bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Dominant Modes of Spring Land Surface Temperature Over Western Eurasia and Their Possible Linkages With Large‐Scale Atmospheric Teleconnection Patterns
Authors: Song Yidi , Chen Haishan , Yang Jingqiu 
Published: February 2022

AbstractPrevious studies suggest that the spring land surface temperature (LST) anomaly over Western Eurasia (WEA; 20°N–70°N, 0–70°E) is a potential driver for Asian even global climate. However, the interannual variability of LST over WEA together with its causes has not received enough attention. Based on multi‐source observations and reanalysis data, three dominant modes of spring LST over WEA were identified, and the roles of atmospheric teleconnection patterns in LST anomalies via altering cloud and water vapor were investigated from the perspective of surface energy budget. The first empirical orthogonal function (EOF1) mode exhibits a homogeneous warming pattern that is closely related to a negatively in‐phase combination of the Scandinavian and East Atlantic/Western Russia (EA/WR) patterns. Under the control of a predominant anomalous anticyclone, the warming is the result of enhanced downward longwave radiation due to more water vapor in a warmer atmosphere associated with anomalous southerly and more incident solar radiation due to reduced cloud cover. The EOF2 mode, which displays a meridional dipole structure, is dominated by the North Atlantic Oscillation. Coupled with an anomalous cyclone and anticyclone over western Europe and around the Caspian Sea, respectively, the former LST anomalies are primarily caused by cloud‐shortwave radiation processes, whereas the latter are dominated by downward longwave radiation due to water vapor. The EOF3 mode, characterized by a zonal dipole pattern, is dominated by the water vapor greenhouse effect related to the Eurasian pattern. The results of the study may provide a valuable signal for climate prediction.
ENSO’s Response to Volcanism in a Data Assimilation‐Based Paleoclimate Reconstruction Over the Common Era
Authors: Dee Sylvia G. , Steiger Nathan J. 
Published: February 2022

AbstractThe tropical response to explosive volcanism remains underconstrained in the paleoclimate record. While the atmosphere cools due to aerosol forcing following volcanic eruptions, modeling evidence suggests that the tropical Pacific responds with compensatory warming. Given the rarity of large volcanic eruptions and the short instrumental record, these modeling results require independent verification. Here, we test for links between volcanism and tropical Pacific dynamics using the newly developed Paleo Hydrodynamics Data Assimilation product (PHYDA), which spans the past 2,000 years. Using Pacific sea surface temperature fields from PHYDA and coincident volcanic eruptions, we test the response of the El Niño–Southern Oscillation (ENSO) to large, tropical volcanic eruptions. We identify a weak El Niño‐like response of the tropical Pacific in the year following sufficiently large, tropical volcanic eruptions. While the response is not significant at the 95% confidence level using superposed epoch analysis (SEA) and self‐organizing maps, a significant result does emerge when employing probability density functions. Our results indicate that the widely used SEA approach, based on composite averaging, may not be sufficiently sensitive to capture an ENSO response in the presence of large internal variability. We additionally conclude that inconsistencies in both the spatial patterns and magnitudes between climate models and PHYDA results indicate that current models overestimate the regional tropical response to volcanic forcing.
Hypermethylation of PDX1, EN2, and MSX1 predicts the prognosis of colorectal cancer
Authors: Lee Yeongun , Dho So Hee , Lee Jiyeon , Hwang Ji-Hyun , Kim Minjung , Choi Won-Young , Lee Jin-Young , Lee Jongwon , Chang Woochul , Lee Min Young , Choi Jungmin , Kim Tae-You , Kim Lark Kyun 
Published: February 2022

AbstractDespite numerous observations regarding the relationship between DNA methylation changes and cancer progression, only a few genes have been verified as diagnostic biomarkers of colorectal cancer (CRC). To more practically detect methylation changes, we performed targeted bisulfite sequencing. Through co-analysis of RNA-seq, we identified cohort-specific DNA methylation markers: CpG islands of the intragenic regions of PDX1, EN2, and MSX1. We validated that these genes have oncogenic features in CRC and that their expression levels are increased in correlation with the hypermethylation of intragenic regions. The reliable depth of the targeted bisulfite sequencing data enabled us to design highly optimized quantitative methylation-specific PCR primer sets that can successfully detect subtle changes in the methylation levels of candidate regions. Furthermore, these methylation levels can divide CRC patients into two groups denoting good and poor prognoses. In this study, we present a streamlined workflow for screening clinically significant differentially methylated regions. Our discovery of methylation markers in the PDX1, EN2, and MSX1 genes suggests their promising performance as prognostic markers and their clinical application in CRC patients.
Prognostic model for time to achieve independent walking in children with Guillain-Barré syndrome
Authors: Chaweekulrat Peerada , Sanmaneechai Oranee 
Published: February 2022

