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Promoters are essential elements of DNA sequence, usually located in the immediate region of the gene transcription start sites, and play a critical role in the regulation of gene transcription. Its importance in molecular biology and genetics has attracted the research interest of researchers, and it has become a consensus to seek a computational method to efficiently identify promoters. Still, existing methods suffer from imbalanced recognition capabilities for positive and negative samples, and their recognition effect can still be further improved. We conducted research on E. coli promoters and proposed a more advanced prediction model, iProL, based on the Longformer pre-trained model in the field of natural language processing. iProL does not rely on prior biological knowledge but simply uses promoter DNA sequences as plain text to identify promoters. It also combines one-dimensional convolutional neural networks and bidirectional long short-term memory to extract both local and global features. Experimental results show that iProL has a more balanced and superior performance than currently published methods. Additionally, we constructed a novel independent test set following the previous specification and compared iProL with three existing methods on this independent test set. [ABSTRACT FROM AUTHOR]

Many state-of-the-art results in natural language processing (NLP) rely on large pre-trained language models (PLMs). These models consist of large amounts of parameters that are tuned using vast amounts of training data. These factors cause the models to memorize parts of their training data, making them vulnerable to various privacy attacks. This is cause for concern, especially when these models are applied in the clinical domain, where data are very sensitive. Training data pseudonymization is a privacy-preserving technique that aims to mitigate these problems. This technique automatically identifies and replaces sensitive entities with realistic but non-sensitive surrogates. Pseudonymization has yielded promising results in previous studies. However, no previous study has applied pseudonymization to both the pre-training data of PLMs and the fine-tuning data used to solve clinical NLP tasks. This study evaluates the effects on the predictive performance of end-to-end pseudonymization of Swedish clinical BERT models fine-tuned for five clinical NLP tasks. A large number of statistical tests are performed, revealing minimal harm to performance when using pseudonymized fine-tuning data. The results also find no deterioration from end-to-end pseudonymization of pre-training and fine-tuning data. These results demonstrate that pseudonymizing training data to reduce privacy risks can be done without harming data utility for training PLMs. [ABSTRACT FROM AUTHOR]

Background: Systematically screening published literature to determine the relevant publications to synthesize in a review is a time-consuming and difficult task. Large language models (LLMs) are an emerging technology with promising capabilities for the automation of language-related tasks that may be useful for such a purpose. Methods: LLMs were used as part of an automated system to evaluate the relevance of publications to a certain topic based on defined criteria and based on the title and abstract of each publication. A Python script was created to generate structured prompts consisting of text strings for instruction, title, abstract, and relevant criteria to be provided to an LLM. The relevance of a publication was evaluated by the LLM on a Likert scale (low relevance to high relevance). By specifying a threshold, different classifiers for inclusion/exclusion of publications could then be defined. The approach was used with four different openly available LLMs on ten published data sets of biomedical literature reviews and on a newly human-created data set for a hypothetical new systematic literature review. Results: The performance of the classifiers varied depending on the LLM being used and on the data set analyzed. Regarding sensitivity/specificity, the classifiers yielded 94.48%/31.78% for the FlanT5 model, 97.58%/19.12% for the OpenHermes-NeuralChat model, 81.93%/75.19% for the Mixtral model and 97.58%/38.34% for the Platypus 2 model on the ten published data sets. The same classifiers yielded 100% sensitivity at a specificity of 12.58%, 4.54%, 62.47%, and 24.74% on the newly created data set. Changing the standard settings of the approach (minor adaption of instruction prompt and/or changing the range of the Likert scale from 1–5 to 1–10) had a considerable impact on the performance. Conclusions: LLMs can be used to evaluate the relevance of scientific publications to a certain review topic and classifiers based on such an approach show some promising results. To date, little is known about how well such systems would perform if used prospectively when conducting systematic literature reviews and what further implications this might have. However, it is likely that in the future researchers will increasingly use LLMs for evaluating and classifying scientific publications. [ABSTRACT FROM AUTHOR]

Background: Automated hypothesis generation (HG) focuses on uncovering hidden connections within the extensive information that is publicly available. This domain has become increasingly popular, thanks to modern machine learning algorithms. However, the automated evaluation of HG systems is still an open problem, especially on a larger scale. Results: This paper presents a novel benchmarking framework Dyport for evaluating biomedical hypothesis generation systems. Utilizing curated datasets, our approach tests these systems under realistic conditions, enhancing the relevance of our evaluations. We integrate knowledge from the curated databases into a dynamic graph, accompanied by a method to quantify discovery importance. This not only assesses hypotheses accuracy but also their potential impact in biomedical research which significantly extends traditional link prediction benchmarks. Applicability of our benchmarking process is demonstrated on several link prediction systems applied on biomedical semantic knowledge graphs. Being flexible, our benchmarking system is designed for broad application in hypothesis generation quality verification, aiming to expand the scope of scientific discovery within the biomedical research community. Conclusions: Dyport is an open-source benchmarking framework designed for biomedical hypothesis generation systems evaluation, which takes into account knowledge dynamics, semantics and impact. All code and datasets are available at: https://github.com/IlyaTyagin/Dyport. [ABSTRACT FROM AUTHOR]

Background: The semantics of entities extracted from a clinical text can be dramatically altered by modifiers, including entity negation, uncertainty, conditionality, severity, and subject. Existing models for determining modifiers of clinical entities involve regular expression or features weights that are trained independently for each modifier. Methods: We develop and evaluate a multi-task transformer architecture design where modifiers are learned and predicted jointly using the publicly available SemEval 2015 Task 14 corpus and a new Opioid Use Disorder (OUD) data set that contains modifiers shared with SemEval as well as novel modifiers specific for OUD. We evaluate the effectiveness of our multi-task learning approach versus previously published systems and assess the feasibility of transfer learning for clinical entity modifiers when only a portion of clinical modifiers are shared. Results: Our approach achieved state-of-the-art results on the ShARe corpus from SemEval 2015 Task 14, showing an increase of 1.1% on weighted accuracy, 1.7% on unweighted accuracy, and 10% on micro F1 scores. Conclusions: We show that learned weights from our shared model can be effectively transferred to a new partially matched data set, validating the use of transfer learning for clinical text modifiers. [ABSTRACT FROM AUTHOR]

Backgrounds: The single-pass long reads generated by third-generation sequencing technology exhibit a higher error rate. However, the circular consensus sequencing (CCS) produces shorter reads. Thus, it is effective to manage the error rate of long reads algorithmically with the help of the homologous high-precision and low-cost short reads from the Next Generation Sequencing (NGS) technology. Methods: In this work, a hybrid error correction method (NmTHC) based on a generative neural machine translation model is proposed to automatically capture discrepancies within the aligned regions of long reads and short reads, as well as the contextual relationships within the long reads themselves for error correction. Akin to natural language sequences, the long read can be regarded as a special "genetic language" and be processed with the idea of generative neural networks. The algorithm builds a sequence-to-sequence(seq2seq) framework with Recurrent Neural Network (RNN) as the core layer. The before and post-corrected long reads are regarded as the sentences in the source and target language of translation, and the alignment information of long reads with short reads is used to create the special corpus for training. The well-trained model can be used to predict the corrected long read. Results: NmTHC outperforms the latest mainstream hybrid error correction methods on real-world datasets from two mainstream platforms, including PacBio and Nanopore. Our experimental evaluation results demonstrate that NmTHC can align more bases with the reference genome without any segmenting in the six benchmark datasets, proving that it enhances alignment identity without sacrificing any length advantages of long reads. Conclusion: Consequently, NmTHC reasonably adopts the generative Neural Machine Translation (NMT) model to transform hybrid error correction tasks into machine translation problems and provides a novel perspective for solving long-read error correction problems with the ideas of Natural Language Processing (NLP). More remarkably, the proposed methodology is sequencing-technology-independent and can produce more precise reads. [ABSTRACT FROM AUTHOR]

Background: Extracting research of domain criteria (RDoC) from high-risk populations like those with post-traumatic stress disorder (PTSD) is crucial for positive mental health improvements and policy enhancements. The intricacies of collecting, integrating, and effectively leveraging clinical notes for this purpose introduce complexities. Methods: In our study, we created a natural language processing (NLP) workflow to analyze electronic medical record (EMR) data and identify and extract research of domain criteria using a pre-trained transformer-based natural language model, all-mpnet-base-v2. We subsequently built dictionaries from 100,000 clinical notes and analyzed 5.67 million clinical notes from 38,807 PTSD patients from the University of Pittsburgh Medical Center. Subsequently, we showcased the significance of our approach by extracting and visualizing RDoC information in two use cases: (i) across multiple patient populations and (ii) throughout various disease trajectories. Results: The sentence transformer model demonstrated high F1 macro scores across all RDoC domains, achieving the highest performance with a cosine similarity threshold value of 0.3. This ensured an F1 score of at least 80% across all RDoC domains. The study revealed consistent reductions in all six RDoC domains among PTSD patients after psychotherapy. We found that 60.6% of PTSD women have at least one abnormal instance of the six RDoC domains as compared to PTSD men (51.3%), with 45.1% of PTSD women with higher levels of sensorimotor disturbances compared to men (41.3%). We also found that 57.3% of PTSD patients have at least one abnormal instance of the six RDoC domains based on our records. Also, veterans had the higher abnormalities of negative and positive valence systems (60% and 51.9% of veterans respectively) compared to non-veterans (59.1% and 49.2% respectively). The domains following first diagnoses of PTSD were associated with heightened cue reactivity to trauma, suicide, alcohol, and substance consumption. Conclusions: The findings provide initial insights into RDoC functioning in different populations and disease trajectories. Natural language processing proves valuable for capturing real-time, context dependent RDoC instances from extensive clinical notes. [ABSTRACT FROM AUTHOR]

