Miracle-dz/UniFAR-FTUs huggingface dataset:
Gut Microbial SNPs Induced by High-Fiber Diet Dominate Nutrition Metabolism and Environmental Adaption of Faecalibacterium prausnitzii in Obese Children

Dietary intervention is effective in human health promotion through modulation of gut microbiota. Diet can cause single-nucleotide polymorphisms (SNPs) to occur in the gut microbiota, and some of these variations may lead to functional changes in human health. In this study, we performed a systematic SNP analysis based on metagenomic data collected from children with Prader–Willi syndrome (PWS, n = 17) and simple obese (SO) children (n = 19), who had better healthy conditions after receiving high-fiber diet intervention. We found that the intervention increased the SNP proportions of Faecalibacterium, Bifidobacterium, and Clostridium and decreased those of Bacteroides in all children. Besides, the PWS children had Collinsella increased and Ruminococcus decreased, whereas the SO had Blautia and Escherichia decreased. There were much more BiasSNPs in PWS than in SO (4,465 vs 303), and only 81 of them appeared in both groups, of which 78 were from Faecalibacterium prausnitzii, and 51 were nonsynonymous mutations. These nonsynonymous variations were mainly related to pathways of environmental adaptation and nutrition metabolism, particularly to carbohydrate and nucleotide metabolism. In addition, dominant strains carrying BiasSNPs in all children shifted from F. prausnitzii AF32-8AC and F. prausnitzii 942/30-2 to F. prausnitzii SSTS Bg7063 and F. prausnitzii JG BgPS064 after the dietary intervention. Furthermore, although the abundance of Bifidobacterium increased significantly by the intervention and became dominant strains responsible for nutrition metabolism, they had less BiasSNPs between the pre- and post-intervention group in comparison with Faecalibacterium. The finding of F. prausnitzii as important functional strains influenced by the intervention highlights the superiority of applying SNP analysis in studies of gut microbiota. This study provided evidence and support for the effect of dietary intervention on gut microbial SNPs, and gave some enlightenments for disease treatment.
Proliferation of SARS-CoV-2 B.1.1.7 Variant in Pakistan-A Short Surveillance Account

The emergence of a more transmissible variant of SARS-CoV-2 (B1. 1.7) in the United Kingdom (UK) during late 2020 has raised major public health concerns. Several mutations have been reported in the genome of the B.1. 1.7 variant including the N501Y and 69-70deletion in the Spike region that has implications on virus transmissibility and diagnostics. Although the B.1. 1.7 variant has been reported by several countries, only three cases have been reported in Pakistan through whole-genome sequencing. Therefore, the objective of the study was to investigate the circulation of B.1. 1.7 variant of concern (VOC) in Pakistani population. We used a two-step strategy for the detection of B.1. 1.7 with initial screening through TaqPathTM COVID-19 CE-IVD RT-PCR kit (ThermoFisher Scientific, Waltham, US) followed by partial spike (S) gene sequencing of a subset of samples having the spike gene target failure (SGTF). From January 01, 2021, to February 21, 2021, a total of 2,650 samples were tested for SARS-CoV-2 and 70.4% (n = 1,867) showed amplification of all the 3 genes (ORF, N, and S). Notably, 29.6% (n=783) samples have been SGTF that represented numbers from all the four provinces and suggest a rather low frequency during the first 3 weeks of January (n = 10, n = 13, and n = 1, respectively). However, the numbers have started to increase in the last week of January, 2021. During February, 726 (93%) cases of SGTF were reported with a peak (n = 345) found during the 3rd week. Based on the partial sequencing of SGTF samples 93.5% (n = 29/31) showed the characteristic N501Y, A570D, P681H, and T716I mutations found in the B.1. 1.7 variant. In conclusion, our findings showed an upsurge of B.1. 1.7 cases in Pakistan during February, 2021 affecting 15 districts and warranting large scale genomic surveillance, strengthening of laboratory network and implementation of appropriate control measures in the country.
Toddlers Using Tablets: They Engage, Play, and Learn

