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2.  Hyperdoping silicon with selenium: solid vs. liquid phase epitaxy 
Scientific Reports  2015;5:8329.
Chalcogen-hyperdoped silicon shows potential applications in silicon-based infrared photodetectors and intermediate band solar cells. Due to the low solid solubility limits of chalcogen elements in silicon, these materials were previously realized by femtosecond or nanosecond laser annealing of implanted silicon or bare silicon in certain background gases. The high energy density deposited on the silicon surface leads to a liquid phase and the fast recrystallization velocity allows trapping of chalcogen into the silicon matrix. However, this method encounters the problem of surface segregation. In this paper, we propose a solid phase processing by flash-lamp annealing in the millisecond range, which is in between the conventional rapid thermal annealing and pulsed laser annealing. Flash lamp annealed selenium-implanted silicon shows a substitutional fraction of ~ 70% with an implanted concentration up to 2.3%. The resistivity is lower and the carrier mobility is higher than those of nanosecond pulsed laser annealed samples. Our results show that flash-lamp annealing is superior to laser annealing in preventing surface segregation and in allowing scalability.
doi:10.1038/srep08329
PMCID: PMC4321182  PMID: 25660096
3.  Effect of hydrogen sulfide on inflammatory cytokines in acute myocardial ischemia injury in rats 
Hydrogen sulfide (H2S) is believed to be involved in numerous physiological and pathophysiological processes, and now it is recognized as the third endogenous signaling gasotransmitter, following nitric oxide and carbon monoxide; however, the effects of H2S on inflammatory factors in acute myocardial ischemia injury in rats have not been clarified. In the present study, sodium hydrosulfide (NaHS) was used as the H2S donor. Thirty-six male Sprague Dawley rats were randomly divided into five groups: Sham, ischemia, ischemia + low-dose (0.78 mg/kg) NaHS, ischemia + medium-dose (1.56 mg/kg) NaHS, ischemia + high-dose (3.12 mg/kg) NaHS and ischemia + propargylglycine (PPG) (30 mg/kg). The rats in each group were sacrificed 6 h after the surgery for sample collection. Compared with the ischemia group, the cardiac damage in the rats in the ischemia + NaHS groups was significantly reduced, particularly in the high-dose group; in the ischemia + PPG group, the myocardial injury was aggravated compared with that in the ischemia group. Compared with the ischemia group, the levels of interleukin (IL)-1β, IL-6 and tumor necrosis factor-α (TNF-α) in the serum of rats in the ischemia + medium- and high-dose NaHS groups were significantly reduced, and the expression of intercellular adhesion molecule-1 (ICAM-1) mRNA and nuclear factor κ-light-chain-enhancer of activated B cells (NF-κB) protein in the myocardial tissues of rats was significantly reduced. In the ischemia + PPG group, the TNF-α, IL-1β and IL-6 levels in the serum were significantly increased, the expression of ICAM-1 mRNA was increased, although without a significant difference, and the expression of NF-κB was increased. The findings of the present study provide novel evidence for the dual effects of H2S on acute myocardial ischemia injury via the modulation of inflammatory factors.
doi:10.3892/etm.2015.2218
PMCID: PMC4316979  PMID: 25667680
hydrogen sulfide; acute myocardial ischemia; rat; inflammatory factor
4.  Carpal Tunnel Syndrome Assessment with Ultrasonography: Value of Inlet-to-Outlet Median Nerve Area Ratio in Patients versus Healthy Volunteers 
PLoS ONE  2015;10(1):e0116777.
Objective
To evaluate the diagnostic value of the Inlet-to-outlet median nerve area ratio (IOR) in patients with clinically and electrophysiologically confirmed carpal tunnel syndrome (CTS).
Methods
Forty-six wrists in 46 consecutive patients with clinical and electrodiagnostic evidence of CTS and forty-four wrists in 44 healthy volunteers were examined with ultrasonography. The cross-sectional area (CSA) of the median nerve was measured at the carpal tunnel inlet (the level of scaphoid-pisiform) and outlet (the level of the hook of the hamate), and the IOR was calculated for each wrist. Ultrasonography and electrodiagnostic tests were performed under blinded conditions. Electrodiagnostic testing combined with clinical symptoms were considered to be the gold standard test. Receiver operating characteristic (ROC) curves were used to evaluate the diagnostic value between the inlet CSA and IOR.
Results
The study population included 16 men and 30 women (mean age, 45.3 years; range, 18–83 years). The control population included 18 men and 26 women (mean age, 50.4 years; range, 18–79 years). The mean inlet CSA was 8.7 mm2 in healthy controls and 14.6mm2 in CTS group (P<0.001). The mean IOR in healthy volunteers (1.0) was smaller than that in patients (1.6, P<0.001). Receiver operating characteristic analysis revealed a diagnostic advantage to using the IOR rather than the inlet CSA (P<0.01). An IOR cutoff value of ≥ 1.3 would yield 93% specificity and 91% sensitivity in the diagnosis of CTS.
Conclusion
The IOR of median nerve area promises to be an effective means in the diagnosis of CTS. A large-scale, randomized controlled trial is required to determine how and when this parameter will be used.
doi:10.1371/journal.pone.0116777
PMCID: PMC4305299  PMID: 25617835
5.  A comprehensive database of Duchenne and Becker muscular dystrophy patients (0–18 years old) in East China 
Background
Currently, there is no cure for Duchenne and Becker muscular dystrophies (DMD/BMD). However, clinical trials with new therapeutic strategies are being conducted or considered. A comprehensive database is critical for patient recruitment and efficacy evaluation. China has the largest population, yet, no comprehensive database for DMD/BMD is available. Our study registered the data of the DMD/BMD patients in East China.
