Miracle-dz/UniFAR-FTUs huggingface dataset:
Chemical Composition and Antimicrobial Activity of Laurus nobilis L. Essential Oils from Bulgaria

Laurel, Laurus nobilis L. is an evergreen plant belonging to the Lauraceae family, native to Southern Europe and the Mediterranean area. This is the first report on the composition and bioactivity of laurel essential oil (EO) from Bulgaria. The oil yield was 0.78%, 0.80%, and 3.25% in the fruits, twigs, and leaves, respectively. The main constituents in the fruit EO were 1,8-cineole (33.3%), α-terpinyl acetate (10.3%), α-pinene (11.0%), β-elemene (7.5%), sabinene (6.3%), β-phellandrene (5.2%), bornyl acetate (4.4%), and camphene (4.3%); those in the twig EO were 1,8-cineole (48.5%), α-terpinyl acetate (13.1%), methyl eugenol (6.6%), β-linalool (3.8%), β-pinene (3.4%), sabinene (3.3%) and terpinene-4-ol (3.3%); and the ones in the leaf EO were 1,8-cineole (41.0%), α-terpinyl acetate (14.4%), sabinene (8.8%), methyl eugenole (6.0%), β-linalool (4.9%), and α-terpineol (3.1%). The antibacterial and antifungal properties of laurel EOs were examined according to the agar well diffusion method. The leaf EO showed antibacterial and antifungal activities against almost all strains of the microorganisms tested, whereas the twig EO was only able to inhibit Staphylococcus aureus. Pseudomonas aeruginosa ATCC 9027 and Escherichia coli ATCC 8739 were the bacterial strains that showed the highest resistance to the laurel EO. The results can benefit the EO industry and biopesticide development.
Using Electronic Health Records to Identify Adverse Drug Events in Ambulatory Care: A Systematic Review

Abstract Objective We identified the methods used and determined the roles of electronic health records (EHRs) in detecting and assessing adverse drug events (ADEs) in the ambulatory setting. Methods We performed a systematic literature review by searching PubMed and Google Scholar for studies on ADEs detected in the ambulatory setting involving any EHR use published before June 2017. We extracted study characteristics from included studies related to ADE detection methods for analysis. Results We identified 30 studies that evaluated ADEs in an ambulatory setting with an EHR. In 27 studies, EHRs were used only as the data source for ADE identification. In two studies, the EHR was used as both a data source and to deliver decision support to providers during order entry. In one study, the EHR was a source of data and generated patient safety reports that researchers used in the process of identifying ADEs. Methods of identification included manual chart review by trained nurses, pharmacists, and/or physicians; prescription review; computer monitors; electronic triggers; International Classification of Diseases codes; natural language processing of clinical notes; and patient phone calls and surveys. Seven studies provided examples of search phrases, laboratory values, and rules used to identify ADEs. Conclusion The majority of studies examined used EHRs as sources of data for ADE detection. This retrospective approach is appropriate to measure incidence rates of ADEs but not adequate to detect preventable ADEs before patient harm occurs. New methods involving computer monitors and electronic triggers will enable researchers to catch preventable ADEs and take corrective action.
Associations of physical activity and gross motor skills with executive function in preschool children from low-income South African settings.

Executive function is foundational for cognitive development. Previous research has shown both gross motor skills and physical activity to be related to executive function. However, evidence for these relationships in the preschool years, as well as in low- and middle-income countries is lacking. Therefore, this study aimed to investigate the relationships between components of executive function (inhibition, shifting and working memory) and gross motor skills (locomotor skills and object control skills) in a sample of preschool children from urban and rural low-income settings in South Africa. Results revealed that inhibition and working memory, but not shifting, were associated with gross motor skills. More specifically: inhibition was associated with both locomotor [β = 0.20, p = 0.047] and object control skills [β = 0.24, p = 0.024], whereas working memory was only associated with locomotor skills [β = 0.21, p = 0.039]. Physical activity was not associated with inhibition and shifting but was negatively associated with working memory. These results elaborate a growing evidence base linking executive function and gross motor skills in the early years, and it is the first to look at specific associations of locomotor and object control skills with executive function in the South African context (a low- and middle-income country).
Working against the biological clock: a review for the Occupational Physician

