Miracle-dz/UniFAR-FTUs huggingface dataset:
Lipopolysaccharide biosynthesis and protein glycosylation in Helicobacter pylori

iv integrity, cell morphology and motility, and the production of outer membrane vesicles (OMVs). The composition of LPS in the mutants was also analysed using mass spectrometry and nuclear magnetic resonance spectroscopy, and the ability of mutants to colonize a mouse model of infection was also studied. The previously unstudied GTs HP1283, HPG27_1230, HP1284, HP0102, HP0805, HP1578 were found to be involved in the biosynthesis of the LPS core region, and the LPS from G27 was found to follow the same general linear structure as strains 26695, SS1, and a serogroup O:3 isolate. The LPS core was found to be essential for the resistance of H. pylori to polymyxin B, and the inner core heptose residues were found to be essential in OMV biogenesis. An additional role for FutA in assembly of the LPS core was suggested by the markedly increased sensitivity of G27ΔfutA to polymyxin B. The LPS size difference (~ 10 kDa) observed between the O-antigen ligase mutant G27ΔwaaL and the Lewis antigen mutant G27ΔHP0826, suggested that the LPS lipid A-core may be smaller than expected, and that the O-antigen might contain more than the Lewis antigen. It is expected that the structural analysis of the LPS from G27 wild-type and the associated LPS mutants constructed in this study will enable determination of the LPS structure and its biosynthetic pathway in H. pylori, which will be crucial for dissecting the role of LPS in H. pylori pathogenesis and immune escape, and could lead to the development of therapeutic drugs targeting the H. pylori LPS biosynthetic pathway.
Synthesis, characterization and application of TiO2/Ag recyclable SERS substrates

In this paper, rutile and anatase TiO2/Ag nanocomposites were prepared by a facile and green photochemical method. The as-prepared samples were investigated by using various spectroscopic and microscopic techniques in detail. Trace detection of rhodamine 6G (R6G) and crystal violet (CV) was studied based on the nanocomposites. Compared to the anatase TiO2/Ag nanocomposite, the rutile TiO2/Ag nanocomposites (Sr3) exhibited the best SERS performance for rhodamine 6G (R6G). Then, the optimized SERS-active substrates (Sr3) were employed to study its recycling properties by degrading R6G and CV in situ. The substrates were able to self-clean. The possible mechanism of the good SERS and photocatalytic performance of the TiO2/Ag nanocomposite (Sr3) was discussed. This work is of importance in theoretical research and practical application based on the SERS effect of nanocomposites.
Bifurcated hydrogen bond in rare sugar by computational study

ABSTRACT The monosaccharides such as D-β-glucose and D-β-idose sugars differ on the hydroxyl group's orientation at the C2-C4 positions. Hydroxyl groups such as OH2, OH3, and OH4 in β-idose are axial, while all (OHs) groups in β-glucose are equatorial. The density functional theory based on the B3LYP/6-31G* level results show that β-glucose is more stable than in β-idose. AIM analysis indicates the existence of intra-molecular hydrogen bond so that β-glucose displays regular intra-molecular hydrogen bond, while β-idose displays bifurcated acceptor intra-molecular hydrogen bond. The NBO analysis has been confirmed that the formation of intra-molecular hydrogen bonds in these two sugars.
Symmetric Assembly of a Sterically Encumbered Allyl Complex: Mechanochemical and Solution Synthesis of the Tris(allyl)beryllate, K[BeA′3] (A′ = 1,3-(SiMe3)2C3H3)

