bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantifying the Dimensionalities and Drivers of Ecosystem Stability at Global Scale
Authors: Chen Jijing , Chi Yonggang , Zhou Wen , Wang Yonglin , Zhuang Jie , Zhao Ning , Ding Jianxi , Song Jun , Zhou Lei 
Published: April 2021

AbstractEcosystem stability is the key to maintain the normal service function of the earth, but the dimensionalities and drivers of stability are highly controversial. A global study on the components of stability, including temporal stability, resistance, and resilience, was analyzed by gross productive production of 130 flux sites, species richness, and climate variables such as precipitation, air temperature, and shortwave radiation over a 24‐year period from 1991 to 2014. Our results provided global‐scale evidence that ecosystem stability must be analyzed as a multidimensional construct, and biome‐specific dimensionality should be considered in exploring ecosystem stability. The effective dimensionalities of ecosystem stability were significantly different among biomes, showing the least in savannas and the most in wetlands. In addition, the climate was predicted to be more important than biodiversity in regulating ecosystem stability on a global scale. The result showed that climates explained up to 70%, 49%, and 39% of the variation in temporal stability, resistance, and resilience of ecosystem function, respectively, while species richness only explained up to 5%, 20%, −11%. These findings give a comprehensive assessment for stability at the global scale and highlight the key role of climate in regulating ecosystem stability.
High-fidelity structured illumination microscopy by point-spread-function engineering
Authors: Wen Gang , Li Simin , Wang Linbo , Chen Xiaohu , Sun Zhenglong , Liang Yong , Jin Xin , Xing Yifan , Jiu Yaming , Tang Yuguo , Li Hui 
Published: April 2021

AbstractStructured illumination microscopy (SIM) has become a widely used tool for insight into biomedical challenges due to its rapid, long-term, and super-resolution (SR) imaging. However, artifacts that often appear in SIM images have long brought into question its fidelity, and might cause misinterpretation of biological structures. We present HiFi-SIM, a high-fidelity SIM reconstruction algorithm, by engineering the effective point spread function (PSF) into an ideal form. HiFi-SIM can effectively reduce commonly seen artifacts without loss of fine structures and improve the axial sectioning for samples with strong background. In particular, HiFi-SIM is not sensitive to the commonly used PSF and reconstruction parameters; hence, it lowers the requirements for dedicated PSF calibration and complicated parameter adjustment, thus promoting SIM as a daily imaging tool.
Phenotypically independent profiles relevant to mental health are genetically correlated
Authors: Roelfs Daniel , Alnæs Dag , Frei Oleksandr , van der Meer Dennis , Smeland Olav B. , Andreassen Ole A. , Westlye Lars T. , Kaufmann Tobias 
Published: April 2021

AbstractGenome-wide association studies (GWAS) and family-based studies have revealed partly overlapping genetic architectures between various psychiatric disorders. Given clinical overlap between disorders, our knowledge of the genetic architectures underlying specific symptom profiles and risk factors is limited. Here, we aimed to derive distinct profiles relevant to mental health in healthy individuals and to study how these genetically relate to each other and to common psychiatric disorders. Using independent component analysis, we decomposed self-report mental health questionnaires from 136,678 healthy individuals of the UK Biobank, excluding data from individuals with a diagnosed neurological or psychiatric disorder, into 13 distinct profiles relevant to mental health, capturing different symptoms as well as social and risk factors underlying reduced mental health. Utilizing genotypes from 117,611 of those individuals with White British ancestry, we performed GWAS for each mental health profile and assessed genetic correlations between these profiles, and between the profiles and common psychiatric disorders and cognitive traits. We found that mental health profiles were genetically correlated with a wide range of psychiatric disorders and cognitive traits, with strongest effects typically observed between a given mental health profile and a disorder for which the profile is common (e.g. depression symptoms and major depressive disorder, or psychosis and schizophrenia). Strikingly, although the profiles were phenotypically uncorrelated, many of them were genetically correlated with each other. This study provides evidence that statistically independent mental health profiles partly share genetic underpinnings and show genetic overlap with psychiatric disorders, suggesting that shared genetics across psychiatric disorders cannot be exclusively attributed to the known overlapping symptomatology between the disorders.
Utidelone inhibits growth of colorectal cancer cells through ROS/JNK signaling pathway
Authors: Li Fuli , Huang Tinglei , Tang Yao , Li Qingli , Wang Jianzheng , Cheng Xiaojiao , Zhang Wenhui , Zhang Baiwen , Zhou Cong , Tu Shuiping 
Published: April 2021

