Miracle-dz/UniFAR-FTUs huggingface dataset:
Protein Palmitoylation in Leukocyte Signaling and Function

Palmitoylation is a post-translational modification (PTM) based on thioester-linkage between palmitic acid and the cysteine residue of a protein. This covalent attachment of palmitate is reversibly and dynamically regulated by two opposing sets of enzymes: palmitoyl acyltransferases containing a zinc finger aspartate-histidine-histidine-cysteine motif (PAT-DHHCs) and thioesterases. The reversible nature of palmitoylation enables fine-tuned regulation of protein conformation, stability, and ability to interact with other proteins. More importantly, the proper function of many surface receptors and signaling proteins requires palmitoylation-meditated partitioning into lipid rafts. A growing number of leukocyte proteins have been reported to undergo palmitoylation, including cytokine/chemokine receptors, adhesion molecules, pattern recognition receptors, scavenger receptors, T cell co-receptors, transmembrane adaptor proteins, and signaling effectors including the Src family of protein kinases. This review provides the latest findings of palmitoylated proteins in leukocytes and focuses on the functional impact of palmitoylation in leukocyte function related to adhesion, transmigration, chemotaxis, phagocytosis, pathogen recognition, signaling activation, cytotoxicity, and cytokine production.
Understanding the Well-Being of Older Chinese Immigrants in Relation to Green Spaces: A Gold Coast Study (Australia)

In recognition of the aging population and the importance of health-supporting urban environments, including urban green spaces, to maintain well-being, scholars and policymakers have increasingly investigated the associations between urban green spaces and the well-being of older people. However, few studies specifically investigate minority older groups such as those with diverse cultural backgrounds, and many studies often ignore the design attributes of green spaces which may contribute to the well-being of those in such groups. In order to address these gaps, this paper explores how green spaces influence the well-being of older Chinese immigrants. This case study analyzes how older Chinese immigrants interact with green spaces on the Gold Coast, Australia, and adopts the value of place as a conceptual framework to understand the relationship. Two qualitative methods, namely, in-depth interviews and travel diaries, were used to collect data. The results show that parks, as a place, play a crucial role in older Chinese immigrants’ ability to undertake outdoor activities. The relationship between green spaces and well-being can be classified into two themes. The first theme is concerned with how older Chinese immigrants perceive and experience green spaces. This finding indicates that green spaces can fulfill their values of keeping healthy, maintaining active lifestyles, and being social, all of which benefit well-being. The second theme relates to daily activities undertaken within green spaces. Issues of accessibility and personal preferences regarding activities complicate the relationship between green spaces and well-being. Good accessibility to green spaces is congruent with older Chinese immigrants’ values of being physically active, while difficulties in conducting preferred activities counteract these values which then generate negative perceptions of green spaces. Overall, there is great potential for understanding how personal values can inform the design of inclusive green spaces for minority or less mobile groups.
Health and Wellbeing in Higher Education: A Comparison of Music and Sport Students Through the Framework of Self Determination Theory

Students in Higher Education report high levels of mental health issues and psychological distress. Paradoxical findings on performance-orientated students, such as athletes and musicians, suggest that the demands of highly skilled vocations may enhance wellbeing while being detrimental to physical and mental health. To provide timely and appropriate help, institutions need to understand what areas of health and wellbeing are compromised in different student groups. In this study, we compared performance-orientated (music and sport) students to other students and the general population on a selection of wellbeing (WHO5, PWS, and WEMWBS), mental and physical health (K10, SF12, and PHQ9), and trait measures (TIPI, LOT-R, and PCS). Through an online survey (N = 273), data were collected from bachelor and master students (n = 135 music, n = 67 sport, n = 71 controls). Students’ scores were compared to the general population, where norm values were available, and analyzed within and between groups. Multiple regression was performed to investigate trait measures as predictors of wellbeing. All groups scored significantly below population norms for wellbeing and mental health. One third were classed as having moderate to severe depression. Musicians scored higher openness to experience than athletes. While sport students showed a highly homogenous within-group profile, music students’ scores differed significantly across study courses (e.g., performance and composition). Predictors for wellbeing were: optimism and emotional stability (all students); additionally conscientiousness (sport and music); and perceived competence (music only). As expected, students reported more health and wellbeing issues than general population. Distinct profiles of wellbeing were apparent for performance-orientated students. Results are in line with Self Determination Theory and suggest the need for institutions to embed health and wellbeing into a ‘living curriculum’ to accommodate the needs of different student groups. The WHO5 emerged as a parsimonious yet sensitive measure for mental health and wellbeing in student populations.
Locality Effect of Coral-Associated Bacterial Community in the Kuroshio Current From Taiwan to Japan

