bluuebunny/crossref_metadata_2025_split huggingface dataset:
Accounting for albedo change to identify climate-positive tree cover restoration
Authors: Hasler Natalia , Williams Christopher A. , Denney Vanessa Carrasco , Ellis Peter W. , Shrestha Surendra , Terasaki Hart Drew E. , Wolff Nicholas H. , Yeo Samantha , Crowther Thomas W. , Werden Leland K. , Cook-Patton Susan C. 
Published: March 2024

AbstractRestoring tree cover changes albedo, which is the fraction of sunlight reflected from the Earth’s surface. In most locations, these changes in albedo offset or even negate the carbon removal benefits with the latter leading to global warming. Previous efforts to quantify the global climate mitigation benefit of restoring tree cover have not accounted robustly for albedo given a lack of spatially explicit data. Here we produce maps that show that carbon-only estimates may be up to 81% too high. While dryland and boreal settings have especially severe albedo offsets, it is possible to find places that provide net-positive climate mitigation benefits in all biomes. We further find that on-the-ground projects are concentrated in these more climate-positive locations, but that the majority still face at least a 20% albedo offset. Thus, strategically deploying restoration of tree cover for maximum climate benefit requires accounting for albedo change and we provide the tools to do so.
Structure and function of Semaphorin-5A glycosaminoglycan interactions
Authors: Nagy Gergely N. , Zhao Xiao-Feng , Karlsson Richard , Wang Karen , Duman Ramona , Harlos Karl , El Omari Kamel , Wagner Armin , Clausen Henrik , Miller Rebecca L. , Giger Roman J. , Jones E. Yvonne 
Published: March 2024

AbstractIntegration of extracellular signals by neurons is pivotal for brain development, plasticity, and repair. Axon guidance relies on receptor-ligand interactions crosstalking with extracellular matrix components. Semaphorin-5A (Sema5A) is a bifunctional guidance cue exerting attractive and inhibitory effects on neuronal growth through the interaction with heparan sulfate (HS) and chondroitin sulfate (CS) glycosaminoglycans (GAGs), respectively. Sema5A harbors seven thrombospondin type-1 repeats (TSR1-7) important for GAG binding, however the underlying molecular basis and functions in vivo remain enigmatic. Here we dissect the structural basis for Sema5A:GAG specificity and demonstrate the functional significance of this interaction in vivo. Using x-ray crystallography, we reveal a dimeric fold variation for TSR4 that accommodates GAG interactions. TSR4 co-crystal structures identify binding residues validated by site-directed mutagenesis. In vitro and cell-based assays uncover specific GAG epitopes necessary for TSR association. We demonstrate that HS-GAG binding is preferred over CS-GAG and mediates Sema5A oligomerization. In vivo, Sema5A:GAG interactions are necessary for Sema5A function and regulate Plexin-A2 dependent dentate progenitor cell migration. Our study rationalizes Sema5A associated developmental and neurological disorders and provides mechanistic insights into how multifaceted guidance functions of a single transmembrane cue are regulated by proteoglycans.
The IL-33/ST2 axis is protective against acute inflammation during the course of periodontitis
Authors: Liu Anhao , Hayashi Mikihito , Ohsugi Yujin , Katagiri Sayaka , Akira Shizuo , Iwata Takanori , Nakashima Tomoki 
Published: March 2024

AbstractPeriodontitis, which is induced by repeated bacterial invasion and the ensuing immune reactions that follow, is the leading cause of tooth loss. Periodontal tissue is comprised of four different components, each with potential role in pathogenesis, however, most studies on immune responses focus on gingival tissue. Here, we present a modified ligature-induced periodontitis model in male mice to analyze the pathogenesis, which captures the complexity of periodontal tissue. We find that the inflammatory response in the peri-root tissues and the expression of IL-6 and RANKL by Thy-1.2− fibroblasts/stromal cells are prominent throughout the bone destruction phase, and present already at an early stage. The initiation phase is characterized by high levels of ST2 (encoded by Il1rl1) expression in the peri-root tissue, suggesting that the IL-33/ST2 axis is involved in the pathogenesis. Both Il1rl1- and Il33-deficient mice exhibit exacerbated bone loss in the acute phase of periodontitis, along with macrophage polarization towards a classically activated phenotype and increased neutrophil infiltration, indicating a protective role of the IL-33/ST2 axis in acute inflammation. Thus, our findings highlight the hidden role of the peri-root tissue and simultaneously advance our understanding of the etiology of periodontitis via implicating the IL-33/ST2 axis.
Using rare genetic mutations to revisit structural brain asymmetry
Authors: Kopal Jakub , Kumar Kuldeep , Shafighi Kimia , Saltoun Karin , Modenato Claudia , Moreau Clara A. , Huguet Guillaume , Jean-Louis Martineau , Martin Charles-Olivier , Saci Zohra , Younis Nadine , Douard Elise , Jizi Khadije , Beauchamp-Chatel Alexis , Kushan Leila , Silva Ana I. , van den Bree Marianne B. M. , Linden David E. J. , Owen Michael J. , Hall Jeremy , Lippé Sarah , Draganski Bogdan , Sønderby Ida E. , Andreassen Ole A. , Glahn David C. , Thompson Paul M. , Bearden Carrie E. , Zatorre Robert , Jacquemont Sébastien , Bzdok Danilo 
Published: March 2024

