Miracle-dz/UniFAR-FTUs huggingface dataset:
All About the RNA: Interferon-Stimulated Genes That Interfere With Viral RNA Processes

Interferon (IFN) signaling induces the expression of a wide array of genes, collectively referred to as IFN-stimulated genes (ISGs) that generally function to inhibit viral replication. RNA viruses are frequently targeted by ISGs through recognition of viral replicative intermediates and molecular features associated with viral genomes, or the lack of molecular features associated with host mRNAs. The ISGs reviewed here primarily inhibit viral replication in an RNA-centric manner, working to sense, degrade, or repress expression of viral RNA. This review focuses on dissecting how these ISGs exhibit multiple antiviral mechanisms, often through use of varied co-factors, highlighting the complexity of the type I IFN response. Specifically, these ISGs can mediate antiviral effects through viral RNA degradation, viral translation inhibition, or both. While the OAS/RNase L pathway globally degrades RNA and arrests translation, ISG20 and ZAP employ targeted RNA degradation and translation inhibition to block viral replication. Meanwhile, SHFL targets translation by inhibiting -1 ribosomal frameshifting, which is required by many RNA viruses. Finally, a number of E3 ligases inhibit viral transcription, an attractive antiviral target during the lifecycle of negative-sense RNA viruses which must transcribe their genome prior to translation. Through this review, we aim to provide an updated perspective on how these ISGs work together to form a complex network of antiviral arsenals targeting viral RNA processes.
Label Representations in Modeling Classification as Text Generation

Several recent state-of-the-art transfer learning methods model classification tasks as text generation, where labels are represented as strings for the model to generate. We investigate the effect that the choice of strings used to represent labels has on how effectively the model learns the task. For four standard text classification tasks, we design a diverse set of possible string representations for labels, ranging from canonical label definitions to random strings. We experiment with T5 on these tasks, varying the label representations as well as the amount of training data. We find that, in the low data setting, label representation impacts task performance on some tasks, with task-related labels being most effective, but fails to have an impact on others. In the full data setting, our results are largely negative: Different label representations do not affect overall task performance.
Transcriptome Analysis of Juvenile Tilapia (Oreochromis niloticus) Blood, Fed With Different Concentrations of Resveratrol

Oreochromis niloticus (genetically improved farmed tilapia, GIFT) often bites the root of Polygonum cuspidatum when it is used as a floating bed, and resveratrol (RES) is mainly accumulated in the root of P. cuspidatum. Blood acts as a pipeline for the fish immune system. Generating blood transcriptomic resources is crucial for understanding molecular mechanisms underlying blood immune responses. In this study, we determined the effects of RES administration on blood transcriptomic response in GIFT. With increasing RES concentration, 133 (0.025 vs. 0.05 g/kg RES), 155 (0.025 vs. 0.1 g/kg RES), and 123 (0.05 vs. 0.1 g/kg RES) genes were detected as significant differentially expressed genes (DEGs). Three and ninety-five shared significant DEGs were found to be enriched among the three (except 0.1 g/kg RES) and four groups (0, 0.025, 0.05, and 0.1 g/kg RES), respectively. To determine the relationship between mitochondrial regulation and RES supplementation, the results of RNA-Seq were analyzed and nine mitochondria-related genes (ATP synthase or mitochondrial-function-related genes) were verified. The results revealed the same expression pattern: cytochrome c isoform X2 (cox2), katanin p60 ATPase-containing subunit A1 isoform X1 (katna1), plasma membrane calcium-transporting ATPase 1-like (atp2b1) and GTP-binding protein A-like (gtpbpal) showed the highest expression in the 0.1 g/kg RES group, while NADH dehydrogenase [ubiquinone] iron-sulfur protein 2 mitochondrial (nad7), ATP synthase subunit beta, mitochondrial (atpb), ATP synthase subunit alpha, mitochondrial-like (atpal), ATP synthase subunit alpha, mitochondrial (atpa) and ATP-dependent Clp protease proteolytic subunit, mitochondrial (clpp) revealed a dose-dependent expression following RES supplementation. Blood Ca2+-ATPase activity, and malondialdehyde, glutathione, and ATP content were significantly increased in the 0.05 (except Ca2+-ATPase activity), 0.1 g/kg RES group when compared with the controls. Eighty-nine shared DGEs were mainly enriched in antigen processing and presentation, cell adhesion molecules and phagosome pathways, based on the comparison between previous reported hepatic and the present blood transcriptome. Our study demonstrated that RES supplementation might improve the resistance to metabolism dysfunction via mitochondrial energy synthesis and/or the respiratory chain (e.g., ATPase).
Building a Part-of-Speech Tagged Corpus for Drenjongke (Bhutia)

