Mindfulness intervention, homogeneous medical concept, and concentrated solution nursing for colorectal cancer patients: a retrospective study.

OBJECTIVE: We aim to explore the differences of the psychological distress of postoperative chemotherapy patients with colorectal cancer between mindfulness intervention combined with homogeneous medical concepts and mindfulness intervention only. METHODS: One hundred patients with colorectal cancer undergoing chemotherapy after surgery from Sep 2020 to Sep 2022 were enrolled and divided into active control group (Solution centered nursing interventions; homogenized medical and nursing professional teams; dedicated personnel responsible for "admission notices"; Regular follow-up after discharge) and mindfulness group (homogeneous medical concept + and concentrated solution + Mindfulness intervention) with 50 cases in each group according to different nursing methods. RESULTS: After nursing, the physical function, emotional function, cognitive function, and social function of the patients in the mindfulness group were significantly higher than those in the active control group. However, the overall life and economic difficulties of the patients in the mindfulness group were significantly lower than those in the active control group (P < 0.05). After nursing, the observation score, description score, action score, intrinsic experience score, non-judgment score and non-reaction score of the mindfulness group were significantly higher than those of the active control group (P < 0.05). CONCLUSION: The implementation of mindfulness intervention in colorectal cancer patients undergoing chemotherapy can alleviate the patients' negative emotions, improve the level of mindfulness, and improve the quality of life of patients.

Medical concept embedding of real-valued electronic health records with application to inflammatory bowel disease.

Deep learning approaches are gradually being applied to electronic health record (EHR) data, but they fail to incorporate medical diagnosis codes and real-valued laboratory tests into a single input sequence for temporal modeling. Therefore, the modeling misses the existing medical interrelations among codes and lab test results that should be exploited to promote early disease detection. To find connections between past diagnoses, represented by medical codes, and real-valued laboratory tests, in order to exploit the full potential of the EHR in medical diagnosis, we present a novel method to embed the two sources of data into a recurrent neural network. Experimenting with a database of Crohn's disease (CD), a type of inflammatory bowel disease, patients and their controls (~1:2.2), we show that the introduction of lab test results improves the network's predictive performance more than the introduction of past diagnoses but also, surprisingly, more than when both are combined. In addition, using bootstrapping, we generalize the analysis of the imbalanced database to a medical condition that simulates real-life prevalence of a high-risk CD group of first-degree relatives with results that make our embedding method ready to screen this group in the population.

SapBERT-Based Medical Concept Normalization Using SNOMED CT.

Word vector representations, known as embeddings, are commonly used for natural language processing. Particularly, contextualized representations have been very successful recently. In this work, we analyze the impact of contextualized and non-contextualized embeddings for medical concept normalization, mapping clinical terms via a k-NN approach to SNOMED CT. The non-contextualized concept mapping resulted in a much better performance (F1-score = 0.853) than the contextualized representation (F1-score = 0.322).

The Medical versus Zoological Concept of Outflow Tract Valves of the Vertebrate Heart.

The anatomical elements that in humans prevent blood backflow from the aorta and pulmonary artery to the left and right ventriclesare the aortic and pulmonary valves, respectively. Each valve regularly consists of three leaflets (cusps), each supported by its valvular sinus. From the medical viewpoint, each set of three leaflets and sinuses is regarded as a morpho-functional unit. This notion also applies to birds and non-human mammals. However, the structures that prevent the return of blood to the heart in other vertebrates are notably different. This has led to discrepancies between physicians and zoologists in defining what a cardiac outflow tract valve is. The aim here is to compare the gross anatomy of the outflow tract valvular system among several groups of vertebrates in order to understand the conceptual and nomenclature controversies in the field.

Patient-Patient Similarity-Based Screening of a Clinical Data Warehouse to Support Ciliopathy Diagnosis.

