Springs ecosystem classification Stevens, Lawrence E.; Schenk, Edward R.; Springer, Abraham E.
Ecological applications,
January 2021, Letnik:
31, Številka:
1
Journal Article
Recenzirano
Springs ecosystems are globally abundant, geomorphologically diverse, and bioculturally productive, but are highly imperiled by anthropogenic activities. More than a century of scientific discussion ...about the wide array of ecohydrological factors influencing springs has been informative, but has yielded little agreement on their classification. This lack of agreement has contributed to the global neglect and degradation of springs ecosystems by the public, scientific, and management communities. Here we review the historical literature on springs classification variables, concluding that site-specific source geomorphology remains the most diagnostic approach. We present a conceptual springs ecosystem model that clarifies the central role of geomorphology in springs ecosystem development, function, and typology. We present an illustrated dichotomous key to terrestrial (non-marine) springs ecosystem types and subtypes, and describe those types. We identify representative reference sites, although data limitations presently preclude selection of continentally or globally representative reference springs of each type. We tested the classification key using data from 244 randomly selected springs of 13 types that were inventoried in western North America. The dichotomous key correctly identified springs type in 87.5% of the cases, with discrepancies primarily due to differentiation of primary vs. secondary typology, and insufficient inventory team training. Using that information, we identified sources of confusion and clarified the key. Among the types that required more detailed explanation were hypocrenes, springs in which groundwater is expressed through phreatophytic vegetation. Overall, springs biodiversity and ecosystem complexity are due, in part, to the co-occurrence of multiple intra-springs microhabitats. We describe microhabitats that are commonly associated with different springs types, reporting at least 13 microhabitats, each of which can support discrete biotic assemblages. Interdisciplinary agreement on basic classification is needed to enhance scientific understanding and stewardship of springs ecosystems, the loss and degradation of which constitute a global conservation crisis.
Current sequencing methods produce large amounts of data, but genome assemblies based on these data are often woefully incomplete. These incomplete and error-filled assemblies result in many ...annotation errors, especially in the number of genes present in a genome. In this paper we investigate the magnitude of the problem, both in terms of total gene number and the number of copies of genes in specific families. To do this, we compare multiple draft assemblies against higher-quality versions of the same genomes, using several new assemblies of the chicken genome based on both traditional and next-generation sequencing technologies, as well as published draft assemblies of chimpanzee. We find that upwards of 40% of all gene families are inferred to have the wrong number of genes in draft assemblies, and that these incorrect assemblies both add and subtract genes. Using simulated genome assemblies of Drosophila melanogaster, we find that the major cause of increased gene numbers in draft genomes is the fragmentation of genes onto multiple individual contigs. Finally, we demonstrate the usefulness of RNA-Seq in improving the gene annotation of draft assemblies, largely by connecting genes that have been fragmented in the assembly process.
SARS-CoV-2 infection can cause severe respiratory COVID-19. However, many individuals present with isolated upper respiratory symptoms, suggesting potential to constrain viral pathology to the ...nasopharynx. Which cells SARS-CoV-2 primarily targets and how infection influences the respiratory epithelium remains incompletely understood. We performed scRNA-seq on nasopharyngeal swabs from 58 healthy and COVID-19 participants. During COVID-19, we observe expansion of secretory, loss of ciliated, and epithelial cell repopulation via deuterosomal cell expansion. In mild and moderate COVID-19, epithelial cells express anti-viral/interferon-responsive genes, while cells in severe COVID-19 have muted anti-viral responses despite equivalent viral loads. SARS-CoV-2 RNA+ host-target cells are highly heterogenous, including developing ciliated, interferon-responsive ciliated, AZGP1high goblet, and KRT13+ “hillock”-like cells, and we identify genes associated with susceptibility, resistance, or infection response. Our study defines protective and detrimental responses to SARS-CoV-2, the direct viral targets of infection, and suggests that failed nasal epithelial anti-viral immunity may underlie and precede severe COVID-19.
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•scRNA-seq on nasopharyngeal swabs of 58 COVID-19 and healthy participants•SARS-CoV-2 induces ciliated cell loss with secretory and deuterosomal expansion•Early, muted anti-viral responses in nasal epithelia in severe COVID-19•Host-virus co-detection maps cell tropism and intrinsic responses to SARS-CoV-2
A study of nasopharyngeal swabs from healthy and COVID-19-infected individuals shows how infection leads to compositional changes in the respiratory epithelium, with early dampened antiviral responses in the nasal epithelia likely underlying and preceding severe disease.
Objetivo: Determinar la correlación entre el resultado de la prueba de reacción en cadena de la polimerasa con transcriptasa reversa (RT-PCR) positiva con los hallazgos reportados por tomografía ...computarizada de alta resolución (TACAR) expresados en CO-RADS (COVID-19 Reporting and Data System) en pacientes con sospecha de enfermedad por coronavirus 2019 (COVID-19). Material y métodos: Incluimos 1,179 pacientes con definición operacional para COVID-19 en quienes se realizó RT-PCR y TACAR al inicio. Estudio retrospectivo, transversal, descriptivo y analítico de marzo a julio de 2020. Resultados: La mediana de edad fue de 57. El 54% de los hombres se afectó con mayor frecuencia, con igualdad en las varianzas. En TACAR la mayoría fue CO-RADS 1 y 5. En el 58% de pacientes la RT-PCR salió positiva. De las categoría CO-RADS 1, 5, 4 y 3, 278 CO-RADS 1 tuvieron PCR negativa y 28 prueba positiva, 601 CO-RADS 5 presentaron PCR positiva y 89 negativa, 45 CO-RADS 4 estimaron PCR positiva y 20 negativa, y 26 CO-RADS 3 obtuvieron PCR positiva y 72 negativa, demostrando tener una relación positiva significativa, con una p ≤ 0.001. Conclusiones: En nuestro estudio la clasificación de CO-RADS en los pacientes con alta sospecha de infección por COVID-19 tiene un alto valor predictivo positivo y el porcentaje de mortalidad obtenido, del 7%, es similar al reportado en otras publicaciones y en la OMS.
