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1.  Factors associated with low unit cohesion in Australian Defence Force members who deployed to the Middle East (2001–2009) 
Introduction
Unit cohesion has been shown to bolster the mental health of military personnel; hence, it is important to identify the characteristics that are associated with low unit cohesion, so that interventions to improve unit cohesion can be targeted and implemented. Little is known about the factors associated with low unit cohesion. This research aims to identify demographic, military service and deployment factors associated with low unit cohesion.
Methods
Data from a self-reported cross-sectional study of 11 411 current or ex-serving Australian military personnel deployed to Iraq or Afghanistan between 2001 and 2009 were used. Multivariable logistic regression was used to investigate the research aims.
Results
Being female (adjusted OR (aOR) (95% CI) 1.35 (1.21 to 1.51)), non-commissioned officer (aOR (95% CI) 1.50 (1.39 to 1.62)), lower ranked (aOR (95% CI) 1.74 (1.51 to 2.01)) or having left military service (aOR (95% CI) 1.71 (1.46 to 2.02)) was associated with reporting low unit cohesion. Potentially modifiable factors such as performing logistic roles on deployment (aOR (95% CI) 1.13 (1.01 to 1.27)), dissatisfaction with work experience on deployment such as working with colleagues who did not do what was expected of them (aOR (95% CI) 4.09 (3.61 to 4.64)), and major problems at home while deployed (aOR (95% CI) 1.50 (1.38 to 1.63)) were also associated with reporting low unit cohesion.
Conclusions
This is the first study to identify demographic, military service and deployment factors associated with low unit cohesion. The modifiable nature of unit cohesion means that military leaders could use this information to identify subgroups for targeted resilience interventions that may reduce vulnerabilities to mental health problems and improve the job satisfaction, preparedness and deployment experiences of serving members.
doi:10.1136/jramc-2015-000484
PMCID: PMC5099321  PMID: 26567321
OCCUPATIONAL & INDUSTRIAL MEDICINE; PREVENTIVE MEDICINE; PUBLIC HEALTH
2.  Basal Tumor Cell Isolation and Patient-Derived Xenograft Engraftment Identify High-Risk Clinical Bladder Cancers 
Scientific Reports  2016;6:35854.
Strategies to identify tumors at highest risk for treatment failure are currently under investigation for patients with bladder cancer. We demonstrate that flow cytometric detection of poorly differentiated basal tumor cells (BTCs), as defined by the co-expression of CD90, CD44 and CD49f, directly from patients with early stage tumors (T1-T2 and N0) and patient-derived xenograft (PDX) engraftment in locally advanced tumors (T3-T4 or N+) predict poor prognosis in patients with bladder cancer. Comparative transcriptomic analysis of bladder tumor cells isolated from PDXs indicates unique patterns of gene expression during bladder tumor cell differentiation. We found cell division cycle 25C (CDC25C) overexpression in poorly differentiated BTCs and determined that CDC25C expression predicts adverse survival independent of standard clinical and pathologic features in bladder cancer patients. Taken together, our findings support the utility of BTCs and bladder cancer PDX models in the discovery of novel molecular targets and predictive biomarkers for personalizing oncology care for patients.
doi:10.1038/srep35854
PMCID: PMC5075783  PMID: 27775025
3.  Bis-biguanide dihydrochloride inhibits intracellular replication of M. tuberculosis and controls infection in mice 
Scientific Reports  2016;6:32725.
While there is an urgent need to develop new and effective drugs for treatment of tuberculosis (TB) and multi-drug resistant TB (MDR-TB), repurposing FDA (U.S. Food and Drug Administration) -approved drugs for development of anti-TB agents may decrease time and effort from bench to bedside. Here, we employed host cell-based high throughput screening (HTS) assay to screen and characterize FDA-approved, off-patent library drugs for anti-Mycobacterium tuberculosis (MTB) activities. The cell-based HTS allowed us to identify an anti-cancer drug of bis-biguanide dihydrochloride (BBD) as potent anti-mycobacteria agent. Further characterization showed that BBD could inhibit intracellular and extracellular growth of M. smegmatis and slow-growing M. bovis BCG. BBD also potently inhibited replication of clinically-isolated MTB and MDR-TB strains. The proof-of-concept study showed that BBD treatment of MTB-infected mice could significantly decrease CFU counts in the lung and spleen. Notably, comparative evaluation showed that MTB CFU counts in BBD-treated mice were lower than those in rifampicin-treated mice. No apparent BBD side effects were found in BBD-treated mice. Thus, our findings support further studies to develop BBD as a new and effective drug against TB and MDR-TB.
doi:10.1038/srep32725
PMCID: PMC5013693  PMID: 27601302
4.  Blood harmane concentrations and dietary protein consumption in essential tremor 
Neurology  2005;65(3):391-396.
