Miracle-dz/UniFAR-FTUs huggingface dataset:
Antinematode Activity of Abomasum Bacterial Culture Filtrates against Haemonchus contortus in Small Ruminants

Simple Summary Haemonchus contortus is an important gastrointestinal nematode parasite of the tropical and sub-tropical regions that cause haemonchosis in small ruminants like goats and sheep. It causes low production, reduced growth and may cause death of the infected animals. Due to the resistance development and environmental issues, the use of anthelmintics can be replaced with biological control, which is an environment friendly alternative. In the present study, three bacteria viz; Comamonas testosteroni, C. jiangduensis and Pseudomonas weihenstephanesis showed significant effect on nematode mortality and egg hatch inhibition. It was also observed that the anthelmintic activity of these bacteria was dose dependent, where 100% bacterial metabolite concentration showed the highest activity. It is suggested that these bacteria may included in the integrated nematode management. Abstract Haemonchosis is a parasitic disease of small ruminants that adversely affects livestock production. Haemonchus contortus is one of the most prevalent nematode parasites that infect the abomasum of small ruminants. This parasite reduces milk production, overall growth and sometimes causes the death of the infected animals. The evaluation of the biocontrol potential of some abomasum bacterial isolates against H. contortus is investigated in this study. Out of which, three isolates—Comamonas testosteroni, Comamonas jiangduensis, Pseudomonas weihenstephanesis—show significant effect against the nematode L3, adult, and egg hatch inhibition assays. Various concentrations of metabolites from these bacteria are prepared and applied in different treatments compared with control. In the case of adult mortality assay, 50% metabolites of C. testosteroni and P. weihenstephanesis show 46% adult mortality, whereas C. jiangduensis shows 40% mortality. It is observed that decreasing the concentration of bacterial metabolite, lowers nematode mortality. The minimum nematode mortality rate is recorded at the lowest filtrates concentration of all the bacterial isolates. The same trend is observed in egg hatch inhibition assay, where the higher concentration of bacterial culture filtrates shows 100% inhibition of H. contortus egg. It is concluded that the effect of bacterial culture filtrates against H. contortus is dose-dependent for their activity against nematode L3, adult, and inhibition of egg hatchment.
Temperature Sensitivity and Composition of Nitrate-Reducing Microbiomes from a Full-Scale Woodchip Bioreactor Treating Agricultural Drainage Water

Denitrifying woodchip bioreactors (WBR), which aim to reduce nitrate (NO3−) pollution from agricultural drainage water, are less efficient when cold temperatures slow down the microbial transformation processes. Conducting bioaugmentation could potentially increase the NO3− removal efficiency during these specific periods. First, it is necessary to investigate denitrifying microbial populations in these facilities and understand their temperature responses. We hypothesized that seasonal changes and subsequent adaptations of microbial populations would allow for enrichment of cold-adapted denitrifying bacterial populations with potential use for bioaugmentation. Woodchip material was sampled from an operating WBR during spring, fall, and winter and used for enrichments of denitrifiers that were characterized by studies of metagenomics and temperature dependence of NO3− depletion. The successful enrichment of psychrotolerant denitrifiers was supported by the differences in temperature response, with the apparent domination of the phylum Proteobacteria and the genus Pseudomonas. The enrichments were found to have different microbiomes’ composition and they mainly differed with native woodchip microbiomes by a lower abundance of the genus Flavobacterium. Overall, the performance and composition of the enriched denitrifying population from the WBR microbiome indicated a potential for efficient NO3− removal at cold temperatures that could be stimulated by the addition of selected cold-adapted denitrifying bacteria.
Dual Memory LSTM with Dual Attention Neural Network for Spatiotemporal Prediction

Spatiotemporal prediction is challenging due to extracting representations being inefficient and the lack of rich contextual dependences. A novel approach is proposed for spatiotemporal prediction using a dual memory LSTM with dual attention neural network (DMANet). A new dual memory LSTM (DMLSTM) unit is proposed to extract the representations by leveraging differencing operations between the consecutive images and adopting dual memory transition mechanism. To make full use of historical representations, a dual attention mechanism is designed to capture long-term spatiotemporal dependences by computing the correlations between the current hidden representations and the historical hidden representations from temporal and spatial dimensions, respectively. Then, the dual attention is embedded into DMLSTM unit to construct a DMANet, which enables the model with greater modeling power for short-term dynamics and long-term contextual representations. An apparent resistivity map (AR Map) dataset is proposed in this paper. The B-spline interpolation method is utilized to enhance AR Map dataset and makes apparent resistivity trend curve continuous derivative in the time dimension. The experimental results demonstrate that the developed method has excellent prediction performance by comparisons with some state-of-the-art methods.
Investigating the Role of Iron Sulfide on the Long-Term Stability of Reduced Uranium under Oxic Groundwater Conditions.

