Intra- and inter-individual genetic differences in gene expression

Genetic variation is known to influence the amount of mRNA produced by a gene. Given that the molecular machines control mRNA levels of multiple genes, we expect genetic variation in the components of these machines would influence multiple genes in a similar fashion. In this study we show that this assumption is correct by using correlation of mRNA levels measured independently in the brain, kidney or liver of multiple, genetically typed, mice strains to detect shared genetic influences. These correlating groups of genes (CGG) have collective properties that account for 40-90% of the variability of their constituent genes and in some cases, but not all, contain genes encoding functionally related proteins. Critically, we show that the genetic influences are essentially tissue specific and consequently the same genetic variations in the one animal may up-regulate a CGG in one tissue but down-regulate the same CGG in a second tissue. We further show similarly paradoxical behaviour of CGGs within the same tissues of different individuals. The implication of this study is that this class of genetic variation can result in complex inter- and intra-individual and tissue differences and that this will create substantial challenges to the investigation of phenotypic outcomes, particularly in humans where multiple tissues are not readily available.

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Status of Muon Collider Research and Development and Future Plans

The status of the research on muon colliders is discussed and plans are outlined for future theoretical and experimental studies. Besides continued work on the parameters of a 3-4 and 0.5 TeV center-of-mass (CoM) energy collider, many studies are now concentrating on a machine near 0.1 TeV (CoM) that could be a factory for the s-channel production of Higgs particles. We discuss the research on the various components in such muon colliders, starting from the proton accelerator needed to generate pions from a heavy-Z target and proceeding through the phase rotation and decay ($\pi \to \mu \nu_{\mu}$) channel, muon cooling, acceleration, storage in a collider ring and the collider detector. We also present theoretical and experimental R & D plans for the next several years that should lead to a better understanding of the design and feasibility issues for all of the components. This report is an update of the progress on the R & D since the Feasibility Study of Muon Colliders presented at the Snowmass'96 Workshop [R. B. Palmer, A. Sessler and A. Tollestrup, Proceedings of the 1996 DPF/DPB Summer Study on High-Energy Physics (Stanford Linear Accelerator Center, Menlo Park, CA, 1997)].Comment: 95 pages, 75 figures. Submitted to Physical Review Special Topics, Accelerators and Beam

Podbat: A Novel Genomic Tool Reveals Swr1-Independent H2A.Z Incorporation at Gene Coding Sequences through Epigenetic Meta-Analysis

Epigenetic regulation consists of a multitude of different modifications that determine active and inactive states of chromatin. Conditions such as cell differentiation or exposure to environmental stress require concerted changes in gene expression. To interpret epigenomics data, a spectrum of different interconnected datasets is needed, ranging from the genome sequence and positions of histones, together with their modifications and variants, to the transcriptional output of genomic regions. Here we present a tool, Podbat (Positioning database and analysis tool), that incorporates data from various sources and allows detailed dissection of the entire range of chromatin modifications simultaneously. Podbat can be used to analyze, visualize, store and share epigenomics data. Among other functions, Podbat allows data-driven determination of genome regions of differential protein occupancy or RNA expression using Hidden Markov Models. Comparisons between datasets are facilitated to enable the study of the comprehensive chromatin modification system simultaneously, irrespective of data-generating technique. Any organism with a sequenced genome can be accommodated. We exemplify the power of Podbat by reanalyzing all to-date published genome-wide data for the histone variant H2A.Z in fission yeast together with other histone marks and also phenotypic response data from several sources. This meta-analysis led to the unexpected finding of H2A.Z incorporation in the coding regions of genes encoding proteins involved in the regulation of meiosis and genotoxic stress responses. This incorporation was partly independent of the H2A.Z-incorporating remodeller Swr1. We verified an Swr1-independent role for H2A.Z following genotoxic stress in vivo. Podbat is open source software freely downloadable from www.podbat.org, distributed under the GNU LGPL license. User manuals, test data and instructions are available at the website, as well as a repository for third party–developed plug-in modules. Podbat requires Java version 1.6 or higher

Emotional ratings and skin conductance response to visual, auditory and haptic stimuli

