Precipitation explains Wood Thrush (Hylocichla mustelina) occupancy patterns in Northern Costa Rica / Patrones de ocurrencia del Zorzal del Bosque (Hylocichla mustelina) explicados por la precipitación en el Norte de Costa Rica

Abstract Introduction: The Wood Thrush is a migratory bird that has experienced dramatic declines in its populations in recent decades. This species overwinters in forest fragments with intermediate levels of habitat modification in Central America. However, more studies detailing the use of remnant forests through time are needed to elucidate the threats this species faces in the wintering grounds. Objective: To understand the effects of environmental and forest structure variables on the occupancy of Wood Thrush in Northern Costa Rica. Methods: The study area was the Área de Conservación Guanacaste (ACG), located in Northern Costa Rica, in December 2016, and during the 2018-2019 migration season. We estimated Wood Thrush occupancy and detection probability in four locations of ACG (dry forest, cloud forest, and two locations in the wet forest) using single-season occupancy models. We also estimated Wood Thrush occupancy and probability of persistence in different months in three vegetation types (open area, secondary forest, and old-growth forest) in the wet forest of ACG using a multi-season occupancy model approach. Results: Wood Thrush occupancy was best described by precipitation in the four locations of the ACG; the probability of occupancy increased with precipitation. The average occupancy of Wood Thrushes varied with vegetation type: open area with shrubs and forest edge (0.69 ± 0.09), secondary forest (0.46 ± 0.1), and old-growth forest (0.61 ± 0.1). Wood Thrush probability of persistence responded partially to changes in precipitation, with an unexpected increase in persistence when the rainfall continued decreasing in the season. Conclusion: Wood Thrush occupancy was best predicted by changes in precipitation considering a larger spatial scale. Its probability of persistence partially varied with precipitation. An increase in persistence closer to Spring migration might be explained by the start of the breeding season of resident birds, potentially reducing territorial conflicts and conserving energy before migration. The long-term protection of wet forests in Northern Costa Rica is of paramount importance for the conservation of Wood Thrushes in their wintering grounds.

Resumen Introducción: El Zorzal del Bosque es un ave migratoria que ha experimentado caídas dramáticas en sus poblaciones en las últimas décadas. Esta especie pasa el invierno en fragmentos de bosque con niveles intermedios de modificación de hábitat en Centroamérica. Sin embargo, se necesitan más estudios que detallen el uso de los bosques remanentes a lo largo del tiempo para dilucidar las amenazas que enfrenta esta especie en las zonas de invernada. Objetivo: Comprender los efectos de variables ambientales y de estructura del bosque en la ocurrencia del Zorzal del Bosque en el Norte de Costa Rica. Métodos: El área de estudio fue el Área de Conservación Guanacaste (ACG), ubicada en el Norte de Costa Rica, en diciembre de 2016, y en la temporada migratoria 2018-2019. Estimamos la ocurrencia y la probabilidad de detección del Zorzal del Bosque en cuatro ubicaciones de ACG (bosque seco, bosque nuboso y dos ubicaciones en el bosque húmedo) utilizando modelos de ocurrencia de una sola temporada. También estimamos la ocurrencia del Zorzal del Bosque y la probabilidad de persistencia en diferentes meses en tres tipos de vegetación (área abierta, bosque secundario y bosque primario) en el bosque húmedo de ACG utilizando un enfoque de modelo de ocurrencia multi-estacional. Resultados: La ocurrencia del Zorzal del Bosque estuvo mejor descrita por la precipitación en las cuatro localidades del ACG; la probabilidad de ocurrencia aumentó con las precipitaciones. La ocurrencia media de zorzales varió con el tipo de vegetación: área abierta con arbustos y borde de bosque (0.69 ± 0.09), bosque secundario (0.46 ± 0.1) y bosque primario (0.61 ± 0.1). La probabilidad de persistencia del zorzal respondió parcialmente a cambios en la precipitación, con un aumento inesperado en la persistencia cuando las precipitaciones continuaron disminuyendo en la temporada. Conclusión: La ocurrecia del Zorzal del Bosque varió con la precipitación considerando una escala espacial mayor. Su probabilidad de persistencia varió parcialmente con la precipitación. Un aumento en la persistencia más cerca de la migración de primavera podría explicarse por el inicio de la temporada de reproducción de las aves residentes, lo que podría reducir los conflictos territoriales y conservar energía antes de la migración. La protección a largo plazo de los bosques húmedos en el norte de Costa Rica es de suma importancia para la conservación de los Zorzales del Bosque en sus zonas de invernada.

