bluuebunny/crossref_metadata_2025_split huggingface dataset:
Temporal and Thematic Analysis of Promotional Waterpipe-Related Posts on Twitter/X in the US
Authors: Ye Puhua , Wu Mengwei , Han Yiwei , Shimazaki Yuka , Cornacchione Ross Jennifer , Sutfin Erin L. , Li Dongmei , Xie Zidian 
Published: October 2024

AbstractIntroductionWaterpipe tobacco smoking (WTS), also known as hookah, shisha, or narghile, is particularly popular among young people in the United States (US). WTS poses serious health risks similar to those of cigarette smoking.MethodsUsing the Twitter/X streaming API (Application Programming Interface), we collected 4,853,562 tweets between March 9, 2021, and March 14, 2023, using waterpipe-related keywords, such as “hookah” and “waterpipe”. After geographical filtering to identify tweets from the US and keyword filtering for the promotional content, we identified 23,803 promotional waterpipe-related tweets. We examined trends in the posting time of these promotional waterpipe-related tweets and identified prevalent topics from these tweets using the BERTopic (Bidirectional Encoder Representations from Transformers) modeling.ResultsThe number of promotional waterpipe-related tweets showed an overall decreasing trend during the study period. The posting of promotional waterpipe-related tweets was more active later in the day. Major topics in the promotional tweets included “Promotion from hookah lounges and online hookah business" (63.97%, 15,227/23,803), "promoting hookah parties and events" (32.26%, 7,679/23,803), and "promoting engineered and durable hookah products" (3.77%, 897/23,803). Twitter/X accounts posting waterpipe-related promotional content have substantial variations in the number of relevant tweets (mean = 2.28, SD = 12.22) and followers (mean = 5,937, SD = 76,770).ConclusionsThis study demonstrates a significant social media activity in promoting waterpipe tobacco smoking. Our findings underscore the urgent need to regulate the promotional content of WTS on social media and promote public health education messages on social media to counteract the promotion of WTS.
Mediation analyses link cardiometabolic factors and liver fat with white matter hyperintensities and cognitive performance: A UK Biobank study
Authors: Askeland-Gjerde Daniel E. , Westlye Lars T. , Andersson Patrik , Korbmacher Max , de Lange Ann-Marie , van der Meer Dennis , Smeland Olav B. , Halvorsen Sigrun , Andreassen Ole A. , Gurholt Tiril P. 
Published: October 2024

AbstractBackgroundLiver fat is associated with cardiometabolic disease, cerebrovascular disease, and dementia. Cerebrovascular disease, most frequently cerebral small vessel disease, identified by MRI as white matter hyperintensities (WMH), often contributes to dementia. However, liver fat’s role in the relationship between cardiometabolic risk, WMH, and cognitive performance is unclear.MethodsIn the UK Biobank cohort (n=32,628; 52.6% female; mean age 64.2±7.7 years; n=23,467 cognitive performance subsample), we used linear regression to investigate associations between cardiometabolic factors measured at baseline and liver fat, WMH, and cognitive performance measured at follow-up, on average, 9.3±2.0 years later. We used structural equation modeling to investigate whether liver fat mediates associations between cardiometabolic factors and WMH and whether WMH mediates associations between liver fat and cognitive performance.ResultsNearly all cardiometabolic factors were significantly associated with liver fat (|r| in [0.03,0.41], p in [1.4x10-8,0〉) and WMH (|r| in [0.05,0.14], p in [1.5x10-13,2.7x10-148]) in regression models. Liver fat was associated with WMH (r=0.09,p=3x10-64) and cognitive performance (r=-0.03,p=1.5x10-7). Liver fat mediated the associations between cardiometabolic factors and WMH (|βmediation| in [0.01,0.03], pmediation in [5.7x10-9,0〉) and WMH mediated the associations between liver fat and cognitive performance (βmediation=-0.01,pmediation≍0).ConclusionsOur findings indicate that liver fat mediates associations between cardiometabolic factors and WMH and that WMH mediates the association between liver fat and cognitive performance. This suggests that liver fat might be important for understanding the effects of cardiometabolic factors on cerebrovascular disease and cognitive function. Experimental studies are warranted to determine relevant targets for preventing vascular-driven cognitive impairment.
What role do adolescents’ independent food purchasing choices play in their dietary quality?
Authors: Shaw Sarah , Crozier Sarah , Cooper Cyrus , Smith Dianna , Barker Mary , Vogel Christina 
Published: October 2024

