Ultraliser: a framework for creating multiscale, high-fidelity and geometrically realistic 3D models for in silico neuroscience.

Ultraliser is a neuroscience-specific software framework capable of creating accurate and biologically realistic 3D models of complex neuroscientific structures at intracellular (e.g. mitochondria and endoplasmic reticula), cellular (e.g. neurons and glia) and even multicellular scales of resolution (e.g. cerebral vasculature and minicolumns). Resulting models are exported as triangulated surface meshes and annotated volumes for multiple applications in in silico neuroscience, allowing scalable supercomputer simulations that can unravel intricate cellular structure-function relationships. Ultraliser implements a high-performance and unconditionally robust voxelization engine adapted to create optimized watertight surface meshes and annotated voxel grids from arbitrary non-watertight triangular soups, digitized morphological skeletons or binary volumetric masks. The framework represents a major leap forward in simulation-based neuroscience, making it possible to employ high-resolution 3D structural models for quantification of surface areas and volumes, which are of the utmost importance for cellular and system simulations. The power of Ultraliser is demonstrated with several use cases in which hundreds of models are created for potential application in diverse types of simulations. Ultraliser is publicly released under the GNU GPL3 license on GitHub (BlueBrain/Ultraliser). SIGNIFICANCE: There is crystal clear evidence on the impact of cell shape on its signaling mechanisms. Structural models can therefore be insightful to realize the function; the more realistic the structure can be, the further we get insights into the function. Creating realistic structural models from existing ones is challenging, particularly when needed for detailed subcellular simulations. We present Ultraliser, a neuroscience-dedicated framework capable of building these structural models with realistic and detailed cellular geometries that can be used for simulations.

Women survivors of intimate partner violence talk about using e-health during pregnancy: a focus group study.

BACKGROUND: Pregnancy is a period of particular vulnerability to experience intimate partner violence against women (IPVAW). eHealth strategies have been implemented to identify women exposed to IPVAW and to combat the abuse and empower them, but there is a lack of evidence on the use of these strategies among pregnant women. This work aims to identify the needs, concerns and preferences of survivors about the use of eHealth strategies to counsel and empower pregnant victims of IPVAW in antenatal care. METHODS: A focus group of six IPVAW survivors who had been pregnant was conducted and open questions about the use of eHealth strategies were asked. The session was recorded, transcribed and thematically analyzed. We identified three main themes: needs and worries of pregnant women experiencing IPVAW, key aspects of video counseling sessions and usefulness of safety planning apps. RESULTS: Women highlighted the relevant role of healthcare professionals-especially midwives-in the identification of IPVAW and the wellbeing of their children as one of the main concerns. They perceived video counseling and safety planning apps as valuable resources. The preferred contents for a video counseling intervention were awareness-raising of the situation, self-esteem and legal advice. They also proposed safety and pregnant-related aspects that should be taken into account in the design of the video counseling sessions and the safety planning app. CONCLUSIONS: Video counseling sessions and safety planning apps are potentially useful tools to counsel and empower women who experience IPVAW during pregnancy. Midwives play a key role in this endeavor.

Evaluation of health outcomes after the implementation of rotational thromboelastometry in patients undergoing cardiac surgery.

BACKGROUND: Viscoelastic tests (rotational thromboelastometry, ROTEM®), together with the implementation of a specific algorithm for coagulation management in cardiac surgery, enable perioperative coagulopathy to be better controlled. METHODS: Retrospective cohort study including 675 patients who underwent cardiac surgery with cardiopulmonary bypass. The incidence of allogeneic blood transfusions and clinical postoperative complications were analyzed before and after ROTEM® implementation. RESULTS: Following viscoelastic testing and the implementation of a specific algorithm for coagulation management, the incidence of any allogeneic blood transfusion decreased (41.4% vs 31.9%, p = .026) during the perioperative period. In the group monitored with ROTEM®, decreased incidence of transfusion was observed for packed red blood cells (31.3% vs 19.8%, p = .002), fresh frozen plasma (9.8% vs 3.8%, p = .008), prothrombin complex concentrate administration (0.9% vs 0.3%, p = .599) and activated recombinant factor VII (0.3% vs 0.0%, p = .603). Increased incidence was observed for platelet transfusion (4.8% vs 6.8%, p = .530) and fibrinogen concentrate (0.9% vs 3.5%, p = .066), tranexamic acid (0.0% vs 0.6%, p = .370) and protamine administration (0.6% vs 0.9%, p = .908). Similar results were observed in the postoperative period, but with a decreased incidence of platelet transfusion (4.8% vs 3.8%, p = .813). In addition, statistically significant reductions were detected in the incidence of postoperative bleeding (9.5% vs 5.3%, p = .037), surgical reexploration (6.0% vs 2.9%, p = .035), and length of Intensive Care Unit (ICU) stay (6.0 days vs 5.3 days, p = .026). CONCLUSIONS: The monitoring of hemostasis by ROTEM® in cardiac surgery, was associated with decreased incidence of allogeneic blood transfusion, clinical hematologic postoperative complications and lengths of ICU stay.

