bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cell-free transcription-translation system: a dual read-out assay to characterize riboswitch function
Authors: Bains Jasleen Kaur , Qureshi Nusrat Shahin , Ceylan Betül , Wacker Anna , Schwalbe Harald 
Published: July 2023

Abstract
Cell-free protein synthesis assays have become a valuable tool to understand transcriptional and translational processes. Here, we established a fluorescence-based coupled in vitro transcription-translation assay as a read-out system to simultaneously quantify mRNA and protein levels. We utilized the well-established quantification of the expression of shifted green fluorescent protein (sGFP) as a read-out of protein levels. In addition, we determined mRNA quantities using a fluorogenic Mango-(IV) RNA aptamer that becomes fluorescent upon binding to the fluorophore thiazole orange (TO). We utilized a Mango-(IV) RNA aptamer system comprising four subsequent Mango-(IV) RNA aptamer elements with improved sensitivity by building Mango arrays. The design of this reporter assay resulted in a sensitive read-out with a high signal-to-noise ratio, allowing us to monitor transcription and translation time courses in cell-free assays with continuous monitoring of fluorescence changes as well as snapshots of the reaction. Furthermore, we applied this dual read-out assay to investigate the function of thiamine-sensing riboswitches thiM and thiC from Escherichia coli and the adenine-sensing riboswitch ASW from Vibrio vulnificus and pbuE from Bacillus subtilis, which represent transcriptional and translational on- and off-riboswitches, respectively. This approach enabled a microplate-based application, a valuable addition to the toolbox for high-throughput screening of riboswitch function.
Changes in Tobacco Dependence and Association With Onset and Progression of Use by Product Type From Waves 1 to 3 of the Population Assessment of Tobacco and Health (PATH) Study
Authors: Strong David R , Pierce John P , White Martha , Stone Matthew D , Abrams David B , Glasser Allison M , Wackowski Olivia A , Cummings K Michael , Hyland Andrew , Taylor Kristie , Edwards Kathryn C , Silveira Marushka L , Kimmel Heather L , Compton Wilson M , Hull Lynn C , Niaura Raymond 
Published: July 2023

Abstract

Introduction
This study examined trajectories of tobacco dependence (TD) in relationship to changes in tobacco product use, and explored the effects of product-specific adding, switching, or discontinued use on dependence over time.

Aims and Methods
Data were analyzed from the first three waves from the Population Assessment of Tobacco and Health (PATH) Study, a nationally representative, longitudinal study of adults and youth in the United States. Data included 9556 wave 1 (2013–2014) adult current established tobacco users aged 18 or older who completed all three interviews and had established use at ≥2 assessments. Mutually exclusive groups included: users of cigarettes only, e-cigarettes only, cigars only, hookah only, any smokeless only, cigarette + e-cigarette dual users, and other multiple product users. A validated 16-item scale assessed TD across product users.

Results
People who used e-cigarettes exclusively at wave 1 had small increases in TD through wave 3. Wave 1 multiple product users’ TD decreased across waves. TD for all other wave 1 user groups remained about the same. For wave 1 cigarette only smokers, switching to another product was associated with lower levels of TD than smokers whose use stayed the same. Movement to no established use of any tobacco product was consistently associated with lower TD for all product users.

Conclusions
Except for wave 1 e-cigarette only users (who experienced small increases in TD), TD among U.S. tobacco product users was stable over time, with daily users less likely to vary from baseline.

Implications
The level of TD among most U.S. tobacco users was stable over the first three waves of the PATH Study and trends in levels of TD were predominantly unrelated to changes in patterns of continued product use. Stable levels of TD suggest a population at persistent risk of health impacts from tobacco. Wave 1 e-cigarette users experienced small increases in levels of TD over time, perhaps due to increases in quantity or frequency of their e-cigarette use or increasing efficiency of nicotine delivery over time.
Recent advances in the genetics of idiopathic pulmonary fibrosis
Authors: Spagnolo Paolo , Lee Joyce S 
Published: July 2023

Purpose of review
Genetics contributes substantially to the susceptibility to idiopathic pulmonary fibrosis (IPF). Genetic studies in sporadic and familial disease have identified several IPF-associated variants, mainly in telomere-related and surfactant protein genes.
Here, we review the most recent literature on genetics of IPF and discuss how it may contribute to disease pathogenesis.