This research paper reports on the generation of the first Drenjongke corpus based on texts taken from a phrase book for beginners, written in the Tibetan script. A corpus of sentences was created after correcting errors in the text scanned through optical character reading (OCR). A total of 34 Part-of-Speech (PoS) tags were defined based on manual annotation performed by the three authors, one of whom is a native speaker of Drenjongke. The first corpus of the Drenjongke language comprises 275 sentences and 1379 tokens, which we plan to expand with other materials to promote further studies of this language.
Intrinsically Self-renewing Neuroprogenitors From the A/J Mouse Spiral Ganglion as Virtually Unlimited Source of Mature Auditory Neurons

Nearly 460 million individuals are affected by sensorineural hearing loss (SNHL), one of the most common human sensory disorders. In mammals, hearing loss is permanent due to the lack of efficient regenerative capacity of the sensory epithelia and spiral ganglion neurons (SGN). Sphere-forming progenitor cells can be isolated from the mammalian inner ear and give rise to inner ear specific cell types in vitro. However, the self-renewing capacities of auditory progenitor cells from the sensory and neuronal compartment are limited to few passages, even after adding powerful growth factor cocktails. Here, we provide phenotypical and functional characterization of a new pool of auditory progenitors as sustainable source for sphere-derived auditory neurons. The so-called phoenix auditory neuroprogenitors, isolated from the A/J mouse spiral ganglion, exhibit robust intrinsic self-renewal properties beyond 40 passages. At any passage or freezing–thawing cycle, phoenix spheres can be efficiently differentiated into mature spiral ganglion cells by withdrawing growth factors. The differentiated cells express both neuronal and glial cell phenotypic markers and exhibit similar functional properties as mouse spiral ganglion primary explants and human sphere-derived spiral ganglion cells. In contrast to other rodent models aiming at sustained production of auditory neurons, no genetic transformation of the progenitors is needed. Phoenix spheres therefore represent an interesting starting point to further investigate self-renewal in the mammalian inner ear, which is still far from any clinical application. In the meantime, phoenix spheres already offer an unlimited source of mammalian auditory neurons for high-throughput screens while substantially reducing the numbers of animals needed.
Acute exacerbations of idiopathic pulmonary fibrosis and the role of corticosteroids

An acute exacerbation of idiopathic pulmonary fibrosis (AEIPF) is a potentially fatal complication of an already debilitating disease. Management is currently centred on delivering excellent supportive care and identifying reversible triggers. Despite growing international awareness and collaboration, no effective therapies have been identified. Corticosteroids are often the mainstay of treatment; however, the evidence base for their use is poor. Here, we review our current understanding of the disease process and how to manage it, with a focus on the role of corticosteroid therapy. Acute exacerbations of IPF cause a rapid deterioration in respiratory status and are challenging to manage. With few other options, corticosteroids are widely used as standard of care; however. the evidence to support this is poor. https://bit.ly/3gvSokN
Identification of Pathways and Key Genes in Venous Remodeling After Arteriovenous Fistula by Bioinformatics Analysis

