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

Patency of the arterial pedal-plantar arch in patients with chronic kidney disease or diabetes mellitus

BACKGROUND Patency of the pedal-plantar arch limits risk of amputation in peripheral artery disease (PAD). We examined patients without chronic kidney disease (CKD)/diabetes mellits (DM) [PAD-control], those with DM without CKD, and those with CKD without DM. METHOD Uni- and multivariate logistic regression was used to assess association of CKD with loss of patency of the pedal-plantar arch and presence of tibial or peroneal vessel occlusion. Multivariate models adjusted for age, sex, hypertension, hyperlipidemia and smoking. RESULTS A total of 419 patients were included [age 75.2 ± 10.3 years, 288 (69%) male]. CKD nearly doubled the unadjusted odds ratio (OR) for loss of patency of the pedal-plantar arch. After adjustment, association remained significant for severe CKD [estimated glomerular filtration rate (eGFR) ≤ 29 ml/min compared with eGFR ≥ 60 ml/min, adjusted (adj.) OR 8.24 (95% confidence interval {CI} 0.99-68.36, p = 0.05)]. CKD was not related to risk of tibial or peroneal artery occlusion [PAD-control versus CKD, adj. OR 1.09 (95% CI 0.49-2.44, p = 0.83)] in contrast to DM [PAD-control versus DM, adj. OR 2.41 (95% CI 1.23-4.72, p = 0.01), CKD versus DM, adj. OR 2.21 (95% CI 0.93-5.22); p = 0.07)]. CONCLUSIONS Below the knee (BTK) vascular pattern differs in patients with either DM or CKD alone. Severe CKD is a risk factor for loss of patency of the pedal-plantar arch

Efficacy Outcomes of Endovascular Versus Surgical Revascularization in Critical Limb Ischemia: Results From a Prospective Cohort Study.

Data on efficacy outcomes of endovascular versus surgical revascularization in patients with critical limb ischemia (CLI) in contemporary practice are limited. In this prospective cohort study, 353 consecutive patients with CLI were enrolled and allocated to endovascular (PTA [percutaneous transluminal angioplasty]), surgical (SURG), or no revascularization (No REVASC) after interdisciplinary consensus. Outcome measures were sustained primary clinical success (sPCS; survival without major amputation, repeated target extremity revascularization, and freedom from CLI), limb salvage, and amputation-free survival. Propensity-matched Kaplan-Meier analyses and stratified log-rank tests were performed. The PTA, SURG, and No REVASC groups consisted of 264, 62, and 27 patients, respectively. Compared to SURG patients, PTA patients were significantly older, had more risk factors, and more often had ischemic lesions. Propensity score-adjusted analyses showed no significant differences: sPCS was 51.3%/52.2%, limb salvage rate 91.5%/93.7%, and major amputation-free survival 90.5%/87.2% at 12 months for PTA and SURG, respectively. Amputation-free survival for the No REVASC group was 69% at 12 months. In conclusion, endovascular and surgical revascularization in CLI has comparable efficacy outcomes after 12 months. Contemporary overall outcome of patients with CLI is considerably better compared to earlier studies

Haemostaseological complication management in caval and iliac venous stenting

Antiplatelet and anticoagulation therapy after venous stenting is still not standardized, data from randomized-controlled trials are missing. Rare prothrombotic disorders and nonresponsiveness to drugs must be taken into account. This case report demonstrates successful haemostaselogical complication management in recurrent rethromboses due to underlying clopidogrel resistance and low responsiveness to anticoagulation with dabigatran after endovascular stent reconstruction of chronic pelvic and caval vein occlusion in a patient with severe postthrombotic syndrome

Multi-Operational Selective Computer-Assisted Targeting of hepatocellular carcinoma-Evaluation of a novel approach for navigated tumor ablation.