Global taxonomic and phylogenetic assembly of AM fungi.

Arbuscular mycorrhizal (AM) fungi are a ubiquitous group of plant symbionts, yet processes underlying their global assembly - in particular the roles of dispersal limitation and historical drivers - remain poorly understood. Because earlier studies have reported niche conservatism in AM fungi, we hypothesized that variation in taxonomic community composition (i.e., unweighted by taxon relatedness) should resemble variation in phylogenetic community composition (i.e., weighted by taxon relatedness) which reflects ancestral adaptations to historical habitat gradients. Because of the presumed strong dispersal ability of AM fungi, we also anticipated that the large-scale structure of AM fungal communities would track environmental conditions without regional discontinuity. We used recently published AM fungal sequence data (small-subunit ribosomal RNA gene) from soil samples collected worldwide to reconstruct global patterns in taxonomic and phylogenetic community variation. The taxonomic structure of AM fungal communities was primarily driven by habitat conditions, with limited regional differentiation, and there were two well-supported clusters of communities - occurring in cold and warm conditions. Phylogenetic structure was driven by the same factors, though all relationships were markedly weaker. This suggests that niche conservatism with respect to habitat associations is weakly expressed in AM fungal communities. We conclude that the composition of AM fungal communities tracks major climatic and edaphic gradients, with the effects of dispersal limitation and historic factors considerably less apparent than those of climate and soil.

Temperature and pH define the realised niche space of arbuscular mycorrhizal fungi.

The arbuscular mycorrhizal (AM) fungi are a globally distributed group of soil organisms that play critical roles in ecosystem function. However, the ecological niches of individual AM fungal taxa are poorly understood. We collected > 300 soil samples from natural ecosystems worldwide and modelled the realised niches of AM fungal virtual taxa (VT; approximately species-level phylogroups). We found that environmental and spatial variables jointly explained VT distribution worldwide, with temperature and pH being the most important abiotic drivers, and spatial effects generally occurring at local to regional scales. While dispersal limitation could explain some variation in VT distribution, VT relative abundance was almost exclusively driven by environmental variables. Several environmental and spatial effects on VT distribution and relative abundance were correlated with phylogeny, indicating that closely related VT exhibit similar niche optima and widths. Major clades within the Glomeraceae exhibited distinct niche optima, Acaulosporaceae generally had niche optima in low pH and low temperature conditions, and Gigasporaceae generally had niche optima in high precipitation conditions. Identification of the realised niche space occupied by individual and phylogenetic groups of soil microbial taxa provides a basis for building detailed hypotheses about how soil communities respond to gradients and manipulation in ecosystems worldwide.

Solanaceae diversity in South America and its distribution in Argentina.

Solanaceae is one of the most diverse families in the Americas, particularly in Argentina where it represents the fourth family in terms of species number. Although checklists for most South American countries have been published, some are outdated and there has been no analysis of Solanaceae diversity at country level. We present an updated summary of Solanaceae diversity in South America, an analysis of its distribution in Argentina, and preliminary conservation assessments for all species endemic to Argentina. Regression analyses were used for evaluating the ratio between taxa/area and endemic/total species, multivariate ordering methods were used to analyze the relationships between Argentine ecoregions, and the IUCN criteria were applied for conservation assessments. Results show that Solanaceae comprises 1611 species in South America. The highest diversity is in Peru, which, together with Ecuador, possesses more diversity than expected for the area; Chile and Brazil have the greatest percentage of endemic species. In Argentina, the Chaco ecoregion hosts the highest number of taxa, but largest number of endemic species is found in the Monte ecoregion. According to the IUCN criteria, 28 endemic species from Argentina are considered threatened. We discuss South American countries and Argentine ecoregions in terms of conservation priorities.

