Crop maps are key inputs for crop inventory production and yield estimation and can inform the implementation of effective farm management practices. Producing these maps at detailed scales requires ...exhaustive field surveys that can be laborious, time-consuming, and expensive to replicate. With a growing archive of remote sensing data, there are enormous opportunities to exploit dense satellite image time series (SITS), temporal sequences of images over the same area. Generally, crop type mapping relies on single-sensor inputs and is solved with the help of traditional learning algorithms such as random forests or support vector machines. Nowadays, deep learning techniques have brought significant improvements by leveraging information in both spatial and temporal dimensions, which are relevant in crop studies. The concurrent availability of Sentinel-1 (synthetic aperture radar) and Sentinel-2 (optical) data offers a great opportunity to utilize them jointly; however, optimizing their synergy has been understudied with deep learning techniques. In this work, we analyze and compare three fusion strategies (input, layer, and decision levels) to identify the best strategy that optimizes optical-radar classification performance. They are applied to a recent architecture, notably, the pixel-set encoder–temporal attention encoder (PSE-TAE) developed specifically for object-based classification of SITS and based on self-attention mechanisms. Experiments are carried out in Brittany, in the northwest of France, with Sentinel-1 and Sentinel-2 time series. Input and layer-level fusion competitively achieved the best overall F-score surpassing decision-level fusion by 2%. On a per-class basis, decision-level fusion increased the accuracy of dominant classes, whereas layer-level fusion improves up to 13% for minority classes. Against single-sensor baseline, multi-sensor fusion strategies identified crop types more accurately: for example, input-level outperformed Sentinel-2 and Sentinel-1 by 3% and 9% in F-score, respectively. We have also conducted experiments that showed the importance of fusion for early time series classification and under high cloud cover condition.
Pathogenic microorganisms entail enormous problems for humans, livestock, and crop plants. A better understanding of the different infection strategies of the pathogens enables us to derive optimal ...treatments to mitigate infectious diseases or develop vaccinations preventing the occurrence of infections altogether. In this review, we highlight the current trends in mathematical modeling approaches and related methods used for understanding host–pathogen interactions. Since these interactions can be described on vastly different temporal and spatial scales as well as abstraction levels, a variety of computational and mathematical approaches are presented. Particular emphasis is placed on dynamic optimization, game theory, and spatial modeling, as they are attracting more and more interest in systems biology. Furthermore, these approaches are often combined to illuminate the complexities of the interactions between pathogens and their host. We also discuss the phenomena of molecular mimicry and crypsis as well as the interplay between defense and counter defense. As a conclusion, we provide an overview of method characteristics to assist non-experts in their decision for modeling approaches and interdisciplinary understanding.
Metabolic cross-feeding interactions are ubiquitous in natural microbial communities. However, it remains generally unclear whether the production and exchange of metabolites incurs fitness costs to ...the producing cells and if so, which ecological mechanisms can facilitate a cooperative exchange of metabolites among unrelated individuals. We hypothesized that positive assortment within structured environments can maintain mutualistic cross-feeding. To test this, we engineered Acinetobacter baylyi and Escherichia coli to reciprocally exchange essential amino acids. Interspecific coculture experiments confirmed that non-cooperating types were selectively favoured in spatially unstructured (liquid culture), yet disfavoured in spatially structured environments (agar plates). Both an individual-based model and experiments with engineered genotypes indicated that a segregation of cross-feeders and non-cooperating auxotrophs stabilized cooperative cross-feeding in spatially structured environments. Chemical imaging confirmed that auxotrophs were spatially excluded from cooperative benefits. Together, these results demonstrate that cooperative cross-feeding between different bacterial species is favoured in structured environments such as bacterial biofilms, suggesting this type of interactions might be common in natural bacterial communities.
Recently, novel techniques introduced to the field of corneal surgery, e.g. Descemet membrane endothelial keratoplasty (DMEK) and corneal crosslinking, extended the therapeutic options. Additionally ...contact lens fitting has developed new alternatives. We herein investigated, whether these techniques have affected volume and spectrum of indications of keratoplasties in both a center more specialized in treating Fuchs' dystrophy (center 1) and a second center that is more specialized in treating keratoconus (center 2).
We retrospectively reviewed the waiting lists for indication, transplantation technique and the patients' travel distances to the hospital at both centers.
