Miracle-dz/UniFAR-FTUs huggingface dataset:
IRF-7 Mediates Type I IFN Responses in Endotoxin-Challenged Mice

IRF-7 mediates robust production of type I IFN via MyD88 of the TLR9 pathway in plasmacytoid dendritic cells (pDCs). Previous in vitro studies using bone marrow-derived dendritic cells lacking either Irf7 or Irf3 have demonstrated that only IRF-3 is required for IFN-β production in the TLR4 pathway. Here, we show that IRF-7 is essential for both type I IFN induction and IL-1β responses via TLR4 in mice. Mice lacking Irf7 were defective in production of both IFN-β and IL-1β, an IFN-β-induced pro-inflammatory cytokine, after LPS challenge. IFN-β production in response to LPS was impaired in IRF-7-deficient macrophages, but not dendritic cells. Unlike pDCs, IRF-7 is activated by the TRIF-, but not MyD88-, dependent pathway via TBK-1 in macrophages after LPS stimulation. Like pDCs, resting macrophages constitutively expressed IRF-7 protein. This basal IRF-7 protein was completely abolished in either Ifnar1−/− or Stat1−/− macrophages, which corresponded with the loss of LPS-stimulated IFN-β induction in these macrophages. These findings demonstrate that macrophage IRF-7 is critical for LPS-induced type I IFN responses, which in turn facilitate IL-1β production in mice.
Deciphering the Pharmacological Mechanisms of Taohe-Chengqi Decoction Extract Against Renal Fibrosis Through Integrating Network Pharmacology and Experimental Validation In Vitro and In Vivo

Taohe-Chengqi decoction (THCQ), a classical traditional Chinese medicinal (TCM) formula, has been extensively used for treating chronic kidney disease (CKD). However, the biological activity and mechanisms of action of its constituents against renal fibrosis have not yet been investigated thoroughly. This study was aimed at devising an integrated strategy for investigating the bioactivity constituents and possible pharmacological mechanisms of the n-butanol extract of THCQ (NE-THCQ) against renal fibrosis. The n-butanol extract of THCQ was prepared by the solvent extraction method. The components of NE-THCQ were analyzed using UPLC-Q/TOF-MS/MS techniques and applied for screening the active components of NE-THCQ according to their oral bioavailability and drug-likeness index. Then, we speculated the potential molecular mechanisms of NE-THCQ against renal fibrosis through pharmacological network analysis. Based on data mining techniques and topological parameters, gene ontology, and pathway enrichment, we established compound-target (C-T), protein-protein interaction (PPI) and compound-target-pathway (C-T-P) networks by Cytoscape to identify the hub targets and pathways. Finally, the potential molecular mechanisms of NE-THCQ against renal fibrosis, as predicted by the network pharmacology analyses, were validated experimentally in renal tubular epithelial cells (HK-2) in vitro and against unilateral ureteral obstruction models in the rat in vivo. We identified 26 components in NE-THCQ and screened seven bioactive ingredients. A total of 118 consensus potential targets associated with renal fibrosis were identified by the network pharmacology approach. The experimental validation results demonstrated that NE-THCQ might inhibit the inflammatory processes, reduce ECM deposition and reverse EMT via PI3K/AKT/mTOR and HIF-1α/VEGF signaling pathways to exert its effect against renal fibrosis. This study identified the potential ingredients of the NE-THCQ by UPLC-Q/TOF-MS/MS and explained the possible mechanisms of NE-THCQ against renal fibrosis by integrating network pharmacology and experimental validation.
Taxonomic Notes on Pycnothelia Dufour and Gymnoderma Nyl. (Cladoniaceae) in Madagascan Region

