Miracle-dz/UniFAR-FTUs huggingface dataset:
BACTERIAL DIVERSITY AND ANTIBIOTIC ACTIVITY IN TEMPERATE AUSTRALIAN MARINE SPONGES

The occurrence of permanent sponge-bacterial associations in five temperate marine sponges from Western Australia (Ircinia sp., Chondrilla australiensis, Echinodictyum clathrioides, Tethya ingalli and Coelosphaera sp.) was investigated using culturing techniques, facilitating both bacterial characterisation and subsequent screening for the presence of antimicrobial activity. Based on biochemical tests, most of the 136 bacterial isolates obtained from the sponges and surrounding water column on several occasions were tentatively identified as members of the Vibrionaceae. Fatty acid methyl ester (FAME) analysis indicated that the isolates represented a broad diversity of 32 distinct bacterial groupings. Most bacterial groups (18) were only ever found associated with sponge tissues, whilst others were found only in the water (6) or were present in the water and one or more sponges (8). For only three bacterial groups was there evidence, based on their presence in host tissues on every sampling occasion and absence from the surrounding water, of a permanent relationship with sponge hosts. One of these groups occurred consistently in three of the sponges species studied (C. australiensis, T. ingalli and Coelosphaera sp.), while the other two were consistently associated with only a single sponge species (T. ingalli and Coelosphaera sp.). Crude extracts of Coelosphaera sp. were not inhibitory to Staphylococcus aureus, but a bacterium from this sponge produced a heat labile, non-dialysable inhibitor of S. aureus. Crude extracts of three other sponge species (Ircinia sp., E. clathrioides and T. ingalli) inhibited S. aureus, but culture supernatants of the bacteria from these sponges did not. These results are discussed in terms of their contribution to understanding sponge microbial diversity and the potential for discovery of new pharmacologically active chemicals.
Structure of the Ebola virus nucleoprotein – RNA complex

Ebola virus is an emerging virus capable of causing a deadly disease in humans. Replication, transcription and packaging of the viral genome is carried out by the viral nucleocapsid. The nucleocapsid is a complex of the viral nucleoprotein, RNA and several other viral proteins. The nucleoprotein NP forms large, RNA-bound, helical filaments and acts as a scaffold for additional viral proteins. The 3.1 Å single-particle cryo-electron microscopy structure of the nucleoprotein-RNA helical filament presented here resembles previous structures determined at lower resolution while providing improved molecular details of protein-protein and protein-RNA interactions. The higher resolution of the structure presented here will facilitate the design and characterization of novel and specific Ebola virus therapeutics targeting the nucleocapsid. Synopsis The 3.1 Å single-particle cryo-electron microscopy structure of the RNA-bound, Ebola virus nucleoprotein helical filament provides molecular details of protein-protein and protein-RNA interactions.
The oxysterol synthesizing enzyme CH25H contributes to the development of intestinal fibrosis

Intestinal fibrosis and stenosis are common complications of Crohn’s disease (CD), frequently requiring surgery. Anti-inflammatory strategies can only partially prevent fibrosis; hence, anti-fibrotic therapies remain an unmet clinical need. Oxysterols are oxidized cholesterol derivatives, with important roles in various biological processes. The enzyme cholesterol 25-hydroxylase (CH25H) converts cholesterol to 25-hydroxycholesterol (25-HC), which modulates immune responses and oxidative stress. In human intestinal samples from CD patients we found a strong correlation of CH25H mRNA expression with the expression of fibrosis markers. We demonstrate reduced intestinal fibrosis in mice deficient for the CH25H enzyme using the sodium dextran sulfate (DSS)-induced chronic colitis model. Additionally, using a heterotopic transplantation model of intestinal fibrosis, we demonstrate reduced collagen deposition and lower concentrations of hydroxyproline in CH25H knockouts. In the heterotopic transplant model, CH25H was expressed in fibroblasts. Taken together, our findings indicate an involvement of oxysterol synthesis in the pathogenesis of intestinal fibrosis.
A significant antihypertensive effect of Holarrhena floribunda supported by an exploratory phytochemical study