Background: A huge amount of research is carried out nowadays in Artificial Intelligence to propose automated ways to analyse medical data with the aim to support doctors in delivering medical diagnoses. However, a main issue of these approaches is the lack of transparency and interpretability of the achieved results, making it hard to employ such methods for educational purposes. It is therefore necessary to develop new frameworks to enhance explainability in these solutions. Results: In this paper, we present a novel full pipeline to generate automatically natural language explanations for medical diagnoses. The proposed solution starts from a clinical case description associated with a list of correct and incorrect diagnoses and, through the extraction of the relevant symptoms and findings, enriches the information contained in the description with verified medical knowledge from an ontology. Finally, the system returns a pattern-based explanation in natural language which elucidates why the correct (incorrect) diagnosis is the correct (incorrect) one. The main contribution of the paper is twofold: first, we propose two novel linguistic resources for the medical domain (i.e, a dataset of 314 clinical cases annotated with the medical entities from UMLS, and a database of biological boundaries for common findings), and second, a full Information Extraction pipeline to extract symptoms and findings from the clinical cases and match them with the terms in a medical ontology and to the biological boundaries. An extensive evaluation of the proposed approach shows the our method outperforms comparable approaches. Conclusions: Our goal is to offer AI-assisted educational support framework to form clinical residents to formulate sound and exhaustive explanations for their diagnoses to patients. [ABSTRACT FROM AUTHOR]

Objective: Suicide is a complex and multifactorial public health problem. Understanding and addressing the various factors associated with suicide is crucial for prevention and intervention efforts. Machine learning (ML) could enhance the prediction of suicide attempts. Method: A systematic review was performed using PubMed, Scopus, Web of Science and SID databases. We aim to evaluate the performance of ML algorithms and summarize their effects, gather relevant and reliable information to synthesize existing evidence, identify knowledge gaps, and provide a comprehensive list of the suicide risk factors using mixed method approach. Results: Forty-one studies published between 2011 and 2022, which matched inclusion criteria, were chosen as suitable. We included studies aimed at predicting the suicide risk by machine learning algorithms except natural language processing (NLP) and image processing. The neural network (NN) algorithm exhibited the lowest accuracy at 0.70, whereas the random forest demonstrated the highest accuracy, reaching 0.94. The study assessed the COX and random forest models and observed a minimum area under the curve (AUC) value of 0.54. In contrast, the XGBoost classifier yielded the highest AUC value, reaching 0.97. These specific AUC values emphasize the algorithm-specific performance in capturing the trade-off between sensitivity and specificity for suicide risk prediction. Furthermore, our investigation identified several common suicide risk factors, including age, gender, substance abuse, depression, anxiety, alcohol consumption, marital status, income, education, and occupation. This comprehensive analysis contributes valuable insights into the multifaceted nature of suicide risk, providing a foundation for targeted preventive strategies and intervention efforts. Conclusions: The effectiveness of ML algorithms and their application in predicting suicide risk has been controversial. There is a need for more studies on these algorithms in clinical settings, and the related ethical concerns require further clarification. Highlights: • Understanding various factors associated with suicide is crucial for prevention and intervention efforts. • Machine learning (ML) could enhance the prediction of suicide attempts. • The neural network (NN) algorithm exhibited the lowest accuracy of 0.70. • The random forest demonstrated the highest accuracy for suicide prediction. [ABSTRACT FROM AUTHOR]

Background: Smoking is a critical risk factor responsible for over eight million annual deaths worldwide. It is essential to obtain information on smoking habits to advance research and implement preventive measures such as screening of high-risk individuals. In most countries, including Denmark, smoking habits are not systematically recorded and at best documented within unstructured free-text segments of electronic health records (EHRs). This would require researchers and clinicians to manually navigate through extensive amounts of unstructured data, which is one of the main reasons that smoking habits are rarely integrated into larger studies. Our aim is to develop machine learning models to classify patients' smoking status from their EHRs. Methods: This study proposes an efficient natural language processing (NLP) pipeline capable of classifying patients' smoking status and providing explanations for the decisions. The proposed NLP pipeline comprises four distinct components, which are; (1) considering preprocessing techniques to address abbreviations, punctuation, and other textual irregularities, (2) four cutting-edge feature extraction techniques, i.e. Embedding, BERT, Word2Vec, and Count Vectorizer, employed to extract the optimal features, (3) utilization of a Stacking-based Ensemble (SE) model and a Convolutional Long Short-Term Memory Neural Network (CNN-LSTM) for the identification of smoking status, and (4) application of a local interpretable model-agnostic explanation to explain the decisions rendered by the detection models. The EHRs of 23,132 patients with suspected lung cancer were collected from the Region of Southern Denmark during the period 1/1/2009-31/12/2018. A medical professional annotated the data into 'Smoker' and 'Non-Smoker' with further classifications as 'Active-Smoker', 'Former-Smoker', and 'Never-Smoker'. Subsequently, the annotated dataset was used for the development of binary and multiclass classification models. An extensive comparison was conducted of the detection performance across various model architectures. Results: The results of experimental validation confirm the consistency among the models. However, for binary classification, BERT method with CNN-LSTM architecture outperformed other models by achieving precision, recall, and F1-scores between 97% and 99% for both Never-Smokers and Active-Smokers. In multiclass classification, the Embedding technique with CNN-LSTM architecture yielded the most favorable results in class-specific evaluations, with equal performance measures of 97% for Never-Smoker and measures in the range of 86 to 89% for Active-Smoker and 91–92% for Never-Smoker. Conclusion: Our proposed NLP pipeline achieved a high level of classification performance. In addition, we presented the explanation of the decision made by the best performing detection model. Future work will expand the model's capabilities to analyze longer notes and a broader range of categories to maximize its utility in further research and screening applications. [ABSTRACT FROM AUTHOR]

Background: COVID-19 is a complex, multi-system disease with varying severity and symptoms. Identifying changes in critically ill COVID-19 patients' proteomes enables a better understanding of markers associated with susceptibility, symptoms, and treatment. We performed plasma antibody microarray and machine learning analyses to identify novel proteins of COVID-19. Methods: A case-control study comparing the concentration of 2000 plasma proteins in age- and sex-matched COVID-19 inpatients, non-COVID-19 sepsis controls, and healthy control subjects. Machine learning was used to identify a unique proteome signature in COVID-19 patients. Protein expression was correlated with clinically relevant variables and analyzed for temporal changes over hospitalization days 1, 3, 7, and 10. Expert-curated protein expression information was analyzed with Natural language processing (NLP) to determine organ- and cell-specific expression. Results: Machine learning identified a 28-protein model that accurately differentiated COVID-19 patients from ICU non-COVID-19 patients (accuracy = 0.89, AUC = 1.00, F1 = 0.89) and healthy controls (accuracy = 0.89, AUC = 1.00, F1 = 0.88). An optimal nine-protein model (PF4V1, NUCB1, CrkL, SerpinD1, Fen1, GATA-4, ProSAAS, PARK7, and NET1) maintained high classification ability. Specific proteins correlated with hemoglobin, coagulation factors, hypertension, and high-flow nasal cannula intervention (P < 0.01). Time-course analysis of the 28 leading proteins demonstrated no significant temporal changes within the COVID-19 cohort. NLP analysis identified multi-system expression of the key proteins, with the digestive and nervous systems being the leading systems. Conclusions: The plasma proteome of critically ill COVID-19 patients was distinguishable from that of non-COVID-19 sepsis controls and healthy control subjects. The leading 28 proteins and their subset of 9 proteins yielded accurate classification models and are expressed in multiple organ systems. The identified COVID-19 proteomic signature helps elucidate COVID-19 pathophysiology and may guide future COVID-19 treatment development. [ABSTRACT FROM AUTHOR]

Background: The Center for Medicare and Medicaid Services (CMS) imposes payment penalties for readmissions following total joint replacement surgeries. This study focuses on total hip, knee, and shoulder arthroplasty procedures as they account for most joint replacement surgeries. Apart from being a burden to healthcare systems, readmissions are also troublesome for patients. There are several studies which only utilized structured data from Electronic Health Records (EHR) without considering any gender and payor bias adjustments. Methods: For this study, dataset of 38,581 total knee, hip, and shoulder replacement surgeries performed from 2015 to 2021 at Novant Health was gathered. This data was used to train a random forest machine learning model to predict the combined endpoint of emergency department (ED) visit or unplanned readmissions within 30 days of discharge or discharge to Skilled Nursing Facility (SNF) following the surgery. 98 features of laboratory results, diagnoses, vitals, medications, and utilization history were extracted. A natural language processing (NLP) model finetuned from Clinical BERT was used to generate an NLP risk score feature for each patient based on their clinical notes. To address societal biases, a feature bias analysis was performed in conjunction with propensity score matching. A threshold optimization algorithm from the Fairlearn toolkit was used to mitigate gender and payor biases to promote fairness in predictions. Results: The model achieved an Area Under the Receiver Operating characteristic Curve (AUROC) of 0.738 (95% confidence interval, 0.724 to 0.754) and an Area Under the Precision-Recall Curve (AUPRC) of 0.406 (95% confidence interval, 0.384 to 0.433). Considering an outcome prevalence of 16%, these metrics indicate the model's ability to accurately discriminate between readmission and non-readmission cases within the context of total arthroplasty surgeries while adjusting patient scores in the model to mitigate bias based on patient gender and payor. Conclusion: This work culminated in a model that identifies the most predictive and protective features associated with the combined endpoint. This model serves as a tool to empower healthcare providers to proactively intervene based on these influential factors without introducing bias towards protected patient classes, effectively mitigating the risk of negative outcomes and ultimately improving quality of care regardless of socioeconomic factors. [ABSTRACT FROM AUTHOR]