The master clock of the biological rhythm, located in the suprachiasmatic nucleus of the anterior hypothalamus, synchronizes the molecular biological clock found in every cell of most peripheral tissues. The human circadian rhythm is largely based on the light-dark cycle. In night shift workers, alteration of the cycle and inversion of the sleep-wake rhythm can result in disruption of the biological clock and induce adverse health effects. This paper offers an overview of the main physiological mechanisms that regulate the circadian rhythm and of the health risks that are associated with its perturbation in shift and night workers. The Occupational Physician should screen shift and night workers for clinical symptoms related to the perturbation of the biological clock and consider preventive strategies to reduce the associated health risks.
Factors associated with the social, individual and programmatic vulnerability of older adults living at home.

OBJECTIVE To verify the occurrence and factors associated to social, individual and programmatic vulnerability among older adults. METHOD A household and cross-sectional survey conducted with 701 community-dwelling older adults. For evaluation of the individual component, we used the frailty phenotype; for the social component, the social vulnerability index was implemented; and for the programmatic component, the Index of access and use of health services. Descriptive and bivariate statistical analyzes and multinomial logistic regression were also carried out (p≤ 0.05). RESULTS It was verified that 15.7% of the older adults lived in areas of high social vulnerability, 31.8% were physically frail and had a moderate programmatic vulnerability score. Older people of a lower age, having lower education and income levels were more likely to live in areas of high or very high social vulnerability. The female gender and the high age groups increased the chances of the frailty condition. It was also observed that the older adults in the 70├ 80-year age group and having lower education were more likely to have medium programmatic vulnerability. CONCLUSION The importance of primary care professionals to consider the multidimensional aspect of vulnerability in identifying older adults who need to be prioritized in health care is evidenced.
In vitro investigation of antimicrobial effects, nanohardness, and cytotoxicity of different glass ionomer restorative materials in dentistry

Aims: The aim of this in vitro study was to investigate the antimicrobial effects, nanohardness, and cytotoxicity of different glass-ionomer restorative materials in dentistry. Materials and Methods: The following glass-ionomer restorative materials were used in our study: Argion (VOCO, Germany), Zirconomer (Shofu Inc., Japan), EQUIA Forte (GC, Japan), Fuji II LC capsule (GC, Japan), and Fuji IX GP capsule (GC, Japan). For the cytotoxicity test, a cell culture without release liquids was used as the control group. Microdilution and a disk diffusion test were used to measure the antimicrobial activity. The MTT (3- [4,5-dimethylthiazol-2-yl] -2,5-diphenyltetrazolium bromide) assay was used to evaluate cytotoxicity. Nanohardness was measured using a nanoindenter device. Results: Our study determined that all restorative materials used in this study inhibited bacterial growth in cultures containing 1 × 102 cfu/ml of the bacterial concentrations (Lactobacillus casei and Streptococcus mutans) and that all restorative materials inhibited fungal growth in the cultures containing <1 × 102 cfu/ml of the fungal strains (Candida albicans). IC50 values obtained for the cytotoxicity test were analyzed using the Chi-square test. After a 72-h incubation period, Zirconomer, EQUIA Forte, Fuji IX GP capsule, and Fuji II LG capsule showed statistically significant lower cell viability values. (P < 0.05). The Kruskal-Wallis analysis was performed on the values obtained from the nanohardness test; the differences between the groups were found to be significant (P < 0.05). Conclusions: All materials tested showed low antimicrobial activity, and the antifungal activity of these materials was found to be lower than their antimicrobial activity. Only Argion showed non-cytotoxic effect. Beginning with the group with the highest nanohardness values and ending with the lowest, the groups are ranked in the following order: Fuji II LC capsule, EQUIA Forte, Argion, Fuji IX GP capsule, and Zirconomer.
Oxidation of h-BN on strongly and weakly interacting metal surfaces