Although very young children have unprecedented access to touchscreen devices, there is limited research on how successfully they operate these devices for play and learning. For infants and toddlers, whose cognitive, fine motor, and executive functions are immature, several basic questions are significant: (1) Can they operate a tablet purposefully to achieve a goal? (2) Can they acquire operating skills and learn new information from commercially available apps? (3) Do individual differences in executive functioning predict success in using and learning from the apps? Accordingly, 31 2-year-olds (M = 30.82 month, SD = 2.70; 18 female) were compared with 29 3-year-olds (M = 40.92 month, SD = 4.82; 13 female) using two commercially available apps with different task and skill requirements: (1) a shape matching app performed across 3 days, and (2) a storybook app with performance compared to that on a matched paper storybook. Children also completed (3) the Minnesota Executive Functioning Scale. An adult provided minimal scaffolding throughout. The results showed: (1) toddlers could provide simple goal-directed touch gestures and the manual interactions needed to operate the tablet (2) after controlling for prior experience with shape matching, toddlers’ increased success and efficiency, made fewer errors, decreased completion times, and required less scaffolding across trials, (3) they recognized more story content from the e-book and were less distracted than from the paper book, (4) executive functioning contributed unique variance to the outcome measures on both apps, and (5) 3-year-olds outperformed 2-year-olds on all measures. The results are discussed in terms of the potential of interactive devices to support toddlers’ learning.
Glioma-Derived Extracellular Vesicles – Far More Than Local Mediators

Extracellular vesicle (EV) secretion is a ubiquitous cellular process with both physiologic and pathologic consequences. EVs are small lipid bilayer vesicles that encompass both microvesicles and exosomes and which are secreted by virtually all cells including cancer cells. In this review, we will focus on the roles of EVs in mediating the crosstalk between glioblastoma (GBM) cells and innate and adaptive immune cells and the potential impact on glioma progression. Glioma-derived EVs contain many bioactive cargoes that can broaden and amplify glioma cell mediated immunosuppressive functions and thereby contribute to shaping the tumor microenvironment. We will discuss evidence demonstrating that the low oxygen (hypoxia) in the GBM microenvironment, in addition to cell-intrinsic effects, can affect intercellular communication through EV release, raising the possibility that properties of the tumor core can more widely impact the tumor microenvironment. Recent advances in glioma-derived EV research have shown their importance not only as message carriers, but also as mediators of immune escape, with the capacity to reprogram tumor infiltrating immune cells. Exploring EV function in cancer-immune crosstalk is therefore becoming an important research area, opening up opportunities to develop EV monitoring for mechanistic studies as well as novel diagnostic glioma biomarker applications. However, robust and reproducible EV analysis is not always routinely established, whether in research or in clinical settings. Taking into account the current state of the art in EV studies, we will discuss the challenges and opportunities for extending the many exciting findings in basic research to a better interpretation of glioma and its response to current and future immunotherapies.
A Comparison in Physical Fitness Attributes, Physical Activity Behaviors, Nutritional Habits, and Nutritional Knowledge Between Elite Male and Female Youth Basketball Players

