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Machine learning methods for compound annotation in non-targeted mass spectrometry—A brief overview of fingerprinting, in silico fragmentation and de novo methods
Get PDFNon-targeted screenings (NTS) are essential tools in different fields, such as forensics, health and environmental sciences. NTSs often employ mass spectrometry (MS) methods due to their high throughput and sensitivity in comparison to, for example, nuclear magnetic resonance–based methods. As the identification of mass spectral signals, called annotation, is labour intensive, it has been used for developing supporting tools based on machine learning (ML). However, both the diversity of mass spectral signals and the sheer quantity of different ML tools developed for compound annotation present a challenge for researchers in maintaining a comprehensive overview of the field.
In this work, we illustrate which ML-based methods are available for compound annotation in non-targeted MS experiments and provide a nuanced comparison of the ML models used in MS data analysis, unravelling their unique features and performance metrics. Through this overview we support researchers to judiciously apply these tools in their daily research. This review also offers a detailed exploration of methods and datasets to show gaps in current methods, and promising target areas, offering a starting point for developers intending to improve existing methodologies.Peer Reviewe
Pichia kudriavzevii (Candida krusei): A systematic review to inform the World Health Organisation priority list of fungal pathogens
No full textIn response to the growing global threat of fungal infections, in 2020 the World Health Organisation (WHO) established an Expert Group to identify priority fungi and develop the first WHO fungal priority pathogen list (FPPL). The aim of this systematic review was to evaluate the features and global impact of invasive infections caused by Pichia kudriavzevii (formerly known as Candida krusei). PubMed and Web of Science were used to identify studies published between 1 January 2011 and 18 February 2021 reporting on the criteria of mortality, morbidity (defined as hospitalisation and length of stay), drug resistance, preventability, yearly incidence, and distribution/emergence. Overall, 33 studies were evaluated. Mortality rates of up to 67% in adults were reported. Despite the intrinsic resistance of P. kudriavzevii to fluconazole with decreased susceptibility to amphotericin B, resistance (or non-wild-type rate) to other azoles and echinocandins was low, ranging between 0 and 5%. Risk factors for developing P. kudriavzevii infections included low birth weight, prior use of antibiotics/antifungals, and an underlying diagnosis of gastrointestinal disease or cancer. The incidence of infections caused by P. kudriavzevii is generally low (∼5% of all Candida-like blood isolates) and stable over the 10-year timeframe, although additional surveillance data are needed. Strategies targeting the identified risk factors for developing P. kudriavzevii infections should be developed and tested for effectiveness and feasibility of implementation. Studies presenting data on epidemiology and susceptibility of P. kudriavzevii were scarce, especially in low- and middle-income countries (LMICs). Thus, global surveillance systems are required to monitor the incidence, susceptibility, and morbidity of P. kudriavzevii invasive infections to inform diagnosis and treatment. Timely species-level identification and susceptibility testing should be conducted to reduce the high mortality and limit the spread of P. kudriavzevii in healthcare facilities.Peer Reviewe
Health service providers' views on barriers and drivers to childhood vaccination of FDMN/Rohingya refugees: a qualitative study in Cox's Bazar, Bangladesh
Get PDFBackground:
Despite established vaccination programs, vaccine-preventable diseases persist among about 900,000 Forcibly Displaced Myanmar Nationals (FDMN)/Rohingya refugees in the world's largest refugee settlement in Bangladesh. Health service providers (HSPs) play a key role in the delivery of childhood vaccination programs. This study explored their views on individual and context barriers and drivers to childhood vaccination in this setting.
Methods:
Informed by the theoretical framework of the Capability-Opportunity-Motivation-Behavior (COM-B) model for behavior change, this qualitative study collected data through eight focus group discussions (FGDs) with community health workers (CHWs) and vaccinators in selected camps with high or low vaccination coverage rates, and through 11 in-depth interviews (IDIs) with key informants working in strategic, management, and administrative roles.
