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1.  The validation of the standard Chinese version of the European Organization for Research and Treatment of Cancer Quality of Life Core Questionnaire 30 (EORTC QLQ-C30) in pre-operative patients with brain tumor in China 
Background
Health related quality of life (HRQOL) has increasingly emphasized on cancer patients. The psychometric properties of the standard Chinese version of the European Organization for Research and Treatment of Cancer Quality of Life Core Questionnaire 30 (EORTC QLQ-C30, version 3.0) in brain tumor patients wasn't proven, and there was no baseline HRQOL in brain tumor patients prior to surgery.
Methods
The questionnaire EORTC QLQ-C30 (version 3.0) was administered at three time points: T1, the first or the second day that patients were hospitalized after the brain tumor suspected or diagnosed by MRI or CT; T2, 1 to 2 days after T1, (T1 and T2 were both before surgery); T3, the day before discharge. Clinical variables included disease histologic types, cognitive function, and Karnofsky Performance Status.
Results
Cronbach's alpha coefficients for multi-item scales were greater than .70 and multitrait scaling analysis showed that most of the item-scale correlation coefficients met the standards of convergent and discriminant validity, except for the cognitive functioning scale. All scales and items exhibited construct validity. Score changes over peri-operation were observed in physical and role functioning scales. Compared with mixed cancer patients assessed after surgery but before adjuvant treatment, brain tumor patients assessed pre-surgery presented better function and fewer symptoms.
Conclusions
The standard Chinese version of the EORTC QLQ-C30 was overall a valid instrument to assess HRQOL in brain tumor patients in China. The baseline HRQOL in brain tumor patients pre-surgery was better than that in mixed cancer patients post-surgery. Future study should modify cognitive functioning scale and examine test-retest reliability and response validity.
doi:10.1186/1471-2288-11-56
PMCID: PMC3112193  PMID: 21513533
2.  An abundance of rare functional variants in 202 drug target genes sequenced in 14,002 people 
Science (New York, N.Y.)  2012;337(6090):100-104.
Rare genetic variants contribute to complex disease risk; however, the abundance of rare variants in human populations remains unknown. We explored this spectrum of variation by sequencing 202 genes encoding drug targets in 14,002 individuals. We find rare variants are abundant (one every 17 bases) and geographically localized, such that even with large sample sizes, rare variant catalogs will be largely incomplete. We used the observed patterns of variation to estimate population growth parameters, the proportion of variants in a given frequency class that are putatively deleterious, and mutation rates for each gene. Overall we conclude that, due to rapid population growth and weak purifying selection, human populations harbor an abundance of rare variants, many of which are deleterious and have relevance to understanding disease risk.
doi:10.1126/science.1217876
PMCID: PMC4319976  PMID: 22604722
3.  Core – shell upconversion nanoparticle – semiconductor heterostructures for photodynamic therapy 
Scientific Reports  2015;5:8252.
Core-shell nanoparticles (CSNPs) with diverse chemical compositions have been attracting greater attention in recent years. However, it has been a challenge to develop CSNPs with different crystal structures due to the lattice mismatch of the nanocrystals. Here we report a rational design of core-shell heterostructure consisting of NaYF4:Yb,Tm upconversion nanoparticle (UCN) as the core and ZnO semiconductor as the shell for potential application in photodynamic therapy (PDT). The core-shell architecture (confirmed by TEM and STEM) enables for improving the loading efficiency of photosensitizer (ZnO) as the semiconductor is directly coated on the UCN core. Importantly, UCN acts as a transducer to sensitize ZnO and trigger the generation of cytotoxic reactive oxygen species (ROS) to induce cancer cell death. We also present a firefly luciferase (FLuc) reporter gene based molecular biosensor (ARE-FLuc) to measure the antioxidant signaling response activated in cells during the release of ROS in response to the exposure of CSNPs under 980 nm NIR light. The breast cancer cells (MDA-MB-231 and 4T1) exposed to CSNPs showed significant release of ROS as measured by aminophenyl fluorescein (APF) and ARE-FLuc luciferase assays, and ~45% cancer cell death as measured by MTT assay, when illuminated with 980 nm NIR light.
doi:10.1038/srep08252
PMCID: PMC4317689  PMID: 25652742
4.  Anti-CD40-induced inflammatory E-cadherin+ dendritic cells enhance T cell responses and antitumour immunity in murine Lewis lung carcinoma 
Background
Agonistic CD40 antibodies have been demonstrated to activate antigen-presenting cells (APCs) and enhance antitumour T cell responses, thereby providing a new therapeutic option in cancer immunotherapy. In agonistic CD40 antibody-mediated inflammatory responses, a novel subset of E-cadherin + dendritic cells (DCs) has been identified, and little is known about the role of these DCs in tumour immunity. This study investigated the effect of anti-CD40-mediated inflammatory E-cadherin + DCs in murine Lewis lung carcinoma (LLC).