The more science advances, the more questions are asked. This compounding growth can make it difficult to keep up with current research directions. Furthermore, this difficulty is exacerbated for junior researchers who enter fields with already large bases of potentially fruitful research avenues. In this paper, we propose a novel task and a recommender system for research directions, RecSOI, that draws from statements of ignorance (SOIs) found in the research literature. By building researchers' profiles based on textual elements, RecSOI generates personalized recommendations of potential research directions tailored to their interests. In addition, RecSOI provides context for the recommended SOIs, so that users can quickly evaluate how relevant the research direction is for them. In this paper, we provide an overview of RecSOI's functioning, implementation, and evaluation, demonstrating its effectiveness in guiding researchers through the vast landscape of potential research directions. [ABSTRACT FROM AUTHOR]

Background: This study aims to propose a semi-automatic method for monitoring the waiting times of follow-up examinations within the National Health System (NHS) in Italy, which is currently not possible to due the absence of the necessary structured information in the official databases. Methods: A Natural Language Processing (NLP) based pipeline has been developed to extract the waiting time information from the text of referrals for follow-up examinations in the Lombardy Region. A manually annotated dataset of 10 000 referrals has been used to develop the pipeline and another manually annotated dataset of 10 000 referrals has been used to test its performance. Subsequently, the pipeline has been used to analyze all 12 million referrals prescribed in 2021 and performed by May 2022 in the Lombardy Region. Results: The NLP-based pipeline exhibited high precision (0.999) and recall (0.973) in identifying waiting time information from referrals' texts, with high accuracy in normalization (0.948-0.998). The overall reporting of timing indications in referrals' texts for follow-up examinations was low (2%), showing notable variations across medical disciplines and types of prescribing physicians. Among the referrals reporting waiting times, 16% experienced delays (average delay = 19 days, standard deviation = 34 days), with significant differences observed across medical disciplines and geographical areas. Conclusions: The use of NLP proved to be a valuable tool for assessing waiting times in follow-up examinations, which are particularly critical for the NHS due to the significant impact of chronic diseases, where follow-up exams are pivotal. Health authorities can exploit this tool to monitor the quality of NHS services and optimize resource allocation. [ABSTRACT FROM AUTHOR]

Background: MicroRNAs play a critical role in regulating gene expression by binding to specific target sites within gene transcripts, making the identification of microRNA targets a prominent focus of research. Conventional experimental methods for identifying microRNA targets are both time-consuming and expensive, prompting the development of computational tools for target prediction. However, the existing computational tools exhibit limited performance in meeting the demands of practical applications, highlighting the need to improve the performance of microRNA target prediction models. Results: In this paper, we utilize the most popular natural language processing and computer vision technologies to propose a novel approach, called TEC-miTarget, for microRNA target prediction based on transformer encoder and convolutional neural networks. TEC-miTarget treats RNA sequences as a natural language and encodes them using a transformer encoder, a widely used encoder in natural language processing. It then combines the representations of a pair of microRNA and its candidate target site sequences into a contact map, which is a three-dimensional array similar to a multi-channel image. Therefore, the contact map's features are extracted using a four-layer convolutional neural network, enabling the prediction of interactions between microRNA and its candidate target sites. We applied a series of comparative experiments to demonstrate that TEC-miTarget significantly improves microRNA target prediction, compared with existing state-of-the-art models. Our approach is the first approach to perform comparisons with other approaches at both sequence and transcript levels. Furthermore, it is the first approach compared with both deep learning-based and seed-match-based methods. We first compared TEC-miTarget's performance with approaches at the sequence level, and our approach delivers substantial improvements in performance using the same datasets and evaluation metrics. Moreover, we utilized TEC-miTarget to predict microRNA targets in long mRNA sequences, which involves two steps: selecting candidate target site sequences and applying sequence-level predictions. We finally showed that TEC-miTarget outperforms other approaches at the transcript level, including the popular seed match methods widely used in previous years. Conclusions: We propose a novel approach for predicting microRNA targets at both sequence and transcript levels, and demonstrate that our approach outperforms other methods based on deep learning or seed match. We also provide our approach as an easy-to-use software, TEC-miTarget, at https://github.com/tingpeng17/TEC-miTarget. Our results provide new perspectives for microRNA target prediction. [ABSTRACT FROM AUTHOR]

Background: The Multi-System Inflammatory Syndrome in Children (MIS-C) can develop several weeks after SARS-CoV-2 infection and requires a distinct treatment protocol. Distinguishing MIS-C from SARS-CoV-2 negative sepsis (SCNS) patients is important to quickly institute the correct therapies. We performed targeted proteomics and machine learning analysis to identify novel plasma proteins of MIS-C for early disease recognition. Methods: A case-control study comparing the expression of 2,870 unique blood proteins in MIS-C versus SCNS patients, measured using proximity extension assays. The 2,870 proteins were reduced in number with either feature selection alone or with a prior COMBAT-Seq batch effect adjustment. The leading proteins were correlated with demographic and clinical variables. Organ system and cell type expression patterns were analyzed with Natural Language Processing (NLP). Results: The cohorts were well-balanced for age and sex. Of the 2,870 unique blood proteins, 58 proteins were identified with feature selection (FDR-adjusted P < 0.005, P < 0.0001; accuracy = 0.96, AUC = 1.00, F1 = 0.95), and 15 proteins were identified with a COMBAT-Seq batch effect adjusted feature selection (FDR-adjusted P < 0.05, P < 0.0001; accuracy = 0.92, AUC = 1.00, F1 = 0.89). All of the latter 15 proteins were present in the former 58-protein model. Several proteins were correlated with illness severity scores, length of stay, and interventions (LTA4H, PTN, PPBP, and EGF; P < 0.001). NLP analysis highlighted the multi-system nature of MIS-C, with the 58-protein set expressed in all organ systems; the highest levels of expression were found in the digestive system. The cell types most involved included leukocytes not yet determined, lymphocytes, macrophages, and platelets. Conclusions: The plasma proteome of MIS-C patients was distinct from that of SCNS. The key proteins demonstrated expression in all organ systems and most cell types. The unique proteomic signature identified in MIS-C patients could aid future diagnostic and therapeutic advancements, as well as predict hospital length of stays, interventions, and mortality risks. [ABSTRACT FROM AUTHOR]

Background: Tremendous research efforts have been made in the Alzheimer's disease (AD) field to understand the disease etiology, progression and discover treatments for AD. Many mechanistic hypotheses, therapeutic targets and treatment strategies have been proposed in the last few decades. Reviewing previous work and staying current on this ever-growing body of AD publications is an essential yet difficult task for AD researchers. Methods: In this study, we designed and implemented a natural language processing (NLP) pipeline to extract gene-specific neurodegenerative disease (ND) -focused information from the PubMed database. The collected publication information was filtered and cleaned to construct AD-related gene-specific publication profiles. Six categories of AD-related information are extracted from the processed publication data: publication trend by year, dementia type occurrence, brain region occurrence, mouse model information, keywords occurrence, and co-occurring genes. A user-friendly web portal is then developed using Django framework to provide gene query functions and data visualizations for the generalized and summarized publication information. Results: By implementing the NLP pipeline, we extracted gene-specific ND-related publication information from the abstracts of the publications in the PubMed database. The results are summarized and visualized through an interactive web query portal. Multiple visualization windows display the ND publication trends, mouse models used, dementia types, involved brain regions, keywords to major AD-related biological processes, and co-occurring genes. Direct links to PubMed sites are provided for all recorded publications on the query result page of the web portal. Conclusion: The resulting portal is a valuable tool and data source for quick querying and displaying AD publications tailored to users' interested research areas and gene targets, which is especially convenient for users without informatic mining skills. Our study will not only keep AD field researchers updated with the progress of AD research, assist them in conducting preliminary examinations efficiently, but also offers additional support for hypothesis generation and validation which will contribute significantly to the communication, dissemination, and progress of AD research. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Background: The advent of high-throughput technologies has led to an exponential increase in uncharacterized bacterial protein sequences, surpassing the capacity of manual curation. A large number of bacterial protein sequences remain unannotated by Kyoto Encyclopedia of Genes and Genomes (KEGG) orthology, making it necessary to use auto annotation tools. These tools are now indispensable in the biological research landscape, bridging the gap between the vastness of unannotated sequences and meaningful biological insights. Results: In this work, we propose a novel pipeline for KEGG orthology annotation of bacterial protein sequences that uses natural language processing and deep learning. To assess the effectiveness of our pipeline, we conducted evaluations using the genomes of two randomly selected species from the KEGG database. In our evaluation, we obtain competitive results on precision, recall, and F1 score, with values of 0.948, 0.947, and 0.947, respectively. Conclusions: Our experimental results suggest that our pipeline demonstrates performance comparable to traditional methods and excels in identifying distant relatives with low sequence identity. This demonstrates the potential of our pipeline to significantly improve the accuracy and comprehensiveness of KEGG orthology annotation, thereby advancing our understanding of functional relationships within biological systems. [ABSTRACT FROM AUTHOR]

Background: While the positive impact of homework completion on symptom alleviation is well-established, the pivotal role of therapists in reviewing these assignments has been under-investigated. This study examined therapists' practice of assigning and reviewing action recommendations in therapy sessions, and how it correlates with patients' depression and anxiety outcomes. Methods: We analyzed 2,444 therapy sessions from community-based behavioral health programs. Machine learning models and natural language processing techniques were deployed to discern action recommendations and their subsequent reviews. The extent of the review was quantified by measuring the proportion of session dialogues reviewing action recommendations, a metric we refer to as "review percentage". Using Generalized Estimating Equations modeling, we evaluated the correlation between this metric and changes in clients' depression and anxiety scores. Results: Our models achieved 76% precision in capturing action recommendations and 71.1% in reviewing them. Using these models, we found that therapists typically provided clients with one to eight action recommendations per session to engage in outside therapy. However, only half of the sessions included a review of previously assigned action recommendations. We identified a significant interaction between the initial depression score and the review percentage (p = 0.045). When adjusting for this relationship, the review percentage was positively and significantly associated with a reduction in depression score (p = 0.032). This suggests that more frequent review of action recommendations in therapy relates to greater improvement in depression symptoms. Further analyses highlighted this association for mild depression (p = 0.024), but not for anxiety or moderate to severe depression. Conclusions: An observed positive association exists between therapists' review of previous sessions' action recommendations and improved treatment outcomes among clients with mild depression, highlighting the possible advantages of consistently revisiting therapeutic homework in real-world therapy settings. Results underscore the importance of developing effective strategies to help therapists maintain continuity between therapy sessions, potentially enhancing the impact of therapy. [ABSTRACT FROM AUTHOR]

