Miracle-dz/UniFAR-FTUs huggingface dataset:
Calculation of coupled bunch effects in the synchrotron light source BESSY VSR

In the last decades, accelerator based synchrotron radiation (SR) has become a central tool for spectroscopic and structural imaging of samples for a wide range of scientific fields, including solid state physics, life science and information technology. The increasing demand for high brilliance and short pulse length is continuously leading to the upgrade or new construction of SR facilities, among which BESSY Variable Pulse Length Storage Ring (BESSY VSR) is the upgrade project for the third generation light source BESSY II, located at Helmholtz-Zentrum Berlin für Materialien und Energie GmbH (HZB), Germany. It will provide a previously uncovered time regime of intense ps bunches in a multi-user facility, achieved by the novel concept of utilizing super conducting (SC) multi-cell cavities. New technological and accelerator physical challenges need to be addressed. This includes coupled bunch effects, a beam-cavity interaction that causes coupled bunch instabilities (CBIs) and transient beam loading. The former are transverse or longitudinal bunch oscillations that spoil the beam quality and the latter is a steady distortion of the longitudinal dynamics, introduced by unevenness in the bunch fill pattern affecting the bunch length and synchronous phase. In the scope of this thesis, the strength of CBIs driven by longitudinal monopole higher order modes (HOMs) and transverse dipole and quadrupole HOMs is evaluated for BESSY VSR, based on analytic calculations and tracking simulations, and compared to the performance of an active bunch-by-bunch feedback (BBFB). Algorithms for tracking codes are derived, and a semi-empirical formula for the estimation of transverse quadrupole CBIs is presented. CBI studies are an integral part of the benchmarking of the cavity models for BESSY VSR and have been accompanying and influencing their entire design process. Based on the BESSY VSR cavity model with highly advanced HOM damping, beam stability is likely to be reached with a BBFB system, independent of the bunch fill pattern. Additionally, measurements of CBIs have been performed at BESSY II and the Metrology Light Source of the Physikalisch-Technische Bundesanstalt (MLS), where the longitudinal long range impedance was characterized. Transient beam loading is evaluated by means of analytic formulas and new experimentally verified tracking codes. For the baseline bunch fill pattern of BESSY VSR, it is shown that the particular setup of cavity frequencies amplifies the transient effect on the long bunch, limiting its elongation and potentially resulting in increased Touschek losses, which has already triggered studies regarding alternative bunch fill pattern.
Detectable Anthropogenic Intensification of the Summer Compound Hot and Dry Events Over Global Land Areas

Compound hot and dry events (CHDEs) pose an increasing threat to global warming and have received growing attention in recent decades. We conducted a detection and attribution analysis (D&A) using the optimal fingerprint technique to analyze the changes in observed CHDEs at continental and sub‐continental scales from 1961 to 2014. The responses of CHDEs changes to anthropogenic (ANT), greenhouse gases (GHG), aerosols (AER), and natural (NAT) forcings were obtained from the Coupled Model Intercomparison Project phase 6 forcing experiment. In a two‐signal D&A analysis that considered ANT and NAT simultaneously, ANT signals were robustly detected and separated from NAT in all continental domains and more than 65% of subcontinental domains (29 out of 44 domains). The trend attributed to the ANT forcing is comparable to the observed trend over domains where the ANT signal is detectable. We also conducted a three‐signal D&A analysis that regressed observation onto GHG, AER, and NAT simultaneously. The GHG signals were detectable in all continents except Oceania, and it contributed dominantly to the observed trend over 22 out of 29 regions where ANT signals had emerged. Multivariate biases correction can largely reduce the models' biases in simulating the marginal distribution and the dependence structure, which can provide a more accurate future risk of CDHEs. We found that limiting global warming to 1.5℃ rather than 2.0℃ can significantly mitigate the impact of compound events in most areas of global land, particularly in South America, Africa, and Oceania.
Timing and Provenance of Volcanic Fluxes Around the Permian‐Triassic Boundary Mass Extinction in South China: U‐Pb Zircon Geochronology, Volcanic Ash Geochemistry and Mercury Isotopes

