PMCC PMCC

Search tips
Search criteria

Advanced
Results 1-25 (98)
 

Clipboard (0)
None

Select a Filter Below

Journals
more »
Year of Publication
1.  Social Trust Prediction Using Heterogeneous Networks 
Along with increasing popularity of social websites, online users rely more on the trustworthiness information to make decisions, extract and filter information, and tag and build connections with other users. However, such social network data often suffer from severe data sparsity and are not able to provide users with enough information. Therefore, trust prediction has emerged as an important topic in social network research. Traditional approaches are primarily based on exploring trust graph topology itself. However, research in sociology and our life experience suggest that people who are in the same social circle often exhibit similar behaviors and tastes. To take advantage of the ancillary information for trust prediction, the challenge then becomes what to transfer and how to transfer. In this article, we address this problem by aggregating heterogeneous social networks and propose a novel joint social networks mining (JSNM) method. Our new joint learning model explores the user-group-level similarity between correlated graphs and simultaneously learns the individual graph structure; therefore, the shared structures and patterns from multiple social networks can be utilized to enhance the prediction tasks. As a result, we not only improve the trust prediction in the target graph but also facilitate other information retrieval tasks in the auxiliary graphs. To optimize the proposed objective function, we use the alternative technique to break down the objective function into several manageable subproblems. We further introduce the auxiliary function to solve the optimization problems with rigorously proved convergence. The extensive experiments have been conducted on both synthetic and real- world data. All empirical results demonstrate the effectiveness of our method.
doi:10.1145/2541268.2541270
PMCID: PMC3983696
Algorithms; Experimentation; Trust prediction; social network; transfer learning; nonnegative matrix factorization
2.  Approximate Algorithms for Computing Spatial Distance Histograms with Accuracy Guarantees 
Particle simulation has become an important research tool in many scientific and engineering fields. Data generated by such simulations impose great challenges to database storage and query processing. One of the queries against particle simulation data, the spatial distance histogram (SDH) query, is the building block of many high-level analytics, and requires quadratic time to compute using a straightforward algorithm. Previous work has developed efficient algorithms that compute exact SDHs. While beating the naive solution, such algorithms are still not practical in processing SDH queries against large-scale simulation data. In this paper, we take a different path to tackle this problem by focusing on approximate algorithms with provable error bounds. We first present a solution derived from the aforementioned exact SDH algorithm, and this solution has running time that is unrelated to the system size N. We also develop a mathematical model to analyze the mechanism that leads to errors in the basic approximate algorithm. Our model provides insights on how the algorithm can be improved to achieve higher accuracy and efficiency. Such insights give rise to a new approximate algorithm with improved time/accuracy tradeoff. Experimental results confirm our analysis.
doi:10.1109/TKDE.2012.149
PMCID: PMC3969837
Molecular simulation; spatial distance histogram; quadtree; scientific databases
3.  Preparation of (+)-Trans-Isoalliin and Its Isomers by Chemical Synthesis and RP-HPLC Resolution 
Naturally occurring (+)-trans-isoalliin, (RCRS)-(+)-trans-S-1-propenyl-L-cysteine sulfoxide, is a major cysteine sulfoxide in onion. The importance of producing it synthetically to support further research is very well recognized. The (+)-trans-isoalliin is prepared by chemical synthesis and reversed-phase (RP)-HPLC. First, S-2-propenyl-L-cysteine (deoxyalliin) is formed from L-cysteine and allyl bromide, which is then isomerized to S-1-propenyl-L-cysteine (deoxyisoalliin) by a base-catalyzed reaction. A mixture of cis and trans forms of deoxyisoalliin is formed and separated by RP-HPLC. Oxidation of the trans form of deoxyisoalliin by H2O2 produces a mixture of (−)- and (+)-trans-isoalliin. Finally, RP-HPLC is used successfully in separating (−)- and (+)-trans-isoalliin, and hence, (+)-trans-isoalliin is synthesized for the first time in this study. In addition, the (±) diastereomers of cis-isoalliin are also separated and purified by RP-HPLC.
doi:10.7171/jbt.14-2502-002
PMCID: PMC3970760
Allium cepa; 1-propenyl-L-cysteine sulfoxide; organosulfur compounds
4.  A New Sparse Simplex Model for Brain Anatomical and Genetic Network Analysis 
The Allen Brain Atlas (ABA) database provides comprehensive 3D atlas of gene expression in the adult mouse brain for studying the spatial expression patterns in the mammalian central nervous system. It is computationally challenging to construct the accurate anatomical and genetic networks using the ABA 4D data. In this paper, we propose a novel sparse simplex model to accurately construct the brain anatomical and genetic networks, which are important to reveal the brain spatial expression patterns. Our new approach addresses the shift-invariant and parameter tuning problems, which are notorious in the existing network analysis methods, such that the proposed model is more suitable for solving practical biomedical problems. We validate our new model using the 4D ABA data, and the network construction results show the superior performance of the proposed sparse simplex model.
PMCID: PMC3939613  PMID: 24579193
5.  Hendra Virus Vaccine, a One Health Approach to Protecting Horse, Human, and Environmental Health 
Emerging Infectious Diseases  2014;20(3):372-379.
