bluuebunny/crossref_metadata_2025 huggingface dataset:
Electrostatic‐spray ionization mass spectrometry sniffing for perfume fingerprinting
Authors: Tobolkina Elena , Qiao Liang , Xu Guobin , Girault Hubert H.
Published: October 2013

RATIONALE

The perfume market is growing significantly, and it is easy to find imitative fragrances of probably all types of perfume. Such imitative fragrances are usually of lower quality than the authentic ones, creating a possible threat for perfume companies. Therefore, it is important to develop efficient chemical analysis techniques to screen rapidly perfume samples.

METHODS

Electrostatic‐spray ionization (ESTASI) was used to analyze directly samples sprayed or deposited on different types of paper. A linear ion trap mass spectrometer was used to detect the ions produced by ESTASI with a modified extended transfer capillary for 'sniffing' ions from the paper.

RESULTS

Several commercial perfumes and a model perfume were analyzed by ESTASI‐sniffing. The results obtained by paper ESTASI‐MS of commercial fragrances were compared with those obtained from ESI‐MS. In addition, a commercial fragrance was first nebulized on the hand and then soaked up by blotting paper, which was afterwards placed on an insulating plate for ESTASI‐MS analysis. Analysis of peptides and proteins was also performed to show that the paper ESTASI‐MS could be used for samples with very different molecular masses.

CONCLUSIONS

Paper ESTASI‐MS yields a rapid fingerprinting characterization of perfume fragrances, avoiding time‐consuming sample‐preparation steps, and thereby performing a rapid screening in a few seconds. Copyright © 2013 John Wiley & Sons, Ltd.
Can ion mobility mass spectrometry and density functional theory help elucidate protonation sites in 'small' molecules?
Authors: Lapthorn Cris , Dines Trevor J. , Chowdhry Babur Z. , Perkins George L. , Pullen Frank S.
Published: October 2013

RATIONALE

Ion mobility spectrometry‐mass spectrometry (IMS‐MS) offers an opportunity to combine measurements and/or calculations of the collision cross‐sections and subsequent mass spectra with computational modelling in order to derive the three‐dimensional structure of ions. IMS‐MS has previously been reported to separate two components for the compound norfloxacin, explained by protonation on two different sites, enabling the separation of protonated isomers (protomers) using ion mobility with distinguishable tandem mass spectrometric (MS/MS) data. This study reveals further insights into the specific example of norfloxacin and wider implications for ion mobility mass spectrometry.

METHODS

Using a quadrupole ion mobility time‐of‐flight mass spectrometer, the IMS and MS/MS spectra of norfloxacin were recorded and compared with theoretical calculations using molecular modelling (density functional theory), and subsequent collision cross‐section calculations using projection approximation.

RESULTS

A third significant component in the ion mobilogram of norfloxacin was observed under similar experimental conditions to those previously reported. The presence of the new component is convoluted by co‐elution with another previously observed component.

CONCLUSIONS

This case demonstrates the potential of combined IMS‐MS/MS with molecular modelling information for increased understanding of 'small‐molecule' fragmentation pathways. Copyright © 2013 John Wiley & Sons, Ltd.
Heavy quark energy loss far from equilibrium in a strongly coupled collision
Authors: Chesler Paul M. , Lekaveckas Mindaugas , Rajagopal Krishna
Published: October 2013

Abstract

We compute and study the drag force acting on a heavy quark propagating through the matter produced in the collision of two sheets of energy in a strongly coupled gauge theory that can be analyzed holographically. Although this matter is initially far from equilibrium, we find that the equilibrium expression for heavy quark energy loss in a homogeneous strongly coupled plasma with the same instantaneous energy density or pressure as that at the location of the quark describes many qualitative features of our results. One interesting exception is that there is a time delay after the initial collision before the heavy quark energy loss becomes significant. At later times, once a liquid plasma described by viscous hydrodynamics has formed, expressions based upon assuming instantaneous homogeneity and equilibrium provide a semi-quantitative description of our results — as long as the rapidity of the heavy quark is not too large. For a heavy quark with large rapidity, the gradients in the velocity of the hydrodynamic fluid result in qualitative consequences for the ‘drag’ force acting on the quark. In certain circumstances, the force required to drag the quark through the plasma can point opposite to the velocity of the quark, meaning that the force that the plasma exerts on a quark moving through it acts in the same direction as its velocity. And, generically, the force includes a component perpendicular to the direction of motion of the quark. Our results support a straightforward approach to modeling the drag on, and energy loss of, heavy quarks with modest rapidity in heavy ion collisions, both before and after the quark-gluon plasma hydrodynamizes, and provide cautionary lessons at higher rapidity.
Linear polarization of gluons and photons in unpolarized collider experiments
Authors: Pisano Cristian , Boer Daniël , Brodsky Stanley J. , Buffing Maarten G. A. , Mulders Piet J.
Published: October 2013

Abstract

We study azimuthal asymmetries in heavy quark pair production in unpolarized electron-proton and proton-proton collisions, where the asymmetries originate from the linear polarization of gluons inside unpolarized hadrons. We provide cross section expressions and study the maximal asymmetries allowed by positivity, for both charm and bottom quark pair production. The upper bounds on the asymmetries are shown to be very large depending on the transverse momentum of the heavy quarks, which is promising especially for their measurements at a possible future Electron-Ion Collider or a Large Hadron electron Collider. We also study the analogous processes and asymmetries in muon pair production as a means to probe linearly polarized photons inside unpolarized protons. For increasing invariant mass of the muon pair the asymmetries become very similar to the heavy quark pair ones. Finally, we discuss the process dependence of the results that arises due to differences in color flow and address the problem with factorization in case of proton-proton collisions.
Effect of Surfactants on Catalytic Activity of Diastase α‐Amylase
Authors: Antony Navya , Balachandran SreedharanNair , Mohanan Puzhavoorparambil V.
Published: October 2013

