bluuebunny/crossref_metadata_2025 huggingface dataset:
Unveiling RNA structure-mediated regulations of RNA stability in wheat
Authors: Wu Haidan , Yu Haopeng , Zhang Yueying , Yang Bibo , Sun Wenqing , Ren Lanying , Li Yuchen , Li Qianqian , Liu Bao , Ding Yiliang , Zhang Huakun
Published: November 2024

Despite the critical role of mRNA stability in post-transcriptional gene regulation, research on this topic in wheat, a vital agricultural crop, remains unclear. Our study investigated the mRNA decay landscape of durum wheat (Triticum turgidum L. ssp. durum, BBAA), revealing subgenomic asymmetry in mRNA stability and its impact on steady-state mRNA abundance. Our findings indicate that the 3’ UTR structure and homoeolog preference for RNA structural motifs can influence mRNA stability, leading to subgenomic RNA decay imbalance. Furthermore, single-nucleotide variations (SNVs) selected for RNA structural motifs during domestication can cause variations in subgenomic mRNA stability and subsequent changes in steady-state expression levels. Our research on the transcriptome stability of polyploid wheat highlights the regulatory role of non-coding region structures in mRNA stability, and how domestication shaped RNA structure, altering subgenomic mRNA stability. These results illustrate the importance of RNA structure-mediated post-transcriptional gene regulation in wheat and pave the way for its potential use in crop improvement.
Microbial and mineral interactions decouple litter quality from soil organic matter formation
Authors: Elias Dafydd M. O. , Mason Kelly E. , Goodall Tim , Taylor Ashley , Zhao Pengzhi , Otero-Fariña Alba , Chen Hongmei , Peacock Caroline L. , Ostle Nicholas J. , Griffiths Robert , Chapman Pippa J. , Holden Joseph , Banwart Steve , McNamara Niall P. , Whitaker Jeanette
Published: November 2024

Current understanding of soil carbon dynamics suggests that plant litter quality and soil mineralogy control the formation of mineral-associated soil organic carbon (SOC). Due to more efficient microbial anabolism, high-quality litter may produce more microbial residues for stabilisation on mineral surfaces. To test these fundamental concepts, we manipulate soil mineralogy using pristine minerals, characterise microbial communities and use stable isotopes to measure decomposition of low- and high-quality litter and mineral stabilisation of litter-C. We find that high-quality litter leads to less (not more) efficient formation of mineral-associated SOC due to soil microbial community shifts which lower carbon use efficiency. Low-quality litter enhances loss of pre-existing SOC resulting in no effect of litter quality on total mineral-associated SOC. However, mineral-associated SOC formation is primarily controlled by soil mineralogy. These findings refute the hypothesis that high-quality plant litters form mineral-associated SOC most efficiently and advance our understanding of how mineralogy and litter-microbial interactions regulate SOC formation.
Arctic freshwater anomaly transiting to the North Atlantic delayed within a buffer zone
Authors: Wang Qiang , Danilov Sergey , Jung Thomas
Published: November 2024

A two-decade-long accumulation of freshwater in the Arctic Ocean’s Beaufort Gyre has recently started to be released. Here we use satellite observations and model simulations to show that changes in wind regimes and sea ice declines are causing freshwater to accumulate close to the export gateways to the North Atlantic. This emerging buffer zone plays an important role in modulating the propagation of freshwater into the subpolar North Atlantic.
Single-cell integration reveals metaplasia in inflammatory gut diseases
Authors: Oliver Amanda J. , Huang Ni , Bartolome-Casado Raquel , Li Ruoyan , Koplev Simon , Nilsen Hogne R. , Moy Madelyn , Cakir Batuhan , Polanski Krzysztof , Gudiño Victoria , Melón-Ardanaz Elisa , Sumanaweera Dinithi , Dimitrov Daniel , Milchsack Lisa Marie , FitzPatrick Michael E. B. , Provine Nicholas M. , Boccacino Jacqueline M. , Dann Emma , Predeus Alexander V. , To Ken , Prete Martin , Chapman Jonathan A. , Masi Andrea C. , Stephenson Emily , Engelbert Justin , Lobentanzer Sebastian , Perera Shani , Richardson Laura , Kapuge Rakeshlal , Wilbrey-Clark Anna , Semprich Claudia I. , Ellams Sophie , Tudor Catherine , Joseph Philomeena , Garrido-Trigo Alba , Corraliza Ana M. , Oliver Thomas R. W. , Hook C. Elizabeth , James Kylie R. , Mahbubani Krishnaa T. , Saeb-Parsy Kourosh , Zilbauer Matthias , Saez-Rodriguez Julio , Høivik Marte Lie , Bækkevold Espen S. , Stewart Christopher J. , Berrington Janet E. , Meyer Kerstin B. , Klenerman Paul , Salas Azucena , Haniffa Muzlifah , Jahnsen Frode L. , Elmentaite Rasa , Teichmann Sarah A.
Published: November 2024

