Finding Related Publications: Extending the Set of Terms Used to Assess Article Similarity.

Recommendation of related articles is an important feature of the PubMed. The PubMed Related Citations (PRC) algorithm is the engine that enables this feature, and it leverages information on 22 million citations. We analyzed the performance of the PRC algorithm on 4584 annotated articles from the 2005 Text REtrieval Conference (TREC) Genomics Track data. Our analysis indicated that the PRC highest weighted term was not always consistent with the critical term that was most directly related to the topic of the article. We implemented term expansion and found that it was a promising and easy-to-implement approach to improve the performance of the PRC algorithm for the TREC 2005 Genomics data and for the TREC 2014 Clinical Decision Support Track data. For term expansion, we trained a Skip-gram model using the Word2Vec package. This extended PRC algorithm resulted in higher average precision for a large subset of articles. A combination of both algorithms may lead to improved performance in related article recommendations

Is EGFR expression altered following postoperative chemotherapy for colorectal adenocarcinoma?

BACKGROUND: There is immunohistochemical evidence to suggest that expression of epidermal growth factor receptor (EGFR) in primary colorectal adenocarcinoma predicts its expression in recurrent disease. This study investigates whether postoperative chemotherapy affects the degree of concordance between EGFR statuses of the two tumors. METHODS: Thirty-three patients were identified from the files of Sunnybrook Health Sciences Center from July 1994 to June 2005. All patients had resection of their primary tumors and their distant recurrences. Eighteen patients received postoperative chemotherapy, 3 of which also received postoperative radiation therapy. Representative primary and recurrent tumor sections were stained using mouse anti-EGFR antibodies and only membranous staining of malignant cells was recorded. Results were reported as negative (no staining), 1+ (positivity in <50% of cells) or 2+ (positivity in >50% of cells). RESULTS: EGFR immunostaining in the 15 patients, who received no postoperative chemotherapy, was decreased in 3 recurrences, remained the same in 10 and increased in 2. In the group of 18 patients who received postoperative chemotherapy, EGFR immunostaining was decreased in 6 recurrences, remained the same in 9 and increased in 3 (p = 0.6598). In patients who received postoperative chemotherapy, the odds ratio for a recurrence to show lower levels of EGFR immunostaining compared to its originally resected primary was 4.75 (CI = 0.94 – 26.73). CONCLUSION: These preliminary data suggest that recurrences following postoperative chemotherapy are likely to have lower levels of EGFR expression compared to cases who receive no chemotherapy. Although the difference of immunostaining profiles between the two groups was not statistically significant, this observation might impact the management of these patients by targeted biologic therapies and its practical implications need further validation in larger series

Correction to: Cluster identification, selection, and description in Cluster randomized crossover trials: the PREP-IT trials

An amendment to this paper has been published and can be accessed via the original article

Increase in contralateral prophylactic mastectomy conversation online unrelated to decision-making

BackgroundThe increased uptake of contralateral prophylactic mastectomy (CPM) among breast cancer patients remains poorly understood. We hypothesized that the increased rate of CPM is represented in conversations on an online breast cancer community and may contribute to patients choosing this operation.MethodsWe downloaded 328,763 posts and their dates of creation from an online breast cancer community from August 1, 2000, to May 22, 2016. We then performed a keyword search to identify posts which mentioned breast cancer surgeries: contralateral prophylactic mastectomy (n&nbsp;=&nbsp;7095), mastectomy (n&nbsp;=&nbsp;10,889), and lumpectomy (n&nbsp;=&nbsp;9694). We graphed the percentage of CPM-related, lumpectomy-related, and mastectomy-related conversations over time. We also graphed the frequency of posts which mentioned multiple operations over time. Finally, we performed a qualitative study to identify factors influencing the observed trends.ResultsSurgically related posts (e.g., mentioning at least one operation) made up a small percentage (n&nbsp;=&nbsp;27,678; 8.4%) of all posts on this community. The percentage of surgically related posts mentioning CPM was found to increase over time, whereas the percentage of surgically related posts mentioning mastectomy decreased over time. Among posts that mentioned more than one operation, mastectomy and lumpectomy were the procedures most commonly mentioned together, followed by mastectomy and CPM. There was no change over time in the frequency of posts that mentioned more than one operation. Our qualitative review found that most posts mentioning a single operation were unrelated to surgical decision-making; rather the operation was mentioned only in the context of the patient's cancer history. Conversely, the most posts mentioning multiple operations centered around the patients' surgical decision-making process.ConclusionsCPM-related conversation is increasing on this online breast cancer community, whereas mastectomy-related conversation is decreasing. These results appear to be primarily informed by patients reporting the types of operations they have undergone, and thus appear to correspond to the known increased uptake of CPM

Thromboembolism risk of COVID-19 is high and associated with a higher risk of mortality: A systematic review and meta-analysis.

