The EPR paradox, Bell's inequality, and the question of locality

Most physicists agree that the Einstein-Podolsky-Rosen-Bell paradox exemplifies much of the strange behavior of quantum mechanics, but argument persists about what assumptions underlie the paradox. To clarify what the debate is about, we employ a simple and well-known thought experiment involving two correlated photons to help us focus on the logical assumptions needed to construct the EPR and Bell arguments. The view presented in this paper is that the minimal assumptions behind Bell's inequality are locality and counterfactual definiteness, but not scientific realism, determinism, or hidden variables, as is often suggested. We further examine the resulting constraints on physical theory with an illustration from the many-worlds interpretation of quantum mechanics -- an interpretation that we argue is deterministic, local, and realist, but that nonetheless violates the Bell inequality.Comment: 28 pages; change of title, minor wording changes, move to TeX forma

Perfect Fluid Quantum Anisotropic Universe: Merits and Challenges

The present paper deals with quantization of perfect fluid anisotropic cosmological models. Bianchi type V and IX models are discussed following Schutz's method of expressing fluid velocities in terms of six potentials. The wave functions are found for several examples of equations of state. In one case a complete wave packet could be formed analytically. The initial singularity of a zero proper volume can be avoided in this case, but it is plagued by the usual problem of non-unitarity of anisotropic quantum cosmological models. It is seen that a particular operator ordering alleviates this problem.Comment: 13 pages, 4 figures; Accepted for publication in Gen Relativ Gravi

Metatranscriptomic Sequencing of a Cyanobacterial Soil-Surface Consortium with and without a Diverse Underlying Soil Microbiome.

Soil surface consortia are easily observed and sampled, allowing examination of their interactions with soil microbiomes. Here, we present metatranscriptomic sequences from Dark Green 1 (DG1), a cyanobacterium-based soil surface consortium, in the presence and absence of an underlying soil microbiome and/or urea

Use of a Climate and Culture Survey to Assess Diversity, Equity, and Inclusion Initiatives at the VCU School of Social Work

The project aimed to create a survey to assess the effectiveness of previously implemented diversity, equity and inclusion (DEI) initiatives, specifically racial equity at the VCU School of Social Work. The VCU School of Social Work has been actively working with their faculty and staff to address DEI at their school and encourage them to become active in DEI initiatives in other areas in the community. School of Social Work leadership was looking for a way to assess if those DEI initiatives met their intended purpose. This project researched ways to assess the effectiveness of DEI initiatives. The result was the creation of an electronic survey distributed to School of Social Work faculty and staff in the fall of 2021

The challenges of long-term invasive mammal management: lessons from the UK

We consider the motivations, strategies, and costs involved in invasive mammal management undertaken in the UK. Widespread established invasive mammals require long‐term management to limit damage or spread, but ongoing management is costly and complex. Long‐term management is most effective where it is applied at a landscape scale, but this requires overarching co‐ordination between multiple stakeholders. Five challenges for successful long‐term management of invasive mammal species are identified as follows: defining landscape‐scale strategies, management co‐ordination, stakeholder and community engagement, sustainable funding, and evidence requirements. We make recommendations on the supportive infrastructure needed for effective landscape‐scale management of invasive mammals to fulfil long‐term conservation aims, as follows. 1. There is a need for evidence‐based Invasive Species Action Plans to provide strategy for the long‐term ongoing management of prioritised species at appropriate scales. 2. Where possible, multispecies approaches to invasive species management should be adopted. 3. Trusted leadership should be identified to take ownership of Action Plans and provide an overarching co‐ordination to bring individuals, organisations, and funders together. 4. Support for a centralised hub for training, data, and knowledge flows will greatly improve scientific outcomes through a searchable evidence base, and via best practice and knowledge sharing

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types

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