bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative analysis of energy use efficiency among Pakistani and Turkish wheat growers
Authors: Imran Muhammad , ul Haq Shamsheer , Ozcatalbas Orhan 
Published: August 2021

AbstractAgriculture is one of the high input energy using sectors which ultimately produces the output energy for the survival of human beings. Wheat is an important cereal in the agriculture production system. It is a major food crop and staple food for many countries in the world. Higher population growth has increased demand for wheat, and this demand has been met through the adoption of modern agricultural practices which are heavily dependent on energy. The current study was planned to examine the input energy use efficiency of rainfed wheat growers in Pakistan and Turkey (countries among the top 10 global wheat producers). A total of 119 wheat growers from the rainfed areas of both countries were randomly selected. The data envelopment analysis was executed to estimate the input energy use efficiency score of the growers. The results of the study revealed that almost a similar source of input energy is used in both countries in wheat cultivation. The largest input energy consumption in Turkey was nitrogen fertilizer (10,531.50 MJ ha−1), while in Pakistan was farmyard manure (12,837.32 MJ ha−1). The Turkish growers have higher energy use efficiency 2.42 as compared to Pakistani growers, whose energy use efficiency was 1.09. Results further revealed that there is a substantial potential for energy savings in both countries by optimizing energy use. The study concluded that the exchange of energy-efficient practices between both countries can significantly reduce energy use and improve the yield of wheat.
Recent Slowdown in the Decline of Arctic Sea Ice Volume Under Increasingly Warm Atmospheric and Oceanic Conditions
Authors: Zhang Jinlun 
Published: August 2021

AbstractA model study shows that the decline of Arctic sea ice volume (SIV) slows down during 2007–2020 with increasingly warm atmospheric and oceanic conditions. The slowdown of the SIV decline is because the decrease in ice export from the Arctic exceeds the decrease in net ice production within the Arctic. The relatively strong decrease in ice export occurs when the increase in ice motion is lower than the decrease in SIV. The relatively weak decrease in net ice production is due to strong increases in ice growth as thinner ice grows faster than thicker ice under freezing conditions. The ice growth increases are closely correlated with and benefit from increases in open water creation caused by enhanced ice divergence and shear as thinner ice is easier to deform.
A Unified Framework for Earthquake Sequences and the Growth of Geological Structure in Fold‐Thrust Belts
Authors: Mallick Rishav , Bürgmann Roland , Johnson Kaj , Hubbard Judith 
Published: August 2021

AbstractObservations of fold growth in fold‐thrust belt settings show that brittle deformation can be localized or distributed. Localized shear is associated with frictional slip on primary faults, while distributed brittle deformation is recognized in the folding of the bulk medium. The interplay of these processes is clearly seen in fault‐bend folds, which are folds cored by a fault with an abrupt change in dip (e.g., a ramp‐décollement system). While the kinematics of fault‐bend folding were described decades ago, the dynamics of these structures remain poorly understood, especially the evolution of fault slip and off‐fault deformation over different periods of the earthquake cycle. In order to investigate the dynamics of fault‐bend folding, we develop a numerical modeling framework that combines a long‐term elasto‐plastic model of folding in a layered medium with a rate‐state frictional model of fault strength evolution in order to simulate geologically and mechanically consistent earthquake sequences. In our simulations, slip on the ramp‐décollement fault and inelastic fold deformation are mechanically coupled processes that build geologic structure. As a result, we observe that folding of the crust (like fault slip) does not occur steadily in time but is modulated by earthquake cycle stresses. We suggest combining seismological and geodetic observations with geological fault models to uncover how elastic and inelastic crustal deformation generate fault‐bend folds. We find that distinguishing between the elastic and inelastic response of the crust to fault slip is possible only in the postseismic period following large earthquakes, indicating that for most fault systems this information currently remains inaccessible.
The Chemistry of Hyperalkaline Springs in Serpentinizing Environments: 1. The Composition of Free Gases in New Caledonia Compared to Other Springs Worldwide
Authors: Monnin Christophe , Quéméneur Marianne , Price Roy , Jeanpert Julie , Maurizot Pierre , Boulart Cédric , Donval Jean‐Pierre , Pelletier Bernard 
Published: August 2021

