Cluster analysis is a valuable unsupervised machine learning technique that is applied in a multitude of domains to identify similarities or clusters in unlabelled data. However, its performance is ...dependent of the characteristics of the data it is being applied to. There is no universally best clustering algorithm, and hence, there are numerous clustering algorithms available with different performance characteristics. This raises the problem of how to select an appropriate clustering algorithm for the given analytical purposes. We present and validate an analysis framework to address this problem. Unlike most current literature which focuses on characterizing the clustering algorithm itself, we present a wider holistic approach, with a focus on the user's needs, the data's characteristics and the characteristics of the clusters it may contain. In our analysis framework, we utilize a softer qualitative approach to identify appropriate characteristics for consideration when matching clustering algorithms to the intended application. These are used to generate a small subset of suitable clustering algorithms whose performance are then evaluated utilizing quantitative cluster validity indices. To validate our analysis framework for selecting clustering algorithms, we applied it to four different types of datasets: three datasets of homemade explosives spectroscopy, eight datasets of publicly available spectroscopy data covering food and biomedical applications, a gene expression cancer dataset, and three classic machine learning datasets. Each data type has discernible differences in the composition of the data and the context within which they are used. Our analysis framework, when applied to each of these challenges, recommended differing subsets of clustering algorithms for final quantitative performance evaluation. For each application, the recommended clustering algorithms were confirmed to contain the top performing algorithms through quantitative performance indices.
Carnivorous plants are mixotrophs that have developed the ability to lure, trap, and digest small organisms and utilize components of the digested bodies. Leaves of Drosophyllum lusitanicum have two ...kinds of glands (emergences): stalked mucilage glands and sessile digestive glands. The stalked mucilage glands perform the primary role in prey lure and trapping. Apart from their role in carnivory, they absorb water condensed from oceanic fog; thus, plants can survive in arid conditions. To better understand the function of carnivorous plant emergences, the molecular composition of their cell walls was investigated using immunocytochemical methods. In this research, Drosophyllum lusitanicum was used as a study system to determine whether cell wall immunocytochemistry differs between the mucilage and digestive glands of other carnivorous plant species. Light and electron microscopy were used to observe gland structure. Fluorescence microscopy revealed the localization of carbohydrate epitopes associated with the major cell wall polysaccharides and glycoproteins. The mucilage gland (emergence) consists of a glandular head, a connecting neck zone, and stalk. The gland head is formed by an outer and inner layer of glandular (secretory) cells and supported by a layer of endodermoid (barrier) cells. The endodermoid cells have contact with a core of spongy tracheids with spiral-shaped thickenings. Lateral tracheids are surrounded by epidermal and parenchymal neck cells. Different patterns of cell wall components were found in the various cell types of the glands. Cell walls of glandular cells generally are poor in both low and highly esterified homogalacturonans (HGs) but enriched with hemicelluloses. Cell walls of inner glandular cells are especially rich in arabinogalactan proteins (AGPs). The cell wall ingrowths in glandular cells are significantly enriched with hemicelluloses and AGPs. In the case of cell wall components, the glandular cells of Drosophyllum lusitanicum mucilage glands are similar to the glandular cells of the digestive glands of Aldrovanda vesiculosa and Dionaea muscipula.
Scalesia pendunculata Hook.f. is the dominant tree in several highlands' areas of the Galapagos Archipelago, yet in inhabited islands the conversion to agricultural fields has reduced its cover. The ...transition to agroforestry systems including the species shows promising scenarios to restore its cover and to provide ecosystem services such as carbon sequestration. Here, based on field gathered data, we model the potential contribution of S. pedunculata stands in the carbon sequestration of Galapagos. Between 2013-2021, 426 S. pedunculata seedlings were planted in the highlands of Santa Cruz and Floreana islands using several restoration technologies, and their height and survival were monitored every three months. A sub-sample of 276 trees alive since 2020 was used to estimate the DBH based on plant age and height. Based on scientific literature, biomass and carbon content were estimated across time. The final modelling included the density of plants in the restoration sites, estimated DBH, potential survival by restoration treatment, and a Brownian noise to add stochastic events. Overall, survival of S. pedunculata was high in control and slightly increased by most restoration treatments. A stand of 530 trees/ha was projected to sequester ~21 Mg C/ha in 10 years. If this is replicated over all Galapagos coffee production would contribute to the reduction of -1.062% of the Galapagos carbon footprint for the same period. This study adds to compiling benefits of restoring Galapagos flora.