The enzyme amylase is one of the hydrolyzing enzymes used in detergent formulation in order to remove soil based on polysaccharides. The effectiveness of the enzyme depends on its compatibility with other ingredients of the formulation. Among the studied additives, comprising anionic surfactants sodium dodecyl hydrogen sulfate (SDS) and dioctyl sodium sulfosuccinate, the cationic surfactant cetyl trimethyl ammonium bromide (CTAB), nonionic surfactants polyoxyethylene sorbitan monooleate and polyoxyethylene octyl phenyl ether, carboxy methyl cellulose and sodium sulfate, only the anionic surfactant SDS and cationic surfactant CTAB showed catalytic enhancement of α‐amylase. The kinetic parameters, Km and kcat, showed an increase in catalytic activity in the micellar pseudophase. The decrease in optimum temperature from 55 to 30 °C and the shift in optimum pH from 5.5 to 7 on the addition of SDS and CTAB for the hydrolysis of starch are very favorable to enhance the washing characteristics.
Volumetric, Compressibility, and Surface Tension Studies on Micellization Behavior of SDS in Aqueous Medium: Effect of Sugars
Authors: Chauhan Suvarcha , Kumar Kuldeep , Singh Kailash , Jyoti Jiwan
Published: October 2013

The densities , velocities of sound , and surface tension , of anionic surfactant sodium dodecyl sulfate in presence of aqueous saccharides (fructose and maltose) with concentrations 0.01 and 0.10 mol kg−1 have been reported over a wide temperature range (293.15–313.15 K) at an interval of 5 K. The apparent molar volume , isentropic compressibility , and apparent molar adiabatic compression values have been calculated using densities and velocities of sound data. Both, and vary non‐linearly at lower concentration of surfactant and tend to achieve linearity at higher concentration of surfactant in presence of saccharides. From the surface tension data, parameters like surface excess , minimum area occupied by the surfactant molecule at the saturated air/solution interface and surface film pressure have been computed. The effect of additives on these parameters has been discussed in terms of different types of the interactions pertaining in the micellar system. An attempt has also been made to draw an inference regarding the effect of these additives on the critical micelle concentration of the surfactant.
Humanities in medicine: preparing for practice
Authors: Ramai Daryl , Shoshanna Goldin Shoshanna
Published: October 2013

None
Docetaxel-induced hypersensitivity pneumonitis mimicking lymphangitic carcinomatosis in a patient with metastatic adenocarcinoma of the lung
Authors: Taj Asma
Published: October 2013

Docetaxel belongs to the taxane family of anti-cancer drugs, which are commonly used in non-small cell lung cancers. They stabilize microtubules by preventing depolymerization, resulting in cell death. Pneumonitis is an uncommon side effect of docetaxel. We report a case of docetaxel induced hypersensitivity pneumonitis mimicking lymphangitic carcinomatosis in a patient with metastatic adenocarcinoma of the lung.
Thrombozytenaggregationshemmer: Was sind die Risiken?
Authors: Curkovic Ivanka , Egbring Marco , Kullak-Ublick Gerd A.
Published: October 2013

Blutungsereignisse, Arzneimittelwechselwirkungen und Therapieversagen sind relevante Risiken einer Therapie mit Plättchenaggregationshemmern. Die neuen Substanzen Prasugrel und Ticagrelor sind stärker wirksam als Clopidogrel und senken ischämische Ereignisse bei Patienten mit akutem Koronarsyndrom effizienter. Sie erhöhen allerdings potenziell auch die Blutungsraten. Eine Therapie mit Clopidogrel birgt das Risiko einer Therapieresistenz bei bis zu 20% der Patienten, die u. a. auf genetischen Polymorphismen und Arzneimittelinteraktionen beruht. Für Prasugrel und Ticagrelor bestehen keine Hinweise, dass genetische Polymorphismen die Wirksamkeit beeinflussen. In Risikosituationen muss die Therapie jedoch sorgfältig angepasst werden, um unerwünschte Wirkungen zu minimieren: So wird bei Patienten >75 Jahre und/oder einem Körpergewicht <60 kg aufgrund des erhöhten Blutungsrisikos eine Prasugrel-Dosisreduktion empfohlen. Ticagrelor ist in Kombination mit starken Cytochrom-P450–3A4-Hemmern kontraindiziert.
In and out: an analysis of epibiotic vs periplasmic bacterial predators
Authors: Pasternak Z , Njagi M , Shani Y , Chanyi R , Rotem O , Lurie-Weinberger M N , Koval S , Pietrokovski S , Gophna U , Jurkevitch E
Published: October 2013