Methods
The phenotype and characteristics of anti-CD40-mediated inflammatory E-cadherin + DCs isolated from the anti-CD40 model were assessed in vitro. The antitumour activity of E-cadherin + DCs were evaluated in vivo by promoting the differentiation of effector CD4+ T cells, CEA-specific CD8+ T cells and CD103+ CD8+ T cells and assessing their resistance to tumour challenge, including variations in tumour volume and survival curves.
Results
Here, we demonstrated that anti-CD40-mediated E-cadherin + inflammatory DCs accumulate in the lungs of Rag1 KO mice and were able to stimulate naïve CD4+ T cells to induce Th1 and Th17 cell differentiation and polarisation and to inhibit regulatory T cell and Th2 responses. Importantly, with the adoptive transfer of E-cadherin + DCs into the Lewis lung cancer model, the inflammatory DCs increased the Th1 and Th17 cell responses and reduced the Treg cell and Th2 responses. Interestingly, following the injection of inflammatory E-cadherin + DCs, the CD103+ CD8+ T cell and CEA-specific CD8+ T cell responses increased and exhibited potent antitumour immunity.
Conclusions
These findings indicate that anti-CD40-induced E-cadherin + DCs enhance T cell responses and antitumour activity in non-small cell lung cancer (NSCLC)-bearing mice and may be used to enhance the efficacy of DC-based peptide vaccines against NSCLC.
Electronic supplementary material
The online version of this article (doi:10.1186/s13046-015-0126-9) contains supplementary material, which is available to authorized users.
doi:10.1186/s13046-015-0126-9
PMCID: PMC4323023  PMID: 25651850
E-cadherin; Dendritic cell; T cell; Lung cancer; Activity
5.  Environmental Surveillance of Human Enteroviruses in Shandong Province, China, 2008 to 2012: Serotypes, Temporal Fluctuation, and Molecular Epidemiology 
Applied and Environmental Microbiology  2014;80(15):4683-4691.
Environmental surveillance is an effective approach in investigating the circulation of polioviruses (PVs) and other human enteroviruses (EVs) in the population. The present report describes the results of environmental surveillance conducted in Shandong Province, China, from 2008 to 2012. A total of 129 sewage samples were collected, and 168 PVs and 1,007 nonpolio enteroviruses (NPEVs) were isolated. VP1 sequencing and typing were performed on all isolates. All PV strains were Sabin-like, with the numbers of VP1 substitutions ranging from 0 to 7. The NPEVs belonged to 19 serotypes, and echovirus 6 (E6), E11, coxsackievirus B3 (CVB3), E3, E12, and E7 were the six main serotypes, which accounted for 18.3%, 14.8%, 14.5%, 12.9%, 9.0%, and 5.7% of NPEVs isolated, respectively. Typical summer-fall peaks of NPEV were observed in the monthly distribution of isolation, and an epidemic pattern of annual circulation was revealed for the common serotypes. Phylogenetic analysis was performed on environmental CVB3 and E3 strains with global reference strains and local strains from aseptic meningitis patients. Shandong strains formed distinct clusters, and a close relationship was observed between local environmental and clinical strains. As an EV-specific case surveillance system is absent in China and many other countries, continuous environmental surveillance should be encouraged to investigate the temporal circulation and phylogeny of EVs in the population.
doi:10.1128/AEM.00851-14
PMCID: PMC4148804  PMID: 24837389
6.  Chemosensillum immunolocalization and ligand specificity of chemosensory proteins in the alfalfa plant bug Adelphocoris lineolatus (Goeze) 
Scientific Reports  2015;5:8073.
Insect chemosensory proteins (CSPs) are a family of small soluble proteins. To date, their physiological functions in insect olfaction remain largely controversial in comparison to odorant binding proteins (OBPs). In present study, we reported the antenna specific expression of three CSPs (AlinCSP4-6) from Adelphocoris lineolatus, their distinct chemosensillum distribution as well as ligand binding capability thus providing the evidence for the possible roles that they could play in semiochemical detection of the plant bug A. lineolatus. The results of qRT-PCR and western blot assay clearly showed that all of these three CSPs are highly expressed in the adult antennae, the olfactory organ of insects. Further cellular investigation of their immunolocalization revealed their dynamic protein expression profiles among different types of antennal sensilla. In a fluorescence competitive binding assay, the selective ligand binding was observed for AlinCSP4-6. In ad`dition, a cooperative interaction was observed between two co-expressed CSPs resulting in an increase of the binding affinities by a mixture of AlinCSP5 and AlinCSP6 to terpenoids which do not bind to individual CSPs. These findings in combination with our previous data for AlinCSP1-3 indicate a possible functional differentiation of CSPs in the A. lineolatus olfactory system.
doi:10.1038/srep08073
PMCID: PMC4308698  PMID: 25627422
7.  Application of a Novel Population of Multipotent Stem Cells Derived from Skin Fibroblasts as Donor Cells in Bovine SCNT 
PLoS ONE  2015;10(1):e0114423.
