Miracle-dz/UniFAR-FTUs huggingface dataset:
Soluble, Colloidal, and Particulate Iron Across the Hydrothermal Vent Mixing Zones in Broken Spur and Rainbow, Mid-Atlantic Ridge

The slow-spreading Mid-Atlantic Ridge (MAR) forms geological heterogeneity throughout the ridge system by deep crustal faults and their resultant tectonic valleys, which results in the existence of different types of hydrothermal vent fields. Therefore, investigating MAR hydrothermal systems opens a gate to understanding the concentration ranges of ecosystem-limiting metals emanating from compositionally distinct fluids for both near-field chemosynthetic ecosystems and far-field transport into the ocean interiors. Here, we present novel data regarding onboard measured, size-fractionated soluble, colloidal, and particulate iron concentrations from the 2018 R/V L’Atalante – ROV Victor research expedition, during which samples were taken from the mixing zone of black smokers using a ROV-assisted plume sampling. Iron size fractionation (<20, 20–200, and >200nm) data were obtained from onboard sequential filtering, followed by measurement via ferrozine assay and spectrophotometric detection at 562nm. Our results showed the persistent presence of a nanoparticulate/colloidal phase (retained within 20–200nm filtrates) even in high-temperature samples. A significant fraction of this phase was retrievable only under treatment with HNO3 – a strong acid known to attack and dissolve pyrite nanocrystals. Upon mixing with colder bottom waters and removal of iron in the higher parts of the buoyant plume, the larger size fractions became dominant as the total iron levels decreased, but it was still possible to detect significant (micromolar) levels of nanoparticulate Fe even in samples collected 5m above the orifice in the rising plume. The coolest sample (<10°C) still contained more than 1μM of only nitric acid-leachable nanoparticle/colloidal, at least 200 times higher than a typical Fe concentration in the non-buoyant plume. Our results support previous reports of dissolved Fe in MAR vent plumes, and we propose that this recalcitrant Fe pool – surviving immediate precipitation – contributes to maintaining high hydrothermal iron fluxes to the deep ocean.
Innate Resistance to Leishmania amazonensis Infection in Rat Is Dependent on NOS2

Leishmania infection causes diverse clinical manifestations in humans. The disease outcome is complicated by the combination of many host and parasite factors. Inbred mouse strains vary in resistance to Leishmania major but are highly susceptible to Leishmania amazonensis infection. However, rats are highly resistant to L. amazonensis infection due to unknown mechanisms. We use the inducible nitric oxide synthase (Nos2) gene knockout rat model (Nos2−/− rat) to investigate the role of NOS2 against leishmania infection in rats. Our results demonstrated that diversion toward the NOS2 pathway is the key factor explaining the resistance of rats against L. amazonensis infection. Rats deficient in NOS2 are susceptible to L. amazonensis infection even though their immune response to infection is still strong. Moreover, adoptive transfer of NOS2 competent macrophages into Nos2−/− rats significantly reduced disease development and parasite load. Thus, we conclude that the distinct L-arginine metabolism, observed in rat macrophages, is the basis of the strong innate resistance to Leishmania. These data highlight that macrophages from different hosts possess distinctive properties and produce different outcomes in innate immunity to Leishmania infections.
Beyond Archaea: The Table Salt Bacteriome

