptive compared to honest acts. Analysis of participants’ inter-brain correlation further revealed that the STS is uniquely involved in deception but not in honesty, especially in females. These results suggest that the STS may play a critical role in spontaneous deception due to mentalizing requirements relating to modulating opponents’ thoughts. To our knowledge, this study was the first to investigate such inter-brain correlates of deception in real face-to-face interactions, and thus is hoped to provide a new path for future complex social behavior research.
The analgesic activities of Stauntonia brachyanthera and YM11 through regulating inflammatory mediators and directly controlling the sodium channel prompt
Authors: Meng Dali , Wang Lei , Du Jingnan , Chen Jianchao , Chen Chao , Xu Wei , Li Chunli
Published: August 2017

The analgesic studies on Stauntonia brachyanthera, a traditional Chinese folk medicine used to treat headache, pains and inflammatory diseases in local areas, showed that the EtOH extracts (EESB) and the characteristic ingredient YM11 could significantly inhibit the acetic acid-induced writhing responses by 43.1% and 78.95%, and decrease the xylene-induced ear edemas by 48.9% and 21.4%, respectively. EESB could significantly increase pain threshold of mice in hot-plate test, but the effect of YM11 was not obviously. Further study in formalin test showed the inhibitory effect of YM11 in 2nd phase was more significant than that in 1st phase, revealed the peripheral analgesic activity of YM11. The ELISA and Western Blot analysis suggested that the analgesic mechanisms of YM11 were related to the inhibitions of the expressions of TNF-α, IL-1β and IL-6, and down-regulations of Nav1.8 protein in the left side of L4–6 DRG regulated by MAPKs, in which the levels of p-ERK, p-JNK and p-p38 were all decreased. In addition, the electrophysiological experiments indicated YM11 could reduce the Nav1.8 currents by 46.01% in small-diameter DRG neurons. Therefore, the analgesic activity of S. brachyanthera might be based on the regulation of inflammatory mediators and the directly control of the sodium channel prompt.
Reliable Multi-Fractal Characterization of Weighted Complex Networks: Algorithms and Implications
Authors: Xue Yuankun , Bogdan Paul
Published: August 2017

Through an elegant geometrical interpretation, the multi-fractal analysis quantifies the spatial and temporal irregularities of the structural and dynamical formation of complex networks. Despite its effectiveness in unweighted networks, the multi-fractal geometry of weighted complex networks, the role of interaction intensity, the influence of the embedding metric spaces and the design of reliable estimation algorithms remain open challenges. To address these challenges, we present a set of reliable multi-fractal estimation algorithms for quantifying the structural complexity and heterogeneity of weighted complex networks. Our methodology uncovers that (i) the weights of complex networks and their underlying metric spaces play a key role in dictating the existence of multi-fractal scaling and (ii) the multi-fractal scaling can be localized in both space and scales. In addition, this multi-fractal characterization framework enables the construction of a scaling-based similarity metric and the identification of community structure of human brain connectome. The detected communities are accurately aligned with the biological brain connectivity patterns. This characterization framework has no constraint on the target network and can thus be leveraged as a basis for both structural and dynamic analysis of networks in a wide spectrum of applications.
Desiccation tolerance in bryophytes: The dehydration and rehydration transcriptomes in the desiccation-tolerant bryophyte Bryum argenteum
Authors: Gao Bei , Li Xiaoshuang , Zhang Daoyuan , Liang Yuqing , Yang Honglan , Chen Moxian , Zhang Yuanming , Zhang Jianhua , Wood Andrew J.
Published: August 2017

The desiccation tolerant bryophyteBryum argenteumis an important component of desert biological soil crusts (BSCs) and is emerging as a model system for studying vegetative desiccation tolerance. Here we present and analyze the hydration-dehydration-rehydration transcriptomes inB. argenteumto establish a desiccation-tolerance transcriptomic atlas.B. argenteumgametophores representing five different hydration stages (hydrated (H0), dehydrated for 2 h (D2), 24 h (D24), then rehydrated for 2 h (R2) and 48 h (R48)), were sampled for transcriptome analyses. Illumina high throughput RNA-Seq technology was employed and generated more than 488.46 million reads. An in-housede novotranscriptome assembly optimization pipeline based on Trinity assembler was developed to obtain a reference Hydration-Dehydration-Rehydration (H-D-R) transcriptome comprising of 76,206 transcripts, with an N50 of 2,016 bp and average length of 1,222 bp. Comprehensive transcription factor (TF) annotation discovered 978 TFs in 62 families, among which 404 TFs within 40 families were differentially expressed upon dehydration-rehydration. Pfam term enrichment analysis revealed 172 protein families/domains were significantly associated with the H-D-R cycle and confirmed early rehydration (i.e. the R2 stage) as exhibiting the maximum stress-induced changes in gene expression.
New 2-aryl-7,8-dimethoxy-3,4-dihydroisoquinolin-2-ium salts as potential antifungal agents: synthesis, bioactivity and structure-activity relationships
Authors: Zhu Lifei , Zhou Bohang , Zhang Bingyu , Xu Mingxuan , Geng Huiling , Zhou Le
Published: August 2017