Recent findings
Recent studies implicate genes involved in telomere maintenance, host defence, cell growth, mammalian target of rapamycin signalling, cell–cell adhesion, regulation of TGF-β signalling and spindle assembly as biological processes involved in the pathogenesis of IPF. Both common and rare genetic variants contribute to the overall risk of IPF; however, while common variants (i.e. polymorphisms) account for most of the heritability of sporadic disease, rare variants (i.e. mutations), mainly in telomere-related genes, are the main contributors to the heritability of familial disease. Genetic factors are likely to also influence disease behaviour and prognosis. Finally, recent data suggest that IPF shares genetic associations – and probably some pathogenetic mechanisms – with other fibrotic lung diseases.

Summary
Common and rare genetic variants are associated with susceptibility and prognosis of IPF. However, many of the reported variants fall in noncoding regions of the genome and their relevance to disease pathobiology remains to be elucidated.
Obesity and thyroid cancer risk
Authors: Burrage Lauren C. , McLeod Donald S.A. , Jordan Susan J. 
Published: July 2023

Purpose of review
This review explores recent evidence assessing the relationship between obesity and thyroid cancer.

Recent findings
Consistent evidence from observational studies suggests that obesity increases the risk of thyroid cancer. The relationship persists when alternative measures of adiposity are used, but the strength of association may vary according to the timing and duration of obesity and how obesity or other metabolic parameters are defined as exposures. Recent studies have reported an association between obesity and thyroid cancers that are larger or have adverse clinicopathologic features, including those with BRAF mutations, thus providing evidence that the association is relevant for clinically significant thyroid cancers. The underlying mechanism for the association remains uncertain but may be driven by disruption in adipokines and growth-signaling pathways.

Summary
Obesity is associated with an increased risk of thyroid cancer, although further research is required to understand the biological mechanisms underpinning this relationship. Reducing the prevalence of obesity is predicted to lessen the future burden of thyroid cancer. However, the presence of obesity does not impact current recommendations for screening or management of thyroid cancer.
A Single Preservation Solution for Static Cold Storage and Hypothermic Oxygenated Perfusion of Marginal Liver Grafts: A Preclinical Study
Authors: Muller Xavier , Rossignol Guillaume , Couillerot Joris , Breton Antoine , Hervieu Valérie , Lesurtel Mickaël , Mohkam Kayvan , Mabrut Jean-Yves 
Published: July 2023

Background.
Hypothermic oxygenated perfusion (HOPE) improves outcomes of marginal liver grafts. However, to date, no preservation solution exists for both static cold storage (SCS) and HOPE.

Methods.
After 30 min of asystolic warm ischemia, porcine livers underwent 6 h of SCS followed by 2 h of HOPE. Liver grafts were either preserved with a single preservation solution (IGL2) designed for SCS and HOPE (IGL2-Machine Perfusion Solution [MPS] group, n = 6) or with the gold-standard University of Wisconsin designed for for SCS and Belzer MPS designed for HOPE (MPS group, n = 5). All liver grafts underwent warm reperfusion with whole autologous blood for 2 h, and surrogate markers of hepatic ischemia–reperfusion injury (IRI) were assessed in the hepatocyte, cholangiocyte, vascular, and immunological compartments.

Results.
After 2 h of warm reperfusion, livers in the IGL2-MPS group showed no significant differences in transaminase release (aspartate aminotransferase: 65.58 versus 104.9 UI/L/100 g liver; P = 0.178), lactate clearance, and histological IRI compared with livers in the MPS group. There were no significant differences in biliary acid composition, bile production, and histological biliary IRI. Mitochondrial and endothelial damage was also not significantly different and resulted in similar hepatic inflammasome activation.

Conclusions.
This preclinical study shows that a novel IGL2 allows for the safe preservation of marginal liver grafts with SCS and HOPE. Hepatic IRI was comparable with the current gold standard of combining 2 different preservation solutions (University of Wisconsin + Belzer MPS). These data pave the way for a phase I first-in-human study and it is a first step toward tailored preservation solutions for machine perfusion of liver grafts.
Symptoms of Depression among Outpatients with Acute Respiratory Infection in Metropolitan Local Government Areas of Kaduna State, Nigeria
Authors: Umeh Gregory C. , Cleenwerck de Kiev Laurent , Mamza Jabani , Atiku Aliyu , Mohammed Suleiman , Hananiya Dauda S. , Onoh Moses , Yahaya Habibu B. , Adeoti Basirat , Musa Rabiat T. , Adegbite Mutiu , Audu Sunday , Daikwo Jeremiah , Iliyasu Neyu , Baloni Amina Mohammed 
Published: July 2023

