bluuebunny/crossref_metadata_2025_split huggingface dataset:
Active learning of ternary alloy structures and energies
Authors: Deshmukh Gaurav , Wichrowski Noah J. , Evangelou Nikolaos , Ghanekar Pushkar G. , Deshpande Siddharth , Kevrekidis Ioannis G. , Greeley Jeffrey 
Published: May 2024

AbstractMachine learning models with uncertainty quantification have recently emerged as attractive tools to accelerate the navigation of catalyst design spaces in a data-efficient manner. Here, we combine active learning with a dropout graph convolutional network (dGCN) as a surrogate model to explore the complex materials space of high-entropy alloys (HEAs). We train the dGCN on the formation energies of disordered binary alloy structures in the Pd-Pt-Sn ternary alloy system and improve predictions on ternary structures by performing reduced optimization of the formation free energy, the target property that determines HEA stability, over ensembles of ternary structures constructed based on two coordinate systems: (a) a physics-informed ternary composition space, and (b) data-driven coordinates discovered by the Diffusion Maps manifold learning scheme. Both reduced optimization techniques improve predictions of the formation free energy in the ternary alloy space with a significantly reduced number of DFT calculations compared to a high-fidelity model. The physics-based scheme converges to the target property in a manner akin to a depth-first strategy, whereas the data-driven scheme appears more akin to a breadth-first approach. Both sampling schemes, coupled with our acquisition function, successfully exploit a database of DFT-calculated binary alloy structures and energies, augmented with a relatively small number of ternary alloy calculations, to identify stable ternary HEA compositions and structures. This generalized framework can be extended to incorporate more complex bulk and surface structural motifs, and the results demonstrate that significant dimensionality reduction is possible in thermodynamic sampling problems when suitable active learning schemes are employed.
Copy number deletion of PLA2G4A affects the susceptibility and clinical phenotypes of schizophrenia
Authors: Gao Zibo , Guo Xinru , Sun Zhouyang , Wu Songyu , Wang Qianyi , Huang Qianlong , Bai Wei , Kou Changgui 
Published: May 2024

AbstractPhospholipase A2(PLA2) superfamily is recognized as being involved in the pathogenesis of schizophrenia by affecting lipid homeostasis in cell membranes. We hypothesized that PLA2 gene copy number variation (CNV) may affect PLA2 enzyme expression and be associated with schizophrenia risk. This study indicated that in the discovery stage, an increased copy number of PLA2G6 and the deletion of PLA2G3, PLA2G4A, PLA2G4F and PLA2G12F was associated with increased risk of schizophrenia. CNV segments involving six PLA2 genes were detected in publicly available datasets, including two deletion segments specific to the PLA2G4A gene. The relationship between the deletion of PLA2G4A and susceptibility to schizophrenia was then reaffirmed in the validation group of 806 individuals. There was a significant correlation between PLA2G4A deletion and the symptoms of poverty of thought in male patients and erotomanic delusion in females. Furthermore, ELISA results demonstrate a significant decrease in peripheral blood cytosolic PLA2(cPLA2) levels in patients with the PLA2G4A deletion genotype compared to those with normal and copy number duplicate genotypes. These data suggest that the functional copy number deletion in the PLA2G4A gene is associated with the risk of schizophrenia and clinical phenotypes by reducing the expression of cPLA2, which may be an indicator of susceptibility to schizophrenia.
EU carbon prices signal high policy credibility and farsighted actors
Authors: Sitarz Joanna , Pahle Michael , Osorio Sebastian , Luderer Gunnar , Pietzcker Robert 
Published: May 2024

AbstractCarbon prices in the EU emissions trading system are a key instrument driving Europe’s decarbonization. Between 2017 and 2021, they surged tenfold, exceeding €80 tCO2−1 and reshaping investment decisions across the electricity and industry sectors. What has driven this increase is an open question. While it coincided with two significant reforms tightening the cap (‘MSR reform’ and ‘Fit for 55’), we argue that a reduced supply of allowances alone cannot fully explain the price rise. A further crucial aspect is that actors must have become more farsighted as the reform signalled policymakers’ credible long-term commitment to climate targets. This is consistent with model results that show historic prices can be better explained with myopic actors, whereas explaining prices after the reforms requires actors to be farsighted. To underline the role of credibility, we test what would happen if a crisis undermines policy credibility such that actors become myopic again, demonstrating that carbon prices could plummet and endanger the energy transition.
De novo design of buttressed loops for sculpting protein functions
Authors: Jiang Hanlun , Jude Kevin M. , Wu Kejia , Fallas Jorge , Ueda George , Brunette T. J. , Hicks Derrick R. , Pyles Harley , Yang Aerin , Carter Lauren , Lamb Mila , Li Xinting , Levine Paul M. , Stewart Lance , Garcia K. Christopher , Baker David 
Published: May 2024