AbstractDuring adolescence, many young people start to make more independent food purchases. Subsequently, these independent food choices will increasingly contribute to their overall diet quality; little is known, however, about this relationship. This study aimed to examine the role adolescents’ independent food purchases play in their diet quality and assess if these relationships vary according to socio-economic status.A convenience sample of adolescents aged 11-18 years and attending secondary school or college in Hampshire, England, were recruited to participate in a one-week cross-sectional observational study. A validated 20-item Food Frequency Questionnaire assessed diet quality. Participants used an ecological momentary assessment mobile phone app to record food purchases.Over seven days, 552 food/drink items were purchased on 253 food purchasing occasions by 80 participants. The majority of purchases (n=329, 60%) were coded as ‘not adhering’ to the UK Eatwell Guide, 32% were coded as ‘adhering’ and 9% fell between these two categories. Healthier food purchasing was associated with better diet quality (β 0.48, (95%CI 0.01, 0.96) p=0.05); results attenuated after adjustment for confounders (β 0.36, (95%CI −0.15, 0.87) p=0.16). Interaction models showed purchasing healthfulness was more strongly associated with diet quality among young people of lower SES (p=0.01). The majority of adolescents’ independent food purchases did not adhere to healthy eating guidelines. For adolescents experiencing socioeconomic disadvantage, these food choices had a more detrimental impact on their overall diet quality than they did for more advantaged adolescents. Future research should focus on identifying ways to support more healthful independent food choices by adolescents to reduce dietary inequalities and improve health and well-being among the next generation of adults.
Effects of the COVID-19 pandemic on TB outcomes in the United States: a Bayesian analysis
Authors: Swartwood Nicole A. , Cohen Ted , Marks Suzanne M. , Hill Andrew N. , Asay Garrett R. Beeler , Self Julie , Feng Pei-Jean I. , Robert Horsburgh C. , Salomon Joshua A. , Menzies Nicolas A. 
Published: October 2024

AbstractBackgroundTuberculosis (TB) cases and deaths in the United States fluctuated substantially during the COVID-19 pandemic. We analyzed multiple data sources to understand the factors contributing to these changes and estimated future TB trends.MethodsWe identified four mechanisms potentially contributing to observed TB trends during 2020– 2023: immigration, respiratory contact rates, rates of accurate diagnosis and treatment initiation, and mortality rates for persons with TB disease. We employed a Bayesian approach to synthesize evidence on how these mechanisms changed during the pandemic and how they might have combined to produce observed 2020–2023 TB data, using a transmission-dynamic model to link mechanisms to TB outcomes. We also simulated a no-pandemic counterfactual scenario that assumed mechanisms followed pre-pandemic trends. We estimated TB outcomes associated with the pandemic until 2035 to capture lagged effects. We evaluated additional scenarios to estimate the individual effect of each mechanism.ResultsOver the 2020–2035 study period, we estimate an additional 2,784 (95% uncertainty interval: 2,164–3,461) TB cases and 1,138 (1,076–1,201) TB deaths in the United States associated with changes occurring during the COVID-19 pandemic. The four mechanisms had offsetting effects – decreases in TB diagnosis rates and increases in TB mortality rates led to more TB deaths, while reductions in contact rates reduced TB deaths. Immigration changes initially reduced TB deaths, but increased deaths over time.DiscussionWhile the direct impacts of the COVID-19 pandemic occurred between 2020–2023, these changes may continue to influence TB incidence and mortality in future years.SummaryThe COVID-19 pandemic disrupted steady declines in U.S. tuberculosis rates. Despite sharp decreases in TB cases over 2020–2021, we projected there would be 2,784 additional TB cases and 1,138 additional TB deaths during 2020–2035 associated with pandemic-related changes.
Predicting the natural yeast phenotypic landscape with machine learning
Authors: Khaiwal Sakshi , Chiara Matteo De , Barré Benjamin P , Barrio-Hernandez Inigo , Stenberg Simon , Beltrao Pedro , Warringer Jonas , Liti Gianni 
Published: October 2024

