Miracle-dz/UniFAR-FTUs huggingface dataset:
SARS-CoV-2 infection is associated with intestinal permeability, systemic inflammation, and microbial dysbiosis in hospitalized COVID-19 patients

Coronavirus disease 2019 (COVID-19) and associated severity has been linked to uncontrolled inflammation and may be associated with changes in the microbiome of mucosal sites including the gastrointestinal tract and oral cavity. These sites play an important role in host-microbe homeostasis and disruption of epithelial barrier integrity during COVID-19 may potentially lead to exacerbated inflammation and immune dysfunction. Outcomes in COVID-19 are highly disparate, ranging from asymptomatic to fatal, and the impact of microbial dysbiosis on disease severity is unclear. Here, we obtained plasma, rectal swabs, oropharyngeal swabs, and nasal swabs from 86 patients hospitalized with COVID-19 and 12 healthy volunteers. We performed 16S rRNA sequencing to characterize the microbial communities in the mucosal swabs and measured circulating cytokines, markers of gut barrier integrity, and fatty acids in the plasma samples. We compared these plasma concentrations and microbiomes between healthy volunteers and the COVID-19 patients who had survived or unfortunately died by the end of study enrollment, and between severe disease and healthy controls, as well as performed a correlation analysis between plasma variables and bacterial abundances. The rectal swabs of COVID-19 patients had reduced abundances of several commensal bacteria including Faecalibacterium prausnitsii, and an increased abundance of the opportunistic pathogens Eggerthella lenta and Hungatella hathewayi. Furthermore, the oral pathogen Scardovia wiggsiae was more abundant in the oropharyngeal swabs of COVID-19 patients who died. The abundance of both H. hathewayi and S. wiggsiae correlated with circulating inflammatory markers including IL-6, highlighting the possible role of the microbiome in COVID-19 severity, and providing potential therapeutic targets for managing COVID-19.
Cold Atmospheric Helium Plasma in the Post-Covid Era: A Promising Tool for the Disinfection of Silicone Endotracheal Prostheses

The COVID-19 pandemic resulted in a high prevalence of laryngotracheal stenosis. The endoluminal tracheal prostheses used to treat this condition are made of medical-grade silicone (MGS). Despite their excellent properties, the main limitation of these prostheses is the formation of a polymicrobial biofilm on their surfaces that interacts with the underlying mucosa, causing local inflammation and interfering with the local healing process, ultimately leading to further complications in the clinical scenario. Cold atmospheric plasma (CAP) shows antibiofilm properties on several microbial species. The present study evaluated the inhibitory effect of CAP on multispecies biofilms grown on MGS surfaces. In addition to the MGS characterization before and after CAP exposure, the cytotoxicity of CAP on immortalized human bronchial epithelium cell line (BEAS-2B) was evaluated. The aging time test reported that CAP could temporarily change the MGS surface wetting characteristics from hydrophilic (80.5°) to highly hydrophilic (< 5°). ATR-FTIR shows no significant alterations in the surficial chemical composition of MGS before and after CAP exposure for 5 min. A significant log reduction of viable cells in mono-species biofilms (log CFU/mL) of C. albicans, S. aureus, and P. aeruginosa (0.636, 0.738, and 1.445, respectively) was detected after CAP exposure. Multi-species biofilms exposed to CAP showed significant viability reduction for C. albicans and S. aureus (1.385 and 0.831, respectively). The protocol was not cytotoxic to BEAS-2B. It could be concluded that CAP can be a simple and effective method to delay the multi-species biofilm formation inside the endotracheal prosthesis.
Exploring the prokaryote-eukaryote interplay in microbial mats from an Andean athalassohaline wetland

