Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment

Enhancing the safety and shelf life of beef and plant-based burgers by combining High Hydrostatic Pressure (HHP) with nisin or a blueberry-derived product

The growing demand for sustainable and healthy dietary options has led to significant interest in plant-based meat alternatives though traditional meats, such as beef, remain dominant in the protein market. High Hydrostatic Pressure (HHP) stands out as a promising technology improving food safety and extending shelf life, while combining HHP with clean-label additives offers potential for process optimization. This study investigates the synergistic effect of HHP combined with nisin (500 IU/g) or blueberry-derived product (4 %) in beef and plant-based burgers to control L. monocytogenes and extend shelf life under slight temperature abuse. In plant-based burgers, HHP (600 MPa, 3 min) combined with additives, effectively delayed L. monocytogenes growth for 104 days during storage, outperforming HHP alone. At lower pressures (300–500 MPa), HHP combined with nisin or blueberry product significantly enhanced pathogen reduction in both matrices, achieving a synergistic effect of up to 1.4 log reduction. HHP (600 MPa), with or without the additives, also extended the storage period of non-inoculated plant-based burgers, maintaining the natural microflora below 3 log CFU/g for 83 days. The blueberry product notably influenced the physicochemical properties (e.g. pH, color) of both matrices, while HHP significantly affected the color of beef burgers. This study provides novel insights into the potential applications of HHP combined with natural antimicrobials, highlighting its effectiveness in plant-based meat alternatives and the significant role of the matrix in the synergistic effect. Future research should focus on sensory analysis and consumer acceptance to align these advancements with market demands

SIVA UAV: A Case Study for the EMC Analysis of Composite Air Vehicles

[EN] The increased use of carbon-fiber composites in unmanned aerial vehicles is a challenge for their EMC assessment by numerical solvers. For accurate and reliable simulations, numerical procedures should be tested not only for individual components, but also within the framework of complete systems. With this aim, this paper presents a benchmark test case based on experimental measurements coming from direct-current injection tests in the SIVA unmanned air vehicle, reproduced by a numerical finite-difference-time-domain solver that employs a new subgridding scheme to treat lossy composite thin panels. Validation was undertaken by applying the feature selective validation method, which quantifies the agreement between experimental and numerical data.This work was supported by the Projects TEC2013-48414C3-{ 1,2,3}-R, TEC2016-79214-C3-{1,2,3}-R, and TEC2015-68766-REDC (Spanish MINECO, EU FEDER), P12-TIC-1442 (J. de Andalucia, Spain), Alhambra-UGRFDTD (AIRBUS DS), and by the CSIRC alhambra.ugr.es supercomputing center.Cabello, MR.; Fernández, S.; Pous, M.; Pascual-Gil, E.; Angulo, LD.; López, P.; Riu, PJ.... (2017). SIVA UAV: A Case Study for the EMC Analysis of Composite Air Vehicles. IEEE Transactions on Electromagnetic Compatibility. 59(4):1103-1113. https://doi.org/10.1109/TEMC.2017.2648507S1103111359

Water table depth modulates productivity and biomass across Amazonian forests

Aim: Water availability is the major driver of tropical forest structure and dynamics. Most research has focused on the impacts of climatic water availability, whereas remarkably little is known about the influence of water table depth and excess soil water on forest processes. Nevertheless, given that plants take up water from the soil, the impacts of climatic water supply on plants are likely to be modulated by soil water conditions. / Location: Lowland Amazonian forests. / Time period: 1971–2019. / Methods: We used 344 long-term inventory plots distributed across Amazonia to analyse the effects of long-term climatic and edaphic water supply on forest functioning. We modelled forest structure and dynamics as a function of climatic, soil-water and edaphic properties. / Results: Water supplied by both precipitation and groundwater affects forest structure and dynamics, but in different ways. Forests with a shallow water table (depth <5 m) had 18% less above-ground woody productivity and 23% less biomass stock than forests with a deep water table. Forests in drier climates (maximum cumulative water deficit < −160 mm) had 21% less productivity and 24% less biomass than those in wetter climates. Productivity was affected by the interaction between climatic water deficit and water table depth. On average, in drier climates the forests with a shallow water table had lower productivity than those with a deep water table, with this difference decreasing within wet climates, where lower productivity was confined to a very shallow water table. / Main conclusions: We show that the two extremes of water availability (excess and deficit) both reduce productivity in Amazon upland (terra-firme) forests. Biomass and productivity across Amazonia respond not simply to regional climate, but rather to its interaction with water table conditions, exhibiting high local differentiation. Our study disentangles the relative contribution of those factors, helping to improve understanding of the functioning of tropical ecosystems and how they are likely to respond to climate change