SummaryMost organisms’ traits result from the complex interplay of many genetic and environmental factors, making their prediction from genotypes difficult. Here, we used machine learning models to explore genotype-phenotype connections for 223 life history traits measured across 1011 genome-sequencedSaccharomyces cerevisiaestrains. Firstly, we used genome-wide association studies to connect genetic variants with the phenotypes. Next, we benchmarked an automated machine learning pipeline that includes preprocessing, feature selection, and hyperparameters optimization in combination with multiple linear and complex machine learning methods. We determined gradient boosting machines as best performing in 65% of predictions and pangenome as best predictor, suggesting a considerable contribution of the accessory genome in controlling phenotypes. The accuracy broadly varied among the phenotypes (r = 0.2-0.9), consistent with varying levels of complexity, with stress resistance being easier to predict compared to growth across carbon and nitrogen nutrients. While no specific genomic features could be linked to the predictions for most phenotypes, machine learning identifies high-impact variants with established relationships to phenotypes despite being rare in the population. Near-perfect accuracies (r>0.95) were achieved when other phenomics data were used to aid predictions, suggesting shared useful information can be conveyed across phenotypes. Overall, our study underscores the power of machine learning to interpret the functional outcome of genetic variants.
Failure to reproduce the effect of procedural memory interference on wakeful consolidation of episodic memory in younger and older adults
Authors: Kamal Lara , Celik Busra , Alpert Griffin , Gonzalez Samantha , Nguyen Vian , Freedberg Michael 
Published: October 2024

AbstractBrown and Robertson (2007) revealed that skill learning interferes with the wakeful consolidation of episodic memories in young adults. This finding is commonly used as evidence that episodic and procedural memories should not be learned in close temporal proximity but has not been reproduced by an independent laboratory. Additionally, older adults experience episodic memory deficits, but it is unknown whether this group is also vulnerable to this type of interference. We aimed to reproduce Brown and Robertson’s (2007) finding in younger adults, while also comparing the magnitude of interference between younger and older adults. Forty younger (18-40 years; n =20) and older adults (≥55 years; n = 20) visited the laboratory in the morning and acquired episodic memories (a list of words) immediately before a procedural finger-tapping (procedural) task. Half of all participants were exposed to a learnable sequential structure. In the afternoon of the same day, participants were asked to recall the episodic memories from the morning session. We found weak evidence of interference for both age groups and no statistical difference in interference between groups. Our results suggest that the interfering effects of these memory types may be negligible or overestimated, and that these memory types can be acquired together without interference.
Uncovering locomotor learning dynamics in people with Parkinson’s disease
Authors: Kim Aram , Schweighofer Nicolas , Petzinger Giselle M. , Finley James M. 
Published: October 2024

AbstractLocomotor learning is important for improving gait and balance impairments in people with Parkinson’s disease (PD). While PD disrupts neural networks involved in motor learning, there is a limited understanding of how PD influences the time course of locomotor learning and retention. Here, we used a virtual obstacle negotiation task to investigate whether the early stages of PD affect the acquisition and retention of locomotor skills. On Day 1, 15 participants with PD and 20 age-matched controls were instructed to achieve a specified level of foot clearance while repeatedly stepping over two different virtual obstacles on a treadmill. We assessed online performance improvement on Day 1 and overnight retention after at least 24 hours on Day 2. We used a hierarchical Bayesian state-space model to estimate the learning rate and the degree of interference between the two obstacles. There was a 93% probability that people with PD learned the locomotor skill faster than controls, but there was limited evidence of group differences in interference between the two heights of obstacles. Both groups improved their performance to a similar magnitude during skill acquisition and performed similarly during retention on Day 2. Notably, a slower learning rate was associated with greater online performance improvement, while lower interference was linked to better overnight retention, and this effect was strongest for the control group. These results highlight that people with early-stage PD retain the ability to use multisensory information to acquire and retain locomotor skills. In particular, our finding that people with early-stage PD learned faster than age-matched controls may reflect the emergence of compensatory motor learning strategies used to offset early motor impairments in people with PD.
Phosphorylation Toggles the SARS-CoV-2 Nucleocapsid Protein Between Two Membrane-Associated Condensate States
Authors: Favetta Bruna , Wang Huan , Cubuk Jasmine , Barai Mayur , Ramirez Cesar , Gormley Adam J. , Murthy Sanjeeva , Soranno Andrea , Shi Zheng , Schuster Benjamin S. 
Published: October 2024

