Miracle-dz/UniFAR-FTUs huggingface dataset:
Children’s wellbeing and their academic achievement: The dangerous discourse of ‘trade-offs’ in education

Research conducted in England over the last decade has documented sustained, significant decreases in children’s wellbeing. While recent changes to curriculum policy promoting children’s wellbeing have been introduced, a notable feature of the discourse surrounding the promotion of children’s wellbeing is that wellbeing is regarded as opposed to, or in tension with, children’s academic achievement. Recently, Gabriel Heller-Sahlgren proposed that there is an inevitable ‘trade-off’ between children’s ‘wellbeing’ and their academic achievement. Using PISA 2012 data, Heller-Sahlgren argues that pupil happiness and high achievement do not go hand in hand; implying policymakers have a decision to make about which they uphold as the priority. In this article, I discuss the theoretical assumptions underpinning transnational comparisons of children’s wellbeing and review evidence from psychology and education to ascertain whether a trade-off is empirically supported. I argue that far from being incompatible, children’s wellbeing and achievement are positively associated. However, this relationship is not straightforward and requires careful disentangling of the hedonic and eudaimonic components of wellbeing. I underline four main gaps in current knowledge of the wellbeing-achievement relationship to date: the need for (1) multidimensional conceptualisation and measurement of wellbeing, (2) exploration of mediating mechanisms/constructs explaining the wellbeing-achievement relationship, (3) objective operationalisation of achievement, and (4) investigation of developmental differences. To conclude, I argue that when making policy recommendations researchers should avoid ‘all or nothing’ thinking which lures governments into false dichotomies.
Fast and Secure Authentication in Virtual Reality Using Coordinated 3D Manipulation and Pointing

There is a growing need for usable and secure authentication in immersive virtual reality (VR). Established concepts (e.g., 2D authentication schemes) are vulnerable to observation attacks, and most alternatives are relatively slow. We present RubikAuth, an authentication scheme for VR where users authenticate quickly and secure by selecting digits from a virtual 3D cube that leverages coordinated 3D manipulation and pointing. We report on results from three studies comparing how pointing using eye gaze, head pose, and controller tapping impact RubikAuth’s usability, memorability, and observation resistance under three realistic threat models. We found that entering a four-symbol RubikAuth password is fast: 1.69–3.5 s using controller tapping, 2.35–4.68 s using head pose and 2.39 –4.92 s using eye gaze, and highly resilient to observations: 96–99.55% of observation attacks were unsuccessful. RubikAuth also has a large theoretical password space: 45n for an n-symbols password. Our work underlines the importance of considering novel but realistic threat models beyond standard one-time attacks to fully assess the observation-resistance of authentication schemes. We conclude with an in-depth discussion of authentication systems for VR and outline five learned lessons for designing and evaluating authentication schemes.
Feature Selection Algorithm based on Sparse Effective Distance combined with sPCA for Microarray Data

Feature selection is an efficient pre-processing method for high-dimensional data. It can promote the accuracy of classifiers by removing redundancy and outliers. However, the traditional feature selection method pay more attention on the correlation between samples and features while ignoring the correlation between samples and samples. When dealing with high-dimensional data with small sample sizes, those methods have poor performance. In this paper, we propose a new feature selection method based on sparse effective distance, which consider the local and global similarities among all the samples. Meanwhile, the proposed feature selection method combine with sparse principal component analysis (sPCA) to improve the sparsity and structure of loadings. The experiments were performed on eight gene expression data sets, and the results show that the proposed method can simultaneously improve the accuracy of classification and the stability.
Supercritical fluid extraction of lignans from seeds and leaves of Schizandra chinensis

Supercritical carbon dioxide was used to extract lignans from seeds and leaves of Schizandra chinensis (Turcz.) Baill. Kinetics of the extraction was found to be controlled by intra-particle diffusion of lignans. The extraction yields were approximately 96% of lignans from seeds and about 26% from leaves, both yields being based on the total lignan content determined from two successive Soxhlet extractions with petroleum ether and methanol. © 1997 John Wiley & Sons, Ltd.
Structural, electronic, and bonding properties of liquid water from first principles

