Revisiting pre-trained remote sensing model benchmarks: resizing and normalization matters

Research in self-supervised learning (SSL) with natural images has progressed rapidly in recent years and is now increasingly being applied to and benchmarked with datasets containing remotely sensed imagery. A common benchmark case is to evaluate SSL pre-trained model embeddings on datasets of remotely sensed imagery with small patch sizes, e.g., 32x32 pixels, whereas standard SSL pre-training takes place with larger patch sizes, e.g., 224x224. Furthermore, pre-training methods tend to use different image normalization preprocessing steps depending on the dataset. In this paper, we show, across seven satellite and aerial imagery datasets of varying resolution, that by simply following the preprocessing steps used in pre-training (precisely, image sizing and normalization methods), one can achieve significant performance improvements when evaluating the extracted features on downstream tasks -- an important detail overlooked in previous work in this space. We show that by following these steps, ImageNet pre-training remains a competitive baseline for satellite imagery based transfer learning tasks -- for example we find that these steps give +32.28 to overall accuracy on the So2Sat random split dataset and +11.16 on the EuroSAT dataset. Finally, we report comprehensive benchmark results with a variety of simple baseline methods for each of the seven datasets, forming an initial benchmark suite for remote sensing imagery

Dopamine drives Drosophila sechellia adaptation to its toxic host

Many insect species are host-obligate specialists. The evolutionary mechanism driving the adaptation of a species to a toxic host is, however, intriguing. We analyzed the tight association of Drosophila sechellia to its sole host, the fruit of Morinda citrifolia, which is toxic to other members of the melanogaster species group. Molecular polymorphisms in the dopamine regulatory protein Catsup cause infertility in D. sechellia due to maternal arrest of oogenesis. In its natural host, the fruit compensates for the impaired maternal dopamine metabolism with the precursor l-DOPA, resuming oogenesis and stimulating egg production. l-DOPA present in morinda additionally increases the size of D. sechellia eggs, what in turn enhances early fitness. We argue that the need of l-DOPA for successful reproduction has driven D. sechellia to become an M. citrifolia obligate specialist. This study illustrates how an insect's dopaminergic system can sustain ecological adaptations by modulating ontogenesis and development. DOI: http://dx.doi.org/10.7554/eLife.03785.00

Optimization of insect odorant receptor trafficking and functional expression via transient transfection in HEK293 cells

Insect odorant receptors show a limited functional expression in various heterologous expression systems including insect and mammalian cells. This may be in part due to the absence of key components driving the release of these proteins from the endoplasmic reticulum and directing them to the plasma membrane. In order to mitigate this problem we took advantage of small export signals within the human HCN1 and Rhodopsin that have been shown to promote protein release from the endoplasmic reticulum and the trafficking of post-Golgi vesicles, respectively. Moreover, we designed a new vector based on a bidirectional expression cassette to drive the functional expression of the insect odorant receptor co-receptor (Orco) and an odor-binding odorant receptor, simultaneously. We show that this new method can be used to reliably express insect odorant receptors in HEK293 cells via transient transfection and that is highly suitable for downstream applications using automated and high-throughput imaging platforms

Immunogenicity and Safety of Adjuvanted Recombinant Zoster Vaccine in Rheumatoid Arthritis Patients on Anti-Cellular Biologic Agents or JAK Inhibitors: A Prospective Observational Study

Rheumatoid arthritis (RA) patients on JAK inhibitors (JAKi) have an increased HZ risk compared to those on biologic DMARDs (bDMARDs). Recently, the Adjuvanted Recombinant Zoster Vaccine (RZV) became available worldwide, showing good effectiveness in patients with inflammatory arthritis. Nevertheless, direct evidence of the immunogenicity of such a vaccine in those on JAKi or anti-cellular bDMARDs is still lacking. This prospective study aimed to assess RZV immunogenicity and safety in RA patients receiving JAKi or anti-cellular bDMARDs that are known to lead to impaired immune response. Patients with classified RA according to ACR/EULAR 2010 criteria on different JAKi or anti-cellular biologics (namely, abatacept and rituximab) followed at the RA clinic of our tertiary center were prospectively observed. Patients received two shots of the RZV. Treatments were not discontinued. At the first and second shots, and one month after the second shot, from all patients with RA, a sample was collected and RZV immunogenicity was assessed and compared between the treatment groups and healthy controls (HCs) receiving RZV for routine vaccination. We also kept track of disease activity at different follow-up times. Fifty-two consecutive RA patients, 44 females (84.61%), with an average age (±SD) of 57.46 ± 11.64 years and mean disease duration of 80.80 ± 73.06 months, underwent complete RZV vaccination between February and June 2022 at our center. At the time of the second shot (1-month follow-up from baseline), anti-VZV IgG titer increased significantly in both groups with similar magnitude (bDMARDs: 2258.76 ± 897.07 mIU/mL; JAKi: 2059.19 ± 876.62 mIU/mL, p < 0.001 for both from baseline). At one-month follow-up from the second shot, anti-VZV IgG titers remained stable in the bDMARDs group (2347.46 ± 975.47) and increased significantly in the JAKi group (2582.65 ± 821.59 mIU/mL, p = 0.03); still, no difference was observed between groups comparing IgG levels at this follow-up time. No RA flare was recorded. No significant difference was shown among treatment groups and HCs. RZV immunogenicity is not impaired in RA patients on JAKi or anti-cellular bDMARDs. A single shot of RZV can lead to an anti-VZV immune response similar to HCs without discontinuing DMARDs

