cOOpD: Reformulating COPD classification on chest CT scans as anomaly detection using contrastive representations

Classification of heterogeneous diseases is challenging due to their complexity, variability of symptoms and imaging findings. Chronic Obstructive Pulmonary Disease (COPD) is a prime example, being underdiagnosed despite being the third leading cause of death. Its sparse, diffuse and heterogeneous appearance on computed tomography challenges supervised binary classification. We reformulate COPD binary classification as an anomaly detection task, proposing cOOpD: heterogeneous pathological regions are detected as Out-of-Distribution (OOD) from normal homogeneous lung regions. To this end, we learn representations of unlabeled lung regions employing a self-supervised contrastive pretext model, potentially capturing specific characteristics of diseased and healthy unlabeled regions. A generative model then learns the distribution of healthy representations and identifies abnormalities (stemming from COPD) as deviations. Patient-level scores are obtained by aggregating region OOD scores. We show that cOOpD achieves the best performance on two public datasets, with an increase of 8.2% and 7.7% in terms of AUROC compared to the previous supervised state-of-the-art. Additionally, cOOpD yields well-interpretable spatial anomaly maps and patient-level scores which we show to be of additional value in identifying individuals in the early stage of progression. Experiments in artificially designed real-world prevalence settings further support that anomaly detection is a powerful way of tackling COPD classification

Checkliste zur Unterstützung der Helmholtz-Zentren bei der Implementierung von Richtlinien für nachhaltige Forschungssoftware

Mit der voranschreitenden Digitalisierung von Forschung und Lehre steigt die Zahl an Software-Lösungen, die an wissenschaftlichen Einrichtungen entstehen und zur Erkenntnisgewinnung genutzt werden. Die – unter dem Stichwort Open Science geforderte – Zugänglichkeit und Nachnutzung von wissenschaftlichen Ergebnissen kann in vielen Fachgebieten nur sichergestellt werden, wenn neben Forschungsdaten auch Programmcode offen zugänglich gemacht wird. Die vorliegende Handreichung richtet sich an Entscheider*innen in den Helmholtz-Zentren, die sich mit der Implementierung von Richtlinien für nachhaltige Forschungssoftware befassen. Sie ergänzt eine Muster-Richtlinie, die den Zentren bereits eine richtungsweisende und nachnutzbare Vorlage zur Erstellung von Regelungen für einen nachhaltigen Umgang mit Forschungssoftware gibt

Proteomic Shifts in Embryonic Stem Cells with Gene Dose Modifications Suggest the Presence of Balancer Proteins in Protein Regulatory Networks

Large numbers of protein expression changes are usually observed in mouse models for neurodegenerative diseases, even when only a single gene was mutated in each case. To study the effect of gene dose alterations on the cellular proteome, we carried out a proteomic investigation on murine embryonic stem cells that either overexpressed individual genes or displayed aneuploidy over a genomic region encompassing 14 genes. The number of variant proteins detected per cell line ranged between 70 and 110, and did not correlate with the number of modified genes. In cell lines with single gene mutations, up and down-regulated proteins were always in balance in comparison to parental cell lines regarding number as well as concentration of differentially expressed proteins. In contrast, dose alteration of 14 genes resulted in an unequal number of up and down-regulated proteins, though the balance was kept at the level of protein concentration. We propose that the observed protein changes might partially be explained by a proteomic network response. Hence, we hypothesize the existence of a class of “balancer” proteins within the proteomic network, defined as proteins that buffer or cushion a system, and thus oppose multiple system disturbances. Through database queries and resilience analysis of the protein interaction network, we found that potential balancer proteins are of high cellular abundance, possess a low number of direct interaction partners, and show great allelic variation. Moreover, balancer proteins contribute more heavily to the network entropy, and thus are of high importance in terms of system resilience. We propose that the “elasticity” of the proteomic regulatory network mediated by balancer proteins may compensate for changes that occur under diseased conditions

Does energy policy hurt international competitiveness of firms? A comparative study for Germany, Switzerland and Austria

This paper investigates the impact of energy policies on the export performance of firms. There has been a long policy debate on potentially negative impacts of cost-increasing energy policies on international competitiveness. We use firm-level data from three countries with similar industry structure but different energy policies: Germany, Switzerland, and Austria. We rely on firm manager assessments on the relevance of energy policy (in terms of taxes, regulations, standards, subsidies and demand stimulation) for their firm operation and link data on the adoption and development of new energy technologies. Regression analyses and matching approaches both show very few impacts of energy policy on export performance, suggesting that either policy impacts on firms’ cost are negligible in the period of study (2012 to 2014) or likely negative impacts are balanced by the adoption of new technology

