Miracle-dz/UniFAR-FTUs huggingface dataset:
Dietary Patterns in Early Childhood and the Risk of Childhood Overweight: The GECKO Drenthe Birth Cohort

Limited and inconsistent evidence exists on the associations between dietary patterns and overweight during childhood. The present study describes dietary patterns of three-year-old Dutch children and associations between childhood overweight and body mass index (BMI) development between 3 and 10 years. In the GECKO Drenthe birth cohort (N = 1306), body height and weight were measured around the age of 3, 4, 5, and 10 years, and overweight was defined according to Cole and Lobstein. A validated food frequency questionnaire (FFQ) was used to measure diet at 3 years. Dietary patterns were derived using principal components analysis (PCA). Using logistic regression analyses, pattern scores were related to overweight at 3 and 10 years. A linear mixed-effect model was used to estimate BMI-SDS development between 3 to 10 years according to quartiles of adherence to the pattern scores. Two dietary patterns were identified: (1) ‘minimally processed foods’, indicating high intakes of vegetables/sauces/savory dishes, and (2) ‘ultra-processed foods’, indicating high intakes of white bread/crisps/sugary drinks. A 1 SD increase in the ‘ultra-processed foods’ pattern score increased the odds of overweight at 10 years (adjusted OR: 1.30; 95%CI: 1.08, 1.57; p = 0.006). The ‘minimally processed foods’ pattern was not associated with overweight. Although a high adherence to both dietary patterns was associated with a higher BMI-SDS up to 10 years of age, a stronger association for the ‘ultra-processed foods’ pattern was observed (p < 0.001). A dietary pattern high in energy-dense and low-fiber ultra-processed foods at 3 years is associated with overweight and a high BMI-SDS later in childhood.
NKG2D Natural Killer Cell Receptor—A Short Description and Potential Clinical Applications

Natural Killer (NK) cells are natural cytotoxic, effector cells of the innate immune system. They can recognize transformed or infected cells. NK cells are armed with a set of activating and inhibitory receptors which are able to bind to their ligands on target cells. The right balance between expression and activation of those receptors is fundamental for the proper functionality of NK cells. One of the best known activating receptors is NKG2D, a member of the CD94/NKG2 family. Due to a specific NKG2D binding with its eight different ligands, which are overexpressed in transformed, infected and stressed cells, NK cells are able to recognize and attack their targets. The NKG2D receptor has an enormous significance in various, autoimmune diseases, viral and bacterial infections as well as for transplantation outcomes and complications. This review focuses on the NKG2D receptor, the mechanism of its action, clinical relevance of its gene polymorphisms and a potential application in various clinical settings.
Outbreak of SARS-CoV-2 Lineage 20I/501Y.V1 in a Nursing Home Underlines the Crucial Role of Vaccination in Both Residents and Staff

Elderly residents in nursing homes are at very high risk of life-threatening COVID-19-related outcomes. In this report, an epidemiological and serological investigation of a SARS-CoV-2 outbreak in an Italian nursing home is described. Among the residents, all but one (19/20) were regularly vaccinated against SARS-CoV-2. In mid-February 2021, a non-vaccinated staff member of the nursing home was diagnosed with the SARS-CoV-2 infection. Following the outbreak investigation, a total of 70% (14/20) of residents aged 77–100 years were found positive. The phylogenetic analysis showed that the outbreak was caused by the SARS-CoV-2 variant of concern 202012/01 (the so-called “UK variant”). However, all but one positive subjects (13/14) were fully asymptomatic. The only symptomatic patient was a vaccinated 86-year-old female with a highly compromised health background and deceased approximately two weeks later. The subsequent serological investigation showed that the deceased patient was the only vaccinated subject that did not develop the anti-spike protein antibody response, therefore being likely a vaccine non-responder. Although the available mRNA SARS-CoV-2 vaccine was not able to prevent several asymptomatic infections, it was able to avert most symptomatic disease cases caused by the SARS-CoV-2 variant of concern 202012/01 in nursing home residents.
Benchmarking DNA Extraction Methods for Phylogenomic Analysis of Sub-Antarctic Rhodococcus and Williamsia Species

