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

Thiel-embalmed cadavers as a novel training model for ultrasound guided, supine, endoscopic combined intrarenal surgery

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Oncological and functional efficacy of nephron-sparing surgery versus radical nephrectomy in renal cell carcinoma stages ≥cT1b: a single institution, matched analysis.

Introduction: The purpose of this paper is to compare oncological outcomes of partial nephrectomy (PN) versus radical nephrectomy (RN) in renal cell carcinoma (RCC) clinical stages ≥T1b, in a retrospective propensity-score matched cohort of a high-volume, tertiary referral center. This paper also aims to compare renal function and complication rates between groups. Material and methods: Our single-institution RCC database was queried to select patients with clinical stages defined by tumor size (T), lymph nodes(N), and metastasis (M) scores of T1b-4 N0 M0, that underwent PN or RN between 2000 and 2014. All images of patients that underwent RN were reviewed, and only patients deemed eligible for PN were included. Medical records were reviewed to obtain data on tumor characteristics, comorbidities, renal function, and complications. After propensity score matching, 152 patients (76 per group) were included in the final analysis. Primary outcomes were cancer specific survival (CSS), overall survival (OS), and clinical progression-free survival (CPFS). Secondary outcomes were renal function preservation and post-operative complication rates. Results: Groups were propensity-score matched. The only parameters that were significantly different between groups were the median follow-up time (RN: 79 months, range 24.1-100.5 vs. PN: 38.5 months, range 20.5-72.1) and a better performance status in the RN group (p = 0.002). The five-year CPFS, CSS, and OS rates were 77.2%, 90.5%, and 86.4%, respectively, in the RN group, and 83.6%, 91.1%, and 82.0%, respectively, in the PN group (p = 0.33, p = 0.55, and p = 0.33, respectively). In the multivariate Cox model, the surgical method was not an independent predictor of CPFS, CSS, or OS. The RN group showed a significantly greater reduction in estimated glomerular filtration rate (RN: 14.1 vs. PN: 5.4 ml/min per 1.73 m²; p \u3c0.03). There was no significant difference in complication rates between the two groups (p = 0.3). The main limitations of this study were its retrospective design and the medium-term follow-up. Conclusions: Our results demonstrated the efficacy and safety of PN in patients with RCC in clinical stages ≥T1b. We observed no significant difference in oncological outcomes between the PN and RN groups at medium-term follow ups. The surgical method did not influence these outcomes. Renal function was preserved significantly more frequently in the PN than in the RN group, but the groups had similar complication rates. These findings suggested that PN could be considered an oncologically safe procedure for treating large RCC tumors; thus, PN should always be considered, when technically feasible, regardless of tumor stage

Thiel-embalmed cadavers as a novel training model for ultrasound-guided supine endoscopic combined intrarenal surgery

Objective To evaluate Thiel-embalmed cadavers (TEC) as a training model for percutaneous nephrolithotomy (PCNL), more specifically for ultrasound (US)-guided supine endoscopic combined intrarenal surgery (ECIRS). Subjects and Methods Thirteen urologists (nine experienced endourologists, four fellows/residents) performed an US-guided supine ECIRS procedure on a TEC. The model was evaluated by way of a questionnaire (5-point Likert scale). Descriptive statistical analysis was performed and results were graphically presented using divergent bar graphs. Results US images were appreciated as lifelike in all aspects. Although distention of the collecting system was not ideal in one out of three TEC, US visualisation of the distended calyces during puncture was good. Skin penetration was more difficult and less realistic in TEC, while kidney puncture and dilatation were deemed very realistic. Ureteric and collecting system anatomy and consistency were similar to real life, although the mucosa appeared paler. US needle guidance was perceived as excellent. Overall, needle puncture assessment was realistic and useful as a training tool. Overall quality and satisfaction of TEC in US-guided supine ECIRS was good to excellent and comparable to a real-life procedure. Overall appropriateness of the TEC model was considered excellent for both initial and advanced supine PCNL training. Conclusion Despite the minor drawbacks of tough skin and non-ideal collecting system dilatation during ureteroscopy, the TEC model was considered good to excellent as a training model for US-guided PCNL, in particular, US-guided needle puncture of the kidney during supine ECIRS

Transvesical approach in robot-assisted bladder diverticulectomy : surgical technique and outcome

