Minority Species Research Articles

Effects of Additives on Crystallization in Thin Organic Films

Controlling the shape and growth of crystals in molecular organic solids has ramifications impacting diverse fields, but remains challenging to fully exploit. Here, crystal shapes in organic thin films are manipulated from aspect ratios of 1 to over 50, with corresponding growth rates decreased by an order of magnitude simply by mixing a structurally dissimilar minority species into the film. These effects are mapped with composition and temperature in mixtures of two model small-molecular-weight organic compounds, revealing a continuous variation in crystal shape and growth rate. Other combinations of molecules are discussed, showing additive shape selection in multicomponent mixtures and enabling customization of crystal shape.

Universal and anomalous behavior in the thermalization of strongly interacting harmonically trapped gas mixtures

We report on the dynamics of thermalization by extending a generalization of the Caldeira–Leggett model, developed in the context of cold atomic gases confined in a harmonic trap, to higher dimensions. Universal characteristics en route to thermalization which appear to be independent of dimensionality are highlighted, which additionally suggest a scaling analogous to turbulent mixing in fluid dynamics. We then focus on features dependent on dimensionality, with particular regard to the role of angular momentum of the two atomic clouds, having in mind the goal of efficient thermalization between the two species. Finally, by considering asymmetry in species numbers, we find that nonlinear interspecies interactions provide a mode locking mechanism between the majority and minority species, relevant to recent experiments involving Fermi–Bose mixtures in the normal phase.

Cross-code gyrokinetic verification and benchmark on the linear collisionless dynamics of the geodesic acoustic mode

The linear properties of the geodesic acoustic modes (GAMs) in tokamaks are investigated by means of the comparison of analytical theory and gyrokinetic numerical simulations. The dependence on the value of the safety factor, finite-orbit-width of the ions in relation to the radial mode width, magnetic-flux-surface shaping, and electron/ion mass ratio are considered. Nonuniformities in the plasma profiles (such as density, temperature, and safety factor), electro-magnetic effects, collisions, and the presence of minority species are neglected. Also, only linear simulations are considered, focusing on the local dynamics. We use three different gyrokinetic codes: the Lagrangian (particle-in-cell) code ORB5, the Eulerian code GENE, and semi-Lagrangian code GYSELA. One of the main aims of this paper is to provide a detailed comparison of the numerical results and analytical theory, in the regimes where this is possible. This helps understanding better the behavior of the linear GAM dynamics in these different regimes, the behavior of the codes, which is crucial in the view of a future work where more physics is present, and the regimes of validity of each specific analytical dispersion relation.

Prediction of Species-Specific Volume Using Different Inventory Approaches by Fusing Airborne Laser Scanning and Hyperspectral Data

Fusion of ALS and hyperspectral data can offer a powerful basis for the discrimination of tree species and enables an accurate prediction of species-specific attributes. In this study, the fused airborne laser scanning (ALS) data and hyperspectral images were used to model and predict the total and species-specific volumes based on three forest inventory approaches, namely the individual tree crown (ITC) approach, the semi-ITC approach, and the area-based approach (ABA). The performances of these inventory approaches were analyzed and compared at the plot level in a complex Alpine forest in Italy. For the ITC and semi-ITC approaches, an ITC delineation algorithm was applied. With the ITC approach, the species-specific volumes were predicted with allometric models for each crown segment and aggregated to the total volume. For the semi-ITC and ABA, a multivariate k-most similar neighbor method was applied to simultaneously predict the total and species-specific volumes using leave-one-out cross-validation at the plot level. In both methods, the ALS and hyperspectral variables were important for volume modeling. The total volume of the ITC, semi-ITC, and ABA resulted in relative root mean square errors (RMSEs) of 25.31%, 17.41%, 30.95% of the mean and systematic errors (mean differences) of 21.59%, −0.27%, and −2.69% of the mean, respectively. The ITC approach achieved high accuracies but large systematic errors for minority species. For majority species, the semi-ITC performed slightly better compared to the ABA, resulting in higher accuracies and smaller systematic errors. The results indicated that the semi-ITC outperformed the two other inventory approaches. To conclude, we suggest that the semi-ITC method is further tested and assessed with attention to its potential in operational forestry applications, especially in cases for which accurate species-specific forest biophysical attributes are needed.

