Miracle-dz/UniFAR-FTUs huggingface dataset:
Mapping Natural Forest Remnants with Multi-Source and Multi-Temporal Remote Sensing Data for More Informed Management of Global Biodiversity Hotspots

Global terrestrial biodiversity hotspots (GBH) represent areas featuring exceptional concentrations of endemism and habitat loss in the world. Unfortunately, geospatial data of natural habitats of the GBHs are often outdated, imprecise, and coarse, and need updating for improved management and protection actions. Recent developments in satellite image availability, combined with enhanced machine learning algorithms and computing capacity, enable cost-efficient updating of geospatial information of these already severely fragmented habitats. This study aimed to develop a more accurate method for mapping closed canopy evergreen natural forest (CCEF) of the Eastern Arc Mountains (EAM) ecoregion in Tanzania and Kenya, and to update the knowledge on its spatial extent, level of fragmentation, and conservation status. We tested 1023 model possibilities stemming from a combination of Sentinel-1 (S1) and Sentinel-2 (S2) satellite imagery, spatial texture of S1 and S2, seasonality derived from Landsat-8 time series, and topographic information, using random forest modelling approach. We compared the best CCEF model with existing spatial forest products from the EAM through independent accuracy assessment. Finally, the CCEF model was used to estimate the fragmentation and conservation coverage of the EAM. The CCEF model has moderate accuracy measured in True Skill Statistic (0.57), and it clearly outperforms other similar products from the region. Based on this model, there are about 296,000 ha of Eastern Arc Forests (EAF) left. Furthermore, acknowledging small forest fragments (1–10 ha) implies that the EAFs are more fragmented than previously considered. Currently, the official protection of EAFs is disproportionally targeting well-studied mountain blocks, while less known areas and small fragments are underrepresented in the protected area network. Thus, the generated CCEF model should be used to design updates and more informed and detailed conservation allocation plans to balance this situation. The results highlight that spatial texture of S2, seasonality, and topography are the most important variables describing the EAFs, while spatial texture of S1 increases the model performance slightly. All in all, our work demonstrates that recent developments in Earth observation allows significant enhancements in mapping, which should be utilized in areas with outstanding biodiversity values for better forest and conservation planning.
Energy supply of the okapi in captivity: intake and digestion trials

In the nutrition of browsing ruminants in captivity, adequate nutrient digestibility and energy content of diet is debated. Problems related to energy-provision and low forage intake have been reported for the okapi and other browsers like the giraffe, particularly during winter. High-fiber concentrates like unmolassed beet pulp have some potential to improve the nutritional management of these species. Using a total of six okapis in captivity, seven feeding trials were carried out at two facilities (A+B) on a structured but opportunistic base. Three trials (A1, A2, B1) were conducted when animals were fed their regular diet including grain based energy concentrates, fruits and vegetables, and alfalfa (Medicago sativa) hay. Two trials (A5, B2) examined the effect of unmolassed beet pulp, and two (A3,4) examined the effect of unmolassed beet pulp+fresh browse. Daily intake and feces production were quantified over 8–12 days. Samples were analyzed for dry matter, crude ash, neutral detergent fiber (NDF)/acid detergent fiber (ADF)/acid detergent lignin (ADL), crude protein, and gross energy. Metabolizable energy content of diets was estimated via a factor (0.83) from digestible energy. The proportion of beet pulp in diets was 13% (A3), 24% (A4), 20% (A5), and 21% (B2). Browse proportion was 11% (A3) and 32% (A4). Daily feed intake ranged between 1.5–1.7% of body weight (BW), digestibility of organic matter between 61–74%. Digestibility of fiber (NDF) was higher in beet pulp diets (A3=39%, A4=60%, A5=54%, B2=61%) than in the others (A1=48%, A2=33%, B1=48%). Supply of metabolizable energy (ME) ranged between 0.50–0.70 MJ ME/(kg BW0.75*day), meeting energy requirements of okapis of 0.50–0.53 MJ ME/(kg BW0.75*day) in general. Diets with beet pulp+browse were not found to be highest, but in the upper level of the range of forage proportions of this study. Palatable browse species were preferred over all other feedstuff offered. The use of unmolassed beet pulp as energy-concentrate for browsing ruminants like the okapi can be recommended because diets high in this high-fibre feedstuff resulted in adequate energy intakes. Zoo Biol 0:1–14, 2006. © 2006 Wiley-Liss, Inc.
Detection, Segmentation, and Model Fitting of Individual Tree Stems from Airborne Laser Scanning of Forests Using Deep Learning

