bluuebunny/crossref_metadata_2025_split huggingface dataset:
Low glucose metabolite 3-phosphoglycerate switches PHGDH from serine synthesis to p53 activation to control cell fate
Authors: Wu Yu-Qing , Zhang Chen-Song , Xiong Jinye , Cai Dong-Qi , Wang Chen-Zhe , Wang Yu , Liu Yan-Hui , Wang Yu , Li Yiming , Wu Jian , Wu Jianfeng , Lan Bin , Wang Xuefeng , Chen Siwei , Cao Xianglei , Wei Xiaoyan , Hu Hui-Hui , Guo Huiling , Yu Yaxin , Ghafoor Abdul , Xie Changchuan , Wu Yaying , Xu Zheni , Zhang Cixiong , Zhu Mingxia , Huang Xi , Sun Xiufeng , Lin Shu-Yong , Piao Hai-Long , Zhou Jianyin , Lin Sheng-Cai 
Published: September 2023

AbstractGlycolytic intermediary metabolites such as fructose-1,6-bisphosphate can serve as signals, controlling metabolic states beyond energy metabolism. However, whether glycolytic metabolites also play a role in controlling cell fate remains unexplored. Here, we find that low levels of glycolytic metabolite 3-phosphoglycerate (3-PGA) can switch phosphoglycerate dehydrogenase (PHGDH) from cataplerosis serine synthesis to pro-apoptotic activation of p53. PHGDH is a p53-binding protein, and when unoccupied by 3-PGA interacts with the scaffold protein AXIN in complex with the kinase HIPK2, both of which are also p53-binding proteins. This leads to the formation of a multivalent p53-binding complex that allows HIPK2 to specifically phosphorylate p53-Ser46 and thereby promote apoptosis. Furthermore, we show that PHGDH mutants (R135W and V261M) that are constitutively bound to 3-PGA abolish p53 activation even under low glucose conditions, while the mutants (T57A and T78A) unable to bind 3-PGA cause constitutive p53 activation and apoptosis in hepatocellular carcinoma (HCC) cells, even in the presence of high glucose. In vivo, PHGDH-T57A induces apoptosis and inhibits the growth of diethylnitrosamine-induced mouse HCC, whereas PHGDH-R135W prevents apoptosis and promotes HCC growth, and knockout of Trp53 abolishes these effects above. Importantly, caloric restriction that lowers whole-body glucose levels can impede HCC growth dependent on PHGDH. Together, these results unveil a mechanism by which glucose availability autonomously controls p53 activity, providing a new paradigm of cell fate control by metabolic substrate availability.
Device-independent certification of indefinite causal order in the quantum switch
Authors: van der Lugt Tein , Barrett Jonathan , Chiribella Giulio 
Published: September 2023

AbstractQuantum theory is compatible with scenarios in which the order of operations is indefinite. Experimental investigations of such scenarios, all of which have been based on a process known as the quantum switch, have provided demonstrations of indefinite causal order conditioned on assumptions on the devices used in the laboratory. But is a device-independent certification possible, similar to the certification of Bell nonlocality through the violation of Bell inequalities? Previous results have shown that the answer is negative if the switch is considered in isolation. Here, however, we present an inequality that can be used to device-independently certify indefinite causal order in the quantum switch in the presence of an additional spacelike-separated observer under an assumption asserting the impossibility of superluminal and retrocausal influences.
Emplacement of the Argyle diamond deposit into an ancient rift zone triggered by supercontinent breakup
Authors: Olierook Hugo K. H. , Fougerouse Denis , Doucet Luc S. , Liu Yebo , Rayner Murray J. , Danišík Martin , Condon Daniel J. , McInnes Brent I. A. , Jaques A. Lynton , Evans Noreen J. , McDonald Bradley J. , Li Zheng-Xiang , Kirkland Christopher L. , Mayers Celia , Wingate Michael T. D. 
Published: September 2023

