bluuebunny/crossref_metadata_2025_split huggingface dataset:
Coordination of microbe–host homeostasis by crosstalk with plant innate immunity
Authors: Ma Ka-Wai , Niu Yulong , Jia Yong , Ordon Jana , Copeland Charles , Emonet Aurélia , Geldner Niko , Guan Rui , Stolze Sara Christina , Nakagami Hirofumi , Garrido-Oter Ruben , Schulze-Lefert Paul 
Published: May 2021

AbstractPlants grown in natural soil are colonized by phylogenetically structured communities of microbes known as the microbiota. Individual microbes can activate microbe-associated molecular pattern (MAMP)-triggered immunity (MTI), which limits pathogen proliferation but curtails plant growth, a phenomenon known as the growth–defence trade-off. Here, we report that, in monoassociations, 41% (62 out of 151) of taxonomically diverse root bacterial commensals suppress Arabidopsis thaliana root growth inhibition (RGI) triggered by immune-stimulating MAMPs or damage-associated molecular patterns. Amplicon sequencing of bacterial 16S rRNA genes reveals that immune activation alters the profile of synthetic communities (SynComs) comprising RGI-non-suppressive strains, whereas the presence of RGI-suppressive strains attenuates this effect. Root colonization by SynComs with different complexities and RGI-suppressive activities alters the expression of 174 core host genes, with functions related to root development and nutrient transport. Furthermore, RGI-suppressive SynComs specifically downregulate a subset of immune-related genes. Precolonization of plants with RGI-suppressive SynComs, or mutation of one commensal-downregulated transcription factor, MYB15, renders the plants more susceptible to opportunistic Pseudomonas pathogens. Our results suggest that RGI-non-suppressive and RGI-suppressive root commensals modulate host susceptibility to pathogens by either eliciting or dampening MTI responses, respectively. This interplay buffers the plant immune system against pathogen perturbation and defence-associated growth inhibition, ultimately leading to commensal–host homeostasis.
Measurement of the QT interval using the Apple Watch
Authors: Spaccarotella Carmen Anna Maria , Migliarino Serena , Mongiardo Annalisa , Sabatino Jolanda , Santarpia Giuseppe , De Rosa Salvatore , Curcio Antonio , Indolfi Ciro 
Published: May 2021

AbstractThe inherited and acquired long QT is a risk marker for potential serious cardiac arrhythmias and sudden cardiac death. Smartwatches are becoming more popular and are increasingly used for monitoring human health. The present study aimed to assess the feasibility and reliability of evaluating the QT interval in lead I, lead II, and V2 lead using a commercially available Apple Watch. One hundred nineteen patients admitted to our Cardiology Division were studied. I, II, and V2 leads were obtained after recording a standard 12-lead ECG. Lead I was recorded with the smartwatch on the left wrist and the right index finger on the crown. Lead II was obtained with the smartwatch on the left lower abdomen and the right index finger on the crown. The V2 lead was recorded with the smartwatch in the fourth intercostal space left parasternal with the right index finger on the crown. There was agreement among the QT intervals of I, II, and V2 leads and the QT mean using the smartwatch and the standard ECG with Spearman’s correlations of 0.886; 0.881; 0.793; and 0.914 (p < 0.001), respectively. The reliability of the QTc measurements between standard and smartwatch ECG was also demonstrated with a Bland–Altman analysis using different formulas. These data show that a smartwatch can feasibly and reliably assess QT interval. These results could have an important clinical impact when frequent QT interval monitoring is required.
A novel application of bubble-eye strain of Carassius auratus for ex vivo fish immunological studies
Authors: Nakajima Hiroto , Miyashita Atsushi , Hamamoto Hiroshi , Sekimizu Kazuhisa 
Published: May 2021

