Search Results (12,706)

Background: Genetic improvement in wheat yield is the most focused research area for the breeding community to ensure sustainable production. Wheat kernel traits and biomass are considered key contributors to enhance crop yield. Methods: This study was designed to explore the genetic diversity of kernel and biomass traits in popular wheat varieties from the US Southern Great Plains using 264 doubled haploid (DH) lines mainly derived from TAM 114 or TAM 204. This population was evaluated in two field environments planted in alpha lattice design during the 2020 crop season. Kernel traits were collected using the hp Scanjet G4010 photo scanner for image capturing and GrainScan v3. software for image analysis. Biomass parameters were collected and processed manually. For genotyping genomic libraries were prepared and sequenced on Illumina NovaSeq 6000 to generate paired end reads of 150 bp. Sequences were aligned to the IWGSC RefSeq genome assembly v2.1 using the Burrows Wheeler Aligner for SNP calling. Results: A total of 59,482 polymorphic SNP markers were retained for genetic analysis after the filtration at 50% missing data and 5% minor allele frequency. To investigate the marker–trait association and the genomic regions, four genome-wide association study models were implemented using the R package GAPIT version 3.5. Based on the Bonferroni correction <8.41 × 10⁻⁷ was used as a threshold to declare marker-trait associations (MTAs) significant. The BLINK model identified 12 MTAs on chromosomes 1A, 2A, 2B, 4A, 4B, and 6B. Conclusions: The identified MTAs can be used to develop diagnostic markers for efficient selection and utilization in recombination breeding and cultivar development process. Full article

Coptis trifolia (threeleaf goldthread) offers a valuable comparative system for investigating the evolution and regulation of benzylisoquinoline alkaloid (BIA) synthesis. In this study, we analyzed the leaf and root transcriptomes of C. trifolia using both long-read and short-read RNA-Sequencing. We assembled 41,926 unigenes (≥500 bp) and identified 37 genes related to BIA biosynthesis, including two transcription factors, bHLH1 and WRKY1. The number of BIA genes identified in C. trifolia was comparable to that in other Coptis species. Transcriptome analysis revealed that most of these genes were more highly expressed in roots than leaves. Consistent with previous studies, C. trifolia contained a single (S)-stylopine synthase (SPS) gene homolog, potentially multifunctional for (S)-canadine synthase (CAS), (S)-cheilanthifoline synthase (CFS), and SPS. Transcriptome and untargeted metabolomic data indicated greater variation in root samples than leaf samples, although slightly more differentially expressed transcripts and metabolites were observed in leaves. Targeted metabolite profiling showed higher BIA accumulation in roots, with epiberberine being the most abundant, followed by coptisine, berberine, and columbamine. These results provide essential genomic resources for comparative analysis of the BIA pathway across Ranunculaceae, targeted gene function studies for metabolic bioengineering, and conservation strategies for C. trifolia, a member of an early-diverging clade within the genus with limited genetic resources. Full article

Acute respiratory infections (ARIs) continue to pose a major global health threat, particularly among vulnerable populations. These infections often present with similar clinical symptoms, complicating accurate diagnosis and facilitating unmonitored transmissions. Genomic surveillance has emerged as an invaluable tool for pathogen identification and monitoring of such infectious pathogens; however, its implementation is frequently limited by high costs. The widespread use of high-throughput sequencing during the COVID-19 pandemic has created an opportunity to repurpose existing genomic platforms for broader respiratory virus surveillance. In this study, we evaluated the feasibility of adapting the Illumina COVIDSeq assay—initially designed for SARS-CoV-2 whole-genome sequencing—for use with Influenza A/B, Respiratory Syncytial Virus (RSV), and Rhinovirus. Positive control samples were processed using two approaches for library preparation: four virus-specific multiple workflows and a combined rapid workflow. Both workflows incorporated pathogen-specific primers for amplification and followed the Illumina COVIDSeq protocol for library preparation and sequencing. Sequencing quality metrics were analysed, including Phred scores, read length distribution, and coverage depth. The study did not identify significant differences in genome coverage and genetic diversity metrics between workflows. Genome Detective consistently identified the correct species across both methods. The findings of this study demonstrate that the COVIDSeq assay can be effectively adapted for multi-pathogen genomic surveillance and that the combined rapid workflow can offer a cost- and labour-efficient alternative with minimal compromise to data quality. Full article

