bluuebunny/crossref_metadata_2025_split huggingface dataset:
Examining the role of common variants in rare neurodevelopmental conditions
Authors: Huang Qin Qin , Wigdor Emilie M. , Malawsky Daniel S. , Campbell Patrick , Samocha Kaitlin E. , Chundru V. Kartik , Danecek Petr , Lindsay Sarah , Marchant Thomas , Koko Mahmoud , Amanat Sana , Bonfanti Davide , Sheridan Eamonn , Radford Elizabeth J. , Barrett Jeffrey C. , Wright Caroline F. , Firth Helen V. , Warrier Varun , Strudwick Young Alexander , Hurles Matthew E. , Martin Hilary C. 
Published: November 2024

AbstractAlthough rare neurodevelopmental conditions have a large Mendelian component1, common genetic variants also contribute to risk2,3. However, little is known about how this polygenic risk is distributed among patients with these conditions and their parents nor its interplay with rare variants. It is also unclear whether polygenic background affects risk directly through alleles transmitted from parents to children, or whether indirect genetic effects mediated through the family environment4 also play a role. Here we addressed these questions using genetic data from 11,573 patients with rare neurodevelopmental conditions, 9,128 of their parents and 26,869 controls. Common variants explained around 10% of variance in risk. Patients with a monogenic diagnosis had significantly less polygenic risk than those without, supporting a liability threshold model5. A polygenic score for neurodevelopmental conditions showed only a direct genetic effect. By contrast, polygenic scores for educational attainment and cognitive performance showed no direct genetic effect, but the non-transmitted alleles in the parents were correlated with the child’s risk, potentially due to indirect genetic effects and/or parental assortment for these traits4. Indeed, as expected under parental assortment, we show that common variant predisposition for neurodevelopmental conditions is correlated with the rare variant component of risk. These findings indicate that future studies should investigate the possible role and nature of indirect genetic effects on rare neurodevelopmental conditions, and consider the contribution of common and rare variants simultaneously when studying cognition-related phenotypes.
Early-twentieth-century cold bias in ocean surface temperature observations
Authors: Sippel Sebastian , Kent Elizabeth C. , Meinshausen Nicolai , Chan Duo , Kadow Christopher , Neukom Raphael , Fischer Erich M. , Humphrey Vincent , Rohde Robert , de Vries Iris , Knutti Reto 
Published: November 2024

Abstract
The observed temperature record, which combines sea surface temperatures with near-surface air temperatures over land, is crucial for understanding climate variability and change1–4. However, early records of global mean surface temperature are uncertain owing to changes in measurement technology and practice, partial documentation5–8, and incomplete spatial coverage9. Here we show that existing estimates of ocean temperatures in the early twentieth century (1900–1930) are too cold, based on independent statistical reconstructions of the global mean surface temperature from either ocean or land data. The ocean-based reconstruction is on average about 0.26 °C colder than the land-based one, despite very high agreement in all other periods. The ocean cold anomaly is unforced, and internal variability in climate models cannot explain the observed land–ocean discrepancy. Several lines of evidence based on attribution, timescale analysis, coastal grid cells and palaeoclimate data support the argument of a substantial cold bias in the observed global sea-surface-temperature record in the early twentieth century. Although estimates of global warming since the mid-nineteenth century are not affected, correcting the ocean cold bias would result in a more modest early-twentieth-century warming trend10, a lower estimate of decadal-scale variability inferred from the instrumental record3, and better agreement between simulated and observed warming than existing datasets suggest2.
Liver X receptor unlinks intestinal regeneration and tumorigenesis
Authors: Das Srustidhar , Parigi S. Martina , Luo Xinxin , Fransson Jennifer , Kern Bianca C. , Okhovat Ali , Diaz Oscar E. , Sorini Chiara , Czarnewski Paulo , Webb Anna T. , Morales Rodrigo A. , Lebon Sacha , Monasterio Gustavo , Castillo Francisca , Tripathi Kumar P. , He Ning , Pelczar Penelope , Schaltenberg Nicola , De la Fuente Marjorie , López-Köstner Francisco , Nylén Susanne , Larsen Hjalte List , Kuiper Raoul , Antonson Per , Hermoso Marcela A. , Huber Samuel , Biton Moshe , Scharaw Sandra , Gustafsson Jan-Åke , Katajisto Pekka , Villablanca Eduardo J. 
Published: November 2024

