RepoMed (Medizinische Hochschule Hannover)
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Programming techniques for improving rule readability for rule-based information extraction natural language processing pipelines of unstructured and semi-structured medical texts
Get PDFBackground Extraction of medical terms and their corresponding values from semi-structured and unstructured texts of medical reports can be a time-consuming and error-prone process. Methods of natural language processing (NLP) can help define an extraction pipeline for accomplishing a structured format transformation strategy. Objectives In this paper, we build an NLP pipeline to extract values of the classification of malignant tumors (TNM) from unstructured and semi-structured pathology reports and import them further to a structured data source for a clinical study. Our research interest is not focused on standard performance metrics like precision, recall, and F-measure on the test and validation data. We discuss how with the help of software programming techniques the readability of rule-based (RB) information extraction (IE) pipelines can be improved, and therefore minimize the time to correct or update the rules, and efficiently import them to another programming language. Methods The extract rules were manually programmed with training data of TNM classification and tested in two separate pipelines based on design specifications from domain experts and data curators. Firstly we implemented each rule directly in one line for each extraction item. Secondly, we reprogrammed them in a readable fashion through decomposition and intention-revealing names for the variable declaration. To measure the impact of both methods we measure the time for the fine-tuning and programming of the extractions through test data of semi-structured and unstructured texts. Results We analyze the benefits of improving through readability of the writing of rules, through parallel programming with regular expressions (REGEX), and the Apache Uima Ruta language (AURL). The time for correcting the readable rules in AURL and REGEX was significantly reduced. Complicated rules in REGEX are decomposed and intention-revealing declarations were reprogrammed in AURL in 5 min. Conclusion We discuss the importance of factor readability and how can it be improved when programming RB text IE pipelines. Independent of the features of the programming language and the tools applied, a readable coding strategy can be proven beneficial for future maintenance and offer an interpretable solution for understanding the extraction and for transferring the rules to other domains and NLP pipelines
Neural correlates of the attention training technique as used in metacognitive therapy: a randomized sham-controlled fMRI study in healthy volunteers
Get PDFIntroduction The Attention Training Technique (ATT) developed as part of metacognitive therapy is a psychotherapeutic treatment method used to enhance top-down attentional flexibility and control. This study investigated potential neurocognitive changes due to ATT and its underlying neural mechanisms using pre-to-post functional magnetic resonance imaging (fMRI). Materials and methods Fifty-four healthy participants were subjected to a randomized, sham-controlled attention training and evaluated using a neurocognitive test battery that partly took place in an fMRI environment. Participants received two doses ATT or sham ATT daily for 1 week. On day eight, all subjects completed the neurocognitive test battery again. Results After the training, the ATT group showed a significant improvement in reaction times regarding attentional disengagement compared to the sham ATT group. fMRI data showed decreased levels of activation in the anterior cingulate cortex (ACC) when comparing the ATT group to the sham ATT group during attentional disengagement post intervention. No ATT > sham ATT effects were found regarding selective auditory attention, working memory performance and inhibitory control. Discussion These findings putatively indicate that ATT facilitates faster attention allocation and increased attentional flexibility in healthy subjects. The fMRI results suggest this ATT-dependent improvement is accompanied by reduced ACC activity, indicating a more flexible attentional state
Data from children after liver transplantation with regard to measles immunity
No full textData from children who underwent liver transplantation at Hannover Medical School (MHH, Germany) and were followed up between January 2021 and December 2022. Including numbers of measles vaccine doses prior to transplant and measles IgG [AU/ml] (measured at Institute of Virology at MHH) after transplantation. Patient data was anonymized
Bioinformatische Analyse des perilymphatischen Proteoms zur Erstellung einer Landkarte des menschlichen Innenohrs
Get PDFPushing the boundaries of innovation: the potential of ex vivo organ perfusion from an interdisciplinary point of view
Get PDFEx vivo machine perfusion (EVMP) is an emerging technique for preserving explanted solid organs with primary application in allogeneic organ transplantation. EVMP has been established as an alternative to the standard of care static-cold preservation, allowing for prolonged preservation and real-time monitoring of organ quality while reducing/preventing ischemia-reperfusion injury. Moreover, it has paved the way to involve expanded criteria donors, e.g., after circulatory death, thus expanding the donor organ pool. Ongoing improvements in EVMP protocols, especially expanding the duration of preservation, paved the way for its broader application, in particular for reconditioning and modification of diseased organs and tumor and infection therapies and regenerative approaches. Moreover, implementing EVMP for in vivo-like preclinical studies improving disease modeling raises significant interest, while providing an ideal interface for bioengineering and genetic manipulation. These approaches can be applied not only in an allogeneic and xenogeneic transplant setting but also in an autologous setting, where patients can be on temporary organ support while the diseased organs are treated ex vivo, followed by reimplantation of the cured organ. This review provides a comprehensive overview of the differences and similarities in abdominal (kidney and liver) and thoracic (lung and heart) EVMP, focusing on the organ-specific components and preservation techniques, specifically on the composition of perfusion solutions and their supplements and perfusion temperatures and flow conditions. Novel treatment opportunities beyond organ transplantation and limitations of abdominal and thoracic EVMP are delineated to identify complementary interdisciplinary approaches for the application and development of this technique
Improving mental well-being in psychocardiology-a feasibility trial for a non-blended web application as a brief metacognitive-based intervention in cardiovascular disease patients.
