Miracle-dz/UniFAR-FTUs huggingface dataset:
Flattening the COVID 19 curve in susceptible forest indigenous tribes using SIR model

COVID 19 is a global threat and globally spreading. The international cooperation involving indigenous peoples and local communities is urgently required in joint prevention to control the epidemic. Currently, many indigenous populations are continuing to face COVID 19. This study is concerned about the dynamic of COVID 19 pandemic among indigenous populations living in the remote Amazon rainforest enclaves. Using the Susceptible Infectious Recovered (SIR) model, the spread of the COVID 19 under 3 intervention scenarios (low, moderate, high) is simulated and predicted in indigenous tribe populations. The SIR model forecasts that without intervention, the epidemic peak may reach within 10 20 days. Nonetheless the peak can be reduced with strict interventions. Under low intervention, the COVID 19 cases are reduced to 73% and 56% of the total populations. While, in the scenario of high intervention, the COVID 19 peaks can be reduced to values ranging from 53% to 15% . To conclude, the simulated interventions tested by SIR model have reduced the pandemic peak and flattened the COVID 19 curve in indigenous populations. Nonetheless, it is mandatory to strengthen all mitigation efforts, reduce exposures, and decrease transmission rate as possible for COVID 19 containment.
Replication of Influenza D Viruses of Bovine and Swine Origin in Ovine Respiratory Explants and Their Attachment to the Respiratory Tract of Bovine, Sheep, Goat, Horse, and Swine

Bovine is considered the main reservoir of influenza D virus (IDV), however, low levels of seropositivity in other farmed species suggest a wide range of potential hosts. Nevertheless, it is not clear whether this scenario is the result of rare spillover events upon contact with bovines, or a lack of adaptation of IDV to these hosts. Among these species, sheep represents a crucial component of the rural economy in many developing countries, but little is known about its role in the ecology of the disease. To evaluate the susceptibility of sheep to IDV viruses of different origin, we used ovine respiratory tissues as an ex vivo model and investigated the infective phenotype of two IDV strains isolated from either bovine (IDV-BOV) or swine (IDV-SW). For translatability purposes, we included a parainfluenza type 3 virus, as positive control, given its known respiratory tropism in sheep. We performed a timed evaluation of the viral infectivity, cell tropism and the associated histopathology, by means of tissue culture infectious dose assays on supernatants and histological/immunohistochemical analyses on explanted tissues, respectively. To further investigate differences in the phenotype of these two strains and to identify the potential targets of replication in the most commonly land-based farmed mammalian species, we carried out virus binding assays on histological sections of the respiratory tract of bovine, caprine, ovine, horse and swine. Our results demonstrated that IDV successfully replicates in nasal, tracheal and lung ovine tissues, suggesting a moderate susceptibility of this species to IDV infection. Interestingly, despite the high genetic identity of these strains, IDV- BOV consistently replicated to higher titers than IDV-SW in all respiratory tracts, suggesting IDV viruses might display considerable levels of variability in their phenotype when crossing the species barrier. Virus binding assays confirmed a superior affinity of the IDV viruses for the bovine upper respiratory tract, and a preference for the pharyngeal epithelium of small ruminants, indicating possible targets to improve the sensitivity of virological sampling for diagnostic and post-mortem purposes. Further pathogenesis and cross-species transmission studies will be necessary to elucidate the ecology of IDV and eventually allow the design of cost-effective surveillance strategies.
Freeze-induced sap absorption in Acer pseudoplatanus: a possible mechanism.

Xylem sap pressure changes in response to imposed temperature regimes were studied using excised stems of young sycamore seedlings (Acer pseudoplatanus L). Experiments confirmed that a rapid decrease in sap pressure (inducing an uptake of water) occurred within the xylem core during freezing. The sequence was reversed by thawing. Measurement of wood diameter or bark thickness revealed no significant changes which might accommodate this sap during freezing. Indeed, investigation of the sapwood density showed an overall increase on freezing. The absorption of water in response to freezing was shown to be operative in deliberately killed tissue, although high tissue water content above about 60% disrupted the response. Experiments using twigs at suprafreezing temperatures induced sap exudation also, but it was only a small fraction of the amounts which could be expected after freeze-induced absorption. Apparently suprafreezing exudation can be explained by thermal expansion effects of gas and sap in the wood.
Automated Analysis of Stroke Mouse Trajectory Data With Traja

