Miracle-dz/UniFAR-FTUs huggingface dataset:
Phytochemical screening and anti-virulence properties of Ceiba pentandra and Ceiba aesculifolia (Malvaceae) bark extracts and fractions

<p><strong>Background</strong>: Inhibition of quorum sensing systems (QSS-I) is a novel strategy in the treatment of bacterial infections. To date, plants are the major source of metabolites with this inhibitory activity. Thus, species of Mexican flora can be important resources for obtaining metabolites with QSS-I activity. </p><p><strong>Hypothesis</strong>: We hypothesized that extracts from species of the genus <em>Ceiba</em> have metabolites with inhibitory activity against bacterial quorum sensing systems. </p><p><strong>Species studied</strong>: <em>Ceiba pentandra </em>(L.) Gaertn. <em> </em>and <em>Ceiba aesculifolia (</em>Kunth) Britten & Baker f. (Malvaceae). </p><p><strong>Study site and years of study</strong><strong>: We collected <em>Ceiba </em>bark in the municipalities of </strong>Tierra Blanca, Veracruz, and Acatlan, Oaxaca, in August 2013. </p><p><strong>Methods</strong>: We determined the effect of extracts from <em>C. aesculifolia</em> and <em>C. pentandra</em> against QSS-regulated phenotypes of <em>Chromobacterium violaceum</em> and <em>Pseudomonas aeruginosa</em>. Extracts were fractionated and the main metabolites were identified. As support in the identification of the species, we carried out an anatomical study of the bark. </p><p><strong>Results</strong>: Hexane and dichloromethane extracts of both species of <em>Ceiba</em> exhibited QSS-I activity. We identified four fractions rich in terpene and sterol compounds with the ability to attenuate virulence factors in <em>P. aerugiosa</em>. The histological analysis appears to support the presence of some differences in the barks that can facilitate identification of the two species. </p><p><strong>Conclusions</strong>: The extracts and fractions of the two species of <em>Ceiba </em>are sources of phytochemicals with the ability to regulate bacterial quorum sensing systems positively or negatively. </p>
Seed Availability Does Not Ensure Regeneration in Northern Ecosystems of the Endangered Limber Pine

Research Highlights: When biotic interactions such as disease alter both the seed production capacity of stands, and seedling survivorship, the relative importance of seed availability versus substrate specificity may alter future regeneration opportunities for plant populations. Background and Objectives: We investigated the importance of disease severity, seed availability, and substrate limitation to the regeneration dynamics of the endangered limber pine, Pinus flexilis, in two ecosystems with varying forest composition, and different histories of white pine blister rust infection (WPBR; Cronartium ribicola). Materials and Methods: A total of 17 stands from the montane ecoregion (Alberta, Canada) were sampled for seed production between 2007–2010, seedling density, and age structure. Model selection using an information theoretic approach compared a series of a priori models and their combinations, based on our hypotheses on the role biotic variables play in the regeneration process. Results: Despite higher rates of WPBR infection, 2.3 times more seed was available for avian dispersers in the southern ecosystem. Recent seedling regeneration did not correspond to seed production (83 versus 251 seedlings/ha, in southern versus northern ecosystems, respectively), resulting in a seven-fold difference in seed to seedling ratios between ecosystems. Models suggest that disease and vegetation cover were important factors explaining the absence of regeneration in 79.4% of the plots sampled, while basal area (BA) of live limber pine, rocky substrates, ecosystem, South aspects, and slope enhanced limber pine regeneration. Seedling age structures suggest that recent regeneration is less likely in more diseased landscapes, than it was historically (40% versus 72.8% of seedlings < 20 years old, respectively, in southern versus northern ecosystems). Conclusions: At the northern limits of limber pine’s range, seed availability does not ensure regeneration, suggesting that other environmental or biotic factors hinder regeneration. Regeneration was consistently predicted to be lower in the southern ecosystem than in the northern ecosystem, suggesting that natural regeneration and the potential for population recovery are ecosystem dependent. We recommend that monitoring recent seedlings will aid the identification of biotic and abiotic factors affecting regeneration.
The Effect of Water Hyacinth, Eichhornia Crassipes, and King-Bo Compound on Some Biological and Biochemical Aspects on Cotton Leaf Worm Spodoptera littoralis (Boisd).

