Miracle-dz/UniFAR-FTUs huggingface dataset:
Variation in the Number and Position of rDNA Loci Contributes to the Diversification and Speciation in Nigella (Ranunculaceae)

Nigella is a small genus belonging to the Ranunculaceae family which is presumably originated and distributed in Aegean and the adjacent Western-Irano-Turanian region. Comparative repeat analysis of N. sativa, N. damascena and N. bucharica was performed using low-pass Illumina genomic reads followed by karyotyping and FISH mapping of seven Nigella species using the in silico identified repeats and ribosomal DNA (rDNA) probes. High- and moderate-copy repeat sequences occupy 57.52, 59.01, and 64.73% of N. sativa, N. damascena and N. bucharica genomes, respectively. Roughly, half of the genomes are retrotransposons (class I transposons), while DNA transposons (class II transposons) contributed to only about 2% of the genomes. The analyzed Nigella species possess large genomes of about 7.4 to 12.4 Gbp/1C. Only two satellite repeats in N. sativa, one in N. damascena and four in N. bucharica were identified, which were mostly (peri)centromeric and represented about 1% of each genome. A high variation in number and position of 45S rDNA loci were found among Nigella species. Interestingly, in N. hispanica, each chromosome revealed at least one 45S rDNA site and one of them occurs in hemizygous condition. Based on the chromosome numbers, genome size and (peri)centromeric satellites, three karyotype groups were observed: Two with 2n = 2x = 12 and a karyotype formula of 10m + 2t (including N. sativa, N. arvensis, N. hispanica as the first group and N. damascena and N. orientalis as the second group) and a more distant group with 2n = 2x = 14 and a karyotype formula of 8m + 2st + 4t (including N. integrifolia and N. bucharica). These karyotype groups agreed with the phylogenetic analysis using ITS and rbcL sequences. We conclude that variation in (peri)centromeric sequences, number and localization of rDNA sites as well as chromosome number (dysploidy) are involved in the diversification of the genus Nigella.
A Microbiota-Dependent Subset of Skin Macrophages Protects Against Cutaneous Bacterial Infection

Microbiota is essential to the development and functional maturation of the immune system. The effects of the gut microbiota on myeloid cells remote from the gut, especially the skin remain unclear. Transcriptomic analysis revealed that type I interferon (IFN) signaling was down-regulated in the skin of germ-free mice compared to that in specific pathogen-free mice. The decrease in type I IFN signaling was closely related to the presence of microbiota and macrophage-specific marker CD169. The absence of CD169+ macrophages resulted in increased bacterial burden and impaired immune responses against Staphylococcus aureus skin infection. CD169+ macrophages mediated the recruitment of γδ T cells as well as the activation of γδ T cells via interleukin (IL)-23. Our findings demonstrate the role of the microbiota in establishment of a specific myeloid cell subset expressing CD169 in the skin and provide evidence of a specific mechanism by which this subset protects against bacterial skin infection.
Bergmann’s Rule Holds in Birds Inhabiting Southern Guinea Forests but Not in the Northern Savanna of Nigeria

The Bergmann’s rule predicts that in endotherms, body sizes will differ with respect to thermal gradients. Larger bodied individuals will inhabit colder environments while in warmer environments, individuals will be smaller-bodied. This hypothesis has been proved and disproved many times due to inconsistencies in body size differences along latitudinal gradients. We tested this hypothesis in 30 Afrotropical resident bird species inhabiting two vegetation types at different latitudes (southern guinea forests and northern savanna) and at different altitudes in Nigeria, West Africa. Using principal component analyses of body mass and wing length, the first principal component, the component of size, indicated that individuals in montane areas were larger than lowland populations in southern guinea forests. However, in the northern guinea savanna, there was no significant difference in body sizes between lowland and montane populations. General linear models show that body size increases as temperature decreases. In species found in both southern guinea forests and northern savanna (i.e., African Thrush Turdus pelios and Snowy-crowned Robin Chat Cossypha niveicapilla), variations in body sizes were significantly dependent on sites. Our study indicates that other macro-scale factors such as vegetation and rainfall patterns might modulate conformity to Bergmann’s rule in Afrotropical environments.
Remote Education/Homeschooling During the COVID-19 Pandemic, School Attendance Problems, and School Return–Teachers’ Experiences and Reflections