We study, from first principles, structural, electronic, and bonding properties of liquid water. Our system is twice as large as that used in previous ab initio simulations and our computed structural properties are in good agreement with the most recent neutron scattering experiments. Moreover, the use of a novel technique, based on the generation of maximally localized Wannier functions, allowed us to describe the molecular charge distribution and the polarization effects in liquid water with a degree of accuracy not previously possible. We find that, in the liquid phase, the water molecule dipole moment has a broad distribution around an average value of about 3.0 D. This value is 60% higher than that of the gas phase and significantly larger than most previous estimates. A considerable increase is also observed in the magnitude of the average eigenvalues of the quadrupole moment tensor. We also find that the anisotropy of the electronic charge distribution of the water molecule is reduced in the liqui.
Dual expression of Atoh1 and Ikzf2 promotes transformation of adult cochlear supporting cells into outer hair cells

Mammalian cochlear outer hair cells (OHCs) are essential for hearing. OHC degeneration causes severe hearing impairment. Previous attempts of regenerating new OHCs from cochlear supporting cells (SCs) had yielded cells lacking Prestin, a key motor protein for OHC function. Thus, regeneration of Prestin+ OHCs remains a challenge for repairing OHC damage in vivo. Here, we reported that successful in vivo conversion of adult cochlear SCs into Prestin+ OHC-like cells could be achieved by simultaneous expression of Atoh1 and Ikzf2, two key transcriptional factors necessary for OHC development. New OHC-like cells exhibited upregulation of hundreds of OHC genes and downregulation of SC genes. Single cell transcriptomic analysis demonstrated that the differentiation status of these OHC-like cells was much more advanced than previously achieved. Thus, we have established an efficient approach to promote regeneration of Prestin+ OHCs and paved the way for repairing damaged cochlea in vivo via transdifferentiation of SCs.
Pre-diabetes linked microRNA miR-193b-3p targets PPARGC1A and increases lipid accumulation in hepatocytes: potential biomarker of fatty liver disease

Distinct plasma microRNA profiles associate with different disease features. Elevated plasma microRNA hsa-miR-193b-3p has been reported in patients with pre-diabetes where early liver dysmetabolism plays a crucial role. MicroRNA target databases revealed that hsa-miR-193b-3p could potentially target PPARGC1A, a master switch transcriptional co-activator that orchestrates the expression of genes involved in multiple metabolic pathways. In this study we evaluated the effects of hsa-miR-193b-3p in the human HepG2 hepatocyte cell line. We show that hsa-miR-193b-3p targets PPARGC1A/PGC1α mRNA 3’UTR and reduces its expression. Overexpression of hsa-miR-193b-3p under hyperglycemia resulted in increased accumulation of intracellular lipid droplets; and quantitative real-time RT-PCR of a panel of 24 genes revealed significant disruption in the expression of genes coordinating glucose uptake, glycolysis, pyruvate metabolism, fatty acid synthesis, fatty acid oxidation, triglyceride synthesis, VLDL secretion, insulin signalling, and mitochondrial biogenesis, dynamics and function. These results provide in vitro evidence that microRNA hsa-miR-193b-3p downregulates PPARGC1A/PGC1α, disrupts downstream metabolic pathways and leads to the accumulation of intracellular lipids in hepatocytes. We propose that microRNA hsa-miR-193b-3p may have potential as a clinically relevant plasma biomarker for metabolic associated fatty liver disease in a pre-diabetic dysglycemic context.
DDX24, a D-E-A-D box RNA helicase, is required for muscle fiber organization and anterior pole specification essential for head regeneration in planarians

