Miracle-dz/UniFAR-FTUs huggingface dataset:
Community size and composition of ammonia oxidizers and denitrifiers in an alluvial intertidal wetland ecosystem

Global nitrogen cycling is mainly mediated by the activity of microorganisms. Nitrogen cycle processes are mediated by functional groups of microorganisms that are affected by constantly changing environmental conditions and substrate availability. In this study, we investigated the temporal and spatial patterns of nitrifier and denitrifier communities in an intertidal wetland. Soil samples were collected over four distinct seasons from three locations with different vegetative cover. Multiple environmental factors and process rates were measured and analyzed together with the community size and composition profiles. We observed that the community size and composition of the nitrifiers and denitrifiers are affected significantly by seasonal factors, while vegetative cover affected the community composition. The seasonal impacts on the community size of ammonia oxidizing archaea (AOA) are much higher than that of ammonia oxidizing bacteria (AOB). The seasonal change was a more important indicator for AOA community composition patterns, while vegetation was more important for the AOB community patterns. The microbial process rates were correlated with both the community size and composition.
A pr 2 00 9 MOND orbits in the Solar System ’ s periphery and confrontation with the obser

We look for MONDian orbital effects in the outer regions of the Solar System by numerically integrating both the MOND and the New-tonian equations of motions with the same initial conditions and investigate the resulting discrepancies. For the interpolating function µ of MOND we examine in details the " simple " form µ(X) = X/(1 + X). Major differences occur in the Oort cloud (r ≈ 50 − 150 kAU) where highly elongated orbits are not allowed by MOND, contrary to Newto-nian mechanics. This fact may have consequences on the composition and the dynamical history of the Oort cloud since the perturbations due to nearby passing stars, interstellar gas clouds and Galactic tides, which in the classical framework change the velocities of the Oort's comets launching them in the inner regions of the Solar System, would be less effective according to MOND. Then, we compare the predicted MOND heliocentric radial shifts ∆r for some trans-Neptunian objects (Pluto and Sedna, r ≈ 40 − 500 AU) and the giant gaseous planets Jupiter, Saturn, Uranus and Neptune (r ≈ 5 − 30 AU) with the optical observations gathered during the last century. The MOND effects for Sedna are orders of magnitude smaller than the present-day orbit accuracy , while those for Pluto over 100 yr are about of the same order of magnitude, or even larger, of its orbit accuracy which will be improved when the New Horizon spacecraft will encounter Pluto in 2015. The MONDian departures ∆r from the Newtonian paths over 80-100 yr for Neptune, Uranus, Saturn and Jupiter are, instead, quite larger than their orbit accuracy according to the latest DE (JPL, NASA), EPM (IAA, RAS) and INPOP (IMCCE) ephemerides in such a way that if µ = X/(1 + X) was valid as interpolating function also at acceleration scales of 10 5 in units of A 0 , its effects should have been detected.
The Small-Scale Environment of Quasars

Where do quasars reside? Are quasars located in environments similar to those of typical L* galaxies, and, if not, how do they differ? An answer to this question will help shed light on the triggering process of quasar activity. We use the Sloan Digital Sky Survey to study the environment of quasars and compare it directly with the environment of galaxies. We find that quasars (Mi ≤ -22, z ≤ 0.4) are located in higher local overdensity regions than are typical L* galaxies. The enhanced environment around quasars is a local phenomenon; the overdensity relative to that around L* galaxies is strongest within 100 kpc of the quasars. In this region, the overdensity is a factor of 1.4 larger than around L* galaxies. The overdensity declines monotonically with scale to nearly unity at ~1 h Mpc, where quasars inhabit environments comparable to those of L* galaxies. The small-scale density enhancement depends on quasar luminosity, but only at the brightest end: the most luminous quasars reside in higher local overdensity regions than do fainter quasars. The mean overdensity around the brightest quasars (Mi ≤ -23.3) is nearly 3 times larger than around L* galaxies, while the density around dimmer quasars (Mi = -22.0 to -23.3) is ~1.4 times that of L* galaxies. By ~0.5 Mpc, the dependence on quasar luminosity is no longer significant. The overdensity on all scales is independent of redshift to z ≤ 0.4. The results suggest a picture in which quasars typically reside in L* galaxies but have a local excess of neighbors within ~0.1-0.5 Mpc; this local density excess likely contributes to the triggering of quasar activity through mergers and other interactions.
Robust Broadcasting of Common and Confidential Messages Over Compound Channels: Strong Secrecy and Decoding Performance