Bdellovibrio and like organisms (BALO) are obligate predators of Gram-negative bacteria, belonging to the α- and δ-proteobacteria. BALO prey using either a periplasmic or an epibiotic predatory strategy, but the genetic background underlying these phenotypes is not known. Here we compare the epibiotic Bdellovibrio exovorus and Micavibrio aeruginosavorus to the periplasmic B. bacteriovorus and Bacteriovorax marinus. Electron microscopy showed that M. aeruginosavorus, but not B. exovorus, can attach to prey cells in a non-polar manner through its longitudinal side. Both these predators were resistant to a surprisingly high number of antibiotic compounds, possibly via 26 and 19 antibiotic-resistance genes, respectively, most of them encoding efflux pumps. Comparative genomic analysis of all the BALOs revealed that epibiotic predators have a much smaller genome (ca. 2.5 Mbp) than the periplasmic predators (ca. 3.5 Mbp). Additionally, periplasmic predators have, on average, 888 more proteins, at least 60% more peptidases, and one more rRNA operon. Fifteen and 219 protein families were specific to the epibiotic and the periplasmic predators, respectively, the latter clearly forming the core of the periplasmic ‘predatome’, which is upregulated during the growth phase. Metabolic deficiencies of epibiotic genomes include the synthesis of inosine, riboflavin, vitamin B6 and the siderophore aerobactin. The phylogeny of the epibiotic predators suggests that they evolved by convergent evolution, with M. aeruginosavorus originating from a non-predatory ancestor while B. exovorus evolved from periplasmic predators by gene loss.
Dispersal network structure and infection mechanism shape diversity in a coevolutionary bacteria-phage system
Authors: Sieber Michael , Robb Matthew , Forde Samantha E , Gudelj Ivana
Published: October 2013

Resource availability, dispersal and infection genetics all have the potential to fundamentally alter the coevolutionary dynamics of bacteria–bacteriophage interactions. However, it remains unclear how these factors synergise to shape diversity within bacterial populations. We used a combination of laboratory experiments and mathematical modeling to test how the structure of a dispersal network affects host phenotypic diversity in a coevolving bacteria-phage system in communities of differential resource input. Unidirectional dispersal of bacteria and phage from high to low resources consistently increased host diversity compared with a no dispersal regime. Bidirectional dispersal, on the other hand, led to a marked decrease in host diversity. Our mathematical model predicted these opposing outcomes when we incorporated modified gene-for-gene infection genetics. To further test how host diversity depended on the genetic underpinnings of the bacteria-phage interaction, we expanded our mathematical model to include different infection mechanisms. We found that the direction of dispersal had very little impact on bacterial diversity when the bacteria-phage interaction was mediated by matching alleles, gene-for-gene or related infection mechanisms. Our experimental and theoretical results demonstrate that the effects of dispersal on diversity in coevolving host–parasite systems depend on an intricate interplay of the structure of the underlying dispersal network and the specifics of the host–parasite interaction.
First biological measurements of deep-sea corals from the Red Sea
Authors: Roder C. , Berumen M. L. , Bouwmeester J. , Papathanassiou E. , Al-Suwailem A. , Voolstra C. R.
Published: October 2013

It is usually assumed that metabolic constraints restrict deep-sea corals to cold-water habitats, with ‘deep-sea’ and ‘cold-water’ corals often used as synonymous. Here we report on the first measurements of biological characters of deep-sea corals from the central Red Sea, where they occur at temperatures exceeding 20°C in highly oligotrophic and oxygen-limited waters. Low respiration rates, low calcification rates and minimized tissue cover indicate that a reduced metabolism is one of the key adaptations to prevailing environmental conditions. We investigated four sites and encountered six species of which at least two appear to be undescribed. One species is previously reported from the Red Sea but occurs in deep cold waters outside the Red Sea raising interesting questions about presumed environmental constraints for other deep-sea corals. Our findings suggest that the present understanding of deep-sea coral persistence and resilience needs to be revisited.
Vanishing of interband light absorption in a persistent spin helix state
Authors: Li Zhou , Marsiglio F. , Carbotte J. P.
Published: October 2013

Spin-orbit coupling plays an important role in various properties of very different materials. Moreover efforts are underway to control the degree and quality of spin-orbit coupling in materials with a concomitant control of transport properties. We calculate the frequency dependent optical conductivity in systems with both Rashba and Dresselhaus spin-orbit coupling. We find that when the linear Dresselhaus spin-orbit coupling is tuned to be equal to the Rashba spin-orbit coupling, the interband optical conductivity disappears. This is taken to be the signature of the recovery of SU(2) symmetry. The presence of the cubic Dresselhaus spin-orbit coupling modifies the dispersion relation of the charge carriers and the velocity operator. Thus the conductivity is modified, but the interband contribution remains suppressed at most but not all photon energies for a cubic coupling of reasonable magnitude. Hence, such a measurement can serve as a diagnostic probe of engineered spin-orbit coupling.
Competitive environments sustain costly altruism with negligible assortment of interactions
Authors: Doncaster C. Patrick , Jackson Adam , Watson Richard A.
Published: October 2013

Competition hinders the evolution of altruism amongst kin when beneficiaries gain at the expense of competing relatives. Altruism is consequently deemed to require stronger kin selection, or trait-selected synergies, or elastic population regulation, to counter this effect. Here we contest the view that competition puts any such demands on altruism. In ecologically realistic scenarios, competition influences both altruism and defection. We show how environments that pit defectors against each other allow strong altruism to evolve even in populations with negligible kin structure and no synergies. Competition amongst defectors presents relative advantages to altruism in the simplest games between altruists and defectors and the most generic models of altruistic phenotypes or genotypes invading non-altruistic populations under inelastic density regulation. Given the widespread inevitability of competition, selection will often favour altruism because its alternatives provide lower fitness. Strong competition amongst defectors nevertheless undermines altruism, by facilitating invasion of unrelated beneficiaries as parasites.
Chemical Toxicity Prediction
Authors: Cronin Mark , Madden Judith , Enoch Steven , Roberts David
Published: October 2013