Methods
A modified registry form of Remudy (http://www.remudy.jp/) was applied to Chinese DMD/BMD patients through the outpatient clinic at Children’s Hospital of Fudan University, Shanghai during the period of August 2011 to December 2013. The data included geographic distribution of patients, age at diagnosis, clinical manifestation, genetic analysis and treatment status.
Results
194 DMD and 35 BMD patients were registered. Most patients lived in East China, namely Jiangsu province, Anhui province, Zhejiang province, Jiangxi province, Shanghai, Fujian province and Shandong province. All individuals aged less than 18 years (age limit to a children’s hospital). Diagnosis was made for a majority of patients during the age of 3–4 (16.6%) and 7–8 (14.8%) years old. Exon deletion was the most frequent genetic mutations (65.5% and 74.3%) followed by point mutations (14.4% and 11.4%), duplications (9.8% and 8.6%) and small insertion/deletion (9.3% and 2.9%) for DMD and BMD, respectively. 82.5% of DMD registrants were ambulatory, and all the BMD registrants were able to walk. 26.3% of DMD registrants have been treated with steroids. Cardiac functions were examined for 46.4% DMD boys and 45.7% BMD boys and respiratory functions were examined for 18.6% DMD boys and 14.3% BMD boys. Four boys with abnormal cardiac function were prescribed for treatment with cardiac medicine. 33.2% of DMD patients are eligible for exon skipping therapy, and among them 9.2% and 4.3% patients are eligible for skipping exon 51 and 53, respectively.
Conclusions
The database is the first linking accurate genetic diagnosis with clinical manifestation and treatment status of dystrophinopathy patients in East China. It provides comprehensive information essential for further patient management, especially for promotion of international cooperation in developing experimental therapies such as exon skipping and read-through of nonsense mutations targeting a subgroup of DMD patient population.
doi:10.1186/s13023-014-0220-7
PMCID: PMC4323212  PMID: 25612904
Duchenne and Becker muscular dystrophy; The CHFU database; Patient management
6.  Construction of cytogenetic map of Gossypium herbaceum chromosome 1 and its integration with genetic maps 
Background
Cytogenetic map can provide not only information of the genome structure, but also can build a solid foundation for genetic research. With the developments of molecular and cytogenetic studies in cotton (Gossypium), the construction of cytogenetic map is becoming more and more imperative.
Results
A cytogenetic map of chromosome 1 (A101) of Gossypium herbaceum (A1) which includes 10 bacterial artificial chromosome (BAC) clones was constructed by using fluorescent in situ hybridization (FISH). Meanwhile, comparison and analysis were made for the cytogenetic map of chromosome 1 (A101) of G. herbaceum with four genetic linkage maps of chromosome 1 (Ah01) of G. hirsutum ((AD)1) and one genetic linkage map of chromosome 1 of (A101) G. arboreum (A2). The 10 BAC clones were also used to be localized on G. raimondii (D5) chromosome 1 (D501), and 2 of them showed clear unique hybridized signals. Furthermore, these 2 BAC clones were also shown localized on chromosome 1 of both A sub-genome and D sub-genome of G. hirsutum.
Conclusion
The comparison of the cytogenetic map with genetic linkage maps showed that most of the identified marker-tagged BAC clones appearing same orders in different maps except three markers showing different positions, which might indicate chromosomal segmental rearrangements. The positions of the 2 BAC clones which were localized on Ah01 and Dh01 chromosomes were almost the same as that on A101 and D501 chromosomes. The corresponding anchored SSR markers of these 2 BAC clones were firstly found to be localized on chromosome D501 (Dh01) as they were not seen mapped like this in any genetic map reported.
doi:10.1186/s13039-015-0106-y
PMCID: PMC4307992  PMID: 25628758
Cotton; BAC-FISH; Cytogenetic map
7.  Indirubins Decrease Glioma Invasion by Blocking Migratory Phenotypes in Both the Tumor and Stromal Endothelial Cell Compartments 
Cancer research  2011;71(16):5374-5380.
Invasion and proliferation in neoplasia require the cooperation of tumor cell and endothelial compartments. Glycogen synthase kinase-3 (GSK-3) is increasingly recognized as a major contributor to signaling pathways that modulate invasion and proliferation. Here we show that GSK-3 inhibitors of the indirubin family reduce invasion of glioma cells and glioma-initiating cell-enriched neurospheres both in vitro and in vivo, and we show that β-catenin signaling plays an important role in mediating these effects. Indirubins improved survival in glioma-bearing mice in which a substantial decrease in blood vessel density was seen in treated animals. In addition, indirubins blocked migration of endothelial cells, suggesting that anti-invasive glioma therapy with GSK-3 inhibitors in vivo not only inhibits invasion of tumor cells, but blocks migration of endothelial cells, which is also required for tumor angiogenesis. Overall, our findings suggest that indirubin inhibition of GSK-3 offers a novel treatment paradigm to target 2 of the most important interacting cellular compartments in heterotypic models of cancer.
doi:10.1158/0008-5472.CAN-10-3026
PMCID: PMC4288480  PMID: 21697283
8.  M-CSF cooperating with NFκB induces macrophage transformation from M1 to M2 by upregulating c-Jun 
Cancer Biology & Therapy  2013;15(1):99-107.
