USING THE EMBL-EBI CLUSTAL OMEGA TOOL TO CALCULATE DIVERSITY OF HEAVY CHAIN PHAGE-DISPLAY LIBRARIES

Here we show that traditional Sanger sequencing combined with analysis tools available from the European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), specifically EMBOSS Transeq and Clustal Omega, is extremely effective in the analysis of naïve phage display antibody libraries for the determination of library size and diversity. The free tools are easy to use and require little manipulation of reads by hand, allowing analysis to be performed on a standard personal computer. Utilization of this technique has applicability to researchers with limited access to deep sequencing. The primary drawback to this analysis methodology is that antibodies with particular molecular or binding properties, desirable or otherwise, are not identifiable by their sequences

Zoogoneticus tequila, a new goodeid fish (Cyprinodontoformes) from the Ameca drainage of Mexico, and a rediagnosis of the genus

http://deepblue.lib.umich.edu/bitstream/2027.42/57161/1/OP725.pd

The Cool Accretion Disk in ESO 243-49 HLX-1: Further Evidence of an Intermediate Mass Black Hole

With an inferred bolometric luminosity exceeding 10^42 erg/s, HLX-1 in ESO 243-49 is the most luminous of ultraluminous X-ray sources and provides one of the strongest cases for the existence of intermediate mass black holes. We obtain good fits to disk-dominated observations of the source with BHSPEC, a fully relativistic black hole accretion disk spectral model. Due to degeneracies in the model arising from the lack of independent constraints on inclination and black hole spin, there is a factor of 100 uncertainty in the best-fit black hole mass M. Nevertheless, spectral fitting of XMM-Newton observations provides robust lower and upper limits with 3000 Msun < M < 3 x 10^5 Msun, at 90% confidence, placing HLX-1 firmly in the intermediate-mass regime. The lower bound on M is entirely determined by matching the shape and peak energy of the thermal component in the spectrum. This bound is consistent with (but independent of) arguments based solely on the Eddington limit. Joint spectral modelling of the XMM-Newton data with more luminous Swift and Chandra observations increases the lower bound to 6000 Msun, but this tighter constraint is not independent of the Eddington limit. The upper bound on M is sensitive to the maximum allowed inclination i, and is reduced to M < 10^5 Msun if we limit i < 75 deg.Comment: 10 pages, 7 figures, accepted for publication in Ap

Electrical lithosphere beneath the Kaapvaal craton, southern Africa

Author Posting. © American Geophysical Union, 2011. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research 116 (2011): B04105, doi:10.1029/2010JB007883.A regional-scale magnetotelluric (MT) experiment across the southern African Kaapvaal craton and surrounding terranes, called the Southern African Magnetotelluric Experiment (SAMTEX), has revealed complex structure in the lithospheric mantle. Large variations in maximum resistivity at depths to 200–250 km relate directly to age and tectonic provenance of surface structures. Within the central portions of the Kaapvaal craton are regions of resistive lithosphere about 230 km thick, in agreement with estimates from xenolith thermobarometry and seismic surface wave tomography, but thinner than inferred from seismic body wave tomography. The MT data are unable to discriminate between a completely dry or slightly “damp” (a few hundred parts per million of water) structure within the transitional region at the base of the lithosphere. However, the structure of the uppermost ∼150 km of lithosphere is consistent with enhanced, but still low, conductivities reported for hydrous olivine and orthopyroxene at levels of water reported for Kaapvaal xenoliths. The electrical lithosphere around the Kimberley and Premier diamond mines is thinner than the maximum craton thickness found between Kimberley and Johannesburg/Pretoria. The mantle beneath the Bushveld Complex is highly conducting at depths around 60 km. Possible explanations for these high conductivities include graphite or sulphide and/or iron metals associated with the Bushveld magmatic event. We suggest that one of these conductive phases (most likely melt-related sulphides) could electrically connect iron-rich garnets in a garnet-rich eclogitic composition associated with a relict subduction slab.In addition to the funding and logistical support provided by SAMTEX consortium members, this work is also supported by research grants from the National Science Foundation (EAR‐0309584 and EAR‐0455242 through the Continental Dynamics Program), the Department of Science and Technology, South Africa, and Science Foundation of Ireland (grant 05/RFP/ GEO001)

Can Drake Passage Observations Match Ekman's Classic Theory?

