The Cityscapes Dataset for Semantic Urban Scene Understanding

Visual understanding of complex urban street scenes is an enabling factor for a wide range of applications. Object detection has benefited enormously from large-scale datasets, especially in the context of deep learning. For semantic urban scene understanding, however, no current dataset adequately captures the complexity of real-world urban scenes. To address this, we introduce Cityscapes, a benchmark suite and large-scale dataset to train and test approaches for pixel-level and instance-level semantic labeling. Cityscapes is comprised of a large, diverse set of stereo video sequences recorded in streets from 50 different cities. 5000 of these images have high quality pixel-level annotations; 20000 additional images have coarse annotations to enable methods that leverage large volumes of weakly-labeled data. Crucially, our effort exceeds previous attempts in terms of dataset size, annotation richness, scene variability, and complexity. Our accompanying empirical study provides an in-depth analysis of the dataset characteristics, as well as a performance evaluation of several state-of-the-art approaches based on our benchmark.Comment: Includes supplemental materia

Rampant exchange of the structure and function of extramembrane domains between membrane and water soluble proteins.

Of the membrane proteins of known structure, we found that a remarkable 67% of the water soluble domains are structurally similar to water soluble proteins of known structure. Moreover, 41% of known water soluble protein structures share a domain with an already known membrane protein structure. We also found that functional residues are frequently conserved between extramembrane domains of membrane and soluble proteins that share structural similarity. These results suggest membrane and soluble proteins readily exchange domains and their attendant functionalities. The exchanges between membrane and soluble proteins are particularly frequent in eukaryotes, indicating that this is an important mechanism for increasing functional complexity. The high level of structural overlap between the two classes of proteins provides an opportunity to employ the extensive information on soluble proteins to illuminate membrane protein structure and function, for which much less is known. To this end, we employed structure guided sequence alignment to elucidate the functions of membrane proteins in the human genome. Our results bridge the gap of fold space between membrane and water soluble proteins and provide a resource for the prediction of membrane protein function. A database of predicted structural and functional relationships for proteins in the human genome is provided at sbi.postech.ac.kr/emdmp

Genealogies of rapidly adapting populations

The genetic diversity of a species is shaped by its recent evolutionary history and can be used to infer demographic events or selective sweeps. Most inference methods are based on the null hypothesis that natural selection is a weak or infrequent evolutionary force. However, many species, particularly pathogens, are under continuous pressure to adapt in response to changing environments. A statistical framework for inference from diversity data of such populations is currently lacking. Toward this goal, we explore the properties of genealogies in a model of continual adaptation in asexual populations. We show that lineages trace back to a small pool of highly fit ancestors, in which almost simultaneous coalescence of more than two lineages frequently occurs. While such multiple mergers are unlikely under the neutral coalescent, they create a unique genetic footprint in adapting populations. The site frequency spectrum of derived neutral alleles, for example, is non-monotonic and has a peak at high frequencies, whereas Tajima's D becomes more and more negative with increasing sample size. Since multiple merger coalescents emerge in many models of rapid adaptation, we argue that they should be considered as a null-model for adapting populations.Comment: to appear in PNA

Genetic draft, selective interference, and population genetics of rapid adaptation

To learn about the past from a sample of genomic sequences, one needs to understand how evolutionary processes shape genetic diversity. Most population genetic inference is based on frameworks assuming adaptive evolution is rare. But if positive selection operates on many loci simultaneously, as has recently been suggested for many species including animals such as flies, a different approach is necessary. In this review, I discuss recent progress in characterizing and understanding evolution in rapidly adapting populations where random associations of mutations with genetic backgrounds of different fitness, i.e., genetic draft, dominate over genetic drift. As a result, neutral genetic diversity depends weakly on population size, but strongly on the rate of adaptation or more generally the variance in fitness. Coalescent processes with multiple mergers, rather than Kingman's coalescent, are appropriate genealogical models for rapidly adapting populations with important implications for population genetic inference.Comment: supplementary illustrations and scripts are available at http://webdav.tuebingen.mpg.de/interference

Effects of a large irrigation reservoir on aquatic and riparian plants: a history of survival and loss

Dammed rivers have unnatural stream flows, disrupted sediment dynamics, and rearranged geomorphologic settings. Consequently, fluvial biota experiences disturbed functioning in the novel ecosystems. The case study is the large irrigation reservoir Alqueva in Guadiana River, Southern Iberia. The study area was divided into three zones: upstream and downstream of the dam and reservoir. For each zone, species composition and land use and land cover (LULC) were compared before and after the Alqueva Dam implementation. Data consist of aquatic and riparian flora composition obtained from 46 surveys and the area (%) of 12 classes of LULC obtained in 90 riverine sampling units through the analysis of historical and contemporary imagery. There was an overall decrease of several endemic species and on the riparian shrublands and aquatic stands, although di erences in the proportion of functional groups were not significant. Nevertheless, compositional diversity shows a significant decline in the upstream zone while landscape diversity shows an accentuated reduction in the reservoir area and downstream of the dam, which is likely related to the loss of the rocky habitats of the ‘old’ Guadiana River and the homogenization of the riverscape due to the irrigation intensification. The mitigation of these critical changes should be site-specific and should rely on the knowledge of the interactions between surrounding lands, ecological, biogeomorphologic, and hydrological components of the fluvial ecosystemsinfo:eu-repo/semantics/publishedVersio