bluuebunny/crossref_metadata_2025_split huggingface dataset:
Widespread shallow mesoscale circulations observed in the trades
Authors: George Geet , Stevens Bjorn , Bony Sandrine , Vogel Raphaela , Naumann Ann Kristin 
Published: July 2023

AbstractUnderstanding the drivers of cloud organization is crucial for accurately estimating cloud feedbacks and their contribution to climate warming. Shallow mesoscale circulations are thought to play an important role in cloud organization, but they have not been observed. Here we present observational evidence for the existence of shallow mesoscale overturning circulations using divergence measurements made during the EUREC4A field campaign in the North Atlantic trades. Meteorological re-analyses reproduce the observed low-level divergence well and confirm the circulations to be mesoscale features (around 200 km across). We find that the shallow mesoscale circulations are associated with large variability in mesoscale vertical velocity and amplify moisture variance at the cloud base. Through their modulation of cloud-base moisture, the circulations influence how efficiently the subcloud layer dries, thus producing moist ascending branches and dry descending branches. The observed moisture variance differs from expectations from large-eddy simulations, which show the largest variance near the cloud top and negligible subcloud variance. The ubiquity of shallow mesoscale circulations, and their coupling to moisture and cloud fields, suggests that the strength and scale of mesoscale circulations are integral to determining how clouds respond to climate change.
Light-induced hexatic state in a layered quantum material
Authors: Domröse Till , Danz Thomas , Schaible Sophie F. , Rossnagel Kai , Yalunin Sergey V. , Ropers Claus 
Published: July 2023

AbstractThe tunability of materials properties by light promises a wealth of future applications in energy conversion and information technology. Strongly correlated materials such as transition metal dichalcogenides offer optical control of electronic phases, charge ordering and interlayer correlations by photodoping. Here, we find the emergence of a transient hexatic state during the laser-induced transformation between two charge-density wave phases in a thin-film transition metal dichalcogenide, 1T-type tantalum disulfide (1T-TaS2). Introducing tilt-series ultrafast nanobeam electron diffraction, we reconstruct charge-density wave rocking curves at high momentum resolution. An intermittent suppression of three-dimensional structural correlations promotes a loss of in-plane translational order caused by a high density of unbound topological defects, characteristic of a hexatic intermediate. Our results demonstrate the merit of tomographic ultrafast structural probing in tracing coupled order parameters, heralding universal nanoscale access to laser-induced dimensionality control in functional heterostructures and devices.
Hole-limited electrochemical doping in conjugated polymers
Authors: Keene Scott T. , Laulainen Joonatan E. M. , Pandya Raj , Moser Maximilian , Schnedermann Christoph , Midgley Paul A. , McCulloch Iain , Rao Akshay , Malliaras George G. 
Published: July 2023

AbstractSimultaneous transport and coupling of ionic and electronic charges is fundamental to electrochemical devices used in energy storage and conversion, neuromorphic computing and bioelectronics. While the mixed conductors enabling these technologies are widely used, the dynamic relationship between ionic and electronic transport is generally poorly understood, hindering the rational design of new materials. In semiconducting electrodes, electrochemical doping is assumed to be limited by motion of ions due to their large mass compared to electrons and/or holes. Here, we show that this basic assumption does not hold for conjugated polymer electrodes. Using operando optical microscopy, we reveal that electrochemical doping speeds in a state-of-the-art polythiophene can be limited by poor hole transport at low doping levels, leading to substantially slower switching speeds than expected. We show that the timescale of hole-limited doping can be controlled by the degree of microstructural heterogeneity, enabling the design of conjugated polymers with improved electrochemical performance.
Transcriptional signatures associated with persisting CD19 CAR-T cells in children with leukemia
Authors: Anderson Nathaniel D. , Birch Jack , Accogli Theo , Criado Ignacio , Khabirova Eleonora , Parks Conor , Wood Yvette , Young Matthew D. , Porter Tarryn , Richardson Rachel , Albon Sarah J. , Popova Bilyana , Lopes Andre , Wynn Robert , Hough Rachael , Gohil Satyen H. , Pule Martin , Amrolia Persis J. , Behjati Sam , Ghorashian Sara 
Published: July 2023