Objectives: The current study aimed to summarize the current evidence on vertical control provided by the bonded rapid palatal expander (BRPE) in pediatric patient populations within 6 months after expansion. Methods: Relevant studies were screened independently by two researchers from the eight databases MEDLINE (PubMed), Web of Science, SCOPUS, Embase, Cochrane, LILACS (Latin American and Caribbean Health Sciences Literature), LIVIVO and Google Scholar, and supplemented by a manual search of the reference lists from studies selected for full-manuscript reading. Relevant data from lateral cephalograms taken pre- and post-expansion was extracted. A meta-analysis was performed with RStudio and a risk of bias assessment of the included articles was completed. Results: Ten relevant studies were included for data extraction, although most had a high risk of bias. The meta-analysis revealed that within 6-month retention after BRPE treatment, there were (1) slight increases in total (0.83 mm), upper (0.57 mm), and lower (0.70 mm) facial height; (2) minimum change in the palatal plane angulation (−0.01°); (3) minimum change in the occlusal angulation (−0.04°); and (4) minimal mandibular plane angulation changes with 0.01° increase in SN-GoGn angle, 0.71° increase in SN-MP angle, 0.17° increase in FMA, and 0.82° increase in PP-GoGn angle. Conclusion: Current evidence indicates that BRPEs may not control or reduce the vertical dimension significantly within 6 months after expansion. Further high-quality studies, particularly on hyperdivergent patients, are needed to clarify whether bonded expanders offer advantages over traditional banded expanders in management of the vertical dimension. Full article

The language used by attorneys at trial could influence case outcomes, impacting fairness and wrongful convictions. At trial, attorneys choose their words to manage impressions the jury forms of the defendant, thereby influencing case outcomes. This study examines whether the abstraction and emotional valence of attorneys’ language at trial influence jurors’ decision-making. In this 2 × 2 factorial experiment, 273 online participants read an attorney’s closing statement regarding a civil case, with the emotional valence of the attorney’s descriptions being either positive or negative, and the abstraction concrete or abstract (e.g., a negative–concrete description being “the cost of removing these cancer-causing chemicals is millions of dollars” vs. the corresponding abstract description, “the cost of removing these health-hazardous chemicals is enormous”). The results revealed that attorney language abstraction and emotional valence influenced jurors’ perceptions of the case: Participants judged the defendant as more liable when exposed to negative–concrete language than positive–concrete language—a difference not present with abstract language. Findings suggest that attorneys might benefit from tailoring their language in closing arguments and that jurors’ decisions can be influenced by how information is conveyed—highlighting implications for courtroom communication and legal outcomes. Full article

The recent advancements in blockchain technology have also expanded its applications to smart agricultural fields, leading to increased research and studies in areas such as supply chain traceability systems and insurance systems. Policies and reward systems built on top of centralized systems face several problems and issues, including data integrity issues, modifications in data readings, third-party banking vulnerabilities, and central point failures. The current paper discusses how farming is becoming a leading cause of water and electricity wastage and introduces a novel idea called IncentiveChain. To keep a limit on the usage of resources in farming, we implemented an application for distributing cryptocurrency to the producers, as the farmers are responsible for the activities in farming fields. Launching incentive schemes can benefit farmers economically and attract more interest and attention. We provide a state-of-the-art architecture and design through distributed storage, which will include using edge points and various technologies affiliated with national agricultural departments and regional utility companies to make IncentiveChain practical. We successfully demonstrate the execution of the IncentiveChain application by transferring crypto-ether from utility company accounts to farmer accounts in a decentralized system application. With this system, the ether is distributed to the farmer more securely using the blockchain, which in turn removes third-party banking vulnerabilities and central, cloud, and blockchain constraints and adds data trust and authenticity. Full article

