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23 pages, 3488 KB  
Article
Variable Density Planting: Using Marigolds as a Model System to Describe a Silvicultural Approach to Increase Structural Diversity
by Gregory J. Ettl, Courtney R. Bobsin, Bernard T. Bormann and Dano E. Holt
Forests 2026, 17(4), 401; https://doi.org/10.3390/f17040401 - 24 Mar 2026
Viewed by 396
Abstract
There is limited information on the effects of irregular-spaced and clumped planting on forest production and structural diversity. We explored Tagetes patula L. development as a model system to demonstrate stand development under varying planting patterns, and conceptualized in the context of Pseudotsuga [...] Read more.
There is limited information on the effects of irregular-spaced and clumped planting on forest production and structural diversity. We explored Tagetes patula L. development as a model system to demonstrate stand development under varying planting patterns, and conceptualized in the context of Pseudotsuga menziesii (Mirb.) Franco mesic production forests of the Pacific Northwestern USA. Two variable planting patterns, clumps of 24 plants and of four plants, were compared to square regular patterns in replicate growing boxes. Spatial patterns were compared post-planting and at maturation, along with stand-level metrics and final dry weights, and stand structural statistics were used to compare production and diversity. The clumped spatial structure of 24-plant clumps was maintained to maturity. Groups of four plants maintained clumping at small scales and regular patterns at larger scales. Initial Regular-Square spacing remained at 2 cm at maturity but became indistinguishable from random patterns at larger scales. There was (1) overall greater mean directional index for the Large-Clumped patterns and greater spatial complexity indices for both clumped patterns, (2) greater social class (size) mean mingling index for small clumps, and (3) higher mean dominance index and mean differentiation index and lower crown volume complexity and height-to-diameter ratios for Regular-Square spacing. The structural complexity was accompanied by limited differences in dried weights by plant tissue (total weight, stem, leaf, flower weight) or plant biometric parameters (stem straightness, crown ratio, crown volume, number of leaves and flowers). The results from irregular planted marigold stand development are discussed in the context of increasing forest stand complexity, potentially without compromising productivity. Full article
(This article belongs to the Section Forest Ecology and Management)
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38 pages, 11590 KB  
Article
Validation of the MODIS Clumping Index: A Case Study in Saihanba National Forest Park
by Siyang Yin, Ziti Jiao, Yadong Dong, Lei Cui, Anxin Ding, Feng Qiu, Qian Zhang, Yongguang Zhang, Xiaoning Zhang, Jing Guo, Rui Xie, Yidong Tong, Zidong Zhu, Sijie Li, Chenxia Wang and Jiyou Jiao
Remote Sens. 2025, 17(22), 3770; https://doi.org/10.3390/rs17223770 - 20 Nov 2025
Viewed by 949
Abstract
The clumping index (CI) describes the level of foliage grouping relative to the random distribution within the canopy. It plays a vital role in the derivation of other important parameters (e.g., the leaf area index, (LAI)) that are usually employed in hydrological, ecological [...] Read more.
The clumping index (CI) describes the level of foliage grouping relative to the random distribution within the canopy. It plays a vital role in the derivation of other important parameters (e.g., the leaf area index, (LAI)) that are usually employed in hydrological, ecological and climatological modeling. In recent years, several satellite-based CI products have been developed using multi-angle reflectance data. However, these products have been validated through the use of a “point-to-point” comparison, which rarely involves a quantitative analysis of spatial representativeness for field-measured CIs in most cases. In this study, we developed a methodological framework to validate the MODIS CI at three different data scales on the basis of intense field measurements, high-resolution unmanned aerial vehicle (UAV) observations and Landsat 8 data. This framework was used to understand the impacts of the scale issue and subpixel variance of the CI in the validation of the MODIS CI for a case study of 12 gridded 500 m pixels in Saihanba National Forest Park, Hebei, China. The results revealed that the MODIS CIs in the study area were in good agreement with the upscaled field CIs (R = 0.75, RMSE = 0.05, bias = 0.02) and UAV CIs. Through a comparison of the observed CIs along the 30 m transects with the 500 m MODIS CIs, we gained insight into the uncertainty caused by the direct “point-to-pixel” evaluation method, which ranged from −0.21~+0.27 for the 10th and 90th percentiles of the observed-MODIS CI error distribution for the twelve pixels. Moreover, semivariogram analysis revealed that the representativeness assessments based on high-resolution albedo and CI maps could reflect the spatial heterogeneity within pixels, whereas the CI map provided more information on the variation in vegetation structures. The average observational footprint needed for a spatially representative sample is approximately 209 m according to an analysis of the high-resolution CI map. The uncertainty of mismatched MODIS land cover types can lead to a deviation of 0.33 in CI estimates, and compared with the CLX method, the scaled-up CI method based on simple arithmetic averages tends to overestimate CIs. In summary, various validation efforts in this case study reveal that the accuracy of the MODIS CIs is generally reliable and in good agreement with that of the upscaled field CIs and UAV CIs; however, with the development of surface process modeling and remote sensing technology, substantial measurements of field CIs in conjunction with high-resolution remotely sensed CI maps derived from single-angle advanced methods are urgently needed for further validation and potential applications. Certainly, such a validation effort will help to improve the understanding of MODIS CI products, which, in turn, will further support the methods and applications of global geospatial information. Full article
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22 pages, 1916 KB  
Article
Freeze-Dried Probiotic Fermented Camel Milk Enriched with Ajwa Date Pulp: Evaluation of Functional Properties, Probiotic Viability, and In Vitro Antidiabetic and Anticancer Activities
by Sally S. Sakr and Hassan Barakat
Foods 2025, 14(15), 2698; https://doi.org/10.3390/foods14152698 - 31 Jul 2025
Cited by 4 | Viewed by 3362
Abstract
Noncommunicable diseases (NCDs) like diabetes and cancer drive demand for therapeutic functional foods. This study developed freeze-dried fermented camel milk (FCM) with Ajwa date pulp (ADP), evaluating its physical and functional properties, probiotic survival, and potential benefits for diabetes and cancer. To achieve [...] Read more.
