Miracle-dz/UniFAR-FTUs huggingface dataset:
The morphogenesis of Nephrolepis exaltata Schott vitrocultures prevailed from stolon apexes, cultivated on aseptic media with auxine content.

This study establishes the influence of various concentrations of auxine on Nephrolepis exaltata Schott vitrocultures. The β indolilbutiric acid (AIB) and α naftilacetic acid (ANA), as growing substances, determine an intensification risogenesis, phylogenesis and calusogenesis at the level of explants prevailed from stolon apexes. Concentrations of 1 mg/l, 1.5 mg/l and 2 mg/l β indolilbutiric acid (AIB) and α naftilacetic acid (ANA), in Murashige-Skoog culture media (1962) [11] influence morphogenesis and organogenesis in a positive way at the level of Nephrolepis exaltata Schott explants.
Multimodal evidence for delayed fear extinction in adolescence and young adulthood

Previous research in rodents and humans points to an evolutionarily conserved profile of blunted fear extinction during adolescence, underpinned by brain structures such as the amygdala and medial prefrontal cortex (mPFC). In this study, we examine age-related effects on the function and structural connectivity of this system in fear extinction in adolescence and young adulthood. Younger age was associated with greater amygdala activity and delayed mPFC engagement to learned threat cues as compared to safety cues. Furthermore, greater structural integrity of the uncinate fasciculus, a white matter tract that connects the amygdala and mPFC, mediated the relationship between age and acceleration of mPFC engagement during extinction. These findings suggest that age-related changes in the structure and function of amygdala-mPFC circuitry may underlie the protracted maturation of fear regulatory processes, rendering younger individuals more vulnerable to anxiety disorders, which emerge during development.
SHANK3 downregulation in the VTA accelerates the extinction of contextual associations induced by non-familiar conspecific interaction

Conditioned place preference (CPP) paradigms, traditionally adopted to study the reinforcing properties of drugs of abuse, have been developed to investigate the neurobiological mechanisms underlying the reinforcing properties of social stimuli. These protocols are largely based on single-housing before and/or during the social stimulus-contextual cues acquisition phase. Here, based on previously established social interaction-induced CPP paradigms, we characterize a place preference task relying on the reinforcing properties of free interaction with a non-familiar (novel) conspecific. The formation of contextual associations induced by the interaction with a novel social stimulus does not require single-housing, necessitates dopamine (DA) receptor 2/3 (D2/3R) activation and undergoes extinction. Interestingly, while extinction of CPP responses is reduced by single-housing, it is accelerated by the downregulation of the autism spectrum disorder (ASD)-related protein SHANK3 in the ventral tegmental area (VTA). Thus, inspired by the literature on drug of abuse-induced contextual learning, we propose that acquisition and extinction of CPP might be used as behavioral assays to assess social-induced contextual association and “social-seeking” dysfunctions in animal models of psychiatric disorders.
The Analysis Of Lecturer Knowledge For Implementation To The Effective Classroom

The purpose of this study was to implementation lecturers’ knowledge about effective classroom and their classroom practices for teaching English. It was also knowing the correspondence between lecturers’ knowledge and the practices. This study designed using qualitative case study approach. The data was obtained using multiple-choice typed test, observation checklist, and interview. The subjects were four English lecturers and their cadets as supporting subject. The data obtained was analyzed using interactive model proposed by Miles and Huberman. The data revealed that the subjects had variety of knowledge about classroom ; one of them had sufficient knowledge , another one showed average result and the other two were emerging. In their classroom practice, two lecturers performed effective classroom skill, but the other two showed average effort in managing their class. For the correspondence, it was found that there were three group of lecturers; the first group has sufficient knowledge and applied it simultaneously, the second group has average knowledge but applied it in more effective ways, and the third group has emerging knowledge and applied it likely to be the same as their knowledge in the classroom practice.
Exploring the Evolutionary Relationship Between Virulence and Drug Resistance

