Miracle-dz/UniFAR-FTUs huggingface dataset:
Conformational communication mediates the reset step in t6A biosynthesis

Abstract The universally conserved N6-threonylcarbamoyladenosine (t6A) modification of tRNA is essential for translational fidelity. In bacteria, t6A biosynthesis starts with the TsaC/TsaC2-catalyzed synthesis of the intermediate threonylcarbamoyl adenylate (TC–AMP), followed by transfer of the threonylcarbamoyl (TC) moiety to adenine-37 of tRNA by the TC-transfer complex comprised of TsaB, TsaD and TsaE subunits and possessing an ATPase activity required for multi-turnover of the t6A cycle. We report a 2.5-Å crystal structure of the T. maritima TC-transfer complex (TmTsaB2D2E2) bound to Mg2+-ATP in the ATPase site, and substrate analog carboxy-AMP in the TC-transfer site. Site directed mutagenesis results show that residues in the conserved Switch I and Switch II motifs of TsaE mediate the ATP hydrolysis-driven reactivation/reset step of the t6A cycle. Further, SAXS analysis of the TmTsaB2D2-tRNA complex in solution reveals bound tRNA lodged in the TsaE binding cavity, confirming our previous biochemical data. Based on the crystal structure and molecular docking of TC–AMP and adenine-37 in the TC-transfer site, we propose a model for the mechanism of TC transfer by this universal biosynthetic system.
Substorms during different storm phases

Abstract. After the deep solar minimum at the end of the solar cycle 23, a small magnetic storm occurred on 20–26 January 2010. The Dst (disturbance storm time) index reached the minimum of −38 nT on 20 January and the prolonged recovery that followed the main phase that lasted for about 6 days. In this study, we concentrate on three substorms that took place (1) just prior to the storm, (2) during the main phase of the storm, and (3) at the end of the recovery of the storm. We analyse the solar wind conditions from the solar wind monitoring spacecraft, the duration and intensity of the substorm events as well as the behaviour of the electrojet currents from the ground magnetometer measurements. We compare the precipitation characteristics of the three substorms. The results show that the F-region electron density enhancements and dominant green and red auroral emission of the substorm activity during the storm recovery resembles average isolated substorm precipitation. However, the energy dissipated, even at the very end of a prolonged storm recovery, is very large compared to the typical energy content of isolated substorms. In the case studied here, the dissipation of the excess energy is observed over a 3-h long period of several consecutive substorm intensifications. Our findings suggest that the substorm energy dissipation varies between the storm phases.
Interactive Effects of CO2 Concentration and Water Regime on Stable Isotope Signatures, Nitrogen Assimilation and Growth in Sweet Pepper

Sweet pepper is among the most widely cultivated horticultural crops in the Mediterranean basin, being frequently grown hydroponically under cover in combination with CO2 fertilization and water conditions ranging from optimal to suboptimal. The aim of this study is to develop a simple model, based on the analysis of plant stable isotopes in their natural abundance, gas exchange traits and N concentration, to assess sweet pepper growth. Plants were grown in a growth chamber for near 6 weeks. Two [CO2] (400 and 800 μmol mol−1), three water regimes (control and mild and moderate water stress) and four genotypes were assayed. For each combination of genotype, [CO2] and water regime five plants were evaluated. Water stress applied caused significant decreases in water potential, net assimilation, stomatal conductance, intercellular to atmospheric [CO2], and significant increases in water use efficiency, leaf chlorophyll content and carbon isotope composition, while the relative water content, the osmotic potential and the content of anthocyanins did change not under stress compared to control conditions support this statement. Nevertheless, water regime affects plant growth via nitrogen assimilation, which is associated with the transpiration stream, particularly at high [CO2], while the lower N concentration caused by rising [CO2] is not associated with stomatal closure. The stable isotope composition of carbon, oxygen, and nitrogen (δ13C, δ18O, and δ15N) in plant matter are affected not only by water regime but also by rising [CO2]. Thus, δ18O increased probably as response to decreases in transpiration, while the increase in δ15N may reflect not only a lower stomatal conductance but a higher nitrogen demand in leaves or shifts in nitrogen metabolism associated with decreases in photorespiration. The way that δ13C explains differences in plant growth across water regimes within a given [CO2], seems to be mediated through its direct relationship with N accumulation in leaves. The changes in the profile and amount of amino acids caused by water stress and high [CO2] support this conclusion. However, the results do not support the use of δ18O as an indicator of the effect of water regime on plant growth.
Collagen content and extracellular matrix cause cytoskeletal remodelling in pancreatic fibroblasts

