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  • Publisher Correction: Community Detection in Complex Networks via Clique Conductance
    Sci. Rep. (IF 4.122) Pub Date : 2018-07-19
    Zhenqi Lu, Johan Wahlström, Arye Nehorai

    A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper.

    更新日期:2018-07-19
  • Author Correction: Depth related adaptations in symbiont bearing benthic foraminifera: New insights from a field experiment on Operculina ammonoides
    Sci. Rep. (IF 4.122) Pub Date : 2018-07-19
    Shai Oron, Sigal Abramovich, Ahuva Almogi-Labin, Julia Woeger, Jonathan Erez

    A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper.

    更新日期:2018-07-19
  • Segmental Additive Tissue Engineering
    Sci. Rep. (IF 4.122) Pub Date : 2018-07-18
    Martina Sladkova, Rawan Alawadhi, Rawan Jaragh Alhaddad, Asmaa Esmael, Shoug Alansari, Munerah Saad, Jenan Mulla Yousef, Lulwa Alqaoud, Giuseppe Maria de Peppo

    Segmental bone defects caused by trauma and disease represent a major clinical problem worldwide. Current treatment options are limited and often associated with poor outcomes and severe complications. Bone engineering is a promising alternative solution, but a number of technical challenges must be addressed to allow for effective and reproducible construction of segmental grafts that meet the size and geometrical requirements needed for individual patients and routine clinical applications. It is important to devise engineering strategies and standard operating procedures that make it possible to scale up the size of bone-engineered grafts, minimize process and product variability, and facilitate technology transfer and implementation. To address these issues, we have combined traditional and modular tissue engineering approaches in a strategy referred to as Segmental Additive Tissue Engineering (SATE). To demonstrate this approach, a digital reconstruction of a rabbit femoral defect was partitioned transversally to the longitudinal axis into segments (modules) with discoidal geometry and defined thickness to enable protocol standardization and effective tissue formation in vitro. Bone grafts corresponding to each segment were then engineered using biomimetic scaffolds seeded with human induced pluripotent stem cell-derived mesodermal progenitors (iPSC-MPs) and a novel perfusion bioreactor with universal design. The SATE strategy enables the effective and reproducible engineering of segmental bone grafts for personalized skeletal reconstruction, and will facilitate technology transfer and implementation of a tissue engineering approach to segmental bone defect therapy.

    更新日期:2018-07-19
  • How different sterols contribute to saponin tolerant plasma membranes in sea cucumbers
    Sci. Rep. (IF 4.122) Pub Date : 2018-07-18
    Emily J. S. Claereboudt, Igor Eeckhaut, Laurence Lins, Magali Deleu

    Sea cucumbers produce saponins as a chemical defense mechanism, however their cells can tolerate the cytotoxic nature of these chemicals. To elucidate the molecular mechanisms behind this tolerance a suite of complementary biophysical tools was used, firstly using liposomes for in vitro techniques then using in silico approaches for a molecular-level insight. The holothuroid saponin Frondoside A, caused significantly less permeabilization in liposomes containing a Δ7 holothuroid sterol than those containing cholesterol and resulted in endothermic interactions versus exothermic interactions with cholesterol containing liposomes. Lipid phases simulations revealed that Frondoside A has an agglomerating effect on cholesterol domains, however, induced small irregular Δ7 sterol clusters. Our results suggest that the structural peculiarities of holothuroid sterols provide sea cucumbers with a mechanism to mitigate the sterol-agglomerating effect of saponins, and therefore to protect their cells from the cytotoxicity of the saponins they produce.

    更新日期:2018-07-19
  • Assembly and Analysis of Unmapped Genome Sequence Reads Reveal Novel Sequence and Variation in Dogs
    Sci. Rep. (IF 4.122) Pub Date : 2018-07-18
    Lindsay A. Holden, Meharji Arumilli, Marjo K. Hytönen, Sruthi Hundi, Jarkko Salojärvi, Kim H. Brown, Hannes Lohi

    Dogs are excellent animal models for human disease. They have extensive veterinary histories, pedigrees, and a unique genetic system due to breeding practices. Despite these advantages, one factor limiting their usefulness is the canine genome reference (CGR) which was assembled using a single purebred Boxer. Although a common practice, this results in many high-quality reads remaining unmapped. To address this whole-genome sequence data from three breeds, Border Collie (n = 26), Bearded Collie (n = 7), and Entlebucher Sennenhund (n = 8), were analyzed to identify novel, non-CGR genomic contigs using the previously validated pseudo-de novo assembly pipeline. We identified 256,957 novel contigs and paired-end relationships together with BLAT scores provided 126,555 (49%) high-quality contigs with genomic coordinates containing 4.6 Mb of novel sequence absent from the CGR. These contigs close 12,503 known gaps, including 2.4 Mb containing partially missing sequences for 11.5% of Ensembl, 16.4% of RefSeq and 12.2% of canFam3.1+ CGR annotated genes and 1,748 unmapped contigs containing 2,366 novel gene variants. Examples for six disease-associated genes (SCARF2, RD3, COL9A3, FAM161A, RASGRP1 and DLX6) containing gaps or alternate splice variants missing from the CGR are also presented. These findings from non-reference breeds support the need for improvement of the current Boxer-only CGR to avoid missing important biological information. The inclusion of the missing gene sequences into the CGR will facilitate identification of putative disease mutations across diverse breeds and phenotypes.

    更新日期:2018-07-19
  • Author Correction: Mutant p53 stimulates cell invasion through an interaction with Rad21 in human ovarian cancer cells
    Sci. Rep. (IF 4.122) Pub Date : 2018-07-18
    Ji-Hye Ahn, Tae Jin Kim, Jae Ho Lee, Jung-Hye Choi

    A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.

    更新日期:2018-07-19
  • Corrigendum: One Step Quantum Key Distribution Based on EPR Entanglement
    Sci. Rep. (IF 4.122) Pub Date : 2018-07-18
    Jian Li, Na Li, Lei-Lei Li, Tao Wang

    Corrigendum: One Step Quantum Key Distribution Based on EPR Entanglement

    更新日期:2018-07-19
  • Evolution of rough-surface geometry and crystalline structures of aligned TiO2 nanotubes for photoelectrochemical water splitting
    Sci. Rep. (IF 4.122) Pub Date : 2018-07-18
    Maryam Zare, Shahram Solaymani, Azizollah Shafiekhani, Slawomir Kulesza, Ştefan Ţălu, Miroslaw Bramowicz

    Nowadays, increasing awareness of environment and fossil fuels protection stimulates intensive research on clean and renewable sources of energy. Production of hydrogen from water through solar-driven splitting reactions is one of the most promising approaches in the field of photoelectrochemistry (PEC). In this work we have fabricated well-aligned, highly-ordered, smooth-mouth TiO2 nanotube arrays (TNAs) in a two-step anodization process of titanium foil, which were then used as photoelectrodes for PEC water splitting. It demonstrates for the first time correspondence between non-linear component characteristics of multiscale rough surface and crystalline structure of annealed TNAs measured at various fabrication stages and their photoelectrochemical response. The as-anodized TNAs with isotropic surface (deduced from AFM and SEM images) and largest figure of merit (according to their PEC performance) were annealed at 450 °C in air. Scale-invariant descriptors of the surface structure of the deposits involved: fractal dimension, corner frequency, roughness, size of nanostructures and their dominant habits. Moreover, X-ray diffraction data processed using the Rietveld method confirmed co-existence of various oxides, for example: TiO2 in the form of anatase, TiO and Ti3O5 phases in the TNAs under study pointing that previous well-established mechanisms of the TNA growth were to certain degree incomplete.

    更新日期:2018-07-19
  • A micron-scale surface topography design reducing cell adhesion to implanted materials
    Sci. Rep. (IF 4.122) Pub Date : 2018-07-18
    Francesco Robotti, Simone Bottan, Federica Fraschetti, Anna Mallone, Giovanni Pellegrini, Nicole Lindenblatt, Christoph Starck, Volkmar Falk, Dimos Poulikakos, Aldo Ferrari

    The micron-scale surface topography of implanted materials represents a complementary pathway, independent of the material biochemical properties, regulating the process of biological recognition by cells which mediate the inflammatory response to foreign bodies. Here we explore a rational design of surface modifications in micron range to optimize a topography comprised of a symmetrical array of hexagonal pits interfering with focal adhesion establishment and maturation. When implemented on silicones and hydrogels in vitro, the anti-adhesive topography significantly reduces the adhesion of macrophages and fibroblasts and their activation toward effectors of fibrosis. In addition, long-term interaction of the cells with anti-adhesive topographies markedly hampers cell proliferation, correlating the physical inhibition of adhesion and complete spreading with the natural progress of the cell cycle. This solution for reduction in cell adhesion can be directly integrated on the outer surface of silicone implants, as well as an additive protective conformal microstructured biocellulose layer for materials that cannot be directly microstructured. Moreover, the original geometry imposed during manufacturing of the microstructured biocellulose membranes are fully retained upon in vivo exposure, suggesting a long lasting performance of these topographical features after implantation.

    更新日期:2018-07-19
  • Electrical Transport and Power Dissipation in Aerosol-Jet-Printed Graphene Interconnects
    Sci. Rep. (IF 4.122) Pub Date : 2018-07-18
    Twinkle Pandhi, Eric Kreit, Roberto Aga, Kiyo Fujimoto, Mohammad Taghi Sharbati, Samane Khademi, A. Nicole Chang, Feng Xiong, Jessica Koehne, Emily M. Heckman, David Estrada

    This paper reports the first known investigation of power dissipation and electrical breakdown in aerosol-jet-printed (AJP) graphene interconnects. The electrical performance of aerosol-jet printed (AJP) graphene was characterized using the Transmission Line Method (TLM). The electrical resistance decreased with increasing printing pass number (n); the lowest sheet resistance measured was 1.5 kΩ/sq. for n = 50. The role of thermal resistance (RTH) in power dissipation was studied using a combination of electrical breakdown thermometry and infrared (IR) imaging. A simple lumped thermal model ( $${\boldsymbol{\Delta }}{\bf{T}}={\bf{P}}{\boldsymbol{\times }}{{\bf{R}}}_{{\bf{TH}}}$$ Δ T = P × R TH ) and COMSOL Multiphysics was used to extract the total RTH, including interfaces. The RTH of AJP graphene on Kapton is ~27 times greater than that of AJP graphene on Al2O3 with a corresponding breakdown current density 10 times less on Kapton versus Al2O3.

