Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome-wide characterization of the PP2C gene family in peanut (Arachis hypogaea L.) and the identification of candidate genes involved in salinity-stress response

Plant protein phosphatase 2C (PP2C) play important roles in response to salt stress by influencing metabolic processes, hormone levels, growth factors, etc. Members of the PP2C family have been identified in many plant species. However, they are rarely reported in peanut. In this study, 178 PP2C genes were identified in peanut, which were unevenly distributed across the 20 chromosomes, with segmental duplication in 78 gene pairs. AhPP2Cs could be divided into 10 clades (A-J) by phylogenetic analysis. AhPP2Cs had experienced segmental duplications and strong purifying selection pressure. 22 miRNAs from 14 different families were identified, targeting 57 AhPP2C genes. Gene structures and motifs analysis exhibited PP2Cs in subclades AI and AII had high structural and functional similarities. Phosphorylation sites of AhPP2C45/59/134/150/35/121 were predicted in motifs 2 and 4, which located within the catalytic site at the C-terminus. We discovered multiple MYB binding factors and ABA response elements in the promoter regions of the six genes (AhPP2C45/59/134/150/35/121) by cis-elements analysis. GO and KEGG enrichment analysis confirmed AhPP2C-A genes in protein binding, signal transduction, protein modification process response to abiotic stimulus through environmental information processing. Based on RNA-Seq data of 22 peanut tissues, clade A AhPP2Cs showed a varying degree of tissue specificity, of which, AhPP2C35 and AhPP2C121 specifically expressed in seeds, while AhPP2C45/59/134/150 expressed in leaves and roots. qRT-PCR indicated that AhPP2C45 and AhPP2C134 displayed significantly up-regulated expression in response to salt stress. These results indicated that AhPP2C45 and AhPP2C134 could be candidate PP2Cs conferring salt tolerance. These results provide further insights into the peanut PP2C gene family and indicate PP2Cs potentially involved in the response to salt stress, which can now be further investigated in peanut breeding efforts to obtain cultivars with improved salt tolerance.
Outcomes of feeding activity of the sea cucumber Holothuria tubulosa on quantity, biochemical composition, and nutritional quality of sedimentary organic matter

Introduction Holothuria tubulosa is one of the most common sea cucumbers in the Mediterranean Sea, generally associated with organically enriched coastal sediments and seagrass beds. As a deposit-feeder, it is responsible for strong bioturbation processes and plays a putative key role in sedimentary carbon cycling and benthic trophodynamics. With the aim of exploring the potential use of holothuroids as a tool for remediating eutrophicated sediments, we investigated the effects of H. tubulosa on sedimentary organic matter quantity, biochemical composition, and nutritional quality. Methods Holothuroids and associated samples of ambient sediments were collected in two sites located in the Central-Western Mediterranean Sea (Sardinia, Italy) and characterized by different trophic status backgrounds: the site of Oristano characterized by sandy-muddy sediments and the presence of mariculture plants (ranked as meso-eutrophic) and the site of Teulada characterized by sandy sediments and Posidonia oceanica meadows (ranked as oligo-mesotrophic). We compared the biochemical composition (proteins, carbohydrates, lipids) of ambient sediment vs sea cucumbers feces and the sedimentary protein content vs protein content in the sediments retrieved in different gut sections (esophagus, mid gut, end gut) of the holothuroid. Results Our results reveal that holothuroids feeding on meso-eutrophic sediments can increase protein (1.5 times) and lipid (1.3 times) content through their defecation, thus making these substrates a more labile food source for other benthic organisms. We report here that H. tubulosa feeding on meso-eutrophic sediment is most likely able to actively select particles rich in labile organic matter with buccal tentacles, as revealed by the protein content in the esophagus that is up to 2-folds higher than that in the source sediment. According to the inverse relationship between assimilation rates and availability of organic substrates and the optimal foraging theory, H. tubulosa feeding on oligo-mesotrophic sediments showed potential assimilation of proteins ca. 25% higher than that of specimens feeding on meso-eutrophic sediments. Discussion Our results reveal that H. tubulosa feeding on meso-eutrophic sediments can profoundly influence the benthic trophic status, specifically modifying the biochemical composition and nutritional quality of organic matter, thus paving the way to its possible use in bioremediation actions of eutrophicated sediments and in Integrated Multi-Trophic Aquaculture systems.
Analysis of Microstrip Dipole Antennas on a Layered Metamaterial Substrate