The broadcast channel with confidential messages (BCC) consists of one transmitter and two receivers, where the transmitter sends a common message to both receivers and, at the same time, a confidential message to one receiver which has to be kept secret from the other one. In this paper, this communication scenario is studied for compound channels, where it is only known to the transmitter and receivers that the actual channel realization is fixed and from a prespecified set of channels. The information theoretic criterion of strong secrecy is analyzed in detail and its impact on the decoding performance of the non-legitimate receiver is characterized. In particular, it is shown that regardless of the computational capabilities and the applied decoding strategy of the non-legitimate receiver, his decoding error always tends to one. This gives a valuable signal processing implication of the strong secrecy criterion and identifies desirable properties of an optimal code design. Further, an achievable strong secrecy rate region is derived and a multiletter outer bound is given. Both together yield a multiletter expression of the strong secrecy capacity region of the compound BCC.
Cooperative Swinging of Complex Pendulum-Like Objects: Experimental Evaluation

Cooperative dynamic object manipulation increases the manipulation repertoire of multiagent teams. As a first step toward cooperative dynamic object manipulation, we present an energy-based controller for cooperative swinging of two-agent pendulum-like objects. Projection of the complex underactuated mechanism onto an abstract cart-pendulum allows us to separate desired and undesired oscillations. The desired oscillation is excited up to a desired energy level, while an undesired oscillation can be actively damped. Communication between the agents is restricted to force feedback. The controller can render leader and follower agents. The follower actively assists the swinging task by imitating the leader's energy flow. Real-world experiments with a robot and a human swinging complex pendulum-like objects are presented. The experimental results indicate that no simultaneous damping of the undesired oscillation is needed, also because it disturbs the human partner. A successful contribution of the robotic follower to the swing-up effort in interaction with a human leader supports the proposed control approach.
Genome-wide quantification of homeolog expression ratio revealed nonstochastic gene regulation in synthetic allopolyploid Arabidopsis

Genome duplication with hybridization, or allopolyploidization, occurs commonly in plants, and is considered to be a strong force for generating new species. However, genome-wide quantification of homeolog expression ratios was technically hindered because of the high homology between homeologous gene pairs. To quantify the homeolog expression ratio using RNA-seq obtained from polyploids, a new method named HomeoRoq was developed, in which the genomic origin of sequencing reads was estimated using mismatches between the read and each parental genome. To verify this method, we first assembled the two diploid parental genomes of Arabidopsis halleri subsp. gemmifera and Arabidopsis lyrata subsp. petraea (Arabidopsis petraea subsp. umbrosa), then generated a synthetic allotetraploid, mimicking the natural allopolyploid Arabidopsis kamchatica. The quantified ratios corresponded well to those obtained by Pyrosequencing. We found that the ratios of homeologs before and after cold stress treatment were highly correlated (r = 0.870). This highlights the presence of nonstochastic polyploid gene regulation despite previous research identifying stochastic variation in expression. Moreover, our new statistical test incorporating overdispersion identified 226 homeologs (1.11% of 20 369 expressed homeologs) with significant ratio changes, many of which were related to stress responses. HomeoRoq would contribute to the study of the genes responsible for polyploid-specific environmental responses.
Transcriptome Fingerprints Distinguish Hallucinogenic and Nonhallucinogenic 5-Hydroxytryptamine 2A Receptor Agonist Effects in Mouse Somatosensory Cortex