OBJECTIVE To facilitate precise local ablation of hepatocellular carcinoma (HCC) in a setting of combined ablation and transarterial chemoembolization (TACE), we evaluated accuracy and efficiency of a novel technique for navigated positioning of ablation probes using intrahepatic tumor referencing and electromagnetic (EM) guidance, in a porcine model. METHODS An angiographic wire with integrated EM reference sensor at its tip was inserted via a transarterial femoral access and positioned in the vicinity of artificial liver tumors. The resulting offset distance between the tumor center and the intrahepatic endovascular EM reference was calculated. Subsequently, EM tracked ablation probes were inserted percutaneously and navigated toward the tumor center, relying on continuous EM guidance via the intrahepatic reference. Targeting accuracy was assessed as the Euclidean distance between the tip of the ablation probe and the tumor center (Target Positioning Error, TPE). Procedural efficiency was assessed as time efforts for tumor referencing and tumor targeting. RESULTS In 6 animals, 124 targeting measurements were performed with an offset distance < 30 mm (clinically most feasible position), resulting in a mean TPE of 2.9 ± 1.6 mm. No significant correlation between the TPE and different intrahepatic offset distances (range 21 to 61 mm, n = 365) was shown as long as the EM reference was placed within the liver. However, the mean TPE increased when placing the EM reference externally on the animal skin (p < 0.01). TPE was similar when targeting under continuous ventilation or in apnea (p = 0.50). Mean time for tumor referencing and navigated targeting was 6.5 ± 3.8 minutes and 14 ± 8 seconds, respectively. CONCLUSION The proposed technique allows precise and efficient navigated positioning of ablation probes into liver tumors in the animal model. We introduce a simple approach suitable for combined ablation and TACE of HCC in a single treatment session

A concept for electromagnetic navigated targeting of liver tumors using an angiographic approach.

BACKGROUND The benefits of using navigation technology for percutaneous local ablation of selected hepatocellular carcinoma (HCC) have been shown. Due to additional efforts in the procedural workflow, barriers to introducing navigation systems on a broad clinical level remain high. In this work, initial steps toward a novel concept for simple and precise targeting of HCC are evaluated. MATERIAL AND METHODS The proposed technique is based on an angiographic approach using an intrahepatic electromagnetic (EM) reference, for consecutive percutaneous navigated positioning of ablation probes. We evaluated the environmental influence of the angiography suite on EM tracking accuracy, the measurement of a 3 D offset from two 2 D fluoroscopy images, and the accuracy and efficiency of the proposed approach in a porcine liver model. RESULTS The C-arm had a major influence on EM tracking accuracy, with an error up to 3.8 mm. The methodology applied for measurement of a 3 D offset from 2 D fluoroscopy images was confirmed to be feasible with a mean error of 0.76 mm. In the porcine liver model experiment, the overall target positioning error (TPE) was 2.0 mm and time for navigated targeting was 17.9 seconds, when using a tracked ablation probe. CONCLUSIONS The initial methodology of the proposed technique was confirmed to be feasible, introducing a novel concept for simple and precise navigated targeting of HCC

Feasibility of stereotactic MRI-based image guidance for the treatment of vascular malformations: a phantom study.

PURPOSE Treatment of vascular malformations requires the placement of a needle within vessels which may be as small as 1 mm, with the current state of the art relying exclusively on two-dimensional fluoroscopy images for guidance. We hypothesize that the combination of stereotactic image guidance with existing targeting methods will result in faster and more reproducible needle placements, as well as reduced radiationexposure, when compared to standard methods based on fluoroscopy alone. METHODS The proposed navigation approach was evaluated in a phantom experiment designed to allow direct comparison with the conventional method. An anatomical phantom of the left forearm was constructed, including an independent control mechanism to indicate the attainment of the target position. Three interventionalists (one inexperienced, two of them frequently practice the conventional fluoroscopic technique) performed 45 targeting attempts utilizing the combined and 45 targeting attempts utilizing the standard approaches. RESULTS In all 45 attempts, the users were able to reach the target when utilizing the combined approach. In two cases, targeting was stopped after 15 min without reaching the target when utilizing only the C-arm. The inexperienced user was faster when utilizing the combined approach and applied significantly less radiation than when utilizing the conventional approach. Conversely, both experienced users were faster when using the conventional approach, in one case significantly so, with no significant difference in radiation dose when compared to the combined approach. CONCLUSIONS This work presents an initial evaluation of a combined navigation fluoroscopy targeting technique in a phantom study. The results suggest that, especially for inexperienced interventionalists, navigation may help to reduce the time and the radiation dose. Future work will focus on the improvement and clinical evaluation of the proposed method