bluuebunny/crossref_metadata_2025_split huggingface dataset:
Combining whole-genome shotgun sequencing and rRNA gene amplicon analyses to improve detection of microbe–microbe interaction networks in plant leaves
Authors: Regalado Julian , Lundberg Derek S , Deusch Oliver , Kersten Sonja , Karasov Talia , Poersch Karin , Shirsekar Gautam , Weigel Detlef 
Published: May 2020

Abstract
Microorganisms from all domains of life establish associations with plants. Although some harm the plant, others antagonize pathogens or prime the plant immune system, support the acquisition of nutrients, tune plant hormone levels, or perform additional services. Most culture-independent plant microbiome research has focused on amplicon sequencing of the 16S rRNA gene and/or the internal transcribed spacer (ITS) of rRNA genomic loci, which show the relative abundance of the microbes to each other. Here, we describe shotgun sequencing of 275 wild Arabidopsis thaliana leaf microbiomes from southwest Germany, with additional bacterial 16S and eukaryotic ITS1 rRNA amplicon data from 176 of these samples. Shotgun data, which unlike the amplicon data capture the ratio of microbe to plant DNA, enable scaling of microbial read abundances to reflect the microbial load on the host. In a more cost-effective hybrid strategy, we show they also allow a similar scaling of amplicon data to overcome compositionality problems. Our wild plants were dominated by bacterial sequences, with eukaryotes contributing only a minority of reads. Microbial membership showed weak associations with both site of origin and plant genotype, both of which were highly confounded in this dataset. There was large variation among microbiomes, with one extreme comprising samples of low complexity and a high load of microorganisms typical of infected plants, and the other extreme being samples of high complexity and a low microbial load. Critically, considering absolute microbial load led to fundamentally different conclusions about microbiome assembly and the interaction networks among major taxa.
Metagenome-assembled genomes reveal unique metabolic adaptations of a basal marine Thaumarchaeota lineage
Authors: Reji Linta , Francis Christopher A 
Published: May 2020

Abstract
Thaumarchaeota constitute an abundant and ubiquitous phylum of Archaea that play critical roles in the global nitrogen and carbon cycles. Most well-characterized members of the phylum are chemolithoautotrophic ammonia-oxidizing archaea (AOA), which comprise up to 5 and 20% of the total single-celled life in soil and marine systems, respectively. Using two high-quality metagenome-assembled genomes (MAGs), here we describe a divergent marine thaumarchaeal clade that is devoid of the ammonia-oxidation machinery and the AOA-specific carbon-fixation pathway. Phylogenomic analyses placed these genomes within the uncultivated and largely understudied marine pSL12-like thaumarchaeal clade. The predominant mode of nutrient acquisition appears to be aerobic heterotrophy, evidenced by the presence of respiratory complexes and various organic carbon degradation pathways. Both genomes encoded several pyrroloquinoline quinone (PQQ)-dependent alcohol dehydrogenases, as well as a form III RuBisCO. Metabolic reconstructions suggest anaplerotic CO2 assimilation mediated by RuBisCO, which may be linked to the central carbon metabolism. We conclude that these genomes represent a hitherto unrecognized evolutionary link between predominantly anaerobic basal thaumarchaeal lineages and mesophilic marine AOA, with important implications for diversification within the phylum Thaumarchaeota.
A neuromarker of individual general fluid intelligence from the white-matter functional connectome
Authors: Li Jiao , Biswal Bharat B. , Meng Yao , Yang Siqi , Duan Xujun , Cui Qian , Chen Huafu , Liao Wei 
Published: May 2020

