Search Results (9)

Neuroblastoma (NB) is an aggressive childhood cancer requiring intensive multimodal therapies in high-risk (HRNB) patients. Currently, invasive surgical biopsies are required to classify NB risk group and assign treatment based on the tumour genetic profile. Circulating tumour DNA (ctDNA) obtained from blood samples can be used to identify tumour biomarkers. Here we applied targeted next-generation sequencing (tNGS) using a panel of 42 genes to analyse 32 NB ctDNA samples for the presence of single-nucleotide variants and copy number changes from 28 patients in all NB risk groups. In two additional ctDNA samples, droplet digital PCR was used to detect hotspot ALK variants. Pathogenic mutations with a variant allele frequency (VAF) > 1% were identified in 13/32 (41%) ctDNA samples. ALK and PTPN11 were the most frequent, each being detected in 4/32 (13%) samples, together with oncogene amplifications. Targeted NGS of ctDNA detected actionable variants, including those absent in the diagnostic primary tumour due to spatial and temporal heterogeneity. Our findings confirm the usefulness of ctDNA in detecting genetic abnormalities in NB. Full article

Ambient particulate matter (PM₁₀) and its chemical composition in polycyclic aromatic hydrocarbons (PAHs) were studied in areas of specific interest, between September 2015 and July 2016. The principal aim of this study was to assess the different PAH source profiles in each area, as well as their potential health risk. In particular, the studied areas were (a) the semiurban industrialized zone of the Municipality of Peloponnese (Meligalas, Messini) of Messinia prefecture, due to the intensive olive-productive activity in the extensive area, (b) the industrialized zone of Oinofyta in Voiotia prefecture, and (c) the urban/traffic center of Athens (Aristotelous). Intense spatial and seasonal variations in PAH levels were observed among the study areas collectively, but also for each one individually. During the winter period, the total PAHs average concentration was 11.45 and 9.84 ng/m³ at Meligalas–Skala (S1, S2 stations), 8.84 ng/m³ at Messini (S3 station), and 6.30 ng/m³ at the center of Athens (Aristotelous). During the summer campaign, the corresponding levels were 0.99, 1.20, and 0.70 ng/m³ (S1, S2, and S3 stations), and 5.84 ng/m³ (Aristotelous), respectively. The highest potential cancer risk of the PAHs mixture was estimated based on winter season measurements taken at the Municipality of Peloponnese. In order to determine PAH sources, two different source apportionment techniques were applied, i.e., diagnostic ratios (DRs) and the positive matrix factorization (PMF) model. Full article

Climate change is undeniably one of the most pressing and critical challenges facing humanity in the 21st century. In this context, monitoring the Earth’s Energy Imbalance (EEI) is fundamental in conjunction with greenhouse gases (GHGs) in order to comprehensively understand and address climate change. The French Uvsq-Sat NG pathfinder mission addresses this issue through the implementation of a Six-Unit CubeSat, which has dimensions of 111.3 × 36.6 × 38.8 cm in its unstowed configuration. Uvsq-Sat NG is a satellite mission spearheaded by the Laboratoire Atmosphères, Observations Spatiales (LATMOS), and supported by the International Satellite Program in Research and Education (INSPIRE). The launch of this mission is planned for 2025. One of the Uvsq-Sat NG objectives is to ensure the smooth continuity of the Earth Radiation Budget (ERB) initiated via the Uvsq-Sat and Inspire-Sat satellites. Uvsq-Sat NG seeks to achieve broadband ERB measurements using state-of-the-art yet straightforward technologies. Another goal of the Uvsq-Sat NG mission is to conduct precise and comprehensive monitoring of atmospheric gas concentrations (CO${}_2$ and CH${}_4$) on a global scale and to investigate its correlation with Earth’s Outgoing Longwave Radiation (OLR). Uvsq-Sat NG carries several payloads, including Earth Radiative Sensors (ERSs) for monitoring incoming solar radiation and outgoing terrestrial radiation. A Near-Infrared (NIR) Spectrometer is onboard to assess GHGs’ atmospheric concentrations through observations in the wavelength range of 1200 to 2000 nm. Uvsq-Sat NG also includes a high-definition camera (NanoCam) designed to capture images of the Earth in the visible range. The NanoCam will facilitate data post-processing acquired via the spectrometer by ensuring accurate geolocation of the observed scenes. It will also offer the capability of observing the Earth’s limb, thus providing the opportunity to roughly estimate the vertical temperature profile of the atmosphere. We present here the scientific objectives of the Uvsq-Sat NG mission, along with a comprehensive overview of the CubeSat platform’s concepts and payload properties as well as the mission’s current status. Furthermore, we also describe a method for the retrieval of atmospheric gas columns (CO${}_2$, CH${}_4$, O${}_2$, H${}_2$O) from the Uvsq-Sat NG NIR Spectrometer data. The retrieval is based on spectra simulated for a range of environmental conditions (surface pressure, surface reflectance, vertical temperature profile, mixing ratios of primary gases, water vapor, other trace gases, cloud and aerosol optical depth distributions) as well as spectrometer characteristics (Signal-to-Noise Ratio (SNR) and spectral resolution from 1 to 6 nm). Full article

