bluuebunny/crossref_metadata_2025_split huggingface dataset:
Forgotten Concepts of Korea’s Welfare State: Productivist Welfare Capitalism and Confucianism Revisited in Family Policy Change
Authors: Gurín Martin 
Published: October 2023

Abstract
Understanding the dominant principle(s) of a welfare regime has been the “higher-level” objective of welfare state analysis. East Asian welfare states are no exception, and thus many contributions have sought to understand the welfare state order of these countries. In this article, we consider the development and current architecture of family policies at the center of welfare regime debate for the case of South Korea. Through this analysis we aim to critically assess current assumptions that both original foundations—productivist welfare capitalism and Confucianism—are theoretically useless for understanding the current welfare state and its development. Instead, this article argues that productivism remains at the heart of family policy in South Korea. The repositioning of productivism, however, and the related focus on social reproduction in the welfare state project, have led to most of the changes introduced to the detriment of Confucianism.
Divergent hepaciviruses, delta-like viruses, and a chu-like virus in Australian marsupial carnivores (dasyurids)
Authors: Harvey Erin , Mifsud Jonathon C O , Holmes Edward C , Mahar Jackie E 
Published: October 2023

Abstract
Although Australian marsupials are characterised by unique biology and geographic isolation, little is known about the viruses present in these iconic wildlife species. The Dasyuromorphia are an order of marsupial carnivores found only in Australia that include both the extinct Tasmanian tiger (thylacine) and the highly threatened Tasmanian devil. Several other members of the order are similarly under threat of extinction due to habitat loss, hunting, disease, and competition and predation by introduced species such as feral cats. We utilised publicly available RNA-seq data from the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) database to document the viral diversity within four Dasyuromorph species. Accordingly, we identified fifteen novel virus sequences from five DNA virus families (Adenoviridae, Anelloviridae, Gammaherpesvirinae, Papillomaviridae, and Polyomaviridae) and three RNA virus taxa: the order Jingchuvirales, the genus Hepacivirus, and the delta-like virus group. Of particular note was the identification of a marsupial-specific clade of delta-like viruses that may indicate an association of deltaviruses with marsupial species. In addition, we identified a highly divergent hepacivirus in a numbat liver transcriptome that falls outside of the larger mammalian clade. We also detect what may be the first Jingchuvirales virus in a mammalian host—a chu-like virus in Tasmanian devils—thereby expanding the host range beyond invertebrates and ectothermic vertebrates. As many of these Dasyuromorphia species are currently being used in translocation efforts to reseed populations across Australia, understanding their virome is of key importance to prevent the spread of viruses to naive populations.
Computational Design of a Highly-Specific HVEM-Based Inhibitor of LIGHT Protein
Authors: Ciura Piotr , Smardz Pamela , Krupa Magdalena A. , Spodzieja Marta , Krupa Pawel , Sieradzan Adam K. 
Published: October 2023

MotivationHVEM-LIGHT binding regulates the immune system response in various ways: it co-stimulates T cell proliferation; promotes B cell differentiation and secretion of immunoglobulins; and enhances dendritic cell maturation. Strong and prolonged stimulation of T cells to proliferate causes high levels of IFN–γ, which leads to chronic inflammation and is the reason for various autoimmune diseases. Therefore, blocking HVEM-LIGHT interaction may be a way to cure these diseases and prevent adverse reaction in organ and tissue transplantation.ResultsIn this work, we designed 62 peptides based on the CRDs of the HVEM structure, differentiating in the number and combination of disulfide bonds present. Based on extensive all-atom MD simulations in state-of-the-art force fields, followed by MM-GBSA binding energy estimation, we selected the most promising CRD2 variants interacting with LIGHT. Several point mutations of these variants provided us with the most strongly binding moiety: the CRD2 with a single disulfide bond (C58-C73) and K54E substitution. This result was supprased only by the truncated variants of CRD2(39-73) with the same disulfide bond present. The binding mechanism was investigated by the use of steered MD simulations, which showed the increased binding affinity of the abovementioned variants, while experimental circular dichroism was used to determine their structural properties.Availability and ImplementationThree PDB models of the LIGHT inhibitors: PM0084527, PM0084528, and PM0084592.Contactpkrupa@ifpan.edu.plSupplementary informationOnline supplementary data is available at: .
CCR5 promotes the migration of CD8+T cells to the leishmanial lesions
Authors: Sacramento Laís Amorim , Amorim Camila Farias , Lombana Claudia G. , Beiting Daniel , Novais Fernanda , Carvalho Lucas P. , Carvalho Edgar M. , Scott Phillip 
Published: October 2023