AbstractIn natural proteins, structured loops have central roles in molecular recognition, signal transduction and enzyme catalysis. However, because of the intrinsic flexibility and irregularity of loop regions, organizing multiple structured loops at protein functional sites has been very difficult to achieve by de novo protein design. Here we describe a solution to this problem that designs tandem repeat proteins with structured loops (9–14 residues) buttressed by extensive hydrogen bonding interactions. Experimental characterization shows that the designs are monodisperse, highly soluble, folded and thermally stable. Crystal structures are in close agreement with the design models, with the loops structured and buttressed as designed. We demonstrate the functionality afforded by loop buttressing by designing and characterizing binders for extended peptides in which the loops form one side of an extended binding pocket. The ability to design multiple structured loops should contribute generally to efforts to design new protein functions.
Affinity gaps among B cells in germinal centers drive the selection of MPER precursors
Authors: Ray Rashmi , Schiffner Torben , Wang Xuesong , Yan Yu , Rantalainen Kimmo , Lee Chang-Chun David , Parikh Shivang , Reyes Raphael A. , Dale Gordon A. , Lin Ying-Cing , Pecetta Simone , Giguere Sophie , Swanson Olivia , Kratochvil Sven , Melzi Eleonora , Phung Ivy , Madungwe Lisa , Kalyuzhniy Oleksandr , Warner John , Weldon Stephanie R. , Tingle Ryan , Lamperti Edward , Kirsch Kathrin H. , Phelps Nicole , Georgeson Erik , Adachi Yumiko , Kubitz Michael , Nair Usha , Crotty Shane , Wilson Ian A. , Schief William R. , Batista Facundo D. 
Published: May 2024

AbstractCurrent prophylactic human immunodeficiency virus 1 (HIV-1) vaccine research aims to elicit broadly neutralizing antibodies (bnAbs). Membrane-proximal external region (MPER)-targeting bnAbs, such as 10E8, provide exceptionally broad neutralization, but some are autoreactive. Here, we generated humanized B cell antigen receptor knock-in mouse models to test whether a series of germline-targeting immunogens could drive MPER-specific precursors toward bnAbs. We found that recruitment of 10E8 precursors to germinal centers (GCs) required a minimum affinity for germline-targeting immunogens, but the GC residency of MPER precursors was brief due to displacement by higher-affinity endogenous B cell competitors. Higher-affinity germline-targeting immunogens extended the GC residency of MPER precursors, but robust long-term GC residency and maturation were only observed for MPER-HuGL18, an MPER precursor clonotype able to close the affinity gap with endogenous B cell competitors in the GC. Thus, germline-targeting immunogens could induce MPER-targeting antibodies, and B cell residency in the GC may be regulated by a precursor–competitor affinity gap.
Alternative platelet differentiation pathways initiated by nonhierarchically related hematopoietic stem cells
Authors: Carrelha Joana , Mazzi Stefania , Winroth Axel , Hagemann-Jensen Michael , Ziegenhain Christoph , Högstrand Kari , Seki Masafumi , Brennan Margs S. , Lehander Madeleine , Wu Bishan , Meng Yiran , Markljung Ellen , Norfo Ruggiero , Ishida Hisashi , Belander Strålin Karin , Grasso Francesca , Simoglou Karali Christina , Aliouat Affaf , Hillen Amy , Chari Edwin , Siletti Kimberly , Thongjuea Supat , Mead Adam J. , Linnarsson Sten , Nerlov Claus , Sandberg Rickard , Yoshizato Tetsuichi , Woll Petter S. , Jacobsen Sten Eirik W. 
Published: May 2024