Water hyacinth, Eichhornia crassipes, is considered as the worst aquatic plant in the world that causes a serious hazard to nation’s developmental activities. The present study was planned to explore the potential of E. crassipes by making its positive attributes outweigh the negative ones. Thus, the present study was carried out to disclose to the effect of E. crassipes extract "extracted by different solvents petroleum ether, acetone, ethanol and water” and kingbo commercial formulation of plant extract on 4 larval instar of Spodoptera littoralis. Some biological aspects were recorded. Also, the phytochemical screening was carried out to E. crassipes extracts. In addition, the efficiency and residual effects of kingbo against S. littoralis under field conditions were also investigated. Obtained results revealed that the percentage of larval mortality was increased with increasing the concentrations of all tested compounds. It also showed that all tested compounds caused reduction in pupal weight compared with control. Results showed that, sterols/terpenoid and flavonoids were the most constitute of E. crassipes. In addition, the present findings showed inhibition effect on total protein content except petroleum ether extract which clarify non-significant effect on 6 instar larval haemolymph. Also, in Esterases pattern were differed than the normal pattern.
Instability phenomena and their control in statics and dynamics: Application to deep and shallow truss and frame structures

In this paper we study the control for nonlinear geometric instability problem of a deep or a shallow truss or yet a frame structure. All the structural models are built with geometrically exact truss and beam finite elements. The proposed models can successfully handle large overall motion under static or dynamic conservative load. The control strategy considers adding a damping from either friction device or viscous damper. This kind of control belong to well-known concept of passivity. Different examples are presented in order to illustrate the proposed theoretical developments.
Neutral processes and high inter-annual turnover shape the assembly of soil bacterial communities in a Mediterranean watershed

There is a renewed interest in recent years on the ecological processes (stochastic vs selective) driving the assembly of microbial communities. Such information could potentially improve our understanding on ecosystem functioning and resilience to disturbances, ecosystem response to environmental shifts, and adoption of sustainable soil management practices. Herein, employing a suite of existing methodologies, we show that stochastic processes have an important role on the assembly of soil bacterial communities at a Mediterranean watershed. Moreover, we document that the relative contribution of assembly processes varies over the years. The observed intensification of stochastic processes was accompanied by a decrease in the contribution of variable selection in favor of homogeneous selection and dispersal and this trend was only marginally affected by land use (natural vs agricultural lands) or soil depth. Our study also revealed a high inter-annual turnover of soil microbial communities that was likely stimulated by the weak environmental selection and the prevailing environmental conditions (drying-wetting cycles) in Mediterranean landscapes, implying potential impacts on ecosystem functioning and our ability to predict soil response to environmental shifts. Using nitrogen mineralization rate (NMR) as a representative function we document highly variable NMR over the sampling years, land uses and soil depths and lack of significant associations with the monitored environmental variables and individual taxa. In summary, our study provides novel insights on the organization and functioning of microbial communities at Mediterranean ecosystems and sets directions towards a more advanced understanding of the relationships among environmental factors, microbial community structure, and ecosystem functioning that could contribute to sustainable management of these severely degraded ecosystems.
Linear Stability Analysis to Determine Boundary Between Stable or Unstable Flow in Nonlinear Simulation of Vorticity Equation