In many solid tumours a desmoplastic reaction takes place, which results in tumour tissue stiffening due to the extensive production of extracellular matrix (ECM) proteins, such as collagen, by stromal cells, mainly fibroblasts (FBs) and cancer-associated fibroblasts (CAFs). In this study, we investigated the effect of collagen stiffness on pancreatic FBs and CAFs, particularly on specific cytoskeleton properties and gene expression involved in tumour invasion. We found that cells become stiffer when they are cultured on stiff substrates and express higher levels of alpha-smooth muscle actin (α-SMA). Also, it was confirmed that on stiff substrates, CAFs are softer than FBs, while on soft substrates they have comparable Young's moduli. Furthermore, the number of spread FBs and CAFs was higher in stiffer substrates, which was also confirmed by Ras-related C3 botulinum toxin substrate 1 (RAC1) mRNA expression, which mediates cell spreading. Although stress fibres in FBs become more oriented on stiff substrates, CAFs have oriented stress fibres regardless of substrate stiffness. Subsequently, we demonstrated that cells' invasion has a differential response to stiffness, which was associated with regulation of Ras homologue family member (RhoA) and Rho-associated, coiled-coil containing protein kinase 1 (ROCK-1) mRNA expression. Overall, our results demonstrate that collagen stiffness modulates FBs and CAFs cytoskeleton remodelling and alters their invasion properties.
Imipramine as an alternative to formamide to detubulate rat ventricular cardiomyocytes

What is the central question of this study? Can imipramine, an antidepressant agent that is a cationic amphiphilic drug that interferes with the phosphatidylinositol 4,5‐bisphosphate (PI(4,5)P2) interactions with proteins maintaining the tubular system, be validated as a new detubulating tool? What is the main finding and its importance? Imipramine was validated as a more efficient and less toxic detubulating agent of cardiomyocytes than formamide. New insights are provided on how PI(4,5)P2 is crucial to maintaining T‐tubule attachment to the cell surface and on the cardiotoxic effects of imipramine overdoses.
Biomedical and genetic characteristics of the Ryukyuans: demographic history, diseases and physical and physiological traits

Abstract Context: The Ryukyu Islands stretch across a southwestern area of the Japanese Archipelago. Because of their unique geographical and historical backgrounds, Ryukyuans have their own genetic and phenotypic characteristics, which have been disclosed in previous anthropological and biomedical studies. Objective: The history, peopling and biomedical and genetic characteristics of Ryukyuans are reviewed and future research directions are discussed. Conclusion: Morphological and genetic studies have suggested the complex demographic history of Ryukyuans and their relationships with other Asian populations. Knowledge of population formation processes is important to understand the distribution of pathogens. In viral infectious diseases, some strains that may be associated with disease symptoms are specific to Ryukyuans. Dramatic changes in diet have played an important role among Ryukyuans in terms of increases in lifestyle-related diseases and mortality risks. To achieve a better understanding of pathogenic disease factors, further integration of findings regarding the genetic and biomedical characteristics of the Ryukyuans is needed.
Neisserial PorB immune enhancing activity and use as a vaccine adjuvant

ABSTRACT Our laboratory has focused on Porin B (PorB), an outer membrane protein from Neisseria meningitidis and TLR2 ligand-based adjuvant, to characterize specific molecular and cellular pathways involved in improved immune responses induced by vaccine adjuvants. PorB’s ability to form micellar nanoparticular multi-molecular organized structures and its interaction with Toll-like receptor 2/1 complexes likely accounts for its potent adjuvant activity. Downstream from this stimulation, we have observed enhanced antigen uptake in antigen presenting cells (APC), greater antigen deposition in secondary lymphoid organs, and promotion of germinal center reactions. In mice, antigen-specific IgGs were increased after PorB adjuvanted vaccination using the model antigen ovalbumin (OVA). Likewise, this formulation resulted in more IL-4 and IFN-γ positive T cells. Mice that received PorB adjuvanted vaccinations benefitted from lower bacterial burdens when challenged with recombinant Listeria monocytogenes expressing OVA. Mouse models lacking MyD88 signaling in various APC types helped identify macrophages as an essential cell type for the adjuvant activity of PorB. We believe the work presented here provides examples of the mechanistic studies required to understand how vaccine adjuvants are contributing to the establishment of protective immunity.
Women have lower chances than men to be resuscitated and survive out-of-hospital cardiac arrest

