julilili42/papers huggingface dataset:
The Evolution of Ecological Diversity in Acidobacteria
2022-02-02

Acidobacteria occur in a large variety of ecosystems worldwide and are particularly abundant and highly diverse in soils. In spite of their diversity, only few species have been characterized to date which makes Acidobacteria one of the most poorly understood phyla among the domain Bacteria. We used a culture-independent niche modeling approach to elucidate ecological adaptations and their evolution for 4,154 operational taxonomic units (OTUs) of Acidobacteria across 150 different, comprehensively characterized grassland soils in Germany. Using the relative abundances of their 16S rRNA gene transcripts, the responses of active OTUs along gradients of 41 environmental variables were modeled using hierarchical logistic regression (HOF), which allowed to determine values for optimum activity for each variable (niche optima). By linking 16S rRNA transcripts to the phylogeny of full 16S rRNA gene sequences, we could trace the evolution of the different ecological adaptations during the diversification of Acidobacteria . This approach revealed a pronounced ecological diversification even among acidobacterial sister clades. Although the evolution of habitat adaptation was mainly cladogenic, it was disrupted by recurrent events of convergent evolution that resulted in frequent habitat switching within individual clades. Our findings indicate that the high diversity of soil acidobacterial communities is largely sustained by differential habitat adaptation even at the level of closely related species. A comparison of niche optima of individual OTUs with the phenotypic properties of their cultivated representatives showed that our niche modeling approach (1) correctly predicts those physiological properties that have been determined for cultivated species of Acidobacteria but (2) also provides ample information on ecological adaptations that cannot be inferred from standard taxonomic descriptions of bacterial isolates. These novel information on specific adaptations of not-yet-cultivated Acidobacteria can therefore guide future cultivation trials and likely will increase their cultivation success.
Aligned Stacking of Nanopatterned 2D Materials for High-Resolution 3D Device Fabrication
2022-02-02

Two-dimensional materials can be combined by placing individual layers on top of each other, so that they are bound only by their van der Waals interaction. The sequence of layers can be chosen arbitrarily, enabling an essentially atomic-level control of the material and thereby a wide choice of properties along one dimension. However, simultaneous control over the structure in the in-plane directions is so far still rather limited. Here, we combine spatially controlled modifications of 2D materials, using focused electron irradiation or electron beam induced etching, with the layer-by-layer assembly of van der Waals heterostructures. The presented assembly process makes it possible to structure each layer with an arbitrary pattern prior to the assembly into the heterostructure. Moreover, it enables a stacking of the layers with accurate lateral alignment, with an accuracy of currently 10 nm, under observation in an electron microscope. Together, this enables the fabrication of almost arbitrary 3D structures with highest spatial resolution.
Echinococcus multilocularis specific antibody, systemic cytokine, and chemokine levels, as well as antigen-specific cellular responses in patients with progressive, stable, and cured alveolar echinococcosis: A 10-year follow-up
2022-02-02

Background The infestation with Echinococcus multilocularis larvae may persist in humans for up to decades without evident clinical symptoms. Longitudinal investigations are needed to understand the dynamic immunological processes in alveolar echinococcosis (AE) patients associated with an active and progressive, a stable or a regressive course of disease. Methodology/Principal findings This study evaluated the E . multilocularis specific antibody responses, systemic cytokine, and chemokine serum levels over a 10-year follow-up period, as well as cellular responsiveness in AE patients. Our results demonstrate a rapid decrease in antibodies against E . multilocularis specific antigen Em2+. Especially in cured patients, these antibodies remained negative, making them a significant predictor for cured AE. E . multilocularis specific IgG4, and indirect hemagglutination IHA decreased later in time, after around 5 years. While total IgE did not show significant dynamics over the course of disease, E . multilocularis specific IgE decreased after one to two years, and increasing levels were a significant predictor of progressive disease. There was no significant change in systemic IL-8, IL-9, CCL18 or CCL20 serum levels over time. Univariate analysis across groups indicated lower IL-8 levels in cured patients; however, this result could not be confirmed by multivariate analysis. Levels of CCL17 decreased during treatment, especially in cured patients, and thus might serve as a predictive or risk factor for progressive disease. Levels of IL-10 and CCL13 decreased during disease, especially after five and ten years of intervention. The E . multilocularis antigen (EmAg) inducible cellular productions of MCP1(CCL13), TARC(CCL17) and PARC(CCL18) were lowest in patients with cured AE and infection-free controls, while the EmAg inducible cellular production of IFN-γ increased after cure. Significant positive cytokine and chemokine correlations were observed in AE patients for IL-9, IL-10, CCL13(MCP-4), CCL17(TARC) and CCL20(LARC)(for all p&lt;0.001). E . multilocularis specific IgG4 response correlated positively with TARC (p&lt;0.001). Both markers enhanced over time in progressive disease and decreased after cure. The levels of IL-8, IL-10, MCP4 and LARC enhanced with AE regression. Conclusions/Significance Repeated biomarker surveys are advisable to evaluate progression or regression of disease during longitudinal follow-up and such analyses can support imaging techniques and improve staging of AE patients.
Quadruple Target Evaluation of Diversity-Optimized Halogen-Enriched Fragments (HEFLibs) Reveals Substantial Ligand Efficiency for AP2-Associated Protein Kinase 1 (AAK1)
2022-02-02