A timely diagnosis is a key challenge for many rare diseases. As an expanding group of rare and severe monogenic disorders with a broad spectrum of clinical manifestations, ciliopathies, notably renal ciliopathies, suffer from important underdiagnosis issues. Our objective is to develop an approach for screening large-scale clinical data warehouses and detecting patients with similar clinical manifestations to those from diagnosed ciliopathy patients. We expect that the top-ranked similar patients will benefit from genetic testing for an early diagnosis. The dependence and relatedness between phenotypes were taken into account in our similarity model through medical concept embedding. The relevance of each phenotype to each patient was also considered by adjusted aggregation of phenotype similarity into patient similarity. A ranking model based on the best-subtype-average similarity was proposed to address the phenotypic overlapping and heterogeneity of ciliopathies. Our results showed that using less than one-tenth of learning sources, our language and center specific embedding provided comparable or better performances than other existing medical concept embeddings. Combined with the best-subtype-average ranking model, our patient-patient similarity-based screening approach was demonstrated effective in two large scale unbalanced datasets containing approximately 10,000 and 60,000 controls with kidney manifestations in the clinical data warehouse (about 2 and 0.4% of prevalence, respectively). Our approach will offer the opportunity to identify candidate patients who could go through genetic testing for ciliopathy. Earlier diagnosis, before irreversible end-stage kidney disease, will enable these patients to benefit from appropriate follow-up and novel treatments that could alleviate kidney dysfunction.

A simple neural vector space model for medical concept normalization using concept embeddings.

OBJECTIVE: Medical concept normalization (MCN), the task of linking textual mentions to concepts in an ontology, provides a solution to unify different ways of referring to the same concept. In this paper, we present a simple neural MCN model that takes mentions as input and directly predicts concepts. MATERIALS AND METHODS: We evaluate our proposed model on clinical datasets from ShARe/CLEF eHealth 2013 shared task and 2019 n2c2/OHNLP shared task track 3. Our neural MCN model consists of an encoder, and a normalized temperature-scaled softmax (NT-softmax) layer that maximizes the cosine similarity score of matching the mention to the correct concept. We adopt SAPBERT as the encoder and initialize the weights in the NT-softmax layer with pre-computed concept embeddings from SAPBERT. RESULTS: Our proposed neural model achieves competitive performance on ShARe/CLEF 2013 and establishes a new state-of-the-art on 2019-n2c2-MCN. Yet this model is simpler than most prior work: it requires no complex pipelines, no hand-crafted rules, and no preprocessing, making it simpler to apply in new settings. DISCUSSION: Analyses of our proposed model show that the NT-softmax is better than the conventional softmax on the MCN task, and both the CUI-less threshold parameter and the initialization of the weight vectors in the NT-softmax layer contribute to the improvements. CONCLUSION: We propose a simple neural model for clinical MCN, an one-step approach with simpler inference and more effective performance than prior work. Our analyses demonstrate future work on MCN may require more effort on unseen concepts.

The influence of homogeneous medical concept combined with focused nursing on the body function of postoperative colostomy patients with colorectal cancer and nursing evaluation / 中国实用护理杂志

