Miracle-dz/UniFAR-FTUs huggingface dataset:
Investigation of the antibacterial efficiency of toothpastes used against dental pathogens

Toothpastes are dental as well as oral hygiene determiners, quality and quantity of toothpaste being the two cardinal points to control the dental health and also the oral hygiene. Dental health deteriorated for dental plaque, dental caries, and periodontal diseases caused by pathogenic bacteria. Toothpaste kill and erase the bacteria from the surface of the teeth and oral cavity but all the toothpastes have not similar antibacterial activity. Four types of toothpaste: Colgate, Close-up, Dabur-Red and Glister were used to observe the comparative antibacterial efficiency considering quality and quantity or doses concentration in an investigation. Experiments were done several times, sound the effective results were observed from Dabur-Red toothpaste in comparison to other toothpastes. Future details research will also open a new avenue to formulate the quality and the dose’s concentration of the best toothpaste for next generation.
Elaboration d’électrodes de pile à combustible par plasma

Cette these en cotutelle resulte de la collaboration entre le laboratoire francais GREMI (Orleans) et le groupe australien SP3 (Universite National Australienne) sur l’optimisation des piles a combustible par procede plasma. Mon projet d’etude concerne le developpement d’une electrode de pile a combustible constituee d’une nanostructure carbonee impregnee d’agregats de catalyseur platine, l’enjeu etant de reduire la quantite de platine tout en conservant de bonnes performances electrochimiques. Durant la premiere partie passee en France, des electrodes traditionnelles non catalysees ont ete impregnees d’agregats de platine sur quelques centaines de nanometres par pulverisation plasma. Cette methode a permis de reduire considerablement la charge de platine par rapport a une electrode traditionnelle catalysee chimiquement tout en reduisant legerement ses performances. La seconde moitie de ma these en Australie concerna la croissance d’un support catalytique carbone de grande surface specifique optimise pour l’application pile a combustible. Des nanofibres de carbone (CNF) ont donc ete deposees sur du papier de carbone recouvert d’une fine couche de nickel en utilisant un procede CVD (Chemical Vapor Deposition) dans un reacteur plasma Helicon que j’ai concu et developpe. La morphologie des CNF a ete caracterisee et optimisee en fonction des parametres plasmas. Ce tapis de CNF a ete impregne d’agregats de platine par pulverisation plasma Helicon. Dans cette nouvelle electrode entierement realisee par plasma, le catalyseur est cette fois reparti sur quelques micrometres ce qui permettra d’augmenter les performances electriques de la pile.
First Molecular Characterisation of Clinical Strains of Mycobacterium ulcerans in Togo (West Africa)

Background: Buruli ulcer is the third most common mycobacterial disease worldwide. Cases most occur in 30 countries but severe cases occur in West Africa countries such as Benin, Cote d’Ivoire and Togo mainly in rural regions. Early diagnosis may prevent severe disability. The molecular technique seems the best solution and new Mycobacterial Interspersed Repetitive Units (MIRU) and variable number tandem repeats (VNTR) typing method are themost reproducible in this regard. They propose geographical, inter and intraspecies differentiation and can be used as a diagnosis tool. Objective: The objective of this study was to investigate the molecular diversity by using MIRUVNTR typing in clinical samples of BU patients in Togo. Study Design: 64 DNA extracts from clinical samples were collected from BU patients in the two principal endemics districts in Togo (Yoto and Zio) with three less endemic districts (Bas Mono, Lacs and Vo). First, IS2404 and KR real-time PCR plus IS2606 conventional PCR were performed. In a second step, the strains were analysed by PCR typing for five specific and sensitive markers MIRU1, VNTR6, ST1, VNTR19 and VNTR9. Results and Conclusion: 71.11% were positive for IS2404, 3.13% were positives for PCR-KR and 31.11% for IS 2606. By MIRU-VNTR typing, 48.86% positive result was found for MIRU1 and 25.00%, 20.31%, 18.75% and 14.06% for VNTR6, ST1, VNTR19 and VNTR9 respectively. One of the samples was negative for all genotyping markers. Two different genetic profiles were identified by MIRU1, ST1 and VNTR loci by gel-analysed of the amplified products. The VNTR profile B (3,1,1,2) corresponding of 3 copies MIRU1, 1 copy VNTR6, 1 copy ST-1 and two copies of VNTR19 was detected in 15.63% of samples and the VNTR profile A (1,1,1,2) corresponding of 1 copy MIRU1, 1 copy VNTR6, 1 copy ST-1 and 2 copies of VNTR19 was detected in 3.13% of samples and confirms the West African genotype (3,1,1) in Togo. Different genetic strains of Mycobacterium ulcerans (M. ulcerans) were co-circulated in the same endemic region in the country. This study has described first the circulating of different genetic strains of M. ulcerans in Togo.
A behavioral approach to personalizing public health

