University of Hamburg
  • Hamburg, Hamburg, Germany
Recent publications
Following recent work by Kollár and Sarnak, we study gaps in the spectra of large connected cubic and quartic graphs with minimum spectral gap. We focus on two sequences of graphs, denoted Δn and Γn which are more ‘symmetric’ compared to the other graphs in these two families, respectively. We prove that (1,5] is a gap interval for Δn, and [(−1+17)/2,3] is a gap interval for Γn. We conjecture that these two are indeed maximal gap intervals. As a by-product, we show that the eigenvalues of Δn lying in the interval [−3,−5] (in particular, its minimum eigenvalue) converge to (1−33)/2 and the eigenvalues of Γn lying in the interval [−4,−(1+17)/2] (and in particular, its minimum eigenvalue) converge to 1−13 as n tends to infinity. The proofs of the above results heavily depend on the following property which can be of independent interest: with few exceptions, all the eigenvalues of connected cubic and quartic graphs with minimum spectral gap are simple.
We present a method which provides a unified framework for most stability theorems that have been proved in graph and hypergraph theory. Our main result reduces stability for a large class of hypergraph problems to the simpler question of checking that a hypergraph H with large minimum degree that omits the forbidden structures is vertex-extendable. This means that if v is a vertex of H and H−v is a subgraph of the extremal configuration(s), then H is also a subgraph of the extremal configuration(s). In many cases vertex-extendability is quite easy to verify. We illustrate our approach by giving new short proofs of hypergraph stability results of Pikhurko, Hefetz-Keevash, Brandt-Irwin-Jiang, Bene Watts-Norin-Yepremyan and others. Since our method always yields minimum degree stability, which is the strongest form of stability, in some of these cases our stability results are stronger than what was known earlier. Along the way, we clarify the different notions of stability that have been previously studied.
Epidemiological studies have linked prolonged febrile seizures (FS) and especially febrile status epilepticus (FSE) in early life to subsequent development of epilepsy. The causality of this association, however, is debated, and the FSE-triggered mechanisms underlying the transformation of a healthy to an epileptic brain remain to be elucidated. There is solid evidence that hyperpolarization-activated cyclic nucleotide-gated (HCN) channels and the resulting h-current (Ih) are involved in this transformation. HCN channels are important regulators of neuronal network activity and shape, particularly during brain development, when activity patterns are crucial for the proper establishment of neuronal connectivity. Primary genetic HCN channel dysfunction promoting FS or secondary dysregulation of HCN channel function triggered by FSE might therefore lead to network derangements that lay the groundwork for the brain to develop epilepsy later in life.
The feasible region Ωind(F) of a graph F is the collection of points (x,y) in the unit square such that there exists a sequence of graphs whose edge densities approach x and whose induced F-densities approach y. A complete description of Ωind(F) is not known for any F with at least four vertices that is not a clique or an independent set. The feasible region provides a lot of combinatorial information about F. For example, the supremum of y over all (x,y)∈Ωind(F) is the inducibility of F and Ωind(Kr) yields the Kruskal-Katona and clique density theorems. We begin a systematic study of Ωind(F) by proving some general statements about the shape of Ωind(F) and giving results for some specific graphs F. Many of our theorems apply to the more general setting of quantum graphs. For example, we prove a bound for quantum graphs that generalizes an old result of Bollobás for the number of cliques in a graph with given edge density. We also consider the problems of determining Ωind(F) when F=Kr−, F is a star, or F is a complete bipartite graph. In the case of Kr− our results sharpen those predicted by the edge-statistics conjecture of Alon et al. while also extending a theorem of Hirst for K4− that was proved using computer aided techniques and flag algebras. The case of the 4-cycle seems particularly interesting and we conjecture that Ωind(C4) is determined by the solution to the triangle density problem, which has been solved by Razborov.
