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2011 William Allan Award Introduction: John M. Opitz 1

Maximilian Muenke
2012 American Journal of Human Genetics  
John Opitz, the winner of the 2011 William Allan Award!  ... 
doi:10.1016/j.ajhg.2012.01.011 pmid:22405083 pmcid:PMC3309199 fatcat:45ntkz66crbirj2szku2yazpve

Learning Visually Grounded Sentence Representations [article]

Douwe Kiela, Alexis Conneau, Allan Jabri, Maximilian Nickel
2018 arXiv   pre-print
We introduce a variety of models, trained on a supervised image captioning corpus to predict the image features for a given caption, to perform sentence representation grounding. We train a grounded sentence encoder that achieves good performance on COCO caption and image retrieval and subsequently show that this encoder can successfully be transferred to various NLP tasks, with improved performance over text-only models. Lastly, we analyze the contribution of grounding, and show that word
more » ... dings learned by this system outperform non-grounded ones.
arXiv:1707.06320v2 fatcat:7aeg4cr5tndinflmp46amycgke

Combining stimulus types for improved coverage in population receptive field mapping

David Linhardt, Maximilian Pawloff, Allan Hummer, Michael Woletz, Martin Tik, Markus Ritter, Ursula Schmidt-Erfurth, Christian Windischberger
2021 NeuroImage  
Retinotopy experiments using population receptive field (pRF) mapping are ideal for assigning regions in the visual field to cortical brain areas. While various designs for visual stimulation were suggested in the literature, all have specific shortcomings regarding visual field coverage. Here we acquired high-resolution 7 Tesla fMRI data to compare pRF-based coverage maps obtained with the two most commonly used stimulus variants: moving bars; rotating wedges and expanding rings. We find that
more » ... timulus selection biases the spatial distribution of pRF centres. In addition, eccentricity values and pRF sizes obtained from wedge/ring or bar stimulation runs show systematic differences. Wedge/ring stimulation results show lower eccentricity values and strongly reduced pRF sizes compared to bar stimulation runs. Statistical comparison shows significantly higher pRF centre numbers in the foveal 2° region of the visual field for wedge/ring compared to bar stimuli. We suggest and evaluate approaches for combining pRF data from different visual stimulus patterns to obtain improved mapping results.
doi:10.1016/j.neuroimage.2021.118240 pmid:34116157 fatcat:iijw6ccxmjdkldaxb5flwxznne

Learning Visually Grounded Sentence Representations

Douwe Kiela, Alexis Conneau, Allan Jabri, Maximilian Nickel
2018 Proceedings of the 2018 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies, Volume 1 (Long Papers)  
We investigate grounded sentence representations, where we train a sentence encoder to predict the image features of a given captioni.e., we try to "imagine" how a sentence would be depicted visually-and use the resultant features as sentence representations. We examine the quality of the learned representations on a variety of standard sentence representation quality benchmarks, showing improved performance for grounded models over non-grounded ones. In addition, we thoroughly analyze the
more » ... t to which grounding contributes to improved performance, and show that the system also learns improved word embeddings.
doi:10.18653/v1/n18-1038 dblp:conf/naacl/KielaCJN18 fatcat:7sda73my3jguhgemoxmje6fhca

Articulated Multi-Instrument 2-D Pose Estimation Using Fully Convolutional Networks

Xiaofei Du, Thomas Kurmann, Ping-Lin Chang, Maximilian Allan, Sebastien Ourselin, Raphael Sznitman, John D. Kelly, Danail Stoyanov
2018 IEEE Transactions on Medical Imaging  
Instrument detection, pose estimation and tracking in surgical videos is an important vision component for computer assisted interventions. While significant advances have been made in recent years, articulation detection is still a major challenge. In this paper, we propose a deep neural network for articulated multi-instrument 2D pose estimation, which is trained on a detailed annotations of endoscopic and microscopic datasets. Our model is formed by a fully convolutional detection-regression
more » ... network. Joints and associations between joint pairs in our instrument model are located by the detection subnetwork and are subsequently refined through a regression subnetwork. Based on the output from the model, the poses of the instruments are inferred using maximum bipartite graph matching. Our estimation framework is powered by deep learning techniques without any direct kinematic information from a robot. Our framework is tested on single-instrument RMIT data, and also on multi-instrument EndoVis and in vivo data with promising results. In addition, the dataset annotations are publicly released along with our code and model.
doi:10.1109/tmi.2017.2787672 pmid:29727290 pmcid:PMC6051486 fatcat:pubjor5rlbgapou2m4bwt37bqi