Transcriptional profiling of Sox17-positive, endoderm-committed mouse embryonic stem cells

Der erste große Schritt in der embryonalen Entwicklung der Vertebraten ist die Bildung der drei Keimblätter - Ektoderm, Mesoderm und Endoderm - während der Gastrulation. Embryonale Zellen des Epiblasten verlieren in diesem Prozess ihre Pluripotenz und schlagen unterschiedliche Entwicklungswege ein, die auf molekularer Ebene nicht vollständig charakterisiert sind. Embryonale Stammzellen (ES Zellen), die aus den pluripotenten Zellen des Epiblasten stammen, exprimieren größtenteils die gleichen Gene wie Epiblastenzellen und können in vitro gezielt in spezialisierte Zelltypen aller drei Keimblätter differenziert werden. Daher geht man davon aus, dass auch zu Beginn der ES Zelldifferenzierung transient Keimblatt-spezifische Gene exprimiert werden. Das während der Gastrulation zwischen Tag 6,0 und 7,5 der Maus- Embryonalentwicklung entstehende endodermale Keimblatt wird auch als definitives Endoderm (DE) bezeichnet. Aus dem DE leiten sich die Organe des gastrointestinalen und respiratorischen Trakts, wie zum Beispiel Leber, Pankreas, Intestinum und Lunge, ab. Neben dem DE entstehen unabhängig von der Gastrulation, zwischen Tag 4,5 bis 5,0 parietales Endoderm (PE) und viscerales Endoderm (VE), die extraembryonales Gewebe bilden. Das direkt dem Epiblasten aufliegende VE spielt zudem eine wichtige Rolle bei der Positionierung der Körperachsen und der Induktion bestimmter embryonaler Strukturen, wie zum Beispiel der Kopffalte. Obwohl sich VE und DE in der Embryonalentwicklung völlig unterschiedlich ableiten lassen, besitzen sie dennoch gemeinsame funktionelle und molekulare Eigenschaften. Beide Endodermderivate exprimieren den Transkriptionsfaktor Sox17, der eine zentrale Rolle bei der Endodermentwicklung spielt. Damit ist Sox17 ein idealer genetischer Marker der Endodermdifferenzierung. Das Ziel dieser Arbeit war es, die frühe Differenzierung von murinen ES Zellen in Sox17-exprimierende endodermale Zellen in vitro zu untersuchen und bisher nicht beschriebene Gene des endodermalen Keimblatts zu charakterisieren. Eine transgene ES Zelllinie wurde etabliert, die das rot-fluoreszierende DsRedExpress-Protein (DsRed) unter der Kontrolle des Sox17 Promotors exprimiert. Es konnte gezeigt werden, dass die ES-Zellen, die ihre Pluripotenz verlieren und endodermale Identität annehmen, das DsRed Transgen in vergleichbarer Weise zum endogenen Sox17 exprimieren und damit ein geeignetes in vitro Modell für Endoderm-Differenzierung darstellen. Die globale Analyse der Genexpression und Untersuchung der Gen-Ontologie zeigten, dass Sox17 exprimierende Zellen dem visceralen, parietalen und definitiven Endoderm zuzuordnen sind. Die Analyse des Transkriptoms erlaubte es zudem neue Endoderm-assozierte Gene zu identifizieren. Die Expression der Gene Prss3, Plet1, 061000O12Rik, Chsy3, 2210011C24Rik, Gm10664, Sel1l3, Cdh6, Slc22a23, Pkdcc, Gpr120, Ttc6 und 210300C02Rik im embryonalen Endoderm und in daraus abgeleiteten Organen in vivo konnte durch in situ Hybridisierung gezeigt werden. Darüber hinaus konnten mit , Rfx6, Cdh6 und 0610010O12Rik Gene identifiziert werden, deren Expression in vitro von SOX17 beeinflusst wird. Diese Ergebnisse unterstreichen die Bedeutung der in dieser Arbeit etablierten Zelllinie zur Identifizierung unbekannter Endoderm-assozierter Gene.The major first step in embryonic development of vertebrates is the formation of three germ layers during the process of gastrulation - the ectoderm, the mesoderm and the endoderm. During gastrulation, embryonic cells of the epiblast loose their pluripotency and adopt different developmental fates. However, the underlying molecular mechanisms have not been fully elucidated. Embryonic stem cells (ESCs) derived from the epiblast largely express the same genes as the pluripotent epiblast cells and in vitro they can be differentiated into cell types of the above mentioned three germ layers. Therefore it is hypothesized that directed ESC differentiation begins with the transient expression of germ layer-specific genes. Endoderm formation in the vertebrate embryo occurs during distinct time periods. In the mouse, the definitive endoderm (DE) forms during gastrulation between day 6.0 and 7.5 of embryonic development, whereas parietal endoderm (PE) and visceral endoderm (VE) arise independently prior to gastrulation between day 4.5 and 5.0. DE gives rise to organs of the gastrointestinal and respiratory tract including thymus, lung, liver, pancreas and intestine, while PE and VE contribute to extra-embryonic tissues. The visceral endoderm surrounding most of the epiblast is important for the induction of embryonic body axes and head folds. Although VE and DE are formed independently during embryonic development, they share common functional and molecular properties. Both endoderm structures express the transcription factor Sox17 which plays a crucial role in endoderm development. Thus, Sox17 is thought to be an ideal marker molecule for endoderm differentiation. The aim of this project was to investigate the early differentiation of murine ES cells into embryoid bodies which express Sox17 and to discover and characterize previously unknown genes important for endoderm formation. For this purpose a transgenic ES cell line was established which expresses the red-fluorescent DsRedExpress (DsRed) protein under the control of the Sox17 promotor. It is shown that ES cells which loose their pluripotency and adopt an endodermal identity express the DsRed transgene in a Sox17 comparable manner. Therefore, the Sox17::DsRed ES cell line represents a suitable in vitro model for endoderm differentiation. Global analysis of gene expression and gene ontology showed that the Sox17 expressing cell population was composed of visceral, parietal and definitive endoderm cells. In addition, the analysis of the Sox17-specific transcriptome identified unknown endoderm- associated genes. In situ hybridisation detected expression of the genes Prss3, Plet1, 061000O12Rik, Chsy3, 2210011C24Rik, Gm10664, Sel1l3, Cdh6, Slc22a23, Pkdcc, Gpr120, Ttc6 and 210300C02Rik within the embryonic endoderm and related organs in vivo. The genes Ocln, Rfx6, Cdh6 and 0610010O12Rik were identified with their expression being directed by SOX17 in vitro. In summary, this work identified previously unknown endoderm-associated genes and made an important contribution to the characterisation of ES cell derived endodermal cell types

