Miracle-dz/UniFAR-FTUs huggingface dataset:
Analyzing the Korean reference genome with meta-imputation increased the imputation accuracy and spectrum of rare variants in the Korean population

Genotype imputation is essential for enhancing the power of association-mapping and discovering rare and indels that are missed by most genotyping arrays. Imputation analysis can be more accurate with a population-specific reference panel or a multi-ethnic reference panel with numerous samples. The National Institute of Health, Republic of Korea, initiated the Korean Reference Genome (KRG) project to identify variants in whole-genome sequences of ∼20,000 Korean participants. In the pilot phase, we analyzed the data from 1,490 participants. The genetic characteristics and imputation performance of the KRG were compared with those of the 1,000 Genomes Project Phase 3, GenomeAsia 100K Project, ChinaMAP, NARD, and TOPMed reference panels. For comparison analysis, genotype panels were artificially generated using whole-genome sequencing data from combinations of four different ancestries (Korean, Japanese, Chinese, and European) and two population-specific optimized microarrays (Korea Biobank Array and UK Biobank Array). The KRG reference panel performed best for the Korean population (R 2 = 0.78–0.84, percentage of well-imputed is 91.9% for allele frequency >5%), although the other reference panels comprised a larger number of samples with genetically different background. By comparing multiple reference panels and multi-ethnic genotype panels, optimal imputation was obtained using reference panels from genetically related populations and a population-optimized microarray. Indeed, the reference panels of KRG and TOPMed showed the best performance when applied to the genotype panels of KBA (R 2 = 0.84) and UKB (R 2 = 0.87), respectively. Using a meta-imputation approach to merge imputation results from different reference panels increased the imputation accuracy for rare variants (∼7%) and provided additional well-imputed variants (∼20%) with comparable imputation accuracy to that of the KRG. Our results demonstrate the importance of using a population-specific reference panel and meta-imputation to assess a substantial number of accurately imputed rare variants.
AcBBX5, a B-box transcription factor from pineapple, regulates flowering time and floral organ development in plants

Flowering is an important factor to ensure the success of plant reproduction, and reasonable flowering time is crucial to the crop yield. BBX transcription factors can regulate several growth and development processes. However, there is little research on whether BBX is involved in flower formation and floral organ development of pineapple. In this study, AcBBX5, a BBX family gene with two conserved B-box domains, was identified from pineapple. Subcellular localization analysis showed that AcBBX5 was located in the nucleus. Transactivation analysis indicated that AcBBX5 had no significant toxic effects on the yeast system and presented transcriptional activation activity in yeast. Overexpression of AcBBX5 delayed flowering time and enlarged flower morphology in Arabidopsis. Meanwhile, the expression levels of AtFT, AtSOC1, AtFUL and AtSEP3 were decreased, and the transcription levels of AtFLC and AtSVP were increased in AcBBX5-overexpressing Arabidopsis, which might lead to delayed flowering of transgenic plants. Furthermore, transcriptome data and QRT-PCR results showed that AcBBX5 was expressed in all floral organs, with the high expression levels in stamens, ovaries and petals. Yeast one-hybrid and dual luciferase assay results showed that AcBBX5 bound to AcFT promoter and inhibited AcFT gene expression. In conclusion, AcBBX5 was involved in flower bud differentiation and floral organ development, which provides an important reference for studying the functions of BBX and the molecular regulation of flower.
The efficacy of a transdiagnostic group cognitive behavioral intervention for Chinese elderly with emotional disorders: A one-year follow-up randomized clinical trial