The ball milling of beryllium chloride with two equivalents of the potassium salt of bis(1,3-trimethylsilyl)allyl anion, K[A′] (A′ = [1,3-(SiMe3)2C3H3]), produces the tris(allyl)beryllate K[BeA’3] (1) rather than the expected neutral BeA’2. The same product is obtained from reaction in hexanes; in contrast, although a similar reaction conducted in Et2O was previously shown to produce the solvated species BeA’2(OEt2), it can produce 1 if the reaction time is extended (16 h). The tris(allyl)beryllate is fluxional in solution, and displays the strongly downfield 9Be NMR shift expected for a three-coordinate Be center (δ22.8 ppm). A single crystal X-ray structure reveals that the three allyl ligands are bound to beryllium in an arrangement with approximate C3 symmetry (Be–C (avg) = 1.805(10) A), with the potassium cation engaging in cation–π interactions with the double bonds of the allyl ligands. Similar structures have previously been found in complexes of zinc and tin, i.e., M[M′A′3L] (M′ = Zn, M = Li, Na, K; M′ = Sn, M = K; L = thf). Density functional theory (DFT) calculations indicate that the observed C3-symmetric framework of the isolated anion ([BeA′3]−) is 20 kJ·mol−1 higher in energy than a C1 arrangement; the K+ counterion evidently plays a critical role in templating the final conformation.
Effect of Lingonberry Extracts on Blood Pressure and Myocardium in Paracetamol Intoxication

In this study we tried to see how (1:1 and 3:1) lingonberry extract act as protective agents of the myocardium and blood pressure in toxicosis induced by paracetamol in rats. Experiments were made on white female Wistar rats, weighing 135 ± 20 g which were divided into 6 groups of 7 animals each: control group (C); Paracetamol treated group (P) 75 mg acetaminophen/100 g bw for 10 days. 1:1 lingonberry hidroalcoholic treated group (Lha), (200 mg/100 g bw (80 μg benzoic acid/100 g bw) for 15 days. 3:1 lingonberry dried extract group (Ld), 100 mg/100 g bw (112 μg benzoic acid/100 g bw), for 15 days. P+Lha (PLha) and P + Ld (PLd) treated group. Blood pressure increases following administration of paracetamol and decreases under treatment with lingonberry extract, more obvious to 3: 1 lingonberry dried extract. Administration of Paracetamol, lingonberry extracts used simple or in combination with Paracetamol does not affect the myocardium histological structure. Histoenzimological there is a slight decrease of SDH activity in the groups P and PLd and an increase in Lha group. CyOx activity is increased in Lha and Ld group. The dried lingonberry extract has no apparent action on the myocardium instead has antihypertensive properties more obvious than the lingonberry alcoholic extract.
Comment la structure des gels laitiers régule-t-elle la biodisponibilité des acides aminés ?

L’impact de la structure de l’aliment sur ses proprietes nutritionnelles est encore mal connu. L’objectif de ce travail etait de voir si des gels laitiers de composition identique obtenus par des procedes de gelification differents presentaient des cinetiques de digestion des proteines et de mise a disposition d’acides amines plasmatiques differentes. A partir d’un lait ecreme traite thermiquement (90°C/10 min), un gel acide et un gel presure de composition identique ont ete concus. Ces deux gels presentent des microstructures similaires (diametre des pores 0.8 μm) et des proprietes rheologiques voisines (facteur de perte tan δ identiques). Ces deux matrices ont ete donnees a des mini-porcs adultes equipes de canules duodenale et jejunale et d’un catheter sanguin. Il ressort que les cinetiques de digestion des proteines laitieres dependent directement du temps de residence de ces aliments dans l’estomac, luimeme pilote par la structure du gel. Les gels acides presentent un temps de residence plus court dans l’estomac que les gels presure. Le nombre de peptides identifies dans la lumiere intestinale tout au long des 7h de digestion etait 3 fois superieur pour le gel acide que pour le gel presure (4349 vs 1443). Le gel acide provoque l’apparition d’un pic precoce et massif d’acides amines essentiels dans le plasma. Le gel presure semble induire plus de satiete que le gel acide. Des donnees supplementaires obtenues in vitro et in silico ont permis de mettre en evidence une forte agglomeration de particules de caseines dans l’estomac pour le gel presure entrainant un temps de sejour superieur ainsi qu’une contraction du reseau proteique suivie d’une expulsion de lactoserum (synerese) provoquant une vidange rapide des proteines seriques.
Ignition Studies of Diisopropyl Ketone, A Second-Generation Biofuel

