bluuebunny/crossref_metadata_2025_split huggingface dataset:
Northward Shift and Narrowing of the ITCZ in 20 Years of AIRS Data
Authors: Aumann Hartmut H. , Broberg Steven , Manning Evan M. 
Published: March 2024

AbstractA time series analysis of Deep Convective Clouds (DCC) in Atmospheric InfraRed Sounder data between 2002 and 2023 shows that the mean latitude of the Inter Tropical Convergence Zone (ITCZ) has shifted northward for land at a rate of about 30 km/decade. The shift for ocean is north as well at about half of the rate for land. Comparisons of our results with the existing literature are complicated by the use of different methodologies and data sources: We used the daily observations of DCCs, which by their association with extreme rain rates are indicators of locally extreme vertical velocity on 15 km horizontal scales, while most of the literature used model or reanalysis gridded data with typically 100 km bins. The southern boundary of the ITCZ shifts north faster than the northern boundary, as qualitatively stated in the literature. The resulting contraction of the ITCZ width with global warming was qualitatively predicted based on theoretical consideration. Our observation of the rate of decrease in the width for ocean is statistically consistent with the contraction deduced from European Centre for Medium Range Forecast Reanalysis and Modern‐Era Retrospective analysis for Research and Applications data. The observed northward shift of the ITCZ was not predicted and is not seen in climate models in the 21st century.
Forecast Skill and Signal‐To‐Noise Ratio for Stratospheric Polar Vortex Variations in Northern Hemisphere Winter Seasonal Hindcasts
Authors: Taguchi M. 
Published: March 2024

AbstractThis study explores seasonal forecast skill and signal‐to‐noise (SN) ratio for stratospheric polar vortex (SPV) variations during Northern winter using hindcast (HC) data of six systems initialized around early November in the Copernicus Climate Change Service database. Results show high skill for December‐January‐February (DJF) mean El Niño/Southern Oscillation and Quasi‐Biennial Oscillation (QBO) variations, although it is suggested that some systems underestimate the QBO amplitude. The ENSO and QBO variations in the HC data are also suggested to be underdispersive having too high SN ratio due to too strong signal and/or too weak noise (spread). The skill for DJF mean SPV variations is limited, with four systems having marginal skill near the 95% level, whereas the SN ratio is suggested to be realistic. It is also shown that no system has skill (evaluated using the Brier Score) at the 95% level in forecasting if each DJF winter experiences one or more major sudden stratospheric warmings, when a bias of the polar vortex strength in each system is simply considered. A comparison of the ensemble members for each system, when divided into two groups by the strength of the QBO‐SPV teleconnection, suggests an increase in the skill for SPV variations for the group of stronger teleconnection. This confirms the idea that the QBO‐SPV teleconnection contributes to the skill for SPV variations, and also suggests that the skill for SPV variations can be improved as the HC QBO and QBO‐SPV teleconnection are better simulated.
Parameterization of the Elevated Convection With a Unified Convection Scheme (UNICON) and Its Impacts on the Diurnal Cycle of Precipitation
Authors: Park Sungsu , Song Chanwoo , Kim Siyun , Kim Juwon 
Published: March 2024

AbstractTo improve the simulation of nocturnal precipitation, we develop a parameterization for the elevated convection that is launched from the level of maximum grid‐mean moist static energy, when grid‐mean vertical flow is upward at the launching interface. The parameterized elevated convection is forced by both cold pool‐driven and partially resolved external mesoscale organized flows. Properties of the external mesoscale flow are estimated from grid‐mean vertical velocity and three dimensional advection tendencies of temperature and moisture. The new parameterization is implemented into a unified convection scheme (UNICON) and tested for both the single‐column case at the Southern Great Plain (SGP) site in US and in global simulations. At the SGP site, the parameterized elevated convection strengthens nocturnal convection, increases nocturnal precipitation, and better simulates the observed diurnal cycle of precipitation. It appears that the elevated and surface‐based convections interact with each other by stabilizing the atmospheric column, which affects subsequent convection. Global simulation shows that the elevated convection mostly occurs over the continents during the night, and also over the oceanic mid‐latitude warm air advection and storm track regions during summer. Without degrading global mean climate, the elevated convection improves the simulation of nocturnal precipitation in the mid‐US but simulates somewhat strong nocturnal precipitation in northeastern Asia. It seems that a key to simulate observed nocturnal precipitation is to appropriately parameterize the impacts of external organized flow on the elevated convection.
A genetic risk score to predict treatment nonresponse in psychotic depression
Authors: ter Hark Sophie E. , Coenen Marieke J. H. , Vos Cornelis F. , Aarnoutse Rob E. , Nolen Willem A. , Birkenhager Tom K. , van den Broek Walter W. , Schellekens Arnt F. A. , Verkes Robbert-Jan , Janzing Joost G. E. 
Published: March 2024