Abstract
Uncontrolled regeneration leads to neoplastic transformation1–3. The intestinal epithelium requires precise regulation during continuous homeostatic and damage-induced tissue renewal to prevent neoplastic transformation, suggesting that pathways unlinking tumour growth from regenerative processes must exist. Here, by mining RNA-sequencing datasets from two intestinal damage models4,5 and using pharmacological, transcriptomics and genetic tools, we identified liver X receptor (LXR) pathway activation as a tissue adaptation to damage that reciprocally regulates intestinal regeneration and tumorigenesis. Using single-cell RNA sequencing, intestinal organoids, and gain- and loss-of-function experiments, we demonstrate that LXR activation in intestinal epithelial cells induces amphiregulin (Areg), enhancing regenerative responses. This response is coordinated by the LXR-ligand-producing enzyme CYP27A1, which was upregulated in damaged intestinal crypt niches. Deletion of Cyp27a1 impaired intestinal regeneration, which was rescued by exogenous LXR agonists. Notably, in tumour models, Cyp27a1 deficiency led to increased tumour growth, whereas LXR activation elicited anti-tumour responses dependent on adaptive immunity. Consistently, human colorectal cancer specimens exhibited reduced levels of CYP27A1, LXR target genes, and B and CD8 T cell gene signatures. We therefore identify an epithelial adaptation mechanism to damage, whereby LXR functions as a rheostat, promoting tissue repair while limiting tumorigenesis.
Spatiotemporal Trajectories of Pedestrian Mobility at the Train Station: evidence of 24 million trajectories
Authors: Apeltauer Tomáš , Uhlík Ondřej , Apeltauer Jiří , Juřík Vojtěch 
Published: November 2024

AbstractUnderstanding pedestrian movement remains crucial for designing efficient and safe transportation structures such as terminals, stations, or airports. The significance of conducting a granular analysis in pedestrian mobility dynamics research is evident in refining crowd behavior modeling. It is essential for gaining insights into potential terminal layouts, crowd management strategies, and evacuation procedures, all of which enhance safety and efficiency. In this context, we offer an original empirical dataset of 24,000,000 samples of trajectory spatial movement at traffic terminals in Havlíčkův Brod and Pardubice, Czech Republic. The dataset was collected using a high-resolution camera system installed at the railway station. Subsequently, algorithmic post-processing was applied to extract anonymous data on the spatial movement of recorded pedestrians. Thanks to this dataset, researchers can delve into the distances between pedestrians in a transportation terminal, considering factors such as group composition, group-to-group distances, and movement speed.
A continuous pursuit dataset for online deep learning-based EEG brain-computer interface
Authors: Forenzo Dylan , Zhu Hao , He Bin 
Published: November 2024

AbstractThis dataset is from an EEG brain-computer interface (BCI) study investigating the use of deep learning (DL) for online continuous pursuit (CP) BCI. In this task, subjects use Motor Imagery (MI) to control a cursor to follow a randomly moving target, instead of a single stationary target used in other traditional BCI tasks. DL methods have recently achieved promising performance in traditional BCI tasks, but most studies investigate offline data analysis using DL algorithms. This dataset consists of ~168 hours of EEG recordings from complex CP BCI experiments, collected from 28 unique human subjects over multiple sessions each, with an online DL-based decoder. The large amount of subject specific data from multiple sessions may be useful for developing new BCI decoders, especially DL methods that require large amounts of training data. By providing this dataset to the public, we hope to help facilitate the development of new or improved BCI decoding algorithms for the complex CP paradigm for continuous object control, bringing EEG-based BCIs closer to real-world applications.
A global overview of marine heatwaves in a changing climate
Authors: Capotondi Antonietta , Rodrigues Regina R. , Sen Gupta Alex , Benthuysen Jessica A. , Deser Clara , Frölicher Thomas L. , Lovenduski Nicole S. , Amaya Dillon J. , Le Grix Natacha , Xu Tongtong , Hermes Juliet , Holbrook Neil J. , Martinez-Villalobos Cristian , Masina Simona , Roxy Mathew Koll , Schaeffer Amandine , Schlegel Robert W. , Smith Kathryn E. , Wang Chunzai 
Published: November 2024