Cloning of mouse ojoplano, a reticular cytoplasmic protein expressed during embryonic development

6 páginas, 4 figuras, 1 tabla de sequencia de datos (NCBI accession number EU683438).Ojoplano (Opo) is a morphogenetic gene playing an important role during embryogenesis in medaka. This report focuses on the identification and characterization of the mouse Opo gene. We examined Opo expression by whole-mount in situ hybridization and in situ hybridization on sagittal sections during mouse embryogenesis. First expression in whole-mounts was detected at Theiler stages 15–17 (E 9.5–10.5 dpc) as a spotted specific staining in migrating neural crest cells and in placodal structures. A complex expression pattern was observed in Theiler stage 22–23 (E 14.5 dpc) in sagittal sections, including expression in skeletal structures (skull, vertebrae, ribs, bones of the locomotor system), in the nasal region, the heart and the eye. Fusion proteins revealed the localization of OPO within the cytoplasm with a reticular distribution that largely overlapped with the endoplasmic reticulum. Opo shows homology to human transcripts linked to a hereditary craniofacial malformation, orofacial cleft 1 (OFC1). The expression of mouse Opo in neural crest derivatives and skull elements further supports this link.This work was supported by the Max Planck Society.Peer reviewe

The Methyltransferase Region of Vesicular Stomatitis Virus L Polymerase Is a Target Site for Functional Intramolecular Insertion

