Miracle-dz/UniFAR-FTUs huggingface dataset:
Nephroprotective Effect from Rose Petals (Rosa damascena) Extract Against Cadmium Toxicity

Cadmium, a heavy metal, is commonly used in industries. It could accumulate in various bodily organs, especially in the kidneys. Due to its antioxidative effect, rose (Rosa damascena) petal may serve to protect organs and tissues against free radicals, generated by cadmium deposition. Hence, this study aims to investigate the nephroprotective effect from rose petal extract against cadmium toxicity. This study was experimentally-designed that involved 25 male Wistar rats, divided into five different groups viz. control (Na-CMC), standard (Quercetin), rose petal methanol extract-I (400 mg/kg BW), extract-II (800 mg/kg BW), and extract-III (1.2g/kg BW). All rats received 7 mg/kgBW of cadmium sulfate peroral 30 minutes following quercetin or rose extract administration. After four weeks of treatment, all rats were sacrificed. Blood and kidney tissue were collected for examinations. Based on lab parameter, it showed that 400 to 1.2 g/kgBW of rose extract was able to maintain similar amount of blood ureum with that of the standard group (p value < 0.05), therefore protecting the tubular part of the kidneys from cadmium damage. The extract III groups exhibited most minimal kidney damage, quantified via lowest EGTI score. Thus, rose petal extract has nephroprotective effect against cadmium toxicity.
Development of an Extreme Gradient Boosting Model Integrated With Evolutionary Algorithms for Hourly Water Level Prediction

The establishment of reliable water level prediction models is vital for urban flood control and planning. In this paper, we develop hybrid models (GA-XGBoost and DE-XGBoost) that couple two evolutionary models, a genetic algorithm (GA) and a differential evolution (DE) algorithm, with the extreme gradient boosting (XGBoost) model for hourly water level prediction. The Jungrang urban basin located on the Han River, South Korea, was selected as a case study for the proposed models. Hourly rainfall and water level data were collected between 2003 and 2020 to construct and evaluate the performance of the selected models. To compare the prediction efficiency, two other tree-based models were chosen: classification and registration tree (CART) and random forest (RF) models. A comparison of the results showed that two hybrid models, GA-XGBoost and DE-XGBoost, outperformed RF and CART in the multistep-ahead prediction of water level, and the relative errors of the hybrid model ranged from [2.18%-9.21%], compared to [3.76%-10.41%] and [2.99%-11.88%] for the RF and CART, respectively. Reliable performance was also supported by other measures. In general, the GA-XGBoost and DE-XGBoost models displayed relatively similar performance despite their small differences. The CART model was not preferable for multistep-ahead water level predictions, even though it yielded the lowest Akaike information criterion (AIC) value. This study verifies that despite having some drawbacks when considering long step-ahead prediction and model complexity, hybrid XGBoost models might be superior to many existing models for hourly water level prediction.
Gender Differences in Computational Thinking Skills among Malaysian’s Primary School Students using Visual Programming

Computational Thinking (CT) is a thought process which utilize computer science concepts to solve problem in the real life. One of the methods to develop CT among the Children is by using visual programming to create computational artifacts such as animation and games. This study collected 50 animation and 47 games projects created by the primary school students in standard 6 (12-year-old) from the eight-week lesson using visual programming Scratch. The purpose of the study is to investigate if there is a significant difference between male and female students on CT skills of flow control, logic, data representation, parallelism, synchronization, user interactivity and abstraction. Source code projects were analyzed for CT skills score. Result from Mann-Whitney U test shows the different was not statistically significant between male and female students on CT skills mentioned previously.
Design and Control of Grid-Connected PWM Rectifiers by Optimizing Fractional Order PI Controller Using Water Cycle Algorithm

