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

Hematopoietic cell transplant specific comorbidity index as a tool in the assessment of non relapse mortality in patients undergoing allogeneic hematopoietic stem cell transplant

Orientadores: Cármino Antonio de Souza, Afonso Celso VigoritoDissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Ciências MédicasResumo: O Transplante de Células Tronco Hematopoiéticas (TCTH) Alogênico representa uma possibilidade de cura para pacientes portadores de doenças hematológicas malignas e benignas. Porém, como qualquer modalidade de tratamento, apresenta efeitos adversos que podem ser graves, inclusive causando a morte. Com o intuito de se avaliar a influência que as comorbidades teriam na mortalidade não relacionada à recidiva (MNRR), foi criada uma ferramenta, o Índice de Comorbidade específico do Transplante de Células Tronco Hematopoiéticas (Hematopoietic Cell Transplant Specific Comorbidity Index - HCT-CI). Nossos objetivos, portanto, foram validar o HCT-CI na população de pacientes submetidos a TCTH Alogênico em nossa instituição, no período de 1993 a 2010, e avaliar outros fatores de riscos envolvidos na MNRR e na Sobrevida Global (SG). Os prontuários de 457 pacientes foram revistos e as informações referentes às comorbidades contidas no HCT-CI foram registradas. A maioria dos pacientes (59%) recebeu o índice 0, seguido de 30% de pacientes com índice de 1-2 e 11% com índice ? 3. Na análise univariada, os pacientes com HCT-CI igual a zero, comparados aos com HCT-CI ?1, apresentaram uma MNRR de 33% vs. 45% (p=0.01) e SG de 53% vs. 35% (p=0.001); nos pacientes que ao transplante apresentavam doença de baixo risco, comparados aos com doença de alto risco, a MNRR foi de 30% vs. 50% (p<0.0001) e SG de 57% vs. 27% (p<0.0001); o tipo de enxerto (medula óssea vs. sangue periférico) apresentou MNRR de 29% vs. 49% (p<0.0001) e SG de 56% vs. 34% (p<0.0001). A análise multivariada confirmou a influência do HCT-CI na MNRR e na SG, do risco da doença sobre a SG e do tipo de enxerto na MNRR. O tipo de condicionamento (baixa dose vs. alta dose) não teve influência na MNRR e SG, tanto na análise univariada quanto na multivariada. Quanto o grupo foi estratificado pelo HCT-CI (0 e ?1) o risco da doença ao transplante e o tipo de enxerto tiveram influência na MNRR e na SG, na análise univariada e multivariada, tanto nos pacientes com HCT-CI 0 e ?1. Não houve influência do tipo de condicionamento. O HCT-CI foi validado na nossa população de pacientes submetidos ao TCTH alogênico e identificamos outros fatores de risco que tiveram influência na MNRR e na SG. O HCT-CI, portanto, deve ser utilizado como guia no planejamento da estratégia terapêutica em pacientes portadores de comorbidadesAbstract: Allogeneic hematopoietic stem cell transplant is an important modality of treatment for patients bearing malignant and benign hematologic diseases, representing a chance of cure. As every treatment, it has a treatment-related mortality, possibly influenced by comorbidities. To better evaluate the influence of comorbidities on Non-Relapse Mortality (NRM) and Overall Survival (OS), the Hematopoietic Cell Transplant Specific Comorbidity Index (HCT-CI) was developed. Our objective was to apply the HCT-CI and to find risk factors for NRM and OS in patients who underwent an allogeneic hematopoietic stem cell transplant in our institution, between 1993 and 2010. Medical charts from 457 patients were reviewed. Most patients (59%) were classified in score 0, followed by 30% of cases with score 1-2 and 11% score 3-7. In a univariate analysis, patients with comorbidity score 0, compared with score ?1 had a NRM of 33% vs. 45% (p=0.01) and OS at 5 years of 53% vs. 35% (p=0.001); patients with low risk disease at transplant, compared with high risk disease, had a NRM of 30% vs. 50% (p<0.0001) and OS of 57% vs. 27% (p<0.0001); graft source (bone marrow vs. peripheral blood) had a NRM of 29% vs. 49% (p<0.0001) and OS 56% vs. 34% (p<0.0001). The multivariate analysis confirmed the influence of HCT-CI score on NRM and OS, disease risk at transplant on OS and graft source on NRM. The conditioning type (low dose vs. high dose) did not influence the NRM and OS in both univariate and multivariate analysis. When stratified by comorbidity (0 and ?1), disease status at transplant and graft source influenced NRM and OS in univariate and multivariate analysis, either in the group of patients with HCT-CI 0 and ?1. The conditioning type had no impact. Based on our data, we were able to validate de HCT-CI in our institution and to identify other risk factors with influence on NRM and OS. The HCT-CI, therefore, could be used to guide the treatment strategy of patients with comorbiditiesMestradoClinica MedicaMestre em Clinica Medic

