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opencc-by-4.0Dec 2019View details →

A GRAPH BASED TAG RECOMMENDATION FOR JUST ABSTRACTED SCIENTIFIC ARTICLES TAGGING

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opencc-zeroJun 2020View details →

Data from: ClinicNet: machine learning for personalized order set recommendations

Objective This study assesses whether neural networks trained on electronic health record (EHR) data can anticipate what individual clinical orders and existing institutional order set templates clinicians will use more accurately than existing decision support tools. Materials and Methods We process 57,624 patients-worth of clinical event EHR data from 2008-2014. We train a feed-forward neural network (ClinicNet) and logistic regression applied to the traditional problem structure of predicting individual clinical items as well as our proposed workflow of predicting existing institutional order set template usage. Results ClinicNet predicts individual clinical orders (precision=0.32, recall=0.47) better than existing institutional order sets (precision=0.15, recall=0.46). The ClinicNet model predicts clinician usage of existing institutional order sets (avg. precision=0.31) with higher average precision than a baseline of order set usage frequencies (avg. precision=0.20) or a logistic regression model (avg. precision=0.12). Discussion Machine learning methods can predict clinical decision-making patterns with greater accuracy and less manual effort than existing static order set templates. This can streamline existing clinical workflows, but may not fit if historical clinical ordering practices are incorrect. For this reason, manually authored content such as order set templates remain valuable for purposeful design of care pathways. ClinicNet's capability of predicting such personalized order set templates illustrates the potential of combining both top-down and bottom-up approaches to delivering clinical decision support content. Conclusion ClinicNet illustrates the capability for machine learning methods applied to the EHR to anticipate both individual clinical orders and existing order set templates, which has the potential to improve upon current standards of practice in clinical order entry.

opencc-by-4.0Aug 2020View details →

[Dataset] Expanding the Number of Reviewers in Open-Source Projects by Recommending Appropriate Developers

A rich collection of review and development data, including information about reviewers, developers and their commits within five large ASF projects and four Gerrit communities.

opencc-by-4.0Oct 2020View details →

Recommending Composite Refactorings for Smell Removal: Heuristics and Evaluation

Short presentation for the paper entitled "Recommending Composite Refactorings for Smell Removal: Heuristics and Evaluation. Abstract. Structural degradation is the process in which quality attributes of a system are negatively impacted. When due attention is not paid to structural degradation, the source code may also become difficult to change. Code smells are recurring structures in the source code that may represent structural degradation. Hence, there are many catalogs and techniques for supporting the removal of code smells through refactoring recommendations, such as a Move Method or a Extract Method. Such recommendations usually consist of single refactorings. However, single refactorings are often not enough for completely removing certain smell occurrences. Moreover, recent studies show that developers most often apply composite refactorings -- i.e., sequences of two or more refactorings -- for removing code smells. Despite showing the importance of performing composite refactorings, existing studies do not provide information on which composite refactoring patterns are recurrent in practice. Therefore, in this work, we conducted an empirical study to extract data from multiple open source systems regarding the composite refactoring practice. This data helped us to find 35 recurring patterns that are effective in removing certain types of code smells. Based on such patterns, we propose a suite of new recommendation heuristics to help developers in applying effective composite refactorings. These heuristics are intended to remove three code smell types, namely Complex Class, Feature Envy, and God Class. After designing the heuristics, we evaluated their effectiveness through a quasi-experiment. This evaluation was conducted with 12 software developers and 9 smelly Java classes. Results indicate that developers considered our heuristics effective or partially effective in more than 93% of the cases. In addition, the evaluation helped us to identify multiple factors that contribute to the acceptance or rejection of the refactoring recommendations. Based on these factors we define new guidelines for the effective recommendation of smell-removal composite refactorings.

opencc-zeroNov 2020View details →

A novel method for detecting extra-home range movements (EHRMs) by animals and recommendations for future EHRM studies

