Qualifikationsarbeiten
http://edoc.rki.de/176904/47
2024-03-29T12:48:55ZClassifying Emergency Department Data to Improve Syndromic Surveillance: From Mixed Data Types to ICD Codes and Syndromes
http://edoc.rki.de/176904/10753
Classifying Emergency Department Data to Improve Syndromic Surveillance: From Mixed Data Types to ICD Codes and Syndromes
Wagner, Birte
Syndromic surveillance systems are used to monitor public health and enable a timely outbreak
detection. Emergency department (ED) data can serve as an important data source for
syndromic surveillance, but a high amount of missing diagnosis codes can make analyses
relying on this information impossible. This study aims at enhancing an ED dataset from a
piloted syndromic surveillance system in Germany to enable the monitoring of an influenza-like
illness (ILI) syndrome.
Routinely collected data from one ED containing mixed-type variables are analysed and
two different approaches are implemented to deal with the missing data. Within the first
approach, the missing diagnosis codes are imputed by predicting them from the remaining
variables, using a multi-class naive Bayes classifier and a deep learning imputation package. In
the second approach, a logistic regression model and a binary naive Bayes classifier are used to
predict the ILI syndrome from all variables except the diagnosis code. The resulting ILI cases
are evaluated on time series level with regard to seasonal patterns.
The diagnosis codes were predicted from mixed-type input variables with sufficient precision
(34.37% F1-measure in the best model). By taking into account the hierarchical structure of
the ICD-10 codes, the performance was improved. Predicting the ILI syndrome independent
of the diagnosis code from the remaining variables worked well (39.63% F1-measure in the
best model) and the predictions showed medical similarity with the ILI syndrome. The models
differed in their sensitivity of including cases, which can be adjusted by changing the threshold
of the classifiers. The resulting ILI cases from all models were positively correlated with the
reference cases on a time series basis (r = 0.865 for best model) and were comparable with an
external data source, a surveillance of severe acute respiratory infections (SARI) (r = 0.867
for best model).
The present study showed that the ED dataset can be enhanced to enable the syndromic
surveillance of an ILI syndrome based on the diagnosis codes, even if this variable is missing.
Additionally, a flexible case definition for an ILI syndrome was developed that is independent
of the diagnosis code and the underlying generic method can be applied to other syndromes
as well.
2023-02-16T00:00:00ZUsing routine emergency department data for syndromic surveillance of acute alcohol intoxication
http://edoc.rki.de/176904/9838
Using routine emergency department data for syndromic surveillance of acute alcohol intoxication
Schlump, Carmen
Background:
The prevalence and intensity of alcohol use varies among subgroups in the population and changes over time. Routine emergency department data provide a potential for monitoring mental health use cases to gather information on frequencies and distri-butions of specified health events in real time. For this purpose, the development of syndrome definitions for the continuous recording and detection of acute changes in alcohol-related visits and acute alcohol intoxications was explored.
Methods:
Routinely collected data from 18 emergency departments in Germany were analysed. Syndrome definitions were developed by combining chief complaints and diagnoses to portray alcohol-related health events presenting to the emergency department. Identified cases were described by characteristics of their distributions and compared to another data source of inpatient health care. Further, cases were presented over time and by separate time period before and during the COVID-19 pandemic.
Results:
From a total of 2,123,492 emergency department attandances, 18,270 cases (0.86%) were identified as alcohol-related visits and 14,141 (0.67%) as acute alcohol intoxica-tions for the observation period between 1 January 2018 to 2 May 2021. Among all acute alcohol intoxications, 71.8% were male and most cases presented in the age category of 45-54 years (20.0%). The syndrome definition continuously recorded cases and displayed acute changes due to the COVID-19 pandemic as well as trends in patient characteristics of identified acute alcohol intoxications.
Conclusion:
The potential and proof of principle for syndromic surveillance of alcohol-related visits, especially acute alcohol intoxications, using emergency department data was demon-strated. The syndrome definition to identify acute alcohol intoxications can be applied for various surveillance purposes. This systematic data collection provides a first foun-dation for timley information on patterns and changes of alcohol consumption to sup-port prevention and intervention efforts in reducing alcohol-related harm.
2022-06-20T00:00:00ZSyndromic surveillance using emergency department data for the monitoring of unspecific acute gastrointestinal infections
http://edoc.rki.de/176904/9067
Syndromic surveillance using emergency department data for the monitoring of unspecific acute gastrointestinal infections
Schranz, Madlen
Background: Timely detection is a prerequisite for the successful prevention and management of gastrointestinal infections. Complimentary to already existing surveillance systems, syndromic surveillance can be used for that purpose. This study analyses data from a piloted syndromic surveillance system in Germany, aiming at the definition of syndromes and the exploration of the system’s ability to monitor seasonal patterns and short-time aberrations of gastrointestinal infections. Methods: Routinely collected data from emergency departments were analysed. Within this paper, two Syndromic Surveillance Health Indicators (SySHI) were created in order to combine complaint information. Syndromes were defined based on a combination of SySHI and a set of ICD-10 diagnoses. Identified cases were stratified by emergency department, age and isolation status. Time series were used to analyse seasonal patterns and combined with an algorithm to perform aberration detection. Results: Between 2012 and 2019 data on 935,032 visits of ten emergency departments were analysed. Of those, 2.7% were identified as cases according to the Syndromic Surveillance Health Indicator. The syndrome definition “unspecific GI without bleeding” identified 3,329 and the syndrome definition “bloody diarrhoea” 589 cases. Time series analysis showed seasonal patterns with peaks in the winter months for the first syndrome. Exemplary for one hospital a total of six signals was created by the algorithm. Conclusion: Emergency department data can be used to define appropriate syndromes for the detection of seasonal patterns and aberrations in case numbers. Syndromes incorporating information on chief complaint and diagnosis were able to identify seasonal fluctuations of gastrointestinal infections.