Anomalous mercury (Hg) contents recorded near the Permian‐Triassic boundary (PTB) are often linked to Siberian Traps Large Igneous Province (STLIP) volcanism and the Permian‐Triassic boundary mass extinction (PTBME). However, mounting evidence indicates that the relation between STLIP volcanism and Hg “anomalies” is not straightforward. This study focuses on the timing and provenance of volcanic fluxes around the PTBME in South China. We constrain carbon isotope (δ13C) and Hg concentration and isotope records by utilizing high‐precision U‐Pb zircon ages from two expanded deep‐water marine sections spanning the Late Permian to Early Triassic in the Nanpanjiang Basin. Results reveal two episodes of Hg enrichment. The oldest episode predates the onset of a large negative δ13C excursion, which is documented to be older than 252.07 ± 0.130 Ma. The second episode occurred between 251.822 ± 0.060 and 251.589 ± 0.062 Ma, coinciding with the nadir of the δ13C excursion. Volcanic ash geochemistry and Hg isotope compositions suggest that mercury was mainly sourced from subduction‐related volcanic arc magmatism in the Tethys region, which peaked between 251.668 ± 0.079 and 251.589 ± 0.052 Ma. These results are compatible with suggestions that regional arc volcanism contributed to the causes of the PTBME in South China and provide evidence that Hg anomalies close to the PTB are not a reliable stratigraphic marker for the PTB extinction event. This study demonstrates that relations between volcanism, environmental perturbations and mass extinction during the Permian‐Triassic transition are better resolved with the aid of high‐precision U‐Pb zircon ages.
The Atlas of Morocco: A Plume‐Assisted Orogeny

We explore the connections between crustal shortening, volcanism, and mantle dynamics in the Atlas of Morocco. In response to compressional forces and strain localization, this intraplate orogen has evolved far from convergent plate margins. Convective effects, such as lithospheric weakening and plume‐related volcanism, contributed in important ways to the building of high topography. We seek to better understand how crustal and mantle processes interacted during the Atlas' orogeny by combining multiple strands of observations, including new and published data. Constraints on crustal and thermal evolution are combined with new analyses of topographic evolution, petrological, and geochemical data from the Anti‐Atlas volcanic fields, and a simple numerical model of the interactions among crustal deformation, a mantle plume, and volcanism. Our findings substantiate that: (a) crustal deformation and exhumation accelerated during the middle/late Miocene, contemporaneous with the onset of volcanism; (b) volcanism has an anorogenic signature with a deep source; (c) a dynamic mantle upwelling supports the high topography. We propose that a mantle plume and the related volcanism weakened the lithosphere beneath the Atlas and that this favored the localization of crustal shortening along pre‐existing structures during plate convergence. This convective‐tectonic sequence may represent a general mechanism for the modification of continental plates throughout the thermo‐chemical evolution of the supercontinental cycle.
Study of groundwater recharge using combined unsaturated‐and saturated‐zone chloride mass balance methods

Understanding groundwater recharge mechanisms is essential for reliable groundwater recharge estimation for sustainable groundwater resource assessment and management, especially in arid and semiarid areas. In this study, chloride, together with stable isotopes (18O and 2H), in 1‐year rainfall, soil water from representative profiles, and groundwater samples, collected in the Ordos Plateau, northern China were analysed. Groundwater recharge was estimated using unsaturated‐ and saturated‐zone chloride mass balance (CMB). An equation that describes the relationship between chloride concentrations in saturated zone water (Csz) and soil water residence time (τ) was derived. With the help of the relationship, chloride concentrations in unsaturated zone water (Cuz) and in groundwater (Csz) can be used to uncover water flow and chloride transport in the unsaturated zone. The relationship between Csz and Cuz indicates that, the groundwater was recharged mainly by intense rainfall events. Small rainfall events did not lead to groundwater recharge but contributed to the flux of chloride to soil surface. Stable isotopic compositions of 18O and 2H provided corroborative evidence of the recharge processes. The relationship between Csz and τ indicates further that there is no source of chloride in the groundwater other than that from precipitation. Thus, Csz can give more reliable recharge estimates. Cuz was influenced by heavy rainfall‐induced runoff, run‐on and bypass flow events and cannot give reliable recharge estimates. However, if used jointly with Csz, Cuz can help to gain insights into recharge processes and yield groundwater recharge estimates with higher certainty. The outcomes of this study can assist for groundwater recharge investigation and assessment in regions where the assumptions and boundary conditions necessary for the correct application of the CMB method may not be met.
‘Like a frog in a well'. A qualitative study of adolescent girls’ life aspirations in Western Nepal

