Miracle-dz/UniFAR-FTUs huggingface dataset:
Signaling in the Tomato Immunity against Fusarium oxysporum

New strategies of control need to be developed with the aim of economic and environmental sustainability in plant and crop protection. Metabolomics is an excellent platform for both understanding the complex plant–pathogen interactions and unraveling new chemical control strategies. GC-MS-based metabolomics, along with a phytohormone analysis of a compatible and incompatible interaction between tomato plants and Fusarium oxysporum f. sp. lycopersici, revealed the specific volatile chemical composition and the plant signals associated with them. The susceptible tomato plants were characterized by the over-emission of methyl- and ethyl-salicylate as well as some fatty acid derivatives, along with an activation of salicylic acid and abscisic acid signaling. In contrast, terpenoids, benzenoids, and 2-ethylhexanoic acid were differentially emitted by plants undergoing an incompatible interaction, together with the activation of the jasmonic acid (JA) pathway. In accordance with this response, a higher expression of several genes participating in the biosynthesis of these volatiles, such as MTS1, TomloxC, TomloxD, and AOS, as well as JAZ7, a JA marker gene, was found to be induced by the fungus in these resistant plants. The characterized metabolome of the immune tomato plants could lead to the development of new resistance inducers against Fusarium wilt treatment.
A Small Molecule Targeting Human MEK1/2 Enhances ERK and p38 Phosphorylation under Oxidative Stress or with Phenothiazines

Small molecules are routinely used to inhibit protein kinases, but modulators capable of enhancing kinase activity are rare. We have previously shown that the small molecule INR119, designed as an inhibitor of MEK1/2, will enhance the activity of its fission yeast homologue, Wis1, under oxidative stress. To investigate the generality of these findings, we now study the effect of INR119 in human cells under similar conditions. Cells of the established breast cancer line MCF-7 were exposed to H2O2 or phenothiazines, alone or combined with INR119. In line with the previous results in fission yeast, the phosphorylation of the MAPKs ERK and p38 increased substantially more with the combination treatment than by H2O2 or phenothiazines, whereas INR119 alone did not affect phosphorylation. We also measured the mRNA levels of TP53 and BAX, known to be affected by ERK and p38 activity. Similarly, the combination of INR119 and phenothiazines increased both mRNAs to higher levels than for phenothiazines alone. In conclusion, the mechanism of action of INR119 on its target protein kinase may be conserved between yeast and humans.
Rotating Bending Fatigue Analysis of Printed Specimens from Assorted Polymer Materials

Fused filament fabrication (FFF), as a form of additive manufacturing (AM), in recent years, has become a popular method to manufacture prototypes, as well as functional parts. FFF is an extrusion process, commonly known as 3D printing, where the object is built by depositing melted material layer by layer. The most common materials, i.e., the materials that are most widely used, are polylactic acid (PLA), acrylonitrile butadiene styrene (ABS) and acrylonitrile styrene acrylate (ASA). Although there are lot of research papers that cover the subject of the determination of mechanical properties and characteristics, theoretically and experimentally, as well as the fatigue characteristics of aforementioned materials, there is a lack of research and scientific papers dealing with the problematics of S–N curves based on the rotating bending fatigue analysis of those materials. Consequently, this paper covers the topic of rotating bending fatigue data for 3D printed specimens of given materials, under different loading values.
Bioactive Compounds, Antioxidant, and Antibacterial Properties of Lonicera caerulea Berries: Evaluation of 11 Cultivars