ABSTRACT This study was focused on two species of lichen-forming fungi from Madagascan Region whose taxonomy has been controversial over the years, Cladonia mascarena Nyl. and Heterodea madagascarea Nyl. While some authors considered C. mascarena to belong to Cladonia, others place it in Pycnothelia Dufour. In this study three loci (ITS rDNA, rpb2 and ef1α) were used to determine the phylogenetic placement of C. mascarena. Our results show that it belongs to Pycnothelia and the combination Pycnothelia mascarena (Nyl.) Nyl. is substantiated. In addition, a key to the genus Pycnothelia is provided. The morphological study of new specimens of Gymnoderma coccocarpum Nyl. and H. madagascarea concluded that these taxa belong to a same species, confirming the extension of Gymnoderma Nyl. to Africa. The overlooked genus Baeoderma Vain. is regarded as a synonym of Gymnoderma, and its type species Baeoderma madagascareum (Nyl.) Vain. is referred to G. coccocarpum.
Understanding Thermostability Factors of Barley Limit Dextrinase by Molecular Dynamics Simulations

Limit dextrinase (LD) is the only endogenous starch-debranching enzyme in barley (Hordeum vulgare, Hv), which is the key factor affecting the production of a high degree of fermentation. Free LD will lose its activity in the mashing process at high temperature in beer production. However, there remains a lack of understanding on the factor affecting the themostability of HvLD at the atomic level. In this work, the molecular dynamics simulations were carried out for HvLD to explore the key factors affecting the thermal stability of LD. The higher value of root mean square deviation (RMSD), radius of gyration (Rg), and surface accessibility (SASA) suggests the instability of HvLD at high temperatures. Intra-protein hydrogen bonds and hydrogen bonds between protein and water decrease at high temperature. Long-lived hydrogen bonds, salt bridges, and hydrophobic contacts are lost at high temperature. The salt bridge interaction analysis suggests that these salt bridges are important for the thermostability of HvLD, including E568–R875, D317–R378, D803–R884, D457–R214, D468–R395, D456–R452, D399–R471, and D541–R542. Root mean square fluctuation (RMSF) analysis identified the thermal-sensitive regions of HvLD, which will facilitate enzyme engineering of HvLD for enhanced themostability.
The Prognostic Significance of Metastatic Nodal Size in Non-surgical Patients With Esophageal Squamous Cell Carcinoma

Background: The present study aimed to determine the prognostic value of the size of metastatic lymph node (LN) in non-surgical patients with esophageal squamous cell carcinoma (ESCC). Methods: Three hundred seventy-six ESCC patients treated with definitive (chemo-) radiotherapy from January 2013 to March 2016 were reviewed. We analyzed potential associations of metastatic nodal size with responses, patterns of failure, and survival. Log-rank testing and Cox proportional hazards regression models were used to assess the impact of the clinical factors on survival. Results: The 3-years over survival (OS) rates following a median follow-up of 28.2 months were 53.2, 46.2, 35.5, and 22.7% for the N0 group, the >0.5 to ≤1 cm group, the >1 to ≤2 cm group, and the >2 cm group, respectively. The progression-free survival (PFS) rates for 2 years were 50.9, 44.2, 26.6, and 23.4% for the N0 group, the >0.5 to ≤1 cm group, the >1 to ≤2 cm group, and the >2 cm group, respectively. The objective response rates (ORR) for the 280 patients with metastatic LNs were 43.1% for the LN >0.5 to ≤1 cm group, 46.9% for the LN >1 to ≤2 cm group, and 25.5% for the LN ≥2 cm group. The LN >2 cm group had the worst ORR of the three groups with LNs. Gross tumor volume (GTV) failure was the most common failure pattern, followed by distant failure and out of GTV LN failure, with incidences of 47.9% (180 of 376), 42% (158 of 376), and 13.8% (52 of 376), respectively. Nodal size correlated statistically with GTV failure and distant failure but not with out-of-GTV nodal failure. After adjusting for age, sex, T category, Primary tumor location, and CRT, the size of metastatic LNs was an independent prognostic factor for OS and PFS in multivariate analyses. Conclusions: Nodal size is one of prognostic factors for non-surgical patients with ESCC and correlated statistically with GTV failure and distant failure.
Honeysuckle leaf blight reduces the growth of infected Amur honeysuckle (Lonicera maackii, Caprifoliaceae) seedlings in a greenhouse experiment1

