bluuebunny/crossref_metadata_2025 huggingface dataset:
The effects of transient, localized electric fields on equatorial electron acceleration and transport toward the inner magnetosphere
Authors: Gabrielse C. , Angelopoulos V. , Runov A. , Turner D. L.
Published: September 2012

Motivated by recent observations of intense electric fields and elevated energetic particle fluxes within flow bursts beyond geosynchronous altitude (Runov et al., 2009, 2011), we apply modeling of particle guiding centers in prescribed but realistic electric fields to improve our understanding of energetic particle acceleration and transport toward the inner magnetosphere through model‐data comparisons. Representing the vortical nature of an earthward traveling flow burst, a localized, westward‐directed transient electric field flanked on either side by eastward fields related to tailward flow is superimposed on a nominal steady state electric field. We simulate particle spectra observed at multiple THEMIS spacecraft located throughout the magnetotail and fit the modeled spectra to observations, thus constraining properties of the electric field model. We find that a simple potential electric field model is capable of explaining the presence and spectral properties of both geosynchronous altitude and “trans‐geosynchronous” injections at higher L‐shells (L > 6.6 RE) in a manner self‐consistent with the injections' inward penetration. In particular, despite the neglect of the magnetic field changes imparted by dipolarization and the inductive electric field associated with them, such a model can adequately describe the physics of both dispersed injections and depletions (“dips”) in energy flux in terms of convective fields associated with earthward flow channels and their return flow. The transient (impulsive), localized, and vortical nature of the earthward‐propagating electric field pulse is what makes this model particularly effective.
Snow dunes: A controlling factor of melt pond distribution on Arctic sea ice
Authors: Petrich Chris , Eicken Hajo , Polashenski Christopher M. , Sturm Matthew , Harbeck Jeremy P. , Perovich Donald K. , Finnegan David C.
Published: September 2012

The location of snow dunes over the course of the ice‐growth season 2007/08 was mapped on level landfast first‐year sea ice near Barrow, Alaska. Landfast ice formed in mid‐December and exhibited essentially homogeneous snow depths of 4–6 cm in mid‐January; by early February distinct snow dunes were observed. Despite additional snowfall and wind redistribution throughout the season, the location of the dunes was fixed by March, and these locations were highly correlated with the distribution of meltwater ponds at the beginning of June. Our observations, including ground‐based light detection and ranging system (lidar) measurements, show that melt ponds initially form in the interstices between snow dunes, and that the outline of the melt ponds is controlled by snow depth contours. The resulting preferential surface ablation of ponded ice creates the surface topography that later determines the melt pond evolution.
The effect of bias feed profile on the linewidth of noisy Josephson flux flow oscillator
Authors: Matrozova Ekaterina A. , Pankratov Andrey L. , Revin Leonid S.
Published: September 2012

For creation of a noisy non-stationary spectrometer operating in the sub-THz frequency range, the emitting power and spectral characteristics of a flux-flow oscillator based on a long Josephson junction are considered. The effect of bias current profiles on the spectral linewidth of a long overlap Josephson junction is investigated and compared with the inline junction geometry. It has been demonstrated that the spectral linewidth can be increased by a factor of three with a moderate reduction of the emitted power.
Hard x-ray photoemission spectroscopy of Bi2S3 thin films
Authors: ten Haaf Sebastian , Balke Benjamin , Felser Claudia , Jakob Gerhard
Published: September 2012

The electronic structure of polycrystalline Bi2S3 thin films deposited by thermal evaporation under high vacuum conditions was investigated with respect to their potential use as absorber materials in p-i-n solar cells by means of hard x-ray photoemission spectroscopy at the PETRA III synchrotron. A clear influence of the post-deposition treatment on the electronic structure could be observed, resulting in a lowering of the Fermi level as well as in a change of the electronic states in the valence band. Furthermore, chemical shifts of Bi2S3 were determined in the bulk-sensitive hard x-ray regime as ΔEB,Bi=1.35 eV and ΔEB,S=−2.80 eV.
The origin of magnetism in perovskite ferroelectric ABO3 nanoparticles (A = K,Li; B = Ta,Nb or A = Ba,Sr,Pb; B = Ti)
Authors: Bahoosh S. G. , Wesselinowa J. M.
Published: September 2012

Using spin Hamiltonian models and Green’s function techniques, we study the ferroic order parameters of ferroelectric nanoparticles, and show how multiferroic behavior can be achieved in such systems. We present a theoretical study suggesting that unexpected ferromagnetic properties of perovskite ferroelectric ABO3 nanoparticles (A = K, Li; B = Ta, Nb or A = Ba, Sr, Pb; B = Ti) observed recently at room temperatures can be explained by considering oxygen vacancies at the surface of the nanocrystalline materials. Such vacancies lead to the appearance of Ta4+ and/or Ta3+ (Ti3+ and/or Ti2+) ions at the surface with nonzero net spin. The resulting different valence compared to the Ta5+ (or Ti4+) with S = 0 in the bulk offers a nonzero magnetization which increases with decreasing particle size. The system shows a multiferroic behavior below a critical size of the nanoparticles and the related polarization tends to a saturation value when the particle size is enhanced.
Thermal conductance at atomically clean and disordered silicon/aluminum interfaces: A molecular dynamics simulation study
Authors: Ih Choi Woon , Kim Kwiseon , Narumanchi Sreekant
Published: September 2012