Abstract Aims Previous studies on sex differences in out-of-hospital cardiac arrest (OHCA) had limited scope and yielded conflicting results. We aimed to provide a comprehensive overall view on sex differences in care utilization, and outcome of OHCA. Methods and results We performed a population-based cohort-study, analysing all emergency medical service (EMS) treated resuscitation attempts in one province of the Netherlands (2006–2012). We calculated odds ratios (ORs) for the association of sex and chance of a resuscitation attempt by EMS, shockable initial rhythm (SIR), and in-hospital treatment using logistic regression analysis. Additionally, we provided an overview of sex differences in overall survival and survival at successive stages of care, in the entire study population and in patients with SIR. We identified 5717 EMS-treated OHCAs (28.0% female). Women with OHCA were less likely than men to receive a resuscitation attempt by a bystander (67.9% vs. 72.7%; P < 0.001), even when OHCA was witnessed (69.2% vs. 73.9%; P < 0.001). Women who were resuscitated had lower odds than men for overall survival to hospital discharge [OR 0.57; 95% confidence interval (CI) 0.48–0.67; 12.5% vs. 20.1%; P < 0.001], survival from OHCA to hospital admission (OR 0.88; 95% CI 0.78–0.99; 33.6% vs. 36.6%; P = 0.033), and survival from hospital admission to discharge (OR 0.49, 95% CI 0.40–0.60; 33.1% vs. 51.7%). This was explained by a lower rate of SIR in women (33.7% vs. 52.7%; P < 0.001). After adjustment for resuscitation parameters, female sex remained independently associated with lower SIR rate. Conclusion In case of OHCA, women are less often resuscitated by bystanders than men. When resuscitation is attempted, women have lower survival rates at each successive stage of care. These sex gaps are likely explained by lower rate of SIR in women, which can only partly be explained by resuscitation characteristics.
A Hydroponic System for Growing Gnotobiotic Vs. Sterile Plants to Study Phytoremediation Processes

In some phytoremediation studies it is desirable to separate and define the specific contribution of plants and root-colonizing bacteria towards contaminant removal. Separating the influence of plants and associated bacteria is a difficult task for soil root environments. Growing plants hydroponically provides more control over the biological factors in contaminant removal. In this study, a hydroponic system was designed to evaluate the role of sterile plant roots, rhizodeposition, and root-associated bacteria in the removal of a model contaminant, phenol. A strain of Pseudomonas pseudoalcaligenes that grows on phenol was inoculated onto plant roots. The introduced biofilm persisted in the root zone and promoted phenol removal over non-augmented controls. These findings indicate that this hydroponic system can be a valuable tool for phytoremediation studies that investigate the effects of biotic and abiotic factors on pollution remediation.
Dexmedetomidine Based Sedation for Post-surgery Critically Ill Adults: A Meta-analysis of Randomized Controlled Trials

