bluuebunny/crossref_metadata_2025_split huggingface dataset:
Proteomic analysis of the pyrenoid-traversing membranes ofChlamydomonas reinhardtiireveals novel components
Authors: Franklin Eric , Wang Lianyong , Cruz Edward Renne , Duggal Keenan , Ergun Sabrina L. , Garde Aastha , Jonikas Martin C. 
Published: November 2024

SummaryPyrenoids are algal CO2-fixing organelles that mediate approximately one-third of global carbon fixation and hold the potential to enhance crop growth if engineered into land plants. Most pyrenoids are traversed by membranes that are thought to supply them with concentrated CO2. Despite the critical nature of these membranes for pyrenoid function, they are poorly understood, with few protein components known in any species.Here we identify protein components of the pyrenoid-traversing membranes from the leading model algaChlamydomonas reinhardtiiby affinity purification and mass spectrometry of membrane fragments. Our proteome includes previously-known proteins as well as novel candidates.We further characterize two of the novel pyrenoid-traversing membrane-resident proteins, Cre10.g452250, which we name Pyrenoid Membrane Enriched 1 (PME1), and LCI16. We confirm their localization, observe that they physically interact, and find that neither protein is required for normal membrane morphology.Taken together, our study identifies the proteome of pyrenoid-traversing membranes and initiates the characterization of a novel pyrenoid-traversing membrane complex, building toward a mechanistic understanding of the pyrenoid.
Neural basis of negative future mental imagery-based simulation in the bipolar disorder spectrum
Authors: Di Simplicio Martina , Visser Renee M. , Alfarano Giorgio , Ji Julie L. , Suri Sana , Holmes Emily A. 
Published: November 2024

AbstractObjectivesDysfunctional mental imagery-based simulations of emotional future events (episodic future simulation) - can contribute to emotional dysregulation in the bipolar disorder spectrum (BPDS). For example, vividly imaging social encounters having a disastrous outcome can trigger low mood. However, episodic future simulation may be perceptually modified to reduce their emotional intensity, which may in turn reduce BPDS mood instability. This study investigates the neural bases of perceptual and emotional characteristics of negative episodic future simulation in BPDS, and of perceptually manipulating such imagery.MethodsEuthymic participants with BPDS (N=20) and healthy controls (HC, N=17) underwent an fMRI scan whilst generating, then perceptually modifying, negative episodic future imagery, and during rest.ResultsNegative episodic future imagery were rated as significantly morerealandunpleasantin the BPDS compared to HC group. Critically, perceptual manipulation of such imagery reduced ratings in the BPDS group to HC levels. Whole-brain analyses of task-based neural activity revealed greater activation in networks including right frontal pole, middle and inferior frontal gyrus and insula during episodic future simulation in BPSD versus HC. BPDS participants showed greater intrinsic resting state functional connectivity within the default mode network than HC participants.ConclusionsFindings suggest dysfunctional episodic future simulation circuitry across default mode network, fronto-parietal and fronto-insular areas may represent a neural mechanism via which mental imagery amplifies emotion in BPDS. Perceptual modifications to dampen such imagery successfully abolished subjective and neural differences between groups, indicating promise as an intervention tool targeting mood instability.
Parenthood, Mental Disorders, and Symptoms Through Adulthood: A Total Population Study
Authors: Andersen ML , Sunde HF , Hart RK , Torvik FA 
Published: November 2024