A numerical method is developed to analyze microstrip dipole antennas on a planar layered metamaterial substrate based on periodic "method of moments" (MoM). In the developed numerical method the spectral domain Green function in conjunction with the "array scanning method" (ASM) is applied. The substrate is made of planar periodic metallic patches inserted in a two layer grounded dielectric slab. Effects of metamaterial loading on input impedance of dipole antennas is investigated using the developed numerical method. It is shown that with metamaterial loading antenna miniaturization is achieved.
Diagnostic and prognostic value of serum S100B in sepsis-associated encephalopathy: A systematic review and meta-analysis

Background In sepsis, brain dysfunction is known as Sepsis-associated encephalopathy (SAE), which often results in severe cognitive and neurological sequelae and increases the risk of death. Our systematic review and meta-analysis aimed to explore the diagnostic and prognostic value of serum S100 calcium-binding protein B (S100B) in SAE patients. Methods We conducted a systematic search of the databases PubMed, Web of Science, Embase, Cochrane databases, CNKI, VIP, and WFSD from their inception dates until August 20, 2022. A Meta-analysis of the included studies was also performed using Review Manager version 5.4 and Stata16.0. Results This meta-analysis included 28 studies with 1401 serum samples from SAE patients and 1591 serum samples from no-encephalopathy septic (NE) patients. The Meta-Analysis showed that individuals with SAE had higher serum S100B level than NE controls (MD, 0.49 [95% CI (0.37)-(0.60), Z =8.29, P < 0.00001]), and the baseline level of serum S100B in septic patients with burn was significantly higher than average (1.96 [95% CI (0.92)-(2.99), Z =3.71, P < 0.0002]) In addition, septic patients with favorable outcomes had lower serum S100B levels than those with unfavorable outcomes (MD, -0.35 [95% CI (-0.50)-(-0.20), Z =4.60, P < 0.00001]). Conclusion Our Meta-Analysis indicates that higher serum S100B level in septic patients are moderately associated with SAE and unfavorable outcomes (The outcomes here mainly refer to the mortality). The serum S100B level may be a useful diagnostic and prognostic biomarker of SAE.
Periodic health checkups reduce the risk of hospitalization in patients with type 2 diabetes

Introduction Periodic health checkups (PHCs) represent a unique system in Japan that is useful for the early detection of lifestyle-related diseases and cardiovascular diseases (CVDs). This study aims to investigate the association of PHCs with the hospitalization risk of patients with type 2 diabetes mellitus (T2DM). Methods A retrospective cohort study was conducted from April 2013 to December 2015 and included participant information such as CVD history, lifestyle, and whether PHC was conducted in addition to regular medical examinations. Difference in clinical data between patients with and without PHC was examined. Furthermore, Cox regression analysis was performed to investigate the independent association of PHCs with hospitalization. Results Herein, 1,256 patients were selected and followed up for 2.35 ± 0.73 years. In the PHC group, body mass index, waist circumference, proportion of patients with a history of CVD, and number of hospitalizations were lower than those in the non-PHC group. Furthermore, the PHC group exhibited a significant association with lower hospitalization risk (hazard ratio = 0.825; 95% confidence interval, 0.684 to 0.997; p = 0.046) in the Cox model. Conclusion This study revealed that PHCs minimized the risk of hospitalization in patients with T2DM. Furthermore, we discussed the effectiveness of PHCs in enhancing health outcomes and reducing health care costs in such patients.
Rhamnogalacturonan-I as a nematode chemoattractant from Lotus corniculatus L. super-growing root culture