The gastrointestinal tract is a multi-organ system crucial for efficient nutrient uptake and barrier immunity. Advances in genomics and a surge in gastrointestinal diseases1,2 has fuelled efforts to catalogue cells constituting gastrointestinal tissues in health and disease3. Here we present systematic integration of 25 single-cell RNA sequencing datasets spanning the entire healthy gastrointestinal tract in development and in adulthood. We uniformly processed 385 samples from 189 healthy controls using a newly developed automated quality control approach (scAutoQC), leading to a healthy reference atlas with approximately 1.1 million cells and 136 fine-grained cell states. We anchor 12 gastrointestinal disease datasets spanning gastrointestinal cancers, coeliac disease, ulcerative colitis and Crohn’s disease to this reference. Utilizing this 1.6 million cell resource (gutcellatlas.org), we discover epithelial cell metaplasia originating from stem cells in intestinal inflammatory diseases with transcriptional similarity to cells found in pyloric and Brunner’s glands. Although previously linked to mucosal healing4, we now implicate pyloric gland metaplastic cells in inflammation through recruitment of immune cells including T cells and neutrophils. Overall, we describe inflammation-induced changes in stem cells that alter mucosal tissue architecture and promote further inflammation, a concept applicable to other tissues and diseases.
A spatial human thymus cell atlas mapped to a continuous tissue axis
Authors: Yayon Nadav , Kedlian Veronika R. , Boehme Lena , Suo Chenqu , Wachter Brianna T. , Beuschel Rebecca T. , Amsalem Oren , Polanski Krzysztof , Koplev Simon , Tuck Elizabeth , Dann Emma , Van Hulle Jolien , Perera Shani , Putteman Tom , Predeus Alexander V. , Dabrowska Monika , Richardson Laura , Tudor Catherine , Kreins Alexandra Y. , Engelbert Justin , Stephenson Emily , Kleshchevnikov Vitalii , De Rita Fabrizio , Crossland David , Bosticardo Marita , Pala Francesca , Prigmore Elena , Chipampe Nana-Jane , Prete Martin , Fei Lijiang , To Ken , Barker Roger A. , He Xiaoling , Van Nieuwerburgh Filip , Bayraktar Omer Ali , Patel Minal , Davies E Graham , Haniffa Muzlifah A. , Uhlmann Virginie , Notarangelo Luigi D. , Germain Ronald N. , Radtke Andrea J. , Marioni John C. , Taghon Tom , Teichmann Sarah A.
Published: November 2024