The aim of this book is to provide the scientific background to using the formation of chemical categories, or groups, of molecules to allow for read-across i.e. the prediction of toxicity from chemical structure. It covers the scientific basis for this approach to toxicity prediction including the methods to group compounds (structural analogues and / or similarity, mechanism of action) and the tools to achieve this. The approaches to perform read-across within a chemical category are also described. The book will provide concise practical guidance for those wishing to apply these methods (in risk / hazard assessment) and will be illustrated with case studies. Chemical Toxicity Prediction is the first book that addresses the concept of category formation and read-across for toxicity prediction specifically. This topic has really taken off in the past few years due to concerns over dealing with the REACH legislation and also due to the availability of the OECD (Q)SAR Toolbox. Much (lengthy and complex) guidance is available on category formation e.g. from the OECD and, to a lesser extent, the European Chemicals Agency but there is no one single source of information that covers all techniques in a concise user-friendly format. There is a real need for this information as in silico toxicology has come to the fore in recent years, primarily as a result of the EU REACH legislation, but also due to many other drivers e.g. reduction of animal testing, Cosmetics regulation. Category formation is seen as the only practical approach to make rational and transparent predictions for complex (human) toxicological endpoints. The book covers all the areas required to create a robust category and perform read-across.
Approaches for Grouping Chemicals into Categories
Authors: Enoch S J , Roberts D. W.
Published: October 2013

This chapter outlines the various methods by which chemical similarity can be defined to allow for chemical category formation. The focus is on three methods: simple analogues, definition of the chemistry associated with molecular initiating events and chemoinformatics. An outline of how each method is used in practice and how they have been developed into in silico tools is presented.
Informing Chemical Categories through the Development of Adverse Outcome Pathways
Authors: Przybylak K R , Schultz T. W.
Published: October 2013

In this chapter, the AOP concept has been briefly described together with its usefulness in chemical category formation and the development of the SARs. It presents how the AOP should be developed, assessed and reported. The main advantage of the AOP in grouping chemicals is the categorisation of compounds based on both intrinsic chemical and biological activity. Such categories of chemicals which share not only MIE but also one or more early key events are more toxicologically meaningful than categories based solely on the MIE.
The State of the Art and Future Directions of Category Formation and Read-Across for Toxicity Prediction
Authors: Cronin M T D
Published: October 2013

This chapter describes the current status, future directions and needs of category formation and read­across to predict toxicity. It is acknowledged that there are several high quality tools and databases for read­across and category formation. Key amongst these tools is the OECD QSAR Toolbox which will require further updates and maintenance in the future. The free availability of toxicity data and information is growing and is essential to support read­across. The future will bring opportunities to use new sources of information, such as from molecular biology. These will undoubtedly inform the new generation of profilers that will be required to assist in grouping for human health endpoints such as repeated dose and reproductive toxicology – areas where profilers are currently lacking. These new profilers will also be linked to Adverse Outcome Pathways, the development of which must be co­ordinated at a global level. Lastly, whilst there has been considerable growth, there is still a need for education and training of scientists to undertake read­across and the preparation of evidence and documentation for regulatory use.
Liver type I regulatory T cells suppress germinal center formation in HBV-tolerant mice
Authors: Xu Long , Yin Wenwei , Sun Rui , Wei Haiming , Tian Zhigang
Published: October 2013

Significance

We present a unique study of a liver-induced systemic tolerance using an intact virus, other than a single protein component-induced liver-persistent model. Liver-educated regulatory cells migrate into peripheral sites and mediate the systemic tolerance. Kupffer cells induce the generation of type 1-like regulatory cells in an IL-10–dependent manner. A possible role of type 1-like regulatory cells in suppressing germinal center formation via secreting IL-10 is demonstrated. We observed that a “regulatory cell-based” tolerizing mechanism, rather than a “clonal deletion” mechanism, provides the possibility of reversing the tolerance by immunotherapeutic approaches.
Positional information, in bits
Authors: Dubuis Julien O. , Tkačik Gašper , Wieschaus Eric F. , Gregor Thomas , Bialek William
Published: October 2013

Significance

In a developing embryo, individual cells need to “know” where they are to do the right thing. How much do they know, and where is this knowledge written down? Here, we show that these questions can be made mathematically precise. In the fruit fly embryo, information about position is thought to be encoded by the concentration of particular protein molecules, and we measure this information, in bits. Just four different kinds of molecules are almost enough to specify the identity of every cell along the long axis of the embryo, and we argue that the way in which this information is distributed reflects an optimization principle, maximizing the information available from a limited number of molecules.
Stability analysis of explicit entropy viscosity methods for non-linear scalar conservation equations
Authors: Bonito Andrea , Guermond Jean-Luc , Popov Bojan
Published: October 2013

We establish the

L
2

L^2

-stability of an entropy viscosity technique applied to nonlinear scalar conservation equations. First- and second-order explicit time-stepping techniques using continuous finite elements in space are considered. The method is shown to be stable independently of the polynomial degree of the space approximation under the standard CFL condition.
Wnt5a signaling promotes apical and basolateral polarization of single epithelial cells
Authors: Gon Hidetoshi , Fumoto Katsumi , Ku Yonson , Matsumoto Shinji , Kikuchi Akira
Published: October 2013