Thermal resistance between layers impedes effective heat dissipation in electronics packaging applications. Thermal conductance for clean and disordered interfaces between silicon (Si) and aluminum (Al) was computed using realistic Si/Al interfaces and classical molecular dynamics with the modified embedded atom method potential. These realistic interfaces, which include atomically clean as well as disordered interfaces, were obtained using density functional theory. At 300 K, the magnitude of interfacial conductance due to phonon-phonon scattering obtained from the classical molecular dynamics simulations was approximately five times higher than the conductance obtained using analytical elastic diffuse mismatch models. Interfacial disorder reduced the thermal conductance due to increased phonon scattering with respect to the atomically clean interface. Also, the interfacial conductance, due to electron-phonon scattering at the interface, was greater than the conductance due to phonon-phonon scattering. This indicates that phonon-phonon scattering is the bottleneck for interfacial transport at the semiconductor/metal interfaces. The molecular dynamics modeling predictions for interfacial thermal conductance for a 5-nm disordered interface between Si/Al were in-line with recent experimental data in the literature.
In vitro electrical-stimulated wound-healing chip for studying electric field-assisted wound-healing process
Authors: Sun Yung-Shin , Peng Shih-Wei , Cheng Ji-Yen
Published: September 2012

The wound-healing assay is an easy and economical way to quantify cell migration under diverse stimuli. Traditional assays such as scratch assays and barrier assays are widely and commonly used, but neither of them can represent the complicated condition when a wound occurs. It has been suggested that wound-healing is related to electric fields, which were found to regulate wound re-epithelialization. As a wound occurs, the disruption of epithelial barrier short-circuits the trans-epithelial potential and then a lateral endogenous electric field is created. This field has been proved invitro as an important cue for guiding the migration of fibroblasts, macrophages, and keratinocytes, a phenomenon termed electrotaxis or galvanotaxis. In this paper, we report a microfluidic electrical-stimulated wound-healing chip (ESWHC) integrating electric field with a modified barrier assay. This chip was used to study the migration of fibroblasts under different conditions such as serum, electric field, and wound-healing-promoting drugs. We successfully demonstrate the feasibility of ESWHC to effectively and quantitatively study cell migration during wound-healing process, and therefore this chip could be useful in drug discovery and drug safety tests.
Raman spectroscopy of the interlayer shear mode in few-layer MoS2 flakes
Authors: Plechinger G. , Heydrich S. , Eroms J. , Weiss D. , Schüller C. , Korn T.
Published: September 2012

Single- and few-layer MoS2 has recently gained attention as an interesting material system for opto-electronics. Here, we report on scanning Raman measurements on few-layer MoS2 flakes prepared by exfoliation. We observe a Raman mode corresponding to a rigid shearing oscillation of adjacent layers. This mode appears at very low Raman shifts between 20 and 30 cm−1. Its position strongly depends on the number of layers, which we independently determine using atomic force microscopy and investigation of the other characteristic Raman modes. Raman spectroscopy of the shear mode, therefore, is a useful tool to determine the number of layers for few-layer MoS2 flakes.
Bark beetle outbreaks, wildfires and defensible space: how much area do we need to treat to protect homes and communities?
Authors: Aronson Glen , Kulakowski Dominik
Published: September 2012

Extensive beetle outbreaks across western North American forests have spurred debates about how to best protect communities from wildfire. Previous work has found that fuels in the wildland–urban interface and especially in the defensible space (40-m radius) around structures are the most important determinants of the flammability of structures during wildfire. We: (1) examined the extent of outbreaks in the western US and their intersection with the wildland-urban interface and its surrounding area and (2) calculated the combined area of defensible space around all wildland-urban interface housing units in the western US. This analysis indicates that: (1) >98% of areas affected by outbreaks are in remote areas rather than in the wildland-urban interface and (2) in the context of limited resources and the goal of protecting homes and communities from wildfire, the area required to create defensible space around all homes in the wildland-urban interface of the western US (which effectively reduces fire risk to structures) is substantially less than that needed to treat all beetle-affected forests (which does not reduce fire risk to structures as effectively). Thus, focussing fuel-reduction treatments in the immediate vicinity of homes and communities rather than in remote beetle-affected forests would be more effective at reducing fire risk to those structures and would incur lower financial and ecological costs.
Shaping acoustic fields as a toolset for microfluidic manipulations in diagnostic technologies
Authors: Reboud Julien , Bourquin Yannyk , Wilson Rab , Pall Gurman S. , Jiwaji Meesbah , Pitt Andrew R. , Graham Anne , Waters Andrew P. , Cooper Jonathan M.
Published: September 2012

