Site Occupancy Research Articles

Spatiotemporal patterns of small carnivores in a human-dominated forest landscape shared with apex predators

ContextRapid increases in human population and the resulting apex predator defaunation are affecting the spatial and temporal dynamics of small carnivores, with uncertain consequences for the ecological community. Documenting the spatiotemporal impact of apex predators and human disturbance on small carnivores becomes crucial to managers overseeing carnivore persistence.ObjectivesAssessing the spatiotemporal responses of five small carnivores to two apex carnivores (tigers Panthera tigris, leopards P. pardus) and human disturbances in Northeast Asia.MethodsWe first applied an occupancy-modelling framework to test whether site occupancy of small carnivores depended on apex carnivore and human disturbance. Then, we calculated the overlap of activity periods between small carnivores and apex predators, as well as the overlap with human/cattle activities using kernel density functions. Finally, we used cross-wavelet analysis to determine the temporal coherence between related species.ResultsSpatially, most small carnivores were independent of tigers and leopards. Compared to apex predators, small carnivores were more likely to use areas with high human activity. Temporally, small carnivores exhibited highly heterogeneous diel overlaps and more in-phase activities with apex predators. However, we found a significant difference in the mean activity time between apex and small carnivore. Meanwhile, small carnivores exhibited low levels of temporal overlap and more out-phase temporal coherence with humans and cattle at shorter periods.ConclusionsApex carnivores and human disturbances don’t limit the space use or intensity of use of small carnivores. Temporal segregation and anti-phase activity are the key role for small carnivores to minimize intraguild predation and human persecution.

How do ecologists estimate occupancy in practice?

Over 20 years ago, ecologists were introduced to the site occupancy model (SOM) for estimating occupancy rates from detection‐nondetection data. In the ensuing decades, the SOM and its hierarchical modeling extensions have become mainstays of quantitative ecology, and estimating occupancy rates has become one of the most common applications of ecological field data. Here, we review 364 peer‐reviewed articles published between 2019–2021 that estimated occupancy. We first document broad patterns in study design and statistical methods to provide educators, developers of methodology and software, and ecologists with a clear picture of the landscape of methodologies used to estimate animal occupancy. Second, we conduct a focused review of a subset of 98 papers that applied the hierarchical SOM, drawing from methodological literature to identify discrepancies between SOM applications and methodological best practices. We discuss limits to statistical power, issues with model checking and model selection procedures, potential problems arising from unmodeled non‐independence, and reproducibility. We highlight areas of rapid advancement in interpreting animal occupancy related to animal movement, imperfect detection, and the occupancy–density relationship. We aim to help readers understand the landscape of methods available, motivate shifts toward robust and reproducible science, and inspire new software and methodological research.

More Pieces of the Puzzle: Transient State Analysis of Dihydroorotate Dehydrogenase B from Lactoccocus lactis.

Dihydroorotate dehydrogenases (DHODs) catalyze the transfer of electrons between dihydroorotate and specific oxidant substrates. Class 1B DHODs (DHODBs) use NAD+ as the oxidant substrate and have a heterodimeric structure that incorporates two active sites, each with a flavin cofactor. One Fe2S2 center lies roughly equidistant between the flavin isoalloxazine rings. This arrangement allows for simultaneous association of reductant and oxidant substrates. Here we describe a series of experiments designed to reveal sequences and contingencies in DHODB chemistry. From these data it was concluded that the resting state of the enzyme is FAD•Fe2S2•FMN. Reduction by either NADH or DHO results in two electrons residing on the FMN cofactor that has a 47 mV higher reduction potential than the FAD. The FAD•Fe2S2•FMNH2 state accumulates with a bisemiquinone state that is an equilibrium accumulation formed from a partial transfer of one electron to the FAD. Pyrimidine reduction is reliant on the availability of the Cys135 proton, as the C135S variant slows orotate reduction by ∼40-fold. The rate of pyrimidine reduction is modulated by occupancy of the FAD site; NADH•FAD•Fe2S2•FMNH2•orotate complex can reduce the pyrimidine at 16 s-1, while NAD+•FAD•Fe2S2•FMNH2•orotate complex reduces the pyrimidine at 5.4 s-1 and the FAD•Fe2S2•FMNH2•orotate complex at 0.6 s-1. This set of effector states account for the apparent discrepancy in the slowest rate observed in transient state single turnover reactions with limiting NADH and the limiting rate observed in steady state.

