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

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

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

Evaluation of ChatGPT Feedback on ELL Writers' Coherence and Cohesion

Since its launch in November 2022, ChatGPT has had a transformative effect on education where students are using it to help with homework assignments and teachers are actively employing it in their teaching practices. This includes using ChatGPT as a tool for writing teachers to grade and generate feedback on students' essays. In this study, we evaluated the quality of the feedback generated by ChatGPT regarding the coherence and cohesion of the essays written by English Language Learners (ELLs) students. We selected 50 argumentative essays and generated feedback on coherence and cohesion using the ELLIPSE rubric. During the feedback evaluation, we used a two-step approach: first, each sentence in the feedback was classified into subtypes based on its function (e.g., positive reinforcement, problem statement). Next, we evaluated its accuracy and usability according to these types. Both the analysis of feedback types and the evaluation of accuracy and usability revealed that most feedback sentences were highly abstract and generic, failing to provide concrete suggestions for improvement. The accuracy in detecting major problems, such as repetitive ideas and the inaccurate use of cohesive devices, depended on superficial linguistic features and was often incorrect. In conclusion, ChatGPT, without specific training for the feedback generation task, does not offer effective feedback on ELL students' coherence and cohesion.Comment: 24 pages, 1 figure

Harnessing novel genetic markers for scald resistance from gene bank spring barley genotypes

Background Scald caused by Rhynchosporium graminicola is a common foliar disease affecting barley production worldwide. Identifying and utilizing scald resistance genes and quantitative trait loci (QTL) to develop barley cultivars with durable and effective resistance to scald is crucial. Results In the present study, we evaluated 275 spring barley genotypes together with 4 commercial check cultivars under controlled conditions and examined the underlying genetics of scald resistance in these genotypes. A significant genetic variation (P value < 0.0001) for scald resistance was observed among the tested barley germplasms. A genome-wide association study (GWAS) identified eight markers-trait associations (MTAs) forming seven QTL located on chromosomes 3H, 6H, and 7H, of which three are novel. The allelic effects of these MTAs were further examined, and favorable alleles associated with scald resistance were identified. Conclusions The identification of QTL for scald resistance, along with favorable allele identification, will be crucial for marker-assisted breeding programs. These findings will facilitate the development of new scald-resistant cultivars and contribute to the sustainability of barley production. Further studies, such as fine-mapping of candidate genes within these identified QTL regions, will help to narrow down the potential causative genetic variants and understand their functional effects on scald resistance

The FoodAuthent Cloud: An Approach Towards A Comprehen-sive Authentication In Food Supply Chains Using Fingerprinting

The research project FoodAuthent aims at establishing framework conditions and incentives to use fingerprinting procedures routinely for food authenticity purposes. In particular, the FoodAuthent system intends to enable the collection, analysis and utilization of chemical "fingerprints" of food products to provide evidence of the authen-ticity of food. For this purpose, cooperatively usable cloud-based food fingerprinting repositories together with standardised data analysis methods are set up as open-source and linked to a discovery service and batch-specific product information

What a girl’s gotta do: the labour of the biopolitical celebrity in austerity Britain

This article debunks the wide-spread view that young female celebrities, especially those who rise to fame through reality shows and other forms of media-orchestrated self-exposure, dodge ‘real’ work out of laziness, fatalism and a misguided sense of entitlement. Instead, we argue that becoming a celebrity in a neoliberal economy such as that of the United Kingdom, where austerity measures disproportionately disadvantage the young, women and the poor is not as irregular or exceptional a choice as previously thought, especially since the precariousness of celebrity earning power adheres to the current demands of the neoliberal economy on its workforce. What is more, becoming a celebrity involves different forms of labour that are best described as biopolitical, since such labour fully involves and consumes the human body and its capacities as a living organism. Weight gain and weight loss, pregnancy, physical transformation through plastic surgery, physical symptoms of emotional distress and even illness and death are all photographically documented and supplemented by extended textual commentary, usually with direct input from the celebrity, reinforcing and expanding on the visual content. As well as casting celebrity work as labour, we also maintain that the workings of celebrity should always be examined in the context of wider cultural and real economies

Healthcare service evolution towards the Internet of Things: an end-user perspective

For the last two decades the Internet of Things (IoT) has been a subject of growing global interest. Particularly dynamic industries such as the healthcare service sector have just begun to understand the benefits of the IoT for the provision of a new, more advanced type of services. However, whilst the healthcare service industry is yet to fully grasp the benefits of information systems for its practitioners and managers, and for patients and families, there is a need for a better understanding of the challenges and opportunities associated to IoT-based healthcare systems as another disruptive wave of technologies. In particular, research on the relevance of users’ skills for adoption of IoT-based healthcare services has been limited. Using the current Internet-based healthcare service landscape as a platform for the formulation and testing of its hypotheses, this paper explores the relationship between patients’ capabilities for effective use of information and communication technologies and the success of IoT-based healthcare services. The resulting theoretical model for effective use of information and communication technologies and the success of IoT-based healthcare services was then validated. The validation was based on data collected from a randomly selected sample of 256 users of Internet-based healthcare services provided by the public healthcare system of the Region of Murcia in Spain. The findings of this research inform future strategies for the implementation of new generations of health and well-being services based on IoT technologies