AbstractDuring recent decades, parenthood has declined in many Western countries. Simultaneously, mental disorders have become more prevalent. We investigated the link between parenthood and mental health in the entire Norwegian-born population aged 31 to 80 from 2006 to 2019 (n=2,234,087). We used logistic regression models on national register data and included sibling- and twin-matched analyses to address unobserved confounders. Parenthood was associated with a lower risk of mental disorders, including depressive and anxiety disorders. For symptoms related to mental disorders, fathers had a reduced risk, while mothers had a slightly elevated risk. Mental health disparities between parents and non-parents were greater among men than among women and persisted across adulthood, before reducing at older ages. Our main findings were largely consistent in sibling- and twin-matched designs. The disparity between parents and non-parents increased over the study period, suggesting stronger selection into parenthood. Our findings highlight parenthood as a significant indicator of mental health inequalities, with its importance growing over time.
The Whole Proteome, Phosphoproteome, and Glycoproteome Landscape of Pan-Cancer Cell Lines Profiled by Mass Spectrometry and Reverse Phase Protein Array
Authors: Wenhao Shi , Tianlong He , Wang Nan , Qian Annan , Liu Yuqiao , Shaojun Tang , Yiying Zhu 
Published: November 2024

AbstractMammalian cancer cell lines are essential model systems in biomedical research. We conducted multi-level proteomics analyses on 54 widely used cancer cell lines derived from various tissue-of-origins using two prominent proteomics technologies: mass spectrometry (MS) and reverse-phase protein array (RPPA). Our analysis identified 10,088 proteins, 33,609 phosphorylation sites across 7,289 phosphoproteins, and 56,350 site-specific glycans on 16,296 glycosylation sites from 5,966 glycoproteins, along with 305 drug-relevant protein and phosphoprotein targets. Our results reveal both consistent and distinct patterns in protein expression and modification between MS and RPPA, underscoring their complementary strengths as discovery tools. Additionally, we identified protein features that distinguish tissue origins across different cell line lineages. This dataset supports model system selection for drug target-related studies in vitro and provides valuable insights into key signaling pathways. Overall, this comprehensive resource enables new opportunities for exploration in cancer biology and offers significant value to research communities focused on biomarker profiling, drug target discovery, and understanding mechanisms across diverse cancer types.
Co-existence of ST-Segment Depression and Exaggerated Blood Pressure Response in Older Runners
Authors: Manabe Kazumasa , Beck Owen N. , Ortega Justus D. , Tanaka Hirofumi 
Published: November 2024

ABSTRACTExercise stress tests are typically performed on symptomatic patients and those at elevated risks of ischemic heart disease. In more recent years, these tests are increasingly recommended for masters athletes who regularly perform exercise training. In the sample of apparently healthy physically active older adults who were recruited for a research study to evaluate exercise economy, we found the coexistence of ST-segment depression and exaggerated BP response in older runners. These findings are consistent with the notion that the screening and assessment of cardiovascular risks should be extended to masters athletes who vigorously train regularly and are seemingly healthy.
GENCODE: massively expanding the lncRNA catalog through capture long-read RNA sequencing
Authors: Kaur Gazaldeep , Perteghella Tamara , Carbonell-Sala Sílvia , Gonzalez-Martinez Jose , Hunt Toby , Mądry Tomasz , Jungreis Irwin , Arnan Carme , Lagarde Julien , Borsari Beatrice , Sisu Cristina , Jiang Yunzhe , Bennett Ruth , Berry Andrew , Cerdán-Vélez Daniel , Cochran Kelly , Vara Covadonga , Davidson Claire , Donaldson Sarah , Dursun Cagatay , González-López Silvia , Gopal Das Sasti , Hardy Matthew , Hollis Zoe , Kay Mike , Montañés José Carlos , Ni Pengyu , Nurtdinov Ramil , Palumbo Emilio , Pulido-Quetglas Carlos , Suner Marie-Marthe , Yu Xuezhu , Zhang Dingyao , Loveland Jane E. , Albà M. Mar , Diekhans Mark , Tanzer Andrea , Mudge Jonathan M. , Flicek Paul , Martin Fergal J , Gerstein Mark , Kellis Manolis , Kundaje Anshul , Paten Benedict , Tress Michael L. , Johnson Rory , Uszczynska-Ratajczak Barbara , Frankish Adam , Guigó Roderic 
Published: November 2024

