Miracle-dz/UniFAR-FTUs huggingface dataset:
Transcriptome analysis of apple leaves infected by the rust fungus Gymnosporangium yamadae at two sporulation stages (spermogonia and aecia) reveals specific host responses, rust pathogenesis-related genes and a shift in the phyllosphere fungal community composition

Apple rust disease caused by Gymnosporangium yamadae is one of the major threats to apple orchards. In this study, dual RNA-seq analysis was conducted to simultaneously monitor gene expression profiles of G. yamadae and infected apple leaves during the formation of rust spermogonia and aecia. The molecular mechanisms underlying this compatible interaction at 10 and 30 days post inoculation (dpi) indicate a significant reaction from the host plant and comprise detoxication pathways at the earliest stage and the induction of secondary metabolism related pathways at 30dpi. Such host reactions have been previously reported in other rust pathosystems and may represent a general reaction to rust infection. G. yamadae transcript profiling indicates a conserved genetic program in spermogonia and aecia that is shared with other rust fungi, whereas secretome prediction reveals the presence of specific secreted candidate effector proteins expressed during apple infection. Unexpectedly, the survey of fungal unigenes in the transcriptome assemblies of inoculated and mock-inoculated apple leaves reveals that G. yamadae infection modifies the fungal community composition in the apple phyllosphere at 30 dpi. Collectively, our results provide novel insights into the compatible apple-apple rust interaction and advance the knowledge of this heteroecious demicyclic rust fungus.
Non-Coding RNAs in Pediatric Solid Tumors

Pediatric solid tumors are a diverse group of extracranial solid tumors representing approximately 40% of childhood cancers. Pediatric solid tumors are believed to arise as a result of disruptions in the developmental process of precursor cells which lead them to accumulate cancerous phenotypes. In contrast to many adult tumors, pediatric tumors typically feature a low number of genetic mutations in protein-coding genes which could explain the emergence of these phenotypes. It is likely that oncogenesis occurs after a failure at many different levels of regulation. Non-coding RNAs (ncRNAs) comprise a group of functional RNA molecules that lack protein coding potential but are essential in the regulation and maintenance of many epigenetic and post-translational mechanisms. Indeed, research has accumulated a large body of evidence implicating many ncRNAs in the regulation of well-established oncogenic networks. In this review we cover a range of extracranial solid tumors which represent some of the rarer and enigmatic childhood cancers known. We focus on two major classes of ncRNAs, microRNAs and long non-coding RNAs, which are likely to play a key role in the development of these cancers and emphasize their functional contributions and molecular interactions during tumor formation.
What can a comparative genomics approach tell us about the pathogenicity of mtDNA mutations in human populations?

Mitochondrial disorders are heterogeneous, showing variable presentation and penetrance. Over the last three decades, our ability to recognize mitochondrial patients and diagnose these mutations, linking genotype to phenotype, has greatly improved. However, it has become increasingly clear that these strides in diagnostics have not benefited all population groups. Recent studies have demonstrated that patients from genetically understudied populations, in particular those of black African heritage, are less likely to receive a diagnosis of mtDNA disease. It has been suggested that haplogroup context might influence the presentation and penetrance of mtDNA disease; thus, the spectrum of mutations that are associated with disease in different populations. However, to date there is only one well‐established example of such an effect: the increased penetrance of two Leber's hereditary optic neuropathy mutations on a haplogroup J background. This paper conducted the most extensive investigation to date into the importance of haplogroup context on the pathogenicity of mtDNA mutations. We searched for proven human point mutations across 726 multiple sequence alignments derived from 33 non‐human species absent of disease. A total of 58 pathogenic point mutations arise in the sequences of these species. We assessed the sequence context and found evidence of population variants that could modulate the phenotypic expression of these point mutations masking the pathogenic effects seen in humans. This supports the theory that sequence context is influential in the presentation of mtDNA disease and has implications for diagnostic practices. We have shown that our current understanding of the pathogenicity of mtDNA point mutations, primarily built on studies of individuals with haplogroups HVUKTJ, will not present a complete picture. This will have the effect of creating a diagnostic inequality, whereby individuals who do not belong to these lineages are less likely to receive a genetic diagnosis.
EFFECT OF CARVACROL ON PRODUCTIVE PERFORMANCE AND SOME IMMUNOLOGICAL PARAMETERS OF GROWING RABBITS