Quantitative characterization of mouse activity, locomotion and walking patterns requires the monitoring of position and activity over long periods of time. Manual behavioral phenotyping, however, is time and skill-intensive, vulnerable to researcher bias and often stressful for the animals. We present examples for using a platform-independent open source trajectory analysis software, Traja, for semi-automated analysis of high throughput mouse home-cage data for neurobehavioral research. Our software quantifies numerous parameters of movement including traveled distance, velocity, turnings, and laterality which are demonstrated for application to neurobehavioral analysis. In this study, the open source software for trajectory analysis Traja is applied to movement and walking pattern observations of transient stroke induced female C57BL/6 mice (30 min middle cerebral artery occlusion) on an acute multinutrient diet intervention (Fortasyn). After stroke induction mice were single housed in Digital Ventilated Cages [DVC, GM500, Tecniplast S.p.A. , Buguggiate (VA), Italy] and activity was recorded 24/7, every 250 ms using a DVC board. Significant changes in activity, velocity, and distance walked are computed with Traja. Traja identified increased walked distance and velocity in Control and Fortasyn animals over time. No diet effect was found in preference of turning direction (laterality) and distance traveled. As open source software for trajectory analysis, Traja supports independent development and validation of numerical methods and provides a useful tool for computational analysis of 24/7 mouse locomotion in home-cage environment for application in behavioral research or movement disorders.
COVID-19 detection from chest X-Ray images using Deep Learning and Convolutional Neural Networks

The COVID-19 pandemic in 2020 has highlighted the need to pull all available resources towards the mitigation of the devastating effects of such ”Black Swan” events. Towards that end, we investigated the option to employ technology in order to assist the diagnosis of patients infected by the virus. As such, several state-of-the-art pre-trained convolutional neural networks were evaluated as of their ability to detect infected patients from chest X-Ray images. A dataset was created as a mix of publicly available X-ray images from patients with confirmed COVID-19 disease, common bacterial pneumonia and healthy individuals. To mitigate the small number of samples, we employed transfer learning, which transfers knowledge extracted by pre-trained models to the model to be trained. The experimental results demonstrate that the classification performance can reach an accuracy of 95% for the best two models.
Genome Wide Association Mapping of Spot Blotch Resistance at Seedling and Adult Plant Stages in Barley

Barley spot blotch (SB) caused by Cochliobolus sativus is one of the major constrains to barley production in warmer regions worldwide. The study was undertaken to identify and estimate effects of loci underlying quantitative resistance to SB at the seedling and adult plant stages. A panel of 261 high input (HI-AM) barley genotypes consisting of released cultivars, advanced breeding lines, and landraces, was screened for resistance to SB. The seedling resistance screening was conducted using two virulent isolates from Morocco (ICSB3 and SB54) while the adult plant stage resistance was evaluated at two hot spot locations, Faizabad and Varanasi, in India under artificial inoculation using a mixture of prevalent virulent isolates. The HI-AM panel was genotyped using DArT-Seq high-throughput genotyping platform. Genome wide association mapping (GWAM) was conducted using 13,182 PAV and 6,311 SNP markers, for seedling and adult plant resistance. Both GLM and MLM model were employed in TASSEL (v 5.0) using principal component analysis and Kinship Matrix as covariates. Final disease rating and Area Under Disease Progress Curve (AUDPC) were used for the evaluation of adult stage plant resistance. The GWAM analysis indicated 23 QTL at the seedling stage (14 for isolate ICSB3 and 9 for isolate SB54), while 15 QTL were detected at the adult plant stage resistance (6 at Faizabad and 9 at Varanasi) and 5 for AUDPC based resistance at Varanasi. Common QTL at seedling and adult plant stages were found across all barley chromosomes. Seedling stage QTL explained together 73.24% of the variance for seedling resistance to isolate ICSB3 and 49.26% for isolate SB54, whereas, QTL for adult plant stage resistance explained together 38.32%, 44.09% and 26.42% of the variance at Faizabad and Varanasi and AUDPC at Varanasi, respectively. Several QTL identified in this study were also reported in previous studies using bi-parental and association mapping populations, corroborating our results. The promising QTL detected at both stages, once validated, can be used for marker assisted selection (MAS) in SB resistance barley breeding program.
Can we prevent Parkinson’s disease with n-3 polyunsaturated fatty acids?