A macroarchaeological view of mobility

Archaeological evidence of mobility is often analyzed using ethnographic-scale models of individual foraging trips and residential moves as a point of reference. Due to site formation processes and the limitations of geochronology, the archaeological record rarely offers the kind of fine-grained resolution needed to identify mobility events at this scale. Here we explore an alternative, macroarchaeological approach that asks how site occupation patterns in a region balance the evolutionary tradeoff between exploration and exploitation. We use a statistical point process model that equates independent-in-time occupations with mobility-driven exploration and dependent-in-time occupations with mobility-driven exploitation. We evaluate the theoretical expectations against the archaeological record of North America using radiocarbon dates from multi-occupation sites. We find strong clustering at short waiting-time intervals of less than under 1000 years, consistent with a model of mobility-driven exploitation at those scales. At longer time scales, waiting times are consistent with a model of mobility-driven exploration. Implications for social learning and niche construction models are explored.

Li+ induced site occupation engineering in Bi3+ activated spinel-type phosphor for multiple optoelectronic applications

The utilization of phosphors for information storage, data encryption, temperature sensing, etc. has been becoming a research hotspot. However, modulating dynamic and pluralistic phosphor emissions is still a huge challenge. Herein, we developed a Li+-induced site occupation engineering in Bi3+ activated Mg2SnO4 (MSO) phosphor with multiple emissions and dynamic afterglow for versatile applications. Experiments and first-principles calculations demonstrated that Bi3+ would simultaneously enter [MgO4] tetrahedron and [SnO6] octahedron to present red and blue emissions, respectively. As Li+ ions were introduced into Mg2SnO4:Bi3+, the preferably generated [LiO4] could hinder the Bi3+ from entering [MgO4] units, so as to force Bi3+ to substitute Sn4+ in [SnO6], thereby leading to strengthened blue emission. Due to the distinct luminescence decay of Bi3+ in tetrahedron and octahedron units, the luminescence colors were regulated from blue to purple and red with enhancing temperature upon UV light excitation, being suitable for luminescence intensity ratio (LIR) thermometer. Moreover, by virtue of the afterglow properties originating from the inherent oxygen vacancies of Mg2SnO4, the dynamic information encryption and anti-counterfeiting by Mg2SnO4:Bi3+, Li+ were achieved. The proposed site occupation engineering can certainly spur several innovative ideas in manufacturing high-performance phosphors for versatile applications.

Kr Adsorption in Porous Carbons: Temperature-Dependent Experimental and Computational Studies†.

The temperature dependence of the adsorption energy of krypton adsorption on activated carbon materials was studied by experiment and simulation. Adsorption isotherms were measured at temperatures from 250 to 330 K and analyzed with Henry's law. The adsorption energy determined from these measurements was found to weaken by more than 10% in this range. Slit pore widths for simulations in this work were modeled by the removal of integral numbers of planes in graphite. Vibrational dynamics of the krypton adsorbate and the carbon atom adsorbent were calculated with the stochastic temperature-dependent effective potential (sTDEP) method, using energetics from density functional theory (DFT) with the many-body dispersion energy method (MBD). Thermal displacements of carbon atoms had a negligible effect on the adsorption energy. The width of the slit pore had the greatest effect on the surface dynamics and the energies of the adsorbate atoms at different temperatures. Assuming a distribution of pore widths, the Boltzmann distribution of site occupancies causes a large weakening of the thermally averaged adsorption energy at higher temperatures.

One-Pot Synthesis of (CrMnFeCoNi)Ox High-Entropy Oxides for Efficient Catalytic Oxidation of Propane: A Promising Substitute for Noble Metal Catalysts.