ABSTRACTCytolytic CD8+T cells mediate immunopathology in cutaneous leishmaniasis without controlling parasites. Here, we identify factors involved in CD8+T cell migration to the lesion that could be targeted to ameliorate disease severity. CCR5 was the most highly expressed chemokine receptor in patient lesions, and the high expression of CCL3 and CCL4, CCR5 ligands, was associated with delayed healing of lesions. To test the requirement for CCR5,Leishmania-infected Rag1-/-mice were reconstituted with CCR5-/-CD8+T cells. We found that these mice developed smaller lesions accompanied by a reduction in CD8+T cell numbers compared to controls. We confirmed these findings by showing that the inhibition of CCR5 with maraviroc, a selective inhibitor of CCR5, reduced lesion development without affecting the parasite burden. Together, these results reveal that CD8+T cells migrate to leishmanial lesions in a CCR5-dependent manner and that blocking CCR5 prevents CD8+T cell-mediated pathology.
DeMixSC: a deconvolution framework that uses single-cell sequencing plus a small benchmark dataset for improved analysis of cell-type ratios in complex tissue samples
Authors: Guo Shuai , Liu Xiaoqian , Cheng Xuesen , Jiang Yujie , Ji Shuangxi , Liang Qingnan , Koval Andrew , Li Yumei , Owen Leah A. , Kim Ivana K. , Aparicio Ana , Shen John Paul , Kopetz Scott , Weinstein John N. , DeAngelis Margaret M. , Chen Rui , Wang Wenyi 
Published: October 2023

AbstractBulk deconvolution with single-cell/nucleus RNA-seq data is critical for understanding heterogeneity in complex biological samples, yet the technological discrepancy across sequencing platforms limits deconvolution accuracy. To address this, we introduce an experimental design to match inter-platform biological signals, hence revealing the technological discrepancy, and then develop a deconvolution framework called DeMixSC using the better-matched, i.e., benchmark, data. Built upon a novel weighted nonnegative least-squares framework, DeMixSC identifies and adjusts genes with high technological discrepancy and aligns the benchmark data with large patient cohorts of matched-tissue-type for large-scale deconvolution. Our results using a benchmark dataset of healthy retinas suggest much-improved deconvolution accuracy. Further analysis of a cohort of 453 patients with age-related macular degeneration supports the broad applicability of DeMixSC. Our findings reveal the impact of technological discrepancy on deconvolution performance and underscore the importance of a well-matched dataset to resolve this challenge. The developed DeMixSC framework is generally applicable for deconvolving large cohorts of disease tissues, and potentially cancer.
sincFold: end-to-end learning of short- and long-range interactions in RNA secondary structure
Authors: Bugnon Leandro A. , Di Persia Leandro , Gerard Matias , Raad Jonathan , Prochetto Santiago , Fenoy Emilio , Chorostecki Uciel , Ariel Federico , Stegmayer Georgina , Milone Diego H. 
Published: October 2023

AbstractMotivationCoding and non-coding RNA molecules participate in many important biological processes. Non-coding RNAs fold into well-defined secondary structures to exert their functions. However, the computational prediction of the secondary structure from a raw RNA sequence is a long-standing unsolved problem, which after decades of almost unchanged performance has now re-emerged thanks to deep learning. Traditional RNA secondary structure prediction algorithms have been mostly based on thermodynamic models and dynamic programming for free energy minimization. More recently deep learning methods have shown competitive performance compared with the classical ones, but still leaving a wide margin for improvement.ResultsIn this work we present sincFold an end-to-end deep learning approach that predicts the nucleotides contact matrix using only the RNA sequence as input. The model is based on 1D and 2D residual neural networks that can learn short- and long-range interaction patterns. We show that structures can be accurately predicted with minimal physical assumptions. Extensive experiments were conducted on several benchmark datasets, considering sequence homology and cross-family validation. sincFold was compared against classical methods and recent deep learning models, showing that it can outperform state-of-the-art methods.AvailabilityThe source code is available athttps://github.com/sinc-lab/sincFold(v0.16) and the web access is provided athttps://sinc.unl.edu.ar/web-demo/sincFoldContactlbugnon@sinc.unl.edu.ar
Chlorophyll to Zeaxanthin Energy Transfer in Non-Photochemical Quenching: An Exciton Annihilation-free Transient Absorption Study
Authors: Lee Tsung-Yen , Lam Lam , Patel-Tupper Dhruv , Roy Partha Pratim , Ma Sophia A. , Lucas-DeMott Aviva , Karavolias Nicholas G. , Niyogi Krishna K. , Fleming Graham R. 
Published: October 2023

