Biomedical text readability after hypernym substitution with fine-tuned large language models

The advent of patient access to complex medical information online has highlighted the need for simplification of biomedical text to improve patient understanding and engagement in taking ownership of their health. However, comprehension of biomedical text remains a difficult task due to the need for domain-specific expertise. We aimed to study the simplification of biomedical text via large language models (LLMs) commonly used for general natural language processing tasks involve text comprehension, summarization, generation, and prediction of new text from prompts. Specifically, we finetuned three variants of large language models to perform substitutions of complex words and word phrases in biomedical text with a related hypernym. The output of the text substitution process using LLMs was evaluated by comparing the pre- and post-substitution texts using four readability metrics and two measures of sentence complexity. A sample of 1,000 biomedical definitions in the National Library of Medicine's Unified Medical Language System (UMLS) was processed with three LLM approaches, and each showed an improvement in readability and sentence complexity after hypernym substitution. Readability scores were translated from a pre-processed collegiate reading level to a post-processed US high-school level. Comparison between the three LLMs showed that the GPT-J-6b approach had the best improvement in measures of sentence complexity. This study demonstrates the merit of hypernym substitution to improve readability of complex biomedical text for the public and highlights the use case for fine-tuning open-access large language models for biomedical natural language processing.

Effect of Recent Abortion Legislation on Twitter User Engagement, Sentiment, and Expressions of Trust in Clinicians and Privacy of Health Information: Content Analysis

BACKGROUND

The Supreme Court ruling in Dobbs v Jackson Women's Health Organization (Dobbs) overrules precedents established by Roe v Wade and Planned Parenthood v Casey and allows states to individually regulate access to abortion care services. While many states have passed laws to protect access to abortion services since the ruling, the ruling has also triggered the enforcement of existing laws and the creation of new ones that ban or restrict abortion. In addition to denying patients the full spectrum of reproductive health care, one major concern in the medical community is how the ruling will undermine trust in the patient-clinician relationship by influencing perceptions of the privacy of patient health information.

OBJECTIVE

This study aimed to study the effect of recent abortion legislation on Twitter user engagement, sentiment, expressions of trust in clinicians, and privacy of health information.

METHODS

We scraped tweets containing keywords of interest between January 1, 2020, and October 17, 2022, to capture tweets posted before and after the leak of the Supreme Court decision. We then trained a Latent Dirichlet Allocation model to select tweets pertinent to the topic of interest and performed a sentiment analysis using Robustly Optimized Bidirectional Encoder Representations from Transformers Pre-training Approach model and a causal impact time series analysis to examine engagement and sentiment. In addition, we used a Word2Vec model to study the terms of interest against a latent trust dimension to capture how expressions of trust for our terms of interest changed over time and used term frequency, inverse-document frequency to measure the volume of tweets before and after the decision with respect to the negative and positive sentiments that map to our terms of interest.

RESULTS

Our study revealed (1) a transient increase in the number of daily users by 576.86% (95% CI 545.34%-607.92%; P<.001), tweeting about abortion, health care, and privacy of health information postdecision leak; (2) a sustained and statistically significant decrease in the average daily sentiment on these topics by 19.81% (95% CI -22.98% to -16.59%; P=.001) postdecision leak; (3) a decrease in the association of the latent dimension of trust across most clinician-related and health information-related terms of interest; (4) an increased frequency of tweets with these clinician-related and health information-related terms and concomitant negative sentiment in the postdecision leak period.

CONCLUSIONS

The study suggests that the Dobbs ruling has consequences for health systems and reproductive health care that extend beyond denying patients access to the full spectrum of reproductive health services. The finding of a decrease in the expression of trust in clinicians and health information-related terms provides evidence to support advocacy and initiatives that proactively address concerns of trust in health systems and services.

