Miracle-dz/UniFAR-FTUs huggingface dataset:
Non-linear mirror instability

Slow dynamical changes in magnetic-field strength and invariance of the particles' magnetic moments generate ubiquitous pressure anisotropies in weakly collisional, magnetized astrophysical plasmas. This renders them unstable to fast, small-scale mirror and firehose instabilities, which are capable of exerting feedback on the macroscale dynamics of the system. By way of a new asymptotic theory of the early nonlinear evolution of the mirror instability in a plasma subject to slow shearing or compression, we show that the instability does not saturate quasilinearly at a steady, low-amplitude level. Instead, the trapping of particles in small-scale mirrors leads to nonlinear secular growth of magnetic perturbations, $\delta B/B \propto t^{2/3}$. Our theory explains recent collisionless simulation results, provides a prediction of the mirror evolution in weakly collisional plasmas and establishes a foundation for a theory of nonlinear mirror dynamics with trapping, valid up to $\delta B/B =O(1)$.
The complex circumstellar and circumbinary environment of V356 Sgr

We analyze 45 spectropolarimetric observations of the eclipsing, interacting binary star V356 Sgr, obtained over a period of 21 years, to characterize the geometry of the system's circumstellar material. After removing interstellar polarization from these data, we find the system exhibits a large intrinsic polarization signature arising from electron scattering. In addition, the lack of repeatable eclipses in the polarization phase curves indicates the presence of a substantial pool of scatterers not occulted by either star. We suggest that these scatterers form either a circumbinary disk coplanar with the gainer's accretion disk or an elongated structure perpendicular to the orbital plane of V356 Sgr, possibly formed by bipolar outflows. We also observe small-scale, cycle-to-cycle variations in the magnitude of intrinsic polarization at individual phases, which we interpret as evidence of variability in the amount of scattering material present within and around the system. This may indicate a mass transfer or mass loss rate that varies on the time-scale of the system's orbital period. Finally, we compare the basic polarimetric properties of V356 Sgr with those of the well studied beta Lyr system; the significant differences observed between the two systems suggests diversity in the basic circumstellar geometry of Roche-lobe overflow systems
STELLAR NUCLEI AND INNER POLAR DISKS IN LENTICULAR GALAXIES

I analyze statistics of the stellar population properties for stellar nuclei and bulges of nearby lenticular galaxies in different environments by using panoramic spectral data of the integral-field spectrograph SAURON retrieved from the open archive of the Isaac Newton Group. I also estimate the fraction of nearby lenticular galaxies having inner polar gaseous disks by exploring the volume-limited sample of early-type galaxies of the ATLAS-3D survey. By inspecting the two-dimensional velocity fields of the stellar and gaseous components with the running tilted-ring technique, I have found seven new cases of inner polar disks. Together with those, the frequency of inner polar disks in nearby S0 galaxies reaches 10%, which is much higher than the frequency of large-scale polar rings. Interestingly, the properties of the nuclear stellar populations in the inner polar ring hosts are statistically the same as those in the whole S0 sample, implying similar histories of multiple gas-accretion events from various directions.
Influence of interface potential on the effective mass in Ge nanostructures

The role of the interface potential on the effective mass of charge carriers is elucidated in this work. We develop a new theoretical formalism using a spatially dependent effective mass that is related to the magnitude of the interface potential. Using this formalism, we studied Ge quantum dots (QDs) formed by plasma enhanced chemical vapour deposition (PECVD) and co-sputtering (sputter). These samples allowed us to isolate important consequences arising from differences in the interface potential. We found that for a higher interface potential, as in the case of PECVD QDs, there is a larger reduction in the effective mass, which increases the confinement energy with respect to the sputter sample. We further understood the action of O interface states by comparing our results with Ge QDs grown by molecular beam epitaxy. It is found that the O states can suppress the influence of the interface potential. From our theoretical formalism, we determine the length scale over which the interface potential influences the effective mass.
Neural signatures of reading-related orthographic processing in braille