AbstractIn this study, we investigated a new application of bubble-eye goldfish (commercially available strain with large bubble-shaped eye sacs) for immunological studies in fishes utilizing the technical advantage of examining immune cells in the eye sac fluid ex vivo without sacrificing animals. As known in many aquatic species, the common goldfish strain showed an increased infection sensitivity at elevated temperature, which we demonstrate may be due to an immune impairment using the bubble-eye goldfish model. Injection of heat-killed bacterial cells into the eye sac resulted in an inflammatory symptom (surface reddening) and increased gene expression of pro-inflammatory cytokines observed in vivo, and elevated rearing temperature suppressed the induction of pro-inflammatory gene expressions. We further conducted ex vivo experiments using the immune cells harvested from the eye sac and found that the induced expression of pro-inflammatory cytokines was suppressed when we increased the temperature of ex vivo culture, suggesting that the temperature response of the eye-sac immune cells is a cell autonomous function. These results indicate that the bubble-eye goldfish is a suitable model for ex vivo investigation of fish immune cells and that the temperature-induced infection susceptibility in the goldfish may be due to functional impairments of immune cells.
Genome-wide identification of the tea plant bHLH transcription factor family and discovery of candidate regulators of trichome formation
Authors: Liu Renjian , Wang Yuyuan , Tang Song , Cai Jiarong , Liu Shaoqun , Zheng Peng , Sun Binmei 
Published: May 2021

AbstractLeaf trichomes play vital roles in plant resistance and the quality of tea. Basic helix-loop-helix (bHLH) transcription factors (TFs) play an important role in regulating plant development and growth. In this study, a total of 134 CsbHLH proteins were identified in the Camellia sinensis var. sinensis (CSS) genome. They were divided into 17 subgroups according to the Arabidopsis thaliana classification. Phylogenetic tree analysis indicated that members of subgroups IIIc-I and IIIc-II might be associated with trichome formation. The expression patterns of CsbHLH116, CsbHLH133, CsbHLH060, CsbHLH028, CsbHLH024, CsbHLH112 and CsbHLH053 from clusters 1, 3 and 5 were similar to the trichome distribution in tea plants. CsbHLH024 and CsbHLH133 were located in the cell nucleus and possessed transcriptional activation ability. They could interact with CsTTG1, which is a regulator of tea trichome formation. This study provides useful information for further research on the function of CsbHLHs in trichome formation.
Niche specificity and functional diversity of the bacterial communities associated with Ginkgo biloba and Panax quinquefolius
Authors: Shehata Hanan R. , Ragupathy Subramanyam , Henry Thomas A. , Newmaster Steven G. 
Published: May 2021

AbstractPlant-associated bacteria can establish mutualistic relationships with plants to support plant health. Plant tissues represent heterogeneous niches with distinct characteristics and may thus host distinct microbial populations. The objectives of this study are to investigate the bacterial communities associated with two medicinally and commercially important plant species; Ginkgo biloba and Panax quinquefolius using high Throughput Sequencing (HTS) of 16S rRNA gene, and to evaluate the extent of heterogeneity in bacterial communities associated with different plant niches. Alpha diversity showed that number of operational taxonomic units (OTUs) varied significantly by tissue type. Beta diversity revealed that the composition of bacterial communities varied between tissue types. In Ginkgo biloba and Panax quinquefolius, 13% and 49% of OTUs, respectively, were ubiquitous in leaf, stem and root. Proteobacteria, Bacteroidetes, Actinobacteria and Acidobacteria were the most abundant phyla in Ginkgo biloba while Proteobacteria, Bacteroidetes, Actinobacteria, Plantomycetes and Acidobacteria were the most abundant phyla in Panax quinquefolius. Functional prediction of these bacterial communities using MicrobiomeAnalyst revealed 5843 and 6251 KEGG orthologs in Ginkgo biloba and Panax quinquefolius, respectively. A number of these KEGG pathways were predicted at significantly different levels between tissues. These findings demonstrate the heterogeneity, niche specificity and functional diversity of plant-associated bacteria.
Plant-expressed virus-like particles reveal the intricate maturation process of a eukaryotic virus
Authors: Castells-Graells Roger , Ribeiro Jonas R. S. , Domitrovic Tatiana , Hesketh Emma L. , Scarff Charlotte A. , Johnson John E. , Ranson Neil A. , Lawson David M. , Lomonossoff George P. 
Published: May 2021

