bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular Distributions and 13C Isotopic Composition of Dicarboxylic Acids, Oxocarboxylic Acids, and α‐dicarbonyls in Wintertime PM2.5 at Three Sites Over Northeast Asia: Implications for Origins and Long‐Range Atmospheric Transport
Authors: Zhao Xiaomai , Pavuluri Chandra Mouli , Dong Zhichao , Xu Zhanjie , Nirmalkar Jayant , Jung Jinsang , Fu Pingqing , Liu Cong‐Qiang 
Published: June 2023

AbstractTo investigate the spatial changes in origins and impact of long‐range transported air masses on organic aerosols (OA) loading and composition over Northeast Asia, fine aerosols (PM2.5) were collected at three sites: Tianjin (TJ), North China and in Padori (PD), and Daejeon (DJ), South Korea, during winter 2019. We studied molecular distributions and compound‐specific stable carbon isotopic composition (δ13C) of dicarboxylic acids, oxocarboxylic acids and α‐dicarbonyls, and carbonaceous and inorganic ionic components in PM2.5. Concentrations of organic carbon was drastically enhanced in haze period compared to that in clean period, but elemental carbon was almost comparable between the two periods. Concentrations of total diacids, oxoacids, and α‐dicarbonyls were higher at TJ followed by DJ and PD during haze period and at DJ followed by TJ and PD during clean period. On average, oxalic acid (C2) was the most abundant among measured species at all three sites, followed by methyl glyoxal (MeGly) and glyoxylic acid (ωC2) at TJ and DJ, and succinic acid (C4) and ωC2 were almost equal and second most abundant followed by MeGly at PD. Based on the mass ratios and linear relations of selected species together with δ13C of diacids and related compounds, we found that contributions of OA from biomass burning/biogenic emissions and their aging were higher at TJ and PD, whereas at DJ, emissions from anthropogenic sources and in situ secondary formation were also important. Furthermore, this study implies that long‐range atmospheric transport of aerosols from source regions to downwind regions are substantial over Northeast Asia.
Genetic diversity and signatures of selection in four indigenous horse breeds of Iran
Authors: Mousavi Seyedeh Fatemeh , Razmkabir Mohammad , Rostamzadeh Jalal , Seyedabadi Hamid-Reza , Naboulsi Rakan , Petersen Jessica L. , Lindgren Gabriella 
Published: June 2023

AbstractIndigenous Iranian horse breeds were evolutionarily affected by natural and artificial selection in distinct phylogeographic clades, which shaped their genomes in several unique ways. The aims of this study were to evaluate the genetic diversity and genomewide selection signatures in four indigenous Iranian horse breeds. We evaluated 169 horses from Caspian (n = 21), Turkmen (n = 29), Kurdish (n = 67), and Persian Arabian (n = 52) populations, using genomewide genotyping data. The contemporary effective population sizes were 59, 98, 102, and 113 for Turkmen, Caspian, Persian Arabian, and Kurdish breeds, respectively. By analysis of the population genetic structure, we classified the north breeds (Caspian and Turkmen) and west/southwest breeds (Persian Arabian and Kurdish) into two phylogeographic clades reflecting their geographic origin. Using the de-correlated composite of multiple selection signal statistics based on pairwise comparisons, we detected a different number of significant SNPs under putative selection from 13 to 28 for the six pairwise comparisons (FDR < 0.05). The identified SNPs under putative selection coincided with genes previously associated with known QTLs for morphological, adaptation, and fitness traits. Our results showedHMGA2andLLPHas strong candidate genes for height variation between Caspian horses with a small size and the other studied breeds with a medium size. Using the results of studies on human height retrieved from the GWAS catalog, we suggested 38 new putative candidate genes under selection. These results provide a genomewide map of selection signatures in the studied breeds, which represent valuable information for formulating genetic conservation and improved breeding strategies for the breeds.
Differential expression of the angiotensin receptors (AT1, AT2, and AT4) in the placental bed of HIV-infected preeclamptic women of African ancestry
Authors: Singh Shoohana , Moodley Jagidesa , Naicker Thajasvarie 
Published: June 2023

