bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evidence of thermophilization in Afromontane forests
Authors: Cuni-Sanchez Aida , Martin Emanuel H. , Uzabaho Eustrate , Ngute Alain S. K. , Bitariho Robert , Kayijamahe Charles , Marshall Andrew R. , Mohamed Nassoro A. , Mseja Gideon A. , Nkwasibwe Aventino , Rovero Francesco , Sheil Douglas , Tinkasimire Rogers , Tumugabirwe Lawrence , Feeley Kenneth J. , Sullivan Martin J. P. 
Published: July 2024

AbstractThermophilization is the directional change in species community composition towards greater relative abundances of species associated with warmer environments. This process is well-documented in temperate and Neotropical plant communities, but it is uncertain whether this phenomenon occurs elsewhere in the tropics. Here we extend the search for thermophilization to equatorial Africa, where lower tree diversity compared to other tropical forest regions and different biogeographic history could affect community responses to climate change. Using re-census data from 17 forest plots in three mountain regions of Africa, we find a consistent pattern of thermophilization in tree communities. Mean rates of thermophilization were +0.0086 °C·y−1 in the Kigezi Highlands (Uganda), +0.0032 °C·y−1 in the Virunga Mountains (Rwanda-Uganda-Democratic Republic of the Congo) and +0.0023 °C·y−1 in the Udzungwa Mountains (Tanzania). Distinct from other forests, both recruitment and mortality were important drivers of thermophilzation in the African plots. The forests studied currently act as a carbon sink, but the consequences of further thermophilization are unclear.
TSG-6+ cancer-associated fibroblasts modulate myeloid cell responses and impair anti-tumor response to immune checkpoint therapy in pancreatic cancer
Authors: Anandhan Swetha , Herbrich Shelley , Goswami Sangeeta , Guan Baoxiang , Chen Yulong , Macaluso Marc Daniel , Jindal Sonali , Natarajan Seanu Meena , Andrewes Samuel W. , Xiong Liangwen , Nagarajan Ashwat , Basu Sreyashi , Tang Derek Ng , Liu Jielin , Min Jimin , Maitra Anirban , Sharma Padmanee 
Published: July 2024

AbstractResistance to immune checkpoint therapy (ICT) presents a growing clinical challenge. The tumor microenvironment (TME) and its components, namely tumor-associated macrophages (TAMs) and cancer-associated fibroblasts (CAFs), play a pivotal role in ICT resistance; however, the underlying mechanisms remain under investigation. In this study, we identify expression of TNF-Stimulated Factor 6 (TSG-6) in ICT-resistant pancreatic tumors, compared to ICT-sensitive melanoma tumors, both in mouse and human. TSG-6 is expressed by CAFs within the TME, where suppressive macrophages expressing Arg1, Mafb, and Mrc1, along with TSG-6 ligand Cd44, predominate. Furthermore, TSG-6 expressing CAFs co-localize with the CD44 expressing macrophages in the TME. TSG-6 inhibition in combination with ICT improves therapy response and survival in pancreatic tumor-bearing mice by reducing macrophages expressing immunosuppressive phenotypes and increasing CD8 T cells. Overall, our findings propose TSG-6 as a therapeutic target to enhance ICT response in non-responsive tumors.
Primordial aqueous alteration recorded in water-soluble organic molecules from the carbonaceous asteroid (162173) Ryugu
Authors: Takano Yoshinori , Naraoka Hiroshi , Dworkin Jason P. , Koga Toshiki , Sasaki Kazunori , Sato Hajime , Oba Yasuhiro , Ogawa Nanako O. , Yoshimura Toshihiro , Hamase Kenji , Ohkouchi Naohiko , Parker Eric T. , Aponte José C. , Glavin Daniel P. , Furukawa Yoshihiro , Aoki Junken , Kano Kuniyuki , Nomura Shin-ichiro M. , Orthous-Daunay Francois-Regis , Schmitt-Kopplin Philippe ,   Hayabusa2-initial-analysis SOM team, Furusho Aogu , Hashiguchi Minako , Fukushima Kazuhiko , Dan Aoki  , McLain Hannah L. , Elsila Jamie E. , Graham Heather V. , Eiler John M. , Hertkorn Norbert , Ruf Alexander , Wolters Cédric , Isa Junko , Vuitton Véronique , Thissen Roland , Sakai Saburo , Sugahara Haruna , Mita Hajime , Chikaraishi Yoshito , Yoshikawa Takaaki , Tanaka Satoru , Morita Mayu , Onose Morihiko , Araoka Daisuke , Kabashima Fumie , Fujishima Kosuke , Sato Hajime , Yamazaki Tomoya , Kimura Yuki , Yurimoto Hisayoshi , Nakamura Tomoki , Noguchi Takaaki , Okazaki Ryuji , Yabuta Hikaru , Sakamoto Kanako , Yada Toru , Nishimura Masahiro , Nakato Aiko , Miyazaki Akiko , Yogata Kasumi , Abe Masanao , Okada Tatsuaki , Usui Tomohiro , Yoshikawa Makoto , Saiki Takanao , Tanaka Satoshi , Terui Fuyuto , Nakazawa Satoru , Watanabe Sei-ichiro , Tsuda Yuichi , Tachibana Shogo 
Published: July 2024