Abstract
Background
Guillain-Barré Syndrome (GBS) is an immune-mediated peripheral neuropathy. Clinical features and outcomes in children differ from adults. Currently, there is no prognostic model to predict outcomes in children and existing models for adults are not suitable.

Objectives
To identify factors that are associated with outcomes and develop clinical model to predict time to independent walking in children with GBS.

Methods
Between 2005 and 2018, 41 patients with GBS were identified by retrospective chart review. Factors associated with independent walking were analyzed with the Kaplan–Meier method. A prediction model was developed based on regression coefficients from Cox’s proportional hazard model.

Results
The disability score at maximum weakness and nerve conduction study results were associated with independent walking and included in the model. Scores range from 0 to 5. A score of 5 predicts 34 days to independent walking while a score of 0 predicts 5 months (mean 158 days, p = 0.008).

Conclusion
This scoring system for pediatric patients provides predicts the time needed to achieve independent walking, an important milestone of recovery for communication with parents, and to assist clinicians to optimize treatment. Further studies of predictive factors and external validation are needed to improve precision of the model.

Impact

This is the first study to create a prognostic scoring system for individual outcomes in children with GBS.

A clinical prognostic model can predict time to achieve independent walking in individual pediatric patients with GBS.

This model can assist clinicians to optimize treatment and guide decisions on rehabilitation to prevent long-term disability.
De novo serine synthesis regulates chondrocyte proliferation during bone development and repair
Authors: Stegen Steve , Loopmans Shauni , Stockmans Ingrid , Moermans Karen , Carmeliet Peter , Carmeliet Geert 
Published: February 2022

AbstractThe majority of the mammalian skeleton is formed through endochondral ossification starting from a cartilaginous template. Cartilage cells, or chondrocytes, survive, proliferate and synthesize extracellular matrix in an avascular environment, but the metabolic requirements for these anabolic processes are not fully understood. Here, using metabolomics analysis and genetic in vivo models, we show that maintaining intracellular serine homeostasis is essential for chondrocyte function. De novo serine synthesis through phosphoglycerate dehydrogenase (PHGDH)-mediated glucose metabolism generates nucleotides that are necessary for chondrocyte proliferation and long bone growth. On the other hand, dietary serine is less crucial during endochondral bone formation, as serine-starved chondrocytes compensate by inducing PHGDH-mediated serine synthesis. Mechanistically, this metabolic flexibility requires ATF4, a transcriptional regulator of amino acid metabolism and stress responses. We demonstrate that both serine deprivation and PHGDH inactivation enhance ATF4 signaling to stimulate de novo serine synthesis and serine uptake, respectively, and thereby prevent intracellular serine depletion and chondrocyte dysfunction. A similar metabolic adaptability between serine uptake and de novo synthesis is observed in the cartilage callus during fracture repair. Together, the results of this study reveal a critical role for PHGDH-dependent serine synthesis in maintaining intracellular serine levels under physiological and serine-limited conditions, as adequate serine levels are necessary to support chondrocyte proliferation during endochondral ossification.
UBE2T-mediated Akt ubiquitination and Akt/β-catenin activation promotes hepatocellular carcinoma development by increasing pyrimidine metabolism
Authors: Zhu Zhenru , Cao Chuanhui , Zhang Dongyan , Zhang Zhihong , Liu Li , Wu Dehua , Sun Jingyuan 
Published: February 2022