Objective:To explore effect of homogeneous medical concept nursing mode combined with focused solution mode on self-efficacy and immunity function and nursing satisfaction analysis of patients with postoperative enterostomy of colorectal cancer.Methods:A total of 102 patients with colorectal cancer undergoing postoperative enterostomy admitted to Suining Central Hospital from December 2019 to December 2020 were selected and divided into control group and observation group according to random number table method, with 52 cases in observation group and 50 cases in control group. The control group received homogeneous medical concept nursing mode, and the observation group combined with the focused solution mode nursing intervention on this basis. The self-efficacy, immune function and nursing satisfaction of the two groups were compared.Results:The general self-efficacy of the observation group was higher than that of the control group ( χ2=2.61, P<0.05). After nursing, the stomato-related self-efficacy score of the observation group was 102.69 ± 12.37, which was higher than that of the control group (90.13±11.22). There was significant difference between the two groups ( t= 5.37, P<0.05). There was no significant difference in peripheral blood CD3+, CD4+ and CD4+/CD8+ and NK levels between 2 groups one day after surgery ( P>0.05). The levels of CD3+, CD4+ and CD4+/CD8+ and NK in peripheral blood of the observation group after nursing care were (67.21 ± 6.21)%, (67.22 ± 8.76)%, (2.65 ± 0.45)% and (19.50 ± 2.05)%, respectively, which were higher than those of the control group (60.32 ± 5.45)%, (60.21 ± 8.25)%, (2.41 ± 0.32)% and (15.62 ± 1.81)%. The differences were statistically significant ( t=5.95, 4.21, 3.11, all P<0.05). The total satisfaction rate of nursing in the observation group was 98.08% (51/52), which was higher than 84.00% (42/50) in the control group, and the difference was statistically significant ( χ2= 2.63, P<0.05). Conclusions:The application of homogenous medical concept nursing mode combined with focused solution mode in colorectal cancer postoperative enterostomy patients is helpful to improve patients' self-efficacy, enhance patients ′ immune function, and improve nursing satisfaction degree, which is worthy of further promotion in clinical practice.

Clinical Concept Extraction with Lexical Semantics to Support Automatic Annotation.

Extracting clinical concepts, such as problems, diagnosis, and treatment, from unstructured clinical narrative documents enables data-driven approaches such as machine and deep learning to support advanced applications such as clinical decision-support systems, the assessment of disease progression, and the intelligent analysis of treatment efficacy. Various tools such as cTAKES, Sophia, MetaMap, and other rules-based approaches and algorithms have been used for automatic concept extraction. Recently, machine- and deep-learning approaches have been used to extract, classify, and accurately annotate terms and phrases. However, the requirement of an annotated dataset, which is labor-intensive, impedes the success of data-driven approaches. A rule-based mechanism could support the process of annotation, but existing rule-based approaches fail to adequately capture contextual, syntactic, and semantic patterns. This study intends to introduce a comprehensive rule-based system that automatically extracts clinical concepts from unstructured narratives with higher accuracy and transparency. The proposed system is a pipelined approach, capable of recognizing clinical concepts of three types, problem, treatment, and test, in the dataset collected from a published repository as a part of the I2b2 challenge 2010. The system's performance is compared with that of three existing systems: Quick UMLS, BIO-CRF, and the Rules (i2b2) model. Compared to the baseline systems, the average F1-score of 72.94% was found to be 13% better than Quick UMLS, 3% better than BIO CRF, and 30.1% better than the Rules (i2b2) model. Individually, the system performance was noticeably higher for problem-related concepts, with an F1-score of 80.45%, followed by treatment-related concepts and test-related concepts, with F1-scores of 76.06% and 55.3%, respectively. The proposed methodology significantly improves the performance of concept extraction from unstructured clinical narratives by exploiting the linguistic and lexical semantic features. The approach can ease the automatic annotation process of clinical data, which ultimately improves the performance of supervised data-driven applications trained with these data.

Improving broad-coverage medical entity linking with semantic type prediction and large-scale datasets.

OBJECTIVES: Biomedical natural language processing tools are increasingly being applied for broad-coverage information extraction-extracting medical information of all types in a scientific document or a clinical note. In such broad-coverage settings, linking mentions of medical concepts to standardized vocabularies requires choosing the best candidate concepts from large inventories covering dozens of types. This study presents a novel semantic type prediction module for biomedical NLP pipelines and two automatically-constructed, large-scale datasets with broad coverage of semantic types. METHODS: We experiment with five off-the-shelf biomedical NLP toolkits on four benchmark datasets for medical information extraction from scientific literature and clinical notes. All toolkits adopt a staged approach of mention detection followed by two stages of medical entity linking: (1) generating a list of candidate concepts, and (2) picking the best concept among them. We introduce a semantic type prediction module to alleviate the problem of overgeneration of candidate concepts by filtering out irrelevant candidate concepts based on the predicted semantic type of a mention. We present MedType, a fully modular semantic type prediction model which we integrate into the existing NLP toolkits. To address the dearth of broad-coverage training data for medical information extraction, we further present WikiMed and PubMedDS, two large-scale datasets for medical entity linking. RESULTS: Semantic type filtering improves medical entity linking performance across all toolkits and datasets, often by several percentage points of F-1. Further, pretraining MedType on our novel datasets achieves state-of-the-art performance for semantic type prediction in biomedical text. CONCLUSIONS: Semantic type prediction is a key part of building accurate NLP pipelines for broad-coverage information extraction from biomedical text. We make our source code and novel datasets publicly available to foster reproducible research.