Research needs, environmental concerns, and logistical considerations for incorporating livestock grazing into coastal upland habitat management

Along the Gulf of Mexico (GoM) coast, natural resource managers continually struggle with managing coastal uplands due to front-end costs, prolonged maintenance, and habitat-specific ecological needs. Prescribed fire, mechanical removal, and chemical treatments are common habitat management techniques used to remove invasive species, clear understory, and achieve other management goals. However, rapid development and changing climate exacerbate the difficulty in using these techniques. A potential alternative or complementary technique is using livestock for habitat management (i.e., targeted or controlled grazing). In other regions of the world, using livestock for conservation or restoration of managed lands has shown to be a less intrusive and more financially viable alternative. To better understand the research needs, logistical, and environmental concerns related to using livestock for habitat management in the coastal uplands of the GoM, we developed and distributed a survey to three groups of land users, including natural resource managers, researchers, and livestock producers in the region. Survey results show that over 96% of respondents are interested in using livestock for habitat management, but less than 10% of respondents were aware of any information that could be used to inform grazing practices for coastal upland habitat management along the Gulf of Mexico coast. There were differences among surveyed groups, but generally small-sized cattle breeds and goats were identified as the livestock with the most potential for environmental benefit and ease of containment. General concerns and areas for further investigation were implementation (e.g., which livestock type to use and grazing intensity), logistical considerations (e.g., fencing and rotational frequency), impacts of grazing on water quality, wildlife, vegetation, and livestock nutrition. Survey respondents overwhelmingly (at least 75% of each group) indicated that livestock grazing ideally would not be a standalone management practice and should be used in conjunction with other habitat management techniques such as prescribed burns, mechanical clearing, or chemical treatments. The results of the survey could be used to develop applied research projects and guidance documents that directly address informational needs related to using livestock for habitat management of coastal uplands along the Gulf of Mexico coast.

Website Usability Analysis of U.S. Military Residency Programs

INTRODUCTION

The Military Match is the residency matching system for medical students attending the Uniformed Services University of Health Sciences, and the students were funded by the Health Professions Scholarship Program through the U.S. Army, Air Force, and Navy. To evaluate and compare military residency programs, students use residency program websites. Often, the residency program's website serves as a key source, or the only point of reference, when considering residency options, especially during times when face-to-face interactions are limited.This report aims to provide a systematic evaluation of military residency programs and their websites.

MATERIALS AND METHODS

Utilizing a previously published website usability scoring system, military residency programs were categorized to objectively and quantitatively analyze their websites. Usability was divided into four categories for quantifiable analysis: accessibility, marketing, content quality, and technology. The methodology for this analysis was replicated from published reports that have examined healthcare website usability. Each website was analyzed and scored in four categories: accessibility, content quality, marketing, and technology. A "General Usability" score was calculated for each website using a composite of the key factors within the four categories. An overall score was generated utilizing the weighted percentage across all four categories. To address deficiencies of the original methodology, a secondary analysis was performed on the listed websites utilizing an automated methodology for website usability.

RESULTS

A comprehensive list of 125 Accreditation Council for Graduate Medical Education U.S. Military residency program websites was compiled. Of these, 96 programs and 106 websites were evaluated. The primary analysis employing usability methodology identified technology as the highest ranked category with a score of 0.749 (SD ± 0.039) (SE 0.005) (P < .05). Marketing and content quality were the lowest scoring categories with mean scores of 0.414 (SD ± 0.054) (SE 0.006) and 0.428 (SD ± 0.229) (SE 0.027), respectively (P < .05). There was no significant difference in overall usability rankings or scores among the 96 residency program websites across the three branches (P < .05).Secondary analysis with the new usability methodology demonstrated military residency websites to exhibit more external backlinking compared to internal backlinking (P < 0.05) and no social media backlinking to any of the 106 analyzed websites. When comparing the three services, the Army had significantly lower external backlinking ranking 43.4 (P < .05) and overall backlinking ranking 56.4 (P < 0.05) when compared to the Navy (mean 48.8 and 71.7, and 43.4). There were no other differences in backlinking rankings across the three branches.

CONCLUSIONS

Residency websites have become a primary way to communicate information to applicants. By assessing the overall usability of the various military residency websites, we determined the effectiveness of these websites to relay information to prospective students interested in applying for military residency. We predict that by improving website accessibility, residency programs increase their effectiveness at communicating information to potential applicants and increase interest in military residency programs.