According to Norway’s Educational Act (§2-1), all children and youths from age 6 to 16 have a right and an obligation to attend free and inclusive education, and most of them attend public schools. Attending school is important for students’ social and academic development and learning; however, some children do not attend school caused by a myriad of possible reasons. Interventions for students with school attendance problems (SAPs) must be individually adopted for each student based on a careful assessment of the difficulties and strengths of individuals and in the student’s environment. Homeschooling might be one intervention for students with SAPs; however, researchers and stakeholders do not agree that this is an optimal intervention. Schools that were closed from the middle of March 2020 due to the COVID-19 pandemic provided an opportunity to investigate remote education more closely. An explorative study was conducted that analyzed 248 teachers’ in-depth perspectives on how to use and integrate experiences from the period of remote education for students with SAPs when schools reopen. Moreover, teachers’ perspectives on whether school return would be harder or easier for SAP students following remote education were investigated. The teachers’ experiences might be useful when planning school return for students who have been absent for prolonged periods.
Development and Maintenance Mechanisms of a Long-Lived Mesoscale Vortex Which Governed the Earlier Stage of the “21.7” Henan Torrential Rainfall Event

From 17 to 22 July 2021, a series of disastrous rainstorms appeared within Henan Province and its surroundings, which rendered 398 dead/missing and a direct economic loss of up to ∼114 billion Yuan. This event was named as the “21.7” Henan torrential rainfall event (TRE), and it could be divided roughly into three stages according to the precipitation features and dominant weather systems. This study mainly focused on the development and maintenance mechanisms of a long-lived (72 h) quasi-stationary mesoscale vortex that governed the earlier stage of the “21.7” TRE. Main results are as follows: 1) the mesoscale vortex formed/maintained in a favorable environment which was characterized by the South-Asia-high associated divergence in the upper troposphere, and the relay transport of relatively cold air by the trough and high-pressure system in the middle troposphere. 2) the vertical stretching due to lower-level convergence and the upward transport of cyclonic vorticity by ascending motions served as the first and second dominant factors for the mesoscale vortex’s rapid development and long-time maintenance, whereas, the import/export transport of anticyclonic/cyclonic vorticity into/from the vortex’s central region and the tilting effects were mainly detrimental for the vortex’s development/maintenance. 3) the air particles that formed the mesoscale vortex mainly came from the levels below 1,500 m, within the regions in lower latitudes. The air particles experienced notable precipitation before the formation of the mesoscale vortex, which contributed to the vortex’s formation through latent heat release.
Age-Specific Activation Patterns and Inter-Subject Similarity During Verbal Working Memory Maintenance and Cognitive Reserve

Cognitive Reserve (CR), according to a recent consensus definition of the NIH-funded Reserve and Resilience collaboratory,1 is constituted by any mechanism contributing to cognitive performance beyond, or interacting with, brain structure in the widest sense. To identity multivariate activation patterns fulfilling this postulate, we investigated a verbal Sternberg fMRI task and imaged 181 people with age coverage in the ranges 20–30 (44 participants) and 55–70 (137 participants). Beyond task performance, participants were characterized in terms of demographics, and neuropsychological assessments of vocabulary, episodic memory, perceptual speed, and abstract fluid reasoning. Participants studied an array of either one, three, or six upper-case letters for 3 s (=encoding phase), then a blank fixation screen was presented for 7 s (=maintenance phase), to be probed with a lower-case letter to which they responded with a differential button press whether the letter was part of the studied array or not (=retrieval phase). We focused on identifying maintenance-related activation patterns showing memory load increases in pattern score on an individual participant level for both age groups. We found such a pattern that increased with memory load for all but one person in the young participants (p < 0.001), and such a pattern for all participants in the older group (p < 0.001). Both patterns showed broad topographic similarities; however, relationships to task performance and neuropsychological characteristics were markedly different and point to individual differences in Cognitive Reserve. Beyond the derivation of group-level activation patterns, we also investigated the inter-subject spatial similarity of individual working memory rehearsal patterns in the older participants’ group as a function of neuropsychological and task performance, education, and mean cortical thickness. Higher task accuracy and neuropsychological function was reliably associated with higher inter-subject similarity of individual-level activation patterns in older participants.
Methodology for the Review and Update of Nutrient Criteria Underpinning Front-of-Pack Labeling: Application to the Glycemic Index Symbol

