ScanComplete: Large-Scale Scene Completion and Semantic Segmentation for 3D Scans

We introduce ScanComplete, a novel data-driven approach for taking an incomplete 3D scan of a scene as input and predicting a complete 3D model along with per-voxel semantic labels. The key contribution of our method is its ability to handle large scenes with varying spatial extent, managing the cubic growth in data size as scene size increases. To this end, we devise a fully-convolutional generative 3D CNN model whose filter kernels are invariant to the overall scene size. The model can be trained on scene subvolumes but deployed on arbitrarily large scenes at test time. In addition, we propose a coarse-to-fine inference strategy in order to produce high-resolution output while also leveraging large input context sizes. In an extensive series of experiments, we carefully evaluate different model design choices, considering both deterministic and probabilistic models for completion and semantic inference. Our results show that we outperform other methods not only in the size of the environments handled and processing efficiency, but also with regard to completion quality and semantic segmentation performance by a significant margin.Comment: Video: https://youtu.be/5s5s8iH0NF

From ethnographic research to big data analytics - A case of maritime energy-efficiency optimization

The shipping industry constantly strives to achieve efficient use of energy during sea voyages. Previous research that can take advantages of both ethnographic studies and big data analytics to understand factors contributing to fuel consumption and seek solutions to support decision making is rather scarce. This paper first employed ethnographic research regarding the use of a commercially available fuel-monitoring system. This was to contextualize the real challenges on ships and informed the need of taking a bigdata approach to achieve energy efficiency(EE).Then this study constructed two machine-learning models based on the recorded voyage data of five different ferries over a one-year period. The evaluation showed that the models generalize well on different training data sets and model outputs indicated a potential for better performance than the existing commercial EE system. How this predictive-analytical approach could potentially impact the design of decision support navigational systems and management practices was also discussed. It is hoped that this inter disciplinary research could provide some enlightenment for a richer methodological framework in future maritime energy research.\ua0\ua9 2020 by the authors

From ethnographic research to big data analytics - A case of maritime energy-efficiency optimization

The shipping industry constantly strives to achieve efficient use of energy during sea voyages. Previous research that can take advantages of both ethnographic studies and big data analytics to understand factors contributing to fuel consumption and seek solutions to support decision making is rather scarce. This paper first employed ethnographic research regarding the use of a commercially available fuel-monitoring system. This was to contextualize the real challenges on ships and informed the need of taking a big data approach to achieve energy efficiency (EE). Then this study constructed two machine-learning models based on the recorded voyage data of five different ferries over a one-year period. The evaluation showed that the models generalize well on different training data sets and model outputs indicated a potential for better performance than the existing commercial EE system. How this predictive-analytical approach could potentially impact the design of decision support navigational systems and management practices was also discussed. It is hoped that this interdisciplinary research could provide some enlightenment for a richer methodological framework in future maritime energy researc

A population study of the minicircles in Trypanosoma cruzi: predicting guide RNAs in the absence of empirical RNA editing

<p>Abstract</p> <p>Background</p> <p>The structurally complex network of minicircles and maxicircles comprising the mitochondrial DNA of kinetoplastids mirrors the complexity of the RNA editing process that is required for faithful expression of encrypted maxicircle genes. Although a few of the guide RNAs that direct this editing process have been discovered on maxicircles, guide RNAs are mostly found on the minicircles. The nuclear and maxicircle genomes have been sequenced and assembled for <it>Trypanosoma cruzi</it>, the causative agent of Chagas disease, however the complement of 1.4-kb minicircles, carrying four guide RNA genes per molecule in this parasite, has been less thoroughly characterised.</p> <p>Results</p> <p>Fifty-four CL Brener and 53 Esmeraldo strain minicircle sequence reads were extracted from <it>T. cruzi </it>whole genome shotgun sequencing data. With these sequences and all published <it>T. cruzi </it>minicircle sequences, 108 unique guide RNAs from all known <it>T. cruzi </it>minicircle sequences and two guide RNAs from the CL Brener maxicircle were predicted using a local alignment algorithm and mapped onto predicted or experimentally determined sequences of edited maxicircle open reading frames. For half of the sequences no statistically significant guide RNA could be assigned. Likely positions of these unidentified gRNAs in <it>T. cruzi </it>minicircle sequences are estimated using a simple Hidden Markov Model. With the local alignment predictions as a standard, the HMM had an ~85% chance of correctly identifying at least 20 nucleotides of guide RNA from a given minicircle sequence. Inter-minicircle recombination was documented. Variable regions contain species-specific areas of distinct nucleotide preference. Two maxicircle guide RNA genes were found.</p> <p>Conclusion</p> <p>The identification of new minicircle sequences and the further characterization of all published minicircles are presented, including the first observation of recombination between minicircles. Extrapolation suggests a level of 4% recombinants in the population, supporting a relatively high recombination rate that may serve to minimize the persistence of gRNA pseudogenes. Characteristic nucleotide preferences observed within variable regions provide potential clues regarding the transcription and maturation of <it>T. cruzi </it>guide RNAs. Based on these preferences, a method of predicting <it>T. cruzi </it>guide RNAs using only primary minicircle sequence data was created.</p

