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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.
The usage of microservices promises a lot of benefits concerning scalability and maintainability, rewriting large monoliths is however not always possible. Especially in scientific projects, pure microservice architectures are therefore not feasible in every project. We propose the utilization of microservice principles for the construction of microsimulations for urban transport. We present a prototypical architecture for the connection of MATSim and AnyLogic, two widely used simulation tools in the context of urban transport simulation. The proposed system combines the two tools into a singular tool supporting civil engineers in decision making on innovative urban transport concepts.
Background:
Huntington’s disease (HD) is a rare, genetic, neurodegenerative and ultimately fatal disease with no cure or progression-delaying treatment currently available. HD is characterized by a triad of cognitive, behavioural and motor symptoms. Evidence on epidemiology and management of HD is limited, especially for Germany. This study aims to estimate the incidence and prevalence of HD and analyze the current routine care based on German claims data.
Methods:
The source of data was a sample of the Institute for Applied Health Research Berlin (InGef) Research Database, comprising data of approximately four million insured persons from approximately 70 German statutory health insurances. The study was conducted in a retrospective cross-sectional design using 2015 and 2016 as a two-year observation period. At least two outpatient or inpatient ICD-10 codes for HD (ICD-10: G10) during the study period were required for case identification. Patients were considered incident if no HD diagnoses in the 4 years prior to the year of case identification were documented. Information on outpatient drug dispensations, medical aids and remedies were considered to describe the current treatment situation of HD patients.
Results:
A 2-year incidence of 1.8 per 100,000 persons (95%-Confidence interval (CI): 1.4–2.4) and a 2-year period prevalence of 9.3 per 100,000 persons (95%-CI: 8.3–10.4) was observed. The prevalence of HD increased with advancing age, peaking at 60–69 years (16.8 per 100,000 persons; 95%-CI: 13.4–21.0) and decreasing afterwards.
The most frequently observed comorbidities and disease-associated symptoms in HD patients were depression (42.9%), dementia (37.7%), urinary incontinence (32.5%), extrapyramidal and movement disorders (30.5%), dysphagia (28.6%) and disorders of the lipoprotein metabolism (28.2%).
The most common medications in HD patients were antipsychotics (66.9%), followed by antidepressants (45.1%). Anticonvulsants (16.6%), opioids (14.6%) and hypnotics (9.7%) were observed less frequently.
Physical therapy was the most often used medical aid in HD patients (46.4%). Nursing services and speech therapy were used by 27.9 and 22.7% of HD patients, respectively, whereas use of psychotherapy was rare (3.2%).
Conclusions:
Based on a representative sample, this study provides new insights into the epidemiology and routine care of HD patients in Germany, and thus, may serve as a starting point for further research.
The topic of electromagnetic compatibility (EMC) remains an important aspect during the planning, installation and operation of automation systems. Communication networks, such as PROFIBUS and PROFINET, are known to be robust and reliable transmission systems. Nevertheless, it is important that a number of fundamental principles needs to be observed to ensure fault-free operation over a long plant lifetime. This paper first describes a number of principles of EMC. On the basis of these principles, six recommendations for action are then developed which are to be observed during the planning of an automation system for use in the manufacturing industry. Finally, an overview is provided of future work for systems in the process industry.
Research into new forms of care for complex chronic diseases requires substantial efforts in the collection, storage, and analysis of medical data. Additionally, providing practical support for those who coordinate the actual care management process within a diversified network of regional service providers is also necessary. For instance, for stroke units, rehabilitation partners, ambulatory actors, as well as health insurance funds. In this paper, we propose the concept of comprehensive and practical receiver-oriented encryption (ROE) as a guiding principle for such data-intensive, research-oriented case management systems, and
illustrate our concept with the example of the IT infrastructure of the project STROKE OWL.