Sulfur occupancy-induced construction of ant-nest-like NiMo/CF(N) electrode for highly efficient hydrogen evolution.

The microstructure of the electrocatalyst plays a critical role in the reaction efficiency and stability during electrochemical water splitting. Designing an efficient and stable electrocatalyst, further clarifying the synthesis mechanism, is still an important problem to be solved urgently. Inspired by the copper pyrometallurgy theory, an exceptionally active NiMo/CF(N) electrode, consisting of an ant-nest-like copper foam substrate (defined as CF(N)) and deposited NiMo layer, was fabricated for the alkaline hydrogen evolution reaction (HER). Our findings expounded the structure construction mechanism and highlighted the pivotal role of the spatial occupancy of sulfur atoms in the construction of the ant-nest-like structure. The NiMo/CF(N) composite, characterized by channels with a 2 µm diameter, showcases strong electronic interactions, increased catalytic active sites, enhanced electron/ion transport, and facilitated gas release during HER. Remarkably, NiMo/CF(N) demonstrates ultralow overpotentials of 21 mV to deliver a current density of 10 mA cm-2 in 1 M KOH. This electrode also exhibits outstanding durability, maintaining a current density of 200 mA cm-2 for 110 h, attributed to the chemical and structural integrity of its catalytic surface and the excellent mechanical properties of the electrode. This work advances the fundamental understanding of constructing micro/nano-structured electrocatalysts for highly efficient water splitting.

Phylogenetic climatic niche evolution and diversification of the Neurergus species (Salamandridae) in the Irano-Anatolian biodiversity hotspot.

This study explores how climate variables influenced the evolution and diversification of Neurergus newts within the Irano-Anatolian biodiversity hotspot. We use a dated phylogenetic tree and climatic niche models to analyze their evolutionary history and ecological preferences. Using genetic data from nuclear (KIAA) and mitochondrial (16s and 12s) genes, we estimate divergence times and identify four major Neurergus clades. The initial speciation event occurred approximately 11.3 million years ago, coinciding with the uplift of the Zagros and Anatolian mountains. This geological transformation isolated newt populations, likely triggering the first speciation event. By integrating potential geographic distribution with climate variables, we reconstruct ancestral niche occupancy profiles. This highlights the critical roles of temperature and precipitation in shaping Neurergus habitat preferences and distribution. We observe both phylogenetic niche conservatism and divergence, with niche divergence playing a dominant role in diversification. This research emphasizes the complex interplay of geography, climate, and ecology in speciation and the vulnerability of isolated mountain newt populations to environmental changes.

Ketanserin exhibits dose- and concentration-proportional serotonin 2A receptor occupancy in healthy individuals: Relevance for psychedelic research.

