Miracle-dz/UniFAR-FTUs huggingface dataset:
Transcriptional analysis in multiple barley varieties identifies signatures of waterlogging response

Waterlogging leads to major crop losses globally, particularly for waterlogging sensitive crops such as barley. Waterlogging reduces oxygen availability and results in additional stresses, leading to the activation of hypoxia and stress response pathways that promote plant survival. Although certain barley varieties have been shown to be more tolerant to waterlogging than others and some tolerance-related QTLs have been identified, the molecular mechanisms underlying this trait are mostly unknown. Transcriptomics approaches can provide very valuable information for our understanding of waterlogging tolerance. Here, we surveyed 21 barley varieties for the differential transcriptional activation of conserved hypoxia-response genes under waterlogging, and selected five varieties with different levels of induction of core hypoxia-response genes. We further characterized their phenotypic response to waterlogging in terms of shoot and root traits. RNA-sequencing to evaluate the genome-wide transcriptional responses to waterlogging of these selected varieties led to the identification of a set of 98 waterlogging-response genes common to the different datasets. Many of these genes are orthologs of the so-called ‘core hypoxia response genes’, thus highlighting the conservation of plant responses to waterlogging. Hierarchical clustering analysis also identified groups of genes with intrinsic differential expression between varieties prior to waterlogging stress. These genes could constitute interesting candidates to study ‘predisposition’ to waterlogging tolerance or sensitivity in barley.
Herpes-like viral elements and universal subtelomeric ribosomal RNA genes in a chromosome-scale thraustochytrid genome assembly

We used long-read sequencing to produce a telomere-to-telomere genome assembly for the heterotrophic stramenopile protist Aurantiochytrium limacinum MYA-1381. Its ∼62 Mbp nuclear genome comprises 26 linear chromosomes with a novel configuration: subtelomeric rDNAs are interspersed with long repeated sequence elements denoted as LOng REpeated - TElomere And Rdna Spacers (LORE-TEARS). These repeats may play a role in chromosome end maintenance. A ∼300 Kbp circular herpesvirus-like genomic element is present at a high copy number. A 269 Kbp related virus-like element was found to reside between two complete sets of rRNA and LORE-TEAR sequences on one end of chromosome 15, indicating recent recombination between the viral and nuclear genome. Our data reveal new types of giant endogenous viral elements originating from herpes-like viruses and existing as either ‘stand-alone’ or integrated elements.
HCCDB v2.0: Decompose the Expression Variations by Single-cell RNA-seq and Spatial Transcriptomics in HCC

Large-scale transcriptomic data are crucial for understanding the molecular features of hepatocellular carcinoma (HCC). By integrating 15 transcriptomic datasets of HCC clinical samples, the first version of HCCDB was released in 2018. The meta-analysis of differentially expressed genes and prognosis-related genes across multiple datasets provides a systematic view of the altered biological processes and the inter-patient heterogeneities of HCC with high reproducibility and robustness. After four years, the database needs to integrate recently published datasets. Furthermore, the latest single-cell and spatial transcriptomics provided a great opportunity to decipher the complex gene expression variations at the cellular level with spatial architecture. Here, we present HCCDB v2.0, an updated version that combines bulk, single-cell, and spatial transcriptomic data of HCC clinical samples. It dramatically expands the bulk sample size, adding 1656 new samples of 11 datasets to the existing 3917 samples, thereby enhancing the reliability of transcriptomic meta-analysis. A total of 182,832 cells and 69,352 spatial spots are added to the single-cell and spatial transcriptomics sections, respectively. A novel single-cell level and 2-dimension (sc-2D) metric was proposed to summarize the cell type-specific and dysregulated gene expression patterns. Results are all graphically visualized in our online portal, allowing users to easily retrieve data through a user-friendly interface and navigate between different views. With extensive clinical phenotypes and transcriptomic data in the database, we show two applications for identifying prognosis-associated cells and tumor microenvironment. HCCDB v2.0 is available at http://lifeome.net/database/hccdb2.
Ancestral glycoprotein hormone-receptor pathway controls growth in C. elegans

