Miracle-dz/UniFAR-FTUs huggingface dataset:
BERT-Kgly: A Bidirectional Encoder Representations From Transformers (BERT)-Based Model for Predicting Lysine Glycation Site for Homo sapiens

As one of the most important posttranslational modifications (PTMs), protein lysine glycation changes the characteristics of the proteins and leads to the dysfunction of the proteins, which may cause diseases. Accurately detecting the glycation sites is of great benefit for understanding the biological function and potential mechanism of glycation in the treatment of diseases. However, experimental methods are expensive and time-consuming for lysine glycation site identification. Instead, computational methods, with their higher efficiency and lower cost, could be an important supplement to the experimental methods. In this study, we proposed a novel predictor, BERT-Kgly, for protein lysine glycation site prediction, which was developed by extracting embedding features of protein segments from pretrained Bidirectional Encoder Representations from Transformers (BERT) models. Three pretrained BERT models were explored to get the embeddings with optimal representability, and three downstream deep networks were employed to build our models. Our results showed that the model based on embeddings extracted from the BERT model pretrained on 556,603 protein sequences of UniProt outperforms other models. In addition, an independent test set was used to evaluate and compare our model with other existing methods, which indicated that our model was superior to other existing models.
Supported Lipid Bilayers and the Study of Two-Dimensional Binding Kinetics

Binding between protein molecules on contacting cells is essential in initiating and regulating several key biological processes. In contrast to interactions between molecules in solution, these events are restricted to the two-dimensional (2D) plane of the meeting cell surfaces. However, converting between the more commonly available binding kinetics measured in solution and the so-called 2D binding kinetics has proven a complicated task since for the latter several factors other than the protein-protein interaction per se have an impact. A few important examples of these are: protein density, membrane fluctuations, force on the bond and the use of auxiliary binding molecules. The development of model membranes, and in particular supported lipid bilayers (SLBs), has made it possible to simplify the studied contact to analyze these effects and to measure 2D binding kinetics of individual protein-protein interactions. We will in this review give an overview of, and discuss, how different SLB systems have been used for this and compare different methods to measure binding kinetics in cell-SLB contacts. Typically, the SLB is functionalized with fluorescently labelled ligands whose interaction with the corresponding receptor on a binding cell can be detected. This interaction can either be studied 1) by an accumulation of ligands in the cell-SLB contact, whose magnitude depends on the density of the proteins and binding affinity of the interaction, or 2) by tracking single ligands in the SLB, which upon interaction with a receptor result in a change of motion of the diffusing ligand. The advantages and disadvantages of other methods measuring 2D binding kinetics will also be discussed and compared to the fluorescence-based methods. Although binding kinetic measurements in cell-SLB contacts have provided novel information on how ligands interact with receptors in vivo the number of these measurements is still limited. This is influenced by the complexity of the system as well as the required experimental time. Moreover, the outcome can vary significantly between studies, highlighting the necessity for continued development of methods to study 2D binding kinetics with higher precision and ease.
A Cage Is a Cage, Unless You Educate. Rhetoric Negatively Impacts Support for a Novel Housing System for Laying Hens Unless the Public Are Educated

It has been proposed that terminology on commercially available eggs can impact the manner in which the eggs are discussed and ultimately consumer support. In this paper we tested if the label of ‘furnished cage’ eggs is a barrier for its support in Australia. Furthermore, we examined if educational interventions could change support and the way furnished cages were discussed. Survey participants (n = 1,157) were recruited by a stratified random sample of Australian adults. The participants were surveyed on their demographics, attitudes toward the poultry industry and animal welfare, and their egg buying behavior. Participants were randomly assigned to one of four treatment groups; two control groups and two educational groups. Participants were shown one of three videos, the control groups were shown a video with general information about chickens, the educated groups were shown one of two almost identical videos that educated them on aspects of the egg-laying industry in Australia, and the welfare implications of different housing systems including furnished systems. The only difference between the two educational videos was the name given to the furnished housing system; one group was introduced to furnished cages, the other was introduced to furnished coops. Educated participants were more likely to support furnished eggs and discuss them more positively than the control groups. When asked to discuss their support for furnished systems, control group participants exposed to the term cage were more likely to discuss the impacts of caged environments than the other treatment groups. The study suggests any negative impacts of housing system terminology can be mitigated through educational interventions.
Results of the Adult COVID-19 Lifestyle Matching Study