AbstractThe oncogene protein ubiquitin-conjugating enzyme E2T (UBE2T) is reported to be upregulated in hepatocellular carcinoma (HCC) and correlated with poor clinical outcomes of HCC patients. However, the underlying mechanism by which UBE2T exerts its oncogenic function in HCC remains largely unexplored. In this study, in vitro and in vivo experiments suggested that UBE2T promoted HCC development including proliferation and metastasis. GSEA analysis indicated that UBE2T was positively correlated with pyrimidine metabolism, and LC/MS-MS metabolomics profiling revealed that the key products of pyrimidine metabolism were significantly increased in UBE2T-overexpressing cells. UBE2T overexpression led to the upregulation of several key enzymes catalyzing de novo pyrimidine synthesis, including CAD, DHODH, and UMPS. Moreover, the utilization of leflunomide, a clinically approved DHODH inhibitor, blocked the effect of UBE2T in promoting HCC progression. Mechanistically, UBE2T increased Akt K63-mediated ubiquitination and Akt/β-catenin signaling pathway activation. The disruption of UBE2T-mediated ubiquitination on Akt, including E2-enzyme-deficient mutation (C86A) of UBE2T and ubiquitination-site-deficient mutation (K8/14 R) of Akt impaired UBE2T’s effect in upregulating CAD, DHODH, and UMPS. Importantly, we demonstrated that UBE2T was positively correlated with p-Akt, β-catenin, CAD, DHODH, and UMPS in HCC tumor tissues. In summary, our study indicates that UBE2T increases pyrimidine metabolism by promoting Akt K63-linked ubiquitination, thus contributing to HCC development. This work provides a novel insight into HCC development and a potential therapeutic strategy for HCC patients.
Retention of deposited ammonium and nitrate and its impact on the global forest carbon sink
Authors: Gurmesa Geshere Abdisa , Wang Ang , Li Shanlong , Peng Shushi , de Vries Wim , Gundersen Per , Ciais Philippe , Phillips Oliver L. , Hobbie Erik A. , Zhu Weixing , Nadelhoffer Knute , Xi Yi , Bai Edith , Sun Tao , Chen Dexiang , Zhou Wenjun , Zhang Yiping , Guo Yingrong , Zhu Jiaojun , Duan Lei , Li Dejun , Koba Keisuke , Du Enzai , Zhou Guoyi , Han Xingguo , Han Shijie , Fang Yunting 
Published: February 2022

AbstractThe impacts of enhanced nitrogen (N) deposition on the global forest carbon (C) sink and other ecosystem services may depend on whether N is deposited in reduced (mainly as ammonium) or oxidized forms (mainly as nitrate) and the subsequent fate of each. However, the fates of the two key reactive N forms and their contributions to forest C sinks are unclear. Here, we analyze results from 13 ecosystem-scale paired15N-labelling experiments in temperate, subtropical, and tropical forests. Results show that total ecosystem N retention is similar for ammonium and nitrate, but plants take up more labelled nitrate ($${20}_{15}^{25}$$201525%) ($${{{{{{\rm{mean}}}}}}}_{{{{{{\rm{minimum}}}}}}}^{{{{{{\rm{maximum}}}}}}}$$meanminimummaximum) than ammonium ($${12}_{8}^{16}$$12816%) while soils retain more ammonium ($${57}_{49}^{65}$$574965%) than nitrate ($${46}_{32}^{59}$$463259%). We estimate that the N deposition-induced C sink in forests in the 2010s is$${0.72}_{0.49}^{0.96}$$0.720.490.96 Pg C yr−1, higher than previous estimates because of a larger role for oxidized N and greater rates of global N deposition.
IL-22 initiates an IL-18-dependent epithelial response circuit to enforce intestinal host defence
Authors: Chiang Hung-Yu , Lu Hsueh-Han , Sudhakar Janaki N. , Chen Yu-Wen , Shih Nien-Shin , Weng Yi-Ting , Shui Jr-Wen 
Published: February 2022