In vertebrates, thyrostimulin is a highly conserved glycoprotein hormone that, besides thyroid stimulating hormone (TSH), is a potent ligand of the TSH receptor. Thyrostimulin is considered the most ancestral glycoprotein hormone and orthologs of its subunits, GPA2 and GPB5, are widely conserved across vertebrate and invertebrate animals. Unlike TSH, however, the functions of the thyrostimulin neuroendocrine system remain largely unexplored. Here, we identify a functional thyrostimulin-like signaling system in Caenorhabditis elegans. We show that orthologs of GPA2 and GPB5, together with thyrotropin-releasing hormone (TRH) related neuropeptides, constitute a neuroendocrine pathway that promotes growth in C. elegans. GPA2/GPB5 signaling is required for normal body size and acts through activation of the glycoprotein hormone receptor ortholog FSHR-1. C. elegans GPA2 and GPB5 increase cAMP signaling by FSHR-1 in vitro. Both subunits are expressed in enteric neurons and promote growth by signaling to their receptor in glial cells and the intestine. Impaired GPA2/GPB5 signaling causes bloating of the intestinal lumen. In addition, mutants lacking thyrostimulin-like signaling show an increased defecation cycle period. Our study suggests that the thyrostimulin GPA2/GPB5 pathway is an ancient enteric neuroendocrine system that regulates intestinal function in ecdysozoans, and may ancestrally have been involved in the control of organismal growth.
Targeted genome editing in polyploids: lessons from Brassica

CRISPR-mediated genome editing has emerged as a powerful tool for creating targeted mutations in the genome for various applications, including studying gene functions, engineering resilience against biotic and abiotic stresses, and increasing yield and quality. However, its utilization is limited to model crops for which well-annotated genome sequences are available. Many crops of dietary and economic importance, such as wheat, cotton, rapeseed-mustard, and potato, are polyploids with complex genomes. Therefore, progress in these crops has been hampered due to genome complexity. Excellent work has been conducted on some species of Brassica for its improvement through genome editing. Although excellent work has been conducted on some species of Brassica for genome improvement through editing, work on polyploid crops, including U’s triangle species, holds numerous implications for improving other polyploid crops. In this review, we summarize key examples from genome editing work done on Brassica and discuss important considerations for deploying CRISPR-mediated genome editing more efficiently in other polyploid crops for improvement.
Estuarine nutrient pollution impact reduction assessment through euphotic zone avoidance/bypass considerations

The feasibility of reducing nutrient pollution impact by redirecting the effluent to depths below the euphotic zone was investigated for the deep estuarine Puget Sound region of the Salish Sea in the Pacific Northwest of America. The hypothesis tested was that the thickness of the outflow layer in deep estuaries may be greater than the euphotic zone depth, allowing a fraction of nutrients to be exported out passively through the layers immediately below. The euphotic zone depth in Puget Sound varies from 8 to 25 m while the depth of the outflow layer can reach up to ≈ 60 m. Outfall relocation strategies were tested on 99% of the anthropogenic nutrient loads currently delivered to Puget Sound. The impact was quantified using the previously established biophysical Salish Sea Model, using gross primary production and exposure to low dissolved oxygen (DO) levels as the metric (< 2 mg/L for hypoxia and < 5 mg/L for impairment). Eliminating nutrient pollution (above natural) from rivers and wastewater reduced hypoxia exposure by 8.1% and 11.2%, respectively. Relocating the outfalls to deeper waters resulted in improvements, but only in the sill-less sub-basins such as Whidbey, where hypoxia and DO impairment exposure decreased (7.9% and 6.8%, respectively). The presence of multiple sills and circulation cells in Puget Sound resulted in increased exposure and rendered nutrient bypass goals unfeasible as originally envisioned. However, an alternate nutrient export pathway was identified through bottom exchange flow out of Puget Sound via Whidbey Basin and Deception Pass. An unexpected reduction in the exchange outflow magnitude (≈ 4%) due additional (22%) freshwater discharged to the estuary bottom was also noted. The potential loss in circulation strength due to rerouting of natural surface freshwater through submerged deep-water outfalls is identified as a new unforeseen anthropogenic impact.
A review of auditory processing and cognitive change during normal ageing, and the implications for setting hearing aids for older adults

Throughout our adult lives there is a decline in peripheral hearing, auditory processing and elements of cognition that support listening ability. Audiometry provides no information about the status of auditory processing and cognition, and older adults often struggle with complex listening situations, such as speech in noise perception, even if their peripheral hearing appears normal. Hearing aids can address some aspects of peripheral hearing impairment and improve signal-to-noise ratios. However, they cannot directly enhance central processes and may introduce distortion to sound that might act to undermine listening ability. This review paper highlights the need to consider the distortion introduced by hearing aids, specifically when considering normally-ageing older adults. We focus on patients with age-related hearing loss because they represent the vast majority of the population attending audiology clinics. We believe that it is important to recognize that the combination of peripheral and central, auditory and cognitive decline make older adults some of the most complex patients seen in audiology services, so they should not be treated as “standard” despite the high prevalence of age-related hearing loss. We argue that a primary concern should be to avoid hearing aid settings that introduce distortion to speech envelope cues, which is not a new concept. The primary cause of distortion is the speed and range of change to hearing aid amplification (i.e., compression). We argue that slow-acting compression should be considered as a default for some users and that other advanced features should be reconsidered as they may also introduce distortion that some users may not be able to tolerate. We discuss how this can be incorporated into a pragmatic approach to hearing aid fitting that does not require increased loading on audiology services.
Socio-hydrological dynamics and water conflicts in the upper Huasco valley, Chile