SummaryThe SARS-CoV-2 Nucleocapsid protein (N) performs several functions during the viral lifecycle, including transcription regulation and viral genome encapsulation. We hypothesized that N toggles between these functions via phosphorylation-induced conformational change, thereby altering N interactions with membranes and RNA. We found that phosphorylation changes how biomolecular condensates composed of N and RNA interact with membranes: phosphorylated N (pN) condensates form thin films, while condensates with unmodified N are engulfed. This partly results from changes in material properties, with pN forming less viscous and elastic condensates. The weakening of protein-RNA interaction in condensates upon phosphorylation is driven by a decrease in binding between pN and unstructured RNA. We show that phosphorylation induces a conformational change in the serine/arginine-rich region of N that increases interaction between pN monomers and decreases nonspecific interaction with RNA. These findings connect the conformation, material properties, and membrane-associated states of N, with potential implications for COVID-19 treatment.
Parasitic-plant parasite utilizes flowering pathways at unconventional stages to form stem-derived galls
Authors: Udandarao Naga Jyothi , Yamashita Yuki , Ushima Ryo , Tsuchida Tsutomu , Bessho-Uehara Kanako 
Published: October 2024

AbstractGalls induced by various organisms exhibit diverse morphological and physiological characteristics, involving complex plant-insect interactions. Most transcriptome analyses to date have focused on leaf-derived galls. To better understand gall formation mechanisms, we investigated stem-derived galls induced by the weevilSmicronyx madaranuson the parasitic plantCuscuta campestrisat gene expression, cellular, and physiological levels. RNA-seq across four developmental stages identified differentially expressed genes and associated gene ontology terms. Consistent with histological observations, genes related to cell division and the cell cycle were upregulated early but decreased as the gall matured. Similar to leaf-derived galls, we found high expression ofPLETHORAand meristem-related homeobox genes in early gall development, suggesting that stem cell induction and maintenance are involved in various gall types. Like leaf- derived galls, the expression of genes related to floral organ development increased through the gall development. However, their expression patterns were dramatically different: downstream genes in the flowering pathway were highly expressed at the initial gall stage, whereas upstream genes were highly expressed later. This suggests that the weevil might activate the flowering pathway at unconventional stages, potentially rerouting the typical flowering cascade to influence gall development. Unlike the decrease in photosynthesis-related genes in leaf-derived galls, we observed an increase in these genes in galls formed on the stem of the holoparasitic plant. Shading experiments confirmed that photosynthesis is crucial for both gall growth and the weevil. This study highlights how gall-inducers can co-opt host resources and genetic pathways, offering new insights into the complexity of plant-insect interactions.
Spatial and seasonal biodiversity variation in a large Mediterranean lagoon using environmental DNA metabarcoding through sponge tissue collection
Authors: Corral-Lou Andrea , Ramón-Laca Ana , Alcaraz Lourdes , Cassidy Robert , Taboada Sergi , Mariani Stefano , Mercado Borja , Vicente Martin , Pérez-Ruzafa Ángel , Gallego Ramón , Riesgo Ana 
Published: October 2024