Introduction: Holarrhena floribunda (G.Don) T.Durand & Schinz is a tree that can grow up to 25 m with white latex in its organs. The bark of this plant is commonly used in traditional medicine to treat dysentery, diarrhea, diabetes, malaria, and high blood pressure. In this study, phytochemical groups were widely investigated on trunk bark as well as on leaves of H. floribunda harvested in Danyi (Togo). Antioxidant activity and antihypertensive properties of the plant extracts were also evaluated on sound guinea pigs.Methods: The hydro-ethanolic extract of the trunk bark was prepared and antioxidant activity was evaluated via the DPPH radical-scavenging and the ferric-reducing antioxidant power (FRAP) methods, and via the determination of the total phenolics content. This hydro-ethanolic extract was used to assess the plant extract effect on blood pressure of sound guinea pigs.Results: So, phytochemical screening revealed that H. floribunda contained most of the phytochemical groups. The 50% inhibitive concentration of that extract by DPPH was 29.80 ± 0.001 μg/mL. The equivalent of Fe2+ by FRAP was 1009.9 ± 0.6 μmol/g of dry extract. The content of phenolic compounds was 139 ± 0.053 mg GAE (gallic acid equivalents)/g of dry extract. Intravenous injection of the extract (10, 20, 40, 80 mg/kg) via the invasive method in guinea pigs under normal strain caused a decrease in diastolic blood pressure, systolic blood pressure, and so in mean arterial pressure (MAP) by dose cumulative and time-dependent.Conclusion: The results show that hydro-ethanolic extract of H. floribunda trunk bark has antihypertensive and antioxidant properties. This might be the reason for the use of that extract for the treatment of hypertension in traditional medicine.
Intuitive Physics: Understanding Dynamics in Real World Physical Scenes

Intuitive physics, or naive physics, is our ability to predict outcomes of a variety of basic physical interactions and to reason about the dynamics of a scene. It is an important ability people have, a crucial part of our intelligence, that helps us deal with the complexity of the surrounding world. Different fields have tried to answer parts of the many questions that one could ask what is the underlying mechanism allowing us to do this type of inference, why do we experience certain illusions, how we can mimic our ability in software systems and robots. This report focuses on the third question by analyzing the newest approaches in machine learning and robotics.
LIDSKÝ KAPITÁL A SOLOWUV MODEL HUMAN CAPITAL AND SOLOW MODEL

This paper aims to discuss the long run output growth with human capital relation. Within recent long run growth models, human capital is being considered as an important variable. But the main discussion is still held about the question how human capital affect real macroeconomic determinants, respectively the real growth and how to define human capital within the model. Here I am trying to determine main directions in which can human capital influence the real output. This paper comes from basic Solow model and it analyses and extends its fundamental conclusions. I am trying to discover question whether the factor of human capital can be an output-leveraging factor at the same level as capital, technology and labor, or in other words whether is it correctly considered in the augmented Solow model as a directly impacting factor of total output.
Eigenvector-based community detection for identifying information hubs in neuronal networks

Eigenvectors of networked systems are known to reveal central, well-connected, network vertices. Here we expand upon the known applications of eigenvectors to define well-connected communities where each is associated with a prominent vertex. This form of community detection provides an analytical approach for analysing the dynamics of information flow in a network. When applied to the neuronal network of the nematode Caenorhabditis elegans, known circuitry can be identified as separate eigenvector-based communities. For the macaque’s neuronal network, community detection can expose the hippocampus as an information hub; this result contradicts current thinking that the analysis of static graphs cannot reveal such insights. The application of community detection on a large scale human connectome (~1.8 million vertices) reveals the most prominent information carrying pathways present during a magnetic resonance imaging scan. We demonstrate that these pathways can act as an effective unique identifier for a subject’s brain by assessing the number of matching pathways present in any two connectomes. Author summary The dynamic response of a network to stimulus can be understood by investigating that system’s eigenvectors. The eigenvectors highlight the most prominent nodes; those that are either a major source or destination for information in the network. Moreover by defining a coordinate system based on multiple eigenvectors, the most prominent communities can be detected with the most prominent node detected alongside those in the community that funnel information towards it. These methods are applied to a variety of brain networks to highlight the circuitry present in a flatworm (Caenorhabditis elegans), the macaque and human subjects. Static graphs representing the connectomes are analysed to provide insights that were previously believed to only be detectable by numerically modelling information flow. Finally, we discovered that brain networks created for human subjects at different times can be identified as belonging to the same subject by investigating the similarity of the prominent communities.
Filamin B and CD13 are components of senescent secretomes that may be involved in primary (stress induced) and paracrine senescence of mesenchymal stromal cells