AbstractPsychotic depression is a severe and difficult-to-treat subtype of major depressive disorder for which higher rates of treatment-resistant depression were found. Studies have been performed aiming to predict treatment-resistant depression or treatment nonresponse. However, most of these studies excluded patients with psychotic depression. We created a genetic risk score (GRS) based on a large treatment-resistant depression genome-wide association study. We tested whether this GRS was associated with nonresponse, nonremission and the number of prior adequate antidepressant trials in patients with a psychotic depression. Using data from a randomized clinical trial with patients with a psychotic depression (n = 122), we created GRS deciles and calculated positive prediction values (PPV), negative predictive values (NPV) and odds ratios (OR). Nonresponse and nonremission were assessed after 7 weeks of treatment with venlafaxine, imipramine or venlafaxine plus quetiapine. The GRS was negatively correlated with treatment response (r = −0.32, p = 0.0023, n = 88) and remission (r = −0.31, p = 0.0037, n = 88), but was not correlated with the number of prior adequate antidepressant trials. For patients with a GRS in the top 10%, we observed a PPV of 100%, a NPV of 73.7% and an OR of 52.4 (p = 0.00072, n = 88) for nonresponse. For nonremission, a PPV of 100%, a NPV of 51.9% and an OR of 21.3 (p = 0.036, n = 88) was observed for patients with a GRS in the top 10%. Overall, an increased risk for nonresponse and nonremission was seen in patients with GRSs in the top 40%. Our results suggest that a treatment-resistant depression GRS is predictive of treatment nonresponse and nonremission in psychotic depression.
Inhibitory and preventive effects of Arnebia euchroma (Royle) Johnst. root extract on Streptococcus mutans and dental caries in rats
Authors: Wu Zeyu , Song Jie , Zhang Yangyang , Yuan Xiyu , Zhao Jin 
Published: March 2024

Abstract
Background
Dental caries is one of the prevalent conditions that threaten oral health. Arnebia euchroma (Royle) Johnst. root (AR) extracts exhibit anti-inflammatory, anti-cancer, and antibacterial properties. This study was designed to investigate the antibacterial impact of AR extract on Streptococcus mutans (S. mutans) UA159 and the anti-caries effect on rats.

Methods
The antibacterial activity of AR extract against S. mutans and its biofilm was determined using the bacterial sensitivity test, the biofilm sensitivity test, and the live-dead staining technique. By fluorescently tagging bacteria, the influence of bacterial adhesion rate was determined. Using a rat caries model, the anti-caries efficacy and safety of AR extract were exhaustively investigated in vivo.

Results
AR extract inhibit not only the growth of S. mutans, but also the generation of S. mutans biofilm, hence destroying and eliminating the biofilm. Moreover, AR extract were able to inhibit S. mutans’ adherence to saliva-encapsulated hydroxyapatite (HAP). Further, in a rat model of caries, the AR extract is able to greatly reduce the incidence and severity of caries lesions on the smooth surface and pit and fissure of rat molars, while exhibiting excellent biosafety.

Conclusions
AR extract exhibit strong antibacterial activity against S. mutans and can lower the incidence and severity of dental cavities in rats. These findings suggest that Arnebia euchroma (Royle) Johnst. could be utilized for the prevention and treatment of dental caries.
Clostridium butyricum MIYAIRI 588 contributes to the maintenance of intestinal microbiota diversity early after haematopoietic cell transplantation
Authors: Fukushima Kentaro , Kudo Hayami , Oka Kentaro , Hayashi Atsushi , Onizuka Makoto , Kusakabe Shinsuke , Hino Akihisa , Takahashi Motomichi , Takeda Kiyoshi , Mori Masaki , Ando Kiyoshi , Hosen Naoki 
Published: March 2024