Single epithelial-derived tumor cells have been shown to induce apical and basolateral (AB) polarity by expression of polarization-related proteins. However, physiological cues and molecular mechanisms for AB polarization of single normal epithelial cells are unclear. When intestinal epithelial cells 6 (IEC6 cells) were seeded on basement membrane proteins (Matrigel), single cells formed an F-actin cap on the upper cell surface, where apical markers accumulated, and a basolateral marker was localized to the rest of the cell surface region, in a Wnt5a signaling–dependent manner. However, these phenotypes were not induced by type I collagen. Rac1 activity in the noncap region was higher than that in the cap region, whereas Rho activity increased toward the cap region. Wnt5a signaling activated and inhibited Rac1 and RhoA, respectively, independently through Tiam1 and p190RhoGAP-A, which formed a tertiary complex with Dishevelled. Furthermore, Wnt5a signaling through Rac1 and RhoA was required for cystogenesis of IEC6 cells. These results suggest that Wnt5a promotes the AB polarization of IEC6 cells through regulation of Rac and Rho activities in a manner dependent on adhesion to specific extracellular matrix proteins.
Functional overlap among distinct G1/S inhibitory pathways allows robust G1 arrest by yeast mating pheromones
Authors: Pope Patricia A. , Pryciak Peter M.
Published: October 2013

In budding yeast, mating pheromones arrest the cell cycle in G1 phase via a pheromone-activated Cdk-inhibitor (CKI) protein, Far1. Alternate pathways must also exist, however, because deleting the cyclin CLN2 restores pheromone arrest to far1∆ cells. Here we probe whether these alternate pathways require the G1/S transcriptional repressors Whi5 and Stb1 or the CKI protein Sic1, whose metazoan analogues (Rb or p27) antagonize cell cycle entry. Removing Whi5 and Stb1 allows partial escape from G1 arrest in far1∆ cln2∆ cells, along with partial derepression of G1/S genes, which implies a repressor-independent route for inhibiting G1/S transcription. This route likely involves pheromone-induced degradation of Tec1, a transcriptional activator of the cyclin CLN1, because Tec1 stabilization also causes partial G1 escape in far1∆ cln2∆ cells, and this is additive with Whi5/Stb1 removal. Deleting SIC1 alone strongly disrupts Far1-independent G1 arrest, revealing that inhibition of B-type cyclin-Cdk activity can empower weak arrest pathways. Of interest, although far1∆ cln2∆ sic1∆ cells escaped G1 arrest, they lost viability during pheromone exposure, indicating that G1 exit is deleterious if the arrest signal remains active. Overall our findings illustrate how multiple distinct G1/S-braking mechanisms help to prevent premature cell cycle commitment and ensure a robust signal-induced G1 arrest.
Identification of the domains of cauliflower mosaic virus protein P6 responsible for suppression of RNA silencing and salicylic acid signalling
Authors: Laird Janet , McInally Carol , Carr Craig , Doddiah Sowjanya , Yates Gary , Chrysanthou Elina , Khattab Ahmed , Love Andrew J. , Geri Chiara , Sadanandom Ari , Smith Brian O. , Kobayashi Kappei , Milner Joel J.
Published: October 2013

Cauliflower mosaic virus (CaMV) encodes a 520 aa polypeptide, P6, which participates in several essential activities in the virus life cycle including suppressing RNA silencing and salicylic acid-responsive defence signalling. We infectedArabidopsiswith CaMV mutants containing short in-frame deletions within the P6 ORF. A deletion in the distal end of domain D-I (the N-terminal 112 aa) of P6 did not affect virus replication but compromised symptom development and curtailed the ability to restore GFP fluorescence in a GFP-silenced transgenicArabidopsisline. A deletion in the minimum transactivator domain was defective in virus replication but retained the capacity to suppress RNA silencing locally. Symptom expression in CaMV-infected plants is apparently linked to the ability to suppress RNA silencing. When transiently co-expressed with tomato bushy stunt virus P19, an elicitor of programmed cell death inNicotiana tabacum, WT P6 suppressed the hypersensitive response, but three mutants, two with deletions within the distal end of domain D-I and one involving the N-terminal nuclear export signal (NES), were unable to do so. Deleting the N-terminal 20 aa also abolished the suppression of pathogen-associated molecular pattern-dependentPR1aexpression following agroinfiltration. However, the two other deletions in domain D-I retained this activity, evidence that the mechanisms underlying these functions are not identical. The D-I domain of P6 when expressed alone failed to suppress either cell death orPR1aexpression and is therefore necessary but not sufficient for all three defence suppression activities. Consequently, concerns about the biosafety of genetically modified crops carrying truncated ORFVI sequences appear unfounded.
A systems level predictive model for global gene regulation of methanogenesis in a hydrogenotrophic methanogen
Authors: Yoon Sung Ho , Turkarslan Serdar , Reiss David J. , Pan Min , Burn June A. , Costa Kyle C. , Lie Thomas J. , Slagel Joseph , Moritz Robert L. , Hackett Murray , Leigh John A. , Baliga Nitin S.
Published: October 2013