AbstractWe report primordial aqueous alteration signatures in water-soluble organic molecules from the carbonaceous asteroid (162173) Ryugu by the Hayabusa2 spacecraft of JAXA. Newly identified low-molecular-weight hydroxy acids (HO-R-COOH) and dicarboxylic acids (HOOC-R-COOH), such as glycolic acid, lactic acid, glyceric acid, oxalic acid, and succinic acid, are predominant in samples from the two touchdown locations at Ryugu. The quantitative and qualitative profiles for the hydrophilic molecules between the two sampling locations shows similar trends within the order of ppb (parts per billion) to ppm (parts per million). A wide variety of structural isomers, including α- and β-hydroxy acids, are observed among the hydrophilic molecules. We also identify pyruvic acid and dihydroxy and tricarboxylic acids, which are biochemically important intermediates relevant to molecular evolution, such as the primordial TCA (tricarboxylic acid) cycle. Here, we find evidence that the asteroid Ryugu samples underwent substantial aqueous alteration, as revealed by the presence of malonic acid during keto–enol tautomerism in the dicarboxylic acid profile. The comprehensive data suggest the presence of a series for water-soluble organic molecules in the regolith of Ryugu and evidence of signatures in coevolutionary aqueous alteration between water and organics in this carbonaceous asteroid.
Hypothalamic hormone deficiency enables physiological anorexia in ground squirrels during hibernation
Authors: Mohr Sarah M. , Dai Pra Rafael , Platt Maryann P. , Feketa Viktor V. , Shanabrough Marya , Varela Luis , Kristant Ashley , Cao Haoran , Merriman Dana K. , Horvath Tamas L. , Bagriantsev Sviatoslav N. , Gracheva Elena O. 
Published: July 2024