Undifferentiated stem cells are better donor cells for somatic cell nuclear transfer (SCNT), resulting in more offspring than more differentiated cells. While various stem cell populations have been confirmed to exist in the skin, progress has been restricted due to the lack of a suitable marker for their prospective isolation. To address this fundamental issue, a marker is required that could unambiguously prove the differentiation state of the donor cells. We therefore utilized magnetic activated cell sorting (MACS) to separate a homogeneous population of small SSEA-4+ cells from a heterogeneous population of bovine embryonic skin fibroblasts (BEF). SSEA-4+ cells were 8-10 μm in diameter and positive for alkaline phosphatase (AP). The percentage of SSEA-4+ cells within the cultured BEF population was low (2-3%). Immunocytochemistry and PCR analyses revealed that SSEA-4+ cells expressed pluripotency-related markers, and could differentiate into cells comprising all three germ layers in vitro. They remained undifferentiated over 20 passages in suspension culture. In addition, cloned embryos derived from SSEA-4 cells showed significant differences in cleavage rate and blastocyst development when compared with those from BEF and SSEA-4− cells. Moreover, blastocysts derived from SSEA-4+ cells showed a higher total cell number and lower apoptotic index as compared to BEF and SSEA-4– derived cells. It is well known that nuclei from pluripotent stem cells yield a higher cloning efficiency than those from adult somatic cells, however, pluripotent stem cells are relatively difficult to obtain from bovine. The SSEA-4+ cells described in the current study provide an attractive candidate for SCNT and a promising platform for the generation of transgenic cattle.
doi:10.1371/journal.pone.0114423
PMCID: PMC4300223  PMID: 25602959
8.  Cross-border collaboration between China and Myanmar for emergency response to imported vaccine derived poliovirus case 
Background
This report describes emergency response following an imported vaccine derived poliovirus (VDPV) case from Myanmar to Yunnan Province, China and the cross-border collaboration between China and Myanmar. Immediately after confirmation of the VDPV case, China disseminated related information to Myanmar with the assistance of the World Health Organization.
Methods
A series of epidemiological investigations were conducted, both in China and Myanmar, including retrospective searches of acute flaccid paralysis (AFP) cases, oral poliovirus vaccine (OPV) coverage assessment, and investigation of contacts and healthy children.
Results
All children <2 years of age had not been vaccinated in the village where the VDPV case had lived in the past 2 years. Moreover, most areas were not covered for routine immunization in this township due to vaccine shortages and lack of operational funds for the past 2 years.
Conclusions
Cross-border collaboration may have prevented a potential outbreak of VDPV in Myanmar. It is necessary to reinforce cross-border collaboration with neighboring countries in order to maximize the leverage of limited resources.
doi:10.1186/s12879-015-0745-y
PMCID: PMC4308939  PMID: 25595618
Vaccine derived poliovirus; Importation; Cross-border collaboration; China; Myanmar
9.  MRA Study on Variation of the Circle of Willis in Healthy Chinese Male Adults 
BioMed Research International  2015;2015:976340.
Aim. To investigate the morphology and variation of the circle of Willis (COW) in healthy Chinese male adults. Materials and Methods. We analyzed cerebral magnetic resonance angiography (MRA) images of 2,246 healthy subjects using typical magnetic resonance imaging (MRI) and MRA. 3D-time of flight (TOF) MRA method was applied to all subjects and the classification was therefore achieved according to the integrity level of COW and the developmental situation of vessels. Results. The overall incidence of COW integrity was 12.24%, with 7.57% nonvariation integral COW. The incidences of partial integrity and nonintegrity were 70.17% and 17.59%, respectively. The integrity rate of anterior circulation was 78.58%, with a close correlation with A1 segment of the anterior cerebral artery (ACA-A1) developmental condition. The developmental variation rate of ACA-A1 was 28.23% and the variation of the right side was higher than that of the left side. The nonintegrity rate of posterior circulation was 83.93% as the hypoplasia of P1 segment of the posterior cerebral artery (PCA-P1) with an incidence rate of 15.85% for PCA-P1 variation. Conclusions. The COW variation is a common phenomenon among the healthy subjects. MRA could enable reflecting the physiological morphology of COW in a comprehensive manner.
