bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exaptation of ancestral cell-identity networks enables C4 photosynthesis
Authors: Swift Joseph , Luginbuehl Leonie H. , Hua Lei , Schreier Tina B. , Donald Ruth M. , Stanley Susan , Wang Na , Lee Travis A. , Nery Joseph R. , Ecker Joseph R. , Hibberd Julian M. 
Published: November 2024

AbstractC4 photosynthesis is used by the most productive plants on the planet, and compared with the ancestral C3 pathway, it confers a 50% increase in efficiency1. In more than 60 C4 lineages, CO2 fixation is compartmentalized between tissues, and bundle-sheath cells become photosynthetically activated2. How the bundle sheath acquires this alternate identity that allows efficient photosynthesis is unclear. Here we show that changes to bundle-sheath gene expression in C4 leaves are associated with the gain of a pre-existing cis-code found in the C3 leaf. From single-nucleus gene-expression and chromatin-accessibility atlases, we uncover DNA binding with one finger (DOF) motifs that define bundle-sheath identity in the major crops C3 rice and C4 sorghum. Photosynthesis genes that are rewired to be strongly expressed in the bundle-sheath cells of C4 sorghum acquire cis-elements that are recognized by DOFs. Our findings are consistent with a simple model in which C4 photosynthesis is based on the recruitment of an ancestral cis-code associated with bundle-sheath identity. Gain of such elements harnessed a stable patterning of transcription factors between cell types that are found in both C3 and C4 leaves to activate photosynthesis in the bundle sheath. Our findings provide molecular insights into the evolution of the complex C4 pathway, and might also guide the rational engineering of C4 photosynthesis in C3 crops to improve crop productivity and resilience3,4.
Social state alters vision using three circuit mechanisms in Drosophila
Authors: Schretter Catherine E. , Hindmarsh Sten Tom , Klapoetke Nathan , Shao Mei , Nern Aljoscha , Dreher Marisa , Bushey Daniel , Robie Alice A. , Taylor Adam L. , Branson Kristin , Otopalik Adriane , Ruta Vanessa , Rubin Gerald M. 
Published: November 2024

Abstract
Animals are often bombarded with visual information and must prioritize specific visual features based on their current needs. The neuronal circuits that detect and relay visual features have been well studied1–8. Much less is known about how an animal adjusts its visual attention as its goals or environmental conditions change. During social behaviours, flies need to focus on nearby flies9–11. Here we study how the flow of visual information is altered when female Drosophila enter an aggressive state. From the connectome, we identify three state-dependent circuit motifs poised to modify the response of an aggressive female to fly-sized visual objects: convergence of excitatory inputs from neurons conveying select visual features and internal state; dendritic disinhibition of select visual feature detectors; and a switch that toggles between two visual feature detectors. Using cell-type-specific genetic tools, together with behavioural and neurophysiological analyses, we show that each of these circuit motifs is used during female aggression. We reveal that features of this same switch operate in male Drosophila during courtship pursuit, suggesting that disparate social behaviours may share circuit mechanisms. Our study provides a compelling example of using the connectome to infer circuit mechanisms that underlie dynamic processing of sensory signals.
Spatially resolved single-cell atlas unveils a distinct cellular signature of fatal lung COVID-19 in a Malawian population
Authors: Nyirenda James , Hardy Olympia M. , Silva Filho João Da , Herder Vanessa , Attipa Charalampos , Ndovi Charles , Siwombo Memory , Namalima Takondwa Rex , Suwedi Leticia , Ilia Georgios , Nyasulu Watipenge , Ngulube Thokozile , Nyirenda Deborah , Mvaya Leonard , Phiri Joseph , Chasweka Dennis , Eneya Chisomo , Makwinja Chikondi , Phiri Chisomo , Ziwoya Frank , Tembo Abel , Makwangwala Kingsley , Khoswe Stanley , Banda Peter , Morton Ben , Hilton Orla , Lawrence Sarah , dos Reis Monique Freire , Melo Gisely Cardoso , de Lacerda Marcus Vinicius Guimaraes , Trindade Maranhão Costa Fabio , Monteiro Wuelton Marcelo , Ferreira Luiz Carlos de Lima , Johnson Carla , McGuinness Dagmara , Jambo Kondwani , Haley Michael , Kumwenda Benjamin , Palmarini Massimo , Denno Donna M. , Voskuijl Wieger , Kamiza Steve Bvuobvuo , Barnes Kayla G. , Couper Kevin , Marti Matthias , Otto Thomas D. , Moxon Christopher A. 
Published: November 2024