Microbial community assembly results from the interaction between biotic and abiotic factors. However, environmental selection is thought to predominantly shape communities in extreme ecosystems. Salar de Huasco, situated in the high altitude Andean Altiplano, represents a poly-extreme ecosystem displaying spatial gradients of physicochemical conditions. To disentangle the influence of abiotic and biotic factors, we studied prokaryotic and eukaryotic communities from microbial mats and underlying sediments across contrasting areas of this athalassohaline ecosystem. The prokaryotic communities were primarily composed of bacteria, notably including a significant proportion of photosynthetic organisms like Cyanobacteria and anoxygenic photosynthetic members of Alpha- and Gammaproteobacteria and Chloroflexi. Additionally, Bacteroidetes, Verrucomicrobia, and Deltaproteobacteria were abundantly represented. Among eukaryotes, photosynthetic organisms (Ochrophyta, Archaeplastida) were predominant, alongside relatively abundant ciliates, cercozoans, and flagellated fungi. Salinity emerged as a key driver for the assembly of prokaryotic communities. Collectively, abiotic factors influenced both prokaryotic and eukaryotic communities, particularly those of algae. However, prokaryotic communities strongly correlated with photosynthetic eukaryotes, suggesting a pivotal role of biotic interactions in shaping these communities. Co-occurrence networks suggested potential interactions between different organisms, such as diatoms with specific photosynthetic and heterotrophic bacteria or with protist predators, indicating influences beyond environmental selection. While some associations may be explained by environmental preferences, the robust biotic correlations, alongside insights from other ecosystems and experimental studies, suggest that symbiotic and trophic interactions significantly shape microbial mat and sediment microbial communities in this athalassohaline ecosystem.
ER-anchored protein sorting controls the fate of two proteasome activators for intracellular organelle communication during proteotoxic stress

Proteotoxic stress, characterized by the accumulation of damaged proteins, poses a significant challenge to cellular homeostasis. To mitigate proteotoxicity eukaryotes employ the proteasome that is regulated by proteasome activators, e.g. transcription factors that promote gene expression of proteasome subunits. As proteotoxicity originates in different compartments, cells need to perceive signals from various locations. Understanding which components integrate signals to address proteotoxicity is essential to develop strategies to cope with proteotoxicity but remain elusive. Here, we identify that the proteasome autoregulatory feedback loop acts as a gatekeeper to facilitate the communication between nucleus and chloroplast. We reveal that the ER-anchored protein sorting system (ERAPS) controls the proteasomal degradation or nuclear translocation of proteasome activators NAC53 and NAC78. While both transcription factors activate the proteasome gene expression, they repress photosynthesis-associated nuclear genes during proteotoxicity through association with a conserved cis-element. Our data implicate a general trade-off between proteasome function and energy metabolism unravelling an unprecedented mechanism of how eukaryotic cells cope with proteotoxicity. Collectively, our discoveries provide a novel conceptual framework in which the proteasome autoregulatory feedback loop coordinates subcellular proteostasis and the trade-off between growth and defence.
Phospholipase D1 Produces Phosphatidic Acid at Sites of Secretory Vesicle Docking and Fusion

Phospholipase D1 (PLD1) activity is essential for the stimulated exocytosis of secretory vesicles where it acts as a lipid-modifying enzyme to produces phosphatidic acid (PA). PLD1 localizes to the plasma membrane and secretory vesicles, and PLD1 inhibition or knockdowns reduce the rate of fusion. However, temporal data resolving when and where PLD1 and PA are required during exocytosis is lacking. In this work, PLD1 and production of PA are measured during the trafficking, docking, and fusion of secretory vesicles in PC12 cells. Using fluorescently-tagged PLD1 and a PA-binding protein, cells were imaged using TIRF microscopy to monitor the presence of PLD1 and the formation of PA throughout the stages of exocytosis. Single docking and fusion events were imaged to measure the recruitment of PLD1 and the formation of PA. PLD1 is present on mobile, docking, and fusing vesicles and also colocalizes with Syx1a clusters. Treatment of cells with PLD inhibitors significantly reduces fusion, but not PLD1 localization to secretory vesicles. Inhibitors also alter the formation of PA; when PLD1 is active, PA slowly accumulates on docked vesicles. During fusion, PA is reduced in cells treated with PLD1 inhibitors, indicating that PLD1 produces PA during exocytosis.
Transcriptional complexity in the insect central complex: single nuclei RNA sequencing of adult brain neurons derived from type 2 neuroblasts