AbstractIn patients undergoing haematopoietic stem-cell transplantation (HSCT), the intestinal microbiota plays an important role in prognosis, transplant outcome, and complications such as graft-versus-host disease (GVHD). Our prior research revealed that patients undergoing HSCT substantially differed from healthy controls. In this retrospective study, we showed that administering Clostridium butyricum MIYAIRI 588 (CBM588) as a live biotherapeutic agent is associated with maintaining intestinal microbiota in the early post-HSCT period. Alpha diversity, which reflects species richness, declined considerably in patients who did not receive CBM588, whereas it remained consistent in those who received CBM588. In addition, β-diversity analysis revealed that CBM588 did not alter the gut microbiota structure at 7–21 days post-HSCT. Patients who developed GVHD showed structural changes in their microbiota from the pre-transplant period, which was noticeable on day 14 before developing GVHD. Enterococcus was significantly prevalent in patients with GVHD after HSCT, and the population of Bacteroides was maintained from the pre-HSCT period through to the post-HSCT period. Patients who received CBM588 exhibited a contrasting trend, with lower relative abundances of both genera Enterococcus and Bacteroides. These results suggest that preoperative treatment with CBM588 could potentially be beneficial in maintaining intestinal microbiota balance.
ISGylation of DRP1 closely balances other post-translational modifications to mediate mitochondrial fission
Authors: Das Palamou , Chakrabarti Oishee 
Published: March 2024

AbstractDynamin related protein 1 (DRP1), a pivotal mitochondrial fission protein, is post-translationally modified by multiple mechanisms. Here we identify a new post-translational modification of DRP1 by the ubiquitin-like protein, interferon-stimulated gene 15 (ISG15). DRP1 ISGylation is mediated by ISG15 E3 ligase, HERC5; this promotes mitochondrial fission. DeISGylation of DRP1 however leads to hyperfusion. Heterologous expression of SARS-CoV2 PLpro, a deISGylating enzyme, results in similar mitochondrial filamentation, significant decrease in total DRP1 protein levels and efflux of mtDNA. We report that deISGylated DRP1 gets ubiquitylated and degraded by TRIM25, instead of PARKIN and MITOL. While the cytosolic pool of DRP1 is primarily ISGylated, both mitochondrial and cytosolic fractions may be ubiquitylated. It is known that phosphorylation of DRP1 at S616 residue regulates its mitochondrial localisation; we show that ISGylation of phospho-DRP1 (S616) renders fission competence at mitochondria. This is significant because DRP1 ISGylation affects its functionality and mitochondrial dynamics in Alzheimer’s disease pathophysiology.
CircHIPK3 regulates fatty acid metabolism through miR-637/FASN axis to promote esophageal squamous cell carcinoma
Authors: Cao Shi-qiang , Xue Song-tao , Li Wen-juan , Hu Guo-sheng , Wu Zhi-gang , Zheng Jian-cong , Zhang Shu-liang , Lin Xiao , Chen Chun , Liu Wen , Zheng Bin 
Published: March 2024

AbstractThe oncogenic role of circRNA in cancers including esophageal cancer (EC) has been well studied. However, whether and how circRNAs are involved in cancer cell metabolic processes remains largely unknown. Here, we reported that circRNA, circHIPK3, is highly expressed in ESCC cell lines and tissues. Knockdown of circHIPK3 significantly restrained cell proliferation, colony formation, migration, and invasion in vitro and inhibited tumor growth in vivo. Mechanistically, circHIPK3 was found to act as a ceRNA by sponging miR-637 to regulate FASN expression and fatty acid metabolism in ESCC cells. Anti-sense oligonucleotide (ASO) targeting circHIPK3 substantially inhibited ESCC both in vitro and in vivo. Therefore, these results uncover a modulatory axis constituting of circHIPK3/miR-637/FASN may be a potential biomarker and therapeutic target for ESCC in the clinic.
Modelling atomic and nanoscale structure in the silicon–oxygen system through active machine learning
Authors: Erhard Linus C. , Rohrer Jochen , Albe Karsten , Deringer Volker L. 
Published: March 2024

AbstractSilicon–oxygen compounds are among the most important ones in the natural sciences, occurring as building blocks in minerals and being used in semiconductors and catalysis. Beyond the well-known silicon dioxide, there are phases with different stoichiometric composition and nanostructured composites. One of the key challenges in understanding the Si–O system is therefore to accurately account for its nanoscale heterogeneity beyond the length scale of individual atoms. Here we show that a unified computational description of the full Si–O system is indeed possible, based on atomistic machine learning coupled to an active-learning workflow. We showcase applications to very-high-pressure silica, to surfaces and aerogels, and to the structure of amorphous silicon monoxide. In a wider context, our work illustrates how structural complexity in functional materials beyond the atomic and few-nanometre length scales can be captured with active machine learning.
RTF2 controls replication repriming and ribonucleotide excision at the replisome
Authors: Conti Brooke A. , Ruiz Penelope D. , Broton Cayla , Blobel Nicolas J. , Kottemann Molly C. , Sridhar Sunandini , Lach Francis P. , Wiley Tom F. , Sasi Nanda K. , Carroll Thomas , Smogorzewska Agata 
Published: March 2024

