Miracle-dz/UniFAR-FTUs huggingface dataset:
Inference of viral quasispecies with a paired de Bruijn graph

MOTIVATION RNA viruses exhibit a high mutation rate and thus they exist in infected cells as a population of closely related strains called viral quasispecies. The viral quasispecies assembly problem asks to characterise the quasispecies present in a sample from high-throughput sequencing data. We study the de novo version of the problem, where reference sequences of the quasispecies are not available. Current methods for assembling viral quasispecies are either based on overlap graphs or on de Bruijn graphs. Overlap graph based methods tend to be accurate but slow, whereas de Bruijn graph based methods are fast but less accurate. RESULTS We present viaDBG, which is a fast and accurate de Bruijn graph based tool for de novo assembly of viral quasispecies. We first iteratively correct sequencing errors in the reads, which allows us to use large k-mers in the de Bruijn graph. To incorporate the paired-end information in the graph, we also adapt the paired de Bruijn graph for viral quasispecies assembly. These features enable the use of long range information in contig construction without compromising the speed of de Bruijn graph based approaches. Our experimental results show that viaDBG is both accurate and fast, whereas previous methods are either fast or accurate but not both. In particular, viaDBG has comparable or better accuracy than SAVAGE, while being at least nine times faster. Furthermore, the speed of viaDBG is comparable to PEHaplo but viaDBG is able to retrieve also low abundance quasispecies, which are often missed by PEHaplo. AVAILABILITY viaDBG is implemented in C ++ and it is publicly available at https://bitbucket.org/bfreirec1/viadbg. All data sets used in this article are publicly available at https://bitbucket.org/bfreirec1/data-viadbg/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Tek (Tie2) is not required for cardiovascular development in zebrafish

ABSTRACT Angiopoietin/TIE signalling plays a major role in blood and lymphatic vessel development. In mouse, Tek (previously known as Tie2) mutants die prenatally due to a severely underdeveloped cardiovascular system. In contrast, in zebrafish, previous studies have reported that although embryos injected with tek morpholinos (MOs) exhibit severe vascular defects, tek mutants display no obvious vascular malformations. To further investigate the function of zebrafish Tek, we generated a panel of loss-of-function tek mutants, including RNA-less alleles, an allele lacking the MO-binding site, an in-frame deletion allele and a premature termination codon-containing allele. Our data show that all these mutants survive to adulthood with no obvious cardiovascular defects. MO injections into tek mutants lacking the MO-binding site or the entire tek locus cause similar vascular defects to those observed in MO-injected +/+ siblings, indicating off-target effects of the MOs. Surprisingly, comprehensive phylogenetic profiling and synteny analyses reveal that Tek was lost in the largest teleost clade, suggesting a lineage-specific shift in the function of TEK during vertebrate evolution. Altogether, these data show that Tek is dispensable for zebrafish development, and probably dispensable in most teleost species. Summary: Mouse Tek mutants and zebrafish tek morphants display severe defects but zebrafish tek mutants do not; we show that tek morpholinos cause off-target effects and that tek is missing in most fish.
PLASMAPHERESIS FOR RESCUE IN SEVERE ENCEPHALOPATHY AND MULTIORGAN FAILURE FROM FULMINANT INFLUENZA (H3N2) INFECTION.

We are presenting a case of 4-years-old previously healthy male with coma, severe acute hepatitis and multiorgan failure in presence of Influenza infection. Literature review highlighted an immune-mediated pathophysiology for such presentations so the child underwent a trial of plasmapheresis which resulted in a rapid clinical improvement and child was discharge in his baseline neurological status by day 14.
Gallic and Ellagic Acids Are Promising Adjuvants to Conventional Amphotericin B for the Treatment of Cutaneous Leishmaniasis

