Miracle-dz/UniFAR-FTUs huggingface dataset:
Elastohydrodynamic lubrication calculations used as a tool to study scuffing

A new Reynolds equation was developed that takes into account the nonlinear viscous behavior of the fluid. The new Reynolds equation considers the nonlinear viscous fluid model of Eyring, the equilibrium equation, the constant mass flow, and the kinematic boundary condition. The new Reynolds equation and the elasticity equation are solved simultaneously by using a system approach and a Newton-Raphson technique. Comparisons are made with results obtained from the classical Reynolds equation. The effects of sliding speed and introducing a bump or a groove within the conjunction are studied. Results are shown for both moderate and heavy loads.
A BLIND METHOD TO DETREND INSTRUMENTAL SYSTEMATICS IN EXOPLANETARY LIGHT CURVES

The study of the atmospheres of transiting exoplanets requires a photometric precision, and repeatability, of one part in ∼104. This is beyond the original calibration plans of current observatories, hence the necessity to disentangle the instrumental systematics from the astrophysical signals in raw data sets. Most methods used in the literature are based on an approximate instrument model. The choice of parameters of the model and their functional forms can sometimes be subjective, causing controversies in the literature. Recently, Morello et al. (, ) have developed a non-parametric detrending method that gave coherent and repeatable results when applied to Spitzer/IRAC data sets that were debated in the literature. Said method is based on independent component analysis (ICA) of individual pixel time-series, hereafter “pixel-ICA”. The main purpose of this paper is to investigate the limits and advantages of pixel-ICA on a series of simulated data sets with different instrument properties, and a range of jitter timescales and shapes, non-stationarity, sudden change points, etc. The performances of pixel-ICA are compared against the ones of other methods, in particular polynomial centroid division, and pixel-level decorrelation method. We find that in simulated cases pixel-ICA performs as well or better than other methods, and it also guarantees a higher degree of objectivity, because of its purely statistical foundation with no prior information on the instrument systematics. The results of this paper, together with previous analyses of Spitzer/IRAC data sets, suggest that photometric precision and repeatability of one part in 104 can be achieved with current infrared space instruments.
Catalytic Mechanism of ATP Hydrolysis in the ATPase Domain of Human DNA Topoisomerase IIα

Human DNA topoisomerase IIα is a biological nanomachine that regulates the topological changes of the DNA molecule and is considered a prime target for anticancer drugs. Despite intensive research, many atomic details about its mechanism of action remain unknown. We investigated the ATPase domain, a segment of the human DNA topoisomerase IIα, using all-atom molecular simulations, multiscale quantum mechanics/molecular mechanics (QM/MM) calculations, and a point mutation study. The results suggested that the binding of ATP affects the overall dynamics of the ATPase dimer. Reaction modeling revealed that ATP hydrolysis favors the dissociative substrate-assisted reaction mechanism with the catalytic Glu87 serving to properly position and polarize the lytic water molecule. The point mutation study complemented our computational results, demonstrating that Lys378, part of the important QTK loop, acts as a stabilizing residue. The work aims to pave the way to a deeper understanding of these important molecular motors and to advance the development of new therapeutics.
Trends in diabetes incidence and associated risk factors among people with HIV in the current treatment era

Objective: To examine type 2 diabetes mellitus incidence and associated risk factors among people with HIV (PWH). Design: A retrospective clinical cohort study of PWH at a Southeastern US academic HIV clinic between 2008 and 2018. Methods: PWH who attended at least two clinic visits were evaluated with demographic and clinical data extracted from the electronic medical record (EMR). Diabetes was defined as: hemoglobin A1C ≥6.5% and/or 2 glucose results >200 mg/dl (at least 30 days apart), diagnosis of diabetes in the EMR, or exposure to diabetes medication. Time to diabetes incidence was computed from the entire clinic population for each year. Multivariable Cox proportional hazard regression models with time-dependent covariates were created to evaluate the independent association between covariates and time to incident diabetes. Results: Among 4113 PWH, we identified 252 incident cases of diabetes. Incidence increased from 1.04 incidents per 1000 person years (PY) in 2008, to 1.55 incidents per 1000 PY in 2018. Body mass index (hazard ratio [HR] 10.5 (6.2, 17.7)), liver disease (HR 1.9 (1.2, 3.1)), steroid exposure (HR 1.5 (1.1, 1.9)), and use of integrase inhibitors (HR 1.5 (1.1, 2.0)) were associated with incident diabetes. Additional associated factors included lower CD4+ cell counts, duration of HIV infection, exposure to nonstatin lipid-lowering therapy, and dyslipidemia. Conclusions: Rapidly increasing incident diabetes rates among PWH were associated with both traditional and HIV-related associated risk factors, particularly body weight, steroid exposure, and use of Integrase Inhibitors. Notably, several of the risk factors identified are modifiable and can be targeted for intervention.
Chronic Traumatic Encephalopathy in a Routine Neuropathology Service in Australia