Background: A dissociative subtype of posttraumatic stress disorder (D-PTSD) was introduced into the 5th edition of the Diagnostic and Statistical Manual of Mental Disorders (DSM-5) but latent profiles and clinical correlates of D-PTSD remain controversial. Objective: The aims of our study were to identify subgroups of individuals with distinct patterns of PTSD symptoms, including dissociative symptoms, by means of latent class analyses (LCA), to compare these results with the categorization of D-PTSD vs. PTSD without dissociative features according to the CAPS-5 interview, and to explore whether D-PTSD is associated with higher PTSD severity, difficulties in emotion regulation, and depressive symptoms. Method: A German sample of treatment-seeking individuals was investigated (N = 352). We conducted an LCA on the basis of symptoms of PTSD and dissociation as assessed by the CAPS-5. Moreover, severity of PTSD (PCL-5), difficulties in emotion regulation (DERS), and depressive symptoms (BDI-II) were compared between patients with D-PTSD according to the CAPS-5 interview and patients without dissociative symptoms. Results: LCA results suggested a 5-class model with one subgroup showing the highest probability to fulfill criteria for the dissociative subtype and high scores on both BDI and DERS. Significantly higher scores on the DERS, BDI and PCL-5 were found in the D-PTSD group diagnosed with the CAPS-5 (n = 75; 35.7%). Sexual trauma was also reported more often by this subgroup. When comparing the dissociative subtype to the LCA results, only a partial overlap could be found. Conclusions: Our findings suggest that patients with D-PTSD have significantly more problems with emotion regulation, more depressive symptoms, and more severe PTSD-symptoms. Given the results of our LCA, we conclude that the dissociative subtype seems to be more complex than D-PTSD as diagnosed by means of the CAPS-5.
Stress granules (SGs) are membrane-less condensates composed of RNA and protein that assemble in response to stress stimuli and disassemble when stress is lifted. Both assembly and disassembly are tightly controlled processes, yet, it remains elusive whether mRNAs in SGs completely recover for translation following stress relief. Using RNA-seq of translating fractions in human cell line, we found that higher fraction of the m6A-modified mRNAs recovered for translation compared to unmodified mRNAs, i.e. 95% vs 84%, respectively. Considering structural mRNA analysis, we found that the m6A modification enhances structuring at nucleotides in its close vicinity. Our results suggest that SG-sequestered mRNAs disassemble nearly completely from SGs and the m6A modification may display some advantage to the mRNAs in their recovery for translation likely by m6A-driven structural stabilization.
The Gulf of Guinea is characterised by a complex hydrology and supports a high species diversity. A recent study has indicated that the area can be considered a refuge for rare taxa. Intensive sampling off the coast of Ghana (Gulf of Guinea) in 2012 on board the R/V F. Nansen resulted in the discovery of a large number of benthic invertebrates, including peracarid crustaceans. A preliminary investigation demonstrated a high diversity of the Cumacea, with 95% of the species being new to science. The most species-rich genus was Eocuma with seven species; six of them proved new to science and are described here. Additionally, the global distribution of Eocuma was analysed with the help of a phylogenetic tree based on morphological characters, Bayesian Binary Markov chain Monte Carlo biogeographic analysis and literature data. The radiation centres of the west African fauna are discussed.
Here, we present a protocol for assessing virus-infected cells using electron cryo-tomography (cryoET). It includes the basic workflows of seeding cells, plunge-freezing, clipping, cryo-focused ion beam milling (cryoFIB-milling), and cryoET, as well as two optional modules: micropatterning and live-cell fluorescence microscopy. We use an A549 human cell line and the virus HAdV5-pIX-mcherry in this protocol, but the comprehensive workflow can be easily transferred to other cell types and different types of virus infection or treatment. For complete details on the use and execution of this protocol, please refer to Pfitzner et al. (2021).
