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1.  Improving accuracy of protein-protein interaction prediction by considering the converse problem for sequence representation 
BMC Bioinformatics  2011;12:409.
With the development of genome-sequencing technologies, protein sequences are readily obtained by translating the measured mRNAs. Therefore predicting protein-protein interactions from the sequences is of great demand. The reason lies in the fact that identifying protein-protein interactions is becoming a bottleneck for eventually understanding the functions of proteins, especially for those organisms barely characterized. Although a few methods have been proposed, the converse problem, if the features used extract sufficient and unbiased information from protein sequences, is almost untouched.
In this study, we interrogate this problem theoretically by an optimization scheme. Motivated by the theoretical investigation, we find novel encoding methods for both protein sequences and protein pairs. Our new methods exploit sufficiently the information of protein sequences and reduce artificial bias and computational cost. Thus, it significantly outperforms the available methods regarding sensitivity, specificity, precision, and recall with cross-validation evaluation and reaches ~80% and ~90% accuracy in Escherichia coli and Saccharomyces cerevisiae respectively. Our findings here hold important implication for other sequence-based prediction tasks because representation of biological sequence is always the first step in computational biology.
By considering the converse problem, we propose new representation methods for both protein sequences and protein pairs. The results show that our method significantly improves the accuracy of protein-protein interaction predictions.
PMCID: PMC3215753  PMID: 22024143
2.  Support vector machine prediction of enzyme function with conjoint triad feature and hierarchical context 
BMC Systems Biology  2011;5(Suppl 1):S6.
Enzymes are known as the largest class of proteins and their functions are usually annotated by the Enzyme Commission (EC), which uses a hierarchy structure, i.e., four numbers separated by periods, to classify the function of enzymes. Automatically categorizing enzyme into the EC hierarchy is crucial to understand its specific molecular mechanism.
In this paper, we introduce two key improvements in predicting enzyme function within the machine learning framework. One is to introduce the efficient sequence encoding methods for representing given proteins. The second one is to develop a structure-based prediction method with low computational complexity. In particular, we propose to use the conjoint triad feature (CTF) to represent the given protein sequences by considering not only the composition of amino acids but also the neighbor relationships in the sequence. Then we develop a support vector machine (SVM)-based method, named as SVMHL (SVM for hierarchy labels), to output enzyme function by fully considering the hierarchical structure of EC. The experimental results show that our SVMHL with the CTF outperforms SVMHL with the amino acid composition (AAC) feature both in predictive accuracy and Matthew’s correlation coefficient (MCC). In addition, SVMHL with the CTF obtains the accuracy and MCC ranging from 81% to 98% and 0.82 to 0.98 when predicting the first three EC digits on a low-homologous enzyme dataset. We further demonstrate that our method outperforms the methods which do not take account of hierarchical relationship among enzyme categories and alternative methods which incorporate prior knowledge about inter-class relationships.
Our structure-based prediction model, SVMHL with the CTF, reduces the computational complexity and outperforms the alternative approaches in enzyme function prediction. Therefore our new method will be a useful tool for enzyme function prediction community.
PMCID: PMC3121122  PMID: 21689481
3.  Glycemic variability in normal glucose tolerance women with the previous gestational diabetes mellitus 
Women with previous gestational diabetes mellitus (pGDM) and postpartum normal glucose tolerance (NGT) may carry impaired islet β cell secretion, insulin resistance and subsequent altered glucose homeostasis. And certain normoglycemic groups at risks of diabetes were presented with elevated glycemic variability. The aim of study was to investigate the glycemic variability in NGT women with pGDM.
Total 48 NGT women with pGDM (pGDM group) and 48 age- and BMI-matched NGT women without pGDM (control group) were recruited in the study. Integrated β cell function was assessed with the Insulin Secretion-Sensitivity Index-2 (ISSI-2) derived from oral glucose tolerance test. All subjects were monitored using the continuous glucose monitoring system for consecutive 72 h. The multiple parameters of glycemic variability included the mean blood glucose (MBG), standard deviation of blood glucose (SDBG), mean of daily differences (MODD), mean amplitude of glycemic excursions (MAGE) and the incremental areas above preprandial glucose values (AUCpp).
