Miracle-dz/UniFAR-FTUs huggingface dataset:
A Hierarchical Deep-Learning Approach for Rapid Windthrow Detection on PlanetScope and High-Resolution Aerial Image Data

Forest damage due to storms causes economic loss and requires a fast response to prevent further damage such as bark beetle infestations. By using Convolutional Neural Networks (CNNs) in conjunction with a GIS, we aim at completely streamlining the detection and mapping process for forest agencies. We developed and tested different CNNs for rapid windthrow detection based on PlanetScope satellite data and high-resolution aerial image data. Depending on the meteorological situation after the storm, PlanetScope data might be rapidly available due to its high temporal resolution, while the acquisition of high-resolution airborne data often takes weeks to a month and is, therefore, used in a second step for more detailed mapping. The study area is located in Bavaria, Germany (ca. 165 km2), and labels for damaged areas were provided by the Bavarian State Institute of Forestry (LWF). Modifications of a U-Net architecture were compared to other approaches using transfer learning (e.g., VGG19) to find the most efficient architecture for the task on both datasets while keeping the computational time low. A custom implementation of U-Net proved to be more accurate than transfer learning, especially on medium (3 m) resolution PlanetScope imagery (intersection over union score (IoU) 0.55) where transfer learning completely failed. Results for transfer learning based on VGG19 on high-resolution aerial image data are comparable to results from the custom U-Net architecture (IoU 0.76 vs. 0.73). When using both architectures on a dataset from a different area (located in Hesse, Germany), however, we find that the custom implementations have problems generalizing on aerial image data while VGG19 still detects most damage in these images. For PlanetScope data, VGG19 again fails while U-Net achieves reasonable mappings. Results highlight the potential of Deep Learning algorithms to detect damaged areas with an IoU of 0.73 on airborne data and 0.55 on Planet Dove data. The proposed workflow with complete integration into ArcGIS is well-suited for rapid first assessments after a storm event that allows for better planning of the flight campaign followed by detailed mapping in a second stage.
A new miniature killifish of the genus Melanorivulus (Cyprinodontiformes: Rivulidae) from the coastal plains of north-eastern Brazil

Melanorivulus atlanticus, new species, is described on the basis of specimens collected in the coastal plains of north-eastern Brazil, constituting the first record of the genus for the Atlantic Forest biogeographical province. The new species together M. decoratus and M. jalapensis form a clade of small species, not surpassing 20 mm SL, mainly diagnosed by the presence of five branchiostegal rays. Melanorivulus atlanticus differs from those two species by a narrow black border along the entire caudal fin in males and the presence of 2 + 1 neuromasts in the mandibular series, besides differing from all congeners by having sexually dimorphic pelvic fin, which is pointed and with seven rays in males, elliptical and with five rays in females. The description of M. atlanticus expands in 670 km to east the known geographic range of the genus.
Summer warming accelerates sub‐arctic peatland nitrogen cycling without changing enzyme pools or microbial community structure

The balance of primary production and decomposition in northern peatlands may shift due to climate change, with potential feedbacks to atmospheric CO2 concentrations. Nitrogen availability will modulate this shift, but little is known about the drivers of soil nitrogen dynamics in these environments. We used a long‐term (9 years) open top chamber (OTC) experiment in an ombrotrophic Sphagnum peat bog in sub‐arctic Sweden, to test for the interactive effects of spring warming, summer warming and winter snow addition on soil nitrogen fluxes, potential activities of nitrogen cycle enzymes, and soil microbial community composition. These simultaneous measurements allowed us to identify the level of organization at which climate change impacts are apparent, an important requirement for developing truly mechanistic understanding. Organic‐N pools and fluxes were an order of magnitude higher than inorganic‐N pools and fluxes. Summer warming approximately doubled fluxes of soil organic nitrogen and ammonia over the growing season. Such a large increase under 1 °C warming is unlikely to be due to kinetic effects, and we propose that it is linked to an observed seasonal decrease in microbial biomass, suggesting that N flux is driven by a substantial late‐season dieback of microbes. This change in N cycle dynamics was not reflected in any of the measured potential peptidase activities. Moreover, the soil microbial community structure was apparently stable across treatments, suggesting a non‐specific microbial dieback. Our results show that in these widespread peat bogs, where many plant species are capable of organic‐N uptake, organic soil N dynamics are quantitatively far more important than the commonly studied inorganic‐N dynamics. Understanding of climate change effects on organic soil N cycling in this system will be advanced by closer investigation of the seasonal dynamics of the microbial biomass and the input of substrates that maintain it.
Deep Semantic Segmentation of Center Pivot Irrigation Systems from Remotely Sensed Data