The accurate simulation of additional interactions at the ATLAS experiment for the analysis of proton–proton collisions delivered by the Large Hadron Collider presents a significant challenge to the computing resources. During the LHC Run 2 (2015–2018), there were up to 70 inelastic interactions per bunch crossing, which need to be accounted for in Monte Carlo (MC) production. In this document, a new method to account for these additional interactions in the simulation chain is described. Instead of sampling the inelastic interactions and adding their energy deposits to a hard-scatter interaction one-by-one, the inelastic interactions are presampled, independent of the hard scatter, and stored as combined events. Consequently, for each hard-scatter interaction, only one such presampled event needs to be added as part of the simulation chain. For the Run 2 simulation chain, with an average of 35 interactions per bunch crossing, this new method provides a substantial reduction in MC production CPU needs of around 20%, while reproducing the properties of the reconstructed quantities relevant for physics analyses with good accuracy.
Background Circulating tumor cells (CTCs) are liquid biopsies that represent micrometastatic disease and may offer unique insights into future recurrences in non-small cell lung cancer (NSCLC). Due to CTC rarity and limited stability, no stable CTC-derived xenograft (CDX) models have ever been generated from non-metastatic NSCLC patients directly. Alternative strategies are needed to molecularly characterize CTCs and means of potential future metastases in this potentially curable patient group. Methods Surgically resected NSCLC primary tumor tissues from non-metastatic patients were implanted subcutaneously in immunodeficient mice to establish primary tumor patient-derived xenograft (ptPDX) models. CTCs were isolated as liquid biopsies from the blood of ptPDX mice and re-implanted subcutaneously into naïve immunodeficient mice to generate liquid biopsy CTC-derived xenograft (CDX) tumor models. Single cell RNA sequencing was performed and validated in an external dataset of non-xenografted human NSCLC primary tumor and metastases tissues. Drug response testing in CDX models was performed with standard of care chemotherapy (carboplatin/paclitaxel). Blockade of MYC, which has a known role in drug resistance, was performed with a MYC/MAX dimerization inhibitor (10058-F4). Results Out of ten ptPDX, two (20%) stable liquid biopsy CDX mouse models were generated. Single cell RNA sequencing analysis revealed an additional regenerative alveolar epithelial type II (AT2)-like cell population in CDX tumors that was also identified in non-xenografted NSCLC patients’ metastases tissues. Drug testing using these CDX models revealed different treatment responses to carboplatin/paclitaxel. MYC target genes and c-MYC protein were upregulated in the chemoresistant CDX model, while MYC/MAX dimerization blocking could overcome chemoresistance to carboplatin/paclitaxel. Conclusions To overcome the lack of liquid biopsy CDX models from non-metastatic NSCLC patients, CDX models can be generated with CTCs from ptPDX models that were originally established from patients’ primary tumors. Single cell analyses can identify distinct drug responses and cell heterogeneities in CDX tumors that can be validated in NSCLC metastases tissues. CDX models deserve further development and study to discover personalized strategies against micrometastases in non-metastatic NSCLC patients.
The reconstruction of the trajectories of charged particles, or track reconstruction, is a key computational challenge for particle and nuclear physics experiments. While the tuning of track reconstruction algorithms can depend strongly on details of the detector geometry, the algorithms currently in use by experiments share many common features. At the same time, the intense environment of the High-Luminosity LHC accelerator and other future experiments is expected to put even greater computational stress on track reconstruction software, motivating the development of more performant algorithms. We present here A Common Tracking Software (ACTS) toolkit, which draws on the experience with track reconstruction algorithms in the ATLAS experiment and presents them in an experiment-independent and framework-independent toolkit. It provides a set of high-level track reconstruction tools which are agnostic to the details of the detection technologies and magnetic field configuration and tested for strict thread-safety to support multi-threaded event processing. We discuss the conceptual design and technical implementation of ACTS, selected applications and performance of ACTS, and the lessons learned.