Abstract. Amur honeysuckle (Lonicera maackii) is an important invasive plant species in the Ohio River Valley. Previous work has shown extensive dieback of honeysuckle in the region, coupled with the appearance of the native fungal pathogen, honeysuckle leaf blight (Insolibasidium deformans). Our goal was to find if the blight causes growth decline or mortality in Amur honeysuckle. Seedlings were grown under greenhouse conditions in 2017. Treated seedlings were sprayed with a spore solution prepared from blighted leaves that were collected from the field. They were placed into a growth chamber with conditions set for optimum spore growth and then returned to the greenhouse after leaf blight began to develop. Growth (height, total stem length, leaf area, and leaf number) and dark-adapted chlorophyll fluorescence (F v/F m) were measured periodically over the growing season. A repeated-measures analysis of aboveground growth indicated that larger, faster-growing plants were more likely to be infected, but their growth rates were subsequently reduced much more than uninfected treated plants and controls. There were positive correlations between F v/F m and RGR (relative growth rate). Blighted leaves had lower values of F v/F m than uninfected leaves. No infected plants died, but this experiment supports our hypothesis that leaf blight causes a significant growth decline in Amur honeysuckle. Future work will determine if the patterns seen under greenhouse conditions hold in the field.
A Preliminary Study to Investigate the Genetic Background of Longevity Based on Whole-Genome Sequence Data of Two Methuselah Dogs

Aging is the largest risk factor in many diseases and mortality alike. As the elderly population is expected to increase at an accelerating rate in the future, these phenomena will pose a growing socio-economic burden on societies. To successfully cope with this challenge, a deeper understanding of aging is crucial. In many aspects, the companion dog is an increasingly popular model organism to study aging, with the promise of producing results that are more applicable to humans than the findings that come from the studies of classical model organisms. In this preliminary study we used the whole-genome sequence of two extremely old dogs – age: 22 and 27 years (or 90–135% more, than the average lifespan of dogs) – in order to make the first steps to understand the genetic background of extreme longevity in dogs. We identified more than ∼80 1000 novel SNPs in the two dogs (7500 of which overlapped between them) when compared to three publicly available canine SNP databases, which included SNP information from850 dogs. Most novel mutations (∼52000 SNPs) were identified at non-coding regions, while 4.6% of the remaining SNPs (n∼1600) were at exons, including 670 missense variants – 76 of which overlapped between the two animals – across 472 genes. Based on their gene ontologies, these genes were related – among others – to gene transcription/translation and its regulation, to immune response and the nervous system in general. We also detected 12 loss-of-function mutations, although their actual effect is unclear. Several genetic pathways were also identified, which pathways may be tempting candidates to be investigated in large sample sizes in order to confirm their relevance in extreme longevity in dogs (and possibly, in humans). We hypothesize a possible link between extreme longevity and the regulation of gene transcription/translation, which hypothesis should be further investigated in the future. This phenomenon could define an interesting direction for future research aiming to better understand longevity. The presented preliminary results highlight the utility of the companion dog in the study of the genetic background of longevity and aging.
Genome-Wide Analysis Reveals Changes in Polled Yak Long Non-coding RNAs in Skeletal Muscle Development

Long non-coding RNAs (lncRNAs) have been extensively studied in recent years. Numerous lncRNAs have been identified in mice, rats, and humans, some of which play important roles in muscle formation and development. However, little is known about lncRNA regulators that affect muscle development in yak (Bos grunniens). LncRNA expression during skeletal muscle development in yak was analyzed by RNA sequencing at three development stages: 3 years (group A), 6 months (group M), and 90-day-old fetuses (group E). A total of 1180 lncRNAs were identified in the three development stages. Compared with group E, 154 were upregulated and 130 were downregulated in group A. Compared with group A, 31 were upregulated and 29 were downregulated in group M. Compared with group E, 147 were upregulated and 149 were downregulated in group M (padj < 0.001, |log2FC| > 1.2). In addition, functional annotation analysis based on gene ontology (GO) and the Kyoto protocol encyclopedia of genes and genomes (KEGG) database showed that differentially expressed lncRNAs (DElncRNAs) were cis–trans target genes. The results showed that DElncRNAs were mainly involved in PI3K-Akt signaling pathway, focal adhesion, MAPK signaling pathway, apoptosis, and p53 signaling pathway. Furthermore, RTL1, IGF2, MEF2C, Pax7, and other well-known muscle development regulators were included in a co-expression network of differentially expressed target genes and lncRNAs. These data will help to further clarify the function of lncRNAs in the different stages of skeletal muscle developmental in yak.
Synthetic Biology Tools for Genome and Transcriptome Engineering of Solventogenic Clostridium