The nonlinear simulation of the vorticity equation is exciting because it provides a more realistic view, it is consistent with the previous investment. However, a linear stability analysis is needed to determine the stability limit of the system, which serves as a guide in determining the flow limits for stable and unstable flows. We use numerical methods to solve this linear stability analysis. This analysis utilizes the Fourier series in the linear form of the vorticity equation, then the vorticity-stream equation containing the Fourier coefficient will be formed in the matrix. Next, numerically using Matlab, we look for the eigenvalues of the matrix to determine the k, beta and Reynolds number values. If one of the eigenvalues has a real positive form given k, beta, and Reynolds number, then the equilibrium solution of the vortex equation is unstable. From graphing the real part of the eigenvalues, which is a function of the Reynolds number for some beta with k = 0.5, we get the critical point of the Reynolds number. By using a Reynolds number greater than the critical Reynolds number give result in an unstable fluid from the simulation. Vice versa, simulation using the Reynolds number, which is smaller than the critical Reynolds number will produce a stable flow. And from the linear stability curve, we know that for k > 1, the flow is stable for every Reynolds number.
Phishing detection using machine learning

Phishing attacks cause a loss of millions of dollars every year. It involves social engineering which makes it much more effective. There are many proposed solutions to solve the problem of phishing using machine learning. This research is partly a study to compare different supervised machine learning algorithms to find the optimal algorithm for phishing detection using machine learning and partly to address the issue of URL shortening service exploitation. URL shortening is used on a daily basis to help reduce the size of the URL, but attackers use these services to hide the original URL of the phishing website. In this research we propose an application that takes in a URL, uses multiple feature extraction techniques to determine whether the URL is phishing or not. We propose a URL unshortener which will return the original URL, compliments the machine learning algorithm increasing its accuracy. The initial accuracy is 92.6% and the False Positive rate is 0.4% but when the URL unshortener is added the accuracy is increased to 96.6%.
Longitudinal Mode Combustion Instabilities in Air Breathing Engines

An investigation of the self-excitation of low frequency (100-600 Hz), longitudinal acoustic modes of a rearward-facing step combustor has been performed. As in combustion instabilities of air breathing propulsion systems, the pressure oscillations are excited by a fluctuating heat release from a flame that is stabilized in a recirculation zone. Flow visualization results and flame radiation intensity data reveal that large vortex structures are responsible for this fluctuating heat release. The vortices are shed at frequencies corresponding to longitudinal acoustic modes of the system or to the first subharmonic of one of the modes. A series of parametric studies were performed to determine the dependence of the vortex shedding frequency upon the step height, mean flow speed, fuel type, and equivalence ratio. It was discovered that the vortex shedding frequency can shift between modes as a result of changes in the chemical reaction time of the reactants or as a result of changes in the mixing process of the cold reactants with the hot products. Detailed investigations into the mechanism of sustenance of the oscillations during instability were performed for several operating conditions. The distribution of the combustion associated with vortex shedding was investigated by measuring the radiation intensity from the flame region. These results were used in Rayleigh's Criterion to determine regions of driving and damping of the oscillations. A one-dimensional linearized acoustic model is used to predict the natural modes of the system and a fluctuating volumetric source is used to model the oscillatory heat release. First, independent driving is applied to determine the system response to driving at different frequencies. One important result is that, the phase difference between the pressure oscillations and the velocity oscillations at the flameholder is very sensitive to the frequency of driving near natural modes of the system. Finally, a velocity-sensitive volumetric source with a time delay is included as feedback to determine the linear stability characteristics of the system. Various mechanisms leading to nonlinear limit cycle behavior are then discussed and compared to experimental data obtained during transition to instability.
Two-Stage Relation Constraint for Semantic Segmentation of Point Clouds

Key to point cloud semantic segmentation is to learn discriminative representations involving of capturing effective relations among points. Many works add hard constraints on points through predefined convolution kernels. Motivated by label propagation algorithm, we develop Dynamic Adjustable Group Propagation (DAGP) with a dynamic adjustable scale module approximating distance parameter. Based on DAGP, we develop a novel Two Stage Propagation framework (TSP) to add intra-group and intergroup relation constraints on representations to enhance the discrimination of features from different group levels. We adopt well-appreciated backbone to extract features for input point cloud and then divide them into groups. DAGP is utilized to propagate information within each group in first stage. To promote information dissemination between groups more efficiently, a selection strategy is introduced to select group-pairs for second stage which propagating labels among selected group-pairs by DAGP. By training with this new learning architecture, the backbone network is enforced to mine relational context information within and between groups without introducing any extra computation burden during inference. Extensive experimental results show that TSP significantly improves the performance of existing popular architectures (PointNet, PointNet++, DGCNN) on large scene segmentation benchmarks (S3DIS, ScanNet) and part segmentation dataset ShapeNet.
Identification of the new species Comatricha macrospora and two other recently recorded species of Comatricha from China