AbstractThe Renin-Angiotensin-Aldosterone System (RAAS) is implicated in the pathophysiology of preeclampsia (PE). There is a paucity of data on uteroplacental angiotensin receptors AT1-2 and 4. We evaluated the immunoexpression of AT1R, AT2R, and AT4R within the placental bed of PE vs. normotensive (N) pregnancies stratified by HIV status. Placental bed (PB) biopsies (n = 180) were obtained from N and PE women. Both groups were stratified by HIV status and gestational age into early-and late onset-PE. Immuno-labeling of AT1R, AT2R, and AT4R was quantified using morphometric image analysis. Immunostaining of PB endothelial cells (EC) and smooth muscle cells of spiral arteries (VSMC) displayed an upregulation of AT1R expression compared to the N group (p < 0.0001). Downregulation of AT2R and AT4R expression was observed in PE vs. N group (p = 0.0042 and p < 0.0001), respectively. AT2R immunoexpression declined between HIV+ve and HIV−ve groups, while AT1R and AT4R displayed an increase. An increase in AT1R expression was noted in the EOPE−ve/+ve and LOPE−ve/+ve compared to N−ve/N+ve. In contrast, AT2R and AT4R expression decreased in EOPE−ve/+ve and LOPE-ve/+ve compared to N−ve/N+ve. We demonstrate a significant downregulation of AT2R and AT4R with a concomitant elevated AT1R immunoexpression within PB of HIV-infected PE women. In addition, a decline in AT2R and AT4R with an increase in AT1R immunoexpression in PE, EOPE, and LOPE vs. normotensive pregnancies, irrespective of HIV status. Thus highlighting differential immunoexpression of uteroplacental RAAS receptors based on pregnancy type, HIV status, and gestational age.
Influence of El Niño on the variability of global shoreline position
Authors: Almar Rafael , Boucharel Julien , Graffin Marcan , Abessolo Gregoire Ondoa , Thoumyre Gregoire , Papa Fabrice , Ranasinghe Roshanka , Montano Jennifer , Bergsma Erwin W. J. , Baba Mohamed Wassim , Jin Fei-Fei 
Published: June 2023

AbstractCoastal zones are fragile and complex dynamical systems that are increasingly under threat from the combined effects of anthropogenic pressure and climate change. Using global satellite derived shoreline positions from 1993 to 2019 and a variety of reanalysis products, here we show that shorelines are under the influence of three main drivers: sea-level, ocean waves and river discharge. While sea level directly affects coastal mobility, waves affect both erosion/accretion and total water levels, and rivers affect coastal sediment budgets and salinity-induced water levels. By deriving a conceptual global model that accounts for the influence of dominant modes of climate variability on these drivers, we show that interannual shoreline changes are largely driven by different ENSO regimes and their complex inter-basin teleconnections. Our results provide a new framework for understanding and predicting climate-induced coastal hazards.
Regioselective stilbene O-methylations in Saccharinae grasses
Authors: Lui Andy C. W. , Pow Kah Chee , Lin Nan , Lam Lydia Pui Ying , Liu Guoquan , Godwin Ian D. , Fan Zhuming , Khoo Chen Jing , Tobimatsu Yuki , Wang Lanxiang , Hao Quan , Lo Clive 
Published: June 2023

AbstractO-Methylated stilbenes are prominent nutraceuticals but rarely produced by crops. Here, the inherent ability of two Saccharinae grasses to produce regioselectively O-methylated stilbenes is reported. A stilbene O-methyltransferase, SbSOMT, is first shown to be indispensable for pathogen-inducible pterostilbene (3,5-bis-O-methylated) biosynthesis in sorghum (Sorghum bicolor). Phylogenetic analysis indicates the recruitment of genus-specific SOMTs from canonical caffeic acid O-methyltransferases (COMTs) after the divergence of Sorghum spp. from Saccharum spp. In recombinant enzyme assays, SbSOMT and COMTs regioselectively catalyze O-methylation of stilbene A-ring and B-ring respectively. Subsequently, SOMT-stilbene crystal structures are presented. Whilst SbSOMT shows global structural resemblance to SbCOMT, molecular characterizations illustrate two hydrophobic residues (Ile144/Phe337) crucial for substrate binding orientation leading to 3,5-bis-O-methylations in the A-ring. In contrast, the equivalent residues (Asn128/Asn323) in SbCOMT facilitate an opposite orientation that favors 3ʹ-O-methylation in the B-ring. Consistently, a highly-conserved COMT is likely involved in isorhapontigenin (3ʹ-O-methylated) formation in wounded wild sugarcane (Saccharum spontaneum). Altogether, our work reveals the potential of Saccharinae grasses as a source of O-methylated stilbenes, and rationalize the regioselectivity of SOMT activities for bioengineering of O-methylated stilbenes.
Single cell and spatial sequencing define processes by which keratinocytes and fibroblasts amplify inflammatory responses in psoriasis
Authors: Ma Feiyang , Plazyo Olesya , Billi Allison C. , Tsoi Lam C. , Xing Xianying , Wasikowski Rachael , Gharaee-Kermani Mehrnaz , Hile Grace , Jiang Yanyun , Harms Paul W. , Xing Enze , Kirma Joseph , Xi Jingyue , Hsu Jer-En , Sarkar Mrinal K. , Chung Yutein , Di Domizio Jeremy , Gilliet Michel , Ward Nicole L. , Maverakis Emanual , Klechevsky Eynav , Voorhees John J. , Elder James T. , Lee Jun Hee , Kahlenberg J. Michelle , Pellegrini Matteo , Modlin Robert L. , Gudjonsson Johann E. 
Published: June 2023