AbstractNeuroimaging studies have uncovered the neural roots of individual differences in human general fluid intelligence (Gf). Gf is characterized by the function of specific neural circuits in brain gray-matter; however, the association between Gf and neural function in brain white-matter (WM) remains unclear. Given reliable detection of blood-oxygen-level-dependent functional magnetic resonance imaging (BOLD-fMRI) signals in WM, we used a functional, rather than an anatomical, neuromarker in WM to identify individual Gf. We collected longitudinal BOLD-fMRI data (in total three times, ~11 months between time 1 and time 2, and ~29 months between time 1 and time 3) in normal volunteers at rest, and identified WM functional connectomes that predicted the individual Gf at time 1 (n = 326). From internal validation analyses, we demonstrated that the constructed predictive model at time 1 predicted an individual’s Gf from WM functional connectomes at time 2 (time 1 ∩ time 2: n = 105) and further at time 3 (time 1 ∩ time 3: n = 83). From external validation analyses, we demonstrated that the predictive model from time 1 was generalized to unseen individuals from another center (n = 53). From anatomical aspects, WM functional connectivity showing high predictive power predominantly included the superior longitudinal fasciculus system, deep frontal WM, and ventral frontoparietal tracts. These results thus demonstrated that WM functional connectomes offer a novel applicable neuromarker of Gf and supplement the gray-matter connectomes to explore brain–behavior relationships.
Rheb1 protects against cisplatin-induced tubular cell death and acute kidney injury via maintaining mitochondrial homeostasis
Authors: Lu Qingmiao , Wang Mingjie , Gui Yuan , Hou Qing , Gu Mengru , Liang Yan , Xiao Bo , Zhao Allan Zijian , Dai Chunsun 
Published: May 2020

AbstractRas homolog enriched in brain (Rheb1), a small GTPase, plays a crucial role in regulating cell growth, differentiation, and survival. However, the role and mechanisms for Rheb1 in tubular cell survival and acute kidney injury (AKI) remain unexplored. Here we found that Rheb1 signaling was activated in kidney tubule of AKI patients and cisplatin-treated mice. A mouse model of tubule-specific deletion of Rheb1 (Tubule-Rheb1−/−) was generated. Compared to control littermates, Tubule-Rheb1−/− mice were phenotypically normal within 2 months after birth but developed more severe kidney dysfunction, tubular cell death including apoptosis, necroptosis and ferroptosis, mitochondrial defect and less PGC-1α expression after cisplatin injection. In primary cultured tubular cells, Rheb1 ablation exacerbated cisplatin-induced cell death and mitochondrial defect. Furthermore, haploinsufficiency for Tsc1 in tubular cells led to Rheb1 activation and mitigated cisplatin-induced cell death, mitochondrial defect and AKI. Together, this study uncovers that Rheb1 may protect against cisplatin-induced tubular cell death and AKI through maintaining mitochondrial homeostasis.
Ciao1 interacts with Crumbs and Xpd to regulate organ growth in Drosophila
Authors: Jung Jean , Yeom Eunbyul , Choi Kwang-Wook 
Published: May 2020

AbstractCiao1 is a component of the cytosolic iron–sulfur cluster assembly (CIA) complex along with MMS19 and MIP18. Xeroderma pigmentosum group D (XPD), a DNA helicase involved in regulation of cell cycle and transcription, is a CIA target for iron–sulfur (Fe/S) modification. In vivo function of Ciao1 and Xpd in developing animals has been rarely studied. Here, we reveal that Ciao1 interacts with Crumbs (Crb), Galla, and Xpd to regulate organ growth in Drosophila. Abnormal growth of eye by overexpressing Crb intracellular domain (Crbintra) is suppressed by reducing the Ciao1 level. Loss of Ciao1 or Xpd causes similar impairment in organ growth. RNAi knockdown of both Ciao1 and Xpd show similar phenotypes as Ciao1 or Xpd RNAi alone, suggesting their function in a pathway. Growth defects caused by Ciao1 RNAi are suppressed by overexpression of Xpd. Ciao1 physically interacts with Crbintra, Galla, and Xpd, supporting their genetic interactions. Remarkably, Xpd RNAi defects can also be suppressed by Ciao1 overexpression, implying a mutual regulation between the two genes. Ciao1 mutant clones in imaginal discs show decreased levels of Cyclin E (CycE) and death-associated inhibitor of apoptosis 1 (Diap1). Xpd mutant clones share the similar reduction of CycE and Diap1. Consequently, knockdown of Ciao1 and Xpd by RNAi show increased apoptotic cell death. Further, CycE overexpression is sufficient to restore the growth defects from Ciao1 RNAi or Xpd RNAi. Interestingly, Diap1 overexpression in Ciao1 mutant clones induces CycE expression, suggesting that reduced CycE in Ciao1 mutant cells is secondary to loss of Diap1. Taken together, this study reveals new roles of Ciao1 and Xpd in cell survival and growth through regulating Diap1 level during organ development.
Weak signal enhancement by nonlinear resonance control in a forced nano-electromechanical resonator
Authors: Chowdhury Avishek , Clerc Marcel G. , Barbay Sylvain , Robert-Philip Isabelle , Braive Remy 
Published: May 2020