Background
β-Carboline alkaloids (e.g., harmane) are highly tremorogenic chemicals. Animal protein (meat) is the major dietary source of these alkaloids. The authors previously demonstrated that blood harmane concentrations were elevated in patients with essential tremor (ET) vs controls. Whether this difference is due to greater animal protein consumption by patients or their failure to metabolize harmane is unknown.
Objective
The aim of this study was to determine whether patients with ET and controls differ with regard to 1) daily animal protein consumption and 2) the correlation between animal protein consumption and blood harmane concentration.
Methods
Data on current diet were collected with a semiquantitative food frequency questionnaire and daily calories and consumption of animal protein and other food types was calculated. Blood harmane concentrations were log-transformed (logHA).
Results
The mean logHA was higher in 106 patients than 161 controls (0.61 ± 0.67 vs 0.43 ± 0.72 g−10/mL, p = 0.035). Patients and controls consumed similar amounts of animal protein (50.2 ± 19.6 vs 49.4 ± 19.1 g/day, p = 0.74) and other food types (animal fat, carbohydrates, vegetable fat) and had similar caloric intakes. In controls, logHA was correlated with daily consumption of animal protein (r = 0.24, p = 0.003); in patients, there was no such correlation (r = −0.003, p = 0.98).
Conclusions
The similarity between patients and controls in daily animal protein consumption and the absence of the normal correlation between daily animal protein consumption and logHA in patients suggests that another factor (e.g., a metabolic defect) may be increasing blood harmane concentration in patients.
doi:10.1212/01.wnl.0000172352.88359.2d
PMCID: PMC4993192  PMID: 16087903
5.  Elevation of blood β-carboline alkaloids in essential tremor 
Neurology  2002;59(12):1940-1944.
Background
β-Carboline alkaloids are normal body constituents but are also potent tremor-producing chemicals that are naturally present in the food chain.
Objective
To explore the hypothesis that high concentrations of β-carboline alkaloids are associated with essential tremor (ET).
Methods
One hundred cases and 100 controls were frequency matched on age, sex, and ethnicity. Blood concentrations of harmane and harmine were quantified by high-performance liquid chromatography, blinded to clinical information.
Results
The mean log blood concentration of harmane was higher in cases than controls (0.72 ± 0.53 vs 0.51 ± 0.64 g−10/mL; p = 0.01). A nonparametric test on nontransformed data (median harmane = 5.21 g−10/mL in cases and 2.28 g−10/mL in controls) confirmed this difference (p = 0.005). The mean log blood concentration of harmine was 0.20 ± 0.48 g−10/mL in cases and 0.10 ± 0.65 g −10/mL in controls (p = 0.20). Log harmane concentrations were stratified based on the median value; 62% of cases vs 39% of controls had a high log harmane concentration (p = 0.001). Mean log harmane concentration was similar in the cases with (0.74 ± 0.58 g−10/mL) and without (0.71 ± 0.50 g−10/mL) an affected relative (p = 0.83).
Conclusions
Blood concentrations of harmane were measured in ET cases compared with controls. Concentrations were elevated in cases with and without a family history of ET.
PMCID: PMC4992345  PMID: 12499487
6.  Genetic variants in adiponectin and blood pressure responses to dietary sodium or potassium interventions: a family-based association study 
Journal of Human Hypertension  2016;30(9):563-570.
Previous studies have shown that genetic factors might have an important role in blood pressure (BP) responses to dietary salt or potassium intake. The aim of this study was to assess the association of common genetic variants of the adiponectin gene with BP responses to controlled dietary sodium or potassium interventions. Subjects (n=334) from 124 families in rural areas of Northern China were recruited. After a 3-day baseline observation, participants sequentially maintained a 7-day low-sodium diet (NaCl, 3 g per day; or sodium, 51.3 mmol per day), followed by a 7-day high-sodium diet (NaCl, 18 g per day; or sodium, 307.8 mmol per day) and a 7-day high-sodium plus potassium supplementation intervention (KCl, 4.5 g per day; or potassium, 60 mmol per day). A total of seven single nucleotide polymorphisms (SNPs) in the adiponectin gene were selected as the study sites. After adjustment for multiple testing, the adiponectin SNP rs16861205 was significantly associated with the diastolic BP (DBP) response to low-salt intervention, and the DBP and mean arterial pressure (MAP) responses to high-salt intervention (P=0.028, 0.023 and 0.027, respectively). SNP rs822394 was associated with the DBP and MAP responses to low-salt intervention and the DBP response to high-salt intervention (P=0.023, 0.030 and 0.033 respectively). Meanwhile, significant association also existed between SNP rs16861194 and the systolic BP response to potassium supplementation intervention (P=0.026). In addition, SNP rs822394 was significantly associated with basal DBP after adjustment for multiple testing (P=0.033). Our study indicated that the genetic polymorphisms in the adiponectin gene are significantly associated with BP responses to dietary sodium and potassium intake.