Dynamics of field-driven population inversion in a confined colloidal mixture.

We study, using Langevin dynamics simulations, the change in composition of a binary colloidal mixture confined in a finite-length channel, induced by an external field. The field-induced transition from a near-bulk composition to an inverted population is studied as a function of time, for different field strengths and system parameters. For state points corresponding to reversible field cycles, the cyclic filling and emptying of the channel by the minority species are compared. Extrapolation of the physical relaxation times to the colloidal regime is performed through a series of simulations at increasing value of the damping parameter. For state points at which the mixture is unstable at zero field, reproducible irreversible cycles are illustrated. For reversible field cycles, the scaling with the particles size of the characteristic cycling time is discussed.

Characteristics of green-blue fluorescence generated from the adaxial sides of leaves of tree species.

We discovered that some tree species have leaves whose adaxial sides show bright green-blue fluorescence upon exposure to ultraviolet irradiation. In total, 141 native Japanese species belonging to 47 families were analyzed, and the brightness of the leaf fluorescence, represented by the L* values (Lab color space) of the pictures, was evaluated. The species possessing the brightest fluorescent leaves, with L* > 50, were Camellia japonica, Camellia sasanqua, and Cleyera japonica of Theaceae, Osmanthus heterophyllus and Ligustrum japonicum of Oleaceae, Aucuba japonica of Garryaceae, and Trochodendron aralioides of Trochodendraceae. These species are propagated by pollination or seed dispersion by birds, except T. aralioides. The fluorescence was specifically observed in the cuticle tissues of the epidermal cells, indicating that the fluorescence is a signal to other organisms that can perceive the fluorescence under natural light. Species possessing the bright leaves represented 5% of the total species tested, while species possessing dark leaves, with L* ≤ 40, represented 88.6%. We deduce that the fluorescence enables the organisms to easily distinguish the minority species possessing bright leaves from the surrounding plants, which were mostly trees species with dark leaves. The structure of A. japonica var. borealis, in which dark leaves only surround its fruits while the rest of the tree is covered by bright leaves, may be useful to signal the presence of fruits to the organisms. We hypothesize that the fluorescence contributes to the propagation of the tree species by helping birds to distinguish these particular trees and/or locate the fruits.

Co-precipitation of rare-earth-doped Y2O3 and MgO nanocomposites for mid-infrared solid-state lasers.

Mid-infrared, solid-state laser materials face three main challenges: (1) need to dissipate heat generated in lasing; (2) luminescence quenching by multiphonon relaxation; and (3) trade-off in high thermal conductivity and small maximum phonon energy. We are tackling these challenges by synthesizing a ceramic nanocomposite in which multiple phases will be incorporated into the same structure. The undoped majority species, MgO, will be the main carrier of high thermal conductivity, and the minority species, Er:Y2O3, will have low maximum phonon energy. There is also an inherent challenge in attempting to make a translucent part from a mixture of two different materials with two different indexes of refraction. A simple, co-precipitation technique has been developed in which both components are synthesized in situ to obtain intimate mixing. These powders compare well to commercially available ceramics, including their erbium spectroscopy, even when mixed as a composite, and can be air-fired to ∼96% of theoretical density, yielding translucent parts. As the amount of Er:Y2O3 increases, the translucency decreases as the number of scattering sites start to coalesce into large patches. If the amount of Er:Y2O3 is sufficiently small and dispersed, the yttria grains will be pinned as individuals in a sea of MgO, leading to optimal translucency.