Increasing evidence suggests tumor-associated macrophages (TAMs) are polarized M2 subtype of macrophage that exerts pro-tumor effects and promote the malignancy of some cancers, but the concrete mechanism is not well defined. Our previous research exhibited that proto-oncogene AP-1 regulated IL-6 expression in macrophages and promoted the formation of M2 macrophages. In this study, we investigate whether extra-cellular stimulus M-CSF help this process or nuclear factor NFκB has a synergistic role in the activation state of polarized M2 subtype of macrophage. RAW 264.7 macrophage and 4T1 mouse breast cancer cells were co-cultured to reconstruct tumor microenvironment. Being co-cultured with 4T1 or its supernatant, the expression of c-Jun, the member of AP-1 family, has a dramatically increase both on the level of gene and on the protein in RAW 264.7 macrophages, but the expression of c-Fos does not increase neither on the level of gene nor on the protein. After co-cultured with 4T1, RAW 264.7 has a higher consumption of M-CSF than RAW 264.7 macrophages alone. With the stimulation of M-CSF, the mRNA of c-Jun increased significantly, but decreased remarkably after adding the anti-M-CSF. And at the same time, p50, the member of NFκB family, has a similar tendency to c-Jun. WB results suggest that with the stimulation of M-CSF, p-Jun in nuclear increases heavily but decreases after the neutralizing antibody added. Coimmunoprecipitation and immunoblotting techniques confirmed that c-Jun and p50 NFκB coprecipitated, and c-Jun protein expression is properly enhanced with rM-CSF effect. In conclusion, M-CSF induces macrophage transformation by upregulating c-Jun with a certain synergy of NFκB. Our study may present a novel therapeutic strategy against cancer.
doi:10.4161/cbt.26718
PMCID: PMC3938528  PMID: 24100343
M-CSF; NFκB; c-Jun; co-culture; transformation
9.  Impact of Glutathione S-Transferase M1 and T1 on Anti-Tuberculosis Drug–Induced Hepatotoxicity in Chinese Pediatric Patients 
PLoS ONE  2014;9(12):e115410.
Background
Anti-tuberculosis drug induced hepatotoxicity (ATDH) is a major adverse drug reaction associated for anti-tuberculosis therapy. The glutathione S-transferases (GST) plays a crucial role in the detoxification of hepatotoxic metabolites of anti-tuberculosis drugs.An association between GSTM1/GSTT1 null mutations and increased risk of ATDH has been demonstrated in adults. Given the ethnic differences and developmental changes, our study aims to investigate the potential impacts of GSTM1/GSTT1genotypes on the development of ATDH in Han Chinese children treated with anti-tuberculosis therapy.
Methods
Children receiving anti-tuberculosis therapy with or without evidence of ATDH were considered as the cases or controls, respectively. The GSTM1 and GSTT1 genotyping were performed using the polymerase chain reaction.
Results
One hundred sixty-three children (20 cases and 143 controls) with a mean age of 4.7 years (range: 2 months-14.1 years) were included. For the GSTM1, 14 (70.0%) cases and 96 (67.1%) controls had homozygous null mutations. For the GSTT1, 13 (65.0%) cases and 97 (67.8%) controls had homozygous null mutations. Neither the GSTM1, nor the GSTT1 polymorphism was significantly correlated with the occurrence of ATHD.
Conclusion
Ourresults did not support the GSTM1 and GSTT1 polymorphisms as the predictors of ADTH in Chinese Han children treated with anti-tuberculosis drugs. An age-related association between pharmacogenetics and ATHD need to be confirmed in the further study.
doi:10.1371/journal.pone.0115410
PMCID: PMC4272297  PMID: 25525805
10.  Robustness analysis on interspecies interaction network for iron and glucose competition between Candida albicans and zebrafish during infection 
BMC Systems Biology  2014;8(Suppl 5):S6.
Candida albicans has emerged as an important model organism for the study of infectious disease. Using high-throughput simultaneously quantified time-course transcriptomics, this study constructed host-pathogen interspecies interaction networks between C. albicans and zebrafish during the adhesion, invasion, and damage stages. Given that iron and glucose have been identified as crucial resources required during the infection process between C. albicans and zebrafish, we focused on the construction of the interspecies networks associated with them. Furthermore, a randomization technique was proposed to identify differentially regulated proteins that are statistically eminent for the three infection stages. The behaviors of the highly connected or differentially regulated proteins identified from the resulting networks were further investigated.
"Robustness" is an important system property that measures the ability of the system tolerating the intrinsic perturbations in a dynamic network. This characteristic provides a systematic and quantitative view to elucidate the dynamics of iron and glucose competition in terms of the interspecies interaction networks. Here, we further estimated the robustness of our constructed interspecies interaction networks for the three infection stages.
The constructed networks and robustness analysis provided significant insight into dynamic interactions related to iron and glucose competition during infection and enabled us to quantify the system's intrinsic perturbation tolerance ability during iron and glucose competition throughout the three infection stages. Moreover, the networks also assist in elucidating the offensive and defensive mechanisms of C. albicans and zebrafish during their competition for iron and glucose. Our proposed method can be easily extended to identify other such networks involved in the competition for essential resources during infection.
doi:10.1186/1752-0509-8-S5-S6
PMCID: PMC4305985  PMID: 25603810
11.  Plateau Effect of Prostate Cancer Risk-Associated SNPs in Discriminating Prostate Biopsy Outcomes 
The Prostate  2013;73(16):1824-1835.