It is increasingly clear that nongenetic elements play a crucial role in the pathogenesis of Parkinson’s disease (PD), yet no modifiable environmental risk factor has been clearly identified. Recent work in animal models of PD supports the contention that n-3 polyunsaturated fatty acids (PUFA) found in fatty fish are neuroprotective in PD. Moreover, a few epidemiological reports suggest that a high intake of fish (and n-3 PUFA) is associated with a lower risk of developing PD. The question remains whether docosahexenoic or eicosapentenoic acid is the brain n-3 PUFA responsible for the observed neuroprotective effect. Despite these encouraging data, the development of n-3 PUFA as drugs is hindered by the fact that they are nonpatentable compounds, at least in their natural form. Nevertheless, owing to their favorable safety profile, it should be a high priority to pursue preclinical and clinical studies on the nutraceutical properties of n-3 PUFA in PD.
EFFECT OF LIGHT AND TEMPERATURE INTERACTIONS ON GROWTH OF CRYPTOMONAS EROSA (CRYPTOPHYCEAE) 1

Cryptomonas erosa Skuja, a planktonic alga, was grown in batch culture at different combinations of light intensity and temperature, under nutrient saturation. Growth was maximal (1.2 divisions · day−1) at 23.5 C and 0.043 ly · min−1, declining sharply with temperature (0.025 divisions‐day−1 at 1 C). With decreasing temperature, the cells showed both light saturation and inhibition at much reduced light intensities. At the same time the compensation light intensity for growth declined towards a minimum of slightly above 0.4 × 10−4 ly · min−1 (~1 ft‐c) at 1 C or <0.1 ly · day−1 (PAR). Cell division was more adversely affected by low temperature than carbon uptake, and the resulting excess production of photosynthate was both stored and excreted. Extreme storage of carbohydrates resulted in cell volumes and carbon content ca. 22 and 30 × greater, respectively, than the maxima observed for cells incubated in the dark, whereas, at growth inhibitory light levels, as much as 57% of the total assimilated carbon was excreted. A marked increase in cell pigment was observed at the lowest light levels (<10−3 ly · min−1), at high temperature. The growth response of C. erosa in culture provides insight into the abundance and distribution of cryptomonads and other small algal flagellates in nature.
Biological Control of Plant-Parasitic Nematodes by Filamentous Fungi Inducers of Resistance: Trichoderma, Mycorrhizal and Endophytic Fungi

Plant-parasitic-nematodes represent a major threat to the agricultural production of different crops worldwide. Due to the high toxicity of chemical nematicides, it is necessary to develop new control strategies against nematodes. In this respect, filamentous fungi can be an interesting biocontrol alternative. The genus Trichoderma, mycorrhizal and endophytic fungi are the main groups of filamentous fungi studied and used as biological control agents (BCAs) against nematodes as resistance inducers. They are able to reduce the damage caused by plant-parasitic nematodes directly by parasitism, antibiosis, paralysis and by the production of lytic enzymes. But they also minimize harm by space and resource-competition, by providing higher nutrient and water uptake to the plant, or by modifying the root morphology, and/or rhizosphere interactions, that constitutes an advantage for the plant-growth. Besides, filamentous fungi are able to induce resistance against nematodes by activating hormone-mediated (salicylic and jasmonic acid, strigolactones among others) plant-defense mechanisms. Additionally, the alteration of the transport of chemical defense components through the plant or the synthesis of plant secondary metabolites and different enzymes can also contribute to enhancing plant defenses. Therefore, the use of filamentous fungi of the mentioned groups as BCAs is a promising durable biocontrol strategy in agriculture against plant-parasitic nematodes.
Global Infodemiology of COVID-19: Focus on Google web searches and Instagram hashtags

