Miracle-dz/UniFAR-FTUs huggingface dataset:
Phylogenetic analysis of Aquilaria Lam. (Thymelaeaceae) based on DNA barcoding

Abstract Aquilaria Lam. is an important group of trees that produce agarwood, which is widely used for manufacturing medicine, perfumes and incense. The members of the genus Aquilaria are close to being extinct due to illegal harvesting and are now protected in many countries. In this study, five DNA barcodes [internal transcribed spacer (ITS), maturase K (matK), psbA-trnH, ribulose bisphosphate carboxylase (rbcL) and trnL-trnF] and their combinations were evaluated for the discrimination of the major (16 out of 21) species of Aquilaria based on three criteria: sequence variation, genetic distances and the discrimination ability. In addition, we attempted to determine the phylogenetic relationship between Aquilaria and Gyrinops species using three phylogenetic analysis methods. We observed that the combination barcode ITS+trnL-trnF had a good discrimination ability based on the best match and best close match methods, provided more genetic information, and clearly indicated the comprehensive phylogenetic relationship between most Aquilaria and Gyrinops species. Considering the overall performance of these barcodes, the ITS+trnL-trnF is a suitable barcode for the identification of Aquilaria species.
Cooperative transmitter structure for improving efficiency in wireless power transfer

Wireless power transfer (WPT) is widely used in portable devices with the advantage of flexibility and conveniences. This paper aims to design a cube transmitter structure, which generates a spatially focused magnetic field providing effective power transfer. The phase shift in multiple coils has been optimized for maximum power transfer efficiency and free positioning in the charging spatial domain. The performance of out-phase multiple coil cube (OPMC) antenna has been compared to that of in-phase multiple coil cube (IPMC) transmitter and traditional single coil. Simulation results show that the OPMC is better and provides higher efficiency wherever the receiver is located inside the cubical region above the cube base.
A Clustering Algorithm for Key Frame Extraction Based on Density Peak

Aiming at the problem of video key frame extraction, a density peak clustering algorithm is proposed, which uses the HSV histogram to transform high-dimensional abstract video image data into quantifiable low-dimensional data, and reduces the computational complexity while capturing image features. On this basis, the density peak clustering algorithm is used to cluster these low-dimensional data and find the cluster centers. Combining the clustering results, the final key frames are obtained. A large number of key frame extraction experiments for different types of videos show that the algorithm can extract different number of key frames by combining video content, overcome the shortcoming of traditional key frame extraction algorithm which can only extract a fixed number of key frames, and the extracted key frames can represent the main content of video accurately.
Vascular Endothelial Function Assessed by Flow-Mediated Vasodilatation in Young Adults Born Very Preterm or With Extremely Low Birthweight: A Regional Cohort Study

Background: Preterm birth and low birthweight have been associated with increased risk of cardiovascular disease in young adults. Endothelial dysfunction is established as an early marker for development of atherosclerotic cardiovascular disease. Previous studies of endothelial function in young adults born very preterm or with extremely low birthweight have, however, shown diverging results. Objective: We aimed to evaluate the risk of cardiovascular disease as measured by vascular endothelial function in young adults born very preterm (<29 weeks of gestation) or with extremely low birthweight (<1,000 g), compared with term-born controls. Methods: This study included 50 young adults born very preterm or with extremely low birthweight and 49 term-born controls born in Norway in the periods 1982–1985, 1991–1992, and 1999–2000 at mean age 28 (±6) years. The endothelial function was assessed by ultrasound measured flow-mediated dilatation (FMD) of the right brachial artery. The arterial diameter was measured at baseline, after release of 5 min of occlusion, and after sublingual administration of nitroglycerine. FMD was reported as absolute and percentage diameter change from baseline and relative to nitroglycerine-induced dilatation. Results: The participants were mainly normal weight non-smokers, without hypertension, diabetes, or established cardiovascular disease. The cases and controls had mean blood pressure 112/71 (SD 12/9) and 112/69 (SD 11/8) mmHg, body mass index 24.0 (SD 4.2) and 24.4 (SD 4.5) kg/m2, and HbA1c 32.7 (SD 2.5) and 33.0 (SD 2.6) mmol/mol, respectively. For both groups, 4 (8%) were smokers. Mean FMD for the adults born very preterm or with extremely low birthweight was 0.17 mm (95% CI 0.14, 0.21) vs. 0.24 mm (95% CI 0.20, 0.28) for the controls (p = 0.01), corresponding to a percentage increase of 5.4% (95% CI 4.2, 6.6) and 7.6% (95% CI 6.2, 8.9), respectively (p = 0.02). The FMD relative to maximal nitroglycerine-induced dilatation was 20% and 31%, respectively (p = 0.001). Conclusions: Young adults born very preterm or with extremely low birthweight have significantly lower FMD compared with the term-born controls suggesting an increased risk of cardiovascular disease.
Trichomonas Vaginalis Infection in Men with High-Risk Sexual Behaviors