2021-12-07T00:00:00ZAnalyse der Restriktion des Humanen Endogenen Retrovirus-K(HML-2) durch das Protein IFI-16
http://edoc.rki.de/176904/8426
Analyse der Restriktion des Humanen Endogenen Retrovirus-K(HML-2) durch das Protein IFI-16
Friedrich, Josephine
Ein Immunsensor für intrazelluläre DNA und viraler Restriktionsfaktor ist das IFI16-Protein. Zu Beginn dieser Arbeit erfolgte der Nachweis der 13-fachen Hemmung der Viruspartikelproduktion von HERV-K(HML-2) durch IFI16. Verwendet wurde dabei der Molekularklon eines rekonstruierten HERV-K113-Provirus, welcher ein vollständiges Provirus-Genom mit offenem Leserahmen für alle viralen Gene und intakte LTR-Sequenzen besitzt. Als Indikator für die virale Partikelproduktion diente die Aktivität der Reversen Transkriptase, die mithilfe des PERT-Assays bestimmt werden konnte. Der Austausch der U3-Region der 5‘LTR mit einem CMV-Promotor resultierte in Außerkraftsetzen der Restriktion. Aufgrund dieser Tatsache wurden im Laufe dieser Arbeit verschiedene Konstrukte generiert, die ermöglichten, die Rolle der LTRs bei der Hemmung von HERV-K113 durch IFI16 zu analysieren. Zu Beginn erfolgte hierfür das Klonieren diverser Luciferase-Konstrukte, die sowohl die Möglichkeit boten, den Effekt von IFI16 auf die alleinstehende 5’LTR und 3’LTR als auch die vollständige LTR von HERV-K113 zu untersuchen. Die Verwendung dieser Luciferase-Konstrukte resultierte jedoch nicht in der Beantwortung der Frage nach der Rolle der LTRs bei der Hemmung von HERV-K113, da keine signifikanten Unterschiede zwischen der entsprechenden Kontrolle und dem IFI16-Expressionsplamid detektiert werden konnten und des Weiteren IFI16 in einigen Zelllinien trotz hoher Transfektionsrate nicht erfolgreich exprimiert wurde. Daher wurden zur Identifikation des funktionellen Bereichs des viralen Genoms, an dem IFI16 seine hemmende Wirkung entfaltet, ergänzende HERV-K(HML-2)-Konstrukte kloniert, die ermöglichen, sukzessiv den Bereich der 5‘ LTR oder der 3’LTR einzugrenzen. Die gewonnenen Daten stützen die Annahme, dass für die Restriktion von HERV-K113 die LTR eine essenzielle Rolle spielt, waren jedoch nicht in der Lage, den dabei funktionellen Bereich des Genoms näher einzugrenzen. Zusätzlich wurden im Rahmen dieser Masterarbeit humane Zelllinien bezüglich ihrer Transfektionseffizienz und hinsichtlich ihrer Volllängen- oder Teil-IFI16-Expression untersucht. Hierbei sind besonders die überzeugenden Daten der Hek293-T und HeLa-Zellen zu erwähnen. Zudem wurde nachgewiesen, dass der Bereich des IFI16-Proteins, welcher lediglich die Pyrindomäne plus Linkerbereich umfasst, zur HERV-K(HML-2) Hemmung ausreicht. Dieser Bereich wurde abschließend in einen bicistronischen lentiviralen Vektor kloniert,
damit Reporterviren generiert und die Transduktionseffizienz verschiedener humanen Zelllinien bestimmt.; An immune sensor for intracellular DNA and viral restriction factor is the interferon-inducible protein 16 (IFI16). At the beginning of this work, the 13-fold inhibition of the viral particle production of HERV-K(HML-2) by IFI16 was demonstrated using the molecular clone of a reconstituted HERV-K113 provirus, which has a complete provirus genome with open reading frame for all viral genes and intact LTR sequences. Within this master thesis, the activity of reverse transcriptase served as an indicator of viral particle production, which could be determined by using a PERT assay. The exchange of the U3-region of the 5’LTR with a CMV-promoter resulted in the annulment of the restriction. Based on this fact, different constructs were generated during this thesis, which made it possible to analyze the role of the LTR in the inhibition of HERV-K113 by IFI16. Initially, this was done by cloning various luciferase constructs that offered the possibility to study the effect of IFI16 on the stand-alone 5'LTR and 3'LTR as well as on the complete LTR of HERV-K113. However, the use of these luciferase constructs did not result in answering the question of the role of the LTRs in inhibiting HERV-K113, as no significant differences could be detected between the corresponding control and the IFI16 expression plasmid and, further, IFI16 was not successfully expressed in some cell lines despite a high transfection rate. Therefore, to identify the functional region of the viral genome at which IFI16 displays its inhibitory effect, complementary HERV-K(HML-2)-constructs were cloned that allowed successively narrowing down the region of the 5' LTR or the 3'LTR. The obtained data verified the assumption that for the restriction of HERV-K113 by IFI16 the LTR plays an essential role but was not able to further identify the functional region of the genome in more detail. In addition, human cell lines were analyzed in this master thesis regarding their transfection efficiency and their full-length or partial IFI16 expression. Here, the convincing data of Hek293T and HeLa cells are particularly worth mentioning. In addition, the region of IFI16 protein containing only the pyrin domain plus linker region was shown to be sufficient for HERV-K(HML-2) inhibition. This region was finally cloned into a bicistronic lentiviral vector to generate reporter viruses and to determine the transduction efficiency of various human cell lines.
2021-06-24T00:00:00Z