Background: Nutrient criteria underlying front-of-pack food labeling programs can play an important role in improving dietary intakes. Currently, no methodology for the development or update of nutrient criteria has been published, nor the methods used by food regulatory bodies. The scientific publication of methodology outlining the development and update of nutrient criteria underpinning front-of-pack food labeling programs highlighting healthier food choices is needed. Objective To develop and provide a globally applicable and transparent methodology for researchers to follow when reviewing existing or developing new nutrient criteria for front-of-pack labeling. Methods The Nutrient Criteria Methodology involved five phases: Phase I, the development of guiding principles; Phase II, collection of information for subsequent phases, including a pre-scope of the literature and selection of food composition database(s) for modeling; Phase III, literature review of all possible nutrients relevant to the nutrient criteria; Phase IV, database modeling to set quantitative limits for each selected nutrient; Phase V, assessment of the criteria against an established nutritional quality assessment tool. As an example, the methodology was applied to the update of the GI Symbol Product Eligibility and Nutrient Criteria (PENC). Results A comprehensive and replicable methodology, based on best practice protocols and ensuring both scientific credibility and practicality of use by industry, was developed. Application of the five phases of the methodology to the GI Symbol PENC highlighted the ability of the methodology to uncover nutritional measures currently missing in many nutrient criteria for front-of-pack food labeling programs and other national food labeling systems, such as glycemic load and the unsaturated to saturated fat ratio. Foods achieving the PENC had a higher Health Star Rating than foods not achieving the PENC. Conclusion Our Nutrient Criteria Methodology can be applied to the development and update of global nutrient criteria underpinning front-of-pack food labeling programs. Further research into the implementation of additional nutritional measures found to be important for human health is recommended, with the goal of the prevention of diet-related disease.
Attachment Security Priming Delayed Negative Information-Related Attentional Disengagement Among Anxiously Attached Individuals: Evidence From Behavioral and Functional MRI Experiments

Although attachment security has been found to attenuate people’s experience of unpleasant information, how it modulates the attentional process toward such information remains unknown. The present study examined this issue by employing the dot-probe task in functional MRI. After completing the Experiences in Close Relationships-Revised questionnaire (ECR-R), 39 participants were asked to complete the dot-probe task in two conditions: the attachment security priming condition and neutral priming condition. The behavioral results revealed that individuals with high level of attachment anxiety exhibited larger attention disengagement from negative traits in the security priming condition than in the control condition. Correspondingly, the brain regions involved in attention regulation and shifting, such as the posterior cingulate and bilateral parietal area, were less activated among high anxiously attached individuals in the security priming condition. These results suggest a role of attachment security priming in regulating the emotional response in anxiously attached individuals during the attentional stage.
Impacts of RNA Mobility Signals on Virus Induced Somatic and Germline Gene Editing

