bluuebunny/crossref_metadata_2025 huggingface dataset:
New Methods of Morphometric Analyses on Scyphozoan Jellyfish Statoliths Including the first Direct Evidence for Statolith Growth Using Calcein as a Fluorescent Marker
Authors: Sötje Ilka , Dishon Tamar , Hoffmann Frank , Holst Sabine
Published: March 2017

Statoliths are the only hard structures in the gelatinous bell of most scyphozoan medusae and investigations on these structures could promote investigations of the understudied population dynamics and phylogeny of jellyfish. We examined the statoliths ofAurelia auritajellyfish of different ages by light microscopic and microtomographic measurements supplemented by scanning electron microscopy. The morphometric analyses confirmed that statolith numbers and sizes increase during jellyfish development and revealed that newly-formed statoliths had similar shapes that may change during statolith growth. Nevertheless, most statoliths had a typical compact rod shape with an aspect ratio of 1–2.5 at all ages and we suggest that the composition of statolith shapes may be taxa specific. We developed a new approach allowing exact measurements of statolith growth for the first time. The application of calcein as a fluorescent marker resulted in clear fluorescent lines within the statoliths, allowing calculations of the statolith side face growth increments (0.1µm/day;n=252). A single-crystal analysis revealed that the calcein incubation did not affect the statolith crystal structure. In conclusion, calcein labeling is an excellent method to follow the growth of bassanite statoliths.
THE LOGIC OF JOINT ABILITY IN TWO-PLAYER TACIT GAMES
Authors: HAWKE PETER
Published: March 2017

Logics of joint strategic ability have recently received attention, with arguably the most influential being those in a family that includes Coalition Logic (CL) and Alternating-time Temporal Logic (ATL). Notably, both CL and ATL bypass the epistemic issues that underpin Schelling-typecoordination problems, by apparently relying on the meta-level assumption of (perfectly reliable) communication between cooperating rational agents. Yet such epistemic issues arise naturally in settings relevant to ATL and CL: these logics are standardly interpreted on structures where agents move simultaneously, opening the possibility that an agent cannot foresee the concurrent choices of other agents. In this paper we introduce a variant of CL we callTwo-Player Strategic Coordination Logic(SCL2). The key novelty of this framework is an operator for capturing coalitional ability when the cooperating agents cannot share strategic information. We identify significant differences in the expressive power and validities of SCL2and CL2, and present a sound and complete axiomatization for SCL2. We briefly address conceptual challenges when shifting attention to games with more than two players and stronger notions of rationality.
Life, lifestyle and location: examining the complexities of psychological distress in young adult Indigenous and non-Indigenous Australians
Authors: Davison B. , Nagel T. , Singh G. R.
Published: March 2017

Mental health is fundamental to an individual’s health and well-being. Mental health disorders affect a substantial portion of the Australian population, with the most vulnerable time in adolescence and young adulthood. Indigenous Australians fare worse than other Australians on almost every measure of physical and mental health. Cross-sectional data from young adults (21–27 years) participating in the Life Course Program, Northern Territory, Australia, is presented. Rates of psychological distress were high in remote and urban residing Indigenous and urban non-Indigenous young adults. This rate was more pronounced in young women, particularly in Indigenous remote and urban residing women. Young adults with high psychological distress also had lower levels of positive well-being, higher perceived stress levels, experienced a higher number of major life events and were at an increased risk of suicidal ideation and/or self-harm. This study supports the need for a continued focus on early screening and treatment at this vulnerable age. The significant association seen between psychological distress and other markers of emotional well-being, particularly risk of suicidal ideation and/or self-harm, highlights the need for a holistic approach to mental health assessment and treatment. A concerted focus on improving the environs of young adults by lowering levels of stress, improving access to adequate housing, educational and employment opportunity, will assist in improving the emotional health of young adults.
Realization of palladium-based optomechanical cantilever hydrogen sensor
Authors: McKeown Steven J. , Wang Xiaozhen , Yu Xin , Goddard Lynford L.
Published: March 2017

Hydrogen has attracted attention as an alternative fuel source and as an energy storage medium. However, the flammability of hydrogen at low concentrations makes it a safety concern. Thus, gas concentration measurements are a vital safety issue. Here we present the experimental realization of a palladium thin film cantilever optomechanical hydrogen gas sensor. We measured the instantaneous shape of the cantilever to nanometer-level accuracy using diffraction phase microscopy. Thus, we were able to quantify changes in the curvature of the cantilever as a function of hydrogen concentration and observed that the sensor’s minimum detection limit was well below the 250 p.p.m. limit of our test equipment. Using the change in curvature versus the hydrogen curve for calibration, we accurately determined the hydrogen concentrations for a random sequence of exposures. In addition, we calculated the change in film stress as a function of hydrogen concentration and observed a greater sensitivity at lower concentrations.
Macrophages induce AKT/β-catenin-dependent Lgr5+ stem cell activation and hair follicle regeneration through TNF
Authors: Wang Xusheng , Chen Haiyan , Tian Ruiyun , Zhang Yiling , Drutskaya Marina S. , Wang Chengmei , Ge Jianfeng , Fan Zhimeng , Kong Deqiang , Wang Xiaoxiao , Cai Ting , Zhou Ying , Wang Jingwen , Wang Jinmei , Wang Shan , Qin Zhihai , Jia Huanhuan , Wu Yue , Liu Jia , Nedospasov Sergei A. , Tredget Edward E. , Lin Mei , Liu Jianjun , Jiang Yuyang , Wu Yaojiong
Published: March 2017

