compositionality
Dotaz
Zobrazit nápovědu
Although metagenomic sequencing is now the preferred technique to study microbiome-host interactions, analyzing and interpreting microbiome sequencing data presents challenges primarily attributed to the statistical specificities of the data (e.g., sparse, over-dispersed, compositional, inter-variable dependency). This mini review explores preprocessing and transformation methods applied in recent human microbiome studies to address microbiome data analysis challenges. Our results indicate a limited adoption of transformation methods targeting the statistical characteristics of microbiome sequencing data. Instead, there is a prevalent usage of relative and normalization-based transformations that do not specifically account for the specific attributes of microbiome data. The information on preprocessing and transformations applied to the data before analysis was incomplete or missing in many publications, leading to reproducibility concerns, comparability issues, and questionable results. We hope this mini review will provide researchers and newcomers to the field of human microbiome research with an up-to-date point of reference for various data transformation tools and assist them in choosing the most suitable transformation method based on their research questions, objectives, and data characteristics.
- Klíčová slova
- compositionality, data preprocessing, human microbiome, machine learning, metagenomics data, normalization,
- Publikační typ
- časopisecké články MeSH
- přehledy MeSH
Owing to their exceptional mechanical, electronic, and phononic transport properties, compositionally complex alloys, including high-entropy alloys, represent an important class of materials. However, the interplay between chemical disorder and electronic correlations, and its influence on electronic structure-derived properties, remains largely unexplored. This is addressed for the archetypal CrMnFeCoNi alloy using resonant and valence band photoemission spectroscopy, electrical resistivity, and optical conductivity measurements, complemented by linear response calculations based on density functional theory. Utilizing dynamical mean-field theory, correlation signatures and damping in the spectra are identified, highlighting the significance of many-body effects, particularly in states distant from the Fermi edge. Electronic transport remains dominated by disorder and potentially short-range order, especially at low temperatures, while visible-spectrum optical conductivity and high-temperature transport are influenced by short quasiparticle lifetimes. These findings improve our understanding of element-specific electronic correlations in compositionally complex alloys and facilitate the development of advanced materials with tailored electronic properties.
- Publikační typ
- časopisecké články MeSH
We studied concentrations of 34 essential and non-essential elements in samples of edible Bay Bolete (Imleria badia) mushrooms added by samples of the growing substrate and bioavailable fraction. The samples were collected from six forested sites affected differently by industrial pollution and underlain by compositionally contrasting bedrock: granite, amphibolite, and peridotite. In all cases, mushrooms behaved as a bioconcentrating system for elements such as Ag, K, P, Rb, S, and Se (BCF > 1) being a bioexcluding system for the rest of the elements analyzed (BCF < 1). Most analyzed elements displayed moderate to high within-mushroom mobility being accumulated preferably in the apical parts of the mushroom's fruiting body (TF > 1). The highest mobility was demonstrated by Cd and Cu. Sodium was the only element with significantly low mobility (TF < 1), and it accumulated preferably in the stipe. Imleria badia seems to be sensitive to the accumulation of elements such as As, Cd, and Pb from the atmospheric deposits. Specific geochemistry of the growing substrate was reflected to different extend in the accumulation of elements such as Ag, Cu, Rb, S, Al, Ca, Fe, Ba, and Na in the mushroom's fruiting bodies.
- Klíčová slova
- Bedrock, Mushroom, Soil, Trace elements, Translocation, Uptake,
- MeSH
- Agaricales * chemie MeSH
- monitorování životního prostředí MeSH
- stopové prvky * analýza MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- stopové prvky * MeSH
The hydrogen sorption properties of single-phase bcc (TiVNb)100-xCrx alloys (x = 0-35) are reported. All alloys absorb hydrogen quickly at 25 °C, forming fcc hydrides with storage capacity depending on the Cr content. A thermodynamic destabilization of the fcc hydride is observed with increasing Cr concentration, which agrees well with previous compositional machine learning models for metal hydride thermodynamics. The steric effect or repulsive interactions between Cr-H might be responsible for this behavior. The cycling performances of the TiVNbCr alloy show an initial decrease in capacity, which cannot be explained by a structural change. Pair distribution function analysis of the total X-ray scattering on the first and last cycled hydrides demonstrated an average random fcc structure without lattice distortion at short-range order. If the as-cast alloy contains a very low density of defects, the first hydrogen absorption introduces dislocations and vacancies that cumulate into small vacancy clusters, as revealed by positron annihilation spectroscopy. Finally, the main reason for the capacity drop seems to be due to dislocations formed during cycling, while the presence of vacancy clusters might be related to the lattice relaxation. Having identified the major contribution to the capacity loss, compositional modifications to the TiVNbCr system can now be explored that minimize defect formation and maximize material cycling performance.