AbstractUtidelone (UTD1), a novel microtubule stabilizing agent, is an epothilone B analogue which was produced by genetic engineering. UTD1 has exhibited broad antitumor activity in multiple solid tumors. However, its activity and mechanism in colorectal cancer (CRC) remain to be studied. In this study, UTD1 dramatically inhibited CRC cell proliferation (with 0.38 µg/ml, 0.77 µg/ml IC50 in RKO and HCT116, respectively) in vitro. Immunofluorescence staining showed that UTD1 induced the formation of microtubule bundling and asters in RKO cells. Flow cytometry analysis demonstrated that UTD1 induced cell cycle to arrest in G2/M phase, subsequent apoptosis. Significantly, UTD1 exhibited stronger effect on inducing apoptosis than paclitaxel and 5-FU, especially in HCT15 cells which is ABCB1 high-expression. UTD1 exposure cleaved caspase-3 and poly ADP-ribose polymerase (PARP), decreased mitochondrial membrane potential, released cytochrome c, increased the production of active oxygen and activated c-Jun N-terminal kinase (JNK), suggesting ROS/JNK pathway was involved in this process. Moreover, UTD1 inhibited tumor growth and was more effective and safer compared with paclitaxel and 5-FU in RKO xenograft in nude mice. Taken together, our findings first indicate that UDT1 inhibits tumor growth in CRC xenograft model and may be a promising agent for CRC treatment.
The role of γ-aminobutyric acid in aluminum stress tolerance in a woody plant, Liriodendron chinense × tulipifera
Authors: Wang Pengkai , Dong Yini , Zhu Liming , Hao Zhaodong , Hu LingFeng , Hu Xiangyang , Wang Guibin , Cheng Tielong , Shi Jisen , Chen Jinhui 
Published: April 2021

AbstractThe aluminum (Al) cation Al3+ in acidic soil shows severe rhizotoxicity that inhibits plant growth and development. Most woody plants adapted to acidic soils have evolved specific strategies against Al3+ toxicity, but the underlying mechanism remains elusive. The four-carbon amino acid gamma-aminobutyric acid (GABA) has been well studied in mammals as an inhibitory neurotransmitter; GABA also controls many physiological responses during environmental or biotic stress. The woody plant hybrid Liriodendron (L. chinense × tulipifera) is widely cultivated in China as a horticultural tree and provides high-quality timber; studying its adaptation to high Al stress is important for harnessing its ecological and economic potential. Here, we performed quantitative iTRAQ (isobaric tags for relative and absolute quantification) to study how protein expression is altered in hybrid Liriodendron leaves subjected to Al stress. Hybrid Liriodendron shows differential accumulation of several proteins related to cell wall biosynthesis, sugar and proline metabolism, antioxidant activity, cell autophagy, protein ubiquitination degradation, and anion transport in response to Al damage. We observed that Al stress upregulated glutamate decarboxylase (GAD) and its activity, leading to increased GABA biosynthesis. Additional GABA synergistically increased Al-induced antioxidant enzyme activity to efficiently scavenge ROS, enhanced proline biosynthesis, and upregulated the expression of MATE1/2, which subsequently promoted the efflux of citrate for chelation of Al3+. We also showed similar effects of GABA on enhanced Al3+ tolerance in Arabidopsis. Thus, our findings suggest a function of GABA signaling in enhancing hybrid Liriodendron tolerance to Al stress through promoting organic acid transport and sustaining the cellular redox and osmotic balance.
A gene that underwent adaptive evolution, LAC2 (LACCASE), in Populus euphratica improves drought tolerance by improving water transport capacity
Authors: Niu Zhimin , Li Guiting , Hu Hongyin , Lv Jiaojiao , Zheng Qiwei , Liu Jianquan , Wan Dongshi 
Published: April 2021