AbstractAsymmetry between the left and right hemisphere is a key feature of brain organization. Hemispheric functional specialization underlies some of the most advanced human-defining cognitive operations, such as articulated language, perspective taking, or rapid detection of facial cues. Yet, genetic investigations into brain asymmetry have mostly relied on common variants, which typically exert small effects on brain-related phenotypes. Here, we leverage rare genomic deletions and duplications to study how genetic alterations reverberate in human brain and behavior. We designed a pattern-learning approach to dissect the impact of eight high-effect-size copy number variations (CNVs) on brain asymmetry in a multi-site cohort of 552 CNV carriers and 290 non-carriers. Isolated multivariate brain asymmetry patterns spotlighted regions typically thought to subserve lateralized functions, including language, hearing, as well as visual, face and word recognition. Planum temporale asymmetry emerged as especially susceptible to deletions and duplications of specific gene sets. Targeted analysis of common variants through genome-wide association study (GWAS) consolidated partly diverging genetic influences on the right versus left planum temporale structure. In conclusion, our gene-brain-behavior data fusion highlights the consequences of genetically controlled brain lateralization on uniquely human cognitive capacities.
Synthetically-primed adaptation of Pseudomonas putida to a non-native substrate D-xylose
Authors: Dvořák Pavel , Burýšková Barbora , Popelářová Barbora , Ebert Birgitta E. , Botka Tibor , Bujdoš Dalimil , Sánchez-Pascuala Alberto , Schöttler Hannah , Hayen Heiko , de Lorenzo Víctor , Blank Lars M. , Benešík Martin 
Published: March 2024

AbstractTo broaden the substrate scope of microbial cell factories towards renewable substrates, rational genetic interventions are often combined with adaptive laboratory evolution (ALE). However, comprehensive studies enabling a holistic understanding of adaptation processes primed by rational metabolic engineering remain scarce. The industrial workhorse Pseudomonas putida was engineered to utilize the non-native sugar D-xylose, but its assimilation into the bacterial biochemical network via the exogenous xylose isomerase pathway remained unresolved. Here, we elucidate the xylose metabolism and establish a foundation for further engineering followed by ALE. First, native glycolysis is derepressed by deleting the local transcriptional regulator gene hexR. We then enhance the pentose phosphate pathway by implanting exogenous transketolase and transaldolase into two lag-shortened strains and allow ALE to finetune the rewired metabolism. Subsequent multilevel analysis and reverse engineering provide detailed insights into the parallel paths of bacterial adaptation to the non-native carbon source, highlighting the enhanced expression of transaldolase and xylose isomerase along with derepressed glycolysis as key events during the process.
Abundant pleiotropy across neuroimaging modalities identified through a multivariate genome-wide association study
Authors: Tissink E. P. , Shadrin A. A. , van der Meer D. , Parker N. , Hindley G. , Roelfs D. , Frei O. , Fan C. C. , Nagel M. , Nærland T. , Budisteanu M. , Djurovic S. , Westlye L. T. , van den Heuvel M. P. , Posthuma D. , Kaufmann T. , Dale A. M. , Andreassen O. A. 
Published: March 2024