Weak Labeling for Cropland Mapping in Africa

Cropland mapping can play a vital role in addressing environmental, agricultural, and food security challenges. However, in the context of Africa, practical applications are often hindered by the limited availability of high-resolution cropland maps. Such maps typically require extensive human labeling, thereby creating a scalability bottleneck. To address this, we propose an approach that utilizes unsupervised object clustering to refine existing weak labels, such as those obtained from global cropland maps. The refined labels, in conjunction with sparse human annotations, serve as training data for a semantic segmentation network designed to identify cropland areas. We conduct experiments to demonstrate the benefits of the improved weak labels generated by our method. In a scenario where we train our model with only 33 human-annotated labels, the F_1 score for the cropland category increases from 0.53 to 0.84 when we add the mined negative labels.Comment: 5 page

Predicting locations of cryptic pockets from single protein structures using the PocketMiner graph neural network

Cryptic pockets expand the scope of drug discovery by enabling targeting of proteins currently considered undruggable because they lack pockets in their ground state structures. However, identifying cryptic pockets is labor-intensive and slow. The ability to accurately and rapidly predict if and where cryptic pockets are likely to form from a structure would greatly accelerate the search for druggable pockets. Here, we present PocketMiner, a graph neural network trained to predict where pockets are likely to open in molecular dynamics simulations. Applying PocketMiner to single structures from a newly curated dataset of 39 experimentally confirmed cryptic pockets demonstrates that it accurately identifies cryptic pockets (ROC-AUC: 0.87) \u3e1,000-fold faster than existing methods. We apply PocketMiner across the human proteome and show that predicted pockets open in simulations, suggesting that over half of proteins thought to lack pockets based on available structures likely contain cryptic pockets, vastly expanding the potentially druggable proteome

Rapid building damage assessment workflow: An implementation for the 2023 Rolling Fork, Mississippi tornado event

Rapid and accurate building damage assessments from high-resolution satellite imagery following a natural disaster is essential to inform and optimize first responder efforts. However, performing such building damage assessments in an automated manner is non-trivial due to the challenges posed by variations in disaster-specific damage, diversity in satellite imagery, and the dearth of extensive, labeled datasets. To circumvent these issues, this paper introduces a human-in-the-loop workflow for rapidly training building damage assessment models after a natural disaster. This article details a case study using this workflow, executed in partnership with the American Red Cross during a tornado event in Rolling Fork, Mississippi in March, 2023. The output from our human-in-the-loop modeling process achieved a precision of 0.86 and recall of 0.80 for damaged buildings when compared to ground truth data collected post-disaster. This workflow was implemented end-to-end in under 2 hours per satellite imagery scene, highlighting its potential for real-time deployment.Comment: In submission to the 2023 ICCV Humanitarian Assistance and Disaster Response Worksho

Active Control of Polariton-Enabled Long-Range Energy Transfer

Optical control is achieved on the excited state energy transfer between spatially separated donor and acceptor molecules, both coupled to the same optical mode of a cavity. The energy transfer occurs through the formed hybrid polaritons and can be switched on and off by means of ultraviolet and visible light. The control mechanism relies on a photochromic component used as donor, whose absorption and emission properties can be varied reversibly through light irradiation, whereas in-cavity hybridization with acceptors through polariton states enables a 6-fold enhancement of acceptor/donor contribution to the emission intensity with respect to a reference multilayer. These results pave the way for synthesizing effective gating systems for the transport of energy by light, relevant for light-harvesting and light-emitting devices, and for photovoltaic cells.Comment: 52 pages, 40 Figures, 202