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Using openEHR Archetypes for Automated Extraction of Numerical Information from Clinical Narratives
(2019)
Up to 80% of medical information is documented by unstructured data such as clinical reports written in natural language. Such data is called unstructured because the information it contains cannot be retrieved automatically as straightforward as from structured data. However, we assume that the use of this flexible kind of documentation will remain a substantial part of a patient’s medical record, so that clinical information systems have to deal appropriately with this type of information description. On the other hand, there are efforts to achieve semantic interoperability between clinical application systems through information modelling concepts like HL7 FHIR or openEHR. Considering this, we propose an approach to transform unstructured documented information into openEHR archetypes. Furthermore, we aim to support the field of clinical text mining by recognizing and publishing the connections between openEHR archetypes and heterogeneous phrasings. We have evaluated our method by extracting the values to three openEHR archetypes from unstructured documents in English and German language.
Radioisotope-guided sentinel lymph node dissection (sLND) has shown high diagnostic reliability in prostate (PCa) and other cancers. To overcome the limitations of the radioactive tracers, magnetometer-guided sLND using superparamagnetic iron oxide nanoparticles (SPIONs) has been successfully used in PCa. This prospective study (SentiMag Pro II, DRKS00007671) determined the diagnostic accuracy of magnetometer-guided sLND in intermediate- and high-risk PCa. Fifty intermediate- or high-risk PCa patients (prostate-specific antigen (PSA) >= 10 ng/mL and/or Gleason score >= 7; median PSA 10.8 ng/mL, IQR 7.4–19.2 ng/mL) were enrolled. After the intraprostatic SPIONs injection a day earlier, patients underwent magnetometer-guided sLND and extended lymph node dissection (eLND, followed by radical prostatectomy. SLNs were detected in in vivo and in ex vivo samples. Diagnostic accuracy of sLND was assessed using eLND as the reference. SLNs were detected in all patients (detection rate 100%), with 447 sentinel lymph nodes SLNs (median 9, IQR 6–12) being identified and 966 LNs (median 18, IQR 15–23) being removed. Thirty-six percent (18/50) of patients had LN metastases (median 2, IQR 1–3). Magnetometer-guided sLND had 100% sensitivity, 97.0% specificity, 94.4% positive predictive value, 100% negative predictive value, 0.0% false negative rate, and 3.0% additional diagnostic value (LN metastases only in SLNs outside the eLND template). In vivo, one positive SLN/LN-positive patient was missed, resulting in a sensitivity of 94.4%. In conclusion, this new magnetic sentinel procedure has high accuracy for nodal staging in intermediate- and high-risk PCa. The reliability of intraoperative SLN detection using this magnetometer system requires verification in further multicentric studies.
We present a simple method to find topics in user reviews that accompany ratings for products or services. Standard topic analysis will perform sub-optimal on such data since the word distributions in the documents are not only determined by the topics but by the sentiment as well. We reduce the influence of the sentiment on the topic selection by adding two explicit topics, representing positive and negative sentiment. We evaluate the proposed method on a set of over 15,000 hospital reviews. We show that the proposed method, Latent Semantic Analysis with explicit word features, finds topics with a much smaller bias for sentiments than other similar methods.
Lemmatization is a central task in many NLP applications. Despite this importance, the number of (freely) available and easy to use tools for German is very limited. To fill this gap, we developed a simple lemmatizer that can be trained on any lemmatized corpus. For a full form word the tagger tries to find the sequence of morphemes that is most likely to generate that word. From this sequence of tags we can easily derive the stem, the lemma and the part of speech (PoS) of the word. We show (i) that the quality of this approach is comparable to state of the art methods and (ii) that we can improve the results of Part-of-Speech (PoS) tagging when we include the morphological analysis of each word.
Mastitis poses a considerable threat to productivity and to animal welfare on modern dairy farms. However, the common way of antibiotic treatment does not always lead to a cure. Unsuccessful cures can, among other reasons, occur due to biofilm formation of the causative agent. This has attracted interest from researchers to introduce promising alternative therapeutic approaches, such as the use of beneficial lactic acid bacteria (LAB). In fact, using LAB for treating mastitis probably requires the formation of a beneficial biofilm by the probiotic bacteria. The present study investigated the ability of five LAB strains, selected on the basis of results from previous studies, to remove and to replace pathogenic biofilms in vitro. For this purpose, Staphylococcus (S.) aureus ATCC 12,600 and two strains—S. xylosus (35/07) and S. epidermidis (575/08)—belonging to the group of coagulase negative staphylococci (CNS) were allowed to form biofilms in a 96-well plate. Subsequently, the LAB were added to the well. The biofilm challenge was evaluated by scraping off and suspending the biofilm cells, followed by a plate count of serial dilutions using selective media. All the LAB strains successfully removed the staphylococcal biofilms. However, only Lactobacillus (L.) rhamnosus ATCC 7469 and L. plantarum 2/37 formed biofilms of their own to replace the pathogenic ones.
Background:
Promoting patient and occupational safety are two key challenges for hospitals. When aiming to improve these two outcomes synergistically, psychosocial working conditions, leadership by hospital management and supervisors, and perceptions of patient and occupational safety climate have to be considered. Recent studies have shown that these key topics are interrelated and form a critical foundation for promoting patient and occupational safety in hospitals. So far, these topics have mainly been studied independently from each other. The present study investigated hospital staffs’ perceptions of four different topics: (1) psychosocial working conditions, (2) leadership, (3) patient safety climate, and (4) occupational safety climate. We present results from a survey in two German university hospitals aiming to detect differences between nurses and physicians.