In both invertebrates such as Drosophila and vertebrates such as mouse or human, the brain contains the most diverse population of cell types of any tissue. It is generally accepted that transcriptional diversity is an early step in generating neuronal and glial diversity, followed by the establishment of a unique gene expression profile that determines neuron morphology, connectivity, and function. In Drosophila, there are two types of neural stem cells, called Type 1 (T1) neuroblasts and Type 2 neuroblasts (T2). In contrast to T1 neuroblasts, T2 neuroblasts generate Intermediate Neural Progenitors (INPs) that expand the number and diversity of neurons. The diversity of T2 neuroblast-derived neurons contributes a large portion of the central complex (CX), a conserved brain region that plays a role in sensorimotor integration, including celestial navigation. Recent work has revealed much of the connectome of the CX, but how this connectome is assembled remains unclear. Mapping the transcriptional diversity of T2 neuroblast-derived neurons, including those projecting to the CX, is a necessary step in linking transcriptional profile to the assembly of the connectome. Here we use single nuclei RNA sequencing of T2 neuroblast- derived adult neurons to identify over 150 distinct cell clusters. We map neurotransmitter and neuropeptide expression and identify unique transcription factor combinatorial codes for each cluster (presumptive neuron subtype). This is a necessary step that directs functional studies to determine whether each transcription factor combinatorial code specifies a distinct neuron type within the central complex. We map several well- characterized columnar neuron subtypes to distinct clusters, and two neuronal classes map to a single cluster. Our data support the hypothesis that each cluster represents a one or a few closely related neuron classes.
Improving peripheral reading with non-invasive transcranial electrical stimulation of early visual areas

We investigated the ability of two non-invasive transcranial electrical stimulation (tES) protocols targeting early visual areas to improve peripheral visual word recognition in separate within-subject, double-blind, sham-controlled experiments with normal observers. English sentences were presented 10 degrees below fixation using a rapid serial visual presentation (RSVP). Transcranial random noise stimulation (tRNS) applied bilaterally on either size of the occipital pole (Oz) elicited a significant performance benefit, but transcranial direct current stimulation (tDCS) applied to Oz did not. These results highlight important factors that may influence the effectiveness of non-invasive brain stimulation methods for enhancing peripheral processing of text, such as stimulation type. While more work is necessary to better understand the relationship between tES and peripheral reading, the present results contribute to the growing body of work implicating tES as a potential tool for enhancing peripheral visual processing.
Evolutionary and Developmental Specialization of Foveal Cell Types in the Marmoset

In primates, high-acuity vision is mediated by the fovea, a small specialized central region of the retina. The fovea, unique to the anthropoid lineage among mammals, undergoes notable neuronal morphological changes during postnatal maturation. However, the extent of cellular similarity across anthropoid foveas and the molecular underpinnings of foveal maturation remain unclear. Here, we used high throughput single cell RNA sequencing to profile retinal cells of the common marmoset (Callithrix jacchus), an early divergent in anthropoid evolution from humans, apes, and macaques. We generated atlases of the marmoset fovea and peripheral retina for both neonates and adults. Our comparative analysis revealed that marmosets share almost all its foveal types with both humans and macaques, highlighting a conserved cellular structure among primate foveas. Furthermore, by tracing the developmental trajectory of cell types in the foveal and peripheral retina, we found distinct maturation paths for each. In-depth analysis of gene expression differences demonstrated that cone photoreceptors and Müller glia, among others, show the greatest molecular divergence between these two regions. Utilizing single-cell ATAC-seq and gene-regulatory network inference, we uncovered distinct transcriptional regulations differentiating foveal cones from their peripheral counterparts. Further analysis of predicted ligand-receptor interactions suggested a potential role for Müller glia in supporting the maturation of foveal cones. Together, these results provide valuable insights into foveal development, structure, and evolution. Significance statement The sharpness of our eyesight hinges on a tiny retinal region known as the fovea. The fovea is pivotal for primate vision and is susceptible to diseases like age-related macular degeneration. We studied the fovea in the marmoset–a primate with ancient evolutionary ties. Our data illustrated the cellular and molecular composition of its fovea across different developmental ages. Our findings highlighted a profound cellular consistency among marmosets, humans, and macaques, emphasizing the value of marmosets in visual research and the study of visual diseases.
3D Nuclei Segmentation by Combining GAN Based Image Synthesis and Existing 3D Manual Annotations