AbstractMarine heatwaves have profoundly impacted marine ecosystems over large areas of the world oceans, calling for improved understanding of their dynamics and predictability. Here, we critically review the recent substantial advances in this active area of research, including the exploration of the three-dimensional structure and evolution of these extremes, their drivers, their connection with other extremes in the ocean and over land, future projections, and assessment of their predictability and current prediction skill. To make progress on predicting and projecting marine heatwaves and their impacts, a more complete mechanistic understanding of these extremes over the full ocean depth and at the relevant spatial and temporal scales is needed, together with models that can realistically capture the leading mechanisms at those scales. Sustained observing systems, as well as measuring platforms that can be rapidly deployed, are essential to achieve comprehensive event characterizations while also chronicling the evolving nature of these extremes and their impacts in our changing climate.
The molybdenum cycle in the oxygenated Neoproterozoic ocean was coupled to manganese carbonate mineralization
Authors: Zhang Bin , Cao Jian , Hu Kai , Liao Zhiwei , Zhang Ruijie , Zhang Yi , Shi Chunhua , Konhauser Kurt O. 
Published: November 2024

AbstractThe Neoproterozoic oxygenation event is a milestone in Earth’s history, yet the redox structure and elemental cycling of the Neoproterozoic ocean remain debated. Here, we investigated iron speciation, molybdenum, and nitrogen isotopes in black shales and manganese carbonates from the upper Ediacaran Doushantuo Formation, South China, to examine the links between redox state, manganese mineralization, and molybdenum cycling. In both lithologies, high pyritic iron ratios (> 0.8) indicate a localized euxinic zone, while estimated seawater molybdenum (1.9‰) and sediment nitrogen isotopic compositions (4.19 ± 1.96‰) resemble modern values, suggesting oxygenated surface waters over euxinic depths. Negative molybdenum isotope in manganese(II) carbonates points to manganese(IV) oxide reduction, acting as a molybdenum shuttle from oxygenated surface to euxinic deep waters. Periodic euxinic contractions drove manganese(II) oxidation and mineralization, shaping molybdenum cycling. This study highlights essential manganese(II) oxidation for manganese carbonate mineralization and offers new insights into molybdenum geochemistry and ancient ocean oxygenation events.
Genetic and phenotypic architecture of human myocardial trabeculation
Authors: McGurk Kathryn A. , Qiao Mengyun , Zheng Sean L. , Sau Arunashis , Henry Albert , Ribeiro Antonio Luiz P. , Ribeiro Antônio H. , Ng Fu Siong , Lumbers R. Thomas , Bai Wenjia , Ware James S. , O’Regan Declan P. 
Published: November 2024

AbstractCardiac trabeculae form a network of muscular strands that line the inner surfaces of the heart. Their development depends on multiscale morphogenetic processes and, while highly conserved across vertebrate evolution, their role in the pathophysiology of the mature heart is not fully understood. Here we report variant associations across the allele frequency spectrum for trabecular morphology in 47,803 participants of the UK Biobank using fractal dimension analysis of cardiac imaging. We identified an association between trabeculation and rare variants in 56 genes that regulate myocardial contractility and ventricular development. Genome-wide association studies identified 68 loci in pathways that regulate sarcomeric function, differentiation of the conduction system and cell fate determination. We found that trabeculation-associated variants were modifiers of cardiomyopathy phenotypes with opposing effects in hypertrophic and dilated cardiomyopathy. Together, these data provide insights into mechanisms that regulate trabecular development and plasticity, and identify a potential role in modifying monogenic disease expression.
Towards an IPCC Atlas for comprehensive climate change risk assessments
Authors: Alegría Andrés , Poloczanska Elvira , Loeschke Sina , Mintenbeck Katja , Poertner Hans 
Published: November 2024

AbstractClimate risk assessments are crucial in quantifying and communicating risks in a clear and concise manner. In light of the rapidly proceeding climatic changes, there is a growing need for a more comprehensive integration and a more effective overview of available and relevant data that go into these assessments, particularly on the temporal and spatial dynamics of risk. In this paper, we describe the advantages, challenges and opportunities for increasing the accessibility of temporal and spatial data needed to support climate risk assessments through the development of an Intergovernmental Panel on Climate Change (IPCC) Atlas, integrated across IPCC Working Groups. We propose that using a climate risk framework to organise this Atlas will result in a more practical resource for understanding and informing risk assessments undertaken by the IPCC, and also make methodologies and results more accessible to a wider audience.
FNDC1 is a myokine that promotes myogenesis and muscle regeneration
Authors: Zhang Rui Xin , Zhai Yuan Yuan , Ding Rong Rong , Huang Jia He , Shi Xiao Chen , Liu Huan , Liu Xiao Peng , Zhang Jian Feng , Lu Jun Feng , Zhang Zhe , Leng Xiang Kai , Li De Fu , Xiao Jun Ying , Xia Bo , Wu Jiang Wei 
Published: November 2024

