bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fertilization controls tiller numbers via transcriptional regulation of a MAX1-like gene in rice cultivation
Authors: Cui Jinying , Nishide Noriko , Mashiguchi Kiyoshi , Kuroha Kana , Miya Masayuki , Sugimoto Kazuhiko , Itoh Jun-Ichi , Yamaguchi Shinjiro , Izawa Takeshi 
Published: June 2023

AbstractFertilization controls various aspects of cereal growth such as tiller number, leaf size, and panicle size. However, despite such benefits, global chemical fertilizer use must be reduced to achieve sustainable agriculture. Here, based on field transcriptome data from leaf samples collected during rice cultivation, we identify fertilizer responsive genes and focus on Os1900, a gene orthologous to Arabidopsis thaliana MAX1, which is involved in strigolactone biosynthesis. Elaborate genetic and biochemical analyses using CRISPR/Cas9 mutants reveal that Os1900 together with another MAX1-like gene, Os5100, play a critical role in controlling the conversion of carlactone into carlactonoic acid during strigolactone biosynthesis and tillering in rice. Detailed analyses of a series of Os1900 promoter deletion mutations suggest that fertilization controls tiller number in rice through transcriptional regulation of Os1900, and that a few promoter mutations alone can increase tiller numbers and grain yields even under minor-fertilizer conditions, whereas a single defective os1900 mutation does not increase tillers under normal fertilizer condition. Such Os1900 promoter mutations have potential uses in breeding programs for sustainable rice production.
Reassessment of growth-climate relations indicates the potential for decline across Eurasian boreal larch forests
Authors: Li Wenqing , Manzanedo Rubén D. , Jiang Yuan , Ma Wenqiu , Du Enzai , Zhao Shoudong , Rademacher Tim , Dong Manyu , Xu Hui , Kang Xinyu , Wang Jun , Wu Fang , Cui Xuefeng , Pederson Neil 
Published: June 2023

AbstractLarch, a widely distributed tree in boreal Eurasia, is experiencing rapid warming across much of its distribution. A comprehensive assessment of growth on warming is needed to comprehend the potential impact of climate change. Most studies, relying on rigid calendar-based temperature series, have detected monotonic responses at the margins of boreal Eurasia, but not across the region. Here, we developed a method for constructing temporally flexible and physiologically relevant temperature series to reassess growth-temperature relations of larch across boreal Eurasia. Our method appears more effective in assessing the impact of warming on growth than previous methods. Our approach indicates widespread and spatially heterogeneous growth-temperature responses that are driven by local climate. Models quantifying these results project that the negative responses of growth to temperature will spread northward and upward throughout this century. If true, the risks of warming to boreal Eurasia could be more widespread than conveyed from previous works.
ALPL-1 is a target for chimeric antigen receptor therapy in osteosarcoma
Authors: Mensali Nadia , Köksal Hakan , Joaquina Sandy , Wernhoff Patrik , Casey Nicholas P. , Romecin Paola , Panisello Carla , Rodriguez René , Vimeux Lene , Juzeniene Asta , Myhre Marit R. , Fåne Anne , Ramírez Carolina Castilla , Maggadottir Solrun Melkorka , Duru Adil Doganay , Georgoudaki Anna-Maria , Grad Iwona , Maturana Andrés Daniel , Gaudernack Gustav , Kvalheim Gunnar , Carcaboso Angel M. , de Alava Enrique , Donnadieu Emmanuel , Bruland Øyvind S. , Menendez Pablo , Inderberg Else Marit , Wälchli Sébastien 
Published: June 2023