In this study, we demonstrated the potential associative effect of combining conventional amphotericin B (Amph B) with gallic acid (GA) and with ellagic acid (EA) in topical formulations for the treatment of cutaneous leishmaniasis in BALB/c mice. Preliminary stability tests of the formulations and in vitro drug release studies with Amph B, GA, Amph B plus GA, EA, and Amph B plus EA were carried out, as well as assessment of the in vivo treatment of BALB/c mice infected with Leishmania major. ABSTRACT In this study, we demonstrated the potential associative effect of combining conventional amphotericin B (Amph B) with gallic acid (GA) and with ellagic acid (EA) in topical formulations for the treatment of cutaneous leishmaniasis in BALB/c mice. Preliminary stability tests of the formulations and in vitro drug release studies with Amph B, GA, Amph B plus GA, EA, and Amph B plus EA were carried out, as well as assessment of the in vivo treatment of BALB/c mice infected with Leishmania major. After 40 days of infection, the animals were divided into 6 groups and treated twice a day for 21 days with a gel containing Amph B, GA, Amph B plus GA, EA, or Amph B plus EA, and the negative-control group was treated with the vehicle. In the animals that received treatment, there was reduction of the lesion size and reduction of the parasitic load. Histopathological analysis of the treatments with GA, EA, and combinations with Amph B showed circumscribed lesions with the presence of fibroblasts, granulation tissue, and collagen deposition, as well as the presence of activated macrophages. The formulations containing GA and EA activated macrophages in all evaluated parameters, resulting in the activation of cells of the innate immune response, which can generate healing and protection. GA and EA produced an associative effect with Amph B, which makes them promising for use with conventional Amph B in the treatment of cutaneous leishmaniasis.
Symbiont-Mediated Digestion of Plant Biomass in Fungus-Farming Insects.

Feeding on living or dead plant material is widespread in insects. Seminal work on termites and aphids has provided profound insights into the critical nutritional role that microbes play in plant-feeding insects. Some ants, beetles, and termites, among others, have evolved the ability to use microbes to gain indirect access to plant substrate through the farming of a fungus on which they feed. Recent genomic studies, including studies of insect hosts and fungal and bacterial symbionts, as well as metagenomics and proteomics, have provided important insights into plant biomass digestion across insect-fungal mutualisms. Advances in understanding of the divergent and complementary functions of complex symbionts not only reveal the mechanism of how these herbivorous insects catabolize plant biomass, but also represent a promising reservoir for carbohydrate-active enzyme discovery, which is of considerable biotechnological interest. Expected final online publication date for the Annual Review of Entomology, Volume 66 is January 11, 2020. Please see http://www.annualreviews. org/page/journal/pubdates for revised estimates.
The Rab5–Rab11 Endosomal Pathway is Required for BDNF-Induced CREB Transcriptional Regulation in Hippocampal Neurons

Brain-derived neurotrophic factor (BDNF) is a key regulator of the morphology and connectivity of central neurons. We have previously shown that BDNF/TrkB signaling regulates the activity and mobility of the GTPases Rab5 and Rab11, which in turn determine the postendocytic sorting of signaling TrkB receptors. Moreover, decreased Rab5 or Rab11 activity inhibits BDNF-induced dendritic branching. Whether Rab5 or Rab11 activity is important for local events only or for regulating nuclear signaling and gene expression is unknown. Here, we investigated, in rat hippocampal neuronal cultures derived from embryos of unknown sex, whether BDNF-induced signaling cascades are altered when early and recycling endosomes are disrupted by the expression of dominant-negative mutants of Rab5 and Rab11. The activity of both Rab5 and Rab11 was required for sustained activity of Erk1/2 and nuclear CREB phosphorylation, and increased transcription of a BDNF-dependent program of gene expression containing CRE binding sites, which includes activity-regulated genes such as Arc, Dusp1, c-fos, Egr1, and Egr2, and growth and survival genes such as Atf3 and Gem. Based on our results, we propose that early and recycling endosomes provide a platform for the integration of neurotrophic signaling from the plasma membrane to the nucleus in neurons, and that this mechanism is likely to regulate neuronal plasticity and survival. SIGNIFICANCE STATEMENT BDNF is a neurotrophic factor that regulates plastic changes in the brain, including dendritic growth. The cellular and molecular mechanisms underlying this process are not completely understood. Our results uncover the cellular requirements that central neurons possess to integrate the plasma membrane into nuclear signaling in neurons. Our results indicate that the endosomal pathway is required for the signaling cascade initiated by BDNF and its receptors at the plasma membrane to modulate BDNF-dependent gene expression and neuronal dendritic growth mediated by the CREB transcription factor. CREB is a key transcription factor regulating circuit development and learning and memory.
Induction Heating in Nanoparticle Impregnated Zeolite

