bluuebunny/crossref_metadata_2025 huggingface dataset:
Freshwater mussels (Anodonta anatina) reduce transmission of a common fish trematode (eye fluke,Diplostomum pseudospathaceum)
Authors: GOPKO M. , MIRONOVA E. , PASTERNAK A. , MIKHEEV V. , TASKINEN J.
Published: August 2017

Recent results suggest that bivalves can play an important role in restraining the spread of various aquatic infections. However, the ability of mussels to remove free-living stages of macroparasites and reduce their transmission is still understudied, especially for freshwater ecosystems. We investigated the influence of the common freshwater mussel (Anodonta anatina) on the transmission of a trematode (eye fluke,Diplostomum pseudospathaceum), which frequently infects fish in farms and natural habitats. In our experiments, mussels caused a significant decrease (P< 0·001) in the abundance of trematode free-living stages, from 6520 to 1770 cercariae L−1on average (about 4-fold in 2 h). Individual clearance rates of mussels were 0·6‒3·7 L per hour (mean 1·9). These tests were followed by experimental infections of rainbow trout (Oncorhynchus mykiss) with different doses ofD. pseudospathaceumcercariae in the presence or absence of mussels. Exposure of fish to cercariae in the presence of mussels significantly (P< 0·05) reduced the infection intensities in fish (by 30–40%) at all exposure doses. Our results indicate that freshwater bivalves can markedly reduce local cercariae densities and could be useful in mitigation of trematodoses harmful to fish farming.
Probabilistic Analysis of the Impact of Vessel Speed Restrictions on Navigational Safety: Accounting for the Right Whale Rule
Authors: Convertino Matteo , Valverde L. James
Published: August 2017

The Right Whale Sighting Advisory System (RWSAS) is a National Oceanic and Atmospheric Administration (NOAA) Fisheries program designed to reduce collisions between vessels and critically endangered North Atlantic right whales. The vessel speed restriction that is part of the RWSAS presents navigation stakeholders with numerous challenges, owing to concerns about increased risks of ship grounding and collisions within ports. In this paper, we present a multi-methodology framework for assessing the impact of the vessel speed restriction on navigational safety. Empirically, we base our discussion in a first-order analysis of ship grounding risk for the Charleston Entrance Channel. Our analysis proceeds in three parts. We begin by using fault and event tree analyses to assess a relevant set of grounding-related event progression and failure probabilities. The influence of alternative vessel speed restrictions on ship grounding risk are then explored via a Bayesian network model that utilises the previously specified fault and event tree models for its partial specification and enumeration. Our analysis suggests that the speed restriction can, under certain reasonable assumptions, be seen to adversely impact the risk of ship grounding accidents in the Charleston Entrance Channel. We conclude with a summary of our findings and recommendations for future research.
DO ENVIRONMENTAL FACTORS AFFECT THE TAXONOMIC RELIABILITY OF LEAF CUTICULAR MICROMORPHOLOGICAL CHARACTERS? A CASE STUDY IN PODOCARPACEAE
Authors: Clugston J. A. R. , Jeffree C. E. , Ahrends A. , Mill R. R.
Published: August 2017

Leaf cuticle micromorphology has been cited as an important set of taxonomic characters in gymnosperms, but previous studies have largely been based on small sample sizes. The premise of this study was to understand whether external factors affect cuticular micromorphology of Podocarpaceae. Two example species, Prumnopitys andina and Podocarpus salignus, were studied. Of 21 sampled characters, nine (c.43% of the total) were visually assessed as being moderately reliable or highly reliable for taxonomic discrimination for both species, with an additional six (c.29%) being moderately reliable or highly reliable for only one or other of the example species, and six characters (c.29%) unreliable for both. Seven of the most variable stomatal characters were selected for further analysis to establish whether environmental factors affect them. The relationship between these seven stomatal characters, the environment and climate was analysed using the R ‘vegan’ package and climate data gathered from WorldClim. Our results showed that both species had larger stomata in moist and shady conditions, and a higher density of (smaller) stomata in sunny and drier conditions. An additional novel finding was the presence of stomata on the adaxial leaf surface in 46% of samples of Prumnopitys andina: the first record of adaxial stomata in this species, highlighting the necessity of studying multiple samples of a given species. In conclusion, these results indicate that larger sample sizes than have hitherto been employed in cuticle micromorphological studies are necessary to fully document the amount of phenotypic variation that exists.
Preface
Authors: DOVIER AGOSTINO
Published: August 2017

Magic squares, chess-like problems, cryptarithmetic puzzles, and similar classes of problems have been extensively used to challenge human reasoning capabilities. Lo Shu magic square can be traced back to 650 B.C., the eight-queens problem was proposed in 1848 by the chess player Max Bazzel TWO × TWO = THREE puzzle appeared in Strand Magazine in 1924. These puzzles are nowadays widely used in constraint programming courses. The first programming language provided with constraint modelling primitives (Sketchpad) has been proposed by the Turing award winner Ivan Sutherland in his PhD thesis (1963). Logemann and Loveland, when implementing the Davis–Putnam procedure (Davis and Putnam 1960) for testing the satisfiability of a propositional formula (SAT), devised an algorithm (Davis–Putnam–Logemann–Loveland (DPLL)) that has become the core of all SAT/and Answer Set Programming solvers (50 years later). It consists in choosing an un-assigned variable, assigning it a value 0 or 1, propagating the chosen value (unit propagation), and proceeding with the alternative value, if the original assignment leads to a contradiction (backtracking). Some years later Waltz (1975) introduced the notion of domain filtering (arc-consistency-based constraint propagation). With this idea the same DPLL scheme can be used for verifying the satisfiability of a constraint satisfaction problem, where the assignment is no longer 0/1 and the unit propagation is replaced by constraint propagation. For a detailed history of these early years achievements, we refer the reader to the works by Loveland et al. (2017), Jaffar and Maher (1994), and Freuder and Mackworth (2006).
The RPMI-1640 vitamin mixture promotes bovine blastocyst developmentin vitroand downregulates gene expression ofTXNIPwith epigenetic modification of associated histones
Authors: Ikeda S. , Sugimoto M. , Kume S.
Published: August 2017