AbstractDriven non-linear resonators can display sharp resonances or even multistable behaviours amenable to induce strong enhancements of weak signals. Such enhancements can make use of the phenomenon of vibrational resonance, whereby a weak low-frequency signal applied to a bistable resonator can be amplified by driving the non-linear oscillator with another appropriately-adjusted non-resonant high-frequency field. Here we demonstrate experimentally and theoretically a significant resonant enhancement of a weak signal by use of a vibrational force, yet in a monostable system consisting of a driven nano-electromechanical nonlinear resonator. The oscillator is subjected to a strong quasi-resonant drive and to two additional tones: a weak signal at lower frequency and a non-resonant driving at an intermediate frequency. We analyse this phenomenon in terms of coherent nonlinear resonance manipulation. Our results illustrate a general mechanism which might have applications in the fields of microwave signal amplification or sensing for instance.
Dual heterogeneous structures lead to ultrahigh strength and uniform ductility in a Co-Cr-Ni medium-entropy alloy
Authors: Du X. H. , Li W. P. , Chang H. T. , Yang T. , Duan G. S. , Wu B. L. , Huang J. C. , Chen F. R. , Liu C. T. , Chuang W. S. , Lu Y. , Sui M. L. , Huang E. W. 
Published: May 2020

AbstractAlloys with ultra-high strength and sufficient ductility are highly desired for modern engineering applications but difficult to develop. Here we report that, by a careful controlling alloy composition, thermomechanical process, and microstructural feature, a Co-Cr-Ni-based medium-entropy alloy (MEA) with a dual heterogeneous structure of both matrix and precipitates can be designed to provide an ultra-high tensile strength of 2.2 GPa and uniform elongation of 13% at ambient temperature, properties that are much improved over their counterparts without the heterogeneous structure. Electron microscopy characterizations reveal that the dual heterogeneous structures are composed of a heterogeneous matrix with both coarse grains (10∼30 μm) and ultra-fine grains (0.5∼2 μm), together with heterogeneous L12-structured nanoprecipitates ranging from several to hundreds of nanometers. The heterogeneous L12 nanoprecipitates are fully coherent with the matrix, minimizing the elastic misfit strain of interfaces, relieving the stress concentration during deformation, and playing an active role in enhanced ductility.
YAP1/TAZ drives ependymoma-like tumour formation in mice
Authors: Eder Noreen , Roncaroli Federico , Domart Marie-Charlotte , Horswell Stuart , Andreiuolo Felipe , Flynn Helen R. , Lopes Andre T. , Claxton Suzanne , Kilday John-Paul , Collinson Lucy , Mao Jun-Hao , Pietsch Torsten , Thompson Barry , Snijders Ambrosius P. , Ultanir Sila K. 
Published: May 2020

