Decreasing time consumption of microscopy image segmentation through parallel processing on the GPU

The computational performance of graphical processing units (GPUs) has improved significantly. Achieving speedup factors of more than 50x compared to single-threaded CPU execution are not uncommon due to parallel processing. This makes their use for high throughput microscopy image analysis very appealing. Unfortunately, GPU programming is not straightforward and requires a lot of programming skills and effort. Additionally, the attainable speedup factor is hard to predict, since it depends on the type of algorithm, input data and the way in which the algorithm is implemented. In this paper, we identify the characteristic algorithm and data-dependent properties that significantly relate to the achievable GPU speedup. We find that the overall GPU speedup depends on three major factors: (1) the coarse-grained parallelism of the algorithm, (2) the size of the data and (3) the computation/memory transfer ratio. This is illustrated on two types of well-known segmentation methods that are extensively used in microscopy image analysis: SLIC superpixels and high-level geometric active contours. In particular, we find that our used geometric active contour segmentation algorithm is very suitable for parallel processing, resulting in acceleration factors of 50x for 0.1 megapixel images and 100x for 10 megapixel images

Essential requirement for JPT2 in NAADP-evoked Ca²⁺ signaling

Nicotinic acid adenine dinucleotide phosphate (NAADP) is a second messenger that releases Ca2+ from acidic organelles through the activation of two-pore channels (TPCs) to regulate endolysosomal trafficking events. NAADP action is mediated by NAADP-binding protein(s) of unknown identity that confer NAADP sensitivity to TPCs. Here, we used a “clickable” NAADP-based photoprobe to isolate human NAADP-binding proteins and identified Jupiter microtubule-associated homolog 2 (JPT2) as a TPC accessory protein required for endogenous NAADP-evoked Ca2+ signaling. JPT2 was also required for the translocation of a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pseudovirus through the endolysosomal system. Thus, JPT2 is a component of the NAADP receptor complex that is essential for TPC-dependent Ca2+ signaling and control of coronaviral entry

Human disc cells in monolayer vs 3D culture: cell shape, division and matrix formation

BACKGROUND: The relationship between cell shape, proliferation, and extracellular matrix (ECM) production, important aspects of cell behavior, is examined in a little-studied cell type, the human annulus cell from the intervertebral disc, during monolayer vs three-dimensional (3D) culture. RESULTS: Three experimental studies showed that cells respond specifically to culture microenvironments by changes in cell shape, mitosis and ECM production: 1) Cell passages showed extensive immunohistochemical evidence of Type I and II collagens only in 3D culture. Chondroitin sulfate and keratan sulfate were abundant in both monolayer and 3D cultures. 2) Cells showed significantly greater proliferation in monolayer in the presence of platelet-derived growth factor compared to cells in 3D. 3) Cells on Matrigel™-coated monolayer substrates became rounded and formed nodular colonies, a finding absent during monolayer growth. CONCLUSIONS: The cell's in vivo interactions with the ECM can regulate shape, gene expression and other cell functions. The shape of the annulus cell changes markedly during life: the young, healthy disc contains spindle shaped cells and abundant collagen. With aging and degeneration, many cells assume a strikingly different appearance, become rounded and are surrounded by unusual accumulations of ECM products. In vitro manipulation of disc cells provides an experimental window for testing how disc cells from given individuals respond when they are grown in environments which direct cells to have either spindle- or rounded-shapes. In vitro assessment of the response of such cells to platelet-derived growth factor and to Matrigel™ showed a continued influence of cell shape even in the presence of a growth factor stimulus. These findings contribute new information to the important issue of the influence of cell shape on cell behavior

Global datasets of leaf photosynthetic capacity for ecological and earth system research

The maximum rate of Rubisco carboxylation (Vcmax) determines leaf photosynthetic capacity and is a key parameter for estimating the terrestrial carbon cycle, but its spatial information is lacking, hindering global ecological research. Here, we convert leaf chlorophyll content (LCC) retrieved from satellite data to Vcmax, based on plants’ optimal distribution of nitrogen between light harvesting and carboxylation pathways. We also derive Vcmax from satellite (GOME-2) observations of sun-induced chlorophyll fluorescence (SIF) as a proxy of leaf photosynthesis using a data assimilation technique. These two independent global Vcmax products agree well (r 2=0.79, RMSE=15.46 μmol m-2 s -1 25 , P<0.001) and compare well with 3672 ground-based measurements (r2=0.68, RMSE=13.55 μmol m-2 s -1 and P<0.001 for SIF; r2=0.55, RMSE=17.55 μmol m-2 s -1 and P<0.001 for LCC). The LCC-derived Vcmax product is also used to constrain the retrieval of Vcmax from TROPOMI SIF data to produce an optimized Vcmax product using both SIF and LCC information. The global distributions of these products are compatible with Vcmax computed from an ecological optimality theory using meteorological variables, but importantly reveal additional information on the influence of land cover, irrigation, soil pH and leaf nitrogen on leaf photosynthetic capacity. These satellite-based approaches and spatial Vcmax products are primed to play a major role in global ecosystem research. The three remote sensing Vcmax products based on SIF, LCC and SIF+LCC are available at https://doi.org/10.5281/zenodo.6466968 (Chen et al., 2020) and the code for implementing the ecological optimality theory is available at https://github.com/SmithEcophysLab/optimal_vcmax_R (Smith, 2020)