doi:10.1155/2015/976340
PMCID: PMC4299360  PMID: 25629057
10.  An Antibody with a Variable Region Coiled-Coil “Knob” Domain 
doi:10.1002/anie.201307939
PMCID: PMC3926434  PMID: 24254636
Antibodies; Protein engineering; Ultralong CDR; Polypeptide; Coiled coil
11.  Limited and Localized Outbreak of Newly Emergent Type 2 Vaccine-Derived Poliovirus in Sichuan, China 
From August 2011 to February 2012, an outbreak caused by type 2 circulating vaccine-derived poliovirus (cVDPV) occurred in Aba County, Sichuan, China. During the outbreak, four type 2 VDPVs (≥0.6% nucleotide divergence in the VP1 region relative to the Sabin 2 strain) were isolated from 3 patients with acute flaccid paralysis (AFP) and one close contact. In addition, a type 2 pre-VDPV (0.3% to 0.5% divergence from Sabin 2) that was genetically related to these type 2 VDPVs was isolated from another AFP patient. These 4 patients were all unimmunized children 0.7 to 1.1 years old. Nucleotide sequencing revealed that the 4 VDPV isolates differed from Sabin 2 by 0.7% to 1.2% in nucleotides in the VP1 region and shared 5 nucleotide substitutions with the pre-VDPV. All 5 isolates were closely related, and all were S2/S3/S2/S3 recombinants sharing common recombination crossover sites. Although the two major determinants of attenuation and temperature sensitivity phenotype of Sabin 2 (A481 in the 5′ untranslated region and Ile143 in the VP1 protein) had reverted in all 5 isolates, one VDPV (strain CHN16017) still retained the temperature sensitivity phenotype. Phylogenetic analysis of the third coding position of the complete P1 coding region suggested that the cVDPVs circulated locally for about 7 months following the initiating oral poliovirus vaccine (OPV) dose. Our findings reinforce the point that cVDPVs can emerge and spread in isolated communities with immunity gaps and highlight the emergence risks of type 2 cVDPVs accompanying the trivalent OPV used. To solve this issue, it is recommended that type 2 OPV be removed from the trivalent OPV or that inactivated polio vaccine (IPV) be used instead.
doi:10.1128/CVI.00196-14
PMCID: PMC4097442  PMID: 24850620
12.  High-Throughput Screening Normalized To Biological Response: Application To Antiviral Drug Discovery 
Journal of biomolecular screening  2013;19(1):10.1177/1087057113496848.
The process of conducting cell-based phenotypic screens can result in datasets from small libraries or portions of large libraries, making accurate hit picking from multiple datasets important for efficient drug discovery. Here, we describe a screen design and data analysis approach that allows for normalization not only between quadrants and plates but also between screens or batches in a robust, quantitative fashion enabling hit-selection from multiple datasets. We independently screened the Microsource Spectrum and NCI Diversity Set II libraries using a cell-based phenotypic HTS assay that uses interferon stimulated response element (ISRE)-driven luciferase-reporter assay to identify interferon (IFN) signal enhancers. Inclusion of a per-plate, per-quadrant IFN dose-response standard curve enabled conversion of ISRE activity to effective IFN concentrations. We identified 45 hits based on a combined z-score ≥ 2.5 from the two libraries, and 25 of 35 available hits were validated in a compound concentration-response assay when tested using fresh compound. The results provide a basis for further analysis of chemical structure in relation to biological function. Together, the results establish an HTS method that can be extended to screening for any class of compounds that influence a quantifiable biological response for which a standard is available.
doi:10.1177/1087057113496848
PMCID: PMC3867592  PMID: 23860224
Phenotypic drug discovery; cell-based assay; Quantitative HTS; Interferon signal enhancer; Statin
13.  Modeling Flight Attendants’ Exposures to Pesticide in Disinsected Aircraft Cabins 
Environmental science & technology  2013;47(24):14275-14281.
Aircraft cabin disinsection is required by some countries to kill insects that may pose risks to public health and native ecological systems. A probabilistic model has been developed by considering the microenvironmental dynamics of the pesticide in conjunction with the activity patterns of flight attendants, to assess their exposures and risks to pesticide in disinsected aircraft cabins under three scenarios of pesticide application. Main processes considered in the model are microenvironmental transport and deposition, volatilization, and transfer of pesticide when passengers and flight attendants come in contact with the cabin surfaces. The simulated pesticide airborne mass concentration and surface mass loadings captured measured ranges reported in the literature. The medians (means±standard devitions) of daily total exposures intakes were 0.24 (3.8±10.0), 1.4 (4.2±5.7) and 0.15 (2.1±3.2) μg/(day kg BW) for scenarios of Residual Application, Preflight and Top-of-Descent spraying, respectively. Exposure estimates were sensitive to parameters corresponding to pesticide deposition, body surface area and weight, surface-to-body transfer efficiencies, and efficiency of adherence to skin. Preflight spray posed 2.0 and 3.1 times higher pesticide exposure risk levels for flight attendants in disinsected aircraft cabins than Top-of-Descent spray and Residual Application, respectively.
doi:10.1021/es403613h
PMCID: PMC3920731  PMID: 24251734
14.  BSeQC: quality control of bisulfite sequencing experiments 
Bioinformatics  2013;29(24):3227-3229.