A total number of 40 New Zealand White rabbit males at 4 weeks of age and averaged 542.50g body weight were used in this study. Animals were distributed randomly into four experimental groups (10 rabbits each). The 1 st group was served as a control group without any supplementation in drinking water. Whereas, the carvacrol was added with concentrations of 0.13, 0.26 and 0.39 ml/liter in drinking water for representing the 2 nd , 3 rd and 4 th
Empirical Spatial Analysis on Fairness of Health Resource Allocation

The paper aims to establish the method to evaluate the demographic fairness,regional fairness and comprehensive situation of health resource allocation and carry out the empirical analysis. With the DEA (Data Envelopment Analysis) method. According to the principle of the Gini coefficient, we established regionalized variables to evaluate demographic fairness and regional fairness of health resource allocation and performed the spatial analysis and evaluation with related spatial analysis methods and ArcGIS software. We analyzed and evaluated the demographic fairness, regional fairness and comprehensive situation of the allocation of health resources in Shandong Province in 2014. The demographic fairness was optimal in Zibo, Dongying, and Weihai and the regional fairness was optimal in Zibo and Jinan. The overall health resource allocation in Shandong Province is in the radial pattern with two centers of Zibo and Jinan. Allocation of health resources is a multidimensional comprehensive problem which is closely related to various factors, such as economy, population, and regional development space. Compared with the conventional analysis methods, the combination of spatial analysis methods and ArcGIS software can reveal the advantages and disadvantages of health resource allocation.
3D Echolocating System For The Visually Impaired Based On Bat SONAR Approach

Video games are becoming widely used today for entertainment and socializing. However, with all the technology there are few games for the blind or the visually impaired people. In the literature, research attempts for wearable and/or assistive systems designed to support visually impaired people are limited in terms of accuracy and support only limited tasks; such as: learning activities, sending SMS, … etc. They use predefi ned tasks and train visually impaired individual to use the system. For navigation and detecting obstacles whilst moving in uncertain environment, visually impaired people would need fruitful research regarding training visually impaired people to understand and interpret the 3D sounds; commonly known as BATS based software. BATS software supports independent mobility for visual impairments individuals benefi t as it provides means to navigate, detect objects, and react to uncertain issues in surrounding using sound navigation and ranging (SONAR). In this paper, we propose a game that allows visually impaired/blind individual to be trained to interpret sounds through the game by play against a sighted opponent (teacher/ relevant or mother for the child). The main idea of the game is to let the sighted player raise sounds; programmed in the game players attack each other’s area. The sighted player mode will have both visuals and audio. According to the Bat system, the blind/visually impaired will have 3D audio, Ultrasonic sensors are used for detecting the obstacles whilst the Servo motors are used to give a precise position and the google glasses to make object type recognition. The sighted opponent will enforce objects occurrences inside the game and the blind/ visually impaired user would be trained use the system in order to be able determine types of the objects, distance to objects compensate the visuals.
In vitro evaluation of antioxidant activity of Caryota mitis Lour. Leaves extracts

Free radicles surly attack different tissues of the body causing serious cell damage and various inflammatory conditions. As a result, there is an urgent need for discovery of new and safe antioxidants of natural sources. DPPH• radicle scavenging assay is an accurate and precise spectrophotometric method used for determination of antioxidant activity, this depends on the measurement of degree of DPPH• color change from violet to yellow spectrophoto metrically. When this technique was applied on the total and different extracts in addition to two pure flavonoids isolated from the leaves of Caryota mitis Lour. , the result revealed that the plant exhibited strong antioxidant activity relative to that of standard ascorbic acid which open the field for industrial formulation of new and safe antioxidant product.
Population Structure Drives Differential Methicillin-resistant Staphylococcus aureus Colonization Dynamics