AbstractRare multipotent stem cells replenish millions of blood cells per second through a time-consuming process, passing through multiple stages of increasingly lineage-restricted progenitors. Although insults to the blood-forming system highlight the need for more rapid blood replenishment from stem cells, established models of hematopoiesis implicate only one mandatory differentiation pathway for each blood cell lineage. Here, we establish a nonhierarchical relationship between distinct stem cells that replenish all blood cell lineages and stem cells that replenish almost exclusively platelets, a lineage essential for hemostasis and with important roles in both the innate and adaptive immune systems. These distinct stem cells use cellularly, molecularly and functionally separate pathways for the replenishment of molecularly distinct megakaryocyte-restricted progenitors: a slower steady-state multipotent pathway and a fast-track emergency-activated platelet-restricted pathway. These findings provide a framework for enhancing platelet replenishment in settings in which slow recovery of platelets remains a major clinical challenge.
A global dataset of diel activity patterns in insect communities
Authors: Wong Mark K. L. , Didham Raphael 
Published: May 2024

AbstractInsect activity powers ecosystems and food production globally. Although insect activity is known to vary with the rise and setting of the sun, there is surprisingly limited empirical information on how insect abundance and richness varies across the 24-hour day–night (diel) cycle. Moreover, commonly used methods for sampling insects such as light traps do not provide suitable comparisons of community properties between diel periods. We present a dataset of 1512 observations of abundance and richness during diurnal and nocturnal periods in insect communities worldwide. The data were collected from 99 studies that systematically sampled insect communities during day and night, using sampling methods minimally influenced by diel variation, such as movement-based interception traps. Spanning six continents, 41 countries and 16 insect orders, the data can support investigations into the factors influencing insect diel preferences as well as the causes and consequences of temporal changes in insect biodiversity. The data also provides key baseline information on the diel activity patterns of insect communities for long-term ecological monitoring. These pursuits take on added significance considering contemporary ‘insect declines’ and increasing anthropogenic impacts on diurnal and nocturnal biodiversity.
Micro-CT data of complete metamorphosis process in Harmonia axyridis
Authors: Shu Runguo , Xiao Yiqi , Zhang Chaowei , Liu Ying , Zhou Hang , Li Fei 
Published: May 2024

AbstractInsect metamorphosis involves significant changes in insect internal structure and is thus a critical focus of entomological research. Investigating the morphological transformation of internal structures is vital to understanding the origins of adult insect organs. Beetles are among the most species-rich groups in insects, but the development and transformation of their internal organs have yet to be systematically documented. In this study, we have acquired a comprehensive dataset that includes 27 detailed whole-body tomographic image sets of Harmonia axyridis, spanning from the prepupal to the pupal stages. Utilizing this data, we have created intricate 3D models of key internal organs, encompassing the brain, ventral nerve cord, digestive and excretion systems, as well as the body wall muscles. These data documented the transformation process of these critical organs and correlations between the origin of adult and larval organs and can be used to enhance the understanding of holometabolous adult organ genesis and offers a valuable reference model for investigating complete metamorphosis in insects.
A chromosome-scale genome assembly of the nipa palm hispid beetle Octodonta nipae
Authors: Tang Baozhen , Yin Chuanlin , He Kang , Tao Shaomin , Fu Lang , Liu Ying , Li Fei , Hou Youming 
Published: May 2024

AbstractNipa palm hispid beetle (Octodonta nipae) is an insect species that is native to Malaysia but has spread to southern China and beyond, seriously threatening palm production. A lack of high-quality genome resources has hindered understanding of the insect’s invasive characteristics and ecological adaptations. Here, we combined Illumina short read, PacBio long-read, and high-throughput chromosome conformation capture (Hi-C) sequencing technologies to generate a high-quality, chromosome-scale genome assembly of nipa palm hispid beetle. The genome assembly was 1.31 Gb in size, consisting of nine chromosomes. The contig and scaffold N50 values were 1.022 Mb and 148.6 Mb, respectively. The genome assembly completeness was estimated at 99.1%. Annotation revealed 16,305 protein-coding genes and 62.16% repeat sequences. This high-quality genome assembly is a valuable resource that will contribute to understanding of the genetic factors underlying the invasive characteristics of nipa palm hispid beetle, ultimately promoting development of efficient control policies.
An experimental investigation of the convective heat transfer augmentation in U-bend double pipe heat exchanger using water-MgO-Cmc fluid
Authors: Gabir Mustafa M. , Albayati Ibrahim M. , Hatami Mohammad , Alkhafaji Dhirgham 
Published: May 2024