T cells develop from circulating precursor cells, which enter the thymus and migrate through specialized subcompartments that support their maturation and selection1. In humans, this process starts in early fetal development and is highly active until thymic involution in adolescence. To map the microanatomical underpinnings of this process in pre- and early postnatal stages, we established a quantitative morphological framework for the thymus—the Cortico-Medullary Axis—and used it to perform a spatially resolved analysis. Here, by applying this framework to a curated multimodal single-cell atlas, spatial transcriptomics and high-resolution multiplex imaging data, we demonstrate establishment of the lobular cytokine network, canonical thymocyte trajectories and thymic epithelial cell distributions by the beginning of the the second trimester of fetal development. We pinpoint tissue niches of thymic epithelial cell progenitors and distinct subtypes associated with Hassall’s corpuscles and identify divergence in the timing of medullary entry between CD4 and CD8 T cell lineages. These findings provide a basis for a detailed understanding of T lymphocyte development and are complemented with a holistic toolkit for cross-platform imaging data analysis, annotation and OrganAxis construction (TissueTag), which can be applied to any tissue.
A multi-omic atlas of human embryonic skeletal development
Authors: To Ken , Fei Lijiang , Pett J. Patrick , Roberts Kenny , Blain Raphael , Polański Krzysztof , Li Tong , Yayon Nadav , He Peng , Xu Chuan , Cranley James , Moy Madelyn , Li Ruoyan , Kanemaru Kazumasa , Huang Ni , Megas Stathis , Richardson Laura , Kapuge Rakesh , Perera Shani , Tuck Elizabeth , Wilbrey-Clark Anna , Mulas Ilaria , Memi Fani , Cakir Batuhan , Predeus Alexander V. , Horsfall David , Murray Simon , Prete Martin , Mazin Pavel , He Xiaoling , Meyer Kerstin B. , Haniffa Muzlifah , Barker Roger A. , Bayraktar Omer , Chédotal Alain , Buckley Christopher D. , Teichmann Sarah A.
Published: November 2024

Human embryonic bone and joint formation is determined by coordinated differentiation of progenitors in the nascent skeleton. The cell states, epigenetic processes and key regulatory factors that underlie lineage commitment of these cells remain elusive. Here we applied paired transcriptional and epigenetic profiling of approximately 336,000 nucleus droplets and spatial transcriptomics to establish a multi-omic atlas of human embryonic joint and cranium development between 5 and 11 weeks after conception. Using combined modelling of transcriptional and epigenetic data, we characterized regionally distinct limb and cranial osteoprogenitor trajectories across the embryonic skeleton and further described regulatory networks that govern intramembranous and endochondral ossification. Spatial localization of cell clusters in our in situ sequencing data using a new tool, ISS-Patcher, revealed mechanisms of progenitor zonation during bone and joint formation. Through trajectory analysis, we predicted potential non-canonical cellular origins for human chondrocytes from Schwann cells. We also introduce SNP2Cell, a tool to link cell-type-specific regulatory networks to polygenic traits such as osteoarthritis. Using osteolineage trajectories characterized here, we simulated in silico perturbations of genes that cause monogenic craniosynostosis and implicate potential cell states and disease mechanisms. This work forms a detailed and dynamic regulatory atlas of bone and cartilage maturation and advances our fundamental understanding of cell-fate determination in human skeletal development.
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

C4 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

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

Postmortem 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

The 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

Eye 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

When 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

Adolescents 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

In 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

Heat 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

Speleothems 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

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

The 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

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

The 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.
Viral N protein hijacks deaminase-containing RNA granules to enhance SARS-CoV-2 mutagenesis
Authors: Li Zhean , Luo Lingling , Ju Xiaohui , Huang Shisheng , Lei Liqun , Yu Yanying , Liu Jia , Zhang Pumin , Chi Tian , Ma Peixiang , Huang Cheng , Huang Xingxu , Ding Qiang , Zhang Yu
Published: November 2024

Host cell-encoded deaminases act as antiviral restriction factors to impair viral replication and production through introducing mutations in the viral genome. We sought to understand whether deaminases are involved in SARS-CoV-2 mutation and replication, and how the viral factors interact with deaminases to trigger these processes. Here, we show that APOBEC and ADAR deaminases act as the driving forces for SARS-CoV-2 mutagenesis, thereby blocking viral infection and production. Mechanistically, SARS-CoV-2 nucleocapsid (N) protein, which is responsible for packaging viral genomic RNA, interacts with host deaminases and co-localizes with them at stress granules to facilitate viral RNA mutagenesis. N proteins from several coronaviruses interact with host deaminases at RNA granules in a manner dependent on its F17 residue, suggesting a conserved role in modulation of viral mutagenesis in other coronaviruses. Furthermore, mutant N protein bearing a F17A substitution cannot localize to deaminase-containing RNA granules and leads to reduced mutagenesis of viral RNA, providing support for its function in enhancing deaminase-dependent viral RNA editing. Our study thus provides further insight into virus-host cell interactions mediating SARS-CoV-2 evolution.
Melanin-like nanoparticles slow cyst growth in ADPKD by dual inhibition of oxidative stress and CREB
Authors: Sun Yongzhan , Zou Quan , Yu Huizheng , Yi Xiaoping , Dou Xudan , Yang Yu , Liu Zhiheng , Yang Hong , Jia Junya , Chen Yupeng , Sun Shao-Kai , Zhang Lirong
Published: November 2024