Planarians have a remarkable ability to undergo whole-body regeneration. The timely establishment of polarity at the wound site followed by the specification of the organizing centers- the anterior pole and the posterior pole, are indispensable for successful regeneration. In planarians, polarity, pole, and positional-information determinants are predominantly expressed by muscles. The molecular toolkit that enables this functionality of planarian muscles however remains poorly understood. Here we report that SMED_DDX24, a D-E-A-D Box RNA helicase and the homolog of human DDX24, is critical for planarian head regeneration. DDX24 is enriched in muscles and its knockdown leads to defective muscle-fiber organization and failure to re-specify anterior pole/organizer. Overall, loss of DDX24 manifests into gross misregulation of many well-characterized positional-control genes and patterning-control genes, necessary for organogenesis and tissue positioning and tissue patterning. In addition, wound-induced Wnt signalling was also upregulated in ddx24 RNAi animals. Canonical WNT-βCATENIN signalling is known to suppress head identity throughout bilateria, including planarians. Modulating this Wnt activity by β-catenin-1 RNAi, the effector molecule of this pathway, partially rescues the ddx24 RNAi phenotype, implying that a high Wnt environment in ddx24 knockdown animals likely impedes their normal head regeneration. Furthermore, at a sub-cellular level, RNA helicases are known to regulate muscle mass and function by regulating their translational landscape. ddx24 knockdown leads to the downregulation of large subunit ribosomal RNA and the 80S ribosome peak, implying its role in ribosome biogenesis and thereby influencing the translational output. This aspect seems to be an evolutionarily conserved role of DDX24. In summary, our work demonstrates the role of a D-E-A-D box RNA helicase in whole-body regeneration through muscle fiber organization, and pole and positional-information re-specification, likely mediated through translation regulation.
Presynaptic NMDA receptors facilitate short-term plasticity and BDNF release at hippocampal mossy fiber synapses

Neurotransmitter release is a highly controlled process by which synapses can critically regulate information transfer within neural circuits. While presynaptic receptors –typically activated by neurotransmitters and modulated by neuromodulators– provide a powerful way of fine-tuning synaptic function, their contribution to activity-dependent changes in transmitter release remains poorly understood. Here, we report that presynaptic NMDA receptors (preNMDARs) at mossy fiber boutons in the rodent hippocampus can be activated by physiologically relevant patterns of activity and selectively enhance short-term synaptic plasticity at mossy fiber inputs onto CA3 pyramidal cells and mossy cells, but not onto inhibitory interneurons. Moreover, preNMDARs facilitate brain-derived neurotrophic factor (BDNF) release and contribute to presynaptic calcium rise. Taken together, our results indicate that by increasing presynaptic calcium, preNMDARs fine tune mossy fiber neurotransmission and can control information transfer during dentate granule cell burst activity that normally occur in vivo.
Detection of hematopoietic stem cell transcriptome in human fetal kidneys and kidney organoids derived from human induced pluripotent stem cells (iPSC)

Background In mammalians, hematopoietic stem cells (HSC) arise in the dorsal aorta from the hemogenic endothelium, followed by their migration to fetal liver and to bone marrow. In zebrafish, kidney is the site of primary hematopoiesis. In humans, the presence of HSC in the fetal or adult kidney has not been established. Methods We analyzed the presence of HSC markers in human fetal kidneys by analysis of single-cell datasets. We then analyzed in kidney organoids derived from iPSC, the presence of hematopoietic markers using transcriptome analyses. Results 12 clusters were identified of stromal, endothelial, and nephron cell type-specific markers in the two fetal stage (17 weeks) kidney datasets. Among these, expression of hematopoietic cells in Cluster 9 showed expression of primitive markers. Moreover, whole transcriptome analysis of our iPSC-derived kidney organoids revealed induction of the primitive hematopoietic transcription factor RUNX1 as found in the human fetal kidney cortex. Conclusions These finding support the presence of cells expressing HSC transcriptome in human kidney. The mechanisms of the appearance of the cells with the same transcriptional features during iPSC-derived kidney organoid generation requires further investigation.
Indian genetic heritage in Southeast Asian populations