The historical accumulation and improper disposal of radioactive waste from extensive extraction and processing activities have caused widespread uranium contamination of groundwater and soils in the United States. Because uranium is a toxic heavy metal and radiological hazard, its migration poses serious human health and ecological risk. While successful remediation has been practiced at selected uranium contaminated sites, recent concerns have been raised over maintaining the long-term immobilization of reduced uranium solids in the subsurface when oxidants re-enter the reducing zone. Previous studies reported that iron sulfide minerals formed during bioreduction may retard UO2 reoxidation by consuming dissolved oxygen, yet limited mechanistic information is available detailing the thermodynamic and kinetic constraints that control UO2 oxidative dissolution in the presence of iron sulfide in groundwater.
Lawsone Derivatives as Efficient Photopolymerizable Initiators for Free-Radical, Cationic Photopolymerizations, and Thiol—Ene Reactions

Two new photopolymerizable vinyl (2-(allyloxy) 1,4-naphthoquinone, HNQA) and epoxy (2-(oxiran-2yl methoxy) 1,4-naphthoquinone, HNQE) photoinitiators derived from lawsone were designed in this paper. These new photoinitiators can be used as one-component photoinitiating systems for the free-radical photopolymerization of acrylate bio-based monomer without the addition of any co-initiators. As highlighted by the electron paramagnetic resonance (EPR) spin-trapping results, the formation of carbon-centered radicals from an intermolecular H abstraction reaction was evidenced and can act as initiating species. Interestingly, the introduction of iodonium salt (Iod) used as a co-initiator has led to (1) the cationic photopolymerization of epoxy monomer with high final conversions and (2) an increase of the rates of free-radical polymerization of the acrylate bio-based monomer; we also demonstrated the concomitant thiol–ene reaction and cationic photopolymerizations of a limonene 1,2 epoxide/thiol blend mixture with the HNQA/Iod photoinitiating system.
Ca2+ Signaling and Its Potential Targeting in Pancreatic Ductal Carcinoma

Simple Summary Pancreatic adenocarcinoma is the fourth most common cause of cancer-related death in the world and is estimated to be the second cause of cancer deaths by 2030. Its complicity of treatment is explained by unique physiology and microenvironment of the exocrine pancreas, where calcium plays an essential role. This review is focused on the Ca2+-dependent proteins and signalization pathways studied so far in pancreatic adenocarcinoma. Ca2+ signaling is suggested as potential and prospective target in pancreatic carcinoma treatment and drug resistance. Abstract Pancreatic cancer (PC) is a major cause of cancer-associated mortality in Western countries (and estimated to be the second cause of cancer deaths by 2030). The main form of PC is pancreatic adenocarcinoma, which is the fourth most common cause of cancer-related death, and this situation has remained virtually unchanged for several decades. Pancreatic ductal adenocarcinoma (PDAC) is inherently linked to the unique physiology and microenvironment of the exocrine pancreas, such as pH, mechanical stress, and hypoxia. Of them, calcium (Ca2+) signals, being pivotal molecular devices in sensing and integrating signals from the microenvironment, are emerging to be particularly relevant in cancer. Mutations or aberrant expression of key proteins that control Ca2+ levels can cause deregulation of Ca2+-dependent effectors that control signaling pathways determining the cells’ behavior in a way that promotes pathophysiological cancer hallmarks, such as enhanced proliferation, survival and invasion. So far, it is essentially unknown how the cancer-associated Ca2+ signaling is regulated within the characteristic landscape of PDAC. This work provides a complete overview of the Ca2+ signaling and its main players in PDAC. Special consideration is given to the Ca2+ signaling as a potential target in PDAC treatment and its role in drug resistance.
A Metabolic Choreography of Maize Plants Treated with a Humic Substance-Based Biostimulant under Normal and Starved Conditions