The title compounds can be considered as simple analogues of quaternary benzo[c]phenanthridine alkaloids (QBAs). In order to develop potent QBA-like antifungal agents, as our continuing study, a series of new title compounds were synthesized and evaluated for bioactivity against five plant pathogenic fungi by the mycelium growth rate method in this study. The SAR were also derived. The majority of the compounds showed good to excellent inhibition activity with average EC50 values of 7.87–20.0 μM for the fungi, superior to sanguinarine and cherythrine (two QBAs) and the commercial fungicide azoxystrobin. Part of the compounds were more active than commercial fungicides thiabendazole or carbendazim against F. solani, F. graminearum and C. gloeosporioides. Six compounds with average EC50 of 3.5–5.1 μg/mL possessed very great potential for development of new antifungal agents. SAR found that substitution patterns of the two aryl-rings significantly affect the activity. There exists a complex interaction effect between substituents of the two aryl-rings on the activity. Generally, the presence of electron-withdrawing groups on the C-ring can significantly increase the activity. These findings will be of great importance for the design of more potent antifungal isoquinoline agents.
Genomic signatures of adaptive introgression from European mouflon into domestic sheep
Authors: Barbato Mario , Hailer Frank , Orozco-terWengel Pablo , Kijas James , Mereu Paolo , Cabras Pierangela , Mazza Raffaele , Pirastru Monica , Bruford Michael W.
Published: August 2017

Mouflon (Ovis aries musimon) became extinct from mainland Europe after the Neolithic, but remnant populations from the Mediterranean islands of Corsica and Sardinia have been used for reintroductions across Europe since the 19th-century. Mouflon x sheep hybrids are larger-bodied than mouflon, potentially showing increased male reproductive success, but little is known about genomic levels of admixture, or about the adaptive significance of introgression between resident mouflon and local sheep breeds. Here we analysed Ovine medium-density SNP array genotypes of 92 mouflon from six geographic regions, along with data from 330 individuals of 16 domestic sheep breeds. We found lower levels of genetic diversity in mouflon than in domestic sheep, consistent with past bottlenecks in mouflon. Introgression signals were bidirectional and affected most mouflon and sheep populations, being strongest in one Sardinian mouflon population. Developing and using a novel approach to identify chromosomal regions with consistent introgression signals, we infer adaptive introgression from mouflon to domestic sheep related to immunity mechanisms, but not in the opposite direction. Further, we infer that Soay and Sarda sheep carry introgressed mouflon alleles involved in bitter taste perception and/or innate immunity. Our results illustrate the potential for adaptive introgression even among recently diverged populations.
The H7N9 influenza A virus infection results in lethal inflammation in the mammalian host via the NLRP3-caspase-1 inflammasome
Authors: Ren Rongrong , Wu Shuxian , Cai Jialin , Yang Yuqin , Ren Xiaonan , Feng Yanling , Chen Lixiang , Qin Boyin , Xu Chunhua , Yang Hua , Song Zhigang , Tian Di , Hu Yunwen , Zhou Xiaohui , Meng Guangxun
Published: August 2017

The avian origin influenza A virus (IAV) H7N9 has caused a considerable number of human infections associated with high rates of death since its emergence in 2013. As a vital component of the host innate immune system, the nucleotide-binding domain leucine-rich repeat containing receptor, pyrin domain containing 3 (NLRP3) inflammasome plays a critical role against H1N1 viral infection. However, the function of NLRP3 inflammasome in host immunological responses to the lethal H7N9 virus is still obscure. Here, we demonstrated that mice deficient for NLRP3 inflammasome components, including NLRP3, caspase-1, and Apoptosis-associated speck-like protein containing a CARD (ASC), were less susceptible to H7N9 viral challenge than wild type (WT) controls. Inflammasome deficiency in these animals led to significantly milder mortality and less pulmonary inflammation compared with WT mice. Furthermore, IL-1 receptor deficient mice also exhibited a higher survival rate than WT controls. Thus, our study reveals that the NLRP3 inflammasome is deleterious for the host during H7N9 infection in mice, which is due to an overwhelming inflammatory response via caspase-1 activation and associated IL-1 signal. Therefore, fine-tuning the activity of NLRP3 inflammasome or IL-1 signaling may be beneficial for the host to control H7N9 associated lethal pathogenesis.
A Novel Fabrication Approach for Multifunctional Graphene-based Thin Film Nano-composite Membranes with Enhanced Desalination and Antibacterial Characteristics
Authors: Hegab Hanaa M. , ElMekawy Ahmed , Barclay Thomas G. , Michelmore Andrew , Zou Linda , Losic Dusan , Saint Christopher P. , Ginic-Markovic Milena
Published: August 2017