AbstractBackgroundThe novel SARS-CoV-2 virus that causes Coronavirus disease (COVID-19) has redefined global health and response to Acute Respiratory Infection (ARI). The outbreak of a cluster of influenza-like illnesses in Wuhan, China, has morphed into a pandemic in the last quarter of 2019, stretching from South East Asia to Europe, The Americas, Africa, and the Australian subcontinent.Materials and MethodsWe shall utilize a cross-sectional, observational design to investigate the prevalence of symptoms of depression among outpatients with ARI and describe the characteristics of outpatients with ARI in Kaduna State.ResultsThe prevalence of symptoms of depression was 19.6% for respondents with symptoms of ARI, and 14.4%, for those without symptoms of ARI. On no risk of depression, we had a higher proportion of the respondents without symptoms of ARI (86%) than those with symptoms of depression (80%) (M=318.4, SD=29.62 case, and M=344.0, SD=14.2 control, r=0.88, CI=13.5 to 6.5, P=0.000952). Likewise, in the category with mild risk of depression, respondents without symptoms of ARI were fewer (10%) than those with symptoms of depression (15%) (M=58.4, SD=26.0 case, and M=42.1, SD=12.7 control, r=0.86, CI=11.8 to 5.8, P=0.0136. There was no significant difference between respondents with symptoms of ARI and without symptoms of ARI in the categories of moderate (M=13.6, SD=5.1 case, and M=11.6, SD=4.6 control, r=0.87, CI=2.3 to 2.1, P=0.178) and high (M=5.6, SD=2.5 case, and M=4.4, SD=3.2 control, r=0.61, CI=1.2 to 1.5, P=0.174) risk of depression.ConclusionSymptoms of depression were commoner among respondents who presented with symptoms of Acute Respiratory Infection (ARI) at the Outpatient Department (OPD). However, further explanatory research is needed to establish causality.
Technical report: A comprehensive comparison between different quantification versions of Nightingale Health’s1H-NMR metabolomics platform
Authors: Bizzarri D. , Reinders M.J.T. , Beekman M. ,   BBMRI-NL, Slagboom P.E. , van den Akker E.B. 
Published: July 2023

Abstract1H-NMR metabolomics data is increasingly used to track various aspects of health and disease. With the availability of larger data resources and continuously improving learning algorithms Nightingale Health has recently updated the quantification and calibration strategy of their platform to further align their reported analytes with clinical standards. Such updates, however, might influence backward replicability and could hamper comparison of repeated measures in longitudinal studies. Based on data of the BBMRI.nl consortium (>25.000 samples across 28 studies), we compared Nightingale data, as originally released in 2014 and 2016, with a re-quantified version of this data released in 2020, of which both versions were based on the same original NMR spectra. Apart from 2 discontinued, and 23 newly defined analytes, we overall observe a high concordance between quantification versions, with 73 out of 222 (33%) showing a mean correlation > 0.9 across the 28 Dutch cohorts. Nevertheless, five metabolites consistently showed relatively low correlations (R<0.7) between platform versions, namely acetoacetate(acace),LDL particle size(ldl_d), saturated fatty acids percentage(sfa_fa), S-HDL-C(s_hdl_c)and sphingomyelins (sm). Previously trained multi-analyte scores, such as our previously published health predictorsMetaboAgeorMetaboHealth, might be particularly sensitive to platform changes. Whereas theMetaboHealthscore replicated well between platform versions, theMetaboAgescore indeed had to be retrained due to discontinued metabolites. Notably, both scores projected on the 2020 re-quantified data did recapitulate the original mortality associations observed in the previous version of the data. Concluding, we urge caution when utilizing data from different quantification versions to avoid mixing analytes capturing different underlying aspects of the NMR spectra, having different units, or simply being discontinued.
An indocyanine green-based liquid biopsy test for circulating tumor cells for pediatric liver cancer
Authors: Espinoza Andres F. , Kureti Pavan , Patel Roma H. , Govindu Saiabhiroop R. , Armbruster Bryan W. , Urbicain Martin , Patel Kalyani R. , Lopez-Terrada Dolores , Vasudevan Sanjeev A. , Woodfield Sarah E. 
Published: July 2023