A new species (Comatricha macrospora) has been collected from the Changbai Mountain National Nature Reserve, Jilin Province, China. Comatricha macrospora has smaller sporocarps and larger spores (about 15–18 μm in diameter) than other species of Comatricha as well as a persistent peridium at the base of the sporotheca. In addition, two newly recorded species of Comatricha—C. tenerrima (M.A. Curtis) G. Lister and C. afroalpina Rammeloo—have been documented in China for the first time, based on material collected from northeast China and the campus of East China Normal University, Fuzhou City, Jiangxi Province. Comatricha tenerrima is characterised by fusiform long-stalked sporocarps and warted pinkish brown spores (about 7–8 μm in diameter). , whereas C. afroalpina occurs on rotting logs and has spores marked by larger warts with an irregular reticulation at their base. Descriptions and scanning electron micrographs for these members of the genus Comatricha are provided. Phylogenetic analyses, based on small subunit ribosomal RNA sequences (SSUrRNA) of Comatricha and related genera, were carried out using Bayesian inference. These analyses confirmed the placement of the new species in the genus Comatricha.
Studying the effects of DNA replication stress on genome integrity and cell viability

I Acknowledgments . II Table of contents . III List of figures. VII List of tables . X List of abbreviations . XI Chapter 1: Introduction . 1 1.1 Genomic instability . 2 1.2 Sources of DNA damage and genomic instability . 2 1.3 Types of DNA damage and genomic rearrangements . 5 1.4 Eukaryotic DNA replication . 7 1.4. 1 Replication initiation . 8 1.4. 2 Replication elongation . 10 1.4. 3 Replication termination . 11 1.5 Replication stress . 11 1.5. 1 Replication fork stalling . 12 1.5. 2 Replication fork collapse . 13 1.5. 3 Replication fork breakage . 14 1.6 The DNA damage response . 15 1.6. 1 DNA damage sensing . 16 1.6. 2 Signal transduction . 18 1.6. 3 Signal effectors . 19 1.7 DNA repair mechanisms. 22 1.7. 1 Non-homologous end joining . 22 1.7. 2 Homologous recombination . 24 1.7. 2.1 Classical double holliday junction . 24 1.7. 2.2 Synthesis-dependent strand annealing. 25 1.7. 2.3 Single strand annealing . 25 1.8 Repair of aberrant replication fork. 27 1.8. 1 Repair of stalled forks . 27 1.8. 2 Repair of collapsed forks . 28 1.8. 3 Repair of broken fork . 30 1.9 Replication stress and cancer . 33 1.10 DNA damage response defects and cancer therapy . 36 1.11 Studies of replication stress response in eukaryotes . 40 1.12 Study Aim . 44 Chapter 2: Materials and Methods . 45 2.1 Cloning . 46 2.1.1 Solutions . 46 2.1.2 Primers . 46 2.1.3 Polymerase chain reaction (PCR) . 48 2.1.4 Annealing of oligonucleotides. 49 2.1.5 Determination of DNA concentration . 49 2.1.6 Agarose gel electrophoresis . 49 2.1.7 Restriction enzyme digestion of plasmid DNA . 50
Rapid statistical methods for inferring intra- and inter-hospital transmission of nosocomial pathogens from whole genome sequence data

