bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification and analysis of differentially expressed trihelix genes in maize (Zea mays) under abiotic stresses
Authors: Zhao Dongbo , Gao Fengju , Guan Peiyan , Gao Jiansheng , Guo Zhihui , Guo Jianjun , Cui Huini , Li Yongjun , Zhang Guijun , Li Zhao , Guo Lianghai 
Published: May 2023

Background
Trihelix transcription factors play important roles in triggering plant growth and imparting tolerance against biotic and abiotic stresses. However, a systematical analysis of the trihelix transcription factor family under heat and drought stresses in maize has not been reported.

Methods
PlantTFDB and TBtools were employed to identify the trihelix domain-containing genes in the maize genome. The heat-regulated transcriptome data for maize were obtained from NCBI to screen differentially expressed ZmTHs genes through statistical analysis. The basic protein sequences, chromosomal localization, and subcellular localization were analyzed using Maize GDB, Expasy, SOMPA, TBtools, and Plant-mPLoc. The conserved motifs, evolutionary relationships, and cis-elements, were analyzed by MEME, MEGA7.0 and PlantCARE software, respectively. The tissue expression patterns of ZmTHs and their expression profiles under heat and drought stress were detected using quantitative real-time PCR (qRT-PCR).

Results
A total of 44 trihelix family members were discovered, and members were distributed over 10 chromosomes in the maize genome. A total of 11 genes were identified that were regulated by heat stress; these were unevenly distributed on chromosomes 1, 2, 4, 5, and 10. ZmTHs encoded a total of 16 proteins, all of which were located in the nucleus; however, ZmTH04.1 was also distributed in the chloroplast. The protein length varied from 206 to 725 amino acids; the molecular weight ranged from 22.63 to 76.40 kD; and the theoretical isoelectric point (pI) ranged from 5.24 to 11.2. The protein’s secondary structures were mainly found to be random coils and α-helices, with fewer instances of elongation chains and β-rotations. Phylogenetic relationship analysis showed that these can be divided into five sub-groups. The conserved domain of ZmTHs was GT1 or MyB_DNA-Bind_4. The protein and gene structure of ZmTHs differed greatly among the subfamilies, while the structures within the subfamilies were similar. The promoter of ZmTHs contained abundant tissue-specific expression cis-acting elements and abiotic stress response elements. qRT-PCR analysis showed that ZmTHs expression levels were significantly different in different tissues. Furthermore, the expression of ZmTH08 was dramatically up-regulated by heat stress, while the expression of ZmTH03, ZmTH04, ZmTH05, ZmTH06, ZmTH07, ZmTH09, ZmTH10, and ZmTH11 were down-regulated by heat stress. Upon PEG-simulated drought stress, ZmTH06 was significantly up-regulated, while ZmTH01 and ZmTH07 were down-regulated.

Conclusions
We performed a genome-wide, systematic identification and analysis of differentially expressed trihelix genes under heat and drought stresses in maize.
Novel immune cell infiltration-related biomarkers in atherosclerosis diagnosis
Authors: Dong Ruoyu , Li Jikuan , Jiang Guangwei , Han Ning , Zhang Yaochao , Shi Xiaoming 
Published: May 2023

Background
Immune cell infiltration (ICI) has a close relationship with the progression of atherosclerosis (AS). Therefore, the current study was aimed to explore the role of genes related to ICI and to investigate potential mechanisms in AS.

Methods
Single-sample gene set enrichment analysis (ssGSEA) was applied to explore immune infiltration in AS and controls. Genes related to immune infitration were mined by weighted gene co-expression network analysis (WGCNA). The function of those genes were analyzed by enrichment analyses of the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO). The interactions among those genes were visualized in the protein-protein interaction (PPI) network, followed by identification of hub genes through Cytoscape software. A receiver operating characteristic (ROC) plot was generated to assess the performance of hub genes in AS diagnosis. The expressions of hub genes were measured by reverse transcription quantitative real-time PCR (RT-qPCR) in human leukemia monocyticcell line (THP-1) derived foam cells and macrophages, which mimic AS and control, respectively.