Dust covering factor, silicate emission and star formation in luminous QSOs

We present Spitzer IRS low resolution, mid-IR spectra of a sample of 25 high luminosity QSOs at 2<z<3.5. When combined with archival IRS observations of local, low luminosity type-I AGNs, the sample spans five orders of magnitude in luminosity. We find that the continuum dust thermal emission at lambda(rest)=6.7um is correlated with the optical luminosity, following the non-linear relation L(6.7um) propto L(5100A)^0.82. We also find an anti correlation between the ratio L(6.7um)/L(5100A) and the [OIII]5007A line luminosity. These effects are interpreted as a decreasing covering factor of the circumnuclear dust as a function of luminosity. Such a result is in agreement with the decreasing fraction of absorbed AGNs as a function of luminosity recently found in various surveys. We clearly detect the silicate emission feature in the average spectrum, but also in four individual objects. These are the Silicate emission in the most luminous objects obtained so far. When combined with the silicate emission observed in local, low luminosity type-I AGNs, we find that the silicate emission strength is correlated with luminosity. The silicate strength of all type-I AGNs also follows a positive correlation with the black hole mass and with the accretion rate. The Polycyclic Aromatic Hydrocarbon (PAH) emission features, expected from starburst activity, are not detected in the average spectrum of luminous, high-z QSOs. The upper limit inferred from the average spectrum points to a ratio between PAH luminosity and QSO optical luminosity significantly lower than observed in lower luminosity AGNs, implying that the correlation between star formation rate and AGN power saturates at high luminosities.Comment: accepted for publication in A&A, 17 pages, 9 figure

Trypanosoma cruzi mitochondrial maxicircles display species- and strain-specific variation and a conserved element in the non-coding region

BACKGROUND: The mitochondrial DNA of kinetoplastid flagellates is distinctive in the eukaryotic world due to its massive size, complex form and large sequence content. Comprised of catenated maxicircles that contain rRNA and protein-coding genes and thousands of heterogeneous minicircles encoding small guide RNAs, the kinetoplast network has evolved along with an extreme form of mRNA processing in the form of uridine insertion and deletion RNA editing. Many maxicircle-encoded mRNAs cannot be translated without this post-transcriptional sequence modification. RESULTS: We present the complete sequence and annotation of the Trypanosoma cruzi maxicircles for the CL Brener and Esmeraldo strains. Gene order is syntenic with Trypanosoma brucei and Leishmania tarentolae maxicircles. The non-coding components have strain-specific repetitive regions and a variable region that is unique for each strain with the exception of a conserved sequence element that may serve as an origin of replication, but shows no sequence identity with L. tarentolae or T. brucei. Alternative assemblies of the variable region demonstrate intra-strain heterogeneity of the maxicircle population. The extent of mRNA editing required for particular genes approximates that seen in T. brucei. Extensively edited genes were more divergent among the genera than non-edited and rRNA genes. Esmeraldo contains a unique 236-bp deletion that removes the 5'-ends of ND4 and CR4 and the intergenic region. Esmeraldo shows additional insertions and deletions outside of areas edited in other species in ND5, MURF1, and MURF2, while CL Brener has a distinct insertion in MURF2. CONCLUSION: The CL Brener and Esmeraldo maxicircles represent two of three previously defined maxicircle clades and promise utility as taxonomic markers. Restoration of the disrupted reading frames might be accomplished by strain-specific RNA editing. Elements in the non-coding region may be important for replication, transcription, and anchoring of the maxicircle within the kinetoplast network

The Pre-History of Urban Scaling

Cities are increasingly the fundamental socio-economic units of human societies worldwide, but we still lack a unified characterization of urbanization that captures the social processes realized by cities across time and space. This is especially important for understanding the role of cities in the history of human civilization and for determining whether studies of ancient cities are relevant for contemporary science and policy. As a step in this direction, we develop a theory of settlement scaling in archaeology, deriving the relationship between population and settled area from a consideration of the interplay between social and infrastructural networks. We then test these models on settlement data from the Pre-Hispanic Basin of Mexico to show that this ancient settlement system displays spatial scaling properties analogous to those observed in modern cities. Our data derive from over 1,500 settlements occupied over two millennia and spanning four major cultural periods characterized by different levels of agricultural productivity, political centralization and market development. We show that, in agreement with theory, total settlement area increases with population size, on average, according to a scale invariant relation with an exponent in the range . As a consequence, we are able to infer aggregate socio-economic properties of ancient societies from archaeological measures of settlement organization. Our findings, from an urban settlement system that evolved independently from its old-world counterparts, suggest that principles of settlement organization are very general and may apply to the entire range of human history