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Data for "Sampling Uncertainty of Research Topics"
(2026-06) Naboka-Krell, Viktoriia
The replication package contains the data and analysis codes for the study "Sampling Uncertainty of Research Topics", which examines the measurement of sampling uncertainty in latent topic models. The dataset comprises 19,059 abstracts submitted to the European Research Consortium for Informatics and Mathematics (ERCIM) and Computational and Financial Econometrics (CFE) conferences between 2007 and 2023. The abstracts have an average length of 158 words (including title) and underwent standardized preprocessing: After removing special characters, numbers, and stopwords, as well as lemmatization (using spaCy with the en_core_web_lg model), a vocabulary of 1,844 unique words remained. **Contents of the ZIP Files** *Data_Simulations.zip* Contains the raw data, processed datasets, and all analysis results relevant to the main study. This includes: - The original abstracts (before and after preprocessing), - The generated bootstrap corpora (for resampling analyses), - The estimated topic models (including document-specific topic weights), - The computed model fit metrics (e.g., sBIC for determining the optimal number of topics), - The Python and R code for data preprocessing, model estimation (including Structural Topic Modeling), and bootstrap analysis, - The results for Figures 1–5 and Tables 1–2 of the paper (e.g., sBIC trends, topic weights, recall metrics). *Algorithm_Confidence_Bands_Word_Clouds.zip* Includes the MATLAB code for generating uncertainty-adjusted word clouds (Figure 6 in the paper). This algorithm visualizes the robustness of topic-word probabilities across bootstrap replications by generating confidence bands for the top words of each topic. *Algorithm_Counts_Top_Flop.zip* Contains the MATLAB code for calculating the top and flop words for selected topics (basis for Figure 7). The code identifies the most and least stable words within a topic across all bootstrap samples, enabling a qualitative assessment of topic stability. *Algorithm_Topic_Time_Series.zip* Includes the code for generating the topic time series (basis for Figure 8). This algorithm aggregates document-specific topic weights on an annual basis and computes confidence bands for the temporal evolution of topic prevalence.
Gender Health Gap: Systemische Versorgungsunterschiede in der Medizin
(2026-06-22) Lutz, JohannaUncovering Medicine
Profiling urinary bile acids by targeted liquid chromatography-tandem mass spectrometry
(2025) Schauermann, Marcel
Bile acids (BA) are C24 steroids synthesized from cholesterol in the liver. Apart from emulsification of fatty food components, they function as endocrine signaling molecules. As such, bile acids bear great potential as future biomarkers in diagnosis and monitoring of metabolic diseases. However, hardly any data exist on BA in urine. Therefore, the present study aimed at developing and implementing a new method for the quantification of urinary bile acids using targeted liquid chromatography-tandem mass spectrometry (LC-MS/MS). The targeted approach included 18 BA: the primary BA cholic acid (CA) and chenodeoxycholic acid (CDCA), and the secondary BA deoxycholic acid (DCA) and lithocholic acid (LCA) as well as glycine and taurine conjugates of these four BA. Furthermore, ursodeoxycholic acid (UDCA) and five BA in their sulfated forms (LCA-S, GLCA-S, TLCA-S, GCDCA-S, GDCA-S) were analyzed. Another goal consisted in presenting first reference values of urinary bile acids during childhood and to investigate their excretion patterns in obese children and adolescents. Finally, potential correlations between urinary bile acids and nutrition were examined. The method required 2 mL of urine and sample preparation consisting of protein precipitation and solid phase extraction. Stable isotopes of BA were included as internal standards (IS). The method was successfully validated and then applied to samples of 80 healthy children as well as 237 obese children of various age groups. The results were presented in three different units ([nmol/L], [nmol BA/mmol Crea] and [nmol/d]). Regardless of the unit, sulfated bile acids (GCDCA-S, GLCA-S, GDCA-S, TLCA-S) dominated in both study groups, CA and GCA were the two dominant non-sulfated BA. Lower bile acid sulfation and amidation in obese children may point to obesity-related limitations in hepatic metabolic capacity. Glycine-amidation appeared to be less prone to obesity-related impairments. Urinary concentration of GCDCA-S decreased with higher carbohydrate intake, while it increased with higher fat or protein intake, respectively.