Humic substance (HS)-based biostimulants show potentials as sustainable strategies for improved crop development and stress resilience. However, cellular and molecular mechanisms governing the agronomically observed effects of HS on plants remain enigmatic. Here, we report a global metabolic reprogramming of maize leaves induced by a humic biostimulant under normal and nutrient starvation conditions. This reconfiguration of the maize metabolism spanned chemical constellations, as revealed by molecular networking approaches. Plant growth and development under normal conditions were characterized by key differential metabolic changes such as increased levels of amino acids, oxylipins and the tricarboxylic acid (TCA) intermediate, isocitric acid. Furthermore, under starvation, the humic biostimulant significantly impacted pathways that are involved in stress-alleviating mechanisms such as redox homeostasis, strengthening of the plant cell wall, osmoregulation, energy production and membrane remodelling. Thus, this study reveals that the humic biostimulant induces a remodelling of inter-compartmental metabolic networks in maize, subsequently readjusting the plant physiology towards growth promotion and stress alleviation. Such insights contribute to ongoing efforts in elucidating modes of action of biostimulants, generating fundamental scientific knowledge that is necessary for development of the biostimulant industry, for sustainable food security.
Synergic Effect of TiO2 Filler on the Mechanical Properties of Polymer Nanocomposites

Nanocomposites with polymer matrix offer excellent opportunities to explore new functionalities beyond those of conventional materials. TiO2, as a reinforcement agent in polymeric nanocomposites, is a viable strategy that significantly enhanced their mechanical properties. The size of the filler plays an essential role in determining the mechanical properties of the nanocomposite. A defining feature of polymer nanocomposites is that the small size of the fillers leads to an increase in the interfacial area compared to traditional composites. The interfacial area generates a significant volume fraction of interfacial polymer, with properties different from the bulk polymer even at low loadings of the nanofiller. This review aims to provide specific guidelines on the correlations between the structures of TiO2 nanocomposites with polymeric matrix and their mechanical properties. The correlations will be established and explained based on interfaces realized between the polymer matrix and inorganic filler. The paper focuses on the influence of the composition parameters (type of polymeric matrix, TiO2 filler with surface modified/unmodified, additives) and technological parameters (processing methods, temperature, time, pressure) on the mechanical strength of TiO2 nanocomposites with the polymeric matrix.
Comparative Analysis of Histone H3K4me3 Distribution in Mouse Liver in Different Diets Reveals the Epigenetic Efficacy of Cyanidin-3-O-glucoside Dietary Intake

Background: Different diets result in significantly different phenotypes through metabolic and genomic reprogramming. Epigenetic marks, identified in humans and mouse models through caloric restriction, a high-fat diet or the intake of specific bioactives, suggest that genomic reprogramming drives this metabolic reprogramming and mediates the effect of nutrition on health. Histone modifications encode the epigenetic signal, which adapts genome functions to environmental conditions, including diets, by tuning the structure and properties of chromatin. To date, the effect of different diets on the genome-wide distribution of critical histone marks has not been determined. Methods: Using chromatin immunoprecipitation sequencing, we investigated the distribution of the trimethylation of lysine 4 of histone H3 in the liver of mice fed for one year with five different diets, including: chow containing yellow corn powder as an extra source of plant bioactives or specifically enriched with cyanidin-3-O-Glucoside, high-fat-enriched obesogenic diets, and caloric-restricted pro-longevity diets. Conclusions: Comparison of the resulting histone mark profiles revealed that functional food containing cyanidin determines a broad effect.
Overview of the Most Promising Radionuclides for Targeted Alpha Therapy: The “Hopeful Eight”

Among all existing radionuclides, only a few are of interest for therapeutic applications and more specifically for targeted alpha therapy (TAT). From this selection, actinium-225, astatine-211, bismuth-212, bismuth-213, lead-212, radium-223, terbium-149 and thorium-227 are considered as the most suitable. Despite common general features, they all have their own physical characteristics that make them singular and so promising for TAT. These radionuclides were largely studied over the last two decades, leading to a better knowledge of their production process and chemical behavior, allowing for an increasing number of biological evaluations. The aim of this review is to summarize the main properties of these eight chosen radionuclides. An overview from their availability to the resulting clinical studies, by way of chemical design and preclinical studies is discussed.
Current Approaches and Tools Used in Drug Development against Parkinson’s Disease