Behavioral policies are increasingly popular in a number of health care contexts. However, evidence of their effectiveness, specifically in low-income and highly disadvantaged populations, is limited. Some positive effects have been found for adaptive interventions, which merge more personalized approaches with advances in data collection and modern analytical methods. These approaches have only recently become feasible, as their implementation requires a confluence of large-scale datasets, contemporary machine learning, and validated behavioral insights. Such methods have considerable potential to improve outcomes without requiring substantial increases in effort on the part of individuals. Using examples from health insurance choice, clinical attendance rates, and prescription of medicines, we present an argument for how adaptive approaches, especially those considering disadvantaged populations explicitly, offer an opportunity to generate equity in public health.
In Silico Interaction of the Active Compounds of Scurrula Atropurpurea with the RANK/RANKL/OPG System in Diabetoporosis

Introduction: Diabetoporosis is a very complex health problem in Indonesia. One approach to the problem is through native Indonesian herbal medicine. The application of Scurrula atropurpurea in the treatment of diabetoporosis has not been revealed, so preliminary in silico study needs to be done. Aim: The purpose of the present study was to analyze the interaction between the active compound of Scurrula atropurpurea and the RANKL/RANK/OPG system in the pathomechanism of osteoporosis in diabetes mellitus. Methods: The procedures of the study included the search for the constituent amino acid of the RANK/RANKL/OPG system, the search for the structure of the active component of Scurrula atropurpurea, 3D modeling of protein structure, protein-ligand docking and visualization, and analysis of protein-ligand bonding interactions. Results: Those bond energies were RANKL-aviculin (–274.96 kJ/mol), RANKL-rutin (–263.12 kJ/mol), RANKL-quercitrin (–256.98 kJ/mol), RANKL-quercetin (–226,50 kJ/mol), RANKL-kaempferol (–221,65 kJ/mol), RANKL-catechin (–214,85 kJ/mol), RANKL-epicatechin (–211.66 kJ/mol), RANKL-caffeine (-171.73 kJ/mol), and RANKL-theobromine (-161.14 kJ/mol). The bond energies were RANK-rutin (-719.26 kJ/mol), RANK-catechin (-680.15 kJ/mol), RANK-caffeine (-654.48 kJ/mol), RANK-theobromine (-651.77 kJ/mol), RANK-quercitrin (-650.68 kJ/mol), RANK-kaempferol (-643.03 kJ/mol), RANK-epicatechin (-641.86 kJ/mol), RANK-quercetin (-641.76 kJ/mol), and RANK-aviculin (-628.62 kJ/mol). Those bond energies were OPG-epicatechin (-590.09 kJ/mol), OPG-theobromine (-578.08 kJ/mol), OPG-caffeine (-568.88 kJ/mol), RANKL-catechin (-560.63 kJ/mol), OPG-quercitrin (-554.50 kJ/mol), OPG-rutin (-547.91 kJ/mol), OPG-quercetin (-545.75 kJ/mol), OPG-kaempferol (-544.48 kJ/mol), and OPG-aviculin (-539.15 kJ/mol). Conclusion: The nine active ingredients of Scurrula atropurpurea do not interfere with the physiological function of RANKL to interact with RANK. The initial interaction of RANK with catechin or rutin will facilitate the bond of RANK to RANKL. When forming a complex with OPG, epicatechin will facilitate its interaction with RANKL.
Influence of organic manures on the growth of diabetes preventive medicinal plant Gynura, Gynura procumbens

