bluuebunny/crossref_metadata_2025_split huggingface dataset:
APOE-ε4 modulates the association among plasma Aβ42/Aβ40, vascular diseases, neurodegeneration and cognitive decline in non-demented elderly adults
Authors: Shi Dai , Xie Siwei , Li Anqi , Wang Qingyong , Guo Hongbo , Han Ying , Xu Huaxi , Gan Wen-Biao , Zhang Lei , Guo Tengfei ,   for the Alzheimer’s Disease Neuroimaging Initiative
Published: March 2022

AbstractIncluding apolipoprotein E-ε4 (APOE-ε4) status and older age into consideration may increase the accuracy of plasma Aβ42/Aβ40 detecting Aβ+ individuals, but the rationale behind this remains to be fully understood. Besides, both Aβ pathology and vascular diseases are related to neurodegeneration and cognitive decline, but it is still not fully understood how APOE-ε4 modulates these relationships. In this study, we examined 241 non-demented Alzheimer’s Disease Neuroimaging Initiative participants to investigate the associations among age, white matter hyperintensities (WMH), hypertension, hyperlipidemia, body mass index (BMI), plasma Aβ42/Aβ40 measured by liquid chromatography tandem mass spectrometry, and 18F-florbetapir Aβ PET as well as their prediction of longitudinal adjusted hippocampal volume (aHCV) and cognition in APOE-ε4 carriers and non-carriers. We found older age predicted faster WMH increase (p = 0.024) and cortical Aβ accumulation (p = 0.043) in APOE-ε4 non-carriers only, whereas lower plasma Aβ42/Aβ40 predicted faster cortical Aβ accumulation (p < 0.018) regardless of APOE-ε4 status. While larger WMH and underweight predicted (p < 0.05) faster decreases in aHCV and cognition in APOE-ε4 non-carriers, lower plasma Aβ42/Aβ40 predicted (p < 0.031) faster decreases in aHCV and cognition in APOE-ε4 carriers. Higher Aβ PET also predicted faster rates of aHCV (p = 0.010) in APOE-ε4 carriers only, but was related to faster rates of cognitive decline (p < 0.022) regardless of APOE-ε4 status. These findings may provide novel insights into understanding different mechanisms underlie neurodegeneration and cognitive decline in non-demented elderly adults with and without APOE-ε4 allele, which may help the design of anti-Alzheimer’s clinical trials.
Acox2 is a regulator of lysine crotonylation that mediates hepatic metabolic homeostasis in mice
Authors: Zhang Yuan , Chen Yuling , Zhang Zhao , Tao Xiang , Xu Sha , Zhang Xinyan , Zurashvili Tinatin , Lu Zhouping , Bayascas José Ramon , Jin Liping , Zhao Jianyuan , Zhou Xiangyu 
Published: March 2022

AbstractAcyl-CoA oxidase 2 (Acox2) is an enzyme involved in peroxisomal bile acid synthesis and branched-chain fatty acid degradation. Acox2 knockout (−/−) mice spontaneously developed liver cancer with marked lymphocytic infiltrate. Tandem-affinity purification coupled with mass spectrometry analysis revealed that Acox2 interacted with methylcrotonoyl-CoA carboxylase followed by co-immunoprecipitation confirmation. Here we reported that non-histone lysine crotonylation (Kcr) levels were downregulated in Acox2−/− mice livers. Interestingly, Kcr signals were concentrated in the nucleus of tumor cells but mostly located in the cytoplasm of adjacent normal liver cells of Acox2−/− mice. Quantitative analysis of the global crotonylome further revealed that 54% (27/50) of downregulated non-histone Kcr sites were located in mitochondrial (11/50) and peroxisomal (17/50) enzymes including Ehhadh, Scp2, Hsd17b4, Crot, Etfa, Cpt1a, Eci1/2, Hadha, Etfdh, and Idh2. Subsequent site-directed mutagenesis and transcriptome analysis revealed that Ehhadh K572cr might have site-specific regulatory roles by downregulating TOP3B expression that lead to increased DNA damage in vitro. Our findings suggested Acox2 is a regulator of Kcr that might play critical role on hepatic metabolic homeostasis.
The world-wide waste web
Authors: Martínez Johann H. , Romero Sergi , Ramasco José J. , Estrada Ernesto 
Published: March 2022