We reviewed a total of 3778 procedures. Fuchs' dystrophy increased at center 1 from 17% (42) to 44% (150) and from 13% (27) to 23% (62) at center 2. In center 1, DMEK increased from zero percent in 2010 to 51% in 2013. In center 2, DMEK was not performed until 2013. The percentage of patients with keratoconus slightly decreased from 15% (36) in 2009 vs. 12% (40) in 2013 in center 1. The respective percentages in center 2 were 28% (57) and 19% (51). In both centers, the patients' travel distances increased.
The results from center 1 suggest that DMEK might increase the total number of keratoplasties. The increase in travel distance suggests that this cannot be fully attributed to recruiting the less advanced patients from the hospital proximity. The increase is rather due to more referrals from other regions. The decrease of keratoconus patients in both centers is surprising and may be attributed to optimized contact lens fitting or even to the effect corneal crosslinking procedure.
Molecular mimicry is the formation of specific molecules by microbial pathogens to avoid recognition and attack by the immune system of the host. Several pathogenic Ascomycota and Zygomycota show ...such a behaviour by utilizing human complement factor H to hide in the blood stream. We call this type of mimicry molecular crypsis. Such a crypsis can reach a point where the immune system can no longer clearly distinguish between self and non-self cells. Thus, a trade-off between attacking disguised pathogens and erroneously attacking host cells has to be made. Based on signalling theory and protein-interaction modelling, we here present a mathematical model of molecular crypsis of pathogenic fungi using the example of Candida albicans. We tackle the question whether perfect crypsis is feasible, which would imply that protection of human cells by complement factors would be useless. The model identifies pathogen abundance relative to host cell abundance as the predominant factor influencing successful or unsuccessful molecular crypsis. If pathogen cells gain a (locally) quantitative advantage over host cells, even autoreactivity may occur. Our new model enables insights into the mechanisms of candidiasis-induced sepsis and complement-associated autoimmune diseases.
Here we present the concept of a protein microarray-based fluorescence immunoassay for multiple biomarker detection in milk extracts by an ordinary smartphone. A multiplex immunoassay was designed on ...a microarray chip, having built-in positive and negative quality controls. After the immunoassay procedure, the 48 microspots were labelled with Quantum Dots (QD) depending on the protein biomarker levels in the sample. QD-fluorescence was subsequently detected by the smartphone camera under UV light excitation from LEDs embedded in a simple 3D-printed opto-mechanical smartphone attachment. The somewhat aberrant images obtained under such conditions, were corrected by newly developed Android-based software on the same smartphone, and protein biomarker profiles were calculated. The indirect detection of recombinant bovine somatotropin (rbST) in milk extracts based on altered biomarker profile of anti-rbST antibodies was selected as a real-life challenge. RbST-treated and untreated cows clearly showed reproducible treatment-dependent biomarker profiles in milk, in excellent agreement with results from a flow cytometer reference method. In a pilot experiment, anti-rbST antibody detection was multiplexed with the detection of another rbST-dependent biomarker, insulin-like growth factor 1 (IGF-1). Milk extract IGF-1 levels were found to be increased after rbST treatment and correlated with the results obtained from the reference method. These data clearly demonstrate the potential of the portable protein microarray concept towards simultaneous detection of multiple biomarkers. We envisage broad application of this 'protein microarray on a smartphone'-concept for on-site testing, e.g., in food safety, environment and health monitoring.
Sentinel-2 scenes are increasingly being used in operational Earth observation (EO) applications at regional, continental and global scales, in near-real time applications, and with multi-temporal ...approaches. On a broader scale, they are therefore one of the most important facilitators of the Digital Earth. However, the data quality and availability are not spatially and temporally homogeneous due to effects related to cloudiness, the position on the Earth or the acquisition plan. The spatio-temporal inhomogeneity of the underlying data may therefore affect any big remote sensing analysis and is important to consider. This study presents an assessment of the metadata for all accessible Sentinel-2 Level-1C scenes acquired in 2017, enabling the spatio-temporal coverage and availability to be quantified, including scene availability and cloudiness. Spatial exploratory analysis of the global, multi-temporal metadata also reveals that higher acquisition frequencies do not necessarily yield more cloud-free scenes and exposes metadata quality issues, e.g. systematically incorrect cloud cover estimation in high, non-vegetated altitudes. The continuously updated datasets and analysis results are accessible as a Web application called EO-Compass. It contributes to a better understanding and selection of Sentinel-2 scenes, and improves the planning and interpretation of remote sensing analyses.
