Miracle-dz/UniFAR-FTUs huggingface dataset:
Properties of Spread-F in High and Low Latitude Ionospheres

The ionospheric spread-F has many significant effects on radio waves that propagation through the Earth's atmosphere, such as refraction, reflection, absorption, time delay, phase change, amplitude change, Doppler shifts, and so on. In this paper, we used the data from DPS-4 Digisondes at low latitude station Hainan (19.4 degrees N, 109.0 degrees E), China, and high altitude stations Yakutsk (62 degrees N, 129 degrees E) and Zhigansk (66 degrees N, 123 degrees E), Russia to study the ionospheric Spread-F (SF) properties during geo-magnetic storm time. Some new results are obtained by data analysis. In Hainan and Yakutsk, SF was observed only in night time, but in Zhigansk it was also observed in day time. The SF seems more activity over Yakutsk. The SSF concerned with equatorial plasma bubble is only observed at low latitude station Hainan and the branch SF is only observed at high latitude stations Yakutsk and Zhigansk. For most cases start time of SF is later if the station latitude is lower. This implies that plasma instability caused ionospheric irregularity is propagation from high latitude to low latitude ionosphere.
Mild Behavioral Impairment and Cerebrovascular Profiles Are Associated with Early Cognitive Impairment in a Community-Based Southeast Asian Cohort

Background: Mild behavioral impairment (MBI) is one of the earliest observable changes when a person experiences cognitive decline and could be an early manifestation of underlying Alzheimer’s disease neuropathology. Limited attention has been given to investigating the clinical applicability of behavioral biomarkers for detection of prodromal dementia. Objective: This study compared the prevalence of self-reported MBI and vascular risk factors in Southeast Asian adults to identify early indicators of cognitive impairment and dementia. Methods: This cohort study utilized baseline data from the Biomarkers and Cognition Study, Singapore (BIOCIS). 607 participants were recruited and classified into three groups: cognitively normal (CN), subjective cognitive decline (SCD), and mild cognitive impairment (MCI). Group comparisons of cognitive-behavioral, neuroimaging, and blood biomarkers data were applied using univariate analyses. Multivariate logistic regression analyses were conducted to investigate the association between cerebrovascular disease, vascular profiles, and cognitive impairment. Results: SCD had significantly higher depression scores and poorer quality of life (QOL) compared to CN. MCI had significantly higher depression scores; total MBI symptoms, MBI-interest, MBI-mood, and MBI-beliefs; poorer sleep quality; and poorer QOL compared to CN. Higher Staals scores, glucose levels, and systolic blood pressure were significantly associated with MCI classification. Fasting glucose levels were significantly correlated with depression, anxiety, MBI-social, and poorer sleep quality. Conclusions: The results reflect current research that behavioral changes are among the first symptoms noticeable to the person themselves as they begin to experience cognitive decline. Self-reported questionnaires may aid in early diagnoses of prodromal dementia. Behavioral changes and diabetes could be potential targets for preventative healthcare for dementia.
MoDAFold: a strategy for predicting the structure of missense mutant protein based on AlphaFold2 and molecular dynamics

Abstract Protein structure prediction is a longstanding issue crucial for identifying new drug targets and providing a mechanistic understanding of protein functions. To enhance the progress in this field, a spectrum of computational methodologies has been cultivated. AlphaFold2 has exhibited exceptional precision in predicting wild-type protein structures, with performance exceeding that of other methods. However, predicting the structures of missense mutant proteins using AlphaFold2 remains challenging due to the intricate and substantial structural alterations caused by minor sequence variations in the mutant proteins. Molecular dynamics (MD) has been validated for precisely capturing changes in amino acid interactions attributed to protein mutations. Therefore, for the first time, a strategy entitled ‘MoDAFold’ was proposed to improve the accuracy and reliability of missense mutant protein structure prediction by combining AlphaFold2 with MD. Multiple case studies have confirmed the superior performance of MoDAFold compared to other methods, particularly AlphaFold2.
Chronic traumatic encephalopathy and aging-related tau astrogliopathy in community-dwelling older persons with and without moderate-to-severe traumatic brain injury