Get PDFBackground Many patients with cardiovascular disease also show a high comorbidity of mental disorders, especially such as anxiety and depression. This is, in turn, associated with a decrease in the quality of life. Psychocardiological treatment options are currently limited. Hence, there is a need for novel and accessible psychological help. Recently, we demonstrated that a brief face-to-face metacognitive therapy (MCT) based intervention is promising in treating anxiety and depression. Here, we aim to translate the face-to-face approach into digital application and explore the feasibility of this approach. Methods We translated a validated brief psychocardiological intervention into a novel non-blended web app. The data of 18 patients suffering from various cardiac conditions but without diagnosed mental illness were analyzed after using the web app over a two-week period in a feasibility trial. The aim was whether a non-blended web app based MCT approach is feasible in the group of cardiovascular patients with cardiovascular disease. Results Overall, patients were able to use the web app and rated it as satisfactory and beneficial. In addition, there was first indication that using the app improved the cardiac patients' subjectively perceived health and reduced their anxiety. Therefore, the approach seems feasible for a future randomized controlled trial. Conclusion Applying a metacognitive-based brief intervention via a non-blended web app seems to show good acceptance and feasibility in a small target group of patients with CVD. Future studies should further develop, improve and validate digital psychotherapy approaches, especially in patient groups with a lack of access to standard psychotherapeutic care
Composition of ex vivo perfusion solutions and kinetics define differential cytokine/chemokine secretion in a porcine cardiac arrest model of lung preservation
Get PDFBackground Ex vivo lung perfusion (EVLP) uses continuous normothermic perfusion to reduce ischemic damage and to improve post-transplant outcomes, specifically for marginal donor lungs after the donation after circulatory death. Despite major efforts, the optimal perfusion protocol and the composition of the perfusate in clinical lung transplantation have not been identified. Our study aims to compare the concentration levels of cytokine/chemokine in different perfusion solutions during EVLP, after 1 and 9 h of cold static preservation (CSP) in a porcine cardiac arrest model, and to correlate inflammatory parameters to oxygenation capacities. Methods Following cardiac arrest, the lungs were harvested and were categorized into two groups: immediate (I-EVLP) and delayed EVLP (D-EVLP), after 1 and 9 h of CSP, respectively. The D-EVLP lungs were perfused with either Steen or modified Custodiol-N solution containing only dextran (CD) or dextran and albumin (CDA). The cytokine/chemokine levels were analyzed at baseline (0 h) and after 1 and 4 h of EVLP using Luminex-based multiplex assays. Results Within 4 h of EVLP, the concentration levels of TNF-α, IL-6, CXCL8, IFN-γ, IL-1α, and IL-1β increased significantly (P < 0.05) in all experimental groups. The CD solution contained lower concentration levels of TNF-α, IL-6, CXCL8, IFN-γ, IL-2, IL-12, IL-10, IL-4, IL-1RA, and IL-18 (P < 0.05) compared with those of the Steen solution. The concentration levels of all experimental groups have correlated negatively with the oxygenation capacity values (P < 0.05). Protein concentration levels did not reach statistical significance for I-EVLP vs. D-EVLP and CD vs. CDA solutions. Conclusion In a porcine cardiac arrest model, a longer period of CSP prior to EVLP did not result in an enhanced protein secretion into perfusates. The CD solution reduced the cytokine/chemokine secretion most probably by iron chelators and/or by the protecting effects of dextran. Supplementing with albumin did not further reduce the cytokine/chemokine secretion into perfusates. These findings may help in optimizing the preservation procedure of the lungs, thereby increasing the donor pool of organs