The efficient catalytic oxidation of propane, as a short-chain alkane, remains challenging in environmental catalysis. High-entropy oxides (HEOs) exhibit advantages in abundant and well-dispersed elemental composition, exceptional thermal stability, and enriched lattice defects. Herein, (CrMnFeCoNi)Ox HEO catalysts are successfully synthesized by using a continuous hydrothermal flow synthesis (CHFS) route, without any subsequent calcination processes. This route yields HEOs with fine particle sizes, high specific surface areas, and abundant near-surface lattice oxygen compared to the traditional coprecipitation method. Notably, the propane conversion over the CHFS-made (CrMnFeCoNi)Ox HEO reaches 90% at 255 °C, with an apparent activation energy of 53.2 kJ/mol, mainly attributed to its enriched lattice oxygen and enhanced oxygen mobility that prevent the accumulation of acetates and the consequent occupation of active sites. In comparison to commercial Pt/Al2O3 and Pd/Al2O3, (CrMnFeCoNi)Ox HEO demonstrates exceptional activity and can maintain long-term stability under high-temperature (upon 650 °C) and moisture-rich conditions (at 2-10 vol %). These attributes highlight its potential as a promising substitute for noble metal catalysts in industrial applications.

Unveiling the structural proteome of an Alzheimer's disease rat brain model.

Studying native protein structures at near-atomic resolution in a crowded environment presents challenges. Consequently, understanding the structural intricacies of proteins within pathologically affected tissues often relies on mass spectrometry and proteomic analysis. Here, we utilized cryoelectron microscopy (cryo-EM) and the Build and Retrieve (BaR) method to investigate protein complexes' structural characteristics such as post-translational modification, active site occupancy, and arrested conformational state in Alzheimer's disease (AD) using brain lysate from a rat model (TgF344-AD). Our findings reveal novel insights into the architecture of these complexes, corroborated through mass spectrometry analysis. Interestingly, it has been shown that the dysfunction of these protein complexes extends beyond AD, implicating them in cancer, as well as other neurodegenerative disorders such as Parkinson's disease, Huntington's disease, and schizophrenia. By elucidating these structural details, our work not only enhances our understanding of disease pathology but also suggests new avenues for future approaches in therapeutic intervention.

Effect of anisotropy field on the resonance frequency and reflection loss shift characteristics of barium hexaferrite ceramics

Abstract For this study, a modified barium hexaferrite based microwave and radar absorbing material was used. Synthesis and characterization of BaFe(12−2x)(MnTi) x O19 (0.1 ≤ x ≤ 1.0) have been prepared by solid state reaction method. The x-ray diffraction patterns reveal that all samples only crystallized into M-type barium hexaferrite after calcination at 1200 °C. Surface morphology images show that the hexagonal flake-like particle is formed at the initial stages of the Mn-Ti substitution level. The magnetic properties measurement reveals that the variation of magnetization values may vary based on preferable site occupation of Mn4+-Ti2+ cations to replace Fe3+ cations. The significant decrease in coercive field (H c) from 3.18 kOe to 0.51 kOe with the increase of Mn-Ti substitution affected the lowering values of anisotropy field (H a ). The maximum reflection loss (RL) positions of BaFe(12−2x)(MnTi) x O19 compositional series are shifted to lower frequency range following the H a trendlines. The maximum RL value equals to 98.42% microwave absorption at 10.5 GHz has been obtained in x = 1.0 (BaFe10Mn0.5Ti0.5O19) composition.

Isotope-dependent site occupation of hydrogen in epitaxial titanium hydride nanofilms

Hydrogen, the smallest and lightest element, readily permeates a variety of materials and modulates their physical properties. Identification of the hydrogen lattice location and its amount in crystals is key to understanding and controlling the hydrogen-induced properties. Combining nuclear reaction analysis (NRA) with the ion channeling technique, we experimentally determined the locations of H and D in epitaxial nanofilms of titanium hydrides from the analysis of the two-dimensional angular mappings of NRA yields. Here we show that 11 at% of H are located at the octahedral site with the remaining H atoms in the tetrahedral site. Density functional theory calculations revealed that the structures with the partial octahedral site occupation are stabilized by the Fermi level shift and Jahn-Teller effect induced by hydrogen. In contrast, D was found to solely occupy the tetrahedral site owing to the mass effect on the zero-point vibrational energy. These findings suggest that site occupation of hydrogen can be controlled by changing the isotope mixture ratio, which leads to promising manifestation of novel hydrogen-related phenomena.