Abstract This study examined the frequency of chronic traumatic encephalopathy-neuropathologic change (CTE-NC) and aging-related tau astrogliopathy (ARTAG) in community-dwelling older adults and tested the hypothesis that these tau pathologies are associated with a history of moderate-to-severe traumatic brain injury (msTBI), defined as a TBI with loss of consciousness >30 minutes. We evaluated CTE-NC, ARTAG, and Alzheimer disease pathologies in 94 participants with msTBI and 94 participants without TBI matched by age, sex, education, and dementia status TBI from the Rush community-based cohorts. Six (3%) of brains showed the pathognomonic lesion of CTE-NC; only 3 of these had a history of msTBI. In contrast, ARTAG was common in older brains (gray matter ARTAG = 77%; white matter ARTAG = 54%; subpial ARTAG = 51%); there were no differences in severity, type, or distribution of ARTAG pathology with respect to history of msTBI. Furthermore, those with msTBI did not have higher levels of PHF-tau tangles density but had higher levels of amyloid-β load (Estimate = 0.339, SE = 0.164, p = 0.040). These findings suggest that CTE-NC is infrequent while ARTAG is common in the community and that both pathologies are unrelated to msTBI. The association of msTBI with amyloid-β, rather than with tauopathies suggests differential mechanisms of neurodegeneration in msTBI.
Household food insecurity and physical activity behaviour in Ecuadorian children and adolescents: findings from the Ecuador 2018 National Health and Nutrition Survey (ENSANUT-2018)

Objective: Ecuador has a high prevalence of household food insecurity (HFI) and is undergoing nutritional and epidemiologic transition. Evidence from high-income countries has reported negative or null associations between HFI and physical activity (PA) in children. It remains uncertain whether the same is true of those from low- and middle-income countries like Ecuador whose environmental and socio-demographic characteristics are distinct from those of high-income countries. We aimed to investigate the association of HFI with PA, sedentary behaviour (SB) and anthropometric indicators in children. Design: Cross-sectional analysis of data from the nationally representative 2018 Ecuadorian National Health and Nutrition Survey. Data were collected on HFI, PA, SB, socio-demographic characteristics and measured height and weight. Unadjusted and adjusted linear, log-binomial and multinomial logistic regression analyses assessed the relationship of HFI with PA, SB, stunting and BMI-for-age. Setting: Ecuador. Participants: 23 621 children aged 5–17 years. Results: Marginal and moderate-severe HFI was prevalent in 24 % and 20 % of the households, respectively. HFI was not associated with PA, SB, stunting nor underweight. Moderate-severe HFI was associated with a lower odds of overweight and obesity. However, adjustment for household assets attenuated this finding for overweight (adjusted OR:0·90, 95 % CI: 0·77, 1·05) and obesity (adjusted OR: 0·88, 95 % CI: 0·71, 1·08). Conclusion: HFI is a burden in Ecuadorian households, but is not associated with PA, SB nor anthropometric indicators in children aged 5–17 years. However, a concerning prevalence of insufficient PA was reported, emphasising the critical need for evidence-based interventions aimed at promoting PA and reducing SB.
A kinesin-13 family kinesin in Trypanosoma brucei regulates cytokinesis and cytoskeleton morphogenesis by promoting microtubule bundling

The early branching eukaryote Trypanosoma brucei divides uni-directionally along the longitudinal cell axis from the cell anterior toward the cell posterior, and the cleavage furrow ingresses along the cell division plane between the new and the old flagella of a dividing bi-flagellated cell. Regulation of cytokinesis in T. brucei involves actomyosin-independent machineries and trypanosome-specific signaling pathways, but the molecular mechanisms underlying cell division plane positioning remain poorly understood. Here we report a kinesin-13 family protein, KIN13-5, that functions downstream of FPRC in the cytokinesis regulatory pathway and determines cell division plane placement. KIN13-5 localizes to multiple cytoskeletal structures, interacts with FPRC, and depends on FPRC for localization to the site of cytokinesis initiation. Knockdown of KIN13-5 causes loss of microtubule bundling at both ends of the cell division plane, leading to mis-placement of the cleavage furrow and unequal cytokinesis, and at the posterior cell tip, causing the formation of a blunt posterior. In vitro biochemical assays demonstrate that KIN13-5 bundles microtubules, providing mechanistic insights into the role of KIN13-5 in cytokinesis and posterior morphogenesis. Altogether, KIN13-5 promotes microtubule bundle formation to ensure cleavage furrow placement and to maintain posterior cytoskeleton morphology in T. brucei.
Abundance and Diversity of Psychrotolerant Cultivable Mycobiota in Winter of a Former Aluminous Shale Mine

