Ensemble pretrained language models to extract biomedical knowledge from literature

OBJECTIVES

The rapid expansion of biomedical literature necessitates automated techniques to discern relationships between biomedical concepts from extensive free text. Such techniques facilitate the development of detailed knowledge bases and highlight research deficiencies. The LitCoin Natural Language Processing (NLP) challenge, organized by the National Center for Advancing Translational Science, aims to evaluate such potential and provides a manually annotated corpus for methodology development and benchmarking.

MATERIALS AND METHODS

For the named entity recognition (NER) task, we utilized ensemble learning to merge predictions from three domain-specific models, namely BioBERT, PubMedBERT, and BioM-ELECTRA, devised a rule-driven detection method for cell line and taxonomy names and annotated 70 more abstracts as additional corpus. We further finetuned the T0pp model, with 11 billion parameters, to boost the performance on relation extraction and leveraged entites' location information (eg, title, background) to enhance novelty prediction performance in relation extraction (RE).

RESULTS

Our pioneering NLP system designed for this challenge secured first place in Phase I-NER and second place in Phase II-relation extraction and novelty prediction, outpacing over 200 teams. We tested OpenAI ChatGPT 3.5 and ChatGPT 4 in a Zero-Shot setting using the same test set, revealing that our finetuned model considerably surpasses these broad-spectrum large language models.

DISCUSSION AND CONCLUSION

Our outcomes depict a robust NLP system excelling in NER and RE across various biomedical entities, emphasizing that task-specific models remain superior to generic large ones. Such insights are valuable for endeavors like knowledge graph development and hypothesis formulation in biomedical research.

The IMPACT framework and implementation for accessible in silico clinical phenotyping in the digital era

Clinical phenotyping is often a foundational requirement for obtaining datasets necessary for the development of digital health applications. Traditionally done via manual abstraction, this task is often a bottleneck in development due to time and cost requirements, therefore raising significant interest in accomplishing this task via in-silico means. Nevertheless, current in-silico phenotyping development tends to be focused on a single phenotyping task resulting in a dearth of reusable tools supporting cross-task generalizable in-silico phenotyping. In addition, in-silico phenotyping remains largely inaccessible for a substantial portion of potentially interested users. Here, we highlight the barriers to the usage of in-silico phenotyping and potential solutions in the form of a framework of several desiderata as observed during our implementation of such tasks. In addition, we introduce an example implementation of said framework as a software application, with a focus on ease of adoption, cross-task reusability, and facilitating the clinical phenotyping algorithm development process.

Positive lifestyle behaviours and emotional health factors are associated with low back pain resilience

PURPOSE

To evaluate the relationship between lifestyle behaviours, emotional health factors, and low back pain (LBP) resilience.

METHODS

This retrospective longitudinal study utilised 1,065 twins with a recent history of LBP from the Washington State Twin Registry. A lifestyle behaviour score was built using variables of body mass index, physical activity engagement, sleep quality, smoking status, and alcohol consumption. An emotional health score was built using variables of the absence of depressed mood, perceived stress, and active coping. The main outcome was LBP resilience, assessed as recovery ("bouncing back"), and sustainability (maintaining high levels of function despite LBP).

RESULTS

After adjusting for covariates, there was no relationship between the lifestyle behaviour score (OR 1.05, 95% CI 0.97-1.15, p = 0.218) and the emotional health score (OR 1.08, 95% CI 0.98-1.19, p = 0.142) with the likelihood of recovering from LBP. There was however, evidence of a positive association between the lifestyle behaviour score (β 0.20, 95% CI 0.04-0.36, p = 0.013), the emotional health score (β 0.22, 95% CI 0.00-0.43, p = 0.049), and greater levels of sustainability. These results were confirmed by a within-pair analysis (lifestyle behaviour score: β 1.79, 95% CI 0.05-3.53, p = 0.043) and (emotional health score: β 0.52, 95% CI 0.09-0.96, p = 0.021) adjusting for genetic and early shared environmental confounding.

CONCLUSION

Findings from this study suggest that people who adopt optimal lifestyle behaviours and positive emotional factors are more likely to be resilient and maintain high levels of function despite suffering from LBP.

