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

How small is small enough? Role of robotics in paediatric urology

The well-known advantages of robotic surgery include improved dexterity, three-dimensional operating view and an improved degree of freedom. Robotic surgery is performed for a wide range of surgeries in urology, which include radical prostatectomy, radical cystectomy, and ureteric reimplantation. Robotic paediatric urology is evolving. The major hindrance in the development of paediatric robotics is, first, the differences in practice patterns in paediatric urology compared with adult urology thereby making development of expertise difficult and secondly it is challenging to conduct proper studies in the paediatric population because of the paucity of cases. The difficulties in conducting these studies include difficulty in designing a proper randomised study, difficulties with blinding, and finally, the ethical issues involved, finally the instruments although in the phase of evolution require a lot of improvement. In this article, we review the relevant articles for paediatric robotic surgery. We emphasise on the technical aspects and results in contemporary paediatric robotic case series

Migration of double J stent into the inferior vena cava and the right atrium

Migration of a ureteric double J stent down into the bladder or up into the kidney is a well known complication. We recently encountered a case where the stent migrated into the vascular system following attempted ureteroscopy for a lower ureteric calculus. The patient required open surgical exploration for stent retrieval

Robotic surgery is ready for prime time in India: For the motion

Robotic surgery with its bundled advantages is still in its burgeoning phase, the best of which is yet to come. The unrivalled suturing ease and motion scaling features, transforming into greater precision, has led to its widespread application in different surgical ramifications. These, coupled with the aforementioned advantages, has led to an increasing number of procedures being performed and that too with improved patient outcomes. It seems that the progressing India is readily accepting this robotic surgical innovation, the use of which is on a continuous rise, with the number of robotic platforms coming up in increasing numbers in many tertiary care Indian centres and a corresponding increase in demand of the same by the patients as well; thereby aptly fulfilling the economics of ′demand and supply′

Laparoendoscopic single-site donor nephrectomy

A donor would prefer a minimally invasive procedure because of lesser morbidity, this may be the reason that laparoscopic donor nephrectomy (LDN) rates have exponentially increased. The rationale dictates that a virtually scarless surgery would be most beneficial to this patient subgroup. In this article, we review the approach, instrumentation, dissection and retrieval issues and the results of laparoendoscopic single-site donor nephrectomy (LESS-DN). The existing literature on LESS-DN was reviewed in Pubmed. The various access sites described for LESS-DN include the umbilicus and Pfannenstiel incision. The steps of LESS-DN duplicate those of standard LDN. There is a paucity of studies comparing LESS-DN with LDN, particularly randomized studies. The most challenging step of LESS-DN is graft retrieval. Authors have described a variety of methods for graft retrieval which include manual methods, and those using retrieval bags. In the majority of the studies, the graft retrieval time is longer in comparison to standard LDN. However, the graft outcome in recipients is comparable. In this article, we also allude to the complications mentioned in various series. LESS-DN is currently an evolving procedure. The procedure requires a high level of skills in laparoscopic surgery. The choice of access site, access site ports and the type of instruments to be used is a matter of surgeon preference. Although the warm ischemia time in most of the series is longer in LESS-DN, this has not translated into poor recipient outcomes. Further work needs to be done to make the retrieval quick

Isolated renal hydatid cyst managed by laparoscopic transperitoneal nephrectomy

Hydatid disease is a cyclozoonotic parasitic infestation caused by the cestode Echinococcus granulosus. Isolated renal involvement is extremely rare. A 45-year-old female, working as a farmer, presented with vague abdominal pain and hydatiduria. Ultrasonography of the abdomen revealed hydatid cyst arising from the right kidney. Computerized tomography scan of the abdomen confirmed the findings. Laparoscopic transperitoneal nephrectomy was performed. Isolated right renal hydatid cyst was removed in toto. Microscopic examination confirmed the diagnosis of hydatid cyst. Transperitoneal laparoscopic approach gives a better working space which helped us to remain outside Gerota's fascia and prevent subsequent cyst rupture

Age-specific prostate specific antigen and prostate specific antigen density values in a community-based Indian population

Introduction: We sought to determine the distribution of serum prostate specific antigen (PSA) levels in a community-based population in the state of Gujarat in India. Materials and Methods: Community screening of subjects residing in Kheda and Anand districts of Gujarat was done with digital rectal examination (DRE), uroflowmetry and transabdominal sonography and serum PSA. In three villages transrectal sonography was done in addition to transabdominal sonography. All patients with a PSA of more than 4 ng/ml and / or abnormal DRE were evaluated. Biopsy-proven prostatic malignancy was detected in 20 patients. Subjects who did not follow up and who had biopsy-proven malignancy were excluded from the analysis, 1899 subjects were analyzed. Results: One thousand seven hundred and eighty-seven (89.17%) had a PSA of < 4 ngml, 180 (8.9%) had a PSA between 4-10 ng/ml, while 37 (1.8 %) had a PSA more than 10ng/ml. There was a statistically significant correlation between age and prostate volume (correlation coefficient 0.33) and between prostate volume and PSA (correlation coefficient 0.50). The age-specific PSA values derived as the 95th percentile value were as follows, 40-49 years (0-2.1), 50-59 years (0-3.4), 60-69 years (0-4.2) and more than 70 years (0-5.0). The 95th percentile value for PSAD was 0.19. Conclusion: Indians need to have separate PSA reference ranges. The age-specific PSA ranges for men in the present study population are on the lower side and the prostate specific antigen density on the higher side

Laparoscopic radical nephrectomy versus open radical nephrectomy in T1-T3 renal tumors: An outcome analysis

Aims: To compare laparoscopic radical nephrectomy (LRN) with open radical nephrectomy (ORN) in T1-T3 renal lesions. Materials and Methods: The records of 65 patients who underwent LRN between January 2002 and December 2006 were entered prospectively in a database. The patients were compared with 56 patients who had undergone ORN between January 2000 and December 2005. The two groups were comparable in terms of age, body mass index (BMI) and tumor size. LRN was compared with ORN in terms of operative room time, blood loss, complications , analgesic requirement, hospital stay and start of oral intake. The oncologic efficacy was evaluated in stages T1 and T2 in terms of cancer-free and overall survival. Results: The laparoscopy group had a significantly shorter hospital stay (5.72, range 3-23 days vs. 9.18, range 4-23 days, p value: < 0.0001), analgesia requirement (175.65, range 50-550 mg vs. 236, range 0-1100 mg of tramadol, p value: < 0.03), hemoglobin decline (1.55, range 0.1 to 4.4 mg/dl vs. 2.25, range 0.2 - 7 mg/dL, p value: < 0.001) and hematocrit drop (4.83, range 0.3 - 12.9 vs. 7.06 range 2 -18, p value: < 0.0001). The majority of specimens showed renal cell carcinoma. In the laparoscopy group, 29 tumors were T1 stage, 18 were T2, while eight were T3. In the open surgery group, 25 tumors were T1, 19 were T2 and 12 were T3. The cancer-free survival rate at 24 months for ORN and LRN in T1 lesions was 91.7% and 93.15% respectively and the patient survival rate was 100% in both groups. The cancer-free survival rate at 24 months for ORN and LRN in T2 lesions was 88.9% and 94.1%, respectively and the patient survival was 100% and 94%, respectively. After LRN, there was one instance of port site metastasis, local recurrence and distant metastasis. All recurrences were distant after ORN. Conclusion: Laparoscopic radical nephrectomy has advantages in terms of shorter hospitalization and a lower analgesia requirement. It is feasible and produces effective cancer control in T1 lesions, comparable to that of its open counterpart in T2 and selected cases of T3 lesions