AbstractMany virus capsids undergo exquisitely choreographed maturation processes in their host cells to produce infectious virions, and these remain poorly understood. As a tool for studying virus maturation, we transiently expressed the capsid protein of the insect virus Nudaurelia capensis omega virus (NωV) in Nicotiana benthamiana and were able to purify both immature procapsids and mature capsids from infiltrated leaves by varying the expression time. Cryo-EM analysis of the plant-produced procapsids and mature capsids to 6.6 Å and 2.7 Å resolution, respectively, reveals that in addition to large scale rigid body motions, internal regions of the subunits are extensively remodelled during maturation, creating the active site required for autocatalytic cleavage and infectivity. The mature particles are biologically active in terms of their ability to lyse membranes and have a structure that is essentially identical to authentic virus. The ability to faithfully recapitulate and visualize a complex maturation process in plants, including the autocatalytic cleavage of the capsid protein, has revealed a ~30 Å translation-rotation of the subunits during maturation as well as conformational rearrangements in the N and C-terminal helical regions of each subunit.
Tryptophan metabolism drives dynamic immunosuppressive myeloid states in IDH-mutant gliomas
Authors: Friedrich Mirco , Sankowski Roman , Bunse Lukas , Kilian Michael , Green Edward , Ramallo Guevara Carina , Pusch Stefan , Poschet Gernot , Sanghvi Khwab , Hahn Markus , Bunse Theresa , Münch Philipp , Gegner Hagen M. , Sonner Jana K. , von Landenberg Anna , Cichon Frederik , Aslan Katrin , Trobisch Tim , Schirmer Lucas , Abu-Sammour Denis , Kessler Tobias , Ratliff Miriam , Schrimpf Daniel , Sahm Felix , Hopf Carsten , Heiland Dieter H. , Schnell Oliver , Beck Jürgen , Böttcher Chotima , Fernandez-Zapata Camila , Priller Josef , Heiland Sabine , Gutcher Ilona , Quintana Francisco J. , von Deimling Andreas , Wick Wolfgang , Prinz Marco , Platten Michael 
Published: May 2021

AbstractThe dynamics and phenotypes of intratumoral myeloid cells during tumor progression are poorly understood. Here we define myeloid cellular states in gliomas by longitudinal single-cell profiling and demonstrate their strict control by the tumor genotype: in isocitrate dehydrogenase (IDH)-mutant tumors, differentiation of infiltrating myeloid cells is blocked, resulting in an immature phenotype. In late-stage gliomas, monocyte-derived macrophages drive tolerogenic alignment of the microenvironment, thus preventing T cell response. We define the IDH-dependent tumor education of infiltrating macrophages to be causally related to a complex re-orchestration of tryptophan metabolism, resulting in activation of the aryl hydrocarbon receptor. We further show that the altered metabolism of IDH-mutant gliomas maintains this axis in bystander cells and that pharmacological inhibition of tryptophan metabolism can reverse immunosuppression. In conclusion, we provide evidence of a glioma genotype-dependent intratumoral network of resident and recruited myeloid cells and identify tryptophan metabolism as a target for immunotherapy of IDH-mutant tumors.
Two three-dimensional polyanionic clusters [M(P4Mo6)2] (M = Co, Zn) exhibiting excellent photocatalytic CO2 reduction performance
Authors: Li Jia-Nian , Du Ze-Yu , Li Ning-Fang , Han Ye-Min , Zang Ting-Ting , Yang Mu-Xiu , Liu Xiao-Mei , Wang Ji-Lei , Mei Hua , Xu Yan 
Published: May 2021

Two captivating molybdophosphate hybrids [M(P4Mo6O31)2]n− (M = Co, Zn) have been successfully synthesized. Compound 1 shows good catalytic activity and the mechanism of its catalysis of the photoreduction of CO2 to CO has been investigated.
FOXD1 is a prognostic biomarker and correlated with macrophages infiltration in head and neck squamous cell carcinoma
Authors: Liang Huazhen , Zhang Chunning , Li Chaoming , Li Changguo , Wang Yanli , Lin Huaming 
Published: May 2021