AbstractDNA replication through a challenging genomic landscape is coordinated by the replisome, which must adjust to local conditions to provide appropriate replication speed and respond to lesions that hinder its progression. We have previously shown that proteasome shuttle proteins, DNA Damage Inducible 1 and 2 (DDI1/2), regulate Replication Termination Factor 2 (RTF2) levels at stalled replisomes, allowing fork stabilization and restart. Here, we show that during unperturbed replication, RTF2 regulates replisome localization of RNase H2, a heterotrimeric enzyme that removes RNA from RNA-DNA heteroduplexes. RTF2, like RNase H2, is essential for mammalian development and maintains normal replication speed. However, persistent RTF2 and RNase H2 at stalled replication forks prevent efficient replication restart, which is dependent on PRIM1, the primase component of DNA polymerase α-primase. Our data show a fundamental need for RTF2-dependent regulation of replication-coupled ribonucleotide removal and reveal the existence of PRIM1-mediated direct replication restart in mammalian cells.
The long and winding road of reprogramming-induced rejuvenation
Authors: Yücel Ali Doğa , Gladyshev Vadim N. 
Published: March 2024

AbstractOrganismal aging is inherently connected to the aging of its constituent cells and systems. Reducing the biological age of the organism may be assisted by reducing the age of its cells - an approach exemplified by partial cell reprogramming through the expression of Yamanaka factors or exposure to chemical cocktails. It is crucial to protect cell type identity during partial reprogramming, as cells need to retain or rapidly regain their functions following the treatment. Another critical issue is the ability to quantify biological age as reprogrammed older cells acquire younger states. We discuss recent advances in reprogramming-induced rejuvenation and offer a critical review of this procedure and its relationship to the fundamental nature of aging. We further comparatively analyze partial reprogramming, full reprogramming and transdifferentiation approaches, assess safety concerns and emphasize the importance of distinguishing rejuvenation from dedifferentiation. Finally, we highlight translational opportunities that the reprogramming-induced rejuvenation approach offers.
Cytokinetic abscission requires actin-dependent microtubule severing
Authors: Advedissian Tamara , Frémont Stéphane , Echard Arnaud 
Published: March 2024

AbstractCell division is completed by the abscission of the intercellular bridge connecting the daughter cells. Abscission requires the polymerization of an ESCRT-III cone close to the midbody to both recruit the microtubule severing enzyme spastin and scission the plasma membrane. Here, we found that the microtubule and the membrane cuts are two separate events that are regulated differently. Using HeLa cells, we uncovered that the F-actin disassembling protein Cofilin-1 controls the disappearance of a transient pool of branched F-actin which is precisely assembled at the tip of the ESCRT-III cone shortly before the microtubule cut. Functionally, Cofilin-1 and Arp2/3-mediated branched F-actin favor abscission by promoting local severing of the microtubules but do not participate later in the membrane scission event. Mechanistically, we propose that branched F-actin functions as a physical barrier that limits ESCRT-III cone elongation and thereby favors stable spastin recruitment. Our work thus reveals that F-actin controls the timely and local disassembly of microtubules required for cytokinetic abscission.
Polycomb-mediated silencing of miR-8 is required for maintenance of intestinal stemness in Drosophila melanogaster
Authors: Veneti Zoe , Fasoulaki Virginia , Kalavros Nikolaos , Vlachos Ioannis S. , Delidakis Christos , Eliopoulos Aristides G. 
Published: March 2024

AbstractBalancing maintenance of self-renewal and differentiation is a key property of adult stem cells. The epigenetic mechanisms controlling this balance remain largely unknown. Herein, we report that the Polycomb Repressive Complex 2 (PRC2) is required for maintenance of the intestinal stem cell (ISC) pool in the adult femaleDrosophila melanogaster. We show that loss of PRC2 activity in ISCs by RNAi-mediated knockdown or genetic ablation of the enzymatic subunit Enhancer of zeste, E(z), results in loss of stemness and precocious differentiation of enteroblasts to enterocytes. Mechanistically, we have identified the microRNAmiR-8as a critical target of E(z)/PRC2-mediated tri-methylation of histone H3 at Lys27 (H3K27me3) and uncovered a dynamic relationship between E(z),miR-8and Notch signaling in controlling stemnessversusdifferentiation of ISCs. Collectively, these findings uncover a hitherto unrecognized epigenetic layer in the regulation of stem cell specification that safeguards intestinal homeostasis.
Extensive photochemical restructuring of molecule-metal surfaces under room light
Authors: Guo Chenyang , Benzie Philip , Hu Shu , de Nijs Bart , Miele Ermanno , Elliott Eoin , Arul Rakesh , Benjamin Helen , Dziechciarczyk Grzegorz , Rao Reshma R. , Ryan Mary P. , Baumberg Jeremy J. 
Published: March 2024