Most neuropharmacological agents and many drugs of abuse modulate the activity of heptahelical G-protein-coupled receptors. Although the effects of these ligands result from changes in cellular signaling, their neurobehavioral activity may not correlate with results of in vitro signal transduction assays. 5-Hydroxytryptamine 2A receptor (5-HT2AR) partial agonists that have similar pharmacological profiles differ in the behavioral responses they elicit. In vitro studies suggest that different agonists acting at the same receptor may establish distinct patterns of signal transduction. Testing this hypothesis in the brain requires a global signal transduction assay that is applicable in vivo. To distinguish the cellular effects of the different 5-HT2AR agonists, we developed an assay for global signal transduction on the basis of high throughput quantification of rapidly modulated transcripts. Study of the responses to agonists in human embryonic kidney 293 cells stably expressing 5-HT2ARs demonstrated that each agonist elicits a distinct transcriptome fingerprint. We therefore studied behavioral and cortical signal transduction responses in wild-type and 5-HT2AR null-mutant mice. The hallucinogenic chemicals (±)-2,5-dimethoxy-4-iodoamphetamine (DOI) and lysergic acid diethylamide (LSD) stimulated a head-twitch behavioral response that was not observed with the nonhallucinogenic lisuride hydrogen maleate (LHM) and was absent in receptor null-mutant mice. We also found that DOI, LSD, and LHM each induced distinct transcriptome fingerprints in somatosensory cortex that were absent in 5-HT2AR null-mutants. Moreover, DOI and LSD showed similarities in the transcriptome fingerprints obtained that were not observed with the behaviorally inactive drug LHM. Our results demonstrate that chemicals acting at the 5-HT2AR induce specific cellular response patterns in vivo that are reflected in unique changes in the somatosensory cortex transcriptome.
Extreme avalanche runout in space and time

The distribution of avalanche runout varies in space and time for individual avalanche paths and from mountain range to mountain range. In this paper, such variations are considered based on the assumption (supported by data worldwide) that the spatial distribution of extreme avalanche runout follows a Gumbel distribution and that the arrival rate of avalanches can be modelled as a Poisson process. The input required is a set of extreme avalanche runout distances for the mountain range and a knowledge of avalanche frequency at the beginning of the runout zone for the path in question. Such information allows theoretical estimation of the effective return period as a function of position, which is very important in zoning applications. In addition, general expressions are derived to relate Gumbel parameters for different mountain ranges to a frequency index to explore general frequency implications from one mountain range to another. The estimated Gumbel parameters imply consistent relationships for expect.
Solar cycle warming at the Earth's surface in NCEP and ERA-40 data: A linear discriminant analysis

[1] The total solar irradiance (TSI) has been measured by orbiting satellites since 1978 to vary on an 11-year cycle by about 0.08%. Because of previous controversies on the reality of solar cycle response at the surface, in this work we discuss the robustness of the solar response with respect to analysis methods, data sets and periods used. Furthermore we concentrate on the globally coherent signal. Two reanalysis data sets are used: one is from National Centers for Environmental Prediction and National Center for Atmospheric Research (NCEP for short) and the other is the European Centre for Medium-Range Weather Forecasts (ECMWF)’s most recent reanalysis denoted by ERA-40. Three analysis methods are considered, with increasing sophistication. Within each data set the analysis results are consistent with each other (i.e., each within the other’s error bars), with the method of linear discriminant analysis (LDA) yielding the smallest error bar and the unfiltered global mean data yielding the largest error bar in the temperature amplitude. All three methods and both data sets are able to demonstrate that the 11-year signal is statistically significant and attributable (i.e., related) to the solar cycle. We deduce the spatial surface pattern over the globe which best distinguishes the solar maximum years from the solar minimum years using the LDA method. The resulting warming pattern shows clearly the polar amplification of warming and the preference for continents over oceans. We propose that the magnitude of the surface warming is consistent with direct solar radiative forcing if positive feedback processes such as ice albedo, water vapor/lapse rate and cloud feedbacks, similar to some of those studied for the greenhouse warming problem, are incorporated. It does not appear to be necessary to invoke some previously proposed exotic indirect mechanisms for an explanation of the observed solar signal. Citation: Tung, K. K. , and C. D. Camp (2008), Solar cycle warming at the Earth’s surface in NCEP and ERA-40 data: A linear discriminant analysis, J. Geophys. Res., 113, D05114, doi:10.1029/2007JD009164.
The City: Understanding how frontline leaders can inspire excellence in the workplace