AbstractDrought severely limits plant development and growth; accordingly, plants have evolved strategies to prevent water loss and adapt to water deficit conditions. However, experimental cases that corroborate these evolutionary processes are limited. The LACCASEs (LACs) family is involved in various plant development and growth processes. Here, we performed an evolutionary analysis ofLACsfromPopulus euphraticaand characterized the functions ofLACsinArabidopsisand poplar. The results showed that inPeuLACs, multiple gene duplications led to apparent functional redundancy as the result of various selective pressures. Among them,PeuLAC2underwent strong positive selection. Heterologous expression analyses showed that the overexpression ofPeuLAC2alters the xylem structure of plants, including thickening the secondary cell wall (SCW) and increasing the fiber cell length and stem tensile strength. Altogether, these changes improve the water transport capacity of plants. The analysis of the physiological experimental results showed thatPeuLAC2-OE lines exhibited a stronger antioxidant response and greater drought tolerance than WT. Three genes screened by transcriptome analysis,NAC025,BG1, andUGT, that are associated with SCW synthesis and drought stress were all upregulated in thePeuLAC2-OE lines, implying that the overexpression ofPeuLAC2thickened the SCW, improved the water transport capacity of the plant, and further enhanced its drought tolerance. Our study highlights that genes that have undergone adaptive evolution may participate in the development of adaptive traits inP. euphraticaand thatPeuLAC2could be a candidate gene for molecular genetic breeding in trees.
The transcription factor SlHY5 regulates the ripening of tomato fruit at both the transcriptional and translational levels
Authors: Wang Weihao , Wang Peiwen , Li Xiaojing , Wang Yuying , Tian Shiping , Qin Guozheng 
Published: April 2021

AbstractLight plays a critical role in plant growth and development, but the mechanisms through which light regulates fruit ripening and nutritional quality in horticultural crops remain largely unknown. Here, we found that ELONGATED HYPOCOTYL 5 (HY5), a master regulator in the light signaling pathway, is required for normal fruit ripening in tomato (Solanum lycopersicum). Loss of function of tomato HY5 (SlHY5) impairs pigment accumulation and ethylene biosynthesis. Transcriptome profiling identified 2948 differentially expressed genes, which included 1424 downregulated and 1524 upregulated genes, in the Slhy5 mutants. In addition, genes involved in carotenoid and anthocyanin biosynthesis and ethylene signaling were revealed as direct targets of SlHY5 by chromatin immunoprecipitation. Surprisingly, the expression of a large proportion of genes encoding ribosomal proteins was downregulated in the Slhy5 mutants, and this downregulation pattern was accompanied by a decrease in the abundance of ribosomal proteins. Further analysis demonstrated that SlHY5 affected the translation efficiency of numerous ripening-related genes. These data indicate that SlHY5 regulates fruit ripening both at the transcriptional level by targeting specific molecular pathways and at the translational level by affecting the protein translation machinery. Our findings unravel the regulatory mechanisms of SlHY5 in controlling fruit ripening and nutritional quality and uncover the multifaceted regulation of gene expression by transcription factors.
A reconciled solution of Meltwater Pulse 1A sources using sea-level fingerprinting
Authors: Lin Yucheng , Hibbert Fiona D. , Whitehouse Pippa L. , Woodroffe Sarah A. , Purcell Anthony , Shennan Ian , Bradley Sarah L. 
Published: April 2021

AbstractThe most rapid global sea-level rise event of the last deglaciation, Meltwater Pulse 1A (MWP-1A), occurred ∼14,650 years ago. Considerable uncertainty regarding the sources of meltwater limits understanding of the relationship between MWP-1A and the concurrent fast-changing climate. Here we present a data-driven inversion approach, using a glacio-isostatic adjustment model to invert for the sources of MWP-1A via sea-level constraints from six geographically distributed sites. The results suggest contributions from Antarctica, 1.3 m (0–5.9 m; 95% probability), Scandinavia, 4.6 m (3.2–6.4 m) and North America, 12.0 m (5.6–15.4 m), giving a global mean sea-level rise of 17.9 m (15.7–20.2 m) in 500 years. Only a North American dominant scenario successfully predicts the observed sea-level change across our six sites and an Antarctic dominant scenario is firmly refuted by Scottish isolation basin records. Our sea-level based results therefore reconcile with field-based ice-sheet reconstructions.
Nickel isotopes link Siberian Traps aerosol particles to the end-Permian mass extinction
Authors: Li Menghan , Grasby Stephen E. , Wang Shui-Jiong , Zhang Xiaolin , Wasylenki Laura E. , Xu Yilun , Sun Mingzhao , Beauchamp Benoit , Hu Dongping , Shen Yanan 
Published: April 2021