The pGDM group had a higher MBG (6.5 ± 0.9 vs. 5.9 ± 0.8 mmol/L, p < 0.05), SDBG (1.3 ± 0.3 vs. 0.9 ± 0.2 mmol/L, p < 0.05), MODD (1.4 ± 0.3 vs. 1.1 ± 0.2 mmol/L, p < 0.05), MAGE (2.7 ± 0.4 vs. 1.8 ± 0.5 mmol/L, p < 0.05), and AUCpp (26.8 ± 3.4 vs. 19.2 ± 3.2 mmol/L·h, p < 0.05), when compared to the control group, and the differences remained significant after adjusting for anthropometric indices and metabolic risk factors. Islet β cell function index ISSI-2 in the pGDM group was lower than in the control group (p < 0.05). MBG, SDBG, MODD, MAGE and AUCpp were all negatively associated with ISSI-2 in the pGDM group (r = −0.31, −0.30, −0.34, −0.48 and −0.54, respectively, p < 0.05), and the correlations remained significant after adjusting for anthropometric indices and metabolic risk factors.
Normal glucose tolerance women with pGDM were presented with elevated glycemic variability, which may be associated with impaired islet β cell function.
PMCID: PMC4581077  PMID: 26405461
Glycemic variability; Normal glucose tolerance; Gestational diabetes mellitus
4.  Spectroscopic Capture and Reactivity of a Low-Spin Cobalt(IV)-Oxo Complex Stabilized by Binding Redox-Inactive Metal Ions 
High-valent cobalt-oxo intermediates are proposed as reactive intermediates in a number of cobalt complex-mediated oxidation reactions. Herein we report the spectroscopic capture of low-spin (S = 1/2) Co(IV)-oxo species in the presence of redox-inactive metal ions, such as Sc3+, Ce3+, Y3+, and Zn2+ and investigation of their reactivity in C-H bond activation and sulfoxidation reactions. Theoretical calculations predict that the binding of Lewis-acidic metal ions to the cobalt-oxo core increases the electrophilicity of the oxygen atom, resulting in the redox tautomerism of a highly unstable [(TAML)CoIII-(O•)]2− species to a more stable [(TAML)CoIV-(O)(Mn+)] core. The present report supports the proposed role of the redox-inactive metal ions in facilitating formation of high-valent metal-oxo cores as a necessary step for oxygen evolution in chemistry and biology.
PMCID: PMC4506312  PMID: 25081948
Cobalt; Oxo ligand; Lewis acid stabilization; Redox tautomerization; Oxygenation
6.  Enamel organic matrix: potential structural role in enamel and relationship to residual basement membrane constituents at the dentin enamel junction 
Connective tissue research  2014;55(0 1):33-37.
Although mature enamel is predominantly composed of mineral, a previously uncharacterized organic matrix layer remains in the post-eruptive tissue that begins at the dentin enamel junction and extends 200–300 µm towards the outer tooth surface. Identification of the composition of this layer has been hampered by its insolubility; however, we have developed a single step method to isolate the organic enamel matrix relatively intact. After dissociative dissolution of the matrix with SDS and urea, initial characterization by Western blotting and gel zymography indicates the presence of type IV and type VII basement membrane collagens and active matrix metalloproteinase-20. When combined with data from transgenic knockout mice and from human mutations, these data suggest that the enamel organic matrix (EOM) and dentin enamel junction may have a structural and functional relationship with basement membranes, e.g. skin. To clarify this relationship, we hypothesize a “foundation” model which proposes that components of the EOM form a support structure that stabilizes the crystalline enamel layer, and bonds it to the underlying dentin along the dentin enamel junction. Since we have also co-localized an active matrix metalloproteinase to this layer, our hypothesis suggests that, under pathologic conditions, MMP-mediated degradation of the EOM could destabilize the enamel–dentin interface.
PMCID: PMC4537066  PMID: 25158177
Basement membrane; dentin enamel junction; mature human enamel; MMP-20; type IV collagen; type VII collagen
7.  Human Adenovirus Type 7 Infection Associated with Severe and Fatal Acute Lower Respiratory Illness and Nosocomial Transmission 
Journal of Clinical Microbiology  2014;53(2):746-749.
A 23-year-old male died of severe pneumonia and respiratory failure in a tertiary hospital in Beijing, and 4 out of 55 close contacts developed fever. Molecular analysis confirmed human adenovirus type 7 (HAdV7) as the causative agent. We highlight the importance of early diagnosis and treatment and proper transmission control of HAdV7.
PMCID: PMC4298532  PMID: 25520444
8.  Non-thermal atmospheric plasmas in dental restoration: improved resin adhesive penetration 
Journal of dentistry  2014;42(8):1033-1042.