AbstractYAP1 gene fusions have been observed in a subset of paediatric ependymomas. Here we show that, ectopic expression of active nuclear YAP1 (nlsYAP5SA) in ventricular zone neural progenitor cells using conditionally-induced NEX/NeuroD6-Cre is sufficient to drive brain tumour formation in mice. Neuronal differentiation is inhibited in the hippocampus. Deletion of YAP1’s negative regulators LATS1 and LATS2 kinases in NEX-Cre lineage in double conditional knockout mice also generates similar tumours, which are rescued by deletion of YAP1 and its paralog TAZ. YAP1/TAZ-induced mouse tumours display molecular and ultrastructural characteristics of human ependymoma. RNA sequencing and quantitative proteomics of mouse tumours demonstrate similarities to YAP1-fusion induced supratentorial ependymoma. Finally, we find that transcriptional cofactor HOPX is upregulated in mouse models and in human YAP1-fusion induced ependymoma, supporting their similarity. Our results show that uncontrolled YAP1/TAZ activity in neuronal precursor cells leads to ependymoma-like tumours in mice.
Trefoil factors share a lectin activity that defines their role in mucus
Authors: Järvå Michael A. , Lingford James P. , John Alan , Soler Niccolay Madiedo , Scott Nichollas E. , Goddard-Borger Ethan D. 
Published: May 2020

AbstractThe mucosal epithelium secretes a host of protective disulfide-rich peptides, including the trefoil factors (TFFs). The TFFs increase the viscoelasticity of the mucosa and promote cell migration, though the molecular mechanisms underlying these functions have remained poorly defined. Here, we demonstrate that all TFFs are divalent lectins that recognise the GlcNAc-α-1,4-Gal disaccharide, which terminates some mucin-like O-glycans. Degradation of this disaccharide by a glycoside hydrolase abrogates TFF binding to mucins. Structural, mutagenic and biophysical data provide insights into how the TFFs recognise this disaccharide and rationalise their ability to modulate the physical properties of mucus across different pH ranges. These data reveal that TFF activity is dependent on the glycosylation state of mucosal glycoproteins and alludes to a lectin function for trefoil domains in other human proteins.
The use of a natural substrate for immobilization of microalgae cultivated in wastewater
Authors: Garbowski Tomasz , Pietryka Mirosława , Pulikowski Krzysztof , Richter Dorota 
Published: May 2020

AbstractThe methods of separation of microalgae has a significant impact in the economic aspects of their cultivation. In this study, pine bark was used as a substrate for immobilization of microalgal biomass cultivated in raw municipal sewage. The experiment was conducted in cylindrical photobioreactors (PBRs) with circulation of wastewater. Biomass was cultivated for 42 days. After that time, abundant growth of the biofilm with microalgae on the surface of pine bark as well as improvement of the quality of treated sewage were observed. The efficiency of removal of nutrients from wastewater was 64–81% for total nitrogen and 97–99% for total phosphorus. Moreover, the concentration of suspended solids in sewage was reduced, which resulted in a decrease in turbidity by more than 90%. Colorimetric analysis and Volatile Matter (VM) content in the substrate showed a decrease in the Higher Heating Value (HHV) and concentration of VM due to the proliferation of biofilm.
Long-term treatment with subcutaneous immunoglobulin in patients with chronic inflammatory demyelinating polyradiculoneuropathy: a follow-up period up to 7 years
Authors: Gentile L. , Mazzeo A. , Russo M. , Arimatea I. , Vita G. , Toscano A. 
Published: May 2020

