Representing Input Transformations by Low-Dimensional Parameter Subspaces

Deep models lack robustness to simple input transformations such as rotation, scaling, and translation, unless they feature a particular invariant architecture or undergo specific training, e.g., learning the desired robustness from data augmentations. Alternatively, input transformations can be treated as a domain shift problem, and solved by post-deployment model adaptation. Although a large number of methods deal with transformed inputs, the fundamental relation between input transformations and optimal model weights is unknown. In this paper, we put forward the configuration subspace hypothesis that model weights optimal for parameterized continuous transformations can reside in low-dimensional linear subspaces. We introduce subspace-configurable networks to learn these subspaces and observe their structure and surprisingly low dimensionality on all tested transformations, datasets and architectures from computer vision and audio signal processing domains. Our findings enable efficient model reconfiguration, especially when limited storage and computing resources are at stake

Initiale Ergebnisse nach perkutanem Aortenklappenersatz bei Hochrisikopatienten an der Universität Rostock

In erfahrenen Händen weist der perkutane Aortenklappenersatz mit dem CoreValve-System für ausgewählte Patienten mit schwerer Aortenklappenstenose eine hohe Erfolgsrate mit niedriger periprozeduraler Mortalität sowie bemerkenswerter klinischer und hämodynamischer Verbesserung auf, die über die bis jetzt beobachtete Zeit von 3 Jahren hinweg erhalten bleibt

SCAN: Multi-hop calibration for mobile sensor arrays

Urban air pollution monitoring with mobile, portable, low-cost sensors has attracted increasing research interest for their wide spatial coverage and affordable expenses to the general public. However, low-cost air quality sensors not only drift over time but also suffer from cross-sensitivities and dependency on meteorological effects. Therefore calibration of measurements from low-cost sensors is indispensable to guarantee data accuracy and consistency to be fit for quantitative studies on air pollution. In this work we propose sensor array network calibration (SCAN), a multi-hop calibration technique for dependent low-cost sensors. SCAN is applicable to sets of co-located, heterogeneous sensors, known as sensor arrays, to compensate for cross-sensitivities and dependencies on meteorological influences. SCAN minimizes error accumulation over multiple hops of sensor arrays, which is unattainable with existing multi-hop calibration techniques. We formulate SCAN as a novel constrained least-squares regression and provide a closed-form expression of its regression parameters. We theoretically prove that SCAN is free from regression dilution even in presence of measurement noise. In-depth simulations demonstrate that SCAN outperforms various calibration techniques. Evaluations on two real-world low-cost air pollution sensor datasets comprising 66 million samples collected over three years show that SCAN yields 16% to 60% lower error than state-of-the-art calibration techniques.</jats:p

A Specific IFIH1 Gain-of-Function Mutation Causes Singleton-Merten Syndrome

Singleton-Merten syndrome (SMS) is an infrequently described autosomal-dominant disorder characterized by early and extreme aortic and valvular calcification, dental anomalies (early-onset periodontitis and root resorption), osteopenia, and acro-osteolysis. To determine the molecular etiology of this disease, we performed whole-exome sequencing and targeted Sanger sequencing. We identified a common missense mutation, c.2465G>A (p.Arg822Gln), in interferon induced with helicase C domain 1 (IFIH1, encoding melanoma differentiation-associated protein 5 [MDA5]) in four SMS subjects from two families and a simplex case. IFIH1 has been linked to a number of autoimmune disorders, including Aicardi-Goutières syndrome. Immunohistochemistry demonstrated the localization of MDA5 in all affected target tissues. In vitro functional analysis revealed that the IFIH1 c.2465G>A mutation enhanced MDA5 function in interferon beta induction. Interferon signature genes were upregulated in SMS individuals’ blood and dental cells. Our data identify a gain-of-function IFIH1 mutation as causing SMS and leading to early arterial calcification and dental inflammation and resorption