Parkinson’s disease is a progressive neurodegenerative disorder characterized by the death of nerve cells in the substantia nigra of the brain. The treatment options for this disease are very limited as currently the treatment is mainly symptomatic, and the available drugs are not able to completely stop the progression of the disease but only to slow it down. There is still a need to search for new compounds with the most optimal pharmacological profile that would stop the rapidly progressing disease. An increasing understanding of Parkinson’s pathogenesis and the discovery of new molecular targets pave the way to develop new therapeutic agents. The use and selection of appropriate cell and animal models that better reflect pathogenic changes in the brain is a key aspect of the research. In addition, computer-assisted drug design methods are a promising approach to developing effective compounds with potential therapeutic effects. In light of the above, in this review, we present current approaches for developing new drugs for Parkinson’s disease.
Association between Reduced Serum Zinc and Diastolic Dysfunction in Maintenance Hemodialysis Patients

Diastolic dysfunction is an emerging challenge among hemodialysis (HD) patients, and the associations between serum zinc with echocardiographic parameters and diastolic function remain uncertain. A total of 185 maintenance HD patients were stratified by the tertiles of serum zinc level to compare their clinical characteristics and echocardiography. Correlations of serum zinc levels with echocardiographic parameters were examined using Pearson’s analysis. Univariate and multivariate logistic regression analyses were performed to investigate the determinants of E/e’ ratio >15 and left atrial volume index (LAVI) > 34 mL/m2, both indicators of diastolic dysfunction. Patients belonging to the first tertile of serum zinc level had a significantly higher E/e’ ratio and LAVI. Serum zinc levels were negatively correlated with E (r = −0.204, p = 0.005), E/e’ ratio (r = −0.217, p = 0.003), and LAVI (r = −0.197, p = 0.007). In a multivariate analysis, older age, diabetes, coronary artery disease, and lower serum zinc levels (OR = 0.974, 95% CI = 0.950–0.999, p = 0.039) were significantly associated with E/e’ ratio >15. Furthermore, diabetes and lower serum zinc levels (OR = 0.978, 95% CI = 0.958–0.999, p = 0.041) were significantly associated with LAVI >34 mL/m2. Reduced serum zinc level was significantly associated with diastolic dysfunction among HD patients. Further prospective studies are warranted to investigate whether zinc supplementation can attenuate cardiac dysfunction in maintenance HD patients.
In Vitro Metabolism of Six C-Glycosidic Flavonoids from Passiflora incarnata L.

Several medical plants, such as Passiflora incarnata L. , contain C-glycosylated flavonoids, which may contribute to their efficacy. Information regarding the bioavailability and metabolism of these compounds is essential, but not sufficiently available. Therefore, the metabolism of the C-glycosylated flavones orientin, isoorientin, schaftoside, isoschaftoside, vitexin, and isovitexin was investigated using the Caco-2 cell line as an in vitro intestinal and epithelial metabolism model. Isovitexin, orientin, and isoorientin showed broad ranges of phase I and II metabolites containing hydroxylated, methoxylated, and sulfated compounds, whereas schaftoside, isoschaftoside, and vitexin underwent poor metabolism. All metabolites were identified via UHPLC-MS or UHPLC-MS/MS using compound libraries containing all conceivable metabolites. Some structures were confirmed via UHPLC-MS experiments with reference compounds after a cleavage reaction using glucuronidase and sulfatase. Of particular interest is the observed cleavage of the C–C bonds between sugar and aglycone residues in isovitexin, orientin, and isoorientin, resulting in unexpected glucuronidated or sulfated luteolin and apigenin derivatives. These findings indicate that C-glycosidic flavones can be highly metabolized in the intestine. In particular, flavonoids with ortho-dihydroxy groups showed sulfated metabolites. The identified glucuronidated or sulfated aglycones demonstrate that enzymes expressed by Caco-2 cells are able to potentially cleave C–C bonds in vitro.
Putative Cooperative ATP–DnaA Binding to Double-Stranded DnaA Box and Single-Stranded DnaA-Trio Motif upon Helicobacter pylori Replication Initiation Complex Assembly