Melanin-like nanoparticles (MNPs) have recently emerged as valuable agents in antioxidant therapy due to their excellent biocompatibility and potent capacity to scavenge various reactive oxygen species (ROS). However, previous studies have mainly focused on acute ROS-related diseases, leaving a knowledge gap regarding their potential in chronic conditions. Furthermore, apart from their well-established antioxidant effects, it remains unclear whether MNPs target other intracellular molecular pathways. In this study, we synthesized ultra-small polyethylene glycol-incorporated Mn2+-chelated MNP (MMPP). We found that MMPP traversed the glomerular filtration barrier and specifically accumulated in renal tubules. Autosomal dominant polycystic kidney disease (ADPKD) is a chronic genetic disorder closely associated with increased oxidative stress and featured by the progressive enlargement of cysts originating from various segments of the renal tubules. Treatment with MMPP markedly attenuated oxidative stress levels, inhibited cyst growth, thereby improving renal function. Interestingly, we found that MMPP effectively inhibits a cyst-promoting gene program downstream of the cAMP-CREB pathway, a crucial signaling pathway implicated in ADPKD progression. Mechanistically, we observed that MMPP directly binds to the bZIP DNA-binding domain of CREB, leading to competitive inhibition of CREB’s DNA binding ability and subsequent reduction in CREB target gene expression. In summary, our findings identify an intracellular target of MMPP and demonstrate its potential for treating ADPKD by simultaneously targeting oxidative stress and CREB transcriptional activity.
Acid Dissociation Constants, Formation Constants, and Other Thermodynamic Parameters
Authors: Kanzaki Ryo
Published: November 2024

In metal–ligand mixture solutions, more than one complex species with different coordination numbers coexist, and each complex behaves as a distinct chemical species. Hence, the first step in characterizing and synthesizing metal complexes is to know the type and concentration of each complex. Stability constants enable us to determine the formation distribution of the metal complexes. In this chapter, complex formation (complexation) equilibria and their equilibrium constants (stability constants) are described. The experimental procedures to determine the thermodynamic parameters of these complexation reactions are then described. The properties of the complexes that those parameters reflect are also discussed.
IR and Raman Spectroscopies
Authors: Teraoka Junji
Published: November 2024

This chapter is concerned with the use of vibrational spectroscopy in the study of the molecular structure of metal complexes. After a brief discussion of the fundamentals of infrared absorption and Raman scattering, the molecular vibrations of ligands of metal complexes will be explored, taking symmetry into consideration. Finally, examples of studies on porphyrin complexes and heme proteins by resonance Raman spectroscopy, saturation Raman spectroscopy, and vibrational circular dichroism will be presented.
Atroposelective synthesis of axially chiral indolizinylpyrroles by catalytic asymmetric Paal–Knorr reaction
Authors: Zhan Wenyan , Hu Jiameng , Chen Xiaoyun , Luo Gen , Song Xiaoxiao
Published: November 2024

A CPA-catalyzed Paal–Knorr reaction of 3-aminoindolizines and 1,4-diketones was described, achieving new five/five-membered indolizinylpyrrole atropisomers.
Ni2+ mediated oxidation and aggregation of o-phenylenediamine: an enhanced photothermal effect for direct, specific and background-free detection of thiophanate-methyl
Authors: Xu Jinju , Qin Ziyi , Liao Chunhui , Lan Tian , Shi Shuyun
Published: November 2024

A novel photothermal platform based on the formation of o-phenylenediamine trimer (triOPD)-Ni2+ aggregates (PCE, 74.4%) for direct, specific, enzyme-free, and background-free detection of thiophanate-methyl.
Orientation-modulated oxygen evolution reaction in epitaxial SrRuO3 films
Authors: Pan Shencheng , Wei Lianjin , Xie Junlong , Lu Zhenjie , Yuan Jiajia , Tang Tian , Meng Leichao , Wang Xin , Zhu Junwu , Fu Yongsheng
Published: November 2024