The center pivot irrigation system (CPIS) is a modern irrigation technique widely used in precision agriculture due to its high efficiency in water consumption and low labor compared to traditional irrigation methods. The CPIS is a leader in mechanized irrigation in Brazil, with growth forecast for the coming years. Therefore, the mapping of center pivot areas is a strategic factor for the estimation of agricultural production, ensuring food security, water resources management, and environmental conservation. In this regard, digital processing of satellite images is the primary tool allowing regional and continuous monitoring with low costs and agility. However, the automatic detection of CPIS using remote sensing images remains a challenge, and much research has adopted visual interpretation. Although CPIS presents a consistent circular shape in the landscape, these areas can have a high internal variation with different plantations that vary over time, which is difficult with just the spectral behavior. Deep learning using convolutional neural networks (CNNs) is an emerging approach that provokes a revolution in image segmentation, surpassing traditional methods, and achieving higher accuracy and efficiency. This research aimed to evaluate the use of deep semantic segmentation of CPIS from CNN-based algorithms using Landsat-8 surface reflectance images (seven bands). The developed methodology can be subdivided into the following steps: (a) Definition of three study areas with a high concentration of CPIS in Central Brazil; (b) acquisition of Landsat-8 images considering the seasonal variations of the rain and drought periods; (c) definition of CPIS datasets containing Landsat images and ground truth mask of 256×256 pixels; (d) training using three CNN architectures (U-net, Deep ResUnet, and SharpMask); (e) accuracy analysis; and (f) large image reconstruction using six stride values (8, 16, 32, 64, 128, and 256). The three methods achieved state-of-the-art results with a slight prevalence of U-net over Deep ResUnet and SharpMask (0.96, 0.95, and 0.92 Kappa coefficients, respectively). A novelty in this research was the overlapping pixel analysis in the large image reconstruction. Lower stride values had improvements quantified by the Receiver Operating Characteristic curve (ROC curve) and Kappa, and fewer errors in the frame edges were also perceptible. The overlapping images significantly improved the accuracy and reduced the error present in the edges of the classified frames. Additionally, we obtained greater accuracy results during the beginning of the dry season. The present study enabled the establishment of a database of center pivot images and an adequate methodology for mapping the center pivot in central Brazil.
Port Bathymetry Mapping Using Support Vector Machine Technique and Sentinel-2 Satellite Imagery

Knowledge of the free draft of ports is essential for the adequate management of ports. To maintain these drafts, it is necessary to carry out dredging periodically, and to conduct bathymetries using traditional techniques, such as echo sounding. However, an echo sounder is very expensive and its accuracy is subject to weather conditions. Thus, the use of recent advancements in remote sensing techniques provide a better solution for mapping and estimating the evolution of the seabed in these areas. This paper presents a cost-effective and practical method for estimating satellite-derived bathymetry for highly polluted and turbid waters at two different ports in the cities of Luarca and Candás in the Principality of Asturias (Spain). The method involves the use of the support vector machine (SVM) technique and open Sentinel-2 satellite imagery, which the European Space Agency has supplied. Models were compared to the bathymetries that were obtained from the in situ data collected by a single beam echo sounder that the Port Service of the Principality of Asturias provided. The most accurate values of the training and testing dataset in Candás, were R2 = 0.911 and RMSE = 0.3694 m, and R2 = 0.8553 and RMSE = 0.4370 m, respectively. The accuracies of the training and testing dataset values in Luarca were R2 = 0.976 and RMSE = 0.4409 m, and R2 = 0.9731 and RMSE = 0.4640 m, respectively. The regression analysis results of the training and testing dataset were consistent. The approaches that have been developed in this work may be included in the monitoring of future dredging activities in ports, especially where the water is polluted, muddy and highly turbid.
The occurrence of polybrominated diphenyl ethers in Brazil: a review

