•Machine learning and text mining approaches are increasingly being used to predict patient outcomes in emergency care.•We use machine learning approaches to quantify the importance of contextual ...free text features in ambulance call data.•Using call handler notes in addition to triage codes improves prediction of unconscious patients requiring conveyance.•Quantifying this gain can help inform emergency medical service policy involving clinical decision support systems.
Pre-hospital emergency medical services use clinical decision support systems (CDSS) to triage calls. Call handlers often supplement this by making free text notes covering key incident information. We investigate whether machine learning approaches using features from such free text notes can improve prediction of unconscious patients who require conveyance.
We analysed a subset of all London Ambulance Service calls that were triaged through the Medical Priority Dispatch System (MPDS) as involving an unconscious or fainting patient in 2018. We use and compare two machine learning algorithms: random forest (RF) and gradient boosting machine (GBM). For each incident, we predict whether the patient will be conveyed to a hospital emergency department or equivalent using as features 1) the MPDS code, 2) the free text notes and 3) the two together. We evaluate model performance using the area under the curve (AUC) metric. Given the imbalance of outcomes (patient conveyed 71 %, not conveyed 29 %), we also consider sensitivity and specificity.
Using only the MPDS code resulted in an AUC of 0.57. Using the text notes gave an improved AUC score of 0.63 and combining the two gave an AUC score of 0.64 (scores were similar for RF and GBM). GBM models scored better on sensitivity (0.93 vs 0.62 for RF in the combined model), but specificity was lower (0.17 vs. 0.56 for RF in the combined model).
Using information contained in the free text notes made by call handlers in combination with MPDS improves prediction of unconscious and fainting patients requiring conveyance to a hospital emergency department (or equivalent) when compared with machine learning models using MPDS codes only. This suggests there is some useful information in unstructured data captured by emergency call handlers that complements MPDS codes. Quantifying this gain can help inform emergency medical service policy when evaluating the decision to expand or augment existing CDSS.
Clinicopathologic data from a population-based endometrial cancer cohort, unselected for age or family history, were analyzed to determine the optimal scheme for identification of patients with ...germline mismatch repair (MMR) gene mutations.
Endometrial cancers from 702 patients recruited into the Australian National Endometrial Cancer Study (ANECS) were tested for MMR protein expression using immunohistochemistry (IHC) and for MLH1 gene promoter methylation in MLH1-deficient cases. MMR mutation testing was performed on germline DNA of patients with MMR-protein deficient tumors. Prediction of germline mutation status was compared for combinations of tumor characteristics, age at diagnosis, and various clinical criteria (Amsterdam, Bethesda, Society of Gynecologic Oncology, ANECS).
Tumor MMR-protein deficiency was detected in 170 (24%) of 702 cases. Germline testing of 158 MMR-deficient cases identified 22 truncating mutations (3% of all cases) and four unclassified variants. Tumor MLH1 methylation was detected in 99 (89%) of 111 cases demonstrating MLH1/PMS2 IHC loss; all were germline MLH1 mutation negative. A combination of MMR IHC plus MLH1 methylation testing in women younger than 60 years of age at diagnosis provided the highest positive predictive value for the identification of mutation carriers at 46% versus ≤ 41% for any other criteria considered.
Population-level identification of patients with MMR mutation-positive endometrial cancer is optimized by stepwise testing for tumor MMR IHC loss in patients younger than 60 years, tumor MLH1 methylation in individuals with MLH1 IHC loss, and germline mutations in patients exhibiting loss of MSH6, MSH2, or PMS2 or loss of MLH1/PMS2 with absence of MLH1 methylation.
Sequence polymorphisms linked to human diseases and phenotypes in genome-wide association studies often affect noncoding regions. A SNP within an intron of the gene encoding Interferon Regulatory ...Factor 4 (IRF4), a transcription factor with no known role in melanocyte biology, is strongly associated with sensitivity of skin to sun exposure, freckles, blue eyes, and brown hair color. Here, we demonstrate that this SNP lies within an enhancer of IRF4 transcription in melanocytes. The allele associated with this pigmentation phenotype impairs binding of the TFAP2A transcription factor that, together with the melanocyte master regulator MITF, regulates activity of the enhancer. Assays in zebrafish and mice reveal that IRF4 cooperates with MITF to activate expression of Tyrosinase (TYR), an essential enzyme in melanin synthesis. Our findings provide a clear example of a noncoding polymorphism that affects a phenotype by modulating a developmental gene regulatory network.
