A remote sensing analysis of Adelie penguin rookeries

The Adelie penguin (Pygoscelis adeliae) makes up the vast majority of bird biomass in the Antarctic. As a major consumer of krill, these birds play an important role in the Antarctic food web, and they have been proposed as an indicator species of the vitality of the Southern Ocean ecosystem. This study explores the terrestrial habitat of the Adelie penguin as a target for remote sensing reconnaissance. Laboratory and groundlevel reflectance measurements of Antarctic materials found in and around penguin rookeries were examined in detail. These analyses suggested data transformation which helped separate penguin rookeries from surrounding areas in Landsat Thematic Mapper imagery. The physical extent of penguin rookeries on Ross and Beaufort Islands, Antarctica, was estimated from the satellite data and compared to published estimates of penguin populations. The results suggest that TM imagery may be used to identify previously undiscovered penguin rookeries, and the imagery may provide a means of developing new population estimation methods for Antarctic ornithology.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/27987/1/0000420.pd

Impact of AlphaFold on structure prediction of protein complexes: The CASP15-CAPRI experiment

We present the results for CAPRI Round 54, the 5th joint CASP-CAPRI protein assembly prediction challenge. The Round offered 37 targets, including 14 homodimers, 3 homo-trimers, 13 heterodimers including 3 antibody-antigen complexes, and 7 large assemblies. On average ~70 CASP and CAPRI predictor groups, including more than 20 automatics servers, submitted models for each target. A total of 21 941 models submitted by these groups and by 15 CAPRI scorer groups were evaluated using the CAPRI model quality measures and the DockQ score consolidating these measures. The prediction performance was quantified by a weighted score based on the number of models of acceptable quality or higher submitted by each group among their five best models. Results show substantial progress achieved across a significant fraction of the 60+ participating groups. High-quality models were produced for about 40% of the targets compared to 8% two years earlier. This remarkable improvement is due to the wide use of the AlphaFold2 and AlphaFold2-Multimer software and the confidence metrics they provide. Notably, expanded sampling of candidate solutions by manipulating these deep learning inference engines, enriching multiple sequence alignments, or integration of advanced modeling tools, enabled top performing groups to exceed the performance of a standard AlphaFold2-Multimer version used as a yard stick. This notwithstanding, performance remained poor for complexes with antibodies and nanobodies, where evolutionary relationships between the binding partners are lacking, and for complexes featuring conformational flexibility, clearly indicating that the prediction of protein complexes remains a challenging problem

Sensitivity analyses of parameters of a M(t) / G / [infinity] stochastic service system

Parameter sensitivity analyses were conducted on a M(t) / G / [infinity] stochastic service system in which (1) the number of constants in an approximating nonhomogeneous Poisson process of inputs, (2) the mean of a Weibull c.d.f. of service time, and (3) the variance of the c.d.f. of service time were traded off in analyses of 24 cases for each of two fitting criteria: an L1 metric implemented by a linear goal program, and an L2 metric implemented by a multilinear least squares regression. The model goodness of fit and estimated total input to the system are both more sensitive to the mean service time than to its variance or to the number of constants in the approximating Poisson input. The fitting criteria give consistent results, but the L2 criterion gives slightly higher estimates of total input to the system over a fixed period of time.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/27308/1/0000329.pd

Impact of AlphaFold on structure prediction of protein complexes: The CASP15-CAPRI experiment

We present the results for CAPRI Round 54, the 5th joint CASP-CAPRI protein assembly prediction challenge. The Round offered 37 targets, including 14 homodimers, 3 homo-trimers, 13 heterodimers including 3 antibody-antigen complexes, and 7 large assemblies. On average similar to 70 CASP and CAPRI predictor groups, including more than 20 automatics servers, submitted models for each target. A total of 21 941 models submitted by these groups and by 15 CAPRI scorer groups were evaluated using the CAPRI model quality measures and the DockQ score consolidating these measures. The prediction performance was quantified by a weighted score based on the number of models of acceptable quality or higher submitted by each group among their five best models. Results show substantial progress achieved across a significant fraction of the 60+ participating groups. High-quality models were produced for about 40% of the targets compared to 8% two years earlier. This remarkable improvement is due to the wide use of the AlphaFold2 and AlphaFold2-Multimer software and the confidence metrics they provide. Notably, expanded sampling of candidate solutions by manipulating these deep learning inference engines, enriching multiple sequence alignments, or integration of advanced modeling tools, enabled top performing groups to exceed the performance of a standard AlphaFold2-Multimer version used as a yard stick. This notwithstanding, performance remained poor for complexes with antibodies and nanobodies, where evolutionary relationships between the binding partners are lacking, and for complexes featuring conformational flexibility, clearly indicating that the prediction of protein complexes remains a challenging problem