The occurrence of polybrominated diphenyl ethers (PBDEs), brominated flame retardants, has been reported in Brazil. These compounds are used in many types of consumer products, such as plastics, foam, electrical wiring and textile coatings; they have become ubiquitous in the environment, in people and in other animals' bodies because of their highly recalcitrant properties as well as their lipophilicity. Recent studies indicate that PBDEs are transported worldwide passively by air and actively through water sources, and can occur in locations as remote as the Arctic environment. This study is the first review to report the PBDEs' presence and concentration in several
Vegetational Diversity and Arthropod Population Response

Studies of agroecosystems during the past 30 years have lead several agri­ cultural scientists to question the commitment of modem industrial agriculture to high intensity monocultural production . Additionally, current research directions in integrated pest management emphasize biological interactions among insect pests, natural enemies, and other crop pests, such as weeds. These inquiries have led to a recent rebirth in interest and research activities on cultural and biological controls in entomology . Vegetational diversity plays a central role in this research renaissance. If one considers it broadly, vegetational diversity involves mixing different kinds of plants in a plant community, but, to paraphrase Vilfredo Pareto ( 1 12), vegetational diversity appears like a bat; within it one can find both birds and mice . More specifically, vegetational diversity varies in three ways: the kinds, the spatial array, and the temporal overlap of the plants in the mixture. In most cases, the mixed plants are different plant species. These plants might be two crops, which is called intercropping; a crop and a weed, which is called weedy culture; or a crop and a beneficial noncrop, which is known by many names including nursery crops, living-mulches, cover­ cropping, etc . In some cases, however, different plant genotypes are mixed (41), including polyvarietal mixtures of agronomically dissimilar genotypes
Limiting the Spread of Resistant Pneumococci: Biological and Epidemiologic Evidence for the Effectiveness of Alternative Interventions

SUMMARY Streptococcus pneumoniae infections are a leading cause of respiratory illness in young children, the elderly, and persons with chronic medical conditions. The emergence of multidrug-resistant pneumococci has compromised the effectiveness of antibiotic therapy for pneumococcal infections. As antibiotic-resistant strains increase in prevalence, there is a need for interventions that minimize the spread of resistant pneumococci. In this review we provide a framework for understanding the spread of pneumococcal resistance and evaluate proposed interventions to reduce this spread. Pneumococci differ from many drug-resistant pathogens because asymptomatic carriers play a key role in transmission of resistant strains and the genes encoding resistance are spread primarily by transformation and conjugative transposons. Evidence suggests that modifications of treatment regimens that have proved effective at limiting resistance in other pathogens may not prevent the spread of pneumococcal resistance. In contrast, programs encouraging more judicious antibiotic use have been shown to be effective. Additionally, a newly developed conjugate pneumococcal vaccine holds great potential as an “antiresistance vaccine” that simultaneously reduces the burden of invasive disease and the prevalence of resistant strains. Several areas of future epidemiologic and laboratory research hold promise to contribute to the reduced spread of pneumococcal resistance.
Apolipoprotein E but Not B Is Required for the Formation of Infectious Hepatitis C Virus Particles