Bacteria containing mycolic acids in their cell envelope are often recalcitrant to cell lysis, so extracting DNA of sufficient quality for third-generation sequencing and high-fidelity genome assembly requires optimization, even when using commercial kits with protocols for hard-to-lyse bacteria. We benchmarked three spin-column-based kits against a classical DNA extraction method employing lysozyme, proteinase K and SDS for six lysozyme-resistant, sub-Antarctic strains of Corynebaceriales. Prior cultivation in broths containing glycine at highly growth-inhibitory concentrations (4.0–4.5%) improved cell lysis using both classical and kit methods. The classical method produced DNA with average fragment sizes of 27–59 Kbp and tight fragment size ranges, meeting quality standards for genome sequencing, assembly and phylogenomic analyses. By 16S rRNA gene sequencing, we classified two strains as Williamsia and four strains as Rhodococcus species. Pairwise comparison of average nucleotide identity (ANI) and alignment fraction (AF), plus genome clustering analysis, confirmed Rhodococcus sp. 1163 and 1168 and Williamsia sp. 1135 and 1138 as novel species. Phylogenetic, lipidomic and biochemical analyses classified psychrotrophic strains 1139 and 1159 as R. qingshengii and R. erythropolis, respectively, using ANI similarity of >98% and AF >60% for species delineation. On this basis, some members of the R. erythropolis genome cluster groups, including strains currently named as R. enclensis, R. baikonurensis, R. opacus and R. rhodochrous, would be reclassified either as R. erythropolis or R. qingshengii.
Therapy Development by Genome Editing of Hematopoietic Stem Cells

Accessibility of hematopoietic stem cells (HSCs) for the manipulation and repopulation of the blood and immune systems has placed them at the forefront of cell and gene therapy development. Recent advances in genome-editing tools, in particular for clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) and CRISPR/Cas-derived editing systems, have transformed the gene therapy landscape. Their versatility and the ability to edit genomic sequences and facilitate gene disruption, correction or insertion, have broadened the spectrum of potential gene therapy targets and accelerated the development of potential curative therapies for many rare diseases treatable by transplantation or modification of HSCs. Ongoing developments seek to address efficiency and precision of HSC modification, tolerability of treatment and the distribution and affordability of corresponding therapies. Here, we give an overview of recent progress in the field of HSC genome editing as treatment for inherited disorders and summarize the most significant findings from corresponding preclinical and clinical studies. With emphasis on HSC-based therapies, we also discuss technical hurdles that need to be overcome en route to clinical translation of genome editing and indicate advances that may facilitate routine application beyond the most common disorders.
A Fully Distributed Protocol with an Event-Triggered Communication Strategy for Second-Order Multi-Agent Systems Consensus with Nonlinear Dynamics

This paper presents the communication strategy for second-order multi-agent systems with nonlinear dynamics. To address the problem of the scarcity of communication channel resources and get rid of using continuous signals among the followers in lead-follower multi-agent systems, a novel event-triggered communication mechanism is proposed in this paper. To avoid employing the centralized information that depends on the Laplacian matrix spectrum, a network protocol with updated coupling gains is proposed, as well as an event-triggered strategy with updated thresholds. To eliminate the ill effects of inter-node communicating noise, relative positions are employed by the protocol instead of absolute positions. By a Lyapunov–Krasovskii functional, it is rigorously proven that the leader-following consensus of MASs is achieved without Zeno behavior, under the control of the proposed protocol with an event-triggered mechanism communication. The effectiveness of the proposed protocol is verified through numerical examples.
In Silico Prediction of Transcription Factor Collaborations Underlying Phenotypic Sexual Dimorphism in Zebrafish (Danio rerio)

