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

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

Fetal volume measurements with three dimensional ultrasound in the first trimester of pregnancy, related to pregnancy outcome, a prospective cohort study

BACKGROUND: First trimester growth restriction is associated with an increased risk of adverse birth outcomes (preterm birth, low birth weight and small for gestational age at birth). The differences between normal and abnormal growth in early pregnancy are small if the fetal size is measured by the crown-rump-length. Three-dimensional ultrasound volume measurements might give more information about fetal development than two-dimensional ultrasound measurements. Detection of the fetus with a small fetal volume might result in earlier detection of high risk pregnancies and a better selection of high risk pregnancies. METHODS: A prospective cohort study, performed at the Máxima Medical Centre, in Eindhoven-Veldhoven, the Netherlands. During the routine first trimester scan with nuchal translucency measurement 500 fetal volumes will be obtained. The gestational age is based on the first day of the last menstrual period in a regular menstrual cycle and by the crown-rump-length. The acquired datasets are collected and stored on a hard disk for offline processing and volume calculation. The investigator who performs the volume measurements is blinded for the results of the first trimester scan. The manual mode will be used to outline the Region Of Interest, the fetal head and rump, in all cross sections. The fetal volumes are calculated with a rotational step of 9°. First, the relation between fetal volume and gestational age, for a set of participants with normal pregnancies (training set), will be assessed. This model will then be used to determine expected values of fetal volume for a normal pregnancy, which will be referred to as expected normal values. Secondly, for a new set of participants with normal pregnancies and a set of participants with complicated pregnancies (together defined as validation set), the observed fetal volumes (FV(observed)) are compared with their expected normal values (FV(expected)) and expressed as a percentage of the expected normal value. The mean difference in percentage error between the set of normal versus complicated pregnancies will then be compared using the independent-samples t-test. Finally, logistic regression analysis will be applied to the validation set of participants to analyze the possibility of predicting the pregnancy outcome after fetal volume calculation in the first trimester, using this percentage error. DISCUSSION: After this study it is clear whether FV measurement in the first trimester can detect high risk pregnancies. If it is possible to detect these pregnancies, more intensive follow up in these pregnancies might result in fewer complicated pregnancies and fewer fetal morbidities

A new semi-automated method for fetal volume measurements with three-dimensional ultrasound: preliminary results

ABSTRACT Objective Complications in pregnancy are suggested to be the result of intrauterine conditions in the first trimester of pregnancy. Three-dimensional ultrasound volume measurements might give more information, compared with two-dimensional measurements. Commonly available methods for volume measurements are not suited for daily practice. This is a report of preliminary results of a promising, more practical semi-automated method for volume calculations with three-dimensional ultrasound. Method Volume datasets of 16 objects (10.2–41.5¿cm3) were obtained. Euclidean shortening flow and Perona and Malik were used as image enhancement techniques. The image gradient was calculated. The points of interest were detected by the iso-intensity and the edge-detection technique. Volume measurements with Volume Computer-aided AnaLysis (VOCAL) are used as a reference. A volume dataset of a first trimester fetus was acquired to test this method in vivo. Results The mathematical calculations with iso-intensity (Perona and Malik: average¿=¿-1.57¿cm3, SD¿=¿4.05; and Euclidean shortening flow: average¿=¿-1.38¿cm3, SD¿=¿2.47) showed results comparable with the VOCAL method (average¿=¿+1.28¿cm3, SD¿=¿2.07). We also succeeded in detecting all voxels in the whole contour of a 12-week fetus. Conclusion Mathematical volume calculations are possible with the semi-automated method. We were able to apply this new method on a first trimester fetus. This new method is promising for future use in the daily practice. © 2012 John Wiley & Sons, Ltd

A new semi-automated method for fetal volume measurements with three-dimensional ultrasound: preliminary results

