[Study on quality status of mineral medicine Calamina].

In this paper, some quality problems of mineral medicine Calamina and calcined Calamina have been discussed after determination and analysis of the quality parameters of a large number of market samples, and the countermeasures are put forward. According to the XRD results, as well as the results of tests included in Chinese Pharmacopoeia(2015 edition), the authenticity of Calamina and calcined Calamina samples were identified. The content of zinc oxide in samples were determined by the method of determination in Chinese Pharmacopoeia. Individually, inductively coupled plasma mass spectrometry(ICP-MS), inductively coupled plasma atomic emission spectrometry(ICP-AES) and atomic fluorescence spectrometry(AFS) methods were used for the determination of impurity elements and harmful elements in Calamina and calcined Calamina samples. Four kinds of impurity elements of magnesium(Mg), iron(Fe), aluminum(Al), calcium(Ca) and five harmful elements such as lead(Pb), cadmium(Cd), arsenic(As), copper(Cu), mercury(Hg) were measured. The study showed that: ① Fake Calamina products on the market were overflowing; ② The mineral origin of the mainstream Calamina in the market is inconsistent with that stipulated in Chinese Pharmacopoeia(2015 edition); ③ The contents of harmful elements Pb and Cd in Calamina and calcined Calamina are generally higher, while the contents of harmful elements As and Cu in some inferior Calaminae are higher; ④ Parts of calcined Calamina were improperly or inadequately processed. In view of these quality problems, the countermeasures are put forward as follows: ① It is suggested that hydrozincite should be approved as the mineral source of Calamina, and be included by Chinese Pharmacopoeia; ② Strengthen the research on the specificity of Calamina identification methods to improve the quality control level; ③ Strengthen the research on the processing of Calamina, and formulate the limit standards for the content of Pb and Cd in Calamina; ④ Carry out research on the artificial synthesis of Calamina and calcined Calamina, in order to cope with the current shortage of Calamina resources and ensure the sustainable development of Calamina medicinal materials.

HIV-1, human interaction database: current status and new features.

The 'Human Immunodeficiency Virus Type 1 (HIV-1), Human Interaction Database', available through the National Library of Medicine at http://www.ncbi.nlm.nih.gov/genome/viruses/retroviruses/hiv-1/interactions, serves the scientific community exploring the discovery of novel HIV vaccine candidates and therapeutic targets. Each HIV-1 human protein interaction can be retrieved without restriction by web-based downloads and ftp protocols and includes: Reference Sequence (RefSeq) protein accession numbers, National Center for Biotechnology Information Gene identification numbers, brief descriptions of the interactions, searchable keywords for interactions and PubMed identification numbers (PMIDs) of journal articles describing the interactions. In addition to specific HIV-1 protein-human protein interactions, included are interaction effects upon HIV-1 replication resulting when individual human gene expression is blocked using siRNA. A total of 3142 human genes are described participating in 12,786 protein-protein interactions, along with 1316 replication interactions described for each of 1250 human genes identified using small interfering RNA (siRNA). Together the data identifies 4006 human genes involved in 14,102 interactions. With the inclusion of siRNA interactions we introduce a redesigned web interface to enhance viewing, filtering and downloading of the combined data set.

The NIH genetic testing registry: a new, centralized database of genetic tests to enable access to comprehensive information and improve transparency.

The National Institutes of Health Genetic Testing Registry (GTR; available online at http://www.ncbi.nlm.nih.gov/gtr/) maintains comprehensive information about testing offered worldwide for disorders with a genetic basis. Information is voluntarily submitted by test providers. The database provides details of each test (e.g. its purpose, target populations, methods, what it measures, analytical validity, clinical validity, clinical utility, ordering information) and laboratory (e.g. location, contact information, certifications and licenses). Each test is assigned a stable identifier of the format GTR000000000, which is versioned when the submitter updates information. Data submitted by test providers are integrated with basic information maintained in National Center for Biotechnology Information's databases and presented on the web and through FTP (ftp.ncbi.nih.gov/pub/GTR/_README.html).

iCn3D: From Web-Based 3D Viewer to Structural Analysis Tool in Batch Mode.

iCn3D was initially developed as a web-based 3D molecular viewer. It then evolved from visualization into a full-featured interactive structural analysis software. It became a collaborative research instrument through the sharing of permanent, shortened URLs that encapsulate not only annotated visual molecular scenes, but also all underlying data and analysis scripts in a FAIR manner. More recently, with the growth of structural databases, the need to analyze large structural datasets systematically led us to use Python scripts and convert the code to be used in Node. js scripts. We showed a few examples of Python scripts at https://github.com/ncbi/icn3d/tree/master/icn3dpython to export secondary structures or PNG images from iCn3D. Users just need to replace the URL in the Python scripts to export other annotations from iCn3D. Furthermore, any interactive iCn3D feature can be converted into a Node. js script to be run in batch mode, enabling an interactive analysis performed on one or a handful of protein complexes to be scaled up to analysis features of large ensembles of structures. Currently available Node. js analysis scripts examples are available at https://github.com/ncbi/icn3d/tree/master/icn3dnode. This development will enable ensemble analyses on growing structural databases such as AlphaFold or RoseTTAFold on one hand and Electron Microscopy on the other. In this paper, we also review new features such as DelPhi electrostatic potential, 3D view of mutations, alignment of multiple chains, assembly of multiple structures by realignment, dynamic symmetry calculation, 2D cartoons at different levels, interactive contact maps, and use of iCn3D in Jupyter Notebook as described at https://pypi.org/project/icn3dpy.