This thesis focuses on ignition of diisopropyl ketone (DIPK), a new biofuel candidate that is produced by endophytic conversion. The ignition delay times behind reflected shockwaves were modeled in a high-pressure shock tube. The ignition delay times were compared to other biofuels and gasoline surrogates. Parametric studies of the ignition delay experiments were performed between 1-10 atm and 900 -1200K. An OH optical sensor was developed in conjunction for the ignition delay experiments. The OH optical sensor uses a microwave discharge lamp to generate light at 308 nm that will then be shined through the combustion reaction. Using Beer-Lambert law the concentration of OH can be obtained during ignition and oxidation of hydrocarbon fuels in a shock tube. DIPK ignition delay time experiments are planned in two shock tubes (located at UCF and UF) to provide ignition and OH time-histories data for model validation.
Mass-loss and equilibrium-moisture-content of 10 wood species during long-term storage at 140°C

During 1-year storage at 140°C, 10 tested wood species lost an average of 37% of their initial mass. With the exception of abachi and thermally modified pine, the average equilibrium-moisture-content of the 10 wood species decreased from initial 11.6 to 6.2% after 180 days, followed by an increase to 7.9% after 1 year.
EFEK KO-KEMOTERAPI FRAKSI ETIL ASETAT AKAR PASAK BUMI DAN DOXORUBICIN TERHADAP PROLIFERASI DAN EKPRESI BAX JARINGAN PAYUDARA TIKUS SD

The use of co-chemotherapy agent was needed since there were some toxicities on the normal tissues caused by the use of doxorubicin. The root of Eurycoma longifolia Jack, a part of plant, has a potential activity as co-chemotherapy. This study aimed to determine the effect of co-chemotherapy of ethyl acetate fraction of E. longifolia Jack roots and doxorubicin against cell proliferation activity by AgNOR method and determine expression of Bax protein of breast tissue in rats induced by DMBA. The rats were divided into five groups: I (baseline), II (DMBA 20 mg/kgBW), III (DMBA, doxorubicin 1.12 mg/kg), IV (DMBA, fraction of 100 mg/kg), and V (DMBA, doxorubicin, fractions). All the rats were sacrificed at week 16. Their breast tissue was evacuated. Cell proliferation and expression was observed using AgNOR method and immunohistochemistry, respectively. Results showed the percentage of p-AgNOR obtained by the healthy group, DMBA group, DMBA+Doxorubicin group, DMBA+ethyl acetate fraction of E. longifolia Jack root group, and DMBA+Doxorubicin+Ethyl acetate fraction of E. longifolia group were 0±0%, 14.67±2.11%, 1.83±1.21%, 6.83±2.03%, and 4.08±0.95%, respectively. The percentage of Bax expression obtained by the healthy group, DMBA group, DMBA+Doxorubicin group, DMBA+ethyl acetate fraction of E. longifolia Jack root group, and DMBA+Doxorubicin+Ethyl acetate fraction of E. longifolia group were 68.82±1.52%, 26.86±3.25%, 44.49±2.06%, 80.92±3.27%, and 78.70±4.87%, respectively. Based on the results, it was concluded that co-chemotherapy agent of ethyl acetate fraction of E. longifolia Jack roots and Doxorubicin could inhibit proliferation and trigger apoptosis through Bax expression in breast tissue of rats induced by DMBA.
Genotypic and phenotypic characterization of winter hardiness in Beta species