The arteriovenous fistula (AVF) is the first choice for vascular access for hemodialysis of renal failure patients. Venous remodeling after exposure to high fistula flow is important for AVF to mature but the mechanism underlying remodeling is still unknown. The objective of this study is to identify the molecular mechanisms that contribute to venous remodeling after AVF. To screen and identify the differentially expressed genes (DEGs) that may involve venous remodeling after AVF, we used bioinformatics to download the public microarray data (GSE39488) from the Gene Expression Omnibus (GEO) and screen for DEGs. We then performed gene ontology (GO) function analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, and gene set enrichment analysis (GSEA) for the functional annotation of DEGs. The protein-protein interaction (PPI) network was constructed and the hub genes were carried out. Finally, we harvested 12 normal vein samples and 12 AVF vein samples which were used to confirm the expressions of the hub genes by immunohistochemistry. A total of 45 DEGs were detected, including 32 upregulated and 13 downregulated DEGs. The biological process (BP) of the GO analysis were enriched in the extrinsic apoptotic signaling pathway, cGMP-mediated pathway signaling, and molting cycle. The KEGG pathway analysis showed that the upregulated DEGs were enriched in glycosaminoglycan biosynthesis and purine metabolism, while the downregulated DEGs were mainly enriched in pathways of glycosaminoglycan biosynthesis, antifolate resistance, and ABC transporters. The GSEA analysis result showed that the top three involved pathways were oxidative phosphorylation, TNFA signaling via NF-K B, and the inflammatory response. The PPI was constructed and the hub genes found through the method of DMNC showed that INHBA and NR4A2 might play an important role in venous remodeling after AVF. The integrated optical density (DOI) examined by immunohistochemistry staining showed that the expression of both INHBA and NR4A2 increased in AVF compared to the control group. Our research contributes to the understanding of the molecular mechanism of venous remodeling after exposure to high fistula flow, which may be useful in treating AVF failure.
A Review of Cross-Domain Text-to-SQL Models

WikiSQL and Spider, the large-scale cross-domain text-to-SQL datasets, have attracted much attention from the research community. The leaderboards of WikiSQL and Spider show that many researchers propose their models trying to solve the text-to-SQL problem. This paper first divides the top models in these two leaderboards into two paradigms. We then present details not mentioned in their original paper by evaluating the key components, including schema linking, pretrained word embeddings, and reasoning assistance modules. Based on the analysis of these models, we want to promote understanding of the text-to-SQL field and find out some interesting future works, for example, it is worth studying the text-to-SQL problem in an environment where it is more challenging to build schema linking and also worth studying combing the advantage of each model toward text-to-SQL.
Transcranial direct current stimulation (tDCS) combined with cognitive training in adolescent boys with ADHD: a double-blind, randomised, sham-controlled trial

Abstract Background Transcranial direct current stimulation (tDCS) could be a side-effect-free alternative to psychostimulants in attention-deficit/hyperactivity disorder (ADHD). Although there is limited evidence for clinical and cognitive effects, most studies were small, single-session and stimulated left dorsolateral prefrontal cortex (dlPFC). No sham-controlled study has stimulated the right inferior frontal cortex (rIFC), which is the most consistently under-functioning region in ADHD, with multiple anodal-tDCS sessions combined with cognitive training (CT) to enhance effects. Thus, we investigated the clinical and cognitive effects of multi-session anodal-tDCS over rIFC combined with CT in double-blind, randomised, sham-controlled trial (RCT, ISRCTN48265228). Methods Fifty boys with ADHD (10–18 years) received 15 weekday sessions of anodal- or sham-tDCS over rIFC combined with CT (20 min, 1 mA). ANCOVA, adjusting for baseline measures, age and medication status, tested group differences in clinical and ADHD-relevant executive functions at posttreatment and after 6 months. Results ADHD-Rating Scale, Conners ADHD Index and adverse effects were significantly lower at post-treatment after sham relative to anodal tDCS. No other effects were significant. Conclusions This rigorous and largest RCT of tDCS in adolescent boys with ADHD found no evidence of improved ADHD symptoms or cognitive performance following multi-session anodal tDCS over rIFC combined with CT. These findings extend limited meta-analytic evidence of cognitive and clinical effects in ADHD after 1–5 tDCS sessions over mainly left dlPFC. Given that tDCS is commercially and clinically available, the findings are important as they suggest that rIFC stimulation may not be indicated as a neurotherapy for cognitive or clinical remediation for ADHD.
Training with Adversaries to Improve Faithfulness of Attention in Neural Machine Translation