    更新日期:2018-07-19
  • Potential of a polyherbal drug to prevent antimicrobial resistance in bacteria to antibiotics
    Sci. Rep. (IF 4.122) Pub Date : 2018-07-18
    Tapas Kumar Sar, Indranil Samanta, Achintya Mahanti, Shabnam Akhtar, Jeevan Ranjan Dash

    Persistence of antibacterial drugs for prolonged period in milk increases the probability of antimicrobial resistance progress. Ceftizoxime was found to be excreted in milk for a prolonged period in goats, cows and buffaloes following intravenous injection of ceftriaxone and ceftizoxime. A single dose of ceftriaxone was administered intravenously in healthy control goats (group I) and a single oral dose of the commercial mammary protective polyherbal drug (1.9 gm) was given one hour prior to intravenous ceftriaxone injection in healthy (group II) and induced mastitic (group III) goats to evaluate milk disposition of ceftizoxime following single intravenous dosing of ceftriaxone at 42.25 mg kg−1.Ceftriaxone/ceftizoxime was analyzed by HPLC. The t1/2α and t1/2β values were 14.755 ± 2.733 and 149.079 ± 18.565 hour, respectively indicating prolonged persistence of ceftizoxime in milk. The polyherbal drug increased the milk concentration at later hours and hastened the excretion of ceftizoxime from milk compared to control group. Ceftriaxone could not be detected in milk. The study suggested that adjunct single or repeated therapy of the polyherbal drug may cause non persistence of ceftriaxone and shorter persistence of ceftizoxime in milk.

    更新日期:2018-07-19
  • Immature particles and capsid-free viral RNA produced by Yellow fever virus-infected cells stimulate plasmacytoid dendritic cells to secrete interferons
    Sci. Rep. (IF 4.122) Pub Date : 2018-07-18
    Laura Sinigaglia, Ségolène Gracias, Elodie Décembre, Matthieu Fritz, Daniela Bruni, Nikaïa Smith, Jean-Philippe Herbeuval, Annette Martin, Marlène Dreux, Frédéric Tangy, Nolwenn Jouvenet

    Plasmacytoid dendritic cells (pDCs) are specialized in the production of interferons (IFNs) in response to viral infections. The Flaviviridae family comprises enveloped RNA viruses such as Hepatitis C virus (HCV) and Dengue virus (DENV). Cell-free flaviviridae virions poorly stimulate pDCs to produce IFN. By contrast, cells infected with HCV and DENV potently stimulate pDCs via short-range delivery of viral RNAs, which are either packaged within immature virions or secreted exosomes. We report that cells infected with Yellow fever virus (YFV), the prototypical flavivirus, stimulated pDCs to produce IFNs in a TLR7- and cell contact- dependent manner. Such stimulation was unaffected by the presence of YFV neutralizing antibodies. As reported for DENV, cells producing immature YFV particles were more potent at stimulating pDCs than cells releasing mature virions. Additionally, cells replicating a release-deficient YFV mutant or a YFV subgenomic RNA lacking structural protein-coding sequences participated in pDC stimulation. Thus, viral RNAs produced by YFV-infected cells reach pDCs via at least two mechanisms: within immature particles and as capsid-free RNAs. Our work highlights the ability of pDCs to respond to a variety of viral RNA-laden carriers generated from infected cells.

    更新日期:2018-07-19
  • Developmental arrest in Drosophila melanogaster caused by mitochondrial DNA replication defects cannot be rescued by the alternative oxidase
    Sci. Rep. (IF 4.122) Pub Date : 2018-07-18
    Ana Paula C. Rodrigues, André F. Camargo, Ana Andjelković, Howard T. Jacobs, Marcos T. Oliveira

    The xenotopic expression of the alternative oxidase AOX from the tunicate Ciona intestinalis in diverse models of human disease partially alleviates the phenotypic effects of mitochondrial respiratory chain defects. AOX is a non-proton pumping, mitochondrial inner membrane-bound, single-subunit enzyme that can bypass electron transport through the cytochrome segment, providing an additional site for ubiquinone reoxidation and oxygen reduction upon respiratory chain overload. We set out to investigate whether AOX expression in Drosophila could counteract the effects of mitochondrial DNA (mtDNA) replication defects caused by disturbances in the mtDNA helicase or DNA polymerase γ. We observed that the developmental arrest imposed by either the expression of mutant forms of these enzymes or their knockdown was not rescued by AOX. Considering also the inability of AOX to ameliorate the phenotype of tko25t, a fly mutant with mitochondrial translation deficiency, we infer that this alternative enzyme may not be applicable to cases of mitochondrial gene expression defects. Finding the limitations of AOX applicability will help establish the parameters for the future putative use of this enzyme in gene therapies for human mitochondrial diseases.

    更新日期:2018-07-19
  • Association between Height and Actinic Keratosis: A Nationwide Population-based Study in South Korea
    Sci. Rep. (IF 4.122) Pub Date : 2018-07-18
    Young Bok Lee, Ji Hyun Lee, Min Ji Kang, Jin-Wou Kim, Dong Soo Yu, Kyung Do Han, Yong Gyu Park

    The association between actinic keratosis (AK) and anthropometric measures has not been investigated. This study aims to evaluate the associations between anthropometric measures and the incidence of AK in South Korea. We analyzed clinical data from individuals aged over 20 years who received a health examination arranged by the national insurance program between 2005 and 2008. Newly diagnosed AK was identified using claims data from baseline to the date of diagnosis or until December 31, 2015. The incidence of AK was highest among the elderly (aged over 60 years) and showed a male bias. The risk of AK increased with greater height. The quintile with the greatest height had an increased risk of AK compared with the quintile with the lowest height (hazard ratio = 1.28, 95% confidence interval: 1.24–1.33) after adjustment for age, sex, income, smoking status, alcohol consumption, hypertension, dyslipidemia, myocardial infarction, congestive heart failure, and chronic obstructive pulmonary disease. This study showed a positive association between the incidence of AK and human height. However, it is unclear whether these findings can be generalized to Koreans who have not received an examination or to populations in other countries.

    更新日期:2018-07-19
  • Control energy of complex networks towards distinct mixture states
    Sci. Rep. (IF 4.122) Pub Date : 2018-07-18
    Sen Nie, H. Eugene Stanley, Shi-Ming Chen, Bing-Hong Wang, Xu-Wen Wang

    Controlling complex networked systems is a real-world puzzle that remains largely unsolved. Despite recent progress in understanding the structural characteristics of network control energy, target state and system dynamics have not been explored. We examine how varying the final state mixture affects the control energy of canonical and conformity-incorporated dynamical systems. We find that the control energy required to drive a network to an identical final state is lower than that required to arrive a non-identical final state. We also demonstrate that it is easier to achieve full control in a conformity-based dynamical network. Finally we determine the optimal control strategy in terms of the network hierarchical structure. Our work offers a realistic understanding of the control energy within the final state mixture and sheds light on controlling complex systems.

    更新日期:2018-07-19
  • Compressing Networks with Super Nodes
    Sci. Rep. (IF 4.122) Pub Date : 2018-07-18
    Natalie Stanley, Roland Kwitt, Marc Niethammer, Peter J. Mucha

    Community detection is a commonly used technique for identifying groups in a network based on similarities in connectivity patterns. To facilitate community detection in large networks, we recast the network as a smaller network of ‘super nodes’, where each super node comprises one or more nodes of the original network. We can then use this super node representation as the input into standard community detection algorithms. To define the seeds, or centers, of our super nodes, we apply the ‘CoreHD’ ranking, a technique applied in network dismantling and decycling problems. We test our approach through the analysis of two common methods for community detection: modularity maximization with the Louvain algorithm and maximum likelihood optimization for fitting a stochastic block model. Our results highlight that applying community detection to the compressed network of super nodes is significantly faster while successfully producing partitions that are more aligned with the local network connectivity and more stable across multiple (stochastic) runs within and between community detection algorithms, yet still overlap well with the results obtained using the full network.

    更新日期:2018-07-19
  • Cord Blood IL-12 Confers Protection to Clinical Malaria in Early Childhood Life
    Sci. Rep. (IF 4.122) Pub Date : 2018-07-18
    Yong Song, Ruth Aguilar, Jing Guo, Maria Nelia Manaca, Augusto Nhabomba, Tamara Katherine Berthoud, Siew-Kim Khoo, Selma Wiertsema, Arnoldo Barbosa, Llorenç Quintó, Ingrid A Laing, Alfredo Mayor, Caterina Guinovart, Pedro L. Alonso, Peter N. LeSouëf, Carlota Dobaño, Guicheng (Brad) Zhang

    Using a well-designed longitudinal cohort, we aimed to identify cytokines that were protective against malaria and to explore how they were influenced by genetic and immunological factors. 349 Mozambican pregnant women and their newborn babies were recruited and followed up for malaria outcomes until 24 months of age. Six Th1 cytokines in cord blood were screened for correlation with malaria incidence, of which IL-12 was selected for further analyses. We genotyped IL-12 polymorphisms in children/mothers and evaluated the genotype-phenotype associations and genetic effects on IL-12 levels. Maternal IL-12 concentrations were also investigated in relation to Plasmodium infections and cord blood IL-12 levels. Our data showed that high background IL-12 levels were prospectively associated with a low incidence of clinical malaria, while IL-12 production after parasite stimulation had the opposite effect on malaria incidence. IL-12 genotypes (IL-12b rs2288831/rs17860508) and the haplotype CGTTAGAG distribution were related to malaria susceptibility and background IL-12 levels. Maternal genotypes also exhibited an evident impact on host genotype-phenotype associations. Finally, a positive correlation in background IL-12 levels between maternal and cord blood was identified. Thus, cord blood background IL-12 concentrations are important for protecting children from clinical malaria, likely mediated by both genotypes (children&mothers) and maternal immunity.