Multiple inducers of in vitro Neutrophil Extracellular Trap (NET) formation (NETosis) have been described. Since there is much variation in study design and results, our aim was to create a ...systematic review of NETosis inducers and perform a standardized in vitro study of NETosis inducers important in (cardiac) wound healing.
In vitro NETosis was studied by incubating neutrophils with PMA, living and dead bacteria (S. aureus and E. coli), LPS, (activated) platelets (supernatant), glucose and calcium ionophore Ionomycin using 3-hour periods of time-lapse confocal imaging.
PMA is a consistent and potent inducer of NETosis. Ionomycin also consistently resulted in extrusion of DNA, albeit with a process that differs from the NETosis process induced by PMA. In our standardized experiments, living bacteria were also potent inducers of NETosis, but dead bacteria, LPS, (activated) platelets (supernatant) and glucose did not induce NETosis.
Our systematic review confirms that there is much variation in study design and results of NETosis induction. Our experimental results confirm that under standardized conditions, PMA, living bacteria and Ionomycin all strongly induce NETosis, but real-time confocal imaging reveal different courses of events.
Breast cancers are complex ecosystems of malignant cells and the tumour microenvironment
. The composition of these tumour ecosystems and interactions within them contribute to responses to cytotoxic ...therapy
. Efforts to build response predictors have not incorporated this knowledge. We collected clinical, digital pathology, genomic and transcriptomic profiles of pre-treatment biopsies of breast tumours from 168 patients treated with chemotherapy with or without HER2 (encoded by ERBB2)-targeted therapy before surgery. Pathology end points (complete response or residual disease) at surgery
were then correlated with multi-omic features in these diagnostic biopsies. Here we show that response to treatment is modulated by the pre-treated tumour ecosystem, and its multi-omics landscape can be integrated in predictive models using machine learning. The degree of residual disease following therapy is monotonically associated with pre-therapy features, including tumour mutational and copy number landscapes, tumour proliferation, immune infiltration and T cell dysfunction and exclusion. Combining these features into a multi-omic machine learning model predicted a pathological complete response in an external validation cohort (75 patients) with an area under the curve of 0.87. In conclusion, response to therapy is determined by the baseline characteristics of the totality of the tumour ecosystem captured through data integration and machine learning. This approach could be used to develop predictors for other cancers.
Laptop computers allow students to type lecture notes instead of relying on the traditional longhand (i.e. paper–pencil) method. The present research compared laptop and longhand note-taking methods ...by investigating how the quality (i.e. complete versus incomplete idea units) and quantity (i.e. total words and total idea units) of typed and handwritten notes differed when students did or did not reply to text messages during a simulated lecture. Accounting for the presence of text messaging while participants took notes situated the present study within the reality facing many students in today’s digital age. Findings indicated that a considerable proportion of the idea units captured in participants’ notes were incomplete, regardless of note-taking method or exposure to distraction during the simulated lecture. However, only the total number of complete idea units stored in student notes meaningfully predicted lecture learning. Furthermore, the presence of digital distraction was particularly disruptive to the quality and quantity of laptop users’ lecture notes relative to longhand note takers. Finally, digital distraction emerged as a more meaningful predictor of lecture learning than note-taking method. Recommendations for improving the quality of student lecture notes are discussed and avenues for future research into note-taking completeness and the interplay between digital distraction and note-taking method are proposed.
Design of a pH sensitive alginate–guar gum hydrogel crosslinked with glutaraldehyde was done for the controlled delivery of protein drugs. Alginate is a non-toxic polysaccharide with favorable pH ...sensitive properties for intestinal delivery of protein drugs. Drug leaching during hydrogel preparation and rapid dissolution of alginate at higher pH are major limitations, as it results in very low entrapment efficiency and burst release of entrapped protein drug, once it enters the intestine. To overcome these limitations, another natural polysaccharide, guargum was included in the alginate matrix along with a cross linking agent to ensure maximum encapsulation efficiency and controlled drug release. The crosslinked alginate–guar gum matrix is novel and the drug loading process used in the study was mild and performed in aqueous environment. The release profiles of a model protein drug (BSA) from test hydrogels were studied under simulated gastric and intestinal media. The beads having an alginate to guar gum percentage combination of 3:1 showed desirable characters like better encapsulation efficiency and bead forming properties in the preliminary studies. The glutaraldehyde concentration giving maximum (100%) encapsulation efficiency and the most appropriate swelling characteristics was found to be 0.5% (w/v). Freeze-dried samples showed swelling ratios most suitable for drug release in simulated intestinal media (∼8.5). Protein release from test hydrogels was minimal at pH 1.2 (∼20%), and it was found to be significantly higher (∼90%) at pH 7.4. Presence of guar gum and glutaraldehyde crosslinking increases entrapment efficiency and prevents the rapid dissolution of alginate in higher pH of the intestine, ensuring a controlled release of the entrapped drug.
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