Skin stem cells can regenerate epidermal appendages; however, hair follicles (HF) lost as a result of injury are barely regenerated. Here we show that macrophages in wounds activate HF stem cells, leading to telogen–anagen transition (TAT) around the wound and de novo HF regeneration, mostly through TNF signalling. Both TNF knockout and overexpression attenuate HF neogenesis in wounds, suggesting dose-dependent induction of HF neogenesis by TNF, which is consistent with TNF-induced AKT signalling in epidermal stem cells in vitro. TNF-induced β-catenin accumulation is dependent on AKT but not Wnt signalling. Inhibition of PI3K/AKT blocks depilation-induced HF TAT. Notably, Pten loss in Lgr5+ HF stem cells results in HF TAT independent of injury and promotes HF neogenesis after wounding. Thus, our results suggest that macrophage-TNF-induced AKT/β-catenin signalling in Lgr5+ HF stem cells has a crucial role in promoting HF cycling and neogenesis after wounding.
Enhancing titres of therapeutic viral vectors using the transgene repression in vector production (TRiP) system
Authors: Maunder H. E. , Wright J. , Kolli B. R. , Vieira C. R. , Mkandawire T. T. , Tatoris S. , Kennedy V. , Iqball S. , Devarajan G. , Ellis S. , Lad Y. , Clarkson N. G. , Mitrophanous K. A. , Farley D. C.
Published: March 2017

A key challenge in the field of therapeutic viral vector/vaccine manufacturing is maximizing production. For most vector platforms, the ‘benchmark’ vector titres are achieved with inert reporter genes. However, expression of therapeutic transgenes can often adversely affect vector titres due to biological effects on cell metabolism and/or on the vector virion itself. Here, we exemplify the novel ‘Transgene Repression In vector Production’ (TRiP) system for the production of both RNA- and DNA-based viral vectors. The TRiP system utilizes a translational block of one or more transgenes by employing the bacterial tryptophan RNA-binding attenuation protein (TRAP), which binds its target RNA sequence close to the transgene initiation codon. We report enhancement of titres of lentiviral vectors expressing Cyclo-oxygenase-2 by 600-fold, and adenoviral vectors expressing the pro-apoptotic gene Bax by >150,000-fold. The TRiP system is transgene-independent and will be a particularly useful platform in the clinical development of viral vectors expressing problematic transgenes.
Local delivery of novel MRTF/SRF inhibitors prevents scar tissue formation in a preclinical model of fibrosis
Authors: Yu-Wai-Man Cynthia , Spencer-Dene Bradley , Lee Richard M. H. , Hutchings Kim , Lisabeth Erika M. , Treisman Richard , Bailly Maryse , Larsen Scott D. , Neubig Richard R. , Khaw Peng T.
Published: March 2017

The myocardin-related transcription factor/serum response factor (MRTF/SRF) pathway represents a promising therapeutic target to prevent fibrosis. We have tested the effects of new pharmacological inhibitors of MRTF/SRF signalling in a preclinical model of fibrosis. CCG-222740, a novel MRTF/SRF inhibitor, markedly decreased SRF reporter gene activity and showed a greater inhibitory effect on MRTF/SRF target genes than the previously described MRTF-A inhibitor CCG-203971. CCG-222740 was also five times more potent, with an IC50 of 5 μM, in a fibroblast-mediated collagen contraction assay, was less cytotoxic, and a more potent inhibitor of alpha-smooth muscle actin protein expression than CCG-203971. Local delivery of CCG-222740 and CCG-203971 in a validated and clinically relevant rabbit model of scar tissue formation after glaucoma filtration surgery increased the long-term success of the surgery by 67% (P < 0.0005) and 33% (P < 0.01), respectively, and significantly decreased fibrosis and scarring histologically. Unlike mitomycin-C, neither CCG-222740 nor CCG-203971 caused any detectable epithelial toxicity or systemic side effects with very low drug levels measured in the aqueous, vitreous, and serum. We conclude that inhibitors of MRTF/SRF-regulated gene transcription such as CCG-222740, potentially represent a new therapeutic strategy to prevent scar tissue formation in the eye and other tissues.
Molecular Characteristics and Serodiagnostic Potential of Dihydrofolate Reductase from Echinococcus granulosus
Authors: Song Xingju , Hu Dandan , Yan Min , Wang Yu , Wang Ning , Gu Xiaobin , Yang Guangyou
Published: March 2017

The larval stage of Echinococcus granulosus causes cystic echinococcosis (CE), a neglected tropical disease that leads to morbidity and mortality in humans and livestock worldwide. Here, we identified and characterized dihydrofolate reductase (Eg-DHFR) from E. granulosus, and evaluated its potential as a diagnostic antigen for sheep CE. Comparison between mammalian (host) DHFR and Eg-DHFR indicates that 45.7% of the 35 active site residues are different. Immunolocalisation analysis showed that native Eg-DHFR was widely distributed in all life-cycle stages of E. granulosus. Recombinant Eg-DHFR (rEg-DHFR) showed typical DHFR enzymatic parameters towards substrate, and was very sensitive to inhibition by methotrexate (IC50 = 27.75 ± 1.03 nM) and aminopterin (IC50 = 63.67 ± 6.76 nM). However, inhibition of DHFR exhibited little protoscolicidal effect in vitro. As there is no reliable method to monitor sheep CE, the immunogenicity of rEg-DHFR was detected, and we developed an indirect ELISA (iELISA) for CE serodiagnosis. The iELISA exhibited diagnostic specificity of 89.58%, diagnostic sensitivity of 95.83%, and the diagnostic accuracy was 91.67% compared with necropsy. Cross-reactivity assay showed analytical specificity of 85.7%. These suggest that rEg-DHFR is an effective antigen for the diagnosis of sheep CE.
Carbon Dots’ Antiviral Functions Against Noroviruses
Authors: Dong Xiuli , Moyer Marsha M. , Yang Fan , Sun Ya-Ping , Yang Liju
Published: March 2017