Spatial transcriptomic technologies enable measurement of expression levels of genes systematically throughout tissue space, deepening our understanding of cellular organizations and interactions within tissues as well as illuminating biological insights in neuroscience, developmental biology and a range of diseases, including cancer. A variety of spatial technologies have been developed and/or commercialized, differing in spatial resolution, sensitivity, multiplexing capability, throughput and coverage. In this paper, we review key enabling spatial transcriptomic technologies and their applications as well as the perspective of the techniques and new emerging technologies that are developed to address current limitations of spatial methodologies. In addition, we describe how spatial transcriptomics data can be integrated with other omics modalities, complementing other methods in deciphering cellar interactions and phenotypes within tissues as well as providing novel insight into tissue organization. Full article

The study investigated the composition and content of Σ₁₅PAH in the surface and core sediments from Dachan Bay (DCB) in Shenzhen city and discussed the effects of urban development and regional energy structure on the marine environment through the spatial distribution, vertical profile, and sources of Σ₁₅PAH. The results indicated that the concentrations of Σ₁₅PAH in the sediments of DCB ranged between 299 ng/g and 2336 ng/g in the surface sediments and between 65 ng/g and 994 ng/g in the core sediments. The horizontal spatial distribution of PAHs content with decreasing concentrations from the coastal to central areas implied the land-based input of PAHs. The vertical profile of high PAHs concentration in 0 cm–60 cm suggested that the PAHs pollution is attributed to the urban development of Shenzhen since 1950, especially after the 1980s. According to features of the low molecular weight (LMW)/high molecular weight (HMW), PAHs diagnostic ratios and their relationships with total organic carbon (TOC) and oil, the pyrogenic PAHs were mainly from the combustion of petroleum and byproducts in the surface and 0 cm–60 cm sediments but from the combustion of biomass in 60 cm–190 cm sediments, which corresponded with the variation of energy structure in surrounding areas. This study suggested that urban development and regional energy structure have a great impact on PAHs distribution in DCB and further controls of land-based pollutant emissions are still needed. Full article

This review highlights the pivotal role of root exudates in the rhizosphere, especially the interactions between plants and microbes and between plants and plants. Root exudates determine soil nutrient mobilization, plant nutritional status, and the communication of plant roots with microbes. Root exudates contain diverse specialized signaling metabolites (primary and secondary). The spatial behavior of these metabolites around the root zone strongly influences rhizosphere microorganisms through an intimate compatible interaction, thereby regulating complex biological and ecological mechanisms. In this context, we reviewed the current understanding of the biological phenomenon of allelopathy, which is mediated by phytotoxic compounds (called allelochemicals) released by plants into the soil that affect the growth, survival, development, ecological infestation, and intensification of other plant species and microbes in natural communities or agricultural systems. Advances in next-generation sequencing (NGS), such as metagenomics and metatranscriptomics, have opened the possibility of better understanding the effects of secreted metabolites on the composition and activity of root-associated microbial communities. Nevertheless, understanding the role of secretory metabolites in microbiome manipulation can assist in designing next-generation microbial inoculants for targeted disease mitigation and improved plant growth using the synthetic microbial communities (SynComs) tool. Besides a discussion on different approaches, we highlighted the advantages of conjugation of metabolomic approaches with genetic design (metabolite-based genome-wide association studies) in dissecting metabolome diversity and understanding the genetic components of metabolite accumulation. Recent advances in the field of metabolomics have expedited comprehensive and rapid profiling and discovery of novel bioactive compounds in root exudates. In this context, we discussed the expanding array of metabolomics platforms for metabolome profiling and their integration with multivariate data analysis, which is crucial to explore the biosynthesis pathway, as well as the regulation of associated pathways at the gene, transcript, and protein levels, and finally their role in determining and shaping the rhizomicrobiome. Full article