ABSTRACT Objective Complications in pregnancy are suggested to be the result of intrauterine conditions in the first trimester of pregnancy. Three-dimensional ultrasound volume measurements might give more information, compared with two-dimensional measurements. Commonly available methods for volume measurements are not suited for daily practice. This is a report of preliminary results of a promising, more practical semi-automated method for volume calculations with three-dimensional ultrasound. Method Volume datasets of 16 objects (10.2–41.5¿cm3) were obtained. Euclidean shortening flow and Perona and Malik were used as image enhancement techniques. The image gradient was calculated. The points of interest were detected by the iso-intensity and the edge-detection technique. Volume measurements with Volume Computer-aided AnaLysis (VOCAL) are used as a reference. A volume dataset of a first trimester fetus was acquired to test this method in vivo. Results The mathematical calculations with iso-intensity (Perona and Malik: average¿=¿-1.57¿cm3, SD¿=¿4.05; and Euclidean shortening flow: average¿=¿-1.38¿cm3, SD¿=¿2.47) showed results comparable with the VOCAL method (average¿=¿+1.28¿cm3, SD¿=¿2.07). We also succeeded in detecting all voxels in the whole contour of a 12-week fetus. Conclusion Mathematical volume calculations are possible with the semi-automated method. We were able to apply this new method on a first trimester fetus. This new method is promising for future use in the daily practice. © 2012 John Wiley & Sons, Ltd

The predictive value of first trimester fetal volume measurements, a prospective cohort study

Objectives To determine if fetal volume (FV) measurements with three-dimensional ultrasound in the first trimester of pregnancy can detect the fetus at risk for preterm birth and/or low birth weight. Methods In this prospective cohort study, 538 participants were included during the routine first trimester ultrasound examination. Volume measurements were performed with VOCAL (9°). Firstly, the relation between FV and gestational age for a set of participants with normal pregnancies (training set), was assessed using multiple linear regression analysis, which was then used to determine the expected normal values. Secondly, for a new set of participants with normal pregnancies and a set of participants with complicated pregnancies (preterm birth and/or low birth weight), i.e. the validation set, the observed fetal volumes (FVobserved) were compared with their expected normal values (FVexpected) and expressed as a percentage of the expected normal value. The difference in mean percentage was then assessed with independent-samples t-test. Finally, logistic regression analysis was applied to the validation set to analyze the ability to predict the pregnancy outcome with FV calculation. Results Linear regression analysis of FV as a predictor of preterm birth and/or low birth weight did not result in significant (p = 0.630 and 0.290, respectively) or clinical relevant results (standardized effect sizes of 0.061 and 0.179, respectively). The predicting quality was also very low (AUC = 0.508 and 0.545 respectively). Conclusions Fetal volume measurements in the first trimester of pregnancy are not useful as a prognostic tool for predicting pregnancies of high risk for preterm birth or a low birth weight

The predictive value of first trimester fetal volume measurements, a prospective cohort study

Objectives: To determine if fetal volume (FV) measurements with three-dimensional ultrasound in the first trimester of pregnancy can detect the fetus at risk for preterm birth and/or low birth weight. Methods: In this prospective cohort study, 538 participants were included during the routine first trimester ultrasound examination. Volume measurements were performed with VOCAL (9 degrees). Firstly, the relation between FV and gestational age for a set of participants with normal pregnancies (training set), was assessed using multiple linear regression analysis, which was then used to determine the expected normal values. Secondly, for a new set of participants with normal pregnancies and a set of participants with complicated pregnancies (preterm birth and/or low birth weight), i.e. the validation set, the observed fetal volumes (FVobserved) were compared with their expected normal values (FVexpected) and expressed as a percentage of the expected normal value. The difference in mean percentage was then assessed with independent-samples t-test. Finally, logistic regression analysis was applied to the validation set to analyze the ability to predict the pregnancy outcome with Pi calculation. Results: Linear regression analysis of FV as a predictor of preterm birth and/or low birth weight did not result in significant (p = 0.630 and 0.290, respectively) or clinical relevant results (standardized effect sizes of 0.061 and 0.179, respectively). The predicting quality was also very low (AUC = 0.508 and 0.545 respectively). Conclusions: Fetal volume measurements in the first trimester of pregnancy are not useful as a prognostic tool for predicting pregnancies of high risk for preterm birth or a low birth weight