AbstractThe immunopathogenesis of psoriasis, a common chronic inflammatory disease of the skin, is incompletely understood. Here we demonstrate, using a combination of single cell and spatial RNA sequencing, IL-36 dependent amplification of IL-17A and TNF inflammatory responses in the absence of neutrophil proteases, which primarily occur within the supraspinous layer of the psoriatic epidermis. We further show that a subset of SFRP2+ fibroblasts in psoriasis contribute to amplification of the immune network through transition to a pro-inflammatory state. The SFRP2+ fibroblast communication network involves production of CCL13, CCL19 and CXCL12, connected by ligand-receptor interactions to other spatially proximate cell types: CCR2+ myeloid cells, CCR7+LAMP3+ dendritic cells, and CXCR4 expressed on both CD8+ Tc17 cells and keratinocytes, respectively. The SFRP2+ fibroblasts also express cathepsin S, further amplifying inflammatory responses by activating IL-36G in keratinocytes. These data provide an in-depth view of psoriasis pathogenesis, which expands our understanding of the critical cellular participants to include inflammatory fibroblasts and their cellular interactions.
Characterization of p38α autophosphorylation inhibitors that target the non-canonical activation pathway
Authors: González Lorena , Díaz Lucía , Pous Joan , Baginski Blazej , Duran-Corbera Anna , Scarpa Margherita , Brun-Heath Isabelle , Igea Ana , Martin-Malpartida Pau , Ruiz Lidia , Pallara Chiara , Esguerra Mauricio , Colizzi Francesco , Mayor-Ruiz Cristina , Biondi Ricardo M. , Soliva Robert , Macias Maria J. , Orozco Modesto , Nebreda Angel R. 
Published: June 2023

Abstractp38α is a versatile protein kinase that can control numerous processes and plays important roles in the cellular responses to stress. Dysregulation of p38α signaling has been linked to several diseases including inflammation, immune disorders and cancer, suggesting that targeting p38α could be therapeutically beneficial. Over the last two decades, numerous p38α inhibitors have been developed, which showed promising effects in pre-clinical studies but results from clinical trials have been disappointing, fueling the interest in the generation of alternative mechanisms of p38α modulation. Here, we report the in silico identification of compounds that we refer to as non-canonical p38α inhibitors (NC-p38i). By combining biochemical and structural analyses, we show that NC-p38i efficiently inhibit p38α autophosphorylation but weakly affect the activity of the canonical pathway. Our results demonstrate how the structural plasticity of p38α can be leveraged to develop therapeutic opportunities targeting a subset of the functions regulated by this pathway.
Dynamic chromatin architecture of the porcine adipose tissues with weight gain and loss
Authors: Jin Long , Wang Danyang , Zhang Jiaman , Liu Pengliang , Wang Yujie , Lin Yu , Liu Can , Han Ziyin , Long Keren , Li Diyan , Jiang Yu , Li Guisen , Zhang Yu , Bai Jingyi , Li Xiaokai , Li Jing , Lu Lu , Kong Fanli , Wang Xun , Li Hua , Huang Zhiqing , Ma Jideng , Fan Xiaolan , Shen Linyuan , Zhu Li , Jiang Yanzhi , Tang Guoqing , Feng Bin , Zeng Bo , Ge Liangpeng , Li Xuewei , Tang Qianzi , Zhang Zhihua , Li Mingzhou 
Published: June 2023

