A tool for evaluating the potential for cost-effective outcomes measurement

Cost related to higher-level outcomes measurement is often very high. However, the cost burden is felt even more by smaller, less well-funded continuing medical education (CME) programs. It is possible to overcome financial and participant-related barriers to measuring Level 6 outcomes, which are patient health outcomes. The Temple University School of Medicine’s Office for Continuing Medical Education developed a sequential tool for attaining cost-effective outcomes measurement for determining the likelihood of a CME intervention to produce significant changes in physician performance. The appropriate selection of the CME topic and specific practice change indictors drive this tool. This tool walks providers through a simple YES or NO decision-making list that guides them toward an accurate prediction of potential programmatic outcomes. Factors considered during the decision-making process include whether: (a) the intended change(s) will have a substantial impact on current practice; (b) the intended practice change(s) are well supported by clinical data, specialty organization/government recommendations, expert opinion, etc; (c) the potential change(s) affects a large population; (d) external factors, such as system pressures, media pressures, financial pressures, patient pressures, safety pressures, etc, are driving this intended change in performance; (e) there is a strong motivation on the part of physicians to implement the intended change(s); and (f) the intended change(s) is relatively easy to implement within any system of practice. If each of these questions can be responded to positively, there is a higher likelihood that the intended practice-related change(s) will occur. Such change can be measured using a simpler and less costly methodology

Geometric Accuracy of Digital Twins for Structural Health Monitoring

We present an exploratory analysis of the geometric accuracy of digital twins generated for existing infrastructure using point clouds. The Level of Geometric Accuracy is a vital specification to measure the twinning quality of the resulting twins. However, there is a lack of a clear definition of the Level of Geometric Accuracy for twins generated in the operation and maintenance stage, especially for structural health monitoring purposes. We critically review existing industry applications and twinning methods. To highlight the technical challenges with creating high-fidelity digital replicas, we present a case study of twinning a bridge using real-world point clouds. We do not provide conclusive methods or results but envisage potential twinning strategies to achieve the desired geometry accuracy. This chapter aims to inform the future development of a geometric accuracy-based evaluation system for use in twinning and updating processes. Since a major barrier for a fully automated twinning workflow is the lack of rigorous interpretation of ‘geometric accuracy’ outside design environments, it is imperative to develop comprehensive standards to guide practitioners and researchers in order to achieve model certainty. As such, this chapter also aims to educate all stakeholders in order to minimise risk when drafting contracts and exchanging digital deliverables

Causes of Defects Associated with Tolerances in Construction: A Case Study

Defects associated with dimensional and geometric variations (tolerance issues) are among the most costly and recurring defects in construction projects, yet the identification and mitigation of the causes of tolerance issues appear to be lacking in the construction industry. To enable the development of widely acceptable solutions for the perennial challenge of tolerance management, a more in-depth understanding of the causes of tolerance issues should be established. The aim of the research presented in this paper is to identify the potential causes of tolerance issues in construction based on a literature review and empirical studies. This research uses a case study approach. The empirical data are collected through direct observations, group interviews, semistructured interviews, and document reviews. Having triangulated the findings, a list of 18 potential causes was derived for the 11 observed tolerance issues in two case study projects. The contribution of this paper to knowledge in engineering management is fourfold: (1) the limitations of prior studies on causes of tolerance issues are revealed, (2) the empirical studies led to not only verifying and refining the causes collected from the literature by considering them in the context of the identified tolerance issues, but also finding new causes in the context of tolerance management when compared to literature, (3) the identified causes provide insight into reasons behind the recurrence of tolerance issues across the industry, and (4) it investigates the causes of tolerance issues while balancing managerial and engineering views. The findings of this study provide a pivotal basis for construction practitioners to develop effective solutions for tolerance management whereby tolerance risks can be identified and mitigated in a prescient manner, which can result in a significant amount of savings

Corroborative Study on Maize Quality, Dry-Milling and Wet-Milling Properties of Selected Maize Hybrids