AbstractArgyle is the world’s largest source of natural diamonds, yet one of only a few economic deposits hosted in a Paleoproterozoic orogen. The geodynamic triggers responsible for its alkaline ultramafic volcanic host are unknown. Here we show, using U-Pb and (U-Th)/He geochronology of detrital apatite and detrital zircon, and U-Pb dating of hydrothermal titanite, that emplacement of the Argyle lamproite is bracketed between 1311 ± 9 Ma and 1257 ± 15 Ma (2σ), older than previously known. To form the Argyle lamproite diatreme complex, emplacement was likely driven by lithospheric extension related to the breakup of the supercontinent Nuna. Extension facilitated production of low-degree partial melts and their migration through transcrustal corridors in the Paleoproterozoic Halls Creek Orogen, a rheologically-weak rift zone adjacent to the Kimberley Craton. Diamondiferous diatreme emplacement during (super)continental breakup may be prevalent but hitherto under-recognized in rift zones at the edges of ancient continental blocks.
Auxin-producing bacteria promote barley rhizosheath formation
Authors: Xu Feiyun , Liao Hanpeng , Yang Jinyong , Zhang Yingjiao , Yu Peng , Cao Yiying , Fang Ju , Chen Shu , Li Liang , Sun Leyun , Du Chongxuan , Wang Ke , Dang Xiaolin , Feng Zhiwei , Cao Yifan , Li Ying , Zhang Jianhua , Xu Weifeng 
Published: September 2023

AbstractThe rhizosheath, or the layer of soil closely adhering to roots, can help plants to tolerate drought under moderate soil drying conditions. Rhizosheath formation is the result of poorly understood interactions between root exudates, microbes, and soil conditions. Here, we study the roles played by the soil microbiota in rhizosheath formation in barley (a dry crop). We show that barley rhizosheath formation is greater in acid soil than in alkaline soil, and inoculation with microbiota from acid soil enhances rhizosheath formation in alkaline soil. The rhizosheath-promoting activity is associated with the presence of Flavobacteriaceae and Paenibacillaceae bacteria that express genes for biosynthesis of indole-3-acetic acid (IAA, a common auxin), as determined by metagenomics and metatranscriptomics. Two bacterial strains isolated from rhizosheath (Chryseobacterium culicis and Paenibacillus polymyxa) produce IAA and enhance barley rhizosheath formation, while their IAA-defective mutants are unable to promote rhizosheath formation. Co-inoculation with the IAA-producing strains enhances barley grain yield in field experiments through an increase in spike number. Our findings contribute to our understanding of barley rhizosheath formation, and suggest potential strategies for crop improvement.
Translating genomic tools to Raman spectroscopy analysis enables high-dimensional tissue characterization on molecular resolution
Authors: Sigle Manuel , Rohlfing Anne-Katrin , Kenny Martin , Scheuermann Sophia , Sun Na , Graeßner Ulla , Haug Verena , Sudmann Jessica , Seitz Christian M. , Heinzmann David , Schenke-Layland Katja , Maguire Patricia B. , Walch Axel , Marzi Julia , Gawaz Meinrad Paul 
Published: September 2023

AbstractSpatial transcriptomics of histological sections have revolutionized research in life sciences and enabled unprecedented insights into genetic processes involved in tissue reorganization. However, in contrast to genomic analysis, the actual biomolecular composition of the sample has fallen behind, leaving a gap of potentially highly valuable information. Raman microspectroscopy provides untargeted spatiomolecular information at high resolution, capable of filling this gap. In this study we demonstrate spatially resolved Raman “spectromics” to reveal homogeneity, heterogeneity and dynamics of cell matrix on molecular levels by repurposing state-of-the-art bioinformatic analysis tools commonly used for transcriptomic analyses. By exploring sections of murine myocardial infarction and cardiac hypertrophy, we identify myocardial subclusters when spatially approaching the pathology, and define the surrounding metabolic and cellular (immune-) landscape. Our innovative, label-free, non-invasive “spectromics” approach could therefore open perspectives for a profound characterization of histological samples, while additionally allowing the combination with consecutive downstream analyses of the very same specimen.
A molecular pyroelectric enabling broadband photo-pyroelectric effect towards self-driven wide spectral photodetection
Authors: Zeng Xi , Liu Yi , Weng Wen , Hua Lina , Tang Liwei , Guo Wuqian , Chen Yaoyao , Yang Tian , Xu Haojie , Luo Junhua , Sun Zhihua 
Published: September 2023