Background: Trichomonas vaginalis is a protozoan pathogen of the human genitourinary tract, which is the cause of trichomoniasis. The disease is one of the most important non-viral sexually transmitted infections in the world. Many studies have been performed on the molecular identification of Trichomonas in men in different parts of the world, but in Iran, such a study has been very limited. We aimed to detect T. vaginalis in urine of men with unusual sexual behavior by wet mount microscopic observation, culturing in TYM-33 and molecular method in Tehran, Iran. Methods: Totally, 47 urine samples were collected from men with high-risk sexual behaviors referred to Health Care Centers in South of Tehran, Iran during 2017–2018. After urine centrifugation and wet mount sediment preparation, the samples were cultured in TYM-33 medium and examined microscopically. Then DNA was extracted from urine sediment samples and finally the 18srRNA gene was amplified by PCR. Results: Thirty-one (65.95%) urine samples were positive for T. vaginalis by PCR. Of these, only 6 (12.76%) were detected positive by wet mount method and 25 (53.19%) by culture and successive passages. Conclusion: The high prevalence of trichomoniasis among men with high-risk sexual behavior in Tehran indicates a potent health risk condition for families. Of course, this percentage is not the real infection rate in ordinary men in Tehran. This situation could be controlled by promoting concurrent diagnosis and treatment of T. vaginalis infection in men and women, as well as strengthening religious beliefs and health education in the individuals.
Effect of Calcium Dobesilate in Preventing Contrast-Induced Nephropathy in Patients with Diabetes and Chronic Kidney Disease

OBJECTIVES: This study assessed the protective effect of calcium dobesilate against contrast-induced nephropathy (CIN) after coronary angiography (CAG) or percutaneous coronary intervention (PCI) in patients with diabetes and chronic kidney disease (CKD). METHODS: A total of 130 patients with diabetes and CKD estimated glomerular filtration rate: 30-90 mL/min/1.73m2 were enrolled and included in the analysis. They were divided into experimental (n=65) and control groups (n=65). Patients in the experimental group were administered oral calcium dobesilate (500 mg) three times daily for 2 days before and 3 days after the procedure. The serum creatinine (SCr), cystatin C (Cys C), and neutrophil gelatinase-associated lipocalin (NGAL) levels were measured before and after the procedure. RESULTS: The mean SCr level at 24h after the procedure was found to be significantly lower in the experimental group than in the control group (79.1±19.6 μmol/L vs. 87.0±19.3 μmol/L, p=0.023). However, the Cys C and NGAL levels were not significantly different between the two groups at all measurement time points (all p>0.05). The incidence of CIN defined by the SCr level was significantly lower in the experimental group than in the control group (3 [4.6%] vs. 13 [20.0%], p=0.017). However, the incidence of CIN defined by the Cys C level was not statistically different between the two groups (7 [10.8%] vs. 7 [10.8%], p=1.000). CONCLUSIONS: This study revealed that calcium dobesilate has no preventive effect against CIN in patients with diabetes and CKD.
Treatment of hepatitis B virus infection in children and adolescents