Volatiles and Nonvolatiles in Flourensia campestris Griseb. (Asteraceae), How Much Do Capitate Glandular Trichomes Matter?

The distribution and ultrastructure of capitate glandular trichomes (GTs) in Flourensia species (Asteraceae) have been recently elucidated, but their metabolic activity and potential biological function remain unexplored. Selective nonvolatile metabolites from isolated GTs were strikingly similar to those found on leaf surfaces. The phytotoxic allelochemical sesquiterpene (-)-hamanasic acid A ((-)-HAA) was the major constituent (ca. 40%) in GTs. Although GTs are quaternary ammonium compounds (QACs)-accumulating species, glycine betaine was not found in GTs; it was only present in the leaf mesophyll. Two (-)-HAA accompanying surface secreted products: compounds 4-hydroxyacetophenone (piceol; 1) and 2-hydroxy-5-methoxyacetophenone (2), which were isolated and fully characterized (GC/MS, NMR), were present in the volatiles found in GTs. The essential oils of fresh leaves revealed ca. 33% monoterpenes, 26% hydrocarbon- and 30% oxygenated sesquiterpenes, most of them related to cadinene and bisabolene derivatives. Present results suggest a main role of GTs in determining the volatile and nonvolatile composition of F. campestris leaves. Based on the known activities of the compounds identified, it can be suggested that GTs in F. campestris would play key ecological functions in plant-pathogen and plant-plant interactions. In addition, the strikingly high contribution of compounds derived from cadinene and bisabolene pathways, highlights the potential of this species as a source of high-valued bioproducts.

Resolution of deep nodes yields an improved backbone phylogeny and a new basal lineage to study early evolution of Asteraceae.

A backbone phylogeny that fully resolves all subfamily and deeper nodes of Asteraceae was constructed using 14 chloroplast DNA loci. The recently named genus Famatinanthus was found to be sister to the Mutisioideae-Asteroideae clade that represents more than 99% of Asteraceae and was found to have the two chloroplast inversions present in all Asteraceae except the nine genera of Barnadesioideae. A monotypic subfamily Famatinanthoideae and tribe Famatinantheae are named herein as new. Relationships among the basal lineages of the family were resolved with strong support in the Bayesian analysis as (Barnadesioideae (Famatinanthoideae (Mutisioideae (Stifftioideae (Wunderlichioideae-Asteroideae))))). Ancestral state reconstruction of ten morphological characters at the root node of the Asteraceae showed that the ancestral sunflower would have had a woody habit, alternate leaves, solitary capitulescences, epaleate receptacles, smooth styles, smooth to microechinate pollen surface sculpturing, white to yellow corollas, and insect-mediated pollination. Herbaceous habit, echinate pollen surface, pubescent styles, and cymose capitulescences were reconstructed for backbone nodes of the phylogeny corresponding to clades that evolved shortly after Asteraceae dispersed out of South America. No support was found for discoid capitula, multiseriate involucres or bird pollination as the ancestral character condition for any node. Using this more resolved phylogenetic tree, the recently described Raiguenrayun cura+Mutisiapollis telleriae fossil should be associated to a more derived node than previously suggested when time calibrating phylogenies of Asteraceae.

NeuroEditor: a tool to edit and visualize neuronal morphologies.