Ultrasonics offers the possibility of developing sophisticated fluid manipulation tools in lab-on-a-chip technologies. Here we demonstrate the ability to shape ultrasonic fields by using phononic lattices, patterned on a disposable chip, to carry out the complex sequence of fluidic manipulations required to detect the rodent malaria parasite
Plasmodium berghei
in blood. To illustrate the different tools that are available to us, we used acoustic fields to produce the required rotational vortices that mechanically lyse both the red blood cells and the parasitic cells present in a drop of blood. This procedure was followed by the amplification of parasitic genomic sequences using different acoustic fields and frequencies to heat the sample and perform a real-time PCR amplification. The system does not require the use of lytic reagents nor enrichment steps, making it suitable for further integration into lab-on-a-chip point-of-care devices. This acoustic sample preparation and PCR enables us to detect
ca.
30 parasites in a microliter-sized blood sample, which is the same order of magnitude in sensitivity as lab-based PCR tests. Unlike other lab-on-a-chip methods, where the sample moves through channels, here we use our ability to shape the acoustic fields in a frequency-dependent manner to provide different analytical functions. The methods also provide a clear route toward the integration of PCR to detect pathogens in a single handheld system.
Activator protein 1 suppresses antitumor T-cell function via the induction of programmed death 1
Authors: Xiao Gang , Deng Anqi , Liu Haifeng , Ge Gaoxiang , Liu Xiaolong
Published: September 2012

T cells play a critical role in tumor immunosurveillance by eliminating newly transformed somatic cells. However, tumor cell variants can escape from immunological control after immunoediting, leading to tumor progression. Whether and how T cells respond to tumor growth remain unclear. Here, we found that tumor-infiltrating T cells exhibited persistently up-regulated expression of the activator protein 1 (AP-1) subunit c-Fos during tumor progression. The ectopic expression of c-Fos in T cells exacerbated tumor growth, whereas the T-cell–specific deletion of c-Fos reduced tumor malignancy. This unexpected immunosuppressive effect of c-Fos was mediated through the induced expression of immune inhibitory receptor programmed death 1 (PD-1) via the direct binding of c-Fos to the AP-1–binding site in the
Pdcd1
(gene encoding PD-1) promoter. A knock-in mutation of this binding site abrogated PD-1 induction, augmented antitumor T-cell function and repressed tumor growth. Taken together, these findings indicate that T-cell c-Fos subsequently induces PD-1 expression in response to tumor progression and that disrupting such induction is essential for repression of tumor growth.
Assistive listening devices drive neuroplasticity in children with dyslexia
Authors: Hornickel Jane , Zecker Steven G. , Bradlow Ann R. , Kraus Nina
Published: September 2012

Children with dyslexia often exhibit increased variability in sensory and cognitive aspects of hearing relative to typically developing peers. Assistive listening devices (classroom FM systems) may reduce auditory processing variability by enhancing acoustic clarity and attention. We assessed the impact of classroom FM system use for 1 year on auditory neurophysiology and reading skills in children with dyslexia. FM system use reduced the variability of subcortical responses to sound, and this improvement was linked to concomitant increases in reading and phonological awareness. Moreover, response consistency before FM system use predicted gains in phonological awareness. A matched control group of children with dyslexia attending the same schools who did not use the FM system did not show these effects. Assistive listening devices can improve the neural representation of speech and impact reading-related skills by enhancing acoustic clarity and attention, reducing variability in auditory processing.
Sulfur isotopes of organic matter preserved in 3.45-billion-year-old stromatolites reveal microbial metabolism
Authors: Bontognali Tomaso R. R. , Sessions Alex L. , Allwood Abigail C. , Fischer Woodward W. , Grotzinger John P. , Summons Roger E. , Eiler John M.
Published: September 2012

The 3.45-billion-year-old Strelley Pool Formation of Western Australia preserves stromatolites that are considered among the oldest evidence for life on Earth. In places of exceptional preservation, these stromatolites contain laminae rich in organic carbon, interpreted as the fossil remains of ancient microbial mats. To better understand the biogeochemistry of these rocks, we performed microscale in situ sulfur isotope measurements of the preserved organic sulfur, including both Δ
33
S and

. This approach allows us to tie physiological inference from isotope ratios directly to fossil biomass, providing a means to understand sulfur metabolism that is complimentary to, and independent from, inorganic proxies (e.g., pyrite). Δ
33
S values of the kerogen reveal mass-anomalous fractionations expected of the Archean sulfur cycle, whereas

values show large fractionations at very small spatial scales, including values below -15‰. We interpret these isotopic patterns as recording the process of sulfurization of organic matter by H
2
S in heterogeneous mat pore-waters influenced by respiratory S metabolism. Positive Δ
33
S anomalies suggest that disproportionation of elemental sulfur would have been a prominent microbial process in these communities.
Molecular analysis of the amphioxus frontal eye unravels the evolutionary origin of the retina and pigment cells of the vertebrate eye
Authors: Vopalensky Pavel , Pergner Jiri , Liegertova Michaela , Benito-Gutierrez Elia , Arendt Detlev , Kozmik Zbynek
Published: September 2012