To investigate the influence of non-thermal plasma treatment on the penetration of a model dental adhesive into the demineralized dentin.
Prepared dentin surfaces were conditioned with Scotchbond Universal etchant for 15 s and sectioned equally perpendicular to the etched surfaces. The separated halves were randomly selected for treatment with an argon plasma brush (input current 6 mA, treatment time 30 s) or gentle argon air blowing (treatment time 30 s, as control). The plasma-treated specimens and control specimens were applied with a model adhesive containing 2,2-bis[4-(2-hydroxy-3-methacryloxypropoxy) phenyl]-propane (BisGMA) and 2-hydroxyethyl methacrylate (HEMA) (mass ratio of 30/70), gently air-dried for 5 s, and light-cured for 20 s. Cross-sectional specimens were characterized using micro-Raman spectral mapping across the dentin, adhesive/dentin interface, and adhesive layer at 1∼micron spatial resolution. SEM was also employed to examine the adhesive/dentin interfacial morphology.
The micro-Raman result disclosed that plasma treatment significantly improved the penetration of the adhesive, evidenced by the apparently higher content of the adhesive at the adhesive/dentin interface as compared to the control. Specifically, the improvement of the adhesive penetration using plasma technique was achieved by dramatically enhancing the penetration of hydrophilic monomer (HEMA), while maintaining the penetration of hydrophobic monomer (BisGMA). Morphological observation at the adhesive/dentin interface using SEM also confirmed the improved adhesive penetration. The results further suggested that plasma treatment could benefit polymerization of the adhesive, especially in the interface region.
The significant role of the non-thermal plasma brush in improving the adhesive penetration into demineralized dentin has been demonstrated. The results obtained may offer a better prospect of using plasma in dental restoration to optimize adhesion between tooth substrate and restorative materials.
PMCID: PMC4211626  PMID: 24859333
non-thermal atmospheric plasmas; dental adhesive; resin penetration; dentin; micro-Raman
9.  Conserved Hydrogen Bonds and Water Molecules in MDR HIV-1 Protease Substrate Complexes 
The success of highly active antiretroviral therapy (HAART) in anti-HIV therapy is severely compromised by the rapidly developing drug resistance. HIV-1 protease inhibitors, part of HAART, are losing their potency and efficacy in inhibiting the target. Multi-drug resistant (MDR) 769 HIV-1 protease (resistant mutations at residues 10, 36, 46, 54, 62, 63, 71, 82, 84, 90) was selected for the present study to understand the binding to its natural substrates. The nine crystal structures of MDR769 HIV-1 protease substrate hepta-peptide complexes were analyzed in order to reveal the conserved structural elements for the purpose of drug design against MDR HIV-1 protease. Our structural studies demonstrated that highly conserved hydrogen bonds between the protease and substrate peptides, together with the conserved crystallographic water molecules, played a crucial role in the substrate recognition, substrate stabilization and protease stabilization. In addition, the absence of the key flap-ligand bridging water molecule might imply a different catalytic mechanism of MDR769 HIV-1 protease compared to that of wild type (WT) HIV-1 protease.
PMCID: PMC4520401  PMID: 23261453
10.  Crystallographic study of multi-drug resistant HIV-1 protease Lopinavir complex: mechanism of drug recognition and resistance 
Lopinavir (LPV) is a second generation HIV-1 protease inhibitor. Drug resistance has rapidly emerged against LPV US FDA approved it on September 15, 2000. Mutations at residues 32I, L33F, 46I, 47A, I54V, V82A, I84V and L90M render the protease drug resistant against LPV. We report the crystal structure of a clinical isolate multi-drug resistant (MDR) 769 HIV-1 protease (resistant mutations at residues 10, 36, 46, 54, 62, 63, 71, 82, 84, 90) complexed with LPV and the in vitro enzymatic IC50 of LPV against MDR 769. The structural and functional studies demonstrate significant drug resistance of MDR 769 against LPV, arising from reduced interactions between LPV and the protease target.
PMCID: PMC4520426  PMID: 23792096
HIV-1 protease; Multi-drug resistance; X-ray crystallography; IC50; Lopinavir
11.  Attitudes toward Physician-Nurse Collaboration in Pediatric Workers and Undergraduate Medical/Nursing Students 
Behavioural Neurology  2015;2015:846498.