AbstractOsteosarcoma (OS) remains a dismal malignancy in children and young adults, with poor outcome for metastatic and recurrent disease. Immunotherapies in OS are not as promising as in some other cancer types due to intra-tumor heterogeneity and considerable off-target expression of the potentially targetable proteins. Here we show that chimeric antigen receptor (CAR) T cells could successfully target an isoform of alkaline phosphatase, ALPL-1, which is highly and specifically expressed in primary and metastatic OS. The target recognition element of the second-generation CAR construct is based on two antibodies, previously shown to react against OS. T cells transduced with these CAR constructs mediate efficient and effective cytotoxicity against ALPL-positive cells in in vitro settings and in state-of-the-art in vivo orthotopic models of primary and metastatic OS, without unexpected toxicities against hematopoietic stem cells or healthy tissues. In summary, CAR-T cells targeting ALPL-1 show efficiency and specificity in treating OS in preclinical models, paving the path for clinical translation.
Pluripotency-independent induction of human trophoblast stem cells from fibroblasts
Authors: Naama Moriyah , Rahamim Moran , Zayat Valery , Sebban Shulamit , Radwan Ahmed , Orzech Dana , Lasry Rachel , Ifrah Annael , Jaber Mohammad , Sabag Ofra , Yassen Hazar , Khatib Areej , Epsztejn-Litman Silvina , Novoselsky-Persky Michal , Makedonski Kirill , Deri Noy , Goldman-Wohl Debra , Cedar Howard , Yagel Simcha , Eiges Rachel , Buganim Yosef 
Published: June 2023

AbstractHuman trophoblast stem cells (hTSCs) can be derived from embryonic stem cells (hESCs) or be induced from somatic cells by OCT4, SOX2, KLF4 and MYC (OSKM). Here we explore whether the hTSC state can be induced independently of pluripotency, and what are the mechanisms underlying its acquisition. We identify GATA3, OCT4, KLF4 and MYC (GOKM) as a combination of factors that can generate functional hiTSCs from fibroblasts. Transcriptomic analysis of stable GOKM- and OSKM-hiTSCs reveals 94 hTSC-specific genes that are aberrant specifically in OSKM-derived hiTSCs. Through time-course-RNA-seq analysis, H3K4me2 deposition and chromatin accessibility, we demonstrate that GOKM exert greater chromatin opening activity than OSKM. While GOKM primarily target hTSC-specific loci, OSKM mainly induce the hTSC state via targeting hESC and hTSC shared loci. Finally, we show that GOKM efficiently generate hiTSCs from fibroblasts that harbor knockout for pluripotency genes, further emphasizing that pluripotency is dispensable for hTSC state acquisition.
Pregnane X receptor agonist nomilin extends lifespan and healthspan in preclinical models through detoxification functions
Authors: Fan Shengjie , Yan Yingxuan , Xia Ying , Zhou Zhenyu , Luo Lingling , Zhu Mengnan , Han Yongli , Yao Deqiang , Zhang Lijun , Fang Minglv , Peng Lina , Yu Jing , Liu Ying , Gao Xiaoyan , Guan Huida , Li Hongli , Wang Changhong , Wu Xiaojun , Zhu Huanhu , Cao Yu , Huang Cheng 
Published: June 2023

AbstractCitrus fruit has long been considered a healthy food, but its role and detailed mechanism in lifespan extension are not clear. Here, by using the nematode C. elegans, we identified that nomilin, a bitter-taste limoloid that is enriched in citrus, significantly extended the animals’ lifespan, healthspan, and toxin resistance. Further analyses indicate that this ageing inhibiting activity depended on the insulin-like pathway DAF-2/DAF-16 and nuclear hormone receptors NHR-8/DAF-12. Moreover, the human pregnane X receptor (hPXR) was identified as the mammalian counterpart of NHR-8/DAF-12 and X-ray crystallography showed that nomilin directly binds with hPXR. The hPXR mutations that prevented nomilin binding blocked the activity of nomilin both in mammalian cells and in C. elegans. Finally, dietary nomilin supplementation improved healthspan and lifespan in D-galactose- and doxorubicin-induced senescent mice as well as in male senescence accelerated mice prone 8 (SAMP8) mice, and induced a longevity gene signature similar to that of most longevity interventions in the liver of bile-duct-ligation male mice. Taken together, we identified that nomilin may extend lifespan and healthspan in animals via the activation of PXR mediated detoxification functions.
Template-jumping prime editing enables large insertion and exon rewriting in vivo
Authors: Zheng Chunwei , Liu Bin , Dong Xiaolong , Gaston Nicholas , Sontheimer Erik J. , Xue Wen 
Published: June 2023