AbstractUsing an adult female miniature pig model with diet-induced weight gain/weight loss, we investigated the regulatory mechanisms of three-dimensional (3D) genome architecture in adipose tissues (ATs) associated with obesity. We generated 249 high-resolution in situ Hi-C chromatin contact maps of subcutaneous AT and three visceral ATs, analyzing transcriptomic and chromatin architectural changes under different nutritional treatments. We find that chromatin architecture remodeling underpins transcriptomic divergence in ATs, potentially linked to metabolic risks in obesity development. Analysis of chromatin architecture among subcutaneous ATs of different mammals suggests the presence of transcriptional regulatory divergence that could explain phenotypic, physiological, and functional differences in ATs. Regulatory element conservation analysis in pigs and humans reveals similarities in the regulatory circuitry of genes responsible for the obesity phenotype and identified non-conserved elements in species-specific gene sets that underpin AT specialization. This work provides a data-rich tool for discovering obesity-related regulatory elements in humans and pigs.
High-throughput measurement of the content and properties of nano-sized bioparticles with single-particle profiler
Authors: Sych Taras , Schlegel Jan , Barriga Hanna M. G. , Ojansivu Miina , Hanke Leo , Weber Florian , Beklem Bostancioglu R. , Ezzat Kariem , Stangl Herbert , Plochberger Birgit , Laurencikiene Jurga , El Andaloussi Samir , Fürth Daniel , Stevens Molly M. , Sezgin Erdinc 
Published: June 2023

AbstractWe introduce a method, single-particle profiler, that provides single-particle information on the content and biophysical properties of thousands of particles in the size range 5–200 nm. We use our single-particle profiler to measure the messenger RNA encapsulation efficiency of lipid nanoparticles, the viral binding efficiencies of different nanobodies, and the biophysical heterogeneity of liposomes, lipoproteins, exosomes and viruses.
Mapping interindividual dynamics of innate immune response at single-cell resolution
Authors: Kumasaka Natsuhiko , Rostom Raghd , Huang Ni , Polanski Krzysztof , Meyer Kerstin B. , Patel Sharad , Boyd Rachel , Gomez Celine , Barnett Sam N. , Panousis Nikolaos I. , Schwartzentruber Jeremy , Ghoussaini Maya , Lyons Paul A. , Calero-Nieto Fernando J. , Göttgens Berthold , Barnes Josephine L. , Worlock Kaylee B. , Yoshida Masahiro , Nikolić Marko Z. , Stephenson Emily , Reynolds Gary , Haniffa Muzlifah , Marioni John C. , Stegle Oliver , Hagai Tzachi , Teichmann Sarah A. 
Published: June 2023

AbstractCommon genetic variants across individuals modulate the cellular response to pathogens and are implicated in diverse immune pathologies, yet how they dynamically alter the response upon infection is not well understood. Here, we triggered antiviral responses in human fibroblasts from 68 healthy donors, and profiled tens of thousands of cells using single-cell RNA-sequencing. We developed GASPACHO (GAuSsian Processes for Association mapping leveraging Cell HeterOgeneity), a statistical approach designed to identify nonlinear dynamic genetic effects across transcriptional trajectories of cells. This approach identified 1,275 expression quantitative trait loci (local false discovery rate 10%) that manifested during the responses, many of which were colocalized with susceptibility loci identified by genome-wide association studies of infectious and autoimmune diseases, including the OAS1 splicing quantitative trait locus in a COVID-19 susceptibility locus. In summary, our analytical approach provides a unique framework for delineation of the genetic variants that shape a wide spectrum of transcriptional responses at single-cell resolution.
COVID-19 vaccination exacerbates ex vivo IL-6 release from isolated PBMCs
Authors: Langgartner Dominik , Winkler Raphael , Brunner-Weisser Jonas , Rohleder Nicolas , Jarczok Marc N. , Gündel Harald , Weimer Katja , Reber Stefan O. 
Published: June 2023