Viral vectors are being engineered to deliver CRISPR/Cas9 components systemically in plants to induce somatic or heritable site-specific mutations. It is hypothesized that RNA mobility signals facilitate entry of viruses or single guide RNAs (sgRNAs) into the shoot apical meristem where germline mutations can occur. Our objective was to understand the impact of RNA mobility signals on virus-induced somatic and germline gene editing in Nicotiana benthamiana and Zea mays. Previously, we showed that foxtail mosaic virus (FoMV) expressing sgRNA induced somatic mutations in N. benthamiana and Z. mays expressing Cas9. Here, we fused RNA mobility signals to sgRNAs targeting the genes encoding either N. benthamiana phytoene desaturase (PDS) or Z. mays high affinity potassium transporter 1 (HKT1). Addition of Arabidopsis thaliana Flowering Locus T (AtFT) and A. thaliana tRNA-Isoleucine (AttRNAIle) did not improve FoMV-induced somatic editing, and neither were sufficient to facilitate germline mutations in N. benthamiana. Maize FT homologs, Centroradialus 16 (ZCN16) and ZCN19, as well as AttRNAIle were found to aid somatic editing in maize but did not enable sgRNAs delivered by FoMV to induce germline mutations. Additional viral guide RNA delivery systems were assessed for somatic and germline mutations in N. benthamiana with the intention of gaining a better understanding of the specificity of mobile signal-facilitated germline editing. Potato virus X (PVX), barley stripe mosaic virus (BSMV), and tobacco rattle virus (TRV) were included in this comparative study, and all three of these viruses delivering sgRNA were able to induce somatic and germline mutations. Unexpectedly, PVX, a potexvirus closely related to FoMV, expressing sgRNA alone induced biallelic edited progeny, indicating that mobility signals are dispensable in virus-induced germline editing. These results show that PVX, BSMV, and TRV expressing sgRNA all have an innate ability to induce mutations in the germline. Our results indicate that mobility signals alone may not be sufficient to enable virus-based delivery of sgRNAs using the viruses, FoMV, PVX, BSMV, and TRV into cell types that result in germline mutations.
Gut Microbiota Characteristics Are Associated With Severity of Acute Radiation-Induced Esophagitis

Background Acute radiation-induced esophagitis (ARIE) is one of the most debilitating complications in patients who receive thoracic radiotherapy, especially those with esophageal cancer (EC). There is little known about the impact of the characteristics of gut microbiota on the initiation and severity of ARIE. Materials and Methods Gut microbiota samples of EC patients undergoing radiotherapy (n = 7) or concurrent chemoradiotherapy (n = 42) were collected at the start, middle, and end of the radiotherapy regimen. Assessment of patient-reported ARIE was also performed. Based on 16S rRNA gene sequencing, changes of the gut microbial community during the treatment regimen and correlations of the gut microbiota characteristics with the severity of ARIE were investigated. Results There were significant associations of several properties of the gut microbiota with the severity of ARIE. The relative abundance of several genera in the phylum Proteobacteria increased significantly as mucositis severity increased. The predominant genera had characteristic changes during the treatment regimen, such as an increase of opportunistic pathogenic bacteria including Streptococcus. Patients with severe ARIE had significantly lower alpha diversity and a higher abundance of Fusobacterium before radiotherapy, but patients with mild ARIE were enriched in Klebsiella, Roseburia, Veillonella, Prevotella_9, Megasphaera, and Ruminococcus_2. A model combining these genera had the best performance in prediction of severe ARIE (area under the curve: 0.907). Conclusion The characteristics of gut microbiota before radiotherapy were associated with subsequent ARIE severity. Microbiota-based strategies have potential use for the early prediction of subsequent ARIE and for the selection of interventions that may prevent severe ARIE.
HLA Diversity in Saudi Population: High Frequency of Homozygous HLA Alleles and Haplotypes

Human leukocyte antigens (HLA) diversity has a tremendous impact on shaping the transplantation practices, transfusion-associated graft versus host disease prevention strategies, and host–pathogen interactions. Here, we conducted a retrospective study of HLA class I and class II homozygosity at allelic and haplotype levels in unrelated individuals genotyped from 2012 to 2016 in a tertiary hospital in the capital of Saudi Arabia. Among 5,000 individuals, 2,773 individuals meet inclusion criteria and were retrospectively analyzed for HLA-A, -B, -C–DRB1, and -DQB1 homozygosity at allelic and haplotype levels. HLA molecular typing was performed using a commercial reverse sequence-specific oligonucleotide (rSSO) kit. We were able to identify 15 HLA-A, 20 HLA-B, 11 HLA-C, 13 HLA-DRB1, and five HLA-DQB1 homozygous alleles demonstrating a very low genetic diversity in the Saudi population. The highest homozygosity in HLA class I was found in locus C followed by A and B (20.3% > 16.1% > 15.5%; p < 0.001) where the most homozygote alleles were A*02 (9.2%), B*51 and B*50 (5.7% and 3.7%), and C*07, C*06, and C*15 (7.2%, 5.48%, and 3.3%) and in HLA class II, the highest homozygosity was found in locus DQB1 compared to DRB1 (31.71% > 19.2%; p < 0.001), with the most common homozygote alleles being DRB1*07 and DRB1*04 (5.33% and 4.2%) and DQB1*02, DQB1*06, and DQB1*03 (13.55%, 7.92%, and 7.64%). The frequency of finding an individual with one homozygote allele was (24.6%), two homozygote alleles (13.5%), three homozygote alleles (4.7%), four homozygote alleles (3.4%), and five alleles were (4.8%). The most frequent homozygote haplotypes are A*23∼C*06∼B*50∼DRB1*07∼DQB1*02 and A*02∼C*06∼B*50∼DRB1*07∼DQB1*02. This study shows low diversity of both class I and II alleles and haplotypes in the Saudi population, which would have a significant impact on shaping the transplantation practices, transfusion-associated graft versus host disease prevention strategies, and host–pathogen interactions.
Transcriptome Analysis of Turbot (Scophthalmus maximus) Infected With Aeromonas salmonicida Reveals a Direct Effect on Leptin Synthesis as a Neuroendocrine Mediator of Inflammation and Metabolism Regulation

