bluuebunny/crossref_metadata_2025_split huggingface dataset:
Short‐Wavelength Electrostatic Wave Measurement Using MMS Spacecraft
Authors: Lalti Ahmad , Khotyaintsev Yuri V. , Graham Daniel B. 
Published: April 2023

AbstractDetermination of the wave mode of short‐wavelength electrostatic waves along with their generation mechanism requires reliable measurement of the wave electric field. We show that for such waves the electric field measured by Magnetospheric MultiScale becomes unreliable when the wavelength is close to the probe‐to‐probe separation. We develop a method, based on spin‐plane interferometry, to reliably determine the full three‐dimensional wave vector of the observed waves. We test the method on synthetic data and then apply it to ion acoustic wave bursts measured in the solar wind. By studying the statistical properties of ion acoustic waves in the solar wind, we retrieve the known results that the wave propagation is predominantly field aligned. We also determine the wavelength of the waves. We find that the nominal value is around 100 m, which when normalized to the Debye length corresponds to scales between 10 and 20 Debye lengths.
Quantifying the Impact of Land Use and Land Cover Change on Moisture Recycling With Convection‐Permitting WRF‐Tagging Modeling in the Agro‐Pastoral Ecotone of Northern China
Authors: Wang Xuejin , Zhang Zhenyu , Zhang Baoqing , Tian Lei , Tian Jie , Arnault Joël , Kunstmann Harald , He Chansheng 
Published: April 2023

AbstractLand use and land cover change (LUCC) can influence the regional atmospheric water budget. In this study, the Weather Research and Forecasting model embedded with evapotranspiration (ET)‐tagging (WRF‐tagging) is used to investigate the atmospheric pathways of ET as well as where and to what extent ET returns as precipitation (P) in the agro‐pastoral ecotone of northern China (APENC). First, we updated the default land use and vegetation indices in the WRF‐tagging with high‐resolution and real‐time datasets. WRF‐tagging modeling reproduces the spatial distribution of P and ET reasonably after updating surface characteristics. Second, we analyzed and quantified the contribution of ET to atmospheric moisture and regional P in the APENC. The water vapor originating as ET is advected in the atmosphere below 600 hPa to hundreds of kilometers by the prevailing winds. Moisture recycling shows that 5.83% of P comes from local ET during the growing season in the core region of the APENC. Furthermore, to quantify the impact of LUCC on moisture recycling, we designed two different vegetation scenarios (Afforestation and Degradation) by changing land use and vegetation indices in the model. Results show that the precipitation recycling ratio increased to 6.31% in the Afforestation scenario, and decreased to 5.19% in the Degradation scenario, demonstrating the non‐neglectable positive feedback of vegetation on P. An analysis of land surface‐precipitation feedback processes indicates that the LUCC‐induced change in precipitation efficiency dominates P changes. Our findings highlight the importance of LUCC on local and regional moisture recycling in the APENC.
The Impact of a Land‐Sea Contrast on Convective Aggregation in Radiative‐Convective Equilibrium
Authors: Dingley Beth , Dagan Guy , Stier Philip , Herbert Ross 
Published: April 2023

AbstractConvective aggregation is an important atmospheric phenomenon which frequently occurs in idealized models in radiative‐convective equilibrium (RCE), where the effects of land, rotation, sea surface temperature gradients, and the diurnal cycle are often removed. This aggregation is often triggered and maintained by self‐generated radiatively driven circulations, for which longwave feedbacks are essential. Many questions remain over how important the driving processes of aggregation in idealized models are in the real atmosphere. We approach this question by adding a continentally sized, idealized tropical rainforest island into an RCE model to investigate how land‐sea contrasts impact convective aggregation and its mechanisms. We show that convection preferentially forms over the island persistently in our simulation. This is forced by a large‐scale, thermally driven circulation. First, a sea‐breeze circulation is triggered by the land‐sea thermal contrast, driven by surface sensible heating. This sea‐breeze circulation triggers convection which then generates longwave heating anomalies. Through mechanism denial tests we find that removing the longwave feedbacks reduces the large‐scale effects of aggregation but does not prevent aggregation from occurring, and thus we highlight there must be another process aiding the aggregation of convection. We also show, by varying the island size, that the aggregated convective cluster appears to have a maximum spatial extent of (10,000 km). These results highlight that the mechanisms of idealized aggregation remain relevant when land is included in the model, and therefore these mechanisms could help us understand convective organization in the real world.
Enhanced Monsoon‐Driven Upwelling in Southeast Asia During the Little Ice Age
Authors: Chen Mengli , Martin Patrick , Ren Haojia , Zhang Run , Samanta Dhrubajyoti , Chen Yi‐Chi , Hughen Konrad A. , Phan Kim Hoang , Vo Si Tuan , Goodkin Nathalie F. 
Published: April 2023