In recent years, the emergence of several highly pathogenic zoonotic diseases in humans has led to a renewed emphasis on the interconnectedness of human, animal, and environmental health, otherwise known as One Health. For example, Hendra virus (HeV), a zoonotic paramyxovirus, was discovered in 1994, and since then, infections have occurred in 7 humans, each of whom had a strong epidemiologic link to similarly affected horses. As a consequence of these outbreaks, eradication of bat populations was discussed, despite their crucial environmental roles in pollination and reduction of the insect population. We describe the development and evaluation of a vaccine for horses with the potential for breaking the chain of HeV transmission from bats to horses to humans, thereby protecting horse, human, and environmental health. The HeV vaccine for horses is a key example of a One Health approach to the control of human disease.
doi:10.3201/eid2003.131159
PMCID: PMC3944873  PMID: 24572697
Hendra virus; HeV; vaccine; HeV vaccine; One Health; G glycoprotein; zoonoses; viruses; zoonotic paramyxovirus; flying foxes; horses; humans; Pteropus bats; Australia; environment; vaccination
6.  Establishing a rabbit model of malignant esophagostenosis using the endoscopic implantation technique for studies on stent innovation 
Background
Stents are recommended in patients with dysphagia caused by esophageal stricture, but an ideal stent does not currently exist. Thus, studies on new esophageal stents are necessary, and suitable animal models are desperately needed for these studies. The aim of this study was to establish a model of malignant esophageal stricture in rabbit for studies on stent innovation.
Methods
A total of 38 New Zealand white rabbits were used in this study. Using the endoscopic submucosal injection technique, VX2 fragments were inoculated into the submucosal layer of the rabbit thoracic esophagus, and an endoscopic follow-up was subsequently performed to observe the tumor development and progression. The self-expandable metal stents were randomly deployed in rabbits with severe esophageal stricture to investigate the safety and feasibility of the animal models for stenting.
Results
An endoscopic implantation procedure for VX2 tumors was completed in 34/38 rabbits, and tumor development was confirmed in 30/34 animals. The success rate of the endoscopic implantation and tumor development were 89.4% (95% CI, 79.6% to 99.2%) and 88.2% (95% CI, 76.9% to 99.5%) respectively. During the endoscopic follow-up period, severe esophageal stricture occurred in 22/30 rabbits with a rate of 73.3% (95% CI, 57.5% to 89.1%), and 12/22 models received stent placement. During and after stent implantation, no severe stent-related complication or mortality occurred in the animal models. The rabbits that received stent placement survived longer than those without stent implantation (the mean survival time: 53.9 days versus 40.3 days, P = 0.016).
Conclusion
The endoscopic method is a safe and effective method for establishing a malignant esophagostenosis model in rabbits. This model can simulate the human body environment for stent deployment and is an excellent tool for the study of stent innovation for the treatment of esophageal cancer.
doi:10.1186/1479-5876-12-40
PMCID: PMC3922539  PMID: 24507720
Esophageal squamous cell carcinoma; Animal model; Endoscopic surgical procedure; Rabbit; Stent therapy
7.  Nur77 Decreases Atherosclerosis Progression in apoE−/− Mice Fed a High-Fat/High-Cholesterol Diet 
PLoS ONE  2014;9(1):e87313.
Rationale
It is clear that lipid disorder and inflammation are associated with cardiovascular diseases and underlying atherosclerosis. Nur77 has been shown to be involved in inflammatory response and lipid metabolism.
Objective
Here, we explored the role of Nur77 in atherosclerotic plaque progression in apoE−/− mice fed a high-fat/high cholesterol diet.
Methods and Results
The Nur77 gene, a nuclear hormone receptor, was highly induced by treatment with Cytosporone B (Csn-B, specific Nur77 agonist), recombinant plasmid over-expressing Nur77 (pcDNA-Nur77), while inhibited by treatment with siRNAs against Nur77 (si-Nur77) in THP-1 macrophage-derived foam cells, HepG2 cells and Caco-2 cells, respectively. In addition, the expression of Nur77 was highly induced by Nur77 agonist Csn-B, lentivirus encoding Nur77 (LV-Nur77), while silenced by lentivirus encoding siRNA against Nur77 (si-Nur77) in apoE−/− mice fed a high-fat/high cholesterol diet, respectively. We found that increased expression of Nur77 reduced macrophage-derived foam cells formation and hepatic lipid deposition, downregulated gene levels of inflammatory molecules, adhesion molecules and intestinal lipid absorption, and decreases atherosclerotic plaque formation.
Conclusion
These observations provide direct evidence that Nur77 is an important nuclear hormone receptor in regulation of atherosclerotic plaque formation and thus represents a promising target for the treatment of atherosclerosis.
doi:10.1371/journal.pone.0087313
PMCID: PMC3909091  PMID: 24498071
8.  Endoscopic mucosal resection with circumferential incision for treatment of rectal carcinoid tumours 
Background
Endoscopic mucosal resection (EMR) is simple and quick and has low complication rates. However, the disadvantage of local recurrence or remnant rate limits the use of this technique. We aimed to analyse the outcomes of conventional EMR and EMR with circumferential incision (CIEMR), a simplified modification of EMR, in the endoscopic treatment of rectal carcinoid tumours.