The origin of vertebrate eyes is still enigmatic. The “frontal eye” of amphioxus, our most primitive chordate relative, has long been recognized as a candidate precursor to the vertebrate eyes. However, the amphioxus frontal eye is composed of simple ciliated cells, unlike vertebrate rods and cones, which display more elaborate, surface-extended cilia. So far, the only evidence that the frontal eye indeed might be sensitive to light has been the presence of a ciliated putative sensory cell in the close vicinity of dark pigment cells. We set out to characterize the cell types of the amphioxus frontal eye molecularly, to test their possible relatedness to the cell types of vertebrate eyes. We show that the cells of the frontal eye specifically coexpress a combination of transcription factors and opsins typical of the vertebrate eye photoreceptors and an inhibitory Gi-type alpha subunit of the G protein, indicating an off-responding phototransductory cascade. Furthermore, the pigmented cells match the retinal pigmented epithelium in melanin content and regulatory signature. Finally, we reveal axonal projections of the frontal eye that resemble the basic photosensory-motor circuit of the vertebrate forebrain. These results support homology of the amphioxus frontal eye and the vertebrate eyes and yield insights into their evolutionary origin.
Direct observation of hydrogen atom dynamics and interactions by ultrahigh resolution neutron protein crystallography
Authors: Chen Julian C.-H. , Hanson B. Leif , Fisher S. Zoë , Langan Paul , Kovalevsky Andrey Y.
Published: September 2012

The 1.1 Å, ultrahigh resolution neutron structure of hydrogen/deuterium (H/D) exchanged crambin is reported. Two hundred ninety-nine out of 315, or 94.9%, of the hydrogen atom positions in the protein have been experimentally derived and resolved through nuclear density maps. A number of unconventional interactions are clearly defined, including a potential O─H…π interaction between a water molecule and the aromatic ring of residue Y44, as well as a number of potential C─H…O hydrogen bonds. Hydrogen bonding networks that are ambiguous in the 0.85 Å ultrahigh resolution X-ray structure can be resolved by accurate orientation of water molecules. Furthermore, the high resolution of the reported structure has allowed for the anisotropic description of 36 deuterium atoms in the protein. The visibility of hydrogen and deuterium atoms in the nuclear density maps is discussed in relation to the resolution of the neutron data.
Coherence brightened laser source for atmospheric remote sensing
Authors: Traverso Andrew J. , Sanchez-Gonzalez Rodrigo , Yuan Luqi , Wang Kai , Voronine Dmitri V. , Zheltikov Aleksei M. , Rostovtsev Yuri , Sautenkov Vladimir A. , Sokolov Alexei V. , North Simon W. , Scully Marlan O.
Published: September 2012

We have studied coherent emission from ambient air and demonstrated efficient generation of laser-like beams directed both forward and backward with respect to a nanosecond ultraviolet pumping laser beam. The generated optical gain is a result of two-photon photolysis of atmospheric O
2
, followed by two-photon excitation of atomic oxygen. We have analyzed the temporal shapes of the emitted pulses and have observed very short duration intensity spikes as well as a large Rabi frequency that corresponds to the emitted field. Our results suggest that the emission process exhibits nonadiabatic atomic coherence, which is similar in nature to Dicke superradiance where atomic coherence is large and can be contrasted with ordinary lasing where atomic coherence is negligible. This atomic coherence in oxygen adds insight to the optical emission physics and holds promise for remote sensing techniques employing nonlinear spectroscopy.
Molecular mechanisms of cobalt-catalyzed hydrogen evolution
Authors: Marinescu Smaranda C. , Winkler Jay R. , Gray Harry B.
Published: September 2012

Several cobalt complexes catalyze the evolution of hydrogen from acidic solutions, both homogeneously and at electrodes. The detailed molecular mechanisms of these transformations remain unresolved, largely owing to the fact that key reactive intermediates have eluded detection. One method of stabilizing reactive intermediates involves minimizing the overall reaction free-energy change. Here, we report a new cobalt(I) complex that reacts with tosylic acid to evolve hydrogen with a driving force of just 30 meV/Co. Protonation of Co
I
produces a transient Co
III
-H complex that was characterized by nuclear magnetic resonance spectroscopy. The Co
III
-H intermediate decays by second-order kinetics with an inverse dependence on acid concentration. Analysis of the kinetics suggests that Co
III
-H produces hydrogen by two competing pathways: a slower homolytic route involving two Co
III
-H species and a dominant heterolytic channel in which a highly reactive Co
II
-H transient is generated by Co
I
reduction of Co
III
-H.
Re-thinking FNI
Authors: Lyngfelt Benjamin
Published: September 2012

This paper discusses the classification of null instantiation phenomena in Construction Grammar and proposes a different treatment of so-called free null instantiation (FNI). Based on e.g. control data, different types of alleged FNI are shown to be more accurately classified as definite (adjunct control), generic (e.g. tough constructions), or unspecified for interpretation (e.g. passives). A striking pattern is that general constructions, such as infinitives and gerunds, license unspecified null instantiation (simply NI), whereas more specific control constructions are associated with a definite (DNI) or generic (GNI) interpretation. Hence, the paper proposes a null instantiation taxonomy that distinguishes (unspecified) NI and the specific subtypes definite (DNI), indefinite (INI), identity of sense (ISNA), and generic (GNI) null instantiation.
Couch-based motion compensation: modelling, simulation and real-time experiments
Authors: Haas Olivier C L , Skworcow Piotr , Paluszczyszyn Daniel , Sahih Abdelhamid , Ruta Mariusz , Mills John A
Published: September 2012

