Miracle-dz/UniFAR-FTUs huggingface dataset:
Tracing growth patterns in cod (Gadus morhua L.) using bioenergetic modelling

Abstract Understanding individual growth in commercially exploited fish populations is key to successful stock assessment and informed ecosystem‐based fisheries management. Traditionally, growth rates in marine fish are estimated using otolith age‐readings in combination with age‐length relationships from field samples, or tag‐recapture field experiments. However, for some species, otolith‐based approaches have been proven unreliable and tag‐recapture experiments suffer from high working effort and costs as well as low recapture rates. An important alternative approach for estimating fish growth is represented by bioenergetic modelling which in addition to pure growth estimation can provide valuable insights into the processes leading to temporal growth changes resulting from environmental and related behavioural changes. We here developed an individual‐based bioenergetic model for Western Baltic cod (Gadus morhua), traditionally a commercially important fish species that however collapsed recently and likely suffers from climate change effects. Western Baltic cod is an ideal case study for bioenergetic modelling because of recently gained in‐situ process knowledge on spatial distribution and feeding behaviour based on highly resolved data on stomachs and fish distribution. Additionally, physiological processes such as gastric evacuation, consumption, net‐conversion efficiency and metabolic rates have been well studied for cod in laboratory experiments. Our model reliably reproduced seasonal growth patterns observed in the field. Importantly, our bioenergetic modelling approach implementing depth‐use patterns and food intake allowed us to explain the potentially detrimental effect summer heat periods have on the growth of Western Baltic cod that likely will increasingly occur in the future. Hence, our model simulations highlighted a potential mechanism on how warming due to climate change affects the growth of a key species that may apply for similar environments elsewhere.
The Effect of Multiple Sclerosis on Family Planning Among Saudi Families

Background Multiple sclerosis (MS) is one of the most common neurological disorders in the world, and it is the leading cause of non-traumatic disability among young adults. While genetic susceptibility plays a role in MS development, the condition is not directly hereditary. Nevertheless, MS tends to aggregate within families, with first-degree relatives of affected individuals facing a higher risk than the general population. Additionally, family planning knowledge is insufficient among MS patients. Hence, this study aimed to assess the influence of MS disease on family planning and define the factors influencing decision-making regarding family planning in multiple sclerosis patients in the Eastern province of Saudi Arabia. Methodology A prospective study was conducted in Eastern Province, Saudi Arabia, during the period of 2022-2023 through directly interviewing the patients using a pre-validated questionnaire. This study would improve counseling and future care plans regarding family planning during patients' visits. Results A total of 57 women with MS were enrolled in this study; 35 (61.4%) patients got pregnant after the onset of the disease, and 46 (97.9%) had healthy children. A total of 23 (40.4%) were previously aborted due to the disease. Only five (8.8%) diseased women experienced relapses of the disease during previous pregnancies. A total of 14 (24.6%) women reported that generally their condition improved during pregnancy and childbirth, and 12 (21.1%) had no change, while four (7%) reported that their condition generally deteriorated. Also, 15 (26.3%) had no change in their condition during the first three months after birth, while four (7%) experienced deteriorated condition. Exactly 71.2% reported that the disease mostly affected their planning for pregnancy, which was of greater extent among 24.6% and partial among 14%. Conclusion Multiple sclerosis affects women's decisions regarding family planning. The most reported causes among affected women included anxiety about weakness and lack of strength during childbirth, concern about possible side effects from MS drugs on the fetus (congenital malformations), worry about not being able to take care of a child due to illness and the severe impact of the disease on their health.
Stringent in-silico identification of putative G-protein-coupled receptors (GPCRs) of the entomopathogenic nematode Heterorhabditis bacteriophora

Abstract The infective juveniles (IJs) of entomopathogenic nematode (EPN) Heterorhabditis bacteriophora find and infect their host insects in heterogeneous soil ecosystems by sensing a universal host cue (CO2) or insect/plant-derived odorants, which bind to various sensory receptors, including G protein-coupled receptors (GPCRs). Nematode chemosensory GPCRs (NemChRs) bind to a diverse set of ligands, including odor molecules. However, there is a lack of information on the NemChRs in EPNs. Here we identified 21 GPCRs in the H. bacteriophora genome sequence in a triphasic manner, combining various transmembrane detectors and GPCR predictors based on different algorithms, and considering inherent properties of GPCRs. The pipeline was validated by reciprocal BLAST, InterProscan, GPCR-CA, and NCBI CDD search. Functional classification of predicted GPCRs using Pfam revealed the presence of four NemChRs. Additionally, GPCRs were classified into various families based on the reciprocal BLAST approach into a frizzled type, a secretin type, and 19 rhodopsin types of GPCRs. Gi/o is the most abundant kind of G-protein, having a coupling specificity to all the fetched GPCRs. As the 21 GPCRs identified are expected to play a crucial role in the host-seeking behavior, these might be targeted to develop novel insect-pest management strategies by tweaking EPN IJ behavior, or to design novel anthelminthic drugs. Our new and stringent GPCR detection pipeline may also be used to identify GPCRs from the genome sequence of other organisms.
Whole-genome and genome-wide association studies improve key agricultural traits of safflower for industrial and medicinal use