This study reported the first assessment of carbon dots’ (CDots) antiviral activity to human norovirus virus-like-particles (VLPs), GI.1 and GII.4 VLPs. CDots with different surface passivation molecules, 2,2′-(ethylenedioxy)bis(ethylamine) (EDA)-CDots and 3-ethoxypropylamine (EPA)-CDots, were synthesized and evaluated. The results indicated both EDA- and EPA- CDots were highly effective to inhibit both strains of VLPs’ bindings to histo-blood group antigens (HBGA) receptors on human cells at CDots concentration of 5 µg/mL, with EDA-CDots achieving 100% inhibition and EPA CDots achieving 85–99% inhibition. At low CDots concentration (2 µg/mL), positively charged EDA-CDots exhibited higher inhibitory effect (~82%) than non-charged EPA-CDots (~60%), suggesting the surface charge status of CDots played a role in the interactions between CDots and the negatively charged VLPs. Both types of CDots also exhibited inhibitory effect on VLP’s binding to their respective antibodies, but much less effective than those to HBGA binding. After CDots treatments, VLPs remained intact, and no degradation was observed on VLPs’ capsid proteins. Taken together, the observed antiviral effects of CDots on noroviruses were mainly through the effective inhibition of VLPs’ binding to HBGA receptors and moderate inhibition of VLPs’ binding to their antibodies, without affecting the integrity of viral capsid protein and the viral particle.
Transcriptomic profiling of 39 commonly-used neuroblastoma cell lines
Authors: Harenza Jo Lynne , Diamond Maura A. , Adams Rebecca N. , Song Michael M. , Davidson Heather L. , Hart Lori S. , Dent Maiah H. , Fortina Paolo , Reynolds C. Patrick , Maris John M.
Published: March 2017

Neuroblastoma cell lines are an important and cost-effective model used to study oncogenic drivers of the disease. While many of these cell lines have been previously characterized with SNP, methylation, and/or mRNA expression microarrays, there has not been an effort to comprehensively sequence these cell lines. Here, we present raw whole transcriptome data generated by RNA sequencing of 39 commonly-used neuroblastoma cell lines. These data can be used to perform differential expression analysis based on a genetic aberration or phenotype in neuroblastoma (e.g., MYCN amplification status, ALK mutation status, chromosome arm 1p, 11q and/or 17q status, sensitivity to pharmacologic perturbation). Additionally, we designed this experiment to enable structural variant and/or long-noncoding RNA analysis across these cell lines. Finally, as more DNase/ATAC and histone/transcription factor ChIP sequencing is performed in these cell lines, our RNA-Seq data will be an important complement to inform transcriptional targets as well as regulatory (enhancer or repressor) elements in neuroblastoma.
Long-term growth data of Escherichia coli at a single-cell level
Authors: Tanouchi Yu , Pai Anand , Park Heungwon , Huang Shuqiang , Buchler Nicolas E. , You Lingchong
Published: March 2017

Long-term, single-cell measurement of bacterial growth is extremely valuable information, particularly in the study of homeostatic aspects such as cell-size and growth rate control. Such measurement has recently become possible due to the development of microfluidic technology. Here we present data from single-cell measurements of Escherichia coli growth over 70 generations obtained for three different growth conditions. The data were recorded every minute, and contain time course data of cell length and fluorescent intensity of constitutively expressed yellow fluorescent protein.
Metagenome sequencing and 98 microbial genomes from Juan de Fuca Ridge flank subsurface fluids
Authors: Jungbluth Sean P. , Amend Jan P. , Rappé Michael S.
Published: March 2017

The global deep subsurface biosphere is one of the largest reservoirs for microbial life on our planet. This study takes advantage of new sampling technologies and couples them with improvements to DNA sequencing and associated informatics tools to reconstruct the genomes of uncultivated Bacteria and Archaea from fluids collected deep within the Juan de Fuca Ridge subseafloor. Here, we generated two metagenomes from borehole observatories located 311 meters apart and, using binning tools, retrieved 98 genomes from metagenomes (GFMs). Of the GFMs, 31 were estimated to be >90% complete, while an additional 17 were >70% complete. Phylogenomic analysis revealed 53 bacterial and 45 archaeal GFMs, of which nearly all were distantly related to known cultivated isolates. In the GFMs, abundant Bacteria included Chloroflexi, Nitrospirae, Acetothermia (OP1), EM3, Aminicenantes (OP8), Gammaproteobacteria, and Deltaproteobacteria, while abundant Archaea included Archaeoglobi, Bathyarchaeota (MCG), and Marine Benthic Group E (MBG-E). These data are the first GFMs reconstructed from the deep basaltic subseafloor biosphere, and provide a dataset available for further interrogation.
Developing a dataset to track aid for reproductive, maternal, newborn and child health, 2003–2013
Authors: Grollman Christopher , Arregoces Leonardo , Martinez-Alvarez Melisa , Pitt Catherine , Powell-Jackson Timothy , Hsu Justine , Greco Giulia , Borghi Josephine
Published: March 2017