Accurate measurements of the structural characteristics of trees such as height, diameter, sweep and taper are an important part of forest inventories in managed forests and commercial plantations. Both terrestrial and aerial LiDAR are currently employed to produce pointcloud data from which inventory metrics can be determined. Terrestrial/ground-based scanning typically provides pointclouds resolutions of many thousands of points per m 2 from which tree stems can be observed and inventory measurements made directly, whereas typical resolutions from aerial scanning (tens of points per m 2 ) require inventory metrics to be regressed from LiDAR variables using inventory reference data collected from the ground. Recent developments in miniaturised LiDAR sensors are enabling aerial capture of pointclouds from low-flying aircraft at high-resolutions (hundreds of points per m 2 ) from which tree stem information starts to become directly visible, enabling the possibility for plot-scale inventories that do not require access to the ground. In this paper, we develop new approaches to automated tree detection, segmentation and stem reconstruction using algorithms based on deep supervised machine learning which are designed for use with aerially acquired high-resolution LiDAR pointclouds. Our approach is able to isolate individual trees, determine tree stem points and further build a segmented model of the main tree stem that encompasses tree height, diameter, taper, and sweep. Through the use of deep learning models, our approach is able to adapt to variations in pointcloud densities and partial occlusions that are particularly prevalent when data is captured from the air. We present results of our algorithms using high-resolution LiDAR pointclouds captured from a helicopter over two Radiata pine forests in NSW, Australia.
Short-Term Ecogeomorphic Evolution of a Fluvial Delta from Hindcasting Intertidal Marsh-Top Elevations (HIME)

Understanding how delta islands grow and change at contemporary, interannual timescales remains a key scientific goal and societal need, but the high-resolution, high frequency morphodynamic data that would be most useful for this are as yet logistically prohibitive. The recorded water levels needed for relative elevation analysis are also often lacking. This paper presents a new approach for hindcasting intertidal marsh-top elevations (HIME) to resolve ecogeomorphic change, even in a young, rapidly changing fluvial delta setting, at sub-decadal temporal resolution and at the spatial resolution of widely available optical remote sensing imagery (e.g., 30 m Landsat). The HIME method first calculates: (i) the probability of land exposure in a set of historical imagery from a user-defined discrete timespan (e.g., months or years); (ii) the probability of water level non-exceedance from water level records, which need not be complete nor coincident with the imagery; and (iii) the systematic variation in local mean water level with distance along the primary hydraulic gradient. The HIME method then combines these inputs to estimate a marsh-top elevation map for each historical timespan of interest. The method was developed, validated, applied, and results analyzed to investigate time-lapse evolution of the Wax Lake Delta in Louisiana, USA, every three years, over two decades (1993–2013). The hindcast maps of delta island extents and elevations evidenced ecogeomorphic system self-organization around four stable attractors, or elevation platforms, at about −0.3 m (subtidal), 0.2 m, 0.4 m, and 0.9 m (supratidal) NAVD88. The HIME results also yielded a time series of net subaerial sediment accumulation, and specific locations and magnitudes of gains and losses, at scales from 30 m to delta-wide (~100 km3) and 6 to 21 years. Average subaerial net sediment accumulation at the Wax Lake Delta (WLD) was estimated as 0.6 cm/yr during the study period. Finally, multiple linear regression models were successfully trained on the HIME elevation maps to model evolving delta island morphologies based on simple geometric factors, such as distance down-delta and position on a delta island; the models also successfully reproduced an average delta topset slope of 1.4 cm. Overall, this study’s development and application of the HIME method added detailed insights to recent, transient ecogeomorphological change at the WLD, and demonstrated the potential of the new approach for accurately reconstructing past intertidal topographies and dynamic change.
Communicating Quantities