The purpose of this study was to compare the attitudes of pediatric workers and undergraduate medical/nursing students toward collaboration. Attitude toward collaboration was measured using an adaptation of the Jefferson Scale of Attitude toward Physician-Nurse Collaboration. The 656 questionnaires were gathered from pediatrician, pediatric interns, and medical students (PIS) and pediatric nurses, nursing interns, and nursing students (NIS). Results showed a statistically significant difference in the total mean scores in attitudes towards collaboration with NIS scoring higher. Among the participants of PIS, the pediatricians obtained the highest mean scores, while, among the participants of NIS, the pediatric nurses got higher mean scores than nursing interns. It is desirable that medical and nurse schools should include interprofessional education in their curriculum to increase the understanding of the complementary roles of physicians and nurses and to encourage establishment of an interdependent relationship between them.
PMCID: PMC4529947  PMID: 26273131
12.  Microbial community changes along the active seepage site of one cold seep in the Red Sea 
The active seepage of the marine cold seeps could be a critical process for the exchange of energy between the submerged geosphere and the sea floor environment through organic-rich fluids, potentially even affecting surrounding microbial habitats. However, few studies have investigated the associated microbial community changes. In the present study, 16S rRNA genes were pyrosequenced to decipher changes in the microbial communities from the Thuwal seepage point in the Red Sea to nearby marine sediments in the brine pool, normal marine sediments and water, and benthic microbial mats. An unexpected number of reads from unclassified groups were detected in these habitats; however, the ecological functions of these groups remain unresolved. Furthermore, ammonia-oxidizing archaeal community structures were investigated using the ammonia monooxygenase subunit A (amoA) gene. Analysis of amoA showed that planktonic marine habitats, including seeps and marine water, hosted archaeal ammonia oxidizers that differed from those in microbial mats and marine sediments, suggesting modifications of the ammonia oxidizing archaeal (AOA) communities along the environmental gradient from active seepage sites to peripheral areas. Changes in the microbial community structure of AOA in different habitats (water vs. sediment) potentially correlated with changes in salinity and oxygen concentrations. Overall, the present results revealed for the first time unanticipated novel microbial groups and changes in the ammonia-oxidizing archaea in response to environmental gradients near the active seepages of a cold seep.
PMCID: PMC4523032  PMID: 26284035
cold seep; Red Sea; 16S rRNA gene; pyrosequencing; ammonia oxidizing archaea
13.  Survey of Wild and Domestic Mammals for Infection with Leishmania infantum following an Outbreak of Desert Zoonotic Visceral Leishmaniasis in Jiashi, People's Republic of China 
PLoS ONE  2015;10(7):e0132493.
In 2008 and 2009, an outbreak of desert-subtype zoonotic visceral leishmaniasis occurred in Jiashi county, Xinjiang, China. So far, no animal reservoir has been identified for this type of visceral leishmaniasis. Therefore, we surveyed the most common mammals (wild and domestic) for Leishmania infections during the outbreak in 2008 and 2009 in order to identify the source of the visceral leishmaniasis in this region. Spleen, liver, bone marrow and blood samples collected from 86 wood mice (Apodemus sylvaticus), 61midday jirds (Meriones meridianus) and 27 Yarkand hares (Lepus yarkandensis) were tested for the presence of Leishmania by microscopy, culture and PCR. All of the animals were found to be negative for Leishmania infections; On the other hand, Leishmania DNA was detected in blood samples collected from livestock reared in the outbreak area: 30.36% (17/56) of sheep, 21.57% (11/51) of goats, 17.78% (8/45) of cattle, and 21.62 (8/37) of donkeys were positive for Leishmania DNA by PCR. The amplified kDNA sequences from the livestock samples matched Leishmania DNA sequences isolated from patients with visceral leishmaniasis in the study area. We suggest that these domestic mammals are a possible reservoir host for Leishmania infantum in the outbreak area.
PMCID: PMC4503304  PMID: 26177101
15.  SS1 (NAL1)- and SS2-Mediated Genetic Networks Underlying Source-Sink and Yield Traits in Rice (Oryza sativa L.) 
PLoS ONE  2015;10(7):e0132060.