Decoding the Role of eg Orbital Occupancy in Co Sites: Mechanistic Insights into Enhanced N2 Activation for Electrocatalytic Nitrate Synthesis

Decoding the Role of e<i>_g</i> Orbital Occupancy in Co Sites: Mechanistic Insights into Enhanced N₂ Activation for Electrocatalytic Nitrate Synthesis

Vegetation influences urban Northern short-tailed shrew site occupancy

Vegetation influences urban Northern short-tailed shrew site occupancy

2-Amino-5-oxo-4-(thiophen-2-yl)-5,6,7,8-tetrahydro-4H-chromene-3-carbonitrile

The crystal structure of the title compound, C14H12N2O2S, reveals two symmetrically independent molecules within the asymmetric unit. Each molecule contains a chromenone core attached to a 2-thiophene ring, cyano, and amino groups. The 2-thiophene ring of one of the two molecules in the asymmetric unit was found to be disordered over two positions, with the major component having a site occupancy factor of 0.837 (2). The 2-thiophene ring is nearly orthogonal to the fused 4H-pyran ring, with dihedral angles between the two sets of planes being 89.5 (5) and 89.63 (8)°. Intermolecular hydrogen bonding, involving N—H...N and N—H...O interactions, creates two distinct motifs leading to the formation of a two-dimensional supramolecular network along the crystallographic ac plane.

Open Sn Framework Structure Hosting Bi Guest atoms-Synthesis, Crystal and Electronic Structure of Na13Sn26Bi.

The large variety of structures of Zintl phases are generally well understood since their anionic substructures follow bonding rules according to the valence concept. But there are also exceptions, which make the semiconductors especially interesting in terms of structure-property relationships. Although several Na-Sn-Pnictides with a variety of structural motives are known, up to this point no ternary compound in the Na-Sn-Bi system has been described. In this paper we present the Zintl-phase Na13Sn25.73Bi1.27 comprising a complex, open-framework structure of Sn atoms, with one mixed Sn/Bi site, hosting Na atoms. An additional Bi atom is loosely connected with only weak contacts to the framework filling a larger cavity within the network. According to band structure calculations of the two ordered variants with either full occupation of the mixed site with Sn or Bi, resulting in Na13Sn26Bi and Na13Sn24Bi3, respectively, both compounds are semiconductors with band gaps of 0.5 eV. A comparison of the band structures with the structurally related binary compounds Na5Sn13 and Na7Sn12 shows that only the perfectly charge balanced Na7Sn12 is a semiconductor whereas Na5Sn13 is metallic. The rather specific electronic situation in the ternary compound is traced back to the loosely bound Bi atom, which acts as a guest atom according to Bix@Na13Sn26-yBiy, with x=1 and y=0.27, capable to change its oxidation state and thus to uptake additional electrons allowing the system to be a semiconductor. Therefore, Na13Sn25.73Bi1.27 can be understood as a rare example of an open framework structure of Sn atoms comprising Bi atoms in the cavities.

A Novel Banana-Shaped Mixed-Metal Co/Fe Polyoxometalate Cluster.