AbstractSerpentinization is a natural process that transforms ferromagnesian minerals such as olivine into serpentine and that produces waters at very high pH and gases enriched in methane (CH4) and hydrogen (H2). We report the composition of gases venting at two springs (Bain des Japonais and Rivière des Kaoris) of the serpentinizing environment of the Prony Bay (New Caledonia) collected eight times between 2011 and 2014, along with in situ measurements (temperature, pH, oxydo‐reduction potential, dissolved oxygen content) of on‐land alkaline springs of the Southern New Caledonia ophiolite. Venting gases are mainly composed of H2, CH4, and N2 and their composition has slightly varied during the 4‐year field survey. An elevated oxygen (O2) content in a high‐pH water sample is due to air uptake during surface flow. O2‐corrected gas compositions along with those published for gas data obtained at similar serpentinizing environments (Italy, Turkey, Philippines, and Oman) show that the H2 and CH4 concentrations display a linear correlation with a slope close to the value corresponding to the CH4 production from carbon dioxide rather from a less oxidized carbon such as carbon monoxide. Although these data are consistent with the stoichiometry of the Sabatier reaction, as such in the gas phase, it is also possible that microbial hydrogenotrophic methanogenesis takes place in the aqueous phase followed by degassing. A diagram is proposed that outlines the partitioning of H2 and CH4 between the gaseous and aqueous phases and the need to consider a two‐phase flow in the hydrology of these hyperalkaline environments.
Role of Microphysics and Convective Autoconversion for the Better Simulation of Tropical Intraseasonal Oscillations (MISO and MJO)
Authors: Dutta Ushnanshu , Hazra Anupam , Chaudhari Hemantkumar S. , Saha Subodh K. , Pokhrel Samir , Shiu Chein‐Jung , Chen Jen‐Ping 
Published: August 2021

AbstractThe seasonal prediction of the Indian summer monsoon (ISM) and Monsoon Intraseasonal Oscillations (MISO), as well as the Madden Julian Oscillations (MJO) that strongly modulate MISO, is of much importance to the agriculture sectors of the Indian Sub‐continent. This study highlights the importance of selecting proper “autoconversion” coefficients for precipitation formation in Coupled Global Climate Model's convective and microphysical schemes in simulating MISO and MJO. With a series of sensitivity experiments, we systematically examined the convective autoconversion and microphysical autoconversion coefficients in the National Centers for Environmental Prediction Coupled Forecast System version 2 (CFSv2). The mean and intraseasonal features of MISO and MJO are improved with a proper combination of autoconversion coefficients, which not only provide a better partition of cloud water and ice but also better feedback between the large‐scale condensation and convective parameterization. The results demonstrate a road map for the improvement of MISO as well as MJO simulation using a coupled climate model.
Therapeutic targets and interventional strategies in COVID-19: mechanisms and clinical studies
Authors: Zhou Yu-Wen , Xie Yao , Tang Lian-Sha , Pu Dan , Zhu Ya-Juan , Liu Ji-Yan , Ma Xue-Lei 
Published: August 2021

AbstractOwing to the limitations of the present efforts on drug discovery against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the lack of the understanding of the biological regulation mechanisms underlying COVID-19, alternative or novel therapeutic targets for COVID-19 treatment are still urgently required. SARS-CoV-2 infection and immunity dysfunction are the two main courses driving the pathogenesis of COVID-19. Both the virus and host factors are potential targets for antiviral therapy. Hence, in this study, the current therapeutic strategies of COVID-19 have been classified into “target virus” and “target host” categories. Repurposing drugs, emerging approaches, and promising potential targets are the implementations of the above two strategies. First, a comprehensive review of the highly acclaimed old drugs was performed according to evidence-based medicine to provide recommendations for clinicians. Additionally, their unavailability in the fight against COVID-19 was analyzed. Next, a profound analysis of the emerging approaches was conducted, particularly all licensed vaccines and monoclonal antibodies (mAbs) enrolled in clinical trials against primary SARS-CoV-2 and mutant strains. Furthermore, the pros and cons of the present licensed vaccines were compared from different perspectives. Finally, the most promising potential targets were reviewed, and the update of the progress of treatments has been summarized based on these reviews.
Circ_0057558 promotes nonalcoholic fatty liver disease by regulating ROCK1/AMPK signaling through targeting miR-206
Authors: Chen Xi , Tan Qing-Qing , Tan Xin-Rui , Li Shi-Jun , Zhang Xing-Xing 
Published: August 2021