Objective: The aim of our case-control study was to find the influence of lifestyle and comorbidities on COVID-19 susceptibility, identify risk factors and protective factors, and identify ways to encourage people to adopt a healthy lifestyle. Methods: Patients with COVID-19 were matched with non-COVID-19 participants in a ratio of 1:2. Univariate analysis was performed using the chi-square test, and multivariate analysis was performed using conditional logistic regression. Results: Multivariate analysis using conditional logistic regression found that alcohol consumption (AC) and a bland diet increased the risk of COVID-19, while college degrees and above, smoking, drinking tea, and exercise, especially walking, significantly reduced the risk of COVID-19. Conclusion: After removing the effects of demographic factors, the study demonstrated that AC significantly reduced the ability of the body to resist COVID-19 infection. Moreover, following a bland diet increased the susceptibility to COVID-19. Notably, people who drank tea and performed regular exercises, especially walking, were significantly less likely to be infected with COVID-19. College degree or above relative illiteracy is COVID-19 protective factors of infection.
Physical Appearance Perfectionism: Psychometric Properties and Factor Structure of an Assessment Instrument in a Representative Sample of Males

Perfectionism is a multidimensional construct with both positive and negative aspects. Recently, the concept of appearance-oriented perfectionism has been introduced, which is associated with body image dissatisfaction and weight and shape control behaviors. The Physical Appearance Perfectionism Scale (PAPS) is a 12-item two-factor instrument developed to assess this new dimension of perfectionism. The aim of the study is to validate the Spanish version of PAPS among a representative sample of 850 male university students in Spain (M = 20 years old; SD = 2.7). Exploratory and confirmatory factorial structure, internal consistency, convergent and concurrent validity, and associated predictor variables analyses have been carried out. Results showed that the Spanish version of the PAPS maintains the original factor structure with all items and proves to be a reliable instrument. Physical appearance-oriented perfectionism is associated with general perfectionism, higher body dissatisfaction, Eating Disorders and Muscle Dysmorphia symptomatology, and compulsive exercise, particularly in the Worry about Imperfection subscale. These variables also act as predictors of physical appearance perfectionism. The use of the PAPS-S and the analysis of its subscales is recommended in the context of body image-related pathologies such as Eating Disorders and Muscle Dysmorphia.
Do Electric Vehicles Mitigate Urban Heat? The Case of a Tropical City

On top of their well known positive impact on air quality and CO2 emissions, electric vehicles generate less exhaust heat compared to traditional vehicles thanks to their high engine efficiency. As such, electric vehicles have the potential to mitigate the excessive heat in urban areas—a problem which has been exacerbated due to urbanisation and climate change. Still, the heat mitigation potential of electric vehicles has not been fully understood. Here, we combine high-resolution traffic heat emission inventories with an urban climate model to simulate the impact of the fleet electrification to the near-surface air temperature in the tropical city of Singapore. We show that a full replacement of traditional internal combustion engine vehicles with electric vehicles reduces the near-surface air temperature by up to 0.6°C. The heat mitigation potential is highest during the morning traffic peak and over areas with the largest traffic density. Interestingly, the reduction in exhaust heat emissions due to the fleet electrification during the evening traffic peak hardly leads to a reduction of near-surface air-temperatures, which is attributed to the different atmospheric conditions during morning and evening. This study presents a new quantification of the city-wide impact of electric vehicles on the air temperature in a tropical urban area. The results may support policy-makers toward designing holistic solutions to address the challenge of climate change adaptation and mitigation in cities.
Multi-Omics Revealed the Protective Effects of Rhamnolipids in Lipopolysaccharide Challenged Broilers