The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes

The release of the 1000(th) complete microbial genome will occur in the next two to three years. In anticipation of this milestone, the Fellowship for Interpretation of Genomes (FIG) launched the Project to Annotate 1000 Genomes. The project is built around the principle that the key to improved accuracy in high-throughput annotation technology is to have experts annotate single subsystems over the complete collection of genomes, rather than having an annotation expert attempt to annotate all of the genes in a single genome. Using the subsystems approach, all of the genes implementing the subsystem are analyzed by an expert in that subsystem. An annotation environment was created where populated subsystems are curated and projected to new genomes. A portable notion of a populated subsystem was defined, and tools developed for exchanging and curating these objects. Tools were also developed to resolve conflicts between populated subsystems. The SEED is the first annotation environment that supports this model of annotation. Here, we describe the subsystem approach, and offer the first release of our growing library of populated subsystems. The initial release of data includes 180 177 distinct proteins with 2133 distinct functional roles. This data comes from 173 subsystems and 383 different organisms

TRAIP promotes DNA damage response during genome replication and is mutated in primordial dwarfism.

DNA lesions encountered by replicative polymerases threaten genome stability and cell cycle progression. Here we report the identification of mutations in TRAIP, encoding an E3 RING ubiquitin ligase, in patients with microcephalic primordial dwarfism. We establish that TRAIP relocalizes to sites of DNA damage, where it is required for optimal phosphorylation of H2AX and RPA2 during S-phase in response to ultraviolet (UV) irradiation, as well as fork progression through UV-induced DNA lesions. TRAIP is necessary for efficient cell cycle progression and mutations in TRAIP therefore limit cellular proliferation, providing a potential mechanism for microcephaly and dwarfism phenotypes. Human genetics thus identifies TRAIP as a component of the DNA damage response to replication-blocking DNA lesions.This work was supported by funding from the Medical Research Council and the European Research Council (ERC, 281847) (A.P.J.), the Lister Institute for Preventative Medicine (A.P.J. and G.S.S.), Medical Research Scotland (L.S.B.), German Federal Ministry of Education and Research (BMBF, 01GM1404) and E-RARE network EuroMicro (B.W), Wellcome Trust (M. Hurles), CMMC (P.N.), Cancer Research UK (C17183/A13030) (G.S.S. and M.R.H), Swiss National Science Foundation (P2ZHP3_158709) (O.M.), AIRC (12710) and ERC/EU FP7 (CIG_303806) (S.S.), Cancer Research UK (C6/A11224) and ERC/EU FP7 (HEALTH-F2- 2010-259893) (A.N.B. and S.P.J.).This is the author accepted manuscript. The final version is available from NPG via http://dx.doi.org/10.1038/ng.345

Racial differences in systemic sclerosis disease presentation: a European Scleroderma Trials and Research group study

Objectives. Racial factors play a significant role in SSc. We evaluated differences in SSc presentations between white patients (WP), Asian patients (AP) and black patients (BP) and analysed the effects of geographical locations.Methods. SSc characteristics of patients from the EUSTAR cohort were cross-sectionally compared across racial groups using survival and multiple logistic regression analyses.Results. The study included 9162 WP, 341 AP and 181 BP. AP developed the first non-RP feature faster than WP but slower than BP. AP were less frequently anti-centromere (ACA; odds ratio (OR) = 0.4, P &lt; 0.001) and more frequently anti-topoisomerase-I autoantibodies (ATA) positive (OR = 1.2, P = 0.068), while BP were less likely to be ACA and ATA positive than were WP [OR(ACA) = 0.3, P &lt; 0.001; OR(ATA) = 0.5, P = 0.020]. AP had less often (OR = 0.7, P = 0.06) and BP more often (OR = 2.7, P &lt; 0.001) diffuse skin involvement than had WP.AP and BP were more likely to have pulmonary hypertension [OR(AP) = 2.6, P &lt; 0.001; OR(BP) = 2.7, P = 0.03 vs WP] and a reduced forced vital capacity [OR(AP) = 2.5, P &lt; 0.001; OR(BP) = 2.4, P &lt; 0.004] than were WP. AP more often had an impaired diffusing capacity of the lung than had BP and WP [OR(AP vs BP) = 1.9, P = 0.038; OR(AP vs WP) = 2.4, P &lt; 0.001]. After RP onset, AP and BP had a higher hazard to die than had WP [hazard ratio (HR) (AP) = 1.6, P = 0.011; HR(BP) = 2.1, P &lt; 0.001].Conclusion. Compared with WP, and mostly independent of geographical location, AP have a faster and earlier disease onset with high prevalences of ATA, pulmonary hypertension and forced vital capacity impairment and higher mortality. BP had the fastest disease onset, a high prevalence of diffuse skin involvement and nominally the highest mortality