Fragment-based drug discovery is one of the most utilized approaches for the identification of novel weakly binding ligands, by efficiently covering a wide chemical space with rather few compounds and by allowing more diverse binding modes to be found. This approach has led to various clinical candidates and approved drugs. Halogen bonding, on the other hand, has gained traction in molecular design and lead optimization, but could offer additional benefits in early drug discovery. Screening halogen-enriched fragments (HEFLibs) could alleviate problems associated with the late introduction of such a highly geometry dependent interaction. Usually, the binding mode is then already dominated by other strong interactions. Due to the fewer competing interactions in fragments, the halogen bond should more often act as an anchor point for the binding mode. Previously, we proposed a fragment library with a focus on diverse binding modes that involve halogens for gaining initial affinity and selectivity. Herein, we demonstrate the applicability of these HEFLibs with a small set of diverse enzymes: the histone-lysine N-methyltransferase DOT1L, the indoleamine 2,3-dioxygenase 1 (IDO1), the AP2-associated protein kinase 1 (AAK1), and the calcium/calmodulin-dependent protein kinase type 1G (CAMK1G). We were able to identify various binding fragments via STD-NMR. Using ITC to verify these initial hits, we determined affinities for many of these fragments. The best binding fragments exhibit affinities in the one-digit micromolar range and ligand efficiencies up to 0.83 for AAK1. A small set of analogs was used to study structure-affinity relationships and hereby analyze the specific importance of each polar interaction. This data clearly suggests that the halogen bond is the most important interaction of fragment 9595 with AAK1.
Robust deep learning object recognition models rely on low frequency information in natural images
2022-02-02

ABSTRACT Machine learning models have difficulty generalizing to data outside of the distribution they were trained on. In particular, vision models are usually vulnerable to adversarial attacks or common corruptions, to which the human visual system is robust. Recent studies have found that regularizing machine learning models to favor brain-like representations can improve model robustness, but it is unclear why. We hypothesize that the increased model robustness is partly due to the low spatial frequency preference inherited from the neural representation. We tested this simple hypothesis with several frequency-oriented analyses, including the design and use of hybrid images to probe model frequency sensitivity directly. We also examined many other publicly available robust models that were trained on adversarial images or with data augmentation, and found that all these robust models showed a greater preference to low spatial frequency information. We show that preprocessing by blurring can serve as a defense mechanism against both adversarial attacks and common corruptions, further confirming our hypothesis and demonstrating the utility of low spatial frequency information in robust object recognition.
Posts About Students on Facebook: A Data Ethics Perspective
2022-02-02

Schools and districts use social media to share announcements and build vibrant communities, but alongside such uses run risks to students' privacy and safety. Using a novel data set of 18 million posts on Facebook by schools and school districts in the United States, we sought to establish how frequently photos of students were shared. Using sequential mixed methods, we estimate that around 4.9 million posts included identifiable images of students and that around 725,000 posts included students' first and last names and their approximate location. We discuss the implications of these findings with a data ethics lens.
Durability of Omicron-neutralizing serum activity following mRNA booster immunization in elderly individuals
2022-02-02

Abstract Elderly individuals are at high risk for severe COVID-19. Due to modest vaccine responses compared to younger individuals and the time elapsed since prioritized vaccinations, the emerging immune-evasive Omicron variant of SARS-CoV-2 is a particular concern for the elderly. Here we longitudinally determined SARS-CoV-2-neutralizing serum activity against different variants in a cohort of 37 individuals with a median age of 82 years. Participants were followed for 10 months after an initial two-dose BNT162b2 vaccination and up to 4.5 months after a BNT162b2 booster. Detectable Omicron-neutralizing activity was nearly absent after two vaccinations but elicited in 89% of individuals by the booster immunization. Neutralizing titers against the Wu01, Delta, and Omicron variants showed similar post-boost declines and 81% of individuals maintained detectable activity against Omicron. Our study demonstrates the mRNA booster effectiveness in inducing Omicron neutralizing activity and provides critical information on vaccine response durability in the highly vulnerable elderly population.
Millennial-scale Land-surface Temperature and Soil Moisture Reconstruction Derived From Last Glacial European Loess Sequences
2022-02-02