AbstractMyogenesis is essential for skeletal muscle formation and regeneration after injury, yet its regulators are largely unknown. Here we identified fibronectin type III domain containing 1 (FNDC1) as a previously uncharacterized myokine. In vitro studies showed that knockdown of Fndc1 in myoblasts reduces myotube formation, while overexpression of Fndc1 promotes myogenic differentiation. We further generated recombinant truncated mouse FNDC1 (mFNDC1), which retains reliable activity in promoting myoblast differentiation in vitro. Gain- and loss-of-function studies collectively showed that FNDC1 promotes cardiotoxin (CTX)-induced muscle regeneration in adult mice. Furthermore, recombinant FNDC1 treatment ameliorated pathological muscle phenotypes in the mdx mouse model of Duchenne muscular dystrophy. Mechanistically, FNDC1 bound to the integrin α5β1 and activated the downstream FAK/PI3K/AKT/mTOR pathway to promote myogenic differentiation. Pharmacological inhibition of integrin α5β1 or of the downstream FAK/PI3K/AKT/mTOR pathway abolished the pro-myogenic effect of FNDC1. Collectively, these results suggested that myokine FNDC1 might be used as a therapeutic agent to regulate myogenic differentiation and muscle regeneration for the treatment of acute and chronic muscle disease.
Fibrillarin homologs regulate translation in divergent cell lineages during planarian homeostasis and regeneration
Authors: Chen Jiajia , Li Yucong , Wang Yan , Wang Hui , Yang Jiaqi , Pan Xue , Zhao Yun , Xu Hao , Jiang Penglei , Qian Pengxu , Wang Hongwei , Xie Zhi , Lei Kai 
Published: November 2024

AbstractTissue homeostasis and regeneration involve complex cellular changes. The role of rRNA modification-dependent translational regulation in these processes remains largely unknown. Planarians, renowned for their ability to undergo remarkable tissue regeneration, provide an ideal model for the analysis of differential rRNA regulation in diverse cell types during tissue homeostasis and regeneration. We investigated the role of RNA 2’-O-methyltransferase, Fibrillarin (FBL), in the planarian Schmidtea mediterranea and identified two FBL homologs: Smed-fbl-1 (fbl-1) and Smed-fbl-2 (fbl-2). Both are essential for planarian regeneration, but play distinct roles: fbl-1 is crucial for progenitor cell differentiation, while fbl-2 is important for late-stage epidermal lineage specification. Different 2’-O-methylation patterns were observed upon fbl-1 and fbl-2 knockdown, suggesting their roles in translation of specific mRNA pools during regeneration. Ribo-seq analysis further revealed differing impacts of fbl-1 and fbl-2 knockdown on gene translation. These findings indicate divergent roles of the duplicate fbl genes in specific cell lineage development in planarians and suggest a role of rRNA modifications in translational regulation during tissue maintenance and regeneration.
Unveiling emissive H-aggregates of benzocoronenediimide, their photophysics and ultrafast exciton dynamics
Authors: Dixit Swati J. N. , Ghosh Rajib , Agarwal Neeraj 
Published: November 2024

Photophysical studies of emissive H-aggregates of t-butyl-substituted benzocoronenediimide (t-But-BCDI) in solution.
General numerical solution of integral equation for long‐range low‐frequency groundwave propagation over irregular terrain
Authors: Wang Dan‐Dan , Lu Qi‐Zirui , Han Chao , Fang Yun , Pu Yu‐Rong 
Published: November 2024

AbstractThe flexibility of the integral equation (IE) method is limited by the available numerical solutions with uniform‐grid schemes. In this paper, a general numerical solution of the IE is presented to predict long‐range low‐frequency (LF) groundwave propagation over irregular terrain. The general numerical solution is re‐derived with the aid of Legendre–Gauss quadrature and interpolation quadrature. The great advantage of the resulting algorithm is that it can freely use non‐uniform grid sizes in the computation area without loss of accuracy. Numerical results in two surface types, including triangular mountain and actual terrain are used to demonstrate the performance of the presented algorithm. Furthermore, it is ascertained that the non‐physical perturbations at long propagation ranges in the IE predictions are caused by the inherent uniform‐grid schemes of the numerical solution rather than the several approximations in the derivation of the IE form.
Postpartum Hemorrhagic Morbidity with Scheduled versus Unscheduled Cesarean Delivery at Term
Authors: Wiley Rachel L. , Chauhan Suneet P. , Johnson Emily A. , Ghose Ipsita , Ciomperlik Hailie N. , Mendez-Figueroa Hector 
Published: November 2024