The serotonin 2A (5-HT2A) receptor is an important target for drug development and the main receptor through which classical psychedelics elucidate their hallucinogenic effects. The 5-HT2A receptor antagonist ketanserin has frequently been used as a tool to block the receptor. Here, we establish the dose-occupancy relation of ketanserin and the cerebral 5-HT2A receptor in healthy participants by conducting a positron emission tomography (PET) study. 120-min PET scans using the 5-HT2A receptor agonist radiotracer [11C]Cimbi-36 were conducted at baseline and after oral doses of either 10, 20, or 40 mg of ketanserin; each participant underwent one or two scans after ketanserin administration. Occupancy was defined as the percent change in neocortex binding potential (BPND), estimated using the simplified reference tissue model (SRTM) with the cerebellum as reference region. Peroral ketanserin intake resulted in a plasma concentration-related increase in cerebral 5-HT2A receptor occupancy with the highest plasma ketanserin concentrations measured after ∼2 h. The relation between mean plasma ketanserin concentrations and 5-HT2A receptor occupancy conformed to a single-site binding model with an estimated EC50 (95 % CI) of 2.52 (0.75; 8.1) ng/mL, which corresponds to a peroral dose of ketanserin of approximately 10 mg. These data elucidate for the first time in humans the cerebral pharmacodynamics of ketanserin, both benefitting its use as a pharmacological tool for probing brain function and adding to its potential for therapeutic use in rescuing a bad psychedelic experience.

"Phosphoproteomic quantification based on phosphopeptide intensity or occupancy? An evaluation based on casein kinase 2 downstream effects".

Quantitative phosphoproteomic data has mostly been reported from experiments comparing relative phosphopeptides intensities in two or more different conditions, while the ideal parameter to compare is phosphopeptides occupancies. This term is scarcely used and therefore barely implemented in phosphoproteomics studies, and this should be of concern for the scientific journals. In order to demonstrate the relevance of this issue, here we show how the method of choice affects the interpretation of the data. The phosphoproteomic profile modulated in two AML cell lines after CK2 inhibition with CIGB-300 or CX-4945 is shown. Following the downstream action of CK2 the phosphosite intensity and occupancy results were compared to validate the best approach for quantitative phosphoproteomic studies. Even when the total number of quantified phosphopeptides was higher by using the intensity calculation, in all the cases the percent of CK2 consensus sequences which were down-regulated in response to CK2 inhibition was higher using the phosphosite occupancy quantification. To note, a high number of CK2 consensus sequences was found down-regulated with at least a 10% or 15% of phosphosite occupancy variation illustrating that low thresholds of occupancy modulation might be indicative of biological effect. Additionally, several biological processes only appear significantly over-represented in the phosphoproteome quantified by occupancy. The functional enrichment analysis per ranges of occupancy variations also illustrated clear differences among AML cell lines subjected to CK2 inhibition by CX-4945. A low overlap between the phosphoproteomes quantified by intensity and occupancy was obtained illustrating that new developments in proteomics techniques are needed to improve the performance of the occupancy approach. Even in such context, results indicate that occupancy quantification performs better than phosphorylation quantification based on intensity reinforcing the importance of such quantification approach to describe phosphoproteomic data.

Evaluating the impact of a ward environment with 20 single occupancy rooms and two four-bedded bays on patient and staff experiences and outcomes in an acute NHS Trust: a mixed-methods study protocol.

INTRODUCTION: Traditionally, wards in acute care hospitals consist predominately of multioccupancy bays with some single rooms. There is an increasing global trend towards a higher proportion of single rooms in hospitals, with the UK National Health Service (NHS) advocating for single-room provision in all new hospital builds. There is limited evidence on the impact of a ward environment incorporating mostly single and some multioccupancy bays on patient care and organisational outcomes. METHODS AND ANALYSES: This study will assess the impact of a newly designed 28-bedded ward environment, with 20 single rooms and two four-bedded bays, on patient and staff experiences and outcomes in an acute NHS Trust in East England. The study is divided into two work packages (WP)-WP1 is a quantitative data extraction of routinely collected patient and staff data while WP2 is a mixed-methods process evaluation consisting of one-to-one, in-depth, semistructured interviews with staff, qualitative observations of work processes on the ward and a quantitative data evaluation of routinely collected process evaluation data from patients and staff. ETHICS AND DISSEMINATION: Ethical approval was obtained from the UK Health Research Authority (IRAS ID: 334395). Study findings will be shared with key stakeholders, published in peer-reviewed high-impact journals and presented at relevant conferences.