oriC is a region of the bacterial chromosome at which the initiator protein DnaA interacts with specific sequences, leading to DNA unwinding and the initiation of chromosome replication. The general architecture of oriCs is universal; however, the structure of oriC and the mode of orisome assembly differ in distantly related bacteria. In this work, we characterized oriC of Helicobacter pylori, which consists of two DnaA box clusters and a DNA unwinding element (DUE); the latter can be subdivided into a GC-rich region, a DnaA-trio and an AT-rich region. We show that the DnaA-trio submodule is crucial for DNA unwinding, possibly because it enables proper DnaA oligomerization on ssDNA. However, we also observed the reverse effect: DNA unwinding, enabling subsequent DnaA–ssDNA oligomer formation—stabilized DnaA binding to box ts1. This suggests the interplay between DnaA binding to ssDNA and dsDNA upon DNA unwinding. Further investigation of the ts1 DnaA box revealed that this box, together with the newly identified c-ATP DnaA box in oriC1, constitute a new class of ATP–DnaA boxes. Indeed, in vitro ATP–DnaA unwinds H. pylori oriC more efficiently than ADP–DnaA. Our results expand the understanding of H. pylori orisome formation, indicating another regulatory pathway of H. pylori orisome assembly.
Effect of 1-Carbaldehyde-3,4-dimethoxyxanthone on Prostate and HPV-18 Positive Cervical Cancer Cell Lines and on Human THP-1 Macrophages

Xanthone derivatives have shown promising antitumor properties, and 1-carbaldehyde-3,4-dimethoxyxanthone (1) has recently emerged as a potent tumor cell growth inhibitor. In this study, its effect was evaluated (MTT viability assay) against a new panel of cancer cells, namely cervical cancer (HeLa), androgen-sensitive (LNCaP) and androgen-independent (PC-3) prostate cancer, and nonsolid tumor derived cancer (Jurkat) cell lines. The effect of xanthone 1 on macrophage functions was also evaluated. The effect of xanthone 1-conditioned THP-1 human macrophage supernatants on the metabolic viability of cervical and prostate cancer cell lines was determined along with its interference with cytokine expression characteristic of M1 profile (IL-1 ≤ β; TNF-α) or M2 profile (IL-10; TGF-β) (PCR and ELISA). Nitric oxide (NO) production by murine RAW264.7 macrophages was quantified by Griess reaction. Xanthone 1 (20 μM) strongly inhibited the metabolic activity of the cell lines and was significantly more active against prostate cell lines compared to HeLa (p < 0.05). Jurkat was the cell most sensitive to the effect of xanthone 1. Compound 1-conditioned IL-4-stimulated THP-1 macrophage supernatants significantly (p < 0.05) inhibited the metabolic activity of HeLa, LNCaP, and PC-3. Xanthone 1 did not significantly affect the expression of cytokines by THP-1 macrophages. The inhibiting effect of compound 1 observed on the production of NO by RAW 264.7 macrophages was moderate. In conclusion, 1-carbaldehyde-3,4-dimethoxyxanthone (1) decreases the metabolic activity of cancer cells and seems to be able to modulate macrophage functions.
Ketogenic Dietary Therapies in Patients with Autism Spectrum Disorder: Facts or Fads? A Scoping Review and a Proposal for a Shared Protocol

Autism spectrum disorder (ASD) is a neurodevelopmental disorder with increasing incidence. An expanding body of literature is examining connections between ASD and dietary interventions. Existing reports suggest a beneficial effect of ketogenic dietary therapies (KDTs) in improving behavioral symptoms in ASD. In this context, the purpose of this scoping review was to identify and map available evidence in the literature about the feasibility and potential efficacy of KDTs in pediatric patients with ASD and to inform clinical practice in the field. Moreover, based on the resulting data from the literature review, we aimed to provide a shared protocol to develop a personalized KDT intervention in patients with ASD. A comprehensive and structured web-based literature search was performed using PubMed and Scopus and it yielded 203 records. Seven papers were finally selected and included in the review. Data were abstracted by independent coders. High variability was identified in study designs and dietary aspects emerged among selected studies. Results supported the effectiveness of KDTs in promoting behavioral improvements. Clinical recommendations on which patients may benefit most from KDTs implementation and difficulties in dietary adherence were discussed.