Background: Antimicrobial resistance has become a serious global problem. A potential post-antibiotic era is threatening present and future medical advances. In Pakistan, the usage of antibiotic is unnecessarily high and due to over exposure to these drugs, bacteria are developing resistance against these drugs. It is necessary to improve public awareness about the rational use of antibiotics in order to bring a change in consumer’s behaviour. Therefore, present study was undertaken to assess the existing knowledge, attitude and practices related to antibiotic usage among university students.
Methods: A cross-sectional study was carried out among university students from Karachi, Pakistan during May-June 2018. 200 students were approached to participate in the study of which 159 agreed to participate (males: 70, females: 89). Pretested questionnaire was distributed to the study subjects and the collected data was analyzed using IBM SPSS version 23.
Results: Substantial number of (33% and 50%) participants were unaware about the differences in antibiotic: anti-inflammatory drugs and antibiotic: antipyretics respectively. 29% of the participants thought it is right to stop antibiotics only based on symptomatic improvement. Thirty nine percent and eighty three percent participants believed that antibiotics should always be prescribed to treat flu like symptoms and pneumonia respectively.
Conclusions: Participants demonstrated average knowledge about antibiotics. Similarly, their attitude and practice toward antibiotic use was associated with misconceptions. An educational intervention is necessary to make them aware about rational use of antibiotics.
Background: Oral cancers (OC) are malignant lesions occurring in the oral cavity that include squamous cell carcinomas (SCC), salivary gland and odontogenic neoplasms. Even though it is the eighth most common malignancy globally but in Pakistan it is the second commonest type of cancer. Lack of awareness about ill-effects of preventable risk factors of oral cancer increases the burden of disease due to the associated high cost of treatment, permanent impairment and high mortality. Hence, awareness can be very helpful in prevention, control and early diagnosis of oral cancer.
Methods: A cross-sectional study was carried out among university students from Karachi, Pakistan during April to May 2018. Three hundred students were approached to participate in the study of which 277 agreed to participate. Pretested questionnaire was distributed and collected data was analysed using IBM SPSS version 23.
Results: There were 125 (45%) males and 152 (55%) females in the study and response rate was 94%. Sixty one percent (154/250) respondents correctly identified smoking, and tobacco chewing as possible causes of oral cancer. Almost one third (74%; 184/250) respondents correctly responded that oral cancer does not spread from person to person through touch or speaking. Sixty six percent (164/250) respondents believed that oral cancer is curable. Mean score of knowledge was higher in females (61%) than males (53%). Significantly higher number of females compared to male participants answered correctly to questions regarding cause of oral cancer, spread of disease and occurrence of oral cancer in AIDS patients.
Conclusions: Participants showed poor knowledge about oral cancer. Female participants showed better knowledge compared to male counterparts. Details about oral cancer should be incorporated in the university curriculum and periodic awareness programs should be organized for students.
Background: India has the third largest HIV epidemic in the world. The Indian epidemic is characterized by low levels in the general population and elevated concentrations among high-risk groups. The present study was planned to determine the awareness of HIV among students from Mumbai University.
Methods: A cross-sectional study was carried out among students from Mumbai University, India during May–June 2017. Two hundred and fifty students were approached to participate in the study of which 199 agreed to participate (males: 132; females: 67). Pretested questionnaire was distributed and collected data was analyzed using IBM SPSS version 23.
Results: Study participants had high knowledge (86%) and attitude score (87%). There was no significant difference between males and female participants for attitude and knowledge, except for one question regarding knowledge about HIV transmission via breastfeeding to child.
Conclusions: Present study showed that there are no misconceptions or negative attitudes regarding HIV among students. A longitudinal study with a larger sample size across India is recommended for further investigation.
Background:
In order to prevent child abuse, instruments measuring child abuse potential (CAP) need to be appropriate, reliable and valid.
Objective:
This study aimed to confirm the 6-factor structure of the Brief Child Abuse Potential Inventory (BCAPI) in a German sample of mothers and fathers, and to examine longitudinal predictors of CAP.