Objective: The classification of hereditary spastic paraplegia (HSP) is based on genetics, and the number of genetic loci continues to increase with new genetic descriptions. Additionally, the number of new variants in known mutations continues to increase. In this paper, we aim to report our experience with genetically confirmed HSPs. Methods: We retrospectively evaluated 10 consecutive children with genetically confirmed HSPs. Results: In this study, we identified six novel mutations, including spastic paraplegia 11 (SPG11), glucosylceramidase beta 2 (GBA2), chromosome 19 open reading frame 12 (C19orf12), 1 in each of the Cytochrome P450 family 7 subfamily B member 1 (CYP7B1) genes, and two different mutations in the intropomyosin-receptor kinase fused gene (TFG) gene. We also identified different clinical phenotypes associated with known mutations. Conclusions: Heterozygous mutations with GBA2 and SPG11 mutation-related HSP are reported for the first time, expanding the known inheritance patterns. We report a novel homozygous chromosome 19 open reading frame 12 (C19orf12) mutation resulting in iron accumulation in the brain, broadening the genetic variants and clinical findings. We determine the first Turkish patients with carnitine palmitoyltransferase IC (CPT1C) and TFG gene mutation-related pure HSP. A pure form of HSP with two novel TFG gene mutations is also identified for the first time. We report the first Turkish patient with kinase D-interacting substrate of 220 kDa (KIDINS220) gene, broadening the clinical spectrum of KIDINS220 variant-related disorders to encompass certain HSPs. Moreover, a novel variant in the oxysterol7-hydroxylase (CYP7B1) gene is reported, expanding the genetic variants and clinical findings relating to SPG5. Full article

Marine mammals are important ecological bio-indicators of marine ecosystems impacted by a plethora of anthropogenic and environmental threats. Genomics detects genetic variation, adaptation to environmental shifts, and susceptibility to diseases in marine mammal species. In this study, eDNA was utilized for the first time in the Pagasitikos Gulf over three consecutive years (2022–2024) in order to detect marine mammal species. Additionally, visual monitoring and eDNA results were compared to reveal the pros and cons of the two methodologies. The gulf was zoned into five different areas with respect to oceanographic features for sampling. DNA extraction was assessed by using a standard protocol of phenol–chloroform followed by PCR amplification using the 16S rRNA gene. A total of 5,209,613 highly filtered sequence reads were attributed to 108 species. Among these, Monachus monachus, Tursiops truncatus, and Ziphius cavirostris species were detected. This novel detection of Z. cavirostris in the relatively shallow waters of the Gulf of Pagasitikos raised the question of whether it was a random event or a new ecological trend. Z. cavirostris and M. monachus appeared to share the same marine areas within the gulf. In the era of the climate crisis, eDNA provides essential information on marine mammals’ ecological status, yields novel detections, and predicts behavioral changes essential to deep-diving species. Full article

The methylation of CpG sites with 5mC mark is a dynamic epigenetic modification. However, the relationship between the methylation and the surrounding genomic sequence context remains poorly explored. Investigation of the allele methylation provides an opportunity to decipher the interplay between differences in the primary DNA sequence and epigenetic variation. Here, we performed high-coverage long-read whole-genome direct DNA sequencing of one individual using Oxford Nanopore technology. We also used Illumina whole-genome sequencing of the parental genomes in order to identify allele-specific methylation sites with a trio-binning approach. We have compared the results of the haplotype-specific methylation detection and revealed that trio binning outperformed other approaches that do not take into account parental information. Also, we analysed the cis-regulatory effects of the genomic variations for influence on CpG methylation. To this end, we have used available Deep Learning models trained on the primary DNA sequence to score the cis-regulatory potential of the genomic loci. We evaluated the functional role of the allele-specific epigenetic changes with respect to gene expression using long-read Nanopore RNA sequencing. Our analysis revealed that the frequency of SNVs near allele-specific methylation positions is approximately four times higher compared to the biallelic methylation positions. In addition, we identified that allele-specific methylation sites are more conserved and enriched at the chromatin states corresponding to bivalent promoters and enhancers. Together, these findings suggest that significant impact on methylation can be encoded in the DNA sequence context. In order to elucidate the effect of the SNVs around sites of allele-specific methylation, we applied the Deep Learning model for detection of the cis-regulatory modules and estimated the impact that a genomic variant brings with respect to changes to the regulatory activity of a DNA loci. We revealed higher cis-regulatory impact variants near differentially methylated sites that we further coupled with transcriptomic long-read sequencing results. Our investigation also highlights technical aspects of allele methylation analysis and the impact of sequencing coverage on the accuracy of genomic phasing. In particular, increasing coverage above 30X does not lead to a significant improvement in allele-specific methylation discovery, and only the addition of trio binning information significantly improves phasing. We investigated genomic variation in a single human individual and coupled computational discovery of cis-regulatory modules with allele-specific methylation (ASM) profiling. In this proof-of-concept analysis, we observed that SNPs located near methylated CpG sites on the same haplotype were enriched for sequence features suggestive of high-impact regulatory potential. This finding—derived from one deeply sequenced genome—illustrates how phased genetic and epigenetic data analyses can jointly put forward a hypotheses about the involvement of regulatory protein machinery in shaping allele-specific epigenetic states. Our investigation provides a methodological framework and candidate loci for future studies of genomic imprinting and cis-mediated epigenetic regulation in humans. Full article