BACKGROUND
Additional prostate cancer (PCa) risk-associated single nucleotide polymorphisms (SNPs) continue to be identified. It is unclear whether addition of newly identified SNPs improves the discriminative performance of biopsy outcomes over previously established SNPs.
METHODS
A total of 667 consecutive patients that underwent prostate biopsy for detection of PCa at Huashan Hospital and Changhai Hospital, Shanghai, China were recruited. Genetic scores were calculated for each patient using various combinations of 29 PCa risk-associated SNPs. Performance of these genetic scores for discriminating prostate biopsy outcomes were compared using the area under a receiver operating characteristic curve (AUC).
RESULTS
The discriminative performance of genetic score derived from a panel of all 29 SNPs (24 previous and 5 new) was similar to that derived from the 24 previously established SNPs, the AUC of which were 0.60 and 0.61, respectively (P = 0.72). When SNPs with the strongest effect on PCa risk (ranked based on contribution to the total genetic variance from an external study) were sequentially added to the models for calculating genetic score, the AUC gradually increased and peaked at 0.62 with the top 13 strongest SNPs. Under the 13-SNP model, the PCa detection rate was 21.52%, 36.74%, and 51.98%, respectively for men with low (<0.5), intermediate (0.5–1.5), and high (>1.5) genetic score, P-trend = 9.91 × 10−6.
CONCLUSION
Genetic score based on PCa risk-associated SNPs implicated to date is a significant predictor of biopsy outcome. Additional small-effect PCa risk-associated SNPs to be discovered in the future are unlikely to further improve predictive performance.
doi:10.1002/pros.22721
PMCID: PMC3910089  PMID: 24037738
prostate; SNPs; genetic score; ChinaPCa; biopsy; AUC
12.  Redesigning the DNA-Targeted Chromophore in Platinum–Acridine Anticancer Agents: A Structure–Activity Relationship Study 
Platinum–acridine hybrid agents show low-nanomolar potency in chemoresistant non-small cell lung cancer (NSCLC), but high systemic toxicity in vivo. To reduce the promiscuous genotoxicity of these agents and improve their pharmacological properties, a modular build–click–screen approach was used to evaluate a small library of twenty hybrid agents containing truncated and extended chromophores of varying basicities. Selected derivatives were resynthesized and tested in five NSCLC cell lines representing large cell, squamous cell, and adenocarcinomas. 7-Aminobenz[c]acridine was identified as a promising scaffold in a hybrid agent (P1–B1) that maintained submicromolar activity in several of the DNA-repair proficient and p53-mutant cancer models, while showing improved tolerability in mice by 32-fold compared to the parent platinum–acridine (P1–A1). The distribution and DNA/RNA adduct levels produced by the acridine- and benz[c]acridine-based analogues in NCI-H460 cells (confocal microscopy, ICP-MS), and their ability to bind G-quadruplex forming DNA sequences (CD spectroscopy, HR-ESMS) were studied. P1–B1 emerges as a less genotoxic, more tolerable, and potentially more target-selective hybrid agent than P1–A1.
doi:10.1002/chem.201404845
PMCID: PMC4244275  PMID: 25302716
anticancer drugs; cellular target; cytotoxicity; DNA adducts; intercalation
13.  Five-year epidemiological survey of valvular heart disease: changes in morbidity, etiological spectrum and management in a cardiovascular center of Southern China 
Journal of Thoracic Disease  2014;6(12):1724-1730.
Objective
The objective of the present study is to analyze the epidemiological profile of patients with abnormal valvular structure and function and highlight the etiological spectrum and management of valvular heart disease (VHD) in a single cardiovascular center of Southern China in five years.
Methods
The retrospective study included 19,428 consecutive patients (9,441 men and 9,987 women with a mean age of 52.03±20.50 years) with abnormal valvular structure and function who were screened by transthoracic echocardiography (TTE) or transesophageal echocardiography (TEE) at the in-patient department of Guangdong General Hospital from January 2009 to December 2013. Data on baseline characteristics, potential etiology, treatment strategies and discharge outcomes were collected from electronic medical records.
Results
There were 13,549 (69.7%) patients with relatively definite etiology for VHD. VHD was rheumatic in 7,197 (37.0%) patients, congenital in 2,697 (13.9%), degenerative in 2,241 (11.5%), ischemic in 2,460 (12.7%). The prevalence decreased significantly in rheumatic VHD from 2009 to 2013 (from 42.8% to 32.8%, P<0.001), but increased markedly in congenital VHD (from 9.0% to 12.3%, P<0.001), ischemic VHD (from 9.2% to 11.3%, P=0.003) and degenerative VHD (from 8.8% to 14.5%, P<0.001). Meantime, the prevalence of ischemic VHD increased after the age of 45, similar to that of degenerative VHD. From 2009 to 2013, the proportion of patients with VHD undergoing open cardiac valvular surgery decreased (from 49.5% to 44.3%, P<0.001) and that of patients treated with general medication increased (from 49.2% to 54.1%, P<0.001). However, there was markedly increment in video-assisted thoracoscopic surgery (VATS) from 2009 to 2013 (from 0.3% to 4.4%, P<0.001). Increasing tendencies were showed in aortic mechanical valve replacement (from 32.1% to 34.5%, P=0.001) and double mechanical valve replacement (from 20.9% to 22.3%, P=0.035), especially in mitral valvuloplasty (from 8.5% to 15.7%, P<0.001). However, the proportion of patients undergoing bioprosthetic valve replacement decreased from 2009 to 2013 (from 26.3% to 15.5%, P<0.001).
