Quantitative mass spectrometry and PAR-CLIP to identify RNA-protein interactions

Systematic analysis of the RNA-protein interactome requires robust and scalable methods. We here show the combination of two completely orthogonal, generic techniques to identify RNA-protein interactions: PAR-CLIP reveals a collection of RNAs bound to a protein whereas SILAC-based RNA pull-downs identify a group of proteins bound to an RNA. We investigated binding sites for five different proteins (IGF2BP1-3, QKI and PUM2) exhibiting different binding patterns. We report near perfect agreement between the two approaches. Nevertheless, they are non-redundant, and ideally complement each other to map the RNA-protein interaction network

Regulation-Structured Dynamic Metabolic Model Provides a Potential Mechanism for Delayed Enzyme Response in Denitrification Process

In a recent study of denitrification dynamics in hyporheic zone sediments, we observed a significant time lag (up to several days) in enzymatic response to the changes in substrate concentration. To explore an underlying mechanism and understand the interactive dynamics between enzymes and nutrients, we developed a trait-based model that associates a community’s traits with functional enzymes, instead of typically used species guilds (or functional guilds). This enzyme-based formulation allows to collectively describe biogeochemical functions of microbial communities without directly parameterizing the dynamics of species guilds, therefore being scalable to complex communities. As a key component of modeling, we accounted for microbial regulation occurring through transcriptional and translational processes, the dynamics of which was parameterized based on the temporal profiles of enzyme concentrations measured using a new signature peptide-based method. The simulation results using the resulting model showed several days of a time lag in enzymatic responses as observed in experiments. Further, the model showed that the delayed enzymatic reactions could be primarily controlled by transcriptional responses and that the dynamics of transcripts and enzymes are closely correlated. The developed model can serve as a useful tool for predicting biogeochemical processes in natural environments, either independently or through integration with hydrologic flow simulators

Abstract

Integrating the social identity and aging literatures, this work tested the hypothesis that there are two independent, but simultaneous, responses by which adults transitioning into old age can buffer themselves against age discrimination: an individual response, which entails adopting a younger subjective age when facing discrimination, and a collective response, which involves increasing identification with the group of older adults. In three experimental studies with a total number of 488 older adults (50 to 75 years of age), we manipulated age discrimination in a job application scenario and measured the effects of both responses on perceived health and self-esteem. Statistical analyses include individual study results as well as a meta-analysis on the combined results of the three studies. Findings show consistent evidence only for the individual response, which was in turn associated with well-being. Furthermore, challenging previous research, the two responses (adopting a younger subjective age and increasing group identification) were not only theoretically, but also empirically distinct. This research complements prior research by signaling the value of considering both responses to discrimination as complementary rather than mutually exclusive

Bunge’s Mathematical Structuralism Is Not a Fiction

In this paper, I explore Bunge’s fictionism in philosophy of mathematics. After an overview of Bunge’s views, in particular his mathematical structuralism, I argue that the comparison between mathematical objects and fictions ultimately fails. I then sketch a different ontology for mathematics, based on Thomasson’s metaphysical work. I conclude that mathematics deserves its own ontology, and that, in the end, much work remains to be done to clarify the various forms of dependence that are involved in mathematical knowledge, in particular its dependence on mental/brain states and material objects

Dynamic, Not Stable:Daily Variations in Subjective Age Bias and Age Group Identification Predict Daily Well-Being in Older Workers

This work examines the hypothesis that older workers' responses to negative events at work depend, in part, on daily fluctuations of subjective age bias (SAB; how old people feel compared to their actual age) and age group identification (age GI). We tested whether SAB and age GI fluctuate over time, whether they influence attributions of negative daily work events as age-related, and thereby predict older workers' daily affect and cognitive engagement in their work. A diary study with 169 older workers (aged 50-70 years) demonstrates that there are substantial daily variations in SAB and GI. Daily fluctuations of SAB and age GI respectively predicted attributions of negative personal (e.g., forgetfulness) and social (e.g., social exclusion) work events to age. Age attributions, in turn, negatively predicted affect and daily cognitive engagement over and above event occurrence. In other words, when confronted with negative daily work events, the short-term dissociation from one's chronological age and age group (i.e., feeling younger and identifying less with other older adults) seems to benefit older workers' well-being

Linear optical properties of one-dimensional Frenkel exciton systems with intersite energy correlations

We analyze the effects of intersite energy correlations on the linear optical properties of one-dimensional disordered Frenkel exciton systems. The absorption line width and the factor of radiative rate enhancement are studied as a function of the correlation length of the disorder. The absorption line width monotonously approaches the seeding degree of disorder on increasing the correlation length. On the contrary, the factor of radiative rate enhancement shows a non-monotonous trend, indicating a complicated scenario of the exciton localization in correlated systems. The concept of coherently bound molecules is exploited to explain the numerical results, showing good agreement with theory. Some recent experiments are discussed in the light of the present theory.Comment: 18 pages, 3 figues, REVTeX, to appear in Physical Review

Regulation-Structured Dynamic Metabolic Model Provides a Potential Mechanism for Delayed Enzyme Response in Denitrification Process