The digital extraction of detailed neuronal morphologies from microscopy data is an essential step in the study of neurons. Ever since Cajal's work, the acquisition and analysis of neuron anatomy has yielded invaluable insight into the nervous system, which has led to our present understanding of many structural and functional aspects of the brain and the nervous system, well beyond the anatomical perspective. Obtaining detailed anatomical data, though, is not a simple task. Despite recent progress, acquiring neuron details still involves using labor-intensive, error prone methods that facilitate the introduction of inaccuracies and mistakes. In consequence, getting reliable morphological tracings usually needs the completion of post-processing steps that require user intervention to ensure the extracted data accuracy. Within this framework, this paper presents NeuroEditor, a new software tool for visualization, editing and correction of previously reconstructed neuronal tracings. This tool has been developed specifically for alleviating the burden associated with the acquisition of detailed morphologies. NeuroEditor offers a set of algorithms that can automatically detect the presence of potential errors in tracings. The tool facilitates users to explore an error with a simple mouse click so that it can be corrected manually or, where applicable, automatically. In some cases, this tool can also propose a set of actions to automatically correct a particular type of error. Additionally, this tool allows users to visualize and compare the original and modified tracings, also providing a 3D mesh that approximates the neuronal membrane. The approximation of this mesh is computed and recomputed on-the-fly, reflecting any instantaneous changes during the tracing process. Moreover, NeuroEditor can be easily extended by users, who can program their own algorithms in Python and run them within the tool. Last, this paper includes an example showing how users can easily define a customized workflow by applying a sequence of editing operations. The edited morphology can then be stored, together with the corresponding 3D mesh that approximates the neuronal membrane.

Rare primary cardiac myxofibrosarcoma in adolescence: Diagnostic challenges and surgical insights.

This article presents a unique case of primary myxofibrosarcoma, an exceptionally rare cardiac neoplasm, in a 16-year-old girl. With fewer than 40 documented cases, this tumor's occurrence in adolescence is particularly uncommon. The patient presented with right-sided paresthesia and subsequent right hemiparesis and dysarthria, along with bilateral pleural effusion. Imaging tests revealed a cerebral ischemic lesion and the presence of a left atrial mass. Initially suspected as a myxoma, the tumor exhibited significant infiltration. Despite prompt excision and cardiac intervention, the patient experienced rapid decompensation and succumbed to heart failure 2 days later. Histopathological analysis revealed an intermediate grade myxofibrosarcoma. This case underscores the diagnostic complexity, emphasizing the need for early identification given the grim prognosis associated with cardiac myxofibrosarcomas, requiring detailed imaging, surgical, and histopathological insights.

Global sampling of plant roots expands the described molecular diversity of arbuscular mycorrhizal fungi.

We aimed to enhance understanding of the molecular diversity of arbuscular mycorrhizal fungi (AMF) by building a new global dataset targeting previously unstudied geographical areas. In total, we sampled 96 plant species from 25 sites that encompassed all continents except Antarctica. AMF in plant roots were detected by sequencing the nuclear SSU rRNA gene fragment using either cloning followed by Sanger sequencing or 454-sequencing. A total of 204 AMF phylogroups (virtual taxa, VT) were recorded, increasing the described number of Glomeromycota VT from 308 to 341 globally. Novel VT were detected from 21 sites; three novel but nevertheless widespread VT (Glomus spp. MO-G52, MO-G53, MO-G57) were recorded from six continents. The largest increases in regional VT number were recorded in previously little-studied Oceania and in the boreal and polar climatic zones - this study providing the first molecular data from the latter. Ordination revealed differences in AM fungal communities between different continents and climatic zones, suggesting that both biogeographic history and environmental conditions underlie the global variation of those communities. Our results show that a considerable proportion of Glomeromycota diversity has been recorded in many regions, though further large increases in richness can be expected in remaining unstudied areas.

Hematocele secondary to rupture of an abdominoscrotal hydrocele.

OBJECTIVE: To describe one case of hematocele secondary to rupture of an abdominoscrotal hydrocele in an adult patient. METHODS AND RESULTS: We report a huge hematocele in a patient with this unusual type of hydrocele that suffered a minimal scrotal trauma. It was a hydrocele that extended through the inguinal canal to the retroperitoneal space. CONCLUSIONS: Abdominoscrotal hydrocele is a rare condition in children and even rarer in adults. The presence of a hematocele requires early surgical treatment.

Global diversity and distribution of nitrogen-fixing bacteria in the soil.

Our knowledge of microbial biogeography has advanced in recent years, yet we lack knowledge of the global diversity of some important functional groups. Here, we used environmental DNA from 327 globally collected soil samples to investigate the biodiversity patterns of nitrogen-fixing bacteria by focusing on the nifH gene but also amplifying the general prokaryotic 16S SSU region. Globally, N-fixing prokaryotic communities are driven mainly by climatic conditions, with most groups being positively correlated with stable hot or seasonally humid climates. Among soil parameters, pH, but also soil N content were most often shown to correlate with the diversity of N-fixer groups. However, specific groups of N-fixing prokaryotes show contrasting responses to the same variables, notably in Cyanobacteria that were negatively correlated with stable hot climates, and showed a U-shaped correlation with soil pH, contrary to other N-fixers. Also, the non-N-fixing prokaryotic community composition was differentially correlated with the diversity and abundance of N-fixer groups, showing the often-neglected impact of biotic interactions among bacteria.