In this paper water cycle algorithm-based fractional order PI controller (FOPI) is proposed for virtual flux-oriented control of a three-phase grid-connected PWM rectifier. FOPI controller makes the PWM rectifier control more robust due to the fractional behavior. Fractional-order controllers have an additional degree of freedom, so a wider range of parameters is available to provide better control and robustness in the plant. The optimization and design of the FOPI controller are done using the water cycle algorithm (WCA). WCA is an optimization method inspired by monitoring the water cycle operation and flow of water bodies like streams and rivers toward the sea. The performance of the FOPI controller is compared with the classical integer order PI controller. The parameters of PI and FOPI controllers are optimized and designed using the WCA technique, leading to WCA-PI and WCA-FOPI controllers. The system is tested using MATLAB/Simulink. The simulation results verify the better performance of WCA-FOPI in terms of settling time, rise time, peak overshoot, and Total Harmonic Distortion (THD) of grid current. A robustness measurement with line filter parametric variations and non-ideal supply voltage (unbalance and distorted supply voltage) is carried out. The WCA-FOPI demonstrates more robustness as compared to WCA-PI. Simulation findings validate the WCA-FOPI controller outcomes as compared to WCA-PI in terms of control effect and robustness.
Improvement of Liver Function from Lemon Pepper Fruit Ethanol Extract in Streptozotocin-Induced Wistar Rats

Diabetes mellitus is usually associated with oxidative stress which can initiate or promote chronic diabetic lesions in various organs. Reactive Oxygen Species accumulation affects liver tissue and may also cause Non-Alcoholic Fatty Liver Disease (NAFLD). Lemon pepper is an alternative medicine that is widely used in the Batak community. Therefore, this study was designed to determine the improvement of liver function from ethanolic extract of lemon (Zanthoxylum acanthopodium) in Wistar rats induced by streptozotocin. In the eksperiment, 25 rats which divided into five groups: control, standard, lemon pepper-1, 2, and 3 (250, 500, and 750 mg/kg BW, respectively) were used. After 14 days of intervention, the ALT and AST levels were measured in all rats. The results showed that the average percentage reduction in the AST levels in lemon pepper I, II, III, and standard groups were 2.64%, 35.76%, 43.59%, and 44.82%, respectively; The average percentage reduction in the ALT levels were 76.19%, 87.20%, 84.99%, and 88.39%, respectively. However, the decrease in each level showed that the increase in the AST level was better than the ALT. Overall it can be concluded that lemon pepper extract can improve the liver function of streptozotocin-induced wistar rats and the most effective dose of ethanolic extract of lemon fruit for improving liver function, especially ALT levels is 750 mg/kg BW.B
Simulating Immunization Campaigns and Vaccine Protection Against COVID-19 Pandemic in Brazil

The vaccine roll-out has currently established a new trend in the fight against COVID-19. In many countries, as vaccination cover rises, the economic and social disruptions are being progressively reduced, bringing more confidence and hope to the population. However, a crucial debate is related to fair access to vaccines, which would lead to stepping up the pace of vaccination in developing countries. Another important issue is how immunization has influenced the control of the infection, deaths, and transmissibility of the new coronavirus in these countries. In this work, we investigate the effects of the rate of vaccination on the COVID-19 epidemic curves, by employing a new data-driven methodology, formulated on the basis of a modified Susceptible-Infected-Recovered model and Machine Learning designs. The data-driven methodology is applied to assess the influence of the vaccines administered in Brazil on the fight against the virus. The impacts of vaccine efficacy and immunization speed are also investigated in our study. Finally, we have found that the use of anti-SARS-CoV-2 vaccines with a low/moderate efficacy can be offset by immunizing a larger proportion of the population more quickly.
A novel RAB11-containing adaptor complex anchoring myosin-5 to secretory vesicles

