Miracle-dz/UniFAR-FTUs huggingface dataset:
Stages of Conceptualization and Formalization in the Design of the Model of the Neuro-Fuzzy Expert System of Professional Selection of Pupils

Buyak B.B. , Tsidilo I.M. , Repskiy V. Í. and Lyalyuk V.P. Stages of Conceptualization and Formalization in the Design of the Model of the Neuro-Fuzzy Expert System of Professional Selection of Pupils. The article describes the problem of designing a neuro-fuzzy expert system of professional selection at the stages of conceptualization and formalization, which involves the definition of concepts, relationships and management mechanisms necessary to describe the solution of problems in the chosen subject field. The structural model of the decision making system for determining the professional selection of students for training in IT specialties is substantiated. Three subsystems are proposed as structural components for studying: psychological peculiarities, personal qualities, factual knowledge, abilities and skills of students. The quality of the system’s operation is determined by the use of various techniques for acquiring knowledge on the basis of which the knowledge base of the neuro-fuzzy system and the combination of the use of fuzzy and stochastic data will be formed.
Xylose-Enriched Ethanol Fermentation Stillage from Sweet Sorghum for Xylitol and Astaxanthin Production

Developing integrated biorefineries requires the generation of high-value co-products produced alongside cellulosic ethanol. Most industrial yeast strains produce ethanol at high titers, but the small profit margins for generating ethanol require that additional high-value chemicals be generated to improve revenue. The aim of this research was to boost xylose utilization and conversion to high-value co-products that can be generated in an integrated biorefinery. Pretreated sweet sorghum bagasse (SSB) was hydrolyzed in sweet sorghum juice (SSJ) followed by ethanol fermentation. Ethanol was removed from the fermentation broth by evaporation to generate a stillage media enriched in xylose. Candida mogii NRRL Y-17032 could easily grow in non-detoxified stillage media, but a high xylitol yield of 0.55 g xylitol/g xylose consumed was achieved after recovered cells were resuspended in synthetic media containing supplemented xylose. Phaffia rhodozyma ATCC 74219 could be cultivated in non-detoxified stillage media, but astaxanthin generation was increased 4-fold (from 17.5 to 71.7 mg/L) in detoxified media. Future processing strategies to boost product output should focus on a two-step process where the stillage media is used as the growth stage, and a synthetic media for the production stage utilizing xylose generated from SSB through selective hemicellulase enzymes.
Δ9-Tetrahydrocannabinol (THC) impairs visual working memory performance

With the sharply increasing prevalence of cannabis use and availability, there is an urgent need to identify cognitive impairments related to its use. It is widely believed that cannabis, or its main psychoactive component Δ9-tetrahydrocannabinol (THC), impairs working memory, i.e., the ability to temporarily hold information in mind. However, our review of the literature yielded surprisingly little empirical support for an effect of THC or cannabis on working memory. We thus conducted a study with 3 main goals: (1) quantify the effect of THC on visual working memory in a well-powered sample (2) test the potential role of cognitive effects (mind wandering and metacognition) in disrupting working memory, and (3) demonstrate how insufficient sample size and task duration reduce the likelihood of detecting a drug effect. We conducted two double-blind, counterbalanced experiments in which healthy adults (N=23, 23) performed a sensitive and validated visual working memory task (the “Discrete Whole-Report task”, 90 trials) after administration of THC (7.5 and/or 15 mg oral) or placebo. We also assessed self-reported ‘mind wandering’ (Exp 1) and metacognitive accuracy about ongoing task performance (Exp 2). THC impaired working memory performance (d = .65), increased mind wandering (Exp 1), and decreased metacognitive accuracy about task performance (Exp 2). Thus, our findings indicate that THC does impair visual working memory, and that this impairment may be related to both increased mind-\ wandering and decreased monitoring of task performance. Finally, we used a downsampling procedure to illustrate the effects of task length and sample size on power to detect the acute effect of THC on working memory.
Chikungunya virus infection impairs osteogenic differentiation of bone marrow-derived mesenchymal stem cells