Rhamnolipid (RL) is a glycolipid biosurfactant and exhibits the following outstanding characteristics: strong antibacterial properties, low toxicity, and high biodegradability. The present research was conducted to explore the protective effects and mechanisms of rhamnolipids as an alternative to antibiotics in LPS (lipopolysaccharide)-challenged broilers. 16S rRNA gene sequencing and metabolomics were used for analyzing the cecal microbial composition and serum metabolites. Dietary antibiotics and RLS supplementation decreased the weight loss rate, enhanced serum immunoglobulin levels, reduced serum diamine oxidase and D-lactate acid concentration, and improved the symptoms of intestinal bleeding and villus height, when broilers were challenged with LPS. The addition of RLS in the diet enhanced serum interleukin-4 and interleukin-10 contents and reduced serum interleukin-6 and tumor necrosis factor-α levels in LPS-challenged broilers compared with the antibiotics group. Spearman’s correlation analysis revealed that RLS may alleviate LPS-induced inflammatory responses through altering the 6-methoxymellein level in broilers. The genus Bacteroides may contribute to the decreased weight loss rate via regulating the serum lysoPC [20:5(5Z,8Z,11Z,14Z,17Z)] secretion. RLS alleviates LPS-induced intestinal injury, enhances the growth and immunity, ameliorates intestinal microflora, and improves serum metabolites in LPS-challenged broilers. RLS exhibited better protective effect than antibiotic supplementation in the diet of LPS-challenged broilers. These findings provide potential regulation strategies and novel insights for RLS enhancing its protective effect in LPS-challenged broilers.
Psychological Treatment Effects Unrelated to Hair-Cortisol and Hair-BDNF Levels in Chronic Tinnitus

Background Currently, there are no objective markers to measure treatment efficacy in chronic (distressing) tinnitus. This study explores whether stress-related biomarkers cortisol and brain-derived neurotrophic factor (BDNF) measured in hair samples of chronic tinnitus patients change after compact multimodal tinnitus-specific cognitive behavioral therapy. Methods In this longitudinal study, hair-cortisol and hair-BDNF levels, self-reported tinnitus-related distress (Tinnitus Questionnaire; TQ), and perceived stress (Perceived Stress Questionnaire; PSQ-20) were assessed before and 3 months after 5 days of treatment in N = 80 chronic tinnitus patients. Linear mixed-effects models with backward elimination were used to assess treatment-induced changes, and a cross-lagged panel model (structural equation model) was used for additional exploratory analysis of the temporal associations between TQ and hair-BDNF. Results At follow-up, a reduction in TQ (p < 0.001) and PSQ-20 scores (p = 0.045) was observed, which was not influenced by baseline hair-cortisol or hair-BDNF levels. No changes in biomarker levels were observed after treatment. The exploratory analysis tentatively suggests that a directional effect of baseline TQ scores on hair-BDNF levels at follow-up (trend; p = 0.070) was more likely than the opposite directional effect of baseline hair-BDNF levels on TQ scores at follow-up (n.s.). Discussion While the treatment effectively reduced tinnitus-related distress and perceived stress in chronic tinnitus patients, this effect was not mirrored in biological changes. However, the lack of changes in hair-cortisol and hair-BDNF levels might have been influenced by the treatment duration, follow-up interval, or confounding medical factors, and therefore must be interpreted with caution. The relationship between tinnitus-related distress and hair-BDNF levels should be explored further to obtain a better understanding of stress-related effects in chronic tinnitus.
Effect of low intensity pulse ultrasound on the neutrophil function and epithelial thickness after skin excision in diabetes mellitus type 2 rats’ model