The transcriptional regulation of gene expression in higher organisms is essential for different cellular and biological processes. These processes are controlled by transcription factors and their combinatorial interplay, which are crucial for complex genetic programs and transcriptional machinery. The regulation of sex-biased gene expression plays a major role in phenotypic sexual dimorphism in many species, causing dimorphic gene expression patterns between two different sexes. The role of transcription factor (TF) in gene regulatory mechanisms so far has not been studied for sex determination and sex-associated colour patterning in zebrafish with respect to phenotypic sexual dimorphism. To address this open biological issue, we applied bioinformatics approaches for identifying the predicted TF pairs based on their binding sites for sex and colour genes in zebrafish. In this study, we identified 25 (e.g., STAT6-GATA4; JUN-GATA4; SOX9-JUN) and 14 (e.g., IRF-STAT6; SOX9-JUN; STAT6-GATA4) potentially cooperating TFs based on their binding patterns in promoter regions for sex determination and colour pattern genes in zebrafish, respectively. The comparison between identified TFs for sex and colour genes revealed several predicted TF pairs (e.g., STAT6-GATA4; JUN-SOX9) are common for both phenotypes, which may play a pivotal role in phenotypic sexual dimorphism in zebrafish.
Indirect Effect of African Swine Fever on the Diet Composition of the Gray Wolf Canis lupus—A Case Study in Belarus

Simple Summary The wild boar population decreased drastically in Eastern Europe after the emergence of a viral disease called African Swine Fever. We studied how the gray wolves’ diet changed in two regions in Belarus during this situation. Wolves mainly hunted wild boar, elk, red deer, roe deer and beaver. The decrease in the wild boar population caused changes in the diet of wolves, but only in Vitebsk region. After the decrease in the wild boar population, wolves in this region hunted wild boar less, but they hunted roe deer and red deer more. The more the wolves consumed wild boar, the less they consumed both deer species (roe deer and red deer). Moreover, the more the wolves consumed elk, the less they consumed beaver. In another region, Grodno, no changes in the wolves’ diet were found. Abstract After the emergence of African swine fever (ASF), the wild boar population numbers fell drastically in Eastern Europe. This situation made it possible to verify the changes in the wolves’ diet that occurred. The material collection was carried out in two regions, Grodno and Vitebsk, in Belarus. In total, 19 species/groups of prey were observed in the gray wolf diet, but the most important were wild boar, elk, red deer, roe deer and beaver. The decrease in the number of wild boar caused changes in the diet of wolves but only in Vitebsk region, where wolves’ diet before the ASF epidemic outbreak consisted mainly of elk and wild boar. After the decrease of wild boar numbers, wolves still mainly hunted elk, but other types of prey included roe deer, red deer and beaver. We found a negative correlation between wild boar and both deer species (roe deer and red deer) in the wolves’ diet. Moreover, the more the wolves consumed elk, the less they consumed beaver. In our opinion, only intensive hunting of wolves by humans can explain the resulting dietary fluctuations between elk and beaver, as well as the fact that wolves did not turn to other food sources.
Quality of Service Provision in Fog Computing: Network-Aware Scheduling of Containers

State-of-the-art scenarios, such as Internet of Things (IoT) and Smart Cities, have recently arisen. They involve the processing of huge data sets under strict time requirements, rendering the use of cloud resources unfeasible. For this reason, Fog computing has been proposed as a solution; however, there remains a need for intelligent allocation decisions, in order to make it a fully usable solution in such contexts. In this paper, a network-aware scheduling algorithm is presented, which aims to select the fog node most suitable for the execution of an application within a given deadline. This decision is made taking the status of the network into account. This scheduling algorithm was implemented as an extension to the Kubernetes default scheduler, and compared with existing proposals in the literature. The comparison shows that our proposal is the only one that can execute all the submitted jobs within their deadlines (i.e., no job is rejected or executed exceeding its deadline) with certain configurations in some of the scenarios tested, thus obtaining an optimal solution in such scenarios.
Antimicrobial, Antioxidant, Anti-Acetylcholinesterase, Antidiabetic, and Pharmacokinetic Properties of Carum carvi L. and Coriandrum sativum L. Essential Oils Alone and in Combination