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•Sequence variation in IRF4 is associated with pigmentation features including freckles•This sequence is located in an enhancer element that affects expression of IRF4•The transcription factors MITF and TFAP2A regulate expression from this element•Together, MITF and IRF4 affect regulation of the pigmentation enzyme TYR
A polymorphism in a noncoding region of IRF4, a transcription factor involved in immune signaling, is found to affect human pigmentation. This polymorphism affects the ability of the transcription factors TFAP2A and MITF to regulate IRF4 levels, which in turn results in reduced levels of the pigmentation enzyme Tyrosinase.
Colorectal cancer (CRC) that displays high microsatellite instability (MSI-H) can be caused by either germline mutations in mismatch repair (MMR) genes, or non-inherited transcriptional silencing of ...the
MLH1
promoter. A correlation between
MLH1
promoter methylation, specifically the ‘C’ region, and
BRAF
V600E status has been reported in CRC studies. Germline MMR mutations also greatly increase risk of endometrial cancer (EC), but no systematic review has been undertaken to determine if these tumour markers may be useful predictors of MMR mutation status in EC patients. Endometrial cancer cohorts meeting review inclusion criteria encompassed 2675 tumours from 20 studies for
BRAF
V600E, and 447 tumours from 11 studies for
MLH1
methylation testing. BRAF V600E mutations were reported in 4/2675 (0.1 %) endometrial tumours of unknown MMR mutation status, and there were 7/823 (0.9 %) total sequence variants in exon 11 and 27/1012 (2.7 %) in exon 15. Promoter
MLH1
methylation was not observed in tumours from 32
MLH1
mutation carriers, or for 13
MSH2
or
MSH6
mutation carriers. MMR mutation-negative individuals with tumour MLH1 and PMS2 IHC loss displayed
MLH1
methylation in 48/51 (94 %) of tumours. We have also detailed specific examples that show the importance of
MLH1
promoter region, assay design, and quantification of methylation. This review shows that
BRAF
mutations occurs so infrequently in endometrial tumours they can be discounted as a useful marker for predicting MMR-negative mutation status, and further studies of endometrial cohorts with known MMR mutation status are necessary to quantify the utility of tumour
MLH1
promoter methylation as a marker of negative germline MMR mutation status in EC patients.
1. Demographic rates such as growth and survival may interact directly as a result of allocation constraints, or indirectly through their relationship with structural characteristics. 2. We explored ...the relationship between growth and survival in a range of rosette-forming species across different habitats, and investigated possible mechanistic explanations for the patterns we found. 3. Results indicated a negative association between growth and survival in small plants across species in different habitats. There was no relationship for large plants. 4. Relative growth rate (RGR) was positively correlated to specific leaf area (SLA), but unrelated to the percentage biomass allocated to roots. This argues against the hypothesized role of allocation to root mass in mediating the growth-survival trade-off. 5. The pattern of biomass partitioning was compared with the predictions of Enquist & Niklas (2002a) Global allocation rules for patterns of biomass partitioning in seed plants. Science 295, 1517-1520. In agreement with their predictions, the overall relationship between above- and below-ground biomass was isometric. However, after accounting for species-specific effects it was found that allocation to roots varied widely between species and was size-dependent, suggesting that the conventional statistical analysis (double-log regression) may be insensitive to biologically important sources of variation.
Reply to J. Moline et al Buchanan, Daniel D; Tan, Yen Y; Walsh, Michael D ...
Journal of clinical oncology,
2014-Jul-20, 2014-07-20, 20140720, Letnik:
32, Številka:
21
Journal Article
Abstract
The concept of adaptive capacity has received significant attention within social-ecological and environmental change research. Within both the resilience and vulnerability literatures ...specifically, adaptive capacity has emerged as a fundamental concept for assessing the ability of social-ecological systems to adapt to environmental change. Although methods and indicators used to evaluate adaptive capacity are broad, the focus of existing scholarship has predominately been at the individual- and household- levels. However, the capacities necessary for humans to adapt to global environmental change are often a function of individual and societal characteristics, as well as cumulative and emergent capacities across communities and jurisdictions. In this paper, we apply a systematic literature review and co-citation analysis to investigate empirical research on adaptive capacity that focus on societal levels beyond the household. Our review demonstrates that assessments of adaptive capacity at higher societal levels are increasing in frequency, yet vary widely in approach, framing, and results; analyses focus on adaptive capacity at many different levels (e.g. community, municipality, global region), geographic locations, and cover multiple types of disturbances and their impacts across sectors. We also found that there are considerable challenges with regard to the ‘fit’ between data collected and analytical methods used in adequately capturing the cross-scale and cross-level determinants of adaptive capacity. Current approaches to assessing adaptive capacity at societal levels beyond the household tend to simply aggregate individual- or household-level data, which we argue oversimplifies and ignores the inherent interactions within and across societal levels of decision-making that shape the capacity of humans to adapt to environmental change across multiple scales. In order for future adaptive capacity research to be more practice-oriented and effectively guide policy, there is a need to develop indicators and assessments that are matched with the levels of potential policy applications.