BackgroundStudies have suggested that there is increased risk of thromboembolism (TE) associated with coronavirus disease 2019 (COVID-19). However, overall arterial and venous TE rates of COVID-19 and effect of TE on COVID-19 mortality is unknown.MethodsWe did a systematic review and meta-analysis of studies evaluating TE in COVID-19. We searched PubMed, Cochrane, and Embase for studies published up to June 12, 2020. Random effects models were used to produce summary TE rates and odds ratios (OR) of mortality in COVID-19 patients with TE compared to those without TE. Heterogeneity was quantified with I 2 .FindingsOf 425 studies identified, 42 studies enrolling 8271 patients were included in the meta-analysis. Overall venous TE rate was 21% (95% CI:17-26%): ICU, 31% (95% CI: 23-39%). Overall deep vein thrombosis rate was 20% (95% CI: 13-28%): ICU, 28% (95% CI: 16-41%); postmortem, 35% (95% CI:15-57%). Overall pulmonary embolism rate was 13% (95% CI: 11-16%): ICU, 19% (95% CI:14-25%); postmortem, 22% (95% CI:16-28%). Overall arterial TE rate was 2% (95% CI: 1-4%): ICU, 5% (95%CI: 3-7%). Pooled mortality rate among patients with TE was 23% (95%CI:14-32%) and 13% (95% CI:6-22%) among patients without TE. The pooled odds of mortality were 74% higher among patients who developed TE compared to those who did not (OR, 1.74; 95%CI, 1.01-2.98; P = 0.04).InterpretationTE rates of COVID-19 are high and associated with higher risk of death. Robust evidence from ongoing clinical trials is needed to determine the impact of thromboprophylaxis on TE and mortality risk of COVID-19.FundingNone

Thromboembolism risk of COVID-19 is high and associated with a higher risk of mortality: A systematic review and meta-analysis.

BackgroundStudies have suggested that there is increased risk of thromboembolism (TE) associated with coronavirus disease 2019 (COVID-19). However, overall arterial and venous TE rates of COVID-19 and effect of TE on COVID-19 mortality is unknown.MethodsWe did a systematic review and meta-analysis of studies evaluating TE in COVID-19. We searched PubMed, Cochrane, and Embase for studies published up to June 12, 2020. Random effects models were used to produce summary TE rates and odds ratios (OR) of mortality in COVID-19 patients with TE compared to those without TE. Heterogeneity was quantified with I 2 .FindingsOf 425 studies identified, 42 studies enrolling 8271 patients were included in the meta-analysis. Overall venous TE rate was 21% (95% CI:17-26%): ICU, 31% (95% CI: 23-39%). Overall deep vein thrombosis rate was 20% (95% CI: 13-28%): ICU, 28% (95% CI: 16-41%); postmortem, 35% (95% CI:15-57%). Overall pulmonary embolism rate was 13% (95% CI: 11-16%): ICU, 19% (95% CI:14-25%); postmortem, 22% (95% CI:16-28%). Overall arterial TE rate was 2% (95% CI: 1-4%): ICU, 5% (95%CI: 3-7%). Pooled mortality rate among patients with TE was 23% (95%CI:14-32%) and 13% (95% CI:6-22%) among patients without TE. The pooled odds of mortality were 74% higher among patients who developed TE compared to those who did not (OR, 1.74; 95%CI, 1.01-2.98; P = 0.04).InterpretationTE rates of COVID-19 are high and associated with higher risk of death. Robust evidence from ongoing clinical trials is needed to determine the impact of thromboprophylaxis on TE and mortality risk of COVID-19.FundingNone