Chikungunya virus (CHIKV) is a positive-sense, single-stranded RNA virus, belonging to the genus alphavirus in the family Togaviridae. The virus is spread by the Aedes species (sp.) mosquitoes in tropical and subtropical regions of the world. CHIKV causes Chikungunya fever (CHIKF), where the acute stage of infection is characterized by high fever, headache, rash, and polyarthralgia. In 30-40% of cases, patients develop a chronic stage with debilitating joint pain persisting for months to years imposing a burden on the population in terms of disability adjusted life years (DALY). Presently, no vaccines or treatment options are available for this infection. Prior investigations reveal that CHIKV infection is associated with bone pathology; however, the molecular mechanism underlying CHIKV-induced bone pathology remains poorly defined. Studies show that disruption of osteogenic differentiation and function of bone marrow-derived mesenchymal stem cells (BMMSCs) can lead to bone pathologies. However, to date pathogenesis of CHIKV infection in this context has not been studied. In the current study, we investigated the susceptibility of BMMSCs to CHIKV and studied the effect of infection on BMMSCs-derived osteogenic cells. To our knowledge, for the first time we report that CHIKV can productively infect BMMSCs. We observed a decrease in the intracellular and extracellular alkaline phosphatase (ALP) activity and reduction in calcium phosphate deposition in infected cells compared to mock-infected control. Thus, we conclude that CHIKV infects BMMSCs and disrupts function of osteogenic cells. Importance Although studies have shown association of bone pathology and CHIKV infection, the pathogenesis of infection causing altered bone homeostasis is not fully understood. Here, we demonstrate for the first time that BMMSCs are susceptible to CHIKV infection. Furthermore, we observe that infection causes disruption in the function of BMMSC- derived osteogenic cells. Impaired function of these osteogenic cells will likely lead to a disruption in bone homeostasis and in part, provides a mechanism for the observed bone pathology associated with CHIKV pathogenesis.
Robust effects of cortical feedback on thalamic firing mode during naturalistic stimulation

Neurons in the dorsolateral geniculate nucleus (dLGN) of the thalamus are contacted by a large number of feedback synapses from cortex, whose role in visual processing is poorly understood. Past studies investigating this role have mostly used simple visual stimuli and anesthetized animals, but corticothalamic (CT) feedback might be particularly relevant during processing of complex visual stimuli, and its effects might depend on behavioral state. Here, we find that CT feedback robustly modulates responses to naturalistic movie clips by increasing response gain and promoting tonic firing mode. Compared to these robust effects for naturalistic movies, CT feedback effects were less consistent for simple grating stimuli. Finally, while CT feedback and locomotion affected dLGN responses in similar ways, we found their effects to be largely independent. We propose that CT feedback and behavioral state use separate routes to powerfully modulate visual information on its way to cortex.
High throughput sequencing combined with null model tests reveals specific plant‐fungi associations linked to seedling establishment and survival

Plant‐fungal interactions are important for plant community assembly, but quantifying these relationships remains challenging. High throughput sequencing of fungal communities allows us to identify plant‐fungal associations at a high level of resolution, but often fails to provide information on taxonomic and functional assignment of fungi. We transplanted seeds of Pinus cembra across an elevational gradient (1850–2250 m a.s.l.) and identified environmental factors and known fungal associates important for seedling establishment and survival. We then applied null model tests to identify taxonomically unassigned fungi associated with pine recruitment. Early seedling establishment was determined by abiotic environmental factors, while seedling survival was predominantly affected by biotic environmental factors (i.e., the abundance of a fungal pathogen known from literature and the distance to adult trees). Null model tests identified known mycorrhizal partners and a large number of unknown operational taxonomic units (OTUs) associated with seedling survival, including saprotrophic and pathogenic species. These results highlight that unknown fungal OTUs, which are usually discarded from analyses, could play a crucial role for plant survival. Synthesis. We conclude that high throughput metabarcoding paired with null model tests, is a valuable approach for identifying hidden plant‐fungal associations within large and complex DNA metabarcoding datasets. Such an approach can be an important tool in illuminating the black box of plant‐microbe interactions, and thus understanding ecosystem dynamics.
An integrated simulation platform for a quadcopter system with fuzzy-tuned PID controllers /Moayad Hani Yacoub Abu Rmilah