Motivation: Bisulfite sequencing (BS-seq) has emerged as the gold standard to study genome-wide DNA methylation at single-nucleotide resolution. Quality control (QC) is a critical step in the analysis pipeline to ensure that BS-seq data are of high quality and suitable for subsequent analysis. Although several QC tools are available for next-generation sequencing data, most of them were not designed to handle QC issues specific to BS-seq protocols. Therefore, there is a strong need for a dedicated QC tool to evaluate and remove potential technical biases in BS-seq experiments.
Results: We developed a package named BSeQC to comprehensively evaluate the quality of BS-seq experiments and automatically trim nucleotides with potential technical biases that may result in inaccurate methylation estimation. BSeQC takes standard SAM/BAM files as input and generates bias-free SAM/BAM files for downstream analysis. Evaluation based on real BS-seq data indicates that the use of the bias-free SAM/BAM file substantially improves the quantification of methylation level.
Availability and implementation: BSeQC is freely available at: http://code.google.com/p/bseqc/.
Contact: wl1@bcm.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
doi:10.1093/bioinformatics/btt548
PMCID: PMC3842756  PMID: 24064417
15.  Intracerebroventricular Transplantation of Ex Vivo Expanded Endothelial Colony-Forming Cells Restores Blood–Brain Barrier Integrity and Promotes Angiogenesis of Mice with Traumatic Brain Injury 
Journal of Neurotrauma  2013;30(24):2080-2088.
Abstract
Endothelial progenitor cells (EPCs) play a key role in tissue repair and regeneration. Previous studies have shown a positive correlation between the number of circulating EPCs and clinical outcomes of patients with traumatic brain injury (TBI). A recent study has further shown that intravenous infusion of human umbilical cord blood-derived endothelial colony-forming cells (ECFCs) improves outcomes of mice subjected to experimental TBI. This follow-up study was designed to determine whether intracerebroventricular (i.c.v.) infusion of ECFCs, which may reduce systemic effects of these cells, could repair the blood–brain barrier (BBB) and promote angiogenesis of mice with TBI. Adult nude mice were exposed to fluid percussion injury and transplanted i.c.v. with ECFCs on day 1 post-TBI. These ECFCs were detected at the TBI zone 3 days after transplantation by SP-DiIC18(3) and fluorescence in situ hybridization. Mice with ECFCs transplant had reduced Evans blue extravasation and brain water content, increased expression of ZO-1 and claudin-5, and showed a higher expression of angiopoietin 1. Consistent with the previous report, mice with ECFCs transplant had also increased microvascular density. Modified neurological severity score and Morris water maze test indicated significant improvements in motor ability, spatial acquisition and reference memory in mice receiving ECFCs, compared to those receiving saline. These data demonstrate the beneficial effects of ECFC transplant on BBB integrity and angiogenesis in mice with TBI.
doi:10.1089/neu.2013.2996
PMCID: PMC3868401  PMID: 23957220
endothelial colony-forming cells, endothelial progenitor cells; transplantation; traumatic brain injury
16.  Two Antarctic penguin genomes reveal insights into their evolutionary history and molecular changes related to the Antarctic environment 
GigaScience  2014;3(1):27.
Background
Penguins are flightless aquatic birds widely distributed in the Southern Hemisphere. The distinctive morphological and physiological features of penguins allow them to live an aquatic life, and some of them have successfully adapted to the hostile environments in Antarctica. To study the phylogenetic and population history of penguins and the molecular basis of their adaptations to Antarctica, we sequenced the genomes of the two Antarctic dwelling penguin species, the Adélie penguin [Pygoscelis adeliae] and emperor penguin [Aptenodytes forsteri].
Results
Phylogenetic dating suggests that early penguins arose ~60 million years ago, coinciding with a period of global warming. Analysis of effective population sizes reveals that the two penguin species experienced population expansions from ~1 million years ago to ~100 thousand years ago, but responded differently to the climatic cooling of the last glacial period. Comparative genomic analyses with other available avian genomes identified molecular changes in genes related to epidermal structure, phototransduction, lipid metabolism, and forelimb morphology.
Conclusions
Our sequencing and initial analyses of the first two penguin genomes provide insights into the timing of penguin origin, fluctuations in effective population sizes of the two penguin species over the past 10 million years, and the potential associations between these biological patterns and global climate change. The molecular changes compared with other avian genomes reflect both shared and diverse adaptations of the two penguin species to the Antarctic environment.
Electronic supplementary material
The online version of this article (doi:10.1186/2047-217X-3-27) contains supplementary material, which is available to authorized users.
doi:10.1186/2047-217X-3-27
PMCID: PMC4322438  PMID: 25671092
Penguins; Avian genomics; Evolution; Adaptation; Antarctica
17.  Complex Structure and Biochemical Characterization of the Staphylococcus aureus Cyclic Diadenylate Monophosphate (c-di-AMP)-binding Protein PstA, the Founding Member of a New Signal Transduction Protein Family* 
The Journal of Biological Chemistry  2014;290(5):2888-2901.
Background: PstA is a cyclic di-AMP receptor and PII-like signal transduction protein.