Herbs and spices have been used since antiquity for their nutritional and health properties, as well as in traditional remedies for the prevention and treatment of many diseases. Therefore, this study aims to perform a chemical analysis of both essential oils (EOs) from the seeds of Carum carvi (C. carvi) and Coriandrum sativum (C. sativum) and evaluate their antioxidant, antimicrobial, anti-acetylcholinesterase, and antidiabetic activities alone and in combination. Results showed that the EOs mainly constitute monoterpenes with γ-terpinene (31.03%), β-pinene (18.77%), p-cymene (17.16%), and carvone (12.20%) being the major components present in C. carvi EO and linalool (76.41%), γ-terpinene (5.35%), and α-pinene (4.44%) in C. sativum EO. In comparison to standards, statistical analysis revealed that C. carvi EO showed high and significantly different (p < 0.05) antioxidant activity than C. sativum EO, but lower than the mixture. Moreover, the mixture exhibited two-times greater ferric ion reducing antioxidant power (FRAP) (IC50 = 11.33 ± 1.53 mg/mL) and equipotent chelating power (IC50 = 31.33 ± 0.47 mg/mL) than the corresponding references, and also potent activity against 2,2-diphenyl-1-picrylhydrazyl (DPPH) (IC50 = 19.00 ± 1.00 mg/mL), β-carotene (IC50 = 11.16 ± 0.84 mg/mL), and superoxide anion (IC50 = 10.33 ± 0.58 mg/mL) assays. Antimicrobial data revealed that single and mixture EOs were active against a panel of pathogenic microorganisms, and the mixture had the ability to kill more bacterial strains than each EO alone. Additionally, the anti-acetylcholinesterase and α-glucosidase inhibitory effect have been studied for the first time, highlighting the high inhibition effect of AChE by C. carvi (IC50 = 0.82 ± 0.05 mg/mL), and especially by C. sativum (IC50 = 0.68 ± 0.03 mg/mL), as well as the mixture (IC50 = 0.63 ± 0.02 mg/mL) compared to the reference drug, which are insignificantly different (p > 0.05). A high and equipotent antidiabetic activity was observed for the mixture (IC50 = 0.75 ± 0.15 mg/mL) when compared to the standard drug, acarbose, which is about nine times higher than each EO alone. Furthermore, pharmacokinetic analysis provides some useful insights into designing new drugs with favorable drug likeness and safety profiles based on a C. carvi and C. sativum EO mixture. In summary, the results of this study revealed that the combination of these EOs may be recommended for further food, therapeutic, and pharmaceutical applications, and can be utilized as medicine to inhibit several diseases.
Surface Texturing of Polyethylene Terephthalate Induced by Excimer Laser in Silver Nanoparticle Colloids

We report on a novel technique of surface texturing of polyethylene terephthalate (PET) foil in the presence of silver nanoparticles (AgNPs). This approach provides a variable surface morphology of PET evenly decorated with AgNPs. Surface texturing occurred in silver nanoparticle colloids of different concentrations under the action of pulse excimer laser. Surface morphology of PET immobilized with AgNPs was observed by AFM and FEGSEM. Atomic concentration of silver was determined by XPS. A presented concentration-controlled procedure of surface texturing of PET in the presence of silver colloids leads to a highly nanoparticle-enriched polymer surface with a variable morphology and uniform nanoparticle distribution.
Extracellular Vesicles of Mesenchymal Stem Cells: Therapeutic Properties Discovered with Extraordinary Success

Mesenchymal stem cells (MSCs), the cells distributed in the stromas of the body, are known for various properties including replication, the potential of various differentiations, the immune-related processes including inflammation. About two decades ago, these cells were shown to play relevant roles in the therapy of numerous diseases, dependent on their immune regulation and their release of cytokines and growth factors, with ensuing activation of favorable enzymes and processes. Such discovery induced great increase of their investigation. Soon thereafter, however, it became clear that therapeutic actions of MSCs are risky, accompanied by serious drawbacks and defects. MSC therapy has been therefore reduced to a few diseases, replaced for the others by their extracellular vesicles, the MSC-EVs. The latter vesicles recapitulate most therapeutic actions of MSCs, with equal or even better efficacies and without the serious drawbacks of the parent cells. In addition, MSC-EVs are characterized by many advantages, among which are their heterogeneities dependent on the stromas of origin, the alleviation of cell aging, the regulation of immune responses and inflammation. Here we illustrate the MSC-EV therapeutic effects, largely mediated by specific miRNAs, covering various diseases and pathological processes occurring in the bones, heart and vessels, kidney, and brain. MSC-EVs operate also on the development of cancers and on COVID-19, where they alleviate the organ lesions induced by the virus. Therapy by MSC-EVs can be improved by combination of their innate potential to engineering processes inducing precise targeting and transfer of drugs. The unique properties of MSC-EVs explain their intense studies, carried out with extraordinary success. Although not yet developed to clinical practice, the perspectives for proximal future are encouraging.
Acetate Kinase a Antisense Delivery by PAMAM Dendrimer for Decreasing Acetate Production and Increasing the Production of Recombinant Albumin in E. coli