AbstractNonalcoholic fatty liver disease (NAFLD) is one of the most prevalent chronic liver disorders that is featured by the extensive deposition of fat in the hepatocytes. Current treatments are very limited due to its unclear pathogenesis. Here, we investigated the function of circ_0057558 and miR-206 in NAFLD. High-fat diet (HFD) feeding mouse was used as an in vivo NAFLD model and long-chain-free fatty acid (FFA)-treated liver cells were used as an in vitro NAFLD model. qRT-PCR was used to measure levels of miR-206, ROCK1 mRNA, and circ_0057558, while Western blotting was employed to determine protein levels of ROCK1, p-AMPK, AMPK, and lipogenesis-related proteins. Immunohistochemistry were performed to examine ROCK1 level. Oil-Red O staining was used to assess the lipid deposition in cells. ELISA was performed to examine secreted triglyceride (TG) level. Dual-luciferase assay was used to validate interactions of miR-206/ROCK1 and circ_0057558/miR-206. RNA immunoprecipitation was employed to confirm the binding of circ_0057558 with miR-206. Circ_0057558 was elevated while miR-206 was reduced in both in vivo and in vitro NAFLD models. miR-206 directly bound with ROCK1 3’-UTR and suppressed lipogenesis and TG secretion through targeting ROCK1/AMPK signaling. Circ_0057558 directly interacted with miR-206 to disinhibit ROCK1/AMPK signaling. Knockdown of circ_0057558 or overexpression of miR-206 inhibited lipogenesis, TG secretion and expression of lipogenesis-related proteins. ROCK1 knockdown reversed the effects of circ_0057558 overexpression. Injection of miR-206 mimics significantly ameliorated NAFLD progression in vivo. Circ_0057558 acts as a miR-206 sponge to de-repress the ROCK1/AMPK signaling and facilitates lipogenesis and TG secretion, which greatly contributes to NAFLD development and progression.
MIR22HG inhibits breast cancer progression by stabilizing LATS2 tumor suppressor
Authors: Deng Xiaochong , Ye Danrong , Hua Kaiyao , Song Hongming , Luo Qifeng , Munankarmy Amik , Liu Diya , Zhou Baian , Zheng Wenfang , Zhou Xiqian , Ji Changle , Wang Xuehui , Yu Yunhe , Fang Lin 
Published: August 2021

AbstractThe long noncoding RNA called MIR22 host gene (MIR22HG) was previously identified as a tumor suppressor in several cancers. However, the biological function of MIR22HG in breast cancer remains unknown. In this study, we aimed to determine the function and molecular mechanism of MIR22HG in breast cancer progression using transcriptomics and biotechnological techniques. Our results showed that MIR22HG expression was lower in the cancerous tissues than in the paired adjacent normal breast tissues. Additionally, MIR22HG was found to be mainly located in the cytoplasm and acted as a miR-629-5p sponge. Notably, MIR22HG stabilized the expression of large tumor suppressor 2 (LATS2), which promoted the LATS2-dependent phosphorylation of YAP1 and suppressed the expression of its downstream target oncogenes, thereby inhibiting the proliferation and migration of breast cancer cells. Therefore, our findings reveal the MIR22HG-dependent inhibition of breast cancer cell proliferation and migration via the miR-629-5p/LATS2 pathway, providing new insights and identifying novel therapeutic targets for breast cancer treatment.
Amnion signals are essential for mesoderm formation in primates
Authors: Yang Ran , Goedel Alexander , Kang Yu , Si Chenyang , Chu Chu , Zheng Yi , Chen Zhenzhen , Gruber Peter J. , Xiao Yao , Zhou Chikai , Witman Nevin , Eroglu Elif , Leung Chuen-Yan , Chen Yongchang , Fu Jianping , Ji Weizhi , Lanner Fredrik , Niu Yuyu , Chien Kenneth R. 
Published: August 2021