The neurobiological reward system in Prolonged Grief Disorder (PGD): A systematic review

Prolonged Grief Disorder (PGD) is a debilitating condition affecting between 7% and 10% of bereaved individuals. Past imaging and psychological studies have proposed links between PGD's characteristic symptoms - in particular, profound yearning - and the neural reward system. We conducted a systematic review to investigate this connection. On December 19, 2019, we searched six bibliographic databases for data on the neurobiology of grief and disordered grief. We excluded studies of the hypothalamic-pituitary-adrenal (HPA) axis, animal studies, and reviews. After abstract and full-text screening, twenty-four studies were included in the final review. We found diverse evidence for the activation of several reward-related regions of the brain in PGD. The data reviewed suggest that compared to normative grief, PGD involves a differential pattern of activity in the amygdala and orbitofrontal cortex (OFC); likely differential activity in the posterior cingulate cortex (PCC), rostral or subgenual anterior cingulate cortex (ACC), and basal ganglia overall, including the nucleus accumbens (NAc); and possible differential activity in the insula. It also appears that oxytocin signaling is altered in PGD, though the exact mechanism is unclear. Our findings appear to be consistent with, though not confirmative of, conceptualizing PGD as a disorder of reward, and identify directions for future research.

Telehealth Impact on Primary Care Related Ambulance Transports

Introduction: Telehealth has been used nominally for trauma, neurological, and cardiovascular incidents in prehospital emergency medical services (EMS). Yet, much less is known about the use of telehealth for low-acuity primary care. We examine the development of one telehealth program and its impact on unnecessary ambulance transports. Objective: The objective of this study is to describe the development and impact of a large-scale telehealth program on ambulance transports. Methods: We describe the patient characteristics and results from a cohort of patients in Houston, Texas who received a prehospital telehealth consultation from an emergency medicine physician. Inclusion criteria were adults and pediatric patients with complaints considered to be non-urgent, primary care related. Data were analyzed for 36 months, from January 2015 through December 2017. Our primary dependent variable was the percentage of patients transported by ambulance. We used descriptive statistics to describe patient demographics, chi-square to examine differences between groups, and logistic regression to explore the effects with multivariate controls including age, gender, race, and chief complaint. Results: A total of 15,067 patients were enrolled (53% female; average age 44 years ± 19 years) over the three-year period. The 3 primary chief complaints were based on abdominal pains (13% of cases), nausea/vomiting/diarrhea (NVD) (9.4%), and back pain (9.3%). Ambulance transports represented 11.2% of all transports in the program, while alternative taxi transportation was used in 75.6%, and the remainder were self- or no-transports. Taxi transportation to an alternate, affiliated clinic (versus ED) was utilized in 5% of incidents. After multivariate controls, older age patients presenting with low-risk, non-acute chest pain, shortness of breath, and dizziness were much more likely to use ambulance transport. Race and gender were not significant predictors of ambulance transport. Conclusions: We found telehealth offers a technology strategy to address potentially unnecessary ambulance transports. Based on prior cost-effectiveness analyses, the reduction of unnecessary ambulance transports translates to an overall reduction in EMS agency costs. Telehealth programs offer a viable solution to support alternate destination and alternate transport programs.

Abstract P3-14-06: The prevention and management of chemotherapy-induced peripheral neuropathy in breast cancer patients: A systematic review

Background: Chemotherapy induced peripheral neuropathy (CIPN) remains a common treatment related adverse event for breast cancer (BC) patients. CIPN interferes with the ability to complete chemotherapy & therefore potentially compromises survival outcomes. CIPN can worsen health-related quality of life and also add to the ongoing morbidity experienced by BC survivors. Previously, systematic reviews & ASCO guidelines have examined CIPN across many cancer types & different chemotherapies, which may lead to the introduction of confounding factors not relevant to BC patients. A recent prospective cohort also identified other specific lifestyle factors associated with CIPN in BC patients (1). From our search, a systematic review specifically looking at CIPN in BC patients has not previously been undertaken.

Methods: We conducted a systematic search in PubMed, EMBASE, CINAHL and CENTRAL. Clinical trials and observational studies for all potential pharmacological and non-pharmacological interventions were included. Risk of bias for full-text papers was assessed using the Cochrane Risk of Bias Assessment or the modified Newcastle Ottawa score.

