PADLoC: LiDAR-Based Deep Loop Closure Detection and Registration using Panoptic Attention

A key component of graph-based SLAM systems is the ability to detect loop closures in a trajectory to reduce the drift accumulated over time from the odometry. Most LiDAR-based methods achieve this goal by using only the geometric information, disregarding the semantics of the scene. In this work, we introduce PADLoC, a LiDAR-based loop closure detection and registration architecture comprising a shared 3D convolutional feature extraction backbone, a global descriptor head for loop closure detection, and a novel transformer-based head for point cloud matching and registration. We present multiple methods for estimating the point-wise matching confidence based on diversity indices. Additionally, to improve forward-backward consistency, we propose the use of two shared matching and registration heads with their source and target inputs swapped by exploiting that the estimated relative transformations must be inverse of each other. Furthermore, we leverage panoptic information during training in the form of a novel loss function that reframes the matching problem as a classification task in the case of the semantic labels and as a graph connectivity assignment for the instance labels. We perform extensive evaluations of PADLoC on multiple real-world datasets demonstrating that it achieves state-of-the-art performance. The code of our work is publicly available at http://padloc.cs.uni-freiburg.de

Few-Shot Panoptic Segmentation With Foundation Models

Current state-of-the-art methods for panoptic segmentation require an immense amount of annotated training data that is both arduous and expensive to obtain posing a significant challenge for their widespread adoption. Concurrently, recent breakthroughs in visual representation learning have sparked a paradigm shift leading to the advent of large foundation models that can be trained with completely unlabeled images. In this work, we propose to leverage such task-agnostic image features to enable few-shot panoptic segmentation by presenting Segmenting Panoptic Information with Nearly 0 labels (SPINO). In detail, our method combines a DINOv2 backbone with lightweight network heads for semantic segmentation and boundary estimation. We show that our approach, albeit being trained with only ten annotated images, predicts high-quality pseudo-labels that can be used with any existing panoptic segmentation method. Notably, we demonstrate that SPINO achieves competitive results compared to fully supervised baselines while using less than 0.3% of the ground truth labels, paving the way for learning complex visual recognition tasks leveraging foundation models. To illustrate its general applicability, we further deploy SPINO on real-world robotic vision systems for both outdoor and indoor environments. To foster future research, we make the code and trained models publicly available at http://spino.cs.uni-freiburg.de

Collaborative Dynamic 3D Scene Graphs for Automated Driving

Maps have played an indispensable role in enabling safe and automated driving. Although there have been many advances on different fronts ranging from SLAM to semantics, building an actionable hierarchical semantic representation of urban dynamic scenes from multiple agents is still a challenging problem. In this work, we present Collaborative URBan Scene Graphs (CURB-SG) that enable higher-order reasoning and efficient querying for many functions of automated driving. CURB-SG leverages panoptic LiDAR data from multiple agents to build large-scale maps using an effective graph-based collaborative SLAM approach that detects inter-agent loop closures. To semantically decompose the obtained 3D map, we build a lane graph from the paths of ego agents and their panoptic observations of other vehicles. Based on the connectivity of the lane graph, we segregate the environment into intersecting and non-intersecting road areas. Subsequently, we construct a multi-layered scene graph that includes lane information, the position of static landmarks and their assignment to certain map sections, other vehicles observed by the ego agents, and the pose graph from SLAM including 3D panoptic point clouds. We extensively evaluate CURB-SG in urban scenarios using a photorealistic simulator. We release our code at http://curb.cs.uni-freiburg.de.Comment: Refined manuscript and extended supplementar

Transcriptomic and proteomic analyses of the Aspergillus fumigatus hypoxia response using an oxygen-controlled fermenter