ABSTRACT This paper is a speleomycological report from a former aluminous shale mine in Janowiec, Poland. Fungi were identified morphologically and molecularly. Microclimatic conditions differed significantly between locations of the study. However, the external environment around the mine did not directly increase the community composition and concentration of fungi in the mine. The density of fungi isolated from the air outside the mine was 63.1 colony forming units (CFU) per 1 cm3 of air. Inside the mine, fungal density ranged from 287.5 to 655 CFU per 1 m3 from the air, 28.4 to 131.1 CFU per 1 cm2 from the rock surfaces and 288.1 to 335.1 CFU per 1 cm3 from the water. Pearson correlation analysis showed that the levels of fungi isolated from the air were correlated positively with temperature, relative humidity and CO2 concentration. The concentration of fungi isolated from the rock surfaces showed a positive correlation with air flow. Five species of filamentous fungi were isolated from the sampled external air, 10 species from the internal air, six species from the rock surface and 11 species from the water. The fungi most frequently isolated from the air and water of the mine belonged to Penicillium spp. , whereas from the rock surface, Geomyces pannorum was most frequently isolated. Some of the fungi present in the mine can be psychrotolerant and pathogenic for humans and animals, and they can also cause degradation of rocks.
Cypin Inhibition as a Therapeutic Approach to Treat Spinal Cord Injury–Induced Mechanical Pain

Cypin (cytosolic postsynaptic density protein 95 interactor) is the primary guanine deaminase in the central nervous system (CNS), promoting the metabolism of guanine to xanthine, an important reaction in the purine salvage pathway. Activation of the purine salvage pathway leads to the production of uric acid (UA). UA has paradoxical effects, specifically in the context of CNS injury as it confers neuroprotection, but it also promotes pain. Since neuropathic pain is a comorbidity associated with spinal cord injury (SCI), we postulated that small molecule cypin inhibitor B9 treatment could attenuate SCI-induced neuropathic pain, potentially by interfering with UA production. However, we also considered that this treatment could hinder the neuroprotective effects of UA and, in doing so, exacerbate SCI outcomes. To address our hypothesis, we induced a moderate midthoracic contusion SCI in female mice and assessed whether transient intrathecal administration of B9, starting at 1 d postinjury (dpi) until 7 dpi, attenuates mechanical pain in hindlimbs at 3 weeks pi. We also evaluated the effects of B9 on the spontaneous recovery of locomotor function. We found that B9 alleviates mechanical pain but does not affect locomotor function. Importantly, B9 does not exacerbate lesion volume at the epicenter. In accordance with these findings, B9 does not aggravate glutamate-induced excitotoxic death of SC neurons in vitro. Moreover, SCI-induced increased astrocyte reactivity at the glial scar is not altered by B9 treatment. Our data suggest that B9 treatment reduces mechanical pain without exerting major detrimental effects following SCI.
Utility of bioelectrical phase angle for cardiovascular risk assessment among individuals with and without diabetes mellitus

Purpose Low values of bioimpedance-derived phase angle (PA) have been associated with various adverse outcomes. We investigated the association of PA with cardiovascular markers in individuals with and without diabetes mellitus (DM). Methods PA was measured in 452 adults (without DM n = 153, T1DM n = 67, T2DM n = 232). Carotid intima-media thickness (IMT), renal resistive index (RRI), ankle-brachial index (ABI) and carotid-femoral Pulse Wave Velocity (cfPWV) were estimated. Furthermore, the levels of high-sensitive Troponin-T [hsTnT], N-terminal brain natriuretic peptide [NT-pro-BNP]) were measured. Results PA values were lower in DM independently of age, gender, and BMI (estimated marginal means 6.21, 5.83, 5.95 for controls, T1DM, T2DM p < .05), a finding which persisted after propensity score matching. PA correlated negatively with IMT (r = −0.181), RRI (r = −0.374), cfPWV (r = −0.358), hsTnT (r = −0.238) and NT-pro-BNP (r = −0.318) (all p < .001). In multivariable analysis, the associations with RRI, cfPWV, hsTnT and NT-pro-BNP remained unchanged. PA values 6.0–6.5° for males and 5.2–5.8° for females were predictive of commonly used cutoffs. The combination of ΑCC/AHA ASCVD Score with PA outperformed either factor in predicting cfPWV, RRI for males and hsTnT, BNP for both genders. Conclusions PA exhibits independent correlations with various parameters pertinent to cardiovascular risk and may be useful for cardiovascular assessment.
CUTTHROAT TROUT TAXONOMY: EXPLORING THE HERITAGE OF COLORADO'S STATE FISH