AbstractIn the context of relapsed and refractory childhood pre-B cell acute lymphoblastic leukemia (R/R B-ALL), CD19-targeting chimeric antigen receptor (CAR)-T cells often induce durable remissions, which requires the persistence of CAR-T cells. In this study, we systematically analyzed CD19 CAR-T cells of 10 children with R/R B-ALL enrolled in the CARPALL trial via high-throughput single-cell gene expression and T cell receptor sequencing of infusion products and serial blood and bone marrow samples up to 5 years after infusion. We show that long-lived CAR-T cells developed a CD4/CD8 double-negative phenotype with an exhausted-like memory state and distinct transcriptional signature. This persistence signature was dominant among circulating CAR-T cells in all children with a long-lived treatment response for which sequencing data were sufficient (4/4, 100%). The signature was also present across T cell subsets and clonotypes, indicating that persisting CAR-T cells converge transcriptionally. This persistence signature was also detected in two adult patients with chronic lymphocytic leukemia with decade-long remissions who received a different CD19 CAR-T cell product. Examination of single T cell transcriptomes from a wide range of healthy and diseased tissues across children and adults indicated that the persistence signature may be specific to long-lived CAR-T cells. These findings raise the possibility that a universal transcriptional signature of clinically effective, persistent CD19 CAR-T cells exists.
A multi-ancestry polygenic risk score improves risk prediction for coronary artery disease
Authors: Patel Aniruddh P. , Wang Minxian , Ruan Yunfeng , Koyama Satoshi , Clarke Shoa L. , Yang Xiong , Tcheandjieu Catherine , Agrawal Saaket , Fahed Akl C. , Ellinor Patrick T. ,   Genes & Health Research Team; the Million Veteran Program, Tsao Philip S. , Sun Yan V. , Cho Kelly , Wilson Peter W. F. , Assimes Themistocles L. , van Heel David A. , Butterworth Adam S. , Aragam Krishna G. , Natarajan Pradeep , Khera Amit V. 
Published: July 2023

AbstractIdentification of individuals at highest risk of coronary artery disease (CAD)—ideally before onset—remains an important public health need. Prior studies have developed genome-wide polygenic scores to enable risk stratification, reflecting the substantial inherited component to CAD risk. Here we develop a new and significantly improved polygenic score for CAD, termed GPSMult, that incorporates genome-wide association data across five ancestries for CAD (>269,000 cases and >1,178,000 controls) and ten CAD risk factors. GPSMultstrongly associated with prevalent CAD (odds ratio per standard deviation 2.14, 95% confidence interval 2.10–2.19,P < 0.001) in UK Biobank participants of European ancestry, identifying 20.0% of the population with 3-fold increased risk and conversely 13.9% with 3-fold decreased risk as compared with those in the middle quintile. GPSMultwas also associated with incident CAD events (hazard ratio per standard deviation 1.73, 95% confidence interval 1.70–1.76,P < 0.001), identifying 3% of healthy individuals with risk of future CAD events equivalent to those with existing disease and significantly improving risk discrimination and reclassification. Across multiethnic, external validation datasets inclusive of 33,096, 124,467, 16,433 and 16,874 participants of African, European, Hispanic and South Asian ancestry, respectively, GPSMultdemonstrated increased strength of associations across all ancestries and outperformed all available previously published CAD polygenic scores. These data contribute a new GPSMultfor CAD to the field and provide a generalizable framework for how large-scale integration of genetic association data for CAD and related traits from diverse populations can meaningfully improve polygenic risk prediction.
Single cell transcriptome sequencing of stimulated and frozen human peripheral blood mononuclear cells
Authors: Derbois Céline , Palomares Marie-Ange , Deleuze Jean-François , Cabannes Eric , Bonnet Eric 
Published: July 2023