    更新日期:2018-07-19
  • The trends of aquacultural nitrogen budget and its environmental implications in China
    Sci. Rep. (IF 4.122) Pub Date : 2018-07-18
    Zhibo Luo, Shanying Hu, Dingjiang Chen

    The rapid development of aquaculture has sustained aquatic food production but has also led to a host of environmental problems, ranging from eutrophication of aquatic ecosystems to global acidification. China has become the world’s largest producer and consumer of aquaculture products. Nitrogen is an essential nutrient in aquaculture ecosystems, and the quantitative environmental fate and impact of nitrogen during aquaculture processes have notable environmental consequences but have received little attention. Here, we established a nitrogen cycling model for China’s aquaculture ecosystem to investigate the creation and fate of reactive nitrogen over a decadal time scale. A nitrogen balance analysis showed that reactive nitrogen input in the aquaculture ecosystem increased from 9.43 Tg N yr−1 in 1978 to 18.54 Tg N yr−1 in 2015, while aquaculture production increased from 0.034 to 1.33 Tg N yr−1 during the same period. The environmental fate analysis showed that nitrogen emissions, accumulation, sediment deposition, and export into the oceans increased by 9.05-fold, 0.24-fold, 9.04-fold, and 2.56-fold, respectively. Finally, we investigated four scenarios representing different consumption levels of aquatic products and provided policy recommendations (larger aquaculture size, standardized aquaculture production model, nutritional element management and balanced dietary structure, etc.) on improved management practices in aquaculture ecosystems.

    更新日期:2018-07-19
  • Trichromatic perception of flower colour improves resource detection among New World monkeys
    Sci. Rep. (IF 4.122) Pub Date : 2018-07-18
    J. D. Hogan, L. M. Fedigan, C. Hiramatsu, S. Kawamura, A. D. Melin

    Many plants use colour to attract pollinators, which often possess colour vision systems well-suited for detecting flowers. Yet, to isolate the role of colour is difficult, as flowers also produce other cues. The study of florivory by Neotropical primates possessing polymorphic colour vision provides an opportunity to investigate the importance of colour directly. Here we determine whether differences in colour vision within a mixed population of wild dichromatic and trichromatic white-faced capuchins (Cebus capucinus imitator) affect flower foraging behaviours. We collected reflectance data for flower foods and modelled their chromatic properties to capuchin colour vision phenotypes. We collected behavioural data over 22 months spanning four years, determined the colour vision phenotype of each monkey based on amino acid variation of the L/M opsin gene from fecal DNA, and compared foraging behaviours of dichromats and trichromats. Most flowers were more conspicuous to trichromats, and trichromats foraged in small flower patches significantly more often. These data demonstrate a difference in wild primate foraging patterns based on colour vision differences, supporting the hypothesis that trichromacy enhances detection of small, ephemeral resources. This advantage, which may also extend to other foods, likely contributes to the maintenance of colour vision polymorphism in Neotropical monkeys.

    更新日期:2018-07-19
  • Determination of risk factors for herpesvirus outbreak in oysters using a broad-scale spatial epidemiology framework
    Sci. Rep. (IF 4.122) Pub Date : 2018-07-18
    Fabrice Pernet, Marine Fuhrmann, Bruno Petton, Joseph Mazurié, Jean-François Bouget, Elodie Fleury, Gaétan Daigle, Pierre Gernez

    Marine diseases have major impacts on ecosystems and economic consequences for aquaculture and fisheries. Understanding origin, spread and risk factors of disease is crucial for management, but data in the ocean are limited compared to the terrestrial environment. Here we investigated how the marine environment drives the spread of viral disease outbreak affecting The Pacific oyster worldwide by using a spatial epidemiology framework. We collected environmental and oyster health data at 46 sites spread over an area of 300 km2 along an inshore-offshore gradient during an epizootic event and conducted risk analysis. We found that disease broke out in the intertidal farming area and spread seaward. Mortalities and virus detection were observed in oysters placed 2 km from the farming areas, but oysters of almost all sites were subclinically infected. Increasing food quantity and quality, growth rate and energy reserves of oyster were associated with a lower risk of mortality offshore whereas increasing turbidity, a proxy of the concentration of suspended particulate matter, and terrestrial inputs, inferred from fatty acid composition of oysters, were associated with a higher risk of mortality. Offshore farming and maintenance of good ecological status of coastal waters are options to limit disease risk in oysters.

    更新日期:2018-07-19
  • Natural menstrual rhythm and oral contraception diversely affect exhaled breath compositions
    Sci. Rep. (IF 4.122) Pub Date : 2018-07-18
    Pritam Sukul, Jochen K. Schubert, Phillip Trefz, Wolfram Miekisch

    Natural menstrual cycle and/or oral contraception diversely affect women metabolites. Longitudinal metabolic profiling under constant experimental conditions is thereby realistic to understand such effects. Thus, we investigated volatile organic compounds (VOCs) exhalation throughout menstrual cycles in 24 young and healthy women with- and without oral contraception. Exhaled VOCs were identified and quantified in trace concentrations via high-resolution real-time mass-spectrometry, starting from a menstruation and then repeated follow-up with six intervals including the next bleeding. Repeated measurements within biologically comparable groups were employed under optimized measurement setup. We observed pronounced and substance specific changes in exhaled VOC concentrations throughout all cycles with low intra-individual variations. Certain blood-borne volatiles changed significantly during follicular and luteal phases. Most prominent changes in endogenous VOCs were observed at the ovulation phase with respect to initial menstruation. Here, the absolute median abundances of alveolar ammonia, acetone, isoprene and dimethyl sulphide changed significantly (P-value ≤ 0.005) by 18.22↓, 13.41↓, 18.02↑ and 9.40↓%, respectively. These VOCs behaved in contrast under the presence of combined oral contraception; e.g. isoprene decreased significantly by 30.25↓%. All changes returned to initial range once the second bleeding phase was repeated. Changes in exogenous benzene, isopropanol, limonene etc. and smoking related furan, acetonitrile and orally originated hydrogen sulphide were rather nonspecific and mainly exposure dependent. Our observations could apprehend a number of known/pre-investigated metabolic effects induced by monthly endocrine regulations. Potential in vivo origins (e.g. metabolic processes) of VOCs are crucial to realize such effects. Despite ubiquitous confounders, we demonstrated the true strength of volatolomics for metabolic monitoring of menstrual cycle and contraceptives. These outcomes may warrant further studies in this direction to enhance our fundamental and clinical understanding on menstrual metabolomics and endocrinology. Counter-effects of contraception can be deployed for future noninvasive assessment of birth control pills. Our findings could be translated toward metabolomics of pregnancy, menopause and post-menopausal complications via breath analysis.

    更新日期:2018-07-19
  • Rapid oral bacteria detection based on real-time PCR for the forensic identification of saliva
    Sci. Rep. (IF 4.122) Pub Date : 2018-07-18
    Ju Yeon Jung, Hyun Kyu Yoon, Sanghyun An, Jee Won Lee, Eu-Ree Ahn, Yeon-Ji Kim, Hyun-Chul Park, Kyungmyung Lee, Jung Ho Hwang, Si-Keun Lim

    This study developed a new method for forensic saliva identification using three oral bacteria, Streptococcus salivarius, Streptococcus sanguinis, and Neisseria subflava, combined with a real-time polymerase chain reaction (RT-PCR) system we called OB mRT-PCR. Analytical sensitivity results showed that the target bacteria were amplified at 102–107 copies/reaction, and analytical specificity was assessed using 24 other viruses, bacteria, and protozoa. To evaluate the OB mRT-PCR kit for forensic applications, saliva from 140 Korean individuals was tested, and at least two target bacteria were detected in all the samples. Additional studies on non-saliva samples demonstrated the specificity of the kit. Comparison of the kit with two conventional saliva test methods, the SALIgAE and RSID-Saliva assays, indicated that it was more sensitive and applicable to saliva samples in long-term storage (up to 14 weeks). Additionally, through amplification of mock forensic items and old DNA samples (isolated without lysis of the bacterial cells, regardless of their Gram-positivity), we found that the kit was applicable to not only saliva swabs, but also DNA samples. We suggest that this simple RT-PCR-based experimental method is feasible for rapid on-site analysis, and we expect this kit to be useful for saliva detection in old forensic DNA samples.

    更新日期:2018-07-19
  • Potent Attractant for Root-Knot Nematodes in Exudates from Seedling Root Tips of Two Host Species
    Sci. Rep. (IF 4.122) Pub Date : 2018-07-18
    Rasa Čepulytė, Wiseborn B. Danquah, George Bruening, Valerie M. Williamson

    Root-knot nematodes (RKN; Meloidogyne spp.) can parasitize over 2,000 plant species and are generally considered to be the most agriculturally damaging group of plant-parasitic nematodes worldwide. Infective juveniles (J2) are non-feeding and must locate and invade a host before their reserves are depleted. However, what attracts J2 to appropriate root entry sites is not known. An aim of this research is to identify semiochemicals that attract RKN to roots. J2 of the three RKN species tested are highly attracted to root tips of both tomato and Medicago truncatula. For both hosts, mutants defective in ethylene signaling were found to be more attractive than those of wild type. We determined that cell-free exudates collected from tomato and M. truncatula seedling root tips were highly attractive to M. javanica J2. Using a pluronic gel-based microassay to monitor chemical fractionation, we determined that for both plant species the active component fractionated similarly and had a mass of ~400 based on size-exclusion chromatography. This characterization is a first step toward identification of a potent and specific attractant from host roots that attracts RKN. Such a compound is potentially a valuable tool for developing novel and safe control strategies.

    更新日期:2018-07-19
  • Endocrine cell type sorting and mature architecture in the islets of Langerhans require expression of Roundabout receptors in β cells
    Sci. Rep. (IF 4.122) Pub Date : 2018-07-18
    Melissa T. Adams, Jennifer M. Gilbert, Jesus Hinojosa Paiz, Faith M. Bowman, Barak Blum

    Pancreatic islets of Langerhans display characteristic spatial architecture of their endocrine cell types. This architecture is critical for cell-cell communication and coordinated hormone secretion. Islet architecture is disrupted in type-2 diabetes. Moreover, the generation of architecturally correct islets in vitro remains a challenge in regenerative approaches to type-1 diabetes. Although the characteristic islet architecture is well documented, the mechanisms controlling its formation remain obscure. Here, we report that correct endocrine cell type sorting and the formation of mature islet architecture require the expression of Roundabout (Robo) receptors in β cells. Mice with whole-body deletion of Robo1 and conditional deletion of Robo2 either in all endocrine cells or selectively in β cells show complete loss of endocrine cell type sorting, highlighting the importance of β cells as the primary organizer of islet architecture. Conditional deletion of Robo in mature β cells subsequent to islet formation results in a similar phenotype. Finally, we provide evidence to suggest that the loss of islet architecture in Robo KO mice is not due to β cell transdifferentiation, cell death or loss of β cell differentiation or maturation.