- Klíčová slova
- cycling, hydrogen storage, multiprincipal element alloys, pair distribution function, positron annihilation spectroscopy, thermodynamics,
- Publikační typ
- časopisecké články MeSH
We conducted a study of elemental compositions of Xerocomellus chrysenteron samples accompanied by samples of related substrate soils. All samples were collected during the harvesting seasons 2021 and 2022 from three forested sites almost unpolluted by recent human activities and underlain by contrasting bedrock (granite, amphibolite, and serpentinite). Elements such as Ag, Cd, K, P, Rb, S, Se, and Zn were the main elements enriched in the mushroom's fruiting bodies relative to the substrate. Concentrations of most elements in mushrooms were not site-dependent, with only Ag, As, Rb, and Se concentrations significantly depending on the bedrock composition. Some elements analyzed in mushrooms displayed temporal features, but such features were not systematic and varied for each element. Most analyzed elements were distributed unevenly within the mushroom's fruiting bodies, with apical parts generally enriched in mobile elements. Mushrooms influenced concentrations of Ag, Cd, K, and Rb and a few other elements in the substrate via uptake, but such influence was very limited and can be responsible for only 2.5-11.5% of total depletion of the affected substrate in the named elements.
- Klíčová slova
- Bedrock, Mushroom, Soil, Trace elements, Translocation, Uptake,
- MeSH
- Agaricales * MeSH
- Basidiomycota * MeSH
- kadmium MeSH
- lidé MeSH
- monitorování životního prostředí MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- kadmium MeSH
To understand how the gut microbiome is impacted by human adaptation to varying environments, we explored gut bacterial communities in the BaAka rainforest hunter-gatherers and their agriculturalist Bantu neighbors in the Central African Republic. Although the microbiome of both groups is compositionally similar, hunter-gatherers harbor increased abundance of Prevotellaceae, Treponema, and Clostridiaceae, while the Bantu gut microbiome is dominated by Firmicutes. Comparisons with US Americans reveal microbiome differences between Africans and westerners but show western-like features in the Bantu, including an increased abundance of predictive carbohydrate and xenobiotic metabolic pathways. In contrast, the hunter-gatherer gut shows increased abundance of predicted virulence, amino acid, and vitamin metabolism functions, as well as dominance of lipid and amino-acid-derived metabolites, as determined through metabolomics. Our results demonstrate gradients of traditional subsistence patterns in two neighboring African groups and highlight the adaptability of the microbiome in response to host ecology.
- MeSH
- Bacteroidetes genetika MeSH
- bakteriální geny MeSH
- bakteriální RNA genetika MeSH
- černoši nebo Afroameričané MeSH
- černoši MeSH
- Firmicutes genetika MeSH
- genové regulační sítě MeSH
- lidé MeSH
- molekulární typizace MeSH
- paleolitická dieta MeSH
- RNA ribozomální 16S genetika MeSH
- sekvenční analýza RNA MeSH
- střevní mikroflóra genetika MeSH
- západní dieta MeSH
- Check Tag
- lidé MeSH
- mužské pohlaví MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- srovnávací studie MeSH
- Geografické názvy
- Spojené státy americké MeSH
- Středoafrická republika MeSH
- Názvy látek
- bakteriální RNA MeSH
- RNA ribozomální 16S MeSH
Highly porous metal-organic frameworks (MOFs), which have undergone exciting developments over the past few decades, show promise for a wide range of applications. However, many studies indicate that they suffer from significant stability issues, especially with respect to their interactions with water, which severely limits their practical potential. Here we demonstrate how the presence of 'sacrificial' bonds in the coordination environment of its metal centres (referred to as hemilability) endows a dehydrated copper-based MOF with good hydrolytic stability. On exposure to water, in contrast to the indiscriminate breaking of coordination bonds that typically results in structure degradation, it is non-structural weak interactions between the MOF's copper paddlewheel clusters that are broken and the framework recovers its as-synthesized, hydrated structure. This MOF retained its structural integrity even after contact with water for one year, whereas HKUST-1, a compositionally similar material that lacks these sacrificial bonds, loses its crystallinity in less than a day under the same conditions.