AbstractZeaxanthin (Zea) is a key component in the energy-dependent, rapidly reversible, non-photochemical quenching process (qE) that regulates photosynthetic light harvesting. Previous transient absorption (TA) studies suggested that Zea can participate in direct quenching via Chlorophyll (Chl) to Zea energy transfer. However, the contamination of intrinsic exciton-exciton annihilation (EEA) makes the assignment of TA signal ambiguous. In this study, we present EEA-free TA data usingNicotiana benthamianathylakoid membranes, including wild type and three NPQ mutants (npq1,npq4, andlut2) generated by CRISPR/Cas9 mutagenesis. Results show a strong correlation between excitation energy transfer from excited Chl Qyto Zea S1and the xanthophyll cycle during qE activation. Notably, a Lut S1signal is absent in thenpq1thylakoids which lack zeaxanthin. Additionally, the fifth-order response analysis shows a reduction in the exciton diffusion length (LD) from 55 ± 5 nm to 38 ± 3 nm under high light illumination, consistent with the reduced range of exciton motion being a key aspect of plants’ response to excess light.
Optoelectronic enhancement of photocurrent by cyanobacteria on sustainable AP-VPP-fabricated PEDOT electrodes
Authors: Wey Laura T. , Yewale Rahul , Hautala Emilia , Hannonen Jenna , Katavisto Kalle , Kvarnström Carita , Allahverdiyeva Yagut , Damlin Pia 
Published: October 2023

AbstractPhotosynthetic microrganisms, including cyanobacteria, can be interfaced with electrodes in biophotovoltaic devices (BPVs) for solar energy conversion. Effective BPV electrodes need to be conductive, transparent, flexible, biocompatible and environmentally friendly, while also being cost-effective, abundant in material and lightweight. The utilization of electrically conducting polymers (CPs), particularly poly(3,4-ethylenedioxythiophene) (PEDOT) fabricated by an atmospheric pressure vapor phase polymerization (AP-VPP) technique, is a promising avenue for BPV applications. However, challenges remain in optimising their performance as CPs are dynamic optoelectronic materials, and their interaction with photosynthetic biocatalysts under a range of conditions has not been explored thoroughly. Here we show that AP-VPP-PEDOT electrodes hold promise for interfacing with cyanobacteria in BPVs to generate green electricity under red and blue light and moderate applied potentials with exogenous electron mediators. The highest non-mediated photocurrent achieved was 0.48 µA cm−2, with a two-layer PEDOT electrode at 0.5 V applied potential and blue light. The highest mediated photocurrent achieved was 2.73 µA cm−2, with a one-layer PEDOT electrode at 0.3 V applied potential and blue light and the exogenous electron mediator 2,6-dichloro-1,4-benzoquinone (DCBQ). The proposed approach to fabricating PEDOT electrodes offers a new pathway for developing sustainable electrodes for BPVs and pinpoints strategies for future optimisation for achieving high-performance outcomes.Abstract Figure
Autophagosome development and chloroplast segmentation occur synchronously for piecemeal degradation of chloroplasts
Authors: Izumi Masanori , Nakamura Sakuya , Otomo Kohei , Ishida Hiroyuki , Hidema Jun , Nemoto Tomomi , Hagihara Shinya 
Published: October 2023