We used x-ray photoemission and absorption spectroscopies to study the influence of thermal molecular oxygen exposure on the h-BN/Co(0001) and h-BN/Au/Co(0001) systems. The spectral analysis was supported by density functional theory calculations. It is shown that oxygen can intercalate h-BN on Co(0001) and also be embedded into its lattice, replacing the nitrogen atoms. Upon substitution, the structures containing one (BN2O) and three (BO3) oxygen atoms in the boron atom environment are formed predominantly. In the case of gold-intercalated h-BN, only the (BN2O) structures are formed; the long-lasting oxygen exposures lead to etching of the h-BN layer.
Common workflow language (CWL)-based software pipeline for de novo genome assembly from long- and short-read data

ABSTRACT Background Here, we created an automated pipeline for the de novoassembly of genomes from Pacific Biosciences long-read and Illumina short-read data using common workflow language (CWL). To evaluate the performance of this pipeline, we assembled the nuclear genomes of the eukaryotes Caenorhabditis elegans (∼100 Mb), Drosophila melanogaster (∼138 Mb), and Plasmodium falciparum (∼23 Mb) directly from publicly accessible nucleotide sequence datasets and assessed the quality of the assemblies against curated reference genomes. Findings We showed a dependency of the accuracy of assembly on sequencing technology and GC content and repeatedly achieved assemblies that meet the high standards set by the National Human Genome Research Institute, being applicable to gene prediction and subsequent genomic analyses. Conclusions This CWL pipeline overcomes current challenges of achieving repeatability and reproducibility of assembly results and offers a platform for the re-use of the workflow and the integration of diverse datasets. This workflow is publicly available via GitHub (https://github.com/vetscience/Assemblosis) and is currently applicable to the assembly of haploid and diploid genomes of eukaryotes.
MDA1, a nucleus-encoded factor involved in the stabilization and processing of the atpA transcript in the chloroplast of Chlamydomonas.

In Chlamydomonas reinhardtii, chloroplast gene expression is tightly regulated post-transcriptionally by gene-specific trans-acting protein factors. Here, we report the molecular identification of an OctotricoPeptide Repeat (OPR) protein, MDA1, which governs the maturation and accumulation of the atpA transcript, encoding subunit α of the chloroplast ATP synthase. As does TDA1, another OPR protein required for the translation of the atpA mRNA, MDA1 targets the atpA 5'-untranslated region (UTR). Unexpectedly, it binds within a region of approximately 100 nt in the middle of the atpA 5'-UTR, at variance with the stabilization factors characterized so far, which bind to the 5'-end of their target mRNA to protect it from 5' → 3' exonucleases. It binds the same region as TDA1, with which it forms a high-molecular-weight complex that also comprises the atpA mRNA. This complex dissociates upon translation, promoting degradation of the atpA mRNA. We suggest that atpA transcripts, once translated, enter the degradation pathway because they cannot reassemble with MDA1 and TDA1, which preferentially bind to de novo transcribed mRNAs.
Early intervention with gastrodin reduces striatal neurotoxicity in adult rats with experimentally-induced diabetes mellitus

Glutamate-induced excitotoxicity in the striatum has an important role in neurodegenerative diseases. It has been reported that diabetes mellitus (DM) induces excitotoxicity in striatal neurons, although the underlying mechanism remains to be fully elucidated. The present study aimed to investigate the effect of gastrodin on DM-induced excitotoxicity in the striatal neurons of diabetic rats. Adult Sprague-Dawley rats were divided into control, diabetic, and gastrodin intervention groups. Diabetes in the rats was induced with a single intraperitoneal injection of streptozotocin (65 mg/kg). In the gastrodin groups, the rats were gavaged with 60 or 120 mg/kg/day gastrodin for 6 weeks, 3 weeks following the induction of diabetes. Pathological alterations in the striatum were assessed using hematoxylin and eosin (H&E) staining. The protein expression levels of phosphorylated (p)-extracellular signal-regulated kinase (ERK)1/2, p-mitogen-activated protein kinase kinase (MEK)1/2, tyrosine receptor kinase B (TrKB) and brain-derived neurotrophic factor (BDNF) in the striatal neurons were evaluated by western blotting and double immunofluorescence. Additionally, the extracellular levels of glutamate were measured by microanalysis followed by high-pressure-liquid-chromatography. In diabetic rats, striatal neuronal degeneration was evident following H&E staining, which revealed the common occurrence of pyknotic nuclei. This was coupled with an increase in glutamate levels in the striatal tissues. The protein expression levels of p-ERK1/2, p-MEK1/2, TrKB and BDNF in the striatal tissues were significantly increased in the diabetic rats compared with those in the normal rats. In the gastrodin groups, degeneration of the striatal neurons was ameliorated. Furthermore, the expression levels of glutamate, p-ERK1/2, p-MEK1/2, TrKB and BDNF in the striatal neurons were decreased. From these findings, it was concluded that reduced neurotoxicity in striatal neurons following treatment with gastrodin may be attributed to its suppressive effects on the expression of p-ERK1/2, p-MEK1/2, BDNF and TrKB.
Phosphatidic acid generated by PLD2 promotes the plasma membrane recruitment of IQGAP1 and neointima formation