Infrequent, long-distance animal movements outside of typical home range areas provide useful insights into resource acquisition, gene flow, and disease transmission within the fields of conservation and wildlife management, yet understanding of these movements is still limited across taxa. To detect these extra-home range movements (EHRMs) in spatial relocation datasets, most previous studies compare relocation points against fixed spatial and temporal bounds, typified by seasonal home ranges (referred to here as the "Fixed-Period" method). However, utilizing home ranges modelled over fixed time periods to detect EHRMs within those periods likely results in many EHRMs going undocumented, particularly when an animal's space use changes within that period of time. To address this, we propose a novel, "Moving-Window" method of detecting EHRMs through an iterative process, comparing each day's relocation data to the preceding period of space use only. We compared the number and characteristics of EHRM detections by both the Moving-Window and Fixed-Period methods using GPS relocations from 33 white-tailed deer (Odocoileus virginianus) in Alabama, USA. The Moving-Window method detected 1.5 times as many EHRMs as the Fixed-Period method and identified 120 unique movements that were undetected by the Fixed-Period method, including some movements that extended nearly 5 km outside of home range boundaries. Additionally, we utilized our EHRM dataset to highlight and evaluate potential sources of variation in EHRM summary statistics stemming from differences in definition criteria among previous EHRM literature. We found that this spectrum of criteria identified between 15.6% and 100.0% of the EHRMs within our dataset. We conclude that variability in terminology and definition criteria previously used for EHRM detection hinders useful comparisons between studies. The Moving-Window approach to EHRM detection introduced here, along with proposed methodology guidelines for future EHRM studies, should allow researchers to better investigate and understand these behaviors across a variety of taxa.

opencc-zeroJan 2021View details →

Clinicians' opinions on recommending aspirin to prevent colorectal cancer to Australians aged 50 to 70 years: A qualitative study

Objectives Australian guidelines recommend all 50 to 70-year-olds without existing contraindications consider taking low-dose aspirin (100 mg – 300 mg per day) for at least 2.5 years to reduce their risk of developing colorectal cancer. We aimed to explore clinicians', practices, knowledge, opinions, and barriers and facilitators to the implementation of these new guidelines. Methods Semi-structured interviews were conducted with clinicians to whom the new guidelines may be applicable (familial cancer clinic staff (geneticists, oncologists and genetic counsellors), gastroenterologists, pharmacists, and general practitioners (GPs)). The Consolidated Framework for Implementation Research (CFIR) underpinned the development of the interview guide. Coding was inductive and themes were developed through consensus between the authors. Emerging themes were mapped onto the CFIR domains: characteristics of the intervention, outer setting, inner setting, individual characteristics and process. Results Sixty-four interviews were completed between March and October 2019. Aspirin was viewed as a safe and cheap option for cancer prevention. GPs were considered by all clinicians as the most important health professionals for implementation of the guidelines. Cancer Council Australia, as a trusted organisation, was an important facilitator to guideline adoption. Uncertainty about aspirin dosage and perceived strength of the evidence, the precise wording of the recommendation, previous changes to guidelines about aspirin, and conflicting findings from trials in older populations were barriers to implementation. Conclusion Widespread adoption of these new guidelines could be an important strategy to reduce the incidence of bowel cancer, but this will require more active implementation strategies focused on primary care and the wider community.

opencc-zeroDec 2014View details →

Data from: Cost effectiveness of the New Zealand diabetes in pregnancy guideline screening recommendations