One of the many possible negative outcomes of pathogen evolution is the emergence of a virulent drug resistant strain. A pathogen may exploit plasmid-mediated gene transfer to gain drug resistance and virulence genes in an attempt to become the exclusive infection. To answer questions on the possible emergence of a virulent drug resistant strain we constructed a nine dimensional SIS model with treatment. We used plasmid-mediated gene transfer by way of superinfection to distribute virulence and drug resistance genes. By examining the resulting system of differential equations at the two extremes of treatment level (%0 and %100), we determined the stability of the single strain endemic infection equilibrium points of interest. In the absence of treatment we determined a set of ancestral conditions which provided constraints on the model parameters. In the presence of treatment we focused on the ability of the virulent drug resistant (AB) strain to invade the avirulent drug resistant (B) strain. We were able to express these invasion conditions in terms of novel reproductive ratios that incorporated both non-superinfection effects and superinfection effects. Our model reveals that plasmid-mediated gene transfer by way of superinfection increases the parameter space allowing for virulence to evolve in a drug resistant population. However, virulence in a drug resistant population is not always more likely to evolve in comparison to virulence in a drug sensitive population. i
Measuring the archaeome: detection and quantification of archaea signatures in the human body

Due to their fundamentally different biology, archaea are consistently overlooked in conventional 16S rRNA gene amplicon surveys. Herein, we evaluate different methodological set-ups to detect and quantify archaea signatures in human samples (nose, oral, appendix, stool, and skin) using amplicon sequencing and quantitative PCR. With our optimized protocol, we were able to increase the detection of archaeal RSVs from one (using a so-called “universal” approach) to 81 RSVs in a representative sample set. Moreover, we confirmed the presence of about 5% archaeal signatures in the human gut, but found, unexpectedly, an almost 1:1 ratio of archaeal to bacterial 16S rRNA genes in appendix and nose samples. This finding indicates a high prevalence of archaeal signatures in body regions thus far not analyzed for the presence of archaea using appropriate methods. In order to assess the archaeome diversity and archaeal abundance, a specific archaea-targeting methodology is required, for which we propose two standard procedures. These methodologies might not only prove useful for analyzing the human archaeome in more detail, but could also be used for other holobionts’ samples.
Characteristics and origins of non-functional Pm21 alleles in Dasypyrum villosum and wheat genetic stocks

Most Dasypyrum villosum resources are highly resistant to wheat powdery mildew that carries Pm21 alleles. However, in the previous studies, four D. villosum lines (DvSus-1 ∼ DvSus-4) and two wheat-D. villosum addition lines (DA6V#1 and DA6V#3) were reported to be susceptible to powdery mildew. In the present study, the characteristics of non-functional Pm21 alleles in the above resources were analyzed after Sanger sequencing. The results showed that loss-of-functions of Pm21 alleles Pm21-NF1 ∼ Pm21-NF3 isolated from DvSus-1, DvSus-2/DvSus-3 and DvSus-4 were caused by two potential point mutations, a 1-bp deletion and a 1281-bp insertion, respectively. The non-functional Pm21 alleles in DA6V#1 and DA6V#3 were same to that in DvSus-4 and DvSus-2/DvSus-3, respectively, indicating that the susceptibilities of the two wheat genetic stocks came from their D. villosum donors. The origins of non-functional Pm21 alleles were also investigated in this study. Except the target variants involved, the sequences of Pm21-NF2 and Pm21-NF3 were identical to that of Pm21-F2 and Pm21-F3 in the resistant D. villosum lines DvRes-2 and DvRes-3, derived from the accessions GRA961 and GRA1114, respectively. It was suggested that the non-functional alleles Pm21-NF2 and Pm21-NF3 originated from the wild-type alleles Pm21-F2 and Pm21-F3. In summary, this study gives an insight into the sequence characteristics of non-functional Pm21 alleles and their origins in natural population of D. villosum.
Both cell-intrinsic and environmental factors constrain speed and persistence in T cell migration