<p>Abstract</p> <p>Background</p> <p><it>Aspergillus fumigatus </it>is a mold responsible for the majority of cases of aspergillosis in humans. To survive in the human body, <it>A. fumigatus </it>must adapt to microenvironments that are often characterized by low nutrient and oxygen availability. Recent research suggests that the ability of <it>A. fumigatus </it>and other pathogenic fungi to adapt to hypoxia contributes to their virulence. However, molecular mechanisms of <it>A. fumigatus </it>hypoxia adaptation are poorly understood. Thus, to better understand how <it>A. fumigatus </it>adapts to hypoxic microenvironments found <it>in vivo </it>during human fungal pathogenesis, the dynamic changes of the fungal transcriptome and proteome in hypoxia were investigated over a period of 24 hours utilizing an oxygen-controlled fermenter system.</p> <p>Results</p> <p>Significant increases in transcripts associated with iron and sterol metabolism, the cell wall, the GABA shunt, and transcriptional regulators were observed in response to hypoxia. A concomitant reduction in transcripts was observed with ribosome and terpenoid backbone biosynthesis, TCA cycle, amino acid metabolism and RNA degradation. Analysis of changes in transcription factor mRNA abundance shows that hypoxia induces significant positive and negative changes that may be important for regulating the hypoxia response in this pathogenic mold. Growth in hypoxia resulted in changes in the protein levels of several glycolytic enzymes, but these changes were not always reflected by the corresponding transcriptional profiling data. However, a good correlation overall (R²= 0.2, p < 0.05) existed between the transcriptomic and proteomics datasets for all time points. The lack of correlation between some transcript levels and their subsequent protein levels suggests another regulatory layer of the hypoxia response in <it>A. fumigatus</it>.</p> <p>Conclusions</p> <p>Taken together, our data suggest a robust cellular response that is likely regulated both at the transcriptional and post-transcriptional level in response to hypoxia by the human pathogenic mold <it>A. fumigatus</it>. As with other pathogenic fungi, the induction of glycolysis and transcriptional down-regulation of the TCA cycle and oxidative phosphorylation appear to major components of the hypoxia response in this pathogenic mold. In addition, a significant induction of the transcripts involved in ergosterol biosynthesis is consistent with previous observations in the pathogenic yeasts <it>Candida albicans </it>and <it>Cryptococcus neoformans </it>indicating conservation of this response to hypoxia in pathogenic fungi. Because ergosterol biosynthesis enzymes also require iron as a co-factor, the increase in iron uptake transcripts is consistent with an increased need for iron under hypoxia. However, unlike <it>C. albicans </it>and <it>C. neoformans</it>, the GABA shunt appears to play an important role in reducing NADH levels in response to hypoxia in <it>A. fumigatus </it>and it will be intriguing to determine whether this is critical for fungal virulence. Overall, regulatory mechanisms of the <it>A. fumigatus </it>hypoxia response appear to involve both transcriptional and post-transcriptional control of transcript and protein levels and thus provide candidate genes for future analysis of their role in hypoxia adaptation and fungal virulence.</p

A proteomic approach to investigating gene cluster expression and secondary metabolite functionality in Aspergillus fumigatus.

A combined proteomics and metabolomics approach was utilised to advance the identification and characterisation of secondary metabolites in Aspergillus fumigatus. Here, implementation of a shotgun proteomic strategy led to the identification of non-redundant mycelial proteins (n = 414) from A. fumigatus including proteins typically under-represented in 2-D proteome maps: proteins with multiple transmembrane regions, hydrophobic proteins and proteins with extremes of molecular mass and pI. Indirect identification of secondary metabolite cluster expression was also achieved, with proteins (n = 18) from LaeA-regulated clusters detected, including GliT encoded within the gliotoxin biosynthetic cluster. Biochemical analysis then revealed that gliotoxin significantly attenuates H2O2-induced oxidative stress in A. fumigatus (p>0.0001), confirming observations from proteomics data. A complementary 2-D/LC-MS/MS approach further elucidated significantly increased abundance (p<0.05) of proliferating cell nuclear antigen (PCNA), NADH-quinone oxidoreductase and the gliotoxin oxidoreductase GliT, along with significantly attenuated abundance (p<0.05) of a heat shock protein, an oxidative stress protein and an autolysis-associated chitinase, when gliotoxin and H2O2 were present, compared to H2O2 alone. Moreover, gliotoxin exposure significantly reduced the abundance of selected proteins (p<0.05) involved in de novo purine biosynthesis. Significantly elevated abundance (p<0.05) of a key enzyme, xanthine-guanine phosphoribosyl transferase Xpt1, utilised in purine salvage, was observed in the presence of H2O2 and gliotoxin. This work provides new insights into the A. fumigatus proteome and experimental strategies, plus mechanistic data pertaining to gliotoxin functionality in the organism

Proteomics of industrial fungi: trends and insights for biotechnology

Filamentous fungi are widely known for their industrial applications, namely, the production of food-processing enzymes and metabolites such as antibiotics and organic acids. In the past decade, the full genome sequencing of filamentous fungi increased the potential to predict encoded proteins enormously, namely, hydrolytic enzymes or proteins involved in the biosynthesis of metabolites of interest. The integration of genome sequence information with possible phenotypes requires, however, the knowledge of all the proteins in the cell in a system-wise manner, given by proteomics. This review summarises the progress of proteomics and its importance for the study of biotechnological processes in filamentous fungi. A major step forward in proteomics was to couple protein separation with high-resolution mass spectrometry, allowing accurate protein quantification. Despite the fact that most fungal proteomic studies have been focused on proteins from mycelial extracts, many proteins are related to processes which are compartmentalised in the fungal cell, e.g. β-lactam antibiotic production in the microbody. For the study of such processes, a targeted approach is required, e.g. by organelle proteomics. Typical workflows for sample preparation in fungal organelle proteomics are discussed, including homogenisation and sub-cellular fractionation. Finally, examples are presented of fungal organelle proteomic studies, which have enlarged the knowledge on areas of interest to biotechnology, such as protein secretion, energy production or antibiotic biosynthesis