Hepatitis B virus (HBV) infection is one of the main causes of morbidity and mortality worldwide. Most children acquire the infection perinatally or during early childhood and develop a chronic hepatitis characterized by a high viral replication and a low-inflammation phase of infection, with normal or only slightly raised aminotransferases. Although a conservative approach in children is usually recommended, different therapies exist and different therapeutic approaches are possible. The main goals of antiviral treatment for children with chronic HBV infection are to suppress viral replication and to warn the disease progression to cirrhosis and hepatocellular carcinoma, although these complications are rare in children. Both United States Food and Drug Administration (US-FDA) and European Medicines Agency (EMA) have approved interferon alfa-2b for children aged 1 year and older, pegylated interferon alfa-2a and lamivudine for children aged 3 years and older, entecavir for use in children aged 2 years and older, and adefovir for use in those 12 years of age and older. Tenofovir disoproxil fumarate is approved by EMA for children aged 2 years and older and by US-FDA for treatment in children aged 12 years and older. Finally, EMA has approved the use of tenofovir alafenamide for treatment of children aged 12 years and older or for children weighing more than 35 kg independent of age. This narrative review will provide the framework for summarizing indications to antiviral therapy in the management of chronic HBV infection in children and adolescents.
Trypsin induces an aversive response in zebrafish by PAR2 activation in keratinocytes

Previously we have shown that trypsin, a protein typically involved in digestion, is released from gills of both fresh and saltwater fishes into surrounding water under stress or injury. We have also shown that each species produces trypsin with different specific activities. In this report, using zebrafish as a model, we identified that trypsin induces an aversive response in zebrafish larvae and adult zebrafish. Since Protease-Activated Receptor 2 (PAR2) responds to trypsin, we tested whether the aversive response is dependent on the activation of PAR2 located on the zebrafish skin cells. Zebrafish larvae treated separately with neomycin and zinc sulfate also showed aversive response indicating neuromast, and olfactory cells are not involved in this aversion. Cultured keratinocytes from zebrafish showed a response to trypsin. Zebrafish larvae subjected to knockdown of par2a also exhibited reduced escape response. Similarly, par2a-deficient mutant larvae displayed no response to trypsin. Since it has been shown that stress activates PAR2 and sends signals to the brain as shown by the increased c-fos expression, we tested c-fos expression in adult zebrafish brains after trypsin treatment of adults and found enhanced c-fos expression by qRT-PCR. Taken together, our results show that the trypsin activates PAR2 on keratinocytes signaling the brain, and this pathway of trypsin-induced escape response will provide a unique communication mechanism in zebrafish. Furthermore, since PAR2 activation also occurs in pain/pruritus sensing, this model might be useful in elucidating components of signaling pathways in pain/pruritus.
Disentangling the Role of Deviant Letter Position on Cognate Word Processing

The way of coding letter position has been extensively assessed during the recognition of native words, leading to the development of a new generation of models that assume more flexible letter position coding schemes compared to classical computational models such as the interactive activation (IA) model. However, determining whether similar letter position encoding mechanisms occur during the bilingual word recognition has been largely less explored despite its implications for the leading model of bilingual word recognition (multilink) as it assumes the input-coding scheme of the IA model. In this study, we aimed to examine this issue through the manipulation of the position of the deviant letter of cognate words (external and internal letters). Two experiments were conducted with Catalan–Spanish bilinguals (a masked priming lexical decision task and a two-alternative forced-choice task) and their respective monolingual controls. The results revealed a differential processing for the first letter in comparison to the other letters as well as modulations as a function of language cue, suggesting amendments to the input-coding scheme of the multilink model.
Genome-Wide Association Study Reveals Novel Genetic Loci for Quantitative Resistance to Septoria Tritici Blotch in Wheat (Triticum aestivum L.)