Hyphal fungi grow rapidly by apical extension, providing a notorious example of polarized growth. The continuous supply of secretory vesicles necessary to meet the demands of the extending tip and the long intracellular distances existing between the tip and the basal septum, often localized > 100 µm away from the former, impose the need of efficient networks of intracellular traffic involving exquisite cooperation between microtubule- and actin-mediated transport. In Aspergillus nidulans kinesin-1 conveys secretory vesicles to the hyphal tip, where they are transferred to myosin-5, which focuses them at the growing apex, thereby determining cell shape. This relay mechanism and the central role played by myosin-5 in hyphal morphogenesis suggested that the mechanisms anchoring secretory vesicles to this motor should involve specific adaptor(s) ensuring the robustness of actomyosin-dependent transport. Secretory vesicles are charged with RAB11, a regulatory GTPase that determines the Golgi to post-Golgi identity transition. By using a combination of shotgun proteomics, GST-RAB pull-down assays, in vitro reconstitution experiments, targeted reverse genetics and multidimensional fluorescence microscopy with endogenously tagged proteins we show that RAB11, the master regulator of fungal exocytosis, mediates myosin-5 engagement both by contacting the motor and by recruiting UDS1, a homologue of an as yet uncharacterized Schizosaccharomyces protein ‘upregulated during mitosis’, which we demonstrate to be a novel RAB11 effector. Analytical ultracentrifugation determined that UDS1 is an elongated dimer and negative-stain electron microscopy showed that, in agreement, UDS1 is rod-shaped. UDS1 does not contact myosin-5 directly, but rather recruits the coiled-coil HMSV, which bridges RAB11/UDS1 to myosin-5. An HMSV-scaffolded complex containing UDS1 and myosin-5 is present in cells, and a RAB11-UDS1-HMSV complex can be reconstituted in vitro in a RAB nucleotide state-dependent manner. In the absence of UDS1/HMSV the steady state levels of myosin-5 at the apical vesicle supply center diminish markedly, such that microtubule-dependent transport spreading vesicles across the apical dome predominates over apex-focused actin-mediated transport. As a consequence, RAB11 and chitin-synthase B (a cargo of the RAB11 pathway) are not focused at the apex, being distributed instead across the apical dome. Therefore, the RAB11 effector UDS1/HMSV cooperates with the GTPase to adapt secretory vesicles to myosin-5, which is required for the apical targeting of RAB11 cargoes and thus for the normal morphology of the hyphae.
GABA and IA Independently Regulate rNST Responses to Afferent Input

Taste responses in the rostral nucleus of the solitary tract (rNST) influence motivated ingestive behavior via ascending pathways, and consummatory reflex behavior via local, brainstem connections. Modifications to the afferent signal within the rNST include changes in gain (the overall rate of neuron activity) and changes in gustatory tuning (the degree to which individual neurons respond to divergent gustatory qualities). These alterations of the sensory signal derive from both synaptic interactions within the nucleus and the constitutive cellular membrane properties of rNST neurons. GABA neurons are well represented within the rNST, as is expression of KV4.3, a channel for a rapidly inactivating outward K+ current (IA). GABAergic synapses suppress rNST responses to afferent input and previous studies showed that this suppression is greater in cells expressing IA, suggesting a possible interaction. Here, we examine the potential interaction between GABAergic inhibition and IA channels in a series of patch clamp experiments. Optogenetic release of GABA suppressed rNST responses to afferent (electrical) stimulation and this effect was greater in cells with IA, confirming an earlier report. We further observed that the composite inhibitory postsynaptic potential was larger in IA positive cells, suggesting one mechanism for the greater afferent suppression. Blocking IA with the channel blocker AmmTX3, enhanced the response to afferent stimulation, suggesting a suppressive role for this channel in regulating afferent input at rest. However, pharmacologic blockade of IA did not suppress GABAergic inhibition, indicating that IA and GABA independently regulate excitatory afferent input.
Droplet-based Single-cell Total RNA-seq Reveals Differential Non-Coding Expression and Splicing Patterns during Mouse Development

In recent years, single-cell transcriptome sequencing has revolutionized biology, allowing for the unbiased characterization of cellular subpopulations. However, most methods amplify the termini of polyadenylated transcripts capturing only a small fraction of the total cellular transcriptome. This precludes the detection of many long non-coding, short non-coding and non-polyadenylated protein-coding transcripts. Additionally, most workflows do not sequence the full transcript hindering the analysis of alternative splicing. We therefore developed VASA-seq to detect the total transcriptome in single cells. VASA-seq is compatible with both plate-based formats and droplet microfluidics. We applied VASA-seq to over 30,000 single cells in the developing mouse embryo during gastrulation and early organogenesis. The dynamics of the total single-cell transcriptome result in the discovery of novel cell type markers many based on non-coding RNA, an in vivo cell cycle analysis and an improved RNA velocity characterization. Moreover, it provides the first comprehensive analysis of alternative splicing during mammalian development.
Environmental and Molecular Modulation of Motor Individuality in Larval Zebrafish