AbstractTargeted insertion of large DNA fragments holds promise for genome engineering and gene therapy. Prime editing (PE) effectively inserts short (<50 bp) sequences. Employing paired prime editing guide RNAs (pegRNAs) has enabled PE to better mediate relatively large insertions in vitro, but the efficiency of larger insertions (>400 bp) remains low and in vivo application has not been demonstrated. Inspired by the efficient genomic insertion mechanism of retrotransposons, we develop a template-jumping (TJ) PE approach for the insertion of large DNA fragments using a single pegRNA. TJ-pegRNA harbors the insertion sequence as well as two primer binding sites (PBSs), with one PBS matching a nicking sgRNA site. TJ-PE precisely inserts 200 bp and 500 bp fragments with up to 50.5 and 11.4% efficiency, respectively, and enables GFP (~800 bp) insertion and expression in cells. We transcribe split circular TJ-petRNA in vitro via a permuted group I catalytic intron for non-viral delivery in cells. Finally, we demonstrate that TJ-PE can rewrite an exon in the liver of tyrosinemia I mice to reverse the disease phenotype. TJ-PE has the potential to insert large DNA fragments without double-stranded DNA breaks and facilitate mutation hotspot exon rewriting in vivo.
Absence of critical thickness for polar skyrmions with breaking the Kittel’s law
Authors: Gong Feng-Hui , Tang Yun-Long , Wang Yu-Jia , Chen Yu-Ting , Wu Bo , Yang Li-Xin , Zhu Yin-Lian , Ma Xiu-Liang 
Published: June 2023

AbstractThe period of polar domain (d) in ferroics was commonly believed to scale with corresponding film thicknesses (h), following the classical Kittel’s law of d ∝ $$\sqrt{h}$$

h

. Here, we have not only observed that this relationship fails in the case of polar skyrmions, where the period shrinks nearly to a constant value, or even experiences a slight increase, but also discovered that skyrmions have further persisted in [(PbTiO3)2/(SrTiO3)2]10 ultrathin superlattices. Both experimental and theoretical results indicate that the skyrmion periods (d) and PbTiO3 layer thicknesses in superlattice (h) obey the hyperbolic function of d = Ah + $$\frac{{{\mbox{B}}}}{h}$$

B

h

other than previous believed, simple square root law. Phase-field analysis indicates that the relationship originates from the different energy competitions of the superlattices with PbTiO3 layer thicknesses. This work exemplified the critical size problems faced by nanoscale ferroelectric device designing in the post-Moore era.
A synthetic dataset of Danish residential electricity prosumers
Authors: Yuan Rui , Pourmousavi S. Ali , Soong Wen L. , Black Andrew J. , Liisberg Jon A. R. , Lemos-Vinasco Julian 
Published: June 2023

AbstractConventional residential electricity consumers are becoming prosumers who not only consume electricity but also produce it. This shift is expected to occur over the next few decades at a large scale, and it presents numerous uncertainties and risks for the operation, planning, investment, and viable business models of the electricity grid. To prepare for this shift, researchers, utilities, policymakers, and emerging businesses require a comprehensive understanding of future prosumers’ electricity consumption. Unfortunately, there is a limited amount of data available due to privacy concerns and the slow adoption of new technologies such as battery electric vehicles and home automation. To address this issue, this paper introduces a synthetic dataset containing five types of residential prosumers’ imported and exported electricity data. The dataset was developed using real traditional consumers’ data from Denmark, PV generation data from the global solar energy estimator (GSEE) model, electric vehicle (EV) charging data generated using package, a residential energy storage system (ESS) operator and a generative adversarial network (GAN) based model to produce synthetic data. The quality of the dataset was assessed and validated through qualitative inspection and three methods: empirical statistics, metrics based on information theory, and evaluation metrics based on machine learning techniques.
Carbon Monitor Europe near-real-time daily CO2 emissions for 27 EU countries and the United Kingdom
Authors: Ke Piyu , Deng Zhu , Zhu Biqing , Zheng Bo , Wang Yilong , Boucher Olivier , Arous Simon Ben , Zhou Chuanlong , Andrew Robbie M. , Dou Xinyu , Sun Taochun , Song Xuanren , Li Zhao , Yan Feifan , Cui Duo , Hu Yifan , Huo Da , Chang Jean-Pierre , Engelen Richard , Davis Steven J. , Ciais Philippe , Liu Zhu 
Published: June 2023

