Miracle-dz/UniFAR-FTUs huggingface dataset:
Nucleolar stress in Drosophila neuroblasts, a model for human ribosomopathies

Different stem cells or progenitor cells display variable threshold requirements for functional ribosomes. For instance, select embryonic neural crest cells or adult bone marrow stem cells, but not others, show lethality due to failures in ribosome biogenesis or function (known as nucleolar stress) in several human ribosomopathies. To determine if various Drosophila neuroblasts display differential sensitivities to nucleolar stress, we used CRISPR-Cas9 to disrupt the Nopp140 gene that encodes two ribosome biogenesis factors (RBFs). Disruption of Nopp140 induced nucleolar stress that arrested larvae in the second instar stage. While the majority of larval neuroblasts arrested development, the Mushroom Body (MB) neuroblasts continued to proliferate as shown by their maintenance of deadpan, a neuroblast-specific transcription factor, and by their continued EdU incorporation. MB neuroblasts in wild type larvae contained more fibrillarin and Nopp140 in their nucleoli as compared to other neuroblasts, indicating that MB neuroblasts stockpile RBFs as they proliferate in late embryogenesis while other neuroblasts normally enter quiescence. A greater abundance of Nopp140 encoded by maternal transcripts in Nopp140−/− MB neuroblasts likely rendered these cells more resilient to nucleolar stress. Summary Statement Nucleolar stress (loss of ribosome production/function) in certain human stem cells or progenitor cells results in disease. In fruit flies, larval Mushroom Body neuroblasts are relatively resilient to nucleolar stress.
Evolution of a Y Chromosome from an X Chromosome

Turnovers of sex chromosomes — where an ancestral sex-determining region is replaced by a new one, or moves to a new genomic location, often on a different chromosome — have rarely been studied within a phylogenetic context that allows the ancestral states to be inferred. Here we compare three closely related species of the fish genus Poecilia, P. reticulata (the guppy), P. picta and P. parae, which reveals that the guppy Y chromosome evolved from an ancestral X chromosome, the first documented case of an X chromosome evolving to become a new Y chromosome. We show that the sex determining locus in all three species is carried on the same chromosome, chromosome 12 in P. reticulata. However, whereas the guppy Y chromosome retains essentially all genes found on the X chromosome, P. picta’s Y chromosome has lost most of them, and is highly degenerated. The few X-linked genes that have retained detectable Y copies in P. picta are almost all homologues of guppy pseudo-autosomal genes. Microsatellite genotyping shows that P. parae also has a degenerated Y chromosome. The guppy Y chromosome must therefore have evolved from an ancestral X chromosome after the split from P. picta and P. parae. Another close relative, the platyfish, must also descend from the same ancestor with a highly degenerated Y chromosome, and its sex chromosome pair is an autosome in both the guppy and P. picta. This evidence for repeated and independent changes supports a role for genetic degeneration in sex chromosome turnovers.
Complete mitochondrial genome sequence of Pseudecheneis Sulcata in the Yarlung Zangbo River, Tibet

Abstract Pseudecheneis sulcata belongs to Sisoridae, Pseudecheneis, which is mainly distributed in India and Tibet of China, and is located in the Motuo and Chayu in the lower reaches of the Yarlung Zangbo River in Tibet. In the present study, we obtained the complete mitochondrial genome sequence of Pseudecheneis sulcata, which was 16,535 bp in length. This genome consisted of 13 protein-coding genes, 22 tRNAgenes, 2 rRNA genes and a non-coding control region. The protein-coding genes have three start codons (GTG, ATG, and CTA) and four stop codons, including three complete stop codons and one incomplete stop codon. To verify the accuracy and utility of newly determined mitogenome sequences by constructing a species phylogenetic relationship tree of species, we expect to use the full mitochondrial gene sequence to interpret related evolutionary events.
Distinct regulation of Nr4a receptors by NFAT and ERK signalling during T cell activation

