Miracle-dz/UniFAR-FTUs huggingface dataset:
Abscisic Acid Deficiency Alters Epicuticular Wax Metabolism and Morphology That Leads to Increased Cuticle Permeability During Sweet Orange (Citrus sinensis) Fruit Ripening

Citrus fruit ripening is coupled with the synthesis and deposition of epicuticular waxes, which reduces water loss during fruit postharvest storage. Although abscisic acid (ABA) is a major regulator of citrus fruit ripening, whether ABA mediates epicuticular wax formation during this process remains poorly understood. We investigated the implication of ABA in cuticle properties and epicuticular wax metabolism, composition, and morphology by comparing the Navelate orange [Citrus sinensis (L.) Osbeck] and its ABA biosynthesis-impaired mutant Pinalate in four ripening stages. ABA deficiency had minor effects on cuticle thickness and epicuticular wax load, but correlated with cuticle permeability. ABA content aligned with mostly fatty acids accumulation in both cultivars, and also with specific alkane, terpenoid, and aldehyde constituents in the parental fruit. In turn, cuticle permeability correlated with the fatty acid profile during fruit ripening in the Navelate and Pinalate, and with primary alcohols, terpenoids, and aldehydes, but only in the mutant fruit. Low ABA levels increased the susceptibility of waxes to crack and were lost from the epicuticular layer. The RNA-seq analysis highlighted the differential regulation of a list of 87 cuticle-related genes between genotypes and ripening stages. Changes in the gene expression of the selected genes in both cultivars were consistent with the content of the aliphatics and terpenoid fractions during ripening. The results suggest a role for ABA in the regulation of fatty acid content and primary alcohol composition, and point out the importance of alkane and triterpenoid for controlling water permeance through fruit cuticles.
MiRNA-Mediated Subpathway Identification and Network Module Analysis to Reveal Prognostic Markers in Human Pancreatic Cancer

Background Pancreatic cancer (PC) remains one of the most lethal cancers. In contrast to the steady increase in survival for most cancers, the 5-year survival remains low for PC patients. Methods We describe a new pipeline that can be used to identify prognostic molecular biomarkers by identifying miRNA-mediated subpathways associated with PC. These modules were then further extracted from a comprehensive miRNA-gene network (CMGN). An exhaustive survival analysis was performed to estimate the prognostic value of these modules. Results We identified 105 miRNA-mediated subpathways associated with PC. Two subpathways within the MAPK signaling and cell cycle pathways were found to be highly related to PC. Of the miRNA-mRNA modules extracted from CMGN, six modules showed good prognostic performance in both independent validated datasets. Conclusions Our study provides novel insight into the mechanisms of PC. We inferred that six miRNA-mRNA modules could serve as potential prognostic molecular biomarkers in PC based on the pipeline we proposed.
Species Diversity With Comprehensive Annotations of Wood-Inhabiting Poroid and Corticioid Fungi in Uzbekistan

Uzbekistan, located in Central Asia, harbors high diversity of woody plants. Diversity of wood-inhabiting fungi in the country, however, remained poorly known. This study summarizes the wood-inhabiting basidiomycte fungi (poroid and corticoid fungi plus similar taxa such as Merismodes, Phellodon, and Sarcodon) (Agaricomycetes, Basidiomycota) that have been found in Uzbekistan from 1950 to 2020. This work is based on 790 fungal occurrence records: 185 from recently collected specimens, 101 from herbarium specimens made by earlier collectors, and 504 from literature-based records. All data were deposited as a species occurrence record dataset in the Global Biodiversity Information Facility and also summarized in the form of an annotated checklist in this paper. All 286 available specimens were morphologically examined. For 138 specimens, the 114 ITS and 85 LSU nrDNA sequences were newly sequenced and used for phylogenetic analysis. In total, we confirm the presence of 153 species of wood-inhabiting poroid and corticioid fungi in Uzbekistan, of which 31 species are reported for the first time in Uzbekistan, including 19 that are also new to Central Asia. These 153 fungal species inhabit 100 host species from 42 genera of 23 families. Polyporales and Hymenochaetales are the most recorded fungal orders and are most widely distributed around the study area. This study provides the first comprehensively updated and annotated the checklist of wood-inhabiting poroid and corticioid fungi in Uzbekistan. Such study should be expanded to other countries to further clarify species diversity of wood-inhabiting fungi around Central Asia.
Genome-Wide Association Mapping and Genomic Prediction of Anther Extrusion in CIMMYT Hybrid Wheat Breeding Program via Modeling Pedigree, Genomic Relationship, and Interaction With the Environment