AbstractThe end-Permian mass extinction (EPME) was the most severe extinction event in the past 540 million years, and the Siberian Traps large igneous province (STLIP) is widely hypothesized to have been the primary trigger for the environmental catastrophe. The killing mechanisms depend critically on the nature of volatiles ejected during STLIP eruptions, initiating about 300 kyr before the extinction event, because the atmosphere is the primary interface between magmatism and extinction. Here we report Ni isotopes for Permian-Triassic sedimentary rocks from Arctic Canada. The δ60Ni data range from −1.09‰ to 0.35‰, and exhibit the lightest δ60Ni compositions ever reported for sedimentary rocks. Our results provide strong evidence for global dispersion and loading of Ni-rich aerosol particles into the Panthalassic Ocean. Our data demonstrate that environmental degradation had begun well before the extinction event and provide a link between global dispersion of Ni-rich aerosols, ocean chemistry changes, and the EPME.
Low-temperature nucleation anomaly in silicate glasses shown to be artifact in a 5BaO·8SiO2 glass
Authors: Xia Xinsheng , Van Hoesen D. C. , McKenzie Matthew E. , Youngman Randall E. , Kelton K. F. 
Published: April 2021

AbstractFor over 40 years, measurements of the nucleation rates in a large number of silicate glasses have indicated a breakdown in the Classical Nucleation Theory at temperatures below that of the peak nucleation rate. The data show that instead of steadily decreasing with decreasing temperature, the work of critical cluster formation enters a plateau and even starts to increase. Many explanations have been offered to explain this anomaly, but none have provided a satisfactory answer. We present an experimental approach to demonstrate explicitly for the example of a 5BaO ∙ 8SiO2 glass that the anomaly is not a real phenomenon, but instead an artifact arising from an insufficient heating time at low temperatures. Heating times much longer than previously used at a temperature 50 K below the peak nucleation rate temperature give results that are consistent with the predictions of the Classical Nucleation Theory. These results raise the question of whether the claimed anomaly is also an artifact in other glasses.
Spin-orbit coupling induced splitting of Yu-Shiba-Rusinov states in antiferromagnetic dimers
Authors: Beck Philip , Schneider Lucas , Rózsa Levente , Palotás Krisztián , Lászlóffy András , Szunyogh László , Wiebe Jens , Wiesendanger Roland 
Published: April 2021

AbstractMagnetic atoms coupled to the Cooper pairs of a superconductor induce Yu-Shiba-Rusinov states (in short Shiba states). In the presence of sufficiently strong spin-orbit coupling, the bands formed by hybridization of the Shiba states in ensembles of such atoms can support low-dimensional topological superconductivity with Majorana bound states localized on the ensembles’ edges. Yet, the role of spin-orbit coupling for the hybridization of Shiba states in dimers of magnetic atoms, the building blocks for such systems, is largely unexplored. Here, we reveal the evolution of hybridized multi-orbital Shiba states from a single Mn adatom to artificially constructed ferromagnetically and antiferromagnetically coupled Mn dimers placed on a Nb(110) surface. Upon dimer formation, the atomic Shiba orbitals split for both types of magnetic alignment. Our theoretical calculations attribute the unexpected splitting in antiferromagnetic dimers to spin-orbit coupling and broken inversion symmetry at the surface. Our observations point out the relevance of previously unconsidered factors on the formation of Shiba bands and their topological classification.
Ontology-driven weak supervision for clinical entity classification in electronic health records
Authors: Fries Jason A. , Steinberg Ethan , Khattar Saelig , Fleming Scott L. , Posada Jose , Callahan Alison , Shah Nigam H. 
Published: April 2021