The synthesis and characterization of a Co/Fe mixed-metal banana-shaped polyoxometalate with the formula [(Co2.5Fe0.5(H2O)PW9O34)2(PW6O26)]16- (Co5Fe) is reported. This transition-metal-substituted polyoxometalate readily assembles from its components in a one-pot reaction and crystallizes in the monoclinic space group P21/c. The structure of Co5Fe can be considered a double sandwich composed by two B-α-{Co2.5Fe0.5PW9O40} Keggin units, in which one coordinatively saturated octahedral metal position is equally occupied by Co(II) and Fe(III) ions with a 50 % of site occupancy. These Keggin units are linked via a hexalacunary Keggin unit {PW6O26}. Single crystal X-ray diffraction and magnetic measurements support the proposed atom arrangement within the crystal structure. Magnetic measurements of these double trimeric unit {Co2.5Fe0.5O13}2 show a combination of antiferromagnetic interactions, the presence of spin frustration, and the first-order spin-orbit coupling of Co(II) ions. Electrocatalytic water oxidation measurements show that Co5Fe displays low stability in both homogeneous and heterogeneous conditions. This is evidenced by the constant increase on the catalytic currents over time together with the appearance of polyoxometalate-derived electrode-bound species that can be responsible for the observed catalytic activity.

Conduction channel creation by interstitial site engineering in otherwise insulating Na6ZnS4 for Na-conducting solid-state electrolytes

Na5.6Zn0.6Ga0.4S4, which retains the crystalline structure of its parent form Na6ZnS4, is described as a new class of Na-conducting solid-state electrolytes (SSEs) for all-solid-state batteries. We demonstrate that while Na6ZnS4 is ionically insulating (1.4 nS cm-1), Ga-substitution results in an astonishing improvement of ionic conductivity (σion) to 70.1 μS cm-1, making Na5.6Zn0.6Ga0.4S4 a practical SSE. This dramatic increase in σion (5 × 104 fold) is associated with an increased Na+ occupancy in interstitial sites as ‘x’ increases in Na6-xZn1-xGaxS4, where interstitial Na ions facilitate long-range Na+ conduction, which is otherwise immobile. Ga-substitution also results in phase-pure Na6-xZn1-xGaxS4, contributing at least partially to the enhancement of σion. Furthermore, Na6-xZn1-xGaxS4 exhibits neither releasing H2S gas nor compromising its crystalline structure for several hours under ambient conditions. Ga-substitution also enhances electrochemical stability. While the anodic limit remains largely unchanged, the cathodic limit is significantly lowered from 0.99 V vs. Na2Sn in Na6ZnS4 to 0.35 V in Na5.6Zn0.6Ga0.4S4, resulting in stable Na alloying/dealloying reactions in a symmetric Na2Sn ‖ Na2Sn cell. These findings are comprehensively supported by various experimental and theoretical methods. Finally, we construct a full cell (Na2Sn ‖ TiS2) and demonstrate the practicality of Na5.6Zn0.6Ga0.4S4 as a promising SSE in all solid-state Na ion batteries.

Differential adsorption of H2S/CH4 by bituminous coal and its competitive adsorption properties

To investigate the adsorption characteristics and competitive adsorption patterns of H2S and CH4 in coal seams, we conducted a combined experimental and molecular simulation study using Ningxia Shuangma bituminous coal as the research subject. The experiments examined the adsorption of single-component H2S and CH4 gases at different temperatures and pressures, while the molecular model of bituminous coal was used to analyze the adsorption patterns of binary gas mixtures under competing conditions. Our experimental results demonstrate that both H2S and CH4 follow Langmuir’s model, with their saturated adsorption positively correlated with pressure but negatively correlated with temperature. Moreover, under identical conditions, H2S exhibits 2.43 times higher saturated adsorption than CH4. Molecular simulations reveal that temperature has a greater impact on H2S compared to CH4; both gases undergo reversible physisorption, where isosteric heat of adsorption decreases linearly with increasing amount of adsorbate molecules; interaction energy for H2S is larger in absolute value than that for CH4, indicating its stronger affinity towards coal surfaces; regarding binary component adsorption, an increase in proportion of H2S within the gas mixture leads to higher saturation adsorptions for both the mixture itself and individual H2S molecules while decreasing saturation adsorption for CH4; Coal adsorption selectivity factor for H2S/CH4 > 1. The preferential occupation of high-energy adsorption sites is more likely to be observed for H2S. The adsorption capacity and competitive adsorption capacity of H2S were greater than that of CH4.