Water table depth modulates productivity and biomass across Amazonian forests

Funding: This work was part of the PhD thesis of the first author, developed at the Graduate Program in Ecology of the National Institute of Amazonian Research (INPA), with a fellowship funded by Coordenação de Aperfeiçoamento de Pessoal de Nível Superior – Brasil (CAPES), Finance Code 001, (88887.141433/2017-00). The authors are also grateful for the financial and research support of the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), Amazonas State Research Foundation (FAPEAM), the Newton Fund via the Natural Environment Research Council (NE/M022021/1 to O.L.P. and F.R.C.C.), PPBio Manaus, Centro de Estudos Integrados da Biodiversidade Amazônica and RAINFOR. We also thank Karina Melgaço, Aurora Levesley and Gabriela Lopez-Gonzalez for curating and managing ForestPlots.net. This was ForestPlots.net Project 26 led by Thaiane Sousa. This is publication number 832 of the Technical Series of the Biological Dynamics of Forest Fragments Project (BDFFP, INPA/STRI).Aim : Water availability is the major driver of tropical forest structure and dynamics. Most research has focused on the impacts of climatic water availability, whereas remarkably little is known about the influence of water table depth and excess soil water on forest processes. Nevertheless, given that plants take up water from the soil, the impacts of climatic water supply on plants are likely to be modulated by soil water conditions. Location : Lowland Amazonian forests. Time period : 1971–2019. Methods : We used 344 long-term inventory plots distributed across Amazonia to analyse the effects of long-term climatic and edaphic water supply on forest functioning. We modelled forest structure and dynamics as a function of climatic, soil-water and edaphic properties. Results : Water supplied by both precipitation and groundwater affects forest structure and dynamics, but in different ways. Forests with a shallow water table (depth <5 m) had 18% less above-ground woody productivity and 23% less biomass stock than forests with a deep water table. Forests in drier climates (maximum cumulative water deficit < −160 mm) had 21% less productivity and 24% less biomass than those in wetter climates. Productivity was affected by the interaction between climatic water deficit and water table depth. On average, in drier climates the forests with a shallow water table had lower productivity than those with a deep water table, with this difference decreasing within wet climates, where lower productivity was confined to a very shallow water table. Main conclusions : We show that the two extremes of water availability (excess and deficit) both reduce productivity in Amazon upland (terra-firme) forests. Biomass and productivity across Amazonia respond not simply to regional climate, but rather to its interaction with water table conditions, exhibiting high local differentiation. Our study disentangles the relative contribution of those factors, helping to improve understanding of the functioning of tropical ecosystems and how they are likely to respond to climate change.Peer reviewe

The global abundance of tree palms

Aim Palms are an iconic, diverse and often abundant component of tropical ecosystems that provide many ecosystem services. Being monocots, tree palms are evolutionarily, morphologically and physiologically distinct from other trees, and these differences have important consequences for ecosystem services (e.g., carbon sequestration and storage) and in terms of responses to climate change. We quantified global patterns of tree palm relative abundance to help improve understanding of tropical forests and reduce uncertainty about these ecosystems under climate change. Location Tropical and subtropical moist forests. Time period Current. Major taxa studied Palms (Arecaceae). Methods We assembled a pantropical dataset of 2,548 forest plots (covering 1,191 ha) and quantified tree palm (i.e., ≥10 cm diameter at breast height) abundance relative to co‐occurring non‐palm trees. We compared the relative abundance of tree palms across biogeographical realms and tested for associations with palaeoclimate stability, current climate, edaphic conditions and metrics of forest structure. Results On average, the relative abundance of tree palms was more than five times larger between Neotropical locations and other biogeographical realms. Tree palms were absent in most locations outside the Neotropics but present in >80% of Neotropical locations. The relative abundance of tree palms was more strongly associated with local conditions (e.g., higher mean annual precipitation, lower soil fertility, shallower water table and lower plot mean wood density) than metrics of long‐term climate stability. Life‐form diversity also influenced the patterns; palm assemblages outside the Neotropics comprise many non‐tree (e.g., climbing) palms. Finally, we show that tree palms can influence estimates of above‐ground biomass, but the magnitude and direction of the effect require additional work. Conclusions Tree palms are not only quintessentially tropical, but they are also overwhelmingly Neotropical. Future work to understand the contributions of tree palms to biomass estimates and carbon cycling will be particularly crucial in Neotropical forests