Background With the global aging, geriatric emotional disorders have received more and more attention. Psychotherapy is an effective approach for alleviating the symptoms associated with emotional disorder, but the number of experienced therapists is low. Studies should be conducted to explore a low-cost and efficient treatment method. Previous findings indicate that transdiagnostic cognitive behavior therapy is an effective approach for treatment of emotional disorders. Group therapy is appropriate for the elderly as they are characterized by high levels of loneliness. In this study, we compared and explored the effects of a transdiagnostic group cognitive behavioral intervention (TD-GCBT), a transdiagnostic individual cognitive behavioral intervention (TD-CBT), and treatment as usual (TAU) on treatment of emotional disorders among the elderly. Method A total of 120 elderly patients diagnosed with emotional disorders were randomly assigned to the TD-GCBT group (40), TD-CBT group (40), and TAU group (40). Changes in symptoms were assessed using HAMD, PHQ-9, HAMA, and GAD-7 scales at baseline, post-treatment (three months), six-month and twelve-months follow-up. The efficacies of the three intervention strategies were compared using linear mixed-effects models. Post-hoc and simple effect analyses were conducted to determine the differences among the three groups. Results The HAMD, PHQ-9, HAMA, and GAD-7 scores revealed a significant effect from baseline to 12 months for time (p < 0.001), group (p < 0.001) and time × group interaction (p < 0.001) in TD-GCBT group compared with the TD-CBT group and TAU group. The effect of TD-GCBT (HAMD: Cohen’s d (3th month, 6th month, 12th month) = 2.69, 3.98, 4.51; HAMA: Cohen’s d = 2.84, 4.13, 5.20) and TD-CBT (HAMD: Cohen’s d = 2.55, 2.87, 2.63; HAMA: Cohen’s d = 2.43, 2.83, 2.78) group was better relative to that of the TAU group (HAMD: Cohen’s d = 0.41, 1.13, 1.46; HAMA: Cohen’s d = 0.64, 1.22, 1.57) (p < 0.001). The scores of the TD-GCBT group showed the most significant decrease compared with the other two groups. Conclusion The findings indicate that TD-GCBT method is effective for treatment of emotional disorders among the elderly. TD-GCBT is effective for alleviating depression and anxiety symptoms up to at least nine months after treatment. The results indicate that TD-GCBT is a cost-effective and resource-effective strategy and can be used an alternative therapy for treatment of mental disorders. Clinical trial registration [https://www.chictr. org.cn], identifier [ChiCTR1900021806].
Toward diverse seed sourcing to upscale ecological restoration in the Brazilian Cerrado

Seed markets are vital to scaling up ecosystem restoration in the Brazilian Cerrado, home of the world’s most species-rich grasslands and savannas. We compiled lists of species traded by four major Cerrado seed supply systems to investigate the representativeness of the species currently available for seed-based restoration. We also identified whether dominant ground-layer species are being sourced for seed production. Seeds from 263 Cerrado species can be purchased for restoration, of which 68% are trees, particularly legumes (24%). 63% of the traded species were found in only one seed supply system. The five most dominant graminoids of the Cerrado ground layer were available for sale, but two additional species uncommon in old-growth areas represented 44% of the sales of a key seed trader in Central Brazil. The expansion of Cerrado seed supply systems should be supported to further increase the number of species on the market. Sourcing seeds from a diversity of herbaceous species is central to facilitating the restoration of species-rich grasslands and savannas in the Cerrado. Recovering the diversity and functioning of old-growth open ecosystems through seeds will depend on increasing the supply and demand for species typical of Cerrado’s ground layer.
η Chamaeleontis: abnormal initial mass function or dynamical evolution?

Context. η Chamaeleontis is a unique young (∼9 Myr) association with 18 systems concentrated in a radius of ≈35 arcmin, i.e. 1 pc at the cluster distance of 97 pc. No other members have been found up to 1.5 degrees from the cluster centre. The cluster mass function is consistent with the IMF of other rich young open clusters in the higher mass range but shows a clear deficit of low mass stars and brown dwarfs with no objects below 0.1 M� . Aims. The aim of this paper is to test whether this peculiar mass function could result from dynamical evolution despite the young age of the cluster. Methods. We performed N-body numerical calculations starting with a log-normal IMF and different initial conditions in terms of number of systems and cluster radius using the code NBODY3. We simulated the cluster dynamical evolution over 10 Myr and compared the results to the observations. Results. We found that it is possible to reproduce η Cha when starting with a very compact configuration (with Ninit = 40 and R0 = 0.005 pc) which suggests that the IMF of the association might not be abnormal. The high initial density might also explain the deficit of wide binaries that is observed in the cluster.
Pharmacogenetics-based population pharmacokinetic analysis and dose optimization of valproic acid in Chinese southern children with epilepsy: Effect of ABCB1 gene polymorphism