Noncommunicable diseases (NCDs) like diabetes and cancer drive demand for therapeutic functional foods. This study developed freeze-dried fermented camel milk (FCM) with Ajwa date pulp (ADP), evaluating its physical and functional properties, probiotic survival, and potential benefits for diabetes and cancer. To achieve this target, six FCM formulations were prepared using ABT-5 starter culture (containing Lactobacillus acidophilus, Bifidobacterium bifidum, and Streptococcus thermophilus) with or without Lacticaseibacillus rhamnosus B-1937 and ADP (12% or 15%). The samples were freeze-dried, and their functional properties, such as water activity, dispersibility, water absorption capacity, water absorption index, water solubility index, insolubility index, and sedimentation, were assessed. Reconstitution properties such as density, flowability, air content, porosity, loose bulk density, packed bulk density, particle density, carrier index, Hausner ratio, porosity, and density were examined. In addition, color and probiotic survivability under simulated gastrointestinal conditions were analyzed. Also, antidiabetic potential was assessed via α-amylase and α-glucosidase inhibition assays, while cytotoxicity was evaluated using the MTT assay on Caco-2 cells. The results show that ADP supplementation significantly improved dispersibility (up to 72.73% in FCM15D+L). These improvements are attributed to changes in particle size distribution and increased carbohydrate and mineral content, which facilitate powder rehydration and reduce clumping. All FCM variants demonstrated low water activity (0.196–0.226), indicating good potential for shelf stability. The reconstitution properties revealed that FCM powders with ADP had higher bulk and packed densities but lower particle density and porosity than controls. Including ADP reduced interstitial air and increased occluded air within the powders, which may minimize oxidation risks and improve packaging efficiency. ADP incorporation resulted in a significant decrease in lightness (L*) and increases in redness (a*) and yellowness (b*), with greater pigment and phenolic content at higher ADP levels. These changes reflect the natural colorants and browning reactions associated with ADP, leading to a more intense and visually distinct product. Probiotic survivability was higher in ADP-fortified samples, with L. acidophilus and B. bifidum showing resilience in intestinal conditions. The FCM15D+L formulation exhibited potent antidiabetic effects, with IC50 values of 111.43 μg mL−1 for α-amylase and 77.21 μg mL−1 for α-glucosidase activities, though lower than control FCM (8.37 and 10.74 μg mL−1, respectively). Cytotoxicity against Caco-2 cells was most potent in non-ADP samples (IC50: 82.22 μg mL−1 for FCM), suggesting ADP and L. rhamnosus may reduce antiproliferative effects due to proteolytic activity. In conclusion, the study demonstrates that ADP-enriched FCM is a promising functional food with enhanced probiotic viability, antidiabetic potential, and desirable physical properties. This work highlights the potential of camel milk and date synergies in combating some NCDs in vitro, suggesting potential for functional food application. Full article
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24 pages, 7790 KB  
Article
Retrieving the Leaf Area Index of Dense and Highly Clumped Moso Bamboo Canopies from Sentinel-2 MSI Data
by Weiliang Fan, Jun Wu, Guang Zheng, Qian Zhang, Xiaojun Xu, Huaqiang Du, Mengxiang Zheng, Kexin Zhang and Feng Zhang
Remote Sens. 2025, 17(11), 1891; https://doi.org/10.3390/rs17111891 - 29 May 2025
Cited by 2 | Viewed by 1289
Abstract
The effects of leaf clumping on leaf area index (LAI, m2·m−2) retrieval have been proved by several studies. For dense and highly clumped Moso bamboo canopies, LAI is usually retrieved using the SAIL-series models that do not account for [...] Read more.