Commercial table salt is a condiment with food preservative properties by decreasing water activity and increasing osmotic pressure. Salt is also a source of halophilic bacteria and archaea. In the present research, the diversity of halotolerant and halophilic microorganisms was studied in six commercial table salts by culture-dependent and culture-independent techniques. Three table salts were obtained from marine origins: Atlantic Ocean, Mediterranean (Ibiza Island), and Odiel marshes (supermarket marine salt). Other salts supplemented with mineral and nutritional ingredients were also used: Himalayan pink, Hawaiian black, and one with dried vegetables known as Viking salt. The results of 16S rRNA gene sequencing reveal that the salts from marine origins display a similar archaeal taxonomy, but with significant variations among genera. Archaeal taxa Halorubrum, Halobacterium, Hallobellus, Natronomonas, Haloplanus, Halonotius, Halomarina, and Haloarcula were prevalent in those three marine salts. Furthermore, the most abundant archaeal genera present in all salts were Natronomonas, Halolamina, Halonotius, Halapricum, Halobacterium, Haloarcula, and uncultured Halobacterales. Sulfitobacter sp. was the most frequent bacteria, represented almost in all salts. Other genera such as Bacillus, Enterococcus, and Flavobacterium were the most frequent taxa in the Viking, Himalayan pink, and black salts, respectively. Interestingly, the genus Salinibacter was detected only in marine-originated salts. A collection of 76 halotolerant and halophilic bacterial and haloarchaeal species was set by culturing on different media with a broad range of salinity and nutrient composition. Comparing the results of 16S rRNA gene metataxonomic and culturomics revealed that culturable bacteria Acinetobacter, Aquibacillus, Bacillus, Brevundimonas, Fictibacillus, Gracilibacillus, Halobacillus, Micrococcus, Oceanobacillus, Salibacterium, Salinibacter, Terribacillus, Thalassobacillus, and also Archaea Haloarcula, Halobacterium, and Halorubrum were identified at least in one sample by both methods. Our results show that salts from marine origins are dominated by Archaea, whereas salts from other sources or salt supplemented with ingredients are dominated by bacteria.
RNA Sequencing Reveals Phenylpropanoid Biosynthesis Genes and Transcription Factors for Hevea brasiliensis Reaction Wood Formation

Given the importance of wood in many industrial applications, much research has focused on wood formation, especially lignin biosynthesis. However, the mechanisms governing the regulation of lignin biosynthesis in the rubber tree (Hevea brasiliensis) remain to be elucidated. Here, we gained insight into the mechanisms of rubber tree lignin biosynthesis using reaction wood (wood with abnormal tissue structure induced by gravity or artificial mechanical treatment) as an experimental model. We performed transcriptome analysis of rubber tree mature xylem from tension wood (TW), opposite wood (OW), and normal wood (NW) using RNA sequencing (RNA-seq). A total of 214, 1,280, and 32 differentially expressed genes (DEGs) were identified in TW vs. NW, OW vs. NW, and TW vs. OW, respectively. GO and KEGG enrichment analysis of DEGs from different comparison groups showed that zeatin biosynthesis, plant hormone signal transduction, phenylpropanoid biosynthesis, and plant–pathogen interaction pathways may play important roles in reaction wood formation. Sixteen transcripts involved in phenylpropanoid biosynthesis and 129 transcripts encoding transcription factors (TFs) were used to construct a TF–gene regulatory network for rubber tree lignin biosynthesis. Among them, MYB, C2H2, and NAC TFs could regulate all the DEGs involved in phenylpropanoid biosynthesis. Overall, this study identified candidate genes and TFs likely involved in phenylpropanoid biosynthesis and provides novel insights into the mechanisms regulating rubber tree lignin biosynthesis.
Changes of Structural and Functional Attention Control Networks in Subclinical Hypothyroidism