Nr4a gene family members are activated by T cell receptor (TCR) signalling and play key roles in Regulatory T cell differentiation and have also been implicated in promoting T cell exhaustion in cancer. The precise signalling pathways that govern their transcription, however, remain unclear. Here we utilise Nr4a3-Tocky mice to elucidate the signalling pathways that govern Nr4a1, 2 and 3 expression in response to physiological stimulation of CD4+ and CD8+ T cells. Our findings reveal that Nr4a1-3 are Src family kinase-dependent. Moreover, Nr4a2 and Nr4a3 are abolished by calcineurin inhibitors and bind NFAT1, highlighting a necessary role for NFAT in the control of Nr4a2 and Nr4a3. Interestingly, the NFAT pathway is redundant for Nr4a1 activation, but all three Nr4a members require ERK signalling for optimal expression. Analysis of T cells expressing constitutively active NFAT1 reveals that NFAT1 alone is sufficient to induce expression of Nr4a2 and Nr4a3, but not Nr4a1. These findings further our understanding of Nr4a regulation, highlighting key differences in the sensitivity of Nr4a1 and Nr4a3 to distal TCR signalling pathways.
Prestress evaluation in prestressed concrete plate-like structures

Condition assessment and capacity evaluation of existing structures using their vibration responses have been subjected to extensive research for many years. Prestressed concrete structures have been one of the main focuses of those studies. In the case of prestressed concrete structures, effective prestress force is the most important parameter for their best performance and yet currently there is no effective method for identifying the prestressing force in an existing prestressed concrete structure. Effect of prestressing is different for different types of structural elements and has to be treated accordingly for its accurate quantification. This paper presents a new approach to evaluate the effective prestress force of plate-like structures with simply supported boundary conditions using their vibration responses. The proposed method quantifies the prestress effect with a reasonable good accuracy, even with noisy measurements using both periodic and impulsive excitations. Prestress estimation can be done using collected data from as less as two measurement locations.
Comprehensive Integrated Platform for Garbage Classification in Reduction, Innocuity, and Resource

Urban garbage collection in three steps and environmental monitoring have become an indispensable link in the green recycling economy of the country. In the process of explosive growth of cities and towns in China, the amount of waste is also expanded in the exponent growth, causing huge environmental and social problems. The current urban area commonly applies the strategy of "mixed collection, centralized transportation, centralized processing", commonly known as the three segment management to recycle and dispose of refuse, which can not effectively solve massive waste issues. This paper is based on the intelligent environmental protection and garbage classification technology to solve the inevitable problems of "sanitation digital management", "solid waste classification & recycling station real-time feedback", and "surrounding environment monitoring", so as to recycle of garbage efficiently and harmlessly. Our initial research results have been applied in the environmental protection projects in many demonstration cities and beautiful villages throughout the country, and good results have been achieved. Based on the research and rich engineering experience, we have proposed and optimized digital dynamic sanitation management, grid large-scale real-time monitoring of solid waste recycling stations feedback, the surrounding water and air quality on-line monitoring subsystems. To overcome difficulties and provide theoretical basis or technical methods, it will strongly support the extensive deployment of garbage recycling in China, and greatly improve the recycling rate of urban and rural waste.
Complete mitochondrial genome sequence and phylogenetic analysis of Lycodes polaris (Sabine, 1824)

Abstract Lycodes polaris is one of the most widely distributed and abundant eelpout species on the Arctic continental shelves with full mitogenome information unavailable. In this paper, complete mitochondrial genome of L. Polaris was determined with 16,595 bp in length, containing 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and 2 non-coding regions (origin of light strand replication and control region). All the protein-coding genes choose ATG as start codon in addition to that COI using GTG. Most genes use TAA or TAG as the stop codon while three others ended with incomplete stop codons. Phylogenetic relationship of L. polaris was also reconstructed. Our result will provide important basis for further studies of L. polaris.
The complete chloroplast genome of sweet tea (Lithocarpus polystachyus)

Abstract Lithocarpus polystachyus, also known as the sweet tea, is a plant of the family Fagaceae. It is widely distributed in southern China, India, and Thailand. The chloroplast (cp) genome of L. polystachyus is 161,217 bp in size containing 122 unique genes, including eight rRNA genes, 37 tRNA genes, and 77 protein-coding genes (PCGs). Phylogenetic analysis exhibited that L. polystachyus was most related to L. balansae.
Suitability Of Largehead hairtail (Trichiurus lepturus) Fish For Hot Smoking