Abstract The climate of the last 50,000 years has been punctuated by oscillations on millennial-to-centennial timescales. Our understanding of this variability derives predominantly from proxy information in ice and marine cores; high-resolution records from land are scarce. Here we quantify land-surface temperature and soil moisture at millennial timescales over continental Europe, for the period spanning 45,000 to 22,000 years before present. We provide the first quantitative terrestrial counterpart to marine and ice-core derived reconstructions for the North Atlantic region. Our terrestrial reconstruction derives from novel isotopic geochemistry and radiocarbon dating of earthworm calcite granules, collected from two temporally overlapping loess palaeosol sequences in the Rhine Valley, Germany. We combine our proxy reconstructions with mesoscale wind and moisture transport modelling. We find that compared with polar and Mediterranean regions, climatic warming from stadial to interstadial phases is attenuated in central-western Europe. The region was dominated by westerly air masses during the last glacial maximum but experienced seasonal variability in wind steadiness. We observe a strong correlation between abrupt temperature variability recorded in the Greenland ice core and the periglacial environments further south. This correlation is likely due to air masses arriving to the Rhine valley are deriving from the North Atlantic.
Oscillations without cortex: Working memory modulates brainwaves in the endbrain of crows
2022-02-02

Summary Complex cognition requires coordinated neuronal activity at the network level. In mammals, this coordination results in distinct dynamics of local field potentials (LFP) that have been central in many models of higher cognition. Because these models are based on mammalian data, they often implicitly assume a cortical organization. Higher associative regions of the brains of birds do not have cortical layering, yet these regions have neuronal single-cell correlates of higher cognition that are very similar to those found in mammals. Here we recorded LFP in the avian equivalent of prefrontal cortex while crows performed a highly controlled and cognitively demanding working memory task, adapted from monkeys. To further ensure that recordings reflected only cognitive processes detached from motor-related activities we trained and monitored the animals to keep their head still. We found signatures in local field potentials, modulated by working memory. Frequencies of a narrow gamma (30-59 Hz) and the beta band (13-19 Hz) contained information about the location of the target items on the screen and were modulated by working memory load. This indicates a critical involvement of these bands in ongoing cognitive processing. We also observed bursts in the beta and gamma frequencies, similar to those observed in monkeys. Such bursts are a vital part of ‘activity silent’ models of working memory. Thus, despite the lack of a cortical organization the avian associative pallium can create LFP signatures reminiscent of those observed in primates. This points towards a critical cognitive function of oscillatory dynamics evolved through convergence in species capable of complex cognition. Relevance statement Contemporary models of higher cognition, like those of working memory, often include temporal dynamics of neural activity such as gamma oscillations. Birds and mammals convergently evolved these cognitive functions and here we show that, despite the large evolutionary distance and largely different brain organization, crows share many of the oscillatory fingerprints reported in primates. This indicates that neural networks required for such LFP phenomena have evolved in parallel and may be critical to higher cognition.
Report on 2112.05078v2
2022-02-02

We consider Markovian open quantum systems subject to stochastic resetting, which means that the dissipative time evolution is reset at randomly distributed times to the initial state.We show that the ensuing dynamics is non-Markovian and has the form of a generalized Lindblad equation.Interestingly, the statistics of quantum-jumps can be exactly derived.This is achieved by combining techniques from the thermodynamics of quantum-jump trajectories with the renewal structure of the resetting dynamics.We consider as an application of our analysis a driven two-level and an intermittent three-level system.Our findings show that stochastic resetting may be exploited as a tool to tailor the statistics of the quantum-jump trajectories and the dynamical phases of open quantum systems.
Additional file 1 of Environmental differences explain subtle yet detectable genetic structure in a widespread pollinator
2022-02-02