AbstractAccurate and complete gene annotations are indispensable for understanding how genome sequences encode biological functions. For twenty years, the GENCODE consortium has developed reference annotations for the human and mouse genomes, becoming a foundation for biomedical and genomics communities worldwide. Nevertheless, collections of important yet poorly-understood gene classes like long non-coding RNAs (lncRNAs) remain incomplete and scattered across multiple, uncoordinated catalogs, slowing down progress in the field. To address these issues, GENCODE has undertaken the most comprehensive lncRNAs annotation effort to date. This is founded on the manual annotation of full-length targeted long-read sequencing, on matched embryonic and adult tissues, of orthologous regions in human and mouse. Altogether 17,931 novel human genes (140,268 novel transcripts) and 22,784 novel mouse genes (136,169 novel transcripts) have been added to the GENCODE catalog representing a 2-fold and 6-fold increase in transcripts, respectively - the greatest increase since the sequencing of the human genome. Novel gene annotations display evolutionary constraints, have well-formed promoter regions, and link to phenotype-associated genetic variants. They greatly enhance the functional interpretability of the human genome, as they help explain millions of previously-mapped “orphan” omics measurements corresponding to transcription start sites, chromatin modifications and transcription factor binding sites. Crucially, our targeted design assigned human-mouse orthologs at a rate beyond previous studies, tripling the number of human disease-associated lncRNAs with mouse orthologs. The expanded and enhanced GENCODE lncRNA annotations mark a critical step towards deciphering the human and mouse genomes.
The fate of artificial transgenes inAcanthamoeba castellanii
Authors: Colp Morgan J. , Blais Cédric , Curtis Bruce A. , Archibald John M. 
Published: November 2024

AbstractIn this study, artificial transformation experiments were performed to investigate how theA. castellaniigenome responds to foreign DNA presented in both circular and linear plasmid form. Nanopore sequencing was used as a high throughput method to screen for transgene DNA in the resulting transformant cultures, and candidate transgene integrations were identified. Molecular biology experiments were performed to validate the sequence data and provide additional context on the fate of transgenes. A method was devised to estimate the rate of read chimerism in nanopore sequencing runs and accurately account for the effects of read chimerism in identifying putative transgene integrations. Based on the experimental data in hand, a potential mechanism for transgene maintenance inA. castellaniiis proposed, one in which incoming foreign DNA is tandemly duplicated and telomeres are added to the ends. This nascent linear molecule is maintained as a transgene-bearing minichromosome, while also allowing for chromosomal integration.
Optimal competitors: the balance of attraction and choices of mutualists, like pollinators, drives facilitation and may promote crop pollination
Authors: Dornhaus Anna , Houston Alasdair I. 
Published: November 2024

AbstractWhen two species use the same resource, this typically leads to competition, such as when different plants aim to attract the same mutualist pollinators. However, more flowers may also attract more pollinators to the area. Depending on which process dominates, one or both ‘competitors’ may actually benefit from the other’s presence: a phenomenon called ‘pollination facilitation’ in plant ecology. For example, it has been argued that strips of wildflowers planted next to crops may attract pollinators who ‘spill over’ into the crop. Here we mathematically examine the tradeoff between facilitation and competition in consumer attraction. We show that contrary to previous claims, no accelerating benefits of densityper seare necessary for facilitation. Instead, under very general assumptions, an imbalance between local competition and joint attraction of consumers can generate a benefit to at least one ‘competitor’. This typically leads to maximal benefit to the crop at a low presence of highly attractive ‘wildflowers’ (i.e. plants that share pollinators with the crop). Our results generalize to many contexts where local competition may trade off with joint attraction of consumers. In such situations, the exact effect of competitor density on attraction of consumers can qualitatively shape outcomes, including facilitation or competition.
Modeling and Optimizing Deep Brain Stimulation to Enhance Gait in Parkinson’s Disease: Personalized Treatment with Neurophysiological Insights
Authors: Azgomi Hamid Fekri , Louie Kenneth H. , Bath Jessica E. , Presbrey Kara N. , Balakid Jannine P. , Marks Jacob H. , Wozny Thomas A. , Galifianakis Nicholas B. , Luciano Marta San , Little Simon , Starr Philip A. , Wang Doris D. 
Published: November 2024