The spin states and electronic structures of the three characteristic crystal planes of SrRuO3 exhibit significant differences. Single-crystal film growth revealed the low spin (001) plane as the most effective for OER.
Bioinspired metal–organic frameworks for aqueous environment decontamination: from laboratory scale to real-world technologies
Authors: Negro Cristina , Guerra Walter D. , Armentano Donatella , Ferrando-Soria Jesús , Grancha Thais , Pardo Emilio
Published: November 2024

Oxamidato-based MOFs in water remediation: the most remarkable examples of the application of oxamidato-based bioMOFs for the selective and efficient removal of emerging pollutants are highlighted in this feature article.
Classification of self-assembled fluorescent probes and their application in cancer diagnosis
Authors: Wu Wenjiao , Huo Fangjun , Yin Caixia
Published: November 2024

The high sensitivity, high selectivity, real-time monitoring capability, non-destructiveness, and versatility of small molecule fluorescent probes make them indispensable and powerful tools in bioscience research.
Large scalable nickel phosphide/nickel@carbon cloth-based flexible composite electrodes for symmetric supercapacitors
Authors: Wei Tao , Cen Meiling , Xu Jing , Zhou Guangmin , Shao Jiao-Jing
Published: November 2024

Electroless deposition of low-cost and large scalable Ni3P/Ni hybrid film on carbon cloth as a flexible composite electrode with remarkable mechanical robustness for high performance supercapacitors.
Controlling the architecture of Au/Pt core–shell nanocubes via platinum growth mode
Authors: Maack Imke , Oldenburg Kevin , Al-Shamery Katharina
Published: November 2024

The nanocrystal surface architectures of cubic bimetallic plasmonic gold antenna-platinum reactor systems for photocatalysis can be controlled via the choice of the reduction agent in nanoparticle synthesis under otherwise identical conditions.
Thiadiazole-based 3D covalent organic framework for efficient anhydrous proton conduction
Authors: Pan Yaoyao , Shan Zhen , Liu Ziya , Su Jian , Zhang Gen
Published: November 2024

The design and synthesis of three-dimensional (3D) covalent organic frameworks (COFs) with exceptional stability and high proton conductivity are critical for advancing high-temperature fuel cells but remain significantly challenging.
Suboxides and subselenides: intermediate reaction products to form Ga2O3, Ga2Se3, In2O3, In2Se3, SnO2, and SnSe2 during molecular-beam epitaxy
Authors: Vogt Patrick , Shang Shun-Li , Liu Zi-Kui
Published: November 2024

General MBE reaction scheme for binary III–VI and IV–VI materials. It presents the complex, consecutive reaction pathways of the adsorbed metal (e.g., Ga), via its subcompound (e.g., Ga2Se), to its solid-state ground state (e.g., Ga2Se3).
Nonadiabatic ab initio chemical reaction dynamics for the photoisomerization reaction of 3,5-dimethylisoxazole via the S1 electronic state
Authors: Kimura Mizuki , Nanbu Shinkoh
Published: November 2024

An advanced molecular dynamics simulation of 3,5-dimethylisoxazole has uncovered two distinct relaxation pathways from the S1 to the S0 state.
Experimental and theoretical investigation on the charge storage performance of NiSb2O6 and its reduced graphene oxide composite – a comparative analysis
Authors: Parul  , Sahoo Surjit , Ratha Satyajit , Sanyal Gopal , Chakraborty Brahmananda , Nayak Saroj Kumar
Published: November 2024

Experimental and theoretical insights into the comparative electrochemical charge storage performances of a NiSb2O6–reduced graphene oxide composite, with its bare counterpart, in neutral electrolytic medium.
Beyond 22% power conversion efficiency in type-II MoSi2As4/MoGe2N4 photovoltaic vdW heterostructure
Authors: Zhang Jing-yi , Wu Xiao-bin , Shi Jun-jie
Published: November 2024