The great ethnolinguistic diversity found today in mainland Southeast Asia (MSEA) reflects multiple migration waves of people in the past. Deeply divergent East Eurasian hunter-gatherers were the first anatomically modern human population known to migrate to the region. Agriculturalists from South China migrated to the region and admixed with the local hunter-gatherers during the Neolithic period. During the Bronze and Iron Ages, the genetic makeup of people in MSEA changed again, indicating an additional influx of populations from South China. Maritime trading between MSEA and India was established at the latest 300 BCE, and the formation of early states in Southeast Asia during the first millennium CE was strongly influenced by Indian culture, and this cultural influence is still prominent today. Several ancient Indian-influenced states were located in present-day Thailand, and various populations in the country are likely to be descendants of people from those states. To systematically explore Indian genetic heritage in MSEA, we generated genome-wide SNP data (the HumanOrigins array) for 119 present-day individuals belonging to 10 ethnic groups from Thailand and co-analyzed them with published data from MSEA using the PCA, ADMIXTURE, f3-statistics, qpAdm, and qpGraph methods. We found South Asian low-level admixture in various MSEA populations which are probably descendants of people from the ancient Indian-influenced states, but failed to find a South Asian genetic component in present-day hunter-gatherer groups and relatively isolated groups from highlands in Northern Thailand. Our results also support close genetic affinity between Kra-Dai-speaking (also known as Tai-Kadai) and Austronesian-speaking populations, which fits a linguistic hypothesis suggesting cladality of the two language families. Author Summary Mainland Southeast Asia is a region with great ethnolinguistic diversity and complex population history. We studied genetic population history of present-day mainland Southeast Asian populations using genome-wide SNP data (the HumanOrigins array). We generated new data for 10 present-day ethnic groups from Thailand, which we further combined with published data from mainland and island Southeast Asians and worldwide populations. We revealed South Asian genetic admixture in various mainland Southeast Asian ethnic groups which are highly influenced by Indian culture, but failed to find it in groups who remained culturally isolated until recently. Our finding suggests that a massive migration of Indian people in the past was responsible for the spread of Indian culture in mainland Southeast Asia. We also found support for a close genetic affinity between Kra-Dai- and Austronesianspeaking populations, which fits a linguistic hypothesis suggesting cladality of the two language families.
The Arabidopsis immune receptor EFR increases resistance to the bacterial pathogens Xanthomonas and Xylella in transgenic sweet orange

Plants employ cell surface receptors to recognize pathogen (or microbe)-associated molecular patterns (PAMPs/MAMPs), which are crucial for immune system activation. The well-studied Arabidopsis thaliana ELONGATION FACTOR-TU RECEPTOR (EFR) recognizes the conserved bacterial PAMP EF-Tu, and the derived peptides elf18 and elf26. The interfamily transfer of EFR has been shown to increase disease resistance in several crops, such as tomato, rice, wheat, and potato. Here, we generated sweet orange (Citrus sinensis) transgenic lines expressing EFR to test if it would confer broad-spectrum resistance against two important citrus bacterial diseases: citrus canker and citrus variegated chlorosis (CVC). Independent EFR transgenic lines gained responsiveness to elf18 and elf26 peptides from Xanthomonas citri and Xylella fastidiosa, as measured by reactive oxygen species (ROS) production, mitogen-activated protein kinase (MAPK) activation and defense gene expression. Consistently, infection assays showed that Citrus-EFR transgenic plants were more resistant to citrus canker and CVC. Our results show that the EFR immune receptor can improve plant immunity in a perennial crop against bacterial pathogens, opening perspectives to engineer durable broad-spectrum disease resistance under field conditions.
Developmental and behavioral phenotypes in a new mouse model of DDX3X syndrome

Background Mutations in the X-linked gene DDX3X account for ~2% of intellectual disability in females, often co-morbid with behavioral problems, motor deficits, and brain malformations. DDX3X encodes an RNA helicase with emerging functions in corticogenesis and synaptogenesis. Methods We generated a Ddx3x haploinsufficient mouse (Ddx3x+/−) with construct validity for DDX3X loss-of-function mutations. We used standardized batteries to assess developmental milestones and adult behaviors, as well as magnetic resonance imaging and immunostaining of cortical projection neurons to capture early postnatal changes in brain development. Results Ddx3x+/− mice show physical, sensory, and motor delays that evolve into behavioral anomalies in adulthood, including hyperactivity, anxiety-like behaviors, cognitive impairments, and motor deficits. Motor function further declines with age. These behavioral changes are associated with a reduction in brain volume, with some regions (e.g., cortex and amygdala) disproportionally affected. Cortical thinning is accompanied by defective cortical lamination, indicating that Ddx3x regulates the balance of glutamatergic neurons in the developing cortex. Conclusions These data shed new light on the developmental mechanisms driving DDX3X syndrome and support face validity of this novel pre-clinical mouse model.
Insights from genomes and genetic epidemiology of SARS-CoV-2 isolates from the state of Andhra Pradesh