Septoria tritici blotch, caused by the fungus Zymoseptoria titici, poses serious and persistent challenges to wheat cultivation in Ethiopia and worldwide. Deploying resistant cultivars is a major component of controlling septoria tritici blotch (STB). Thus, the objective of this study was to elucidate the genomic architecture of STB resistance in an association panel of 178 bread wheat genotypes. The association panel was phenotyped for STB resistance, phenology, yield, and yield-related traits in three locations for 2 years. The panel was also genotyped for single nucleotide polymorphism (SNP) markers using the genotyping-by-sequencing (GBS) method, and a total of 7,776 polymorphic SNPs were used in the subsequent analyses. Marker-trait associations were also computed using a genome association and prediction integrated tool (GAPIT). The study then found that the broad-sense heritability for STB resistance ranged from 0.58 to 0.97 and 0.72 to 0.81 at the individual and across-environment levels, respectively, indicating the presence of STB resistance alleles in the association panel. Population structure and principal component analyses detected two sub-groups with greater degrees of admixture. A linkage disequilibrium (LD) analysis in 338,125 marker pairs also detected the existence of significant (p ≤ 0.01) linkage in 27.6% of the marker pairs. Specifically, in all chromosomes, the LD between SNPs declined within 2.26–105.62 Mbp, with an overall mean of 31.44 Mbp. Furthermore, the association analysis identified 53 loci that were significantly (false discovery rate, FDR, <0.05) associated with STB resistance, further pointing to 33 putative quantitative trait loci (QTLs). Most of these shared similar chromosomes with already published Septoria resistance genes, which were distributed across chromosomes 1B, 1D, 2A, 2B, 2D, 3A,3 B, 3D, 4A, 5A, 5B, 6A, 7A, 7B, and 7D. However, five of the putative QTLs identified on chromosomes 1A, 5D, and 6B appeared to be novel. Dissecting the detected loci on IWGSC RefSeq Annotation v2.1 revealed the existence of disease resistance-associated genes in the identified QTL regions that are involved in plant defense responses. These putative QTLs explained 2.7–13.2% of the total phenotypic variation. Seven of the QTLs (R2 = 2.7–10.8%) for STB resistance also co-localized with marker-trait associations (MTAs) for agronomic traits. Overall, this analysis reported on putative QTLs for adult plant resistance to STB and some important agronomic traits. The reported and novel QTLs have been identified previously, indicating the potential to improve STB resistance by pyramiding QTLs by marker-assisted selection.
A longitudinal study on respiratory viral infection for healthy volunteers

Human-to-human transmission by means of droplets is an important route of infection for respiratory viruses. Therefore, outbreaks are thought to spread via asymptomatic and/or mildly symptomatic infected persons. We reported previously that several viruses were detected in children regardless of their health condition. Respiratory tract viral infection is one of the most common and important diseases of children. When we consider their range of movement, adults might spread viruses to the community more easily than children. Although asymptomatic rates may vary depending on the host's age and the virus, little is known about what respiratory viruses are present in adults with subclinical or mild symptoms. In this study, we investigated how often, how long, and what respiratory viruses were present in asymptomatic adults. Gargle samples obtained by rinsing the throat with distilled water were collected from participants once a week and subjected to two-step real-time PCR to detect respiratory viruses. Sixteen singleplex real-time PCRs were employed for the detection of the following respiratory viral pathogens: parainfluenza viruses (PIVs) 1, 2, 3, and 4, respiratory syncytial virus (RSV), human metapneumovirus (hMPV), enterovirus (EV)/ rhinovirus (RV), human bocavirus (hBoV), human parechovirus (hPeV), adenovirus (AdV), human coronaviruses (hCoV) OC43, NL63, 229E, and HKU-1, and influenza virus (FluV) type C, and one-step real-time reverse transcription (RT)-PCR was used for detection FluV A and B.
Pulmonary alveolar proteinosis with an unusual bronchoscopic complication

Pulmonary alveolar proteinosis (PAP) is a rare respiratory syndrome, which can be challenging to diagnose given its non‐specific presentation and imaging findings. While most primary cases of PAP have an autoimmune basis, the triggers for the disease are uncertain with occupational factors increasingly thought to be important. We report the unusual complication of pneumomediastinum and bilateral pneumothoraces following endobronchial ultrasound‐guided transbronchial needle aspirate in the setting of PAP. We discuss the possible physiological mechanisms of this complication, which appears to be more common in conditions with reduced lung compliance.
Online mathematics supports in lieu of university tutorials during COVID-19: student and lecturer perspectives