Abstract Chronic traumatic encephalopathy (CTE) is a neuropathological diagnosis defined by a unique pattern of hyperphosphorylated tau (p-tau) accumulation that begins in neocortical regions of the brain. It is associated with a range of neuropsychological symptoms, but a definitive diagnosis can only be made by postmortem brain examination. In 2018, we instituted CTE screening for all autopsy brains as part of our routine departmental protocol by performing p-tau immunohistochemistry on a restricted set of 3 neocortical blocks (frontal, temporal, and parietal). This strategy allowed us to identify 4 cases of low-stage CTE from 180 consecutive autopsies. Two of the 4 cases had a documented history of brain injury; for the remaining 2 cases, there was a long history of treatment-resistant tonic/clonic epilepsy suggesting that undocumented brain injuries may have occurred. Our experience indicates that 3-block CTE screening is useful in identifying CTE in routine practice. The results of this study further support the association between prior head injuries and CTE and demonstrate that, albeit uncommon, CTE does occur in the general population. Our findings suggest that p-tau screening should be routinely pursued in brain autopsy, particularly where there is a documented or likely history of traumatic brain injury.
Stromal cells of the endometrium and decidua: in search of a name and an identity

Abstract Human endometrial and decidual stromal cells are the same cells in different environments (nonpregnancy and pregnancy, respectively). Although some authors consider decidual stromal cells to arise solely from the differentiation of endometrial stromal cells, this is a debatable issue given that decidualization processes do not end with the formation of the decidua, as shown by the presence of stromal cells from both the endometrium and decidua in both undifferentiated (nondecidualized) and decidualized states. Furthermore, recent functional and transcriptomic results have shown that there are differences in the decidualization process of endometrial and decidual stromal cells, with the latter having a greater decidualization capacity than the former. These differences suggest that in the terminology and study of their characteristics, endometrial and decidual stromal cells should be clearly distinguished, as should their undifferentiated or decidualized status. There is, however, considerable confusion in the designation and identification of uterine stromal cells. This confusion may impede a judicious understanding of the functional processes in normal and pathological situations. In this article, we analyze the different terms used in the literature for different types of uterine stromal cells, and propose that a combination of differentiation status (undifferentiated, decidualized) and localization (endometrium, decidua) criteria should be used to arrive at a set of accurate, unambiguous terms. The cell identity of uterine stromal cells is also a debatable issue: phenotypic, functional, and transcriptomic studies in recent decades have related these cells to different established cells. We discuss the relevance of these associations in normal and pathological situations. Summary Sentence Decidual stromal cells show a greater capacity for decidualization than endometrial stromal cells, so studies of these stromal cells should clearly distinguish between these two cell types. Graphical Abstract Decidualization from precursor endometrial stromal cells (preEnSCs) to decidualized endometrial stromal cells (dEnSCs) in the endometrium, and from precursor decidual stromal cells (preDSCs) to decidualized decidual stromal cells (dDSCs) in the decidua. Figure created in BioRender.com
Maternal high-fat diet modifies epigenetic marks H3K27me3 and H3K27ac in bone to regulate offspring osteoblastogenesis in mice

ABSTRACT Studies from both humans and animal models indicated that maternal chronic poor-quality diet, especially a high fat diet (HFD), is significantly associated with reduced bone density and childhood fractures in offspring. When previously studied in a rat model, our data suggested that maternal HFD changes epigenetic marks such as DNA methylation and histone modifications to control osteoblast metabolism. In mouse embryonic and postnatal offspring bone samples, a ChIP-sequencing (ChIP-Seq)-based genome-wide method was used to locate the repressive histone mark H3K27me3 (mediated via the polycomb histone methyltransferase, Ezh2) and expressive histone mark H3K27ac (p300/CBP mediated) throughout the genome. Using isolated mouse embryonic cells from foetal calvaria (osteoblast-like cells), H3K27me3 ChIP-Seq showed that 147 gene bodies and 26 gene promoters in HFD embryotic samples had a greater than twofold increase in H3K27me peaks compared to controls. Among the HFD samples, Pthlh and Col2a1 that are important genes playing roles during chondro- and osteogenesis had significantly enriched levels of H3K27me3. Their decreased mRNA expression was confirmed by real-time PCR and standard ChIP analysis, indicating a strong association with Ezh2 mediated H3K27me3 epigenetic changes. Using embryonic calvaria osteoblastic cells and offspring bone samples, H3K27ac ChIP-Seq analysis showed that osteoblast inhibitor genes Tnfaip3 and Twist1 had significantly enriched peaks of H3K27ac in HFD samples compared to controls. Their increased gene expression and association with H3K27ac were also confirmed by real-time PCR and standard ChIP analysis. These findings indicate that chronic maternal HFD changes histone trimethylation and acetylation epigenetic marks to regulate expression of genes controlling osteoblastogenesis.
Psychological flexibility moderates the influence of fear avoidance on outcomes after mild traumatic brain injury

