University of Notre Dame

About: University of Notre Dame is a education organization based out in Notre Dame, Indiana, United States. It is known for research contribution in the topics: Population & Large Hadron Collider. The organization has 22238 authors who have published 55201 publications receiving 2032925 citations. The organization is also known as: University of Notre Dame du Lac & University of Notre Dame, South Bend.

Quantification of mesocosm fish and amphibian species diversity via environmental DNA metabarcoding.

Abstract: Freshwater fauna are particularly sensitive to environmental change and disturbance. Management agencies frequently use fish and amphibian biodiversity as indicators of ecosystem health and a way to prioritize and assess management strategies. Traditional aquatic bioassessment that relies on capture of organisms via nets, traps and electrofishing gear typically has low detection probabilities for rare species and can injure individuals of protected species. Our objective was to determine whether environmental DNA (eDNA) sampling and metabarcoding analysis can be used to accurately measure species diversity in aquatic assemblages with differing structures. We manipulated the density and relative abundance of eight fish and one amphibian species in replicated 206-L mesocosms. Environmental DNA was filtered from water samples, and six mitochondrial gene fragments were Illumina-sequenced to measure species diversity in each mesocosm. Metabarcoding detected all nine species in all treatment replicates. Additionally, we found a modest, but positive relationship between species abundance and sequencing read abundance. Our results illustrate the potential for eDNA sampling and metabarcoding approaches to improve quantification of aquatic species diversity in natural environments and point the way towards using eDNA metabarcoding as an index of macrofaunal species abundance.

Windowed cross-correlation and peak picking for the analysis of variability in the association between behavioral time series

Abstract: Cross-correlation and most other longitudinal analyses assume that the association between 2 variables is stationary. Thus, a sample of occasions of measurement is expected to be representative of the association between variables regardless of the time of onset or number of occasions in the sample. The authors propose a method to analyze the association between 2 variables when the assumption of stationarity may not be warranted. The method results in estimates of both the strength of peak association and the time lag when the peak association occurred for a range of starting values of elapsed time from the beginning of an experiment.

MIT Cheetah 3: Design and Control of a Robust, Dynamic Quadruped Robot

Abstract: This paper introduces a new robust, dynamic quadruped, the MIT Cheetah 3. Like its predecessor, the Cheetah 3 exploits tailored mechanical design to enable simple control strategies for dynamic locomotion and features high-bandwidth proprioceptive actuators to manage physical interaction with the environment. A new leg design is presented that includes proprioceptive actuation on the abduction/adduction degrees of freedom in addition to an expanded range of motion on the hips and knees. To make full use of these new capabilities, general balance and locomotion controllers for Cheetah 3 are presented. These controllers are embedded into a modular control architecture that allows the robot to handle unexpected terrain disturbances through reactive gait modification and without the need for external sensors or prior environment knowledge. The efficiency of the robot is demonstrated by a low Cost of Transport (CoT) over multiple gaits at moderate speeds, with the lowest CoT of 0.45 found during trotting. Experiments showcase the ability to blindly climb up stairs as a result of the full system integration. These results collectively represent a promising step toward a platform capable of generalized dynamic legged locomotion.

A High-Resolution Survey of Low-Redshift QSO Absorption Lines: Statistics and Physical Conditions of O VI Absorbers

Abstract: Using high-resolution ultraviolet spectra of 16 low-z QSOs obtained with the E140M echelle mode of the Space Telescope Imaging Spectrograph, we study the physical conditions and statistics of O VI absorption in the intergalactic medium (IGM) at -->z zabs zQSO) O VI systems comprising 77 individual components, and we find 14 proximate systems ( -->zabs ? zQSO) containing 34 components. For intervening systems (components) with rest-frame equivalent width -->Wr > 30 m?, the number of O VI absorbers per unit redshift -->dN/dz = 15.6?2.4+2.9 -->(21.0?2.8+3.2) , and this decreases to -->dN/dz = 0.9?0.5+1.0 -->(0.3?0.3+0.7) for -->Wr > 300 m?. The number per redshift increases steeply as zabs approaches zQSO; we find that -->dN/dz is 3-10 times higher within 2500 km s?1 of zQSO. The most striking difference between intervening and proximate systems is that some proximate absorbers have substantially lower H I/O VI ratios. The lower ratios in proximate systems could be partially due to ionization effects, but these proximate absorbers must also have significantly higher metallicities. We find that 37% of the intervening O VI absorbers have velocity centroids that are well aligned with corresponding H I absorption. If the O VI and the H I trace the same gas, the relatively small differences in line widths imply that the absorbers are cool, with -->T T ? 105.5 K if the metallicity is high enough to cause the associated broad Ly? absorption to be too weak to detect. We show that 53% of the intervening O VI systems are complex multiphase absorbers that can accommodate both lower metallicity collisionally ionized gas with -->T > 105 K and cold photoionzed gas.

Glycosylation of Pichia pastoris-derived proteins.

Abstract: The Pichia pastoris system for expression of heterologous recombinant proteins is being used increasingly because of the large yields of properly folded proteins that result and the ease of scaling preparations into large-biomass fermentors. Another advantage of this system centres on the type of glycosylation that results, generally yielding protein-bound oligosaccharides that are of much shorter chain length than found in Saccharomyces cerevisiae. This review is a summary of the current state of knowledge of glycosylation of proteins in this methylotrophic yeast.