AbstractPlants distribute many nutrients to chloroplasts during leaf development and maturation. When leaves senesce or experience sugar starvation, the autophagy machinery degrades chloroplast proteins to facilitate efficient nutrient reuse. Here, we report on the intracellular dynamics of an autophagy pathway responsible for piecemeal degradation of chloroplast components. Through live-cell monitoring of chloroplast morphology, we observed the formation of chloroplast budding structures in sugar-starved leaves. These buds were then released and incorporated into the vacuolar lumen as an autophagic cargo termed a Rubisco-containing body. The budding structures did not accumulate in mutants of core autophagy machinery, suggesting that autophagosome creation is required for forming chloroplast buds. Simultaneous tracking of chloroplast morphology and autophagosome development revealed that the isolation membranes of autophagosomes interact closely with part of the chloroplast surface before forming chloroplast buds. Chloroplasts then protrude at the site associated with the isolation membranes, which divide synchronously with autophagosome maturation. This autophagy-related division does not require DYNAMIN-RELATED PROTEIN 5B, which constitutes the division ring for chloroplast proliferation in growing leaves. An unidentified division machinery may thus fragment chloroplasts for degradation in coordination with the development of the chloroplast-associated isolation membrane.
Gap-free X and Y chromosomes ofSalix arbutifoliareveal an evolutionary change from male to female heterogamety in willows, without a change in the sex-determining region
Authors: Wang Yi , Gong Guangnan , Zhang Rengang , Hörandl Elvira , Zhang Zhixiang , Charlesworth Deborah , He Li 
Published: October 2023

AbstractIn theVetrixclade ofSalix, a genus of woody flowering plants, sex determination involves chromosome 15, but an XY system has changed to a ZW system. We used genome sequencing (with chromosome conformation capture (Hi-C) and PacBio HiFi high-fidelity reads) to study the evolutionary history of the sex-linked regions before and after the transition. We assembled chromosome level gap-free X and Y chromosomes ofSalix arbutifolia, and distinguished the haplotypes in the 15X- and 15Y-linked regions. This revealed “micro-heteromorphism” differentiating the haplotypes of the Y- and X-linked regions, including insertions, deletions and duplications. Unusually, the X-linked region is considerably larger than the corresponding Y region, and we show that this primarily reflects extensive accumulation of repetitive sequences and gene duplications. The phylogenies of single-copy orthogroups within the sex-linked regions ofS. arbutifolia(X and Y) andS. purpurea(Z and W) indicate that they possess a common ancestral sex-linked region that is physically small and located in a repeat-rich region near the chromosome 15 centromere. During the change in heterogamety, the W-linked region was derived from the X-linked one and the Z from the Y. The W may subsequently have evolved a region in which recombination became suppressed. We also detected accumulation of genes with opposite sex-biases in the sex-linked regions.
Interleukin 11-induced microRNAs as functional mediators and circulating biomarkers of cardiac fibrosis
Authors: Tikhomirov Roman , Reilly-O’Donnell Benedict , Lucarelli Carla , Srivastava Prashant Kumar , Anwar Maryam , Yiu Chi Him Kendrick , Dielesen Julia , Piella Santiago Nicolas , Kwan Zoe , Zaccagnini Germana , Mansfield Catherine , Tessari Maddalena , Menicanti Lorenzo , Greco Simona , Leszek Przemysław , Faggian Giuseppe , Emanueli Costanza , Martelli Fabio , Gorelik Julia 
Published: October 2023