The paper presents a couch-based active motion compensation strategy evaluated in simulation and validated experimentally using both a research and a clinical Elekta Precise Table™. The control strategy combines a Kalman filter to predict the surrogate motion used as a reference by a linear model predictive controller with the control action calculation based on estimated position and velocity feedback provided by an observer as well as predicted couch position and velocity using a linearized state space model. An inversion technique is used to compensate for the dead-zone nonlinearity. New generic couch models are presented and applied to model the Elekta Precise Table™ dynamics and nonlinearities including dead zone. Couch deflection was measured for different manufacturers and found to be up to 25 mm. A feed-forward approach is proposed to compensate for such couch deflection. Simultaneous motion compensation for longitudinal, lateral and vertical motions was evaluated using arbitrary trajectories generated from sensors or loaded from files. Tracking errors were between 0.5 and 2 mm RMS. A dosimetric evaluation of the motion compensation was done using a sinusoidal waveform. No notable differences were observed between films obtained for a fixed- or motion-compensated target. Further dosimetric improvement could be made by combining gating, based on tracking error together with beam on/off time, and PSS compensation.
Extended cleavage specificity of the mast cell chymase from the crab-eating macaque (Macaca fascicularis): an interesting animal model for the analysis of the function of the human mast cell chymase
Authors: Thorpe Michael , Yu Jing , Boinapally Vamsi , Ahooghalandari Parvin , Kervinen Jukka , Garavilla Lawrence de , Hellman Lars
Published: September 2012

Serine proteases are the major protein constituents within mast cell secretory granules. These proteases are subdivided into chymases and tryptases depending on their primary cleavage specificity. Here, we present the extended cleavage specificity of the macaque mast cell chymase and compare the specificity with human chymase (HC) and dog chymase (DC) that were produced in the same insect cell expression host. The macaque chymase (MC) shows almost identical characteristics as the HC, including both primary and extended cleavage specificities as well as sensitivity to protease inhibitors, whereas the DC differs in several of these characteristics. Although previous studies have shown that mouse mast cell protease-4 (mMCP-4) is similar in its hydrolytic specificity to the HC, mouse mast cells contain several related enzymes. Thus mice may not be the most appropriate model organism for studying HC activity and inhibition. Importantly, macaques express only one chymase and, as primates, are closely related to human general physiology. In addition, the human and macaque enzymes both cleave angiotensin I (Ang I) in the same way, generating primarily angiotensin II (Ang II) and they do not further degrade the peptide like most rodent enzymes do. Both enzymes also cleave two additional potential in vivo substrates, fibronectin and secretory leukocyte protease inhibitor (SLPI) in a similar way. Given the fact that both HC and MC are encoded by a single gene with high sequence homology and that many physiological processes are similar between these species, the macaque may be a very interesting model to study the physiological role of the chymase and to determine the potency and potential side-effects of various chymase inhibitors designed for therapeutic human use.
Prediction of welfare outcomes for broiler chickens using Bayesian regression on continuous optical flow data
Authors: Roberts Stephen J. , Cain Russell , Dawkins Marian Stamp
Published: September 2012

Currently, assessment of broiler (meat) chicken welfare relies largely on labour-intensive or post-mortem measures of welfare. We here describe a method for continuously and robustly monitoring the welfare of living birds while husbandry changes are still possible. We detail the application of Bayesian modelling to motion data derived from the output of cameras placed in commercial broiler houses. We show that the forecasts produced by the model can be used to accurately assess certain key aspects of the future health and welfare of a flock. The difference between healthy flocks and less-healthy ones becomes predictable days or even weeks before clinical symptoms become apparent. Hockburn (damaged leg skin, usually only seen in birds of two weeks or older) can be well predicted in flocks of only 1–2 days of age, using this approach. Our model combines optical flow descriptors of bird motion with robust multivariate forecasting and provides a sparse, efficient model with sparsity-inducing priors to achieve maximum predictive power with the minimum number of key variables.
Bottom-up effects of host-plant species diversity and top-down effects of ants interactively increase plant performance
Authors: Moreira Xoaquín , Mooney Kailen A. , Zas Rafael , Sampedro Luis
Published: September 2012

While plant diversity is well known to increase primary productivity, whether these bottom-up effects are enhanced by reciprocal top-down effects from the third trophic level is unknown. We studied whether pine tree species diversity, aphid-tending ants and their interaction determined plant performance and arthropod community structure. Plant diversity had a positive effect on aphids, but only in the presence of mutualistic ants, leading to a threefold greater number of both groups in the tri-specific cultures than in monocultures. Plant diversity increased ant abundance not only by increasing aphid number, but also by increasing ant recruitment per aphid. The positive effect of diversity on ants in turn cascaded down to increase plant performance; diversity increased plant growth (but not biomass), and this effect was stronger in the presence of ants. Consequently, bottom-up effects of diversity within the same genus and guild of plants, and top-down effects from the third trophic level (predatory ants), interactively increased plant performance.
Intraguild predation provides a selection mechanism for bacterial antagonistic compounds
Authors: Leisner J. J. , Haaber J.
Published: September 2012