Abstract Safflower (Carthamus tinctorius) is widely cultivated around the world for its seeds and flowers. The presence of linoleic acid (LA) in its seeds and hydroxysafflor yellow A (HSYA) in its flowers are the crucial traits that enable safflower to be used for industrial and medicinal purposes. Understanding the genetic control of these traits is essential for optimizing the quality of safflower and its breeding. To further this research, we present a chromosome-scale assembly of the genome of the safflower variety ‘Chuanhonghua 1’, which was achieved using an integrated strategy combining Illumina, Oxford Nanopore, and Hi-C sequencing. We obtained a 1.17-Gb assembly with a contig N50 of 1.08 Mb, and all assembled sequences were assigned to 12 pseudochromosomes. Safflower’s evolution involved the core eudicot γ-triplication event and a whole-genome duplication event, which led to large-scale genomic rearrangements. Extensive genomic shuffling has occurred since the divergence of the ancestor of dicotyledons. We conducted metabolite and transcriptome profiles with time- and part-dependent changes and screened candidate genes that significantly contribute to seed lipid biosynthesis. We also analyzed key gene families that participate in LA and HSYA biosynthesis. Additionally, we re-sequenced 220 safflower lines and carried out a genome-wide association study using high-quality SNP data for eight agronomic traits. We identified SNPs related to important traits in safflower. Besides, the candidate gene HH_034464 (CtCGT1) was shown to be involved in the biosynthesis of HSYA. Overall, we provide a high-quality reference genome and elucidate the genetic basis of LA and HSYA biosynthesis in safflower. This vast amount of data will benefit further research for functional gene mining and breeding in safflower.
Crinoid Anchoring Strategies for Soft-Bottom Dwelling

Abstract During the geologic history of crinoids, many groups have modified their distal stems to function as anchors in soft sediments, but more so in the Paleozoic than in later times. Major strategies were passively implanting anchors, cirral root systems, coils, and stemless reclining. In Paleozoic roots, the stereom usually consists of crystallographically individualized ossicles, but articulations may be hidden by a tough cuticle that protected the living tissue of immersed parts and stiffened them with cortical stereom. Post-Paleozoic representatives produced similar anchoring structures by different fabricational pathways, including non-articulated root systems.
The effects of anxiety on taste perception: The role of awareness

Prior research indicate that emotional states can alter taste perception, but the underlying mechanisms remain unclear. This study explores whether taste perception changes due to the mere evocation of emotions or the cognitive awareness of emotions. The first experiment investigated how anxiety affects taste perception when individuals are aware of their anxiety. Participants watched videos inducing relaxation or anxiety, then were divided into groups focusing on their emotions and those who did not, and the taste perception was measure. The second experiment investigated the influence of awareness directed toward emotions on taste evaluation, without manipulating emotional states. This focused on cognitive processing of taste through evaluations of visual stimuli. Results showed that sweetness perception is suppressed by the evocation of anxiety, whereas bitterness perception is enhanced only by anxiety with awareness. These findings indicate that the mechanisms by which emotional states affect taste perception may differ depending on taste quality.
Dissecting genomic regions and underlying sheath blight resistance traits in rice ( Oryza sativa L.) using a genome‐wide association study

Abstract The productivity of rice is greatly affected by the infection of the plant pathogenic fungus Rhizoctonia solani, which causes a significant grain yield reduction globally. There exist a limited number of rice accessions that are available to develop sheath blight resistance (ShB). Our objective was to identify a good source of the ShB resistance, understand the heritability, and trait interactions, and identify the genomic regions for ShB resistance traits by genome‐wide association studies (GWAS). In the present study, a set of 330 traditional landraces and improved rice varieties were evaluated for ShB resistance and created a core panel of 192 accessions used in the GWAS. This panel provides a more considerable amount of genetic variance and found a significant phenotypic variation among the panel of rice accessions for all the agro‐morphological and disease‐resistance traits over the seasons. The infection rate of ShB and disease reaction were calculated as percent disease index (PDI) and area under the disease progress curve (AUDPC). The correlation analysis showed a significant positive association between PDIs and AUPDC and a negative association between PDI and plant height, flag leaf length, and grain yield. The panel was genotyped with 133 SSR microsatellite markers, resulting in a genome coverage of 314.83 Mb, and the average distance between markers is 2.53 Mb. By employing GLM and MLM (Q + K) models, 30 marker–trait associations (MTAs) were identified with targeted traits over the seasons. Among these QTLs, eight were found to be novel and located on 2, 4, 8, 10, and 12 chromosomes, which explained the phenotypic variation ranging from 5% to 15%. With the GWAS approach, six candidate genes were identified. Os05t0566400, Os08t0155900, and Os09t0567300 were found to be associated with defense mechanisms against ShB. These findings provided insights into the novel donors of IC283139, IC 277248, Sivappuchithirai Kar, and Bowalia. The promising genomic regions on 10 of 12 chromosomes associated with ShB would be useful in developing rice varieties with durable disease resistance.
Genome-Wide Identiﬁcation and Analysis of the ABCF Gene Family in Triticum aestivum