doi:10.1038/jhh.2016.5
PMCID: PMC4981730  PMID: 27011258
7.  Folate-Chitosan Nanoparticles Loaded with Ursolic Acid Confer Anti-Breast Cancer Activities in vitro and in vivo 
Scientific Reports  2016;6:30782.
Ursolic acid (UA) has proved to have broad-spectrum anti-tumor effects, but its poor water solubility and incompetent targeting property largely limit its clinical application and efficiency. Here, we synthesized a nanoparticle-based drug carrier composed of chitosan, UA and folate (FA-CS-UA-NPs) and demonstrated that FA-CS-UA-NPs could effectively diminish off-target effects and increase local drug concentrations of UA. Using MCF-7 cells as in vitro model for anti-cancer mechanistic studies, we found that FA-CS-UA-NPs could be easily internalized by cancer cells through a folate receptor-mediated endocytic pathway. FA-CS-UA-NPs entered into lysosome, destructed the permeability of lysosomal membrane, and then got released from lysosomes. Subsequently, FA-CS-UA-NPs localized into mitochondria but not nuclei. The prolonged retention of FA-CS-UA-NPs in mitochondria induced overproduction of ROS and destruction of mitochondrial membrane potential, and resulted in the irreversible apoptosis in cancer cells. In vivo experiments showed that FA-CS-UA-NPs could significantly reduce breast cancer burden in MCF-7 xenograft mouse model. These results suggested that FA-CS-UA-NPs could further be explored as an anti-cancer drug candidate and that our approach might provide a platform to develop novel anti-cancer drug delivery system.
doi:10.1038/srep30782
PMCID: PMC4965748  PMID: 27469490
8.  Experimentally simulating quantum walks with self-collimated light 
Scientific Reports  2016;6:28610.
In self-collimated photonic crystal, periodically arranged air holes of sub-wavelength scale provide flattened equi-frequency curves perpendicular to the ΓM direction, which allow light or photons propagating in a quasi-uniform medium without diffraction. Here we for the first time experimentally simulate four-step single-photon discrete time quantum walks with classical light in such a photonic crystal chip fabricated on silicon-on-insulator. Similarities between theoretical expectations and experimental results are higher than 0.98. The functional area is compact and can be extended to construct more complicated linear quantum circuits.
doi:10.1038/srep28610
PMCID: PMC4926089  PMID: 27353428
9.  Th17-related cytokines contribute to recall-like expansion/effector function of HMBPP-specific Vγ2Vδ2 T cells after Mycobacterium tuberculosis infection or vaccination 
European journal of immunology  2015;45(2):442-451.
Whether cytokines can influence the adaptive immune response by antigen-specific γδ T cells during infections or vaccinations remains unknown. We previously demonstrated that, during BCG/Mycobacterium tuberculosis (Mtb) infections, Th17-related cytokines markedly upregulated when phosphoantigen-specific VγVδ2 T cells expanded. In this study, we examined the involvement of Th17-related cytokines in the recall-like responses of Vγ2Vδ2 T cells following Mtb infection or vaccination against TB. Treatment with IL-17A/IL-17F or IL-22 expanded phosphoantigen 4-hydroxy-3-methyl-but-enyl pyrophosphate (HMBPP)-stimulated Vγ2Vδ2 T cells from BCG-vaccinated macaques but not from naïve animals, and IL-23 induced greater expansion than the other Th17-related cytokines. Consistently, Mtb infection of macaques also enhanced the ability of IL-17/IL-22 or IL-23 to expand HMBPP-stimulated Vγ2Vδ2 T cells. When evaluating IL-23 signaling as a prototype, we found that HMBPP/IL-23-expanded Vγ2Vδ2 T cells from macaques infected with Mtb or vaccinated with BCG or Listeria ΔactA prfA*-ESAT6/Ag85B produced IL-17, IL-22, IL-2, and IFN-γ. Interestingly, HMBPP/IL-23-induced production of IFN-γ in turn facilitated IL-23-induced expansion of HMBPP-activated Vγ2Vδ2 T cells. Furthermore, HMBPP/IL-23-induced proliferation of Vγ2Vδ2 T cells appeared to require APC contact and involve the conventional and novel protein kinase C signaling pathways. These findings suggest that Th17-related cytokines can contribute to recall-like expansion and effector function of Ag-specific γδ T cells after infection or vaccination.
doi:10.1002/eji.201444635
PMCID: PMC4916493  PMID: 25141829
γδ T cells; IL-17/IL-22; IL-23; Phosphoantigen; Tuberculosis
10.  Design of Hydrogen Storage Alloys/Nanoporous Metals Hybrid Electrodes for Nickel-Metal Hydride Batteries 
Scientific Reports  2016;6:27601.