The Kuroshio Current (KC) is one of the fastest water currents in the world, running through the western boundary of the North Pacific Ocean. The KC strongly influences the regional hydroclimate by creating temperature, salinity, and pH gradients from tropical to subtropical and temperate zones, including regions with rich coral reef habitats. Microbial community composition of corals is influenced by various environmental factors, including salinity, pH, and geographical location. However, to date, it is unclear how coral-associated microbial communities would respond to the same water current running through different locations with a time lag. Therefore, we hypothesized that the locations subjected to the KC at higher latitudes experience similar but sequential lag in environmental variability compared to those at lower latitudes, and thus the coral communities of both will respond similarly, but at different times. In this year-long study, we compared the bacterial communities of Acropora muricata at Taiwan, Okinawa, and Kochi subjected to the KC. We found that site-specific conditions and site latitude may have stronger effects on bacterial composition and dynamics than a water current. Consequently, we suggest that latitude largely determines the temperature tolerance range of coral microbiota. Additionally, among the dominant coral associated bacteria, Endozoicomonas from A. muricata and Stylophora pistillata forms distinct phylogroups, while Acinetobacter is more likely a host generalist.
Prognostic Value of Circulating MG53 Levels in Acute Myocardial Infarction

Background: Mitsugumin 53 (MG53), a muscle-specific protein belonging to the TRIM family, has been demonstrated to protect the heart against oxidative injury. Although previous studies indicated that ischemic hearts released MG53 into circulation in mice, its effects in humans remains unknown. We aimed to evaluate the prognostic value of MG53 in patients with ST-segment elevation myocardial infarction (STEMI). Methods: Serum levels of MG53 were measured in 300 patients with STEMI, all patients were followed for 3 years. The primary endpoint was major adverse cardiovascular events (MACE), defined as a composite of cardiovascular (CV) death, heart failure causing-rehospitalization, recurrent myocardial infarction (MI), and stroke. Results: Patients with a higher concentration of serum MG53 tended to be older, with a history of diabetes. MG53 levels were also highly associated with indicators reflecting heart function, such as left ventricular ejection fraction (LVEF), N terminal pro B type natriuretic peptide (NT-pro-BNP), and cardiac troponin I (cTnI) at baseline. Kaplan-Meier survival curves demonstrated that patients with MG53 levels above the cutoff value (132.17 pg/ml) were more likely to have MACEs. Moreover, it was found to be a significant predictor of CV death (HR: 6.12; 95% CI: 2.10–17.86; p = 0.001). Furthermore, the C-statistic and Integrated Discrimination Improvement (IDI) values for MACEs were improved with MG53 as an independent risk factor or when combined with cTnI. Conclusions: MG53 is a valuable prognostic marker of MACE in patients with AMI, independent of established conventional risk factors, highlighting the significance of MG53 in risk stratification post-MI.
Modeling Cell-Free Protein Synthesis Systems—Approaches and Applications

