Adopting Text Mining on Rehabilitation Therapy Repositioning for Stroke

Stroke is a common disabling disease that severely affects the daily life of patients. Accumulating evidence indicates that rehabilitation therapy can improve movement function. However, no clear guidelines have specific and effective rehabilitation therapy schemes, and the development of new rehabilitation techniques has been relatively slow. This study used a text mining approach, the ABC model, to identify an existing rehabilitation candidate therapy method that is most likely to be repositioned for stroke. In the model, we built the internal links of stroke (A), assessment scales (B), and rehabilitation therapies (C) in PubMed and the links were related to upper limb function measurements for patients with stroke. In the first step, using E-utility, we retrieved both stroke-related assessment scales and rehabilitation therapy records and then compiled two datasets, which were called Stroke_Scales and Stroke_Therapies, respectively. In the next step, we crawled all rehabilitation therapies co-occurring with the Stroke_Therapies and then named them as All_Therapies. Therapies that were already included in Stroke_Therapies were deleted from All_Therapies; therefore, the remaining therapies were the potential rehabilitation therapies, which could be repositioned for stroke after subsequent filtration by a manual check. We identified the top-ranked repositioning rehabilitation therapy and subsequently examined its clinical validation. Hand-arm bimanual intensive training (HABIT) was ranked the first in our repositioning rehabilitation therapies and had the most interaction links with Stroke_Scales. HABIT significantly improved clinical scores on assessment scales [Fugl-Meyer Assessment (FMA) and action research arm test (ARAT)] in the clinical validation study for acute stroke patients with upper limb dysfunction. Therefore, based on the ABC model and clinical validation, HABIT is a promising repositioned rehabilitation therapy for stroke, and the ABC model is an effective text mining approach for rehabilitation therapy repositioning. The findings in this study would be helpful in clinical knowledge discovery

H5N1 Influenza a Virus Replicates Productively in Pancreatic Cells and Induces Apoptosis and Pro-Inflammatory Cytokine Response

The inflammatory response and apoptosis have been proved to have a crucial role in the pathogenesis of the influenza A virus (IAV). Previous studies indicated that while IAV commonly causes pancreatitis and pancreatic damage in naturally and experimentally infected animals, the molecular mechanisms of the pathogenesis of IAV infection are less reported. In the present study, we showed for the first time that both avian-like (α-2,3-linked) and human-like (α-2,6-linked) sialic acid (SA) receptors were expressed by the mouse pancreatic cancer cell line PAN02 and the human pancreatic cancer cell line PANC-1. Using growth kinetics experiments, we also showed that PAN02 and PANC-1 cells supported the productive replication of the H5N1 highly pathogenic avian influenza while exhibited the limited replication of IAV subtypes H1N1 and H7N2 in vitro. The in vivo infection of H5N1 in pancreatic cells was confirmed by the histopathological and immunohistochemical staining of pancreas tissue from mice. Other than H1N1 and H7N2, severe damage and extensive positive signals were observed in pancreas of H5N1 infected mice. All three virus subtypes induced apoptosis but also triggered the infected PAN02 and PANC-1 cells to release pro-inflammatory cytokines and chemokines including interferon (IFN)-α, IFN-β, IFN-γ, chemokine (C-C motif) ligand 2 (CCL2), tumor necrosis factor (TNF)-α, and interleukin (IL)-6. Notably, the subtypes of H5N1 could significantly upregulate these cytokines and chemokines in both two cells when compared with H1N1 and H7N2. The present data provide further understanding of the pathogenesis of H5N1 IAV in pancreatic cells derived from humans and mammals and may also benefit the development of new treatment against H5N1 influenza virus infection

Spatiotemporal dynamic of subtropical forest carbon storage and its resistance and resilience to drought in China

Subtropical forests are rich in vegetation and have high photosynthetic capacity. China is an important area for the distribution of subtropical forests, evergreen broadleaf forests (EBFs) and evergreen needleleaf forests (ENFs) are two typical vegetation types in subtropical China. Forest carbon storage is an important indicator for measuring the basic characteristics of forest ecosystems and is of great significance for maintaining the global carbon balance. Drought can affect forest activity and may even lead to forest death and the stability characteristics of different forest ecosystems varied after drought events. Therefore, this study used meteorological data to simulate the standardized precipitation evapotranspiration index (SPEI) and the Biome-BGC model to simulate two types of forest carbon storage to quantify the resistance and resilience of EBF and ENF to drought in the subtropical region of China. The results show that: 1) from 1952 to 2019, the interannual drought in subtropical China showed an increasing trend, with five extreme droughts recorded, of which 2011 was the most severe one; 2) the simulated average carbon storage of the EBF and ENF during 1985-2019 were 130.58 t·hm-2 and 78.49 t·hm-2, respectively. The regions with higher carbon storage of EBF were mainly concentrated in central and southeastern subtropics, where those of ENF mainly distributed in the western subtropic; 3) The median of resistance of EBF was three times higher than that of ENF, indicating the EBF have stronger resistance to extreme drought than ENF. Moreover, the resilience of two typical forest to 2011 extreme drought and the continuous drought events during 2009 - 2011 were similar. The results provided a scientific basis for the response of subtropical forests to drought, and indicating that improve stand quality or expand the plantation of EBF may enhance the resistance to drought in subtropical China, which provided certain reference for forest protection and management under the increasing frequency of drought events in the future