Die Verlangerung des Vegetationszeitraumes von Zuckerruben (Beta vulgaris L.) verspricht eine deutliche Ertragssteigerung. Einen Ansatz dafur bietet der Anbau von Winterzuckerruben. Voraussetzung dafur ist unter anderem eine ausreichende Winterharte. Um die genetische Variation fur dieses Merkmal zu untersuchen, wurden in der vorliegenden Arbeit mehrortige Feldversuche mit einem genetisch diversen Beta vulgaris Sortiment durchgefuhrt. Dabei wurden signifikante Genotyp-, Umwelteffekte, sowie Genotyp-Umweltinteraktionen entdeckt. In einem Teil des Sortiments wurde anschliesend mit Hilfe von EcoTILLING Sequenzvariationen in dem Gen BvFL1identifiziert, die einen Einfluss auf das Schossverhalten vor Winter und auf Winterharte hatten. In einer bi-parentalen Zuckerrubenpopulation mit 238 F2:3 Nachkommenschaften wurden QTLs mit Effekt auf einen Frostschadensindex und Uberlebensraten in der Klimakammer identifiziert, die zwischen 13% und 17% der phanotypischen Variation erklaren.
Dual Functionalized Freestanding TiO2 Nanotube Arrays Coated with Ag Nanoparticles and Carbon Materials for Dye-Sensitized Solar Cells

Highly ordered, freestanding TiO2 nanotube arrays (TiO2 NTAs) were prepared using an electrochemical method. The barrier layer was etched to open the bottom of each array, aptly named “open-ended TiO2 NTAs”. These arrays were coated with silver nanoparticles (Ag NPs) and/or carbon materials to enhance electron generation and transport. The energy conversion efficiency of the resulting dye-sensitized solar cells (DSSCs) with open-ended freestanding TiO2 NTAs, when coated with Ag NPs, increased from 5.32% to 6.14% (by 15%) due to plasmonic interactions. Meanwhile, coating the open-ended freestanding TiO2 NTAs with carbon materials increased the energy conversion efficiency from 5.32% to 6.07% (by 14%), due to π-π conjugation. When the Ag NPs and carbon materials were simultaneously applied to the open-ended freestanding TiO2 NTAs, the energy conversion efficiency increased from 5.32% to 6.91%—an enhancement of 30%, due to the additive effects of plasmonics and π-π conjugation.
Magnetic, structural and surface properties of functionalized maghemite nanoparticles for copper and lead adsorption

In this study, magnetic nanocomposites were developed and used as adsorbents for lead and copper from aqueous media. Structural, surface, magnetic and textural properties of functionalized maghemite nanoparticles synthesized by alkaline co-precipitation were studied. The surfaces of the iron oxide nanoparticles (Nps) were modified with different chemical agents such as fatty and amino acids, silica (SiO2), mesoporous silica (SBA-15), hydroxyapatite, multiwall carbon nanotubes (MWCNTs) and ethylenediaminetetraacetic acid (EDTA), obtaining NPs with mean particle sizes ranging from 7 to 16 nm according to Rietveld refinement and TEM images analysis. The physicochemical surface properties of the functionalized materials were studied via zeta potential (ζ) and Fourier transform infrared (FTIR) spectroscopy. Mossbauer spectroscopy (MS) as a function of temperature and DC magnetometry were used to study the magnetic properties. The superparamagnetic relaxation was studied by MS. The resolved spectra at 20 K confirm the presence of nanomaghemite phase. Besides, the saturation magnetization varies from 12 to 62 emu g−1. A nitrogen adsorption–desorption technique was used to determine the specific surface area and to study the porous structure. The functionalized γ-Fe2O3 Nps exhibited a Brunauer–Emmett–Teller (BET) specific surface area ranging from 74 to 214 m2 g−1 and revealed remarkable uptake capacities to remove Cu(II) and Pb(II) species from aqueous solutions.
Climate change effect on storm drainage networks by storm water management model

