PALS and Open Source

PALS has been working with open source technologies including an electronic resource management (ERM) system, an openURL link resolver, a discovery tool, and an integrated library system (ILS). While these tools provide benefits to your staff and patrons, there are challenges in the configuration and setup. In this session we will share our experiences with working in the open source community - both the obstacles and opportunities

Optical Readout in a Multi-Module System Test for the ATLAS Pixel Detector

The innermost part of the ATLAS experiment at the LHC, CERN, will be a pixel detector. The command messages and the readout data of the detector are transmitted over an optical data path. The readout chain consists of many components which are produced at several locations around the world, and must work together in the pixel detector. To verify that these parts are working together as expected a system test has been built up. In this paper the system test setup and the operation of the readout chain is described. Also, some results of tests using the final pixel detector readout chain are given.Comment: 6 pages, 10 figures, Pixel 2005 proceedings preprin

Automatically detecting asymmetric running using time and frequency domain features

Human motion analysis technologies have been widely employed to identify injury determining factors and provide objective and quantitative feedback to athletes to help prevent injury. However, most of these technologies are: ex- pensive, restricted to laboratory environments, and can require significant post processing. This reduces their ecological validity, adoption and usefulness. In this paper, we present a novel wearable inertial sensor framework to accurately distinguish between symmetrical and asymmetrical running patterns in an unconstrained environment. The framework can automatically classify symmetry/asymmetry using Short Time Fourier Trans- form (STFT) and other time domain features in conjunction with a customized Random Forest classifier. The accuracy of the designed framework is up to 94% using 3-D accelerometer and 3-D gyroscope data from a sensor node attached on the upper back of a subject. The upper back inertial sensors data were then down-sampled by a factor of 4 to simulate utilizing low-cost inertial sensors whilst also facilitating a decrease of the computational cost to achieve near real-time application. We conclude that the proposed framework can potentially pave the way for employing low-cost sensors, such as those used in smartphones, attached on the upper back to provide injury related and performance feedback in real-time in unconstrained environments

Ecological and Genomic Attributes of Novel Bacterial Taxa That Thrive in Subsurface Soil Horizons.

While most bacterial and archaeal taxa living in surface soils remain undescribed, this problem is exacerbated in deeper soils, owing to the unique oligotrophic conditions found in the subsurface. Additionally, previous studies of soil microbiomes have focused almost exclusively on surface soils, even though the microbes living in deeper soils also play critical roles in a wide range of biogeochemical processes. We examined soils collected from 20 distinct profiles across the United States to characterize the bacterial and archaeal communities that live in subsurface soils and to determine whether there are consistent changes in soil microbial communities with depth across a wide range of soil and environmental conditions. We found that bacterial and archaeal diversity generally decreased with depth, as did the degree of similarity of microbial communities to those found in surface horizons. We observed five phyla that consistently increased in relative abundance with depth across our soil profiles: Chloroflexi, Nitrospirae, Euryarchaeota, and candidate phyla GAL15 and Dormibacteraeota (formerly AD3). Leveraging the unusually high abundance of Dormibacteraeota at depth, we assembled genomes representative of this candidate phylum and identified traits that are likely to be beneficial in low-nutrient environments, including the synthesis and storage of carbohydrates, the potential to use carbon monoxide (CO) as a supplemental energy source, and the ability to form spores. Together these attributes likely allow members of the candidate phylum Dormibacteraeota to flourish in deeper soils and provide insight into the survival and growth strategies employed by the microbes that thrive in oligotrophic soil environments.IMPORTANCE Soil profiles are rarely homogeneous. Resource availability and microbial abundances typically decrease with soil depth, but microbes found in deeper horizons are still important components of terrestrial ecosystems. By studying 20 soil profiles across the United States, we documented consistent changes in soil bacterial and archaeal communities with depth. Deeper soils harbored communities distinct from those of the more commonly studied surface horizons. Most notably, we found that the candidate phylum Dormibacteraeota (formerly AD3) was often dominant in subsurface soils, and we used genomes from uncultivated members of this group to identify why these taxa are able to thrive in such resource-limited environments. Simply digging deeper into soil can reveal a surprising number of novel microbes with unique adaptations to oligotrophic subsurface conditions

SO2 Emissions and Lifetimes: Estimates from Inverse Modeling Using In Situ and Global, Space-Based (SCIAMACHY and OMI) Observations