The City is a large complex government organization that provides a diverse array of services to the community from recreation to engineering. The City has undergone services reviews resulting in improvements in technology, structure, and process in order to improve efficiencies and increase accountability to the community. In addition to the service improvements, expectations of leaders have changed in order to meet the new and changing demands of the transforming organization. In 2012, the City released its first corporate business plan that articulated the goals and objectives of the organization; one of the goals specifically outlined the City’s desire to inspire excellence in the workplace. This study took this corporate goal and considered it in the context of frontline leaders across the organization, and this inquiry investigated the question: how frontline leaders could inspire excellence in the workplace? Short and long-term recommendations resulted from this research inquiry, which included (1) increase the awareness of inspiring excellence, (2) develop a frontline leader excellence retreat, (3) develop a vision of inspiring excellence, (4) create a leadership framework for excellence, (5) develop a decision making framework, and (6) create an organizational culture of excellence . This action research project was conducted in accordance with the Royal Roads University (2011) Research Ethics Policy. Every effort was taken to ensure that the research was conducted fairly, with respect and met all legal requirements. In general, the study was of low risk to both the organization and its participants, and these efforts were enhanced by keeping the organization confidential and removing all organizational identifiers. Inspiring Excellence in the Workplace 3 ACKNOWLEDGEMENTS This research project would not have been possible without the support and guidance of many dedicated, supportive, and committed leaders, including the City’s leaders who participated in this research project. Although everyone who was involved was vital to the success of this study, I would like to acknowledge a few individuals for their belief in me. First, I would like to thank whole heartedly my supervisor, Tammy Dewar, who was my guide. She provided me with sound judgement and attuned feedback while allowing me to think outside of the box and explore the inquiry freely. Secondly, I would like to acknowledge the incredible inquiry team that assisted this process. Everyone on the inquiry team was amazing. I would like to express a special thank you to inquiry team member Cheryl Williams, graduate of the Masters in Leadership program in 2011. Cheryl brought incredible insights, reasoning, and support to me and the inquiry process. This inquiry initiative would not have been possible without my organizational sponsor, Christina Nikiforuk. As an advocate for continuous improvement and excellence at the City, Christina supported this project full heartedly. She was an incredible source of insight and
Selection of Reference Genes for qRT-PCR Analysis of Gene Expression in Stipa grandis during Environmental Stresses

Stipa grandis P. Smirn. is a dominant plant species in the typical steppe of the Xilingole Plateau of Inner Mongolia. Selection of suitable reference genes for the quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR) is important for gene expression analysis and research into the molecular mechanisms underlying the stress responses of S. grandis. In the present study, 15 candidate reference genes (EF1 beta, ACT, GAPDH, SamDC, CUL4, CAP, SNF2, SKIP1, SKIP5, SKIP11, UBC2, UBC15, UBC17, UCH, and HERC2) were evaluated for their stability as potential reference genes for qRT-PCR under different stresses. Four algorithms were used: GeNorm, NormFinder, BestKeeper, and RefFinder. The results showed that the most stable reference genes were different under different stress conditions: EF1beta and UBC15 during drought and salt stresses; ACT and GAPDH under heat stress; SKIP5 and UBC17 under cold stress; UBC15 and HERC2 under high pH stress; UBC2 and UBC15 under wounding stress; EF1beta and UBC17 under jasmonic acid treatment; UBC15 and CUL4 under abscisic acid treatment; and HERC2 and UBC17 under salicylic acid treatment. EF1beta and HERC2 were the most suitable genes for the global analysis of all samples. Furthermore, six target genes, SgPOD, SgPAL, SgLEA, SgLOX, SgHSP90 and SgPR1, were selected to validate the most and least stable reference genes under different treatments. Our results provide guidelines for reference gene selection for more accurate qRT-PCR quantification and will promote studies of gene expression in S. grandis subjected to environmental stress.
A "Two-Tier" Labour Market for Fixed-Term Jobs? Evaluating Evidence from West Germany Using Quantile Regression