Smoking is not linked to the development of anti-peptidylarginine deiminase 4 autoantibodies in rheumatoid arthritis

Laura C. Cappelli, Maximilian F. Konig, Allan C. Gelber, Clifton O. Bingham, Erika Darrah
2018 Arthritis Research & Therapy  
Defining environmental factors responsible for development of autoimmunity in rheumatoid arthritis (RA) is critical for understanding mechanisms of disease initiation and propagation. Notably, a history of cigarette smoking has been implicated in the genesis of RA and is associated with worse disease outcomes. Antibodies to peptidylarginine deiminase 4 (PAD4) are also associated with more severe RA. A subset of patients who have PAD4 autoantibodies that cross-react with PAD3 (anti-PAD3/4) are
more » ... the highest risk for interstitial lung disease, and this risk is augmented by a history of cigarette smoking. It is unclear, however, if smoking is etiologically linked to the development of anti-PAD4 antibodies. Methods: Patients were included in this study if they had physician-diagnosed RA as well as DNA, serum, and a date-matched clinical assessment (n = 274). Anti-PAD4 and anti-CCP antibodies were measured by immunoprecipitation and ELISA, respectively; shared epitope (SE) status was determined by HLA-DRβ1 genotyping. Logistic regression analysis was used to evaluate associations of smoking with PAD4 antibodies, with adjustment for relevant demographic and clinical features. Stratified analyses by disease duration and shared epitope status were also performed. Results: Anti-PAD4 antibodies were present in 25% of RA patients, with 50% of these individuals having anti-PAD3/4 cross-reactive antibodies. Anti-PAD4 antibodies were significantly associated with a longer disease duration, SE alleles, and anti-CCP antibodies. Importantly, there were no significant differences in smoking history between anti-PAD4 positive and negative groups in univariate analyses, stratified analyses, or multivariable models. However, an inverse relationship between smoking and anti-PAD4 antibodies was suggested by a lower prevalence of current smokers among patients with anti-PAD3/4 antibodies compared to antibody negative individuals (p = 0.04). Further, the lowest levels of anti-PAD4 antibodies were observed in current smokers (p = 0.14), and a significant association of SE and anti-PAD4 antibodies was only present among never smokers (p = 0.01). Conclusions: Smoking history was not associated with anti-PAD4 antibodies in patients with RA. The finding that anti-PAD4 antibodies were not associated with smoking suggests that other environmental factors may contribute to the development of autoimmunity to PAD4 in these patients.
doi:10.1186/s13075-018-1533-z pmid:29566742 pmcid:PMC5865363 fatcat:sgimsyagvzfa5cflfbblpeyeuu

Patch-based adaptive weighting with segmentation and scale (PAWSS) for visual tracking in surgical video

Xiaofei Du, Maximilian Allan, Sebastian Bodenstedt, Lena Maier-Hein, Stefanie Speidel, Alessio Dore, Danail Stoyanov
2019 Medical Image Analysis  
Multi-part appearance model ( Allan et al., 2015 ) and articulated degrees-of-freedom ( Allan et al., 2018 ) of robotic instruments can be used to align the prior model with low level optical flow  ...  Then, it was improved by combining constraints from feature points, temporal motion model with stereo setup ( Allan et al., 2014 ) .  ... 
doi:10.1016/j.media.2019.07.002 pmid:31299494 pmcid:PMC6988132 fatcat:4yscspuewng7paowuqde3ttooy