AbstractCountries globally trade with tons of waste materials every year, some of which are highly hazardous. This trade admits a network representation of the world-wide waste web, with countries as vertices and flows as directed weighted edges. Here we investigate the main properties of this network by tracking 108 categories of wastes interchanged in the period 2001–2019. Although, most of the hazardous waste was traded between developed nations, a disproportionate asymmetry existed in the flow from developed to developing countries. Using a dynamical model, we simulate how waste stress propagates through the network and affects the countries. We identify 28 countries with low Environmental Performance Index that are at high risk of waste congestion. Therefore, they are at threat of improper handling and disposal of hazardous waste. We find evidence of pollution by heavy metals, by volatile organic compounds and/or by persistent organic pollutants, which are used as chemical fingerprints, due to the improper handling of waste in several of these countries.
Predictive models for the selection of thermally tolerant corals based on offspring survival
Authors: Quigley K. M. , van Oppen M. J. H. 
Published: March 2022

AbstractFinding coral reefs resilient to climate warming is challenging given the large spatial scale of reef ecosystems. Methods are needed to predict the location of corals with heritable tolerance to high temperatures. Here, we combine Great Barrier Reef-scale remote sensing with breeding experiments that estimate larval and juvenile coral survival under exposure to high temperatures. Using reproductive corals collected from the northern and central Great Barrier Reef, we develop forecasting models to locate reefs harbouring corals capable of producing offspring with increased heat tolerance of an additional 3.4° heating weeks (~3 °C). Our findings predict hundreds of reefs (~7.5%) may be home to corals that have high and heritable heat-tolerance in habitats with high daily and annual temperature ranges and historically variable heat stress. The locations identified represent targets for protection and consideration as a source of corals for use in restoration of degraded reefs given their potential to resist climate change impacts and repopulate reefs with tolerant offspring.
Trade-off between reducing mutational accumulation and increasing commitment to differentiation determines tissue organization
Authors: Demeter Márton , Derényi Imre , Szöllősi Gergely J. 
Published: March 2022

AbstractSpecies-specific differences control cancer risk across orders of magnitude variation in body size and lifespan, e.g., by varying the copy numbers of tumor suppressor genes. It is unclear, however, how different tissues within an organism can control somatic evolution despite being subject to markedly different constraints, but sharing the same genome. Hierarchical differentiation, characteristic of self-renewing tissues, can restrain somatic evolution both by limiting divisional load, thereby reducing mutation accumulation, and by increasing cells’ commitment to differentiation, which can “wash out” mutants. Here, we explore the organization of hierarchical tissues that have evolved to limit their lifetime incidence of cancer. Estimating the likelihood of cancer in the presence of mutations that enhance self-proliferation, we demonstrate that a trade-off exists between mutation accumulation and the strength of washing out. Our results explain differences in the organization of widely different hierarchical tissues, such as colon and blood.
Large-scale cryovolcanic resurfacing on Pluto
Authors: Singer Kelsi N. , White Oliver L. , Schmitt Bernard , Rader Erika L. , Protopapa Silvia , Grundy William M. , Cruikshank Dale P. , Bertrand Tanguy , Schenk Paul M. , McKinnon William B. , Stern S. Alan , Dhingra Rajani D. , Runyon Kirby D. , Beyer Ross A. , Bray Veronica J. , Ore Cristina Dalle , Spencer John R. , Moore Jeffrey M. , Nimmo Francis , Keane James T. , Young Leslie A. , Olkin Catherine B. , Lauer Tod R. , Weaver Harold A. , Ennico-Smith Kimberly 
Published: March 2022

AbstractThe New Horizons spacecraft returned images and compositional data showing that terrains on Pluto span a variety of ages, ranging from relatively ancient, heavily cratered areas to very young surfaces with few-to-no impact craters. One of the regions with very few impact craters is dominated by enormous rises with hummocky flanks. Similar features do not exist anywhere else in the imaged solar system. Here we analyze the geomorphology and composition of the features and conclude this region was resurfaced by cryovolcanic processes, of a type and scale so far unique to Pluto. Creation of this terrain requires multiple eruption sites and a large volume of material (>104 km3) to form what we propose are multiple, several-km-high domes, some of which merge to form more complex planforms. The existence of these massive features suggests Pluto’s interior structure and evolution allows for either enhanced retention of heat or more heat overall than was anticipated before New Horizons, which permitted mobilization of water-ice-rich materials late in Pluto’s history.
Electric control of a canted-antiferromagnetic Chern insulator
Authors: Cai Jiaqi , Ovchinnikov Dmitry , Fei Zaiyao , He Minhao , Song Tiancheng , Lin Zhong , Wang Chong , Cobden David , Chu Jiun-Haw , Cui Yong-Tao , Chang Cui-Zu , Xiao Di , Yan Jiaqiang , Xu Xiaodong 
Published: March 2022