A corroborative study was conducted on the maize quality properties of test weight, pycnometer density, tangential abrasive dehulling device (TADD), time-to-grind on the Stenvert hardness tester (SHT), 100-kernel weight, kernel size distribution, and proximate composition as well as maize dry- and wet-millability by six participating laboratories. Suggested operating procedures were given to compare their measurements and provide the variance structure within and between laboratories and hybrids. Partial correlation coefficient among maize quality properties varied among laboratories. The repeatability and reproducibility precision values were acceptably low for the physical quality tests, except for TADD and SHT time-to-grind measurements. The yields of dry- and wet-milled products and their correlation with maize quality properties were dependent on the collaborating laboratory. This paper highlights the importance of laboratory variation when considering which maize hybrids are best suited for dry-milling and wet-milling

Proteins in stool as biomarkers for non-invasive detection of colorectal adenomas with high risk of progression

Screening to detect colorectal cancer (CRC) in an early or premalignant state is an effective method to reduce CRC mortality rates. Current stool-based screening tests, e.g. fecal immunochemical test (FIT), have a suboptimal sensitivity for colorectal adenomas and difficulty distinguishing adenomas at high risk of progressing to cancer from those at lower risk. We aimed to identify stool protein biomarker panels that can be used for the early detection of high-risk adenomas and CRC. Proteomics data (LC–MS/MS) were collected on stool samples from adenoma (n = 71) and CRC patients (n = 81) as well as controls (n = 129). Colorectal adenoma tissue samples were characterized by low-coverage whole-genome sequencing to determine their risk of progression based on specific DNA copy number changes. Proteomics data were used for logistic regression modeling to establish protein biomarker panels. In total, 15 of the adenomas (15.8%) were defined as high risk of progressing to cancer. A protein panel, consisting of haptoglobin (Hp), LAMP1, SYNE2, and ANXA6, was identified for the detection of high-risk adenomas (sensitivity of 53% at specificity of 95%). Two panels, one consisting of Hp and LRG1 and one of Hp, LRG1, RBP4, and FN1, were identified for high-risk adenomas and CRCs detection (sensitivity of 66% and 62%, respectively, at specificity of 95%). Validation of Hp as a biomarker for high-risk adenomas and CRCs was performed using an antibody-based assay in FIT samples from a subset of individuals from the discovery series (n = 158) and an independent validation series (n = 795). Hp protein was significantly more abundant in high-risk adenoma FIT samples compared to controls in the discovery (p = 0.036) and the validation series (p = 9e-5). We conclude that Hp, LAMP1, SYNE2, LRG1, RBP4, FN1, and ANXA6 may be of value as stool biomarkers for early detection of high-risk adenomas and CRCs

Combining Structure and Sequence Information Allows Automated Prediction of Substrate Specificities within Enzyme Families

An important aspect of the functional annotation of enzymes is not only the type of reaction catalysed by an enzyme, but also the substrate specificity, which can vary widely within the same family. In many cases, prediction of family membership and even substrate specificity is possible from enzyme sequence alone, using a nearest neighbour classification rule. However, the combination of structural information and sequence information can improve the interpretability and accuracy of predictive models. The method presented here, Active Site Classification (ASC), automatically extracts the residues lining the active site from one representative three-dimensional structure and the corresponding residues from sequences of other members of the family. From a set of representatives with known substrate specificity, a Support Vector Machine (SVM) can then learn a model of substrate specificity. Applied to a sequence of unknown specificity, the SVM can then predict the most likely substrate. The models can also be analysed to reveal the underlying structural reasons determining substrate specificities and thus yield valuable insights into mechanisms of enzyme specificity. We illustrate the high prediction accuracy achieved on two benchmark data sets and the structural insights gained from ASC by a detailed analysis of the family of decarboxylating dehydrogenases. The ASC web service is available at http://asc.informatik.uni-tuebingen.de/

Multitarget Stool DNA Test Performance in an Average-Risk Colorectal Cancer Screening Population