Additional file 1: Table S1. Microsatellite loci used in this work, with original locus names [127], the primer mixes they were assigned to, repeat units (motifs), size ranges, annealing temperatures (Tm), forward and reverse primer sequences (5’–3’) as well as information on null alleles and stuttering. Table S2. Basic population genetic statistics for each sampling location encompassing diploid (‘dpds’) and both haploid and diploid individuals (‘mpds’). N: number of individuals; NA: number of alleles; NE: number of effective alleles; AR: allelic richness, rarefied for seven individuals (k); uHE: unbiased expected heterozygosity; HO: observed heterozygosity. Observed heterozygosity values between ‘dpds’ and ‘mpds’ are largely congruent, as SPAGeDi, even though capable of working with mixed-ploidy data sets, does not include haploid individuals in calculating this metric. Table S3. Below the diagonal: Multilocus pairwise Fst values calculated with GenAlEx and based on a data set containing diploid individuals only. Above the diagonal: Corresponding FDR-corrected P values. Marginally significant Fst values and P values are indicated in bold. See Table S8 for population names. Table S4. Above the diagonal: Multilocus pairwise Fst values computed with polysat and based on a data set containing both haploid and diploid individuals. Below the diagonal: Corresponding bootstrap-derived upper 95% confidence intervals. See Table S8 for population names. Table S5. Above the diagonal: Multilocus pairwise Fst values calculated with polysat and based on a data set containing diploid individuals only. Below the diagonal: Corresponding bootstrap-derived upper 95% confidence intervals. See Table S8 for population names. Table S6. Discriminant analysis of principal components (DAPC) result showing the assignment of individuals to clusters identified de novo. Table S7. Pearson correlation coefficients of environmental variables at population locations harbouring both haploid and diploid individuals. See Table S9 for the abbreviations used. Table S8. Populations sampled, including their abbreviations, locations, and the number of individuals. ‘cpds’: full data set after exclusion of full siblings and clones; ‘pop10’: ‘cpds’ after excluding populations with fewer than 10 individuals; ‘mpds’: mixed-ploidy data set encompassing both haploid males and diploid females; ‘dpds’: data set containing diploid individuals only. Table S9. Environmental variables used. Those in bold were retained after stepwise elimination with a variance inflation factor ≥ 10. Table S10. Resistance matrix derived from Circuitscape, where higher values indicate higher predicted resistance to inter-population dispersal. See Table S8 for population names.
Frequency and Associations of Adverse Reactions of COVID-19 Vaccines Reported to Pharmacovigilance Systems in the European Union and the United States
2022-02-03

Introduction This study aims to provide a risk assessment of the adverse reactions related to the COVID-19 vaccines manufactured by AstraZeneca, Janssen, Moderna, and Pfizer-BioNTech which have been in use in the European Union and the United States between December 2020 and October 2021. Methods Data from the European Database of Suspected Adverse Drug Reaction (EudraVigilance) and the Vaccine Adverse Events Reporting System (VAERS) from 2020 to October 2021 are analysed. More than 7.8 million adverse reactions of about 1.6 million persons are included. The adverse reactions are classified with the Common Toxicity Criteria (CTC) categories. COVID-19 vaccine exposures and adverse reactions reported between December 2020 and October 2021 are compared to influenza vaccine exposures and adverse reactions reported between 2020 and 2021. The population-level vaccine exposures to COVID-19 and influenza vaccines comprised about 451 million and 437 million exposures, respectively. Absolute and relative risk estimates are calculated by CTC categories and COVID-19 vaccines for the EU and US populations aged 18 years and older. Results A higher risk of reporting serious adverse reactions was observed for the COVID-19 vaccines in comparison to the influenza vaccines. Individuals age 65 and older were associated with a higher frequency of death, hospitalisations, and life-threatening reactions than younger individuals (relative risk estimates between 1.49 99% CI [1.44–1.55] and 8.61 99% CI [8.02–9.23]). Outcome onset of serious adverse reactions occurred within the first 7 days after vaccination in about 77.6–89.1% of cases. The largest absolute risks were observed for allergic, constitutional reactions, dermatological, gastrointestinal, neurological reactions, and localised and non-localised pain. The largest relative risks between COVID-19 vs. influenza vaccines were observed for allergic reactions, arrhythmia, general cardiovascular events, coagulation, haemorrhages, gastrointestinal, ocular, sexual organs reactions, and thrombosis. Conclusion The present study provides an overview of adverse reactions frequently reported to the pharmacovigilance systems following COVID-19 vaccination in the EU and US populations. Despite the limitations of passive reporting systems, these results may inform further clinical research investigating in more detail the pathophysiological mechanisms potentially associated with the COVID-19 vaccines.
Noninteracting fermionic systems with localized losses: Exact results in the hydrodynamic limit
2022-02-03

We investigate the interplay between unitary and nonunitary dynamics after a quantum quench in a noninteracting fermionic chain. In particular, we consider the effect of localized loss processes, for which fermions are added and removed incoherently at the center of the chain. We focus on the hydrodynamic limit of large distances from the localized losses and of long times, with their ratio being fixed. In this limit, the localized losses gives rise to an effective imaginary delta potential (nonunitary impurity), and the time-evolution of the local correlation functions admits a simple hydrodynamic description in terms of the fermionic occupations in the initial state and the reflection and transmission amplitudes of the impurity. We derive this hydrodynamic framework from the ab initio calculation of the microscopic dynamics. This allows us to analytically characterize the effect of losses for several theoretically relevant initial states, such as a uniform Fermi sea, homogeneous product states, or the inhomogeneous state obtained by joining two Fermi seas. In this latter setting, when both gain and loss processes are present, we observe the emergence of exotic nonequilibrium steady states with stepwise uniform density profiles. In all instances, for strong loss and gain rates the coherent dynamics of the system is arrested, which is a manifestation of the celebrated quantum Zeno effect.