AbstractThe interplay between band topology and magnetism can give rise to exotic states of matter. For example, magnetically doped topological insulators can realize a Chern insulator that exhibits quantized Hall resistance at zero magnetic field. While prior works have focused on ferromagnetic systems, little is known about band topology and its manipulation in antiferromagnets. Here, we report that MnBi2Te4 is a rare platform for realizing a canted-antiferromagnetic (cAFM) Chern insulator with electrical control. We show that the Chern insulator state with Chern number C = 1 appears as the AFM to canted-AFM phase transition happens. The Chern insulator state is further confirmed by observing the unusual transition of the C = 1 state in the cAFM phase to the C = 2 orbital quantum Hall states in the magnetic field induced ferromagnetic phase. Near the cAFM-AFM phase boundary, we show that the dissipationless chiral edge transport can be toggled on and off by applying an electric field alone. We attribute this switching effect to the electrical field tuning of the exchange gap alignment between the top and bottom surfaces. Our work paves the way for future studies on topological cAFM spintronics and facilitates the development of proof-of-concept Chern insulator devices.
Lung type II alveolar epithelial cells collaborate with CCR2+ inflammatory monocytes in host defense against poxvirus infection
Authors: Yang Ning , Luna Joseph M. , Dai Peihong , Wang Yi , Rice Charles M. , Deng Liang 
Published: March 2022

AbstractThe pulmonary immune system consists of a network of tissue-resident cells as well as immune cells that are recruited to the lungs during infection and/or inflammation. How these immune components function during an acute poxvirus infection is not well understood. Intranasal infection of mice with vaccinia virus causes lethal pneumonia and systemic dissemination. Here we report that vaccinia C7 is a crucial virulence factor that blocks activation of the transcription factor IRF3. We provide evidence that type II alveolar epithelial cells (AECIIs) respond to pulmonary infection of vaccinia virus by inducing IFN-β and IFN-stimulated genes via the activation of the MDA5 and STING-mediated nucleic acid-sensing pathways and the type I IFN positive feedback loop. This leads to the recruitment and activation of CCR2+ inflammatory monocytes in the infected lungs and subsequent differentiation into Lyve1− interstitial macrophages (Lyve1− IMs), which efficiently engulf viral particles and block viral replication. Our results provide insights into how innate immune sensing of viral infection by lung AECIIs influences the activation and differentiation of CCR2+ inflammatory monocytes to defend against pulmonary poxvirus infection.
A hierarchical transcriptional network activates specific CDK inhibitors that regulate G2 to control cell size and number in Arabidopsis
Authors: Nomoto Yuji , Takatsuka Hirotomo , Yamada Kesuke , Suzuki Toshiya , Suzuki Takamasa , Huang Ying , Latrasse David , An Jing , Gombos Magdolna , Breuer Christian , Ishida Takashi , Maeo Kenichiro , Imamura Miyu , Yamashino Takafumi , Sugimoto Keiko , Magyar Zoltán , Bögre László , Raynaud Cécile , Benhamed Moussa , Ito Masaki 
Published: March 2022

AbstractHow cell size and number are determined during organ development remains a fundamental question in cell biology. Here, we identified a GRAS family transcription factor, called SCARECROW-LIKE28 (SCL28), with a critical role in determining cell size in Arabidopsis. SCL28 is part of a transcriptional regulatory network downstream of the central MYB3Rs that regulate G2 to M phase cell cycle transition. We show that SCL28 forms a dimer with the AP2-type transcription factor, AtSMOS1, which defines the specificity for promoter binding and directly activates transcription of a specific set of SIAMESE-RELATED (SMR) family genes, encoding plant-specific inhibitors of cyclin-dependent kinases and thus inhibiting cell cycle progression at G2 and promoting the onset of endoreplication. Through this dose-dependent regulation of SMR transcription, SCL28 quantitatively sets the balance between cell size and number without dramatically changing final organ size. We propose that this hierarchical transcriptional network constitutes a cell cycle regulatory mechanism that allows to adjust cell size and number to attain robust organ growth.
An adaptive synaptic array using Fowler–Nordheim dynamic analog memory
Authors: Mehta Darshit , Rahman Mustafizur , Aono Kenji , Chakrabartty Shantanu 
Published: March 2022

