Evaluating the Pharmacological Mechanism of Chinese Medicine Si-Wu-Tang through Multi-Level Data Integration

Si-Wu-Tang (SWT) is a Traditional Chinese Medicine (TCM) formula widely used for the treatments of gynecological diseases. To explore the pharmacological mechanism of SWT, we incorporated microarray data of SWT with our herbal target database TCMID to analyze the potential activity mechanism of SWT''s herbal ingredients and targets. We detected 2,405 differentially expressed genes in the microarray data, 20 of 102 proteins targeted by SWT were encoded by these DEGs and can be targeted by 2 FDA-approved drugs and 39 experimental drugs. The results of pathway enrichment analysis of the 20 predicted targets were consistent with that of 2,405 differentially expressed genes, elaborating the potential pharmacological mechanisms of SWT. Further study from a perspective of protein-protein interaction (PPI) network showed that the predicted targets of SWT function cooperatively to perform their multi-target effects. We also constructed a network to combine herbs, ingredients, targets and drugs together which bridges the gap between SWT and conventional medicine, and used it to infer the potential mechanisms of herbal ingredients. Moreover, based on the hypothesis that the same or similar effects between different TCM formulae may result from targeting the same proteins, we analyzed 27 other TCM formulae which can also treat the gynecological diseases, the subsequent result provides additional insight to understand the potential mechanisms of SWT in treating amenorrhea. Our bioinformatics approach to detect the pharmacology of SWT may shed light on drug discovery for gynecological diseases and could be utilized to investigate other TCM formulae as well.     

An Overview of the Genetic Structure within the Italian Population from Genome-Wide Data

In spite of the common belief of Europe as reasonably homogeneous at genetic level, advances in high-throughput genotyping technology have resolved several gradients which define different geographical areas with good precision. When Northern and Southern European groups were considered separately, there were clear genetic distinctions. Intra-country genetic differences were also evident, especially in Finland and, to a lesser extent, within other European populations. Here, we present the first analysis using the 125,799 genome-wide Single Nucleotide Polymorphisms (SNPs) data of 1,014 Italians with wide geographical coverage. We showed by using Principal Component analysis and model-based individual ancestry analysis, that the current population of Sardinia can be clearly differentiated genetically from mainland Italy and Sicily, and that a certain degree of genetic differentiation is detectable within the current Italian peninsula population. Pair-wise F_ST statistics Northern and Southern Italy amounts approximately to 0.001 between, and around 0.002 between Northern Italy and Utah residents with Northern and Western European ancestry (CEU). The Italian population also revealed a fine genetic substructure underscoring by the genomic inflation (Sardinia vs. Northern Italy = 3.040 and Northern Italy vs. CEU = 1.427), warning against confounding effects of hidden relatedness and population substructure in association studies.     

Rumor Diffusion and Convergence during the 3.11 Earthquake: A Twitter Case Study

We focus on Internet rumors and present an empirical analysis and simulation results of their diffusion and convergence during emergencies. In particular, we study one rumor that appeared in the immediate aftermath of the Great East Japan Earthquake on March 11, 2011, which later turned out to be misinformation. By investigating whole Japanese tweets that were sent one week after the quake, we show that one correction tweet, which originated from a city hall account, diffused enormously. We also demonstrate a stochastic agent-based model, which is inspired by contagion model of epidemics SIR, can reproduce observed rumor dynamics. Our model can estimate the rumor infection rate as well as the number of people who still believe in the rumor that cannot be observed directly. For applications, rumor diffusion sizes can be estimated in various scenarios by combining our model with the real data.     

Workplace Social Capital and Mental Health among Chinese Employees: A Multi-Level,Cross-Sectional Study

Background

Whereas the majority of previous research on social capital and health has been on residential neighborhoods and communities, the evidence remains sparse on workplace social capital. To address this gap in the literature, we examined the association between workplace social capital and health status among Chinese employees in a large, multi-level, cross-sectional study.

Methods

By employing a two-stage stratified random sampling procedure, 2,796 employees were identified from 35 workplaces in Shanghai during March to November 2012. Workplace social capital was assessed using a validated and psychometrically tested eight-item measure, and the Chinese language version of the WHO-Five Well-Being Index (WHO-5) was used to assess mental health. Control variables included sex, age, marital status, education level, occupation status, smoking status, physical activity, and job stress. Multilevel logistic regression analysis was conducted to explore whether individual- and workplace-level social capital was associated with mental health status.