Analysis of Hepatitis C Virus cis-elements involved in the Initiation of Negative-Strand RNA Synthesis
(2026-03) Malik, Attiya Qadoos
Hepatitis C Virus infects approximately 3 % of the global population. Because infection often remains asymptomatic for long periods, many cases progress unnoticed to severe liver diseases such as cirrhosis, hepatocellular carcinoma or chronic liver failure. HCV possesses a positive-strand RNA genome that replicates via negative-strand RNA intermediate. While many aspects of HCV replication are well studied, comparatively little is known about the cis-acting RNA elements on the positive-strand genome that are involved in the initiation of negative-strand RNA synthesis. Studying negative-strand RNA synthesis poses major technical challenges, particularly due to background signals that obscure accurate detection. The background signals arise from false priming (1) during in vitro-transcription and (2) during reverse transcription due to the strong hairpin structure at the 3´end of the RNA genome and (3) contaminating residual plasmid DNA and transfected RNA that serves as a false template during cDNA synthesis. Furthermore, it is essential to measure negative-strand RNA synthesis uncoupled from other viral processes such as translation and positive-strand RNA replication. To address these challenges, an HCV subgenomic (4th generation) replicon system was developed combined with a highly optimized strand-specific RNA detection assay. The system allows precise detection of newly synthesized negative-strand RNA with negligible background. Template DNA contamination from in vitro-transcribed RNA was (nearly) completely eliminated by two rounds of DNase digestion followed by RNA purification using Monarch kit columns. Total RNA extracted using TRIzol also underwent additional DNase treatments, acidic phenol/chloroform extraction and column-based purification to further enhance RNA quality. To selectively detect RNA new transcribed only after transfection of the replicon, 5EU-labelling was used in combination with Click iT chemistry. The 5EU-labelled nascent RNA was biotinylated, captured using streptavidin beads, and subjected to ten stringent washing steps before analysis by RT-qPCR. High temperature conditions during reverse transcription (65 °C) and qPCR (62 °C) further minimized nonspecific amplification. This approach reduced the background signals from polymerase deficient negative controls to only 0.02 - 0.035 %, representing an approximately 975-fold improvement over earlier methods in the Niepmann laboratory using 1st generation replicon system and conventional RNA purification procedures. Using this highly sensitive platform, the study identified the SLI-II region of the HCV 5´UTR as the minimal essential cis-acting element required for the initiation of negative-strand RNA synthesis. The SLI-III domain, which comprises the IRES region of the HCV 5´UTR, supported about 34.5 % of the overall efficiency of the negative-strand RNA synthesis. In contrast, mutations disrupting binding of eIF3 or the 40S subunit (∆IIIb and mutIIId/e) caused a drastic reduction in negative-strand RNA levels, both in SLI-III as well as in complete 5´UTR construct. These findings underscore the essential role of an intact HCV 5´UTR in genome replication and suggest that recruitment of eIF3 and the small ribosomal 40S subunit positively regulate negative-strand RNA synthesis. Similar to the PCBP2 protein, these factors may bridge the 5´- and 3´-ends of the viral genome, promoting genome circularization. Competitive binding of NS5B dimer or oligomer to the 5´UTR may disrupt this interaction, enabling replication via NS5B binding to the 3´-end. Such interactions may function as a checkpoint determining whether the genome undergoes translation and/or replication. Detection of negative-strand RNA is currently reliable only from 24 hpt onward, and further optimization is required to analyse initiation events at earlier time points.
Klinische Bewährung von Freiendbrücken unter besonderer Berücksichtigung der gesetzlichen Vorgaben in der vertragszahnärztlichen Versorgung
(2025) Rau, Katharina Maria
Ziel: Mit der vorliegenden retrospektiven Longitudinalstudie sollte die klinische Bewährung von Freiendbrücken, unter Berücksichtigung verschiedener Einflussfaktoren und der gesetzlichen Vorgaben in der vertragszahnärztlichen Versorgung, untersucht werden. Material und Methode: Aus einem Patientenkollektiv von über 25.000 Patienten der Poliklinik für Zahnärztliche Prothetik der Justus-Liebig-Universität Gießen wurden mithilfe eines internen EDV-Programmes (Multizentrische Dokumentation) 72 Patienten mit insgesamt 79 Freiendbrücken herausgefiltert, die den Einschlusskriterien entsprachen. Der Untersuchungszeitraum erstreckte sich dabei von September 2005 bis Oktober 2024. Zur statistischen Analyse der Daten wurde die Überlebenszeitanalyse nach Kaplan-Meier mit Gruppenvergleichen durchgeführt. Zum Vergleich statistischer Signifikanzen der neun untersuchten Faktoren wurde der von SPSS angebotene Log-Rank-Test, Breslow-Test sowie der Tarone-Ware-Test verwendet. Ergebnisse: Bei 79 Freiendbrücken und 72 Patienten lag die mittlere Beobachtungsdauer bei 5,44 ± 4,42 Jahren. Der längste dokumentierte Zeitraum erstreckte sich über 17,03 Jahre. Alle neun Variablen, die betrachtet und in die Statistik mit einbezogen wurden, hatten keinen signifikanten Einfluss (p>0,05) auf die Überlebenswahrscheinlichkeit der Freiendbrücken. Mithilfe der Überlebenszeitanalyse konnte eine mittlere Überlebenszeit von 13,49 ± 0,90 Jahren ermittelt werden bei einem Konfidenzintervall von 11,73 bis 15,26 Jahren. Die 5-Jahres-Überlebensrate betrug 85,6%, nach 10 sowie nach 15 Jahren lag sie bei 68,2%. Eine Unterschreitung der 90%igen Überlebenswahrscheinlichkeit fand nach 4,85 Jahren statt, während die 50%ige Überlebenswahrscheinlichkeit nicht unterschritten wurde. Das durchschnittliche Patientenalter bei Eingliederung lag bei 57,48 ± 14,28 Jahren. Insgesamt wurden 12 (15,19%) Freiendbrücken im Verlauf funktionsuntüchtig. Zudem wurden drei Retentionsverluste dokumentiert.