AbstractGenetic pleiotropy is abundant across spatially distributed brain characteristics derived from one neuroimaging modality (e.g. structural, functional or diffusion magnetic resonance imaging [MRI]). A better understanding of pleiotropy across modalities could inform us on the integration of brain function, micro- and macrostructure. Here we show extensive genetic overlap across neuroimaging modalities at a locus and gene level in the UK Biobank (N = 34,029) and ABCD Study (N = 8607). When jointly analysing phenotypes derived from structural, functional and diffusion MRI in a genome-wide association study (GWAS) with the Multivariate Omnibus Statistical Test (MOSTest), we boost the discovery of loci and genes beyond previously identified effects for each modality individually. Cross-modality genes are involved in fundamental biological processes and predominantly expressed during prenatal brain development. We additionally boost prediction of psychiatric disorders by conditioning independent GWAS on our multimodal multivariate GWAS. These findings shed light on the shared genetic mechanisms underlying variation in brain morphology, functional connectivity, and tissue composition.
Engineering biology and climate change mitigation: Policy considerations
Authors: Symons Jonathan , Dixon Thomas A. , Dalziell Jacqueline , Curach Natalie , Paulsen Ian T. , Wiskich Anthony , Pretorius Isak S. 
Published: March 2024

AbstractEngineering biology (EngBio) is a dynamic field that uses gene editing, synthesis, assembly, and engineering to design new or modified biological systems. EngBio applications could make a significant contribution to achieving net zero greenhouse gas emissions. Yet, policy support will be needed if EngBio is to fulfil its climate mitigation potential. What form should such policies take, and what EngBio applications should they target? This paper reviews EngBio’s potential climate contributions to assist policymakers shape regulations and target resources and, in so doing, to facilitate democratic deliberation on desirable futures.
Casein kinase II promotes piRNA production through direct phosphorylation of USTC component TOFU-4
Authors: Zhang Gangming , Zheng Chunwei , Ding Yue-he , Mello Craig 
Published: March 2024

AbstractPiwi-interacting RNAs (piRNAs) are genomically encoded small RNAs that engage Piwi Argonaute proteins to direct mRNA surveillance and transposon silencing. Despite advances in understanding piRNA pathways and functions, how the production of piRNA is regulated remains elusive. Here, using a genetic screen, we identify casein kinase II (CK2) as a factor required for piRNA pathway function. We show that CK2 is required for the localization of PRG-1 and for the proper localization of several factors that comprise the ‘upstream sequence transcription complex’ (USTC), which is required for piRNA transcription. Loss of CK2 impairs piRNA levels suggesting that CK2 promotes USTC function. We identify the USTC component twenty-one-U fouled-up 4 (TOFU-4) as a direct substrate for CK2. Our findings suggest that phosphorylation of TOFU-4 by CK2 promotes the assembly of USTC and piRNA transcription. Notably, during the aging process, CK2 activity declines, resulting in the disassembly of USTC, decreased piRNA production, and defects in piRNA-mediated gene silencing, including transposons silencing. These findings highlight the significance of posttranslational modification in regulating piRNA biogenesis and its implications for the aging process. Overall, our study provides compelling evidence for the involvement of a posttranslational modification mechanism in the regulation of piRNA biogenesis.
Defects in the cell wall and its deposition caused by loss-of-function of three RLKs alter root hydrotropism in Arabidopsis thaliana
Authors: Chang Jinke , Li Xiaopeng , Shen Juan , Hu Jun , Wu Liangfan , Zhang Xueyao , Li Jia 
Published: March 2024

AbstractRoot tips can sense moisture gradients and grow into environments with higher water potential. This process is called root hydrotropism. Here, we report three closely related receptor-like kinases (RLKs) that play critical roles in root hydrotropism: ALTERED ROOT HYDROTROPIC RESPONSE 1 (ARH1), FEI1, and FEI2. Overexpression of these RLKs strongly reduce root hydrotropism, but corresponding loss-of-function mutants exhibit an increased hydrotropic response in their roots. All these RLKs show polar localization at the plasma membrane regions in root tips. The biosynthesis of the cell wall, cutin, and wax (CCW) is significantly impaired in root tips of arh1-2 fei1-C fei2-C. A series of known CCW mutants also exhibit increased root hydrotropism and reduced osmotic tolerance, similar to the characteristics of the triple mutant. Our results demonstrat that the integrity of the cell wall, cutin, and root cap wax mediate a trade-off between root hydrotropism and osmotic tolerance.
RETRACTED ARTICLE: Metal free cross-dehydrogenative N-N coupling of primary amides with Lewis basic amines
Authors: Kathiravan Subban , Dhillon Prakriti , Zhang Tianshu , Nicholls Ian A. 
Published: March 2024