Very little is known about how lipid signaling regulates intima hyperplasia after vascular injury. Herein, we report that deletion and pharmacological inhibition of phospholipase D (PLD)2, which generates the signaling lipid phosphatidic acid (PA), reduced neointimal formation in the mouse carotid artery ligation model. PLD2 deficiency inhibits migration of vascular smooth muscle cells (VSMCs) into the intima in mice as well as migration and formation of membrane ruffles in primary VSMCs. PA specifically binds to the IQ motif–containing guanosine triphosphatase–activating protein 1 (IQGAP1) scaffold protein. The binding between PA and IQGAP is required for the plasma membrane recruitment of IQGAP1. Similar to PLD2 inhibition, knockdown of IQGAP1 blocks ruffle formation and migration in VSMCs, which are rescued by expression of the exogenous IQGAP1 but not the PA binding–deficient mutant. These data reveal that the PLD2‐PA‐IQGAP1 pathway plays an important role in VSMC migration and injury‐induced vascular remodeling, and implicate PLD2 as a candidate target for therapeutic interventions. —Wang, Z. , Cai, M. , Tay, L. W. R. , Zhang, F. , Wu, P., Huynh, A. , Cao, X. , Di Paolo, G. , Peng, J., Milewicz, D. M. , Du, G. Phosphatidic acid generated by PLD2 promotes the plasma membrane recruitment of IQGAP1 and neointima formation. FASEB J. 33, 6713–6725 (2019). www.fasebj. org
How accurately do routinely reported HIV viral load suppression proportions reflect progress towards the 90-90-90 target in the population on antiretroviral treatment in Khayelitsha, South Africa?

BACKGROUND The Joint United Nations Programme on HIV/AIDS (UNAIDS) third 90-90-90 target requires 90% of patients on antiretroviral treatment (ART) to be virally suppressed (<1 000 copies/mL). In Khayelitsha, Cape Town, South Africa viral load (VL) suppression of <400 copies/mL was reported as 89% in 2016, but only 56% of patients had a result recorded in routine data. We conceived a VL 'cascade' to represent the steps required for an expected VL to be reported as complete in routine data and thus contribute to reported VL suppression: among those for whom a VL is 'expected', a sample must be collected and tested ('done'), a result must be 'filed' in the patient folder, 'noted' by a clinician and electronically 'captured'. The low reported completion suggested gaps along the VL cascade and cast doubt on the validity of reported suppression. OBJECTIVES To assess the validity of routinely reported VL suppression and identify barriers to VL completion. METHODS A retrospective cohort study between 1 July 2015 and 30 June 2016, which included all Khayelitsha patients receiving ART, with a routine VL expected, was conducted. We obtained data routinely captured on site and VL data from the laboratory system. A sample of 1 035 patient folders was reviewed. VL suppression was calculated using laboratory data, including all tests done, and compared with reported suppression based on on-site captured electronic data. Successful progression through each step on the VL cascade was estimated. We used logistic regression to identify factors associated with laboratory data and reported VL testing. RESULTS Of 22 991 patients for whom a routine VL test was due, 84% were done, 79% filed, 76% noted and 55% captured. Using all laboratory data, VL suppression was estimated as 82%, 87%, 89% and 91% at the 50, 200, 400 and 1 000 copies/mL thresholds, respectively, but reported suppression using captured results was 80%, 86%, 88% and 89% at those thresholds. Routine VL testing is more likely to be done in children <15 years old (adjusted odds ratio (aOR) 1.89, 95% confidence interval (CI) 1.45 - 2.48) and pregnant women (aOR 1.90, 95% CI 1.28 - 2.81) than in men, adjusted for facility. CONCLUSIONS Despite a low reported completion, VL testing completion was high. Reported suppression using captured data was similar to suppression calculated using all laboratory data, which provided an accurate measure of progress towards the 90-90-90 target. More work is needed to reach the 16% of patients missed by routine testing.
Sensing of cell-associated HTLV by plasmacytoid dendritic cells is regulated by dense β-galactoside glycosylation