AbstractPostmortem single-cell studies have transformed understanding of lower respiratory tract diseases (LRTDs), including coronavirus disease 2019 (COVID-19), but there are minimal data from African settings where HIV, malaria and other environmental exposures may affect disease pathobiology and treatment targets. In this study, we used histology and high-dimensional imaging to characterize fatal lung disease in Malawian adults with (n = 9) and without (n = 7) COVID-19, and we generated single-cell transcriptomics data from lung, blood and nasal cells. Data integration with other cohorts showed a conserved COVID-19 histopathological signature, driven by contrasting immune and inflammatory mechanisms: in US, European and Asian cohorts, by type I/III interferon (IFN) responses, particularly in blood-derived monocytes, and in the Malawian cohort, by response to IFN-γ in lung-resident macrophages. HIV status had minimal impact on histology or immunopathology. Our study provides a data resource and highlights the importance of studying the cellular mechanisms of disease in underrepresented populations, indicating shared and distinct targets for treatment.
An organotypic atlas of human vascular cells
Authors: Barnett Sam N. , Cujba Ana-Maria , Yang Lu , Maceiras Ana Raquel , Li Shuang , Kedlian Veronika R. , Pett J. Patrick , Polanski Krzysztof , Miranda Antonio M. A. , Xu Chuan , Cranley James , Kanemaru Kazumasa , Lee Michael , Mach Lukas , Perera Shani , Tudor Catherine , Joseph Philomeena D. , Pritchard Sophie , Toscano-Rivalta Rebecca , Tuong Zewen K. , Bolt Liam , Petryszak Robert , Prete Martin , Cakir Batuhan , Huseynov Alik , Sarropoulos Ioannis , Chowdhury Rasheda A. , Elmentaite Rasa , Madissoon Elo , Oliver Amanda J. , Campos Lia , Brazovskaja Agnieska , Gomes Tomás , Treutlein Barbara , Kim Chang N. , Nowakowski Tomasz J. , Meyer Kerstin B. , Randi Anna M. , Noseda Michela , Teichmann Sarah A. 
Published: November 2024

AbstractThe human vascular system, comprising endothelial cells (ECs) and mural cells, covers a vast surface area in the body, providing a critical interface between blood and tissue environments. Functional differences exist across specific vascular beds, but their molecular determinants across tissues remain largely unknown. In this study, we integrated single-cell transcriptomics data from 19 human organs and tissues and defined 42 vascular cell states from approximately 67,000 cells (62 donors), including angiotypic transitional signatures along the arterial endothelial axis from large to small caliber vessels. We also characterized organotypic populations, including splenic littoral and blood–brain barrier ECs, thus clarifying the molecular profiles of these important cell states. Interrogating endothelial–mural cell molecular crosstalk revealed angiotypic and organotypic communication pathways related to Notch, Wnt, retinoic acid, prostaglandin and cell adhesion signaling. Transcription factor network analysis revealed differential regulation of downstream target genes in tissue-specific modules, such as those of FOXF1 across multiple lung vascular subpopulations. Additionally, we make mechanistic inferences of vascular drug targets within different vascular beds. This open-access resource enhances our understanding of angiodiversity and organotypic molecular signatures in human vascular cells, and has therapeutic implications for vascular diseases across tissues.
Eye movements of children with and without developmental dyslexia in an alphabetic script during alphabetic and logographic tasks
Authors: Trauzettel-Klosinski Susanne , Faisst Theda , Schick Vera , Righetti Giulia , Braun Christoph , Cordey-Henke Angelika , Sun Ching-Chu , Kuester-Gruber Stephan 
Published: November 2024