Tree-oriented silviculture: a new approach for coppice stands

Abstract: Tree-oriented silviculture is an innovative approach of forest management aimed at enhancing a limited number of early-selected crop trees whose growth is favored over the full rotation period by applying frequent thinning in their neighborhood. This approach was originally applied to high forests, but can also be applied to coppices to maintain or improve biodiversity by selecting valuable timber trees and/or minority species as target trees. The main limitation of this silvicultural option is the need of specialized and qualified operators in all the phases, from selection of crop trees to logging operations. In this study, experimental trials were established by the Forest Research Centre of Arezzo (Italy) to verify the suitability of this approach to different structural and enviromental conditions. In coppices characterized by fast growing species such as chestnut, tree-oriented silviculture has been applied to a limited number of crop trees (50-100 ha) to obtain more valuable and larger-sized assortments in a shorter rotation period, reducing at the same time the silvicultural costs. In mixed coppices, where the ordinary management (coppicing) was applied, the abandonment or the conversion into high forest gave rise to a progressive loss in terms of species composition. Contrastingly, thinning focused around a few (5-20) trees of sporadic species allowed to maintain a high level of biodiversity, and led to favorable conditions for growth and regeneration of these species.

Pre-treatment minority HIV-1 drug resistance mutations and long term virological outcomes: is prediction possible?

BackgroundAlthough the use of highly active antiretroviral therapy in HIV positive individuals has proved to be effective in suppressing the virus to below detection limits of commonly used assays, virological failure associated with drug resistance is still a major challenge in some settings. The prevalence and effect of pre-treatment resistance associated variants on virological outcomes may also be underestimated because of reliance on conventional population sequencing data which excludes minority species. We investigated long term virological outcomes and the prevalence and pattern of pre-treatment minority drug resistance mutations in individuals initiating HAART at a local HIV clinic.MethodsPatient’s records of viral load results and CD4 cell counts from routine treatment monitoring were used and additional pre-treatment blood samples for Sanger sequencing were obtained. A selection of pre-treatment samples from individuals who experienced virological failure were evaluated for minority resistance associated mutations to 1 % prevalence and compared to individuals who achieved viral suppression.ResultsAt least one viral load result after 6 months or more of treatment was available for 65 out of 78 individuals followed for up to 33 months. Twenty (30.8 %) of the 65 individuals had detectable viremia and eight (12.3 %) of them had virological failure (viral load > 1000 RNA copies/ml) after at least 6 months of HAART. Viral suppression, achieved by month 8 to month 13, was followed by low level viremia in 10.8 % of patients and virological failure in one patient after month 20. There was potentially reduced activity to Emtricitabine or Tenofovir in three out of the eight cases in which minority drug resistance associated variants were investigated but detectable viremia occurred in one of these cases while the activity of Efavirenz was generally reduced in all the eight cases.ConclusionsEarly viral suppression was followed by low level viremia for some patients which may be an indication of failure to sustain viral suppression over time. The low level viremia may also be representing early stages of resistance development. The mutation patterns detected in the minority variants showed potential reduced drug sensitivity which highlights their potential to dominate after treatment initiation.Trial registrationNot applicable.Electronic supplementary materialThe online version of this article (doi:10.1186/s12985-016-0628-x) contains supplementary material, which is available to authorized users.

Identification of Oligosaccharides in Feces of Breast-fed Infants and Their Correlation with the Gut Microbial Community

Glycans in breast milk are abundant and found as either free oligosaccharides or conjugated to proteins and lipids. Free human milk oligosaccharides (HMOs) function as prebiotics by stimulating the growth of beneficial bacteria while preventing the binding of harmful bacteria to intestinal epithelial cells. Bacteria have adapted to the glycan-rich environment of the gut by developing enzymes that catabolize glycans. The decrease in HMOs and the increase in glycan digestion products give indications of the active enzymes in the microbial population. In this study, we quantitated the disappearance of intact HMOs and characterized the glycan digestion products in the gut that are produced by the action of microbial enzymes on HMOs and glycoconjugates from breast milk. Oligosaccharides from fecal samples of exclusively breast-fed infants were extracted and profiled using nanoLC-MS. Intact HMOs were found in the fecal samples, additionally, other oligosaccharides were found corresponding to degraded HMOs and non-HMO based compounds. The latter compounds were fragments of N-glycans released through the cleavage of the linkage to the asparagine residue and through cleavage of the chitobiose core of the N-glycan. Marker gene sequencing of the fecal samples revealed bifidobacteria as the dominant inhabitants of the infant gastrointestinal tracts. A glycosidase from Bifidobacterium longum subsp. longum was then expressed to digest HMOs in vitro, which showed that the digested oligosaccharides in feces corresponded to the action of glycosidases on HMOs. Similar expression of endoglycosidases also showed that N-glycans were released by bacterial enzymes. Although bifidobacteria may dominate the gut, it is possible that specific minority species are also responsible for the major products observed in feces. Nonetheless, the enzymatic activity correlated well with the known glycosidases in the respective bacteria, suggesting a direct relationship between microbial abundances and catabolic activity.