Conclusions
Despite a significant shift from rheumatic towards degenerative etiology from 2009 to 2013, rheumatic VHD remains the leading etiology in Southern China, with a significant increase in the prevalence of ischemic, congenital and degenerative VHD. General medication and cardiac valvular surgery remain the main treatment options. The proportion of VATS increased markedly from 2009 to 2013, and mechanical valve replacement and mitral valvuloplasty showed an increasing tendency.
doi:10.3978/j.issn.2072-1439.2014.11.21
PMCID: PMC4283290  PMID: 25589965
Epidemiological; valvular heart disease (VHD); etiology; cardiac valvular surgery
14.  Undifferentiated embryonal sarcoma of liver: a multi-institutional experience with 9 cases 
To summarize the clinicopathological features, therapeutic regimens and outcomes for the patients with undifferentiated embryonal sarcoma of the liver (UESL), 9 cases of UESL were retrospectively reviewed. Complete clinical history, lab studies, imaging examinations and pathological findings were collected for analysis. Overall survival and progression free survival were assessed by Kaplan-Meier Survival Analysis. The patients were 6 to 37 years old, and included 6 males and 3 females. The tumor size ranged from 5 to 26 cm. Pathologically, the tumors consisted of proliferations of medium sized spindle, oval or stellate shaped pleomorphic cells loosely or compactly arranged in an edematous or myxoid matrix, with scattered bizarre multinucleated giant cells. All of the 9 cases were treated with radical resections, 6 of 9 cases received chemothrepy for postoperative treatment. All follow-up data were available, 4 of 9 cases had recurrence, and 2 patients were died. Time to recurrence in these cases was 19, 4, 29, 14 months. The mean overall survival (OS) was 58.25 ± 9.1 months and the mean progression-free survival (PFS) was 39.55 ± 11.6 months. UESL is a potential treatable malignance when treated with combined multiagent chemotherapy after resection.
PMCID: PMC4313983
Liver; undifferentiated embryonal sarcoma; hepatectomy; prognosis
15.  Inherited predisposition to breast cancer among African American women 
African Americans have a disproportionate burden of aggressive young-onset breast cancer. Genomic testing for inherited predisposition to breast cancer is increasingly common in clinical practice, but comprehensive mutation profiles remain unknown for most minority populations. We evaluated 289 patients who self-identified as African American with primary invasive breast cancer and with personal or family cancer history or tumor characteristics associated with high genetic risk for all classes of germline mutations in known breast cancer susceptibility genes using a validated targeted capture and multiplex sequencing approach. Sixty-eight damaging germline mutations were identified in 65 (22 %, 95 % CI 18–28 %) of the 289 subjects. Proportions of patients with unequivocally damaging mutations in a breast cancer gene were 26 % (47/180; 95 % confident interval [CI] 20–33 %) of those with breast cancer diagnosis before age 45; 25 % (26/103; 95 % CI 17–35 %) of those with triple-negative breast cancer (TNBC); 29 % (45/156; 95 % CI 22–37 %) of those with a first or second degree relative with breast cancer before age 60 or with ovarian cancer; and 57 % (4/7; 95 % CI 18–90 %) of those with both breast and ovarian cancer. Of patients with mutations, 80 % (52/65) carried mutations in BRCA1 and BRCA2 genes and 20 % (13/65) carried mutations in PALB2, CHEK2, BARD1, ATM, PTEN, or TP53. The mutational allelic spectrum was highly heterogeneous, with 57 different mutations in 65 patients. Of patients meeting selection criteria other than family history (i.e., with young age at diagnosis or TNBC), 48 % (64/133) had very limited information about the history of cancer in previous generations of their families. Mutations in BRCA1 and BRCA2 or another breast cancer gene occur in one in four African American breast cancer patients with early onset disease, family history of breast or ovarian cancer, or TNBC. Each of these criteria defines patients who would benefit from genomic testing and novel therapies targeting DNA repair pathways.
doi:10.1007/s10549-014-3195-0
PMCID: PMC4298662  PMID: 25428789
Breast cancer; Next-generation sequencing; African American; Inherited susceptibility
16.  C3a Receptor Antagonist Ameliorates Inflammatory and Fibrotic Signals in Type 2 Diabetic Nephropathy by Suppressing the Activation of TGF-β/smad3 and IKBα Pathway 
PLoS ONE  2014;9(11):e113639.
Objective
Diabetic nephropathy (DN) is a serious complication for patients with diabetes mellitus (DM). Emerging evidence suggests that complement C3a is involved in the progression of DN. The aim of this study was to investigate the effect of C3a Receptor Agonist (C3aRA) on DN and its potential mechanism of action in rats with type 2 diabetes mellitus (T2DM).
Methods
T2DM was induced in SD rats by a high fat diet (HFD) plus repeated low dose streptozocin (STZ) injections. T2DM rats were treated with vehicle or C3aRA for 8 weeks. Biochemical analysis, HE and PAS stains were performed to evaluate the renal function and pathological changes. Human renal glomerular endothelial cells (HRGECs) were cultured and treated with normal glucose (NG), high glucose (HG), HG+C3a, HG+C3a+C3aRA and HG+C3a+BAY-11-7082 (p-IKBα Inhibitor) or SIS3 (Smad3 Inhibitor), respectively. Real-time PCR, immunofluorescent staining and western blot were performed to detect the mRNA and protein levels, respectively.