ABSTRACTBackground and AimsHepatoblastoma (HB) and hepatocellular carcinoma (HCC) are the most common malignant hepatocellular tumors seen in children. The aim of this work was to develop a liquid biopsy test for circulating tumor cells (CTCs) for these tumors that would be less invasive and provide information about the real-time state of tumors in response to therapies.MethodsFor this test, we utilized indocyanine green (ICG), a far-red fluorescent dye that is used clinically to identify malignant liver cells in the body during surgery. We assessed ICG accumulation in cell lines with fluorescence microscopy and flow cytometry. For our CTC test, we developed a panel of liver tumor-specific markers, ICG, Glypican-3 (GPC3), and DAPI and tested this panel with cell lines and non-cancer control blood samples. We then used this panel to analyze whole blood samples for CTC burden with a cohort of 14 HB and HCC patients and correlated with patient characteristics and outcomes.ResultsWe showed that ICG accumulation is specific to liver cancer cells, compared to non-malignant liver cells, non-liver solid tumor cells, and non-malignant cells and can be used to identify liver tumor cells in a mixed population of cells. Experiments with the ICG/GPC3/DAPI panel showed that it specifically tagged malignant liver cells. With patient samples, we found that CTC burden from sequential blood samples from the same patients mirrored the patients’ responses to therapy.ConclusionsOur novel ICG-based liquid biopsy test for CTCs can be used to specifically count CTCs in the blood of pediatric liver cancer patients.Impact and implicationsThis manuscript represents the first report of circulating tumor cells in the blood of pediatric liver cancer patients. The novel and innovative assay for CTCs shown in this paper will facilitate future work examining the relationship between CTC numbers and patient outcomes, forming the foundation for incorporation of liquid biopsy into routine clinical care for these patients.Graphical abstractOverview of novel liquid biopsy test for circulating tumor cells for pediatric liver cancer. Figure made with Biorender.
ChatGPT sits the DFPH exam: large language model performance and potential to support public health learning
Authors: Davies Nathan P , Wilson Robert , Winder Madeleine S , Tunster Simon J , McVicar Kathryn , Thakrar Shivan T , Williams Joe , Reid Allan 
Published: July 2023

AbstractBackgroundArtificial intelligence-based large language models, like ChatGPT, have been rapidly assessed for both risks and potential in health-related assessment and learning. However, their application in public health professional exams have not yet been studied. We evaluated the performance of ChatGPT in part of the Faculty of Public Health’s Diplomat exam (DFPH).MethodsChatGPT was provided with a bank of 119 publicly available DFPH question parts from past papers. Its performance was assessed by two active DFPH examiners. The degree of insight and level of understanding apparently displayed by ChatGPT was also assessed.ResultsChatGPT passed 3 of 4 papers, surpassing the current pass rate. It performed best on questions relating to research methods. Its answers had a high floor. Examiners identified ChatGPT answers with 73.6% accuracy and human answers with 28.6% accuracy. ChatGPT provided a mean of 3.6 unique insights per question and appeared to demonstrate a required level of learning on 71.4% of occasions.ConclusionsLarge language models have rapidly increasing potential as a learning tool in public health education. However, their factual fallibility and the difficulty of distinguishing their responses from that of humans pose potential threats to teaching and learning.
Post-birth exposure contrasts for children during the Household Air Pollution Intervention Network randomized controlled trial
Authors: Pillarisetti Ajay , Ye Wenlu , Balakrishnan Kalpana , Rosa Ghislaine , Díaz-Artiga Anaité , Underhill Lindsay J. , Steenland Kyle , Peel Jennifer L. , Kirby Miles A. , McCracken John , Waller Lance , Chang Howard , Wang Jiantong , Dusabimana Ephrem , Ndagijimana Florien , Sambandam Sankar , Mukhopadhyay Krishnendu , Kearns Katherine A. , Campbell Devan , Kremer Jacob , Rosenthal Joshua , Ghosh Ahana , Clark Maggie , Checkley William , Clasen Thomas , Naeher Luke , Piedrahita Ricardo , Johnson Michael 
Published: July 2023