AbstractClimate change impacts ocean nutrient availability and will likely alter the marine food web. While climate models predict decreased average ocean productivity, the extent of these changes, especially in the marginal seas upon which large human populations depend, is not well understood. Here, we reconstructed changes in seawater phosphate concentration and nitrate source over the past 400 years, which reveals a more than 50% decline in residence time of seawater phosphate, and 8%–48% decline in subsurface nitrogen supply following the coldest period of Little Ice Age. Our data indicates a link between surface ocean nutrient supply and the East Asian Summer Monsoon strength in an economically important marginal sea. As climate models predict that the East Asian Summer monsoon will strengthen in the future, our study implies that surface ocean primary productivity may increase in the South China Sea, contrary to the predicted decrease in global average ocean productivity.
Structure of Post‐Midnight Enhancements in Electron Density at the Low Latitude F‐Layer Ionosphere
Authors: Liu Libo , Yang Yuyan , Zhang Ruilong , Tariq M. Arslan , Le Huijun , Chen Yiding , Zhang Hui , Li Guozhu , Yue Xinan 
Published: April 2023

AbstractIt has previously found that at Sanya (109.6°E, 18.3°N) a post‐midnight enhancement in the F2‐layer peak electron density (NmF2) is often accompanied by the increase in the bottom side F layer electron density (Ne) and a reduction in the top side F layer Ne. We conduct a case study to explore the complete spatial coverage of the post‐midnight enhancements of electron density in the low latitude ionosphere. The total electron content (TEC) data are retrieved from the Beidou Geostationary Earth Orbit (GEO) satellite signals recorded by a network of Global Navigation Satellite System (GNSS) receivers in Asia‐Australia. The F2‐layer peak parameters and the altitudinal profiles of Ne are measured by the ionosonde, and incoherent scatter radar at Sanya (109.6°E, 18.3°N). The GEO‐TEC does not always completely follow the enhancement of NmF2. The enhancements may peak roughly simultaneously or with significant time shifts in the west‐east direction, even in the GEO‐TEC series recorded by a GNSS receiver in an event, which indicates possibly the enhancement of different longitudinal scales. Further, in the cases the enhancement is clustered in a limited area. The low latitude enhancements show a hemispheric asymmetry; they occur mainly in the northern hemisphere and usually have no correspondingly magnetic conjugate symmetrical features in the southern hemisphere. The hemispheric asymmetry of the enhancements highlights that both the field‐aligned plasma transport and electric fields are possibly responsible for regulating the limited spatial presence of post‐midnight enhancements in the low latitude ionosphere.
Genomic insights into the coupling of aChlorella-like microeukaryote and sulfur bacteria in the chemocline of permanently stratified Lake Cadagno
Authors: Saini Jaspreet S , Manni Mosè , Hassler Christel , Cable Rachel N , Duhaime Melissa B , Zdobnov Evgeny M 
Published: April 2023

AbstractMeromictic Lake Cadagno is a permanently stratified system with a persistent microbial bloom within the oxic-anoxic boundary called the chemocline. The association between oxygenic and anoxygenic photosynthesis within the chemocline has been known for at least two decades. Although anoxygenic purple and green sulfur bacteria have been well studied, reports on oxygenic phytoplankton have remained sparse since their discovery in the 1920s. Nearly a century later, this study presents the first near-complete genome of a photosynthetic microbial eukaryote from the chemocline of Lake Cadagno, provisionally named Chlorella-like MAG. The 18.9 Mbp nuclear genome displays a high GC content (71.5%), and the phylogenetic placement suggests that it is a novel species of the genus Chlorella of Chlorophytes. Functional annotation of the Chlorella-like metagenome-assembled genome predicted 10,732 protein-coding genes, with an approximate 0.6% proportion potentially involved in carbon, sulfur, and nitrogen (C, N, and S) metabolism. In addition to C4 photosynthesis, this study detected genes for heat shock proteins (HSPs) in the Chlorella-like algae, consistent with the other Chlorella species. Altogether, the genomic insights in this study suggest the cooperation of photosynthetic algae with phototrophic sulfur bacteria via C, N, and S metabolism, which may aid their collective persistence in the Lake Cadagno chemocline. Furthermore, this work additionally presents the chloroplast genome of Cryptomonas-like species, which was likely to be presumed as cyanobacteria in previous studies because of the presence of phycobilisomes.
Mesophilic and thermophilic viruses are associated with nutrient cycling during hyperthermophilic composting
Authors: Liao Hanpeng , Liu Chen , Ai Chaofan , Gao Tian , Yang Qiu-E , Yu Zhen , Gao Shaoming , Zhou Shungui , Friman Ville-Petri 
Published: April 2023