Heat capacity measurements were performed for Se, Se90Te10, Se80Te20, and Se70Te30 materials in the 230-630 K temperature range. Both glassy and crystalline Cp dependences were found to be identical within the experimental error. The compositional dependence of the N-type undercooled liquid Cp evolution was explained on the basis of free-volume theory; vibrational and chemical contributions to heat capacity were found to be roughly similar for all Se-Te compositions. The thermal behavior in the Se-Te chalcogenide system was thoroughly studied: glass transition, cold crystallization, and melting were investigated in dependence on composition and various experimental conditions (heating rate, particle size, and pre-nucleation period). The kinetics of the structural relaxation and crystallization processes are described in terms of the Tool-Narayanaswamy-Moynihan and Johnson-Mehl-Avrami models. The complexity of these processes is thoroughly discussed with regard to the compositionally determined changes of molecular structures. The discussion is conducted in terms of the mutual interplay between the thermodynamics and kinetics in this system.
- Publikační typ
- časopisecké články MeSH
The ferromagnetic shape memory (FSM) behavior of glass-coated Fe47‑x Mn24+x Ga29 (x = 0-8 at. %) microwires has been investigated through temperature-dependent magnetization and ac magnetic susceptibility measurements. Magnetization measurements as a function of temperature reveal an abrupt increase and decrease in magnetization upon cooling and heating, respectively, indicating characteristic thermal hysteresis (ΔT hys ) behavior typically associated with a magnetic-field-induced "diffusionless" martensitic transformation. The magnitude and width of ΔT hys are strongly correlated with the Fe/Mn atomic ratio; notably, the Fe45Mn26Ga29 microwire exhibits a very large ΔT hys width of 98 K, which is attributed to local deformation involving the motion of Fe and Mn atoms. Furthermore, an antiferromagnetic transition is observed in a low-temperature region, shifting from 22 to 41 K depending on composition. This shift is attributed to variations in local exchange interactions arising from unequal occupation of Fe and Mn 3d orbitals. These findings highlight a compositionally driven design strategy that enables precise tuning of FSM behavior, making Fe-Mn-Ga microwires promising candidates for use in tunable magnetic actuation and sensing technologies.
- Klíčová slova
- Fe-based Heusler alloys, L21 structure, Martensitic transformation, ac magnetic susceptibility, magnetic hysteresis, magnetic shape memory,
- Publikační typ
- časopisecké články MeSH
Metals are the backbone of manufacturing owing to their strength and formability. Compared to polymers they have high mass density. There is, however, one exception: magnesium. It has a density of only 1.7 g/cm3, making it the lightest structural material, 4.5 times lighter than steels, 1.7 times lighter than aluminum, and even slightly lighter than carbon fibers. Yet, the widespread use of magnesium is hampered by its intrinsic brittleness. While other metallic alloys have multiple dislocation slip systems, enabling their well-known ductility, the hexagonal lattice of magnesium offers insufficient modes of deformation, rendering it intrinsically brittle. We have developed a quantum-mechanically derived treasure map which screens solid solution combinations with electronic bonding, structure and volume descriptors for similarity to the ductile magnesium-rare earth alloys. Using this insight we synthesized a surprisingly simple, compositionally lean, low-cost and industry-compatible new alloy which is over 4 times more ductile and 40% stronger than pure magnesium. The alloy contains 1 wt.% aluminum and 0.1 wt.% calcium, two inexpensive elements which are compatible with downstream recycling constraints.
- Publikační typ
- časopisecké články MeSH