Quadcopters are powerful flying robots that are given great interest for their various emerging applications. A quadcopter is an under-actuated system that is naturally unstable and, hence, requires a robust controller to perform rotational and translational maneuvering with high stability. This thesis develops an integrated simulation platform with visualization capability for a quadrotor unmanned aerial vehicle (UAV). The nonlinear dynamic equations of motion for the six degrees of freedom of a quadcopter have been derived from the first principles. The quadcopter dynamical model has been stabilized by PID and fuzzy-tuned PID controllers in order to test and compare their performance. The simulation platform for the quadcopter was developed using MATLAB and Simulink and integrated with the FlightGear Flight simulator in order to visualize the quadcopter motion in real time. The simulation results have shown the effectiveness of the two proposed controllers during altitude, attitude and path tracking control. However, performance indicators of the time response curves for positions and attitude have shown that the fuzzy-tuned PID controller could stabilize the quadcopter more efficiently and provided a faster response and smaller overshoots. Fuzzy-tuned PID controllers have reduced the overshoot along the vertical axis from 10.6% to 4.25%. It enabled the quadcopter to strictly track the planned path with very small tracking errors and time delay. The response of this controller was leading the response of the conventional PID controller by 1.13s during path tracking. The developed simulation platform significantly reduces the time-consuming and intensive testing on expensive quadcopter prototypes and, hence, shortens the total development time and design cost. The simulation platform is a promising tool that is very useful for students and researchers who would like to study and analyze the performance of quadcopter systems.
Modulation of peptidoglycan synthesis by recycled cell wall tetrapeptides

The bacterial cell wall is made of peptidoglycan (PG), a polymer that is essential for maintenance of cell shape and survival. During growth, bacteria remodel their PG, releasing fragments that are predominantly re-internalized by the cell, where they are recycled for synthesis of new PG. Although the PG recycling pathway is widely conserved, its components are not essential and its roles in cell wall homeostasis are not well-understood. Here, we identified LdcV, a Vibrio cholerae L,D-carboxypeptidase that cleaves the terminal D-Alanine from recycled murotetrapeptides. In the absence of ldcV, recycled tetrapeptides accumulated in the cytosol, leading to two toxic consequences for the cell wall. First, incorporation of tetrapeptide-containing PG precursors into the cell wall led to reduction in D,D-cross-linkage between stem peptides, diminishing PG integrity. Second, tetrapeptide accumulation led to a decrease in canonical UDP-pentapeptide precursors, reducing PG synthesis. Thus, LdcV and the recycling pathway promote optimal cell wall assembly and composition. Furthermore, Ldc substrate preference for murotetrapeptides containing canonical (D-Alanine) vs. non-canonical (D-Methionine) D-amino acids is conserved, suggesting that accumulation of tetrapeptide recycling intermediates may modulate PG homeostasis in environments enriched in non-canonical-muropeptides via substrate competition.
Metabolomic profiling reveals developmentally regulated biosynthesis of polyprenols and dolichols in the malaria parasite

The cis-polyisoprenoid lipids namely polyprenols (POH), dolichols (DOH) and their derivatives are linear polymers of several isoprene units and have recently gained special attention due to several breakthroughs in the field including improvements in the analytical techniques for their analysis, partial identification of their enzymatic machinery, and the discovery of new biological functions beyond glycosylation. In eukaryotes, POH and DOH are synthesized as a mixture of four or more homologues of different length with one or two predominant species with sizes varying among organisms. Interestingly, POH are hardly detectable in eukaryotic cells under normal conditions with the exception of plants and sporulating yeast. Our metabolomics studies revealed that cis-polyisoprenoids are more prevalent and diverse in the protozoan parasite Plasmodium falciparum than previously postulated as we uncovered the active biosynthesis of medium-long POH and DOH (15 to 19 isoprene units). Moreover, a distinctive POH and DOH profile both within the intraerythrocytic asexual cycle and between asexual and gametocyte stages was observed. These results suggest that cis-polyisoprenoid biosynthesis is developmentally regulated. In addition, we confirmed that DOH biosynthesis occurs via reduction of the POH to DOH by an active polyprenol reductase (PfPPRD) and metabolomics analyses of a PfPPRD conditional mutant suggest that a salvage mechanism of DOH may exist.
Biological Control of Seedling Damping – Off of Sugar Beet Plant