The aim of the study was to evaluate 11 cultivars of blue honeysuckle (Lonicera caerulea L.) for bioactive compounds, antioxidant capacity, and the antibacterial activity of berries. Total phenolic contents (TPCs) and total anthocyanin contents (TACs) were established by using ethanolic extracts. For contents of organic acids and saccharides, aqueous extracts were used, and vitamin C was determined by using oxalic acid solution. DPPH• radical scavenging capacity was evaluated by using ethanolic extracts; antibacterial activity was assessed by using both ethanolic and aqueous extracts. The TPC varied from 364.02 ± 0.41 mg/100 g in ‘Vostorg’ to 784.5 ± 0.3 mg/100 g in ‘Obilnaja’, and TAC ranged from 277.8 ± 1.1 mg/100 g in ‘Čelnočnaja’ to 394.1 ± 8.4 mg/100 g in ‘Nimfa’. Anthocyanins comprised 53.8% of total phenolic contents on average. Among organic acids, citric acid was predominant, averaging 769.41 ± 5.34 mg/100 g, with malic and quinic acids amounting to 289.90 ± 2.64 and 45.00 ± 0.37 mg/100 g on average, respectively. Contents of vitamin C were 34.26 ± 0.25 mg/100 g on average. Organic acids were most effective in the inhibition of both Gram-positive and Gram-negative bacteria tested. In conclusion, berries of L. caerulea are beneficial not only for fresh consumption, but also as a raw material or ingredients of foods with high health-promoting value.
The last frontier for global non-communicable disease action: The emergency department—A cross-sectional study from East Africa

Abstract Background Deaths due to non-communicable diseases (NCDs) have surpassed those due to communicable diseases globally and are projected to do so in Africa by 2030. Despite demonstrated effectiveness in high-income country (HIC) settings, the ED is a primary source of NCD care that has been under-prioritized in Africa. In this study, we assess the burden of leading NCDs and NCD risk factors in Kenyan Casualty Department patients, to inform interventions targeting patients with NCDs in emergency care settings. Methods Using the WHO STEPwise approach to surveillance (STEPS) tool and the Personal Health Questionnaire (PHQ-9), we conducted a survey of 923 adults aged 18 and over at Kenyatta National Hospital Emergency Department (KNH ED), the largest hospital in East Africa between May-October 2018. We used descriptive statistics and covariate-adjusted logistic analysis to analyze results. We included the following socio-demographic variables in our models: age, income, household size (t-test), sex, education, marital status, work status, and poverty status (chi-squared test or fisher's exact test). Findings More than a third of respondents had hypertension (35.8%, n=225/628), one in five had raised blood sugar or diabetes (18.3%, n=61/333), and more than one in ten reported having cardiovascular disease (11.7%, n=90/769). Having lower levels of education was associated with tobacco use (OR 6.0, 95% CI 2.808-12.618, p < 0.0001), while those with higher levels of education reported increased alcohol use (OR 0.620 (95% CI 0.386-0.994, p = 0.0472). While a predominant proportion of respondents had had some form of screening for either hypertension (80.3%, n=630/772), blood sugar (42.6%, n=334/767) or cholesterol (13.9%, n=109/766), the proportion of those on treatment was low, with the highest proportion being half of those diagnosed with hypertension reporting taking medication(51.6%, n=116/225). Determinants of disease burden were age, sex, and income. Interpretation Comprehension of the unique epidemiology and characteristics of patients presenting to the ED is key to guide care in African populations. Patient-driven interventions, and collaboration with community-based stakeholders such as patient navigators, are ideal considerations to sustainably address NCDs leveraging the ED in the resource-limited setting. Funding Hecht-Albert Global Health Pilot Innovation Award for Junior Faculty, Global Health Leadership Institute, Yale University.
De Novo 1q21.3q22 Duplication Revaluation in a “Cold” Complex Neuropsychiatric Case with Syndromic Intellectual Disability

Syndromic intellectual disability often obtains a genetic diagnosis due to the combination of first and next generation sequencing techniques, although their interpretation may require revaluation over the years. Here we report on a composite neuropsychiatric case whose phenotype includes moderate intellectual disability, spastic paraparesis, movement disorder, and bipolar disorder, harboring a 1.802 Mb de novo 1q21.3q22 duplication. The role of this duplication has been reconsidered in the light of negativity of many other genetic exams, and of the possible pathogenic role of many genes included in this duplication, potentially configuring a contiguous gene-duplication syndrome.
Combined Peridynamics and Discrete Multiphysics to Study the Effects of Air Voids and Freeze-Thaw on the Mechanical Properties of Asphalt

