![150400-Thumbnail Image.png](https://d1rbsgppyrdqq4.cloudfront.net/s3fs-public/styles/width_400/public/2021-08/150400-Thumbnail%20Image.png?versionId=WFEnCncJSEzAng.Xha5.KW4BlhAkxD_j&X-Amz-Content-Sha256=UNSIGNED-PAYLOAD&X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIASBVQ3ZQ42ZLA5CUJ/20240610/us-west-2/s3/aws4_request&X-Amz-Date=20240610T171342Z&X-Amz-SignedHeaders=host&X-Amz-Expires=120&X-Amz-Signature=a1cba49cf89568a3d01eef3f1b735ba287f0b6195a2a65c9cbcdf031f3aa8460&itok=6FaGkBLK)
![150443-Thumbnail Image.png](https://d1rbsgppyrdqq4.cloudfront.net/s3fs-public/styles/width_400/public/2021-08/150443-Thumbnail%20Image.png?versionId=0neP0asFBPIOIFptE2uqC45r2AxEz5iC&X-Amz-Content-Sha256=UNSIGNED-PAYLOAD&X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIASBVQ3ZQ42ZLA5CUJ/20240615/us-west-2/s3/aws4_request&X-Amz-Date=20240615T054028Z&X-Amz-SignedHeaders=host&X-Amz-Expires=120&X-Amz-Signature=df114e714b944f12903052a276220ae7b1d2562527eb46f88d5acc27026e6550&itok=SHJUbOaW)
![149362-Thumbnail Image.png](https://d1rbsgppyrdqq4.cloudfront.net/s3fs-public/styles/width_400/public/2021-08/149362-Thumbnail%20Image.png?versionId=K8Ln8fg2OEHYCZTN.jrBR8qXTDbHIjrl&X-Amz-Content-Sha256=UNSIGNED-PAYLOAD&X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIASBVQ3ZQ42ZLA5CUJ/20240615/us-west-2/s3/aws4_request&X-Amz-Date=20240615T074849Z&X-Amz-SignedHeaders=host&X-Amz-Expires=120&X-Amz-Signature=ba5bc10361fe1cd882c7994e9eae1f19b70768013718d11759e8316f2db55c2b&itok=7_vE1rr0)
![149312-Thumbnail Image.png](https://d1rbsgppyrdqq4.cloudfront.net/s3fs-public/styles/width_400/public/2021-08/149312-Thumbnail%20Image.png?versionId=3f4V7e4o2v6ZhI_th_SDhfqHpSv7N.z9&X-Amz-Content-Sha256=UNSIGNED-PAYLOAD&X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIASBVQ3ZQ42ZLA5CUJ/20240615/us-west-2/s3/aws4_request&X-Amz-Date=20240615T101709Z&X-Amz-SignedHeaders=host&X-Amz-Expires=120&X-Amz-Signature=e2a8af6e68643b0fe2e2f7abeb033cd054a45c38506b09ccb16ed9d9db1cf71e&itok=6fd_PVdO)
The global transport and deposition of anthropogenic nitrogen (N) to downwind ecosystems are significant and continue to increase. Indeed, atmospheric deposition can be a significant source of N to many watersheds, including those in remote, unpopulated areas. Bacterial denitrification in lake sediments may ameliorate the effects of N loading by converting nitrate (NO3-) to N2 gas. Denitrification also produces nitrous oxide (N2O), a potent greenhouse gas. The ecological effects of atmospheric N inputs in terrestrial ecosystems and the pelagic zone of lakes have been well documented; however, similar research in lake sediments is lacking. This project investigates the effects N of deposition on denitrification and N2O production in lakes. Atmospheric N inputs might alter the availability of NO3- and other key resources to denitrifiers. Such altered resources could influence denitrification, N2O production, and the abundance of denitrifying bacteria in sediments. The research contrasts these responses in lakes at the ends of gradients of N deposition in Colorado and Norway. Rates of denitrification and N2O production were elevated in the sediments of lakes subject to anthropogenic N inputs. There was no evidence, however, that N deposition has altered sediment resources or the abundance of denitrifiers. Further investigation into the dynamics of nitric oxide, N2O, and N2 during denitrification found no difference between deposition regions. Regardless of atmospheric N inputs, sediments from lakes in both Norway and Colorado possess considerable capacity to remove NO3- by denitrification. Catchment-specific properties may influence the denitrifying community more strongly than the rate of atmospheric N loading. In this regard, sediments appear to be insulated from the effects of N deposition compared to the water column. Lastly, surface water N2O concentrations were greater in high-deposition lakes compared to low-deposition lakes. To understand the potential magnitude of deposition-induced N2O production, the greenhouse gas inventory methodology of Intergovernmental Panel on Climate Change was applied to available datasets. Estimated emissions from lakes are 7-371 Gg N y-1, suggesting that lakes could be an important source of N2O.
![130370-Thumbnail Image.png](https://d1rbsgppyrdqq4.cloudfront.net/s3fs-public/styles/width_400/public/2021-04/130370-Thumbnail%20Image.png?versionId=r1BJpf8yxqds5e1m_5oeGTnCIq0RcpXV&X-Amz-Content-Sha256=UNSIGNED-PAYLOAD&X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIASBVQ3ZQ42ZLA5CUJ/20240530/us-west-2/s3/aws4_request&X-Amz-Date=20240530T154040Z&X-Amz-SignedHeaders=host&X-Amz-Expires=120&X-Amz-Signature=3922d2a2882968d59c264b4579d3833b1a84402c6548cfe729a82ad7dc5016c3&itok=hqxA9aRn)
Background:
Drosophila gene expression pattern images document the spatiotemporal dynamics of gene expression during embryogenesis. A comparative analysis of these images could provide a fundamentally important way for studying the regulatory networks governing development. To facilitate pattern comparison and searching, groups of images in the Berkeley Drosophila Genome Project (BDGP) high-throughput study were annotated with a variable number of anatomical terms manually using a controlled vocabulary. Considering that the number of available images is rapidly increasing, it is imperative to design computational methods to automate this task.