AbstractEmbryonic development is largely conserved among mammals. However, certain genes show divergent functions. By generating a transcriptional atlas containing >30,000 cells from post-implantation non-human primate embryos, we uncover that ISL1, a gene with a well-established role in cardiogenesis, controls a gene regulatory network in primate amnion. CRISPR/Cas9-targeting of ISL1 results in non-human primate embryos which do not yield viable offspring, demonstrating that ISL1 is critically required in primate embryogenesis. On a cellular level, mutant ISL1 embryos display a failure in mesoderm formation due to reduced BMP4 signaling from the amnion. Via loss of function and rescue studies in human embryonic stem cells we confirm a similar role of ISL1 in human in vitro derived amnion. This study highlights the importance of the amnion as a signaling center during primate mesoderm formation and demonstrates the potential of in vitro primate model systems to dissect the genetics of early human embryonic development.
An integrated in vivo/in vitro framework to enhance cell-free biosynthesis with metabolically rewired yeast extracts
Authors: Rasor Blake J. , Yi Xiunan , Brown Hunter , Alper Hal S. , Jewett Michael C. 
Published: August 2021

AbstractCell-free systems using crude cell extracts present appealing opportunities for designing biosynthetic pathways and enabling sustainable chemical synthesis. However, the lack of tools to effectively manipulate the underlying host metabolism in vitro limits the potential of these systems. Here, we create an integrated framework to address this gap that leverages cell extracts from host strains genetically rewired by multiplexed CRISPR-dCas9 modulation and other metabolic engineering techniques. As a model, we explore conversion of glucose to 2,3-butanediol in extracts from flux-enhanced Saccharomyces cerevisiae strains. We show that cellular flux rewiring in several strains of S. cerevisiae combined with systematic optimization of the cell-free reaction environment significantly increases 2,3-butanediol titers and volumetric productivities, reaching productivities greater than 0.9 g/L-h. We then show the generalizability of the framework by improving cell-free itaconic acid and glycerol biosynthesis. Our coupled in vivo/in vitro metabolic engineering approach opens opportunities for synthetic biology prototyping efforts and cell-free biomanufacturing.
Bioengineered embryoids mimic post-implantation development in vitro
Authors: Girgin Mehmet U. , Broguiere Nicolas , Hoehnel Sylke , Brandenberg Nathalie , Mercier Bastien , Arias Alfonso Martinez , Lutolf Matthias P. 
Published: August 2021

AbstractThe difficulty of studying post-implantation development in mammals has sparked a flurry of activity to develop in vitro models, termed embryoids, based on self-organizing pluripotent stem cells. Previous approaches to derive embryoids either lack the physiological morphology and signaling interactions, or are unconducive to model post-gastrulation development. Here, we report a bioengineering-inspired approach aimed at addressing this gap. We employ a high-throughput cell aggregation approach to simultaneously coax mouse embryonic stem cells into hundreds of uniform epiblast-like aggregates in a solid matrix-free manner. When co-cultured with mouse trophoblast stem cell aggregates, the resulting hybrid structures initiate gastrulation-like events and undergo axial morphogenesis to yield structures, termed EpiTS embryoids, with a pronounced anterior development, including brain-like regions. We identify the presence of an epithelium in EPI aggregates as the major determinant for the axial morphogenesis and anterior development seen in EpiTS embryoids. Our results demonstrate the potential of EpiTS embryoids to study peri-gastrulation development in vitro.
Seasonal Arctic sea ice forecasting with probabilistic deep learning
Authors: Andersson Tom R. , Hosking J. Scott , Pérez-Ortiz María , Paige Brooks , Elliott Andrew , Russell Chris , Law Stephen , Jones Daniel C. , Wilkinson Jeremy , Phillips Tony , Byrne James , Tietsche Steffen , Sarojini Beena Balan , Blanchard-Wrigglesworth Eduardo , Aksenov Yevgeny , Downie Rod , Shuckburgh Emily 
Published: August 2021

AbstractAnthropogenic warming has led to an unprecedented year-round reduction in Arctic sea ice extent. This has far-reaching consequences for indigenous and local communities, polar ecosystems, and global climate, motivating the need for accurate seasonal sea ice forecasts. While physics-based dynamical models can successfully forecast sea ice concentration several weeks ahead, they struggle to outperform simple statistical benchmarks at longer lead times. We present a probabilistic, deep learning sea ice forecasting system, IceNet. The system has been trained on climate simulations and observational data to forecast the next 6 months of monthly-averaged sea ice concentration maps. We show that IceNet advances the range of accurate sea ice forecasts, outperforming a state-of-the-art dynamical model in seasonal forecasts of summer sea ice, particularly for extreme sea ice events. This step-change in sea ice forecasting ability brings us closer to conservation tools that mitigate risks associated with rapid sea ice loss.
Self-assembling human heart organoids for the modeling of cardiac development and congenital heart disease
Authors: Lewis-Israeli Yonatan R. , Wasserman Aaron H. , Gabalski Mitchell A. , Volmert Brett D. , Ming Yixuan , Ball Kristen A. , Yang Weiyang , Zou Jinyun , Ni Guangming , Pajares Natalia , Chatzistavrou Xanthippi , Li Wen , Zhou Chao , Aguirre Aitor 
Published: August 2021