Results
We observed that the proportions of 27 immune cells were significantly elevated in AS. Subsequent integrative analyses of differential expression and WGCNA identified 99 immune cell-related differentially expressed genes (DEGs) between AS and control. Those DEGs were associated with tryptophan metabolism and extracellular matrix (ECM)-related functions. Moreover, by constructing the PPI network, we found 11 hub immune cell-related genes in AS. The expression pattern and receiver ROC analyses in two independent datasets showed that calsequestrin 2 (CASQ2), nexilin F-Actin binding protein (NEXN), matrix metallopeptidase 12 (MMP12), C-X-C motif chemokine ligand 10 (CXCL10), phospholamban (PLN), heme oxygenase 1 (HMOX1), ryanodine receptor 2 (RYR2), chitinase 3 like 1 (CHI3L1), matrix metallopeptidase 9 (MMP9), actin alpha cardiac muscle 1 (ACTC1) had good performance in distinguishing AS from control samples. Furthermore, those biomarkers were shown to be correlated with angiogenesis and immune checkpoints. In addition, we found 239 miRNAs and 47 transcription factor s (TFs), which may target those biomarkers and regulate their expressions. Finally, we found that RT-qPCR results were consistent with sequencing results.
Emotions and Language Learning Instructed Second Language Acquisition
Authors: Dewaele Jean‐Marc , Botes Elouise 
Published: January 2025

Abstract
This is an overview of applied linguistic work on four foreign language learner emotions, inspired by various branches of psychology, especially Positive Psychology. The emotions that have been selected are Foreign Language Classroom Anxiety (FLCA), Foreign Language Enjoyment (FLE), Foreign Language Boredom (FLB), and Foreign Language Peace of Mind (FLPOM). The adoption of A more holistic approach by applied linguists from 2014 has led to the inclusion of at least two emotions in the same research designs. The four emotions have generated strong responses within the applied linguistic community. They have been—and are being—investigated in a wide variety of contexts with different language combinations and learner profiles. The aim of researchers is to locate the sources and effects of these emotions in order to propose ways in which FL teachers can create a positive classroom atmosphere conducive to learning and well‐being. The four emotions selected represent different levels of valence and activation. FLE is a positive, medium‐to‐high activating emotion. FLPOM is a positive, low activating emotion originating in the Chinese cultural tradition. FLCA is a negative, medium‐to‐high activating emotion. Finally, FLB is a negative emotion with extremely low levels of activation.
Early Bilingual Education
Authors: Hickey Tina M. , Cameron‐Faulkner Thea 
Published: January 2025

Abstract
This chapter considers bilingual education in the early years, for children up to six years. The different models of one‐way and two‐way immersion education are outlined, in a variety of international contexts, and research on their outcomes is summarized. The pedagogical approaches used in early bilingual education are explored and recent developments and ongoing challenges are considered.
Grammatical Features of Hedging
Authors: Mihatsch Wiltrud 
Published: January 2025

Abstract

The terms “hedge” for types of expressions and “hedging” for their strategic communicative use encompass a variety of formal procedures and communicative functions, which, although often not easily delineated, must be clearly distinguished in analysis and application. In this entry, I will distinguish hedges operating on the propositional level, that is, approximators, from illocutionary hedges, that is, mitigators. One important link between hedges belonging to these different levels is their general metacommunicative contribution. This explains why synchronically, approximators may be employed as mitigators, and certain mitigators may also be employed as approximators. In some cases, such discourse effects may become part of the conventional meaning of an expression, leading to polysemy. This also explains why approximators and mitigators are formally highly heterogeneous and range from well‐established devices to discourse strategies. Approximators flexibilizing the interpretation of lexical items, the so‐called adaptors, tend to have narrow scope over lexical expressions and syntagms containing lexical expressions, especially nouns. Rounders, that is, approximators modifying numerals such as
roughly
, are often adverbs, which also have narrow scope. Mitigators are employed to guarantee self‐image preservation and they are linked to a series of interactional goals. Most mitigators have scope over speech acts and can occupy a variety of syntactic positions. They are often detached from the host sentence and may appear at the right or left sentence periphery. While approximators tend to be lexical or possibly grammatical items, most well‐established mitigators belong to the category of pragmatic markers.
Linear Unit Grammar—A Real‐Time Grammar
Authors: Mauranen Anna 
Published: January 2025