Findings:
Barriers and drivers were evident across all COM factors for HSPs and caregivers. Among HSPs, knowledge around vaccination acted both as a barrier and driver, while communication skills and confidence in vaccination served as drivers. Caregivers' lack of awareness of vaccination, concerns and mistrust were described as main barriers. Context barriers included information system deficiencies, family dynamics, HSPs' working conditions, and vaccination site accessibility. Context drivers included effective communication, mobilization, and incentives. Differences between high and low coverage camps in Cox's Bazar included variations in HSPs' knowledge, communication strategies, incentive use, and stakeholder collaboration.
Discussion:
For better vaccination coverage in the camps, context-related changes regarding collaboration, health workforce and the use of incentives seem necessary. Caregivers' mistrust toward vaccination needs to be considered under the social and historical background of the Rohingya community, and further addressed with targeted communication and campaigning.Peer Reviewe
The predictive value of supervised machine learning models for insomnia symptoms through smartphone usage behavior
Get PDFIntroduction:
Digital phenotyping can be an innovative and unobtrusive way to improve the detection of insomnia. This study explores the correlations between smartphone usage features (SUF) and insomnia symptoms and their predictive value for detecting insomnia symptoms.
Methods:
In an observational study of a German convenience sample, the Insomnia Severity Index (ISI) and smartphone usage data (e.g., time the screen was active, longest time the screen was inactive in the night) for the previous 7 days were obtained. SUF (e.g., min, mean) were calculated from the smartphone usage data. Correlation analyses between the ISI and SUF were conducted. For the specification of the machine learning models (ML), 80 % of the data was allocated to training, 20 % to testing, and five-fold cross-validation was used. Six algorithms (support vector machine, XGBoost, Random Forest, k-Nearest-Neighbor, Naive Bayes, and Logistic Regressions) were specified to predict ISI scores ≥15.
Results:
752 participants (51.1 % female, mean ISI = 10.23, mean age = 41.92) were included in the analyses. Small correlations between some of the SUF and insomnia symptoms were found. In the ML models, sensitivity was low, ranging from 0.05 to 0.27 in the testing subsample. Random Forest and Naive Bayes were the best-performing algorithms. Yet, their AUCs (0.57, 0.58 respectively) in the testing subsample indicated a low discrimination capacity.
Conclusions:
Given the small magnitude of the correlations and low discrimination capacity of the ML models, SUFs, as measured in this study, do not appear to be sufficient for detecting insomnia symptoms. Further research is necessary to explore whether examining intra-individual variations and subpopulations or employing alternative smartphone sensors yields more promising outcomes.Peer Reviewe
HIV-Jahresbericht 2023
Get PDFGemäß § 7 Abs. 3 IfSG ist der direkte oder indirekte Nachweis einer HIV-Infektion nichtnamentlich unmittelbar an das RKI zu melden. Als HIV-Neudiagnosen werden die Meldungen gezählt, bei denen es sich entweder nach Kenntnis der Laboreinrichtung oder der diagnostizierenden Einrich-tung um eine Erstdiagnose in Deutschland handelt oder aber ein negativer HIV-Antikörpertest nach dem Jahr 2001 angegeben wurde und bei denen nach einem Abgleich mit allen an das RKI gemelde-ten Fällen keine frühere Meldung identifizierbar ist. Wie das Epidemiologische Bulletin 40/2024 ausführt, wurden dem RKI bis zum 1.5.2024 für das Jahr 2023 insgesamt 3.321 gesicherte HIV-Neudiagnosen gemeldet. Dies stellt keine wesentliche Änderung zum Vorjahr dar, in dem 3.279 gesicherte HIV-Neudiagnosen gemeldet wurden. Für 2023 ist zu berücksichtigen, dass auch in diesem Meldejahr noch in erheblichem Umfang HIV-Meldungen von aus der Ukraine nach Deutschland geflüchteten Personen erfolgten und anzunehmen ist, dass bei den meisten dieser Fälle die HIV-Diagnose und der Behandlungsbeginn bereits in der Ukraine erfolgten. Folglich handelt es sich hier meistens nicht um tatsächliche Neudiagnosen, sondern um einen erstmaligen Nachweis der HIV-Infektion in Deutschland.Peer Reviewe