Diverse environmental conditions surrounding preimplantation embryos, including available nutrients, affect their metabolism and development in both short- and long-term manner. Thioredoxin-interacting protein (TXNIP) is a possible marker for preimplantation stress that is implicated inin vitrofertilization- (IVF) induced long-term DOHaD effects. B vitamins, as participants in one-carbon metabolism, may affect preimplantation embryos by epigenetic alterations of metabolically and developmentally important genes.In vitro-produced bovine embryos were cultured with or without Roswell Park Memorial Institute 1640 vitamin mixture, containing B vitamins and B vitamin-like substances, from day 3 after IVF and we evaluated blastocyst development andTXNIPmessenger RNA (mRNA) expression in the blastocysts by reverse transcription-quantitative polymerase chain reaction. The degree of trimethylation of histone H3 lysine 27 (H3K27me3) atTXNIPpromoter was examined semi-quantitatively by chromatin immunoprecipitation polymerase chain reaction. Total H3K27me3 were also compared between the groups by Western blot analysis. The vitamin treatment significantly increased the rates of blastocyst development (P<0.05) and their hatching (P<0.001) from the zona pellucida by day 8. The mRNA expression ofTXNIPwas lower (P<0.01) in blastocysts in the vitamin-mixture-treated group concomitant with higher (P<0.05) level of H3K27me3 of its promoter compared with the control group. The total H3K27me3 in the vitamin-mixture-treated group was also higher (P<0.01) than that in the control group. The epigenetic control of genes related to important metabolic processes during the periconceptional period by nutritional conditionsin uteroand/orin vitromay have possible implication for the developmental programming during this period that may impact the welfare and production traits of farm animals.
A Systems Comparison of Contrasting Organic Weed Management Strategies
Authors: Brown Bryan , Gallandt Eric R.
Published: August 2017

Weed management strategies differ in their ability to control weeds, and often have unique agroecological implications. To provide growers with an improved sense of trade-offs between weed control and ecological effects, we implemented several prominent organic weed management strategies in yellow onion in 2014 and 2015. Strategies included cultivation of weed seedlings during the early, weed-sensitive “critical period” of the crop; frequent cultivation events to ensure “zero seed rain”; and weed suppression with polyethylene or natural mulches. As expected, end-of-season weed biomass and weed seed production were greatest in the critical period system and nearly zero for the zero seed rain system. Weeds were also well controlled in natural mulch systems. Average onion yield per treatment was 50.7 Mg ha−1. In 2014, the critical period system and the polyethylene mulch systems demonstrated yield loss, likely due to weed competition and excessive soil temperature, respectively. Onion soluble solids content was also diminished in these systems in 2014, but bulb firmness was greatest in unmulched systems. Carabid beetles, earthworms, soil compaction, soil nitrate, and microbial biomass were affected by weed management strategy, with natural-mulched systems generally performing most favorably. However, these effects were not substantial enough to affect yield of a subsequent sweet corn crop grown in weed-free conditions. In contrast, sweet corn managed with only early-season cultivations demonstrated yield loss (P=0.004) in plots where the critical period treatment was implemented the prior year, indicating that weed competition resulting from abundant weed seed production in that system was the most influential legacy effect of the weed management strategies.
Habituation based synaptic plasticity and organismic learning in a quantum perovskite
Authors: Zuo Fan , Panda Priyadarshini , Kotiuga Michele , Li Jiarui , Kang Mingu , Mazzoli Claudio , Zhou Hua , Barbour Andi , Wilkins Stuart , Narayanan Badri , Cherukara Mathew , Zhang Zhen , Sankaranarayanan Subramanian K. R. S. , Comin Riccardo , Rabe Karin M. , Roy Kaushik , Ramanathan Shriram
Published: August 2017

A central characteristic of living beings is the ability to learn from and respond to their environment leading to habit formation and decision making. This behavior, known as habituation, is universal among all forms of life with a central nervous system, and is also observed in single-cell organisms that do not possess a brain. Here, we report the discovery of habituation-based plasticity utilizing a perovskite quantum system by dynamical modulation of electron localization. Microscopic mechanisms and pathways that enable this organismic collective charge-lattice interaction are elucidated by first-principles theory, synchrotron investigations, ab initio molecular dynamics simulations, and in situ environmental breathing studies. We implement a learning algorithm inspired by the conductance relaxation behavior of perovskites that naturally incorporates habituation, and demonstrate learning to forget: a key feature of animal and human brains. Incorporating this elementary skill in learning boosts the capability of neural computing in a sequential, dynamic environment.
Origin of charge transfer and enhanced electron–phonon coupling in single unit-cell FeSe films on SrTiO3
Authors: Zhang Huimin , Zhang Ding , Lu Xiaowei , Liu Chong , Zhou Guanyu , Ma Xucun , Wang Lili , Jiang Peng , Xue Qi-Kun , Bao Xinhe
Published: August 2017