8 9 T cells are key effector cells in the immune system that are well-known for their ability to adapt their shape and 10 behavior to environmental cues. It has been suggested that these highly diverse, context-dependent migration 11 patterns reflect an optimization process – where T cells adjust motility parameters such as speed and persistence 12 to aid their search for antigen. Whereas models investigating such ”search strategies” typically treat speed and 13 persistence as independent variables, one aspect of cell motility was recently found to be conserved across 14 a large variety of cell types: fast-moving cells turn less frequently. This raises the question whether T cells 15 can tune speed and persistence independently of each other. We therefore investigated to what extent this 16 universal coupling between cell speed and persistence (UCSP) shapes the behavior of migrating T cells. We 17 first show that the UCSP emerges spontaneously in an in silico Cellular Potts Model (CPM) of T cell migration. 18 Our model shows a link between the UCSP and cell shape dynamics, which put an upper bound on both the 19 speed and the persistence a cell can reach. We then use the CPM to examine how environmental constraints 20 affect motility patterns of T cells migrating in the crowded environments they also face in vivo, and show that T 21 cells completely lose their speed-persistence coupling when confined in a densely packed environment such 22 as the epidermis. Thus, although our model further highlights the validity of the UCSP in migrating cells, it 23 also demonstrates that environmental factors may overrule this coupling. Our data show that T cell motility 24 parameters are subject to both cell-intrinsic and extrinsic constraints, suggesting that ”optimal” T cell search 25 strategies may not always be attainable in vivo. 26
Stream diatoms exhibit weak niche conservation along global environmental and climatic gradients

Niche conservatism (NC) describes the scenario in which species retain similar characteristics or traits over time and space, and thus has potentially important implications for understanding their biogeographic distributions. Evidence consistent with NC includes similar niche properties across geographically distant regions. We investigated whether NC was evident in stream diatom morphospecies by modeling species responses to environmental and climatic variables in a set of calibration sites (from the US) and then evaluated the models with test sets (from France, Finland, New Zealand, Antilles and La Réunion). We also examined whether diatom species showed congruency in environmental niche optima and niche breadths between the study regions, and whether species occupancy and functional traits influenced the observed patterns. We used boosted regression tree models with local environmental variables and climatic variables as predictors. We detected low NC in both environmental and climate models and a lack of consistent differences in NC between widely distributed and regionally rare species and among functional groups. For all species, diatom environmental and climatic optima varied clearly between the regions but showed some positive relationships especially for pH and total phosphorus. Diatom niche breadths were only weakly correlated between the US and the other regions. We demonstrated that diatoms showed overall relatively little NC globally, and NC was especially low for climatic variables. Collectively, these findings suggest that there may exist locally adapted lineages within the diatom morphospecies or diatoms possess some adaptation potential for differences in temperature. We argue that in diatoms, environmental and especially climate models may not be transferrable in space globally but need regional diatom data for calibration because species niches seem to differ among geographical regions.
Bayesian Classification of Microbial Communities Based on 16S rRNA Metagenomic Data

We propose a Bayesian method for the classification of 16S rRNA metagenomic profiles of bacterial abundance, by introducing a Poisson-Dirichlet-Multinomial hierarchical model for the sequencing data, constructing a prior distribution from sample data, calculating the posterior distribution in closed form; and deriving an Optimal Bayesian Classifier (OBC). The proposed algorithm is compared to state-of-the-art classification methods for 16S rRNA metagenomic data, including Random Forests and the phylogeny-based Metaphyl algorithm, for varying sample size, classification difficulty, and dimensionality (number of OTUs), using both synthetic and real metagenomic data sets. The results demonstrate that the proposed OBC method, with either noninformative or constructed priors, is competitive or superior to the other methods. In particular, in the case where the ratio of sample size to dimensionality is small, it was observed that the proposed method can vastly outperform the others. Author summary Recent studies have highlighted the interplay between host genetics, gut microbes, and colorectal tumor initiation/progression. The characterization of microbial communities using metagenomic profiling has therefore received renewed interest. In this paper, we propose a method for classification, i.e., prediction of different outcomes, based on 16S rRNA metagenomic data. The proposed method employs a Bayesian approach, which is suitable for data sets with small ration of number of available instances to the dimensionality. Results using both synthetic and real metagenomic data show that the proposed method can outperform other state-of-the-art metagenomic classification algorithms.
The Antimicrobial Properties Of Extracts Obtained From Begonia Goegoensis N.E.Br. Leaf Against Pseudomonas Aeruginosa Isolates