Guinea Pig Model for Evaluating the Potential Public Health Risk of Swine and Avian Influenza Viruses

BACKGROUND: The influenza viruses circulating in animals sporadically transmit to humans and pose pandemic threats. Animal models to evaluate the potential public health risk potential of these viruses are needed. METHODOLOGY/PRINCIPAL FINDINGS: We investigated the guinea pig as a mammalian model for the study of the replication and transmission characteristics of selected swine H1N1, H1N2, H3N2 and avian H9N2 influenza viruses, compared to those of pandemic (H1N1) 2009 and seasonal human H1N1, H3N2 influenza viruses. The swine and avian influenza viruses investigated were restricted to the respiratory system of guinea pigs and shed at high titers in nasal tracts without prior adaptation, similar to human strains. None of the swine and avian influenza viruses showed transmissibility among guinea pigs; in contrast, pandemic (H1N1) 2009 virus transmitted from infected guinea pigs to all animals and seasonal human influenza viruses could also horizontally transmit in guinea pigs. The analysis of the receptor distribution in the guinea pig respiratory tissues by lectin histochemistry indicated that both SAα2,3-Gal and SAα2,6-Gal receptors widely presented in the nasal tract and the trachea, while SAα2,3-Gal receptor was the main receptor in the lung. CONCLUSIONS/SIGNIFICANCE: We propose that the guinea pig could serve as a useful mammalian model to evaluate the potential public health threat of swine and avian influenza viruses

Attenuation of Vaccinia Tian Tan Strain by Removal of Viral TC7L-TK2L and TA35R Genes

Vaccinia Tian Tan (VTT) was attenuated by deletion of the TC7L-TK2L and TA35R genes to generate MVTT3. The mutant was generated by replacing the open reading frames by a gene encoding enhanced green fluorescent protein (EGFP) flanked by loxP sites. Viruses expressing EGFP were then screened for and purified by serial plaque formation. In a second step the marker EGFP gene was removed by transfecting cells with a plasmid encoding cre recombinase and selecting for viruses that had lost the EGFP phenotype. The MVTT3 mutant was shown to be avirulent and immunogenic. These results support the conclusion that TC7L-TK2L and TA35R deletion mutants can be used as safe viral vectors or as platform for vaccines

Characterization of an Artificial Swine-Origin Influenza Virus with the Same Gene Combination as H1N1/2009 Virus: A Genesis Clue of Pandemic Strain

Pandemic H1N1/2009 influenza virus, derived from a reassortment of avian, human, and swine influenza viruses, possesses a unique gene segment combination that had not been detected previously in animal and human populations. Whether such a gene combination could result in the pathogenicity and transmission as H1N1/2009 virus remains unclear. In the present study, we used reverse genetics to construct a reassortant virus (rH1N1) with the same gene combination as H1N1/2009 virus (NA and M genes from a Eurasian avian-like H1N1 swine virus and another six genes from a North American triple-reassortant H1N2 swine virus). Characterization of rH1N1 in mice showed that this virus had higher replicability and pathogenicity than those of the seasonal human H1N1 and Eurasian avian-like swine H1N1 viruses, but was similar to the H1N1/2009 and triple-reassortant H1N2 viruses. Experiments performed on guinea pigs showed that rH1N1 was not transmissible, whereas pandemic H1N1/2009 displayed efficient transmissibility. To further determine which gene segment played a key role in transmissibility, we constructed a series of reassortants derived from rH1N1 and H1N1/2009 viruses. Direct contact transmission studies demonstrated that the HA and NS genes contributed to the transmission of H1N1/2009 virus. Second, the HA gene of H1N1/2009 virus, when combined with the H1N1/2009 NA gene, conferred efficient contact transmission among guinea pigs. The present results reveal that not only gene segment reassortment but also amino acid mutation were needed for the generation of the pandemic influenza virus

Characterization of the sesame (Sesamum indicum L.) global transcriptome using Illumina paired-end sequencing and development of EST-SSR markers