Anther extrusion (AE) is the most important male floral trait for hybrid wheat seed production. AE is a complex quantitative trait that is difficult to phenotype reliably in field experiments not only due to high genotype-by-environment effects but also due to the short expression window in the field condition. In this study, we conducted a genome-wide association scan (GWAS) and explored the possibility of applying genomic prediction (GP) for AE in the CIMMYT hybrid wheat breeding program. An elite set of male lines (n = 603) were phenotype for anther count (AC) and anther visual score (VS) across three field experiments in 2017–2019 and genotyped with the 20K Infinitum is elect SNP array. GWAS produced five marker trait associations with small effects. For GP, the main effects of lines (L), environment (E), genomic (G) and pedigree relationships (A), and their interaction effects with environments were used to develop seven statistical models of incremental complexity. The base model used only L and E, whereas the most complex model included L, E, G, A, and G × E and A × E. These models were evaluated in three cross-validation scenarios (CV0, CV1, and CV2). In cross-validation CV0, data from two environments were used to predict an untested environment; in random cross-validation CV1, the test set was never evaluated in any environment; and in CV2, the genotypes in the test set were evaluated in only a subset of environments. The prediction accuracies ranged from −0.03 to 0.74 for AC and −0.01 to 0.54 for VS across different models and CV schemes. For both traits, the highest prediction accuracies with low variance were observed in CV2, and inclusion of the interaction effects increased prediction accuracy for AC only. In CV0, the prediction accuracy was 0.73 and 0.45 for AC and VS, respectively, indicating the high reliability of across environment prediction. Genomic prediction appears to be a very reliable tool for AE in hybrid wheat breeding. Moreover, high prediction accuracy in CV0 demonstrates the possibility of implementing genomic selection across breeding cycles in related germplasm, aiding the rapid breeding cycle.
Pathophysiology of Blood–Brain Barrier Permeability Throughout the Different Stages of Ischemic Stroke and Its Implication on Hemorrhagic Transformation and Recovery

The blood–brain barrier (BBB) is a dynamic interface responsible for maintaining the central nervous system homeostasis. Its unique characteristics allow protecting the brain from unwanted compounds, but its impairment is involved in a vast number of pathological conditions. Disruption of the BBB and increase in its permeability are key in the development of several neurological diseases and have been extensively studied in stroke. Ischemic stroke is the most prevalent type of stroke and is characterized by a myriad of pathological events triggered by an arterial occlusion that can eventually lead to fatal outcomes such as hemorrhagic transformation (HT). BBB permeability seems to follow a multiphasic pattern throughout the different stroke stages that have been associated with distinct biological substrates. In the hyperacute stage, sudden hypoxia damages the BBB, leading to cytotoxic edema and increased permeability; in the acute stage, the neuroinflammatory response aggravates the BBB injury, leading to higher permeability and a consequent risk of HT that can be motivated by reperfusion therapy; in the subacute stage (1–3 weeks), repair mechanisms take place, especially neoangiogenesis. Immature vessels show leaky BBB, but this permeability has been associated with improved clinical recovery. In the chronic stage (>6 weeks), an increase of BBB restoration factors leads the barrier to start decreasing its permeability. Nonetheless, permeability will persist to some degree several weeks after injury. Understanding the mechanisms behind BBB dysregulation and HT pathophysiology could potentially help guide acute stroke care decisions and the development of new therapeutic targets; however, effective translation into clinical practice is still lacking. In this review, we will address the different pathological and physiological repair mechanisms involved in BBB permeability through the different stages of ischemic stroke and their role in the development of HT and stroke recovery.
Bixin Attenuates Experimental Autoimmune Encephalomyelitis by Suppressing TXNIP/NLRP3 Inflammasome Activity and Activating NRF2 Signaling