Methanogens catalyze the critical methane-producing step (called methanogenesis) in the anaerobic decomposition of organic matter. Here, we present the first predictive model of global gene regulation of methanogenesis in a hydrogenotrophic methanogen,Methanococcus maripaludis. We generated a comprehensive list of genes (protein-coding and noncoding) forM. maripaludisthrough integrated analysis of the transcriptome structure and a newly constructed Peptide Atlas. The environment and gene-regulatory influence network (EGRIN) model of the strain was constructed from a compendium of transcriptome data that was collected over 58 different steady-state and time-course experiments that were performed in chemostats or batch cultures under a spectrum of environmental perturbations that modulated methanogenesis. Analyses of the EGRIN model have revealed novel components of methanogenesis that included at least three additional protein-coding genes of previously unknown function as well as one noncoding RNA. We discovered that at least five regulatory mechanisms act in a combinatorial scheme to intercoordinate key steps of methanogenesis with different processes such as motility, ATP biosynthesis, and carbon assimilation. Through a combination of genetic and environmental perturbation experiments we have validated the EGRIN-predicted role of two novel transcription factors in the regulation of phosphate-dependent repression of formate dehydrogenase—a key enzyme in the methanogenesis pathway. The EGRIN model demonstrates regulatory affiliations within methanogenesis as well as between methanogenesis and other cellular functions.
The Effect of Cylinder Bore Distortion on Lube Oil Consumption and Blow-By
Authors: Kagnici Fatih , Akalin Ozgen
Published: October 2013

It is well known that cylinder bore deformations during engine operation cause a number of problems in piston ring lubrication. Particularly, the deterioration of piston ring and cylinder bore conformability results in a significant increase in lubricating oil consumption. Therefore, measurement and identification of cylinder bore distortion has been an important subject for engine designers. In this study, an analytical lubricating oil consumption model was developed for a diesel engine. Piston stiffness was identified as an important input parameter for the oil consumption model, and the stiffness matrix of the piston was calculated using finite element simulations. In addition, finite element analysis was performed to determine the distorted cylinder block shape in engine running conditions. Pressure curves and loads obtained in actual engine tests were used in the analysis. The Fourier coefficients of a distorted cylinder bore was calculated which characterize the deformed bore orders. Using these Fourier coefficients, several distorted bore shapes were regenerated, including a straight bore and the effect of each order on total lube oil consumption was investigated by means of the oil consumption model.
Non-C2 Lie Bracket Averaging for Nonsmooth Extremum Seekers
Authors: Scheinker Alexander , Krstić Miroslav
Published: October 2013

A drawback of extremum seeking-based control is the introduction of a high frequency oscillation into a system's dynamics, which prevents even stable systems from settling at their equilibrium points. In this paper, we develop extremum seeking-based controllers whose control efforts, unlike that of traditional extremum seeking-based schemes, vanish as the system approaches equilibrium. Because the controllers that we develop are not differentiable at the origin, in proving a form of stability of our control scheme we start with a more general problem and extend the semiglobal practical stability result of Moreau and Aeyels to develop a relationship between systems and their averages even for systems which are nondifferentiable at a point. More specifically, in order to apply the practical stability results to our control scheme, we extend the Lie bracket averaging result of Kurzweil, Jarnik, Sussmann, Liu, Gurvits, and Li to non-C2 functions. We then improve on our previous results on model-independent semiglobal exponential practical stabilization for linear time-varying single-input systems under the assumption that the time-varying input vector, which is otherwise unknown, satisfies a persistency of excitation condition over a sufficiently short window.
Integrative Annotation of Variants from 1092 Humans: Application to Cancer Genomics
Authors: Khurana Ekta , Fu Yao , Colonna Vincenza , Mu Xinmeng Jasmine , Kang Hyun Min , Lappalainen Tuuli , Sboner Andrea , Lochovsky Lucas , Chen Jieming , Harmanci Arif , Das Jishnu , Abyzov Alexej , Balasubramanian Suganthi , Beal Kathryn , Chakravarty Dimple , Challis Daniel , Chen Yuan , Clarke Declan , Clarke Laura , Cunningham Fiona , Evani Uday S. , Flicek Paul , Fragoza Robert , Garrison Erik , Gibbs Richard , Gümüş Zeynep H. , Herrero Javier , Kitabayashi Naoki , Kong Yong , Lage Kasper , Liluashvili Vaja , Lipkin Steven M. , MacArthur Daniel G. , Marth Gabor , Muzny Donna , Pers Tune H. , Ritchie Graham R. S. , Rosenfeld Jeffrey A. , Sisu Cristina , Wei Xiaomu , Wilson Michael , Xue Yali , Yu Fuli ,   1000 Genomes Project Consortium, Dermitzakis Emmanouil T. , Yu Haiyuan , Rubin Mark A. , Tyler-Smith Chris , Gerstein Mark
Published: October 2013

Identifying Important Identifiers

Each of us has millions of sequence variations in our genomes. Signatures of purifying or negative selection should help identify which of those variations is functionally important.

Khurana
et al.

(
1235587
) used sequence polymorphisms from 1092 humans across 14 populations to identify patterns of selection, especially in noncoding regulatory regions. Noncoding regions under very strong negative selection included binding sites of some chromatin and general transcription factors (TFs) and core motifs of some important TF families. Positive selection in TF binding sites tended to occur in network hub promoters. Many recurrent somatic cancer variants occurred in noncoding regulatory regions and thus might indicate mutations that drive cancer.
Selective Gas Transport Through Few-Layered Graphene and Graphene Oxide Membranes
Authors: Kim Hyo Won , Yoon Hee Wook , Yoon Seon-Mi , Yoo Byung Min , Ahn Byung Kook , Cho Young Hoon , Shin Hye Jin , Yang Hoichang , Paik Ungyu , Kwon Soongeun , Choi Jae-Young , Park Ho Bum
Published: October 2013

Gas Separations

When gas separation membranes are made thinner, they usually allow permeating gases to pass through faster. However, a thinner membrane may be poorer at separating between gas species.