INTRODUCTION: We set out to evaluate the performance of a multitarget stool DNA (MT-sDNA) in an average-risk colonoscopy-controlled colorectal cancer (CRC) screening population. MT-sDNA stool test results were evaluated against fecal immunochemical test (FIT) results for the detection of different lesions, including molecularly defined high-risk adenomas and several other tumor characteristics. METHODS: Whole stool samples (n = 1,047) were prospectively collected and subjected to an MT-sDNA test, which tests for KRAS mutations, NDRG4 and BMP3 promoter methylation, and hemoglobin. Results for detecting CRC (n = 7), advanced precancerous lesions (advanced adenoma [AA] and advanced serrated polyps; n = 119), and non-AAs (n = 191) were compared with those of FIT alone (thresholds of 50, 75, and 100 hemoglobin/mL). AAs with high risk of progression were defined by the presence of specific DNA copy number events as measured by low-pass whole genome sequencing. RESULTS: The MT-sDNA test was more sensitive than FIT alone in detecting advanced precancerous lesions (46% (55/119) vs 27% (32/119), respectively, P < 0.001). Specificities among individuals with nonadvanced or negative findings (controls) were 89% (791/888) and 93% (828/888) for MT-sDNA and FIT testing, respectively. A positive MT-sDNA test was associated with multiple lesions (P = 0.005), larger lesions (P = 0.03), and lesions with tubulovillous architecture (P = 0.04). The sensitivity of the MT-sDNA test or FIT in detecting individuals with high-risk AAs (n = 19) from individuals with low-risk AAs (n = 52) was not significantly different. DISCUSSION: In an average-risk screening population, the MT-sDNA test has an increased sensitivity for detecting advanced precancerous lesions compared with FIT alone. AAs with a high risk of progression were not detected with significantly higher sensitivity by MT-sDNA or FIT

Molecular profiling of longitudinally observed small colorectal polyps: A cohort study

Background: Knowledge of the natural history of colorectal adenomas is limited because these lesions are removed upon detection. The few studies in which small adenomas have been left in situ for a limited period of time, have shown that most lesions remain stable or even completely regress. Specific DNA copy number changes (‘cancer associated events’ or CAEs) are associated with progression of adenomas to cancer. In this study we evaluated whether molecular features of progression correlated with growth of small polyps. Methods: Small (6–9 mm) colorectal precursor lesions detected on CT-colonography (CTC) were left in situ and re-evaluated with CTC after three years. Based o

Fusion transcripts and their genomic breakpoints in polyadenylated and ribosomal RNA-minus RNA sequencing data

BACKGROUND: Fusion genes are typically identified by RNA sequencing (RNA-seq) without elucidating the causal genomic breakpoints. However, non–poly(A)-enriched RNA-seq contains large proportions of intronic reads that also span genomic breakpoints. RESULTS: We have developed an algorithm, Dr. Disco, that searches for fusion transcripts by taking an entire reference genome into account as search space. This includes exons but also introns, intergenic regions, and sequences that do not meet splice junction motifs. Using 1,275 RNA-seq samples, we investigated to what extent genomic breakpoints can be extracted from RNA-seq data and their implications regarding poly(A)-enriched and ribosomal RNA–minus RNA-seq data. Comparison with whole-genome sequencing data revealed that most genomic breakpoints are not, or minimally, transcribed while, in contrast, the genomic breakpoints of all 32 TMPRSS2-ERG–positive tumours were present at RNA level. We also revealed tumours in which the ERG breakpoint was located before ERG, which co-existed with additional deletions and messenger RNA that incorporated intergenic cryptic exons. In breast cancer we identified rearrangement hot spots near CCND1 and in glioma near CDK4 and MDM2 and could directly associate this with increased expression. Furthermore, in all datasets we find fusions to intergenic regions, often spanning multiple cryptic exons that potentially encode neo-antigens. Thus, fusion transcripts other than classical gene-to-gene fusions are prominently present and can be identified using RNA-seq. CONCLUSION: By using the full potential of non–poly(A)-enriched RNA-seq data, sophisticated analysis can reliably identify expressed genomic breakpoints and their transcriptional effects

TGF-β in tolerance, development and regulation of immunity

AbstractThe TGF-β superfamily is an ancient metazoan protein class which cuts across cell and tissue differentiation, developmental biology and immunology. Its many members are regulated at multiple levels from intricate control of gene transcription, post-translational processing and activation, and signaling through overlapping receptor structures and downstream intracellular messengers. We have been interested in TGF-β homologues firstly as key players in the induction of immunological tolerance, the topic so closely associated with Ray Owen. Secondly, our interests in how parasites may manipulate the immune system of their host has also brought us to study the TGF-β pathway in infections with longlived, essentially tolerogenic, helminth parasites. Finally, within the spectrum of mammalian TGF-β proteins is an exquisitely tightly-regulated gene, anti-Müllerian hormone (AMH), whose role in sex determination underpins the phenotype of freemartin calves that formed the focus of Ray’s seminal work on immunological tolerance