Construction of Clinical Biobanks and the Medical Ethics

Nowadays, various types and forms of clinical biobanks have been gradually established worldwide, which have become one of the important components and research platforms of life science and related disease researches in the medical system. This article mainly introduces the construction, management and operation of clinical biobanks, and discusses the medical ethics faced by it

On the Construction of Biobank in General Hospitals

Objective: Discussion on a series of biospecimen related issues are conducted, such as collection and preservation, quality control, as well as management and application, during the construction of human tissue biobank in a general hospital. Methods: To develop a set of standardized operational procedures and to collect tissue samples, such as whole blood, serum, plasma, fresh frozen tissues, cerebrospinal fluid, and paraffin-embedded tissues, which were classified and made aliquots according to different requirements, and stored at -80℃ temperature refrigerator or in liquid nitrogen. At the same time, a set of information management software was used to realize management of the biobank. Results: Currently, there are more than 20,000 specimens of various benign and malignant cases, which cover 380 diseases, being collected in the biological database in our hospital. These specimens include paraffin-embedded tissue, fresh frozen tissue, femoral head, whole blood, plasma, serum and cerebrospinal fluid, etc. A large number of these specimensare beneficial is used in clinical research at present. Conclusion: The establishment of biological sample bank can maximize the value of non-reborn human tissue specimens, and provide normal control standards as well as benign and malignant disease standards for clinical diagnosis and treatment, which is of great significance to the research of disease pathogenesis and the development of detection technology

BioConceptVec: creating and evaluating literature-based biomedical concept embeddings on a large scale

Capturing the semantics of related biological concepts, such as genes and mutations, is of significant importance to many research tasks in computational biology such as protein-protein interaction detection, gene-drug association prediction, and biomedical literature-based discovery. Here, we propose to leverage state-of-the-art text mining tools and machine learning models to learn the semantics via vector representations (aka. embeddings) of over 400,000 biological concepts mentioned in the entire PubMed abstracts. Our learned embeddings, namely BioConceptVec, can capture related concepts based on their surrounding contextual information in the literature, which is beyond exact term match or co-occurrence-based methods. BioConceptVec has been thoroughly evaluated in multiple bioinformatics tasks consisting of over 25 million instances from nine different biological datasets. The evaluation results demonstrate that BioConceptVec has better performance than existing methods in all tasks. Finally, BioConceptVec is made freely available to the research community and general public via https://github.com/ncbi-nlp/BioConceptVec.Comment: 33 pages, 6 figures, 7 tables, accepted by PLOS Computational Biolog

Graph Reasoning for Question Answering with Triplet Retrieval

Answering complex questions often requires reasoning over knowledge graphs (KGs). State-of-the-art methods often utilize entities in questions to retrieve local subgraphs, which are then fed into KG encoder, e.g. graph neural networks (GNNs), to model their local structures and integrated into language models for question answering. However, this paradigm constrains retrieved knowledge in local subgraphs and discards more diverse triplets buried in KGs that are disconnected but useful for question answering. In this paper, we propose a simple yet effective method to first retrieve the most relevant triplets from KGs and then rerank them, which are then concatenated with questions to be fed into language models. Extensive results on both CommonsenseQA and OpenbookQA datasets show that our method can outperform state-of-the-art up to 4.6% absolute accuracy.Comment: Findings of ACL 202

Total body bone mineral density and various spinal disorders: a Mendelian randomization study

IntroductionObservational studies have yielded inconsistent findings regarding the correlation between bone mineral density (BMD) and various spinal disorders. To explore the relationship between total-body BMD and various spinal disorders further, we conducted a Mendelian randomization analysis to assess this association.MethodsTwo-sample bidirectional Mendelian randomization (MR) analysis was employed to investigate the association between total-body BMD and various spinal disorders. The inverse-variance weighted (IVW) method was used as the primary effect estimate, and additional methods, including weighted median, MR-Egger, simple mode, and weighted mode, were used to assess the reliability of the results. To examine the robustness of the data further, we conducted a sensitivity analysis using alternative bone-density databases, validating the outcome data.ResultsMR revealed a significant positive association between total-body BMD and the prevalence of spondylosis and spinal stenosis. When total-body BMD was considered as the exposure factor, the analysis demonstrated an increased risk of spinal stenosis (IVW odds ratio [OR] 1.23; 95% confidence interval [CI], 1.14–1.32; P < 0.001) and spondylosis (IVW: OR 1.24; 95%CI, 1.16–1.33; P < 0.001). Similarly, when focusing solely on heel BMD as the exposure factor, we found a positive correlation with the development of both spinal stenosis (IVW OR 1.13, 95%CI, 1.05–1.21; P < 0.001) and spondylosis (IVW OR 1.10, 95%CI, 1.03–1.18; P = 0.0048). However, no significant associations were found between total-body BMD and other spinal disorders, including spinal instability, spondylolisthesis/spondylolysis, and scoliosis (P > 0.05).ConclusionThis study verified an association of total-body BMD with spinal stenosis and with spondylosis. Our results imply that when an increasing trend in BMD is detected during patient examinations and if the patient complains of numbness and pain, the potential occurrence of conditions such as spondylosis or spinal stenosis should be investigated and treated appropriately

Analysis on the Nutritional Components and Texture Characteristics of Prefabricated Grilled Fish with Different Fish Species

To explore the development value of different freshwater fish productions of prefabricated grilled fish and realize the diversified development of prefabricated grilled fish categories, an analysis was hereby carried out on the nutritional and textural characteristics of prefabricated grilled fish processed from six common freshwater fish. The results showed that there was no significant difference in the moisture and ash content (P>0.05), the protein content ranged from 21.87%~24.28%, and the fat content was low in all six types of grilled fish. Besides, the content of glutamic acid, aspartic acid and lysine was high, and that of the total essential amino acids ranged from 7.71~9.42 g/100 g. Among them, that of common carp and Wuchang fish was higher, followed by tilapia and grass carp, Wuchang fish, common carp and tilapia had a high fresh amino acid content. The ratio of the essential amino acids to the total amino acids of the six grilled fish was about 40%, which was a high-quality animal protein source. According to the amino acid score, the first limiting amino acid of all six grilled fish was methionine+cysteine, common carp had the highest essential amino acid index, followed by tilapia. Besides, a total of 22 fatty acids were detected in the six grilled fish species, which had a high proportion of unsaturated fatty acids. Tilapia and Wuchang fish contained high functional fatty acids with a high nutritional value, such as eicosapentaenoic acid and docosahexaenoic acid. Through the principal component analysis, the comprehensive score of nutritional indicators followed the order of tilapia>Wuchang fish>common carp>grass carp>crucian carp>pincer fish, while in terms of textural characteristics, the elasticity and chewiness of tilapia and Wuchang fish were significantly（P<0.05）higher than those of traditional common carp and grass carp, and the hardness was lower. In this case, it could be tentatively inferred that tilapia and Wuchang fish had a better muscle texture. As raw materials of grilled fish, all these six freshwater fish were excellent protein sources, reasonable amino acid composition and rich fatty acids, among which, tilapia and Wuchang fish produced prefabricated grilled fish with better nutrition and better taste. Overall, this study provides a theoretical basis for the development of grilled fish in multiple categories and the extension of the "breeding+processing" industry chain