ABSTRACT Our previous studies have found that hepatitis C virus (HCV) particles are enriched in apolipoprotein E (apoE) and that apoE is required for HCV infectivity and production. Studies by others, however, suggested that both microsomal transfer protein (MTP) and apoB are important for HCV production. To define the roles of apoB and apoE in the HCV life cycle, we developed a single-cycle HCV growth assay to determine the correlation of HCV assembly with apoB and apoE expression, as well as the influence of MTP inhibitors on the formation of HCV particles. The small interfering RNA (siRNA)-mediated knockdown of apoE expression remarkably suppressed the formation of HCV particles. However, apoE expressed ectopically could restore the defect of HCV production posed by the siRNA-mediated knockdown of endogenous apoE expression. In contrast, apoB-specific antibodies and siRNAs had no significant effect on HCV infectivity and production, respectively, suggesting that apoB does not play a significant role in the HCV life cycle. Additionally, two MTP inhibitors, CP-346086 and BMS-2101038, efficiently blocked secretion of apoB-containing lipoproteins but did not affect HCV production unless apoE expression and secretion were inhibited. At higher concentrations, however, MTP inhibitors blocked apoE expression and secretion and consequently suppressed the formation of HCV particles. Furthermore, apoE was found to be sensitive to trypsin digestion and to interact with NS5A in purified HCV particles and HCV-infected cells, as demonstrated by coimmunoprecipitation. Collectively, these findings demonstrate that apoE but not apoB is required for HCV assembly, probably via a specific interaction with NS5A.
Macro-ecology of plankton–seabird associations in the North Pacific Ocean

In conjunction with the North Pacific Continuous Plankton Recorder program, we conducted surveys of seabirds from June 2002 to June 2007. Here, we tested the hypotheses of (i) east–west variations in coupled plankton and seabird abundance, and (ii) that surface-feeding and diving seabirds vary in their relationships to primary productivity and mesozooplankton species abundance and diversity. To test these hypotheses, we developed statistical models for 20 species of seabirds and 12 zooplankton taxonomic groups. Seabird density was highly variable between seasons, but was consistently higher in the western than eastern North Pacific. Seabird diversity was greater in the east. Zooplankton abundance did not differ between regions. We found associations at the “bulk” level between seabird density and net primary productivity, but only one association between seabirds and total zooplankton abundance or diversity. However, we found many relationships between seabird species and the abundance of different zooplankton summarized at the genus or family level. Some of these taxonomic relationships reflect direct predator–prey interactions, while others may reflect zooplankton that serve as ecological indicators of other prey, such as micronekton, upon which the birds may feed. Surface or near-surface feeding, mostly piscivorous seabirds, did not differ systematically from diving, mainly planktivorous seabirds in their zooplankton associations. Seabirds apparently respond to zooplankton taxonomic groupings more so than bulk zooplankton characteristics, such as abundance or diversity. Macro-ecological studies of remote marine ecosystems using zooplankton and seabirds as ecological indicators provide a framework for understanding and assessing spatial and temporal variations in these difficult-to-study pelagic environments.
Host Volatile Attractants and Traps for Detection of Tetropium fuscum (F.), Tetropium castaneum L., and Other Longhorned Beetles (Coleoptera: Cerambycidae)

Abstract Cortical and sapwood volatiles were collected in situ from red spruce, Picea rubens (Sarg.), trees infested with Tetropium fuscum (F.), to determine the relative concentrations and enantiomer ratios of monoterpenes emitted. This information was used to create a synthetic “spruce blend” lure that was tested in various trap designs for efficacy in capturing T. fuscum, and Tetropium castaneum L. in field bioassays conducted on McNabs Island, Nova Scotia, in 2001 and 2002 and in Poland and Switzerland in 2002. Response of other cerambycid species was measured opportunistically. Cross-vane pan traps baited with spruce blend caught significantly more T. fuscum than unbaited traps or traps baited with racemic α-pinene, ethanol, or both. The addition of an ethanol lure to spruce blend–baited traps significantly increased capture of T. fuscum and T. castaneum. There were no significant differences among trap designs in mean catch of either Tetropium species. Spruce blend was also significantly attractive to Monochamus urussovii (Fischer) and, when paired with an ethanol lure, was significantly attractive to Spondylis buprestoides L. Asemum striatum L. was significantly attracted to racemic α-pinene but was not attracted to spruce blend or spruce blend plus ethanol. None of the lures tested were significantly attractive to Stictoleptura rubra L. or Alosterna tabacicolor (DeGeer).
Investigating trophic relationships of pinnipeds in Alaska and Washington using stable isotope ratios of nitrogen and carbon