Pythium ultimum causal of damping –off in sugar beet, which is one of the most destructive diseases in this crop worldwide.During the study, twelve bacterial isolates were isolated from rhizosphere soil of sugar beet crop. Three isolates of them showed antifungal activity against these phytopathogen. These isolates were identified as: Bacillus amyloliquefaciens , Bacillus pseudomycodies and Bacillus sp. by standard tests and the application of biolog system.Three species of fungi as Trichoderma spp.were successfully used by several investigators to control . In vivo, results of seeds soaking with tested B. amyloliquefaciens showed that the most effective in controlling damping –off disease(80%) followed by B. pseudomycodies (66.67%). While, T. viride recorded value of survival plants (60%), T. hamatum and T.harzianum (53.33%, 23.33%, respectively). At the same time seeds coating with T.harzianum was the most effective in controlling disease indicated that (86.67%), followed by B. pseudomycodies , B. amyloliquefaciens , T. viride , Bacillus sp.and T. hamatum(80.00%, 73.33%, 50.00%, 46.67%, 40.00 % respectively) in soil infested with P. ultimum.
Integrated disease management of downy mildew in bottle gourd (Lagenaria siceraria (Mol.) Stand)

Downy mildew disease of bottle gourd (Lagenaria siceraria (Mol.) Standl) is one of the most important foliar diseases, causing significant loss in India. downy mildew disease found to cause serious losses in bottle gourd crop throughout Rajasthan and other states. Characteristic symptoms are first appear as pale green area on the upper surface of leaves that changes to bright yellow angular or rectangular spots. Leaf spot are irregular or blocky in appearance and are delimited by leaf veins. The minimum disease incidence (4.09%) and maximum yield (338.5q/ha) were observed in treatment T5(T0+ Seed treatment with carbendazim 12%+ mancozeb 63% @ 3 g/kg and drenching of Captan 70% +Hexaconazole 5% WP @ 0.1% 15 days after germination followed by spraying of Tebuconazole 50% + Trifloxystrobin 25% @1g/l + spray with (Imidacloprid 17.8 SL @ 7.5 ml/ 15 l + Neem oil 0.2%) followed by Fosetyl-Al @ 0.1% followed by spraying of Tebuconazole 50% + Trifloxystrobin 25% @1g/l + spray with (Imidacloprid 17.8 SL @ 7.5 ml/ 15 l + Neem oil 0.2%) followed by Fosetyl-Al @ 0.1% at 10 days interval) while maximum disease incidence (28.54%)and minimum yield (225.7 q/ha)were observed in treatment T7(Control). Natural products such as herbal extracts may provide alternatives to synthetic fungicides.
The complete mitochondrial genome sequence of Osteobrama belangeri (Cyprinidae) and its comparison with other related Cypriniformes fish species

Abstract The complete mitogenome of Osteobrama belangeri is described using Ion Torrent (PGM sequencer), which was 16,609 bp in size comprising 13 mRNAs, teo rRNA genes, 22 tRNAs, and 926 bp as D-Loop control region, in addition to gene order and organization, being similar to most of the other related Cypriniformes fish mitogenome of NCBI databases. The all 22 tRNAs were packed into a typical clover-leaf structure. In the present study, the mitogenome has 99% similarity to the complete mitogenome sequence of O. belangeri mitogenome details previously and also would be helpful in understanding the phylogenetics, population genetics, and evolution of family Cyprinidae fishes.
A Web-based Sample Size Calculator for Reliability Studies