Search for dark matter produced in association with bottom or top quarks in √s = 13 TeV pp collisions with the ATLAS detector

A search for weakly interacting massive particle dark matter produced in association with bottom or top quarks is presented. Final states containing third-generation quarks and miss- ing transverse momentum are considered. The analysis uses 36.1 fb−1 of proton–proton collision data recorded by the ATLAS experiment at √s = 13 TeV in 2015 and 2016. No significant excess of events above the estimated backgrounds is observed. The results are in- terpreted in the framework of simplified models of spin-0 dark-matter mediators. For colour- neutral spin-0 mediators produced in association with top quarks and decaying into a pair of dark-matter particles, mediator masses below 50 GeV are excluded assuming a dark-matter candidate mass of 1 GeV and unitary couplings. For scalar and pseudoscalar mediators produced in association with bottom quarks, the search sets limits on the production cross- section of 300 times the predicted rate for mediators with masses between 10 and 50 GeV and assuming a dark-matter mass of 1 GeV and unitary coupling. Constraints on colour- charged scalar simplified models are also presented. Assuming a dark-matter particle mass of 35 GeV, mediator particles with mass below 1.1 TeV are excluded for couplings yielding a dark-matter relic density consistent with measurements

Pollen Video Library for Benchmarking Detection, Classification, Tracking and Novelty Detection Tasks