AbstractPeripheral blood mononuclear cells (PBMCs) are blood cells that are a critical part of the immune system used to fight off infection, defending our bodies from harmful pathogens. In biomedical research, PBMCs are commonly used to study global immune response to disease outbreak and progression, pathogen infections, for vaccine development and a multitude of other clinical applications. Over the past few years, the revolution in single-cell RNA sequencing (scRNA-seq) has enabled an unbiased quantification of gene expression in thousands of individual cells, which provides a more efficient tool to decipher the immune system in human diseases. In this work, we generate scRNA-seq data from human PBMCs at high sequencing depth (>100,000 reads/cell) for more than 30,000 cells, in resting, stimulated, fresh and frozen conditions. The data generated can be used for benchmarking batch correction and data integration methods, and to study the effect of freezing-thawing cycles on the quality of immune cell populations and their transcriptomic profiles.
Causal associations between inflammatory bowel disease and primary biliary cholangitis: a two-sample bidirectional Mendelian randomization study
Authors: Zhao Jiaxi , Li Kaixin , Liao Xiaoyang , Zhao Qian 
Published: July 2023

AbstractInflammatory bowel disease (IBD) has been reported to be associated with hepatobiliary diseases. Previous observational and Mendelian randomization (MR) studies have suggested a causal association between IBD and primary sclerosing cholangitis (PSC). However, it is unclear whether IBD has a causal association with primary biliary cholangitis (PBC): another autoimmune liver disease. We obtained genome-wide association study (GWAS) statistics from published GWASs for PBC, UC, and CD. We screened qualified instrumental variables (IVs) based on the three major assumptions of MR. To determine the causal relationships between UC or CD and PBC, two-sample MR analyses were performed using inverse variance-weighted (IVW), MR-Egger, and weighted median (WM) methods, and sensitivity analyses were conducted to validate the robustness of the results. We also conducted reverse MR analysis to reveal the causal association between PBC and UC or CD. UC was associated with a higher risk of PBC (OR 1.35, 95% CI 1.05–1.73, P = 0.02) in the IVW method, and CD was associated with an increased risk of PBC (OR 1.18, 95% CI 1.03–1.36, P = 0.02) in IVW. The weighted median and MR-Egger regression of both diseases showed a consistent direction but were not statistically significant. Results of the reverse MR analysis did not suggest genetic susceptibility that PBC was associated with an increased risk of UC (OR 1.05, 95% CI 0.95–1.17, P = 0.34) or CD (OR 1.1, 95% CI 0.99–1.20, P = 0.06). The present study revealed that IBD subtypes could increase the incidence of PBC, but in turn, PBC did not increase the incidence of IBD subtypes. Understanding that IBD and PBC constitute mutual risk factors can help with the clinical management of both diseases.
Amelogenin peptide analyses reveal female leadership in Copper Age Iberia (c. 2900–2650 BC)
Authors: Cintas-Peña Marta , Luciañez-Triviño Miriam , Montero Artús Raquel , Bileck Andrea , Bortel Patricia , Kanz Fabian , Rebay-Salisbury Katharina , García Sanjuán Leonardo 
Published: July 2023

AbstractGiven the absence of written records, the main source of information available to analyze gender inequalities in early complex societies is the human body itself. And yet, for decades, archaeologists have struggled with the sex estimation of poorly preserved human remains. Here we present an exceptional case study that shows how ground-breaking new scientific methods may address this problem. Through the analysis of sexually dimorphic amelogenin peptides in tooth enamel, we establish that the most socially prominent person of the Iberian Copper Age (c. 3200–2200 BC) was not male, as previously thought, but female. The analysis of this woman, discovered in 2008 at Valencina, Spain, reveals that she was a leading social figure at a time where no male attained a remotely comparable social position. Only other women buried a short time after in the Montelirio tholos, part of the same burial area, appear to have enjoyed a similarly high social position. Our results invite to reconsider established interpretations about the political role of women at the onset of early social complexity, and question traditionally held views of the past. Furthermore, this study anticipates the changes that newly developed scientific methods may bring to prehistoric archaeology and the study of human social evolution.
The neurobiological effects of mind–body exercise: a systematic review and meta-analysis of neuroimaging studies
Authors: Han Yvonne M. Y. , Chan Melody M. Y. , Choi Coco X. T. , Law Maxwell C. H. , Ahorsu Daniel Kwasi , Tsang Hector W. H. 
Published: July 2023