AbstractHydrazides, N-N containing structural motifs, are important due to their presence in a wide variety of biologically significant compounds. While the homo N-N coupling of two NH moieties to form the hydrazide N-N bond is well developed, the cross-dehydrogenative hetero N-N coupling remains very unevolved. Here we present an efficient intermolecular N-N cross-coupling of a series of primary benzamides with broad range of Lewis basic primary and secondary amines using PhI(OAc)2as both a terminal oxidant and a cross-coupling mediator, without the need for metal catalysts, high temperatures, and inert atmospheres, and with substantial potential for use in the late-stage functionalization of drugs.
Quantifying the interfacial triboelectricity in inorganic-organic composite mechanoluminescent materials
Authors: Pan Xin , Zhuang Yixi , He Wei , Lin Cunjian , Mei Lefu , Chen Changjian , Xue Hao , Sun Zhigang , Wang Chunfeng , Peng Dengfeng , Zheng Yanqing , Pan Caofeng , Wang Lixin , Xie Rong-Jun 
Published: March 2024

AbstractMechanoluminescence (ML) sensing technologies open up new opportunities for intelligent sensors, self-powered displays and wearable devices. However, the emission efficiency of ML materials reported so far still fails to meet the growing application requirements due to the insufficiently understood mechano-to-photon conversion mechanism. Herein, we propose to quantify the ability of different phases to gain or lose electrons under friction (defined as triboelectric series), and reveal that the inorganic-organic interfacial triboelectricity is a key factor in determining the ML in inorganic-organic composites. A positive correlation between the difference in triboelectric series and the ML intensity is established in a series of composites, and a 20-fold increase in ML intensity is finally obtained by selecting an appropriate inorganic-organic combination. The interfacial triboelectricity-regulated ML is further demonstrated in multi-interface systems that include an inorganic phosphor-organic matrix and organic matrix-force applicator interfaces, and again confirmed by self-oxidization and reduction of emission centers under continuous mechanical stimulus. This work not only gives direct experimental evidences for the underlying mechanism of ML, but also provides guidelines for rationally designing high-efficiency ML materials.
Precise prediction of phase-separation key residues by machine learning
Authors: Sun Jun , Qu Jiale , Zhao Cai , Zhang Xinyao , Liu Xinyu , Wang Jia , Wei Chao , Liu Xinyi , Wang Mulan , Zeng Pengguihang , Tang Xiuxiao , Ling Xiaoru , Qing Li , Jiang Shaoshuai , Chen Jiahao , Chen Tara S. R. , Kuang Yalan , Gao Jinhang , Zeng Xiaoxi , Huang Dongfeng , Yuan Yong , Fan Lili , Yu Haopeng , Ding Junjun 
Published: March 2024

AbstractUnderstanding intracellular phase separation is crucial for deciphering transcriptional control, cell fate transitions, and disease mechanisms. However, the key residues, which impact phase separation the most for protein phase separation function have remained elusive. We develop PSPHunter, which can precisely predict these key residues based on machine learning scheme. In vivo and in vitro validations demonstrate that truncating just 6 key residues in GATA3 disrupts phase separation, enhancing tumor cell migration and inhibiting growth. Glycine and its motifs are enriched in spacer and key residues, as revealed by our comprehensive analysis. PSPHunter identifies nearly 80% of disease-associated phase-separating proteins, with frequent mutated pathological residues like glycine and proline often residing in these key residues. PSPHunter thus emerges as a crucial tool to uncover key residues, facilitating insights into phase separation mechanisms governing transcriptional control, cell fate transitions, and disease development.
Genetic similarity between relatives provides evidence on the presence and history of assortative mating
Authors: Sunde Hans Fredrik , Eftedal Nikolai Haahjem , Cheesman Rosa , Corfield Elizabeth C. , Kleppesto Thomas H. , Seierstad Anne Caroline , Ystrom Eivind , Eilertsen Espen Moen , Torvik Fartein Ask 
Published: March 2024

AbstractAssortative mating – the non-random mating of individuals with similar traits – is known to increase trait-specific genetic variance and genetic similarity between relatives. However, empirical evidence is limited for many traits, and the implications hinge on whether assortative mating has started recently or many generations ago. Here we show theoretically and empirically that genetic similarity between relatives can provide evidence on the presence and history of assortative mating. First, we employed path analysis to understand how assortative mating affects genetic similarity between family members across generations, finding that similarity between distant relatives is more affected than close relatives. Next, we correlated polygenic indices of 47,135 co-parents from the Norwegian Mother, Father, and Child Cohort Study (MoBa) and found genetic evidence of assortative mating in nine out of sixteen examined traits. The same traits showed elevated similarity between relatives, especially distant relatives. Six of the nine traits, including educational attainment, showed greater genetic variance among offspring, which is inconsistent with stable assortative mating over many generations. These results suggest an ongoing increase in familial similarity for these traits. The implications of this research extend to genetic methodology and the understanding of social and economic disparities.
Engineering the pore environment of antiparallel stacked covalent organic frameworks for capture of iodine pollutants
Authors: Xie Yinghui , Rong Qiuyu , Mao Fengyi , Wang Shiyu , Wu You , Liu Xiaolu , Hao Mengjie , Chen Zhongshan , Yang Hui , Waterhouse Geoffrey I. N. , Ma Shengqian , Wang Xiangke 
Published: March 2024