A two-dimensional type-II MoSi2As4/MoGe2N4 van der Waals heterostructure with a high power conversion efficiency of 22.09% was designed, making it a potential candidate material in the field of photovoltaics.
Interplay between conformational flexibility, intermolecular H-bonding and 3d-metal cation extraction ability in a series of thiacalix[4]arene lower rim disubstituted Schiff base derivatives
Authors: Strelnikova Iuliia V. , Ovsyannikov Alexander S. , Gubaidullin Aidar T. , Agarkov Artem S. , Kleshnina Sophiya R. , Iova A. A. , Furer Victor L. , Vandyukov Alexander E. , Solovieva Svetlana E. , Antipin Igor S.
Published: November 2024

The study revealed the enhanced conformational flexibility of thiacalix[4]arene Schiff base derivatives, which drastically affected their coordination and H-bonding behavior.
Simple carbenes as hydrogen bond acceptors: ab initio determination of nucleophilicities and reduced nucleophilicities
Authors: Alkorta Ibon , Legon Anthony
Published: November 2024

Conflated straight lines indicate that the nine carbenes have same reduced nucleophilicities when forming hydrogen bonds with Lewis acids HX.
Light driven photoswitches: three classes of molecular systems that result in a single photoproduct via a conical intersection and an exothermic reverse reaction
Authors: Zilberg Shmuel
Published: November 2024

A common feature of molecular photoswitches is the selectivity of their photo-processes.
Desulfurization of isothiocyanates by a divalent germanium amide
Authors: Stancil Thad R. , Fortney Vanessa A. , Murphy Julia K. , Gembicky Milan , Rheingold Arnold L. , Weinert Charles S.
Published: November 2024

A germanium(ii) amide abstracts a sulfur atom from isothiocyanates.
Sulfur oxidation mediated controllable reconstruction on LiCo1.9Fe0.1O4 for boosted electrochemical water oxidation
Authors: Xiong Bing , Tan Haige , Wang Yangkai , Sang Tian , Li Weiwei , Wang Jianlin , Huang Qiuping , Li Na , Fu Zhengping , Lu Yalin
Published: November 2024

Appropriate contact between catalysts and reactants calls for optimized exposure of active sites in the near-surface region, which can be accomplished by tuning the surface reconstruction degree.
Binding of base-stabilized borylenes with transition metals and formation of metal only Lewis pairs
Authors: Chakraborty Barsha , Hazarika Raj Rishi , Braunschweig Holger , Phukan Ashwini K.
Published: November 2024

Quantum chemical calculations predict that base-stabilized borylenes can not only strongly bind to transition metal complexes but could also facilitate the formation of metal-only Lewis pairs with Lewis acidic fragments.
Simultaneously improving the efficiencies of organic photovoltaic devices and modules by finely manipulating the aggregation behaviors of Y-series molecules
Authors: Li Yaohui , Jia Ziyan , Huang Peihao , Gao Chuanlin , Wang Yufei , Xue Shuangxi , Lu Shirong , (Michael) Yang Yang
Published: November 2024

We have developed a novel liquid additive that boosts J-aggregation in NFAs through enhanced non-covalent interactions with the BTP core, leading to a record efficiency for thick-film (≥200 nm), large-area OPV modules.
Correction: Exploring the variability of PFAS in urban sewage: a comparison of emissions in commercial versus municipal urban areas
Authors: Krlovic N. , Saracevic E. , Derx J. , Gundacker C. , Krampe J. , Kreuzinger N. , Zessner M. , Zoboli O.
Published: November 2024

Correction for ‘Exploring the variability of PFAS in urban sewage: a comparison of emissions in commercial versus municipal urban areas’ by N. Krlovic et al., Environ. Sci.: Processes Impacts, 2024, 26, 1868–1878, https://doi.org/10.1039/D4EM00415A.
Recent advances in bifunctional carbon-based single-atom electrocatalysts for rechargeable zinc–air batteries
Authors: Chen Yang , Wang Gan , Li Junhua , He Ting , Zhang Yi , Zhang Heng , Liu You-Nian
Published: November 2024

The review delves into six modulation strategies of carbon-based single-atom catalysts, emphasizing the relationship between electronic structure and performance to aid in the development of bifunctional electrocatalysts for zinc–air batteries.