Introduction The soil houses a tremendous amount of micro-organisms, many of which are plant parasites and pathogens by feeding off plant roots for sustenance. Such root pathogens and parasites often rely on plant-secreted signaling molecules in the rhizosphere as host guidance cues. Here we describe the isolation and characterization of a chemoattractant of plant-parasitic root-knot nematodes (Meloidogyne incognita, RKN). Methods The Super-growing Root (SR) culture, consisting of excised roots from the legume species Lotus corniculatus L. , was found to strongly attract infective RKN juveniles and actively secrete chemoattractants into the liquid culture media. The chemo-attractant in the culture media supernatant was purified using hydrophobicity and anion exchange chromatography, and found to be enriched in carbohydrates. Results Monosaccharide analyses suggest the chemo-attractant contains a wide array of sugars, but is enriched in arabinose, galactose and galacturonic acid. This purified chemoattractant was shown to contain pectin, specifically anti-rhamnogalacturonan-I and anti-arabinogalactan protein epitopes but not anti-homogalacturonan epitopes. More importantly, the arabinose and galactose sidechain groups were found to be essential for RKN-attracting activities. This chemo-attractant appears to be specific to M. incognita, as it wasn’t effective in attracting other Meloidogyne species nor Caenorhabditis elegans. Discussion This is the first report to identify the nematode attractant purified from root exudate of L corniculatus L. Our findings re-enforce pectic carbohydrates as important chemicals mediating micro-organism chemotaxis in the soil, and also highlight the unexpected utilities of the SR culture system in root pathogen research.
Inhibition of specific signaling pathways rather than epigenetic silencing of effector genes is the leading mechanism of innate tolerance

Introduction Macrophages activated through a pattern-recognition receptor (PRR) enter a transient state of tolerance characterized by diminished responsiveness to restimulation of the same receptor. Signaling-based and epigenetic mechanisms are invoked to explain this innate tolerance. However, these two groups of mechanisms should result in different outcomes. The epigenetic scenario (silencing of effector genes) predicts that activation of a PRR should broadly cross-tolerize to agonists of unrelated PRRs, whereas in the signaling-based scenario (inhibition of signaling pathways downstream of specific PRRs), cross-tolerization should occur only between agonists utilizing the same PRR and/or signaling pathway. Also, the so-called non-tolerizeable genes have been described, which acquire distinct epigenetic marks and increased responsiveness to rechallenge with the same agonist. The existence of such genes is well explained by epigenetic mechanisms but difficult to explain solely by signaling mechanisms. Methods To evaluate contribution of signaling and epigenetic mechanisms to innate tolerance, we tolerized human macrophages with agonists of TLR4 or NOD1 receptors, which signal via distinct pathways, and assessed responses of tolerized cells to homologous restimulation and to cross-stimulation using different signaling, metabolic and transcriptomic read-outs. We developed a transcriptomics-based approach to distinguish responses to secondary stimulation from continuing responses to primary stimulation. Results We found that macrophages tolerized with a NOD1 agonist lack responses to homologous restimulation, whereas LPS-tolerized macrophages partially retain the ability to activate NF-κB pathway upon LPS rechallenge, which allows to sustain low-level expression of a subset of pro-inflammatory genes. Contributing to LPS tolerance is blockade of signaling pathways required for IFN-β production, resulting in ‘pseudo-tolerization’ of IFN-regulated genes. Many genes in NOD1- or TLR4-tolerized macrophages are upregulated as the result of primary stimulation (due to continuing transcription and/or high mRNA stability), but do not respond to homologous restimulation. Hyperresponsiveness of genes to homologous rechallenge is a rare and inconsistent phenomenon. However, most genes that have become unresponsive to homologous stimuli show unchanged or elevated responses to agonists of PRRs signaling via distinct pathways. Discussion Thus, inhibition of specific signaling pathways rather than epigenetic silencing is the dominant mechanism of innate tolerance.
Genetic diversity and structure of the 4th cycle breeding population of Chinese fir (Cunninghamia lanceolata (lamb.) hook)