A pot experiment was carried out to evaluate the effects of various organic manures on the growth performance and biomass production of Gynura procumbens in the net house of the Department of Soil, Water and Environment, University of Dhaka. Seven types of manures, viz. ACI, BGF-1, Mazim, Vermicompost, Sufola, GTS and Poultry litter composts were used separately at the rate of 15 ton/ha. Highest height (78cm) in poultry litter compost, leaf number (208.33 no./plant) in sufola manure, leaf area (53.64 cm2/plant) in vermicompost, and branch (3.67 no./plant), girth (3.07cm/plant), fresh weight (202.28g/plant) and dry weight (22.44g/plant) were recorded in poultry litter compost treatment at harvest. Height, leaf area, and fresh and dry weights of leaf varied significantly (p≤ 0.5) and increased with time. Results showed that the overall best growth performance was achieved in poultry litter compost. J. Biodivers. Conserv. Bioresour. Manag. 2018, 4(2): 61-66
Synergetic effect of non-complementary 5’ AT-rich sequences on the development of a multiplex TaqMan real-time PCR for specific and robust detection of Clavibacter michiganensis and C. michiganensis subsp. nebraskensis

Clavibacter is an agriculturally important genus comprising a single species, Clavibacter michiganensis, and multiple subspecies, including, C. michiganensis subsp. nebraskensis which causes Goss’s wilt/blight of corn and accounts for high yield losses - listed among the five most significant diseases of corn in the United States of America. Our research objective was to develop a robust and rapid multiplex TaqMan real-time PCR (qPCR) to detect C. michiganensis in general and C. michiganensis subsp. nebraskensis with enhanced reliability and accuracy by adding non-complementary AT sequences to the 5’ end of the forward and reverse primers. Comparative genomic analyses were performed to identify unique and conserved gene regions for primer and probe design. The unique genomic regions, ABC transporter ATP-binding protein CDS/ABC-transporter permease and MFS transporter were determined for specific detection of C. michiganensis and C. m. subsp. nebraskensis, respectively. The AT-rich sequences at the 5’ position of the primers enhanced the reaction efficiency and sensitivity of rapid qPCR cycling; the reliability, accuracy and high efficiency of the developed assay was confirmed after testing with 59 strains from inclusivity and exclusivity panels – no false positives or false negatives were detected. The assays were also validated through naturally and artificially infected corn plant samples; all samples were detected for C. michiganensis and C. m. subsp. nebraskensis with 100% accuracy. The assay with 5’ AT-rich sequences detected up to 10- and 100-fg of C. michiganensis and C. michiganensis subsp. nebraskensis genome targets, respectively. No adverse effect was observed when sensitivity assays were spiked with host genomic DNA. Addition of 5’ AT rich sequences enhanced the qPCR reaction efficiency from 0.82 (M = -3.83) and 0.91 (M = -3.54) to 1.04 (with optimum slope value; M = -3.23) for both C. michiganensis and C. michiganensis subsp. nebraskensis, respectively; a increase of 10-fold sensitivity was also obtained with C. michiganensis primer set. The methodology proposed here can be used to optimize the reaction efficiency and to harmonize the diagnostic protocols which have prodigious applications in routine diagnostics, biosecurity and microbial forensics.
Ginkgo biloba Alleviates Cisplatin-Mediated Neurotoxicity in Rats via Modulating APP/Aβ/P2X7R/P2Y12R and XIAP/BDNF-Dependent Caspase-3 Apoptotic Pathway

Neurotoxicity is an obvious adverse effect in Patients encountering a complete course of chemotherapy. The present work is conducted to evaluate the neuroprotective effect of Ginkgo biloba (Ginkgo) against the neurotoxicity induced by Cisplatin (Cis) in rats. Forty male Wistar albino rats were arranged into four groups: (1) Control group, rats were given saline; (2) Cis group, rats were injected by Cis 2 mg/kg body weight i.p., twice a week starting on the fifth day for thirty days; (3) Ginkgo group, rats were administered Ginkgo (50 mg/kg orally) daily for thirty days; and (4) Ginkgo+Cis group, rats received Ginkgo (50 mg/kg orally) daily and on the fifth day, rats were injected with Cis (2 mg/Kg body weight i.p.) twice a week for thirty days. Cis significantly increased Gamma glutamyltransferase (GGT) and Acetyl Cholinesterase (CHE) as compared to the control group and also disturbed cerebral oxidative/antioxidant redox. Co-administration of Ginkgo and Cis reversed the adverse effect of Cis on the brain tissue. Moreover, co-administration of Ginkgo and Cis ameliorated Cis induced brain damage by reducing Amyloid precursor protein (APP), amyloid β (Aβ), P2Y12R and P2X7R mRNA expressions and proteins. Furthermore, Ginkgo regulated XIAP/BDNF expressions with a consequent decrease of caspase-3 and DNA fragmentation%. The current results concluded that concurrent treatment with Ginkgo can mitigate neurotoxicity mediated by Cis in experimental animals through exhibiting antioxidant effect by restoring cerebral oxidative/antioxidant redox and anti-apoptotic effect via regulating cerebral APP/Aβ/P2Y12R/P2X7R and XIAP/BDNF signaling pathways.
Complete mitochondrial genome analysis of Leptomias sp. (Coleoptera, Curculionidae) from Southeast Tibet of China

