BACKGROUND: High-throughput sequencing is a powerful tool that is extensively applied in biological studies. However, sequencers may produce low-quality bases, leading to ambiguous bases, 'N's. PCR duplicates introduced in library preparation are conventionally removed in genomics studies, and several deduplication tools have been developed for this purpose. Two identical reads may appear different due to ambiguous bases and the existing tools cannot address 'N's correctly or efficiently. RESULTS: Here we proposed and implemented TrieDedup, which uses the trie (prefix tree) data structure to compare and store sequences. TrieDedup can handle ambiguous base 'N's, and efficiently deduplicate at the level of raw sequences. We also reduced its memory usage by approximately 20% by implementing restrictedDict in Python. We benchmarked the performance of the algorithm and showed that TrieDedup can deduplicate reads up to 270-fold faster than pairwise comparison at a cost of 32-fold higher memory usage. CONCLUSIONS: The TrieDedup algorithm may facilitate PCR deduplication, barcode or UMI assignment, and repertoire diversity analysis of large-scale high-throughput sequencing datasets with its ultra-fast algorithm that can account for ambiguous bases due to sequencing errors.

The calculation of Tumor Stroma Ratio (TSR) is a challenging medical issue that could improve predictions of neoadjuvant chemotherapy benefits and patient prognoses. Although several studies on breast cancer and deep learning methods have achieved promising results, the drawbacks that pixel-level semantic segmentation processes could not extract core tumor regions containing both tumor pixels and stroma pixels make it difficult to accurately calculate TSR. In this paper, we propose a Vague-Segment Technique (VST) consisting of a designed SwinV2UNet module and a modified Suzuki algorithm. Specifically, the SwinV2UNet identifies tumor pixels and generate pixel-level classification results, based on which the modified Suzuki algorithm extracts the contour of core tumor regions in terms of cosine angle. Through this way, VST obtains vaguely segmentation results of core tumor regions containing both tumor pixels and stroma pixels, where the TSR could be calculated by the formula of Intersection over Union (IOU). For the training and evaluation, we utilize the well-known The Cancer Genome Atlas (TCGA) database to create an annotated dataset, while 150 images with TSR annotations from real cases are also collected. The experimental results illustrate that the proposed VST could generate better tumor identification results compared with state-of-the-art methods, where the extracted core tumor regions lead to more consistencies of calculated TSR with senior experts compared to junior pathologists. The experimental results demonstrate the superiority of our proposed pipeline, which has promise for future clinical application.

Tone mapping aims to convert high dynamic range (HDR) images to low dynamic range (LDR) representations, a critical task in the camera imaging pipeline. In recent years, 3-Dimensional LookUp Table (3D LUT) based methods have gained attention due to their ability to strike a favorable balance between enhancement performance and computational efficiency. However, these methods often fail to deliver satisfactory results in local areas since the look-up table is a global operator for tone mapping, which works based on pixel values and fails to incorporate crucial local information. To this end, this paper aims to address this issue by exploring a novel strategy that integrates global and local operators by utilizing closed-form Laplacian pyramid decomposition and reconstruction. Specifically, we employ image-adaptive 3D LUTs to manipulate the tone in the low-frequency image by leveraging the specific characteristics of the frequency information. Furthermore, we utilize local Laplacian filters to refine the edge details in the high-frequency components in an adaptive manner. Local Laplacian filters are widely used to preserve edge details in photographs, but their conventional usage involves manual tuning and fixed implementation within camera imaging pipelines or photo editing tools. We propose to learn parameter value maps progressively for local Laplacian filters from annotated data using a lightweight network. Our model achieves simultaneous global tone manipulation and local edge detail preservation in an end-to-end manner. Extensive experimental results on two benchmark datasets demonstrate that the proposed method performs favorably against state-of-the-art methods.

SUMMARY: Community curation-harnessing community intelligence in knowledge curation, bears great promise in dealing with the flood of biological knowledge. To exploit the full potential of the scientific community for knowledge curation, multiple biological wikis (bio-wikis) have been built to date. However, none of them have achieved a substantial impact on knowledge curation. One of the major limitations in bio-wikis is insufficient community participation, which is intrinsically because of lack of explicit authorship and thus no credit for community curation. To increase community curation in bio-wikis, here we develop AuthorReward, an extension to MediaWiki, to reward community-curated efforts in knowledge curation. AuthorReward quantifies researchers' contributions by properly factoring both edit quantity and quality and yields automated explicit authorship according to their quantitative contributions. AuthorReward provides bio-wikis with an authorship metric, helpful to increase community participation in bio-wikis and to achieve community curation of massive biological knowledge. AVAILABILITY: http://cbb.big.ac.cn/software. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.