Structure diagram of binary Lennard-Jones clusters.

We analyze the structure diagram for binary clusters of Lennard-Jones particles by means of a global optimization approach for a large range of cluster sizes, compositions, and interaction energies and present a publicly accessible database of 180 000 minimal energy structures (http://softmattertheory.lu/clusters.html). We identify a variety of structures such as core-shell clusters, Janus clusters, and clusters in which the minority species is located at the vertices of icosahedra. Such clusters can be synthesized from nanoparticles in agglomeration experiments and used as building blocks in colloidal molecules or crystals. We discuss the factors that determine the formation of clusters with specific structures.

Tunable filter Raman spectroscopy of purified semiconducting and metallic carbon nanotubes

Tunable filter Raman spectroscopy is used to efficiently produce Raman excitation maps of unpurified and type-purified single walled carbon nanotubes (SWCNTs). Maps with fine excitation resolution (1 nm) are created over a wide wavelength range (727 to 980 nm), extending from metallic to semiconducting resonances. At a given wavelength, the wide bandwidth (>3,000 cm–1) allows the comparison of the G band with the radial breathing mode (RBM), and shows the 2D band and other less prominent bands. Materials examined included unsorted powders, aqueous sorted semiconductors, aqueous sorted metals, and polyfluorene sorted semiconductors in toluene. The Raman excitation profiles of the G band are broad, relative to the RBM bands. The maps offer evidence of minority species contamination, except in the case of the polyfluorene sorted semiconductors. Tunable Raman spectroscopy data help validate the simpler fixed wavelength Raman spectroscopy approaches to purity assessment.

Complete Genome Sequence of a Reference Stock of Simian Immunodeficiency Virus RNA (SIVmac251/32H/L28) Determined by Deep Sequencing.

A reference preparation for simian immunodeficiency virus (SIV) RNA nucleic acid assays was characterized by complete genome deep sequencing. The entire coding sequence and flanking long terminal repeats, including minority species, were determined. This information will inform SIV research investigations and aid evaluation and development of amplification assays for SIV RNA quantification.

Nanoscale Solvation Leads to Spontaneous Formation of a Bicarbonate Monolayer on Rutile (110) under Ambient Conditions: Implications for CO2 Photoreduction

The chemical state of a catalyst in operando is particularly important for catalysts that target minority species, such as atmospheric CO2 which has a concentration of only 400 ppm. A reaction can be promoted by the selective binding of reactants or hindered by molecules that block active sites. We show that adsorbed CO2, a very weakly bonded species on TiO2, is unlikely to play the key role in CO2 photoreduction under ambient conditions, at least on rutile (110), as the vast majority of unsaturated Ti sites are terminated by a different, much more strongly bound carbonaceous species: adsorbed bicarbonate (HCO3). Using a combination of scanning tunneling microscopy (STM) and surface spectroscopies, we show that atmospheric CO2 readily and stably displaces adsorbed H2O on rutile (110), creating a self-assembled monolayer of HCO3 and H that is stable at room temperature even in vacuum. This reaction occurs on near-ideal, stoichiometric rutile (110) and does not require surface defects, such as O vacancies, ...