Multiple sclerosis (MS), an autoimmune and degenerative disease, is characterized by demyelination and chronic neuroinflammation. Bixin is a carotenoid isolated from the seeds of Bixa orellana that exhibits various potent pharmacological activities, including antioxidant, anti-inflammatory, and anti-tumor properties. However, the effects of bixin on MS have not yet been examined. To evaluate the effects and underlying molecular mechanisms of bixin on MS, experimental autoimmune encephalomyelitis (EAE) was established in C57BL/6 mice, which were treated via intragastric administration of bixin solutions. To evaluate the molecular mechanisms of bixin, quantitative reverse-transcription PCR, western blot, immunohistochemistry, flow cytometry, and enzyme-linked immunosorbent assay analyses were performed. We found that bixin significantly improved the symptoms and pathology in EAE mice, reduced the release of inflammatory cytokines TNF-α, IL-6, IL-8, IL-17, and IFN-γ, and increased the expression of the anti-inflammatory cytokine IL-10. And bixin reduced the proportion of Th1 and Th17 cells in the spleen and CNS, and suppressed microglia aggregation, and TXNIP/NLRP3 inflammasome activity by scavenging excessive reactive oxygen species (ROS) in EAE mice. Furthermore, bixin inhibited inflammation and oxidative stress via activating nuclear factor erythroid 2-related factor 2 (NRF2), and its downstream genes in EAE mice, meanwhile, these effects were suppressed upon treatment with an NRF2 inhibitor, ML385. Bixin prevented neuroinflammation and demyelination in EAE mice primarily by scavenging ROS through activation of the NRF2 signaling pathway. Taken together, our results indicate that bixin is a promising therapeutic candidate for treatment of MS.
Fighting Strategies Against the Novel Coronavirus Pandemic: Impact on Global Economy

Sudden outbreak of a new pathogen in numbers of pneumonic patients in Wuhan province during December 2019 has threatened the world population within a short period of its occurrence. This respiratory tract–isolated pathogen was initially named as novel coronavirus 2019 (nCoV-2019), but later termed as SARS-CoV-2. The rapid spreading of this infectious disease received the label of pandemic by the World Health Organization within 4 months of its occurrence, which still seeks continuous attention of the researchers to prevent the spread and for cure of the infected patients. The propagation of the disease has been recorded in 215 countries, with more than 25.5 million cases and a death toll of more than 0.85 million. Several measures are taken to control the disease transmission, and researchers are actively engaged in finding suitable therapeutics to effectively control the disease to minimize the mortality and morbidity rates. Several existing potential candidates were explored in the prevention and treatment of worsening condition of COVID-19 patients; however, none of the formulation has been approved for the treatment but used under medical supervision. In this article, a focus has been made to highlight on current epidemiology on the COVID-19 infection, clinical features, diagnosis, and transmission, with special emphasis on treatment measures of the disease at different stages of clinical research and the global economic influence due to this pandemic situation. Progress in the development on vaccine against COVID-19 has also been explored as important measures to immunize people. Moreover, this article is expected to provide information to the researchers, who are constantly combating in the management against this outbreak.
Will SARS-CoV-2 Infection Elicit Long-Lasting Protective or Sterilising Immunity? Implications for Vaccine Strategies (2020)

In December 2019, an outbreak of a novel coronavirus (SARS-CoV-2) in Wuhan, China resulted in the current COVID-19 global pandemic. The human immune system has not previously encountered this virus, raising the important question as to whether or not protective immunity is generated by infection. Growing evidence suggests that protective immunity can indeed be acquired post-infection—although a handful of reinfection cases have been reported. However, it is still unknown whether the immune response to SARS-CoV-2 leads to some degree of long-lasting protection against the disease or the infection. This review draws insights from previous knowledge regarding the nature and longevity of immunity to the related virus, SARS-CoV, to fill the gaps in our understanding of the immune response to SARS-CoV-2. Deciphering the immunological characteristics that give rise to protective immunity against SARS-CoV-2 is critical to guiding vaccine development and also predicting the course of the pandemic. Here we discuss the recent evidence that characterises the adaptive immune response against SARS-CoV-2 and its potential implications for the generation of memory responses and long-term protection.
How general is cognitive ability in non-human animals? A meta-analytical and multi-level reanalysis approach

