OBIA: An Open Biomedical Imaging Archive.

With the development of artificial intelligence (AI) technologies, biomedical imaging data play an important role in scientific research and clinical application, but the available resources are limited. Here we present Open Biomedical Imaging Archive (OBIA), a repository for archiving biomedical imaging and related clinical data. OBIA adopts five data objects (Collection, Individual, Study, Series, and Image) for data organization, and accepts the submission of biomedical images of multiple modalities, organs, and diseases. In order to protect personal privacy, OBIA has formulated a unified de-identification and quality control process. In addition, OBIA provides friendly and intuitive web interfaces for data submission, browsing, and retrieval, as well as image retrieval. As of September 2023, OBIA has housed data for a total of 937 individuals, 4136 studies, 24,701 series, and 1,938,309 images covering 9 modalities and 30 anatomical sites. Collectively, OBIA provides a reliable platform for biomedical imaging data management and offers free open access to all publicly available data to support research activities throughout the world. OBIA can be accessed at https://ngdc.cncb.ac.cn/obia.

McAN: a novel computational algorithm and platform for constructing and visualizing haplotype networks.

Haplotype networks are graphs used to represent evolutionary relationships between a set of taxa and are characterized by intuitiveness in analyzing genealogical relationships of closely related genomes. We here propose a novel algorithm termed McAN that considers mutation spectrum history (mutations in ancestry haplotype should be contained in descendant haplotype), node size (corresponding to sample count for a given node) and sampling time when constructing haplotype network. We show that McAN is two orders of magnitude faster than state-of-the-art algorithms without losing accuracy, making it suitable for analysis of a large number of sequences. Based on our algorithm, we developed an online web server and offline tool for haplotype network construction, community lineage determination, and interactive network visualization. We demonstrate that McAN is highly suitable for analyzing and visualizing massive genomic data and is helpful to enhance the understanding of genome evolution. Availability: Source code is written in C/C++ and available at https://github.com/Theory-Lun/McAN and https://ngdc.cncb.ac.cn/biocode/tools/BT007301 under the MIT license. Web server is available at https://ngdc.cncb.ac.cn/bit/hapnet/. SARS-CoV-2 dataset are available at https://ngdc.cncb.ac.cn/ncov/. Contact: songshh@big.ac.cn (Song S), zhaowm@big.ac.cn (Zhao W), baoym@big.ac.cn (Bao Y), zhangzhang@big.ac.cn (Zhang Z), ybxue@big.ac.cn (Xue Y).

GSA-Human: Genome Sequence Archive for Human.

The Genome Sequence Archive for Human (GSA-Human) is a data repository specialized for human genetic related data derived from biomedical researches, and also supports the data collection and management of National Key Research and Development Projects. GSA-Human has a data security management strategy according to the national regulations of human genetic resources. It provides two different models of data access: Open-access and Controlled-access. Open-access data are universally and freely accessible for global researchers, while Controlled-access ensures that data are accessed only by authorized users with the permission of the Data Access Committee (DAC). Till July 2021, GSA-Human has housed more than 5.27 PB of data from 750 datasets.

Drought stress introduces growth, physiological traits and ecological stoichiometry changes in two contrasting Cunninghamia lanceolata cultivars planted in continuous-plantation soils.