Kim
et al.

(p.
91
) examined the permeability and selectivity of layered graphene and graphene oxide membranes. Gas molecules diffuse through defective pores and channels that form between the layers. Controlling these structures tuned the properties of the membranes to allow the extraction of carbon dioxide from other gases.

Li
et al.

(p.
95
) describe membranes as thin as 1.8 nanometers made from only two to three layers of graphene oxide. Small defects within the layers allowed hydrogen to pass through, separating it from carbon dioxide and nitrogen.
Fungal Small RNAs Suppress Plant Immunity by Hijacking Host RNA Interference Pathways
Authors: Weiberg Arne , Wang Ming , Lin Feng-Mao , Zhao Hongwei , Zhang Zhihong , Kaloshian Isgouhi , Huang Hsien-Da , Jin Hailing
Published: October 2013

RNA on the Attack

Plant microbial pathogens often work through protein effectors that are delivered into the plant cells to disrupt critical cellular functions.

Weiberg
et al.

(p.
118
; see the Perspective by

Baulcombe

) have now found that small RNAs (sRNAs) of the fungus
Botrytis cinerea
can play a similar role. After fungal infection of tomato or
Arabidopsis
leaves, the plant cells contained a suite of fungal-derived sRNAs. Three sRNAs were found to bind to the plant's own Argonaute protein, thereby silencing the plant's fungal defense genes.
Surviving in a Marine Desert: The Sponge Loop Retains Resources Within Coral Reefs
Authors: de Goeij Jasper M. , van Oevelen Dick , Vermeij Mark J. A. , Osinga Ronald , Middelburg Jack J. , de Goeij Anton F. P. M. , Admiraal Wim
Published: October 2013

Sponge Pump

“Darwin's Paradox” asks how productive and diverse ecosystems like coral reefs thrive in the marine equivalent of a desert.

De Goeij
et al.

(p.
108
) now show that coral reef sponges are part of a highly efficient recycling pathway for dissolved organic matter (DOM), converting it, via rapid sponge-cell turnover, into cellular detritus that becomes food for reef consumers. DOM transfer through the sponge loop approaches the gross primary production rates required for the entire coral reef ecosystem.
Fine-Tuning Photosynthesis
Authors: Rochaix Jean-David
Published: October 2013

A potassium channel helps to fine-tune the photosynthetic machinery of plants to changes in environmental conditions.

[Also see Report by

Carraretto
et al.

]
Small RNA—the Secret of Noble Rot
Authors: Baulcombe David
Published: October 2013

Small RNA from a fungal pathogen is transferred to cells of a plant host where it silences the mRNA for defense proteins.

[Also see Report by

Weiberg
et al.

]
A Risky Science Communication Environment for Vaccines
Authors: Kahan Dan M.
Published: October 2013

Neglecting the science of science communication puts the value of decision-relevant science at risk.

[Also see Perspective by
Bauch and Galvani
]
Winning the Translational Race: Making Good Choices in Biomarker Assay Development for the Clinic
Authors: Kennedy Richard , Timmons James A.
Published: October 2013

In an effort to develop more tailored approaches to managing disease, there has been a surge in biomarker research aimed at providing truly personalized medicine. The increase in interest over the past 20 years suggests great promise that biomarkers will transform patient treatment. However, despite the optimism and intense research, relatively few are in routine clinical use today. Attention has now turned to actively translating actionable biomarkers and biomarker signatures into clinical utility—not an easy task. The major reasons for clinical failure of biomarkers are poor experimental design and inappropriate choice of assay. It is therefore critical to carefully construct biomarker discovery and validation studies using the most appropriate assays, and to develop these into validated analytical methods suitable for clinical practice. This webinar will review the unprecedented range of technology choices, and provide insight into the challenges confronting researchers when selecting the right biomarker to pursue and the best assay to develop for the clinic.
For Researchers, IPCC Leaves a Deep Impression
Authors: Kintisch Eli
Published: October 2013

It's not clear how much impact a massive new report on climate change will have on policymakers, but it is clear that the work of the Intergovernmental Panel on Climate Change (IPCC) has left a deep mark on global science.
Large-Scale Gene Comparisons Boost Tree of Life Studies
Authors: Pennisi Elizabeth
Published: October 2013

Building family trees is getting a lot easier with new methods that pull out hundreds of genetic markers to compare.
NIH Seeks Better Database for Genetic Diagnosis
Authors: Marshall Eliot
Published: October 2013

NIH builds ClinGen—a clinical reference site for all human gene variants.
The Power of Negative Thinking
Authors: Couzin-Frankel Jennifer
Published: October 2013

Gaining ground in the ongoing struggle to coax researchers to share negative results.
What's Lost When a Meeting Goes Virtual
Authors: Mervis Jeffrey
Published: October 2013

This summer, NASA's Lunar Science Forum became the largest scientific gathering to embrace the new world of cyber meetings. The experience drew mixed reviews.
Meetings That Flatter, but May Not Deliver
Authors: Cohen Jon
Published: October 2013