Objective: To determine the effect of Low Intensity Pulse Ultrasound (LIPUS) on the neutrophil function and epithelial thickness after skin excision in diabetes mellitus type 2 rats’ model (an Immunohistochemistry Study on Matrix Metalloproteinase-9). Material and Methods: Thirty-six Sprague dawley rats were divided into six groups: DM2, DM4, DM7, DML2, DML4, and DML7, each of which consist of 6 rats. Rats that matched the inclusion criteria were made into diabetes mellitus type 2 by injecting Nicotinamide and Streptozotocin. In all rat’s excision wound was made with punch biopsy in the back area. DML group received LIPUS therapy in the wound area (frequency: 3 MHz, intensity: 0.5 W/cm2, duty cycle: 20%, duration: 3 minutes every day) for two days (DML2), four days (DML4) and seven days (DML7). In the wound tissue an immunohistochemical examination was performed with Polyclonal Antibody MMP-9 to observe MMP-9 expression and and Periodic Acid-Schiff staining to observe epithelial thickness. Results: Two-Way ANOVA and PostHoc LSD test showed lower level of MMP-9 expressions in the DML group than in the DM group, whereas the epithelial thickness in the DML group was found higher than in the DM group. The Pearson test showed a correlation between the level of MMP9 expressions and epithelial thickness (p=0.000;
Finger Tapping as a Biomarker to Classify Cognitive Status in 80+-Year-Olds

This study examined the association between finger tapping and cognitive function in a group of 225 elderly participants (116 males; age 79–92 years; M = 82.5; SD = 2.4). Finger tapping was assessed in two conditions: self-selected pace and fast pace. Based on cognitive assessments, including the MoCA and CERA-NP test battery, participants were classified as cognitively healthy individuals (CHI), participants with mild cognitive impairments (MCI), and those with possible MCI (pMCI). Results of the analyses show significant differences between groups, sex and the group × sex interaction in four parameters for the self-selected pace condition and eight parameters for the fast pace condition. These parameters were used for classification by means of linear discriminant analysis (LDA). The first LDA component showed significant differences between CHI and pMCI and between CHI and MCI. Furthermore, the second LDA component showed significant differences between CHI and pMCI as well as between pMCI and MCI. Nevertheless, the algorithm correctly classified only 50% of participants, regardless of group, suggesting that tapping parameters are only partially useful for classification in early stages of dementia. We discuss these findings in terms of the diadochokinetic nature of finger tapping as associated with the age-related degeneration of cortical and subcortical motor areas.
Phthalate Esters in Tap Water, Southern Thailand: Daily Exposure and Cumulative Health Risk in Infants, Lactating Mothers, Pregnant and Nonpregnant Women

Human exposure to phthalate esters (PAEs) via drinking water has generated public health concerns due to their endocrine disruptive abilities. This study reports on the occurrence and fate of six PAEs in raw and tap water samples collected from provincial waterworks located in Songkhla Province, Southern Thailand. In addition, the daily exposure and cumulative health risk of susceptible populations due to drinking tap water were evaluated by using four different reference dose (RfDs) sources. The maximum concentrations of PAEs in raw water were between 1.68 and 4.84 and 0.52 and 1.24 µg/L in tap water. Moreover, the levels of PAEs in the tap water samples indicated the poor PAEs removal efficiency of the conventional treatment process (59.9–69.1%). The contribution of water to the daily intake of PAEs did not exceed 0.37% in all the groups. Furthermore, both the individual and cumulative risk assessment showed negligible noncarcinogenic and antiandrogenic risk for all the groups. Nevertheless, the cumulative risk showed an increasing trend in the order of infants > lactating mothers > pregnant women > nonpregnant women, suggesting that infants are more vulnerable. In additional, the newly proposed RfDAA yielded higher hazard quotient and hazard index estimates, which indicates it is a more sensitive tool than other RfDs for the assessment of the individual and mixture risk of pollutants. The carcinogenic risk of DEHP was acceptable in every group. However, we recommend a future cumulative risk assessment of vulnerable groups considering their simultaneous exposure to all chemicals that have antiandrogenic effects via tap water.
Epidemiological Study of Lung Cancer in Iran: A Systematic Review