Abstract
While decomposition of organic matter by bacteria plays a major role in nutrient cycling in terrestrial ecosystems, the significance of viruses remains poorly understood. Here we combined metagenomics and metatranscriptomics with temporal sampling to study the significance of mesophilic and thermophilic bacteria and their viruses on nutrient cycling during industrial-scale hyperthermophilic composting (HTC). Our results show that virus-bacteria density dynamics and activity are tightly coupled, where viruses specific to mesophilic and thermophilic bacteria track their host densities, triggering microbial community succession via top-down control during HTC. Moreover, viruses specific to mesophilic bacteria encoded and expressed several auxiliary metabolic genes (AMGs) linked to carbon cycling, impacting nutrient turnover alongside bacteria. Nutrient turnover correlated positively with virus–host ratio, indicative of a positive relationship between ecosystem functioning, viral abundances, and viral activity. These effects were predominantly driven by DNA viruses as most detected RNA viruses were associated with eukaryotes and not associated with nutrient cycling during the thermophilic phase of composting. Our findings suggest that DNA viruses could drive nutrient cycling during HTC by recycling bacterial biomass through cell lysis and by expressing key AMGs. Viruses could hence potentially be used as indicators of microbial ecosystem functioning to optimize productivity of biotechnological and agricultural systems.
Heroin and its metabolites: relevance to heroin use disorder
Authors: Milella Michele Stanislaw , D’Ottavio Ginevra , De Pirro Silvana , Barra Massimo , Caprioli Daniele , Badiani Aldo 
Published: April 2023

AbstractHeroin is an opioid agonist commonly abused for its rewarding effects. Since its synthesis at the end of the nineteenth century, its popularity as a recreational drug has ebbed and flowed. In the last three decades, heroin use has increased again, and yet the pharmacology of heroin is still poorly understood. After entering the body, heroin is rapidly deacetylated to 6-monoacetylmorphine (6-MAM), which is then deacetylated to morphine. Thus, drug addiction literature has long settled on the notion that heroin is little more than a pro-drug. In contrast to these former views, we will argue for a more complex interplay among heroin and its active metabolites: 6-MAM, morphine, and morphine-6-glucuronide (M6G). In particular, we propose that the complex temporal pattern of heroin effects results from the sequential, only partially overlapping, actions not only of 6-MAM, morphine, and M6G, but also of heroin per se, which, therefore, should not be seen as a mere brain-delivery system for its active metabolites. We will first review the literature concerning the pharmacokinetics and pharmacodynamics of heroin and its metabolites, then examine their neural and behavioral effects, and finally discuss the possible implications of these data for a better understanding of opioid reward and heroin addiction. By so doing we hope to highlight research topics to be investigated by future clinical and pre-clinical studies.
Orbitofrontal cortex microRNAs support long-lasting heroin seeking behavior in male rats
Authors: Zanda Mary Tresa , Floris Gabriele , Daws Stephanie E. 
Published: April 2023