Abstract Leptomias sp. belongs to Coleoptera, Curculionidae, Leptomias Faust. It is mainly distributed in the Himalayas and Yarlung Zangbo River valleys in Tibet. It is the first time to report the complete mitochondrial genome of Leptomias sp. , which featured a typical circular molecule of 16,801 bp in length, including 13 PCGs, 22 tRNAs, two rRNAs, and one control region. The overall nucleotide composition was 38.7% of A, 10.0% of G, 34.3% of T, and 17.0% of C. The content of A + T was higher than G + C. In this study, we also determined that Leptomias sp. was the sister to the Sympiezomias velatus based the phylogenetic analysis of nucleotide sequence datasets. This study provides a useful resource for further studies on conservation and population genetics of Leptomias species.
Defining the role and control of the lpxO gene in Klebsiella pneumoniae

Antimicrobial resistance (AMR) is fast becoming one of the greatest challenges to human mortality this century. In recent years the number of reported infections by multi-drug resistant (MDR) bacteria has seen a rapid rise. As a result, the efficacy of currently used antibiotics is decreasing, with infections by MDR bacteria increasingly difficult to treat. In more and more cases, the use of last-line drugs is becoming necessary. However, this in turn has resulted in increasing reports of last-line drug resistance, presenting a dangerous cycle that leaves us potentially short of treatment options. As a result, elucidating the intrinsic resistance mechanisms that pathogens employ, and their importance in generating an AMR phenotype, is essential to developing a comprehensive and effective antimicrobial strategy. Furthermore, identifying specific resistance mechanisms and their contribution to AMR presents potential targets for inhibitory drugs in combination with existing antimicrobials. This project looks at the role of the transcription regulator RamA in generating an AMR phenotype in the Gram-negative bacterium Klebsiella pneumoniae. K. pneumoniae is a major cause of nosocomial infections in the immunocompromised, with MDR isolates resistant to the last-line drug colistin rapidly increasing in prevalence. K. pneumoniae RamA regulates genes associated with virulence and resistance, able to modulate outer membrane permeability through altered influx and efflux. Overexpression of ramA has also been shown to upregulate the dioxygenase LpxO, a lipid A modifying enzyme associated with increased resistance to colistin, polymyxin B, and the human cationic antimicrobial peptide LL-37. Our study seeks to define the relative importance of RamA and LpxO in relation to polymyxin B, colistin and LL-37; specifically how RamA-mediated lpxO-overexpression confers this phenotype. In this regard, we have performed MIC and relative survival assay studies with wild-type K. pneumoniae, ramAand lpxO-overexpressing strains, in order to define the role of these genes in the relevant phenotypes.
A BEM for the Hydrodynamic Analysis of Oscillating Water Column Systems in Variable Bathymetry

In this work, a novel Boundary Element Method (BEM) is developed and applied to the investigation of the performance of Oscillating Water Column (OWC) systems, taking into account the interaction of the incident wave field with the bottom topography. The modelling includes the effect of additional upwave walls and barriers used to modify the resonance characteristics of the device and improve its performance as the U-OWC configuration. Numerical results illustrating the effects of depth variation in conjunction with other parameters—such as chamber dimensions as well as the parameters associated with the turbine and power take-off system—on the device performance are presented and discussed. Finally, a case study is presented regarding the potential installation of an OWC in a selected port site in the Black Sea, characterized by a good wave energy potential, on the coast of Romania.
Time‐lagged inverse‐distance weighting for air temperature analysis in an equatorial urban area (Guayaquil, Ecuador)