Methods
A total of 59 consecutive patients with rectal carcinoid tumours without regional lymph node enlargement confirmed by endoscopic ultrasonography were included in the study. These patients underwent endoscopic treatment from January 2009 to September 2011 and were randomly designated into CIEMR (n = 31) or EMR group (n = 28). En bloc resection rate, pathological complete resection rate, procedure time, complications and follow-up outcomes were analysed.
Results
The en bloc resection rate was not significantly different between the CIEMR and EMR groups (100% versus 96.55%, P > 0.05). The pathological complete resection rate was higher in the CIEMR group than in the EMR group (96.7% versus 82.14%, P < 0.05). The overall complication rate, delayed bleeding and procedure time were not significantly different between the two groups. No recurrence was observed in either the EMR or CIEMR group.
Conclusions
CIEMR optimises the procedure of EMR and simplifies the technique of endoscopic submucosal dissection; thus, it has a better histologically complete resection rate and more acceptable complication rate than EMR. Thus, CIEMR may be preferable to conventional EMR for resection of rectal carcinoid tumours less than 15 mm.
doi:10.1186/1477-7819-12-23
PMCID: PMC3912495  PMID: 24472342
CIEMR; Endoscopic mucosal resection (EMR); Rectal carcinoid tumours
9.  Comparison of Endoscopic Submuscosal Implantation vs. Surgical Intramuscular Implantation of VX2 Fragments for Establishing a Rabbit Esophageal Tumor Model for Mimicking Human Esophageal Squamous Carcinoma 
PLoS ONE  2014;9(1):e85326.
Purpose
This study was undertaken to establish a rabbit esophageal tumor model for mimicking human esophageal squamous carcinoma (ESC) by endoscopic and surgical implantation of VX2 tumors.
Methods
Fragments of a VX2 tumour were endoscopically implanted in the submucosal layer of the thoracic esophagus of 32 New Zealand white rabbits, while 34 animals received surgical implantation into the muscular layer. Then, the animals were studied endoscopically and pathologically. The safety and efficiency of the two methods and the pathological features of the animal models were analyzed.
Results
Both the endoscopic and the surgical method had a relatively high success rate of tumor implantation [93.7% (30/32) vs. 97.1% (33/34)] and tumor growth [86.7% (26/30) vs. 81.8% (27/33)], and the variation in the results was not statistically significant (P>0.05). Compared with those produced by the surgical method, the models produced by the endoscopic method had a higher rate of severe esophageal stricture [61.5% (16/26) vs. 29.6% (8/27)] and of intra-luminal tumor growth [73.1% (19/26) vs. 37.0% (10/27)], and had a lower rate of tumor invasion of adjacent organs [53.8% (14/26) vs. 81.5% (22/27)]; all of these results were statistically significant (P<0.05). However, the difference in the survival time and the rates of tumor regional/distant metastasis [38.5% (10/26) vs. 51.8% (14/27)] between the two methods were not statistically significant (P>0.05).
Conclusion
The endoscopic and surgical methods are both safe and effective for establishment of VX2 tumors in the rabbit esophagus. The models produced by the two methods have different pathologic features mimicking that of human ESC. We recommend the models for studies on surgical procedures and minimally invasive treatments.
doi:10.1371/journal.pone.0085326
PMCID: PMC3901654  PMID: 24475043
10.  Porphyromonas gingivalis Infection Reduces Regulatory T Cells in Infected Atherosclerosis Patients 
PLoS ONE  2014;9(1):e86599.
Increasing evidence has shown periodontal pathogen Porphyromonas gingivalis (P.gingivalis) infection contributes to atherosclerosis (AS) progression. P.gingivalis fimbriae act as an important virulence factor in AS. Regulatory T cells (Tregs) may play a crucial role in autoimmune response during this process. However, whether P.gingivalis infection is associated with Tregs dysregulation during AS is still unknown and the prevalence of different P.gingivalis FimA genotypes during this process is unclear. Here we analyzed the distribution of Tregs and in P.gingivalis-infected atherosclerotic patients to reveal the relationship between P.gingivalis infection and Tregs reduction/dysfunction and to elucidate their role in periodontitis-AS interaction. FimA genotype was also examined to determine the prevalence of fimbriae. Our results showed that P.gingivalis infection reduced Tregs in atherosclerotic patients compared with non-atherosclerotic patients and health controls. Concentration of TGF-β1, which plays an important role in the development of Tregs, also decreased in P.gingivalis infected patients. Furthermore, type II FimA seems to show higher prevalence than the other five detected types. The population of Tregs further decreased in patients with type II FimA compared with the other types. P.gingivlias FimA genotype II was the dominant type associated with decreased Treg population. These results indicate that P.gingivalis infection may be associated with Tregs dysregulation in AS; type II FimA may be a predominant genotype in this process.
doi:10.1371/journal.pone.0086599
PMCID: PMC3900568  PMID: 24466164
11.  The BDNF/TrkB Signaling Pathway Is Involved in Heat Hyperalgesia Mediated by Cdk5 in Rats 
PLoS ONE  2014;9(1):e85536.
