Miracle-dz/UniFAR-FTUs huggingface dataset:
The Influence of Context on the Abstraction Level of Children’s Conversations in the Preschool Classroom

ABSTRACT Research Findings: Conversing abstract concepts boost children’s language learning. Despite the numerous studies on the linguistic environment of early childhood education settings (ECE), most of this work disregards contextual factors that may influence abstract conversations and omits characteristics of children’s verbal participation in these interactions. We examined how preschool classroom contexts influenced the abstraction level of children’s conversations and how the context and conversational partners’ language influenced children’s verbal participation. We analyzed 2,928 utterances in 453 natural teacher and peer conversations during a one-week period in a preschool classroom. Bayesian analysis showed that children and teachers used significantly more abstract talk in small-group activities coded as math and science than other coded settings. Moreover, Bayesian analysis revealed that the abstraction level of conversational partners’ turns influenced that of children’s talk beyond the characteristics of the context. Interestingly, this association was moderated by the partner (teacher or peer). Practice or Policy: The inconsistent association between measurements of ECE quality and children’s outcomes invites practitioners to reevaluate what these measurements should assess. This study suggests the need to pay greater attention to the features of ECE settings that are conducive to children’s development, such as learning materials, grouping, and peer interactions.
Spatial and temporal variability of aerosol particles in Arctic spring

The objective of this work is to investigate the variability in the aerosol particle number concentration in Arctic spring. The Indirect and Semi‐Direct Aerosol Campaign (ISDAC) was conducted during April 2008 in the vicinities of Fairbanks and Barrow, Alaska. Aircraft‐based measurements of total aerosol particle number concentration (Na) in the size range of 0.12–3 µm diameter were obtained using a passive cavity aerosol spectrometer probe (PCASP‐100X). The analysis considers Na during cloud‐free periods in biomass burning (BB) and non‐BB aerosol loading scenarios, the latter including background cases and cases with elevated concentration in layers. The BB cases had air masses originating mainly from Russian and Asian forest and crop fires, whereas the non‐BB cases originated predominantly from Arctic or oceanic regions. The average Na for all non‐BB cases was 127 cm−3, while that for all BB cases was Na = 720 cm−3. These estimates do not, however, capture the details of aerosol particle layers encountered during most flights. Variability in Na was considered for constant altitude (horizontal) flight legs ranging from 50 to 650 km in length, as well as for vertical flight profiles up to 7 km above sea level. When aerosol particle layers were encountered, Na rapidly increased from 20 to 550 cm−3, and reached up to 2200 cm−3 within air masses dominated by BB plumes. The observed variability in Na may have important implications for estimating cloud microphysical properties as well as estimates of particle properties used in global climate model simulations, because averaging over large space‐ or time‐scales may not represent real atmospheric conditions. The analysis demonstrates the difficulty in interpreting average aerosol particle characteristics along longer flight legs, particularly during cases with higher particle loading that varies over shorter distance scales and time periods. Copyright © 2012 Royal Meteorological Society and Crown in the right of Canada.
Resting-state functional brain network alternations related to non-suicidal and suicidal self-injurious behaviors in adolescents with depression

Background: Nonsuicidal self-injury (NSSI) and suicidal attempt (SA) frequently occur during depressed adolescents, but the underlying neurobiological mechanisms are poorly understood. This study sought to investigate neurobiological alternations that underpin adolescent NSSI with or without a history of SA, specifically using functional connectivity (FC) analysis. Methods: We collected self-reported questionnaires and resting-state fMRI data from depressed adolescents (N = 114), and they were divided into three groups: clinical control (non-self-harm), NSSI-only, and NSSI+SA based on their history of self-harm. Alternations of FC patterns were identified through support vector machine-based classification. Results: Adolescent NSSI with or without a history of SA exhibited both overlapping and divergent neurobiological alternations. Referring to the alternations of FC in the NSSI group, the alternations of intra-/inter-network FCs among the Control, SalVAtten, Limbic, and Default networks persist in depressed adolescents with a history of both NSSI and SA, while some new alternations appear, including inter-network FCs among the Limbic, DorsAttn, and Visual networks. Limitations: Cross-sectional design. Retrospective self-report on the history of self-harm behaviors and severity of depression symptoms. The modest sample size. Conclusions: The emphasis of this study on the network basis could extend the existing evidence at a circuit level, and may explain an underlying neurobiological mechanism pertaining to the continuum of self-destructiveness in adolescents.
A nanobody-based strategy for rapid and scalable purification of native human protein complexes