We created a dataset to generate estimates of donor-reported ‘official development assistance’ and private grants (ODA+) to reproductive, maternal, newborn and child health (RMNCH) by donor, recipient country and activity type over the period 2003–2013. We collected disbursement information from the Organisation for Economic Co-operation and Development Creditor Reporting System (CRS) in January 2015. All 2.1 million records across all sectors were coded based on donor name, project title, short and long descriptions, and CRS code describing the purpose of the disbursement. We classified records according to the degree to which they would promote attainment of Millennium Development Goals 4 and 5 (reproductive and sexual health, maternal and newborn health, and child health). We also classified records according to whether they supported prenatal and neonatal health (PNH). The dataset includes project funding as well as allocating shares of general budget support, health sector support and basket funding. The data can be used to analyse resource flows to RMNCH or to other purposes or beneficiaries of ODA+.
The global avian invasions atlas, a database of alien bird distributions worldwide
Authors: Dyer Ellie E. , Redding David W. , Blackburn Tim M.
Published: March 2017

The introduction of species to locations where they do not naturally occur (termed aliens) can have far-reaching and unpredictable environmental and economic consequences. Therefore there is a strong incentive to stem the tide of alien species introduction and spread. In order to identify broad patterns and processes of alien invasions, a spatially referenced, global dataset on the historical introductions and alien distributions of a complete taxonomic group is required. Here we present the Global Avian Invasions Atlas (GAVIA)—a new spatial and temporal dataset comprising 27,723 distribution records for 971 alien bird species introduced to 230 countries and administrative areas spanning the period 6000BCE—AD2014. GAVIA was initiated to provide a unified database of records on alien bird introductions, incorporating records from all stages of invasion, including introductions that have failed as well as those that have succeeded. GAVIA represents the most comprehensive resource on the global distribution of alien species in any major taxon, allowing the spatial and temporal dynamics of alien bird distributions to be examined.
Low Dimensional String-like Relaxation Underpins Superionic Conduction in Fluorites and Related Structures
Authors: Annamareddy Ajay , Eapen Jacob
Published: March 2017

Among the superionic conductors that show a Faraday transition – the continuous increase in the ionic conductivity over a range of temperatures – the fluorite structures have enjoyed incisive examinations over the past four decades; yet the fundamental nature of superionicity has remained largely inconclusive. Departing from the traditional quasi-static defect framework, we provide weighty evidence for string-like dynamical structures that govern the fast ion conduction process in fluorites. We show that lower temperatures encourage the growth of longer but slowly relaxing strings and vice-versa – a direct manifestation of heterogeneous dynamics. Remarkably, the ionic conductivity is inversely correlated to the lifetime of the ions that participate in the strings and not explicitly to the ion population. Our analysis methodology, which resolves a long-standing disagreement on defect structures and the mechanism of ionic transport in fcc fluorite structures, is well-positioned to describe the dynamics of low dimensional conduction in a larger class of superionic conductors.
Stressor exposure has prolonged effects on colonic microbial community structure in Citrobacter rodentium-challenged mice
Authors: Galley Jeffrey D. , Mackos Amy R. , Varaljay Vanessa A. , Bailey Michael T.
Published: March 2017

Stressor exposure significantly affects the colonic mucosa-associated microbiota, and exacerbates Citrobacter rodentium-induced inflammation, effects that can be attenuated with probiotic Lactobacillus reuteri. This study assessed the structure of the colonic mucosa-associated microbiota in mice exposed to a social stressor (called social disruption), as well as non-stressed control mice, during challenge with the colonic pathogen C. rodentium. Mice were exposed to the social stressor or home cage control conditions for six consecutive days and all mice were challenged with C. rodentium immediately following the first exposure to the stressor. In addition, mice received probiotic L. reuteri, or vehicle as a control, via oral gavage following each stressor exposure. The stressor-exposed mice had significant differences in microbial community composition compared to non-stressed control mice. This difference was first evident following the six-cycle exposure to the stressor, on Day 6 post-C. rodentium challenge, and persisted for up to 19 days after stressor termination. Mice exposed to the stressor had different microbial community composition regardless of whether they were treated with L. reuteri or treated with vehicle as a control. These data indicate that stressor exposure affects the colonic microbiota during challenge with C. rodentium, and that these effects are long-lasting and not attenuated by probiotic L. reuteri.
Environmental DNA in subterranean biology: range extension and taxonomic implications for Proteus
Authors: Gorički Špela , Stanković David , Snoj Aleš , Kuntner Matjaž , Jeffery William R. , Trontelj Peter , Pavićević Miloš , Grizelj Zlatko , Năpăruş-Aljančič Magdalena , Aljančič Gregor
Published: March 2017