AbstractOne of the major problems of using nanofluids in heat exchange applications is the forming and deposition of nanoparticles on the inner surface of the heat exchanger. In this paper, Water-Cmc fluid is used as a surfactant for nanoparticles to prevent deposition and congregation. The pressure drops and heat transfer in U-bend double pipe heat exchanger based on water-MgO-Cmc fluid, are examined. Nanoparticles of Magnesium Oxide (MgO) and Carboxymethyl Cellulose (Cmc) are used with pure water as a base fluid. The experimental rig and procedures are designed to facilitate various operational conditions such as flow rate, volume concentration of MgO particles and weight concentration of Cmc particles. Furthermore, convective heat transfer coefficient, heat exchanger effectiveness, pressure drop, friction factor, under different conditions, are measured. The results demonstrate convective heat transfer coefficient of U-bend double pipe heat exchangers is enhanced by 35% for 1 MgO vol.% and 0.2 Cmc wt.% compared to base fluid (Water-Cmc). It is concluded that pressure drops are directly proportion to the increase of MgO nanoparticles at same Cmc concentration by 23% at 0.2 wt.%. Whilst, friction factor of the system is inversely proportion to the increase of volumetric flow rate of water-MgO-Cmc fluid. An increase in MgO nanoparticle concentration increases the friction factor, hence maximum friction factor enhancement by 38% for MgO concentration of 1 vol.%. The effectiveness of heat exchanger is slightly increased by 8% with increase of MgO concentration and flow rate. Finally, thermo-physical characteristics of water-MgO-Cmc fluid at various temperatures, are measured
An omics-based characterization of Wolfiporia cocos reveals three CYP450 members involved in the biosynthetic pathway of pachymic acid
Authors: Liu Heping , Jing Naliang , Li Fengfeng , Wang Keyue , Tang Jing , Zhao Qin , Zhang Yipeng , Noushahi Hamza Armghan , Xu Ran , Wang Xuekui , Zhu Wenjun , Feng Shengqiu , Shu Shaohua , Mei Zhinan 
Published: May 2024

AbstractWolfiporia cocos is a medicinal mushroom used in China. It biosynthesizes pachymic acid (PA), a main therapeutic triterpene associated with therapies. Nowadays, the unknown PA biosynthesis leads to difficulties in increasing its content in W. cocos. Herein, we report sequencing, assembling, and characterization of the genome and several transcriptomes of W. cocos. Sequence mining determined candidate genes that encode lanosterol synthase, sterol O-acyltransferase, and sterol C-24 methyltransferase likely involved in the steps from lanosterol to PA. Gene cluster analysis identified four CYP450 cDNAs likely involved in the biosynthesis of PA, namely WcCYP64-1, WcCYP64-2, WcCYP52, and WcCYP_FUM15, which were subjected to both overexpression and silencing in mycelia. The overexpression of each of WcCYP64-1, WcCYP52 and WcCYP_FUM15 increased the content of PA, 16α-hydroxytrametenolic acid, eburicoic acid, and tumulosic acid, while the silencing of each gene either significantly or slightly decreased the contents of these four compounds, indicating their involvement in the PA biosynthesis. In addition, different temperatures affected the expression of these genes and the formation of PA. By contrast, the overexpression and silencing of WcCYP64-2 did not alter the formation of these compounds. Taken together, these findings determine more potential steps in the biosynthetic pathway of PA for metabolic engineering.
A metagenomic analysis of the phase 2 Anopheles gambiae 1000 genomes dataset reveals a wide diversity of cobionts associated with field collected mosquitoes
Authors: Pastusiak Andrzej , Reddy Michael R. , Chen Xiaoji , Hoyer Isaiah , Dorman Jack , Gebhardt Mary E. , Carpi Giovanna , Norris Douglas E. , Pipas James M. , Jackson Ethan K. 
Published: May 2024

AbstractThe Anopheles gambiae 1000 Genomes (Ag1000G) Consortium previously utilized deep sequencing methods to catalogue genetic diversity across African An. gambiae populations. We analyzed the complete datasets of 1142 individually sequenced mosquitoes through Microsoft Premonition’s Bayesian mixture model based (BMM) metagenomics pipeline. All specimens were confirmed as either An. gambiae sensu stricto (s.s.) or An. coluzzii with a high degree of confidence ( > 98% identity to reference). Homo sapiens DNA was identified in all specimens indicating contamination may have occurred either at the time of specimen collection, preparation and/or sequencing. We found evidence of vertebrate hosts in 162 specimens. 59 specimens contained validated Plasmodium falciparum reads. Human hepatitis B and primate erythroparvovirus-1 viral sequences were identified in fifteen and three mosquito specimens, respectively. 478 of the 1,142 specimens were found to contain bacterial reads and bacteriophage-related contigs were detected in 27 specimens. This analysis demonstrates the capacity of metagenomic approaches to elucidate important vector-host-pathogen interactions of epidemiological significance.
Bio-inspired surface structures promote optical transmittance and hydrophobicity in cellulose-based films for self-cleaning perovskite solar cells
Authors: Daghigh Shirazi Hamidreza , Mirmohammadi Seyed Mehran , Mousavi Seyede Maryam , Markkanen Magnus , Halme Janne , Jokinen Ville , Vapaavuori Jaana 
Published: May 2024