The present study was designed to evaluate the antibacterial property of crude extracts of the leaves of Begonia goegoensis N.E. Br. prepared in different solvent systems against Pseudomonas aeruginosa (ATCC 27583) and β -lactamases producing Pseudomonas aeruginosa (MBL-positive Pseudomonas aeruginosa ) strains. Therefore, five kinds of solvents were used to extract the active ingredients from the leaves of Begonia goegoensis : ethanol, methanol, ethyl acetate, hexane, and dichloromethane. The testing of antibacterial activity of the plant extracts was carried out in vitro by Kirby-Bauer disc diffusion technique. Subsequently, the present study has shown that ethanolic extract from the leaves of Begonia goegoensis exhibited strong activity against Pseudomonas aeruginosa (inhibition zone diameter ranged from 12 mm to 13 mm), while methanolic leaf extract screened revealed less profound activity (within 11–12.5 mm). Moreover, it has been observed that ethyl acetate, hexane and dichloromethane extracts obtained from leaves of Begonia goegoensis revealed no antibacterial activity against P. aeruginosa and MBL-positive Pseudomonas aeruginosa strains. MBL-positive Pseudomonas aeruginosa was also susceptible to ethanolic and methanolic extracts (inhibition zone diameter ranged from 12.5 mm to 15.5 mm). Thus, the spectrum of activity observed in the present study indicate that the alcoholic leaf extract of Begonia goegoensis could be a possible source to obtain new and effective herbal medicines to treat various infectious diseases, including infections, caused by drug resistant microorganisms.
SimFection: a digital resource for vaccination education

Abstract Vaccination coverage in the United Kingdom is below the level recommended by the World Health Organisation, and when vaccination coverage is not sufficient, outbreaks of infectious diseases can occur. In 2015, coverage of the first dose of the Measles-Mumps-Rubella vaccine declined in the United Kingdom for the first time since 2008, indicating a need to raise public awareness and understanding of the importance of vaccination to public health. Identifying 16 – 18-year olds as a target audience, being future parents who would make decisions regarding vaccination of their children, a digital educational resource (‘SimFection’) was developed to deliver key messages about the spread and control of vaccine-preventable infectious diseases (identified via school curricula). The process of development utilised an iterative approach, involving a cyclic process of prototyping, testing, analysis and refinement with a range of audiences including students, schoolchildren, and trainee teachers. The completed resource is now available online for free download.
A simple, rapid method for detecting seven common invasive fish species in Europe from environmental DNA

Biological invasions are a global threat to biodiversity, and many arise from deliberate introductions. The American freshwater fish Micropterus salmoides and Ameiurus spp. (Ameiurus melas and Ameiurus nebulosus) were introduced to Europe for recreational fishing, Gambusia holbrooki and Gambusia affinis were introduced for mosquito population control, and Lepomis gibbosus was introduced as an ornamental species. The Asiatic Pseudorasbora parva was acquired inadvertently as an accompanying species in fish consignments. This article presents a novel approach for detecting these species directly from water samples based on a panel of five taxon‐specific primers within 16S rDNA. The primers were validated from tissue, in aquarium experiments, and from Ebro River water samples (Spain). With a simple polymerase chain reaction (PCR) protocol, followed by visualization in agarose gel or capillary electrophoresis, it was possible to detect these species from environmental DNA concentrations as low as 0.89–100 pg mL–¹. This sensitive and economical tool can be used to control European invasions of these species and to preserve native biodiversity.
Influence of NAADP and bafilomycine A1 on activity of ATPase in liver postmitochondrial fraction

