Constructing ab initio models of ultra-thin Al–AlOx–Al barriers

The microscopic structure of ultra-thin oxide barriers often plays a major role in modern nano-electronic devices. In the case of superconducting electronic circuits, their operation depends on the electrical nonlinearity provided by one or more such oxide layers in the form of ultra-thin tunnel barriers (also known as Josephson junctions). Currently available fabrication techniques manufacture an amorphous oxide barrier, which is attributed as a major noise source within the device. The nature of this noise is currently an open question and requires both experimental and theoretical investigation. Here, we present a methodology for constructing atomic-scale computational models of Josephson junctions using a combination of molecular mechanics, empirical and ab initio methods. These junctions consist of ultra-thin amorphous aluminium-oxide layers sandwiched between crystalline aluminium. The stability and structure of these barriers as a function of density and stoichiometry are investigated, which we compare with experimentally observed parameters.     

Tree fine root Ca/Al molar ratio – Indicator of Al and acidity stress

Many Aloe species are exploited as natural products. Generally, the leaves are unsustainably picked from wild plants to meet the market demand. Basic scientific information on seed biology and the ways of increasing levels of secondary metabolites in seedlings is still lacking for Aloe species. This study investigated seed germination requirements and evaluated levels of secondary metabolites in seedlings of Aloe arborescens, an important species in traditional medicine. The highest percentage germination (78%) and the fastest germination rate (GR) (10% d^? 1) with a mean germination time (MGT) of 9 days were achieved at 20°C under a 16-h photoperiod. At 25°C, maximum percentage germination (67%) (P < 0.05), higher GR (13% d^? 1) and shorter MGT (6 days) were obtained under constant light. These results indicate that temperature and light play a significant role in germination of A. arborescens seeds. Increasing osmotic pressure on seeds decreased percentage germination, whereas buffering the solution to a range of pH values (4–10) did not significantly affect germination. Smoke–water (1:500 v/v), smoke-isolated karrikinolide (10^? 8 and 10^? 9 M) and potassium nitrate (10^? 3 and 10^? 4 M) significantly promoted germination compared with the control at 25°C (supra-optimal temperature) under a 16-h photoperiod. These treatments were also effective in increasing secondary metabolite levels (flavonoids and phenolics) in A. arborescens seedlings.     

Distribution of Microorganisms in the Al–Fe–Humus Podzols of Natural and Anthropogenically Impacted Boreal Spruce Forests

Natural and anthropogenically induced seasonal variations in the abundance and biomass of various groups of microorganisms in the Al–Fe–humus podzols of boreal spruce forests were analyzed. The fungal biomass in these soils was found to be considerably higher than the bacterial biomass. The microbial population was mainly concentrated in a thin surface layer (10–15 cm in thickness), which included the forest litter and the upper mineral root-inhabited soil horizon and greatly differed from other soil horizons in morphology and other properties. This layer was found to be optimal with respect to hydrothermal and nutritional conditions and is characterized by profound seasonal variations in the abundance and biomass of microbiota. The high acidity, typical of the Al–Fe–humus podzols, resulted from the metabolism of their microbial communities. In the polluted podzols, the population of prokaryotes increased and that of eukaryotes decreased.     

Thermal and pressure-induced martensitic phase transformations in a Ni–Al alloy modelled by Sutton–Chen embedded atom method

The Ni–Al alloys which exhibit the thermoelastic martensitic phase transformations in the composition range from 60 to 65 atomic percentage (at.%) of Ni are widely used in the high technology applications. In this study, both thermal and pressure-induced phase transformations in Ni-37.5 at.%Al alloy model were investigated by a molecular dynamics (MD) method. Physical interactions between atoms in the alloy system were modelled using the Sutton–Chen version of the embedded atom method based on many-body interactions. The potential parameters for cross interactions between Ni and Al atoms were estimated by optimising the results obtained from the MD simulations, taking into account the experimental data including the crystal lattice properties of the model alloy in high temperature phase.     

A Low-Cost Al(OH)3-Modified Fire-Retardant and Shuttle-Limiting Separator for Safe and Stable Lithium–Sulfur Batteries

Lithium–sulfur battery (LSB) possesses high theoretical energy density, but its poor cycling stability and safety issues significantly restrict progress in practical applications. Herein, a low-cost and simple Al(OH)₃-based modification of commercial separator, which renders the battery outstanding fire-retardant and stable cycling, is reported. The modification is carried out by a simple blade coating of an ultrathin composite layer, mainly consisting of Al(OH)₃ nanoparticles and conductive carbon, on the cathode side of the separator. The Al(OH)₃ shows strong chemical absorption ability toward Lewis-based polysulfides and outstanding fire retardance through a self-decomposition mechanism under high heat, while the conductive carbon material acts as a top current collector to prevent dead polysulfide. LSB using the Al(OH)₃-modified separator shows an extremely low average capacity decade per cycle during 1000 cycles at 2 C (0.029%, 1 C = 1600 mA g⁻¹). The pouch cell exhibiting high energy density (426 Wh kg⁻¹) can also steadily cycle for more than 100 cycles with high capacity retention (70.2% at 0.1 C). The effectiveness and accessibility of this Al(OH)₃ modification strategy will hasten the practical application progress of LSBs.     