Optimizing a custom tiling microarray for low input detection and identification of unamplified virus targets

Viruses are major pathogens causing foodborne illnesses and are often present at low levels in foods, thus requiring sensitive techniques for their detection in contaminated foods. The lack of efficient culture methods for many foodborne viruses and the potential for multi-species viral contamination have driven investigation toward non-amplification based methods for virus detection and identification. A custom DNA microarray (FDA_EVIR) was assessed for its sensitivity in the detection and identification of low-input virus targets, human hepatitis A virus, norovirus, and coxsackievirus, individually and in combination. Modifications to sample processing were made to accommodate low input levels of unamplified virus targets, which included addition of carrier cDNA, RNase treatment, and optimization of DNase I-mediated target fragmentation. Amplification-free detection and identification of foodborne viruses were achieved in the range of 250–500 copies of virus RNA. Alternative data analysis methods were employed to distinguish the genotypes of the viruses particularly at lower levels of target input and the single probe-based analysis approach made it possible to identify a minority species in a multi-virus complex. The oligonucleotide array is shown to be a promising platform to detect foodborne viruses at low levels close to what are anticipated in food or environmental samples.

Overwintering of Vineyard Yeasts: Survival of Interacting Yeast Communities in Grapes Mummified on Vines.

The conversion of grape must into wine involves the development and succession of yeast populations differing in species composition. The initial population is formed by vineyard strains which are washed into the must from the crushed grapes and then completed with yeasts coming from the cellar environment. As the origin and natural habitat of the vineyard yeasts are not fully understood, this study addresses the possibility, that grape yeasts can be preserved in berries left behind on vines at harvest until the spring of the next year. These berries become mummified during the winter on the vines. To investigate whether yeasts can survive in these overwintering grapes, mummified berries were collected in 16 localities in the Tokaj wine region (Hungary-Slovakia) in early March. The collected berries were rehydrated to recover viable yeasts by plating samples onto agar plates. For the detection of minority species which would not be detected by direct plating, an enrichment step repressing the propagation of alcohol-sensitive yeasts was also included in the process. The morphological, physiological, and molecular analysis identified 13 basidiomycetous and 23 ascomycetous species including fermentative yeasts of wine-making relevance among the 3879 isolates. The presence of viable strains of these species demonstrates that the grapes mummified on the vine can serve as a safe reservoir of yeasts, and may contribute to the maintenance of grape-colonizing yeast populations in the vineyard over years, parallel with other vectors and habitats. All basidiomycetous species were known phylloplane yeasts. Three Hanseniaspora species and pigmented Metschnikowia strains were the most frequent ascomycetes. Other fermentative yeasts of wine-making relevance were detected only in the enrichment cultures. Saccharomyces (S. paradoxus, S. cerevisiae, and S. uvarum) were recovered from 13% of the samples. No Candida zemplinina was found. The isolates with Aureobasidium morphology turned out to belong to Aureobasidium subglaciale, Kabatiella microsticta, or Columnosphaeria fagi. The ascomyceteous isolates grew at high concentrations of sugars with Wickerhamomyces anomalus being the most tolerant species. Complex interactions including antagonism (growth inhibition, contact inhibition, competition for nutrients) and synergism (crossfeeding) among the isolates and with Botrytis cinerea shape the composition of the overwintering communities.

Complete Genome Sequence of the WHO International Standard for HIV-2 RNA Determined by Deep Sequencing.

The World Health Organization (WHO) International Standard for HIV-2 RNA nucleic acid assays was characterized by complete genome deep sequencing. The entire coding sequence and flanking long terminal repeats (LTRs), including minority species, were assigned subtype A. This information will aid design, development, and evaluation of HIV-2 RNA amplification assays.

Accounting for the Dynamic Oxidative Behavior of Nickel Anodes.

The dynamic behavior of the anodic peak for amorphous nickel oxy/hydroxide (a-NiOx) films in basic media was investigated. Chronocoulometry of films with known nickel concentrations reveals that a total of four electrons per nickel site comprise the signature anodic peak at 1.32 V during the first oxidative scan, and two electrons are passed through the associated cathodic peak on the reverse scan. The anodic and cathodic signals each contain two electrons on the successive scans. Catalytic oxygen evolution reaction (OER) was detected within the anodic peak, which is at a lower potential than is widely assumed. In order to rationalize these experimental results, we propose that the four-electron oxidation event is the conversion of the film from nickel(II) hydroxide ([Ni(II)-OH](-)) to a higher valent nickel peroxide species (e.g., Ni(IV)-OO or Ni(III)-OO·). The subsequent reduction of the nickel peroxide species is confined by a chemical step resulting in the accumulation of [Ni(II)-OOH](-), which is then oxidized by two electrons to form Ni(IV)-OO during the subsequent oxidative scan on the time scale of a cyclic voltammetric experiment. Our proposed mechanism and the experimental determination that each nickel site is oxidized by four electrons helps link the myriad of seemingly disparate literature data related to OER catalysis by nickel electrodes. The faster catalysis that occurs at higher oxidative potentials is derived from a minority species and is not elaborated here.