Interface charge transfer and electron–phonon coupling have been suggested to play a crucial role in the recently discovered high-temperature superconductivity of single unit-cell FeSe films on SrTiO3. However, their origin remains elusive. Here, using ultraviolet photoemission spectroscopy and element-sensitive X-ray photoemission spectroscopy, we identify the strengthened Ti–O bond that contributes to the interface enhanced electron–phonon coupling and unveil the band bending at the FeSe/SrTiO3 interface that leads to the charge transfer from SrTiO3 to FeSe films. We also observe band renormalization that accompanies the onset of superconductivity. Our results not only provide valuable insights into the mechanism of the interface-enhanced superconductivity, but also point out a promising route toward designing novel superconductors in heterostructures with band bending-induced charge transfer and interfacial enhanced electron–phonon coupling.
Measuring inter-protein pairwise interaction energies from a single native mass spectrum by double-mutant cycle analysis
Authors: Sokolovski Miri , Cveticanin Jelena , Hayoun Déborah , Korobko Ilia , Sharon Michal , Horovitz Amnon
Published: August 2017

The strength and specificity of protein complex formation is crucial for most life processes and is determined by interactions between residues in the binding partners. Double-mutant cycle analysis provides a strategy for studying the energetic coupling between amino acids at the interfaces of such complexes. Here we show that these pairwise interaction energies can be determined from a single high-resolution native mass spectrum by measuring the intensities of the complexes formed by the two wild-type proteins, the complex of each wild-type protein with a mutant protein, and the complex of the two mutant proteins. This native mass spectrometry approach, which obviates the need for error-prone measurements of binding constants, can provide information regarding multiple interactions in a single spectrum much like nuclear Overhauser effects (NOEs) in nuclear magnetic resonance. Importantly, our results show that specific inter-protein contacts in solution are maintained in the gas phase.
Erratum: Ubiquitous overexpression of the DNA repair factor dPrp19 reduces DNA damage and extends Drosophila life span
Authors: Garschall Kathrin , Dellago Hanna , Gáliková Martina , Schosserer Markus , Flatt Thomas , Grillari Johannes
Published: August 2017

Correction to: npj Aging and Mechanisms of Disease, advance online publication, 15 March 2017; doi:10.1038/s41514-017-0005-z
Single Microfluidic Electrochemical Sensor System for Simultaneous Multi-Pulmonary Hypertension Biomarker Analyses
Authors: Lee GeonHui , Lee JuKyung , Kim JeongHoon , Choi Hak Soo , Kim Jonghan , Lee SangHoon , Lee HeaYeon
Published: August 2017

Miniaturized microfluidic biosensors have recently been advanced for portable point-of-care diagnostics by integrating lab-on-a-chip technology and electrochemical analysis. However, the design of a small, integrated, and reliable biosensor for multiple and simultaneous electrochemical analyses in a single device remains a challenge. Here, we present a simultaneous microfluidic electrochemical biosensing system to detect multiple biomarkers of pulmonary hypertension diseases in a single device. The miniaturized biosensor, which is composed of five chambers, is precisely and individually controlled using in-house-built pneumatic microvalves to manipulate the flow pathway. Each chamber is connected to an electrochemical sensor designed to detect four different biomarkers plus a reference control. Our design allows for loading of multiple reagents for simultaneous analyses. On the basis of the developed microfluidic electrochemical sensor system, we successfully detected four well-defined pulmonary hypertension-associated biomarkers, namely, fibrinogen, adiponectin, low-density lipoprotein, and 8-isoprostane. This novel approach offers a new platform for a rapid, miniaturized, and sensitive diagnostic sensor in a single device for various human diseases.
Grouping by feature of cross-modal flankers in temporal ventriloquism
Authors: Klimova Michaela , Nishida Shin’ya , Roseboom Warrick
Published: August 2017

Signals in one sensory modality can influence perception of another, for example the bias of visual timing by audition: temporal ventriloquism. Strong accounts of temporal ventriloquism hold that the sensory representation of visual signal timing changes to that of the nearby sound. Alternatively, underlying sensory representations do not change. Rather, perceptual grouping processes based on spatial, temporal, and featural information produce best-estimates of global event properties. In support of this interpretation, when feature-based perceptual grouping conflicts with temporal information-based in scenarios that reveal temporal ventriloquism, the effect is abolished. However, previous demonstrations of this disruption used long-range visual apparent-motion stimuli. We investigated whether similar manipulations of feature grouping could also disrupt the classical temporal ventriloquism demonstration, which occurs over a short temporal range. We estimated the precision of participants’ reports of which of two visual bars occurred first. The bars were accompanied by different cross-modal signals that onset synchronously or asynchronously with each bar. Participants’ performance improved with asynchronous presentation relative to synchronous - temporal ventriloquism - however, unlike the long-range apparent motion paradigm, this was unaffected by different combinations of cross-modal feature, suggesting that featural similarity of cross-modal signals may not modulate cross-modal temporal influences in short time scales.
Metastable exohedrally decorated Borospherene B40
Authors: Saha Santanu , Genovese Luigi , Goedecker Stefan
Published: August 2017