AbstractBroadband spectral photoresponse has shown bright prospects for various optoelectronic devices, while fulfilling high photoactivity beyond the material bandgap is a great challenge. Here, we present a molecular pyroelectric, N-isopropylbenzylaminium trifluoroacetate (N-IBATFA), of which the broadband photo-pyroelectric effects allow for self-driven wide spectral photodetection. As a simple organic binary salt, N-IBATFA possesses a large polarization (~9.5 μC cm−2), high pyroelectric coefficient (~6.9 μC cm−2 K−1) and figures-of-merits (FV = 187.9 × 10−2 cm2 μC−1; FD = 881.5 × 10−5 Pa−0.5) comparable to the state-of-art pyroelectric materials. Particularly, such intriguing attributes endow broadband photo-pyroelectric effect, namely, transient currents covering ultraviolet (UV, 266 nm) to near-infrared (NIR, 1950 nm) spectral regime, which breaks the restriction of its optical absorption and thus allows wide UV-NIR spectral photodetection. Our finding highlights the potential of molecular system as high-performance candidates toward self-powered wide spectral photodetection.
Composition of cetacean communities worldwide shapes their contribution to ocean nutrient cycling
Authors: Gilbert Lola , Jeanniard-du-Dot Tiphaine , Authier Matthieu , Chouvelon Tiphaine , Spitz Jérôme 
Published: September 2023

AbstractDefecation by large whales is known to fertilise oceans with nutrients, stimulating phytoplankton and ecosystem productivity. However, our current understanding of these processes is limited to a few species, nutrients and ecosystems. Here, we investigate the role of cetacean communities in the worldwide biological cycling of two major nutrients and six trace nutrients. We show that cetaceans release more nutrients in mesotrophic to eutrophic temperate waters than in oligotrophic tropical waters, mirroring patterns of ecosystem productivity. The released nutrient cocktails also vary geographically, driven by the composition of cetacean communities. The roles of small cetaceans, deep diving cetaceans and baleen whales differ quantitatively and functionally, with contributions of small cetaceans and deep divers exceeding those of large whales in some areas. The functional diversity of cetacean communities expands beyond their role as top predators to include their role as active nutrient vectors, which might be equally important to local ecosystem dynamics.
Nongenetic surface engineering of mesenchymal stromal cells with polyvalent antibodies to enhance targeting efficiency
Authors: Ye Tenghui , Liu Xi , Zhong Xianghua , Yan Ran , Shi Peng 
Published: September 2023

AbstractSystemic infusion is a prevalent administration method for mesenchymal stromal cells (MSCs) in clinical trials. However, the inability to deliver a large number of therapeutic cells to diseased tissue is a substantial barrier. Here, we demonstrate that surface engineering of MSCs with polyvalent antibodies can effectively improve the targeting efficiency of MSCs to diseased tissue. The polyvalent antibody is directly synthesized on the cell surface via DNA template-directed biomolecule assembly. The data show that engineered MSCs exhibit superior adhesion to inflamed endothelium in vitro and in vivo. In female mouse models of acute inflammation and inflammatory bowel disease, engineered MSCs show enhanced targeting efficiency and therapeutic efficacy in damaged tissues. Notably, the entire procedure for polyvalent functionalization only requires the simple mixing of cells and solutions under physiological conditions within a few hours, which significantly reduces preparation processes and manufacturing costs and minimizes the impact on the cells. Thus, our study provides a strategy for improved MSC-based regenerative medicine.
Selecting cardiac magnetic resonance images suitable for annotation of pulmonary arteries using an active-learning based deep learning model
Authors: van der Veen Werner , Benjamins Jan-Walter , Yeung Ming Wai , van der Harst Pim 
Published: September 2023

AbstractAn increasing and aging patient population poses a growing burden on healthcare professionals. Automation of medical imaging diagnostics holds promise for enhancing patient care and reducing manpower required to accommodate an increasing patient-population. Deep learning, a subset of machine learning, has the potential to facilitate automated diagnostics, but commonly requires large-scaled labeled datasets. In medical domains, data is often abundant but labeling is a laborious and costly task. Active learning provides a method to optimize the selection of unlabeled samples that are most suitable for improvement of the model and incorporate them into the model training process. This approach proves beneficial when only a small number of labeled samples are available. Various selection methods currently exist, but most of them employ fixed querying schedules. There is limited research on how the timing of a query can impact performance in relation to the number of queried samples. This paper proposes a novel approach called dynamic querying, which aims to optimize the timing of queries to enhance model development while utilizing as few labeled images as possible. The performance of the proposed model is compared to a model trained utilizing a fully-supervised training method, and its effectiveness is assessed based on dataset size requirements and loss rates. Dynamic querying demonstrates a considerably faster learning curve in relation to the number of labeled samples used, achieving an accuracy of 70% using only 24 samples, compared to 82% for a fully-supervised model trained on the complete training dataset of 1017 images.
Variability in donor leukocyte counts confound the use of common RNA sequencing data normalization strategies in transcriptomic biomarker studies performed with whole blood
Authors: O’Connell Grant C. 
Published: September 2023