A practical fabrication technique is presented to tackle the trade-off between the water flux and salt rejection of thin film composite (TFC) reverse osmosis (RO) membranes through controlled creation of a thinner active selective polyamide (PA) layer. The new thin film nano-composite (TFNC) RO membranes were synthesized with multifunctional poly tannic acid-functionalized graphene oxide nanosheets (pTA-f-GO) embedded in its PA thin active layer, which is produced through interfacial polymerization. The incorporation of pTA-f-GOL into the fabricated TFNC membranes resulted in a thinner PA layer with lower roughness and higher hydrophilicity compared to pristine membrane. These properties enhanced both the membrane water flux (improved by 40%) and salt rejection (increased by 8%) of the TFNC membrane. Furthermore, the incorporation of biocidal pTA-f-GO nanosheets into the PA active layer contributed to improving the antibacterial properties by 80%, compared to pristine membrane. The fabrication of the pTA-f-GO nanosheets embedded in the PA layer presented in this study is a very practical, scalable and generic process that can potentially be applied in different types of separation membranes resulting in less energy consumption, increased cost-efficiency and improved performance.
Evolution of the electronic band structure of twisted bilayer graphene upon doping
Authors: Huang Shengqiang , Yankowitz Matthew , Chattrakun Kanokporn , Sandhu Arvinder , LeRoy Brian J.
Published: August 2017

The electronic band structure of twisted bilayer graphene develops van Hove singularities whose energy depends on the twist angle between the two layers. Using Raman spectroscopy, we monitor the evolution of the electronic band structure upon doping using the G peak area which is enhanced when the laser photon energy is resonant with the energy separation of the van Hove singularities. Upon charge doping, the Raman G peak area initially increases for twist angles larger than a critical angle and decreases for smaller angles. To explain this behavior with twist angle, the energy separation of the van Hove singularities must decrease with increasing charge density demonstrating the ability to modify the electronic and optical properties of twisted bilayer graphene with doping.
Involvement of Transient Receptor Potential Cation Channel Member A1 activation in the irritation and pain response elicited by skin-lightening reagent hydroquinone
Authors: Tai Yan , Wang Chuan , Wang Zhihua , Liang Yi , Du Junying , He Dongwei , Fan Xiaoyan , Jordt Sven-Eric , Liu Boyi
Published: August 2017

Hydroquinone (HQ) is one of the most frequently used and effective skin-lightening products to treat skin hyperpigmentation disorders, including postinflammatory hyperpigmentation, melasma and solar lentigines. HQ is also widely used in cosmetic products for skin whitening. However, HQ treatment can evoke substantial skin irritation, a side effect that remains poorly understood. Here we demonstrate that HQ is an activator of the peripheral irritant receptor transient receptor potential (TRP) cation channel member A1 (TRPA1). HQ failed to activate TRPV1, TRPV4 or TRPM8. HQ-induced TRPA1 activation was dependent on essential redox-sensitive cysteine and lysine residues within N-terminus of channel protein. HQ elicited Ca2+ influx in a subpopulation of mouse sensory neurons sensitive to the TRPA1 agonist, mustard oil. HQ-induced neuronal responses were significantly reduced by TRPA1 inhibitors, and reduced in neurons isolated from Trpa1-deficient mice. In mice, intraplantar injection of HQ at clinically relevant concentrations elicited both acute pain and persistent mechanical hyperalgesia which were almost completely abolished by TRPA1 inhibitors. These findings identify TRPA1 as a molecular target for HQ and provide insights into the mechanism of HQ-induced skin irritation. These findings also suggest that selective TRPA1 antagonists may be useful to counteract HQ-induced skin irritation.
Gaussian network model can be enhanced by combining solvent accessibility in proteins
Authors: Zhang Hua , Jiang Tao , Shan Guogen , Xu Shiqi , Song Yujie
Published: August 2017

Gaussian network model (GNM), regarded as the simplest and most representative coarse-grained model, has been widely adopted to analyze and reveal protein dynamics and functions. Designing a variation of the classical GNM, by defining a new Kirchhoff matrix, is the way to improve the residue flexibility modeling. We combined information arising from local relative solvent accessibility (RSA) between two residues into the Kirchhoff matrix of the parameter-free GNM. The undetermined parameters in the new Kirchhoff matrix were estimated by using particle swarm optimization. The usage of RSA was motivated by the fact that our previous work using RSA based linear regression model resulted out higher prediction quality of the residue flexibility when compared with the classical GNM and the parameter free GNM. Computational experiments, conducted based on one training dataset, two independent datasets and one additional small set derived by molecular dynamics simulations, demonstrated that the average correlation coefficients of the proposed RSA based parameter-free GNM, called RpfGNM, were significantly increased when compared with the parameter-free GNM. Our empirical results indicated that a variation of the classical GNMs by combining other protein structural properties is an attractive way to improve the quality of flexibility modeling.
Identifying the miRNA signature associated with survival time in patients with lung adenocarcinoma using miRNA expression profiles
Authors: Yerukala Sathipati Srinivasulu , Ho Shinn-Ying
Published: August 2017

