Miracle-dz/UniFAR-FTUs huggingface dataset:
BalLeRMix +: mixture model approaches for robust joint identification of both positive selection and long-term balancing selection

Abstract Summary The growing availability of genomewide polymorphism data has fueled interest in detecting diverse selective processes affecting population diversity. However, no model-based approaches exist to jointly detect and distinguish the two complementary processes of balancing and positive selection. We extend the BalLeRMix B-statistic framework described in Cheng and DeGiorgio (2020) for detecting balancing selection and present BalLeRMix+, which implements five B statistic extensions based on mixture models to robustly identify both types of selection. BalLeRMix+ is implemented in Python and computes the composite likelihood ratios and associated model parameters for each genomic test position. Availability and implementation BalLeRMix+ is freely available at https://github.com/bioXiaoheng/BallerMixPlus. Supplementary information Supplementary data are available at Bioinformatics online.
Strategic traits of bacteria and archaea vary widely within substrate use groups.

Quantitative traits such as maximum growth rate and cell radial diameter are one facet of ecological strategy variation across bacteria and archaea. Another facet is substrate-use pathways, such as iron reduction or methylotrophy. Here we ask how these two facets intersect, using a large compilation of data for culturable species and examining seven quantitative traits (genome size, signal-transduction protein and histidine kinase counts, growth temperature, temperature adjusted maximum growth rate, cell radial diameter, and 16S rRNA operon copy number). Overall, quantitative trait variation within groups of organisms possessing a particular substrate-use pathway was very broad, outweighing differences between substrate-use groups. Although some substrate-use groups had significantly different means for some quantitative traits, standard deviation of quantitative trait values within each substrate use pathway mostly averaged between 1.6 and 1.8 times larger than standard deviation across group means. Most likely this wide variation reflects ecological strategy: for example, fast maximum growth rate is likely to express an early-successional or copiotrophic strategy, and maximum growth varies widely within most substrate-use pathways. In general, it appears that these quantitative traits express different and complementary information about ecological strategy, compared to substrate use.
Sesamol ameliorates hepatic lipid accumulation and oxidative stress in steatosis HepG2 cells via the PPAR signaling pathway.

Non-alcoholic fatty liver disease (NAFLD) is a chronic hepatopathy caused by disordered lipid metabolism in the liver. Sesamol, a phenolic compound derived from sesame oil, has been shown to inhibit obesity, hyperlipidemia, and atherosclerosis in previous investigations. However, the preventive effect of sesamol against hepatic steatosis and oxidative stress in NAFLD has not been well-studied. In this work, sesamol was observed to alleviate lipid accumulation and oxidative stress in high oleic acid (300 μM)/cholesterol (25 μM) induced HepG2 cells, thus indicating that sesamol was involved in regulating hepatic lipid metabolism and oxidative injury. Mechanism studies found that the activated peroxisome proliferator-activated receptors (PPAR) signaling pathway by sesamol intervention up-regulated gene and protein expressions related to fatty acid oxidation and cholesterol efflux and catabolism, thus accelerating lipid consumption and reducing intracellular lipid accumulation in the process of NAFLD. These data suggested that sesamol can effectively ameliorate hepatic steatosis and sesamol riched sesamol oil may be a potential agent for finding therapeutic strategies to treat the NAFLD. PRACTICAL APPLICATIONS: Sesamol and sesamol-rich sesame oil have received much attention due to their performance on hepatic lipid regulation. The results of this study indicate that sesamol treatment could ameliorate hepatic steatosis by inhibiting lipid accumulation and oxidative stress, thus demonstrating that sesamol and sesame oil can be used for functional foods and nutraceutical applications in the future. In addition, the present work provides knowledge of the effects of sesamol on NAFLD and involved mechanisms, and further supplies nutritional guidelines for sesame oil consumption.
HyperAttentionDTI: improving drug-protein interaction prediction by sequence-based deep learning with attention mechanism

MOTIVATION Identifying drug-target interactions (DTIs) is a crucial step in drug repurposing and drug discovery. Accurately identifying DTIs in silico can significantly shorten development time and reduce costs. Recently, many sequence-based methods are proposed for DTI prediction and improve performance by introducing the attention mechanism. However, these methods only model single non-covalent inter-molecular interactions among drugs and proteins and ignore the complex interaction between atoms and amino acids. RESULTS In this paper, we propose an end-to-end bio-inspired model based on the convolutional neural network (CNN) and attention mechanism, named HyperAttentionDTI, for predicting DTIs. We use deep CNNs to learn the feature matrices of drugs and proteins. To model complex non-covalent inter-molecular interactions among atoms and amino acids, we utilize the attention mechanism on the feature matrices and assign an attention vector to each atom or amino acid. We evaluate HpyerAttentionDTI on three benchmark datasets and the results show that our model achieves significantly improved performance compared to the state-of-the-art baselines. Moreover, a case study on the human Gamma-aminobutyric acid receptors confirm that our model can be used as a powerful tool to predict DTIs. AVAILABILITY The codes of our model are available at https://github.com/zhaoqichang/HpyerAttentionDTI and https://zenodo.org/record/5039589. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Association between the use of exchange devices for peritoneal dialysis fluids and peritonitis incidence: A nationwide cohort study