Results
T2DM rats showed worse renal morphology and impaired renal function compared with control rats, including elevated levels of serum creatinine (CREA), blood urea nitrogen (BUN) and urine albumin excretion (UACR), as well as increased levels of C3a, C3aR, IL-6, p-IKBα, collagen I, TGF-β and p-Smad3 in the kidney of T2DM rats and C3a-treated HRGECs. In contrast, C3aRA treatment improved renal function and morphology, reduced CREA, UACR and the intensity of PAS and collagen I staining in the kidney of T2DM rats, and decreased C3a, p-IKBα, IL-6, TGF-β, p-Smad3 and collagen I expressions in HRGECs and T2DM rats.
Conclusion
C3a mediated pro-inflammatory and pro-fibrotic responses and aggravated renal injury in T2DM rats. C3aRA ameliorated T2DN by inhibiting IKBα phosphorylation and cytokine release, and also TGF-β/Smad3 signaling and ECM deposition. Therefore, complement C3a receptor is a potential therapeutic target for DN.
doi:10.1371/journal.pone.0113639
PMCID: PMC4244104  PMID: 25422985
17.  mir-155 regulates cardiac allograft rejection by targing the expression of suppressor of cytokine signaling-1 (DOCS1) in dendritic cells 
Previously, we observed that mir-155 is induced during dendritic cell (DC) differentiation. We now demon-strated convincing evidence indicating that mir-155 promotes DC maturation and regulates its capacity for antigen presentation and induction of alloreactive T cell activation. Interestingly, the induction of miR-155 expression in DCs is dependent on the TLR4/Myd88/NF-κB signaling. Our mechanistic studies further revealed that SOCS1 is a direct target for mir-155, and by binding to its 3’UTR, mir-155 is likely to affect SOCS1 translation. Suppression of mir-155 expression in DCs significantly attenuated LPS-induced DC maturation along with reduced capability to stimulate allogeneic T cell proliferation. As a result, administration of antagomiR-155 provided protection for cardiac allografts from rejection. Together, our data support that suppression of miR-155 in DCs could be a viable therapeutic strategy for prevention and treatment of allograft rejection in clinical setting of transplantation.
PMCID: PMC4276246  PMID: 25550988
miR-155; dendritic cells; immune response; allograft
18.  Delineation of Early and Later Adult Onset Depression by Diffusion Tensor Imaging 
PLoS ONE  2014;9(11):e112307.
Background
Due to a lack of evidence, there is no consistent age of onset to define early onset (EO) versus later onset (LO) major depressive disorder (MDD). Fractional anisotropy (FA), derived from diffusion tensor imaging (DTI), has been widely used to study neuropsychiatric disorders by providing information about the brain circuitry, abnormalities of which might facilitate the delineation of EO versus LO MDD.
Method
In this study, 61 pairs of untreated, non-elderly, first-episode MDD patients and healthy controls (HCs) aged 18–45 years old received DTI scans. The voxel-based analysis method (VBM), classification analysis, using the Statistical Package for the Social Sciences (SPSS), and regression analyses were used to determine abnormal FA clusters and their correlations with age of onset and clinical symptoms.
Results
Classification analysis suggested in the best model that there were two subgroups of MDD patients, delineated by an age of onset of 30 years old, by which MDD patients could be divided into EO (18–29 years old) and LO (30–45 years old) groups. LO MDD was characterized by decreased FA, especially in the white matter (WM) of the fronto-occipital fasciculus and posterior limb of internal capsule, with a negative correlation with the severity of depressive symptoms; in marked contrast, EO MDD showed increased FA, especially in the WM of the corpus callosum, corticospinal midbrain and inferior fronto-occipital fasciculus, while FA of the WM near the midbrain had a positive correlation with the severity of depressive symptoms.
Conclusion
Specific abnormalities of the brain circuitry in EO vs. LO MDD were delineated by an age of onset of 30 years old, as demonstrated by distinct abnormal FA clusters with opposite correlations with clinical symptoms. This DTI study supported the evidence of an exact age for the delineation of MDD, which could have broad multidisciplinary importance.
Trial Registration
ClinicalTrials.gov NCT00703742
doi:10.1371/journal.pone.0112307
PMCID: PMC4231105  PMID: 25393297
19.  Evaluation of Reported Prostate Cancer Risk-Associated SNPs From Genome-Wide Association Studies of Various Racial Populations in Chinese Men 
The Prostate  2013;73(15):1623-1635.
BACKGROUND
Several genome-wide association studies (GWAS) of prostate cancer (PCa) have identified many single nucleotide polymorphisms (SNPs) that are significantly associated with PCa risk in various racial groups. The objective of this study is to evaluate which of these SNPs are associated with PCa risk in Chinese men and estimate their strength of association.
METHODS
All SNPs that were reported to be associated with PCa risk in GWAS from populations of European, African American, Japanese, and Chinese descent were evaluated in 1,922 PCa cases and 2,175 controls selected from the Chinese Consortium for Prostate Cancer Genetics (ChinaPCa). A logistic regression analysis was used to estimate allelic odds ratios (ORs) of these SNPs for PCa.