ABSTRACT Adolescents’ aspirations are important for a healthy transition into adulthood. Knowledge about girls’ aspirations and their formation in a low-income context is scant. Framed within life course theory, this qualitative study aimed to understand adolescent girls’ life aspirations, with a specific focus on school, work, family life, health and diets, and explore how aspirations are shaped within girls’ everyday life context, in Nawalpur and Parasi, two districts in the plains of Western Nepal. Data collection involved interviewing 17 adolescent girls (11–19 years) using creative elicitation techniques: timeline drawing and network mapping. Thematic analyses revealed unique aspiration profiles of younger, older, and married adolescent girls. While younger girls were present-oriented and aspired high, older girls balanced aspirations with reality and in turn, adjusted their aspirations. Married women had mostly resigned themselves to their present lives and transferred their lost aspirations onto their children. Findings underscore how girls’ feelings, others in their daily lives, gendered norms, and structural factors, are related to different domains of aspirations during different stages of adolescence. Results give direction to integrated policies and programs that aim to sustain and cultivate adolescent girls’ aspirations at specific stages of adolescence.
UV resistance and biodegradation of PLA-based polymeric blends doped with PBS, PBAT, TPS

Abstract The design of new biodegradable polymers is important for solving the fossil resource and environmental pollution problems associated with conventional plastics. New PLA-based mixtures with the addition of PBAT, PBS and TPS, with different contents, were prepared to investigate their behavior after accelerated aging, as well as their potential for the biodegradation process. Their mechanical properties, mass, hardness, morphology, gloss and color change during UV irradiation progress, have been investigated. The samples were exposed to UV radiation for 21 d, their accelerated aging properties, were assessed weekly and compared with the non-aged samples. The degree of disintegration was determined after soil burial. The results showed that the mechanical properties, especially formability, as well as gloss and color, changed significantly after accelerated aging. All tested matrices are degradable, as shown by soil burial tests. Testing the stability of the functional properties of biodegradable plastics, which are assessed by end users, is important for the wider use of these plastics.
Divergent iron-regulatory states contribute to heterogeneity in breast cancer aggressiveness

Primary tumors with similar mutational profiles can progress to vastly different outcomes where transcriptional state, rather than mutational profile, predicts prognosis. A key challenge is to understand how distinct tumor cell states are induced and maintained. In triple negative breast cancer cells, invasive behaviors and aggressive transcriptional signatures linked to poor patient prognosis can emerge in response to contact with collagen type I. Herein, collagen-induced migration heterogeneity within a TNBC cell line was leveraged to identify transcriptional programs associated with invasive versus non-invasive phenotypes and implicate molecular switches. Phenotype-guided sequencing revealed that invasive cells upregulate iron uptake and utilization machinery, anapleurotic TCA cycle genes, actin polymerization promoters, and a distinct signature of Rho GTPase activity and contractility regulating genes. The non-invasive cell state is characterized by actin and iron sequestration modules along with glycolysis gene expression. These unique tumor cell states are evident in patient tumors and predict divergent outcomes for TNBC patients. Glucose tracing confirmed that non-invasive cells are more glycolytic than invasive cells, and functional studies in cell lines and PDO models demonstrated a causal relationship between phenotype and metabolic state. Mechanistically, the OXPHOS dependent invasive state resulted from transient HO-1 upregulation triggered by contact with dense collagen that reduced heme levels and mitochondrial chelatable iron levels. This induced expression of low cytoplasmic iron response genes regulated by ACO1/IRP1. Knockdown or inhibition of HO-1, ACO1/IRP1, MRCK, or OXPHOS abrogated invasion. These findings support an emerging theory that heme and iron flux serve as important regulators of TNBC aggressiveness.
Persistence of intact HIV-1 proviruses in the brain during antiretroviral therapy