Lung adenocarcinoma is a multifactorial disease. MicroRNA (miRNA) expression profiles are extensively used for discovering potential theranostic biomarkers of lung cancer. This work proposes an optimized support vector regression (SVR) method called SVR-LUAD to simultaneously identify a set of miRNAs referred to the miRNA signature for estimating the survival time of lung adenocarcinoma patients using their miRNA expression profiles. SVR-LUAD uses an inheritable bi-objective combinatorial genetic algorithm to identify a small set of informative miRNAs cooperating with SVR by maximizing estimation accuracy. SVR-LUAD identified 18 out of 332 miRNAs using 10-fold cross-validation and achieved a correlation coefficient of 0.88 ± 0.01 and mean absolute error of 0.56 ± 0.03 year between real and estimated survival time. SVR-LUAD performs well compared to some well-recognized regression methods. The miRNA signature consists of the 18 miRNAs which strongly correlates with lung adenocarcinoma: hsa-let-7f-1, hsa-miR-16-1, hsa-miR-152, hsa-miR-217, hsa-miR-18a, hsa-miR-193b, hsa-miR-3136, hsa-let-7g, hsa-miR-155, hsa-miR-3199-1, hsa-miR-219-2, hsa-miR-1254, hsa-miR-1291, hsa-miR-192, hsa-miR-3653, hsa-miR-3934, hsa-miR-342, and hsa-miR-141. Gene ontology annotation and pathway analysis of the miRNA signature revealed its biological significance in cancer and cellular pathways. This miRNA signature could aid in the development of novel therapeutic approaches to the treatment of lung adenocarcinoma.
Host Delivered RNAi, an efficient approach to increase rice resistance to sheath blight pathogen (Rhizoctonia solani)
Authors: Tiwari Ila Mukul , Jesuraj Arun , Kamboj Richa , Devanna B. N. , Botella Jose R. , Sharma T. R.
Published: August 2017

Rhizoctonia solani, the causal agent of rice sheath blight disease, causes significant losses worldwide as there are no cultivars providing absolute resistance to this fungal pathogen. We have used Host Delivered RNA Interference (HD-RNAi) technology to target two PATHOGENICITY MAP KINASE 1 (PMK1) homologues, RPMK1-1 and RPMK1-2, from R. solani using a hybrid RNAi construct. PMK1 homologues in other fungal pathogens are essential for the formation of appressorium, the fungal infection structures required for penetration of the plant cuticle, as well as invasive growth once inside the plant tissues and overall viability of the pathogen within the plant. Evaluation of transgenic rice lines revealed a significant decrease in fungal infection levels compared to non-transformed controls and the observed delay in disease symptoms was further confirmed through microscopic studies. Relative expression levels of the targeted genes, RPMK1-1 and RPMK1-2, were determined in R. solani infecting either transgenic or control lines with significantly lower levels observed in R. solani infecting transgenic lines carrying the HD-RNAi constructs. This is the first report demonstrating the effectiveness of HD-RNAi against sheath blight and offers new opportunities for durable control of the disease as it does not rely on resistance conferred by major resistance genes.
Arginyl dipeptides increase the frequency of NaCl-elicited responses via epithelial sodium channel alpha and delta subunits in cultured human fungiform taste papillae cells
Authors: Xu Jiao-Jiao , Elkaddi Nadia , Garcia-Blanco Alvaro , Spielman Andrew I. , Bachmanov Alexander A. , Chung Hau Yin , Ozdener Mehmet Hakan
Published: August 2017

Salty taste is one of the five basic tastes and is often elicited by NaCl. Because excess sodium intake is associated with many health problems, it could be useful to have salt taste enhancers that are not sodium based. In this study, the regulation of NaCl-induced responses was investigated in cultured human fungiform taste papillae (HBO) cells with five arginyl dipeptides: Ala-Arg (AR), Arg-Ala (RA), Arg-Pro (RP), Arg-Glu (RE), and Glu-Arg (ER); and two non-arginyl dipeptides: Asp-Asp (DD) and Glu-Asp (ED). AR, RA, and RP significantly increased the number of cell responses to NaCl, whereas no effect was observed with RE, ER, DD, or ED. We also found no effects with alanine, arginine, or a mixture of both amino acids. Pharmacological studies showed that AR significantly increased responses of amiloride-sensitive but not amiloride-insensitive cells. In studies using small interfering RNAs (siRNAs), responses to AR were significantly decreased in cells transfected with siRNAs against epithelial sodium channel ENaCα or ENaCδ compared to untransfected cells. AR dramatically increased NaCl-elicited responses in cells transfected with NHE1 siRNA but not in those transfected with ENaCα or ENaCδ siRNAs. Altogether, AR increased responses of amiloride-sensitive cells required ENaCα and ENaCδ.
Use antibiotics in cell culture with caution: genome-wide identification of antibiotic-induced changes in gene expression and regulation
Authors: Ryu Ann H. , Eckalbar Walter L. , Kreimer Anat , Yosef Nir , Ahituv Nadav
Published: August 2017