RESULTS
Among the 53 SNPs, 50 were polymorphic in the Chinese population. Of which, 10 and 24 SNPs were significantly associated with PCa risk in Chinese men at P < 0.001 and <0.05, respectively. These 24 significant SNPs included 17, 5, and 2 SNPs that were originally discovered in European, Japanese, and Chinese descent, respectively. The estimated ORs ranged from 1.10 to 1.49 and the direction of association was consistent with previous studies. When ORs were estimated separately for PCa with Gleason score ≤7 and ≥8, a marginally significant difference in ORs was found only for two of the 24 SNPs (P = 0.02 and 0.04).
CONCLUSION
About half of PCa risk-associated SNPs identified in GWAS of various populations are associated with PCa risk in Chinese men. Information on PCa risk-associated SNPs and their ORs may facilitate risk assessment of PCa risk in Chinese men.
doi:10.1002/pros.22629
PMCID: PMC3928594  PMID: 24038036
prostate cancer; SNPs; genome-wide association; Chinese
20.  Prediction of Prostate Cancer From Prostate Biopsy in Chinese Men Using a Genetic Score Derived From 24 Prostate Cancer Risk-Associated SNPs 
The Prostate  2013;73(15):1651-1659.
BACKGROUND.
Twenty-four prostate cancer (PCa) risk-associated single nucleotide polymorphisms (SNPs) in Chinese men have been cataloged. We evaluated whether these SNPs can independently predict outcomes of prostate biopsy, and improve the predictive performance of existing clinical variables.
METHODS.
Three hundred eight consecutive patients that underwent prostate biopsy for detection of PCa at Huashan Hospital, Shanghai, China between April 2011 and August 2012 were recruited. Clinical variables such as serum prostate-specific antigen (PSA) levels and peripheral blood samples were collected prior to a 10-core biopsy. A genetic score based on these 24 PCa associated SNPs was calculated for each individual.
RESULTS.
Among 308 patients underwent prostate biopsy, 141 (45.8%) were diagnosed with PCa. Genetic score was significantly higher in patients with PCa (median = 1.30) than without (median = 0.89), P = 3.81 × 10−6. The difference remained significant after adjusting for age and total PSA, P = 0.007. The PCa detection rate increased with increasing genetic score; 26.3%, 43.2%, and 60.0% for men with lower (<0.5), average (0.5–1.5), and higher (>1.5) genetic score, respectively, P−trend = 0.0003. For patients with moderately elevated PSA levels (1.6–20 ng/ml), the PCa detection rate was 31.2% overall and was 16.7%, 31.2%, and 40.9% for men with lower (<0.5), average (0.5–1.5), and higher (>1.5) genetic score, respectively, P−trend = 0.03. For patients with PSA 2: 20 ng/ml, however, the PCa detection rates were high (>69%) regardless of genetic score.
CONCLUSION.
A genetic score based on PCa risk-associated SNPs is an independent predictor of prostate biopsy outcomes in Chinese men and may be helpful to determine the need for prostate biopsy among patients within a ‘‘gray zone’’ of PCa risk.
doi:10.1002/pros.22661
PMCID: PMC3909876  PMID: 23868750
ChinaPCa; SNPs; risk assessment; PSA
21.  Nosocomial Neonatal Legionellosis Associated with Water in Infant Formula, Taiwan 
Emerging Infectious Diseases  2014;20(11):1921-1924.
We report 2 cases of neonatal Legionella infection associated with aspiration of contaminated water used in hospitals to make infant formula. The molecular profiles of Legionella strains isolated from samples from the infants and from water dispensers were indistinguishable. Our report highlights the need to consider nosocomial legionellosis among neonates who have respiratory symptoms.
doi:10.3201/eid2011.140542
PMCID: PMC4214307  PMID: 25340315
water; infant formula; Legionella; neonatal legionellosis; neonate; nosocomial infection; Taiwan; bacteria
22.  OCT4 Expression and Vasculogenic Mimicry Formation Positively Correlate with Poor Prognosis in Human Breast Cancer 
To evaluate the prognostic value of OCT4 expression and vasculogenic mimicry (VM) in human breast cancer, we examined OCT4 expression and VM formation using immunohistochemistry and CD31/PAS (periodic acid-schiff) double staining on 90 breast cancer specimens. All patients were followed up for five–149 months following surgery. Survival curves were generated using Kaplan-Meier method. Multivariate analysis was performed using Cox regression model to assess the prognostic values. Results showed positive correlation between OCT4 expression and VM formation (p < 0.05). Both OCT4 expression and VM were also positively correlated with lymph node metastasis, higher histological grade, and Nottingham prognostic index (p < 0.05). Patients with OCT4 expression or VM formation exhibited poorer overall survival (OS) and disease-free survival (DFS) than OCT4-negative or VM-negative patients (p < 0.05). OCT4-positive/VM-positive patients also had the worst OS and DFS (p < 0.05). In multivariate survival analysis, VM, Nottingham prognostic index (NPI), and Her2 were independent prognostic factors related to OS and OCT4-positive/VM-positive patients, whereas NPI and Her2 were independent predictors of DFS. These results suggest that a combined OCT4 expression/VM could improve the prognostic judgment for breast cancer patients.
doi:10.3390/ijms151119634
PMCID: PMC4264130  PMID: 25353179
OCT4; vasculogenic mimicry; breast cancer
23.  Relief of cannabis withdrawal symptoms and cannabis quitting strategies in people with schizophrenia 
Psychiatry research  2013;209(3):273-278.