The experimental discovery of borospherene, the only non-carbon fullerene observed in nature, has generated a lot of interest in the scientific community and led to the theoretical prediction of various endohedrally and exohedrally decorated borospherene. We apply Minima Hopping Method (MHM), a global geometry optimization algorithm at the density functional level to check the stability of recently proposed exohedrally decorated borospherenes M6@B40 for (M = Li, Na, K, Rb, Be, Mg, Ca, Sr, Sc and Ti). By performing short MHM runs, we find that the proposed fullerene structures are not global minima. Our new lowest energy structures are significantly deformed and of much lower symmetry. These low energy structures spontaneously aggregate by forming chemical bonds when they are brought together. Therefore, it would be challenging to synthesize bulk materials made out of the theoretically postulated exohedrally decorated borospherenes such as B40M6 which might have technologically useful properties.
Interactions of the Calcite {10.4} Surface with Organic Compounds: Structure and Behaviour at Mineral – Organic Interfaces
Authors: Hakim S. S. , Olsson M. H. M. , Sørensen H. O. , Bovet N. , Bohr J. , Feidenhans’l R. , Stipp S. L. S.
Published: August 2017

The structure and the strength of organic compound adsorption on mineral surfaces are of interest for a number of industrial and environmental applications, oil recovery, CO2 storage and contamination remediation. Biomineralised calcite plays an essential role in the function of many organisms that control crystal growth with organic macromolecules. Carbonate rocks, composed almost exclusively of calcite, host drinking water aquifers and oil reservoirs. In this study, we examined the ordering behaviour of several organic compounds and the thickness of the adsorbed layers formed on calcite {10.4} surfaces. We used X-ray reflectivity (XRR) to study calcite {10.4} surfaces that were prepared in three alcohols: methanol, isopropanol and pentanol and one carboxylic acid: octanoic acid. All molecules adsorbed in self-assembled layers, where thickness depended on the density and the length of the molecule. For methanol and isopropanol, molecular dynamic simulations (MD) provided complementary information, which allowed us to develop a surface model. Branching in isopropanol induced slightly less ordering because of the additional degree of freedom. Pentanol and octanoic acid adsorbed as single monolayers. The results of this work indicate that adhered organic compounds from the surrounding environment can affect the surface behaviour, depending on properties of the organic compound.
Genome-wide expression differences in anti-Vegf and dexamethasone treatment of inflammatory angiogenesis in the rat cornea
Authors: Mirabelli Pierfrancesco , Mukwaya Anthony , Lennikov Anton , Xeroudaki Maria , Peebo Beatrice , Schaupper Mira , Lagali Neil
Published: August 2017

Angiogenesis as a pathological process in the eye can lead to blindness. In the cornea, suppression of angiogenesis by anti-VEGF treatment is only partially effective while steroids, although effective in treating inflammation and angiogenesis, have broad activity leading to undesirable side effects. In this study, genome-wide expression was investigated in a suture-induced corneal neovascularization model in rats, to investigate factors differentially targeted by dexamethasone and anti-Vegf. Topical treatment with either rat-specific anti-Vegf, dexamethasone, or normal goat IgG (sham) was given to sutured corneas for 48 hours, after which in vivo imaging, tissue processing for RNA microarray, and immunofluorescence were performed. Dexamethasone suppressed limbal vasodilation (P < 0.01) and genes in PI3K-Akt, focal adhesion, and chemokine signaling pathways more effectively than anti-Vegf. The most differentially expressed genes were confirmed by immunofluorescence, qRTPCR and Western blot. Strong suppression of Reg3g and the inflammatory chemokines Ccl2 and Cxcl5 and activation of classical complement pathway factors C1r, C1s, C2, and C3 occurred with dexamethasone treatment, effects absent with anti-Vegf treatment. The genome-wide results obtained in this study provide numerous potential targets for specific blockade of inflammation and angiogenesis in the cornea not addressed by anti-Vegf treatment, as possible alternatives to broad-acting immunosuppressive therapy.
Mitochondrial division inhibitor-1 is neuroprotective in the A53T-α-synuclein rat model of Parkinson’s disease
Authors: Bido Simone , Soria Federico N. , Fan Rebecca Z. , Bezard Erwan , Tieu Kim
Published: August 2017

Alpha-synuclein (α-syn) is involved in both familial and sporadic Parkinson’s disease (PD). One of the proposed pathogenic mechanisms of α-syn mutations is mitochondrial dysfunction. However, it is not entirely clear the impact of impaired mitochondrial dynamics induced by α-syn on neurodegeneration and whether targeting this pathway has therapeutic potential. In this study we evaluated whether inhibition of mitochondrial fission is neuroprotective against α-syn overexpressionin vivo. To accomplish this goal, we overexpressed human A53T-α- synuclein (hA53T-α-syn) in the rat nigrostriatal pathway, with or without treatment using the small molecule Mitochondrial Division Inhibitor-1 (mdivi-1), a putative inhibitor of the mitochondrial fission Dynamin-Related Protein-1 (Drp1). We show here that mdivi-1 reduced neurodegeneration, α-syn aggregates and normalized motor function. Mechanistically, mdivi-1 reduced mitochondrial fragmentation, mitochondrial dysfunction and oxidative stress. Thesein vivoresults support the negative role of mutant α-syn in mitochondrial function and indicate that mdivi-1 has a high therapeutic potential for PD.
Employing high-frequency alternating magnetic fields for the non-invasive treatment of prosthetic joint infections
Authors: Chopra Rajiv , Shaikh Sumbul , Chatzinoff Yonatan , Munaweera Imalka , Cheng Bingbing , Daly Seth M. , Xi Yin , Bing Chenchen , Burns Dennis , Greenberg David E.
Published: August 2017