Results: Of 706 records being identified, 601 unique citations were screened with 21 full text papers retrieved for assessment, and 16 studies included in the qualitative assessment. We identified 10 randomised controlled trials (RCTs), one observational cohort study, and five controlled before-and-after studies (CBA). Pharmacological interventions which were investigated included calcium/magnesium infusion, glutamine, amifostine, goshajinkigan, omega 3 fatty acids, acetyl-L-carnitine, pregabalin, alpha-lipoic acid and minocycline. Non-pharmacological interventions included body mass index & lifestyle factors, electroacupuncture, exercise, limb hypothermia, carbon dioxide limb bathing and limb compression therapy. All trials identified were investigating primary prevention of CIPN in the setting of taxane chemotherapy. Improvements in the incidence of CIPN were reported with omega 3 fatty acids, glutamine and alpha-lipoic acid, but only one of these studies is a published RCT. In two of the studies, the benefit was identified only on physical examination, but no significant benefit with nerve conduction (NCS) testing. On subgroup analysis of trials investigating exercise, there was a benefit in the use of high intensity exercise versus low intensity exercise, particularly in patients <50 years old within a healthy weight range. Mixed results were seen with goshajinkigan. An increase in CIPN was seen with antioxidant use, electroacupuncture and acetyl L carnitine. Majority of the RCTs were associated with a high overall risk of bias.

Conclusions: There has been a paucity of research on CIPN in BC patients. There were no interventions identified in this systematic review which show a clear clinical benefit in the prevention of CIPN in BC patients. BC patients may have specific lifestyle and hormonal factors which influence CIPN and this should prompt ongoing specific patient focussed research within this subgroup with large, blinded, randomised controlled trials.

Greenlee, et al. Natl Cancer Inst 2017; 109(2).

Citation Format: Roberts KE, Feng S, Adsett I, Rickett K, Woodward N. The prevention and management of chemotherapy-induced peripheral neuropathy in breast cancer patients: A systematic review [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P3-14-06.

Production and separation of carrier-free ⁷Be

A high-purity carrier-free (7)Be was efficiently isolated following proton bombardment of a lithium hydroxide-aluminum target. The separation of beryllium from lithium and aluminum was achieved through a hydrochloric acid elution system utilizing cation exchange chromatography. The beryllium recovery, +99%, was assessed through gamma spectroscopy while the chemical purity was established by mass spectrometry. The decontamination factors of beryllium from lithium and aluminum were determined to be 6900 and 300, respectively.

BMPR2 mutations in pulmonary arterial hypertension with congenital heart disease

The aim of the present study was to determine if patients with both pulmonary arterial hypertension (PAH), due to pulmonary vascular obstructive disease, and congenital heart defects (CHD), have mutations in the gene encoding bone morphogenetic protein receptor (BMPR)-2. The BMPR2 gene was screened in two cohorts: 40 adults and 66 children with PAH/CHD. CHDs were patent ductus arteriosus, atrial and ventricular septal defects, partial anomalous pulmonary venous return, transposition of the great arteries, atrioventicular canal, and rare lesions with systemic-to-pulmonary shunts. Six novel missense BMPR2 mutations were found in three out of four adults with complete type C atrioventricular canals and in three children. One child had an atrial septal defect and patent ductus arteriosus; one had an atrial septal defect, patent ductus arteriosus and partial anomalous pulmonary venous return; and one had an aortopulmonary window and a ventricular septal defect. Bone morphogenetic protein receptor 2 mutations were found in 6% of a mixed cohort of adults and children with pulmonary arterial hypertension/congenital heart defects. The current findings compliment recent reports in mouse models implicating members of the bone morphogenetic protein/transforming growth factor-beta pathway inducing cardiac anomalies analogous to human atrioventricular canals, septal defects and conotruncal congenital heart defects. The small number of patients studied and the ascertainment bias inherent in selecting for pulmonary arterial hypertension require further investigation.

Nutrition assessment of the critically ill child

Nutrition assessment is an integral part of the evaluation of the critically ill child. The goal of nutrition assessment is to identify those children who are malnourished and those who are at risk of becoming malnourished. Malnutrition is known to affect wound healing, infection rate, mortality, and morbidity, making early identification of children at risk essential. An initial assessment consists of a complete history and physical examination. The history and physical examination findings are then evaluated in conjunction with appropriate laboratory and anthropometric measurements. Through vigilant nutrition assessment, prompt, appropriate nutrition support can be provided to the critically ill child.

Treatment of Stanford type B aortic dissection with stent-grafts: preliminary results

PURPOSE

To evaluate the feasibility and safety of endovascular stent-graft placement in treating Stanford type B aortic dissection.

MATERIALS AND METHODS

Seven patients underwent endovascular stent-graft placement for type B aortic dissection. Five patients had acute and two had chronic dissection. In five patients, the proximal entry tear was within 2 cm of the origin of the left subclavian artery, and in two patients it was beyond this site. In three patients, the noncovered proximal portion of the stent-graft was placed across the origin of the left subclavian artery. The efficacy of the procedure was assessed at follow-up studies 3, 6, 12, and 24 months after intervention.