Official reindeer herding statistics are an invaluable source of data for both social and natural scientists wishing to understand and model ecological systems in the Arctic. However, as with all official statistics, reindeer herding statistics are subject to certain distortions emerging from the way they are collected and processed as well as from a priori assumptions. In this article, we analyse Soviet/Russian reindeer herding statistics in order to reveal these distortions and assumptions and show how these statistics should be interpreted. Particularly, we analyse reindeer ownership categories and reindeer age/sex categories, spatial organization of the data, so-called magical numbers (statistical parameters used by the state to assess the quality of reindeer herding management), and the manner of collecting statistics. We show that official Soviet/Russian statistics reflected the world as the state wanted to see it, even if it obviously did not completely correspond to the world ‘out there’. In Soviet times, the state even made systematic attempts to change this world to better correspond to the statistics, which, however, was never fully achieved. On the basis of this analysis, we offer some recommendations for how an interested researcher should read and understand Russian reindeer herding statistics.
We introduce a Python package that provides simple and unified access to a collection of datasets from fundamental physics research—including particle physics, astroparticle physics, and hadron- and nuclear physics—for supervised machine learning studies. The datasets contain hadronic top quarks, cosmic-ray-induced air showers, phase transitions in hadronic matter, and generator-level histories. While public datasets from multiple fundamental physics disciplines already exist, the common interface and provided reference models simplify future work on cross-disciplinary machine learning and transfer learning in fundamental physics. We discuss the design and structure and line out how additional datasets can be submitted for inclusion. As showcase application, we present a simple yet flexible graph-based neural network architecture that can easily be applied to a wide range of supervised learning tasks. We show that our approach reaches performance close to dedicated methods on all datasets. To simplify adaptation for various problems, we provide easy-to-follow instructions on how graph-based representations of data structures, relevant for fundamental physics, can be constructed and provide code implementations for several of them. Implementations are also provided for our proposed method and all reference algorithms.
There have been recurrent calls in the field of educational assessment to design theoretically substantiated and empirically supported cognitive models that could be used for assessment purposes. Cognitive models, a simplified depiction of problem-solving processes employed while working on a task of interest, may demonstrate knowledge and skills possessed by individuals at different learning and performance levels. Such models could have significant implications for the assessment of crucial abilities, such as reading comprehension, which is of utmost importance to academic and personal growth. As such, this qualitative study focuses on developing a cognitive model of L2 (second language) reading comprehension. The cognitive model blends the characteristics of three types of cognitive models (i.e., the cognitive model of test specifications, domain mastery, and task performance). The study also aims to offer insights into L2 reading assessments conducted in English-medium instruction settings, where the effective execution of L2 reading processes is crucial.
Using a vector field in R4, we provide an example of a robust heteroclinic cycle between two equilibria that displays a mix of features exhibited by well-known types of low-dimensional heteroclinic structures, including simple, quasi-simple and pseudo-simple cycles. Our cycle consists of two equilibria on one coordinate axis and two connections. One of the connections is one-dimensional while the other is two-dimensional. We compare our heteroclinic cycle to others in the literature that are similar in architecture, and illustrate how the standard methods used to analyse those cycles fail to provide sufficient information on the attraction properties of our example. The instability of two subcycles contained in invariant three-dimensional subspaces seems to indicate that our cycle is generically completely unstable. Although this cycle is one of the simplest possible and exists in low-dimension, the complete study of the stability of our cycle by using the standard techniques for return map reduction is not possible given the hybrid nature of the return map.
We consider locally finite, connected, quasi-transitive graphs and show that every such graph with more than one end is a tree amalgamation of two other such graphs. This can be seen as a graph-theoretical version of Stallings' splitting theorem for multi-ended finitely generated groups and indeed it implies this theorem. Our result also leads to a characterisation of accessible graphs. We obtain applications of our results for planar graphs (answering a variant of a question by Mohar in the affirmative) and graphs without thick ends.
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13,692 members
Kersten Peldschus
  • Diagnostic and Interventional Radiology Department and Clinic
Hauke R Heekeren
  • Department of Psychology
Mathias Fischer
  • Department of Informatics
20146, Hamburg, Hamburg, Germany
Head of institution
Prof. Dr. Dr. h.c. Dieter Lenzen
+49 (0)4152 87-1528
+49 (0)4152 87-2332