For a while now I’ve been trying to figure out precisely why so many people really struggle when it comes to making thematic maps where the purpose is to communicate something about the spatial pattern of numbers. Why do so many pick the wrong map type, select inappropriate classification schemes, use poor colours and so on? Sometimes it’s down to a lack of knowledge and understanding. Sometimes, it’s simply down to the fact that so many people now make maps using software that preselects any number of variables and they neither understand what’s going on or why they would change things. Sometimes it’s down to a lack of time. Sometimes, well.there’s got to be other more fundamental reasons. I then happened across what I found to be an insightful blog post by Santiago Ortiz on Visual.ly (Ortiz, 2012) and think I found the answer that had been staring me in the face for so long. I contacted Ortiz and was granted permission to reprint much of his blog here which I think provides a really valuable insight into why it’s just so fundamentally difficult to map patterns of quantitative data. Ortiz posed the following question at a workshop on interactive data visualisation in 2010: ‘let’s try and find all possible ways to visualize a ludicrously small set of data of two numbers. Afterwards, let’s try and pick the best visualization’. With such a tiny dataset, you would think both exercises could be completed in less than 5 min. Yet, the exercise lasted over 2 h without having actually accomplished either of the two tasks. Not only was the number of possible ways to visualize two values far higher than expected, but also each single visualisation method admitted multiple and interesting variations and opened new questions and discussions. The following is a list of different ways to visualize two numbers. In many cases, the visualisation depends directly on the unit, meaning, interpretation and context of the values. Some of the examples might be seen as variations of the same theme, while others will be perceived as excessively eccentric or even esoteric. The list is, quite probably, not exhaustive! The numbers: 75 and 37
Light and electron microscopic and energy dispersive X-ray microanalysis studies of globoids in protein bodies of embryo tissues and the aleurone layer of rice (Otyza sativa L.) grains

To understand the differences in mineral nutrient storage within tissues and organs of rice (Oryza sativa L.) grains, the distribution of globoids in rice embryo and endosperm tissues was examined using light and transmission electron microscopy and energy dispersive X-ray microanalysis was used to study globoid composition. Globoids were found in most embryo tissues, including provascular cells, and their location and size in sections of protein bodies is described. While P, Mg, and K were commonly detected in all globoids, other elements such as Ca, Mn, Fe, and Zn were sometimes detected in globoids of specific tissues and (or) regions. High peak-to-background ratios for P were obtained in globoids of scutellar and aleurone cells, and moderately high values were detected in ground meristem regions of the mesocotyl and coleoptile. Relatively high K levels were found in globoids in parenchyma cells of the scutellum and coleorhiza; in provascular cells of the radicle; and in ground meristem cells from the .
Interactions between Foliar Pathogens and the Saprophytic Microflora of the Wheat (Triticum aestivum L.) Phylloplane

Hyphal interference between 10 saprophytic micro-organisms isolated from wheat phylloplane against four target pathogens (Septoria tritici, Alternaria triticimaculans, Bipolaris sorokiniana and Drechslera tritici-repentis) were studied microscopically. Antagonism was measured as the ability of the saprophytic micro-organisms to induce morphological changes of hyphae and spores of the pathogens and to reduce conidial germination. Typical reactions included formation of chlamydospores, encircled hyphae, plasmolysis, vacuolation and granulation of hyphae. Ungerminated malformed conidia, lysis, and the formation of inflated germ tubes on germinating conidia were also observed. Paecilomyces lilacinus and Bacillus sp. possessed the greatest capacity for interference. Fusarium moniliforme var. anthophilum, Epicoccum nigrum and Chaetomium globosum were next in order of the range and severity of interference. Spore germination of S. tritici was significantly reduced in the presence of P. lilacinus, F. moniliforme var. anthophilum, E. nigrum, Bacillus sp. , Cryptococcus sp. and Nigrospora sphaerica, with levels of inhibition of up to 69%, Paecilomyces lilacinus, Cryptococcus sp. , F. moniliforme var. anthophilum and N. sphaerica caused a reduction of spore germination of 47-60% with the greatest effect being- against B. sorokiniana. Chaetomium globosum, P. lilacinus, Rhodotorula rubra and Bacillus sp. significantly reduced spore germination of A. triticimaculans. E. nigrum, F. moniliforme var anthophilum, Stemphylium sp. , P. lilacinus and Bacillus sp. caused the greatest reduction in D. tritici-repentis. Greenhouse experiments on pathogen-antagonist interactions on the wheat phylloplane showed the potential value of some of the antagonists for controlling the pathogens. If parasitism occurs in nature, the native micro-organisms might be useful for biological control by competing with the pathogens and so regulating their colonization of wheat leaves.
Estimation of calcium intake by Meadow Pipit nestlings in an acidified area