Objective: This study aimed to explore the structural changes in patients with subclinical hypothyroidism (SCH) using voxel-based morphometry (VBM) and to investigate the altered attentional control networks using functional MRI (fMRI) during the performance of a modified Stroop task with Chinese characters. Methods: High-resolution three-dimensional (3D) T1-weighted images and an fMRI scan were taken from 18 patients with SCH and 18 matched control subjects. The Montreal Cognitive Assessment Chinese-revised (MoCA-CR) and the Stroop task were used to evaluate the cognitive and attention control of the participants. Results: Compared to controls, the VBM results showed decreased gray matter volumes (GMVs) in bilateral prefrontal cortices (PFCs, including middle, medial, and inferior frontal gyri), cingulate gyrus, precuneus, left middle temporal gyrus, and insula in patients with SCH. The fMRI results showed a distributed network of brain regions in both groups, consisting of PFCs (including superior and middle and inferior frontal cortices), anterior cingulate cortex (ACC), posterior cingulate cortex, and precuneus, as well as the insula and caudate nucleus. Compared to controls, the SCH group had lower activation of the above brain areas, especially during the color-naming task. In addition, the normalized GMV (nGMV) was negatively correlated with thyroid-stimulating hormone (TSH) level (r = −0.722, p < 0.001). Conclusion: Results indicate that patients with SCH exhibit reduced GMVs, altered BOLD signals, and activation in regions associated with attention control, which further suggest that patients with SCH may have attentional control deficiency, and the weakened PFC–ACC–precuneus brain network might be one of the neural mechanisms. Negative correlations between nGMV and TSH suggest that TSH elevation may induce abnormalities in the cortex.
Astrocytes Downregulate Inflammation in Lipopolysaccharide-Induced Acute Respiratory Distress Syndrome: Applicability to COVID-19

Background: An acute respiratory distress syndrome (ARDS) is caused by the increased amounts of pro-inflammatory cytokines and neutrophil-mediated tissue injury. To date, there is no effective treatment for the ARDS available, while the need for one is growing due to the most severe complications of the current coronavirus disease-2019 (COVID-19) pandemic. The human astrocytes (AstroRx) have shown immunomodulatory properties in the central nervous system (CNS). This study aimed to evaluate the capacity of astrocytes to decrease lung inflammation and to be applied as a treatment therapy in ARDS. Methods: First, we assessed the ability of clinical-grade AstroRx to suppress T-cell proliferation in a mixed lymphocyte reaction test. Next, we tested the therapeutical potential of AstroRx cells in a lipopolysaccharide (LPS)-based ARDS mouse model by injecting AstroRx intravenously (i.v). We determined the degree of lung injury by using a severity scoring scale of 0–2, based on the American Thoracic Society. The scoring measured the presence of neutrophils, fibrin deposits, and the thickening of alveolar walls. The state of inflammation was further assessed by quantifying the immune-cell infiltration to the bronchoalveolar lavage fluid (BALF) and by the presence of proinflammatory cytokines and chemokines in the BALF and serum. Results: We detected that AstroRx cells were capable to suppress T-cell proliferation in vitro after exposure to the mitogen concanavalin A (ConA). In vivo, AstroRx cells were able to lower the degree of lung injury in LPS-treated animals compared with the sham injected animals (P = 0.039). In this study, 30% of AstroRx treated mice showed no lung lesions (responder mice), these mice presented a steady number of eosinophils, T cells, and neutrophils comparable with the level of naïve control mice. The inflammatory cytokines and chemokines, such as TNFα, IL1b, IL-6, and CXCL1, were also kept in check in responder AstroRx-treated mice and were not upregulated as in the sham-injected mice (P < 0.05). As a result, the LPS-treated ARDS mice had a higher survival rate when they were treated with AstroRx. Conclusions: Our results demonstrate that the immunosuppressive activity of AstroRx cells support the application of AstroRx cells as a cell therapy treatment for ARDS. The immunoregulatory activity may also be a part of the mechanism of action of AstroRx reported in the amyotrophic lateral sclerosis (ALS) neurodegenerative disease.
Psychosocial Health and Physical Activity in People With Major Depression in the Context of COVID-19