Bacteriocins are bacterial proteinaceous toxins with bacteriostatic or bacteriocidal activity towards other bacteria. The current theory on their biological role concerns especially colicins, with underlying social interactions described as an example of spite. This leads to a rock–paper–scissors game between colicin producers and sensitive and resistant variants. The generality of this type of selection mechanism has previously been challenged with lactic acid bacterial (LAB) bacteriocins as an example. In the natural environment of LAB, batch cultures are the norm opposed to the natural habitats ofEscherichia coliwhere continuous cultures are prevailing. This implies that fitness for LAB, to a large degree, is related to survival rates (bottleneck situations) rather than to growth rates. We suggest that the biological role of LAB bacteriocins is to enhance survival in the stationary growth phase by securing a supply of nutrients from lysed target cells. Thus, this social interaction is an example of selfishness rather than of spite. Specifically, it fits into an ecological model known as intraguild predation (IGP), which is a combination of competition and predation where the predator (LAB bacteriocin producer) and prey (bacteriocin susceptible bacteria) share similar and often limited resources. We hypothesize that IGP may be a common phenomenon promoting microbial production of antagonistic compounds.
The yield of experimental yeast populations declines during selection
Authors: Jasmin Jean-Nicolas , Dillon Marcus M. , Zeyl Clifford
Published: September 2012

The trade-off between growth rate and yield can limit population productivity. Here we tested for this life-history trade-off in replicate haploid and diploid populations ofSaccharomyces cerevisiaepropagated in glucose-limited medium in batch cultures for 5000 generations. The yield of single clones isolated from the haploid lineages, measured as both optical and population density at the end of a growth cycle, declined during selection and was negatively correlated with growth rate. Initially, diploid populations did not pay this cost of adaptation but haploidized after about 1000–3000 generations of selection, and this ploidy transition was associated with a decline in yield caused by reduced cell size. These results demonstrate the experimental evolution of a trade-off between growth rate and yield, caused by antagonistic pleiotropy, during adaptation in haploids and after an adaptive transition from diploidy to haploidy.
The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression
Authors: Derrien Thomas , Johnson Rory , Bussotti Giovanni , Tanzer Andrea , Djebali Sarah , Tilgner Hagen , Guernec Gregory , Martin David , Merkel Angelika , Knowles David G. , Lagarde Julien , Veeravalli Lavanya , Ruan Xiaoan , Ruan Yijun , Lassmann Timo , Carninci Piero , Brown James B. , Lipovich Leonard , Gonzalez Jose M. , Thomas Mark , Davis Carrie A. , Shiekhattar Ramin , Gingeras Thomas R. , Hubbard Tim J. , Notredame Cedric , Harrow Jennifer , Guigó Roderic
Published: September 2012

The human genome contains many thousands of long noncoding RNAs (lncRNAs). While several studies have demonstrated compelling biological and disease roles for individual examples, analytical and experimental approaches to investigate these genes have been hampered by the lack of comprehensive lncRNA annotation. Here, we present and analyze the most complete human lncRNA annotation to date, produced by the GENCODE consortium within the framework of the ENCODE project and comprising 9277 manually annotated genes producing 14,880 transcripts. Our analyses indicate that lncRNAs are generated through pathways similar to that of protein-coding genes, with similar histone-modification profiles, splicing signals, and exon/intron lengths. In contrast to protein-coding genes, however, lncRNAs display a striking bias toward two-exon transcripts, they are predominantly localized in the chromatin and nucleus, and a fraction appear to be preferentially processed into small RNAs. They are under stronger selective pressure than neutrally evolving sequences—particularly in their promoter regions, which display levels of selection comparable to protein-coding genes. Importantly, about one-third seem to have arisen within the primate lineage. Comprehensive analysis of their expression in multiple human organs and brain regions shows that lncRNAs are generally lower expressed than protein-coding genes, and display more tissue-specific expression patterns, with a large fraction of tissue-specific lncRNAs expressed in the brain. Expression correlation analysis indicates that lncRNAs show particularly striking positive correlation with the expression of antisense coding genes. This GENCODE annotation represents a valuable resource for future studies of lncRNAs.
Long noncoding RNAs are rarely translated in two human cell lines
Authors: Bánfai Balázs , Jia Hui , Khatun Jainab , Wood Emily , Risk Brian , Gundling William E. , Kundaje Anshul , Gunawardena Harsha P. , Yu Yanbao , Xie Ling , Krajewski Krzysztof , Strahl Brian D. , Chen Xian , Bickel Peter , Giddings Morgan C. , Brown James B. , Lipovich Leonard
Published: September 2012

Data from the Encyclopedia of DNA Elements (ENCODE) project show over 9640 human genome loci classified as long noncoding RNAs (lncRNAs), yet only ∼100 have been deeply characterized to determine their role in the cell. To measure the protein-coding output from these RNAs, we jointly analyzed two recent data sets produced in the ENCODE project: tandem mass spectrometry (MS/MS) data mapping expressed peptides to their encoding genomic loci, and RNA-seq data generated by ENCODE in long polyA+ and polyA− fractions in the cell lines K562 and GM12878. We used the machine-learning algorithm RuleFit3 to regress the peptide data against RNA expression data. The most important covariate for predicting translation was, surprisingly, the Cytosol polyA− fraction in both cell lines. LncRNAs are ∼13-fold less likely to produce detectable peptides than similar mRNAs, indicating that ∼92% of GENCODE v7 lncRNAs are not translated in these two ENCODE cell lines. Intersecting 9640 lncRNA loci with 79,333 peptides yielded 85 unique peptides matching 69 lncRNAs. Most cases were due to a coding transcript misannotated as lncRNA. Two exceptions were an unprocessed pseudogene and a bona fide lncRNA gene, both with open reading frames (ORFs) compromised by upstream stop codons. All potentially translatable lncRNA ORFs had only a single peptide match, indicating low protein abundance and/or false-positive peptide matches. We conclude that with very few exceptions, ribosomes are able to distinguish coding from noncoding transcripts and, hence, that ectopic translation and cryptic mRNAs are rare in the human lncRNAome.
Personal and population genomics of human regulatory variation
Authors: Vernot Benjamin , Stergachis Andrew B. , Maurano Matthew T. , Vierstra Jeff , Neph Shane , Thurman Robert E. , Stamatoyannopoulos John A. , Akey Joshua M.
Published: September 2012

