We Could, but Should We? Ethical Considerations for Providing Access to GeoCities and Other Historical Digital Collections

We live in an era in which the ways that we can make sense of our past are evolving as more artifacts from that past become digital. At the same time, the responsibilities of traditional gatekeepers who have negotiated the ethics of historical data collection and use, such as librarians and archivists, are increasingly being sidelined by the system builders who decide whether and how to provide access to historical digital collections, often without sufficient reflection on the ethical issues at hand. It is our aim to better prepare system builders to grapple with these issues. This paper focuses discussions around one such digital collection from the dawn of the web, asking what sorts of analyses can and should be conducted on archival copies of the GeoCities web hosting platform that dates to 1994.This research was supported by the Natural Sciences and Engineering Research Council of Canada, the Social Sciences and Humanities Research Council of Canada, the US National Science Foundation (grants 1618695 and 1704369), the Andrew W. Mellon Foundation, Start Smart Labs, and Compute Canada

InterPoll: Crowd-Sourced Internet Polls

Crowd-sourcing is increasingly being used to provide answers to online polls and surveys. However, existing systems, while taking care of the mechanics of attracting crowd workers, poll building, and payment, provide little to help the survey-maker or pollster in obtaining statistically significant results devoid of even the obvious selection biases. This paper proposes InterPoll, a platform for programming of crowd-sourced polls. Pollsters express polls as embedded LINQ queries and the runtime correctly reasons about uncertainty in those polls, only polling as many people as required to meet statistical guarantees. To optimize the cost of polls, InterPoll performs query optimization, as well as bias correction and power analysis. The goal of InterPoll is to provide a system that can be reliably used for research into marketing, social and political science questions. This paper highlights some of the existing challenges and how InterPoll is designed to address most of them. In this paper we summarize some of the work we have already done and give an outline for future work

The Vein Patterning 1 (VEP1) Gene Family Laterally Spread through an Ecological Network

Lateral gene transfer (LGT) is a major evolutionary mechanism in prokaryotes. Knowledge about LGT— particularly, multicellular— eukaryotes has only recently started to accumulate. A widespread assumption sees the gene as the unit of LGT, largely because little is yet known about how LGT chances are affected by structural/functional features at the subgenic level. Here we trace the evolutionary trajectory of VEin Patterning 1, a novel gene family known to be essential for plant development and defense. At the subgenic level VEP1 encodes a dinucleotide-binding Rossmann-fold domain, in common with members of the short-chain dehydrogenase/reductase (SDR) protein family. We found: i) VEP1 likely originated in an aerobic, mesophilic and chemoorganotrophic α-proteobacterium, and was laterally propagated through nets of ecological interactions, including multiple LGTs between phylogenetically distant green plant/fungi-associated bacteria, and five independent LGTs to eukaryotes. Of these latest five transfers, three are ancient LGTs, implicating an ancestral fungus, the last common ancestor of land plants and an ancestral trebouxiophyte green alga, and two are recent LGTs to modern embryophytes. ii) VEP1's rampant LGT behavior was enabled by the robustness and broad utility of the dinucleotide-binding Rossmann-fold, which provided a platform for the evolution of two unprecedented departures from the canonical SDR catalytic triad. iii) The fate of VEP1 in eukaryotes has been different in different lineages, being ubiquitous and highly conserved in land plants, whereas fungi underwent multiple losses. And iv) VEP1-harboring bacteria include non-phytopathogenic and phytopathogenic symbionts which are non-randomly distributed with respect to the type of harbored VEP1 gene. Our findings suggest that VEP1 may have been instrumental for the evolutionary transition of green plants to land, and point to a LGT-mediated ‘Trojan Horse’ mechanism for the evolution of bacterial pathogenesis against plants. VEP1 may serve as tool for revealing microbial interactions in plant/fungi-associated environments

ConvBKI: Real-Time Probabilistic Semantic Mapping Network with Quantifiable Uncertainty

In this paper, we develop a modular neural network for real-time semantic mapping in uncertain environments, which explicitly updates per-voxel probabilistic distributions within a neural network layer. Our approach combines the reliability of classical probabilistic algorithms with the performance and efficiency of modern neural networks. Although robotic perception is often divided between modern differentiable methods and classical explicit methods, a union of both is necessary for real-time and trustworthy performance. We introduce a novel Convolutional Bayesian Kernel Inference (ConvBKI) layer which incorporates semantic segmentation predictions online into a 3D map through a depthwise convolution layer by leveraging conjugate priors. We compare ConvBKI against state-of-the-art deep learning approaches and probabilistic algorithms for mapping to evaluate reliability and performance. We also create a Robot Operating System (ROS) package of ConvBKI and test it on real-world perceptually challenging off-road driving data.Comment: arXiv admin note: text overlap with arXiv:2209.1066

Genome-scale network model of metabolism and histone acetylation reveals metabolic dependencies of histone deacetylase inhibitors

Abstract Histone acetylation plays a central role in gene regulation and is sensitive to the levels of metabolic intermediates. However, predicting the impact of metabolic alterations on acetylation in pathological conditions is a significant challenge. Here, we present a genome-scale network model that predicts the impact of nutritional environment and genetic alterations on histone acetylation. It identifies cell types that are sensitive to histone deacetylase inhibitors based on their metabolic state, and we validate metabolites that alter drug sensitivity. Our model provides a mechanistic framework for predicting how metabolic perturbations contribute to epigenetic changes and sensitivity to deacetylase inhibitors.https://deepblue.lib.umich.edu/bitstream/2027.42/148146/1/13059_2019_Article_1661.pd

Dagstuhl News January - December 2011

"Dagstuhl News" is a publication edited especially for the members of the Foundation "Informatikzentrum Schloss Dagstuhl" to thank them for their support. The News give a summary of the scientific work being done in Dagstuhl. Each Dagstuhl Seminar is presented by a small abstract describing the contents and scientific highlights of the seminar as well as the perspectives or challenges of the research topic