Background: The use of exchange devices for peritoneal dialysis (PD) fluids is a common practice in Japan. Evidence on the effectiveness of exchange devices in preventing PD-related peritonitis is scarce. We evaluated the association between the use of exchange devices for PD fluids and peritonitis incidence. Methods: We retrospectively enrolled 3845 patients, aged ≥20 years, receiving PD for ≥3 months, with available data on the exchange procedure for PD fluids and peritonitis incidence that was obtained from the Japan Renal Data Registry, a nationwide annual survey. The patients were grouped according to whether the manual or device PD fluid exchange method was used. The onset of peritonitis was defined as a leukocyte count of >100/µL (neutrophils ≥50%) in PD effluents. We applied quasi-Poisson regression analyses to estimate the incidence rate ratio (IRR). Age, sex, PD vintage, body mass index, automated PD use, residual kidney function, comorbidities, haemoglobin and serum albumin were adjusted as potential confounders. Results: Older age, automated PD use, diabetes as comorbidity and lower haemoglobin levels were associated with the use of exchange devices for PD fluids. Patients using devices for PD fluid exchange (69.2%) had an increased risk of peritonitis of 37% (IRR: 1.37, 95% confidence interval (CI): 1.07–1.75) and 28% (IRR: 1.28, 95% CI: 1.00–1.63) in the crude and multivariate adjustment models, respectively. Conclusions: The use of exchange devices for PD fluids and peritonitis incidence showed no favourable association. There may remain possible residual confounding by indication.
Male–female differences in acute thoracic aortic dissection: a systematic review and meta-analysis

Abstract OBJECTIVES This study aims to systematically review published literature on male–female differences in presentation, management and outcomes in patients diagnosed with acute thoracic aortic dissection (AD). METHODS A systematic literature search was conducted for studies published between 1 January 1999 and 19 October 2020 investigating mortality and morbidity in adult patients diagnosed with AD. Patient and treatment characteristics were compared with odds ratios (ORs) and standardized mean differences and a meta-analysis using a random-effects model was performed for early mortality. Overall survival and reoperation were visualized by pooled Kaplan–Meier curves. RESULTS Nine studies investigating type A dissections (AD-A), 1 investigating type B dissections (AD-B) and 3 investigating both AD-A and AD-B were included encompassing 18 659 patients. Males were younger in both AD-A (P < 0.001) and AD-B (P < 0.001), and in AD-A patients males had more distally extended dissections [OR 0.57, 95% confidence interval (CI) 0.46–0.70; P < 0.001]. Longer operation times were observed for males in AD-A (standardized mean difference 0.29, 95% CI 0.17–0.41; P < 0.001) while male patients were less often treated conservatively in AD-B (OR 0.65, 95% CI 0.58–0.72; P < 0.001). The pooled early mortality risk ratio for males versus females was 0.94 (95% CI 0.84–1.06, P = 0.308) in AD-A and 0.92 (95% CI 0.83–1.03, P = 0.143) in AD-B. Pooled overall mortality in AD-A showed no male–female difference, whereas male patients had more reinterventions during follow-up. CONCLUSIONS This systematic review shows male–female differences in AD patient and treatment characteristics, comparable early and overall mortality and inconsistent outcome reporting. As published literature is scarce and heterogeneous, large prospective studies with standardized reporting of male–female characteristics and outcomes are clearly warranted. Improved knowledge of male–female differences in AD will help shape optimal individualized care for both males and females. Clinical registration number PROSPERO, ID number: CRD42020155926.
Pharmacological Modulation of Immune Responses by Nutritional Components

The incidence of noncommunicable diseases (NCDs) has increased over the last few decades, and one of the major contributors to this is lifestyle, especially diet. High intake of saturated fatty acids and low intake of dietary fiber is linked to an increase in NCDs. Conversely, a low intake of saturated fatty acids and a high intake of dietary fiber seem to have a protective effect on general health. Several mechanisms have been identified that underlie this phenomenon. In this review, we focus on pharmacological receptors, including the aryl hydrocarbon receptor, binding partners of the retinoid X receptor, G-coupled protein receptors, and toll-like receptors, which can be activated by nutritional components and their metabolites. Depending on the nutritional component and the receptors involved, both proinflammatory and anti-inflammatory effects occur, leading to an altered immune response. These insights may provide opportunities for the prevention and treatment of NCDs and their inherent (sub)chronic inflammation. Significance Statement This review summarizes the reported effects of nutritional components and their metabolites on the immune system through manipulation of specific (pharmacological) receptors, including the aryl hydrocarbon receptor, binding partners of the retinoid X receptor, G-coupled protein receptors, and toll-like receptors. Nutritional components, such as vitamins, fibers, and unsaturated fatty acids are able to resolve inflammation, whereas saturated fatty acids tend to exhibit proinflammatory effects. This may aid decision makers and scientists in developing strategies to decrease the incidence of noncommunicable diseases.
Association between asthma status and prenatal antibiotic prescription fills among women in a Medicaid population

