Natural language processing (NLP) to facilitate abstract review in medical research: the application of BioBERT to exploring the 20-year use of NLP in medical research.

BACKGROUND: Abstract review is a time and labor-consuming step in the systematic and scoping literature review in medicine. Text mining methods, typically natural language processing (NLP), may efficiently replace manual abstract screening. This study applies NLP to a deliberately selected literature review problem, the trend of using NLP in medical research, to demonstrate the performance of this automated abstract review model. METHODS: Scanning PubMed, Embase, PsycINFO, and CINAHL databases, we identified 22,294 with a final selection of 12,817 English abstracts published between 2000 and 2021. We invented a manual classification of medical fields, three variables, i.e., the context of use (COU), text source (TS), and primary research field (PRF). A training dataset was developed after reviewing 485 abstracts. We used a language model called Bidirectional Encoder Representations from Transformers to classify the abstracts. To evaluate the performance of the trained models, we report a micro f1-score and accuracy. RESULTS: The trained models' micro f1-score for classifying abstracts, into three variables were 77.35% for COU, 76.24% for TS, and 85.64% for PRF. The average annual growth rate (AAGR) of the publications was 20.99% between 2000 and 2020 (72.01 articles (95% CI: 56.80-78.30) yearly increase), with 81.76% of the abstracts published between 2010 and 2020. Studies on neoplasms constituted 27.66% of the entire corpus with an AAGR of 42.41%, followed by studies on mental conditions (AAGR = 39.28%). While electronic health or medical records comprised the highest proportion of text sources (57.12%), omics databases had the highest growth among all text sources with an AAGR of 65.08%. The most common NLP application was clinical decision support (25.45%). CONCLUSIONS: BioBERT showed an acceptable performance in the abstract review. If future research shows the high performance of this language model, it can reliably replace manual abstract reviews.

Meta-analysis using Python: a hands-on tutorial.

BACKGROUND: Meta-analysis is a central method for quality evidence generation. In particular, meta-analysis is gaining speedy momentum in the growing world of quantitative information. There are several software applications to process and output expected results. Open-source software applications generating such results are receiving more attention. This paper uses Python's capabilities to provide applicable instruction to perform a meta-analysis. METHODS: We used the PythonMeta package with several modifications to perform the meta-analysis on an open-access dataset from Cochrane. The analyses were complemented by employing Python's zEpid package capable of creating forest plots. Also, we developed Python scripts for contour-enhanced funnel plots to assess funnel plots asymmetry. Finally, we ran the analyses in R and STATA to check the cross-validity of the results. RESULTS: A stepwise instruction on installing the software and packages and performing meta-analysis was provided. We shared the Python codes for meta-analysts to follow and generate the standard outputs. Our results were similar to those yielded by R and STATA. CONCLUSION: We successfully produced standard meta-analytic outputs using Python. This programming language has several flexibilities to improve the meta-analysis results even further.

Fulminant and Diffuse Cerebral Toxoplasmosis as the First Manifestation of HIV Infection: A Case Presentation and Review of the Literature.

BACKGROUND One of the most common causes of central nervous system (CNS) opportunistic infections in immunocompromised patients is toxoplasmosis. It can cause focal or disseminated brain lesions leading to neurological deficit, coma, and death. Prompt management with optimal antibiotics is vital. However, the diagnosis of cerebral toxoplasmosis is challenging in infected individuals with human immunodeficiency virus (HIV). The possible diagnosis is based on clinical presentation, imaging, and specific serologic investigations. The diagnosis can be confirmed by histopathological examination and/or by finding nucleic material in the spinal cerebrospinal fluid (CSF) examination. CASE REPORT We present a review of the literature with a rare illustrative case of diffuse CNS toxoplasmosis as the first manifestation of HIV infection in a young patient. Brain MRI showed diffuse, ring-enhancing lesions, and significant midline shift. Decompressive hemicraniectomy for control of intracranial pressure and anti-infectious therapy were performed. CONCLUSIONS This should raise awareness that cerebral toxoplasmosis can occur in pediatric patients with HIV infection, and, more importantly, as the first manifestation of AIDS. Although the prognosis is often poor, early diagnosis and immediate treatment of this life-threatening opportunistic infection can improve outcomes.

Zinc and copper levels in severe heart failure and the effects of atrial fibrillation on the zinc and copper status.

Oxidative stress is involved in the pathogenesis of congestive heart failure (CHF). Some trace elements serve as antioxidant defenses. The purpose of this study was to analyze the effect of atrial fibrillation (AF) on zinc (Zn) and copper (Cu) levels in patients with advanced CHF. In this prospective study, serum Zn and Cu levels in 78 patients with clinically advanced CHF, i.e., New York Heart Association (NYHA) functional class III or IV (40 patients with AF and 38 in sinus rhythm) were measured using atomic absorption spectrophotometry. All patients also had a left ventricular ejection fraction (EF) of <35%. We recruited 40 volunteers with nearly the same age and weight as control. They had normal EF. There was no significant difference between patients with AF and those with sinus rhythm regarding serum Zn and Cu levels. However, both groups showed significant hypozincemia (p < 0.000) and a decreased Zn/Cu ratio (p < 0.03) compared with control group. Serum Cu levels were similar in the two groups and did not differ significantly from the control group. In patients with advanced CHF, irrespective of the rhythm, profound hypozincemia, and a decreased Zn/Cu ratio were present, which could be secondary to the activation of the renin-angiotensin-aldosterone system and CHF medications. The results suggest the need for more studies focusing on possible benefits with Zn nutriceutical replacement in patients with advanced CHF.