Objective: To compare the cost-effectiveness of 2 possible screening strategies for gestational diabetes mellitus (GDM) from the perspective of the New Zealand health system, developed as part of a gestational diabetes guideline. Design: A decision analytic model was built comparing 2-step screening (glycated haemoglobin (HbA1c) test at first booking and a 2 h 75 g oral glucose tolerance test (OGTT) as a single test at 24–28 weeks) with 3-step screening (HbA1c test at first booking and a 1 h glucose challenge test (GCT) followed by a 2 h 75 g OGTT when indicated from 24–28 weeks) using a 9-month time horizon. Setting: A hypothetical cohort of 62 000 pregnant women in New Zealand. Methods: Probabilities, costs and benefits were derived from the literature, and supplementary data was obtained from National Women's Annual Clinical Reports. Main outcome measures, screening and treatment costs (NZ$2013) and effect on health outcomes (incidence of complications). Results: The total cost for both strategies under baseline assumptions shows that the 2-step screening strategy would cost NZ$1.38 m more than the 3-step screening strategy overall. The additional cost per case detected was NZ$12 460 per case. The model found that the 2-step screening strategy identifies 12 more women with diabetes and 111 more women with GDM when compared against the 3-step screening strategy. We assessed the effect of changing the sensitivity and specificity of the OGTT. The baseline model assumed that the 2 h 75 g OGTT has a sensitivity and specificity of 95%. The 2-step strategy becomes more cost-effective when the diagnostic accuracy measures are improved. Conclusions: Adopting a 2-step strategy would moderately increase the number of GDM cases detected at the same time as moderately increasing the number of women with false negatives at a significant cost to the health system. Further evidence on the benefits of the 2 different approaches would be welcome.

opencc-zeroDec 2018View details →

Data from: A clinical decision support system learned from data to personalize treatment recommendations towards preventing breast cancer metastasis

Objective: A Clinical Decision Support System (CDSS) that can amass Electronic Health Record (EHR) and other patient data holds promise to provide accurate classification and guide treatment choices. Our objective is to develop the Decision Support System for Making Personalized Assessments and Recommendations Concerning Breast Cancer Patients (DPAC), which is a CDSS learned from data that recommends the optimal treatment decisions based on a patient's features. Method: We developed a Bayesian network architecture called Causal Modeling with Internal Layers (CAMIL), and an algorithm called Treatment Feature Interactions (TFI), which learns from data the interactions needed in a CAMIL model. Using the TFI algorithm, we learned interactions for six treatments from the Lynn Sage Data Set (LSDS). We created a CAMIL model using these interactions, resulting in a DPAC which recommends treatments towards preventing 5-year breast cancer metastasis. Results: In a 5-fold cross-validation analysis, we compared the probability of being metastasis free in 5 years for patients who made decisions recommended by DPAC to those who did not. These probabilities are (the probability for those making the decisions appears first): chemotherapy (.938, .872); breast/chest wall radiation (.939, .902); nodal field radiation (.940, .784); antihormone (.941, .906); HER2 inhibitors (.934, .880); neadjuvant therapy (.931, .837). In an application of DPAC to the independent METABRIC dataset, the probabilities for chemotherapy were (.845, .788). Discussion: Patients who took the advice of DPAC had, as a group, notably better outcomes than those who did not. We conclude that DPAC is effective at amassing and analyzing data towards treatment recommendations. Some of the findings in DPAC are controversial. For example, DPAC says that chemotherapy increases the chances of metastasis for many node negative patients. This controversy shows the importance of developing a conclusive version of DPAC to ensure we provide patients with the best patient-specific treatment recommendations.

opencc-zeroDec 2016View details →

Data from: Multivariate phylogenetic comparative methods: evaluations, comparisons, and recommendations