Standard cell culture guidelines often use media supplemented with antibiotics to prevent cell contamination. However, relatively little is known about the effect of antibiotic use in cell culture on gene expression and the extent to which this treatment could confound results. To comprehensively characterize the effect of antibiotic treatment on gene expression, we performed RNA-seq and ChIP-seq for H3K27ac on HepG2 cells, a human liver cell line commonly used for pharmacokinetic, metabolism and genomic studies, cultured in media supplemented with penicillin-streptomycin (PenStrep) or vehicle control. We identified 209 PenStrep-responsive genes, including transcription factors such as ATF3 that are likely to alter the regulation of other genes. Pathway analyses found a significant enrichment for “xenobiotic metabolism signaling” and “PXR/RXR activation” pathways. Our H3K27ac ChIP-seq identified 9,514 peaks that are PenStrep responsive. These peaks were enriched near genes that function in cell differentiation, tRNA modification, nuclease activity and protein dephosphorylation. Our results suggest that PenStrep treatment can significantly alter gene expression and regulation in a common liver cell type such as HepG2, advocating that antibiotic treatment should be taken into account when carrying out genetic, genomic or other biological assays in cultured cells.
Modelling the evolution of transcription factor binding preferences in complex eukaryotes
Authors: Rosanova Antonio , Colliva Alberto , Osella Matteo , Caselle Michele
Published: August 2017

Transcription factors (TFs) exert their regulatory action by binding to DNA with specific sequence preferences. However, different TFs can partially share their binding sequences due to their common evolutionary origin. This “redundancy” of binding defines a way of organizing TFs in “motif families” by grouping TFs with similar binding preferences. Since these ultimately define the TF target genes, the motif family organization entails information about the structure of transcriptional regulation as it has been shaped by evolution. Focusing on the human TF repertoire, we show that a one-parameter evolutionary model of the Birth-Death-Innovation type can explain the TF empirical repartition in motif families, and allows to highlight the relevant evolutionary forces at the origin of this organization. Moreover, the model allows to pinpoint few deviations from the neutral scenario it assumes: three over-expanded families (including HOX and FOX genes), a set of “singleton” TFs for which duplication seems to be selected against, and a higher-than-average rate of diversification of the binding preferences of TFs with a Zinc Finger DNA binding domain. Finally, a comparison of the TF motif family organization in different eukaryotic species suggests an increase of redundancy of binding with organism complexity.
A Neural Marker of Obsessive-Compulsive Disorder from Whole-Brain Functional Connectivity
Authors: Takagi Yu , Sakai Yuki , Lisi Giuseppe , Yahata Noriaki , Abe Yoshinari , Nishida Seiji , Nakamae Takashi , Morimoto Jun , Kawato Mitsuo , Narumoto Jin , Tanaka Saori C
Published: August 2017

Obsessive-compulsive disorder (OCD) is a common psychiatric disorder with a lifetime prevalence of 2–3%. Recently, brain activity in the resting state is gathering attention for exploring altered functional connectivity in psychiatric disorders. Although previous resting-state functional magnetic resonance imaging studies investigated the neurobiological abnormalities of patients with OCD, there are concerns that should be addressed. One concern is the validity of the hypothesis employed. Most studies used seed-based analysis of the fronto-striatal circuit, despite the potential for abnormalities in other regions. A hypothesis-free study is a promising approach in such a case, while it requires researchers to handle a dataset with large dimensions. Another concern is the reliability of biomarkers derived from a single dataset, which may be influenced by cohort-specific features. Here, our machine learning algorithm identified an OCD biomarker that achieves high accuracy for an internal dataset (AUC = 0.81; N = 108) and demonstrates generalizability to an external dataset (AUC = 0.70; N = 28). Our biomarker was unaffected by medication status, and the functional networks contributing to the biomarker were distributed widely, including the frontoparietal and default mode networks. Our biomarker has the potential to deepen our understanding of OCD and to be applied clinically.
Diversity, distribution and different habitat use among the tropical freshwater eels of genus Anguilla
Authors: Arai Takaomi , Abdul Kadir Siti Raudah
Published: August 2017

Along with the mysteries of their ecology, freshwater eels have fascinated biologists for centuries. However, information concerning species diversity, geographic distribution, and life histories of the tropical anguillid eels in the Indo-Pacific region are highly limited. Comprehensive research on the species composition, distribution and habitat use among tropical anguillid eels in the Peninsular Malaysia were conducted for four years. A total of 463 specimens were collected in the northwestern peninsular area. The dominant species was A. bicolor bicolor constituting of 88.1% of the total eels, the second one was A. bengalensis bengalensis at 11.7%, while A. marmorata was the least abundant at 0.2%. A. bicolor bicolor was widely distributed from upstream to downstream areas of the rivers. In comparison, A. bengalensis bengalensis preferred to reside from the upstream to midstream areas with no tidal zones, cooler water temperatures and higher elevation areas. The habitat preference might be different between sites due to inter-species interactions and intra-specific plasticity to local environmental conditions. These results suggest that habitat use in the tropical anguillid eels might be more influenced by ambient environmental factors, such as salinity, temperature, elevation, river size and carrying capacity, than ecological competition, such as interspecific competition.
An unusual role for the phytyl chains in the photoprotection of the chlorophylls bound to Water-Soluble Chlorophyll-binding Proteins
Authors: Agostini Alessandro , Palm Daniel M. , Schmitt Franz-Josef , Albertini Marco , Valentin Marilena Di , Paulsen Harald , Carbonera Donatella
Published: August 2017

