CHDbase: A Comprehensive Knowledgebase for Congenital Heart Disease-related Genes and Clinical Manifestations.

Congenital heart disease (CHD) is one of themost common causes of major birth defects, with a prevalence of 1%. Although an increasing number of studies have reported the etiology of CHD, the findings scattered throughout the literature are difficult to retrieve and utilize in research and clinical practice. We therefore developed CHDbase, an evidence-based knowledgebase of CHD-related genes and clinical manifestations manually curated from 1114 publications, linking 1124susceptibility genes and 3591 variations to more than 300 CHD types and related syndromes. Metadata such as the information of each publication and the selected population and samples, the strategy of studies, and the major findings of studies were integrated with each item of the research record. We also integrated functional annotations through parsing ∼ 50 databases/tools to facilitate the interpretation of these genes and variations in disease pathogenicity. We further prioritized the significance of these CHD-related genes with a gene interaction network approach and extracted a core CHD sub-network with 163 genes. The clear genetic landscape of CHD enables the phenotype classification based on the shared genetic origin. Overall, CHDbase provides a comprehensive and freely available resource to study CHD susceptibilities, supporting a wide range of users in the scientific and medical communities. CHDbase is accessible at http://chddb.fwgenetics.org.

Simplifying Weighted Heterogeneous Networks by Extracting h-Structure via s-Degree.

In this study, we developed a method to extract the core structure of weighted heterogeneous networks by transforming the heterogeneous networks into homogeneous networks. Using the standardized z-score, we define the s-degree by summing all the z-scores of adjacent edges into base-nodes for a weighted heterogeneous network. Then, we rank all the s-degrees in decreasing order to obtain the core structure via the h-index of a base-homogeneous-network. After reducing all adjacent edges between the attribute nodes and base-nodes to the core structure, we obtain the heterogeneous core structure of the weighted network, which is called the h-structure. We find that the h-structure in a heterogeneous network contains less than 1% nodes and edges, which results in the construction of a highly effective simplification of a weighted heterogeneous network. Two practical cases, the citation network and the co-purchase network, were examined in this study.

Identifying "hot papers" and papers with "delayed recognition" in large-scale datasets by using dynamically normalized citation impact scores.

"Hot papers" (HPs) are papers which received a boost of citations shortly after publication. Papers with "delayed recognition" (DRs) received scarcely impact over a long time period, before a considerable citation boost started. DRs have attracted a lot of attention in scientometrics and beyond. Based on a comprehensive dataset with more than 5,000,000 papers published between 1980 and 1990, we identified HPs and DRs. In contrast to many other studies on DRs, which are based on raw citation counts, we calculated dynamically field-normalized impact scores for the search of HPs and DRs. This study is intended to investigate the differences between HPs (n = 323) and DRs (n = 315). The investigation of the journals which have published HPs and DRs revealed that some journals (e.g. Physical Review Letters and PNAS) were able to publish significantly more HPs than other journals. This pattern did not appear in DRs. Many HPs and DRs have been published by authors from the USA; however, in contrast to other countries, authors from the USA have published statistically significantly more HPs than DRs. Whereas "Biochemistry & Molecular Biology," "Immunology," and "Cell Biology" have published significantly more HPs than DRs, the opposite result arrived for "Surgery" and "Orthopedics." The results of the analysis of certain properties of HPs and DRs (e.g. number of pages) suggest that the emergence of DRs is an unpredictable process.

Extracting h-Backbone as a Core Structure in Weighted Networks.

Determining the core structure of complex network systems allows us to simplify them. Using h-bridge and h-strength measurements in a weighted network, we extract the h-backbone core structure. We find that focusing on the h-backbone in a network allows greater simplification because it has fewer edges and thus fewer adjacent nodes. We examine three practical applications: the co-citation network in an information system, the open flight network in a social system, and coauthorship in network science publications.

Sequence analysis of annually normalized citation counts: an empirical analysis based on the characteristic scores and scales (CSS) method.

In bibliometrics, only a few publications have focused on the citation histories of publications, where the citations for each citing year are assessed. In this study, therefore, annual categories of field- and time-normalized citation scores (based on the characteristic scores and scales method: 0 = poorly cited, 1 = fairly cited, 2 = remarkably cited, and 3 = outstandingly cited) are used to study the citation histories of papers. As our dataset, we used all articles published in 2000 and their annual citation scores until 2015. We generated annual sequences of citation scores (e.g., [Formula: see text]) and compared the sequences of annual citation scores of six broader fields (natural sciences, engineering and technology, medical and health sciences, agricultural sciences, social sciences, and humanities). In agreement with previous studies, our results demonstrate that sequences with poorly cited (0) and fairly cited (1) elements dominate the publication set; sequences with remarkably cited (3) and outstandingly cited (4) periods are rare. The highest percentages of constantly poorly cited papers can be found in the social sciences; the lowest percentages are in the agricultural sciences and humanities. The largest group of papers with remarkably cited (3) and/or outstandingly cited (4) periods shows an increasing impact over the citing years with the following orders of sequences: [Formula: see text] (6.01%), which is followed by [Formula: see text] (1.62%). Only 0.11% of the papers (n = 909) are constantly on the outstandingly cited level.