AbstractEye movements (EM) during naming alphabetic versus logographic stimuli in children with and without developmental dyslexia (DD) were examined for each stimulus separately to identify conspicuous characteristics that influence naming performance. 40 children (group DD = 18; control group C = 22) were taught Chinese characters. EM were recorded during naming alphabetic words, pictures and Chinese characters. Main variables were articulation latencies, numbers and durations of fixations, secondary variables were fixation locations and error rates. Group DD showed significantly longer latencies and more fixations while reading words, but only insignificantly more fixations while naming pictures and Chinese characters. However, their error rate was significantly higher during naming Chinese characters but correlated neither with severity of phonological deficit nor with visual complexity. Their first fixation was significantly more often on the center of characters, in group C on the left. In both groups, EM variables were influenced by conspicuous features of characters, such as visual complexity, composition and structure. EM variables and scanning behavior while naming Chinese characters indicate holistic processing in the visuo-spatial pathway and were affected by conspicuous features of characters. The higher error rate in group DD could be determined by several factors, without a major role of the phonological deficit.
Anisotropy parameters from shapes of ion-ion correlation features of fragmenting molecules
Authors: Olsson Emelie , Wallner Måns , Squibb Richard J. , Ideböhn Veronica , Parriani Marco , Parkes Michael A. , Price Stephen D. , Eland John H.D. , Feifel Raimund 
Published: November 2024

AbstractWhen a molecule loses two electrons, Coulomb repulsion makes the resulting doubly charged system likely to fragment into two singly charged ions. These monocations can be detected in a correlated fashion using multiplex time-of-flight spectroscopy. The island shapes in the ion-ion coincidence maps derived from such two-body dissociations contain detailed information on the physical processes underlying the fragmentation. Here, a simple method is presented where a fit function is used to determine the anisotropy parameter β of the molecular distribution from the peak shape of the time-of-flight difference of the two ions. The validity of the method is demonstrated by performing fits to simulated peak shapes, recovering the β value of the input angular distribution, and by comparison of experimental peak shapes to β values known from the literature.
Victimization experiences, internalizing problems and family bonds among adolescents from the UK: multi-group structural equation modeling using an intersectionality-informed approach
Authors: Birnkammer Susanne , Booker Cara L. , Calvano Claudia 
Published: November 2024

AbstractAdolescents from marginalized backgrounds are at increased risk for victimization experiences, which was shown for ethnic minorities and females. However, an intersectional approach has rarely been taken in research. Using the Understanding Society Youth Panel, multigroup structural equation models were conducted to identify cross-group variation among adolescents aged 10–15 years in the relation between victimization experiences (verbal, physical and cyberbullying, discrimination) and internalizing problems (loneliness, emotional problems, life satisfaction), along with a mediating effect of family bonds (family support, parental communication). The groups white male (n = 280), white female (n = 280), Black, Asian and minority ethnic (BAME) male (n = 219) and BAME female (n = 279) were included in the analyses. Across all groups, victimization experiences were negatively associated with family bonds. Only among BAME male adolescents, experiences of victimization were related to more internalizing problems. No mediating effects of family bonds on the relation between victimization and internalizing problems were identified in any group. The results support an intersectionality-informed approach and the necessity of implementing preventative anti-bullying and family strengthening interventions among adolescents.
An improved transcriptome annotation reveals asymmetric expression and distinct regulation patterns in allotetraploid common carp
Authors: Wang Qi , Huang Yang Meidi , Yu Shuangting , Chen Yingjie , Wang Kaikuo , Zhang Yan , Zhao Ran , Li Jiongtang 
Published: November 2024

AbstractIn allotetraploid common carp, protein-coding homoeologs presented divergent expression levels between the two subgenomes. However, whether subgenome dominance occurs in other transcriptional and post-transcriptional events remains unknown. Using Illumina RNA sequencing and PacBio full-length sequencing, we refined the common carp transcriptome annotation and explored differences in four transcriptional and post-transcriptional events between the two subgenomes. The results revealed that the B subgenome presented more alternative splicing events, as did lncRNAs and circRNAs. However, the expression levels, tissue specificity, sequence features, and functions of lncRNAs and circRNAs did not significantly differ between the two subgenomes, suggesting a common regulatory mechanism shared by the two subgenomes. Furthermore, both the number and base substitution frequency of RNA editing events were greater in the B subgenome. Functional analyses of these transcriptional events also revealed subgenome bias. Genes that undergo alternative splicing in the A subgenome participate in more biological processes, and lncRNA targets show a preference between subgenomes. CircRNA host genes in the B subgenome were associated with more biological functions, and RNA editing preferentially occurred in noncoding regions or led to nonsynonymous mutations in the B subgenome. Taken together, the refined transcriptome annotation revealed complicated and imbalanced expression strategies in allotetraploid common carp.
Power sector benefits of flexible heat pumps in 2030 scenarios
Authors: Roth Alexander , Gaete-Morales Carlos , Kirchem Dana , Schill Wolf-Peter 
Published: November 2024

