CLET: Computation of Latencies in Event-related potential Triggers using photodiode on virtual reality apparatuses

To investigate event-related activity in human brain dynamics as measured with EEG, triggers must be incorporated to indicate the onset of events in the experimental protocol. Such triggers allow for the extraction of ERP, i.e., systematic electrophysiological responses to internal or external stimuli that must be extracted from the ongoing oscillatory activity by averaging several trials containing similar events. Due to the technical setup with separate hardware sending and recording triggers, the recorded data commonly involves latency differences between the transmitted and received triggers. The computation of these latencies is critical for shifting the epochs with respect to the triggers sent. Otherwise, timing differences can lead to a misinterpretation of the resulting ERPs. This study presents a methodical approach for the CLET using a photodiode on a non-immersive VR (i.e., LED screen) and an immersive VR (i.e., HMD). Two sets of algorithms are proposed to analyze the photodiode data. The experiment designed for this study involved the synchronization of EEG, EMG, PPG, photodiode sensors, and ten 3D MoCap cameras with a VR presentation platform (Unity). The average latency computed for LED screen data for a set of white and black stimuli was 121.98 ± 8.71 ms and 121.66 ± 8.80 ms, respectively. In contrast, the average latency computed for HMD data for the white and black stimuli sets was 82.80 ± 7.63 ms and 69.82 ± 5.52 ms. The codes for CLET and analysis, along with datasets, tables, and a tutorial video for using the codes, have been made publicly available

Copernicus for urban resilience in Europe

The urban community faces a significant obstacle in effectively utilising Earth Observation (EO) intelligence, particularly the Copernicus EO program of the European Union, to address the multifaceted aspects of urban sustainability and bolster urban resilience in the face of climate change challenges. In this context, here we present the efforts of the CURE project, which received funding under the European Union’s Horizon 2020 Research and Innovation Framework Programme, to leverage the Copernicus Core Services (CCS) in supporting urban resilience. CURE provides spatially disaggregated environmental intelligence at a local scale, demonstrating that CCS can facilitate urban planning and management strategies to improve the resilience of cities. With a strong emphasis on stakeholder engagement, CURE has identified eleven cross-cutting applications between CCS that correspond to the major dimensions of urban sustainability and align with user needs. These applications have been integrated into a cloud-based platform known as DIAS (Data and Information Access Services), which is capable of delivering reliable, usable and relevant intelligence to support the development of downstream services towards enhancing resilience planning of cities throughout Europe

Biodiversity mediates top-down control in eelgrass ecosystems: a global comparative-experimental approach

Nutrient pollution and reduced grazing each can stimulate algal blooms as shown by numerous experiments. But because experiments rarely incorporate natural variation in environmental factors and biodiversity, conditions determining the relative strength of bottom-up and top-down forcing remain unresolved. We factorially added nutrients and reduced grazing at 15 sites across the range of the marine foundation species eelgrass (Zostera marina) to quantify how top-down and bottom-up control interact with natural gradients in biodiversity and environmental forcing. Experiments confirmed modest top-down control of algae, whereas fertilisation had no general effect. Unexpectedly, grazer and algal biomass were better predicted by cross-site variation in grazer and eelgrass diversity than by global environmental gradients. Moreover, these large-scale patterns corresponded strikingly with prior small-scale experiments. Our results link global and local evidence that biodiversity and top-down control strongly influence functioning of threatened seagrass ecosystems, and suggest that biodiversity is comparably important to global change stressors.National Science Foundation [OCE-1031061]info:eu-repo/semantics/publishedVersio

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

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

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

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

Analysis of LhcSR3, a Protein Essential for Feedback De-Excitation in the Green Alga Chlamydomonas reinhardtii

To prevent photodamage by excess light, plants use different proteins to sense pH changes and to dissipate excited energy states. In green microalgae, however, the LhcSR3 gene product is able to perform both pH sensing and energy quenching functions

Habitat-Specific Population Growth of a Farmland Bird

BACKGROUND: To assess population persistence of species living in heterogeneous landscapes, the effects of habitat on reproduction and survival have to be investigated. METHODOLOGY/PRINCIPAL FINDINGS: We used a matrix population model to estimate habitat-specific population growth rates for a population of northern wheatears Oenanthe oenanthe breeding in farmland consisting of a mosaic of distinct habitat (land use) types. Based on extensive long-term data on reproduction and survival, habitats characterised by tall field layers (spring- and autumn-sown crop fields, ungrazed grasslands) displayed negative stochastic population growth rates (log lambda(s): -0.332, -0.429, -0.168, respectively), that were markedly lower than growth rates of habitats characterised by permanently short field layers (pastures grazed by cattle or horses, and farmyards, log lambda(s): -0.056, +0.081, -0.059). Although habitats differed with respect to reproductive performance, differences in habitat-specific population growth were largely due to differences in adult and first-year survival rates, as shown by a life table response experiment (LTRE). CONCLUSIONS/SIGNIFICANCE: Our results show that estimation of survival rates is important for realistic assessments of habitat quality. Results also indicate that grazed grasslands and farmyards may act as source habitats, whereas crop fields and ungrazed grasslands with tall field layers may act as sink habitats. We suggest that the strong decline of northern wheatears in Swedish farmland may be linked to the corresponding observed loss of high quality breeding habitat, i.e. grazed semi-natural grasslands