Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative HIV-1 Phylogenies Characterized by PR/RT, Pol and Near-Full-Length Genome Sequences

In an effort to evaluate the accuracy of HIV-1 phylogenies based on genomes of increasing length, we developed a comprehensive near-full-length HIV-1 genome RT–PCR assay and performed a comparative evaluation via phylogenetic analyses. To this end, we conducted comparative analyses of HIV-1 phylogenies derived based on HIV-1 PR/RT (2253–3359 in the HXB2 genome) and pol region (2253–5250 in the HXB2 genome) sequences isolated from 134 HIV-1-infected patients in Cyprus (2017–2019). The HIV-1 genotypic subtypes determined using six subtyping tools (REGA 3.0, COMET 2.3, jpHMM, SCUEAL, Stanford, and Geno2pheno) were compared to investigate the discrepancies generated among different tools. To evaluate the accuracy of defined HIV-1 phylogenies, the samples exhibiting at least one discrepant subtyping result among different subtyping tools in both PR/RT and pol regions or only in the pol region (n = 38) were selected for near-full-length HIV-1 genome (790–8795 in HXB2 genome) sequencing using a newly developed RT–PCR/sequencing assay. The obtained sequences were employed for HIV-1 genotypic subtype determination and subjected to comparative phylogenetic-based analyses. It was observed that 39.6% of the 134 samples presented discrepancies in the PR/RT region, while 28.4% presented discrepancies in the pol region. REGA 3.0 produced the fewest discrepancies collectively in both regions and was selected for subsequent subtyping and comparative phylogenetic analyses of near-full-length HIV-1 genome sequences. The analyses of near-full-length HIV-1 genome sequences identified 68.4% of the 38 ‘discrepant samples’ (n = 26) as belonging to uncharacterized recombinant HIV-1 strains, while 21.1% were circulating recombinant forms (CRFs) (n = 8) and 10.5% belonged to pure group M subtypes (n = 4). The findings demonstrated a significant reduction of 11.2% in discrepancies when pol region sequences were used compared to PR/RT region sequences, indicating that increased nucleotide sequence lengths are directly correlated with more consistent subtype classification. The results also revealed that if the discrepancy in pol region subtyping results persists, then there is a high likelihood (89.5%) that the query sequence is a recombinant HIV-1 strain, 68.4% of which belong to uncharacterized recombinant HIV-1 strains. The results of this study showed that REGA 3.0 presented the best performance in subtyping recombinant HIV-1 strains, while Stanford performed better in defining phylogenies of pure group M subtypes. The study highlights that, especially in populations with polyphyletic HIV-1 epidemics resulting in a high prevalence of recombinant HIV-1 strains, neither PR/RT nor pol region sequences are reliable for the determination of HIV-1 genotypic subtypes in samples showing discrepancies among different subtyping tools, and only near-full-length or full-length HIV-1 genome sequences are sufficiently accurate.
Losses in coplanar waveguide resonators at millikelvin temperatures

We study the loss rate for a set of lambda/2 coplanar waveguide resonators at millikelvin temperatures (20 mK - 900mK) and different applied powers (3E-19 W - 1E-12 W). The loss rate becomes power independent below a critical power. For a fixed power, the loss rate increases significantly with decreasing temperature. We show that this behavior can be caused by two-level systems in the surrounding dielectric materials. Interestingly, the influence of the two-level systems is of the same order of magnitude for the different material combinations. That leads to the assumption that the nature of these two-level systems is material independent.
Study of the structure of a meteor complex near the earth's orbit. 1. Description of the model

The mechanism which forms meteor swarms and causes them to evolve consists of process which lead, on one hand, to concentration, and on the other hand, to scattering. The authors show that this mechanism leads to a hyperbolic intensity distribution of meteor swarms. By starting out from the most general qualitative concepts concerning the origin and evolution of meteor material, the authors have obtained a model for the probable structure of a meteor complex which reflects its systematic nature. The next step will be to check experimentally whether or not this model is accurate.
D-branes and synthetic/$C^{\infty}$-algebraic symplectic/calibrated geometry, I: Lemma on a finite algebraicness property of smooth maps from Azumaya/matrix manifolds