Seasonal habitat-use patterns of large mammals in a human-dominated landscape.

Large mammals in temperate climates typically display seasonal patterns of habitat use. However, these patterns are often overlooked because large mammals are usually surveyed at annual intervals. In addition, most studies focus on a single species and ignore other species with which the focal species could interact. Knowing seasonal patterns of habitat use in multiple species and understanding factors that cause these patterns can provide further detail on population dynamics and guide effective conservation planning. Here, using dynamic occupancy modeling, we analyze 11 years of camera-trap data collected in northwestern Anatolia, Turkey, to investigate seasonal habitat use of 8 large-mammal species: Brown Bear (Ursus arctos), Eurasian Lynx (Lynx lynx), Gray Wolf (Canis lupus), Red Fox (Vulpes vulpes), Wild Boar (Sus scrofa), Roe Deer (Capreolus capreolus), European Hare (Lepus europaeus), and Red Deer (Cervus elaphus). For each species, we study the strength of seasonality in habitat use and its dependence on human population density and elevation, which have been shown to affect distributions of species in the region. Although all species exhibited seasonality in habitat use, the strength of this seasonality varied among species; it was strongest in Wild Boar, Roe Deer, and Brown Bear. Moreover, except for Brown Bear, all species tended to avoid sites close to humans. The species responded differently to changing elevation; increasing elevation had both positive and negative effects on species-specific colonization and desertion probabilities, and these effects were likely related to either feeding habits or tendency to avoid humans. These results indicate that seasonality should be taken into consideration in population studies. However, because species differ, seasonality patterns should be identified separately for each species of interest, as differences in these patterns can explain the underlying dynamics of habitat-use patterns more accurately.

Data and bills of materials for buildings designed for mass timber, structural steel, and reinforced concrete based on the 2021 international building code provisions.

This article presents and describes a dataset for the bills of materials for the buildings constructed with mass timber (MT), structural steel (SS), and reinforced concrete (RC), which are generated using Athena's Impact Estimator for Buildings (IE4B) software to conduct a whole building life-cycle assessment (WBLCA). These data are associated with the research article Environmental Impact Assessment of Mass Timber, Structural Steel, and Reinforced Concrete Buildings Based on the 2021 International Building Code Provisions [1]. This dataset was utilized to estimate their environmental impacts but can be used to estimate the costs of buildings constructed with MT, SS, and RC building materials. These data could be replicated using the same layout, system boundaries, reference study period (RSP), and building assemblies' information as used in the published work [1]. This dataset is related to conceptual design of a building with 11 apartment units per floor. However, a detailed design that includes the analysis of interior architectural finishes such as internal partitions within the units, kitchen and washroom fixtures, internal doors, flooring, and so on, could be developed and analyzed to obtain a more comprehensive estimates of life cycle assessment. This dataset was originally developed to compare the environmental impacts of structural materials selection for three common framing typologies.

Mesocarnivore sensitivity to natural and anthropogenic disturbance leads to declines in occurrence and concern for species persistence.

Understanding mesocarnivore responses to both natural and anthropogenic disturbance is crucial for understanding species' potential to maintain landscape persistence into the future. We examined the response of five mesocarnivore species (bobcat, coyote, fisher, gray fox, and red fox) to both types of disturbances and climatic conditions. The Northeastern U.S. has experienced multiple large-scale disturbances, such as a mass defoliation event following larval spongy moth outbreak and high densities of infrastructure that divide the natural landcover into roadless zones where these species inhabit. Using dynamic occupancy models in a Bayesian framework, we aimed to (1) examine variation in species' responses over a 4-year study by estimating variation in site-level occupancy, colonization and extirpation of each species in the state of Rhode Island relative to natural disturbance (i.e., defoliation event), anthropogenic disturbance (i.e., parceling of natural landcover bounded by roads, distance to roads), and climate (i.e., seasonal precipitation) and (2) compare current occurrence trends to predicted asymptotic occupancy to identify key variables contributing to distribution instability. Our findings indicated declines in the occurrence of both fox species, and fisher. There was variation in mesocarnivore response to disturbance among the species. We found gray fox and fisher occupancy dynamics to be sensitive to all forms of disturbance and coyote occurrence was positively associated with anthropogenic disturbance. Although bobcat and red fox were predicted to respond positively to future climate scenarios, fisher and gray fox were not, and persistence of fisher and gray fox in a landscape of disturbance relies on large areas with high forest and shrubland cover. With the wide-spread spongy moth outbreak across much of southern New England, our findings indicate that efforts to conserve forested lands may be crucial in maintaining the persistence of several mesocarnivore species in this region experiencing large-scale disturbance.

