“Show me the Data”: A Recipe for Quality Improvement Success in an Academic Surgical Department

Background Surgeons in academic medical centers have traditionally taken a siloed approach to reducing postoperative complications. We initiated a project focusing on transparency and sharing of data in order to engage surgeons in collaborative quality improvement. Its key features were the development of a comprehensive Department Quality Dashboard and the creation of a Clinical Operations Council that oversaw quality. The purpose of this study was to assess the impact of those efforts. Study Design We compared inpatient outcomes before and after our intervention, allowing one quarter as the diffusion period. The outcomes analyzed were: risk-adjusted length of stay (LOS), mortality and direct cost and unadjusted incidence of complications and 30-day all-cause readmissions, as determined by the Vizient Clinical Database. We examined the outcomes of three groups: Group 1 (Surgery), Group 2 - all other surgical departments (Other Surgery) and Group 3 - all other patients (Non-Surgery). Two-tailed Students’s t-test was used for analysis and a p value of <0.05 considered statistically significant. Results Group 1 demonstrated statistically significant improvements in mortality (p=0.01), LOS (p=0.002), cost (p=0.0001) and complications (p=0.02) while the all-cause readmission rate was unchanged, resulting in mean decrease of 0.55 LOS days and direct cost savings of $2300 per surgical admission. The comparison groups had only modest decreases in some of the analyzed outcomes and an increase in complication rates. Conclusions These data suggest that a collaborative, data-driven and transparent approach to assessing the quality of surgical care can yield significant improvements in patient outcomes

Monte Carlo Simulations of HIV Capsid Protein Homodimer

Capsid protein (CA) is the building block of virus coats. To help understand how the HIV CA proteins self-organize into large assemblies of various shapes, we aim to computationally evaluate the binding affinity and interfaces in a CA homodimer. We model the N- and C-terminal domains (NTD and CTD) of the CA as rigid bodies and treat the five-residue loop between the two domains as a flexible linker. We adopt a transferrable residue-level coarse-grained energy function to describe the interactions between the protein domains. In seven extensive Monte Carlo simulations with different volumes, a large number of binding/unbinding transitions between the two CA proteins are observed, thus allowing a reliable estimation of the equilibrium probabilities for the dimeric vs monomeric forms. The obtained dissociation constant for the CA homodimer from our simulations, 20–25 μM, is in reasonable agreement with experimental measurement. A wide range of binding interfaces, primarily between the NTDs, are identified in the simulations. Although some observed bound structures here closely resemble the major binding interfaces in the capsid assembly, they are statistically insignificant in our simulation trajectories. Our results suggest that although the general purpose energy functions adopted here could reasonably reproduce the overall binding affinity for the CA homodimer, further adjustment would be needed to accurately represent the relative strength of individual binding interfaces

A checklist of the hawkmoths (Lepidoptera: Sphingidae) of the Cayman Islands: with implications for the pollination of the ghost orchid \u3ci\u3eDendrophylax fawcettii \u3c/i\u3eRolfe (Orchidaceae: Angraecinae) and consideration of bat predation

This checklist synthesises historic collections of Sphingidae (Lepidoptera) made during the summer months in the Cayman Islands in 1938 and 1975 with modern records drawn from a variety of sources. We report observations and collections made in all seasons of the year and provide natural history and larval food details. Four species, Phryxus caicus (Cramer) in all three islands, plus Isognathus rimosa (Grote), Enyo lugubris (Linnaeus), and Eumorpha satellitia (Linnaeus) in Grand Cayman only, are here reported as new records, for a total of 25 sphingid species occurring in the Cayman Islands. Seven species are new records for Grand Cayman, five are added for Little Cayman and two for Cayman Brac. Potential hawkmoth pollinators for the Cayman Islands endemic ghost orchid, Dendrophylax fawcettii Rolfe (Orchidaceae: Angraecinae) are reviewed and Cayman records of hawkmoths as prey of the big-eared bat Macrotus waterhousii minor Gundlach (Phyllostomidae) are discussed. The hawkmoths (Lepidoptera: Sphingidae) of the Cayman Islands are the only moths to have received more than passing treatment as a group in the published literature. The catalogue provided by Askew (1994) remains the most recent, and with one exception, is based only on collections made in the early rainy seasons of 1938 and 1975. The results of the Oxford University Biological Expedition to all three Cayman Islands, conducted between April and August 1938, were reported by Jordan (1940), and those of the Royal Society–Cayman Islands Government Expedition to Little Cayman in June–July 1975 by Askew (1980). These combined lists, to which Askew (1994) was able to add the 1911 specimen of Pachylia ficus (Linnaeus) from Grand Cayman deposited at the Natural History Museum, London by T.M. Savage English, resulted in a total of twenty-one species of Sphingidae reported from the Cayman Islands as of 1994. Since that time, insect collections have been established at the National Trust for the Cayman Islands, the Department of Environment and the Department of Agriculture. The authors have also made personal collections. Particularly since the advent of digital equipment, photographic images of hawkmoths made by resident and visiting naturalists have provided significant primary records and supplemental data. This checklist synthesises the historic collections and the modern records, reports occurrence for all months of the year, and provides natural history information where available. We assess the larval food plant availability, the affinities and permanence of the sphingid fauna of the islands