AbstractThe neurobiological effects of mind–body exercise on brain activation, functional neural connections and structural changes in the brain remain elusive. This systematic review and coordinate-based meta-analysis investigated the changes in resting-state and task-based brain activation, as well as structural brain changes before and after mind–body exercise compared to waitlist or active controls based on published structural or functional magnetic resonance imaging randomized controlled trials or cross-sectional studies. Electronic database search and manual search in relevant publications yielded 34 empirical studies with low-to-moderate risk of bias (assessed by Cochrane risk-of-bias tool for randomized trials or Joanna Briggs Institute’s critical appraisal checklist for analytical cross-sectional studies) that fulfilled the inclusion criteria, with 26 studies included in the narrative synthesis and 8 studies included in the meta-analysis. Coordinate-based meta-analysis showed that, while mind–body exercise enhanced the activation of the left anterior cingulate cortex within the default mode network (DMN), it induced more deactivation in the left supramarginal gyrus within the ventral attention network (uncorrected ps < 0.05). Meta-regression with duration of mind–body practice as a factor showed that, the activation of right inferior parietal gyrus within the DMN showed a positive association with increasing years of practice (voxel-corrected p < 0.005). Although mind–body exercise is shown to selectively modulate brain functional networks supporting attentional control and self-awareness, the overall certainty of evidence is limited by small number of studies. Further investigations are needed to understand the effects of both short-term and long-term mind–body exercise on structural changes in the brain.PROSPERO registration number: CRD42021248984.
A mindful approach to controlling intrusive thoughts
Authors: Ashton S. M. , Sambeth A. , Quaedflieg C. W. E. M. 
Published: July 2023

AbstractIntrusive thoughts of negative experiences can pose a threat to our well-being. To some extent, unwanted memories can be intentionally controlled via an executive control mechanism that downregulates the occurrence of intrusions. Mindfulness training can improve executive control. It is not known whether mindfulness training can be used as an intervention to improve intentional memory control and reduce intrusions. To this end, 148 healthy participants completed a 10-day app-based mindfulness training or an active control task. At baseline, inhibitory control and working memory were assessed as measures of executive functioning. Post-mindfulness training, intrusions were assessed via the Think/No-Think task. It was expected that mindfulness training would reduce intrusions. Furthermore, we hypothesised that this would be moderated by baseline executive functioning. Results revealed that, contrary to our hypothesis, both groups increased equally in dispositional mindfulness between baseline and post-test. As such, our exploratory analysis revealed that higher dispositional mindfulness across both groups resulted in fewer intrusions and enhanced the ability to downregulate intrusions over time. Furthermore, this effect was moderated by inhibitory control at baseline. These results provide insight into factors that can improve the ability to control unwanted memories, which could have considerable implications for treatments in psychopathologies characterized by the frequent occurrence of intrusive thoughts.Protocol registrationThe stage 1 protocol for this Registered Report was accepted in principle on 11th March, 2022. The protocol, as accepted by the journal, can be found at:https://doi.org/10.17605/OSF.IO/U8SJN.
Hybridization of the swarming and interior point algorithms to solve the Rabinovich–Fabrikant system
Authors: Sabir Zulqurnain , Said Salem Ben , Al-Mdallal Qasem 
Published: July 2023

AbstractIn this study, a trustworthy swarming computing procedure is demonstrated for solving the nonlinear dynamics of the Rabinovich–Fabrikant system. The nonlinear system’s dynamic depends upon the three differential equations. The computational stochastic structure based on the artificial neural networks (ANNs) along with the optimization of global search swarming particle swarm optimization (PSO) and local interior point (IP) algorithms, i.e., ANNs-PSOIP is presented to solve the Rabinovich–Fabrikant system. An objective function based on the differential form of the model is optimized through the local and global search methods. The correctness of the ANNs-PSOIP scheme is observed through the performances of achieved and source solutions, while the negligible absolute error that is around 10−05–10−07 also represent the worth of the ANNs-PSOIP algorithm. Furthermore, the consistency of the ANNs-PSOIP scheme is examined by applying different statistical procedures to solve the Rabinovich–Fabrikant system.
Shared hotspot mutations in oncogenes position dogs as an unparalleled comparative model for precision therapeutics
Authors: Rodrigues Lucas , Watson Joshua , Feng Yuan , Lewis Benjamin , Harvey Garrett , Post Gerald , Megquier Kate , White Michelle E. , Lambert Lindsay , Miller Aubrey , Lopes Christina , Zhao Shaying 
Published: July 2023