Treatment of prosthetic joint infection (PJI) usually requires surgical replacement of the infected joint and weeks of antibiotic therapy, due to the formation of biofilm. We introduce a non-invasive method for thermal destruction of biofilm on metallic implants using high-frequency (>100 kHz) alternating magnetic fields (AMF). In vitro investigations demonstrate a >5-log reduction in bacterial counts after 5 minutes of AMF exposure. Confocal and scanning electron microscopy confirm removal of biofilm matrix components within 1 minute of AMF exposure, and combination studies of antibiotics and AMF demonstrate a 5-log increase in the sensitivity of Pseudomonas aeruginosa to ciprofloxacin. Finite element analysis (FEA) simulations demonstrate that intermittent AMF exposures can achieve uniform surface heating of a prosthetic knee joint. In vivo studies confirm thermal damage is confined to a localized region (<2 mm) around the implant, and safety can be achieved using acoustic monitoring for the presence of surface boiling. These initial studies support the hypothesis that AMF exposures can eradicate biofilm on metal implants, and may enhance the effectiveness of conventional antibiotics.
Shedding new light on the Crab with polarized X-rays
Authors: Chauvin M. , Florén H.-G. , Friis M. , Jackson M. , Kamae T. , Kataoka J. , Kawano T. , Kiss M. , Mikhalev V. , Mizuno T. , Ohashi N. , Stana T. , Tajima H. , Takahashi H. , Uchida N. , Pearce M.
Published: August 2017

Strong magnetic fields, synchrotron emission, and Compton scattering are omnipresent in compact celestial X-ray sources. Emissions in the X-ray energy band are consequently expected to be linearly polarized. X-ray polarimetry provides a unique diagnostic to study the location and fundamental mechanisms behind emission processes. The polarization of emissions from a bright celestial X-ray source, the Crab, is reported here for the first time in the hard X-ray band (~20–160 keV). The Crab is a complex system consisting of a central pulsar, a diffuse pulsar wind nebula, as well as structures in the inner nebula including a jet and torus. Measurements are made by a purpose-built and calibrated polarimeter, PoGO+. The polarization vector is found to be aligned with the spin axis of the pulsar for a polarization fraction, PF = (20.9 ± 5.0)%. This is higher than that of the optical diffuse nebula, implying a more compact emission site, though not as compact as, e.g., the synchrotron knot. Contrary to measurements at higher energies, no significant temporal evolution of phase-integrated polarisation parameters is observed. The polarization parameters for the pulsar itself are measured for the first time in the X-ray energy band and are consistent with observations at optical wavelengths.
Global and local excitation and inhibition shape the dynamics of the cortico-striatal-thalamo-cortical pathway
Authors: Rădulescu Anca , Herron Joanna , Kennedy Caitlin , Scimemi Annalisa
Published: August 2017

The cortico-striatal-thalamo-cortical (CSTC) pathway is a brain circuit that controls movement execution, habit formation and reward. Hyperactivity in the CSTC pathway is involved in obsessive compulsive disorder (OCD), a neuropsychiatric disorder characterized by the execution of repetitive involuntary movements. The striatum shapes the activity of the CSTC pathway through the coordinated activation of two classes of medium spiny neurons (MSNs) expressing D1 or D2 dopamine receptors. The exact mechanisms by which balanced excitation/inhibition (E/I) of these cells controls the network dynamics of the CSTC pathway remain unclear. Here we use non-linear modeling of neuronal activity and bifurcation theory to investigate how global and local changes in E/I of MSNs regulate the activity of the CSTC pathway. Our findings indicate that a global and proportionate increase in E/I pushes the system to states of generalized hyper-activity throughout the entire CSTC pathway. Certain disproportionate changes in global E/I trigger network oscillations. Local changes in the E/I of MSNs generate specific oscillatory behaviors in MSNs and in the CSTC pathway. These findings indicate that subtle changes in the relative strength of E/I of MSNs can powerfully control the network dynamics of the CSTC pathway in ways that are not easily predicted by its synaptic connections.
Increased sporadic extremes decrease the intraseasonal variability in the Indian summer monsoon rainfall
Authors: Karmakar Nirupam , Chakraborty Arindam , Nanjundiah Ravi S.
Published: August 2017

The Indian summer monsoon (ISM) shows quasi-rhythmic intraseasonal oscillations (ISO) manifested as alternate ‘active’ phases of copious rainfall and quiescent phases of ‘break’. Within these periodic phases, the daily rainfall shows large variability and exhibits spatiotemporally sporadic extreme rainfall events. The recent decades have witnessed a significant increase in the number of these extreme rainfall events, especially in the quiescent phases. This increase is accompanied by a decreasing trend in the mean monsoon rainfall and a weakening variance of its low-frequency ISO (LF-ISO) cycle. However, any physical link between this apparent paradox of increased extreme rainfall events and weakened slower-time-scale components is not yet reported. Here, using observations and numerical model simulations, we show that the occurrence of extreme rainfall events, primarily in the break phase of an LF-ISO cycle, reduce the intensity of the following active phase by stabilizing the atmosphere. We found that extreme events in a monsoon break leads to a reduction in the vertical shear of zonal winds and an increase in the static stability of the atmosphere in the following break-to-active transition and active phases. These conditions oppose the initiation and development of an active phase and lessen its intensity. This reduces the LF-ISO intensity and mean ISM rainfall.
Chronic low-level expression of HIV-1 Tat promotes a neurodegenerative phenotype with aging
Authors: Dickens Alex M. , Yoo Seung Wan , Chin Alfred C. , Xu Jiadi , Johnson Tory P. , Trout Amanda L. , Hauser Kurt F. , Haughey Norman J.
Published: August 2017