Recycling of the endo-lysosomal organelles occur by permanent in the cell. This store is thought to be the acidic store because V-type of H+-ATPase is responsible for their acidification. Bafilomycine A1 is a selective inhibitor of vacuolar H+ ATPase, and is often used as anticancer drug. However, it is not clear if applying of bafilomycine A1 is safe for normal cells. Endo-lysosomes are important cellular Ca2+ storage, sensitive to nicotinic acid adenine dinucleotide phosphate (NAADP). Hepatocytes were shown to have NAADP-sensitive acidic store. But the correlation between acidic store and endoplasmatic reticulum or plasmatic membrane during endo-lysosomal organelles recycling and fusion is still unknown. The main goal of this study was to examine influence of bafilomycine A1 and NAADP on activity of Na+/K+-ATPase, basal Mg2+-ATPase and Ca2+-ATPase of plasmatic membrane (PM) and endoplasmatic reticulum (ER) for better understanding of the relationship between acidic organelles and PM/ER. Besides possibility of bafilomycine A1 applying as anticancer drug is examined. All experiments were conducted using rat liver postmitochondrial fraction. It was shown that SERCA activity is increasing under bafilomycine A1 presence, as well as NAADP. At the same time, changes in PMCA activity was not found. Preincubation of rat liver postmitochondrial fraction with bafilomycine A1 completely prevented NAADPinduced increasing of SERCA activity. Bafilomycine A1 decreased activity of Na+/K+ATPase and amplificated NAADP-induced decreasing of this pump. Applying of NAADP caused more intensive decrease in Na+/K+-ATPase activity after preincubation of this fraction with bafilomycine A1. It was also shown that bafilomycine A1 caused increasing of basal Mg2+-ATPase activity and NAADP intensify bafilomycine A1-induced changes of function of this pump. These effects are realized due to changes of pH inside the endolysosomal ogranels, acidification of incubation medium, as well as calcium concentration in local contact sites. A conclusion was made that NAADP-sensitive store is bafilomycine A1-sensitive, which also has direct contact sites to ER, but not to PM. Besides, existing of NAADPsensitive, but bafilomycine-insensitive store in this fraction is supposed, which is more likely represented by endosomes. So, applying bafilomycine A1 in anticancer therapy may cause a damage of endo-lysosomal organelles recycling in healthy cells.
Development of and Therapeutic Applications for Novel Inhibitors of Deoxycytidine Kinase

Author(s): Armijo, Amanda Lee | Advisor(s): Radu, Caius G. ; Czernin, Johannes | Abstract: Deoxycytidine kinase (dCK), a rate-limiting enzyme in the deoxyribonucleotide salvage pathway, participates in the production of deoxyribonucleoside triphosphates (dNTPs). dCK is highly expressed in hematopoietic tissues and many cancers. In addition, dCK is responsible for the phosphorylation, and thus activation of several antiviral and anticancer nucleoside analog pro-drugs. Austin, Toy, and colleagues have demonstrated that dCK deficient mice (dCK-/-) have severe developmental defects of the lymphoid and hematopoietic progenitor cells, indicating that dCK is pivotal for their normal development. Further study of the T, B, and erythroid lineages revealed nucleotide pool imbalances resulting in replication stress and cell cycle arrest in the early stages of DNA replication. Dual inactivation of both dCK and thymidine kinase 1 (TK1) in vivo supported our hypothesis that salvage of thymidine by TK1 was responsible for the allosteric block of the de novo pathway enzyme, ribonucleotide reductase, consequentially perturbing the nucleotide pools. These findings and the role of dCK in cancer led to our interest in developing a small molecule inhibitor. Positron Emission Tomography and the dCK-specific substrate, 18F-L-1-(2'-deoxy-2'-F luoroarabinofuranosyl) Cytosine, proved useful in the quick identification of top performing dCK inhibitors in vivo. Following a high throughput screen and a structure-activity relationship study we successfully identified high potency small molecule inhibitors of dCK (dCKi). The combination of the dCKi with pharmacological perturbations of de novo dNTP synthesis, via thymidine, in acute lymphoblastic leukemia cells depletes deoxycytidine triphosphate pools leading to DNA replication stress, cell cycle arrest, and apoptosis in vivo, without detectable toxicity to normal tissues. The results from our studies further our understanding of nucleotide metabolism in normal hematopoiesis and hematological malignancies, and identify dCK as a new therapeutic target in hematological malignancies.
Virological examination of conjunctival swabs in clinically healthy horses

The aim of the study was to determine the presence of the equine influenza virus (EIV), the equine arteritis virus (EAV), and the equine herpesvirus (EHV) in the conjunctival sac of clinically healthy horses. Fifty horses of both sexes and various breeds and ages were included in the study. Virus isolation was carried out in cell cultures (the Madin-Darby canine kidney, green monkey kidney and rabbit kidney cells) from conjunctival swabs. The hemaglutination assay was carried out in order to identify EI viral amplification. The study revealed no presence of the above listed viruses in the conjunctival sac of clinically healthy horses.