AbstractNaturally occurring canine cancers have remarkable similarities to their human counterparts. To better understand these similarities, we investigated 671 client-owned dogs from 96 breeds with 23 common tumor types, including those whose mutation profile are unknown (anal sac carcinoma and neuroendocrine carcinoma) or understudied (thyroid carcinoma, soft tissue sarcoma and hepatocellular carcinoma). We discovered mutations in 50 well-established oncogenes and tumor suppressors, and compared them to those reported in human cancers. As in human cancer, TP53 is the most commonly mutated gene, detected in 22.5% of canine tumors overall. Canine tumors share mutational hotspots with human tumors in oncogenes including PIK3CA, KRAS, NRAS, BRAF, KIT and EGFR. Hotspot mutations with significant association to tumor type include NRAS G61R and PIK3CA H1047R in hemangiosarcoma, ERBB2 V659E in pulmonary carcinoma, and BRAF V588E (equivalent of V600E in humans) in urothelial carcinoma. Our findings better position canines as a translational model of human cancer to investigate a wide spectrum of targeted therapies.
Unsteady mix convectional stagnation point flow of nanofluid over a movable electro-magnetohydrodynamics Riga plate numerical approach
Authors: Nasir Saleem , Berrouk Abdallah S. , Gul Taza , Zari Islam , Alghamdi Wajdi , Ali Ishtiaq 
Published: July 2023

AbstractThe flow at a time-independent separable stagnation point on a Riga plate under thermal radiation and electro-magnetohydrodynamic settings is examined in this research. Two distinct base fluids-H2O and C2H6O2 and TiO2 nanostructures develop the nanocomposites. The flow problem incorporates the equations of motion and energy along with a unique model for viscosity and thermal conductivity. Similarity components are then used to reduce these model problem calculations. The Runge Kutta (RK-4) function yields the simulation result, which is displayed in graphical and tabular form. For both involved base fluid theories, the nanofluids flow and thermal profiles relating to the relevant aspects are computed and analyzed. According to the findings of this research, the C2H6O2 model heat exchange rate is significantly higher than the H2O model. As the volume percentage of nanoparticles rises, the velocity field degrades while the temperature distribution improves. Moreover, for greater acceleration parameters, TiO2/ C2H6O2has the highest thermal coefficient whereas TiO2/ H2O has the highest skin friction coefficient. The key observation is that C2H6O2 base nanofluid has a little higher performance than H2O nanofluid.
Target of selective auditory attention can be robustly followed with MEG
Authors: Kurmanavičiūtė Dovilė , Kataja Hanna , Jas Mainak , Välilä Anne , Parkkonen Lauri 
Published: July 2023

AbstractSelective auditory attention enables filtering of relevant acoustic information from irrelevant. Specific auditory responses, measurable by magneto- and electroencephalography (MEG/EEG), are known to be modulated by attention to the evoking stimuli. However, such attention effects have typically been studied in unnatural conditions (e.g. during dichotic listening of pure tones) and have been demonstrated mostly in averaged auditory evoked responses. To test how reliably we can detect the attention target from unaveraged brain responses, we recorded MEG data from 15 healthy subjects that were presented with two human speakers uttering continuously the words “Yes” and “No” in an interleaved manner. The subjects were asked to attend to one speaker. To investigate which temporal and spatial aspects of the responses carry the most information about the target of auditory attention, we performed spatially and temporally resolved classification of the unaveraged MEG responses using a support vector machine. Sensor-level decoding of the responses to attended vs. unattended words resulted in a mean accuracy of $$79\% \pm 2 \%$$

79
%
±
2
%

(N = 14) for both stimulus words. The discriminating information was mostly available 200–400 ms after the stimulus onset. Spatially-resolved source-level decoding indicated that the most informative sources were in the auditory cortices, in both the left and right hemisphere. Our result corroborates attention modulation of auditory evoked responses and shows that such modulations are detectable in unaveraged MEG responses at high accuracy, which could be exploited e.g. in an intuitive brain–computer interface.