Evolution of leapfrog migration: A test of competition-based hypotheses.

Leapfrog migration is a common migration pattern in birds where the breeding and wintering latitudes between populations are in reversed latitudinal sequence. Competition for wintering and breeding sites has been suggested to be an ultimate factor, and several competitor-based hypotheses have been proposed to explain this pattern. If wintering sites close to the breeding sites are favored, competitive exclusion could force subdominant individuals to winter further away. Competitive exclusion could be mediated either through body size or by prior occupancy. The alternative "spring predictability" hypothesis assumes competition for sufficiently close wintering areas, allowing the birds to use autocorrelated weather cues to optimally time spring migration departure. To test predictions and assumptions of these hypotheses, we combined morphometrics, migration, and weather data from four populations of common ringed plover breeding along a latitudinal (56-68° N) and climatic gradient (temperate to Arctic). Critical for our evaluation was that two populations were breeding on the same latitude in subarctic Sweden with the same distance to the closest potential wintering site, but differed in breeding phenology, and wintered in West Africa and Europe, respectively. Thus, while breeding on the same latitude, their winter distribution overlapped with that of an Arctic and temperate population. Body size was largest within the temperate population, but there was no size difference between the two subarctic populations. Populations wintering in Europe arrived there before populations wintering in Africa. The largest variation in the arrival of meteorological spring occurred at the temperate breeding site, while there was almost no difference among the other sites. In general, temperatures at the northernmost wintering area correlated well with each breeding site prior to breeding site-specific spring arrival. Based on these observations, we conclude that competitive exclusion through body-size-related dominance cannot explain leapfrog migration. Furthermore, the assumptions on which the "spring predictability" hypothesis is based did not match the observed wintering ranges either. However, we could not reject the hypothesis that competitive exclusion mediated by prior occupancy in the wintering area could lead to leapfrog migration, and therefore, this hypothesis should be retained as working hypothesis for further work.

Predicting continuous amyloid PET values with CSF tau phosphorylation occupancies.

INTRODUCTION: Cerebrospinal fluid (CSF) tau phosphorylation at multiple sites is associated with cortical amyloid and other pathologic changes in Alzheimer's disease. These relationships can be non-linear. We used an artificial neural network to assess the ability of 10 different CSF tau phosphorylation sites to predict continuous amyloid positron emission tomography (PET) values. METHODS: CSF tau phosphorylation occupancies at 10 sites (including pT181/T181, pT217/T217, pT231/T231 and pT205/T205) were measured by mass spectrometry in 346 individuals (57 cognitively impaired, 289 cognitively unimpaired). We generated synthetic amyloid PET scans using biomarkers and evaluated their performance. RESULTS: Concentration of CSF pT217/T217 had low predictive error (average error: 13%), but also a low predictive range (ceiling 63 Centiloids). CSF pT231/T231 has slightly higher error (average error: 19%) but predicted through a greater range (87 Centiloids). DISCUSSION: Tradeoffs exist in biomarker selection. Some phosphorylation sites offer greater concordance with amyloid PET at lower levels, while others perform better over a greater range. HIGHLIGHTS: Novel pTau isoforms can predict cortical amyloid burden. pT217/T217 accurately predicts cortical amyloid burden in low-amyloid individuals. Traditional CSF biomarkers correspond with higher levels of amyloid.