Objective: Treatment for bladder diverticula may become necessary in case of incomplete bladder emptying or recurrent urinary tract infections (UTIs). When bladder outlet obstruction is present, a simultaneous desobstructive procedure can be performed. In this video, we present our technique for a transvesical approach in robot-assisted bladder diverticulectomy (RABD) and discuss its outcomes.Patients and Surgical Procedure: We retrospectively analyzed the outcomes of 23 patients who underwent a transvesical RABD between March 2015 and May 2020 at the OLV hospital of Aalst. After retrograde filling, a cystotomy is performed. The orifices are identified and the bladder diverticulum is observed. The mucosa covering the diverticular neck is incised and the plane between the mucosa and the muscularis is identified. The mucosa is separated from the surrounding structures. The base of the diverticulum is transected using cautery. The defect is closed with a barbed suture.Results: Median age was 66 years (interquartile range [IQR] 60-69). The number of diverticula removed ranged from 1 to 3. Ten patients were treated with diverticulectomy alone, 12 underwent a simultaneous adenomectomy, 1 a radical prostatectomy. Median operative was 140 minutes (IQR 120-180), median estimated blood loss was 250 mL (IQR 28-438). Median catheterization time was 2 days (IQR 1-5), median hospitalization time 3 days (IQR 2-4). One patient developed urinary leakage after catheter removal, one patient developed a UTI. Median follow-up was 9 months (IQR 3.5-14). No late postoperative complications nor relapse were recorded. Average postvoid residual was 42 mL (IQR 0-111), with a median decline of 120 mL (IQR -402 to -33).Conclusions: Transvesical approach for RABD is a safe and reliable technique that gives the advantage of a quick localization of the diverticulum and orifices, and direct access to the prostate when simultaneous desobstruction is necessary. Catheterization time is short. No relapse has been observed

PERI-OPERATIVE OUTCOMES OF OPEN VERSUSROBOT-ASSISTED SIMPLE PROSTATECTOMY: RESULTS FROMTWO HIGH-VOLUME CENTRES

INTRODUCTION AND OBJECTIVE: Simple prostatectomy isthe treatment of choice for symptomatic benign prostatic hyperplasia(BPH), and it should be recommended in prostate glands>80cc.Although functional outcomes of the open approach (OSP) are un-doubtedly favourable, the robotic approach (RASP) is gainingconsensus thanks to its safety and reduced morbidity. However, data ofRASP is scarce, and the majority of published series described smallcohorts with short follow-up. We aimed to investigate perioperativeoutcomes of RASP and OSP in a large cohort of patients from twourological referral centres.METHODS: We analyzed data of 357 consecutive men withsymptomatic BPH who received OSP or RASP at two referral centres[OLV Hospital (Aalst, Belgium) and United Hospitals (Ancona, Italy)]from 2011 to 2021. Multivariable regressions (MVA) investigated vari-ables associated with postoperative complications after adjusting forage, Body Mass Index (BMI), Charlson Comorbidity Index (CCI),prostate volume, concurrent bladder stone or diverticula, indwellingcatheter, surgical approach (OSP vs. RASP), operative time (OT) andestimated blood loss (EBL).RESULTS: A total of 201 (56%) and 156 (44%) men receivedOSP and RASP, respectively. Overall, median (interquartile range[IQR]) age and CCI were 70 (65-76) years and 3 (2-4), with no differ-ences between the groups (both p>0.05). Median [IQR] prostate vol-ume was slightly higher in the RASP vs. OSP group (median: 164 vs.153 cc; p[0.08). As compared to men receiving OSP, OT was longer inthe RASP group (124 vs. 89 minutes), with lower EBL (395 vs. 761 ml),shorter catheterisation time (3 vs. 10 days) and length of stay (LOS) (4vs. 8 days; all medians; all p<0.001). The rate of overall post-operativecomplications was higher in the OSP vs. RASP group (33% vs. 24%;p[0.05), especially of Clavien-Dindo grade 3 (15% vs. 5%;p[0.003), with higher rates of postoperative blood transfusions (28%vs. 1%; p<0.001). On MVA, the probability of postoperativecomplications was higher for older men (odds ratio [OR]: 1.13; 95%confidence interval [CI]: 1.07, 1.23; p[0.047) and for men who hadhigher EBL (OR: 1.45; 95%CI: 1.02, 1.53; p[0.001), whereas theassociation between surgical approach and overall postoperativecomplications was not statistically significant (OR: 0.88; 95% CI 0.64,1.27; p[0.1).CONCLUSIONS: As compared to OSP, RASP allows for lowerpostoperative complications and blood transfusions and thus, it mightbe considered an option for the treatment of symptomatic BPH ac-cording to physician's preference