AbstractIn this paper we present an adaptive synaptic array that can be used to improve the energy-efficiency of training machine learning (ML) systems. The synaptic array comprises of an ensemble of analog memory elements, each of which is a micro-scale dynamical system in its own right, storing information in its temporal state trajectory. The state trajectories are then modulated by a system level learning algorithm such that the ensemble trajectory is guided towards the optimal solution. We show that the extrinsic energy required for state trajectory modulation can be matched to the dynamics of neural network learning which leads to a significant reduction in energy-dissipated for memory updates during ML training. Thus, the proposed synapse array could have significant implications in addressing the energy-efficiency imbalance between the training and the inference phases observed in artificial intelligence (AI) systems.
Exploring a blue-light-sensing transcription factor to double the peak productivity of oil in Nannochloropsis oceanica
Authors: Zhang Peng , Xin Yi , He Yuehui , Tang Xianfeng , Shen Chen , Wang Qintao , Lv Nana , Li Yun , Hu Qiang , Xu Jian 
Published: March 2022

AbstractOleaginous microalgae can produce triacylglycerol (TAG) under stress, yet the underlying mechanism remains largely unknown. Here, we show that, in Nannochloropsis oceanica, a bZIP-family regulator NobZIP77 represses the transcription of a type-2 diacylgycerol acyltransferase encoding gene NoDGAT2B under nitrogen-repletion (N+), while nitrogen-depletion (N−) relieves such inhibition and activates NoDGAT2B expression and synthesis of TAG preferably from C16:1. Intriguingly, NobZIP77 is a sensor of blue light (BL), which reduces binding of NobZIP77 to the NoDGAT2B-promoter, unleashes NoDGAT2B and elevates TAG under N−. Under N+ and white light, NobZIP77 knockout fully preserves cell growth rate and nearly triples TAG productivity. Moreover, exposing the NobZIP77-knockout line to BL under N− can double the peak productivity of TAG. These results underscore the potential of coupling light quality to oil synthesis in feedstock or bioprocess development.
Highly efficient prime editing by introducing same-sense mutations in pegRNA or stabilizing its structure
Authors: Li Xiaosa , Zhou Lina , Gao Bao-Qing , Li Guangye , Wang Xiao , Wang Ying , Wei Jia , Han Wenyan , Wang Zixian , Li Jifang , Gao Runze , Zhu Junjie , Xu Wenchao , Wu Jing , Yang Bei , Sun Xiaodong , Yang Li , Chen Jia 
Published: March 2022

AbstractPrime editor (PE), which is developed by combining Cas9 nickase and an engineered reverse transcriptase, can mediate all twelve types of base substitutions and small insertions or deletions in living cells but its efficiency remains low. Here, we develop spegRNA by introducing same-sense mutations at proper positions in the reverse-transcription template of pegRNA to increase PE’s base-editing efficiency up-to 4,976-fold (on-average 353-fold). We also develop apegRNA by altering the pegRNA secondary structure to increase PE’s indel-editing efficiency up-to 10.6-fold (on-average 2.77-fold). The spegRNA and apegRNA can be combined to further enhance editing efficiency. When spegRNA and apegRNA are used in PE3 and PE5 systems, the efficiencies of sPE3, aPE3, sPE5 and aPE5 systems are all enhanced significantly. The strategies developed in this study realize highly efficient prime editing at certain previously uneditable sites.
Crystal structure and cellular functions of uPAR dimer
Authors: Yu Shujuan , Sui Yaqun , Wang Jiawei , Li Yongdong , Li Hanlin , Cao Yingping , Chen Liqing , Jiang Longguang , Yuan Cai , Huang Mingdong 
Published: March 2022

AbstractReceptor dimerization of urokinase-type plasminogen activator receptor (uPAR) was previously identified at protein level and on cell surface. Recently, a dimeric form of mouse uPAR isoform 2 was proposed to induce kidney disease. Here, we report the crystal structure of human uPAR dimer at 2.96 Å. The structure reveals enormous conformational changes of the dimer compared to the monomeric structure: D1 of uPAR opens up into a large expanded ring that captures a β-hairpin loop of a neighboring uPAR to form an expanded β-sheet, leading to an elongated, highly intertwined dimeric uPAR. Based on the structure, we identify E49P as a mutation promoting dimer formation. The mutation increases receptor binding to the amino terminal fragment of its primary ligand uPA, induces the receptor to distribute to the basal membrane, promotes cell proliferation, and alters cell morphology via β1 integrin signaling. These results reveal the structural basis for uPAR dimerization, its effect on cellular functions, and provide a basis to further study this multifunctional receptor.
Estimation of the bidirectional relationship between schizophrenia and inflammatory bowel disease using the mendelian randomization approach
Authors: Qian Li , He Xiaoyan , Gao Fengjie , Fan Yajuan , Zhao Binbin , Ma Qingyan , Yan Bin , Wang Wei , Ma Xiancang , Yang Jian 
Published: March 2022