Largehead hairtail fish(Trichiuru lepturus) used in the present study has no industrial use in Egypt up to now. The study aimed to investigate the suitability of this fish for preparing hot smoked steaks. Physical, chemical, and technological characteristics of fresh and smoked fish were studied. Two trials were done for preparing smoked fish steaks, skin-on and skin-off. The hot smoked (skin-off) steaks were highly accepted by panelists because of its pleasant flavor and good golden brown color. The results of the chemical analysis of fresh and skin-off flesh showed that the hot smoking process lowered the moisture content of the fresh sample from 73.15 to 66.68%, a relative decrease in both crude protein and total lipids, while an increase in ash, Na, Mg and slight decrease in other minerals content of fresh fish steaks. The total essential amino acids in the fresh and smoked fish represented 46.05 and 43.21 g/100g protein, respectively.Triacylglycerols fraction considered the main compound of total lipids of both fresh and smoked steaks. Monoacylglycerols, and hydrocarbons appeared and a slight increase in diacylglycerols and free fatty acids fractions were noted in smoked steaks of smoked flesh. The level of saturated fatty acids (SFA) of smoked fish was relatively increased, while, the polyunsaturated fatty acids(PUFA) were relatively decreased. Docosahexaenoic acid (DHA)and eicosapentaenoic acid (EPA) were found to be the major n-3 PUFA.The ratios of n-3/n-6 were 7.64 and 6.53 of fresh and smoked largehead hairtail fish (LHF) steaks, respectively.
Characterization of the complete chloroplast genome sequence of Galinsoga parviflora and its phylogenetic implications

Abstract Galinsoga parviflora is an invasive weed in southwest of Chinese agricultural systems and commonly used as medicine and food. In this study, the complete chloroplast genome of the G. parviflora was assembled from the whole genome Illumina sequencing data. The circular genome is 151,811 bp in size, which composed of one large single-copy (LSC) and one small single-copy (SSC) regions of 83,594 bp and 18,141 bp, respectively, and separated by a pair of inverted repeat (IR) regions of 25,038 bp each. It encodes a total of 113 gene species (80 protein-coding, 29 tRNA, and four rRNA species), in which 19 of them with double copies. The overall GC content is 37.7% while the GC content of the LSC, SSC, and IR regions are 35.8%, 31.3%, and 43.1%, separately. Phylogenetic analysis indicated that Galinsoga parviflora was closely related to Galinsoga quadriradiata.
Supplementation in Autoimmune Thyroid Hashimoto’s Disease. Vitamin D and Selenium

This review aims to present the importance of nutrients for thyroid health in light of autoimmune Hashimoto’s disease. Authors focus mainly on vitamin D and selenium function in the body, metabolism, serum concentration in patients, replenishment outcome after singular or combined the treatment and dose. Vitamin D is essential for immune regulation and yields inflammatory properties. Selenium plays an important role in thyroid metabolism by protecting it from oxidative damage during iodine metabolism and by taking part in thyroid hormone production. Hashimoto is a complex disease and cross-curricular therapies probably will find more interest than one-way therapy.
The complete chloroplast genome of Curcuma longa L. (Zingiberaceae)

Abstract Curcuma longa L. is a widely distributed medicinal plant in Southeast Asia, especially in China. In this study, we reported and characterized the complete chloroplast genome sequence of C. longa. The chloroplast genome was determined to be 162,255 bp in length. It contained large single-copy (LSC) and small single-copy (SSC) regions of 86,975 bp and 15,776 bp, respectively, which were separated by a pair of 29,752 bp inverted repeat (IR) regions. The genome is predicted to contain 133 genes, including 87 protein-coding genes, 38 tRNA genes, and eight rRNA genes. The overall GC content of the genome is 36.2%. A phylogenetic tree reconstructed by 23 chloroplast genomes reveals that C. longa is mostly related to Curcuma roscoeana, with bootstrap support values of 100%.
Maize residues changes soil fungal composition and decrease soil microbial co-ocurrence networks complexity