Comparison of soil eDNA to camera traps for assessing mammal and bird community composition and site use.

Species detections often vary depending on the survey methods employed. Some species may go undetected when using only one approach in community-level inventory and monitoring programs, which has management and conservation implications. We conducted a comparative study of terrestrial mammal and bird detections in the spring and summer of 2021 by placing camera traps at 30 locations across a large military installation in northern Michigan, USA and testing replicate soil samples from these sites for environmental DNA (eDNA) using an established vertebrate metabarcoding assay. We detected a total of 48 taxa from both survey methods: 26 mammalian taxa (excluding humans, 24 to species and two to genus) and 22 avian taxa (21 to species and one to genus). We detected a relatively even distribution of mammalian taxa on cameras (17) and via eDNA analysis (15), with seven taxa detected from both methods. Most medium-to-large carnivores were detected only on cameras, whereas semi-fossorial small mammals were detected only via eDNA analysis. We detected higher bird diversity with camera traps (18 taxa) compared to eDNA analysis (eight taxa; four taxa were detected with both methods), but cameras alone were most effective at detecting smaller birds that frequently occupy arboreal environments. We also used Bayesian spatial occupancy models for two widely distributed game species (white-tailed deer, Odocoileus virginianus, and ruffed grouse, Bonasa umbellus) that were moderately detected with both survey methods and found species-specific site use (occupancy) estimates were similar between cameras and eDNA analysis. Concordant with similar studies, our findings suggest that a combination of camera trap and eDNA surveys could be most useful for assessing the composition of terrestrial mammal communities. Camera traps may be most efficient for assessing bird diversity but can be complemented with eDNA analysis, particularly for species that spend considerable time on the ground.

Accounting for imperfect detection when estimating species-area relationships and beta-diversity.

Ecologists have historically quantified fundamental biodiversity patterns, including species-area relationships (SARs) and beta diversity, using observed species counts. However, imperfect detection may often bias derived community metrics and subsequent community models. Although several statistical methods claim to correct for imperfect detection, their performance in species-area and ß-diversity research remains unproven. We examine inaccuracies in the estimation of SARs and ß-diversity parameters that emerge from imperfect detection, and whether such errors can be mitigated using a non-parametric diversity estimator (iNEXT.3D) and Multi-Species Occupancy Models (MSOMs). We simulated 28,350 sampling regimes of 2835 fragmented communities, varying the mean and standard deviation of species detection probabilities, and the number of sampling repetitions. We then quantified the bias, accuracy, and precision of derived estimates of model coefficients for SARs and the effects of patch area on ß-diversity (pairwise Sørensen similarity). Imperfect detection biased estimates of all evaluated parameters, particularly when mean detection probabilities were low, and there were few sampling repetitions. Observed counts consistently underestimated species richness and SAR z-values, and overestimated SAR c-values; iNEXT.3D and MSOMs only partially resolved these biases. iNEXT.3D provided the best estimates of SAR z-values, although MSOM estimates were generally comparable. All three methods accurately estimated pairwise Sørensen similarity in most circumstances, but only MSOMs provided unbiased estimates of the coefficients of models examining covariate effects on ß-diversity. Even when using iNEXT.3D or MSOMs, imperfect detection consistently caused biases in SAR coefficient estimates, calling into question the robustness of previous SAR studies. Furthermore, the inability of observed counts and iNEXT.3D to estimate ß-diversity model coefficients resulted from a systematic, area-related bias in Sørensen similarity estimates. Importantly, MSOMs corrected for these biases in ß-diversity assessments, even in suboptimal scenarios. Nonetheless, as estimator performance consistently improved with increasing sampling repetitions, the importance of appropriate sampling effort cannot be understated.

Characterization of the SWI/SNF complex and nucleosome organization in sorghum.