HIV-1 reservoir cells that circulate in peripheral blood during suppressive antiretroviral therapy (ART) have been well characterized, but little is known about the dissemination of HIV-1-infected cells across multiple anatomical tissues, especially the central nervous system (CNS). Here, we performed single-genome, near full-length HIV-1 next-generation sequencing to evaluate the proviral landscape in distinct anatomical compartments, including multiple CNS tissues, from 3 ART-treated participants at autopsy. While lymph nodes and, to a lesser extent, gastrointestinal and genitourinary tissues represented tissue hotspots for the persistence of intact proviruses, we also observed intact proviruses in CNS tissue sections, particularly in the basal ganglia. Multi-compartment dissemination of clonal intact and defective proviral sequences occurred across multiple anatomical tissues, including the CNS, and evidence for the clonal proliferation of HIV-1-infected cells was found in the basal ganglia, in the frontal lobe, in the thalamus and in periventricular white matter. Deep analysis of HIV-1 reservoirs in distinct tissues will be informative for advancing HIV-1 cure strategies.
Intent matters: how flow and forms of information impact collective navigation

The phenomenon of collective navigation has received considerable interest in recent years. A common line of thinking, backed by theoretical studies, is that collective navigation can improve navigation efficiency through the ‘many-wrongs’ principle, whereby individual error is reduced by comparing the headings of neighbours. When navigation takes place in a flowing environment, each individual’s trajectory is influenced by drift. Consequently, a potential discrepancy emerges between an individual’s intended heading and its actual heading. In this study we develop a theoretical model to explore whether collective navigation benefits are altered according to the form of heading information transmitted between neighbours. Navigation based on each individual’s intended heading is found to confer robust advantages across a wide spectrum of flows, via both a marked improvement in migration times and a capacity for a group to overcome flows unnavigable by solitary individuals. Navigation based on individual’s actual headings is far less effective, only offering an improvement under highly favourable currents. For many currents, sharing actual heading information can even lead to journey times that exceed those of individual navigators.
Comparative genomics between Colombian clinical isolates of Monophasic Variant Salmonella Typhimurium and international clonal lineages

In Colombia, Salmonella Typhimurium monophasic variant (MVST) is the fourth serovar recovered in laboratory surveillance of acute diarrheal disease (ADD). Given its rapid worldwide dissemination, increasing multidrug-resistance, and the emergence of different endemic clones, it is considered an emerging public health problem. This study compared 21 Colombian clinical isolates and 27 MVST genomes from Europe, Asia, the United States, and Australia to know the gene pool and to define similarities with international clones. Eighty percent of the Colombian MVST isolates formed a lineage divided into 2 clones, while 4 genomes were associated with the European ST34 and USA lineages. These two Colombian clones emerged in relatively recent events, in which possible spread was established during 2011 and 2012, exhibiting a diversity of plasmids and prophages, adapting to the Colombian population after differentiation. These results are a clear example of the high plasticity of MVST, evidencing the need for active genomic surveillance to monitor the circulation of new clonal lineages.
Locomotor effects of a fibrosis-based immune response in stickleback fish