Strains of Clostridium genus are used for production of various value-added products including fuels and chemicals. Development of any commercially viable production process requires a combination of both strain and fermentation process development strategies. The strain development in Clostridium sp. could be achieved by random mutagenesis, and targeted gene alteration methods. However, strain improvement in Clostridium sp. by targeted gene alteration method was challenging due to the lack of efficient tools for genome and transcriptome engineering in this organism. Recently, various synthetic biology tools have been developed to facilitate the strain engineering of solventogenic Clostridium. In this review, we consolidated the recent advancements in toolbox development for genome and transcriptome engineering in solventogenic Clostridium. Here we reviewed the genome-engineering tools employing mobile group II intron, pyrE alleles exchange, and CRISPR/Cas9 with their application for strain development of Clostridium sp. Next, transcriptome engineering tools such as untranslated region (UTR) engineering and synthetic sRNA techniques were also discussed in context of Clostridium strain engineering. Application of any of these discussed techniques will facilitate the metabolic engineering of clostridia for development of improved strains with respect to requisite functional attributes. This might lead to the development of an economically viable butanol production process with improved titer, yield and productivity.
Hot and Cool Executive Function in Elite- and Amateur- Adolescent Athletes From Open and Closed Skills Sports

Background Executive functions (EFs) not only play an important role in shaping adolescent’s goal-directed, future-oriented cognitive skills under relatively abstract, non-affective conditions (Cool EF), but also under motivationally significant, affective conditions (Hot EF). Empirical evidence suggest a link between EF, exercise and physical activity, specifically elite adult athletes appear to outperform amateur athletes in Cool EF; however, no previous studies have examined the relationship between Hot and Cool EFs and impulsivity during the developmentally sensitive period of adolescence comparing different types of sport (open- vs. closed-skills), and levels (elite athletes vs. amateurs). Methods A total 86 boys and girls between 13 and 15 years of age (mean: 14.0, SD: 0.79) from different sports (track-and-field; team handball) were recruited. Participants were further divided into two groups: (a) 40 elite, and (b) 46 amateur athletes. They completed four Cool EF tasks including Trail-Making Test, Trail-Walking-Test, Flanker task, n-back-task, and one Hot EF task on Game of Dice task. Data on subjective impulsivity (UPPS Impulsive Behavior Scale; Barratt Impulsiveness Scale-15) was also collected. Results There was a significant overall effect for expertise in favor of elite athletes (Wilks’ Lambda = 0.61, F(14,69) = 3.19, p = 0.001, ηp2 = 0.393), but no overall main effect for type of sport or an interaction for expertise by type of sport. Specifically, elite athletes showed significantly better performances on dual tasks. For Hot EF, there were no main effects for type of sport, expertise level, training experience or training duration. We also found positive correlations among Cool EF and impulsivity measures, and between Hot EF and Impulsivity, but no significant relationship between Cool and Hot EF. Conclusion The current understanding of the decisive cognitive abilities does not correspond to sporting reality, so that the tests frequently used are not sensitive enough to distinguish between elite and amateur athletes or different sports. However, it should also be remembered that the factors underlying complex sporting performance are multidimensional and are obviously difficult to trace back to selected partial aspects. Without being able to answer this question conclusively, we proposed a 4-D classification of experimental paradigms, in which we differentiate between tasks of different specificity, between Cool and Hot EF, and between task complexity, and type of sport.
The Effect of Probiotics on T-2 Mycotoxin Induced Apoptosis in Chicken Liver Tissue