Water-Soluble Chlorophyll Proteins (WSCPs) fromBrassicaceaeare non-photosynthetic proteins which tetramerize upon binding four chlorophyll (Chl) molecules. The bound Chls are highly photostable, despite the lack of bound carotenoids known, in Chl-containing photosynthetic proteins, to act as singlet oxygen and Chl triplet (3Chl) quenchers. Although the physiological function of WSCPs is still unclear, it is likely to be related to their biochemical stability and their resistance to photodegradation. To get insight into the origin of this photostability, the properties of the3Chl generated in WSCPs upon illumination were investigated. We found that, unlike the excited singlet states, which are excitonic states, the triplet state is localized on a single Chl molecule. Moreover, the lifetime of the3Chl generated in WSCPs is comparable to that observed in other Chl-containing systems and is reduced in presence of oxygen. In contrast to previous observations, we found that WSCP actually photosensitizes singlet oxygen with an efficiency comparable to that of Chl in organic solvent. We demonstrated that the observed resistance to photooxidation depends on the conformation of the phytyl moieties, which in WSCP are interposed between the rings of Chl dimers, hindering the access of singlet oxygen to the oxidizable sites of the pigments.
Environmental concern-based site screening of carbon dioxide geological storage in China
Authors: Cai Bofeng , Li Qi , Liu Guizhen , Liu Lancui , Jin Taotao , Shi Hui
Published: August 2017

Environmental impacts and risks related to carbon dioxide (CO2) capture and storage (CCS) projects may have direct effects on the decision-making process during CCS site selection. This paper proposes a novel method of environmental optimization for CCS site selection using China’s ecological red line approach. Moreover, this paper established a GIS based spatial analysis model of environmental optimization during CCS site selection by a large database. The comprehensive data coverage of environmental elements and fine 1 km spatial resolution were used in the database. The quartile method was used for value assignment for specific indicators including the prohibited index and restricted index. The screening results show that areas classified as having high environmental suitability (classes III and IV) in China account for 620,800 km2 and 156,600 km2, respectively, and are mainly distributed in Inner Mongolia, Qinghai and Xinjiang. The environmental suitability class IV areas of Bayingol Mongolian Autonomous Prefecture, Hotan Prefecture, Aksu Prefecture, Hulunbuir, Xilingol League and other prefecture-level regions not only cover large land areas, but also form a continuous area in the three provincial-level administrative units. This study may benefit the national macro-strategic deployment and implementation of CCS spatial layout and environmental management in China.
TRPC6 counteracts TRPC3-Nox2 protein complex leading to attenuation of hyperglycemia-induced heart failure in mice
Authors: Oda Sayaka , Numaga-Tomita Takuro , Kitajima Naoyuki , Toyama Takashi , Harada Eri , Shimauchi Tsukasa , Nishimura Akiyuki , Ishikawa Tatsuya , Kumagai Yoshito , Birnbaumer Lutz , Nishida Motohiro
Published: August 2017

Excess production of reactive oxygen species (ROS) caused by hyperglycemia is a major risk factor for heart failure. We previously reported that transient receptor potential canonical 3 (TRPC3) channel mediates pressure overload-induced maladaptive cardiac fibrosis by forming stably functional complex with NADPH oxidase 2 (Nox2). Although TRPC3 has been long suggested to form hetero-multimer channels with TRPC6 and function as diacylglycerol-activated cation channels coordinately, the role of TRPC6 in heart is still obscure. We here demonstrated that deletion of TRPC6 had no impact on pressure overload-induced heart failure despite inhibiting interstitial fibrosis in mice. TRPC6-deficient mouse hearts 1 week after transverse aortic constriction showed comparable increases in fibrotic gene expressions and ROS production but promoted inductions of inflammatory cytokines, compared to wild type hearts. Treatment of TRPC6-deficient mice with streptozotocin caused severe reduction of cardiac contractility with enhancing urinary and cardiac lipid peroxide levels, compared to wild type and TRPC3-deficient mice. Knockdown of TRPC6, but not TRPC3, enhanced basal expression levels of cytokines in rat cardiomyocytes. TRPC6 could interact with Nox2, but the abundance of TRPC6 was inversely correlated with that of Nox2. These results strongly suggest that Nox2 destabilization through disrupting TRPC3-Nox2 complex underlies attenuation of hyperglycemia-induced heart failure by TRPC6.
Red-edge position of habitable exoplanets around M-dwarfs
Authors: Takizawa Kenji , Minagawa Jun , Tamura Motohide , Kusakabe Nobuhiko , Narita Norio
Published: August 2017