This study examined the response to cannabis withdrawal symptoms and use of quitting strategies to maintain abstinence in people with schizophrenia. A convenience sample of 120 participants with schizophrenia who had at least weekly cannabis use and a previous quit attempt without formal treatment were administered the 176-item Marijuana Quit Questionnaire to characterize their “most serious” (self-defined) quit attempt. One hundred thirteen participants had withdrawal symptoms, of whom 104 (92.0%) took some action to relieve a symptom, most commonly nicotine use (75%). 90% of withdrawal symptoms evoked an action for relief in a majority of participants experiencing them, most frequently anxiety (95.2% of participants) and cannabis craving (94.4%). 96% of participants used one or more quitting strategies to maintain abstinence during their quit attempt, most commonly getting rid of cannabis (72%) and cannabis paraphernalia (67%). Religious support or prayer was the quitting strategy most often deemed “most helpful” (15%). Use of a self-identified most helpful quitting strategy was associated with significantly higher one-month (80.8% vs. 73.6%) and one-year (54.9% vs. 41.3%) abstinence rates. Actions to relieve cannabis withdrawal symptoms in people with schizophrenia are common. Promotion of effective quitting strategies may aid relapse prevention.
doi:10.1016/j.psychres.2013.07.044
PMCID: PMC3804059  PMID: 23969281
Schizophrenia; Cannabis; Drug withdrawal symptoms; Coping behavior; Abstinence
24.  Transcriptome Sequencing and Profiling of Expressed Genes in Phloem and Xylem of Ramie (Boehmeria nivea L. Gaud) 
PLoS ONE  2014;9(10):e110623.
Ramie (Boehmeria nivea L. Gaud) is a highly versatile herbaceous plant which is widely cropped in southern China. The success of this herbaceous plant relies on wide use in modern industry. Understanding the profiling of expressed genes in phloem and xylem of ramie is crucial for improving its industrial performance. Herein, we uncover the transcriptome profile in phloem and xylem in present study. Using Illumina paired-end sequencing technology, 57 million high quality reads were generated. De novo assembly yielded 87,144 unigenes with an average length of 635 bp. By sequence similarity searching for public databases, a total of 32,541 (41.77%) unigenes were annotated for their function. Among these genes, 57,873 (66.4%) and 28,678 (32.9%) unigenes were assigned to categories of Gene Ontology and Orthologous Groups database, respectively. By searching against the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG), 18,331 (21.0%) unigenes were mapped to 125 pathways. The metabolic pathways were assigned the most unigene (4,793, 26.2%). Furthermore, Pol II and Pol III subunits as well as the genes of Galactose metabolism pathway had higher expression in phloem compared to xylem. In addition, fatty acid metabolism pathway genes showed more abundant in xylem than phloem. These results suggest that high activities of RNA synthesis and Galactose metabolism pathway promises fiber synthesis in phloem. The present study is the initial exploration to uncover the fiber biosynthesis difference between phloem and xylem in ramie through the analysis of deep sequencing data.
doi:10.1371/journal.pone.0110623
PMCID: PMC4213010  PMID: 25354139
25.  The role of TGF-β signaling and apoptosis in innate and adaptive immunity in zebrafish: a systems biology approach 
BMC Systems Biology  2014;8(1):116.
Background
The immune system is a key biological system present in vertebrates. Exposure to pathogens elicits various defensive immune mechanisms that protect the host from potential threats and harmful substances derived from pathogens such as parasites, bacteria, and viruses. The complex immune system of humans and many other vertebrates can be divided into two major categories: the innate and the adaptive immune systems. At present, analysis of the complex interactions between the two subsystems that regulate host defense and inflammatory responses remains challenging.
Results
Based on time-course microarray data following primary and secondary infection of zebrafish by Candida albicans, we constructed two intracellular protein–protein interaction (PPI) networks for primary and secondary responses of the host. 57 proteins and 341 PPIs were identified for primary infection while 90 proteins and 385 PPIs were identified for secondary infection. There were 20 proteins in common while 37 and 70 proteins specific to primary and secondary infection. By inspecting the hub proteins of each network and comparing significant changes in the number of linkages between the two PPI networks, we identified TGF-β signaling and apoptosis as two of the main functional modules involved in primary and secondary infection.
Smad7, a member of the inhibitor SMADs, was identified to be a key protein in TGF-β signaling involved in secondary infection only. Indeed, the Smad7-dependent feedback system is related to the TGF-β signaling pathway and the immune response, suggesting that Smad7 may be an important regulator of innate and adaptive immune responses in zebrafish. Furthermore, we found that apoptosis was differentially involved in the two infection phases; more specifically, whereas apoptosis was promoted in response to primary infection, it was inhibited during secondary infection.
Conclusions
Our initial in silico analyses pave the way for further investigation into the interesting roles played by the TGF-β signaling pathway and apoptosis in innate and adaptive immunity in zebrafish. Such insights could lead to therapeutic advances and improved drug design in the continual battle against infectious diseases.
Electronic supplementary material
The online version of this article (doi:10.1186/s12918-014-0116-0) contains supplementary material, which is available to authorized users.
doi:10.1186/s12918-014-0116-0
PMCID: PMC4224695  PMID: 25341656
C. albicans; Zebrafish; Infection; Protein-protein interaction; Dynamic; Modeling; Immune; Adapt immune

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