Background: Using dexmedetomidine (Dex) as a sedative agent may benefit the clinical outcomes of post-surgery patients. We reviewed randomized controlled trials (RCTs) to assess whether use of a Dex could improve the outcomes in post-surgery critically ill adults. Methods: We searched Medline, Embase, PubMed, and the Cochrane databases for RCTs comparing Dex with propofol or a placebo in post-operative patients, all included RCTs should be published in English before Jul 2016. Citations meeting inclusion criteria were full screened, and trial available data were abstracted independently and the Cochrane risk of bias tool was used for quality assessment. Results: Sixteen RCTs involving 2568 patients were subject to this meta-analysis. The use of a Dex sedative regimen was associated with a reduce delirium prevalence [odd ratio (OR):0.33, 95% confidence intervals (CI): 0.24–0.45, I2= 5%, P<0.001], a shorter the length of ICU stay [mean difference (MD): −0.60, 95%CI: −0.69 to −0.50, I2=40%, P<0.001] and the length of hospital stay [MD: −0.68, 95%CI: −1.21 to −0.16, I2=0%, P=0.01]. However, using of Dex could not shorter the duration of mechanical ventilation [MD: −10.18. 95%CI: −31.08–10.72, I2=99%, P=0.34], but could shorter the time to extubation in post-surgery patients [MD: −47.46, 95%CI: −84.63–10.67, I2=98%, P=0.01]. Conclusion: The use of a Dex sedative regimen was associated with a reduce delirium prevalence, a shorter the length of ICU and hospital stay, and a shorter time to extubation in post-surgery critical ill patients.
A small molecular inhibitor of LRRK1 identified by homology modeling and virtual screening suppresses osteoclast function, but not osteoclast differentiation, in vitro

We used TGFβ activation kinase 1 as a template to build a 3D structure of the human LRRK1 kinase domain (hLRRK1 KD) and performed small molecule docking. One of the chemicals (IN04) that docked into the pocket was chosen for evaluation of biological effects on osteoclasts (OCs) in vitro. INO4 at 16 nM completely blocked ATP binding to hLRRK1 KD in an in vitro pulldown assay. In differentiation and pit assays, while the number of OCs on bone slices were comparable for OCs treated with IN04 and DMSO, IN04 treatment of OCs significantly impaired their ability to resorb bone. The area of pits on bone slices was reduced by 43% at 5 μM and 83% at 10 μM as compared to DMSO. Individual pits appeared smaller and shallower. F-actin staining revealed that DMSO-treated OCs displayed clear actin rings, and F-actin forms a peripheral sealing zone. By contrast, IN04-treated OCs showed disarranged F-actin in the cytoplasm, and F-actin failed to form a sealing zone on bone slices. IN04 treatment had no effects on OC-derived coupling factor production nor on osteoblast nodule formation. Our data indicate IN04 is a potent inhibitor of LRRK1, suppressing OC function with no effect on OC formation.
Herpes Simplex Virus 1 Tegument Protein UL46 Inhibits TANK-Binding Kinase 1-Mediated Signaling

HSV-1 has evolved multiple strategies to evade host antiviral responses and establish a lifelong latent infection, but the molecular mechanisms by which HSV-1 interrupts antiviral innate immunity are not completely understood. As TBK1 is very critical for antiviral innate immunity, it is of great interest to reveal the immune evasion mechanism of HSV-1 by targeting TBK1. In the present study, HSV-1 UL46 was found to inhibit the activation of IFN-I by targeting TBK1, suggesting that the evasion of TBK1 mediated antiviral innate immunity by HSV-1 UL46. Findings in this study will provide new insights into the host-virus interaction and help develop new approaches against HSV-1 infection. ABSTRACT TANK-binding kinase 1 (TBK1) is a key component of the antiviral immunity signaling pathway. It activates downstream interferon regulatory factor 3 (IRF3) and subsequent type I interferon (IFN-I) production. Herpes simplex virus type 1 (HSV-1) can antagonize host antiviral immune responses and lead to latent infection. Here, HSV-1 tegument protein UL46 was demonstrated to downregulate TBK1-dependent antiviral innate immunity. UL46 interacted with TBK1 and reduced TBK1 activation and its downstream signaling. Our results showed that UL46 impaired the interaction of TBK1 and IRF3 and downregulated the activation of IRF3 by inhibiting the dimerization of TBK1 to reduce the IFN-I production induced by TBK1 and immunostimulatory DNA. The IFN-I and its downstream antiviral genes induced by UL46-deficient HSV-1 (ΔUL46 HSV-1) were higher than those of wild-type HSV-1 (WT HSV-1). In addition, the stable knockdown of TBK1 facilitated the replication of ΔUL46 HSV-1, but not WT HSV-1. Together, these findings reveal a novel mechanism of immune evasion by HSV-1. IMPORTANCE HSV-1 has evolved multiple strategies to evade host antiviral responses and establish a lifelong latent infection, but the molecular mechanisms by which HSV-1 interrupts antiviral innate immunity are not completely understood. As TBK1 is very critical for antiviral innate immunity, it is of great interest to reveal the immune evasion mechanism of HSV-1 by targeting TBK1. In the present study, HSV-1 UL46 was found to inhibit the activation of IFN-I by targeting TBK1, suggesting that the evasion of TBK1 mediated antiviral innate immunity by HSV-1 UL46. Findings in this study will provide new insights into the host-virus interaction and help develop new approaches against HSV-1 infection.
Natural Regression of Frailty Among Community-Dwelling Older Adults: A Systematic Review and Meta-Analysis.