Ekman's theory of the wind-driven ocean surface boundary layer assumes a constant eddy viscosity and predicts that the current rotates with depth at the same rate as it decays in amplitude. Despite its wide acceptance, Ekman current spirals are difficult to observe. This is primarily because the spirals are small signals that are easily masked by ocean variability and cannot readily be separated from the geostrophic component. This study presents a method for estimating ageostrophic currents from shipboard acoustic Doppler current profiler data in Drake Passage and finds that observations are consistent with Ekman's theory. By taking into account the sampling distributions of wind stress and ageostrophic velocity, the authors find eddy viscosity values in the range of 0.08–0.12 m2 s−1 that reconcile observations with the classic theory in Drake Passage. The eddy viscosity value that most frequently reconciles observations with the classic theory is 0.094 m2 s−1, corresponding to an Ekman depth scale of 39 m

State owned enterprises as bribe payers: the role of institutional environment

Our paper draws attention to a neglected channel of corruption—the bribe payments by state-owned enterprises (SOEs). This is an important phenomenon as bribe payments by SOEs fruitlessly waste national resources, compromising public welfare and national prosperity. Using a large dataset of 30,249 firms from 50 countries, we show that, in general, SOEs are less likely to pay bribes for achieving organizational objectives owing to their political connectivity. However, in deteriorated institutional environments, SOEs may be subjected to potential managerial rent-seeking behaviors, which disproportionately increase SOE bribe propensity relative to privately owned enterprises. Specifically, our findings highlight the importance of fostering democracy and rule of law, reducing prevalence of corruption and shortening power distance in reducing the incidence of SOE bribery

Expert consensus and recommendations on safety criteria for active mobilization of mechanically ventilated critically ill adults

Introduction: The aim of this study was to develop consensus recommendations on safety parameters for mobilizing adult, mechanically ventilated, intensive care unit (ICU) patients. Methods: A systematic literature review was followed by a meeting of 23 multidisciplinary ICU experts to seek consensus regarding the safe mobilization of mechanically ventilated patients. Results: Safety considerations were summarized in four categories: respiratory, cardiovascular, neurological and other. Consensus was achieved on all criteria for safe mobilization, with the exception being levels of vasoactive agents. Intubation via an endotracheal tube was not a contraindication to early mobilization and a fraction of inspired oxygen less than 0.6 with a percutaneous oxygen saturation more than 90% and a respiratory rate less than 30 breaths/minute were considered safe criteria for in- and out-of-bed mobilization if there were no other contraindications. At an international meeting, 94 multidisciplinary ICU clinicians concurred with the proposed recommendations. Conclusion: Consensus recommendations regarding safety criteria for mobilization of adult, mechanically ventilated patients in the ICU have the potential to guide ICU rehabilitation whilst minimizing the risk of adverse events

Ejecta Evolution Following a Planned Impact into an Asteroid: The First Five Weeks

The impact of the DART spacecraft into Dimorphos, moon of the asteroid Didymos, changed Dimorphos' orbit substantially, largely from the ejection of material. We present results from twelve Earth-based facilities involved in a world-wide campaign to monitor the brightness and morphology of the ejecta in the first 35 days after impact. After an initial brightening of ~1.4 magnitudes, we find consistent dimming rates of 0.11-0.12 magnitudes/day in the first week, and 0.08-0.09 magnitudes/day over the entire study period. The system returned to its pre-impact brightness 24.3-25.3 days after impact through the primary ejecta tail remained. The dimming paused briefly eight days after impact, near in time to the appearance of the second tail. This was likely due to a secondary release of material after re-impact of a boulder released in the initial impact, through movement of the primary ejecta through the aperture likely played a role.Comment: 16 pages, 5 Figures, accepted in the Astrophysical Journal Letters (ApJL) on October 16, 202