Native isolation of proteins in high yield and purity is a major bottleneck for analysis of their three- dimensional structure, function, and interactome. Here, we present a streamlined workflow for the rapid production of proteins or protein complexes using lentiviral transduction of human suspension cells, combined with highly-specific nanobody-mediated purification and proteolytic elution. (1) First, generation of a plasmid coding for a protein of interest fused to an N- or C- terminal GFP or ALFA peptide tag is rapidly achieved using the lentiviral plasmid toolkit we have designed. (2) Human suspension cell lines stably expressing the tagged fusion protein can be generated in <5 days using lentiviral transduction. (3) Leveraging the picomolar affinity of the GFP and ALFA nanobodies for their respective tags, proteins expressed even at low levels can be specifically captured from the resulting cell lysate in a variety of conditions, including detergents and mild denaturants. (4) Finally, rapid and specific elution of tagged or untagged proteins under native conditions is achieved within minutes at 4°C using an engineered SUMO protease. We demonstrate the wide applicability of the method by purifying multiple challenging soluble and membrane protein complexes to high purity from human cells. Our strategy is also directly compatible with many widely used GFP expression plasmids, cell lines and transgenic model organisms; is faster than alternative approaches, requiring ∼8 days from cloning to purification; and results in substantially improved yields and purity.
Early alterations of thalamo- and hippocampo-cortical functional connectivity are biomarkers of epileptogenesis after traumatic brain injury

The Epilepsy Bioinformatics Study for Antiepileptogenic Therapy (EpiBioS4Rx) study is a prospective multicenter clinical observational study to identify early biomarkers of epileptogenesis after moderate-to-severe traumatic brain injury (TBI). In this preliminary analysis of 37 patients, using a seed-based approach applied to acute (i.e., ≤ 14 days) functional magnetic resonance (MRI) imaging data, we directly test the hypothesis that the epileptogenic process following brain trauma is associated with functional changes within hippocampal and thalamo-cortical networks. Additionally, we hypothesize that the network connectivity involving thalamic and hippocampal circuits underlying early and late-onset epileptogenesis would differ. The three groups did not differ by sex distribution (χ2(2) = 1.8, p = . 407), age (H(2) = 4.227, p = . 121), admission Glasgow Coma Scale (H(2) = 3.850, p = . 146) or postinjury day of the MRI session (H(2) = . 695, p = . 706). The primary finding is that patients with early seizures, a sign of early epileptogenesis, exhibited pattern 1, namely, an increased positive connectivity in thalamic and hippocampal networks, as compared to patients who had no epileptogenesis, or late epileptogenesis (p < .05, FWE-corrected at the cluster level). In contrast, this finding was absent in those patients who exhibited late seizures, with the latter group displayed pattern 2, namely, a lower positive and higher negative connectivity in the hippocampal network, as compared to patients who had no signs of epileptogenesis (p < .05, FWE-corrected at the cluster level). Patients with either pattern 1 or pattern 2 connectivity profiles in thalamic and hippocampal networks were significantly predictive of late (i.e., between 7 days and 2 years) epileptogenesis following brain trauma. A Receiver Operating Characteristic (ROC) Curve analysis model that included thalamic and hippocampal functional connectivity values presented an Area Under the Curve (AUC) 87.7, specificity 86.7, and sensitivity 84.6. Our results indicate that dysfunction in hippocampal and thalamo-cortical networks are potential biomarkers for early and late epileptogenesis following a TBI.
Connectomes for 40,000 UK Biobank participants: A multi-modal, multi-scale brain network resource