The characteristics and evolutionary forces acting on regulatory variation in humans remains elusive because of the difficulty in defining functionally important noncoding DNA. Here, we combine genome-scale maps of regulatory DNA marked by DNase I hypersensitive sites (DHSs) from 138 cell and tissue types with whole-genome sequences of 53 geographically diverse individuals in order to better delimit the patterns of regulatory variation in humans. We estimate that individuals likely harbor many more functionally important variants in regulatory DNA compared with protein-coding regions, although they are likely to have, on average, smaller effect sizes. Moreover, we demonstrate that there is significant heterogeneity in the level of functional constraint in regulatory DNA among different cell types. We also find marked variability in functional constraint among transcription factor motifs in regulatory DNA, with sequence motifs for major developmental regulators, such as HOX proteins, exhibiting levels of constraint comparable to protein-coding regions. Finally, we perform a genome-wide scan of recent positive selection and identify hundreds of novel substrates of adaptive regulatory evolution that are enriched for biologically interesting pathways such as melanogenesis and adipocytokine signaling. These data and results provide new insights into patterns of regulatory variation in individuals and populations and demonstrate that a large proportion of functionally important variation lies beyond the exome.
Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements
Authors: Kundaje Anshul , Kyriazopoulou-Panagiotopoulou Sofia , Libbrecht Max , Smith Cheryl L. , Raha Debasish , Winters Elliott E. , Johnson Steven M. , Snyder Michael , Batzoglou Serafim , Sidow Arend
Published: September 2012

Gene regulation at functional elements (e.g., enhancers, promoters, insulators) is governed by an interplay of nucleosome remodeling, histone modifications, and transcription factor binding. To enhance our understanding of gene regulation, the ENCODE Consortium has generated a wealth of ChIP-seq data on DNA-binding proteins and histone modifications. We additionally generated nucleosome positioning data on two cell lines, K562 and GM12878, by MNase digestion and high-depth sequencing. Here we relate 14 chromatin signals (12 histone marks, DNase, and nucleosome positioning) to the binding sites of 119 DNA-binding proteins across a large number of cell lines. We developed a new method for unsupervised pattern discovery, the Clustered AGgregation Tool (CAGT), which accounts for the inherent heterogeneity in signal magnitude, shape, and implicit strand orientation of chromatin marks. We applied CAGT on a total of 5084 data set pairs to obtain an exhaustive catalog of high-resolution patterns of histone modifications and nucleosome positioning signals around bound transcription factors. Our analyses reveal extensive heterogeneity in how histone modifications are deposited, and how nucleosomes are positioned around binding sites. With the exception of the CTCF/cohesin complex, asymmetry of nucleosome positioning is predominant. Asymmetry of histone modifications is also widespread, for all types of chromatin marks examined, including promoter, enhancer, elongation, and repressive marks. The fine-resolution signal shapes discovered by CAGT unveiled novel correlation patterns between chromatin marks, nucleosome positioning, and sequence content. Meta-analyses of the signal profiles revealed a common vocabulary of chromatin signals shared across multiple cell lines and binding proteins.
The single nucleotide polymorphism CRTh2 rs533116 is associated with allergic asthma and increased expression of CRTh2
Authors: Campos Alberto E. , MacLean E. , Davidson C. , Palikhe N. S. , Storie J. , Tse C. , Brenner D. , Mayers I. , Vliagoftis H. , El‐Sohemy A. , Cameron L.
Published: September 2012

Background

CRTh2 (chemoattractant‐receptor homologous molecule expressed on Th2 cells) is expressed by Th2 cells and other cells involved in allergic inflammation. Single nucleotide polymorphisms (SNPs) in CRTh2 (rs11571288, rs545659, rs634681) have been associated with various phenotypes of allergy in ethnically distinct populations. Here, we assessed the association between CRTh2 rs533116 and allergic asthma, expression of CRTh2 and Th2 cytokine production.

Methods

CRTh2 rs533116 was genotyped in an ethnically diverse population (n = 1282). The proportion of cells expressing CRTh2 was determined in peripheral blood from subjects with allergic airways disease and controls as well as with in vitro differentiated Th2 cells. Receptor function was assessed by stimulating Th2 cells with the CRTh2‐specific agonist 13,14‐dihydro‐15‐keto‐PGD2 (DK‐PGD2) and measuring IL‐4 and IL‐13 by intracellular staining and ELISA.