Source leaf/sink capacity (SS) traits are important determinants of grain yield (GY) of rice. To understand the genetic basis of the SS relationship in rice, five SS and GY traits of rice were genetically dissected using two reciprocal introgression populations. Seventy-three QTL affecting the SS and GY traits were identified, most of which were detected in one of the parental genetic backgrounds (GBs). Two major QTL at bins 4.7 (SS1) and 3.12 (SS2) were associated consistently with all measured SS and yield traits in both GBs across two contrasting environments. Strong interactions between SS1/SS2 and the detected QTL led us to the discovery of genetic networks affecting the SS and GY traits. The SS1 acted as a regulator controlling two groups of downstream QTL affecting the source leaf width and grain number per panicle (GNP). SS2 functioned as a regulator positively regulating different groups of downstream QTL affecting the source leaf length, GNP, grain weight, and GY. Map-based cloning of SS1 indicates that SS1 is NAL1 involved in polar auxin/IAA transport. Different alleles at NAL1 were apparently able to qualitatively and/or quantitatively control the IAA transport from the apical meristem to different plant tissues and thus regulate those downstream loci/pathways controlling different SS traits of rice. There was a functional allele and a non-functional mutation in the parents at each of the QTL downstream of SS1 or SS2, which were detectable only in the presence of the functional allele of SS1 or SS2. Our results provided direct evidence that SS and yield traits in rice are controlled by complex signaling pathways and suggest further improvement of rice yield potential with enhanced and balanced SS relationships can be achieved by accurately manipulating allelic combinations at loci in the SS1 and SS2 mediated pathways.
PMCID: PMC4498882  PMID: 26162098
16.  Choroidal thickness and high myopia: a cross-sectional study and meta-analysis 
BMC Ophthalmology  2015;15:70.
The purpose of this study was to examine the choroidal thickness of patients with high myopia using enhanced depth imaging optical coherence tomography (EDI-OCT) and compare them with healthy subjects.
We first conducted a cross-sectional study and then performed a meta-analysis to address this issue further. Using enhanced depth imaging optical coherence tomography (EDI-OCT), the macular choroidal thickness of high myopic eyes and normal control eyes were measured and compared at each location. Univariate and multivariate linear regression analyses were performed to assess the association between choroidal thickness and clinical factors such as axial length (AL), spherical equivalent (SE), and central corneal thickness. In the high myopic eyes, subgroup analysis of macular choroidal thickness was performed in eyes with or without lacquer cracks and choroidal neovascularization (CNV). The meta-analyses were conducted using the Stata software package.
The high myopic eyes had a thinner choroid than the control eyes at all macular locations (all P < 0.001). Multivariable linear regression analysis showed that the subfoveal choroidal thickness (SFCT) was not significantly thinner in association with the diagnosis. Subgroup analysis showed that the high myopia with CNV and with lacquer cracks had a significantly thinner choroid than without CNV or lacquer crack eyes. The result of our cross-sectional study is consistent with the results of the further meta-analysis with the pooled weighted mean difference (WMD) of −116.30 μm (95 % CI: −145.68, −86.92) for SFCT.
The present study, along with the comprehensive meta-analysis, indicated that in the Chinese population, the choroidal thickness in high myopic eyes was thinner than that of normal control eyes, even across different subgroups. This might be secondary to the longer AL but it is not an independent factor. The presence of CNV and of lacquer cracks is associated strongly with eyes with thinner macular choroids.
PMCID: PMC4490603  PMID: 26138613
Choroidal thickness; High myopia; Optical coherence tomography
17.  Diffusion basis spectrum imaging detects and distinguishes coexisting subclinical inflammation, demyelination, and axonal injury in experimental autoimmune encephalomyelitis mice 
NMR in biomedicine  2014;27(7):843-852.
Clinicopathological paradox has significantly hampered the effective assessment of the efficacy of therapeutic intervention of multiple sclerosis. The neuroimaging biomarkers of tissue injury could guide a more effective treatment by accurately reflecting the underlying subclinical pathologies. Diffusion tensor imaging-derived directional diffusivity and anisotropy indices have been applied to characterize white matter disorders. However, these biomarkers are sometimes confounded by complex pathologies seen in multiple sclerosis and its animal models. Recently, a novel diffusion basis spectrum imaging has been developed to quantitatively assess axonal injury, demyelination, and inflammation in a mouse model of inflammatory demyelination. Lenaldekar, which inhibits T-cell expansion in a non-cytolytic manner, has been shown to suppress relapses and preserve white matter integrity in mice with experimental autoimmune encephalomyelitis. In this study, relapsing-remitting experimental autoimmune encephalomyelitis was induced through active immunization of SJL/J mice with a myelin proteolipid protein peptide. We evaluated the therapeutic efficacy of Lenaldekar treatment via daily clinical score, cross-sectional ex vivo diffusion basis spectrum imaging examination, and histological analysis. Lenaldekar greatly reduced relapse severity and protected white matter integrity in these experimental autoimmune encephalomyelitis mice. Diffusion basis spectrum imaging-derived axial diffusivity, radial diffusivity and restricted diffusion tensor fraction accurately reflected axon, myelin integrity and inflammation associated cellularity change, respectively. These results support the potential use of diffusion basis spectrum imaging as an effective outcome measure for preclinical drug evaluation.