AbstractEcosystem monitoring is a fundamental tool to avert biodiversity loss, gathering valuable information that can be used to develop conservation policies, evaluating management outcomes, and guiding science-based decision-making. The Mar Menor costal lagoon (South-East of Spain) has experienced episodes of eutrophication due to intensive agriculture and other human activities, causing mass mortalities of marine fauna. In this scenario, biodiversity monitoring is crucial to evaluate the status of fauna and flora and take appropriate measures. Here, our main objective was to assess faunal composition and its spatial and temporal structure associated with the pillars used to support the built recreational well-being facilities along the Mar Menor. We capitalised on the many sea sponges that settle on these structures by collecting tissue samples for subsequent extraction of filtered environmental DNA (i.e. ‘natural sampler DNA’, nsDNA) in northern and southern areas of the lagoon, both in spring and summer. We metabarcoded all samples at the cytochrome oxidase subunit I gene (COI), and reliably identified 76 taxa belonging to nine different phyla, with annelids, poriferans, molluscs and cnidarians being the richest groups. We detected emblematic species of threatened status, such as pipefishes (genusSyngnathus) and the piddock clam,Pholas dactylus, and others known to become invasive, such as the ascidiansStyela canopusandBotrylloides niger, the barnacleAmphibalanus amphitrite, and the polychaetesBranchiomma bairdiandBranchiomma boholense. The use of common and widely distributed sponges as natural eDNA samplers allowed us to characterise both spatial and temporal diversity, further emphasizing the importance of this low-cost approach to monitoring biological communities in shallow coastal ecosystems.
Small molecule-directed differentiation of submerged-cultured human nasal airway epithelia for respiratory disease modelling
Authors: Dreyer Henriette H.M. , Ithakisiou Georgia-Nefeli , Spelier Sacha , Iwanski Malina K. , Katrukha Eugene , Terstappen Jonne , Rodenburg Lisa W. , den Hertog-Oosterhoff Loes A. , Smits Shannon M.A. , van der Windt Isabelle S. , Azink Lotte T. , Bijlard Linda H.M. , Passier Koen , van Beuningen Sam F.B. , Lebbink Robert Jan , Haarman Eric G. , van der Ent Cornelis K. , Kapitein Lukas C. , Bont Louis J. , Beekman Jeffrey M. , Amatngalim Gimano D. 
Published: October 2024

AbstractSubmerged cultures of undifferentiated or transformed epithelial cells are widely used in respiratory research due to their ease of use and scalability. However, these systems fail to capture the cellular diversity of the human airway epithelium. In this study, we developed anin vitromodel where cryopreserved human nasal epithelial cells, collected by brushings, are differentiated under submerged conditions on standard plastic cultureware. By applying small-molecule inhibitors targeting Notch and BMP signaling, we achieved efficient differentiation of cultures containing basal, secretory, and ciliated cells. This approach supports scalable culturing of both 2D epithelial monolayers and 3D organoids, validated as (personalized) disease models for primary ciliary dyskinesia, cystic fibrosis, and respiratory syncytial virus infection. This model offers a cost-effective, scalable platform that combines the simplicity of traditional cultures with the cellular complexity of the human airway epithelium, providing a valuable tool for respiratory disease research.
Charting the landscape of cytoskeletal diversity in microbial eukaryotes
Authors: Mikus Felix , Ramos Armando Rubio , Shah Hiral , Olivetta Marine , Borgers Susanne , Hellgoth Jonas , Saint-Donat Clémence , Araújo Margarida , Bhickta Chandni , Cherek Paulina , Bilbao Jone , Txurruka Estibalitz , Leisch Nikolaus , Schwab Yannick , Husnik Filip , Seoane Sergio , Probert Ian , Guichard Paul , Hamel Virginie , Dey Gautam , Dudin Omaya 
Published: October 2024

AbstractMicrobial eukaryotes are small and often resistant to standard labelling and imaging techniques, and therefore remain understudied – despite their critical ecological importance - with the exception of a few established models. Here, we use Ultrastructure Expansion Microscopy (U-ExM) to carry out high-resolution volumetric imaging of over 200 cultured planktonic eukaryotes across major lineages. By combining U-ExM with pan- and specific immuno-labelling, we reveal novel microtubule and centrin-containing elements and assign molecular identities to enigmatic cytoskeletal structures observed previously only by electron microscopy. Our investigation represents the first systematic survey of the extensive cytoskeletal diversity on display across the eukaryotic tree, including the major species groups of dinoflagellates, haptophytes, ciliates, euglenids, cryptomonads, and green algae. Our U-ExM approach extends to mixed environmental samples, paving the way for environmental cell biology at ultrastructural resolution and unprecedented scale, a crucial step towards understanding and protecting complex ecosystems in the face of biodiversity loss.