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ArXiv May 2024Hyperpolarized (HP) C MRI has shown promise as a valuable modality for measurements of metabolism and is currently in human trials at 15 research sites worldwide. With...
Hyperpolarized (HP) C MRI has shown promise as a valuable modality for measurements of metabolism and is currently in human trials at 15 research sites worldwide. With this growth it is important to adopt standardized data storage practices as it will allow sites to meaningfully compare data. In this paper we (1) describe data that we believe should be stored and (2) demonstrate pipelines and methods that utilize the Digital Imaging and Communications in Medicine (DICOM) standard. This includes proposing a set of minimum set of information that is specific to HP C MRI studies. We then show where the majority of these can be fit into existing DICOM Attributes, primarily via the "Contrast/Bolus" module. We also demonstrate pipelines for utilizing DICOM for HP C MRI. DICOM is the most common standard for clinical medical image storage and provides the flexibility to accommodate the unique aspects of HP C MRI, including the HP agent information but also spectroscopic and metabolite dimensions. The pipelines shown include creating DICOM objects for studies on human and animal imaging systems with various pulse sequences. We also show a python-based method to efficiently modify DICOM objects to incorporate the unique HP C MRI information that is not captured by existing pipelines. Moreover, we propose best practices for HP C MRI data storage that will support future multi-site trials, research studies and technical developments of this imaging technique.
PubMed: 38764595
DOI: No ID Found -
American Journal of Obstetrics and... May 2024Gestational diabetes mellitus affects up to 10% of pregnancies and is classified into subtypes gestational diabetes subtype A1 (GDMA1) (managed by lifestyle...
BACKGROUND
Gestational diabetes mellitus affects up to 10% of pregnancies and is classified into subtypes gestational diabetes subtype A1 (GDMA1) (managed by lifestyle modifications) and gestational diabetes subtype A2 (GDMA2) (requiring medication). However, whether these subtypes are distinct clinical entities or more reflective of an extended spectrum of normal pregnancy endocrine physiology remains unclear.
OBJECTIVE
Integrated bulk RNA-sequencing (RNA-seq), single-cell RNA-sequencing (scRNA-seq), and spatial transcriptomics harbors the potential to reveal disease gene signatures in subsets of cells and tissue microenvironments. We aimed to combine these high-resolution technologies with rigorous classification of diabetes subtypes in pregnancy. We hypothesized that differences between preexisting type 2 and gestational diabetes subtypes would be associated with altered gene expression profiles in specific placental cell populations.
STUDY DESIGN
In a large case-cohort design, we compared validated cases of GDMA1, GDMA2, and type 2 diabetes mellitus (T2DM) to healthy controls by bulk RNA-seq (n=54). Quantitative analyses with reverse transcription and quantitative PCR of presumptive genes of significant interest were undertaken in an independent and nonoverlapping validation cohort of similarly well-characterized cases and controls (n=122). Additional integrated analyses of term placental single-cell, single-nuclei, and spatial transcriptomics data enabled us to determine the cellular subpopulations and niches that aligned with the GDMA1, GDMA2, and T2DM gene expression signatures at higher resolution and with greater confidence.
RESULTS
Dimensional reduction of the bulk RNA-seq data revealed that the most common source of placental gene expression variation was the diabetic disease subtype. Relative to controls, we found 2052 unique and significantly differentially expressed genes (-2
2 thresholds; q<0.05 Wald Test) among GDMA1 placental specimens, 267 among GDMA2, and 1520 among T2DM. Several candidate marker genes (chorionic somatomammotropin hormone 1 [CSH1], period circadian regulator 1 [PER1], phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit beta [PIK3CB], forkhead box O1 [FOXO1], epidermal growth factor receptor [EGFR], interleukin 2 receptor subunit beta [IL2RB], superoxide dismutase 3 [SOD3], dedicator of cytokinesis 5 [DOCK5], suppressor of glucose, and autophagy associated 1 [SOGA1]) were validated in an independent and nonoverlapping validation cohort (q<0.05 Tukey). Functional enrichment revealed the pathways and genes most impacted for each diabetes subtype, and the degree of proximal similarity to other subclassifications. Surprisingly, GDMA1 and T2DM placental signatures were more alike by virtue of increased expression of chromatin remodeling and epigenetic regulation genes, while albumin was the top marker for GDMA2 with increased expression of placental genes in the wound healing pathway. Assessment of these gene signatures in single-cell, single-nuclei, and spatial transcriptomics data revealed high specificity and variability by placental cell and microarchitecture types. For example, at the cellular and spatial (eg, microarchitectural) levels, distinguishing features were observed in extravillous trophoblasts (GDMA1) and macrophages (GDMA2). Lastly, we utilized these data to train and evaluate 4 machine learning models to estimate our confidence in predicting the control or diabetes status of placental transcriptome specimens with no available clinical metadata. CONCLUSION
Consistent with the distinct association of perinatal outcome risk, placentae from GDMA1, GDMA2, and T2DM-affected pregnancies harbor unique gene signatures that can be further distinguished by altered placental cellular subtypes and microarchitectural niches.