135 Erciyes Med J 2019; 41(2): 135-40 • DOI: 10.14744/etd.2019. 37974 ORIGINAL ARTICLE – OPEN ACCESS This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License. Tiziana Squillaro , Servet Özcan , Nicola Alessio , Mustafa Burak Acar , Giovanni Di Bernardo , Mariarosa Anna Beatrice Melone , Gianfranco Peluso , Umberto Galderisi Filamin B and CD13 Are Components of Senescent Secretomes That May Be Involved in Primary (Stress Induced) and Paracrine Senescence of Mesenchymal Stromal Cells Objective: In the present study we aim to evaluate whether some of the proteins previously identified in the secretome of senescent bone marrow (BM)and adipose (A)-mesenchymal stromal cells (MSCs) could be involved in regulation of senescence phenomena. Materials and Methods: Among the identified proteins, we selected Filamin B (FLNB) and Aminopeptidase N (CD13) that were exclusively found in the secretome of senescent cells. We silenced their mRNA expression in BM-MSCs by means of RNA interference technology and induced acute senescence by hydrogen peroxide treatment. Our goal was to evaluate if FLNB or CD13 silencing may affect onset of senescence. Results: Our preliminary data showed that CD13 protein could be a key factor involved in the regulation and determination of both primary and paracrine induced senescence in human BM-MSCs. On the other hand, Filamin B seems not to be involved in the determination of primary senescence whereas its presence could be part of the mechanism that regulates the senescence induction in human BM-MSCs by paracrine signaling. Conclusion: Our study provides a useful base for identifying the complex extracellular protein networks involved in the regulation of MSC cellular senescence.
REPRODUCTIVE QUALITY OF ROOSTERS WITH NORMAL AND MODIFIED GENOME

To date, progress has been made in the production of transgenic poultry: effective gene constructs have been obtained, and efficient systems for recombinant DNA delivery into target cells have been created. However, when breeding a genetically modified poultry, problems may arise with transgenic offspring, in particular its low viability or limited number. This paper is the first to report on histological structure of the testes and the composition of spermatogenic cells in the seminiferous tubules of transgenic roostersand on the quality and fertilizing ability of their semen. The study was carried out on transgenic roosters which were obtained by us in different ways based on chicken ( Gallus gallus L.) Pervomaiskaya breed and their non-transgenic analogues (vivarium of Ernst Federal Science Center for Animal Husbandry, 2017-2018). group I was transgenic roosters after introduction of the lentiviral vector pWRSV into chicken embryos in vivo ( n = 4); group II was transgenic roosters obtained by transplantation of transformed in vitro donor spermatogonia into the testes of sterile recipient roosters ( n = 5). The control group included non-transgenic roosters selected as analogues (breed, age). Sperm was collected once every 2-3 days in penicillin vials heated to 30  C by ab- dominal massage carried by the same technician. The following semen indicators were investigated: ejaculate volume, sperm motility and concentration in the ejaculate, the head and acrosome area, total spermatozoa length, flagella length. The criteria for evaluation of the fertilizing capacity of semen were the egg fertilization and the hatching of the younger generation. The histological structure of the seminiferous tubules and the composition of spermatogenic cells were also studied. Our exper-iments show that the quantitative and qualitative indicators of sperm in transgenic roosters decrease compared to the control. The volume of ejaculate, the concentration and motility of spermatozoa were 19, 15 and 1 % lower in group I and 38, 29 and 2 % lower in group II. However, there are no deviations in the safety of the acrosome in transgenic roosters when compared to the control individ- uals. Histological analysis of testes of the transgenic and non-transgenic roosters also reveals no significant pathological disturbances in the seminiferous tubules. Nevertheless, an insignificant decrease in the number of spermatogenic cells in transgenic individuals occurs when compared to the control ones (up to 19 %). The fertilizing capacity of the transgenic roosters’ semen is also lower than that of the control roosters. In group I the differences with the control group for the percentage of chick hatching were 15 %, in the group 2 — 10 % (р < 0.05), which may indicate some negative effect of the integration of the transgene on the functional state of the germ cells in the studied genetically modified individuals.
Mislocalization and clearance of neuronal Rhes as a novel hallmark of tauopathies