Metabarcoding of soil environmental DNA to estimate plant diversity globally.

Introduction: Traditional approaches to collecting large-scale biodiversity data pose huge logistical and technical challenges. We aimed to assess how a comparatively simple method based on sequencing environmental DNA (eDNA) characterises global variation in plant diversity and community composition compared with data derived from traditional plant inventory methods. Methods: We sequenced a short fragment (P6 loop) of the chloroplast trnL intron from from 325 globally distributed soil samples and compared estimates of diversity and composition with those derived from traditional sources based on empirical (GBIF) or extrapolated plant distribution and diversity data. Results: Large-scale plant diversity and community composition patterns revealed by sequencing eDNA were broadly in accordance with those derived from traditional sources. The success of the eDNA taxonomy assignment, and the overlap of taxon lists between eDNA and GBIF, was greatest at moderate to high latitudes of the northern hemisphere. On average, around half (mean: 51.5% SD 17.6) of local GBIF records were represented in eDNA databases at the species level, depending on the geographic region. Discussion: eDNA trnL gene sequencing data accurately represent global patterns in plant diversity and composition and thus can provide a basis for large-scale vegetation studies. Important experimental considerations for plant eDNA studies include using a sampling volume and design to maximise the number of taxa detected and optimising the sequencing depth. However, increasing the coverage of reference sequence databases would yield the most significant improvements in the accuracy of taxonomic assignments made using the P6 loop of the trnL region.

Dominance, diversity, and niche breadth in arbuscular mycorrhizal fungal communities.

Classical theory identifies resource competition as the major structuring force of biotic communities and predicts that (i) levels of dominance and richness in communities are inversely related, (ii) narrow niches allow dense "packing" in niche space and thus promote diversity, and (iii) dominants are generalists with wide niches, such that locally abundant taxa also exhibit wide distributions. Current empirical support, however, is mixed. We tested these expectations using published data on arbuscular mycorrhizal (AM) fungal community composition worldwide. We recorded the expected negative relationship between dominance and richness and, to a degree, the positive association between local and global dominance. However, contrary to expectations, dominance was pronounced in communities where more specialists were present and, conversely, richness was higher in communities with more generalists. Thus, resource competition and niche packing appear to be of limited importance in AM fungal community assembly; rather, patterns of dominance and diversity seem more consistent with habitat filtering and stochastic processes.

Living in extreme environments: distribution of Lyciumhumile (Solanaceae), an endemic halophyte from the Altiplano-Puna region, South America.

Very few Solanaceae species are able to grow in saline soils; one of them is Lyciumhumile. This species is endemic to the Altiplano-Puna region (Central Andes, South America) where there are multiple extreme environmental conditions such as hypersaline soils. Here we present an updated description and distribution of L.humile including its new record for Bolivia at the edges of "Salar de Uyuni", the largest salt flat in the world; we discuss its ecological role in saline environments by analyzing soil salinity and cover-abundance values ​​of the studied sites. According to IUCN criteria, we recommend a category of Least Concern for L.humile, but the growing development of lithium mining in saline environments of the Altiplano-Puna region may potentially threaten exclusive communities.

New insights into the salt tolerance of the extreme halophytic species Lycium humile (Lycieae, Solanaceae).

Knowledge about Solanaceae species naturally adapted to salinity is scarce, despite the fact that a considerable number of Solanaceae has been reported growing in saline environments. Lycium humile Phil. inhabits extreme saline soils in the Altiplano-Puna region (Central Andes, South America) and represents a promising experimental model to study salt tolerance in Solanaceae plants. Seeds, leaves and roots were collected from a saline environment (Salar del Diablo, Argentina). Seeds were scarified and 30 days after germination salt treatments were applied by adding NaCl salt pulses (up to 750 or 1000 mM). Different growth parameters were evaluated, and leaf spectral reflectance, endogenous phytohormone levels, antioxidant capacity, proline and elemental content, and morpho-anatomical characteristics in L. humile under salinity were analyzed both in controlled and natural conditions. The multiple salt tolerance mechanisms found in this species are mainly the accumulation of the phytohormone abscisic acid, the increase of the antioxidant capacity and proline content, together with the development of a large leaf water-storage parenchyma that allows Na+ accumulation and an efficient osmotic adjustment. Lycium humile is probably one of the most salt-tolerant Solanaceae species in the world, and, in controlled conditions, can effectively grow at high NaCl concentrations (at least, up to 750 mM NaCl) but also, in the absence of salts in the medium. Therefore, we propose that natural distribution of L. humile is more related to water availability, as a limiting factor of growth in Altiplano-Puna saline habitats, than to high salt concentrations in the soils.