Impact of phosphorus mineral source (Al–P or Fe–P) and pH on cluster-root formation and carboxylate exudation in Lupinus albus L.

Lupinus albus L. were grown in rhizoboxes containing a soil amended with sparingly available Fe–P or Al–P (100 μg P g⁻¹ soil/resin mixture). Root halves of individual plants were supplied with nutrient solution (minus P) buffered at either pH 5.5 or 7.5, to assess whether the source of mineral-bound P and/or pH influence cluster-root growth and carboxylate exudation. The P-amended soil was mixed 3:1 (w/w) with anion-exchange resins to allow rapid fixation of carboxylates. Treatments lasted 10 weeks. Forty percent and 30% of the root mass developed as cluster roots in plants grown on Fe–P and Al–P respectively, but cluster-root growth was the same on root-halves grown at pH 5.5 or 7.5. Mineral-bound P source (Al– or Fe–P) had no influence on the types of carboxylates measured in soil associated with cluster roots—citrate (and trace amounts of malate and fumarate) was the only major carboxylate detected. The [citrate] in the rhizosphere of cluster roots decreased with increased shoot P status (suggesting a systemic effect) and also, only for plants grown on Al–P, with decreased pH in the root environment (suggesting a local effect). In a separate experiment using anion exchange resins pre-loaded with malate or citrate, we measured malate (50%) and citrate (79%) recovery after 30 days in soil. We therefore, also conclude that measurements of [citrate] and [malate] at the root surface may be underestimated and would be greater than the 40- and 1.6-μmol g⁻¹ root DM, respectively estimated by us and others because of decomposition of carboxylates around roots prior to sampling.     

Autophagy–physiology and pathophysiology

“Autophagy” is a highly conserved pathway for degradation, by which wasted intracellular macromolecules are delivered to lysosomes, where they are degraded into biologically active monomers such as amino acids that are subsequently re-used to maintain cellular metabolic turnover and homeostasis. Recent genetic studies have shown that mice lacking an autophagy-related gene (Atg5 or Atg7) cannot survive longer than 12 h after birth because of nutrient shortage. Moreover, tissue-specific impairment of autophagy in central nervous system tissue causes massive loss of neurons, resulting in neurodegeneration, while impaired autophagy in liver tissue causes accumulation of wasted organelles, leading to hepatomegaly. Although autophagy generally prevents cell death, our recent study using conditional Atg7-deficient mice in CNS tissue has demonstrated the presence of autophagic neuron death in the hippocampus after neonatal hypoxic/ischemic brain injury. Thus, recent genetic studies have shown that autophagy is involved in various cellular functions. In this review, we introduce physiological and pathophysiological roles of autophagy.     

Uni-directional Interaction and Plant–Pollinator–Robber Coexistence

A mathematical model for the plant-pollinator-robber interaction is studied to understand the factors leading to the widespread occurrence and stability of such interactions. In the interaction, a flowering plant provides resource for its pollinator and the pollinator has both positive and negative effects on the plant. A nectar robber acts as a plant predator, consuming a common resource with the pollinator, but with a different functional response. Using dynamical systems theory, mechanisms of species coexistence are investigated to show how a robber could invade the plant-pollinator system and persist stably with the pollinator. In addition, circumstances are demonstrated in which the pollinator's positive and negative effects on the plant could determine the robber's invasibility and the three-species coexistence.     

Magnetic–Plasmonic FePt@Ag Core–Shell Nanoparticles and Their Magnetic and SERS Properties

Magnetic–plasmonic FePt@Ag core–shell nanoparticles (NPs) with different Ag shell thicknesses were successfully synthesized using a seed-mediated method. They presented not only localized surface plasmon resonance in the visible region, but also superparamagnetic behavior at room temperature. When normalized by the weight of FePt, the saturation magnetization of the FePt@Ag NPs was found to be higher than that of FePt NPs, suggesting that the Ag shell effectively passivated the FePt NP surfaces, avoiding the direct interaction between the FePt core and surface capping ligands that typically forms a magnetically dead layer in FePt NPs. Despite the high colloidal stability and the small size of the FePt@Ag NPs, the NPs were easily separated using a permanent magnet. The surface enhanced Raman scattering (SERS) activity of the FePt@Ag NPs was then examined using thiophenol as a Raman reporter molecule and was found to be equivalent to that of Ag NPs. Moreover, the SERS activity of the FePt@Ag NPs was enhanced when a magnetic field was applied during the preparation of the SERS substrate (FePt@Ag NP film). These FePt@Ag NPs hold promise as dual-functional sensing probes for environmental and diagnostic applications.     