Background
Cyclin-dependent kinase 5 (Cdk5) has been shown to play an important role in mediating inflammation-induced heat hyperalgesia. However, the underlying mechanism remains unclear. The aim of this study was to determine whether roscovitine, an inhibitor of Cdk5, could reverse the heat hyperalgesia induced by peripheral injection of complete Freund's adjuvant (CFA) via the brain-derived neurotrophic factor (BDNF)-tyrosine kinase B (TrkB) signaling pathway in the dorsal horn of the spinal cord in rats.
Results
Heat hyperalgesia induced by peripheral injection of CFA was significantly reversed by roscovitine, TrkB-IgG, and the TrkB inhibitor K252a, respectively. Furthermore, BDNF was significantly increased from 0.5 h to 24 h after CFA injection in the spinal cord dorsal horn. Intrathecal adminstration of the Cdk5 inhibitor roscovitine had no obvious effects on BDNF levels. Increased TrkB protein level was significantly reversed by roscovitine between 0.5 h and 6 h after CFA injection. Cdk5 and TrkB co-immunoprecipitation results suggested Cdk5 mediates the heat hyperalgesia induced by CFA injection by binding with TrkB, and the binding between Cdk5 and TrkB was markedly blocked by intrathecal adminstration of roscovitine.
Conclusion
Our data suggested that the BDNF-TrkB signaling pathway was involved in CFA-induced heat hyperalgesia mediated by Cdk5. Roscovitine reversed the heat hyperalgesia induced by peripheral injection of CFA by blocking BDNF/TrkB signaling pathway, suggesting that severing the close crosstalk between Cdk5 and the BDNF/TrkB signaling cascade may present a potential target for anti-inflammatory pain.
doi:10.1371/journal.pone.0085536
PMCID: PMC3897472  PMID: 24465591
12.  Retinal Nerve Fiber Layer Thickness Changes in Parkinson Disease: A Meta-Analysis 
PLoS ONE  2014;9(1):e85718.
Background
Parkinson disease (PD) is a neurodegenerative process that leads to a selective loss of dopaminergic neurons, mainly in the basal ganglia of the brain. Numerous studies have analyzed the ability of optical coherence tomography (OCT) to detect retinal nerve fiber layer (RNFL) thickness abnormalities and changes in PD, but the results have not always been consistent. Therefore, we carried out a meta-analysis to evaluate the RNFL thickness measured with OCT in PD.
Methods and Findings
Case-control studies were selected through an electronic search of the Cochrane Controlled Trials Register, PUBMED and EMBASE. For the continuous outcomes, we calculated the weighted mean difference (WMD) and 95% confidence interval (CI). The statistical analysis was performed by RevMan 5.0 software. Thirteen case-control studies were included in the present meta-analysis, containing a total of 644 eyes in PD patients and 604 eyes in healthy controls. The results of our study showed that there was a significant reduction in average RNFL thickness in patients with PD compared to healthy controls (WMD = −5.76, 95% CI: −8.99 to −2.53, P = 0.0005). Additionally, differences of RNFL thickness in superior quadrant (WMD = −4.44, 95% CI: −6.93 to −1.94, P = 0.0005), inferior quadrant (WMD = −7.56, 95% CI: −11.33 to −3.78, P<0.0001), nasal quadrant (WMD = −3.12, 95% CI: −5.63 to −0.61, P = 0.01) and temporal quadrant (WMD = −4.63, 95% CI: −7.20 to −2.06, P = 0.0004) were all significant between the two groups.
Conclusion
In view of these results and the noninvasive nature of OCT technology, we surmise that OCT could be a useful tool for evaluating the progression of the Parkinson disease.
Trial Registration
ClinicalTrials.gov NCT01928212
doi:10.1371/journal.pone.0085718
PMCID: PMC3897496  PMID: 24465663
13.  A comprehensive microRNA expression profile of the backfat tissue from castrated and intact full-sib pair male pigs 
BMC Genomics  2014;15:47.
Background
It is widely known that castration has a significant effect on the accumulation of adipose tissue. microRNAs (miRNAs) are known to be involved in fat deposition and to be regulated by the androgen-induced androgen receptor (AR). However, there is little understanding of the relationship between miRNAs and fat deposition after castration. In this study, the high-throughput SOLiD sequencing approach was used to identify and characterize miRNA expression in backfat from intact and castrated full-sib male 23-week-old pigs. The patterns of adipogenesis and fat deposition were compared between castrated and intact male pigs.
Results
A total of 366 unique miRNA genes were identified, comprising 174 known pre-miRNAs and 192 novel pre-miRNAs. One hundred and sixty-seven pre-miRNAs were common to both castrated (F3) and intact (F4) male pig small RNA libraries. The novel pre-miRNAs encoded 153 miRNAs/miRNA*s and 141 miRNAs/miRNA*s in the F3 and F4 libraries, respectively. One hundred and seventy-seven miRNAs, including 45 up- and 132 down-regulated, had more than 2-fold differential expression between the castrated and intact male pigs (p-value < 0.001). Thirty-five miRNAs were further selected, based on the expression abundance and differentiation between the two libraries, to predict their targets in KEGG pathways. KEGG pathway analyses suggested that miRNAs differentially expressed between the castrated and intact male pigs are involved in proliferation, apoptosis, differentiation, migration, adipose tissue development and other important biological processes. The expression patterns of eight arbitrarily selected miRNAs were validated by stem-loop reverse-transcription quantitative polymerase chain reaction. These data confirmed the expression tendency observed with SOLiD sequencing. miRNA isomiRs and mirtrons were also investigated in this study. Mirtrons are a recently described category of miRNA relying on splicing rather than processing by the microprocessor complex to generate the RNAi pathway. The functions of miRNAs important for regulating fat deposition were also investigated in this study.