AbstractMammalian hibernators survive prolonged periods of cold and resource scarcity by temporarily modulating normal physiological functions, but the mechanisms underlying these adaptations are poorly understood. The hibernation cycle of thirteen-lined ground squirrels (Ictidomys tridecemlineatus) lasts for 5–7 months and comprises weeks of hypometabolic, hypothermic torpor interspersed with 24–48-h periods of an active-like interbout arousal (IBA) state. We show that ground squirrels, who endure the entire hibernation season without food, have negligible hunger during IBAs. These squirrels exhibit reversible inhibition of the hypothalamic feeding center, such that hypothalamic arcuate nucleus neurons exhibit reduced sensitivity to the orexigenic and anorexigenic effects of ghrelin and leptin, respectively. However, hypothalamic infusion of thyroid hormone during an IBA is sufficient to rescue hibernation anorexia. Our results reveal that thyroid hormone deficiency underlies hibernation anorexia and demonstrate the functional flexibility of the hypothalamic feeding center.
Characterising the genetic architecture of changes in adiposity during adulthood using electronic health records
Authors: Venkatesh Samvida S. , Ganjgahi Habib , Palmer Duncan S. , Coley Kayesha , Linchangco Gregorio V. , Hui Qin , Wilson Peter , Ho Yuk-Lam , Cho Kelly , Arumäe Kadri ,   Million Veteran Program,   Estonian Biobank Research Team, Metspalu Andres , Milani Lili , Esko Tõnu , Mägi Reedik , Nelis Mari , Hudjashov Georgi , Wittemans Laura B. L. , Nellåker Christoffer , Vainik Uku , Sun Yan V. , Holmes Chris , Lindgren Cecilia M. , Nicholson George 
Published: July 2024

AbstractObesity is a heritable disease, characterised by excess adiposity that is measured by body mass index (BMI). While over 1,000 genetic loci are associated with BMI, less is known about the genetic contribution to adiposity trajectories over adulthood. We derive adiposity-change phenotypes from 24.5 million primary-care health records in over 740,000 individuals in the UK Biobank, Million Veteran Program USA, and Estonian Biobank, to discover and validate the genetic architecture of adiposity trajectories. Using multiple BMI measurements over time increases power to identify genetic factors affecting baseline BMI by 14%. In the largest reported genome-wide study of adiposity-change in adulthood, we identify novel associations with BMI-change at six independent loci, including rs429358 (APOE missense variant). The SNP-based heritability of BMI-change (1.98%) is 9-fold lower than that of BMI. The modest genetic correlation between BMI-change and BMI (45.2%) indicates that genetic studies of longitudinal trajectories could uncover novel biology of quantitative traits in adulthood.
Wavelength-tunable high-fidelity entangled photon sources enabled by dual Stark effects
Authors: Chen Chen , Yan Jun-Yong , Babin Hans-Georg , Wang Jiefei , Xu Xingqi , Lin Xing , Yu Qianqian , Fang Wei , Liu Run-Ze , Huo Yong-Heng , Cai Han , Sha Wei E. I. , Zhang Jiaxiang , Heyn Christian , Wieck Andreas D. , Ludwig Arne , Wang Da-Wei , Jin Chao-Yuan , Liu Feng 
Published: July 2024

AbstractThe construction of a large-scale quantum internet requires quantum repeaters containing multiple entangled photon sources with identical wavelengths. Semiconductor quantum dots can generate entangled photon pairs deterministically with high fidelity. However, realizing wavelength-matched quantum-dot entangled photon sources faces two difficulties: the non-uniformity of emission wavelength and exciton fine-structure splitting induced fidelity reduction. Typically, these two factors are not independently tunable, making it challenging to achieve simultaneous improvement. In this work, we demonstrate wavelength-tunable entangled photon sources based on droplet-etched GaAs quantum dots through the combined use of AC and quantum-confined Stark effects. The emission wavelength can be tuned by ~1 meV while preserving an entanglement fidelity f exceeding 0.955(1) in the entire tuning range. Based on this hybrid tuning scheme, we finally demonstrate multiple wavelength-matched entangled photon sources with f > 0.919(3), paving the way towards robust and scalable on-demand entangled photon sources for quantum internet and integrated quantum optical circuits.
The cysteine-rich virulence factor NipA of Arthrobotrys flagrans interferes with cuticle integrity of Caenorhabditis elegans
Authors: Emser Jennifer , Wernet Nicole , Hetzer Birgit , Wohlmann Elke , Fischer Reinhard 
Published: July 2024