The effects of leaf clumping on leaf area index (LAI, m2·m−2) retrieval have been proved by several studies. For dense and highly clumped Moso bamboo canopies, LAI is usually retrieved using the SAIL-series models that do not account for leaf clumping, although these retrievals are subsequently successfully validated by indirect ground-based methods that do account for leaf clumping. In order to explore these two seemingly contradictory results, LAIs of 21 Moso bamboo canopies retrieved by the GOST2 model (incorporating leaf clumping), the 4SAIL model and the SNAP tool (both without leaf clumping), respectively, were validated against ground-based LAI estimations, including the direct allometric method and indirect digital hemispherical photograph (DHP) methods. LAIs retrieved by GOST2 show strong agreement with the surrogate truth estimated by the allometric method (R2 = 0.79, RMSE = 3.03), but underestimations of retrieved LAIs by 4SAIL and the SNAP tool reach up to 27.6 and 28.8, respectively, due to lack of consideration of leaf clumping. These results indicate the following: (1) Depending on gap analysis-based clumping index (Ω) algorithms, leaf clumping corrections in indirect ground-based LAI estimations are unsuccessful for highly clumped Moso bamboo canopies due to heavy overlapped leaves; (2) LAIs of dense and highly clumped Moso bamboo canopies can be retrieved from satellite remote sensing data through canopy reflectance models with leaf clumping consideration; (3) The misunderstanding of LAI ranges of Moso bamboo canopies by previous studies (2.2–6.5) can be attributed to the application of gap analysis-based Ω for indirect ground-based LAI estimations; and (4) Effective leaf area index (Le) derived from satellite remote sensing data, and validated using gap analysis-based Le/Ω, could be erroneously interpreted as LAI. Full article
(This article belongs to the Section Forest Remote Sensing)
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17 pages, 3550 KB  
Article
Meso-Scale Breakage Characteristics of Recycling Construction and Demolition Waste Subgrade Material Under Compaction Effort
by Lu Han, Weiliang Gao, Yaping Tao and Lulu Liu
Materials 2025, 18(11), 2439; https://doi.org/10.3390/ma18112439 - 23 May 2025
Cited by 2 | Viewed by 845
Abstract
The application of construction and demolition waste (CDW) as roadbed filler faces challenges due to the variable mechanical properties caused by fragile recycled brick aggregates. This study elucidates the breakage mechanism of CDW fillers under compaction effort through a combination of standardized laboratory [...] Read more.
The application of construction and demolition waste (CDW) as roadbed filler faces challenges due to the variable mechanical properties caused by fragile recycled brick aggregates. This study elucidates the breakage mechanism of CDW fillers under compaction effort through a combination of standardized laboratory compaction tests and discrete element method (DEM) simulations. Furthermore, the breakage evolution patterns of mixed fills comprising recycled concrete and brick aggregates at various mixing ratios were revealed. A DEM model was developed to characterize recycled concrete and brick aggregates, adopting polygonal clumps for particles >4.75 mm and spherical clumps for finer fractions. The results indicate that particle breakage progresses through three distinct stages: linear fragment stage (0–200 kJ/m3, 50% of total breakage), deceleration growth stage (200–1000 kJ/m3, 38% of total breakage), and residual crushing stage (1000–2684.9 kJ/m3, 12% of total breakage). Recycled concrete aggregates form a skeleton restraining deep cracks, while brick aggregates enhance stability through energy dissipation and void filling. However, exceeding 30% brick content impedes skeleton development. Critically, a 30% brick content optimizes performance, achieving peak dry density with 25% lower compression deformation than concrete-only fillers, while limiting breakage index rise. These results provide a science-based strategy to optimize CDW roadbed design, improving recycling efficiency and supporting sustainable infrastructure. Full article
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21 pages, 4967 KB  
Article
Evaluation of MODIS and VIIRS BRDF Parameter Differences and Their Impacts on the Derived Indices
by Chenxia Wang, Ziti Jiao, Yaowei Feng, Jing Guo, Zhilong Li, Ge Gao, Zheyou Tan, Fangwen Yang, Sizhe Chen and Xin Dong
Remote Sens. 2025, 17(11), 1803; https://doi.org/10.3390/rs17111803 - 22 May 2025
Cited by 4 | Viewed by 1608
Abstract
Multi-angle remote sensing observations play an important role in the remote sensing of solar radiation absorbed by land surfaces. Currently, the Moderate Resolution Imaging Spectroradiometer (MODIS) and Visible Infrared Imaging Radiometer Suite (VIIRS) teams have successively applied the Ross–Li kernel-driven bidirectional reflectance distribution [...] Read more.