Studying population genetic structure and diversity is crucial for the marker-assisted selection and breeding of coniferous tree species. In this study, using RAD-seq technology, we developed 343,644 high-quality single nucleotide polymorphism (SNP) markers to resolve the genetic diversity and population genetic structure of 233 Chinese fir selected individuals from the 4th cycle breeding program, representing different breeding generations and provenances. The genetic diversity of the 4th cycle breeding population was high with nucleotide diversity (Pi ) of 0.003, and Ho and He of 0.215 and 0.233, respectively, indicating that the breeding population has a broad genetic base. The genetic differentiation level between the different breeding generations and different provenances was low (Fst < 0.05), with population structure analysis results dividing the 233 individuals into four subgroups. Each subgroup has a mixed branch with interpenetration and weak population structure, which might be related to breeding rather than provenance, with aggregation from the same source only being in the local branches. Our results provide a reference for further research on the marker-assisted selective breeding of Chinese fir and other coniferous trees.
Corneal dendritic cells in diabetes mellitus: A narrative review

Diabetes mellitus is a global public health problem with both macrovascular and microvascular complications, such as diabetic corneal neuropathy (DCN). Using in-vivo confocal microscopy, corneal nerve changes in DCN patients can be examined. Additionally, changes in the morphology and quantity of corneal dendritic cells (DCs) in diabetic corneas have also been observed. DCs are bone marrow-derived antigen-presenting cells that serve both immunological and non-immunological roles in human corneas. However, the role and pathogenesis of corneal DC in diabetic corneas have not been well understood. In this article, we provide a comprehensive review of both animal and clinical studies that report changes in DCs, including the DC density, maturation stages, as well as relationships between the corneal DCs, corneal nerves, and corneal epithelium, in diabetic corneas. We have also discussed the associations between the changes in corneal DCs and various clinical or imaging parameters, including age, corneal nerve status, and blood metabolic parameters. Such information would provide valuable insight into the development of diagnostic, preventive, and therapeutic strategies for DM-associated ocular surface complications.
S-wave velocity characteristics and mineralization of the southern tibet detachment system-yalaxiangbo dome

A series of extensional structures, including the southern Tibet detachment system (STDS), the north-south trending rifts (NSTR), and the northern Himalayan gneiss dome (NHGD), developed from the collision and compression between the Indian and Eurasian plates. These tectonic movements were accompanied by magmatism and polymetallic mineralization. Cuona Rift (CR) is located on the STDS next to the Yalaxiangbo Dome (YD) and passes through the Zhegucuo-longzi fault (ZLF), the Lhozhag fault (LZF), the Rongbu-Gudui fault (RGF), the Cuonadong dome (CD), and the YD. The study area contains numerous metal deposits, such as rare metal ore, lead zinc ore, gold deposits, and two geothermal fields, i.e., the Cuona geothermal field (CGF) and the Gudui geothermal field (GGF). Current research on the geological structures from the STDS to the YD is mainly based on magnetotelluric and natural seismic imaging. These surveys have a low resolution, making it impossible to image the shallow crust in detail. This study obtained about a 112 km S-wave velocity profile from the STDS to the YD using the multichannel surface wave imaging method. The profile results indicated that the average thickness of the sedimentary layer from the STDS to the YD is 400–500 m, while it is more than 800 m at certain fault zones. The CD is connected to the high-velocity body below the Zhaxikang ore concentration area (ZOCA) and may have the same provenance. The thermal conductivity reveals that the CGF, the GGF, and the ZOCA have high values and a more intense thermal radiation capacity. This drives the migration and circulation of the thermal fluids in the CGF and the GGF, causing them to continuously transmit heat to the shallow surface along the fault system. The migration of the thermal fluids extracts useful elements from the geological bodies through which it flows. When these elements mix with the atmospheric infiltration water, it precipitates to form the Zhaxikang hydrothermal superimposed transformation type lead-zinc polymetallic deposit.
Detailed genetic and clinical analysis of a novel de novo variant in HPRT1: Case report of a female patient from Saudi Arabia with Lesch–Nyhan syndrome