AbstractAlthough high-frequency deep brain stimulation (DBS) is effective at relieving many motor symptoms of Parkinson’s disease (PD), its effects on gait can be variable and unpredictable. This is due to 1) a lack of standardized and robust metrics for gait assessment in PD patients, 2) the challenges of performing a thorough evaluation of all the stimulation parameters space that can alter gait, and 3) a lack of understanding for impacts of stimulation on the neurophysiological signatures of walking. In this study, our goal was to develop a data-driven approach to identify optimal, personalized DBS stimulation parameters to improve gait in PD patients and identify the neurophysiological signature of improved gait. Local field potentials from the globus pallidus and electrocorticography from the motor cortex of three PD patients were recorded using an implanted bidirectional neural stimulator during overground walking. A walking performance index (WPI) was developed to assess gait metrics with high reliability. DBS frequency, amplitude, and pulse width on the “clinically-optimized” stimulation contact were then systemically changed to study their impacts on gait metrics and underlying neural dynamics. We developed a Gaussian Process Regressor (GPR) model to map the relationship between DBS settings and the WPI. Using this model, we identified and validated personalized DBS settings that significantly improved gait metrics. Linear mixed models were employed to identify neural spectral features associated with enhanced walking performance. We demonstrated that improved walking performance was linked to the modulation of neural activity in specific frequency bands, with reduced beta band power in the pallidum and increased alpha band pallidal-motor cortex coherence synchronization during key moments of the gait cycle. Integrating WPI and GPR to optimize DBS parameters underscores the importance of developing and understanding personalized, data-driven interventions for gait improvement in PD.
Protein associations and protein–metabolite interactions with depressive symptoms and the p-factor
Authors: Whipp Alyce M , Drouard Gabin , Rose Richard J , Pulkkinen Lea , Kaprio Jaakko 
Published: November 2024

AbstractDespite increasing mental health problems among young people, few studies have examined associations between plasma proteins and mental health, and interactions between proteins and metabolites in association with mental health problems remain underexplored. In 730 twins, we quantified associations between plasma proteins measured at age 22 with 21 indicators representing either depressive symptoms or the p-factor, collected from questionnaires and interviews completed by different raters (e.g., self-report, teachers) through adolescence to young adulthood (12 to 22 years), and tested for interactions with metabolites. We found 47 proteins associated with depressive symptoms or the p-factor (FDR<0.2), 9 being associated with both. Two proteins, contactin-1 and mast/stem cell growth factor receptor kit, positively interacted with valine levels in explaining p-factor variability. In conclusion, our study demonstrates strong associations between plasma proteins and mental health and provides evidence for proteome– metabolome interactions in explaining higher levels of mental health problems.
Spatial Patterns of COVID-19 Mortality: Examining Socioeconomic Determinants in U.S. Counties Using Cluster Analysis
Authors: Wardrup Robert Ross 
Published: November 2024

AbstractAimThis study aims to investigate the spatial patterns of COVID-19 mortality across U.S. counties and identify the socioeconomic determinants that influence these mortality trends, using spatial epidemiological methods.Subject and MethodsWe conducted a spatial analysis of COVID-19 mortality data from over 3,000 U.S. counties, applying cluster detection techniques, including SatScan, to identify areas with significant mortality trends. Spatial regression models, including spatial lag and spatial error models, were employed to examine the impact of socioeconomic variables, such as race, income inequality, and insurance rates, on COVID-19 mortality. The analysis controlled for multicollinearity and spatial autocorrelation in the data.ResultsCounties with higher proportions of Black populations and higher uninsured rates exhibited significantly lower COVID-19 trends over the study period. Spatial clustering revealed regions in the northwestern and eastern/northeastern United States with a mix of positive and negative mortality rate trends. The spatial lag model showed the strongest fit, confirming the importance of spatial dependency in explaining mortality patterns.ConclusionThis study highlights the significant spatial disparities in COVID-19 mortality across U.S. counties. The findings emphasize the need for targeted public health interventions in vulnerable regions to address these disparities.
Multicenter Comparison of AI Deep Learning Reconstruction, Iterative Reconstruction, and Filtered Back Projection for Coronary Artery Calcification Scoring
Authors: Winkler Alena R. , Campos June D. , Winkler Mark L. 
Published: November 2024