Nuclei segmentation is an important task in cell biology analysis that requires accurate and reliable methods, especially within complex low signal to noise ratio images with crowded cells populations. In this context, deep learning-based methods such as Stardist have emerged as the best performing solutions for segmenting nucleus. Unfortunately, the performances of such methods rely on the availability of vast libraries of ground truth hand-annotated data-sets, which become especially tedious to create for 3D cell cultures in which nuclei tend to overlap. In this work, we present a workflow to segment nuclei in 3D in such conditions when no specific ground truth exists. It combines the use of a robust 2D segmentation method, Stardist 2D, which have been trained on thousands of already available ground truth datasets, with the generation of pair of 3D masks and synthetic fluorescence volumes through a conditional GAN. It allows to train a Stardist 3D model with 3D ground truth masks and synthetic volumes that mimic our fluorescence ones. This strategy allows to segment 3D data that have no available ground truth, alleviating the need to perform manual annotations, and improving the results obtained by training Stardist with the original ground truth data.
Understanding the global patterns of Venezuelan migration: determinants of an expanding diaspora

ABSTRACT The economic, political and humanitarian crisis in Venezuela intensified since 2015 and has led to the largest migration crisis in the region’s modern history. In parallel, the composition of the major destination countries has changed fundamentally. This paper investigates the factors determining the choice of destination country of Venezuelan migrants in the pre- and post-2015 period. Exploiting the United Nations migration dataset (for 230 countries from 1990 to 2017), we apply a Poisson Pseudo-Maximum Likelihood (PPML) estimator to a modified gravity model of migration. The results suggest that Venezuelans were generally choosing a certain destination country based on economic criteria in times of relative stability (1990 to 2015). However, this determinant loses its importance during times of crisis (2015 to 2017), when Venezuelans were primarily immigrating to geographically proximate nations. Consistently for both periods Venezuelans appear to migrate in larger numbers to destinations with an already established network of compatriots.
Evolution of grain sizes and orientations during phase transitions in hydrous Mg2SiO4

Transformation microstructures in mantle minerals, such as (Mg,Fe)2SiO4, are critical for predicting the rheological properties of rocks and the interpretation of seismic observations. We present in situ multigrain X‐ray diffraction experiments on hydrous Mg2SiO4 at the P/T conditions relevant for deep cold subducting slabs (up to 40 GPa and 850°C) at a low experimental strain rate (~4 * 10−6s−1). We monitor the orientations of hundreds of grains and grain size variations during the series of α‐β‐γ (forsterite‐wadsleyite‐ringwoodite) phase transformations. Microtextural results indicate that the β and an intermediate γ* phase grow incoherently relatively to the host α phase consistent with a nucleation and growth model. The β and γ phases exhibit orientation relationships which are in agreement with previous ex situ observations. The β and intermediate γ* show texturing due to moderate differential stress in the sample. Both the α‐β and α‐γ transformation induce significant reductions of the mean sample grain size of up to 90% that starts prior to the appearance of the daughter phase. Apart from the γ*, in the newly formed β and γ phases, the nucleation rate is faster than the growth rate, inhibiting the formation of large grains. These results on grain orientations and grain size reductions in relation to transformation kinetics should allow refining existing slab strength models.
Asperity break after 12 years: The Mw6.4 2015 Lefkada (Greece) earthquake

The Mw6.4 earthquake sequence of 2015 in western Greece is analyzed using seismic data. Multiple point source modeling, nonlinear slip patch, and linear slip inversions reveal a coherent rupture image with directivity toward the southwest and several moment release episodes, reflected in the complex aftershock distribution. The key feature is that the 2015 earthquake ruptured a strong asperity, which was left unbroken in between two large subevents of the Mw6.2 Lefkada doublet in 2003. This finding and the well‐analyzed Cephalonia earthquake sequence of 2014 provide strong evidence of segmentation of the major dextral Cephalonia‐Lefkada Transform Fault (CTF), being related to extensional duplex transform zones. We propose that the duplexes extend farther to the north and that the CTF runs parallel to the western coast of Lefkada and Cephalonia Islands, considerably closer to the inhabited islands than previously thought. Generally, this study demonstrates faulting complexity across short time scales (earthquake doublets) and long time scales (seismic gaps).
How Can We Maximize Phylogenetic Diversity? Parameterized Approaches for Networks