Background: Telemedicine has experienced rapid growth in recent years, aiming to enhance medical efficiency and reduce the workload of healthcare professionals. During the COVID-19 pandemic in 2019, it became especially crucial, enabling remote screenings and access to healthcare services while maintaining social distancing. Online consultation platforms have emerged, but the demand has strained the availability of medical professionals, directly leading to research and development in automated medical consultation. Specifically, there is a need for efficient and accurate medical dialogue summarization algorithms to condense lengthy conversations into shorter versions focused on relevant medical facts. The success of large language models like generative pre-trained transformer (GPT)-3 has recently prompted a paradigm shift in natural language processing (NLP) research. In this paper, we will explore its impact on medical dialogue summarization. Methods: We present the performance and evaluation results of two approaches on a medical dialogue dataset. The first approach is based on fine-tuned pre-trained language models, such as bert-based summarization (BERTSUM) and bidirectional auto-regressive Transformers (BART). The second approach utilizes a large language models (LLMs) GPT-3.5 with inter-context learning (ICL). Evaluation is conducted using automated metrics such as ROUGE and BERTScore. Results: In comparison to the BART and ChatGPT models, the summaries generated by the BERTSUM model not only exhibit significantly lower ROUGE and BERTScore values but also fail to pass the testing for any of the metrics in manual evaluation. On the other hand, the BART model achieved the highest ROUGE and BERTScore values among all evaluated models, surpassing ChatGPT. Its ROUGE-1, ROUGE-2, ROUGE-L, and BERTScore values were 14.94%, 53.48%, 32.84%, and 6.73% higher respectively than ChatGPT's best results. However, in the manual evaluation by medical experts, the summaries generated by the BART model exhibit satisfactory performance only in the "Readability" metric, with less than 30% passing the manual evaluation in other metrics. When compared to the BERTSUM and BART models, the ChatGPT model was evidently more favored by human medical experts. Conclusion: On one hand, the GPT-3.5 model can manipulate the style and outcomes of medical dialogue summaries through various prompts. The generated content is not only better received than results from certain human experts but also more comprehensible, making it a promising avenue for automated medical dialogue summarization. On the other hand, automated evaluation mechanisms like ROUGE and BERTScore fall short in fully assessing the outputs of large language models like GPT-3.5. Therefore, it is necessary to research more appropriate evaluation criteria. [ABSTRACT FROM AUTHOR]

Background: Laboratory data can provide great value to support research aimed at reducing the incidence, prolonging survival and enhancing outcomes of cancer. Data is characterized by the information it carries and the format it holds. Data captured in Alberta's biomarker laboratory repository is free text, cluttered and rouge. Such data format limits its utility and prohibits broader adoption and research development. Text analysis for information extraction of unstructured data can change this and lead to more complete analyses. Previous work on extracting relevant information from free text, unstructured data employed Natural Language Processing (NLP), Machine Learning (ML), rule-based Information Extraction (IE) methods, or a hybrid combination between them. Methods: In our study, text analysis was performed on Alberta Precision Laboratories data which consisted of 95,854 entries from the Southern Alberta Dataset (SAD) and 6944 entries from the Northern Alberta Dataset (NAD). The data covers all of Alberta and is completely population-based. Our proposed framework is built around rule-based IE methods. It incorporates topics such as Syntax and Lexical analyses to achieve deterministic extraction of data from biomarker laboratory data (i.e., Epidermal Growth Factor Receptor (EGFR) test results). Lexical analysis compromises of data cleaning and pre-processing, Rich Text Format text conversion into readable plain text format, and normalization and tokenization of text. The framework then passes the text into the Syntax analysis stage which includes the rule-based method of extracting relevant data. Rule-based patterns of the test result are identified, and a Context Free Grammar then generates the rules of information extraction. Finally, the results are linked with the Alberta Cancer Registry to support real-world cancer research studies. Results: Of the original 5512 entries in the SAD dataset and 5017 entries in the NAD dataset which were filtered for EGFR, the framework yielded 5129 and 3388 extracted EGFR test results from the SAD and NAD datasets, respectively. An accuracy of 97.5% was achieved on a random sample of 362 tests. Conclusions: We presented a text analysis framework to extract specific information from unstructured clinical data. Our proposed framework has shown that it can successfully extract relevant information from EGFR test results. [ABSTRACT FROM AUTHOR]

Importance: Large language models (LLMs) like OpenAI's ChatGPT are powerful generative systems that rapidly synthesize natural language responses. Research on LLMs has revealed their potential and pitfalls, especially in clinical settings. However, the evolving landscape of LLM research in medicine has left several gaps regarding their evaluation, application, and evidence base. Objective: This scoping review aims to (1) summarize current research evidence on the accuracy and efficacy of LLMs in medical applications, (2) discuss the ethical, legal, logistical, and socioeconomic implications of LLM use in clinical settings, (3) explore barriers and facilitators to LLM implementation in healthcare, (4) propose a standardized evaluation framework for assessing LLMs' clinical utility, and (5) identify evidence gaps and propose future research directions for LLMs in clinical applications. Evidence review: We screened 4,036 records from MEDLINE, EMBASE, CINAHL, medRxiv, bioRxiv, and arXiv from January 2023 (inception of the search) to June 26, 2023 for English-language papers and analyzed findings from 55 worldwide studies. Quality of evidence was reported based on the Oxford Centre for Evidence-based Medicine recommendations. Findings: Our results demonstrate that LLMs show promise in compiling patient notes, assisting patients in navigating the healthcare system, and to some extent, supporting clinical decision-making when combined with human oversight. However, their utilization is limited by biases in training data that may harm patients, the generation of inaccurate but convincing information, and ethical, legal, socioeconomic, and privacy concerns. We also identified a lack of standardized methods for evaluating LLMs' effectiveness and feasibility. Conclusions and relevance: This review thus highlights potential future directions and questions to address these limitations and to further explore LLMs' potential in enhancing healthcare delivery. [ABSTRACT FROM AUTHOR]

Background: The provision of data sharing statements (DSS) for clinical trials has been made mandatory by different stakeholders. DSS are a device to clarify whether there is intention to share individual participant data (IPD). What is missing is a detailed assessment of whether DSS are providing clear and understandable information about the conditions for data sharing of IPD for secondary use. Methods: A random sample of 200 COVID-19 clinical trials with explicit DSS was drawn from the ECRIN clinical research metadata repository. The DSS were assessed and classified, by two experienced experts and one assessor with less experience in data sharing (DS), into different categories (unclear, no sharing, no plans, yes but vague, yes on request, yes with specified storage location, yes but with complex conditions). Results: Between the two experts the agreement was moderate to substantial (kappa=0.62, 95% CI [0.55, 0.70]). Agreement considerably decreased when these experts were compared with a third person who was less experienced and trained in data sharing ("assessor") (kappa=0.33, 95% CI [0.25, 0.41]; 0.35, 95% CI [0.27, 0.43]). Between the two experts and under supervision of an independent moderator, a consensus was achieved for those cases, where both experts had disagreed, and the result was used as "gold standard" for further analysis. At least some degree of willingness of DS (data sharing) was expressed in 63.5% (127/200) cases. Of these cases, around one quarter (31/127) were vague statements of support for data sharing but without useful detail. In around half of the cases (60/127) it was stated that IPD could be obtained by request. Only in in slightly more than 10% of the cases (15/127) it was stated that the IPD would be transferred to a specific data repository. In the remaining cases (21/127), a more complex regime was described or referenced, which could not be allocated to one of the three previous groups. As a result of the consensus meetings, the classification system was updated. Conclusion: The study showed that the current DSS that imply possible data sharing are often not easy to interpret, even by relatively experienced staff. Machine based interpretation, which would be necessary for any practical application, is currently not possible. Machine learning and / or natural language processing techniques might improve machine actionability, but would represent a very substantial investment of research effort. The cheaper and easier option would be for data providers, data requestors, funders and platforms to adopt a clearer, more structured and more standardised approach to specifying, providing and collecting DSS. Trial registration: The protocol for the study was pre-registered on ZENODO (https://zenodo.org/record/7064624#.Y4DIAHbMJD8). [ABSTRACT FROM AUTHOR]

Deep Self-Attention Network (Transformer) is an encoder–decoder architectural model that excels in establishing long-distance dependencies and is first applied in natural language processing. Due to its complementary nature with the inductive bias of convolutional neural network (CNN), Transformer has been gradually applied to medical image processing, including kidney image processing. It has become a hot research topic in recent years. To further explore new ideas and directions in the field of renal image processing, this paper outlines the characteristics of the Transformer network model and summarizes the application of the Transformer-based model in renal image segmentation, classification, detection, electronic medical records, and decision-making systems, and compared with CNN-based renal image processing algorithm, analyzing the advantages and disadvantages of this technique in renal image processing. In addition, this paper gives an outlook on the development trend of Transformer in renal image processing, which provides a valuable reference for a lot of renal image analysis. [ABSTRACT FROM AUTHOR]