General intelligence has been a topic of high interest for over a century. Traditionally, research on general intelligence was based on principal component analyses and other dimensionality reduction approaches. The advent of high-speed computing has provided alternative statistical tools that have been used to test predictions of human general intelligence. In comparison, research on general intelligence in non-human animals is in its infancy and still relies mostly on factor-analytical procedures. Here, we argue that dimensionality reduction, when incorrectly applied, can lead to spurious results and limit our understanding of ecological and evolutionary causes of variation in animal cognition. Using a meta-analytical approach, we show, based on 555 bivariate correlations, that the average correlation among cognitive abilities is low (r = 0.185; 95% CI: 0.087–0.287), suggesting relatively weak support for general intelligence in animals. We then use a case study with relatedness (genetic) data to demonstrate how analysing traits using mixed models, without dimensionality reduction, provides new insights into the structure of phenotypic variance among cognitive traits, and uncovers genetic associations that would be hidden otherwise. We hope this article will stimulate the use of alternative tools in the study of cognition and its evolution in animals.
Extracellular Vesicles Are Key Regulators of Tumor Neovasculature

Tumor progression involves a series of biologically important steps in which the crosstalk between cancer cells and the surrounding environment is an important issue. Angiogenesis is a key tumorigenic phenomenon for cancer progression. Tumor-related extracellular vesicles (EVs) modulate the tumor microenvironment (TME) through cell-to-cell communication. Tumor cells in a hypoxic TME release more EVs than cells in a normoxic environment due to uncontrollable tumor proliferation. Tumor-derived EVs in the TME influence endothelial cells (ECs), which then play multiple roles, contributing to tumor angiogenesis, loss of the endothelial vascular barrier by binding to ECs, and subsequent endothelial-to-mesenchymal transition. In contrast, they also indirectly induce tumor angiogenesis through the phenotype switching of various cells into cancer-associated fibroblasts, the activation of tumor-associated ECs and platelets, and remodeling of the extracellular matrix. Here, we review current knowledge regarding the involvement of EVs in tumor vascular-related cancer progression.
Intricate Distribution Patterns of Six Cytotypes of Allium oleraceum at a Continental Scale: Niche Expansion and Innovation Followed by Niche Contraction With Increasing Ploidy Level

The establishment and success of polyploids are thought to often be facilitated by ecological niche differentiation from diploids. Unfortunately, most studies compared diploids and polyploids, ignoring variation in ploidy level in polyploids. To fill this gap, we performed a large-scale study of 11,163 samples from 1,283 populations of the polyploid perennial geophyte Allium oleraceum with reported mixed-ploidy populations, revealed distribution ranges of cytotypes, assessed their niches and explored the pattern of niche change with increasing ploidy level. Altogether, six ploidy levels (3x−8x) were identified. The most common were pentaploids (53.6%) followed by hexaploids (22.7%) and tetraploids (21.6%). Higher cytotype diversity was found at lower latitudes than at higher latitudes (>52° N), where only tetraploids and pentaploids occurred. We detected 17.4% of mixed-ploidy populations, usually as a combination of two, rarely of three, cytotypes. The majority of mixed-ploidy populations were found in zones of sympatry of the participating cytotypes, suggesting they have arisen through migration (secondary contact zone). Using coarse-grained variables (climate, soil), we found evidence of both niche expansion and innovation in tetraploids related to triploids, whereas higher ploidy levels showed almost zero niche expansion, but a trend of increased niche unfilling of tetraploids. Niche unfilling in higher ploidy levels was caused by a contraction of niche envelopes toward lower continentality of the climate and resulted in a gradual decrease of niche breadth and a gradual shift in niche optima. Field-recorded data indicated wide habitat breadth of tetraploids and pentaploids, but also a pattern of increasing synanthropy in higher ploidy levels. Wide niche breadth of tetra- and pentaploids might be related to their multiple origins from different environmental conditions, higher “age”, and retained sexuality, which likely preserve their adaptive potential. In contrast, other cytotypes with narrower niches are mostly asexual, probably originating from a limited range of contrasting environments. Persistence of local ploidy mixtures could be enabled by the perenniality of A. oleraceum and its prevalence of vegetative reproduction, facilitating the establishment and decreasing exclusion of minority cytotype due to its reproductive costs. Vegetative reproduction might also significantly accelerate colonization of new areas, including recolonization of previously glaciated areas.
Developing and Validating Tests of Reading and Listening Comprehension for Fifth and Sixth Grade Students in Portugal

