Modelling antiferromagnetic interfaces with MuMax3

In this thesis, we investigate how compensated as well as uncompensated antiferromagnetic interfaces can be modelled in the open source software package MuMax3, which has been developed within our own research group DyNaMat and is predominantly used to study static and dynamic effects in ferromagnets. This implementation allows us to give a realistic description of static effects in ferromagnets due to the presence of an antiferromagnetic interface

Modelling compensated antiferromagnetic interfaces with MuMax3

We show how compensated antiferromagnetic spins can be implemented in the micromagnetic simulation program MuMax3. We demonstrate that we can model spin flop coupling as a uniaxial anisotropy for small canting angles and how we can take into account the exact energy terms for strong coupling between a ferromagnet and compensated antiferromagnet. We also investigate the training effect in biaxial antiferromagnets and reproduce the training effect in a polycrystalline IrMn/CoFe bilayer.Comment: 11 pages + Supplementary Material (10 pages

Detecting post-stroke aphasia using EEG-based neural envelope tracking of natural speech

[Objective]. After a stroke, one-third of patients suffer from aphasia, a language disorder that impairs communication ability. The standard behavioral tests used to diagnose aphasia are time-consuming and have low ecological validity. Neural tracking of the speech envelope is a promising tool for investigating brain responses to natural speech. The speech envelope is crucial for speech understanding, encompassing cues for processing linguistic units. In this study, we aimed to test the potential of the neural envelope tracking technique for detecting language impairments in individuals with aphasia (IWA). [Approach]. We recorded EEG from 27 IWA in the chronic phase after stroke and 22 controls while they listened to a story. We quantified neural envelope tracking in a broadband frequency range as well as in the delta, theta, alpha, beta, and gamma frequency bands using mutual information analysis. Besides group differences in neural tracking measures, we also tested its suitability for detecting aphasia using a Support Vector Machine (SVM) classifier. We further investigated the required recording length for the SVM to detect aphasia and to obtain reliable outcomes. [Results]. IWA displayed decreased neural envelope tracking compared to controls in the broad, delta, theta, and gamma band. Neural tracking in these frequency bands effectively captured aphasia at the individual level (SVM accuracy 84%, AUC 88%). High-accuracy and reliable detection could be obtained with 5-7 minutes of recording time. [Significance]. Our study shows that neural tracking of speech is an effective biomarker for aphasia. We demonstrated its potential as a diagnostic tool with high reliability, individual-level detection of aphasia, and time-efficient assessment. This work represents a significant step towards more automatic, objective, and ecologically valid assessments of language impairments in aphasia

Fast micromagnetic simulations on GPU : recent advances made with mumax³

In the last twenty years, numerical modeling has become an indispensable part of magnetism research. It has become a standard tool for both the exploration of new systems and for the interpretation of experimental data. In the last five years, the capabilities of micromagnetic modeling have dramatically increased due to the deployment of graphical processing units (GPU), which have sped up calculations to a factor of 200. This has enabled many studies which were previously unfeasible. In this topical review, we give an overview of this modeling approach and show how it has contributed to the forefront of current magnetism research

A dual sgRNA approach for functional genomics in Arabidopsis thaliana

Reverse genetics uses loss-of-function alleles to interrogate gene function. The advent of CRISPR/Cas9-based gene editing now allows the generation of knock-out alleles for any gene and entire gene families. Even in the model plant Arabidopsis thaliana, gene editing is welcomed as T-DNA insertion lines do not always generate null alleles. Here, we show efficient generation of heritable mutations in Arabidopsis using CRISPR/Cas9 with a workload similar to generating overexpression lines. We obtain for several different genes Cas9 null-segregants with bi-allelic mutations in the T2 generation. While somatic mutations were predominantly generated by the canonical non-homologous end joining (cNHEJ) pathway, we observed inherited mutations that were the result of synthesis-dependent microhomology-mediated end joining (SD-MMEJ), a repair pathway linked to polymerase theta (PolQ). We also demonstrate that our workflow is compatible with a dual sgRNA approach in which a gene is targeted by two sgRNAs simultaneously. This paired nuclease method results in more reliable loss-of-function alleles that lack a large essential part of the gene. The ease of the CRISPR/Cas9 workflow should help in the eventual generation of true null alleles of every gene in the Arabidopsis genome, which will advance both basic and applied plant research