BertMCN: Mapping colloquial phrases to standard medical concepts using BERT and highway network.

In the last few years, people started to share lots of information related to health in the form of tweets, reviews and blog posts. All these user generated clinical texts can be mined to generate useful insights. However, automatic analysis of clinical text requires identification of standard medical concepts. Most of the existing deep learning based medical concept normalization systems are based on CNN or RNN. Performance of these models is limited as they have to be trained from scratch (except embeddings). In this work, we propose a medical concept normalization system based on BERT and highway layer. BERT, a pre-trained context sensitive deep language representation model advanced state-of-the-art performance in many NLP tasks and gating mechanism in highway layer helps the model to choose only important information. Experimental results show that our model outperformed all existing methods on two standard datasets. Further, we conduct a series of experiments to study the impact of different learning rates and batch sizes, noise and freezing encoder layers on our model.

Medical concept normalization in French using multilingual terminologies and contextual embeddings.

INTRODUCTION: Concept normalization is the task of linking terms from textual medical documents to their concept in terminologies such as the UMLS®. Traditional approaches to this problem depend heavily on the coverage of available resources, which poses a problem for languages other than English. OBJECTIVE: We present a system for concept normalization in French. We consider textual mentions already extracted and labeled by a named entity recognition system, and we classify these mentions with a UMLS concept unique identifier. We take advantage of the multilingual nature of available terminologies and embedding models to improve concept normalization in French without translation nor direct supervision. MATERIALS AND METHODS: We consider the task as a highly-multiclass classification problem. The terms are encoded with contextualized embeddings and classified via cosine similarity and softmax. A first step uses a subset of the terminology to finetune the embeddings and train the model. A second step adds the entire target terminology, and the model is trained further with hard negative selection and softmax sampling. RESULTS: On two corpora from the Quaero FrenchMed benchmark, we show that our approach can lead to good results even with no labeled data at all; and that it outperforms existing supervised methods with labeled data. DISCUSSION: Training the system with both French and English terms improves by a large margin the performance of the system on a French benchmark, regardless of the way the embeddings were pretrained (French, English, multilingual). Our distantly supervised method can be applied to any kind of documents or medical domain, as it does not require any concept-labeled documents. CONCLUSION: These experiments pave the way for simpler and more effective multilingual approaches to processing medical texts in languages other than English.

Learning structured medical information from social media.

Our goal is to summarise and aggregate information from social media regarding the symptoms of a disease, the drugs used and the treatment effects both positive and negative. To achieve this we first apply a supervised machine learning method to automatically extract medical concepts from natural language text. In an environment such as social media, where new data is continuously streamed, we need a methodology that will allow us to continuously train with the new data. To attain such incremental re-training, a semi-supervised methodology is developed, which is capable of learning new concepts from a small set of labelled data together with the much larger set of unlabelled data. The semi-supervised methodology deploys a conditional random field (CRF) as the base-line training algorithm for extracting medical concepts. The methodology iteratively augments to the training set sentences having high confidence, and adds terms to existing dictionaries to be used as features with the base-line model for further classification. Our empirical results show that the base-line CRF performs strongly across a range of different dictionary and training sizes; when the base-line is built with the full training data the F1 score reaches the range 84%-90%. Moreover, we show that the semi-supervised method produces a mild but significant improvement over the base-line. We also discuss the significance of the potential improvement of the semi-supervised methodology and found that it is significantly more accurate in most cases than the underlying base-line model.