One of the big problems facing municipalities is the management and control of urban flooding where urban drainage systems are under growing pressure due to increases in urbanization, population and changes in the climate. Urban flooding causes environmental and infrastructure damage, especially to roads, this damage increasing maintenance costs. The aim of the present study is to develop a decision support tool to identify the performance of storm networks to address future risks associated with climate change in the Middle East region and specifically, illegal sewer connections in the storm networks of Karbala city, Iraq. The storm water management model has been used to simulate Karbala’s storm drainage network using continuous hourly rainfall intensity data from 2008 to 2016. The results indicate that the system is sufficient as designed before consideration of extra sewage due to an illegal sewer connection. Due to climate changes in recent years, rainfall intensity has increased reaching 33.54 mm/h, this change led to flooding in 47% of manholes. Illegal sewage will increase flooding in the storm system at this rainfall intensity from between 39% to 52%.
IN VIVO TEST OF ANTIMALARIAL ACTIVITY FROM DICHLOROMETHANE-ETHYL ACETATE-METHANOL FRACTIONS OF MUNDU’S BARK(GARCINIA DULCIS (ROXB.) IN SWISS WEBSTER MICE

Objective: Genus Garcinia is well-known having rich xanthone compound contents and several of those are having biological activity as antimalarial. The aims of this research wereto determine in vivo antiplasmodialactivityof dichloromethane-ethyl acetate-methanol fractions of Mundu’s bark ( Garciniadulcis (Roxb.) Kurz) especially fraction Vagainst Plasmodium berghei and to determineeffective dose. Methods : Making fraction V from ethyl acetate extractsof Mundu’s bark with vacuum column chromatographymethod was applied using dichloromethane-ethyl acetate-methanol. The product was monitored by thin layer chromatography using silica gel GF-254 and a mobile phase of chloroform: ethyl acetate (6:4). The same profiles from eluent composed fraction 18 and 19 were categorized as fraction V.Those were tested in each of groups animals with a doseof 12.5; 25; 50 and 100 mg/kg body weight. Antimalarial activityassessments have been performed with the in vivoPlasmodium berghei test. Plasmodial activity was obtained by calculating percentage of parasitaemia, parasitaemia inhibition and ED 50 determination. ED 50 value determined based on the relationship between dose and the percentage of parasite growth inhibition by probit analysis. Results : In this research, Antiplasmodial activity of fraction V from Mundu’s bark displayed in dose of 50 mg/kg bw and 100 mg/kg bw with inhibition parasite growth by values of 47.255% and 12.761%, respectively. Conclusion : According to the research, fraction V of Mundu’s bark ( Garcinia dulcis (Roxb.) Kurz) had the most potential antiplasmodial activity by in vivo test for male Swiss-Webster mice. The value of ED 50 was reached by 47.424 mg/kg bw. Keywords : Mundu’s bark, Antiplasmodial activity, ED 50 .
Highly Efficient and Reproducible Nonfullerene Solar Cells from Hydrocarbon Solvents

With chlorinated solvents unlikely to be permitted for use in solution-processed organic solar cells in industry, there must be a focus on developing nonchlorinated solvent systems. Here we report high-efficiency devices utilizing a low-bandgap donor polymer (PffBT4T-2DT) and a nonfullerene acceptor (EH-IDTBR) from hydrocarbon solvents and without using additives. When mesitylene was used as the solvent, rather than chlorobenzene, an improved power conversion efficiency (11.1%) was achieved without the need for pre- or post-treatments. Despite altering the processing conditions to environmentally friendly solvents and room-temperature coating, grazing incident X-ray measurements confirmed that active layers processed from hydrocarbon solvents retained the robust nanomorphology obtained with hot-processed chlorinated solvents. The main advantages of hydrocarbon solvent-processed devices, besides the improved efficiencies, were the reproducibility and storage lifetime of devices. Mesitylene devices showed b.
Micellization of pH-sensitive poly(butadiene)-block-poly(2 vinylpyridine)-block-poly(ethylene oxide) triblock copolymers: Complex formation with anionic surfactants