The RING E3 ligase KEEP ON GOING modulates JASMONATE ZIM-DOMAIN12 stability

Jasmonate (JA) signaling in plants is mediated by the JASMONATE ZIM-DOMAIN (JAZ) proteins that repress the activity of several transcription factors regulating JA-inducible gene expression. The hormone JA-isoleucine triggers the interaction of JAZ repressor proteins with the F-box protein CORONATINE INSENSITIVE1 (COI1), part of an S-phase kinase-associated protein1/Cullin1/F-box protein COI1 (SCFCOI1) E3 ubiquitin ligase complex, and their degradation by the 26S proteasome. In Arabidopsis (Arabidopsis thaliana), the JAZ family consists of 13 members. The level of redundancy or specificity among these members is currently not well understood. Here, we characterized JAZ12, encoded by a highly expressed JAZ gene. JAZ12 interacted with the transcription factors MYC2, MYC3, and MYC4 in vivo and repressed MYC2 activity. Using tandem affinity purification, we found JAZ12 to interact with SCFCOI1 components, matching with observed in vivo ubiquitination and with rapid degradation after treatment with JA. In contrast to the other JAZ proteins, JAZ12 also interacted directly with the E3 RING ligase KEEP ON GOING (KEG), a known repressor of the ABSCISIC ACID INSENSITIVE5 transcription factor in abscisic acid signaling. To study the functional role of this interaction, we circumvented the lethality of keg loss-of-function mutants by silencing KEG using an artificial microRNA approach. Abscisic acid treatment promoted JAZ12 degradation, and KEG knockdown led to a decrease in JAZ12 protein levels. Correspondingly, KEG overexpression was capable of partially inhibiting COI1-mediated JAZ12 degradation. Our results provide additional evidence for KEG as an important factor in plant hormone signaling and a positive regulator of JAZ12 stability

A nanobody modulates the p53 transcriptional program without perturbing its functional architecture

The p53 transcription factor plays an important role in genome integrity. To perform this task, p53 regulates the transcription of genes promoting various cellular outcomes including cell cycle arrest, apoptosis or senescence. The precise regulation of this activity remains elusive as numerous mechanisms, e.g. posttranslational modifications of p53 and (non-)covalent p53 binding partners, influence the p53 transcriptional program. We developed a novel, non-invasive tool to manipulate endogenous p53. Nanobodies (Nb), raised against the DNA-binding domain of p53, allow us to distinctively target both wild type and mutant p53 with great specificity. Nb3 preferentially binds ‘structural’ mutant p53, i.e. R175H and R282W, while a second but distinct nanobody, Nb139, binds both mutant and wild type p53. The co-crystal structure of the p53 DNA-binding domain in complex with Nb139 (1.9 Å resolution) reveals that Nb139 binds opposite the DNA-binding surface. Furthermore, we demonstrate that Nb139 does not disturb the functional architecture of the p53 DNA-binding domain using conformation-specific p53 antibody immunoprecipitations, glutaraldehyde crosslinking assays and chromatin immunoprecipitation. Functionally, the binding of Nb139 to p53 allows us to perturb the transactivation of p53 target genes. We propose that reduced recruitment of transcriptional co-activators or modulation of selected post-transcriptional modifications account for these observations

Learned Fear of Gastrointestinal Sensations in Healthy Adults

Background & Aims Gastrointestinal symptom-specific fear and anxiety are important determinants of gastrointestinal symptom perception. We studied learning of fear toward innocuous gastrointestinal sensations as a putative mechanism in the development of gastrointestinal symptom-specific fear and anxiety. Methods Fifty-two healthy subjects (26 women) received 2 types of esophageal balloon distention at a perceptible but nonpainful intensity (conditioned stimulus [CS], the innocuous sensation) and at a painful intensity (unconditioned stimulus [US]). Subjects were assigned randomly to 1 of 2 groups. During the learning phase, the innocuous CS preceded the painful US in the experimental group (n = 26). In the control group (n = 26), on the contrary, the US never followed the CS directly. During a subsequent extinction phase, both groups received only CS distention—the painful US was no longer administered. Indexes of fear learning toward the innocuous CS distention included the skin conductance response, fear-potentiated startle (measured by the eye-blink electromyogram), and self-reported expectancy of the US. Results During the learning phase, only the experimental group learned to fear the innocuous gastrointestinal CS, based on the increase in US expectancy (compared with the control group, P = .04), increased skin conductance response (compared with the control group, P = .03), and potentiated startle reflex (compared with the control group, P = .001) in response to the CS. The differences between the experimental and control groups in US expectancy and skin conductance, but not fear-potentiated startle, disappeared during the extinction phase. Conclusions Fear toward innocuous gastrointestinal sensations can be established through associative learning in healthy human beings. This may be an important mechanism in the development of fear of gastrointestinal symptoms, implicated in the pathophysiology of functional gastrointestinal disorders

In-situ estimation of ice crystal properties at the South Pole using LED calibration data from the IceCube Neutrino Observatory

The IceCube Neutrino Observatory instruments about 1 km3 of deep, glacial ice at the geographic South Pole using 5160 photomultipliers to detect Cherenkov light emitted by charged relativistic particles. A unexpected light propagation effect observed by the experiment is an anisotropic attenuation, which is aligned with the local flow direction of the ice. Birefringent light propagation has been examined as a possible explanation for this effect. The predictions of a first-principles birefringence model developed for this purpose, in particular curved light trajectories resulting from asymmetric diffusion, provide a qualitatively good match to the main features of the data. This in turn allows us to deduce ice crystal properties. Since the wavelength of the detected light is short compared to the crystal size, these crystal properties do not only include the crystal orientation fabric, but also the average crystal size and shape, as a function of depth. By adding small empirical corrections to this first-principles model, a quantitatively accurate description of the optical properties of the IceCube glacial ice is obtained. In this paper, we present the experimental signature of ice optical anisotropy observed in IceCube LED calibration data, the theory and parametrization of the birefringence effect, the fitting procedures of these parameterizations to experimental data as well as the inferred crystal properties.</p