Background: Several studies have been conducted using 'infodemiological' methods in COVID-19 research, but studies focusing to examine the extent of infodemic monikers (misinformation) on the internet is very limited. Aim: We aimed to investigate the internet search behavior related to COVID-19 and the extent of infodemic monikers circulating in Google and Instagram during the pandemic period in the world. Methods: Using Google Trends and Instagram hashtags (#), we explored the internet search activities and behaviors related to COVID-19 pandemic all over the world from February 20, 2020, to May 06, 2020. Briefly, we investigated the names used to identify the virus, health and risk perception, life during the lockdown, and also information related to the adoption of infodemic monikers related to COVID-19. We computed the average peak volume (APC) with a 95% confidence interval (CI) during the study period. Results: The top five COVID-19 related terms used in Google searches were "coronavirus", "corona", "COVID", "virus", "corona virus", and "COVID-19". Countries with a higher number of COVID-19 cases have greater Google searches queries related to COVID-19. "coronavirus ozone", "coronavirus laboratory", "coronavirus 5G", "coronavirus conspiracy" and "coronavirus bill gates" are widely circulated infodemic monikers on the internet. Searches related to 'tips and cures' to COVID-19 spiked when the US president suggested an unproven drug as a 'miracle cure' and suggested injecting disinfectant to treat COVID-19. Around two-thirds (66.1%) of the Instagram users use "COVID-19", and "coronavirus" hashtags to disperse the information related to COVID-19. Conclusion: Globally, there is a growing interest in COVID-19 and a large number of infodemic monikers are circulating on the internet. Therefore, mass media regulators and health organizers should be vigilant to diminish the infodemic monikers dispersing on the internet and also should take serious actions against those spreading misinformation in social media.
Quantification of model and data uncertainty in a network analysis of cardiac myocyte mechanosignalling

Cardiac myocytes transduce changes in mechanical loading into cellular responses via interacting cell signalling pathways. We previously reported a logic-based ordinary differential equation model of the myocyte mechanosignalling network that correctly predicts 78% of independent experimental results not used to formulate the original model. Here, we use Monte Carlo and polynomial chaos expansion simulations to examine the effects of uncertainty in parameter values, model logic and experimental validation data on the assessed accuracy of that model. The prediction accuracy of the model was robust to parameter changes over a wide range being least sensitive to uncertainty in time constants and most affected by uncertainty in reaction weights. Quantifying epistemic uncertainty in the reaction logic of the model showed that while replacing ‘OR’ with ‘AND’ reactions greatly reduced model accuracy, replacing ‘AND’ with ‘OR’ reactions was more likely to maintain or even improve accuracy. Finally, data uncertainty had a modest effect on assessment of model accuracy. This article is part of the theme issue ‘Uncertainty quantification in cardiac and cardiovascular modelling and simulation’.
The influence of environmental factors on the persistence of Zoophthora radicans conidia

Abstract The ability ofZoophthora radicansconidia to infect and induce mycosis inPlutella xylostellalarvae was dramatically reduced after just 24 hr field exposure in the Cameron Highlands, Malaysia. In laboratory studies some conidia retained infectivity for up to 16 days on the surface of foliage or soil. The rate at which conidia lost infectivity was greater on the adaxial leaf surface than on the abaxial leaf surface and greater on soil with a low moisture content than on soil with a higher moisture content. One hour of simulated heavy rainfall had no impact on the ability of primary conidia on either the adaxial or abaxial leaf surface to induce mycosis in test larvae; 3 hr rainfall significantly reduced the level of infection induced in larvae bioassayed on the adaxial leaf surface. When primary conidia were incubated on leaf surfaces under conditions of high humidity to encourage capilliconidia development and then subjected to heavy rainfall, 1 hr of exposure significantly reduced the level of mycosis induced in test larvae bioassayed on adaxial but not abaxial leaf surfaces. Exposure of primary conidia to natural, temperate solar radiation for 4 hr did not affect the level of mycosis induced in test larvae. Ultraviolet and simulated tropical solar radiation were both damaging to conidia, although capilliconidia were significantly more tolerant to radiation than primary conidia. The ability to induce mycosis in test larvae was not affected by 1 hr of exposure to simulated tropical solar radiation but 4 hr exposure significantly reduced the level of mycosis induced in test larvae. Eight hours of exposure had no further affect on the level of mycosis induced by secondary capilliconidia but did reduce the level induced by primary conidia. Solar radiation is considered to be the major environmental factor affectingZ. radicanspersistence. The results are discussed in relation to the use ofZ. radicansforP. xylostellacontrol.
Common Mycorrhizal Network Induced JA/ET Genes Expression in Healthy Potato Plants Connected to Potato Plants Infected by Phytophthora infestans