Fusarium graminearum (Fg) can cause different diseases in cereals and maize crops worldwide, and a correct management of previous crop residues could decrease disease incidence and/or severity. Bacterial, fungal and Fusarium communities were studied by metabarcoding approach in 8 agricultural fields with wheat-maize rotation system in Brittany, France, during three years. Additionally, shift in microbial communities were evaluated under mesocosm experiments in soils amended or not with maize residues and/or Fg isolate. Bacterial communities composition were highly influenced by crop soil origin in both environmental and mesocosm soils, while bacteria co-occurrence network complexity was decreased by maize residues in environmental samples and Fg treatment in mesocosm samples. Maize residues altered slightly bacteria-fungi co-occurrence networks, while all treatments on mesoscosm experiments showed lower complexity in bacteria-fungi networks than Control Soil treatment. A clear input of fungal genera Epicoccum, Fusarium, Vishniacozyma, Articulospora, Papiliotrema, Sarocladium, Xenobotryosphaeria, Ramularia, Cladosporium, Cryptococcus and Bullera from maize residues to soil were observed for both environmental and mesocosm samples. Moreover, an increase of F. graminearum and F. avenaceum was observed in soils whe maize residues were presented. Finally, microbial co-occurrence networks reported some OTUs significant correlated to Fusarium spp. OTUs, such as those assigned to Epicoccum, Vishniacozyma and Sarocladium fungal genera, previously reported as efficient biocontrol agents versus Fusarium spp. Moreover, a decrease of complexity was observed for soil bacterial and bacterial-fungal networks due to maize addition in both environmental and mesocoms communities.
Screening of some Sumatran medicinal plants and selected secondary metabolites for their cytotoxic potential against MCF-7 and HSC-3 cell lines

In continuation of our study of Sumatran plants and bioactivities of their constituents particularly their cytotoxic activities, we re-extracted lichen Stereocaulon graminosum Schaer (Stereocaulaceae), and isolated atranorin (1) and stictic acid (4). These isolated compounds have been tested for their cytotoxic activities against human breast adenocarcinoma cancer cell (MCF-7) and human oral squamous carcinoma cancer cell (HSC-3) using MTT assay with a slight modification. Some methanolic extracts of the leaves of Elephantopus scaber, Piper betle, Andrographis paniculata, rhizomes of Boesenbergia pandurata, Alpinia galanga, Kaempferia galanga and isolated compounds; ethyl haematommate (2), olivatolic acid (3), deoxyelephantopin (5), andrographolide (6), hydroxychavicol (7), eugenol (8), curcumin (9), pinostrobin (10), pinocembrin (11), alpinetin (12), α-mangostin (13), angiopteroside (14), and stevioside (15) from Sumatran traditional medicinal plants have also been tested.
Effect of Phaseolus vulgaris on E. coli induced peritonitis and bacteraemia in mice

Infectious or non-infectious peritonitis leads to systemic inflammation due to violation of the peritoneum which is often fatal. Evidences suggest that common bean (Phaseolus vulgaris L.) is a source of nutrients and contains phenolic compounds having antioxidant activity and its consumption has been linked with improved health benefits. The aim of the present investigation was evaluate the in vitro antibacterial, antioxidant activity and protective potential of the methanolic extract of P. vulgaris in E. coli induced model of peritonitis in albino wistar rats. Rats were pre-treated with 200 mg/kg and 400 mg/kg/bwt dose for 3 days and fourth day with E. coli (1×108 CFU/ml) strain and consecutively 3 days treatment. Mortality was monitored for 14 days. After the death of rats or completion of the experiment rats were sacrifice and kidney were used for our protocol. Colonies were count and statically analysis was done. Results showed dose dependent antibacterial activity. Thus the methanolic extract of P. vulgaris exhibited significant protection against E. coli induced peritonitis in normal rats. It significantly reduced the viable cells of E. coli when inoculated in rats. Activity is attributed to flavonoids and phenolic compounds. The present study thus suggests that methanolic extract of P. vulgaris significantly reverses peritoneal infection by E. coli in rats. It can be suggest that this medicinal formulation will be used as herbal medicine with no side effects. The high content of phenolic compounds, antioxidant activity and antibacterial activity of P. vulgaris indicate that they may impart health benefits when consumed and should be regarded as a valuable source of antioxidants. Thus, consumption of P. vulgaris seed along with coats might be recommended to gaining better nutritive benefits. Keywords: P. vulgaris, Peritonitis, Antioxidant, Antibacterial, E. coli
Identification and target prediction of small miRNA