Effects of Zn2+/Si4+ co-doping on the cation distribution, crystal structure, and microwave dielectric characteristics of spinel-structured MgAl2O4 ceramics

Investigating the relationship between the structure and dielectric properties of cation-mixed spinel ceramics is crucial for overcoming the limitations of conventional microwave materials. In this study, MgAl2-x(Zn0.5Si0.5)xO4 (x = 0, 0.02, 0.04, 0.06, and 0.08) ceramics were prepared by a solid-state reaction method. The co-substitution for Al with Zn2+/Si4+ induces Al3+ cations for preferential occupation of the 8a site in the oxygen tetrahedra, forming a solid-solution ceramic at x ≤ 0.06. Enhanced ionic diffusion and compressive stress contribute to a dense microstructure (ρ > 95%) with uniform grain-size distribution after heating at 1650 °C for 4 h. Raman and 27Al NMR spectra reveal a relationship between cation distribution and covalency, consistent with the results of Rietveld refinement. The increases in cation disorder and degree of inversion are accompanied by an enhanced covalency of the Al–O bonds, which reduces intrinsic dielectric loss. In addition, the combination of Shannon ion polarizability and bond valence theory suggests that the increases in permittivity (εr) and the temperature coefficient of resonant frequency (τf) are related to the high polarizability of the dopant ions and the abnormal polarizability derived from the decreasing bond valence of the Al2–O site. The sample at x = 0.06 exhibits a low εr of 8.31, high Q × f of 194,159 GHz (at ∼11.35 GHz), and τf of -30.8 ppm/°C, indicating superior microwave application prospects as compared with traditional Mg-Al spinel ceramics.

Iron and phosphate species regulates arsenic speciation and potential mobility in contaminated soils

Arsenic in soils poses a high environmental risk. The understanding of arsenic geochemical speciation, mobility, and other potential factors in contaminated soils is crucial for appropriate remediation strategy development and environmental assessment. The objective of this study was to investigate the arsenic oxidation state and its form in each step of sequential extraction applied to different types of contaminated soils, and to analyze the impact of sequential extraction forms of soil Fe and phosphate. Soil samples were collected from three agricultural regions: acid mine drainage (AMD)-impacted red soils (n = 5, 61.1–248.6 mg As/kg) and As-contaminated groundwater-impacted soil including yellow soils (n = 6, 23.2–32.1 mg As/kg) and chestnut soils (n = 5, 9.0–13.3 mg As/kg). The results of sequential extraction revealed that As was primarily associated with Fe(III) oxyhydroxides. The highest proportion of amorphous Fe(III) oxyhydroxide-bound As was observed in the southern red soils, which was attributable to the coprecipitation/immobilization of high Fe and As concentration levels in AMD during irrigation. The amount of adsorbed As (mass fraction) increased linearly with increasing amounts of As and is related to the presence of both amorphous and crystalline Fe phases in the soils. This demonstrates the immobilization role of reactive Fe phases in controlling the potential mobility of As in contaminated soils impacted by As-contaminated groundwater and AMD. Soil phosphate, with mass concentrations 2–4 orders of magnitude higher than those of As, occupied most of the Fe(III) oxyhydroxide reactive sites. Phosphate-extractable As was 4.3–80.7 mg/kg, accounting for 18.3–76.0 % (median of 33.5 %) of total As, indicating the competitive effect of phosphate on the desorptive release of As. The AMD-impacted paddy soil exhibited much higher proportions of phosphate-extractable As and a predominance of As(III) in the water-soluble extract, revealing the high potential mobility and toxicity of As in flooded soil. The dominant occupation of Fe adsorption sites by soil phosphate likely contributes to low efficiency of soil Fe in immobilizing As. To reduce As mobility, it is imperative to develop future strategies for phosphates used as sustainable fertilizer to support crop culture.

Luminescence improvement via site environment adjustment and site occupancy regulation of Eu2+ in Ca8MgSi4O16Cl2

Luminescence improvement via site environment adjustment and site occupancy regulation of Eu2+ in Ca8MgSi4O16Cl2