The ultra-stable Y (H-USY) zeolite is used as catalyst for the conversion of plastic feedstocks into high added value products through catalytic cracking technologies. However, the energy requirements associated with these processes are still high. On the other hand, induction heating by magnetic nanoparticles has been exploited for different applications such as cancer treatment by magnetic hyperthermia, improving of water electrolysis and many other heterogeneous catalytic processes. In this work, the heating efficiency of γ-Fe2O3 nanoparticle impregnated zeolites is investigated in order to determine the potential application of this system in catalytic reactions promoted by acid catalyst centers under inductive heating. The γ-Fe2O3 nanoparticle impregnated zeolite has been investigated by X-ray diffraction, electron microscopy, ammonia temperature program desorption (NH3-TPD), H2 absorption, thermogravimetry and dc and ac-magnetometry. It is observed that the diffusion of the magnetic nanoparticles in the pores of the zeolite is possible due to a combined micro and mesoporous structure and, even when fixed in a solid matrix, they are capable of releasing heat as efficiently as in a colloidal suspension. This opens up the possibility of exploring the application at higher temperatures.
Research on the Active VitaminD_3's transformation by microorganism (I)——25(OH)D_3's Biology Translation

According to the biology characteristics of target fungoid, some actinomyces were screened. Only the target actinomyces could translate VD_3 into active VD_3--25(OH)D_3. And then HPLC and TLC were used to detect the activities of the actinomyces. All of the results showed that actinomyces TN-955 had the excellent translation function.
FIBTEM clot firmness parameters correlate well with the fibrinogen concentration measured by the Clauss assay in patients and healthy subjects

Abstract The Clauss assay is the assay most often used for measuring plasma fibrinogen levels. However, the FIBTEM-assay, determined using thromboelastometry (ROTEM) can also be used to estimate fibrinogen levels. A major advantage of the FIBTEM is that it can provide information about fibrinogen levels within minutes, while the Clauss assay needs 30–60 min before the result is available. The aim of this study was to investigate the correlation between fibrinogen levels measured by the Clauss assay and results from the FIBTEM-assay. We included 111 patients ≥18 years for whom both ROTEM analyses and a fibrinogen measurement using the Clauss assay were available. In addition, ROTEM and Clauss measurements from 75 healthy subjects were included. Spearman correlation was used to determine the association between the results of both assays. The patients included were mostly patients with major trauma or undergoing large surgery (e.g. cardiac surgery or liver transplantation). Strong correlations were found between FIBTEM clot firmness parameters and fibrinogen levels measured by the Clauss assay in patients (Spearman’s correlation coefficients (rs) above 0.80 (p < .001) for all subgroups) and healthy subjects (rs = 0.66, p < .001). The correlation between early FIBTEM parameters (clot firmness at 5 or 10 min) and the maximum clot firmness was almost perfect (rs above 0.96). Also, the correlation between the α-angle and FIBTEM parameters was strong (rs above 0.7). In conclusion, strong correlations were found between early FIBTEM parameters and fibrinogen levels.
Advances research in plant nitrogen, phosphorus and their stoichiometry in terrestrial ecosystems: a review

Nitrogen (N), phosphorus (P) and their stoichiometry play pivotal roles in plant structure and functions, development and ecological strategies in terrestrial ecosystems due to their coupling with each other and their irreplaceability. Plant N and P can be influenced by biotic and abiotic factors, such as individual traits, climate change and human disturbance, and it is those factors that determine the plant community composition and structure that fi- nally affect the ecosystem processes. According to previous studies, there is an allometric relationship between N and P. Relationships between plant N and P depend on the soil nutrient condition and species plasticity in N and P. Understanding the relationships between plant N and P in major ecological gradients can further our knowledge about vegetation restoration, succession, biodiversity, ecosystem trophic structure and biogeochemical cycles. This information could help predict potential changes in terrestrial ecosystems in response to future climate change. We review recent advances in the influencing factors and mechanism of stoichiometry in order to improve understanding of plant responses to global change.
Gender Differences in the Personality Correlates of Reactive and Proactive Aggression in a Spanish Sample of Young Adults