Prior to recent molecular testing, larger spots and more scales above the lateral line were phenotypic traits associated with greenback cutthroat trout Oncorhynchus clarkii stomias as compared to Colorado River cutthroat trout O. c. pleuriticus. However, these two subspecies could not be separated consistently on the basis of those characteristics. As a result, geographic range had become the default approach for establishing subspecies designation. In 2007, researchers at the University of Colorado and others used mitrochondrial DNA (mtDNA), microsatellites, and amplified fragment length polymorphisms (AFLPs) to suggest there was a genetic basis for separating greenback cutthroat trout from Colorado River cutthroat trout. The primary concern raised by that study was that five of the nine greenback cutthroat trout populations they examined actually displayed genetic fingerprints more similar to Colorado River cutthroat trout from Trappers Lake, Colorado (Lineage CR). A finding that attracted less attention was the discovery of an alleged greenback cutthroat trout population west of the Continental Divide near Gunnison, Colorado, in West Antelope Creek. Recovery Team partners used the same AFLP test to canvass cutthroat trout populations for genetic purity across Colorado. Results indicate that the West Antelope Creek population is not unique, as 46 additional populations sharing the ―greenback‖ genetic fingerprint (Lineage GB) have now been identified west of the Continental Divide. It is therefore questionable whether West Antelope Creek fish are really greenback cutthroat trout as suggested in the 2007 study, or whether they simply represent diversity within Colorado River cutthroat trout. Given their broad geographic distribution and lack of a robust East Slope source from which to stock, it seems unlikely that these Lineage GB populations were established by anthropogenic means. A more parsimonious explanation would suggest they are aboriginal to Colorado's West Slope. Interestingly, no Lineage GB populations have been discovered in the White and Yampa river basins. This region appears to be a stronghold for Lineage CR cutthroat trout and coincides with the native range of Colorado's only other native salmonid, the mountain whitefish Prosopium williamsoni. Perhaps Lineage GB fish were already present in southwestern Colorado when Lineage CR and mountain whitefish invaded the state from the Green River drainage.
Quasi 2-layer morphodynamic model and Lagrangian study of bedload

Conventional morphodynamic models are typically based on a coupled system of hydrodynamic equations, a bed-update equation, and a sediment-transport equation. However, the sediment-transport equation is almost invariably empirical, with numerous options available in the literature. Bed morphological evolution predicted by a conventional model can be very sensitive to the choice of sediment-transport formula. This thesis presents a physics-based model, where the shallow water-sediment-mixture flow is idealised as being divided into two layers of variable (in time and space) densities: the lower layer concerned with bedload transport, and the upper layer representing sediment in suspension. The model is referred to as a Quasi-2-Layer (Q2L) model in order to distinguish it from typical 2-Layer models representing stratified flow by two layers of different but constant and uniform densities. The present model, which does not require the selection of a particular empirical formula for sediment transport rates, is satisfactorily validated against widely used empirical expressions for bedload and total transport rates. Analytical solutions to the model are derived for steady uniform flow over an erodible bed. Case studies show that the Q2L model, in contrast to conventional morphodynamic approaches, yields more realistic results by inherently including the influence of the bed slope on the sediment transport. This conclusion is validated against experimental data from a steep sloping duct. An analytical study using the Q2L model investigates the influence of bed-slope on bedload transport; the resulting expressions are in turn used to modify empirical sediment transport formulae (derived for horizontal beds) in order to render them applicable to arbitrary streamwise slopes. The Q2L model provides an alternative approach to studying sedimenttransport phenomena, whose adequate analysis cannot be undertaken following con-
Longitudinal changes in home food availability and concurrent associations with food and nutrient intake among children at 24–48 months