The farnesyltransferase inhibitor lonafarnib reduces tau inclusion burden and atrophy in familial tauopathy models by inhibiting farnesylation on the Ras GTPase, Rhes, and activating autophagy. While hinting at a role of Rhes in tau aggregation, it is unclear how translatable these results are for sporadic forms of tauopathy. We used a combination of quantitative pathology using multiplex immunofluorescence for Rhes, several tau post-translational modifications, and single nucleus RNA sequence analysis to interrogate Rhes presence and distribution in human cortical neurons and Rhes relation to tau and TDP-43 changes. snRNA data suggest that Rhes is found in all cortical neuron subpopulations, not only in striatum cells. Histologic investigation in hippocampal formation from multiple postmortem cases in five different tauopathies and healthy controls and TDP-43 proteinopathy showed that nearly all neurons in control brains display a pattern of diffuse cytoplasmic Rhes positivity. However, in the presence of abnormal tau, but not TDP-43 inclusions, the patterns of neuronal cytoplasmic Rhes tend to present as either punctiform or fully absent. Our findings reinforce the relevance of the link between Rhes changes and tau pathology suggested by in vivo and in vitro models of tauopathy and support a potential clinical application of lonafarnib to tauopathies.
miR-21 blocks obesity in mice: a potential therapy for humans

microRNAs are promising drug targets in obesity and metabolic disorders. miR-21 expression is upregulated in obese white adipose tissue (WAT), however, its physiological role in WAT has not been fully explored. We aimed to dissect the underlying molecular mechanisms of miR-21 in treating obesity, diabetes, and insulin resistance. We demonstrated, in human and mice, that elevated miR-21 expression is associated with metabolically healthy obesity. miR-21 mimic affected the expression of genes associated with adipogenesis, thermogenesis, and browning in 3T3-L1 adipocytes. In addition, it blocked high fat diet-induced weight gain in obese mice, without modifying food intake or physical activity. This was associated with metabolic enhancements, WAT browning and thermogenic programming, and brown AT induction through VEGF-A, p53, and TGF{beta}1 signaling pathways. Our findings add a novel role of miR-21 in the regulation of obesity and a potential therapy for both obesity and T2D without altering caloric intake and physical activities.
A review of evidence about use and performance of species distribution modelling ensembles like BIOMOD

The idea of combining predictions from different models into an ensemble has gained considerable popularity in species distribution modelling, partly due to free and comprehensive software such as the R package BIOMOD. However, despite proliferation of ensemble models, we lack oversight of how and where they are used for modelling distributions, and how well they perform. Here, we present such an overview.
Abstract P21: Saliva as a testing specimen with or without pooling for SARS-CoV-2 detection by multiplex RT-PCR test