AbstractEx vivo culturing of isolated PBMCs from individuals vaccinated with the coronavirus disease 2019 (COVID-19) vaccine BNT162b1 revealed a pronounced T cell response in the presence of the receptor binding domain (RBD) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein. The latter was 10-fold more pronounced than the ex vivo response of PBMCs from the same individuals to other common pathogen T cell epitope pools, suggesting COVID-19 vaccination to induce RBD-specific T cell responses and not to facilitate T cell (re)activity in general. In the current study we investigated whether COVID-19 vaccination long-lastingly affects plasma interleukin (IL)-6 concentrations, complete blood counts, ex vivo IL-6 and IL-10 secretion of PBMCs cultured under basal conditions or in the presence of concanavalin (Con) A and lipopolysaccharide (LPS), salivary cortisol and α-amylase, mean arterial pressure (MAP), heart rate (HR) as well as mental and physical health status. The study was initially designed to investigate whether the presence vs. absence of own pets during urban upbringing has protective effects against psychosocial stress-induced immune activation during adulthood. However, as COVID-19 vaccines were approved while the study was ongoing and as, therefore, both vaccinated and non-vaccinated individuals have been recruited, we were able to stratify our data set with respect to the COVID-19 vaccination status and to assess the long-lasting effects of COVID-19 vaccination on physiological immunological, cardiovascular and psychosomatic health parameters. This data is presented in the current study. We show that isolated PBMCs from individuals vaccinated against COVID-19 show a ~ 600-fold increase in basal and a ~ 6000-fold increase in ConA-induced proinflammatory IL-6 secretion, and a ~ 2-fold increase in basal and ConA-induced antiinflammatory IL-10 secretion, both in comparison with non-vaccinated individuals. In contrast, LPS-induced ex vivo IL-6 and IL-10 secretions were not affected by vaccination status, as were plasma IL-6 concentrations, complete blood counts, salivary cortisol and α-amylase, cardiovascular measures and psychosomatic health. In summary, our findings are of relevance for many clinical studies ran before/during the pandemic, clearly indicating that consideration of participants’ vaccination status is critical, at least when assessing ex vivo PBMC functionality.
Symbolic innovation at the onset of the Upper Paleolithic in Eurasia shown by the personal ornaments from Tolbor-21 (Mongolia)
Authors: Rigaud Solange , Rybin Evgeny P. , Khatsenovich Arina M. , Queffelec Alain , Paine Clea H. , Gunchinsuren Byambaa , Talamo Sahra , Marchenko Daria V. , Bolorbat Tsedendorj , Odsuren Davaakhuu , Gillam J. Christopher , Izuho Masami , Fedorchenko Alexander Yu. , Odgerel Dashdorjgochoo , Shelepaev Roman , Hublin Jean-Jacques , Zwyns Nicolas 
Published: June 2023

AbstractFigurative depictions in art first occur ca. 50,000 years ago in Europe, Africa, and Southeast Asia. Considered by most as an advanced form of symbolic behavior, they are restricted to our species. Here, we report a piece of ornament interpreted as a phallus-like representation. It was found in a 42,000 ca.-year-old Upper Paleolithic archaeological layer at the open-air archaeological site of Tolbor-21, in Mongolia. Mineralogical, microscopic, and rugosimetric analyses points toward the allochthonous origin of the pendant and a complex functional history. Three-dimensional phallic pendants are unknown in the Paleolithic record, and this discovery predates the earliest known sexed anthropomorphic representation. It attests that hunter-gatherer communities used sex anatomical attributes as symbols at a very early stage of their dispersal in the region. The pendant was produced during a period that overlaps with age estimates for early introgression events betweenHomo sapiensand Denisovans, and in a region where such encounters are plausible.
Transcriptome and metabonomics combined analysis revealed the energy supply mechanism involved in fruiting body initiation in Chinese cordyceps
Authors: He Li , Xie Fang , Zhou Gang , Chen Zhao He , Wang Jing Yi , Wang Cheng Gang 
Published: June 2023

AbstractChinese cordyceps was one of most valuable traditional Chinese medicine fungi. To elucidate the molecular mechanisms related to energy supply mechanism involved in the initiation and formation of primordium in Chinese cordyceps, we performed the integrated metabolomic and transcriptomic analyses of it at pre-primordium period, primordium germination period and after-primordium period, respectively. Transcriptome analysis showed that many genes related to ‘starch and sucrose metabolism’, ‘fructose and mannose metabolism’, ‘linoleic acid metabolism’, ‘fatty acids degradation’ and ‘glycerophospholipid metabolism’ were highly up-regulated at primordium germination period. Metabolomic analysis showed many metabolites regulated by these genes in these metabolism pathways were also markedly accumulated at this period. Consequently, we inferred that carbohydrate metabolism and β-oxidation pathway of palmitic acid and linoleic acid worked cooperatively to generate enough acyl-CoA, and then entered TCA cycle to provide energy for fruiting body initiation. Overall, our finding provided important information for further exploring the energy metabolic mechanisms of realizing the industrialization of Chinese cordyceps artificial cultivation.