In vitro systems are ideal setups to investigate the basic principles of biochemical reactions and subsequently the bricks of life. Cell-free protein synthesis (CFPS) systems mimic the transcription and translation processes of whole cells in a controlled environment and allow the detailed study of single components and reaction networks. In silico studies of CFPS systems help us to understand interactions and to identify limitations and bottlenecks in those systems. Black-box models laid the foundation for understanding the production and degradation dynamics of macromolecule components such as mRNA, ribosomes, and proteins. Subsequently, more sophisticated models revealed shortages in steps such as translation initiation and tRNA supply and helped to partially overcome these limitations. Currently, the scope of CFPS modeling has broadened to various applications, ranging from the screening of kinetic parameters to the stochastic analysis of liposome-encapsulated CFPS systems and the assessment of energy supply properties in combination with flux balance analysis (FBA).
Population Structure of Double-Stranded RNA Mycoviruses That Infect the Rice Blast Fungus Magnaporthe oryzae in Japan

Various viruses infect Magnaporthe oryzae (syn. Pyricularia oryzae), which is a well-studied fungus that causes rice blast disease. Most research has focused on the discovery of new viruses and the hypovirulence-associated traits conferred by them. Therefore, the diversity and prevalence of viruses in wild fungal populations have not been explored. We conducted a comprehensive screening of M. oryzae mycoviruses from various regions in Japan using double-stranded RNA (dsRNA) electrophoresis and RT-PCR assays. We detected three mycoviruses, Magnaporthe oryzae virus 2 (MoV2), Magnaporthe oryzae chrysovirus 1 (MoCV1), and Magnaporthe oryzae partitivirus 1 (MoPV1), among 127 of the 194 M. oryzae strains screened. The most prevalent virus was MoPV1 (58.8%), which often co-infected in a single fungal strain together with MoV2 or MoCV1. MoV2 and MoCV1 were found in 22.7 and 10.8% of strains, respectively, and they were usually distributed in different regions so that mixed-infection with these two mycoviruses was extremely rare. The predominance of MoPV1 in M. oryzae is supported by significant negative values from neutrality tests, which indicate that the population size of MoPV1 tends to increase. Population genetic analyses revealed high nucleotide diversity and the presence of phylogenetically diverse subpopulations among the MoV2 isolates. This was not the case for MoPV1. Furthermore, studies of a virus-cured M. oryzae strain revealed that MoV2 does not cause any abnormalities or symptoms in its host. However, a leaf sheath inoculation assay showed that its presence slightly increased the speed of mycelial growth, compared with virus-free mycelia. These results demonstrate that M. oryzae in Japan harbors diverse dsRNA mycovirus communities with wide variations in their population structures among different viruses.
Tre2-Bub2-Cdc16 Family Proteins Based Nomogram Serve as a Promising Prognosis Predicting Model for Melanoma

Tre2-Bub2-Cdc16 (TBC) proteins are conserved in eukaryotic organisms and function as negative feedback dominating the GAPs for Rab GTPases, while the function of TBC proteins in melanoma remains unclear. In this study, we observed the differential expression of 33 TBC genes in TCGA datasets classified by clinical features. Seven prognostic-associated TBC genes were identified by LASSO Cox regression analysis. Mutation analysis revealed distinctive frequency alteration in the seven prognostic-associated TBCs between cases with high and low scores. High-risk score and cluster 1 based on LASSO Cox regression and consensus clustering analysis were relevant to clinical features and unfavorable prognosis. GSVA analysis showed that prognostic-associated TBCs were related to metabolism and protein transport signaling pathway. Correlation analysis indicated the relationship between the prognostic-associated TBCs with RAB family members, invasion-related genes and immune cells. The prognostic nomogram model was well established to predict survival in melanoma. What’s more, interference of one of the seven TBC proteins TBC1D7 was confirmed to inhibit the proliferation, migration and invasion of melanoma cells in vitro. In summary, we preliminarily investigated the impact of TBCs on melanoma through multiple bioinformatics analysis and experimental validation, which is helpful for clarifying the mechanism of melanoma and the development of anti-tumor drugs.
Intestinal Dysbiosis in, and Enteral Bacterial Therapies for, Systemic Autoimmune Diseases