The vertebrate immune system provides an impressively effective defense against parasites and pathogens. However, these benefits must be balanced against a range of costly side-effects including energy loss and risks of auto-immunity. These costs might include biomechanical impairment of movement, but little is known about the intersection between immunity and biomechanics. Here, we show that a fibrosis immune response in threespine stickleback (Gasterosteus aculeatus) has collateral effects on their locomotion. When freshwater stickleback are infected with the tapeworm parasite Schistocephalus solidus, they face an array of fitness consequences ranging from impaired body condition and fertility to an increased risk of mortality. To fight the infection, some stickleback will initiate a fibrosis immune response in which they produce excess collagenous tissue in their coelom. Although fibrosis is effective at reducing infection, some populations of stickleback actively suppress this immune response, possibly because the costs of fibrosis outweigh the benefits. Here we quantify the locomotor effects of the fibrosis immune response in the absence of parasites to investigate whether there are collateral costs of fibrosis that could help explain why some fish forego this effective defense. To do this, we induce fibrosis in stickleback and then test their C-start escape performance. Additionally, we measure the severity of fibrosis, body stiffness, and body curvature during the escape response. We were able to estimate performance costs of fibrosis by including these variables as intermediates in a structural equation model. This model reveals that among control fish without fibrosis, there is a performance cost associated with increased body stiffness. However, fish with fibrosis did not experience this cost but rather displayed increased performance with higher fibrosis severity. This result demonstrates that the adaptive landscape of immune responses can be complex with the potential for wide reaching and unexpected fitness consequences.
Opto-seq reveals input-specific immediate early gene induction in ventral tegmental area cell types

The ventral tegmental area (VTA) is a critical node in circuits governing motivated behavior and is home to diverse populations of neurons that release dopamine, GABA, glutamate, or combinations of these neurotransmitters. The VTA receives inputs from many brain regions, but a comprehensive understanding of input-specific activation of VTA neuronal subpopulations is lacking. To address this, we combined optogenetic stimulation of select VTA inputs with single-nucleus RNA sequencing (snRNAseq) and highly multiplexed in situ hybridization to identify distinct neuronal clusters and characterize their spatial distribution and activation patterns. Quantification of immediate early gene (IEG) expression revealed that different inputs activated select VTA subpopulations, which demonstrated cell-type specific IEG programs. Within dopaminergic subpopulations IEG induction levels correlated with differential expression of ion channel genes. This new transcriptomics-guided circuit analysis reveals the diversity of VTA activation driven by distinct inputs and provides a resource for future analysis of VTA cell types.
Cognitive Model Discovery via Disentangled RNNs

Computational cognitive models are a fundamental tool in behavioral neuroscience. They instantiate in software precise hypotheses about the cognitive mechanisms underlying a particular behavior. Constructing these models is typically a difficult iterative process that requires both inspiration from the literature and the creativity of an individual researcher. Here, we adopt an alternative approach to learn parsimonious cognitive models directly from data. We fit behavior data using a recurrent neural network that is penalized for carrying information forward in time, leading to sparse, interpretable representations and dynamics. When fitting synthetic behavioral data from known cognitive models, our method recovers the underlying form of those models. When fit to laboratory data from rats performing a reward learning task, our method recovers simple and interpretable models that make testable predictions about neural mechanisms.
High performers demonstrate greater neural synchrony than low performers across behavioral domains

Heterogeneity in brain activity gives rise to heterogeneity in behavior, which in turn comprises our distinctive characteristics as individuals. Studying the path from brain to behavior, however, often requires making assumptions about how similarity in behavior scales with similarity in brain activity. Here, we expand upon recent work which proposes a theoretical framework for testing the validity of such assumptions. Using intersubject representational similarity analysis in two independent movie-watching fMRI datasets, we probe how brain-behavior relationships vary as a function of behavioral domain and participant sample. We find evidence that, in some cases, the neural similarity of two individuals is not correlated with behavioral similarity. Rather, individuals with higher behavioral scores are more similar to other high scorers whereas individuals with lower behavioral scores are dissimilar from everyone else. Ultimately, our findings motivate a more extensive investigation of both the structure of brain-behavior relationships and the tacit assumption that people who behave similarly will demonstrate shared patterns of brain activity.