Multi-angle remote sensing observations play an important role in the remote sensing of solar radiation absorbed by land surfaces. Currently, the Moderate Resolution Imaging Spectroradiometer (MODIS) and Visible Infrared Imaging Radiometer Suite (VIIRS) teams have successively applied the Ross–Li kernel-driven bidirectional reflectance distribution function (BRDF) model to integrate multi-angle observations to produce long time series BRDF model parameter products (MCD43 and VNP43), which can be used for the inversion of various surface parameters and the angle correction of remote sensing data. Even though the MODIS and VIIRS BRDF products originate from sensors and algorithms with similar designs, the consistency between BRDF parameters for different sensors is still unknown, and this likely affects the consistency and accuracy of various downstream parameter inversions. In this study, we applied BRDF model parameter time-series data from the overlapping period of the MODIS and VIIRS services to systematically analyze the temporal and spatial differences between the BRDF parameters and derived indices of the two sensors from the site scale to the region scale in the red band and NIR band, respectively. Then, we analyzed the sensitivity of the BRDF parameters to variations in Normalized Difference Hotspot–Darkspot (NDHD) and examined the spatiotemporal distribution of zero-valued pixels in the BRDF parameter products generated by the constraint method in the Ross–Li model from both sensors, assessing their potential impact on NDHD derivation. The results confirm that among the three BRDF parameters, the isotropic scattering parameters of MODIS and VIIRS are more consistent, whereas the volumetric and geometric-optical scattering parameters are more sensitive and variable; this performance is more pronounced in the red band. The indices derived from the MODIS and VIIRS BRDF parameters were compared, revealing increasing discrepancies between the albedo and typical directional reflectance and the NDHD. The isotropic scattering parameter and the volumetric scattering parameter show responses that are very sensitive to increases in the equal interval of the NDHD, indicating that the differences between the MODIS and VIIRS products may strongly influence the consistency of NDHD estimation. In addition, both MODIS and VIIRS have a large proportion of zero-valued pixels (volumetric and geometric-optical parameter layers), whereas the spatiotemporal distribution of zero-valued pixels in VIIRS is more widespread. While the zero-valued pixels have a minor influence on reflectance and albedo estimation, such pixels should be considered with attention to the estimation accuracy of the vegetation angular index, which relies heavily on anisotropic characteristics, e.g., the NDHD. This study reveals the need in optimizing the Clumping Index (CI)-NDHD algorithm to produce VIIRS CI product and highlights the importance of considering BRDF product quality flags for users in their specific applications. The method used in this study also helps improve the theoretical framework for cross-sensor product consistency assessment and clarify the uncertainty in high-precision ecological monitoring and various remote sensing applications. Full article
(This article belongs to the Special Issue Remote Sensing of Solar Radiation Absorbed by Land Surfaces)
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16 pages, 1402 KB  
Article
Prevalence, Antimicrobial Resistance, and Virulence Potential of Staphylococcus aureus in Donkeys from Nigeria
by Onyinye Josephine Okorie-Kanu, Madubuike Umunna Anyanwu, Obichukwu Chisom Nwobi, Regina Yaya Tambe-Ebot, Nkechi Harriet Ikenna-Ezeh, Chukwuemeka Calistus Okolo, Lynda Onyinyechi Obodoechi, Patience Chinasa Ugwu, Ifeyinwa Riona Okosi, Ishmael Festus Jaja and James Wabwire Oguttu
Antibiotics 2025, 14(5), 453; https://doi.org/10.3390/antibiotics14050453 - 29 Apr 2025
Cited by 1 | Viewed by 2359
Abstract
Background: Animal-associated antimicrobial-resistant staphylococci pose a One Health concern, as they can spread into the environment and cause serious infections. Yet, donkeys in Nigeria have been largely overlooked as potential reservoirs of these pathogens. Aim/Objectives: To isolate Staphylococcus aureus from donkeys in Obollo-Afor, [...] Read more.
Background: Animal-associated antimicrobial-resistant staphylococci pose a One Health concern, as they can spread into the environment and cause serious infections. Yet, donkeys in Nigeria have been largely overlooked as potential reservoirs of these pathogens. Aim/Objectives: To isolate Staphylococcus aureus from donkeys in Obollo-Afor, southeast Nigeria, assess their antimicrobial resistance profiles, and evaluate their virulence potential. Materials and Methods: Staphylococci were isolated from the nasal swabs of 250 donkeys, using mannitol salt agar, confirmed biochemically, with Staphylococcus aureus identified via a latex agglutination test and mass spectrometry. The resistance profiles of the isolates, including in regard to methicillin, inducible clindamycin, and β-lactamase production, were determined using disc diffusion, while vancomycin resistance was assessed through the use of agar dilution. The virulence factors were evaluated phenotypically. Results: Of the 250 samples, 11 (4.4%) contained S. aureus and 239 (95.6%) grew other Staphylococcus species. The resistance rates of the 11 S. aureus isolates to gentamicin, penicillin, tigecycline, cefoxitin, linezolid, and chloramphenicol were 45.5%, 66.7%, 54.5%, 27.3%, 36.4%, and 18.1%, respectively. The phenotypic methicillin-resistant S. aureus prevalence was 1.2%. Additionally, 23.5% of the S. aureus isolates were multidrug resistant, with a mean antibiotic resistance index of 0.25. All the S. aureus isolates exhibited virulence factors like clumping factor expression, catalase, caseinase, lecithinase, and gelatinase activity, while the occurrence of haemagglutinin, biofilm, pellicle, and hemolysin occurred in 27.3%, 54.5%, 36.4%, 72.2%, respectively. Conclusion: Although a small percentage of donkeys in Nigeria may harbor S. aureus, these animals are potentially spreading antimicrobial resistance, including multidrug and methicillin resistance, to humans and the environment. Full article
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27 pages, 5909 KB  
Article
A Phenologically Simplified Two-Stage Clumping Index Product Derived from the 8-Day Global MODIS-CI Product Suite
by Ge Gao, Ziti Jiao, Zhilong Li, Chenxia Wang, Jing Guo, Xiaoning Zhang, Anxin Ding, Zheyou Tan, Sizhe Chen, Fangwen Yang and Xin Dong
Remote Sens. 2025, 17(2), 233; https://doi.org/10.3390/rs17020233 - 10 Jan 2025
Cited by 1 | Viewed by 1813
Abstract
The clumping index (CI) is a key structural parameter that quantifies the nonrandomness of the spatial distribution of vegetation canopy leaves. Investigating seasonal variations in the CI is crucial, especially for estimating the leaf area index (LAI) and studying global carbon and water [...] Read more.