Objective: The aim of this study was to establish a population pharmacokinetic (PPK) model of valproic acid (VPA) in pediatric patients with epilepsy in southern China, and provide guidance for individualized medication of VPA therapy. Methods: A total of 376 VPA steady-state trough concentrations were collected from 103 epileptic pediatric patients. The PPK parameter values for VPA were calculated by using the nonlinear mixed-effects modeling (NONMEM) method, and a one-compartment model with first-order absorption and elimination processes was applied. Covariates included demographic information, concomitant medications and selected gene polymorphisms. Goodness-of-fit (GOF), bootstrap analysis, and visual predictive check (VPC) were used for model evaluation. In addition, we used Monte Carlo simulations to propose dose recommendations for different subgroup patients. Results: A significant effect of the patient age and ABCB1 genotypes was observed on the VPA oral clearance (CL/F) in the final PPK model. Compared with patients with the ABCB1 rs3789243 AA genotype, CL/F in patients with GG and AG genotypes was increased by 8% and reduced by 4.7%, respectively. The GOF plots indicated the satisfactory predictive performance of the final model, and the evaluation by bootstrap and VPC showed that a stable model had been developed. A table of individualized dosing regimens involving age and ABCB1 genotype was constructed based on the final PPK model. Conclusion: This study quantitatively investigated the effects of patient age and ABCB1 rs3789243 variants on the pharmacokinetic variability of VPA. The PPK models could be beneficial to individual dose optimization in epileptic children on VPA therapy.
Spatial distribution and influencing factors of mountainous geological disasters in southwest China: A fine-scale multi-type assessment

Abstract: Geological disasters have long been a constant threat to socioeconomic development and human life and property. Many studies focus on the occurred geological disasters and ignore the potential risk events. Fine-scale multi-type analysis of Potential Geological Disasters Spots (PGDSs) is a necessary but insufficiently explored research field in China’s mountainous areas. Taking Meigu County (Sichuan Province, Southwest China), a typical disaster-prone region, as the study area. Average nearest neighbor (ANN), standard deviational ellipse (SDE), kernel density estimation (KDE), and ordinary least squares (OLS) regression are used to assess the spatial distribution of potential geological disasters spots and their influencing factors. The findings show that: potential geological disasters spots have a significant spatial heterogeneity and exhibited a prominent clustering characteristic. They were distributed in an elevation range of 1,500–2000 m, which receives an average monthly rainfall of more than 240 mm, as well as in highly foliated (0.6 < Normalized Difference Vegetation Index (NDVI) < 0.8), west-facing (247.5–292.5°), and slopes of 10–20°. In addition, slope, aspect, population density, and rainfall were found as the main influencing factors. The results provide practical rural development measures with support for potential geological disasters spots avoidance and preparedness.
Hammering with the telescope

The rapid pace in which various Artificial Intelligence and Machine Learning tools are developed, both within the research community and outside of it, often discourages the involved researchers from taking time to consider potential consequences and applications of the technical advances, especially the unintended ones. While there are notable exceptions to this “gold rush” tendency, individuals and groups providing careful analyses and recommendations for future actions, their adoption remains, at best, limited. This essay presents an analysis of the ethical (and not only) challenges connected with the applications of AI/ML methods in the socio-legal domain.
Temporal and spatial characteristics of submesoscale motions in the Bohai Sea