Recent years have seen increased interest in phylogenetic comparative analyses of multivariate datasets, but to date the varied proposed approaches have not been extensively examined. Here we review the mathematical properties required of any multivariate method, and specifically evaluate existing multivariate phylogenetic comparative methods in this context. Phylogenetic comparative methods based on the full multivariate likelihood are robust to levels of covariation among trait dimensions and are insensitive to the orientation of the dataset, but display increasing model misspecification as the number of trait dimensions increases. This is because the expected evolutionary covariance matrix (V) used in the likelihood calculations becomes more ill-conditioned as trait dimensionality increases, and as evolutionary models become more complex. Thus, these approaches are only appropriate for datasets with few traits and many species. Methods that summarize patterns across trait dimensions treated separately (e.g., SURFACE) incorrectly assume independence among trait dimensions, resulting in nearly a 100% model misspecification rate. Methods using pairwise composite likelihood are highly sensitive to levels of trait covariation, the orientation of the dataset, and the number of trait dimensions. The consequences of these debilitating deficiencies is that a user can arrive at differing statistical conclusions, and therefore biological inferences, simply from a dataspace rotation, like principal component analysis. By contrast, algebraic generalizations of the standard phylogenetic comparative toolkit that use the trace of covariance matrices are insensitive to levels of trait covariation, the number of trait dimensions, and the orientation of the dataset. Further, when appropriate permutation tests are used, these approaches display acceptable Type I error and statistical power. We conclude that methods summarizing information across trait dimensions, as well as pairwise composite likelihood methods should be avoided, while algebraic generalizations of the phylogenetic comparative toolkit provide a useful means of assessing macroevolutionary patterns in multivariate data. Finally, we discuss areas in which multivariate phylogenetic comparative methods are still in need of future development; namely highly multivariate Ornstein-Uhlenbeck models and approaches for multivariate evolutionary model comparisons.

opencc-zeroDec 2015View details →

Data from: Assessing the sustainability of African lion trophy hunting, with recommendations for policy

While trophy hunting provides revenue for conservation, it must be carefully managed to avoid negative population impacts, particularly for long-lived species with low natural mortality rates. Trophy hunting has had negative effects on lion populations throughout Africa, and the species serves as an important case study to consider the balance of costs and benefits, and to consider the effectiveness of alternative strategies to conserve exploited species. Age-restricted harvesting is widely recommended to mitigate negative effects of lion hunting, but this recommendation was based on a population model parameterized with data from a well-protected and growing lion population. Here, we used demographic data from lions subject to more typical conditions, including source–sink dynamics between a protected National Park and adjacent hunting areas in Zambia's Luangwa Valley, to develop a stochastic population projection model and evaluate alternative harvest scenarios. Hunting resulted in population declines over a 25-yr period for all continuous harvest strategies, with large declines for quotas >1 lion/concession (~0.5 lion/1,000 km2) and hunting of males younger than seven years. A strategy that combined periods of recovery, an age limit of ≥7 yr, and a maximum quota of ~0.5 lions shot/1,000 km2 yielded a risk of extirpation <10%. Our analysis incorporated the effects of human encroachment, poaching, and prey depletion on survival, but assumed that these problems will not increase, which is unlikely. These results suggest conservative management of lion trophy hunting with a combination of regulations. To implement sustainable trophy hunting while maintaining revenue for conservation of hunting areas, our results suggest that hunting fees must increase as a consequence of diminished supply. These findings are broadly applicable to hunted lion populations throughout Africa and to inform global efforts to conserve exploited carnivore populations.

opencc-zeroJun 2016View details →

Management of persistent non-specific low back pain in primary care: A review of current guideline recommendations

AGREE II Summary Score Sheets

FIGURE 9 in A new species of poison-dart frog (Anura: Dendrobatidae) from Manu province, Amazon region of southeastern Peru, with notes on its natural history, bioacoustics, phylogenetics, and recommended conservation status

FIGURE 9. Currently known distribution of Ameerega shihuemoy (orange circles). The main natural protected areas in the Madre de Dios region are shown in green. Amarakaeri Communal Reserve covers an area of 402.335,62 ha; A. shihuemoy has been found at six localities inside this reserve.

FIGURE 10. A in A new species of poison-dart frog (Anura: Dendrobatidae) from Manu province, Amazon region of southeastern Peru, with notes on its natural history, bioacoustics, phylogenetics, and recommended conservation status

FIGURE 10. A, dorsal, and B, ventral view of the body; C, lateral view of head; and D, ventral view of the hand, of the adult holotype CBF 3900 of Ameerega yungicola. Scale on every picture. Photos by Daniela Rössler.