Effect of Intraoperative High Positive End-Expiratory Pressure (PEEP) With Recruitment Maneuvers vs Low PEEP on Postoperative Pulmonary Complications in Obese Patients: A Randomized Clinical Trial (vol 321, pg 2292, 2019)

status: publishe

Effect of Intraoperative High Positive End-Expiratory Pressure (PEEP) With Recruitment Maneuvers vs Low PEEP on Postoperative Pulmonary Complications in Obese Patients: A Randomized Clinical Trial.

IMPORTANCE An intraoperative higher level of positive end-expiratory positive pressure (PEEP) with alveolar recruitment maneuvers improves respiratory function in obese patients undergoing surgery, but the effect on clinical outcomes is uncertain

Effect of intraoperative high Positive End-Expiratory Pressure (PEEP) with recruitment maneuvers vs low PEEP on postoperative pulmonary complications in obese patients : a randomized clinical trial

IMPORTANCE An intraoperative higher level of positive end-expiratory positive pressure (PEEP) with alveolar recruitment maneuvers improves respiratory function in obese patients undergoing surgery, but the effect on clinical outcomes is uncertain. OBJECTIVE To determine whether a higher level of PEEP with alveolar recruitment maneuvers decreases postoperative pulmonary complications in obese patients undergoing surgery compared with a lower level of PEEP. DESIGN, SETTING, AND PARTICIPANTS Randomized clinical trial of 2013 adults with body mass indices of 35 or greater and substantial risk for postoperative pulmonary complications who were undergoing noncardiac, nonneurological surgery under general anesthesia. The trial was conducted at 77 sites in 23 countries from July 2014-February 2018; final follow-up: May 2018. INTERVENTIONS Patients were randomized to the high level of PEEP group (n = 989), consisting of a PEEP level of 12 cm H2O with alveolar recruitment maneuvers (a stepwise increase of tidal volume and eventually PEEP) or to the low level of PEEP group (n = 987), consisting of a PEEP level of 4 cm H2O. All patients received volume-controlled ventilation with a tidal volume of 7 mL/kg of predicted body weight. MAIN OUTCOMES AND MEASURES The primary outcomewas a composite of pulmonary complications within the first 5 postoperative days, including respiratory failure, acute respiratory distress syndrome, bronchospasm, new pulmonary infiltrates, pulmonary infection, aspiration pneumonitis, pleural effusion, atelectasis, cardiopulmonary edema, and pneumothorax. Among the 9 prespecified secondary outcomes, 3 were intraoperative complications, including hypoxemia (oxygen desaturation with SpO(2) 1 minute). RESULTS Among 2013 adults who were randomized, 1976 (98.2%) completed the trial (mean age, 48.8 years; 1381 [69.9%] women; 1778 [90.1%] underwent abdominal operations). In the intention-to-treat analysis, the primary outcome occurred in 211 of 989 patients (21.3%) in the high level of PEEP group compared with 233 of 987 patients (23.6%) in the low level of PEEP group (difference, -2.3%[95% CI, -5.9% to 1.4%]; risk ratio, 0.93 [95% CI, 0.83 to 1.04]; P =.23). Among the 9 prespecified secondary outcomes, 6 were not significantly different between the high and low level of PEEP groups, and 3 were significantly different, including fewer patients with hypoxemia (5.0% in the high level of PEEP group vs 13.6% in the low level of PEEP group; difference, -8.6%[95% CI, -11.1% to 6.1%]; P <.001). CONCLUSIONS AND RELEVANCE Among obese patients undergoing surgery under general anesthesia, an intraoperative mechanical ventilation strategy with a higher level of PEEP and alveolar recruitment maneuvers, compared with a strategy with a lower level of PEEP, did not reduce postoperative pulmonary complications