Background: Systemic lupus erythematosus (SLE) is a rare autoimmune disorder characterized by an unpredictable course of flares and remission with diverse manifestations. Lupus nephritis, one of the major disease manifestations of SLE for organ damage and mortality, is a key component of lupus classification criteria. Accurately identifying lupus nephritis in electronic health records (EHRs) would therefore benefit large cohort observational studies and clinical trials where characterization of the patient population is critical for recruitment, study design, and analysis. Lupus nephritis can be recognized through procedure codes and structured data, such as laboratory tests. However, other critical information documenting lupus nephritis, such as histologic reports from kidney biopsies and prior medical history narratives, require sophisticated text processing to mine information from pathology reports and clinical notes. In this study, we developed algorithms to identify lupus nephritis with and without natural language processing (NLP) using EHR data from the Northwestern Medicine Enterprise Data Warehouse (NMEDW). Methods: We developed five algorithms: a rule-based algorithm using only structured data (baseline algorithm) and four algorithms using different NLP models. The first NLP model applied simple regular expression for keywords search combined with structured data. The other three NLP models were based on regularized logistic regression and used different sets of features including positive mention of concept unique identifiers (CUIs), number of appearances of CUIs, and a mixture of three components (i.e. a curated list of CUIs, regular expression concepts, structured data) respectively. The baseline algorithm and the best performing NLP algorithm were externally validated on a dataset from Vanderbilt University Medical Center (VUMC). Results: Our best performing NLP model incorporated features from both structured data, regular expression concepts, and mapped concept unique identifiers (CUIs) and showed improved F measure in both the NMEDW (0.41 vs 0.79) and VUMC (0.52 vs 0.93) datasets compared to the baseline lupus nephritis algorithm. Conclusion: Our NLP MetaMap mixed model improved the F-measure greatly compared to the structured data only algorithm in both internal and external validation datasets. The NLP algorithms can serve as powerful tools to accurately identify lupus nephritis phenotype in EHR for clinical research and better targeted therapies. [ABSTRACT FROM AUTHOR]

Background: Thousands of genes have been associated with different Mendelian conditions. One of the valuable sources to track these gene-disease associations (GDAs) is the Online Mendelian Inheritance in Man (OMIM) database. However, most of the information in OMIM is textual, and heterogeneous (e.g. summarized by different experts), which complicates automated reading and understanding of the data. Here, we used Natural Language Processing (NLP) to make a tool (Gene-Phenotype Association Discovery (GPAD)) that could syntactically process OMIM text and extract the data of interest. Results: GPAD applies a series of language-based techniques to the text obtained from OMIM API to extract GDA discovery-related information. GPAD can inform when a particular gene was associated with a specific phenotype, as well as the type of validation—whether through model organisms or cohort-based patient-matching approaches—for such an association. GPAD extracted data was validated with published reports and was compared with large language model. Utilizing GPAD's extracted data, we analysed trends in GDA discoveries, noting a significant increase in their rate after the introduction of exome sequencing, rising from an average of about 150–250 discoveries each year. Contrary to hopes of resolving most GDAs for Mendelian disorders by now, our data indicate a substantial decline in discovery rates over the past five years (2017–2022). This decline appears to be linked to the increasing necessity for larger cohorts to substantiate GDAs. The rising use of zebrafish and Drosophila as model organisms in providing evidential support for GDAs is also observed. Conclusions: GPAD's real-time analyzing capacity offers an up-to-date view of GDA discovery and could help in planning and managing the research strategies. In future, this solution can be extended or modified to capture other information in OMIM and scientific literature. [ABSTRACT FROM AUTHOR]

Artificial intelligence (AI) is a transformative technology with many benefits, but also risks when applied to healthcare and cardiac surgery in particular. Surgeons must be aware of AI and its application through generative pre-trained transformers (GPT/ChatGPT) to fully understand what this offers to clinical care, decision making, training, research and education. Clinicians must appreciate that the advantages and potential for transformative change in practice is balanced by risks typified by validation, ethical challenges and medicolegal concerns. ChatGPT should be seen as a tool to support and enhance the skills of surgeons, rather than a replacement for their experience and judgment. Human oversight and intervention will always be necessary to ensure patient safety and to make complex decisions that may require a refined understanding of individual patient circumstances. [ABSTRACT FROM AUTHOR]

Background: While the positive impact of homework completion on symptom alleviation is well-established, the pivotal role of therapists in reviewing these assignments has been under-investigated. This study examined therapists' practice of assigning and reviewing action recommendations in therapy sessions, and how it correlates with patients' depression and anxiety outcomes. Methods: We analyzed 2,444 therapy sessions from community-based behavioral health programs. Machine learning models and natural language processing techniques were deployed to discern action recommendations and their subsequent reviews. The extent of the review was quantified by measuring the proportion of session dialogues reviewing action recommendations, a metric we refer to as "review percentage". Using Generalized Estimating Equations modeling, we evaluated the correlation between this metric and changes in clients' depression and anxiety scores. Results: Our models achieved 76% precision in capturing action recommendations and 71.1% in reviewing them. Using these models, we found that therapists typically provided clients with one to eight action recommendations per session to engage in outside therapy. However, only half of the sessions included a review of previously assigned action recommendations. We identified a significant interaction between the initial depression score and the review percentage (p = 0.045). When adjusting for this relationship, the review percentage was positively and significantly associated with a reduction in depression score (p = 0.032). This suggests that more frequent review of action recommendations in therapy relates to greater improvement in depression symptoms. Further analyses highlighted this association for mild depression (p = 0.024), but not for anxiety or moderate to severe depression. Conclusions: An observed positive association exists between therapists' review of previous sessions' action recommendations and improved treatment outcomes among clients with mild depression, highlighting the possible advantages of consistently revisiting therapeutic homework in real-world therapy settings. Results underscore the importance of developing effective strategies to help therapists maintain continuity between therapy sessions, potentially enhancing the impact of therapy. [ABSTRACT FROM AUTHOR]

Purpose: Convolution operator-based neural networks have shown great success in medical image segmentation over the past decade. The U-shaped network with a codec structure is one of the most widely used models. Transformer, a technology used in natural language processing, can capture long-distance dependencies and has been applied in Vision Transformer to achieve state-of-the-art performance on image classification tasks. Recently, researchers have extended transformer to medical image segmentation tasks, resulting in good models. Methods: This review comprises publications selected through a Web of Science search. We focused on papers published since 2018 that applied the transformer architecture to medical image segmentation. We conducted a systematic analysis of these studies and summarized the results. Results: To better comprehend the benefits of convolutional neural networks and transformers, the construction of the codec and transformer modules is first explained. Second, the medical image segmentation model based on transformer is summarized. The typically used assessment markers for medical image segmentation tasks are then listed. Finally, a large number of medical segmentation datasets are described. Conclusion: Even if there is a pure transformer model without any convolution operator, the sample size of medical picture segmentation still restricts the growth of the transformer, even though it can be relieved by a pretraining model. More often than not, researchers are still designing models using transformer and convolution operators. [ABSTRACT FROM AUTHOR]

Objective: Clinical deep phenotyping and phenotype annotation play a critical role in both the diagnosis of patients with rare disorders as well as in building computationally-tractable knowledge in the rare disorders field. These processes rely on using ontology concepts, often from the Human Phenotype Ontology, in conjunction with a phenotype concept recognition task (supported usually by machine learning methods) to curate patient profiles or existing scientific literature. With the significant shift in the use of large language models (LLMs) for most NLP tasks, we examine the performance of the latest Generative Pre-trained Transformer (GPT) models underpinning ChatGPT as a foundation for the tasks of clinical phenotyping and phenotype annotation. Materials and methods: The experimental setup of the study included seven prompts of various levels of specificity, two GPT models (gpt-3.5-turbo and gpt-4.0) and two established gold standard corpora for phenotype recognition, one consisting of publication abstracts and the other clinical observations. Results: The best run, using in-context learning, achieved 0.58 document-level F1 score on publication abstracts and 0.75 document-level F1 score on clinical observations, as well as a mention-level F1 score of 0.7, which surpasses the current best in class tool. Without in-context learning, however, performance is significantly below the existing approaches. Conclusion: Our experiments show that gpt-4.0 surpasses the state of the art performance if the task is constrained to a subset of the target ontology where there is prior knowledge of the terms that are expected to be matched. While the results are promising, the non-deterministic nature of the outcomes, the high cost and the lack of concordance between different runs using the same prompt and input make the use of these LLMs challenging for this particular task. [ABSTRACT FROM AUTHOR]

Background: Oxygen saturation, a key indicator of COVID-19 severity, poses challenges, especially in cases of silent hypoxemia. Electronic health records (EHRs) often contain supplemental oxygen information within clinical narratives. Streamlining patient identification based on oxygen levels is crucial for COVID-19 research, underscoring the need for automated classifiers in discharge summaries to ease the manual review burden on physicians. Method: We analysed text lines extracted from anonymised COVID-19 patient discharge summaries in German to perform a binary classification task, differentiating patients who received oxygen supplementation and those who did not. Various machine learning (ML) algorithms, including classical ML to deep learning (DL) models, were compared. Classifier decisions were explained using Local Interpretable Model-agnostic Explanations (LIME), which visualize the model decisions. Result: Classical ML to DL models achieved comparable performance in classification, with an F-measure varying between 0.942 and 0.955, whereas the classical ML approaches were faster. Visualisation of embedding representation of input data reveals notable variations in the encoding patterns between classic and DL encoders. Furthermore, LIME explanations provide insights into the most relevant features at token level that contribute to these observed differences. Conclusion: Despite a general tendency towards deep learning, these use cases show that classical approaches yield comparable results at lower computational cost. Model prediction explanations using LIME in textual and visual layouts provided a qualitative explanation for the model performance. [ABSTRACT FROM AUTHOR]