AbstractAnimals protect themself from microbial attacks by robust skins or a cuticle as in Caenorhabditis elegans. Nematode-trapping fungi, like Arthrobotrys flagrans, overcome the cuticle barrier and colonize the nematode body. While lytic enzymes are important for infection, small-secreted proteins (SSPs) without enzymatic activity, emerge as crucial virulence factors. Here, we characterized NipA (nematode induced protein) which A. flagrans secretes at the penetration site. In the absence of NipA, A. flagrans required more time to penetrate C. elegans. Heterologous expression of the fungal protein in the epidermis of C. elegans led to blister formation. NipA contains 13 cysteines, 12 of which are likely to form disulfide bridges, and the remaining cysteine was crucial for blister formation. We hypothesize that NipA interferes with cuticle integrity to facilitate fungal entry. Genome-wide expression analyses of C. elegans expressing NipA revealed mis-regulation of genes associated with extracellular matrix (ECM) maintenance and innate immunity.
Fungal melanin suppresses airway epithelial chemokine secretion through blockade of calcium fluxing
Authors: Reedy Jennifer L. , Jensen Kirstine Nolling , Crossen Arianne J. , Basham Kyle J. , Ward Rebecca A. , Reardon Christopher M. , Brown Harding Hannah , Hepworth Olivia W. , Simaku Patricia , Kwaku Geneva N. , Tone Kazuya , Willment Janet A. , Reid Delyth M. , Stappers Mark H. T. , Brown Gordon D. , Rajagopal Jayaraj , Vyas Jatin M. 
Published: July 2024

AbstractRespiratory infections caused by the human fungal pathogenAspergillus fumigatusare a major cause of mortality for immunocompromised patients. Exposure to these pathogens occurs through inhalation, although the role of the respiratory epithelium in disease pathogenesis has not been fully defined. Employing a primary human airway epithelial model, we demonstrate that fungal melanins potently block the post-translational secretion of the chemokines CXCL1 and CXCL8 independent of transcription or the requirement of melanin to be phagocytosed, leading to a significant reduction in neutrophil recruitment to the apical airway both in vitro and in vivo.Aspergillus-derived melanin, a major constituent of the fungal cell wall, dampened airway epithelial chemokine secretion in response to fungi, bacteria, and exogenous cytokines. Furthermore, melanin muted pathogen-mediated calcium fluxing and hindered actin filamentation. Taken together, our results reveal a critical role for melanin interaction with airway epithelium in shaping the host response to fungal and bacterial pathogens.
Programmed cell death regulator BAP2 is required for IRE1-mediated unfolded protein response in Arabidopsis
Authors: Pastor-Cantizano Noelia , Angelos Evan R. , Ruberti Cristina , Jiang Tao , Weng Xiaoyu , Reagan Brandon C. , Haque Taslima , Juenger Thomas E. , Brandizzi Federica 
Published: July 2024

AbstractEnvironmental and physiological situations can challenge the balance between protein synthesis and folding capacity of the endoplasmic reticulum (ER) and cause ER stress, a potentially lethal condition. The unfolded protein response (UPR) restores ER homeostasis or actuates programmed cell death (PCD) when ER stress is unresolved. The cell fate determination mechanisms of the UPR are not well understood, especially in plants. Here, we integrate genetics and ER stress profiling with natural variation and quantitative trait locus analysis of 350 natural accessions of the model species Arabidopsis thaliana. Our analyses implicate a single nucleotide polymorphism to the loss of function of the general PCD regulator BON-ASSOCIATED PROTEIN2 (BAP2) in UPR outcomes. We establish that ER stress-induced BAP2 expression is antagonistically regulated by the UPR master regulator, inositol-requiring enzyme 1 (IRE1), and that BAP2 controls adaptive UPR amplitude in ER stress and ignites pro-death mechanisms in conditions of UPR insufficiency.
Regulatory mechanism of cold-inducible diapause in Caenorhabditis elegans
Authors: Horikawa Makoto , Fukuyama Masamitsu , Antebi Adam , Mizunuma Masaki 
Published: July 2024