Recent studies have shown that a number of common autoimmune diseases have perturbations of their intestinal microbiome (dysbiosis). These include: Celiac Disease (CeD), Multiple Sclerosis (MS), Rheumatoid Arthritis (RA), Sjogren’s Syndrome (SS), and Type 1 diabetes (T1D). All of these have intestinal microbiomes that are different from healthy controls. There have been numerous studies using animal models of single probiotics (monoclonal) or mixtures of probiotics (polyclonal) and even complete microbiota transfer (fecal microbial transfer-FMT) to inhibit or delay the onset of autoimmune diseases such as the aforementioned common ones. However, proportionally, fewer clinical trials have utilized monoclonal therapies or FMT than polyclonal therapies for treating autoimmune diseases, even though bacterial mono-therapies do inhibit the development of autoimmune diseases and/or delay the onset of autoimmune diseases in rodent models of those autoimmune diseases. In this review then, we review the previously completed and currently ongoing clinical trials that are testing bacterial therapies (FMT, monoclonal, and polyclonal) to treat common autoimmune dseases and discuss the successes in using bacterial monotherapies to treat rodent models of these common autoimmune diseases.
Data-driven Ensemble Visualization

Numerical simulations have an inherent sensitivity to input parameters, which in many cases are not estimated perfectly. By using different parameterizations, an ensemble of simulations is generated in order to sample from the space of possible outcomes. Investigating every single member of this ensemble separately is tedious and often not possible, which is why major trends and similarities in the ensemble members are searched, introducing additional uncertainty by the methods used therefore. Further, dependencies between different quantities at different forecast times can reveal which errors propagate in time and where additional measurements might have improved the accuracy of the simulation. When relating differences in the realizations to initial parameters, metrics have to be found to compare different simulation outcomes. Clustering analysis is used to group similar members together; however, its outcome varies depending on the specific parameters used for the clustering. By sampling systematically in the clustering space, we create an ensemble of clusterings hinting at sensitivities present. Multiple linked views support the user in finding a suitable clustering and provide insights into the quality and effects of it. Summary visualizations show the variability of cluster sizes, cluster-memberships of each data-point as well as uncertainties in feature visualizations such as contour plots. Specific clusterings or clusters can be selected and all views are updated interactively. Using these methods, we present a workflow assisting the user in clustering tasks which is applied exemplary on the forecasts of tropical cyclone Karl in 2016. Correlation analysis in the ensemble data gives hints on dependencies between different regions, quantities and time steps. Appearing correlation patterns are sensitive to the exact locations correlated to each other, and correspondences between patterns over time-steps have to be established. We present a grid point clustering algorithm which provides a statistically coherent region to which other quantities are correlated to. By further clustering spatial structures of high correlation, regions of coherent features in the ensemble are indicated. Connected correlation structures are automatically tracked over time by combining optical-flow-based forward and backward tracking. The tracking quality and confidence is controlled using a split-merge diagram and a color coded swipe-path gives an immediate overview over a selected tracked structure. In the above mentioned real case, we were able to relate uncertainties in the exact position of cyclone Karl with the erroneous forecast of a heavy precipitation event in Norway a few days later.
Endogenous retroviral gene elements (syncytin-Rum1 and BERV-K1), interferon-τ, and pregnancy associated glycoprotein-1 are differentially expressed in maternal and fetal tissues during the first 50 days of gestation in beef heifers1