ABSTRACT Objectives Psychological factors contribute to poorer long-term outcomes following mild traumatic brain injury (mTBI); however, the exact psychological mechanisms that underly this relationship are not well understood. This study examined the relationship between psychological flexibility, fear avoidance, and outcomes over the first 6 months after mTBI Method Adults with mTBI-completed measures of psychological flexibility, fear avoidance, post-concussion symptoms, and functional status at baseline (<3 months post-injury; N = 152), and 3-month (N = 133) and 6-month follow-up (N = 102). A conceptually derived moderation-mediation analysis was used to test the mediating effect of fear avoidance on post-concussion symptoms and functional outcomes, and the moderating effects of psychological flexibility on fear avoidance. Results Fear avoidance had a significant indirect effect on the relationship between post-concussion symptoms and functional status across all three time points. Psychological flexibility was found to significantly moderate these effects. Only low levels of psychological flexibility had a significant influence on the mediating effects of high fear avoidance on functional status at 6-month follow-up. Conclusions Psychological flexibility may influence mTBI recovery by exerting an influence on fear avoidance. These initial findings provide a potential theoretical explanation of how fear avoidance can become maladaptive with time after mTBI.
Safeguarding in Church: Children and Young People’s Perceptions of Safety in Religious and Other Faith-Based Settings

Organizations that interact with children and young people have a duty of care to ensure the safety of those children and young people from any manner of abuse, particularly from child sexual abuse. Faith-based (“religious”) organizations are of particular interest due to the number of victims/survivors speaking out about their experiences of grooming, child sexual abuse, and other forms of harm in religious organizations. Focusing on addressing the risks and improving safeguarding efforts, prevention activities benefit from giving children agency and a voice. We conducted a study using two focus groups with children and young people involved with two different Christian denominations. We conducted activities and led discussions regarding their views about safety in the context of the faith-based organization with which they engage. Children and young people described different potentially unsafe situations, their likely frequency, and the level of impact such situations would have from their own point of view. They also described how they thought adults in their faith-based organization would see them. Thematic analysis of the data supported four themes related to young people’s sense of safety: concerning behavior of adults and other young people, fear of judgment by others (adults and peers), sense of or lack of empowerment due to power dynamics, and the importance of a sense of “familiarity. ” Visual comparisons of the data on scatterplots suggested differences not only in the level of impact and frequency of potentially unsafe situations between young people and adults but also between the two denominations. Children and young people can provide a wealth of information regarding their safety concerns when involved in programs and services at faith-based organizations. Clergy and other faith-based organizational leaders should consider how the context in which young people are involved (including interdenominational and interfaith difference, as well as the diverse types of activities young people are involved with) can affect their safety concerns.
Zona pellucida removal by acid Tyrode's solution affects pre- and post-implantation development and gene expression in mouse embryos

Abstract The zona pellucida plays a crucial role in the process of fertilization to early embryonic development, including cellular arrangement and communication between blastomeres. However, little is known regarding the role of the zona pellucida in pre- and post-implantation embryonic development associated with gene expression. We investigated the effect of zona pellucida removal on pre- and post-implantation development of mouse embryos. After zona pellucida removal of two-cell stage embryos was performed by acid Tyrode's solution, which is commonly used for zona pellucida treatment, compaction occurred earlier in zona pellucida-free than zona pellucida-intact embryos. In addition, the expression of differentiation-related genes in the inner cell mass and trophectoderm was significantly altered in zona pellucida-free blastocyst compared with zona pellucida-intact embryos. After embryo transfer, the rate of implantation and live fetuses was lower in zona pellucida-free embryos than in control embryos, whereas the fetal weight at E17.5 was not different. However, placental weight significantly increased in zona pellucida-free embryos. RNA-sequencing analysis of the placenta showed that a total of 473 differentially expressed genes significantly influenced the biological process. The present study suggests that zona pellucida removal by acid Tyrode's solution at the two-cell stage not only disturbs the expression pattern of inner cell mass-/trophectoderm-related genes but affects the post-implantation development of mouse embryos. Overall, this study provides deeper insight into the role of the zona pellucida during early embryonic development and the viability of post-implantation development. Summary Sentence Zona pellucida removal by acid Tyrode's solution affects the inner cell mass/trophectoderm differentiation; a lower fetal rate, higher placental weight, and a total of 473 differentially expressed genes during post-implantation development in mice. Graphical Abstract
Obesity and outcomes in patients undergoing upper airway surgery for obstructive sleep apnea