MicroRNAs: exploring a new dimension in the pathogenesis of kidney cancer

Renal cell carcinoma (RCC) is the most common neoplasm of the adult kidney. The role of the von-Hippel-Lindeau (VHL) tumour suppressor gene is well established in RCC with a loss of VHL protein leading to accumulated hypoxia-induced factor (HIF) and the subsequent transcriptional activation of multiple downstream targets. Recently, microRNAs (miRNAs) have been shown to be differentially expressed in RCC and their role in RCC pathogenesis is emerging. This month, in BMC Medicine, Gleadle and colleagues show that certain miRNAs are regulated by VHL in either a hypoxia-inducible factor (HIF)-dependent or HIF-independent manner in RCC. They also show that miRNA expression correlates with the survival of RCC patients

Revision and Update of the Consensus Definitions of Invasive Fungal Disease From the European Organization for Research and Treatment of Cancer and the Mycoses Study Group Education and Research Consortium.

BACKGROUND: Invasive fungal diseases (IFDs) remain important causes of morbidity and mortality. The consensus definitions of the Infectious Diseases Group of the European Organization for Research and Treatment of Cancer and the Mycoses Study Group have been of immense value to researchers who conduct clinical trials of antifungals, assess diagnostic tests, and undertake epidemiologic studies. However, their utility has not extended beyond patients with cancer or recipients of stem cell or solid organ transplants. With newer diagnostic techniques available, it was clear that an update of these definitions was essential. METHODS: To achieve this, 10 working groups looked closely at imaging, laboratory diagnosis, and special populations at risk of IFD. A final version of the manuscript was agreed upon after the groups' findings were presented at a scientific symposium and after a 3-month period for public comment. There were several rounds of discussion before a final version of the manuscript was approved. RESULTS: There is no change in the classifications of "proven," "probable," and "possible" IFD, although the definition of "probable" has been expanded and the scope of the category "possible" has been diminished. The category of proven IFD can apply to any patient, regardless of whether the patient is immunocompromised. The probable and possible categories are proposed for immunocompromised patients only, except for endemic mycoses. CONCLUSIONS: These updated definitions of IFDs should prove applicable in clinical, diagnostic, and epidemiologic research of a broader range of patients at high-risk

Non-L\'evy mobility patterns of Mexican Me'Phaa peasants searching for fuelwood

We measured mobility patterns that describe walking trajectories of individual Me'Phaa peasants searching and collecting fuelwood in the forests of "La Monta\~na de Guerrero" in Mexico. These one-day excursions typically follow a mixed pattern of nearly-constant steps when individuals displace from their homes towards potential collecting sites and a mixed pattern of steps of different lengths when actually searching for fallen wood in the forest. Displacements in the searching phase seem not to be compatible with L\'evy flights described by power-laws with optimal scaling exponents. These findings however can be interpreted in the light of deterministic searching on heavily degraded landscapes where the interaction of the individuals with their scarce environment produces alternative searching strategies than the expected L\'evy flights. These results have important implications for future management and restoration of degraded forests and the improvement of the ecological services they may provide to their inhabitants.Comment: 15 pages, 4 figures. First version submitted to Human Ecology. The final publication will be available at http://www.springerlink.co

Organochlorine Pesticides in Consumer Fish and Mollusks of Liaoning Province, China: Distribution and Human Exposure Implications

Fish and mollusk samples were collected from markets located in 12 cities in Liaoning province, China, during August and September 2007, and 22 organochlorine pesticides (OCPs) were detected. DDT, HCH, endosulfan, chlordane, and HCB were the dominating OCPs, with mean concentrations and ranges of, respectively, 15.41 and 0.57 to 177.56 ng/g, 0.84 and below detection limit (BDL) to 22.99 ng/g, 1.31 and BDL to 13.1 ng/g, 1.05 and BDL to 15.68 ng/g, and 0.63 and BDL to 9.21 ng/g in all fish and mollusk samples. The concentrations of other OCPs generally were low and were detectable in a minority of samples, reflecting the low levels of these OCPs in the study region. In general, OCP concentrations were obviously higher in fish than in mollusks, and higher in freshwater fish than in marine fish, which indicated, first, that freshwater fish are more easily influenced than seawater fish and mollusks by OCP residues in agricultural areas and, second, that there are different biota accumulation factors for OCPs between fish and mollusk. To learn the consumption of fish and mollusk, 256 questionnaires were sent to families in 12 cities of Liaoning province. Using the contamination data, average estimated daily intakes of OCPs via fish and mollusk consumption were calculated, which were used for exposure assessment. The public health risks caused by exposure to OCPs in the course of fish and mollusk consumption were compared to noncancer benchmarks and cancer benchmarks