Abstract When the first national lockdown due to the COVID-19 pandemic occurred, all higher educational institutions in Ireland moved to remote learning and have effectively remained in this mode ever since. The situation presented enormous challenges for many mathematics lecturers who had not delivered lectures or tutorials online before. This study looks closely at what a traditional (in-person) mathematics tutorial encompasses and examines learners’ needs with respect to support within a remotely delivered module. The work focuses on how well various formats of remote support address the affordances of the traditional in-person tutorial. The range of support formats explored here includes live tutorials, written homework with feedback, group work via breakout rooms in Zoom, a discussion forum and instant formative feedback through Canvas quizzes and the e-assessment tool Numbas. The effectiveness of the different formats of remote support is assessed through examining student engagement and student and lecturer feedback. Six student cohorts, of levels ranging from first year to MSc level, across three different departments, taking either a mathematics or statistics module, participated in the study and were surveyed on their experience and future preferences. The work highlights some of the key issues surrounding remote support within mathematics modules and discusses the findings in the context of the implications for a lecturer and the factors to consider when deciding on a strategy for remote learning. The paper also analyses student interaction and notes the aspects of remote mathematics support that will have value beyond the pandemic.
Effects of a group-based lifestyle medicine for depression: A pilot randomized controlled trial

Given the growing evidence that a range of lifestyle factors are involved in the etiology of depression, a ‘lifestyle medicine’ approach can be potentially safe and cost-effective to prevent or treat depression. To examine the effects and acceptability of a group-based, integrative lifestyle medicine intervention as a standalone treatment for managing depressive symptoms, a pilot randomized controlled trial (RCT) was conducted in a Chinese adult population in 2018. Participants (n = 31) with PHQ-9 score above the cut-off of ≥ 10, which was indicative of moderate to severe depression, were recruited from the general community in Hong Kong and randomly assigned to lifestyle medicine group (LM group) or care-as-usual group (CAU group) in a ratio of 1:1. Participants in the LM group received 2-hour group sessions once per week for six consecutive weeks, which covered diet, exercise, mindfulness, psychoeducation, and sleep management. Linear mixed-effects model analyses showed that the LM group had a significant reduction in PHQ-9 scores compared to the CAU group at immediate posttreatment and 12-week posttreatment follow-up (d = 0.69 and 0.73, respectively). Moreover, there were significantly greater improvements in anxiety, stress, and insomnia symptoms (measured by DASS-21 and ISI) at all time points in the LM group (d = 0.42–1.16). The results suggests that our 6-week group-based, integrative lifestyle intervention program is effective in lowering depressive, anxiety, stress, and insomnia symptoms in the Chinese population. Further studies in clinical populations with a larger sample size and longer follow-up are warranted.
Football Match Dynamics Explored by Recurrence Analysis

A widely accepted notion of football matches in performance analysis (PA) is to consider them as dynamic interaction processes with emerging behaviors. The description and analysis of these processes requires specific methods. Recurrence analysis is a technique for analyzing complex systems in many domains like astrophysics, earth sciences, engineering, biology, cardiology, and neuroscience. Its general concept is to examine the recurrence behavior of a system, as in when, how often and how close its trajectory in a phase space returns to a previous state. The aim of the study is to apply recurrence analysis to football matches. Positional data from 21 football matches of a German Bundesliga team were examined. The phase space was made up of the field players' x,y-positions at each second of the match. For each pair of seconds, the average distance of all the players between their positions at these two time points was calculated. Recurrence plots (RPs) were obtained by color-coding these distances. With a recurrence threshold of rt = 9 m and a minimum line length of lmin = 3 s, general recurrence parameters were calculated to characterize the individual recurrence behaviors of each match. Three football-specific recurrence parameters were defined to represent recurrence properties of open play. RPs showed commonalities (typical features indicating set plays and continuous gameplay) as well as unique structures during each match (number, distribution, and sequence of typical features). The recurrence parameters showed several significant correlations with traditional performance indicators like number of goals and passes completed, e.g., the correlation between number of goals and recurrence rate is r = −0.622 (p = 0.003). By extending the sample and design of recurrence studies, there is great potential for recurrence analysis to improve both the practical and theoretical potential of performance analysis.