Abstract Objective Pregnant women with asthma have increased frequency of respiratory viral infections and exacerbations. Because of these risks, women with asthma may be subject to increased surveillance during pregnancy and may, therefore, be at increased risk of antibiotic receipt. The objective of this study was to assess the relationship between maternal asthma and outpatient prenatal antibiotic prescription fills to inform antibiotic stewardship. Methods We included women who delivered a singleton, term, non-low birthweight, and otherwise healthy infant enrolled in the Tennessee Medicaid Program. Maternal asthma and prenatal antibiotic fills were ascertained from healthcare encounters and outpatient pharmacy claims. We examined the association between maternal asthma and prenatal antibiotic fills using modified Poisson regression. Results Our study population included 168354 pregnant women, 4% of whom had asthma. Women with asthma had an increased risk of filling at least one prenatal antibiotic prescription (adjusted risk ratio [aRR] 1.27, 95% confidence interval [CI] 1.25-1.28) and had an increased number of fills during pregnancy (aRR 1.54, 95% CI 1.51-1.57) compared to women without asthma. Among those who filled at least one antibiotic prescription, women with asthma had earlier first prenatal antibiotic prescription fill and increased likelihood of filling at least one course of broad-spectrum antibiotics during pregnancy (versus narrow-spectrum). Conclusions Pregnant women with asthma had more outpatient antibiotic prescription fills than pregnant women without asthma. These findings highlight that pregnant women with asthma disproportionately fill more antibiotic prescriptions during pregnancy, providing data that may inform antibiotic stewardship.
Family-focused campus-based university event increases perceived knowledge, science capital and aspirations across a wide demographic

ABSTRACT Creative ways of delivering informal science events in community settings are viewed as key to engaging new audiences and participants whom scientists find hard to reach, however, the impact of ‘formal’ setting events is often overlooked. Here, through a mixed-methods approach, we analyse a large-scale family-focused public engagement event hosted within a university campus setting. We aimed to explore the profile of visitors attending together with the impact and perceived knowledge gained. Analysis from two consecutive years of data collection found that the university-based event attracted new visitors annually, with almost half having not attended other science events/attractions within the last year. An increase in perceived knowledge was shown amongst all study participants, being significantly amplified in those from low progression to higher education postcode areas. Both immediate and longer-term positive impact was reported by participants with increases in components of science capital observed as well as enhanced positive perception of the university and its students. This data exemplifies the benefit of university-hosted events in widening participation and public understanding of science.
The role of communication professionals in fostering a culture of public engagement

ABSTRACT This study initially reports on qualitative interviews (n = 17) with scientists at two Long Term Ecological Research (LTER) sites in the northeastern United States. These interviews suggest the need for greater attention to the role of communication professionals and institutional leadership in fostering high-quality public engagement. The study also reports on a follow-up quantitative survey (n = 68) conducted to better understand the degree to which LTER scientists’ views about communication professionals were meaningfully associated with perceptions about the need for robust engagement funding. The project was initially designed based on the Integrated Behavioral Model to assess how individual LTER scientists’ engagement-related attitudes, normative beliefs, and efficacy beliefs affected their communication activities. However, the combined results highlight the potential value of additional research and theorization aimed at better understanding the factors that might lead to greater cooperation between scientists and organizational communicators.
Standing out in a small crowd: The role of display size in attracting attention

ABSTRACT Strong evidence supporting the top-down modulation of attention has come from studies in which participants learned to suppress a singleton in a heterogeneous four-item display. These studies have been criticized on the grounds that the displays are so sparse that the singleton is not actually salient. We argue that similar evidence of suppression has been found with substantially larger displays where salience is not in question. Additionally, we examine the results of applying salience models to four-item displays, and find prominent markers of salience at the location of the singleton. We conclude that small heterogeneous displays do not preclude strong salience signals. Beyond that, we reflect on how further basic research on salience may speed resolution of the attentional capture debate.
The progress revisited: How the dispute between stimulus-driven and contingent-capture advocates is hampered by a blindness for change