Aim: The aim of the study was to identify, target, and predict small miRNA. Materials and Methods: Small RNA with <50 nucleotides long non-coding RNA has various functions such as gene regulation, we took one such RNA from non-coding RNA database from NCBI and analyzed its structure and function. Quality of small RNA sequencing data of Drosophila melanogaster downloaded from NCBI was checked using next-generation sequencing, FastQC and adapters were removed using cutadapt tool. The quality check was performed before and after trimming. Results: From the data, we have obtained the miRNA which had the highest score seemed to have many regulatory functions and it is surprising to know how one miRNA could be responsible for 10 important functions. Conclusion: Earlier it was considered that the exon part was more clinically significant, but the current trend is that the miRNA which is obtained from the intron part is of equal importance and has a lot of clinical significance which could be discovered in future large scale researches.
Developing a microscopic image dataset in support of intelligent phytoplankton detection using deep learning

Phytoplankton plays an important role in marine ecological environment and aquaculture. However, the recognition and detection of phytoplankton rely on manual operations. As the foundation of achieving intelligence and releasing human labour, a phytoplankton microscopic image dataset PMID2019 for phytoplankton automated detection is presented. The PMID2019 dataset contains 10 819 phytoplankton microscopic images of 24 different categories. We leverage microscopes to collect images of phytoplankton in the laboratory environment. Each object in the images is manually labelled with a bounding box and category of ground-truth. In addition, living cells move quickly making it difficult to capture images of them. In order to generalize the dataset for in situ applications, we further utilize Cycle-GAN to achieve the domain migration between dead and living cell samples. We built a synthetic dataset to generate the corresponding living cell samples from the original dead ones. The PMID2019 dataset will not only benefit the development of phytoplankton microscopic vision technology in the future, but also can be widely used to assess the performance of the state-of-the-art object detection algorithms for phytoplankton recognition. Finally, we illustrate the performances of some state-of-the-art object detection algorithms, which may provide new ideas for monitoring marine ecosystems.
Complete mitochondrial genome of red panda (Ailurus fulgens) and its phylogenetic analysis

Abstract In this study, we reported the complete mitochondrial genome sequence of a red panda (Ailurus fulgens). The mitogenome (GenBank accession number MK886830) length is 16,517 bp and exhibits the typical structure of mammalian mitochondrial genomes contains 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs, and one control region. The tRNASer (AGY) gene failed to form the typical clover-leaf secondary structure as it lacked the dihydrouridine (DHU) arm. phylogenetically, our sequence cluster together with genus Ailurus, which showed a closer genetic relationship. The mitogenome provides new data to further elucidation and understand the phylogeny of red pandas.
Inter-specific variation of maternal thyroid hormones associate with migration, mode of development, and captivity: a phylogenetic comparative analysis

Animals’ life-history traits vary largely along many continuums across species and several physiological parameters have been proposed as possible mediators that drive the life-history variation, such as metabolic rates, glucocorticoids, and oxidative stress. Interestingly, thyroid hormones (THs), despite closely interacting with these physiological parameters, have never been considered as such mediators. Because of the crucial effects on embryonic development, THs can also induce transgenerational plasticity when transferred into developing offspring, for instance, via egg yolks in birds. In this study, we compiled a unique data set of maternal yolk THs in 34 bird species across 17 families and 6 orders and analysed them with data of life-history traits along several life-history continuums. Our phylogenetic mixed models estimated higher deposition of the two most important forms of THs – T3 and T4 -- in both concentrations and total amounts in migratory species than resident species, and larger total amounts of T3 in precocial species than in altricial species. However, maternal THs did not show clear associations with any traits of the pace- of-life syndrome. When taking environmental factors into account, we found that captive species also deposited higher TH concentrations and larger amounts in the egg yolks than wild species. These findings suggest that THs are likely involved in the evolution of life-history variation or vice versa. Accordingly we proposed many angles for further studies.