An efficient assessment of reading and linguistic abilities in school children requires reliable and valid measures. Moreover, measures which include specific test forms for different academic grade levels, that are vertically equated, allow the direct comparison of results across multiple time points and avoid floor and ceiling effects. Two studies were conducted to achieve these goals. The purpose of the first study was to develop tests of reading and listening comprehension in European Portuguese, with vertically scaled test forms for students in the fifth and sixth grades, using Rasch model analyses. The purpose of the second study was to collect evidence for the validity of these tests based on the relationships of test scores with other variables. The samples included 454 and 179 students for the first and second study, respectively. The data from both studies provided evidence for good psychometric characteristics for the test forms: unidimensionality and local independence, as well as adequate reliability and evidence of validity. The developed test forms are an important contribution in the Portuguese educational context as they allow for the assessment of students’ performance in these skills across multiple time points and can be used both in research and practice.
Case Report: Overlapping Multiple Sclerosis With Anti-N-Methyl-D-Aspartate Receptor Encephalitis: A Case Report and Review of Literature

Anti-N-methyl-D-aspartate receptor (NMDAR) encephalitis is an autoimmune disorder mediated by NMDAR antibodies, typically manifesting as behavioral complaints, psychosis, seizures, movement disorders, hypoventilation, and autonomic dysfunction. In recent years, the predisposing factors and pathophysiological mechanisms of anti-NMDAR encephalitis have been tried to be clarified. It has been recognized that an overlap may be observed between anti-NMDAR encephalitis and inflammatory demyelinating disease. However, anti-NMDAR encephalitis is rarely associated with multiple sclerosis. Here, we describe a Chinese female patient diagnosed with relapsing remitting multiple sclerosis who developed anti-NMDAR encephalitis. Further, we discuss the previously reported literature.
Feasibility and Safety of Bilateral Hybrid EEG/EOG Brain/Neural–Machine Interaction

Cervical spinal cord injuries (SCIs) often lead to loss of motor function in both hands and legs, limiting autonomy and quality of life. While it was shown that unilateral hand function can be restored after SCI using a hybrid electroencephalography/electrooculography (EEG/EOG) brain/neural hand exoskeleton (B/NHE), it remained unclear whether such hybrid paradigm also could be used for operating two hand exoskeletons, e.g., in the context of bimanual tasks such as eating with fork and knife. To test whether EEG/EOG signals allow for fluent and reliable as well as safe and user-friendly bilateral B/NHE control, eight healthy participants (six females, mean age 24.1 ± 3.2 years) as well as four chronic tetraplegics (four males, mean age 51.8 ± 15.2 years) performed a complex sequence of EEG-controlled bilateral grasping and EOG-controlled releasing motions of two exoskeletons visually presented on a screen. A novel EOG command performed by prolonged horizontal eye movements (>1 s) to the left or right was introduced as a reliable switch to activate either the left or right exoskeleton. Fluent EEG control was defined as average “time to initialize” (TTI) grasping motions below 3 s. Reliable EEG control was assumed when classification accuracy exceeded 80%. Safety was defined as “time to stop” (TTS) all unintended grasping motions within 2 s. After the experiment, tetraplegics were asked to rate the user-friendliness of bilateral B/NHE control using Likert scales. Average TTI and accuracy of EEG-controlled operations ranged at 2.14 ± 0.66 s and 85.89 ± 15.81% across healthy participants and at 1.90 ± 0.97 s and 81.25 ± 16.99% across tetraplegics. Except for one tetraplegic, all participants met the safety requirements. With 88 ± 11% of the maximum achievable score, tetraplegics rated the control paradigm as user-friendly and reliable. These results suggest that hybrid EEG/EOG B/NHE control of two assistive devices is feasible and safe, paving the way to test this paradigm in larger clinical trials performing bimanual tasks in everyday life environments.