Blind readers use a tactile reading systems consisting of raised dot arrays: braille/⠃⠗⠇. How does the human brain implement reading by touch? The current study looked for signatures of reading-specific orthographic processes in braille, separate from low-level somatosensory responses and semantic retrieval. Of specific interest were responses in posterior parietal cortices (PPC), because of their role in high-level tactile perception. Congenitally blind, proficient braille readers read real words and pseudowords by touch while undergoing fMRI. We leveraged the system of contractions in English braille, where one or more braille cells can represent combinations of English print letters (e.g., “ing” ⠬, “one” ⠐⠕), making it possible to separate physical and uncontracted letter-length. All words in the study consisted of 4 braille cells, but their corresponding Roman spellings varied from 4 to 7 letters (e.g., “con-c-er-t” ⠒⠉⠻⠞. contracted: 4 cells; uncontracted: 7 letters). We found that the bilateral supramarginal gyrus (SMG) in the PPC increased its activity as the uncontracted word length increased. By contrast, in the hand region of primary somatosensory cortex (S1), activity increased as a function of a low-level somatosensory feature: dot-number per word. The PPC also showed greater response to pseudowords than real words and distinguished between real and pseudowords in multi-voxel-pattern analysis. Parieto-occipital, early visual and ventral occipito-temporal, as well as prefrontal cortices also showed sensitivity to the real-vs-pseudoword distinction. We conclude that PPC is involved in sublexical orthographic processing for braille, possibly due to braille’s tactile modality. Significance statement Blind readers use tactile reading systems of raised dot arrays: braille. To identify signatures of orthographic processing for reading by touch, and dissociate it from tactile and linguistic process, we leveraged the system of contractions in English braille, where one or more braille characters represents combinations of English print letters. Blind proficient braille readers read real words and pseudowords during fMRI scans. While all words consisted of 4 braille characters, the uncontracted spelling ranged from 4-7 letters. Activity in bilateral-posterior-parietal cortices, just posterior to primary-somatosensory cortex, increased with uncontracted word length, independent of tactile complexity (number of raised dots per word). By contrast, primary-somatosensory activity increased with tactile complexity. The posterior-parietal cortices contribute to tactile reading.
Sensory tuning in neuronal movement commands

Movement control is critical for successful interaction with our environment. However, movement does not occur in complete isolation of sensation, and this is particularly true of eye movements. Here we show that the neuronal eye movement commands emitted by the superior colliculus, a structure classically associated with oculomotor control, encompass a robust visual sensory representation of eye movement targets. Thus, similar saccades towards different images are associated with different saccade-related “motor” bursts. Such sensory tuning in superior colliculus saccade motor commands appeared for all image manipulations that we tested, from simple visual features to real-life object images, and it was also strongest in the most motor neurons in the deeper collicular layers. Visual-feature discrimination performance in the motor commands was also stronger than in visual responses. Comparing superior colliculus motor command feature discrimination performance to that in the primary visual cortex during steady gaze fixation revealed that collicular motor bursts possess a reliable peri-saccadic sensory representation of the peripheral saccade target’s visual appearance, exactly when retinal input is most uncertain. Consistent with this, we found that peri-saccadic perception is altered as a function of saccade target visual features. Therefore, superior colliculus neuronal movement commands likely serve a fundamentally sensory function.
FIRST INSIGHTS IN A NON-RODENT MODEL SPECIES OF THE OLFACTORY LIMBUS. THE RED FOX (Vulpes vulpes) AS A CASE IN POINT

The mammalian olfactory systems can be divided into several subsystems based on the anatomical location of their neuroreceptor cells and the family of receptors they express. The more in depth studied systems are the main olfactory system and the vomeronasal system, whose first integrative enters are the main and the accessory olfactory bulb, respectively. In addition, there is a range of olfactory subsystems which converge to the transition zone located between the main olfactory bulb and the accessory olfactory bulb. , which has been termed as olfactory limbus (OL) and includes specialized glomeruli which receive uncanonical sensory afferences and interact with the MOB and AOB. Beyond the laboratory rodents, there is a lack of information regarding the olfactory subsystems of carnivores. We have focused on the specific study of the olfactory limbus of the fox, performing serial histological sections, general and specific histological stainings, including both double and simple immunohistochemical and lectin-histochemical labeling techniques. As a result, we have been able to determine that the OL of the fox shows an uncommon development with a high degree of development and complexity. This makes this species a novel mammalian model that could provide a wider understanding of non-canonical pathways involved in the processing of chemosensory cues.
Silencing hippocampal CA2 reduces behavioral flexibility in spatial learning

The hippocampus is a key structure involved in learning and remembering spatial information. However the extent to which hippocampal region CA2 is involved in these processes remains unclear. Here we show that chronically silencing dorsal CA2 impairs reversal learning in the Morris water maze. After platform relocation, CA2-silenced mice spent more time in the vicinity of the old platform location and less time in the new target quadrant. Accordingly, behavioral strategy analysis revealed increased perseverance in navigating to the old location during the first day and an increased use of non-spatial strategies during the second day of reversal learning. Confirming previous indirect indications, these results demonstrate that CA2 is recruited when mice must flexibly adapt their behavior as task contingencies change. We discuss how these findings can be explained by recent theories of CA2 function and outline testable predictions to understand the underlying neural mechanisms. Demonstrating a direct involvement of CA2 in spatial learning, this work lends further support to the notion that CA2 plays a fundamental role in hippocampal information processing.
Clinical PARP inhibitors allosterically induce PARP2 retention on DNA