We lay down an elementary yet fundamental lemma concerning a finite algebraicness property of a smooth map from an Azumaya/matrix manifold with a fundamental module to a smooth manifold. This gives us a starting point to build a synthetic (synonymously, $C^{\infty}$-algebraic) symplectic geometry and calibrated geometry that are both tailored to and guided by D-brane phenomena in string theory and along the line of our previous works D(11.1) (arXiv:1406.0929 [math.DG]) and D(11.2) (arXiv:1412.0771 [hep-th]).
Cut-off Point of Glutathione Peroxidase(GSH-PX) for the Diagnosis of Endometritis in Dairy Cows

The cut-off point of a diagnostic test is the determination of the minimum value at which an individual can be diagnosed as sick. To obtain a good position, an analysis is carried out using a statistical ROC Curve (Receiver Operating Characteristic), which is used in determining the value of the diagnosis with the highest sensitivity and specificity. The cut-off value of glutathione peroxidase (GSH-Px) for the diagnosis of uterine diseases is not described. The minimum tolerable value can be described for 130 U/g Hb; the value has been used as a limit under which it has a marginal deficiency of Se. Therefore, the objective of this work was to determine the cut-off point of the GSH-Px values that allows diagnosing cows with endometritis, in dairy herds in the province of Santa Fe, Argentina. We used 115 Holstein cows between 21 and 56 postpartum days, from dairy establishments in the province of Santa Fe, Argentina. Blood samples were obtained by puncturing the coccygeal vein for determination of GSH-Px. At the same time, the uterine status of the cows was characterized in two groups: healthy cows (VS, by its initials in Spanish) and cows with endometritis, either clinical and subclinical (VE, by its initials in Spanish). To create a ROC curve, the VS and VE diagnoses must be entered under a binary system as 0 (VS) and 1 (VE). The obtained results indicate that the point or cut value for the GSH-Px was of 222 U/g Hb with a sensitivity of 81.4% and a specificity of 33.9%. That is to say, above that value, the possibility of suffering endometritis decreases significantly. We can conclude that the cut-off point of 222 U/g Hb obtained for this group of cows from establishments in the province of Santa Fe, could be considered in the future as a complementary tool to diagnose endometritis.
The Importance of Signal Strength Index in Optical Coherence Tomography Angiography: A Study of Eyes with Pseudoexfoliation Syndrome

Purpose To evaluate the effect of the signal strength index (SSI) on a comparison of the vascular and structural OCT measurements between eyes with pseudoexfoliation syndrome (PXF) and healthy controls of Asian-Indian origin. Methods In this cross-sectional study, 33 eyes of 33 PXF patients and 40 healthy eyes of 40 controls underwent OCT and OCT angiography (OCTA). Eyes with intraocular pressure (IOP) >21mmHg, glaucomatous disc changes, or any other ocular pathology were excluded. Peripapillary vessel density (VD) and retinal nerve fiber layer (RNFL) thickness were determined from the optic disc scans. Parafoveal VD and ganglion cell complex (GCC) thickness were measured from the macular scans. These parameters were compared between the groups using mixed effect models after adjusting for clinical confounders such as IOP, as well as SSI of the scans. Results The 2 groups were demographically similar. Average RNFL (94µm vs 100µm, p = 0.01) and GCC (91µm vs 95µm, p = 0.03) were thinner in the PXF group compared to controls. The average peripapillary VD appeared lower in the PXF groups compared to controls (58.2% vs 58.8%, p = 0.04), but after adjusting for IOP and SSI, no difference was noted (p = 0.39). After accounting for confounders, parafoveal VD in the PXF group was significantly lower compared to controls (44.3% vs 46.8%, p = 0.008). Conclusion Peripapillary RNFL thickness, parafoveal GCC thickness and parafoveal VD were decreased in eyes with PXF when compared to controls. VD measurements are associated with the SSI and, therefore, clinicians and researchers evaluating OCTA scans quantitatively must consider the SSI value during analysis and interpretation.
Long-Term Prognosis Value of Paravalvular Leak and Patient–Prosthesis Mismatch following Transcatheter Aortic Valve Implantation: Insight from the France-TAVI Registry