Introduction: Major depression is a psychiatric disease associated with physical inactivity, which in turn affects mental and physical health. A randomized controlled trial is being implemented to facilitate physical activity in people with major depression. In March 2020, Swiss state authorities temporarily legislated a lockdown to contain the Coronavirus disease-19 (COVID-19), which influenced health, behavior and research. The aim of this study was to find out whether data gathered before and during/after the lockdown among in-patients with major depression differ with regard to psychosocial health, physical activity and related attitudes and to establish whether baseline data have been affected by the lockdown. Methods: This is a cross-sectional analysis within a randomized controlled trial. Physically inactive, adult in-patients diagnosed with major depression were recruited from four Swiss psychiatric clinics between January 2019 and December 2020. Psychosocial health was measured with questionnaires pertaining to stress, sleep and health-related quality of life. Physical activity was measured with the Simple Physical Activity Questionnaire. Explicit attitudes were measured with seven questionnaires pertaining to physical activity-related motivation and volition. Implicit attitudes toward physical activity were captured with a single target implicit association test. Results: The sample consisted of 165 participants (n = 119 before lockdown, n = 46 during/after lockdown). No statistically significant differences were found between in-patients with major depression assessed before and during/after the COVID-19 lockdown with regard to psychosocial health (stress, p = 0.51; sleep, p = 0.70; physical component of health-related quality of life, p = 0.55; mental component of health-related quality of life, p = 0.64), self-reported physical activity (p = 0.16) and explicit as well as implicit attitudes toward physical activity (p = 0.94). Hence, the COVID-19-induced lockdown seems not to have led to group differences. Conclusion: Baseline data gathered in in-patients suffering from major depression who are physically inactive upon admission to in-patient treatment in Switzerland seem to be unaffected by the COVID-19-induced lockdown. To assess changes in said population regarding psychosocial health and physical activity patterns over time, longitudinal data are needed.
Exploring the Conceptual Constructs of Learners’ Goal Commitment, Grit, and Self-Efficacy

Although learners’ success in learning has generally been attributed to cognitive factors, non-cognitive issues in education should be taken into consideration in the process of learning which affects learners’ achievement. One of these issues, which become popular among researchers in the previous decade is grit, that is, posited as passion and perseverance thanks to its enduring quality and the other is self-efficacy. Another factor is goal commitment that talks about the way to reach a goal or insistent determinations to achieve a goal. The proposed review attempts to focus on these three factors in regulating students’ learning achievement. Accordingly, some educational suggestions are offered for teachers, students, and syllabus designers.
Bioinformatics Analysis Explores Potential Hub Genes in Nonalcoholic Fatty Liver Disease

Background: Nonalcoholic fatty liver disease (NAFLD) is now recognized as the most prevalent chronic liver disease worldwide. However, the dysregulated gene expression for NAFLD is still poorly understood. Material and methods: We analyzed two public datasets (GSE48452 and GSE89632) to identify differentially expressed genes (DEGs) in NAFLD. Then, we performed a series of bioinformatics analyses to explore potential hub genes in NAFLD. Results: This study included 26 simple steatosis (SS), 34 nonalcoholic steatohepatitis (NASH), and 13 healthy controls (HC). We observed 6 up- and 19 down-regulated genes in SS, and 13 up- and 19 down-regulated genes in NASH compared with HC. Meanwhile, the overlapping pathways between SS and NASH were PI3K-Akt signaling pathway and pathways in cancer. Then, we screened out 10 hub genes by weighted Gene Co-Expression Network Analysis (WGCNA) and protein-protein interaction (PPI) networks. Eventually, we found that CYP7A1/GINS2/PDLIM3 were associated with the prognosis of hepatocellular carcinoma (HCC) in the TCGA database. Conclusion: Although further validation is still needed, we provide useful and novel information to explore the potential candidate genes for NAFLD prognosis and therapeutic options.
Is There a Histone Code for Cellular Quiescence?