Objective Obesity is frequently debated as a factor associated with increased postoperative complications. Specifically, upper airway surgeries for obstructive sleep apnea (OSA), a common comorbidity among obese patients, may be complicated by obesity’s impact on intraoperative ventilation. The aim of this retrospective study was to analyze the association of various degrees of obesity with postoperative outcomes in patients undergoing surgery for OSA. Methods The American College of Surgeons National Surgical Quality Improvement database between 2015 and 2019 was used to create a sample of patients diagnosed with OSA who underwent uvulopalatopharyngoplasty, tracheotomy, and surgeries at the base of tongue, maxilla, palate, or nose/turbinate. Inverse probability-weighted logistic regression and unadjusted multivariable logistic regression were used to compare outcomes of non-obese and obesity class 1, class 2, and class 3 groups (World Health Organization classification). Primary outcome was a composite of 30-day readmissions, reoperations, and/or postoperative complications, and a secondary outcome was all-cause same-day hospital admission. Results There were 1929 airway surgeries identified. The inverse probability-weighted regression comparing class 1, class 2, and class 3 obesity groups to non-obese patients showed no association between obesity and composite outcome and no association between obesity and hospital admission (all p-values > 0.05). Conclusion These results do not provide evidence that obesity is associated with poorer outcomes or hospital admission surrounding upper airway surgery for OSA. While these data points towards the safety of upper airway surgery in obese patients with OSA, larger prospective studies will aid in elucidating the impact of obesity.
Biochemical and structural characterization of hepatitis A virus 2C reveals an unusual ribonuclease activity on single-stranded RNA

Abstract The HAV nonstructural protein 2C is essential for virus replication; however, its precise function remains elusive. Although HAV 2C shares 24–27% sequence identity with other 2Cs, key motifs are conserved. Here, we demonstrate that HAV 2C is an ATPase but lacking helicase activity. We identified an ATPase-independent nuclease activity of HAV 2C with a preference for polyuridylic single-stranded RNAs. We determined the crystal structure of an HAV 2C fragment to 2.2 Å resolution, containing an ATPase domain, a region equivalent to enterovirus 2C zinc-finger (ZFER) and a C-terminal amphipathic helix (PBD). The PBD of HAV 2C occupies a hydrophobic pocket (Pocket) in the adjacent 2C, and we show the PBD–Pocket interaction is vital for 2C functions. We identified acidic residues that are essential for the ribonuclease activity and demonstrated mutations at these sites abrogate virus replication. We built a hexameric-ring model of HAV 2C, revealing the ribonuclease-essential residues clustering around the central pore of the ring, whereas the ATPase active sites line up at the gaps between adjacent 2Cs. Finally, we show the ribonuclease activity is shared by other picornavirus 2Cs. Our findings identified a previously unfound activity of picornavirus 2C, providing novel insights into the mechanisms of virus replication.
MiR-495-3p regulates myoblasts proliferation and differentiation through targeting cadherin 2

Abstract MircoRNAs (miRNAs) play an important role in skeletal muscle development. Previous study had found that miR-495-3p was differentially expressed in fetal and adult goat skeletal muscle, but its function in myogenic proliferation and differentiation are unclear. Herein, we found the expression of miR-495-3p in C2C12 was downregulated during proliferation stage and upregulated during differentiation stage. Functionally, overexpression of miR-495-3p in C2C12 inhibited proliferation, and promoted myogenic differentiation. Mechanistically, the luciferase reporter assay demonstrated that cadherin 2 (CDH2) was a potential target gene of miR-495-3p. Importantly, overexpression of miR-495-3p inhibited CDH2 expression. Furthermore, knockdown of CDH2 in C2C12 inhibited proliferation and promoted myogenic differentiation. Together, the results showed that miR-495-3p inhibits C2C12 proliferation and promotes myogenic differentiation through targeting CDH2.
Psychological Resilience Level after Cognitive-Behavior Therapy in Old People with Empty Nest Syndrome - A single-case Experimental Design

ABSTRACT Objectives The aim of this study was to investigate the impact of Cognitive-Behavior Therapy (CBT) on resilience in old people with “empty nest syndrome. ” Methods Three older adults with empty nest syndrome underwent CBT for 8 weeks in a single-case experimental design. Changes in resilience were tracked through measurements at baseline, intervention, and follow-up. Visual analysis as well as an effect size index of Percentage of Nonoverlapping Data (PND) were then analyzed. Results CBT resulted in a significant increase in psychological resilience for all three participants across the intervention phase. Follow-up data showed that all subjects were able to maintain their resiliency four weeks after the intervention. Conclusions This single-case experimental study supports the hypothesis that CBT improves resiliency in old people with empty nest syndrome. Clinical Implications Cognitive Behavior Therapy is effective in increasing resiliency in old people with empty nest syndrome. The culture dynamics is an important component in the emergence and persistence of empty nest syndrome.