AbstractIL-18 is emerging as an IL-22-induced and epithelium-derived cytokine which contributes to host defence against intestinal infection and inflammation. In contrast to its known role in Goblet cells, regulation of barrier function at the molecular level by IL-18 is much less explored. Here we show that IL-18 is a bona fide IL-22-regulated gate keeper for intestinal epithelial barrier. IL-22 promotes crypt immunity both via induction of phospho-Stat3 binding to theIl-18gene promoter and viaIl-18independent mechanisms. In organoid culture, while IL-22 primarily increases organoid size and inhibits expression of stem cell genes, IL-18 preferentially promotes organoid budding and induces signature genes of Lgr5+stem cells via Akt-Tcf4 signalling. During adherent-invasiveE. coli(AIEC) infection, systemic administration of IL-18 corrects compromised T-cell IFNγ production and restores Lysozyme+Paneth cells inIl-22−/−mice, but IL-22 administration fails to restore these parameters inIl-18−/−mice, thereby placing IL-22-Stat3 signalling upstream of the IL-18-mediated barrier defence function. IL-18 in return regulates Stat3-mediated anti-microbial response in Paneth cells, Akt-Tcf4-triggered expansion of Lgr5+stem cells to facilitate tissue repair, and AIEC clearance by promoting IFNγ+T cells.
Re-engineered BCG overexpressing cyclic di-AMP augments trained immunity and exhibits improved efficacy against bladder cancer
Authors: Singh Alok Kumar , Praharaj Monali , Lombardo Kara A. , Yoshida Takahiro , Matoso Andres , Baras Alex S. , Zhao Liang , Srikrishna Geetha , Huang Joy , Prasad Pankaj , Powell Jonathan D. , Kates Max , McConkey David , Pardoll Drew M. , Bishai William R. , Bivalacqua Trinity J. 
Published: February 2022

AbstractIn addition to its role as a TB vaccine, BCG has been shown to elicit heterologous protection against many other pathogens including viruses through a process termed trained immunity. Despite its potential as a broadly protective vaccine, little has been done to determine if BCG-mediated trained immunity levels can be optimized. Here we re-engineer BCG to express high levels of c-di-AMP, a PAMP recognized by stimulator of interferon genes (STING). We find that BCG overexpressing c-di-AMP elicits more potent signatures of trained immunity including higher pro-inflammatory cytokine responses, greater myeloid cell reprogramming toward inflammatory and activated states, and enhances epigenetic and metabolomic changes. In a model of bladder cancer, we also show that re-engineered BCG induces trained immunity and improved functionality. These results indicate that trained immunity levels and antitumor efficacy may be increased by modifying BCG to express higher levels of key PAMP molecules.
Restoring circadian gene profiles in clock networks using synthetic feedback control
Authors: Foo Mathias , Akman Ozgur E. , Bates Declan G. 
Published: February 2022

AbstractThe circadian system—an organism’s built-in biological clock—is responsible for orchestrating biological processes to adapt to diurnal and seasonal variations. Perturbations to the circadian system (e.g., pathogen attack, sudden environmental change) often result in pathophysiological responses (e.g., jetlag in humans, stunted growth in plants, etc.) In view of this, synthetic biologists are progressively adapting the idea of employing synthetic feedback control circuits to alleviate the effects of perturbations on circadian systems. To facilitate the design of such controllers, suitable models are required. Here, we extend our recently developed model for the plant circadian clock—termed the extended S-System model—to model circadian systems across different kingdoms of life. We then use this modeling strategy to develop a design framework, based on an antithetic integral feedback (AIF) controller, to restore a gene’s circadian profile when it is subject to loss-of-function due to external perturbations. The use of the AIF controller is motivated by its recent successful experimental implementation. Our findings provide circadian biologists with a systematic and general modeling and design approach for implementing synthetic feedback control of circadian systems.
Dataset on electrical single-family house and heat pump load profiles in Germany
Authors: Schlemminger Marlon , Ohrdes Tobias , Schneider Elisabeth , Knoop Michael 
Published: February 2022

AbstractThis paper describes a dataset of residential electricity household and heat pump load profiles, measured in 38 single-family houses in Northern Germany. We provide data per household of apparent, active and reactive power (W), voltage (V), current (A) and the power factor (no unit) in 10 seconds to 60 minutes temporal resolution from May 2018 to the end of 2020. We validated the dataset both in itself, comparing different measurements that should produce the same results, and externally to standard load profiles and found no major inconsistencies. We identified an average consumption per single-family house with 2.38 inhabitants of 2829 kWh for the household and an additional 4993 kWh for the heat pump. The dataset can support the understanding of patterns in electrical load curves and can help to estimate the additional load on distribution networks induced by heat pumps.
Transcriptome analysis of genes associated with autolysis of Coprinus comatus
Authors: Guo Hong-Bo , Zhang Zhi-Fei , Wang Jia-Qing , Wang Si-Yu , Yang Ji-Kang , Xing Xi-Yao , Qi Xiao-Jian , Yu Xiao-Dan 
Published: February 2022