Results

In total, 34.9% of workers reported poor mental health (WHO-5<13). After controlling for individual-level socio-demographic and lifestyle variables, compared to workers with the highest quartile of personal social capital, workers with the third, second, and lowest quartiles exhibited 1.39 to 3.54 times greater odds of poor mental health, 1.39 (95% CI: 1.10–1.75), 1.85 (95% CI: 1.38–2.46) and 3.54 (95% CI: 2.73–4.59), respectively. Corresponding odds ratios for workplace-level social capital were 0.95 (95% CI: 0.61–1.49), 1.14 (95% CI: 0.72–1.81) and 1.63 (95% CI: 1.05–2.53) for the third, second, and lowest quartiles, respectively.

Conclusions

Higher workplace social capital is associated with lower odds of poor mental health among Chinese employees. Promoting social capital at the workplace may contribute to enhancing employees’ mental health in China.     

Data from a Study of a Neuroallergic Family

Migraine and other types of headaches, serous meningites, encephalomyelites related to the employment of serums and vaccines, including Alazhuanin's hemorrhagic encephalitis, acute hemorrhagic encephalitis, parainfectious encephalites, nervous system damage of arthritic origin (primarily chorea minor), vascular diseases of the nervous system in periarteritis nodosa, cerebral thromboangiitis obliterans in Winiwarter-Buerger's disease, serous and toxic neurites and polyneurites, the Guillain-Barre syndrome, Landry's paralysis, polyneurites resulting from treatment with salvarsan and sulfonamides, certain cases of Meniere's syndrome, demyelinating diseases of the nervous system (multiple sclerosis, related acute and chronic disseminated encephalites, encephalitis periaxialis diffusa, and other forms of sclerous leuco encephalites and, finally, epilepsy (1-24) are diseases of the nervous system associated with immune pathology reactions to various antigens (foods, inhalational, medicamental, viral, bacterial and other foreign agents, and autoantigens).     

Geographical,botanical and chemical profile of monofloral Italian honeys as food quality guarantee and territory brand

Bees represent an important element for the preservation of plant biodiversity. During their activities, bees cover a large area around the hive and their products strictly reflect the distinctive traits of these environments. In honey, the floral diversity of the areas inspected by bees is revealed by their pollen spectra. The present work characterized 460 Italian unifloral honeys by melissopalynological and physicochemical analyses. Obtained data contributed to: confirm the botanical identity of the samples; determine the plant biodiversity revealed in each honey; differentiate the samples of the same monofloral typology in relation to their geographical origin; and identify peculiar floristic associations in the Italian regions. Moreover, gas chromatographic analysis was carried out on rare unifloral honey to study their sugar profiles. This work provided the scientific base to create a valid tool able to assign a territorial brand and an authenticity guarantee to the honey, protecting the consumers from adulterations.     

Diffusion of Messages from an Electronic Cigarette Brand to Potential Users through Twitter

Objective

This study explores the presence and actions of an electronic cigarette (e-cigarette) brand, Blu, on Twitter to observe how marketing messages are sent and diffused through the retweet (i.e., message forwarding) functionality. Retweet networks enable messages to reach additional Twitter users beyond the sender’s local network. We follow messages from their origin through multiple retweets to identify which messages have more reach, and the different users who are exposed.

Methods

We collected three months of publicly available data from Twitter. A combination of techniques in social network analysis and content analysis were applied to determine the various networks of users who are exposed to e-cigarette messages and how the retweet network can affect which messages spread.

Results

The Blu retweet network expanded during the study period. Analysis of user profiles combined with network cluster analysis showed that messages of certain topics were only circulated within a community of e-cigarette supporters, while other topics spread further, reaching more general Twitter users who may not support or use e-cigarettes.

Conclusions

Retweet networks can serve as proxy filters for marketing messages, as Twitter users decide which messages they will continue to diffuse among their followers. As certain e-cigarette messages extend beyond their point of origin, the audience being exposed expands beyond the e-cigarette community. Potential implications for health education campaigns include utilizing Twitter and targeting important gatekeepers or hubs that would maximize message diffusion.     

中国五省市甲型肝炎病毒基因分型的研究

为了解甲型肝炎（甲肝）病毒（ＨＡＶ）在中国几个城市的基因型分布,选择浙江杭州、江苏启东、安徽铜陵、云南昆明和上海市等的甲肝病人粪便标本或血清标本,以逆转录－套式聚合酶链反应（ＲＴ－ｎＰＣＲ）扩增合成ＨＡＶ ＶＰ１／２Ａ交接区基因区,并进行直接核苷酸序列分析和差异比较。结果表明,从这些城市甲肝病人分离到的１７株ＨＡＶ株均属基因Ⅰ型,为ＩＡ和ＩＢ亚型;所有ＨＡＶ株间核苷酸差异均小于１５％,但约５０％Ｈ     

Surgeons' Exposure to Radiation in Single- and Multi-Level Minimally Invasive Transforaminal Lumbar Interbody Fusion; A Prospective Study