Most plants are connected belowground via common mycorrhizal networks (CMNs). In their presence, the transmission of warning signals from diseased to uninfected plants has been reported. However, current studies have all been conducted in pots making it difficult to discriminate direct from indirect contribution of hyphae to the transmission of the signals. Here, we conducted an in vitro study with potato plantlets connected by a CMN of the arbuscular mycorrhizal fungus Rhizophagus irregularis. The plantlets were grown in physically separated compartments and their connection ensured only by the CMN. The donor potato plantlets were infected by Phytophthora infestans and defense genes analyzed 24, 48 and 120 h post-infection (hpi) in the uninfected receiver potato plantlets. Twenty-four hpi by the pathogen, PAL, PR-1b, ERF3, and LOX genes were significantly upregulated, whereas no significant transcript variation was noticed 48 and 120 hpi. The exact nature of the warning signals remains unknown but was not associated to microorganisms other than the AMF or to diffusion mechanisms through the growth medium or induced by volatile compounds. The defense response appeared to be transitory and associated with the jasmonic acid or ethylene pathway. These findings demonstrate the direct involvement of hyphae in the transmission of warning signals from diseased to uninfected potato plantlets and their indubitable role in providing a route for activating defense responses in uninfected plants.
Leishmanicidal Potential of Hardwickiic Acid Isolated From Croton sylvaticus

Leishmania is a parasitic protozoon responsible for the neglected tropical disease Leishmaniasis. Approximately, 350 million people are susceptible and close to 70,000 death cases globally are reported annually. The lack of effective leishmanicides, the emergence of drug resistance and toxicity concerns necessitate the pursuit for effective antileishmanial drugs. Natural compounds serve as reservoirs for discovering new drugs due to their chemical diversity. Hardwickiic acid (HA) isolated from the stembark of Croton sylvaticus was evaluated for its leishmanicidal potential against Leishmania donovani and L. major promastigotes. The susceptibility of the promastigotes to HA was determined using the 3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyltetrazolium bromide/phenazine methosulfate colorimetric assay with Amphotericin B serving as positive control. HA showed a significant antileishmanial activity on L. donovani promastigotes with an IC50 value of 31.57± 0.06 µM with respect to the control drug, amphotericin B with IC50 of 3.35 ± 0.14 µM). The cytotoxic activity was observed to be CC50 = 247.83 ± 6.32 µM against 29.99 ± 2.82 µM for curcumin, the control, resulting in a selectivity index of SI = 7.85. Molecular modeling, docking and dynamics simulations of selected drug targets corroborated the observed antileishmanial activity of HA. Novel insights into the mechanisms of binding were obtained for trypanothione reductase (TR), pteridine reductase 1 (PTR1), and glutamate cysteine ligase (GCL). The binding affinity of HA to the drug targets LmGCL, LmPTR1, LdTR, LmTR, LdGCL, and LdPTR1 were obtained as -8.0, -7.8, -7.6, -7.5, -7.4 and -7.1 kcal/mol, respectively. The role of Lys16, Ser111, and Arg17 as critical residues required for binding to LdPTR1 was reinforced. HA was predicted as a Caspase-3 stimulant and Caspase-8 stimulant, implying a possible role in apoptosis, which was shown experimentally that HA induced parasite death by loss of membrane integrity. HA was also predicted as antileishmanial molecule corroborating the experimental activity. Therefore, HA is a promising antileishmanial molecule worthy of further development as a biotherapeutic agent.