Europe’s obligate cave-dwelling amphibianProteus anguinusinhabits subterranean waters of the north-western Balkan Peninsula. Because only fragments of its habitat are accessible to humans, this endangered salamander’s exact distribution has been difficult to establish. Here we introduce a quantitative real time polymerase chain reaction-based environmental DNA (eDNA) approach to detect the presence ofProteususing water samples collected from karst springs, wells or caves. In a survey conducted along the southern limit of its known range, we established a likely presence ofProteusat seven new sites, extending its range to Montenegro. Next, using specific molecular probes to discriminate the rare black morph ofProteusfrom the closely related white morph, we detected its eDNA at five new sites, thus more than doubling the known number of sites. In one of these we found both black and whiteProteuseDNA together. This finding suggests that the two morphs may live in contact with each other in the same body of groundwater and that they may be reproductively isolated species. Our results show that the eDNA approach is suitable and efficient in addressing questions in biogeography, evolution, taxonomy and conservation of the cryptic subterranean fauna.
Synergistic Effects of Micro-electrolysis-Photocatalysis on Water Treatment and Fish Performance in Saline Recirculating Aquaculture System
Authors: Ye Zhangying , Wang Shuo , Gao Weishan , Li Haijun , Pei Luowei , Shen Mingwei , Zhu Songming
Published: March 2017

A new physico-chemical process for TAN (total ammonia nitrogen) removal and disinfection is introduced in saline recirculating aquaculture system (RAS), in which the biofilter is replaced with an integrated electrolysis cell and an activated carbon filter. The electrolysis cell which is based on micro current electrolysis combined with UV-light was self-designed. After the fundamental research, a small pilot scale RAS was operated for 30 days to verify the technical feasibility. The system was stocked by 42 GIFT tilapia (Oreochromis niloticus) fish with the rearing density of 13 kg/m3. During the experiments, the TAN concentration remained below 1.0 mg/L. The nitrite concentration was lower than 0.2 mg/L and the nitrate concentration had increased continuously to 12.79 mg/L at the end. Furthermore, the concentration of residual chlorine in culture ponds remained below 0.3 mg/L, ORP maintained slight fluctuations in the range of 190~240 mV, and pH of the water showed the downtrend. Tilapia weight increased constantly to 339.3 ± 10 g. For disinfection, the active chlorine generated by electrochemical treatment caused Escherichia coli inactivation. Enzyme activity assay indicated that the activity of glutamate dehydrogenase, carbonic anhydrase and glutamic pyruvic transaminase increased within the normal range. The preliminary feasibility was verified by using this physico-chemical technology in the RAS.
Elevated angiopoietin 2 in aqueous of patients with neovascular age related macular degeneration correlates with disease severity at presentation
Authors: Ng Danny S. , Yip Yolanda W. , Bakthavatsalam Malini , Chen Li J. , Ng Tse K. , Lai Timothy Y. , Pang Calvin P. , Brelén Mårten E.
Published: March 2017

Angiopoietin 2 (ANG2) is a proangiogenic cytokine which may have an implication in neovascular age related macular degeneration (nAMD). In 24 eyes of 24 subjects presenting with treatment naïve nAMD and 26 eyes of 26 control patients, aqueous humor samples were collected at the time of intervention (intravitreal injection of anti-vascular endothelial growth factor or cataract extraction). Best corrected visual acuity (BCVA) with and central macular thickness (CMT) using optical coherence tomography (OCT) were measured before each injection in the nAMD group. Aqueous cytokine levels were determined by immunoassay using a multiplex array (Quansys Biosciences, Logan, UT). Levels of ANG2 in the aqueous were significantly higher in nAMD patients than those of the control group (p < 0.0001), so were hepatocyte growth factor (HGF), interleukin-8 (IL-8) and tissue inhibitor of metalloproteinase 1 (TIMP 1), all with p < 0.001. ANG2 correlated with worse BCVA (r = 0.44, p-value = 0.027) and greater CMT (r = 0.66, p-value < 0.0001) on optical coherence tomography (OCT). ANG2 is upregulated in patients with nAMD and correlates with severity of disease at presentation.
Potential of biosynthesized silver nanoparticles using Stenotrophomonas sp. BHU-S7 (MTCC 5978) for management of soil-borne and foliar phytopathogens
Authors: Mishra Sandhya , Singh Braj Raj , Naqvi Alim H. , Singh H. B.
Published: March 2017

Stenotrophomonas sp. is emerging as a popular microbe of global concern with various potential ecological roles. Biosynthesis of gold and silver nanoparticles (AgNPs) using this bacterial strain has shown promising applications in life sciences. However, there is no report on efficient agricultural applications of biosynthesized AgNPs using Stenotrophomonas sp. In this regard, successful biosynthesis of AgNPs using Stenotrophomonas sp. BHU-S7 (MTCC 5978) was monitored by Uv-visible spectrum showing surface plasmon resonance (SPR) peak at 440 nm. The biosynthesized AgNPs were spherical with an average mean size of ~12 nm. The antifungal efficacy of biosynthesized AgNPs against foliar and soil-borne phytopathogens was observed. The inhibitory impact of AgNPs (2, 4, 10 μg/ml) on conidial germination was recorded under in vitro conditions. Interestingly, sclerotia of Sclerotium rolfsii exposed to AgNPs failed to germinate on PDA medium and in soil system. Moreover, AgNPs treatment successfully managed collar rot of chickpea caused by S. rolfsii under greenhouse conditions. The reduced sclerotia germination, phenolic acids induction, altered lignification and H2O2 production was observed to be the probable mechanisms providing protection to chickpea against S. rolfsii. Our data revealed that AgNPs treated plants are better equipped to cope with pathogen challenge pointing towards their robust applications in plant disease management.
The effects of self-selected light-dark cycles and social constraints on human sleep and circadian timing: a modeling approach
Authors: Skeldon Anne C. , Phillips Andrew J. K. , Dijk Derk-Jan
Published: March 2017