Fast Folding Dynamics of an Intermediate State in RNase H Measured by Single-Molecule FRET.

We have studied the folding kinetics of the core intermediate (I) state of RNase H by using a combination of single-molecule FRET (smFRET) and hidden Markov model analysis. To measure fast dynamics in thermal equilibrium as a function of the concentration of the denaturant GdmCl, a special FRET labeled variant, RNase H 60-113, which is sensitive to folding of the protein core, was immobilized on PEGylated surfaces. Conformational transitions between the unfolded (U) state and the I state could be described by a two-state model within our experimental time resolution, with millisecond mean residence times. The I state population was always a minority species in the entire accessible range of denaturant concentrations. By introducing the measured free energy differences between the U and I states as constraints in global fits of the GdmCl dependence of FRET histograms of a differently labeled RNase H variant (RNase H 3-135), we were able to reveal the free energy differences and, thus, population ratios of all three macroscopic state ensembles, U, I and F (folded state) as a function of denaturant concentration.

Electrospray mass spectrometry as a tool to characterize phospholipid composition of plant cakes

Phospholipids (PL) are components of increased value in nutritional applications, especially those rich in polyunsaturated fatty acids (PUFA) such as α‐linolenic acid (ALA, 18:3 n‐3) and linoleic acid (LA, 18:2 n‐6). Currently, the oil processing industry generates by‐products in the form of oilseed and plant cakes that can be valorized for food/feed applications. With the aim of diversifying PL sources and improving their identification in terms of fatty acid (FA) composition, plant cakes obtained from five different sources (camelina, flaxseed, hemp, sesame, walnut) were extracted and analyzed by lipidomics approach using three analytical methods of mass spectrometry (MS): (i) shotgun; (ii) reverse phase liquid chromatography (RPLC) in multiple reaction monitoring (MRM) mode; and (iii) normal phase liquid chromatography (NPLC) with data dependant scan MS fragmentation. We obtained complementary information: while shotgun allowed identifying PL species, RPLC associated to MRM enabled to access high sensitivity and to focus on minority species. Then, NPLC in data dependant scan led to the identification of lysophospholipids and cardiolipin species besides phosphatidylcholine (PC). Among, the five plant cakes analyzed, camelina cake showed the highest percentage of ALA. If ALA was also found in flaxseed and hemp cakes, it was in a lesser extent. Moreover, ALA was located on the sn‐2 position of the glycerol backbone, a valuable position for nutritional applications.Practical applications: The food industry generates large amounts of by‐products, and most of them remain unused. Among them, degumming pastes, i.e., by‐products from the oil refining process, could be valuable sources of phospholipids (PL). These phospholipids present interesting properties, as emulsifiers, thickening agents, or antioxidants, for food or cosmetic industries. Moreover, depending on the plant source, the fatty acid composition in phospholipids could be different from that of the oil (mainly composed of triglycerides instead of phospholipids), especially for α‐linolenic acid (ALA, 18:3 n‐3). Among, the five plant cakes analyzed (camelina, flaxseed, hemp, sesame, walnut), camelina cake showed the highest percentage of ALA. If ALA was also found in flaxseed and hemp cakes, it was in a lesser extent. Moreover, ALA was located in the sn‐2 position of the glycerol, a valuable position for nutritional applications. On the whole, using powerful and complementary analytical procedures for PL characterization allowed widening the potential sources of this type of lipids.Workflow of the plant cake lipid analysis based on three analytical methods of mass spectrometry.