Background: Transcatheter aortic valve implantation (TAVI) is the preferred treatment for symptomatic severe aortic stenosis (AS) in a majority of patients across all surgical risks. Patients and methods: Paravalvular leak (PVL) and patient–prosthesis mismatch (PPM) are two frequent complications of TAVI. Therefore, based on the large France-TAVI registry, we planned to report the incidence of both complications following TAVI, evaluate their respective risk factors, and study their respective impacts on long-term clinical outcomes, including mortality. Results: We identified 47,494 patients in the database who underwent a TAVI in France between 1 January 2010 and 31 December 2019. Within this population, 17,742 patients had information regarding PPM status (5138 with moderate-to-severe PPM, 29.0%) and 20,878 had information regarding PVL (4056 with PVL ≥ 2, 19.4%). After adjustment, the risk factors for PVL ≥ 2 were a lower body mass index (BMI), a high baseline mean aortic gradient, a higher body surface area, a lower ejection fraction, a smaller diameter of TAVI, and a self-expandable TAVI device, while for moderate-to-severe PPM we identified a younger age, a lower BMI, a larger body surface area, a low aortic annulus area, a low ejection fraction, and a smaller diameter TAVI device (OR 0.85; 95% CI, 0.83–0.86) as predictors. At 6.5 years, PVL ≥ 2 was an independent predictor of mortality and was associated with higher mortality risk. PPM was not associated with increased risk of mortality. Conclusions: Our analysis from the France-TAVI registry showed that both moderate-to-severe PPM and PVL ≥ 2 continue to be frequently observed after the TAVI procedure. Different risk factors, mostly related to the patient’s anatomy and TAVI device selection, for both complications have been identified. Only PVL ≥ 2 was associated with higher mortality during follow-up.
Development of High-Fiber, Low Fat Chicken Nuggets

Dietary fiber intake is significantly below the recommended daily allowances worldwide, making fortification of foods with dietary fiber a vital strategy. Simultaneously, there is a trend towards increased consumption of processed meat products containing substantial amounts of fat, making processed meat products an excellent vehicle to deliver fiber. In this study, the effects of adding four types of dietary fiber (Resistant Starch (RS), Polydextrose (POD), Fructooligosaccharides (FOS) and Galactooligosaccharides (GOS)) to chicken nuggets were investigated. Fibers were added at three levels (5, 10 and 15%) to replace 33.33, 66.66, and 100%, respectively, of the chicken skin. The difference between the removed quantity of chicken skin and added fiber was compensated with water. Chicken nuggets were evaluated by measuring color, texture, proximate composition, yield and consumers’ acceptability. Results indicated that replacement of the chicken skin entirely with dietary fiber is possible without negatively affecting the final product quality.
Recent updates in the treatment of diabetic polyneuropathy

Distal symmetric diabetic peripheral polyneuropathy (DPN) is the most common form of neuropathy in the world, affecting 30 to 50% of diabetic individuals and resulting in significant morbidity and socioeconomic costs. This review summarizes updates in the diagnosis and management of DPN. Recently updated clinical criteria facilitate bedside diagnosis, and a number of new technologies are being explored for diagnostic confirmation in specific settings and for use as surrogate measures in clinical trials. Evolving literature indicates that distinct but overlapping mechanisms underlie neuropathy in type 1 versus type 2 diabetes, and there is a growing focus on the role of metabolic factors in the development and progression of DPN. Exercise-based lifestyle interventions have shown therapeutic promise. A variety of potential disease-modifying and symptomatic therapies are in development. Innovations in clinical trial design include the incorporation of detailed pain phenotyping and biomarkers for central sensitization.
Research on the Impact of Pro-Environment Game and Guilt on Environmentally Sustainable Behaviour