Whole genome sequence (WGS) data for bacterial pathogens can provide evidence as to the source of nosocomial infection, and more specifically the ability to distinguish between intra- and inter-hospital transmission. This is currently achieved either through using SNP thresholds, which can lack statistical robustness, or by constructing phylogenetic trees, which can be computationally expensive and difficult to interpret. Here we compare two alternative statistical approaches using 1022 genomes of methicillin resistant Staphylococcus aureus (MRSA) clone ST22. In 71% of cases both methods predict the same hospital origin, which is also supported by the ML tree. Robust assignments are divided approximately equally between intra-hospital transmission and inter-hospital transmission. Our approaches are rapid and produce intuitive output that could inform on immediate infection control priorities, as well as providing long-term data on inter-hospital transmission networks. We discuss the strengths and weakness of our methods, and the generalisability of this approach. One Sentence Summary We present rapid statistical methods for distinguishing intra- versus inter-hospital transmission of bacterial pathogens using whole genome sequence data; these methods do not require the use of SNP thresholds or the generation and interpretation of phylogenetic trees.
Efficient protocol for mass micropropagation of Artemisia annua L.

An efficient protocol for mass micropropagation of Artemisia annua L. was developed. The shoots were in vitro cultivated on a full and half strengths MS supplemented with BAP and IBA for shoot and root induction from stem tip explants. Maximum number of shoots (19.1) with an average shoot height of 3.6 cm was achieved at full MS medium + 1.0 mg/L BAP, after four weeks of cultivation. The best plant rooting (100%), with 7.4 average roots’ number per explant and average root length of 15.1 cm, was obtained at 1⁄2 MS medium + 0.1 mg/L IBA + 2.0% sucrose, after five weeks of cultivation. Under these growing conditions, an increase of total phenolic and flavonoid content of A. annua tissues was registered. The multiplied plants were successfully ex vitro adapted and 65% survival was achieved on the mixture of soil, perlite and sand (2: 1: 1 v/v/v) used for acclimatization. The amounts of phenols and flavonoids, as well as total antioxidant activity of ex vitro plants, were significantly higher compared to those in the in vitro plants, but similar to the levels measured in vivo. The effective protocol for shoot micropropagation that was developed, could enable a large scale commercial production of A. annua.
Deep Brain Stimulation of the Ventromedial Prefrontal Cortex Disrupts Consolidation of Fear Memories

Anxiety disorders pose one of the biggest threats to mental health worldwide, yet current therapeutics have been mostly ineffective due to issues with relapse, efficacy, and toxicity. Deep brain stimulation (DBS) is a promising therapy for treatment-resistant psychiatric disorders including anxiety, but very little is known about the effects of DBS on fear memories. In this study, we used a modified plus-maze discriminative task and showed that DBS of the ventromedial prefrontal cortex (vmPFC) was able to disrupt consolidation, but not acquisition or retrieval of fear memories. We validated these results using a tone-footshock fear conditioning paradigm. We further demonstrated short-term changes in dopaminergic receptor and c-Fos expression in the ventral hippocampus (vHPC) and established a partial casual role of dopamine 2 receptors in this effect. Lastly, we showed changes in neurotransmitter levels in the vHPC. This study highlights the potential therapeutic effect of vmPFC DBS to treat anxiety disorders.
63-level Reduce Switch Asymmetrical Cascaded H-Bridge Multilevel Inverter

Extensive research has been carried out on multilevel inverters (MLIs) during recent years, as they are used in many applications. The main problem in MLI is high number of Total Harmonic Distortions (THD's) in output at low voltage levels and switching losses because of the use of large number of switches to produce high quality output. This paper presents the design of 63-level Reduce Switch Asymmetrical Cascaded H-Bridge Multi Level Inverter (RS-ASCHBMLI) that can produce high quality output with less THD, without utilizing high number of switches. Inverter design uses asymmetric (unequal) voltage sources as an input. Switching control unit utilizes voltage Reference technique to control level generating circuitry. Level creating circuitry produces only positive levels of voltage across H-Bridge terminals. H-Bridge is used to generate polarities. THD obtain through this technique is 1.02 % by using only nine semiconductor switches.