Transcriptional Cofactor TBLR1 Controls Lipid Mobilization in White Adipose Tissue

Maria Rohm, Anke Sommerfeld, Daniela Strzoda, Allan Jones, Tjeerd P. Sijmonsma, Gottfried Rudofsky, Christian Wolfrum, Carsten Sticht, Norbert Gretz, Maximilian Zeyda, Lukas Leitner, Peter P. Nawroth (+4 others)
2013 Cell Metabolism  
Lipid mobilization (lipolysis) in white adipose tissue (WAT) critically controls lipid turnover and adiposity in humans. While the acute regulation of lipolysis has been studied in detail, the transcriptional determinants of WAT lipolytic activity remain still largely unexplored. Here we show that the genetic inactivation of transcriptional cofactor transducin beta-likerelated 1(TBLR1) blunts the lipolytic response of white adipocytes through the impairment of cAMPdependent signal transduction.
more » ... Indeed, mice lacking TBLR1 in adipocytes are defective in fasting-induced lipid mobilization and, when placed on a high-fatdiet, show aggravated adiposity, glucose intolerance, and insulin resistance. TBLR1 levels are found to increase under lipolytic conditions in WAT of both human patients and mice, correlating with serum free fatty acids (FFAs). As a critical regulator of WAT cAMP signaling and lipid mobilization, proper activity of TBLR1 in adipocytes might thus represent a critical molecular checkpoint for the prevention of metabolic dysfunction in subjects with obesityrelated disorders.
doi:10.1016/j.cmet.2013.02.010 pmid:23499424 fatcat:sfxngeebube7fh7brzalhwitxy

Combined 2D and 3D tracking of surgical instruments for minimally invasive and robotic-assisted surgery

Xiaofei Du, Maximilian Allan, Alessio Dore, Sebastien Ourselin, David Hawkes, John D. Kelly, Danail Stoyanov
2016 International Journal of Computer Assisted Radiology and Surgery  
Max Allan would like to acknowledge the financial support of the Rabin Ezra foundation as well as EPSRC funding for DTP in Medical and Biomedical Imaging at University College London.  ... 
doi:10.1007/s11548-016-1393-4 pmid:27038963 pmcid:PMC4893384 fatcat:wn2feqvsk5h4ffpd3cyp2hy4qm

miR-200 deficiency promotes lung cancer metastasis by activating cancer-associated fibroblasts [article]

Bin Xue, Chen-Hua Chuang, Haydn M Prosser, Cesar Seigi Fuziwara, Claudia Chan, Neil Sahasrabudhe, Maximilian Kühn, Yalei Wu, Jingqi Chen, Anne Biton, Caifu Chen, John Erby Wilkinson (+5 others)
2020 bioRxiv   pre-print
Lung adenocarcinoma, the most prevalent lung cancer subtype, is characterized by its high propensity to metastasize. Despite the importance of metastasis in lung cancer mortality, its underlying cellular and molecular mechanisms remain largely elusive. Here, we identified miR-200 miRNAs as potent suppressors for lung adenocarcinoma metastasis. miR-200 expression is specifically repressed in mouse metastatic lung adenocarcinomas, and miR-200 decrease strongly correlates with poor patient
more » ... . Consistently, deletion of mir-200c/141 in the KrasLSL-G12D/+; Trp53flox/flox lung adenocarcinoma mouse model significantly promoted metastasis, generating a desmoplastic tumor stroma highly reminiscent of metastatic human lung cancer. miR-200 deficiency in lung cancer cells promotes the proliferation and activation of adjacent cancer-associated fibroblasts (CAFs), which in turn elevates the metastatic potential of cancer cells. miR-200 regulates the functional interaction between cancer cells and CAFs, at least in part, by targeting Notch ligand Jagged1 and Jagged2 in cancer cells and inducing Notch activation in adjacent CAFs. Hence, the interaction between cancer cells and CAFs constitutes an essential mechanism to promote metastatic potential.
doi:10.1101/2020.09.02.276550 fatcat:thgvogyejnbexmxwx2gjnymr6u