Abstract

The
Linear Unit Grammar
(LUG) seeks to bridge the gap between ongoing speech and conventional grammatical analysis. In other words, it closes the gap between the linearity, or temporal dynamics, of discourse and the hierarchy of grammar. It seeks to capture the listener's experience of speech segmentation and analyses this in terms of a theoretical model which can also feed into a fine‐tuned analysis by more traditional grammars. LUG consists of two main stages: (a) breaking down a stretch of discourse into intuitive chunks and (b) imposing an analytical framework on those chunks. Together, these stages result in a grammatical analysis of continuous discourse such as spontaneous speech. A fundamental assumption underpinning the model is that speech processing involves segmenting the speech we hear into meaningful units, but that these units cannot be determined beforehand in formal terms. Recently, evidence from cognitive research has shown that this is roughly what takes place in language processing. It is much like perceptual processing more generally, which consists in chunking up incoming information and processing it rapidly into more abstract representations. This corresponds to LUG's first stage. Once the chunks are discovered, for example, experimentally by asking listeners to chunk up speech they hear, the grammatical analysis can be applied to these chunks in phase two. LUG is non‐hierarchical, and by accounting for the whole speech flow, remains close to the language experience of a learner, facilitating their grasp of linguistic structure and appreciating its relevance.
Multilingualism and Attitudes
Authors: Ó Riagáin Pádraig 
Published: January 2025

Abstract
Language attitudes are defined as evaluative reactions to language, and research on the topic is spread across the social sciences. Language attitudes research has created a very large body of data which has an impressive geographical range and which has generally yielded consistent results concerning how people evaluate different language varieties and speakers of those varieties. The article presents a selective and critical account of the findings from this research. It is organized around the main methodological approaches involved—that is, experimental, ethnographic, and survey methods. The research shows that languages, dialects, and accents used within a given society can be ordered on a hierarchy of prestige, broadly corresponding to the socioeconomic status of the social groups that use them. A significant policy issue concerns the extent to which, and in what contexts, language attitudes in multilingual contexts lead to the normalization of linguistic diversity or, alternatively, to added hostility and conflicts among those in different ethnolinguistic groups. The article briefly considers some methodological shortcomings in each approach and concludes by noting some integrative developments that are likely to shape future research in this field.
Grammar and Evaluation
Authors: Hidalgo‐Downing Laura 
Published: January 2025

Abstract
Grammatical and lexical resources in a language like English are used by speakers to express evaluation, which is concerned with the expression of a speaker's attitude toward, viewpoint on or feelings about what is being talked about. Although some grammatical categories, such as modal verbs, adverbs, adjectives, and some grammatical patterns, are prototypically used to express evaluation and the related concepts of stance and appraisal, different grammars and monographs approach the relation between grammar and evaluation in different ways. This entry addresses three main issues in the study of grammar and evaluation. First, approaches to evaluation differ depending on whether they adopt a narrower approach, focusing only on modality, or a broader one, which includes attitudinal meanings as well as modality. Second, the concept of evaluation itself is subject to different interpretations; some approaches adopt the concept of “stance” as an overarching notion that includes evaluation as its actual instantiation in discourse, while other approaches use the terms “stance,” “attitude,” and “appraisal” as near synonyms of evaluation. Third, some key aspects regarding the relation between grammar and evaluation are the source of ongoing debates, such as the extent to which it is possible to distinguish between the grammatical and the lexical marking of evaluation, the extent to which evaluation is expressed explicitly or implicitly and the difficulties in identifying evaluation in discourse.
Pragmatic Markers in Dutch
Authors: Foolen Ad , van der Wouden Ton 
Published: January 2025