    更新日期:2018-07-19
  • Reduction of the forming voltage through tailored oxygen non-stoichiometry in tantalum oxide ReRAM devices
    Sci. Rep. (IF 4.122) Pub Date : 2018-07-18
    Katharina Skaja, Michael Andrä, Vikas Rana, Rainer Waser, Regina Dittmann, Christoph Baeumer

    In this study, we investigated the influence of oxygen non-stoichiometry on the resistive switching performance of tantalum oxide based memristive devices. Thin-films of tantalum oxide were deposited with varying sputter power and oxygen partial pressure. The electroforming voltage was found to decrease with increasing power density or decreased oxygen partial pressure, while the endurance remained stable and the resistance window ROFF/RON was found to increase. In-depth XPS analysis connects these observations to a controllable oxygen sub-stoichiometry in the sputter-deposited films. Our analysis shows that the decrease of the forming voltage results from an increase in carrier density in the as-prepared thin-films, which is induced by the presence of oxygen vacancies.

    更新日期:2018-07-19
  • Menthol, a unique urinary volatile compound, is associated with chronic inflammation in interstitial cystitis
    Sci. Rep. (IF 4.122) Pub Date : 2018-07-18
    Muhammad Shahid, Min Young Lee, Austin Yeon, Eunho Cho, Vikram Sairam, Luis Valdiviez, Sungyong You, Jayoung Kim

    Chronic inflammation is a potential systemic risk factor for many bladder dysfunctions, including interstitial cystitis (IC). However, the underlying mechanism through which a healthy bladder protects itself from inflammatory triggers remains unknown. In this study, we identified odor compounds in urine obtained from IC patients and healthy controls. Using comprehensive solid-phase microextraction-gas chromatography-time-of-flight-mass spectrometry (SPME-GC-TOF-MS) profiling and bioinformatics, we found that levels of urinary volatile metabolites, such as menthol, were significantly reduced in IC patients, compared to healthy controls. In an attempt to understand the mechanistic meaning of our volatile metabolites data and the role of menthol in the immune system, we performed two independent experiments: (a) cytokine profiling, and (b) DNA microarray. Our findings suggest that lipopolysaccharide (LPS)-stimulated inflammatory events, such as the production and secretion of inflammatory cytokines (e.g., TNF-α, IL-6, and IL-1β) and the activation of NF-κB and associated proteins within a large signaling network (e.g., Akt, TLR1, TNFAIP3, and NF-κB), are suppressed by the presence of menthol. These findings broaden our knowledge on the role of urinary menthol in suppressing inflammatory events and provide potential new strategies for alleviating both the odor and inflammation associated with IC.

    更新日期:2018-07-19
  • U6 can be used as a housekeeping gene for urinary sediment miRNA studies of IgA nephropathy
    Sci. Rep. (IF 4.122) Pub Date : 2018-07-18
    Zhi-Yu Duan, Guang-Yan Cai, Ji-Jun Li, Ru Bu, NanNan Wang, Pei Yin, Xiang-Mei Chen

    Recent studies have indicated that urinary sediment miRNAs not only are able to serve as non-invasive diagnostic biomarkers for IgA nephropathy (IgAN) but may also be closely related to several clinical and pathological indicators. However, the lack of a suitable internal reference miRNA has hampered research into urinary sediment miRNAs. To date, U6 has been used as a reference gene in urinary sediment miRNA studies mostly based on the results from studies using tissue samples and cell lines. In a total of 330 IgAN patients, 164 disease control patients and 130 normal control patients, there was no significant difference in U6 levels. We also compared the U6 levels in different types of primary glomerular disease groups (IgA nephropathy, membranous nephropathy, minimal change nephrosis and focal segmental glomerular sclerosis). The results confirmed that there was no significant difference in the expression of U6 in different primary glomerular disease groups. Moreover, treatment had no significant effect on the expression levels of U6 in IgA nephropathy. Therefore, U6 is an excellent housekeeping gene for urinary sediment miRNA studies of IgA nephropathy.

    更新日期:2018-07-19
  • A dual-fMRI investigation of the iterated Ultimatum Game reveals that reciprocal behaviour is associated with neural alignment
    Sci. Rep. (IF 4.122) Pub Date : 2018-07-18
    Daniel J. Shaw, Kristína Czekóová, Rostislav Staněk, Radek Mareček, Tomáš Urbánek, Jiří Špalek, Lenka Kopečková, Jan Řezáč, Milan Brázdil

    Dyadic interactions often involve a dynamic process of mutual reciprocity; to steer a series of exchanges towards a desired outcome, both interactants must adapt their own behaviour according to that of their interaction partner. Understanding the brain processes behind such bidirectional reciprocity is therefore central to social neuroscience, but this requires measurement of both individuals’ brains during real-world exchanges. We achieved this by performing functional magnetic resonance imaging (fMRI) on pairs of male individuals simultaneously while they interacted in a modified iterated Ultimatum Game (iUG). In this modification, both players could express their intent and maximise their own monetary gain by reciprocating their partner’s behaviour – they could promote generosity through cooperation and/or discourage unfair play with retaliation. By developing a novel model of reciprocity adapted from behavioural economics, we then show that each player’s choices can be predicted accurately by estimating expected utility (EU) not only in terms of immediate payoff, but also as a reaction to their opponent’s prior behaviour. Finally, for the first time we reveal that brain signals implicated in social decision making are modulated by these estimates of EU, and become correlated more strongly between interacting players who reciprocate one another.

    更新日期:2018-07-19
  • Mechanical interactions between bacteria and hydrogels
    Sci. Rep. (IF 4.122) Pub Date : 2018-07-18
    Nehir Kandemir, Waldemar Vollmer, Nicholas S. Jakubovics, Jinju Chen

    Mechanical interactions between bacterial cells and extracellular polymeric substance are essential in determining biofilm assembly and disassembly as well the mechanical characteristics of biofilms. However, the physics of these mechanical interactions in different cell culture conditions are poorly understood. We created typical artificial biofilm consisting of planktonic bacteria and hydrogel, in the absence of metabolic or regulatory effect. We have demonstrated that the cell culture medium can significantly affect the mechanical interactions between bacterial cells and hydrogels. The stiffness of the bacteria-hydrogel artificial biofilm cannot be simply attributed by the summation of the contribution from the bacteria and hydrogel based on the mathematical models and computational models. We have revealed that the tryptone component of Luria-Bertani broth medium plays an important role in stiffening effect of bacteria-hydrogel construct. Such significant stiffening effect can be explained by the following mechanism: the presence of tryptone in cell culture medium may enable the bacteria itself to crosslink the hydrogel polymer chains. Our findings have also demonstrated the synergy of modelling and innovative experiments which would potentially impact the biofilm control strategies.

    更新日期:2018-07-19
  • Non-canonicaly recruited TCRαβCD8αα IELs recognize microbial antigens
    Sci. Rep. (IF 4.122) Pub Date : 2018-07-18
    Lukasz Wojciech, Edyta Szurek, Michal Kuczma, Anna Cebula, Wessam R. Elhefnawy, Maciej Pietrzak, Grzegorz Rempala, Leszek Ignatowicz

    In the gut, various subsets of intraepithelial T cells (IELs) respond to self or non-self-antigens derived from the body, diet, commensal and pathogenic microbiota. Dominant subset of IELs in the small intestine are TCRαβCD8αα+ cells, which are derived from immature thymocytes that express self-reactive TCRs. Although most of TCRαβCD8αα+ IELs are thymus-derived, their repertoire adapts to microbial flora. Here, using high throughput TCR sequencing we examined how clonal diversity of TCRαβCD8αα+ IELs changes upon exposure to commensal-derived antigens. We found that fraction of CD8αα+ IELs and CD4+ T cells express identical αβTCRs and this overlap raised parallel to a surge in the diversity of microbial flora. We also found that an opportunistic pathogen (Staphylococcus aureus) isolated from mouse small intestine specifically activated CD8αα+ IELs and CD4+ derived T cell hybridomas suggesting that some of TCRαβCD8αα+ clones with microbial specificities have extrathymic origin. We also report that CD8ααCD4+ IELs and Foxp3CD4+ T cells from the small intestine shared many αβTCRs, regardless whether the later subset was isolated from Foxp3CNS1 sufficient or Foxp3CNS1 deficient mice that lacks peripherally-derived Tregs. Overall, our results imply that repertoire of TCRαβCD8αα+ in small intestine expends in situ in response to changes in microbial flora.

    更新日期:2018-07-19
  • Weighted Betweenness Preferential Attachment: A New Mechanism Explaining Social Network Formation and Evolution
    Sci. Rep. (IF 4.122) Pub Date : 2018-07-18
    Alexandru Topirceanu, Mihai Udrescu, Radu Marculescu

    The dynamics of social networks is a complex process, as there are many factors which contribute to the formation and evolution of social links. While certain real-world properties are captured by the degree-driven preferential attachment model, it still cannot fully explain social network dynamics. Indeed, important properties such as dynamic community formation, link weight evolution, or degree saturation cannot be completely and simultaneously described by state of the art models. In this paper, we explore the distribution of social network parameters and centralities and argue that node degree is not the main attractor of new social links. Consequently, as node betweenness proves to be paramount to attracting new links – as well as strengthening existing links –, we propose the new Weighted Betweenness Preferential Attachment (WBPA) model, which renders quantitatively robust results on realistic network metrics. Moreover, we support our WBPA model with a socio-psychological interpretation, that offers a deeper understanding of the mechanics behind social network dynamics.