Background: There is no comprehensive study addressing all the epidemiological aspects of Lung cancer (LC) in Iran, therefore this systematic review investigated the epidemiological aspects of lung cancer in Iran. Methods: The search was performed until the Aug. 2020 on the in international databases based on PRISMA protocol by Pulmonary Neoplasms, Lung Neoplasm, Neoplasm, Lung, Lung Cancer, Cancer, Pulmonary Cancer, Cancer, Pulmonary, Cancers, Cancer of the Lung, Iran, incidence, death, risk factors keywords and different combinations of them. Articles that evaluated epidemiological aspects of lung cancer were included in the analysis. Results: Of 1420 articles, 82 cases were entered the analysis. Based on studies, in Iran, lung cancer has been the most common cancer and its prevalence is increasing. Squamous cell carcinoma and adenocarcinoma is the most common type of lung cancer in men and women, respectively. Cigarette smoking, human papilloma virus (HPV) infection, mustard gas, occupational risk factors and genetic factors considered as the major reported risk factors for lung cancer and vegetarian diet as a protective factor. Conclusion: In according to the increasing trend of incidence and mortality of lung cancer in Iran, elimination of the major risk factors can decrease this issue and national comprehensive planning should be considered in health promotion plans.
Safety and immunogenicity of BNT162b2 mRNA COVID-19 vaccine in adolescents with rheumatic diseases treated with immunomodulatory medications

Abstract Objectives Adolescents with juvenile-onset autoimmune inflammatory rheumatic diseases (AIIRDs) could be at risk for disease flare secondary to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection or to withholding anti-inflammatory therapy. While vaccination can protect against coronavirus disease 2019 (COVID-19), safety and immunogenicity data regarding anti-SARS-CoV-2 vaccines among adolescents with AIIRDs are limited. This international, prospective, multicentre study evaluated the safety and immunogenicity of the BNT162b2 anti-SARS-CoV-2 vaccine among adolescents and young adults with juvenile-onset AIIRDs, 80% of whom are on chronic immunomodulatory therapy. Methods Vaccine side effects, disease activity and short-term efficacy were evaluated after 3 months in 91 patients. Anti-spike S1/S2 IgG antibody levels were evaluated in 37 patients and 22 controls 2–9 weeks after the second dose. Results A total of 91 patients and 40 healthy controls were included. The safety profile was good, with 96.7% (n = 88) of patients reporting mild or no side effects and no change in disease activity. However, three patients had transient acute symptoms: two following the first vaccination (renal failure and pulmonary haemorrhage) and one following the second dose (mild lupus flare vs viral infection). The seropositivity rate was 97.3% in the AIIRD group compared with 100% among controls. However, anti-S1/S2 antibody titres were significantly lower in the AIIRD group compared with controls [242 (S.d. 136.4) vs 387.8 (57.3) BAU/ml, respectively; P < 0.0001]. No cases of COVID-19 were documented during the 3 month follow-up. Conclusion Vaccination of juvenile-onset AIIRD patients demonstrated good short-term safety and efficacy and a high seropositivity rate but lower anti-S1/S2 antibody titres compared with healthy controls. These results should encourage vaccination of adolescents with juvenile-onset AIIRDs, even while on immunomodulation.
Thermal analysis of fused deposition modeling process based finite element method: Simulation and parametric study

Abstract Fused deposition modeling (FDM) is an advanced additive manufacturing (AM) method for rapid prototyping technique and to produce functional components with complex geometry. However, the process is mostly appropriate to polymer-based raw materials for several fields of application. In this study, a 3-D computational model is developed to analyze the transient heat transfer problem and investigate the inter-layer adhesion behavior, which affects the mechanical behavior of the final part. The developed model is validated based on published experimental and analytical data. The numerical model is utilized to predict the temperature evolution in the interface region between layers. The time history of temperature is coupled with a mathematical model describing the bonding potential to predict the bonding formation. In addition, the developed model is combined with design exploration tools to investigate the relationship between key process parameters and their impact on the output variables using design of experiment (DEO) and response surface methods. Moreover, due to the 3-D nature of the developed model, it could be coupled with a structural computational tool for further thermomechanical analysis.