AbstractCongenital heart defects constitute the most common human birth defect, however understanding of how these disorders originate is limited by our ability to model the human heart accurately in vitro. Here we report a method to generate developmentally relevant human heart organoids by self-assembly using human pluripotent stem cells. Our procedure is fully defined, efficient, reproducible, and compatible with high-content approaches. Organoids are generated through a three-step Wnt signaling modulation strategy using chemical inhibitors and growth factors. Heart organoids are comparable to age-matched human fetal cardiac tissues at the transcriptomic, structural, and cellular level. They develop sophisticated internal chambers with well-organized multi-lineage cardiac cell types, recapitulate heart field formation and atrioventricular specification, develop a complex vasculature, and exhibit robust functional activity. We also show that our organoid platform can recreate complex metabolic disorders associated with congenital heart defects, as demonstrated by an in vitro model of pregestational diabetes-induced congenital heart defects.
Oral immune dysfunction is associated with the expansion of FOXP3+PD-1+Amphiregulin+ T cells during HIV infection
Authors: Bhaskaran N. , Schneider E. , Faddoul F. , Paes da Silva A. , Asaad R. , Talla A. , Greenspan N. , Levine A. D. , McDonald D. , Karn J. , Lederman M. M. , Pandiyan P. 
Published: August 2021

AbstractResidual systemic inflammation and mucosal immune dysfunction persist in people living with HIV, despite treatment with combined anti-retroviral therapy, but the underlying immune mechanisms are poorly understood. Here we report that the altered immune landscape of the oral mucosa of HIV-positive patients on therapy involves increased TLR and inflammasome signaling, localized CD4+ T cell hyperactivation, and, counterintuitively, enrichment of FOXP3+ T cells. HIV infection of oral tonsil cultures in vitro causes an increase in FOXP3+ T cells expressing PD-1, IFN-γ, Amphiregulin and IL-10. These cells persist even in the presence of anti-retroviral drugs, and further expand when stimulated by TLR2 ligands and IL-1β. Mechanistically, IL-1β upregulates PD-1 expression via AKT signaling, and PD-1 stabilizes FOXP3 and Amphiregulin through a mechanism involving asparaginyl endopeptidase, resulting in FOXP3+ cells that are incapable of suppressing CD4+ T cells in vitro. The FOXP3+ T cells that are abundant in HIV-positive patients are phenotypically similar to the in vitro cultured, HIV-responsive FOXP3+ T cells, and their presence strongly correlates with CD4+ T cell hyper-activation. This suggests that FOXP3+ T cell dysregulation might play a role in the mucosal immune dysfunction of HIV patients on therapy.
A guanidine-degrading enzyme controls genomic stability of ethylene-producing cyanobacteria
Authors: Wang Bo , Xu Yao , Wang Xin , Yuan Joshua S. , Johnson Carl H. , Young Jamey D. , Yu Jianping 
Published: August 2021

AbstractRecent studies have revealed the prevalence and biological significance of guanidine metabolism in nature. However, the metabolic pathways used by microbes to degrade guanidine or mitigate its toxicity have not been widely studied. Here, via comparative proteomics and subsequent experimental validation, we demonstrate that Sll1077, previously annotated as an agmatinase enzyme in the model cyanobacterium Synechocystis sp. PCC 6803, is more likely a guanidinase as it can break down guanidine rather than agmatine into urea and ammonium. The model cyanobacterium Synechococcus elongatus PCC 7942 strain engineered to express the bacterial ethylene-forming enzyme (EFE) exhibits unstable ethylene production due to toxicity and genomic instability induced by accumulation of the EFE-byproduct guanidine. Co-expression of EFE and Sll1077 significantly enhances genomic stability and enables the resulting strain to achieve sustained high-level ethylene production. These findings expand our knowledge of natural guanidine degradation pathways and demonstrate their biotechnological application to support ethylene bioproduction.