Nickel metal hydride (Ni-MH) batteries have demonstrated key technology advantages for applications in new-energy vehicles, which play an important role in reducing greenhouse gas emissions and the world’s dependence on fossil fuels. However, the poor high-rate dischargeability of the negative electrode materials—hydrogen storage alloys (HSAs) limits applications of Ni-MH batteries in high-power fields due to large polarization. Here we design a hybrid electrode by integrating HSAs with a current collector of three-dimensional bicontinuous nanoporous Ni. The electrode shows enhanced high-rate dischargeability with the capacity retention rate reaching 44.6% at a discharge current density of 3000 mA g−1, which is 2.4 times that of bare HSAs (18.8%). Such a unique hybrid architecture not only enhances charge transfer between nanoporous Ni and HSAs, but also facilitates rapid diffusion of hydrogen atoms in HSAs. The developed HSAs/nanoporous metals hybrid structures exhibit great potential to be candidates as electrodes in high-performance Ni-MH batteries towards applications in new-energy vehicles.
doi:10.1038/srep27601
PMCID: PMC4895169  PMID: 27270184
11.  Modulation of electronic properties from stacking orders and spin-orbit coupling for 3R-type MoS2 
Scientific Reports  2016;6:24140.
Two-dimensional crystals stacked by van der Waals coupling, such as twisted graphene and coupled graphene-BN layers with unusual phenomena have been a focus of research recently. As a typical representative, with the modulation of structural symmetry, stacking orders and spin-orbit coupling, transitional metal dichalcogenides have shown a lot of fascinating properties. Here we reveal the effect of stacking orders with spin-orbit coupling on the electronic properties of few-layer 3R-type MoS2 by first principles methods. We analyze the splitting of states at the top of valence band and the bottom of conduction band, following the change of stacking order. We find that regardless of stacking orders and layers’ number, the spin-up and spin-down channels are evidently separated and can be as a basis for the valley dependent spin polarization. With a model Hamiltonian about the layer’s coupling, the band splitting can be effectively analyzed by the coupling parameters. It is found that the stacking sequences, such as abc and abca, have the stronger nearest-neighbor coupling which imply the popular of periodic abc stacking sequence in natural growth of MoS2.
doi:10.1038/srep24140
PMCID: PMC4823783  PMID: 27053462
12.  Inhibition of Ebola and Marburg Virus Entry by G Protein-Coupled Receptor Antagonists 
Journal of Virology  2015;89(19):9932-9938.
ABSTRACT
Filoviruses, consisting of Ebola virus (EBOV) and Marburg virus (MARV), are among the most lethal infectious threats to mankind. Infections by these viruses can cause severe hemorrhagic fevers in humans and nonhuman primates with high mortality rates. Since there is currently no vaccine or antiviral therapy approved for humans, there is an urgent need to develop prophylactic and therapeutic options for use during filoviral outbreaks and bioterrorist attacks. One of the ideal targets against filoviral infection and diseases is at the entry step, which is mediated by the filoviral glycoprotein (GP). In this report, we screened a chemical library of small molecules and identified numerous inhibitors, which are known G protein-coupled receptor (GPCR) antagonists targeting different GPCRs, including histamine receptors, 5-HT (serotonin) receptors, muscarinic acetylcholine receptor, and adrenergic receptor. These inhibitors can effectively block replication of both infectious EBOV and MARV, indicating a broad antiviral activity of the GPCR antagonists. The time-of-addition experiment and microscopic studies suggest that GPCR antagonists block filoviral entry at a step following the initial attachment but prior to viral/cell membrane fusion. These results strongly suggest that GPCRs play a critical role in filoviral entry and GPCR antagonists can be developed as an effective anti-EBOV/MARV therapy.