Using a model of methicillin-resistant Staphylococcus aureus (MRSA) within an intensive care unit (ICU), we explore how differing hospital population structures impact these infection dynamics.Using a stochastic compartmental model of an 18-bed ICU, we compared the rates of MRSA acquisition across three potential population structures: a Single Staff Type (SST) model with nurses and physicians as a single staff type, a model with separate staff types for nurses and physicians (Nurse-MD model), and a Metapopulation model where each nurse was assigned a group of patients. By varying the proportion of time spent with the assigned patient group (γ) within the Metapopulation model, we explored whether simpler models may be acceptable approximations to more realistic patient-healthcare staff contact patterns.The SST, Nurse-MD, and Metapopulation models had a mean annual number of cumulative MRSA acquisitions of 40.6, 32.2 and 19.6 respectively. All models were sensitive to the same parameters in the same direction, although the Metapopulation model was less sensitive. The number of acquisitions varied non-linearly by values of γ, with values below 0.40 resembling the Nurse-MD model, while values above that converged toward the metapopulation structure.The population structure of a modeled hospital has considerable impact on model results, with the SST model having more than double the acquisition rate of the more structured Metapopulation model. While the direction of parameter sensitivity remained the same, the magnitude of these differences varied, producing different infection rates across relatively similar populations. The non-linearity of the model’s response to differing values of γ suggests only a narrow space of relatively dispersed nursing assignments where simple model approximations are appropriate.Simplifying assumptions around how a hospital population is modeled, especially assuming random mixing, may overestimate infection rates and the impact of interventions.
Sunflower response to inoculation with single and mixed species of arbuscular mycorrhizal fungi: Agronomic characteristics

The impact of indigenous arbuscular mycorrhizal fungi (AMF) on agronomic characteristics of sunflower (Helianthus annuus L.) was evaluated in a pot experiment. The indigenous AMF, including Glomus intraradices, Glomus mosseae, and Glomus viscosum, were isolated from an agricultural field in which cotton and sunflower plants were grown. The most abundant species (G. viscosum) was multiplied in a monospecific culture. Sunflower plants were inoculated with the mixture of three selected AMF species or solely with G. viscosum. The number of leaves, shoot length, head diameter, above ground biomass, and seeds mass were significantly higher in the plant inoculated with AMF mixture followed by individual inoculation with G. viscosum followed by the control. AMF mixture outperformed the G. viscosumby increasing mycorrhizal dependency and mycorrhizal inoculation effect of sunflower. The results indicate that AMF mixture could be considered as a good inoculum for improving growth and yield of sunflower in sustainable agriculture.
Whole-Genome Sequencing Redefines Shewanella Taxonomy

The genus Shewanella encompasses a diverse group of Gram negative, primarily aquatic bacteria with a remarkable ecological relevance, an outstanding set of metabolic features and an emergent clinical importance. The rapid expansion of the genus over the 2000 s has prompted questions on the real taxonomic position of some isolates and species. Recent work by us and others identified inconsistencies in the existing species classification. In this study we aimed to clarify such issues across the entire genus, making use of the genomic information publicly available worldwide. Phylogenomic analyses, including comparisons based on genome-wide identity indexes (digital DNA-DNA hybridization and Average Nucleotide Identity) combined with core and accessory genome content evaluation suggested that the taxonomic position of 64 of the 131 analyzed strains should be revisited. Based on the genomic information currently available, emended descriptions for some Shewanella species are proposed. Our study establishes for the first time a whole-genome based phylogeny for Shewanella spp. including a classification at the subspecific level.
Eaten or beaten? Severe population decline of the invasive lizard Podarcis siculus (Rafinesque-Schmaltz, 1810) after an eradication project in Athens, Greece