Submesoscale motions are ubiquitous in the ocean, playing a significant role in energy transfer, mass transport, and biogeochemical processes. However, little attention has been drawn to the submesoscale dynamics in shallow coastal waters. In the present study, submesoscale motions in the Bohai Sea, a typical shallow sea with mean depth of about 18 m, are studied using a validated high-resolution (~ 500 m) model based on Regional Oceanic Modeling System (ROMS). The results show that submesoscale structures in the Bohai Sea are mainly located in the shallow coastal regions, the Bohai Strait, the areas around islands and headlands, and mostly tend to be parallel to the isobaths. The periodic variations of submesoscale motions are closely related to the tidal, spring-neap, and seasonal cycles in the Bohai Sea. The spring-neap variations of submesoscale motions are mainly attributed to the curl of vertical mixing, which is stronger during spring tides than neap tides. Compared with winter, the stronger background horizontal and vertical density variance in summer are conducive to frontogenesis, resulting in more active submesoscale motions. The results in this study are expected to contribute to enriching our knowledge about submesoscale dynamics in shallow coastal seas.
Nutrient composition (Si:N) as driver of plankton communities during artificial upwelling

Artificial upwelling brings nutrient-rich deep water to the sun-lit surface to boost fisheries or carbon sequestration. Deep water sources under consideration range widely in inorganic silicon (Si) relative to nitrogen (N). Yet, little is known about how such differences in nutrient composition may influence the effectiveness of the fertilization. Si is essential primarily for diatoms that may increase food web and export efficiency via their large size and ballasting mineral shells, respectively. With a month-long mesocosm study in the subtropical North Atlantic, we tested the biological response to artificial upwelling with varying Si:N ratios (0.07-1.33). Community biomass increased 10-fold across all mesocosms, indicating that basic bloom dynamics were upheld despite the wide range in nutrient composition. Key properties of these blooms, however, were influenced by Si. Photosynthetic capacity and nutrient-use efficiency doubled from Si-poor to Si-rich upwelling, leading to C:N ratios as high as 17, well beyond Redfield. Si-rich upwelling also resulted in 6-fold higher diatom abundance and mineralized Si and a corresponding shift from smaller towards larger phytoplankton. The pronounced change in both plankton quantity (biomass) and quality (C:N ratio, size and mineral ballast) for trophic transfer and export underlines the pivotal role of Si in shaping the response of oligotrophic regions to upwelled nutrients. Our findings indicate a benefit of active Si management during artificial upwelling with the potential to optimize fisheries production and CO2 removal.
Reconsidering children’s illness uncertainty and management experiences with female Japanese cancer survivors

The aim of this study is to examine the illness uncertainties (IU) that children experience and the ways they manage them in order to construct a long-term, comprehensive developmental care for children with illness. Semi-structured, in-person interviews were conducted with six Japanese female adolescent cancer survivors, all recruited from the same hospital in Tokyo, Japan. Using directed content analysis, all transcriptions that fell under the definition “the person is unable to construct the meaning of an illness related event of her/his self or another, and is aware of the state” were coded with the codes defined from the data, which were then cross-referenced with the existing literature. The results indicated new aspects of children’s IU; uncertainties regarding hospitalization and the necessity to distinguish and examine IU with and without answers. In terms of IU management, we discuss the informative value “role models,” and depict how uncertainty acceptance may be a new form of solution.
When less is more: Visitation by generalist pollinators can have neutral or negative effects on plant reproduction

Selection for specialized coevolutionary relationships can arise if generalized opportunistic pollinators, while still delivering some pollen, operate as less effective pollen delivery agents. Nevertheless, generalization could buffer high-latitude communities from loss of specialist pollinator species by providing some pollination service. Currently, there is limited understanding of the ecosystem services provided by generalized pollinators and whether they increase the fitness of the plants they visit. Network data and thorough observations of floral visitors, paired with estimates of seed set, offer some insight into the role of generalists, which in turn can inform us about how plants are likely to respond to ecosystem disturbances, such as losses of some pollinators, or changes in land cover. Here, we report on plant-pollinator visitation networks in Canada with high levels of generalization and examine the effects of generalization on seed set under different disturbance histories. We also then take a case study of one crop wild relative, Rubus arcticus or Arctic raspberry, and report on a near-complete characterization of pollinator interactions in different environmental conditions. Our findings indicate that generalized pollinators, though frequent and robust to variable temperatures and moisture conditions, do not appear to play a strong role in increasing the reproductive output of many plant species, and may provide only a weak buffer against the stronger effects of disturbance.
Thymoquinone protects the testes of hypothyroid rats by suppressing pro-inflammatory cytokines and oxidative stress and promoting SIRT1 testicular expression