PMCID: PMC4071074  PMID: 24816651
Multiple sclerosis; diffusion MRI; axon injury; inflammation; demyelination; DBSI; Lenaldekar; EAE
18.  A Mechanistic study of Plasma Treatment Effects on Demineralized Dentin Surfaces for Improved Adhesive/Dentin Interface Bonding 
Clinical plasma medicine  2014;2(1):11-16.
Our previous work has shown that non-thermal plasma treatment of demineralized dentin significantly (p<0.05) improved adhesive/dentin bonding strength for dental composite restoration as compared with the untreated controls. This study is to achieve mechanistic understanding of the plasma treatment effects on dentin surface through investigating the plasma treated dentin surfaces and their interaction with adhesive monomer, 2-Hydroxyethyl methacrylate (HEMA). The plasma treated dentin surfaces from human third molars were evaluated by water contact angle measurements and scanning electron microscopy (SEM). It was found that plasma-treated dentin surface with subsequent HEMA immersion (Plasma/HEMA Treated) had much lower water contact angle compared with only plasma-treated (Plasma Treated) or only HEMA immersed (HEMA Treated) dentin surfaces. With prolong water droplet deposition time, water droplets spread out completely on the Plasma/HEMA Treated dentin surfaces. SEM images of Plasma/HEMA Treated dentin surfaces verified that dentin tubules were opened-up and filled with HEMA monomers. Extracted type I collagen fibrils, which was used as simulation of the exposed dentinal collagen fibrils after acid etching step, were plasma treated and analyzed with Fourier transform infrared spectroscopy (FT-IR) and circular dichroism (CD) spectra. FT-IR spectra of the Plasma/HEMA Treated collage fibrils showed broadened amide I peak at 1660 cm−1 and amide II at 1550 cm−1, which indicate secondary structure changes of the collagen fibrils. CD spectra indicated that 67.4% collagen helix structures were denatured after plasma treatment. These experimental results demonstrate that non-thermal argon plasma treatment was very effective in loosing collagen structure and enhancing adhesive monomer penetration, which are beneficial to thicker hybrid layer and longer resin tag formation, and consequently enhance adhesive/dentin interface bonding.
PMCID: PMC4175472  PMID: 25267936
Plasma treatment; demineralized dentin surface; adhesive penetration; adhesive/dentin bonding: denatured collagen
19.  Limited Unilateral Decompression and Pedicle Screw Fixation with Fusion for Lumbar Spinal Stenosis with Unilateral Radiculopathy: A Retrospective Analysis of 25 Cases 
Lumbar spinal stenosis is conventionally treated with surgical decompression. However, bilateral decompression and laminectomy is more invasive and may not be necessary for lumbar stenosis patients with unilateral radiculopathy. We aimed to report the outcomes of unilateral laminectomy and bilateral pedicle screw fixation with fusion for patients with lumbar spinal stenosis and unilateral radiculopathy.
Patients with lumbar spinal stenosis with unilateral lower extremity radiculopathy who received limited unilateral decompression and bilateral pedicle screw fixation were included and evaluated using visual analog scale (VAS) pain and the Oswestry Disability Index (ODI) scores preoperatively and at follow-up visits. Ligamentum flavum thickness of the involved segments was measured on axial magnetic resonance images.
Twenty-five patients were included. The mean preoperative VAS score was 6.6±1.6 and 4.6±3.1 for leg and back pain, respectively. Ligamentum flavum thickness was comparable between the symptomatic and asymptomatic side (p=0.554). The mean follow-up duration was 29.2 months. The pain in the symptomatic side lower extremity (VAS score, 1.32±1.2) and the back (VAS score, 1.75±1.73) significantly improved (p=0.000 vs. baseline for both). The ODI improved significantly postoperatively (6.60±6.5; p=0.000 vs. baseline). Significant improvement in VAS pain and ODI scores were observed in patients receiving single or multi-segment decompression fusion with fixation (p<0.01).