AbstractBackgroundCardiac fibrosis can be triggered by several pathologies, including ischemic heart disease and aortic stenosis (AS). Cardiac fibrosis is brought about by uncontrolled extracellular matrix (ECM) deposition by myofibroblasts. Interleukin-11 (IL-11) has been firmly demonstrated to be a major trigger of multi-organ fibrosis. However, the molecular mechanisms underpinning IL-11-induced fibrosis requires further characterisation. Recent studies indicate that microRNA (miRNA) dysregulation contributes to the pathogenesis of cardiac fibrosis and can be targeted therapeutically. In this study, we explored the hypothesis that miRNAs act as downstream effectors of IL-11-induced cardiac fibrosis. Moreover, we investigated the translational potential of IL-11-regulated miRNAs as circulating biomarkers of cardiac fibrosis in AS patients.Methods and ResultsUsing computational approaches, we identified miRNA-497-5p and miRNA-27b-5p as potential new downstream profibrotic effectors of IL-11 in fibroblasts. We next confirmed that both miRNAs increased in healthy rat CF stimulated with IL-11 and in CF derived from post-infarction failing hearts. At the functional level, miRNA-497-5p and miRNA-27b-5p inhibition indirectly reduced the mRNA expression of collagen 1 (Col1a1). Conversely, transfection of CFs with mimics for each of the two miRNAs promoted fibroblast-to-myofibroblast transition and increased Col1a1 levels. We provided evidences that miRNA-27b-5p and miRNA-497-5p converge to promote hypoxia-inducible factor 1 signalling, by targeting its regulator EGLN (PHD) family members. The clinical relevance of our findings was confirmed using left ventricle (LV) specimens obtained from surgical patients with AS. The miRNA-27b-5p and miRNA-497-5p measured in the LV, peripheral plasma and plasma extracellular vesicles correlated with the severity of LV fibrosis, indicating these miRNAs’ potential as new circulating biomarkers of cardiac fibrosis.ConclusionsIn this study, we have newly identified the potential value of miRNA-27b-5p and miRNA-497-5p as actionable biomarkers of the profibrotic response to IL-11 in the heart. Future studies should validate the translational potential of the miRNAs as new clinical biomarkers and therapeutic targets.
Antibodies utilizing VL6-57 light chains target a convergent cryptic epitope on SARS-CoV-2 spike protein driving the genesis of Omicron variants
Authors: Yan Qihong , Gao Xijie , Liu Banghui , Hou Ruitian , He Ping , Ma Yong , Zhang Yudi , Zhang Yanjun , Li Zimu , Chen Qiuluan , Wang Jingjing , Huang Xiaohan , Liang Huan , Chen Xianying , Niu Xuefeng , He Jun , Chen Ling , Zhao Jincun , Xiong Xiaoli 
Published: October 2023

AbstractContinued evolution of SARS-CoV-2 generates variants to challenge antibody immunity established by infection and vaccination. A connection between population immunity and genesis of virus variants has long been suggested but its molecular basis remains poorly understood. Here, we identify a class of SARS-CoV-2 neutralising public antibodies defined by their shared usage of VL6-57 light chains. Although heavy chains of diverse genotypes are utilized, convergent HCDR3 rearrangements have been observed among these public antibodies to cooperate with germline VL6-57 LCDRs to target a convergent epitope defined by RBD residues S371-S373-S375. Antibody repertoire analysis identifies that this class of VL6-57 antibodies is present in SARS-CoV-2-naïve individuals and is clonally expanded in most COVID-19 patients. We confirm that Omicron specific substitutions at S371, S373 and S375 mediate escape of antibodies of the VL6-57 class. These findings support that this class of public antibodies constitutes immune pressure promoting the introduction of S371L/F-S373P-S375F in Omicron variants. The results provide further molecular evidences to support that antigenic evolution of SARS-CoV-2 is driven by antibody mediated population immunity.
Arabidopsis AGO1 N-terminal Poly-Q domain promotes phase separation and association with stress granules during heat stress
Authors: Blagojevic Aleksandar , Baldrich Patricia , Schiaffini Marlene , Lechner Esther , Baumberger Nicolas , Hammann Philippe , Elmayan Taline , Garcia Damien , Vaucheret Hervé , Meyers Blake C. , Genschik Pascal 
Published: October 2023

SUMMARYInArabidopsis thaliana, ARGONAUTE1 (AGO1) plays a central role in microRNA (miRNA) and small interfering RNA (siRNA)-mediated silencing. Nuclear AGO1 is loaded with miRNAs and exported to the cytosol where it associates to the rough ER to conduct miRNA-mediated translational repression, mRNA cleavage and biogenesis of phased siRNAs. These latter, as well as other cytosolic siRNAs, are loaded into cytosolic AGO1, but in which compartment this happens is not known. Moreover, the effect of stress on AGO1 localization is still unclear. Here, we show that a 37°C heat stress (HS) promotes AGO1 protein accumulation in cytosolic condensates where it co-localizes with components of siRNA bodies and of stress granules (SGs). AGO1 contains a prion-like domain in its poorly characterized N-terminal Poly-Q domain, which, is sufficient to undergo phase separation, independent of the presence or absence of SGS3. HS only moderately affects the small RNA repertoire, the loading of AGO1 by miRNAs and the signatures of target cleavage, suggesting that its localization in condensates protects AGO1 rather than promotes or impairs its activity in reprograming gene expressing during stress. Collectively, our work shed new light on the impact of high temperature on a main effector of RNA silencing in plants.