The widespread use of combinational antiretroviral therapies (cART) in developed countries has changed the course of Human Immunodeficiency Virus (HIV) infection from an almost universally fatal disease to a chronic infection for the majority of individuals. Although cART has reduced the severity of neurological damage in HIV-infected individuals, the likelihood of cognitive impairment increases with age, and duration of infection. As cART does not suppress the expression of HIV non-structural proteins, it has been proposed that a constitutive production of HIV regulatory proteins in infected brain cells may contribute to neurological damage. However, this assumption has never been experimentally tested. Here we take advantage of the leaky tetracycline promoter system in the Tat-transgenic mouse to show that a chronic very low-level expression of Tat is associated with astrocyte activation, inflammatory cytokine expression, ceramide accumulation, reductions in brain volume, synaptic, and axonal damage that occurs over a time frame of 1 year. These data suggest that a chronic low-level production of Tat may contribute to progressive neurological damage in virally suppressed HIV-infected individuals.
Revealing extracellular electron transfer mediated parasitism: energetic considerations
Authors: Moscoviz Roman , Flayac Clément , Desmond-Le Quéméner Elie , Trably Eric , Bernet Nicolas
Published: August 2017

Extracellular electron transfer (EET) is a mechanism that allows energetic coupling between two microorganisms or between a microorganism and an electrode surface. EET is either supported by direct physical contacts or mediated by electron shuttles. So far, studies dealing with interspecies EET (so-called IET) have mainly focused on possible syntrophic interactions between microorganisms favoured by this mechanism. In this article, the case of fermentative bacteria receiving extracellular electrons while fermenting a substrate is considered. A thermodynamical analysis based on metabolic energy balances was applied to re-investigate experimental data from the literature. Results suggest that the observations of a decrease of cell biomass yields of fermentative electron-accepting species, as mostly reported, can be unravelled by EET energetics and correspond to parasitism in case of IET. As an illustration, the growth yield decrease of Propionibacterium freudenreichii (−14%) observed in electro-fermentation experiments was fully explained by EET energetics when electrons were used by this species at a potential of −0.12 ± 0.01 V vs SHE. Analysis of other cases showed that, in addition to EET energetics in Clostridium pasteurianum, biological regulations can also be involved in such biomass yield decrease (−33% to −38%). Interestingly, the diminution of bacterial biomass production is always concomitant with an increased production of reduced compounds making IET-mediated parasitism and electro-fermentation attractive ways to optimize carbon fluxes in fermentation processes.
Increased plasma levels of lncRNA H19 and LIPCAR are associated with increased risk of coronary artery disease in a Chinese population
Authors: Zhang Zhen , Gao Wei , Long Qing-Qing , Zhang Jian , Li Ya-Fei , liu Dong-Chen , Yan Jian-Jun , Yang Zhi-Jian , Wang Lian-Sheng
Published: August 2017

Recent studies in animal models and humans show that long non-coding RNAs (lncRNAs) are involved in the development of atherosclerosis, which contributes to the pathological foundation of coronary artery disease (CAD). LncRNAs in plasma and serum have been considered as promising novel biomarkers for diagnosis and prognosis of cardiovascular diseases, especially CAD. We here measured the circulating levels of 8 individual lncRNAs which are known to be relevant to atherosclerosis in the plasma samples from 300 patients with CAD and 180 control subjects by using quantitative real-time reverse transcription-polymerase chain reaction (qRT-PCR) methods. We found that the plasma level of H19 and long intergenic non-coding RNA predicting cardiac remodeling (LIPCAR) were significantly increased in patients with CAD. The area under the receiver operating characteristic curve was 0.631 for H19 and 0.722 for LIPCAR. Multivariate logistic regression analyses indicated that plasma H19 and LIPCAR were independent predictors for CAD, even after adjustment for traditional cardiovascular risk factors. Further studies identified that plasma levels of H19 and LIPCAR were also increased in CAD patients with heart failure compared to those with normal cardiac function. Taken together, our results suggest that increased plasma levels of H19 and LIPCAR are associated with increased risk of CAD and may be considered as novel biomarkers for CAD.
Verteporfin inhibits growth of human glioma in vitro without light activation
Authors: Al-Moujahed Ahmad , Brodowska Katarzyna , Stryjewski Tomasz P. , Efstathiou Nikolaos E. , Vasilikos Ioannis , Cichy Joanna , Miller Joan W. , Gragoudas Evangelos , Vavvas Demetrios G.
Published: August 2017