Abstract
Pragmatic markers (PMs) contextualize speech acts and propositional content. They can be subcategorized on the basis of syntactic and functional criteria. Three subgroups of PMs in Dutch are focused on: discourse particles, focus particles, and modal particles. In this overview, recent research is summarized, both synchronic descriptive work and diachronic, sociolinguistic, psycholinguistic, and applied linguistic studies. Desiderata for future research are pointed out. Existing research on German PMs can be of use here, because Dutch and German are rather similar in their inventory of PMs and the positions they can take in the linear structure of the sentence. At the same time, there are subtle differences between the two languages, as shown in contrastive studies on German and Dutch PMs.
Hierarchical Spin‐Polarized Nanosheet Array for Boosting Ampere‐Level Water Oxidation Under Magnetic Field
Authors: Li Haifan , Quan Quan , Dong Hongliang , Zhang Yuxuan , Xie Pengshan , Chen Dong , Yin Di , Wong Chun‐Yuen , Ho Johnny C. 
Published: January 2025

AbstractThe spin‐polarization strategy by manipulating magnetic electrocatalysts can promote the spin‐sensitive oxygen evolution reaction (OER) while developing efficient spin‐polarized materials toward ampere‐level OER is still challenging. Herein, a hierarchical inter‐doped (Ru‐Ni)Ox nanosheet array in situ grown on nickel foam is designed, which exhibits a distinguished overpotential of 286 mV at 1 A cm−2 under 0.4 T magnetic field and a steady lifespan of 200 h at the ampere current density (i.e., 1 A cm−2), outperforming most reported state‐of‐art spin‐selective OER catalysts in alkaline electrolytes Integrating intrinsic and interfacial spin‐polarization on the inter‐doped (Ru‐Ni)Ox nanosheet array can significantly boost the catalytic activity for ampere‐level OER under a magnetic field. Specifically, the spin‐aligned Ru sites optimize the rate‐determined O─O coupling step to reduce the thermodynamic barrier of OER. Meanwhile, the charge transfer kinetics is promoted due to the accelerating spin‐selective electron transfer via spin pinning at the ferromagnetic‐antiferromagnetic interface. The design of a hierarchical spin‐polarized structure that integrates intrinsic and interfacial spin‐polarization strategies provides an additional route to developing a spin‐polarized OER catalyst capable of serving ampere current densities.
Light‐Driven Ion Intercalation in Carbon Nitride for High‐Temperature‐Resilient Information Storage and Encryption
Authors: Zhang Shuai , Kong Lingqiao , Yan Bingzhen , Ma Long , Ruan Qiushi 
Published: January 2025

AbstractInformation storage and encryption systems often suffer from degradation and instability at elevated temperatures. This work introduces a robust ion‐based information storage and encryption system that demonstrates exceptional temperature resistance up to 350 °C, achieved through the immobilization of monoatomic cations (Li+, Na+, and K+) in carbon nitride via light exposure. By creating electron trap states within the carbon nitride matrix, light exposure enables photo‐charging of the material, transforming it into a capacitor capable of dynamic, reversible color changes for encoding and encrypting information. Notably, the ionic state of the material serves as the foundation for data storage, offering an inherent security feature where trapped electrons are quenched upon air exposure. This encrypted information can be reactivated through light charging. This study establishes a novel paradigm for high‐temperature information storage, using light to control ion movement with precision and security.
Constructing the Dirac Electronic Behavior Database of Under‐Stress Transition Metal Dichalcogenides for Broad Applications
Authors: Wu Xiao , Sun Mingzi , Yu Haitao , Xing Zhiguo , Kou Jiahao , Liang Shipeng , Wang Zhong Lin , Huang Bolong 
Published: January 2025