AbstractGene expression data generated from whole blood via next generation sequencing is frequently used in studies aimed at identifying mRNA-based biomarker panels with utility for diagnosis or monitoring of human disease. These investigations often employ data normalization techniques more typically used for analysis of data originating from solid tissues, which largely operate under the general assumption that specimens have similar transcriptome composition. However, this assumption may be violated when working with data generated from whole blood, which is more cellularly dynamic, leading to potential confounds. In this study, we used next generation sequencing in combination with flow cytometry to assess the influence of donor leukocyte counts on the transcriptional composition of whole blood specimens sampled from a cohort of 138 human subjects, and then subsequently examined the effect of four frequently used data normalization approaches on our ability to detect inter-specimen biological variance, using the flow cytometry data to benchmark each specimens true cellular and molecular identity. Whole blood samples originating from donors with differing leukocyte counts exhibited dramatic differences in both genome-wide distributions of transcript abundance and gene-level expression patterns. Consequently, three of the normalization strategies we tested, including median ratio (MRN), trimmed mean of m-values (TMM), and quantile normalization, noticeably masked the true biological structure of the data and impaired our ability to detect true interspecimen differences in mRNA levels. The only strategy that improved our ability to detect true biological variance was simple scaling of read counts by sequencing depth, which unlike the aforementioned approaches, makes no assumptions regarding transcriptome composition.
A large quantitative analysis of written language challenges the idea that all languages are equally complex
Authors: Koplenig Alexander , Wolfer Sascha , Meyer Peter 
Published: September 2023

AbstractOne of the fundamental questions about human language is whether all languages are equally complex. Here, we approach this question from an information-theoretic perspective. We present a large scale quantitative cross-linguistic analysis of written language by training a language model on more than 6500 different documents as represented in 41 multilingual text collections consisting of ~ 3.5 billion words or ~ 9.0 billion characters and covering 2069 different languages that are spoken as a native language by more than 90% of the world population. We statistically infer the entropy of each language model as an index of what we call average prediction complexity. We compare complexity rankings across corpora and show that a language that tends to be more complex than another language in one corpus also tends to be more complex in another corpus. In addition, we show that speaker population size predicts entropy. We argue that both results constitute evidence against the equi-complexity hypothesis from an information-theoretic perspective.
Prevalence of plasma lipid abnormalities and associated risk factors among Iranian adults based on the findings from STEPs survey 2021
Authors: Khanali Javad , Ghasemi Erfan , Rashidi Mohammad-Mahdi , Ahmadi Naser , Ghamari Seyyed-Hadi , Azangou-Khyavy Mohammadreza , Malekpour Mohammad-Reza , Abbasi-Kangevari Mohsen , Hashemi Seyedeh Melika , Naderian Mohammadreza , Rezaei Negar , Dilmaghani-Marand Arezou , Farzi Yosef , Kazemi Ameneh , Yoosefi Moein , Hajebi Amirali , Rezaei Shahabeddin , Azadnajafabad Sina , Fattahi Nima , Nasserinejad Maryam , Abdolhamidi Elham , Haghshenas Rosa , Rezaei Nazila , Djalalinia Shirin , Larijani Bagher , Farzadfar Farshad 
Published: September 2023