    更新日期:2018-07-19
  • Evaluating the potential of residual Pap test fluid as a resource for the metaproteomic analysis of the cervical-vaginal microbiome
    Sci. Rep. (IF 4.122) Pub Date : 2018-07-18
    Somaieh Afiuni-Zadeh, Kristin L. M. Boylan, Pratik D. Jagtap, Timothy J. Griffin, Joel D. Rudney, Marnie L. Peterson, Amy P. N. Skubitz

    The human cervical-vaginal area contains proteins derived from microorganisms that may prevent or predispose women to gynecological conditions. The liquid Pap test fixative is an unexplored resource for analysis of microbial communities and the microbe-host interaction. Previously, we showed that the residual cell-free fixative from discarded Pap tests of healthy women could be used for mass spectrometry (MS) based proteomic identification of cervical-vaginal proteins. In this study, we reprocessed these MS raw data files for metaproteomic analysis to characterize the microbial community composition and function of microbial proteins in the cervical-vaginal region. This was accomplished by developing a customized protein sequence database encompassing microbes likely present in the vagina. High-mass accuracy data were searched against the protein FASTA database using a two-step search method within the Galaxy for proteomics platform. Data was analyzed by MEGAN6 (MetaGenomeAnalyzer) for phylogenetic and functional characterization. We identified over 300 unique peptides from a variety of bacterial phyla and Candida. Peptides corresponding to proteins involved in carbohydrate metabolism, oxidation-reduction, and transport were identified. By identifying microbial peptides in Pap test supernatants it may be possible to acquire a functional signature of these microbes, as well as detect specific proteins associated with cervical health and disease.

    更新日期:2018-07-19
  • Spatiotemporal epidemiology of rabies at an interface between domestic dogs and wildlife in South Africa
    Sci. Rep. (IF 4.122) Pub Date : 2018-07-18
    Michael Grover, Paul R. Bessell, Anne Conan, Pim Polak, Claude T. Sabeta, Bjorn Reininghaus, Darryn L. Knobel

    We characterized the spatiotemporal epidemiology of rabies from January 2009 through March 2014 across the interface between a wildlife reserve and communal livestock farming area in South Africa. Brain tissue from 344 animals of 28 different species were tested for lyssavirus antigen. Of these, 146 (42.4%) samples tested positive, of which 141 (96.6%) came from dogs. Brain samples of dogs were more likely to test positive for lyssavirus antigen if they were found and destroyed in the reserve, compared to samples originating from dogs outside the reserve (65.3% vs. 45.5%; odds ratio (OR) = 2.26, 95% confidence interval (CI) = 1.27–4.03), despite rabies surveillance outside the reserve being targeted to dogs that have a higher index of suspicion due to clinical or epidemiological evidence of infection. In the reserve, dogs were more likely to test positive for rabies if they were shot further from villages (OR = 1.42, 95% CI 1.18–1.71) and closer to water points (OR = 0.41, 95% CI 0.21–0.81). Our results provide a basis for refinement of existing surveillance and control programs to mitigate the threat of spillover of rabies to wildlife populations.

    更新日期:2018-07-19
  • How driving rates determine the statistics of driven non-equilibrium systems with stationary distributions
    Sci. Rep. (IF 4.122) Pub Date : 2018-07-18
    Bernat Corominas-Murtra, Rudolf Hanel, Leonardo Zavojanni, Stefan Thurner

    Sample space reducing (SSR) processes offer a simple analytical way to understand the origin and ubiquity of power-laws in many path-dependent complex systems. SRR processes show a wide range of applications that range from fragmentation processes, language formation to search and cascading processes. Here we argue that they also offer a natural framework to understand stationary distributions of generic driven non-equilibrium systems that are composed of a driving- and a relaxing process. We show that the statistics of driven non-equilibrium systems can be derived from the understanding of the nature of the underlying driving process. For constant driving rates exact power-laws emerge with exponents that are related to the driving rate. If driving rates become state-dependent, or if they vary across the life-span of the process, the functional form of the state-dependence determines the statistics. Constant driving rates lead to exact power-laws, a linear state-dependence function yields exponential or Gamma distributions, a quadratic function produces the normal distribution. Logarithmic and power-law state dependence leads to log-normal and stretched exponential distribution functions, respectively. Also Weibull, Gompertz and Tsallis-Pareto distributions arise naturally from simple state-dependent driving rates. We discuss a simple physical example of consecutive elastic collisions that exactly represents a SSR process.

    更新日期:2018-07-19
  • Triptolide attenuates proteinuria and podocyte apoptosis via inhibition of NF-κB/GADD45B
    Sci. Rep. (IF 4.122) Pub Date : 2018-07-18
    Ling Wang, Liwen Zhang, Qing Hou, Xiaodong Zhu, Zhaohong Chen, Zhihong Liu

    Podocyte injury is a primary contributor to proteinuria. Triptolide is a major active component of Tripterygium wilfordii Hook F that exhibits potent antiproteinuric effects. We used our previously developed in vivo zebrafish model of inducible podocyte-target injury and found that triptolide treatment effectively alleviated oedema, proteinuria and foot process effacement. Triptolide also inhibited podocyte apoptosis in our zebrafish model and in vitro. We also examined the mechanism of triptolide protection of podocyte. Whole-genome expression profiles of cultured podocytes demonstrated that triptolide treatment downregulated apoptosis pathway-related GADD45B expression. Specific overexpression of gadd45b in zebrafish podocytes abolished the protective effects of triptolide. GADD45B is a mediator of podocyte apoptosis that contains typical NF-κB binding sites in the promoter region, and NF-κB p65 primarily transactivates this gene. Triptolide inhibited NF-κB signalling activation and binding of NF-κB to the GADD45B promoter. Taken together, our findings demonstrated that triptolide attenuated proteinuria and podocyte apoptosis via inhibition of NF-κB/GADD45B signalling, which provides a new understanding of the antiproteinuric effects of triptolide in glomerular diseases.

    更新日期:2018-07-19
  • Magnetic resonance as a local probe for kagomé magnetism in Barlowite Cu4(OH)6FBr
    Sci. Rep. (IF 4.122) Pub Date : 2018-07-18
    K. M. Ranjith, C. Klein, A. A. Tsirlin, H. Rosner, C. Krellner, M. Baenitz

    Temperature- and field-dependent 1H-, 19F-, and 79,81Br-NMR measurements together with zero - field 79,81Br-NQR measurements on polycrystalline samples of barlowite, Cu4(OH)6FBr are conducted to study the magnetism and possible structural distortions on a microscopic level. The temperature dependence of the 79,81Br-NMR spin-lattice relaxation rates 1/T1 indicate a phase transition at TN $$\simeq $$ ≃ 15 K which is of magnetic origin, but with an unusually weak slowing down of fluctuations below TN. Moreover, 1/T1T scales linear with the bulk susceptibility which indicates persisting spin fluctuations down to 2 K. Quadupolare resonance (NQR) studies reveal a pair of zero-field NQR- lines associated with the two isotopes of Br with the nuclear spins of I = 3/2. Quadrupole coupling constants of vQ ≃ 28.5 MHz and 24.7 MHz for 79Br- and 81Br-nuclei are determined from Br-NMR and the asymmetry parameter of the electric field gradient was estimated to η ≃ 0.2. The Br-NQR lines are consistent with our findings from Br-NMR and they are relatively broad, even above TN. This broadening and the relative large η value suggests a symmetry reduction at the Br- site reflecting the presence of a local distortion in the lattice. Our density-functional calculations show that the displacements of Cu2 atoms located between the kagome planes do not account for this relatively large η. On the other hand, full structural relaxation, including the deformation of kagome planes, leads to a better agreement with the experiment.

    更新日期:2018-07-19
  • GOATOOLS: A Python library for Gene Ontology analyses
    Sci. Rep. (IF 4.122) Pub Date : 2018-07-18
    D. V. Klopfenstein, Liangsheng Zhang, Brent S. Pedersen, Fidel Ramírez, Alex Warwick Vesztrocy, Aurélien Naldi, Christopher J. Mungall, Jeffrey M. Yunes, Olga Botvinnik, Mark Weigel, Will Dampier, Christophe Dessimoz, Patrick Flick, Haibao Tang

    The biological interpretation of gene lists with interesting shared properties, such as up- or down-regulation in a particular experiment, is typically accomplished using gene ontology enrichment analysis tools. Given a list of genes, a gene ontology (GO) enrichment analysis may return hundreds of statistically significant GO results in a “flat” list, which can be challenging to summarize. It can also be difficult to keep pace with rapidly expanding biological knowledge, which often results in daily changes to any of the over 47,000 gene ontologies that describe biological knowledge. GOATOOLS, a Python-based library, makes it more efficient to stay current with the latest ontologies and annotations, perform gene ontology enrichment analyses to determine over- and under-represented terms, and organize results for greater clarity and easier interpretation using a novel GOATOOLS GO grouping method. We performed functional analyses on both stochastic simulation data and real data from a published RNA-seq study to compare the enrichment results from GOATOOLS to two other popular tools: DAVID and GOstats. GOATOOLS is freely available through GitHub: https://github.com/tanghaibao/goatools .

    更新日期:2018-07-19
  • Inactivation of TCA cycle enhances Staphylococcus aureus persister cell formation in stationary phase
    Sci. Rep. (IF 4.122) Pub Date : 2018-07-18
    Ying Wang, Martin Saxtorph Bojer, Shilpa Elizabeth George, Zhihao Wang, Peter Ruhdal Jensen, Christiane Wolz, Hanne Ingmer

    Persister cells constitute a small subpopulation of bacteria that display remarkably high antibiotic tolerance and for pathogens such as Staphylococcus aureus are suspected as culprits of chronic and recurrent infections. Persisters formed during exponential growth are characterized by low ATP levels but less is known of cells in stationary phase. By enrichment from a transposon mutant library in S. aureus we identified mutants that in this growth phase displayed enhanced persister cell formation. We found that inactivation of either sucA or sucB, encoding the subunits of the α-ketoglutarate dehydrogenase of the tricarboxylic acid cycle (TCA cycle), increased survival to lethal concentrations of ciprofloxacin by 10–100 fold as did inactivation of other TCA cycle genes or atpA encoding a subunit of the F1F0 ATPase. In S. aureus, TCA cycle activity and gene expression are de-repressed in stationary phase but single cells with low expression may be prone to form persisters. While ATP levels were not consistently affected in high persister mutants they commonly displayed reduced membrane potential, and persistence was enhanced by a protein motive force inhibitor. Our results show that persister cell formation in stationary phase does not correlate with ATP levels but is associated with low membrane potential.