Geographic Object-Based Image Analysis – Towards a new paradigm Blaschke, Thomas; Hay, Geoffrey J.; Kelly, Maggi ...
ISPRS journal of photogrammetry and remote sensing,
January 2014, 2014, 2014-Jan, 2014-01-00, 20140101, Letnik:
87, Številka:
100
Journal Article
Recenzirano
Odprti dostop
The amount of scientific literature on (Geographic) Object-based Image Analysis – GEOBIA has been and still is sharply increasing. These approaches to analysing imagery have antecedents in earlier ...research on image segmentation and use GIS-like spatial analysis within classification and feature extraction approaches. This article investigates these development and its implications and asks whether or not this is a new paradigm in remote sensing and Geographic Information Science (GIScience). We first discuss several limitations of prevailing per-pixel methods when applied to high resolution images. Then we explore the paradigm concept developed by Kuhn (1962) and discuss whether GEOBIA can be regarded as a paradigm according to this definition. We crystallize core concepts of GEOBIA, including the role of objects, of ontologies and the multiplicity of scales and we discuss how these conceptual developments support important methods in remote sensing such as change detection and accuracy assessment. The ramifications of the different theoretical foundations between the ‘per-pixel paradigm’ and GEOBIA are analysed, as are some of the challenges along this path from pixels, to objects, to geo-intelligence. Based on several paradigm indications as defined by Kuhn and based on an analysis of peer-reviewed scientific literature we conclude that GEOBIA is a new and evolving paradigm.
Urban green mapping has become an operational task in city planning, urban land management, and quality of life assessments. As a multi-dimensional, integrative concept, urban green comprising ...several ecological, socio-economic, and policy-related aspects. In this paper, the author advances the representation of urban green by deriving scale-adapted, policy-relevant units. These so-called geons represent areas of uniform green valuation under certain size and homogeneity constraints in a spatially explicit representation. The study accompanies a regular monitoring scheme carried out by the urban municipality of the city of Salzburg, Austria, using optical satellite data. It was conducted in two stages, namely SBG_QB (10.2 km², QuickBird data from 2005) and SBG_WV (140 km², WorldView-2 data from 2010), within the functional urban area of Salzburg. The geon delineation was validated by several quantitative measures and spatial analysis techniques, as well as ground documentation, including panorama photographs and visual interpretation. The spatial association pattern was assessed by calculating Global Moran's I with incremental search distances. The final geonscape, consisting of 1083 units with an average size of 13.5 ha, was analyzed by spatial metrics. Finally, categories were derived for different types of functional geons. Future research paths and improvements to the described strategy are outlined.
Purpose
To propose additional items for established dry eye disease (DED) instruments that cover blepharitis-specific signs and symptoms and to determine the association between the clinical findings ...and subjective complaints.
Methods
Thirty-one patients with blepharitis and DED were prospectively included in the pretest period for selecting suitable questions. In the main phase of the study, the selected questions were then tested on 68 patients with blepharitis and DED and 20 controls without blepharitis or DED. Pearson’s coefficient of correlation was calculated between the blepharitis-specific questions, tear break-up time (TBUT), the Schirmer test score, and the ocular surface disease index (OSDI) score; and the similarity between the blepharitis-specific questions, OSDI questions, and objective parameters for DED was assessed via hierarchical clustering. Furthermore, the discriminatory power of the blepharitis-specific questions was investigated with the receiver operating characteristic (ROC) curve.
Results
The additional question about heavy eyelids revealed a significant correlation with the OSDI score (
r
= 0.45,
p
< 0.001) and Schirmer score (
r
= − 0.32,
p
= 0.006). Cluster analysis demonstrated the similarity between the question about heavy eyelids and TBUT. In addition, the OSDI questionnaire had the highest discriminatory power in ROC analysis, and the OSDI score significantly correlated with the specific questions about eyelids sticking together (
r
= 0.47,
p
< 0.0001) and watery or teary eyes (
r
= 0.34,
p
= 0.003).
Conclusions
The blepharitis-specific additional questions were closely associated with objective parameters for DED. The question about heavy eyelids might be well suited for recording the symptoms of hyposecretory and hyperevaporative dry eye with blepharitis.
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