The micellization of three tailor-made triblock copolymers, such as PB100–P2VP100–PEO104, PB185–P2VP108–PEO154, and PB37–P2VP115–PEO241, having similar total molecular weights and constant poly(2-vinylpyridine) (P2VP) sequence lengths, was investigated as a function of pH and sodium dodecyl sulfate (SDS) concentration. At pH 7 the formation of intermicellar aggregates was observed, especially for copolymers of low poly(ethylene oxide) (PEO) content. A pH decrease from 7 to 3 leads to a particle size increase due to the electrostatic repulsion of the protonated P2VP chains. The influence of the PEO sequence length was also observed for zeta potential values. At pH 3, in the absence of SDS, core–shell–corona micelles are formed whereas in the presence of small amount of SDS (degree of neutralization DN = 0%–50%), a complex is formed between SDS and the protonated P2VP which leads to the shrinkage of the shell and thus to a decrease of the micellar sizes. For higher DN values, the micellar sizes increase due to the formation of large agglomerates and a transition occurs from a monomodal to a bimodal size distribution. Furthermore, it turned out that secondary aggregation, such as intermicellar aggregation, can completely be avoided if the degree of polymerization (DPn) of the water-soluble block is significantly higher than the DPn of the water-insoluble sequence. © 2017 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2017, 134, 45313.
How enzymes are adsorbed on soil solid phase and factors limiting its activity: A Review

Abstract A majority of biochemical reactions are often catalysed by different types of enzymes. Adsorption of the enzyme is an imperative phenomenon, which protects it from physical or chemical degradation resulting in enzyme reserve in soil. This article summarizes some of the key results from previous studies and provides information about how enzymes are adsorbed on the surface of the soil solid phase and how different factors affect enzymatic activity in soil. Many studies have been done separately on the soil enzymatic activity and adsorption of enzymes on solid surfaces. However, only a few studies discuss enzyme adsorption on soil perspective; hence, we attempted to facilitate the process of enzyme adsorption specifically on soil surfaces. This review is remarkably unmatched, as we have thoroughly reviewed the relevant publications related to protein adsorption and enzymatic activity. Also, the article focuses on two important aspects, adsorption of enzymes and factors limiting the activity of adsorbed enzyme, together in one paper. The first part of this review comprehensively lays emphasis on different interactions between enzymes and the soil solid phase and the kinetics of enzyme adsorption. In the second part, we encircle various factors affecting the enzymatic activity of the adsorbed enzyme in soil.
A Simple and Sensitive GC-ECD Method for Detecting Synthetic Pyrethroid Insecticide Residues in Vegetable and Fruit Samples

A gas chromatographic-electron capture detection (GC-ECD) method was developed for determinating six synthetic pyrethroids insecticides (i.e. cyhalothrin, permethrin, cyfluthrin, cypermethrin, fenvalerate, and deltamethrin) which have been widely used in fruit orchards and vegetable growing. The synthetic pyrethroid insecticides were extracted using dichloromethane and cleaned up by loading onto the graphitized carbon cartridge. Limit of detection (LOD) ranged from 1 to 5 ng g-1 and limit of quantitation (LOQ) ranged from 2.5 to 10 ng g-1. The relative standard deviation (RSD) of intra-batch and inter-batch ranged from 1.8 to 7.4% and 8.9 to 15.7%, respectively. Recoveries at spiked levels (5, 10 and 50 ng g-1.) ranged from 96.8-109.3%, 86.5-96.9% and 83.8-98.4%, respectively. The developed method was successfully applied to quantify pyrethroid residues in fruit and vegetable samples from Chiang Mai province, northern Thailand. All samples had detectable levels of at least one synthetic pyrethoid insecticide residue. This developed method is practical for analysis of six synthetic pyrethroid insecticide residues, especially for screening of large quantities of samples because of its short extraction time. Moreover, GC-ECD which is a typical equipment in organic trace laboratory was successfully employed and provided practical achievement of sensitivity.