: The ATP-binding cassette (ABC) superfamily of proteins is a group of evolutionarily conserved proteins. The ABCF subfamily is involved in ribosomal synthesis, antibiotic resistance, and transcriptional regulation. However, few studies have investigated the role of ABCF in wheat ( Triticum aestivum ) immunity. Here, we identiﬁed 18 TaABCF s and classiﬁed them into four categories based on their domain characteristics. Functional similarity between Arabidopsis and wheat ABCF genes was predicted using phylogenetic analysis. A comprehensive genome-wide analysis of gene structure, protein motifs, chromosomal location, and cis-acting elements was also performed. Tissue-speciﬁc analysis and expression proﬁling under temperature, hormonal, and viral stresses were performed using real-time quantitative reverse transcription polymerase chain reaction after randomly selecting one gene from each group. The results revealed that all TaABCF genes had the highest expression at 25 ◦ C and responded to methyl jasmonate induction. Notably, TaABCF2 was highly expressed in all tissues except the roots, and silencing it signiﬁcantly increased the accumulation of Chinese wheat mosaic virus or wheat yellow mosaic virus in wheat leaves. These results indicated that TaABCF may function in response to viral infection, laying the foundation for further studies on the mechanisms of this protein family in plant defence.
Blueberry and cranberry pangenomes as a resource for future genetic studies and breeding efforts

Abstract Domestication of cranberry and blueberry began in the United States in the early 1800s and 1900s, respectively, and in part owing to their flavors and health-promoting benefits are now cultivated and consumed worldwide. The industry continues to face a wide variety of production challenges (e.g. disease pressures), as well as a demand for higher-yielding cultivars with improved fruit quality characteristics. Unfortunately, molecular tools to help guide breeding efforts for these species have been relatively limited compared with those for other high-value crops. Here, we describe the construction and analysis of the first pangenome for both blueberry and cranberry. Our analysis of these pangenomes revealed both crops exhibit great genetic diversity, including the presence–absence variation of 48.4% genes in highbush blueberry and 47.0% genes in cranberry. Auxiliary genes, those not shared by all cultivars, are significantly enriched with molecular functions associated with disease resistance and the biosynthesis of specialized metabolites, including compounds previously associated with improving fruit quality traits. The discovery of thousands of genes, not present in the previous reference genomes for blueberry and cranberry, will serve as the basis of future research and as potential targets for future breeding efforts. The pangenome, as a multiple-sequence alignment, as well as individual annotated genomes, are publicly available for analysis on the Genome Database for Vaccinium—a curated and integrated web-based relational database. Lastly, the core-gene predictions from the pangenomes will serve useful to develop a community genotyping platform to guide future molecular breeding efforts across the family.
Benefit of perioperative radiotherapy for hepatocellular carcinoma: a quality-based systematic review and meta-analysis