AbstractExposure to household air pollution is a leading cause of ill-health globally. The Household Air Pollution Intervention Network (HAPIN) randomized controlled trial evaluated the impact of a free liquefied petroleum gas stove and fuel intervention on birth outcomes and maternal and child health. As part of HAPIN, an extensive exposure assessment was conducted. Here, we report on PM2.5and CO exposures of young children (≤ 15 months old) reconstructed using a Bluetooth-beacon based time-activity monitoring system coupled with microenvironmental pollutant monitors. Median (IQR) exposures to PM2.5were 65.1 (33 – 128.2) µg/m3in the control group and 22.9 (17.2 – 35.3) µg/m3 in the intervention group; for CO, median (IQR) exposures were 1.1 (0.3 – 2.9) ppm and 0.2 (0 – 0.7) ppm for control and intervention group, respectively. Exposure reductions were stable over time and consistent with previous findings for the children’s mothers. In the intervention group, 75% of children’s reconstructed exposures were below the WHO interim target guideline value of 35 µg/m3, while 26% were below the standard in the control group. Our findings suggest that an LPG fuel and stove intervention can substantially reduce children’s exposure to household air pollution.
Online Database of Clinical Algorithms with Race and Ethnicity
Authors: Visweswaran Shyam , Sadhu Eugene M. , Morris Michele M. , Vis Anushka R. , Samayamuthu Malarkodi Jebathilagam 
Published: July 2023

ABSTRACTSome clinical algorithms incorporate an individual’s race, ethnicity, or both as an input variable or predictor in determining diagnoses, prognoses, treatment plans, or risk assessments. Inappropriate use of race and ethnicity in clinical algorithms at the point of care may exacerbate health disparities and promote harmful practices of race-based medicine. We identified 42 risk calculators that use race as a predictor, five laboratory test results with different reference ranges recommended for different races, one therapy recommendation based on race, 15 medications with guidelines for initiation and monitoring based on race, and four medical devices with differential racial performance. Information on these clinical algorithms are freely available athttp://www.clinical-algorithms-with-race-and-ethnicity.org. This resource aims to raise awareness about the use of race in clinical algorithms and to track the progress made toward eliminating its inappropriate use. The database will be actively updated to include clinical algorithms based on race that were missed, along with additional characteristics of these algorithms.
Functional variations in gamma-secretase activity are critical determinants of the clinical, biomarker, and cognitive progression of autosomal dominant Alzheimer’s disease
Authors: Schultz Stephanie A. , Liu Lei , Schultz Aaron P. , Fitzpatrick Colleen D. , Levin Raina , Bellier Jean-Pierre , Shirzadi Zahra , Joseph-Mathurin Nelly , Chen Charles D. , Benzinger Tammie L.S. , Day Gregory S. , Farlow Martin R. , Gordon Brian A. , Hassenstab Jason J. , Jack Clifford R. , Jucker Mathias , Karch Celeste M. , Lee Jae-Hong , Levin Johannes , Perrin Richard J. , Schofield Peter R , Xiong Chengjie , Johnson Keith A. , McDade Eric , Bateman Randall J. , Sperling Reisa A. , Selkoe Dennis J. , Chhatwal Jasmeer P. ,   Dominantly Inherited Alzheimer Network Investigators
Published: July 2023

ABSTRACTBackgroundThe balance between production, clearance, and toxicity of Aβ peptides is central to Alzheimer’s disease (AD) pathobiology. Though highly variable in terms of age at symptom onset (AAO), hundreds of variants inPSEN1cause autosomal dominant forms of AD (ADAD) with nearly complete penetrance. PSEN1 forms the catalytic core of the γ-secretase complex and thereby directly mediates the production of longer, aggregation-prone Aβ peptides relative to shorter, non-aggregating peptides. We hypothesized that the broad AAO and biomarker heterogeneity seen across ADAD would be predictable based on mutation-specific differences in the production of Aβ species.MethodsAβ-37, 38, 40, 42, and 43 production was quantified from 161 uniquePSEN1variants expressed in HEK293 cells. Prediction of AAO was carried out in 106 variants with available AAO and then replicated in 55 variants represented across 190 PSEN1 mutation carriers who have detailed cognitive and biomarker data from the Dominantly Inherited Alzheimer’s Network (DIAN).ResultsVariations in Aβ production across the 161 mutations examined in cell-based models were highly predictive of AAO. In those with correspondingin vivodata from the DIAN study, our cell-based γ-secretase composite was strongly associated with biomarker and cognitive trajectories.ConclusionsThese findings elucidate the critical link between γ-secretase function, Aβ production, and AD progression and offer mechanistic support for the amyloid hypothesis. The approach used here represents a powerful tool to account for heterogeneity in disease progression in ADAD clinical trials and to assess the pathogenicity of variants of unknown significance or with limited family history.