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

Impact of opioid-free analgesia on pain severity and patient satisfaction after discharge from surgery: multispecialty, prospective cohort study in 25 countries

Background: Balancing opioid stewardship and the need for adequate analgesia following discharge after surgery is challenging. This study aimed to compare the outcomes for patients discharged with opioid versus opioid-free analgesia after common surgical procedures.Methods: This international, multicentre, prospective cohort study collected data from patients undergoing common acute and elective general surgical, urological, gynaecological, and orthopaedic procedures. The primary outcomes were patient-reported time in severe pain measured on a numerical analogue scale from 0 to 100% and patient-reported satisfaction with pain relief during the first week following discharge. Data were collected by in-hospital chart review and patient telephone interview 1 week after discharge.Results: The study recruited 4273 patients from 144 centres in 25 countries; 1311 patients (30.7%) were prescribed opioid analgesia at discharge. Patients reported being in severe pain for 10 (i.q.r. 1-30)% of the first week after discharge and rated satisfaction with analgesia as 90 (i.q.r. 80-100) of 100. After adjustment for confounders, opioid analgesia on discharge was independently associated with increased pain severity (risk ratio 1.52, 95% c.i. 1.31 to 1.76; P < 0.001) and re-presentation to healthcare providers owing to side-effects of medication (OR 2.38, 95% c.i. 1.36 to 4.17; P = 0.004), but not with satisfaction with analgesia (beta coefficient 0.92, 95% c.i. -1.52 to 3.36; P = 0.468) compared with opioid-free analgesia. Although opioid prescribing varied greatly between high-income and low- and middle-income countries, patient-reported outcomes did not.Conclusion: Opioid analgesia prescription on surgical discharge is associated with a higher risk of re-presentation owing to side-effects of medication and increased patient-reported pain, but not with changes in patient-reported satisfaction. Opioid-free discharge analgesia should be adopted routinely

Hepato-bronchial fistula secondary to perforated sigmoid diverticulitis: a case report

Abstract Background Patients with diverticulitis are predisposed to hepatic abscesses via seeding through the portal circulation. Hepatic abscesses are well-documented sequelae of diverticulitis, however instances of progression to hepato-bronchial fistulization are rare. We present a case of diverticulitis associated with hepatic abscess leading to hepato-bronchial fistulization, which represents a novel disease course not yet reported in the literature. Case Presentation A 61-year-old Caucasian man presented with a history of unintentional weight loss and dyspnea both at rest and with exertion. He had a significant tobacco and alcohol misuse history. A massive right-sided pleural effusion was found on chest X-ray, which responded partially to chest tube insertion. A computed tomography scan of his thorax confirmed the presence of innumerable lung abscesses as well as a complex pleural effusion. An indeterminate tiny air pocket at the dome of the liver was also noted. A follow-up computed tomography scan of his abdomen revealed a decompressed hepatic abscess extending into the right pleural space and the right lower lobe. A sigmoid-rectal fistula was also revealed with focal colonic thickening, presumed to be the sequelae of remote or chronic diverticulitis. An interventional radiologist inserted a percutaneous drain into the decompressed hepatic abscess and the instillation of contrast revealed immediate filling of the right pleural space, lung parenchyma, and bronchial tree, confirming a hepato-bronchial fistula. After two concurrent chest tube insertions failed to drain the remaining pleural effusion completely, surgical lung decortication was conducted. Markedly thickened pleura were seen and a significant amount of gelatinous inflammatory material was debrided from the lower thoracic cavity. He recovered well and was discharged 10 days post-thoracotomy on oral antibiotics. The percutaneous liver abscess tube was removed 3 weeks post-discharge from hospital after the drain check revealed that the fistula and abscess had entirely resolved. Conclusions Refractory right-sided pleural effusion combined with constitutional symptoms should alert clinicians to search for possible hepatic abscess, especially in the context of diverticulitis. The rupture of an untreated hepatic abscess could lead to death from profound sepsis or rarely, as in this case, a hepato-bronchial fistula. Timely investigation and a multidisciplinary treatment approach can lead to improved patient outcomes

Environment-Adaptable Fast Multi-Resolution (EAF-MR) optimization in large-scale RF-FPGA systems

Abstract Software-defined radio (SDR) can have high communication quality with a reconfigurable RF front-end. One of the main challenges of a reconfigurable RF front-end is finding an optimal configuration among all possible configurations. In order to efficiently find an optimal configuration, Environment-Adaptable Fast (EAF) optimization utilizes calculated signal-to-interference-and-noise ratio (SINR) and narrows down the searching space (Jun et al., Environment-adaptable efficient optimization for programming of reconfigurable Radio Frequency (RF) receivers, 2014). However, we found several limitations for applying the EAF optimization to a realistic large-scale Radio Frequency-Field Programmable Gate Array (RF-FPGA) system. In this paper, we first investigated two estimation issues of RF impairments: a saturation bias of nonlinearity estimates and limited resources for RF impairment estimation. Using the estimated results, the SINR formula was calculated and used for the Environment-Adaptable Fast Multi-Resolution (EAF-MR) optimization, which was designed by applying the EAF optimization to multi-resolution optimization. Finally, our simulation set-up demonstrated the efficiency improvement of the EAF-MR optimization for a large-scale RF-FPGA

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 science. © The Author(s) 2019. Published by Oxford University Press