IMPORTANCE Infection of Ebola virus and Marburg virus can cause severe illness in humans with a high mortality rate, and currently there is no FDA-approved vaccine or therapeutic treatment available. The 2013-2015 epidemic in West Africa underscores a lack of our understanding in the infection and pathogenesis of these viruses and the urgency of drug discovery and development. In this study, we have identified numerous inhibitors that are known G protein-coupled receptor (GPCR) antagonists targeting different GPCRs. These inhibitors can effectively block replication of both infectious EBOV and MARV, indicating a broad antiviral activity of the GPCR antagonists. Our results strongly suggest that GPCRs play a critical role in filoviral entry and GPCR antagonists can be developed as an effective anti-EBOV/MARV therapy.
doi:10.1128/JVI.01337-15
PMCID: PMC4577884  PMID: 26202243
13.  Hierarchy Low CD4+/CD8+ T-Cell Counts and IFN-γ Responses in HIV-1+ Individuals Correlate with Active TB and/or M.tb Co-Infection 
PLoS ONE  2016;11(3):e0150941.
Objective
Detailed studies of correlation between HIV-M.tb co-infection and hierarchy declines of CD8+/CD4+ T-cell counts and IFN-γ responses have not been done. We conducted case-control studies to address this issue.
Methods
164 HIV-1-infected individuals comprised of HIV-1+ATB, HIV-1+LTB and HIV-1+TB- groups were evaluated. Immune phenotyping and complete blood count (CBC) were employed to measure CD4+ and CD8+ T-cell counts; T.SPOT.TB and intracellular cytokine staining (ICS) were utilized to detect ESAT6, CFP10 or PPD-specific IFN-γ responses.
Results
There were significant differences in median CD4+ T-cell counts between HIV-1+ATB (164/μL), HIV-1+LTB (447/μL) and HIV-1+TB- (329/μL) groups. Hierarchy low CD4+ T-cell counts (<200/μL, 200-500/μL, >500/μL) were correlated significantly with active TB but not M.tb co-infection. Interestingly, hierarchy low CD8+ T-cell counts were not only associated significantly with active TB but also with M.tb co-infection (P<0.001). Immunologically, HIV-1+ATB group showed significantly lower numbers of ESAT-6-/CFP-10-specific IFN-γ+ T cells than HIV-1+LTB group. Consistently, PPD-specific IFN-γ+CD4+/CD8+ T effector cells in HIV-1+ATB group were significantly lower than those in HIV-1+LTB group (P<0.001).
Conclusions
Hierarchy low CD8+ T-cell counts and effector function in HIV-1-infected individuals are correlated with both M.tb co-infection and active TB. Hierarchy low CD4+ T-cell counts and Th1 effector function in HIV-1+ individuals are associated with increased frequencies of active TB, but not M.tb co-infection.
doi:10.1371/journal.pone.0150941
PMCID: PMC4784913  PMID: 26959228
14.  Necroptosis in Niemann–Pick disease, type C1: a potential therapeutic target 
Cell Death & Disease  2016;7(3):e2147-.
Niemann–Pick disease, type C1 (NPC1) is a neurodegenerative, lysosomal storage disorder due to mutation of the NPC1 gene. The NPC1 phenotype is characterized by progressive neuronal dysfunction, including cerebellar ataxia and dementia. There is histological evidence of neuroinflammation and progressive neuronal loss, with cerebellar Purkinje cells particularly vulnerable to loss of NPC1 function. Necroptosis was evaluated as a mechanism of neuronal loss. Receptor-interacting protein kinase 1 (RIP1) and RIP3 are key components of the necrosomal complex that regulates necroptotic cell death. We report increased expression of RIP1 and RIP3 in NPC1 fibroblasts, NPC1 iPS cell-derived neuronal precursors, and in cerebellar tissue from both NPC1 mice and patients. Our data suggest a positive correlation between NPC1 neurological disease severity and assembly of the necrosome complex. Furthermore, we demonstrate that pharmacological inhibition of RIP1 decreases cell death both in vitro and in vivo. Treatment of Npc1-mutant mice with necrostatin-1, an allosteric inhibitor of RIP1, significantly delayed cerebellar Purkinje cell loss, progression of neurological symptoms, and death. Collectively, our data identified necroptosis as a key component of the molecular network that contributes to neuronal loss in NPC1 and establish that inhibition of necroptosis is a potential therapeutic intervention.
doi:10.1038/cddis.2016.16
PMCID: PMC4823930  PMID: 26986514
15.  Elevated serum IL-35 and increased expression of IL-35-p35 or -EBI3 in CD4+CD25+ T cells in patients with active tuberculosis 
Despite the recent appreciation of interleukin 35 (IL-35) function in inflammatory diseases, little is known for IL-35 response in patients with active tuberculosis (ATB). In the current study, we demonstrated that ATB patients exhibited increases in serum IL-35 and in mRNA expression of both subunits of IL-35 (p35 and EBI3) in white blood cells and peripheral blood mononuclear cells. Consistently, anti-TB drug treatment led to reduction in serum IL-35 level and p35 or EBI3 expression. TB infection was associated with expression of p35 or EBI3 protein in CD4+ but not CD8+ T cells. Most p35+CD4+ T cells and EBI3+CD4+ T cells expressed Treg-associated marker CD25. Our findings may be important in understanding immune pathogenesis of TB. IL-35 in the blood may potentially serve as a biomarker for immune status and prognosis in TB.