PARP1 and PARP2 detect DNA breaks, which activates their catalytic production of poly(ADP-ribose) that recruits repair factors and releases PARP1/2 from DNA. PARP inhibitors (PARPi) are used in cancer treatment and target PARP1/2 catalytic activity, interfering with repair and increasing PARP1/2 persistence on DNA damage. Additionally, certain PARPi exert allosteric effects that increase PARP1 retention on DNA. However, no clinical PARPi exhibit this allosteric behavior toward PARP1. In contrast, we show that certain clinical PARPi exhibit an allosteric effect that retains PARP2 on DNA breaks in a manner that depends on communication between the catalytic and DNA-binding regions. Using a PARP2 mutant that mimics an allosteric inhibitor effect, we observed increased PARP2 retention at cellular damage sites. The new PARPi AZD5305 also exhibited a clear reverse allosteric effect on PARP2. Our results can help explain the toxicity of clinical PARPi and suggest ways to improve PARPi moving forward.
Flagellar Genes Are Associated with the Colonization Persistence Phenotype of the Drosophila melanogaster Microbiota

Despite the growing body of research on the microbiota, the mechanisms by which the microbiota colonizes a host can still be further elucidated. This study identifies bacterial genes that are associated with the colonization persistence phenotype of the microbiota in Drosophila melanogaster, which reveals specific bacterial factors that influence the establishment of the microbiota within its host. ABSTRACT In this work, we use Drosophila melanogaster as a model to identify bacterial genes necessary for bacteria to colonize their hosts independent of the bulk flow of diet. Early work on this model system established that dietary replenishment drives the composition of the D. melanogaster gut microbiota, and subsequent research has shown that some bacterial strains can stably colonize, or persist within, the fly independent of dietary replenishment. Here, we reveal transposon insertions in specific bacterial genes that influence the bacterial colonization persistence phenotype by using a gene association approach. We initially established that different bacterial strains persist at various levels, independent of dietary replenishment. We then repeated the analysis with an expanded panel of bacterial strains and performed a metagenome-wide association (MGWA) study to identify distinct bacterial genes that are significantly correlated with the level of colonization by persistent bacterial strains. Based on the MGWA study, we tested if 44 bacterial transposon insertion mutants from 6 gene categories affect bacterial persistence within the flies. We identified that transposon insertions in four flagellar genes, one urea carboxylase gene, one phosphatidylinositol gene, one bacterial secretion gene, and one antimicrobial peptide (AMP) resistance gene each significantly influenced the colonization of D. melanogaster by an Acetobacter fabarum strain. Follow-up experiments revealed that each flagellar mutant was nonmotile, even though the wild-type strain was motile. Taken together, these results reveal that transposon insertions in specific bacterial genes, including motility genes, are necessary for at least one member of the fly microbiota to persistently colonize the fly. IMPORTANCE Despite the growing body of research on the microbiota, the mechanisms by which the microbiota colonizes a host can still be further elucidated. This study identifies bacterial genes that are associated with the colonization persistence phenotype of the microbiota in Drosophila melanogaster, which reveals specific bacterial factors that influence the establishment of the microbiota within its host. The identification of specific genes that affect persistence can help inform how the microbiota colonizes a host. Furthermore, a deeper understanding of the genetic mechanisms of the establishment of the microbiota could aid in the further development of the Drosophila microbiota as a model for microbiome research.
Arithmetic and Hyperbolic Structures in String Theory