AbstractChronic Inflammatory Demyelinating Polyneuropathy (CIDP) is a rare and heterogeneous acquired sensory-motor polyneuropathy with autoimmune pathogenesis. Intravenous immunoglobulins (IVIG) are a well-established therapy for CIDP: it is well known that at least two-thirds of these patients need these infusions for several years. More recently, Subcutaneous Immunoglobulins (SCIg) have been proved to be effective: this finding has been confirmed either in isolated cases or in few randomized trials. However, it appeared that the longest SCIg treatment follow up lasted no longer than 48 months. We report herein the results of a long-term SCIg treatment with a follow up period up to 7 years (84 months), considering safety, tolerability and patients’ perception of SCIg treatment in a CIDP population. We studied 17 patients (10 M; 7 F) with a diagnosis of CIDP, defined according to the EFNS/PNS criteria, successfully treated with IVIG every 4/6 weeks before being switched to SCIg treatment. Clinical follow-up included, apart from a routinely clinical assessment, the administration of Medical Research Council (MRC) sum-score, the Overall Neuropathy Limitation Scale (ONLS) and the Life Quality Index questionnaire (LQI). The results showed that, in the majority of this pre-selected group of CIDP patients (16/17), SCIg were well tolerated and were preferred over IVIG. Strength and motor functions remained stable or even improved during the long term follow-up (up to 84 months) with benefits on walking capability and resistance, manual activity performances and fatigue reduction.
The role of the adaptor molecule STING during Schistosoma mansoni infection
Authors: Souza Cláudia , Sanches Rodrigo C. O. , Assis Natan R. G. , Marinho Fábio V. , Mambelli Fábio S. , Morais Suellen B. , Gimenez Enrico G. T. , Guimarães Erika S. , Castro Tiago B. R. , Oliveira Sergio C. 
Published: May 2020

AbstractSchistosomiasis is a human parasitic disease responsible for serious consequences for public health, as well as severe socioeconomic impacts in developing countries. Here, we provide evidence that the adaptor molecule STING plays an important role inSchistosoma mansoniinfection.S. mansoniDNA is sensed by cGAS leading to STING activation in murine embryonic fibroblasts (MEFs). Sting−/−and C57BL/6 (WT) mice were infected with schistosome cercariae in order to assess parasite burden and liver pathology. Sting−/−miceshowedworm burden reduction but no change in the number of eggs or granuloma numbers and area when compared to WT animals. Immunologically, a significant increase in IFN-γ production by the spleen cells was observed in Sting−/−animals. Surprisingly, Sting−/−mice presented an elevated percentage of neutrophils in lungs, bronchoalveolar lavage, and spleens. Moreover, Sting−/−neutrophils exhibited increased survival rate, but similar ability to kill schistosomulain vitrowhen stimulated with IFN-γ when compared to WT cells. Finally, microbiota composition was altered in Sting−/−mice, revealing a more inflammatory profile when compared to WT animals. In conclusion, this study demonstrates that STING signaling pathway is important forS. mansoniDNA sensing and the lack of this adaptor molecule leads to enhanced resistance to infection.
Implications of personality and parental education on healthy lifestyles among adolescents
Authors: Yañez Aina M , Bennasar-Veny Miquel , Leiva Alfonso , García-Toro Mauro 
Published: May 2020