Metabolomic and elemental analysis of camel and bovine urine by GC–MS and ICP–MS

Recent studies from the author’s laboratory indicated that camel urine possesses antiplatelet activity and anti-cancer activity which is not present in bovine urine. The objective of this study is to compare the volatile and elemental components of bovine and camel urine using GC–MS and ICP–MS analysis. We are interested to know the component that performs these biological activities. The freeze dried urine was dissolved in dichloromethane and then derivatization process followed by using BSTFA for GC–MS analysis. Thirty different compounds were analyzed by the derivatization process in full scan mode. For ICP–MS analysis twenty eight important elements were analyzed in both bovine and camel urine. The results of GC–MS and ICP–MS analysis showed marked difference in the urinary metabolites. GC–MS evaluation of camel urine finds a lot of products of metabolism like benzene propanoic acid derivatives, fatty acid derivatives, amino acid derivatives, sugars, prostaglandins and canavanine. Several research reports reveal the metabolomics studies on camel urine but none of them completely reported the pharmacology related metabolomics. The present data of GC–MS suggest and support the previous studies and activities related to camel urine.     

Viscoelastic and Thermal Properties of Collagen–Xanthan Gum and Collagen–Maltodextrin Suspensions During Heating and Cooling

The purpose of this work was to investigate the viscoelastic properties of aqueous suspensions of crude collagen powder extracted from bovine hides and nonsubmitted to the hydrolysis reaction that leads to gelatin. The studied variables included the collagen concentration and the addition of xanthan gum or maltodextrin at varied concentrations during heating/cooling of the mixtures. Differential scanning calorimetry thermograms showed that the addition of polysaccharides decreased the endothermic peak areas observed at the denaturation temperature of collagen. The rheological properties of the pure collagen suspensions were highly dependent on concentration: 4% and 6% collagen suspensions presented a great increase in the storage modulus after heating/cooling, whereas for concentrations of 8% and 10% G′ decreased during heating and did not recover its original value after heating/cooling. The frequency sweeps showed that the thermal treatment was responsible by the strengthening of the interactions that formed the polymer network. Addition of 0.1% xanthan gum to collagen suspensions increased the gel strength, especially after heating/cooling of the system, whereas increasing gum concentration to 0.3% resulted in a weaker gel, which could indicate thermodynamic incompatibility between the biopolymers. Mixtures of collagen and maltodextrin resulted in more fluid structures than those obtained with pure collagen at the same collagen concentration and the range of temperatures in which these mixtures behaved as a gel decreased with increasing concentrations of both collagen and maltodextrin, suggesting incompatibilities between the biopolymers.     

mRNA-based therapeutics–Advances and perspectives

In this review we discuss features of mRNA synthesis and modifications used to minimize immune response and prolong efficiency of the translation process in vivo. Considerable attention is given to the use of liposomes and nanoparticles containing lipids and polymers for the mRNA delivery. Finally we briefly discuss mRNAs which are currently in the clinical trials for cancer immunotherapy, vaccination against infectious diseases, and replacement therapy.     

Physicomechanical Characterization and Optimization of EDTA–mPEG and Avicel®–EDTA–mPEG In Situ Melt Dispersion Mini-Pellets

The purpose of this study was to develop a physicomechanically customizable oral metal chelatory in situ hot melt dispersion mini-pellet entity which could be utilized within a binary drug delivery system. Avicel^® RC/CL type R-591 was included within the in situ hot melt dispersion mini-pellet formulations to determine the physicomechanical effect this compound would have on the mini-pellet formulations. The physicomechanical properties of the hot melt in situ mini-pellet formulations were mathematically fitting to regression curves. Physicomechanical adjustment of the in situ hot melt dispersion mini-pellet formulations could be mathematically predicted with the derived regression curve equations. The addition of Avicel^® RC/CL type R-591 increased the physicomechanical properties such as matrix hardness and increased total disintegration of the in situ hot melt dispersion mini-pellet formulations. The utilization of a physicomechanically customizable oral metal chelatory in situ hot melt dispersion mini-pellet entity within a binary drug delivery system would to achieve a synergistically enhance the activity of a drug-carrying entity or a permeation enhancing entity within a single drug delivery unit. The experimental results indicated that weights of the pellets that achieved optimal hardness ranged between 35 and 45 mg. The melt–dispersion formulations disintegrated within shorter time periods and maintained higher ethylenediaminetetraacetic acid (EDTA) concentrations whereas melt–dispersion formulations which included Avicel^® had superior physicomechanical properties. Disintegration times ranged between 1,000 s for melt–dispersions containing EDTA and methyloxy polyethylene glycol 2000 (mPEG) only, to >6,000 s for melt–dispersions comprising EDTA, mPEG, and Avicel^®.     