Results:
We present a computational method to annotate gene expression pattern images automatically. The proposed method uses the bag-of-words scheme to utilize the existing information on pattern annotation and annotates images using a model that exploits correlations among terms. The proposed method can annotate images individually or in groups (e.g., according to the developmental stage). In addition, the proposed method can integrate information from different two-dimensional views of embryos. Results on embryonic patterns from BDGP data demonstrate that our method significantly outperforms other methods.
Conclusion:
The proposed bag-of-words scheme is effective in representing a set of annotations assigned to a group of images, and the model employed to annotate images successfully captures the correlations among different controlled vocabulary terms. The integration of existing annotation information from multiple embryonic views improves annotation performance.
![130385-Thumbnail Image.png](https://d1rbsgppyrdqq4.cloudfront.net/s3fs-public/styles/width_400/public/2021-04/130385-Thumbnail%20Image.png?versionId=rAUYk60iZoWmfXG7vA4QlIqXtvnbWUAk&X-Amz-Content-Sha256=UNSIGNED-PAYLOAD&X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIASBVQ3ZQ42ZLA5CUJ/20240614/us-west-2/s3/aws4_request&X-Amz-Date=20240614T031323Z&X-Amz-SignedHeaders=host&X-Amz-Expires=120&X-Amz-Signature=595e4bcaee06a2169c09ad00103b17e9520f6e0b4ae233b67a9297f1b88b1de4&itok=whrkTp87)
![130320-Thumbnail Image.png](https://d1rbsgppyrdqq4.cloudfront.net/s3fs-public/styles/width_400/public/2021-04/130320-Thumbnail%20Image.png?versionId=88ytKIF82b6vJW83BmdHpse0aB9xIggf&X-Amz-Content-Sha256=UNSIGNED-PAYLOAD&X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIASBVQ3ZQ42ZLA5CUJ/20240530/us-west-2/s3/aws4_request&X-Amz-Date=20240530T153726Z&X-Amz-SignedHeaders=host&X-Amz-Expires=120&X-Amz-Signature=10923590cf158ddcd9f0faae9fa7e11cac4be04751b6cec78b64f3ec57e10086&itok=-BhZSDXs)
X-ray free-electron lasers provide novel opportunities to conduct single particle analysis on nanoscale particles. Coherent diffractive imaging experiments were performed at the Linac Coherent Light Source (LCLS), SLAC National Laboratory, exposing single inorganic core-shell nanoparticles to femtosecond hard-X-ray pulses. Each facetted nanoparticle consisted of a crystalline gold core and a differently shaped palladium shell. Scattered intensities were observed up to about 7 nm resolution. Analysis of the scattering patterns revealed the size distribution of the samples, which is consistent with that obtained from direct real-space imaging by electron microscopy. Scattering patterns resulting from single particles were selected and compiled into a dataset which can be valuable for algorithm developments in single particle scattering research.
![130321-Thumbnail Image.png](https://d1rbsgppyrdqq4.cloudfront.net/s3fs-public/styles/width_400/public/2021-04/130321-Thumbnail%20Image.png?versionId=Qz8AVLilG_wPQvC4pSqXEh9tMCf4_cfX&X-Amz-Content-Sha256=UNSIGNED-PAYLOAD&X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIASBVQ3ZQ42ZLA5CUJ/20240615/us-west-2/s3/aws4_request&X-Amz-Date=20240615T011115Z&X-Amz-SignedHeaders=host&X-Amz-Expires=120&X-Amz-Signature=61ca77ee4cdd66df5ea8d38d91f0022d2278ccc3fbb29d6b1121299ff3bf1b21&itok=DBBpN6q4)
![130323-Thumbnail Image.png](https://d1rbsgppyrdqq4.cloudfront.net/s3fs-public/styles/width_400/public/2021-04/130323-Thumbnail%20Image.png?versionId=xIO9hccUSBcdZG5dySeB6H3lyyMV76LX&X-Amz-Content-Sha256=UNSIGNED-PAYLOAD&X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIASBVQ3ZQ42ZLA5CUJ/20240615/us-west-2/s3/aws4_request&X-Amz-Date=20240615T062155Z&X-Amz-SignedHeaders=host&X-Amz-Expires=120&X-Amz-Signature=79299f38e4d9d6f3c4a9d69153d61d7eeba89139c7661d34e0aa9c6818edd0c8&itok=xKmmsAUJ)
![130324-Thumbnail Image.png](https://d1rbsgppyrdqq4.cloudfront.net/s3fs-public/styles/width_400/public/2021-04/130324-Thumbnail%20Image.png?versionId=PveDVC78niKm2jnCV1n5j8d.nZMVYlW5&X-Amz-Content-Sha256=UNSIGNED-PAYLOAD&X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIASBVQ3ZQ42ZLA5CUJ/20240615/us-west-2/s3/aws4_request&X-Amz-Date=20240615T055241Z&X-Amz-SignedHeaders=host&X-Amz-Expires=120&X-Amz-Signature=f100248e2eb35027fdbec5e775eb90bf5f3b296c3770ae4834864667815f45bb&itok=3Mi5m02G)