AbstractHeat pumps play a major role in decreasing fossil fuel use in heating. They increase electricity demand, but could also foster the system integration of variable renewable energy sources. We analyze three scenarios for expanding decentralized heat pumps in Germany by 2030, focusing on the role of buffer heat storage. Using an open-source power sector model, we assess costs, capacity investments, and emissions effects. We find that investments in solar photovoltaics can cost-effectively accompany the roll-out of heat pumps in case wind power expansion potentials are limited. Results further show that short-duration heat storage substantially reduces the need for firm capacity and battery storage. Larger heat storage sizes do not substantially change the results. Increasing the number of heat pumps from 1.7 to 10 million units could annually save more than half of Germany’s private and commercial natural gas consumption and around half of households’ building-related CO2 emissions.
Central European warm phases recorded by episodic speleothem growth during MIS 3
Authors: Klose Jennifer , Weber Michael , Scholz Denis 
Published: November 2024

AbstractSpeleothems provide exceptional age control and are a valuable archive for the identification of warm phases in temperate climates. Here we present a speleothem composite record from Germany, which shows episodic growth during the last glacial period, coinciding with several Greenland Interstadials. Using a combined approach of high-resolution solution and in-situ laser ablation 230Th/U-dating, we were able to precisely constrain the timing and duration of several particularly warm phases during Marine Isotope Stage 3. Climatic conditions favourable for speleothem growth occurred episodically until 32,000 years ago, much longer than reported from existing speleothem records. The inception of speleothem growth lags the onset of Greenland Interstadials and covers approximately 88% of their total duration during early, and approximately 25% during middle and late Marine Isotope Stage 3. This indicates progressive climatic cooling during Marine Isotope Stage 3, with the speleothem growth phases representing persistent Central European warm phases.
Inferring the regional distribution of Visceral Leishmaniasis incidence from data at different spatial scales
Authors: Nightingale Emily S. , Subramanian Swaminathan , Schwarzer Ashley R. , Chapman Lloyd A. C. , Jambulingam Purushothaman , Cameron Mary M. , Brady Oliver J. , Medley Graham F. , Lucas Tim C. D. 
Published: November 2024

Abstract
Background
As cases of visceral leishmaniasis (VL) in India dwindle, there is motivation to monitor elimination progress on a finer geographic scale than sub-district (block). Low-incidence projections across geographically- and demographically- heterogeneous communities are difficult to act upon, and equitable elimination cannot be achieved if local pockets of incidence are overlooked. However, maintaining consistent surveillance at this scale is resource-intensive and not sustainable in the long-term.

Methods
We analysed VL incidence across 45,000 villages in Bihar state, exploring spatial autocorrelation and associations with local environmental conditions in order to assess the feasibility of inference at this scale. We evaluated a statistical disaggregation approach to infer finer spatial variation from routinely-collected, block-level data, validating against observed village-level incidence.

Results
This disaggregation approach does not estimate village-level incidence more accurately than a baseline assumption of block-homogeneity. Spatial auto-correlation is evident on a block-level but weak between neighbouring villages within the same block, possibly suggesting that longer-range transmission (e.g., due to population movement) may be an important contributor to village-level heterogeneity.

Conclusions
Increasing the range of reactive interventions to neighbouring villages may not improve their efficacy in suppressing transmission, but maintaining surveillance and diagnostic capacity in areas distant from recently observed cases - particularly along routes of population movement from endemic regions - could reduce reintroduction risk in currently unaffected villages. The reactive, spatially-targeted approach to VL surveillance limits interpretability of data observed at the village level, and hence the feasibility of routinely drawing and validating inference at this scale.
Aerodynamics-guided machine learning for design optimization of electric vehicles
Authors: Tran Jonathan , Fukami Kai , Inada Kenta , Umehara Daisuke , Ono Yoshimichi , Ogawa Kenta , Taira Kunihiko 
Published: November 2024