    更新日期:2018-07-19
  • Advances in single-scan time-encoding magnetic resonance imaging
    Sci. Rep. (IF 4.122) Pub Date : 2018-07-18
    Sina Marhabaie, Geoffrey Bodenhausen, Philippe Pelupessy

    Time-encoding MRI is a single-scan method that uses traditional k-encoding only in one direction. In the orthogonal “time-encoding” direction, a string of echoes appears in an order that depends on the position of the corresponding spin packets. In one variant of time-encoding, this is achieved by using a series of selective pulses and appropriate gradients in both k-encoding and time-encoding directions. Although time-encoding offers some advantages over traditional single-scan Fourier methods such as echo planar imaging (EPI), the original time-encoding sequence also has some drawbacks that limit its applications. In this work, we show how one can improve several aspects of the original time-encoding sequence. By using an additional gradient pulse one can change the order in which the echoes appear, leading to identical echo times for all echoes, and hence to a uniform signal attenuation due to transverse relaxation and a reduction in average signal attenuation due to diffusion. By rearranging positive and negative gradients one can reduce the switching rate of the gradients. Furthermore, we show how one can implement time-encoding sequences in an interleaved fashion in order to reduce signal attenuation due to transverse relaxation and diffusion, while increasing the spatial resolution.

    更新日期:2018-07-19
  • Nano@lignocellulose intercalated montmorillonite as adsorbent for effective Mn(II) removal from aqueous solution
    Sci. Rep. (IF 4.122) Pub Date : 2018-07-18
    Yuhong An, Xiaotao Zhang, Ximing Wang, Zhangjing Chen, Xiangwen Wu

    This paper describes the preparation of nano@lignocellulose (nano@LC) and a nano@lignocellulose/montmorillonite (nano@LC/MT) nanocomposite, as well as the capacity of the nano@LC/MT for adsorbing manganese ions from aqueous solution. The structure of nano@LC and nano@LC/MT was characterised by Fourier-transform infrared spectroscopy, X-ray diffraction, Scanning electron microscopy, and Transmission electron microscopy, which revealed that the diffraction peak of montmorillonite almost disappeared, infrared bands of the functional groups shifted, and morphology of the material changed after the formation of the composite. The optimum conditions for the adsorption of Mn(II) on the nano@LC/MT nanocomposite were investigated in detail by changing the initial Mn(II) concentration, pH, adsorption temperature, and time. The results revealed that the adsorption capacity of the nano@LC/MT nanocomposite for Mn(II) reached 628.0503 mg/g at a Mn(II) initial concentration of 900 mg/L, solution pH 5.8, adsorption temperature 55 °C, and adsorption time 160 min. Adsorption kinetics experiments revealed good agreement between the experimental data and the pseudo-second order kinetic model. The experimental data was satisfactorily fitted to the Langmuir isotherm. Adsorption-desorption results showed that nano@LC/MT exhibited excellent reusability. The adsorption mechanism was investigated through FT-IR and EDX spectroscopic analyses. The results suggested that nano@LC/MT have great potential in removing Mn(II) from water.

    更新日期:2018-07-19
  • Motion cues modulate responses to emotion in movies
    Sci. Rep. (IF 4.122) Pub Date : 2018-07-18
    Eran Dayan, Avi Barliya, Beatrice de Gelder, Talma Hendler, Rafael Malach, Tamar Flash

    Film theorists and practitioners suggest that motion can be manipulated in movie scenes to elicit emotional responses in viewers. However, our understanding of the role of motion in emotion perception remains limited. On the one hand, movies continuously depict local motion- movements of objects and humans, which are crucial for generating emotional responses. Movie scenes also frequently portray global motion, mainly induced by large camera movements, global motion being yet another source of information used by the brain during natural vision. Here we used functional MRI to elucidate the contributions of local and global motion to emotion perception during movie viewing. Subjects observed long (1 min) movie segments depicting emotional or neutral content. Brain activity in areas that showed preferential responses to emotional content was strongly linked over time with frame-wide variations in global motion, and to a lesser extent with local motion information. Similarly, stronger responses to emotional content were recorded within regions of interest whose activity was attuned to global and local motion over time. Since global motion fields are experienced during self-motion, we suggest that camera movements may induce illusory self-motion cues in viewers that interact with the movie’s narrative and with other emotional cues in generating affective responses.

    更新日期:2018-07-19
  • Electrostatic Tuning of the Ligand Binding Mechanism by Glu27 in Nitrophorin 7
    Sci. Rep. (IF 4.122) Pub Date : 2018-07-18
    Stefania Abbruzzetti, Alessandro Allegri, Axel Bidon-Chanal, Hideaki Ogata, Giancarlo Soavi, Giulio Cerullo, Stefano Bruno, Chiara Montali, F. Javier Luque, Cristiano Viappiani

    Nitrophorins (NP) 1–7 are NO-carrying heme proteins found in the saliva of the blood-sucking insect Rhodnius prolixus. The isoform NP7 displays peculiar properties, such as an abnormally high isoelectric point, the ability to bind negatively charged membranes, and a strong pH sensitivity of NO affinity. A unique trait of NP7 is the presence of Glu in position 27, which is occupied by Val in other NPs. Glu27 appears to be important for tuning the heme properties, but its influence on the pH-dependent NO release mechanism, which is assisted by a conformational change in the AB loop, remains unexplored. Here, in order to gain insight into the functional role of Glu27, we examine the effect of Glu27 → Val and Glu27 → Gln mutations on the ligand binding kinetics using CO as a model. The results reveal that annihilation of the negative charge of Glu27 upon mutation reduces the pH sensitivity of the ligand binding rate, a process that in turn depends on the ionization of Asp32. We propose that Glu27 exerts a through-space electrostatic action on Asp32, which shifts the pKa of the latter amino acid towards more acidic values thus reducing the pH sensitivity of the transition between open and closed states.

    更新日期:2018-07-19
  • Renoprotective effects of a factor Xa inhibitor: fusion of basic research and a database analysis
    Sci. Rep. (IF 4.122) Pub Date : 2018-07-18
    Yuya Horinouchi, Yasumasa Ikeda, Keijo Fukushima, Masaki Imanishi, Hirofumi Hamano, Yuki Izawa-Ishizawa, Yoshito Zamami, Kenshi Takechi, Licht Miyamoto, Hiromichi Fujino, Keisuke Ishizawa, Koichiro Tsuchiya, Toshiaki Tamaki

    Renal tubulointerstitial injury, an inflammation-associated condition, is a major cause of chronic kidney disease (CKD). Levels of activated factor X (FXa), a blood coagulation factor, are increased in various inflammatory diseases. Therefore, we investigated the protective effects of an FXa inhibitor against renal tubulointerstitial injury using unilateral ureteral obstruction (UUO) mice (a renal tubulointerstitial fibrosis model) and the Food and Drug Administration Adverse Events Reporting System (FAERS) database. The renal expression levels of FX and the FXa receptors protease-activated receptor (PAR)-1 and PAR-2 were significantly higher in UUO mice than in sham-operated mice. UUO-induced tubulointerstitial fibrosis and extracellular matrix expression were suppressed in UUO mice treated with the FXa inhibitor edoxaban. Additionally, edoxaban attenuated UUO-induced macrophage infiltration and inflammatory molecule upregulation. In an analysis of the FAERS database, there were significantly fewer reports of tubulointerstitial nephritis for patients treated with FXa inhibitors than for patients not treated with inhibitors. These results suggest that FXa inhibitors exert protective effects against CKD by inhibiting tubulointerstitial fibrosis.

    更新日期:2018-07-19
  • MDC1 methylation mediated by lysine methyltransferases EHMT1 and EHMT2 regulates active ATM accumulation flanking DNA damage sites
    Sci. Rep. (IF 4.122) Pub Date : 2018-07-18
    Sugiko Watanabe, Makoto Iimori, David Virya Chan, Eiji Hara, Hiroyuki Kitao, Yoshihiko Maehara

    Chromatin dynamics mediated by post-translational modifications play a crucial role in cellular response to genotoxic stress for the maintenance of genome integrity. MDC1 is a pivotal chromatin adaptor in DNA damage response (DDR) and its methylation is essential to recruit repair factors at DNA double-strand break (DSB) sites, yet their precise molecular mechanisms remain elusive. Here we identified euchromatic histone-lysine N-methyltransferase 1 (EHMT1) and EHMT2 as novel regulators of MDC1, which is required for the accumulation of DDR factors e.g. 53BP1 and RAP80, at the DSB sites. MDC1 interacts mainly with EHMT1, which is facilitated by DNA damage-initiated ATM signalling, and EHMT2 dominantly modulates methylation of MDC1 lysine 45. This regulatory modification promotes the interaction between MDC1 and ATM to expand activated ATM on damaged chromatin and dysfunctional telomere. These findings identify EHMT1 and EHMT2 as DDR components, with implications for genome-integrity maintenance through proper dynamic methylation of MDC1.

    更新日期:2018-07-19
  • Quantitative muscle MRI to follow up late onset Pompe patients: a prospective study
    Sci. Rep. (IF 4.122) Pub Date : 2018-07-18
    Sebastian Figueroa-Bonaparte, Jaume Llauger, Sonia Segovia, Izaskun Belmonte, Irene Pedrosa, Elena Montiel, Paula Montesinos, Javier Sánchez-González, Alicia Alonso-Jiménez, Eduard Gallardo, Isabel Illa, Jordi Díaz-Manera

    Late onset Pompe disease (LOPD) is a slow, progressive disorder characterized by skeletal and respiratory muscle weakness. Enzyme replacement therapy (ERT) slows down the progression of muscle symptoms. Reliable biomarkers are needed to follow up ERT-treated and asymptomatic LOPD patients in clinical practice. In this study, 32 LOPD patients (22 symptomatic and 10 asymptomatic) underwent muscle MRI using 3-point Dixon and were evaluated at the time of the MRI with several motor function tests and patient-reported outcome measures, and again after one year. Muscle MRI showed a significant increase of 1.7% in the fat content of the thigh muscles in symptomatic LOPD patients. In contrast, there were no noteworthy differences between muscle function tests in the same period of time. We did not observe any significant changes either in muscle MRI or in muscle function tests in asymptomatic patients over the year. We conclude that 3-point Dixon muscle MRI is a useful tool for detecting changes in muscle structure in symptomatic LOPD patients and could become part of the current follow-up protocol in daily clinics.