Recent discussion of fixed-term contracts tends to ignore the considerable variation in the quality of these jobs and the wages associated with them (e.g. Booth et al., 2002). In this paper the authors develop the concept of a “two-tier” labour market for fixed-term contracts in Germany and test this concept using quantile regression. Using data from the German Socio-Economic Panel (SOEP) they find that those with high-wage fixed-term contracts earn only slightly less than permanent counterparts, those with low-wage temporary jobs earn much less, indicating that Ordinary Least Squares (OLS) regression misses important aspects of the wage structure of fixed-term workers.
Light-Induced Oxidative Stress, N-Formylkynurenine, and Oxygenic Photosynthesis

Light stress in plants results in damage to the water oxidizing reaction center, photosystem II (PSII). Redox signaling, through oxidative modification of amino acid side chains, has been proposed to participate in this process, but the oxidative signals have not yet been identified. Previously, we described an oxidative modification, N-formylkynurenine (NFK), of W365 in the CP43 subunit. The yield of this modification increases under light stress conditions, in parallel with the decrease in oxygen evolving activity. In this work, we show that this modification, NFK365-CP43, is present in thylakoid membranes and may be formed by reactive oxygen species produced at the Mn4CaO5 cluster in the oxygen-evolving complex. NFK accumulation correlates with the extent of photoinhibition in PSII and thylakoid membranes. A modest increase in ionic strength inhibits NFK365-CP43 formation, and leads to accumulation of a new, light-induced NFK modification (NFK317) in the D1 polypeptide. Western analysis shows that D1 degradation and oligomerization occur under both sets of conditions. The NFK modifications in CP43 and D1 are found 17 and 14 Angstrom from the Mn4CaO5 cluster, respectively. Based on these results, we propose that NFK is an oxidative modification that signals for damage and repair in PSII. The data suggest a two pathway model for light stress responses. These pathways involve differential, specific, oxidative modification of the CP43 or D1 polypeptides.
Population genomics meet Lagrangian simulations: Oceanographic patterns and long larval duration ensure connectivity among Paracentrotus lividus populations in the Adriatic and Ionian seas

Abstract Connectivity between populations influences both their dynamics and the genetic structuring of species. In this study, we explored connectivity patterns of a marine species with long‐distance dispersal, the edible common sea urchin Paracentrotus lividus, focusing mainly on the Adriatic–Ionian basins (Central Mediterranean). We applied a multidisciplinary approach integrating population genomics, based on 1,122 single nucleotide polymorphisms (SNPs) obtained from 2b‐RAD in 275 samples, with Lagrangian simulations performed with a biophysical model of larval dispersal. We detected genetic homogeneity among eight population samples collected in the focal Adriatic–Ionian area, whereas weak but significant differentiation was found with respect to two samples from the Western Mediterranean (France and Tunisia). This result was not affected by the few putative outlier loci identified in our dataset. Lagrangian simulations found a significant potential for larval exchange among the eight Adriatic–Ionian locations, supporting the hypothesis of connectivity of P. lividus populations in this area. A peculiar pattern emerged from the comparison of our results with those obtained from published P. lividus cytochrome b (cytb) sequences, the latter revealing genetic differentiation in the same geographic area despite a smaller sample size and a lower power to detect differences. The comparison with studies conducted using nuclear markers on other species with similar pelagic larval durations in the same Adriatic–Ionian locations indicates species‐specific differences in genetic connectivity patterns and warns against generalizing single‐species results to the entire community of rocky shore habitats.