Comparison of Kjeldahl Method for Determination of Crude Protein in Cereal Grains and Oilseeds with Generic Combustion Method: Collaborative Study

Seven laboratories participated in a collaborative study to extend the applicability of the AOAC generic combustion method for determination of crude protein in animal feed (990.03) to include determination in cereal grains and oilseeds. In the study, method 990.03 was compared with the AOAC mercury catalyst Kjeldahl method for determination of protein in grains (979.09) and crude protein in animal feed (954.01). The study also evaluated the effect on the results of fineness of grind. For determination of crude protein in grains and oilseeds by the combustion method, standard deviations for repeatability and reproducibility ranged from 0.10 to 0.37 and from 0.25 to 0.54, respectively, and relative standard deviations for repeatability and reproducibility ranged from 0.77 to 2.57% and from 1.24 to 3.15%, respectively. The combustion method was adopted first action by AOAC International for determination of crude protein in cereal grains and oilseeds containing 0.2- 20% nitrogen.

Effect of Feeding a Low Vitamin a Diet to Beef Steers on Calpain 1 Activation during Meat Aging

ObjectivesThe objective of the study was to determine if a vitamin A deficient diet during beef finishing influences calpain 1 activation during meat aging.Materials and MethodsSixty-four steers of approximately 7 mo of age were subjected to a 14-d acclimation period followed by a 95-d growing period on a low vitamin A diet (1017 IU vitamin A/kg DM) designed to deplete liver vitamin A stores. Steers were assigned to a randomized complete blocked design with a 2 × 2 arrangement of treatments (breed: commercial Angus, n = 32, and purebred Simmental, n = 32; and a Low Vitamin A diet or a control diet). The low Vitamin A (LVA) treatment was a finishing diet with no supplemental vitamin A (723 IU vitamin A/kg DM). The control (CON) treatment was the LVA diet plus supplementation with 2200 IU vitamin A/kg DM for a total of 2923 IU vitamin A/kg DM. Serum retinol concentrations were monitored at the beginning and end of treatment. Upon completion of finishing, steers were slaughtered in two groups at a commercial plant. After fabrication, boneless strip loins (IMPS 180) were collected and transported to NDSU. Samples (approximately 40 g) were collected from the anterior portion of the strip loin on d-2 and d-7 of aging and immediately frozen. Protein was extracted from meat samples in fractionation buffers to yield sarcoplasmic and myofibrillar portions, separated by SDS-PAGE, and transferred to PVDF membranes. Immunoblot analysis was done using anti-desmin (d-2 and d-7) and anti-calpain 1 (d-2) antibodies, and results were visualized and documented. A pooled control was run on all membranes and set to a value of one for normalizing results. All experimental data were analyzed using the Proc Mixed procedure of SAS with breed of steers, dietary treatments, their interaction and slaughter date used as a fixed effect.ResultsCalpain 1 autolysis in the sarcoplasmic protein fraction of the d-2 aged loin samples were not affected by treatment or breed. The myofibrillar protein fraction from Angus loins had greater (P = 0.02) accumulation of the 76 kDa calpain 1 autolysis product than that from the Simmental loins; the myofibrillar fraction of the loins from the LVA treatment tended (P = 0.07) to have more 76 kDa calpain 1 autolysis product than that from the CON. There were not any differences (P > 0.19) in the 80 kDa calpain 1 band or the 78 kDa calpain 1 intermediate autolysis product in the myofibrillar fraction. There was a treatment by breed interaction (P = 0.01) for desmin in the d-7 aged loins where Angus loins from the CON treatment had less accumulation of the 46 kDa band than Angus loins on the LVA treatment and Simmental loins from either treatment.ConclusionVitamin A restriction increased protein proteolysis in Angus but not in Simmental steers. The increased calpain 1 autolysis in Angus vs. Simmental, regardless of Vitamin A treatment, indicates a genetic difference that may be the driver for the increased protein degradation in steers a restricted vitamin A diet.

Petawatt Laser Guiding and Electron Beam Acceleration to 8 GeV in a Laser-Heated Capillary Discharge Waveguide

Guiding of relativistically intense laser pulses with peak power of 0.85 PW over 15 diffraction lengths was demonstrated by increasing the focusing strength of a capillary discharge waveguide using laser inverse bremsstrahlung heating. This allowed for the production of electron beams with quasimonoenergetic peaks up to 7.8 GeV, double the energy that was previously demonstrated. Charge was 5 pC at 7.8 GeV and up to 62 pC in 6 GeV peaks, and typical beam divergence was 0.2 mrad.