Schedules of survival, growth and reproduction are key life‐history traits. Data on how these traits vary among species and populations are fundamental to our understanding of the ecological ...conditions that have shaped plant evolution. Because these demographic schedules determine population growth or decline, such data help us understand how different biomes shape plant ecology, how plant populations and communities respond to global change and how to develop successful management tools for endangered or invasive species. Matrix population models summarize the life cycle components of survival, growth and reproduction, while explicitly acknowledging heterogeneity among classes of individuals in the population. Matrix models have comparable structures, and their emergent measures of population dynamics, such as population growth rate or mean life expectancy, have direct biological interpretations, facilitating comparisons among populations and species. Thousands of plant matrix population models have been parameterized from empirical data, but they are largely dispersed through peer‐reviewed and grey literature, and thus remain inaccessible for synthetic analysis. Here, we introduce the compadre Plant Matrix Database version 3.0, an open‐source online repository containing 468 studies from 598 species world‐wide (672 species hits, when accounting for species studied in more than one source), with a total of 5621 matrices. compadre also contains relevant ancillary information (e.g. ecoregion, growth form, taxonomy, phylogeny) that facilitates interpretation of the numerous demographic metrics that can be derived from the matrices. Synthesis. Large collections of data allow broad questions to be addressed at the global scale, for example, in genetics (genbank), functional plant ecology (try, bien, d3) and grassland community ecology (nutnet). Here, we present compadre, a similarly data‐rich and ecologically relevant resource for plant demography. Open access to this information, its frequent updates and its integration with other online resources will allow researchers to address timely and important ecological and evolutionary questions.
The ability to initiate an action quickly when needed and the ability to cancel an impending action are both fundamental to action control. It is often presumed that they are qualitatively distinct ...processes, yet they have largely been studied in isolation and little is known about how they relate to one another. Comparing previous experimental results shows a similar time course for response initiation and response inhibition. However, the exact time course varies widely depending on experimental conditions, including the frequency of different trial types and the urgency to respond. For example, in the stop-signal task, where both action initiation and action inhibition are involved and could be compared, action inhibition is typically found to be much faster. However, this apparent difference is likely due to there being much greater urgency to inhibit an action than to initiate one in order to avoid failing at the task. This asymmetry in the urgency between action initiation and action inhibition makes it impossible to compare their relative time courses in a single task. Here, we demonstrate that when action initiation and action inhibition are measured separately under conditions that are matched as closely as possible, their speeds are not distinguishable and are positively correlated across participants. Our results raise the possibility that action initiation and action inhibition may not necessarily be qualitatively distinct processes but may instead reflect complementary outcomes of a single decision process determining whether or not to act.
The time courses of initiating an action and canceling an action have largely been studied in isolation, and little is known about their relationship. Here, we show that when measured under comparable conditions the speeds of action initiation and action inhibition are the same. This finding raises the possibility that these two functions may be more closely related than previously assumed, with potentially important implications for their underlying neural basis.
Coexistence between large carnivores and humans is a global conservation concern. Montana (USA) is home to recovering grizzly bear (Ursus arctos) populations and increasing human–grizzly ...interactions. In 2019, we administered a survey of Montanans to investigate factors influencing normative beliefs about grizzly bear population sizes and quantify the relationship between these beliefs and satisfaction with grizzly management in the state. Using a linear regression (r2 = .61), we found that residents with positive attitudes and emotional dispositions toward grizzlies or who trusted the agency were more likely to believe grizzly populations were too low. Residents who believed hunting should be used to manage conflict, were themselves hunters, had vicarious wildlife experience with property damage, believed grizzly populations were expanding, or were older were more likely to believe populations were too high. We found a negative quadratic relationship between normative grizzly bear population size beliefs and satisfaction with management, suggesting an optimal “Goldilocks” zone where coexistence is most possible. In practice, if observed Goldilocks zones are incompatible with population numbers required to meet conservation goals, considering factors influencing these beliefs may help bolster acceptance of larger population sizes.
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