Participants and setting:
Two waves of data were collected from 197 mothers and 191 fathers of children aged 10–21 months for the “Kinder in Deutschland–KiD 0–3” in-depth study. Families were stratified based on prior self-report data for screening purposes.
Methods:
138 fathers and 147 mothers were included in the analysis (invalid: 25% mothers, 30% fathers). First, validity of reporting was examined. Second, confirmatory factor analysis (CFA) was employed to assess factor structure. Third, internal reliability and criterion validity were examined. Finally, multivariate poisson regressions investigated longitudinal predictors of CAP in mothers.
Results:
A previously established six-factor structure was confirmed for mothers but not fathers. CFA failed for fathers due to large numbers of variables with zero variance. For mothers, internal consistency and criterion validity were good. BCAPI score at follow-up was associated with baseline BCAPI score (β= 00.08), stress (β= 0.06), education (β=-0.19) and alcohol use(β= .58).
Conclusions:
Findings confirm the six-factor structure of the BCAPI among German mothers. The clinical use of the BCAPI in fathers is not recommended as it might produce data that are hard to interpret. Further research with fathers is needed to establish if this is due to limitations with this dataset or with the questionnaire.
Targeted panel sequencing in pediatric primary cardiomyopathy supports a critical role of TNNI3
(2019)
The underlying genetic mechanisms and early pathological events of children with primary cardiomyopathy (CMP) are insufficiently characterized. In this study, we aimed to characterize the mutational spectrum of primary CMP in a large cohort of patients ≤18 years referred to a tertiary center. Eighty unrelated index patients with pediatric primary CMP underwent genetic testing with a panel-based next-generation sequencing approach of 89 genes. At least one pathogenic or probably pathogenic variant was identified in 30/80 (38%) index patients. In all CMP subgroups, patients carried most frequently variants of interest in sarcomere genes suggesting them as a major contributor in pediatric primary CMP. In MYH7, MYBPC3, and TNNI3, we identified 18 pathogenic/probably pathogenic variants (MYH7 n = 7, MYBPC3 n = 6, TNNI3 n = 5, including one homozygous (TNNI3 c.24+2T>A) truncating variant. Protein and transcript level analysis on heart biopsies from individuals with homozygous mutation of TNNI3 revealed that the TNNI3 protein is absent and associated with upregulation of the fetal isoform TNNI1. The present study further supports the clinical importance of sarcomeric mutation-not only in adult-but also in pediatric primary CMP. TNNI3 is the third most important disease gene in this cohort and complete loss of TNNI3 leads to severe pediatric CMP.
In this study, we investigated injection molded wood-polypropylene composites based on various wood sources and their decay resistance against white rot (Trametes versicolor) and brown rot (Coniophora puteana) in a laboratory test according to EN 15534-1:2014. The manufactured composites consisted of poplar (Populus spp.), willow (Salix spp.), European beech (Fagus sylvatica L.), Norway spruce (Picea abies (L.) H. Karst.), and a commercial wood source (Arbocel® C100), respectively. All formulations were compounded on a co-rotating twin screw extruder and subsequently injection molded to wood–PP specimens with a wood content of 60% or 70% by weight. It was found that the test procedure had a significant effect on the mechanical properties. Loss in mechanical properties was primarily caused by moisture and less by fungal decay. Moisture caused a loss in the modulus of rupture and modulus of elasticity of 34 to 45% and 29 to 73%, respectively. Mean mass and wood mass losses were up to a maximum of 3.7% and 5.3%, respectively. The high resistance against fungal decay was generally attributed to the encapsulation of wood by the polymer matrix caused by sample preparation, and enhanced by reduced moisture uptake during the preconditioning procedure. Notable differences with respect to the wood particle source and decay fungi were also observed. Structural characterization confirmed the decay pattern of the fungi such as void cavities close the surface and the deposition of calcium oxalates.