This paper demonstrates the use of peridynamics and discrete multiphysics to assess micro crack formation and propagation in asphalt at low temperatures and under freezing conditions. Three scenarios are investigated: (a) asphalt without air voids under compressive load, (b) asphalt with air voids and (c) voids filled with freezing water. The first two are computed with Peridynamics, the third with peridynamics combined with discrete multiphysics. The results show that the presence of voids changes the way cracks propagate in the material. In asphalt without voids, cracks tend to propagate at the interface between the mastic and the aggregate. In the presence of voids, they ‘jump’ from one void to the closest void. Water expansion is modelled by coupling Peridynamics with repulsive forces in the context of Discrete Multiphysics. Freezing water expands against the voids’ internal surface, building tension in the material. A network of cracks forms in the asphalt, weakening its mechanical properties. The proposed methodology provides a computational tool for generating samples of ‘digital asphalt’ that can be tested to assess the asphalt properties under different operating conditions.
Palm Fruit Bioactive Complex (PFBc), a Source of Polyphenols, Demonstrates Potential Benefits for Inflammaging and Related Cognitive Function

Cognitive function is a key aspect of healthy aging. Inflammation associated with normal aging, also called inflammaging is a primary risk factor for cognitive decline. A diet high in fruits and vegetable and lower in calories, particularly a Mediterranean Diet, may lower the risk of age-related cognitive decline due in part to the associated high intake of antioxidants and polyphenols. A phenolic, Palm Fruit Bioactive complex (PFBc) derived from the extraction process of palm oil from oil palm fruit (Elaeis guineensis), is reported to offset inflammation due to its high antioxidant, especially vitamin E, and polyphenol content. The benefit is thought to be achieved via the influence of antioxidants on gene expression. It is the purpose of this comprehensive review to discuss the etiology, including gene expression, of mild cognitive impairment (MCI) specific to dietary intake of antioxidants and polyphenols and to focus on the potential impact of nutritional interventions specifically PFBc has on MCI. Several in vitro, in vivo and animal studies support multiple benefits of PFBc especially for improving cognitive function via anti-inflammatory and antioxidant mechanisms. While more human studies are needed, those completed thus far support the benefit of consuming PFBc to enhance cognitive function via its anti-inflammatory antioxidant functions.
Biochemical Properties and Anti-Biofilm Activity of Chitosan-Immobilized Papain

Chitosan, the product of chitin deacetylation, is an excellent candidate for enzyme immobilization purposes. Here we demonstrate that papain, an endolytic cysteine protease (EC: 3.4.22.2) from Carica papaya latex immobilized on the matrixes of medium molecular (200 kDa) and high molecular (350 kDa) weight chitosans exhibits anti-biofilm activity and increases the antimicrobials efficiency against biofilm-embedded bacteria. Immobilization in glycine buffer (pH 9.0) allowed adsorption up to 30% of the total protein (mg g chitosan−1) and specific activity (U mg protein−1), leading to the preservation of more than 90% of the initial total activity (U mL−1). While optimal pH and temperature of the immobilized papain did not change, the immobilized enzyme exhibited elevated thermal stability and 6–7-fold longer half-life time in comparison with the soluble papain. While one-half of the total enzyme dissociates from both carriers in 24 h, this property could be used for wound-dressing materials design with dosed release of the enzyme to overcome the relatively high cytotoxicity of soluble papain. Our results indicate that both soluble and immobilized papain efficiently destroy biofilms formed by Staphylococcus aureus and Staphylococcus epidermidis. As a consequence, papain, both soluble and immobilized on medium molecular weight chitosan, is capable of potentiating the efficacy of antimicrobials against biofilm-embedded Staphylococci. Thus, papain immobilized on medium molecular weight chitosan appears a presumably beneficial agent for outer wound treatment for biofilms destruction, increasing antimicrobial treatment effectiveness.
An Interesting Molecule: γ-Aminobutyric Acid. What Can We Learn from Hydra Polyps?

Neuronal excitability is controlled primarily by γ-aminobutyric acid (GABA) in the central and peripheral nervous systems of vertebrate as well as invertebrate organisms. Besides its recognized neurotransmitter functions, GABA also plays a fundamental role in neurogenesis and synaptogenesis during embryonic development. In addition, GABAergic mechanisms are also involved in disorders of various peripheral tissues, ranging from diabetes to hypothyroidism to inflammatory responses. The discovery of the molecule and the history of its biosynthetic pathways in vertebrate and invertebrate phyla are summarized here. The occurrence and distribution of GABA, GABA-synthesizing enzymes, and receptors to GABA in the freshwater polyp Hydra vulgaris (Cnidaria: Hydrozoa), endowed with an early evolved nervous system, are discussed in relation to possible interactions with the microbiota, a stable component of Hydra polyps; their contribution to the evolution of nervous systems through microbe–neuronal interactions is proposed.
Methane Production Rate during Anoxic Litter Decomposition Depends on Si Mass Fractions, Nutrient Stoichiometry, and Carbon Quality