I offer a close reading of Hölderlin’s “Mnemosyne“ (“Reif sind, in Feuer getaucht…”) that situates it in terms of its links to Greek tragedy and Homer. The essay explores Hölderlin’s focus on Achilles and the death of the Greek heroes Patroklos and Ajax against the notion of “poetic transport.” I also look at Hölderlin’s 2nd Böhlendorff Letter that traffics in the relation between antiquity and modernity. The essay also offers a reading of the second stanza of “Mnemosyne” in terms of Rousseau’s essay on “The Reveries of the Solitary Walker” and its appeal to the poet. As Hölderlin pursues the tense relation between memory and death, he poses questions about ethical responsibility that challenge the human being to find a path between wallowing in too excessive grief that ends in unbounded subjectivity and affirming the sense of the other that extends beyond our own self-preoccupation. Full article

Augmented Reality (AR) continues to generate interest as a pedagogical tool in contexts where English is a Foreign Language (EFL). However, its role in developing higher-order cognitive skills, such as inferencing, remains underexplored. This exploratory, mixed-methods study investigates whether AR can scaffold inference-making in advanced EFL learners. Forty-seven university students in XX were assigned to either a control group (CG) or an experimental group (EG). Both groups read Edgar Allan Poe’s “The Tell-Tale Heart” in digital format. The CG received a conventional inference-based comprehension lesson, while the EG engaged with two interactive AR scenes developed using the Onirix Studio platform. Pre- and post-tests assessed inferential comprehension, and qualitative data were gathered through open-ended responses. While the CG demonstrated modest post-test gains and the EG showed a slight decline, neither change reached statistical significance. Notably, qualitative findings revealed that a salient AR element—a ticking clock—likely prompted misinterpretation in the EG, disrupting symbolic reasoning and contributing to schema misalignment. However, some learners exhibited metacognitive insight suggestive of productive struggle. These results suggest that AR may hold untapped potential for developing metacognitive reflection and critical literacy. Directions for future research are outlined. Full article

In advanced manufacturing, nanotechnology, and aerospace fields, the demand for precision is increasing. Driven by this demand, multi-degree-of-freedom grating encoders have become particularly crucial in high-precision displacement and angle measurement. Over the years, these encoders have evolved from one-dimensional systems to complex multi-degree-of-freedom measurement solutions that can achieve real-time synchronization. There can also be high-resolution feedback. Its structure is relatively compact, the signal output is also very stable, and the integration degree is high. This gives it a significant advantage in complex measurement tasks. Recently, there have been new developments. The functions of grating encoders in terms of principle, system architecture, error modeling, and signal processing strategies have all been expanded. For instance, accuracy can be improved by integrating multiple reading-heads, while innovative strategies such as error decoupling and robustness enhancement have further advanced system performance. This article will focus on the development of two-dimensional, three-dimensional and multi-degree-of-freedom grating encoders, exploring how the measurement degrees of freedom have evolved, and emphasizing key developments in spatial decoupling, error compensation and system integration. At the same time, it will also discuss some challenges, such as error coupling, system stability and intelligent algorithms for integrating real-time error correction. The future of grating encoders holds great potential. Their applications in precision control, semiconductor calibration, calibration systems, and next-generation intelligent manufacturing technologies can bring promising progress to both industrial and scientific fields. Full article