Results

CRTh2 rs533116 was associated with allergic asthma in White people (2.67 [1.09–6.55], P < 0.05), and expression of CRTh2 was higher in subjects with allergic airways disease compared to controls (P < 0.05). Among allergic individuals, the AA genotype was significantly associated with more eosinophils and higher expression of CRTh2 by both CD4+ T cells and eosinophils (P < 0.05). In vitro, the AA genotype was associated with a higher proportion of CRTh2+ cells during Th2 differentiation as well as more IL‐4 and IL‐13 expression following DK‐PGD2 stimulation (P < 0.05).

Conclusions

These findings show an association between CRTh2 rs533116 and allergic asthma and suggest this may be mediated by elevated expression of CRTh2, leading to higher numbers of circulating eosinophils and Th2 cytokine production.
The effects of six electronic apex locators on pacemaker function: an in vitro study
Authors: Gomez G. , Duran‐Sindreu F. , Jara Clemente F. , Garofalo R. R. , Garcia M. , Bueno R. , Roig M.
Published: September 2012

Aim

To assess the effects of six electronic apex locators (EALs) on pacemaker function in vitro.

Methodology

Six EALs (Mini Apex Locator®, Dentaport ZX®, Novapex®, Raypex5®, Root ZX mini®, and Justy II®) were tested for electromagnetic interference (EMI) with one pacemaker (Saint Jude Medical). The pacemaker, with a single electrode, was immersed in a saline solution bath adjusted to 400–800 ohms to simulate the electrical resistance of the human body and to register the activity by the system. The pacemaker was tested with each of the EALs to analyse the presence of EMI with the EAL switched on, the EAL switched off and during EAL operation. Each series of tests began with a 15‐second baseline recording (R0) and continued until all the recording conditions had been covered. The conditions were as follows: R1: recording with the lead of the EAL <2 cm from the tip of the electrode; R2: recording with the lead of the EAL <2 cm from the generator; R3: recording with the lead of the EAL <2 cm from the sensing arc; and R4: recording with the lead of the EAL 15 cm from the sensing arc. If any of the EALs produced interference, its characteristics were categorized.

Results

When the lead of the EAL was <2 cm from the tip of the electrode, the majority of the EALs tested produced only background noise. Only one (the Mini Apex Locator) resulted in EMI that was detected as false heart activity. When the EAL was <2 cm from the generator, just one EAL detected background noise (the Mini Apex Locator). When the EAL was <2 cm from the sensing arc or 15 cm from the sensing arc, the recordings were not affected by any of the EALs. There were no significant differences amongst the EALs analysed with respect to the production of EMI.

Conclusions

EMI occurred when the EALs were placed close to the tip of the electrode and occasionally when close to the pacemaker; however, no EMI was detected when the EALs were placed near to or 15 cm from the sensing arc in this laboratory experimental model.
Differential responses to predator cues between two mosquito species breeding in different habitats
Authors: OHBA SHIN‐YA , OHTSUKA MASAKAZU , SUNAHARA TOSHIHIKO , SONODA YURI , KAWASHIMA EMIKO , TAKAGI MASAHIRO
Published: September 2012

1. Natural selection favours females who can correctly assess the predation risk and hence avoid high‐risk oviposition sites and reduce the mortality rate of their offspring. In spite of the potential significance of such behaviour, relatively few studies have assessed the relationship between oviposition behaviour and predation risk.

2. The present study aimed to determine the sublethal effects of predators on oviposition site selection by gravid females, the foraging activity of larvae, and the life history traits of two mosquito species that breed in different habitats, Aedes albopictus Skuse (container breeder) and Culex tritaeniorhynchus Giles (wetland breeder).

3. Female C. tritaeniorhynchus avoided laying eggs at oviposition sites in the presence of a predator cue. In contrast, female A. albopictus laid eggs in both the absence and presence of the predator cue.

4. To examine the effects of predator cues on larval behaviour, experiments were conducted in the absence and presence of a predator cue. Although larval activity was lower in the presence of the predator cue than that in its absence in both species, C. tritaeniorhynchus responded to the predator cue more strongly than A. albopictus. Female A. albopictus that had been reared with caged predators exhibited an extended larval development period, whereas the adult C. tritaeniorhynchus reared in the presence of predators were smaller than those reared in their absence.

5. This finding might explain why C. tritaeniorhynchus avoid laying eggs in predator‐conditioned water, for example to increase the fitness of their offspring, but A. albopictus either cannot detect predator cues or are not sensitive to them.
Rachycentron canadum (cobia) Lectin Promoted Mitogenic Response in Mice BALB/c Splenocytes
Authors: Coriolano M. C. , de Melo C. M. L. , Santos A. J. G. , Pereira V. R. A. , Coelho L. C. B. B.
Published: September 2012

The mitogenic lectins are invaluable tools to study the biochemical changes associated with lymphocyte activation and proliferation of various immune cells. Rachycentron canadum lectin (RcaL) was detected and purified from serum of cobia fish. The aim of this study was to evaluate the proliferative response and cytokine production in splenocytes of mice in vitro stimulated with RcaL lectin; Canavalia ensiformis lectin (Con A) was used as positive control. A high proliferation index was induced by RcaL in relation to control cells. Furthermore, RcaL induced higher IL‐2 and IL‐6 production in relation to control. The cell viability was 90% in splenocytes treated with RcaL lectin, but RcaL promoted significant late apoptosis after 24 and 48 h in relation to control. RcaL induced proliferative responses suggesting that this lectin can be used as a mitogenic agent in immunostimulatory assays.