AbstractWith the urgent need to implement the EU countries pledges and to monitor the effectiveness of Green Deal plan, Monitoring Reporting and Verification tools are needed to track how emissions are changing for all the sectors. Current official inventories only provide annual estimates of national CO2 emissions with a lag of 1+ year which do not capture the variations of emissions due to recent shocks including COVID lockdowns and economic rebounds, war in Ukraine. Here we present a near-real-time country-level dataset of daily fossil fuel and cement emissions from January 2019 through December 2021 for 27 EU countries and UK, which called Carbon Monitor Europe. The data are calculated separately for six sectors: power, industry, ground transportation, domestic aviation, international aviation and residential. Daily CO2 emissions are estimated from a large set of activity data compiled from different sources. The goal of this dataset is to improve the timeliness and temporal resolution of emissions for European countries, to inform the public and decision makers about current emissions changes in Europe.
Bioinformatics and system biology approach to identify potential common pathogenesis for COVID-19 infection and osteoarthritis
Authors: Chen Ziyi , Wang Wenjuan , Jue Hao , Hua Yinghui 
Published: June 2023

AbstractA growing of evidence has showed that patients with osteoarthritis (OA) had a higher coronavirus 2019 (COVID-19) infection rate and a poorer prognosis after infected it. Additionally, scientists have also discovered that COVID-19 infection might cause pathological changes in the musculoskeletal system. However, its mechanism is still not fully elucidated. This study aims to further explore the sharing pathogenesis of patients with both OA and COVID-19 infection and find candidate drugs. Gene expression profiles of OA (GSE51588) and COVID-19 (GSE147507) were obtained from the Gene Expression Omnibus (GEO) database. The common differentially expressed genes (DEGs) for both OA and COVID-19 were identified and several hub genes were extracted from them. Then gene and pathway enrichment analysis of the DEGs were performed; protein–protein interaction (PPI) network, transcription factor (TF)-gene regulatory network, TF-miRNA regulatory network and gene-disease association network were constructed based on the DEGs and hub genes. Finally, we predicted several candidate molecular drugs related to hub genes using DSigDB database. The receiver operating characteristic curve (ROC) was applied to evaluate the accuracy of hub genes in the diagnosis of both OA and COVID-19. In total, 83 overlapping DEGs were identified and selected for subsequent analyses. CXCR4, EGR2, ENO1, FASN, GATA6, HIST1H3H, HIST1H4H, HIST1H4I, HIST1H4K, MTHFD2, PDK1, TUBA4A, TUBB1 and TUBB3 were screened out as hub genes, and some showed preferable values as diagnostic markers for both OA and COVID-19. Several candidate molecular drugs, which are related to the hug genes, were identified. These sharing pathways and hub genes may provide new ideas for further mechanistic studies and guide more individual-based effective treatments for OA patients with COVID-19 infection.
Using machine learning to detect coronaviruses potentially infectious to humans
Authors: Gonzalez-Isunza Georgina , Jawaid M. Zaki , Liu Pengyu , Cox Daniel L. , Vazquez Mariel , Arsuaga Javier 
Published: June 2023

AbstractEstablishing the host range for novel viruses remains a challenge. Here, we address the challenge of identifying non-human animal coronaviruses that may infect humans by creating an artificial neural network model that learns from spike protein sequences of alpha and beta coronaviruses and their binding annotation to their host receptor. The proposed method produces a human-Binding Potential (h-BiP) score that distinguishes, with high accuracy, the binding potential among coronaviruses. Three viruses, previously unknown to bind human receptors, were identified: Bat coronavirus BtCoV/133/2005 and Pipistrellus abramus bat coronavirus HKU5-related (both MERS related viruses), and Rhinolophus affinis coronavirus isolate LYRa3 (a SARS related virus). We further analyze the binding properties of BtCoV/133/2005 and LYRa3 using molecular dynamics. To test whether this model can be used for surveillance of novel coronaviruses, we re-trained the model on a set that excludes SARS-CoV-2 and all viral sequences released after the SARS-CoV-2 was published. The results predict the binding of SARS-CoV-2 with a human receptor, indicating that machine learning methods are an excellent tool for the prediction of host expansion events.
Colour opponency is widespread across the mouse subcortical visual system and differentially targets GABAergic and non-GABAergic neurons
Authors: Feord R. C. , Gomoliszewska A. , Pienaar A. , Mouland J. W. , Brown T. M. 
Published: June 2023