Many of the cells in our bodies are quiescent, that is, temporarily not dividing. Under certain physiological conditions such as during tissue repair and maintenance, quiescent cells receive the appropriate stimulus and are induced to enter the cell cycle. The ability of cells to successfully transition into and out of a quiescent state is crucial for many biological processes including wound healing, stem cell maintenance, and immunological responses. Across species and tissues, transcriptional, epigenetic, and chromosomal changes associated with the transition between proliferation and quiescence have been analyzed, and some consistent changes associated with quiescence have been identified. Histone modifications have been shown to play a role in chromatin packing and accessibility, nucleosome mobility, gene expression, and chromosome arrangement. In this review, we critically evaluate the role of different histone marks in these processes during quiescence entry and exit. We consider different model systems for quiescence, each of the most frequently monitored candidate histone marks, and the role of their writers, erasers and readers. We highlight data that support these marks contributing to the changes observed with quiescence. We specifically ask whether there is a quiescence histone “code,” a mechanism whereby the language encoded by specific combinations of histone marks is read and relayed downstream to modulate cell state and function. We conclude by highlighting emerging technologies that can be applied to gain greater insight into the role of a histone code for quiescence.
Limitations of Antibiotic MIC-Based PK-PD Metrics: Looking Back to Move Forward

Within a few years after the first successful clinical use of penicillin, investigations were conducted in animal infection models to explore a range of factors that were considered likely to influence the antibacterial response to the drug. Those studies identified that the response was influenced by not only the total daily dose but also the interval between individual doses across the day, and whether penicillin was administered in an intermittent or continuous manner. Later, as more antibiotics were discovered and developed, antimicrobial pharmacologists began to measure antibiotic concentrations in biological fluids. This enabled the linking of antibacterial response at a single time point in an animal or in vitro infection model with one of three summary pharmacokinetic (PK) measures of in vivo exposure to the antibiotic. The summary PK exposure measures were normalised to the minimum inhibitory concentration (MIC), an in vitro measure of the pharmacodynamic (PD) potency of the drug. The three PK-PD indices (ratio of maximum concentration to MIC, ratio of area under the concentration-time curve to MIC, time concentration is above MIC) have been used extensively since the 1980s. While these MIC-based summary PK-PD metrics have undoubtedly facilitated the development of new antibiotics and the clinical application of both new and old antibiotics, it is increasingly recognised that they have a number of substantial limitations. In this article we use a historical perspective to review the origins of the three traditional PK-PD indices before exploring in detail their limitations and the implications arising from those limitations. Finally, in the interests of improving antibiotic development and dosing in patients, we consider a model-based approach of linking the full time-course of antibiotic concentrations with that of the antibacterial response. Such an approach enables incorporation of other factors that can influence treatment outcome in patients and has the potential to drive model-informed precision dosing of antibiotics into the future.
Effects of Different Recovery Positions on the Postpercutaneous Liver Biopsy Complications: A Metaanalysis

Objective: We aim to evaluate the effects of different recovery positions on the adverse events and the patient acceptability in those who underwent percutaneous liver biopsy (PLB). Methods: A literature search was conducted in the Cochrane Library, Embase, Scopus, PubMed, CNKI, Sinomed, and Wanfang databases. The time for the article extraction was until July 2020. The articles were screened by two independent researchers, together with the bias risk evaluation and data extraction. The RevMan 5.4 software was utilized for the metaanalysis. Results: Finally, two articles involving 180 subjects were eligible for this study. Metaanalysis showed that at T0, the alternation between right-side and combined position (CRP) would induce an elevation of post-PLB pain compared with the dorsal/supine position (SRP) [WMD = −2.00, 95% CI (−3.54, −0.47), p = 0.01]. There were no statistical differences in the postoperative pain among the CRP, SRP, and right-side position (RRP). The patient acceptability of SRP and RRP was higher than that of the CRP. Finally, two eligible studies were included, which showed no incidence of pneumothorax and abdominal bleeding. Conclusions: CRP would induce post-PLB pain at T0. SRP was the most acceptable position for the cases that underwent PLB. There were no statistical differences in the incidence of pneumothorax and abdominal bleeding. Systematic Review Registration: https://www.crd. york.ac. uk/PROSPERO, identifier: CRD42020196633.