AbstractRecovery from opioid use disorder (OUD) and maintenance of abstinence from opioid use is hampered by perseverant drug cravings that may persist for months after cessation of drug use. Drug cravings can intensify during the abstinence period, a phenomenon referred to as the ‘incubation of craving’ that has been well-described in preclinical studies. We previously reported that animals that self-administered heroin at a dosage of 0.075 mg/kg/infusion (HH) paired with discrete drug cues displayed robust incubation of heroin craving behavior after 21 days (D) of forced abstinence, an effect that was not observed with a lower dosage (0.03 mg/kg/infusion; HL). Here, we sought to elucidate molecular mechanisms underlying long-term heroin seeking behavior by profiling microRNA (miRNA) pathways in the orbitofrontal cortex (OFC), a brain region that modulates incubation of heroin seeking. miRNAs are small noncoding RNAs with long half-lives that have emerged as critical regulators of drug seeking behavior but their expression in the OFC has not been examined in any drug exposure paradigm. We employed next generation sequencing to detect OFC miRNAs differentially expressed after 21D of forced abstinence between HH and HL animals, and proteomics analysis to elucidate miRNA-dependent translational neuroadaptations. We identified 55 OFC miRNAs associated with incubation of heroin craving, including miR-485-5p, which was significantly downregulated following 21D forced abstinence in HH but not HL animals. We bidirectionally manipulated miR-485-5p in the OFC to demonstrate that miR-485-5p can regulate long-lasting heroin seeking behavior after extended forced abstinence. Proteomics analysis identified 45 proteins selectively regulated in the OFC of HH but not HL animals that underwent 21D forced abstinence, of which 7 were putative miR-485-5p target genes. Thus, the miR-485-5p pathway is dysregulated in animals with a phenotype of persistent heroin craving behavior and OFC miR-485-5p pathways may function to support long-lasting heroin seeking.
Immunological and prognostic significance of tumour necrosis in colorectal cancer
Authors: Kastinen Meeri , Sirniö Päivi , Elomaa Hanna , Ahtiainen Maarit , Väyrynen Sara A. , Herzig Karl-Heinz , Meriläinen Sanna , Aro Raila , Häivälä Reetta , Rautio Tero , Saarnio Juha , Wirta Erkki-Ville , Helminen Olli , Seppälä Toni T. , Kuopio Teijo , Böhm Jan , Tuomisto Anne , Mecklin Jukka-Pekka , Mäkinen Markus J. , Väyrynen Juha P. 
Published: April 2023

Abstract
Background
Colorectal cancer (CRC) causes the second most cancer deaths worldwide, but the disease course varies according to tumour characteristics and immunological factors. Our objective was to examine the associations of tumour necrosis with tumour characteristics, immune cell infiltrates, serum cytokine concentrations, as well as prognosis in CRC.

Methods
Three independent CRC cohorts, including 1413 patients, were analysed. Associations of the areal percentage of tumour necrosis with clinicopathologic parameters, tumour infiltrating immune cells, cytokine concentrations in systemic and mesenteric vein blood, and survival were examined.

Results
Higher tumour necrosis percentage associated with shorter colorectal cancer-specific survival independent of tumour grade, T, N or M-class, mismatch repair status, BRAF status, and other possible confounding factors. In the largest cohort (N = 1100), the HR for high tumour necrosis percentage (≥40% vs. <3%) was 3.22 (95% CI 1.68–6.17, Ptrend < 0.0001). Tumour necrosis percentage positively correlated with peripheral serum levels of CXCL8, a proinflammatory chemokine, and negatively correlated with mesenteric serum levels of CXCL10 and mast cell densities in the invasive margin of the tumour.

Conclusions
Our results support the value of tumour necrosis as a prognostic factor in colorectal cancer. CXCL8 may have a role in the systemic effects of tumour necrosis.
BCL-G: 20 years of research on a non-typical protein from the BCL-2 family
Authors: Hartman Mariusz L. , Czyz Malgorzata 
Published: April 2023

AbstractProteins from the BCL-2 family control cell survival and apoptosis in health and disease, and regulate apoptosis-unrelated cellular processes. BCL-Gonad (BCL-G, also known as BCL2-like 14) is a non-typical protein of the family as its long isoform (BCL-GL) consists of BH2 and BH3 domains without the BH1 motif. BCL-G is predominantly expressed in normal testes and different organs of the gastrointestinal tract. The complexity of regulatory mechanisms of BCL-G expression and post-translational modifications suggests that BCL-G may play distinct roles in different types of cells and disorders. While several genetic alterations of BCL2L14 have been reported, gene deletions and amplifications prevail, which is also confirmed by the analysis of sequencing data for different types of cancer. Although the studies validating the phenotypic consequences of genetic manipulations of BCL-G are limited, the role of BCL-G in apoptosis has been undermined. Recent studies using gene-perturbation approaches have revealed apoptosis-unrelated functions of BCL-G in intracellular trafficking, immunomodulation, and regulation of the mucin scaffolding network. These studies were, however, limited mainly to the role of BCL-G in the gastrointestinal tract. Therefore, further efforts using state-of-the-art methods and various types of cells are required to find out more about BCL-G activities. Deciphering the isoform-specific functions of BCL-G and the BCL-G interactome may result in the designing of novel therapeutic approaches, in which BCL-G activity will be either imitated using small-molecule BH3 mimetics or inhibited to counteract BCL-G upregulation. This review summarizes two decades of research on BCL-G.
The hunger strikes back: an epigenetic memory for autophagy
Authors: González-Rodríguez Patricia , Füllgrabe Jens , Joseph Bertrand 
Published: April 2023