AbstractTemperature is a critical environmental cue that controls the development and lifespan of many animal species; however, mechanisms underlying low-temperature adaptation are poorly understood. Here, we describe cold-inducible diapause (CID), another type of diapause induced by low temperatures in Caenorhabditis elegans. A premature stop codon in heat shock factor 1 (hsf-1) triggers entry into CID at 9 °C, whereas wild-type animals enter CID at 4 °C. Furthermore, both wild-type and hsf-1(sy441) mutant animals undergoing CID can survive for weeks, and resume growth at 20 °C. Using epistasis analysis, we demonstrate that neural signalling pathways, namely tyraminergic and neuromedin U signalling, regulate entry into CID of the hsf-1 mutant. Overexpression of anti-ageing genes, such as hsf-1, XBP1/xbp-1, FOXO/daf-16, Nrf2/skn-1, and TFEB/hlh-30, also inhibits CID entry of the hsf-1 mutant. Based on these findings, we hypothesise that regulators of the hsf-1 mutant CID may impact longevity, and successfully isolate 16 long-lived mutants among 49 non-CID mutants via genetic screening. Furthermore, we demonstrate that the nonsense mutation of MED23/sur-2 prevents CID entry of the hsf-1(sy441) mutant and extends lifespan. Thus, CID is a powerful model to investigate neural networks involving cold acclimation and to explore new ageing mechanisms.
A diverse proteome is present and enzymatically active in metabolite extracts
Authors: House Rachel J. , Soper-Hopper Molly T. , Vincent Michael P. , Ellis Abigail E. , Capan Colt D. , Madaj Zachary B. , Wolfrum Emily , Isaguirre Christine N. , Castello Carlos D. , Johnson Amy B. , Escobar Galvis Martha L. , Williams Kelsey S. , Lee Hyoungjoo , Sheldon Ryan D. 
Published: July 2024

AbstractMetabolite extraction is the critical first-step in metabolomics experiments, where it is generally regarded to inactivate and remove proteins. Here, arising from efforts to improve extraction conditions for polar metabolomics, we discover a proteomic landscape of over 1000 proteins within metabolite extracts. This is a ubiquitous feature across several common extraction and sample types. By combining post-resuspension stable isotope addition and enzyme inhibitors, we demonstrate in-extract metabolite interconversions due to residual transaminase activity. We extend these findings with untargeted metabolomics where we observe extensive protein-mediated metabolite changes, including in-extract formation of glutamate dipeptide and depletion of total glutathione. Finally, we present a simple extraction workflow that integrates 3 kDa filtration for protein removal as a superior method for polar metabolomics. In this work, we uncover a previously unrecognized, protein-mediated source of observer effects in metabolomics experiments with broad-reaching implications across all research fields using metabolomics and molecular metabolism.
Whole exome sequencing analysis identifies genes for alcohol consumption
Authors: Kang Jujiao , Deng Yue-Ting , Wu Bang-Sheng , Liu Wei-Shi , Li Ze-Yu , Xiang Shitong , Yang Liu , You Jia , Gong Xiaohong , Jia Tianye , Yu Jin-Tai , Cheng Wei , Feng Jianfeng 
Published: July 2024

AbstractAlcohol consumption is a heritable behavior seriously endangers human health. However, genetic studies on alcohol consumption primarily focuses on common variants, while insights from rare coding variants are lacking. Here we leverage whole exome sequencing data across 304,119 white British individuals from UK Biobank to identify protein-coding variants associated with alcohol consumption. Twenty-five variants are associated with alcohol consumption through single variant analysis and thirteen genes through gene-based analysis, ten of which have not been reported previously. Notably, the two unreported alcohol consumption-related genes GIGYF1 and ANKRD12 show enrichment in brain function-related pathways including glial cell differentiation and are strongly expressed in the cerebellum. Phenome-wide association analyses reveal that alcohol consumption-related genes are associated with brain white matter integrity and risk of digestive and neuropsychiatric diseases. In summary, this study enhances the comprehension of the genetic architecture of alcohol consumption and implies biological mechanisms underlying alcohol-related adverse outcomes.
Decreased ENSO post-2100 in response to formation of a permanent El Niño-like state under greenhouse warming
Authors: Geng Tao , Cai Wenju , Jia Fan , Wu Lixin 
Published: July 2024

