Predicting Emergency Department Volume Using Forecasting Methods to Create a “Surge Response” for Noncrisis Events

Objectives:  This study investigated whether emergency department (ED) variables could be used in mathematical models to predict a future surge in ED volume based on recent levels of use of physician capacity. The models may be used to guide decisions related to on‐call staffing in non–crisis‐related surges of patient volume. Methods:  A retrospective analysis was conducted using information spanning July 2009 through June 2010 from a large urban teaching hospital with a Level I trauma center. A comparison of significance was used to assess the impact of multiple patient‐specific variables on the state of the ED. Physician capacity was modeled based on historical physician treatment capacity and productivity. Binary logistic regression analysis was used to determine the probability that the available physician capacity would be sufficient to treat all patients forecasted to arrive in the next time period. The prediction horizons used were 15 minutes, 30 minutes, 1 hour, 2 hours, 4 hours, 8 hours, and 12 hours. Five consecutive months of patient data from July 2010 through November 2010, similar to the data used to generate the models, was used to validate the models. Positive predictive values, Type I and Type II errors, and real‐time accuracy in predicting noncrisis surge events were used to evaluate the forecast accuracy of the models. Results:  The ratio of new patients requiring treatment over total physician capacity (termed the care utilization ratio [CUR]) was deemed a robust predictor of the state of the ED (with a CUR greater than 1 indicating that the physician capacity would not be sufficient to treat all patients forecasted to arrive). Prediction intervals of 30 minutes, 8 hours, and 12 hours performed best of all models analyzed, with deviances of 1.000, 0.951, and 0.864, respectively. A 95% significance was used to validate the models against the July 2010 through November 2010 data set. Positive predictive values ranged from 0.738 to 0.872, true positives ranged from 74% to 94%, and true negatives ranged from 70% to 90% depending on the threshold used to determine the state of the ED with the 30‐minute prediction model. Conclusions:  The CUR is a new and robust indicator of an ED system’s performance. The study was able to model the tradeoff of longer time to response versus shorter but more accurate predictions, by investigating different prediction intervals. Current practice would have been improved by using the proposed models and would have identified the surge in patient volume earlier on noncrisis days.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/92015/1/j.1553-2712.2012.01359.x.pd

Facilitation of a tropical seagrass by a chemosymbiotic bivalve increases with environmental stress

Facilitation of foundation species is critical to the structure, function and persistence of ecosystems. Understanding the dependence of the strength of this facilitation on environmental conditions is important for informed ecosystem management and for predicting the impacts of global change. In coastal seagrass habitats, chemosymbiotic lucinid bivalves can facilitate seagrasses by decreasing potentially toxic levels of sulphide in sediment porewater. However, variation in the strength of lucinid–seagrass facilitation with environmental context has not been experimentally investigated. We tested the hypothesis that the presence of the tiger lucine Codakia orbicularis becomes more important to the growth and survival of the seagrass Thalassia testudinum under decreased light availability and increased sulphide stress. In a mesocosm experiment, we reduced average ambient-light to T. testudinum by 64% and/or increased sediment porewater sulphide concentrations by ~200% and compared growth and tissue chemistry of T. testudinum with and without C. orbicularis. We found that T. testudinum was better able to maintain growth under shading and sulphide stress when C. orbicularis was present. C. orbicularis strongly decreased sediment porewater sulphide, an effect that minimized sulphur build-up in seagrass tissue and was likely achieved through bioirrigation as well as chemoautotrophy. The relative effects of C. orbicularis on T. testudinum growth were strongest in the presence of environmental stressors. Synthesis. The strength of lucinid–seagrass facilitation increases under environmental conditions that hinder the ability of seagrass to detoxify sulphide. Our results provide evidence of a potential mechanism by which the spatiotemporal association between lucinids and seagrasses is maintained and support the incorporation of interspecific facilitation into conservation and restoration strategies for foundation species in the face of increasing anthropogenic impact and global change

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

Smoke, curtains and mirrors: the production of race through time and title registration

This article analyses the temporal effects of title registration and their relationship to race. It traces the move away from the retrospection of pre-registry common law conveyancing and toward the dynamic, future-oriented Torrens title registration system. The Torrens system, developed in early colonial Australia, enabled the production of ‘clean’, fresh titles that were independent of their predecessors. Through a process praised by legal commentators for ‘curing’ titles of their pasts, this system produces indefeasible titles behind its distinctive ‘curtain’ and ‘mirror’, which function similarly to magicians’ smoke and mirrors by blocking particular realities from view. In the case of title registries, those realities are particular histories of and relationships with land, which will not be protected by property law and are thus made precarious. Building on interdisciplinary work which theorises time as a social tool, I argue that Torrens title registration produces a temporal order which enables land market coordination by rendering some relationships with land temporary and making others indefeasible. This ordering of relationships with land in turn has consequences for the human subjects who have those relationships, cutting futures short for some and guaranteeing permanence to others. Engaging with Renisa Mawani and other critical race theorists, I argue that the categories produced by Torrens title registration systems materialise as race

Human and mouse essentiality screens as a resource for disease gene discovery.

The identification of causal variants in sequencing studies remains a considerable challenge that can be partially addressed by new gene-specific knowledge. Here, we integrate measures of how essential a gene is to supporting life, as inferred from viability and phenotyping screens performed on knockout mice by the International Mouse Phenotyping Consortium and essentiality screens carried out on human cell lines. We propose a cross-species gene classification across the Full Spectrum of Intolerance to Loss-of-function (FUSIL) and demonstrate that genes in five mutually exclusive FUSIL categories have differing biological properties. Most notably, Mendelian disease genes, particularly those associated with developmental disorders, are highly overrepresented among genes non-essential for cell survival but required for organism development. After screening developmental disorder cases from three independent disease sequencing consortia, we identify potentially pathogenic variants in genes not previously associated with rare diseases. We therefore propose FUSIL as an efficient approach for disease gene discovery

Phyto-oestrogens and breast cancer chemoprevention

Phytoestrogens are polyphenol compounds of plant origin that exhibit a structural similarity to the mammalian steroid hormone 17β-oestradiol. In Asian nations the staple consumption of phyto-oestrogen-rich foodstuffs correlates with a reduced incidence of breast cancer. Human dietary intervention trials have noted a direct relationship between phyto-oestrogen ingestion and a favourable hormonal profile associated with decreased breast cancer risk. However, these studies failed to ascertain the precise effect of dietary phyto-oestrogens on the proliferation of mammary tissue. Epidemiological and rodent studies crucially suggest that breast cancer chemoprevention by dietary phyto-oestrogen compounds is dependent on ingestion before puberty, when the mammary gland is relatively immature. Phyto-oestrogen supplements are commercially marketed for use by postmenopausal women as natural and safe alternatives to hormone replacement therapy. Of current concern is the effect of phyto-oestrogen compounds on the growth of pre-existing breast tumours. Data are contradictory, with cell culture studies reporting both the oestrogenic stimulation of oestrogen receptor-positive breast cancer cell lines and the antagonism of tamoxifen activity at physiological phyto-oestrogen concentrations. Conversely, phyto-oestrogen ingestion by rodents is associated with the development of less aggressive breast tumours with reduced metastatic potential. Despite the present ambiguity, current data do suggest a potential benefit from use of phyto-oestrogens in breast cancer chemoprevention and therapy. These aspects are discussed