The switch defective/sucrose non-fermentable (SWI/SNF) multisubunit complex plays an important role in the regulation of gene expression by remodeling chromatin structure. Three SWI/SNF complexes have been identified in Arabidopsis including BAS, SAS, and MAS. Many subunits of these complexes are involved in controlling plant development and stress response. However, the function of these complexes has hardly been studied in other plant species. In this study, we identified the subunits of the SWI/SNF complex in sorghum and analyzed their evolutionary relationships in six grass species. The grass species conserved all the subunits as in Arabidopsis, but gene duplication occurred diversely in different species. Expression pattern analysis in sorghum (Sorghum bicolor) showed that most of the subunit-encoding genes were expressed constitutively, although the expression level was different. Transactivation assays revealed that SbAN3, SbGIF3, and SbSWI3B possessed transactivation activity, which suggests that they may interact with the pre-initiation complex (PIC) to activate transcription. We chose 12 subunits in sorghum to investigate their interaction relationship by yeast two-hybrid assay. We found that these subunits displayed distinct interaction patterns compared to their homologs in Arabidopsis and rice. This suggests that different SWI/SNF complexes may be formed in sorghum to perform chromatin remodeling functions. Through the integrated analysis of MNase-seq and RNA-seq data, we uncovered a positive relationship between gene expression levels and nucleosome phasing. Furthermore, we found differential global nucleosome enrichments between leaves and roots, as well as in response to PEG treatment, suggesting that dynamics of nucleosome occupancy, which is probably mediated by the SWI/SNF complex, may play important roles in sorghum development and stress response.

Multiphase Reconstruction of Heterogeneous Materials Using Machine Learning and Quality of Connection Function.

Establishing accurate structure-property linkages and precise phase volume accuracy in 3D microstructure reconstruction of materials remains challenging, particularly with limited samples. This paper presents an optimized method for reconstructing 3D microstructures of various materials, including isotropic and anisotropic types with two and three phases, using convolutional occupancy networks and point clouds from inner layers of the microstructure. The method emphasizes precise phase representation and compatibility with point cloud data. A stage within the Quality of Connection Function (QCF) repetition loop optimizes the weights of the convolutional occupancy networks model to minimize error between the microstructure's statistical properties and the reconstructive model. This model successfully reconstructs 3D representations from initial 2D serial images. Comparisons with screened Poisson surface reconstruction and local implicit grid methods demonstrate the model's efficacy. The developed model proves suitable for high-quality 3D microstructure reconstruction, aiding in structure-property linkages and finite element analysis.

Unveiling the translational dynamics of lychee (Litchi chinesis Sonn.) in response to cold stress.

Cold stress poses a significant threat to the quality and productivity of lychee (Litchi chinensis Sonn.). While previous research has extensively explored the genomic and transcriptomic responses to cold stress in lychee, the translatome has not been thoroughly investigated. This study delves into the translatomic landscape of the 'Xiangjinfeng' cultivar under both control and low-temperature conditions using RNA sequencing and ribosome profiling. We uncovered a significant divergence between the transcriptomic and translatomic responses to cold exposure. Additionally, bioinformatics analyses underscored the crucial role of codon occupancy in lychee's cold tolerance mechanisms. Our findings reveal that the modulation of translation via codon occupancy is a vital strategy to abiotic stress. Specifically, the study identifies ribosome stalling, particularly at the E site AAU codon, as a key element of the translation machinery in lychee's response to cold stress. This work enhances our understanding of the molecular dynamics of lychee's reaction to cold stress and emphasizes the essential role of translational regulation in the plant's environmental adaptability.

Quantification and site-specific analysis of co-occupied N- and O-glycopeptides.