Background: Limited evidence exists comprehensively assessing physical fitness attributes, physical activity behaviors, nutritional habits, and nutritional knowledge according to sex in basketball players during early adolescence. Insight of this nature could be used to optimize the training process and lifestyles in young basketball players. Objective: To compare physical fitness attributes, physical activity levels, nutritional habits, and nutritional knowledge between elite male and female basketball players under 14 years of age (U-14). Methods: Twenty-three U-14 basketball players (male, n = 13 and female, n = 10) from the same elite basketball academy (Spanish Asociación de Clubes de Baloncesto [ACB] League) participated in this study. Physical fitness attributes were assessed using a basketball-specific test battery (countermovement jump, drop jump, linear sprint, Lane Agility Drill, 505 change-of-direction, and repeated-change-of-direction tests), while physical activity levels (Physical Activity Questionnaire for Adolescents, PAQ-A), nutritional habits (Turconi questionnaire), and nutritional knowledge (Turconi questionnaire) were assessed using questionnaires. Results: Male players exhibited better physical fitness in all tests (p <0.001 to 0.036, effect size = −0.44 to −0.76, intermediate to strong) compared to female players. Male players also performed more physical activity in their leisure time (p = 0.036) than females. No significant differences in nutritional habits and nutritional knowledge were evident between sexes (p > 0.05). Of note, a high proportion of players declared never or only sometimes eating fruit (males: 23%; females: 40%) and vegetables (males: 46%; females: 70%). In addition, relatively poor nutritional knowledge was evident in all players with the group correctly answering <50% of nutritional questions overall (4.57 ± 1.88 out of 11 points, 42%) and according to sex (males: 4.07 ± 2.10, 37%; females: 5.20 ± 1.40, 47%). Conclusion: These findings emphasize the necessity to perform individualized prescription of training stimuli across sexes to optimize the physical preparedness and development of youth basketball players. Additionally, strategies such as nutrition-focused education interventions may be necessary in this population given the low consumption of fruits and vegetables, as well as the poor nutritional knowledge observed in players.
eStroop: Implementation, Standardization, and Systematic Comparison of a New Voice-Key Version of the Traditional Stroop Task

The Stroop effect is a well-documented phenomenon, demonstrating both interference and facilitation effects. Many versions of the Stroop task were created, according to the purposes of its applications, varying in numerous aspects. While many versions are developed to investigate the mechanisms of the effect itself, the Stroop effect is also considered a general measure of attention, inhibitory control, and executive functions. In this paper, we implement “eStroop”: a new digital version based on verbal responses, measuring the main processes involved in the traditional effect. eStroop features four categories of stimuli in four different colors: (1) geometrical shapes, (2) neutral words, (3) congruent words, and (4) incongruent words. The results of the administration to 307 University students confirm the Stroop effect and offer baseline data for future research and clinical testing. Direct comparisons with other recent versions of the task are discussed, offering insights into differences and similarities between different task variables.
Larval Fish Assemblage Structure at Coastal Fronts and the Influence of Environmental Variability

Within the coastal zone, oceanographic features, such as fronts, can have major effects on the abundance and distribution of larval fish. We investigated the effects of fronts on larval fish assemblages by jointly collecting physical (ADCP and CTD) and biological (larvae) data in the nearshore waters of the south coast of South Africa, on four separate neap-tide occasions. Accumulation of fish larvae at predominantly internal wave-associated fronts was observed, with higher larval densities inshore of and within the front than farther offshore. On each occasion, larvae of coastal species with pelagic eggs (Mugillidae and Sparidae) were numerically dominant at the front itself, while inshore of the front, larvae of coastal species with benthic eggs (Gobiesocidae and Gobiidae) were more abundant. Offshore catches mainly comprised Engraulidae (pelagic species with pelagic eggs) larvae, which were generally restricted to the bottom, where current velocities were onshore on each occasion. On the occasion when fast (>100 cm/s) currents prevailed, however, accumulation of the larvae of coastal species occurred offshore of the front, and larvae were mixed throughout the water column. Thus, larval occurrence at these coastal frontal systems was strongly affected by the degree of mixing by currents, which on most occasions resulted in onshore retention. The results underline the importance of frontal systems in determining the nearshore distributions of fish larvae, particularly by retaining coastal fish species in the inshore region. The environmental variability observed at these frontal systems has potential implications for larval connectivity of fish populations.
Student Engagement in Mathematics Flipped Classrooms: Implications of Journal Publications From 2011 to 2020