ABSTRACTObjectiveTo validate the feasibility of AI Deep Learning Reconstruction for Coronary Artery Calcification Scoring in order to decrease radiation exposure on a 4cm detector CT scanner. This is the first such validation on devices that are most commonly utilized for this procedure.MethodsData from 105 consecutive patients referred for Coronary Artery Calcification Scoring (CACS) in 4 centers was reconstructed with Filtered Back Projection (FBP), Iterative Reconstruction (Hybrid-IR), and AI Deep Learning Reconstruction (AI DLR), and analyzed both quantitatively and qualitatively to determine if AI DLR can be routinely used for this purpose. Additional phantom testing was performed to determine if further dose reduction can be accomplished with AI DLR while maintaining or improving image quality compared to current Hybrid-IR reconstruction.ResultsQuantitively, there was excellent agreement between the three reconstructions (FBP, Hybrid IR and AI DLR) with an interclass coefficient of 0.99. The mean CACS for Filtered Back Projection Reconstructions was 111.05. The mean CACS for Hybrid-IR was 91.30. The mean CACS for AI Deep Learning Reconstructions was 93.50. Qualitatively, image quality was consistently better with AI DLR than with Hybrid-IR at both soft tissue and lung windowing. Based on our phantom experiments, AI DLR allows for dose reduction of at least a 37% without any image quality penalty compared to Hybrid-IR.ConclusionsThe use of AI DLR for use in CACS on 4 cm coverage CT scanner has been quantitatively and qualitatively validated for use for the first time. AI DLR produces qualitatively and quantitively better image quality than Hybrid-IR at the same dose level, and produces good agreement in categorization of Agatston scores. In vivo and in vitro evaluations show that AI DLR will allow for an at least a 37% further dose reduction on a 4 cm coverage CT scanner.
Perspectives on the implementation of post-validation surveillance for lymphatic filariasis in the Pacific Islands: A Nominal Group Technique-based study protocol
Authors: Craig Adam T , Lawford Harriet , Viali Satupaitea , Tuitama George , Lau Colleen L 
Published: November 2024

AbstractIntroductionLymphatic filariasis (LF) is a neglected tropical disease caused by parasitic worms, transmitted via mosquito bites. Significant global efforts have led to the interruption of LF transmission, with eight of the 16 previously endemic Pacific Island countries and territories (PICTs) validated by WHO as having eliminated the disease as a public health problem. Post-validation surveillance (PVS) is recommended to verify the absence of a resurgence in transmission; however, there are no guidelines on how to implement such surveillance effectively.AimThis protocol outlines a research study that aims to explore, synthesise, and prioritise the perspectives of LF program staff from LF-eliminated PICTs. The study will focus on identifying the challenges faced in implementing PVS in the PICT settings and determining corresponding context-relevant operational research priorities.MethodThe study will employ a nominal group technique (NGT) involving representatives from LF-eliminated PICTs. The NGT will adhere to a structured process for generating, ranking, and prioritising ideas, followed by group discussions, debates, and the collation of shared views.DiscussionThe research will provide insights into the most significant challenges faced in implementing PVS in the PICTs. It will also identify priority areas where operational research is required to inform policy and practice. To our knowledge, this study is the first to apply a rigorous consensus group method to distil challenges and research priorities for LF PVS in PICTs. We expect this research to inform the development of national and regional LF guidelines.