AbstractIn the electronic health record, using clinical notes to identify entities such as disorders and their temporality (e.g. the order of an event relative to a time index) can inform many important analyses. However, creating training data for clinical entity tasks is time consuming and sharing labeled data is challenging due to privacy concerns. The information needs of the COVID-19 pandemic highlight the need for agile methods of training machine learning models for clinical notes. We present Trove, a framework for weakly supervised entity classification using medical ontologies and expert-generated rules. Our approach, unlike hand-labeled notes, is easy to share and modify, while offering performance comparable to learning from manually labeled training data. In this work, we validate our framework on six benchmark tasks and demonstrate Trove’s ability to analyze the records of patients visiting the emergency department at Stanford Health Care for COVID-19 presenting symptoms and risk factors.
Analysis of SARS-CoV-2 genomic epidemiology reveals disease transmission coupled to variant emergence and allelic variation
Authors: Bandoy D J Darwin R. , Weimer Bart C. 
Published: April 2021

AbstractThe spread of SARS-CoV-2 created a pandemic crisis with > 150,000 cumulative cases in > 65 countries within a few months. The reproductive number (R) is a metric to estimate the transmission of a pathogen during an outbreak. Preliminary published estimates were based on the initial outbreak in China. Whole genome sequences (WGS) analysis found mutational variations in the viral genome; however, previous comparisons failed to show a direct relationship between viral genome diversity, transmission, and the epidemic severity. COVID-19 incidences from different countries were modeled over the epidemic curve. Estimates of the instantaneous R (Wallinga and Teunis method) with a short and standard serial interval were done. WGS were used to determine the populations genomic variation and that underpinned creation of the pathogen genome identity (GENI) score, which was merged with the outbreak curve in four distinct phases. Inference of transmission time was based on a mutation rate of 2 mutations/month. R estimates revealed differences in the transmission and variable infection dynamics between and within outbreak progression for each country examined. Outside China, our R estimates observed propagating dynamics indicating that other countries were poised to move to the takeoff and exponential stages. Population density and local temperatures had no clear relationship to the outbreak progression. Integration of incidence data with the GENI score directly predicted increases in cases as the genome variation increased that led to new variants. Integrating the outbreak curve, dynamic R, and SNP variation found a direct association between increasing cases and transmission genome evolution. By defining the epidemic curve into four stages and integrating the instantaneous country-specific R with the GENI score, we directly connected changes in individual outbreaks based on changes in the virus genome via SNPs. This resulted in the ability to forecast potential increases in cases as well as mutations that may defeat PCR screening and the infection process. By using instantaneous R estimations and WGS, outbreak dynamics were defined to be linked to viral mutations, indicating that WGS, as a surveillance tool, is required to predict shifts in each outbreak that will provide actionable decision making information. Integrating epidemiology with genome sequencing and modeling allows for evidence-based disease outbreak tracking with predictive therapeutically valuable insights in near real time.
Differential characterization of stress sensitivity and its main control mechanism in deep pore-fracture clastic reservoirs
Authors: Han Denglin , Wang Huachao , Wang Chenchen , Yuan Wenfang , Zhang Juan , Lin Wei , Hu Rongrong 
Published: April 2021

AbstractStress sensitivity in reservoirs is critical during the exploitation of oil and gas fields. As a deep clastic reservoir under strong tectonic compression, the Ahe Formation in the northern tectonic zone of the Kuqa depression exhibited strong stress sensitivity effect. However, the conventional evaluation method by using permeability damage rate as a constraint restricts the mechanistic understanding of the strong stress sensitivity effect. In this study, morphology of stress sensitivity test curve, coupled with rate change of permeability and extent of irreversible damage in actual sample measurement through micro-CT in-situ scanning, is used to characterize differentially. The strong stress sensitivity effects of the studied intervals can be divided into three types: (1) rapid change in permeability–weak irreversible damage, (2) moderate change in permeability–strong irreversible damage and (3) moderate change in permeability–moderate irreversible damage. The strong stress sensitivity is caused by the micro-pores and micro-fractures, which are widely developed in the studied reservoir. The mechanisms caused by the two types of pore are different. The stress sensitivity effects in micro-fracture-rich reservoirs are characterized by rapid change in permeability and weak irreversible damage. Meanwhile, the stress sensitivity effects in micro-pore-rich reservoirs are manifested as moderate change in permeability and strong irreversible damage. The study shows that the differences in the content of micro-pores and micro-fractures and their reverse mechanisms of stress sensitivity co-create different types of stress sensitivity within the samples. Accordingly, the differences of the stress sensitivity type in macroscopic samples are caused by the competition between the microscopic differences of pore types.