The (cost) effectiveness of procedural sedation and analgesia versus general anaesthesia for hysteroscopic myomectomy, a multicentre randomised controlled trial : PROSECCO trial, a study protocol

BACKGROUND: In women with abnormal uterine bleeding, fibroids are a frequent finding. In case of heavy menstrual bleeding and presence of submucosal type 0-1 fibroids, hysteroscopic resection is the treatment of first choice, as removal of these fibroids is highly effective. Hysteroscopic myomectomy is currently usually performed in the operating theatre. A considerable reduction in costs and a higher patient satisfaction are expected when procedural sedation and analgesia with propofol (PSA) in an outpatient setting is applied. However, both safety and effectiveness - including the necessity for re-intervention due to incomplete resection - have not yet been evaluated. METHODS: This study is a multicentre randomised controlled trial with a non-inferiority design and will be performed in the Netherlands. Women > 18 years with a maximum of 3 symptomatic type 0 or 1 submucosal fibroids with a maximum diameter of 3.5 cm are eligible to participate in the trial. After informed consent, 205 women will be randomised to either hysteroscopic myomectomy using procedural sedation and analgesia with propofol in an outpatient setting or hysteroscopic myomectomy using general anaesthesia in a clinical setting in the operating theatre. Primary outcome will be the percentage of complete resections, based on transvaginal ultrasonography 6 weeks postoperatively. Secondary outcomes are cost effectiveness, menstrual blood loss (Pictorial blood assessment chart), quality of life, pain, return to daily activities/work, hospitalization, (post) operative complications and re-interventions. Women will be followed up to one year after hysteroscopic myomectomy. DISCUSSION: This study may demonstrate comparable effectiveness of hysteroscopic myomectomy under procedural sedation and analgesia versus general anaesthesia in a safe and patient friendly environment, whilst achieving a significant cost reduction. TRIAL REGISTRATION: Dutch trial register, number NTR5357 . Registered 11th of August 2015

The (cost) effectiveness of procedural sedation and analgesia versus general anaesthesia for hysteroscopic myomectomy, a multicentre randomised controlled trial : PROSECCO trial, a study protocol

BACKGROUND: In women with abnormal uterine bleeding, fibroids are a frequent finding. In case of heavy menstrual bleeding and presence of submucosal type 0-1 fibroids, hysteroscopic resection is the treatment of first choice, as removal of these fibroids is highly effective. Hysteroscopic myomectomy is currently usually performed in the operating theatre. A considerable reduction in costs and a higher patient satisfaction are expected when procedural sedation and analgesia with propofol (PSA) in an outpatient setting is applied. However, both safety and effectiveness - including the necessity for re-intervention due to incomplete resection - have not yet been evaluated. METHODS: This study is a multicentre randomised controlled trial with a non-inferiority design and will be performed in the Netherlands. Women > 18 years with a maximum of 3 symptomatic type 0 or 1 submucosal fibroids with a maximum diameter of 3.5 cm are eligible to participate in the trial. After informed consent, 205 women will be randomised to either hysteroscopic myomectomy using procedural sedation and analgesia with propofol in an outpatient setting or hysteroscopic myomectomy using general anaesthesia in a clinical setting in the operating theatre. Primary outcome will be the percentage of complete resections, based on transvaginal ultrasonography 6 weeks postoperatively. Secondary outcomes are cost effectiveness, menstrual blood loss (Pictorial blood assessment chart), quality of life, pain, return to daily activities/work, hospitalization, (post) operative complications and re-interventions. Women will be followed up to one year after hysteroscopic myomectomy. DISCUSSION: This study may demonstrate comparable effectiveness of hysteroscopic myomectomy under procedural sedation and analgesia versus general anaesthesia in a safe and patient friendly environment, whilst achieving a significant cost reduction. TRIAL REGISTRATION: Dutch trial register, number NTR5357 . Registered 11th of August 2015