Background: Hypothyroidism has been linked to many testicular structural and dysfunctional changes in males. Thymoquinone (TQ) has shown a potent testicular protective effect through its antioxidant, anti-inflammatory, antiapoptotic, fertility-enhancing, and endocrine modulatory activities. Objectives: This study aimed to investigate the efficacy of TQ in preserving the testicular structure of a model of experimentally induced hypothyroidism in rats and identify the mechanism behind this effect. Materials and methods: Propylthiouracil (PTU) was used to induce hypothyroidism in adult male Wistar rats, who were then treated with TQ (50 mg/kg/body weight) for 4 weeks and compared to the untreated rats. Thyroid hormonal profile, oxidants/antioxidants profile, and serum testosterone levels were assessed. Gene expression and immune expression of SIRT1 and pro-inflammatory cytokines TNF-α and NF-κB were also assessed in the testicular tissue. Results: TQ administration successfully improved PTU-induced disturbance in the thyroid hormonal profile (T3, T4, and TSH), serum testosterone level, and pancreatic antioxidants compared to the untreated hypothyroid group. TQ significantly downregulated (p = 0.001, p ˂ 0.001) TNF-α and NF-κB transcription, while it significantly upregulated (p = 0.01) SIRT1 transcription in the testes of hypothyroid rats. TQ markedly relieved the histopathological testicular changes induced by PTU and significantly increased (p = 0.002, p = 0.01) the sectional area of seminiferous tubules and germinal epithelial height, respectively. TUNEL-positive apoptotic germinal cells were significantly decreased (p ˂ 0.001), while PCNA-positive proliferating germinal cells and androgen receptor expression were significantly increased (p ˂ 0.001) in the testes of TQ-treated hypothyroid rats. Conclusion: Thymoquinone could limit the hypothyroidism-induced structural changes in the testis, mostly through the upregulation of SIRT1 expression, which seems to mediate its promising antioxidant, anti-inflammatory and antiapoptotic effects that were evident in this study. Therefore, TQ is recommended as an adjuvant safe supplement in managing hypothyroidism, especially in males.
Affection of facial artifacts caused by micro-expressions on electroencephalography signals

Macro-expressions are widely used in emotion recognition based on electroencephalography (EEG) because of their use as an intuitive external expression. Similarly, micro-expressions, as suppressed and brief emotional expressions, can also reflect a person’s genuine emotional state. Therefore, researchers have started to focus on emotion recognition studies based on micro-expressions and EEG. However, compared to the effect of artifacts generated by macro-expressions on the EEG signal, it is not clear how artifacts generated by micro-expressions affect EEG signals. In this study, we investigated the effects of facial muscle activity caused by micro-expressions in positive emotions on EEG signals. We recorded the participants’ facial expression images and EEG signals while they watched positive emotion-inducing videos. We then divided the 13 facial regions and extracted the main directional mean optical flow features as facial micro-expression image features, and the power spectral densities of theta, alpha, beta, and gamma frequency bands as EEG features. Multiple linear regression and Granger causality test analyses were used to determine the extent of the effect of facial muscle activity artifacts on EEG signals. The results showed that the average percentage of EEG signals affected by muscle artifacts caused by micro-expressions was 11.5%, with the frontal and temporal regions being significantly affected. After removing the artifacts from the EEG signal, the average percentage of the affected EEG signal dropped to 3.7%. To the best of our knowledge, this is the first study to investigate the affection of facial artifacts caused by micro-expressions on EEG signals.