We mapped functional and structural brain networks for more than 40,000 UK Biobank participants. Structural connectivity was estimated with tractography and diffusion MRI. Resting-state functional MRI was used to infer regional functional connectivity. We provide high-quality structural and functional connectomes for multiple parcellation granularities, several alternative measures of interregional connectivity, and a variety of common data pre-processing techniques, yielding more than one million connectomes in total and requiring more than 200,000 hours of compute time. For a single subject, we provide 28 out-of-the-box versions of structural and functional brain networks, allowing users to select, e.g., the parcellation and connectivity measure that best suit their research goals. Furthermore, we provide code and intermediate data for the time-efficient reconstruction of more than 1,000 different versions of a subject’s connectome based on an array of methodological choices. All connectomes are available via the UK Biobank data sharing platform and our connectome mapping pipelines are openly available. In this report, we describe our connectome resource in detail for users, outline key considerations in developing an efficient pipeline to map an unprecedented number of connectomes, and report on the quality control procedures that were completed to ensure connectome reliability and accuracy. We demonstrate that our structural and functional connectivity matrices meet a number of quality control checks and replicate previously established findings in network neuroscience. We envisage that our resource will enable new studies of the human connectome in health, disease and aging at an unprecedented scale.
Characterization of a mouse model of ICF syndrome reveals enhanced CD19 activation in inducing hypogammaglobulinemia

Immunodeficiency, centromeric instability and facial anomalies (ICF) syndrome is a rare autosomal recessive disorder characterized by DNA hypomethylation and antibody deficiency. It is caused by mutations in DNMT3B, ZBTB24, CDCA7 or HELLS. While progress has been made in elucidating the roles of these genes in regulating DNA methylation, little is known about the pathogenesis of the life-threatening hypogammaglobulinemia phenotype. Here we show that mice deficient for Zbtb24 in the hematopoietic lineage recapitulate major clinical features of patients with ICF syndrome. Specifically, Vav-Cre-mediated ablation of Zbtb24 does not affect lymphocyte development but results in reduced plasma cells and low levels of IgM, IgG1 and IgA. Zbtb24-deficient mice are hyper- and hypo-responsive to T-dependent and Tindependent type 2 antigens, respectively, and marginal zone B cell activation is impaired. B cells from Zbtb24-deficient mice display elevated CD19 phosphorylation. Heterozygous disruption of Cd19 can revert the hypogammaglobulinemia phenotype in these mice. Mechanistically, Il5ra (interleukin-5 receptor subunit alpha) is derepressed in Zbtb24-deficient B cells, and elevated IL-5 signaling enhances CD19 phosphorylation. Our results reveal a novel link between IL-5 signaling and CD19 activation and suggest that abnormal CD19 activity contributes to immunodeficiency in ICF syndrome. SIGNIFICANCE STATEMENT ICF syndrome is a rare immunodeficiency disorder first reported in the 1970s. The lack of appropriate animal models has hindered the investigation of the pathogenesis of antibody deficiency, the major cause of death in ICF syndrome. Here we show that, in mice, disruption of Zbtb24, one of the ICF-related genes, in the hematopoietic lineage results in low levels of immunoglobulins. Characterization of these mice reveals abnormal B cell activation due to elevated CD19 phosphorylation. Mechanistically, Il5ra (interleukin-5 receptor subunit alpha) is derepressed in Zbtb24-deficient B cells, and increased IL-5 signaling enhances CD19 phosphorylation.
VirRep: accurate identification of viral genomes from human gut metagenomic data via a hybrid language representation learning framework

Accurate identification of viral genomes from metagenomic data provides a broad avenue for studying viruses in the human gut. Here, we introduce VirRep, a novel virus identification method based on a hybrid language representation learning framework. VirRep employs a context-aware encoder and a composition-focused encoder to incorporate the learned knowledge and known biological insights to better describe the source of a DNA sequence. We benchmarked VirRep on multiple human gut virome datasets under different conditions and demonstrated significant superiority than state-of-the-art methods and even combinations of them. A comprehensive validation has also been conducted on real human gut metagenomes to show the great utility of VirRep in identifying high-quality viral genomes that are missed by other methods.
signifinder enables the identification of tumor cell states and cancer expression signatures in bulk, single-cell and spatial transcriptomic data