"Predatory" conferences—meetings, sometimes sparsely attended, that seem to come into being primarily to make money—have become a cottage industry in scientific communication.
Salivary Biomarkers: Toward Future Clinical and Diagnostic Utilities
Authors: Yoshizawa Janice M. , Schafer Christopher A. , Schafer Jason J. , Farrell James J. , Paster Bruce J. , Wong David T. W.
Published: October 2013

The pursuit of timely, cost-effective, accurate, and noninvasive diagnostic methodologies is an endeavor of urgency among clinicians and scientists alike. Detecting pathologies at their earliest stages can significantly affect patient discomfort, prognosis, therapeutic intervention, survival rates, and recurrence. Diagnosis and monitoring often require painful invasive procedures such as biopsies and repeated blood draws, adding undue stress to an already unpleasant experience. The discovery of saliva-based microbial, immunologic, and molecular biomarkers offers unique opportunities to bypass these measures by utilizing oral fluids to evaluate the condition of both healthy and diseased individuals. Here we discuss saliva and its significance as a source of indicators for local, systemic, and infectious disorders. We highlight contemporary innovations and explore recent discoveries that deem saliva a mediator of the body's physiological condition. Additionally, we examine the current state of salivary diagnostics and its associated technologies, future aspirations, and potential as the preferred route of disease detection, monitoring, and prognosis.
Recent Advances in Understanding Enteric Pathogenic Escherichia coli
Authors: Croxen Matthew A. , Law Robyn J. , Scholz Roland , Keeney Kristie M. , Wlodarska Marta , Finlay B. Brett
Published: October 2013

Although
Escherichia coli
can be an innocuous resident of the gastrointestinal tract, it also has the pathogenic capacity to cause significant diarrheal and extraintestinal diseases. Pathogenic variants of
E. coli
(pathovars or pathotypes) cause much morbidity and mortality worldwide. Consequently, pathogenic
E. coli
is widely studied in humans, animals, food, and the environment. While there are many common features that these pathotypes employ to colonize the intestinal mucosa and cause disease, the course, onset, and complications vary significantly. Outbreaks are common in developed and developing countries, and they sometimes have fatal consequences. Many of these pathotypes are a major public health concern as they have low infectious doses and are transmitted through ubiquitous mediums, including food and water. The seriousness of pathogenic
E. coli
is exemplified by dedicated national and international surveillance programs that monitor and track outbreaks; unfortunately, this surveillance is often lacking in developing countries. While not all pathotypes carry the same public health profile, they all carry an enormous potential to cause disease and continue to present challenges to human health. This comprehensive review highlights recent advances in our understanding of the intestinal pathotypes of
E. coli
.
Update on Tick-Borne Rickettsioses around the World: a Geographic Approach
Authors: Parola Philippe , Paddock Christopher D. , Socolovschi Cristina , Labruna Marcelo B. , Mediannikov Oleg , Kernif Tahar , Abdad Mohammad Yazid , Stenos John , Bitam Idir , Fournier Pierre-Edouard , Raoult Didier
Published: October 2013

Tick-borne rickettsioses are caused by obligate intracellular bacteria belonging to the spotted fever group of the genusRickettsia. These zoonoses are among the oldest known vector-borne diseases. However, in the past 25 years, the scope and importance of the recognized tick-associated rickettsial pathogens have increased dramatically, making this complex of diseases an ideal paradigm for the understanding of emerging and reemerging infections. Several species of tick-borne rickettsiae that were considered nonpathogenic for decades are now associated with human infections, and novelRickettsiaspecies of undetermined pathogenicity continue to be detected in or isolated from ticks around the world. This remarkable expansion of information has been driven largely by the use of molecular techniques that have facilitated the identification of novel and previously recognized rickettsiae in ticks. New approaches, such as swabbing of eschars to obtain material to be tested by PCR, have emerged in recent years and have played a role in describing emerging tick-borne rickettsioses. Here, we present the current knowledge on tick-borne rickettsiae and rickettsioses using a geographic approach toward the epidemiology of these diseases.
Pathogenesis and Current Approaches to Control of Varicella-Zoster Virus Infections
Authors: Gershon Anne A. , Gershon Michael D.
Published: October 2013

Varicella-zoster virus (VZV) was once thought to be a fairly innocuous pathogen. That view is no longer tenable. The morbidity and mortality due to the primary and secondary diseases that VZV causes, varicella and herpes zoster (HZ), are significant. Fortunately, modern advances, including an available vaccine to prevent varicella, a therapeutic vaccine to diminish the incidence and ameliorate sequelae of HZ, effective antiviral drugs, a better understanding of VZV pathogenesis, and advances in diagnostic virology have made it possible to control VZV in the United States. Occult forms of VZV-induced disease have been recognized, including zoster sine herpete and enteric zoster, which have expanded the field. Future progress should include development of more effective vaccines to prevent HZ and a more complete understanding of the consequences of VZV latency in the enteric nervous system.
An Atypical Clostridium Strain Related to the Clostridium botulinum Group III Strain Isolated from a Human Blood Culture
Authors: Bouvet Philippe , Ruimy Raymond , Bouchier Christiane , Faucher Nathalie , Mazuet Christelle , Popoff Michel R.
Published: October 2013

A nontoxigenic strain isolated from a fatal human case of bacterial sepsis was identified as a
Clostridium
strain from
Clostridium botulinum
group III, based on the phenotypic characters and 16S rRNA gene sequence, and was found to be related to the mosaic
C. botulinum
D/C strain according to a multilocus sequence analysis of 5 housekeeping genes.