Can we trust that the attention heatmaps produced by a neural machine translation (NMT) model reflect its true internal reasoning? We isolate and examine in detail the notion of faithfulness in NMT models. We provide a measure of faithfulness for NMT based on a variety of stress tests where model parameters are perturbed and measuring faithfulness based on how often the model output changes. We show that our proposed faithfulness measure for NMT models can be improved using a novel differentiable objective that rewards faithful behaviour by the model through probability divergence. Our experimental results on multiple language pairs show that our objective function is effective in increasing faithfulness and can lead to a useful analysis of NMT model behaviour and more trustworthy attention heatmaps. Our proposed objective improves faithfulness without reducing the translation quality and it also seems to have a useful regularization effect on the NMT model and can even improve translation quality in some cases.
AMesure: A Web Platform to Assist the Clear Writing of Administrative Texts

This article presents the AMesure platform, which aims to assist writers of French administrative texts in simplifying their writing. This platform includes a readability formula specialized for administrative texts and it also uses various natural language processing (NLP) tools to analyze texts and highlight a number of linguistic phenomena considered difficult to read. Finally, based on the difficulties identified, it offers pieces of advice coming from official plain language guides to users. This paper describes the different components of the system and reports an evaluation of these components.
TMU Japanese-English Multimodal Machine Translation System for WAT 2020

We introduce our TMU system submitted to the Japanese<->English Multimodal Task (constrained) for WAT 2020 (Nakazawa et al., 2020). This task aims to improve translation performance with the help of another modality (images) associated with the input sentences. In a multimodal translation task, the dataset is, by its nature, a low-resource one. Our method used herein augments the data by generating noisy translations and adding noise to existing training images. Subsequently, we pretrain a translation model on the augmented noisy data, and then fine-tune it on the clean data. We also examine the probabilistic dropping of either the textual or visual context vector in the decoder. This aims to regularize the network to make use of both features while training. The experimental results indicate that translation performance can be improved using our method of textual data augmentation with noising on the target side and probabilistic dropping of either context vector.
Automatic Classification of Students on Twitter Using Simple Profile Information

Obtaining social media demographic information using machine learning is important for efficient computational social science research. Automatic age classification has been accomplished with relative success and allows for the study of youth populations, but student classification—determining which users are currently attending an academic institution—has not been thoroughly studied. Previous work (He et al., 2016) proposes a model which utilizes 3 tweet-content features to classify users as students or non-students. This model achieves an accuracy of 84%, but is restrictive and time intensive because it requires accessing and processing many user tweets. In this study, we propose classification models which use 7 numerical features and 10 text-based features drawn from simple profile information. These profile-based features allow for faster, more accessible data collection and enable the classification of users without needing access to their tweets. Compared to previous models, our models identify students with greater accuracy; our best model obtains an accuracy of 88.1% and an F1 score of . 704. This improved student identification tool has the potential to facilitate research on topics ranging from professional networking to the impact of education on Twitter behaviors.
Investigations of impurity-free vacancy disordering in (Al)InGaAs(P)/InGaAs quantum wells

In this work, controlled band gap modifications in InGaAsP/InGaAs and AlInGaAs/InGaAs quantum well structures using different encapsulating layers are studied and compared. Photoluminescence spectroscopy was used for monitoring the changes in the optical properties of the quantum wells due to interdiffusion. X-ray photoelectron spectroscopy was used to investigate the interfacial reaction between the QW structure and dielectric capping layer. The results are compared and discussed based on the sublattices' interdiffusion, promotion or suppression under different dielectric capping layers.
Mass-Transfer Characteristics of Surface Aerators and Gas-Inducing Impellers