Calcium availability might limit reproductive output in birds either by effects on eggshell formation or on skeletal growth of nestlings. Quantitative data on calcium intake by nestlings of free-living passerines are needed to test the second hypothesis. In an acidified area of the Jeseniky Mountains (Czech Republic), estimates were made of calcium requirements and intake in Meadow Pipit Anthus pratensis nestlings during the nestling period. Analyses of nestling diet, determined by neck ligatures, showed that only snail shells were an important source of calcium. During the whole nestling period dry matter intake per nestling was 31.1 g, of which snail shells contributed 0.626 g. The total calcium necessary for successful development of each nestling was estimated as 139.8 mg. Arthropods in the diet provided only 16% of the calcium requirement. However, sufficient calcium was ensured by intake of snails (mainly Arianta arbustorum), despite their low abundance in the area.
Distribución geográfica y ecoepidemiología de la fauna de triatominos (Reduviidae: Triatominae) en la Isla Margarita del departamento de Bolívar, Colombia

Introduction. Information concerning to triatomine diversity and some eco-epidemiologic aspects on Margarita Island has been recorded only from two of the five counties on the island. Knowledge about species habitat and their natural infection is essential to establish the risk for Chagas disease in endemic areas. Objective. The distribution of triatomine insect fauna and its infection with Trypanosoma cruzi was described in order to establish and to stratify the risk of Chagas disease transmission. Material and methods. Each of the 5 counties on Margarita Island were surveyed for triatomid insects inside and outside each dwelling. In the extradomicilary area, searches were conducted in the palms and bird nests located within forests and in pastures near domiciles. Infection with T. cruzi was determined amplifying by PCR the DNA extracted from triatomine feces. Results. Five species of Reduviidae were recovered among the 1,154 triatomines captured in the 5 counties. Triatoma maculata and Rhodnius pallescens showed high infection rates within dwellings and as well as in the peridomestic areas in Mompos and Talaigua Nuevo. On the palm trees, only R. pallescens and Eratyrus cuspidatus were found infected, and only in San Fernando and Margarita. In Cicuco, only R. pallescens was infected. Presence of Triatoma dimidiata was also ascertained.Conclusion. Infected triatomines were present in houses and on palm trees in all counties on the island. These observations indicate a potential risk of Chagas across the entire island; furthermore the presence of T. dimidiata, a very efficient Chagas vector, emphasizes the need to establish its epidemiological status on the island.
Mapping Floristic Patterns of Trees in Peruvian Amazonia Using Remote Sensing and Machine Learning

Recognition of the spatial variation in tree species composition is a necessary precondition for wise management and conservation of forests. In the Peruvian Amazonia, this goal is not yet achieved mostly because adequate species inventory data has been lacking. The recently started Peruvian national forest inventory (INFFS) is expected to change the situation. Here, we analyzed genus-level variation, summarized through non-metric multidimensional scaling (NMDS), in a set of 157 INFFS inventory plots in lowland to low mountain rain forests (<2000 m above sea level) using Landsat satellite imagery and climatic, edaphic, and elevation data as predictor variables. Genus-level floristic patterns have earlier been found to be indicative of species-level patterns. In correlation tests, the floristic variation of tree genera was most strongly related to Landsat variables and secondly to climatic variables. We used random forest regression, under varying criteria of feature selection and cross-validation, to predict the floristic composition on the basis of Landsat and environmental data. The best model explained >60% of the variation along NMDS axes 1 and 2 and 40% of the variation along NMDS axis 3. We used this model to predict the three NMDS dimensions at a 450-m resolution over all of the Peruvian Amazonia and classified the pixels into 10 floristic classes using k-means classification. An indicator analysis identified statistically significant indicator genera for 8 out of the 10 classes. The results are congruent with earlier studies, suggesting that the approach is robust and can be applied to other tropical regions, which is useful for reducing research gaps and for identifying suitable areas for conservation.
Efficacy of new bacterial phytase in poultry diets