Invasive species have been recognised as an important hazard to native communities. Amongst the mitigation measures that have been proposed to confront biological invasions, eradication projects are certainly the most drastic. In this short communication, a successful eradication project against a recently established population of the Italian wall lizard (Podarcissiculus) in Athens, Greece, is reported. To this aim, the Hellenic Herpetological Society received unforeseen aid from stray cats and, possibly, from the Οcellated skink (Chalcidesocellatus) and vegetation growth. Within three years, the initial thriving P.siculus population has shrunk to very few individuals.
Characterisation of an Arabidopsis mutant with altered greening characteristics

Two plastid-to-nucleus signalling pathways had previously been identified by studies on genomes uncoupled (gun) mutants of Arabidopsis. A pathway responding to the state of plastid protein synthesis was . disrupted in gunl mutants. Unlike the wild type, the mutants show expression of nuclear photosynthesis genes in the presence of norflurazon, which results in chloroplast photooxidation, or in the presence of lincomycin, an inhibitor of plastid translation. The aim of this study was to understand ---·-·-. the role of plastid protein synthesis in plastid-to-nucleus signalling. Five putative gunl-like mutants from a new collection of Arabidopsis gun mutants with a green fluorescent protein (GFP) reporter gene under the control of a tobacco RbcS (encoding ribulose-1,5-bisphosphate carboxylase small subunit) promoter were examined further. One of the mutant lines, PR48.2N, showed two-fold higher transcript abundance of nuclear photosynthesis genes, RBCS and LHCBJ (encoding light-harvesting chlorophyll a/b-binding protein 1 ), compared to wild type with or without treatments of norflurazon or lincomycin. Pigment analysis of PR48.2N seedlings illumin~ted for 16 hours after being subjected to various lengths of dark treatment demonstrated that the mutant line accumulated less chlorophyll than wild type after short periods of darkness (2-4 days) but showed an enhanced ability to green after prolonged dark treatments (5-10 days). Consistent with the enhanced greening ability, transcript abundance of nuclear photosynthesis genes was higher and there was more thylakoid membrane in chloroplasts in greened PR48.2N seedlings after prolonged darkness compared to the wild type. Microarray analysis indicated that a group of transcripts encoding seed storage proteins, oleosins and late embryogenesis abundant proteins showed very low abundance in PR48.2N seedlings. The promoter regions of the genes shared some ciselements possibly involved in regulation by abscisic acid (ABA). However, the ABA content of PR48.2N seedlings was not significantly different to wild type, although the
Leveraging biobank-scale rare and common variant analyses to identify ASPHD1 as the main driver of reproductive traits in the 16p11.2 locus

Whereas genome-wide association studies (GWAS) allowed identifying thousands of associations between variants and traits, their success rate in pinpointing causal genes has been disproportionately low. Here, we integrate biobank-scale phenotype data from carriers of a rare copy-number variant (CNV), Mendelian randomization and animal modeling to identify causative genes in a GWAS locus for age at menarche (AaM). We show that the dosage of the 16p11.2 BP4-BP5 interval is correlated positively with AaM in the UK and Estonian biobanks and 16p11.2 clinical cohorts, with a directionally consistent trend for pubertal onset in males. These correlations parallel an increase in reproductive tract disorders in both sexes. In support of these observations, 16p11.2 mouse models display perturbed pubertal onset and structurally altered reproductive organs that track with CNV dose. Further, we report a negative correlation between the 16p11.2 dosage and relative hypothalamic volume in both humans and mice, intimating a perturbation in the gonadotropin-releasing hormone (GnRH) axis. Two independent lines of evidence identified candidate causal genes for AaM; Mendelian randomization and agnostic dosage modulation of each 16p11.2 gene in zebrafish gnrh3:egfp models. ASPHD1, expressed predominantly in brain and pituitary gland, emerged as a major phenotype driver; and it is subject to modulation by KCTD13 to exacerbate GnRH neuron phenotype. Together, our data highlight the power of an interdisciplinary approach to elucidate disease etiologies underlying complex traits.
Preadaptation to the vertical: an extra dimension to the natural history and nesting habits of the Tree Bumble Bee, Bombus (Pyrobombus) hypnorum