Aeromonas salmonicida subsp. salmonicida is the causative agent of furunculosis, a disease affecting numerous fish species worldwide. It is a highly pathogenic bacterium for turbot, whose farming production represents an important economic activity in several European countries and China. To better understand the response of this organism to A. salmonicida, we conducted RNA-Seq analysis of the head kidney from experimentally infected and uninfected turbot juveniles at 24 hours post-infection (hpi). As expected, among the differentially expressed genes (DEGs) between infected and uninfected fish, we observed the modulation of a multitude of immune-related genes but also a high representation of genes linked to metabolism. Interestingly, one of the most upregulated genes was that encoding the hormone leptin. Leptin is a multifunctional hormone/cytokine that has been shown to play roles in the immune system, stress response, food intake, metabolism and energy balance. We used recombinant human leptin to elucidate its role during infection with A. salmonicida in turbot (anorexigenic activity, ability to modulate metabolism and the immune response, and its effect on survival and bacterial load during infection). We found that the intraperitoneal administration of leptin was able to alter the response to the bacteria at the immune level, but especially at the metabolic level, which resulted in a higher survival rate without affecting the bacterial load. Based on this, we hypothesized that leptin could offer great potential as a therapeutic treatment during furunculosis outbreaks by reducing the impact of sepsis. Our results reveal the complex interplay between bacterial activity and the regulation of food intake, metabolism and inflammation.
Intrinsic Functional Connectivity in the Default Mode Network Differentiates the Combined and Inattentive Attention Deficit Hyperactivity Disorder Types

Neuroimaging studies have revealed neurobiological differences in ADHD, particularly studies examining connectivity disruption and anatomical network organization. However, the underlying pathophysiology of ADHD types remains elusive as it is unclear whether dysfunctional network connections characterize the underlying clinical symptoms distinguishing ADHD types. Here, we investigated intrinsic functional network connectivity to identify neural signatures that differentiate the combined (ADHD-C) and inattentive (ADHD-I) presentation types. Applying network-based statistical (NBS) and graph theoretical analysis to task-derived intrinsic connectivity data from completed fMRI scans, we evaluated default mode network (DMN) and whole-brain functional network topology in a cohort of 34 ADHD participants (aged 8–17 years) defined using DSM-IV criteria as predominantly inattentive (ADHD-I) type (n = 15) or combined (ADHD-C) type (n = 19), and 39 age and gender-matched typically developing controls. ADHD-C were characterized from ADHD-I by reduced network connectivity differences within the DMN. Additionally, reduced connectivity within the DMN was negatively associated with ADHD-RS hyperactivity-impulsivity subscale score. Compared with controls, ADHD-C but not ADHD-I differed by reduced connectivity within the DMN; inter-network connectivity between the DMN and somatomotor networks; the DMN and limbic networks; and between the somatomotor and cingulo-frontoparietal, with ventral attention and dorsal attention networks. However, graph-theoretical measures did not significantly differ between groups. These findings provide insight into the intrinsic networks underlying phenotypic differences between ADHD types. Furthermore, these intrinsic functional connectomic signatures support neurobiological differences underlying clinical variations in ADHD presentations, specifically reduced within and between functional connectivity of the DMN in the ADHD-C type.