BACKGROUND: The decrease in Cunninghamia lanceolata (Lamb.) production on continuously planted soil is an essential problem. In this study, two-year-old seedlings of two cultivars (a normal cultivar, NC, and a super cultivar, SC) were grown in two types of soil (not planted (NP) soil; continuously planted (CP) soil) with three watering regimes, and the interactive effects on plant growth and physiological traits were investigated in a greenhouse experiment. The water contents of the soil in the control (CK) (normal water content), medium water content (MWC) and low water content (LWC) treatments reached 75-80 %, 45-50 % and 20-25 % of the field water capacity, respectively. RESULTS: The results indicated that the CP soil had a negative effect on growth and physiological traits and that the LWC treatment caused even more severe and comprehensive negative effects. In both cultivars, the CP soil significantly decreased the height increment (HI), basal diameter increment (DI), dry matter accumulation (DMA), net photosynthetic rate (Pn), total chlorophyll content (TChl), carotenoid content (Caro) and photosynthetic nitrogen use efficiency (PNUE). Compared to the NP soil, the CP soil also decreased the proline and soluble protein contents, nitrogen use efficiency (NUE) and phosphorus use efficiency (PUE) and increased the nitrogen:phosphorus ratio in roots, stems and leaves. The LWC treatment decreased growth and photosynthesis, changed ecological stoichiometry, induced oxidative stress, promoted water use efficiency and damaged chloroplast ultrastructure. Significant increases in ascorbate peroxidase (APX), peroxidase (POD), soluble protein and proline contents were found in the LWC treatment. Compared with the NC, the SC was more tolerant to the CP soil and water stress, as indicated by the higher levels of DMA, Pn, and WUE. After exposure to the CP soil and watering regimes, the decreases in biomass accumulation and gas exchange were more pronounced. CONCLUSIONS: The combination of drought and CP soil may have detrimental effects on C. lanceolata growth, and low water content enhances the impacts of CP soil stress on C. lanceolata seedlings. The superiority of the SC over the NC is significant in Chinese fir plantation soil. Therefore, continuously planted soil can be utilized to cultivate improved varieties of C. lanceolata and maintain water capacity. This can improve their growth and physiological performance to a certain extent.

The Genome Sequence Archive Family: Toward Explosive Data Growth and Diverse Data Types.

The Genome Sequence Archive (GSA) is a data repository for archiving raw sequence data, which provides data storage and sharing services for worldwide scientific communities. Considering explosive data growth with diverse data types, here we present the GSA family by expanding into a set of resources for raw data archive with different purposes, namely, GSA (https://ngdc.cncb.ac.cn/gsa/), GSA for Human (GSA-Human, https://ngdc.cncb.ac.cn/gsa-human/), and Open Archive for Miscellaneous Data (OMIX, https://ngdc.cncb.ac.cn/omix/). Compared with the 2017 version, GSA has been significantly updated in data model, online functionalities, and web interfaces. GSA-Human, as a new partner of GSA, is a data repository specialized in human genetics-related data with controlled access and security. OMIX, as a critical complement to the two resources mentioned above, is an open archive for miscellaneous data. Together, all these resources form a family of resources dedicated to archiving explosive data with diverse types, accepting data submissions from all over the world, and providing free open access to all publicly available data in support of worldwide research activities.

The Global Landscape of SARS-CoV-2 Genomes, Variants, and Haplotypes in 2019nCoVR.

On January 22, 2020, China National Center for Bioinformation (CNCB) released the 2019 Novel Coronavirus Resource (2019nCoVR), an open-access information resource for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). 2019nCoVR features a comprehensive integration of sequence and clinical information for all publicly available SARS-CoV-2 isolates, which are manually curated with value-added annotations and quality evaluated by an automated in-house pipeline. Of particular note, 2019nCoVR offers systematic analyses to generate a dynamic landscape of SARS-CoV-2 genomic variations at a global scale. It provides all identified variants and their detailed statistics for each virus isolate, and congregates the quality score, functional annotation, and population frequency for each variant. Spatiotemporal change for each variant can be visualized and historical viral haplotype network maps for the course of the outbreak are also generated based on all complete and high-quality genomes available. Moreover, 2019nCoVR provides a full collection of SARS-CoV-2 relevant literature on the coronavirus disease 2019 (COVID-19), including published papers from PubMed as well as preprints from services such as bioRxiv and medRxiv through Europe PMC. Furthermore, by linking with relevant databases in CNCB, 2019nCoVR offers data submission services for raw sequence reads and assembled genomes, and data sharing with NCBI. Collectively, SARS-CoV-2 is updated daily to collect the latest information on genome sequences, variants, haplotypes, and literature for a timely reflection, making 2019nCoVR a valuable resource for the global research community. 2019nCoVR is accessible at https://bigd.big.ac.cn/ncov/.