Abstract
Background: Forkhead Box D1 (FOXD1) is differentially expressed in various tumors. However, its role and correlation with immune cell infiltration remains uncertain in head and neck squamous cell carcinoma (HNSC).
Methods: FOXD1 expression was analyzed in The Cancer Genome Atlas (TCGA) pan-cancer data. The clinical prognosis influence of FOXD1 was evaluated by clinical survival data of TCGA. Enrichment analysis of FOXD1 was performed using R packages ‘clusterProfiler’. We downloaded the immune cell infiltration score of TCGA samples from published articles, and analyzed the correlation between immune cell infiltration level and FOXD1 expression.
Results: FOXD1 was highly expressed and associated with poorer overall survival (OS, P&lt;0.0001), disease-specific survival (DSS, P=0.00011), and progression-free interval (PFI, P&lt;0.0001) in HNSC and some other tumors. In addition, FOXD1 expression was significantly correlated with infiltration of immune cells. Tumor-associated macrophages (TAMs) infiltration increased in tissues with high FOXD1 expression in HNSC. Immunosuppressive genes such as PD-L1, IL-10, TGFB1, and TGFBR1 were significantly positively correlated with FOXD1.
Conclusions: Our study suggests FOXD1 to be an oncogene and act as an indicator of poor prognosis in HNSC. FOXD1 might contribute to the TAM infiltration in HNSC. High FOXD1 may be associated with tumor immunosuppression status.
Identification of m6A methyltransferase-related lncRNA signature for predicting immunotherapy and prognosis in patients with hepatocellular carcinoma
Authors: Li Lili , Xie Rongrong , Lu Guangrong 
Published: May 2021

Abstract
N6-methyladenosine (m6A) methyltransferase has been shown to be an oncogene in a variety of cancers. Nevertheless, the relationship between the long non-coding RNAs (lncRNAs) and hepatocellular carcinoma (HCC) remains elusive. We integrated the gene expression data of 371 HCC and 50 normal tissues from The Cancer Genome Atlas (TCGA) database. Differentially expressed protein-coding genes (DE-PCGs)/lncRNAs (DE-lncRs) analysis and univariate regression and Kaplan–Meier (K–M) analysis were performed to identify m6A methyltransferase-related lncRNAs. Three prognostic lncRNAs were selected by univariate and LASSO Cox regression analyses to construct the m6A methyltransferase-related lncRNA signature. Multivariate Cox regression analyses illustrated that this signature was an independent prognostic factor for overall survival (OS) prediction. The Gene Set Enrichment Analysis (GSEA) suggested that the m6A methyltransferase-related lncRNAs were involved in the immune-related biological processes (BPs) and pathways. Besides, we discovered that the lncRNAs signature was correlated with the tumor microenvironment (TME) and the expression of critical immune checkpoints. Tumor Immune Dysfunction and Exclusion (TIDE) analysis revealed that the lncRNAs could predict the clinical response to immunotherapy. Our study had originated a prognostic signature for HCC based on the potential prognostic m6A methyltransferase-related lncRNAs. The present study had deepened the understanding of the TME status of HCC patients and laid a theoretical foundation for the choice of immunotherapy.
Handheld bioprinting strategies for in situ wound dressing
Authors: Li Hongbin , Cheng Feng , Orgill Dennis P. , Yao Junjie , Zhang Yu Shrike 
Published: May 2021

Abstract
Handheld bioprinting has recently attracted considerable attention as a technology to deliver biomaterials and/or cells to injury sites by using freeform, user-instructed deposition approaches, specifically targeted towards in situ wound dressing and healing. In this review, we present a concise introduction of handheld bioprinting, and a thorough discussion on design and manufacture of handheld bioprinters and choice over bioinks. Finally, the advantages, challenges, and prospective of the said technologies are elaborated. It is believed that handheld bioprinting will play an essential role in the field of in situ wound healing mainly due to its excellent portability, user-friendliness, cost-effectiveness, and amenability to various wound needs.
The physiological role of estrogen receptor functional domains
Authors: Arao Yukitomo , Korach Kenneth S. 
Published: May 2021

Abstract
Estrogen receptor (ER) is a member of the nuclear receptor superfamily whose members share conserved domain structures, including a DNA-binding domain (DBD) and ligand-binding domain (LBD). Estrogenic chemicals work as ligands for activation or repression of ER-mediated transcriptional activity derived from two transactivation domains: AF-1 and AF-2. AF-2 is localized in the LBD, and helix 12 of the LBD is essential for controlling AF-2 functionality. The positioning of helix 12 defines the ER alpha (ERα) ligand properties as agonists or antagonists. In contrast, it is still less well defined as to the ligand-dependent regulation of N-terminal AF-1 activity. It has been thought that the action of selective estrogen receptor modulators (SERMs) is mediated by the regulation of a tissue specific AF-1 activity rather than AF-2 activity. However, it is still unclear how SERMs regulate AF-1 activity in a tissue-selective manner. This review presents some recent observations toward information of ERα mediated SERM actions related to the ERα domain functionality, focusing on the following topics. (1) The F-domain, which is connected to helix 12, controls 4-hydroxytamoxifen (4OHT) mediated AF-1 activation associated with the receptor dimerization activity. (2) The zinc-finger property of the DBD for genomic sequence recognition. (3) The novel estrogen responsive genomic DNA element, which contains multiple long-spaced direct-repeats without a palindromic ERE sequence, is differentially recognized by 4OHT and E2 ligand bound ERα transactivation complexes.
Repetition Priming in Treatment of Anomia
Authors: Tabrizi Rana , Walton Logan , Simon Emily , Silkes JoAnn P. 
Published: May 2021