Analysis of lignin–carbohydrate and lignin–lignin linkages after hydrolase treatment of xylan–lignin,glucomannan–lignin and glucan–lignin complexes from spruce wood

Xylan–lignin (XL), glucomannan–lignin (GML) and glucan–lignin (GL) complexes were isolated from spruce wood, hydrolyzed with xylanase or endoglucanase/β-glucosidase, and analyzed by analytical pyrolysis and 2D-NMR. The enzymatic hydrolysis removed most of the polysaccharide moieties in the complexes, and the lignin content and relative abundance of lignin–carbohydrate linkages increased. Analytical pyrolysis confirmed the action of the enzymatic hydrolysis, with strong decreases of levoglucosane and other carbohydrate-derived products. Unexpectedly it also revealed that the hydrolase treatment alters the pattern of lignin breakdown products, resulting in higher amounts of coniferyl alcohol. From the anomeric carbohydrate signals in the 2D-NMR spectra, phenyl glycoside linkages (undetectable in the original complexes) could be identified in the hydrolyzed GML complex. Lower amounts of glucuronosyl and benzyl ether linkages were also observed after the hydrolysis. From the 2D-NMR spectra of the hydrolyzed complexes, it was concluded that the lignin in GML is less condensed than in XL due to its higher content in β-O-4′ ether substructures (62 % of side chains in GML vs 53 % in XL) accompanied by more coniferyl alcohol end units (16 vs 13 %). In contrast, the XL lignin has more pinoresinols (11 vs 6 %) and dibenzodioxocins (9 vs 2 %) than the GML (and both have ~13 % phenylcoumarans and 1 % spirodienones). Direct 2D-NMR analysis of the hydrolyzed GL complex was not possible due to its low solubility. However, after sample acetylation, an even less condensed lignin than in the GML complex was found (with up to 72 % β-O-4′ substructures and only 1 % pinoresinols). The study provides evidence for the existence of structurally different lignins associated to hemicelluloses (xylan and glucomannan) and cellulose in spruce wood and, at the same time, offers information on some of the chemical linkages between the above polymers.     

Gene–gene and gene–environment interactions in ulcerative colitis

Genome-wide association studies (GWAS) have identified at least 133 ulcerative colitis (UC) associated loci. The role of genetic factors in clinical practice is not clearly defined. The relevance of genetic variants to disease pathogenesis is still uncertain because of not characterized gene–gene and gene–environment interactions. We examined the predictive value of combining the 133 UC risk loci with genetic interactions in an ongoing inflammatory bowel disease (IBD) GWAS. The Wellcome Trust Case–Control Consortium (WTCCC) IBD GWAS was used as a replication cohort. We applied logic regression (LR), a novel adaptive regression methodology, to search for high-order interactions. Exploratory genotype correlations with UC sub-phenotypes [extent of disease, need of surgery, age of onset, extra-intestinal manifestations and primary sclerosing cholangitis (PSC)] were conducted. The combination of 133 UC loci yielded good UC risk predictability [area under the curve (AUC) of 0.86]. A higher cumulative allele score predicted higher UC risk. Through LR, several lines of evidence for genetic interactions were identified and successfully replicated in the WTCCC cohort. The genetic interactions combined with the gene-smoking interaction significantly improved predictability in the model (AUC, from 0.86 to 0.89, P = 3.26E?05). Explained UC variance increased from 37 to 42 % after adding the interaction terms. A within case analysis found suggested genetic association with PSC. Our study demonstrates that the LR methodology allows the identification and replication of high-order genetic interactions in UC GWAS datasets. UC risk can be predicted by a 133 loci and improved by adding gene–gene and gene–environment interactions.     

Dose–response and threshold effects in cytotoxicity and apoptosis

Cell death can occur as an active, programmed event in response to cytotoxic injury or to endogenous growth limiting factors; the latter serve to maintain homeostasis of cell number in tissues. Cells seem to use different pathways for programmed death, as reflected by their different morphology and different biochemistry. Severe cell damage leading to incapacitation of essential cell functions such as ATP synthesis or the maintenance of membrane potential may lead to “necrosis”. In any event, the incidence and rate of cell death increase with increasing signal intensity. Cytotoxic injury requires a certain number of primary insults; cell death will therefore occur only beyond a definable threshold. Growth factor control of cell death is receptor-mediated with dose–response relations including threshold phenomena follow the general principles of receptor kinetics. The occurrence of programmed cell death during the stages of carcinogenesis introduces a reversible component into this disease. Therefore, there may exist thresholds of dose or durations of exposure to certain carcinogens below which irreversible disease is not generated.