One of the possible signs of life on distant habitable exoplanets is the red-edge, which is a rise in the reflectivity of planets between visible and near-infrared (NIR) wavelengths. Previous studies suggested the possibility that the red-edge position for habitable exoplanets around M-dwarfs may be shifted to a longer wavelength than that for Earth. We investigated plausible red-edge position in terms of the light environment during the course of the evolution of phototrophs. We show that phototrophs on M-dwarf habitable exoplanets may use visible light when they first evolve in the ocean and when they first colonize the land. The adaptive evolution of oxygenic photosynthesis may eventually also use NIR radiation, by one of two photochemical reaction centers, with the other center continuing to use visible light. These “two-color” reaction centers can absorb more photons, but they will encounter difficulty in adapting to drastically changing light conditions at the boundary between land and water. NIR photosynthesis can be more productive on land, though its evolution would be preceded by the Earth-type vegetation. Thus, the red-edge position caused by photosynthetic organisms on habitable M-dwarf exoplanets could initially be similar to that on Earth and later move to a longer wavelength.
A simple quantum voting scheme with multi-qubit entanglement
Authors: Xue Peng , Zhang Xin
Published: August 2017

We propose a simple quantum voting scenario with a set of pairs of particles in a multi-particle entangled state. This scenario is suitable for large scale general votings. We also provide a proof of security of our scheme against the most general type of attack by generalizing Shor and Preskill’s proof of security of the other schemes.
Endocannabinoid tone is higher in healthy lean South Asian than white Caucasian men
Authors: Kantae Vasudev , Nahon Kimberly J. , Straat Maaike E. , Bakker Leontine E. H. , Harms Amy C. , van der Stelt Mario , Hankemeier Thomas , Jazet Ingrid M. , Boon Mariëtte R. , Rensen Patrick C. N.
Published: August 2017

South Asians have a higher risk to develop obesity and related disorders compared to white Caucasians. This is likely in part due to their lower resting energy expenditure (REE) as related with less energy-combusting brown adipose tissue (BAT). Since overactivation of the endocannabinoid system is associated with obesity and low BAT activity, we hypothesized that South Asians have a higher endocannabinoid tone. Healthy lean white Caucasian (n = 10) and South Asian (n = 10) men were cold-exposed to activate BAT. Before and after cooling, REE was assessed and plasma was collected for analysis of endocannabinoids and lipids. At thermoneutrality, South Asians had higher plasma levels of 2-arachidonoylglycerol (2-AG; 11.36 vs 8.19 pmol/mL, p < 0.05), N-arachidonylethanolamine (AEA; 1.04 vs 0.89 pmol/mL, p = 0.05) and arachidonic acid (AA; 23.24 vs 18.22 nmol/mL, p < 0.001). After pooling of both ethnicities, plasma 2-AG but not AEA positively correlated with triglycerides (R2 = 0.32, p < 0.05) and body fat percentage (R2 = 0.18, p < 0.05). Interestingly, AA negative correlated with REE (R2 = 0.46, p < 0.001) and positively with body fat percentage (R2 = 0.33, p < 0.01). Cooling increased endocannabinoids. In conclusion, South Asian compared to white Caucasian men have higher endocannabinoid tone. This suggests that endocannabinoids may, at least in part, underlie the disadvantageous metabolic phenotype of South Asians later in life.
Comprehensive validation of T- and B-cell deficiency in rag1-null zebrafish: Implication for the robust innate defense mechanisms of teleosts
Authors: Tokunaga Yumie , Shirouzu Masamichi , Sugahara Ryota , Yoshiura Yasutoshi , Kiryu Ikunari , Ototake Mitsuru , Nagasawa Takahiro , Somamoto Tomonori , Nakao Miki
Published: August 2017

rag1−/− zebrafish have been employed in immunological research as a useful immunodeficient vertebrate model, but with only fragmentary evidence for the lack of functional adaptive immunity. rag1-null zebrafish exhibit differences from their human and murine counterparts in that they can be maintained without any specific pathogen-free conditions. To define the immunodeficient status of rag1−/− zebrafish, we obtained further functional evidence on T- and B-cell deficiency in the fish at the protein, cellular, and organism levels. Our developed microscale assays provided evidence that rag1−/− fish do not possess serum IgM protein, that they do not achieve specific protection even after vaccination, and that they cannot induce antigen-specific CTL activity. The mortality rate in non-vaccinated fish suggests that rag1−/− fish possess innate protection equivalent to that of rag1+/− fish. Furthermore, poly(I:C)-induced immune responses revealed that the organ that controls anti-viral immunity is shifted from the spleen to the hepatopancreas due to the absence of T- and B-cell function, implying that immune homeostasis may change to an underside mode in rag-null fish. These findings suggest that the teleost relies heavily on innate immunity. Thus, this model could better highlight innate immunity in animals that lack adaptive immunity than mouse models.
Decoupling between the response of coral calcifying fluid pH and calcification to ocean acidification
Authors: Comeau S. , Cornwall C. E. , McCulloch M. T.
Published: August 2017