Abstract We hypothesized that the endogenous retroviruses [ERV: syncytin-Rum1 and (BERV-K1)], and pregnancy hormones [interferon-τ (IFN-τ), and pregnancy associated glycoprotein-1 (PAG-1)] would be differentially expressed whereas progesterone and insulin concentrations in maternal blood would remain steady during early gestation. To test this hypothesis Angus crossbred heifers (n = 46; ∼15 mo of age; BW = 363 ± 35 kg) were fed native grass hay, supplemented with cracked corn to gain 0.3 kg/d, and given ad libitum access to water. All heifers were subjected to a 5-d CO-Synch + CIDR estrous synchronization protocol and AI (breeding = d 0). Ovariohysterectomies were performed on d 16, 22, 28, 34, 40, and 50 of gestation and at d 16 of the estrous cycle for non-pregnant (NP) controls. Utero-placental tissues [maternal caruncle (CAR); maternal intercaruncular endometrium (ICAR); and fetal membranes, (FM, chorion on d 16, chorioallantois on d 22 to 50)] were collected from the uterine horn ipsilateral to the corpus luteum (CL). Tissues were flash frozen and stored at –80°C. Expression of mRNA was evaluated using qPCR. In CAR, syncytin-Rum1 expression was greater (P < 0.01) on d 50 (81.5-fold) compared with NP controls or any other day of early pregnancy. In contrast, syncytin-Rum1 expression in I-CAR only tended (P = 0.09) to change across days of early pregnancy and did not differ (P = 0.27) in FM tissues. In CAR, the expression of BERV-K1 was not different (P > 0.79) at d 16 and 22, was intermediate at d 28, 34, and 40, and was greatest on d 50 (108-fold increase compared with NP). Expression of BERV-K1 in FM was increased (P < 0.01) on d 28, 34, and 50 compared with NP controls, but at d 40 did not differ from NP controls. The mRNA expression of IFN-τ in FM at d 22 was greater (P < 0.01) than all other days of gestation. In CAR, expression of PAG-1 increased (P < 0.001) dramatically on d 40 (20,000-fold) and d 50 (86,000-fold) compared with NP heifers (P < 0.01). In ICAR, expression of PAG-1 was greater (P < 0.05) on d 28 and 40 (fold increases of 113 and 102, respectively, compared with NP). Insulin concentrations were not different (P = 0.53) but progesterone was greater (P < 0.01) on d 16, 22, 28, 34, and 40 compared with d 50 of gestation. These data confirm differential ERV, IFN-τ, and PAG-1 gene expression during critical time points of early gestation in utero-placental tissues.
A more accurate account of the effect of k-space sampling and signal decay on the effective spatial resolution in functional MRI

The effects of k-space sampling and signal decay on the effective spatial resolution of MRI and functional MRI (fMRI) are commonly assessed by means of the magnitude point-spread function (PSF), defined as the absolute values (magnitudes) of the complex MR imaging PSF. It is commonly assumed that this magnitude PSF signifies blurring, which can be quantified by its full-width at half-maximum (FWHM). Here we show that the magnitude PSF fails to accurately represent the true effects of k-space sampling and signal decay. Firstly, a substantial part of the width of the magnitude PSF is due to MRI sampling per se. This part is independent of any signal decay and its effect depends on the spatial frequency composition of the imaged object. Therefore, it cannot always be expected to introduce blurring. Secondly, MRI reconstruction is typically followed by taking the absolute values (magnitude image) of the reconstructed complex image. This introduces a non-linear stage into the process of image formation. The complex imaging PSF does not fully describe this process, since it does not reflect the stage of taking the magnitude image. Its corresponding magnitude PSF fails to correctly describe this process, since convolving the original pattern with the magnitude PSF is different from the true process of taking the absolute following a convolution with the complex imaging PSF. Lastly, signal decay can have not only a blurring, but also a high-pass filtering effect. This cannot be reflected by the strictly positive width of the magnitude PSF. As an alternative, we propose to first approximate the MRI process linearly. We then model the linear approximation by decomposing it into a signal decay-independent MR sampling part and an approximation of the signal decay effect. We approximate the latter as a convolution with a Gaussian PSF or, if the effect is that of high-pass filtering, as reversing the effect of a convolution with a Gaussian PSF. We show that for typical high-resolution fMRI at 7 Tesla, signal decay in Spin-Echo has a moderate blurring effect (FWHM = 0.89 voxels, corresponds to 0.44 mm for 0.5 mm wide voxels). In contrast, Gradient-Echo acts as a moderate high-pass filter that can be interpreted as reversing a Gaussian blurring with FWHM = 0.59 voxels (0.30 mm for 0.5 mm wide voxels). Our improved approximations and findings hold not only for Gradient-Echo and Spin-Echo fMRI but also for GRASE and VASO fMRI. Our findings support the correct planning, interpretation, and modeling of high-resolution fMRI.