Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Actively implementing an evidence-based feeding guideline for critically ill patients (NEED): a multicenter, cluster-randomized, controlled trial

Background: Previous cluster-randomized controlled trials evaluating the impact of implementing evidence-based guidelines for nutrition therapy in critical illness do not consistently demonstrate patient benefits. A large-scale, sufficiently powered study is therefore warranted to ascertain the effects of guideline implementation on patient-centered outcomes. Methods: We conducted a multicenter, cluster-randomized, parallel-controlled trial in intensive care units (ICUs) across China. We developed an evidence-based feeding guideline. ICUs randomly allocated to the guideline group formed a local "intervention team", which actively implemented the guideline using standardized educational materials, a graphical feeding protocol, and live online education outreach meetings conducted by members of the study management committee. ICUs assigned to the control group remained unaware of the guideline content. All ICUs enrolled patients who were expected to stay in the ICU longer than seven days. The primary outcome was all-cause mortality within 28 days of enrollment. Results: Forty-eight ICUs were randomized to the guideline group and 49 to the control group. From March 2018 to July 2019, the guideline ICUs enrolled 1399 patients, and the control ICUs enrolled 1373 patients. Implementation of the guideline resulted in significantly earlier EN initiation (1.20 vs. 1.55 mean days to initiation of EN; difference − 0.40 [95% CI − 0.71 to − 0.09]; P = 0.01) and delayed PN initiation (1.29 vs. 0.80 mean days to start of PN; difference 1.06 [95% CI 0.44 to 1.67]; P = 0.001). There was no significant difference in 28-day mortality (14.2% vs. 15.2%; difference − 1.6% [95% CI − 4.3% to 1.2%]; P = 0.42) between groups. Conclusions: In this large-scale, multicenter trial, active implementation of an evidence-based feeding guideline reduced the time to commencement of EN and overall PN use but did not translate to a reduction in mortality from critical illness. Trial registration: ISRCTN, ISRCTN12233792. Registered November 20th, 2017

Actively implementing an evidence-based feeding guideline for critically ill patients (NEED): a multicenter, cluster-randomized, controlled trial.

BackgroundPrevious cluster-randomized controlled trials evaluating the impact of implementing evidence-based guidelines for nutrition therapy in critical illness do not consistently demonstrate patient benefits. A large-scale, sufficiently powered study is therefore warranted to ascertain the effects of guideline implementation on patient-centered outcomes.MethodsWe conducted a multicenter, cluster-randomized, parallel-controlled trial in intensive care units (ICUs) across China. We developed an evidence-based feeding guideline. ICUs randomly allocated to the guideline group formed a local "intervention team", which actively implemented the guideline using standardized educational materials, a graphical feeding protocol, and live online education outreach meetings conducted by members of the study management committee. ICUs assigned to the control group remained unaware of the guideline content. All ICUs enrolled patients who were expected to stay in the ICU longer than seven days. The primary outcome was all-cause mortality within 28 days of enrollment.ResultsForty-eight ICUs were randomized to the guideline group and 49 to the control group. From March 2018 to July 2019, the guideline ICUs enrolled 1399 patients, and the control ICUs enrolled 1373 patients. Implementation of the guideline resulted in significantly earlier EN initiation (1.20 vs. 1.55 mean days to initiation of EN; difference - 0.40 [95% CI - 0.71 to - 0.09]; P = 0.01) and delayed PN initiation (1.29 vs. 0.80 mean days to start of PN; difference 1.06 [95% CI 0.44 to 1.67]; P = 0.001). There was no significant difference in 28-day mortality (14.2% vs. 15.2%; difference - 1.6% [95% CI - 4.3% to 1.2%]; P = 0.42) between groups.ConclusionsIn this large-scale, multicenter trial, active implementation of an evidence-based feeding guideline reduced the time to commencement of EN and overall PN use but did not translate to a reduction in mortality from critical illness.Trial registrationISRCTN, ISRCTN12233792 . Registered November 20th, 2017

Actively implementing an evidence-based feeding guideline for critically ill patients (NEED): a multicenter, cluster-randomized, controlled trial (vol 26, 46, 2022)

BackgroundPrevious cluster-randomized controlled trials evaluating the impact of implementing evidence-based guidelines for nutrition therapy in critical illness do not consistently demonstrate patient benefits. A large-scale, sufficiently powered study is therefore warranted to ascertain the effects of guideline implementation on patient-centered outcomes.MethodsWe conducted a multicenter, cluster-randomized, parallel-controlled trial in intensive care units (ICUs) across China. We developed an evidence-based feeding guideline. ICUs randomly allocated to the guideline group formed a local "intervention team", which actively implemented the guideline using standardized educational materials, a graphical feeding protocol, and live online education outreach meetings conducted by members of the study management committee. ICUs assigned to the control group remained unaware of the guideline content. All ICUs enrolled patients who were expected to stay in the ICU longer than seven days. The primary outcome was all-cause mortality within 28 days of enrollment.ResultsForty-eight ICUs were randomized to the guideline group and 49 to the control group. From March 2018 to July 2019, the guideline ICUs enrolled 1399 patients, and the control ICUs enrolled 1373 patients. Implementation of the guideline resulted in significantly earlier EN initiation (1.20 vs. 1.55 mean days to initiation of EN; difference - 0.40 [95% CI - 0.71 to - 0.09]; P = 0.01) and delayed PN initiation (1.29 vs. 0.80 mean days to start of PN; difference 1.06 [95% CI 0.44 to 1.67]; P = 0.001). There was no significant difference in 28-day mortality (14.2% vs. 15.2%; difference - 1.6% [95% CI - 4.3% to 1.2%]; P = 0.42) between groups.ConclusionsIn this large-scale, multicenter trial, active implementation of an evidence-based feeding guideline reduced the time to commencement of EN and overall PN use but did not translate to a reduction in mortality from critical illness.Trial registrationISRCTN, ISRCTN12233792 . Registered November 20th, 2017