Aim
Marine habitats and their dynamics are difficult to systematically monitor, particularly those in remote locations. This is the case with the sub‐Antarctic ecosystem of the giant kelp Macrocystis ...pyrifera, which was already noted by Charles Darwin in his accounts on the Voyage of the Beagle and recorded on the nautical charts made during that expedition. We combined these and other nautical charts from the 19th and early 20th centuries with surveys conducted in the 1970s and 1980s and satellite detection algorithms from 1984 to 2019, to analyse kelp distribution through time and the factors that correlate with it.
Location
Marine ecoregions of Channels and Fjords of Southern Chile, Falkland Islands (Malvinas), and the island of South Georgia.
Taxon
Macrocystis pyrifera.
Methods
We characterised 309 giant kelp forests by their coastal geospatial attributes. Statistically significant variables were included in a conditional inference tree to predict kelp forest size. Sea surface temperature (SST) records were analysed to confirm temperature ranges over the last four decades. Nautical charts, historical surveys, aerial photogrammetry, unmanned aerial vehicle (UAV) surveys and satellite imagery were overlaid to assess spatial distribution of kelp forest canopies, spanning the period 1829–2020.
Results
Considering the extensive natural and human caused changes over the last two centuries, this diverse kelp ecosystem is remarkably persistent. We found that the ocean currents and wave exposure, combined with the geomorphological settings of the coastline are the most critical factors predicting the extent of the kelp forests.
Main conclusions
We have described the long‐term ecological persistence of the kelp forests in this vastly under‐studied region that offers a conceptual biogeographical model supporting the global importance proposed by Charles Darwin 200 years ago (Darwin, 1845). In the current context of global change, the need for conservation of this persistent and well‐preserved marine ecosystem has never been more important.
Triple negative tumors are more aggressive than other breast cancer subtypes and there is a lack of specific therapeutic targets on them. Since muscarinic receptors have been linked to tumor ...progression, we investigated the effect of metronomic therapy employing a traditional anti-cancer drug, paclitaxel plus muscarinic agonists at low doses on this type of tumor. We observed that MDA-MB231 tumor cells express muscarinic receptors, while they are absent in the non-tumorigenic MCF-10A cell line, which was used as control. The addition of carbachol or arecaidine propargyl ester, a non-selective or a selective subtype 2 muscarinic receptor agonist respectively, plus paclitaxel reduces cell viability involving a down-regulation in the expression of ATP “binding cassette” G2 drug transporter and epidermal growth factor receptor. We also detected an inhibition of tumor cell migration and anti-angiogenic effects produced by those drug combinations in vitro and in vivo (in NUDE mice) respectively. Our findings provide substantial evidence about subtype 2 muscarinic receptors as therapeutic targets for the treatment of triple negative tumors.
The radical cure of Plasmodium vivax and P. ovale requires treatment with primaquine or tafenoquine to clear dormant liver stages. Either drug can induce haemolysis in individuals with ...glucose-6-phosphate dehydrogenase (G6PD) deficiency, necessitating screening. The reference diagnostic method for G6PD activity is ultraviolet (UV) spectrophotometry; however, a universal G6PD activity threshold above which these drugs can be safely administered is not yet defined. Our study aimed to quantify assay-based variation in G6PD spectrophotometry and to explore the diagnostic implications of applying a universal threshold.