&lt;p&gt;&lt;strong&gt;Dataset description&lt;/strong&gt;&lt;/p&gt;&lt;p&gt;This dataset contains microscopic images and videos of pollen gathered between Feb. and Aug. 2020 in Graz, Austria.&lt;/p&gt;&lt;p&gt;Pollen images of 16 types:&nbsp;...&lt;strong&gt;images_16_types.zip&lt;/strong&gt;&lt;/p&gt;&lt;ul&gt;&lt;li&gt;Acer Pseudoplatanus&lt;/li&gt;&lt;li&gt;Aesculus Carnea&lt;/li&gt;&lt;li&gt;Alnus&lt;/li&gt;&lt;li&gt;Anthoxanthum&lt;/li&gt;&lt;li&gt;Betula Pendula&lt;/li&gt;&lt;li&gt;Brassica&lt;/li&gt;&lt;li&gt;Carpinus&lt;/li&gt;&lt;li&gt;Corylus&lt;/li&gt;&lt;li&gt;Dactylis Glomerata&lt;/li&gt;&lt;li&gt;Fraxinus&lt;/li&gt;&lt;li&gt;Pinus Nigra&lt;/li&gt;&lt;li&gt;Platanus&lt;/li&gt;&lt;li&gt;Populus Nigra&lt;/li&gt;&lt;li&gt;Prunus Avium&lt;/li&gt;&lt;li&gt;Sequoiadendron Giganteum&lt;/li&gt;&lt;li&gt;Taxus Baccata&lt;/li&gt;&lt;/ul&gt;&lt;p&gt;Pollen video library&nbsp;...&lt;strong&gt;pollen_video_library.zip&lt;/strong&gt;&lt;/p&gt;&lt;ul&gt;&lt;li&gt;Each type of pollen is in a separate folder, there may be multiple videos per type.&lt;/li&gt;&lt;li&gt;In each pollen folder, we included images cropped from the videos by YOLO object detection algorithm trained on a subset of pollen images as described in [1].&lt;/li&gt;&lt;li&gt;Cropped file name structure&nbsp;[Video file name]_[TrackingID]_[Image index of a grain]_[Frame index in video]&lt;ul&gt;&lt;li&gt;Example, if a grain has 5 images, the file name would be: &nbsp;Anthoxanthum-grass-20200530-122652_0000000_001_00001.jpg Anthoxanthum-grass-20200530-122652_0000000_002_00002.jpg ... Anthoxanthum-grass-20200530-122652_0000000_005_00005.jpg&lt;/li&gt;&lt;/ul&gt;&lt;/li&gt;&lt;/ul&gt;&lt;p&gt;Field data over 3 days are gathered in Graz in spring 2020.&nbsp;...&lt;strong&gt;pollen_field_data.zip&lt;/strong&gt;&lt;/p&gt;&lt;p&gt;&nbsp;&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Version 2:&lt;/strong&gt;&lt;/p&gt;&lt;p&gt;For experiments of mitigating the distribution shift of pollen identification on field data, there are 5 types selected from field data and manually labeled by the expert. The data are zipped in &lt;strong&gt;"the manual_labeled_field_data_5_types.zip"&lt;/strong&gt;&nbsp;&lt;/p&gt;&lt;p&gt;The "&lt;strong&gt;images_5_types_9010_train.zip&lt;/strong&gt;" and "&lt;strong&gt;images_5_types_9010_val.zip&lt;/strong&gt;" contain 5 types selected from library data (&lt;strong&gt;images_16_types.zip&lt;/strong&gt;), &nbsp;and these correspond to field data.&nbsp;&lt;/p&gt;&lt;p&gt;The "&lt;strong&gt;images_3_types_for_ablation_study.zip&lt;/strong&gt;" contains data on 3 levels of pollen grain hydration. These data are used for the ablation study of model generalization in pollen identification.&nbsp;&lt;/p&gt;&lt;p&gt;Sample code to load the data and visualize the images is in&nbsp;...plot_pollen_sample.py. Download and extract the file&nbsp;...&lt;strong&gt;images_16_types.zip&lt;/strong&gt;&nbsp;in the same folder as&nbsp;...plot_pollen_sample.py&nbsp;to run the example.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Dependecies:&lt;/strong&gt;&lt;/p&gt;&lt;ul&gt;&lt;li&gt;opencv&lt;/li&gt;&lt;li&gt;numpy&lt;/li&gt;&lt;li&gt;matplotlib&lt;/li&gt;&lt;/ul&gt;&lt;p&gt;&lt;strong&gt;Credit&lt;/strong&gt;&lt;/p&gt;&lt;p&gt;[1] N. Cao, M. Meyer, L. Thiele, and O. Saukh. 2020. Automated Pollen Detection with an Affordable Technology. In Proceedings of the International Conference on Embedded Wireless Systems and Networks (EWSN). 108–119.&lt;/p&gt;&lt;p&gt;@inproceedings{namcao2020pollen, &nbsp;title = {Automated Pollen Detection with an Affordable Technology}, &nbsp;author = {Nam Cao and Matthias Meyer and Lothar Thiele and Olga Saukh}, &nbsp;booktitle = {Proceedings of the International Conference on Embedded Wireless Systems and Networks (EWSN)}, &nbsp;pages={108–119} &nbsp;month = {2}, &nbsp;year = {2020}, }&lt;/p&gt;&lt;p&gt;Appears in the Proceedings of the 3rd Workshop on Data Acquisition To Analysis (DATA '20)&lt;/p&gt