Why do we go to sleep late and struggle to wake up on time? Historically, light-dark cycles were dictated by the solar day, but now humans can extend light exposure by switching on artificial lights. We use a mathematical model incorporating effects of light, circadian rhythmicity and sleep homeostasis to provide a quantitative theoretical framework to understand effects of modern patterns of light consumption on the human circadian system. The model shows that without artificial light humans wakeup at dawn. Artificial light delays circadian rhythmicity and preferred sleep timing and compromises synchronisation to the solar day when wake-times are not enforced. When wake-times are enforced by social constraints, such as work or school, artificial light induces a mismatch between sleep timing and circadian rhythmicity (‘social jet-lag’). The model implies that developmental changes in sleep homeostasis and circadian amplitude make adolescents particularly sensitive to effects of light consumption. The model predicts that ameliorating social jet-lag is more effectively achieved by reducing evening light consumption than by delaying social constraints, particularly in individuals with slow circadian clocks or when imposed wake-times occur after sunrise. These theory-informed predictions may aid design of interventions to prevent and treat circadian rhythm-sleep disorders and social jet-lag.
Comprehensive track-structure based evaluation of DNA damage by light ions from radiotherapy-relevant energies down to stopping
Authors: Friedland W. , Schmitt E. , Kundrát P. , Dingfelder M. , Baiocco G. , Barbieri S. , Ottolenghi A.
Published: March 2017

Track structures and resulting DNA damage in human cells have been simulated for hydrogen, helium, carbon, nitrogen, oxygen and neon ions with 0.25–256 MeV/u energy. The needed ion interaction cross sections have been scaled from those of hydrogen; Barkas scaling formula has been refined, extending its applicability down to about 10 keV/u, and validated against established stopping power data. Linear energy transfer (LET) has been scored from energy deposits in a cell nucleus; for very low-energy ions, it has been defined locally within thin slabs. The simulations show that protons and helium ions induce more DNA damage than heavier ions do at the same LET. With increasing LET, less DNA strand breaks are formed per unit dose, but due to their clustering the yields of double-strand breaks (DSB) increase, up to saturation around 300 keV/μm. Also individual DSB tend to cluster; DSB clusters peak around 500 keV/μm, while DSB multiplicities per cluster steadily increase with LET. Remarkably similar to patterns known from cell survival studies, LET-dependencies with pronounced maxima around 100–200 keV/μm occur on nanometre scale for sites that contain one or more DSB, and on micrometre scale for megabasepair-sized DNA fragments.
Microstructural tissue-engineering in the rachis and barbs of bird feathers
Authors: Lingham-Soliar Theagarten
Published: March 2017

Feathers do not have to be especially strong but they do need to be stiff and at the same time resilient and to have a high work of fracture. Syncitial barbule fibres are the highest size-class of continuous filaments in the cortex of the rachis of the feather. However, the rachis can be treated as a generalized cone of rapidly diminishing volume. This means that hundreds of syncitial barbule fibres of the rachis may have to be terminated before reaching the tip – creating potentially thousands of inherently fatal crack-like defects. Here I report a new microstructural architecture of the feather cortex in which most syncitial barbule fibres deviate to the right and left edges of the feather rachis from far within its borders and extend into the barbs, side branches of the rachis, as continuous filaments. This novel morphology adds significantly to knowledge of β-keratin self-assembly in the feather and helps solve the potential problem of fatal crack-like defects in the rachidial cortex. Furthermore, this new complexity, consistent with biology’s robust multi-functionality, solves two biomechanical problems at a stroke. Feather barbs deeply ‘rooted’ within the rachis are also able to better withstand the aerodynamic forces to which they are subjected.
Nephronectin plays critical roles in Sox2 expression and proliferation in dental epithelial stem cells via EGF-like repeat domains
Authors: Arai Chieko , Yoshizaki Keigo , Miyazaki Kanako , Saito Kan , Yamada Aya , Han Xue , Funada Keita , Fukumoto Emiko , Haruyama Naoto , Iwamoto Tsutomu , Takahashi Ichiro , Fukumoto Satoshi
Published: March 2017

Tooth development is initiated by epithelial-mesenchymal interactions via basement membrane (BM) and growth factors. In the present study, we found that nephronectin (Npnt), a component of the BM, is highly expressed in the developing tooth. Npnt localizes in the BM on the buccal side of the tooth germ and shows an expression pattern opposite that of the dental epithelial stem cell marker Sox2. To identify the roles of Npnt during tooth development, we performed knockdown and overexpression experiments using ex vivo organ and dental epithelial cell cultures. Our findings showed that loss of Npnt induced ectopic Sox2-positive cells and reduced tooth germ size. Over expression of Npnt showed increased proliferation, whereas the number of Sox2-positive cells was decreased in dental epithelial cells. Npnt contains 5 EGF-like repeat domains, as well as an RGD sequence and MAM domain. We found that the EGF-like repeats are critical for Sox2 expression and cell proliferation. Furthermore, Npnt activated the EGF receptor (EGFR) via the EGF-like repeat domains and induced the PI3K-Akt signaling pathway. Our results indicate that Npnt plays a critical scaffold role in dental epithelial stem cell differentiation and proliferation, and regulates Sox2 expression during tooth development.
Fundamental properties of resonances
Authors: Ceci S. , Hadžimehmedović M. , Osmanović H. , Percan A. , Zauner B.
Published: March 2017