Innate behavioral biases such as human handedness are a ubiquitous form of inter-individual variation that are not strictly hardwired into the genome and are influenced by diverse internal and external cues. Yet, genetic and environmental factors modulating behavioral variation remain poorly understood, especially in vertebrates. To identify genetic and environmental factors that influence behavioral variation, we take advantage of larval zebrafish light-search behavior. During light-search, individuals preferentially turn in leftward or rightward loops, in which directional bias is sustained and non-heritable, and maintained by a habenula-rostral PT circuit. Here we use a medium-throughput recording strategy and unbiased analysis to show that significant individual to individual variation exists in wildtype larval zebrafish turning preference. We classify stable left, right, and unbiased turning types, with most individuals exhibiting a directional preference. Raising larvae at elevated temperature selectively reduces the leftward turning type and impacts rostral PT neurons, specifically. Exposure to conspecifics, variable salinity, environmental enrichment, and physical disturbance does not significantly impact inter-individual turning bias. Pharmacological manipulation of Notch signaling and carrying a mutant allele of a known Notch pathway affecter gene, gsx2, disrupted turn bias individuality in a dose-dependent manner. These results establish that larval zebrafish is a powerful vertebrate model for inter-individual variation with sensitivity to specific environmental perturbations and gene dosage.
In vivo serial passaging of human-simian immunodeficiency virus clones identifies viral characteristics that enhance persistent viral replication

We previously reported that a human immunodeficiency virus type 1 with a simian immunodeficiency virus vif substitution (HSIV-vifNL4-3) could replicate in pigtailed macaques (PTMs), demonstrating that Vif is a species-specific tropism factor of primate lentiviruses. However, infections did not result in high peak viremia or setpoint plasma viral loads, as observed during SIV infection of PTMs. Here, we characterized variants isolated from one of the original infected animals with CD4 depletion after nearly four years of infection to identify determinants of increased replication fitness. In our studies, we found that the HSIV-vif clones did not express the HIV-1 Vpr protein due to interference from the vpx open reading frame in singly spliced vpr mRNA. To examine whether these viral genes contribute to persistent viral replication, we generated infectious HSIV-vif clones expressing either the HIV-1 Vpr or SIV Vpx protein. And then to determine viral fitness determinants of HSIV-vif, we conducted three rounds of serial in vivo passaging in PTMs, starting with an initial inoculum containing a mixture of CXCR4-tropic (Vpr- HSIV-vifNL4-3 isolated at 196 (C/196) and 200 (C/200) weeks post-infection from a PTM with depressed CD4 counts) and CCR5-tropic HSIV (Vpr+ HSIV-vif derivatives based NL-AD8 and Bru-Yu2 and a Vpx expressing HSIV-vifYu2). Interestingly, all infected PTMs showed peak plasma viremia close to or above 105 copies/ml and persistent viral replication for more than 20 weeks. The passage 3 PTM showed peak viral loads greater than 105 viral RNA copies/ml. Infectious molecular clones (IMCs) recovered from the passage 3 PTM (HSIV-P3 IMCs) included mutations required for HIV-1 Vpr expression and those mutations encoded by the CXCR4-tropic HSIV-vifNL4-3 isolates C/196 and C/200. The data indicate that the biological isolates selected during long-term infection acquired HIV-1 Vpr expression to enhance their replication fitness in PTMs. Further passaging of HSIV-P3 IMCs in vivo may generate pathogenic variants with higher replication capacity, which will be a valuable resource as challenge virus in vaccine and cure studies.
Orientation dependent proton transverse relaxation in the human brain white matter: The magic angle effect on a cylindrical helix