In Situ Formation of Ag Nanoparticles in Mesoporous TiO2 Films Decorated on Bamboo via Self-Sacrificing Reduction to Synthesize Nanocomposites with Efficient Antifungal Activity.

We developed a novel green approach for the in situ fabrication of Ag NPs in mesoporous TiO2 films via the bamboo self-sacrificing reduction of Ag(NH3)2+ ions, which can inhibit fungal growth on the bamboo surface. Mesoporous anatase TiO2 (MT) films were first synthesized on bamboo via a hydrothermal method. Then, Ag NPs with a 5.3 nm mean diameter were incorporated into the pore channels of optimal MT/bamboo (MTB) samples at room temperature without the addition of reducing agents, such that the Ag NPs were almost entirely embedded into the MT films. Our analysis indicated that the solubilized lignin from bamboo, which is rich in oxygen-containing functional groups, serves as a green reductant for reducing the Ag(NH3)2+ ions to Ag NPs. Antifungal experiments with Trichoderma viride under dark conditions highlighted that the antifungal activity of the Ag/MT/bamboo samples were greater than those of naked bamboo, MTB, and Ag/bamboo, suggesting that these hybrid nanomaterials produce a synergistic antifungal effect that is unrelated to photoactivity. The inhibition of Penicillium citrinum effectively followed a similar trend. This newly developed bamboo protection method may provide a sustainable, eco-friendly, and efficient method for enhancing the antifungal characteristics of traditional bamboo, having the potential to prolong the service life of bamboo materials, particularly under dark conditions.

[D-Leu-4]-OB3 and MA-[D-Leu-4]-OB3, small molecule synthetic peptide leptin mimetics, improve glycemic control in diet-induced obese (DIO) mice.

We have previously shown that following oral delivery in dodecyl maltoside (DDM), [D-Leu-4]-OB3 and its myristic acid conjugate, MA-[D-Leu-4]-OB3, improved energy balance and glucose homeostasis in genetically obese/diabetic mouse models. More recently, we have provided immunohistochemical evidence indicating that these synthetic peptide leptin mimetics cross the blood-brain barrier and concentrate in the area of the arcuate nucleus of the hypothalamus in normal C57BL/6J and Swiss Webster mice, in genetically obese ob/ob mice, and in diet-induced obese (DIO) mice. In the present study, we describe the effects of oral delivery of [D-Leu-4]-OB3 and MA-[D-Leu-4]-OB3 on glycemic control in diet-induced (DIO) mice, a non-genetic rodent model of obesity and its associated insulin resistance, which more closely recapitulates common obesity and diabetes in humans. Male C57BL/6J and DIO mice, 17, 20, and 28 weeks of age, were maintained on a low-fat or high-fat diet and given vehicle (DDM) alone or [D-Leu-4]-OB3 or MA-[D-Leu-4]-OB3 in DDM by oral gavage for 12 or 14 days. Body weight gain, food and water intake, fasting blood glucose, oral glucose tolerance, and serum insulin levels were measured. Our data indicate that (1) [D-Leu-4]-OB3 and MA-[D-Leu-4]-OB3 restore glucose tolerance in male DIO mice maintained on a high-fat diet to levels comparable to those of non-obese C57BL/6J wild-type mice of the same age and sex maintained on a low-fat diet; and (2) the influence of [D-Leu-4]-OB3 and MA-[D-Leu-4]-OB3 on glycemic control appears to be independent of their effects on energy balance. These results suggest that [D-Leu-4]-OB3 and/or MA-[D-Leu-4]-OB3 may have application to the management of the majority of cases of common obesity in humans, a state characterized at least in part, by leptin resistance resulting from a defect in leptin transport across the blood-brain barrier. They further suggest that these small molecule synthetic peptide leptin mimetics, through their influence on glycemic control, may prevent the pre-diabetic state associated with most cases of common obesity from escalating into overt type 2 diabetes mellitus.