Objective This study aimed to compare the composite maternal hemorrhagic outcomes (CMHOs) among term (≥37 weeks) singletons who had scheduled versus unscheduled cesarean deliveries (CDs). A subgroup analysis was done for those without prior uterine surgeries.
Study Design Retrospectively, we identified all singletons at term who had CDs. The unscheduled CDs included individuals admitted with a plan for vaginal delivery with at least 1 hour of attempted labor. CMHOs included any of the following: estimated blood loss of ≥1,000 mL, use of uterotonics (excluding prophylactic oxytocin) or Bakri balloon, surgical management of hemorrhage, blood transfusion, hysterectomy, thromboembolism, admission to intensive care unit, or maternal death. Multivariable Poisson regression models with robust error variance were used to estimate adjusted relative risks (aRRs) with 95% confidence intervals (CIs).
Results Of 8,623 deliveries in the study period, 2,691 (31.2%) had CDs at term, with 1,709 (67.3%) scheduled CDs, and 983 (36.5%) unscheduled CDs. Overall, the rate of CMHO was 23.3%, and the rate of blood transfusion was 4.1%. CMHOs were two-fold higher among unscheduled (34.5%) than scheduled CDs (16.9%; aRR = 2.18; 95% CI: 1.81–2.63). The aRRs for blood transfusion and surgical interventions to manage postpartum hemorrhage were three times higher with unscheduled than scheduled CDs. The subgroup analysis indicated that among the cohorts without prior uterine surgery, the rate of the CMHOs was significantly higher when the CD was unscheduled versus scheduled (aRR 1.85; 95% CI 1.45–2.37).
Conclusion Compared to scheduled CDs, the composite hemorrhagic adverse outcomes were significantly higher with unscheduled CDs.
Key Points
In-vivo stress measurements in kitesurfing and wakeboarding: implications on load control and preventive approaches – an in-vivo field study
Authors: Sander Frank , Neuse Nina , Ren Xiping , Bader Rainer , Klinkmann Gerd , Lutter Christoph , Tischer Thomas 
Published: November 2024

AbstractThe trend sports kitesurfing and wakeboarding are increasingly gaining popularity. Tricks and high jumps – both in the air and over obstacles – are performed with increasing difficulty. Repeated high loads on the body, particularly when landing after a jump, can lead to overuse and acute injuries directly related to peak forces, particularly in the lower extremities.There is a lack of detailed analyses of these forces resulting from wakeboarding or kitesurfing, although such data would be relevant for the analysis of injury mechanisms and the subsequent development of prevention strategies. This study is the first of its kind in which the loads on the lower extremity during wakeboarding and kitesurfing were subjected to in-vivo measurements during various maneuvers.Six wakeboarders and 12 kitesurfers (6 with loop bindings and 6 with fixed bindings) were investigated (mean age 33.1 ± 9.9 years). Jump height, hang time, acceleration, and the maximum vertical ground reaction force of both feet during takeoff and landing were recorded by means of sensor insoles (Moticon, Germany) on the feet of the athletes and simultaneously by a height and acceleration sensor (PIQ Sport Intelligence) on the board. A statistical analysis was performed.The data showed that wakeboarders were exposed to higher loads than kitesurfers, with significant differences occurring only between wakeboarders and kitesurfers with loop bindings and between kitesurfers with loop bindings and fixed bindings. High mean forces occurred during the landing of wakeboarders (rear foot 24.24 N/kg ± 8.82; front foot 20.33 N/kg ± 5.05) compared to kitesurfers with loop bindings (rear foot 12.09 N/kg ± 5.6; front foot 12.23 N/kg ± 4.92) as well as partially in kitesurfers with fixed shoe bindings (front foot 13.61 N/kg ± 5.92). Forces during lift-off were comparable in the rear foot (wakeboarders, kitesurfers with fixed bindings, kitesurfers with loop bindings 14.17 ± 6.37 vs. 16.39 ± 4.99 vs. 14.72 ± 5.13 N/kg). Similarly, despite the higher average acceleration force of the wakeboarders (4.16 g ± 1.02), there was no statistically significant difference (p = 0.166) compared to the kitesurfers.The in-vivo forces acting on the lower extremities during wakeboarding and kitesurfing are high (highest absolute values of 3012 N and relative values of 31.71 N/Kg). In addition, fixed boot bindings allow for the generation of higher forces than strap bindings. The results of our study have important implications on load control and preventive approaches in these two sports.