Spatial Distribution Balance Analysis of Hospitals in Wuhan

The spatial distribution pattern of hospitals in Wuhan indicates a core in the central urban areas and a sparse distribution in the suburbs, particularly at the center of suburbs. This study aims to improve the gravity and Huff models to analyze healthcare accessibility and resources. Results indicate that healthcare accessibility in central urban areas is better than in the suburbs, where it increasingly worsens for the suburbs. A shortage of healthcare resources is observed in large-scale and high-class hospitals in central urban areas, whereas the resources of some hospitals in the suburbs are redundant. This study proposes the multi-criteria evaluation (MCE) analysis model for the location assessment in constructing new hospitals, which can effectively ameliorate healthcare accessibility in suburban areas. This study presents implications for the planning of urban healthcare facilities

RCSANet: A Full Convolutional Network for Extracting Inland Aquaculture Ponds from High-Spatial-Resolution Images

Numerous aquaculture ponds are intensively distributed around inland natural lakes and mixed with cropland, especially in areas with high population density in Asia. Information about the distribution of aquaculture ponds is essential for monitoring the impact of human activities on inland lakes. Accurate and efficient mapping of inland aquaculture ponds using high-spatial-resolution remote-sensing images is a challenging task because aquaculture ponds are mingled with other land cover types. Considering that aquaculture ponds have intertwining regular embankments and that these salient features are prominent at different scales, a Row-wise and Column-wise Self-Attention (RCSA) mechanism that adaptively exploits the identical directional dependency among pixels is proposed. Then a fully convolutional network (FCN) combined with the RCSA mechanism (RCSANet) is proposed for large-scale extraction of aquaculture ponds from high-spatial-resolution remote-sensing imagery. In addition, a fusion strategy is implemented using a water index and the RCSANet prediction to further improve extraction quality. Experiments on high-spatial-resolution images using pansharpened multispectral and 2 m panchromatic images show that the proposed methods gain at least 2–4% overall accuracy over other state-of-the-art methods regardless of regions and achieve an overall accuracy of 85% at Lake Hong region and 83% at Lake Liangzi region in aquaculture pond extraction

On the rules of continuity and symmetry for the data quality of street networks - Fig 1

<p><b>Geometry of road networks and related concepts demonstrated</b>: nodes and segments (a); one-way, two-way streets, single-line, and double-line representations (b) natural streets (in the same color) formed by every-best-fit (c) and self-best-fit (d) strategies.</p

Measured parallelism corresponding to the road pairs in Fig 3.

<p>Measured parallelism corresponding to the road pairs in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0200334#pone.0200334.g003" target="_blank">Fig 3</a>.</p

On the rules of continuity and symmetry for the data quality of street networks

<div><p>Knowledge or rule-based approaches are needed for quality assessment and assurance in professional or crowdsourced geographic data. Nevertheless, many types of geographic knowledge are statistical in nature and are therefore difficult to derive rules that are meaningful for this purpose. The rules of continuity and symmetry considered in this paper can be thought of as two concrete forms of the first law of geography, which may be used to formulate quality measures at the individual level without referring to ground truth. It is not clear, however, how much the rules can be faithful. Hence, the main objective is to test if the rules are consistent with street network data over the world. Specifically, for the rule of continuity we identify natural streets that connect smoothly in a network, and measure the spatial order of information (e.g. names, highway level, speed, etc.) along the streets. The measure is based on spatial auto-correlation indicators adapted for one dimension. For the rule of symmetry, we device an algorithm that recognize parallel road pairs (e.g. dual carriageways), and examine to what extent attributes in the pairs are identical. The two rules are tested against 28 cities selected from OpenStreetMap data worldwide; two professional data sets are used to show more insights. We found that the rules are consistent with street networks from a wide range of cities of different characteristics, and also noted cases with varying degrees of agreement. As a side-effect, we discussed possible limitations of the autocorrelation indicators used, where cautions are needed when interpreting the results. In addition, we present techniques that performed the tests automatically, which can be applied to new data to further verify (or falsify) our findings, or extended as quality assurance tools to detect data items that do not satisfy the rules and to suggest possible corrections according to the rules.</p></div