Planning a validation study of a questionnaire or measurement tool requires consideration for testing the validity and reliability aspects of the measurement tool. When it comes to the reliability aspect, a number of commonly used statistical coefficients such as Cronbach’s alpha, intraclass correlation, kappa and Pearson’s correlation coefficients would be considered to provide empirical evidence of the reliability of the tool during the validation process. To ensure that the reliability is accurately assessed, a researcher must consider the sample size requirement for the statistical analyses. In this article, I will introduce a newly developed web-based sample size calculator, which includes the ability to calculate the sample sizes of these four important coefficients. I will also show how to use the calculator for each of the coefficients.
Residual quantification and oxidative stress induced by malachite green after subacute and sublethal exposure in red tilapia

Background and Aim: Malachite green (MG) is an effective antiparasitic and antifungal chemical for treatment of fish. However, MG is reported to be a potential carcinogen. Yet, it is widely used in aquaculture despite its prohibition for use in food-producing animals by the EU and USFDA. The present study quantified MG residues and evaluated the oxidative stress in red tilapia when exposed to subacute and sublethal concentrations of MG. Materials and Methods: Red tilapia exposed to subacute (0.105 mg/L for 20 days) and sublethal (0.053 mg/L for 60 days) concentrations were evaluated for total plasma protein, total immunoglobulin, nitroblue tetrazolium activity, malondialdehyde, reduced glutathione (GSH), and catalase (CAT) activity levels. The residues of MG and leuco-MG (LMG) were also quantified in the fish muscles using liquid chromatography–tandem mass spectrometry. Results: Fish exposed to subacute concentration showed higher CAT on day 10 in the liver and days 5 and 15 in the spleen, whereas in fish exposed to the sublethal concentration, higher levels of GSH were observed on day 1 in the kidney and day 50 in the spleen. Fish muscle was able to accumulate the sum of MG and LMG of 108.04 µg/kg for subacute (day 20) and 82.68 µg/kg for sublethal (day 60). Conclusion: This study showed that red tilapia was able to adapt to the stress caused by exposure to MG at sublethal concentration.
The complete mitogenome of red-collared lorikeet (Trichoglossus rubritorquis) and its phylogenetic analysis

Abstract The complete mitogenome of a lorikeet, Trichoglossus rubritorquis (Psittaciformes, Loriidae), was determined first in the genus Trichoglossus. The assembled mitogenome was 17,915 bp and composed of 13 protein-coding genes, 22 tRNAs, two rRNAs and two control regions. Nucleotide composition of T. rubritorquis mitogenome was 30.20% A, 33.30% C, 14.04% G, and 22.46% T, with an A + T bias of 52.66%. ML tree based on 13 protein-coding genes indicated that, Melopsittacus undulatus of the family Psittacidae was the closest related species to T. rubritorquis. This result suggested that lorikeets might still be in the family Psittacidae.
Codon-optimized TDP-43 mediates neurodegeneration in a Drosophila model of ALS/FTLD

Transactive response DNA binding protein-43 (TDP-43) is known to mediate neurodegeneration associated with amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). The exact mechanism by which TDP-43 exerts toxicity in the brains of affected patients remains unclear. In a novel Drosophila melanogaster model, we report gain-of-function phenotypes due to misexpression of insect codon-optimized version of human wild-type TDP-43 (CO-TDP-43) using both the binary GAL4/UAS system and direct promoter fusion constructs. The CO-TDP-43 model showed robust tissue specific phenotypes in the adult eye, wing, and bristles in the notum. Compared to non-codon optimized transgenic flies, the CO-TDP-43 flies produced increased amount of high molecular weight protein, exhibited pathogenic phenotypes, and showed cytoplasmic aggregation with both nuclear and cytoplasmic expression of TDP-43. Further characterization of the adult retina showed a disruption in the morphology and function of the photoreceptor neurons with the presence of acidic vacuoles that are characteristic of autophagy. Based on our observations, we propose that TDP-43 has the propensity to form toxic protein aggregates via a gain-of-function mechanism, and such toxic overload leads to activation of protein degradation pathways such as autophagy. The novel codon optimized TDP-43 model is an excellent resource that could be used in genetic screens to identify and better understand the exact disease mechanism of TDP-43 proteinopathies and find potential therapeutic targets.