Distant supervision for medical concept normalization.

We consider the task of Medical Concept Normalization (MCN) which aims to map informal medical phrases such as "loosing weight" to formal medical concepts, such as "Weight loss". Deep learning models have shown high performance across various MCN datasets containing small number of target concepts along with adequate number of training examples per concept. However, scaling these models to millions of medical concepts entails the creation of much larger datasets which is cost and effort intensive. Recent works have shown that training MCN models using automatically labeled examples extracted from medical knowledge bases partially alleviates this problem. We extend this idea by computationally creating a distant dataset from patient discussion forums. We extract informal medical phrases and medical concepts from these forums using a synthetically trained classifier and an off-the-shelf medical entity linker respectively. We use pretrained sentence encoding models to find the k-nearest phrases corresponding to each medical concept. These mappings are used in combination with the examples obtained from medical knowledge bases to train an MCN model. Our approach outperforms the previous state-of-the-art by 15.9% and 17.1% classification accuracy across two datasets while avoiding manual labeling.

Salience of Medical Concepts of Inside Clinical Texts and Outside Medical Records for Referred Cardiovascular Patients.

Outside medical records (OMRs) accompanying referred patients are frequently sent as faxes from external healthcare providers. Accessing useful and relevant information from these OMRs in a timely manner is a challenging task due to a combination of the presence of machine-illegible information and the limited system interoperability inherent in healthcare. Little research has been done on investigating information in OMRs. This paper evaluated overlapping and non-overlapping medical concepts captured from digitally faxed OMRs for patients transferring to the Department of Cardiovascular Medicine and from clinical consultant notes generated at the Mayo Clinic. We used optical character recognition (OCR) techniques to make faxed OMRs machine-readable and used natural language processing (NLP) techniques to capture clinical concepts from both machine-readable OMRs and Mayo clinical notes. We measured the level of overlap in medical concepts between OMRs and Mayo clinical narratives in the quantitative approaches and assessed the salience of concepts specific to Cardiovascular Medicine by calculating the ratio of those mentioned concepts relative to an independent clinical corpus. Among the concepts collected from the OMRs, 11.19% of those were also present in the Mayo clinical narratives that were generated within the 3 months after their initial encounter at the Mayo Clinic. For those common concepts, 73.97% were identified in initial consultant notes (ICNs) and 26.03% were captured over subsequent follow-up consultant notes (FCNs). These findings implied that information collected from the OMRs is potentially informative for patient care, but some valuable information (additionally identified in FCNs) collected from the OMRs is not fully used in an earlier stage of the care process. The concepts collected from the ICNs have the highest salience to Cardiovascular Medicine (0.112) compared to concepts in OMRs and concepts in FCNs. Additionally, unique concepts captured in ICNs (unseen in OMRs or FCNs) carried the most salient information (0.094), which demonstrated that ICNs provided the most informative concepts for the care of transferred patients.

Medical concept normalization in social media posts with recurrent neural networks.

Text mining of scientific libraries and social media has already proven itself as a reliable tool for drug repurposing and hypothesis generation. The task of mapping a disease mention to a concept in a controlled vocabulary, typically to the standard thesaurus in the Unified Medical Language System (UMLS), is known as medical concept normalization. This task is challenging due to the differences in the use of medical terminology between health care professionals and social media texts coming from the lay public. To bridge this gap, we use sequence learning with recurrent neural networks and semantic representation of one- or multi-word expressions: we develop end-to-end architectures directly tailored to the task, including bidirectional Long Short-Term Memory, Gated Recurrent Units with an attention mechanism, and additional semantic similarity features based on UMLS. Our evaluation against a standard benchmark shows that recurrent neural networks improve results over an effective baseline for classification based on convolutional neural networks. A qualitative examination of mentions discovered in a dataset of user reviews collected from popular online health information platforms as well as a quantitative evaluation both show improvements in the semantic representation of health-related expressions in social media.