AbstractCoprinus comatus, widely known as “Jituigu”, is an important commodity and food in China. The yield of C. comatus, however, is substantially reduced by the autolysis of the fruiting bodies after harvest. To gain insight into the molecular mechanism underlying this autolysis, we divided the growth of C. comatus fruiting bodies into four stages: infant stage (I), mature stage (M), discolored stage (D), and autolysis stage (A). We then subjected these stages to de novo transcriptomic analysis using high-throughput Illumina sequencing. A total of 12,946 unigenes were annotated and analyzed with the Gene Ontology (GO), Clusters of Orthologous Groups of proteins (COG), and Kyoto Encyclopedia of Genes and Genomes (KEGG). We analyzed the differentially expressed genes (DEGs) between stages I and M, M and D, and D and A. Because the changes from M to D are thought to be related to autolysis, we focused on the DEGs between these two stages. We found that the pathways related to metabolic activity began to vary in the transition from M to D, including pathways named as autophagy—yeast, peroxisome, and starch and sucrose metabolism. This study also speculates the possible process of the autolysis of Coprinus comatus. In addition, 20 genes of interest were analyzed by quantitative real-time PCR to verify their expression profiles at the four developmental stages. This study, which is the first to describe the transcriptome of C. comatus, provides a foundation for future studies concerning the molecular basis of the autolysis of its fruiting bodies.
Topological synchronization of chaotic systems
Authors: Lahav Nir , Sendiña-Nadal Irene , Hens Chittaranjan , Ksherim Baruch , Barzel Baruch , Cohen Reuven , Boccaletti Stefano 
Published: February 2022

AbstractA chaotic dynamics is typically characterized by the emergence of strange attractors with their fractal or multifractal structure. On the other hand, chaotic synchronization is a unique emergent self-organization phenomenon in nature. Classically, synchronization was characterized in terms of macroscopic parameters, such as the spectrum of Lyapunov exponents. Recently, however, we attempted a microscopic description of synchronization, called topological synchronization, and showed that chaotic synchronization is, in fact, a continuous process that starts in low-density areas of the attractor. Here we analyze the relation between the two emergent phenomena by shifting the descriptive level of topological synchronization to account for the multifractal nature of the visited attractors. Namely, we measure the generalized dimension of the system and monitor how it changes while increasing the coupling strength. We show that during the gradual process of topological adjustment in phase space, the multifractal structures of each strange attractor of the two coupled oscillators continuously converge, taking a similar form, until complete topological synchronization ensues. According to our results, chaotic synchronization has a specific trait in various systems, from continuous systems and discrete maps to high dimensional systems: synchronization initiates from the sparse areas of the attractor, and it creates what we termed as the ‘zipper effect’, a distinctive pattern in the multifractal structure of the system that reveals the microscopic buildup of the synchronization process. Topological synchronization offers, therefore, a more detailed microscopic description of chaotic synchronization and reveals new information about the process even in cases of high mismatch parameters.
Refractive index measurements of solid deuterium–tritium
Authors: Iwano Keisuke , Zhang Jiaqi , Iwamoto Akifumi , Iwasa Yuki , Shigemori Keisuke , Hara Masanori , Hatano Yuji , Norimatsu Takayoshi , Yamanoi Kohei 
Published: February 2022

AbstractPhysical properties of tritium (T) and deuterium (D) have been of great interest as a fuel for nuclear fusion. However, several kinds of the physical properties in a cryogenic environment have not been reported. Optical properties in liquid and solid phases are indispensable for the quality control of the DT fuel. We study the dependence of the refractive index of solid DT on temperature. A dedicated cryogenic system has been developed and forms a transparent solid DT in a prism cell. Refractive index measurements based on Snell’s law were conducted. The refractive indexes of solid DT are from 1.1618 ± 0.0002 to 1.1628 ± 0.0002 in the temperature range of 19.40 K to 17.89 K.