While Si influences nutrient stoichiometry and decomposition of graminoid litter, it is still unclear how Si influences anoxic litter decomposition and CH4 formation in graminoid dominated fen peatlands. First, Eriophorum vaginatum plants were grown under different Si and P availabilities, then shoots and roots were characterized regarding their proportions of C, Si, N and P and regarding C quality. Subsequently the Eriophorum shoots were subjected to anoxic decomposition. We hypothesized; that (I) litter grown under high Si availability would show a higher Si but lower nutrient mass fractions and a lower share of recalcitrant carbon moieties; (II) high-Si litter would show higher CH4 and CO2 production rates during anoxic decomposition; (III) methanogenesis would occur earlier in less recalcitrant high-Si litter, compared to low-Si litter. We found a higher Si mass fraction that coincides with a general decrease in C and N mass fractions and decreased share of recalcitrant organic moieties. For high-Si litter, the CH4 production rate was higher, but there was no long-term influence on the CO2 production rate. More labile high-Si litter and a differential response in nutrient stoichiometry led to faster onset of methanogenesis. This may have important implications for our understanding of anaerobic carbon turnover in graminoid-rich fens.
Designing Interpretable Recurrent Neural Networks for Video Reconstruction via Deep Unfolding

Deep unfolding methods design deep neural networks as learned variations of optimization algorithms through the unrolling of their iterations. These networks have been shown to achieve faster convergence and higher accuracy than the original optimization methods. In this line of research, this paper presents novel interpretable deep recurrent neural networks (RNNs), designed by the unfolding of iterative algorithms that solve the task of sequential signal reconstruction (in particular, video reconstruction). The proposed networks are designed by accounting that video frames’ patches have a sparse representation and the temporal difference between consecutive representations is also sparse. Specifically, we design an interpretable deep RNN (coined reweighted-RNN) by unrolling the iterations of a proximal method that solves a reweighted version of the <inline-formula> <tex-math notation="LaTeX">$\ell _{1}$ </tex-math></inline-formula>-<inline-formula> <tex-math notation="LaTeX">$\ell _{1}$ </tex-math></inline-formula> minimization problem. Due to the underlying minimization model, our reweighted-RNN has a different thresholding function (alias, different activation function) for each hidden unit in each layer. In this way, it has higher network expressivity than existing deep unfolding RNN models. We also present the derivative <inline-formula> <tex-math notation="LaTeX">$\ell _{1}$ </tex-math></inline-formula>-<inline-formula> <tex-math notation="LaTeX">$\ell _{1}$ </tex-math></inline-formula>-RNN model, which is obtained by unfolding a proximal method for the <inline-formula> <tex-math notation="LaTeX">$\ell _{1}$ </tex-math></inline-formula>-<inline-formula> <tex-math notation="LaTeX">$\ell _{1}$ </tex-math></inline-formula> minimization problem. We apply the proposed interpretable RNNs to the task of video frame reconstruction from low-dimensional measurements, that is, sequential video frame reconstruction. The experimental results on various datasets demonstrate that the proposed deep RNNs outperform various RNN models.
Physiological Responses of Salinized Fenugreek (Trigonella foenum-graecum L.) Plants to Foliar Application of Salicylic Acid

Considering the detrimental effects of salt stress on the physiological mechanisms of plants in terms of growth, development and productivity, intensive efforts are underway to improve plant tolerance to salinity. Hence, an experiment was conducted to assess the impact of the foliar application of salicylic acid (SA; 0.5 mM) on the physiological traits of fenugreek (Trigonella foenum-graecum L.) plants grown under three salt concentrations (0, 75, and 150 mM NaCl). An increase in salt concentration generated a decrease in the chlorophyll content index (CCI); however, the foliar application of SA boosted the CCI. The malondialdehyde content increased in salt-stressed fenugreek plants, while a reduction in content was observed with SA. Likewise, SA application induced an accumulation of proline, total phenolics, and flavonoids. Moreover, further increases in total free amino acids and shikimic acid were observed with the foliar application of SA, in either control or salt-treated plants. Similar results were obtained for ascorbate peroxidase, peroxidase, polyphenol oxidase, and catalase with SA application. Hence, we concluded that the foliar application of SA ameliorates salinity, and it is a growth regulator that improves the tolerance of fenugreek plants under salt stress.
Two peptides targeting endothelial receptors are internalized into murine brain endothelial cells