Human T Lymphotropic virus (HTLV) infection can persist in individuals resulting, at least in part, from viral escape of the innate immunity, including inhibition of type I interferon response in infected T-cells. Plasmacytoid dendritic cells (pDCs) are known to bypass viral escape by their robust type I interferon production. Here, we demonstrated that pDCs produce type I interferons upon physical cell contact with HTLV-infected cells, yet pDC activation inversely correlates with the ability of the HTLV-producing cells to transmit infection. We show that pDCs sense surface associated-HTLV present with glycan-rich structure referred to as biofilm-like structure, which thus represents a newly described viral structure triggering the antiviral response by pDCs. Consistently, heparan sulfate proteoglycans and especially the cell surface pattern of terminal β-galactoside glycosylation, modulate the transmission of the immunostimulatory RNA to pDCs. Altogether, our results uncover a function of virus-containing cell surface-associated glycosylated structures in the activation of innate immunity.
Analysis of estimation of electromagnetic dosimetric values from non-ionizing radiofrequency fields in conventional road vehicle environments

Abstract A high number of wireless technologies can be found operating in vehicular environments with the aim of offering different services. The dosimetric evaluation of this kind of scenarios must be performed in order to assess their compatibility with current exposure limits. In this work, a dosimetric evaluation inside a conventional car is performed, with the aid of an in-house 3D Ray Launching computational code, which has been compared with measurement results of wireless sensor networks located inside the vehicle. These results can aid in an adequate assessment of human exposure to non-ionizing radiofrequency fields, taking into account the impact of the morphology and the topology of the vehicle for current as well as for future exposure limits.
Identification of Antimalarial Compounds That Require CLAG3 for Their Uptake by Plasmodium falciparum-Infected Erythrocytes

During the intraerythrocytic asexual cycle malaria parasites acquire nutrients and other solutes through a broad selectivity channel localized at the membrane of the infected erythrocyte termed the plasmodial surface anion channel (PSAC). The protein product of the Plasmodium falciparum clonally variant clag3.1 and clag3.2 genes determines PSAC activity. ABSTRACT During the intraerythrocytic asexual cycle malaria parasites acquire nutrients and other solutes through a broad selectivity channel localized at the membrane of the infected erythrocyte termed the plasmodial surface anion channel (PSAC). The protein product of the Plasmodium falciparum clonally variant clag3.1 and clag3.2 genes determines PSAC activity. Switches in the expression of clag3 genes, which are regulated by epigenetic mechanisms, are associated with changes in PSAC-dependent permeability that can result in resistance to compounds toxic for the parasite, such as blasticidin S. Here, we investigated whether other antimalarial drugs require CLAG3 to reach their intracellular target and consequently are prone to parasite resistance by epigenetic mechanisms. We found that the bis-thiazolium salts T3 (also known as albitiazolium) and T16 require the product of clag3 genes to enter infected erythrocytes. P. falciparum populations can develop resistance to these compounds via the selection of parasites with dramatically reduced expression of both genes. However, other compounds previously demonstrated or predicted to enter infected erythrocytes through transport pathways absent from noninfected erythrocytes, such as fosmidomycin, doxycycline, azithromycin, lumefantrine, or pentamidine, do not require expression of clag3 genes for their antimalarial activity. This suggests that they use alternative CLAG3-independent routes to access parasites. Our results demonstrate that P. falciparum can develop resistance to diverse antimalarial compounds by epigenetic changes in the expression of clag3 genes. This is of concern for drug development efforts because drug resistance by epigenetic mechanisms can arise quickly, even during the course of a single infection.