PubMed: 38763341
DOI: 10.1016/j.ajog.2024.05.014 -
The Journal of Adolescent Health :... Jun 2024To assess the relevance of the Sustainable Development Goals (SDGs) framework for adolescent health measurement, both in terms of age disaggregation and different health...
PURPOSE
To assess the relevance of the Sustainable Development Goals (SDGs) framework for adolescent health measurement, both in terms of age disaggregation and different health domains captured, and how the adolescent health indicators recommended by the Global Action for Measurement of Adolescent Health (GAMA) can complement the SDG framework.
METHODS
We conducted a desk review to systematically map all 248 SDG indicators using the UN metadata repository in three steps: 1) age-related mandates for SDG reporting; 2) linkages between the SDG indicators and priority areas for adolescent health measurement; 3) comparison between the GAMA indicators and the SDG framework.
RESULTS
Of the 248 SDG indicators, 35 (14%) targeted an age range overlapping with adolescence (10-19 years) and 33 (13%) called for age disaggregation. Only one indicator (3.7.2 "adolescent birth rate") covered the entire 10-19 age range. Almost half (41%) of the SDG indicators were directly related to adolescent health, but only 33 of those (13% of all SDG indicators) overlapped with the ages 10-19, and 15 (6% of all SDG indicators) explicitly mandated age disaggregation. Among the 47 GAMA indicators, five corresponded to existing SDG indicators, and eight were adolescent-specific age adaptations. Several GAMA indicators shed light on aspects not tracked in the SDG framework, such as obesity, mental health, physical activity, and bullying among 10-19-year-olds.
DISCUSSION
Adolescent health cannot be monitored comprehensively with the SDG framework alone. The GAMA indicators complement this framework via age-disaggregated adaptations and by tracking aspects of adolescent health currently absent from the SDGs.
Topics: Humans; Adolescent; Sustainable Development; Adolescent Health; Global Health; Child; Health Status Indicators; Goals; Female; Young Adult; Male
PubMed: 38762262
DOI: 10.1016/j.jadohealth.2024.01.004 -
The Journal of Adolescent Health :... Jun 2024
Topics: Humans; Adolescent; Child; Adolescent Health; Female; Infant, Newborn; Infant; Metadata; Child Health; Health Status Indicators; Male; Maternal Health
PubMed: 38762254
DOI: 10.1016/j.jadohealth.2024.01.006 -
Scientific Reports May 2024The underutilization of digestate-derived polymers presents a pressing environmental concern as these valuable materials, derived from anaerobic digestion processes,...
The underutilization of digestate-derived polymers presents a pressing environmental concern as these valuable materials, derived from anaerobic digestion processes, remain largely unused, contributing to pollution and environmental degradation when left unutilized. This study explores the recovery and utilization of biodegradable polymers from biomass anaerobic digestate to enhance the performance of solar photovoltaic (PV) cells while promoting environmental sustainability. The anaerobic digestion process generates organic residues rich in biodegradable materials, often considered waste. However, this research investigates the potential of repurposing these materials by recovering and transforming them into high-quality coatings or encapsulants for PV cells. The recovered biodegradable polymers not only improve the efficiency and lifespan of PV cells but also align with sustainability objectives by reducing the carbon footprint associated with PV cell production and mitigating environmental harm. The study involves a comprehensive experimental design, varying coating thickness, direct normal irradiance (DNI) (A), dry bulb temperature (DBT) (B), and relative humidity (C) levels to analyze how different types of recovered biodegradable polymers interact with diverse environmental conditions. Optimization showed that better result was achieved at A = 8 W/m, B = 40 °C and C = 70% for both the coated material studied. Comparative study showed that for enhanced cell efficiency and cost effectiveness, EcoPolyBlend coated material is more suited however for improving durability and reducing environmental impact NanoBioCelluSynth coated material is preferable choice. Results show that these materials offer promising improvements in PV cell performance and significantly lower environmental impact, providing a sustainable solution for renewable energy production. This research contributes to advancing both the utilization of biomass waste and the development of eco-friendly PV cell technologies, with implications for a more sustainable and greener energy future. This study underscores the pivotal role of exploring anaerobic digestate-derived polymers in advancing the sustainability and performance of solar photovoltaic cells, addressing critical environmental and energy challenges of our time.Please confirm if the author names are presented accurately and in the correct sequence (given name, middle name/initial, family name). Author 7 Given name: [Ashok] Last name [Kumar Yadav]. Also, kindly confirm the details in the metadata are correct.correct.