In arid regions of north-central Chile, mining activities and agricultural land use changes lead to competing water demands, water insecurity, and related conflicts. Different local and external user groups rely on the scarce water resources. This case study investigates socio-hydrological transformations in the upper Huasco valley. It builds on a mixed method approach that combines remote sensing assessments (Corona, Landsat, Sentinel-2) with a set of social science methods including interviews and an analysis of Twitter tweets. Against the backdrop of the recent mega drought, results show that the upper Huasco valley faces adverse environmental impacts and conflicts over mining activities as well as an expansion of export-oriented agriculture. While water availability largely depends on the cryosphere, remote sensing analyses show a drastic glacier decrease in the vicinity of the mining project, where three glaciers completely disappeared since 2000. Furthermore, an expansion of the cultivated area from 2,000 ha in the 1990s to about 3,210 ha occurred in the 2000s. Agricultural expansion has come to a halt and only a slight increase of 100 ha can be detected over the last decade. Interview and social media data show local concerns and discourses on issues of water scarcity and quality related to these land use changes. The study stresses the necessity of integrative assessments for a better understanding of water scarcity and water-related conflicts. Equitable water governance in climate-sensitive areas requires contextualizing land use changes and the precarious drinking water situation from a socio-hydrological perspective.
Application and Study of Precipitation Schemes in Weather Simulation in Summer and Winter over China

Through simulation of summer and winter precipitation cases in China, the cloud precipitation schemes of model were examined. Results indicate that it is discrepant between convective precipitation simulated by the Kain-Fritsch (KF) scheme and Betts-Miller (BM) scheme in summer, the former scheme is better than the latter in this case. The ambient atmosphere may be varied by different convective schemes. The air is wetter and the updraft is stronger in the KF scheme than in the BM scheme, which can induce the more grid scale precipitation in the KF scheme, i.e., the different cumulus schemes may have the different and important effect on the grid scale precipitation. However, there is almost no convective rain in winter in northern China, so the effect of cumulus precipitation on the grid scale precipitation can be disregarded. Therefore, the gird scale precipitation is primary in the winter of northern China.
Assessment of past and future land use/cover change over Tordzie watershed in Ghana

Land use/ land cover (LULC) change has been identified as the main driving force of global change. The study investigated LULC change in Tordzie watershed in Ghana and predicted the future development. The supervised classification procedure was applied to Landsat images of 1987, 2003, and 2017. The cellular automata–Markov model embedded in IDRISI 17 software was employed to model LULC for the years 2030 and 2050. The trend of LULC change was exploited from 1987 to 2003, from 2003 to 2017, and projected to 2030 and 2050. Settlement and crop land, respectively, increased from 2.68% to 16.46% in 1987 to 3.65% and 53.47% in 2003 and finally to 20.61% and 58.52% in 2017. Vegetation cover declined from 23.2% in 1987 to 13.9% in 2003 and finally to 11.3% in 2017. The annual rate of change was determined. In 2030 and 2050, the dominant land use type will be crop land (56%). However, it decreased between 2017 and 2030 by −1.73%. The findings of the study are very relevant to land and water resource planners, policy formulators and implementers, and environmental and climate change advocates. Sustainable land use policy and its implementation are recommended. Graphical Abstract
m6A-related lncRNAs predict prognosis and indicate cell cycle in gastric cancer

Background: N6-methyladenosine (m6A) modification is a common epigenetic methylation modification of RNA, which plays an important role in gastric carcinogenesis and progression by regulating long non-coding RNA (lncRNA). This study is aimed to investigate the potential prognostic signatures of m6A -related lncRNAs in STAD. Methods: The m6A-related lncRNAs with the most significant impact on gastric cancer prognosis in the TCGA database were identified by bioinformatics and machine learning methods. The m6A-related lncRNA prognostic model (m6A-LPS) and nomogram was constructed by Cox regression analysis with the minimum absolute contraction and selection operator (LASSO) algorithm. The functional enrichment analysis of m6A-related lncRNAs was also investigated. The miRTarBase, miRDB and TargetScan databases were utilized to establish a prognosis-related network of competing endogenous RNA (ceRNA) by bioinformatics methods. The correlation of AL391152.1 expressions and cell cycle were experimentally testified by qRT-PCR and flow cytometry. Results: In total, 697 lncRNAs that were identified as m6A-related lncRNAs in GC samples. The survival analysis showed that 18 lncRNAs demonstrated prognostic values. A risk model with 11 lncRNAs was established by Lasso Cox regression, and can predict the prognosis of GC patients. Cox regression analysis and ROC curve indicated that this lncRNA prediction model was an independent risk factor for survival rates. Functional enrichment analysis and ceRNA network revealed that the nomogram was notably associated with cell cycle. qRT-PCR and flow cytometry revealed that downregulation of GC m6A-related lncRNA AL391152.1 could decrease cyclins expression in SGC7901 cells. Conclusion: A m6A-related lncRNAs prognostic model was established in this study, which can be applied to predict prognosis and cell cycle in gastric cancer.
Advances in the adsorption of heavy metal ions in water by UiO-66 composites