AbstractRadioiodine capture from nuclear fuel waste and contaminated water sources is of enormous environmental importance, but remains technically challenging. Herein, we demonstrate robust covalent organic frameworks (COFs) with antiparallel stacked structures, excellent radiation resistance, and high binding affinities toward I2, CH3I, and I3− under various conditions. A neutral framework (ACOF-1) achieves a high affinity through the cooperative functions of pyridine-N and hydrazine groups from antiparallel stacking layers, resulting in a high capacity of ~2.16 g/g for I2 and ~0.74 g/g for CH3I at 25 °C under dynamic adsorption conditions. Subsequently, post-synthetic methylation of ACOF-1 converted pyridine-N sites to cationic pyridinium moieties, yielding a cationic framework (namely ACOF-1R) with enhanced capacity for triiodide ion capture from contaminated water. ACOF-1R can rapidly decontaminate iodine polluted groundwater to drinking levels with a high uptake capacity of ~4.46 g/g established through column breakthrough tests. The cooperative functions of specific binding moieties make ACOF-1 and ACOF-1R promising adsorbents for radioiodine pollutants treatment under practical conditions.
Cell-fate conversion of intestinal cells in adult Drosophila midgut by depleting a single transcription factor
Authors: Guo Xingting , Wang Chenhui , Zhang Yongchao , Wei Ruxue , Xi Rongwen 
Published: March 2024

AbstractThe manipulation of cell identity by reprograming holds immense potential in regenerative medicine, but is often limited by the inefficient acquisition of fully functional cells. This problem can potentially be resolved by better understanding the reprogramming process using in vivo genetic models, which are currently scarce. Here we report that both enterocytes (ECs) and enteroendocrine cells (EEs) in adultDrosophilamidgut show a surprising degree of cell plasticity. Depleting the transcription factor Tramtrack in the differentiated ECs can initiate Prospero-mediated cell transdifferentiation, leading to EE-like cells. On the other hand, depletion of Prospero in the differentiated EEs can lead to the loss of EE-specific transcription programs and the gain of intestinal progenitor cell identity, allowing cell cycle re-entry or differentiation into ECs. We find that intestinal progenitor cells, ECs, and EEs have a similar chromatin accessibility profile, supporting the concept that cell plasticity is enabled by pre-existing chromatin accessibility with switchable transcription programs. Further genetic analysis with this system reveals that the NuRD chromatin remodeling complex, cell lineage confliction, and age act as barriers to EC-to-EE transdifferentiation. The establishment of this genetically tractable in vivo model should facilitate mechanistic investigation of cell plasticity at the molecular and genetic level.
Substantially reducing global PM2.5-related deaths under SDG3.9 requires better air pollution control and healthcare
Authors: Yue Huanbi , He Chunyang , Huang Qingxu , Zhang Da , Shi Peijun , Moallemi Enayat A. , Xu Fangjin , Yang Yang , Qi Xin , Ma Qun , Bryan Brett A. 
Published: March 2024

AbstractThe United Nations’ Sustainable Development Goal (SDG) 3.9 calls for a substantial reduction in deaths attributable to PM2.5 pollution (DAPP). However, DAPP projections vary greatly and the likelihood of meeting SDG3.9 depends on complex interactions among environmental, socio-economic, and healthcare parameters. We project potential future trends in global DAPP considering the joint effects of each driver (PM2.5 concentration, death rate of diseases, population size, and age structure) and assess the likelihood of achieving SDG3.9 under the Shared Socioeconomic Pathways (SSPs) as quantified by the Scenario Model Intercomparison Project (ScenarioMIP) framework with simulated PM2.5 concentrations from 11 models. We find that a substantial reduction in DAPP would not be achieved under all but the most optimistic scenario settings. Even the development aligned with the Sustainability scenario (SSP1-2.6), in which DAPP was reduced by 19%, still falls just short of achieving a substantial (≥20%) reduction by 2030. Meeting SDG3.9 calls for additional efforts in air pollution control and healthcare to more aggressively reduce DAPP.