Since the conceptual distinction of reactive and proactive aggression has been proposed, numerous studies have tried to disentangle the correlates of each function of aggression. While reactive aggression tends to be more strongly related to impulsivity, angry reactivity, or hostility, proactive aggression has proved to be more associated with psychopathic traits and goal-directed behaviors. However, in addition to the current debate about the actual distinction of reactive and proactive aggression, the study of gender differences is still scarce. Thus, the aim of the current study is to evaluate the distinctiveness of reactive and proactive aggression by means of the examination of their differential personality correlates (i.e., HEXACO, psychopathic traits, and impulsivity facets), as well as the assessment of gender differences in those relationships. To that end, a sample composed of 326 young adults aged 18–34 was recruited in Spain. The results evidenced unique associations of reactive and proactive aggression with a set of personality traits, including the HEXACO factors, psychopathic traits, and impulsivity facets, both at raw and residual level. Furthermore, when all the variables were entered in the model, proactive aggression remained strongly related to the factor of Honesty/humility and Emotionality, whereas reactive aggression remained associated with the impulsive/irresponsive factor of psychopathy and, specifically, with the facet of negative urgency, as well as with lack of Agreeableness. Likewise, some gender differences emerged as regards certain correlates. Specifically, proactive aggression was related with lack of Agreeableness and sensation seeking only in males and with the impulsive/irresponsive factor of psychopathy only in females, although these differences were not statistically significant. The conceptual and practical implications of these finding are discussed in terms of prevention.
Significant reduction of indeterminate (atypical) diagnosis after implementation of The Paris System for Reporting Urinary Cytology: A single‐institution study of more than 27,000 cases

Urinary cytology is a noninvasive and cost‐effective diagnostic and surveillance test in the clinical management of urothelial carcinoma (UC). The Paris System for Reporting Urinary Cytology (TPS), published in 2016, introduced definite diagnostic criteria aimed at improving performance in detecting high‐grade UC (HGUC) and decreasing the indeterminate (atypical) diagnosis.
Determination of the Infectious Agent of Translucent Post-Larva Disease (TPD) in Penaeus vannamei

A new emerging disease called “translucent post-larvae disease” (TPD) or “glass post-larvae disease” (GPD) of Penaeus vannamei, characterized by pale or colorless hepatopancreas and digestive tract, has become an urgent threat to the shrimp farming industry. Following this clue that treatment of an antibacterial agent could alleviate the disease, systematic investigation of the potential infectious agent of TPD was conducted using bacterial identification and artificial challenge tests to fulfill Koch’s postulates. A dominant bacterial isolate, Vp-JS20200428004-2, from the moribund individuals was isolated and identified as Vibrio parahaemolyticus based on multi-locus sequence analysis. However, Vp-JS20200428004-2 differed from the V. parahaemolyticus that caused typical acute hepatopancreatic necrosis disease. Immersion challenge tests revealed that Vp-JS20200428004-2 could cause 100% mortality within 40 h at a dose of 1.83 × 106 CFU/mL, and experimental infected shrimp showed similar clinical signs of TPD. The Vp-JS20200428004-2 could be re-isolated and identified from the experimental infected individuals. Moreover, histopathological analysis of diseased samples indicated that Vp-JS20200428004-2 caused severe necrosis and sloughing of epithelial cells of the hepatopancreas and midgut in shrimp individuals both naturally and experimentally infected. Our present results indicated that Vp-JS20200428004-2 is a highly virulent infectious agent associated with the TPD and deserves further attention.
Experimental study of Punica granatum flower Polyphenol's effect on IL-6,TXB2's and PPAR-γ mRNA's expression in IR rats