AbstractThe molecule-metal interface is of paramount importance for many devices and processes, and directly involved in photocatalysis, molecular electronics, nanophotonics, and molecular (bio-)sensing. Here the photostability of this interface is shown to be sensitive even to room light levels for specific molecules and metals. Optical spectroscopy is used to track photoinduced migration of gold atoms when functionalised with different thiolated molecules that form uniform monolayers on Au. Nucleation and growth of characteristic surface metal nanostructures is observed from the light-driven adatoms. By watching the spectral shifts of optical modes from nanoparticles used to precoat these surfaces, we identify processes involved in the photo-migration mechanism and the chemical groups that facilitate it. This photosensitivity of the molecule-metal interface highlights the significance of optically induced surface reconstruction. In some catalytic contexts this can enhance activity, especially utilising atomically dispersed gold. Conversely, in electronic device applications such reconstructions introduce problematic aging effects.
Efficient all-small-molecule organic solar cells processed with non-halogen solvent
Authors: Gao Wei , Ma Ruijie , Dela Peña Top Archie , Yan Cenqi , Li Hongxiang , Li Mingjie , Wu Jiaying , Cheng Pei , Zhong Cheng , Wei Zhanhua , Jen Alex K.-Y. , Li Gang 
Published: March 2024

AbstractAll-small-molecule organic solar cells with good batch-to-batch reproducibility combined with non-halogen solvent processing show great potential for commercialization. However, non-halogen solvent processing of all-small-molecule organic solar cells are rarely reported and its power conversion efficiencies are very difficult to improve. Herein, we designed and synthesized a small molecule donor BM-ClEH that can take advantage of strong aggregation property induced by intramolecular chlorine-sulfur non-covalent interaction to improve molecular pre-aggregation in tetrahydrofuran and corresponding micromorphology after film formation. Tetrahydrofuran-fabricated all-small-molecule organic solar cells based on BM-ClEH:BO-4Cl achieved high power conversion efficiencies of 15.0% in binary device and 16.1% in ternary device under thermal annealing treatment. In contrast, weakly aggregated BM-HEH without chlorine-sulfur non-covalent bond is almost inefficient under same processing conditions due to poor pre-aggregation induced disordered π-π stacking, indistinct phase separation and exciton dissociation. This work promotes the development of non-halogen solvent processing of all-small-molecule organic solar cells and provides further guidance.
Quantitative pathogenicity and host adaptation in a fungal plant pathogen revealed by whole-genome sequencing
Authors: Amezrou Reda , Ducasse Aurélie , Compain Jérôme , Lapalu Nicolas , Pitarch Anais , Dupont Laetitia , Confais Johann , Goyeau Henriette , Kema Gert H. J. , Croll Daniel , Amselem Joëlle , Sanchez-Vallet Andrea , Marcel Thierry C. 
Published: March 2024

AbstractKnowledge of genetic determinism and evolutionary dynamics mediating host-pathogen interactions is essential to manage fungal plant diseases. Studies on the genetic architecture of fungal pathogenicity often focus on large-effect effector genes triggering strong, qualitative resistance. It is not clear how this translates to predominately quantitative interactions. Here, we use the Zymoseptoria tritici-wheat model to elucidate the genetic architecture of quantitative pathogenicity and mechanisms mediating host adaptation. With a multi-host genome-wide association study, we identify 19 high-confidence candidate genes associated with quantitative pathogenicity. Analysis of genetic diversity reveals that sequence polymorphism is the main evolutionary process mediating differences in quantitative pathogenicity, a process that is likely facilitated by genetic recombination and transposable element dynamics. Finally, we use functional approaches to confirm the role of an effector-like gene and a methyltransferase in phenotypic variation. This study highlights the complex genetic architecture of quantitative pathogenicity, extensive diversifying selection and plausible mechanisms facilitating pathogen adaptation.