Individual-level data were pooled from studies that used G6PD spectrophotometry. Studies were identified via PubMed search (25 April 2018) and unpublished contributions from contacted authors (PROSPERO: CRD42019121414). Studies were excluded if they assessed only individuals with known haematological conditions, were family studies, or had insufficient details. Studies of malaria patients were included but analysed separately. Included studies were assessed for risk of bias using an adapted form of the Quality Assessment of Diagnostic Accuracy Studies-2 (QUADAS-2) tool. Repeatability and intra- and interlaboratory variability in G6PD activity measurements were compared between studies and pooled across the dataset. A universal threshold for G6PD deficiency was derived, and its diagnostic performance was compared to site-specific thresholds. Study participants (n = 15,811) were aged between 0 and 86 years, and 44.4% (7,083) were women. Median (range) activity of G6PD normal (G6PDn) control samples was 10.0 U/g Hb (6.3-14.0) for the Trinity assay and 8.3 U/g Hb (6.8-15.6) for the Randox assay. G6PD activity distributions varied significantly between studies. For the 13 studies that used the Trinity assay, the adjusted male median (AMM; a standardised metric of 100% G6PD activity) varied from 5.7 to 12.6 U/g Hb (p < 0.001). Assay precision varied between laboratories, as assessed by variance in control measurements (from 0.1 to 1.5 U/g Hb; p < 0.001) and study-wise mean coefficient of variation (CV) of replicate measures (from 1.6% to 14.9%; p < 0.001). A universal threshold of 100% G6PD activity was defined as 9.4 U/g Hb, yielding diagnostic thresholds of 6.6 U/g Hb (70% activity) and 2.8 U/g Hb (30% activity). These thresholds diagnosed individuals with less than 30% G6PD activity with study-wise sensitivity from 89% (95% CI: 81%-94%) to 100% (95% CI: 96%-100%) and specificity from 96% (95% CI: 89%-99%) to 100% (100%-100%). However, when considering intermediate deficiency (<70% G6PD activity), sensitivity fell to a minimum of 64% (95% CI: 52%-75%) and specificity to 35% (95% CI: 24%-46%). Our ability to identify underlying factors associated with study-level heterogeneity was limited by the lack of availability of covariate data and diverse study contexts and methodologies.
Our findings indicate that there is substantial variation in G6PD measurements by spectrophotometry between sites. This is likely due to variability in laboratory methods, with possible contribution of unmeasured population factors. While an assay-specific, universal quantitative threshold offers robust diagnosis at the 30% level, inter-study variability impedes performance of universal thresholds at the 70% level. Caution is advised in comparing findings based on absolute G6PD activity measurements across studies. Novel handheld quantitative G6PD diagnostics may allow greater standardisation in the future.
The newly created Kawésqar National Park (KNP) and National Reserve (KNR) in southern Chile consists of diverse terrestrial and marine habitats, which includes the southern terminus of the Andes, the ...Southern Patagonia Ice Fields, sub-Antarctic rainforests, glaciers, fjords, lakes, wetlands, valleys, channels, and islands. The marine environment is influenced by wide ranging hydrological factors such as glacier melt, large terrigenous inputs, high precipitation, strong currents, and open ocean water masses. Owing to the remoteness, rugged terrain, and harsh environmental conditions, little is known about this vast region, particularly the marine realm. To this end, we conducted an integrated ecological assessment using SCUBA and remote cameras down to 600 m to examine this unique and largely unexplored ecosystem. Kelp forests (primarily Macrocystis pyrifera) dominate the nearshore ecosystem and provide habitat for myriad benthic organisms. In the fjords, salinity was low and both turbidity and nutrients from terrigenous sources were high, with benthic communities dominated by active suspension feeders (e.g., Bivalvia, Ascidiacea, and Bryozoa). Areas closer to the Pacific Ocean showed more oceanic conditions with higher salinity and lower turbidity, with benthic communities experiencing more open benthic physical space in which predators (e.g., Malacostraca and Asteroidea) and herbivorous browsers (e.g., Echinoidea and Gastropoda) were more conspicuous components of the community compared to the inner fjords. Hagfish (Myxine sp.) was the most abundant and frequently occurring fish taxa observed on deep-sea cameras (80% of deployments), along with several taxa of sharks (e.g., Squaliformes, Etmopteridae, Somniosidae, Scyliorhinidae), which collectively were also observed on 80% of deep-sea camera deployments. The kelp forests, deep fjords, and other nearshore habitats of the KNR represent a unique ecosystem with minimal human impacts at present. The KNR is part of the ancestral territory of the indigenous Kawésqar people and their traditional knowledge, including the importance of the land-sea connection in structuring the marine communities of this region, is strongly supported by our scientific findings.
Charles Darwin never doubted the common ancestry of the human races. But he was open-minded about whether the races might nevertheless be so different from each other that they ought to be classified ...not as varieties of one species but as distinct species. He pondered this varieties-or-species question on and off for decades, from his time aboard the Beagle through to the publication of the Descent of Man. A constant throughout was his concern with something that he first learned on the Beagle voyage and that, on the face of it, seemed to favour the species ranking: the different races, he was told, play host to distinct species of lice. This paper reconstructs the long run of Darwin's reflections and interactions on race, lice and history, using his extended correspondence with Henry Denny – curator of the scientific collections of the Leeds Philosophical and Literary Society, and Britain's leading expert in the natural history of lice – as a window onto the social world whose imprint is everywhere in the pages of the Descent.
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