Conclusions
This study expands the number of fat-deposition-related miRNAs in pig. The results also indicate that castration can significantly affect the expression patterns of fat-related miRNAs. The differentially expressed miRNAs may play important roles in fat deposition after castration.
doi:10.1186/1471-2164-15-47
PMCID: PMC3901342  PMID: 24443800
Male pig; MicroRNA; Fat deposition; Castration
14.  Diploid, but not haploid, human embryonic stem cells can be derived from microsurgically repaired tripronuclear human zygotes 
Cell Cycle  2013;12(2):302-311.
Human embryonic stem cells have shown tremendous potential in regenerative medicine, and the recent progress in haploid embryonic stem cells provides new insights for future applications of embryonic stem cells. Disruption of normal fertilized embryos remains controversial; thus, the development of a new source for human embryonic stem cells is important for their usefulness. Here, we investigated the feasibility of haploid and diploid embryo reconstruction and embryonic stem cell derivation using microsurgically repaired tripronuclear human zygotes. Diploid and haploid zygotes were successfully reconstructed, but a large proportion of them still had a tripolar spindle assembly. The reconstructed embryos developed to the blastocyst stage, although the loss of chromosomes was observed in these zygotes. Finally, triploid and diploid human embryonic stem cells were derived from tripronuclear and reconstructed zygotes (from which only one pronucleus was removed), but haploid human embryonic stem cells were not successfully derived from the reconstructed zygotes when two pronuclei were removed. Both triploid and diploid human embryonic stem cells showed the general characteristics of human embryonic stem cells. These results indicate that the lower embryo quality resulting from abnormal spindle assembly contributed to the failure of the haploid embryonic stem cell derivation. However, the successful derivation of diploid embryonic stem cells demonstrated that microsurgical tripronuclear zygotes are an alternative source of human embryonic stem cells. In the future, improving spindle assembly will facilitate the application of triploid zygotes to the field of haploid embryonic stem cells.
doi:10.4161/cc.23103
PMCID: PMC3575459  PMID: 23255130
triploid zygotes; haploid; spindle assembly; human embryonic stem cells
15.  Functional Analysis LRP6 Novel Mutations in Patients with Coronary Artery Disease 
PLoS ONE  2014;9(1):e84345.
Background
Genetic architecture of coronary artery disease (CAD) is still to be defined. Since low density lipoprotein receptor-related protein 6 (LRP6) gene play critical roles in Wnt signal transduction which are important for vascular development and endodermis specification, we therefore resequenced it to search for mutations in CAD patients.
Methods
We systemically sequenced all the exons and promoter region of LRP6 gene in a sample of 380 early onset CAD patients and 380 control subjects in Chinese.
Results
In total, we identified 5 patient-specific mutations including K82N (two patients), S488Y (one patient), P1066T (two patients), P1206H (two patients) and I1264V (one patient) All these mutations located at the extracellular domain of LRP6 gene. In vitro functional analysis of patient-specific mutations demonstrated that these mutations resulted in a significant reduction in both protein level transporting to cell membrane and downstream Wnt signal activity. Furthermore, we found that LRP6 novel mutations attenuated proliferation and migration of human umbilical vein endothelial cells (HUVECs) when compared with wild type (WT) LRP6.
Conclusion
Our results demonstrated that these loss-of-function variants might contribute to disease liability in a subset of CAD and defects in Wnt signal activation might be important contributing factors for the onset of CAD.
doi:10.1371/journal.pone.0084345
PMCID: PMC3888387  PMID: 24427284
16.  Generation of high-performance binding proteins for peptide motifs by affinity clamping 
Methods in enzymology  2013;523:285-302.
We describe concepts and methodologies for generating “Affinity Clamps”, a new class of recombinant binding proteins that achieve high affinity and high specificity toward short peptide motifs of biological importance, which is a major challenge in protein engineering. The Affinity Clamping concept exploits the potential of nonhomologous recombination of protein domains in generating large changes in protein function and the inherent binding affinity and specificity of the so-called modular interaction domains toward short peptide motifs. Affinity Clamping creates a clamshell architecture that clamps onto a target peptide. The design processes involve (i) choosing a starting modular interaction domain appropriate for the target and applying structure-guided modifications, (ii) attaching a second domain, termed “enhancer domain” and (iii) optimizing the peptide-binding site located between the domains by directed evolution. The two connected domains work synergistically to achieve high levels of affinity and specificity that are unattainable with either domain alone. Because of the simple and modular architecture, affinity clamps are particularly well suited as building blocks for designing more complex functionalities. Affinity Clamping represents a major advance in protein design that is broadly applicable to the recognition of peptide motifs.
doi:10.1016/B978-0-12-394292-0.00013-8
PMCID: PMC3757518  PMID: 23422435
molecular recognition; nonhomologous recombination; directed evolution; domain interface; affinity reagents; modular domain; molecular scaffold
17.  Features and treatment modality of iliopsoas abscess and its outcome: a 6-year hospital-based study 
BMC Infectious Diseases  2013;13:578.