Background: Digital mental health interventions (DMHIs) may reduce treatment access issues for those experiencing depressive and/or anxiety symptoms. DMHIs that incorporate relational agents may offer unique ways to engage and respond to users and to potentially help reduce provider burden. This study tested Woebot for Mood & Anxiety (W-MA-02), a DMHI that employs Woebot, a relational agent that incorporates elements of several evidence-based psychotherapies, among those with baseline clinical levels of depressive or anxiety symptoms. Changes in self-reported depressive and anxiety symptoms over 8 weeks were measured, along with the association between each of these outcomes and demographic and clinical characteristics. Methods: This exploratory, single-arm, 8-week study of 256 adults yielded non-mutually exclusive subsamples with either clinical levels of depressive or anxiety symptoms at baseline. Week 8 Patient Health Questionnaire-8 (PHQ-8) changes were measured in the depressive subsample (PHQ-8 ≥ 10). Week 8 Generalized Anxiety Disorder-7 (GAD-7) changes were measured in the anxiety subsample (GAD-7 ≥ 10). Demographic and clinical characteristics were examined in association with symptom changes via bivariate and multiple regression models adjusted for W-MA-02 utilization. Characteristics included age, sex at birth, race/ethnicity, marital status, education, sexual orientation, employment status, health insurance, baseline levels of depressive and anxiety symptoms, and concurrent psychotherapeutic or psychotropic medication treatments during the study. Results: Both the depressive and anxiety subsamples were predominantly female, educated, non-Hispanic white, and averaged 38 and 37 years of age, respectively. The depressive subsample had significant reductions in depressive symptoms at Week 8 (mean change =—7.28, SD = 5.91, Cohen's d = -1.23, p < 0.01); the anxiety subsample had significant reductions in anxiety symptoms at Week 8 (mean change = -7.45, SD = 5.99, Cohen's d = -1.24, p < 0.01). No significant associations were found between sex at birth, age, employment status, educational background and Week 8 symptom changes. Significant associations between depressive and anxiety symptom outcomes and sexual orientation, marital status, concurrent mental health treatment, and baseline symptom severity were found. Conclusions: The present study suggests early promise for W-MA-02 as an intervention for depression and/or anxiety symptoms. Although exploratory in nature, this study revealed potential user characteristics associated with outcomes that can be investigated in future studies. Trial Registration: This study was retrospectively registered on ClinicalTrials.gov (#NCT05672745) on January 5th, 2023. [ABSTRACT FROM AUTHOR]

Objective: To develop a Chinese Diabetes Mellitus Ontology (CDMO) and explore methods for constructing high-quality Chinese biomedical ontologies. Materials and methods: We used various data sources, including Chinese clinical practice guidelines, expert consensus, literature, and hospital information system database schema, to build the CDMO. We combined top-down and bottom-up strategies and integrated text mining and cross-lingual ontology mapping. The ontology was validated by clinical experts and ontology development tools, and its application was validated through clinical decision support and Chinese natural language medical question answering. Results: The current CDMO consists of 3,752 classes, 182 fine-grained object properties with hierarchical relationships, 108 annotation properties, and over 12,000 mappings to other well-known medical ontologies in English. Based on the CDMO and clinical practice guidelines, we developed 200 rules for diabetes diagnosis, treatment, diet, and medication recommendations using the Semantic Web Rule Language. By injecting ontology knowledge, CDMO enhances the performance of the T5 model on a real-world Chinese medical question answering dataset related to diabetes. Conclusion: CDMO has fine-grained semantic relationships and extensive annotation information, providing a foundation for medical artificial intelligence applications in Chinese contexts, including the construction of medical knowledge graphs, clinical decision support systems, and automated medical question answering. Furthermore, the development process incorporated natural language processing and cross-lingual ontology mapping to improve the quality of the ontology and improved development efficiency. This workflow offers a methodological reference for the efficient development of other high-quality Chinese as well as non-English medical ontologies. [ABSTRACT FROM AUTHOR]

Background: Epi-transcriptome regulation through post-transcriptional RNA modifications is essential for all RNA types. Precise recognition of RNA modifications is critical for understanding their functions and regulatory mechanisms. However, wet experimental methods are often costly and time-consuming, limiting their wide range of applications. Therefore, recent research has focused on developing computational methods, particularly deep learning (DL). Bidirectional long short-term memory (BiLSTM), convolutional neural network (CNN), and the transformer have demonstrated achievements in modification site prediction. However, BiLSTM cannot achieve parallel computation, leading to a long training time, CNN cannot learn the dependencies of the long distance of the sequence, and the Transformer lacks information interaction with sequences at different scales. This insight underscores the necessity for continued research and development in natural language processing (NLP) and DL to devise an enhanced prediction framework that can effectively address the challenges presented. Results: This study presents a multi-scale self- and cross-attention network (MSCAN) to identify the RNA methylation site using an NLP and DL way. Experiment results on twelve RNA modification sites (m6A, m1A, m5C, m5U, m6Am, m7G, Ψ, I, Am, Cm, Gm, and Um) reveal that the area under the receiver operating characteristic of MSCAN obtains respectively 98.34%, 85.41%, 97.29%, 96.74%, 99.04%, 79.94%, 76.22%, 65.69%, 92.92%, 92.03%, 95.77%, 89.66%, which is better than the state-of-the-art prediction model. This indicates that the model has strong generalization capabilities. Furthermore, MSCAN reveals a strong association among different types of RNA modifications from an experimental perspective. A user-friendly web server for predicting twelve widely occurring human RNA modification sites (m6A, m1A, m5C, m5U, m6Am, m7G, Ψ, I, Am, Cm, Gm, and Um) is available at http://47.242.23.141/MSCAN/index.php. Conclusions: A predictor framework has been developed through binary classification to predict RNA methylation sites. [ABSTRACT FROM AUTHOR]

Background: GPT-4-based ChatGPT demonstrates significant potential in various industries; however, its potential clinical applications remain largely unexplored. Methods: We employed the New England Journal of Medicine (NEJM) quiz "Image Challenge" from October 2021 to March 2023 to assess ChatGPT's clinical capabilities. The quiz, designed for healthcare professionals, tests the ability to analyze clinical scenarios and make appropriate decisions. We evaluated ChatGPT's performance on the NEJM quiz, analyzing its accuracy rate by questioning type and specialty after excluding quizzes which were impossible to answer without images. ChatGPT was first asked to answer without the five multiple-choice options, and then after being given the options. Results: ChatGPT achieved an 87% (54/62) accuracy without choices and a 97% (60/62) accuracy with choices, after excluding 16 image-based quizzes. Upon analyzing performance by quiz type, ChatGPT excelled in the Diagnosis category, attaining 89% (49/55) accuracy without choices and 98% (54/55) with choices. Although other categories featured fewer cases, ChatGPT's performance remained consistent. It demonstrated strong performance across the majority of medical specialties; however, Genetics had the lowest accuracy at 67% (2/3). Conclusion: ChatGPT demonstrates potential for diagnostic applications, suggesting its usefulness in supporting healthcare professionals in making differential diagnoses and enhancing AI-driven healthcare. [ABSTRACT FROM AUTHOR]

Herbicide and pesticide exposure [e.g., agent orange (AO)] is associated with an increased risk of multiple myeloma (MM) due to the contaminant, 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). However, it is unclear whether TCDD/AO exposure (AO exposure hereafter) increases the risk of progression of monoclonal gammopathy of undetermined significance (MGUS) to MM. We sought to evaluate the association in a nationwide study of US Veterans. A natural language processing algorithm was used to confirm MGUS and progression to MM. We included Veterans who were diagnosed with MGUS from 10/1/1999 to 12/31/2021 and served during the Vietnam War Era from 1/9/1962 to 5/7/1975. AO exposure was stratified according to three TCDD exposure levels: high (1/9/1962–11/30/1965), medium (12/1/1965–12/31/1970), or low (1/1/1971–5/7/1975). The association between AO exposure and progression was analyzed using multivariable Fine-Gray subdistribution hazard model with death as a competing event. The analytic cohort included 10,847 Veterans with MGUS, of whom 26.3% had AO exposure and 7.4% progressed to MM over a median follow-up of 5.2 years. In multivariable analysis, high exposure was associated with an increased progression rate (multivariable-adjusted hazard ratio 1.48; 95% confidence interval 1.02–2.16), compared to Veterans with no exposure. This information is critical to inform progression risk in patients diagnosed with MGUS and prior AO exposure. It is also applicable to MGUS patients with occupational TCDD exposure from herbicides and pesticides. [ABSTRACT FROM AUTHOR]

Purpose: The study aims to enhance the efficiency and accuracy of literature reviews on normal tissue complication probability (NTCP) in head and neck cancer patients using radiation therapy. It employs meta-analysis (MA) and natural language processing (NLP). Material and methods: The study consists of two parts. First, it employs MA to assess NTCP models for xerostomia, dysphagia, and mucositis after radiation therapy, using Python 3.10.5 for statistical analysis. Second, it integrates NLP with convolutional neural networks (CNN) to optimize literature search, reducing 3256 articles to 12. CNN settings include a batch size of 50, 50–200 epoch range and a 0.001 learning rate. Results: The study's CNN-NLP model achieved a notable accuracy of 0.94 after 200 epochs with Adamax optimization. MA showed an AUC of 0.67 for early-effect xerostomia and 0.74 for late-effect, indicating moderate to high predictive accuracy but with high variability across studies. Initial CNN accuracy of 66.70% improved to 94.87% post-tuning by optimizer and hyperparameters. Conclusion: The study successfully merges MA and NLP, confirming high predictive accuracy for specific model-feature combinations. It introduces a time-based metric, words per minute (WPM), for efficiency and highlights the utility of MA and NLP in clinical research. [ABSTRACT FROM AUTHOR]