BACKGROUND AND OBJECTIVES Frailty is a dynamic process with potential transitions over time. However, there is limited understanding of the patterns of frailty improvement. We conducted a systematic review and meta-analysis to estimate the natural rate of frailty regression among community-dwelling older adults aged at least 60 years. RESEARCH DESIGN AND METHODS Systematic searches for studies reporting frailty improvement were performed in 5 databases (Medline, Embase, CINAHL plus, Web of Science, and PsycINFO) from inception until January 2019. RESULTS Twenty-five studies from 26 countries were included. Among a baseline population of more than 50,000 individuals, the pooled prevalence of pre-frailty and frailty was 50.5% (95% confidence interval [CI] 47.8-53.3) and 12.8% (95% CI 9.1-17.0), respectively. During a median follow-up of 3.0 (range 1-10.0) years, 23.3% of surviving pre-frail individuals regressed to a robust state and 35.2% of surviving frail individuals reversed to a pre-frail or robust state. The pooled remission rates among people with pre-frailty and frailty were 80.4 (95% CI 61.7-104.6) and 135.3 (95% CI 98.1-186.5) per 1,000 person-years, respectively. Frailty and pre-frailty improvement rates varied by sex, diagnostic criteria, study region, and follow-up duration. The remission rates were significantly reduced when accounting for progressions to death. The heterogeneity of included studies was high which reflected considerable differences in methodological approach. DISCUSSION AND IMPLICATIONS Although frailty is highly prevalent in older people, natural remission is possible and common. Improved understanding of the factors that confer increased likelihood of frailty regression may support the design of interventions to reduce the burden of frailty.
Impact of Dry Eye on Visual Acuity and Contrast Sensitivity: Dry Eye Assessment and Management Study

Supplemental digital content is available in the text. SIGNIFICANCE Identification of the association of specific signs of dry eye disease with specific visual function deficits may allow for more targeted approaches to treatment. PURPOSE The purpose of this study was to explore the association of dry eye signs and symptoms with visual acuity (VA) and contrast sensitivity in the Dry Eye Assessment and Management study. METHODS Baseline data from participants in the Dry Eye Assessment and Management study were used in this secondary cross-sectional analysis. Standardized procedures were used to obtain results on the Ocular Surface Disease Index (OSDI), high-contrast logMAR VA, contrast sensitivity, tear film debris, tear breakup time (TBUT), corneal fluorescein staining, meibomian gland evaluation, conjunctival lissamine green staining, and Schirmer test scores. Generalized linear models that included age, refractive error status, and cataract status were used to assess the association between VA and contrast sensitivity with OSDI score and each dry eye sign. The Hochberg procedure was used to account for multiple comparisons. RESULTS Among 487 participants (974 eyes), worse VA was associated with worse mean score on the OSDI vision subscale (39.4 for VA 20/32 or worse vs. 32.4 for VA 20/16 or better; adjusted linear trend, P = .02); scores were not associated with contrast sensitivity. Severe meibomian gland plugging and abnormal secretions were associated with worse mean log contrast sensitivity (1.48 for severe vs. 1.54 for not plugged [P = .04] and 1.49 for obstructed vs. 1.57 for clear [P = .002], respectively). Longer TBUT was associated with better mean log contrast sensitivity (1.57 for TBUT >5 seconds and 1.51 for TBUT ≤2 seconds, P < .0001). CONCLUSIONS Worse VA rather than worse contrast sensitivity drives vision-related symptoms in dry eye. Greater tear film instability was associated with worse contrast sensitivity.