The Tree Bumble Bee, Bombus hypnorum, is a native of forest environments but has now successfully colonised urban areas. To better understand its success in an anthropogenic context, this review considers aspects of its natural history and nesting habits using a combination of published literature, anecdotal field observations by entomologists from a number of countries, and information from the BWARS database. Where man’s influence is minimal, B. hypnorum appears to nest almost exclusively in tree cavities. Modern woodlands tend to be managed and nest-cavity poor. Urban areas with gardens provide foraging opportunities together with a large supply of well-insulated and well-protected aboveground nest sites. B. hypnorum currently appears to do better in urban areas than managed woodlands, and quite possibly better than it ever did in primeval forest. In Britain, where it was first found in 2001, its notable success appears to reflect the absolute quantity of suitable anthropogenic, and specifically urban, nesting habitat. Conspicuous nest placement has resulted in more nest records for this recent arrival than exist for any native British bumble bee species. In “helping itself” to an anthropogenic nesting niche, B. hypnorum highlights how important appropriate nesting sites are in determining which bumble bee species can live in any given area. Detailed information on nest site preferences and availability needs to inform conservation measures for threatened native species.
Structures and electronic properties of domain walls in BiFeO3 thin films

Abstract Domain walls (DWs) in ferroelectrics are atomically sharp and can be created, erased, and reconfigured within the same physical volume of ferroelectric matrix by external electric fields. They possess a myriad of novel properties and functionalities that are absent in the bulk of the domains, and thus could become an essential element in next-generation nanodevices based on ferroelectrics. The knowledge about the structure and properties of ferroelectric DWs not only advances the fundamental understanding of ferroelectrics, but also provides guidance for the design of ferroelectric-based devices. In this article, we provide a review of structures and properties of DWs in one of the most widely studied ferroelectric systems, BiFeO3 thin films. We correlate their conductivity and photovoltaic properties to the atomic-scale structure and dynamic behaviors of DWs.
Allopatric Speciation in Asia Contributed to the Diversity Anomaly between Eastern Asia and Eastern North America: Evidence from Anchored Phylogenomics of Stewartia (Theaceae)

Premise of research. The disjunct distribution of plant genera between eastern Asia (EA) and eastern North America (ENA) has long attracted the attention of biologists and biogeographers. For most genera that have been studied, there are more species in EA than in ENA, and the diversity anomaly may have resulted from the greater physiographical heterogeneity in EA than in ENA in conjunction with climate and sea level changes. However, few empirical studies have explicitly tested the association between species diversity and allopatric speciation events. The genus Stewartia (Theaceae) displays this diversity anomaly, with two species in ENA and 21 species in EA, but the phylogeny of this group has not been resolved because of insufficient data. Methodology. Here, we sampled 15 species of Stewartia (65%) and generated data from over 500 nuclear loci using the anchored phylogenomic approach to produce a robust phylogeny of Stewartia. In addition, biogeographical analyses were performed to elucidate the natural history of Stewartia, including estimated times of divergence, ancestral areas, and speciation patterns. Pivotal results. Our parsimony, Bayesian, and species tree analyses produced congruent phylogenies with high resolution of the interspecific relationships within Stewartia. Speciation in Asia was mostly allopatric between the Japanese Islands and the Asian continent during the Miocene and the early Pliocene, while the two ENA species represent lineages from different times, with S. malacodendron being the first lineage to split off from the remaining species and S. ovata coming later as sister to the deciduous species of Asian Stewartia. Conclusions. The results provide direct evidence for the importance of allopatry in the differential diversity between EA and ENA.