Objectives Sensitive and high throughput molecular testing availability is essential during the COVID-19 pandemic. The vast majority of the SARS-CoV-2 molecular assays use nasopharyngeal or oropharyngeal swab specimens collected from suspected individuals. However, collecting these specimens has apparent drawbacks, including discomfort to patients and exposure risk to healthcare workers. Methods We developed and validated of QuantiVirus™ SARS-CoV-2 multiplex test using saliva as the testing specimens with pooling. Results The analytical sensitivity (LOD) was confirmed to be 100-200 copies/mL. For clinical evaluation, 85 known positive and 90 knowns negative NPS specimens were showed a positive predictive agreement of 100% and a negative predictive agreement of 98.9%. Twenty paired NPS and saliva samples were tested and showed overall 80% concordance rate without significant difference between NPS and saliva specimens by Wilcoxon signed-rank test (p=0.13). On a large scale of saliva-based population screening, the positive test rate was 1.79% among 389 saliva specimens. Furthermore, saliva sample pooling up to 6 samples for SARS-CoV-2 detection is feasible with sensitivity of 94.8% and specificity of 100%. Conclusions These results demonstrated that the clinical performance of saliva-based testing is comparable to that of NPS-based testing, and that pooling of saliva specimens for SARS-CoV-2 detection is feasible. Citation Format: Qing Sun, Jonathan Li, Hui Ren, Larry Pastor, Yulia Loginova, Joseph Wong, Zhao Zhang, Aiguo Zhang, Chuanyi Mark Lu, Michael Sha. Saliva as a testing specimen with or without pooling for SARS-CoV-2 detection by multiplex RT-PCR test [abstract]. In: Proceedings of the AACR Virtual Meeting: COVID-19 and Cancer; 2021 Feb 3-5. Philadelphia (PA): AACR; Clin Cancer Res 2021;27(6_Suppl):Abstract nr P21.
Havens for threatened Australian mammals: the contributions of fenced areas and offshore islands to the protection of mammal species susceptible to introduced predators

Context Many Australian mammal species are highly susceptible to predation by introduced domestic cats (Felis catus) and European red foxes (Vulpes vulpes). These predators have caused many extinctions and have driven large distributional and population declines for many more species. The serendipitous occurrence of, and deliberate translocations of mammals to, ‘havens’ (cat- and fox-free offshore islands, and mainland fenced exclosures capable of excluding cats and foxes) has helped avoid further extinction. Aims The aim of this study was to conduct a stocktake of current island and fenced havens in Australia and assess the extent of their protection for threatened mammal taxa that are most susceptible to cat and fox predation. Methods Information was collated from diverse sources to document (1) the locations of havens and (2) the occurrence of populations of predator-susceptible threatened mammals (naturally occurring or translocated) in those havens. The list of predator-susceptible taxa (67 taxa, 52 species) was based on consensus opinion from >25 mammal experts. Key results Seventeen fenced and 101 island havens contain 188 populations of 38 predator-susceptible threatened mammal taxa (32 species). Island havens cover a larger cumulative area than fenced havens (2152 km2 versus 346 km2), and reach larger sizes (largest island 325 km2, with another island of 628 km2 becoming available from 2018; largest fence: 123 km2). Islands and fenced havens contain similar numbers of taxa (27 each), because fenced havens usually contain more taxa per haven. Populations within fences are mostly translocated (43 of 49; 88%). Islands contain translocated populations (30 of 139; 22%); but also protect in situ (109) threatened mammal populations. Conclusions Havens are used increasingly to safeguard threatened predator-susceptible mammals. However, 15 such taxa occur in only one or two havens, and 29 such taxa (43%) are not represented in any havens. The taxon at greatest risk of extinction from predation, and in greatest need of a haven, is the central rock-rat (Zyzomys pedunculatus). Implications Future investment in havens should focus on locations that favour taxa with no (or low) existing haven representation. Although havens can be critical for avoiding extinctions in the short term, they cover a minute proportion of species’ former ranges. Improved options for controlling the impacts of cats and foxes at landscape scales must be developed and implemented.
LQR optimized BP neural network PI controller for speed control of brushless DC motor

This paper proposes a linear quadratic regulator (LQR) optimized back propagation neural network (BPNN) PI controller called LN-PI for the speed control of brushless direct current (BLDC) motor. The controller adopts BPNN to adjust the gain K P and K I of PI, which improves the dynamic characteristics and robustness of the controller. Moreover, LQR is adopted to optimize the output of BPNN so as to make it close to the target PI gains. Finally, the optimized control output is inputted into the BLDC motor system to achieve speed control. The performance analysis of the proposed controller is presented to compare with traditional PI controller, neural network PI controller and LQR optimized PI controller under MATLAB/Simulink, the results shows that the proposed controller effectively improves the response speed, reduces the steady-state error and enhances the anti-interference ability.