Limited laminectomy and unilateral spinal decompression followed by bilateral pedicle screw fixation with fusion achieves satisfactory outcomes in patients with spinal stenosis and unilateral radiculopathy. This procedure is less damaging to structures that are important for maintaining posterior stability of the spine.
PMCID: PMC4534742  PMID: 26279816
Lumbar spinal stenosis; Unilateral radiculopathy; Unilateral decompression; Pedicle screw instrumentation
20.  Comorbidity and survival among women with ovarian cancer: evidence from prospective studies 
Scientific Reports  2015;5:11720.
The relationship between comorbidity and ovarian cancer survival has been controversial so far. Therefore, we conducted a meta-analysis to summarize the existing evidence from prospective studies on this issue. Relevant studies were identified by searching the PubMed, EMBASE, and ISI Web of Science databases through the end of January 2015. Two authors independently performed the eligibility evaluation and data abstraction. Random-effects models were used to estimate summary hazard ratios (HRs) and 95% confidence intervals (CIs) for overall survival. Eight prospective studies involving 12,681 ovarian cancer cases were included in the present study. The summarized HR for presence versus absence of comorbidity was 1.20 (95% CI = 1.11–1.30, n = 8), with moderate heterogeneity (I2 = 31.2%, P = 0.179). In addition, the summarized HR for the highest compared with the lowest category of the Charlson’s comorbidity index was 1.68 (95% CI = 1.50–1.87, n = 2), without heterogeneity (I2 = 0%, P = 0.476). Notably, a significant negative impact of comorbidity on ovarian cancer survival was observed in most subgroup analyses stratified by the study characteristics and whether there was adjustment for potential confounders. In conclusion, the findings of this meta-analysis suggest that underlying comorbidity is consistently associated with decreased survival in patients with ovarian cancer. Comorbidity should be taken into account when managing these patients.
PMCID: PMC4484350  PMID: 26118971
21.  Acylation of Antioxidant of Bamboo Leaves with Fatty Acids by Lipase and the Acylated Derivatives’ Efficiency in the Inhibition of Acrylamide Formation in Fried Potato Crisps 
PLoS ONE  2015;10(6):e0130680.
This study selectively acylated the primary hydroxyl groups on flavonoids in antioxidant of bamboo leaves (AOB) using lauric acid with Candida antarctica lipase B in tert-amyl-alcohol. The separation and isolation of acylated derivatives were performed using silica gel column chromatography with a mixture of dichloromethane/diethyl ether/methanol as eluents. Both thin layer chromatography and high-performance liquid chromatography analyses confirmed the high efficiency of the isolation process with the purified orientin-6″-laurate, isoorientin-6″-laurate, vitexin-6″-laurate, and isovitexin-6″-laurate that were obtained. The addition of AOB and acylated AOB reduced acrylamide formation in fried potato crisps. Results showed that 0.05% AOB and 0.05% and 0.1% acylated AOB groups significantly (p < 0.05) reduced the content of acrylamide in potato crisps by 30.7%, 44.5%, and 46.9%, respectively.
PMCID: PMC4476655  PMID: 26098744
22.  The decreased expression of miR-625 predicts poor prognosis of esophageal squamous cell carcinoma 
Background: Previous study has detected the expression of miR-625 in esophageal squamous cell carcinoma (ESCC) and found that miR-625 was related to tumor depth, stage, and metastasis of ESCC. However, the prognostic value of miR-625 in ESCC has not yet been reported. Methods: Real-time quantitative PCR was employed to measure the expression level of miR-625 in clinical ESCC tissues. Survival curves were made using the Kaplan-Meier method, and the log rank test was used to analyze the differences between clinicopathological characteristics and survival in ESCC patients. Results: The expression level of miR-625 in ESCC tissues was significantly lower than that in adjacent non-tumor tissues (1.00 ± 0.38 vs. 3.25 ± 1.83, P < 0.0001). Low miR-625 expression was observed to be closely correlated with lymph node metastasis (P = 0.01), distant metastasis (P = 0.007), tumor differentiation (P = 0.04), and advanced TNM stage (P = 0.005). The 5-year overall survival rate in the low expression group was 38.1%, compared with 68.8% in the high expression group (log-rank test, P = 0.001). Multivariate Cox regression analysis showed that miR-625 expression level (HR = 3.72, 95% CI: 1.36-8.78, P = 0.005) was an independent factor in predicting the overall survival of ESCC patients. Conclusion: Our findings provide the convincing evidence for the first time that the down-regulation of miR-625 may serve as a novel molecular marker to predict the aggressive tumor progression and unfavorable prognosis of ESCC patients.