    更新日期:2018-07-19
  • Nuclear Norm Clustering: a promising alternative method for clustering tasks
    Sci. Rep. (IF 4.122) Pub Date : 2018-07-18
    Yi Wang, Yi Li, Chunhong Qiao, Xiaoyu Liu, Meng Hao, Yin Yao Shugart, Momiao Xiong, Li Jin

    Clustering techniques are widely used in many applications. The goal of clustering is to identify patterns or groups of similar objects within a dataset of interest. However, many cluster methods are neither robust nor sensitive to noises and outliers in real data. In this paper, we present Nuclear Norm Clustering (NNC, available at https://sourceforge.net/projects/nnc/), an algorithm that can be used in various fields as a promising alternative to the k-means clustering method. The NNC algorithm requires users to provide a data matrix M and a desired number of cluster K. We employed simulated annealing techniques to choose an optimal label vector that minimizes nuclear norm of the pooled within cluster residual matrix. To evaluate the performance of the NNC algorithm, we compared the performance of both 15 public datasets and 2 genome-wide association studies (GWAS) on psoriasis, comparing our method with other classic methods. The results indicate that NNC method has a competitive performance in terms of F-score on 15 benchmarked public datasets and 2 psoriasis GWAS datasets. So NNC is a promising alternative method for clustering tasks.

    更新日期:2018-07-19
  • Magnetoelectric Spin Wave Modulator Based On Synthetic Multiferroic Structure
    Sci. Rep. (IF 4.122) Pub Date : 2018-07-18
    Michael Balinskiy, Andres C. Chavez, Anthony Barra, Howard Chiang, Gregory P. Carman, Alexander Khitun

    We describe a spin wave modulator – spintronic device aimed to control spin wave propagation by an electric field. The modulator consists of a ferromagnetic film serving as a spin wave bus combined with a synthetic multiferroic comprising piezoelectric and magnetostrictive materials. Its operation is based on the stress-mediated coupling between the piezoelectric and magnetostrictive materials. By applying an electric field to the piezoelectric layer, the stress is produced. In turn, the stress changes the direction of the easy axis in the magnetostrictive layer and affects spin wave transport. We present experimental data on a prototype consisting of a piezoelectric [Pb(Mg1/3Nb2/3)O3](1-x) –[PbTiO3]x substrate, and 30 nm layer of magnetostrictive Ni film, where the film is attached to a 30 nm thick Ni81Fe19 spin wave bus. We report spin wave signal modulation in Ni81Fe19 layer by an electric field applied across the piezoelectric layer. The switching between the spin wave conducting and non-conducting states is achieved by applying ±0.3 MV/m electric field. We report over 300% modulation depth detected 80 μm away from the excitation port at room temperature. The demonstration of the spin wave modulator provides a new direction for spin-based device development by utilizing an electric field for spin current control.

    更新日期:2018-07-19
  • Carbon dioxide stimulates lake primary production
    Sci. Rep. (IF 4.122) Pub Date : 2018-07-18
    Mohammed Hamdan, Pär Byström, Erin R. Hotchkiss, Mohammed J. Al-Haidarey, Jenny Ask, Jan Karlsson

    Gross primary production (GPP) is a fundamental ecosystem process that sequesters carbon dioxide (CO2) and forms the resource base for higher trophic levels. Still, the relative contribution of different controls on GPP at the whole-ecosystem scale is far from resolved. Here we show, by manipulating CO2 concentrations in large-scale experimental pond ecosystems, that CO2 availability is a key driver of whole-ecosystem GPP. This result suggests we need to reformulate past conceptual models describing controls of lake ecosystem productivity and include our findings when developing models used to predict future lake ecosystem responses to environmental change.

    更新日期:2018-07-19
  • Crystal structure and substrate binding mode of ectonucleotide phosphodiesterase/pyrophosphatase-3 (NPP3)
    Sci. Rep. (IF 4.122) Pub Date : 2018-07-18
    Christoph Döhler, Matthias Zebisch, Norbert Sträter

    Ectonucleotide phosphodiesterase/pyrophosphatase-3 (NPP3) is a membrane-bound glycoprotein that regulates extracellular levels of nucleotides. NPP3 is known to contribute to the immune response on basophils by hydrolyzing ATP and to regulate the glycosyltransferase activity in Neuro2a cells. Here, we report on crystal structures of the nuclease and phosphodiesterase domains of rat NPP3 in complex with different substrates, products and substrate analogs giving insight into details of the catalytic mechanism. Complex structures with a phosphate ion, the product AMP and the substrate analog AMPNPP provide a consistent picture of the coordination of the substrate in which one zinc ion activates the threonine nucleophile whereas the other zinc ion binds the phosphate group. Co-crystal structures with the dinucleotide substrates Ap4A and UDPGlcNAc reveal a binding pocket for the larger leaving groups of these substrates. The crystal structures as well as mutational and kinetic analysis demonstrate that the larger leaving groups interact only weakly with the enzyme such that the substrate affinity is dominated by the interactions of the first nucleoside group. For this moiety, the nucleobase is stacked between Y290 and F207 and polar interactions with the protein are only formed via water molecules thus explaining the limited nucleobase selectivity.

    更新日期:2018-07-19
  • Engineering the oleaginous red yeast Rhodotorula glutinis for simultaneous β-carotene and cellulase production
    Sci. Rep. (IF 4.122) Pub Date : 2018-07-18
    Hong-Wei Pi, Marimuthu Anandharaj, Yi-Ying Kao, Yu-Ju Lin, Jui-Jen Chang, Wen-Hsiung Li

    Rhodotorula glutinis, an oleaginous red yeast, intrinsically produces several bio-products (i.e., lipids, carotenoids and enzymes) and is regarded as a potential host for biorefinery. In view of the limited available genetic engineering tools for this yeast, we have developed a useful genetic transformation method and transformed the β-carotene biosynthesis genes (crtI, crtE, crtYB and tHMG1) and cellulase genes (CBHI, CBHII, EgI, EgIII, EglA and BGS) into R. glutinis genome. The transformant P4-10-9-63Y-14B produced significantly higher β-carotene (27.13 ± 0.66 mg/g) than the wild type and also exhibited cellulase activity. Furthermore, the lipid production and salt tolerance ability of the transformants were unaffected. This is the first study to engineer the R. glutinis for simultaneous β-carotene and cellulase production. As R. glutinis can grow in sea water and can be engineered to utilize the cheaper substrates (i.e. biomass) for the production of biofuels or valuable compounds, it is a promising host for biorefinery.

    更新日期:2018-07-19
  • Automatic multiple zebrafish tracking based on improved HOG features
    Sci. Rep. (IF 4.122) Pub Date : 2018-07-18
    Yun-Xiang Bai, Shu-Hui Zhang, Zhi Fan, Xing-Yu Liu, Xin Zhao, Xi-Zeng Feng, Ming-Zhu Sun

    As an excellent model organism, zebrafish have been widely applied in many fields. The accurate identification and tracking of individuals are crucial for zebrafish shoaling behaviour analysis. However, multi-zebrafish tracking still faces many challenges. It is difficult to keep identified for a long time due to fish overlapping caused by the crossings. Here we proposed an improved Histogram of Oriented Gradient (HOG) algorithm to calculate the stable back texture feature map of zebrafish, then tracked multi-zebrafish in a fully automated fashion with low sample size, high tracking accuracy and wide applicability. The performance of the tracking algorithm was evaluated in 11 videos with different numbers and different sizes of zebrafish. In the Right-tailed hypothesis test of Wilcoxon, our method performed better than idTracker, with significant higher tracking accuracy. Throughout the video of 16 zebrafish, the training sample of each fish had only 200–500 image samples, one-fifth of the idTracker’s sample size. Furthermore, we applied the tracking algorithm to analyse the depression and hypoactivity behaviour of zebrafish shoaling. We achieved correct identification of depressed zebrafish among the fish shoal based on the accurate tracking results that could not be identified by a human.

    更新日期:2018-07-19
  • Crystal structure of an L chain optimised 14F7 anti-ganglioside Fv suggests a unique tumour-specificity through an unusual H-chain CDR3 architecture
    Sci. Rep. (IF 4.122) Pub Date : 2018-07-18
    Kaare Bjerregaard-Andersen, Hedda Johannesen, Noha Abdel-Rahman, Julie Elisabeth Heggelund, Helene Mykland Hoås, Fana Abraha, Paula A. Bousquet, Lene Støkken Høydahl, Daniel Burschowsky, Gertrudis Rojas, Stefan Oscarson, Geir Åge Løset, Ute Krengel

    Targeted cancer immunotherapy offers increased efficacy concomitantly with reduced side effects. One antibody with promising clinical potential is 14F7, which specifically recognises the NeuGc GM3 ganglioside. This antigen is found in the plasma membrane of a range of tumours, but is essentially absent from healthy human cells. 14F7 can discriminate NeuGc GM3 from the very similar NeuAc GM3, a common component of cell membranes. The molecular basis for this unique specificity is poorly understood. Here we designed and expressed 14F7-derived single-chain Fvs (scFvs), which retained the specificity of the parent antibody. Detailed expression and purification protocols are described as well as the synthesis of the NeuGc GM3 trisaccharide. The most successful scFv construct, which comprises an alternative variable light chain (VLA), allowed structure determination to 2.2 Å resolution. The structure gives insights into the conformation of the important CDR H3 loop and the suspected antigen binding site. Furthermore, the presence of VLA instead of the original VL elucidates how this subdomain indirectly stabilises the CDR H3 loop. The current work may serve as a guideline for the efficient production of scFvs for structure determination.