The blood-brain barrier (BBB) is one of the main obstacles for therapies targeting brain diseases. Most macromolecules fail to pass the tight BBB, formed by brain endothelial cells interlinked by tight junctions. A wide range of small, lipid-soluble molecules can enter the brain parenchyma via diffusion, whereas macromolecules have to transcytose via vesicular transport. Vesicular transport can thus be utilized as a strategy to deliver brain therapies. By conjugating BBB targeting antibodies and peptides to therapeutic molecules or nanoparticles, it is possible to increase uptake into the brain. Previously, the synthetic peptide GYR and a peptide derived from melanotransferrin (MTfp) have been suggested as candidates for mediating transcytosis in brain endothelial cells (BECs). Here we study uptake, intracellular trafficking, and translocation of these two peptides in BECs. The peptides were synthesized, and binding studies to purified endocytic receptors were performed using surface plasmon resonance. Furthermore, the peptides were conjugated to a fluorophore allowing for live-cell imaging studies of their uptake into murine brain endothelial cells. Both peptides bound to low-density lipoprotein receptor-related protein 1 (LRP-1) and the human transferrin receptor, while lower affinity was observed against the murine transferrin receptor. The MTfp showed a higher binding affinity to all receptors when compared to the GYR peptide. The peptides were internalized by the bEnd.3 mouse endothelial cells within 30 min of incubation and frequently co-localized with endo-lysosomal vesicles. Moreover, our in vitro Transwell translocation experiments confirmed that GYR was able to cross the murine barrier and indicated the successful translocation of MTfp. Thus, despite binding to endocytic receptors with different affinities, both peptides are able to transcytose across the murine BECs.
Potential of Fumagillin and Agaricus blazei Mushroom Extract to Reduce Nosema ceranae in Honey Bees

Simple Summary Nosemosis is a disease in bees that causes severe problems for their vitality, reproduction and productivity. Traditionally, the treatment involves the application of fumagillin, an antibiotic with proven effect. Recently, fumagillin production and registration has faced problems worldwide, leading to the absence of adequate treatment. Motivated by the reported health issues and the occurrence of residues after fumagillin application, scientists around the world have sought a medication or a supplement that could help beekeepers to control Nosema. Current trends include the search for alternative non-antibiotic treatments. In a laboratory (cage) experiment, we studied the effect of fumagillin and natural extract of mushroom Agaricus blazei on the survival of Nosema infected bees, Nosema spore loads and levels of immune-related gene expression and oxidative stress markers. The results undoubtedly confirmed the anti-Nosema effect of fumagillin, as seen in better bee survival and monitored parameters; its application without Nosema infection (preventive) caused disturbance in some of the parameters. The application of A. blazei extract, however, showed positive effects in both preventive and curative applications. These beneficial properties of A. blazei extract indicate a potential that needs to be further investigated. Abstract Depending on the infection level and colony strength, Nosema ceranae, a microsporidian endoparasite of the honey bee may have significant consequences on the health, reproduction and productivity of bee colonies. Despite exerting some side effects, fumagillin is most often used for Nosema control. In this study, in a cage experiment, N. ceranae infected bees were treated with fumagillin or the extract of Agaricus blazei mushroom, a possible alternative for Nosema control. Bee survival, Nosema spore loads, the expression levels of immune-related genes and parameters of oxidative stress were observed. Fumagillin treatment showed a negative effect on monitored parameters when applied preventively to non-infected bees, while a noticeable anti-Nosema effect and protection from Nosema-induced immunosuppression and oxidative stress were proven in Nosema-infected bees. However, a protective effect of the natural A. blazei extract was detected, without any side effects but with immunostimulatory activity in the preventive application. The results of this research suggest the potential of A. blazei extract for Nosema control, which needs to be further investigated.