Methods:
We performed a cross-sectional study using a standardized paper-based questionnaire. The survey was conducted with nurses and physicians to assess the four topics. The instruments mainly consisted of scales of the German version of the COPSOQ (Copenhagen Psychosocial Questionnaire), one scale of the Copenhagen Burnout Inventory (CBI), scales to assess leadership and transformational leadership, scales to assess patient safety climate using the Hospital Survey on Patient Safety Culture (HSPSC), and analogous items to assess occupational safety climate.
Results:
A total of 995 completed questionnaires out of 2512 distributed questionnaires were returned anonymously. The overall response rate was 39.6%. The sample consisted of 381 physicians and 567 nurses. We found various differences with regard to the four topics. In most of the COPSOQ and the HSPSC-scales, physicians rated psychosocial working conditions and patient safety climate more positively than nurses. With regard to occupational safety, nurses
indicated higher occupational risks than physicians.
Conclusions:
The WorkSafeMed study combined the assessment of the four topics psychosocial working conditions, leadership, patient safety climate, and occupational safety climate in hospitals. Looking at the four topics provides an overview of where improvements in hospitals may be needed for nurses and physicians. Based on these results,
improvements in working conditions, patient safety climate, and occupational safety climate are required for health care professionals in German university hospitals – especially for nurses.
The objective of this study was to investigate the association between teat skin colonization and intramammary infection (IMI) with Staphylococcus aureus or Streptococcus agalactiae at the quarter level in herds with automatic milking systems. Milk and teat skin samples from 1,142 quarters were collected from 300 cows with somatic cell count >200,000 cells/mL from 8 herds positive for Strep. agalactiae. All milk and teat skin samples were cultured on calf blood agar and selective media. A subset of samples from 287 quarters was further analyzed using a PCR assay (Mastit4 PCR; DNA Diagnostic A/S, Risskov, Denmark). Bacterial culture detected Staph. aureus in 93 (8.1%) of the milk samples and 75 (6.6%) of the teat skin samples. Of these, 15 (1.3%) quarters were positive in both the teat skin and milk samples. Streptococcus agalactiae was cultured in 84 (7.4%) of the milk samples and 4 (0.35%) of the teat skin samples. Of these, 3 (0.26%) quarters were positive in both the teat skin and milk samples. The PCR detected Staph. aureus in 29 (10%) of the milk samples and 45 (16%) of the teat skin samples. Of these, 2 (0.7%) quarters were positive in both the teat skin and milk samples. Streptococcus agalactiae was detected in 40 (14%) of the milk samples and 51 (18%) of the teat skin samples. Of these, 16 (5.6%) quarters were positive in both the teat skin and milk samples. Logistic regression was used to investigate the association between teat skin colonization and IMI at the quarter level. Based on bacterial culture results, teat skin colonization with Staph. aureus resulted in 7.8 (95% confidence interval: 2.9; 20.6) times higher odds of Staph. aureus IMI, whereas herd was observed as a major confounder. However, results from the PCR analyses did not support this association. Streptococcus agalactiae was isolated from the teat skin with both PCR and bacterial culture, but the number of positive teat skin samples detected by culture was too low to proceed with further analysis. Based on the PCR results, Strep. agalactiae on teat skin resulted in 3.8 (1.4; 10.1) times higher odds of Strep. agalactiae IMI. Our results suggest that Staph. aureus and Strep. agalactiae on teat skin may be a risk factor for IMI with the same pathogens. Focus on proper teat skin hygiene is therefore recommended also in AMS.
The NOA project collects and stores images from open access publications and makes them findable and reusable. During the project a focus group workshop was held to determine whether the development is addressing researchers’ needs. This took place before the second half of the project so that the results could be considered for further development since addressing users’ needs is a big part of the project. The focus was to find out what content and functionality they expect from image repositories.
In a first step, participants were asked to fill out a survey about their images use. Secondly, they tested different use cases on the live system. The first finding is that users have a need for finding scholarly images but it is not a routine task and they often do not know any image repositories. This is another reason for repositories to become more open and reach users by integrating with other content providers. The second finding is that users paid attention to image licenses but struggled to find and interpret them while also being unsure how to cite images. In general, there is a high demand for reusing scholarly images but the existing infrastructure has room to improve.
This feasibility study investigates the flexural properties of biocomposites containing woven flax textiles (plain, twill, satin) and woven twill patterned hybrid textiles containing flax-/glass or flax-/carbon mixture for lightweight applications. Synthetic fibers are integrated as weft and flax fibers are integrated as warp yarns using a double-rapier weaving machine with a Jacquard attachment. The corresponding biocomposites are manufactured via vacuum infusion process using a biobased epoxy resin as a matrix. The manufactured biocomposites are analyzed with regard to their density and flexural properties. The results show that the use of hybrid textiles offers a promising solution for the manufacture of biocomposites with a higher biobased content and significantly improved flexural properties. Furthermore, the introduction of high-performance synthetic fibers in textiles enables the manufacture of biocomposites with an isotropic mechanical performance.
The paper sheds light on the change in the concept of obedience within the Society of Jesus since the 1960s. In the aftermath of the Second Vatican Council, a so-called crisis of authority and obedience took place in the Catholic Church and the religious orders. As a consequence, the notions of responsibility and conscience came to the fore in the Jesuit definition of obedience. The religious concept of obedience, that is the obedience towards God, was reassessed as a service to humanity. The paper analyzes how the change in the concept of obedience gave rise to the promotion of social justice, which the Society of Jesus proclaimed at General Congregation 32 in 1974/75. By including the promotion of social justice into their central mission, Jesuits not only fundamentally transformed their self-conception, but also their ethical values. The paper argues that the pursuit of social justice became a form of religious obedience.