    更新日期:2018-07-19
  • Familial Associations in Testicular Cancer with Other Cancers
    Sci. Rep. (IF 4.122) Pub Date : 2018-07-18
    Luyao Zhang, Hongyao Yu, Otto Hemminki, Asta Försti, Kristina Sundquist, Kari Hemminki

    Familial risks for testicular cancer (TC) are among the highest of all cancers. However, data are limited for histological types of TC and for possible familial associations of TC with other cancers. We used the nationwide Swedish Family-Cancer Database for years 1958 to 2015 to analyse familial relative risks (RR) for 11,138 TC patients when first-degree relatives were diagnosed with TC or other cancer in reference to those without a family history. A total of 191 familial TCs were found, which accounted for 2.0% of all TC. The RR was 5.06 when one family member was diagnosed with TC with no significant difference between seminoma and nonseminoma. However, the risk for nonseminoma was 33.59 when two family members were affected. Internally consistent familial associations of TC, particularly of seminoma, were found with breast and nervous system cancers and melanoma. Individual significant associations were found for a number of sites, including ovarian, endometrial and prostate cancers. Our results suggest that nonseminoma may have a stronger genetic background than seminoma but seminoma shares more familial associations with discordant cancers. Clustering of TC with hormone-dependent cancers of the breast, ovary, endometrium and prostate may suggest mechanistic links and possibly gene-environment interactions.

    更新日期:2018-07-19
  • An integrative approach to discovering cryptic species within the Bemisia tabaci whitefly species complex
    Sci. Rep. (IF 4.122) Pub Date : 2018-07-18
    Soňa Vyskočilová, Wee Tek Tay, Sharon van Brunschot, Susan Seal, John Colvin

    Bemisia tabaci is a cryptic whitefly-species complex that includes some of the most damaging pests and plant-virus vectors of a diverse range of food and fibre crops worldwide. We combine experimental evidence of: (i) differences in reproductive compatibility, (ii) hybrid verification using a specific nuclear DNA marker and hybrid fertility confirmation and (iii) high-throughput sequencing-derived mitogenomes, to show that the “Mediterranean” (MED) B. tabaci comprises at least two distinct biological species; the globally invasive MED from the Mediterranean Basin and the “African silver-leafing” (ASL) from sub-Saharan Africa, which has no associated invasion records. We demonstrate that, contrary to its common name, the “ASL” does not induce squash silver-leafing symptoms and show that species delimitation based on the widely applied 3.5% partial mtCOI gene sequence divergence threshold produces discordant results, depending on the mtCOI region selected. Of the 292 published mtCOI sequences from MED/ASL groups, 158 (54%) are low quality and/or potential pseudogenes. We demonstrate fundamental deficiencies in delimiting cryptic B. tabaci species, based solely on partial sequences of a mitochondrial barcoding gene. We advocate an integrative approach to reveal the true species richness within cryptic species complexes, which is integral to the deployment of effective pest and disease management strategies.

    更新日期:2018-07-19
  • Natural Course of Clinically Isolated Syndrome: A Longitudinal Analysis Using a Markov Model
    Sci. Rep. (IF 4.122) Pub Date : 2018-07-18
    Yuli Hou, Yujuan Jia, Jingtian Hou

    Clinically isolated syndrome (CIS) refers to the initial clinical episode with symptoms suggestive of multiple sclerosis (MS). Due to limited number of long-term follow-up studies, progression pattern from CIS to more advanced stages remains unclear. In the current study, we constructed a Markov model to simulate the natural course of CIS. The model estimated the probabilities of transition from CIS to more advanced disease stages and the duration needed for the progression. The analysis showed: (1) CIS is a solid disease identity: more than 85% of the subjects with a diagnosis of CIS progress to RRMS or more advanced stages within 20 years; (2) the reduction of life expectancy in subjects with CIS is marginal.

    更新日期:2018-07-19
  • Prior object-knowledge sharpens properties of early visual feature-detectors
    Sci. Rep. (IF 4.122) Pub Date : 2018-07-18
    Christoph Teufel, Steven C. Dakin, Paul C. Fletcher

    Early stages of visual processing are carried out by neural circuits activated by simple and specific features, such as the orientation of an edge. A fundamental question in human vision is how the brain organises such intrinsically local information into meaningful properties of objects. Classic models of visual processing emphasise a one-directional flow of information from early feature-detectors to higher-level information-processing. By contrast to this view, and in line with predictive-coding models of perception, here, we provide evidence from human vision that high-level object representations dynamically interact with the earliest stages of cortical visual processing. In two experiments, we used ambiguous stimuli that, depending on the observer’s prior object-knowledge, can be perceived as either coherent objects or as a collection of meaningless patches. By manipulating object knowledge we were able to determine its impact on processing of low-level features while keeping sensory stimulation identical. Both studies demonstrate that perception of local features is facilitated in a manner consistent with an observer’s high-level object representation (i.e., with no effect on object-inconsistent features). Our results cannot be ascribed to attentional influences. Rather, they suggest that high-level object representations interact with and sharpen early feature-detectors, optimising their performance for the current perceptual context.

    更新日期:2018-07-19
  • Author Correction: Evolution of extrema features reveals optimal stimuli for biological state transitions
    Sci. Rep. (IF 4.122) Pub Date : 2018-07-18
    Joshua Chang, David Paydarfar

    A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper.

    更新日期:2018-07-19
  • Reading and Myopia: Contrast Polarity Matters
    Sci. Rep. (IF 4.122) Pub Date : 2018-07-18
    Andrea C. Aleman, Min Wang, Frank Schaeffel

    In myopia the eye grows too long, generating poorly focused retinal images when people try to look at a distance. Myopia is tightly linked to the educational status and is on the rise worldwide. It is still not clear which kind of visual experience stimulates eye growth in children and students when they study. We propose a new and perhaps unexpected reason. Work in animal models has shown that selective activation of ON or OFF pathways has also selective effects on eye growth. This is likely to be true also in humans. Using custom-developed software to process video frames of the visual environment in realtime we quantified relative ON and OFF stimulus strengths. We found that ON and OFF inputs were largely balanced in natural environments. However, black text on white paper heavily overstimulated retinal OFF pathways. Conversely, white text on black paper overstimulated ON pathways. Using optical coherence tomography (OCT) in young human subjects, we found that the choroid, the heavily perfused layer behind the retina in the eye, becomes about 16 µm thinner in only one hour when subjects read black text on white background but about 10 µm thicker when they read white text from black background. Studies both in animal models and in humans have shown that thinner choroids are associated with myopia development and thicker choroids with myopia inhibition. Therefore, reading white text from a black screen or tablet may be a way to inhibit myopia, while conventional black text on white background may stimulate myopia.

    更新日期:2018-07-19
  • Paeonin extracted from potatoes protects gastric epithelial cells from H2O2-induced oxidative damage in vitro by PI3K/Akt-mediated Nrf2 signaling pathway
    Sci. Rep. (IF 4.122) Pub Date : 2018-07-18
    Jiping Xiao, Bo Chen, Qiong Wang, Lijuan Yang, Huachun Guo

    In this study, it is aimed to investigate the antioxidant mechanism of new extracts from potatoes. Four pigments, namely, Petunin, Paeonin, Malvidin and Pelargonidin, were extracted from potatoes by high performance liquid chromatography (HPLC). Our results showed that the cellular morphology and cell viability were significantly altered in gastric mucosal epithelial cells (GES-1) treated with different hydrogen peroxide (H2O2) concentrations over time (P < 0.05). Paeonin presented the strongest anti-oxidative effects on H2O2-treated cells, in both a dose- and time-dependent manner, determined by ARE-luciferase activity and HO-1 mRNA expression. After pre-treatment with Paeonin in H2O2-exposed cells, Keap1, Nrf2, HO-1 and NQO1 protein expressions were remarkably up-regulated. Furthermore, immunostaining of Nrf2 expression was obviously elevated in the H2O2 + Paeonin group over time. The GSH content in the H2O2 + Paeonin group was notably lower than that in the H2O2 + Paeonin + GSK690693 group. Paeonin promoted cell cycle with augmented Cyclin D1 and p27 protein expressions. Moreover, Paeonin suppressed apoptosis with increased Bcl2, total Caspase3 and total Caspase8 protein expressions and decreased Bax, p-Caspase3 and p-Caspase8 protein expression in H2O2-treated cells. These results suggested that Paeonin might exert an anti-oxidative role by activating Nrf2 signaling pathway with the changes of cell cycle and apoptosis.

    更新日期:2018-07-19
  • Ranking genome-wide correlation measurements improves microarray and RNA-seq based global and targeted co-expression networks
    Sci. Rep. (IF 4.122) Pub Date : 2018-07-18
    Franziska Liesecke, Dimitri Daudu, Rodolphe Dugé de Bernonville, Sébastien Besseau, Marc Clastre, Vincent Courdavault, Johan-Owen de Craene, Joel Crèche, Nathalie Giglioli-Guivarc’h, Gaëlle Glévarec, Olivier Pichon, Thomas Dugé de Bernonville

    Co-expression networks are essential tools to infer biological associations between gene products and predict gene annotation. Global networks can be analyzed at the transcriptome-wide scale or after querying them with a set of guide genes to capture the transcriptional landscape of a given pathway in a process named Pathway Level Coexpression (PLC). A critical step in network construction remains the definition of gene co-expression. In the present work, we compared how Pearson Correlation Coefficient (PCC), Spearman Correlation Coefficient (SCC), their respective ranked values (Highest Reciprocal Rank (HRR)), Mutual Information (MI) and Partial Correlations (PC) performed on global networks and PLCs. This evaluation was conducted on the model plant Arabidopsis thaliana using microarray and differently pre-processed RNA-seq datasets. We particularly evaluated how dataset × distance measurement combinations performed in 5 PLCs corresponding to 4 well described plant metabolic pathways (phenylpropanoid, carbohydrate, fatty acid and terpene metabolisms) and the cytokinin signaling pathway. Our present work highlights how PCC ranked with HRR is better suited for global network construction and PLC with microarray and RNA-seq data than other distance methods, especially to cluster genes in partitions similar to biological subpathways.

    更新日期:2018-07-19
Some contents have been Reproduced with permission of the American Chemical Society.
Some contents have been Reproduced by permission of The Royal Society of Chemistry.
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