We measured stable-nitrogen (δ15N) and stable-carbon (δ13C) isotope ratios in muscle and hair from 7 northern fur seals (Callorhinus ursinus) from the Pribilof Islands, Alaska, and 27 Steller sea lions (Eumetopias jubatus), and 14 harbor seals (Phoca vitulina) from the Gulf of Alaska and coast of Washington State, in order to contrast dietary information derived from isotopic vs. available conventional dietary studies. Stable-nitrogen-isotope analysis of muscle revealed that harbor seals were enriched over sea lions (mean δ15N = 18.6‰vs. 17.5‰) which were in turn enriched over northern fur seals (mean δ15N = 16.6‰). Trophic segregation among these species likely results primarily from differential reliance on herring (Clupea harengus), Atka mackerel (Pleurogrammus monopterygius), and large vs. small walleye pollock (Theregra chalcogramma). According to their δ15N values, adult male Steller sea lions showed a higher trophic position than adult females (mean δ15N: 18.0‰vs. 17.2‰), whereas adult female northern fur seals were trophically higher than juvenile male fur seals (mean δ15N: 16.5‰vs. 15.0‰). Each of these observed differences likely resulted from differential reliance on squid or differences in the size range of pollock consumed. Three northern fur seal pups showed higher δ15N enrichment over adults (mean 17.7‰vs. 15.8‰) due to their reliance on their mother's milk. Stable-carbon isotope measurements of hair revealed a cline toward more negative values with latitude. Segregation in hair δ13C between Steller sea lions and harbor seals off the coast of Washington (mean δ13C: −13.6‰vs.−15.0‰) reflected the greater association of harbor seals with freshwater input from the Columbia River. Our study demonstrates the utility of the stable isotope approach to augment conventional dietary analyses of pinnipeds and other marine mammals.
An expanded phylogeny of the Dennstaedtiaceae ferns: Oenotrichia falls within a non-monophyletic Dennstaedtia, and Saccoloma is polyphyletic

Abstract. Recent studies have transferred several species previously attributed to the fern genus Oenotrichia to other genera, and even out of the Dennstaedtiaceae to other families. However, the relationship of the type species, O. maxima from New Caledonia, has not previously been investigated using DNA sequences. With phylogenetic analyses of chloroplast DNA sequences, we verify the placement of Oenotrichia within the Dennstaedtiaceae. Moreover, O. maxima actually nests along with Leptolepia in a clade of Dennstaedtia. Dennstaedtia itself is non-monophyletic, with a second clade being more closely related to Microlepia. We outline what is required to resolve the generic taxonomy of this group. We also find that samples attributed to Saccoloma are polyphyletic, with some falling inside the Dennstaedtiaceae and others outside.
Variation in demography, condition and dietary quality of hares Lepus europaeus from high-density and low-density populations

Abstract Numbers of European hares Lepus europaeus have declined throughout Europe due to agricultural intensification. However, hares are more common in intensive arable areas than in pastural areas. To identify factors limiting populations, functional explanations for differences in density of hares were sought. We compared demography (litter size, prenatal mortality and participation in breeding by females), body condition (urinary and serum nitrogen, kidney fat, bone marrow fat, skeletal size and body weight), and dietary quality of hares from parts of England and Wales where they are present at relatively high densities (arable habitats) and at relatively low densities (pastural habitats). In pastural areas a lower proportion of adult females were lactating in late winter than in arable areas. Recruitment was therefore lower in pastural than in arable habitats. Hares from pastural areas were smaller, lighter and had less fat than those from arable areas, but dietary quality was similar. Thus hares in low-density populations from pastural areas were able to obtain a good-quality diet, but expended more energy and were unable to maintain body condition as well as those from arable areas. Pastural habitat, which in England and Wales is relatively warm and wet, is suboptimal for hares. The reduced recruitment and chance of survival of hares in the pastural habitats we describe may explain the differences in density of hares in arable and pastural habitats. Efforts to conserve the hare should focus on the reduction of predation and exposure to unfavourable weather by the provision of year-round vegetative cover (such as fallow land, rough grassland and shelterbelts), to increase the chances of survival of leverets and adult hares.