Phthalate esters (PAEs) are endocrine-disrupting chemicals that pose potential risks to human health. Water and sediments are crucial carriers and storage media for the migration and transformation of PAEs. In this study, six congeners of PAEs were measured in water and sediment samples to elucidate their spatial distribution, congener profiles, and ecological risks in the middle-lower Hanjiang River during the wet and dry seasons. The concentration of the Σ₆PAEs ranged from 592 to 2.75 × 10³ ng/L with an average of 1.47 × 10³ ng/L in surface water, while the concentration of the Σ₆PAEs ranged from 1.12 × 10³ to 6.61 × 10³ ng/g with an average of 2.69 × 10³ ng/g in sediments. In general, PAE concentrations were ranked as sediment > water, and dry season > wet season. DEHP and DBP were the dominant PAEs in the middle-lower Hanjiang River in surface water and sediments. SPSS analysis showed that dissolved organic carbon (DOC) in surface water was significantly correlated with the concentration of DBP, DEHP, and the ∑₆PAEs, while organic matter (OM) was significantly correlated with the concentration of the ∑₆PAEs in sediments. The concentrations of PAEs were irregularly distributed and varied significantly in surface water and sediments. Compared with other regions at home and abroad, the pollution levels of surface water and sediments in the middle-lower Hanjiang River were relatively low and not enough to have a negative impact on the local water’s ecological environment. However, the supervision of land-based discharge should still be strengthened. Full article

A method is developed in this paper to calculate the spatial gain of a vertical line array when the plane-wave assumption is not applicable and when the oceanic ambient noise is correlated. The proposed optimal array gain (OAG), which can evaluate the array’s performance and effectively guide its deployment, can be given by an equation in which the noise gain (NG) is subtracted from the signal gain (SG); hence, a high SG and a negative NG can enhance the performance of the array. OAGs and SGs with different array locations are simulated and analyzed based on the sound propagation properties of the direct-arrival zone (DAZ) and the reliable acoustic path (RAP) using ray theory. SG and NG are related to the correlation coefficients of the signals and noise, respectively, and the vertical correlation is determined by the structures of the multipath arrivals. The SG in the DAZ is always high because there is little difference between the multipath waves, while the SG in the RAP changes with the source-receiver range because of the variety of structure in the multiple arrivals. The SG under different conditions is simulated in this work. The “dual peak” structure can often be observed in the vertical directionality pattern of the noise because of the presence of bottom reflection and deep sound channel. When the directions of the signal and noise are close, the conventional beamformer will enhance the correlation of not only the signals but also the noise; thus, the directivity of the signals and noise are analyzed. Under the condition of having a typical sound speed profile, the OAG in some areas of the DAZ and RAP can achieve high values and even exceed the ideal gain of horizontal line array 10 logN dB, while, in some other areas, it will be lowered because of the influence of the NG. The proposed method of gain analysis can provide analysis methods for vertical arrays in the deep ocean under many conditions with references. The theory and simulation are tested by experimental data. Full article

A comparison between efforts to detect methane anomalies by a simple band ratio approach from the Airborne Visual Infrared Imaging Spectrometer-Classic (AVIRIS-C) data for the Kern Front oil field, Central California, and the Coal Oil Point marine hydrocarbon seep field, offshore southern California, was conducted. The detection succeeded for the marine source and failed for the terrestrial source, despite these sources being of comparable strength. Scene differences were investigated in higher spectral and spatial resolution collected by the AVIRIS-C successor instrument, AVIRIS Next Generation (AVIRIS-NG), by a sensitivity study. Sensitivity to factors including water vapor, aerosol, planetary boundary layer (PBL) structure, illumination and viewing angle, and surface albedo clutter were explored. The study used the residual radiance method, with sensitivity derived from MODTRAN (MODerate resolution atmospheric correction TRANsmission) simulations of column methane (XCH₄). Simulations used the spectral specifications and geometries of AVIRIS-NG and were based on a uniform or an in situ vertical CH₄ profile, which was measured concurrent with the AVIRIS-NG data. Small but significant sensitivity was found for PBL structure and water vapor; however, highly non-linear, extremely strong sensitivity was found for surface albedo error. For example, a 10% decrease in the surface albedo corresponded to a 300% XCH₄ increase over background XCH₄ to compensate for the total signal, less so for stronger plumes. This strong non-linear sensitivity resulted from the high percentage of surface-reflected radiance in the airborne at-sensor total radiance. Coarse spectral resolution and feedback from interferents like water vapor underlay this sensitivity. Imaging spectrometry like AVIRIS and the Hyperspectral InfraRed Imager (HyspIRI) candidate satellite mission, have the advantages of contextual spatial information and greater at-sensor total radiance. However, they also face challenges due to their relatively broad spectral resolution compared to trace gas specific orbital sensors, e.g., the Greenhouse gases Observing SATellite (GOSAT), which is especially applicable to trace gas retrievals over scenes with high spectral albedo variability. Results of the sensitivity analysis are applicable for the residual radiance method and CH₄ profiles used in the analysis, but they illustrate potential significant challenges in CH₄ retrievals using other approaches. Full article