All resonances, from hydrogen nuclei excited by the high-energy gamma rays in deep space to newly discovered particles produced in Large Hadron Collider, should be described by the same fundamental physical quantities. However, two distinct sets of properties are used to describe resonances: the pole parameters (complex pole position and residue) and the Breit-Wigner parameters (mass, width, and branching fractions). There is an ongoing decades-old debate on which one of them should be abandoned. In this study of nucleon resonances appearing in the elastic pion-nucleon scattering we discover an intricate interplay of the parameters from both sets, and realize that neither set is completely independent or fundamental on its own.
WT1 expression in breast cancer disrupts the epithelial/mesenchymal balance of tumour cells and correlates with the metabolic response to docetaxel
Authors: Artibani Mara , Sims Andrew H. , Slight Joan , Aitken Stuart , Thornburn Anna , Muir Morwenna , Brunton Valerie G. , Del-Pozo Jorge , Morrison Linda R. , Katz Elad , Hastie Nicholas D. , Hohenstein Peter
Published: March 2017

WT1 is a transcription factor which regulates the epithelial-mesenchymal balance during embryonic development and, if mutated, can lead to the formation of Wilms’ tumour, the most common paediatric kidney cancer. Its expression has also been reported in several adult tumour types, including breast cancer, and usually correlates with poor outcome. However, published data is inconsistent and the role of WT1 in this malignancy remains unclear. Here we provide a complete study of WT1 expression across different breast cancer subtypes as well as isoform specific expression analysis. Using in vitro cell lines, clinical samples and publicly available gene expression datasets, we demonstrate that WT1 plays a role in regulating the epithelial-mesenchymal balance of breast cancer cells and that WT1-expressing tumours are mainly associated with a mesenchymal phenotype. WT1 gene expression also correlates with CYP3A4 levels and is associated with poorer response to taxane treatment. Our work is the first to demonstrate that the known association between WT1 expression in breast cancer and poor prognosis is potentially due to cancer-related epithelial-to-mesenchymal transition (EMT) and poor chemotherapy response.
Mind-wandering and alterations to default mode network connectivity when listening to naturalistic versus artificial sounds
Authors: Gould van Praag Cassandra D. , Garfinkel Sarah N. , Sparasci Oliver , Mees Alex , Philippides Andrew O. , Ware Mark , Ottaviani Cristina , Critchley Hugo D.
Published: March 2017

Naturalistic environments have been demonstrated to promote relaxation and wellbeing. We assess opposing theoretical accounts for these effects through investigation of autonomic arousal and alterations of activation and functional connectivity within the default mode network (DMN) of the brain while participants listened to sounds from artificial and natural environments. We found no evidence for increased DMN activity in the naturalistic compared to artificial or control condition, however, seed based functional connectivity showed a shift from anterior to posterior midline functional coupling in the naturalistic condition. These changes were accompanied by an increase in peak high frequency heart rate variability, indicating an increase in parasympathetic activity in the naturalistic condition in line with the Stress Recovery Theory of nature exposure. Changes in heart rate and the peak high frequency were correlated with baseline functional connectivity within the DMN and baseline parasympathetic tone respectively, highlighting the importance of individual neural and autonomic differences in the response to nature exposure. Our findings may help explain reported health benefits of exposure to natural environments, through identification of alterations to autonomic activity and functional coupling within the DMN when listening to naturalistic sounds.
Stepwise analysis of MIR9 loci identifies miR-9-5p to be involved in Oestrogen regulated pathways in breast cancer patients
Authors: Barbano Raffaela , Pasculli Barbara , Rendina Michelina , Fontana Andrea , Fusilli Caterina , Copetti Massimiliano , Castellana Stefano , Valori Vanna Maria , Morritti Maria , Graziano Paolo , Luigi Ciuffreda , Coco Michelina , Picardo Francesco , Mazza Tommaso , Evron Ella , Murgo Roberto , Maiello Evaristo , Esteller Manel , Fazio Vito Michele , Parrella Paola
Published: March 2017

miR-9 was initially identified as an epigenetically regulated miRNA in tumours, but inconsistent findings have been reported so far. We analysed the expression of miR-9-5p, miR-9-3p, pri-miRs and MIR9 promoters methylation status in 131 breast cancer cases and 12 normal breast tissues (NBTs). The expression of both mature miRs was increased in tumours as compared to NBTs (P < 0.001) and negatively correlated with ER protein expression (P = 0.005 and P = 0.003, for miR-9-3p and miR-9-5p respectively). In addition, miR-9-5p showed a significant negative correlation with PgR (P = 0.002). Consistently, miR-9-5p and miR-9 3p were differentially expressed in the breast cancer subgroups identified by ER and PgR expression and HER2 amplification. No significant correlation between promoter methylation and pri-miRNAs expressions was found either in tumours or in NBTs. In the Luminal breast cancer subtype the expression of miR-9-5p was associated with a worse prognosis in both univariable and multivariable analyses. Ingenuity Pathway Analysis exploring the putative interactions among miR-9-5p/miR-9-3p, ER and PgR upstream and downstream regulators suggested a regulatory loop by which miR-9-5p but not miR-9-3p is induced by steroid hormone receptor and acts within hormone-receptor regulated pathways.
Proteomic analysis indicates that mitochondrial energy metabolism in skeletal muscle tissue is negatively correlated with feed efficiency in pigs
Authors: Fu Liangliang , Xu Yueyuan , Hou Ye , Qi Xiaolong , Zhou Lian , Liu Huiying , Luan Yu , Jing Lu , Miao Yuanxin , Zhao Shuhong , Liu Huazhen , Li Xinyun
Published: March 2017