Active learning: a step towards automating medical concept extraction.

OBJECTIVE: This paper presents an automatic, active learning-based system for the extraction of medical concepts from clinical free-text reports. Specifically, (1) the contribution of active learning in reducing the annotation effort and (2) the robustness of incremental active learning framework across different selection criteria and data sets are determined. MATERIALS AND METHODS: The comparative performance of an active learning framework and a fully supervised approach were investigated to study how active learning reduces the annotation effort while achieving the same effectiveness as a supervised approach. Conditional random fields as the supervised method, and least confidence and information density as 2 selection criteria for active learning framework were used. The effect of incremental learning vs standard learning on the robustness of the models within the active learning framework with different selection criteria was also investigated. The following 2 clinical data sets were used for evaluation: the Informatics for Integrating Biology and the Bedside/Veteran Affairs (i2b2/VA) 2010 natural language processing challenge and the Shared Annotated Resources/Conference and Labs of the Evaluation Forum (ShARe/CLEF) 2013 eHealth Evaluation Lab. RESULTS: The annotation effort saved by active learning to achieve the same effectiveness as supervised learning is up to 77%, 57%, and 46% of the total number of sequences, tokens, and concepts, respectively. Compared with the random sampling baseline, the saving is at least doubled. CONCLUSION: Incremental active learning is a promising approach for building effective and robust medical concept extraction models while significantly reducing the burden of manual annotation.

A comprehensive study of named entity recognition in Chinese clinical text.

OBJECTIVE: Named entity recognition (NER) is one of the fundamental tasks in natural language processing. In the medical domain, there have been a number of studies on NER in English clinical notes; however, very limited NER research has been carried out on clinical notes written in Chinese. The goal of this study was to systematically investigate features and machine learning algorithms for NER in Chinese clinical text. MATERIALS AND METHODS: We randomly selected 400 admission notes and 400 discharge summaries from Peking Union Medical College Hospital in China. For each note, four types of entity-clinical problems, procedures, laboratory test, and medications-were annotated according to a predefined guideline. Two-thirds of the 400 notes were used to train the NER systems and one-third for testing. We investigated the effects of different types of feature including bag-of-characters, word segmentation, part-of-speech, and section information, and different machine learning algorithms including conditional random fields (CRF), support vector machines (SVM), maximum entropy (ME), and structural SVM (SSVM) on the Chinese clinical NER task. All classifiers were trained on the training dataset and evaluated on the test set, and micro-averaged precision, recall, and F-measure were reported. RESULTS: Our evaluation on the independent test set showed that most types of feature were beneficial to Chinese NER systems, although the improvements were limited. The system achieved the highest performance by combining word segmentation and section information, indicating that these two types of feature complement each other. When the same types of optimized feature were used, CRF and SSVM outperformed SVM and ME. More specifically, SSVM achieved the highest performance of the four algorithms, with F-measures of 93.51% and 90.01% for admission notes and discharge summaries, respectively.

Discussion on fundamental medical concept enhancing the overall quality of medical students in the department of geriatrics during clinical practice / 中华医学教育探索杂志

It is important to explore the fundamental medical concepts which can enhance the overall quality of medical students in the department of geriatrics during clinical practice. These funda-mental medical concepts include medical humanistic spirit,holistic medicine,health management and patient-physician communication. Specific measures include improving emotional communication of clini-cal interns in department of geriatrics with elderly patients,training student's thinking as a whole towards multiple system disease in the elderly,training students to assess and manage elderly patients from a vari-ety of perspectives and improving doctor-patient communication skills by routine clinical teaching and teaching ward round. All these concepts will help improve the working ability and medical ethics of clini-cal interns and enable them to adapt to the clinical work quickly. So they can become qualified doctors.