<p>Abstract</p> <p>Background</p> <p>Sesame is an important oil crop, but limited transcriptomic and genomic data are currently available. This information is essential to clarify the fatty acid and lignan biosynthesis molecular mechanism. In addition, a shortage of sesame molecular markers limits the efficiency and accuracy of genetic breeding. High-throughput transcriptomic sequencing is essential to generate a large transcriptome sequence dataset for gene discovery and molecular marker development.</p> <p>Results</p> <p>Sesame transcriptomes from five tissues were sequenced using Illumina paired-end sequencing technology. The cleaned raw reads were assembled into a total of 86,222 unigenes with an average length of 629 bp. Of the unigenes, 46,584 (54.03%) had significant similarity with proteins in the NCBI nonredundant protein database and Swiss-Prot database (E-value < 10^-5). Of these annotated unigenes, 10,805 and 27,588 unigenes were assigned to gene ontology categories and clusters of orthologous groups, respectively. In total, 22,003 (25.52%) unigenes were mapped onto 119 pathways using the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG). Furthermore, 44,750 unigenes showed homology to 15,460 <it>Arabidopsis </it>genes based on BLASTx analysis against The Arabidopsis Information Resource (TAIR, Version 10) and revealed relatively high gene coverage. In total, 7,702 unigenes were converted into SSR markers (EST-SSR). Dinucleotide SSRs were the dominant repeat motif (67.07%, 5,166), followed by trinucleotide (24.89%, 1,917), tetranucleotide (4.31%, 332), hexanucleotide (2.62%, 202), and pentanucleotide (1.10%, 85) SSRs. AG/CT (46.29%) was the dominant repeat motif, followed by AC/GT (16.07%), AT/AT (10.53%), AAG/CTT (6.23%), and AGG/CCT (3.39%). Fifty EST-SSRs were randomly selected to validate amplification and to determine the degree of polymorphism in the genomic DNA pools. Forty primer pairs successfully amplified DNA fragments and detected significant amounts of polymorphism among 24 sesame accessions.</p> <p>Conclusions</p> <p>This study demonstrates that Illumina paired-end sequencing is a fast and cost-effective approach to gene discovery and molecular marker development in non-model organisms. Our results provide a comprehensive sequence resource for sesame research.</p

BrAPI-an application programming interface for plant breeding applications

Motivation: Modern genomic breeding methods rely heavily on very large amounts of phenotyping and genotyping data, presenting new challenges in effective data management and integration. Recently, the size and complexity of datasets have increased significantly, with the result that data are often stored on multiple systems. As analyses of interest increasingly require aggregation of datasets from diverse sources, data exchange between disparate systems becomes a challenge. Results: To facilitate interoperability among breeding applications, we present the public plant Breeding Application Programming Interface (BrAPI). BrAPI is a standardized web service API specification. The development of BrAPI is a collaborative, community-based initiative involving a growing global community of over a hundred participants representing several dozen institutions and companies. Development of such a standard is recognized as critical to a number of important large breeding system initiatives as a foundational technology. The focus of the first version of the API is on providing services for connecting systems and retrieving basic breeding data including germplasm, study, observation, and marker data. A number of BrAPI-enabled applications, termed BrAPPs, have been written, that take advantage of the emerging support of BrAPI by many databases

Electromagnetic forming of AA1060 sheet based on mixed forces generated by a three-coil dual-power system

Abstract The electromagnetic force used in electromagnetic forming is mainly divided into attraction and repulsion. Dual-coil attractive electromagnetic forming can be used in the field of sheet pit repair. However, the magnetic field and eddy current generated by the two coils compete with each other, and the energy utilization rate is low. Therefore, a compensation coil is introduced, and an electromagnetic forming scheme of a three-coil dual-power sheet based on mixed force is proposed and verified by simulation. It is found that the three-coil mixed force can effectively improve the competition between the magnetic field and eddy current. The loading of the mixing force is not a simple superposition of attraction and repulsion, but the mutual promotion of the two. The forming displacement of the three-coil mixed force forming scheme is 582% higher than that of the dual-coil attraction forming scheme, and 89% higher than that of the attract first and then repel forming scheme. The forming effect of the three-coil mixing force is related to the number of turns of the compensation coil. The research results can improve the energy utilization rate of electromagnetic forming and provide a new idea for the loading scheme of electromagnetic forming force field

The Potential Environmental Impact of PAHs on Soil and Water Resources in Air Deposited Coal Refuse Sites in Niangziguan Karst Catchment, Northern China

Long-term deposition of coal spoil piles may lead to serious pollution of soil and water resources in the dumping sites and surrounding areas. Karst aquifers are highly sensitive to environmental pollution. In this study, the occurrence and release/mobilization of polycyclic aromatic hydrocarbons (PAHs) in coal waste and coal spoils fire gas mineral (CSFGM) were evaluated by field and indoor investigations at Yangquan city, one of the major coal mining districts in the karst areas of northern China. Field investigations showed that dumping of coal waste over decades has resulted in soil and water pollution via spontaneous combustion and leaching of coal spoil piles. Indoor analysis revealed that the 2-ring and 3-ring PAHs contribute to 65&#8211;80% of the total PAHs in coal spoils, with naphthalene (Nap), Chrysene (Chr), and Phenanthrene (Phe) as the dominant compounds. Based on a heating/burning simulation experiment, the production of PAHs is temperature-dependent and mainly consists of low-ring PAHs: 2-ring, 3-ring, and part of the 4-ring PAHs. The PAHs in the leachate are light-PAHs (Nap, 20.06 ng/L; Phe, 4.76 ng/L) with few heavy-PAHs. The distribution modes of PAHs in two soil profiles suggest that the precipitation caused downward movement of PAHs and higher mobility of light-PAHs