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

Effect of angiotensin-converting enzyme inhibitor and angiotensin receptor blocker initiation on organ support-free days in patients hospitalized with COVID-19

IMPORTANCE Overactivation of the renin-angiotensin system (RAS) may contribute to poor clinical outcomes in patients with COVID-19. Objective To determine whether angiotensin-converting enzyme (ACE) inhibitor or angiotensin receptor blocker (ARB) initiation improves outcomes in patients hospitalized for COVID-19. DESIGN, SETTING, AND PARTICIPANTS In an ongoing, adaptive platform randomized clinical trial, 721 critically ill and 58 non–critically ill hospitalized adults were randomized to receive an RAS inhibitor or control between March 16, 2021, and February 25, 2022, at 69 sites in 7 countries (final follow-up on June 1, 2022). INTERVENTIONS Patients were randomized to receive open-label initiation of an ACE inhibitor (n = 257), ARB (n = 248), ARB in combination with DMX-200 (a chemokine receptor-2 inhibitor; n = 10), or no RAS inhibitor (control; n = 264) for up to 10 days. MAIN OUTCOMES AND MEASURES The primary outcome was organ support–free days, a composite of hospital survival and days alive without cardiovascular or respiratory organ support through 21 days. The primary analysis was a bayesian cumulative logistic model. Odds ratios (ORs) greater than 1 represent improved outcomes. RESULTS On February 25, 2022, enrollment was discontinued due to safety concerns. Among 679 critically ill patients with available primary outcome data, the median age was 56 years and 239 participants (35.2%) were women. Median (IQR) organ support–free days among critically ill patients was 10 (–1 to 16) in the ACE inhibitor group (n = 231), 8 (–1 to 17) in the ARB group (n = 217), and 12 (0 to 17) in the control group (n = 231) (median adjusted odds ratios of 0.77 [95% bayesian credible interval, 0.58-1.06] for improvement for ACE inhibitor and 0.76 [95% credible interval, 0.56-1.05] for ARB compared with control). The posterior probabilities that ACE inhibitors and ARBs worsened organ support–free days compared with control were 94.9% and 95.4%, respectively. Hospital survival occurred in 166 of 231 critically ill participants (71.9%) in the ACE inhibitor group, 152 of 217 (70.0%) in the ARB group, and 182 of 231 (78.8%) in the control group (posterior probabilities that ACE inhibitor and ARB worsened hospital survival compared with control were 95.3% and 98.1%, respectively). CONCLUSIONS AND RELEVANCE In this trial, among critically ill adults with COVID-19, initiation of an ACE inhibitor or ARB did not improve, and likely worsened, clinical outcomes. TRIAL REGISTRATION ClinicalTrials.gov Identifier: NCT0273570

Effect of screening programme on mortality from breast cancer. Women might not accept mammography if benefit is lower than is currently thought.

CommentLetterinfo:eu-repo/semantics/publishe

Risks of osteoporosis associated with breast cancer treatment: the need to access to preventive treatment.

The results of available clinical studies suggest that breast cancer treatment significantly affect bone turnover, BMD and fracture risk. This is for instance the case for all third-generation aromatase inhibitors. For these reasons it is recommended that breast cancer patients exercise regularly and take daily calcium (1500 mg) and vitamin D (800UI) supplements. Most experts recommend that all women starting medical castration or aromatase inhibitor therapy should be assessed for their risk of osteoporosis and undergo bone mineral density (BMD) measurement by dual-energy X-ray absorptiometry (DEXA). Patients with pre-existing osteopenia and osteoporosis should be evaluated for conditions which worsen skeletal health, such as vitamin D deficiency, hyperparathyroidism, hyperthyroidism and hyper-calcuria. If these patients have a BMD score of -2.5 or lower, a low BMD (T-score between -1 and -2.5) and additional risk factors for osteoporosis or fragility fractures, bisphosphonate therapy should be considered. The optimal duration of bisphosphonate therapy is unknown. It should probably be given for as long as aromatase inhibitor therapy is continued. In addition, bisphosphonate therapy may also reduce the risk of bone metastases. This approach seems to be cost effective based on an economic evaluation model.EditorialSCOPUS: ed.jinfo:eu-repo/semantics/publishe

Management of BRCA1/2 associated breast cancer: A systematic qualitative review of the state of knowledge in 2006

Introduction: The optimal clinical management of breast cancer (BC) arising in BRCA1/2 mutations carriers is a difficult issue complicated by the risk of subsequent malignancies and by the potential differences in response to local and systemic therapies. Aim: Systematically review the difference in outcome after breast conservation therapy (BCT) and uni-or bilateral mastectomy in BRCA1/2 related BC. Material and methods: We selected 20 studies, for which we evaluated the methodology, the characteristics of the populations, biases, confounding risk factors and outcomes. Results: All studies are retrospective, entailed by numerous biases. They varied with respect to patients' number, selection, and confounding factors. Hereditary BC patients carried an increased risk of ipsilateral recurrence in 5/17 studies, a worse survival in 4/14, an increased risk of contralateral BC in 14/16. Conclusion: Except for contralateral risk, the presence of a BRCA mutation does not seem to offer additional prognostic information. Large prospective trials, stratified for risk reduction strategies are warranted. © 2006 Elsevier Ltd. All rights reserved.SCOPUS: ar.jinfo:eu-repo/semantics/publishe

Influence of HRT on prognostic factors for breast cancer: A systematic review after the Women's Health Initiative trial

SCOPUS: re.jinfo:eu-repo/semantics/publishe

Desire for a child and breast cancer

About 10% of breast cancers occur in women who are younger than 40 years of age. For many of them, the breast cancer diagnosis will occur when they are still planning pregnancy. Most breast cancers are diagnosed at an early stage of the disease, i.e. stage I or II, which is associated with a high survival rate (5 years-survival ranging between 97% and 79% respectively) (1). Many of these patients will use adjuvant endocrine therapy. This treatment has no direct impact on their fertility, but postpones a possible pregnancy, since pregnancy is contra-indicated during Tamoxifen treatment. On the other hand, chemotherapy increases the risk of premature ovarian failure, of early menopause, and of definitive sterility. This may result in an increased risk of depression and impaired quality of life. Furthermore, those women who remain fertile will often be advised to avoid pregnancy in the near future, in order to ensure the absence of breast cancer recurrence. Nevertheless, fertility decreases with age. Possible strategies, which permit optimal treatment of breast cancer and maintain the possibility of pregnancy, should be systematically discussed with the patient as soon as possible during treatment planning (2). Gynecologists and surgeons should encourage such patients to participate in multi-center studies evaluating strategies to preserve their fertility. Life continues after cancer; the prospect of pregnancy and child birth are part of a positive project.SCOPUS: re.jinfo:eu-repo/semantics/publishe