Feed efficiency (FE) is a highly important economic trait in pig production. Investigating the molecular mechanisms of FE is essential for trait improvement. In this study, the skeletal muscle proteome of high-FE and low-FE pigs were investigated by the iTRAQ approach. A total of 1780 proteins were identified, among which 124 proteins were differentially expressed between the high- and low-FE pigs, with 74 up-regulated and 50 down-regulated in the high-FE pigs. Ten randomly selected differentially expressed proteins (DEPs) were validated by Western blotting and quantitative PCR (qPCR). Gene ontology (GO) analysis showed that all the 25 DEPs located in mitochondria were down-regulated in the high-FE pigs. Furthermore, the glucose-pyruvate-tricarboxylic acid (TCA)-oxidative phosphorylation energy metabolism signaling pathway was found to differ between high- and low-FE pigs. The key enzymes involved in the conversion of glucose to pyruvate were up-regulated in the high-FE pigs. Thus, our results suggested mitochondrial energy metabolism in the skeletal muscle tissue was negatively correlated with FE in pigs, and glucose utilization to generate ATP was more efficient in the skeletal muscle tissue of high-FE pigs. This study offered new targets and pathways for improvement of FE in pigs.
Tissue resident memory T cells in the human conjunctiva and immune signatures in human dry eye disease
Authors: Bose Tanima , Lee Ryan , Hou Aihua , Tong Louis , Chandy K. George
Published: March 2017

Non-recirculating resident memory (TRM) and recirculating T cells mount vigorous immune responses to both self and foreign antigens in barrier tissues like the skin, lung and gastrointestinal tract. Using impression cytology followed by flow cytometry we identified two TRM subsets and four recirculating T-subsets in the healthy human ocular surface. In dry eye disease, principal component analysis (PCA) revealed two clusters of patients with distinct T-cell signatures. Increased conjunctival central memory and naïve T cells characterized Cluster-1 patients, and increased CD8+ TRMs and CD4+ recirculating memory T cells characterized Cluster-2 patients. Interestingly these T-cell signatures are associated with different clinical features: the first signature correlated with increased ocular redness, and the second with reduced tear break up times. These findings open the door to immune-based characterization of dry eye disease and T-subset specific immunotherapies to suppress T-subsets involved in disease. They may also help with patient stratification during clinical trials of immunomodulators.
Nano-inspired smart interfaces: fluidic interactivity and its impact on heat transfer
Authors: Kim Beom Seok , Lee Byoung In , Lee Namkyu , Choi Geehong , Gemming Thomas , Cho Hyung Hee
Published: March 2017

Interface-inspired convection is a key heat transfer scheme for hot spot cooling and thermal energy transfer. An unavoidable trade-off of the convective heat transfer is pressure loss caused by fluidic resistance on an interface. To overcome this limitation, we uncover that nano-inspired interfaces can trigger a peculiar fluidic interactivity, which can pursue all the two sides of the coin: heat transfer and fluidic friction. We demonstrate the validity of a quasi-fin effect of Si-based nanostructures based on conductive capability of heat dissipation valid under the interactivity with fluidic viscous sublayer. The exclusive fluid-interface friction is achieved when the height of the nanostructures is much less than the thickness of the viscous sublayers in the turbulent regime. The strategic nanostructures show an enhancement of heat transfer coefficients in the wall jet region by more than 21% without any significant macroscale pressure loss under single-phase impinging jet. Nanostructures guaranteeing fluid access via an equivalent vacancy larger than the diffusive path length of viscid flow lead to local heat transfer enhancement of more than 13% at a stagnation point. Functional nanostructures will give shape to possible breakthroughs in heat transfer and its optimization can be pursued for engineered systems.
Stimulation of adult hippocampal neurogenesis by physical exercise and enriched environment is disturbed in a CADASIL mouse model
Authors: Klein C. , Schreyer S. , Kohrs F. E. , Elhamoury P. , Pfeffer A. , Munder T. , Steiner B.
Published: March 2017

In the course of CADASIL (Cerebral Autosomal Dominant Arteriopathy with Subcortical Infarcts and Leukoencephalopathy), a dysregulated adult hippocampal neurogenesis has been suggested as a potential mechanism for early cognitive decline. Previous work has shown that mice overexpressing wild type Notch3 and mice overexpressing Notch3 with a CADASIL mutation display impaired cell proliferation and survival of newly born hippocampal neurons prior to vascular abnormalities. Here, we aimed to elucidate how the long-term survival of these newly generated neurons is regulated by Notch3. Knowing that adult neurogenesis can be robustly stimulated by physical exercise and environmental enrichment, we also investigated the influence of such stimuli as potential therapeutic instruments for a dysregulated hippocampal neurogenesis in the CADASIL mouse model. Therefore, young-adult female mice were housed in standard (STD), environmentally enriched (ENR) or running wheel cages (RUN) for either 28 days or 6 months. Mice overexpressing mutated Notch3 and developing CADASIL (TgN3R169C), and mice overexpressing wild type Notch3 (TgN3WT) were used. We found that neurogenic stimulation by RUN and ENR is apparently impaired in both transgenic lines. The finding suggests that a disturbed neurogenic process due to Notch3-dependent micromilieu changes might be one vascular-independent mechanism contributing to cognitive decline observed in CADASIL.