AbstractDiscovering and utilizing the unique optoelectronic properties of transition metal dichalcogenides (TMDCs) is of great significance for developing next‐generation electronic devices. In particular, research on Dirac state modulations of TMDCs under external strains is lacking. To fill this research gap, it has established a comprehensive database of 90 types of TMDCs and their response behaviors under external strains have been systematically investigated regarding the presence of Dirac cones and electronic structure evolutions. Among all the conditions, 27.3% of the TMDCs are Dirac materials with three distinct types of Dirac cones, which are mainly attributed to the electron localizations induced by external strains. TMDCs based on tellurides with 1H phase favor the formation of Dirac cones under stresses, leading to metallic‐like properties and ultra‐fast charge transportation. Correlations among Dirac cones, energy, electronic properties, and lattice structures have been revealed, offering critical references for modulating the properties of well‐known TMDCs. More importantly, it has confirmed that the phase transition points are not sufficient for the appearance of Dirac cones. This work provides critical guidance to facilitate the development of TMDCs‐based superconducting and optoelectronic devices for broad applications.
Structure‐Guided Engineering of Oleate Hydratase for the Synthesis of Small Chiral Alcohols without Decoy Molecule
Authors: Härterich Natalie , Schneider Andreas , Horz Philip , Travnicek Nicolas D. , Hauer Bernhard 
Published: January 2025

AbstractSmall and chiral secondary alcohols are sought‐after compounds that are frequently used in the synthesis of biologically active compounds. However, their stereochemically correct synthesis remains a challenge for the chemical industry. Synthetic routes are restrained by multiple steps and thus low atom efficiency. Here we employ engineered variants from the oleate hydratase from E. meningoseptica to produce chiral C5‐C8 secondary alcohols within a single step. First, we established a two‐phase system (2‐PS) to trap the volatile substrates/products which facilitated semi‐rational mutagenesis in the active site and tunnel of the enzyme. These efforts led to variants with an up to 20‐fold increase in catalytic activity and >99% ee, notably, without the use of a decoy molecule. Computational analysis indicated structural changes in the tunnel radius, ligand transport and energy profiles, which gave us hints to explain the enhanced performance of the variants. Interestingly, scaling up the reaction volume demonstrated significant increases in product concentrations, leading up to a 100‐fold increase in comparison to the current benchmark. This new 2‐PS and the engineered enzyme variants offer a promising approach for a scalable, asymmetric hydration of small unactivated alkenes, which would drastically ease the access to chiral alcohol‐based pheromones or drugs.
Expanding the Functions of KHSRP Protein: Insights into DNA G‐Quadruplex Binding
Authors: Russomanno Pasquale , Zizza Pasquale , Cerofolini Linda , D'Aria Federica , Iachettini Sara , Di Vito Serena , Biroccio Annamaria , Amato Jussara , Fragai Marco , Pagano Bruno 
Published: January 2025

AbstractKHSRP (KH‐type splicing regulatory protein) is a multifunctional nucleic acid‐binding protein that regulates various cellular processes, with critical roles in controlling gene expression. G‐quadruplexes (G4s) are noncanonical nucleic acid structures involved in essential cellular activities, including gene expression, and are recognized as potential therapeutic targets in cancer. The biological functions of G4s are mediated by proteins making their formation highly dynamic within cells. Therefore, the recognition of G4s by specific proteins is crucial for modulating physiological and pathological pathways. Given the growing interest in DNA G4s, a deeper understanding of the proteins that interact with them and their molecular recognition is imperative. This study demonstrates that KHSRP binds to these DNA structures. Biophysical analyses provide insights into the thermodynamics, kinetics, and structural aspects of these interactions, showing that G4 structural variability significantly influences KHSRP binding, in which the KH3 protein domain plays a key role. Validation of these interactions in cancer cells further highlights their biological relevance. Notably, the G4 ligand pyridostatin affects KHSRP/G4 interactions both in vitro and in cells, suggesting that small molecules can modulate this molecular recognition. These findings underscore KHSRP's potential role in regulating cellular mechanisms through binding to G4‐forming DNA, positioning it as a possible therapeutic target in cancer.