Abstract In recent years many researchers have described the reduced mycotoxin toxicity caused by probiotic bacteria. Since reduction under gastrointestinal conditions of the bioavailability of mycotoxins by probiotics is not fully investigated in birds, the aim of the study was to determine the effect of probiotic on T-2 mycotoxicosis induced apoptosis in broiler’s liver. For the study, twelve 1-days old broilers were divided equally into T-2 toxin (T2) and probiotic with T-2 (P+T2) groups. From the first experimental day, probiotic Enterococcus faecium DSM 7134 was administered in drinking water to P+T2 group. From the fourth day, T-2 toxin was given for three consecutive days to T2 toxin group. At 8th experimental day chicken were sacrificed, liver was fixed in buffered 10% formalin, embedded into paraffin, slices 5 μm in thickness were cut followed by immunohistochemical staining with polyclonal primary antibodies p21 and p53 (Abcam, UK) according to the manufacturers’ guidelines (IHC kit, Abcam, UK). Blood samples were taken by cardiac puncture to measure liver enzymes. Immunohistochemical staining revealed strong expression of p53 and p21 antibodies in hepatocytes nuclei as well as around blood vessels in T-2 toxin group’s chicken liver tissue. Staining by both antibodies was less intensive in P+T2 group. Enzyme analysis showed significantly increased (p<0.05) blood aspartate transaminase and alanine transaminase concentrations by 33.87% and 68.03% respectfully in T2 toxin group, while enzyme concentrations were decreased in P+T2 group. The obtained results showed reduced features of liver apoptosis in treatment with probiotic bacteria.
If I knew they were the expression of creativity in people with blindness, I would rate them higher - Bias in Evaluating the Work of People with Blindness

Abstract Objective: In our pilot study, we tested to what extent subjective understanding and aesthetic appreciation of em-bossed drawings were dependent on the information that their creators were people with disability. Method: Our research was carried out in a gallery of contemporary art with 30 adults who were non-experts in the field of visual arts. Subjects were asked to view the current exhibition and then evaluate their subjective understanding and aesthetic appreciation (liking and interest) of 12 embossed drawings on seven-point scales. Results: Participants who were aware that persons with blindness had created the drawings (the informed group) in contrast to those who remained unaware (the uninformed group) declared – both – greater subjective understanding and higher appreciation of the exhibited works. In the informed group (N = 15), in comparison to the uninformed group (N = 15), the correlation between appreciation and subjective understanding of artwork was stronger. Conclusions: We discuss our pattern of results considering the attributional approach to creativity (Kasof, 1995) and the model of a cognitive mastering process of aesthetic experiences (Leder, Belke, Oeberst, & Augustin, 2004). Our results can be used, among others, by educators working in art galleries and museums.
Characteristics of African Swine Fever Virus Isolated from Domestic Pigs and Wild Boars in the Russian Federation and South Ossetia

Abstract The article presents the results of a comparative study of the biological, molecular and genetic characteristics of African swine fever virus (ASFV) isolates, obtained from domestic pigs and wild boars in the Russian Federation and South Ossetia from 2016 to 2018. The studied isolates caused the death of pigs manifesting, as a rule, signs of an acute or subacute form of the disease when using various methods of infection including intramuscular, direct contact, intranasal and oral routes. The virus was hemadsorbing, belonging to serotype 8 and genotype II, and accumulated in the blood with a titer of 6.5 to 7.5 lg HAU50/cm3. The ASFV isolates circulating in the central region of Russia were found to have an insertion of 10 base pairs in the intergenic region I73R/I329L. However, the ASFV isolated in the Irkutsk region and South Ossetia, as well as Georgia 2007/1 (FR682468.1), lacked this insertion.
Health–Aware and Fault–Tolerant Control of an Octorotor UAV System Based on Actuator Reliability

Abstract A major goal in modern flight control systems is the need for improving reliability. This work presents a health-aware and fault-tolerant control approach for an octorotor UAV that allows distributing the control effort among the available actuators based on their health information. However, it is worth mentioning that, in the case of actuator fault occurrence, a reliability improvement can come into conflict with UAV controllability. Therefore, system reliability sensitivity is redefined and modified to prevent uncontrollable situations during the UAV’s mission. The priority given to each actuator is related to its importance in system reliability. Moreover, the proposed approach can reconfigure the controller to compensate actuator faults and improve the overall system reliability or delay maintenance tasks.