The clumping index (CI) is a key structural parameter that quantifies the nonrandomness of the spatial distribution of vegetation canopy leaves. Investigating seasonal variations in the CI is crucial, especially for estimating the leaf area index (LAI) and studying global carbon and water cycles. However, accurate estimations of the seasonal CI have substantial challenges, e.g., from the need for accurate hot spot measurements, i.e., the typical feature of the bidirectional reflectance distribution function (BRDF) shape in the current CI algorithm framework. Therefore, deriving a phenologically simplified stable CI product from a high-frequency CI product (e.g., 8 days) to reduce the uncertainty of CI seasonality and simplify CI applications remains important. In this study, we applied the discrete Fourier transform and an improved dynamic threshold method to estimate the start of season (SOS) and end of season (EOS) from the CI time series and indicated that the CI exhibits significant seasonal variation characteristics that are generally consistent with the MODIS land surface phenology (LSP) product (MCD12Q2), although seasonal differences between them probably exist. Second, we divided the vegetation cycle into two phenological stages based on the MODIS LSP product, ignoring the differences mentioned above, i.e., the leaf-on season (LOS, from greenup to dormancy) and the leaf-off season (LFS, after dormancy and before greenup of the next vegetation cycle), and developed the phenologically simplified two-stage CI product for the years 2001–2020 using the MODIS 8-day CI product suite. Finally, we assessed the accuracy of this CI product (RMSE = 0.06, bias = 0.01) via 95 datasets from 14 field-measured sites globally. This study revealed that the CI exhibited an approximately inverse trend in terms of phenological variation compared with the NDVI. Globally, based on the phenologically simplified two-stage CI product, the CILOS is smaller than the CILFS across all land cover types. Compared with the LFS stage, the quality for this CI product is better in the LOS stage, where the QA is basically identified as 0 and 1, accounting for more than ~90% of the total quality flag, which is significantly higher than that in the LFS stage (~60%). This study provides relatively reliable CI datasets that capture the general trend of seasonal CI variations and simplify potential applications in modeling ecological, meteorological, and other surface processes at both global and regional scales. Therefore, this study provides both new perspectives and datasets for future research in relation to CI and other biophysical parameters, e.g., the LAI. Full article
(This article belongs to the Section Atmospheric Remote Sensing)
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19 pages, 4707 KB  
Article
Coppice and Coppice-with-Standard Stands Systems: Implications for Forest Management and Biodiversity
by Sajad Ghanbari, Pedro Álvarez-Álvarez, Ayeshe Esmaili, Samira Sasanifar, Seyed Mohmmad Moein Sadeghi, Kiomars Sefidi and Ivan Eastin
Forests 2025, 16(1), 116; https://doi.org/10.3390/f16010116 - 10 Jan 2025
Viewed by 2455
Abstract
Examining forest stand structures is crucial for effective forest management, as it provides essential insights into current conditions and informs future strategies. Coppice systems, a historic forest management practice with centuries of documented use across various regions, play a vital role in supporting [...] Read more.
Examining forest stand structures is crucial for effective forest management, as it provides essential insights into current conditions and informs future strategies. Coppice systems, a historic forest management practice with centuries of documented use across various regions, play a vital role in supporting unique flora and fauna, making them integral to conservation efforts. This study has two primary objectives: (i) to evaluate how various forest management approaches impact species composition and structural characteristics of forest stands, and (ii) to assess and compare diversity within these stands using a range of indices. In this research, two management systems in Iran’s Arasbaran forests were compared: the traditional coppice system and the coppice-with-standard (CWS) stands system. Fieldwork was conducted in 24 sample plots for each management system, where quantitative indicators and biodiversity indices were employed to evaluate and compare stand characteristics. The findings revealed that the CWS system exhibited higher mean values for tree height, diameter at the breast height (DBH), and basal area compared to the coppice system. Coppice stands had a sprout clump density of 546 per hectare, primarily composed of Quercus macranthera, while the CWS stands had a combined tree and sprout clump density of 421 per hectare. Diversity assessments showed that species diversity, as measured by Pielou’s index, was higher in the coppice system (1.42) than in the CWS system (1.01). However, species richness, represented by the Menhinik index, was lower in both systems, with values of 0.31 for the coppice system and 0.19 for the CWS system. These results suggest that the CWS system is more effective in promoting growth and stand development, whereas the coppice system may better support biodiversity. The findings have practical implications for forest managers and policymakers in Iran and other regions with similar forest ecosystems. For instance, if the objective is to enhance biodiversity and ecosystem resilience, the coppice system—with its higher diversity indices—may be the preferred choice. On the other hand, if the aim is to boost timber production while maintaining a baseline level of biodiversity, the CWS system could be more suitable. Full article
(This article belongs to the Section Forest Ecology and Management)
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15 pages, 5760 KB  
Article
Retinal Dystrophy Associated with Homozygous Variants in NRL
by Jordi Maggi, James V. M. Hanson, Lisa Kurmann, Samuel Koller, Silke Feil, Christina Gerth-Kahlert and Wolfgang Berger
Genes 2024, 15(12), 1594; https://doi.org/10.3390/genes15121594 - 12 Dec 2024
Cited by 5 | Viewed by 2258
Abstract
Background/Objectives: Neural retina leucine zipper (NRL) is a transcription factor involved in the differentiation of rod photoreceptors. Pathogenic variants in the gene encoding NRL have been associated with autosomal dominant retinitis pigmentosa and autosomal recessive clumped pigmentary retinal degeneration. Only a dozen [...] Read more.