Protein glycosylation is a complex post-translational modification that is generally classified as N- or O-linked. Site-specific analysis of glycopeptides is accomplished with a variety of fragmentation methods, depending on the type of glycosylation being investigated and the instrumentation available. For instance, collisional dissociation methods are frequently used for N-glycoproteomic analysis with the assumption that one N-sequon exists per tryptic peptide. Alternatively, electron-based methods are indispensable for O-glycosite localization. However, the presence of simultaneously N- and O-glycosylated peptides could suggest the necessity of electron-based fragmentation methods for N-glycoproteomics, which is not commonly performed. Thus, we quantified the prevalence of N- and O-glycopeptides in mucins and other glycoproteins. A much higher frequency of co-occupancy within mucins was detected whereas only a negligible occurrence occurred within non-mucin glycoproteins. This was demonstrated from analyses of recombinant and/or purified proteins, as well as more complex samples. Where co-occupancy occurred, O-glycosites were frequently localized to the Ser/Thr within the N-sequon. Additionally, we found that O-glycans in close proximity to the occupied Asn were predominantly unelaborated core 1 structures, while those further away were more extended. Overall, we demonstrate electron-based methods are required for robust site-specific analysis of mucins, wherein co-occupancy is more prevalent. Conversely, collisional methods are generally sufficient for analyses of other types of glycoproteins.

The spatial extent and the dispersal strategy of species shape the occupancy frequency distribution of stream insect assemblages.

Several theoretical models have been proposed as the underlying mechanisms behind occupancy frequency distribution (OFD) patterns. For instance, the metapopulation dynamic model predicts bimodal OFD pattern indicating the dominance of dispersal processes in structuring the assemblages, while the niche-based model predicts unimodal right-skewed OFD pattern, and thus assemblages are driven mostly by niche processes. However, it is well known that the observed OFD pattern reflects the interplay of several other factors (e.g. habitat heterogeneity, species specificity and sampling protocol parameters). It follows that the individual contribution of each factor to the OFD pattern is rather complicated to explore. Our main objective was to examine the role of the spatial extent of the sampling and the dispersal strategies of species in shaping OFD pattern. For this, we collected samples of stream insect assemblages inhabiting near-natural streams in the Pannon Ecoregion. We formed groups of species representing contrasting dispersal strategies (referred to as dispersal groups). Applying a computer program algorithm, we produced samples with different spatial extent. We found that with increasing spatial extent, the OFD pattern changed from bimodal to unimodal for active dispersers. Insect groups with different dispersal strategies differed in the strength of support for OFD patterns within all spatial extent. Furthermore, the strength of support for OFD patterns varied across dispersal groups differently as the spatial extent increased. Our results reflected underlying changes in mechanisms structuring assemblages along an increasing spatial extent. We also assumed that the stream insect dispersal strategy influences the relative role of dispersal and niche processes particularly as spatial extent increases from stream reaches to the extent of adjacent valleys. We could define spatial extents and dispersal strategies within which unique metacommunity processes could underlie the organisation of assemblages.

Occupancy Prediction in IoT-Enabled Smart Buildings: Technologies, Methods, and Future Directions.

In today's world, a significant amount of global energy is used in buildings. Unfortunately, a lot of this energy is wasted, because electrical appliances are not used properly or efficiently. One way to reduce this waste is by detecting, learning, and predicting when people are present in buildings. To do this, buildings need to become "smart" and "cognitive" and use modern technologies to sense when and how people are occupying the buildings. By leveraging this information, buildings can make smart decisions based on recently developed methods. In this paper, we provide a comprehensive overview of recent advancements in Internet of Things (IoT) technologies that have been designed and used for the monitoring of indoor environmental conditions within buildings. Using these technologies is crucial to gathering data about the indoor environment and determining the number and presence of occupants. Furthermore, this paper critically examines both the strengths and limitations of each technology in predicting occupant behavior. In addition, it explores different methods for processing these data and making future occupancy predictions. Moreover, we highlight some challenges, such as determining the optimal number and location of sensors and radars, and provide a detailed explanation and insights into these challenges. Furthermore, the paper explores possible future directions, including the security of occupants' data and the promotion of energy-efficient practices such as localizing occupants and monitoring their activities within a building. With respect to other survey works on similar topics, our work aims to both cover recent sensory approaches and review methods used in the literature for estimating occupancy.