Phylogenetic Diversity (PD) is a measure of the overall biodiversity of a set of present-day species (taxa) within a phylogenetic tree. We consider an extension of PD to phylogenetic networks. Given a phylogenetic network with weighted edges and a subset S of leaves, the all-paths phylogenetic diversity of S is the summed weight of all edges on a path from the root to some leaf in S . The problem of finding a bounded-size set S that maximizes this measure is polynomial-time solvable on trees, but NP-hard on networks. We study the latter from a parameterized perspective. While this problem is W[2] -hard with respect to the size of S (and W[1] -hard with respect to the size of the complement of S ), we show that it is FPT with respect to several other parameters, including the phylogenetic diversity of S , the acceptable loss of phylogenetic diversity, the number of reticulations in the network, and the treewidth of the underlying graph.
Klíč ke květeně České republiky

Nove, zcela přepracovane vydani Klice ke květeně Ceske republiky zahrnuje nejnovějsich poznatky ze systematiky i terenni botaniky. Obsahuje zpracovani vice než 3700 druhů a poddruhů rostlin, perokresby a strucný text s popisy rostlin a udaji o jejich rozsiřeni, nejcastějsich stanovistich a době květu. Klic je urcen vsem zajemcům o urcovani rostlin, zejmena botanikům, studentům, ucitelům a ochranařům.
Quantitative estimation of the contribution of dust sources to Chinese loess using detrital zircon U‐Pb age patterns

The origin and provenance of the loess deposits of the Chinese Loess Plateau (CLP) are still debated. In order to pinpoint the dust sources, surface samples from the piedmont of the Northeastern Tibetan Plateau, the Gobi Altai Mountains, and modern eolian dunes from the Tengger desert and Mu Us sand field were analyzed by using the detrital zircon dating technique. In order to quantitatively discriminate the content of different potential sources, zircon grains of different ages were grouped according to their tectonic origin. Zircon grains aged from 1300 to 550 Ma were assigned to the Northeastern Tibetan Plateau, and grains aged from 550 to 0 Ma to the Northeastern Tibetan Plateau or the Gobi Altai Mountains, or to a combination of the two. Zircon ages of around 2.8 Ga to 1.3 Ga may be a mixture of sources from the Northeastern Tibetan Plateau, Gobi Altai Mountains, or North China Craton. Sediments from the Tengger desert and Mu Us sand field consist of a mixture of the three sources and exhibit a high degree of spatial variability in terms of their source. In the northern part of the two deserts, 43–83% of the sediments are derived from the Gobi Altai Mountains, while in the south, material from the Northeastern Tibetan Plateau comprises 51–98% of the sediments. Loess deposits from the CLP also comprise a mixture of the three different sources, with material from the Northeastern Tibetan Plateau making the dominant contribution (65–100%), with material from the North China Craton and the Gobi Altai Mountains comprising 0–35% and 0–40% of the loess deposits, respectively. The contributions from the three sources to the loess deposits on CLP vary spatially. Application of the novel statistical method of provenance group analysis demonstrates that the loess deposits comprise a mixture of material from a broad region of northern China and that the Northeastern Tibetan Plateau material makes the dominant contribution.
Global-Scale Decadal Hyper Modes

This article discusses the idea of stochastic global-scale multi-decadal Hyper Modes. The chapter will first illustrate the spatial pattern and time-scales of the leading mode of global-scale multi decadal climate variability in observations and model simulations. It is further shown that the main characteristic of the leading mode of global-scale multi-decadal variability can be simulated in the absence of any ocean dynamics and by atmospheric teleconnections only. In a simple stochastic model for the Hyper Modes, local (basin-wide) modes of variability act mostly on interannual timescales forced by atmospheric white noise. Most of these modes have a weak link to the tropical regions via atmospheric teleconnections, which on longer (decadal) time-scales become more dominant. The tropical link provides a synchronization of the local modes to near global multi-decadal Hyper Modes. The persistence of higher latitudes SST variability with an exponentially decreasing mixing into the deeper oceans leads to a power spectrum with a low-frequency tail and different slope compared to a red noise power spectrum. The main elements of this stochastic model do not involve any ocean dynamics beyond local vertical mixing.