Evaluating the factors responsible for differing species-specific sensitivities to declining seawater pH is central to understanding the mechanisms via which ocean acidification (OA) affects coral calcification. We report here the results of an experiment comparing the responses of the coral Acropora yongei and Pocillopora damicornis to differing pH levels (8.09, 7.81, and 7.63) over an 8-week period. Calcification of A. youngei was reduced by 35% at pH 7.63, while calcification of P. damicornis was unaffected. The pH in the calcifying fluid (pHcf) was determined using δ11B systematics, and for both species pHcf declined slightly with seawater pH, with the decrease being more pronounced in P. damicornis. The dissolved inorganic carbon concentration at the site of calcification (DICcf) was estimated using geochemical proxies (B/Ca and δ11B) and found to be double that of seawater DIC, and increased in both species as seawater pH decreased. As a consequence, the decline of the saturation state at the site of calcification (Ωcf) with OA was partially moderated by the DICcf increase. These results highlight that while pHcf, DICcf and Ωcf are important in the mineralization process, some corals are able to maintain their calcification rates despite shifts in their calcifying fluid carbonate chemistry.
Cross-buckled structures for stretchable and compressible thin film silicon solar cells
Authors: Nam Jiyoon , Seo Bowook , Lee Youngjoo , Kim Dong-Ho , Jo Sungjin
Published: August 2017

Increasing interests in stretchable electronic devices have resulted in vigorous research activities, most of which are focused on structural configurations. Diverse structural configurations are available for stretchability, including stiff-island, serpentine, and buckled structures. With easily deformable shapes and simple fabrication processes, buckled structures have the potential to realize stretchability. However, conventional buckled structures exhibit stretchability only in a single-axis direction. In the present study, a new type of cross-buckled structure, which can overcome the limitations of conventional buckled structures is developed. The stretchable thin film solar cells with the cross-buckled structure showed stable mechanical and electrical characteristics under both stretching and compressing conditions. The cross-buckled structure for stretchable electronic devices is expected to broaden the fields of wearable electronics, stretchable displays, and biocompatible applications.
Polarization invariant plasmonic nanostructures for sensing applications
Authors: Tobing Landobasa Y. M. , Goh Geat-Yee , Mueller Aaron D. , Ke Lin , Luo Yu , Zhang Dao-Hua
Published: August 2017

Optics-based sensing platform working under unpolarized light illumination is of practical importance in the sensing applications. For this reason, sensing platforms based on localized surface plasmons are preferred to their integrated optics counterparts for their simple mode excitation and inexpensive implementation. However, their optical response under unpolarized light excitation is typically weak due to their strong polarization dependence. Herein, the role of rotational symmetry for realizing robust sensing platform exhibiting strong optical contrast and high sensitivity is explored. Specifically, gammadion and star-shaped gold nanostructures with different internal and external rotational symmetries are fabricated and studied in detail, from which their mode characteristics are demonstrated as superposition of their constituent longitudinal plasmons that are in conductive coupling with each other. We demonstrate that introducing and increasing internal rotational symmetry would lead to the enhancement in optical contrast up to ~3x under unpolarized light illumination. Finally, we compare the sensing performances of rotationally symmetric gold nanostructures with a more rigorous figure-of-merit based on sensitivity, Q-factor, and spectral contrast.
Conformational modulation of influenza virus hemagglutinin: characterization and in vivo efficacy of monomeric form
Authors: Seok Jong Hyeon , Kim Jeongwon , Lee Dan Bi , Cho Ki Joon , Lee Ji-Hye , Bae Garam , Chung Mi Sook , Kim Kyung Hyun
Published: August 2017

Mutational changes that mostly occur at the head region of hemagglutinin (HA) lead to the emergence of new epidemic influenza viruses, whereas HA antigens have been modified to generate broadly neutralizing antibodies toward highly conserved epitopes in the HA stem. Interestingly, a recent analysis of serum antibody repertoires showed that broadly neutralizing antibodies bind to HA monomer at a conserved region occluded at the intermonomer interface of HA trimer and confer protection in animal models. We showed previously that the recombinant HA ectodomain from a pandemic strain A/Korea/01/2009 was monomeric in solution and crystal structure. In order to examine the potential antigenicity of a monomeric form, we designed HA monomer that incorporates mutations to destabilize trimer conformations. Starting with the HA trimer from a seasonal strain A/Thailand/CU44/2006, mutations were introduced at the intermonomer interface, Ser199 of HA1 and Gly47, Arg75, Phe88, Val91, and Arg106 of HA2. Two mutants, F88E and V91W, were characterized to form a monomer and their double mutant F88E/V91W monomer was selected as an antigen. Animal studies showed that the HA monomer induced protective immunity in vivo, comparable to the trimer, albeit low antibody titers in sera.