Game strategies are widely used by companies to attract users and increase their stickiness. At the same time, the protection of the ecological environment is also an important expression of corporate social responsibility. This paper explores the integration of social responsibility with gaming strategies from the psychological perspective of game withdrawal, and explores the incorporation of social responsibility as an element in gamification design to reduce user withdrawal behaviour, thereby increasing individual’s environmentally sustainable behaviour. We evidenced our hypothesis through two studies. Study one proved our hypothesis by recruiting 106 university undergraduates (from Wuhan University, mean age 20, of whom 47 were female and 59 were male) to prove our hypothesis by recalling previous experiences with different types of games. Study two further tested our hypothesis by manipulating participants’ guilt through randomly recruiting 196 participants (mean age 35, of whom 88 were female and 108 were male, 35 of them were students, 107 were office workers and 54 were from other sectors) from different industries through the questionnaire research website Credamo. The findings show that incorporating social responsibility elements into the design of games can make users engage in pro-social behaviour while playing the game, and the guilt that users feel because of the game will be compensated by pro-social behaviour, thus reducing the game frequency and duration and improving the intent of pro-social behaviour. At the same time, players’ self-control moderates the effect of guilt on game play volume under a socially responsible gamification design.
Influence of country governance factors and national culture on corporate sustainability practice: an inter-Country study

Abstract A growing number of studies have investigated organisational-level and sectorial-level determinants of corporate sustainability practice (hereinafter referred to as CSP) such as Board attributes, audit committee meetings, shareholders’ activism, ownership structure and sustainability-linked compensation, and industry type. However, most studies have been conducted at the country level, as there have been calls to conduct an investigation using intercountry evidence; therefore, studies that focus on country-level governance factors affecting CSP are scarce. Against this backdrop, the current study investigates country-level governance factors (i.e., Voice and Accountability; Political Stability and Absence of Violence/Terrorism; Government Effectiveness; Regulatory Quality; Rule of Law; and Control of Corruption) and national culture dimensions proposed by Hofstede (i.e., Power distance; Individualism; Masculinity; Uncertainty avoidance; Long-term orientation; and Indulgence) affecting CSP in an international context of 204 oil and gas firms cutting across 36 countries over a 10-year period (2011–2020). Result from the analysis using multivariate regression, generalised linear models regression and discriminant analysis reveals that the country-level governance factor strongly promoting CSP is the rule of law, whilst four of the national culture factor positively influence on CSP except power distance and masculinity. This current study contributes to knowledge by presenting empirical evidence that country-level and national culture factors affect CSP. The study, thus, argues for the inclusion of country governance factors and cultural dimension that may affect CSP in addition to other well-known factors affecting sustainability practice. The study also adds to literature by providing empirical support for the Hofstede Model on national cultural dimensions affecting accounting and organisational practice.
COVID-19-Related Self-Stigma, Post-Traumatic Stress Disorder, Insomnia, and Smartphone Addiction Among Frontline Government Workers with COVID-19 Pandemic Control Duties