Over the last decade, many studies and some clinical trials have proposed gene expression signatures as a valuable tool for understanding cancer mechanisms, defining subtypes, monitoring patient prognosis, and therapy efficacy. However, technical and biological concerns about reproducibility have been raised. Technical reproducibility is a major concern: we currently lack a computational implementation of the proposed signatures, which would provide detailed signature definition and assure reproducibility, dissemination, and usability of the classifier. Another concern regards intratumor heterogeneity, which has never been addressed when studying these types of biomarkers using bulk transcriptomics. With the aim of providing a tool able to improve the reproducibility and usability of gene expression signatures, we propose signifinder, an R package that provides the infrastructure to collect, implement, and compare expression-based signatures from cancer literature. The included signatures cover a wide range of biological processes from metabolism and programmed cell death, to morphological changes, such as quantification of epithelial or mesenchymal-like status. Collected signatures can score tumor cell characteristics, such as the predicted response to therapy or the survival association, and can quantify microenvironmental information, including hypoxia and immune response activity. signifinder has been used to characterize tumor samples and to investigate intra-tumor heterogeneity, extending its application to single-cell and spatial transcriptomic data. Through these higher-resolution technologies, it has become increasingly apparent that the single-sample score assessment obtained by transcriptional signatures is conditioned by the phenotypic and genetic intratumor heterogeneity of tumor masses. Since the characteristics of the most abundant cell type or clone might not necessarily predict the properties of mixed populations, signature prediction efficacy is lowered, thus impeding effective clinical diagnostics. Through signifinder, we offer general principles for interpreting and comparing transcriptional signatures, as well as suggestions for additional signatures that would allow for more complete and robust data inferences. We consider signifinder a useful tool to pave the way for reproducibility and comparison of transcriptional signatures in oncology.
Diet quality alters the consequences of gradual phenotypic plasticity for individual performance

Organisms exhibit reversible physiological adjustments as a response to rapidly changing environments. Yet, such plasticity of the phenotype is gradual and may lag behind the environmental fluctuations, thereby affecting the long-term average performance of the organisms. By supplying energy and essential compounds for optimal tissue building, food determines the range of possible phenotypic changes and potentially the rate at which they occur. Here, we assess how differences in the dietary supply of essential lipids modulate the phenotypic plasticity of an ectotherm facing thermal fluctuations. We use three phytoplankton strains to create a gradient of polyunsaturated fatty acids and sterols supply for Daphnia magna under constant and fluctuating temperatures. We used three different fluctuation periodicities to unravel the temporal dynamics of gradual plasticity and its long-term consequences on D. magna performance measured as juvenile somatic growth rate. In agreement with gradual plasticity theory, we show that in D.magna, fluctuation periodicity determines the differential between observed growth rates and those expected from constant conditions. Most importantly, we show that diet modulates both the size and the direction of the growth rate differential. Overall, we demonstrate that the nutritional context is essential for predicting ectotherm consumers’ performance in fluctuating thermal environments.
Inducible expression of the restriction enzyme uncovered genome-wide distribution and dynamic behavior of histones H4K16ac and H2A.Z at DNA double-strand breaks in Arabidopsis