We present a tunable diode-laser absorption spectroscopy (TDLAS) system operating at 1.5711 µm for CO₂ gas concentration measurements. The system can operate in either a traditional direct-mode (dTDLAS) sawtooth wavelength scan or a recently demonstrated wavelength-toggled single laser differential-absorption lidar (WTSL-DIAL) mode using precompensated current pulses. The use of such precompensated pulses offsets the slow thermal constants of the diode laser, leading to fast toggling between ON and OFF-resonance wavelengths. A short measurement time is indeed pivotal for atmospheric sensing, where ambient factors, such as turbulence or mechanical vibrations, would otherwise deteriorate sensitivity, precision and accuracy. Having a system able to operate in both modes allows us to benchmark the novel experimental procedure against the well-established dTDLAS method. The theory behind the new WTSL-DIAL method is also expanded to include the periodicity of the current modulation, fundamental for the calculation of the OFF-resonance wavelength. A two-detector scheme is chosen to suppress the influence of laser intensity fluctuations in time (1/f noise), and its performance is eventually benchmarked against a one-detector approach. The main difference between dTDLAS and WTSL-DIAL, in terms of signal processing, lies in the fact that while the former requires time-consuming data processing, which limits the maximum update rate of the instrument, the latter allows for computationally simpler and faster concentration readings. To compare other performance metrics, the update rate was kept at 2 kHz for both methods. To analyze the dTDLAS data, a four-parameter Lorentzian fit was performed, where the fitting function comprised the six main neighboring absorption lines centered around 1.5711 µm. Similarly, the spectral overlap between the same lines was considered when analyzing the WTSL-DIAL data in real time. Our investigation shows that, for the studied time intervals, the WTSL-DIAL approach is 3.65 ± 0.04 times more precise; however, the dTDLAS-derived CO₂ concentration measurements are less subject to systematic errors, in particular pressure-induced ones. The experimental results are accompanied by a thorough explanation and discussion of the models used, as well as their advantages and limitations. Full article

In educational technology environments, the ability to customize digital text presentation offers opportunities to enhance learning experiences through typographical adjustments. This study investigated how digital letter spacing (LS) manipulations affect reading comprehension (RC), reading speed, calibration of comprehension (CoC), and preferences in emergent readers. We examined 163 second graders and 126 third graders as they read digital texts in Hebrew under two conditions: standard LS (100%) and increased LS (150%). The results revealed developmental differences in response to spacing manipulations: increased LS significantly improved RC in second graders, whereas it showed an opposite trend for third graders. Reading rate remained stable across conditions for both groups. Children also demonstrated more accurate CoC under their individually optimal LS condition, suggesting that their comprehension monitoring was responsive to typographical features that supported reading. Preferences analysis indicated a higher numerical proportion of participants favoring the standard LS condition over the increased LS condition in both grades. These findings imply that by integrating adaptive typographical features into educational technology, educators can enhance performance in developing readers, supporting differentiated instruction in increasingly digital learning environments. Full article

In recent years, Bionic reading has been introduced as a means to combat superficial reading and low comprehension rates. This paper investigates eye movements between participants who read a passage in standard font and an additional Bionic font passage. It was found that Bionic font does not significantly change eye movements when reading. Fixation durations, number of fixations and reading speeds were not significantly different between the two formats. Furthermore, fixations were spread throughout the word and not only on leading characters, even when using Bionic font; hence, participants were not able to “auto-complete” the words. Additionally, Bionic font did not facilitate easier processing of low-frequency or unfamiliar words. Overall, it would appear that Bionic font, in the short term, does not affect reading. Further investigation is needed to determine whether a long-term intervention with Bionic font is more meaningful than standard interventions. Full article