FIGURE 6 in A new species of poison-dart frog (Anura: Dendrobatidae) from Manu province, Amazon region of southeastern Peru, with notes on its natural history, bioacoustics, phylogenetics, and recommended conservation status

FIGURE 6. Tadpole of Ameerega shihuemoy at Gosner stage 25: (A) dorsal, (B) ventral, (C) lateral, (D) Oral disc at Gosner stage 41, (E) Free-living tadpole at Gosner stage 25. Photos by S. J. Serrano.

FIGURE 5 in A new species of poison-dart frog (Anura: Dendrobatidae) from Manu province, Amazon region of southeastern Peru, with notes on its natural history, bioacoustics, phylogenetics, and recommended conservation status

FIGURE 5. Spectrograms of advertisement calls of morphologically similar species of Ameerega. A) A. shihuemoy, recorded at Manu Learning Centre, Madre de Dios, Peru 12 June 2014 (temperature not noted). B) A. boliviana, recorded from Correo- Apolo, La Paz, Bolivia. C) A. simulans recorded from Marcapata, Cusco, Peru. D) A. picta recorded from Madidi National Park, Bolivia. E) A. yungicola recorded from Caranavi, Yungas, Bolivia. F) A. hahneli, recorded from Shintuya, Madre de Dios, Peru. G) A. macero, recorded at Manu Learning Centre, Madre de Dios, Peru.

FIGURE 2. A in A new species of poison-dart frog (Anura: Dendrobatidae) from Manu province, Amazon region of southeastern Peru, with notes on its natural history, bioacoustics, phylogenetics, and recommended conservation status

FIGURE 2. A, dorsal; B, and ventral views of the body of the subadult female paratype MHNC 14561 (SVL = 20.7 mm); C, dorsal; D, and ventral views of the body of the subadult male paratype MHNC 4779 (SVL = 17.4 mm); E, adult male carrying tadpoles; F, adult male paratype MHNC 15863. Photos by J.C. Chaparro (A-D), R. Coronel (E), R. Santa Cruz (F).

FIGURE 4 in A new species of poison-dart frog (Anura: Dendrobatidae) from Manu province, Amazon region of southeastern Peru, with notes on its natural history, bioacoustics, phylogenetics, and recommended conservation status

FIGURE 4. Box plots representing the median (black horizontal line), interquartile range (box), range (whiskers) and outside values (circles) of call parameters comparison among Ameerega shihuemoy, A. boliviana, A. hahneli, A. picta, A. simulans and A. yungicola where: a) note duration (ms), b) calling rate, c) fundamental frequency (Hz) and d) dominant frequency (Hz).

FIGURE 3 in A new species of poison-dart frog (Anura: Dendrobatidae) from Manu province, Amazon region of southeastern Peru, with notes on its natural history, bioacoustics, phylogenetics, and recommended conservation status

FIGURE 3. Color patterns of Ameerega shihuemoy from tadpole to adult MUSM 31692. Photos by Marcus Brent-Smith.

FIGURE 1. A in A new species of poison-dart frog (Anura: Dendrobatidae) from Manu province, Amazon region of southeastern Peru, with notes on its natural history, bioacoustics, phylogenetics, and recommended conservation status

FIGURE 1. A, dorsal, and B, ventral view of the body; C, lateral view of head; D, and tympanum under skin; E, mouth showing choanae details; F, ventral view of the hand; G, and foot, of the adult female holotype MHNC 15488 (SVL = 25.7 mm) of Ameerega shihuemoy sp. nov. Scale on every picture. Photos by J.C. Chaparro.

FIGURE 7 in A new species of poison-dart frog (Anura: Dendrobatidae) from Manu province, Amazon region of southeastern Peru, with notes on its natural history, bioacoustics, phylogenetics, and recommended conservation status

FIGURE 7. Maximum Likelihood (ML) phylogeny of Ameerega based on 16S ribosomal RNA gene. Numbers above nodes are bootstrap values.