Introduction: Although surgery is the standard curative modality for hepatocellular carcinoma, more than two-thirds experience intrahepatic recurrence. Since no standard perioperative treatment has been established, the authors performed a meta-analysis to evaluate the benefits of perioperative radiotherapy (RT). Methods: The PubMed, MEDLINE, EMBASE, and Cochrane Library were searched until May 2023. Randomized or propensity-matched studies evaluating at least five major clinical factors investigating benefit of perioperative RT, were included. The main effect measure were the pooled odds ratios (OR) regarding the benefit of perioperative RT using 2-year overall survival (OS) and 1-year disease-free survival (DFS) data. Results: Seven studies (five randomized and two propensity-matched studies) involving 815 patients were included. The pooled ORs for 1-year DFS and 2-year OS were 0.359 (95% CI: 0.246–0.523) and 0.371 (95% CI: 0.293–0.576), respectively, favoring perioperative RT, with very low heterogeneity. In the subgroup analyses, the benefits of OS and DFS were consistent between the two subgroups [portal vein thrombosis (PVT) and narrow resection margin (RM) groups]. In the PVT subgroup, the pooled OS rates at both 1-year and 2-year (75.6 vs. 36.9%, P<0.001; 25.6 vs. 9.9%, P=0.004) and DFS rates at both 1-year and 2-year (25.2 vs. 10.3%, P=0.194; 11.9 vs. 3.0%, P=0.022) were higher in the perioperative RT group. In the narrow RM subgroup, the surgery and RT groups showed higher pooled OS rates for both 1-year and 2-year (97.3 vs. 91.9%, P=0.042; 90.4 vs. 78.7%, P=0.051) and DFS (88.1 vs. 72.6%, P<0.001; 70.1 vs. 51.7%, P<0.001). Grade 5 toxicity was not reported, and three studies reported grade ≥3 or higher liver function test abnormalities, ranging from 4.8–19.2%. Conclusion: The present study supports the oncological benefits of perioperative RT, for cases with high-risk of recurrence. Oncologic outcomes between subgroups differed according to clinical indications.
Comparison of perioperative outcomes of selective arterial clipping guided by near-infrared fluorescence imaging using indocyanine green versus undergoing standard robotic-assisted partial nephrectomy: a systematic review and meta-analysis

Background: This study employs a meta-analytic approach to investigate the impact of robotic-assisted partial nephrectomy, with and without near-infrared fluorescence imaging (NIRF-RAPN vs S-RAPN), on patients’ perioperative outcomes and postoperative changes in renal function. Materials and methods: The authors conducted a comprehensive and rigorous systematic review and cumulative meta-analysis of primary outcomes following the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses), AMSTAR (Assessing the Methodological Quality of Systematic Reviews) Guidelines, and Risk-of-Bias Tool (RoB2). To ensure a thorough search, the authors systematically searched five major databases, including Medline, PubMed, Cochrane Library, Scopus, and Web of Science, from databases’ inception to April 2023. Results: No significant differences were found between the two groups in terms of age (P=0.19), right side (P=0.54), BMI (P=0.39), complexity score (P=0.89), tumor size (P=0.88), operating time (P=0.39), estimated blood loss (P=0.47), length of stay (P=0.87), complications (P=0.20), transfusion (P=0.36), and positive margins (P=0.38). However, it is noteworthy that the NIRF-RAPN group exhibited significant reductions in warm ischemia time (P=0.001), the percentage change in estimated glomerular filtration rate at discharge (P=0.01) compared to the S-RAPN group. Conclusion: This meta-analysis provides evidence that the group undergoing NIRF-RAPN showed a statistically significant protective effect on the estimated glomerular filtration rate (eGFR).
GproteinDb in 2024: new G protein-GPCR couplings, AlphaFold2-multimer models and interface interactions

Abstract G proteins are the major signal proteins of ∼800 receptors for medicines, hormones, neurotransmitters, tastants and odorants. GproteinDb offers integrated genomic, structural, and pharmacological data and tools for analysis, visualization and experiment design. Here, we present the first major update of GproteinDb greatly expanding its coupling data and structural templates, adding AlphaFold2 structure models of GPCR–G protein complexes and advancing the interactive analysis tools for their interfaces underlying coupling selectivity. We present insights on coupling agreement across datasets and parameters, including constitutive activity, agonist-induced activity and kinetics. GproteinDb is accessible at https://gproteindb.org.
A longitudinal prospective study of septoplasty impact on headache and allergic rhinitis in patients with septal deviation

Objective To measure the severity of allergic rhinitis (AR) and different types of headaches in patients with septal deviation before and after septoplasty. Methods This multicentre, prospective, longitudinal, observational study enrolled patients with deviated nasal septum, nasal symptoms and headaches associated with persistent AR lasting at least 2 months without resolution. The nasal obstruction evaluation (NOSE) scale, immunoglobulin-E (Ig-E) levels and visual analogue scale (VAS) for headache pain severity were evaluated before and after septoplasty using Wilcoxon signed-rank test. Results A total of 196 patients were enrolled in the study (102 males; 94 females). A total of 134 patients (68%) were diagnosed with severe AR and 166 (85%) experienced headaches with AR. The majority (100 of 166 patients; 60%) had sinusoidal headaches, while 25% (42 of 166 patients) reported a combination of sinusoidal headache and migraine and 14% (24 of 166 patients) experienced migraines. A comparison of preoperative and postoperative Ig-E levels, NOSE and VAS scores demonstrated that septoplasty significantly improved AR symptoms and headaches. Although there were significant improvements in headaches overall post-septoplasty, only the sinusoidal components improved, while migraine remained unaffected. Conclusion Septoplasty improved AR and sinusoidal headaches in patients with septal deviation, but migraines remained unaffected.