PMCID: PMC4846911  PMID: 27158354
Human active pulmonary tuberculosis; interleukin-35; p35; EBI3; CD4+CD25+ T cells
16.  The influence of inhaled multi-walled carbon nanotubes on the autonomic nervous system 
Background
Heart rate and cardiovascular function are regulated by the autonomic nervous system. Heart rate variability (HRV) as a marker reflects the activity of autonomic nervous system. The prognostic significance of HRV in cardiovascular disease has been reported in clinical and epidemiological studies. The present study focused on the influence of inhaled multi-walled carbon nanotubes (MWCNTs) on autonomic nervous system by HRV analysis.
Methods
Male Sprague–Dawley rats were pre-implanted with a telemetry device and kept in the individual cages for recovery. At week four after device implantation, rats were exposed to MWCNTs for 5 h at a concentration of 5 mg/m3. The real-time EKGs were recorded by a telemetry system at pre-exposure, during exposure, 1 day and 7 days post-exposure. HRV was measured by root mean square of successive differences (RMSSD); the standard deviation of inter-beat (RR) interval (SDNN); the percentage of successive RR interval differences greater than 5 ms (pNN5) and 10 ms (pNN10); low frequency (LF) and high frequency (HF).
Results
Exposure to MWCNTs increased the percentage of differences between adjacent R-R intervals over 10 ms (pNN10) (p < 0.01), RMSSD (p < 0.01), LF (p < 0.05) and HF (p < 0.01).
Conclusions
Inhalation of MWCNTs significantly alters the balance between sympathetic and parasympathetic nervous system. Whether such transient alterations in autonomic nervous performance would alter cardiovascular function and raise the risk of cardiovascular events in people with pre-existing cardiovascular conditions warrants further study.
doi:10.1186/s12989-016-0119-7
PMCID: PMC4750189  PMID: 26864021
Inhalation; Multi-walled carbon nanotubes; Autonomic nervous system; Heart rate variability
18.  Learning To Fold Proteins Using Energy Landscape Theory 
Israel journal of chemistry  2014;54(8-9):1311-1337.
This review is a tutorial for scientists interested in the problem of protein structure prediction, particularly those interested in using coarse-grained molecular dynamics models that are optimized using lessons learned from the energy landscape theory of protein folding. We also present a review of the results of the AMH/AMC/AMW/AWSEM family of coarse-grained molecular dynamics protein folding models to illustrate the points covered in the first part of the article. Accurate coarse-grained structure prediction models can be used to investigate a wide range of conceptual and mechanistic issues outside of protein structure prediction; specifically, the paper concludes by reviewing how AWSEM has in recent years been able to elucidate questions related to the unusual kinetic behavior of artificially designed proteins, multidomain protein misfolding, and the initial stages of protein aggregation.
doi:10.1002/ijch.201300145
PMCID: PMC4189132  PMID: 25308991
19.  A weighted and integrated drug-target interactome: drug repurposing for schizophrenia as a use case 
BMC Systems Biology  2015;9(Suppl 4):S2.
Background
Computational pharmacology can uniquely address some issues in the process of drug development by providing a macroscopic view and a deeper understanding of drug action. Specifically, network-assisted approach is promising for the inference of drug repurposing. However, the drug-target associations coming from different sources and various assays have much noise, leading to an inflation of the inference errors. To reduce the inference errors, it is necessary and critical to create a comprehensive and weighted data set of drug-target associations.