Background/Objectives: Neural retina leucine zipper (NRL) is a transcription factor involved in the differentiation of rod photoreceptors. Pathogenic variants in the gene encoding NRL have been associated with autosomal dominant retinitis pigmentosa and autosomal recessive clumped pigmentary retinal degeneration. Only a dozen unrelated families affected by recessive NRL-related retinal dystrophy have been described. The purpose of this study was to expand the genotypic spectrum of this disease by reporting clinical and genetic findings of two unrelated families. Methods: Index patients affected by retinal dystrophy were genetically tested by whole-exome sequencing (WES) and whole-genome sequencing (WGS). Segregation analysis within the families was performed for candidate variants. A minigene assay was performed to functionally characterize a variant suspected to affect splicing. Results: Variant filtering revealed homozygous NRL variants in both families. The variant in patient A was a small deletion encompassing the donor splice site of exon 1 of transcript NM_006177.3. The minigene assay revealed that this variant led to two aberrant transcripts that used alternative cryptic donor splice sites located in intron 1. In patient B, a stop-gain variant was identified in the last exon of NRL in a homozygous state due to maternal uniparental disomy of chromosome 14. Conclusions: Our study expands the genotypic spectrum of autosomal recessive NRL-related retinal dystrophy. Moreover, it underscores the importance of actively maintaining bioinformatic pipelines for variant detection and the utility of minigene assays in functionally characterizing candidate splicing variants. Full article
(This article belongs to the Special Issue Study of Inherited Retinal Diseases—Volume II)
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17 pages, 5871 KB  
Article
DNA Damage, Cell Death, and Alteration of Cell Proliferation Insights Caused by Copper Oxide Nanoparticles Using a Plant-Based Model
by Sazada Siddiqui
Biology 2024, 13(10), 805; https://doi.org/10.3390/biology13100805 - 9 Oct 2024
Cited by 10 | Viewed by 2176
Abstract
The speedy growth of copper oxide nanoparticle (CuO NP) manufacturing due to their wide application in industries has caused concerns due to their increased discharge into the environment from both purposeful and accidental sources. Their presence at an elevated concentration in the environment [...] Read more.
The speedy growth of copper oxide nanoparticle (CuO NP) manufacturing due to their wide application in industries has caused concerns due to their increased discharge into the environment from both purposeful and accidental sources. Their presence at an elevated concentration in the environment can cause potential hazards to the plant kingdom, specifically to staple food crops. However, limited research is available to determine the consequences of CuO NPs. The present study aimed to assess the morphological and cytological changes induced by CuO NPs on Pisum sativum L., a key staple food crop. Seeds of Pisum sativum were exposed to various concentrations of CuO NPs (0, 25, 50, 75, 100, and 125 ppm) for 2 h, and their effects on seed germination (SG), radicle length (RL), cell proliferation kinetics (CPK), mitotic index (MI), cell death (CD), micronucleus frequency (MNF), and chromosomal aberration frequency (CAF) were studied. The results indicate a significant reduction in SG, RL, CPK, and MI and a significant dose-dependent increase in CD, MNF, and CAF. CuO NP treatment has led to abnormal meiotic cell division, increased incidence of micronucleus frequency, and chromosomal aberration frequency. Additionally, the CuO NP-treated groups showed an increase in the percentage of aberrant meiotic cells such as laggard (LG), double bridge (DB), stickiness (STC), clumped nuclei (CNi), precocious separation (PS), single bridge (SB), and secondary association (SA). CuO NP treatment led to reductions in SG as follows: 55% at 24 h, 60.10% at 48 h, and 65% at 72 h; reductions in RL as follows: 0.55 ± 0.021 cm at 24 h, 0.67 ± 0.01 cm at 48 h, and 0.99 ± 0.02 cm at 72 h; reductions in CPK as follows: 34.98% at prophase, 7.90% at metaphase, 3.5% at anaphase, and 0.97% at telophase. It also led to a 57.45% increase in CD, a 39.87% reduction in MI, and a 60.77% increase in MNF at a higher concentration of 125 ppm. The findings of this study clearly show that CuO NPs have a genotoxic effect on the food crop plant Pisum sativum. Full article
(This article belongs to the Section Plant Science)
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18 pages, 5217 KB  
Article
Effect of the Particle Size Distribution of the Ballast on the Lateral Resistance of Continuously Welded Rail Tracks
by Jafar Chalabii, Morteza Esmaeili, Dániel Gosztola, Szabolcs Fischer and Majid Movahedi Rad
Infrastructures 2024, 9(8), 129; https://doi.org/10.3390/infrastructures9080129 - 6 Aug 2024
Cited by 7 | Viewed by 3430
Abstract
While the effect of ballast degradation on lateral resistance is noteworthy, limited research has delved into the specific aspect of ballast breakage in this context. This study is dedicated to assessing the influence of breakage on sleeper lateral resistance. For simplicity, it is [...] Read more.