Results: Apo-PstA and complex crystal structures reveal a novel cyclic di-AMP-binding mode and induced conformational changes.
Conclusion: PstA has a similar fold but distinct signal transduction properties from classic PII proteins, which function in nitrogen metabolism.
Significance: Identification of common features allows for rational prediction of cyclic di-AMP-binding sites.
Signaling nucleotides are integral parts of signal transduction systems allowing bacteria to cope with and rapidly respond to changes in the environment. The Staphylococcus aureus PII-like signal transduction protein PstA was recently identified as a cyclic diadenylate monophosphate (c-di-AMP)-binding protein. Here, we present the crystal structures of the apo- and c-di-AMP-bound PstA protein, which is trimeric in solution as well as in the crystals. The structures combined with detailed bioinformatics analysis revealed that the protein belongs to a new family of proteins with a similar core fold but with distinct features to classical PII proteins, which usually function in nitrogen metabolism pathways in bacteria. The complex structure revealed three identical c-di-AMP-binding sites per trimer with each binding site at a monomer-monomer interface. Although distinctly different from other cyclic-di-nucleotide-binding sites, as the half-binding sites are not symmetrical, the complex structure also highlighted common features for c-di-AMP-binding sites. A comparison between the apo and complex structures revealed a series of conformational changes that result in the ordering of two anti-parallel β-strands that protrude from each monomer and allowed us to propose a mechanism on how the PstA protein functions as a signaling transduction protein.
doi:10.1074/jbc.M114.621789
PMCID: PMC4316997  PMID: 25505271
Bacterial Signal Transduction; Bioinformatics; Crystal Structure; Nucleotide; Staphylococcus aureus (S. aureus); Complex
18.  Fitting magnetic field gradient with Heisenberg-scaling accuracy 
Scientific Reports  2014;4:7390.
The linear function is possibly the simplest and the most used relation appearing in various areas of our world. A linear relation can be generally determined by the least square linear fitting (LSLF) method using several measured quantities depending on variables. This happens for such as detecting the gradient of a magnetic field. Here, we propose a quantum fitting scheme to estimate the magnetic field gradient with N-atom spins preparing in W state. Our scheme combines the quantum multi-parameter estimation and the least square linear fitting method to achieve the quantum Cramér-Rao bound (QCRB). We show that the estimated quantity achieves the Heisenberg-scaling accuracy. Our scheme of quantum metrology combined with data fitting provides a new method in fast high precision measurements.
doi:10.1038/srep07390
PMCID: PMC4260217  PMID: 25487218
19.  The treatment and research for posttraumatic stress disorder with Chinese medicine 
European Journal of Psychotraumatology  2014;5:10.3402/ejpt.v5.26524.
There is no disease called posttraumatic stress disorder (PTSD) in traditional Chinese medicine (TCM). However, Huangdi's Canon of Medicine written in about 200 BC, one of the most famous TCM classics, recorded diseases with similar etiology, pathogenesis, and clinical symptoms. Moreover, contemporary TCM also attaches great importance to diseases caused by trauma. Especially after 2008, there is a mini-rush of study on PTSD as a result of Sichuan earthquake. Referring to ancient and modern literature, we summarize the TCM treatment of PTSD and wish to contribute to the further study on TCM remedy for PTSD.
doi:10.3402/ejpt.v5.26524
PMCID: PMC4265179  PMID: 25511728
TCM; PTSD; trauma; depression; research
20.  Appropriate treatment strategies improve survival of hepatocellular carcinoma patients with portal vein tumor thrombus 
World Journal of Gastroenterology : WJG  2014;20(45):17141-17147.
AIM: To evaluate the survival benefits of different treatment strategies for hepatocellular carcinoma (HCC) patients with portal vein tumor thrombus (PVTT) and to determine the prognosis factors.
METHODS: Between 2007 and 2009, 338 HCC patients treated for PVTT were retrospectively studied. The patients were divided into 4 groups that underwent different treatments: the conservative treatment group (n = 75), the transarterial chemoembolization (TACE) group (n = 86), the hepatic resection group (n = 90), and the hepatic resection associated with postoperative TACE group (n = 87). Survival rates were determined using the Kaplan-Meier method and differences between the groups were identified through log-rank analysis. Cox’s proportional hazard model was used to identify the risk factors for survival.
RESULTS: The mean survival periods for patients in the conservative treatment, TACE, hepatic resection and hepatic resection associated with postoperative TACE groups were 3.8, 7, 8.2 and 15.1 mo, respectively. Significant differences were observed in the survival rates. For the surgical resection associated with postoperative TACE group, the survival rates after 1, 2 and 3 years were 49%, 37% and 19%, respectively. These results were significantly higher than those of the other groups (P < 0.05). Meanwhile, the 1, 2 and 3 year survival rates for the surgical resection group were 28%, 20% and 15%, whereas those for the TACE group were 17.5%, 0% and 0%, respectively. These values significantly increased after hepatic resection compared with those after TACE (P < 0.05).