Aim To investigate Punica granatum flower Polyphenol's effect on peroxisome proliferator-activated receptor-γ(PPAR-γ)mRNA's expression in heart and IL-6,TXB2's content of blood serum in insulin resistance (IR) rats which were induced by low dose of streptozotocin(STZ) and high calorie food.Methods Male SD rats were randomly divided into normal group,model group,greating group.The rats of normal group were fed with common food while the others with high calorie food and injected with low dose of STZ.Fasting plasma glucose(FPG),fasting insulin(FIns),IL-6 and TXB2 level of all rats were measured by routine methods,and insulin sensitivity index(ISI)was calculated accordingly.At the end of experimental treatment,the total mRNAs of heart tissues were extracted and the genic fragments of PPAR-γ were amplificated in order to detect their expression levels.Results Punica granatum flower Polyphenol could reduce the FPG,FIns,IL-6 and TXB2 level in model rats ,increase the PPAR-γ mRNA's expression and enhance ISI effectively.Conclusion Punica granatum flower Polyphenol can ameliorate IR conditon of the model rats and its mechanism is probably related to its effect of enhancing the genic expression level of PPAR-γ.
Isolation and PCR identification of 12 strains of inclusion body hepatitis virus from clinical broilers.

The 12 virus strains isolated originally from livers of broiler chickens with inclusion body hepatitis were characterized during chicken embryo kidney(CEK)cell culture.12 isolates of fowl adenovirus groupⅠ were identified based on virus morphology,cytopathogenic effect(CPE)and sequence analysis.The virus particles were non-enveloped,from 70 to 80nm in diameter,and had icosahedrad.Different affections could be observed in embryo eggs during different periods.The virus caused CPE in CEK cells.An avian adenovirus-specific polymerase chain reaction(PCR)was developed.The primers were from the conserved hexon sequence data of the chicken embryo lethal orphan(CELO)avian adenovirus.An avian adenovirus-specific 508bp product was amplified by these primers from hexon.These results confirmed that the 12 isolates were members of chicken inclusion body hepatitis caused by fowl adenovirus groups.The inclusion body hepatitis specific PCR assay was sensitive,specific,rapid and simple,which would be useful for the clinical diagnosis of inclusion body hepatitis virus infection.
Metabolic Roles of Androgen Receptor and Tip60 in Androgen-Dependent Prostate Cancer

Androgen receptor (AR)-mediated signaling is essential for the growth and differentiation of the normal prostate and is the primary target for androgen deprivation therapy in prostate cancer. Tat interactive protein 60 kDa (Tip60) is a histone acetyltransferase that is critical for AR activation. It is well known that cancer cells rewire their metabolic pathways in order to sustain aberrant proliferation. Growing evidence demonstrates that the AR and Tip60 modulate key metabolic processes to promote the survival of prostate cancer cells, in addition to their classical roles. AR activation enhances glucose metabolism, including glycolysis, tricarboxylic acid cycle and oxidative phosphorylation, as well as lipid metabolism in prostate cancer. The AR also interacts with other metabolic regulators, including calcium/calmodulin-dependent kinase kinase 2 and mammalian target of rapamycin. Several studies have revealed the roles of Tip60 in determining cell fate indirectly by modulating metabolic regulators, such as c-Myc, hypoxia inducible factor 1α (HIF-1α) and p53 in various cancer types. Furthermore, Tip60 has been shown to regulate the activity of key enzymes in gluconeogenesis and glycolysis directly through acetylation. Overall, both the AR and Tip60 are master metabolic regulators that mediate cellular energy metabolism in prostate cancer, providing a framework for the development of novel therapeutic targets in androgen-dependent prostate cancer.
Revealing Solute Clusters in Coalescence by Atom Probe Tomography Analysis

Abstract Experimentally revealing dynamic evolution and growth behavior of small solute clusters in alloys remains a technical challenge. To date, the coalescence of the solute clusters has seldom been experimentally addressed. To address the challenge, we used atom probe tomography (APT) to access boundary information of solute clusters and identify those in close contact. By systematically investigating the population and size evolution of the clusters in close contact with aging time, we unveiled important information regarding the clusters in coalescence with the exsitu experimental technique. In this work, the maximum separation method was employed to identify clusters in APT datasets of naturally aged Al–Zn–Mg alloy. Coalescence was found to significantly contribute to the growth of small clusters and remained predominant for the formation and growth of large Guinier–Preston II ${\rm \lpar G}{\rm P}_{{\eta }^{\prime}}\rpar$ zones after 3 months aging.