Arbuscular Mycorrhizal Fungal Communities in the Soils of Desert Habitats.

Deserts cover a significant proportion of the Earth's surface and continue to expand as a consequence of climate change. Mutualistic arbuscular mycorrhizal (AM) fungi are functionally important plant root symbionts, and may be particularly important in drought stressed systems such as deserts. Here we provide a first molecular characterization of the AM fungi occurring in several desert ecosystems worldwide. We sequenced AM fungal DNA from soil samples collected from deserts in six different regions of the globe using the primer pair WANDA-AML2 with Illumina MiSeq. We recorded altogether 50 AM fungal phylotypes. Glomeraceae was the most common family, while Claroideoglomeraceae, Diversisporaceae and Acaulosporaceae were represented with lower frequency and abundance. The most diverse site, with 35 virtual taxa (VT), was in the Israeli Negev desert. Sites representing harsh conditions yielded relatively few reads and low richness estimates, for example, a Saudi Arabian desert site where only three Diversispora VT were recorded. The AM fungal taxa recorded in the desert soils are mostly geographically and ecologically widespread. However, in four sites out of six, communities comprised more desert-affiliated taxa (according to the MaarjAM database) than expected at random. AM fungal VT present in samples were phylogenetically clustered compared with the global taxon pool, suggesting that nonrandom assembly processes, notably habitat filtering, may have shaped desert fungal assemblages.

The Morelloid clade of Solanum L. (Solanaceae) in Argentina: nomenclatural changes, three new species and an updated key to all taxa.

Since the publication of the Solanaceae treatment in "Flora Argentina" in 2013 exploration in the country and resolution of outstanding nomenclatural and circumscription issues has resulted in a number of changes to the species of the Morelloid clade of Solanum L. (Solanaceae) for Argentina. Here we describe three new species: Solanum hunzikeri Chiarini & Cantero, sp. nov., from wet high elevation areas in Argentina (Catamarca, Salta and Tucumán) and Bolivia (Chuquisaca and Tarija), S. marmoratum Barboza & S. Knapp, sp. nov., from central Argentina in Catamarca, La Pampa, La Rioja, San Juan and San Luis, and S. tiinae Barboza & S. Knapp, sp. nov., from the mountains of Jujuy, La Rioja, Salta and Tucumán. We provide descriptions, illustrations and distribution maps for all new taxa. A table of nomenclatural changes and additional taxa now known to occur in Argentina summarizes additions and changes since the "Flora Argentina". We also provide an updated key, including all new taxa for the country, to facilitate identification and further exploration.

Organic extracts of Larrea divaricata Cav. induced apoptosis on tumoral MCF7 cells with an higher cytotoxicity than nordihydroguaiaretic acid or paclitaxel.

The methanolic and methane dichloride extracts of aerial parts of Larrea divaricata Cay. (Jarilla) plants exhibited a pronounced cytotoxic effect by arresting cell viability at a level of 35% against the MCF-7 cell line, a human breast adenocarcinoma, while only a weak cytotoxic effect was observed for the aqueous extract. Apoptosis was detected by flow cytometry, using annexin V and by cytological detection with fluorescein diacetate / propidium iodide staining. The annexin V, as well as the uptake of fluorescein diacetate/propidium iodide staining, revealed that methanolic and methane dichloride extracts of L. divaricata treatment of cells resulted in a rapid plasma membrane perturbation and triggered cellular death (>70%). Methanolic extracts were submitted to further treatment by bioassay-guided purification, involving fractionation and chromatography. 0.1% (w/w) nordihydroguaiaretic acid (NDGA) was found, which displayed weak citotoxic activity.