The human emotional reactions to stimuli delivered by different sensory modalities is a topic of interest for many disciplines, from Human-Computer-Interaction to cognitive sciences. Different databases of stimuli eliciting emotional reaction are available, tested on a high number of participants. Interestingly, stimuli within one database are always of the same type. In other words, to date, no data was obtained and compared from distinct types of emotion-eliciting stimuli from the same participant. This makes it difficult to use different databases within the same experiment, limiting the complexity of experiments investigating emotional reactions. Moreover, whereas the stimuli and the participants’ rating to the stimuli are available, physiological reactions of participants to the emotional stimuli are often recorded but not shared. Here, we test stimuli delivered either through a visual, auditory, or haptic modality in a within participant experimental design. We provide the results of our study in the form of a MATLAB structure including basic demographics on the participants, the participant’s self-assessment of his/her emotional state, and his/her physiological reactions (i.e., skin conductance)

Inverse modeling of global and regional CH_4 emissions using SCIAMACHY satellite retrievals

Methane retrievals from the Scanning Imaging Absorption Spectrometer for Atmospheric Chartography (SCIAMACHY) instrument onboard ENVISAT provide important information on atmospheric CH_4 sources, particularly in tropical regions which are poorly monitored by in situ surface observations. Recently, Frankenberg et al. (2008a, 2008b) reported a major revision of SCIAMACHY retrievals due to an update of spectroscopic parameters of water vapor and CH_4. Here, we analyze the impact of this revision on global and regional CH_4 emissions estimates in 2004, using the TM5-4DVAR inverse modeling system. Inversions based on the revised SCIAMACHY retrievals yield ∼20% lower tropical emissions compared to the previous retrievals. The new retrievals improve significantly the consistency between observed and assimilated column average mixing ratios and the agreement with independent validation data. Furthermore, the considerable latitudinal and seasonal bias correction of the previous SCIAMACHY retrievals, derived in the TM5-4DVAR system by simultaneously assimilating high-accuracy surface measurements, is reduced by a factor of ∼3. The inversions result in significant changes in the spatial patterns of emissions and their seasonality compared to the bottom-up inventories. Sensitivity tests were done to analyze the robustness of retrieved emissions, revealing some dependence on the applied a priori emission inventories and OH fields. Furthermore, we performed a detailed validation of simulated CH_4 mixing ratios using NOAA ship and aircraft profile samples, as well as stratospheric balloon samples, showing overall good agreement. We use the new SCIAMACHY retrievals for a regional analysis of CH_4 emissions from South America, Africa, and Asia, exploiting the zooming capability of the TM5 model. This allows a more detailed analysis of spatial emission patterns and better comparison with aircraft profiles and independent regional emission estimates available for South America. Large CH_4 emissions are attributed to various wetland regions in tropical South America and Africa, seasonally varying and opposite in phase with CH_4 emissions from biomass burning. India, China and South East Asia are characterized by pronounced emissions from rice paddies peaking in the third quarter of the year, in addition to further anthropogenic emissions throughout the year

Labour in a single shot: critical perspectives on Antje Ehmann and Harun Farocki's global video project

This collection of essays offers a critical assessment of Labour in a Single Shot, a groundbreaking documentary video workshop. From 2011 to 2014, curator Antje Ehmann and film- and videomaker Harun Farocki produced an art project of truly global proportions. They travelled to fifteen cities around the world to conduct workshops inspired by cinema history’s first film, Workers Leaving the Lumière Factory, shot in 1895 by the Lumière brothers in France. While the workshop videos are in colour and the camera was not required to remain static, Ehmann and Farocki’s students were tasked with honouring the original Lumière film’s basic parameters of theme and style. The fascinating result is a collection of more than 550 short videos that have appeared in international exhibitions and on an open-access website, offering the widest possible audience the opportunity to ponder contemporary labour in multiple contexts around the world.https://library.oapen.org/handle/20.500.12657/5163

The Future of Agent-Based Modeling

In this paper, I elaborate on the role of agent-based (AB) modeling for macroeconomic research. My main tenet is that the full potential of the AB approach has not been realized yet. This potential lies in the modular nature of the models, which is bought by abandoning the straitjacket of rational expectations and embracing an evolutionary perspective. I envisage the foundation of a Modular Macroeconomic Science, where new models with heterogeneous interacting agents, endowed with partial information and limited computational ability, can be created by recombining and extending existing models in a unified computational framework