Background
Percutaneous drainage (PCD) and surgical intervention are two primary treatment options for iliopsoas abscess (IPA). However, there is currently no consensus on when to use PCD or surgical intervention, especially in patients with gas-forming IPA. This study compared the characteristics of patients with gas-forming and non-gas forming IPA and their mortality rates under different treatment modalities. An algorithm for selecting appropriate treatment for IPA patients is proposed based on our findings.
Methods
Eighty-eight IPA patients between July 2007 and February 2013 were enrolled in this retrospective study. Patients < 18 years of age or with an incomplete course of treatment were excluded. Demographic information, clinical characteristics, and outcomes of different treatment approaches were compared between gas-forming IPA and non-gas forming IPA patients.
Results
Among the 88 enrolled patients, 27 (31%) had gas-forming IPA and 61 (69%) had non-gas forming IPA. The overall intra-hospital mortality rate was 25%. The gas-forming IPA group had a higher intra-hospital mortality rate (12/27, 44.0%) than the non-gas forming IPA group (10/61, 16.4%) (P < 0.001). Only 2 of the 13 patients in the gas-forming IPA group initially accepting PCD had a good outcome (success rate = 15.4%). Three of the 11 IPA patients with failed initial PCD expired, and 8 of the 11 patients with failed initial PCD accepted salvage operation, of whom 5 survived. Seven of the 8 gas-forming IPA patients accepting primary surgical intervention survived (success rate = 87.5%). Only 1 of the 6 gas-forming IPA patients who accepted antibiotics alone, without PCD or surgical intervention, survived (success rate = 16.7%). In the non-gas forming IPA group, 23 of 61 patients initially accepted PCD, which was successful in 17 patients (73.9%). The success rate of PCD was much higher in the non-gas forming group than in the gas-forming group (P <0.01).
Conclusions
Based on the high failure rate of PCD and the high success rate of surgical intervention in our samples, we recommend early surgical intervention with appropriate antibiotic treatment for the patients with gas-forming IPA. Either PCD or primary surgical intervention is a suitable treatment for patients with non-gas forming IPA.
doi:10.1186/1471-2334-13-578
PMCID: PMC3878923  PMID: 24321123
Iliopsoas abscess; Percutaneous drainage; Psoas abscess; Pyomyositis; Surgery
18.  Organizational Culture and Its Relationship with Hospital Performance in Public Hospitals in China 
Health Services Research  2011;46(6 Pt 2):2139-2160.
Objective
To measure perceptions of organizational culture among employees of public hospitals in China and to determine whether perceptions are associated with hospital performance.
Data Sources
Hospital, employee, and patient surveys from 87 Chinese public hospitals conducted during 2009.
Study Design
Developed and administered a tool to assess organizational culture in Chinese public hospitals. Used factor analysis to create measures of organizational culture. Analyzed the relationships between employee type and perceptions of culture and between perceptions of culture and hospital performance using multivariate models.
Principal Findings
Employees perceived the culture of Chinese public hospitals as stronger in internal rules and regulations, and weaker in empowerment. Hospitals in which employees perceived that the culture emphasized cost control were more profitable and had higher rates of outpatient visits and bed days per physician per day but also had lower levels of patient satisfaction. Hospitals with cultures perceived as customer-focused had longer length of stay but lower patient satisfaction.
Conclusions
Managers in Chinese public hospitals should consider whether the culture of their organization will enable them to respond effectively to their changing environment.
doi:10.1111/j.1475-6773.2011.01336.x
PMCID: PMC3392996  PMID: 22092228
Business and management; comparative health systems/international health; hospitals; organization theory
19.  Does breastfeeding contribute to the racial gap in reading and math test scores? 
Annals of epidemiology  2013;23(10):10.1016/j.annepidem.2013.06.091.
Purpose
The aim of this study was to examine the impact of divergent breastfeeding practices between Caucasian and African American mothers on the lingering achievement test gap between Caucasian and African American children.
Methods
The Child Development Supplement of the Panel Study of Income Dynamics, beginning in 1997, followed a cohort of 3563 children aged 0–12 years. Reading and math test scores from 2002 for 1928 children were linked with breastfeeding history. Regression analysis was used to examine associations between ever having been breastfed and duration of breastfeeding and test scores, controlling for characteristics of child, mother, and household.
Results
African American students scored significantly lower than Caucasian children by 10.6 and 10.9 points on reading and math tests, respectively. After accounting for the impact of having been breastfed during infancy, the racial test gap decreased by 17% for reading scores and 9% for math scores.