AbstractUnder transient greenhouse warming, El Niño-Southern Oscillation (ENSO) is projected to increase pre-2100, accompanied by an easier establishment of atmospheric convection in the equatorial eastern Pacific, where sea surface temperature (SST) warms faster than surrounding regions. After 2100, how ENSO variability may change remains unknown. Here we find that under a high emission scenario, ENSO variability post-2100 reverses from the initial increase to an amplitude far smaller than that of the 20th century. The fast eastern warming persists and shrinks the equatorial Pacific non-convective area, such that establishing convection in the non-convective area, as during an El Niño, requires smaller convective anomaly, inducing weaker wind anomalies leading to reduced ENSO SST variability. The nonlinear ENSO response is thus a symptom of the persistent El Niño-like warming pattern. Therefore, the oscillatory ENSO impact could be replaced by that from the permanent El Niño-like mean condition with cumulative influences on affected regions.
On-demand transposition across light-matter interaction regimes in bosonic cQED
Authors: Valadares Fernando , Huang Ni-Ni , Chu Kyle Timothy Ng , Dorogov Aleksandr , Chua Weipin , Kong Lingda , Song Pengtao , Gao Yvonne Y. 
Published: July 2024

AbstractThe diverse applications of light-matter interactions in science and technology stem from the qualitatively distinct ways these interactions manifest, prompting the development of physical platforms that can interchange between regimes on demand. Bosonic cQED employs the light field of high-Q superconducting cavities coupled to nonlinear circuit elements, harnessing the rich dynamics of their interaction for quantum information processing. However, implementing fast switching of the interaction regime without deteriorating the cavity coherence is a significant challenge. We present an experiment that achieves this feat, combining nanosecond-scale frequency tunability of a transmon coupled to a cavity with lifetime of hundreds of microseconds. Our implementation affords a range of useful capabilities for quantum information processing; from fast creation of cavity Fock states using resonant interaction and interchanging tomography techniques at qualitatively distinct interaction regimes on the fly, to the suppression of unwanted cavity-transmon dynamics during idle evolution. By bringing flux tunability into the bosonic cQED toolkit, our work opens up the possibility to probe the full range of light-matter interaction dynamics within a single platform and provides valuable pathways towards robust and versatile quantum information processing.
Developmental trajectories of EEG aperiodic and periodic components in children 2–44 months of age
Authors: Wilkinson Carol L. , Yankowitz Lisa D. , Chao Jerry Y. , Gutiérrez Rodrigo , Rhoades Jeff L. , Shinnar Shlomo , Purdon Patrick L. , Nelson Charles A. 
Published: July 2024

AbstractThe development of neural circuits has long-lasting effects on brain function, yet our understanding of early circuit development in humans remains limited. Here, periodic EEG power features and aperiodic components were examined from longitudinal EEGs collected from 592 healthy 2–44 month-old infants, revealing age-dependent nonlinear changes suggestive of distinct milestones in early brain maturation. Developmental changes in periodic peaks include (1) the presence and then absence of a 9-10 Hz alpha peak between 2-6 months, (2) nonlinear changes in high beta peaks (20-30 Hz) between 4-18 months, and (3) the emergence of a low beta peak (12-20 Hz) in some infants after six months of age. We hypothesized that the emergence of the low beta peak may reflect maturation of thalamocortical network development. Infant anesthesia studies observe that GABA-modulating anesthetics do not induce thalamocortical mediated frontal alpha coherence until 10-12 months of age. Using a small cohort of infants (n = 23) with EEG before and during GABA-modulating anesthesia, we provide preliminary evidence that infants with a low beta peak have higher anesthesia-induced alpha coherence compared to those without a low beta peak.