Effects of hot boning and moisture enhancement on the eating quality of cull cow beef

The effects of chilling method and moisture enhancement were examined for improving eating quality of semimembranosus (SM) and longissimus lumborum (LL) from 62 cull beef cows. Chilling method included hot boning muscles after 45 to 60 min postmortem or conventional chilling for 24 h. Moisture enhancement included 1) a non-injected control (CONT) or injection processing (10% of product weight) using 2) Sodium Tripolyphosphate/salt (Na/STP), 3) Sodium Citrate (NaCIT), 4) Calcium Ascorbate (CaASC), or 5) Citrus Juices (CITRUS). Chilling method by moisture enhancement treatment interactions (P<0.09) were due to decreased hue, chroma and sarcomere length values in hot boned vs. conventionally chilled product (SM and LL) for CaASC vs. other moisture enhancement treatments. Chilling method by moisture enhancement treatment interactions (P<0.05) were due to decreased shear force and increased tenderness in conventionally chilled vs. hot boned LL using CaASC vs. Na/STP. Moisture enhancement can improve tenderness of cull cow beef depending on combinations of chilling method and moisture enhancement treatments used.

International guidelines for the diagnosis and management of hereditary haemorrhagic telangiectasia

BACKGROUND

HHT is an autosomal dominant disease with an estimated prevalence of at least 1/5000 which can frequently be complicated by the presence of clinically significant arteriovenous malformations in the brain, lung, gastrointestinal tract and liver. HHT is under-diagnosed and families may be unaware of the available screening and treatment, leading to unnecessary stroke and life-threatening hemorrhage in children and adults.

OBJECTIVE

The goal of this international HHT guidelines process was to develop evidence-informed consensus guidelines regarding the diagnosis of HHT and the prevention of HHT-related complications and treatment of symptomatic disease.

METHODS

The overall guidelines process was developed using the AGREE framework, using a systematic search strategy and literature retrieval with incorporation of expert evidence in a structured consensus process where published literature was lacking. The Guidelines Working Group included experts (clinical and genetic) from eleven countries, in all aspects of HHT, guidelines methodologists, health care workers, health care administrators, HHT clinic staff, medical trainees, patient advocacy representatives and patients with HHT. The Working Group determined clinically relevant questions during the pre-conference process. The literature search was conducted using the OVID MEDLINE database, from 1966 to October 2006. The Working Group subsequently convened at the Guidelines Conference to partake in a structured consensus process using the evidence tables generated from the systematic searches.

RESULTS

The outcome of the conference was the generation of 33 recommendations for the diagnosis and management of HHT, with at least 80% agreement amongst the expert panel for 30 of the 33 recommendations.

Lissencephaly with cerebellar hypoplasia (LCH): a heterogeneous group of cortical malformations

Detailed classification of brain malformations such as lissencephaly has led to the positional cloning of genes required for normal neuronal migration and the identification of unique molecular pathways governing brain structure. While classical magnetic resonance imaging (MRI) patterns of lissencephaly involve primarily the cerebral cortex, malformations in this spectrum can be associated with significant cerebellar underdevelopment and have recently been referred to as lissencephaly with cerebellar hypoplasia (LCH). The phenotypic features of 34 children were found to define 6 subtypes of LCH. Two of these (LCHa and LCHb) were associated with mutation in the LIS1, DCX and RELN genes, respectively. Gene mutations that exemplify four additional classes (LCHc, d, e and f) remained to be determined. Phenotypic features included small head circumference, cortical malformation ranging from agyria to simplification of the gyral pattern and from near normal cortical thickness to marked thickening of the cortical gray matter. Cerebellar manifestations ranged from midline hypoplasia to diffuse volume reduction and disturbed foliation. We conclude that LCH is within the spectrum of DCX and LIS1 mutations, that LCH associated with RELN mutation is distinguished by the severity of cerebellar and hippocampal involvement, and that several distinctive patterns indicate additional genetic mutations that can produce LCH.