Conclusions
Study findings indicate that breastfeeding explains 17% and 9% of the observed gaps in reading and math scores, respectively, between African Americans and Caucasians, an effect larger than most recent educational policy interventions. Renewed efforts around policies and clinical practices that promote and remove barriers for African American mothers to breastfeed should be implemented.
doi:10.1016/j.annepidem.2013.06.091
PMCID: PMC3836202  PMID: 23880156
Breastfeeding; Academic achievement; Child development
20.  Pancreaticobiliary maljuction combining with pancreas divisum: Report of four cases 
Pancreaticobiliary maljunction (PBM) is an unusual anomalous condition in which the pancreatic duct and bile duct merge outside the duodenal wall and form a long common channel. Pancreas divisum (PD) is a congenital anomaly in which the dorsal and ventral pancreatic ducts fail to fuse. Endoscopic retrograde cholangiopancreatography (ERCP) is the gold standard for diagnosing PD and magnetic resonance cholangiopancreatography (MRCP) is the non-invasive choice. In this study, four cases of patients with unusual PBM in addition to PD are described. The patients presented with abdominal pain, which was caused by distal biliary stricture diagnosed by MRCP. The patients received ERCP and had a good prognosis.
doi:10.3892/etm.2013.1403
PMCID: PMC3861473  PMID: 24348755
pancreaticobiliary maljunction; pancreas divisum; diagnosis; therapy
21.  Cloning and expression analysis of a novel high-mobility group box 2 homologue from Lampetra japonica 
High-mobility group box 2 (HMGB2) is a nonhistone architectural protein that plays important roles in many biological processes. In this study, we cloned a homologue of the HMGB2 from the lymphocyte-like cells of Lampetra japonica (L. japonica). Sequence analysis reveals that L. japonica HMGB2 contains two highly conserved motifs and shares more than 70 % identity with the homologues from other vertebrate species. Subsequently, Lj-HMGB2 was subcloned into the pET-28a(+) and pIRES2 AcGFP1-Nuc vector and expressed in Rosetta blue (DE3) and Hela cell lines, respectively. The recombinant L. japonica HMGB2 (rLj-HMGB2) with apparent molecular mass of 22 kDa was further purified by His-Bind affinity chromatography. Real-time quantitative PCR indicates that the expression level of Lj-HMGB2 was particularly up-regulated in intestines after challenged with lipopolysaccharide, while up-regulated in lymphocyte-like cells and heart after challenged with concanavalin A in vivo. In addition, rLj-HMGB2 could induce the generation of proinflammatory mediators in the activated human acute monocytic leukemia cell line (THP1), which suggested that Lj-HMGB2 may participate in the immune response of the lampreys.
doi:10.1007/s10695-013-9871-x
PMCID: PMC3948571  PMID: 24158500
Lampetra japonica; HMGB2; Proinflammatory
22.  Single arc volumetric-modulated arc therapy is sufficient for nasopharyngeal carcinoma: a dosimetric comparison with dual arc VMAT and dynamic MLC and step-and-shoot intensity-modulated radiotherapy 
Background
The performance of single arc VMAT (VMAT1) for nasopharyngeal carcinoma (NPC) on the Axesse linac has not been well described in previous studies. The purpose of this study is to assess the feasibility of VMAT1 for NPC by comparing the dosimetry, delivery efficiency, and accuracy with dual arc VMAT (VMAT2), dynamic MLC intensity-modulated radiotherapy (dIMRT), and step-and-shoot intensity-modulated radiotherapy (ssIMRT).
Methods
Twenty consecutive patients with non-metastatic NPC were selected to be planned with VMAT1, VMAT2, dIMRT and ssIMRT using Monaco 3.2 TPS on the Axesse™ linear accelerator. Three planning target volumes (PTVs), contoured as high risk, moderate risk and low risk regions, were set to receive median absorbed-dose (D50%) of 72.6 Gy, 63.6 Gy and 54 Gy, respectively. The Homogeneity Index (HI), Conformity Index (CI), Dose Volume Histograms (DVHs), delivery efficiency and accuracy were all evaluated.
Results
Mean HI of PTV72.6 is better with VMAT1(0.07) and VMAT2(0.07) than dIMRT(0.09) and ssIMRT(0.09). Mean HI of PTV63.6 is better with VMAT1(0.21) and VMAT2(0.21) than dIMRT and ssIMRT. Mean CI of PTV72.6 is also better with VMAT1(0.57) and VMAT2(0.57) than dIMRT(0.49) and ssIMRT(0.5). Mean CI of PTV63.6 is better with VMAT1(0.76) and VMAT2(0.76) than dIMRT(0.73) and ssIMRT(0.73). VMAT had significantly improved homogeneity and conformity compared with IMRT. There was no significant difference between VMAT1 and VMAT2 in PTV coverage. Dose to normal tissues was acceptable for all four plan groups. VMAT1 and VMAT2 showed no significant difference in normal tissue sparring, whereas the mean dose of the parotid gland of dIMRT was significantly reduced compared to VMAT1 and VMAT2. The mean delivery time for VMAT1, VMAT2, dIMRT and ssIMRT was 2.7 min, 3.9 min, 5.7 min and 14.1 min, respectively. VMAT1 reduced the average delivery time by 29.8%, 51.1% and 80.8% compared with VMAT2, dIMRT and ssIMRT, respectively. VMAT and IMRT could all be delivered accurately based on our quality assurance standards.