In a recent study of denitrification dynamics in hyporheic zone sediments, we observed a significant time lag (up to several days) in enzymatic response to the changes in substrate concentration. To explore an underlying mechanism and understand the interactive dynamics between enzymes and nutrients, we developed a trait-based model that associates a community’s traits with functional enzymes, instead of typically used species guilds (or functional guilds). This enzyme-based formulation allows to collectively describe biogeochemical functions of microbial communities without directly parameterizing the dynamics of species guilds, therefore being scalable to complex communities. As a key component of modeling, we accounted for microbial regulation occurring through transcriptional and translational processes, the dynamics of which was parameterized based on the temporal profiles of enzyme concentrations measured using a new signature peptide-based method. The simulation results using the resulting model showed several days of a time lag in enzymatic responses as observed in experiments. Further, the model showed that the delayed enzymatic reactions could be primarily controlled by transcriptional responses and that the dynamics of transcripts and enzymes are closely correlated. The developed model can serve as a useful tool for predicting biogeochemical processes in natural environments, either independently or through integration with hydrologic flow simulators

Shake table testing of a tuned mass damper inerter (Tmdi)-equipped structure and nonlinear dynamic modeling under harmonic excitations

This paper presents preliminary experimental results from a novel shaking table testing campaign investigating the dynamic response of a two-degree-of-freedom (2DOF) physical specimen with a grounded inerter under harmonic base excitation and contributes a nonlinear dynamic model capturing the behavior of the test specimen. The latter consists of a primary mass connected to the ground through a high damping rubber isolator (HDRI) and a secondary mass connected to the primary mass through a second HDRI. Further, a flywheel-based rack-and-pinion inerter prototype device is used to connect the secondary mass to the ground. The resulting specimen resembles the tuned mass damper inerter (TMDI) configuration with grounded inerter analytically defined and numerically assessed by the authors in a number of previous publications. Physical specimens with three different inerter coefficients are tested on the shake table under sine-sweep excitation with three different amplitudes. Experimental frequency response functions (FRFs) are derived manifesting a softening nonlinear behavior of the specimens and enhanced vibration suppression with increased inerter coefficient. Further, a 2DOF parametric nonlinear model of the specimen is established accounting for non-ideal inerter device behavior and its potential to characterize experimental response time-histories, FRFs, and force-displacement relationships of the HDRIs and of the inerter is verified

The transformative potential of reflective diaries for elite English cricketers

The sport of cricket has a history of its players suffering from mental health issues. The psychological study of cricket and, in particular, the attendant demands of participating at an elite level has not previously received rigorous academic attention. This study explored ten elite male cricketers’ experiences of keeping a daily reflective diary for one month during the competitive season. The aim was to assess how valuable qualitative diaries are in this field. Participants were interviewed regarding their appraisal of the methodology as a self‐help tool that could assist coping with performance pressures and wider life challenges. Three outcomes were revealed: first, that diary keeping was an effective opportunity to reflect upon the past and enhance one’s self (both as an individual and a performer); second, that diary keeping acted as a form of release that allowed participants to progress; and third, that diary keeping allowed participants to discover personal patterns of success that increased the likeliness of optimum performance

Airborne observations of the Eyjafjalla volcano ash cloud over Europe during air space closure in April and May 2010

© Author(s) 2011. This work is distributed under the Creative Commons Attribution 3.0 LicenseAirborne lidar and in-situ measurements of aerosols and trace gases were performed in volcanic ash plumes over Europe between Southern Germany and Iceland with the Falcon aircraft during the eruption period of the Eyjafjalla1 volcano between 19 April and 18 May 2010. Flight planning and measurement analyses were supported by a refined Meteosat ash product and trajectory model analysis. The volcanic ash plume was observed with lidar directly over the volcano and up to a distance of 2700 km downwind, and up to 120 h plume ages. Aged ash layers were between a few 100 m to 3 km deep, occurred between 1 and 7 km altitude, and were typically 100 to 300 km wide. Particles collected by impactors had diameters up to 20 μm diameter, with size and age dependent composition. Ash mass concentrations were derived from optical particle spectrometers for a particle density of 2.6 g cm-3 and various values of the refractive index (RI, real part: 1.59; 3 values for the imaginary part: 0, 0.004 and 0.008). The mass concentrations, effective diameters and related optical properties were compared with ground-based lidar observations. Theoretical considerations of particle sedimentation constrain the particle diameters to those obtained for the lower RI values. The ash mass concentration results have an uncertainty of a factor of two. The maximum ash mass concentration encountered during the 17 flights with 34 ash plume penetrations was below 1 mg m-3. The Falcon flew in ash clouds up to about 0.8 mg m-3 for a few minutes and in an ash cloud with approximately 0.2 mg -3 mean-concentration for about one hour without engine damage. The ash plumes were rather dry and correlated with considerable CO and SO2 increases and O3 decreases. To first order, ash concentration and SO2 mixing ratio in the plumes decreased by a factor of two within less than a day. In fresh plumes, the SO2 and CO concentration increases were correlated with the ash mass concentration. The ash plumes were often visible slantwise as faint dark layers, even for concentrations below 0.1 mg m-3. The large abundance of volatile Aitken mode particles suggests previous nucleation of sulfuric acid droplets. The effective diameters range between 0.2 and 3 μm with considerable surface and volume contributions from the Aitken and coarse mode aerosol, respectively. The distal ash mass flux on 2 May was of the order of 500 (240-1600) kgs -1. The volcano induced about 10 (2.5-50) Tg of distal ash mass and about 3 (0.6-23) Tg of SO2 during the whole eruption period. The results of the Falcon flights were used to support the responsible agencies in their decisions concerning air traffic in the presence of volcanic ash.Peer reviewe