Characterization of cell-type specific circular RNAs associated with colorectal cancer metastasis

Colorectal cancer (CRC) is the most common gastrointestinal malignancy and a leading cause of cancer deaths in the United States. More than half of CRC patients develop metastatic disease (mCRC) with an average 5-year survival rate of 13%. Circular RNAs (circRNAs) have recently emerged as important tumorigenesis regulators; however, their role in mCRC progression remains poorly characterized. Further, little is known about their cell-type specificity to elucidate their functions in the tumor microenvironment (TME). To address this, we performed total RNA sequencing (RNA-seq) on 30 matched normal, primary and metastatic samples from 14 mCRC patients. Additionally, five CRC cell lines were sequenced to construct a circRNA catalog in CRC. We detected 47 869 circRNAs, with 51% previously unannotated in CRC and 14% novel candidates when compared to existing circRNA databases. We identified 362 circRNAs differentially expressed in primary and/or metastatic tissues, termed circular RNAs associated with metastasis (CRAMS). We performed cell-type deconvolution using published single-cell RNA-seq datasets and applied a non-negative least squares statistical model to estimate cell-type specific circRNA expression. This predicted 667 circRNAs as exclusively expressed in a single cell type. Collectively, this serves as a valuable resource, TMECircDB (accessible at https://www.maherlab.com/tmecircdb-overview), for functional characterization of circRNAs in mCRC, specifically in the TME

DANSR: A tool for the detection of annotated and novel small RNAs

Existing small noncoding RNA analysis tools are optimized for processing short sequencing reads (17-35 nucleotides) to monitor microRNA expression. However, these strategies under-represent many biologically relevant classes of small noncoding RNAs in the 36-200 nucleotides length range (tRNAs, snoRNAs, etc.). To address this, we developed DANSR, a tool for the detection of annotated and novel small RNAs using sequencing reads with variable lengths (ranging from 17-200 nt). While DANSR is broadly applicable to any small RNA dataset, we applied it to a cohort of matched normal, primary, and distant metastatic colorectal cancer specimens to demonstrate its ability to quantify annotated small RNAs, discover novel genes, and calculate differential expression. DANSR is available as an open source tool

A heuristic method for determining CO2 efficiency in transportation planning

Background CO2 emissions are generally considered the most important indicator to determine the global warming effects. Their evaluation in the case of a transportation infrastructure is generally not easy and could be achieved through a separate balance

Integrated analysis of genomic and transcriptomic data for the discovery of splice-associated variants in cancer

Somatic mutations within non-coding regions and even exons may have unidentified regulatory consequences that are often overlooked in analysis workflows. Here we present RegTools ( www.regtools.org ), a computationally efficient, free, and open-source software package designed to integrate somatic variants from genomic data with splice junctions from bulk or single cell transcriptomic data to identify variants that may cause aberrant splicing. We apply RegTools to over 9000 tumor samples with both tumor DNA and RNA sequence data. RegTools discovers 235,778 events where a splice-associated variant significantly increases the splicing of a particular junction, across 158,200 unique variants and 131,212 unique junctions. To characterize these somatic variants and their associated splice isoforms, we annotate them with the Variant Effect Predictor, SpliceAI, and Genotype-Tissue Expression junction counts and compare our results to other tools that integrate genomic and transcriptomic data. While many events are corroborated by the aforementioned tools, the flexibility of RegTools also allows us to identify splice-associated variants in known cancer drivers, such as TP53, CDKN2A, and B2M, and other genes

Changing patterns in diagnostic strategies and the treatment of blunt injury to solid abdominal organs

Background: In recent years there has been increasing interest shown in the nonoperative management (NOM) of blunt traumatic injury. The growing use of NOM for blunt abdominal organ injury has been made possible because of the progress made in the quality and availability of the multidetector computed tomography (MDCT) scan and the development of minimally invasive intervention options such as angioembolization. Aim: The purpose of this review is to describe the changes that have been made over the past decades in the management of blunt trauma to the liver, spleen and kidney. Results: The management of blunt abdominal injury has changed considerably. Focused assessment with sonography for trauma (FAST) examination has replaced diagnostic peritoneal lavage as diagnostic modality in the primary survey. MDCT scanning with intravenous contrast is now the gold standard diagnostic modality in hemodynamically stable patients with intra-abdominal fluid detected with FAST. One of the current discussions in the l erature is whether a whole body MDCT survey should be implemented in the primary survey. Conclusions The progress in imaging techniques has contributed to NOM being currently the treatment of choice for hemodynamically stable patients. Angioembolization can be used as an adjunct to NOM and has increased the succe