AbstractThe transition to electric vehicles is driving a fundamental shift in the automobile design process. Changes in constraints afforded by the absence of a combustion engine create new opportunities for modifying vehicle geometries. Current approaches to optimizing vehicle aerodynamics require a vast amount of computational studies and physical experiments, which are expensive when performing parameter sweeps over conceivable geometric configurations, suggesting the need for more efficient surrogate models to assist analysis. Here we analyze a dataset of industry-quality automobile geometries with their associated aerodynamic performance obtained from experimentally validated, high-fidelity large-eddy simulations. We show that a relationship between these geometries and their respective aerodynamics can be extracted in a low-dimensional manner by leveraging a nonlinear autoencoder which is simultaneously trained to estimate the drag coefficient from the latent variables. We perform aerodynamic design optimization of vehicle designs by making use of the learned aerodynamic relationship in the low-order space obtained by the model. We demonstrate that the aerodynamic trends for the geometries produced from the optimization process show agreement with validation simulations. The findings of this work demonstrate the application of data-driven approaches to the analysis and design of vehicles in a production environment.
Increased potentiation of 5-fluorouracil induced thymidylate synthase inhibition by 5,10-methylenetetrahydrofolate (arfolitixorin) compared to leucovorin in patients with colorectal liver metastases; The Modelle-001 Trial
Authors: Taflin Helena , Odin Elisabeth , Carlsson Göran , Gustavsson Bengt , Hemmingsson Oskar , Wettergren Yvonne , Urbanowicz Krzysztof , Turyn Jacek , Smolenski Ryszard T. , Peters Godefridus J. 
Published: November 2024

Abstract
Background
5-Fluorouracil (5-FU) is a cornerstone in treatment of colorectal cancer (CRC) and is usually combined with leucovorin (LV) to enhance the antitumour effect by increase thymidylate synthase (TS) inhibition, the key target enzyme for 5-FU. Arfolitixorin (Arfo) is an active form of the reduced folate, [6 R]-5,10-methylenetetrahydrofolate ([6 R]-MeTHF and in contrast to LV, does not need to be metabolized. The Modelle-001 was designed to explore whether a single intravenous bolus injection of Arfo as compared to LV, together with 5-FU increases the inhibition of TS, levels of folate concentrations and polyglutamylation in CRC liver metastases (CRLM) and liver parenchyma.

Patients and methods
Thirty patients with CRLM received either LV (60 mg/m2) or Arfo (30 mg/m2 or 120 mg/m2) in combination with 5-FU preoperatively. Levels of folates and and TS inhibition were measured.

Results
Significantly higher MeTHF levels and higher TS inhibition were measured in the Arfo groups compared to LV60, and there was a difference in folate poly-glutamylation between the groups.

Conclusion
The Modelle-001 Trial demonstrated significantly higher levels of MeTHF in metastases following Arfo compared to LV. This resulted in a greater increase TS inhibition in metastases although not statistically significant.
Molecular condensation of the CO/NF-YB/NF-YC/FT complex gates floral transition in Arabidopsis
Authors: Huang Xiang , Ma Zhiming , He Danxia , Han Xiao , Liu Xu , Dong Qiong , Tan Cuirong , Yu Bin , Sun Tiedong , Nordenskiöld Lars , Lu Lanyuan , Miao Yansong , Hou Xingliang 
Published: November 2024

AbstractThe plant master photoperiodic regulator CONSTANS (CO) interacts with Nuclear Factor-Y subunits B2 (NF-YB2) and C9 (NF-YC9) and transcriptionally activates the florigen gene FLOWERING LOCUS T (FT), regulating floral transition. However, the molecular mechanism of the functional four-component complex assembly in the nucleus remains elusive. We report that co-phase separation of CO with NF-YB2/NF-YC9/FT precisely controls heterogeneous CO assembly and FT transcriptional activation. In response to light signals, CO proteins form functional percolation clusters from a diffuse distribution in a B-box-motif-dependent manner. Multivalent coassembly with NF-YC9 and NF-YB2 prevents inhibitory condensate formation and is necessary to maintain proper CO assembly and material properties. The intrinsically disordered region (IDR) of NF-YC9, containing a polyglutamine motif, fine-tunes the functional properties of CO/NF-YB/NF-YC condensates. Specific FT promoter recognition with polyelectrolyte partitioning also enables the fluidic functional properties of CO/NF-YB/NF-YC/FT condensates. Our findings offer novel insights into the tunable macromolecular condensation of the CO/NF-YB/NF-YC/FT complex in controlling flowering in the photoperiod control.