AbstractSeveral studies have shown an association between personality and health status. The aim of this study was to evaluate the association between personality traits, parental education and health-related lifestyles in a cohort of Spanish adolescents. This is a longitudinal study with a source population of 1,123 third-year students (aged 14–15) in secondary schools in Spain. At the baseline evaluation sociodemographic variables, parental education and personality (Big Five Questionnaire for Children) were collected. At 18 months of follow-up health related lifestyles, including adherence to a healthy diet (KidMed index), tobacco and alcohol consumption, physical exercise, sleep problems and recreative screen and social network time were collected. A total of 824 adolescents (73.4%) completed the 18 months assessment and 695 (84.3%) presented valid data. Higher conscientiousness was associated to a lower risk for non-adherence to Mediterranean diet (OR = 0.7, 95% CIs=0.5–0.9), tobacco (OR = 0.5, 95% CIs=0.3–0.7) and alcohol consumption (OR = 0.6, 95% CIs=0.5–0.8), excessive use of screens (OR = 0.7, 95% CIs=0.5–0.9) and social network sites (OR = 0.7, 95% CIs=0.5–0.8). Higher levels of extraversion was significantly related to a lower risk of physical inactivity (OR = 0.7, 95% CIs=0.6–0.9), but they are at a higher risk of low adherence to Mediterranean diet (OR = 1.3, 95% CIs=1.0–1.7), tobacco (OR = 2.7, 95% CIs=1.7–4.3) and alcohol consumption (OR = 1.9, 95% CIs=1.5–2.4) and excessive use of social network sites (OR = 1.6, 95% CIs=1.3–1.9). High levels of emotional instability were associated with tobacco consumption (OR = 1.5, 95% CIs=1.0–2.2) and sleep problems (OR = 2.0, 95% CIs=1.5–2.7). Finally, we found an association with lower parental education and adolescents’ low adherence to Mediterranean diet (OR = 1.6, 95% CIs=1.0–2.4) and sleep problems (OR = 1.8, 95% CIs=1.0–3.0). Cluster analysis of health-related behaviours indicated the presence of two different clusters (unhealthy and healthy adolescents) that were associated with personality traits. Conscientiousness, extraversion, emotional instability and parental education are independent factors associated with the acquisition of adolescent healthy lifestyles.
The early local and systemic Type I interferon responses to ultraviolet B light exposure are cGAS dependent
Authors: Skopelja-Gardner Sladjana , An Jie , Tai Joyce , Tanaka Lena , Sun Xizhang , Hermanson Payton , Baum Rebecca , Kawasumi Masaoki , Green Richard , Gale Michael , Kalus Andrea , Werth Victoria P. , Elkon Keith B. 
Published: May 2020

AbstractMost systemic lupus erythematosus (SLE) patients are photosensitive and ultraviolet B light (UVB) exposure worsens cutaneous disease and precipitates systemic flares of disease. The pathogenic link between skin disease and systemic exacerbations in SLE remains elusive. In an acute model of UVB-triggered inflammation, we observed that a single UV exposure triggered a striking IFN-I signature not only in the skin, but also in the blood and kidneys. The early IFN-I signature was significantly higher in female compared to male mice. The early IFN-I response in the skin was almost entirely, and in the blood partly, dependent on the presence of cGAS, as was skin inflammatory cell infiltration. Inhibition of cGAMP hydrolysis augmented the UVB-triggered IFN-I response. UVB skin exposure leads to cGAS-activation and both local and systemic IFN-I signature and could contribute to acute flares of disease in susceptible subjects such as patients with SLE.
Mapping the mechanical properties of paintings via nanoindentation: a new approach for cultural heritage studies
Authors: Tiennot Mathilde , Paardekam Erik , Iannuzzi Davide , Hermens Erma 
Published: May 2020

AbstractA comprehensive understanding of the behaviour of the heterogenous layers within the paint stratigraphies in historical paintings is crucial to evaluate their long term stability. We aim to refine nanoindentation as a new tool to investigate the mechanical behaviour of historical oil paints, by adapting the probes and the protocol already used in biomechanical research on soft tissues. The depth-controlled indentation profile performed with a spherical probe provides an evaluation of the non-linear viscoelastic behaviour of the individual layers in paint at local scale. The technique is non-destructive and guarantees the integrity of the surface after indentation. The mapping of elasticity demonstrates the properties’ heterogeneity of the composite material within the paint layers, as well as between the individual layers and their interfaces.
Near-threshold fatigue crack propagation without oxide-induced crack closure
Authors: Tazoe Koki , Tanaka Hiroto , Oka Masanori , Yagawa Genki 
Published: May 2020

AbstractAn accurate value for the threshold stress intensity factor range, ΔKth, is a key parameter for studying crack-like defects. However, it is difficult to obtain accurate ΔKthvalues due to oxide-induced crack closure. In this study, we report conditions for minimizing the effects of oxide-induced crack closure near the threshold region, where a concave curve of the effect on the loading frequency on oxide-induced crack closure is achieved. The resulting conditions allow for an accurate determination of ΔKth, which is a key material parameter relating to the pertinent loading ratio.