Mathematics is one of the core STEM (science, technology, engineering, and mathematics) subject disciplines. Engaging students in learning mathematics helps retain students in STEM fields and thus contributes to the sustainable development of society. To increase student engagement, some mathematics instructors have redesigned their courses using the flipped classroom approach. In this review, we examined the results of comparative studies published between 2011 and 2020 to summarize the effects of this instructional approach (vs. traditional lecturing) on students’ behavioral, emotional, and cognitive engagement with mathematics courses. Thirty-three articles in K–12 and higher education contexts were included for analysis. The results suggest that the use of the flipped classroom approach may increase some aspects of behavioral engagement (e.g., interaction and attention/participation), emotional engagement (e.g., course satisfaction), and cognitive engagement (e.g., understanding of mathematics). However, we discovered that several aspects (e.g., students’ attendance, mathematics anxiety, and self-regulation) of student engagement have not been thoroughly explored and are worthy of further study. The results of this review have important implications for future flipped classroom practice (e.g., engaging students in solving real-world problems), and for research on student engagement (e.g., using more objective measures, such as classroom observation) in mathematics education.
Elevated Hydrostatic Pressure Causes Retinal Degeneration Through Upregulating Lipocalin-2

Elevation of intraocular pressure is a major risk factor for glaucoma development, which causes the loss of retinal ganglion cells (RGCs). Lipocalin 2 (Lcn2) is upregulated in glaucomatous retinae; however, whether Lcn2 is directly involved in glaucoma is debated. In this study, retinal explant cultures were subjected to increased water pressure using a two-chamber culture device, and Lcn2 protein levels were examined by immunoblotting. In situ TdT-mediated dUTP nick and labeling (TUNEL) and glial fibrillary acidic protein (GFAP) immunohistochemical assays were performed to assess apoptosis and gliosis, respectively. The neurotoxicity of Lcn2 in the retinal explant culture was determined with exogenous administration of recombinant Lcn2. The Lcn2 protein levels, percentage of TUNEL-positive cells, and GFAP-positive area were significantly higher in retinae cultured under 50 cm H2O pressure loads compared to those cultured under 20 cm H2O. We found that Lcn2 exhibited neurotoxicity in retinae at dose of 1 μg/ml. The negative effects of increased hydrostatic pressure were attenuated by the iron chelator deferoxamine. This is the first report demonstrating the direct upregulation of Lcn2 by elevating hydrostatic pressure. Modulating Lcn2 and iron levels may be a promising therapeutic approach for retinal degeneration.
Isolation and Identification of a High-Yield Ethyl Caproate-Producing Yeast From Daqu and Optimization of Its Fermentation

Baijiu is an important fermented product in China. A yeast named YX3307 that is capable of producing a large amount of ethyl caproate (EC) was isolated from Daqu, a crude fermentation starter for Baijiu. This yeast was identified as Clavispora lusitaniae on the basis of its morphological properties, physiological and biochemical characteristics, and 26S rDNA sequence. Single-factor experiments were conducted to obtain the optimum fermentation conditions for EC production by YX3307. The highest EC yield (62.0 mg/L) from YX3307 was obtained with the following culture conditions: inoculum size 7.5% (v/v), seed cell age 30 h, sorghum hydrolysate medium (SHM) with a sugar content of 10 Brix and an initial pH of 6.0; incubation at 28°C with shaking at 180 rpm for 32 h; addition of 10% (v/v) anhydrous ethanol and 0.04% (v/v) caproic acid at 32 and 40 h, respectively, static culture at 20°C until 72 h. YX3307 synthesized more EC than ethyl acetate, ethyl lactate, ethyl butyrate, and ethyl octanoate. An intracellular enzyme or cell membrane enzyme was responsible for EC synthesis. YX3307 can produce many flavor compounds that are important for high-quality Baijiu. Thus, it has potential applications in improving the flavor and quality of Baijiu.
Identification and Validation of a Prognostic 5-Protein Signature for Biochemical Recurrence Following Radical Prostatectomy for Prostate Cancer