Topics: Biomass; Solar Energy; Polymers; Recycling; Anaerobiosis
PubMed: 38755253
DOI: 10.1038/s41598-024-62048-5 -
Scientific Data May 2024Nanomaterials hold great promise for improving our society, and it is crucial to understand their effects on biological systems in order to enhance their properties and...
Nanomaterials hold great promise for improving our society, and it is crucial to understand their effects on biological systems in order to enhance their properties and ensure their safety. However, the lack of consistency in experimental reporting, the absence of universally accepted machine-readable metadata standards, and the challenge of combining such standards hamper the reusability of previously produced data for risk assessment. Fortunately, the research community has responded to these challenges by developing minimum reporting standards that address several of these issues. By converting twelve published minimum reporting standards into a machine-readable representation using FAIR maturity indicators, we have created a machine-friendly approach to annotate and assess datasets' reusability according to those standards. Furthermore, our NanoSafety Data Reusability Assessment (NSDRA) framework includes a metadata generator web application that can be integrated into experimental data management, and a new web application that can summarize the reusability of nanosafety datasets for one or more subsets of maturity indicators, tailored to specific computational risk assessment use cases. This approach enhances the transparency, communication, and reusability of experimental data and metadata. With this improved FAIR approach, we can facilitate the reuse of nanosafety research for exploration, toxicity prediction, and regulation, thereby advancing the field and benefiting society as a whole.
Topics: Metadata; Nanostructures; Risk Assessment
PubMed: 38755173
DOI: 10.1038/s41597-024-03324-x -
International Journal of Medical... Aug 2024Alcohol is often consumed in a social context. We aim to investigate whether social mobile sensing is associated with real-world social interactions and alcohol...
BACKGROUND
Alcohol is often consumed in a social context. We aim to investigate whether social mobile sensing is associated with real-world social interactions and alcohol consumption. In addition, we investigate how social restriction policies implemented during the COVID-19 pandemic have influenced these associations.
METHODS
We conducted a smartphone-based ecological momentary assessment (EMA) study for 7 days over a 213-day period from 8 August 2020 to 9 March 2021 in Germany, including both no-lockdown and lockdown stages. Participants used a smartphone application which passively collects data on social behavior (e.g., app usage, phone calls, SMS). Moreover, we assessed real-world social interactions and alcohol consumption via daily questionnaires.
RESULTS
We found that each one-hour increase in social media usage was associated with a 40.2% decrease in the average number of drinks consumed. Mediation analysis suggested that social media usage decreases alcohol intake through decreased real-world social interactions. Notably, we did not find that any significant influence of the lockdown stage on the association between social mobile sensing and alcohol intake.
CONCLUSIONS
Our study suggests that people who use more social media drink less, likely due to reduced face-to-face social interactions. This highlights the potential of social mobile sensing as an objective measure of social activity and its implications for understanding alcohol consumption behavior.
Topics: Humans; COVID-19; Smartphone; Male; Female; Adult; Alcohol Drinking; Social Media; Germany; Ecological Momentary Assessment; Middle Aged; Mobile Applications; Young Adult; SARS-CoV-2; Social Interaction
PubMed: 38754285
DOI: 10.1016/j.ijmedinf.2024.105486 -
Bundesgesundheitsblatt,... Jun 2024The interoperability Working Group of the Medical Informatics Initiative (MII) is the platform for the coordination of overarching procedures, data structures, and...