Liquid-side mass-transfer coefficients (kLa) were measured in surface aerators and self-inducing-type reactors. The measurements were made in 1.0- and 1.5-m-i.d. cylindrical and 8.2 × 8.2-m square tanks using physical absorption of oxygen. The effect of liquid submergence was investigated in detail. Further, the effects of the diameter of the tank, the ratio of the impeller diameter to the tank diameter, and the clearance of the impeller from the tank bottom were also studied. Three different impeller designs were investigated as surface aerators. Single and multiple impellers were employed in the case of self-inducing reactors. The power consumption was varied in the range of 30−1000 W/m3. Suitable correlations were developed for both types of reactors.
Using the unusual weak N…CO bond as a solvation probe

Most chemical (or biochemical) reactions take place in a liquid solvent. Water is the natural solvent of biochemical reactions, and is increasingly used for organic synthesis. As water is not an inert solvent, modelling such a complex environment and evaluating the solvation effects on the electronic structure of the solute is a challenge. The unusual weak bond is used here as a probe of the solvation effects. Several solvation models were tested: a continuum, 1027 TIP3P water molecules and a microsolvation model complemented by a continuum or by TIP3P molecules. First, we show that the combination of the topological analysis of the electron localisation function (ELF) and the theory of atoms in molecules (AIM) is a robust way to evaluate and rationalise the strength and the accuracy of a given solvation model. These analyses demonstrate that a polarisable continuum model (PCM) is less accurate than a quantum mechanics/molecular mechanics (QM/MM) calculation where only the probe molecule is included in the QM region. We also show that solvating the solute and its first solvation shell embedded in a PCM leads to the same polarisation effect as a costly QM/MM calculation with 30 H2O included in the QM part and approximately 1000 classical water molecules. Finally, beyond this work, we show here that the combined ELF and AIM analyses can open up new opportunities for the electronic description of environment effects, for example in dynamical calculations.
Extraction of heptavalent technetium from nuclear waste streams with 2-nitrophenyl octyl ether

Technetium-99, in the form of Tc(VII), is one of major problems in the management and disposal of nuclear waste in view of its long half-life in combination with high geochemical mobility. Solvent extraction is an important separation technique to remove 99Tc from liquid nuclear waste streams. 2-nitrophenyl octyl ether (NPOE) shows high extraction ability for Tc(VII) from water and NaOH solutions (>99.5%) in spite of the lack of donating atoms. Upon extraction from alkaline solutions, TcO4- associates with NPOE molecules in 1:1 stoichiometry where the co-extracted cation is expected to play an important role in the extraction mechanism. At pH > 4 the Tc(VII) distribution is relatively insensitive towards changes in pH, while at decreasing pH (<4) the distribution ratio decreases sharply. The strong dependency of the Tc(VII) distribution on the acidity is very useful for developing efficient extraction-stripping systems. This study showed that NPOE is an excellent compound for the removal of technetium from alkaline nuclear wastes.
Phase transitions of sea-salt/water mixtures at low temperatures: Implications for ozone chemistry in the polar marine boundary layer

We present laboratory experiments employing differential scanning calorimetry as well as flow cell microscopy to study the microphysics of aqueous NaCl and sea-salt solutions and droplets at temperatures below 273 K. The freezing and melting points of ice and other precipitates were determined in NaCl and sea-salt bulk samples as well as in emulsion samples. Using flow cell microscopy, we have determined the deliquescence and efflorescence relative humidities of NaCl and sea-salt droplets at temperatures between 249 and 273 K, extending the existing room temperature data to polar conditions. Our measurements suggest that sea-salt aerosols will most likely be liquid most of the time under polar marine boundary conditions. In addition, we show that sea-salt aerosols or seawater spray deposited on the polar ice pack will remain partly liquid down to 230 K, with concentrations of Cl− and Br− increasing by more than an order of magnitude upon cooling when compared to normal seawater concentrations. This is likely to enhance the rate at which heterogeneous bromine activation reactions occur in the sea-salt deposits. Such reaction rate enhancements with decreasing temperatures are currently not implemented in chemical models, and might help explain the fast bromine activation and subsequent ozone destruction observed during ozone depletion events in the polar marine boundary layer in spring.