RESULTS

The procedure was technically and clinically successful in six patients (86%). The left subclavian artery remained patent in all patients. In two patients with involvement of aortic branches, endovascular stent-graft placement restored adequate blood flow to the compromised branches. One patient was readmitted 1 month later because the dissection extended into the ascending aorta. In all but this patient, closure of the entry tear and thrombosis of the false lumen along the stent-graft were achieved. All false lumina shrank considerably. The mean follow-up time was 14 months (range, 1-25 months).

CONCLUSION

Type B aortic dissections within and beyond 2 cm of the origin of the left subclavian artery can be treated safely and effectively by means of endovascular stent-graft placement.

Balance and ankle range of motion in community-dwelling women aged 64 to 87 years: a correlational study

BACKGROUND AND PURPOSE

This study investigated the relationship between balance measures and ankle range of motion (ROM) in community-dwelling elderly women with no health problems. Identification of modifiable factors associated with balance may enable clinicians to design treatments to help reduce the risk of falls in elderly people.

SUBJECTS

The sample consisted of 34 women between the ages of 64 and 87 years (mean=74.7, SD=6.0).

METHODS

Goniometry was used to determine bilateral ankle active-assistive range of motion (AAROM) and passive range of motion. Balance capabilities were measured with the Functional Reach Test (FRT) and the Tinetti Performance-Oriented Mobility Assessment (POMA). Balance data for the FRT, POMA balance subtest, POMA gait subtest, and POMA total score were correlated with ankle ROM using the Pearson product moment correlation coefficient (PCC).

RESULTS

Correlations between ROM and balance scores were found, ranging from.29 to.63. The POMA gait subtest and FRT resulted in higher correlations with ROM than did the POMA balance subtest (left total AAROM PCC=.63,.51, and.31). Correlations using composite ankle ROM scores were higher than individual motions. The strongest correlation existed between bilateral, total ankle AAROM and the POMA gait subtest scores (PCC=. 63)

CONCLUSION AND DISCUSSION

Correlations exist between ankle ROM and balance in community-dwelling elderly women. Additional research is needed to determine whether treatment directed at increasing ankle ROM can improve balance.

Ventilatory strategies for the critically ill infant and child

As newer modes of mechanical ventilation and adjuncts to ventilation continue to be developed and studied, pediatric critical care practitioners are going to have many exciting options for the treatment of the critically ill infant and child. All who provide care to these critically ill patients must continue to evaluate these varied ventilatory strategies.

A pharmacological study of the responses induced by muscarinic agonists on the isolated superior cervical ganglion of the guinea-pig

We have studied the muscarinic agonist induced responses on the guinea-pig superior cervical ganglion in vitro, as recorded from the internal carotid nerve using a grease-gap. The principal response was a depolarization, but a small hyperpolarizing response could be revealed under certain conditions. We determined the pA2 of a number of muscarinic antagonists against the muscarine induced depolarization. Four selective antagonists and atropine appeared to act competitively. The rank order of their pA2s was 4-DAMP (8.5), atropine (8.4), pirenzepine (8.0), methoctramine (7.2) and AF-DX 116 (6.3). In addition to muscarine, we assessed the potency and relative maximum response of nine other muscarinic compounds to depolarize this preparation: carbachol, 5-methylfurmethide, oxotremorine, oxotremorine-M, pilocarpine, RS 86, AF102B and two novel compounds L-670548 and L-679512. L-670548 was the most potent and AF102B was the least potent agonist tested. Only AF102B evoked a maximum depolarization that was significantly smaller than muscarine. A hyperpolarizing response to carbachol (1 microM) could be recorded when the superfusing medium contained 0.3 microM pirenzepine and only 0.1 mM CaCl2 (cf. usual 2.5 mM). This response was relatively small compared to that evoked on the superior cervical ganglion of the rat. It was blocked by the cardioselective antagonists methoctramine (0.1-0.3 microM) and AF-DX 116 (0.3-1.0 microM). Of the 10 agonists tested, only carbachol, oxotremorine and oxotremorine-M reproducibly evoked a hyperpolarizing response. It was concluded that muscarinic agonists can induce a depolarization of the guinea-pig superior cervical ganglion mediated by M1 receptors. The activation of cardiac-like M2 receptors resulted in a hyperpolarizing response that was relatively small.