AbstractHistorical and demographical human cohorts of populations exposed to famine, as well as animal studies, revealed that exposure to food deprivation is associated to lasting health-related effects for the exposed individuals, as well as transgenerational effects in their offspring that affect their diseases’ risk and overall longevity. Autophagy, an evolutionary conserved catabolic process, serves as cellular response to cope with nutrient starvation, allowing the mobilization of an internal source of stored nutrients and the production of energy. We review the evidence obtained in multiple model organisms that support the idea that autophagy induction, including through dietary regimes based on reduced food intake, is in fact associated to improved health span and extended lifespan. Thereafter, we expose autophagy-induced chromatin remodeling, such as DNA methylation and histone posttranslational modifications that are known heritable epigenetic marks, as a plausible mechanism for transgenerational epigenetic inheritance of hunger.
Radiation induces IRAK1 expression to promote radioresistance by suppressing autophagic cell death via decreasing the ubiquitination of PRDX1 in glioma cells
Authors: Li Jing , Sun Yuchen , Zhao Xu , Ma Yuan , Xie Yuchen , Liu Siqi , Hui Beina , Shi Xiaobo , Sun Xuanzi , Zhang Xiaozhi 
Published: April 2023

AbstractRadiotherapy is the standard adjuvant treatment for glioma patients; however, the efficacy is limited by radioresistance. The function of Interleukin-1 receptor associated kinase 1 (IRAK1) in tumorigenesis and radioresistance remains to be elucidated. IRAK1 expression and its correlation with prognosis were analyzed in glioma tissues. We found that glioma patients with overexpressed IRAK1 show a poor prognosis. Notably, ionizing radiation (IR) remarkably induces IRAK1 expression, which was decreased by STING antagonist H-151 treatment. JASPAR prediction, ChIP assays, and dual luciferase reporter assays indicated that transcription factor FOXA2, suppressed by STING inhibition, directly binds to the IRAK1 promoter region and activates its transcription. IRAK1 knockdown inhibits malignancy and enhances the radiosensitivity of glioma in vitro and in vivo. To explore the potential IRAK1 interacting targets mediating the radioresistance of glioma cells, IP/Co-IP, LC-MS/MS, GST pull-down, and ubiquitination analyses were conducted. Mechanistically, IRAK1 bound to PRDX1, a major member of antioxidant enzymes, and further prevents ubiquitination and degradation of PRDX1 mediated by E3 ubiquitin ligase HECTD3; Both the DOC and HECT domains of HECTD3 directly interacted with PRDX1 protein. Overexpression of PRDX1 reverses the radiotherapy sensitization effect of IRAK1 depletion by diminishing autophagic cell death. These results suggest the IRAK1-PRDX1 axis provides a potential therapeutic target for glioma patients.
PLCG2 can exist in eccDNA and contribute to the metastasis of non-small cell lung cancer by regulating mitochondrial respiration
Authors: Yang Yongfeng , Yang Ying , Huang Hong , Song Tingting , Mao Shengqiang , Liu Dan , Zhang Li , Li Weimin 
Published: April 2023

AbstractExtrachromosomal circular DNAs (eccDNAs) participate in tumorigenesis and tumor progression. However, the role and mechanism of eccDNAs have yet to be elucidated in non-small cell lung cancer (NSCLC). In our research, three surgically matched NSCLC tissue samples, NSCLC cell lines (H1299, A549, and H460), and a normal lung cell line (MRC-5) were used as study objects. High-throughput eccDNA sequencing and bioinformatics analysis were performed to study the distribution pattern and level of eccDNA expression. The upregulated candidate eccDNA-encoding PLCG2 was validated by routine PCR. Plasmid transfection, RNA interference, qRT‒PCR and western blotting experiments were used to verify the expression level of PLCG2. Our results showed that the chromosome distribution, length distribution, and genomic annotation of the eccDNAs were comparable between the NSCLC and normal groups. Nevertheless, there were no significant differences in eccDNAs between NSCLC tissues and matched normal lung tissues. The eccDNA derived from PLCG2 was upregulated in NSCLC cells. TCGA analysis and immunohistochemistry showed that PLCG2 was highly expressed in lung cancer tissues and tended to be associated with poor outcome. We also demonstrated that PLCG2 can promote metastasis through the regulation of mitochondrial respiration. These results suggested that PLCG2 identified by eccDNA sequencing acts as an oncogene and might be a new biomarker for NSCLC diagnosis and prognosis evaluation.