A longitudinal study of plasma BAFF levels in mothers and their infants in Uganda, and correlations with subsets of B cells

Caroline Rönnberg, Allan Lugaajju, Anna Nyman, Ulf Hammar, Matteo Bottai, Maximilian Julius Lautenbach, Christopher Sundling, Fred Kironde, Kristina E. M. Persson, Yolande Richard
2021 PLoS ONE  
Formal analysis: Caroline Rönnberg, Allan Lugaajju, Anna Nyman, Ulf Hammar, Matteo Bottai, Maximilian Julius Lautenbach, Christopher Sundling, Kristina E. M. Persson. Funding acquisition: Kristina E.  ...  Writing -original draft: Caroline Rönnberg, Allan Lugaajju. Writing -review & editing: Allan Lugaajju, Christopher Sundling, Kristina E. M. Persson. 30.  ... 
doi:10.1371/journal.pone.0245431 pmid:33465125 fatcat:6k6kw3myobhl5bzstgz3fa52ki

The TanDEM-X Mission Phases - Ten Years of Bistatic Acquisition and Formation Planning

Markus Bachmann, Thomas Kraus, Allan Bojarski, Maximilian Schandri, Johannes Boer, Thomas Busche, Jose Luis Bueso Bello, Christo Grigorov, Ulrich Steinbrecher, Stefan Buckreuss, Gerhard Krieger, Manfred Zink
2021 IEEE Journal of Selected Topics in Applied Earth Observations and Remote Sensing  
From 1992 to 1999, he was with the Ludwig Maximilians University, Munich, where he conducted multidisciplinary research on neuronal modeling and nonlinear information processing in biological and technical  ...  Allan Bojarski received the Dipl. -Ing. degree in aerospace engineering from the Technical University of Munich, Munich, Germany, in 2014.  ...  Maximilian Schandri received the B.Sc. and M.Sc. degrees in physics from the University of Erlangen-Nuremberg, Erlangen, Germany, in 2016 and 2018, respectively.  ... 
doi:10.1109/jstars.2021.3065446 fatcat:gr6znk7wonfzrpw5opvwrow2mq

Cryptococcus neoformans Ex Vivo Capsule Size Is Associated With Intracranial Pressure and Host Immune Response in HIV-associated Cryptococcal Meningitis

Emma J. Robertson, Grace Najjuka, Melissa A. Rolfes, Andrew Akampurira, Neena Jain, Janani Anantharanjit, Maximilian von Hohenberg, Manlio Tassieri, Allan Carlsson, David B. Meya, Thomas S. Harrison, Bettina C. Fries (+2 others)
2013 Journal of Infectious Diseases  
Background. The Cryptococcus neoformans polysaccharide capsule is a well-characterized virulence factor with immunomodulatory properties. The organism and/or shed capsule is postulated to raise intracranial pressure (ICP) in cryptococcal meningitis (CM) by mechanical obstruction of cerebrospinal fluid (CSF) outflow. Little is known regarding capsule phenotype in human cryptococcosis. We investigated the relationship of ex vivo CSF capsular phenotype with ICP and CSF immune response, as well as
more » ... n vitro phenotype. Methods. In total, 134 human immunodeficiency virus (HIV)-infected Ugandan adults with CM had serial lumbar punctures with measurement of CSF opening pressures, quantitative cultures, ex vivo capsule size and shedding, viscosity, and CSF cytokines; 108 had complete data. Induced capsular size and shedding were measured in vitro for 48 C. neoformans isolates. Results. Cryptococcal strains producing larger ex vivo capsules in the baseline ( pretreatment) CSF correlated with higher ICP (P = .02), slower rate of fungal clearance (P = .02), and paucity of CSF inflammation, including decreased CSF white blood cell (WBC) count (P < .001), interleukin (IL)-4 (P = .02), IL-6 (P = .01), IL-7 (P = .04), IL-8 (P = .03), and interferon γ (P = .03). CSF capsule shedding did not correlate with ICP. On multivariable analysis, capsule size remained independently associated with ICP. Ex vivo capsular size and shedding did not correlate with that of the same isolates grown in vitro. Conclusions. Cryptococcal capsule size ex vivo is an important contributor to virulence in human cryptococcal meningitis.
doi:10.1093/infdis/jit435 pmid:23945372 pmcid:PMC3864387 fatcat:tjtjbaqaxrfqdbziq5keehyfga