Background: In the context of increasing population aging, ongoing drug-resistant pathogens and the COVID-19 epidemic, the changes in the epidemiological and clinical characteristics of patients with pneumonia remain unclear. This study aimed to assess the trends in hospitalization, case fatality, comorbidities, and isolated pathogens of pneumonia-related adult inpatients in Guangzhou during the last decade. Methods: We retrospectively enrolled hospitalized adults who had doctor-diagnosed pneumonia in the First Affiliated Hospital of Guangzhou Medical University from January 1, 2013 to December 31, 2022. A natural language processing system was applied to automatically extract the clinical data from electronic health records. We evaluated the proportion of pneumonia-related hospitalizations in total hospitalizations, pneumonia-related in-hospital case fatality, comorbidities, and species of isolated pathogens during the last decade. Binary logistic regression analysis was used to assess predictors for patients with prolonged length of stay (LOS). Results: A total of 38,870 cases were finally included in this study, with 70% males, median age of 64 (53, 73) years and median LOS of 7.9 (5.1, 12.8) days. Although the number of pneumonia-related hospitalizations showed an upward trend, the proportion of pneumonia-related hospitalizations decreased from 199.6 per 1000 inpatients in 2013 to 123.4 per 1000 in 2021, and the case fatality decreased from 50.2 per 1000 in 2013 to 23.9 per 1000 in 2022 (all P < 0.05). The most common comorbidities were chronic obstructive pulmonary disease, lung malignancy, cardiovascular diseases and diabetes. The most common pathogens were Pseudomonas aeruginosa, Candida albicans, Acinetobacter baumannii, Stenotrophomonas maltophilia, Klebsiella pneumoniae, and Staphylococcus aureus. Glucocorticoid use during hospitalization (Odd Ratio [OR] = 1.86, 95% Confidence Interval (CI): 1.14–3.06), immunosuppressant use during hospitalization (OR = 1.99, 1.14–3.46), ICU admission (OR = 16.23, 95%CI: 11.25–23.83), receiving mechanical ventilation (OR = 3.58, 95%CI: 2.60–4.97), presence of other underlying diseases (OR = 1.54, 95%CI: 1.15–2.06), and elevated procalcitonin (OR = 1.61, 95%CI: 1.19–2.19) were identified as independent predictors for prolonged LOS. Conclusion: The proportion of pneumonia-related hospitalizations and the in-hospital case fatality showed downward trends during the last decade. Pneumonia inpatients were often complicated by chronic underlying diseases and isolated with gram-negative bacteria. ICU admission was a significant predictor for prolonged LOS in pneumonia inpatients. [ABSTRACT FROM AUTHOR]

Background: With more clinical trials are offering optional participation in the collection of bio-specimens for biobanking comes the increasing complexity of requirements of informed consent forms. The aim of this study is to develop an automatic natural language processing (NLP) tool to annotate informed consent documents to promote biorepository data regulation, sharing, and decision support. We collected informed consent documents from several publicly available sources, then manually annotated them, covering sentences containing permission information about the sharing of either bio-specimens or donor data, or conducting genetic research or future research using bio-specimens or donor data. Results: We evaluated a variety of machine learning algorithms including random forest (RF) and support vector machine (SVM) for the automatic identification of these sentences. 120 informed consent documents containing 29,204 sentences were annotated, of which 1250 sentences (4.28%) provide answers to a permission question. A support vector machine (SVM) model achieved a F-1 score of 0.95 on classifying the sentences when using a gold standard, which is a prefiltered corpus containing all relevant sentences. Conclusions: This study provides the feasibility of using machine learning tools to classify permission-related sentences in informed consent documents. [ABSTRACT FROM AUTHOR]

Background: Unmet social needs may impair health and access to health care, and intervening on these holds particular promise in high-risk patient populations, such as those with multiple chronic conditions. Our objective was to identify social needs in a patient population at significant risk—Medicare enrollees with multiple chronic illnesses enrolled in care management services—and measure their prevalence prior to any systematic screening. Methods: We partnered with Renova Health, an independent Medicare Chronic Care Management (CCM) provider with patients in 10 states during our study period (January 2017 through August 2020). Our data included over 3,000 Medicare CCM patients, representing nearly 20,000 encounters. We used a dictionary-based natural language processing approach to ascertain the prevalence of six domains of barriers to care (food insecurity, housing instability, utility hardship) and unmet social needs (health care affordability, need for supportive services, transportation) in notes taken during telephonic Medicare CCM patient encounters. Results: Barriers to care, specifically need for supportive services (2.4%) and health care affordability (0.8%), were the most prevalent domains identified. Transportation as a barrier to care came up relatively less frequently in CCM encounters (0.1%). Unmet social needs were identified at a comparatively lower rate, with potential housing instability (0.3%) flagged most followed by potential utility hardship (0.2%) and food insecurity (0.1%). Conclusions: There is substantial untapped opportunity to systematically screen for social determinants of health and unmet social needs in care management. [ABSTRACT FROM AUTHOR]

Background: Protein–protein interactions (PPIs) are heavily involved in many biological processes. Consequently, the identification of PPIs in the model plant Arabidopsis is of great significance to deeply understand plant growth and development, and then to promote the basic research of crop improvement. Although many experimental Arabidopsis PPIs have been determined currently, the known interactomic data of Arabidopsis is far from complete. In this context, developing effective machine learning models from existing PPI data to predict unknown Arabidopsis PPIs conveniently and rapidly is still urgently needed. Results: We used a large-scale pre-trained protein language model (pLM) called ESM-1b to convert protein sequences into high-dimensional vectors and then used them as the input of multilayer perceptron (MLP). To avoid the performance overestimation frequently occurring in PPI prediction, we employed stringent datasets to train and evaluate the predictive model. The results showed that the combination of ESM-1b and MLP (i.e., ESMAraPPI) achieved more accurate performance than the predictive models inferred from other pLMs or baseline sequence encoding schemes. In particular, the proposed ESMAraPPI yielded an AUPR value of 0.810 when tested on an independent test set where both proteins in each protein pair are unseen in the training dataset, suggesting its strong generalization and extrapolating ability. Moreover, the proposed ESMAraPPI model performed better than several state-of-the-art generic or plant-specific PPI predictors. Conclusion: Protein sequence embeddings from the pre-trained model ESM-1b contain rich protein semantic information. By combining with the MLP algorithm, ESM-1b revealed excellent performance in predicting Arabidopsis PPIs. We anticipate that the proposed predictive model (ESMAraPPI) can serve as a very competitive tool to accelerate the identification of Arabidopsis interactome. [ABSTRACT FROM AUTHOR]

In this paper, we present a framework for developing a Learning Health System (LHS) to provide means to a computerized clinical decision support system for allied healthcare and/or nursing professionals. LHSs are well suited to transform healthcare systems in a mission-oriented approach, and is being adopted by an increasing number of countries. Our theoretical framework provides a blueprint for organizing such a transformation with help of evidence based state of the art methodologies and techniques to eventually optimize personalized health and healthcare. Learning via health information technologies using LHS enables users to learn both individually and collectively, and independent of their location. These developments demand healthcare innovations beyond a disease focused orientation since clinical decision making in allied healthcare and nursing is mainly based on aspects of individuals' functioning, wellbeing and (dis)abilities. Developing LHSs depends heavily on intertwined social and technological innovation, and research and development. Crucial factors may be the transformation of the Internet of Things into the Internet of FAIR data & services. However, Electronic Health Record (EHR) data is in up to 80% unstructured including free text narratives and stored in various inaccessible data warehouses. Enabling the use of data as a driver for learning is challenged by interoperability and reusability. To address technical needs, key enabling technologies are suitable to convert relevant health data into machine actionable data and to develop algorithms for computerized decision support. To enable data conversions, existing classification and terminology systems serve as definition providers for natural language processing through (un)supervised learning. To facilitate clinical reasoning and personalized healthcare using LHSs, the development of personomics and functionomics are useful in allied healthcare and nursing. Developing these omics will be determined via text and data mining. This will focus on the relationships between social, psychological, cultural, behavioral and economic determinants, and human functioning. Furthermore, multiparty collaboration is crucial to develop LHSs, and man-machine interaction studies are required to develop a functional design and prototype. During development, validation and maintenance of the LHS continuous attention for challenges like data-drift, ethical, technical and practical implementation difficulties is required. [ABSTRACT FROM AUTHOR]

Gain-of-function (GOF) variants give rise to increased/novel protein functions whereas loss-of-function (LOF) variants lead to diminished protein function. Experimental approaches for identifying GOF and LOF are generally slow and costly, whilst available computational methods have not been optimized to discriminate between GOF and LOF variants. We have developed LoGoFunc, a machine learning method for predicting pathogenic GOF, pathogenic LOF, and neutral genetic variants, trained on a broad range of gene-, protein-, and variant-level features describing diverse biological characteristics. LoGoFunc outperforms other tools trained solely to predict pathogenicity for identifying pathogenic GOF and LOF variants and is available at https://itanlab.shinyapps.io/goflof/. [ABSTRACT FROM AUTHOR]

Purpose: Today, the Internet provides access to many patients' experiences, which is crucial in assessing the quality of healthcare services. This paper introduces a model for detecting cancer patients' opinions about healthcare services in the Persian language, both positive and negative. Method: To achieve the objectives of this study, a combination of sentiment analysis (SA) and topic modeling approaches was employed. All pertinent comments made by cancer patients were collected from the patient feedback form of the Tehran University of Medical Science (TUMS) Cancer Institute (CI) in Iran, from March to October 2021. Conventional evaluation metrics such as accuracy, precision, recall, and F-measure were utilized to assess the performance of the proposed model. Result: The experimental findings revealed that the proposed SA model achieved accuracies of 89.3%, 92.6%, and 90.8% in detecting patients' sentiments towards general services, healthcare services, and life expectancy, respectively. Based on the topic modeling results, the topic "Metastasis" exhibited lower sentiment scores compared to other topics. Additionally, cancer patients expressed dissatisfaction with the current appointment booking service, while topics such as "Good experience," "Affable staff", and "Chemotherapy" garnered higher sentiment scores. Conclusion: The combined use of SA and topic modeling offers valuable insights into healthcare services. Policymakers can utilize the knowledge obtained from these topics and associated sentiments to enhance patient satisfaction with cancer institution services. [ABSTRACT FROM AUTHOR]