This thesis consists of an introductory text followed by two separate parts which may be read independently of each other. In Part I we analyze certain hyperbolic structures arising when studying gravity in the vicinity of spacelike singularities (the BKL-limit). In this limit, spatial points decouple and the dynamics exhibits ultralocal behaviour which may be mapped to an auxiliary problem given in terms of a (possibly chaotic) hyperbolic billiard. In all supergravities arising as low-energy limits of string theory or M-theory, the billiard dynamics takes place within the fundamental Weyl chambers of certain hyperbolic Kac-Moody algebras, suggesting that these algebras generate hidden infinite-dimensional symmetries of gravity. We investigate the modification of the billiard dynamics when the original gravitational theory is formulated on a compact spatial manifold of arbitrary topology, revealing fascinating mathematical structures known as galleries. We further use the conjectured hyperbolic symmetry E10 to generate and classify certain cosmological (S-brane) solutions in eleven-dimensional supergravity. Finally, we show in detail that eleven-dimensional supergravity and massive type IIA supergravity are dynamically unified within the framework of a geodesic sigma model for a particle moving on the infinite-dimensional coset space E10/K(E10). Part II of the thesis is devoted to a study of how (U-)dualities in string theory provide powerful constraints on perturbative and non-perturbative quantum corrections. These dualities are typically given by certain arithmetic groups G(Z) which are conjectured to be preserved in the effective action. The exact couplings are given by moduli-dependent functions which are manifestly invariant under G(Z), known as automorphic forms. We discuss in detail various methods of constructing automorphic forms, with particular emphasis on a special class of functions known as (non-holomorphic) Eisenstein series. We provide detailed examples for the physically relevant cases of SL(2,Z) and SL(3,Z), for which we construct their respective Eisenstein series and compute their (non-abelian) Fourier expansions. We also discuss the possibility that certain generalized Eisenstein series, which are covariant under the maximal compact subgroup K(G), could play a role in determining the exact effective action for toroidally compactified higher derivative corrections. Finally, we propose that in the case of rigid Calabi-Yau compactifications in type IIA string theory, the exact universal hypermultiplet moduli space exhibits a quantum duality group given by the Picard modular group SU(2,1;Z[i]). To verify this proposal we construct an SU(2,1;Z[i])-invariant Eisenstein series, and we present preliminary results for its Fourier expansion which reveals the expected contributions from D2-brane and NS5-brane instantons.
Turbulent states in plane Couette flow with rotation

Shearing and rotational forces in fluids can significantly alter the transport of momentum. A numerical investigation was undertaken to study the role of these forces using plane Couette flow subject to rotation about an axis perpendicular to both wall-normal and streamwise directions. Using a set of progressively higher Reynolds numbers up to Re = 5200, we find that the momentum flux, measured by the wall shear stress, for a given Re is a non-monotonic function of rotation number, Ro. For low-to-moderate Reynolds numbers, we find a maximum that is associated with flow fields that are dominated by downstream vortices and calculations of 2D vortices capture the maximum also quantitatively. For higher Reynolds numbers, a second stronger maximum emerges at smaller rotation numbers, closer to non-rotating plane Couette flow. It is carried by flows with a markedly 3D structure and cannot be captured by 2D vortex studies. As the Reynolds number increases, this maximum becomes stronger and eventually overtakes the one associated with the 2D flow state.
Acyl plastoquinol is a major substance that co-migrates with triacylglycerol in cyanobacteria

Various studies have suggested the presence of triacylglycerol in cyanobacteria, but no convincing evidence exists. We purified a substance co-migrating with triacylglycerol and determined its structure using mass spectrometry, gas chromatography, and 1H- and 13C-NMR. The major components were palmitoyl and stearoyl plastoquinols (acyl plastoquinol). Acyl plastoquinol has never been described before. The level of acyl plastoquinol was 0.4% of the total lipids. We still do not have clear evidence for the presence of triacylglycerol. If present, the maximum triacylglycerol level, must be at most 10% of acyl plastoquinol or less. The Synechocystis Slr2103 protein was suggested to synthesize triacylglycerol, but the product could be acyl plastoquinol. The possible roles of this novel compound in photosynthesis should be a new focus of research.
Simulating the formation of massive seed black holes in the early Universe – II. Impact of rate coefficient uncertainties

We investigate how uncertainties in the chemical and cooling rate coefficients relevant for a metal-free gas influence our ability to determine the critical ultraviolet field strength required to suppress H2 cooling in high-redshift atomic cooling halos. The suppression of H2 cooling is a necessary prerequisite for the gas to undergo direct collapse and form an intermediate mass black hole. These black holes can then act as seeds for the growth of the supermassive black holes (SMBHs) observed at redshifts $z \sim 6$. The viability of this model for SMBH formation depends on the critical ultraviolet field strength, Jcrit: if this is too large, then too few seeds will form to explain the observed number density of SMBHs. We show in this paper that there are five key chemical reactions whose rate coefficients are uncertain enough to significantly affect Jcrit. The most important of these is the collisional ionization of hydrogen by collisions with other hydrogen atoms, as the rate for this process is very poorly constrained at the low energies relevant for direct collapse. The total uncertainty introduced into Jcrit by this and the other four reactions could in the worst case approach a factor of five. We also show that the use of outdated or inappropriate values for the rates of some chemical reactions in previous studies of the direct collapse mechanism may have significantly affected the values of Jcrit determined by these studies.