Purpose:
Repetition priming has been suggested as a method for targeting implicit processes in anomia treatment. Prior studies have used masked priming for this purpose. This study extends that work with visible primes, a more clinically feasible approach.

Method:
This study used a single-subject design across three participants with aphasia. Treatment involved repeated exposure to identity primes (trained condition) or sham primes (untrained condition) paired with pictures. Analyses assessed acquisition effects for trained items and untrained items that were seen during the training period, generalization to untrained items that had not been seen, and generalization to broader language skills, immediately and 3 months post-treatment.

Results:
All participants improved in naming trained items immediately after treatment, with greater improvements for trained than for untrained items. All participants maintained some degree of improvement on trained items 3 months post-treatment, although the degree differed across participants. Inconsistent generalization occurred to unexposed items. Improvements were noted in some areas of broader language ability, although these varied.

Conclusions:
These data suggest a repetition priming treatment paradigm may increase naming accuracy for individuals with anomia and may benefit other aspects of language. Participant factors may have influenced response to treatment. Directions for future investigation are discussed.
The X-CLASS survey: A catalogue of 1646 X-ray-selected galaxy clusters up to z ∼ 1.5
Authors: Koulouridis E. , Clerc N. , Sadibekova T. , Chira M. , Drigga E. , Faccioli L. , Le Fèvre J. P. , Garrel C. , Gaynullina E. , Gkini A. , Kosiba M. , Pacaud F. , Pierre M. , Ridl J. , Tazhenova K. , Adami C. , Altieri B. , Baguley J.-C. , Cabanac R. , Cucchetti E. , Khalikova A. , Lieu M. , Melin J.-B. , Molham M. , Ramos-Ceja M. E. , Soucail G. , Takey A. , Valtchanov I. 
Published: May 2021

Context. Cosmological probes based on galaxy clusters rely on cluster number counts and large-scale structure information. X-ray cluster surveys are well suited for this purpose because they are far less affected by projection effects than optical surveys, and cluster properties can be predicted with good accuracy.
Aims. The XMM Cluster Archive Super Survey, X-CLASS, is a serendipitous search of X-ray-detected galaxy clusters in 4176 XMM-Newton archival observations until August 2015. All observations are clipped to exposure times of 10 and 20 ks to obtain uniformity, and they span ∼269 deg2 across the high-Galactic latitude sky (|b| > 20°). The main goal of the survey is the compilation of a well-selected cluster sample suitable for cosmological analyses.
Methods. We describe the detection algorithm, the visual inspection, the verification process, and the redshift validation of the cluster sample, as well as the cluster selection function computed by simulations. We also present the various metadata that are released with the catalogue, along with two different count-rate measurements, an automatic one provided by the pipeline, and a more detailed and accurate interactive measurement. Furthermore, we provide the redshifts of 124 clusters obtained with a dedicated multi-object spectroscopic follow-up programme.
Results. With this publication, we release the new X-CLASS catalogue of 1646 well-selected X-ray-detected clusters over a wide sky area, along with their selection function. The sample spans a wide redshift range, from the local Universe up to z ∼ 1.5, with 982 spectroscopically confirmed clusters, and over 70 clusters above z = 0.8. The redshift distribution peaks at z ∼ 0.1, while if we remove the pointed observations it peaks at z ∼ 0.3. Because of its homogeneous selection and thorough verification, the cluster sample can be used for cosmological analyses, but also as a test-bed for the upcoming eROSITA observations and other current and future large-area cluster surveys. It is the first time that such a catalogue is made available to the community via an interactive database which gives access to a wealth of supplementary information, images, and data.