It is well known that sudden variations of air temperature have the potential to cause severe impacts on human health. Therefore, it becomes necessary to provide information capable of quantifying the severity of the problem, considering that the continuous increase of temperature due to global warming and urban development will cause more intense effects in heavily populated areas. Due to its geographical location and local characteristics, Ecuador, a country located on the western coast of South America, is characterized by a high vulnerability to climatic extremes. The present research develops an evaluation of urban climate change effects through the analysis of extreme temperature indices using four meteorological stations situated in the city of Guayaquil (southwest Ecuador). Since the available data are not adequate for extreme temperature indices criteria, it was necessary to employ an infilling method for times series in an innovative way that can be applicable at the small scale. Thus, a cross‐correlation‐enhanced inverse distance weighting (CC‐IDW) method was proposed. The method entails a spatial interpolation based on data of urban stations situated outside of Guayaquil by taking into account cross‐correlation among times series at precise lags that leads to an improvement in the way of estimating the missing values. Subsequently, a homogeneity test, data quality control and the calculation of extreme temperature indices chosen from those proposed by the World Meteorological Organization (WMO) were implemented. The results show that there is a general tendency of warming with quite homogenous temperatures for all considered stations. However, it should be recognized that the climate pattern of this region is strongly modulated by the El Niño Southern Oscillation (ENSO) cycle. Only for two extreme indices: the highest maximum temperature (TXx) and the warm days (TX90p), are the resulting trend co‐efficients statistically significant. The study suggests a deteriorated climatic condition due to heat stress that warrants further study using the available database for the city of Guayaquil.
On Hadamard and Kronecker products in covariance structures for genotype × environment interaction

When including genotype × environment interactions (G × E) in genomic prediction models, Hadamard or Kronecker products have been used to model the covariance structure of interactions. The relation between these two types of modeling has not been made clear in genomic prediction literature. Here, we demonstrate that a certain model based on a Hadamard formulation and another using the Kronecker product lead to exactly the same statistical model. Moreover, we illustrate how a multiplication of entries of covariance matrices is related to modeling locus × environmental‐variable interactions explicitly. Finally, we use a wheat and a maize data set to illustrate that the environmental covariance E can be specified easily, also if no information on environmental variables – such as temperature or precipitation – is available. Given that lines have been tested in different environments, the corresponding environmental covariance can simply be estimated from the training set as phenotypic covariance between environments. To achieve a high level of increase in predictive ability, the environmental covariance has to be defined appropriately and records on the performance of the lines of the test set under different environmental conditions have to be included in the training set.
Insights from five decades of monitoring habitat and breeding populations of American woodcock

1. Habitat loss and degradation are contributing to severe declines in many North American bird species. For American woodcock Scolopax minor (‘woodcock’), loss of preferred young forest habitat matrices are generally attributed as the primary drivers of range-wide population declines in eastern North America, but regional patterns in abundance or habitat availability have not been assessed in Nova Scotia, the northeastern-most portion of the range. 2. Our objectives were to (a) identify regions of similar trends over the past five decades, (b) evaluate spatiotemporal relationships in the effect of habitat availability on abundance across the province and (c) provide recommendations for woodcock management priorities in Nova Scotia to target local population declines. 3.Using50yearsofstandardisedsurveysandhabitatmeasures,weinvestigatedwood-cock population trends and local habitat availability by applying a novel spatially-explicit model with Integrated Nested Laplace Approximation. 4. Province-level declines were primarily driven by losses of breeding woodcock in the north and south of the province, while the central region experienced growth. The proportion of area around a survey route comprised of clear-cut, harvested forest was the most important habitat and ultimately range wide. The temporally and spatially extensive surveys used here provide a remarkably comprehensive avian monitoring dataset. Coupled with modern analytical tools, our study system serves as an example of how long-term avian survey efforts are capable of informing management regionally to achieve broader conservation targets.
The complete mitogenome of the Lepturacanthus savala (Perciformes: Trichiuridae) from the Yellow Sea

Abstract Lepturacanthus savala is a commercially important marine fish belonging to the family Trichiuridae, with a wide distribution in the Indian-Western Pacific coastal waters. In this study, the complete mitochondrial genome of L. savala has been determined by primer walking methods. The mitogenome is 17,146 bp in length containing 13 protein-coding genes, 2 ribosomal RNA genes, 21 transfer RNA genes, a control region, and an origin of light-chain replication region. The base composition is 28.9% for A, 29.0% for C, 15.7% for G, and 26.4% for T. The maximum-likelihood tree based on whole mitogenome showed that it is the closest related species of Trichiurus.