Phytase produced by Escherichia coli was fed to broiler chicks fed graded levels of available phosphorus (0.25–45%). A positive control involved Natuphos® a fungal phytase commonly used in poultry nutrition. Feeding diets with only 0.25% available phosphorus from 1 to 13 d of age resulted in reduced feed intake and weight gain, with associated loss in tibia weight, tibia ash and tibia phosphorus content (P < 0.01). Adding 600 IU phytase kg−1 diet corrected these problems, and both sources were equally efficacious for most parameters studied. Key words: Phosphorus, phytase, chicken
Effects of Maturity and Postharvest Techniques on Keeping Quality of Melons

Maturity of netted muskmelons (Cucumis melo L., var. reticulatus, cvs Earl′s Favourite and Napoleon) is difficult to estimate by their appearance. Ethylene and flavor volatiles production of the melons were found to be good indicators in estimating maturity.Keeping qualities of the melons during postharvest storage were highly dependent on the fruit′s maturity and on storage methods. Modified atmosphere in seal-packaging with polyethylene bags and ethylene-removing treatment on seal-packaging were effective to maintain qualities of the melons which were at proper maturity stage for harvesting (ethylene production: 0.3μl/kg/h). Keeping-quality periods of the melons were 1 week at 20°C, 2 weeks at 10°C or 3-4 weeks at 4°C, and were not prolonged by low pressure storage.
Sources of nutrients to rooted submerged macrophytes growing in a nutrient‐rich stream

1. The relative contribution of roots and leaves to nutrient uptake by submerged stream macrophytes was tested in experiments where plants were grown in an outdoor flow-channel system. Water was supplied from a nutrient-rich stream with inorganic nitrogen and phosphorus concentrations typical of Danish streams. 2. Four submerged macrophyte species were tested, Elodea canadensis, Callitriche cophocarpa, Ranunculus aquatilis and Potamogeton crispus, and all species were able to satisfy their demand for mineral nutrients by leaf nutrient uptake alone. This was evident from manipulative experiments showing that removal of the roots had no negative impact on the relative growth rate of the plants. Further, the organic N and P concentrations of the plant tissue was constant with time for the de-rooted plants. 3. Enrichment of water and/or sediment had no effect on the relative growth rate of two species, E. canadensis and C. cophocarpa, indicating that in situ nutrient availability was sufficient to cover the needs for growth. Despite the lack of a response in growth rate, a reduced root/shoot biomass ratio was observed with nutrient enrichment of water and/or sediment, and an increased tissue-P concentration in response to open-water enrichment. 4. The open-water nutrient concentrations of the stream in which the experiments were performed are in the upper part of the range found for Danish farmland streams (the majority of Danish streams). Still, however, the negligible effect of nutrient enrichment on the growth of submerged macrophytes observed suggests that mineral nutrient availability might play a minor role in controlling macrophyte growth in most Danish streams.
An Indo-Pacific goby (Teleostei: Gobioidei) from West Africa, with systematic notes on Butis and related eleotridine genera

An eleotridine gobioid fish recently found at Port Harcourt, Nigeria, is identified as the Indo-west Pacific Prionobutis koilomatodon (Bleeker). On the basis of head sensory papillae (free neuromast) patterns, this species is now transferred to the Indo-west Pacific genus Butis Bleeker. A systematic description of the Port Harcourt Butis koilomatodon is accompanied by observations on biology. Occurrence of this species in West Africa is believed to be the result of accidental transport in the ballast water of ships.