AbstractIt has been reported that schizophrenia (SCZ) and inflammatory bowel disease (IBD) are related. However, whether there is a bidirectional interaction between them remains unclear. The aim of this study was to conduct a bidirectional Mendelian randomization (MR) analysis to elucidate the causal relationship between SCZ and IBD and its subtypes, including Crohn’s disease (CD) and ulcerative colitis (UC). Single-nucleotide polymorphisms (SNPs) extracted from the summary data of genome-wide association studies were used as genetic instruments. MR was performed using the inverse-variance-weighted method. The MR-Egger and weighted median methods were used for sensitivity analyses. Analysis using 70 SNPs as genetic instruments showed that SCZ was associated with an increased risk of IBD (OR = 1.14, 95% CI: 1.09–1.20, P = 9.21 × 10−8), CD (OR = 1.16, 95% CI: 1.07–1.25, P = 1.42 × 10−4), and UC (OR = 1.14, 95% CI: 1.07–1.21, P = 2.72 × 10−5). The results of the sensitivity analyses were robust and no evidence of pleiotropy was observed. Bidirectional MR analyses showed no causal effects of IBD, CD, or UC on SCZ. This study suggests that SCZ has causal effects on IBD and its subtypes, whereas IBD has no effect on SCZ. Brain-gut axis interactions may help clarify the causal relationship between SCZ and IBD. However, further studies are needed to elucidate the biological mechanisms behind the brain-gut interactions.
Native range estimates for red-listed vascular plants
Authors: Borgelt Jan , Sicacha-Parada Jorge , Skarpaas Olav , Verones Francesca 
Published: March 2022

AbstractBesides being central for understanding both global biodiversity patterns and associated anthropogenic impacts, species range maps are currently only available for a small subset of global biodiversity. Here, we provide a set of assembled spatial data for terrestrial vascular plants listed at the global IUCN red list. The dataset consists of pre-defined native regions for 47,675 species, density of available native occurrence records for 30,906 species, and standardized, large-scale Maxent predictions for 27,208 species, highlighting environmentally suitable areas within species’ native regions. The data was generated in an automated approach consisting of data scraping and filtering, variable selection, model calibration and model selection. Generated Maxent predictions were validated by comparing a subset to available expert-drawn range maps from IUCN (n = 4,257), as well as by qualitatively inspecting predictions for randomly selected species. We expect this data to serve as a substitute whenever expert-drawn species range maps are not available for conducting large-scale analyses on biodiversity patterns and associated anthropogenic impacts.
Comprehensive spectral libraries for various rabbit eye tissue proteomes
Authors: Qin Guoting , Zhang Pengzhi , Sun Mingxia , Fu Wenjiang , Cai Chengzhi 
Published: March 2022

AbstractRabbits have been widely used for studying ocular physiology and pathology due to their relatively large eye size and similar structures with human eyes. Various rabbit ocular disease models, such as dry eye, age-related macular degeneration, and glaucoma, have been established. Despite the growing application of proteomics in vision research using rabbit ocular models, there is no spectral assay library for rabbit eye proteome publicly available. Here, we generated spectral assay libraries for rabbit eye compartments, including conjunctiva, cornea, iris, retina, sclera, vitreous humor, and tears using fractionated samples and ion mobility separation enabling deep proteome coverage. The rabbit eye spectral assay library includes 9,830 protein groups and 113,593 peptides. We present the data as a freely available community resource for proteomic studies in the vision field. Instrument data and spectral libraries are available via ProteomeXchange with identifier PXD031194.
A worldwide epidemiological database for COVID-19 at fine-grained spatial resolution
Authors: Guidotti Emanuele 
Published: March 2022

AbstractThis database provides the daily time-series of COVID-19 cases, deaths, recovered people, tests, vaccinations, and hospitalizations, for more than 230 countries, 760 regions, and 12,000 lower-level administrative divisions. The geographical entities are associated with identifiers to match with hydrometeorological, geospatial, and mobility data. The database includes policy measures at the national and, when available, sub-national levels. The data acquisition pipeline is open-source and fully automated. As most governments revise the data retrospectively, the database always updates the complete time-series to mirror the original source. Vintage data, immutable snapshots of the data taken each day, are provided to ensure research reproducibility. The latest data are updated on an hourly basis, and the vintage data are available since April 14, 2020. All the data are available in CSV files or SQLite format. By unifying the access to the data, this work makes it possible to study the pandemic on a global scale with high resolution, taking into account within-country variations, nonpharmaceutical interventions, and environmental and exogenous variables.