CONCLUSION: Surgical resection is the most effective therapeutic strategy for HCC patients with PVTT and results in high hepatic functional reserve. For patients who can tolerate the procedure, postoperative TACE is necessary to prevent recurrence and prolong the survival period.
doi:10.3748/wjg.v20.i45.17141
PMCID: PMC4258584  PMID: 25493028
Hepatocellular carcinoma; Portal vein tumor thrombosis; Conservative treatment; Transarterial chemoembolization; Surgical resection; Postoperative transarterial chemoembolization
21.  Metastatic Recurrence in a Pancreatic Cancer Patient Derived Orthotopic Xenograft (PDOX) Nude Mouse Model Is Inhibited by Neoadjuvant Chemotherapy in Combination with Fluorescence-Guided Surgery with an Anti-CA 19-9-Conjugated Fluorophore 
PLoS ONE  2014;9(12):e114310.
The aim of this study is to determine the efficacy of neoadjuvant chemotherapy (NAC) with gemcitabine (GEM) in combination with fluorescence-guided surgery (FGS) on a pancreatic cancer patient derived orthotopic xenograft (PDOX) model. A PDOX model was established from a CA19-9-positive, CEA-negative tumor from a patient who had undergone a pancreaticoduodenectomy for pancreatic adenocarcinoma. Mice were randomized to 4 groups: bright light surgery (BLS) only; BLS+NAC; FGS only; and FGS+NAC. An anti-CA19-9 or anti-CEA antibody conjugated to DyLight 650 was administered intravenously via the tail vein of mice with the pancreatic cancer PDOX 24 hours before surgery. The PDOX was brightly labeled with fluorophore-conjugated anti-CA19-9, but not with a fluorophore-conjugated anti-CEA antibody. FGS was performed using the fluorophore-conjugated anti-CA19-9 antibody. FGS had no benefit over BLS to prevent metastatic recurrence. NAC in combination with BLS did not convey an advantage over BLS to prevent metastatic recurrence. However, FGS+NAC significantly reduced the metastatic recurrence frequency to one of 8 mice, compared to FGS only after which metastasis recurred in 6 out of 8 mice, and BLS+NAC with metastatic recurrence in 7 out of 8 mice (p = 0.041). Thus NAC in combination with FGS can reduce or even eliminate metastatic recurrence of pancreatic cancer sensitive to NAC. The present study further emphasizes the power of the PDOX model which enables metastasis to occur and thereby identify the efficacy of NAC in combination with FGS on metastatic recurrence.
doi:10.1371/journal.pone.0114310
PMCID: PMC4252107  PMID: 25463150
22.  Improved Detection Limit in Rapid Detection of Human Enterovirus 71 and Coxsackievirus A16 by a Novel Reverse Transcription–Isothermal Multiple-Self-Matching-Initiated Amplification Assay 
Journal of Clinical Microbiology  2014;52(6):1862-1870.
Rapid detection of human enterovirus 71 (EV71) and coxsackievirus A16 (CVA16) is important in the early phase of hand-foot-and-mouth disease (HFMD). In this study, we developed and evaluated a novel reverse transcription–isothermal multiple-self-matching-initiated amplification (RT-IMSA) assay for the rapid detection of EV71 and CVA16 by use of reverse transcriptase, together with a strand displacement DNA polymerase. Real-time RT-IMSA assays using a turbidimeter and visual RT-IMSA assays to detect EV71 and CVA16 were established and completed in 1 h, and the reported corresponding real-time reverse transcription–loop-mediated isothermal amplification (RT-LAMP) assays targeting the same regions of the VP1 gene were adopted as parallel tests. Through testing VP1 RNAs transcribed in vitro, the real-time RT-IMSA assays exhibited better linearity of quantification, with R2 values of 0.952 (for EV71) and 0.967 (for CVA16), than the real-time RT-LAMP assays, which had R2 values of 0.803 (for EV71) and 0.904 (for CVA16). Additionally, the detection limits of the real-time RT-IMSA assays (approximately 937 for EV71 and 67 for CVA16 copies/reaction) were higher than those of real-time RT-LAMP assays (approximately 3,266 for EV71 and 430 for CVA16 copies/reaction), and similar results were observed in the visual RT-IMSA assays. The new approaches also possess high specificities for the corresponding targets, with no cross-reactivity observed. In clinical assessment, compared to commercial reverse transcription-quantitative PCR (qRT-PCR) kits, the diagnostic sensitivities of the real-time RT-IMSA assays (96.4% for EV71 and 94.6% for CVA16) were higher than those of the real-time RT-LAMP assays (91.1% for EV71 and 90.8% for CVA16). The visual RT-IMSA assays also exhibited the same results. In conclusion, this proof-of-concept study suggests that the novel RT-IMSA assay is superior to the RT-LAMP assay in terms of detection limit and has the potential to rapidly detect EV71 and CVA16 viruses.
doi:10.1128/JCM.03298-13
PMCID: PMC4042787  PMID: 24648558
23.  Epidemiological and viral genome characteristics of the first human H7N9 influenza infection in Guangdong Province, China 
Journal of Thoracic Disease  2014;6(12):1785-1793.