Purpose The duties related to COVID-19 control and prevention may have caused psychological stress for the individuals in charge (eg, frontline government workers) and have reportedly led to mental health issues, such as insomnia and post-traumatic stress disorder (PTSD). However, the prevalence of these COVID-19-related disorders and their associated factors remain unclear. Therefore, the purpose of the present study was to investigate the prevalence rates of insomnia, PTSD, COVID-19-related self-stigma, and smartphone addiction, along with the identification of risk factors and protective factors for Taiwan frontline government workers with COVID-19 pandemic control duties. Methods The survey was carried out with 151 participants between September and October 2021. All participants completed the Fear of COVID-19 Scale (assessing fear of COVID-19), Self-Stigma Scale (assessing self-stigma during the COVID-19 pandemic), Smartphone Application-Based Addiction Scale (assessing the risk of smartphone addiction), Insomnia Severity Index (assessing insomnia), Impacts of Event Scale-6 (assessing PTSD), and a self-designed set of questions assessing trait resilience. Results The results showed that the prevalence rate was 31.1% for insomnia and 33.8% for PTSD. Furthermore, service duration (adjusted odds ratio [AOR] = 0.93; 95% confidence interval [CI] = 0.86, 0.999) and trait resilience (AOR = 0.19; 95% CI = 0.08, 0.46) were protective factors and fear of COVID-19 (AOR = 1.91; 95% CI = 1.02, 3.57) was a risk factor for insomnia. Fear of COVID-19 (AOR = 2.63; 95% CI = 1.35, 5.14), self-stigma (AOR = 3.62; 95% CI = 1.19, 11.02), and smartphone addiction (AOR = 1.09, 95% CI = 1.001, 1.19) were risk factors, and trait resilience was a protective factor (AOR = 0.58; 95% CI = 0.29, 1.17) for PTSD. Conclusion The findings demonstrated a high prevalence of insomnia and PTSD. Risk-reducing strategies and protective factor promotion strategies are recommended to help reduce the symptoms of insomnia and PTSD among Taiwan frontline government workers.
Identifying Hub Genes and Immune Cell Infiltration for the Progression of Carotid Atherosclerotic Plaques in the Context of Predictive and Preventive Using Integrative Bioinformatics Approaches and Machine-Learning Strategies

Emerging evidence shows that carotid atherosclerosis is related to the activation of immune-related pathways and inflammatory cell infiltration. However, the immune-linked pathways that helped in the advancement of the carotid atherosclerotic plaque and the association of such plaques with the infiltration status of the body's immune cells still unclear. Here, the expression profiles of the genes expressed during the progression of the carotid atherosclerotic plaques were retrieved from the Gene Expression Omnibus database and 178 differentially expressed genes were examined. The Weighted Gene Coexpression Network Analysis technique identified one of the brown modules showed the greatest correlation with carotid atherosclerotic plaques. In total, 66 intersecting genes could be detected after combining the DEGs. LASSO regression analysis was subsequently performed to obtain five hub genes as potential biomarkers for carotid atherosclerotic plaques. The functional analysis emphasized the vital roles played by the inflammation- and immune system-related pathways in this disease. The immune cell infiltration results highlighted the significant correlation among the CD4+ T cells, B cells, macrophages, and CD8+ T cells. Thereafter, the gene expression levels and the diagnostic values related to every hub gene were further validated. The above results indicated that macrophages, B cells, CD4+ T cells, and CD8 + T cells were closely related to the formation of the advanced-stage carotid atherosclerotic plaques. Based on the results, it could be hypothesized that the expression of hub genes (C3AR1, SLAMF8, TMEM176A, FERMT3, and GIMAP4) assisted in the advancement of the early-stage to advanced-stage carotid atherosclerotic plaque through immune-related signaling pathways. This may help to provide novel strategies for the treatment of carotid plaque in the context of predictive, preventive, and personalized medicine.
Contributions to Succession in a Family Business from the Perspective of Global University Entrepreneurial Spirit Students’ Survey (GUESSS)

Relationship between family support and organizational commitment is investigated, in the attitude of succession in a family business, and, this one, in the succession intention. Therefore, the research operationalizes constructs studied by the Global University Entrepreneurial Spirit Students’ Survey, in a survey with 289 university students from the Federal University in Brazil. Structural modeling showed satisfactory adjustment indices to support the seven hypotheses of the study: family support assumes an important explanatory capacity for the variation of affective commitment (R2=38%), as well as of normative commitment (R2=41%); commitment (affective and normative) assumes an important explanatory capacity for the variation in the succession attitude (R2=49%); and, the suggested relationship between the succession attitude and the succession intention (β=0.775; t=22.772, p=0.000), in addition to being supported, demonstrates the greater explanatory capacity of the predictor construct variation (R2=60%). It was concluded, therefore, that prior planning, with actions that mobilize future family members (successors) can result in the achievement of the longevity of these companies.