Results
In this study, we created a weighted and integrated drug-target interactome (WinDTome) to provide a comprehensive resource of drug-target associations for computational pharmacology. We first collected drug-target interactions from six commonly used drug-target centered data sources including DrugBank, KEGG, TTD, MATADOR, PDSP Ki Database, and BindingDB. Then, we employed the record linkage method to normalize drugs and targets to the unique identifiers by utilizing the public data sources including PubChem, Entrez Gene, and UniProt. To assess the reliability of the drug-target associations, we assigned two scores (Score_S and Score_R) to each drug-target association based on their data sources and publication references. Consequently, the WinDTome contains 546,196 drug-target associations among 303,018 compounds and 4,113 genes. To assess the application of the WinDTome, we designed a network-based approach for drug repurposing using mental disorder schizophrenia (SCZ) as a case. Starting from 41 known SCZ drugs and their targets, we inferred a total of 264 potential SCZ drugs through the associations of drug-target with Score_S higher than two in WinDTome and human protein-protein interactions. Among the 264 SCZ-related drugs, 39 drugs have been investigated in clinical trials for SCZ treatment and 74 drugs for the treatment of other mental disorders, respectively. Compared with the results using other Score_S cutoff values, single data source, or the data from STITCH, the inference of 264 SCZ-related drugs had the highest performance.
Conclusions
The WinDTome generated in this study contains comprehensive drug-target associations with confidence scores. Its application to the SCZ drug repurposing demonstrated that the WinDTome is promising to serve as a useful resource for drug repurposing.
doi:10.1186/1752-0509-9-S4-S2
PMCID: PMC4474536  PMID: 26100720
20.  Cu4 Cluster Doped Monolayer MoS2 for CO Oxidation 
Scientific Reports  2015;5:11230.
The catalytic oxidation of CO molecule on a thermodynamically stable Cu4 cluster doped MoS2 monolayer is investigated by density functional theory (DFT) where the reaction proceeds in a new formation order of COOOCO* (O2* + 2CO* → COOOCO*), OCO* (COOOCO* → CO2 + OCO*), and CO2 (OCO* → CO2) desorption with the corresponding reaction barrier values of 0.220 eV, 0.370 eV and 0.119 eV, respectively. Therein, the rate-determining step is the second one. This low barrier indicates high activity of this system where CO oxidation could be realized at room temperature (even lower). As a result, the Cu4 doped MoS2 could be a candidate for CO oxidation with lower cost and higher activity without poisoning and corrosion problems.
doi:10.1038/srep11230
PMCID: PMC4459236  PMID: 26052674
21.  A Powerful Association Test of Multiple Genetic Variants Using a Random-Effects Model 
Statistics in medicine  2013;33(11):1816-1827.
There is an emerging interest in sequencing-based association studies of multiple rare variants. Most association tests suggested in the literature involve collapsing rare variants with or without weighting. Recently, a variance-component score test, SKAT, was proposed to address the limitations of collapsing method. Although SKAT was shown to outperform most of the alternative tests, its applications and power might be restricted and influenced by missing genotypes. In this paper, we suggest a new method based on testing whether the fraction of causal variants in a region is zero. The new association test, TREM, is derived from a random-effects model, allows for missing genotypes and the choice of weighting function is not required when common and rare variants are analyzed simultaneously. We performed simulations to study the type I error rates and power of four competing tests under various conditions on the sample size, genotype missing rate, variant frequency, effect directionality, and the number of non-causal rare variant and/or causal common variant. The simulation results showed that TREM was a valid test and less sensitive to the inclusion of non-causal rare variants and/or low effect common variants, or to the presence of missing genotypes. When the effects were more consistent in the same direction, TREM also had better power performance. Finally, an application to the Shanghai breast cancer study showed that rare causal variants at the FGFR2 gene were detected by TREM and SKAT, but TREM produced more consistent results for different sets of rare and common variants.
doi:10.1002/sim.6068
PMCID: PMC4008649  PMID: 24338936
association test; random-effects model; rare variant; sequencing-based study
22.  Using Ontology Fingerprints to disambiguate gene name entities in the biomedical literature 
Ambiguous gene names in the biomedical literature are a barrier to accurate information extraction. To overcome this hurdle, we generated Ontology Fingerprints for selected genes that are relevant for personalized cancer therapy. These Ontology Fingerprints were used to evaluate the association between genes and biomedical literature to disambiguate gene names. We obtained 93.6% precision for the test gene set and 80.4% for the area under a receiver-operating characteristics curve for gene and article association. The core algorithm was implemented using a graphics processing unit-based MapReduce framework to handle big data and to improve performance. We conclude that Ontology Fingerprints can help disambiguate gene names mentioned in text and analyse the association between genes and articles.