Background: Biochemical recurrence (BCR) is an indicator of prostate cancer (PCa)-specific recurrence and mortality. However, there is a lack of an effective prediction model that can be used to predict prognosis and to determine the optimal method of treatment for patients with BCR. Hence, the aim of this study was to construct a protein-based nomogram that could predict BCR in PCa. Methods: Protein expression data of PCa patients was obtained from The Cancer Proteome Atlas (TCPA) database. Clinical data on the patients was downloaded from The Cancer Genome Atlas (TCGA) database. Lasso and Cox regression analyses were conducted to select the most significant prognostic proteins and formulate a protein signature that could predict BCR. Subsequently, Kaplan–Meier survival analysis and Cox regression analyses were conducted to evaluate the performance of the prognostic protein-based signature. Additionally, a nomogram was constructed using multivariate Cox regression analysis. Results: We constructed a 5-protein-based prognostic prediction signature that could be used to identify high-risk and low-risk groups of PCa patients. The survival analysis demonstrated that patients with a higher BCR showed significantly worse survival than those with a lower BCR (p < 0.0001). The time-dependent receiver operating characteristic curve showed that the signature had an excellent prognostic efficiency for 1, 3, and 5-year BCR (area under curve in training set: 0.691, 0.797, 0.808 and 0.74, 0.739, 0.82 in the test set). Univariate and multivariate analyses indicated that this 5-protein signature could be used as independent prognosis marker for PCa patients. Moreover, the concordance index (C-index) confirmed the predictive value of this 5-protein signature in 3, 5, and 10-year BCR overall survival (C-index: 0.764, 95% confidence interval: 0.701–0.827). Finally, we constructed a nomogram to predict BCR of PCa. Conclusions: Our study identified a 5-protein-based signature and constructed a nomogram that could reliably predict BCR. The findings might be of paramount importance for the prediction of PCa prognosis and medical decision-making. Subjects: Bioinformatics, oncology, urology.
An Eco-Friendly Slow-Release Urea Fertilizer Based on Waste Mulberry Branches for Potential Agriculture and Horticulture Applications

Development of a compound fertilizer for agricultural and horticultural applications remains an important challenge in the field of biomass synthesis on account of its raw material source and biodegradability. In this work, an eco-friendly slow-release urea fertilizer (SRUF) employing mulberry branch-g-poly(acrylic acid-co-acrylamide) (MB/P(AA-co-AM)) superabsorbent was prepared. The MB/P(AA-co-AM) superabsorbent was blended with sodium alginate, urea, and CaCl2 solutions to accomplish this synthesis process. The synthesis conditions of the SRUF and its application performance were examined. The results showed that under the optimal synthesis conditions the water absorbency and water absorbency rate of the SRUF reached 420.0 g/g and 60.0 (g/g)/min in deionized water, respectively. The water retention of the SRUF was 7.2 wt % after 25 d. The urea release in deionized water and soil both exhibited a typical slow release behavior. A degradation rate of 32.0 wt % was attained for the SRUF while it was buried .
A prospective case–control study to evaluate oral health status before and after intervention using different dental aids in children with visual impairment

Background: A major dental concern in children with special health-care needs is poor oral hygiene, which results in increased incidences of dental caries, gingivitis, and periodontal disease. Aims: The study intended to determine if there was a difference in the oral health status of children with visual impairment and normal children and to evaluate the efficacy of the frequently used dental aids. Settings and Design: The study population included 90 children, 45 children with visual impairment (study group) with age- and sex-matched 45 normal children (control group). Both the groups were further divided into three intervention subgroups. Subgroup A: manual toothbrushes, Subgroup B: manual toothbrush with medicated mouthwashes, and Subgroup C: powered toothbrushes. Materials and Methods: For each subject, oral hygiene index simplified (OHIS), Turesky-Gilmore-Glickman modification of the Quigley-Hein Plaque Index (TQPHI), and decayed missing filled teeth (DMFT) indices were recorded at baseline, i.e., before any intervention. This was followed by oral prophylaxis by ultrasonic scaling. The three indices were recorded in 0 (baseline), 30 days (1 month), 90 days (3 months), and 180 days (6 months), respectively. Statistical Analysis Used: ANOVA test, Chi-square test, and student paired test were used for statistical analysis. Results: The mean TQHPI and OHIS values of mouthwashes at the end of 6 months were 1.01 and 1.60, respectively, which were lower than manual and power brushes. No statistically significant reduction in the DMFT scores with the use of any of the adjuncts was noted. Conclusions: Among the dental aids used in the study, mouthwash showed a significant reduction in plaque and oral hygiene scores as compared to powered toothbrushes and manual brushes alone.