Verteporfin (VP), a light-activated drug used in photodynamic therapy for the treatment of choroidal neovascular membranes, has also been shown to be an effective inhibitor of malignant cells. Recently, studies have demonstrated that, even without photo-activation, VP may still inhibit certain tumor cell lines, including ovarian cancer, hepatocarcinoma and retinoblastoma, through the inhibition of the YAP-TEAD complex. In this study, we examined the effects of VP without light activation on human glioma cell lines (LN229 and SNB19). Through western blot analysis, we identified that human glioma cells that were exposed to VP without light activation demonstrated a downregulation of YAP-TEAD-associated downstream signaling molecules, including c-myc, axl, CTGF, cyr61 and survivin and upregulation of the tumor growth inhibitor molecule p38 MAPK. In addition, we observed that expression of VEGFA and the pluripotent marker Oct-4 were also decreased. Verteporfin did not alter the Akt survival pathway or the mTor pathway but there was a modest increase in LC3-IIB, a marker of autophagosome biogenesis. This study suggests that verteporfin should be further explored as an adjuvant therapy for the treatment of glioblastoma.
Non-sequential double ionization with near-single cycle laser pulses
Authors: Chen A. , Kübel M. , Bergues B. , Kling M. F. , Emmanouilidou A.
Published: August 2017

A three-dimensional semiclassical model is used to study double ionization of Ar when driven by a near-infrared and near-single-cycle laser pulse for intensities ranging from 0.85 × 1014 W/cm2 to 5 × 1014 W/cm2. Asymmetry parameters, distributions of the sum of the two electron momentum components along the direction of the polarization of the laser field and correlated electron momenta are computed as a function of the intensity and of the carrier envelope phase. A very good agreement is found with recently obtained results in kinematically complete experiments employing near-single-cycle laser pulses. Moreover, the contribution of the direct and delayed pathways of double ionization is investigated for the above observables. Finally, an experimentally obtained anti-correlation momentum pattern at higher intensities is reproduced with the three-dimensional semiclassical model and shown to be due to a transition from strong to soft recollisions with increasing intensity.
Mechanism of Photodamage of the Oxygen Evolving Mn Cluster of Photosystem II by Excessive Light Energy
Authors: Zavafer Alonso , Koinuma Wataru , Chow Wah Soon , Cheah Mun Hon , Mino Hiroyuki
Published: August 2017

Photodamage to Photosystem II (PSII) has been attributed either to excessive excitation of photosynthetic pigments or by direct of light absorption by Mn4CaO5 cluster. Here we investigated the time course of PSII photodamage and release of Mn in PSII-enriched membranes under high light illumination at 460 nm and 660 nm. We found that the loss of PSII activity, assayed by chlorophyll fluorescence, is faster than release of Mn from the Mn4CaO5 cluster, assayed by EPR. Loss of PSII activity and Mn release was slower during illumination in the presence of exogenous electron acceptors. Recovery of PSII activity was observed, after 30 min of addition of electron donor post illumination. The same behavior was observed under 460 and 660 nm illumination, suggesting stronger correlation between excessive excitation and photodamage compared to direct light absorption by the cluster. A unified model of PSII photodamage that takes into account present and previous literature reports is presented.
Minimal Long-Term Neurobehavioral Impairments after Endovascular Perforation Subarachnoid Hemorrhage in Mice
Authors: Fanizzi Claudia , Sauerbeck Andrew D. , Gangolli Mihika , Zipfel Gregory J. , Brody David L. , Kummer Terrance T.
Published: August 2017

Cognitive deficits are among the most severe and pervasive consequences of aneurysmal subarachnoid hemorrhage (SAH). A critical step in developing therapies targeting such outcomes is the characterization of experimentally-tractable pre-clinical models that exhibit multi-domain neurobehavioral deficits similar to those afflicting humans. We therefore searched for neurobehavioral abnormalities following endovascular perforation induction of SAH in mice, a heavily-utilized model. We instituted a functional screen to manage variability in injury severity, then assessed acute functional deficits, as well as activity, anxiety-related behavior, learning and memory, socialization, and depressive-like behavior at sub-acute and chronic time points (up to 1 month post-injury). Animals in which SAH was induced exhibited reduced acute functional capacity and reduced general activity to 1 month post-injury. Tests of anxiety-related behavior including central area time in the elevated plus maze and thigmotaxis in the open field test revealed increased anxiety-like behavior at subacute and chronic time-points, respectively. Effect sizes for subacute and chronic neurobehavioral endpoints in other domains, however, were small. In combination with persistent variability, this led to non-significant effects of injury on all remaining neurobehavioral outcomes. These results suggest that, with the exception of anxiety-related behavior, alternate mouse models are required to effectively analyze cognitive outcomes after SAH.
Smartphone-based multi-contrast microscope using color-multiplexed illumination
Authors: Jung Daeseong , Choi Jun-Ho , Kim Soocheol , Ryu Suho , Lee Wonchan , Lee Jong-Seok , Joo Chulmin
Published: August 2017

We present a portable multi-contrast microscope capable of producing bright-field, dark-field, and differential phase contrast images of thin biological specimens on a smartphone platform. The microscopy method is based on an imaging scheme termed “color-coded light-emitting-diode (LED) microscopy (cLEDscope),” in which a specimen is illuminated with a color-coded LED array and light transmitted through the specimen is recorded by a color image sensor. Decomposition of the image into red, green, and blue colors and subsequent computation enable multi-contrast imaging in a single shot. In order to transform a smartphone into a multi-contrast imaging device, we developed an add-on module composed of a patterned color micro-LED array, specimen stage, and miniature objective. Simple installation of this module onto a smartphone enables multi-contrast imaging of transparent specimens. In addition, an Android-based app was implemented to acquire an image, perform the associated computation, and display the multi-contrast images in real time. Herein, the details of our smartphone module and experimental demonstrations with various biological specimens are presented.
The manipulation of gene expression and the biosynthesis of Vitamin C, E and folate in light-and dark-germination of sweet corn seeds
Authors: Liu Fengyuan , Xiang Nan , Hu Jian Guang , Shijuan Yan , Xie Lihua , Brennan Charles Stephen , Huang Wenjie , Guo Xinbo
Published: August 2017