DNA double-strand breaks (DSBs) are among the most serious types of DNA damage and cause mutations and chromosomal rearrangements. In eukaryotes, DSBs are immediately repaired in coordination with chromatin remodeling for the deposition of DSB-related histone modifications and variants. To elucidate the details of DSB-dependent chromatin remodeling throughout the genome, artificial DSBs need to be reproducibly induced at various genomic loci. Recently, in mammals, a comprehensive method for elucidating chromatin remodeling at multiple DSB loci via chemically induced expression of a restriction enzyme was developed. However, this DSB induction system is not suitable for investigating chromatin remodeling during and after DSB repair, and such approach has not been performed in plants. Here, we established a transgenic Arabidopsis plant harboring a restriction enzyme gene Sbf I driven by a heat-inducible promoter. Using this transgenic plant, we performed chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) of histones H4K16ac and H2A.Z and investigated dynamics of these histone marks around the endogenous 623 Sbf I recognition sites. We also precisely quantified DSB efficiency at all cleavage sites using the DNA resequencing data obtained by ChIP-seq procedures. From the results, Sbf I-induced DSBs were detected at 360 loci and induced the transient deposition of H4K16ac and H2A.Z around these regions. Interestingly, we also observed the co-localization of H4K16ac and H2A.Z at some DSB loci. Overall, DSB-dependent chromatin remodeling was found to be a highly conserved between plants and animals. These findings provide new insights into chromatin remodeling that occurs in response to DSBs in Arabidopsis.
Effect of number of diffusion encoding directions in Neonatal Diffusion Tensor Imaging using Tract-Based Spatial Statistical analysis

Diffusion Tensor Imaging (DTI) has been used to study the developing brain in early childhood, infants and in utero studies. In infants, number of used diffusion encoding directions has traditionally been smaller in earlier studies down to the minimum of 6 orthogonal directions. While the more recent studies often involve more directions, number of used directions remains an issue when acquisition time is optimized without compromising on data quality and in retrospective studies. Variability in the number of used directions may introduce bias and uncertainties to the DTI scalar estimates that affect cross-sectional and longitudinal study of the brain. We analyzed DTI images of 133 neonates, each data having 54 directions after quality control, to evaluate the effect of number of diffusion weighting directions from 6 to 54 with interval of 6 to the DTI scalars with Tract-based spatial statistics (TBSS) analysis. The TBSS analysis was applied to DTI scalar maps, and the mean Region of Interest (ROI) values were extracted using JHU atlas. We found significant bias in ROI mean values when only 6 directions were used (positive in FA, negative in MD, AD, RD), while when using 24 directions and above, the difference to scalar values calculated from 54 direction DTI was negligible. Using DTI measurements from data with at least 24 directions may be used in comparisons with DTI measurements from data with higher numbers of directions.
Purification and characterization of a novel anti-tumour galactose binding lectin from Euphorbia caducifolia latex

A galactose specific lectin was isolated from the latex of Euphorbia caducifolia to investigate the therapeutical aspects protein. Protein was purified from latex serum with two different affinity matrices and confirmed to contain 8 isoforms called isolectin with a molecular weight of 32 and 32.5 kDa. Preliminary studies state the specificity towards galactose, but its affinity with lactose is more favourable even at low concentrations. Circular spectrometry suggests the predominance β conformation is high in comparison to others as like most of the other latex lectins. Haemagglutination activity of the protein with different thermal and pH ranges shows maximum activity at pH 6-8 and 60-70°C. In therapeutically, it is noticed that the galactose specific lectin showed mitogenicity with human macrophages and anti-cancer properties on human cervical cancer cells.
Adjacent LSTM-Based Page Scheduling for Hybrid DRAM/NVM Memory Systems

Recent advances in memory technologies have led to the rapid growth of hybrid systems that combine traditional DRAM and Non Volatile Memory (NVM) technologies, as the latter provide lower cost per byte, low leakage power and larger capacities than DRAM, while they can guarantee comparable access latency. Such kind of heterogeneous memory systems impose new challenges in terms of page placement and migration among the alternative technologies of the heterogeneous memory system. In this paper, we present a novel approach for efficient page placement on heterogeneous DRAM/NVM systems. We design an adjacent LSTM-based approach for page placement, which strongly relies on page accesses prediction, while sharing knowledge among pages with behavioral similarity. The proposed approach leads up to 65.5% optimized performance compared to existing approaches, while achieving near-optimal results and saving 20.2% energy consumption on average. Moreover, we propose a new page replacement policy, namely clustered-LRU , achieving up to 8.1% optimized performance, compared to the default Least Recently Used (LRU) policy.