PMCID: PMC4538131  PMID: 26309624
MiRNA-625; esophageal cancer; ESCC; clinicopathological features; prognosis
23.  Significantly decreased mRNA levels of BDNF and MEK1 genes in treatment-resistant depression 
Neuroreport  2014;25(10):753-755.
The aim of the current study was to investigate whether the levels of mRNA expression of brain-derived neurotrophin factor (BDNF) and a related gene MEK1 were more obviously decreased in treatment-resistant depression (TRD). In total, 50 patients with major depressive disorder (including 26 with TRD and 24 with treatment-responsive depression) and 48 healthy controls were enrolled. BDNF and MEK1 mRNA levels in blood samples from all patients and controls were measured using reverse transcriptase-PCR. BDNF and MEK1 mRNA levels were significantly reduced in patients with major depressive disorder when compared with healthy controls (BDNF: P<0.01; MEK1: P<0.001), as well as among treatment-resistant depressive patients as compared with treatment-responsive depressive patients (BDNF: P<0.001; MEK1: P<0.01). Our findings support the hypothesis that BDNF and MEK1 mRNA expression levels are more obviously decreased in patients with TRD.
PMCID: PMC4465888  PMID: 24709918
brain-derived neurotrophin factor; mitogen-activated protein kinase kinase 1; treatment-resistant depression; treatment-responsive depression
24.  Pyrosequencing revealed shifts of prokaryotic communities between healthy and disease-like tissues of the Red Sea sponge Crella cyathophora 
PeerJ  2015;3:e890.
Sponge diseases have been widely reported, yet the causal factors and major pathogenic microbes remain elusive. In this study, two individuals of the sponge Crella cyathophora in total that showed similar disease-like characteristics were collected from two different locations along the Red Sea coast separated by more than 30 kilometers. The disease-like parts of the two individuals were both covered by green surfaces, and the body size was much smaller compared with adjacent healthy regions. Here, using high-throughput pyrosequencing technology, we investigated the prokaryotic communities in healthy and disease-like sponge tissues as well as adjacent seawater. Microbes in healthy tissues belonged mainly to the Proteobacteria, Cyanobacteria and Bacteroidetes, and were much more diverse at the phylum level than reported previously. Interestingly, the disease-like tissues from the two sponge individuals underwent shifts of prokaryotic communities and were both enriched with a novel clade affiliated with the phylum Verrucomicrobia, implying its intimate connection with the disease-like Red Sea sponge C. cyathophora. Enrichment of the phylum Verrucomicrobia was also considered to be correlated with the presence of algae assemblages forming the green surface of the disease-like sponge tissues. This finding represents an interesting case of sponge disease and is valuable for further study.
PMCID: PMC4465955  PMID: 26082867
Low microbial abundance; Verrucomicrobia; Sponge symbiont; Disease-like sponge
25.  Transcriptional responses of invasive and indigenous whiteflies to different host plants reveal their disparate capacity of adaptation 
Scientific Reports  2015;5:10774.
The whitefly Bemisia tabaci contains more than 35 cryptic species. The higher adaptability of Middle East-Asia Minor 1 (MEAM1) cryptic species has been recognized as one important factor for its invasion and displacement of other indigenous species worldwide. Here we compared the performance of the invasive MEAM1 and the indigenous Asia II 3 whitefly species following host plant transfer from a suitable host (cotton) to an unsuitable host (tobacco) and analyzed their transcriptional responses. After transfer to tobacco for 24 h, MEAM1 performed much better than Asia II 3. Transcriptional analysis showed that the patterns of gene regulation were very different with most of the genes up-regulated in MEAM1 but down-regulated in Asia II 3. Whereas carbohydrate and energy metabolisms were repressed in Asia II 3, the gene expression and protein metabolisms were activated in MEAM1. Compared to the constitutive high expression of detoxification genes in MEAM1, most of the detoxification genes were down-regulated in Asia II 3. Enzymatic activities of P450, GST and esterase further verified that the detoxification of MEAM1 was much higher than that of Asia II 3. These results reveal obvious differences in responses of MEAM1 and Asia II 3 to host transfer.
PMCID: PMC4455138  PMID: 26041313

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