ABSTRACT Luck, Gaspelin, Folk, Remington, and Theeuwes [2021. Progress toward resolving the attentional capture debate. Visual Cognition, 29(1), 1–21. https://doi.org/10.1080/13506285.2020. 1848949] argue that the debate regarding attentional capture has changed in such a way that there is now some consensus. However, even though a certain degree of agreement has been reached on the question whether locations can be preattentively inhibited or facilitated, the different views underlying the debate did not change fundamentally. The major question as to whether or not attentional control is contingent upon the non-spatial control settings of an observer is still not settled. In the present commentary I argue that the main reason for this is that current notions do not incorporate the possibility that the underlying processes are dynamic. To really move the debate forward, it is necessary to recognize that not only behaviour but also the underlying processes change over time.
Scale Bridging in Computational Modelling of Quasi-Brittle Fracture of Cementitious Composites

Computational prediction damage in cementitious composites, as steel fibre reinforced ones, under mechanical, thermal, etc. loads, manifested as creation of micro-fractured zones, followed by potential initiation and evolution of macroscopic cracks, is a rather delicate matter, due to the necessity of bridging between micro-and macro-scales. This short paper presents a relatively simple approach, based on the nonlocal viscoelasticity model, coupled with cohesive crack analysis, using extended finite element techniques. Such model admits proper verification of its existence and convergence results, from the physical and mathematical formulation up to software implementation of relevant algorithms. Its practical applicability is documented on a sequence of representative computational examples.
Formulation Optimization and Characterization of Spray-Dried Medium Chain Triglycerides-Rich Oil

Medium chain triglycerides (MCT) are important substrates of the energy metabolism and anabolic processes in mammals. In this study, MCT-rich oil was encapsulated in the mixing ratios of maltodextrin and protein by spray drying to produce spray-dried MCT-rich oil (SMCT). Spray-dried conditions were an inlet temperature of 200 °C, an outlet temperature of 90 °C, and a flow rate of 0.70 L/h. Box–Behnken experimental design and response surface methodology were applied for modeling the influence of formulation variables on powder recovery of SMCT. The key variables were concentration of maltodextrin (10-30% W/W), total protein (5–15% w/w), and MCT-rich oil (5–15% w/w). The microparticles were characterized in terms of particle morphology, yield, Carr's index, moisture content, flowability, hygroscopicity, and powder diffraction. The highest yield of SMCT was 41.19% obtained under the optimized conditions (maltodextrin concentration of 15% w/w, total protein concentration of 8% w/w, MCT-rich oil concentration of 15%). Experimentally obtained values were consistent with those predicted by the model, indicating the suitability of the employed model and the success of the model in optimizing the formulation.
Palm Kernel Ash and Eggshell Ash as Partial Replacement of Cement in Interlocking Brick Production

This research uses eggshell ash and palm kernel shell ash as a partial replacement for cement in brick production. Previous researchers have used different materials as a replacement for cement. This research seeks to determine the best eggshell ash and palm kernel ash ratio as a partial replacement for cement in brick production. The experiment uses 5, 10, 15, and 20% eggshell ash and palm kernel shell ash for a partial replacement of cement. This research performs the compressive strength, water absorption, efflorescence, fire resistance, colour, sound and size tests to determine the quality of the brick containing eggshell ash and palm kernel shell ash as a partial replacement for cement. The results show that the best ratio for replacing cement in brick production is 15% eggshell ash and palm kernel shell.
Nonlinear Vibration and Stability Analysis of Functionally Graded Nanobeam Subjected to External Parametric Excitation and Thermal Load

Analysis of vibration stability of simply supported Euler-Bernoulli functionally graded (FG) nanobeam embedded in viscous elastic medium with thermal effect under external parametric excitation is presented in this work. An attempt has been made for the first time is investigating the effect of thermal load on dynamic behavior, amplitude response, instability region and bifurcation points of functionally graded nanobeam. Thermal loads are supposed to be uniform, linear or nonlinear distribution along the thickness direction. Nonlocal continuum theory and the principle of the minimum total potential energy are applied to derive the governing equations. The partial differential equations (PDE) are transported to the ordinary differential equations (ODE) by using the Petrov-Galerkin method and the multiple time scales method are manipulated to solve the motion equation. To study the effect of external parametric excitation and thermal effect, different temperature distributions along the thickness such as uniform, linear, and nonlinear distribution are considered. Moreover, stable and unstable regions and bifurcation points are determined. It is obtained that the thermal load can affect the amplitude response of FG nanobeam. Also, it is observed that the instability of the system is affected by the detuning parameter and the parametric excitation amplitude plays great role in the instability of system. Nanobeams are used in many devices like nanoresonators, nanosensors and nanoswitches. This paper is helpful for designing and manufacturing nanoscale structures specially nanoresonators under different thermal loads.