AbstractDeveloping suitable light management layers can improve the lifetime and efficiency of solar cells and other optoelectronics. Here, a bioinspired approach to produce all-biobased films with high anisotropic light scattering and superhydrophobicity is presented as a route toward sustainable light management layers for photovoltaics. The multifunctional films are achieved by replicating leek leaves onto cellulose acetate, producing hierarchical surface structures. The free-standing films show a transmittance of ≈94% and a haze of ≈54% at the wavelength of 550 nm. Moreover, anisotropic advancing contact angles of up to 160° and 156° in cross directions are achieved through tailoring a carnauba wax coating. Using the replica as the light management layer on perovskite solar cells improved the power conversion efficiency by 6 ± 0.3%. Meanwhile, the surface water repellency facilitates self-cleaning, ensuring maximum incident light over time by tackling dirt accumulation. Furthermore, the method can be potentially employed to fabricate substrates from virtually any leaf or patterned surface as the initial replication template.
Underestimation of carbon dioxide emissions from organic-rich agricultural soils
Authors: Liang Zhi , Hermansen Cecilie , Weber Peter L. , Pesch Charles , Greve Mogens H. , de Jonge Lis W. , Mäenpää Maarit , Leifeld Jens , Elsgaard Lars 
Published: May 2024

AbstractOrganic-rich agricultural soils, including drained peatlands, are hotspots for biogenic CO2 emissions. Due to microbial mineralisation, the organic carbon (OC) content of these soils transitions to that of mineral soils, but it remains unclear how the residual OC content controls the rate of CO2 emission. Here we show that area-scaled CO2 emissions from topsoils with >6% OC are not controlled by OC content and OC density in a comprehensive laboratory incubation experiment. National greenhouse gas inventories assign area-scaled CO2 emission factors to soils with >12% OC, while soils with 6-12% OC are mostly disregarded or treated with lower emission factors. In this respect, our results suggest that CO2 emissions from organic soils could be underestimated by up to 40% in the Danish national inventory submission to the United Nations Framework Convention on Climate Change (UNFCCC). We conclude that global underestimation of area-scaled CO2 emissions from 6-12% OC soils occurs in countries with large proportions of organic soils in transition from organic to organo-mineral soils due to agricultural management. Refining CO2 emission estimates for 6-12% OC soils is critical for the accuracy of national inventories, but also for recognising the climate benefits of initiatives to rewet drained organic soils.
Aging atlas reveals cell-type-specific effects of pro-longevity strategies
Authors: Gao Shihong Max , Qi Yanyan , Zhang Qinghao , Guan Youchen , Lee Yi-Tang , Ding Lang , Wang Lihua , Mohammed Aaron S. , Li Hongjie , Fu Yusi , Wang Meng C. 
Published: May 2024

AbstractOrganismal aging involves functional declines in both somatic and reproductive tissues. Multiple strategies have been discovered to extend lifespan across species. However, how age-related molecular changes differ among various tissues and how those lifespan-extending strategies slow tissue aging in distinct manners remain unclear. Here we generated the transcriptomic Cell Atlas of Worm Aging (CAWA, http://mengwanglab.org/atlas) of wild-type and long-lived strains. We discovered cell-specific, age-related molecular and functional signatures across all somatic and germ cell types. We developed transcriptomic aging clocks for different tissues and quantitatively determined how three different pro-longevity strategies slow tissue aging distinctively. Furthermore, through genome-wide profiling of alternative polyadenylation (APA) events in different tissues, we discovered cell-type-specific APA changes during aging and revealed how these changes are differentially affected by the pro-longevity strategies. Together, this study offers fundamental molecular insights into both somatic and reproductive aging and provides a valuable resource for in-depth understanding of the diversity of pro-longevity mechanisms.