Purpose To overcome some limitations of prior orientation-dependent proton transverse relaxation formalisms in white matter (WM) with a novel framework based on the generalized magic angle effect function. Methods A cylindrical helix model was developed embracing anisotropic rotational and translational diffusion of restricted molecules in human brain WM, with the former characterized by an axially symmetric system. Transverse relaxation rates R2 and were divided into isotropic and anisotropic parts, , with α denoting an open angle and ε0 an orientation (Φ) offset from DTI-derived primary diffusivity direction. The proposed framework (Fit A) was compared with prior models without ε0 on previously published water and methylene proton transverse relaxation rates from developing, healthy, and pathological WM at 3T. Goodness of fit was represented by root-mean-square error (RMSE). F-test and linear correlation were used with statistical significance set to P ≤ 0.05. Results Fit A significantly (P<0.01) outperformed prior models as demonstrated by reduced RMSEs, e.g., 0.349 vs. 0.724 in myelin water. Fitted ε0 was in good agreement with calculated ε0 from directional diffusivities. Compared with those from healthy adult, the fitted , and α from neonates were substantially reduced but ε0 increased, consistent with incomplete myelination. Significant positive and negative (α and ) correlations were found with aging (demyelination) in elderly. Conclusion The developed framework can better characterize orientation dependences from a wide range of proton transverse relaxation measurements in human brain WM, shedding new light on myelin microstructural alterations at the molecular level.
Methylphenidate as a causal test of translational and basic neural coding hypotheses

Most systems neuroscience studies fall into one of two categories: basic science work aimed at understanding the relationship between neurons and behavior, or translational work aimed at developing treatments for neuropsychiatric disorders. Here we use these two approaches to inform and enhance each other. Our study both tests hypotheses about basic science neural coding principles and elucidates the neuronal mechanisms underlying new, clinically relevant behavioral effects of systemically administered methylphenidate (Ritalin). We discovered that orally administered methylphenidate, used clinically to treat Attention Deficit Hyperactivity Disorder (ADHD) and generally to enhance cognition (Lakhan & Kirchgessner, 2012; Maher, 2008), increases spatially selective visual attention, enhancing visual performance at only the attended location. And as predicted by our previous work (Ni et al., 2018), we found that this causal manipulation enhances vision in rhesus macaques specifically when it decreases the mean correlated variability of neurons in visual area V4. Our findings demonstrate that the visual system is a platform for understanding the neural underpinnings of both complex cognitive processes (basic science) and neuropsychiatric disorders (translation). Addressing basic science hypotheses, our results are consistent with a scenario in which methylphenidate has cognitively specific effects by working through naturally selective cognitive mechanisms. Clinically, our findings suggest that the often staggeringly specific symptoms of neuropsychiatric disorders may be caused and treated by leveraging general mechanisms.
Dysregulation of the Tweak/Fn14 pathway in skeletal muscle of spinal muscular atrophy mice

Spinal muscular atrophy (SMA) is a childhood neuromuscular disorder caused by depletion of the survival motor neuron (SMN) protein. SMA is characterized by the selective death of spinal cord motor neurons, leading to progressive muscle wasting. Loss of skeletal muscle in SMA is a combination of denervation-induced muscle atrophy and intrinsic muscle pathologies. Elucidation of the pathways involved is essential to identify the key molecules that contribute to and sustain muscle pathology. The tumor necrosis factor-like weak inducer of apoptosis (TWEAK)/TNF receptor superfamily member fibroblast growth factor inducible 14 (Fn14) pathway has been shown to play a critical role in the regulation of denervation-induced muscle atrophy as well as muscle proliferation, differentiation and metabolism in adults. However, it is not clear whether this pathway would be important in highly dynamic and developing muscle. We thus investigated the potential role of the TWEAK/Fn14 pathway in SMA muscle pathology, using the severe Taiwanese Smn-/-;SMN2 and the less severe Smn2B/- SMA mice, which undergo a progressive neuromuscular decline in the first three post-natal weeks. Here, we report significantly dysregulated expression of the TWEAK/Fn14 pathway during disease progression in skeletal muscle of the two SMA mouse models. In addition, siRNA-mediated Smn knockdown in C2C12 myoblasts suggests a genetic interaction between Smn and the TWEAK/Fn14 pathway. Further analyses of SMA, Tweak-/- and Fn14-/- mice revealed dysregulated myopathy, myogenesis and glucose metabolism pathways as a common skeletal muscle feature, and providing further evidence in support of a relationship between the TWEAK/Fn14 pathway and Smn. Finally, a pharmacological intervention (Fc-TWEAK) to upregulate the activity of the TWEAK/Fn14 pathway improved disease phenotypes in the two SMA mouse models. Our study provides novel mechanistic insights into the molecular players that contribute to muscle pathology in SMA and into the role of the TWEAK/Fn14 pathway in developing muscle.