Top-down constraints on global sulfur dioxide (SO2) emissions are inferred through inverse modeling using SO2 column observations from two satellite instruments (SCIAMACHY and OMI). We first evaluated the S02 column observations with surface SO2 measurements by applying local scaling factors from a global chemical transport model (GEOS-Chem) to SO2 columns retrieved from the satellite instruments. The resulting annual mean surface SO2 mixing ratios for 2006 exhibit a significant spatial correlation (r=0.86, slope=0.91 for SCIAMACHY and r=0.80, slope = 0.79 for OMI) with coincident in situ measurements from monitoring networks throughout the United States and Canada. We evaluate the GEOS-Chem simulation of the SO2 lifetime with that inferred from in situ measurements to verity the applicability of GEOS-Chem for inversion of SO2 columns to emissions. The seasonal mean SO2 lifetime calculated with the GEOS-Chem model over the eastern United States is 13 h in summer and 48 h in winter, compared to lifetimes inferred from in situ measurements of 19 +/- 7 h in summer and 58 +/- 20 h in winter. We apply SO2 columns from SCIAMACHY and OMI to derive a top-down anthropogenic SO2 emission inventory over land by using the local GEOS-Chem relationship between SO2 columns and emissions. There is little seasonal variation in the top-down emissions (<15%) over most major industrial regions providing some confidence in the method. Our global estimate for annual land surface anthropogenic SO2 emissions (52.4 Tg S/yr from SCIAMACHY and 49.9 Tg S / yr from OMI) closely agrees with the bottom-up emissions (54.6 Tg S/yr) in the GEOS-Chem model and exhibits consistency in global distributions with the bottom-up emissions (r = 0.78 for SCIAMACHY, and r = 0.77 for OMI). However, there are significant regional differences

“A very orderly retreat”: Democratic transition in East Germany, 1989-90

East Germany's 1989-90 democratisation is among the best known of East European transitions, but does not lend itself to comparative analysis, due to the singular way in which political reform and democratic consolidation were subsumed by Germany's unification process. Yet aspects of East Germany's democratisation have proved amenable to comparative approaches. This article reviews the comparative literature that refers to East Germany, and finds a schism between those who designate East Germany's transition “regime collapse” and others who contend that it exemplifies “transition through extrication”. It inquires into the merits of each position and finds in favour of the latter. Drawing on primary and secondary literature, as well as archival and interview sources, it portrays a communist elite that was, to a large extent, prepared to adapt to changing circumstances and capable of learning from “reference states” such as Poland. Although East Germany was the Soviet state in which the positions of existing elites were most threatened by democratic transition, here too a surprising number succeeded in maintaining their position while filing across the bridge to market society. A concluding section outlines the alchemy through which their bureaucratic power was transmuted into property and influence in the “new Germany”

The Role of Convection in Redistributing Formaldehyde to the Upper Troposphere Over North America and the North Atlantic during the Summer 2004 INTEX Campaign

Measurements of CH2O from a tunable diode laser absorption spectrometer (TDLAS) were acquired onboard the NASA DC-8 during the summer 2004 INTEX-NA (Intercontinental Chemical Transport Experiment - North America) campaign to test our understanding of convection and production mechanisms in the upper troposphere (UT, 6-12-km) over continental North America and the North Atlantic Ocean. Point-by-point comparisons with box model calculations, when MHP (CH3OOH) measurements were available for model constraint, resulted in a median CH2O measurement/model ratio of 0.91 in the UT. Multiple tracers were used to arrive at a set of UT CH2O background and perturbed air mass periods, and 46% of the TDLAS measurements fell within the latter category. At least 66% to 73% of these elevated UT observations were caused by enhanced production from CH2O precursors rather than direct transport of CH2O from the boundary layer. This distinction is important, since the effects from the former can last for over a week or more compared to one day or less in the case of convective transport of CH2O itself. In general, production of CH2O from CH4 was found to be the dominant source term, even in perturbed air masses. This was followed by production from MHP, methanol, PAN type compounds, and ketones, in descending order of their contribution. In the presence of elevated NO from lightning and potentially from the stratosphere, there was a definite trend in the CH2O discrepancy, which for the highest NO mixing ratios produced a median CH2O measurement/model ratio of 3.9 in the 10-12-km range. Discrepancies in CH2O and HO2 in the UT with NO were highly correlated and this provided further information as to the possible mechanism(s) responsible. These discrepancies with NO are consistent with additional production sources of both gases involving CH3O2 + NO reactions, most likely caused by unmeasured hydrocarbons

Computational design of a red fluorophore ligase for site-specific protein labeling in living cells

Chemical fluorophores offer tremendous size and photophysical advantages over fluorescent proteins but are much more challenging to target to specific cellular proteins. Here, we used Rosetta-based computation to design a fluorophore ligase that accepts the red dye resorufin, starting from Escherichia coli lipoic acid ligase. X-ray crystallography showed that the design closely matched the experimental structure. Resorufin ligase catalyzed the site-specific and covalent attachment of resorufin to various cellular proteins genetically fused to a 13-aa recognition peptide in multiple mammalian cell lines and in primary cultured neurons. We used resorufin ligase to perform superresolution imaging of the intermediate filament protein vimentin by stimulated emission depletion and electron microscopies. This work illustrates the power of Rosetta for major redesign of enzyme specificity and introduces a tool for minimally invasive, highly specific imaging of cellular proteins by both conventional and superresolution microscopies.National Institutes of Health (U.S.) (Grant DP1 OD003961)National Institutes of Health (U.S.) (R01 GM072670)American Chemical Societ