Conclusions
In the treatment of NPC using the Axesse™ linear accelerator, single arc VMAT has shown superiority to double arc VMAT, dIMRT and ssIMRT in delivery efficiency, without compromise to the PTV coverage. However, there is still room for improvement in terms of OAR sparing.
doi:10.1186/1748-717X-8-237
PMCID: PMC3854543  PMID: 24125432
Radiotherapy; Volumetric modulated arc therapy; Radiotherapy; Intensity modulated; Nasopharyngeal carcinoma; Plan evaluation; Dosimetry
23.  Hydrogen/Deuterium Exchange Mass Spectrometry and Site-Directed Disulfide Cross-Linking Suggest an Important Dynamic Interface between the Two Lysostaphin Domains 
Lysostaphin is a peptidoglycan hydrolase secreted by Staphylococcus simulans. It can specifically lyse Staphylococcus aureus and is being tested as a novel antibacterial agent. The protein contains an N-terminal catalytic domain and a C-terminal cell wall targeting domain. Although the two domains from homologous enzymes were structurally determined, the structural organization of lysostaphin domains remains unknown. We used hydrogen/deuterium exchange mass spectrometry (H/DX-MS) and site-directed disulfide cross-linking to probe the interface between the lysostaphin catalytic and targeting domains. H/DX-MS-mediated comparison of peptides from full-length lysostaphin and the separated domains identified four peptides of lower solvent accessibility in the full-length protein. Cross-linking analysis using cysteine pair substitutions within those peptides showed that two pairs of cysteines can form disulfide bonds, supporting the domain association role of the targeted peptides. The cross-linked mutant exhibited a binding capacity to S. aureus that was similar to that of the wild-type protein but reduced bacteriolytic activity probably because of restraint in conformation. The diminished activity was further reduced with increasing NaCl concentrations that can cause contractions of bacterial peptidoglycan. The lytic activity, however, could be fully recovered by reducing the disulfide bonds. These results suggest that lysostaphin may require dynamic association of the two domains for coordinating substrate binding and target cleavage on the elastic peptidoglycan. Our study will help develop site-specific PEGylated lysostaphin to treat systemic S. aureus infections.
doi:10.1128/AAC.02348-12
PMCID: PMC3623330  PMID: 23380729
24.  The effects of morphine on basal neuronal activities in the lateral and medial pain pathways 
Neuroscience letters  2012;525(2):173-178.
Numerous studies indicate that morphine suppresses pain-evoked activities in both spinal and supraspinal regions. However, little is known about the effect of morphine on the basal brain activity in the absence of pain. The present study was designed to assess the effects of single-dose morphine on the spontaneous discharge of many simultaneously recorded single units, as well as their functional connections, in the lateral pain pathway, including the primary somatosensory cortex (SI) and ventral posterolateral thalamus (VPL), and medial pain pathway, including the anterior cingulate cortex (ACC) and medial dorsal thalamus (MD), in awake rats. Morphine (5mg/kg) was administered intraperitoneally before the recording. Naloxone plus morphine and normal saline injections were performed respectively as controls. The results showed that morphine administration produced significant changes in the spontaneous neuronal activity in more than one third of the total recorded neurons, with primary activation in the lateral pathway while both inhibition and activation in the medial pathway. Naloxone pretreatment completely blocked the effects induced by morphine. In addition, the correlated activities between and within both pain pathways was exclusively suppressed after morphine injection. These results suggest that morphine may play different roles in modulating neural activity in normal versus pain states. Taken together, this is the first study investigating the morphine modulation of spontaneous neuronal activity within parallel pain pathways. It can be helpful for revealing neuronal population coding for the morphine action in the absence of pain, and shed light on the supraspinal mechanisms for preemptive analgesia.
doi:10.1016/j.neulet.2012.07.032
PMCID: PMC3465732  PMID: 22841696
morphine; spontaneous activity; the primary somatosensory cortex; the anterior cingulate cortex; thalamus
25.  AFDC/TANF Exits and Re-entries for Families Raising Children with Educational Disabilities 
Children and youth services review  2012;34(9):1756-1761.
Having a child with a disability is considered a barrier to self-sufficiency among welfare recipients. This study examines the impact of children’s educational disability on single-mother families’ welfare exits and re-entries for a cohort of children in a metropolitan region in Missouri, who were born between 1982 and 1994, and received AFDC/TANF at least once from 1990 through 2008 (N=4,928). A semiparametric proportional hazards model for recurrent events is used to analyze the relationship between a child’s educational disability and family welfare exit and re-entry. Results show that families with children with disabilities (the disability group) are less likely to exit and more likely to re-enter the welfare system than families with children without disabilities (the nondisability group). After the 1996 welfare reform, the welfare exit rate increases more for the disability group than for the nondisability group, while the welfare re-entry rate decreases less for the disability group than for the nondisability group.
doi:10.1016/j.childyouth.2012.05.011
PMCID: PMC3398742  PMID: 22822283
Children with disabilities; Poverty; Welfare reform; Single-parent families; Special education

Results 1-25 (98)