The innovative adsorbents known as the Metal-organic Framework (MOFs) had a high specific surface area, various structural types, and good chemical stability. MOFs have been produced through hydrothermal, mechanochemical, microwave-assisted, gelation, and other synthesis methods, and the solvothermal process is one of them that researchers frequently utilize. The UiO materials have a more comprehensive application potential than different subtypes of MOFs among the numerous MOFs that have been synthesized. The synthesis of MOFs and their composites, as well as the adsorption characteristics of UiO materials in the adsorption of various heavy metal ions, have all been examined and summarized in this study.
16S rRNA gene sequencing reveals the correlation between the gut microbiota and the susceptibility to pathological scars

The gut microbiome profile in patients with pathological scars remains rarely known, especially those patients who are susceptible to pathological scars. Previous studies demonstrated that gut microbial dysbiosis can promote the development of a series of diseases via the interaction between gut microbiota and host. The current study aimed to explore the gut microbiota of patients who are prone to suffer from pathological scars. 35 patients with pathological scars (PS group) and 40 patients with normal scars (NS group) were recruited for collection of fecal samples to sequence the 16S ribosomal RNA (16S rRNA) V3-V4 region of gut microbiota. Alpha diversity of gut microbiota showed a significant difference between NS group and PS group, and beta diversity indicated that the composition of gut microbiota in NS and PS participants was different, which implied that dysbiosis exhibits in patients who are susceptible to pathological scars. Based on phylum, genus, species levels, we demonstrated that the changing in some gut microbiota (Firmicutes; Bacteroides; Escherichia coli, etc.) may contribute to the occurrence or development of pathological scars. Moreover, the interaction network of gut microbiota in NS and PS group clearly revealed the different interaction model of each group. Our study has preliminary confirmed that dysbiosis exhibits in patients who are susceptible to pathological scars, and provide a new insight regarding the role of the gut microbiome in PS development and progression.
Seasonal patterns in the epidemiology of Bell's palsy in Hungary

Introduction Epidemiological data on Bell's palsy are vital for elucidating disease prevalence and enhancing therapeutic options. Our objective was to explore the prevalence and possible risk factors associated with Bell's palsy recurrence in the Clinical Center of the University of Debrecen service area. Secondary data analysis was performed using hospital discharge data, including patient information and comorbidities. Methods Data was obtained from the Clinical Center of the University of Debrecen, on Bell's palsy patients who were treated at the hospital between January 1, 2015 and December 31, 2021. Multiple logistic regression analysis was used to examine the factors associated with Bell's palsy recurrence. Results Of the 613 patients analyzed, 5.87% had recurrent paralysis, and the median time interval between episodes was 315 days. Hypertension was significantly associated with Bell's palsy recurrence. Moreover, seasonal distribution analysis revealed that the number of Bell's palsy episodes was higher in colder seasons, with spring and winter having a significantly higher number of episodes than summer and autumn. Discussion This study provides insights into the prevalence and associated risk factors of Bell's palsy recurrence, which could aid in its management and help reduce the long-term consequences of the disease. Further research is necessary to determine the precise mechanisms underlying these findings.
Management of keratoconus: an updated review

Keratoconus is the most common corneal ectatic disorder. It is characterized by progressive corneal thinning with resultant irregular astigmatism and myopia. Its prevalence has been estimated at 1:375 to 1:2,000 people globally, with a considerably higher rate in the younger populations. Over the past two decades, there was a paradigm shift in the management of keratoconus. The treatment has expanded significantly from conservative management (e.g., spectacles and contact lenses wear) and penetrating keratoplasty to many other therapeutic and refractive modalities, including corneal cross-linking (with various protocols/techniques), combined CXL-keratorefractive surgeries, intracorneal ring segments, anterior lamellar keratoplasty, and more recently, Bowman’s layer transplantation, stromal keratophakia, and stromal regeneration. Several recent large genome-wide association studies (GWAS) have identified important genetic mutations relevant to keratoconus, facilitating the development of potential gene therapy targeting keratoconus and halting the disease progression. In addition, attempts have been made to leverage the power of artificial intelligence-assisted algorithms in enabling earlier detection and progression prediction in keratoconus. In this review, we provide a comprehensive overview of the current and emerging treatment of keratoconus and propose a treatment algorithm for systematically guiding the management of this common clinical entity.