The L-protein of vesicular stomatitis virus (VSV) is a single-chain multi-domain RNA-dependent RNA polymerase. Previously reported attempts of intramolecular insertions of fluorescent proteins into the L-protein resulted in temperature-sensitive and highly attenuated polymerase activity. Here, we describe a novel insertion site that was selected based on in silico prediction. Of five preselected locations, insertion of the fluorescent protein mCherry in the VSV polymerase between amino acids 1620 and 1621 preserved polymerase function even after extended passaging and showed only mild attenuation compared to wildtype VSV polymerase. High magnification fluorescence imaging revealed a corpuscular cytosolic pattern for the L-protein. To confirm that the insertion site tolerates inclusion of proteins others than mCherry, we cloned mWasabi into the same position in L, generating a VSV-LmWasabi, which was also functional. We also generated a functional dual-color-dual-insertion VSV construct with intramolecularly labeled P and L-proteins. Together, our data present an approach to tag VSV polymerase intramolecularly without perturbing enzymatic activity. This L fusion protein might enable future tracing studies to monitor intracellular location of the VSV transcription and replication machinery in real-time life-imaging studies

Induction and Selection of Sox17-Expressing Endoderm Cells Generated from Murine Embryonic Stem Cells

Embryonic stem (ES) cells offer a valuable source for generating insulin-producing cells. However, current differentiation protocols often result in heterogeneous cell populations of various developmental stages. Here we show the activin A-induced differentiation of mouse ES cells carrying a homologous dsRed-IRES-puromycin knock-in within the Sox17 locus into the endoderm lineage. Sox17-expressing cells were selected by fluorescence-assisted cell sorting (FACS) and characterized at the transcript and protein level. Treatment of ES cells with high concentrations of activin A for 10 days resulted in up to 19% Sox17-positive cells selected by FACS. Isolated Sox17-positive cells were characterized by defini- tive endoderm-specific Sox17/Cxcr4/Foxa2 transcripts, but lacked pluripotency-associated Oct4 mRNA and protein. The Sox17-expressing cells showed downregulation of extraembryonic endoderm (Sox7, Afp, Sdf1)-, mesoderm (Foxf1, Meox1)- and ectoderm (Pax6, NeuroD6)-specific transcripts. The presence of Hnf4α, Hes1 and Pdx1 mRNA demonstrated the expression of primitive gut/foregut cell-specific markers. Ngn3, Nkx6.1 and Nkx2.2 transcripts in Sox17-positive cells were determined as properties of pancreatic endocrine progenitors. Immunocytochemistry of activin A-induced Sox17-positive embryoid bodies revealed coexpression of Cxcr4 and Foxa2. Moreover, the histochemical demonstration of E-cadherin-, Cxcr4-, Sox9-, Hnf1β- and Ngn3-positive epithelial-like structures underlined the potential of Sox17-positive cells to further differentiate into the pancreatic lineage. By reducing the heterogeneity of the ES cell progeny, Sox17-expressing cells are a suitable model to evaluate the effects of growth and differentiation factors and of culture conditions to delineate the differentiation process for the generation of pancreatic cells in vitro.Dieser Beitrag ist mit Zustimmung des Rechteinhabers aufgrund einer (DFG-geförderten) Allianz- bzw. Nationallizenz frei zugänglich

Point Mutations in the Glycoprotein Ectodomain of Field Rabies Viruses Mediate Cell Culture Adaptation through Improved Virus Release in a Host Cell Dependent and Independent Manner

Molecular details of field rabies virus (RABV) adaptation to cell culture replication are insufficiently understood. A better understanding of adaptation may not only reveal requirements for efficient RABV replication in cell lines, but may also provide novel insights into RABV biology and adaptation-related loss of virulence and pathogenicity. Using two recombinant field rabies virus clones (rRABV Dog and rRABV Fox), we performed virus passages in three different cell lines to identify cell culture adaptive mutations. Ten passages were sufficient for the acquisition of adaptive mutations in the glycoprotein G and in the C-terminus of phosphoprotein P. Apart from the insertion of a glycosylation sequon via the mutation D247N in either virus, both acquired additional and cell line-specific mutations after passages on BHK (K425N) and MDCK-II (R346S or R350G) cells. As determined by virus replication kinetics, complementation, and immunofluorescence analysis, the major bottleneck in cell culture replication was the intracellular accumulation of field virus G protein, which was overcome after the acquisition of the adaptive mutations. Our data indicate that limited release of extracellular infectious virus at the plasma membrane is a defined characteristic of highly virulent field rabies viruses and we hypothesize that the observed suboptimal release of infectious virions is due to the inverse correlation of virus release and virulence in vivo