While the effect of ballast degradation on lateral resistance is noteworthy, limited research has delved into the specific aspect of ballast breakage in this context. This study is dedicated to assessing the influence of breakage on sleeper lateral resistance. For simplicity, it is assumed that ballast breakage has already occurred. Accordingly, nine granularity variations finer than No. 24 were chosen for simulation, with No. 24 as the assumed initial particle size distribution. Initially, a DEM model was validated for this purpose using experimental outcomes. Subsequently, employing this model, the lateral resistance of different particle size distributions was examined for a 3.5 mm displacement. The track was replaced by a reinforced concrete sleeper in the models, and no rails or rail fasteners were considered. The sleeper had a simplified model with clumps, the type of which was the so-called B70 and was applied in Western Europe. The sleeper was taken into consideration as a rigid body. The crushed stone ballast was considered as spherical grains with the addition that they were divided into fractions (sieves) in weight proportions (based on the particle distribution curve) and randomly generated in the 3D model. The complete 3D model was a 4.84 × 0.6 × 0.57 m trapezoidal prism with the sleeper at the longitudinal axis centered and at the top of the model. Compaction was performed with gravity and slope walls, with the latter being deleted before running the simulation. During the simulation, the sleeper was moved horizontally parallel to its longitudinal axis and laterally up to 3.5 mm in static load in the compacted ballast. The study successfully established a relationship between lateral resistance and ballast breakage. The current study’s findings indicate that lateral resistance decreases as ballast breakage increases. Moreover, it was observed that the rate of lateral resistance decrease becomes zero when the ballast breakage index reaches 0.6. Full article
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12 pages, 2189 KB  
Article
Habitat Characteristics of the Endangered Himalayan Red Panda in Panchthar–Ilam–Taplejung Corridor, Eastern Nepal
by Anjali Limbu, Arjun Thapa, Laxman Khanal, Sandesh Gurung, Nicolas James Cruz and Tej Bahadur Thapa
Ecologies 2024, 5(3), 342-353; https://doi.org/10.3390/ecologies5030021 - 3 Jul 2024
Cited by 1 | Viewed by 6047
Abstract
The Panchthar–Ilam–Taplejung Corridor in Eastern Nepal, managed through community forestry, is a crucial habitat for the Himalayan red panda, an endangered carnivore threatened by forest degradation and illegal trade. We deployed the altitude line intercept and ten-tree plotless methods to evaluate the distribution [...] Read more.
The Panchthar–Ilam–Taplejung Corridor in Eastern Nepal, managed through community forestry, is a crucial habitat for the Himalayan red panda, an endangered carnivore threatened by forest degradation and illegal trade. We deployed the altitude line intercept and ten-tree plotless methods to evaluate the distribution of Himalayan red pandas and the environmental factors affecting them within four community forests, namely Singhadevi, Chitre-Hile, Chhipchhipe, and Kalikhop-Dadehli, of the corridor. We established a total of 23 transects and 92 plots, identifying 41 plots with evidence of the Himalayan red panda’s presence. The sign occurrence revealed a clumped distribution of the species across all four community forests. The Himalayan red panda signs were observed between 2200 m and 2700 m above sea level (asl) and the majority of them were from habitats with a moderate slope within elevations of 2400 m to 2500 m asl. The primary sites for the defecation were large horizontal tree branches (78.12%), followed by forest ground (15.62%) and rocks (6.25%). The dominant tree species in their habitats included Lithocarpus pachyphylla (Importance value index, IVI = 45.05), Symplocus theifolia (IVI = 37.19), Symplocos pyrifolia (IVI = 20.99), Quercus lamellosa (IVI = 19.25), and Magnolia campbellii (IVI = 17.25). Among the thirteen environmental variables examined, proximity to water, distance to road, bamboo density, and Normalized Difference Vegetation Index were identified as the major factors influencing the Himalayan red panda’s distribution. This research provides crucial insights to develop site-specific habitat management plans for community forestry. Full article
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19 pages, 3811 KB  
Article
Neighborhood Competition and Understory-Associated Vegetation Are Important Factors Influencing the Natural Regeneration of Subtropical Mountain Forests
by Zizhuo Wang, Kunrong Qin, Wen Fang and Haiyang Wang
Forests 2024, 15(6), 1017; https://doi.org/10.3390/f15061017 - 12 Jun 2024
Cited by 4 | Viewed by 2185
Abstract
Natural regeneration is deemed essential for maintaining biodiversity and ecosystem stability. Previous studies, however, have primarily concentrated on regions exhibiting limited environmental and climatic variability, overlooking the classification of natural regeneration based on age and source. Research conducted at the mesoscale, characterized by [...] Read more.