AbstractThe study aimed to estimate the prevalence of lipid abnormalities in Iranian adults by demographic characterization, geographical distribution, and associated risk factors using national and sub-national representative samples of the STEPs 2021 survey in Iran. In this population-based household survey, a total of 18,119 individuals aged over 25 years provided blood samples for biochemical analysis. Dyslipidemia was defined by the presence of at least one of the lipid abnormalities of hypertriglyceridemia (≥ 150 mg/dL), hypercholesterolemia (≥ 200 mg/dL), high LDL-C (≥ 130 mg/dL), and low HDL-C (< 50 mg/dL in women, < 40 mg/dL in men), or self-reported use of lipid-lowering medications. Mixed dyslipidemia was characterized as the coexistence of high LDL-C with at least one of the hypertriglyceridemia and low HDL-C. The prevalence of each lipid abnormality was determined by each population strata, and the determinants of abnormal lipid levels were identified using a multiple logistic regression model. The prevalence was 39.7% for hypertriglyceridemia, 21.2% for hypercholesterolemia, 16.4% for high LDL-C, 68.4% for low HDL-C, and 81.0% for dyslipidemia. Hypercholesterolemia and low HDL-C were more prevalent in women, and hypertriglyceridemia was more prevalent in men. The prevalence of dyslipidemia was higher in women (OR = 1.8), obese (OR = 2.8) and overweight (OR = 2.3) persons, those residents in urban areas (OR = 1.1), those with inappropriate physical activity (OR = 1.2), patients with diabetes (OR = 2.7) and hypertension (OR = 1.9), and participants with a history (OR = 1.6) or familial history of CVDs (OR = 1.2). Mixed dyslipidemia prevalence was 13.6% in women and 11.4% in men (P < 0.05). The prevalence of lipid abnormalities was highly heterogeneous among provinces, and East Azarbaijan with 85.3% (81.5–89.1) and Golestan with 68.5% (64.8–72.2) had the highest and lowest prevalence of dyslipidemia, respectively. Although the prevalence of high cholesterol and LDL-C had a descending trend in the 2016–2021 period, the prevalence of dyslipidemia remained unchanged. There are modifiable risk factors associated with dyslipidemia that can be targeted by the primary healthcare system. To modify these risk factors and promote metabolic health in the country, action plans should come to action through a multi-sectoral and collaborative approach.
Experimental study on the impact of indoor air quality on creativity by Serious Brick Play method
Authors: Arikrishnan Shmitha , Roberts Adam Charles , Lau Wee Siang , Wan Man Pun , Ng Bing Feng 
Published: September 2023

AbstractCompanies are increasingly asking their employees to find creative solutions to their problems. However, the office environment may reduce an employee’s creative potential. In this study, the role of indoor air quality parameters (PM2.5, TVOC, and CO2) in maintaining a creative environment (involving lateral thinking ability) was evaluated by Serious Brick Play (SBP), an adaptation of the LEGO Serious Play (LSP) framework. This study was conducted in a simulated office space with 92 participants over a period of 6 weeks. The SBP required participants to address a challenge by building using Lego bricks, and then describe the solution within a given timeframe. The creations and descriptions were then graded in terms of originality, fluency, and build. The results indicated that higher TVOC levels were significantly associated with lower-rated creative solutions. A 71.9% reduction in TVOC (from 1000 ppb), improves an individual’s full creative potential by 11.5%. Thus, maintaining a low TVOC level will critically enhance creativity in offices.
Octopod Hox genes and cephalopod plesiomorphies
Authors: Barrera Grijalba Cristian Camilo , Rodríguez Monje Sonia Victoria , Gestal Camino , Wollesen Tim 
Published: September 2023

AbstractFew other invertebrates captivate our attention as cephalopods do. Octopods, cuttlefish, and squids amaze with their behavior and sophisticated body plans that belong to the most intriguing among mollusks. Little is, however, known about their body plan formation and the role of Hox genes. The latter homeobox genes pattern the anterior–posterior body axis and have only been studied in a single decapod species so far. Here, we study developmental Hox and ParaHox gene expression in Octopus vulgaris.Hox genes are expressed in a near-to-staggered fashion, among others in homologous organs of cephalopods such as the stellate ganglia, the arms, or funnel. As in other mollusks Hox1 is expressed in the nascent octopod shell rudiment. While ParaHox genes are expressed in an evolutionarily conserved fashion, Hox genes are also expressed in some body regions that are considered homologous among mollusks such as the cephalopod arms and funnel with the molluscan foot. We argue that cephalopod Hox genes are recruited to a lesser extent into the formation of non-related organ systems than previously thought and emphasize that despite all morphological innovations molecular data still reveal the ancestral molluscan heritage of cephalopods.