The Influence of Metallicity on Stellar Differential Rotation and Magnetic Activity

Christoffer Karoff, Travis S. Metcalfe, Ângela R. G. Santos, Benjamin T. Montet, Howard Isaacson, Veronika Witzke, Alexander I. Shapiro, Savita Mathur, Guy R. Davies, Mikkel N. Lund, Rafael A. Garcia, Allan S. Brun (+11 others)
2018 Astrophysical Journal  
Observations of Sun-like stars over the last half-century have improved our understanding of how magnetic dynamos, like that responsible for the 11-year solar cycle, change with rotation, mass and age. Here we show for the first time how metallicity can affect a stellar dynamo. Using the most complete set of observations of a stellar cycle ever obtained for a Sun-like star, we show how the solar analog HD 173701 exhibits solar-like differential rotation and a 7.4-year activity cycle. While the
more » ... uration of the cycle is comparable to that generated by the solar dynamo, the amplitude of the brightness variability is substantially stronger. The only significant difference between HD 173701 and the Sun is its metallicity, which is twice the solar value. Therefore, this provides a unique opportunity to study the effect of the higher metallicity on the dynamo acting in this star and to obtain a comprehensive understanding of the physical mechanisms responsible for the observed photometric variability. The observations can be explained by the higher metallicity of the star, which is predicted to foster a deeper outer convection zone and a higher facular contrast, resulting in stronger variability.
doi:10.3847/1538-4357/aaa026 fatcat:pillwgphqncvxiq3xymn27r3hi

Genetic screens identify a context-specific PI3K/p27Kip1 node driving extrahepatic biliary cancer

Chiara Falcomata, Stefanie Barthel, Angelika Ulrich, Sandra Diersch, Christian Veltkamp, Lena Rad, Fabio Boniolo, Myriam Solar, Katja Steiger, Barbara Seidler, Magdalena Zukowska, Joanna Madej (+22 others)
2021 Cancer Discovery  
Biliary tract cancer ranks among the most lethal human malignancies, representing an unmet clinical need. Its abysmal prognosis is tied to an increasing incidence and a fundamental lack of mechanistic knowledge regarding the molecular basis of the disease. Here, we show that the Pdx1-positive extrahepatic biliary epithelium is highly susceptible toward transformation by activated PIK3CAH1047R but refractory to oncogenic KrasG12D. Using genome-wide transposon screens and genetic loss-of-function
more » ... experiments, we discover context-dependent genetic interactions that drive extrahepatic cholangiocarcinoma (ECC) and show that PI3K signaling output strength and repression of the tumor suppressor p27Kip1 are critical context-specific determinants of tumor formation. This contrasts with the pancreas, where oncogenic Kras in concert with p53 loss is a key cancer driver. Notably, inactivation of p27Kip1 permits KrasG12D-driven ECC development. These studies provide a mechanistic link between PI3K signaling, tissue-specific tumor suppressor barriers, and ECC pathogenesis, and present a novel genetic model of autochthonous ECC and genes driving this highly lethal tumor subtype. SIGNIFICANCE: We used the first genetically engineered mouse model for extrahepatic bile duct carcinoma to identify cancer genes by genome-wide transposon-based mutagenesis screening. Thereby, we show that PI3K signaling output strength and p21Kip1 function are critical determinants for context-specific ECC formation.
doi:10.1158/2159-8290.cd-21-0209 pmid:34282029 pmcid:PMC7612573 fatcat:pdgzjsf2gfgu5cuop7r35tsqci
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