Background: Hypoxanthine-guanine phosphoribosyltransferase (HPRT1) deficiency is an inborn error of purine metabolism responsible for Lesch–Nyhan syndrome (LNS). The disease is inherited in an X-linked recessive manner and predominantly affects male individuals. Female individuals can carry a mutation as heterozygotes, but typically, they are asymptomatic because of the random inactivation of the affected allele. Nevertheless, although rare, heterozygote female individuals may manifest LNS with full characteristics. Herein, we describe a female patient from Saudi Arabia with LNS. Results: The patient (a 4-year-old girl) presented with typical characteristics of the disease, which include global developmental delay, self-mutilation, hyperuricemia, hypotonia, speech delay, spasticity, and seizures. Her general biochemical laboratory results were normal except for high levels of uric acid. The abdominal MRI\MRS, mostly unremarkable, showed bilateral echogenic foci within the renal collecting system. Genetic testing (whole-exome sequencing, iterative variant filtering, segregation analysis, and Sanger sequencing) pointed a novel de novo frameshift variant in HPRT1. X-inactivation assay using HpaII showed the presence of a 100% skewed X chromosome carrying the affected allele. RT-PCR of the cDNA indicated complete loss of the expression of the normal allele. Conclusion: Our study presents a female patient who has a severe case of LNSand found to be the 15th female patient with the disease in the world. The study emphasizethe need for a streamlined protocol that will help an early and accurate diagnosis of female LNS patients to avoid unnecessary interventions that lead to costly patient care.
‘Looking before and after’: Can simple eye tracking patterns distinguish poetic from prosaic texts?

Introduction The study of ‘serious’ literature has recently developed into an emerging field called neurocognitive poetics that applies cognitive neuroscientific techniques to examine how we understand and appreciate poetry. The current research used eye-tracking techniques on a small sample of young adults to see if and how the reading of short pieces of poetry differed from the reading of matched prosaic texts. Methods With ‘proof of concept’ intentions reflecting arguments first proposed by 19th Century literary figures, there was a particular focus on the differences between the reading of poetry and prose in terms number and frequency of fixations and regressive eye movements back and forth within the texts in this two-by-two experimental design (poetry vs. prose x need vs. no need for final line reappraisal). Results It was found that poetic pieces compared to prosaic pieces were associated with more and longer fixations and more regressive eye movements throughout the text. The need to reappraise meaning at the prompt of a final line was only significantly associated with more regressive eye movements. Comparisons examining the 4 text conditions (poetic reappraisal, poetic non-reappraisal, prosaic reappraisal, and prosaic non-reappraisal) showed that the poetic reappraisal condition was characterised by significantly more regressive eye movements as well as longer fixations compared to the prosaic non-reappraisal condition. No significant correlations were found between self-reported literary familiarity and eye tracking patterns. Discussion Despite limitations, this proof-of-concept study provides insights into reading patterns that can help to define objectively the nature of poetic material as requiring slower reading particularly characterised by more and longer fixations and eye movements backwards through the texts compared to the faster, more linear reading of prose. Future research using these, and other psychophysiological metrics can begin to unpack the putative cognitive benefits of reading literary material.
Semi-quantitative risk assessment of marine mammal oil exposure: A case study in the western Gulf of Mexico

Marine mammals are highly vulnerable to oil spills, although the effects at both individual and population levels are not fully understood. A first approximation to evaluate the possible consequences of oil spills on marine life is using ecological risk assessments, which are analytical tools used to assess the likelihood of adverse environmental effects due to exposure to stressors derived from human activities. We developed a semi-quantitative framework to evaluate the risk of oil spill exposure on marine mammals that combines the likelihood of exposure based on species-specific biological and ecological traits, and the feasibility of encounter, which considers not only the overlap between the distribution of the species and the total affected area by a spill but also considers the distribution of spilled oil within this area, thus reducing the uncertainty in the estimate. We applied our framework to assess the risk of exposure of eight cetaceans to scenarios of large heavy oil (API gravity<22) spills originating from three hypothetical deep-water wells in the western Gulf of Mexico. High habitat suitability areas obtained using the maximum entropy (MaxEnt) modeling approach were used as a proxy for the geographic regions where each species is likely to be distributed, and oil spill scenarios were generated using numerical models incorporating transport, dispersion, and oil degradation. The analysis allowed identifying those species for which there is a significant risk of exposure in each spill scenario. However, our results suggest that the risk does not appear to be high for any species under any scenario. The information generated by our risk assessment is key to developing management plans in those areas of the Gulf of Mexico where deep-water activities of the hydrocarbon industry are currently being developed or planned.