Natural regeneration is deemed essential for maintaining biodiversity and ecosystem stability. Previous studies, however, have primarily concentrated on regions exhibiting limited environmental and climatic variability, overlooking the classification of natural regeneration based on age and source. Research conducted at the mesoscale, characterized by increased environmental variability and the incorporation of neighborhood competition and understory-associated vegetation, enhances our comprehension of the multifaceted influences on natural regeneration. To comprehend this issue, this study implemented 60 plots, each measuring 20 m × 20 m, across five distinct areas of Chongqing, China. Twenty explanatory variables were chosen from five diverse categories: understory vegetation, neighborhood competition, stand structure, climatic factors, and environmental factors. And the naturally regenerated species were classified into seedlings and saplings, as well as endogenous and exogenous species, based on their age and origin. We examined the response of the different categories of natural regeneration to various factors and constructed a structural equation model (SEM) for significant factors to investigate their direct and indirect effects on natural regeneration. A total of 61 regenerated tree species belonging to 29 families and 42 genera were found in the study area, and the naturally regenerating species with high importance values were Quercus fabri, Robinia pseudoacacia, Alangium chinense, Cunninghamia lanceolata, and Ligustrum lucidum. It was found that neighborhood competition and understory-associated vegetation explained the largest proportion (more than 50%) of the variation in the different categories of natural regeneration, and forests with clumped distribution (W), a high mingling index (M) and strong competition (H) had a reduced natural regeneration capacity. Understory-associated herbs significantly reduced natural regeneration and the crowdedness index (C) significantly inhibited the understory-associated herbs, thus indirectly promoting natural regeneration. The shrub cover is significantly and positively correlated with the number of naturally regenerated plants and can be used as an indicator of a forest community’s regeneration potential. Understanding the differences in the importance of various factors at the mesoscale, as well as their direct and indirect impacts, can help us further comprehend the mechanisms of natural regeneration and provide a foundation for the sustainable development of forests. Full article
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19 pages, 3227 KB  
Article
Hyperspectral Leaf Area Index and Chlorophyll Retrieval over Forest and Row-Structured Vineyard Canopies
by Luke A. Brown, Harry Morris, Andrew MacLachlan, Francesco D’Adamo, Jennifer Adams, Ernesto Lopez-Baeza, Erika Albero, Beatriz Martínez, Sergio Sánchez-Ruiz, Manuel Campos-Taberner, Antonio Lidón, Cristina Lull, Inmaculada Bautista, Daniel Clewley, Gary Llewellyn, Qiaoyun Xie, Fernando Camacho, Julio Pastor-Guzman, Rosalinda Morrone, Morven Sinclair, Owen Williams, Merryn Hunt, Andreas Hueni, Valentina Boccia, Steffen Dransfeld and Jadunandan Dashadd Show full author list remove Hide full author list
Remote Sens. 2024, 16(12), 2066; https://doi.org/10.3390/rs16122066 - 7 Jun 2024
Cited by 9 | Viewed by 5164
Abstract
As an unprecedented stream of decametric hyperspectral observations becomes available from recent and upcoming spaceborne missions, effective algorithms are required to retrieve vegetation biophysical and biochemical variables such as leaf area index (LAI) and canopy chlorophyll content (CCC). In the context of missions [...] Read more.
As an unprecedented stream of decametric hyperspectral observations becomes available from recent and upcoming spaceborne missions, effective algorithms are required to retrieve vegetation biophysical and biochemical variables such as leaf area index (LAI) and canopy chlorophyll content (CCC). In the context of missions such as the Environmental Mapping and Analysis Program (EnMAP), Precursore Iperspettrale della Missione Applicativa (PRISMA), Copernicus Hyperspectral Imaging Mission for the Environment (CHIME), and Surface Biology Geology (SBG), several retrieval algorithms have been developed based upon the turbid medium Scattering by Arbitrarily Inclined Leaves (SAIL) radiative transfer model. Whilst well suited to cereal crops, SAIL is known to perform comparatively poorly over more heterogeneous canopies (including forests and row-structured crops). In this paper, we investigate the application of hybrid radiative transfer models, including a modified version of SAIL (rowSAIL) and the Invertible Forest Reflectance Model (INFORM), to such canopies. Unlike SAIL, which assumes a horizontally homogeneous canopy, such models partition the canopy into geometric objects, which are themselves treated as turbid media. By enabling crown transmittance, foliage clumping, and shadowing to be represented, they provide a more realistic representation of heterogeneous vegetation. Using airborne hyperspectral data to simulate EnMAP observations over vineyard and deciduous broadleaf forest sites, we demonstrate that SAIL-based algorithms provide moderate retrieval accuracy for LAI (RMSD = 0.92–2.15, NRMSD = 40–67%, bias = −0.64–0.96) and CCC (RMSD = 0.27–1.27 g m−2, NRMSD = 64–84%, bias = −0.17–0.89 g m−2). The use of hybrid radiative transfer models (rowSAIL and INFORM) reduces bias in LAI (RMSD = 0.88–1.64, NRMSD = 27–64%, bias = −0.78–−0.13) and CCC (RMSD = 0.30–0.87 g m−2, NRMSD = 52–73%, bias = 0.03–0.42 g m−2) retrievals. Based on our results, at the canopy level, we recommend that hybrid radiative transfer models such as rowSAIL and INFORM are further adopted for hyperspectral biophysical and biochemical variable retrieval over heterogeneous vegetation. Full article
(This article belongs to the Section Environmental Remote Sensing)
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