Objectives: To describe changes in home food availability during early childhood, including modified, developmentally sensitive obesogenic scores, and to determine whether home food availability is associated with food and nutrient intakes of children concurrently, over time. Design: Data were drawn from the STRONG Kids 2 longitudinal, birth cohort to achieve the study objectives. Home food availability was assessed with the Home Food Inventory (HFI) and included fifteen food groups (e.g. fruit and vegetables) and three obesogenic scores (one original and two modified). Food and nutrient intakes were measured using the Block FFQ and included twenty-seven food groups and eighteen nutrients (e.g. vitamins A and C, protein). HFI and FFQ were completed by trained researchers or mothers, respectively, at 24, 36 and 48 months. Repeated-measures ANOVA and Spearman’s correlations were used to achieve the study objectives. Setting: Central Illinois, USA. Participants: Participants were 468 children at 24, 36 and 48 months of age. Results: Availability of less nutritious foods and obesogenic foods and beverages increased as children aged, and availability of both nutritious and less nutritious foods were associated with child food and nutrient intake. The three obesogenic scores demonstrated similar, positive associations with the intake of energy, saturated fat, added sugars and kilocalories from sweets. Conclusion: These findings offer novel insight into changes in home food availability and associations with food and nutrient intake during early childhood. Additional attention is needed examining antecedents (e.g. built environments, purchasing behaviours) and consequences (e.g. child diet quality and weight) of home food availability.
Sustaining healthy long-term host-microbiome interactions in a physiologically relevant dynamic gingival tissue model

Host-oral microbiome interactions are known to be critical in maintaining local and systemic health of the human body, although they are difficult to study in both clinical and in vitro applications. Despite efforts, recapitulation of gingival architecture and physiological characteristics of the periodontal niche cannot be achieved by traditional tissue engineering strategies. Here, we advanced our humanized three-dimensional gingival model by co-culturing it with a healthy patient-derived microbiomes for seven days within an oral bioreactor that mimics native salivary dynamics. Our results indicated long-term host and microbiome viability, host barrier integrity and physiological response, and preservation of healthy microbial populations and interbacterial dialogues. The model has proven useful in successfully mimicking tissue homeostasis at the interface of the periodontal niche and suitable for the introduction of immune cells. Future studies will focus on using the model as a comparator of periodontal inflammation and identifying biomarkers associated with eubiotic/dysbiotic profiles. Graphical Abstract Created partially in biorender.com.
Immunomodulatory Porous Regenerative Scaffolds for in situ Vascular Engineering

The 70-year quest for synthetic vascular graft (sVG) endothelialization has not led to completely healed endothelium in clinically used sVGs. In humans, healing is limited to the vicinity of anastomotic regions (pannus ingrowth) and does not reach the middle regions of sVGs. Here, we conducted proof-of-concept implantation of immunomodulatory porous regenerative scaffolds for in situ vascular engineering (IMPRESSIVE) as interposition grafts in sheep carotid arteries. These scaffolds are based on a new polyurethane (PU) material featuring a 40 µm precision porous structure optimized for angiogenesis. The modulus of the PU was adjusted to match that of natural arteries. The implantation study revealed rapid healing in IMPRESSIVE sVGs. In side-by-side comparison with standard polytetrafluoroethylene (PTFE) grafts, the luminal surfaces of PU grafts were almost completely covered with nucleated cells, while healing in PTFE grafts was limited to several millimeters within anastomotic regions. Endothelialization was observed in the middle regions of PU grafts and overall endothelialization increased significantly compared to PTFE grafts. Densities of mononuclear cells, foreign body giant cells (FBGCs), and endothelial cells within graft walls of PU grafts were also significantly higher than those in PTFE grafts, suggesting transmural cellular infiltration may play a key role in overall improved healing. High percentages of macrophages in pores of PU grafts show Type 1 (CCR7+) and Type 2 (mannose receptor, MR+) characteristics. We also discovered that FBGCs exist in a diverse spectrum of phenotypes. Dually activated FBGCs (CCR7+MR+, G1/2) dominate the population of FBGCs associated with pro-healing PU grafts. These observations suggest a complex, balanced pro-healing response from macrophages and FBGCs. The IMPRESSIVE approach may enable complete endothelialization in pro-healing sVGs and have wide applications in implantable devices and tissue engineering.