Background: Child abuse and neglect (CAN) is prevalent, associated with long-term adversities, and often undetected. Primary care settings offer a unique opportunity to identify CAN and facilitate referrals, when warranted. Electronic health records (EHR) contain extensive information to support healthcare decisions, yet time constraints preclude most providers from thorough EHR reviews that could indicate CAN. Strategies that summarize EHR data to identify CAN and convey this to providers has potential to mitigate CAN-related sequelae. This study used expert review/consensus and Natural Language Processing (NLP) to develop and test a lexicon to characterize children who have experienced or are at risk for CAN and compared machine learning methods to the lexicon + NLP approach to determine the algorithm's performance for identifying CAN. Methods: Study investigators identified 90 CAN terms and invited an interdisciplinary group of child abuse experts for review and validation. We then used NLP to develop pipelines to finalize the CAN lexicon. Data for pipeline development and refinement were drawn from a randomly selected sample of EHR from patients seen at pediatric primary care clinics within a U.S. academic health center. To explore a machine learning approach for CAN identification, we used Support Vector Machine algorithms. Results: The investigator-generated list of 90 CAN terms were reviewed and validated by 25 invited experts, resulting in a final pool of 133 terms. NLP utilized a randomly selected sample of 14,393 clinical notes from 153 patients to test the lexicon, and.03% of notes were identified as CAN positive. CAN identification varied by clinical note type, with few differences found by provider type (physicians versus nurses, social workers, etc.). An evaluation of the final NLP pipelines indicated 93.8% positive CAN rate for the training set and 71.4% for the test set, with decreased precision attributed primarily to false positives. For the machine learning approach, SVM pipeline performance was 92% for CAN + and 100% for non-CAN, indicating higher sensitivity than specificity. Conclusions: The NLP algorithm's development and refinement suggest that innovative tools can identify youth at risk for CAN. The next key step is to refine the NLP algorithm to eventually funnel this information to care providers to guide clinical decision making. [ABSTRACT FROM AUTHOR]

Introduction: Accurate identification of venous thromboembolism (VTE) is critical to develop replicable epidemiological studies and rigorous predictions models. Traditionally, VTE studies have relied on international classification of diseases (ICD) codes which are inaccurate – leading to misclassification bias. Here, we developed ClotCatcher, a novel deep learning model that uses natural language processing to detect VTE from radiology reports. Methods: Radiology reports to detect VTE were obtained from patients admitted to Emory University Hospital (EUH) and Grady Memorial Hospital (GMH). Data augmentation was performed using the Google PEGASUS paraphraser. This data was then used to fine-tune ClotCatcher, a novel deep learning model. ClotCatcher was validated on both the EUH dataset alone and GMH dataset alone. Results: The dataset contained 1358 studies from EUH and 915 studies from GMH (n = 2273). The dataset contained 1506 ultrasound studies with 528 (35.1%) studies positive for VTE, and 767 CT studies with 91 (11.9%) positive for VTE. When validated on the EUH dataset, ClotCatcher performed best (AUC = 0.980) when trained on both EUH and GMH dataset without paraphrasing. When validated on the GMH dataset, ClotCatcher performed best (AUC = 0.995) when trained on both EUH and GMH dataset with paraphrasing. Conclusion: ClotCatcher, a novel deep learning model with data augmentation rapidly and accurately adjudicated the presence of VTE from radiology reports. Applying ClotCatcher to large databases would allow for rapid and accurate adjudication of incident VTE. This would reduce misclassification bias and form the foundation for future studies to estimate individual risk for patient to develop incident VTE. [ABSTRACT FROM AUTHOR]

Background: Determining a protein's quaternary state, i.e. the number of monomers in a functional unit, is a critical step in protein characterization. Many proteins form multimers for their activity, and over 50% are estimated to naturally form homomultimers. Experimental quaternary state determination can be challenging and require extensive work. To complement these efforts, a number of computational tools have been developed for quaternary state prediction, often utilizing experimentally validated structural information. Recently, dramatic advances have been made in the field of deep learning for predicting protein structure and other characteristics. Protein language models, such as ESM-2, that apply computational natural-language models to proteins successfully capture secondary structure, protein cell localization and other characteristics, from a single sequence. Here we hypothesize that information about the protein quaternary state may be contained within protein sequences as well, allowing us to benefit from these novel approaches in the context of quaternary state prediction. Results: We generated ESM-2 embeddings for a large dataset of proteins with quaternary state labels from the curated QSbio dataset. We trained a model for quaternary state classification and assessed it on a non-overlapping set of distinct folds (ECOD family level). Our model, named QUEEN (QUaternary state prediction using dEEp learNing), performs worse than approaches that include information from solved crystal structures. However, it successfully learned to distinguish multimers from monomers, and predicts the specific quaternary state with moderate success, better than simple sequence similarity-based annotation transfer. Our results demonstrate that complex, quaternary state related information is included in such embeddings. Conclusions: QUEEN is the first to investigate the power of embeddings for the prediction of the quaternary state of proteins. As such, it lays out strengths as well as limitations of a sequence-based protein language model approach, compared to structure-based approaches. Since it does not require any structural information and is fast, we anticipate that it will be of wide use both for in-depth investigation of specific systems, as well as for studies of large sets of protein sequences. A simple colab implementation is available at: https://colab.research.google.com/github/Furman-Lab/QUEEN/blob/main/QUEEN_prediction_notebook.ipynb. [ABSTRACT FROM AUTHOR]

Background: In the healthcare domain today, despite the substantial adoption of electronic health information systems, a significant proportion of medical reports still exist in paper-based formats. As a result, there is a significant demand for the digitization of information from these paper-based reports. However, the digitization of paper-based laboratory reports into a structured data format can be challenging due to their non-standard layouts, which includes various data types such as text, numeric values, reference ranges, and units. Therefore, it is crucial to develop a highly scalable and lightweight technique that can effectively identify and extract information from laboratory test reports and convert them into a structured data format for downstream tasks. Methods: We developed an end-to-end Natural Language Processing (NLP)-based pipeline for extracting information from paper-based laboratory test reports. Our pipeline consists of two main modules: an optical character recognition (OCR) module and an information extraction (IE) module. The OCR module is applied to locate and identify text from scanned laboratory test reports using state-of-the-art OCR algorithms. The IE module is then used to extract meaningful information from the OCR results to form digitalized tables of the test reports. The IE module consists of five sub-modules, which are time detection, headline position, line normalization, Named Entity Recognition (NER) with a Conditional Random Fields (CRF)-based method, and step detection for multi-column. Finally, we evaluated the performance of the proposed pipeline on 153 laboratory test reports collected from Peking University First Hospital (PKU1). Results: In the OCR module, we evaluate the accuracy of text detection and recognition results at three different levels and achieved an averaged accuracy of 0.93. In the IE module, we extracted four laboratory test entities, including test item name, test result, test unit, and reference value range. The overall F1 score is 0.86 on the 153 laboratory test reports collected from PKU1. With a single CPU, the average inference time of each report is only 0.78 s. Conclusion: In this study, we developed a practical lightweight pipeline to digitalize and extract information from paper-based laboratory test reports in diverse types and with different layouts that can be adopted in real clinical environments with the lowest possible computing resources requirements. The high evaluation performance on the real-world hospital dataset validated the feasibility of the proposed pipeline. [ABSTRACT FROM AUTHOR]

Background: Breastfeeding is a critical health intervention in infants. Recent literature reported that the COVID-19 pandemic resulted in significant mental health issues in pregnant and breastfeeding women due to social isolation and lack of direct professional support. These maternal mental health issues affected infant nutrition and decreased breastfeeding rates during COVID-19. Twitter, a popular social media platform, can provide insight into public perceptions and sentiment about various health-related topics. With evidence of significant mental health issues among women during the COVID-19 pandemic, the perception of infant nutrition, specifically breastfeeding, remains unknown. Methods: We aimed to understand public perceptions and sentiment regarding breastfeeding during the COVID-19 pandemic through Twitter analysis using natural language processing techniques. We collected and analyzed tweets related to breastfeeding and COVID-19 during the pandemic from January 2020 to May 2022. We used Python software (v3.9.0) for all data processing and analyses. We performed sentiment and emotion analysis of the tweets using natural language processing libraries and topic modeling using an unsupervised machine-learning algorithm. Results: We analyzed 40,628 tweets related to breastfeeding and COVID-19 generated by 28,216 users. Emotion analysis revealed predominantly "Positive emotions" regarding breastfeeding, comprising 72% of tweets. The overall tweet sentiment was positive, with a mean weekly sentiment of 0.25 throughout, and was affected by external events. Topic modeling revealed six significant themes related to breastfeeding and COVID-19. Passive immunity through breastfeeding after maternal vaccination had the highest mean positive sentiment score of 0.32. Conclusions: Our study provides insight into public perceptions and sentiment regarding breastfeeding during the COVID-19 pandemic. Contrary to other topics we explored in the context of COVID (e.g., ivermectin, disinformation), we found that breastfeeding had an overall positive sentiment during the pandemic despite the documented rise in mental health challenges in pregnant and breastfeeding mothers. The wide range of topics on Twitter related to breastfeeding provides an opportunity for active engagement by the medical community and timely dissemination of advice, support, and guidance. Future studies should leverage social media analysis to gain real-time insight into public health topics of importance in child health and apply targeted interventions. [ABSTRACT FROM AUTHOR]