Revealing dynamic regulations and the related key proteins of myeloma-initiating cells by integrating experimental data into a systems biological model.

MOTIVATION: The growth and survival of myeloma cells are greatly affected by their surrounding microenvironment. To understand the molecular mechanism and the impact of stiffness on the fate of myeloma-initiating cells (MICs), we develop a systems biological model to reveal the dynamic regulations by integrating reverse-phase protein array data and the stiffness-associated pathway. RESULTS: We not only develop a stiffness-associated signaling pathway to describe the dynamic regulations of the MICs, but also clearly identify three critical proteins governing the MIC proliferation and death, including FAK, mTORC1 and NFκB, which are validated to be related with multiple myeloma by our immunohistochemistry experiment, computation and manually reviewed evidences. Moreover, we demonstrate that the systematic model performs better than widely used parameter estimation algorithms for the complicated signaling pathway. AVAILABILITY AND IMPLEMENTATION: We can not only use the systems biological model to infer the stiffness-associated genetic signaling pathway and locate the critical proteins, but also investigate the important pathways, proteins or genes for other type of the cancer. Thus, it holds universal scientific significance. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Public awareness, emotional reactions and human mobility in response to the COVID-19 outbreak in China - a population-based ecological study.

BACKGROUND: The outbreak of COVID-19 generated severe emotional reactions, and restricted mobility was a crucial measure to reduce the spread of the virus. This study describes the changes in public emotional reactions and mobility patterns in the Chinese population during the COVID-19 outbreak. METHODS: We collected data on public emotional reactions in response to the outbreak through Weibo, the Chinese Twitter, between 1st January and 31st March 2020. Using anonymized location-tracking information, we analyzed the daily mobility patterns of approximately 90% of Sichuan residents. RESULTS: There were three distinct phases of the emotional and behavioral reactions to the COVID-19 outbreak. The alarm phase (19th-26th January) was a restriction-free period, characterized by few new daily cases, but a large amount public negative emotions [the number of negative comments per Weibo post increased by 246.9 per day, 95% confidence interval (CI) 122.5-371.3], and a substantial increase in self-limiting mobility (from 45.6% to 54.5%, changing by 1.5% per day, 95% CI 0.7%-2.3%). The epidemic phase (27th January-15th February) exhibited rapidly increasing numbers of new daily cases, decreasing expression of negative emotions (a decrease of 27.3 negative comments per post per day, 95% CI -40.4 to -14.2), and a stabilized level of self-limiting mobility. The relief phase (16th February-31st March) had a steady decline in new daily cases and decreasing levels of negative emotion and self-limiting mobility. CONCLUSIONS: During the COVID-19 outbreak in China, the public's emotional reaction was strongest before the actual peak of the outbreak and declined thereafter. The change in human mobility patterns occurred before the implementation of restriction orders, suggesting a possible link between emotion and behavior.

Biomaterials and tissue engineering in traumatic brain injury: novel perspectives on promoting neural regeneration.

Traumatic brain injury is a serious medical condition that can be attributed to falls, motor vehicle accidents, sports injuries and acts of violence, causing a series of neural injuries and neuropsychiatric symptoms. However, limited accessibility to the injury sites, complicated histological and anatomical structure, intricate cellular and extracellular milieu, lack of regenerative capacity in the native cells, vast variety of damage routes, and the insufficient time available for treatment have restricted the widespread application of several therapeutic methods in cases of central nervous system injury. Tissue engineering and regenerative medicine have emerged as innovative approaches in the field of nerve regeneration. By combining biomaterials, stem cells, and growth factors, these approaches have provided a platform for developing effective treatments for neural injuries, which can offer the potential to restore neural function, improve patient outcomes, and reduce the need for drugs and invasive surgical procedures. Biomaterials have shown advantages in promoting neural development, inhibiting glial scar formation, and providing a suitable biomimetic neural microenvironment, which makes their application promising in the field of neural regeneration. For instance, bioactive scaffolds loaded with stem cells can provide a biocompatible and biodegradable milieu. Furthermore, stem cells-derived exosomes combine the advantages of stem cells, avoid the risk of immune rejection, cooperate with biomaterials to enhance their biological functions, and exert stable functions, thereby inducing angiogenesis and neural regeneration in patients with traumatic brain injury and promoting the recovery of brain function. Unfortunately, biomaterials have shown positive effects in the laboratory, but when similar materials are used in clinical studies of human central nervous system regeneration, their efficacy is unsatisfactory. Here, we review the characteristics and properties of various bioactive materials, followed by the introduction of applications based on biochemistry and cell molecules, and discuss the emerging role of biomaterials in promoting neural regeneration. Further, we summarize the adaptive biomaterials infused with exosomes produced from stem cells and stem cells themselves for the treatment of traumatic brain injury. Finally, we present the main limitations of biomaterials for the treatment of traumatic brain injury and offer insights into their future potential.

2019nCoVAS: Developing the Web Service for Epidemic Transmission Prediction, Genome Analysis, and Psychological Stress Assessment for 2019-nCoV.

Since the COVID-19 epidemic is still expanding around the world and poses a serious threat to human life and health, it is necessary for us to carry out epidemic transmission prediction, whole genome sequence analysis, and public psychological stress assessment for 2019-nCoV. However, transmission prediction models are insufficiently accurate and genome sequence characteristics are not clear, and it is difficult to dynamically assess the public psychological stress state under the 2019-nCoV epidemic. Therefore, this study develops a 2019nCoVAS web service (http://www.combio-lezhang.online/2019ncov/home.html) that not only offers online epidemic transmission prediction and lineage-associated underrepresented permutation (LAUP) analysis services to investigate the spreading trends and genome sequence characteristics, but also provides psychological stress assessments based on such an emotional dictionary that we built for 2019-nCoV. Finally, we discuss the shortcomings and further study of the 2019nCoVAS web service.

Pore structure characterization of Chang-7 tight sandstone using MICP combined with N2GA techniques and its geological control factors.

Understanding the pore networks of unconventional tight reservoirs such as tight sandstones and shales is crucial for extracting oil/gas from such reservoirs. Mercury injection capillary pressure (MICP) and N2 gas adsorption (N2GA) are performed to evaluate pore structure of Chang-7 tight sandstone. Thin section observation, scanning electron microscope, grain size analysis, mineral composition analysis, and porosity measurement are applied to investigate geological control factors of pore structure. Grain size is positively correlated with detrital mineral content and grain size standard deviation while negatively related to clay content. Detrital mineral content and grain size are positively correlated with porosity, pore throat radius and withdrawal efficiency and negatively related to capillary pressure and pore-to-throat size ratio; while interstitial material is negatively correlated with above mentioned factors. Well sorted sediments with high debris usually possess strong compaction resistance to preserve original pores. Although many inter-crystalline pores are produced in clay minerals, this type of pores is not the most important contributor to porosity. Besides this, pore shape determined by N2GA hysteresis loop is consistent with SEM observation on clay inter-crystalline pores while BJH pore volume is positively related with clay content, suggesting N2GA is suitable for describing clay inter-crystalline pores in tight sandstones.