AbstractColour vision plays many important roles in animal behaviour but the brain pathways processing colour remain surprisingly poorly understood, including in the most commonly used laboratory mammal, mice. Indeed, particular features of mouse retinal organisation present challenges in defining the mechanisms underlying colour vision in mice and have led to suggestions that this may substantially rely on ‘non-classical’ rod-cone opponency. By contrast, studies using mice with altered cone spectral sensitivity, to facilitate application of photoreceptor-selective stimuli, have revealed widespread cone-opponency across the subcortical visual system. To determine the extent to which such findings are truly reflective of wildtype mouse colour vision, and facilitate neural circuit mapping of colour-processing pathways using intersectional genetic approaches, we here establish and validate stimuli for selectively manipulating excitation of the native mouse S- and M-cone opsin classes. We then use these to confirm the widespread appearance of cone-opponency (> 25% of neurons) across the mouse visual thalamus and pretectum. We further extend these approaches to map the occurrence of colour-opponency across optogenetically identified GABAergic (GAD2-expressing) cells in key non-image forming visual centres (pretectum and intergeniculate leaflet/ventral lateral geniculate; IGL/vLGN). Strikingly, throughout, we find S-ON/M-OFF opponency is specifically enriched in non-GABAergic cells, with identified GABAergic cells in the IGL/VLGN entirely lacking this property. Collectively, therefore, we establish an important new approach for studying cone function in mice, confirming a surprisingly extensive appearance of cone-opponent processing in the mouse visual system and providing new insight into functional specialisation of the pathways processing such signals.
Effect of the 2020 hypersensitivity pneumonitis guideline on the pathologic diagnosis of interstitial pneumonia
Authors: Ozasa Mutsumi , Bychkov Andrey , Zaizen Yoshiaki , Tabata Kazuhiro , Uegami Wataru , Yamano Yasuhiko , Kataoka Kensuke , Johkoh Takeshi , Mukae Hiroshi , Kondoh Yasuhiro , Fukuoka Junya 
Published: June 2023

AbstractIt was reported that the 2020 guideline for hypersensitivity pneumonitis (HP) might result in the overdiagnosis of fibrotic HP (fHP). fHP and other types of interstitial pneumonias have several overlapping characteristics, and a high diagnostic concordance rate of fHP is rarely obtained. Therefore, we investigated the impact of the 2020 HP guideline on the pathological diagnosis of cases previously diagnosed as interstitial pneumonia. We identified 289 fibrotic interstitial pneumonia cases from 2014 to 2019 and classified them into four categories according to the 2020 HP guideline: typical, probable, and indeterminate for fHP and alternative diagnosis. The original pathological diagnosis of 217 cases were compared to their classification as either typical, probable, or indeterminate for fHP according to the 2020 guideline. The clinical data, including serum data and pulmonary function tests, were compared among the groups. Diagnoses changed from non-fHP to fHP for 54 (25%) of the 217 cases, of which, 8 were typical fHP and 46 were probable fHP. The ratio of typical and probable fHP cases to the total number of VATS cases was significantly lower when using transbronchial lung cryobiopsy (p < 0.001). The clinical data of these cases bore a more remarkable resemblance to those diagnosed as indeterminate for fHP than to those diagnosed as typical or probable. The pathological criteria in the new HP guidelines increase the diagnosis of fHP. However, it is unclear whether this increase leads to overdiagnosis, and requires further investigation. Transbronchial lung cryobiopsy may not be helpful when using the new criteria to impart findings for fHP diagnosis.
The mere presence of a smartphone reduces basal attentional performance
Authors: Skowronek Jeanette , Seifert Andreas , Lindberg Sven 
Published: June 2023

AbstractThe smartphone has become an indispensable part of everyday life. It enables endless possibilities and offers persistent access to a multiplicity of entertainment, information, and social contacts. The development towards a greater use and a persistent presence of the smartphone does not only lead to advantages, but also raises potential for negative consequences and a negative influence on attention. In this research, the hypothesis of the mere smartphone presence leading to cognitive costs and a lower attention is being tested. The smartphone may use limited cognitive resources and consequently lead to a lower cognitive performance. To investigate this hypothesis, participants aged 20–34 perform a concentration and attention test in the presence and absence of a smartphone. The results of the conducted experiment imply that the mere presence of a smartphone results in lower cognitive performance, which supports the hypothesis of the smartphone presence using limited cognitive resources. The study as well as the subsequent results and the resulting practical implications are presented and discussed in this paper.