Schluckimpfstoff-abgeleitete Polioviren in Abwasserproben an weiteren Orten in Deutschland nachgewiesen
Get PDFWeltpoliotag 2024: Politische Krisen werden von Gesundheitskrisen begleitet
Get PDFDer Weltpoliotag wird jährlich am 24. Oktober begangen und erinnert daran, wie weit die globale Gemeinschaft im Kampf gegen Polio ge¬kommen ist. Seit dem Beginn der „Global Polio Eradication Initiative“ durch die WHO und ihre Partner im Jahr 1988 gibt es aktuell nur noch zwei Länder mit endemischer Polioviruszirkulation. Seit mehreren Jahren stellen jedoch Ausbrüche durch zirkulie-rende vakzineabgeleitete Polioviren (cVDPV) ein weitaus größeres Problem als Erkrankungen durch Poliowildviren dar. Fälle von akuten schlaffen Pa¬resen oder anhaltende cVDPV-Nachweise im Abwasser gibt es derzeit in 41 Ländern, vorwiegend in Afrika. Im Jahr 2024 steht Gaza exemplarisch für die Herausforderungen, die bei der Polioeradikation in Krisenregionen bestehen. Die humanitäre Lage ist verheerend und im August 2024 übermittelten die Gesundheitsbehörden in Gaza einen Poliofall durch cVDPV2 bei einem ungeimpften zehn Monate alten Kind. Es ist wichtig, die bisherigen Anstrengungen im Kampf gegen Polio fortzusetzen und zu intensivieren.PoliomyelitisWeltpoliotagvakzineabgeleitete PoliovirenPoliowildvirenPolioeradikatio
Wastewater-based Surveillance on SARS-CoV-2
No full textThe SARS-CoV-2 viral load in wastewater is being tested at selected wastewater treatment plants (WWTP) in Germany as part of AMELAG (“Abwassermonitoring für die epidemiologische Lagebewertung”, German for wastewater monitoring for epidemiological situation assessment). Data from 168 WWTP are currently included in the analyses. For the calendar week 40 data from 84 WWTP were available. Data from other WWTP are provided continuously.
A steep increase in the aggregated SARS-CoV-2 viral load can be observed for the last two weeks. The development observed over the last few weeks may still change due to late notifications, especially from WWTP with large population coverage
Diabetes mellitus, cardiovascular and chronic respiratory diseases in Germany and Europe - results of the European Health Interview Survey (EHIS 3, 2018 – 2020)
Get PDFBackground: In Europe, the health situation is primarily influenced by non-communicable diseases. Comparable information on key indicators for the European region can highlight potential areas for improvement in prevention and care.
Method: Based on EHIS 3, age-standardised prevalences of three disease groups and two indicators of self-assessed health among those affected were presented for Germany (n = 22,708) and the average of 29 European countries (n = 301,960).
Results: The disease prevalence estimates in Germany were higher compared to the European average: diabetes 8.4 % vs. 7.4 %, cardiovascular diseases 6.8 % vs. 5.7 %, chronic respiratory diseases 11.4 % vs. 7.9 %. Likewise, the proportion with self-assessed very good or good general health among those affected was also higher in Germany (diabetes 35.8 % vs. 30.7 %, cardiovascular diseases 25.3 % vs. 18.9 %, chronic respiratory diseases 44.7 % vs. 41.9 %). For limitations in everyday activities, higher proportions were found in Germany for diabetes (65.6 % vs. 60.6 %) and chronic respiratory diseases (64.5 % vs. 57.6 %). Germany showed similar gender-, age- and education-specific differences for disease prevalence, but in part less pronounced differences for the indicators of self-assessed health than the European average.
Conclusions: Further analysis of the differences for the indicators considered between Germany and the European average and the possible underlying factors, such as differences in prevention, diagnosis, disease severity and care, is required. The educational inequalities observed across Europe suggest considerable potential for promoting health equity.Peer Reviewe