Coronavirus disease (COVID-19) emerged from a city in China and has now spread as a global pandemic affecting millions of individuals. The causative agent, SARS-CoV-2 is being extensively studied in terms of its genetic epidemiology using genomic approaches. Andhra Pradesh is one of the major states of India with the third-largest number of COVID-19 cases with limited understanding of its genetic epidemiology. In this study, we have sequenced 293 SARS-CoV-2 genome isolates from Andhra Pradesh with a mean coverage of 13,324X. We identified 564 high-quality SARS-CoV-2 variants, out of which 15 are novel. A total of 18 variants mapped to RT-PCR primer/probe sites, and 4 variants are known to be associated with an increase in infectivity. Phylogenetic analysis of the genomes revealed the circulating SARS-CoV-2 in Andhra Pradesh majorly clustered under the clade A2a (94%), while 6% fall under the I/A3i clade, a clade previously defined to be present in large numbers in India. To the best of our knowledge, this is the most comprehensive genetic epidemiological analysis performed for the state of Andhra Pradesh.
Oral epithelial cells distinguish between Candida species with high or low pathogenic potential through miRNA regulation

Oral epithelial cells monitor microbiome composition and initiate immune response upon dysbiosis, as in case of Candida imbalances. Comparison of healthy oral epithelial cell responses revealed that the inability of C. parapsilosis to induce a robust antifungal response was due to activation of various inflammation-independent pathways, while C. albicans robustly activated inflammation cascades. Regarding posttranscriptional regulation, several miRNAs were altered by both species. For C. parapsilosis, the applied dose directly correlated with changes in transcriptomic responses. Carbohydrate metabolism, hypoxia- and cardiovascular development-related responses dominate after C. parapsilosis stimulus, whereas C. albicans altered inflammatory responses. Subsequent analyses of HIF1-α and HSC-activation pathways predicted target genes through which miRNA-dependent regulation of yeast-specific functions may occur, supporting the observed responses. Thus, C. parapsilosis is recognized as a commensal at low doses by the oral epithelium; however, increased fungal burden activates different pathways, some of which overlap with inflammatory processes induced by C. albicans. Impact statement Altered miRNA regulation discriminates between C. albicans and C. parapsilosis in human oral epithelial cells
Quantifying cell transitions in C. elegans with data-fitted landscape models

Increasing interest has emerged in new mathematical approaches that simplify the study of complex differentiation processes by formalizing Waddington’s landscape metaphor. However, a rational method to build these landscape models remains an open problem. Building on pioneering work by Corson and Siggia (2012, 2017) we study vulval development in C. elegans by developing a framework based on Catastrophe Theory (CT) and approximate Bayesian computation (ABC) to build data-fitted landscape models. We first identify the candidate qualitative landscapes, and then use CT to build the simplest model consistent with the data, which we quantitatively fit using ABC. The resulting model suggests that the underlying mechanism is a quantifiable two-step decision controlled by EGF and Notch-Delta signals, where a non-vulval/vulval decision is followed by a bistable transition to the two vulval states. This new model fits a broad set of data and makes several novel predictions.
Envelope reconstruction of speech and music highlights unique tracking of speech at low frequencies

The human brain tracks amplitude fluctuations of both speech and music, which reflects acoustic processing in addition to the processing of higher-order features and one’s cognitive state. Comparing neural tracking of speech and music envelopes can elucidate stimulus-general mechanisms, but direct comparisons are confounded by differences in their envelope spectra. Here, we use a novel method of frequency-constrained reconstruction of stimulus envelopes using EEG recorded during passive listening. We expected to see music reconstruction match speech in a narrow range of frequencies, but instead we found that speech was reconstructed better than music for all frequencies we examined. Additionally, speech envelope tracking at low frequencies, below 1 Hz, was uniquely associated with increased weighting over parietal channels. Our results highlight the importance of low-frequency speech tracking and its origin from speech-specific processing in the brain.