Background
The first H7N9 human case in south of China was confirmed in Guangdong Province on August 2013, outside of the typical influenza season. For investigating the H7N9 virus source and transmission in the local community, we analyze the epidemiology and genome features of the virus isolated from the first human infection detected in Guangdong Province.
Methods
The data including medical records, exposure history and time line of events for the H7N9 patient and close contacts was collected. Variation and genetic signatures of H7N9 virus in Guangdong was analyzed using ClustalW algorithm and comparison with mutations associated with changes in biological characteristics of the virus.
Results
The female patient had a history of poultry exposure, and she was transferred from a local primary hospital to an intensive care unit (ICU) upon deterioration. No additional cases were reported. Similar to previous infections with avian influenza A (H7N9) virus, the patient presented with both upper and lower respiratory tract symptoms. Respiratory failure progressed quickly, and the patient recovered 4 weeks after the onset of symptoms. Genome analysis of the virus indicated that the predicted antigen city and internal genes of the virus are similar to previously reported H7N9 viruses. The isolated virus is susceptible to neuraminidase (NA) inhibitors but resistant to adamantine. Although this virus contains some unique mutations that were only detected in avian or environment-origin avian influenza A (H7N9) viruses, it is still quite similar to other human H7N9 isolates.
Conclusions
The epidemiological features and genome of the first H7N9 virus in Guangdong Province are similar to other human H7N9 infections. This virus may have existed in the environment and live poultry locally; therefore, it is important to be alert of the risk of H7N9 re-emergence in China, including emergence outside the typical influenza season.
doi:10.3978/j.issn.2072-1439.2014.12.09
PMCID: PMC4283329  PMID: 25589974
Avian influenza virus; epidemiology; H7N9; viral genome
24.  Comparative Transcriptome Analysis to Reveal Genes Involved in Wheat Hybrid Necrosis 
Wheat hybrid necrosis is an interesting genetic phenomenon that is found frequently and results in gradual death or loss of productivity of wheat. However, the molecular basis and mechanisms of this genetic phenomenon are still not well understood. In this study, the transcriptomes of wheat hybrid necrosis F1 and its parents (Neimai 8 and II469) were investigated using digital gene expression (DGE). A total of 1300 differentially expressed genes were identified, indicating that the response to hybrid necrosis in wheat is complicated. The assignments of the annotated genes based on Gene Ontology (GO) revealed that most of the up-regulated genes belong to “universal stress related”, “DNA/RNA binding”, “protein degradation” functional groups, while the down-regulated genes belong to “carbohydrate metabolism” and “translation regulation” functional groups. These findings suggest that these pathways were affected by hybrid necrosis. Our results provide preliminarily new insight into the underlying molecular mechanisms of hybrid necrosis and will help to identify important candidate genes involved in wheat hybrid necrosis.
doi:10.3390/ijms151223332
PMCID: PMC4284769  PMID: 25522166
Triticumaestivum; hybrid necrosis; digital gene expression; transcriptome
25.  Efficacy of tumor-targeting Salmonella typhimurium A1-R in combination with anti-angiogenesis therapy on a pancreatic cancer patient-derived orthotopic xenograft (PDOX) and cell line mouse models 
Oncotarget  2014;5(23):12346-12357.
The aim of the present study was to examine the efficacy of tumor-targeting Salmonella typhimurium A1-R treatment following anti-vascular endothelial growth factor (VEGF) therapy on VEGF-positive human pancreatic cancer. A pancreatic cancer patient-derived orthotopic xenograft (PDOX) that was VEGF-positive and an orthotopic VEGF-positive human pancreatic cancer cell line (MiaPaCa-2-GFP) as well as a VEGF-negative cell line (Panc-1) were tested. Nude mice with these tumors were treated with gemcitabine (GEM), bevacizumab (BEV), and S. typhimurium A1-R. BEV/GEM followed by S. typhimurium A1-R significantly reduced tumor weight compared to BEV/GEM treatment alone in the PDOX and MiaPaCa-2 models. Neither treatment was as effective in the VEGF-negative model as in the VEGF-positive models. These results demonstrate that S. typhimurium A1-R following anti-angiogenic therapy is effective on pancreatic cancer including the PDOX model, suggesting its clinical potential.
PMCID: PMC4322966  PMID: 25402324
Pancreatic cancer; Salmonella typhimurium A1-R; patient-derived orthotopic xenograft (PDOX); orthotopic; nude mice; GFP; VEGF; anti-angiogenic therapy; bevacizumab; gemcitabine

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