The interoperability Working Group of the Medical Informatics Initiative (MII) is the platform for the coordination of overarching procedures, data structures, and interfaces between the data integration centers (DIC) of the university hospitals and national and international interoperability committees. The goal is the joint content-related and technical design of a distributed infrastructure for the secondary use of healthcare data that can be used via the Research Data Portal for Health. Important general conditions are data privacy and IT security for the use of health data in biomedical research. To this end, suitable methods are used in dedicated task forces to enable procedural, syntactic, and semantic interoperability for data use projects. The MII core dataset was developed as several modules with corresponding information models and implemented using the HL7® FHIR® standard to enable content-related and technical specifications for the interoperable provision of healthcare data through the DIC. International terminologies and consented metadata are used to describe these data in more detail. The overall architecture, including overarching interfaces, implements the methodological and legal requirements for a distributed data use infrastructure, for example, by providing pseudonymized data or by federated analyses. With these results of the Interoperability Working Group, the MII is presenting a future-oriented solution for the exchange and use of healthcare data, the applicability of which goes beyond the purpose of research and can play an essential role in the digital transformation of the healthcare system.
Topics: Humans; Datasets as Topic; Electronic Health Records; Germany; Health Information Interoperability; Medical Informatics; Medical Record Linkage; Systems Integration
PubMed: 38753022
DOI: 10.1007/s00103-024-03888-4 -
PloS One 2024In a recent study (doi: 10.1371/journal.pone.0265662), associations were identified between owner-reported dog health status and diet, whereby those fed a vegan diet...
In a recent study (doi: 10.1371/journal.pone.0265662), associations were identified between owner-reported dog health status and diet, whereby those fed a vegan diet were perceived to be healthier. However, the study was limited because it did not consider possible confounding from variables not included in the analysis. The aim of the current study was to extend these earlier findings, using different modelling techniques and including multiple variables, to identify the most important predictors of owner perceptions of dog health. From the original dataset, two binary outcome variables were created: the 'any health problem' distinguished dogs that owners perceived to be healthy ("no") from those perceived to have illness of any severity; the 'significant illness' variable distinguished dogs that owners perceived to be either healthy or having mild illness ("no") from those perceived to have significant or serious illness ("yes"). Associations between these health outcomes and both owner-animal metadata and healthcare variables were assessed using logistic regression and machine learning predictive modelling using XGBoost. For the any health problem outcome, best-fit models for both logistic regression (area under curve [AUC] 0.842) and XGBoost (AUC 0.836) contained the variables dog age, veterinary visits and received medication, whilst owner age and breed size category also featured. For the significant illness outcome, received medication, veterinary visits, dog age and were again the most important predictors for both logistic regression (AUC 0.903) and XGBoost (AUC 0.887), whilst breed size category, education and owner age also featured in the latter. Any contribution from the dog vegan diet variable was negligible. The results of the current study extend the previous research using the same dataset and suggest that diet has limited impact on owner-perceived dog health status; instead, dog age, frequency of veterinary visits and receiving medication are most important.
Topics: Dogs; Animals; Humans; Surveys and Questionnaires; Dog Diseases; Male; Female; Ownership; Perception; Health Status; Diet, Vegan; Logistic Models
PubMed: 38748734
DOI: 10.1371/journal.pone.0280173 -
Social Studies of Science May 2024Biobanks are becoming ubiquitous infrastructures in zoology and other non-human life sciences. They promise to store frozen research samples for the long term for future...
Biobanks are becoming ubiquitous infrastructures in zoology and other non-human life sciences. They promise to store frozen research samples for the long term for future use. That use remains speculative but nevertheless needs to be anticipated. Following the establishment of a physical and digital infrastructure for frozen samples in an animal biobanking project, this article explores how the future is anticipated to remember the past, and how frozen objects are shaped accordingly. Situating the biobank between mundane freezing routines in a research lab and the 'dry' and 'wet' collections of natural history museums, I argue that frozen research objects need to be conserved in two separate ways. The unavailability of cryo-objects in cold storage forces researchers to store materials independently of metadata, while retaining a link between them that allows for their reunion after thawing. The result is a split object, leading a double life at sub-zero and room temperature, linked only through the surface of special plastic containers. Following the making of such split objects, this article offers an elaboration of Radin's 'planned hindsight' as well as a reflection on the universality and particularity of biobanks as standardized scientific memory.
PubMed: 38747550
DOI: 10.1177/03063127241252081