Database URL: http://www.ontologyfingerprint.org
doi:10.1093/database/bav034
PMCID: PMC4390608  PMID: 25858285
23.  Colorectal cancer drug target prediction using ontology-based inference and network analysis 
Identification of novel drug targets is a critical step in drug development. Many recent studies have produced multiple types of data, which provides an opportunity to mine the relationships among them to predict drug targets. In this study, we present a novel integrative approach that combines ontology reasoning with network-assisted gene ranking to predict new drug targets. We utilized colorectal cancer (CRC) as a proof-of-concept use case to illustrate the approach. Starting from FDA-approved CRC drugs and the relationships among disease, drug, gene, pathway, and SNP in an ontology representing PharmGKB data, we inferred 113 potential CRC drug targets. We further prioritized these genes based on their relationships with CRC disease genes in the context of human protein–protein interaction networks. Thus, among the 113 potential drug targets, 15 were selected as the promising drug targets, including some genes that are supported by previous studies. Among them, EGFR, TOP1 and VEGFA are known targets of FDA-approved drugs. Additionally, CCND1 (cyclin D1), and PTGS2 (prostaglandin-endoperoxide synthase 2) have reported to be relevant to CRC or as potential drug targets based on the literature search. These results indicate that our approach is promising for drug target prediction for CRC treatment, which might be useful for other cancer therapeutics.
doi:10.1093/database/bav015
PMCID: PMC4375358  PMID: 25818893
24.  A comparative study of disease genes and drug targets in the human protein interactome 
BMC Bioinformatics  2015;16(Suppl 5):S1.
Background
Disease genes cause or contribute genetically to the development of the most complex diseases. Drugs are the major approaches to treat the complex disease through interacting with their targets. Thus, drug targets are critical for treatment efficacy. However, the interrelationship between the disease genes and drug targets is not clear.
Results
In this study, we comprehensively compared the network properties of disease genes and drug targets for five major disease categories (cancer, cardiovascular disease, immune system disease, metabolic disease, and nervous system disease). We first collected disease genes from genome-wide association studies (GWAS) for five disease categories and collected their corresponding drugs based on drugs' Anatomical Therapeutic Chemical (ATC) classification. Then, we obtained the drug targets for these five different disease categories. We found that, though the intersections between disease genes and drug targets were small, disease genes were significantly enriched in targets compared to their enrichment in human protein-coding genes. We further compared network properties of the proteins encoded by disease genes and drug targets in human protein-protein interaction networks (interactome). The results showed that the drug targets tended to have higher degree, higher betweenness, and lower clustering coefficient in cancer Furthermore, we observed a clear fraction increase of disease proteins or drug targets in the near neighborhood compared with the randomized genes.
Conclusions
The study presents the first comprehensive comparison of the disease genes and drug targets in the context of interactome. The results provide some foundational network characteristics for further designing computational strategies to predict novel drug targets and drug repurposing.
doi:10.1186/1471-2105-16-S5-S1
PMCID: PMC4402590  PMID: 25861037
25.  CD4+ T cells are required to contain early extrathoracic TB dissemination and sustain multi-effector functions of CD8+ T and CD3− lymphocytes 
The possibility that CD4+ T cells can act as “innate-like” cells to contain very-early M. tuberculosis (Mtb) dissemination and function as master helpers to sustain multiple effector functions of CD8+ T cells and CD3-negative lymphocytes during development of adaptive immunity against primary tuberculosis(TB) has not been demonstrated. We showed that pulmonary Mtb infection of CD4-depleted macaques surprisingly led to very-early extrathoracic Mtb dissemination, whereas CD4 deficiency clearly resulted in rapid TB progression. CD4 depletion during Mtb infection revealed the ability of CD8+ T cells to compensate and rapidly differentiate to Th17-like/Th1-like, and cytotoxic-like effectors, but these effector functions were subsequently unsustainable due to CD4 deficiency. While CD3-negative non-T lymphocytes in presence of CD4+ T cells developed predominant Th22-like and NK-like (perforin production) responses to Mtb infection, CD4 depletion abrogated these Th22-/NK-like effector functions and favored IL-17 production by CD3-negative lymphocytes. CD4-depleted macaques exhibited no or few pulmonary T effector cells constitutively producing IFN-γ, TNFα, IL-17, IL-22, and perforin at the endpoint of more severe TB, but presented pulmonary IL-4+ T effectors. TB granulomas in CD4-depleted macaques contained fewer IL-22+ and perforin+ cells despite presence of IL-17+ and IL-4+ cells. These results implicate previously-unknown “innate-like” ability of CD4+ T cells to contain extrathoracic Mtb dissemination at very early stage. Data also suggest that CD4+ T cells are required to sustain multiple effector functions of CD8+ T cells and CD3-negative lymphocytes and to prevent rapid TB progression during Mtb infection of nonhuman primates.
doi:10.4049/jimmunol.1301373
PMCID: PMC4104690  PMID: 24489088
CD4+ T cell depletion; T effector cells; Mycobacterium tuberculosis; Primates; tuberculosis

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