This study investigates the potential interrelationship between gene expression and biosynthesis of vitamin C, E and folate in sweet corn sprouts. Germination of sweet corn kernels was conducted in light and dark environments to determine if this relationship was regulated by photo-illumination. Results indicated that light and dark environments affected the DHAR, TMT and GTPCH expression and that these genes were the predominant genes of vitamin C, E and folate biosynthesis pathways respectively during the germination. Levels of vitamin C and folate increased during the germination of sweet corn seeds while vitamin E had a declining manner. Sweet corn sprouts had higher vitamin C and E levels as well as relevant gene expression levels in light environment while illumination had little influence on the folate contents and the gene expression levels during the germination. These results indicate that there might be a collaborative relationship between vitamin C and folate regulation during sweet corn seed germination, while an inhibitive regulation might exist between vitamin C and E.
Regulation of Osteoclast Differentiation by Myosin X
Authors: Tasca Amy , Astleford Kristina , Lederman Ari , Jensen Eric D. , Lee Beth S. , Gopalakrishnan Rajaram , Mansky Kim C.
Published: August 2017

Osteoclasts begin as mononuclear cells that fuse to form multinuclear cells able to resorb bone. The mechanisms that regulate all the steps of osteoclast differentiation are not entirely known. MYO10, an unconventional myosin, has previously been shown in mature osteoclasts to play a role in attachment and podosome positioning. We determined that MYO10 is also expressed early during osteoclast differentiation. Loss of MYO10 expression in osteoclast precursors inhibits the ability of mononuclear osteoclasts to fuse into multinuclear osteoclasts. Expression ofNfatc1,Dc-stamp,Ctsk, andβ3integrinis reduced in the osteoclasts with reduced MYO10 expression. A slight reduction in the osteoclasts ability to migrate, as well as a reduction in SMAD 1/5/8 phosphorylation are also noted with reduced MYO10 expression. Interestingly we also detected a change in the ability of the osteoclast precursors to form tunneling nanotubes (TNTs), which suggests that MYO10 may regulate the presence of TNTs through its interaction with the cytoskeletal proteins.
Plant organ evolution revealed by phylotranscriptomics in Arabidopsis thaliana
Authors: Lei Li , Steffen Joshua G. , Osborne Edward J. , Toomajian Christopher
Published: August 2017

The evolution of phenotypes occurs through changes both in protein sequence and gene expression levels. Though much of plant morphological evolution can be explained by changes in gene expression, examining its evolution has challenges. To gain a new perspective on organ evolution in plants, we applied a phylotranscriptomics approach. We combined a phylostratigraphic approach with gene expression based on the strand-specific RNA-seq data from seedling, floral bud, and root of 19Arabidopsis thalianaaccessions to examine the age and sequence divergence of transcriptomes from these organs and how they adapted over time. Our results indicate that, among the sense and antisense transcriptomes of these organs, the sense transcriptomes of seedlings are the evolutionarily oldest across all accessions and are the most conserved in amino acid sequence for most accessions. In contrast, among the sense transcriptomes from these same organs, those from floral bud are evolutionarily youngest and least conserved in sequence for most accessions. Different organs have adaptive peaks at different stages in their evolutionary history; however, all three show a common adaptive signal from the Magnoliophyta to Brassicale stage. Our research highlights how phylotranscriptomic analyses can be used to trace organ evolution in the deep history of plant species.
Chloroplast genomes of Arabidopsis halleri ssp. gemmifera and Arabidopsis lyrata ssp. petraea: Structures and comparative analysis
Authors: Asaf Sajjad , Khan Abdul Latif , Khan Muhammad Aaqil , Waqas Muhammad , Kang Sang-Mo , Yun Byung-Wook , Lee In-Jung
Published: August 2017

We investigated the complete chloroplast (cp) genomes of non-model Arabidopsis halleri ssp. gemmifera and Arabidopsis lyrata ssp. petraea using Illumina paired-end sequencing to understand their genetic organization and structure. Detailed bioinformatics analysis revealed genome sizes of both subspecies ranging between 154.4~154.5 kbp, with a large single-copy region (84,197~84,158 bp), a small single-copy region (17,738~17,813 bp) and pair of inverted repeats (IRa/IRb; 26,264~26,259 bp). Both cp genomes encode 130 genes, including 85 protein-coding genes, eight ribosomal RNA genes and 37 transfer RNA genes. Whole cp genome comparison of A. halleri ssp. gemmifera and A. lyrata ssp. petraea, along with ten other Arabidopsis species, showed an overall high degree of sequence similarity, with divergence among some intergenic spacers. The location and distribution of repeat sequences were determined, and sequence divergences of shared genes were calculated among related species. Comparative phylogenetic analysis of the entire genomic data set and 70 shared genes between both cp genomes confirmed the previous phylogeny and generated phylogenetic trees with the same topologies. The sister species of A. halleri ssp. gemmifera is A. umezawana, whereas the closest relative of A. lyrata spp. petraea is A. arenicola.