Although minimally invasive transforaminal lumbar interbody fusion (MIS-TLIF) has widely been developed in patients with lumbar diseases, surgeons risk exposure to fluoroscopic radiation. However, to date, there is no studies quantifying the effective dose during MIS-TLIF procedure, and the radiation dose distribution is still unclear. In this study, the surgeons'' radiation doses at 5 places on the bodies were measured and the effective doses were assessed during 31 consecutive 1- to 3-level MIS-TLIF surgeries. The operating surgeon, assisting surgeon, and radiological technologist wore thermoluminescent dosimeter on the unshielded thyroid, chest, genitals, right middle finger, and on the chest beneath a lead apron. The doses at the lens and the effective doses were also calculated. Mean fluoroscopy times were 38.7, 53.1, and 58.5 seconds for 1, 2, or 3 fusion levels, respectively. The operating surgeon''s mean exposures at the lens, thyroid, chest, genitals, finger, and the chest beneath the shield, respectively, were 0.07, 0.07, 0.09, 0.14, 0.32, and 0.05 mSv in 1-level MIS-TLIF; 0.07, 0.08, 0.09, 0.18, 0.34, and 0.05 mSv in 2-level; 0.08, 0.09, 0.14, 0.15, 0.36, and 0.06 mSv in 3-level; and 0.07, 0.08, 0.10, 0.15, 0.33, and 0.05 mSv in all cases. Mean dose at the operating surgeon''s right finger was significantly higher than other measurements parts (P<0.001). The operating surgeon''s effective doses (0.06, 0.06, and 0.07 mSv for 1, 2, and 3 fusion levels) were low, and didn''t differ significantly from those of the assisting surgeon or radiological technologist. Revision MIS-TLIF was not associated with higher surgeons'' radiation doses compared to primary MIS-TLIF. There were significantly higher surgeons'' radiation doses in over-weight than in normal-weight patients. The surgeons'' radiation exposure during MIS-TLIF was within the safe level by the International Commission on Radiological Protection''s guidelines. The accumulated radiation exposure, especially to surgeon''s hands, should be carefully monitored.     

Can Abundance of Protists Be Inferred from Sequence Data: A Case Study of Foraminifera

Protists are key players in microbial communities, yet our understanding of their role in ecosystem functioning is seriously impeded by difficulties in identification of protistan species and their quantification. Current microscopy-based methods used for determining the abundance of protists are tedious and often show a low taxonomic resolution. Recent development of next-generation sequencing technologies offered a very powerful tool for studying the richness of protistan communities. Still, the relationship between abundance of species and number of sequences remains subjected to various technical and biological biases. Here, we test the impact of some of these biological biases on sequence abundance of SSU rRNA gene in foraminifera. First, we quantified the rDNA copy number and rRNA expression level of three species of foraminifera by qPCR. Then, we prepared five mock communities with these species, two in equal proportions and three with one species ten times more abundant. The libraries of rDNA and cDNA of the mock communities were constructed, Sanger sequenced and the sequence abundance was calculated. The initial species proportions were compared to the raw sequence proportions as well as to the sequence abundance normalized by rDNA copy number and rRNA expression level per species. Our results showed that without normalization, all sequence data differed significantly from the initial proportions. After normalization, the congruence between the number of sequences and number of specimens was much better. We conclude that without normalization, species abundance determination based on sequence data was not possible because of the effect of biological biases. Nevertheless, by taking into account the variation of rDNA copy number and rRNA expression level we were able to infer species abundance, suggesting that our approach can be successful in controlled conditions.     

Citing a Data Repository: A Case Study of the Protein Data Bank

The Protein Data Bank (PDB) is the worldwide repository of 3D structures of proteins, nucleic acids and complex assemblies. The PDB’s large corpus of data (> 100,000 structures) and related citations provide a well-organized and extensive test set for developing and understanding data citation and access metrics. In this paper, we present a systematic investigation of how authors cite PDB as a data repository. We describe a novel metric based on information cascade constructed by exploring the citation network to measure influence between competing works and apply that to analyze different data citation practices to PDB. Based on this new metric, we found that the original publication of RCSB PDB in the year 2000 continues to attract most citations though many follow-up updates were published. None of these follow-up publications by members of the wwPDB organization can compete with the original publication in terms of citations and influence. Meanwhile, authors increasingly choose to use URLs of PDB in the text instead of citing PDB papers, leading to disruption of the growth of the literature citations. A comparison of data usage statistics and paper citations shows that PDB Web access is highly correlated with URL mentions in the text. The results reveal the trend of how authors cite a biomedical data repository and may provide useful insight of how to measure the impact of a data repository.