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

Direct innominate artery cannulation for selective antegrade cerebral perfusion during deep hypothermic circulatory arrest in aortic surgery

ObjectiveTo demonstrate a novel, reproducible, and effective method of direct innominate artery cannulation using a 14F pediatric venous cannula to establish antegrade cerebral protection (ACP) in patients undergoing aortic surgery that requires an open distal anastomosis or hemiarch replacement.MethodsWe reviewed prospectively gathered data on all patients who had undergone replacement of the ascending aorta or hemiarch with an open distal anastomosis using deep hypothermic circulatory arrest and direct innominate artery cannulation with a 14F pediatric venous cannula at our institution. After central cannulation and cooling to 25°C to 28°C, all patients had ACP initiated by way of a direct innominate cannula placed over a guidewire.ResultsFifty patients underwent direct innominate artery cannulation with our technique from 2010 to 2012. The operative mortality was 2% (n = 1), and the rates of neurologic morbidity were acceptable and similar to those with other methods of ACP delivery: stroke (2%, n = 1), seizure (0%, n = 0), and delirium (18%, n = 9). The mean operative time was 31 ± 9, 19 ± 5, 100 ± 39, 141 ± 39, and 259 ± 63 minutes for cooling, circulatory arrest, crossclamp, cardiopulmonary bypass, and total operative time, respectively. No local or arterial complications were observed.ConclusionsDirect cannulation of the innominate artery using a 14F pediatric venous cannula is a simple, reproducible, safe, and effective technique for establishing ACP in patients undergoing aortic surgery that requires an open distal anastomosis or hemiarch replacement. This technique avoids the additional time and potential local complications associated with other established methods for delivering ACP, such as axillary cannulation

Simulation and skills training in mitral valve surgery

ObjectiveLimited exposure and visualization and technical complexity have affected resident training in mitral valve surgery. We propose simulation-based learning to improve skill acquisition in mitral valve surgery.MethodsAfter reviewing instructional video recordings of mitral annuloplasty in porcine and plastic models, 11 residents (6 integrated and 5 traditional) performed porcine model mitral annuloplasty. Video-recorded performance was reviewed by attending surgeon providing audio formative feedback superimposed on video recordings; recordings were returned to residents for review. After 3-week practice with plastic model, residents repeated porcine model mitral annuloplasty. Performance assessments initially (prefeedback) and at 3 weeks (postfeedback) were based on review of video recordings on 5-point rating scale (5, good; 3, average; 1, poor) of 11 components. Ratings were averaged for composite score.ResultsTime to completion improved from mean 31 ± 9 minutes to 25 ± 6 minutes after 3-week practice (P = .03). At 3 weeks, improvement in technical components was achieved by all residents, with prefeedback scores varying from 2.4 ± 0.6 for needle angles to 3.0 ± 0.5 for depth of bites and postfeedback scores of 3.1 ± 0.8 for tissue handling to 3.6 ± 0.8 for suture management and tension (P ≤ .001). Interrater reliability was greater than 0.8. In this sample, composite scores of first-year integrated and traditional residents were lower than those of senior level residents; comparatively, third-year integrated residents demonstrated good technical proficiency.ConclusionsSimulation-based learning with formative feedback results in overall improved performance of simulated mitral annuloplasty. In complex surgical procedures, simulation may provide necessary early graduated training and practice. Importantly, a “passing” grade can be established for proficiency-based advancement

Hypophosphatemia promotes lower rates of muscle ATP synthesis

Hypophosphatemia can lead to muscle weakness and respiratory and heart failure, but the mechanism is unknown. To address this question, we noninvasively assessed rates of muscle ATP synthesis in hypophosphatemic mice by using in vivo saturation transfer [(31)P]-magnetic resonance spectroscopy. By using this approach, we found that basal and insulin-stimulated rates of muscle ATP synthetic flux (V(ATP)) and plasma inorganic phosphate (P(i)) were reduced by 50% in mice with diet-induced hypophosphatemia as well as in sodium-dependent P(i) transporter solute carrier family 34, member 1 (NaPi2a)-knockout (NaPi2a(−/−)) mice compared with their wild-type littermate controls. Rates of V(ATP) normalized in both hypophosphatemic groups after restoring plasma P(i) concentrations. Furthermore, V(ATP) was directly related to cellular and mitochondrial P(i) uptake in L6 and RC13 rodent myocytes and isolated muscle mitochondria. Similar findings were observed in a patient with chronic hypophosphatemia as a result of a mutation in SLC34A3 who had a 50% reduction in both serum P(i) content and muscle V(ATP). After oral P(i) repletion and normalization of serum P(i) levels, muscle V(ATP) completely normalized in the patient. Taken together, these data support the hypothesis that decreased muscle ATP synthesis, in part, may be caused by low blood P(i) concentrations, which may explain some aspects of muscle weakness observed in patients with hypophosphatemia.—Pesta, D. H., Tsirigotis, D. N., Befroy, D. E., Caballero, D., Jurczak, M. J., Rahimi, Y., Cline, G. W., Dufour, S., Birkenfeld, A. L., Rothman, D. L., Carpenter, T. O., Insogna, K., Petersen, K. F., Bergwitz, C., Shulman, G. I. Hypophosphatemia promotes lower rates of muscle ATP synthesis

Identification of Very Low-Risk Subgroups of Patients with Primary Mediastinal Large B-Cell Lymphoma Treated with R-CHOP

Background R-CHOP can cure approximately 75% of patients with primary mediastinal large B-cell lymphoma (PMLBCL), but prognostic factors have not been sufficiently evaluated yet. R-da- EPOCH is potentially more effective but also more toxic than R-CHOP. Reliable prognostic classification is needed to guide treatment decisions. Materials and Methods We analyzed the impact of clinical prognostic factors on the outcome of 332 PMLBCL patients <= 65 years treated with R-CHOP +/- radiotherapy in a multicenter setting in Greece and Cyprus. Results With a median follow-up of 69 months, 5-year freedom from progression (FFP) was 78% and 5-year lymphoma specific survival (LSS) was 89%. On multivariate analysis, extranodal involvement (E/IV) and lactate dehydrogenase (LDH) >= 2 times upper limit of normal (model A) were significantly associated with FFP; E/IV and bulky disease (model B) were associated with LSS. Both models performed better than the International Prognostic Index (IPI) and the age-adjusted IPI by Harrel’s C rank parameter and Akaike information criterion. Both models A and B defined high-risk subgroups (13%-27% of patients [pts]) with approximately 19%-23% lymphoma-related mortality. They also defined subgroups composing approximately one-fourth or one-half of the patients, with 11% risk of failure and only 1% or 4% 5-year lymphoma-related mortality. Conclusion The combination of E/IV with either bulky disease or LDH >= 2 times upper limit of normal defined high-risk but not very-high-risk subgroups. More importantly, their absence defined subgroups comprising approximately one-fourth or one-half of the pts, with 11% risk of failure and minimal lymphoma-related mortality, who may not need more intensive treatment such as R-da-EPOCH. Implications for Practice By analyzing the impact of baseline clinical characteristics on outcomes of a large cohort of patients with primary mediastinal large B-cell lymphoma homogeneously treated with R-CHOP with or without radiotherapy, we developed novel prognostic indices which can aid in deciding which patients can be adequately treated with R-CHOP and do not need more intensive regimens such as R-da-EPOCH. The new indices consist of objectively determined characteristics (extranodal disease or stage IV, bulky disease, and markedly elevated serum lactate dehydrogenase), which are readily available from standard initial staging procedures and offer better discrimination compared with established risk scores (International Prognostic Index [IPI] and age-adjusted IPI)

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