Background: Acetate accumulation in the culture medium is known as an inhibitor in recombinant protein production in Escherichia coli. Various approaches have been proposed and evaluated to overcome this challenge and reduce the concentration of acetate. In this study, we examined the effect of acetate kinase A antisense on acetate production rate in E. coli We also used PAMAM dendrimers as a suitable delivery agent for antisense transformation into E. coli host cell. Objective: This study aimed to decrease acetate production as a by-product using an antisense-dendrimer complex to increase mass cell and subsequently recombinant Albumin production in E. coli. Materials and Methods: Here, to study the effect of this treatment on recombinant protein production, we used pET22b/HAS construct. The ackA gene expression was inhibited by designed antisense to reduce acetate concentration in culture medium. AckA antisense was transferred to E. coli by PAMAM dendrimer. Finally, ackA expression and recombinant Albumin production were evaluated Real-Time PCR and densitometry, respectively. Results: Our data showed, designed antisense lead to reduction of acetate kinase gene expression and subsequently acetate concentration in the culture medium. Finally, acetate concentration reduction and cell mass increase result in enhanced recombinant Alb production in the treated group (1.25 mg.mL-1) compare to the control group ( 0.59 mg.mL-1). Conclusions: Reduction of acetate in E. coli fermentation process decreased the recombinant Alb production following cell growth and cell mass increase. In the current study, we showed that an antisense can be a useful tool for ackA gene expression reduction. Also, we noted that PAMAM dendrimer could be a proper delivery agent for oligonucleotide antisense transformation into bacterial cells.
Hepatitis C Virus Glycan-Dependent Interactions and the Potential for Novel Preventative Strategies

Chronic hepatitis C virus (HCV) infections continue to be a major contributor to liver disease worldwide. HCV treatment has become highly effective, yet there are still no vaccines or prophylactic strategies available to prevent infection and allow effective management of the global HCV burden. Glycan-dependent interactions are crucial to many aspects of the highly complex HCV entry process, and also modulate immune evasion. This review provides an overview of the roles of viral and cellular glycans in HCV infection and highlights glycan-focused advances in the development of entry inhibitors and vaccines to effectively prevent HCV infection.
Novel Anticancer and Treatment Sensitizing Compounds against Pancreatic Cancer

Simple Summary Pancreatic cancer is a disease of unmet clinical needs. Considering the poor prognosis and high treatment resistance of this devastating disease, the search for the development, understanding and characterization of potential treatments and/or treatment sensitizers is of clinical importance. The synergy between natural remedies and state-of-the-art cancer treatments has been poorly considered despite evidence of antioxidant, antimicrobial and antitumor capabilities. Moreover, natural chemical compounds have been the source of many approved drugs. This review collates novel and natural compounds explored for their preclinical anticancer, chemosensitizing and radiosensitizing effects for pancreatic cancer. Here, we highlight a number of natural sources in very early preclinical testing that may hold potential to enhance treatment sensitization, and in turn, reduce treatment resistance and toxicity via lowering treatment dose requirements. Abstract The isolation of chemical compounds from natural origins for medical application has played an important role in modern medicine with a range of novel treatments having emerged from various natural forms over the past decades. Natural compounds have been exploited for their antioxidant, antimicrobial and antitumor capabilities. Specifically, 60% of today’s anticancer drugs originate from natural sources. Moreover, the combination of synthetic and natural treatments has shown applications for (i) reduced side effects, (ii) treatment sensitization and (iii) reduction in treatment resistance. This review aims to collate novel and natural compounds that are being explored for their preclinical anticancer, chemosensitizing and radiosensitizing effects on Pancreatic Ductal Adenocarcinoma (PDAC), which is a lethal disease with current treatments being inefficient and causing serve side effects. Two key points are highlighted by this work: (i) the availability of a range of natural compounds for potentially new therapeutic approaches for PDAC, (ii) potential synergetic impact of natural compounds with advanced chemo- and radio-therapeutic modalities for PDAC.